bluuebunny/crossref_metadata_2025_split huggingface dataset:
Conserved changes in secondary structure and aggregation properties ofin vitroevolved proteins for thermo stability
Authors: Kundharapu Satyamurthy 
Published: February 2017

AbstractMost of the screening strategies of directed evolution involved in thermo stability deals with aggregation of proteins either directly or indirectly. Here in this work I investigated what happens in aggregation property and secondary structure of the protein when it improved its thermo stability by incorporating certain amino acid changes in the protein. To study these changes I picked randomly 12 different proteins and I analyzed their 25 different thermo stable mutants. I used open access online Software to get the aggregation propensity values and values for different secondary structure elements propensities of proteins. I compared the aggregation propensity and predicted secondary structure values of thermo stable mutants with their parent Wild type proteins. The stable mutants followed three different conserved patterns to improve their thermo stability.
Modern machine learning outperforms GLMs at predicting spikes
Authors: Benjamin Ari S. , Fernandes Hugo L. , Tomlinson Tucker , Ramkumar Pavan , VerSteeg Chris , Chowdhury Raeed , Miller Lee , Kording Konrad Paul 
Published: February 2017

AbstractNeuroscience has long focused on finding encoding models that effectively ask “what predicts neural spiking?” and generalized linear models (GLMs) are a typical approach. It is often unknown how much of explainable neural activity is captured, or missed, when fitting a GLM. Here we compared the predictive performance of GLMs to three leading machine learning methods: feedforward neural networks, gradient boosted trees (using XGBoost), and stacked ensembles that combine the predictions of several methods. We predicted spike counts in macaque motor (M1) and somatosensory (S1) cortices from standard representations of reaching kinematics, and in rat hippocampal cells from open field location and orientation. In general, the modern methods (particularly XGBoost and the ensemble) produced more accurate spike predictions and were less sensitive to the preprocessing of features. This discrepancy in performance suggests that standard feature sets may often relate to neural activity in a nonlinear manner not captured by GLMs. Encoding models built with machine learning techniques, which can be largely automated, more accurately predict spikes and can offer meaningful benchmarks for simpler models.
Improved LC-MS chromatographic alignment increases the accuracy of label-free quantitative proteomics: Comparison of spectral counting versus ion intensity-based proteomic quantification strategies
Authors: Ng Daniel H.J. , Humphries Jonathan D. , Selley Julian N. , Warwood Stacey , Knight David , Byron Adam , Humphries Martin J. 
Published: February 2017

AbstractThe ability to provide an unbiased qualitative and quantitative description of the global changes to proteins in a cell or an organism would permit the systems-wide study of complex biological systems. Label-free quantitative shotgun proteomic strategies (including LC-MS ion intensity quantification and spectral counting) are attractive because of their relatively low cost, ease of implementation, and the lack of multiplexing restrictions when comparing multiple samples. Owing to improvements in the resolution and sensitivity of mass spectrometers, and the availability of analytical software packages, protein quantification by LC-MS ion intensity has increased in popularity. Here, we have addressed the importance of chromatographic alignment on protein quantification, and then assessed how spectral counting compares to ion intensity-based proteomic quantification. Using a spiked-in protein strategy, we analysed two situations that commonly arise in the application of proteomics to cell biology: (i) samples with a small number of proteins of differential abundance in a larger non-changing background, and (ii) samples with a larger number of proteins of differential abundance. To perform these assessments on biologically relevant samples, we used isolated integrin adhesion complexes (IACs). Technical replicate analysis of isolated IACs resulted in a range of alignment scores using the Progenesis QI software package and demonstrated that higher LC-MS chromatographic alignment scores increased the precision of protein quantification. Furthermore, implementation of a simple sample batch-running strategy enabled good chromatographic alignment for hundreds of samples over multiple batches. Finally, we applied the sample batch-running strategy and compared quantification by LC-MS ion intensity to spectral counting and found that quantification by LC-MS ion intensity was more accurate and precise. In summary, these results demonstrate that chromatographic alignment is important for precise and accurate protein quantification based on LC-MS ion intensity and accordingly we present a simple sample re-ordering strategy to facilitate improved alignment. These findings are not only relevant to label-free quantification using Progenesis QI but may be useful to the wide range of MS-based quantification strategies that rely on chromatographic alignment.
α-tubulin acetylation and detyrosination correlate with starvation-induced autophagy in tobacco cells
Authors: Lytvyn Dmytro I. , Yemets Alla I. , Blume Yaroslav B. 
Published: February 2017

ABSTRACTRecent data has enabled discovery of novel functions of microtubules (MTs) in the regulation of autophagy development under physiologic/stressful conditions in yeast and animal cells. MTs participate in maturation and traffic of autophagosomes through their dynamic state changes and post-translational modifications of tubulin, including acetylation. We demonstrated the involvement of tobacco cell MTs in the development of starvation-induced autophagy via tubulin acetylation and denitrotyrosination. Induced metabolic stress caused by prolonged cultivation of BY-2 suspension cells results in glucose depletion in the culture medium and following increased rates of protein hydrolysis and autophagy. Development of autophagy was strongly accompanied by α-tubulin acetylation and detyrosination. Both post-translational modifications were caused by changes in the molecular microenvironment of the tobacco cell MTs that was revealed via Co-IP assay. The termination of autophagy led to the development of programmed cell death that was characterised by nucleosomal DNA fragmentation and decreases in α-tubulin acetylation and detyrosination. Our data suggest the role of the functional state of MTs in the mediation of plant autophagy via changes in the tubulin microenvironment and in its post-translational modifications.SUMMARY STATEMENTThe main findings cover a possible impact of plant microtubular cytoskeleton to starvation-induced autophagy development. It can be realized by means of tubulin post-translational modifications, acetylation in the first place.
Stable association of a Drosophila-derived microbiota with its animal partner and the nutritional environment upon transfer between populations and generations
Authors: Téfit Mélisandre A. , Gillet Benjamin , Joncour Pauline , Hughes Sandrine , Leulier François 
Published: February 2017

AbstractIn the past years, the fruit flyDrosophila melanogasterhas been extensively used to study the relationship between animals and their associated microbes. Compared to the one of wild populations, the microbiota of laboratory-reared flies is less diverse, and comprises fewer bacterial taxa; nevertheless, the main commensal bacteria found in fly microbiota always belong to theAcetobacteraceaeandLactobacillaceaefamilies. The bacterial communities associated with the fly are environmentally acquired, and the partners engage in a perpetual re-association process. Adult flies constantly ingest and excrete microbes from and onto their feeding substrate, which are then transmitted to the next generation developing within this shared habitat. We wanted to analyze the potential changes in the bacterial community during its reciprocal transfer between the two compartments of the niche (i.e. the fly and the diet). To address this question, we used a diverse, wild-derived microbial community and analyzed its relationship with the fly population and the nutritive substrate in a given habitat. Here we show that the community was overall well maintained upon transmission to a new niche, to a new fly population and to their progeny, illustrating the stable association of a Drosophila-derived microbiota with its fly partner and the nutritional environment. These results highlight the preponderant role of the nutritional substrate in the dynamics of Drosophila/microbiota interactions, and the need to fully integrate this variable when performing such studies.
Eelgrass leaf surface microbiomes are locally variable and highly correlated with epibiotic eukaryotes
Authors: Bengtsson Mia M. , Bühler Anton , Brauer Anne , Dahlke Sven , Schubert Hendrik , Blindow Irmgard 
Published: February 2017

ABSTRACTEelgrass(Zostera marina)is a marine foundation species essential for coastal ecosystem services around the northern hemisphere. Like all macroscopic organisms, it possesses a microbiome which may play critical roles in modulating the interaction of eelgrass with its environment. For example, its leaf surface microbiome could inhibit or attract eukaryotic epibionts which may overgrow the eelgrass leading to reduced primary productivity and subsequent eelgrass meadow decline. We used amplicon sequencing of the 16S and 18S rRNA genes of prokaryotes and eukaryotes to assess the leaf surface microbiome (prokaryotes) as well as eukaryotic epibionts in-and outside lagoons on the German Baltic Sea coast. Bacterial microbiomes varied substantially both between sites inside lagoons and between open coastal and lagoon sites. Water depth, leaf area and biofilm chlorophyllaconcentration explained a large amount of variation in both bacterial and eukaryotic community composition. Communities of bacterial and eukaryotic epibionts were highly correlated, and network analysis revealed disproportionate co-occurrence between a limited number of eukaryotic taxa and several bacterial taxa. This suggests that eelgrass leaf surface biofilms are a mosaic of the microbiomes of several eukaryotes, in addition to that of the eelgrass itself, and underlines that eukaryotic microbial diversity should be taken into account in order to explain microbiome assembly and dynamics in aquatic environments.
PGC-1α coordinates with Bcl-2 to control cell cycle in U251 cells through reducing ROS
Authors: Yao Kun , Fu Xufeng , Xing Du , Li Yan , Han Bing , Zexi Chen , Yang Shanshan , Wei Ran , Zhou Jiaqi , Cui Qinghua 
Published: February 2017

AbstractB-cell lymphoma 2 (Bcl-2) has a dual function, acting both as an oncogene and an anti-tumor gene. It is well known that Bcl-2 exerts its tumor promoting function through the mitochondrial pathway. However, the mechanism by which Bcl-2 suppresses tumor formation is not well understood. We have previously shown that Bcl-2 inhibits cell cycle progression from the G0/G1to the S phase after serum starvation, and that quiescent Bcl-2 expressing cells maintained a significant lower level of mitochondrial reactive oxygen species (ROS) than the control cells. Based on the fact that ROS mediate cell cycle progression, and are controlled by peroxisome proliferator-activated receptor-γ co-activator 1α (PGC-1α), a key molecule induced by prolonged starvation and involved in mitochondrial metabolism, we hypothesized that PGC-1α might be related with the cell cycle function of Bcl-2. Here, we showed that PGC-1α was upregulated upon Bcl-2 overexpression and downregulated following Bcl-2 knockdown during serum starvation. Knockdown of PGC-1α activated Bcl-2 expression. Taken together, our results suggest that after serum depletion, PGC-la might coordinate with Bcl-2 to reduce ROS, which in turn delay cell cycle progression.Summary statementPGC-1α coordinate with Bcl-2 delay cell cycle progression to reduce ROS after serum depletion in human glioma U251 cells.
High-throughput live-imaging of embryos in microwell arrays using a modular, inexpensive specimen mounting system
Authors: Donoughe Seth , Kim Chiyoung , Extavour Cassandra G. 
Published: February 2017

AbstractLive-imaging embryos in a high-throughput manner is essential for shedding light on a wide range of questions in developmental biology, but it is difficult and costly to mount and image embryos in consistent conditions. Here, we present OMMAwell, a simple, reusable device that makes it easy to mount up to hundreds of embryos in arrays of agarose microwells with customizable dimensions and spacing. OMMAwell can be configured to mount specimens for upright or inverted microscopes, and includes a reservoir to hold live-imaging medium to maintain constant moisture and osmolarity of specimens during time-lapse imaging. All device components can be cut from a sheet of acrylic using a laser cutter. Even a novice user will be able to cut the pieces and assemble the device in less than an hour. At the time of writing, the total materials cost is less than five US dollars. We include all device design files in a commonly used format, as well as complete instructions for its fabrication and use. We demonstrate a detailed workflow for designing a custom mold and employing it to simultaneously live-image dozens of embryos at a time for more than five days, using embryos of the cricketGryllus bimaculatusas an example. Further, we include descriptions, schematics, and design files for molds that can be used with 14 additional vertebrate and invertebrate species, including most major traditional laboratory models and a number of emerging model systems. Molds have been user-tested for embryos including zebrafish (Danio rerio), fruit fly (Drosophila melanogaster), coqui frog (Eleutherodactylus coqui), annelid worm (Capitella teleta), amphipod crustacean (Parhyale hawaiensis), red flour beetle (Tribolium castaneum), and three-banded panther worm (Hofstenia miamia), as well mouse organoids (Mus musculus). Finally, we provide instructions for researchers to customize OMMAwell inserts for embryos or tissues not described herein.Summary StatementThisTechniques and Resourcesarticle describes an inexpensive, customizable device for mounting and live-imaging a wide range of tissues and species; complete design files and instructions for assembly are included.
Contesting lifestyle risk and gendering coronary candidacy: lay epidemiology of heart disease in Finland in the 1970s
Authors: Jauho Mikko 
Published: February 2017

AbstractThis study addresses two issues currently under critical discussion in the epidemiology of cardiovascular diseases (CVD), the relative neglect of women and the individualised nature of key risk factors. It focuses on the North Karelia project (NKP), a community programme aimed at coronary heart disease (CHD) prevention in a predominantly rural Finnish region in the early 1970s, that is, during a period when the epidemiological understanding of CVD still was relatively new and actively promoted. Adopting the notions of lay epidemiology and coronary candidacy, culturally mediated explanatory models lay people use to assess who is likely to develop heart disease and why, the study shows that locals targeted by the project critically engaged with both of these bias. Based on the rich materials resulting from project activities the study shows, first, how many locals subsumed the individualised and lifestyle‐based approach to CHD prevention promoted by NKP under a more general framework emphasising the health effects of ongoing structural changes in the area, and second, how women constructed themselves as viable coronary candidates. The case supports the position in the current discussions on lay expertise that wants to integrate lay experiences more firmly into epidemiological studies and public health.
Hyperemesis gravidarum and cardiometabolic risk factors in adolescents: a follow‐up of the Northern Finland Birth Cohort 1986
Authors: Koot MH , Grooten IJ , Sebert S , Koiranen M , Järvelin MR , Kajantie E , Painter RC , Roseboom TJ 
Published: February 2017

ObjectiveTo investigate the long‐term consequences of prenatal exposure to maternal hyperemesis gravidarum upon offspring cardiometabolic risk factors.DesignThis study is part of the prospective follow‐up of the Northern Finland Birth Cohort 1986.SettingBetween 1 July 1985 and 30 June 1986 all pregnant women in two provinces of Finland were recruited at first antenatal visit (99% of eligible participated).PopulationA total of 8953 women with liveborn singleton offspring who consented to having their children followed‐up were included.MethodsHyperemesis gravidarum (HG) was defined as hospitalisation during pregnancy for HG based on the International Classification of Disease (ICD) code. Women who were not hospitalised for HG during pregnancy were used as a reference group. Data on pregnancy and birth outcomes were obtained via medical records and questionnaires; 6462 adolescents, aged 16 years, underwent anthropometric measurements (HG n = 42, reference n = 6420) and 5648 adolescents had a fasting blood sample taken (HG n = 36, reference n = 5612).Main outcome measuresBody mass index (BMI), blood pressure, fasting glucose, and lipid levels in offspring.ResultsMultivariate regression analyses showed no differences in offspring BMI (kg/m2; adjusted percentage difference HG versus reference, 2.2; 95% CI −0.1, 4.6), systolic blood pressure (adjusted difference 2.1 mmHg; 95% CI −1.5, 5.6), and fasting blood glucose (mmol/l; adjusted percentage difference, 2.3; 95% CI −0.6, 5.4), between adolescents born to mothers with and without HG.ConclusionsWe found no evidence that prenatal exposure to HG has negative consequences for cardiometabolic health of offspring at the age of 16 years.Tweetable abstractHyperemesis gravidarum does not affect cardiometabolic health in adolescent offspring.
Trends in operative vaginal delivery, 2005–2013: a population‐based study
Authors: Merriam AA , Ananth CV , Wright JD , Siddiq Z , D'Alton ME , Friedman AM 
Published: February 2017

ObjectiveThe objectives of this study were to determine temporal trends in forceps and vacuum delivery and factors associated with operative vaginal delivery.DesignRetrospective cohort.SettingPopulation‐based study of US birth records.PopulationUS births from 2005 to 2013.MethodsThis study evaluated forceps and vacuum extraction during vaginal delivery in live‐born, non‐anomalous singleton gestations from ≥ 36 to < 42 weeks of gestation. The primary outcomes were vacuum, forceps and overall operative delivery. Obstetric, medical and demographic characteristics associated with operative vaginal delivery were analysed. Multivariable logistic regression models were developed to determine factors associated with forceps/vacuum use.ResultsA total of 22 598 971 vaginal deliveries between 2005 and 2013 were included in the analysis. In all, 1 083 318 (4.8%) were vacuum‐assisted and 237 792 (1.1%) were by forceps. Both vacuum and forceps deliveries decreased over the study period; vacuum deliveries decreased from 5.8% in 2005 to 4.1% in 2013, and forceps deliveries decreased from 1.4% to 0.9% during the same period. The adjusted odds ratio for forceps delivery was 0.70 (95% CI 0.69–0.72) in 2013 with 2005 as a reference. For vacuum delivery the odds ratio was 0.68 (95% CI 0.67–0.69) comparing the same years.ConclusionForceps and vacuum deliveries decreased during the study period. Low rates of operative delivery pose a challenge for resident education and may limit the degree to which women have access to alternatives to caesarean delivery. Initiatives that allow future generations of obstetricians to develop expertise in performing operative deliveries in the setting of decreased volume are an urgent resident education priority.Tweetable abstractForceps and vacuum delivery decreased significantly in the USA from 2005 to 2013.
Spontaneous and indicated preterm delivery risk is increased among overweight and obese women without prepregnancy chronic disease
Authors: Kim SS , Mendola P , Zhu Y , Hwang BS , Grantz KL 
Published: February 2017

ObjectiveTo investigate the independent impact of prepregnancy obesity on preterm delivery among women without chronic diseases by gestational age, preterm category and parity.DesignA retrospective cohort study.SettingData from the Consortium on Safe Labor (CSL) in the USA (2002–08).PopulationSingleton deliveries at ≥23 weeks of gestation in the CSL (43 200 nulliparas and 63 129 multiparas) with a prepregnancy body mass index (BMI) ≥18.5 kg/m2 and without chronic diseases.MethodsAssociation of prepregnancy BMI and the risk of preterm delivery was examined using Poisson regression with normal weight as reference.Main outcome measuresPreterm deliveries were categorised by gestational age (extremely, very, moderate to late) and category (spontaneous, indicated, no recorded indication).ResultsRelative risk of spontaneous preterm delivery was increased for extremely preterm among obese nulliparas (1.26, 95% CI: 0.94–1.70 for overweight; 1.88, 95% CI: 1.30–2.71 for obese class I; 1.99, 95% CI: 1.32–3.01 for obese class II/III) and decreased for moderate to late preterm delivery among overweight and obese multiparas (0.90, 95% CI: 0.83–0.97 for overweight; 0.87, 95% CI: 0.78–0.97 for obese class I; 0.79, 95% CI: 0.69–0.90 for obese class II/III). Indicated preterm delivery risk was increased with prepregnancy BMI in a dose–response manner for extremely preterm and moderate to late preterm among nulliparas, as it was for moderate to late preterm delivery among multiparas.ConclusionsPrepregnancy BMI was associated with increased risk of preterm delivery even in the absence of chronic diseases, but the association was heterogeneous by preterm categories, gestational age and parity.Tweetable abstractObese nulliparas without chronic disease had higher risk for spontaneous delivery <28 weeks of gestation.
Cruciform position for trauma resuscitation
Authors: Mitra Biswadev , Fitzgerald Mark C , Olaussen Alexander , Thaveenthiran Prasanthan , Bade‐Boon Jordan , Martin Katherine , Smit De Villiers , Cameron Peter A 
Published: February 2017

AbstractMultiply injured patients represent a particularly demanding subgroup of trauma patients as they require urgent simultaneous clinical assessments using physical examination, ultrasound and invasive monitoring together with critical management, including tracheal intubation, thoracostomies and central venous access. Concurrent access to multiple body regions is essential to facilitate the concept of ‘horizontal’ resuscitation. The current positioning of trauma patient, with arms adducted, restricts this approach. Instead, the therapeutic cruciform positioning, with arms abducted at 90°, allows planning and performing of multiple life‐saving interventions simultaneously. This positioning also provides a practical surgical field with improved sterility and procedural access.