bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Masquelet induced-membrane technique: an option for a tertiary-referral conflict setting
Authors: Ley Paul , Gosselin Richard A , Villar Richard 
Published: May 2019

Abstract
A post-traumatic, infected, non-union of a long bone is a significant challenge to orthopaedic surgeons, especially in zones of conflict and humanitarian settings. We describe a 32-year-old man treated with the two-stage Masquelet procedure for an infected non-union, and the processes required to achieve clinical bony union. The initial injury was a gunshot wound through the left proximal tibia, which lay untreated for three months before the first definitive surgical procedure. Subsequent management required 13 procedures over 18 months with clinical union being achieved 4.5 years after wounding. The management of an infected non-union of a long bone in zones of conflict is difficult. However, a successful outcome is still possible and the Masquelet procedure a suitable choice; amputation is not always the correct solution. There is a need in the humanitarian sector for healthcare facilities within easy reach of a zone of conflict that can undertake complex reconstructive procedures.
Linear bias forecasts for emission line cosmological surveys
Authors: Merson Alexander , Smith Alex , Benson Andrew , Wang Yun , Baugh Carlton 
Published: May 2019

Abstract
We forecast the linear bias for  Hα-emitting galaxies at high redshift. To simulate a Euclid-like and a WFIRST-like survey, we place galaxies into a large-volume dark matter halo lightcone by sampling a library of luminosity-dependent halo occupation distributions (HODs), which is constructed using a physically motivated galaxy formation model. We calibrate the dust attenuation in the lightcones such that they are able to reproduce the  Hα luminosity function or the  Hα cumulative number counts. The angle-averaged galaxy correlation function is computed for each survey in redshift slices of width Δ z = 0.2. In each redshift bin the linear bias can be fitted with a single, scale-independent value that increases with increasing redshift. Fitting for the evolution of linear bias with redshift, we find that our Euclid-like and WFIRST-like surveys are both consistent within error with the relation b(z) = 0.7z + 0.7. Our bias forecasts are consistent with bias measurements from the HiZELS survey. We find that the Euclid-like and WFIRST-like surveys yield linear biases that are broadly consistent within error, most likely due to the HOD for the WFIRST-like survey having a steeper power-law slope towards larger halo masses.
Accounting for multiplicity in calculating eta Earth
Authors: Zink Jon K , Hansen Bradley M S 
Published: May 2019

ABSTRACT
Using the updated exoplanet population parameters of our previous study, which includes the planetary radius updates from Gaia DR2 and an inferred multiplicity distribution, we provide a revised η⊕ calculation. This is achieved by sampling planets from our derived population model and determining which planets meet our criterion for habitability. To ensure robust results, we provide probabilities calculated over a range of upper radius limits. Our most optimistic criterion for habitability provides an η⊕ value of $0.34\pm 0.02 \frac{\rm planets}{\rm star}$. We also consider the effects of multiplicity and the number of habitable planets each system may contain. Our calculation indicates that $6.4\pm 0.5{{\ \rm per\ cent}}$ of GK dwarfs have more than one planet within their habitable zone. This optimistic habitability criterion also suggests that $0.036\pm 0.009{{\ \rm per\ cent}}$ of solar-like stars will harbour five or more habitable planets. These tightly packed highly habitable systems should be extremely rare, but still possible. Even with our most pessimistic criterion, we still expect that $1.8\pm 0.2{{\ \rm per\ cent}}$ of solar-like stars harbour more than one habitable planet.
The mass-loss, expansion velocities, and dust production rates of carbon stars in the Magellanic Clouds
Authors: Nanni Ambra , Groenewegen Martin A T , Aringer Bernhard , Rubele Stefano , Bressan Alessandro , van Loon Jacco Th , Goldman Steven R , Boyer Martha L 
Published: May 2019

ABSTRACT
The properties of carbon stars in the Magellanic Clouds (MCs) and their total dust production rates are predicted by fitting their spectral energy distributions (SED) over pre-computed grids of spectra reprocessed by dust. The grids are calculated as a function of the stellar parameters by consistently following the growth for several dust species in their circumstellar envelopes, coupled with a stationary wind. Dust radiative transfer is computed taking as input the results of the dust growth calculations. The optical constants for amorphous carbon are selected in order to reproduce different observations in the infrared and optical bands of Gaia Data Release 2. We find a tail of extreme mass-losing carbon stars in the Large Magellanic Cloud (LMC) with low gas-to-dust ratios that is not present in the Small Magellanic Cloud (SMC). Typical gas-to-dust ratios are around 700 for the extreme stars, but they can be down to ∼160–200 and ∼100 for a few sources in the SMC and in the LMC, respectively. The total dust production rate for the carbon star population is ∼1.77 ± 0.45 × 10−5 M⊙ yr−1, for the LMC, and ∼2.52 ± 0.96 × 10−6 M⊙ yr−1, for the SMC. The extreme carbon stars observed with the Atacama Large Millimeter Array and their wind speed are studied in detail. For the most dust-obscured star in this sample the estimated mass-loss rate is ∼6.3 × 10−5 M⊙ yr−1. The grids of spectra are available at:1 and included in the SED-fitting python package for fitting evolved stars.2
Caver Web 1.0: identification of tunnels and channels in proteins and analysis of ligand transport
Authors: Stourac Jan , Vavra Ondrej , Kokkonen Piia , Filipovic Jiri , Pinto Gaspar , Brezovsky Jan , Damborsky Jiri , Bednar David 
Published: May 2019

AbstractCaver Web 1.0 is a web server for comprehensive analysis of protein tunnels and channels, and study of the ligands’ transport through these transport pathways. Caver Web is the first interactive tool allowing both the analyses within a single graphical user interface. The server is built on top of the abundantly used tunnel detection tool Caver 3.02 and CaverDock 1.0 enabling the study of the ligand transport. The program is easy-to-use as the only required inputs are a protein structure for a tunnel identification and a list of ligands for the transport analysis. The automated guidance procedures assist the users to set up the calculation in a way to obtain biologically relevant results. The identified tunnels, their properties, energy profiles and trajectories for ligands’ passages can be calculated and visualized. The tool is very fast (2–20 min per job) and is applicable even for virtual screening purposes. Its simple setup and comprehensive graphical user interface make the tool accessible for a broad scientific community. The server is freely available at https://loschmidt.chemi.muni.cz/caverweb.
Single-molecule visualization of the effects of ionic strength and crowding on structure-mediated interactions in supercoiled DNA molecules
Authors: Scott Shane , Shaheen Cynthia , McGuinness Brendon , Metera Kimberly , Kouzine Fedor , Levens David , Benham Craig J , Leslie Sabrina 
Published: May 2019

Abstract
DNA unwinding is an important cellular process involved in DNA replication, transcription and repair. In cells, molecular crowding caused by the presence of organelles, proteins, and other molecules affects numerous internal cellular structures. Here, we visualize plasmid DNA unwinding and binding dynamics to an oligonucleotide probe as functions of ionic strength, crowding agent concentration, and crowding agent species using single-molecule CLiC microscopy. We demonstrate increased probe–plasmid interaction over time with increasing concentration of 8 kDa polyethylene glycol (PEG), a crowding agent. We show decreased probe–plasmid interactions as ionic strength is increased without crowding. However, when crowding is introduced via 10% 8 kDa PEG, interactions between plasmids and oligos are enhanced. This is beyond what is expected for normal in vitro conditions, and may be a critically important, but as of yet unknown, factor in DNA’s proper biological function in vivo. Our results show that crowding has a strong effect on the initial concentration of unwound plasmids. In the dilute conditions used in these experiments, crowding does not impact probe–plasmid interactions once the site is unwound.
M1CR0B1AL1Z3R—a user-friendly web server for the analysis of large-scale microbial genomics data
Authors: Avram Oren , Rapoport Dana , Portugez Shir , Pupko Tal 
Published: May 2019

Abstract
Large-scale mining and analysis of bacterial datasets contribute to the comprehensive characterization of complex microbial dynamics within a microbiome and among different bacterial strains, e.g., during disease outbreaks. The study of large-scale bacterial evolutionary dynamics poses many challenges. These include data-mining steps, such as gene annotation, ortholog detection, sequence alignment and phylogeny reconstruction. These steps require the use of multiple bioinformatics tools and ad-hoc programming scripts, making the entire process cumbersome, tedious and error-prone due to manual handling. This motivated us to develop the M1CR0B1AL1Z3R web server, a ‘one-stop shop’ for conducting microbial genomics data analyses via a simple graphical user interface. Some of the features implemented in M1CR0B1AL1Z3R are: (i) extracting putative open reading frames and comparative genomics analysis of gene content; (ii) extracting orthologous sets and analyzing their size distribution; (iii) analyzing gene presence–absence patterns; (iv) reconstructing a phylogenetic tree based on the extracted orthologous set; (v) inferring GC-content variation among lineages. M1CR0B1AL1Z3R facilitates the mining and analysis of dozens of bacterial genomes using advanced techniques, with the click of a button. M1CR0B1AL1Z3R is freely available at https://microbializer.tau.ac.il/.
Opioid Use and Rate of Nicotine Metabolism Among Pregnant Smokers
Authors: Oncken Cheryl , Mead Erin L , Dornelas Ellen A , Kuo Chia-Ling , Sankey Heather Z , Kranzler Henry R , Thurlow Sheila 
Published: May 2019

Abstract

Introduction
Smokers who use opioids smoke more cigarettes per day (CPD) than non-opioid users, which could be due to the effects of opioids on nicotine metabolism. Moreover, nicotine metabolism increases during pregnancy, potentially making quitting more difficult for pregnant smokers. We examined nicotine metabolism and its association with opioid use (OU) and CPD in pregnant smokers.

Methods
We recruited pregnant women who smoked at least 5 CPD for a clinical trial of smoking cessation. Plasma nicotine metabolite ratio (NMR; trans-3′-hydroxycotinine (3HC)/cotinine)—a biomarker of nicotine metabolism—OU (involving methadone, buprenorphine, fentanyl, oxycodone, or tramadol), and CPD were assessed at baseline. We used linear regression to examine the associations between log-transformed NMR, OU, and CPD, adjusting for race/ethnicity and menthol smoking.

Results
Among 129 pregnant smokers, 25 (19%) were opioid users; most were maintained on methadone (n = 14). Compared to non-OU smokers, OU smokers had higher median CPD (10.0 vs. 7.0, p = .0007), serum 3HC (81.0 vs. 42.0 ng/mL, p = .0001), and NMR (0.63 vs. 0.43, p &lt; .0001). In addition, methadone-maintained smokers had a higher median NMR than non-OU smokers (0.66 vs. 0.43, p = .0004). Adjusting for covariates, log-transformed NMR was greater in OU smokers (p = .012), specifically methadone-maintained smokers (p = .024), than non-OU smokers.

Conclusions
Our preliminary results show that OU is associated with a higher NMR in pregnant smokers. A larger study sample is needed to replicate this finding, examine potential mechanisms, and determine its clinical significance.

Implications
Among pregnant smokers, we observed that nicotine metabolism was significantly faster among opioid users—the majority of whom were on methadone maintenance—compared to nonusers, which could have implications for smoking cessation. Further studies are needed to replicate this finding, evaluate potential mechanisms, and determine its clinical significance.
Evaluation of a Screening Method for the Detection of Colistin-Resistant Enterobacteriaceae in Stool
Authors: Turbett Sarah E , Desrosiers Lisa , Andrews-Dunleavey Catherine , Becker Margaret , Walker Allison Taylor , Esposito Douglas , Woodworth Kate Russell , Branda John A , Rosenberg Eric , Ryan Edward T , LaRocque Regina 
Published: May 2019

Abstract
Emergence of mobile colistin resistance (mcr)–containing Enterobacteriaceae is a public health threat, prompting enhanced surveillance through the Centers for Disease Control and Prevention. We evaluated a selective culture medium for the isolation of Enterobacteriaceae with non-wild-type colistin minimum inhibitory concentrations, including those with mcr-1 genes, in spiked stool samples.
Evidence for enhanced Bruton’s tyrosine kinase activity in transitional and naïve B cells of patients with granulomatosis with polyangiitis
Authors: von Borstel Anouk , Abdulahad Wayel H , Sanders Jan Stephan , Rip Jasper , Neys Stefan F H , Hendriks Rudi W , Stegeman Coen A , Heeringa Peter , Rutgers Abraham , Corneth Odilia B J 
Published: May 2019

Abstract

Objectives
To determine Bruton’s tyrosine kinase (BTK) protein and phosphorylation levels in B cell subsets of granulomatosis with polyangiitis (GPA) patients and to investigate the effect of BTK blockade on in vitro B cell cytokine production, subset distribution and (auto)antibody production.

Methods
BTK protein and phosphorylation levels were determined by flow cytometry in peripheral blood B cells of 29 untreated GPA patients [9 active and 20 remission GPA patients (10 ANCA– and 10 ANCA+)], 9 age- and sex-matched healthy controls (HCs) and 9 untreated active RA patients. The effect of BTK blockade on in vitro B cell cytokine production, subset distribution and (auto)antibody production was determined in the same donors in peripheral blood mononuclear cell cultures.

Results
BTK protein levels were significantly increased in transitional and naïve B cells of active GPA and RA patients compared with remission GPA patients and HCs. Both B cell subsets of active patients were more sensitive to B cell receptor stimulation, as BTK and phospholipase Cγ2 phosphorylation were increased in these patients. In vitro BTK blockade had profound effects on B cell cytokine production, plasma cell formation and (auto)antibody production in both GPA patients and HCs. Interestingly, the effect of BTK blockade was less pronounced in active GPA patients, possibly due to increased activation of B cells.

Conclusion
We show that BTK protein and phosphorylation levels are most profoundly increased in newly emerging B cells of active GPA patients compared with remission patients. BTK blockade greatly inhibits in vitro B cell effector functions in GPA patients and HCs. These promising data identify BTK as an interesting novel therapeutic target in the treatment of GPA.
The inherently democratic nature of technology assessment
Authors: Grunwald Armin 
Published: May 2019

AbstractTechnology assessment (TA) emerged more than fifty years ago to provide information supply, decision support, and orientation for democratic processes and institutions in many democratic countries. This historical observation alone, however, does not justify speaking of an inherent relationship between TA and democracy. The latter requires taking a conceptual view. Arguments supporting the thesis of the inherently democratic nature of TA will be given based on pragmatist approaches developed by John Dewey and Jürgen Habermas. This perspective on TA has specific implications for the inclusion of the knowledge and perspectives of stakeholders, people affected and citizens involved in TA processes, as well as the necessity to develop or strengthen thinking in alternative options. Furthermore, it makes clear that in the current crisis of democracy in many countries, TA cannot take a distant and neutral position.
Parental PM2.5 Exposure-Promoted Development of Metabolic Syndrome in Offspring Is Associated With the Changes of Immune Microenvironment
Authors: Zhang Jia , Zeng Xuejiao , Du Xihao , Pan Kun , Song Liying , Song Weimin , Xie Yuquan , Zhao Jinzhuo 
Published: May 2019

Abstract
Parental exposure to ambient fine particulate matter (PM2.5) has been associated with some of adverse health outcomes in offspring. The association between parental PM2.5 exposure and the development of metabolic syndrome (MetS) in offspring, and the effects of parental PM2.5 exposure on the susceptibility of offspring mice to PM2.5, has not been evaluated. The C57BL/6 parental mice (male and female mice) were exposed to filtered air (FA) or concentrated PM2.5 (PM) using Shanghai-METAS for a total of 16 weeks. At week 12 during the exposure, we allowed the parental male and female mice to breed offspring mice. The male offspring mice were divided into 4 groups and exposed to PM and FA again. The results showed that whether the parental mice were exposed to PM2.5 or not, the offspring mice exposure to PM2.5 appeared the elevation of blood pressure, insulin resistance, impairment of glucose tolerance, and dyslipidemia when compared to the offspring mice exposure to FA. More importantly, no matter what the offspring mice were exposed to, parental PM exposure overwhelmingly impacted the fasting blood insulin, homeostasis model assessment-insulin resistance, serous low-density lipoprotein cholesterol, and total cholesterol, splenic T helper cell 17 (Th17) and Treg cells, serous interleukin (IL)-17A, IL-6, and IL-10 in offspring mice. The results suggested that the parental exposure to air pollution might induce the development of MetS in offspring and might enhance the susceptibility of offspring to environmental hazards. The effects of parental PM exposure on offspring might be related to the changes of immune microenvironment.
Gabapentin for Peri-operative Pain Management for Office Uterine Aspiration: A Randomized Controlled Trial [10H]
Authors: Gray Beverly , Hagey Jill , Crabtree Donna , Weber Jeremy , Pieper Carl , Haddad Lisa 
Published: May 2019

INTRODUCTION:
Gabapentin, used to treat neuropathic and chronic pain, has also been used to reduce post-surgical pain in a variety of clinical settings. We investigated if the addition of gabapentin to the routine oral sedation regimen would reduce peri-operative pain from uterine aspiration.

METHODS:
IRB approval and informed consent were obtained. We enrolled patients seeking first trimester uterine aspiration with oral sedation in a randomized double-blind placebo-controlled trial to receive placebo or 600 mg of oral gabapentin in addition to oral sedation and paracervical block. Our primary outcome was pain 5-minutes after procedure measured on a VAS (100 mm) pain scale. Secondary outcomes measured included pain at a variety of time points, post-operative pain medication use, anxiety and nausea. This study was powered to detect a 16 mm difference in pain. To assess the effect of gabapentin at the 5-minute post-op assessment, we fit a linear regression controlling for baseline pain.

RESULTS:
96 patients were randomized (95 completed study protocol). Patients receiving gabapentin reported similar pain scores compared to placebo at the 5-minute post-op assessment (p = 0.56). Anxiety measures were similar between groups at several time points. Gabapentin was well-tolerated and side effects were similar between groups. 15% of women receiving gabapentin versus 31% receiving placebo recorded using narcotic pain medication within 24 hours of the procedure (p = 0.06).

CONCLUSION:
Gabapentin did not have a significant effect on the 5-minute post-operative pain measurement or anxiety. The trend toward decreased opioid usage in the post-operative period amongst the gabapentin users warrants future investigation.
Attempted and Successful VBAC Across Geographic Areas in the United States [25H]
Authors: Greene Madelyne , Hsiang-Hui Daphne Kuo , Hartenbach Ellen , Shrider Emily , Ehrenthal Deborah 
Published: May 2019

INTRODUCTION:
Rates of Cesarean delivery continue to increase in the US and globally. Efforts to reduce the number of unnecessary Cesarean sections include renewed support for vaginal birth after Cesarean (VBAC). Previous research has demonstrated that trends in trial of labor after Cesarean (TOLAC) and successful VBAC may differ across geographic areas.

METHODS:
Using combined 2014 and 2015 national vital statistics data, we describe rates of attempted (TOLAC) and successful VBAC among low-risk (term, singleton, vertex), in-hospital births occurring in counties across the NCHS 6-level rural-urban measurement classification. Using logistic regression modeling, we describe patterns in TOLAC and VBAC rates across geographic areas, both unadjusted and adjusted for demographic characteristics, health services use (e.g. WIC, prenatal care), and medical risk factors. The UW-Madison IRB exempted this study.

RESULTS:
There were 153,758 documented attempted VBAC deliveries in 2014 and 2015, with an overall VBAC success rate of 72.0%. Rates of both any TOLAC and successful VBAC were significantly lower among institutions in more rural areas across the country (TOLAC unadjusted OR 0.543, 95% CI 0.461-0.506, and VBAC unadjusted OR 0.463, 95% CI 0.437-0.489 in rural county hospitals compared to large metropolitan centers). Controlling for various factors did not substantially alter these patterns.

CONCLUSION:
Hospitals in more rural areas in the US may be less likely to attempt TOLAC and successfully deliver via VBAC. Hospitals in different geographic areas may have vastly different access to resources and specialists that can support VBAC and high-quality clinical decision making to reduce the number of unnecessary Cesarean sections.
Baby Boxes and Breastfeeding: A Study of the Impact of Safe Sleeping Environments on Infant Feeding Method [26H]
Authors: Pantoja Rachel , Herrine Gail , Zhao Huaquing , Swiecki-Sikora Allison Leigh , Kiani Kayvon , Datwani Hema 
Published: May 2019

INTRODUCTION:
The benefits of breastfeeding for both a newborn and mother are well established. Parents often co-sleep with their children for ease of breastfeeding. However, co-sleeping is associated with sleep-related deaths. To alleviate this burden, Temple University Hospital (TUH) provided all newly delivered mothers with a Baby Box, a box with a firm mattress, for a safe sleeping environment. The purpose of this project was to study the impact of a safe sleeping environment on breastfeeding rates.

METHODS:
This is a retrospective study of patients between May 2016 and May 2018 who delivered at TUH and were provided a Baby Box prior to hospital discharge. A phone survey was performed after discharge. Categorical variables were analyzed using Pearson chi-squared test. This study on review by the TUH IRB was given exempt status.

RESULTS:
Of 4,394 eligible women, 26% reported exclusive breastfeeding of their infant. Approximately 26% of those exclusively breastfeeding reported using the Baby Box for infant sleep, and 54% reported that breastfeeding was easier while using the Baby Box. Approximately 32% of those who exclusively breastfed reported co-sleeping with their infant. There was no statistically significant difference between feeding method and use of the Baby Box.

CONCLUSION:
With the use of the baby box, the number of participants exclusively breastfeeding was low. Of those who exclusively breastfeed, there was a high rate of co-sleeping, despite being provided with a safe sleeping environment. This study demonstrates the need for continued efforts to promote breastfeeding and safe sleeping in this patient population.