bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identifying spatial domain by adapting transcriptomics with histology through contrastive learning
Authors: Zeng Yuansong , Yin Rui , Luo Mai , Chen Jianing , Pan Zixiang , Lu Yutong , Yu Weijiang , Yang Yuedong 
Published: February 2023

AbstractRecent advances in spatial transcriptomics have enabled measurements of gene expression at cell/spot resolution meanwhile retaining both the spatial information and the histology images of the tissues. Accurately identifying the spatial domains of spots is a vital step for various downstream tasks in spatial transcriptomics analysis. To remove noises in gene expression, several methods have been developed to combine histopathological images for data analysis of spatial transcriptomics. However, these methods either use the image only for the spatial relations for spots, or individually learn the embeddings of the gene expression and image without fully coupling the information. Here, we propose a novel method ConGI to accurately exploit spatial domains by adapting gene expression with histopathological images through contrastive learning. Specifically, we designed three contrastive loss functions within and between two modalities (the gene expression and image data) to learn the common representations. The learned representations are then used to cluster the spatial domains on both tumor and normal spatial transcriptomics datasets. ConGI was shown to outperform existing methods for the spatial domain identification. In addition, the learned representations have also been shown powerful for various downstream tasks, including trajectory inference, clustering, and visualization.
PPICT: an integrated deep neural network for predicting inter-protein PTM cross-talk
Authors: Zhu Fei , Deng Lei , Dai Yuhao , Zhang Guangyu , Meng Fanwang , Luo Cheng , Hu Guang , Liang Zhongjie 
Published: February 2023

AbstractPost-translational modifications (PTMs) fine-tune various signaling pathways not only by the modification of a single residue, but also by the interplay of different modifications on residue pairs within or between proteins, defined as PTM cross-talk. As a challenging question, less attention has been given to PTM dynamics underlying cross-talk residue pairs and structural information underlying protein–protein interaction (PPI) graph, limiting the progress in this PTM functional research. Here we propose a novel integrated deep neural network PPICT (Predictor for PTM Inter-protein Cross-Talk), which predicts PTM cross-talk by combining protein sequence-structure-dynamics information and structural information for PPI graph. We find that cross-talk events preferentially occur among residues with high co-evolution and high potential in allosteric regulation. To make full use of the complex associations between protein evolutionary and biophysical features, and protein pair features, a heterogeneous feature combination net is introduced in the final prediction of PPICT. The comprehensive test results show that the proposed PPICT method significantly improves the prediction performance with an AUC value of 0.869, outperforming the existing state-of-the-art methods. Additionally, the PPICT method can capture the potential PTM cross-talks involved in the functional regulatory PTMs on modifying enzymes and their catalyzed PTM substrates. Therefore, PPICT represents an effective tool for identifying PTM cross-talk between proteins at the proteome level and highlights the hints for cross-talk between different signal pathways introduced by PTMs.
‘Come as you are’: place attachment to Islamic third spaces in the United States
Authors: Mohammed Hassnaa 
Published: February 2023

Abstract
Our global community necessitates the understanding of emergent hybrid typologies of religious spaces and their role in community development. Islamic third spaces are informal socio-religious environments that serve the unmet needs of acculturated generations of US Muslims. Using a place attachment framework, the study illustrates how the social and physical designs of two third spaces curate inclusive and contextually driven experiences for their members. This is done through an exploration of data from twenty-four in-depth semi-structured interviews with attendees of two Islamic third spaces. Findings indicated that, in addition to social and physical features of third spaces, contextual influences affecting US Muslims served a crucial role in participants place attachment. We conclude that attachment to third spaces provides a basis for community development processes, such as social cohesion and integration within the US populous.
Temporal hierarchy of cortical responses reflects core-belt-parabelt organization of auditory cortex in musicians
Authors: Benner Jan , Reinhardt Julia , Christiner Markus , Wengenroth Martina , Stippich Christoph , Schneider Peter , Blatow Maria 
Published: February 2023

Abstract
Human auditory cortex (AC) organization resembles the core-belt-parabelt organization in nonhuman primates. Previous studies assessed mostly spatial characteristics; however, temporal aspects were little considered so far. We employed co-registration of functional magnetic resonance imaging (fMRI) and magnetoencephalography (MEG) in musicians with and without absolute pitch (AP) to achieve spatial and temporal segregation of human auditory responses. First, individual fMRI activations induced by complex harmonic tones were consistently identified in four distinct regions-of-interest within AC, namely in medial Heschl’s gyrus (HG), lateral HG, anterior superior temporal gyrus (STG), and planum temporale (PT). Second, we analyzed the temporal dynamics of individual MEG responses at the location of corresponding fMRI activations. In the AP group, the auditory evoked P2 onset occurred ~25 ms earlier in the right as compared with the left PT and ~15 ms earlier in the right as compared with the left anterior STG. This effect was consistent at the individual level and correlated with AP proficiency. Based on the combined application of MEG and fMRI measurements, we were able for the first time to demonstrate a characteristic temporal hierarchy (“chronotopy”) of human auditory regions in relation to specific auditory abilities, reflecting the prediction for serial processing from nonhuman studies.
Context-based modulations of 3D vision are expertise dependent
Authors: Li Zhen , Chang Dorita H F 
Published: February 2023

Abstract
An object’s identity can influence depth-position judgments. The mechanistic underpinnings underlying this phenomenon are largely unknown. Here, we asked whether context-dependent modulations of stereoscopic depth perception are expertise dependent. In 2 experiments, we tested whether training that attaches meaning (i.e. classification labels) to otherwise novel, stereoscopically presented objects changes observers’ sensitivity for judging their depth position. In Experiment 1, observers were randomly assigned to 3 groups: a Greeble-classification training group, an orientation-discrimination training group, or a no-training group, and were tested on their stereoscopic depth sensitivity before and after training. In Experiment 2, participants were tested before and after training while fMRI responses were concurrently imaged. Behaviorally, stereoscopic performance was significantly better following Greeble-classification (but not orientation-discrimination, or no-) training. Using the fMRI data, we trained support vector machines to predict whether the data were from the pre- or post-training sessions. Results indicated that classification accuracies in V4 were higher for the Greeble-classification group as compared with the orientation-discrimination group for which accuracies were at chance level. Furthermore, classification accuracies in V4 were negatively correlated with response times for Greeble identification. We speculate that V4 is implicated in an expertise-dependent, object-tuning manner that allows it to better guide stereoscopic depth retrieval.
Alcohol septal ablation versus surgical septal myectomy of obstructive hypertrophic cardiomyopathy: systematic review and meta-analysis
Authors: Yokoyama Yujiro , Shimoda Tomonari , Shimada Yuichi J , Shimamura Junichi , Akita Keitaro , Yasuda Risako , Takayama Hiroo , Kuno Toshiki 
Published: February 2023

AbstractOBJECTIVESTo elucidate the optimal septal reduction therapy for obstructive hypertrophic cardiomyopathy, we conducted a meta-analysis comparing alcohol septal ablation (ASA) and septal myectomy.METHODSMEDLINE, EMBASE and Cochrane CENTRAL were searched to identify studies investigating the outcomes of ASA and septal myectomy in patients with obstructive hypertrophic cardiomyopathy in January 2023. The primary outcome of interest was all-cause mortality in studies with ≥1 year of follow-up. The secondary outcomes of interest comprised left ventricular outflow tract (LVOT) pressure gradient reduction and reoperations of LVOT. A subgroup analysis of all-cause mortality including studies with follow-up ≥5 years was performed.RESULTS27 observational studies were included (15 968 patients). Analysis demonstrated similar all-cause mortality [hazard ratio (HR) (95% confidence interval) (CI) 1.24 (0.88–1.76); P = 0.21; I2 = 56%]. In contrast, ASA was associated with less reduction of LVOT pressure gradient and a reoperation rate [weighted mean difference (95% CI) 11.04 mmHg (5.60–16.48); P &lt; 0.01; I2 = 64%, HR (95% CI) 9.14 (6.55–12.75); P &lt; 0.001; I2 = 0%, respectively]. The subgroup analysis with follow-up ≥5 years revealed higher long-term mortality with ASA [HR (95% CI) 1.50 (1.04–2.15); P = 0.03; I2 = 52%].CONCLUSIONSAlthough both septal reduction therapies were associated with similar all-cause mortality, ASA was associated with a higher rate of reoperation and less reduction of LVOT pressure gradient. Furthermore, all-cause mortality with follow-up ≥5 years showed favourable outcomes with septal myectomy, although the result is only hypothesis-generating given a subgroup analysis.
Upstream innovation leakage in Uganda’s coffee planting material pipeline
Authors: Diiro Gracious , Kawooya Dick , Lybbert Travis J , Wunsch-Vincent Sacha 
Published: February 2023

AbstractPolicies and institutions shape the incentives that influence innovation, technology adoption and productivity. We characterise the robusta coffee planting material pipeline in Uganda that connects upstream innovation in improved germplasm to downstream coffee producers. A nationally representative survey of coffee nursery operators reveals poor and heterogeneous production practices, potentially reflecting shifting policy priorities. The majority of smallholder coffee farmers consequently get inferior, disease-prone seedlings—thereby locking in decades of continued low productivity. Given Uganda’s ambition to drastically increase coffee production, detecting, understanding and addressing these problems should be a top priority as a prerequisite to effective agricultural policy and enhanced productivity.
A recent experience on the role of influenza vaccination on cardiovascular events
Authors: Sosa-Liprandi María Inés , Zaidel Ezequiel José , Sosa-Liprandi Álvaro 
Published: February 2023

AbstractThe purpose of this review is to update the recent information regarding the role of influenza vaccination (IV) as a strategy to reduce cardiovascular (CV) events. During the last 2 years, new meta-analysis, guidelines, and two randomized controlled trials (RCTs) were published. The IAMI trial added information regarding the safety and efficacy of IV right after an acute myocardial infarction hospitalization. A significant reduction in the primary endpoint—including mortality—was observed. More recently, the influenza vaccine to prevent vascular events trial (IVVE) trial did not meet the primary CV endpoint in patients with heart failure (HF). However, a significant reduction was observed during the seasonal peaks of Influenza circulation. COVID-19 pandemic provoked recruitment difficulties in these trials, as well as an altered influenza seasonality and incidence. Further analysis of IVVE trial is needed to clarify the precise role of IV in patients with HF. A recent meta-analysis of RCTs and observational studies indicated that IV was safe and effective to reduce CV events, and it was included in the most updated guideline. Despite these benefits, and the recommendations for its prescription by scientific societies and health regulatory agencies, the vaccination rate remains below than expected globally. The correct understanding of implementation barriers, which involve doctors, patients, and their context, is essential when continuous improvement strategies are planned, in order to improve the IV rate in at-risk subjects.
Influenza and cardiovascular disease pathophysiology: strings attached
Authors: Skaarup Kristoffer Grundtvig , Modin Daniel , Nielsen Lene , Jensen Jens Ulrik Stæhr , Biering-Sørensen Tor 
Published: February 2023

AbstractA link between influenza infection and cardiovascular morbidity has been known for almost a century. This narrative review examined the cardiovascular complications associated with influenza and the potential mechanisms behind this relationship. The most common reported cardiovascular complications are cardiovascular death, myocardial infarction, and heart failure hospitalization. There are multiple proposed mechanisms driving the increased risk of cardiovascular complications. These mechanics involve influenza-specific effects such as direct cardiac infection and endothelial dysfunction leading to plaque destabilization and rupture, but also hypoxaemia and systemic inflammatory responses including increased metabolic demand, biomechanical stress, and hypercoagulability. The significance of the individual effects is unclear, and thus whether influenza directly or indirectly causes cardiovascular events is unknown. In conclusion, the risk of acute cardiovascular morbidity and mortality is elevated during influenza infection. The proposed underlying pathophysiological mechanisms support this association, but systemic responses to infection may drive this relationship.
Cultural transmission of reproductive success impacts genomic diversity, coalescent tree topologies, and demographic inferences
Authors: Guez Jérémy , Achaz Guillaume , Bienvenu François , Cury Jean , Toupance Bruno , Heyer Évelyne , Jay Flora , Austerlitz Frédéric 
Published: February 2023

Abstract
Cultural transmission of reproductive success has been observed in many human populations as well as other animals. Cultural transmission of reproductive success consists of a positive correlation of nongenetic origin between the progeny size of parents and children. This correlation can result from various factors, such as the social influence of parents on their children, the increase of children’s survival through allocare from uncles and aunts, or the transmission of resources. Here, we study the evolution of genomic diversity over time under cultural transmission of reproductive success. Cultural transmission of reproductive success has a threefold impact on population genetics: (1) the effective population size decreases when cultural transmission of reproductive success starts, mimicking a population contraction, and increases back to its original value when cultural transmission of reproductive success stops; (2) coalescent tree topologies are distorted under cultural transmission of reproductive success, with higher imbalance and a higher number of polytomies; and (3) branch lengths are reduced nonhomogenously, with a higher impact on older branches. Under long-lasting cultural transmission of reproductive success, the effective population size stabilizes but the distortion of tree topology and the nonhomogenous branch length reduction remain, yielding U-shaped site frequency spectra under a constant population size. We show that this yields a bias in site frequency spectra-based demographic inference. Considering that cultural transmission of reproductive success was detected in numerous human and animal populations worldwide, one should be cautious because inferring population past histories from genomic data can be biased by this cultural process.
Weather model based atmospheric corrections of Sentinel-1 InSAR deformation data at Turkish volcanoes
Authors: Dogru Fikret , Albino Fabien , Biggs Juliet 
Published: February 2023

SUMMARYOne of the main constraints on the use of satellite radar data for monitoring natural hazards is the existence of atmospheric signals. In particular, volcanic deformation can be difficult to identify because atmospheric phase delays can mask or even mimic ground deformation signals. Eliminating atmospheric signals is particularly crucial for high-relief volcanoes such as Ağrı, Tendürek, Acigöl, Göllüdağ and Hasandağ in the Eastern and Central Anatolia. To overcome the atmospheric effects, we use high-resolution ECMWF weather models coupled with an empirical phase-elevation approach for correcting Sentinel-1 interferograms. We apply these methods to two areas of Turkey, the first of which covers three volcanoes in Central Anatolia (Acigöl, Göllüdağ, Hasandağ) between January 2016 and December 2018 and the second covers two volcanoes in Eastern Anatolia (Ağrı, Tendürek) between September 2016 and December 2018. The reduction in standard deviation (quality factor) is calculated for both ascending and descending tracks and the atmospheric corrections are found to perform better on descending interferograms in both cases. Then, we use a least-squares approach to produce a time-series. For Central Anatolia, we used 416 ascending and 415 descending interferograms to create 144 and 145 cumulative displacement maps, respectively, and for Eastern Anatolia, we used 390 ascending and 380 descending interferograms to produce 137 and 130 cumulative displacement maps, respectively. We find that the temporal standard deviation before atmospheric corrections ranges between 0.9 and 3.7 cm for the five volcanoes in the region and is consistently higher on ascending track data, which is acquired at the end of the day when solar heating is greatest. Atmospheric correction reduces the standard deviation to 0.5–2.5 cm. Residual signals might be due to the ice-cap at Ağrı and agriculture near Acigöl. We conclude that these volcanoes did not experience significant magmatic deformation during this time period, despite the apparent signals visible in individual uncorrected interferograms. We demonstrate that atmospheric corrections are vital when using InSAR for monitoring the deformation of high-relief volcanoes in arid continental climates such as Turkey.
Generating colorful carrot germplasm through metabolic engineering of betalains pigments
Authors: Deng Yuan-Jie , Duan Ao-Qi , Liu Hui , Wang Ya-Hui , Zhang Rong-Rong , Xu Zhi-Sheng , Xiong Ai-Sheng 
Published: February 2023

Abstract
Betalains are tyrosine-derived plant pigments exclusively found in the Caryophyllales order and some higher fungi and generally classified into two groups: red-violet betacyanins and yellow-orange betaxanthins. Betalains attract great scientific and economic interest because of their relatively simple biosynthesis pathway, attractive colors and health-promoting properties. Co-expressing two core genes BvCYP76AD1 and BvDODA1 with or without a glycosyltransferase gene MjcDOPA5GT allowed the engineering of carrot (an important taproot vegetable) to produce a palette of unique colors. The highest total betalains content, 943.2 μg·g−1 DW, was obtained in carrot taproot transformed with p35S:RUBY which produces all of the necessary enzymes for betalains synthesis. Root-specific production of betalains slightly relieved tyrosine consumption revealing the possible bottleneck in betalains production. Furthermore, a unique volcano-like phenotype in carrot taproot cross-section was created by vascular cambium-specific production of betalains. The betalains-fortified carrot in this study is thus anticipated to be used as functional vegetable and colorful carrot germplasm in breeding to promote health.
A Constrained Mean Curvature Flow and Alexandrov–Fenchel Inequalities
Authors: Mei Xinqun , Wang Guofang , Weng Liangjun 
Published: February 2023

Abstract
In this article, we study a locally constrained mean curvature flow for star-shaped hypersurfaces with capillary boundary in the half-space. We prove its long-time existence and the global convergence to a spherical cap. Furthermore, the capillary quermassintegrals defined in [29] evolve monotonically along the flow, and hence we establish a class of new Alexandrov–Fenchel inequalities for convex hypersurfaces with capillary boundary in the half-space.
Lost Daughters: Affective Framings of Women Embracing Islam
Authors: van den Brandt Nella 
Published: February 2023

Abstract
This article draws upon and contributes to current discussions in the study of conversion, Muslims in Europe, and gender and emotion by taking media productions as an ethnographic starting point for analyzing the subject position of women who converted to Islam. In contemporary Western European contexts, the phenomenon of conversion to Islam evokes various affective responses, including bewilderment, concern, and fear. This article assesses the frames through which female converts to Islam are represented in the media and particularly explores the existing focus on mother and daughter relationships. Based upon an analysis of the emotions named and generated, this article argues that such affective framings contribute to the shaping of the subject position of female converts to Islam. It moreover demonstrates that emotions such as concern, sadness, grief, and fear are the result of, as well as constructively infuse, contemporary debates on religious and cultural diversity in the Netherlands in which Islam and Muslims are considered to pose a “problem” for Europe.
Increase of PEth after Single Consumption of Alcohol and Evaluation of a Volumetric DBS Filter Paper Device
Authors: Stöth Frederike , Koch Kevin , Bantle Matthias , Pütz Philipp , Wortmann Felix , Weinmann Wolfgang 
Published: February 2023

Abstract
Direct alcohol biomarkers are of growing interest for the assessment of alcohol consumption, with particular interest in phosphatidylethanol (PEth) in recent years. PEth is only formed when alcohol is present in the body. However, there is no statement about how much the PEth concentration increases after single moderate alcohol consumption. This study was conducted to determine the increase in PEth concentrations after a single drinking event. Additionally, a new volumetric sampling device (volumetric dried blood spot cards (DBSV)) was evaluated, which was designed to simplify further sampling processes and to allow for easy self-sampling. Dried blood samples from 31 volunteers were collected before and after single alcohol consumption with a mean maximum breath alcohol concentration of 0.4 mg/L (range: 0.30–0.55 mg/L). PEth concentrations were determined after automated extraction by liquid chromatography--tandem mass spectrometry. PEth 16:0/18:1 and PEth 16:0/18:2 concentrations increased to an average of 45 ng/mL each in patients starting below 20 ng/mL (range: 25.0–57.0 ng/mL for PEth 16:0/18:1; range 26.8–62.3 ng/mL for PEth 16:0/18:2). PEth concentrations in patients starting above 20 ng/mL increased by a mean of 30 ng/mL (range: 6.2–71.3 ng/mL for PEth 16:0/18:1; range 8.8–65.3 ng/mL for PEth 16:0/18:2). In addition, the comparison of the new sampling device DBSV with a standard filter paper card (with volumetrically applied 20 µL of blood samples) yielded a close agreement for the determined PEth concentrations in 24 forensic samples and three external controls. Therefore, the sampling device DBSV proved to be suitable for the determination of PEth concentrations in blood.