bluuebunny/crossref_metadata_2025_split huggingface dataset:
Detection and classification of SARS‐CoV‐2 using high‐resolution melting analysis
Authors: Sun Liying , Xiu Leshan , Zhang Chi , Xiao Yan , Li Yamei , Zhang Lulu , Ren Lili , Peng Junping 
Published: March 2022

SummaryCoronavirus disease 2019 (COVID‐19), which is caused by severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2), has recently posed a significant threat to global public health. The objective of this study was to develop and evaluate a rapid, expandable and sequencing‐free high‐resolution melting (HRM) approach for the direct detection and classification of SARS‐CoV‐2. Thirty‐one common pathogens that can cause respiratory tract infections were used to evaluate the specificity of the method. Synthetic RNA with serial dilutions was utilized to determine the sensitivity of the method. Finally, the clinical performance of the method was assessed using 290 clinical samples. The one‐step multiplex HRM could accurately identify SARS‐CoV‐2 and differentiate mutations in each marker site within approximately 2 h. For each target, the limit of detection was lower than 10 copies/reaction, and no cross‐reactivity was observed among organisms within the specificity testing panel. The method showed good uniformity for SARS‐CoV‐2 detection with a consistency of 100%. Regarding the clade classification performance, the results showed good concordance compared with sequencing, with the rate of agreement being 95.1% (78/82). The one‐step multiplex HRM method is a rapid method for SARS‐CoV‐2 detection and classification.
Controlling critical mistag‐associated false discoveries in metagenetic data
Authors: Richardson Rodney T. 
Published: March 2022

Abstract

Metagenetic methods are commonplace within ecological and environmental research. One concern with these methods is the phenomenon of ‘critical mistagging’, where sequences from one sample are erroneously inferred to have originated from another sample due to errors in the attachment, PCR replication or sequencing of sample‐specific dual‐index tags. For studies using PCR‐based library preparation on large sample sizes, the most cost‐effective approach to limiting mistag‐associated false detections involves using an unsaturated Latin square dual‐indexing design. This allows researchers to estimate mistagging rates during sequencing but the statistical procedures for filtering out detections using this mistag rate have received little attention.

I propose a straightforward method to limit mistag‐associated false discoveries during metabarcoding applications. I analysed two Illumina metabarcoding datasets produced using unsaturated Latin square designs to explore the distribution of mistagged sequences across dual‐index combinations on a per taxon basis. I tested these data for conformity to the assumptions that (a) mistagging follows a binomial distribution (i.e. X ~ B(n, p)) where p, the probability of a sequence being mistagged, varies minimally across taxa and (b) mistags are distributed uniformly across dual‐index combinations. I provide R functions that estimate the 95th percentile of expected mistags per dual‐index combination for each taxon under these assumptions.

I show that mistagging rates were consistent across taxa within the datasets analysed and that modelling mistagging as a binomial process with uniform distribution across dual‐index combinations enabled robust control of mistag‐associated false discoveries.

I propose that this method of taxon‐specific filtering of detections based on the maximum mistags expected per dual‐index combination should be broadly accepted during metagenetic analysis, provided that control sample mistag abundances follow a near‐uniform distribution. When this assumption is violated, data may be better fit by assuming that the distribution of mistags across combinations follows Poisson characteristics (i.e. X ~Pois(λ)), with λ empirically estimated from the abundance distribution of mistags among control samples. I provide a second R function for this case. Both functions and demonstrations associated with this work are freely available at https://github.com/RTRichar/ModellingCriticalMistags.
Drosophila Sirtuin 6 mediates developmental diet‐dependent programming of adult physiology and survival
Authors: Shukla Namrata , Kolthur‐Seetharam Ullas 
Published: March 2022

AbstractOrganisms in the wild experience unpredictable and diverse food availability throughout their lifespan. Over‐/under‐nutrition during development and in adulthood is known to dictate organismal survival and fitness. Studies using model systems have also established long‐term effects of developmental dietary alterations on life‐history traits. However, the underlining genetic/molecular factors, which differentially couple nutrient inputs during development with fitness later in life are far less understood. Using Drosophila and loss/gain of function perturbations, our serendipitous findings demonstrate an essential role of Sirtuin 6 in regulating larval developmental kinetics, in a nutrient‐dependent manner. The absence of Sirt6 affected ecdysone and insulin signalling and led to accelerated larval development. Moreover, varying dietary glucose and yeast during larval stages resulted in enhanced susceptibility to metabolic and oxidative stress in adults. We also demonstrate an evolutionarily conserved role for Sirt6 in regulating physiological homeostasis, physical activity and organismal lifespan, known only in mammals until now. Our results highlight gene‐diet interactions that dictate thresholding of nutrient inputs and physiological plasticity, operative across development and adulthood. In summary, besides showing its role in invertebrate ageing, our study also identifies Sirt6 as a key factor that programs macronutrient‐dependent life‐history traits.
Molecular chaperone heat shock protein 70 inhibitors suppress conditioned place preference induced by morphine exposure in male rats
Authors: Wei Shoupeng , Li Yu‐ling , Gong Qi , Liang Hui , Bernardi Rick E. , Liang Jian‐hui 
Published: March 2022

AbstractPrevious studies have indicated a role for molecular chaperone heat shock protein 70 (Hsp70) in the development of behavioural sensitization to morphine in rodents, suggesting that Hsp70 expression following morphine exposure is involved in molecular changes that may underlie addiction vulnerability. The current study was carried out to investigate the role of Hsp70 in the positive reinforcing properties of morphine using conditioned place preference (CPP) in male rats. An unbiased CPP procedure of three phases (pre‐conditioning: d1–d3; conditioning: d4–d6; and testing: d7) was used. During the conditioning phase, morphine injections (5 mg/kg, subcutaneously) were administered to induce significant place preference. To explore the effect of Hsp70 on the development and expression of morphine CPP, Hsp70 inhibitors (PES, KNK437 and methylene blue) were administered into the lateral ventricle prior to either morphine conditioning sessions or a morphine challenge on the test day. Furthermore, Hsp70 expression within the mesocorticolimbic system was measured after the treatment with KNK437, a transcriptional inhibitor. We found that PES and KNK437, respectively, injected intracerebroventricularly dose‐dependently attenuated both the development and expression of morphine CPP. Methylene blue treatment demonstrated an attenuation of the development, but had no effect on the expression of morphine CPP. Following KNK437 treatment, Hsp70 expression was significantly inhibited in the shell of nucleus accumbens (NAc) during both the development and expression of morphine CPP. The findings suggest that Hsp70 in the NAc shell plays an important role in the reinforcing effects of morphine and may be involved in the development of morphine dependence.
A de novo variant in the bovine ADAMTSL4 gene in an Original Braunvieh calf with congenital cataract
Authors: Häfliger Irene M. , Wolf‐Hofstetter Sonja , Casola Christina , Hetzel Udo , Seefried Franz R. , Drögemüller Cord 
Published: March 2022

AbstractInherited forms of cataract are a heterogeneous group of eye disorders known in livestock species. Clinicopathological analysis of a single case of impaired vision in a newborn Original Braunvieh calf revealed nuclear cataract. Whole‐genome sequencing of the parent‐offspring trio revealed a de novo mutation of ADAMTSL4 in this case. The heterozygous p.Arg776His missense variant affects a conserved residue of the ADAMTSL4 gene that encodes a secreted glycoprotein expressed in the lens throughout embryonic development. In humans, ADAMTSL4 genetic variants cause recessively inherited forms of subluxation of the lens. Given that ADAMTSL4 is a functional candidate gene for inherited disorders of the lens, we suggest that heterozygosity for the identified missense variant may have caused the congenital cataract in the affected calf. Cattle populations should be monitored for unexplained cataract cases, with subsequent DNA sequencing a hypothesized pathogenic effect of heterozygous ADAMTSL4 variants could be confirmed.
Review article: current and emerging therapies for the management of cirrhosis and its complications
Authors: Tapper Elliot B. , Ufere Nneka N. , Huang Daniel Q. , Loomba Rohit 
Published: March 2022

AbstractBackgroundCirrhosis is increasingly common and morbid. Optimal utilisation of therapeutic strategies to prevent and control the complications of cirrhosis are central to improving clinical and patient‐reported outcomes.MethodsWe conducted a narrative review of the literature focusing on the most recent advances.ResultsWe review the aetiology‐focused therapies that can prevent cirrhosis and its complications. These include anti‐viral therapies, psychopharmacological therapy for alcohol‐use disorder, and the current landscape of clinical trials for non‐alcoholic steatohepatitis. We review the current standard of care and latest developments in the management of hepatic encephalopathy (HE), ascites and hepatorenal syndrome. We evaluate the promise and drawbacks of chemopreventative therapies that have been examined in trials and observational studies which may reduce the risk of hepatocellular carcinoma and cirrhosis complications. Finally, we examine the therapies which address the non‐pain symptoms of cirrhosis including pruritis, muscle cramps, sexual dysfunction and fatigue.ConclusionThe improvement of clinical and patient‐reported outcomes for patients with cirrhosis is possible by applying evidence‐based pharmacotherapeutic approaches to the prevention and treatment of cirrhosis complications.
‘People like me don’t do well at school’: The roles of identity compatibility and school context in explaining the socioeconomic attainment gap
Authors: Easterbrook Matthew J. , Nieuwenhuis Marlon , Fox Kerry J. , Harris Peter R. , Banerjee Robin 
Published: March 2022

BackgroundSchool students who are eligible for reduced or free school meals (FSM) – an indicator of economic disadvantage – have lower academic attainment than their peers.AimsWe investigated whether identity compatibility – the perceived compatibility between one’s social identities and the stereotype of a high‐achieving student – contributes to this socioeconomic attainment gap, and whether the association between socioeconomic status and identity compatibility is moderated by school context.SampleOur sample was 4,629 students aged 15–16 years old across 29 schools in England.MethodWe assessed students’ perceptions of identity compatibility via self‐report questionnaires 8 months prior to them taking national, standardized exams.ResultsMultilevel regression analyses revealed a negative indirect effect from eligibility for FSM to exam results via identity compatibility. These effects existed even while accounting for students’ gender and language status, other psychological variables known to predict academic attainment, and their previous exam results. Furthermore, school context moderated the relationship between FSM eligibility and identity compatibility. In line with the identities in context model of educational inequalities, there was a significant negative association between FSM and identity compatibility only for students attending schools in which there was previously a relatively large socioeconomic attainment gap.ConclusionsOur results demonstrate the importance of social psychological variables in explaining educational inequalities, and of the local educational context in determining the educational experience of students from lower socioeconomic status backgrounds.
Lipopolysaccharide increases exosomes secretion from endothelial progenitor cells by toll‐like receptor 4 dependent mechanism
Authors: Xia Liang , Wang Xiaotian , Yao Weidong , Wang Meihui , Zhu Junhui 
Published: March 2022

AbstractBackground InformationEndothelial progenitor cells (EPCs) can exert angiogenic effects by a paracrine mechanism, where exosomes work as an important mediator. Recent studies reported functional expression of toll‐like receptor (TLR) 4 on human EPCs and dose‐dependent effects of lipopolysaccharide (LPS) on EPC angiogenic properties. To study the effects of TLR4/LPS signaling on EPC‐derived exosomes (Exo) and clarify the mechanism, we investigated the role of LPS on exosomes secretion from human EPCs and tested their anti‐oxidation/senescence functions. We employed the inhibitors of the plasma membrane Ca2+‐ATPase (PMCA), endoplasmic reticulum Ca2+‐ATPase (ERCA), PLC‐IP3 pathway and store‐operated calcium entry to assess the effects of LPS on EPC intracellular calcium signalings which critical for exosome secretion.ResultsLPS induced the release of Exo in a TLR4‐dependent manner in vitro, which effect can be partly abrogated by an membrane‐permeable IP 3 R antagonist, 2‐aminoethyl diphenylborinate (2‐APB), but not PLC inhibitor, U‐73122. The LPS can significantly delay the fallback of [Ca2+]i after isolating the cellular PMCA activity, and disturb PMCA 1/4 expression. The distribution of elevated intracellular calcium seemed coincident with the development of the multivesicular bodies (MVBs). furthermore, the anti‐oxidation/senescence properties of LPS‐induced Exo were validated by the senescence‐associated β‐galactosidase activity assay and reactive oxygen species (ROS) related H2DCF‐DA assay.ConclusionsThe mechanism of PMCA downregulation and IP3R‐dependent ER Ca2+ release may contribute to the pro‐exosomal effects of LPS on EPCs.SignificanceThis study provides new insights into the potential role of LPS/TLR4 pathway in regulating EPC‐derived exosomes, which may help to develop some feasible approach to manipulate the Exo secretion and promote the clinical application of EPCs therapy in future.
Patch testing in drug reaction with eosinophilia and systemic symptoms (DRESS): A literature review
Authors: de Groot Anton C. 
Published: March 2022

AbstractThe literature on positive patch test results in drug reaction with eosinophilia and systemic symptoms (DRESS) is reviewed. One hundred and five drugs were identified that have together caused 536 positive patch tests in 437 DRESS patients. By far, the most reactions (n = 145) were caused by carbamazepine, followed by amoxicillin, isoniazid, phenytoin, ethambutol, fluindione, phenobarbital, rifampicin, and ceftriaxone; 43 drugs each caused a single case only. The drug classes causing the highest number of reactions were anticonvulsants (39%), beta‐lactam antibiotics (20%), antituberculosis agents (11%), non‐beta‐lactam antibiotics (6%), and iodinated contrast media (5%). The sensitivity of patch testing (percentage of positive reactions) is high for anticonvulsants (notably carbamazepine), beta‐lactam antibiotics (notably amoxicillin), and, possibly, iodinated contrast media. Allopurinol and sulfasalazine frequently cause DRESS but never give positive patch tests. Patch testing in DRESS appears to be safe, although mild recurrence of DRESS symptoms, mostly skin reactions, may not be rare. Multiple drug hypersensitivity was found to occur in 16% of all patients, but it is argued that the true frequency is higher. Clinical aspects of DRESS, including diagnosing the disease and identifying culprit drugs (patch tests, intradermal tests, in vitro tests, challenge tests) are also provided, emphasizing the role of patch testing.
Searching for refuge: A framework for identifying site factors conferring resistance to climate‐driven vegetation change
Authors: Raiho Ann M. , Scharf Henry R. , Roland Carl A. , Swanson David K. , Stehn Sarah E. , Hooten Mevin B. 
Published: March 2022

AbstractAimClimate change is occurring at accelerated rates in high latitude regions such as Alaska, causing alterations in woody plant growth and associated ecosystem patterns and processes. Our aim is to assess the magnitude and speed that climate‐induced changes in woody plant distribution and volume may be reduced and/or slowed by relatively static landscape features like physical characteristics (e.g. depth to gravel, mineral cover percent and slope degree) and/or edaphic properties (e.g. soil organic matter, soil pH and site wetness rating) that resist climate‐vegetation responses.LocationWe leveraged a large field data set collected across a network of Alaskan national parks, which allows for comprehensive spatial data analysis over a uniquely large spatial extent.MethodsTo learn about the conditions that may either impede or accelerate vegetation changes in northern Alaska, we used a Bayesian hierarchical model to identify which landscape features may decelerate change or offer refuge for plant species. Our model quantifies the contribution of fast (‘dynamic’) versus slow (‘static’) changing variables to predict plant volume and categorize landscape types into either robust or nonrobust to climate changes.ResultsWe found that two landscape features, low soil wetness and low soil organic matter comprising 63.1% of sites in the data set, were the most likely landscape features to inhibit vegetation expansion. We also found that fewer numbers of sites have the potential to offer refuge to existing plant species (5.43% on average) because few sites had high soil wetness as a landscape feature.Main conclusionsOur analyses highlight the importance of incorporating static covariates representing landscape resistance to vegetation change for improving realism in forecasts of vegetation change in Alaska.
The role of artificial light at night and road density in predicting the seasonal occurrence of nocturnally migrating birds
Authors: La Sorte Frank A. , Johnston Alison , Rodewald Amanda D. , Fink Daniel , Farnsworth Andrew , Van Doren Benjamin M. , Auer Tom , Strimas‐Mackey Matthew 
Published: March 2022

AbstractAimArtificial light at night (ALAN) and roads are known threats to nocturnally migrating birds. How associations with ALAN and roads are defined in combination for these species at the population level across the full annual cycle has not been explored.LocationWestern Hemisphere.MethodsWe estimated range‐wide exposure, predictor importance and the prevalence of positive associations with ALAN and roads at a weekly temporal resolution for 166 nocturnally migrating bird species in three orders: Passeriformes (n = 104), Anseriformes (n = 27) and Charadriiformes (n = 35). We clustered Passeriformes based on the prevalence of positive associations.ResultsPositive associations with ALAN and roads were more prevalent for Passeriformes during migration when exposure and importance were highest. Positive associations with ALAN and roads were more prevalent for Anseriformes and Charadriiformes during the breeding season when exposure was lowest. Importance was uniform for Anseriformes and highest during migration for Charadriiformes. Our cluster analysis identified three groups of Passeriformes, each having similar associations with ALAN and roads. The first occurred in eastern North America during migration where exposure, prevalence, and importance were highest. The second wintered in Mexico and Central America where exposure, prevalence and importance were highest. The third occurred throughout North America where prevalence was low, and exposure and importance were uniform. The first and second were comprised of dense habitat specialists and long‐distance migrants. The third was comprised of open habitat specialists and short distance migrants.Main conclusionsOur findings suggest ALAN and roads pose the greatest risk during migration for Passeriformes and during the breeding season for Anseriformes and Charadriiformes. Our results emphasise the close relationship between ALAN and roads, the diversity of associations dictated by taxonomy, exposure, migration strategy and habitat and the need for more informed and comprehensive mitigation strategies where ALAN and roads are treated as interconnected threats.
The important role of animal social status in vertebrate seed dispersal
Authors: Bartel Savannah L. , Orrock John L. 
Published: March 2022

AbstractSeed dispersal directly affects plant establishment, gene flow and fitness. Understanding patterns in seed dispersal is, therefore, fundamental to understanding plant ecology and evolution, as well as addressing challenges of extinction and global change. Our ability to understand dispersal is limited because seeds may be dispersed by multiple agents, and the effectiveness of these agents can be highly variable both among and within species. We provide a novel framework that links seed dispersal to animal social status, a key component of behaviour. Because social status affects individual resource access and movement, it provides a critical link to two factors that determine seed dispersal: the quantity of seeds dispersed and the spatial patterns of dispersal. Social status may have unappreciated effects on post‐dispersal seed survival and recruitment when social status affects individual habitat use. Hence, environmental changes, such as selective harvesting and urbanisation, that affect animal social structure may have unappreciated consequences for seed dispersal. This framework highlights these exciting new hypotheses linking environmental change, social structure and seed dispersal. By outlining experimental approaches to test these hypotheses, we hope to facilitate studies across a wide diversity of plant‐animal networks, which may uncover emerging hotspots or significant declines in seed dispersal.
A multi‐laboratory assessment of lupus anticoagulant assays performed on the ACL TOP 50 family for harmonized testing in a large laboratory network
Authors: Favaloro Emmanuel J. , Mohammed Soma , Vong Ronny , Chapman Kent , Swanepoel Priscilla , Kershaw Geoffrey , Cai Nancy , Just Sarah , Connelly Lynne , Brighton Timothy , Pasalic Leonardo 
Published: March 2022

AbstractIntroductionLupus anticoagulant (LA) testing is commonly performed within hemostasis laboratories, and the ACL TOP 50 family of instruments represent a new “single platform” of hemostasis instrumentation. Our aim was to evaluate these instruments and manufacturer reagents or alternatives for utility in LA testing.MethodsComparative evaluations of LA testing using newly installed ACL TOPs 550 and 750 as well as comparative assessments with existing “reference,” predominantly Stago, instrumentation, and reagents. Evaluations comprised both dilute Russell viper venom time (dRVVT) and activated partial thromboplastin time (APTT)‐based assays. Establishment of normal reference ranges (NRR).ResultsThe HemosIL dRVVT‐based assays showed good comparability with the existing Stago reference method (R > 0.9) and could be considered as verified as fit for purpose. A variety of APTT assays was additionally evaluated for LA utility, and we identified from the assessment good utility of a non‐Werfen solution in Hyphen BioMed Cephen reagents. NRR were established based on ≥120 normal individual plasma samples.ConclusionThis evaluation of LA reagents on ACL TOP 50 Family instruments identified overall acceptable performance of both dRVVT (Werfen solution) and APTT (non‐Werfen solution) to enable harmonization of LA testing in our large network.