bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fine mapping of candidate effector genes for heart rate
Authors: Ramírez Julia , van Duijvenboden Stefan , Young William J. , Chen Yutang , Usman Tania , Orini Michele , Lambiase Pier D. , Tinker Andrew , Bell Christopher G. , Morris Andrew P. , Munroe Patricia B. 
Published: July 2024

AbstractAn elevated resting heart rate (RHR) is associated with increased cardiovascular mortality. Genome-wide association studies (GWAS) have identified > 350 loci. Uniquely, in this study we applied genetic fine-mapping leveraging tissue specific chromatin segmentation and colocalization analyses to identify causal variants and candidate effector genes for RHR. We used RHR GWAS summary statistics from 388,237 individuals of European ancestry from UK Biobank and performed fine mapping using publicly available genomic annotation datasets. High-confidence causal variants (accounting for > 75% posterior probability) were identified, and we collated candidate effector genes using a multi-omics approach that combined evidence from colocalisation with molecular quantitative trait loci (QTLs), and long-range chromatin interaction analyses. Finally, we performed druggability analyses to investigate drug repurposing opportunities. The fine mapping pipeline indicated 442 distinct RHR signals. For 90 signals, a single variant was identified as a high-confidence causal variant, of which 22 were annotated as missense. In trait-relevant tissues, 39 signals colocalised with cis-expression QTLs (eQTLs), 3 with cis-protein QTLs (pQTLs), and 75 had promoter interactions via Hi-C. In total, 262 candidate genes were highlighted (79% had promoter interactions, 15% had a colocalised eQTL, 8% had a missense variant and 1% had a colocalised pQTL), and, for the first time, enrichment in nervous system pathways. Druggability analyses highlighted ACHE, CALCRL, MYT1 and TDP1 as potential targets. Our genetic fine-mapping pipeline prioritised 262 candidate genes for RHR that warrant further investigation in functional studies, and we provide potential therapeutic targets to reduce RHR and cardiovascular mortality.
Low-calorie diets are effective for weight loss in patients undergoing benign upper gastrointestinal surgery: a systematic review and meta-analysis
Authors: Chowdhury Nibir , Hasnan Syarafina , Ullah Shahid , Thompson Sarah K. 
Published: July 2024

Abstract
Background
Obesity may increase surgical complexity in patients undergoing abdominal surgery by limiting visualization and increasing the risk of peri-operative complications. A preoperative reduction in weight and liver volume may improve surgical outcomes. The aim of our study was to evaluate the efficacy of a low-calorie diet (LCD) versus a very low-calorie diet (VLCD) in reducing weight and liver volume prior to laparoscopic surgery.

Methods
A systematic search was conducted using the following inclusion criteria: obese patients undergoing preoperative weight loss using a VLCD or LCD, evaluation of liver volume reduction, and the use of an imaging modality before and after the diet.

Results
A total of 814 patients from 21 different studies were included in this systematic review and meta-analysis, with 544 female patients (66.8%) and a mean age range between 24 and 54 years old. There was a total mean weight loss of 6.42% and mean liver volume reduction of 16.7%. Meta-analysis demonstrated that a preoperative diet (LCD or VLCD) significantly reduced weight [SMD = − 0.68; 95% CI (− 0.93, − 0.42), I2 = 82%, p ≤ 0.01] and liver volume [SMD = − 2.03; 95% CI (− 4.00, − 0.06), I2 = 94%, p ≤ 0.01]. When assessed individually, a VLCD led to significant weight reduction [SMD = − 0.79; CI (− 1.24; − 0.34), p ≤ 0.01, I2 = 90%], as did an LCD [SMD = − 0.60; CI (− 0.90; − 0.29), p ≤ 0.01, I2 = 68%). Similarly, there was a significant reduction in liver volume following a VLCD [SMD = − 1.40; CI (− 2.77, − 0.03), p ≤ 0.01, I2 = 96%], and an LCD [SMD = − 2.66; CI (− 6.13, 0.81), p ≤ 0.01, I2 = 93%]. However, there was no significant difference between the two regimens.

Conclusions
Preoperative restrictive calorie diets are effective in reducing weight and liver volume prior to laparoscopic surgery. Whilst a VLCD was better than an LCD at reducing both weight and liver volume, the difference was not significant.

Graphical abstract
Responding to the workforce crisis: consensus recommendations from the Second Workforce Summit of the American Society of Pediatric Nephrology
Authors: Soranno Danielle E. , Amaral Sandra , Ashoor Isa , Atkinson Meredith A. , Barletta Gina-Marie , Braun Michael C. , Carlson Joann , Carter Caitlin , Chua Annabelle , Dharnidharka Vikas R. , Drake Keri , Erkan Elif , Feig Dan , Goldstein Stuart L. , Hains David , Harshman Lyndsay A. , Ingulli Elizabeth , Kula Alexander J. , Leonard Mary , Mannemuddhu Sudha , Menon Shina , Modi Zubin J. , Moxey-Mims Marva , Nada Arwa , Norwood Victoria , Starr Michelle C. , Verghese Priya S. , Weidemann Darcy , Weinstein Adam , Smith Jodi 
Published: July 2024

Abstract
Importance
Pediatric patients with complex medical problems benefit from pediatric sub-specialty care; however, a significant proportion of children live greater than 80 mi. away from pediatric sub-specialty care.

Objective
To identify current knowledge gaps and outline concrete next steps to make progress on issues that have persistently challenged the pediatric nephrology workforce.

Evidence review
Workforce Summit 2.0 employed the round table format and methodology for consensus building using adapted Delphi principles. Content domains were identified via input from the ASPN Workforce Committee, the ASPN’s 2023 Strategic Plan survey, the ASPN’s Pediatric Nephrology Division Directors survey, and ongoing feedback from ASPN members. Working groups met prior to the Summit to conduct an organized literature review and establish key questions to be addressed. The Summit was held in-person in November 2023. During the Summit, work groups presented their preliminary findings, and the at-large group developed the key action statements and future directions.

Findings
A holistic appraisal of the effort required to cover inpatient and outpatient sub-specialty care will help define faculty effort and time distribution. Most pediatric nephrologists practice in academic settings, so work beyond clinical care including education, research, advocacy, and administrative/service tasks may form a substantial amount of a faculty member’s time and effort. An academic relative value unit (RVU) may assist in creating a more inclusive assessment of their contributions to their academic practice. Pediatric sub-specialties, such as nephrology, contribute to the clinical mission and care of their institutions beyond their direct billable RVUs. Advocacy throughout the field of pediatrics is necessary in order for reimbursement of pediatric sub-specialist care to accurately reflect the time and effort required to address complex care needs. Flexible, individualized training pathways may improve recruitment into sub-specialty fields such as nephrology.

Conclusions and relevance
The workforce crisis facing the pediatric nephrology field is echoed throughout many pediatric sub-specialties. Efforts to improve recruitment, retention, and reimbursement are necessary to improve the care delivered to pediatric patients.

Graphical Abstract
Effect of Background Scattering on Efimov Scenario for Overlapping Narrow Feshbach Resonances
Authors: Hamodi-Gzal Fatema , Khaykovich Lev 
Published: July 2024

AbstractEfimov physics in the vicinity of two overlapping narrow Feshbach resonances can be explored within a framework of a three-channel model where a non-interacting open channel is coupled to two closed molecular channels. Here, we determine how it compares to the extended two-channel model, which includes an open channel with finite background scattering and a single molecular channel. We identify the parameter range in which the three-channel model surpasses the extended two-channel model. Furthermore, the three-channel model is extended to include background scattering, and then both models are applied to the experimentally relevant system of bosonic lithium atoms polarized on two different energy levels, with an isolated and two overlapping narrow Feshbach resonances, respectively. We confirm, in agreement with previous studies, that being small, the background scattering length in lithium has a negligible effect on the Efimov features in the case of isolated resonance. However, in the case of overlapping Feshbach resonances, the inclusion of background scattering improves the performance of the theory with respect to the experimentally measured position of the Efimov resonance.
Cognition and Activity of Daily Living Function in people with Parkinson’s disease
Authors: Bode Merle , Kalbe Elke , Liepelt-Scarfone Inga 
Published: July 2024

AbstractThe ability to perform activities of daily living (ADL) function is a multifaceted construct that reflects functionality in different daily life situations. The loss of ADL function due to cognitive impairment is the core feature for the diagnosis of Parkinson’s disease dementia (PDD). In contrast to Alzheimer’s disease, ADL impairment in PD can be compromised by various factors, including motor and non-motor aspects. This narrative review summarizes the current state of knowledge on the association of cognition and ADL function in people with PD and introduces the concept of “cognitive ADL” impairment for those problems in everyday life that are associated with cognitive deterioration as their primary cause. Assessment of cognitive ADL impairment is challenging because self-ratings, informant-ratings, and performance-based assessments seldomly differentiate between “cognitive” and “motor” aspects of ADL. ADL function in PD is related to multiple cognitive domains, with attention, executive function, and memory being particularly relevant. Cognitive ADL impairment is characterized by behavioral anomalies such as trial-and-error behavior or task step omissions, and is associated with lower engagement in everyday behaviors, as suggested by physical activity levels and prolonged sedentary behavior. First evidence shows that physical and multi-domain interventions may improve ADL function, in general, but the evidence is confounded by motor aspects. Large multicenter randomized controlled trials with cognitive ADL function as primary outcome are needed to investigate which pharmacological and non-pharmacological interventions can effectively prevent or delay deterioration of cognitive ADL function, and ultimately the progression and conversion to PDD.
Elective full pulpotomy in mature permanent teeth diagnosed with symptomatic irreversible pulpitis: a two years retrospective study
Authors: Jiménez-Martín Cristina , Martín-González Jenifer , Crespo-Gallardo Isabel , Montero-Miralles Paloma , Cabanillas-Balsera Daniel , Segura-Egea Juan J. 
Published: July 2024

Abstract
Aim
To investigate the outcome of elective full pulpotomy, using calcium silicate-based cements (CSBC), after 2 years, in symptomatic mature permanent teeth with carious lesions, diagnosed as irreversible pulpitis, and analyse the capacity of Wolters et al. (2017) classification to predict the likelihood of treatment failure.

Methods
The treatment records of 56 patients with symptomatic mature teeth with carious lesions, diagnosed as irreversible pulpitis and treated by elective full pulpotomy, using CSBCs as pulp capping materials, were reviewed. Thirteen teeth were excluded. The remaining 43 teeth were evaluated retrospectively at 24 months. Fisher`s exact test with the Lancaster’s mid-P adjustment was used to assess different outcomes amongst the diagnostic categories.

Results
Four of the cases failed before 24 months and required root canal treatment (RCT). Overall success rate at 2 years was 90.7% (39 of 43). An inverse, but non-significant, correlation was observed between the severity of pulpitis according to the Wolters classification and the treatment success rate (p > 0.05). The type of CSBC used was associated to the success rate (OR = 10.5; 95% C.I. = 0.5 – 207.4; p = 0.027), being 82% with Endosequence and 100% with Biodentine. Postoperative pain associated significantly to lower success rate (66.7%) (Odds ratio = 8.0; 95% C.I. = 0.7 – 95.9; p = 0.047).

Conclusions
Elective full pulpotomy using a CSBC was a successful choice for the treatment of mature permanent teeth with symptoms indicative of irreversible pulpitis. There were no significant differences between the success rate of mild, moderate and severe pulpitis. Postoperative pain could be considered a risk marker for failure of full pulpotomy. The term “irreversible pulpitis” should be re-signified to indicate the need for access to the pulp chamber, rather than an indication for extraction or RCT.
Synchronous citizen science with dogs
Authors: Pelgrim Madeline H. , Tidd Zachary , Byrne Molly , Johnston Angie M. , Buchsbaum Daphna 
Published: July 2024

Abstract
Citizen science approaches have grown in popularity over the years, partly due to their ability to reach a wider audience and produce more generalizable samples. In dogs, these studies, though, have been limited in their controls over materials or experimental protocols, with guardians typically reporting results without researcher supervision. Over two studies, we explored and validated a synchronous citizen science approach. We had dog guardians act as experimenters while being supervised by a researcher over Zoom. In study 1, we demonstrated that synchronous citizen science produced equivalent levels of performance to in-lab designs in a choice task. Consistent with past in-lab research, dogs selected a treat (vs. an empty plate) in a two-alternative forced-choice task. In study 2, we showed that Zoom methods are also appropriate for studies utilizing looking time measures. We explored dogs’ looking behaviors when a bag of treats was placed in an unreachable location, and dogs’ guardians were either attentive or inattentive while dogs attempted to retrieve the treats. Consistent with past work, dogs in the attentive condition looked at their guardian for longer periods and had a shorter latency to first look than dogs in the inattentive condition. Overall, we have demonstrated that synchronous citizen science studies with dogs are feasible and produce valid results consistent with those found in a typical lab setting.
On circuit diameter bounds via circuit imbalances
Authors: Dadush Daniel , Koh Zhuan Khye , Natura Bento , Végh László A. 
Published: July 2024

AbstractWe study the circuit diameter of polyhedra, introduced by Borgwardt, Finhold, and Hemmecke (SIAM J. Discrete Math.29(1), 113–121 (2015)) as a relaxation of the combinatorial diameter. We show that the circuit diameter of a system$$\{x\in \mathbb {R}^n:\, Ax=b,\, \mathbb {0}\le x\le u\}$${x∈Rn:Ax=b,0≤x≤u}for$$A\in \mathbb {R}^{m\times n}$$A∈Rm×nis bounded by$$O(m\min \{m, n - m\}\log (m+\kappa _A)+n\log n)$$O(mmin{m,n-m}log(m+κA)+nlogn), where$$\kappa _A$$κAis the circuit imbalance measure of the constraint matrix. This yields a strongly polynomial circuit diameter bound if e.g., all entries ofAhave polynomially bounded encoding length inn. Further, we present circuit augmentation algorithms for LPs using the minimum-ratio circuit cancelling rule. Even though the standard minimum-ratio circuit cancelling algorithm is not finite in general, our variant can solve an LP in$$O(mn^2\log (n+\kappa _A))$$O(mn2log(n+κA))augmentation steps.
Guidelines for clinical evaluation of chronic kidney disease in early stages
Authors: Sugawara Yuka , Kanda Eiichiro , Hamano Takayuki , Itano Seiji , Okada Hirokazu , Tomori Koji , Watanabe Yusuke , Asakura Wataru , Isaka Yoshitaka , Iseki Kunitoshi , Usui Tomoko , Suzuki Yusuke , Tanaka Mototsugu , Nishimura Rimei , Fukami Kei , Matsushita Kunihiro , Wada Jun , Watada Hirotaka , Ueki Kohjiro , Kashihara Naoki , Nangaku Masaomi ,   Research Working Group for Establishing Guidelines for Clinical Evaluation of Chronic Kidney Disease
Published: July 2024

Abstract
Background
For the development of pharmaceutical products in kidney field, appropriate surrogate endpoints which can predict long-term prognosis are needed as an alternative to hard endpoints, such as end-stage kidney disease. Though international workshop has proposed estimated glomerular filtration rate (GFR) slope reduction of 0.5–1.0 mL/min/1.73 m /year and 30% decrease in albuminuria/proteinuria as surrogate endpoints in early and advanced chronic kidney disease (CKD), it was not clear whether these are applicable to Japanese patients.

Methods
We analyzed J-CKD-DB and CKD-JAC, Japanese databases/cohorts of CKD patients, and J-DREAMS, a Japanese database of patients with diabetes mellitus to investigate the applicability of eGFR slope and albuminuria/proteinuria to the Japanese population. Systematic review on those endpoints was also conducted including the results of clinical trials published after the above proposal.

Results
Our analysis showed an association between eGFR slope and the risk of end-stage kidney disease. A 30% decrease in albuminuria/proteinuria over 2 years corresponded to a 20% decrease in the risk of end-stage kidney disease patients with baseline UACR ≥ 30 mg/gCre or UPCR ≥ 0.15 g/gCre in the analysis of CKD-JAC, though this analysis was not performed on the other database/cohort. Those results suggested similar trends to those of the systematic review.

Conclusion
The results suggested that eGFR slope and decreased albuminuria/proteinuria may be used as a surrogate endpoint in clinical trials for early CKD (including diabetic kidney disease) in Japanese population, though its validity and cutoff values must be carefully considered based on the latest evidence and other factors.
AI-assisted Segmentation Tool for Brain Tumor MR Image Analysis
Authors: Lee Myungeun , Kim Jong Hyo , Choi Wookjin , Lee Ki Hong 
Published: July 2024

Abstract
TumorPrism3D software was developed to segment brain tumors with a straightforward and user-friendly graphical interface applied to two- and three-dimensional brain magnetic resonance (MR) images. The MR images of 185 patients (103 males, 82 females) with glioblastoma multiforme were downloaded from The Cancer Imaging Archive (TCIA) to test the tumor segmentation performance of this software. Regions of interest (ROIs) corresponding to contrast-enhancing lesions, necrotic portions, and non-enhancing T2 high signal intensity components were segmented for each tumor. TumorPrism3D demonstrated high accuracy in segmenting all three tumor components in cases of glioblastoma multiforme. They achieved a better Dice similarity coefficient (DSC) ranging from 0.83 to 0.91 than 3DSlicer with a DSC ranging from 0.80 to 0.84 for the accuracy of segmented tumors. Comparative analysis with the widely used 3DSlicer software revealed TumorPrism3D to be approximately 37.4% faster in the segmentation process from initial contour drawing to final segmentation mask determination. The semi-automated nature of TumorPrism3D facilitates reproducible tumor segmentation at a rapid pace, offering the potential for quantitative analysis of tumor characteristics and artificial intelligence-assisted segmentation in brain MR imaging.
Exploring the use of Rasch modelling in “common content” items for multi-site and multi-year assessment
Authors: Hope David , Kluth David , Homer Matthew , Dewar Avril , Goddard-Fuller Rikki , Jaap Alan , Cameron Helen 
Published: July 2024

AbstractRasch modelling is a powerful tool for evaluating item performance, measuring drift in difficulty over time, and comparing students who sat assessments at different times or at different sites. Here, we use data from thirty UK medical schools to describe the benefits of Rasch modelling in quality assurance and the barriers to using it. Sixty “common content” multiple choice items were offered to all UK medical schools in 2016-17, and a further sixty in 2017-18, with five available in both years. Thirty medical schools participated, for sixty total datasets across two sessions, and 14,342 individual sittings. Schools selected items to embed in written assessment near the end of their programmes. We applied Rasch modelling to evaluate unidimensionality, model fit statistics and item quality, horizontal equating to compare performance across schools, and vertical equating to compare item performance across time. Of the sixty sittings, three provided non-unidimensional data, and eight violated goodness of fit measures. Item-level statistics identified potential improvements in item construction and provided quality assurance. Horizontal equating demonstrated large differences in scores across schools, while vertical equating showed item characteristics were stable across sessions. Rasch modelling provides significant advantages in model- and item- level reporting compared to classical approaches. However, the complexity of the analysis and the smaller number of educators familiar with Rasch must be addressed locally for a programme to benefit. Furthermore, due to the comparative novelty of Rasch modelling, there is greater ambiguity on how to proceed when a Rasch model identifies misfitting or problematic data.
An experimental evaluation of Siamese Neural Networks for robot localization using omnidirectional imaging in indoor environments
Authors: Cabrera Juan José , Román Vicente , Gil Arturo , Reinoso Oscar , Payá Luis 
Published: July 2024

AbstractThe objective of this paper is to address the localization problem using omnidirectional images captured by a catadioptric vision system mounted on the robot. For this purpose, we explore the potential of Siamese Neural Networks for modeling indoor environments using panoramic images as the unique source of information. Siamese Neural Networks are characterized by their ability to generate a similarity function between two input data, in this case, between two panoramic images. In this study, Siamese Neural Networks composed of two Convolutional Neural Networks (CNNs) are used. The output of each CNN is a descriptor which is used to characterize each image. The dissimilarity of the images is computed by measuring the distance between these descriptors. This fact makes Siamese Neural Networks particularly suitable to perform image retrieval tasks. First, we evaluate an initial task strongly related to localization that consists in detecting whether two images have been captured in the same or in different rooms. Next, we assess Siamese Neural Networks in the context of a global localization problem. The results outperform previous techniques for solving the localization task using the COLD-Freiburg dataset, in a variety of lighting conditions, specially when using images captured in cloudy and night conditions.
Domain independent heuristics for online stochastic contingent planning
Authors: Blumenthal Oded , Shani Guy 
Published: July 2024

AbstractPartially observable Markov decision processes (POMDP) are a useful model for decision-making under partial observability and stochastic actions. Partially Observable Monte-Carlo Planning (POMCP) is an online algorithm for deciding on the next action to perform, using a Monte-Carlo tree search approach, based on the UCT algorithm for fully observable Markov-decision processes. POMCP develops an action-observation tree, and at the leaves, uses a rollout policy to provide a value estimate for the leaf. As such, POMCP is highly dependent on the rollout policy to compute good estimates, and hence identify good actions. Thus, many practitioners who use POMCP are required to create strong, domain-specific heuristics. In this paper, we model POMDPs as stochastic contingent planning problems. This allows us to leverage domain-independent heuristics that were developed in the planning community. We suggest two heuristics, the first is based on the well-known $$h_{add}$$

h

add

heuristic from classical planning, and the second is computed in belief space, taking the value of information into account.