bluuebunny/crossref_metadata_2025_split huggingface dataset:
A comparison of Oxford nanopore library strategies for bacterial genomics
Authors: Sauvage Thomas , Cormier Alexandre , Delphine Passerini 
Published: October 2023

Abstract
Background
Oxford nanopore Technologies (ONT) provides three main library preparation strategies to sequence bacterial genomes. These include tagmentation (TAG), ligation (LIG) and amplification (PCR). Despite ONT’s recommendations, making an informed decision for preparation choice remains difficult without a side-by-side comparison. Here, we sequenced 12 bacterial strains to examine the overall output of these strategies, including sequencing noise, barcoding efficiency and assembly quality based on mapping to curated genomes established herein.

Results
Average read length ranged closely for TAG and LIG (> 5,000 bp), while being drastically smaller for PCR (< 1,100 bp). LIG produced the largest output with 33.62 Gbp vs. 11.72 Gbp for TAG and 4.79 Gbp for PCR. PCR produced the most sequencing noise with only 22.7% of reads mappable to the curated genomes, vs. 92.9% for LIG and 87.3% for TAG. Output per channel was most homogenous in LIG and most variable in PCR, while intermediate in TAG. Artifactual tandem content was most abundant in PCR (22.5%) and least in LIG and TAG (0.9% and 2.2%). Basecalling and demultiplexing of barcoded libraries resulted in ~ 20% data loss as unclassified reads and 1.5% read leakage.

Conclusion
The output of LIG was best (low noise, high read numbers of long lengths), intermediate in TAG (some noise, moderate read numbers of long lengths) and less desirable in PCR (high noise, high read numbers of short lengths). Overall, users should not accept assembly results at face value without careful replicon verification, including the detection of plasmids assembled from leaked reads.
An investigation of psychoactive polypharmacy and related gender-differences in older adults with dementia: a retrospective cohort study
Authors: Trenaman Shanna C , Quach Jack , Bowles Susan K , Kirkland Susan , Andrew Melissa K 
Published: October 2023

Abstract
Background
Older adults living with dementia may express challenging responsive behaviours. One management strategy is pharmacologic treatment though these options often have limited benefit, which may lead to multiple treatments being prescribed.

Methods
The aim of the present study was to describe psychoactive medication polypharmacy and explore factors associated with psychoactive polypharmacy in a cohort of older adults living with dementia in Nova Scotia, Canada, including a gender-stratified analysis. This was a retrospective cohort study of those aged 65 years or older with a recorded diagnosis of dementia between 2005 and 2015. Medication dispensation data was collected from April 1, 2010, or dementia diagnosis (cohort entry) to either death or March 31, 2015 (cohort exit). Psychoactive medication claims were captured. Psychoactive medication polypharmacy was defined as presence of three or more psychoactive prescription medications dispensed to one subject and overlapping for more than 30 days. Psychoactive polypharmacy episodes were described in duration, quantity, and implicated medications. Regression analysis examined factors associated with experience and frequency of psychoactive polypharmacy. All analysis were stratified by gender.

Results
The cohort included 15,819 adults living with dementia (mean age 80.7 years; 70.0% female), with 99.4% (n = 15,728) receiving at least one psychoactive medication over the period of follow-up. Psychoactive polypharmacy was present in 19.3% of the cohort. The gender specific logistic regressions demonstrated that for both men and women a younger age was associated with an increased risk of psychoactive polypharmacy (women: OR 0.97, 95%CI[0.96, 0.98], men: OR 0.96, 95%CI[0.95, 0.97]). Men were less likely to experience psychoactive polypharmacy if their location of residence was urban (OR 0.86, 95%CI[0.74, 0.99]). There was no significant association between location of residence (urban or rural) and psychoactive polypharmacy for women living with dementia. Antidepressants were the most dispensed medication class, while quetiapine was the most dispensed medication.

Conclusions
This study suggests that of adults living with dementia those of younger ages were more likely to experience psychoactive polypharmacy and that men living with dementia in rural locations may benefit from increased access to non-pharmacological options for dementia management.
Identifying the impact of social isolation and loneliness on psychological well-being among the elderly in old-age homes of India: the mediating role of gender, marital status, and education
Authors: Mishra Bijeta , Pradhan Jalandhar , Dhaka Suman 
Published: October 2023

Abstract
Background
Social isolation and loneliness can be detrimental to the overall functioning of the older adults. The study examines the impact of social isolation and loneliness on the psychological well-being of older adults residing in various old-age homes in India and investigates the mediating role of gender, marital status, and education level in the way social isolation and loneliness affect psychological well-being.

Methods
Data has been collected from 320 individuals aged sixty years or above. Data were collected using standardized measures like Lubben Social Network Scale- 6, revised UCLA Loneliness Scale, and shortened version of psychological well-being scale by Ryff & Keyes (1995). Multivariate and mediation analysis were performed to understand the associations of social isolation and loneliness with psychological well-being.

Results
A statistically significant MANOVA effect was obtained for social isolation (F = 3.836, p < .01), and loneliness (F = 3.782, p < .01). Gender and education as independent factors were significantly associated with the psychological well-being of individuals. However, both gender and education did not mediate the impact of social isolation and loneliness on the psychological well-being of older adults. Further, marital status had a partial mediating effect on the relationship between social isolation, loneliness, and psychological well-being.

Conclusions
The findings of the study can be incorporated into measures aiming at alleviation of feelings of social isolation and loneliness among the elderly. Further, the findings can be used to design various intervention strategies aimed at the reduction of social isolation and loneliness among older adults and the restoration of their psychological well-being.
Study protocol for prospective multi-institutional phase III trial of standard of care therapy with or without stereotactic ablative radiation therapy for recurrent ovarian cancer (SABR-ROC)
Authors: Kim Yong Bae , Byun Hwa Kyung , Wee Chan Woo , Kim Hojin , Kim Seyoung , Yang Gowoon , Kim Jina , Park Sang Joon , Lee Jung-Yun 
Published: October 2023

Abstract
Background
Efforts have been made to investigate the role of salvage radiotherapy (RT) in treating recurrent ovarian cancer (ROC). Stereotactic ablative radiation therapy (SABR) is a state-of-the-art therapy that uses intensity modulation to increase the fractional dose, decrease the number of fractions, and target tumors with high precision.

Methods
The SABR-ROC trial is a phase 3, multicenter, randomized, prospective study to evaluate whether the addition of SABR to the standard of care significantly improves the 3-year overall survival (OS) of patients with ROC. Patients who have completed the standard treatment for primary epithelial ovarian cancer are eligible. In addition, patients with number of metastases ≤ 10 and maximum diameter of each metastatic site of gross tumor ≤ 5 cm are allowed. Randomization will be stratified by (1) No. of the following clinical factors met, platinum sensitivity, absence of ascites, normal level of CA125, and ECOG performance status of 0–1; 0–3 vs. 4; (2) site of recurrence; with vs. without lymph nodes; and (3) PARP inhibitor; use vs. non-use. The target number of patients to be enrolled in this study is 270. Participants will be randomized in a 1:2 ratio. Participants in Arm 2 will receive SABR for recurrent lesions clearly identified in imaging tests as well as the standard of care (Arm 1) based on treatment guidelines and decisions made in multidisciplinary discussions. The RT fraction number can range from 1 to 10, and the accepted dose range is 16–45 Gy. The RT Quality Assurance (QA) program consists of a three-tiered system: general credentialing, trial-specific credentialing, and individual case reviews.

Discussion
SABR appears to be preferable as it does not interfere with the schedule of systemic treatment by minimizing the elapsed days of RT. The synergistic effect between systemic treatment and SABR is expected to reduce the tumor burden by eradicating gross tumors identified through imaging with SABR and controlling microscopic cancer with systemic treatment. It might also be beneficial for quality-of-life preservation in older adults or heavily treated patients.

Trial registration
This trial was registered at ClinicalTrials.gov (NCT05444270) on June 29th, 2022.
Heavy metal deposition and parameter change of soft contact lenses by exposure to particulate matter
Authors: Jung Won Young , Kim Jin Woo , Kim So Ra , Park Mijung 
Published: October 2023

Abstract
Background
Particulate matter (PM) is known to contain heavy metals and be harmful to the tissues and organs of the human body including the eyes. As such, in this study, the deposition of heavy metals from PM on soft contact lenses was examined, and changes in the lens parameters were further investigated.

Methods
Six types of soft contact lenses were exposed to captured PM10 for eight hours. The central thickness, water content, refractive power, and oxygen transmissibility of each contact lens were measured after analyzing the amounts of six heavy metals adsorbed on the contact lenses.

Results
Lead, manganese, barium, arsenic, vanadium, and cadmium were detected in the captured PM, and only lead was adsorbed on all soft contact lenses except senofilcon C. The largest deposition was 23.21 ± 0.70 (10− 3)µg/lens of the lead on lotrafilcon B. The oxygen transmissibility of nelfilcon A exhibited statistically significant changes, however, it was within the ISO standard tolerance. Nevertheless, changes in the central thickness, water content, and refractive power of each soft contact lens were not statistically significant.

Conclusions
This study revealed that a considerable amount of lead in PM10 was adsorbed on soft contact lenses. Amongst lens parameters, only oxygen transmissibility changed significantly. Thus, wearing soft contact lenses under high PM10 concentration might affect the physiology of the eyes.
Vision degrading myodesopsia assessed with optos ultra-widefield scanning laser ophthalmoscope
Authors: Lin Tiezhu , Shi Cheng , Wu Bing , Pazo Emmanuel Eric , Shen Lijun 
Published: October 2023

Abstract
Background
To investigate the diagnostic sensitivity of Optos imaging for vision degrading myodesopsia (VDM).

Methods
A total of 420 eyes from 345 patients with VDM were collected in this cross-sectional study. All eyes were classified as having posterior vitreous detachment (PVD) or not having PVD. The sensitivity of Optos imaging for the visibility of vitreous floaters was evaluated. The associated factors with the visibility of vitreous floaters on Optos images were analyzed in univariate and multivariate logistic regression analyses.

Results
The mean age of all patients was 56.19 ± 13.89 years old, and 66.67% of patients were female. The vitreous floaters were visible on the ultrasound B scan in all eyes, but only in 47.62% of Optos images (55.29% in eyes with PVD and 15% in eyes without PVD). In the multiple binary logistic regression analysis, age (OR = 1.094, 95%CI = 1.063–1.125, P < 0.001), spherical equivalent (OR = 0.869, 95%CI = 0.791–0.955, P = 0.004) and the distance of the floaters from the retina (OR = 1.191, 95%CI = 1.059–1.339, P = 0.003) were significantly correlated with the visibility of vitreous floaters on Optos images. On Optos images, 25.71% of VDM eyes presented additional retinal abnormalities.

Conclusions
Optos imaging has a low sensitivity for vitreous floaters, particularly in eyes without PVD. On Optos imaging, floaters were more visible in older patients, eyes with greater myopia, and floaters that were further from the retina.
Relationship between adiponectin and blood pressure in obese Latino adolescent boys with a family history of type 2 diabetes
Authors: Hijazin Kristin , Smith Brandon , Garrett Coleby , Knox Allan , Kelly Louise A. 
Published: October 2023

Abstract
introduction
Adipokines are associated with several pathological states including, metabolic syndrome, obesity, insulin resistance and type 2 diabetes. One of these adipokines, adiponectin is of particular interest as it has been shown to have numerous anti-inflammatory effects, However, the association between adiponectin and blood pressure remains inconclusive especially in the Latino adolescent with obesity.

Purpose
To investigate the relationship between plasma adiponectin and blood pressure in Latino adolescents’ boys with obesity and a with a family history of Type 2 diabetes.

Methods
Thirty two Latino adolescent males with obesity aged 14–17 years with a family history of type 2 diabetes underwent a frequently sampled glucose tolerance test (FSIVGTT) to measure insulin sensitivity. Body composition was assessed using dual energy x-ray absorptiometry. Obesity was defined as having a BMI percentile ≥95. Blood pressure was assessed using the Dinamap automated blood pressure monitor, and the average of three readings was used in the analysis. Fasting plasma adiponectin was determined using radioimmunoassay.

Results
There were moderate positive significant correlations for adiponectin and Systolic blood pressure(SBP) (rho = 0.436, p < 0.027) and Diastolic blood pressure(DBP) (rho = 0.41,p < 0.028). A multivariate liner regression showed that plasma adiponectin could significantly detect 19% of the variance in SBP (p = 0.017, and 33% for DBP (p = 0.017). In a simple linear regression adiponectin was not related to any of our variables (p < 0.05).

Conclusion
In conclusion, adiponectin was positively and significantly correlated to blood pressure in Latino adolescent with obesity. Future studies should investigate this relationship in a large sample of Latino adolescent youth.
A cross-sectional survey exploring HIV and HCV prevalence among men who purchase sex in Dnipro, Ukraine
Authors: Lazarus Lisa , Herpai Nicole , Pavlova Daria , Gill Amaanat , Cholette François , McClarty Leigh M. , Isac Shajy , Lopatenko Anna , Pickles Michael , Mishra Sharmistha , Shaw Souradet Y. , Lorway Robert , McKinnon Lyle R. , Sandstrom Paul , Blanchard James , Balakireva Olga , Becker Marissa L. ,   on behalf of the Dynamics Study Team, Aral Sevgi , Bondar Tetiana , Cheuk Eve , Daniuk Christina , Forget Evelyn , Lee Emma , Ma Huiting , Moses Stephen , Murney Maureen , Nguien Nam-Mykhailo , Shakarishvili Ani , Tarasova Tatiana 
Published: October 2023

Abstract
Background
HIV programming in Ukraine largely targets “key population” groups. Men who purchase sex are not directly reached. The aim of our study was to explore the prevalence of sexually transmitted and blood-borne infections (STBBIs) among men who purchase sex from female sex workers.

Methods
Following geographic mapping and population size estimation at each “hotspot”, we conducted a cross-sectional bio-behavioural survey with men who purchase sex between September 2017 and March 2018 in Dnipro, Ukraine. Eligibility criteria included purchasing sex services at a “hotspot” and being ≥ 18 years. Participants completed a structured questionnaire, followed by HIV/HCV rapid testing and a dried blood spot (DBS) sample collection for confirmatory serology.

Results
The study enrolled 370 participants. The median age was 32 (interquartile range [IQR] = 27–38) and the median age of first purchase of sexual services was 22 (IQR = 19–27). Over half (56%) of participants reported ever testing for HIV; four participants (2%, N = 206) reported having tested positive for HIV, with three out of the four reporting being on ART. Forty percent of participants had ever tested for HCV, with three (2%, N = 142) having ever tested positive for HCV. In DBS testing, nine participants (2.4%) tested positive for HIV and 24 (6.5%) tested positive for ever having an HCV infection.

Conclusion
Prevalence of HIV and HCV in this population was high. Given high rates of study enrolment and testing, efforts should be made to reach men who purchase sex with expanded STBBI programming.
Phytochemical analysis, in vitro and in silico effects from Alstonia boonei De Wild stem bark on selected digestive enzymes and adipogenesis in 3T3-L1 preadipocytes
Authors: Anyanwu Gabriel O. , Ejike Uju D. , Gyebi Gideon A. , Rauf Khalid , Nisar-Ur-Rehman  , Iqbal Jamshed , Zaib Sumera , Usunobun Usunomena , Onyeneke Eusebius C. , Alotaibi Badriyah S. , Batiha Gaber El-Saber 
Published: October 2023

Abstract
Background
Obesity is a global health issue arising from the unhealthy accumulation of fat. Medicinal plants such as Alstonia boonei stem bark has been reported to possess body weight reducing effect in obese rats. Thus, this study sought to investigate the in vitro and in silico effects of fractions from Alstonia boonei stem bark on selected obesity-related digestive enzymes and adipogenesis in 3T3-L1 preadipocytes.

Method
Two fractions were prepared from A. boonei: crude alkaloid fraction (CAF) and crude saponin fraction (CSF), and their phytochemical compounds were profiled using Liquid chromatography with tandem mass spectrometry (LCMS/MS). The fractions were assayed for inhibitory activity against lipase, α-amylase and α-glucosidase, likewise their antiadipogenic effect in 3T3-L1 adipocytes. The binding properties with the 3 enzymes were also assessed using in silico tools.

Results
Eleven alkaloids and six saponin phytochemical compounds were identified in the CAF and CSF using LCMS/MS. The CAF and CSF revealed good inhibitory activity against pancreatic lipase enzyme, but weak and good activity against amylase respectively while only CSF had inhibitory activity against α-glucosidase. Both fractions showed antiadipogenic effect in the clearance of adipocytes and reduction of lipid content in 3T3-L1 adipocytes. The LCMS/MS identified compounds (41) from both fractions demonstrated good binding properties with the 3 enzymes, with at least the top ten compounds having higher binding energies than the reference inhibitors (acarbose and orlistat). The best two docked compounds to the three enzymes were firmly anchored in the substrate binding pockets of the enzymes. In a similar binding pattern as the reference acarbose, Estradiol-17-phenylpropionate (-11.0 kcal/mol) and 3α-O-trans-Feruloyl-2 α -hydroxy-12-ursen-28-oic acid (-10.0 kcal/mol) interacted with Asp197 a catalytic nucleophile of pancreatic amylase. Estradiol-17-phenylpropionate (-10.8 kcal/mol) and 10-Hydroxyyohimbine (-10.4 kcal/mol) interacted with the catalytic triad (Ser152-Asp176-His263) of pancreatic lipase while Estradiol-17-phenylpropionate (-10.1 kcal/mol) and 10-Hydroxyyohimbine (-9.9 kcal/mol) interacted with Asp616 and Asp518 the acid/base and nucleophilic residues of modelled α-glucosidase.

Conclusion
The antiobesity effect of A. boonei was displayed by both the alkaloid and saponin fractions of the plant via inhibition of pancreatic lipase and adipogenesis.
A qualitative investigation of uninsured patient and primary care provider perspectives on specialty care eConsults
Authors: Bifulco Lauren , Grzejszczak Lynsey , Velez Idiana , Angelocci Tracy , Anderson Daren 
Published: October 2023

AbstractBackgroundUninsured and underinsured patients face specialty care access disparities that prevent them from obtaining the care they need and negatively impact their health and well-being. We aimed to understand how making specialty care electronic consultations (eConsults) available at a multi-site Federally Qualified Health Center (FQHC) in central Texas affected uninsured patients’ care-seeking experiences and impacted their ability to receive the needed care.MethodsWe used concepts from Ecological Systems Theory to examine individual, interpersonal, organization-level, social, and health policy environment factors that impacted patients’ access to specialty care and the use of eConsults. We conducted thematic analysis of semi-structured, qualitative interviews with patients about seeking specialty care while uninsured and with uninsured patients and FQHC PCPs about their experience using eConsults to obtain specialists’ recommendations.ResultsPatients and PCPs identified out-of-pocket cost, stigma, a paucity of local specialists willing to see uninsured patients, time and difficulty associated with travel and transportation to specialty visits, and health policy limitations as barriers to obtaining specialty care. Benefits of using eConsults for uninsured patients included minimizing/avoiding financial stress, expanding access to care, expanding scope of primary care, and expediting access to specialists. Concerns about the model included patients’ limited understanding of eConsults, concern about cost, and worry whether eConsults could appropriately meet their specialty needs.ConclusionsFindings suggest that eConsults delivered in a primary care FQHC addressed uninsured patients’ specialty care access concerns. They helped to address financial and geographic barriers, provided time and cost savings to patients, expanded FQHC PCPs’ knowledge and care provision options, and allowed patients to receive more care in primary care.
Single-nucleus transcriptome inventory of giant panda reveals cellular basis for fitness optimization under low metabolism
Authors: Yang Shangchen , Lan Tianming , Wei Rongping , Zhang Ling , Lin Lin , Du Hanyu , Huang Yunting , Zhang Guiquan , Huang Shan , Shi Minhui , Wang Chengdong , Wang Qing , Li Rengui , Han Lei , Tang Dan , Li Haimeng , Zhang Hemin , Cui Jie , Lu Haorong , Huang Jinrong , Luo Yonglun , Li Desheng , Wan Qiu-Hong , Liu Huan , Fang Sheng-Guo 
Published: October 2023

Abstract
Background
Energy homeostasis is essential for the adaptation of animals to their environment and some wild animals keep low metabolism adaptive to their low-nutrient dietary supply. Giant panda is such a typical low-metabolic mammal exhibiting species specialization of extremely low daily energy expenditure. It has low levels of basal metabolic rate, thyroid hormone, and physical activities, whereas the cellular bases of its low metabolic adaptation remain rarely explored.

Results
In this study, we generate a single-nucleus transcriptome atlas of 21 organs/tissues from a female giant panda. We focused on the central metabolic organ (liver) and dissected cellular metabolic status by cross-species comparison. Adaptive expression mode (i.e., AMPK related) was prominently displayed in the hepatocyte of giant panda. In the highest energy-consuming organ, the heart, we found a possibly optimized utilization of fatty acid. Detailed cell subtype annotation of endothelial cells showed the uterine-specific deficiency of blood vascular subclasses, indicating a potential adaptation for a low reproductive energy expenditure.

Conclusions
Our findings shed light on the possible cellular basis and transcriptomic regulatory clues for the low metabolism in giant pandas and helped to understand physiological adaptation response to nutrient stress.