bluuebunny/crossref_metadata_2025_split huggingface dataset:
Large conformational changes of a highly dynamic pre-protein binding domain in SecA
Authors: Ernst Isabel , Haase Maximilian , Ernst Stefan , Yuan Shuguang , Kuhn Andreas , Leptihn Sebastian 
Published: August 2018

AbstractSecA is an essential molecular motor for the translocation of proteins across the membrane via the bacterial Sec secretion system. While the Sec system is found in all cells from archaea to multicellular eukaryotes, the SecA protein is mainly found in bacteria. The mechanism of how the motor protein works on a molecular level is still under dispute but it is well established that SecA binds ATP and uses its hydrolysis for the translocation of substrates. In this work, we addressed the question of which conformational changes the protein might undergo during protein translocation. To this end, we investigated the molecular movements of SecA in the absence or the presence of ATP using single-molecule FRET measurements and in silico normal mode analyses. Our results demonstrate that the pre-protein binding domain of SecA is highly dynamic in the absence of the nucleotide and moves towards the helical wing domain in an ATP-bound state.
Direct quantification of nanoparticle surface hydrophobicity
Authors: Valsesia Andrea , Desmet Cloé , Ojea-Jiménez Isaac , Oddo Arianna , Capomaccio Robin , Rossi François , Colpo Pascal 
Published: August 2018

AbstractHydrophobicity is an important parameter for the risk assessment of chemicals, but standardised quantitative methods for the determination of hydrophobicity cannot be applied to nanomaterials. Here we describe a method for the direct quantification of the surface energy and hydrophobicity of nanomaterials. The quantification is obtained by comparing the nanomaterial binding affinity to two or more engineered collectors, i.e. surfaces with tuned hydrophobicity. In order to validate the concept, the method is applied to a set of nanoparticles with varying degrees of hydrophobicity. The technique described represents an alternative to the use of other methods such as hydrophobic interaction chromatography or water–octanol partition, which provide only qualitative values of hydrophobicity.
The first annotated set of scanning electron microscopy images for nanoscience
Authors: Aversa Rossella , Modarres Mohammad Hadi , Cozzini Stefano , Ciancio Regina , Chiusole Alberto 
Published: August 2018

AbstractIn this paper, we present the first publicly available human-annotated dataset of images obtained by the Scanning Electron Microscopy (SEM). A total of roughly 22,000 SEM images at the nanoscale are classified into 10 categories to form 4 labeled training sets, suited for image recognition tasks. The selected categories span the range of 0D objects such as particles, 1D nanowires and fibres, 2D films and coated surfaces as well as patterned surfaces, and 3D structures such as microelectromechanical system (MEMS) devices and pillars. Additional categories such as tips and biological are also included to expand the spectrum of possible images. A preliminary degree of hierarchy is introduced, by creating a subtree structure for the categories and populating them with the available images, wherever possible.
Computational workflow to study the seasonal variation of secondary metabolites in nine different bryophytes
Authors: Peters Kristian , Gorzolka Karin , Bruelheide Helge , Neumann Steffen 
Published: August 2018

AbstractIn Eco-Metabolomics interactions are studied of non-model organisms in their natural environment and relations are made between biochemistry and ecological function. Current challenges when processing such metabolomics data involve complex experiment designs which are often carried out in large field campaigns involving multiple study factors, peak detection parameter settings, the high variation of metabolite profiles and the analysis of non-model species with scarcely characterised metabolomes. Here, we present a dataset generated from 108 samples of nine bryophyte species obtained in four seasons using an untargeted liquid chromatography coupled with mass spectrometry acquisition method (LC/MS). Using this dataset we address the current challenges when processing Eco-Metabolomics data. Here, we also present a reproducible and reusable computational workflow implemented in Galaxy focusing on standard formats, data import, technical validation, feature detection, diversity analysis and multivariate statistics. We expect that the representative dataset and the reusable processing pipeline will facilitate future studies in the research field of Eco-Metabolomics.
An acquisition, curation and management workflow for sustainable, terabyte-scale marine image analysis
Authors: Schoening Timm , Köser Kevin , Greinert Jens 
Published: August 2018

AbstractOptical imaging is a common technique in ocean research. Diving robots, towed cameras, drop-cameras and TV-guided sampling gear: all produce image data of the underwater environment. Technological advances like 4K cameras, autonomous robots, high-capacity batteries and LED lighting now allow systematic optical monitoring at large spatial scale and shorter time but with increased data volume and velocity. Volume and velocity are further increased by growing fleets and emerging swarms of autonomous vehicles creating big data sets in parallel. This generates a need for automated data processing to harvest maximum information. Systematic data analysis benefits from calibrated, geo-referenced data with clear metadata description, particularly for machine vision and machine learning. Hence, the expensive data acquisition must be documented, data should be curated as soon as possible, backed up and made publicly available. Here, we present a workflow towards sustainable marine image analysis. We describe guidelines for data acquisition, curation and management and apply it to the use case of a multi-terabyte deep-sea data set acquired by an autonomous underwater vehicle.
Interplanetary dust delivery of water to the atmospheres of Pluto and Triton
Authors: Poppe A. R. , Horányi M. 
Published: August 2018

Context. Both Pluto and Triton possess thin, N2-dominated atmospheres controlled by sublimation of surface ices.
Aims. We aim to constrain the influx and ablation of interplanetary dust grains into the atmospheres of both Pluto and Triton in order to estimate the rate at which oxygen-bearing species are introduced into both atmospheres.
Methods. We use (i) an interplanetary dust dynamics model to calculate the flux and velocity distributions of interplanetary dust grains relevant for both Pluto and Triton and (ii) a model for the ablation of interplanetary dust grains in the atmospheres of both Pluto and Triton. We sum the individual ablation profiles over the incoming mass and velocity distributions of interplanetary dust grains in order to determine the vertical structure and net deposition of water to both atmospheres.
Results. Our results show that <2% of silicate grains ablate at either Pluto or Triton while approximately 75% and >99% of water ice grains ablate at Pluto and Triton, respectively. From ice grains, we calculate net water influxes to Pluto and Triton of ~3.8 kg day−1 (8.5 × 103 H2O cm−2 s−1) and ~370 kg day−1 (6.2 × 105 H2O cm−2 s−1), respectively. The significant difference in total water deposition between Pluto and Triton is due to the presence of Triton within Neptune’s gravity well, which both enhances interplanetary dust particle (IDP) fluxes due to gravitational focusing and accelerates grains before entry into Triton’s atmosphere, thereby causing more efficient ablation.
Conclusions. We conclude that water deposition from dust ablation plays only a minor role at Pluto due to its relatively low flux. At Triton, water deposition from IDPs is more significant and may play a role in the alteration of atmospheric and ionospheric chemistry. We also suggest that meteoric smoke and smaller, unablated grains may serve as condensation nuclei for the formation of hazes at both worlds.
D-Dimer and TAT Measurement in Patients with Deep Venous Thrombosis: Utility in Diagnosis and Judgement of Anticoagulant Treatment Effectiveness
Authors: Speiser Wolfgang , Mallek Reinhold , Koppensteiner Renate , Andreas Stümpflen , Kapiotis Stylianos , Minar Erich , Ehringer Herbert , Lechner Klaus 
Published: August 2018

SummaryThe plasma levels of thrombin-antithrombin III-complexes (TAT) and the fibrin split product D-Dimer were measured in 39 patients with phlebographically proven acute DVT: 34 patients had proximal DVT, 5 had calf DVT The sensitivity of D-Dimer and TAT measurements in the diagnosis of proximal DVT was found to be dependent on the duration of symptoms: 0 to 7 days (n = 27): elevated D-Dimer levels (>120 ng/ml) = 1, D-Dimer Latex test positive (>500 ng/ml) = 1, elevated TAT levels (>6 ng/ml) = 0.88. Eight to 14 days (n = 7): elevated D-Dimer levels = 1, D-Dimer Latex test positive = 0.33, elevated TAT levels = 0.66; specificity: elevated D-Dimer: 0.48, D-Dimer Latex test: 1, elevated TAT: 0.76. Calf DVT patients (n = 5) had elevated D-Dimer levels, negative Latex tests and 3 of them had normal TAT values. Hemostatic and fibrinolytic parameters were also determined in 13 patients during heparin treatment of proximal DVT. Elevated D-Dimer and TAT levels rapidly decreased after initiation of anticoagulant therapy. In 2 of 13 patients a marked increase in D-Dimer and TAT levels was observed in periods of ineffective heparinization, documented by normal or only slightly prolonged thrombin clotting times. We conclude from our results that 1) D-Dimer El A measurement, in contrast to TAT measurement, shows a very high sensitivity in the diagnosis of DVT, 2) due to low specificity this test can only be used to exclude thrombosis in patients with suspected DVT, and 3) the determination of the plasma levels of D-Dimer and TAT may be useful for judging the effect of anticoagulant treatment on thrombotic processes.
The Effects of Long-Term Using Once-A-Month Injectable Contraceptive Norethisterone Enanthate/ Estradiol Valerate on Coagulation in the Chinese
Authors: Meng Yuan-Xiang , Jiang Hai-Ying , Lu Feng-Ying 
Published: August 2018

SummarySixty-four Chinese women were studied for the effects of injecting once-a-month contraceptive norethisterone enanthate/ estradiol valerate between 2 to 4 1/2 years on certain coagulation and fibrinolytic parameters, and 59 women not receiving any steroidal contraception were controls. In both groups there was no significant change in PT, fibrinogen, factor X activity, AT III antigen, AT III activity and fibrinolytic activity expressed by euglobulin lysis time. There was no significant difference in mean levels of factor VIIIR:Ag between the two groups, although a sub-group women in treatment group had higher than accepted levels of factor VIIIR:Ag.
Stress Induced Release of Plasminogen Activator from Lysosomes
Authors: Beard E. L , Busuttil R. W , Gottshalk S. K 
Published: August 2018

SummaryMild hemorrhage was found to bring about a slight increase in the plasminogen activator activity of the blood serum of albino rats. This change coincided with a minor increase in the plasminogen activator activity of the liver microsomes of these rats and a significant increase in that of the liver lysosomes. Presumably the stress was sufficient to increase lysosomal permeability allowing for a greater outflow of plasminogen activator into the body fluids.Drum trauma and acid phosphatase injections brought about a similar release of plasminogen activator and acid phosphatase which intensified when the two were applied together. Rats which had previously been made resistant to drum trauma responded only slightly to either stress alone but their resistance was overcome when both stresses were applied together.
Plasmatic and Thrombocytic Anti-Plasmins and Anti-Activators II.
Authors: den Ottolander G. J. H , Leijnse B , Cremer-Elfrink H. M. J 
Published: August 2018

SummaryValues for inhibitors in plasma and in platelets against plasmin and against different activators were measured in normal test persons. The influence of freezing and thawing, of heating to 60° C and of destruction in other ways was assessed. The reaction pattern of all these inhibitors was established. It appears that there are differences in behaviour amongst these inhibitors. In patients with a high and with a low anti-UK there was no correlation with the levels of inhibitors directed against blood activator, obtained in several ways, SK and tissue activator.The conclusion is that anti-UK is not representative for anti-activator activity in general. There are indications that blood activator liberated with different stimuli is one substance.
Plasmatic and Platelet Anti-Plasmins and Anti-Activators
Authors: den Ottolander G. J. H , Leijnse B , Cremer-Elfrink M. J. H 
Published: August 2018

SummaryThe values for plasmatic and thrombocytic anti-plasmin and anti-UK were determined in normal test persons and in 107 patients with different diseases.In 12 patients with a fresh venous thrombosis the values of these inhibitors were within normal limits.In 6 patients with liver cirrhosis no significantly lowered values were found.Also in patients with different haematological diseases no abnormality was found. A relationship between plasmatic and thrombocytic anti-UK was found.
Fibrinolysis and Alimentary Lipaemia in Whites and Bantus; Their Relationship and Response to Intravenous Heparin
Authors: Lackner H , Sougin-Mibashan R 
Published: August 2018

Summary and Conclusion1. Diurnal variation in fibrinolysis is marked in the Whites and almost absent in the Bantu. >2. The difference in fibrinolytic activity beween White and Bantu has been confirmed, but was found to decrease over the course of the morning due to diurnal variation in the White subjects.3. The ingestion of butter fat does not inhibit fibrinolysis to any appreciable extent in either White or Bantu.4. The accelerating effect of heparin on fibrinolysis was found to be present in lipaemic plasma, but appears to be distinct from the fat-clearing effect.
Convenient New Bedside and Laboratory Method for the Control of Anticoagulant Therapy
Authors: Hartert H 
Published: August 2018

SummaryA new simple method is described for the determination of thromboplastin time on 0.02 ml of capillary blood. It employs an automatic pipette with a disposable mouthpiece (sections of a plastic capillary tube), which is replaced by a new one after each determination. The automatic pipette may be used in the same way for pipetting the thromboplastin suspension into the test tube. The latter is the only utensil, which has to be cleaned after the determination.In comparison with other procedures of thromboplastin time determinations, the new micro-method has been found as reliable as “macro”-methods using venous blood.
6-oxo-Prostaglandin F1α and Thromboxane B2 in Uterine Vein Blood - A Possible Role in Menstrual Bleeding
Authors: Goodfellow C F , Paton R C , Salmon J A , Moncada S , Clayton J K , Davies J A , McNicol G P 
Published: August 2018

SummaryThe role of the haemostatic system in relation to menstrual bleeding is poorly understood. Platelet retention to glass beads and plasma concentrations of 6-oxo-PGFα and thromboxane B2 were measured in uterine and peripheral venous blood obtained from 18 women undergoing abdominal hysterectomy. Concentrations of 6-oxo-PGFα were significantly (p<0.01) higher in uterine (1.4 ± 0.3 ng/ml, mean ± SEM) than in peripheral vein blood (0.2 ±0.1 ng/ml) as was the level of thromboxane B2 (0.5 + 0.1 and 0.2 ± 0.1 ng/ml, respectively). Platelet retention in uterine vein blood (11 ± 4%) was significantly lower than in peripheral blood (42 ±4%; p<0.01) and the degree of platelet retention correlated inversely with the plasma concentration of 6-oxo-PGFα (r −0.43; p<0.01). There was a significant rank correlation between time since menstruation and concentrations of 6-oxo-PGFα in uterine (τ + 0.69; p<0.001) and peripheral (τ + 0.56; p<0.05) vein blood. The results indicate that an increased local production of prostacyclin (PGI2) relative to thromboxane A2 at the time of menstruation could contribute to the mechanism of uterine bleeding.
Protein C Level at Birth
Authors: Polack B , Pouzol P , Amiral J , Kolodie L 
Published: August 2018

SummaryThe protein C level was determined, on cord blood, for 30 healtly newborns by electro-immuno assay using a monospecific antiserum. For the newborns the mean level of protein C related antigen is about one third of normal adults’ mean level. There is a good correlation between Protein C related antigen and prothrombin related antigen. The low level of these vitamin-K-dependent proteins is probably a consequence of partial liver immaturity at birth. Using two-dimensional immuno-electrophoresis we were unable to detect subcarboxylated forms of protein C. However these abnormal forms could be seen in vitamin-K deficiencies of neonates.
Randomized Quality Improvement Trial of Opting-In Versus Opting-Out to Increase Influenza Vaccination Rates during Pregnancy
Authors: Wootton Susan , Blackwell Sean , Saade George , Berens Pamela , Hutchinson Maria , Green Charles , Sridhar Sujatha , Elam Kara , Tyson Jon 
Published: August 2018

Introduction Despite strong recommendations, only 40.6% of pregnant women attending two prenatal clinics were vaccinated against influenza during the 2009 pandemic. We tested whether an opting-out approach would improve vaccine uptake.
Methods We conducted a randomized quality improvement (QI) trial to compare opting-out with conventional opting-in consent for influenza immunization. Women age ≥ 18 years attending the University of Texas Health Science Center at Houston (UTHealth) or UT-Medical Branch (UTMB) prenatal clinics during the 2010–2011 influenza season, were eligible.
Results We enrolled 280 women (140 UTHealth, 140 UTMB). Both groups had similar mean age (26.0 ± 5.5 years), mean gestational age (19.4 ± 9.5 weeks), and percent with underlying health conditions (20.7%). Vaccination rates with opting-in and opting-out were similar among all (83 vs. 84%), UTHealth (87 vs. 93%), and UTMB patients (79 vs.76%) (p > 0.05). In subsamples of patients assessed, consent strategy did not significantly affect maternal recall of information provided.
Conclusion While prenatal influenza vaccination uptake doubled from the 2009–2010 influenza season, opting-out did not perform better than opting-in, a conclusion opposite that we would have reached had this been a nonconcurrent trial. Vaccination rates dropped posttrial; hence, continued research is needed to increase the prenatal influenza immunizations.
Predictors of Hand Dexterity after Single-Digit Replantation
Authors: Kawamura Kenji , Omokawa Shohei , Shimizu Takamasa , Iida Akio , Tanaka Yasuhito , Nakanishi Akito 
Published: August 2018

Background Microsurgical replantation of the thumb and digits has become an increasingly familiar technique in clinical practice worldwide. However, successful digit replantation does not always provide better hand function than revision amputation. Little information is available regarding predictors of motor skill activities of replanted hands. Therefore, we retrospectively evaluated hand dexterity after single-digit replantation at a minimum follow-up of 1 year and analyzed the factors influencing dexterity.
Methods This retrospective cohort study included 23 patients treated for amputation injuries at our institution from 2014 to 2015. Patients with amputations from Tamai's zone 2 to 5 of the thumb (3 patients), index finger (11 patients), or middle finger (9 patients) who underwent digital replantation surgery and were followed up for more than 1 year were included. Follow-up evaluations were conducted at an average of 23 months postoperatively (range: 13–25 months). We hypothesized that possible factors influencing hand dexterity after single-digit replantation were patient age, injured finger, key pinch strength, Semmes–Weinstein test result, and percentage of total active motion. Relationships between the outcome variable, which was the result of the Purdue Pegboard Test of hand dexterity, and explanatory variables were analyzed using Spearman's correlation coefficient. A p-value of < 0.05 indicated statistical significance.
Results No postoperative complications occurred. Univariate analysis indicated that decreased hand dexterity after single-digit replantation was significantly associated with older age (p = 0.001) and poor recovery of sensation, as shown by the Semmes–Weinstein test (p = 0.012).
Conclusion Patient age was a risk factor for low hand dexterity after replantation surgery. Recovery of finger sensitivity enhanced dexterity of motor skill activities following finger replantation surgery.
Inferring dynamic topology for decoding spatiotemporal structures in complex heterogeneous networks
Authors: Wang Shuo , Herzog Erik D. , Kiss István Z. , Schwartz William J. , Bloch Guy , Sebek Michael , Granados-Fuentes Daniel , Wang Liang , Li Jr-Shin 
Published: August 2018

Significance
Inferring connections forms a critical step toward understanding large and diverse complex networks. To date, reliable and efficient methods for the reconstruction of network topology from measurement data remain a challenge due to the high complexity and nonlinearity of the system dynamics. These obstacles also form a bottleneck for analyzing and controlling the dynamic structures (e.g., synchrony) and collective behavior in such complex networks. The novel contribution of this work is to develop a unified data-driven approach to reliably and efficiently reveal the dynamic topology of complex networks in different scales—from cells to societies. The developed technique provides guidelines for the refinement of experimental designs toward a comprehensive understanding of complex heterogeneous networks.
Serious games may improve physician heuristics in trauma triage
Authors: Mohan Deepika , Fischhoff Baruch , Angus Derek C. , Rosengart Matthew R. , Wallace David J. , Yealy Donald M. , Farris Coreen , Chang Chung-Chou H. , Kerti Samantha , Barnato Amber E. 
Published: August 2018

Significance
Americans can expect to experience at least one meaningful diagnostic medical error in their lifetime. One plausible source of those errors is physicians’ reliance on heuristics that are generally useful but can fail in diagnostically challenging situations. Based on previous research and clinical experience, we identified heuristics that might cause diagnostic errors in trauma triage. We sought to improve physicians’ heuristic judgment by providing simulated experience with two “serious” video games. In a randomized controlled trial, both games had positive effects, whereas equivalent exposure to traditional medical education had none. By complementing physicians’ natural ways of thinking, such simulated experiences might transfer to actual triage and other high-pressure decisions.
Global analysis of mutations driving microevolution of a heterozygous diploid fungal pathogen
Authors: Ene Iuliana V. , Farrer Rhys A. , Hirakawa Matthew P. , Agwamba Kennedy , Cuomo Christina A. , Bennett Richard J. 
Published: August 2018

Significance
Evolution acts on mutations that naturally arise within the genome and are shaped both by intrinsic genomic features and by the cellular environment. We catalog the mutations arising in a heterozygous diploid yeast during passaging in vitro and in the mammalian host. We establish genome-wide mutation rates and reveal that “microscale” changes (base substitutions and short-track recombination events) are the primary drivers of microevolution, although chromosomal-level changes also occur in specific host environments. Our results define mutation hotspots, including those adjoining recombination tracts, and indicate that many mutations are purged from the population due to purifying selection. Together, these data provide a high-resolution picture of how the heterozygous diploid genome of a fungal pathogen undergoes evolution over short time scales.