bluuebunny/crossref_metadata_2025_split huggingface dataset:
Stress and a sedentary lifestyle are associated with irritable bowel syndrome in medical students from Peru: a cross-sectional study
Authors: Vasquez-Rios George , Machicado Jorge D. , Ticse Ray , Ruiz Eloy F. , Gamero Maria T. , Pezua Adriana , Marcos Luis A. , Tagle Martin 
Published: August 2019

Background
Previous studies suggest that medical students may have higher rates of irritable bowel syndrome as compared to the general population. We hypothesized lifestyle characteristics may be associated to irritable bowel syndrome.

Methods
A cross-sectional survey was conducted in 2015 among students in their fourth, fifth, sixth and seven years of a medical school in Peru. Volunteer participants responded to questions pertaining to demographics, surveys including the Rome III criteria and the Self-reported Stress questionnaire. Regression models were performed to establish variables independently associated with irritable bowel syndrome.

Results
Out of 452 students, 346 responded the survey (response rate: 76.5%; female rate: 47%; median age: 22 years). The irritable bowel syndrome prevalence in respondents was 9.5% (95% confidence interval: 6.7%–13.1%). On univariate analysis, being a senior medical student (odds ratio: 2.8; 95% confidence interval: 1.3–5.9; P < 0.01), mental illness (odds ratio: 3.3; 95% confidence interval: 1.6–6.8; P = 0.002), psychiatric medication use (odds ratio: 2.8; 95% confidence interval: 1.4–5.9; P = 0.005), sedentary lifestyle (odds ratio: 4.4; 95% confidence interval: 1.8–11; P = 0.001) and stress (odds ratio: 4.4; 95% confidence interval: 2.1–9.3; P < 0.001) were associated to irritable bowel syndrome. On a multivariate analysis, a sedentary lifestyle (odds ratio: 3.2; 95% confidence interval: 1.25–8.20; P = 0.01) and stress (odds ratio: 3.0; 95% confidence interval: 1.35–6.67; P < 0.01) were independently associated with irritable bowel syndrome.

Conclusion
The prevalence of irritable bowel syndrome in medical students from Peru is slightly lower compared to the global prevalence of irritable bowel syndrome. Stress and a sedentary lifestyle were independent risk factors associated with irritable bowel syndrome. Our study suggests that lifestyle modifications and stress coping techniques could have an impact to reduce the rates of irritable bowel syndrome in medical students.
Paediatric traumatic brain injury
Authors: Coulter Ian C. , Forsyth Rob J. 
Published: August 2019

Purpose of review
To provide a summary of recent developments in the field of paediatric traumatic brain injury (TBI).

Recent findings
The epidemiology of paediatric TBI with falling rates of severe TBI, and increasing presentations of apparently minor TBI. There is growing interest in the pathophysiology and outcomes of concussion in children, and detection of ‘significant’ injury, arising from concern about risks of long-term chronic traumatic encephalopathy. The role of decompressive craniectomy in children is still clarifying.

Summary
Paediatric TBI remains a major public health issue.
The health literacy of hospitalized trauma patients: We should be screening for deficiencies
Authors: Weinberg Jordan A. , Shehada Mahmoud Z. , Chapple Kristina M. , Israr Sharjeel , Jones Michael D. , Jacobs Jordan V. , Bogert James N. 
Published: August 2019

BACKGROUND
Although the impact of health literacy (HL) on trauma patient outcomes remains unclear, recent studies have demonstrated that trauma patients with deficient HL have poor understanding of their injuries, are less likely to comply with follow-up, and are relatively less satisfied with physician communication. In this study, we sought to determine if HL deficiency was associated with comprehension of discharge instructions.

METHODS
In this prospective study, hospitalized trauma patients underwent evaluation of HL prior to discharge. Newest Vital Sign (NVS) instrument was used to score HL as deficient, marginal, or proficient. Three days postdischarge, patients were telephonically administered a six-point scored questionnaire regarding comprehension of discharge instructions. A general linear model was used to determine the association between HL and comprehension of discharge instructions.

RESULTS
Sixty-three patients were administered both NVS and discharge instruction questionnaire. Ten (15.9%) patients scored as deficient in HL on the NVS screen, 16 (25.4%) as marginally proficient, and 37 (58.7%) as proficient. The HL proficiency significantly predicted follow-up score with increasing proficiency associated with higher scores on the discharge comprehension assessment (p < 0.001). Adjusted mean scores (± SE) for deficient, marginal, and proficient patients were 2.8 ± 0.5, 3.2 ± 0.4, and 4.7 ± 0.2. Post hoc comparisons demonstrated significant differences between proficient with marginal proficiency (p = 0.002) and deficient proficiency (p = 0.001).

CONCLUSION
Performance on bedside test of HL among trauma inpatients predicted ability to comprehend instructions following hospital discharge. This study supports the value of HL screening prior to discharge. The HL-deficient patients may benefit from a transitional care program to improve comprehension of discharge instructions after leaving the hospital.

LEVEL OF EVIDENCE
Therapeutic/Care Management, level III.
End-tidal carbon dioxide underestimates plasma carbon dioxide during emergent trauma laparotomy leading to hypoventilation and misguided resuscitation: A Western Trauma Association Multicenter Study
Authors: Campion Eric M. , Robinson Caitlin K. , Brant Nicholson , Ferrigno Lisa , McIntyre Robert , Biesterveld Ben , Alam Hasan , Callcut Rachael , Mishra Somya , Platt Blake , Moore Margaret M. , Nahmias Jeffry , Grigorian Areg , Dance Sarah , Britton Linda , Schroeppel Thomas , Rodriquez Jennifer , Shatz David , Becker James , Spalding M. Chance , Wolff Timothy W. , Privette Alicia R. , Eriksson Evert , Sahi Saad Liaqat , Patel Anish , Moore Scott M. , Stiles Anquonette L. , Moore Ernest E. , Cohen Mitchell J. , Sauaia Angela , Burlew Clay Cothren , Urban Shane , Osi Udekwu Pascal , Nguyen Megan , Dibbert Ashley , Conroy Amanda , Ross Erin , Nunez Garcia Brenda , Albertson Spencer , Dunn Julie , Alnachaoukati Omar , Stillman Zachery , Decker Cassandra , Heise Holly , Burton Josh S. 
Published: August 2019

BACKGROUND
End-tidal carbon dioxide (ETCO2) is routinely used during elective surgery to monitor ventilation. The role of ETCO2 monitoring in emergent trauma operations is poorly understood. We hypothesized that ETCO2 values underestimate plasma carbon dioxide (pCO2) values during resuscitation for hemorrhagic shock.

METHODS
Multicenter trial was performed analyzing the correlation between ETCO2 and pCO2 levels.

RESULTS
Two hundred fifty-six patients resulted in 587 matched pairs of ETCO2 and pCO2. Correlation between these two values was very poor with an R
2 of 0.04. 40.2% of patients presented to the operating room acidotic and hypercarbic with a pH less than 7.30 and a pCO2 greater than 45 mm Hg. Correlation was worse in patients that were either acidotic or hypercarbic. Forty-five percent of patients have a difference greater than 10 mm Hg between ETCO2 and pCO2. A pH less than 7.30 was predictive of an ETCO2 to pCO2 difference greater than 10 mm Hg. A difference greater than 10 mm Hg was predictive of mortality independent of confounders.

CONCLUSION
Nearly one half (45%) of patients were found to have an ETCO2 level greater than 10 mm Hg discordant from their PCO2 level. Reliance on the discordant values may have contributed to the 40% of patients in the operating room that were both acidotic and hypercarbic. Early blood gas analysis is warranted, and a lower early goal of ETCO2 should be considered.

LEVEL OF EVIDENCE
Therapeutic, level IV.
A novel protocol to maintain continuous access to thawed plasma at a rural trauma center
Authors: Hannigan Cara , Ologun Gabriel , Trecartin Andrew , Colom Lauren , Bloomdahl Ry , Seyer Amanda , LaRock Lisa , Tubby Barbara , Cagir Burt , Granet Jason , Behm Robert 
Published: August 2019

BACKGROUND
Early administration of plasma improves mortality in massively transfused patients, but the thawing process causes delay. Small rural centers have been reluctant to maintain thawed plasma due to waste concerns. Our 254-bed rural Level II trauma center initiated a protocol allowing continuous access to thawed plasma, and we hypothesized its implementation would not increase waste or cost.

METHODS
Two units of thawed plasma are continuously maintained in the trauma bay blood refrigerator. After 3 days, these units are replaced with freshly thawed plasma and returned to the blood bank for utilization prior to their 5-day expiration date. The blood bank monitors and rotates the plasma. Only trauma surgeons can use the plasma stored in the trauma bay. Wasted units and cost were measured over a 12-month period and compared with the previous 2 years.

RESULTS
The blood bank thawed 1127 units of plasma during the study period assigning 274 to the trauma bay. When compared with previous years, we found a significant increase in waste (p < 0.001) and cost (p = 0.020) after implementing our protocol. It cost approximately US $125/month extra to maintain continuous access to thawed plasma during the study period.

DISCUSSION
A protocol to maintain thawed plasma in the trauma bay at a rural Level II trauma center resulted in a miniscule increase in waste and cost when considering the scope of maintaining a trauma center. We think this cost is also minimal when compared with the value of having immediate access to thawed plasma. Constant availability of thawed plasma can be offered at smaller rural centers without a meaningful impact on cost.

LEVEL OF EVIDENCE
Economic and Value-based Evaluations, Level III.
De novo genome assembly of the meadow brown butterfly, Maniola jurtina
Authors: Singh Kumar Saurabh , Hosken David J. , Wedell Nina , ffrench-Constant Richard , Bass Chris , Baxter Simon , Paszkiewicz Konrad , Sharma Manmohan D 
Published: August 2019

AbstractBackgroundMeadow brown butterflies (Maniola jurtina) on the Isles of Scilly represent an ideal model in which to dissect the links between genotype, phenotype and long-term patterns of selection in the wild - a largely unfulfilled but fundamental aim of modern biology. To meet this aim, a clear description of genotype is required.FindingsHere we present the draft genome sequence of M. jurtina to serve as an initial genetic resource for this species. Seven libraries were constructed using DNA from multiple wild caught females and sequenced using Illumina, PacBio RSII and MinION technology. A novel hybrid assembly approach was employed to generate a final assembly with an N50 of 214 kb (longest scaffold 2.9 Mb). The genome encodes a total of 36,294 genes. 90.3% and 88.7% of core BUSCO (Benchmarking Universal Single-Copy Orthologs) Arthropoda and Insecta gene sets were recovered as complete single-copies from this assembly. Comparisons with 17 other Lepidopteran species placed 86.5% of the assembled genes in orthogroups.ConclusionsOur results provide the first high-quality draft genome and annotation of the butterfly M. jurtina.
Attentional Networks during the Menstrual Cycle
Authors: Cohen Zahira Z. , Gotlieb Neta , Erez Offer , Wiznitzer Arnon , Arbel Oded , Matas Devorah , Koren Lee , Henik Avishai 
Published: August 2019

AbstractThe menstrual cycle is characterized partially by fluctuations of the ovarian hormones estradiol (E2) and progesterone (P4), which are implicated in the regulation of cognition. Research on attention in the different stages of the menstrual cycle is sparse, and the three attentional networks (alerting, orienting and executive) and their interaction were not explored during the menstrual cycle. In the current study, we used the ANT-I (attentional network test – interactions) to examine two groups of women: naturally cycling (NC) – those with a regular menstrual cycle, and oral contraceptives (OC) – those using OC and characterized with low and steady ovarian hormone levels. We tested their performance at two time points that fit, in natural cycles, the early follicular phase and the early luteal phase. We found no differences in performance between NC and OC in low ovarian hormone states (Both phases for the OC group and early follicular phase for the NC group). However, the NC group in the early luteal phase exhibited the same pattern of responses for alerting and no-alerting conditions, resulting in a better conflict resolution (executive) when attention is oriented to the target. Results-driven exploratory regression analysis of E2 and P4 suggested that change in P4 from early follicular to early luteal phases was a mediator for the alerting effect found. In conclusion, the alerting state found with or without alertness manipulation suggests that there is a progesterone mediated activation of the alerting system during the mid-luteal phase.
Structure of the host cell recognition and penetration machinery of a Staphylococcus aureus bacteriophage
Authors: Kizziah James L. , Manning Keith A. , Dearborn Altaira D. , Dokland Terje 
Published: August 2019

ABSTRACTStaphylococcus aureus is a common cause of infections in humans. The emergence of virulent, antibiotic-resistant strains of S. aureus is a significant public health concern. Most virulence and resistance factors in S. aureus are encoded by mobile genetic elements, and transduction by bacteriophages represents the main mechanism for horizontal gene transfer. The baseplate is a specialized structure at the tip of bacteriophage tails that plays key roles in host recognition, cell wall penetration, and DNA ejection. We have used high-resolution cryo-electron microscopy to determine the structure of the S. aureus bacteriophage 80α baseplate at 3.7 Å resolution, allowing atomic models to be built for most of the major tail and baseplate proteins, including two tail fibers, a trimeric receptor binding protein, and part of the tape measure protein. Our structure provides a structural basis for understanding host recognition, cell wall penetration and DNA ejection in viruses infecting Gram-positive bacteria. Comparison to other phages demonstrate the modular design of baseplate proteins, and the adaptations to the host that take place during the evolution of staphylococci and other pathogens.
Effects of pathogenic CNVs on biochemical markers: a study on the UK Biobank
Authors: Bracher-Smith Matthew , Kendall Kimberley M , Rees Elliott , Einon Mark , O’Donovan Michael C , Owen Michael J , Kirov George 
Published: August 2019

ABSTRACTBackgroundPathogenic copy number variants (CNVs) increase risk for medical disorders, even among carriers free from neurodevelopmental disorders. The UK Biobank recruited half a million adults who provided samples for biochemical and haematology tests which have recently been released. We wanted to assess how the presence of pathogenic CNVs affects these biochemical test results.MethodsWe called all CNVs from the Affymetrix microarrays and selected a set of 54 CNVs implicated as pathogenic (including their reciprocal deletions/duplications) and present in five or more persons. We used linear regression analysis to establish their association with 28 biochemical and 23 haematology tests.ResultsWe analysed 421k participants who passed our CNV quality control filters and self-reported as white British or Irish descent. There were 268 associations between CNVs and biomarkers that were significant at a false discovery rate of 0.05. Deletions at 16p11.2 had the highest number of significant associations, but several rare CNVs had higher effect sizes indicating that the lack of significance was likely due to the reduced statistical power for rarer events. The distribution of values can be visualised on our interactive website:http://kirov.psycm.cf.ac.uk/.ConclusionsCarriers of many pathogenic CNVs have changes in biochemical and haematology tests, and many of those are associated with adverse health consequences. These changes did not always correlate with increases in diagnosed medical disorders in this population. Carriers should have regular blood tests in order to identify and treat adverse medical consequences early. Levels of cholesterol and related lipids were unexpectedly lower in carriers of CNVs associated with increased weight gain, most likely due to the use of statins by such people.
Hybridization and diversification are positively correlated across vascular plant families
Authors: Mitchell Nora , Whitney Kenneth D. 
Published: August 2019

ABSTRACTHybridization has experimental and observational ties to evolutionary processes and outcomes such as adaptation, speciation, and radiation. Although it has been hypothesized that hybridization and diversification are correlated, this idea remains largely untested empirically. Here, we use a hybridization database on 195 plant families, life history information, and a time-calibrated family-level phylogeny to test for phylogenetically-corrected associations between hybridization and diversification rates, while also taking into account life-history traits that may be correlated with both processes. We show that diversification and hybridization are positively correlated using three different methods to estimate diversification rates and two different metrics of hybridization. Moreover, the relationship remains detectable when incorporating the correlations between diversification and two other life history characteristics, perenniality and woodiness. We further provide potential mechanisms for this association under three different scenarios: hybridization may drive diversification, diversification may drive hybridization, or both hybridization and diversification may jointly be driven by other factors. We suggest future studies to disentangle the causal structure.
Age-related decline in metabolite heavy isotope content in rodent organs
Authors: Li Xiyan , Snyder Michael P. 
Published: August 2019

AbstractHeavy isotopes are discriminated by biological systems due to kinetic isotopic effects at the biochemical/metabolic levels. How these heavy isotopes are enriched or depleted over a long term is unclear, but artificial manipulation of heavy isotope content in various organisms has produced significant impacts on biological functions, suggesting the origin may arise with intrinsic mechanisms for a functional outcome. Our previous study has revealed an age-associated decline in metabolite heavy isotope content (HIC) in the budding yeast, which could be reversed in part by supplementing heavy water, and consequently, also increased yeast lifespans. In the current study, we report a similar age-dependent decline in HIC from three types of mouse tissues: brain, heart, and skeletal muscles. Furthermore, individual tissues exhibited different patterns of HIC change over age, which appeared to match their development and maturation timelines. These results have demonstrated that age-dependent decline in HIC also exists in mammals, which is likely a traceable feature of development and perhaps aging. Thus, we believe that reversing the decline in HIC could have the potential to extend the healthspan of humans.
Global Genetic Cartography of Urban Metagenomes and Anti-Microbial Resistance
Authors: Danko David , Bezdan Daniela , Afshinnekoo Ebrahim , Ahsanuddin Sofia , Bhattacharya Chandrima , Butler Daniel J , Chng Kern Rei , Donnellan Daisy , Hecht Jochen , Jackson Katelyn , Kuchin Katerina , Karasikov Mikhail , Lyons Abigail , Mak Lauren , Meleshko Dmitry , Mustafa Harun , Mutai Beth , Neches Russell Y , Ng Amanda , Nikolayeva Olga , Nikolayeva Tatyana , Png Eileen , Ryon Krista , Sanchez Jorge L , Shaaban Heba , Sierra Maria A , Thomas Dominique , Young Ben , Abudayyeh Omar O. , Alicea Josue , Bhattacharyya Malay , Blekhman Ran , Castro-Nallar Eduardo , Cañas Ana M , Chatziefthimiou Aspassia D , Crawford Robert W , De Filippis Francesca , Deng Youping , Desnues Christelle , Dias-Neto Emmanuel , Dybwad Marius , Elhaik Eran , Ercolini Danilo , Frolova Alina , Gankin Dennis , Gootenberg Jonathan S. , Graf Alexandra B , Green David C , Hajirasouliha Iman , Hernandez Mark , Iraola Gregorio , Jang Soojin , Kahles Andre , Kelly Frank J , Knights Kaymisha , Kyrpides Nikos C , Łabaj Paweł P , Lee Patrick K H , Leung Marcus H Y , Ljungdahl Per , Mason-Buck Gabriella , McGrath Ken , Meydan Cem , Mongodin Emmanuel F , Moraes Milton Ozorio , Nagarajan Niranjan , Nieto-Caballero Marina , Noushmehr Houtan , Oliveira Manuela , Ossowski Stephan , Osuolale Olayinka O , Özcan Orhan , Paez-Espino David , Rascovan Nicolas , Richard Hugues , Rätsch Gunnar , Schriml Lynn M , Semmler Torsten , Sezerman Osman U , Shi Leming , Shi Tieliu , Song Le Huu , Suzuki Haruo , Court Denise Syndercombe , Tighe Scott W , Tong Xinzhao , Udekwu Klas I , Ugalde Juan A , Valentine Brandon , Vassilev Dimitar I , Vayndorf Elena , Velavan Thirumalaisamy P , Wu Jun , Zambrano María M , Zhu Jifeng , Zhu Sibo , Mason Christopher E ,   The International MetaSUB Consortium
Published: August 2019

AbstractWe have created a global atlas of 4,728 metagenomic samples from mass-transit systems in 60 cities across 3 years. This is the first systematic, worldwide study cataloging the urban microbial ecosystem. We identify taxonomically-defined microorganisms collected across three years. This atlas provides an annotated, geospatial profile of microbial strains, functional characteristics AMR markers, and novel genetic elements, including 10,928 viral, 1302 bacteria, and 2 archaea novel species. We identify 4,424 species of urban microorganisms and a consistent “core” of 31 species found in nearly all samples that is largely distinct from any human commensal microbiome. Profiles of AMR genes show geographic variation in type and density. Together, these results constitute a high-resolution, global metagenomic atlas, which enables the discovery of new genetic components, highlights potential forensic applications, and provides an essential first draft of the global AMR burden of the world’s cities.
On the distribution of tract lengths during adaptive introgression
Authors: Shchur Vladimir , Svedberg Jesper , Medina Paloma , Corbett-Detig Russ , Nielsen RASMUS 
Published: August 2019

ABSTRACTAdmixture is increasingly being recognized as an important factor in evolutionary genetics. The distribution of genomic admixture tracts, and the resulting effects on admixture linkage disequilibrium, can be used to date the timing of admixture between species or populations. However, the theory used for such prediction assumes selective neutrality despite the fact that many famous examples of admixture involve natural selection acting for or against admixture. In this paper, we investigate the effects of positive selection on the distribution of tract lengths. We develop a theoretical framework that relies on approximating the trajectory of the selected allele using a logistic function. By numerically calculating the expected allele trajectory, we also show that the approach can be extended to cases where the logistic approximation is poor due to the effects of genetic drift. Using simulations, we show that the model is highly accurate under most scenarios. We use the model to show that positive selection on average will tend to increase the admixture tract length. However, perhaps counter-intuitively, conditional on the allele frequency at the time of sampling, positive selection will actually produce shorter expected tract lengths. We discuss the consequences of our results in interpreting the timing of the introgression of EPAS1 from Denisovans into the ancestors of Tibetans.