Tag: mol

Scaling of MD with domain decomposition on JUWELS Cluster – Developers discussions

GROMACS version: 2024-dev-20240201-787d96c7a9-unknownGROMACS modification: YesI’m conducting some performance tests on the JUWELS Cluster, trying to see the improvement in performance that DD can bring within a single node. GROMACS build infoHere, GROMACS was built using GCC v11.4.0, uses OpenMP and OpenMPI v4.1.5, and builds its own FFTW v3.3.8. JUWELS Cluster…

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A Simple Overview for Proteins Molecular Dynamics Simulations Using GROMACS

About Gromacs – Gromacs. s.d. Consulté le 5 mai 2023. www.gromacs.org/About_Gromacs Baker, D., Sali, A.: Protein structure prediction and structural genomics. Science 294(5540), 93–96 (2001). doi.org/10.1126/science.1065659 Beckstein, O., et al.: Ion channel gating: insights via molecular simulations. FEBS Lett. 555(1), 85–90 (2003). doi.org/10.1016/s0014-5793(03)01151-7 CrossRef  Google Scholar  Bowman, A.L., Ridder, L.,…

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The Evolution from HG19 to HG38

Welcome to another blog post! ‍ Reference genomes are essential benchmarks of a species’ genome that facilitate the accurate comparison of individual genomes and are crucial tools for identifying genetic variants and diagnosing rare diseases. Here, we will explore the evolution of the human reference genome, focusing on the transition…

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Inferring divergence times within pikas (Ochotona spp.) using mtDNA and relaxed molecular dating techniques.

Inferring divergence times within pikas (Ochotona spp.) using mtDNA and relaxed molecular dating techniques. Inferring divergence times within pikas (Ochotona spp.) using mtDNA and relaxed molecular dating techniques. Mol Phylogenet Evol. 2009 Oct; 53(1):1-12. Animals Animals DNA, Mitochondrial …

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Antimicrobial potential of Streptomyces coeruleofuscus SCJ isolated from microbiologically unexplored garden soil in Northwest Morocco

Zaman, S. B. et al. A review on antibiotic resistance: Alarm bells are ringing. Cureus doi.org/10.7759/cureus.1403 (2017). Article  PubMed  PubMed Central  Google Scholar  Peterson, E. & Kaur, P. Antibiotic resistance mechanisms in bacteria: Relationships between resistance determinants of antibiotic producers, environmental bacteria, and clinical pathogens. Front. Microbiol. 9, 2928 (2018)….

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Sperm-specific histone H1 in highly condensed sperm nucleus of Sargassum horneri

Cho, C. et al. Haploinsufficiency of protamine-1 or-2 causes infertility in mice. Nat. Genet. 28, 82–86 (2001). Article  CAS  PubMed  Google Scholar  Oliva, R. Protamines and male infertility. Hum. Reprod. Update 12, 417–435 (2006). Article  CAS  PubMed  Google Scholar  Balhorn, R. The protamine family of sperm nuclear proteins. Genome Biol….

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Twisted DNA Increases CRISPR Off-target Effects

At the end of 2023, the FDA approved Casgevy for sickle cell disease, its first approval for a therapeutic that used the genome editing tool clustered regulatory interspaced palindromic repeats (CRISPR) to specifically inactivate a human gene as a treatment for a genetic disease. While CRISPR-based gene therapies could potentially…

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Genomic insights into Plasmodium vivax population structure and diversity in central Africa | Malaria Journal

Hamblin MT, Di Rienzo A. Detection of the signature of natural selection in humans: evidence from the Duffy blood group locus. Am J Hum Genet. 2000;66:1669–79. Article  CAS  PubMed  PubMed Central  Google Scholar  Hamblin MT, Thompson EE, Di Rienzo A. Complex signatures of natural selection at the Duffy blood group…

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N6-methyladenosine modification positively regulate Japanese encephalitis virus replication | Virology Journal

Burgess HM, Depledge DP, Thompson L, Srinivas KP, Grande RC, Vink EI, Abebe JS, Blackaby WP, Hendrick A, Albertella MR, Kouzarides T, Stapleford KA, Wilson AC, Mohr I. Targeting the m6A RNA modification pathway blocks SARS-CoV-2 and HCoV-OC43 replication. Genes Dev. 2021;35:1005–19. Article  CAS  PubMed  PubMed Central  Google Scholar  Chambers…

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Causality-enriched epigenetic age uncouples damage and adaptation

Gladyshev, V. N. et al. Molecular damage in aging. Nat. Aging 1, 1096–1106 (2021). Article  PubMed  PubMed Central  Google Scholar  Sziráki, A., Tyshkovskiy, A. & Gladyshev, V. N. Global remodeling of the mouse DNA methylome during aging and in response to calorie restriction. Aging Cell 17, e12738 (2018). Article  PubMed …

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Comparison of capture-based mtDNA sequencing performance between MGI and illumina sequencing platforms in various sample types | BMC Genomics

Hu T, Chitnis N, Monos D, Dinh A. Next-generation sequencing technologies: an overview. Hum Immunol. 2021;82(11):801–11. Article  CAS  Google Scholar  Jeon SA, Park JL, Park SJ, Kim JH, Goh SH, Han JY, Kim SY. Comparison between MGI and Illumina sequencing platforms for whole genome sequencing. Genes Genomics. 2021;43(7):713–24. Article  CAS …

Continue Reading Comparison of capture-based mtDNA sequencing performance between MGI and illumina sequencing platforms in various sample types | BMC Genomics

Altered quorum sensing and physiology of Staphylococcus aureus during spaceflight detected by multi-omics data analysis

CDC. (ed CDC) (U.S. Department of Health and Human Services, CDC; 2019, Atlanta, GA, 2019). Krismer, B., Weidenmaier, C., Zipperer, A. & Peschel, A. The commensal lifestyle of Staphylococcus aureus and its interactions with the nasal microbiota. Nat. Rev. Microbiol. 15, 675–687 (2017). Article  CAS  PubMed  Google Scholar  Somerville, G….

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Would purchasing 5 micrograms of CYP2D6 and trying to convert codeine to morphine at home work?

It’s perhaps more serious chemistry than most people are capable or interested in, but there is a simple, two step process for making a mixture of dihydroheroin and 6-monoacetyldihydromorphine (its main metabolite and equally active) as HBr salts suitable for injection or smoking. 1. Codeine freebase converted to dihydrocodeine base…

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Harmonic bond lammps – LAMMPS Beginners

srz1994 December 29, 2023, 1:46pm 1 Dear LAMMPS users, I am attempting to utilize the harmonic bond potential in LAMMPS. I’m a bit confused about the meaning of the statement in the LAMMPS manual: “Note that the usual 1/2 factor is included in K.” The formula provided in the documentation…

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Neutrophil extracellular trap-induced intermediate monocytes trigger macrophage activation syndrome in adult-onset Still’s disease | BMC Medicine

Wang MY, Jia JC, Yang CD, Hu QY. Pathogenesis, disease course, and prognosis of adult-onset Still’s disease: an update and review. Chin Med J (Engl). 2019;132(23):2856–64. Article  CAS  PubMed  Google Scholar  Feist E, Mitrovic S, Fautrel B. Mechanisms, biomarkers and targets for adult-onset Still’s disease. Nat Rev Rheumatol. 2018;14(10):603–18. Article …

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Notch signaling in thyrocytes is essential for adult thyroid function and mammalian homeostasis

Brent, G. A. Mechanisms of thyroid hormone action. J. Clin. Invest. 9, 3035–3043 (2012). Article  Google Scholar  Iwen, K. A., Oelkrug, R. & Brabant, G. Effects of thyroid hormones on thermogenesis and energy partitioning. J. Mol. Endocrinol. 60, R157–R170 (2018). Article  PubMed  CAS  Google Scholar  Biondi, B. & Wartofsky, L….

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Exploring the Latest Advances in Transcriptomics

Since the idea of genetic regulation was first postulated back in the 1950s, our scientific understanding of the transcriptome has deepened greatly.1 Looking into the transcriptome of cells and tissues has helped scientists to understand the biological processes that drive both health and disease; however, the complex and occasionally mysterious…

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De novo variants underlying monogenic syndromes with intellectual disability in a neurodevelopmental cohort from India

Russell PSS, Nagaraj S, Vengadavaradan A, Russell S, Mammen PM, Shankar SR, et al. Prevalence of intellectual disability in India: a meta-analysis. World J Clin Pediatr. 2022;11:206–14. Article  PubMed  PubMed Central  Google Scholar  Winnepenninckx B, Rooms L, Kooy RF. Mental retardation: a review of the genetic causes. Br J Dev…

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Seroprevalence and Molecular Characterization of B. abortus

Introduction Brucellosis is a zoonotic disease caused by Brucella spp., a gram-negative facultative intracellular coccobacillus.1 These microorganisms can infect livestock, wildlife, and humans, causing significant public concern and substantial agricultural economic loss. Currently, at least six novel Brucella species have been identified: Brucella pinnipedialis, Brucella ceti,2 Brucella papionis,3 Brucella microti,4…

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Two Phase 3 Trials of Datopotamab Deruxtecan Plus Durvalumab Initiated in Patients Across Two Breast Cancer Subtypes | Antibodies

Two Phase 3 Trials of Datopotamab Deruxtecan Plus Durvalumab Initiated in Patients Across Two Breast Cancer Subtypes Details Category: Antibodies Published on Tuesday, 19 December 2023 09:37 Hits: 742 TROPION-Breast04 is evaluating Daiichi Sankyo and AstraZeneca’s datopotamab deruxtecan plus durvalumab as neoadjuvant treatment for early-stage triple negative and HR…

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LncRNA/circRNA-mRNA networks in CARAS | JIR

Introduction Combined allergic rhinitis and asthma syndrome (CARAS), a new terminology introduced by the World Allergy Organization (WAO) in 2004, is an allergic reaction that occurs in the respiratory tract, including upper respiratory tract allergy (allergic rhinitis, AR) and lower respiratory tract allergy (asthma, AS).1,2 The incidence of AS in…

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Characterization of the Spectrum of Mitochondrial DNA Nucleotide Substitutions in Human Populations in High Altitude Environments

Burtscher, J., Mallet, R.T., Pialoux, V., et al., Adaptive responses to hypoxia and/or hyperoxia in humans, Antioxid. Redox Signal., 2022, vol. 37, pp. 887—912. doi.org/10.1089/ars.2021.0280 Article  PubMed  Google Scholar  Chandel, N.S., McClintock, D.S., Feliciano, C.E., et al., Reactive oxygen species generated at mitochondrial complex III stabilize hypoxia-inducible factor-1alpha during hypoxia: a…

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Frontiers Publishing Partnerships | Construction of recombinant adenovirus-5 vector to prevent replication-competent adenovirus occurrence

Introduction In recent years, recombinant adenoviral vectors have been used in different fields of biomedical sciences such as in vitro and in vivo gene transfer, vaccine development, and gene therapy (Russell, 2000; Mitani and Kubo, 2002). Multiple features of recombinant adenoviral vectors such as high packaging capacity for transgene insertion,…

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Analysis of sepsis combined with pulmonary infection by mNGS

Introduction Sepsis is one of the major diseases that poses a serious threat to human health, and its incidence and in-hospital mortality rates remain high despite the continuous updating of sepsis guidelines.1 Its main clinical manifestations are elevated body temperature, chills, and rapid heart rate, and it is most common…

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A super-pangenome of the North American wild grape species | Genome Biology

Alston JM, Sambucci O. Grapes in the world economy. In: Cantu D, Walker MA, editors. The grape genome. Springer International Publishing; 2019. p. 1–24. Google Scholar  Rahemi A, Dodson Peterson JC, Lund KT. Grape rootstocks and related species. Cham: Springer International Publishing; 2022. Walker MA, Heinitz C, Riaz S, Uretsky…

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Characterization of runs of Homozygosity revealed genomic inbreeding and patterns of selection in indigenous sahiwal cattle

Almeida OAC, Moreira GCM, Rezende FM et al (2019) Identification of selection signatures involved in performance traits in a paternal broiler line. BMC Genomics 20:1–20. doi.org/10.1186/s12864-019-5811-1 Article  Google Scholar  Alshawi A, Essa A, Al-Bayatti S, Hanotte O (2019) Genome Analysis Reveals Genetic Admixture and Signature of Selection for Productivity and…

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Assessment of genetic diversity, population structure and wolf-dog hybridisation in the Eastern Romanian Carpathian wolf population

Kershaw, F. et al. The Coalition for Conservation Genetics: Working across organizations to build capacity and achieve change in policy and practice. Conserv. Sci. Pract. 4, e12635 (2022). Article  Google Scholar  Waits, L. P. & Paetkau, D. Noninvasive genetic sampling tools for wildlife biologists: a review of applications and recommendations…

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Sequencing 101: Structural variation – PacBio

Over the last 50 years, many monumental achievements in genetics and biology have unfolded before our eyes. From the invention of DNA sequencing technologies to the completion of the human genome project and the emergence of genomic medicine, we have made many intellectual and technological leaps in our understanding of…

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Plasma cell-free DNA 5-hydroxymethylcytosine and whole-genome sequencing signatures for early detection of esophageal cancer

Waters JK, Reznik SI. Update on management of squamous cell esophageal cancer. Curr Oncol Rep. 2022;24:375–85. Article  PubMed  Google Scholar  Sung H, Ferlay J, Siegel RL, Laversanne M, Soerjomataram I, Jemal A, Bray F. Global cancer statistics 2020: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185…

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Perception of genomic newborn screening among peripartum mothers

Therrell BL, Padilla CD, Loeber JG, Kneisser I, Saadallah A, Borrajo GJC, et al. Current status of newborn screening worldwide: 2015. Semin Perinatol. 2015;39:171–87. Article  PubMed  Google Scholar  Battelino T, Kržišnik C, Pavlin K. Early detection and follow-up of children with phenylketonuria in Slovenia. Zdr Vestn. 1994;63:25–8. Google Scholar  Lampret…

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Validation of Oxford nanopore sequencing for improved New World Leishmania species identification via analysis of 70-kDA heat shock protein | Parasites & Vectors

Akhoundi M, Downing T, Votypka J, Kuhls K, Lukes J, Cannet A, et al. Leishmania infections: molecular targets and diagnosis. Mol Aspects Med. 2017;57:1–29. Article  PubMed  Google Scholar  Akhoundi M, Kuhls K, Cannet A, Votypka J, Marty P, Delaunay P, et al. A historical overview of the classification, evolution, and…

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First complete mitogenome of Massarineae and its contribution to phylogenetic implications in Pleosporales

Crous, P. W. et al. Fungal Planet description sheets: 214–280. Persoonia 32, 184–306 (2014). Article  PubMed  PubMed Central  Google Scholar  Zhang, Y. et al. Multi-locus phylogeny of Pleosporales: A taxonomic, ecological and evolutionary re-evaluation. Stud. Mycol. 64, 85–105 (2009). Article  PubMed  PubMed Central  Google Scholar  Schoch, C. L. et al….

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A Database of RNA Modifications

Modomics – A Database of RNA Modifications RsmA from Thermus thermophilus – protein summary. ID Card: Full name: Ribosomal RNA small subunit methyltransferase A Synonym: KsgA, TTHA0083 GI: 55980052 COG: COG0030 UniProt: Q5SM60 Structures: | 3FUT | 3FUU | 3FUW | 3FUV | 3FUX | Enzyme type: methyltransferase Position of…

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TWAS revealed significant causal loci for milk production and its composition in Murrah buffaloes

Cao, C. et al. Power analysis of transcriptome-wide association study: Implications for practical protocol choice. PLoS Genet. 17(2), e1009405 (2021). Article  CAS  PubMed  PubMed Central  Google Scholar  De Camargo, G. M. F. et al. Prospecting major genes in dairy buffaloes. BMC Genomics 16, 1–14 (2015). Article  Google Scholar  El-Halawany, N….

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Arsenic is a potent co-mutagen of ultraviolet light

Barnes, J. L., Zubair, M., John, K., Poirier, M. C. & Martin, F. L. Carcinogens and DNA damage. Biochem. Soc. Trans. 46, 1213–1224 (2018). Article  CAS  PubMed  PubMed Central  Google Scholar  Ames, B. N., Durston, W. E., Yamasaki, E. & Lee, F. D. Carcinogens are mutagens: a simple test system…

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Multipli fix ti/spring commands – LAMMPS

m.adibi December 16, 2023, 6:30am 1 Greetings, I am trying to calculate the free energy of complex crystals where there are two types of atoms. I know that fix ti/spring can be used to find the free energy of simple crystals with only a single atom type. Now I was…

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First report of cutaneous leishmaniasis caused by Leishmania donovani in Ethiopia | Parasites & Vectors

Alvar J, Vélez ID, Bern C, Herrero M, Desjeux P, Cano J, et al. Leishmaniasis worldwide and global estimates of its incidence. PLoS ONE. 2012. doi.org/10.1371/journal.pone.0035671. Article  PubMed  PubMed Central  Google Scholar  Gadisa E, Tsegaw T, Abera A, Elnaiem DE, Den Boer M, Aseffa A, et al. Eco-epidemiology of visceral…

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Gadolinium Oxide Nanoparticles reinforce immune response

Boyi Yu,1– 4 Xuanyi Lu,5 Xianglong Feng,1– 4 Ting Zhao,1– 4 Jiaxin Li,1– 4 Yudie Lu,5 Fei Ye,1– 4 Xiongxiong Liu,1– 4 Xiaogang Zheng,1– 4 Zheyu Shen,5 Xiaodong Jin,1– 4 Weiqiang Chen,1– 4 Qiang Li1– 4 1Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, People’s Republic of…

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Diversity and dissemination of viruses in pathogenic protozoa

Wang, A. L. & Wang, C. C. Viruses of the protozoa. Annu. Rev. Microbiol. 45, 251–263 (1991). Article  CAS  PubMed  Google Scholar  Banik, G., Stark, D., Rashid, H. & Ellis, J. Recent advances in molecular biology of parasitic viruses. Infect. Disord. – Drug Targets 14, 155–167 (2015). Article  Google Scholar …

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PRRG4 regulates mitochondrial function and promotes migratory behaviors of breast cancer cells through the Src-STAT3-POLG axis | Cancer Cell International

Sung H, Ferlay J, Siegel RL, Laversanne M, Soerjomataram I, Jemal A, Bray F. Global cancer statistics 2020: GLOBOCAN estimates of incidence and mortality Worldwide for 36 cancers in 185 countries. CA Cancer J Clin. 2021;71(3):209–49. doi.org/10.3322/caac.21660. Article  PubMed  Google Scholar  Hu G, Chong RA, Yang Q, Wei Y, Blanco…

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Chromosome-level genome assembly of the Stoliczka’s Asian trident bat (Aselliscus stoliczkanus)

Dobson, G. E. On a new genus and species of Rhinolophidae, with description of a new species of Vesperus, and notes on some other species of insectivorous bats from Persia. J. Asiat. Soc. Bengal. 40, 455–461 (1871). Google Scholar  Bates, P., Bumrungsri, S., Francis, C., Csorba, G. & Furey, N….

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Precision Medicine: A New Era in Cancer Therapy

Precision medicine can offer improved clinical outcomes by assessing the unique characteristics of tumors, such as their likelihood of developing resistance to chemotherapy. Stay up to date on the latest science with Brush Up Summaries.  Precision Medicine in Cancer Precision medicine for cancer treatment involves tailoring treatments to an individual…

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Fatty Acid Metabolism-Related lncRNAs as Biomarkers for SKCM

Introduction Skin cutaneous melanoma (SKCM), as one of the most aggressive types of cancer due to its elevated degree of heterogeneity, has gained increasing attention during the past few decades.1 Also known as “the cancer that rises with the sun”,2 melanoma originates from cancerous melanocytes due to molecular or genetic…

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Maternal dominance contributes to subgenome differentiation in allopolyploid fishes

Otto, S. P. & Whitton, J. Polyploid incidence and evolution. Annu. Rev. Genet. 34, 401–437 (2000). Article  CAS  PubMed  Google Scholar  Van de Peer, Y., Maere, S. & Meyer, A. The evolutionary significance of ancient genome duplications. Nat. Rev. Genet. 10, 725–732 (2009). Article  PubMed  Google Scholar  Comai, L. The…

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SOCS3 inhibiting JAK-STAT pathway enhances oncolytic adenovirus efficacy by potentiating viral replication and T-cell activation

Kaufman HL, Kohlhapp FJ, Zloza A. Oncolytic viruses: a new class of immunotherapy drugs. Nat Rev Drug Discov. 2015;14:642–62. Article  CAS  PubMed  PubMed Central  Google Scholar  Kessler T, Wick W. Oncolytic virotherapy: potentially a game-changing tumor treatment. Cancer Cell. 2021;39:753–5. Article  CAS  PubMed  Google Scholar  Koch J, Schober SJ, Hindupur…

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Identification of Differentially Expressed Genes in Human Colorectal Cancer Using RNASeq Data Validated on the Molecular Level with Real-Time PCR

Allam RM, Al-Abd AM, Khedr A, Sharaf OA, Nofal SM, Khalifa AE, Mosli HA, Abdel-Naim AB (2018) Fingolimod interrupts the cross talk between estrogen metabolism and sphingolipid metabolism within prostate cancer cells. Toxicol Lett 291:77–85 Article  CAS  PubMed  Google Scholar  Andrews S et al (2010) FastQC: a quality control tool…

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File:FAM86B1 540px.gif – Wikipedia

Summary DescriptionFAM86B1 540px.gif English: Protein structure of human FAM86B1 isoform 1 predicted by AlphaFold. Colored by secondary structure, with alpha helices in red and beta strands in yellow. The SKL2 peroxisomal targeting signal is shown in green. Remaining coils are blue. gif shows FAM86B1 slowly spinning, so that the full…

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Archaic Introgression Shaped Human Circadian Traits | Genome Biology and Evolution

Abstract When the ancestors of modern Eurasians migrated out of Africa and interbred with Eurasian archaic hominins, namely, Neanderthals and Denisovans, DNA of archaic ancestry integrated into the genomes of anatomically modern humans. This process potentially accelerated adaptation to Eurasian environmental factors, including reduced ultraviolet radiation and increased variation in…

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Viruses under the Antarctic Ice Shelf are active and potentially involved in global nutrient cycles

Rignot, E., Jacobs, S., Mouginot, J. & Scheuchl, B. Ice-shelf melting around antarctica. Science (80-) 341, 266–270 (2013). Article  ADS  CAS  Google Scholar  Wadham, J. L. et al. Ice sheets matter for the global carbon cycle. Nat. Commun. 10, 1–17 (2019). Google Scholar  Adusumilli, S., Fricker, H. A., Medley, B.,…

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Potential energy associated with a molecule – LAMMPS

I am trying to simuate ring polymers in lammps. I want to put constraint on its area by associating a potential energy porpotional to its area .The area can be calculated from all its positions of beads if provided in a serial manner .I am trying it by creating a…

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Chromosome-level genome assembly of the Asian spongy moths Lymantria dispar asiatica

Boukouvala, M. C. et al. Lymantria dispar (L.) (Lepidoptera: Erebidae): Current Status of Biology, Ecology, and Management in Europe with Notes from North America. Insects 13 (2022). Keena M. A., Richards, J. Y. Comparison of Survival and Development of Gypsy Moth Lymantria dispar L. (Lepidoptera: Erebidae) Populations from Different Geographic…

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Whole mitochondrial and chloroplast genome sequencing of Tunisian date palm cultivars: diversity and evolutionary relationships | BMC Genomics

Johnson DV, Al-Khayri JM, Jain SM. Introduction: Date Production Status and Prospects in Africa and the Americas. In: Al-Khayri J, Jain S, Johnson D, editors. Date Palm Genetic Resources and Utilization: Volume 1: Africa and the Americas. Springer Netherlands, Dordrecht; 2015. p. 1–18. doi.org/10.1007/978-94-017-9694-1_1 Gros-Balthazard M, Hazzouri KM, Flowers JM. Genomic…

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Increasing Widespread Accessibility of Molecular Testing for Oncology Research

Advancements in cancer diagnostics and monitoring have revolutionized the way we understand and treat this complex disease. The advent of molecular technologies for analyzing nucleic acids has made it possible to detect, analyze and monitor cancer more precisely and sensitively than ever before. Furthermore, it has made noninvasive liquid biopsy…

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Drug repositioning using multiple gene expression profiles

Chuo University’s Professor Y-h. Taguchi places focus on drug repositioning using multiple gene expression profiles In my previous manuscripts (1-3), I introduced our studies of in silico drug repositioning using gene expression profiles. Nevertheless, in these studies, we could use the single gene expression profile to perform in silico drug…

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dashed PDB file/OXT residues

I think it is clear what is going on once you do a few things. Download and read the header of the PDB file for 3odu: HEADER SIGNALING PROTEIN, HYDROLASE 11-AUG-10 3ODU TITLE THE 2.5 A STRUCTURE OF THE CXCR4 CHEMOKINE RECEPTOR IN COMPLEX WITH TITLE 2 SMALL MOLECULE ANTAGONIST…

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Topological structures and syntenic conservation in sea anemone genomes

Putnam, N. H. et al. Sea anemone genome reveals ancestral eumetazoan gene repertoire and genomic organization. Science 317, 86–94 (2007). Article  ADS  CAS  PubMed  Google Scholar  Chapman, J. A. et al. The dynamic genome of Hydra. Nature 464, 592–596 (2010). Article  ADS  CAS  PubMed  PubMed Central  Google Scholar  Srivastava, M….

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metadynamics restart: CHOLESKY

Dear developers and users: I wish to ask what to do,  if using a restart file from a previous metadynamic run  (updated to inp extension: please, see the attached) CP2K terminates with a notice Cholesky decompose failed: the matrix is not positive definite or * *    |      …

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Molecular Techniques | SpringerLink

Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, Brown CG, Hall KP, Evers DJ, Barnes CL, Bignell HR et al (2008) Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456:53–59 CrossRef  CAS  PubMed  PubMed Central  Google Scholar  Büyükköroğlu G, Dora DD, Özdemir F, Hızel C (2018)…

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Heavy-chain antibody targeting of CD38 NAD+ hydrolase ectoenzyme to prevent fibrosis in multiple organs

Asano, Y. & Varga, J. Rationally-based therapeutic disease modification in systemic sclerosis: Novel strategies. Semin. Cell Dev. Biol. 101, 148–160. doi.org/10.1016/j.semcdb.2019.12.007 (2019). Article  Google Scholar  Allanore, Y. et al. Systemic sclerosis. Nat. Rev. Dis. Prim. 1, 15002. doi.org/10.1038/nrdp.2015.2 (2015). Article  PubMed  Google Scholar  Varga, J. & Abraham, D. Systemic sclerosis:…

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Cas9-induced targeted integration of large DNA payloads in primary human T cells via homology-mediated end-joining DNA repair

Khan, S. et al. Role of recombinant DNA technology to improve life. Int. J. Genomics Proteomics 2016, 2405954 (2016). Google Scholar  Spolski, R., Li, P. & Leonard, W. J. Biology and regulation of IL-2: from molecular mechanisms to human therapy. Nat. Rev. Immunol. 18, 648–659 (2018). Article  CAS  PubMed  Google…

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High-throughput sequencing of Diatoms using V4 region of 18S rRNA gene in Bayug Island, Iligan City, Philippines

Almarez DN, Almarez FJS, Baulete EM. 2014. Bayug Island Aquasilvi Program: An Eco-Governance Strategy for Climate Change Adaptation and Mitigation. J Govern Dev 10(2): 35-54. DOI: 10.32890/jgd. Alongi DM. 2014. Carbon cycling and storage in mangrove forests. Ann Rev Mar Sci 6: 195-219. DOI: 10.1146/annurev-marine-010213-135020. Balint M, Pfenninger M, Grossart…

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The Protective Mechanism of TFAM on Mitochondrial DNA and its Role in Neurodegenerative Diseases

Annesley SJ, Fisher PR (2019) Mitochondria in health and disease. Cells 8(7). doi.org/10.3390/cells8070680 Cannino G, Ferruggia E, Luparello C, Rinaldi AM (2009) Cadmium and mitochondria. Mitochondrion 9(6):377–384. doi.org/10.1016/j.mito.2009.08.009 Article  CAS  PubMed  Google Scholar  Bonora M, Missiroli S, Perrone M, Fiorica F, Pinton P, Giorgi C (2021) Mitochondrial control of genomic…

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Reproxalap in Patients with Seasonal Allergic Conjunctivitis

Introduction Reproxalap, a novel chemical entity in late-stage clinical development for the treatment of ocular inflammation, chemically sequesters a class of small molecules known as reactive aldehyde species (RASP). Via covalent binding to amine and thiol residues, RASP modulate the structure and function of proteins in an analog manner1 depending…

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A laboratory ice machine as a cold oligotrophic artificial microbial niche for biodiscovery

Flemming, H.-C. & Wuertz, S. Bacteria and archaea on earth and their abundance in biofilms. Nat. Rev. Microbiol. 17, 247–260 (2019). Article  CAS  PubMed  Google Scholar  Flemming, H.-C., Neu, T. R. & Wozniak, D. J. The EPS matrix: The “house of biofilm cells”. J. Bacteriol. 189, 7945–7947 (2007). Article  CAS …

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Phyloecology of nitrate ammonifiers and their importance relative to denitrifiers in global terrestrial biomes

Steffen, W. et al. Planetary boundaries: guiding human development on a changing planet. Science 347, 1259855 (2015). Article  PubMed  Google Scholar  Kanter, D. R. et al. Nitrogen pollution policy beyond the farm. Nat. Food 1, 27–32 (2020). Article  ADS  Google Scholar  Tian, H. et al. A comprehensive quantification of global…

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An ncRNA transcriptomics-based approach to design siRNA molecules against SARS-CoV-2 double membrane vesicle formation and accessory genes | BMC Infectious Diseases

When compared to the genomes of other RNA viruses, coronaviruses have been found to possess largest genome sizes. They are capable of establishing reservoirs in both human and zoonotic populations, enabling their transmission and circulation among a range of animal hosts, including bats, pangolins, civets, cats, mice, pigs, whales, dogs,…

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Generating a New sgRNA Vector, pGL3-U6-sgRNA-PGK-mRFP-T2A-PuroR, to Improve Base Editing

doi: 10.32371/jger/246146. Epub 2022 Dec 17. Affiliations Expand Affiliation 1 Center for Molecular and Cellular Biosciences, School of Biological, Environmental, and Earth Sciences, University of Southern Mississippi, Hattiesburg, Mississippi 39406, United States of America. Free PMC article Item in Clipboard Tolulope E Ayo et al. J Genome Ed Regul. 2022. Free…

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Regulation of the ER-Resident Mannosidase EDEM2 in HEK293 Cells

Abstract EDEM2 plays an important role as the first enzyme that acts during mannose trimming of N-glycosylated proteins in the ERAD machinery. Although EDEM2 expression has been reported to be transcriptionally regulated by the IRE1-sXBP1 pathway, very little is known about how endogenous EDEM2 protein expression is regulated. In this…

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Analysis of geometric morphometrics and molecular phylogeny for Anopheles species in the Republic of Korea

World Health Organization (WHO). WHO malaria report. 2022 www.who.int/publications/i/item/9789240064898 (2022). Savi, M. K. An overview of malaria transmission mechanisms, control, and modeling. Med. Sci. 11, 3 (2023). Google Scholar  Bahk, Y. Y. et al. Epidemiological characteristics of re-emerging vivax malaria in the Republic of Korea (1993–2017). Korean J. Parasitol. 56,…

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Construction of a risk stratification model integrating ctDNA to predict response and survival in neoadjuvant-treated breast cancer | BMC Medicine

Sung H, Ferlay J, Siegel RL, Laversanne M, Soerjomataram I, Jemal A, Bray F. Global Cancer Statistics 2020: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA Cancer J Clin. 2021;71(3):209–49. Article  PubMed  Google Scholar  Giaquinto AN, Sung H, Miller KD, Kramer JL, Newman LA,…

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Insight into chloroplast genome structural variation of the Mongolian endemic species Adonis mongolica (Ranunculaceae) in the Adonideae tribe

Wang, W. T. Revision of Adonis (Ranunculaceae). Bull. Bot. Res. 14, 1–31 (1994). Google Scholar  Gao, T. et al. Evaluating the feasibility of using candidate DNA Barcodes in discriminating species of the large Asteraceae family. BMC Evol. Biol. 10, 324 (2016). Article  Google Scholar  Conti, F. et al. Adonis fucensis…

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IJMS | Free Full-Text | Spontaneous Mutations in Saccharomyces cerevisiae mtDNA Increase Cell-to-Cell Variation in mtDNA Amount

This is an early access version, the complete PDF, HTML, and XML versions will be available soon. Open AccessArticle by 1, 1 and 2,* 1 Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow 119991, Russia 2 Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia…

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Panel-based RNA fusion sequencing improves diagnostics of pediatric acute myeloid leukemia

Rasche M, Zimmermann M, Borschel L, Bourquin J, Dworzak M, Klingebiel T, et al. Successes and challenges in the treatment of pediatric acute myeloid leukemia: a retrospective analysis of the AML-BFM trials from 1987 to 2012. Leukemia. 2018;32:2167–77. Article  PubMed  PubMed Central  Google Scholar  Manola KN. Cytogenetics of pediatric acute…

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Transition of allele-specific DNA hydroxymethylation at regulatory loci is associated with phenotypic variation in monozygotic twins discordant for psychiatric disorders | BMC Medicine

Lichtenstein P, Yip BH, Bjork C, Pawitan Y, Cannon TD, Sullivan PF, Hultman CM. Common genetic determinants of schizophrenia and bipolar disorder in Swedish families: a population-based study. Lancet. 2009;373(9659):234–9. Article  PubMed  Google Scholar  Maurano MT, Humbert R, Rynes E, Thurman RE, Haugen E, Wang H, Reynolds AP, Sandstrom R,…

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Dispersal from the Qinghai-Tibet plateau by a high-altitude butterfly is associated with rapid expansion and reorganization of its genome

Zachos, J., Pagani, H., Sloan, L., Thomas, E. & Billups, K. Trends, rhythms, and aberrations in global climate 65 Ma to present. Science 292, 686–693 (2001). Article  ADS  CAS  PubMed  Google Scholar  Favre, A. et al. The role of the uplift of the Qinghai-Tibetan Plateau for the evolution of Tibetan…

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RPTOR mutation: a novel predictor of efficacious immunotherapy in melanoma

Li Z, Gao Y, Cao Y et al (2023) Extracellular RNA in Melanoma: advances, challenges, and opportunities. Front Cell Dev Biol 11:1141543. doi.org/10.3389/fcell.2023.1141543 Article  PubMed  PubMed Central  Google Scholar  Hamid O, Cowey CL, Offner M, Faries M, Carvajal RD (2019) Efficacy, Safety, and tolerability of approved combination BRAF and MEK…

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Wide bovine tick-borne pathogen spectrum: Predominancy of Theileria annulata and the first molecular detection of Ehrlichia minasensis in Turkey

Agina OA, Shaari MS, Isa NMM, Ajat M, Zamri-Saad M, Hamzah H (2020) Clinical pathology, immunopathology and advanced vaccine technology in bovine theileriosis: A review. Pathogens 9:697. doi.org/10.3390/pathogens9090697 Article  PubMed  PubMed Central  CAS  Google Scholar  Aktas M (2014) A survey of ixodid tick species and molecular identification of tick-borne pathogens….

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Screening for lipid nanoparticles that modulate the immune activity of helper T cells towards enhanced antitumour activity

Huang, Q., Zeng, J. & Yan, J. COVID-19 mRNA vaccines. J. Genet. Genomics 48, 107–114 (2021). Article  CAS  PubMed  PubMed Central  Google Scholar  Huang, S., Zhu, Y., Zhang, L. & Zhang, Z. Recent advances in delivery systems for genetic and other novel vaccines. Adv. Mater. 34, e2107946 (2022). Article  PubMed …

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Genetic architecture of cardiac dynamic flow volumes

Virani, S. S. et al. Heart disease and stroke statistics-2021 update: a report from the American Heart Association. Circulation 143, e254–e743 (2021). Article  PubMed  Google Scholar  Nauffal, V. et al. Genetics of myocardial interstitial fibrosis in the human heart and association with disease. Nat. Genet. 55, 777–786 (2023). Article  CAS …

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Origin and evolution of the triploid cultivated banana genome

Rouard, M. et al. Three new genome assemblies support a rapid radiation in Musa acuminata (wild banana). Genome Biol. Evol. 10, 3129–3140 (2018). CAS  PubMed  PubMed Central  Google Scholar  Langhe, E. D., Vrydaghs, L., Maret, P. D., Perrier, X. & Denham, T. Why bananas matter: an introduction to the history…

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A CNN based m5c RNA methylation predictor

Hammad, M. et al. A novel end-to-end deep learning approach for cancer detection based on microscopic medical images. Biocybern. Biomed. Eng. 42(3), 737–748 (2022). Article  Google Scholar  Hammad, M. et al. Efficient multimodal deep-learning-based covid-19 diagnostic system for noisy and corrupted images. J. King Saud Univ.-Sci. 34(3), 101898 (2022). Article …

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Uncovering myocardial infarction genetic signatures using GWAS exploration in Saudi and European cohorts

Benjamin, E. J. et al. Heart disease and stroke statistics-2019 update: A report from the American Heart Association. Circulation 139, e56–e528 (2019). Article  PubMed  Google Scholar  Yusuf, S. et al. Effect of potentially modifiable risk factors associated with myocardial infarction in 52 countries (the INTERHEART study): Case-control study. Lancet 364,…

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Huge Etotal difference between TIP4p implicit VS explicit methods from the manual script – LAMMPS Beginners

Have you read the manual: Yes. I used the scripts from Lammps manualMD simulation experience: Yes, several years, with Gromacs, Amber and OpenMMLammps experience: No. Started recentlyLammps version: 20230208Lammps execution command: mpirun -np xxx lmp -in in.tip4pCan you provide your input scripts and results: Yes. Please check this: Input scripts…

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A minimally invasive, field-applicable CRISPR/Cas biosensor to aid in the detection of Pseudogymnoascus destructans, the causative fungal agent of white-nose syndrome in bats

doi: 10.1111/1755-0998.13902. Online ahead of print. Affiliations Expand Affiliations 1 U.S. Geological Survey, Wetland and Aquatic Research Center, Gainesville, Florida, USA. 2 Washington Department of Fish and Wildlife, Olympia, Washington, USA. 3 Cherokee Nation System Solutions, Contractor to the U.S. Geological Survey, Gainesville, Florida, USA. Item in Clipboard Adam A…

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In situ metagenomics: A platform for rapid sequencing and analysis of metagenomes in less than one day

doi: 10.1111/1755-0998.13909. Online ahead of print. Affiliations Expand Affiliations 1 Microbiome Analysis Laboratory, Systems Biology Department, CNB-CSIC, Madrid, Spain. 2 Departamento de Ecoloxía e Bioloxía Animal, Centro de Investigación Mariña, Universidade de Vigo, Vigo, Spain. 3 Department of Biogeochemistry and Microbial Ecology, National Museum of Natural Sciences (MNCN-CSIC), Madrid, Spain….

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Haplotype-resolved genome of heterozygous African cassava cultivar TMEB117 (Manihot esculenta)

Wang, P. et al. The genome evolution and domestication of tropical fruit mango. Genome Biol 21 (2020). Tang, C. et al. The rubber tree genome reveals new insights into rubber production and species adaptation. Nat Plants 2 (2016). Bredeson, J. V. et al. Sequencing wild and cultivated cassava and related…

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Glabridin improves autoimmune disease in Trex1-deficient mice by reducing type I interferon production | Molecular Medicine

Bustin SA, Benes V, Garson JA, Hellemans J, Huggett J, Kubista M, Mueller R, Nolan T, Pfaffl MW, Shipley GL, Vandesompele J, Wittwer CT. The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. Clin Chem. 2009;55:611–22. Article  CAS  PubMed  Google Scholar  Chen Q, Sun L, Chen ZJ….

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Freshwater Viral Metagenome Analyses Targeting dsDNA Viruses

doi: 10.1007/978-1-0716-3515-5_3. Affiliations Expand Affiliations 1 Division of Environmental Materials, Honam National Institute of Biological Resources, Mokpo, Republic of Korea. 2 Department of Biological Sciences and Bioengineering, Inha University, Incheon, Republic of Korea. chojc@inha.ac.kr. Item in Clipboard Kira Moon et al. Methods Mol Biol. 2024. Show details Display options Display options…

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Effects of diabetes mellitus and glycemic traits on cardiovascular morpho-functional phenotypes | Cardiovascular Diabetology

American Diabetes A. Economic costs of Diabetes in the U.S. in 2017. Diabetes Care. 2018;41(5):917–28. Article  Google Scholar  Linssen PBC, Veugen MGJ, Henry RMA, van der Kallen CJH, Kroon AA, Schram MT, Brunner-La Rocca HP, Stehouwer CDA. Associations of (pre)Diabetes with right ventricular and atrial structure and function: the Maastricht…

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The MetaInvert soil invertebrate genome resource provides insights into below-ground biodiversity and evolution

FAO, ITPS, GSBI, CBD & EC. State of knowledge of soil biodiversity – Status, challenges and potentialities, Report 2020. (FAO). doi.org/10.4060/cb1928en. 2020. Potapov, A. M. et al. Feeding habits and multifunctional classification of soil-associated consumers from protists to vertebrates. Biol. Rev. 97, 1057–1117 (2022). Article  PubMed  Google Scholar  García-Palacios, P.,…

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From Metagenomics to Ecogenomics: NGS-Based Approaches for Discovery of New Circular DNA Single-Stranded Viral Species

doi: 10.1007/978-1-0716-3515-5_7. Affiliations Expand Affiliations 1 Departamento de Biotecnología Agrícola, Instituto Politécnico Nacional, CIIDIR Unidad Sinaloa, Guasave, Sinaloa, Mexico. 2 Department of Plant Biochemistry, Center for Plant Molecular Biology (ZMBP), Eberhard Karls University, Tübingen, Germany. 3 Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga-Consejo Superior de Investigaciones…

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Metagenomics reveals effects of fluctuating water conditions on functional pathways in plant litter microbial community

Keller, J. K. Wetlands and the global carbon cycle: what might the simulated past tell us about the future?. New Phytol. 192, 789–792 (2011). Article  CAS  PubMed  Google Scholar  Dolinar, N., Rudolf, M., Šraj, N. & Gaberščik, A. Environmental changes affect ecosystem services of the intermittent Lake Cerknica. Ecol. Complex….

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How to group atoms as molecules in reax – LAMMPS General Discussion

Using Aug 2023 version of Lammps This is a rather basic issue. I am following the paper by Kim to model , water, ethahol and phosphoric acid adsorbed to TiO2 using their ff.Reactive MD-force field: Kim, S.-Y., van Duin, A. C. T., and Kubicki, J. D., 2012, Molecular dynamics simulations…

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HER2 low expression breast cancer subtyping and their correlation with prognosis and immune landscape based on the histone modification related genes

Barzaman, K. et al. Breast cancer: Biology, biomarkers, and treatments. Int. Immunopharmacol. 84, 106535 (2020). Article  CAS  PubMed  Google Scholar  Siegel, R. L., Miller, K. D., Wagle, N. S. & Jemal, A. Cancer statistics, 2023. CA Cancer J. Clin. 73(1), 17–48 (2023). Article  PubMed  Google Scholar  Mueller, C., Haymond, A.,…

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An error occurred in the pull code to implement the methane gas compression process under a certain – User discussions

Jiang December 8, 2023, 2:40pm 1 GROMACS version:2018.8GROMACS modification: Yes/NoHere post your questionHere is my code, I want to construct methane gas under certain temperature and pressure conditions by applying pressure to the graphene above, but I am not very clear about how to define the direction of stretching in…

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CircRNA and Stroke: New Insight of Potential Biomarkers and Therapeutic Targets

Diener HC, Hankey GJ (2020) Primary and secondary Prevention of ischemic Stroke and Cerebral Hemorrhage: JACC Focus Seminar. J Am Coll Cardiol 75(15):1804–1818 Article  PubMed  Google Scholar  Dou Z, Yu Q, Wang G, Wu S, Reis C, Ruan W, Yan F, Chen G (2020) Circular RNA expression profiles alter significantly…

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New Symmetry Annotation Feature for Macromolecular Assemblies

In an effort to improve the understanding of the structure and function of macromolecular assemblies, a new feature has been introduced to annotate and display symmetry in these structures. This new process, powered by Ananas, provides global symmetry data for each new assembly on a weekly basis. This underlying data…

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Future-focused therapeutics | Scientist Live

Base editing is bringing the next breakthrough in cell and gene therapy, explains Michelle Fraser. Cell and gene therapies (CGTs) hold the promise to transform medicine for patients globally. These therapies work by correcting DNA to treat a genetic disease, or by modifying cells from the immune system to specifically…

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Advancements in Non-human Forensic DNA Analysis

Alahi MEE, Mukhopadhyay SC (2017) Detection methodologies for pathogen and toxins: a review. Sensors 1885:17 Google Scholar  Aly SM, Sabri DM (2015) Next generation sequencing (NGS): a golden tool in forensic toolkit. Archiwum Medycyny Sądowej i Kryminologii/Archives of Forensic Medicine and Criminology 65(4):260–271 Google Scholar  Amendt J, Richards CS, Campobasso…

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Psychological impact of additional findings detected by genome-wide Non-Invasive Prenatal Testing (NIPT): TRIDENT-2 study

Lo YMD, Corbetta N, Chamberlain PF, Rai V, Sargent IL, Redman CWG, et al. Presence of fetal DNA in maternal plasma and serum. Lancet. 1997;350:485–7. Article  CAS  PubMed  Google Scholar  Warsof SL, Larion S, Abuhamad AZ. Overview of the impact of noninvasive prenatal testing on diagnostic procedures. Prenat Diagn. 2015;35:972–9….

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