bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Utility of SOX10 Immunohistochemical Staining in Breast Pathology
Authors: Rammal Rayan , Goel Kanika , Elishaev Esther , Rinda Soong T , Jones Mirka W , Zhao Chengquan , Clark Beth Z , Carter Gloria J , Yu Jing , Fine Jeffrey L , Villatoro Tatiana M , Harinath Lakshmi , Bhargava Rohit 
Published: August 2022

Abstract

Objectives
SOX10 expression helps identify melanocytic lesions. Over time, novel uses have been identified, such as expression in triple-negative breast cancer (TNBC). We evaluated the usefulness of SOX10 in breast pathology—specifically, identification and subtyping of TNBC and distinction from gynecologic carcinomas, use as a myoepithelial marker, and in the distinction of usual ductal hyperplasia (UDH) from atypical ductal hyperplasia (ADH).

Methods
Several breast and gynecologic carcinoma tissue microarrays containing a total of 492 cases were stained with SOX10. Whole sections of 34 ADH, 50 UDH, and 29 ductal carcinoma in situ (DCIS) samples were also stained with SOX10.

Results
SOX10 expression was identified in 67% of consecutive TNBC cases. Expression was mostly seen in nonapocrine, androgen receptor (AR)–negative TNBCs. All gynecologic carcinomas (n = 157) were negative. All UDH cases showed mosaic SOX10 expression, while all ADH cases lacked expression. All estrogen receptor (ER)–positive DCIS (n = 19) specimens were negative for SOX10, while 2 of 10 ER-negative DCIS specimens were positive for SOX10. The latter 2 cases showed SOX10-positive invasive carcinomas.

Conclusions
SOX10 identifies nonluminal AR-type TNBC and is useful in distinguishing TNBC from gynecologic carcinomas. SOX10 can distinguish UDH from ADH. SOX10 is not useful in distinguishing ADH from DCIS.
Investigating the Use of Grammar Learning Strategies in Hungary and Poland: A Comparative Study
Authors: Pawlak Mirosław , Csizér Kata 
Published: August 2022

Abstract
Although there is consensus that second language grammar instruction is needed, some controversial issues remain. Whatever instructional options are selected, it is vital that they allow the development of not only explicit knowledge but also implicit or at least automatized knowledge that can be used in real-time interaction. Since this aim is difficult to achieve, students need to learn this subsystem on their own and this process can be aided by adept use of grammar learning strategies (GLS). However, research in this area is scarce, existing tools have not been validated in different contexts, and no cross-country comparisons have been made. The study addresses these gaps by examining the use of GLS by university students majoring in English in Hungary (N = 205) and Poland (N = 173). Data were collected by means of a standardized questionnaire and subjected to principal component analysis and correlational analysis. Independent- and paired-samples t-tests as well as regression analyses were also run. Some differences were found between the two contexts but overall patterns of GLS use were strikingly similar.
Chemical footprints mediate habitat selection in co-occurring aphids
Authors: Porras Mitzy F , McCartney Nathaniel , Raspotnig Günther , Rajotte Edwin G 
Published: August 2022

Abstract
Habitat selection is a critical process that shapes the spatial distribution of species at local and regional scales. The mechanisms underlying habitat preference rely on environmental factors, species traits, and ecological interactions with other species. Here, we examined spatial segregation between two co-occurring aphid species (Rhopalosiphum maidis and R. padi) on wheat plants. We hypothesized that spatial segregation between these aphid species was mediated by aphid cuticular compounds left as chemical “footprints” on plant surfaces. Combining field and laboratory experiments, we first examined how plant microsites alter fitness by measuring the fecundity of each species. Next, we tested whether intra- and interspecific pre-inhabitation modified habitat selection in both aphid species. Both aphid species preferred and exhibited higher fecundity on wheat stems versus leaves. Laboratory trials showed that R. maidis pre-inhabitation altered R. padi spatial preference. By gas chromatography-mass spectrometry analysis and bioassays testing the effects of aphid density and footprint extracts, we found a density-dependent response, with R. padi avoiding locations previously inhabited by R. maidis. The chemical analysis of footprint crude extracts revealed a highly abundant compound, 1-hexacosanol, and when presented in the synthetic form, also elicited R. padi displacement. Altogether, it indicated that R. maidis footprints altered R. padi habitat selection with cuticular compounds playing a relevant role in the habitat selection process in co-occurring aphid species.
Anthropogenic noise and light alter temporal but not spatial breeding behavior in a wild frog
Authors: Cronin Andrew D , Smit Judith A H , Halfwerk Wouter 
Published: August 2022

AbstractIncreasing urbanization has led to large-scale land-use changes, exposing persistent populations to drastically altered environments. Sensory pollutants, including low-frequency anthropogenic noise and artificial light at night (ALAN), are typically associated with urban environments and known to impact animal populations in a variety of ways. Both ALAN and anthropogenic noise can alter behavioral and physiological processes important for survival and reproduction, including communication and circadian rhythms. Although noise and light pollution typically co-occur in urbanized areas, few studies have addressed their combined impact on species’ behavior. Here, we assessed how anthropogenic noise and ALAN can influence spatial and temporal variation in breeding activity of a wild frog population. By exposing artificial breeding sites inside a tropical rainforest to multiple sensory environments, we found that both anthropogenic noise and ALAN impact breeding behavior of túngara frogs (Engystomops pustulosus), albeit in different ways. Males arrived later in the night at their breeding sites in response to anthropogenic noise. ALAN, on the other hand, led to an increase in calling effort. We found no evidence that noise or light pollution either attracted frogs to or repelled frogs from breeding sites. Thus, anthropogenic noise may negatively affect calling males by shifting the timing of sexual signaling. Conversely, ALAN may increase the attractiveness of calling males. These changes in breeding behavior highlight the complex ways that urban multisensory pollution can influence behavior and suggest that such changes may have important ecological implications for the wildlife that are becoming increasingly exposed to urban multisensory pollution.
CRISPRCasStack: a stacking strategy-based ensemble learning framework for accurate identification of Cas proteins
Authors: Zhang Tianjiao , Jia Yuran , Li Hongfei , Xu Dali , Zhou Jie , Wang Guohua 
Published: August 2022

AbstractCRISPR-Cas system is an adaptive immune system widely found in most bacteria and archaea to defend against exogenous gene invasion. One of the most critical steps in the study of exploring and classifying novel CRISPR-Cas systems and their functional diversity is the identification of Cas proteins in CRISPR-Cas systems. The discovery of novel Cas proteins has also laid the foundation for technologies such as CRISPR-Cas-based gene editing and gene therapy. Currently, accurate and efficient screening of Cas proteins from metagenomic sequences and proteomic sequences remains a challenge. For Cas proteins with low sequence conservation, existing tools for Cas protein identification based on homology cannot guarantee identification accuracy and efficiency. In this paper, we have developed a novel stacking-based ensemble learning framework for Cas protein identification, called CRISPRCasStack. In particular, we applied the SHAP (SHapley Additive exPlanations) method to analyze the features used in CRISPRCasStack. Sufficient experimental validation and independent testing have demonstrated that CRISPRCasStack can address the accuracy deficiencies and inefficiencies of the existing state-of-the-art tools. We also provide a toolkit to accurately identify and analyze potential Cas proteins, Cas operons, CRISPR arrays and CRISPR-Cas locus in prokaryotic sequences. The CRISPRCasStack toolkit is available at https://github.com/yrjia1015/CRISPRCasStack.
ComABAN: refining molecular representation with the graph attention mechanism to accelerate drug discovery
Authors: Yan Huihui , Xie Yuanyuan , Liu Yao , Yuan Leer , Sheng Rong 
Published: August 2022

Abstract
An unsolved challenge in developing molecular representation is determining an optimal method to characterize the molecular structure. Comprehension of intramolecular interactions is paramount toward achieving this goal. In this study, ComABAN, a new graph-attention-based approach, is proposed to improve the accuracy of molecular representation by simultaneously considering atom–atom, bond–bond and atom-bond interactions. In addition, we benchmark models extensively on 8 public and 680 proprietary industrial datasets spanning a wide variety of chemical end points. The results show that ComABAN has higher prediction accuracy compared with the classical machine learning method and the deep learning-based methods. Furthermore, the trained neural network was used to predict a library of 1.5 million molecules and picked out compounds with a classification result of grade I. Subsequently, these predicted molecules were scored and ranked using cascade docking, molecular dynamics simulations to generate five potential candidates. All five molecules showed high similarity to nanomolar bioactive inhibitors suppressing the expression of HIF-1α, and we synthesized three compounds (Y-1, Y-3, Y-4) and tested their inhibitory ability in vitro. Our results indicate that ComABAN is an effective tool for accelerating drug discovery.
Small compound-based direct cell conversion with combinatorial optimization of pathway regulations
Authors: Nakamura Toru , Iwata Michio , Hamano Momoko , Eguchi Ryohei , Takeshita Jun-ichi , Yamanishi Yoshihiro 
Published: August 2022

AbstractMotivationDirect cell conversion, direct reprogramming (DR), is an innovative technology that directly converts source cells to target cells without bypassing induced pluripotent stem cells. The use of small compounds (e.g. drugs) for DR can help avoid carcinogenic risk induced by gene transfection; however, experimentally identifying small compounds remains challenging because of combinatorial explosion.ResultsIn this article, we present a new computational method, COMPRENDRE (combinatorial optimization of pathway regulations for direct reprograming), to elucidate the mechanism of small compound-based DR and predict new combinations of small compounds for DR. We estimated the potential target proteins of DR-inducing small compounds and identified a set of target pathways involving DR. We identified multiple DR-related pathways that have not previously been reported to induce neurons or cardiomyocytes from fibroblasts. To overcome the problem of combinatorial explosion, we developed a variant of a simulated annealing algorithm to identify the best set of compounds that can regulate DR-related pathways. Consequently, the proposed method enabled to predict new DR-inducing candidate combinations with fewer compounds and to successfully reproduce experimentally verified compounds inducing the direct conversion from fibroblasts to neurons or cardiomyocytes. The proposed method is expected to be useful for practical applications in regenerative medicine.Availability and implementationThe code supporting the current study is available at the http://labo.bio.kyutech.ac.jp/~yamani/comprendre.Supplementary informationSupplementary data are available at Bioinformatics online.
Sertoli cells require TDP-43 to support spermatogenesis
Authors: Zomer Helena D , Osuru Hari Prasad , Chebolu Apoorv , Rayl Jeremy M , Timken Madeline , Reddi Prabhakara P 
Published: August 2022

Abstract
TAR DNA binding protein of 43 kD (TDP-43) is an evolutionarily conserved, ubiquitously expressed transcription factor and RNA-binding protein with major human health relevance. TDP-43 is present in Sertoli and germ cells of the testis and is aberrantly expressed in the sperm of infertile men. Sertoli cells play a key role in spermatogenesis by offering physical and nutritional support to male germ cells. The current study investigated the requirement of TDP-43 in Sertoli cells. Conditional knockout (cKO) of TDP-43 in mouse Sertoli cells caused failure of spermatogenesis and male subfertility. The cKO mice showed decreased testis weight, and low sperm count. Testis showed loss of germ cell layers, presence of vacuoles, and sloughing of round spermatids, suggesting loss of contact with Sertoli cells. Using a biotin tracer, we found that the blood-testis barrier (BTB) was disrupted as early as postnatal day 24 and worsened in adult cKO mice. We noted aberrant expression of the junction proteins connexin-43 (gap junction) and N-cadherin (ectoplasmic specialization). Oil Red O staining showed a decrease in lipid droplets (phagocytic function) in tubule cross-sections, Sertoli cells cytoplasm, and in the lumen of seminiferous tubules of cKO mice. Finally, qRT-PCR showed upregulation of genes involved in the formation and/or maintenance of Sertoli cell junctions as well as in the phagocytic pathway. Sertoli cells require TDP-43 for germ cell attachment, formation and maintenance of BTB, and phagocytic function, thus indicating an essential role for TDP-43 in the maintenance of spermatogenesis.
Was Henry David Thoreau a Good Naturalist? An Approach for Assessing Data from Historical Natural History Records
Authors: Primack Richard B , Miller-Rushing Abraham J , Miller Tara K 
Published: August 2022

abstractEcologists are increasingly combining historical observations made by naturalists with modern observations to detect the ecological effects of climate change. This use of historical observations raises the following question: How do we know that historical data are appropriate to use to answer current ecological questions? In the present article, we address this question for environmental philosopher Henry David Thoreau, author of Walden. Should we trust his observations? We qualitatively and quantitatively evaluate Thoreau's observations using a three-step framework: We assess the rigor, accuracy, and utility of his observations to investigate changes in plants and animals over time. We conclude that Thoreau was an accurate observer of nature and a reliable scientist. More importantly, we describe how this simple three-step approach could be used to assess the accuracy of other scientists and naturalists.
When Law-And-Order Politics Fail: Media Fragmentation and Protective Factors That Limit the Politics of Fear
Authors: Lee Murray , Ellis Justin R , Keel Chloe , Wickes Rebecca , Jackson Jonathan 
Published: August 2022

Abstract
Law-and-order politics has long been a topic of scholarly work. The leveraging of fear of crime for political capital has been of particular concern. In the 2018 election in the Australian state of Victoria, crime and law-and-order became prominent political issues, particularly through racialized discourse about ‘African gangs’. That election provides a case study here. This article turns the traditional analysis of the politics of fear of crime around and considers some of the key reasons why law-and-order politics failed to gain decisive political traction in this instance. Media fragmentation and diversification continues to challenge the primacy of political primary definers in unpredictable ways. As such, electoral strategies that seek to leverage fear of crime and community insecurity need to be understood in the context of broader individual, community and social protective factors that might mitigate fear of crime.
Asteraceae as a model system for evolutionary studies: from fossils to genomes
Authors: Palazzesi Luis , Pellicer Jaume , Barreda Viviana D , Loeuille Benoît , Mandel Jennifer R , Pokorny Lisa , Siniscalchi Carolina M , Tellería M Cristina , Leitch Ilia J , Hidalgo Oriane 
Published: August 2022

Abstract
With c. 24 700 species (10% of all flowering plants), Asteraceae are one of the largest and most phenotypically diverse angiosperm families, with considerable economic and ecological importance. Asteraceae are distributed worldwide, from nearly polar latitudes all the way to the tropics, and occur across a diverse range of habitats from extreme deserts to swamps and from lowland rainforests to alpine tundra. Altogether, these characteristics make this family an outstanding model system to address a broad range of eco-evolutionary questions. In this review, we summarize recent progress in our understanding of Asteraceae on the basis of joint efforts by specialists in the fields of palaeobotany, cytogenetics, comparative genomics and phylogenomics. We will highlight how these developments are opening up new possibilities for integrating fields and better comprehending evolution beyond Asteraceae.
Preoperative brain connectome predicts postoperative changes in processing speed in moyamoya disease
Authors: Gao Mengxia , Lam Charlene L M , Lui Wai M , Lau Kui Kai , Lee Tatia M C 
Published: August 2022

AbstractMoyamoya disease is a rare cerebrovascular disorder associated with cognitive dysfunction. It is usually treated by surgical revascularization, but research on the neurocognitive outcomes of revascularization surgery is controversial. Given that neurocognitive impairment could affect the daily activities of patients with moyamoya disease, early detection of postoperative neurocognitive outcomes has the potential to improve patient management. In this study, we applied a well-established connectome-based predictive modelling approach to develop machine learning models that used preoperative resting-state functional connectivity to predict postoperative changes in processing speed in patients with moyamoya disease. Twelve adult patients with moyamoya disease (age range: 23–49 years; female/male: 9/3) were recruited prior to surgery and underwent follow-up at 1 and 6 months after surgery. Twenty healthy controls (age range: 24–54 years; female/male: 14/6) were recruited and completed the behavioural test at baseline, 1-month follow-up and 6-month follow-up. Behavioural results indicated that the behavioural changes in processing speed at 1 and 6 months after surgery compared with baseline were not significant. Importantly, we showed that preoperative resting-state functional connectivity significantly predicted postoperative changes in processing speed at 1 month after surgery (negative network: ρ = 0.63, Pcorr = 0.017) and 6 months after surgery (positive network: ρ = 0.62, Pcorr = 0.010; negative network: ρ = 0.55, Pcorr = 0.010). We also identified cerebro-cerebellar and cortico-subcortical connectivities that were consistently associated with processing speed. The brain regions identified from our predictive models are not only consistent with previous studies but also extend previous findings by revealing their potential roles in postoperative neurocognitive functions in patients with moyamoya disease. Taken together, our findings provide preliminary evidence that preoperative resting-state functional connectivity might predict the post-surgical longitudinal neurocognitive changes in patients with moyamoya disease. Given that processing speed is a crucial cognitive ability supporting higher neurocognitive functions, this study’s findings offer important insight into the clinical management of patients with moyamoya disease.
Control of hybrid DC/AC microgrid system employing fuel cell and solar photovoltaic sources using grey wolf optimization
Authors: Al-Antaki Ahmed M , Golubchik T V , Al-Furaiji Mushtaq A , Mohammed H J 
Published: August 2022

Abstract
The outcome of this study is to improve and enhance the power quality of the hybrid DC/AC microgrid (MG). The photovoltaic (PV) system and the proton exchange membrane fuel cell (PEMFC) are used as renewable energy sources to deliver the optimum active power to the utility grid. The MG system based on the PV system, PEMFC and voltage source inverter is modelled mathematically. Also, the maximum power point tracking (MPPT)-based grey wolf optimization (GWO) is used to increase the PV module efficiency and enhance performance. Also, to improve the PEMFC performance, a digital proportional-integral controller is used to control the PEMFC circuit. The proposed inverter is controlled using synchronous reference frame theory, called the direct-quadrature (dq) control method. Hence, the performance of the proposed MG system is tested using MATLAB® for various weather and loading conditions. From the simulation results, the proposed MG system can deliver and absorb an active power based on the PV and fuel cell characteristics. As a result, the hybrid DC/AC MG is enhanced in terms of stabilization of the DC-bus voltage. Also, the power quality of the MG is improved using GWO optimization based on MPPT. Finally, good results are achieved using GWO in terms of the total harmonic distortion of the output current of 2.3% and higher efficiency of 98.9%.
Breaking Down the Breakpoints: Rationale for the 2022 Clinical and Laboratory Standards Institute Revised Piperacillin-Tazobactam Breakpoints Against Enterobacterales
Authors: Tamma Pranita D , Harris Patrick N A , Mathers Amy J , Wenzler Eric , Humphries Romney M 
Published: August 2022

Abstract
Piperacillin-tazobactam (PTZ) is one of the most common antibiotics administered to hospitalized patients. Its broad activity against gram-negative, gram-positive, and anaerobic pathogens; efficacy in clinical trials across diverse infection types and patient populations; and generally favorable toxicity profile make it a particularly appealing antibiotic agent. PTZ susceptibility interpretive criteria (ie, breakpoints) for the Enterobacterales were initially established in 1992, as the drug was undergoing approval by the US Food and Drug Administration. In the ensuing 30 years, changes in the molecular epidemiology of the Enterobacterales and its impact on PTZ susceptibility testing, mounting pharmacokinetic/pharmacodynamic data generated from sophisticated techniques such as population pharmacokinetic modeling and Monte Carlo simulation, and disturbing safety signals in a large clinical trial prompted the Clinical Laboratory and Standards Institute (CLSI) to review available evidence to determine the need for revision of the PTZ breakpoints for Enterobacterales. After an extensive literature review and formal voting process, the susceptibility criteria were revised in the 2022 CLSI M100 document to the following: ≤8/4 µg/mL (susceptible), 16/4 µg/mL (susceptible dose-dependent), and ≥32/4 µg/mL (resistant). Herein, we provide a brief overview of the CLSI process of antibiotic breakpoint revisions and elaborate on the available data that ultimately led to the decision to revise the PTZ breakpoints.
Reflections on the post-Covid city
Authors: Glaeser Edward L 
Published: August 2022

Abstract
What will COVID-19 and the shift to remote work do to the cities of the world? The temporary disruptions have been enormous and remain enormous as of the late summer of 2022. Offices remain vacant in many large cities. Within the US, the pandemic sped up the longer-term movement of people and firms to the sunbelt. Looking forward, there seem to be two possible scenarios, depending on the pandemic events of the future. If COVID-19 is only the first of a wave of deadly global disease events, then the urban renaissance that began thirty years ago could end. If COVID-19 is a one-off pandemic, then the impact of disease and telecommuting on urban life will be more limited. The enduring demand of people to enjoy urban amenities, and the value of learning face-to-face should enable cities to survive this shock. The stark gap between these two scenarios highlights the importance of global investments in public health that can reduce the risk of future pandemics.