bluuebunny/crossref_metadata_2025 huggingface dataset:
Predicting Survival From Out-of-Hospital Cardiac Arrest
Authors: Lindholm Daniel J. , Campbell Jack P.
Published: May 2019

Objective:

To determine the effect of a return of spontaneous circulation (RO SC) on survival to hospital discharge as compared to other established predictors of survival.

Methods:

A retrospective case review of all out-of-hospital primary cardiac arrests from 01 January, 1992 to 31 December 1994 was conducted. The relative values of age, race, gender, presenting cardiac rhythm, witnessed event, initiation of CPR by bystanders, response time intervals, and return of spontaneous circulation (ROSC) in an Utstein-template database were tested as predictors of survival of patients who had suffered a cardiac arrest in the out-of-hospital setting. The ROSC was defined as return of spontaneous circulation prior to and present upon arrival at the emergency department. Predictors were evaluated for statistical significance using a logistic regression analysis (p < 0.05). Odds ratios (OR) and 95% confidence intervals (CI) with positive and negative predictive values (PPV, NPV) were calculated.

Results:

Of 832 patients with primary cardiac arrest, 153 (18.4%) had ROSC and 67 (8.1%) survived to hospital discharge. Comparing survivors to nonsurvivors, the mean values for age were 64 to 67 years, with 59.7% to 36.1% being witnessed, 35.8% to 23.9% having bystander CPR initiated, 88.1% to 48.4% having ventricular fibrillation (V-fib) and 82.1% to 64.0% having ROSC. An initial electro-cardiographic rhythm of V-fib (p = 0.009; OR = 2.2; CI = 1.2-3.9), and ROSC (p < 0.0001; OR = 5.2; CI = 3.6-7.5) are statistically significant predictors of survival to hospital discharge. The PPV was 13.8% for V-fib and 35.9% for ROSC, and the NPV was 98.0% for V-fib and 98.2% for ROSC.

Conclusion:

Presenting V-fib and out-of-hospital ROSC are significant predictors of survival from cardiac arrest. Failure to obtain ROSC in the out-of-hospital setting strongly suggests consideration for terminating resuscitation efforts.
A Classroom Simulation of the Syrian Conflict
Authors: Frank Richard W. , Genauer Jessica
Published: May 2019

This article describes a semester-long classroom simulation of the Syrian conflict designed for an introductory international relations (IR) course. The simulation culminates with two weeks of multi-stakeholder negotiations addressing four issues: humanitarian aid, economic sanctions, ceasefire, and political transition. Students randomly play one of 15 roles involving three actor types: states, non-state actors, and international organizations. This article outlines the costs and benefits of simulation design options toward encouraging students’ understanding of IR concepts, and it proposes a course plan for tightly integrating lectures, readings, assessment, and simulation—regardless of class size or length. We highlight this integration through a discussion of two weeks’ worth of material—domestic politics and war, and non-state actors—and the incorporation of bargaining concepts and frameworks into the two weeks of simulated multi-stakeholder negotiations.
Recent advances in research on draught ruminants
Authors: Pearson R. A. , Zerbini E. , Lawrence P. R.
Published: May 2019

A feeding system, draught cows, disease/work interactions and animal power introduction in a farming system, four areas of recent research on draught ruminants which are important to future development of animal power, are reviewed. A new feeding system for draught animals is described which enables food requirements and the effects of work on live weight and milk production to be calculated.

Recent data on the energy cost of walking are appraised. Research on working cows, mainly in Ethiopia, has shown that undernutrition has a greater effect on milk yield than work, which has a transient effect. The length of the post-partum anoestrous period increases with decrease in body condition. Body-weight loss increases with increasing work load. It is suggested that dairy cows delay conception by 1 day for every day of work done. Work has little effect on food intake or digestive parameters. Although it is associated with an overall increase in food intake of cows, even of un-supplemented forage diets, the increase is not sufficient to meet all the extra energy needs for work. Food intake of both working and non-working cows increases during lactation.

Disease limits the working capacity of draught animals and work can exacerbate disease. These effects were investigated using Trypanosoma evansi in Indonesia and T. congolense in The Gambia. In both studies, infected animals were able to do much less work than non-infected ones and the severity of the effect depended greatly on the strain of trypanosome used. In general, increasing the plane of nutrition did not ameliorate the effects of the disease, nor in the Gambian study did it prevent loss of appetite in infected animals.

The technical and agronomic innovations necessary for the introduction of animal power into an inland valley region of central Nigeria are described and some of the sociological implications discussed.
Genetic and phenotypic parameter estimates for feeding pattern and performance test traits in pigs
Authors: Hall A. D. , Hill W. G. , Bampton P. R. , Webb A. J.
Published: May 2019

The data used in these analyses were compiled from individual feeding records of 1832 pigs from 70 sire families using FIRE (food intake recording equipment) system from Hunday Electronics Ltd at the Cotswold Pig Development Company. Pigs were on test between 45 (s.d. 2·76) kg and 95 (s.d. 6·78) kg. Daily food intake (DFI kg), food intake per visit (FlV kg), number of visits per day (NV), duration of each visit (TV min), time in the feeder per day (TD min), feeding rate (FR kg/min) and number of non-feeding visits per day (NFV), were measured as means of test and DFI was also recorded as means of bi-weekly periods of test. Performance test traits ofbackfat depth off test (BF mm), food conversion ratio (ECR kg/kg) and average daily gain (ADG kg), over the test period, were also measured.

Parameters were estimated by restricted maximum likelihood with a multivariate individual animal model. DFI had a heritability of 0·21 ranging from 0·18 to 0·26 over the four test periods. Correlations between DFI in each test period were high (rg = 0·75 to 0·99). DFI was highly correlated with performance test traits (0·61 to 0·78) but had low correlations with feeding pattern traits (0·0 to 0·24). The heritabilities of feeding pattern traits were low (0·06 to 0·11) with the exception of FIV (0·27) and NV (0·34) but correlations between feeding pattern traits were high. FIV, NV and TV were moderately correlated with ADG (rg = 0·49, -0·29, 0·33 respectively), BF (rg = 0·35, -0·15, 0·17 respectively) and ECR (rg = -0·12, 0·31, -0·27 respectively). Feeding patterns may be changed substantially by selection and the genetic correlations with performance test traits indicate that feeding patterns traits can be usefully incorporated in selection criteria to improve somewhat the accuracy of selection.
A genetic and economic analysis of nucleus breeding plans designed to improve dairy breeds in Brazil
Authors: Lobo C. H. , Allaire F. R.
Published: May 2019

The objective of this research was to design and compare nucleus breeding plans that might be recommended to the breeders of Brazilian dairy cattle. Plans for native dairy breeds were compared for the change of genetic merit in milk yield and in the economic return at 25-year investment periods. Effects of nucleus herd and commercial population sizes on genetic gain and net income were examined. Investment value of plans was studied for differences in the efficiency of embryo transfer techniques and in the sale price of cows and young bulls on genetic merit. Parent selection was based on records on individuals (for females), their full- and half-sibs, their dam, full-and half-sibs of their sire and their dam and their grandam. Within herd sire selection was restricted to a maximum of one bull per full-sib family. No matings of full-sibs were allowed. Annual economic summaries considered the age distribution of animals within herds. Alternative plans were investigated for their revenue, expense and net income streams and their investment value. The cumulative genetic gain of selected animals in lactational milk production was 1639 kg and 1435 kg for large plans with 64 donors (L) and small plans with 32 donors (S), respectively. The initial genetic lift for a population size of 20 000 animals was equal to 279 kg. When the size of the commercial population was increased to 50 000 animals, the lift was increased by 10%. Profitability in the different plans was achieved after the sale of cows and young bulls. The difference between cumulative discounted net returns at year 25 for L and S was proportional to the sale prices placed on the genetic merit of cows and bulls. The programmes of genetic improvement described were profitable and should be recommended to the breeders of Brazilian dairy cattle. Considering the criteria of gain to cost, the smaller plan seems to be the most reasonable to implement.
Phenotypic variation in live weight and live-weight changes of lactating Holstein-Friesian cows
Authors: Koenen E. P. C. , Groen A. F. , Gengler N.
Published: May 2019

This study quantified individual phenotypic variation in live weight and live-weight changes during the first three lactations and estimated the effects of age, lactation week and pregnancy on live weight. Data comprised weekly averaged live weight (calculated from daily observations) during 452 lactations of 239 Holstein-Friesian cows. Unadjusted mean live weights were 553 (s.d. 50), 611 (s.d. 55) and 654 (s.d. 57) kg during first, second and third parity, respectively. Estimated effect of growth during parity was 46, 52 and 23 kg for the first three parities. Mean maximum weight loss was 26, 22 and 22 kg for first, second and third parity and variation was large among individuals. Week of lactation when cows had their maximum weight loss ranged from 7 weeks in first lactation to 13 weeks in third lactation. Estimated maximum effect of pregnancy on live weight during the lactation varied from 27 to 59 kg. Phenotypic variance in live weight increased with parity. Repeatabilities of live-weight observations within parity were 0.85 . Across parities, high repeatabilities were found for calving weight and mean live weight but not for parameters associated with maximum weight loss. Correlations between weekly means and mean live weight during the whole of lactation were high. It was concluded that single live-weight observations of heifers are a good measurement of mean live weight during the first three panties.
Pig growth and conformation monitoring using image analysis
Authors: Marchant J. A. , Schofield C. P. , White R. P.
Published: May 2019

Machine vision can be used to collect images of pigs and analyse them to identify and measure specific areas and dimensions related to their growth, shape and hence conformation. This information could improve the stockman’s ability to maximize production efficiency and also to monitor health by detecting abnormalities in growth rates. This work introduces fully automated algorithms which find the plan view outline of animals in a normal housing situation, divide the outline into major body components and measure specified dimensions and areas. Special attention is paid to determining whether the results are sufficiently repeatable to be useful in estimating these parameters. Problems in compensating for changes in the optical geometry are outlined and methods proposed to deal with them. The repeatability of the image analysis process coupled with the subsequent signal processing for outlier rejection gives s.e. values on areas of < 0·005 and on linear dimensions of < 0·0025. For example, the plan view area less head and neck (A4) can be used to predict the weight of the group of pigs at 34 kg, 66 kg and 98 kg with standard errors of 0·25 kg, 0·17 kg and 0·39 kg respectively when using manual weighing results to calibrate the system. If an individual pig is weighed once at 75 days (e.g. 34 kg) to calibrate the A4-to-weight relationship, subsequent A4 measurements can be used to predict its weight when 125 days old (approx. 80 kg) to within 1 kg. This matches the accuracy of the manual weighing system used in the trials. The effect of pig gender on the area to weight relationships is not significant (P= 0·074), but there is a small yet significant gender effect with the linear dimensions.
Digestion site and extent of carbohydrate fractions in steers offered by-product diets, as determined by detergent and enzymatic methods
Authors: Taniguchi K. , Zhao Y. , Uchikawa H. , Obitsu T.
Published: May 2019

The objective was to elucidate the influences of two analytical methods, which employed neutral detergent or enzymes, on the digestion of carbohydrate fractions in the rumen and post-rumen of steers. Structural carbohydrates in diets and digesta were directly measured using both procedures and the contents of non-fibre carbohydrates (NFC) and non-fibre non-starch polysaccharides (NFSP) were estimated by subtracting the structural carbohydrates and other components from the organic matter. Carbohydrate sources were Italian ryegrass and rolled barley in the control diet and, in each of other three diets, Italian ryegrass and rolled barley plus either beet pulp, citrus pulp or soya-bean hulls. All diets contained similar proportions of dry matter as crude protein, structural carbohydrates and NFC but the starch proportion of the NFC was different in each diet, as follows: control (0·62), beet pulp (0·48), citrus pulp (0·30) and soya-bean hulls (0·63). Four Holstein steers with ruminal, duodenal and Heal cannulas were offered the four diets in a 4 × 4 Latin-square design. Estimated digestibilities of the structural carbohydrates in the rumen and the whole tract were greater (P < 0·01) when the detergent method was used than when the enzymatic method was used. The maximal difference in the ruminal digestion among the four diets was only 0·05 by the detergent method but 0·17 by the enzymatic method. Conversely, the digestibility of NFC in the rumen, as estimated from the detergent structural carbohydrates was less (P < 0.01) than that estimated from enzymatic structural carbohydrates with no evident differences among the four diets. Starch digestibility in the rumen was extensive for all diets but the ruminal digestibility of NFSP was much lower in the control and soya-bean hull diets, especially when it was estimated using the detergent method. The duodenal flow of microbial protein was greater (P < 0·05) for the beet pulp and citrus pulp diets than for the control. The acetate concentration of the ruminal fluids ranged from 84 for the control diet to 128 mmol/l for the soya-bean hulls diet. The digestion of carbohydrate fractions and the fermentation characteristics in the rumen suggested that the enzymatic method is the more appropriate method for fractionating carbohydrates.
The Normative Power of Secularism. Tunisian Ennahda's Discourse on Religion, Politics, and the State (2011–2016)
Authors: Pfeifer Hanna
Published: May 2019

By critically engaging the literature on the inclusion-moderation hypothesis, this paper seeks to show how the normative structure of secularism constitutes, enables, and restricts the discursive space in which Islamists can justify political action. It analyzes changes in Tunisian Ennahda's discourse (2011–2016) as an attempt to navigate between standards of recognition imposed on them by the normative power of secularism on the one hand, and what they can convincingly integrate into their own platform on the other hand.
The 3‐D Velocity Models and Seismicity Highlight Forearc Deformation Due to Subducting Features (Central Vanuatu)
Authors: Foix O. , Crawford W. C. , Koulakov I. , Baillard C. , Régnier M. , Pelletier B. , Garaebiti E.
Published: May 2019

The central Vanuatu forearc is characterized by a reduced convergence rate at the trench, significant uplift of the overriding plate, and the presence of large forearc islands. Volcanic activity and intermediate‐depth seismicity behind the forearc are among the highest on Earth. These features are presumed to be associated with the subduction of a large seamount chain and an immersed ridge. We used a catalog of P and S arrivals from a local seismological network to construct the first 3‐D velocity model of the region and to relocate earthquakes beneath the forearc. The 3‐D model reveals a highly heterogeneous velocity distribution in the first 40 km beneath the surface. Trench‐parallel low P and S velocity zones in the upper tens of kilometers beneath the western edges of the two largest forearc islands correlate to the major features entering into subduction and suggest highly fractured and probably water‐infiltrated features. Trench‐parallel high‐velocity zones at 5–15‐km depth, further to the east, may be part of a continuous consolidated rock structure that acts as a backstop. Thick overriding plate crust (29 ± 3 km) in the forearc is consistent with the presence of continental remnants. The earthquake distribution is generally heterogeneous, suggesting a complex fault structure and variable stress. Earthquakes are, however, well aligned at the plate interface in between the subducting features, where they constrain the angle of subduction to be 15° on average, down to 10–15‐km depth.
Fluid Injection Experiments in Shale at Elevated Confining Pressures: Determination of Flaw Sizes From Mechanical Experiments
Authors: Chandler Michael R. , Mecklenburgh Julian , Rutter Ernest , Lee Peter
Published: May 2019

Triaxial experiments and direct fluid injection experiments have been conducted at confining pressures up to 100 MPa on Mancos shale, Whitby mudstone, Penrhyn slate, and Pennant sandstone. Experiments were conducted with sample axes lying both parallel and perpendicular to layering in the materials. During triaxial failure Penrhyn slate was stronger for samples with cleavage parallel to maximum principal stress, but the two orientations in the shales displayed similar failure stresses. Initial flaw sizes of around 40 μm were calculated from the triaxial data using the wing crack model, with the shales having shorter initial flaws than the nonshales. During direct fluid injection, breakdown was rapid, with no discernible gap between fracture initiation and breakdown. Breakdown pressure increased linearly with confining pressure but was less sensitive to confining pressure than expected from existing models. A fracture mechanics‐based model is proposed to determine the initial flaw size responsible for breakdown in injection experiments. Flaw sizes determined in this way agree reasonably with those determined from the triaxial data in the nonshales at low confining pressures. As confining pressure rises, a threshold is reached, above which the fluid injection experiments suggest a lower initial flaw length of around 10 μm. This threshold is interpreted as being due to the partial closure of flaws. In the shales an initial flaw length of around 10 μm was determined at all confining pressures, agreeing reasonably with those determined through the triaxial experiments.
Structure and Variability of the Antilles Current at 26.5°N
Authors: Meinen Christopher S. , Johns William E. , Moat Ben I. , Smith Ryan H. , Johns Elizabeth M. , Rayner Darren , Frajka‐Williams Eleanor , Garcia Rigoberto F. , Garzoli Silvia L.
Published: May 2019

Observations from five different systems provide a robust picture of the structure and variability of the Antilles Current, an important contributor to the oceanic flux budget, at 26.5°N during 2005–2015. The analysis includes three direct measurement technologies (current meters, shipboard acoustic Doppler current profilers, and lowered acoustic Doppler current profilers) and two geostrophy‐based measurement technologies (conductivity‐temperature‐depth profilers and pressure‐equipped inverted echo sounders). The direct systems are shown to produce weaker, and less variable, Antilles Current transport estimates than the geostrophy‐based systems. The record‐length‐mean geostrophic estimate for the Antilles Current is 4.7 Sverdrups (Sv; 1 Sv = 106 m3/s), and the daily temporal standard deviation is 7.5 Sv. The variations of the Antilles Current transport exceed those of the entire basin‐wide meridional overturning circulation, illustrating the impact of this unusual current. Seasonal variability shows a maximum northward transport in August–September; however, the seasonal component of the variability is weak, and aliasing of higher frequencies is still a problem even with 10.5 years of data. The dominant time scales of variability in the spectra are at 70 and 180 days, and there is indication of westward propagation of Rossby Wave‐like features into the region at a speed of 9 cm/s. There is no significant correlation between the Antilles Current transport variations and those of the Florida Current at 27°N, in phase or at lags/leads of up to 5 years, likely reflecting the varying coastal wave/wall jet time scales for information to pass from the basin interior through the Bahamas Islands.
A Conceptual Framework for the Scale‐Specific Stochastic Modeling of Transitions in Tropical Cyclone Intensities
Authors: Prasanth Sai , Rao P. S. C. , Marks F. D.
Published: May 2019

At any given time, a tropical cyclone (TC) vortex has multiple intensity pathways that are possible. We conceptualize this problem as a scenario where each of the TC's intensity pathways is a distinct attractor basin, and a combination of several external and internal factors across multiple scales dictates as to which of the many pathways the TC vortex actually takes. As with any complex system, it is difficult to know the details of the multiscale processes that cause or initiate the tipping of the TC vortex into an attractor basin. A stochastic shock arising from any of the various scales within a TC vortex and the subsequent cross‐scale energy transactions may rapidly increase the probability of the vortex intensifying or weakening. To address this problem and apply our conceptual framework to actual TC case studies, we formulate a novel scale‐specific stochastic model that examines the multiscale energetics at and across individual wave numbers within the TC vortex. The stochastic term is modeled in a realistic manner in that the lower and higher wave numbers are treated differently. High‐resolution Hurricane Weather and Research Forecast model outputs of two Bay of Bengal TCs, Phailin (intensifying) and Lehar (weakening), are used as case studies. An ensemble of intensity pathways is generated, and the nonstationary probability distributions of the intensity transitions at each time are examined. Our approach is another step toward an improved understanding of the stochastic dynamics of multiscale transitions of a TC vortex.
Prediction of 24-hour sodium excretion from spot urine samples in South African adults: a comparison of four equations
Authors: Charlton Karen , Ware Lisa J. , Chidumwa Glory , Cockeran Marike , Schutte Aletta E. , Naidoo Nirmala , Kowal Paul
Published: May 2019

Repeated 24-hour urine collection is considered to be the gold standard for assessing salt intake. This is often impractical in large-population studies, especially in low–middle-income countries. Equations to estimate 24-hour urinary salt excretion from a spot urine sample have been developed, but have not been widely validated in African populations. This study aimed to systematically assess the validity of four existing equations to predict 24-hour urinary sodium excretion (24UNa) from spot urine samples in a nationally representative sample of South Africans. Spot and 24-hour urine samples were collected in a subsample (n = 438) of participants from the World Health Organisation Study on global AGEing and adult health (SAGE) Wave 2 in South Africa in 2015. Measured 24UNa values were compared with predicted 24UNa values from the Kawasaki, Tanaka, INTERSALT and Mage equations using Bland–Altman plots. In this subsample (mean age 52.8 ± 16.4 years; body mass index 30.2 ± 8.2 kg/m2; 76% female; 73% black African; 42% hypertensive), all four equations produced a significantly different population estimate compared with the measured median value of 6.7 g salt/day (IQR 4.4–10.5). Although INTERSALT underestimated salt intake (−3.77 g/d; −1.64 to −7.09), the other equations overestimated by 1.28 g/d (−3.52; 1.97), 6.24 g/d (2.22; 9.45), and 17.18 g/d (8.42; 31.96) for Tanaka, Kawasaki, and Mage, respectively. Bland–Altman curves indicated unacceptably wide levels of agreement. Use of these equations to estimate population level salt intake from spot urine samples in South Africans is not recommended.
A high-fat diet promotes depression-like behavior in mice by suppressing hypothalamic PKA signaling
Authors: Vagena Eirini , Ryu Jae Kyu , Baeza-Raja Bernat , Walsh Nicola M. , Syme Catriona , Day Jonathan P. , Houslay Miles D. , Baillie George S.
Published: May 2019

Obesity is associated with an increased risk of depression. The aim of the present study was to investigate whether obesity is a causative factor for the development of depression and what is the molecular pathway(s) that link these two disorders. Using lipidomic and transcriptomic methods, we identified a mechanism that links exposure to a high-fat diet (HFD) in mice with alterations in hypothalamic function that lead to depression. Consumption of an HFD selectively induced accumulation of palmitic acid in the hypothalamus, suppressed the 3′, 5′-cyclic AMP (cAMP)/protein kinase A (PKA) signaling pathway, and increased the concentration of free fatty acid receptor 1 (FFAR1). Deficiency of phosphodiesterase 4A (PDE4A), an enzyme that degrades cAMP and modulates stimulatory regulative G protein (Gs)-coupled G protein-coupled receptor signaling, protected animals either from genetic- or dietary-induced depression phenotype. These findings suggest that dietary intake of saturated fats disrupts hypothalamic functions by suppressing cAMP/PKA signaling through activation of PDE4A. FFAR1 inhibition and/or an increase of cAMP signaling in the hypothalamus could offer potential therapeutic targets to counteract the effects of dietary or genetically induced obesity on depression.
Complement C3 activation regulates the production of tRNA-derived fragments Gly-tRFs and promotes alcohol-induced liver injury and steatosis
Authors: Zhong Fudi , Hu Zhigao , Jiang Keqing , Lei Biao , Wu Zhan , Yuan Guandou , Luo Hongliang , Dong Chunqiang , Tang Bo , Zheng Chaowen , Yang Shuai , Zeng Yonglian , Guo Zhenya , Yu Shuiping , Su Huizhao , Zhang Guo , Qiu Xiaoqiang , Tomlinson Stephen , He Songqing
Published: May 2019

Complement is known to play a role in alcoholic fatty liver disease (AFLD), but the underlying mechanisms are poorly understood, thereby constraining the development of a rational approach for therapeutic intervention in the complement system. C3 deficiency has been shown to impart protective effects against ethanol-induced hepatic steatosis and inflammation. Here we demonstrate a protection effect in wild-type mice by treatment with CR2-Crry, a specific inhibitor of C3 activation. The expression of glycine transfer (t) RNA-derived fragments (Gly-tRFs) is upregulated in ethanol-fed mice and inhibition of Gly-tRFs in vivo decreases chronic ethanol feeding-induced hepatosteatosis without affecting inflammation. The expression of Gly-tRF was downregulated in C3-deficient or CR2-Crry-treated mice, but not in C5-deficient mice; Gly-tRF expression was restored by the C3 activation products C3a or Asp (C3a-des-Arg) via the regulation of CYP2E1. Transcriptome profiling of hepatic tissues showed that Gly-tRF inhibitors upregulate the expression of sirtuin1 (Sirt1) and subsequently affect downstream lipogenesis and β-oxidation pathways. Mechanistically, Gly-tRF interacts with AGO3 to downregulate Sirt1 expression via sequence complementarity in the 3′ UTR. Notably, the expression levels of C3d, CYP2E1 and Gly-tRF are upregulated, whereas Sirt1 is decreased in AFLD patients compared to healthy controls. Collectively, our findings suggest that C3 activation products contribute to hepatosteatosis by regulating the expression of Gly-tRF. Complement inhibition at the C3 activation step and treatment with Gly-tRF inhibitors may be potential and precise therapeutic approaches for AFLD.
BioWordVec, improving biomedical word embeddings with subword information and MeSH
Authors: Zhang Yijia , Chen Qingyu , Yang Zhihao , Lin Hongfei , Lu Zhiyong
Published: May 2019

Distributed word representations have become an essential foundation for biomedical natural language processing (BioNLP), text mining and information retrieval. Word embeddings are traditionally computed at the word level from a large corpus of unlabeled text, ignoring the information present in the internal structure of words or any information available in domain specific structured resources such as ontologies. However, such information holds potentials for greatly improving the quality of the word representation, as suggested in some recent studies in the general domain. Here we present BioWordVec: an open set of biomedical word vectors/embeddings that combines subword information from unlabeled biomedical text with a widely-used biomedical controlled vocabulary called Medical Subject Headings (MeSH). We assess both the validity and utility of our generated word embeddings over multiple NLP tasks in the biomedical domain. Our benchmarking results demonstrate that our word embeddings can result in significantly improved performance over the previous state of the art in those challenging tasks.
Polymorphic transition and nucleation pathway of barium dititanate (BaTi2O5) during crystallization from undercooled liquid
Authors: Ge Xuan , Hu Qiaodan , Lu Wenquan , Cao Sheng , Yang Liang , Xu Mingqin , Xia Mingxu , Li Jianguo
Published: May 2019

The nucleation pathway plays an important role in vitrification, preparation of glass-ceramic composites and synthesis of metastable materials. In this paper, we studied the nucleation pathway of a novel ferroelectric BaTi2O5 (BT2) during crystallization from undercooled liquid by aerodynamic levitation (ADL) containerless processing and structural analysis. An interesting polymorphic transition of BT2 regulated by the undercooling was observed during the crystallization process: the ferroelectric monoclinic phase (γ-BT2) was fabricated at low undercoolings and the paraelectric orthorhombic metastable phase (β-BT2) was obtained from hypercooled liquid. This polymorphic transition phenomenon corresponds to a non-classical nucleation pathway: metastable β-BT2 preferentially nucleates from undercooled melt and γ-BT2 is generated from β phase by solid-state phase transition. The two-step nucleation pathway stems from the structural heredity between the undercooled liquid and crystals. A stronger structural homology exists between the undercooled melt and β-BT2 than γ-BT2 based on diffraction data and atomic configurations analysis. This structural homology coupled with nucleation barrier calculation was used to elucidate the non-classical nucleation pathway of BT2 crystallization: the similarity of the structural unit (Ti-O polyhedra) between the undercooled liquid and the metastable β-BT2 reduces the nucleation barrier and contributes to the preferential precipitation of β-like clusters. This work reveals the formation route of BT2 from cooling melt, which not only benefits the synthesis and application of this novel functional material but also provides a guideline of the crystallization process of titanates from melt at atomic level.
Kinetic Investigation and Dissolution Behavior of Cyanide Alternative Gold Leaching Reagents
Authors: Birich Alexander , Stopic Srecko , Friedrich Bernd
Published: May 2019

Raising social awareness and environmental specifications on cyanide application force gold industry to search for alternative leaching reagents. Therefore, researchers worldwide investigate cyanide alternatives for gold recovery since several decades. Often the research activities cannot be compared directly, since different input materials and experimental conditions are used. Over the course of this study, different promising cyanide alternative reagents were investigated in terms of their capability of pure gold dissolution at different temperatures. All experiments took place under identical conditions by using uniform samples of 99.99% gold disks, to enable a comparability. Thiosulfate as one of the most promising reagent thiosulfate according to literature revealed an insufficient leaching behavior. The gold dissolution was hindered due to the formation of a sulfide passive layer. Also in the thiourea trials, a surface precipitation took place, though gold dissolution did not stop. The halogens iodine, bromine and the well-known gold solvent aqua regia dissolved gold very fast (up to ~1,000 mg·h−1·cm−2). Methanosulfonic acid (MSA) was not capable to extract any gold. The experiments were compared with cyanide trials at identical conditions. The average dissolution rate of investigated reagents at 25 °C shows following order: aqua regia > iodine > bromine > cyanide > thiourea > thiosulfate > MSA.
Predatory bacteria can protect SKH-1 mice from a lethal plague challenge
Authors: Findlay James S. , Flick-Smith Helen C. , Keyser Emma , Cooper Ian A. , Williamson E. Diane , Oyston Petra C. F.
Published: May 2019

With the rise of antimicrobial resistance, novel ways to treat bacterial infections are required and the use of predatory bacteria may be one such approach. Bdellovibrio species have been shown in vitro to predate on a wide range of other Gram-negative bacteria, including CDC category A/B pathogens such as Yersinia pestis. The data reported here show that treatment of SKH-1 mice with Bdellovibrio bacteriovorus HD100 provided significant protection from a lethal challenge of Yersinia pestis CO92. This is the first report of protection conferred by predation in vivo against a systemic pathogen challenge. However, this protective effect was not observed in a preliminary study with Balb/c mice. Therefore the effects of the predatory bacteria are complex and may be dependent on immune status/genetics of the host. Overall, predatory bacteria may have utility as a therapeutic modality but further work is required to understand the predator-host interaction.
Populations of the coral species Montastraea cavernosa on the Belize Barrier Reef lack vertical connectivity
Authors: Eckert Ryan J. , Studivan Michael S. , Voss Joshua D.
Published: May 2019

Larval connectivity among and within coral reefs is important for sustaining coral metapopulations, enhancing ecosystem resilience through species and genetic diversity, and maintaining reef ecosystems’ structure and functions. This study characterized genetic structure and assessed horizontal and vertical connectivity among populations of the ubiquitous gonochoric broadcast spawning coral Montastraea cavernosa in Belize. Using nine polymorphic microsatellite loci, we genotyped M. cavernosa colonies from four depth zones at four study sites within Belizean marine management zones. Study sites were selected within South Water Caye Marine Reserve (3 sites) and Glover’s Reef Marine Reserve (1 site). Strong contemporary genetic differentiation was observed between relatively shallow M. cavernosa populations (10 m, 16 m) and relatively deep (25 m, 35 m) populations, coinciding with a transition from reef crest to reef slope. These results were consistent across both marine reserves. Vertical and horizontal migration models suggest that all populations were historically panmictic, with little unidirectional migration. The relative local isolation of shallow and mesophotic M. cavernosa populations in Belize, coupled with the importance of Belize’s upper mesophotic populations as potential larval sources for other areas in the Tropical Western Atlantic, reinforces the need for management strategies that conserve coral populations across all depth zones.
Assessing matrix quality by Raman spectroscopy helps predict fracture toughness of human cortical bone
Authors: Unal Mustafa , Uppuganti Sasidhar , Timur Selin , Mahadevan-Jansen Anita , Akkus Ozan , Nyman Jeffry S.
Published: May 2019

Developing clinical tools that assess bone matrix quality could improve the assessment of a person’s fracture risk. To determine whether Raman spectroscopy (RS) has such potential, we acquired Raman spectra from human cortical bone using microscope- and fiber optic probe-based Raman systems and tested whether correlations between RS and fracture toughness properties were statistically significant. Calculated directly from intensities at wavenumbers identified by second derivative analysis, Amide I sub-peak ratio I1670/I1640, not I1670/I1690, was negatively correlated with Kinit (N = 58; R2 = 32.4%) and J-integral (R2 = 47.4%) when assessed by Raman micro-spectroscopy. Area ratios (A1670/A1690) determined from sub-band fitting did not correlate with fracture toughness. There were fewer correlations between RS and fracture toughness when spectra were acquired by probe RS. Nonetheless, the I1670/I1640 sub-peak ratio again negatively correlated with Kinit (N = 56; R2 = 25.6%) and J-integral (R2 = 39.0%). In best-fit general linear models, I1670/I1640, age, and volumetric bone mineral density explained 50.2% (microscope) and 49.4% (probe) of the variance in Kinit. I1670/I1640 and v1PO4/Amide I (microscope) or just I1670/I1640 (probe) were negative predictors of J-integral (adjusted-R2 = 54.9% or 37.9%, respectively). While Raman-derived matrix properties appear useful to the assessment of fracture resistance of bone, the acquisition strategy to resolve the Amide I band needs to be identified.
Combining patch-clamping and fluorescence microscopy for quantitative reconstitution of cellular membrane processes with Giant Suspended Bilayers
Authors: Velasco-Olmo Ariana , Ormaetxea Gisasola Julene , Martinez Galvez Juan Manuel , Vera Lillo Javier , Shnyrova Anna V.
Published: May 2019

In vitro reconstitution and microscopic visualization of membrane processes is an indispensable source of information about a cellular function. Here we describe a conceptionally novel free-standing membrane template that facilitates such quantitative reconstitution of membrane remodelling at different scales. The Giant Suspended Bilayers (GSBs) spontaneously swell from lipid lamella reservoir deposited on microspheres. GSBs attached to the reservoir can be prepared from virtually any lipid composition following a fast procedure. Giant unilamellar vesicles can be further obtained by GSB detachment from the microspheres. The reservoir stabilizes GSB during deformations, mechanical micromanipulations, and fluorescence microscopy observations, while GSB-reservoir boundary enables the exchange of small solutes with GSB interior. These unique properties allow studying macro- and nano-scale membrane deformations, adding membrane-active compounds to both sides of GSB membrane and applying patch-clamp based approaches, thus making GSB a versatile tool for reconstitution and quantification of cellular membrane trafficking events.
Magnitude and reasons for pre-diagnosis attrition among presumptive multi-drug resistant tuberculosis patients in Bago Region, Myanmar: A mixed methods study
Authors: Oo Tun , Kyaw Khine Wut Yee , Soe Kyaw Thu , Saw Saw , Satyanarayana Srinath , Aung Si Thu
Published: May 2019

In Myanmar, Rifampicin resistant tuberculosis (RR-TB, a proxy for Multi-drug resistant TB) case detection is very low. Our study objectives were to assess the proportion of eligible TB patients who had not undergone RR-TB testing (Xpert-MTB/Rif tests) in Bago Region, Myanmar and to understand the reasons and solutions for non-testing. We conducted a mixed-methods study involving analysis of routinely collected programme data followed by key informant interviews (KIIs) with 32 health care providers. From October 2016 to March 2017, of the 2,331 eligible patients, 1,066 (46%) had not undergone Xpert-MTB/Rif testing. Patients from townships without Xpert-MTB/Rif testing facilities, new TB patients, patients whose HIV status was negative or unknown and extra pulmonary TB patients were less likely to undergo Xpert-MTB/Rif testing. From the health care providers’ perspective, the most common reasons for non-testing were: (a) lack of awareness of the eligibility criteria; (b) difficulties in collecting sputum and transportation from eligible patients to the testing sites. We conclude that nearly half of eligible patients were not tested for RR-TB. Training of health care providers about the latest eligibility criteria and improvement in sputum collection and transportation systems particularly for townships without Xpert-MTB/Rif testing facilities are required to improve RR-TB testing.
Functional duplication of Rap1 in methylotrophic yeasts
Authors: Malyavko Alexander N. , Petrova Olga A. , Zvereva Maria I. , Dontsova Olga A.
Published: May 2019

The telomere regulator and transcription factor Rap1 is the only telomere protein conserved in yeasts and mammals. Its functional repertoire in budding yeasts is a particularly interesting field for investigation, given the high evolutionary diversity of this group of unicellular organisms. In the methylotrophic thermotolerant speciesHansenula polymorphaDL-1 the RAP1 gene is duplicated (HpRAP1A and HpRAP1B). Here, we report the functional characterization of the two paralogues fromH.polymorphaDL-1. We uncover distinct (but overlapping) DNA binding preferences of HpRap1A and HpRap1B proteins. We show that only HpRap1B is able to recognize telomeric DNA directly and to protect it from excessive recombination, whereas HpRap1A is associated with subtelomere regions. Furthermore, we identify specific binding sites for both HpRap1A and HpRap1B within promoters of a large number of ribosomal protein genes (RPGs), implicating Rap1 in the control of the RP regulon inH.polymorpha. Our bioinformatic analysis suggests that RAP1 was duplicated early in the evolution of the “methylotrophs” clade, and the two genes evolved independently. Therefore, our characterization of Rap1 paralogues inH.polymorphamay be relevant to other “methylotrophs”, yielding valuable insights into the evolution of budding yeasts.
Statistical Properties and Predictability of Extreme Epileptic Events
Authors: Frolov Nikita S. , Grubov Vadim V. , Maksimenko Vladimir A. , Lüttjohann Annika , Makarov Vladimir V. , Pavlov Alexey N. , Sitnikova Evgenia , Pisarchik Alexander N. , Kurths Jürgen , Hramov Alexander E.
Published: May 2019

The use of extreme events theory for the analysis of spontaneous epileptic brain activity is a relevant multidisciplinary problem. It allows deeper understanding of pathological brain functioning and unraveling mechanisms underlying the epileptic seizure emergence along with its predictability. The latter is a desired goal in epileptology which might open the way for new therapies to control and prevent epileptic attacks. With this goal in mind, we applied the extreme event theory for studying statistical properties of electroencephalographic (EEG) recordings of WAG/Rij rats with genetic predisposition to absence epilepsy. Our approach allowed us to reveal extreme events inherent in this pathological spiking activity, highly pronounced in a particular frequency range. The return interval analysis showed that the epileptic seizures exhibit a highly-structural behavior during the active phase of the spiking activity. Obtained results evidenced a possibility for early (up to 7 s) prediction of epileptic seizures based on consideration of EEG statistical properties.
Metamaterial emitter for thermophotovoltaics stable up to 1400 °C
Authors: Chirumamilla Manohar , Krishnamurthy Gnanavel Vaidhyanathan , Knopp Katrin , Krekeler Tobias , Graf Matthias , Jalas Dirk , Ritter Martin , Störmer Michael , Petrov Alexander Yu , Eich Manfred
Published: May 2019

High temperature stable selective emitters can significantly increase efficiency and radiative power in thermophotovoltaic (TPV) systems. However, optical properties of structured emitters reported so far degrade at temperatures approaching 1200 °C due to various degradation mechanisms. We have realized a 1D structured emitter based on a sputtered W-HfO2 layered metamaterial and demonstrated desired band edge spectral properties at 1400 °C. To the best of our knowledge the temperature of 1400 °C is the highest reported for a structured emitter, so far. The spatial confinement and absence of edges stabilizes the W-HfO2 multilayer system to temperatures unprecedented for other nanoscaled W-structures. Only when this confinement is broken W starts to show the well-known self-diffusion behavior transforming to spherical shaped W-islands. We further show that the oxidation of W by atmospheric oxygen could be prevented by reducing the vacuum pressure below 10−5 mbar. When oxidation is mitigated we observe that the 20 nm spatially confined W films survive temperatures up to 1400 °C. The demonstrated thermal stability is limited by grain growth in HfO2, which leads to a rupture of the W-layers, thus, to a degradation of the multilayer system at 1450 °C.
A Systematic Review of the Clinical Efficacy and Safety of CFTR Modulators in Cystic Fibrosis
Authors: Habib Al-Rahim R. , Kajbafzadeh Majid , Desai Sameer , Yang Connie L. , Skolnik Kate , Quon Bradley S.
Published: May 2019

Several placebo-controlled trials have been recently published evaluating novel therapies targeting the defective CFTR protein. This systematic review examines the clinical efficacy and safety of CFTR modulators in individuals with cystic fibrosis (CF) with specific genetic mutations. Online sources were searched for placebo-controlled, parallel-design clinical trials investigating CFTR modulators from January 1, 2005 to March 31, 2018. The primary outcome of interest was FEV1% predicted (ppFEV1). Fourteen RCTs met our eligibility criteria. The largest improvement in ppFEV1 favouring treatment was observed for ivacaftor (IVA) in G551D individuals (≥6 years old). Both tezacaftor-ivacaftor (TEZ-IVA) and lumacaftor-ivacaftor (LUM-IVA) also improved ppFEV1 in F508del homozygous individuals but there was increased reporting of respiratory adverse events with LUM-IVA compared to placebo. IVA also significantly improved ppFEV1 in a sub-group of individuals ≥18 years old with an R117H mutation. No significant improvements in ppFEV1 were observed for IVA, LUM, or TEZ in F508del homozygous individuals, LUM or LUM-IVA in F508del heterozygous individuals, or ataluren in individuals with a nonsense mutation. Significant improvements in ppFEV1 and other clinical outcomes were observed for IVA in G551D individuals, TEV-IVA and LUM-IVA in F508del homozygous individuals, and IVA in adults with a R117H mutation.