bluuebunny/crossref_metadata_2025_split huggingface dataset:
Differential expression of a brain aging biomarker across discrete chronic pain disorders
Authors: Hung Peter Shih-Ping , Zhang Jia Y. , Noorani Alborz , Walker Matthew R. , Huang Megan , Zhang Jason W. , Laperriere Normand , Rudzicz Frank , Hodaie Mojgan 
Published: February 2022

Abstract
Chronic pain has widespread, detrimental effects on the human nervous system and its prevalence and burden increase with age. Machine learning techniques have been applied on brain images to produce statistical models of brain aging. Specifically, the Gaussian process regression is particularly effective at predicting chronological age from neuroimaging data which permits the calculation of a brain age gap estimate (brain-AGE). Pathological biological processes such as chronic pain can influence brain-AGE. Because chronic pain disorders can differ in etiology, severity, pain frequency, and sex-linked prevalence, we hypothesize that the expression of brain-AGE may be pain specific and differ between discrete chronic pain disorders. We built a machine learning model using T1-weighted anatomical MRI from 812 healthy controls to extract brain-AGE for 45 trigeminal neuralgia (TN), 52 osteoarthritis (OA), and 50 chronic low back pain (BP) subjects. False discovery rate corrected Welch t tests were conducted to detect significant differences in brain-AGE between each discrete pain cohort and age-matched and sex-matched controls. Trigeminal neuralgia and OA, but not BP subjects, have significantly larger brain-AGE. Across all 3 pain groups, we observed female-driven elevation in brain-AGE. Furthermore, in TN, a significantly larger brain-AGE is associated with response to Gamma Knife radiosurgery for TN pain and is inversely correlated with the age at diagnosis. As brain-AGE expression differs across distinct pain disorders with a pronounced sex effect for female subjects. Younger women with TN may therefore represent a vulnerable subpopulation requiring expedited chronic pain intervention. To this end, brain-AGE holds promise as an effective biomarker of pain treatment response.
Gut-derived serotonin and its emerging roles in immune function, inflammation, metabolism and the gut–brain axis
Authors: Banskota Suhrid , Khan Waliul I. 
Published: February 2022

Purpose of review
To shed light on the recently uncovered diverse role of serotonin (5-hydroxytryptamine; 5-HT) in the regulation of immune functions, inflammation, metabolism, and gut–brain axis.

Recent findings
Peripheral 5-HT which accounts for approximately 95% of the total is largely synthesized in the gut by enterochromaffin cells. Enterochromaffin cells release 5-HT in response to various stimuli including microbial products. Released 5-HT influences secretomotor, sensory and immune functions as well as inflammatory processes in the gut. 5-HT released from enterochromaffin cells enters circulation and is taken up and concentrated in platelets. 5-HT released from the activated platelets interacts with different organs to alter their metabolic activity. 5-HT also serves as a link in the gut–brain axis.

Summary
Emerging evidence regarding the role of peripheral 5-HT in the regulation of various physiological and pathophysiological conditions opens up new targets for researchers to explore and for clinicians to treat and manage different diseases associated with the altered 5-HT signalling.
How to present quality of life outcomes after focal therapy: using validated instruments and novel statistical methods
Authors: Clements Matthew B. 
Published: February 2022

Purpose of review
To provide an up-to-date summary of widely used patient-reported measures for focal therapy quality of life outcomes and review contemporary analytic methods and recommendations for data visualization.

Recent findings
Measures such as pad-use, or preferably validated instruments such as the International Consultation on Incontinence Questionnaire, MSKCC Prostate Quality of Life Survey, or Expanded Prostate Cancer Index (EPIC) should be used for urinary function assessment. Sexual Function can be assessed with the International Index of Erectile Function or EPIC, but researchers must be careful to account for patients that are not currently sexually active when analyzing outcomes. Measurement of baseline function is crucial for a meaningful understanding of post-treatment outcomes. When multiple measurements are collected, longitudinal models such as generalized estimating equations or linear mixed effects models are preferred. Whenever possible, the data visualization should mirror the hypothesis testing for clarity of interpretation, and use of restricted cubic splines or generalized additive models are preferred to illustrate non-linear trajectories in quality of life after treatment.

Summary
Advances in both the measurement of patient quality of life with validated instruments and statistical methods have allowed for a more complete understanding and reporting of outcomes, which can be applied to the evaluation of focal therapy for prostate cancer.
Health Care Experiences During Pregnancy and Parenting with an Opioid Use Disorder
Authors: Kim Jane , Busse Morgan , Kantrowitz-Gordon Ira , Altman Molly R. 
Published: February 2022

Abstract

Purpose:
The purpose of this study was to describe the experience of individuals with opioid use disorder (OUD) during the perinatal period.

Study Design and Methods:
We convened focus groups of patients with OUD who had been pregnant and were parenting. Participants who were 18 and older, English-speaking, self-identified as pregnant or parenting, and actively using opioids or in recovery from OUD were recruited using snowball and convenience sampling in resident treatment facilities and outpatient settings. Data were recorded, transcribed, and analyzed for themes.

Results:
Twenty-four participants were recruited, 10 of whom were actively receiving residential recovery services. Most participants had been pregnant from 4 weeks to 2 years prior to our focus group session; none reported being currently pregnant. Nineteen participants had custody of some, or all, of their children. They identified four key themes related to their care: (1) disrespectful care, (2) fear of accessing services, (3) inconsistencies in care received, and (4) limited health and social services.

Clinical Implications:
Participants reported overall negative interactions across different health care settings and lack of social resources to promote ongoing recovery and successful parenting. Nurses should be aware of the lasting impressions they have on their patients. Recognition of their own biases, person-first language, and partnership building skills with patients can help attenuate OUD stigma, promote positive nurse–patient relationships, and support new parents in recovery and infant bonding.
Use of Insoluble Dietary Fiber and Probiotics for Bowel Preparation Before Colonoscopy: A Prospective Study
Authors: Kudou Kensuke , Kimura Koich , Tsutsumi Ryosuke , Hashimoto Naotaka , Wada Hiroya , Ikeda Tetsuo 
Published: February 2022

Background:
In screening colonoscopy, patients usually have to ingest large amounts of bowel-cleansing agents, including polyethylene glycol (PEG). This is difficult and has various side effects; thus, patients avoid undergoing a colonoscopy. We tested a novel bowel preparation method before colonoscopy using insoluble dietary fiber and probiotics (PB).

Methods:
This was a prospective clinical study conducted between October 2018 and March 2019 at a general hospital. Forty participants were randomly assigned to low-volume PEG solution diet (MoviPrep), wheat bran fiber (WBF) and probiotic Bifidobacterium animalis subsp. lactis GCL2505 (PB GCL2505), or standard-volume regimen (1.0 to 1.5 L of MoviPrep) (control group). The patient compliance and the quality of bowel preparation were evaluated.

Results:
Forty individuals aged 38 to 83 years were randomly assigned to the WBF with PB (n=20) and control (n=20) groups. All participants underwent bowel preparation before colonoscopy according to each protocol. The mean required volume of MoviPrep was significantly lower in the WBF with PB group than in the control group (582.5 vs. 1305 mL, P<0.0001). Successful bowel-cleansing rates were not significantly different between the 2 groups; however, the ratio of the Harefield Cleansing Scale grades C and D was significantly lower in the WBF with PB group than in the control group (P=0.0471).

Conclusions:
The intake of WBF and GCL2505 before colonoscopy reduces the required PEG quantities while maintaining bowel-cleansing quality. This novel, minimally invasive pretreatment method makes colonoscopy more accessible contributing to the prevention and early treatment of colorectal cancer.
EXPERIMENTAL INVESTIGATION OF PULSE STERILIZATION OF VIRAL INFECTION
Authors: Chumakov Volodymyr , Ostryzhnyi Mykhailo , Kharchenko Oksana , Naumenko Krystina , Zagorodnya Svitlana , Muraveinyk Vasiliy , Tarasevich Aleksandr 
Published: February 2022

AbstractThe results of experimental investigations of the effect of high-intensity pulsed UV radiation on the influenza virus type A (H1N1) are presented. The research methodology is developed and the structure of the experiments is described. An end-face plasma accelerator was used as a radiation source, which provides a power pulsed discharge in an open atmosphere. The high efficiency of inactivation of the infectiousness of the virus was shown within a short period of time. The possibility of providing urgent 100% sterilization of a viral infection has been shown for the first time. A model for calculating the efficiency of pulse sterilization has been developed. The prospects for the application of pulse sterilization technology to combat coronavirus infection are considered.
Performance of polygenic risk scores in screening, prediction, and risk stratification
Authors: Hingorani AD. , Gratton J. , Finan C. , Schmidt AF. , Patel R. , Sofat R. , Kuan V. , Langenberg C. , Hemingway H. , Morris JK. , Wald NJ. 
Published: February 2022

AbstractBackgroundThe clinical value of polygenic risk scores has been questioned. We sought to clarify performance in population screening, individual risk prediction and population risk stratification by analysing 926 polygenic risk scores for 310 diseases from the Polygenic Score (PGS) Catalog.MethodsPolygenic risk scores in the PGS Catalog are reported using hazard ratios or odds ratios per standard deviation, or the area under the receiver operating characteristic curve sometimes expressed as theC-index. We used this information to produce estimates of performance in: (a)population screening— by calculating the detection rate (DR5) for a 5% false positive rate (FPR) and the population odds of becoming affected given a positive result (OAPR); (b)individual risk prediction— by calculating the individual odds of becoming affected for a person with a particular polygenic score; and (c)population risk stratification— by calculating the odds of becoming affected for groups of individuals in different portions of a polygenic risk score distribution. We use coronary artery disease and breast cancer as illustrative examples.FindingsPopulation screening performance: The medianDR5for all polygenic risk scores and all diseases studied was 11% [interquartile range 8 − 18%]. The medianDR5was 12% [9 − 19] for polygenic risk scores for CAD and 10% [9 − 12] for breast cancer, with populationOAPRsof 1:8 and 1: 21 respectively, with background 10-year odds of 1:19 and 1:41 respectively, which are typical for these diseases at age 50.Individual risk prediction: The corresponding 10-year odds of becoming affected for individuals aged 50 with a polygenic risk score at the 2.5th, 25th, 75thand 97.5thcentile were 1:54, 1:29, 1:15, and 1:8 for CAD and 1:91, 1:56, 1:34, and 1:21 for breast cancer.Population risk stratification: At age 50, stratifying into quintile groups of CAD risk yielded 10-year odds of 1: 41 and 1: 11 for the lowest and highest quintile groups respectively. The 10-year odds was 1: 7 for the upper 2.5% of the polygenic risk score distribution for CAD, a group that contributed 7% of cases. The corresponding estimates for breast cancer were 1: 72 and 1: 26 for lowest and highest quintiles; and 1:19 for the upper 2.5% of the distribution, which contributed 6% of cases.InterpretationPolygenic risk scores perform poorly in population screening, individual risk prediction, and population risk stratification.FundingBritish Heart Foundation; UK Research and Innovation; National Institute of Health and Care Research.
A Multi-Component Telehealth Intervention to Improve Oncofertility Care Delivery among Young Cancer Patients: A Pilot Study
Authors: Yang Emily , Dornisch Anna , Nerb Laura , Helsten Teresa , Kaiser Bonnie N. , Aristizabal Paula , Armenian Saro , Torno Lilibeth L. , Baca Nicole M. , Genensen Mark C. , Su H. Irene , Romero Sally A. D. 
Published: February 2022

AbstractPurposeOncofertility care for pediatric, adolescent, and young adult cancer patients remains under-implemented across adult and pediatric oncology settings. We pilot tested an electronic health record (EHR)-enabled multi-component oncofertility intervention (including screening, referral, and fertility consult) in an adult academic oncology program and systematically assessed intervention fit to pediatric and community oncology programs.MethodsUsing surveys (n=33), audits (n=143), and interviews (n=21) guided by implementation science frameworks, we pilot tested the EHR-enabled intervention for oncofertility care in young cancer patients at an adult oncology program and evaluated implementation outcomes. We interviewed healthcare providers from seven regional oncology and fertility programs about intervention fit to their clinical contexts.ResultsWe recruited 33 healthcare providers from an adult oncology setting and 15 healthcare providers from seven additional oncology and fertility settings. At the adult oncology setting, the intervention was found to be appropriate, acceptable, and feasible and improved the screening of fertility needs (from 30% pre- to 51% post-intervention), yet some patients did not receive appropriate referrals to fertility consults. Providers across all settings suggested content and context modifications, such as adding options to the intervention or allowing the screening component to pop up at a second visit, to improve and adapt the intervention to better fit their clinical care contexts.ConclusionsWe found that the EHR-enabled intervention increased the rate of goal-concordant oncofertility care delivery at an adult oncology program. We also identified facilitators, barriers, and needed adaptations to the intervention required for implementation and scaling up across diverse oncology settings.
Avoiding false positive SARS-CoV-2 rapid antigen test results with point-of-care molecular testing on residual test buffer
Authors: LeBlanc Jason J , McCracken Gregory R. , Goodall Barbara , Hatchette Todd F , Barrett Lisa , Ross John , Davidson Ross J , Patriquin Glenn 
Published: February 2022

AbstractObjectivesAntigen-based rapid diagnostic tests (Ag-RDTs) have been widely used for the detection of SARS-CoV-2 during the Covid-19 pandemic. In settings of low disease prevalence, such as asymptomatic community testing, national guidelines recommend molecular confirmation of positive Ag-RDT results. This often requires patients to be recalled for repeat specimen recollection and subsequent testing in reference laboratories. This project assessed the use of a point-of-care molecular method for SARS-CoV-2 detection on-site at a volunteer-led asymptomatic community testing site, using the residual test buffer (RTB) from positive Ag-RDTs.MethodsThe Abbott COVID-19 ID NOW assay was performed on RTB from two Ag-RDTs: the Abbott Panbio COVID-19 Ag Rapid Test Device and the BTNX Rapid Response COVID-19 Antigen Rapid Test Device. All RTBs were tested using real-time RT-PCR at a reference laboratory using the ThermoFisher TaqPath COVID-19 Combo kit which was used to assign positive Ag-RDTs results as true or false positives. Analytical specificity of the ID NOW was assessed with a panel of various respiratory organisms.ResultsOf 419 positive Ag-RDTs from 5148 tests performed, ID NOW testing of the RTB was positive in 100% of the samples characterized as true positives by RT-PCR. No SARS-CoV-2 detections by ID NOW were observed from 10 specimens characterized as false positive Ag-RDTs, or from contrived specimens with various respiratory organisms.ConclusionsThe use of on-site molecular testing on RTB provides a suitable option for rapid confirmatory testing of positive Ag-RDTs, thereby obviating the need for specimen recollection for molecular testing at local reference laboratories.
Biophysical fitness landscape of the SARS-CoV-2 Delta variant receptor binding domain
Authors: Patrick Casey , Upadhyay Vaibhav , Lucas Alexandra , Mallela Krishna M.G. 
Published: February 2022

AbstractAmong the five known SARS-CoV-2 variants of concern, Delta is the most virulent leading to severe symptoms and increased number of deaths. Our study seeks to examine how the biophysical parameters of the Delta variant correlate to the clinical observations. Receptor binding domain (RBD) is the first point of contact with the human host cells and is the immunodominant form of the spike protein. Delta variant RBD contains two novel mutations L452R and T478K. We examined the effect of single mutations as well as the double mutation on RBD expression in human Expi293 cells, RBD stability using urea and thermal denaturation, and RBD binding to angiotensin converting enzyme 2 (ACE2) receptor and to neutralizing antibodies using isothermal titration calorimetry. Delta variant RBD showed significantly higher expression compared to the wild-type RBD, and the increased expression is due to L452R mutation. Despite their non-conservative nature, none of the mutations significantly affected RBD structure and stability. All mutants showed similar binding affinity to ACE2 and to Class 1 antibodies (CC12.1 and LY-CoV016) as that of the wild-type. Delta double mutant L452R/T478K showed no binding to Class 2 antibodies (P2B-2F6 and LY-CoV555) and a hundred-fold weaker binding to a Class 3 antibody (REGN10987), and the decreased antibody binding is determined by the L452R mutation. These results indicate that the immune escape from neutralizing antibodies, rather than receptor binding, is the main biophysical parameter determining the fitness landscape of the Delta variant RBD and is determined by the L452R mutation.
Generalization in Sensorimotor Networks Configured with Natural Language Instructions
Authors: Riveland Reidar , Pouget Alexandre 
Published: February 2022

AbstractOne of humans’ most fundamental cognitive feats is the ability to interpret linguistic instructions in order to perform novel tasks without any explicit experience with the task. Yet, the computations that the brain might use to accomplish such a feat remains poorly understood. Here we use the latest advances in Natural Language Processing to create a neural model of generalization based on linguistic instructions. Models are trained on a set of commonly studied psychophysical tasks, and receive instructions embedded by a pre-trained language model. Our best models can perform a previously unseen task with a performance of 83% correct on average based solely on linguistic instructions (i.e. 0-shot learning). We found that language scaffolds sensorimotor representations such that activity for interrelated tasks share a common geometry with the semantic representations of instructions, allowing language to cue the proper composition of practiced skills in unseen settings. Finally, we show how this model can generate a linguistic description of a novel task it has identified using only motor feedback, which can subsequently guide a partner model to perform the task. Our models offer several experimentally testable predictions outlining how linguistic information must be represented in order to facilitate flexible and general cognition in the human brain.
Neuromuscular embodiment of feedback control elements in Drosophila flight
Authors: Whitehead Samuel C. , Leone Sofia , Lindsay Theodore , Meiselman Matthew R. , Cowan Noah , Dickinson Michael , Yapici Nilay , Stern David L. , Shirangi Troy , Cohen Itai 
Published: February 2022

ABSTRACTWhile insects like Drosophila are flying, aerodynamic instabilities require that they make millisecond-timescale adjustments to their wing motion to stay aloft and on course. These stabilization reflexes can be modeled as a proportional-integral (PI) controller; however, it is unclear how such control might be instantiated in insects at the level of muscles and neurons. Here, we show that the b1 and b2 motor units—prominent components of the fly’s steering muscles system—modulate specific elements of the PI controller: the angular displacement (integral, I) and angular velocity (proportional, P), respectively. Moreover, these effects are observed only during the stabilization of pitch. Our results provide evidence for an organizational principle in which each muscle contributes to a specific functional role in flight control, a finding that highlights the power of using top-down behavioral modeling to guide bottom-up cellular manipulation studies.
Genetic Algorithm with Rank Selection optimises robust parameter estimation for systems biology models
Authors: Douilhet Gemma , Niranjan Mahesan , Vallejo Andres , Clayton Kalum , Davies James , Sirvent Sofia , Pople Jenny , Ardern-Jones Michael R , Polak Marta E 
Published: February 2022

ABSTRACTThe ability to reliably predict and infer cellular responses to environmental exposures would offer a major advance in the investigation of immune regulation in health and disease. One possible approach is the use of in silico modelling. Design of such a mathematical kinetic model would be based on existing knowledge of a biological system and utilise a partial data set to parameterise. However, the process of parameter estimation, key for the accuracy of the model, is difficult to conduct by hand, and thus a computational alternative is necessary. We report the utility of Genetic Algorithm with Rank Selection (GARS) as a parameter estimation tool on multiple biological models, including heat shock, signal transduction via ERK, circadian rhythm and NFκB systems, where it showed strong accuracy and superiority to the Extended Kalman Filter method, Algebraic Difference Equations, and MATLAB fminsearch approaches. GARS parameter estimation is a valuable tool for biological data because it reliably infers system behaviour from partial data sets, allowing for the prediction of cellular responses to environmental exposures.