bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inference of phylogenetic trees directly from raw sequencing reads using Read2Tree
Authors: Dylus David , Altenhoff Adrian , Majidian Sina , Sedlazeck Fritz J. , Dessimoz Christophe 
Published: April 2023

AbstractCurrent methods for inference of phylogenetic trees require running complex pipelines at substantial computational and labor costs, with additional constraints in sequencing coverage, assembly and annotation quality, especially for large datasets. To overcome these challenges, we present Read2Tree, which directly processes raw sequencing reads into groups of corresponding genes and bypasses traditional steps in phylogeny inference, such as genome assembly, annotation and all-versus-all sequence comparisons, while retaining accuracy. In a benchmark encompassing a broad variety of datasets, Read2Tree is 10–100 times faster than assembly-based approaches and in most cases more accurate—the exception being when sequencing coverage is high and reference species very distant. Here, to illustrate the broad applicability of the tool, we reconstruct a yeast tree of life of 435 species spanning 590 million years of evolution. We also apply Read2Tree to >10,000Coronaviridaesamples, accurately classifying highly diverse animal samples and near-identical severe acute respiratory syndrome coronavirus 2 sequences on a single tree. The speed, accuracy and versatility of Read2Tree enable comparative genomics at scale.
Fibrillin microfibril structure identifies long-range effects of inherited pathogenic mutations affecting a key regulatory latent TGFβ-binding site
Authors: Godwin Alan R. F. , Dajani Rana , Zhang Xinyang , Thomson Jennifer , Holmes David F. , Adamo Christin S. , Sengle Gerhard , Sherratt Michael J. , Roseman Alan M. , Baldock Clair 
Published: April 2023

AbstractGenetic mutations in fibrillin microfibrils cause serious inherited diseases, such as Marfan syndrome and Weill–Marchesani syndrome (WMS). These diseases typically show major dysregulation of tissue development and growth, particularly in skeletal long bones, but links between the mutations and the diseases are unknown. Here we describe a detailed structural analysis of native fibrillin microfibrils from mammalian tissue by cryogenic electron microscopy. The major bead region showed pseudo eightfold symmetry where the amino and carboxy termini reside. On the basis of this structure, we show that a WMS deletion mutation leads to the induction of a structural rearrangement that blocks interaction with latent TGFβ-binding protein-1 at a remote site. Separate deletion of this binding site resulted in the assembly of shorter fibrillin microfibrils with structural alterations. The integrin αvβ3-binding site was also mapped onto the microfibril structure. These results establish that in complex extracellular assemblies, such as fibrillin microfibrils, mutations may have long-range structural consequences leading to the disruption of growth factor signaling and the development of disease.
HIT-UAV: A high-altitude infrared thermal dataset for Unmanned Aerial Vehicle-based object detection
Authors: Suo Jiashun , Wang Tianyi , Zhang Xingzhou , Chen Haiyang , Zhou Wei , Shi Weisong 
Published: April 2023

AbstractWe present the HIT-UAV dataset, a high-altitude infrared thermal dataset for object detection applications on Unmanned Aerial Vehicles (UAVs). The dataset comprises 2,898 infrared thermal images extracted from 43,470 frames in hundreds of videos captured by UAVs in various scenarios, such as schools, parking lots, roads, and playgrounds. Moreover, the HIT-UAV provides essential flight data for each image, including flight altitude, camera perspective, date, and daylight intensity. For each image, we have manually annotated object instances with bounding boxes of two types (oriented and standard) to tackle the challenge of significant overlap of object instances in aerial images. To the best of our knowledge, the HIT-UAV is the first publicly available high-altitude UAV-based infrared thermal dataset for detecting persons and vehicles. We have trained and evaluated well-established object detection algorithms on the HIT-UAV. Our results demonstrate that the detection algorithms perform exceptionally well on the HIT-UAV compared to visual light datasets, since infrared thermal images do not contain significant irrelevant information about objects. We believe that the HIT-UAV will contribute to various UAV-based applications and researches. The dataset is freely available athttps://pegasus.ac.cn.
Two decades of fumigation data from the Soybean Free Air Concentration Enrichment facility
Authors: Aspray Elise Kole , Mies Timothy A. , McGrath Jesse A. , Montes Christopher M. , Dalsing Bradley , Puthuval Kannan K. , Whetten Andrew , Herriott Jelena , Li Shuai , Bernacchi Carl J. , DeLucia Evan H. , Leakey Andrew D. B. , Long Stephen P. , McGrath Justin M. , Miglietta Franco , Ort Donald R. , Ainsworth Elizabeth A. 
Published: April 2023

AbstractThe Soybean Free Air Concentration Enrichment (SoyFACE) facility is the longest running open-air carbon dioxide and ozone enrichment facility in the world. For over two decades, soybean, maize, and other crops have been exposed to the elevated carbon dioxide and ozone concentrations anticipated for late this century. The facility, located in East Central Illinois, USA, exposes crops to different atmospheric concentrations in replicated octagonal ~280 m2 Free Air Concentration Enrichment (FACE) treatment plots. Each FACE plot is paired with an untreated control (ambient) plot. The experiment provides important ground truth data for predicting future crop productivity. Fumigation data from SoyFACE were collected every four seconds throughout each growing season for over two decades. Here, we organize, quality control, and collate 20 years of data to facilitate trend analysis and crop modeling efforts. This paper provides the rationale for and a description of the SoyFACE experiments, along with a summary of the fumigation data and collation process, weather and ambient data collection procedures, and explanations of air pollution metrics and calculations.
Global 3-hourly wind-wave and swell data for wave climate and wave energy resource research from 1950 to 2100
Authors: Jiang Xingjie , Xie Botao , Bao Ying , Song Zhenya 
Published: April 2023

AbstractOcean wave climate, including wind waves and swells, is essential to human marine activities and global or regional climate systems, and is highly related to harnessing wave energy resources. In this study, a global 3-hourly instantaneous wave dataset was established with the third-generation wave model MASNUM-WAM and wind forcings derived from the products of the First Institute of Oceanography-Earth System Model version 2.0, the climate model coupled with wave model, under the unified framework of the Coupled Model Intercomparison Project phase 6. This dataset contains 17 wave parameters, including the information associated with wave energy and spectral shape geometries, from one historical (1950–2014) simulation and three future (2015–2100) scenario experiments (ssp125, ssp245, and ssp585). Moreover, all the parameters can be accessed separately in the form of wind waves and swells. The historical results show that the simulated wave characteristics agree well with satellite observations and the ERA5 reanalysis products. This dataset can provide the community with a unique and informative data source for wave climate and wave energy resource research.
Degradation of paper products due to volatile organic compounds
Authors: Alam Izhar , Sharma Chhaya 
Published: April 2023

AbstractPaper and packaging materials a lignocellulose-based natural biodegradable polymer that spontaneously releases acetic acid, aldehydes, alcohol, and ester-based volatile organic compounds (VOCs) upon ageing and these VOCs start degrading the paper products and decline their mechanical strength properties. The reactivity of the paper of unbleached wheat straw pulp towards acetic acid and hexanal, which has been proven to have more degrading effects on paper than other VOCs, was considered in this work. The papers were exposed to these volatile compounds for 90 days in an air-tight vessel under ambient environmental conditions. The results showed that hexanal was more destructive than acetic acid with regards to cellulose degradation and depletion in the mechanical strength properties. The paper properties like, tensile, tear and burst index, viscosity, pH and carbonyl group content was measured. The growth of the carbonyl group, evidence of the ageing effects in the paper, detected more in the paper exposed to acetic acid. However, the strength of paper properties declined more with hexanal. FE-SEM analysis of the sample showed the development of pores and damage of cellulose fibre upon ageing. Similarly, the damaging effects of VOCs on cellulose, hemicelluloses and lignin were confirmed by significantly reduced peak detection through FT-IR \analysis. The high crystallinity index of the paper products due to exposure to VOCs was detected by XRD analysis, which confirmed the degradation of the low molecular weight cellulose molecule. Thus, the results are strongly recommended that VOCs that generates due to natural or artificial ageing could be the leading cause of paper degradation.
Efficient shallow learning as an alternative to deep learning
Authors: Meir Yuval , Tevet Ofek , Tzach Yarden , Hodassman Shiri , Gross Ronit D. , Kanter Ido 
Published: April 2023

AbstractThe realization of complex classification tasks requires training of deep learning (DL) architectures consisting of tens or even hundreds of convolutional and fully connected hidden layers, which is far from the reality of the human brain. According to the DL rationale, the first convolutional layer reveals localized patterns in the input and large-scale patterns in the following layers, until it reliably characterizes a class of inputs. Here, we demonstrate that with a fixed ratio between the depths of the first and second convolutional layers, the error rates of the generalized shallow LeNet architecture, consisting of only five layers, decay as a power law with the number of filters in the first convolutional layer. The extrapolation of this power law indicates that the generalized LeNet can achieve small error rates that were previously obtained for the CIFAR-10 database using DL architectures. A power law with a similar exponent also characterizes the generalized VGG-16 architecture. However, this results in a significantly increased number of operations required to achieve a given error rate with respect to LeNet. This power law phenomenon governs various generalized LeNet and VGG-16 architectures, hinting at its universal behavior and suggesting a quantitative hierarchical time–space complexity among machine learning architectures. Additionally, the conservation law along the convolutional layers, which is the square-root of their size times their depth, is found to asymptotically minimize error rates. The efficient shallow learning that is demonstrated in this study calls for further quantitative examination using various databases and architectures and its accelerated implementation using future dedicated hardware developments.
The efficacy of bimatoprost ophthalmic solution combined with NB-UVB phototherapy in non-segmental and segmental vitiligo: a single-blind randomized controlled study
Authors: Silpa-archa Narumol , Likittanasombat Surachanee , Apinuntham Chalermkwan , Pruksaeakanan Chutipon , Charoenpipatsin Norramon , Chaiyabutr Chayada , Wongpraparut Chanisada 
Published: April 2023

AbstractBimatoprost ophthalmic solution 0.03% (PGF2α analogues) combined with narrowband ultraviolet B (NB-UVB) was reported to be an effective treatment for vitiligo. To investigate the efficacy and safety of treatment for non-segmental/segmental vitiligo compared among bimatoprost ophthalmic solution 0.01% combined with NB-UVB phototherapy, bimatoprost monotherapy, and placebo. This single-blind randomized controlled study enrolled stable Thai vitiligo patients with at least three similarly sized lesions in the same anatomical area. The treatment duration was 6 months with 1- and 2-month post-treatment follow-ups. The 3 selected lesions on each patient were randomized to receive combination therapy, monotherapy, or placebo. The Vitiligo Area Scoring Index (VASI) was used to evaluate lesion response. Of the 25 initially enrolled subjects, 19 patients were analyzed. There were 13 and 6 non-segmental and segmental vitiligo cases, respectively. Eight and 11 cases had face/neck and non-face/neck lesions, respectively. Non-segmental vitiligo and non-face/neck vitiligo patients in the combination group had significant improvement in VASI score at 3 months, 6 months, and at the 2-month follow-up. No side effects were observed/reported. Bimatoprost combination therapy was shown to be safe and effective for treating Thai patients with non-segmental vitiligo in non-face/neck areas of the body.
Engineering benefits of replacing natural sand with manufactured sand in landfill construction
Authors: Pillai Anjali G. , Gali Madhavi Latha 
Published: April 2023

AbstractTranslational sliding failures in landfills are often triggered by inadequate shear strength of interfaces in liners and covers. Geosynthetic Clay Liners (GCL) are used in different components of landfills to contain the leachate. GCLs are usually placed above a compacted sand subgrade to develop higher shear resistance. In the context of depleting natural sand resources, the present study explores the feasibility of replacing natural sand with manufactured sand (Msand) in landfill construction. Interface shear tests were performed on GCL in contact with river sand and Msand of similar gradation to evaluate the shear strength at different normal stresses and hydration conditions. It is found that Msand provides higher interface shear strength with GCL compared to river sand. Digital image analysis of tested specimens of GCL showed that variation in particle morphology of the two sands has direct influence on the microlevel interaction mechanisms governing the shear strength. Quantification of morphological parameters showed that Msand particles are angular and rough compared to natural sand particles, leading to higher particle interlocking. Hydration of the GCL reduced the interface shear strength, the effect being less in case of Msand. The study highlights that replacement of natural sand with Msand has added benefits.
Watching the human retina breath in real time and the slowing of mitochondrial respiration with age
Authors: Kaynezhad Pardis , Tachtsidis Ilias , Sivaprasad Sobha , Jeffery Glen 
Published: April 2023

AbstractThe retina has the greatest metabolic demand in the body particularly in dark adaptation when its sensitivity is enhanced. This requires elevated level of perfusion to sustain mitochondrial activity. However, mitochondrial performance declines with age leading to reduced adaptive ability. We assessed human retina metabolism in vivo using broad band near-infrared spectroscopy (bNIRS), which records colour changes in mitochondria and blood as retinal metabolism shifts in response to changes in environmental luminance. We demonstrate a significant sustained rise in mitochondrial oxidative metabolism in the first 3 min of darkness in subjects under 50 years old. This was not seen in those over 50 years. Choroidal oxygenation declines in < 50 s as mitochondrial metabolism increases, but gradually rises in the > 50 s. Significant group differences in blood oxygenation are apparent in the first 6 min, consistent with mitochondrial demand leading hemodynamic changes. A greater coupling between mitochondrial oxidative metabolism with hemodynamics is revealed in subjects older than 50, possibly due to reduced capacity in the older retina. Rapid in vivo assessment of retinal metabolism with bNIRS provides a route to understanding fundamental physiology and early identification of retinal disease before pathology is established.
Deciphering the spectrum of cutaneous lymphomas expressing TFH markers
Authors: Donzel Marie , Trecourt Alexis , Balme Brigitte , Harou Olivier , Mauduit Claire , Bachy Emmanuel , Guesquières Hervé , Fontaine Juliette , Ortonne Nicolas , Perier-Muzet Marie , Dalle Stéphane , Traverse-Glehen Alexandra 
Published: April 2023

AbstractT-follicular helper (TFH) markers are expressed in the microenvironnement of marginal zone B-cell lymphoma (MZL), and in lymphomas arising from TFH-cells, sometimes making the differential diagnosis difficult. In the skin, the “TFH-spectrum” is poorly defined, going from primary cutaneous lymphoproliferative disorder with small/medium CD4+ T-cells (SMLPD) to cutaneous localizations of systemic angioimmunoblastic T-cell lymphoma (cAITL), and may pass through intermediate forms (primary cutaneous T-follicular helper derived lymphoma, not otherwise specified (PCTFHL,NOS)). We retrospectively analyzed 20 MZL, 13 SMLPD, 5 PCTFHL, and 11 cAITL clinically, histologically, and molecularly, to define tools to differentiate them. Characteristics that might favor the diagnosis of MZL over SMLPD are: multiple skin nodules (p < 0.001), nodular architecture (p < 0.01), residual germinal centers with follicular dendritic cell network (p < 0.001), monotypic plasma cells (p < 0.001), and few staining with PD1 (p = 0.016) or CXCL13 (p = 0.03). PCTFHL and cAITL presented as multiple (p < 0.01) lesions, in older patients (p < 0.01), with systemic symptoms and/or biological alterations (p < 0.01). Immunophenotypic loss of T-cell markers (p < 0.001), BCL6 (p = 0.023) and/or CD10 staining (p = 0.08), and a higher proliferative index (≥ 30%, p = 0.039) favoured these diagnoses over SMLPD. Pathogenic variants were observed by genomic sequencing in 47% of MZL (TNFAIP3 (32%), EP300 (21%), NOTCH2 (16%), KMT2D (16%), CARD11 (10.5%)), 8% of SMLPD (TET2), 40% of PCTFHL (SOCS1 (20%), ARID1A (20%)) and 64% of cAITL (TET2 (63.6%), RHOA (36.4%), NOTCH1 (9%)). This study characterizes the various clinical and histological features between cutaneous lymphomas expressing TFH markers and highlights the value of the interest of screening for genomic mutations in difficult cases.
Identification of immune and Toll-like receptor signaling pathway related feature lncRNAs to construct diagnostic nomograms for acute ischemic stroke
Authors: Su Zhuo-Yi , Yu Zi-Qiao , Yao Bo , Zhao De-Xi 
Published: April 2023

AbstractWe aimed to identify the immune and Toll-like receptor (TLR) signaling pathway related feature lncRNAs to construct the diagnostic nomograms for acute ischemic stroke (AIS). Two AIS-associated expression profiles GSE16561 and GSE22255 were downloaded from NCBI Gene Expression Omnibus, the former was the training set and the latter was the validation set. The differential expression genes (DEGs) and lncRNAs (DElncRNAs) related to TLR signaling pathway were identified between AIS and control groups. The single sample gene set enrichment analysis (ssGSEA) was applied to evaluate the immune infiltration. The immune and TLR signaling pathway related DElncRNAs were determined. Three optimization algorithms were utilized to select the immune and TLR signaling pathway related feature lncRNAs to construct the diagnostic nomograms of AIS. Based on the lncRNA signature, a ceRNA network was constructed. 37 DEGs and 28 DElncRNAs related to TLR signaling pathway were identified in GSE16561. 16 immune cell types exhibited significant differences in distribution between AIS and control groups. 28 immune and TLR signaling pathway related DElncRNAs were determined. 8 immune and TLR signaling pathway related feature lncRNAs were selected. The diagnostic nomograms of AIS performed well in both datasets. A ceRNA network was constructed consisting of 7 immune and TLR signaling pathway related feature lncRNAs as well as 19 AIS related miRNAs and 21 TLR signaling pathway related genes. LINC00173, LINC01089, LINC02210, MIR600HG, SNHG14, TP73-AS1, LINC00680 and CASC2 may be the potential biomarkers of AIS diagnosis, and TLR signaling pathway may be a promising immune related therapeutic target for AIS.
Solution of road network problem with the help of m-polar fuzzy graph using isometric and antipodal concept
Authors: Mondal Uttam , Mahapatra Tanmoy , Xin Qin , Pal Madhumangal 
Published: April 2023

AbstractThe isometry in crisp graph theory is a well-known fact. But, isometry under a fuzzy environment was developed recently and studied many facts. In a m-polar fuzzy graph, we have to think m components for each node and edge. Since, in our consideration, we consider m components for each nodes as well as edges, therefore we can not handle this type of situation using fuzzy model as their is a single components for this concept. Again, we can not apply bipolar or intuitionistic fuzzy graph model as each edges or nodes have just two components. Thus, these mPFG models give more efficient fuzziness results than other fuzzy model. Also, it is very interesting to develop and analyze such types of mPFGs with examples and related theorems. Considering all those things together, we have presented isometry under a m-polar fuzzy environment. In this paper, we have discussed the isometric m-polar fuzzy graph along with many exciting facts about it. Metric space properties have also been implemented on m-polar fuzzy isometric graph. We also have initiated a generalized fuzzy graph, namely antipodal m-polar fuzzy graphs, along with several issues. The degree of it is also presented along with edge regularity properties. We also give a relation between m-polar fuzzy antipodal graphs and their underlying crisp graphs. Its properties have also been discussed on m-polar fuzzy odd as well as even cycles, complete graphs, etc. Finally, a real-life application on a road network system in a m-polar fuzzy environment using the $$\mu$$
μ
-distance concept is also presented.
Repeated unilateral handgrip contractions alter functional connectivity and improve contralateral limb response times
Authors: Andrushko Justin W. , Levenstein Jacob M. , Zich Catharina , Edmond Evan C. , Campbell Jon , Clarke William T. , Emir Uzay , Farthing Jonathan P. , Stagg Charlotte J. 
Published: April 2023

AbstractIn humans, motor learning is underpinned by changes in sensorimotor network functional connectivity (FC). Unilateral contractions increase FC in the ipsilateral primary motor cortex (M1) and supplementary motor area (SMA); areas involved in motor planning and execution of the contralateral hand. Therefore, unilateral contractions are a promising approach to augment motor performance in the contralateral hand. In a within-participant, randomized, cross-over design, 15 right-handed adults had two magnetic resonance imaging (MRI) sessions, where functional-MRI and MR-Spectroscopic Imaging were acquired before and after repeated right-hand contractions at either 5% or 50% maximum voluntary contraction (MVC). Before and after scanning, response times (RTs) were determined in both hands. Nine minutes of 50% MVC contractions resulted in decreased handgrip force in the contracting hand, and decreased RTs and increased handgrip force in the contralateral hand. This improved motor performance in the contralateral hand was supported by significant neural changes: increased FC between SMA-SMA and increased FC between right M1 and right Orbitofrontal Cortex. At a neurochemical level, the degree of GABA decline in left M1, left and right SMA correlated with subsequent behavioural improvements in the left-hand. These results support the use of repeated handgrip contractions as a potential modality for improving motor performance in the contralateral hand.