bluuebunny/crossref_metadata_2025_split huggingface dataset:
Flexible optimal bus‐schedule bridging for metro operation‐interruption
Authors: Lai Yuanwen , Liang Jianhong , Rao Yinsheng , Fan Yanhui , Zhan Renyan , Easa Said , Wang Shuyi 
Published: April 2024

AbstractUnder the sudden interruption of the metro, it is significant to dispatch emergency bridging buses to evacuate stranded passengers to improve linkage management and service reliability. Aiming at the problem of emergency bridging bus scheduling, considering the remaining capacity of conventional buses, passenger tolerance, and site convenience, a flexible combined emergency bridging bus scheduling model is constructed based on the constraints of vehicle capacity, dispatching capacity, and maximum evacuation times of emergency bridging bus, aiming at minimizing the maximum evacuation time and passenger delay. The improved Harris hawk algorithm is used to solve the model, and the evacuation plan of the demand‐responsive and station‐station bridging lines is obtained. The maximum evacuation time is 41 min, and the average delay of stranded passengers is 19 min. The results show that the maximum evacuation time is 10% and 27% less than the fixed combined and single scheduling. The average delay is 16% and 42% less than the fixed combination and traditional single scheduling. The sensitivity analysis of the influencing factors of emergency bridging bus scheduling is conducted. The results show that the flexible combined emergency bridging bus scheduling model constructed in this paper can improve evacuation efficiency and reduce passenger travel delays.
A novel algorithm for open switch fault detection and fault tolerant control of interleaved DC‐DC boost converters
Authors: Zandi Omid , Poshtan Javad 
Published: April 2024

AbstractThis paper presents a novel algorithm for fault diagnosis and fault tolerant control of interleaved boost converters (IBCs) in the presence of single or double simultaneous open‐circuit faults (OCFs) in power switches. An innovative diagnosis signal (recorded by a cheap current sensor) will be introduced whose waveform mainly depends on the healthy or faulty condition of the converter. Since the diagnosis signal is periodic in the steady‐state operation of the converters, its Fourier Series coefficients, together with the duty cycle of the converter are used as distinguishing features for fault diagnosis of the OCFs in the converter. The well‐known Kalman filter is utilized for robust estimation of the Fourier‐based features. Finally, the modulation of the remaining healthy phases is rearranged in a way that the pre‐fault performance recovers. The proposed algorithm is verified in a laboratory four‐phase IBC setup in which the experimental results show its satisfactory performance. Also, the structure of the proposed method is straightforward and can be implemented in the same microcontroller which is used for voltage and current regulation of the converter.
De-risking pension plans: the impact on firm value from lump-sum buyouts
Authors: Jorgensen Randy , Obonyo Tirimba , Wingender John R. 
Published: April 2024

AbstractFirms have attempted to de-risk their pension obligations by offering its pension beneficiaries a lump-sum distribution instead of the guaranteed payments to be paid to retirees in a defined benefit pension plan. We examine the stock market reaction to the announcement of these offerings using event study methodologies. We find a statistically significant positive cumulative abnormal returns for the 20-day period prior to the event, the 20-day period after the event, and for the entire 41-day event period surrounding the announcement. We also find that the cumulative abnormal returns are higher the more liabilities a firm has and increases with the level of funding of the pension plan. Our results contribute to the literature on pensions by finding that firms that buy out their pensioners’ defined benefit payments via a lump-sum distribution experience an increase in firm value. There is a significant amount of analysis of such buyouts in the literature and in the press, but our results are the first to examine and document the increase in value derived from such pension changes. We also more fully develop the motivations for such events from a cost/benefit perspective.
Career decisions in artistic professions during the COVID-19 pandemic in Germany—an experimental study
Authors: Seitz Matthias , Frick Ulrich , Tallon Miles , Gotthardt Karina , Rakoczy Katrin 
Published: April 2024

AbstractThe COVID-19 pandemic has had a significant impact on the professional situation in artistic professions. Repeated lockdowns resulted in the cancellation of cultural events and exacerbated economic challenges, depriving artists and people working in the culture industry of their primary source of income. Such drastic conditions could lead to important professional decisions, including career changes. This study aimed to determine the factors that could influence career decisions among artistic professionals during a second pandemic lockdown period in Germany. To examine whether health concerns or financial struggles are more important in shaping artistic professionals’ decisions to change or stay in their profession, a vignette experiment was conducted in an online survey (n = 788) in the winter of 2020–2021. In the experiment’s 2*3-factorial randomised design, all respondents were asked to put themselves in the role of artists and make decisions about career changes under different income conditions or with different health prospects. The vignette experiment revealed that income losses related to career changes decreased the willingness to change careers, whereas health prospects (hypothetical differences in vaccine efficacy) did not affect the decisions. In addition, other variables were found to explain career decisions; female gender and signs of a depressive disorder were associated with greater willingness for career turnover, whereas a higher educational level and status of earning one’s livelihood in the culture industry were associated with a diminished tendency for career turnover. The latter impact factor was interpreted as a kind of “don´t give up effect” that is particularly observable among artistic professionals.
Discrepancies in corrected calcium versus ionised calcium in a geriatric population: an observational study
Authors: Suryapranata Alexandra P S P , Keijsers Carolina J P W , Kurstjens Steef , Van Strien Astrid M 
Published: April 2024

Abstract

Background
Calcium can be measured as ionised (Ca-ionised) or albumin-adjusted total calcium (Ca-albumin). Current clinical guidelines predominantly utilise Ca-albumin, despite Ca-ionised being the gold standard. Discrepancies can occur between these measurement modalities and can lead to clinical dilemmas. It remains unclear how large these discrepancies are in older patients. This study investigated the discrepancies between Ca-ionised and Ca-albumin in geriatric patients.

Methods
This is an observational study of all geriatric patients (n = 876) in the Jeroen Bosch Hospital (January 2018 and January 2021) in whom both Ca-ionised and Ca-albumin were measured. Misclassification of calcaemic state (i.e. low, normal or high) was calculated (percentages), the measure of agreement was described using Cohen’s Kappa and for the continuous data Pearson’s correlation coefficient was used. Relevant categories of age and renal function were considered for effect modification effects and studied by interaction terms in a regression model.

Results
In one-third of the measurements, there was a misclassification. Ca-albumin measurements failed to identify 28% of hypocalcaemia. In 3.5%, hypercalcemia based on Ca-albumin was not confirmed by Ca-ionised. The correlation coefficient between Ca-ionised and Ca-albumin was 0.743 (P = 0.01) and measure of agreement by Kappa was 0.213 (P &lt; 0.001). In the oldest old (≥ 85 years) and patients with eGFR &lt;30 ml/min/1.73 m2 ,the agreement by Kappa was lower, with values of 0.192 and 0.104, respectively.

Conclusion
There is a discrepancy between Ca-albumin and Ca-ionised in one-third of the geriatric patients, leading to clinical dilemmas. In the oldest old and patients with renal dysfunction, this problem is most pronounced.
Understanding the association between pain and delirium in older hospital inpatients: systematic review and meta-analysis
Authors: White Nicola , Bazo-Alvarez Juan Carlos , Koopmans Michel , West Emily , Sampson Elizabeth L 
Published: April 2024

Abstract

Objective
Delirium and pain are common in older adults admitted to hospital. The relationship between these is unclear, but clinically important. We aimed to systematically review the association between pain (at rest, movement, pain severity) and delirium in this population.

Methods
PubMed, EMBASE, CINAHL, PsycINFO, Cochrane and Web of Science were searched (January 1982–November 2022) for Medical Subject Heading terms and synonyms (‘Pain’, ‘Analgesic’, ‘Delirium’). Study eligibility: (1) validated pain measure as exposure, (2) validated delirium tool as an outcome; participant eligibility: (1) medical or surgical (planned/unplanned) inpatients, (2) admission length ≥ 48 h and (3) median cohort age over 65 years. Study quality was assessed with the Newcastle Ottawa Scale. We collected/calculated odds ratios (ORs) for categorical data and standard mean differences (SMDs) for continuous data and conducted multi-level random-intercepts meta-regression models. This review was prospectively registered with PROSPERO [18/5/2020] (CRD42020181346).

Results
Thirty studies were selected: 14 reported categorical data; 16 reported continuous data. Delirium prevalence ranged from 2.2 to 55%. In the multi-level analysis, pain at rest (OR 2.14; 95% confidence interval [CI] 1.39–3.30), movement (OR 1.30; 95% CI 0.66–2.56), pain categorised as ‘severe’ (OR 3.42; 95% CI 2.09–5.59) and increased pain severity when measured continuously (SMD 0.33; 95% CI 0.08–0.59) were associated with an increased delirium risk. There was substantial heterogeneity in both categorical (I2 = 0%–77%) and continuous analyses (I2 = 85%).

Conclusion
An increase in pain was associated with a higher risk of developing delirium. Adequate pain management with appropriate analgesia may reduce incidence and severity of delirium.
Challenges and patient outcomes in chronic subdural haematoma at the level of a regional care system A multi-centre, mixed-methods study from the East of England
Authors: Stubbs Daniel James , Khanna Sam , Davies Benjamin M , Vivian Mark E , Bashford Tom , Adatia Krishma , Chen Ping , Clarkson Peter John , McGlennan Catherine , Indurawage Lalani , Patel Martyn , Tyagunenko Rada , Burnstein Rowan , Menon David K , Hutchinson Peter J , Joannides Alexis ,   on behalf of the SENIOR-C team
Published: April 2024

Abstract

Background
Chronic subdural haematoma (cSDH) is a common neurosurgical pathology affecting older patients with other health conditions. A significant proportion (up-to 90%) of referrals for surgery in neurosciences units (NSU) come from secondary care. However, the organisation of this care and the experience of patients repatriated to non-specialist centres are currently unclear.

Objectives
This study aimed to clarify patient outcome in non-specialist centres following NSU discharge for cSDH surgery and to understand key system challenges. The study was set within a representative neurosurgical care system in the east of England.

Design and methods
We performed a retrospective cohort analysis of patients referred for cSDH surgery. Alongside case record review, patient and staff experience were explored using surveys as well as an interactive c-design workshop. Challenges were identified from thematic analysis of survey responses and triangulated by focussed workshop discussions.

Results
Data on 381 patients referred for cSDH surgery from six centres was reviewed. One hundred and fifty-six (41%) patients were repatriated following surgery. Sixty-one (39%) of those repatriated suffered an inpatient complication (new infection, troponin rise or renal injury) following NSU discharge, with 58 requiring institutional discharge or new care. Surveys for staff (n = 42) and patients (n = 209) identified that resourcing, communication, and inter-hospital distance posed care challenges. This was corroborated through workshop discussions with stakeholders from two institutions.

Conclusions
A significant amount of perioperative care for cSDH is delivered outside of specialist centres. Future improvement initiatives must recognise the system-wide nature of delivery and the challenges such an arrangement presents.
Development and implementation of ambulatory care pharmacy services at an internal medicine clinic
Authors: Wells Casey , Warren Anne Carrington , Scott Mollie Ashe 
Published: April 2024

Abstract

Purpose
This report describes the step-by-step process that led to expansion of ambulatory care pharmacy services at a newly established internal medicine clinic within a patient-centered medical home in North Carolina.

Summary
Implementation of clinical pharmacist services at the clinic was led by a postgraduate year 2 (PGY2) pharmacy resident and guided by the 9 steps described in the book Building a Successful Ambulatory Care Practice: A Complete Guide for Pharmacists. After a needs assessment and review of the demographics and insurance status of the clinic’s target population, it was determined that pharmacist services would focus on quality measures including diabetes nephropathy screening, diabetes eye examination, blood glucose control in diabetes, discharge medication reconciliation, annual wellness visits, and medication adherence in diabetes, hypercholesterolemia, and hypertension. Clinic appointments were conducted under 3 models: a pharmacist-physician covisit model, a “floor model” of pharmacist consultation on drug information or medication management issues during medical resident sign-out sessions with supervising physicians (medical residents could also see patients along with the pharmacist at a covisit appointment), and a covisit model of stacked physician and pharmacist appointments. The pharmacist’s services were expanded from 2 half-day clinic sessions per week initially to 5 or 6 half-day clinic sessions by the end of the residency year.

Conclusion
By the fourth quarter of the first PGY2 residency year in which ambulatory care pharmacy services were provided in the clinic, the clinical and financial impact of those services justified the addition of a second full-time pharmacist to the clinic team.
Surveying biomedical relation extraction: a critical examination of current datasets and the proposal of a new resource
Authors: Huang Ming-Siang , Han Jen-Chieh , Lin Pei-Yen , You Yu-Ting , Tsai Richard Tzong-Han , Hsu Wen-Lian 
Published: April 2024

Abstract
Natural language processing (NLP) has become an essential technique in various fields, offering a wide range of possibilities for analyzing data and developing diverse NLP tasks. In the biomedical domain, understanding the complex relationships between compounds and proteins is critical, especially in the context of signal transduction and biochemical pathways. Among these relationships, protein–protein interactions (PPIs) are of particular interest, given their potential to trigger a variety of biological reactions. To improve the ability to predict PPI events, we propose the protein event detection dataset (PEDD), which comprises 6823 abstracts, 39 488 sentences and 182 937 gene pairs. Our PEDD dataset has been utilized in the AI CUP Biomedical Paper Analysis competition, where systems are challenged to predict 12 different relation types. In this paper, we review the state-of-the-art relation extraction research and provide an overview of the PEDD’s compilation process. Furthermore, we present the results of the PPI extraction competition and evaluate several language models’ performances on the PEDD. This paper’s outcomes will provide a valuable roadmap for future studies on protein event detection in NLP. By addressing this critical challenge, we hope to enable breakthroughs in drug discovery and enhance our understanding of the molecular mechanisms underlying various diseases.
GLIMMERS: glioma molecular markers exploration using long-read sequencing
Authors: Thongrattana Wichayapat , Arigul Tantip , Suktitipat Bhoom , Pithukpakorn Manop , Sathornsumetee Sith , Wongsurawat Thidathip , Jenjaroenpun Piroon 
Published: April 2024

Abstract

Summary
The revised WHO guidelines for classifying and grading brain tumors include several copy number variation (CNV) markers. The turnaround time for detecting CNVs and alterations throughout the entire genome is drastically reduced with the customized read incremental approach on the nanopore platform. However, this approach is challenging for non-bioinformaticians due to the need to use multiple software tools, extract CNV markers and interpret results, which creates barriers due to the time and specialized resources that are necessary. To address this problem and help clinicians classify and grade brain tumors, we developed GLIMMERS: glioma molecular markers exploration using long-read sequencing, an open-access tool that automatically analyzes nanopore-based CNV data and generates simplified reports.

Availability and implementation
GLIMMERS is available at https://gitlab.com/silol_public/glimmers under the terms of the MIT license.
NeoAgDT: optimization of personal neoantigen vaccine composition by digital twin simulation of a cancer cell population
Authors: Mösch Anja , Grazioli Filippo , Machart Pierre , Malone Brandon 
Published: April 2024

Abstract

Motivation
Neoantigen vaccines make use of tumor-specific mutations to enable the patient’s immune system to recognize and eliminate cancer. Selecting vaccine elements, however, is a complex task which needs to take into account not only the underlying antigen presentation pathway but also tumor heterogeneity.

Results
Here, we present NeoAgDT, a two-step approach consisting of: (i) simulating individual cancer cells to create a digital twin of the patient’s tumor cell population and (ii) optimizing the vaccine composition by integer linear programming based on this digital twin. NeoAgDT shows improved selection of experimentally validated neoantigens over ranking-based approaches in a study of seven patients.

Availability and implementation
The NeoAgDT code is published on Github: https://github.com/nec-research/neoagdt.
A data-adaptive methods in detecting exogenous methyltransferase accessible chromatin in human genome using nanopore sequencing
Authors: Tu Kailing , Li Xuemei , Zhang Qilin , Huang Wei , Xie Dan 
Published: April 2024

Abstract

Motivation
Identifying chromatin accessibility is one of the key steps in studying the regulation of eukaryotic genomes. The combination of exogenous methyltransferase and nanopore sequencing provides an strategy to identify open chromatin over long genomic ranges at the single-molecule scale. However, endogenous methylation, non-open-chromatin-specific exogenous methylation and base-calling errors limit the accuracy and hinders its application to complex genomes.

Results
We systematically evaluated the impact of these three influence factors, and developed a model-based computational method, methyltransferase accessible genome region finder (MAGNIFIER), to address the issues. By incorporating control data, MAGNIFIER attenuates the three influence factors with data-adaptive comparison strategy. We demonstrate that MAGNIFIER is not only sensitive to identify the open chromatin with much improved accuracy, but also able to detect the chromatin accessibility of repetitive regions that are missed by NGS-based methods. By incorporating long-read RNA-seq data, we revealed the association between the accessible Alu elements and non-classic gene isoforms.

Availability and implementation
Freely available on web at https://github.com/Goatofmountain/MAGNIFIER.
Sensitivity analysis for matched observational studies with continuous exposures and binary outcomes
Authors: Zhang Jeffrey , Small Dylan S , Heng Siyu 
Published: April 2024

Summary
Matching is one of the most widely used study designs for adjusting for measured confounders in observational studies. However, unmeasured confounding may exist and cannot be removed by matching. Therefore, a sensitivity analysis is typically needed to assess a causal conclusion’s sensitivity to unmeasured confounding. Sensitivity analysis frameworks for binary exposures have been well established for various matching designs and are commonly used in various studies. However, unlike the binary exposure case, there still lacks valid and general sensitivity analysis methods for continuous exposures, except in some special cases such as pair matching. To fill this gap in the binary outcome case, we develop a sensitivity analysis framework for general matching designs with continuous exposures and binary outcomes. First, we use probabilistic lattice theory to show that our sensitivity analysis approach is finite population exact under Fisher’s sharp null. Second, we prove a novel design sensitivity formula as a powerful tool for asymptotically evaluating the performance of our sensitivity analysis approach. Third, to allow effect heterogeneity with binary outcomes, we introduce a framework for conducting asymptotically exact inference and sensitivity analysis on generalized attributable effects with binary outcomes via mixed-integer programming. Fourth, for the continuous outcome case, we show that conducting an asymptotically exact sensitivity analysis in matched observational studies when both the exposures and outcomes are continuous is generally NP-hard, except in some special cases such as pair matching. As a real data application, we apply our new methods to study the effect of early-life lead exposure on juvenile delinquency. An implementation of the methods in this work is available in the R package doseSens.
Genetic divergences provide evidence to accept a new Mediterranean genus Antalia (Apiaceae) and insights into allopatric divergence extended to the Pliocene
Authors: Doğru-Koca Aslı 
Published: April 2024

Abstract
Narrow endemism is the core of plant diversity in flora of the Mediterranean Basin, which is among the world’s 36 biodiversity hotspots. The Mediterranean genus Kundmannia (Careae, Apioideae) comprises just three species, K. sicula, K. anatolica, and K. syriaca. Notably, K. sicula has a wide distribution from the western Mediterranean to Greece, while K. anatolica and K. syriaca occur only in Turkey’s Taurus Mountains, which is a phylogeographical hotspot. Initially, the aim herein was to determine the phylogenetic placement of the genus Kundmannia based on DNA sequences, but it later developed to describing a new genus, Antalia gen. nov., and revealing historical events that acted as drivers in the genetic divergence between Kundmannia and Antalia. Both ribosomal and combined chloroplast multilocus sequences were used to unravel the phylogenetic topology. Toward this aim, morphological characteristics were examined. Based on this, Antalia differs from Kundmannia by its shorter bracteoles and petals, the colour of the petals, and smaller fruits. The phylogenetic results revealed that the genus Kundmannia is nested within the tribe Careae and is not monophyletic. Antalia, which is genetically separate from Kundmannia, is described as a new genus. Detailed morphological descriptions and identification keys are provided. Causes of the genetic disjunction between Antalia and Kundmannia were carefully considered in a time-calibrated phylogenetic framework. The Mediterranean Sea has acted as a relatively effective barrier between these genera since the Messinian salinity crisis. The unwinged mericarps seem to have facilitated the work of the barrier. Historical events during and after the Pliocene and allopatric vicariance seem to have been the most important drivers of evolution between Kundmannia and Antalia and within Antalia.