bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clinical Utility of the Neuropsychological Assessment Battery Judgment Subtest in the Evaluation of Older Adults
Authors: Donders Jacobus , Maher Tracy 
Published: May 2024

Abstract

Objective
The purpose of this retrospective archival study was to explore the clinical utility of the Judgment subtest of the Neuropsychological Assessment Battery (NAB) in older adults who were referred because of cognitive concerns. Specifically, we were interested in how NAB Judgment covaried with other measures of executive functioning.

Method
226 adults, aged 61–89 years (48% dementia, 35% mild cognitive impairment, 18% cognitively intact) completed NAB Judgment. They also completed Trail Making Test (TMT) A and B. In addition, Behavior Rating Inventory of Executive Function (BRIEF–A) informant and self-reports were obtained to measure executive functioning in daily life.

Results
Scores on NAB Judgment did not correlate significantly with BRIEF–A informant ratings. However, there was a statistically significant correlation between BRIEF–A informant ratings and TMT B. Better performance on TMT B was associated with fewer informant concerns. Furthermore, subgroups with versus without informant BRIEF–A Metacognition indices in the range of impairment demonstrated a statistically significant difference on TMT B but not on Judgment.

Conclusions
Executive functioning in older adults should not be assessed using NAB Judgment alone. Such an evaluation should be supplemented with other in-person tests as well as informant ratings of daily functioning.
The Breast-Pectoralis Flap: A New Advance in Autologous Breast Reconstruction—A Preliminary Report on 20 Cases
Authors: Delay Emmanuel , Michel Gautier , Mambour Gwenola , Meruta Andreea Carmen , Frobert Paul , Perez Simon 
Published: May 2024

Abstract

Background
In the past, several publications have described breast reconstruction techniques that utilize the contralateral breast; however, interest diminished because of technical difficulty, scarring, and poor aesthetic results.

Objectives
This study aimed to present a new breast reconstruction technique that uses a combination of the breast-pectoralis flap and the abdominal advancement flap.

Methods
This retrospective study analyzed the results and complications of 20 consecutive breast reconstructions with the breast-pectoralis flap technique.

Results
The authors present a series of 20 breast reconstructions that utilized the breast-pectoralis flap. Delayed breast reconstruction was performed in 13 cases (65%), breast reconstruction in 5 patients (25%) with Poland syndrome, sequela correction after a chest wall sarcoma in 1 patient (5%), and sequela correction after breast cystic lymphangioma resection in 1 patient (5%). One complication required surgical reintervention without long-term consequences. The outcomes were considered very good in 50% of the cases, good in 45%, and fair in 5%.

Conclusions
The combination of the breast-pectoralis flap and the abdominal advancement flap is an interesting advance in breast reconstruction. Evaluation of the presented cases suggests wider indications for this technique.

Level of Evidence: 4
danRerLib: a Python package for zebrafish transcriptomics
Authors: Schwartz Ashley V , Sant Karilyn E , George Uduak Z 
Published: May 2024

Abstract

Summary
Understanding the pathways and biological processes underlying differential gene expression is fundamental for characterizing gene expression changes in response to an experimental condition. Zebrafish, with a transcriptome closely mirroring that of humans, are frequently utilized as a model for human development and disease. However, a challenge arises due to the incomplete annotations of zebrafish pathways and biological processes, with more comprehensive annotations existing in humans. This incompleteness may result in biased functional enrichment findings and loss of knowledge. danRerLib, a versatile Python package for zebrafish transcriptomics researchers, overcomes this challenge and provides a suite of tools to be executed in Python including gene ID mapping, orthology mapping for the zebrafish and human taxonomy, and functional enrichment analysis utilizing the latest updated Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. danRerLib enables functional enrichment analysis for GO and KEGG pathways, even when they lack direct zebrafish annotations through the orthology of human-annotated functional annotations. This approach enables researchers to extend their analysis to a wider range of pathways, elucidating additional mechanisms of interest and greater insight into experimental results.

Availability and implementation
danRerLib, along with comprehensive documentation and tutorials, is freely available. The source code is available at https://github.com/sdsucomptox/danrerlib/ with associated documentation and tutorials at https://sdsucomptox.github.io/danrerlib/. The package has been developed with Python 3.9 and is available for installation on the package management systems PIP (https://pypi.org/project/danrerlib/) and Conda (https://anaconda.org/sdsu_comptox/danrerlib) with additional installation instructions on the documentation website.
Neonicotinoids differentially modulate nicotinic acetylcholine receptors in immature and antral follicles in the mouse ovary
Authors: Mourikes Vasiliki E , Santacruz-Márquez Ramsés , Deviney Ashley , Neff Alison , Laws Mary J , Flaws Jodi A 
Published: May 2024

Abstract
Neonicotinoids are the most widely used insecticides in the world. They are synthetic nicotine derivatives that act as nicotinic acetylcholine receptor agonists. Although parent neonicotinoids have low affinity for the mammalian nicotinic acetylcholine receptor, they can be activated in the environment and the body to positively charged metabolites with high affinity for the mammalian nicotinic acetylcholine receptor. Imidacloprid, the most popular neonicotinoid, and its bioactive metabolite desnitro-imidacloprid differentially interfere with ovarian antral follicle physiology in vitro, but their effects on ovarian nicotinic acetylcholine receptor subunit expression are unknown. Furthermore, ovarian nicotinic acetylcholine receptor subtypes have yet to be characterized in the ovary. Thus, this work tested the hypothesis that ovarian follicles express nicotinic acetylcholine receptors and their expression is differentially modulated by imidacloprid and desnitro-imidacloprid in vitro. We used polymerase chain reaction, RNA in situ hybridization, and immunohistochemistry to identify and localize nicotinic acetylcholine receptor subunits (α2, 4, 5, 6, 7 and β1, 2, 4) expressed in neonatal ovaries (NO) and antral follicles. Chrnb1 was expressed equally in NO and antral follicles. Chrna2 and Chrnb2 expression was higher in antral follicles compared to NO and Chrna4, Chrna5, Chrna6, Chrna7, and Chrnb4 expression was higher in NO compared to antral follicles. The α subunits were detected throughout the ovary, especially in oocytes and granulosa cells. Imidacloprid and desnitro-imidacloprid dysregulated the expression of multiple nicotinic acetylcholine receptor subunits in NO, but only dysregulated one subunit in antral follicles. These data indicate that mammalian ovaries contain nicotinic acetylcholine receptors, and their susceptibility to imidacloprid and desnitro-imidacloprid exposure varies with the stage of follicle maturity.
Estimating brain and eye lens dose for the cardiologist in interventional cardiology—are the dose levels of concern?
Authors: Hulthén Markus , Tsapaki Virginia , Karambatsakidou Angeliki 
Published: May 2024

Abstract

Objectives
To establish conversion coefficients (CCs), between mean absorbed dose to the brain and eye lens of the cardiologist and the air kerma-area product, PKA, for a set of projections in cardiac interventional procedures. Furthermore, by taking clinical data into account, a method to estimate the doses per procedure, or annual dose, is presented.

Methods
Thermoluminescence dosimeters were used together with anthropomorphic phantoms, simulating a cardiologist performing an interventional cardiac procedure, to estimate the CCs for the brain and eye lens dose for nine standard projections, and change in patient size and x-ray spectrum. Additionally, a single CC has been estimated, accounting for each projections fraction of use in the clinic and associated PKA using clinical data from the dose monitoring system in our hospital.

Results
The maximum CCs for the eye lens and segment of the brain, is 5.47 μGy/Gycm2 (left eye lens) and 1.71 μGy/Gycm2 (left brain segment). The corresponding weighted CCs: are 3.39 μGy/Gycm2 and 0.89 μGy/Gycm2, respectively.

Conclusions
Conversion coefficients have been established under actual scatter conditions, showing higher doses on the left side of the operator. Using modern interventional x-ray equipment, interventional cardiac procedures will not cause high radiation dose levels to the operator when a ceiling mounted shield is used, otherwise there is a risk that the threshold dose values for cataract will be reached.

Advance in knowledge
In addition to the CCs for the different projections, methods for deriving a single CC per cardiac interventional procedure and dose per year were introduced.
Randomized clinical trial on D2 lymphadenectomy versus D2 lymphadenectomy plus complete mesogastric excision in patients undergoing gastrectomy for cancer (DCGC01 study)
Authors: Xie Daxing , Shen Jie , Liu Liang , Cao Beibei , Xiao Aitang , Qin Jichao , Wu Jianhong , Yan Qun , Hu Yuanlong , Yang Chuanyong , Cao Zhixin , Hu Junbo , Yin Ping , Gong Jianping 
Published: May 2024

Abstract

Background
It is unknown whether D2 lymphadenectomy + complete mesogastric excision for gastric cancer improves survival compared with just D2 lymphadenectomy.

Methods
Between September 2014 and June 2018, patients with advanced gastric cancer were randomly assigned (1 : 1) to laparoscopic D2 lymphadenectomy or D2 lymphadenectomy + complete mesogastric excision gastrectomy. The modified intention-to-treat population was defined as patients who had pathologically confirmed gastric adenocarcinoma (pT1 N1–3 M0 and pT2–4 N0–3 M0). The primary endpoint was 3-year disease-free survival. Secondary endpoints were the recurrence pattern and overall survival.

Results
The median follow-up of patients in the D2 lymphadenectomy group (169 patients) and patients in the D2 lymphadenectomy +complete mesogastric excision group (169 patients) was 55 (interquartile range 37–60) months and 51 (interquartile range 40–60) months respectively. Recurrence occurred in 50 patients in the D2 lymphadenectomy group (29.6%) versus 33 patients in the D2 lymphadenectomy + complete mesogastric excision group (19.5%) (P = 0.032). The 3-year disease-free survival was 75.5% (95% c.i. 68.3% to 81.3%) in the D2 lymphadenectomy group versus 85.0% (95% c.i. 78.7% to 89.6%) in the D2 lymphadenectomy + complete mesogastric excision group (log rank P = 0.042). The HR for recurrence in the D2 lymphadenectomy + complete mesogastric excision group versus the D2 lymphadenectomy group was 0.64 (95% c.i. 0.41 to 0.99) by Cox regression (P = 0.045). The 3-year overall survival rate was 77.5% (95% c.i. 70.4% to 83.1%) in the D2 lymphadenectomy group versus 85.8% (95% c.i. 79.6% to 90.2%) in the D2 lymphadenectomy + complete mesogastric excision group (log rank P = 0.058). The HR for death in the D2 lymphadenectomy + complete mesogastric excision group versus the D2 lymphadenectomy group was 0.64 (95% c.i. 0.41 to 1.02) (P = 0.058).

Conclusion
Compared with conventional D2 dissection, D2 lymphadenectomy + complete mesogastric excision is associated with better disease-free survival, but there is no statistically significant difference in overall survival.

Registration number
NCT01978444 (http://www.clinicaltrials.gov).
Gallstones as a cause in presumed acute alcoholic pancreatitis: observational multicentre study
Authors: Sissingh Noor J , de Rijk Fleur E M , Timmerhuis Hester C , Umans Devica S , Anten Marie-Paule G F , Bouwense Stefan A W , van Delft Foke , van Eijck Brechje C , Erkelens Willemien G , Hazen Wouter L , Kuiken Sjoerd D , Quispel Rutger , Romkens Tessa E H , Schwartz Matthijs P , Seerden Tom C , Spanier B W Marcel , Verlaan Tessa , Vleggaar Frank P , Voermans Rogier P , Verdonk Robert C , van Hooft Jeanin E 
Published: May 2024

Abstract

Background
Data on the incidence and clinical relevance of gallstones in patients with suspected acute alcoholic pancreatitis are lacking and are essential to minimize the risk of recurrent acute pancreatitis. The aim of this study was to assess the incidence of gallstones and the associated rate of recurrent acute pancreatitis in patients with presumed acute alcoholic pancreatitis.

Methods
Between 2008 and 2019, 23 hospitals prospectively enrolled patients with acute pancreatitis. Those diagnosed with their first episode of presumed acute alcoholic pancreatitis were included in this study. The term gallstones was used to describe the presence of cholelithiasis or biliary sludge found during imaging. The primary outcome was pancreatitis recurrence during 3 years of follow-up.

Results
A total of 334 patients were eligible for inclusion, of whom 316 were included in the follow-up analysis. Gallstone evaluation, either during the index admission or during follow-up, was performed for 306 of 334 patients (91.6%). Gallstones were detected in 54 patients (17.6%), with a median time to detection of 6 (interquartile range 0–42) weeks. During follow-up, recurrent acute pancreatitis occurred in 121 of 316 patients (38.3%), with a significantly higher incidence rate for patients with gallstones compared with patients without gallstones (59% versus 34.2% respectively; P &lt; 0.001), while more patients with gallstones had stopped drinking alcohol at the time of their first recurrence (41% versus 24% respectively; P = 0.020). Cholecystectomy was performed for 19 patients with gallstones (36%). The recurrence rate was lower for patients in the cholecystectomy group compared with patients who did receive inadequate treatment or no treatment (5/19 versus 19/34 respectively; P = 0.038).

Conclusion
Gallstones were found in almost one in every five patients diagnosed with acute alcoholic pancreatitis. Gallstones were associated with a higher rate of recurrent pancreatitis, while undergoing cholecystectomy was associated with a reduction in this rate.
The weed, asbestos pipe and disposable tree: unmuting multispecies Flemish and Norwegian circular site stories for diverse circular economies
Authors: Wuyts Wendy 
Published: May 2024

Abstract
This study explores diverse circular economies and methods of multispecies ethnography in Vorselaar, Belgium and Røros, Norway, to identify care-full justice in small-scale places and to challenge traditional anthropocentric and capitalocentric models. This study unearths circular site stories in Vorselaar’s community-driven sustainability practices and Røros’s integration of cultural heritage in its sustainability approach, highlighting the need for a broader, care-centric perspective in circular economy discourse. The results demonstrate the universality and adaptability of diverse circular economies in fostering narratives of multispecies justice and the need for emphasising multispecies justice and bioregionalism to foster biodiversity, human wellbeing and their need for belonging and ecological citizenship.
Determination of Clinically Acceptable Analytical Variation of Cardiac Troponin at Decision Thresholds
Authors: Pickering John W , Kavsak Peter , Christenson Robert H , Troughton Richard W , Pemberton Christopher J , Richards A Mark , Joyce Laura , Than Martin P 
Published: May 2024

Abstract

Background
Clinical decision-making for risk stratification for possible myocardial infarction (MI) uses high-sensitivity cardiac troponin (hs-cTn) thresholds that range from the limit of detection to several-fold higher than the upper reference limit (URL). To establish a minimum analytical variation standard, we can quantify the effect of variation on the population clinical measures of safety (sensitivity) and effectiveness [proportion below threshold, or positive predictive value (PPV)].

Methods
From large datasets of patients investigated for possible MI with the Abbott hs-cTnI and Roche hs-cTnT assays, we synthesized datasets of 1 000 000 simulated patients. Troponin concentrations were randomly varied several times based on absolute deviations of 0.5 to 3 ng/L and relative changes of 2% to 20% around the low-risk threshold (5 ng/L) and URLs, respectively.

Results
For both assays at the low-risk thresholds, there were negligible differences in sensitivity (&lt;0.3%) with increasing analytical variation. The proportion of patients characterized as low risk reduced by 30% to 29% (Roche) and 53% to 44% (Abbott). At the URL, increasing analytical variation also did not change sensitivity; the PPV fell by less than 3%. For risk stratification, increased delta thresholds (change between serial troponin concentrations) increased sensitivity at the cost of a decreased percentage of patients below the delta threshold, with the largest changes at the greatest analytical variation.

Conclusions
At the low-risk threshold, analytical variation up to 3 ng/L minimally impacted the safety metric (sensitivity) but marginally reduced effectiveness. Similarly, at the URL even relative variation up to 25% minimally impacted safety metrics and effectiveness. Analytical variation for delta thresholds did not negatively impact sensitivity but decreased effectiveness.
FLT4 causes developmental disorders of the cardiovascular and lymphovascular systems via pleiotropic molecular mechanisms
Authors: Monaghan Richard M , Naylor Richard W , Flatman Daisy , Kasher Paul R , Williams Simon G , Keavney Bernard D 
Published: May 2024

Abstract

Aims
Rare, deleterious genetic variants in FLT4 are associated with Tetralogy of Fallot (TOF), the most common cyanotic congenital heart disease. The distinct genetic variants in FLT4 are also an established cause of Milroy disease, the most prevalent form of primary hereditary lymphoedema. The phenotypic features of these two conditions are non-overlapping, implying pleiotropic cellular mechanisms during development.

Methods and results
In this study, we show that FLT4 variants identified in patients with TOF, when expressed in primary human endothelial cells, cause aggregation of FLT4 protein in the perinuclear endoplasmic reticulum, activating proteostatic and metabolic signalling, whereas lymphoedema-associated FLT4 variants and wild-type (WT) FLT4 do not. FLT4 TOF variants display characteristic gene expression profiles in key developmental signalling pathways, revealing a role for FLT4 in cardiogenesis distinct from its role in lymphatic development. Inhibition of proteostatic signalling abrogates these effects, identifying potential avenues for therapeutic intervention. Depletion of flt4 in zebrafish caused cardiac phenotypes of reduced heart size and altered heart looping. These phenotypes were rescued with coinjection of WT human FLT4 mRNA, but incompletely or not at all by mRNA harbouring FLT4 TOF variants.

Conclusion
Taken together, we identify a pathogenic mechanism for FLT4 variants predisposing to TOF that is distinct from the known dominant negative mechanism of Milroy-causative variants. FLT4 variants give rise to conditions of the two circulatory subdivisions of the vascular system via distinct developmental pleiotropic molecular mechanisms.
Pathway-based, reaction-specific annotation of disease variants for elucidation of molecular phenotypes
Authors: Orlic-Milacic Marija , Rothfels Karen , Matthews Lisa , Wright Adam , Jassal Bijay , Shamovsky Veronica , Trinh Quang , Gillespie Marc E , Sevilla Cristoffer , Tiwari Krishna , Ragueneau Eliot , Gong Chuqiao , Stephan Ralf , May Bruce , Haw Robin , Weiser Joel , Beavers Deidre , Conley Patrick , Hermjakob Henning , Stein Lincoln D , D’Eustachio Peter , Wu Guanming 
Published: May 2024

Abstract
Germline and somatic mutations can give rise to proteins with altered activity, including both gain and loss-of-function. The effects of these variants can be captured in disease-specific reactions and pathways that highlight the resulting changes to normal biology. A disease reaction is defined as an aberrant reaction in which a variant protein participates. A disease pathway is defined as a pathway that contains a disease reaction. Annotation of disease variants as participants of disease reactions and disease pathways can provide a standardized overview of molecular phenotypes of pathogenic variants that is amenable to computational mining and mathematical modeling. Reactome (https://reactome.org/), an open source, manually curated, peer-reviewed database of human biological pathways, in addition to providing annotations for &gt;11 000 unique human proteins in the context of ∼15 000 wild-type reactions within more than 2000 wild-type pathways, also provides annotations for &gt;4000 disease variants of close to 400 genes as participants of ∼800 disease reactions in the context of ∼400 disease pathways. Functional annotation of disease variants proceeds from normal gene functions, described in wild-type reactions and pathways, through disease variants whose divergence from normal molecular behaviors has been experimentally verified, to extrapolation from molecular phenotypes of characterized variants to variants of unknown significance using criteria of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Reactome’s data model enables mapping of disease variant datasets to specific disease reactions within disease pathways, providing a platform to infer pathway output impacts of numerous human disease variants and model organism orthologs, complementing computational predictions of variant pathogenicity.
Database URL: https://reactome.org/