bluuebunny/crossref_metadata_2025_split huggingface dataset:
Major adverse cardiovascular events’ reduction and their association with glucose‐lowering medications and glycemic control among patients with type 2 diabetes: A retrospective cohort study using electronic health records
Authors: Hsu Haowen , Kocis Paul Thomas , Pichardo‐Lowden Ariana , Hwang Wenke 
Published: October 2024

AbstractBackgroundCardiovascular diseases are a common cause of death among patients with type 2 diabetes (T2DM). Major adverse cardiovascular event (MACE) risks can be significantly reduced under adequate glycemic control (GC). This study aims to identify factors that influence MACE risk among patients with T2DM, including Hemoglobin A1c variability score (HVS) and early use of MACE‐preventive glucose‐lowering medications (GLMs).MethodsWe conducted a longitudinal cohort study to retrospectively review electronic health records between 2011 and 2022. Patients with T2DM ≥18 years without previous stroke or acute myocardial infarction (AMI) were included. Cox regression was utilized to investigate MACE risk factors and compare MACE risk reduction associated with early use of MACE‐preventive GLMs.ResultsA total of 19 685 subjects were included, with 5431 having MACE, including 4453 strokes, 977 AMI, and 1 death. There were 11 123 subjects with good baseline GC. Subjects with good baseline GC had 0.837 (confidence interval [CI]: 0.782–0.895) times lower MACE risk than their counterpart. Subjects with a single MACE‐preventive GLM at baseline with continuous use >365 days showed a decreased MACE hazard ratio (0.681; CI: 0.635–0.731). Among all MACE‐preventive GLMs, semaglutide provided a more significant MACE‐preventive effect.ConclusionsThis study identified that GLM, early GC, and HVS are MACE determinants among patients with T2DM. Novel GLM, adequate GC, and reduction of HVS can benefit MACE outcomes.image
Revisiting the Briggs Ancient DNA Damage Model: A Fast Maximum Likelihood Method to Estimate Post‐Mortem Damage
Authors: Zhao Lei , Henriksen Rasmus Amund , Ramsøe Abigail , Nielsen Rasmus , Korneliussen Thorfinn Sand 
Published: October 2024

ABSTRACTOne essential initial step in the analysis of ancient DNA is to authenticate that the DNA sequencing reads are actually from ancient DNA. This is done by assessing if the reads exhibit typical characteristics of post‐mortem damage (PMD), including cytosine deamination and nicks. We present a novel statistical method implemented in a fast multithreaded programme, ngsBriggs that enables rapid quantification of PMD by estimation of the Briggs ancient damage model parameters (Briggs parameters). Using a multinomial model with maximum likelihood fit, ngsBriggs accurately estimates the parameters of the Briggs model, quantifying the PMD signal from single and double‐stranded DNA regions. We extend the original Briggs model to capture PMD signals for contemporary sequencing platforms and show that ngsBriggs accurately estimates the Briggs parameters across a variety of contamination levels. Classification of reads into ancient or modern reads, for the purpose of decontamination, is significantly more accurate using ngsBriggs than using other methods available. Furthermore, ngsBriggs is substantially faster than other state‐of‐the‐art methods. ngsBriggs offers a practical and accurate method for researchers seeking to authenticate ancient DNA and improve the quality of their data.
The Ribosomal Operon Database: A Full‐Length rDNA Operon Database Derived From Genome Assemblies
Authors: Krabberød Anders K. , Stokke Embla , Thoen Ella , Skrede Inger , Kauserud Håvard 
Published: October 2024

ABSTRACTCurrent rDNA reference sequence databases are tailored towards shorter DNA markers, such as parts of the 16/18S marker or the internally transcribed spacer (ITS) region. However, due to advances in long‐read DNA sequencing technologies, longer stretches of the rDNA operon are increasingly used in environmental sequencing studies to increase the phylogenetic resolution. There is, therefore, a growing need for longer rDNA reference sequences. Here, we present the ribosomal operon database (ROD), which includes eukaryotic full‐length rDNA operons fished from publicly available genome assemblies. Full‐length operons were detected in 34.1% of the 34,701 examined eukaryotic genome assemblies from NCBI. In most cases (53.1%), more than one operon variant was detected, which can be due to intragenomic operon copy variability, allelic variation in non‐haploid genomes, or technical errors from the sequencing and assembly process. The highest copy number found was 5947 in Zea mays. In total, 453,697 unique operons were detected, with 69,480 operon variant clusters remaining after intragenomic clustering at 99% sequence identity. The operon length varied extensively across eukaryotes, ranging from 4136 to 16,463 bp, which will lead to considerable polymerase chain reaction (PCR) bias during amplification of the entire operon. Clustering the full‐length operons revealed that the different parts (i.e., 18S, 28S, and the hypervariable regions V4 and V9 of 18S) provide divergent taxonomic resolution, with 18S, the V4 and V9 regions being the most conserved. The ROD will be updated regularly to provide an increasing number of full‐length rDNA operons to the scientific community.
good: An R package for modelling count data
Authors: Agis David , Tur Jordi , Moriña David , Puig Pedro , Fernández‐Fontelo Amanda 
Published: October 2024

Abstract

Organisms‐related data often appear as counts. The Poisson distribution is the most popular choice for modelling count data, but this distribution assumes equidispersion, which is usually not satisfied in real‐world data. Deviations from the Poisson assumption lead to discrete‐valued distributions that can fit over‐ and/or underdispersion.

Although models for count data with over‐dispersion have been widely considered in the literature, models for underdispersion—the opposite phenomenon—have received less attention because underdispersion is relatively common only in certain research fields, including ecology.

The Good distribution is a flexible option for modelling count data with over‐dispersion or underdispersion, although no R packages are available so far offering functionalities such as calculating quantiles, probabilities, etc., of a Good distribution or providing a method for modelling a Good‐distributed output based on a number of potential predictors.

This paper presents the R package good, which computes the standard probabilistic functions, generates random samples from a population following a Good distribution and estimates the Good regression.
Public perceptions of opioid misuse recovery and related resources in a nationally representative sample of United States adults
Authors: Golan Olivia , Kresovich Alex , Drymon Christina , Ducharme Lori , Flanagan Balawajder Elizabeth , Borowiecki Mateusz , Lamuda Phoebe , Taylor Bruce , Pollack Harold , Schneider John 
Published: October 2024

AbstractAimsTo understand how the US public defines recovery from opioid misuse and the recovery‐related resources it views as most helpful, and to compare differences by opioid misuse history and demographic characteristics.DesignObservational study of data from the nationally representative AmeriSpeak® Panel survey administered in October/November 2021.SettingUnited States.Participants6515 adults (≥ 18 years).MeasurementsRespondents ranked 10 definitions of recovery (religious in nature; spiritual in nature; physical/mental in nature; contributing to society; enhanced quality of life; seeking professional help; having a sense of purpose; moderate/controlled substance use; no drug use; abstaining from all substance use) and 9 resources that might contribute to recovery (primary care physician; intensive inpatient program; residential rehabilitation program; self‐help group; therapist/psychologist/social worker; prescribed medication; talking to family/friends; spiritual/natural healer; faith‐based organization). We explored differences in rankings by opioid misuse history (personal vs. family/friend vs. no history) and demographic characteristics (race, sex, age) using multivariable ordinal logistic regression.FindingsSeeking professional help was the most endorsed recovery definition overall [mean (M) = 6.97, standard error (SE) = 0.03]. Those with personal opioid misuse history ranked enhanced quality of life (B = 0.16, P = 0.049) and having a sense of purpose (B = 0.16, P = 0.029) significantly higher, and ranked abstaining from substance use (B = ‐0.20, P = 0.009) significantly lower as recovery definitions than those without a history of opioid misuse. Compared with White respondents, Black (B = 0.60, P < 0.001) and Hispanic (B = 0.55, P < 0.001) respondents defined recovery as more religious in nature. Residential rehabilitation program was identified as the most helpful resource for recovery (M = 7.16, SE = 0.02), while prescribed medication received a relatively low ranking overall (M = 4.05, SE = 0.03). Those with family/friend opioid misuse history ranked prescribed medication as less helpful than others (B = ‐0.14, P = 0.003).ConclusionsThe general US public's views around recovery from opioid misuse appear to focus on abstinence and formal treatment receipt, while people with a history of opioid misuse place less emphasis on abstinence and greater emphasis on other aspects of well‐being.
Borderline tumours of the ovary: A 37‐year experience at a tertiary referral centre
Authors: McBain Rosie , Kashyap Aidan , Bishop Milly , Vicario Estefania , Volchek Mila , Naaman Yael , Rajadevan Niveditha , Jones Antonia , Neesham Deborah , McNally Orla 
Published: October 2024

IntroductionBorderline ovarian tumours (BOT) are a common epithelial ovarian tumours. Typically diagnosed at an early stage with a good prognosis, many BOT are treated conservatively. Recurrence is common. This update to our last audit in 1997 represents one of the largest audits of BOT to date.Materials and MethodsAll patients with BOT managed at ‘the hospital’ from 1984 to 2021 were included. Expert pathology review was available.ResultsThere were 549 cases included. The recurrence rate was 5% (n = 29/549) with 1.4% (n = 8/549) undergoing malignant transformation. Three of the eight women who recurred as cancer died from their disease. Frozen section was predictive of histologic diagnosis in 92% (n = 55/60) of serous tumours (SBOT), but only 62% (n = 54/87) of mucinous tumours (MBOT). In MBOT where the appendix appeared normal intra‐operatively, it was histologically benign in all cases (n = 63). In SBOT, the recurrence rate was 5/23 (22%), 12/52 (23%), 1/29 (3%) and 3% (P = <0.01) for unilateral cystectomy, unilateral oophorectomy ± cystectomy, bilateral oophorectomy, and bilateral oophorectomy with hysterectomy, respectively, as index procedure. In MBOT this correlated to 2/20 (10%), 3/93 (3%), 0 and 1/58 (2%), respectively.DiscussionThis study describes important information correlating first surgical procedure and fertility‐sparing surgery to recurrence and malignant transformation. For all BOT subtypes, fertility‐preserving surgery increased the risk of recurrence and hysterectomy was not superior to removal of both ovaries. In MBOT, frozen section is of limited utility and the macroscopically normal appendix is very unlikely to be anything but benign, if MBOT is the true histologic diagnosis.
Diagnostic Value of the Voltage‐to‐Mass Ratio in Biopsy‐Proven Cardiac Amyloidosis
Authors: Jiang Zihan , Zhuang Shengsheng , Tang Min , Tian Zhuang , Zhang Shuyang 
Published: October 2024

ABSTRACTObjectivesThe calculation of left ventricular mass varies in different studies, and reference values of the voltage‐to‐mass ratio for diagnosing cardiac amyloidosis (CA) are lacking. This study aimed to determine the value of the voltage‐to‐mass ratio in diagnosing CA and provide an optimal cut‐off value for different calculation methods.MethodsWe reviewed the electrocardiograms and echocardiograms of 213 consecutive biopsy‐proven CA patients, 236 hypertrophic cardiomyopathy (HCM) patients, 100 hypertensive heart disease patients, and 181 healthy controls. Left ventricular mass was calculated using linear and cross‐sectional area (CSA) methods. The voltage‐to‐mass ratios were compared between the CA group and other groups. The voltage‐to‐mass ratio obtained was used to build multivariate logistic regression models that predicted the log odds of developing CA.ResultsThe CA group had a significantly lower voltage‐to‐mass ratio than the HCM, hypertensive heart disease, and healthy control groups. The voltage‐to‐mass ratio was an independent factor significantly associated with the CA diagnosis after adjusting for baseline characteristics. Linear and CSA methods yielded areas under the ROC curve of 0.86 and 0.90, respectively. Using the CSA method, the optimal cut‐off was 16.42 mV/mm2/m2, with 89.0% sensitivity and 80.8% specificity.ConclusionThe voltage‐to‐mass ratio could differentiate patients with CA, HCM, and hypertensive heart disease from healthy controls, potentially providing an accurate and non‐invasive alternative to current expensive and invasive diagnostic techniques.
An extended substrate spectrum of the proton organic cation antiporter and relation to other cation transporters
Authors: Ali Khan Cauzar , Kirsch Nicolai , Brockmöller Jürgen , Redeker Kyra‐Elisa Maria 
Published: October 2024

AbstractMost central nervous system (CNS) active drugs are organic cations, which need carrier proteins for efficient transfer through the blood–brain barrier (BBB). A genetically still unidentified proton organic cation (H+/OC) antiporter is found in several tissues, including endothelial cells of the BBB. We characterized the substrate spectrum of the H+/OC antiporter and the overlap in substrate spectrum with OCTN1, OCTN2 or OCT3 by screening 87 potential substrates for transport activity. Based on high antiport rates, 45 of the tested substances were substrates of the H+/OC antiporter. They included antidepressants (like tranylcypromine or nortriptyline), antipsychotics (like levomepromazine) and local anaesthetics. Concentration‐dependent transport was confirmed for 38 of the substrates. Transport uptake depending on a pH gradient across the cell membrane confirmed that 43 drugs were indeed substrates of the H+/OC antiporter. However, the patterns of pH dependence differed between the substrates, possibly indicating different modes of transport or the existence of multiple antiporter proteins. The substrate overlap between the H+/OC antiporter and OCTN1, OCTN2 or OCT3 was minimal, indicating that the latter three are not the proteins underlying the H+/OC antiporter activity. Overall, about 50% of positively charged drugs may be substrates of the antiporter, which may be the most important membrane transport protein for many drugs.
Social Inclusion Through Making Neighbourhood Connections: Experiences of Older Adults With Intellectual Disabilities of Local Volunteering and Leisure, Facilitated by Local Connectors
Authors: Boland Geraldine , Potter Anne‐Marie , de Paor Eilin , Guerin Suzanne 
Published: October 2024

ABSTRACTBackgroundThe social networks of adults with intellectual disabilities are often small and may be limited to family, paid staff and others with disabilities. This study explored the social inclusion of six individuals who joined mainstream leisure clubs or became local volunteers.MethodThis qualitative intervention study provided structured support and education to local connectors, existing members of clubs/organisations who provided one‐to‐one support to new members with intellectual disabilities. After 4 months, qualitative interviews were conducted to explore the experiences of the six participants with disability. Data were analysed using content analysis.FindingsIndividuals joining mainstream leisure clubs or volunteering, with natural supporters, creates opportunities for making new acquaintances and expanding social networks. Finding local connectors and opportunities for shared volunteering or leisure activities based on personal goals/interests are key to individuals forming new acquaintances close to where they live. Barriers and facilitators to participation are identified.ConclusionsAdults with intellectual disabilities becoming volunteers or joining mainstream leisure clubs has the potential to lead to enhanced opportunities for social inclusion in their neighbourhoods. Implications for policy and practice are examined. Recommendations for further research are explored. A Valued Social Role Checklist developed from this study offers a tool when sourcing social roles.
Adverse events after chemodenervation with onabotulinum neurotoxin A in children with hypertonia and sialorrhea
Authors: Krieger Jacqueline , Prosser Laura , Evans Sarah Helen 
Published: October 2024

AbstractAimTo identify the incidence and type of adverse events reported after chemodenervation with onabotulinum neurotoxin A (BoNT‐A) in children with hypertonia and sialorrhea and compare adverse events in the on‐label or off‐label use of BoNT‐A with regard to dose, patient's age, and location of the injection.MethodUsing a retrospective chart review, we studied BoNT‐A injections occurring from January 2017 to December 2020 in patients at a pediatric hospital. The electronic health record was examined to identify adverse events reported within 2 months of the injection. Data included the patient's age, sex, race, and ethnicity, as well as the type of toxin injected, the dose, the location of injection, and the patient's weight.ResultsWe analyzed 1733 procedures. Adverse events were infrequent (2.5%) and not serious, most commonly reported as pain or discomfort. All adverse events were temporary and there were no deaths. We did not observe a meaningful difference in the frequency of adverse events for injections that exceeded the 2022 US Food and Drug Administration (FDA)‐approved maximum dose compared to injections that were within the FDA‐approved dose range. The likelihood of adverse events did not increase with higher doses of BoNT‐A. More adverse events were reported for injection into the salivary glands (4.37%) than into the extremities (2.26%).InterpretationHigher doses of injected BoNT‐A in a pediatric population may be safe. Further work is needed to investigate the relationship between dose and efficacy.
Using technology to support diabetes care in hospital: Guidelines from the Joint British Diabetes Societies for Inpatient Care (JBDS‐IP) group and Diabetes Technology Network (DTN) UK
Authors: Avari Parizad , Choudhary Pratik , Lumb Alistair , Misra Shivani , Rayman Gerry , Flanagan Daniel , Dhatariya Ketan ,   the Joint British Diabetes Societies for Inpatient Care (JBDS‐IP) group
Published: October 2024

AbstractThis article summarises the Joint British Diabetes Societies for Inpatient Care (JBDS‐IP) Group guidelines on the use of technology to support diabetes care in hospital. The guideline incorporates two main areas: (i) use of wearable technology devices to improve diabetes management in hospital (including continuous glucose monitoring and insulin pump therapy) and (ii) information technology. Although it is reasonable to extrapolate from the evidence available, that devices developed to enhance diabetes care outside hospital will show similar benefits, there are challenges posed within the inpatient setting in hospital. This guidance provides a pragmatic approach to supporting self‐management in individuals using wearable technology admitted to hospital. Furthermore, it also aims to provide a best practice guide for using information technology to monitor diabetes care and communicate between health professionals.
Association of initial serum sodium change and clinical outcome in patients with diabetes receiving sodium–glucose cotransporter‐2 inhibitor therapy: A multicentre database analysis in Taiwan
Authors: Cheng Yu‐Wen , Chan Yi‐Hsin , Chuang Chi , Chen Shao‐Wei , Chao Tze‐Fan , Kao Yi‐Wei 
Published: October 2024

AbstractAimThe study aimed to assess the impact of varying degrees of initial serum sodium change among patients with type 2 diabetes (T2D) starting sodium–glucose cotransporter‐2 inhibitor (SGLT2i) therapy and their subsequent clinical outcome.MethodsWe used medical data from a multicentre health care provider in Taiwan and recruited 4400 patients with T2D with baseline normal serum sodium (135–145 mmol/L) and follow‐up serum sodium measures available after 3 months of SGLT2i treatment from 1 June 2016 to 31 December 2021.ResultsAfter a median of 2.9 (2.4, 3.4) months of SGLT2i treatment, overall, there was a minimal change in serum sodium levels (from 139.6 ± 2.4 to 139.5 ± 3.7 mmol/L). Most patients (87.8%) maintained normal sodium levels, while 8.6% (n = 378) experienced hyponatraemia (<135 mmol/L) and 3.6% (n = 158) hypernatraemia (>145 mmol/L). Factors independently associated with hyponatraemia included cancer history, chronic lung disease, insulin use, higher glycated haemoglobin, impaired liver function, lower baseline sodium and greater initial decline in kidney function. Conversely, factors linked to hypernatraemia included older age, absence of cancer history, loop diuretic and non‐steroidal anti‐inflammatory drug use, higher baseline sodium and a lesser initial decline in kidney function. Over a median of 26.0 months of follow‐up, hyponatraemia shortly after starting SGLT2i therapy was associated with significantly increased risks of major adverse cardiovascular events [hazard ratio (HR): 2.52; 95% confidence interval (CI): 1.83–3.48], heart failure for hospitalization (HR: 1.66; 95% CI: 1.16–2.37), major adverse renal events (HR: 2.27; 95% CI: 1.73–2.96) and all‐cause death (HR: 2.98; 95% CI: 2.17–4.11) after adjusting for clinically relevant factors. Non‐linear analysis indicated that a more pronounced initial decline in serum sodium levels correlated steeply with higher risks of these adverse events.ConclusionWhile most patients with T2D maintain stable serum sodium homeostasis on SGLT2i therapy, a subset may experience dysnatraemic events with potential worse clinical consequences. Physicians should be vigilant about monitoring sodium levels and considering the associated risks when initiating SGLT2i therapy in patients with risk.