bluuebunny/crossref_metadata_2025_split huggingface dataset:
Full Exceptional Collections and Stability Conditions for Dynkin Quivers
Authors: Otani Takumi 
Published: May 2024

Abstract
For a stability condition $\sigma $ on a triangulated category, Dimitrov–Katzarkov introduced the notion of a $\sigma $-exceptional collection. In this paper, we study full $\sigma $-exceptional collections in the derived category of an acyclic quiver. In particular, we prove that any stability condition $\sigma $ on the derived category of a Dynkin quiver admits a full $\sigma $-exceptional collection.
Dislocation: Toward a Framework for the Study of Crises
Authors: Klopf Nadine , Nabers Dirk 
Published: May 2024

Abstract
The paper develops a conceptual framework for the analysis of crises. It rests on the central argument that crises cannot be restricted to exceptional occurrences or temporarily delimited events, but we approach crisis as ontologically constitutive for our everyday lives. The concept of “discursive dislocation” is the cornerstone of this endeavor, as it grasps multiple aspects of sociopolitical instability, including societal deficiencies, fragilities, and political failures. Through theoretically advancing the concept of dislocation, we systematize three dimensions of crisis as permanent, recurring, and ephemeral dislocation. This allows us to analyze crises not only in their immediate environment but also makes it possible to understand them in their broader sociopolitical context. The conceptual framework is illustrated with the example of the COVID-19 pandemic in the United States, which reveals how the construction of the pandemic as a crisis is embedded in the historically ingrained self-portrayal of the United States, and how crisis responses are invoked to serve particular sociopolitical purposes in retaining an established American identity.
The Case for an Expressive Logic of Action
Authors: Duque Marina G 
Published: May 2024

Abstract
How can scholars theorize about phenomena like the eroding support, within the West, for the liberal democratic practices that once defined the post-1945 international order? Cumulative evidence shows that resentment toward out-groups shapes public attitudes toward issues like immigration and globalization, bolstering support for isolationist foreign policies in Western democracies. Yet, these findings contrast with the logics of action—based on means-end calculations, shared norms, practices, or habit—that IR scholars use to develop theory. Because existing logics provide a limited vocabulary to theorize about group processes with crucial symbolic and affective features, an important dimension of foreign policy behavior remains undertheorized. In this article, I draw on multi-disciplinary research to develop an expressive logic of action, whereby political behavior expresses an actor's social identification. Based on this logic, group attachment provides a compelling motivation for political behavior, whose activation depends on an interaction between issue framing and psychological dispositions. By focusing on the distinctive features of expressive behavior and specifying the mechanisms behind this behavior, an expressive logic encourages theory development and refinement across domains.
Sliding motility of Bacillus cereus mediates vancomycin pseudo-resistance during antimicrobial susceptibility testing
Authors: Schmid Paul J , Forstner Patrick , Kittinger Clemens 
Published: May 2024

Abstract

Background
The glycopeptide vancomycin is the antimicrobial agent-of-choice for the treatment of severe non-gastrointestinal infections with members of Bacillus cereus sensu lato (s.l.). Recently, sporadic detection of vancomycin-resistant phenotypes emerged, mostly for agar diffusion testing such as the disc diffusion method or gradient test (e.g. Etest®) method.

Results
In this work, we were able to disprove a preliminarily assumed high resistance to vancomycin in an isolate of B. cereus s.l. using broth microdilution and agar dilution. Microscopic imaging during vancomycin susceptibility testing showed spreading towards the inhibition zone, which strongly suggested sliding motility. Furthermore, transcriptomic analysis using RNA-Seq on the nanopore platform revealed several key genes of biofilm formation (e.g. calY, tasA, krsEABC) to be up-regulated in pseudo-resistant cells, substantiating that bacterial sliding is responsible for the observed mobility. Down-regulation of virulence (e.g. hblABCD, nheABC, plcR) and flagellar genes compared with swarming cells also confirmed the non-swarming phenotype of the pseudo-resistant isolate.

Conclusions
The results highlight an insufficiency of agar diffusion testing for vancomycin susceptibility in the B. cereus group, and reference methods like broth microdilution are strongly recommended. As currently no guideline mentions interfering phenotypes in antimicrobial susceptibility testing of B. cereus s.l., this knowledge is essential to obtain reliable results on vancomycin susceptibility. In addition, this is the first report of sliding motility undermining accurate antimicrobial susceptibility testing in B. cereus s.l. and may serve as a basis for future studies on bacterial motility in susceptibility testing and its potential impact on treatment efficacy.
Ceftaroline fosamil treatment patterns and outcomes in adults with community-acquired pneumonia: a real-world multinational, retrospective study
Authors: Soriano Alex , Bassetti Matteo , Gogos Charalambos , Ferry Tristan , de Pablo Raul , Ansari Wajeeha , Kantecki Michal , Schweikert Bernd , Luna Gustavo , Blasi Francesco 
Published: May 2024

Abstract

Background
This multicentre, observational, retrospective chart review study assessed ceftaroline fosamil treatment patterns and outcomes in adults hospitalized with community-acquired pneumonia (CAP) in usual care settings.

Methods
Anonymized patient data were extracted from hospital records of adults with CAP who received ≥4 consecutive IV ceftaroline fosamil doses at sites in Brazil, Colombia, France, Greece, Italy, Russia and Spain.

Results
The dataset included 185 patients (58.9% male; mean age 62.2 years), of whom 128 (69.2%) had severe CAP defined by CURB-65, PSI/PORT score or physician judgement. Streptococcus pneumoniae (n = 44; 23.8%) and Staphylococcus aureus [MSSA (n = 15) and MRSA (n = 14)] were the most frequently identified pathogens. Clinical response occurred in 151 (81.6%) patients overall, and in 104 (81.3%) severe CAP patients. Response within ≤4 and &gt;4 days occurred in 79 (42.7%) and 62 (33.5%) patients (unknown, n = 10), respectively. Twenty (10.8%) patients required readmission within 30 days. Thirty-day all-cause mortality rates were 9.7% (n = 18) overall and 10.2% (n = 13) in severe CAP. In sensitivity analysis using ICU admission as a more objective marker of severe CAP (n = 75), clinical response and 30 day mortality occurred in 57 (76.0%) and 10 (13.3%) patients, respectively. Overall, clinical response to ceftaroline fosamil was associated with &gt;60% shorter length of ICU stay (3.6 versus 9.2 days), and &gt;30% lower hospital costs ($8449 versus $12 559) versus non-responders.

Conclusions
Ceftaroline fosamil was effective in treating adults with CAP, including severe CAP, in Europe and Latin America. Clinical response to ceftaroline fosamil was associated with reductions in healthcare resource use compared with non-responders.
Knowledge-guided generative artificial intelligence for automated taxonomy learning from drug labels
Authors: Fang Yilu , Ryan Patrick , Weng Chunhua 
Published: May 2024

Abstract

Objectives
To automatically construct a drug indication taxonomy from drug labels using generative Artificial Intelligence (AI) represented by the Large Language Model (LLM) GPT-4 and real-world evidence (RWE).

Materials and Methods
We extracted indication terms from 46 421 free-text drug labels using GPT-4, iteratively and recursively generated indication concepts and inferred indication concept-to-concept and concept-to-term subsumption relations by integrating GPT-4 with RWE, and created a drug indication taxonomy. Quantitative and qualitative evaluations involving domain experts were performed for cardiovascular (CVD), Endocrine, and Genitourinary system diseases.

Results
2909 drug indication terms were extracted and assigned into 24 high-level indication categories (ie, initially generated concepts), each of which was expanded into a sub-taxonomy. For example, the CVD sub-taxonomy contains 242 concepts, spanning a depth of 11, with 170 being leaf nodes. It collectively covers a total of 234 indication terms associated with 189 distinct drugs. The accuracies of GPT-4 on determining the drug indication hierarchy exceeded 0.7 with “good to very good” inter-rater reliability. However, the accuracies of the concept-to-term subsumption relation checking varied greatly, with “fair to moderate” reliability.

Discussion and Conclusion
We successfully used generative AI and RWE to create a taxonomy, with drug indications adequately consistent with domain expert expectations. We show that LLMs are good at deriving their own concept hierarchies but still fall short in determining the subsumption relations between concepts and terms in unregulated language from free-text drug labels, which is the same hard task for human experts.
Spatial and temporal distribution of Scirtothrips dorsalis (Thysanoptera: Thripidae) and their natural enemies in Florida strawberry fields
Authors: Kaur Gagandeep , Stelinski Lukasz L , Martini Xavier , Boyd Nathan , Mallinger Rachel , Lahiri Sriyanka 
Published: May 2024

Abstract
Given the recent invasion of Scirtothrips dorsalis Hood in North America, there is limited information regarding their distribution and population dynamics in cultivated small fruit crops. Therefore, we investigated the spatial and temporal distribution of S. dorsalis and their natural enemies in commercially produced strawberry fields in Florida. During 2 consecutive strawberry production seasons, 4 and 6 geographically separated strawberry fields were sampled and were divided into grids with 30–40 sampling points per field. At each sampling point, 4–5 leaf and flower samples were collected, and sticky traps were deployed. We quantified the occurrence of S. dorsalis as well as potential natural enemies, including Orius spp., Geocoris spp., and other predators such as long-legged flies. During both years, most of the S. dorsalis and natural enemies were found on field borders, and counts progressively diminished further into the interiors of plots and away from field edges. Cluster and outlier analysis revealed that S. dorsalis formed statistically significant clusters and that these “hot spots” remained in the same general locations throughout the season. There was a strong relationship between the occurrence of natural enemies and the presence of S. dorsalis, but the number of natural enemies was generally low compared to S. dorsalis. Our results indicate that targeting field borders for chemical control or planting strawberries away from natural areas containing potential alternative hosts for thrips may be an effective strategy for reducing agricultural inputs; however, future field assessments are needed to determine if these methods could replace the treatment of entire fields.
Three Early Linguistic Layers in Haredi Hebrew
Authors: Sender Dina 
Published: May 2024

Abstract
A close examination of contemporary Hebrew as spoken by Haredi, or ultra-Orthodox, communities in Israel reveals linguistic layers from several historical and cultural contexts. This article looks at elements from three of these layers: Jewish religious literature, the Yiddish language and outdated Israeli Hebrew. An analysis of these elements sheds light on how Haredi Hebrew differs from ‘general’ Israeli Hebrew and how these differences reflect linguistic perceptions and socio-cultural values that distinguish Haredim from the broader Israeli population. In addition to demonstrating the intricate interplay between language and society, analysis offers insight into the dynamic nature of Hebrew language evolution.
Prevalence of PTSD in Active Duty Members with Mild Traumatic Brain Injury: Systematic Review and Meta-analysis
Authors: Lai Choang , Kostas-Polston Elizabeth A , Engler Mary B , Capple Kathryn A , Froelicher Erika Sivarajan 
Published: May 2024

ABSTRACT

Introduction
Traumatic brain injury (TBI), particularly mild TBI (mTBI), is a significant health concern for U.S. active duty service members (ADSMs), with potential implications for psychiatric outcomes including PTSD. Despite recognizing this association, the prevalence of PTSD among ADSMs with mTBI remains unclear.

Materials and Methods
The review followed the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. A thorough search in PubMed, CINAHL, Embase, and PsycINFO databases from 2008 to 2024 focused on identifying studies involving ADSMs with PTSD and mTBI. The R software (version 4.3.2) was employed for meta-analysis with the “meta” and “meta prop” packages.

Results
Eight reviewed studies revealed a pooled prevalence estimate of PTSD among ADSMs with mTBI at 36% (95% CI, 30%-41%, P &lt; .01, I2 = 96%). Cohort studies indicated a slightly higher prevalence of 38% (95% CI, 19%-59%, P &lt; .01, I2 = 98%), whereas cross-sectional studies provided a marginally lower prevalence of 34% (95% CI, 27%-40%, P &lt; .01, I2 = 92%).

Conclusion
Methodological differences, including diagnostic criteria variability, contribute to the observed variability in prevalence estimates. Despite methodological challenges, this study provides crucial insights into the pooled prevalence of comorbid PTSD and mTBI within the military, emphasizing the need for standardized methodologies and further research to refine understanding and support strategies for affected individuals.
Primordial aminoacyl-tRNA synthetases preferred minihelices to full-length tRNA
Authors: Tang Guo Qing , Hu Hao , Douglas Jordan , Carter Charles W 
Published: May 2024

Abstract
Aminoacyl-tRNA synthetases (AARS) and tRNAs translate the genetic code in all living cells. Little is known about how their molecular ancestors began to enforce the coding rules for the expression of their own genes. Schimmel et al. proposed in 1993 that AARS catalytic domains began by reading an ‘operational’ code in the acceptor stems of tRNA minihelices. We show here that the enzymology of an AARS urzyme•TΨC-minihelix cognate pair is a rich in vitro realization of that idea. The TΨC-minihelixLeu is a very poor substrate for full-length Leucyl-tRNA synthetase. It is a superior RNA substrate for the corresponding urzyme, LeuAC. LeuAC active-site mutations shift the choice of both amino acid and RNA substrates. AARS urzyme•minihelix cognate pairs are thus small, pliant models for the ancestral decoding hardware. They are thus an ideal platform for detailed experimental study of the operational RNA code.
SeqCAT: Sequence Conversion and Analysis Toolbox
Authors: Kornrumpf Kevin , Kurz Nadine S , Drofenik Klara , Krauß Lukas , Schneider Carolin , Koch Raphael , Beißbarth Tim , Dönitz Jürgen 
Published: May 2024

Abstract
Dealing with sequence coordinates in different formats and reference genomes is challenging in genetic research. This complexity arises from the need to convert and harmonize datasets of different sources using alternating nomenclatures. Since manual processing is time-consuming and requires specialized knowledge, the Sequence Conversion and Analysis Toolbox (SeqCAT) was developed for daily work with genetic datasets. Our tool provides a range of functions designed to standardize and convert gene variant coordinates based on various sequence types. Its user-friendly web interface provides easy access to all functionalities, while the Application Programming Interface (API) enables automation within pipelines. SeqCAT provides access to human genomic, protein and transcript data, utilizing various data resources and packages and extending them with its own unique features. The platform covers a wide range of genetic research needs with its 14 different applications and 3 info points, including search for transcript and gene information, transition between reference genomes, variant mapping, and genetic event review. Notable examples are ‘Convert Protein to DNA Position’ for translation of amino acid changes into genomic single nucleotide variants, or ‘Fusion Check’ for frameshift determination in gene fusions. SeqCAT is an excellent resource for converting sequence coordinate data into the required formats and is available at: https://mtb.bioinf.med.uni-goettingen.de/SeqCAT/.
ChemFH: an integrated tool for screening frequent false positives in chemical biology and drug discovery
Authors: Shi Shaohua , Fu Li , Yi Jiacai , Yang Ziyi , Zhang Xiaochen , Deng Youchao , Wang Wenxuan , Wu Chengkun , Zhao Wentao , Hou Tingjun , Zeng Xiangxiang , Lyu Aiping , Cao Dongsheng 
Published: May 2024

Abstract
High-throughput screening rapidly tests an extensive array of chemical compounds to identify hit compounds for specific biological targets in drug discovery. However, false-positive results disrupt hit compound screening, leading to wastage of time and resources. To address this, we propose ChemFH, an integrated online platform facilitating rapid virtual evaluation of potential false positives, including colloidal aggregators, spectroscopic interference compounds, firefly luciferase inhibitors, chemical reactive compounds, promiscuous compounds, and other assay interferences. By leveraging a dataset containing 823 391 compounds, we constructed high-quality prediction models using multi-task directed message-passing network (DMPNN) architectures combining uncertainty estimation, yielding an average AUC value of 0.91. Furthermore, ChemFH incorporated 1441 representative alert substructures derived from the collected data and ten commonly used frequent hitter screening rules. ChemFH was validated with an external set of 75 compounds. Subsequently, the virtual screening capability of ChemFH was successfully confirmed through its application to five virtual screening libraries. Furthermore, ChemFH underwent additional validation on two natural products and FDA-approved drugs, yielding reliable and accurate results. ChemFH is a comprehensive, reliable, and computationally efficient screening pipeline that facilitates the identification of true positive results in assays, contributing to enhanced efficiency and success rates in drug discovery. ChemFH is freely available via https://chemfh.scbdd.com/.
Histone deacetylase Hos2 regulates protein expression noise by potentially modulating the protein translation machinery
Authors: Lin Wei-Han , Opoc Florica J G , Liao Chia-Wei , Roy Kevin R , Steinmetz Lars M , Leu Jun-Yi 
Published: May 2024

Abstract
Non-genetic variations derived from expression noise at transcript or protein levels can result in cell-to-cell heterogeneity within an isogenic population. Although cells have developed strategies to reduce noise in some cellular functions, this heterogeneity can also facilitate varying levels of regulation and provide evolutionary benefits in specific environments. Despite several general characteristics of cellular noise having been revealed, the detailed molecular pathways underlying noise regulation remain elusive. Here, we established a dual-fluorescent reporter system in Saccharomyces cerevisiae and performed experimental evolution to search for mutations that increase expression noise. By analyzing evolved cells using bulk segregant analysis coupled with whole-genome sequencing, we identified the histone deacetylase Hos2 as a negative noise regulator. A hos2 mutant down-regulated multiple ribosomal protein genes and exhibited partially compromised protein translation, indicating that Hos2 may regulate protein expression noise by modulating the translation machinery. Treating cells with translation inhibitors or introducing mutations into several Hos2-regulated ribosomal protein genes—RPS9A, RPS28B and RPL42A—enhanced protein expression noise. Our study provides an effective strategy for identifying noise regulators and also sheds light on how cells regulate non-genetic variation through protein translation.
IRF2BP2 counteracts the ATF7/JDP2 AP-1 heterodimer to prevent inflammatory overactivation in acute myeloid leukemia (AML) cells
Authors: Fischer Sabrina , Weber Lisa Marie , Stielow Bastian , Frech Miriam , Simon Clara , Geller Merle , Könnecke Julie , Finkernagel Florian , Forné Ignasi , Nist Andrea , Bauer Uta-Maria , Stiewe Thorsten , Neubauer Andreas , Liefke Robert 
Published: May 2024

Abstract
Acute myeloid leukemia (AML) is a hematological malignancy characterized by abnormal proliferation and accumulation of immature myeloid cells in the bone marrow. Inflammation plays a crucial role in AML progression, but excessive activation of cell-intrinsic inflammatory pathways can also trigger cell death. IRF2BP2 is a chromatin regulator implicated in AML pathogenesis, although its precise role in this disease is not fully understood. In this study, we demonstrate that IRF2BP2 interacts with the AP-1 heterodimer ATF7/JDP2, which is involved in activating inflammatory pathways in AML cells. We show that IRF2BP2 is recruited by the ATF7/JDP2 dimer to chromatin and counteracts its gene-activating function. Loss of IRF2BP2 leads to overactivation of inflammatory pathways, resulting in strongly reduced proliferation. Our research indicates that a precise equilibrium between activating and repressive transcriptional mechanisms creates a pro-oncogenic inflammatory environment in AML cells. The ATF7/JDP2-IRF2BP2 regulatory axis is likely a key regulator of this process and may, therefore, represent a promising therapeutic vulnerability for AML. Thus, our study provides new insights into the molecular mechanisms underlying AML pathogenesis and identifies a potential therapeutic target for AML treatment.
Evolution of grain size distribution in the circumgalactic medium
Authors: Hirashita Hiroyuki 
Published: May 2024

Abstract
In order to theoretically understand dust properties in the circumgalactic medium (CGM), we construct a dust evolution model that incorporates the evolution of grain size distribution. We treat the galaxy and the CGM as separate one-zone objects, and consider the mass exchange between them. We take into account dust production and interstellar dust processing for the galaxy based on our previous models, and newly incorporate sputtering in the hot phase and shattering in the cool phase for the CGM. We find that shattering increases the dust destruction (sputtering) efficiency in the CGM. The functional shape of the grain size distribution in the CGM evolves following that in the galaxy, but it is sensitive to the balance between sputtering and shattering in the CGM. For an observational test, we discuss the wavelength dependence of the reddening in the CGM traced by background quasar colors, arguing that, in order to explain the observed reddening level, a rapid inflow from the CGM to the galaxy is favored because of quick dust/metal enrichment. Small grain production by shattering in the CGM also helps to explain the rise of dust extinction toward short wavelengths.