bluuebunny/crossref_metadata_2025_split huggingface dataset:
Antimicrobial Susceptibility Patterns Among a Large, Nationwide Cohort of Chryseobacterium Species Clinical Isolates
Authors: Pham Jonathan , Calvaresi Emilia , Fisher Mark 
Published: November 2023

Abstract

Background
Chryseobacterium species are ubiquitous in nature that can be found in soil, water, sinks, and medical devices. They have been implicated in various infections including ventilator-associated pneumonia, catheter-related bloodstream infections (CRBSI), skin and soft tissue infections, and meningitis. C. indologenes has been shown to possess an extended-spectrum beta-lactamase (ESBL) and metallo-β-lactamase (MBL) that render it resistant to most antibiotics. Antimicrobial susceptibility testing (AST) data are required to help clinicians choose effective empiric antibiotics and to investigate potential resistance mechanisms.

Methods
Chryseobacterium spp. identification was determined prior to submission by client laboratories or performed in our laboratory by MALDI-TOF (Bruker Biotyper) or 16S rRNA gene sequencing. AST was performed on Chryseobacterium species isolates received from across the United States between April 2004 and December 2018. AST was performed using custom-made broth microdilution panels, and minimal inhibitory concentrations (MICs) were interpreted using CLSI M100 MIC breakpoints for non-Enterobacterales organisms. Isolates from a range of clinical specimens including blood, respiratory, wound, tissue, bone, and body fluids were included. Quality control was performed using Escherichia coli ATCC 25922 and Pseudomonas aeruginosa ATCC 27853. Results were included only if the QC values were within range. The MIC50, MIC90, and MIC ranges for antimicrobials for frequently tested Chryseobacterium species were determined.

Results
AST was completed for 245 Chryseobacterium species clinical isolates, and the most frequently tested species were C. gleum/ indologenes (n = 78), C. hominis (n = 25), C. taklimakanense (n = 14), C. anthropi/ haifense (n = 12), C. arthrospharae (n = 12), C. bernardetii/jejuense (n = 3), C. pallidum (n = 3), and C. solincola/treverense (n = 3). 84 isolates were unable to be identified to species level, and were grouped as “Chryseobacterium spp.” Regarding susceptibility, across all Chryseobacterium species, the antibiotics with the most activity included minocycline (97.8%), trimethoprim-sulfamethoxazole (TMP-SMX; 95.5%), levofloxacin (92.3%), and ciprofloxacin (82.8%). Comparing the β-lactams, piperacillin-tazobactam had the most activity (59.7%), whereas ceftazidime (42.2%), cefepime (44.3%), meropenem (41.2%), and imipenem (46.3%) had similar low activity. The highest resistance rates were found for tobramycin (96%), aztreonam (94.6%), and gentamicin (62.7%). Among the Chryseobacterium isolates, certain species were found to be largely pan-susceptible, including C. anthropic/haifense, C. hominis, and C. taklimakanense.

Conclusions
Chryseobacterium species display significant resistance against β-lactam antibiotics, which are often used for empiric therapy. Minocycline, TMP-SMX, and fluoroquinolones have the most activity against Chryseobacterium species clinical isolates.
IMPACT OF CMA ON DIAGNOSIS AND CLINICAL MANAGEMENT OF NEONATES: A RETROSPECTIVE SINGLE CENTER STUDY OF A 10-YEAR COHORT
Authors: Rosti Ozgur , Williams Eli , Fan Jinbo 
Published: November 2023

Abstract

Introduction
Congenital anomalies are one of the leading causes of mortality in neonatal period. The burden of genetic disease is high in neonates with congenital anomalies. Chromosomal microarray analysis (CMA) is the “first-tier” cytogenetic diagnostic test for individuals with multiple congenital anomalies. The aim of this study is to assess the diagnostic yield and clinical management impact of CMA in a large neonatal cohort over a 10-year period at a single medical center.

Methods
This is a retrospective study of a cohort of neonates tested by CMA at UVA Cytogenetics Laboratory between the years of 2013-2022. All individuals had either an isolated (major) congenital anomaly (CA) or multiple congenital malformations (MCA). We evaluated the diagnostic yield of the CMA in this neonate cohort and the frequency of positive CMA findings for specific phenotypes, as well as impact of CMA findings in the clinical management of patients.

Results
Of the 965 patients analyzed, 656 (68%) had normal results, 166 (17%) patients only had variants of uncertain significance (VUS), 128 (13%) patients had pathogenic alterations (thus confirmed genetic diagnosis), and 15 (2%) patients only had absence of heterozygosity (AOH) regions meeting our reporting criteria. Further details on presence of specific CNVs in the cohort and, positivity per presence/absence of multiple and specific anomalies is still ongoing and will be given in the presentation. For patients received a genetic diagnosis through CMA analysis, genetic findings were considered beneficial for clinical management, and a direct change to medical management occurred.

Conclusion
s: In this study, we found that the overall diagnostic yield for CMA in this neonate cohort is at approximately 13%. The confirmed genetic diagnosis affected the clinical management/treatment plan of this subset of neonatal patients. While first-tier testing for MCA and other indications is increasingly moving to ES/GS approaches, CMA continues to offer diagnostic and actionable genetic information in a timely matter. Overall, the implementation of CMA to a neonatal cohort at our center has increased the proportion of patients receiving a confirmed genetic diagnosis and affected the management/treatment plan of a subset of neonatal patients.
CytogeneticsPlatelet inhibition testing: whole blood point-of-care vs traditional platelet aggregometry
Authors: Achram Robert , Barrette Eileen , Guarner Jeannette , Smith Geoffrey , Maier Cheryl L 
Published: November 2023

Abstract
Monitoring drug response to ensure optimal platelet suppression is necessary in select patients on dual antiplatelet therapy (DAPT). At our institution, responses to aspirin (ASA) and P2Y12 inhibitors (P2Y12-Is) are assessed by light transmission aggregometry (LTA) using the Helena AggRAM assay. This method requires platelet-rich plasma (PRP) and is labor intensive. Platelet mapping using thromboelastography (TEG) is an alternate method, which offers point-of-care testing on whole blood. Here, we aimed to evaluate the concordance of our LTA assay with TEG, as well as the VerifyNow® PRUTest. We aimed to run testing on at least 20 patient samples; however, at the time of abstract submission, only 10 samples were available. Ten blood samples from 8 patients on dual anti-platelet therapy were collected in preparation for neurologic stent placement. Prepared PRP was analyzed by LTA on the Helena AggRAM assay. The maximal amplitude of the aggregation curves was recorded in the presence of high dose (HD) ADP, low dose (LD) ADP, and arachidonic acid (AA). Whole blood was analyzed by TEG using PlateletMapping ADP & AA assay cartridges on the Haemonetics® TEG 6s analyzer, and by the VerifyNow® PRUTest. Thresholds to qualify platelet suppression as optimal or suboptimal were defined a priori following established guidelines. Concordance between methods was calculated using the following formula: (optimal/optimal + suboptimal/suboptimal) / total number of samples. Pearson correlation between units of measure was also determined. For P2Y12-I response, concordance between LTA and TEG was 70% (correlation was r = 0.76 between TEG and LTA with HD ADP, and r = 0.70 between TEG and LTA with LD ADP). Concordance between VerifyNow® and LTA was 60% (correlation was r = 0.84 between VerifyNow® and LTA with HD ADP, and r = 0.78 between VerifyNow® and LTA with LD ADP). Finally, concordance between VerifyNow® and TEG was 30% (correlation was r = 0.81). Regarding ASA response, concordance was 80% between LTA and TEG (correlation was r = 0.31). To summarize, overall concordance ranged from 30 to 80% across platforms. For P2Y12 inhibition, results obtained from LTA with HD ADP and VerifyNow® had the strongest correlation (r = 0.84). Interestingly, the correlation between VerifyNow® and TEG was similarly elevated (r = 0.81), but concordance was poor (30%). When comparing TEG to LTA, the strongest correlation was between LTA with HD ADP and TEG (r value = 0.76). Concerning ASA inhibition, concordance between LTA and TEG was acceptable; however, correlation was weak (80%; r = 0.31). Results from this preliminary study support the potential use of TEG to monitor platelet response to therapy. We plan to continue our testing to include a minimum of 20 samples, and also consider patient outcomes, before implementing any laboratory workflow changes.
The Million Patient Labset: A large, de-identified dataset of longitudinal clinical laboratory results from one million patients
Authors: Spies Nicholas , Zhang Ray , Jackups Ronald 
Published: November 2023

Abstract
Laboratory testing is integral to the diagnosis and treatment of disease. Advances in electronic medical records and computation have initiated an era of ‘big data’ for laboratory medicine. However, most health data continues to exist in isolated and inaccessible information silos, limiting public utility. To address this gap, we have developed a large, de-identified, longitudinal dataset of laboratory results from over one million patients, called the Million Patient Labset (MPL), which is free and open to the public. The MPL was produced from the combination of two large healthcare systems with IRB and information security approvals. It includes 1,112,550 patients from across 1,920 healthcare sites in two states from 2017 through 2021, with 4,404 different clinical assays represented. Sites included primary care clinics, secondary care facilities for dialysis, infusions, rehabilitation, and other subspecialties, and tertiary centers for major surgery, trauma care, cancer care, and other complex medical services. Assays having fewer than 100 results were excluded. Limited patient demographic and encounter metadata are also included. Protected health information was de-identified in accordance with Health Insurance Portability and Accountability Act of 1996 (HIPAA) safe harbor standards. Service dates and times were altered to obscure absolute timestamps, while approximately preserving interval lengths between test results of the same patient, and general age and time of testing averages across patients. Time of day, day of week, and seasonality were approximately preserved. Data were validated through randomly selected comparisons against the original patient records, prior to destroying re-identification keys. In conclusion, we have produced a large de-identified open-access dataset of clinical laboratory results from over one million real patients. We hope this resource will be valuable for researchers exploring human clinical variation, medical artificial intelligence, reference interval optimization, and other data-driven studies.
CytogeneticsPathBrowser: an educational tool to convert textbook images and captions into flashcards
Authors: Hung Stevephen , Woddor Navitha , Barzaga Maikel Benitez , Prado Ilianne Vega , Soriano Carla Ayala , Mamilla Divya , Sepulveda Jorge 
Published: November 2023

Abstract

Background
Competence in reaching the correct diagnosis from analysis of clinical pathology specimens requires exposure to a large volume and breadth of cases. Images from textbooks are critical resources that supplement actual cases with well curated information. However, learning from textbooks has several setbacks. Images from individual textbooks are limited in number and often do not adequately capture variation of the disease entity. Textbooks also do not usually provide a platform for learners to assess their diagnostic abilities. This burdens the learner with creating flashcards for self-assessment, which is manually intensive.

Methods
To address these limitations, we developed PathBrowser, a web browser-accessible program that leverages the PyMuPDF Python package (Artifex) to extract images and captions from textbooks in PDF format. Captions are written to the image files using ExifTool (Phil Harvey), making the images searchable by keywords. The program then displays the image while hiding the caption, challenging the user to enter the appropriate diagnosis. To minimize work by the user to prepare flashcard questions and answers, the program can automatically generate quiz questions by using natural language processing tools and a Naïve Bayes (NB) classifier (NLTK and SpaCy packages) to identify important terms from the caption as either diagnoses or cytologic features.

Results
As a proof of principle, we used PathBrowser to build an image repository of myeloblasts and common mimickers, including reactive lymphocytes and chronic lymphoid leukemias, towards training junior pathology residents to identify blasts in peripheral blood and body fluids. In total, PathBrowser extracted 173 images (63 myeloblasts and 110 non-blasts) from 2 textbook sources (Atlas of Diagnostic Hematology by Salama et al., and Hematopathology by Jaffe et al.). We trained a NB classifier to label images as “myeloblast” or “non-myeloblast,” based on keywords in the caption. We manually ascertained that PathBrowser extracted the appropriate caption from 30/30 (100%) images of myeloblasts. Of these, the NB classifier correctly extracted the term “myeloblast” in 28 (93%) images. A survey of pathology residents showed that 89% of respondents agreed the program is a useful pathology learning tool.

Conclusions
We developed a program that makes reading from textbooks an interactive learning experience. By automating the manual-intensive steps of extracting images and captions and preparing flashcards with quiz questions using caption terms classified by machine learning tools, learners can focus on recognizing the diagnostic features represented by the images. Finally, our program enables the rapid generation of a repository of images from diverse sources, so that learners can browse a wide spectrum of disease entities and their variants.
Spatial differencing for sample selection models with ‘site-specific’ unobserved local effects
Authors: Klein Alexander , Tchuente Guy 
Published: November 2023

Summary
This paper proposes an estimator which combines spatial differencing with a two-step sample selection estimator. We derive identification, estimation, and inference results from ‘site-specific’ unobserved effects. These effects operate at a spatial scale that cannot be captured by administrative borders. Therefore, we use spatial differencing. We show that under justifiable assumptions, the estimator is consistent and asymptotically normal. A Monte Carlo experiment illustrates the small sample properties of our estimator. We apply our procedure to the estimation of a female wage offer equation in the United States and the results show the relevance of spatial differencing to account for ‘site-specific’ unobserved effects.
Teaching positive psychology lessons in an intensive English program
Authors: Rogers Carolee , McMurry Benjamin L , Dewey Dan P 
Published: November 2023

Abstract
This article investigates the effectiveness of positive psychology interventions (PPIs) in an intensive English program for non-matriculated university students. Interventions based on the PERMA model were implemented through weekly 65-minute lessons given during the first class of each week. These were followed by short daily activities during the rest of the week. Using positive psychology topics as the content, students concurrently engaged in language learning activities. Each participant was asked to complete a questionnaire at the end of the semester consisting of five open-ended questions relating to the PPIs, the lessons, the activities, the topics, and how they felt the PPIs affected their language learning and their life outside of class. Two raters individually reviewed each student response and marked them as positive, neutral, or negative. On the whole, the learners viewed the PPIs as being helpful for their well-being without detracting from their linguistic development.
Language teacher wellbeing: an individual–institutional pact
Authors: Gregersen Tammy , MacIntyre Peter 
Published: November 2023

Abstract
Although positive psychology (PP) is characterized as a tripartite approach to human flourishing that considers emotions, traits, and institutions, to date the role of institutions has been relatively overlooked. This is particularly problematic when exploring language teacher wellbeing because a teacher’s ability to thrive is also dependent upon the context in which they work. Combining the results of a web survey on teacher wellbeing with relevant concepts from PP on the collective responsibility of individuals and institutions, this study provides a podium from which teachers’ voices can be heard. When asked for specific advice on positively confronting challenges (particularly stemming from the Covid-19 pandemic), teachers’ recommendations coalesced around the four themes of doing your best: teaching practices, positive leadership, and positive attitudes and gratitude. The purpose of this study is to listen to teachers’ voices and provide implications for making more positive institutions.
ORFans in Mitochondrial Genomes of Marine Polychaete Polydora
Authors: Selifanova Maria , Demianchenko Oleg , Noskova Elizaveta , Pitikov Egor , Skvortsov Denis , Drozd Jana , Vatolkina Nika , Apel Polina , Kolodyazhnaya Ekaterina , Ezhova Margarita A , Tzetlin Alexander B , Neretina Tatiana V , Knorre Dmitry A 
Published: November 2023

Abstract
Most characterized metazoan mitochondrial genomes are compact and encode a small set of proteins that are essential for oxidative phosphorylation, as well as rRNA and tRNA for their expression. However, in rare cases, invertebrate taxa have additional open reading frames (ORFs) in their mtDNA sequences. Here, we sequenced and analyzed the mitochondrial genome of a polychaete worm, Polydora cf. ciliata, part of whose life cycle takes place in low-oxygen conditions. In the mitogenome, we found three “ORFan” regions (544, 1,060, and 427 bp) that have no resemblance to any standard metazoan mtDNA gene but lack stop codons in one of the reading frames. Similar regions are found in the mitochondrial genomes of three other Polydora species and Bocardiella hamata. All five species share the same gene order in their mitogenomes, which differ from that of other known Spionidae mitogenomes. By analyzing the ORFan sequences, we found that they are under purifying selection pressure and contain conservative regions. The codon adaptation indices (CAIs) of the ORFan genes were in the same range of values as the CAI of conventional protein-coding genes in corresponding mitochondrial genomes. The analysis of the P. cf. ciliata mitochondrial transcriptome showed that ORFan-544, ORFan-427, and a portion of the ORFan-1060 are transcribed. Together, this suggests that ORFan-544 and ORFan-427 encode functional proteins. It is likely that the ORFans originated when the Polydora/Bocardiella species complex separated from the rest of the Spionidae, and this event coincided with massive gene rearrangements in their mitochondrial genomes and tRNA-Met duplication.
Associations of Folate/Folic Acid Supplementation Alone and in Combination With Other B Vitamins on Dementia Risk and Brain Structure: Evidence From 466 224 UK Biobank Participants
Authors: Ling Yitong , Yuan Shiqi , Huang Xiaxuan , Tan Shanyuan , Cheng Hongtao , Xu Anding , Lyu Jun 
Published: November 2023

Abstract
Previous researchers have tried to explore the association between folate/folic acid intake and dementia incidence, but the results remain controversial. We evaluated the associations of folate/folic acid supplementation alone and in combination with other B vitamins on dementia risk and brain structure. A total of 466 224 UK Biobank participants were investigated. Cox proportional hazards models were used to assess the associations between folate/folic acid supplementation status and the risk of Alzheimer’s disease (AD) and vascular dementia (VD). Multivariable linear regression models were employed to evaluate the association between folate/folic acid supplementation status and brain structure. In the final model, folate/folic acid supplementation alone was significantly associated with a higher risk of AD (hazard ratio [HR] = 1.34, 95% confidence interval [CI] = 1.06–1.69, p = .015) and VD (HR = 1.61, 95% CI = 1.21–2.13, p = .001). Folate/folic acid supplementation alone was associated with a reduction in the hippocampus (β = −95.25 mm3, 95% CI = −165.31 to −25.19 mm3, p = .014) and amygdala (β = −51.85 mm3, 95% CI = −88.02 to −15.68 mm3, p = .012). The risk of AD and VD, as well as brain structure, in the group with combined folate/folic acid supplementation and other B vitamins did not show a statistically significant difference compared to the reference group (all p &gt; .05). Folate/folic acid supplementation alone is significantly associated with a higher risk of AD and VD, as well as adverse alterations in brain structure. However, when combined with other B vitamins, these detrimental effects can be counteracted.
Long-stranded non-coding RNAs temporal-specific expression profiles reveal longissimus dorsi muscle development and intramuscular fat deposition in Tianzhu white yak
Authors: He Zhaohua , Wang Xiangyan , Qi Youpeng , Zhu Chune , Zhao Zhidong , Zhang Xiaolan , Liu Xiu , Li Shaobin , Zhao Fangfang , Wang Jiqing , Shi Bingang , Hu Jiang 
Published: November 2023

Abstract
The process of muscle development and intramuscular fat (IMF) deposition is quite complex and controlled by both mRNAs and ncRNAs. Long-stranded non-coding RNAs (LncRNAs) are involved in various biological processes in mammals while also playing a critical role in muscle development and fat deposition. In the present study, RNA-Seq was used to comprehensively study the expression of lncRNAs and mRNAs during muscle development and intramuscular fat deposition in postnatal Tianzhu white yaks at three stages, including 6 mo of age (calve, n = 6), 30 mo of age (young cattle, n = 6) and 54 mo of age (adult cattle, n = 6). The results indicated that a total of 2,101 lncRNAs and 20,855 mRNAs were screened across the three stages, of which the numbers of differential expression (DE) lncRNAs and DE mRNAs were 289 and 1,339, respectively, and DE lncRNAs were divided into eight different expression patterns based on expression trends. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that some DE mRNAs overlapped with target genes of lncRNAs, such as NEDD4L, SCN3B, AGT, HDAC4, DES, MYH14, KLF15 (muscle development), ACACB, PCK2, LIPE, PIK3R1, PNPLA2, and MGLL (intramuscular fat deposition). These DE mRNAs were significantly enriched in critical muscle development and IMF deposition-related pathways and GO terms, such as AMPK signaling pathway, PI3K-Akt signaling pathway, PPAR signaling pathway, etc. In addition, lncRNA-mRNA co-expression network analysis revealed that six lncRNAs (MSTRG.20152.2, MSTRG.20152.3, XR_001351700.1, MSTRG.8190.1, MSTRG.4827.1, and MSTRG.11486.1) may play a major role in Tianzhu white yak muscle development and lipidosis deposition. Therefore, this study enriches the database of yak lncRNAs and could help to further explore the functions and roles of lncRNAs in different stages of muscle development and intramuscular fat deposition in the Tianzhu white yak.