bluuebunny/crossref_metadata_2025_split huggingface dataset:
Causes and consequences of intraspecific variation in animal responses to anthropogenic noise
Authors: Harding Harry R , Gordon Timothy A C , Eastcott Emma , Simpson Stephen D , Radford Andrew N 
Published: June 2019

AbstractAnthropogenic noise is a recognized global pollutant, affecting a wide range of nonhuman animals. However, most research considers only whether noise pollution has an impact, ignoring that individuals within a species or population exhibit substantial variation in responses to stress. Here, we first outline how intrinsic characteristics (e.g., body size, condition, sex, and personality) and extrinsic factors (e.g., environmental context, repeated exposure, prior experience, and multiple stressors) can affect responses to environmental stressors. We then present the results of a systematic search of the anthropogenic-noise literature, identifying articles that investigated intraspecific variation in the responses of nonhuman animals to noise. This reveals that fewer than 10% of articles (51 of 589) examining impacts of noise test experimentally for intraspecific variation in responses; of those that do, more than 75% report significant effects. We assess these existing studies to determine the current scope of research and findings to-date, and to provide suggestions for good practice in the design, implementation, and reporting of robust experiments in this field. We close by explaining how understanding intraspecific variation in responses to anthropogenic noise is crucial for improving how we manage captive animals, monitor wild populations, model species responses, and mitigate effects of noise pollution on wildlife. Our aim is to stimulate greater knowledge and more effective management of the harmful consequences of this global pollutant.
Taxonomy of dark- and white-barked birches related to Betula pendula and B. pubescens (Betulaceae) in Ukraine based on both morphological traits and DNA markers
Authors: Tarieiev Andrii , Olshanskyi Igor , Gailing Oliver , Krutovsky Konstantin V 
Published: June 2019

Abstract
Distribution, taxonomy, nomenclature and molecular genetic data are presented for two closely related pairs of birch taxa: (1) dark-barked Betula pubescens var. sibakademica (Baran.) Kuzeneva (basionym B. sibakademica Baranov) and white-barked B. pubescens var. pubescens, and (2) dark-barked B. kotulae Zaverucha = B. pendula var. obscura (Kotula ex Fiek) Olšavská (basionym B. obscura Kotula ex Fiek, heterotypic synonym B. kotulae) and white-barked B. pendula, respectively. Using published data and sequences obtained in this study, it was found that, although these pairs can be distinguished not only by morphological characters but also by two diagnostic single nucleotide polymorphisms (SNPs) in the internal transcribed spacers ITS1 and ITS2, no sequence differences within each pair were detected. These results suggest that the colour of the bark cannot be used as a taxonomic trait at the species level, and the dark-barked birches within each pair should not be treated as separate species or varieties, but as forms, respectively. Therefore, we reassessed the taxonomic status of B. sibakademica and B. kotulae using morphological traits and molecular genetic markers and suggest that B. pubescens f. sibakademica (Baranov) Tarieiev comb. nov. and B. pendula f. obscura (Kotula ex Fiek) Tarieiev comb. nov. should be used for them, respectively. Betula pubescens f. sibakademica was described in Ukraine for the first time.
Growth of two Atlantic Coast Piping Plover populations
Authors: Weithman Chelsea E , Robinson Samantha G , Hunt Kelsi L , Altman Jon , Bellman Henrietta A , DeRose-Wilson Audrey L , Walker Katie M , Fraser James D , Karpanty Sarah M , Catlin Daniel H 
Published: June 2019

AbstractSpecies listed under the U.S. Endangered Species Act are required to meet stated recovery goals for delisting. These goals often are developed early in the species’ conservation history and may need to be updated or refined as new information becomes available. The Atlantic Coast Piping Plover (Charadrius melodus), which was listed more than 30 yr ago, has not met recovery goals through much of its range. Initial recovery goals included maintaining a reproductive output of 1.5 fledged chicks per pair for 5 yr. This goal was based on modelling that assumed equal survival rates for adults throughout the range, but recent studies suggest that demographic rates may vary with latitude. To investigate latitudinal variation, we developed demographic and population growth estimates for 2 breeding populations of Piping Plovers on the U.S. Atlantic Coast on Fire Island, New York (40.7°N), and on the Outer Banks of North Carolina (35.3°N) in 2013–2017. Breeding success (nest success and pre-fledge chick survival) varied annually but was lower in North Carolina than New York. Average adult true survival in New York (x̅ = 0.73, SE = 0.04) was similar to average survival in North Carolina (x̅ = 0.69, SE = 0.07). Annual post-fledging survival for both sites, however, was variable and often higher than had been previously reported for Atlantic Coast Piping Plovers (0.43–0.66 for New York; 0.31 and 1.0 for North Carolina). While the estimated reproductive output needed for a stationary population for both sites was similar (1.10 chicks per pair for New York, 95% CI: 0.83–1.41; 1.08 for North Carolina, 95% CI: 0.67–1.59), only the New York population achieved or exceeded these values during our study. Our findings suggest that understanding annual and latitudinal demographic variability would be helpful in refining recovery goals.
Combined alignments of sequences and domains characterize unknown proteins with remotely related protein search PSISearch2D
Authors: Yang Minglei , Zhang Wenliang , Yao Guocai , Zhang Haiyue , Li Weizhong 
Published: June 2019

Abstract
Iterative homology search has been widely used in identification of remotely related proteins. Our previous study has found that the query-seeded sequence iterative search can reduce homologous over-extension errors and greatly improve selectivity. However, iterative homology search remains challenging in protein functional prediction. More sensitive scoring models are highly needed to improve the predictive performance of the alignment methods, and alignment annotation with better visualization has also become imperative for result interpretation. Here we report an open-source application PSISearch2D that runs query-seeded iterative sequence search for remotely related protein detection. PSISearch2D retrieves domain annotation from Pfam, UniProtKB, CDD and PROSITE for resulting hits and demonstrates combined domain and sequence alignments in novel visualizations. A scoring model called C-value is newly defined to re-order hits with consideration of the combination of sequence and domain alignments. The benchmarking on the use of C-value indicates that PSISearch2D outperforms the original PSISearch2 tool in terms of both accuracy and specificity. PSISearch2D improves the characterization of unknown proteins in remote protein detection. Our evaluation tests show that PSISearch2D has provided annotation for 77 695 of 139 503 unknown bacteria proteins and 140 751 of 352 757 unknown virus proteins in UniProtKB, about 2.3-fold and 1.8-fold more characterization than the original PSISearch2, respectively. Together with advanced features of auto-iteration mode to handle large-scale data and optional programs for global and local sequence alignments, PSISearch2D enhances remotely related protein search.
The hypoxic expression of the glucose transporter RAG1 reveals the role of the bHLH transcription factor Sck1 as a novel hypoxic modulator in Kluyveromyces lactis
Authors: Santomartino Rosa , Ottaviano Daniela , Camponeschi Ilaria , Landicho Tracy Ann Alcarpio , Falato Luca , Visca Andrea , Soulard Alexandre , Lemaire Marc , Bianchi Michele Maria 
Published: June 2019

ABSTRACT
Glucose is the preferred nutrient for most living cells and is also a signaling molecule that modulates several cellular processes. Glucose regulates the expression of glucose permease genes in yeasts through signaling pathways dependent on plasma membrane glucose sensors. In the yeast Kluyveromyces lactis, sufficient levels of glucose induction of the low-affinity glucose transporter RAG1 gene also depends on a functional glycolysis, suggesting additional intracellular signaling. We have found that the expression of RAG1 gene is also induced by hypoxia in the presence of glucose, indicating that glucose and oxygen signaling pathways are interconnected. In this study we investigated the molecular mechanisms underlying this crosstalk. By analyzing RAG1 expression in various K. lactis mutants, we found that the bHLH transcriptional activator Sck1 is required for the hypoxic induction of RAG1 gene. The RAG1 promoter region essential for its hypoxic induction was identified by promoter deletion experiments. Taken together, these results show that the RAG1 glucose permease gene is synergistically induced by hypoxia and glucose and highlighted a novel role for the transcriptional activator Sck1 as a key mediator in this mechanism.
Dartington Hall and the Quest for ‘Life in its Completeness’, 1925–45
Authors: Neima Anna 
Published: June 2019

Abstract
In the wake of the First World War, reformers across the Western world questioned laissez-faire liberalism, the self-oriented and market-driven ruling doctrine of the nineteenth century. This philosophy was blamed, variously, for the war, for industrialization and for urbanization; for a way of life shorn of any meaning beyond getting and keeping; for the too great faith in materialism and in science; and for the loss of a higher, transcendent meaning that gave a unifying purpose to individual existence and to society as a whole. For many, the cure to these ills lay in reforming the liberal social framework in ways that made it more fulfilling to the whole person and that strengthened ties between individuals. This article looks at Dartington Hall as an outstanding practical example of this impulse to promote holistic, integrated living – exploring the project as an interlinked constellation of experiments in education, the arts, agriculture and social organization; and also looking at how Dartington’s philosophy and trajectory matched those of other such enterprises begun in interwar Britain and further afield, making it a bellwether of changes in reformist thinking across the century.
Challenges and Prospects for Testing the Mother’s Curse Hypothesis
Authors: Dowling Damian K , Adrian Rebecca E 
Published: June 2019

Abstract
Maternal inheritance of mitochondrial DNA (mtDNA) renders selection blind to mutations whose effects are limited to males. Evolutionary theory predicts this will lead to the accumulation of a male-specific genetic load within the mitochondrial genomes of populations; that is, a pool of mutations that negatively affects male, but not female, fitness components. This principle has been termed the Mother’s Curse hypothesis. While the hypothesis has received some empirical support, its relevance to natural populations of metazoans remains unclear, and these ambiguities are compounded by the lack of a clear predictive framework for studies attempting to test Mother’s Curse. Here, we seek to redress this by outlining the core predictions of the hypothesis, as well as the key features of the experimental designs that are required to enable direct testing of the predictions. Our goal is to provide a roadmap for future research seeking to elucidate the evolutionary significance of the Mother’s Curse hypothesis.
The Impact of Unconscious Bias in Healthcare: How to Recognize and Mitigate It
Authors: Marcelin Jasmine R , Siraj Dawd S , Victor Robert , Kotadia Shaila , Maldonado Yvonne A 
Published: June 2019

AbstractThe increasing diversity in the US population is reflected in the patients who healthcare professionals treat. Unfortunately, this diversity is not always represented by the demographic characteristics of healthcare professionals themselves. Patients from underrepresented groups in the United States can experience the effects of unintentional cognitive (unconscious) biases that derive from cultural stereotypes in ways that perpetuate health inequities. Unconscious bias can also affect healthcare professionals in many ways, including patient-clinician interactions, hiring and promotion, and their own interprofessional interactions. The strategies described in this article can help us recognize and mitigate unconscious bias and can help create an equitable environment in healthcare, including the field of infectious diseases.
Susceptibility of carbapenemase-producing Enterobacterales (CPE) to nitroxoline
Authors: Fuchs Frieder , Hamprecht Axel 
Published: June 2019

AbstractBackgroundInfections caused by carbapenemase-producing Enterobacterales (CPE) constitute a major global health concern and are associated with increased morbidity and mortality. Nitroxoline is an old antibiotic, which has recently been re-launched for the treatment of uncomplicated urinary tract infection. Because of low resistance rates it could be an interesting option for treatment of MDR isolates, yet data on CPE susceptibility are scarce.ObjectivesTo analyse the in vitro activity of nitroxoline against CPE.MethodsMICs of nitroxoline were determined by agar dilution for a collection of well-characterized carbapenemase producers (n = 105), producing OXA-48-like (n = 36), VIM (n = 21), IMI (n = 9), IMP (n = 6), NDM (n = 22), KPC (n = 11), OXA-58 (n = 2) and GES (n = 2). For comparison, MICs of ertapenem, imipenem and meropenem were determined by agar gradient diffusion.ResultsFor all 105 isolates, the MIC50/90 of nitroxoline was 8/16 mg/L. All Escherichia coli isolates (30/30, 100%) showed low MICs of 2–8 mg/L and were susceptible to nitroxoline. MICs of 32 mg/L were recorded for five isolates of VIM- and IMI-producing Enterobacter cloacae (n = 3) and OXA- and VIM-producing Klebsiella pneumoniae (n = 2).ConclusionsNitroxoline exhibited excellent in vitro activity against most isolates producing common and rare carbapenemases. If the current EUCAST susceptibility breakpoint of ≤16 mg/L for E. coli in uncomplicated urinary tract infections was applied, 95.2% (100/105) of isolates would be classified as susceptible. Nitroxoline could therefore be an alternative oral option for treatment of uncomplicated urinary tract infections caused by CPE.
Identification of Subterranean Termite Genus, Reticulitermes (Blattodea: Rhinotermitidae) in Taiwan
Authors: Wu Chia-Chien , Tsai Cheng-Lung , Liang Wei-Ren , Takematsu Yoko , Li Hou-Feng 
Published: June 2019

Abstract
Species identification in the genus Reticulitermes is often difficult because of ambiguous morphological characters. Challenges in Reticulitermes spp. recognition have also been encountered in East Asia, including Taiwan. Because of unknown Reticulitermes taxa in Taiwan and the possible origin of alien Reticulitermes kanmonensis Takematsu in Japan and Korea, reexamining Reticulitermes fauna in Taiwan is imperative. To clarify the Reticulitermes fauna in Taiwan, this study applied two mitochondrial genes (cytochrome oxidase subunit II [COII] and 16S rDNA) and morphological characters for species delimitation. Reticulitermes specimens collected from 63 localities across the main and adjacent islands of Taiwan were analyzed. Phylogenetic analyses, morphological comparisons, and ecological traits suggested the existence of three species in Taiwan: Reticulitermes flaviceps (Oshima), R. kanmonensis, and Reticulitermes leptomandibularis Hsia and Fan. Altitudinal distributions among the three Reticulitermes termites tended to differ: R. flaviceps adapted to low hills, but R. kanmonensis and R. leptomandibularis occurred in medium mountainous areas. The combined data, including haplotype diversities and distribution range, suggest that 1) R. flaviceps is an endemic species and only found in Taiwan; 2) R. kanmonensis and R. leptomandibularis are both native species in Taiwan and China; 3) Japanese R. kanmonensis populations originated from southern China and/or Taiwan and that Korean populations were possibly introduced from Japan.
Type IV tibial tubercle fracture—Salter–Harris type II variant
Authors: Andrews Kyle A , Gillette Marshall , Shah Ronit V , Mckean Lucas A , Sanford Christopher G 
Published: June 2019

AbstractFractures about the tibial tubercle are uncommon fracture patterns, seen most often in adolescent males as they approach skeletal maturity. Compartment syndrome has a high association with these fractures requiring close monitoring, and a heightened level of suspicion. Tibial tubercle fractures are typically stratified using the Ogden classification. The type of intra-articular involvement and degree of displacement guide appropriate treatment. This report highlights a 14-year-old male patient who suffered a type IV tibial tubercle fracture with a unique Salter–Harris II, or transitional, component posteriorly that was unable to be closed reduced and developed compartment syndrome. He underwent fasciotomy, open reduction, and temporary external fixation. Once the status of the soft tissues improved, he underwent staged open reduction and internal fixation with skin grafting. The patient’s fracture and soft tissues healed and he currently ambulates without assistance or pain, and has returned to all desired activities including competitive sports.
Identifying optical turbulence profiles for realistic tomographic error in adaptive optics
Authors: Farley O J D , Osborn J , Morris T , Fusco T , Neichel B , Correia C , Wilson R W 
Published: June 2019

ABSTRACT
For extremely large telescopes, adaptive optics will be required to correct the Earth’s turbulent atmosphere. The performance of tomographic adaptive optics is strongly dependent on the vertical distribution (profile) of this turbulence. An important way in which this manifests is the tomographic error, arising from imperfect measurement and reconstruction of the turbulent phase at altitude. Conventionally, a small number of reference profiles are used to obtain this error in simulation; however these profiles are not constructed to be representative in terms of tomographic error. It is therefore unknown whether these simulations are providing realistic performance estimates. Here, we employ analytical adaptive optics simulation that drastically reduces computation times to compute tomographic error for 10 691 measurements of the turbulence profile gathered by the Stereo-SCIDAR instrument at ESO Paranal. We assess for the first time the impact of the profile on tomographic error in a statistical manner. We find, in agreement with previous work, that the tomographic error is most directly linked with the distribution of turbulence into discrete, stratified layers. Reference profiles are found to provide mostly higher tomographic error than expected, which we attribute to the fact that these profiles are primarily composed of averages of many measurements resulting in unrealistic, continuous distributions of turbulence. We propose that a representative profile should be defined with respect to a particular system, and that as such simulations with a large statistical sample of profiles must be an important step in the design process.
Quantifying gene selection in cancer through protein functional alteration bias
Authors: Brandes Nadav , Linial Nathan , Linial Michal 
Published: June 2019

Abstract
Compiling the catalogue of genes actively involved in cancer is an ongoing endeavor, with profound implications to the understanding and treatment of the disease. An abundance of computational methods have been developed to screening the genome for candidate driver genes based on genomic data of somatic mutations in tumors. Existing methods make many implicit and explicit assumptions about the distribution of random mutations. We present FABRIC, a new framework for quantifying the selection of genes in cancer by assessing the effects of de-novo somatic mutations on protein-coding genes. Using a machine-learning model, we quantified the functional effects of ∼3M somatic mutations extracted from over 10 000 human cancerous samples, and compared them against the effects of all possible single-nucleotide mutations in the coding human genome. We detected 593 protein-coding genes showing statistically significant bias towards harmful mutations. These genes, discovered without any prior knowledge, show an overwhelming overlap with known cancer genes, but also include many overlooked genes. FABRIC is designed to avoid false discoveries by comparing each gene to its own background model using rigorous statistics, making minimal assumptions about the distribution of random somatic mutations. The framework is an open-source project with a simple command-line interface.
Risk of Wnt/β-catenin signalling pathway gene polymorphisms in primary Sjögren’s syndrome
Authors: Fernández-Torres Javier , Pérez-Hernández Nonanzit , Hernández-Molina Gabriela , Martínez-Nava Gabriela A , Garrido-Rodríguez Daniela , López-Reyes Alberto , Rodríguez-Pérez José M 
Published: June 2019

AbstractObjectiveTo explore genetic polymorphisms of the Wnt/β-catenin signalling pathway in primary SS (PSS).MethodsWe included 98 patients with PSS and 165 healthy volunteers. Genomic DNA was extracted from peripheral blood samples. Through an open-array platform of low density, we genotyped 25 polymorphisms from 14 genes (WISP1, DKK1, SOST, FRZB, LRP1, LRP4, LRP5, LRP6, GSKB, ADAMTS5, GDF5, FMN2, ADIPOQ and COL11A1) involved in the Wnt/β-catenin signalling pathway. We compared the allelic and genotypic frequencies with Fisher’s exact test and logistic regression analysis adjusted by age, gender and individual admixture, as well as bootstrap-resampling analysis. We assessed the gene–gene interaction by the multifactor dimensionality reduction method.ResultsWe found a positive significant association with four polymorphisms: LRP5 rs606989, FRZB rs409238, GSK3B rs2037547 and ADIPOQ rs2241766. All of them conferred risk for PSS, being the highest among subjects carrying three to four risk alleles (P &lt; 0.001). According to a multifactor dimensionality reduction analysis, the best models included the LRP5 (rs606989), FRZB (rs409238) and ADIPOQ (rs2241766) polymorphisms.ConclusionLRP5, FRZB and ADIPOQ genes related in the Wnt/β-catenin signalling pathway increased the risk of PSS. Further research is needed to establish their functional role in this clinical entity.
Shuffling through the Bargain Bin: Real-Estate Holdings of Public Firms*
Authors: Demirci Irem , Gurun Umit G , Yönder Erkan 
Published: June 2019

Abstract
Constructing a novel database on the real-estate holdings of public firms, we show that distressed firms sell their real-estate assets at a discount relative to healthy firms. We find that distress discount in real-estate assets is less pronounced for sellers with less liquidity-constrained industry peers and in machinery-heavy industries. We also document that asset redeployability and the availability of potential buyers are two important property-specific determinants of the distress discount. Additionally, firms’ property portfolios that are less redeployable with less potential buyers exacerbate the negative impact of financial distress on the cost of borrowing.