bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prediction of Aortic Contrast Enhancement on Dynamic Hepatic Computed Tomography—Performance Comparison of Machine Learning Methods and Simulation Software
Authors: Masuda Takanori , Nakaura Takeshi , Higaki Toru , Funama Yoshinori , Sato Tomoyasu , Masuda Shouko , Yoshiura Takayuki , Arao Shinichi , Hiratsuka Junichi , Hirai Toshinori , Awai Kazuo 
Published: March 2022

Objectives
The aim of this study was to compare prediction ability between ensemble machine learning (ML) methods and simulation software for aortic contrast enhancement on dynamic hepatic computed tomography.

Methods
We divided 339 human hepatic dynamic computed tomography scans into 2 groups. One group consisted of 279 scans used to create cross-validation data sets, the other group of 60 scans were used as test data sets. To evaluate the effect of the patient characteristics on enhancement, we calculated changes in the contrast medium dose per enhancement of the abdominal aorta in the hepatic arterial phase. The parameters for ML were the patient sex, age, height, body weight, body mass index, and cardiac output. We trained 9 ML regressors by applying 5-fold cross-validation, integrated the predictions of all ML regressors for ensemble learning and the simulations, and used the training and test data to compare their Pearson correlation coefficients.

Results
Comparison of different ML methods showed that the Pearson correlation coefficient for the real and predicted contrast medium dose per enhancement of the abdominal aorta was highest with ensemble ML (r = 0.786). It was higher than that obtained with the simulation software (r = 0.350). With ensemble ML, the Bland-Altman limit of agreement [mean difference, 5.26 Hounsfield units (HU); 95% limit of agreement, −112.88 to 123.40 HU] was narrower than that obtained with the simulation software (mean difference, 11.70 HU; 95% limit of agreement, −164.71 to 188.11 HU).

Conclusion
The performance for predicting contrast enhancement of the abdominal aorta in the hepatic arterial phase was higher with ensemble ML than with the simulation software.
Is Free Breathing Possible During Computed Tomography–Guided Percutaneous Transthoracic Lung Biopsy? The Clinical Experience in 585 Cases
Authors: Han Ji-Yeon , Lee Ki-Nam , Choi Seok Jin , Baek Jin Wook , Kim Dasom , Lee Hongyeul , Yoon Yoo Sang , Choo Hye Jung , Heo Young Jin , Park Jinyoung , Kim Dong Hyun 
Published: March 2022

Objective
The aim of the study was to retrospectively evaluate the safety and accuracy of computed tomography (CT)–guided percutaneous transthoracic needle biopsy (PTNB) of lung lesions during quiet breathing.

Methods
We investigated the diagnostic performance and complication rate of 585 procedures in 563 patients (357 men; mean age, 67.7 years), who underwent CT-guided PTNBs during quiet breathing, aided by a respiratory targeting technique from May 2017 to July 2019. Differences between the cases with and without respiratory targeting were analyzed. Logistic regression analyses were performed to examine the development of pneumothorax and hemoptysis.

Results
Percutaneous transthoracic needle biopsy samples were successfully obtained in 574 of 585 procedures (98.1%). Final diagnoses included: 410 malignant cases, 119 benign cases, and 45 indeterminate cases. The sensitivity, specificity, and accuracy of diagnosis were 94.4%, 100%, and 95.7%, respectively. Use of respiratory targeting was associated with younger age (P = 0.004), smaller lesion size (P < 0.001), peripheral location (P = 0.003), shorter distance from the diaphragm (P < 0.001), lower lobe location (P < 0.001), prone position (P = 0.004), and visible motion artifact (P < 0.001). Pneumothorax and hemoptysis rates were 22.9% and 7.9%, respectively. Upon multivariate analysis, emphysema (P = 0.002) was the only independent risk factor for pneumothorax, whereas distance from the pleura greater than 2 cm (P < 0.001), tissue sampling 3 times or more (P = 0.003), and a less experienced operator (P < 0.001) were risk factors for hemoptysis.

Conclusions
Computed tomography–guided PTNB during quiet breathing with respiratory targeting yielded high diagnostic performance with a slightly higher rate of complications. Free-breathing PTNB can be applied in clinical practice, based on lesion location and risk factors for complications.
Diagnosis of Primary Scrotal Lymphedema Using 99mTc-Sulfur Colloid Lymphoscintigram
Authors: Rhee Annie , Flug Jonathan A. , Casey William J. , Roarke Michael C. , Rebecca Alanna M. , Yang Ming 
Published: March 2022

Abstract
We report a case of a 19-year-old man who presented with severe scrotal swelling. His medical history was notable for severe global edema at birth. Most areas of swelling had resolved by adolescence with exception of the scrotum and the left lower extremity. 99mTc-filtered sulfur colloid lymphoscintigraphy of the lower extremities demonstrated prominent dermal backflow into the superficial scrotum and thighs, which were confirmed on the SPECT/CT images, and correlated with findings on MR lymphangiogram. Lymphoscintigram and MR lymphangiogram may provide complementary information to aid diagnosis and management of primary scrotal lymphedema.
FPGA Acceleration of GWAS Permutation Testing
Authors: Swiel Yaniv , Brandenburg Jean-Tristan , Hayat Mahtaab , Chen Wenlong Carl , Cox Mitchell A. , Hazelhurst Scott 
Published: March 2022

MotivationGenome-wide association studies (GWASs) analyse genetic variation over the genomes of many individuals in an attempt to identify single nucleotide polymorphisms (SNPs) associated with complex phenotypes. To capture a large amount of genetic variation and increase the chance of detecting associated SNPs, modern GWASs include millions of SNPs sampled from thousands of individuals. The cumulative probability of false associations increases with the number of SNPs included in the analysis. A GWAS, therefore, needs to control the number of false associations. Permutation testing is a straightforward and accurate method of controlling the false positive rate, but it is very computationally expensive (and slow) so there is a need for a permutation testing accelerator that can process modern GWAS datasets in reasonable time.ResultsFPGAs (Field-Programmable Gate Arrays) are reconfigurable integrated circuits which provide a high level of parallelisation that can be harnessed to accelerate GWAS permutation testing. This work presents an accessible FPGA-based tool (designed to run on a cloud-based AWS EC2 FPGA instance) that accelerates GWAS permutation testing for continuous phenotypes. The tool implements two known GWAS permutation testing algorithms: maxT permutation testing and adaptive permutation testing. The speed of the FPGA-based tool was compared to the speed of PLINK (a popular CPU-based tool) running on 40 Intel Xeon 4114 CPU cores using an imputed breast cancer dataset of 13.7 million SNPs sampled from 3652 individuals. For 1000 maxT permutations, the FPGA-based algorithm’s run time was 22 minutes while PLINK’s run time was almost 7 days; for 100 million adaptive permutations, the FPGA-based algorithm’s run time was 325 minutes and PLINK’s run time was about 8.5 days. For 700 million adaptive permutations of the same dataset (an almost unfeasible workload for PLINK running on a 40-core CPU) the run time of the FPGA-accelerated algorithm was 33 hours.AvailabilityAn EC2 AMI (FPGA_perm) in the us-east-1 region is available. Instructions, source code and sample data are available at https://github.com/witseie/fpgaperm.
Anthropogenic impacts on threatened species erode functional diversity in turtles and crocodilians
Authors: Rodríguez-Caro R.C. , Graciá E. , Blomberg S.P. , Cayuela H. , Grace M. , Carmona C.P. , Pérez-Mendoza H.A. , Giménez A. , Salguero-Gómez R. 
Published: March 2022

ABSTRACTThe Anthropocene is tightly associated with a drastic loss of species worldwide and the disappearance of their key ecosystem functions. The on-going reduction in ecosystem functionality is driven by global and local threats. The orders Testudines (turtles and tortoises) and Crocodilia (crocodiles, alligators, and gharials) contain numerous threatened, long-lived species for which their functional diversity and potential erosion by anthropogenic impacts remains unknown. Here, we examine 259 (69%) of the existing 375 species of Testudines and Crocodilia, quantifying their life history strategies (i.e., schedules of survival, development, and reproduction) from open-access data on their demography, ancestry, and threats. We find that the loss of functional diversity in simulated extinction scenarios of threatened species is greater than expected by chance. Moreover, the effects of unsustainable local consumption, diseases, and pollution are associated with specific functional strategies. In contrast, climate change, habitat disturbance, and global trade affect all species independent of their life history strategy. Importantly, the loss of functional diversity for threatened species by habitat disturbance is twice that for all other threats. Our findings highlight the importance of conservation programmes focused on preserving the functional diversity of life history strategies jointly with the phylogenetic representativity of these highly threatened groups.
Black Queen Hypothesis, partial privatization, and quorum sensing evolution
Authors: Souza Lucas Santana , Irie Yasuhiko , Eda Shigetoshi 
Published: March 2022

AbstractMicroorganisms produce costly cooperative goods whose benefit is partially shared with nonproducers, called ‘mixed’ goods. The Black Queen Hypothesis predicts that partially privatization of benefits from the mixed goods has two major evolutionary implications. First, to favor strains producing several mixed goods over nonproducing strains. Second, to favor the maintenance of cooperative traits through different strains instead of having all cooperative traits present in a single strain (metabolic specialization). Despite the importance of quorum sensing regulation of mixed goods, it is not clear how partial privatization of benefits affects quorum sensing evolution. Here, we studied the influence of partial privatization of benefits on the evolution of quorum sensing. We developed a mathematical population genetics model of an unstructured microbial population considering four strains that differ in their ability to produce an autoinducer (quorum sensing signaling molecule) and a mixed good. Our model assumes that the production of the autoinducers and the mixed goods is constitutive and/or depends on quorum sensing. Our results suggest that partially privatized benefits cannot foster quorum sensing. This result occurs because: (1) a strain that produces both autoinducer and good (fully producing strain) cannot persist in the population; (2) the strain only producing the autoinducer and the strain producing mixed goods in response to the autoinducers cannot coexist, i.e., metabolic specialization cannot be fostered.
The AppNL-G-F mouse model of Alzheimer’s disease is refractory to regulatory T cell treatment
Authors: Yshii Lidia , Mascali Loriana , Kouser Lubna , Lemaitre Pierre , Marino Marika , Dooley James , Burton Oliver , Haughton Jeason , Callaerts-Vegh Zsuzsanna , De Strooper Bart , Holt Matthew G. , Pasciuto Emanuela , Liston Adrian 
Published: March 2022

AbstractBackgroundAlzheimer’s Disease is a neurodegenerative disease with a neuroinflammatory component. Due to the multifunctional capacity of regulatory T cells to prevent and reverse inflammation, regulatory T cells have been proposed as a potential therapeutic in Alzheimer’s Disease, either as a direct cell therapy or through the use of IL2 as a biologic to expand the endogenous population.MethodsHere we characterize the longitudinal immunological changes occurring in T cells in the AppNL-G-F mouse model of Alzheimer’s disease.ResultsAge-dependent immunological changes, in both the brain and periphery, occurred in parallel in both AppNL-G-F mice and control AppNL mice. As the endogenous IL2 axis was disturbed with age, we sought to determine the effect of IL2 supplementation on disease progression. Using a genetic model of IL2 provision in the periphery or in the brain, we found that expanding regulatory T cells in either location was unable to alter the progression of key pathological events or behavioral changes.ConclusionThese results suggest that either the AppNL-G-F mouse model does not recapitulate key regulatory T cell-dependent process of Alzheimer’s disease, or that regulatory T cell therapy is not a promising candidate for APP-mutation-driven Alzheimer’s disease.
B cells are addicted to immunoglobulin production in the ER
Authors: Caganova Marieta , Taskiran Hakan , Zong Yue , Zach Andreas , Kabrani Eleni , Schmidt Kristin , Goffing Paul , Jellusova Julia , Rajewsky Klaus 
Published: March 2022

AbstractResting B cell dependence on the B cell antigen receptor (BCR) has been attributed solely to its signaling competence. We have recently shown that the presence of the BCR is vital for endoplasmic reticulum (ER) homeostasis and mitochondrial function both in primary B cells and Burkitt lymphoma (BL) cell lines. Unexpectedly, in BL Ramos cells this role has been shown to be independent of BCR signals from the cell membrane. Now, we provide evidence that also in mouse resting B cells ER-resident immunoglobulin (Ig) heavy chains control ER homeostasis, calcium storage and mitochondrial homeostasis through ER-mitochondria contacts. These findings demonstrate that BCR expression shapes cellular fitness already at the stage of assembly in the ER and uncover a new layer of B cell dependence on the production of Ig heavy chains in the ER. Sensing protein expression in the ER, with counterselection of compromised cells, might well operate also in other differentiated cells.
A Spatiotemporal Reconstruction of the C. elegans Pharyngeal Cuticle Reveals a Structure Rich in Phase-Separating Proteins
Authors: Kamal Muntasir , Tokmakjian Levon , Knox Jessica , Mastrangelo Peter , Ji Jingxiu , Cai Hao , Wojciechowski Jakub W. , Hughes Michael P. , Takács Kristóf , Chu Xiaoquan , Pei Jianfeng , Grolmusz Vince , Kotulska Malgorzata , Forman-Kay Julie D. , Roy Peter J. 
Published: March 2022

AbstractRoughly 4.5 million species of ecdysozoan animals repeatedly shed their old cuticle and construct a new one underneath to accommodate growth. How cuticles are constructed is not well understood. Here, we systematically mine gene expression datasets to uncover the spatiotemporal blueprint for how the chitin-based pharyngeal cuticle of the nematode Caenorhabditis elegans is built. We demonstrate that the blueprint correctly predicts expression patterns and functional relevance to cuticle development. We find that as larvae prepare to molt, catabolic enzymes are upregulated and the genes that encode chitin synthase, chitin cross-linkers, and homologs of amyloid regulators subsequently peak in expression. 48% of the gene products secreted during the molt are predicted to be intrinsically disordered proteins (IDPs), many of which belong to four distinct families that are expressed in overlapping waves. These include the IDPAs, IDPBs, and IDPCs that are introduced for the first time here. We find that all four families have sequence properties known to drive phase separation and show in vitro phase separation for one of these proteins. This systematic analysis reveals the massive contribution that IDPs make to the cuticle and highlights how reversibly phase-separating materials may facilitate cuticle disassembly and reassembly during the molt.
A re-emerging arbovirus in livestock in China: Early genomic surveillance and phylogeographic analysis
Authors: Su Shuo 
Published: March 2022

AbstractViruses in livestock represent a great risk to public health due to the close contact of their hosts with humans and the potential long-range transportation though animal trade. Here, we show how to predict outbreaks of potential zoonotic pathogens and use spatially-explicit phylogeographic and phylodynamic approaches to provide estimates of key epidemiological parameters. First, we use metagenomic next generation sequencing (mNGS) to identify a Getah virus (GETV) as the pathogen responsible for a re-emerging swine disease in China. The GETV isolate is able to replicate in a variety of cell lines including human cells and shows high pathogenicity in a mouse model suggesting a potential public health risk. We obtained 16 complete genomes and 78 E2 gene sequences from viral strains collected within China from 2017 to 2021 through large-scale surveillance among livestock, pets and mosquitoes. Moreover, phylogenetic analysis reveals that three major GETV lineages are responsible for the current epidemic in livestock in China. We identify three potential positively selected sites and mutations of interest in E2, which may impact the transmissibility and pathogenicity of the virus. We then reconstruct the evolutionary and dispersal history of the virus and test the impact of several environmental factors on the viral genetic diversity through time and on the dispersal dynamic of viral lineages. Of note, we identify temporal variation in livestock meat consumption as a main predictor of viral genetic diversity through time. Finally, phylogeographic analyses indicate that GETV preferentially circulates within areas associated with relatively higher mean annual temperature and pig population density. Our results highlight the importance of continuous surveillance of GETV among livestock in southern Chinese regions associated with relatively high temperatures, and the need to control mosquitoes in the livestock farms. Our analyses of GETV also provide a baseline for future studies of the molecular epidemiology and early warning of emerging arboviruses in China.
The asymmetric ABA response on both sides of root tip is important for tomato root hydrotropism by mediating proton efflux and cell elongation
Authors: Yuan Wei , Liu Jianping , Dai Hui , Zhang Qian , Xu Weifeng , Zhang Jianhua , Li Ying 
Published: March 2022

SummaryHydrotropism is an important adaptation of plant roots to the uneven distribution of water, and the current research on hydrotropism is mainly focused on Arabidopsis thaliana. We examined hydrotropism in tomato (Solanum lycopersicum) primary roots. We used RNA sequencing to detect the gene expression on both sides (dry and wet side) of root tips (5 mm from the root cap junction) by splitting root tips longitudinally into two halves. We found that hydrostimulation induced the asymmetric cell elongation between the dry side (lower water potential) and wet side of root tips (higher water potential). ABA biosynthesis gene ABA4 was induced on the dry side as compared to the wet side of root tips. Chemical inhibitors that block ABA biosynthesis can disrupt hydrotropism, and ABA biosynthesis mutant not showed significantly reduced hydrotropism. Furthermore, asymmetric H+ efflux was found in wild-type but not in root tips of ABA biosynthesis mutant not after hydrostimulation. Our results suggest that the asymmetric ABA response on both sides of root tip mediate asymmetric H+ efflux, and then drive the asymmetric cell elongation, which allows the root to bend towards the wet side to take up more water.Graphical abstractInvolvement of ABA-mediated asymmetric H+ efflux in root hydrotropism.Compared to the wet side of root tip (higher water potential), the dry side (lower water potential) induces the expression of ABA biosynthesis gene ABA4, thus enhancing proton efflux to promoting cell elongation on the dry side. Because H+ efflux and cell elongation on the dry side of the root tip are higher than that on the wet side, the asymmetric growth of cells on both sides allows the root to bend towards the wet side for taking up more water.In BriefThe asymmetric ABA response on both sides of root tip (dry side and wet side) sequently mediates root asymmetric H+ efflux, and then drives the asymmetric cell elongation on both sides of root tip, which allows the root to bend towards the wet side for absorbing more water.HighlightsHydrotropic bending requires asymmetric cell elongation on the root two sides.Asymmetric expression of ABA biosynthesis gene ABA4 is required for root hydrotropism.The H+ efflux on the dry side of the root is increased.ABA-associated asymmetric H+ efflux driven root hydrotropic bending.
Rhythm of relationships in a social fish over the course of a full year in the wild
Authors: Aslak Ulf , Monk Christopher T. , Brockmann Dirk , Arlinghaus Robert 
Published: March 2022

AbstractAnimals are expected to adjust their social behaviour to cope with challenges in their environment. Therefore, for fish populations, in temperate regions with seasonal and daily environmental oscillations, characteristic rhythms of social relationships should be pronounced. To date, most research concerning fish social networks and biorhythms has occurred in artificial laboratory environments or over confined temporal scales of days to weeks. By contrast, little is known about the social networks of wild, freely roaming fish, including how seasonal and diurnal rhythms modulate social networks over the course of a full year. The advent of high-resolution acoustic telemetry enables us to quantify detailed social interactions in the wild over time-scales sufficient to examine seasonal rhythms at whole-ecosystems scales. Our objective was to explore the rhythms of social interactions in a social fish population at various time-scales over one full year in the wild by examining high-resolution snapshots of dynamic social network. To that end, we tracked the behaviour of 36 adult common carp,Cyprinus carpio, in a 25 ha lake and constructed temporal social networks among individuals across various time-scales, where social interactions were defined by proximity. We compared the network structure to a temporally shuffled null model to examine the importance of social attraction, and checked for persistent characteristic groups (“friendships”) over time. The clustering within the carp social network tended to be more pronounced during daytime than nighttime throughout the year. Social attraction, particularly during daytime, was a key driver for interactions. Shoaling behavior substantially increased during daytime in the wintertime, whereas in summer carp interacted less frequently, but the interaction duration increased. Characteristic groups were more common in the summer months and during nighttime, where the social memory of carp lasted up to two weeks. We conclude that social relationships of carp change diurnally and seasonally. These patterns were likely driven by predator avoidance, seasonal shifts in lake temperature, visibility, forage availability and the presence of anoxic zones. The techniques we employed can be applied generally to high-resolution biotelemetry data to reveal social structures across other fish species at ecologically realistic scales.
Multi-level cellular and functional annotation of single-cell transcriptomes
Authors: Mikolajewicz Nicholas , Brown Kevin R. , Moffat Jason , Han Hong 
Published: March 2022

AbstractSingle-cell RNA-sequencing (scRNA-seq) offers unprecedented insight into heterogenous biology, allowing for the interrogation of cellular populations and gene expression programs at single-cell resolution. Here, we introduce scPipeline, a single-cell analytic toolbox that offers modular workflows for multi-level cellular annotation and user-friendly analysis reports. Novel methods that are introduced to facilitate scRNA-seq annotation include: (i) co-dependency index (CDI)-based differential expression; (ii) cluster resolution optimization using a marker-specificity criterion; (iii) marker-based cell-type annotation with Miko scoring; and (iv) gene program discovery using scale-free shared nearest neighbor network (SSN) analysis. Our unsupervised and supervised procedures were validated using a diverse collection of scRNA-seq datasets and we provide illustrative examples of cellular and transcriptomic annotation of developmental and immunological scRNA-seq atlases. Overall, scPipeline provides a flexible computational framework for in-depth scRNA-seq analysis.