bluuebunny/crossref_metadata_2025_split huggingface dataset:
Can low-carbohydrate diets be recommended for reducing cardiovascular risk?
Authors: Berger Amy , Thorn Eric 
Published: July 2022

Purpose of review
This review provides a rationale for implementing carbohydrate restriction as a dietary therapy to improve biomarkers of cardiovascular health and suggests that this will require a paradigm shift away from what is currently promulgated as a ‘heart-healthy’ diet.

Recent findings
Type 2 diabetes mellitus (T2DM), metabolic syndrome, and related co-morbidities are major risk factors for cardiovascular disease (CVD). Ideally, then, a diet intended to support cardiovascular health should be one that improves or reverses these underlying risk factors. Carbohydrate restriction is effective for this purpose as well as for favorably impacting atherogenic dyslipidemia. Recent consensus reports from select national organizations have endorsed low-carbohydrate diets for improving glycemia and cardiovascular risk. Reluctance among public health organizations and some clinicians to more widely promote this therapeutic nutritional approach is driven primarily by the increase in serum low-density lipoprotein cholesterol (LDL-C) observed in a proportion of individuals who adopt a low-carbohydrate diet. Here we explore the rationale for using carbohydrate restriction to improve cardiovascular health by way of favorably impacting T2DM and insulin resistance, and why this salutary effect outweighs the potential adverse effects of an increase in serum LDL-C.

Summary
Carbohydrate restriction is a logical foundation for a dietary intervention intended to reduce CVD risk, particularly among individuals with T2DM or metabolic syndrome.
The Influence of Practice Structure on Urologists’ Treatment of Men With Low-Risk Prostate Cancer
Authors: Mitchell Jean M. , Gresenz Carole Roan 
Published: July 2022

Background:
Vertical and horizontal integration among health care providers has transformed the practice arrangements under which many physicians work.

Objective:
To examine the influence of type of practice structure, and by implication the financial incentives associated with each structure, on treatment received among men newly diagnosed with low-risk prostate cancer.

Research Design:
We compiled a unique database from cancer registry records from 4 large states, Medicare enrollment and claims for the years 2005−2014 and SK & A physician surveys corroborated by extensive internet searches. We estimated a multinomial logit model to examine the influence of urologist practice structure on type of initial treatment received.

Results:
The probability of being monitored with active surveillance was 7.4% and 4.2% points higher for men treated by health system and nonhealth system employed urologists (P<0.01), respectively, in comparison to men treated by single specialty urology practices. Among multispecialty practices, the rate of active surveillance use was 3% points higher compared with single specialty urology practices(P<0.01). Use of intensity modulated radiation therapy among urologists with ownership in intensity modulated radiation therapy was 17.4% points higher compared with urologists working in small single specialty practices.

Conclusions:
Physician practice structure attributes are significantly associated with type of treatment received but few studies control for such factors. Our findings—coupled with the observation that urologist practice structure shifted substantially over this time period due to mergers of small urology groups—provide one explanation for the limited uptake of active surveillance among men with low-risk disease in the US.
The Role of Social Risk Factors in Dialysis Quality and Patient Outcomes Under a Medicare Quality Incentive Program
Authors: Breck Andrew , Marr Jeffrey , Turenne Marc , Esposito Dominick 
Published: July 2022

Background:
There have been critical improvements in dialysis care and mortality in the last decade. These improvements track with the implementation of the end-stage renal disease (ESRD) Quality Incentive Program (QIP) beginning in 2012, which aligns Medicare payments to dialysis facilities with performance on quality measures. This study explores whether the improvements in dialysis care and patient outcomes under the ESRD QIP have been shared equally among patient groups.

Methods:
Our analyses focus on 4 social risk factors: Black race, Hispanic ethnicity, dual eligibility for Medicare and Medicaid, and rurality. We estimated multivariable regressions using longitudinal Medicare and Consolidated Renal Operations in a Web-Enabled Network data.

Results:
ESRD QIP payment reductions were more common at dialysis facilities with higher proportions of Black and dual-eligible ESRD patients. Patients with dual eligibility and Black race had persistently worse relative outcomes as the ESRD QIP was implemented. This finding was true for differences in outcomes when comparing patients within and across facilities and was not affected by the addition of specific quality measures to the ESRD QIP measure set. Hispanic patients and patients at rural facilities have generally not had worse outcomes since the start of the ESRD QIP.

Conclusions:
There is no evidence of widening disparities in dialysis care or patient outcomes across patient groups under the ESRD QIP, which is a longstanding and well-publicized concern with value-based purchasing programs. Relative changes between patient groups since the start of ESRD QIP have not favored any patient group. Many disparities in dialysis quality measures and assessment of dialysis facility payment reductions persist.
Active surveillance for non-muscle-invasive bladder cancer: fallacy or opportunity?
Authors: von Deimling Markus , Pallauf Maximilian , Bianchi Alberto , Laukhtina Ekaterina , Karakiewicz Pierre I. , Rink Michael , Shariat Shahrokh F. , Pradere Benjamin 
Published: July 2022

Purpose of review
This review aims to analyze the current place of active surveillance (AS) in non-muscle-invasive bladder cancer (NMIBC).

Recent findings
A growing body of evidence suggests that AS protocols for pTa low-grade (TaLG) NMIBC are safe and feasible. However, current guidelines have not implemented AS due to a lack of high-quality data. Available studies included pTa tumors, with only one study excluding pT1-NMIBC. Inclusion/exclusion criteria were heterogeneously defined based on tumor volume, number of tumors, carcinoma in situ (CIS), or high-grade (HG) NMIBC. Tumor volume <10 mm and <5 lesions were used as cut-offs. Positive urinary cytology (UC) or cancer-related symptoms precluded inclusion. Surveillance within the first year consisted of quarterly cystoscopy. AS stopped upon the presence of cancer-related symptoms, change in tumor morphology, positive UC, or patient's request. With a median time on AS of 16 months, two-thirds of the patients failed AS. Progression to muscle-invasive bladder cancer (MIBC) was rare and occurred only in patients with pT1-NIMBC at inclusion.

Summary
AS in NMIBC is an attractive concept in the era of personalized medicine, but strong evidence is still awaited. A more precise definition of patient inclusion, follow-up, and failure criteria is required to improve its implementation in daily clinical practice.
Pediatric Medical Traumatic Stress in Inflammatory Bowel Disease, Pancreatitis, and Cystic Fibrosis
Authors: Cuneo Addison A. , Abu-El-Haija Maisam , Marsac Meghan L. , Verstraete Sofia , Heyman Melvin B. , Ly Ngoc , Perito Emily R. 
Published: July 2022

Objectives:Known as pediatric medical traumatic stress (PMTS), posttraumatic stress symptoms from medical experiences have not been explored in children with chronic gastrointestinal diseases. This cross-sectional study of children and adolescents with inflammatory bowel disease, chronic pancreatitis and cystic fibrosis, aimed to (1) estimate the prevalence of medical potentially traumatic events (PTEs) and PMTS, (2) explore potential risk factors for PMTS, and (3) explore potential consequences of PMTS.Methods:This cross-sectional study used validated, self-report measures to evaluate PTEs and PMTS. Descriptive statistics and regression analyses were used to achieve study objectives.Results:Over two-thirds of children reported a medical potentially traumatic event (91 of 132, 69%). Forty-eight had PMTS symptoms (36%). PMTS was associated with medication burden, emergency and intensive care visits, and parent posttraumatic stress disorder in multivariate analysis. Potential consequences associated with PMTS included school absenteeism, home opioid use, poor quality of life, and parent missed work.Conclusions:A substantial portion of our cohort reported medical PTEs and PMTS. The exploratory analysis identified potential associations between PMTS and illness factors, parent posttraumatic stress disorder, and functional impairments. Further studies of PMTS detection, prevention and treatment are integral to optimizing these children’s health and quality of life.
Fat Malabsorption and Ursodeoxycholic Acid Treatment in Children With Reduced Organic Solute Transporter-α (SLC51A) Expression
Authors: Tronstad Rune Rose , Berland Siren , Tjora Erling , El Jellas Khadija , Aukrust Ingvild , Kristensen Kurt , Tveitnes Dag , Molven Anders , Marschall Hanns-Ulrich , Rao Anuradha , Dawson Paul A. 
Published: July 2022

Objectives:
A bile acid homeostasis disorder was suspected in 2 siblings and their second cousin who presented in infancy with fat malabsorption, severe fat-soluble vitamin deficiency, rickets, and mild liver involvement. Our aims were to identify the genetic cause, describe the disease, and evaluate the response to ursodeoxycholic acid (UDCA) treatment.

Methods:
Whole exome sequencing, immunohistochemistry of duodenal biopsies and candidate variant testing in a cell-based model was performed. Fecal fat excretion, serum bile acids, 7α-hydroxy-4-cholesten-3-one (C4), and fibroblast growth factor 19 (FGF19) were quantified in both siblings on and off UDCA treatment.

Results:
A novel homozygous variant of SLC51A, which encodes the bile acid carrier organic solute transporter (OST)-α, was identified in all affected children. OSTα protein expression was readily detected by immunohistochemistry in duodenum of pediatric control subjects but not in the affected siblings. The siblings had low serum levels of bile acids and C4 and high serum levels of FGF19 consistent with repression of hepatic bile acid synthesis. On treatment with UDCA, fecal fat excretion was reduced and serum levels of C4, FGF19, and liver enzymes normalized.

Conclusions:
We report an apparent deficiency of OSTα associated with early onset fat malabsorption and mild liver involvement. The clinical presentation partially overlaps previous reports for 3 patients with OSTα or OSTβ deficiency and extends the clinical spectrum associated with loss of SLC51A expression. Our data suggest that repression of hepatic bile acid synthesis contributes to fat malabsorption in OSTα-OSTβ deficiency but can be partly reversed with UDCA treatment.
Reasons Affecting the Choice of Patient-Identified Goals Set by Occupational Therapists in Low Vision Rehabilitation
Authors: Smith Theresa M. 
Published: July 2022

Background:
Goal setting is done in collaboration with the patient, but patient-identified (PID) goals are not always addressed. The purpose of this study was to determine reasons PID goals are not set in low-vision rehabilitation and for which tasks.

Methods:
Occupational therapists completed an individualized survey to determine from 15 probable reasons why they did not set a PID for specific tasks.

Results and Conclusion:
PID goals were not set for 3 activities of daily living, 13 instrumental activities of daily living, 4 social participation, and 10 leisure tasks. Further research is needed to understand how prioritization of PID goals differs between therapists and patients.
Social Determinants of Health for Older Adults With Low Vision
Authors: Bryant Kimberly D. , Wengerd Lauren , Smith Cristina R. 
Published: July 2022

Objective:
To analyze the literature to increase understanding and awareness of how the social determinants of health can impact visual impairment in the elderly population.

Methods:
The authors used secondary and tertiary data sources on the subject area.

Results:
Although there has been minimal data collected on the effect of social determinants of health on visual impairment for older adults, more evidence is needed to show the influence of the social inequalities involved in the onset of low vision for the elderly population and to increase education on the resources available to improve function impacted by visual impairment.
SMAP design: A multiplex PCR amplicon and gRNA design tool to screen for natural and CRISPR-induced genetic variation
Authors: Develtere Ward , Waegneer Evelien , Debray Kevin , Van Glabeke Sabine , Maere Steven , Ruttink Tom , Jacobs Thomas B. 
Published: July 2022

ABSTRACTMultiplex amplicon sequencing is a versatile method to identify genetic variation in natural or mutagenized populations through eco-tilling or multiplex CRISPR screens. Such genotyping screens require reliable and specific primer designs, combined with simultaneous gRNA design for CRISPR screens. Unfortunately, current tools are unable to combine multiplex gRNA and primer design into a high-throughput and easy-to-use manner with high design flexibility. Here, we report the development of a bioinformatics tool called SMAP design to overcome these limitations. We tested SMAP design on several plant and non-plant genomes and obtained designs for more than 80-90% of the target genes, depending on the genome and gene family. We validated the primer designs with Illumina multiplex amplicon sequencing and Sanger sequencing in Arabidopsis and soybean. We also used SMAP design to perform eco-tilling by tilling PCR amplicons across nine candidate genes putatively associated with haploid induction in Cichorium intybus. We screened 60 accessions of chicory and witloof and identified thirteen knockout haplotypes and their carriers. SMAP design is an easy-to-use command-line tool that generates highly specific gRNA and/or primer designs for any number of loci for CRISPR or natural variation screens and is compatible with other SMAP modules for seamless downstream analysis.
Reconstructing protein interactions across time using phylogeny-aware graph neural networks
Authors: Moi David , Dessimoz Christophe 
Published: July 2022

AbstractMotivationGenes which are involved in the same biological processes tend to co-evolve. Thus, metabolic pathways, protein complexes, and other kinds of protein-protein interactions can be inferred by looking for correlated patterns of gene retention and loss across the tree of life—a technique called phylogenetic profiling. Recent methodological developments on phylogenetic profiling have focused on scalability improvements to take advantage of the rapidly accumulating genomic data. However, state-of-the-art methods assume that the correlation resulting from co-evolving proteins is uniform across all species considered. This is reasonable for interactions already present at the root of the species considered, but less so for ones that emerge in more recent lineages. To address this challenge and take advantage of recent developments in deep learning methods, we introduce a phylogenetic profiling method which processes large gene co-phylogenies using neural networks.ResultsWe show that post-processing conventional phylogenetic profiles using deep neural networks can improve predictions, but requires onerous training on specific phylogenies. Overcoming this limitation by taking the topology of the species tree as an input, Graph Neural Networks are shown to outperform all other methods when interaction detection is not centered on just one species of interest, while also predicting when interactions appeared and in which taxa they are present.ConclusionGraph Neural Networks constitute a promising new approach for phylogenetic profiling. Our work is a first foray into “dynamic phylogenetic profiling”—the reconstruction of pairwise protein interaction across time.AvailabilityAll of the code is available on the project Git at https://github.com/DessimozLab/HogProf/tree/master/pyprofiler/notebooks/Graphnet. Datasets used are hosted at http://humap2.proteincomplexes.org/download and https://string-db.org/cgi/download.Contactdmoi@unil.ch
Mapping the unicellular transcriptome of the ascending thoracic aorta to changes in mechanosensing and mechanoadaptation during aging
Authors: Farra Yasmeen M. , Rivera Cristobal , Silvestro Michele , Matz Jacqueline , Pratama Yogi , Kumari Puja , Vlahos John , Ramkhelawon Bhama , Bellini Chiara 
Published: July 2022

ABSTRACTAortic stiffening is an inevitable manifestation of chronological aging, yet the mechano-molecular programs that orchestrate region- and layer-specific adaptations along the length and through the wall of the aorta are incompletely defined. Here, we show that the decline in passive cyclic distensibility is more pronounced in the ascending thoracic (ATA) compared to distal segments of the aorta and that tissues in both the medial and adventitial compartments of the ATA stiffen during aging. Single-cell RNA sequencing of aged ATA tissues reveals altered cellular senescence, remodeling, and inflammatory responses accompanied by enrichment of T-lymphocytes and rarefaction of vascular smooth muscle cells, compared to young samples. T-lymphocytes accumulate in the adventitia and likely promote fibrosis, while activation of mechanosensitive piezo-1 enhances medial vasoconstriction. These results portray the immuno-mechanical aging of the ATA as a process that culminates in a stiffer conduit permissive to the accrual of multi-gerogenic signals priming to disease development.
Simulation study of Cell Transmembrane Potential and Electroporation Induced by Time-Varying Magnetic Fields
Authors: Guo Fei , Qian Kun , Li Xin , Deng Hao 
Published: July 2022

AbstractIn this work, an improved simulation model was proposed to assess the transmembrane potential (TMP) evolution on the cellular membrane exposed to time-varying magnetic fields (TMFs). Comparatively, we extended the research on TMP induced by TMF to the electroporation phenomenon by introducing the Smoluchowski function, thereby predicting the occurrence of electroporation. The simulation results based on our numerical model showed that with exposure to the sub-microsecond trapezoidal pulsed magnetic field (PMF), the pore density did not reach the conventional electroporation criterion (1014m−2) even if the TMP exceeded the electroporation threshold (∼1V); however, with the same energy import, it was easier for the nanosecond pulse to electroporate the membrane evidenced by higher pore density. Further, the capability of predicting the occurrence of electroporation was verified by extending our simulation model to compare experimental results. The comparative analysis showed that our simulation model has predictive and guiding significance for experimental studies and practical applications.
Hybrid Rank Aggregation (HRA): A novel rank aggregation method for ensemble-based feature selection
Authors: Jain Rahi , Xu Wei 
Published: July 2022

AbstractBackgroundFeature selection (FS) reduces the dimensions of high dimensional data. Among many FS approaches, ensemble-based feature selection (EFS) is one of the commonly used approaches. The rank aggregation (RA) step influences the feature selection of EFS. Currently, the EFS approach relies on using a single RA algorithm to pool feature performance and select features. However, a single RA algorithm may not always give optimal performance across all datasets.Method and ResultsThis study proposes a novel hybrid rank aggregation (HRA) method to perform the RA step in EFS which allows the selection of features based on their importance across different RA techniques. The approach allows creation of a RA matrix which contains feature performance or importance in each RA technique followed by an unsupervised learning-based selection of features based on their performance/importance in RA matrix. The algorithm is tested under different simulation scenarios for continuous outcomes and several real data studies for continuous, binary and time to event outcomes and compared with existing RA methods. The study found that HRA provided a better or at par robust performance as compared to existing RA methods in terms of feature selection and predictive performance of the model.ConclusionHRA is an improvement to current single RA based EFS approaches with better and robust performance. The consistent performance in continuous, categorical and time to event outcomes suggest the wide applicability of this method. While the current study limits the testing of HRA on cross-sectional data with input features of a continuous distribution, it could be applied to longitudinal and categorical data.
A Data-Driven Biopsychosocial Framework Determining the Spreading of Chronic Pain
Authors: Tanguay-Sabourin Christophe , Fillingim Matt , Parisien Marc , Guglietti Gianluca V , Zare Azin , Norman Jax , Da-ano Ronrick , Perez Jordi , Thompson Scott J , Martel Marc O , Roy Mathieu , Diatchenko Luda , Vachon-Presseau Etienne 
Published: July 2022

AbstractChronic pain conditions are complex syndromes characterized by a mosaic of biological, psychological, and social factors. We derived predictive models for the number of co- existing pain sites in the UK Biobank and identified a common risk score that classified different chronic pain conditions in cross-sectional data, predicted the development of chronic pain in pain-free individuals, and determined the spreading of chronic pain to multiple sites or its recovery nine years later. The features with the strongest prognosis included sleeplessness, feeling ‘fed-up’, tiredness, stressful life events, and a BMI > 30. The risk score for pain was associated with an inflammatory blood marker, a polygenic risk score for pain, and a neuroimaging-based marker for sustained pain. The demonstration of a common biopsychosocial risk factor for different clinical pain conditions may help better characterize a general chronic pain syndrome, tailor research protocols, optimize patient randomization in clinical trials, and improve pain management.