bluuebunny/crossref_metadata_2025_split huggingface dataset:
VS38c and CD38-Multiepitope Antibodies Provide Highly Comparable Minimal Residual Disease Data in Patients With Multiple Myeloma
Authors: Broijl Annemiek , de Jong Augustinus C M , van Duin Mark , Sonneveld Pieter , Kühnau Jesper , van der Velden Vincent H J 
Published: September 2021

Abstract

Objectives
To compare flow cytometric minimal residual disease (MRD) data obtained using the EuroFlow approach, including the CD38-multiepitope (ME) antibody or the VS38c antibody.

Methods
We evaluated 29 bone marrow samples from patients with multiple myeloma (MM), of whom 15 had received daratumumab within the past 6 months. We evaluated MRD data and fluorescence intensities.

Results
Qualitative MRD data were 100% concordant between the 2 approaches. In MRD-positive samples (n = 14), MRD levels showed an excellent correlation (R2 = 0.999). Whereas VS38c staining was strong in both normal plasma cells and MM cells, independent of daratumumab treatment, staining intensities for CD38 were lower in MM cells compared with normal plasma cells, and on both cell types CD38 expression was significantly reduced in daratumumab-treated patients.

Conclusions
Both CD38-ME and VS38c allow reliable MRD detection in MM patients, but the high expression of VS38c allows easier identification of MM cells, especially in daratumumab-treated patients.
Expanding the Spectrum of Adult NTRK3-Rearranged Spindle Cell Neoplasms: A Recurrent NTRK3-SQSTM1 Fusion Spindle Cell Tumor With Deceptively Bland Morphology
Authors: Punjabi Lavisha S , Sittampalam Kesavan 
Published: September 2021

Abstract

Objectives
NTRK-rearranged spindle cell neoplasms (other than infantile fibrosarcoma) are an emerging entity of tumors that demonstrate wide variation in clinical and histopathologic features. We report a case of an NTRK-rearranged spindle cell neoplasm bearing a deceptively bland morphology.

Methods
We performed histopathologic, immunohistochemical, and molecular evaluation on resection tissue. We also conducted a literature review on adult NTRK3-rearranged spindle cell neoplasms.

Results
The tumor presented as a recurrent ankle mass in an elderly patient. Histologically, it was composed of bland spindle cells set in a fibrous to edematous stroma. Blood vessels were interspersed with subtle perivascular hyalinization and scattered lymphoid aggregates. Immunohistochemically, the spindle cells expressed CD34 and S100 while being negative for SOX10. The tumor also showed cytoplasmic reactivity for pan–tyrosine receptor kinase immunohistochemistry. Next-generation sequencing identified an NTRK3-SQSTM1 fusion. To the best of our knowledge, this fusion pair has not been previously reported in adult NTRK-rearranged mesenchymal tumors.

Conclusions
Altogether, this rare and diagnostically challenging case of an NTRK3-rearranged spindle cell tumor with low-grade morphology is in contrast to many of the reported adult NTRK3-rearranged mesenchymal tumors. Recognition of low-grade NTRK-rearranged tumors demands close attention to clues in morphology and immunoprofiles.
Laboratory Predictors of Hemolytic Anemia in Patients With Systemic Loxoscelism
Authors: Jacobs Jeremy W , Bastarache Lisa , Thompson Mary Ann 
Published: September 2021

Abstract

Objectives
To develop a sensitive and specific protocol for detecting preclinical hemolysis in patients with brown recluse spider (BRS) bites by comparing a large cohort of individuals with brown recluse spider (BRS) bites with and without hemolytic anemia.

Methods
A cross-sectional, retrospective analysis of clinical features and laboratory values, including urinalysis (UA) and peripheral blood results, and timing of positive laboratory values prior to a significant drop in hematocrit was performed to evaluate effective predictors of clinically significant hemolysis.

Results
In total, 275 patients with BRS bites were identified (64 with hemolytic anemia). Sensitivity and specificity of UA positive for blood (with and without microscopic hematuria) for detecting hemolysis were 72% and 75%, respectively. The combination of elevated serum total bilirubin (TB) and lactate dehydrogenase (LDH) had greater sensitivity (94%) and specificity (91%) for detecting patients developing hemolysis. When TB and LDH were evaluated prior to a significant decrease in hematocrit, they were positive in 82% of cases, while UA was positive for blood prior to a hematocrit decrease in 38% of cases.

Conclusions
Serum TB and LDH levels are more effective at detecting preclinical hemolysis than UA and should be serially analyzed to triage patients with BRS bites before life-threatening hemolysis occurs.
Racial/Ethnic Differences in Actigraphy, Questionnaire, and Polysomnography Indicators of Healthy Sleep: The Multi-Ethnic Study of Atherosclerosis
Authors: Chung Joon , Goodman Matthew , Huang Tianyi , Wallace Meredith L , Johnson Dayna A , Bertisch Suzanne , Redline Susan 
Published: September 2021

Abstract
We utilized the comprehensive sleep assessment of the Multi-Ethnic Study of Atherosclerosis (2010–2013), a cohort of US White, Black, Chinese, and Hispanic adults and older adults (n = 1,736; mean age = 68.3 years), to draw 13 sleep dimensions and create composite Sleep Health Scores to quantify multidimensional sleep health disparities. After age and sex adjustment in linear regression, compared with White participants, Black participants showed the greatest global sleep disparity, followed by Hispanic and Chinese participants. We estimated relative “risk” (RR) of obtaining favorable sleep compared with White adults at the component level according to race/ethnicity (lower is worse). The largest disparities were in objectively measured sleep timing regularity (RRBlack = 0.37, 95% confidence interval (CI): 0.29, 0.47; RRHispanic = 0.64, 95% CI: 0.52, 0.78; RRChinese = 0.70, 95% CI: 0.54, 0.90) and duration regularity (RRBlack = 0.55, 95% CI: 0.47, 0.65; RRHispanic = 0.76, 95% CI: 0.66, 0.88; RRChinese = 0.74, 95% CI: 0.61, 0.90) after sex and age adjustment. Disparities in duration and continuity were also apparent, and Black adults were additionally disadvantaged in % slow-wave sleep (N3), sleepiness, and sleep timing (24-hour placement). Sleep timing regularity, duration regularity, duration, and continuity may comprise a multidimensional cluster of targets to reduce racial/ethnic sleep disparities.
Associations of Binge Drinking and Heavy Alcohol Use on Sugar and Fat Intake in a Cohort of Southern People Living with HIV
Authors: Rosen Erika M , Primeaux Stefany D , Simon Liz , Welsh David A , Molina Patricia E , Ferguson Tekeda F 
Published: September 2021

Abstract

Aims
To assess whether binge drinking and heavy alcohol use are associated with increased sugar and fat consumption among a Southern cohort of people living with HIV (PWH).

Methods
This was a cross-sectional analysis of PWH enrolled in the New Orleans Alcohol use in HIV (NOAH) Study (n = 215). Binge and heavy drinking were identified through a 30-day Alcohol Timeline-Followback and dietary intake was assessed through a 24-hour dietary recall.

Results
Participants were 65.4% male, 83.3% Black, with a mean age of 49.2 ± 9.9. Heavy drinkers consumed more total calories than abstainers (P = 0.035) and low-to-moderate drinkers (P = 0.024), and binge drinkers consumed more calories than non-binge drinkers (P = 0.025). Binge and heavy drinkers had significantly higher intake of total and saturated fat in grams. However, substantially increased caloric intake among these participants led to non-significant associations for alcohol use with high total and saturated fat intake as a percent of total energy intake (%TEI). Binge drinkers had lower odds of consuming high sugar as a %TEI (odds ratio: 0.31 [0.14, 0.68]). Additionally, sugar intake predicted total and saturated fat intake, and this association was slightly higher among binge drinkers (total fat P-value: 0.12).

Conclusions
In this population of PWH, while binge and heavy drinking predicted higher caloric and fat intake in grams, binge drinkers were less likely to consume a high-sugar diet. This analysis suggests that interventions focused on reduced alcohol use may be especially beneficial in reducing metabolic disease burden in PWH if supplemented with information on incorporating lower energy-dense foods with reduced fat.
Content externalism without thought experiments?
Authors: Morgan Jonathan Brink 
Published: September 2021

Abstract
A recent argument against content internalism bucks tradition: it abandons Twin-Earth-style thought experiments and instead claims that internalism is inconsistent with plausible principles relating belief contents and truth values. Call this (for reasons that will become obvious) the transparency argument. Here, it is shown that there is a structurally parallel argument against content internalism’s foil: content externalism. Preserving the transparency argument while fending off the parallel argument against externalism requires that (i) content-determination and truth-value-determination are implausibly linked together and that (ii) eternalism about belief contents is true. Given these requirements, there may be reason to prefer simple, thought-experiment-based arguments against internalism – the sort of arguments that the transparency argument is meant to supersede.
RhizoVision Explorer: open-source software for root image analysis and measurement standardization
Authors: Seethepalli Anand , Dhakal Kundan , Griffiths Marcus , Guo Haichao , Freschet Gregoire T , York Larry M 
Published: September 2021

Abstract
Roots are central to the function of natural and agricultural ecosystems by driving plant acquisition of soil resources and influencing the carbon cycle. Root characteristics like length, diameter and volume are critical to measure to understand plant and soil functions. RhizoVision Explorer is an open-source software designed to enable researchers interested in roots by providing an easy-to-use interface, fast image processing and reliable measurements. The default broken roots mode is intended for roots sampled from pots and soil cores, washed and typically scanned on a flatbed scanner, and provides measurements like length, diameter and volume. The optional whole root mode for complete root systems or root crowns provides additional measurements such as angles, root depth and convex hull. Both modes support providing measurements grouped by defined diameter ranges, the inclusion of multiple regions of interest and batch analysis. RhizoVision Explorer was successfully validated against ground truth data using a new copper wire image set. In comparison, the current reference software, the commercial WinRhizo™, drastically underestimated volume when wires of different diameters were in the same image. Additionally, measurements were compared with WinRhizo™ and IJ_Rhizo using a simulated root image set, showing general agreement in software measurements, except for root volume. Finally, scanned root image sets acquired in different labs for the crop, herbaceous and tree species were used to compare results from RhizoVision Explorer with WinRhizo™. The two software showed general agreement, except that WinRhizo™ substantially underestimated root volume relative to RhizoVision Explorer. In the current context of rapidly growing interest in root science, RhizoVision Explorer intends to become a reference software, improve the overall accuracy and replicability of root trait measurements and provide a foundation for collaborative improvement and reliable access to all.
Visual recognition and coevolutionary history drive responses of amphibians to an invasive predator
Authors: Melotto Andrea , Ficetola Gentile Francesco , Alari Elisa , Romagnoli Samuele , Manenti Raoul 
Published: September 2021

Abstract
During biotic invasions, native prey are abruptly exposed to novel predators and are faced with unprecedented predatory pressures. Under these circumstances, the lack of common evolutionary history may hamper predator recognition by native prey, undermining the expression of effective antipredator responses. Nonetheless, mechanisms allowing prey to overcome evolutionary naïveté exist. For instance, in naïve prey, history of coevolution with similar native predators or detection of general traits characterizing predators can favor the recognition of stimuli released by invasive predators. However, few studies have assessed how these mechanisms shape prey response at the community level. Here, we evaluated behavioral responses in naïve larvae of 13 amphibian species to chemical and visual cues associated with an invasive predator, the American red swamp crayfish (Procambarus clarkii). Moreover, we investigated how variation among species responses was related to their coexistence with similar native crayfish predators. Amphibian larvae altered their behavior in presence of visual stimuli of the alien crayfish, while chemical cues elicited feeble and contrasting behavioral shifts. Activity reduction was the most common and stronger response, whereas some species exhibited more heterogeneous strategies also involving distancing and rapid escape response. Interestingly, species sharing coevolutionary history with the native crayfish were able to finely tune their response to the invasive one, performing bursts to escape. These results suggest native prey can respond to invasive predators through recognition of generic risk cues (e.g., approaching large shapes), still the capability of modulating antipredator strategies may also depend on their coevolutionary history with similar native predators.
Population differences in the effect of context on personality in an invasive lizard
Authors: Brand Jack A , Naimo Annalise C , Michelangeli Marcus , Martin Jake M , Sih Andrew , Wong Bob B M , Chapple David G 
Published: September 2021

Abstract
Within populations, individuals often differ consistently in their average level of behavior (i.e., animal personality), as well as their response to environmental change (i.e., behavioral plasticity). Thus, changes in environmental conditions might be expected to mediate the structure of animal personality traits. However, it is currently not well understood how personality traits change in response to environmental conditions, and whether this effect is consistent across multiple populations within the same species. Accordingly, we investigated variation in personality traits across two ecological contexts in the invasive delicate skink (Lampropholis delicata). Specifically, lizards from three different populations were repeatedly measured for individual activity in group behavioral assays under differing levels of food availability. We found that environmental context had a clear effect on the structure of lizard personality, where activity rates were not repeatable in the absence of food, but were repeatable in the presence of food resources. The difference in repeatability of activity rates across contexts appeared to be largely driven by an increase in among-individual variance when tested in the presence of food resources. However, this was only true for one of the populations tested, with food context having no effect on the expression of personality traits in the other two populations. Our results highlight the important role of environmental context in mediating the structure of animal personality traits and suggest that this effect may vary among populations.
Condition-dependent sexual reproduction is driven by benefits, not costs of sex
Authors: Lever Jessica , Drapes Sally , Hall Matthew D , Booksmythe Isobel 
Published: September 2021

AbstractFacultative sexual organisms must allocate resources to both asexual and sexual reproduction. Optimal patterns of investment in sex depend on the relative costs and benefits of each reproductive mode, and may consequently be context- and condition-dependent. Two proposed explanations for the observed variation in investment in sex among facultative sexual lineages invoke alternative condition-dependent scenarios. Under the fitness-associated sex hypothesis, sex is predicted when individuals are in poor condition or experience stressful environments. Under the resource-demanding sex hypothesis, sex is only affordable to individuals in good condition experiencing favourable environments. Direct tests of these contrasting hypotheses are rare; moreover, investment in different components of sexual reproduction responds differently to cues promoting sex, and may be subject to different energetic constraints. Using genotypes of facultative sexual Daphnia carinata that differ in their level of investment in sex, we manipulated resource availability while accounting for day length (a seasonal cue for sex) to evaluate these hypotheses. The sexual response to day length depended on resource availability: increased day lengths and reduced food availability increased the production of sexual eggs, and relative investment in males, in a manner consistent with the fitness-associated sex hypothesis. The pattern of condition-dependence was specific to each component of reproductive investment – while male production covaried with asexual fecundity across genotypes, increased sexual egg production was associated with reduced asexual reproduction. Our results suggest that investment in sex is determined largely by its context-dependent advantages, and that this investment is not moderated by immediate costs to asexual reproduction.
Conditional natal dispersal provides a mechanism for populations tracking resource pulses after fire
Authors: Stillman Andrew N , Lorenz Teresa J , Siegel Rodney B , Wilkerson Robert L , Johnson Matthew , Tingley Morgan W 
Published: September 2021

AbstractAnimals that persist in spatially structured populations face the challenge of tracking the rise and fall of resources across space and time. To combat these challenges, theory predicts that species should use conditional dispersal strategies that allow them to emigrate from patches with declining resources and colonize new resource patches as they appear. We studied natal dispersal movements in the black-backed woodpecker (Picoides arcticus), a species known for its strong association with recent post-fire forests in western North America. We radio-tracked juveniles originating from seven burned areas and tested hypotheses that environmental and individual factors influence dispersal distance and emigration rates—investigating emigration while additionally accounting for imperfect detection with a novel Bayesian model. We found that juveniles were more likely to leave natal areas and disperse longer distances if they were heavier or hatched in older burned areas where resources are increasingly scarce. Juveniles were also more likely to leave their natal burn if they hatched in a nest closer to the fire perimeter. While dispersing across the landscape, black-backed woodpeckers selected for burned forest relative to unburned available habitat. Together, these results strongly support the hypothesis that black-backed woodpecker populations track resource pulses across fire-prone landscapes, with conditional natal dispersal acting as a mechanism for locating and colonizing newly burned areas. Lending empirical support to theoretical predictions, our findings suggest that changes in resource distribution may shape dispersal patterns and, consequently, the distribution and persistence of spatially structured populations.
Assessing deep learning methods in cis-regulatory motif finding based on genomic sequencing data
Authors: Zhang Shuangquan , Ma Anjun , Zhao Jing , Xu Dong , Ma Qin , Wang Yan 
Published: September 2021

Abstract
Identifying cis-regulatory motifs from genomic sequencing data (e.g. ChIP-seq and CLIP-seq) is crucial in identifying transcription factor (TF) binding sites and inferring gene regulatory mechanisms for any organism. Since 2015, deep learning (DL) methods have been widely applied to identify TF binding sites and predict motif patterns, with the strengths of offering a scalable, flexible and unified computational approach for highly accurate predictions. As far as we know, 20 DL methods have been developed. However, without a clear and systematic assessment, users will struggle to choose the most appropriate tool for their specific studies. In this manuscript, we evaluated 20 DL methods for cis-regulatory motif prediction using 690 ENCODE ChIP-seq, 126 cancer ChIP-seq and 55 RNA CLIP-seq data. Four metrics were investigated, including the accuracy of motif finding, the performance of DNA/RNA sequence classification, algorithm scalability and tool usability. The assessment results demonstrated the high complementarity of the existing DL methods. It was determined that the most suitable model should primarily depend on the data size and type and the method’s outputs.
Exploring the immune evasion of SARS-CoV-2 variant harboring E484K by molecular dynamics simulations
Authors: Wu Leyun , Peng Cheng , Yang Yanqing , Shi Yulong , Zhou Liping , Xu Zhijian , Zhu Weiliang 
Published: September 2021

Abstract
Although the current coronavirus disease 2019 (COVID-19) vaccines have been used worldwide to halt spread of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the emergence of new SARS-CoV-2 variants with E484K mutation shows significant resistance to the neutralization of vaccine sera. To better understand the resistant mechanism, we calculated the binding affinities of 26 antibodies to wild-type (WT) spike protein and to the protein harboring E484K mutation, respectively. The results showed that most antibodies (~85%) have weaker binding affinities to the E484K mutated spike protein than to the WT, indicating the high risk of immune evasion of the mutated virus from most of current antibodies. Binding free energy decomposition revealed that the residue E484 forms attraction with most antibodies, while the K484 has repulsion from most antibodies, which should be the main reason of the weaker binding affinities of E484K mutant to most antibodies. Impressively, a monoclonal antibody (mAb) combination was found to have much stronger binding affinity with E484K mutant than WT, which may work well against the mutated virus. Based on binding free energy decomposition, we predicted that the mutation of four more residues on receptor-binding domain (RBD) of spike protein, viz., F490, V483, G485 and S494, may have high risk of immune evasion, which we should pay close attention on during the development of new mAb therapeutics.
Representation of molecules for drug response prediction
Authors: An Xin , Chen Xi , Yi Daiyao , Li Hongyang , Guan Yuanfang 
Published: September 2021

Abstract
The rapid development of machine learning and deep learning algorithms in the recent decade has spurred an outburst of their applications in many research fields. In the chemistry domain, machine learning has been widely used to aid in drug screening, drug toxicity prediction, quantitative structure–activity relationship prediction, anti-cancer synergy score prediction, etc. This review is dedicated to the application of machine learning in drug response prediction. Specifically, we focus on molecular representations, which is a crucial element to the success of drug response prediction and other chemistry-related prediction tasks. We introduce three types of commonly used molecular representation methods, together with their implementation and application examples. This review will serve as a brief introduction of the broad field of molecular representations.