bluuebunny/crossref_metadata_2025_split huggingface dataset:
Towards a Standardized Classification of the Hepatobiliary Manifestations in Cystic Fibrosis (CFHBI): A Joint ESPGHAN/NASPGHAN Position Paper
Authors: Bodewes Frank A.J.A. , Freeman Alvin Jay , Weymann Alexander , Debray Dominique , Scheers Isabelle , Verkade Henkjan J. , Narkewicz Michael R. 
Published: January 2024

AbstractThe broad spectrum of hepatobiliary involvement in cystic fibrosis (CF) has been commonly referred to as cystic fibrosis liver disease (CFLD). However, differences in the definitions of CFLD have led to variations in reported prevalence, incidence rates, and standardized recommendations for diagnosis and therapies.Harmonizing the description of the spectrum of hepatobiliary involvement in all people with CF (pwCF) is deemed essential for providing a reliable account of the natural history, which in turn supports the development of meaningful clinical outcomes in patient care and research.Recognizing this necessity, The European Society for Paediatric Gastroenterology Hepatology and Nutrition (ESPGHAN) and the North American Society for Pediatric Gastroenterology, Hepatology and Nutrition (NASPGHAN) commissioned and tasked a committee to develop and propose a systematic classification of the CF hepatobiliary manifestations to increase uniformity, accuracy, and comparability for clinical, registry, and research purposes. This report describes the committee's combined expert position statement on hepatobiliary involvement in CF, which has been endorsed by NASPGHAN and ESPGHAN.We recommend using CFHBI (Cystic Fibrosis Hepato‐Biliary Involvement) as the updated term to describe and classify all hepatobiliary manifestations in all pwCF. CFHBI encompasses the current extensive spectrum of phenotypical, clinical, or diagnostic expressions of liver involvement observed in pwCF. We present a schematic categorization of CFHBI, which may also be used to track and classify the changes and development of CFHBI in pwCF over time. The proposed classification for CFHBI is based on expert consensus and has not been validated for clinical practice and research purposes. Achieving validation should be an important aim for future research.
Focused Cardiac Ultrasound Diagnosis of Dilated Cardiomyopathy
Authors: Perera AG Nuwan D. , Noorbakhsh Kathleen A. , Marin Jennifer R. , Azhdam Devora B. 
Published: January 2024

Abstract
We report the case of a 6-year-old boy presenting to the emergency department after a syncopal event during a flu-like illness. Intermittent ventricular tachycardia was noted during Emergency Medical Services transport, and a focused cardiac ultrasound (FOCUS) in the emergency department revealed a dilated left ventricle and left atrium as well as severe global systolic dysfunction. Point-of-care ultrasound findings prompted expedited evaluation and management of this critically ill patient.
The Knotted Urethral Catheter—Description of a Novel Technique and Steps for Removal
Authors: Rampersad Barbara , Paul Joanne F. 
Published: January 2024

Abstract
The spontaneous intravesicular knotting of a feeding tube used for urethral catheterization is a rare but documented complication. The reported incidence in the world literature is 0.2 per 100,000, with only 40 cases reported. Removal of these intravesicular knots has been attempted in a number of ways, such as the use of a guide wire to untangle the knot, use of excess lubrication and traction with or without anesthetic, and percutaneous or open cystostomy. This cystoscopic technique for removal has not been previously described.
Based on our experience and published recommendations, we formulate an algorithm for removal. We outline steps for prevention and techniques from simple to complex, which can be used to remove knotted catheters.
Although a rare complication of catheterization in children, catheter knotting can be troublesome. Following the steps suggested in this algorithm may avoid the use of more invasive techniques for removal.
Risk Factors Affecting Clinical Outcomes of Low-risk Early-stage Human Papillomavirus–Associated Endocervical Adenocarcinoma Treated by Surgery Alone: Application of Silva Pattern
Authors: Bae Bong Kyung , Bae Hyunsik , Cho Won Kyung , Kim Byoung-Gie , Choi Chel Hun , Kim Tae-Joong , Lee Yoo-Young , Lee Jeong-Won , Kim Hyun-Soo , Park Won 
Published: January 2024

This study aimed to report the clinical outcomes and risk factors for survival of patients with low-risk early-stage human papillomavirus–associated (HPVA) endocervical adenocarcinoma (EAC) treated with surgery alone. This retrospective study obtained the clinicopathological data of patients with early-stage HPVA EAC who underwent surgery between 2012 and 2018. The Silva pattern of invasion was determined by reviewing pathology slides. Locoregional recurrence-free survival (RFS), RFS, and overall survival were calculated, and the risk factors for survival were analyzed. One hundred seventeen patients with a median follow-up of 5.2 years (0.5–9.7 yr) were included. The most common histologic type was usual (94/117, 80.3%). The Silva pattern was A in 79 patients (67.5%), B in 30 (25.6%), and C in 8 (6.8%). The 5-year locoregional RFS, RFS, and overall survival rates were 92.4%, 87.8%, and 97.2%, respectively. The presence of intermediate-risk factors and Silva pattern C were significantly associated with worse survival. Based on these findings, patients were categorized into 2 groups: Group 1 (Silva pattern A or Silva pattern B without intermediate-risk factors) and Group 2 (Silva pattern B with intermediate-risk factors or Silva pattern C). Group 2 showed significantly worse outcomes than Group 1, including the 5-year locoregional RFS (98.6% vs 68.0%), RFS (96.4% vs 54.6%), and overall survival (100.0% vs 86.5%). In conclusion, surgery alone for early-stage HPVA EAC resulted in favorable outcomes. Consideration of the Silva pattern, in addition to well-known risk factors, could help in precise risk group stratification of low-risk, early-stage HPVA EAC.
A Mixed-Methods Analysis of Deception Detection by Neurodiverse Young Adults
Authors: Coburn Kelly L. , Miller Gillian N. , Martin Lucas A. , Kana Rajesh K. 
Published: January 2024

Purpose:
Differences in social cognition between autistic and nonautistic people may put autistic people at greater risk of being deceived. To inform communication interventions related to deception, the purposes of this mixed-methods study were to examine the deception detection strategies used by young adults with varying levels of autistic traits and to explore whether those strategies differed between groups or in terms of accuracy.

Methods:
Fifty-one young adults with varying levels of autistic traits watched a series of videos. For each video, the participant judged whether the recorded speaker was truthful and gave the reasoning for their judgment. Inductive thematic analysis was used to identify themes in participants' stated reasons, which were used to quantitatively examine (1) between-group differences based on self-reported autistic traits and (2) theme-based differences in accuracy.

Results:
Thematic analysis of the open-ended responses yielded four major themes: subjective descriptions of the person, nonverbal communication, observable features of the response, and nebulous reasons. Statistical analyses indicated no significant group differences in frequency of use of the four themes. When the four themes were compared with each other, observable response features yielded significantly more accurate judgments than nonverbal communication or subjective descriptions.

Discussion:
Findings are discussed within the framework of speech–language pathologists' role in helping communicators determine a speaker's truthfulness, with the ultimate goal of avoiding deception and/or manipulation. Suggestions for incorporating research findings into the design of communication interventions are included.
Pathogen detection in childhood exacerbated asthma in Sri Lanka, role and characteristics of Mycoplasma pneumoniae and antibiotic stewardship
Authors: Wijesooriya Lakmini Inoka , Chalker Victoria , Perera Priyantha , Sunil-Chandra N.P. 
Published: January 2024

Abstract
Asthma is a significant public health concern, particularly in children. Exacerbation of asthma (EOA) is life-threatening and respiratory infections (RIs) play a crucial role. Though viruses play a significant role in EOA, patients are empirically treated with antibiotics; in particular, macrolides are prescribed for unconfirmed M. pneumoniae infections. Although EOA and M. pneumoniae have been reported in many countries, no published data in Sri Lanka. The present study aimed to identify common respiratory viruses, typical respiratory bacterial pathogens, and M. pneumoniae in children with EOA and relate them with the compatibility of antimicrobial use.
A case-control study was conducted in the pediatric unit of North Colombo Teaching Hospital, Sri Lanka, involving two groups of children between 5-15 years. Group-1: children with EOA, Group-2: children with stable asthma (SA). Each group consisted of 100 children. Sputum/throat swabs were tested for common respiratory viruses using specific fluoresceinated monoclonal antibodies (MAbs) with direct immunofluorescent staining, typical bacterial pathogens by routine culture and M. pneumoniae by RT-PCR. Macrolide-resistance in M. pneumoniae was detected using conventional PCR and sequencing for specific genetic mutations in the 23S rRNA gene. M. pneumoniae was genotyped using nested multilocus sequence typing (MLST), which targeted eight housekeeping genes (ppa, pgm, gyrB, gmk, glyA, atpA, arcC, adk).
There was no significant difference in demographic data between the two groups. There was no statistically significant difference in age gender and geographical location between the two groups. In children with EOA, antibiotics were used in 66%, and macrolides in 42%. Samples consisted of 78% sputum and 22% throat swabs. Adenovirus virus was the most common respiratory virus identified, and it was significantly higher in children with EOA compared to those with SA, but no significant difference in typical bacteria findings between the two groups. M. pneumoniae was detected in one patient in the group of 100 children with EOA with none detected in the SA group. The M. pneumoniae was macrolide sensitive, and as per MLST analysis, it was ST14. The empiric use of antibiotics in children with asthma may be better targeted with pathogen screening to inform treatment to minimize antibiotic resistance.
ESPressoscope: a small and powerful platform for in situ microscopy
Authors: Li Ethan , Saggiomo Vittorio , Ouyang Wei , Prakash Manu , Diederich Benedict 
Published: January 2024

AbstractMicroscopy is essential for detecting, identifying, analyzing, and measuring small objects. Access to modern microscopy equipment is crucial for scientific research, especially in the biomedical and analytical sciences. However, the high cost of equipment, limited availability of parts, and challenges associated with transporting equipment often limit the accessibility and operational capabilities of these tools, particularly in field sites and other remote or resource-limited settings. Thus, there is a need for affordable and accessible alternatives to traditional microscopy systems. We address this challenge by investigating the feasibility of using a simple microcontroller board not only as a portable and field-ready digital microscope, but furthermore as a versatile platform which can easily be adapted to a variety of imaging applications. By adding a few external components, we demonstrate that a low-cost ESP32 camera board can be used to build an autonomous in situ platform for digital time-lapse imaging of cells. This platform, which we call the ESPressoscope, can be adapted to applications ranging from monitoring incubator cell cultures in the lab to observing ecological phenomena in the sea, and it can be adapted for other techniques such as microfluidics or spectrophotometry. The ESPressoscope achieves a low power consumption and small size, which makes it ideal for field research in environments and applications where microscopy was previously infeasible. Its Wi-Fi connectivity enables integration with external image processing and storage systems, including on cloud platforms when internet access is available. Finally, we present several web browser-based tools to help users operate and manage the ESPressoscope’s software. Our findings demonstrate the potential for low-cost, portable microscopy solutions to enable new and more accessible experiments for biological and analytical applications.
nail: software for high-speed, high-sensitivity protein sequence annotation
Authors: Roddy Jack W. , Rich David H. , Wheeler Travis J. 
Published: January 2024

Abstract“Fast is fine, but accuracy is final.”-- Wyatt EarpBackgroundThe extreme diversity of newly sequenced organisms and considerable scale of modern sequence databases lead to a tension between competing needs for sensitivity and speed in sequence annotation, with multiple tools displacing the venerable BLAST software suite on one axis or another. Alignment based on profile hidden Markov models (pHMMs) has demonstrated state of art sensitivity, while recent algorithmic advances have resulted in hyper-fast annotation tools with sensitivity close to that of BLAST.ResultsHere, we introduce a new tool that bridges the gap between advances in these two directions, reaching speeds comparable to fast annotation methods such as MMseqs2 while retaining most of the sensitivity offered by pHMMs. The tool, callednail, implements a heuristic approximation of the pHMM Forward/Backward (FB) algorithm by identifying a sparse subset of the cells in the FB dynamic programming matrix that contains most of the probability mass. The method produces an accurate approximation of pHMM scores and E-values with high speed and small memory requirements. On a protein benchmark,nailrecovers the majority of recall difference between MMseqs2 and HMMER, with run time ∼26x faster than HMMER3 (only ∼2.4x slower than MMseqs2’s sensitive variant).nailis released under the open BSD-3-clause license and is available for download athttps://github.com/TravisWheelerLab/nail.
The MKK3 module integrates nitrate and light signals to modulate secondary dormancy inArabidopsis thaliana
Authors: Regnard Sarah , Otani Masahiko , Keruzore Marc , Teinturier Alizée , Blondel Marc , Kawakami Naoto , Krapp Anne , Colcombet Jean 
Published: January 2024

AbstractSeed dormancy corresponds to a reversible blockage of germination. Primary dormancy is established during seed maturation while secondary dormancy is set up on the dispersed seed, following an exposure to unfavourable factors. Both dormancies are relieved in response to environmental factors, such as light, nitrate and coldness. QTL analyses for preharvest sprouting identified MKK3 kinase in cereals as a player in dormancy control. Here, we showed that MKK3 also plays a role in secondary dormancy in Arabidopsis within a signalling module composed of MAP3K13/14/19/20, MKK3 and clade-C MAPKs. Seeds impaired in this module acquired heat-induced secondary dormancy more rapidly than WT seeds and this dormancy is less sensitive to nitrate, a signal able to release dormancy. We also demonstrated that MPK7 was strongly activated in the seed during dormancy release, especially in response to light and nitrate. This activation was greatly reduced inmap3k13/14/19/20andmkk3mutants. Finally, we showed that the module was not regulated, and apparently did not regulate, the genes controlling ABA/GA hormone balance, one of the crucial mechanisms of seed dormancy control. Overall, our work identified a whole new MAPK module controlling seed germination and enlarged the panel of functions of the MKK3-related modules in plants.
Organic macromolecules transport a significant proportion of the calcium precursor for nacre formation
Authors: Macías-Sánchez Elena , Huang Xing , Willinger Marc G. , Rodríguez-Navarro Alejandro , Checa Antonio 
Published: January 2024

AbstractThe mechanism of nacre formation in gastropods involves a vesicular system that transports organic and mineral precursors from the mantle epithelium to the mineralization chamber. Between them lies the surface membrane, a thick organic structure that covers the mineralization chamber and the forming nacre. The surface membrane is a dynamic structure that grows by the addition of vesicles on the outer side and recedes by the formation of interlamellar membranes on the inner side. By using a combination of electron microscopy imaging and spectroscopy, we have monitored the journey of the vesicles from the mantle epithelium to the mineralization chamber, focusing on the elemental composition of the organic structures at each stage. Our data reveal that transport occurs in lipid bilayer vesicles through exocytosis from the outer mantle epithelium. After release into the surface membrane, chitin undergoes a process of self-assembly and interaction with proteins, resulting in progressive changes of the internal structure of the surface membrane until the final structure of the interlamellar membranes is acquired. Finally, these detach from the inner side of the surface membrane. Elemental analysis revealed the transport of a considerable amount of calcium bound to proteins, likely forming calcium-protein complexes.
Unusual migratory strategy a key factor driving interactions at wind energy facilities in at-risk bats
Authors: Campbell Caitlin J. , Nelson David M. , Nagel Juliet , Clerc Jeff , Weller Theodore J. , Weiringa Jamin G. , Fraser Erin , Longstaffe Fred J. , Hale Amanda M. , Lout Meghan , Pruitt Lori , Guralnick Robert , Vander Zanden Hannah B. 
Published: January 2024

AbstractSeasonal movement strategies are poorly understood for most animals, impeding broader understanding of processes underlying migration and limiting practical conservation needs. Here we develop and implement a framework for integrating multiple sources of endogenous markers, in particular stable hydrogen isotope data, that capture and scale dynamics from the movements of individuals to that of continental migration. We assembled and integrated thousands of new isotopic measurements from bat fur with existing datasets and applied this framework to reveal migratory patterns of three broadly distributed bat species most at risk for fatalities at wind energy facilities. Our findings show that the species comprising the lowest proportion of wind turbine fatalities (silver-haired bats) exhibits expected movements to lower latitudes in autumn and higher latitudes in spring. Surprisingly, the two species with higher wind turbine fatality rates (hoary and eastern red bats) have more complex movements, including significant movement to higher latitudes during autumn. We term this unique strategy “pell-mell” migration, during which some individuals are as likely to move to higher latitudes as lower latitudes, relative to their individual summering grounds, in early autumn, after which they move to similar or lower latitudes to overwinter. The pell-mell migratory period corresponds with peak fatalities at wind energy facilities, and bats moving northward during autumn are associated with mortality at those facilities. Our results provide direct support for the hypothesis that bat fatalities at wind energy facilities are related to migration and highlight the importance of migratory distance as an ultimate driver of increased interactions with wind energy facilities, which appears significantly greater for species that travel widely across latitudes in the autumn.
Novel mutation leading to splice donor loss in a conserved site ofDMDcauses cryptorchidism
Authors: Chen Jianhai , Jia Yangying , Zhong Jie , Zhang Kun , Dai Hongzheng , He Guanglin , Li Fuping , Zeng Li , Fan Chuanzhu , Xu Huayan 
Published: January 2024

AbstractBackgroundAs one of the most common congenital abnormalities in male births, cryptorchidism has been found to have a polygenic etiology according to previous studies of common variants. However, little is known about genetic predisposition of rare variants for cryptorchidism, since rare variants have larger effective size on diseases than common variants.MethodsIn this study, a cohort of 115 Chinese probands with cryptorchidism was analyzed using whole-genome sequencing (WGS), alongside 19 parental controls and 2136 unaffected men. Additionally, CRISPR-Cas9 editing of a conserved variant was performed in a mouse model, with MRI screening utilized to observe the phenotype.ResultsIn 30 of 115 patients (26.1%), we identified four novel genes (ARSH,DMD,MAGEA4, andSHROOM2) affecting at least five unrelated patients and four known genes (USP9Y,UBA1,BCORL1, andKDM6A) with the candidate rare pathogenic variants affecting at least two cases. Burden tests of rare variants revealed the genome-wide significances for newly identified genes (p< 2.5×10-6) under the Bonferroni correction. Surprisingly, novel and known genes were mainly from X chromosome (seven on X and one on Y) and all rare X-chromosomal segregating variants exhibited a maternal inheritance rather thande novoorigin. CRISPR-Cas9 mouse modeling of a splice donor loss variant inDMD(NC_000023.11:g.32454661C>G), which resides in a conserved site across vertebrates, replicated bilateral cryptorchidism phenotypes, confirmed by Magnetic resonance imaging (MRI) at 4 and 10 weeks.ConclusionOur results revealed the role of theDMDgene mutation in causing cryptorchidism. The results also suggest that maternal-X inheritance of pathogenic defects could have a predominant role in the development of cryptorchidism.
Exploring Beauty Product Accessibility for Individuals with Upper Extremity Disabilities
Authors: Fullmer Niko , Cone Hannah , Gumarang Jeanette , Kieffer Emily , Bae Soyoung Esther , Rosario Emily R 
Published: January 2024

AbstractObjectiveThis study explores the accessibility of beauty products for individuals with upper extremity disabilities.MethodsParticipants with varied upper extremity impairments used Rare Beauty makeup products over two weeks. Assessments of hand function and questionnaires evaluated usability and satisfaction.ResultsProduct features like bottle shape, cap design, and texture significantly influenced usability for those with hand and arm impairments. Notably, individuals with fine motor skill impairments reported easier gripping with larger bottle sizes and ease of opening with cap enhancements. The unique product shape and enhanced caps were also found to be more accessible for participants across all ability levels. Overall, the products were well-received, with most participants finding them comfortable and user-friendly.ConclusionsThe study emphasizes the need for inclusive design in the beauty industry, catering to those with upper extremity disabilities. It reveals the importance of ergonomic and adaptable product features to enhance usability and accessibility.Plain Language summaryThis study investigated the use of beauty products by people with upper extremity disabilities. Participants tried Rare Beauty makeup for two weeks and provided feedback. Results showed that product design, like bottle shape and cap ease, significantly impacts usability for those with hand and arm function impairments. Key findings included better grip on certain products for those with fine motor skill challenges. Overall, participants found the products comfortable and easy to use, highlighting the importance of inclusive design in beauty products for people with disabilities.