bluuebunny/crossref_metadata_2025_split huggingface dataset:
One thousand soils for molecular understanding of belowground carbon cycling
Authors: Bowman Maggie M. , Heath Alexis E. , Varga Tamas , Battu Anil K. , Chu Rosalie K. , Toyoda Jason , Cheeke Tanya E. , Porter Stephanie S. , Moffett Kevan , Letendre Brittany , Qafoku Odeta , Bargar John R. , Mans Douglas , Hess Nancy , Graham Emily B. 
Published: December 2022

AbstractWhile significant progress has been made in understanding global carbon (C) cycling, the mechanisms regulating belowground C fluxes and storage are still uncertain. New molecular technologies have the power to elucidate these processes, yet we have no widespread standardized implementation of molecular techniques. To address this gap, we introduce the Molecular Observation Network (MONet), a decadal vision from the Environmental Molecular Sciences Laboratory (EMSL), to develop a national network for understanding the molecular composition, physical structure, and hydraulic and biological properties of soil and water. These data are essential for advancing the next generation of multiscale Earth systems models. In this paper, we discuss the 1000 Soils Pilot for MONet, including a description of standardized sampling materials and protocols and a use case to highlight the utility of molecular-level and microstructural measurements for assessing the impacts of wildfire on soil. While the 1000 Soils Pilot generated a plethora of data, we focus on assessments of soil organic matter (SOM) chemistry via Fourier-transform ion cyclotron resonance-mass spectrometry and microstructural properties via X-ray Computed Tomography to highlight the effects of recent fire history in forested ecosystems on belowground C cycling. We observed decreases in soil respiration, microbial biomass, and potential enzyme activity in soils with high frequency burns. Additionally, the nominal oxidation state of carbon in SOM increased with burn frequency in surface soils. This results in a quantifiable shift in the molecular signature of SOM and shows that wildfire may result in oxidation of SOM and structural changes to soil pore networks that persist into deeper soils.
Egg hatching success is significantly influenced by the time of thermal stress in multiple hard tick species
Authors: Ajayi Oluwaseun M. , Oyen Kennan J. , Davies Benjamin , Finch Geoffrey , Piller Benjamin D. , Harmeyer Alison A. , Wendeln Katherine , Perretta Carlie , Rosendale Andrew J. , Benoit Joshua B. 
Published: December 2022

AbstractTicks are blood-feeding arthropods responsible for the transmission of disease-causing pathogens to a wide range of vertebrate hosts, including livestock and humans. Tick-borne diseases have been implicated in significant economic losses to livestock production, and this threat will increase as these obligate parasites widen their geographical ranges. Just like in other ectotherms, thermal stress due to changing global temperatures has been shown to influence tick survival and distribution. However, studies on the influence of extreme temperatures in ticks have focused on advanced, mobile stages, ignoring stages that are immobile and cannot move to more favorable microhabitats. In this study, low- and high-temperature regimens were assessed in relation to egg viability for hard tick species -Amblyomma maculatum(Gulf Coast tick),Ixodes scapularis(black-legged tick),Dermacentor variabilis(American dog tick), andRhipicephalus sanguineus(Brown dog tick). Tick eggs exposed early in development were significantly more susceptible to thermal stress when compared with those exposed later in development. In our tested models, treatment was more important for egg hatching than species differences. Lastly, there was evidence of extreme thermal exposure significantly altering the hatching times of tick eggs for specific treatments. These results provide insights into the critical period for tick egg viability and potential tick control strategies as the globe continues to experience climate change.
Effect of Size Variability, Filamentation and Division Dynamics on Escherichia coli Allometry
Authors: Kale Tanvi , Khatri Dhruv , Athale Chaitanya A. 
Published: December 2022

AbstractThe cell surface area (SA) increase with volume (V) for cells is determined by growth and regulation of size and shape. Most studies of the rod-shaped model bacteriumEscherichia colihave focussed on the phenomenology or molecular mechanisms governing such scaling. Here, we proceed to examine the role of population statistics and cell division dynamics in such scaling by a combination of microscopy, image analysis and statistical simulations. We find that while cells sampled from mid-log cultures follow a 2/3 exponent, similar to geometric (Platonic) solids, drug induced filamentous cells have higher exponent values. Modulating the growth rate to change the proportion of filamentous cells, we find SA-V scales with an exponent>2/3, exceeding that predicted by the geometric scaling law. However, since increasing growth rates alter the mean and spread of population cell size distributions, we use statistical modeling to disambiguate between the effect of the mean size and variability. Simulating (i) increasing mean cell length with a constant standard deviation (s.d.) and (ii) a constant mean length with increasing s.d. results in scaling exponents that exceed the 2/3 geometric law, when population variability is included. In order to overcome possible effects of statistical sampling of unsynchronized cell populations, we virtually ‘synchronized’ the estimation of SA-V scaling from single cell growth experiments. We find the exponent depends on the stage with the maximal cell length heterogeneity and scaling exponent observed during the intermediate period between birth (B) and division (D) stages. These results point to a need to consider population statistics and a role for cell growth and division when estimating SA-V scaling of bacterial cells.
Neuroecological selection for musical features through spatial reciprocity in long-term partnerships
Authors: Schruth David M. 
Published: December 2022

AbstractChemical sensing via olfaction constitutes a most ancient form of inter-organism communication. But acoustical signaling via tonal and rhythmic patterning is also common among higher vertebrates. Animals that live in well ventilated habitats and move in diasporic ways have further evolved more spectrally varied and discretized call structure. But unlike song in birds, researchers have struggled to locate isolated nucleii specialized for music cognition. The brain stem, midbrain, hindbrain, and forebrain, however, all largely associate with aspects of musical performance, perception, memory, and emotion. I hypothesized that spectral features of musical display evolved as honest signals of spatial cognition for precarious locomotor tasks associated with nurturing and protecting vulnerable offspring. I investigated possible connections between motor, visual, and spatial cognitive areas in relation to both signaler production and receiver processing of acoustical features of musical output. Brain component volume fractions of 42 parts from 48 primates were compiled, from a single source, and compared against a vocal complexity index (ARDI) as well as individual musical feature scores: including tone, interval, repetition, transposition rhythm, and unique syllable count. Structures for spatial and visual perception as well as motor control and emotional processing associated moderately with areas used by species who produce calls with both temporal and spectral musical features. These findings are consistent with a dual (both receiver- and signaler-side) function of musical signals. Associations with spatio-social areas (e.g. schizocortex and insula) support direct selection for a paralimbic-based neighbor orienting [PIANO] sensory modality for mapping and anticipating movement of fellow arboreal cohabitants. Associations with motor areas (e.g. LGN, mid-brain, and thalamus) support the complementary model that signaler capacities for spatio-motive emplacement [ME] are indirectly selected by conspecific receivers. This dual manifestation in low-parity species that locomote in diasporic ways through (arboreally) diffuse habitats, is compatible with musicality serving as courtship signals by long-term mates with consistent and reliable spatial capacities directly relevant to care of vulnerable (arboreal) offspring.
Combination of personalized computational modeling and machine-learning for optimization of left ventricular pacing site in cardiac resynchronization therapy
Authors: Dokuchaev Arsenii , Chumarnaya Tatiana , Bazhutina Anastasia , Khamzin Svyatoslav , Lebedeva Viktoria , Lyubimtseva Tamara , Zubarev Stepan , Lebedev Dmitry , Solovyova Olga 
Published: December 2022

ABSTRACTBackgroundThe 30-50% non-response rate to cardiac resynchronisation therapy (CRT) calls for improved patient selection and optimized pacing lead placement.ObjectiveThe study aimed to develop a novel technique using patient-specific cardiac models and machine learning (ML) to predict an optimal left ventricular (LV) pacing site (ML-PS) that maximizes the likelihood of LV ejection fraction (LVEF) improvement in a given CRT candidate. To validate the approach, we evaluated whether the distance DPSbetween the clinical LV pacing site (ref-PS) and ML-PS is associated with improved response rate and magnitude.Materials and MethodsWe reviewed retrospective data for 57 CRT recipients. A positive response was defined as a more than 10% LVEF improvement. Personalized models of ventricular activation and ECG were created from MRI and CT images. The characteristics of ventricular activation during intrinsic rhythm and biventricular (BiV) pacing with ref-PS were derived from the models and used in combination with clinical data to train supervised ML classifiers. The best logistic regression model classified CRT responders with a high accuracy of 0.77 (ROC AUC=0.84). The LR classifier, model simulations and Bayesian optimization with Gaussian process regression were combined to identify an optimal ML-PS that maximizes the ML-score of CRT response over the LV surface in each patient.ResultsThe optimal ML-PS improved the ML-score by 17±14% over the ref-PS. Twenty percent of the non-responders were reclassified as positive at ML-PS. Selection of positive patients with a max ML-score >0.5 demonstrated an improved clinical response rate. The distance DPSwas shorter in the responders. The max ML-score and DPSwere found to be strong predictors of CRT response (ROC AUC=0.85). In the group with max ML-score>0.5 and DPS< 30 mm, the response rate was 83% compared to 14% in the rest of the cohort. LVEF improvement in this group was higher than in the other patients (16±8% vs 7±8%).ConclusionA new technique combining clinical data, personalized heart modelling and supervised ML demonstrates the potential for use in clinical practice to assist in optimizing patient selection and predicting optimal LV pacing lead position in HF candidates for CRT.
The estimated disease burden of COVID-19 in Japan from 2020 to 2021
Authors: Tsuzuki Shinya , Beutels Philippe 
Published: December 2022

AbstractBackgroundTo date, it is not fully understood to what extent COVID-19 has burdened society in Japan. This study aimed to estimate the total disease burden due to COVID-19 in Japan during 2020-2021.MethodsWe stratify disease burden estimates by age group and present it as absolute Quality Adjusted Life Years (QALYs) lost and QALYs lost per 100,000 persons. The total estimated value of QALYs lost consists of (1) QALYs lost brought by deaths due to COVID-19, (2) QALYs lost brought by inpatient cases, (3) QALYs lost brought by outpatient cases, and (4) QALYs lost brought by long-COVID.FindingsQALYs lost due to COVID-19 was estimated as 286,781·7 for two years, 114·0 QALYs per 100,000 population per year. 71·3% of them were explained by the burden derived from deaths. Probabilistic sensitivity analysis showed that the burden of outpatient cases was the most sensitive factor.InterpretationThe large part of disease burden due to COVID-19 in Japan from the beginning of 2020 to the end of 2021 was derived from Wave 3, 4, and 5 and the proportion of QALYs lost due to morbidity in the total burden increased gradually. The estimated disease burden was smaller than that in other high-income countries. It will be our future challenge to take other indirect factors into consideration.FundingsThis research was funded by JSPS KAKENHI [Grant number 20K10546]. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Crossmodal visual predictions elicit spatially specific early visual cortex activity but later than real visual stimuli
Authors: Stange Liesa , Ossandón José P. , Röder Brigitte 
Published: December 2022

AbstractPrevious studies have indicated that crossmodal visual predictions are instrumental in controlling early visual cortex activity. The exact time course and spatial precision of such crossmodal top-down influences on visual cortex have been unknown. In the present study, participants were exposed to audio-visual combinations comprising one of two sounds and a Gabor patch either in the top left or in the bottom right visual field. Event related potentials (ERP) were recorded to these frequent crossmodal combinations (Standards) as well as to trials in which the visual stimulus was omitted (Omissions) or the visual and auditory stimuli were recombined (Deviants). Standards and Deviants elicited an ERP between 50 and 100 ms of opposite polarity known as a C1 effect commonly associated with retinotopic processing in early visual cortex. In contrast, a C1 effect was not observed in Omission trials. Spatially specific Omission and Mismatch effects (Deviants minus Standards) started only later with a latency of 230 ms and 170 ms, respectively.These results suggest that crossmodal visual predictions control visual cortex activity in a spatially specific manner. However, visual predictions do not elicit neural responses that mimic stimulus-driven activity but rather seem to affect early visual cortex via distinct neural mechanisms.
Do early indicators of euthyroid sick syndrome predict longer-term post-bariatric weight loss? A hypothesis-generating preliminary study
Authors: Fowler Natasha , Adler Sarah , Najarian Thomas , Rowsemitt Carol N. , Safer Debra L. 
Published: December 2022

AbstractBackgroundDespite bariatric surgery’s success for most patients, up to 30% do not experience optimal weight loss outcomes. Reasons remain incompletely understood. Thyroid hormones, due to their role in energy expenditure, have received study. Yet research to date is inconclusive regarding the impact of standard thyroid markers (e.g., thyroid stimulating hormone, or TSH) on weight regulation after bariatric surgery. This prospective observational study investigates whether the early development of euthyroid sick syndrome (ESS) predicts reduced longer-term post-bariatric weight loss. ESS develops during periods of stress (e.g., critical illness, severe infection, famine) and is thought to serve a protective function by suppressing metabolism and conserving weight. Levels of metabolically active free triiodothyronine (FT3) drop, levels of non-catabolic reverse 3,3’,5’-triiodothyronine (rT3) rise, and TSH levels remain euthyroid. Reductions in the ratio of FT3to rT3significantly predict outcomes in critically ill patients with ESS yet have been unexamined in intentional weight loss among post-bariatric patients. Hence this hypothesis-generating preliminary study investigated whether early changes in the FT3:rT3ratio predict weight changes at 1-2 years post-bariatric surgeryMethodsTwenty-three adult patients undergoing Roux-en-Y gastric bypass (n=12) or sleeve gastrectomy (n=11) were recruited from a bariatric surgery clinic. The TSH, FT4, FT3, rT3, and self-reported hypothyroid symptoms were collected 2-weeks pre-surgery and between 2 weeks to 3 months post-surgery. Body mass index was measured pre-surgery and 1-2 years post-surgery.ResultsReductions in the FT3:rT3ratio from pre- to early post-surgery significantly predicted reduced weight loss at 1 (p= 0.03) and 2 years (p= 0.02) post-surgery. No other thyroid-related markers nor hypothyroid symptoms were predictive.ConclusionsAlthough replication with larger samples is needed due to sizeable study attrition, this small exploratory study provides provocative support that early changes in the FT3:rT3ratio associated with ESS predict longer-term reductions in post-bariatric surgery weight loss. Clinical implications are discussed.
Splicing annotation of endometrial cancer GWAS risk loci reveals potentially causal variants and supports a role forNF1andSKAP1as susceptibility genes
Authors: Canson Daffodil M. , O’Mara Tracy A. , Spurdle Amanda B. , Glubb Dylan M. 
Published: December 2022

ABSTRACTAlternative splicing contributes to cancer development. Indeed, splicing analysis of cancer genome-wide association study (GWAS) risk variants has revealed likely causal variants. To systematically assess GWAS variants for splicing effects, we developed a prioritization workflow using a combination of splicing prediction tools, alternative transcript isoform and splicing quantitative trait locus (sQTL) annotations. Application of this workflow to candidate causal variants from 16 endometrial cancer GWAS risk loci highlighted single nucleotide polymorphisms (SNPs) that were predicted to upregulate alternative transcripts. For two variants, sQTL data supported the predicted impact on splicing. At the 17q11.2 locus, the protective allele for rs7502834 was associated with increased splicing of an exon inNF1alternative transcript encoding a truncated protein in adipose tissue and is consistent with an endometrial cancer transcriptome-wide association study (TWAS) finding in adipose tissue. Notably,NF1haploinsufficiency is protective for obesity, a well-established risk factor for endometrial cancer. At the 17q21.32 locus, the rs2278868 risk allele was predicted to upregulate aSKAP1transcript that is subject to nonsense mediated decay, concordant with a corresponding sQTL in lymphocytes. This is consistent with a TWAS finding that indicates decreasedSKAP1expression in blood increases endometrial cancer risk. As SKAP1 is involved in T-cell immune responses, decreasedSKAP1expression may impact endometrial tumor immunosurveillance. In summary, our analysis has identified potentially causal endometrial cancer GWAS risk variants with plausible biological mechanisms and provides a splicing annotation workflow to aid interpretation of other GWAS datasets.
Understanding the mechanism of the SARS CoV-2 coinfection with other respiratory viruses
Authors: Ponnusamy Kalaiarasan , Srinivasan RadhaKrishnan Venkatraman , Marwal Robin , Datta Meena , Dhar Mahesh Shankar , Chaudhary Urmila , Sharma Uma , Kumari Swati , Sharma Kalpana , Gogia Hema , Madan Preeti , Kabra Sandhya , Rakshit Partha 
Published: December 2022

AbstractCoinfections have a potential role in increased morbidity and mortality rates during pandemics. Our investigation is aimed at evaluating the viral coinfection prevalence in COVID-19 patients. Rapid diagnostic tests are tools with a paramount impact both on improving patient care. Particularly in the case of respiratory infections, it is of great importance to quickly confirm/exclude the involvement of pathogens. The COVID-19 pandemic has been associated with changes in respiratory virus infections worldwide, which have differed between virus types. In this paper, we systematically searched the percentage of coinfection of various respiratory viruses in COVID-19-positive samples. We included patients of all ages, in all settings. The main outcome was the proportion of patients with viral coinfection. By describing the differences in changes between viral species across different geographies over the course of the COVID-19 pandemic, we may better understand the complex factors involved in the community cocirculation of respiratory viruses.
State-dependency of behavioural traits is a function of the life-stage in a holometabolous insect
Authors: Singh Pragya , Wolthaus Jonas , Schielzeth Holger , Müller Caroline 
Published: December 2022

AbstractState variables, such as body condition, are important predictors of behavioural traits. Depending on the state of an individual, the costs and benefits associated with different behavioural decisions can vary. An individual’s state could affect its average behavioural response and also the behavioural repeatability. Moreover, even for the same state, different behavioural strategies may be adaptive depending on the individual’s life-stage. Here, we manipulated the body condition in larvae and adults of a holometabolous insect species,Athalia rosae, using starvation. We assessed the effects of starvation on the behavioural traits of post-contact immobility (PCI) and activity levels and tested their repeatability. Our results show state-dependency of behaviour, although the effect varied with life-stage. Starved larvae exhibited shorter PCI duration and higher activity levels, whereas starved adults were less active than non-starved individuals. Moreover, although most behavioural repeatability estimates were significant in both life-stages, we did not find any significant effect of starvation on the estimates. Next, we calculated standardised effect sizes to compare starvation effects across life stages. We found that starvation had a larger and opposite effect in the larval stage than during the adult stage for all behavioural traits. Finally, we conducted microcosm and no-choice bioassay experiments to examine the benefits and costs, respectively, of the behaviour elicited by starvation in the larval stage. We observed that starved larvae located food faster than non-starved larvae but were also attacked sooner by a predator, possibly due to their higher activity levels. Together, our results demonstrate that behavioural state-dependence is a function of the life-stage of an individual. Moreover, the behavioural strategy exhibited can be adaptive for a specific life-stage with respect to certain functions, like foraging, but also carry costs, like risk of predation.
Structure-optimized sgRNA selection with PlatinumCRISPr for efficient Cas9 generation of knock-outs
Authors: Haussmann Irmgard U. , Dix Thomas C. , McQuarrie David W. J. , Dezi Veronica , Hans Abdullah I. , Arnold Roland , Soller Matthias 
Published: December 2022

AbstractA single guide RNA (sgRNA) directs Cas9 nuclease for gene-specific scission of double-stranded DNA. High Cas9 activity is essential for efficient gene editing to generate gene deletions and gene replacements by homologous recombination. However, cleavage efficiency is below 50% for more than half of randomly selected sgRNA sequences in human cell culture screens or model organisms. We used in vitro assays to determine intrinsic molecular parameters for maximal sgRNA activity including correct folding of sgRNAs and Cas9 structural information. From comparison of over 10 data sets, we find major constraints in sgRNA design originating from defective secondary structure of the sgRNA, sequence context of the seed region, GC context and detrimental motifs, but we also find considerable variation among different prediction tools when applied to different data sets. To aid selection of efficient sgRNAs, we developed web-based PlatinumCRISPr, an sgRNA design tool to evaluate base-pairing and sequence composition parameters for optimal design of highly efficient sgRNAs for Cas9 genome editing named PlatinumCRISPr. We applied this tool to select sgRNAs to efficiently generate gene deletions inDrosophila Ythdc1andYthdf, that bind toN6methylated adenosines (m6A) in mRNA. However, we discovered, that generating small deletions with sgRNAs and Cas9 leads to ectopic reinsertion of the deleted DNA fragment elsewhere in the genome. These insertions can be removed by standard genetic recombination and chromosome exchange. These new insights into sgRNA design and the mechanisms of CRISPR-Cas9 genome editing advances efficient use of this technique for safer applications in humans.