bluuebunny/crossref_metadata_2025_split huggingface dataset:
Part I: Crossfit-Related Injury Characteristics Presenting to Sports Medicine Clinic
Authors: Stracciolini Andrea , Quinn Bridget , Zwicker Rebecca L. , Howell David R. , Sugimoto Dai 
Published: February 2020

Objective:
To investigate CrossFit-related injuries presenting to a pediatric sports medicine clinic.

Design:
Retrospective review of pediatric CrossFit-related injuries from between January 1, 2003, and June 31, 2016.

Setting:
Pediatric sports medicine clinic at a tertiary-level academic medical center.

Patients:
Patients with injury related to CrossFit participation.

Independent Variables:
Sex, age, injury site, diagnosis, diagnostic imaging, and treatment.

Main Outcome Measures:
Annual CrossFit-related injury proportion (%) over time.

Results:
One hundred fifteen medical identified (N = 55 female; mean age, 25.2 ± 10.4 years). Proportion of CrossFit-related injuries presenting to clinic relative to overall clinic volume consistently increased over time (Pearson r = 0.825; P = 0.022). Injury location included head (0.08%), trunk/spine (25.2%), upper extremity (27.0%), and lower extremity (47.0%). Common injured joints included knee (27%), spine (24.3%), and shoulder (16.5%). Nearly half of patients had a single diagnostic imaging (49.6%; 57 of 115). Most common diagnostics included magnetic resonance imaging (60.0%; 69 of 115), plain radiographs (51.3%; 59 of 115), ultrasound (10.4%; 12 of 115), and computerized tomographic scan (9.6%; 11 of 115). Most commonly prescribed treatments included physical/occupational therapy (38.3%; 44 of 115), activity modification (19.1%; 22 of 115), crutches/brace/splinting/compression sleeve (13.0%; 15 of 115), and non–steroidal anti-inflammatory medications (10.4%; 12 of 115).

Conclusions:
CrossFit-related injury proportion presenting to a pediatric sports medicine clinic increased over time. A notable proportion of injuries occurred to the trunk and spine. Advanced imaging was obtained in approximately half of these youth athletes. Further research in youth CrossFit athletes is required surrounding mechanism of injury to prevent future injury in this mode of training for youth athletes.
Nutrition and health of edible insects
Authors: van Huis Arnold 
Published: February 2020

Purpose of review
Elucidate the effect of insects as feed and food on nutrition and health of humans and animals.

Recent findings
A new sector is developing of insects as food and feed. The academic interest is growing exponentially. In addition to their high nutritional values, there are also health benefits. These relate to prebiotic effects of insect products, such as chitin on humans and animals. Insects have a large reservoir of antimicrobial peptides. Some insect species have shown to have antioxidant properties.

Summary
The increasing demand for meat and the limited amount of land availability prompt the search for alternative protein sources. Insects require less land and have a lower environmental impact than meat products. In addition to having a high nutritional value, they have also health benefits. Several edible insect species can be grown on organic side streams, in this way contributing to a circular economy. The number of scientific articles increased exponentially, and more than 290 start-ups are now engaging in its production and marketing. Food safety issues are not a major issue but need to be carefully checked when organic waste streams are used. The main strategies related to consumer issues are disguising the insects in familiar products and making them tasty.
The establishment and application of sialoscintigraphic reference values from patients with obstructive sialadenitis
Authors: Chen Yen-Chun , Han Deng-Yu , Chang Chi-Ching , Su Chin-Hui , Hung Shih-Han , Hsu Chung-Huei 
Published: February 2020

Aim
To evaluate feasibility of establishing a clinically applicable reference value through those unaffected salivary gland on sialoscintigraphic data obtained from patients presented with obstructive sialadenitis affected a single gland.

Materials and methods
Ninety-one patients suffered from single salivary gland swelling, pain/tenderness and received sialoscintigraphic examinations were retrospectively enrolled. The quantitative data parameters, including the uptake ratio, maximal accumulation, maximal excretion, time to maximal (T
max) and time to minimal (T
min) activity of the affected and unaffected glands, were calculated for analysis. Data were also obtained and recorded for comparison from 50 patients who fulfill the American–European criteria for the diagnosis of Sjogren’s syndrome.

Results
The maximal excretion appeared to be the best indicator for distinguishing affected and unaffected glands of obstructive diseases, for parotid and submandibular glands (P = 0.0002 and P < 0.0001, respectively). The area under the receiver-operating characteristic curve (AUC) is 0.82 for submandibular glands. In patients with Sjogren’s syndrome, the maximal excretion and T
min were the best parameters, for parotid (P = 0.002 and P < 0.0001, respectively) and submandibular glands (P < 0.0001 and P = 0.002, respectively). Uptake ratio was a good parameter for submandibular gland (P < 0.0001). The AUC of maximal excretion and uptake ratio for submandibular glands is 0.81 and 0.77, respectively.

Conclusion
Quantitative data obtained from the unaffected glands of patients with obstructive sialadenitis could be used as reference values for the functional evaluation of salivary gland disorders with maximal excretion as one of the reliable parameters.
The rise and fall of the model for end-stage liver disease score and the need for an optimized machine learning approach for liver allocation
Authors: Vagefi Parsia A. , Bertsimas Dimitris , Hirose Ryutaro , Trichakis Nikolaos 
Published: February 2020

Purpose of review
The Model for End-Stage Liver Disease (MELD) has been used to rank liver transplant candidates since 2002, and at the time bringing much needed objectivity to the liver allocation process. However, and despite numerous revisions to the MELD score, current liver allocation still does not allow for equitable access to all waitlisted liver candidates.

Recent findings
An optimized prediction of mortality (OPOM) was developed utilizing novel machine-learning optimal classification tree models trained to predict a liver candidate's 3-month waitlist mortality or removal. When compared to MELD and MELD-Na, OPOM more accurately and objectively prioritized candidates for liver transplantation based on disease severity. In simulation analysis, OPOM allowed for more equitable allocation of livers with a resultant significant number of additional lives saved every year when compared with MELD-based allocation.

Summary
Machine learning technology holds the potential to help guide transplant clinical practice, and thus potentially guide national organ allocation policy.
Beta amyloid levels in cerebrospinal fluid of HIV-infected people vary by exposure to antiretroviral therapy
Authors: Fields Jerel Adam , Swinton Mary K. , Soontornniyomkij Benchawanna , Carson Aliyah , Achim Cristian L. 
Published: February 2020

Background:
HIV-associated neurocognitive disorders (HAND) persist despite the widespread implementation of combined antiretroviral therapy (ART). As people with HIV (PWH) age on ART regimens, the risk of age-related comorbidities, such as Alzheimer's disease may increase. However, questions remain as to whether HIV or ART will alter such risks. Beta amyloid (Aβ) and phosphorylated-tau (p-tau) proteins are associated with Alzheimer's disease and their levels are altered in the CSF of Alzheimer's disease cases.

Methods:
To better understand how these Alzheimer's disease-related markers are affected by HIV infection and ART, postmortem CSF collected from 70 well characterized HIV+ decedents was analyzed for Aβ1–42, Aβ1–40, and p-tau levels.

Results:
Aβ1–42 and Aβ1–40 CSF levels were higher in cases that were exposed to ART. Aβ1–42 and Aβ1–40 CSF levels were also higher in cases on protease inhibitors compared with those with no exposure to protease inhibitors. Aβ1–42 and Aβ1–40 levels in CSF were lowest in HIV+ cases with HIV-associated dementia (HAD) and levels were highest in those diagnosed with asymptomatic neurocognitive impairment (ANI) and minor neurocognitive disorder (MND). Aβ1–42 and Aβ1–40 were inversely related with p-tau levels in all cases, as previously reported.

Conclusion:
These data suggest that ART exposure is associated with increased levels of Aβ1–42 and Aβ1–40 in the CSF. Also, HAD, but not ANI/MND diagnosis is associated with decreased levels of Aβ1–42 and Aβ1–40 in CSF, potentially suggesting impaired clearance. These data suggest that HIV infection and ART may impact pathogenic mechanisms involving Aβ1–42 and Aβ1–40, but not p-tau.
Assessing the validity of and factors that influence accurate self-reporting of HIV status after testing: a population-based study
Authors: Chasimpha Steady J.D. , Mclean Estelle M. , Dube Albert , McCormack Valerie , dos-Santos-Silva Isabel , Glynn Judith R. 
Published: February 2020

Objectives:
To assess the validity of self-reported HIV status, and investigate factors that influence accurate reporting of HIV-positive status, in a population tested and informed of their HIV test result.

Design:
Prospective cohort study.

Methods:
We compared self-reported HIV status with biomarker-confirmed HIV test status among participants of Karonga Health and Demographic Surveillance Site in rural northern Malawi. We linked information on HIV test results to subsequent self-reported HIV status, and calculated sensitivity, specificity, positive predictive value and negative predictive value for self-reported HIV status (considered as a diagnostic test). We used Poisson regression with robust variance estimators to examine predictors of accurate self-reporting of HIV-positive status.

Results:
Among 17 445 adults who tested for HIV, were recorded as having received their HIV test results, and had a subsequent self-reported HIV status between 2007 and 2018: positive predictive value of self-reported HIV status was 98.0% (95% confidence interval: 97.3–98.7); negative predictive value was 98.3 (98.1–98.5); sensitivity was 86.1% (84.5–87.7); and specificity was 99.8% (99.7–99.9). Among true HIV-positive people, those who were younger, interviewed in community settings, and had tested for HIV longer ago were more likely to misreport their HIV-positive status.

Conclusion:
In this setting, self-report provides good estimates of test-detected HIV prevalence, suggesting that it can be used when HIV test results are not available. Despite frequent HIV testing, younger people and those interviewed in community settings were less likely to accurately report their HIV-positive status. More research on barriers to self-reporting of HIV status is needed in these subgroups.
The cognitive costs, contraindications and complications of epilepsy surgery in adults
Authors: Baxendale Sallie 
Published: February 2020

Purpose of reviewAccess to epilepsy surgery is rapidly growing throughout the world. While it is an established and effective treatment for seizures, epilepsy surgery has the potential to exacerbate cognitive comorbidities of the condition.Recent findingsNot all surgical patients experience a postoperative decline in cognitive function. Postoperative cognitive function depends upon the functional integrity of the tissue to be removed and the functional reserve of the structures that remainin situ. While developments in surgical technique can reduce the cognitive morbidity of epilepsy surgery, the same procedure may result in different cognitive outcomes for different candidates, depending on their preoperative characteristics and postoperative trajectories. Multivariate models can be used to identify those most at risk of cognitive decline. There remains a significant lack of research into clinical interventions aimed at reducing the impact of surgically induced cognitive deficits on the lives of the patients who experience them.SummaryAccurate identification of the cognitive risks associated with surgery, based on an individual's personal risk profile rather than the generic risks associated with the procedure, is now recognized as a mandatory part of the preoperative evaluation and is one of the pillars of informed consent for the procedure.
Global multi-environment resistance QTL for foliar late blight resistance in tetraploid potato with tropical adaptation
Authors: Lindqvist-Kreuze Hannele , de Boeck Bert , Unger Paula , Gemenet Dorcus , Li Xianping , Pan Zhechao , Sui Qinjun , Qin Junhong , Woldegjorgis Gebremedhin , Negash Kassaye , Seid Ibrahim , Hirut Betaw , Gastelo Manuel , De Vega Jose , Bonierbale Merideth 
Published: February 2020

AbstractThe identification of environmentally stable and globally predictable resistance to potato late blight is challenged by the crop’s clonal and polyploid nature and the pathogen’s rapid evolution. Genome-wide analysis (GWA) of multi-environment trials can add precision to breeding for complex traits. A diversity panel of tetraploid potato germplasm bread for multiple resistance and quality traits was genotyped by genotyping by sequencing (GBS) and phenotyped for late blight resistance in a trait observation network spanning three continents addressed by the International Potato Center’s (CIP’s) breeding program. The aims of this study were to (i) identify QTL underlying resistance in and across environments and (ii) develop prediction models to support the global deployment and use of promising resistance sources in local breeding and variety development programs. Health-indexedin vitroplants of 380 clones and varieties were distributed from CIP headquarters in Peru to China and Ethiopia and tuber seed was produced centrally in each country. Phenotypes were recorded as rAUDPC following field exposure to local isolates ofPhytophthora infestans, Stringent filtering for individual read depth >60 resulted in 3,239 tetraploid SNPs. Meanwhile, 55,748 diploid SNPs were identified using diploidized data and individual read depth>17. The kinship matrix was utilized to obtain BLUP and identify best performing germplasm in each and all environments. Genotypes with high levels of resistance in all environments were identified from the B3, LBHT and B3-LTVR populations. GWA identified stable QTL for late blight resistance in chromosome 9 and environment specific QTL in chromosomes 3, 5, 6 and 10.
phyr: An R package for phylogenetic species-distribution modelling in ecological communities
Authors: Li Daijiang , Dinnage Russell , Nell Lucas , Helmus Matthew R. , Ives Anthony 
Published: February 2020

SummaryModel-based approaches are increasingly popular in ecological studies. A good example of this trend is the use of joint species distribution models to ask questions about ecological communities. However, most current applications of model-based methods do not include phylogenies despite the well-known importance of phylogenetic relationships in shaping species distributions and community composition. In part, this is due to lack of accessible tools allowing ecologists to fit phylogenetic species distribution models easily.To fill this gap, the R packagephyr(pronounced fire) implements a suite of metrics, comparative methods and mixed models that use phylogenies to understand and predict community composition and other ecological and evolutionary phenomena. Thephyrworkhorse functions are implemented in C++ making all calculations and model estimations fast.phyrcan fit a variety of models such as phylogenetic joint-species distribution models, spatiotemporal-phylogenetic autocorrelation models, and phylogenetic trait-based bipartite network models.phyralso estimates phylogenetically independent trait correlations with measurement error to test for adaptive syndromes and performs fast calculations of common alpha and beta phylogenetic diversity metrics. Allphyrmethods are united under Brownian motion or Ornstein-Uhlenbeck models of evolution and phylogenetic terms are modelled as phylogenetic covariance matrices.The functions and model formula syntax we propose inphyrserves as a simple and unified framework that ignites the use of phylogenies to address a variety of ecological questions.
ErrorX: automated error correction for immune repertoire sequencing datasets
Authors: Sevy Alexander M 
Published: February 2020

AbstractMotivationRecent advances in DNA sequencing technology have allowed deep profiling of B- and T-cell receptor sequences on an unprecedented scale. However, sequencing errors pose a significant challenge in expanding the scope of these experiments. Errors can arise both by PCR during library preparation and by miscalled bases on the sequencing instrument itself. These errors compromise the validity of biological conclusions drawn from the data.ResultsTo address these concerns I have developed ErrorX, a software for automated error correction of B- and T-cell receptor NGS datasets. ErrorX uses deep learning to automatically identify bases that have a high probability of being erroneous. In benchmark studies, ErrorX reduced the overall error rate of public datasets by up to 36% with a false positive rate of 0.05% or less. Since ErrorX is a pure bioinformatics approach, it can be directly applied to any existing antibody or T-cell receptor sequencing datasets to infer sites of probable error without any changes in library preparation.AvailabilityErrorX is free for non-commercial use, with both a command-line interface and GUI available for Mac, Linux, and Windows operating systems, and full documentation available. Pre-compiled binaries are available athttps://endeavorbio.com/downloads/.
Basal forebrain-derived acetylcholine encodes valence-free reinforcement prediction error
Authors: Sturgill JF , Hegedus P , Li SJ , Chevy Q , Siebels A , Jing M , Li Y , Hangya B , Kepecs A 
Published: February 2020

AbstractAcetylcholine (Ach) is released by the cholinergic basal forebrain (CBF) throughout the cortical mantle and is implicated in behavioral functions ranging from arousal to attention to learning. Yet what signal ACh provides to cortex remains unresolved, hindering our understanding of its functional roles. Here we demonstrate that the CBF signals unsigned reinforcement prediction error, in contrast to dopamine (DA) neurons that encode reward prediction error. We show that both CBF neuronal activity and acetylcholine (ACh) release at cortical targets signal reinforcement delivery, acquire responses to predictive stimuli and show diminished responses to expected outcomes, hallmarks of a prediction error. To compare ACh with DA, we simultaneously monitored the activity of both neuromodulators during a serial reversal learning task. ACh tracked learning as swiftly as DA during acquisition but lagged slightly during extinction, suggesting that these neuromodulators play complementary roles in reinforcement as their patterns of innervation, cellular targets, and signaling mechanisms are themselves complementary. Through retrograde viral tracing we show that the cholinergic and dopaminergic systems engage overlapping upstream circuits, accounting for their coordination during learning. This predictive and valence-free signal explains how ACh can proactively and retroactively improve the processing of behaviorally important stimuli, be they good or bad.
Live cell imaging of single neurotrophin receptor molecules on human neuron in Alzheimer’s disease
Authors: Barabás Klaudia , Kobolák Julianna , Godó Soma , Ernszt Dávid , Kecskés Miklós , Varga Csaba , Kardos József , Jánosi Tibor Z. , Fujiwara Takahiro , Kusumi Akihiro , Téglási Annamária , Dinnyés András , Ábrahám István M. 
Published: February 2020

AbstractThe changes in the receptor dynamics such as the surface movement of the receptor molecules on the plasma membrane are essential to receptor function. However, whether the receptor dynamics are affected by disease conditions is unknown. Neurotrophin receptors such as TrkA and p75NTRplay a critical role in neuronal survival and their functions are highly affected in Alzheimer’s disease (AD). Using live-cell single-molecule imaging of neurotrophin receptors we examined the surface trafficking of TrKA and p75NTRmolecules on human induced pluripotent stem cells (hiPSCs) derived live neurons from presenilin 1 (PSEN1) mutant AD patients and healthy subjects. Here we report that surface trafficking of p75NTRmolecules on neurites is faster than that of TrkA molecules in healthy controls. The surface dynamics of TrkA molecules were elevated in AD patients compared to healthy individuals. In contrast, the surface movement of p75NTRwas significantly smaller in AD patients compared to healthy individuals. Interestingly, amyloid beta1-42(Aβ1-42) administration increased the surface trafficking of both TrkA and p75NTRin healthy hiPSCs neurons. These findings provides the first evidence that the surface diffusion of TrkA and p75NTRmolecules are altered in patients suffering from AD. Our data also suggest that Aβ1-42may responsible for the alteration of the surface movements of TrkA but not for p75NTR.One Sentence SummaryThe surface movements of neurotrophin receptors such as TrkA and p75NTRare altered in neurons derived from patients suffering from familial Alzheimer’s disease.
Systematic review protocol: Quantitative susceptibility mapping of brain iron accumulation in neurodegenerative diseases
Authors: Ravanfar Parsa , Loi Samantha , Van Rheenen Tamsyn , Bush Ashley , Desmond Patricia , Cropley Vanessa , Moffat Bradford , Velakoulis Dennis , Pantelis Christos 
Published: February 2020

AbstractIron has been found to play an important role in neurodegeneration. Quantitative susceptibility mapping (QSM) is a relatively new – and the most accurate - MRI technique available for assessment of iron deposition in the brain. There is a rapidly growing number of studies using QSM to investigate brain iron distribution in neurodegenerative diseases including but not limited to Alzheimer’s disease, Parkinson’s disease, Amyotrophic lateral sclerosis, Huntington disease and Wilson’s disease. These studies have shown increased iron deposition in the brain regions that are associated with the pathology of the disease. Additionally, QSM is found to be accurate in differential diagnosis of neurodegenerative diseases where clinical presentations are indistinguishable. Structural changes evidenced by QSM are reported to precede the onset of clinical manifestation of neurodegenerative diseases suggesting its benefit in early diagnosis. To our knowledge, no systematic review of QSM findings in neurodegenerative diseases has been published before. A systematic synthesis and conclusion of the existing evidence can improve our understanding of the pathophysiology of neurodegeneration, describe the clinical and research utility of QSM, and point out the direction for future studies in neuropsychiatric disorders.This document is a systematic review protocol developed in accordance with Preferred reporting items for systematic review and meta-analysis protocols (PRISMA-P) guideline. This protocol is prepared as a guide for conducting a systematic review of studies investigating brain iron and microstructural changes in neurodegenerative diseases using quantitative susceptibility mapping (QSM). This protocol has also been submitted to Prospective Register of Systematic Reviews (PROSPERO) for registration. By publishing this protocol, we aim to enhance clarity and transparency of our systematic review and minimise the risk of bias in the process of its development.