bluuebunny/crossref_metadata_2025_split huggingface dataset:
Designing isolation guidelines for COVID-19 patients utilizing rapid antigen tests: a simulation study using viral dynamics models
Authors: Jeong Yong Dam , Ejima Keisuke , Kim Kwang Su , Joohyeon Woo , Iwanami Shoya , Fujita Yasuhisa , Jung Il Hyo , Shibuya Kenji , Iwami Shingo , Bento Ana I. , Ajelli Marco 
Published: January 2022

AbstractAppropriate isolation guidelines for COVID-19 patients are warranted. Currently, isolating for fixed time is adapted in most countries. However, given the variability in viral dynamics between patients, some patients may no longer be infectious by the end of isolation (thus they are redundantly isolated), whereas others may still be infectious. Utilizing viral test results to determine ending isolation would minimize both the risk of ending isolation of infectious patients and the burden due to redundant isolation of noninfectious patients. In our previous study, we proposed a computational framework using SARS-CoV-2 viral dynamics models to compute the risk and the burden of different isolation guidelines with PCR tests. In this study, we extend the computational framework to design isolation guidelines for COVID-19 patients utilizing rapid antigen tests. Time interval of tests and number of consecutive negative tests to minimize the risk and the burden of isolation were explored. Furthermore, the approach was extended for asymptomatic cases. We found the guideline should be designed considering various factors: the infectiousness threshold values, the detection limit of antigen tests, symptom presence, and an acceptable level of releasing infectious patients. Especially, when detection limit is higher than the infectiousness threshold values, more consecutive negative results are needed to ascertain loss of infectiousness. To control the risk of releasing of infectious individuals under certain levels, rapid antigen tests should be designed to have lower detection limits than infectiousness threshold values to minimize the length of prolonged isolation, and the length of prolonged isolation increases when the detection limit is higher than the infectiousness threshold values, even though the guidelines are optimized for given conditions.
Clinical evaluation of the Diagnostic Analyzer for Selective Hybridization (DASH): a point-of-care PCR test for rapid detection of SARS-CoV-2 infection
Authors: Achenbach Chad J , Caputo Matthew , Hawkins Claudia , Balmert Lauren C , Qi Chao , Odorisio Joseph , Dembele Etienne , Jackson Alema , Abbas Hiba , Frediani Jennifer K , Levy Joshua M , Rebolledo Paulina A. , Kempker Russell R. , Esper Annette M. , Lam Wilbur A. , Martin Greg S. , Murphy Robert L 
Published: January 2022

AbstractBackgroundRapid and accurate testing for SARS-CoV-2 is an essential tool in the medical and public health response to the COVID-19 pandemic. An ideal test for COVID-19 would combine the sensitivity of laboratory-based PCR combined with the speed and ease of use of point-of-care (POC) or home-based rapid antigen testing.MethodsTo evaluate the performance of the Diagnostic Analyzer for Selective Hybridization (DASH) SARS-CoV-2 POC PCR (sample insertion to result time of 16 minutes), we conducted a cross-sectional study of adults with and without symptoms of COVID-19 at four clinical sites. We collected two bilateral anterior nasal swabs from each participant and information on COVID-19 symptoms, vaccination, and exposure. One swab was tested with the DASH SARS-CoV-2 POC PCR and the second in a central laboratory using Cepheid Xpert Xpress SARS-CoV-2 PCR. We assessed test concordance and calculated sensitivity, specificity, negative and positive predictive values using Xpert as the “gold standard.”ResultsWe enrolled 315 and analyzed 313 participants with median age 42 years; 65% were female, 62% symptomatic, 75% had received ≥2 doses of mRNA COVID-19 vaccine, and 16% currently COVID-19 positive. There were concordant results for 307 tests indicating an overall agreement for DASH of 0.98 [95% CI 0.96, 0.99] compared to Xpert. DASH performed at 0.96 [95% CI 0.86, 1.00] sensitivity and 0.98 [95% CI 0.96, 1.00] specificity, with a positive predictive value of 0.85 [95% CI 0.73, 0.96] and negative predictive value of 0.996 [95% CI 0.99, 1.00]. The six discordant tests between DASH and Xpert all had high Ct values (>30) on the respective positive assay. DASH and Xpert Ct values were highly correlated (R=0.89 [95% CI 0.81, 0.94]).ConclusionsDASH POC SARS-CoV-2 PCR was accurate, easy to use, and provided fast results in real-life clinical settings with an overall performance similar to an EUA-approved laboratory-based PCR. Its compact design and ease of use are optimal for a variety of healthcare, and potentially community settings, including areas with lack of access to central laboratory-based PCR testing.SummaryDASH is an accurate, easy to use, and fast point-of-care test with applications for diagnosis and screening of SARS-CoV-2 infection.
Substantial immune response in Omicron infected breakthrough and unvaccinated individuals against SARS-CoV-2 variants of concerns
Authors: Yadav Pragya D. , Sapkal Gajanan N. , Sahay Rima R. , Potdar Varsha A. , Deshpande Gururaj R. , Patil Deepak Y. , Nyayanit Dimpal A. , Shete Anita M. , Shastri Jayanthi , Awate Pradeep , Malhotra Bharti , Abraham Priya 
Published: January 2022

AbstractThe recent emergence of highly mutated SARS-CoV-2 Omicron variant has debilitating effect on public health system of the affected countries worldwide. Currently India is facing third wave of COVID-19 pandemic and going through a severe crisis. Within short span of time, the variant has shown high transmissibility and capability of evading the immune response generated against natural infection and vaccination. The immune escape potential of Omicron is a serious concern and further needs to be explored. In the present study, we have assessed the IgG and neutralizing antibody (NAb) response in breakthrough individuals vaccinated with two doses ChAdOx1 nCoV-19 vaccine (n=25), breakthrough individuals vaccinated with two doses of BNT162b2 mRNA vaccine (n=8) and unvaccinated individuals (n=6). All these individuals were infected with Omicron variant. The IgG antibody activity in the sera of the ChAdOx1 nCoV-19 and BNT162b2 mRNA breakthrough individuals was comparable with S1-RBD, while it was lesser in BNT162b2 mRNA breakthrough individuals with N protein and inactivated whole antigen IgG ELISA. BNT162b2 mRNA breakthrough individuals showed moderate reduction in NAb GMTs compared to ChAdOx1 nCoV-19 against Alpha, Beta and Delta. However, 3-fold higher reduction was observed with omicron variant in BNT162b2 mRNA than ChAdOx1 nCoV-19. Apparently, Alpha variant was modestly resistant to the sera of unvaccinated individuals than Beta, Delta and Omicron. Our study demonstrated substantial immune response in the individuals infected with Omicron. The neutralizing antibodies could effectively neutralize the Omicron and other VOCs including the most prevalent Delta variant.
An efficient CRISPR-Cas9 enrichment sequencing strategy for characterizing complex and highly duplicated genomic regions. A case study in the Prunus salicina LG3-MYB10 genes cluster
Authors: Fiol Arnau , Jurado-Ruiz Federico , López-Girona Elena , Aranzana Maria José 
Published: January 2022

ABSTRACTGenome complexity is largely linked to diversification and crop innovation. Examples of regions with duplicated genes with relevant roles in agricultural traits are found in many crops. In both duplicated and non-duplicated genes, much of the variability in agronomic traits is caused by large as well as small and middle scale structural variants (SVs), which highlights the relevance of the identification and characterization of complex variability between genomes for plant breeding. Here we improve and demonstrate the use of CRISPR-Cas9 enrichment combined with long-read sequencing technology to resolve the MYB10 region in the linkage group 3 (LG3) of Japanese plum (Prunus salicina), which has a length from 90 kb to 271 kb according to the P. salicina genomes available. We demonstrate the high complexity of this region, with homology levels between Japanese plum varieties comparable to those between Prunus species. We cleaved MYB10 genes in five plum varieties using the Cas9 enzyme guided by a pool of crRNAs. The barcoded fragments were then pooled and sequenced in a single MinION Oxford Nanopore Technologies (ONT) run, yielding 194 Mb of sequence. The enrichment was confirmed by aligning the long reads to the plum reference genomes, with a mean read on-target value of 4.5% and a depth per sample of 11.9x. From the alignment, 3,261 SNPs and 287 SVs were called and phased. A de novo assembly was constructed for each variety, which also allowed detection, at the haplotype level, of the variability in this region. CRISPR-Cas9 enrichment is a versatile and powerful tool for long-read targeted sequencing even on highly duplicated and/or polymorphic genomic regions, being especially useful when a reference genome is not available. Potential uses of this methodology as well as its limitations are further discussed.
Preclinical Characterization of Relatlimab, a Human LAG-3–Blocking Antibody, Alone or in Combination With Nivolumab
Authors: Thudium Kent , Selby Mark , Zorn Julie A. , Rak Gregory , Wang Xi-Tao , Bunch Roderick Todd , Hogan Jason M. , Strop Pavel , Korman Alan J. 
Published: January 2022

AbstractNovel therapeutic approaches combining immune checkpoint inhibitors are needed to improve clinical outcomes for patients with cancer. Lymphocyte-activation gene 3 (LAG-3) is an immune checkpoint molecule that inhibits T-cell activity and antitumor immune responses, acting through an independent mechanism from that of programmed death-1 (PD-1) and cytotoxic T lymphocyte associated antigen-4 (CTLA-4). Here, we describe the development and preclinical characterization of relatlimab, a human antibody that binds to human LAG-3 with high affinity and specificity to block the interaction of LAG-3 with the ligands MHC II and fibrinogen like protein-1, and to reverse LAG-3–mediated inhibition of T-cell function in vitro. Consistent with previous reports, in mouse models, the combined blockade of LAG-3 and PD-1 with surrogate antibodies resulted in enhanced anti-tumor activity greater than the individual blockade of either receptor. In toxicity studies in cynomolgus monkeys, relatlimab was generally well tolerated when combined with nivolumab. These results are consistent with findings from the RELATIVITY-047 phase 2/3 trial showing that relatlimab combined with nivolumab is a well-tolerated regimen that demonstrated superior progression-free survival compared with nivolumab monotherapy in patients with unresectable or metastatic melanoma.SynopsisPreclinical studies demonstrate that relatlimab specifically blocks the interaction between LAG-3 and its ligands, and provide a biological rationale for combining relatlimab with the anti−PD-1 antibody nivolumab as an effective cancer immunotherapeutic strategy.
Interaction among bacterial cells triggers exit from lag phase
Authors: Ardré Maxime , Doulcier Guilhem , Brenner Naama , Rainey Paul B. 
Published: January 2022

AbstractThe relationship between the number of cells colonizing a new environment and time for resumption of growth is a subject of long-standing interest. In microbiology this is known as the “inoculum effect”. Its mechanistic basis is unclear with possible explanations ranging from the independent actions of individual cells, to collective actions of populations of cells. Progress requires precise measurement of lag time distributions while at the same time, experimentally controlling inoculum size. Here we use a millifluidic droplet device in which the growth dynamics of hundreds of populations founded by different numbers of Pseudomonas fluorescens cells, ranging from a single cell, to one thousand cells, were followed in real time. Our data show that lag phase decreases with inoculum size. The average decrease, variance across droplets, and distribution shapes, follow predictions of extreme value theory, where the inoculum lag time is determined by the minimum value sampled from the single-cell distribution. Our experimental results show that exit from lag phase depends on strong interactions among cells, consistent with a “leader-cell” triggering end of lag phase for the entire population.
MX2 viral substrate breadth and inhibitory activity are regulated by protein phosphorylation
Authors: Betancor Gilberto , Bangham Madeleine , Jeon Jun Ki , Shah Kanisha , Lynham Steven , Jimenez-Guardeño Jose M , Malim Michael H 
Published: January 2022

AbstractHuman immunodeficiency virus type-1 (HIV-1) infection is potently inhibited by human myxovirus resistance 2 (MX2/MxB), which binds to the viral capsid and blocks the nuclear import of viral DNA. We have recently shown that phosphorylation is a key regulator of MX2 antiviral activity, with phosphorylation of serine residues at positions 14, 17 and 18 repressing MX2 function. Here, we extend the study of MX2 post-translational modifications, and identify serine and threonine phosphorylation in all domains of MX2. By substituting these residues with aspartic acid or alanine, hence mimicking the presence or absence of a phosphate group, respectively, we identified key positions that control MX2 antiviral activity. Aspartic acid substitutions of residues Ser306 or Thr334 and alanine substitutions of Thr343 yielded proteins with substantially reduced antiviral activity, whereas the presence of aspartic acid at positions Ser28, Thr151 or Thr343 resulted in enhanced activity: referred to as hypermorphic mutants. In some cases, these hypermorphic mutations, particularly when paired with other MX2 mutations (e.g., S28D/T151D or T151D/T343A) acquired the capacity to inhibit HIV-1 Capsid mutants known to be insensitive to wild type MX2, such as P90A or T210K, as well as MX2-resistant retroviruses such as equine infectious anaemia virus (EIAV) and murine leukaemia virus (MLV). This work highlights the complexity and importance of MX2 phosphorylation in the regulation of antiviral activity, and in the selection of susceptible viral substrates.Author summaryProductive infection by human immunodeficiency virus type-1 (HIV-1) requires the import of viral replication complexes into the nuclei of infected cells. Myxovirus resistance 2 (MX2/MxB) blocks this step, halting nuclear accumulation of viral DNA and virus replication. We recently demonstrated how phosphorylation of a stretch of three serines in the amino-terminal domain of MX2 inhibits the antiviral activity. Here, we identify additional positions in MX2 whose phosphorylation status reduces or enhances antiviral function (hypomorphic and hypermorphic variants, respectively). Importantly, hypermorphic mutant proteins not only increased inhibitory activity against wild type HIV-1, but can also exhibit antiviral capabilities against HIV-1 Capsid mutant viruses that are resistant to wild type MX2. Furthermore, some of these proteins were also able to inhibit retroviruses that are insensitive to MX2. Therefore, we propose that phosphorylation comprises a major element of MX2 regulation and substrate determination.
Biogenic methane cycling is controlled by microbial cohorts
Authors: Mondav Rhiannon , Martin Gaëtan , Peura Sari , Garcia Sarahi L. 
Published: January 2022

AbstractThe generation and consumption of methane by aquatic microbial communities is an important contribution to the global carbon budget. We sought to broaden understanding of consortia members and interactions by combining multiple methods including analysis of natural and cultivated microbial communities. By analysing the microbial community composition and co-occurrence patterns of a lake time-series we were able to identify potential consortia involved in methane cycling. In combination with methane flux, we also analysed the community composition and co-occurrence patterns of reduced microbial model communities with inoculum from the same lake. While the network analyses confirmed many known associations, when combined with results from mixed cultures, we noted new players in methane cycling. Cultivated model communities were shown to be an effective method to explore the rarer but still important players in methane cycling and for identifying new putative members. Here we show that using multiple methods to approach the complex problem of methane cycling consortia yields not just insights into the known taxa but highlights potential new members creating new hypotheses to be tested.
L-threonine mediated DAF-16/HSF-1 activation inhibits ferroptosis and increases healthspan
Authors: Kim Juewon , Jo Yunju , Cho Donghyun , Ryu Dongryeol 
Published: January 2022

SummaryThe pathways that impact longevity in the wake of dietary restriction (DR) pathway remain still ill-defined. Most studies have focused on nutrient limitation and perturbations of energy metabolism to explain the beneficial effects of DR. We showed that the essential amino acid L-threonine was elevated in Caenorhabditis elegans under DR, and that L-threonine supplementation increased its healthspan. To elucidate the underlying mechanism, we conducted metabolic and transcriptomic profiling using LC-MS/MS and RNA-seq analyses in worms that were fed with RNAi to induce loss of function of key candidate mediators and evaluated healthspan. L-threonine supplementation and loss-of-threonine dehydrogenase, which govern L-threonine metabolism, increased the healthspan of C. elegans by attenuating ferroptosis in a ferritin-dependent manner. Tran-scriptomic analysis of C. elegans supplemented with L-threonine showed that FTN-1 encoding ferritin was elevated, implying FTN-1 is an essential mediator of longevity promotion through L-threonine. Organismal ferritin levels were positively correlated with chronological aging and L-thre-onine supplementation further increased ferritin levels, which protected against age-associated ferroptosis through the DAF-16 and HSF-1 pathways. Our investigation uncovered the role of a distinct and universal metabolite, L-threonine, in DR-mediated improvement in organismal healthspan, suggesting it could be an effective intervention for preventing senescence progression and age-induced ferroptosis.
Choice of 16S ribosomal RNA primers impacts urinary microbiota profiling
Authors: Heidrich Vitor , Inoue Lilian T. , Asprino Paula F. , Bettoni Fabiana , Mariotti Antonio C.H. , Bastos Diogo A. , Jardim Denis L.F. , Arap Marco A. , Camargo Anamaria A. 
Published: January 2022

AbstractAccessibility to next-generation sequencing (NGS) technologies has enabled the profiling of microbial communities living in distinct habitats. 16S ribosomal RNA (rRNA) gene sequencing is widely used for microbiota profiling with NGS technologies. Since most used NGS platforms generate short reads, sequencing the full-length 16S rRNA gene is impractical. Therefore, choosing which 16S rRNA hypervariable region to sequence is critical in microbiota profiling studies. All nine 16S rRNA hypervariable regions are taxonomically informative, but due to variability in profiling performance for specific clades, choosing the ideal 16S rRNA hypervariable region will depend on the bacterial composition of the habitat under study. Recently, NGS allowed the identification of microbes in the urinary tract, and urinary microbiota has become an active research area. However, there is no current study evaluating the performance of different 16S rRNA hypervariable regions for urinary microbiota profiling. We collected urine samples from male volunteers and profiled their urinary microbiota by sequencing a panel of six amplicons encompassing all nine 16S rRNA hypervariable regions. After systematically comparing their performance, we show that V1V2 hypervariable regions better assess the taxa commonly present in urine samples and V1V2 amplicon sequencing is more suitable for urinary microbiota profiling. We believe our results will be helpful to guide this crucial methodological choice in future urinary microbiota studies.
Structural Ramifications of Spike Protein D614G Mutation in SARS-CoV-2
Authors: Dokainish Hisham M. , Sugita Yuji 
Published: January 2022

AbstractA single mutation from aspartate to glycine at position 614 has dominated all circulating variants of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). D614G mutation induces structural changes in the Spike (S) protein that strengthen the virus infectivity. Here, we use molecular dynamics simulations to dissect the effects of mutation and 630-loop rigidification on wild-type structure. The introduction of mutation with ordered 630-loop induces structural changes toward S-G614 Cryo-EM structure. An ordered 630-loop weakens the stabilizing interactions of the anionic D614, suggesting its disorder in wild-type. The mutation allosterically alters the receptor binding domain (RBD) forming an asymmetric and mobile Down conformation, which facilitate Up transition. The loss of D614_K854 salt-bridge upon mutation, generally stabilize S-protein protomer, including the fusion peptide proximal region that mediates membrane fusion. Understanding of the molecular basis of D614G is crucial as it dominates in all variants of concern including Delta and Omicron.
Neutralizing immunity in vaccine breakthrough infections from the SARS-CoV-2 Omicron and Delta variants
Authors: Servellita Venice , Syed Abdullah M. , Brazer Noah , Saldhi Prachi , Garcia-Knight Miguel , Sreekumar Bharath , Khalid Mir M. , Ciling Alison , Chen Pei-Yi , Kumar G. Renuka , Gliwa Amelia S. , Nguyen Jenny , Sotomayor-Gonzalez Alicia , Zhang Yueyuan , Frias Edwin , Prostko John , Hackett John , Andino Raul , Doudna Jennifer , Ott Melanie , Chiu Charles Y. 
Published: January 2022

SummaryVirus-like particle (VLP) and live virus assays were used to investigate neutralizing immunity to Delta and Omicron SARS-CoV-2 variants in 239 samples from 125 fully vaccinated individuals. In uninfected, non-boosted individuals, VLP neutralization titers to Delta and Omicron were reduced 2.7-fold and 15.4-fold, respectively, compared to wild-type (WT), while boosted individuals (n=23) had 18-fold increased titers. Delta breakthrough infections (n=39) had 57-fold and 3.1-fold titers whereas Omicron breakthrough infections (n=14) had 5.8-fold and 0.32-fold titers compared to uninfected non-boosted and boosted individuals, respectively. The difference in titers (p=0.049) was related to a higher proportion of moderate to severe infections in the Delta cohort (p=0.014). Correlation of neutralizing and spike quantitative antibody titers was decreased with Delta or Omicron compared to WT. Neutralizing antibodies in Delta and Omicron breakthrough infections increase overall, but the relative magnitude of increase is greater in more clinically severe infection and against the specific infecting variant.