bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tra1 controls the transcriptional landscape of the aging cell
Authors: Bari Khaleda Afrin , Berg Matthew D , Genereaux Julie , Brandl Christopher J , Lajoie Patrick 
Published: October 2022

Abstract
Gene expression undergoes considerable changes during the aging process. The mechanisms regulating the transcriptional response to cellular aging remain poorly understood. Here, we employ the budding yeast Saccharomyces cerevisiae to better understand how organisms adapt their transcriptome to promote longevity. Chronological lifespan assays in yeast measure the survival of nondividing cells at stationary phase over time, providing insights into the aging process of postmitotic cells. Tra1 is an essential component of both the yeast Spt-Ada-Gcn5 acetyltransferase/Spt-Ada-Gcn5 acetyltransferase-like and nucleosome acetyltransferase of H4 complexes, where it recruits these complexes to acetylate histones at targeted promoters. Importantly, Tra1 regulates the transcriptional response to multiple stresses. To evaluate the role of Tra1 in chronological aging, we took advantage of a previously characterized mutant allele that carries mutations in the TRA1 PI3K domain (tra1Q3). We found that loss of functions associated with tra1Q3 sensitizes cells to growth media acidification and shortens lifespan. Transcriptional profiling reveals that genes differentially regulated by Tra1 during the aging process are enriched for components of the response to stress. Notably, expression of catalases (CTA1, CTT1) involved in hydrogen peroxide detoxification decreases in chronologically aged tra1Q3 cells. Consequently, they display increased sensitivity to oxidative stress. tra1Q3 cells are unable to grow on glycerol indicating a defect in mitochondria function. Aged tra1Q3 cells also display reduced expression of peroxisomal genes, exhibit decreased numbers of peroxisomes, and cannot grow on media containing oleate. Thus, Tra1 emerges as an important regulator of longevity in yeast via multiple mechanisms.
Rat Mammary carcinoma susceptibility 3 (Mcs3) pleiotropy, socioenvironmental interaction, and comparative genomics with orthologous human 15q25.1-25.2
Authors: Duderstadt Emily L , Samuelson David J 
Published: October 2022

Abstract
Genome-wide association studies of breast cancer susceptibility have revealed risk-associated genetic variants and nominated candidate genes; however, the identification of causal variants and genes is often undetermined by genome-wide association studies. Comparative genomics, utilizing Rattus norvegicus strains differing in susceptibility to mammary tumor development, is a complimentary approach to identify breast cancer susceptibility genes. Mammary carcinoma susceptibility 3 (Mcs3) is a Copenhagen (COP/NHsd) allele that confers resistance to mammary carcinomas when introgressed into a mammary carcinoma susceptible Wistar Furth (WF/NHsd) genome. Here, Mcs3 was positionally mapped to a 7.2-Mb region of RNO1 spanning rs8149408 to rs107402736 (chr1:143700228–150929594, build 6.0/rn6) using WF.COP congenic strains and 7,12-dimethylbenz(a)anthracene-induced mammary carcinogenesis. Male and female WF.COP-Mcs3 rats had significantly lower body mass compared to the Wistar Furth strain. The effect on female body mass was observed only when females were raised in the absence of males indicating a socioenvironmental interaction. Furthermore, female WF.COP-Mcs3 rats, raised in the absence of males, did not develop enhanced lobuloalveolar morphologies compared to those observed in the Wistar Furth strain. Human 15q25.1-25.2 was determined to be orthologous to rat Mcs3 (chr15:80005820–82285404 and chr15:83134545–84130720, build GRCh38/hg38). A public database search of 15q25.1-25.2 revealed genome-wide significant and nominally significant associations for body mass traits and breast cancer risk. These results support the existence of a breast cancer risk-associated allele at human 15q25.1-25.2 and warrant ultrafine mapping of rat Mcs3 and human 15q25.1-25.2 to discover novel causal genes and variants.
Post-operative anastomotic leakage and collagen changes in patients with rectal cancer undergoing neoadjuvant chemotherapy vs chemoradiotherapy
Authors: Jiang Wei , Wang Huaiming , Zheng Jixiang , Zhao Yandong , Xu Shuoyu , Zhuo Shuangmu , Wang Hui , Yan Jun 
Published: October 2022

Abstract

Background
A significant difference in the anastomotic leakage (AL) rate has been observed between patients with locally advanced rectal cancer who have undergone preoperative chemotherapy and those undergoing preoperative chemoradiotherapy. This study aimed to quantitatively analyse collagen structural changes caused by preoperative chemoradiotherapy and illuminate the relationship between collagen changes and AL.

Methods
Anastomotic distal and proximal “doughnut” specimens from the Sixth Affiliated Hospital of Sun Yat-sen University (Guangzhou, China) were quantitatively assessed for collagen structural changes between patients with and without preoperative radiotherapy using multiphoton imaging. Then, patients treated with preoperative chemoradiotherapy were used as a training cohort to construct an AL–SVM classifier by the Mann–Whitney U test and support vector machine (SVM). An independent test cohort from the Fujian Province Cancer Hospital (Fuzhou, China) was used to validate the AL–SVM classifier.

Results
A total of 207 patients were included from the Sixth Affiliated Hospital of Sun Yat-sen University. The AL rate in the preoperative chemoradiotherapy group (n = 107) was significantly higher than that in the preoperative chemotherapy group (n = 100) (21.5% vs 7.0%, P = 0.003). A fully quantitative analysis showed notable morphological and spatial distribution feature changes in collagen in the preoperative chemoradiotherapy group. Then, the patients who received preoperative chemoradiotherapy were used as a training cohort to construct the AL–SVM classifier based on five collagen features and the tumor distance from the anus. The AL–SVM classifier showed satisfactory discrimination and calibration with areas under the curve of 0.907 and 0.856 in the training and test cohorts, respectively.

Conclusions
The collagen structure may be notably altered by preoperative radiotherapy. The AL–SVM classifier was useful for the individualized prediction of AL in rectal cancer patients undergoing preoperative chemoradiotherapy.
SARS-CoV-2 Serosurveys: How Antigen, Isotype and Threshold Choices Affect the Outcome
Authors: Binder Raquel A , Fujimori Gavin F , Forconi Catherine S , Reed George W , Silva Leandro S , Lakshmi Priya Saikumar , Higgins Amanda , Cincotta Lindsey , Dutta Protiva , Salive Marie-Claire , Mangolds Virginia , Anya Otuwe , Calvo Calle J Mauricio , Nixon Thomas , Tang Qiushi , Wessolossky Mireya , Wang Yang , Ritacco Dominic A , Bly Courtney S , Fischinger Stephanie , Atyeo Caroline , Oluoch Peter O , Odwar Boaz , Bailey Jeffrey A , Maldonado-Contreras Ana , Haran John P , Schmidt Aaron G , Cavacini Lisa , Alter Galit , Moormann Ann M 
Published: October 2022

Abstract

Background
Evaluating the performance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) serological assays and clearly articulating the utility of selected antigens, isotypes, and thresholds is crucial to understanding the prevalence of infection within selected communities.

Methods
This cross-sectional study, implemented in 2020, screened PCR–confirmed coronavirus disease 2019 patients (n = 86), banked prepandemic and negative samples (n = 96), healthcare workers and family members (n = 552), and university employees (n = 327) for anti–SARS-CoV-2 receptor-binding domain, trimeric spike protein, and nucleocapsid protein immunoglobulin (Ig)G and IgA antibodies with a laboratory-developed enzyme-linked immunosorbent assay and tested how antigen, isotype and threshold choices affected the seroprevalence outcomes. The following threshold methods were evaluated: (i) mean + 3 standard deviations of the negative controls; (ii) 100% specificity for each antigen-isotype combination; and (iii) the maximal Youden index.

Results
We found vastly different seroprevalence estimates depending on selected antigens and isotypes and the applied threshold method, ranging from 0.0% to 85.4%. Subsequently, we maximized specificity and reported a seroprevalence, based on more than one antigen, ranging from 9.3% to 25.9%.

Conclusions
This study revealed the importance of evaluating serosurvey tools for antigen-, isotype-, and threshold-specific sensitivity and specificity, to interpret qualitative serosurvey outcomes reliably and consistently across studies.
Organizational and Technical Security Considerations for Laboratory Cloud Computing
Authors: Krumm Niklas 
Published: October 2022

Abstract

Background
Clinical and anatomical pathology services are increasingly utilizing cloud information technology (IT) solutions to meet growing requirements for storage, computation, and other IT services. Cloud IT solutions are often considered on the promise of low cost of entry, durability and reliability, scalability, and features that are typically out of reach for small- or mid-sized IT organizations. However, use of cloud-based IT infrastructure also brings additional security and privacy risks to organizations, as unfamiliarity, public networks, and complex feature sets contribute to an increased surface area for attacks.

Content
In this best-practices guide, we aim to help both managers and IT professionals in healthcare environments understand the requirements and risks when using cloud-based IT infrastructure within the laboratory environment. We will describe how technical, operational, and organizational best practices that can help mitigate security, privacy, and other risks associated with the use of could infrastructure; furthermore, we identify how these best practices fit into healthcare regulatory frameworks.
Among organizational best practices, we identify the need for specific hiring requirements, relationships with parent IT groups, mechanisms for reviewing and auditing security practices, and sound practices for onboarding and offboarding employees. Then, we highlight selected specific operational security, account security, and auditing/logging best practices. Finally, we describe how individual cloud technologies have specific resource-level security features.

Summary
We emphasize that laboratory directors, managers, and IT professionals must ensure that the fundamental organizational and process-based requirements are addressed first, to establish the groundwork for technical security solutions and successful implementation of cloud infrastructure.
Automated selection of changepoints using empirical P-values and trimming
Authors: Quinn Matthew , Chung Arlene , Glass Kimberly 
Published: October 2022

Abstract

Objectives
One challenge that arises when analyzing mobile health (mHealth) data is that updates to the proprietary algorithms that process these data can change apparent patterns. Since the timings of these updates are not publicized, an analytic approach is necessary to determine whether changes in mHealth data are due to lifestyle behaviors or algorithmic updates. Existing methods for identifying changepoints do not consider multiple types of changepoints, may require prespecifying the number of changepoints, and often involve nonintuitive parameters. We propose a novel approach, Automated Selection of Changepoints using Empirical P-values and Trimming (ASCEPT), to select an optimal set of changepoints in mHealth data.

Materials and Methods
ASCEPT involves 2 stages: (1) identification of a statistically significant set of changepoints from sequential iterations of a changepoint detection algorithm; and (2) trimming changepoints within linear and seasonal trends. ASCEPT is available at https://github.com/matthewquinn1/changepointSelect.

Results
We demonstrate ASCEPT’s utility using real-world mHealth data collected through the Precision VISSTA study. We also demonstrate that ASCEPT outperforms a comparable method, circular binary segmentation, and illustrate the impact when adjusting for changepoints in downstream analysis.

Discussion
ASCEPT offers a practical approach for identifying changepoints in mHealth data that result from algorithmic updates. ASCEPT’s only required parameters are a significance level and goodness-of-fit threshold, offering a more intuitive option compared to other approaches.

Conclusion
ASCEPT provides an intuitive and useful way to identify which changepoints in mHealth data are likely the result of updates to the underlying algorithms that process the data.
3M™ Petrifilm™ Rapid Yeast and Mold Count Plate for the Enumeration of Yeasts and Molds in Dried Cannabis Flower: AOACOfficial MethodSM 2014.05
Authors: Schumacher April , Lingle Cari , Silbernagel Karen M 
Published: October 2022

AbstractBackgroundThe 3MTM Petrifilm™ Rapid Yeast and Mold Count (RYM) Plate is a sample-ready culture medium system which contains nutrients supplemented with antibiotics, a cold-water-soluble gelling agent, and an indicator system that facilitates yeast and mold enumeration.ObjectiveThe 3M Petrifilm RYM Plate was validated for the enumeration of yeast and mold in dried cannabis flower through the AOAC Emergency Response Validation process.MethodsThe performance of the 3M Petrifilm RYM Plate was compared to dichloran rose bengal chloramphenicol (DRBC) agar. Matrix data were normalized by log10 transformation and performance indicators included repeatability, difference of means, and inclusivity/exclusivity.ResultsThese studies demonstrated the 3M Petrifilm RYM Plate method detects and enumerates yeasts and molds from dried cannabis flower at low, medium, and high contamination levels. The average log counts at 25 or 28°C for 60 to 72 h were equivalent to the average log counts of the DRBC reference method at low, medium and high levels. In strain studies, all 71 yeasts and molds tested produced typical colony morphology on 3M Petrifilm RYM Plates. Of the 32 non-target bacterial strains tested, none were detected on 3M Petrifilm RYM Plates.ConclusionThe 3M Petrifilm RYM Plate is a reliable method for the enumeration of live yeast and mold in dried cannabis flower.HighlightsThe 3M Petrifilm RYM Plate allows for rapid detection of yeast and mold within 60 to 72 h of incubation. Up to 40 sample-ready plates can be stacked during incubation to save space.
Constraining Tamil Transnational Political Action: Security Governance Practices beyond the Sending State
Authors: Craven Catherine Ruth 
Published: October 2022

AbstractThis paper examines the security governance of the Tamil diaspora through a practice lens. It takes as its starting point the observation that the Tamil diaspora community has historically been subjected to complex and multi-scalar security governance. How this continues after the end of the Sri Lankan civil war period remains empirically and theoretically underexamined, with studies focusing instead on Tamil diaspora organizing. This paper addresses this gap by mapping and theorizing contemporary constraints to Tamil transnational political action (TPA), building on the growing literature on the transnational repression of diaspora. Further, it proposes to move beyond the state-centrism and liberal bias inherent in this literature, by centering security governance practices. Based on a review of existing literature and historical and ethnographic data collected through mixed-method fieldwork among the Tamil diaspora community between 2015 and 2018, this paper concludes that key security governance practices that constrain Tamil TPA, such as proscription, counterterrorism policing, and formal diplomatic practices, have continued since the end of the civil war, each revealing complex global security entanglements beyond the diaspora sending state.
Social Determinants of Adherence to Treatment for Tuberculosis Infection and Disease Among Children, Adolescents, and Young Adults: A Narrative Review
Authors: Leddy Anna M , Jaganath Devan , Triasih Rina , Wobudeya Eric , Bellotti de Oliveira Marcia C , Sheremeta Yana , Becerra Mercedes C , Chiang Silvia S 
Published: October 2022

AbstractGlobal efforts to eliminate tuberculosis (TB) must address the unique barriers that children (ages 0 through 9 years) and adolescents/young adults (AYA; ages 10 through 24 years) face in adhering to treatment for TB infection and disease. We conducted a narrative review to summarize current knowledge on the social determinants of treatment adherence among these age groups to guide efforts and policy to address their unique needs. Our findings revealed that research on TB treatment adherence among children and AYA is still in its nascent stage. The current literature revealed structural/community-, health system-, household-, and individual-level factors that influence treatment adherence and varied with developmental stage. There is a need to develop multilevel interventions to address the unique challenges that children and AYA face in adhering to TB treatment.
Tuberculosis in Children Living With HIV: Ongoing Progress and Challenges
Authors: Vonasek Bryan J , Rabie Helena , Hesseling Anneke C , Garcia-Prats Anthony J 
Published: October 2022

Abstract
There has been much recent progress on control of the tuberculosis (TB) and human immunodeficiency virus (HIV) epidemics globally. However, advances in children have lagged behind, and TB-HIV coinfection continues to be a major driver of pediatric mortality in many settings. This review highlights recent research findings in the areas of prevention, diagnosis, and treatment of HIV-associated childhood TB. Key areas for future research are defined. Current prevention efforts such as vaccination, TB symptom screening, and TB preventive treatment are demonstrated as beneficial but need to be optimized for children living with HIV (CLHIV). Diagnosis of HIV-associated TB in children remains a major challenge, depending heavily on clinicians’ ability to judge an array of signs, symptoms, and imaging findings, but there are a growing number of promising diagnostic tools with improved accuracy and feasibility. Treatment of TB-HIV coinfection has also seen recent progress with more evidence demonstrating the safety and effectiveness of shorter regimens for treatment of TB infection and disease and improved understanding of interactions between antiretrovirals and TB medications. However, several evidence gaps on drug-drug interactions persist, especially for young children and those with drug-resistant TB. Accelerated efforts are needed in these areas to build upon current progress and reduce the burden of TB on CLHIV.
Pediatric Tuberculosis Diagnostics: Present and Future
Authors: Basile Francesca Wanda , Nabeta Pamela , Ruhwald Morten , Song Rinn 
Published: October 2022

Abstract
The current diagnostic abilities for the detection of pediatric tuberculosis are suboptimal. Multiple factors contribute to the under-diagnosis of intrathoracic tuberculosis in children, namely the absence of pathognomonic features of the disease, low bacillary loads in respiratory specimens, challenges in sample collection, and inadequate access to diagnostic tools in high-burden settings. Nonetheless, the 2020s have witnessed encouraging progress in the area of novel diagnostics. Recent WHO-endorsed rapid molecular assays hold promise for use in service decentralization strategies, and new policy recommendations include stools as an alternative, child-friendly specimen for testing with the GeneXpert assay. The pipeline of promising assays in mid/late-stage development is expanding, and novel pediatric candidate biomarkers based on the host immune response are being identified for use in diagnostic and triage tests. For a new test to meet the pediatric target product profiles prioritized by the WHO, it is key that the peculiarities and needs of the hard-to-reach pediatric population are considered in the early planning phases of discovery, validation, and implementation studies.
Platelet aggregation with various morphologies of neutrophils in arterial thrombus in a patient with Coronavirus disease: a case report
Authors: Tanaka Chiharu , Hiraiwa Shinichiro , Otsuka Hiroyuki , Yamaguchi Masaomi 
Published: October 2022

Abstract
Arterial thromboembolism is a life-threatening condition in COVID-19 patients; however, the mechanism of hypercoagulopathy remains unknown. A 62-year-old man with a history of obesity was diagnosed with COVID-19 pneumonia. After hospitalisation, unfractionated heparin was administered because of increased D-dimer levels; nevertheless, an arterial embolism in the left lower limb developed on the following day. Enhanced computed tomography revealed an occluded left iliac artery and intra-aortic thrombus at the juxtarenal level. Urgent thrombectomy was performed. On post-operative day 6, coumadin was initiated to treat the remaining thrombus. The patient was discharged without any complications. The removed thrombus pathologically presented platelet aggregation and degenerated neutrophils that were in various time axes; some neutrophils had clear margins of nuclear membrane, whereas others had pyknotic and fragment nuclei. We believe that the platelet formation and the neutrophils in several time axes could be key factors in promoting thrombus formation in COVID-19 patients.
Sustainable Development Goals (SDG) indicators for municipalities: a comprehensive monitoring approach from Germany
Authors: Jossin Jasmin , Peters Oliver 
Published: October 2022

Abstract
While the 2030 agenda addresses the United Nation member states primarily at their national levels, municipalities play a crucial role in implementing all of the 17 SDGs and many of the 169 targets. These processes must be monitored and evaluated. However, the UN indicators are not sufficiently applicable to the local context. Therefore, a multi-stakeholder working group was formed in Germany to develop a comprehensive set of Sustainable Development Goal (SDG) indicators for municipalities, together with additional instruments to support local SDG monitoring such as an SDG data portal. The first catalogue which included 47 core SDG indicators was published in 2018. According to consecutive evaluations and practical tests, the indicator set was substantially expanded and revised to a final number of 120 SDG indicators. About half of the 120 indicators are provided with local-level data and the other half must be assessed individually for comprehensive local SDG monitoring. Likewise, accompanying tools were relaunched with additional functionalities. Although this new and unique set of indicators now covers a majority of the municipally relevant targets, there are still some decisive monitoring gaps for various reasons. The strengths and weaknesses of our methodological approach, as well as implications for future research and practical developments, are discussed.