bluuebunny/crossref_metadata_2025_split huggingface dataset:
Loss of NDST1 N-sulfotransferase activity is associated with autosomal recessive intellectual disability
Authors: Khosrowabadi Elham , Mignon-Ravix Cécile , Riccardi Florence , Cacciagli Pierre , Desnous Béatrice , Sigaudy Sabine , Milh Mathieu , Villard Laurent , Kjellén Lena , Molinari Florence 
Published: December 2023

Abstract
Intellectual Disability (ID) is the major cause of handicap, affecting nearly 3% of the general population, and is highly genetically heterogenous with more than a thousand genes involved. Exome sequencing performed in two independent families identified the same missense variant, p.(Gly611Ser), in the NDST1 (N-deacetylase/N-sulfotransferase member 1) gene. This variant had been previously found in ID patients of two other families but has never been functionally characterized. The NDST1 gene encodes a bifunctional enzyme that catalyzes both N-deacetylation and N-sulfation of N-acetyl-glucosamine residues during heparan sulfate (HS) biosynthesis. This step is essential because it influences the downstream enzymatic modifications and thereby determines the overall structure and sulfation degree of the HS polysaccharide chain. To discriminate between a rare polymorphism and a pathogenic variant, we compared the enzymatic properties of wild-type and mutant NDST1 proteins. We found that the p.(Gly611Ser) variant results in a complete loss of N-sulfotransferase activity while the N-deacetylase activity is retained. NDST1 shows the highest and the most homogeneous expression in the human cerebral structures compared to the other members of the NDST gene family. These results indicate that a loss of NDST1 N-sulfation activity is associated with impaired cognitive functions.
Development of a breast cancer prognostic model based on vesicle-mediated transport-related genes to predict immune landscape and clinical drug therapy
Authors: Zhu Xiaotao , Wang Fan , Wang Mingzhen , Lv Lin , Fang Linghui , Song Jialu , Wang Xiaohui , Ding Fengsheng 
Published: December 2023

Abstract

Background
Vesicle-mediated transport, vital for substance exchange and intercellular communication, is linked to tumor initiation and progression. This work was designed to study the role of vesicle-mediated transport-related genes (VMTRGs) in breast cancer (BC)prognosis.

Methods
Univariate Cox analysis was utilized to screen prognosis-related VMTRGs. BC samples underwent unsupervised clustering based on VMTRGs to analyze survival, clinical factors, and immune cell abundance across different subtypes. We constructed a risk model using univariate Cox and LASSO regression analysis, with validation conducted using GEO datasets. Subsequently, we performed tumor mutational burden analysis, and immune landscape analysis on both groups. Ultimately, we conducted immunophenoscore (IPS) scoring to forecast immunotherapy and performed drug sensitivity analysis.

Results
We identified 102 VMTRGs associated with BC prognosis. Using these 102 VMTRGs, BC patients were classified into 3 subtypes, with Cluster3 patients showing significantly better survival rates. We constructed a prognostic model for BC based on 12 VMTRGs that effectively predicted patient survival. Riskscore was an independent prognostic factor for BC patients. According to median risk score, high-risk group (HRG) had higher TMB values. The immune landscape of the HRG exhibited characteristics of cold tumor, with higher immune checkpoint expression levels and lower IPS scores, whereas Gemcitabine, Nilotinib, and Oxaliplatin were more suitable for treating low-risk group.

Conclusion
We classified BC subtypes and built a prognostic model based on VMTRGs. The genes in the prognostic model may serve as potential targets for BC therapy.
Understanding Medication Nonadherence in Crohn’s Disease Patients: A Qualitative Evaluation
Authors: Brady Robert E , Salwen-Deremer Jessica K , Tunnell Natalie C , Winter Michael W 
Published: December 2023

Abstract

Background
Immune-modifying medications are widely available and recognized as valuable by most gastroenterologists. However, approximately 40% of patients with Crohn’s disease (CD) do not comply with regimens using these medications, resulting in complications, hospitalization, and surgeries. We sought to identify factors that motivate adherence or nonadherence with medication recommendations for CD.

Methods
We conducted qualitative interviews with patients living with CD who were identified as adherent or nonadherent to immune-modifying medication recommendations by their treating gastroenterologist. Semistructured interview guides were developed based on an established framework for understanding health behaviors. We conducted content analysis of the resulting qualitative data using an inductive-deductive approach to identify emergent themes that influence medication decision-making.

Results
Twenty-five patients with CD completed interviews for this study. Interviews were independently coded and analyzed for thematic content. Two broad domains emerged comprising (1) themes reflected in the Theoretical Domains Framework and (2) novel themes specific to medication decision-making in CD. Adherent patients conveyed a sense of trust in science and healthcare provider expertise, while nonadherent patients were more likely to express beliefs in their ability to self-manage CD, concern about risks associated with medication, and a general ambivalence to treatment.

Conclusions
There are clear cognitive, behavioral, and relational factors that guide patients’ medication-related decision-making. Several of the factors share features of other behavioral change and decision-making processes, while others are specific to the experience of patients with CD. A fuller understanding of these factors is essential to developing effective behavioral interventions to improve adherence to evidence-based treatment recommendations.
Aortic growth after arch reconstruction with patch augmentation: a 2-decade experience
Authors: Recco Dominic P , Kizilski Shannen B , Ghosh Reena M , Piekarski Breanna , Prakash Ashwin , Hoganson David M 
Published: December 2023

Abstract

OBJECTIVES
Optimal aortic sizing during aortic arch reconstruction remains unknown. Negative effects of arch under- or oversizing are well-published. We aimed to characterize longitudinal aortic growth after patch-augmented arch reconstruction to identify the initial reconstructed arch size that results in normal mid-term arch dimensions.

METHODS
Single-centre, retrospective review of infants undergoing Damus-Kaye-Stansel (DKS) or non-DKS patch-augmented aortic arch reconstruction between 2000 and 2021. Ascending aorta, proximal and distal transverse arch, aortic isthmus (AIsth) and descending aorta dimensions were measured in postoperative echocardiograms (&lt;3 months from index operation) and cross-sectional imaging (&gt;12 months). Longitudinal changes to aortic dimensions and z-scores were analysed. Secondary outcomes included reintervention, valve and ventricular function, mortality and transplantation.

RESULTS
Fifty-four patients (16 DKS, 38 non-DKS) were included. At 6.3 [2.2, 12.0]-year follow-up, all aortic segments grew significantly in both groups, while z-scores remained unchanged except for non-DKS proximal and distal transverse arch z-scores, which significantly increased (P &lt; 0.05 each). When stratified by initial postoperative z-score (z &lt; −1, −1 ≤ z ≤ 1, z &gt; 1), non-DKS patients with initial AIsth z-score &lt;−1 had a final z-score significantly smaller than both the targeted z-score zero (P = 0.014) and final z-score in a group with initial postoperative z-score ±1 (P = 0.009). Valve and ventricular function remained stable. Eighteen patients required reintervention, 1 died and 1 underwent transplant.

CONCLUSIONS
Over mid-term follow-up, aortic growth after arch reconstruction with patch augmentation was proportional when repaired to normal z-score dimensions, aside from proximal transverse arch, which disproportionately dilated. AIsth undersizing prevailed mid-term and trended towards a higher reintervention rate. Initial reconstruction between z-score 0 and +1 resulted in maintenance of that z-score size at mid-term follow-up. Overall, it is crucial to achieve targeted aortic sizing at index operation to maintain appropriate aortic dimensions over time and reduce reintervention risk with specific focus on the AIsth.
Measuring prognostic awareness in patients with advanced cancer: a scoping review and interpretive synthesis of the impact of hope
Authors: Mathews Jean , Merchant Shaila , Galica Jacqueline , Palmer Michael J , O’Donnell Jennifer , Koven Rachel , Booth Christopher , Brundage Michael 
Published: December 2023

Abstract

Background
Assessment of prognostic awareness (PA) in patients with advanced cancer is challenging because patient responses often indicate their hopes. The objectives of this scoping review were to summarize studies that measured PA in patients with advanced cancer and to synthesize data about how PA was measured and whether hope was incorporated into the measurement.

Methods
MEDLINE and Embase databases were searched from inception to December 14, 2021. Data regarding the impact of hope on assessment of PA were extracted when studies reported on patients’ beliefs about prognosis and patients’ beliefs about their doctor’s opinion about prognosis. An interpretive synthesis approach was used to analyze the data and to generate a theory regarding the incorporation of hope into the assessment of PA.

Results
In total, 52 studies representing 23 766 patients were included. Most were conducted in high-income countries and measured PA based on the goal of treatment (curable vs incurable). Five studies incorporated hope into the assessment of PA and reported that among patients who responded that their treatment goal was a cure, an average of 30% also acknowledged that their doctors were treating them with palliative intent. Interpretive synthesis of the evidence generated a trinary conceptualization of PA patients who are aware and accepting of their prognosis; aware and not accepting; and truly unaware. Each of these groups will benefit from different types of interventions to support their evolving PA.

Conclusion
The trinary conceptualization of PA may promote understanding of the impact of hope in the assessment of PA and guide future research.
On the anisotropic distribution of clusters in the local Universe
Authors: Schaller Matthieu 
Published: December 2023

ABSTRACT
In his 2021 lecture to the Canadian Association of Physicists Congress, P.J.E. Peebles pointed out that the brightest extragalactic radio sources tend to be aligned with the plane of the de Vaucouleur Local Supercluster up to redshifts of z = 0.02 ($d_{\rm MW}\approx 85~\rm {Mpc}$). He then asked whether such an alignment of clusters is anomalous in the standard Lambda cold dark matter (ΛCDM) framework. In this letter, we employ an alternative, absolute orientation agnostic, measure of the anisotropy based on the inertia tensor axial ratio of these brightest sources and use a large cosmological simulation from the flamingo suite to measure how common such an alignment of structures is. We find that only 3.5 per cent of randomly selected regions display an anisotropy of their clusters more extreme than the one found in the local Universe’s radio data. This sets the region around the Milky Way as a 1.85σ outlier. Varying the selection parameters of the objects in the catalogue, we find that the clusters in the local Universe are never more than 2σ away from the simulations’ prediction for the same selection. We thus conclude that the reported anisotropy, whilst noteworthy, is not in tension with the ΛCDM paradigm.
CHLOROPLAST UNUSUAL POSITIONING 1 is a plant-specific actin polymerization factor regulating chloroplast movement
Authors: Kong Sam-Geun , Yamazaki Yosuke , Shimada Atsushi , Kijima Saku T , Hirose Keiko , Katoh Kaoru , Ahn Jeongsu , Song Hyun-Geun , Han Jae-Woo , Higa Takeshi , Takano Akira , Nakamura Yuki , Suetsugu Noriyuki , Kohda Daisuke , Uyeda Taro Q P , Wada Masamitsu 
Published: December 2023

Abstract
Plants have unique responses to fluctuating light conditions. One such response involves chloroplast photorelocation movement, which optimizes photosynthesis under weak light by the accumulation of chloroplasts along the periclinal side of the cell, which prevents photodamage under strong light by avoiding chloroplast positioning toward the anticlinal side of the cell. This light-responsive chloroplast movement relies on the reorganization of chloroplast actin (cp-actin) filaments. Previous studies have suggested that CHLOROPLAST UNUSUAL POSITIONING 1 (CHUP1) is essential for chloroplast photorelocation movement as a regulator of cp-actin filaments. In this study, we conducted comprehensive analyses to understand CHUP1 function. Functional, fluorescently tagged CHUP1 colocalized with and was coordinately reorganized with cp-actin filaments on the chloroplast outer envelope during chloroplast movement in Arabidopsis thaliana. CHUP1 distribution was reversibly regulated in a blue light- and phototropin-dependent manner. X-ray crystallography revealed that the CHUP1-C-terminal domain shares structural homology with the formin homology 2 (FH2) domain, despite lacking sequence similarity. Furthermore, the CHUP1-C-terminal domain promoted actin polymerization in the presence of profilin in vitro. Taken together, our findings indicate that CHUP1 is a plant-specific actin polymerization factor that has convergently evolved to assemble cp-actin filaments and enables chloroplast photorelocation movement.
Radio galaxy zoo: towards building the first multipurpose foundation model for radio astronomy with self-supervised learning
Authors: Slijepcevic Inigo V , Scaife Anna M M , Walmsley Mike , Bowles Micah , Wong O Ivy , Shabala Stanislav S , White Sarah V 
Published: December 2023

Abstract
In this work, we apply self-supervised learning with instance differentiation to learn a robust, multipurpose representation for image analysis of resolved extragalactic continuum images. We train a multi-use model which compresses our unlabelled data into a structured, low dimensional representation which can be used for a variety of downstream tasks (e.g. classification, similarity search). We exceed baseline supervised Fanaroff–Riley classification performance by a statistically significant margin, with our model reducing the test set error by up to half. Our model is also able to maintain high classification accuracy with very few labels, with only $7.79{{\ \rm per\ cent}}$ error when only using 145 labels. We further demonstrate that by using our foundation model, users can efficiently trade off compute, human labelling cost and test set accuracy according to their respective budgets, allowing for efficient classification in a wide variety of scenarios. We highlight the generalizability of our model by showing that it enables accurate classification in a label scarce regime with data from the new MIGHTEE survey without any hyperparameter tuning, where it improves upon the baseline by $\sim 8{{\ \rm per\ cent}}$. Visualizations of our labelled and un-labelled data show that our model’s representation space is structured with respect to physical properties of the sources, such as angular source extent. We show that the learned representation is scientifically useful even if no labels are available by performing a similarity search, finding hybrid sources in the RGZ DR1 data set without any labels. We show that good augmentation design and hyperparameter choice can help achieve peak performance, while emphasizing that optimal hyperparameters are not required to obtain benefits from self-supervised pre-training.
Enabling novel paradigms: a biological questions-based approach to human chemical hazard and drug safety assessment
Authors: Berridge Brian R , Bucher John R , Sistare Frank , Stevens James L , Chappell Grace A , Clemons Meredith , Snow Samantha , Wignall Jessica , Shipkowski Kelly A 
Published: December 2023

Abstract
Throughput needs, costs of time and resources, and concerns about the use of animals in hazard and safety assessment studies are fueling a growing interest in adopting new approach methodologies for use in product development and risk assessment. However, current efforts to define “next-generation risk assessment” vary considerably across commercial and regulatory sectors, and an a priori definition of the biological scope of data needed to assess hazards is generally lacking. We propose that the absence of clearly defined questions that can be answered during hazard assessment is the primary barrier to the generation of a paradigm flexible enough to be used across varying product development and approval decision contexts. Herein, we propose a biological questions-based approach (BQBA) for hazard and safety assessment to facilitate fit-for-purpose method selection and more efficient evidence-based decision-making. The key pillars of this novel approach are bioavailability, bioactivity, adversity, and susceptibility. This BQBA is compared with current hazard approaches and is applied in scenarios of varying pathobiological understanding and/or regulatory testing requirements. To further define the paradigm and key questions that allow better prediction and characterization of human health hazard, a multidisciplinary collaboration among stakeholder groups should be initiated.
The Creation and Validation of an Ankle Bone Age Atlas and Data Predicting Remaining Ankle Growth
Authors: Pennock Andrew T. , Bomar James D. , Pedowitz Jason M. , Carveth Stephen L. 
Published: December 2023

Background:
The purpose of the current study was 2-fold: (1) to create and validate an ankle bone age atlas spanning the pediatric and adolescent years and (2) to utilize this atlas in conjunction with distal tibia/fibular growth data as measured on serial radiographs to develop a predictive growth model for the lower extremity.

Methods:
Radiographs were surveyed to identify distinguishable, reproducible, radiographic features. Radiographic features of the tibia, fibula, hindfoot, and midfoot from 270 patients were identified and a “standard” for each age/sex was selected to create an atlas. A separate cohort of 90 ankle radiographs was selected to validate the atlas. A subcohort of 41 patients with left-hand radiographs within 3 months of ankle imaging was used to compare the 2 bone age approaches. Harris growth lines were evaluated in 304 serial images of the distal tibia to determine the remaining growth.

Results:
The distal tib/fib ossification centers provided the best age assessment for early childhood (male age: 1 to 8 y; female age: 1 to 4 y). The ossification/fusion of the calcaneal apophysis provided the best age assessment in the preadolescent stage (male age: 6 to 14 y; female age: 5 to 12 y). The closure of the distal tib/fib physes best determined skeletal maturity (male age: 14 to 16 y; female age: 12 to 14 y). The ankle atlas had excellent interobserver and intraobserver reliability (intraclass correlation coefficient=0.993, P<0.001 and 0.998, P<0.001), respectively. We found an excellent correlation between the patient’s chronologic age and ankle bone age (r=0.984; P<0.001). Ankle bone age assessment and Greulich and Pyle were correlated (r
s=0.822, P<0.001). We found that males with a bone age of ≥15 years and females with a bone age of ≥13 years had ≤2 mm of residual growth of the distal tibia/fibula physes.

Conclusions:
bone age can be determined using ankle films ordered to assess/treat ankle injuries. This tool, along with our growth remaining table, may have important clinical implications when managing patients with ankle trauma with premature physeal closure.

Level of Evidence:
IV
The Assessment of Radial Peripapillary Capillary Vessel Density in Adult Children of Patients With Primary Open Angle Glaucoma
Authors: Bayraktar Serdar , Hondur Gözde , Şekeroğlu Mehmet Ali , Altaş Fatma Büşra , Yeşilyaprak Nurtaç , Çevik Seda , Şen Emine , Elgin Ufuk 
Published: December 2023

Précis:
The observed decrease in radial peripapillary capillary vessel density among adult children of individuals with primary open angle glaucoma, in comparison to controls, suggests the possibility of early microvascular alterations in the eyes of these at-risk individuals.

Purpose:
To compare the radial peripapillary capillary vessel density (RPCVD) and peripapillary retinal nerve fiber layer (RNFL) thickness values of eyes between healthy adults with a maternal or paternal history of primary open angle glaucoma (POAG) and age-matched healthy controls without a family history of POAG.

Materials and Methods:
RPCVD values and RNFL thicknesses in the peripapillary region and 4 quadrants (superior, inferior, nasal, and temporal) were evaluated using optical coherence tomography angiography among 30 adult children of patients with POAG and 30 age-matched healthy controls without a family history of POAG.

Results:
The mean whole image RPCVD (51.6±1.7% vs. 49.8±1.7%, P=0.0006) and average RPCVD (54.7±1.7% vs. 53.2±2.1%, P=0.006) values were significantly lower in the adult children of patients with POAG compared with age-matched healthy controls without a family history of POAG. There was no difference in terms of RNFL thickness values in any region.

Conclusion:
Despite having similar RNFL thickness values to the control group, the observation of lower RPCVD in the eyes of adult children of POAG patients may indicate potential early vascular alterations. The result of the present study encourages further longitudinal studies to determine the potential importance of the underlying vascular alterations in these high-risk individuals.