bluuebunny/crossref_metadata_2025_split huggingface dataset:
Counterpropagating topological and quantum Hall edge channels
Authors: Shamim Saquib , Shekhar Pragya , Beugeling Wouter , Böttcher Jan , Budewitz Andreas , Mayer Julian-Benedikt , Lunczer Lukas , Hankiewicz Ewelina M. , Buhmann Hartmut , Molenkamp Laurens W. 
Published: May 2022

AbstractThe survival of the quantum spin Hall edge channels in presence of an external magnetic field has been a subject of experimental and theoretical research. The inversion of Landau levels that accommodates the quantum spin Hall effect is destroyed at a critical magnetic field, and a trivial insulating gap appears in the spectrum for stronger fields. In this work, we report the absence of this transport gap in disordered two dimensional topological insulators in perpendicular magnetic fields of up to 16 T. Instead, we observe that a topological edge channel (from band inversion) coexists with a counterpropagating quantum Hall edge channel for magnetic fields at which the transition to the insulating regime is expected. For larger fields, we observe only the quantum Hall edge channel with transverse resistance close to h/e2. By tuning the disorder using different fabrication processes, we find evidence that this unexpected ν = 1 plateau originates from extended quantum Hall edge channels along a continuous network of charge puddles at the edges of the device.
Nuclear oligo hashing improves differential analysis of single-cell RNA-seq
Authors: Kim Hyeon-Jin , Booth Greg , Saunders Lauren , Srivatsan Sanjay , McFaline-Figueroa José L. , Trapnell Cole 
Published: May 2022

AbstractSingle-cell RNA sequencing (scRNA-seq) offers a high-resolution molecular view into complex tissues, but suffers from high levels of technical noise which frustrates efforts to compare the gene expression programs of different cell types. “Spike-in” RNA standards help control for technical variation in scRNA-seq, but using them with recently developed, ultra-scalable scRNA-seq methods based on combinatorial indexing is not feasible. Here, we describe a simple and cost-effective method for normalizing transcript counts and subtracting technical variability that improves differential expression analysis in scRNA-seq. The method affixes a ladder of synthetic single-stranded DNA oligos to each cell that appears in its RNA-seq library. With improved normalization we explore chemical perturbations with broad or highly specific effects on gene regulation, including RNA pol II elongation, histone deacetylation, and activation of the glucocorticoid receptor. Our methods reveal that inhibiting histone deacetylation prevents cells from executing their canonical program of changes following glucocorticoid stimulation.
Proteogenomic characterization of 2002 human cancers reveals pan-cancer molecular subtypes and associated pathways
Authors: Zhang Yiqun , Chen Fengju , Chandrashekar Darshan S. , Varambally Sooryanarayana , Creighton Chad J. 
Published: May 2022

AbstractMass-spectrometry-based proteomic data on human tumors—combined with corresponding multi-omics data—present opportunities for systematic and pan-cancer proteogenomic analyses. Here, we assemble a compendium dataset of proteomics data of 2002 primary tumors from 14 cancer types and 17 studies. Protein expression of genes broadly correlates with corresponding mRNA levels or copy number alterations (CNAs) across tumors, but with notable exceptions. Based on unsupervised clustering, tumors separate into 11 distinct proteome-based subtypes spanning multiple tissue-based cancer types. Two subtypes are enriched for brain tumors, one subtype associating with MYC, Wnt, and Hippo pathways and high CNA burden, and another subtype associating with metabolic pathways and low CNA burden. Somatic alteration of genes in a pathway associates with higher pathway activity as inferred by proteome or transcriptome data. A substantial fraction of cancers shows high MYC pathway activity without MYC copy gain but with mutations in genes with noncanonical roles in MYC. Our proteogenomics survey reveals the interplay between genome and proteome across tumor lineages.
Organophotoredox-catalyzed semipinacol rearrangement via radical-polar crossover
Authors: Kodo Taiga , Nagao Kazunori , Ohmiya Hirohisa 
Published: May 2022

AbstractOver the past century, significant progress in semipinacol rearrangement involving 1,2-migration of α-hydroxy carbocations has been made in the areas of catalysis and total synthesis of natural products. To access the α-hydroxy carbocation intermediate, conventional acid-mediated or electrochemical approaches have been employed. However, the photochemical semipinacol rearrangement has been underdeveloped. Herein, we report the organophotoredox-catalyzed semipinacol rearrangement via radical-polar crossover (RPC). A phenothiazine-based organophotoredox catalyst facilitates the generation of an α-hydroxy non-benzylic alkyl radical followed by oxidation to the corresponding carbocation, which can be exploited to undergo the semipinacol rearrangement. As a result, the photochemical approach enables decarboxylative semipinacol rearrangement of β-hydroxycarboxylic acid derivatives and alkylative semipinacol type rearrangement of allyl alcohols with carbon electrophiles, producing α-quaternary or α-tertiary carbonyls bearing sp3-rich scaffolds.
Image registration method using representative feature detection and iterative coherent spatial mapping for infrared medical images with flat regions
Authors: Wang Hao-Jen , Lee Chia-Yen , Lai Jhih-Hao , Chang Yeun-Chung , Chen Chung-Ming 
Published: May 2022

AbstractIn the registration of medical images, nonrigid registration targets, images with large displacement caused by different postures of the human body, and frequent variations in image intensity due to physiological phenomena are substantial problems that make medical images less suitable for intensity-based image registration modes. These problems also greatly increase the difficulty and complexity of feature detection and matching for feature-based image registration modes. This research introduces an automatic image registration algorithm for infrared medical images that offers the following benefits: effective detection of feature points in flat regions (cold patterns) that appear due to changes in the human body’s thermal patterns, improved mismatch removal through coherent spatial mapping for improved feature point matching, and large-displacement optical flow for optimal transformation. This method was compared with various classical gold standard image registration methods to evaluate its performance. The models were compared for the three key steps of the registration process—feature detection, feature point matching, and image transformation—and the results are presented visually and quantitatively. The results demonstrate that the proposed method outperforms existing methods in all tasks, including in terms of the features detected, uniformity of feature points, matching accuracy, and control point sparsity, and achieves optimal image transformation. The performance of the proposed method with four common image types was also evaluated, and the results verify that the proposed method has a high degree of stability and can effectively register medical images under a variety of conditions.
Differential effects of stress-related and stress-unrelated humor in remitted depression
Authors: Braniecka Anna , Wołkowicz Iwona , Orylska Anna , Antosik-Wójcińska Anna Z. , Chrzczonowicz-Stępień Agnieszka , Bolek Ewelina 
Published: May 2022

AbstractEnhancing emotion regulation among previously depressed people is crucial for improving their resilience and reducing relapse. Therefore, emphasis is placed on determining effective regulation strategies, particularly those that, besides down-regulating negative emotions, also up-regulate positive emotions. One promising strategy, with great potential in both these respects, is humor. It is unclear, however, what type of humor is most adaptive in remitted depression. This study compared two distinct humor-based strategies: stress-related humor and stress-unrelated humor. Outpatients with remitted depression (N = 94) participated in a randomized experiment evoking personal stress and the subsequent application of stress-related humor, stress-unrelated humor, or a non-humorous regulation. They repeatedly reported positive and negative emotions (at four time points) and experienced distress (at three time points). There were also assessments of selective attention, subsequent performance, effort, and intrusive thoughts. Unlike non-humorous regulation, humor-based strategies had adaptive consequences, both immediately and after a delay; however, stress-unrelated humor was most beneficial and was the only effective strategy when attention deficits were present. Humor, especially if unrelated to stressors, might broaden the repertoire of powerful emotion regulation strategies in remitted depression. Humorous focusing on distress can be detrimental for patients with attention impairment.Clinical trial registration: The study was registered under the number ISRCTN86314628 (20/09/2021).
Integrated computational analysis reveals HOX genes cluster as oncogenic drivers in head and neck squamous cell carcinoma
Authors: Shenoy U Sangeetha , Morgan Richard , Hunter Keith , Kabekkodu Shama Prasada , Radhakrishnan Raghu 
Published: May 2022

AbstractAlterations in homeobox (HOX) gene expression are involved in the progression of several cancer types including head and neck squamous cell carcinoma (HNSCC). However, regulation of the entire HOX cluster in the pathophysiology of HNSCC is still elusive. By using different comprehensive databases, we have identified the significance of differentially expressed HOX genes (DEHGs) in stage stratification and HPV status in the cancer genome atlas (TCGA)-HNSCC datasets. The genetic and epigenetic alterations, druggable genes, their associated functional pathways and their possible association with cancer hallmarks were identified. We have performed extensive analysis to identify the target genes of DEHGs driving HNSCC. The differentially expressed HOX cluster-embedded microRNAs (DEHMs) in HNSCC and their association with HOX-target genes were evaluated to construct a regulatory network of the HOX cluster in HNSCC. Our analysis identified sixteen DEHGs in HNSCC and determined their importance in stage stratification and HPV infection. We found a total of 55 HNSCC driver genes that were identified as targets of DEHGs. The involvement of DEHGs and their targets in cancer-associated signaling mechanisms have confirmed their role in pathophysiology. Further, we found that their oncogenic nature could be targeted by using the novel and approved anti-neoplastic drugs in HNSCC. Construction of the regulatory network depicted the interaction between DEHGs, DEHMs and their targets genes in HNSCC. Hence, aberrantly expressed HOX cluster genes function in a coordinated manner to drive HNSCC. It could provide a broad perspective to carry out the experimental investigation, to understand the underlying oncogenic mechanism and allow the discovery of new clinical biomarkers for HNSCC.
Validation of quantitative fatty acid signature analysis for estimating the diet composition of free-ranging killer whales
Authors: Remili Anaïs , Dietz Rune , Sonne Christian , Iverson Sara J. , Roy Denis , Rosing-Asvid Aqqalu , Land-Miller Haley , Pedersen Adam F. , McKinney Melissa A. 
Published: May 2022

AbstractAccurate diet estimates are necessary to assess trophic interactions and food web dynamics in ecosystems, particularly for apex predators like cetaceans, which can regulate entire food webs. Quantitative fatty acid analysis (QFASA) has been used to estimate the diets of marine predators in the last decade but has yet to be implemented on free-ranging cetaceans, from which typically only biopsy samples containing outer blubber are available, due to a lack of empirically determined calibration coefficients (CCs) that account for fatty acid (FA) metabolism. Here, we develop and validate QFASA for killer whales using full blubber from managed-care and free-ranging individuals. First, we compute full, inner, and outer blubber CCs from the FA signatures across the blubber layers of managed-care killer whales and their long-term diet items. We then run cross-validating simulations on the managed-care individuals to evaluate the accuracy of diet estimates by comparing full-depth and depth-specific estimates to true diets. Finally, we apply these approaches to subsistence-harvested killer whales from Greenland to test the utility of the method for free-ranging killer whales, particularly for the outer blubber. Accurate diet estimates for the managed-care killer whales were only achieved using killer whale-specific and blubber-layer-specific CCs. Modeled diets for the Greenlandic killer whales largely consisted of seals (75.9 ± 4.7%) and/or fish (20.4 ± 2.4%), mainly mackerel, which was consistent with stomach content data and limited literature on this population. Given the remote habitats and below surface feeding of most cetaceans, this newly developed cetacean-specific QFASA method, which can be applied to outer-layer biopsies, offers promise to provide a significant new understanding of diet dynamics of free-ranging odontocetes and perhaps other cetacean species throughout the world’s oceans.
Ultrahigh strength ductile microalloyed steel with a very low yield ratio developed by quenching and partitioning heat treatment
Authors: Fida Hassan S. , AlWadei H. 
Published: May 2022

AbstractIn this study, a microalloyed low carbon steel was subjected to quenching and partitioning (Q&P) heat treatment processes. The primary ferrite-pearlite microstructure of the steel was transformed into a bainitic microstructure containing interlath and sporadic blocks of retained austenite. The applied heat treatment process partitioned the carbon into the retained austenite to a weight percentage of 0.136. The microalloyed low-carbon steel acquired a continuous yield with high yield strength, a gigapascal level of ultimate tensile strength (i.e., ~ 1.1 GPa), and a very low yield ratio (i.e., 0.55) while retaining reasonable ductility and toughness when compared to the preheat-treated values.
Detecting sleep outside the clinic using wearable heart rate devices
Authors: Perez-Pozuelo Ignacio , Posa Marius , Spathis Dimitris , Westgate Kate , Wareham Nicholas , Mascolo Cecilia , Brage Søren , Palotti Joao 
Published: May 2022

AbstractThe adoption of multisensor wearables presents the opportunity of longitudinal monitoring of sleep in large populations. Personalized yet device-agnostic algorithms can sidestep laborious human annotations and objectify cross-cohort comparisons. We developed and tested a heart rate-based algorithm that captures inter- and intra-individual sleep differences in free-living conditions and does not require human input. We evaluated it on four study cohorts using different research- and consumer-grade devices for over 2000 nights. Recording periods included both 24 h free-living and conventional lab-based night-only data. We compared our optimized method against polysomnography, sleep diaries and sleep periods produced through a state-of-the-art acceleration based method. Against sleep diaries, the algorithm yielded a mean squared error of 0.04–0.06 and a total sleep time (TST) deviation of $$-$$
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2.70 (± 5.74) and 12.80 (± 3.89) minutes, respectively. When evaluated with PSG lab studies, the MSE ranged between 0.06 and 0.11 yielding a time deviation between $$-$$
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29.07 and $$-$$
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55.04 minutes. These results showcase the value of this open-source, device-agnostic algorithm for the reliable inference of sleep in free-living conditions and in the absence of annotations.
Effect of the stacking order, annealing temperature and atmosphere on crystal phase and optical properties of Cu2SnS3
Authors: Zaki M. Y. , Sava F. , Simandan I. D. , Buruiana A. T. , Mihai C. , Velea A. , Galca A. C. 
Published: May 2022

AbstractCu2SnS3 (CTS) is emerging as a promising absorber for the next generation thin film solar cells (TFSC) due to its excellent optical and electronic properties, earth-abundance and eco-friendly elemental composition. In addition, CTS can be used as precursor films for the Cu2ZnSnS4 (CZTS) synthesis. The optical properties of CTS are influenced by stoichiometry, crystalline structure, secondary phases and crystallite size. Routes for obtaining CTS films with optimized properties for TFSC are still being sought. Here, the CTS thin films synthesized by magnetron sputtering on soda lime glass (SLG) using Cu and SnS2 targets in two different stacks, were studied. The SLG\Cu\SnS2 and SLG\SnS2\Cu stacks were annealed in S and Sn + S atmospheres, at various temperatures. Both stacks show a polymorphic structure, and higher annealing temperatures favor the monoclinic CTS phase formation. Morphology is influenced by the stacking order since a SnS2 top layer generates several voids on the surface due to the evaporation of SnS, while a Cu top layer provides uniform and void-free surfaces. The films in the copper-capped stack annealed under Sn + S atmosphere have the best structural, morphological, compositional and optical properties, with tunable band gaps between 1.18 and 1.37 eV. Remarkably, secondary phases are present only in a very low percent (< 3.5%) in samples annealed at higher temperatures. This new synthesis strategy opens the way for obtaining CTS thin films for solar cell applications, that can be used also as intermediary stage for CZTS synthesis.
The use of high-affinity polyhistidine binders as masking probes for the selection of an NDM-1 specific aptamer
Authors: Sabrowski Wiebke , Dreymann Nico , Möller Anja , Czepluch Denise , Albani Patricia P. , Theodoridis Dimitrios , Menger Marcus M. 
Published: May 2022

AbstractThe emergence of carbapenemase-producing multi-drug resistant Enterobacteriaceae poses a dramatic, world-wide health risk. Limited treatment options and a lack of easy-to-use methods for the detection of infections with multi-drug resistant bacteria leave the health-care system with a fast-growing challenge. Aptamers are single stranded DNA or RNA molecules that bind to their targets with high affinity and specificity and can therefore serve as outstanding detection probes. However, an effective aptamer selection process is often hampered by non-specific binding. When selections are carried out against recombinant proteins, purification tags (e.g. polyhistidine) serve as attractive side targets, which may impede protein target binding. In this study, aptamer selection was carried out against N-terminally hexa-histidine tagged New Delhi metallo-ß-lactamase 1. After 14 selection rounds binding to polyhistidine was detected rather than to New Delhi metallo-ß-lactamase 1. Hence, the selection strategy was changed. As one aptamer candidate showed remarkable binding affinity to polyhistidine, it was used as a masking probe and selection was restarted from selection round 10. Finally, after three consecutive selection rounds, an aptamer with specific binding properties to New Delhi metallo-ß-lactamase 1 was identified. This aptamer may serve as a much-needed detection probe for New Delhi metallo-ß-lactamase 1 expressing Enterobacteriaceae.
Structure-based assessment and druggability classification of protein–protein interaction sites
Authors: Alzyoud Lara , Bryce Richard A. , Al Sorkhy Mohammad , Atatreh Noor , Ghattas Mohammad A. 
Published: May 2022

AbstractThe featureless interface formed by protein–protein interactions (PPIs) is notorious for being considered a difficult and poorly druggable target. However, recent advances have shown PPIs to be druggable, with the discovery of potent inhibitors and stabilizers, some of which are currently being clinically tested and approved for medical use. In this study, we assess the druggability of 12 commonly targeted PPIs using the computational tool, SiteMap. After evaluating 320 crystal structures, we find that the PPI binding sites have a wide range of druggability scores. This can be attributed to the unique structural and physiochemical features that influence their ligand binding and concomitantly, their druggability predictions. We then use these features to propose a specific classification system suitable for assessing PPI targets based on their druggability scores and measured binding-affinity. Interestingly, this system was able to distinguish between different PPIs and correctly categorize them into four classes (i.e. very druggable, druggable, moderately druggable, and difficult). We also studied the effects of protein flexibility on the computed druggability scores and found that protein conformational changes accompanying ligand binding in ligand-bound structures result in higher protein druggability scores due to more favorable structural features. Finally, the drug-likeness of many published PPI inhibitors was studied where it was found that the vast majority of the 221 ligands considered here, including orally tested/marketed drugs, violate the currently acceptable limits of compound size and hydrophobicity parameters. This outcome, combined with the lack of correlation observed between druggability and drug-likeness, reinforces the need to redefine drug-likeness for PPI drugs. This work proposes a PPI-specific classification scheme that will assist researchers in assessing the druggability and identifying inhibitors of the PPI interface.
Risk factors associated with preterm birth after IVF/ICSI
Authors: Li Jian , Shen Jinhua , Zhang Xiaoli , Peng Yangqin , Zhang Qin , Hu Liang , Reichetzeder Christoph , Zeng Suimin , Li Jing , Tian Mei , Gong Fei , Lin Ge , Hocher Berthold 
Published: May 2022

AbstractIn vitro fertilization/intracytoplasmic sperm injection (IVF/ICSI) is associated with an increased risk of preterm (33rd–37th gestational week) and early preterm birth (20th–32nd gestational week). The underlying general and procedure related risk factors are not well understood so far. 4328 infertile women undergoing IVF/ICSI were entered into this study. The study population was divided into three groups: (a) early preterm birth group (n = 66), (b) preterm birth group (n = 675) and (c) full-term birth group (n = 3653). Odds for preterm birth were calculated by stepwise multivariate logistic regression analysis. We identified seven independent risk factors for preterm birth and four independent risk factors for early preterm birth. Older (> 39) or younger (< 25) maternal age (OR: 1.504, 95% CI 1.108–2.042, P = 0.009; OR: 2.125, 95% CI 1.049–4.304, P = 0.036, respectively), multiple pregnancy (OR: 9.780, 95% CI 8.014–11.935, P < 0.001; OR: 8.588, 95% CI 4.866–15.157, P < 0.001, respectively), placenta previa (OR: 14.954, 95% CI 8.053–27.767, P < 0.001; OR: 16.479, 95% CI 4.381–61.976, P < 0.001, respectively), and embryo reduction (OR: 3.547, 95% CI 1.736–7.249, P = 0.001; OR: 7.145, 95% CI 1.990–25.663, P = 0.003, respectively) were associated with preterm birth and early preterm birth, whereas gestational hypertension (OR: 2.494, 95% CI 1.770–3.514, P < 0.001), elevated triglycerides (OR: 1.120, 95% CI 1.011–1.240, P = 0.030) and shorter activated partial thromboplastin time (OR: 0.967, 95% CI 0.949–0.985, P < 0.001) were associated only with preterm birth. In conclusion, preterm and early preterm birth risk factors in patients undergoing assisted IVF/ICSI are in general similar to those in natural pregnancy. The lack of some associations in the early preterm group was most likely due to the lower number of early preterm birth cases. Only embryo reduction represents an IVF/ICSI specific risk factor.