bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of tissue type and season on the detection of regulated sugarcane viruses by high throughput sequencing
Authors: Bolus Stephen , Wathen-Dunn Kate , Grinstead Samuel C. , Hu Xiaojun , Malapi Martha , Mollov Dimitre 
Published: September 2023

AbstractHigh throughput sequencing (HTS) can supplement and may replace diagnostic tests for plant pathogens. However, the methodology and processing of HTS data must first be optimized and standardized to ensure the sensitivity and repeatability of the results. Importation of sugarcane into the United States is highly regulated, and sugarcane plants are subjected to strict quarantine measures and diagnostic testing, especially for the presence of certain viruses of regulatory concern. Here, we tested whether HTS could reliably detect four RNA and three DNA sugarcane viruses over three seasons (fall, winter, and spring) and in three tissue types (root, stem, and leaves). Using HTS on ribosomal depleted total RNA samples, we reliably detected RNA viruses in all tissue types and across all seasons, but we failed to confidently detect DNA viruses in some samples. We recommend that future optimization be employed to ensure the robust and reliable detection of all regulated sugarcane viruses by HTS.
Dissociation between neuroanatomical and symptomatic subtypes in schizophrenia
Authors: Chai Chao , Ding Hao , Du Xiaotong , Xie Yingying , Man Weiqi , Zhang Yu , Ji Yi , Liang Meng , Zhang Bin , Ning Yuping , Zhuo Chuanjun , Yu Chunshui , Qin Wen 
Published: September 2023

Abstract

Background
Schizophrenia is a complex and heterogeneous syndrome with high clinical and biological stratification. Identifying distinctive subtypes can improve diagnostic accuracy and help precise therapy. A key challenge for schizophrenia subtyping is understanding the subtype-specific biological underpinnings of clinical heterogeneity. This study aimed to investigate if the machine learning (ML)-based neuroanatomical and symptomatic subtypes of schizophrenia are associated.

Methods
A total of 314 schizophrenia patients and 257 healthy controls from four sites were recruited. Gray matter volume (GMV) and Positive and Negative Syndrome Scale (PANSS) scores were employed to recognize schizophrenia neuroanatomical and symptomatic subtypes using K-means and hierarchical methods, respectively.

Results
Patients with ML-based neuroanatomical subtype-1 had focally increased GMV, and subtype-2 had widespread reduced GMV than the healthy controls based on either K-means or Hierarchical methods. In contrast, patients with symptomatic subtype-1 had severe PANSS scores than subtype-2. No differences in PANSS scores were shown between the two neuroanatomical subtypes; similarly, no GMV differences were found between the two symptomatic subtypes. Cohen’s Kappa test further demonstrated an apparent dissociation between the ML-based neuroanatomical and symptomatic subtypes (P > 0.05). The dissociation patterns were validated in four independent sites with diverse disease progressions (chronic vs. first episodes) and ancestors (Chinese vs. Western).

Conclusions
These findings revealed a replicable dissociation between ML-based neuroanatomical and symptomatic subtypes of schizophrenia, which provides a new viewpoint toward understanding the heterogeneity of schizophrenia.
Generalizability of Self-Supervised Training Models for Digital Pathology: A Multicountry Comparison in Colorectal Cancer
Authors: Shao Zhuchen , Dai Liuxi , Jonnagaddala Jitendra , Chen Yang , Wang Yifeng , Fang Zijie , Zhang Yongbing 
Published: September 2023

PURPOSE In this multicountry study, we aim to explore the effectiveness of self-supervised learning (SSL) in colorectal cancer (CRC)–related predictive tasks using large amount of unlabeled digital pathology imaging data. METHODS We adopted SimSiam to conduct self-supervised pretraining on two large whole-slide image CRC data sets from the United States and Australia. The SSL pretrained encoder is then used in several predictive tasks, including supervised predictive tasks (tissue classification, microsatellite instability v microsatellite stability classification), and weakly supervised predictive tasks (polyp type classification and adenoma grading, and 5-year survival prediction). Performance on the tasks was compared between models using SSL pretraining and those using ImageNet pretraining, and performance for one-country pretraining was compared with two-country pretraining. RESULTS We demonstrate that SSL pretraining outperforms ImageNet pretraining in predictive tasks, that is, SSL pretraining outperforms the ImageNet pretraining by 3.01% of [Formula: see text] score on average over supervised predictive tasks and 1.53% of AUC on average over weakly supervised predictive tasks. Furthermore, two-country SSL pretraining has shown more stable performance than single-country pretraining, that is, two-country pretraining outperforms at least one of the single-country pretrainings by 1.93% of [Formula: see text] on average over supervised predictive tasks and 1.36% of AUC on average over weakly-supervised predictive tasks. CONCLUSION We find that using unlabeled image data for SSL pretraining in CRC related tasks is more effective than using ImageNet pretraining. Furthermore, SSL pretraining using data from multiple countries achieve more stable performance and better generalization than single-country pretraining.
Tirzepatide Immunogenicity on Pharmacokinetics, Efficacy, and Safety: Analysis of Data From Phase 3 Studies
Authors: Mullins Garrett R , Hodsdon Michael E , Li Ying Grace , Anglin Greg , Urva Shweta , Schneck Karen , Bardos Jennifer N , Martins Ricardo Fonseca , Brown Katelyn , Calderon Boris 
Published: September 2023

Abstract

Context
Antidrug antibodies (ADA) can potentially affect drug pharmacokinetics, safety, and efficacy.

Objective
This work aimed to evaluate treatment-emergent (TE) ADA in tirzepatide (TZP)-treated participants across 7 phase 3 trials and their potential effect on pharmacokinetics, efficacy, and safety.

Methods
ADA were assessed at baseline and throughout the study until end point, defined as week 40 (SURPASS-1, -2, and -5) or week 52 (SURPASS-3, -4, Japan-Mono, and Japan-Combo). Samples for ADA characterization were collected at SURPASS trial sites. Participants included ADA-evaluable TZP-treated patients with type 2 diabetes (N = 5025). Interventions included TZP 5, 10, or 15 mg. ADA were detected and characterized for their ability to cross-react with native glucose-dependent insulinotropic polypeptide (nGIP) and glucagon-like peptide-1 (nGLP-1), neutralize tirzepatide activity on GIP and GLP-1 receptors, and neutralize nGIP and nGLP-1.

Results
TE ADA developed in 51.1% of tirzepatide-treated patients. Proportions were similar across dose groups. Maximum ADA titers ranged from 1:20 to 1: 81 920 among TE ADA+ patients. Neutralizing antibodies (NAb) against TZP activity on GIP and GLP-1 receptors were observed in 1.9% and 2.1% of patients, respectively. Less than 1.0% of patients had cross-reactive NAb against nGIP or nGLP-1. TE ADA status, ADA titer, and NAb status had no effect on the pharmacokinetics or efficacy of TZP. More TE ADA+ patients experienced hypersensitivity reactions or injection site reactions than TE ADA– patients. The majority of hypersensitivity and injection site reactions were nonserious and nonsevere, and most events occurred and/or resolved irrespective of TE ADA status or titer.

Conclusion
Immunogenicity did not affect TZP pharmacokinetics or efficacy. The majority of hypersensitivity or injection site reactions experienced by TE ADA+ patients were mild to moderate in severity.
Cripping the Archive: Analyzing Archival Disorder in the Yamashita Family Archives and Karen Tei Yamashita’sLetters to Memory
Authors: Stefan Hayley C. 
Published: September 2023

AbstractThis article outlines a crip archival analysis of Karen Tei Yamashita’s creative family memoir Letters to Memory (2017) and the separate Yamashita Family Archives; the analysis revolves around the concept of disorder. The book and digital archives move the daily lived experience of incarceration out of chronological order, encouraging new connections across a massive collection of materials: letters, photographs, federal surveillance documents, paintings, sermons, and other ephemera surrounding World War II Japanese American incarceration. Their respective acts of assembling and retelling destabilize the dominant narrative of a resolved family or national trauma to reflect divergent embodied experiences of distress and disability effected by racial debilitation. Offering concentric analysis of textual and archival reordering via Asian American studies, disability studies, and digital humanities, this article adds alternative dimensions to the ongoing legacy of incarceration by inviting readers to create new constellations of meaning through examining temporal and embodied disorder. Reading the physical book and digital archives together also acts as a model for how literary studies scholars might complicate our attention to embodiment beyond narrative analysis, by thinking about disability and madness in the design and structure of texts and digital media. Through cripping the archive, the author calls for a reconceptualization of mad and disabled bodyminds as not only content to be examined, but also users and creators whose disorder animates alternative ways of knowing personal and state violence.
Structural Effect of Water-Soluble Zinc Porphyrins in a Visible-Light Driven NADH Regeneration System Catalyzed by Rhodium Pentamethylcyclopentadienyl Complex
Authors: Takeuchi Mika , Amao Yutaka 
Published: September 2023

Abstract
The effect of ionic substituents (4-sulfonatophenyl, 4-carboxyphenyl, 4-methylpyridyl, and 4-N,N,N-trimethylaminophenyl-groups) of water-soluble zinc porphyrin (ZnP) on the visible light-driven NADH regeneration by a system of triethanolamine, ZnP, and rhodium complex [Cp*Rh(bpy)(H2O)]2+ (Cp* = pentamethylcyclopentadienyl, bpy = 2,2′-bipyridyl) was studied to provide significant guidance for hybridization with a wide range of oxidoreductases.
Vertical Jump Testing after Anterior Cruciate Ligament Reconstruction: A Systematic Review and Meta-analysis
Authors: DUTAILLIS BENJAMIN , DIAMOND LAURA E. , LAZARCZUK STEPHANIE L. , TIMMINS RYAN G. , BOURNE MATTHEW N. 
Published: September 2023

ABSTRACT

Introduction
Recently, there has been a call for vertical jump testing via force–plate analysis to be included in the assessment of individuals after anterior cruciate ligament reconstruction (ACLR) and as part of return-to-play criteria. However, a synthesis of current literature is needed to help guide clinicians on what tests to perform, which force–plate metrics to assess, and how these may change over the time course of rehabilitation.

Methods
Four online databases were searched from inception to July 2022. The Downs and Black checklist was used to assess study quality. Multilevel meta-analyses and meta-regressions were undertaken in conjunction with a best evidence synthesis.

Results
Forty-two articles were included, capturing 2375 participants with a history of ACLR. Reconstructed limbs displayed 1) lower peak eccentric forces, concentric forces, landing forces, and lower eccentric and concentric impulses (standardized means difference [SMD] = −1.84 to −0.46) than uninjured contralateral limbs during bilateral countermovement jumps (CMJ) and drop vertical jumps (DVJ); 2) lower jump heights and reactive strength indices (RSI), and longer contact times than uninjured contralateral limbs during unilateral CMJ and DVJ (SMD = −0.86 to 0.26); and 3) lower jump heights, RSI, and longer contact times during bilateral and unilateral CMJ, and unilateral DVJ, than uninjured controls (SMD = −1.19 to 1.08). Meta-regression revealed that time postsurgery was a significant moderator (P < 0.05) for 1) bilateral CMJ height, peak concentric force, and peak landing force; 2) between-limb differences in unilateral CMJ height; and 3) differences in unilateral DVJ height, RSI, and contact time between reconstructed limbs and healthy controls with no history of injury.

Conclusions
Individuals with a history of ACLR display chronic deficits in vertical jumping performance during a range of bilateral and unilateral tasks, which may have implications for return-to-play criteria and the design of interventions targeted at restoring long-term deficits in explosive lower limb strength after ACLR.
A realist process evaluation of an intervention to promote competencies in interprofessional collaboration among interdisciplinary integrated care teams for older people: Study protocol.
Authors: O'Donnell Deirdre , Ahern Emer , Davies Carmel , De Brún Aoife , Donnelly Sarah , Doran Thelma , Drury Anne , Dunne Nikki , Finucane Lillian , Harnett PJ , Harrison Reema , Lang Deirdre , McAuliffe Eilish , McCarthy Mary , McGuigan Catherine , Ní Shé Éidín , O'Donoghue Gráinne , O'Shea Marie , Radomska Apolonia , Travers John , Whitty Helen , Devaney Catherine 
Published: September 2023

Background: International policy is increasingly committed to placing interdisciplinary team-working at the centre of health and social care integration across the lifespan. The National Clinical Programme for Older People in Ireland has a critical role in the design and implementation of the National Older Person’s Service Model, which aims to shift the delivery of care away from acute hospitals towards community-based care. Interdisciplinary Community Specialist Teams for older persons (CST-OPs) play an important role in this service model. To support the development of competencies for interprofessional collaboration and an interdisciplinary team-based approach to care integration, a culture shift will be required within care delivery. Design: This study builds upon a collaborative partnership project which co-designed a framework describing core competencies for interprofessional collaboration in CST-OPs. A realist-informed process evaluation of the framework will be undertaken as the competencies described in the framework are being fostered in newly developed CST-OPs under the national scale-up of the service model. Realist evaluation approaches reveal what worked, why it worked (or did not), for whom and under what circumstances. Three iterative and integrated work packages are proposed which combine multiple methods of data collection, analysis and synthesis. Prospective data collection will be undertaken within four CST-OPs, including qualitative exploration of the care experiences of older people and family carers. Discussion: The realist explanatory theory will provide an understanding of how interprofessional collaboration can be fostered and sustained in various contexts of care integration for older people. It will underpin curriculum development for team-based education and training of health and social care professionals, a key priority area in the national Irish health strategy. It will provide healthcare leaders with knowledge of the resources and supports required to harness the benefits of interprofessional collaboration and to realise the goals of integrated care for older people.
Lab-scale and on-field industrial composting of biodegradable plastic blends for packaging
Authors: Chong Zhi Kai , Hofmann Alexander , Haye Marie , Wilson Sharon , Sohoo Ihsanullah , Alassali Ayah , Kuchta Kerstin 
Published: September 2023

Background: The acceptance of compostable plastic packaging in industrial composting plants is not universal despite available certification due to the persistence of plastic residues after composting. To better understand this discrepancy, this study compared the disintegration rates of two blends designed for rigid packaging (polylactic acid based) and soft packaging (polybutylene succinate based) in lab-scale composting tests and in an industrial composting plant. Methods: A lab-scale composting test was conducted in triplicates according to ISO 20200 for 4, 8 and 12 weeks to check the disintegration potential of the blends. Duplicate test material were then exposed in the compost pile of an industrial composting plant for a duration of 3 weeks and compared with a supplementary lab-scale test of the same duration. Results: The rigid packaging samples (1 mm thickness) retained on average 76.4%, 59.0% and 55.7% of its mass after 4, 8 and 12 weeks respectively in the lab-scale. In the plant, the remaining mass was 97.2% and 99.5%, much higher compared to the average of 68.9% after 3 weeks in the supplementary lab-scale test. The soft packaging samples (109±9 µm sample thickness) retained on average 45.4%, 10.9% and 0.3% of its mass after 4, 8 and 12 weeks respectively in the lab-scale. In the plant, a high remaining mass was also observed (94.0% and 93.8%). The supplementary lab-scale test showed similar remaining mass but higher fragmentation after 3 weeks. Conclusions: The results show that the samples achieved significant disintegration in the lab-scale but not in the plant. The difference between the tests that might further contribute to the differing degradation rates is the composition and heterogeneity of the composting substrate. Therefore, the substrate composition and thermophilic composting duration of individual plants are important considerations to determine the suitability of treating compostable plastic in real-world conditions.
Rotate: A command-line program to rotate circular DNA sequences to start at a given position or string
Authors: Durbin Richard , De Sanctis Bianca , Blumer Moritz 
Published: September 2023

Sequences derived from circular DNA molecules (i.e. most bacterial, viral and plastid genomes) are expected to be linearised and rotated to a common start position for most downstream analyses including alignment. Despite this being a common and straightforward task, available software is either limited to a small number of input sequences, lacks the option to specify a custom anchor string, or requires a commercial license. Here, we present rotate, a simple, open source command line program written in C with no external dependencies, which can rotate a set of input sequences to a custom anchor string (allowing for a specified number of mismatches), or offset the input sequences to the desired position. The combination of both functionalities allows the rotation of all input sequences to any desired starting position, enabling downstream analysis. rotate is extremely fast and scales linearly with the number of input sequences, taking only seconds to rotate over a thousand mitochondrial sequences.
STUDY OF TRENDS IN THE INFLUENCE OF A UNIVERSITY TEACHER’S LEVEL OF PROFESSIONAL IDENTIFICATION ON THE FEATURES OF SELF-ATTITUDE MANIFESTATION
Authors: Busygina Tatyana A. 
Published: September 2023

Цель. В статье анализируется взаимосвязь особенностей самоотношения преподавателя вуза и профессиональной идентификации. Раскрываются основные подходы в изучении полюсов самоотношения педагогов, особенности взаимодействия и взаимовлияния с профессиональным самосознанием. Осознание тождественности с профессией, положительное отношение педагога к себе как к профессионалу повышает уровень самоуважения, генерализованно распространяясь на позитивное, принимающее отношение к себе на уровне личности.
Но наряду с позитивным профессиональным сценарием, в жизни преподавателя мы можем наблюдать проявления кризисных аспектов, истоки которых содержатся в негативном полюсе самоотношения – низком интересе к своей личности, разочаровании в себе, низком уровне самоуважения, самокритике, невыраженном контакте с пониманием и осознанием своих желаний, потребностей, аспектов эмоционально-чувственной сферы.
Методология проведения работы. В процессе исследования был проведен теоретический анализ литературных источников. Эмпирическое исследование, выявляющее взаимосвязь полюса самоотношения от уровня профессиональной идентификации, было проведено на выборке из 130 преподавателей российских вузов обоих полов со стажем более 18лет с помощью психодиагностических методик. Количественная обработка результатов произведена на базе статистических программы STATISTICA 6.0.
Результаты. В результате эмпирического исследования нами были получены выводы о том, что преподаватель с развитой профессиональной идентификацией может опираться на нее как на фактор, способствующий самопринятию, самоуважению и самореализации.
Психологическая работа с негативным и позитивным полюсом самоотношения может стать мерой предупреждении эмоционального выгорания и успешного выхода из кризисных состояний.
Область применения результатов. Результаты исследования помогут углубить представления о значимости психологической работы со стрессовыми ситуациями, развитием позитивного самоотношения, самоуважения, самоинтереса на базе укрепления профессионального самосознания педагогов, а также в создании психологических программ по развитию эмоциональной компетентности и профилактике профессионального выгорания преподавателей вузов
LEVELS OF SITUATIONAL AND PERSONAL ANXIETY IN YOUNG MEN WITH INTERNET ADDICTION STUDYING AT A MEDICAL UNIVERSITY
Authors: Yaskevich Roman A. , Moskalenko Olga L. 
Published: September 2023

Purpose. To study the influence of Internet addiction on indicators of situational and personal anxiety in young men studying at a medical university.
Materials and methods. The study included 66 male students enrolled in the 3rd year of the Medical Faculty of the Medical University. To assess the level of Internet addiction, we used the CIAS scale (Chen Internet addiction Scale) adapted by V.L. Malygin and K.A. Feklisov To identify and assess the severity of situational (reactive) and personal anxiety, we used the STAI (State-Trait Anxiety Inventory) scale of self-assessment of the anxiety level by C.D. Spielberger in the modification of Yu.L. Khanin.
Results. Among the young men studying at the medical university – 94,8% of the surveyed had different levels of personal anxiety, among which the share of persons with high levels accounted for more than a third – 36,2%. A pronounced and stable pattern of Internet addictive behavior according to the CIAS scale was found in 6.9% of the surveyed young men studying at a medical university. It was found that all young men (100%) with a pronounced and stable pattern of Internet addiction noted high levels of personal anxiety.
Conclusion. High levels of personal anxiety were revealed in young men with a pronounced and stable pattern of Internet addiction
Political Media Rhetoric: an Integrated Approach to The Study of Speech Practices in Political Media Discourse
Authors: Dobrosklonskaya T. , Loginova Polina 
Published: September 2023

The article outlines a new integrated approach to the study of political media communications, represented as a separate discipline — political media rhetoric. The academic demand for media rhetoric as a new branch of media linguistic and rhetoric studies is determined by the growing interest to the rhetoric aspect of political media discourse and hence the necessity of introducing a complex systemic approach to its analysis. The theory of political media rhetoric is constructed on the basis of key assumptions of classical rhetoric, media linguistics, media stylistics and other disciplines related to the study of media discourse in the aspect of political communications.
The article defines historical roots of the formation of media rhetoric,
its academic goals, methodology, and its place within general structure of humanities. The subject of political media rhetoric is the actualization of different speech rhetorical practices in the sphere of political media discourse.
The basic category of political media rhetoric is represented by a polycode multimodal rhetoric mediatext, functioning within the system of political media communications. The research potential of political media rhetoric has been analyzed on the material of public speeches of the French modern politicians. The conducted research shows that the terminology and methodology of political media rhetoric can be effectively applied as a complex systemic approach to the study of rhetoric media practices in the sphere of political media communications.