bluuebunny/crossref_metadata_2025_split huggingface dataset:
scMAPA: Identification of cell-type–specific alternative polyadenylation in complex tissues
Authors: Bai Yulong , Qin Yidi , Fan Zhenjiang , Morrison Robert M , Nam KyongNyon , Zarour Hassane M , Koldamova Radosveta , Padiath Quasar Saleem , Kim Soyeon , Park Hyun Jung 
Published: April 2022

Abstract

Background
Alternative polyadenylation (APA) causes shortening or lengthening of the 3ʹ-untranslated region (3ʹ-UTR) of genes (APA genes) in diverse cellular processes such as cell proliferation and differentiation. To identify cell-type–specific APA genes in scRNA-Seq data, current bioinformatic methods have several limitations. First, they assume certain read coverage shapes in the scRNA-Seq data, which can be violated in multiple APA genes. Second, their identification is limited between 2 cell types and not directly applicable to the data of multiple cell types. Third, they do not control undesired source of variance, which potentially introduces noise to the cell-type–specific identification of APA genes.

Findings
We developed a combination of a computational change-point algorithm and a statistical model, single-cell Multi-group identification of APA (scMAPA). To avoid the assumptions on the read coverage shape, scMAPA formulates a change-point problem after transforming the 3ʹ biased scRNA-Seq data to represent the full-length 3ʹ-UTR signal. To identify cell-type–specific APA genes while adjusting for undesired source of variation, scMAPA models APA isoforms in consideration of the cell types and the undesired source. In our novel simulation data and data from human peripheral blood mononuclear cells, scMAPA outperforms existing methods in sensitivity, robustness, and stability. In mouse brain data consisting of multiple cell types sampled from multiple regions, scMAPA identifies cell-type–specific APA genes, elucidating novel roles of APA for dividing immune cells and differentiated neuron cells and in multiple brain disorders.

Conclusions
scMAPA elucidates the cell-type–specific function of APA events and sheds novel insights into the functional roles of APA events in complex tissues.
Deep learning inversion of Rayleigh-wave dispersion curves with geological constraints for near-surface investigations
Authors: Chen Xinhua , Xia Jianghai , Pang Jingyin , Zhou Changjiang , Mi Binbin 
Published: April 2022

SUMMARY
With the emergence of massive seismic data sets, surface wave methods using deep learning (DL) can effectively obtain shear wave velocity (Vs) structure for non-invasive near-surface investigations. Previous studies on DL inversion for deep geophysical investigation have a reference model to generate the training data set, while near-surface investigations have no model. Therefore, we systematically give a set of training data set generation processes. In the process, we use both prior information and the observed data to constrain the data set so that the DL inversion model can learn the local geological characteristics of the survey area. Because the space of inverted Vs models is constrained and thus narrowed, the inversion non-uniqueness can be reduced. Furthermore, the mean squared error, which is commonly used as loss function, may cause a poor fitting accuracy of phase velocities at high frequencies in near-surface applications. To make the fitting accuracy evenly in all frequency bands, we modify the loss function into a weighted mean squared relative error. We designed a convolutional neural network (CNN) to directly invert fundamental-mode Rayleigh-wave phase velocity for 1-D Vs models. To verify the feasibility and reliability of the proposed algorithm, we tested and compared it with the Levenberg–Marquardt (L-M) inversion and neighbourhood algorithm (NA) using field data from the Lawrence experiment (USA) and the Wuwei experiment (China). In both experiments, the inverted Vs models by CNN are consistent with the borehole information and are similar to that from existing methods after fine tuning of model parameters. The average root mean squares errors (RMSEs) of the CNN, NA and L-M methods are also similar, except in the Lawrence experiment, the RMSE of CNN is 17.33 m s−1 lower than previous studies using the L-M method. Moreover, the comparison of different loss functions for the Wuwei experiment indicates that the modified loss function can achieve higher accuracy than the traditional one. The proposed CNN is therefore ideally suited for rapid, repeated near-surface subsurface imaging and monitoring under similar geological settings.
Pre-processing data to reduce biases: full matching incorporating an instrumental variable in population-based studies
Authors: Cerna-Turoff Ilan , Maurer Katherine , Baiocchi Michael 
Published: April 2022

AbstractBackgroundEpidemiologists are often concerned with unobserved biases that produce confounding in population-based studies. We introduce a new design approach—‘full matching incorporating an instrumental variable (IV)’ or ‘Full-IV Matching’—and illustrate its utility in reducing observed and unobserved biases to increase inference accuracy. Our motivating example is tailored to a central question in humanitarian emergencies—the difference in sexual violence risk by displacement setting.MethodsWe conducted a series of 1000 Monte Carlo simulations generated from a population-based survey after the 2010 Haitian earthquake and included earthquake damage severity as an IV and the unmeasured variable of ‘social capital’. We compared standardized mean differences (SMDs) for covariates after different designs to understand potential biases. Mean risk differences (RDs) were used to assess each design’s accuracy in estimating the oracle of the simulated data set.ResultsNaive analysis and pair matching equivalently performed. Full matching reduced imbalances between exposed and comparison groups across covariates, except for the unobserved covariate of ‘social capital’. Pair and full matching overstated differences in sexual violence risk when displaced to a camp vs a community [pair: RD = 0.13, 95% simulation interval (SI) 0.09–0.16; full: RD = 0.11, 95% SI 0.08–0.14). Full-IV Matching reduced imbalances across observed covariates and importantly ‘social capital’. The estimated risk difference (RD = 0.07, 95% SI 0.03–0.11) was closest to the oracle (RD = 0.06, 95% SI 0.4–0.8).ConclusionFull-IV Matching is a novel approach that is promising for increasing inference accuracy when unmeasured sources of bias likely exist.
Exploring the “Military Time”: Historical Timing, Civil–Military Relations, and the Military Revolution in Russia and Japan
Authors: Kadercan Burak 
Published: April 2022

AbstractWhat is the relationship between civil–military relations and the emergence as well as diffusion of military innovations? More precisely, how do civil–military relations affect a state's capacity for adopting military innovations? While both topics, military innovations and civil–military relations, have individually attracted considerable scholarly attention, very few studies deal with them in tandem. This study builds on the existing research on the relationship between “historical timing,” civil–military relations, and the diffusion of military reforms and advances an analytical framework that treats “time” as an explanatory dynamic, using the reception of the “military revolution” on Russia and Japan as exploratory cases. In both cases, historical timing played crucial roles in defining the “balance of [political] power” between the rulers and the existing military establishment, which then led to diverging paths in terms of adopting and internalizing the military reforms associated with the aforementioned revolution.
Inwardness: Comparative Religious Philosophy in Modern Egypt
Authors: El Shakry Omnia 
Published: April 2022

AbstractThis article centers the Islamic philosopher ʿUthman Amin in order to explore the intellectual exchange between Muslim and Christian scholars in twentieth-century Egypt. Specifically, I look at inwardness, intellectual dialogue, and interreligious friendships in a field that has traditionally been dominated by scholarship on the relationship between Islam and politics or Islam and the law. I elucidate Amin’s philosophy of inwardness and its attendant virtues of seclusion, spiritual contemplation, and the jihad of the self—paying particular attention to reading as an illuminative embodied practice—through the lens of an Islamic discursive tradition. How might we understand the concept of an Islamic discursive tradition, as a philosophy of reasoned and embodied religion, within the context of such interreligious encounters? Amin, I argue, was engaged in an experimentum mentis in which inwardness provided an angle of lucidity from which Islam and Christianity could gaze upon one another. In so doing, I demonstrate the heuristic value of theorizations of tradition by Alasdair MacIntyre and Talal Asad to studies of interreligious encounter and scholarly exchange.
Prognostic Factors for In-Hospital Mortality of Geriatric Burns From the US National Inpatient Sample 2016 to 2018
Authors: Yi Yangtian , Vrouwe Sebastian Q , Gottlieb Lawrence J , Rubin Daniel S 
Published: April 2022

Abstract
Older adults with an acute burn experience a high frequency of in-hospital mortality. However, traditional burn mortality prediction models are less accurate for older adults likely because they do not account for geriatric specific factors, such as frailty. This study aims to investigate the impact of frailty on in-hospital mortality in older adult burn patients. Patients ≥50 years of age with an acute burn diagnosis in the National Inpatient Sample (2016–2018) were included in the cohort. Three multivariable logistic regression models to predict in-hospital mortality were generated and compared. The models were 1) age and percent total body surface area, 2) age, percent total body surface area and the Elixhauser Comorbidity Index, and 3) age, percent total body surface area, and Hospital Frailty Risk Score. A total of 60,515 weighted discharges were included in the cohort. In-hospital mortality increased with age, as 3.3% of 50- to 64-year-olds, 5.3% of 65- to 74-year-olds, 6.6% of 75- to 84-year-olds, and 9.9% of ≥85-year-olds died during the acute burn admission (P &lt; .001). The multivariable model that included Hospital Frailty Risk Score had a higher area under the receiver operating characteristics curve than the model with age and percent total body surface area (0.84 vs 0.79; P &lt; .001) and the model with Elixhauser Comorbidity Index (0.84 vs 0.83; P = .013). Frailty improved prediction of in-hospital mortality for older adult acute burn patients and burn specialists should consider implementing a frailty instrument to evaluate older adults with an acute burn injury.
Analyses of Bloodmeal Hosts and Prevalence of Rickettsia parkeri in the Gulf Coast Tick Amblyomma maculatum (Acari: Ixodidae) From a Reconstructed Piedmont Prairie Ecosystem, North Carolina
Authors: Johnson Connie R , Ponnusamy Loganathan , Richards Allen L , Apperson Charles S 
Published: April 2022

Abstract
Host feeding patterns and the prevalence of infection with Rickettsia parkeri were determined for the primary vector, Amblyomma maculatum Koch as well as sympatric tick species A. americanum (Linnaeus) and Dermacentor variabilis (Say) collected from a reconstructed prairie in the Piedmont region of North Carolina during 2011 and 2012. The occurrence of R. parkeri among A. maculatum adults and nymphs was 36.9% (45/122) and 33.3% (2/6), respectively. Rickettsia parkeri was detected in a single male A. americanum 2.3% (1/43). A PCR-reverse line blot hybridization assay of a 12S rDNA fragment amplified from remnant larval and nymphal bloodmeals of host-seeking ticks was used to identify bloodmeal hosts. Of the tick samples tested, bloodmeal host identification was successful for 29.3% (12/41) of adult A. americanum and 39.2% (20/51) of adult D. variabilis. For A. maculatum, bloodmeal host identification was successful for 50% (61/122) of adults collected from vegetation and 100% (4/4) of nymphs removed from cotton rats (Sigmodon hispidus Say and Ord). The cotton rat was the most common bloodmeal host with 59.0% (36/61) identified for adult A. maculatum. No statistically significant association was observed, however, between bloodmeal host and pathogen prevalence for any tick species. While the cotton rat was an important bloodmeal host for A. maculatum nymphs, this vertebrate did not appear to be the primary source of R. parkeri infection for A. maculatum.
Blow Flies (Diptera: Calliphoridae) and the American Diet: Effects of Fat Content on Blow Fly Development
Authors: Noblesse A P , Meeds A W , Weidner L M 
Published: April 2022

Abstract
Forensic entomology is an important field of forensic science that utilizes insect evidence in criminal investigations. Blow flies (Diptera: Calliphoridae) are among the first colonizers of remains and are frequently used in determining the minimum postmortem interval (mPMI). Blow fly development is influenced by a variety of factors including temperature and feeding substrate. Unfortunately, dietary fat content remains an understudied factor in the development process, which is problematic given the high rates of obesity in the United States. To study the effects of fat content on blow flies we investigated survivorship, adult weight, and development time (overall and by sex) of Lucilia sericata (Meigen) and Phormia regina (Meigen) on ground beef with 10%, 20%, or 27% fat. As fat content increased, survivorship decreased across both species with significant impact to P. regina. While P. regina adults were generally larger than L. sericata across all fat levels, only L. sericata demonstrated a significant (P &lt; 0.05) difference in weight by sex. Overall development times did not vary by fat content, excluding 27% for P. regina. Additionally, development times did not vary by sex for P. regina but did differ (P &lt; 0.05) for L. sericata with females taking longer to develop. These findings provide insight into the effect of fat content on blow fly development, a factor that should be considered when estimating an mPMI. By understanding how fat levels affect the survivorship and development of the species studied here, we can begin improving the practice of insect evidence analysis in casework.
Evaluating the Efficacy of a New Alternating Pressure Air Mattress Aimed at Reducing Pressure Injuries During the Transport of Combat Casualties
Authors: Lavender Steven A , Kachlan Anas , Pennells Simon E , Spence David 
Published: April 2022

ABSTRACT

Introduction
The development of pressure ulcers during aeromedical transport of combat casualties is an issue that continues to exist, especially during long transport flights. This study investigated the potential for a new intervention, an air-inflated insulating mattress pad (IMP) that has a pump system designed to alternate the pressurization of air cells under the patient, thus temporally shifting the pressure concentration locations.

Materials and Methods
In a repeated measures design study, 12 participants experienced the following four simulated transport conditions, each for 90 minutes: (1) The North Atlantic Treaty Organization (NATO) litter by itself (control condition), (2) the NATO litter covered with the standard mattress pad (Warrior Evacuation Pad), (3) the NATO litter covered with the air-inflated mattress (IMP), and (4) the NATO litter, covered with the standard mattress pad that was covered by the insulating mattress pad. Peak pressure readings were obtained every 15 seconds under the head, torso, pelvis, legs, and heels.

Results
While both mattress pads significantly reduced the peak pressures relative to the litter-only condition, the new IMP with the alternating cell pressurizations, by itself or in combination with the standard mattress pad, further reduced the peak pressures under the regions with the localized highest pressures, namely the head, pelvis, and heels. Moreover, the IMP with alternating pressure introduced the most variability in the peak pressure readings, which reduces the peak pressure exposure periods for specific tissue locations.

Conclusions
The IMP with alternating cell pressurizations could further reduce the likelihood of pressure injuries during aeromedical transport of combat casualties.
Simple interpretation of the seemingly complicated X-ray spectral variation of NGC 5548
Authors: Midooka Takuya , Ebisawa Ken , Mizumoto Misaki , Sugawara Yasuharu 
Published: April 2022

ABSTRACT
NGC 5548 is a very well-studied Seyfert 1 galaxy in broad wavelengths. Previous multiwavelength observation campaigns have indicated that its multiple absorbers are highly variable and complex. A previous study applied a two-zone partial covering model with different covering fractions to explain the complex X-ray spectral variation and reported a correlation between one of the covering fractions and the photon index of the power-law continuum. However, it is not straightforward to physically understand such a correlation. In this paper, we propose a model to avoid this unphysical situation; the central X-ray emission region is partially covered by clumpy absorbers composed of double layers. These ‘double partial coverings’ have precisely the same covering fraction. Based on our model, we have conducted an extensive spectral study using the data taken by XMM–Newton, Suzaku, and NuSTAR in the range of 0.3–78 keV for 16 yr. Consequently, we have found that the X-ray spectral variations are mainly explained by independent changes of the following three components; (1) the soft excess spectral component below ∼1 keV, (2) the cut-off power-law normalization, and (3) the partial covering fraction of the clumpy absorbers. In particular, spectral variations above ∼1 keV are mostly explained only by the changes of the partial covering fraction and the power-law normalization. In contrast, the photon index and all the other spectral parameters are not significantly variable.
Determining the aberrations in a nearly diffraction-limited spectrograph
Authors: Sánchez B , Watson A M , Cuevas S 
Published: April 2022

ABSTRACT
We present a method to determine the static aberrations in a nearly diffraction-limited spectrograph introduced, for example, by alignment or manufacturing errors. We consider an instrument with two stages separated by a slit or image slicer located in the intermediate focal plane. In such a spectrograph, it is not trivial to distinguish aberrations in the first stage, before the slit, from those in the second, after the slit. However, our method achieves this. Measuring these aberrations separately opens the possibility of reducing them, by realignment or other means, and thereby improving the optical performance of the instrument. The method is based on fitting models to multiple images of a point source, with controlled displacements of the source perpendicular to the slit and controlled defocuses of the second stage or the detector. Fitting models to these images allows the determination of the aberrations in both stages. Our key discovery is that the displaced and defocused images provide additional information which allows us to break the ambiguity between the two stages. We present simulations that validate the performance of the method.
Molecular Phylogeny Reveals the Past Transoceanic Voyages of Drywood Termites (Isoptera, Kalotermitidae)
Authors: Buček Aleš , Wang Menglin , Šobotník Jan , Hellemans Simon , Sillam-Dussès David , Mizumoto Nobuaki , Stiblík Petr , Clitheroe Crystal , Lu Tomer , González Plaza Juan José , Mohagan Alma , Rafanomezantsoa Jean-Jacques , Fisher Brian , Engel Michael S. , Roisin Yves , Evans Theodore A. , Scheffrahn Rudolf , Bourguignon Thomas 
Published: April 2022

AbstractTermites are major decomposers in terrestrial ecosystems and the second most diverse lineage of social insects. The Kalotermitidae form the second-largest termite family and are distributed across tropical and subtropical ecosystems, where they typically live in small colonies confined to single wood items inhabited by individuals with no foraging abilities. How the Kalotermitidae have acquired their global distribution patterns remains unresolved. Similarly, it is unclear whether foraging is ancestral to Kalotermitidae or was secondarily acquired in a few species. These questions can be addressed in a phylogenetic framework. We inferred time-calibrated phylogenetic trees of Kalotermitidae using mitochondrial genomes of ∼120 species, about 27% of kalotermitid diversity, including representatives of 21 of the 23 kalotermitid genera. Our mitochondrial genome phylogenetic trees were corroborated by phylogenies inferred from nuclear ultraconserved elements derived from a subset of 28 species. We found that extant kalotermitids shared a common ancestor 84 Ma (75–93 Ma 95% highest posterior density), indicating that a few disjunctions among early-diverging kalotermitid lineages may predate Gondwana breakup. However, most of the ∼40 disjunctions among biogeographic realms were dated at &lt;50 Ma, indicating that transoceanic dispersals, and more recently human-mediated dispersals, have been the major drivers of the global distribution of Kalotermitidae. Our phylogeny also revealed that the capacity to forage is often found in early-diverging kalotermitid lineages, implying the ancestors of Kalotermitidae were able to forage among multiple wood pieces. Our phylogenetic estimates provide a platform for critical taxonomic revision and future comparative analyses of Kalotermitidae.
RING 3.0: fast generation of probabilistic residue interaction networks from structural ensembles
Authors: Clementel Damiano , Del Conte Alessio , Monzon Alexander Miguel , Camagni Giorgia F , Minervini Giovanni , Piovesan Damiano , Tosatto Silvio C E 
Published: April 2022

AbstractResidue interaction networks (RINs) are used to represent residue contacts in protein structures. Thanks to the advances in network theory, RINs have been proved effective as an alternative to coordinate data in the analysis of complex systems. The RING server calculates high quality and reliable non-covalent molecular interactions based on geometrical parameters. Here, we present the new RING 3.0 version extending the previous functionality in several ways. The underlying software library has been re-engineered to improve speed by an order of magnitude. RING now also supports the mmCIF format and provides typed interactions for the entire PDB chemical component dictionary, including nucleic acids. Moreover, RING now employs probabilistic graphs, where multiple conformations (e.g. NMR or molecular dynamics ensembles) are mapped as weighted edges, opening up new ways to analyze structural data. The web interface has been expanded to include a simultaneous view of the RIN alongside a structure viewer, with both synchronized and clickable. Contact evolution across models (or time) is displayed as a heatmap and can help in the discovery of correlating interaction patterns. The web server, together with an extensive help and tutorial, is available from URL: https://ring.biocomputingup.it/.