bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prevalence of Rheumatic Diseases and Quality of Life in the Saraguro Indigenous People, Ecuador
Authors: Guevara Sergio V. , Feicán Elsa A. , Peláez Ingris , Valdiviezo Wilson A. , Montaleza Maria A. , Molina Gladis M. , Ortega Nelly R. , Delgado Jorge A. , Chimbo Lidia E. , Hernandez María V. , Sanin Luz H. , Cervera Ricard 
Published: August 2019

Rheumatic diseases are more prevalent and aggressive in indigenous population groups, providing medical attention for which poses a challenge for the rheumatologist.

Objective
To estimate the prevalence of musculoskeletal (MSK) disorders and rheumatic diseases in the Saraguro indigenous people in Ecuador, as well as to identify the main factors associated with the health status of this population.

Methods
This observational, cross-sectional study focused on the community was conducted using the COPCORD (Community-Oriented Program for Control of Rheumatic Diseases) methodology. The required data were obtained using the following instruments: (1) a screening for MSK disorders and rheumatic diseases; (2) a sociodemographic questionnaire; (3) a functional capacity Health Assessment Questionnaire Disability Index questionnaire; and (4) the quality of life EQ-5D-3L (EuroQoL) questionnaire. The rheumatologists working with the indigenous community were responsible for examining and treating study participants suffering from MSK disorders.

Results
The study sample comprised 2687 individuals, with mean age of 44 (SD, 19.9) years, 1690 (62.9%) of whom were women; Kichwa speakers comprised 32.4% (872), and 1244 (46.3%) reported MSK pain. The most prevalent conditions were as follows: low back pain (9.3%), hand osteoarthritis (OA, 7.2%), knee OA (6.5%), rheumatic regional pain syndrome (5.8%), fibromyalgia (1.8%), and rheumatoid arthritis (1.3%). Lower education level, unemployment, cooking with firewood, and rheumatic diseases were associated with a lower quality of life.

Conclusions
Musculoskeletal disorders, rheumatic diseases, and rheumatoid arthritis were found to be highly prevalent in the studied population. Rheumatoid arthritis and hand OA had the most significant impact on the quality of life.
One-Piece Fronto-orbital Distraction With Midline Splitting But Without Bandeau for Metopic Craniosynostosis
Authors: Fawzy Hossam Hassan , Choi Jong-Woo , Ra Young-Shin 
Published: August 2019

Background
Distraction osteogenesis has gained popularity in the treatment of different types of craniosynostosis. We aimed to present the technique of 1-piece fronto-orbital distraction with midline splitting osteotomy but without bandeau for the treatment of metopic craniosynostosis, and the protocol of outcome evaluation using craniometric, volumetric, and morphologic parameters based on 3-dimensional computer simulation.

Methods
This retrospective study included 9 patients with isolated metopic craniosynostosis who underwent surgical correction with distraction osteogenesis between December 2015 and February 2018. The osteotomy was designed in the form of 1-piece fronto-orbital distraction without separation of the orbital bandeau accompanied by midline splitting osteotomy. This was followed by the application of 2 pairs of cranial distractors to produce anterolateral expansion. The 3-dimensional files from preoperative and postdistraction computed tomographic data were used for the measurement of craniometric, volumetric, and morphologic parameters.

Results
The postdistraction craniometric measurement revealed a 12.52% increase in the interfrontal angle. Moreover, there were increases in the bifrontal diameter, diagonal diameters, and interorbital distance. Volumetric measurements revealed an increase in the total cranial volume by 228.1 ± 110.19 cm3. The anterior compartmental volume increased by 33.24%. Morphologic evaluation in the form of curvature analysis showed shrinkage of the surface area of abnormal curvature from 29.5 ± 6.71 cm2 preoperatively to 3.85 ± 3.66 cm2 after distraction.

Conclusions
The technique of 1-piece fronto-orbital distraction with midline splitting osteotomy but without bandeau is an effective surgical option for the treatment of metopic craniosynostosis. The postdistraction outcomes demonstrated the correction of various forms of dysmorphology in metopic craniosynostosis.
Scope of Hand Surgery Using Surgeon Administered Local/Regional Anaesthesia
Authors: Sim Wei Ping , Ng Hannah Jia Hui , Tan Shoun , Bajaj Sanjay Laxmandasji , Rajaratnam Vaikunthan 
Published: August 2019

Introduction
Hand and wrist surgeries are often carried out under local/regional anesthesia. We describe our experience using Surgeon Administered Local/Regional Anaesthesia (SALoRA) without sedation to deliver acute and elective hand surgery anesthesia in a tertiary public hospital in Singapore. This is in comparison to wide awake local anesthesia no tourniquet, which has been increasing in popularity.

Methods
Retrospective analysis was conducted on all surgeries performed under SALoRA between January 1, 2013, to December 31, 2016, at our institution. Surgeries on areas other than the hand, wrist, forearm, and elbow were excluded. The records were reviewed to analyze the demographics of the patients, profile of cases performed, and their outcomes.

Results
Of a total of 3016 cases performed, 1994 patients (1275 men; age, 45.78 ± 16 years) fulfilled the inclusion criteria and were available for analysis for the study period. The case distribution was similar to most other published data on day hand surgery cases. Tourniquet was used in 1357 (68%) of cases with an average operation time of 26 ± 19 minutes. Mean tourniquet use was 24 ± 15 minutes. Detailed analysis will be presented.

Conclusion
This study shows the versatility of SALoRA in delivering hand surgery in a cost-effective manner. A wide spectrum of surgeries in the hand, wrist, forearm, and elbow can be performed using SALoRA safely. This has increased productivity, efficiency, and use of resources. SALoRA has the advantage of a guaranteed and reliable bloodless field, quick turnaround time without the need of extra personnel and resources needed for patient monitoring to abide by Joint Commission International requirements and the potential risk of systemic adrenaline effects.
Persistent Neuroinflammation and Brain-Specific Immune Priming in a Novel Survival Model of Murine Pneumosepsis
Authors: Denstaedt Scott J. , Spencer-Segal Joanna L. , Newstead Michael , Laborc Klaudia , Zeng Xianying , Standiford Theodore J. , Singer Benjamin H. 
Published: August 2019

ABSTRACT
Pneumonia is the leading cause of sepsis and septic shock. Patients who survive pneumonia are vulnerable to long-term complications including increased risk of neurocognitive dysfunction. This study investigated the immune response and long-term complications of a non-surgical mouse model of Klebsiella pneumoniae pneumosepsis with antibiotic treatment. Pneumosepsis resulted in acutely enhanced expression of inflammatory cytokines, chemokines, and damage-associated molecular patterns in the brain and spleen. Despite resolution of infection, murine pneumosepsis survivors demonstrated a deficit in exploratory locomotor behavior at 2 weeks. This was associated with brain-specific persistent inflammatory gene expression and infiltrating myeloid cells in the brain. The brain inflammatory response was also primed in response to secondary challenge with lipopolysaccharide. The findings of this study demonstrate behavioral and inflammatory outcomes that parallel observations in other models of sepsis, but that have not previously been described in antibiotic-treated pneumonia models, highlighting a common pathway to the development of chronic brain dysfunction in sepsis survival.
Assessment of Bias in Estimates of Sexual Network Degree using Prospective Cohort Data
Authors: Uong Stephen , Rosenberg Eli S. , Goodreau Steven M. , Luisi Nicole , Sullivan Patrick , Jenness Samuel M. 
Published: August 2019

ABSTRACTBackgroundSexual network degree, a count of ongoing partnerships, plays a critical role in the transmission dynamics of human immunodeficiency virus (HIV) and other sexually transmitted infections (STI). Researchers often quantify degree using self-reported cross-sectional data on the day of survey, which may result in bias because of uncertainty about future sexual activity.MethodsWe evaluated the bias of a cross-sectional degree measure with a prospective cohort study of men who have sex with men (MSM). At baseline, we asked men about whether recent sexual partnerships were ongoing. We confirmed the true, ongoing status of those partnerships at baseline at follow-up. With logistic regression, we estimated the partnership-level predictors of baseline measure accuracy. With Poisson regression, we estimated the longitudinally confirmed degree as a function of baseline predicted degree.ResultsAcross partnership types, the baseline ongoing status measure was 70% accurate, with higher negative predictive value (91%) than positive predictive value (39%). Partnership exclusivity and racial pairing were associated with higher accuracy. Baseline degree generally overestimated confirmed degree. Bias, or number of ongoing partners different than predicted at baseline, was -0.28 overall, ranging from -1.91 to -0.41 for MSM with any ongoing partnerships at baseline. Comparing MSM of the same baseline degree, the level of bias was stronger for black compared to white MSM, and for younger compared to older MSM.ConclusionsResearch studies may overestimate degree when it is quantified cross-sectionally. Adjustment and structured sensitivity analyses may account for bias in studies of HIV or STI prevention interventions.
Peripheral Biomarkers of Tobacco-Use Disorder: A Systematic Review
Authors: Newton Dwight F. 
Published: August 2019

AbstractIntroductionTobacco use disorder (TUD) is a major worldwide healthcare burden resulting in 7 million deaths annually. TUD has few approved cessation aids, all of which are associated a high rate of relapse within one year. Biomarkers of TUD severity, treatment response, and risk of relapse have high potential clinical utility to identify ideal responders and guide additional treatment resources.MethodsA MEDLINE search was performed using the terms biomarkers, dihydroxyacetone phosphate, bilirubin, inositol, cotinine, adrenocorticotropic hormone, cortisol, pituitary-adrenal system, homovanillic acid, dopamine, pro-opiomelanocortin, lipids, lipid metabolism all cross-referenced with tobacco-use disorder.ResultsThe search yielded 424 results, of which 57 met inclusion criteria. The most commonly studied biomarkers were those related to nicotine metabolism, the hypothalamic-pituitary-adrenal (HPA) axis, and cardiovascular (CVD) risk. Nicotine metabolism was most associated with severity of dependence and treatment response, where as HPA axis and CVD markers showed less robust associations with dependence and relapse risk.ConclusionsNicotine-metabolite ratio, cortisol, and atherogenicity markers appear to be the most promising lead biomarkers for further investigation, though the body of literature is still preliminary. Longitudinal, repeated-measures studies are required to determine the directionality of the observed associations and determine true predictive power of these biomarkers. Future studies should also endeavour to study populations with comorbid psychiatric disorders to determine differences in utility of certain biomarkers.
Genetically encoded cell-death indicators (GEDI) to detect an early irreversible commitment to neurodegeneration
Authors: Linsley Jeremy W. , Shah Kevan , Castello Nicholas , Chan Michelle , Haddad Dominic , Mancini Jay , Oza Viral , Wang Shijie , Javaherian Ashkan , Kokel David , Finkbeiner Steven 
Published: August 2019

AbstractCell death is a critical process that occurs normally in health and disease. However, its study is limited due to available technologies that only detect very late stages in the process or specific death mechanisms. Here, we report the development of a new fluorescent biosensor called genetically encoded death indicator (GEDI). GEDI specifically detects an intracellular Ca2+ level that cells achieve early in the cell death process and marks a stage at which cells are irreversibly committed to die. The time-resolved nature of GEDI delineates a binary demarcation of cell life and death in real time, reformulating the definition of cell death. We demonstrate that GEDI acutely and accurately reports death of rodent and human neurons in vitro, and show GEDI enables a novel automated imaging platform for single cell detection of neuronal death in vivo in zebrafish larvae. With a quantitative pseudo-ratiometric signal, GEDI facilitates high-throughput analysis of cell death in time lapse imaging analysis, providing the necessary resolution and scale to identify early factors leading to cell death in studies of neurodegeneration.
SHIFT: speedy histological-to-immunofluorescent translation of whole slide images enabled by deep learning
Authors: Burlingame Erik A. , McDonnell Mary , Schau Geoffrey F. , Thibault Guillaume , Lanciault Christian , Morgan Terry , Johnson Brett E. , Corless Christopher , Gray Joe W. , Chang Young Hwan 
Published: August 2019

ABSTRACTSpatially-resolved molecular profiling by immunostaining tissue sections is a key feature in cancer diagnosis, subtyping, and treatment, where it complements routine histopathological evaluation by clarifying tumor phenotypes. In this work, we present a deep learning-based method called speedy histological-to-immunofluorescent translation (SHIFT) which takes histologic images of hematoxylin and eosin-stained tissue as input, then in near-real time returns inferred virtual immunofluorescence (IF) images that accurately depict the underlying distribution of phenotypes without requiring immunostaining of the tissue being tested. We show that deep learning-extracted feature representations of histological images can guide representative sample selection, which improves SHIFT generalizability. SHIFT could serve as an efficient preliminary, auxiliary, or substitute for IF by delivering multiplexed virtual IF images for a fraction of the cost and in a fraction of the time required by nascent multiplexed imaging technologies.KEY POINTSSpatially-resolved molecular profiling is an essential complement to histopathological evaluation of cancer tissues.Information obtained by immunofluorescence imaging is encoded by features in histological images.SHIFT leverages previously unappreciated features in histological images to facilitate virtual immunofluorescence staining.Feature representations of images guide sample selection, improving model generalizability.
PalaeoChip Arctic1.0: An optimised eDNA targeted enrichment approach to reconstructing past environments
Authors: Murchie Tyler J. , Kuch Melanie , Duggan Ana , Ledger Marissa L. , Roche Kévin , Klunk Jennifer , Karpinski Emil , Hackenberger Dirk , Sadoway Tara , MacPhee Ross , Froese Duane , Poinar Hendrik 
Published: August 2019

SummaryAncient environmental DNA has been established as a viable biomolecular proxy for tracking taxonomic presence through time in a local environment, even in the total absence of primary tissues. It is thought that sedimentary ancient DNA (sedaDNA) survives through mineral binding. And while these organo-mineral complexes likely facilitate long-term preservation, they also challenge our ability to release and isolate target molecules. Two limitations in sedaDNA extraction impede many palaeoenvironmental reconstructions: the post-extraction carryover of enzymatic inhibitors, and sedaDNA loss when attempting to reduce inhibitor co-elution. Here, we present an optimised eDNA targeted enrichment approach for reconstructing past environments. Our new extraction protocol with targeted enrichment averages a 14.6-fold increase in on-target plant and animal DNA compared to a commercial soil extraction kit, and a 22.6-fold increase compared to a PCR metabarcoding approach. To illustrate the effectiveness of the PalaeoChip Arctic1.0 protocol, we present results of plant and animal presence from permafrost samples and discuss new potential evidence for the late survival (ca. 9685 BP) of mammoth (Mammuthus sp.) and horse (Equus sp.) in the Klondike Region of Yukon, Canada. This approach translates to a more diverse and sensitive dataset with increased sequencing efficiency of ecologically informative sedaDNA.
Mercator: An R Package for Visualization of Distance Matrices
Authors: Abrams Zachary B. , Coombes Caitlin E. , Li Suli , Coombes Kevin R. 
Published: August 2019

AbstractSummaryUnsupervised data analysis in many scientific disciplines is based on calculating distances between observations and finding ways to visualize those distances. These kinds of unsupervised analyses help researchers uncover patterns in large-scale data sets. However, researchers can select from a vast number of different distance metrics, each designed to highlight different aspects of different data types. There are also numerous visualization methods with their own strengths and weaknesses. To help researchers perform unsupervised analyses, we developed the Mercator R package. Mercator enables users to see important patterns in their data by generating multiple visualizations using different standard algorithms, making it particularly easy to compare and contrast the results arising from different metrics. By allowing users to select the distance metric that best fits their needs, Mercator helps researchers perform unsupervised analyses that use pattern identification through computation and visual inspection.Availability and ImplementationMercator is freely available at the Comprehensive R Archive Network (https://cran.r-project.org/web/packages/Mercator/index.html)ContactKevin.Coombes@osumc.eduSupplementary informationSupplementary data are available at Bioinformatics online.
Flies exploit predictable perspectives and backgrounds to enhance iridescent signal salience and mating success
Authors: White Thomas E. , Vogel-Ghibely Nina , Butterworth Nathan J. 
Published: August 2019

AbstractCommunication requires both the encoding of information and its effective transmission, but little is known about display traits that primarily serve to enhance efficacy. Here we examined the visual courtships of Lispe cana, a cursorial fly that lives and mates in heterogeneous foreshores, and tested the prediction that males should seek to enhance signal salience and consequent fitness through the flexible choice of display locations. We show that courting males access the field of view of females by straddling them and holding their wings closed, before moving ahead to present their structurally coloured faces in ritualised dances. Males preferentially present these UV-white signals against darker backgrounds, and the magnitude of contrast predicts female attention, which in turn predict mating success. Our results demonstrate a striking interplay between the physical and attentional manipulation of receivers and reveal novel routes to the enhancement of signal efficacy in noisy environments.
EPIFANY – A method for efficient high-confidence protein inference
Authors: Pfeuffer Julianus , Sachsenberg Timo , Dijkstra Tjeerd M. H. , Serang Oliver , Reinert Knut , Kohlbacher Oliver 
Published: August 2019

AbstractAccurate protein inference under the presence of shared peptides is still one of the key problems in bottom-up proteomics. Most protein inference tools employing simple heuristic inference strategies are efficient, but exhibit reduced accuracy. More advanced probabilistic methods often exhibit better inference quality but tend to be too slow for large data sets.Here we present a novel protein inference method, EPIFANY, combining a loopy belief propagation algorithm with convolution trees for efficient processing of Bayesian networks. We demonstrate that EPIFANY combines the reliable protein inference of Bayesian methods with significantly shorter runtimes. On the 2016 iPRG protein inference benchmark data EPIFANY is the only tested method which finds all true-positive proteins at a 5% protein FDR without strict pre-filtering on PSM level, yielding an increase in identification performance (+10% in the number of true positives and +35% in partial AUC) compared to previous approaches. Even very large data sets with hundreds of thousands of spectra (which are intractable with other Bayesian and some non-Bayesian tools) can be processed with EPIFANY within minutes. The increased inference quality including shared peptides results in better protein inference results and thus increased robustness of the biological hypotheses generated.EPIFANY is available as open-source software for all major platforms at https://OpenMS.de/epifany.
An ethnobotanical study of the genusElymus
Authors: Frawley Emma S. , Ciotir Claudia , Micke Brooke , Rubin Matthew J. , Miller Allison J. 
Published: August 2019

AbstractGrains of domesticated grasses (Poaceae) have long been a global food source and constitute the bulk of calories in the human diet. Recent efforts to establish more sustainable agricultural systems have focused in part on the development of herbaceous, perennial crops. Perennial plants have extensive root systems that stabilize soil and absorb water and nutrients at greater rates than their annual counterparts; consequently, perennial grasses are important potential candidates for grain domestication. While most contemporary grass domesticates consumed by humans are annual plants, there are over 7,000 perennial grass species that remain largely unexplored for domestication purposes. Documenting ethnobotanical uses of wild perennial grasses could aid in the evaluation of candidate species forde novocrop development. The objectives of this study are 1) to provide an ethnobotanical survey of the grass genusElymus; and 2) to investigate floret size variation in species used by people.Elymusincludes approximately 150 perennial species distributed in temperate and subtropical regions, of which at least 21 taxa have recorded nutritional, medicinal, and/or material uses.Elymusspecies used for food by humans warrant pre-breeding and future analyses to assess potential utility in perennial agricultural systems.