bluuebunny/crossref_metadata_2025 huggingface dataset:
Swimming, gliding, and rolling toward the mainstream: cell biology of marine protists
Authors: Collier Jackie L. , Rest Joshua S.
Published: May 2019

Marine protists are a polyphyletic group of organisms playing major roles in the ecology and biogeochemistry of the oceans, including performing much of Earth’s photosynthesis and driving the carbon, nitrogen, and silicon cycles. In addition, marine protists occupy key positions in the tree of life, including as the closest relatives of metazoans. Despite all the reasons to better understand them, knowledge of the cell biology of most marine protist lineages is sparse. This is beginning to change thanks to vibrant growth in the development of new model organisms. Here, we survey some recent advances in studying the cell biology of marine protists toward understanding the functional basis of their unique features, gaining new perspectives on universal eukaryotic biology, and for understanding homologous biology within metazoans and the evolution of metazoan traits.
Toward Unsettling Histories of Domesticity
Authors: Burton Antoinette
Published: May 2019

In this response to the roundtable, Burton emphasizes the unsettled and unsettling character of domesticity and challenges facile definitions of its global history. She offers ways of reading the essays in pairs, backwards and forwards in time, and together as a kind of prospective course syllabus.
A 3-Dimensional Quantitative Analysis of Volume Loss Following Submental Cryolipolysis
Authors: Jain Mohit , Savage Nicholas E , Spiteri Kelly , Snell Broughton J
Published: May 2019

Background

Cryolipolysis is a proven and effective means of fat reduction; however, there are no standardized means of measuring volume reduction.

Objectives

We aim to assess the volume loss using a 3-dimensional (3D) analysis following submental cryolipolysis.

Methods

A retrospective cohort study between April 2016 and August 2018 was performed. Thirty-five patients underwent a single 45-minute cycle of cryolipolysis to the submental region using the CoolSculpting System. A 3-fold analysis was performed employing an independent observer assessment of 2-dimensional photographs and 3D volumetric analysis utilizing the Vectra XT system, and patient satisfaction was measured with the FACE-Q questionnaire.

Results

Our results suggested the mean (standard deviation) pretreatment volume (n = 35) was 104.12 cm3 (28.78). The 6-week mean posttreatment volume (n = 26) was 81.55 cm3 (21.29). The mean volume reduction found at 6 weeks posttreatment showed a reduction of 22.46 cm3 (19.10) (95% CI 14.74 to 30.17, P < 0.0001). The 12-week mean posttreatment volume (n = 24) was 82.24 cm3 (23.97). The 12-week posttreatment demonstrated a reduction of 22.30 cm3 (14.04) (95% CI 16.37 to 28.23, P < 0.0001). The mean percentage correct for each reviewer correctly identifying the pretreatment and posttreatment photograph was 76.33% (7.14). Patient satisfaction showed a mean FACE-Q score of 54.10 (20.41).

Conclusions

The study further affirms that submental cryolipolysis is an efficacious and safe, noninvasive method for reducing submental adiposity resulting in notable patient satisfaction rates. Furthermore, results suggest that patients can have a volume loss of about 20% on average, allowing them to be more confident and comfortable with their appearance.

Level of Evidence: 4
C-InterSecture—a computational tool for interspecies comparison of genome architecture
Authors: Nuriddinov M , Fishman V
Published: May 2019

Motivation

Recent development of Hi-C technique, a biochemical method to study 3D genome architecture, provided large amount of information describing spatial organization of chromosomes in different cell types and species. While multiple tools are available for analysis and comparison of Hi-C data of different cell types, there are almost no resources for systematic interspecies comparison.

Results

To fill this gap, we developed C-InterSecture, a computational pipeline allowing systematic comparison of genome architecture between species. C-InterSecture allows statistical comparison of contact frequencies of individual pairs of loci, as well as interspecies comparison of contacts pattern within defined genomic regions, i.e. topologically associated domains. We employed C-InterSecture to compare mammalian and avian genome organization and showed how evolutionary changes of genomic distance affect 3D architecture of vertebrate’s genome.

Availability and implementation

C-InterSecture is implemented as a collection of python scripts freely available on GitHub repository at https://github.com/NuriddinovMA/C-InterSecture. Jucebox-compatible .hic files produced by C-InterSecture are available at http://genedev.bionet.nsc.ru/site/CIntersecture.html.

Supplementary information

Supplementary data are available at Bioinformatics online.
SPar-K: a method to partition NGS signal data
Authors: Groux Romain , Bucher Philipp
Published: May 2019

We present SPar-K (Signal Partitioning with K-means), a method to search for archetypical chromatin architectures by partitioning a set of genomic regions characterized by chromatin signal profiles around ChIP-seq peaks and other kinds of functional sites. This method efficiently deals with problems of data heterogeneity, limited misalignment of anchor points and unknown orientation of asymmetric patterns.

Availability and implementation

SPar-K is a C++ program available on GitHub https://github.com/romaingroux/SPar-K and Docker Hub https://hub.docker.com/r/rgroux/spar-k.

Supplementary information

Supplementary data are available at Bioinformatics online.
Environmental Variables Influencing Chironomid Assemblages (Diptera: Chironomidae) in Lowland Rivers of Central Poland
Authors: Leszczyńska Joanna , Grzybkowska Maria , Głowacki Łukasz , Dukowska Małgorzata
Published: May 2019

Chironomids (Diptera: Chironomidae) are a family of dipterans with a global distribution. Owing to their great functional diversity and ability to adapt to a wide range of environmental conditions, they often dominate in freshwater macroinvertebrate communities, playing a key role in the cycling of organic matter and the flow of energy in aquatic ecosystems. Our aim was to analyze the structure of chironomid assemblages and identify the environmental factors, including current velocity, river width, water depth, water temperature, dissolved oxygen, percentage of substrate covered by vascular plants, inorganic bottom substrate, and quantity of benthic (BPOM) and transported (TPOM) particulate organic matter, that underpin variation in species richness across a set of lowland rivers in central Poland, differing by stream order and abiotic parameters. Using an Information Theoretic Approach, we formulated a set of alternative models based on previously published work, with models fitted in a Bayesian framework using Integrated Nested Laplace Approximation. The species richness of chironomids increased with river order, achieving a maximum in third and fourth order rivers, but decreased at higher orders. The best-fitting models included a positive effect of inorganic substrate index and dissolved oxygen on chironomid species richness. The quality structure of chironomid assemblages reflected the assumptions of the River Continuum Concept showing that species richness was under the influence of factors operating at both a micro- (inorganic bottom substrate) and macro-scale (dissolved oxygen).
Study on the mantle discontinuity structures beneath Northeast China with time–frequency phase-weighted stacks of ambient noise correlations
Authors: Li Songlin , Huang Jinli , Liu Zhikun , Zhang Yi
Published: May 2019

In this study, we use continuous waveforms recorded by 258 seismic stations from permanent and temporary networks in Northeast China from September 2009 to August 2011. Using ambient noise cross-correlations and time–frequency phase-weighted stacking based on the S-transform, we retrieve the P waves reflected on 410-km and 660-km discontinuities, we employ a 3-D P-wave velocity model as references to make time–depth conversion and then obtain the lateral depth variations of the two mantle discontinuities. Our results show that beneath the Changbaishan volcano, the 410-km discontinuity is depressed and is relatively thin, indicating the presence of high-temperature materials above the discontinuity. This implies that the Changbaishan volcano formed by upwelling of mantle melting associated with dehydration of the subducting Pacific slab. In the southeast margin of the study region, the 660-km discontinuity is depressed by ∼21 km, indicating the existence of low-temperature materials above the discontinuity. These results support the hypothesis that the Pacific slab has subducted beneath Northeast China and has stagnated at the bottom of the mantle transition zone. In addition, we determine that the 660-km discontinuity at 123.6°E–126.2°E, to the west of this stagnant slab, is slightly uplifted at a small scale, which may have been caused by upwelling melting formed by vertical tearing of the stagnant slab. Moreover, we preliminarily investigate the discontinuities beneath the northern part of the study region. The results show that the 410-km discontinuity is significantly depressed beneath the northeastern margin of the study region, which we attribute to reflected P-wave signals on the boundary between hydrous and anhydrous wadsleyite. The large-scale depression of the 660-km discontinuity observed beneath the northeastern part of the study region may be related to the existence of the stagnant slab.
Advancing perspectives on health literacy in childhood and youth
Authors: Bröder Janine , Okan Orkan , Bauer Ullrich , Schlupp Sandra , Pinheiro Paulo
Published: May 2019

Children and young people’s importance as core target population for health literacy has been highlighted throughout the literature due to the relevance of the early life phases for maintaining, restoring and promoting health during the life course. Transferring health literacy concepts to the target population, however, requires proper testing of their applicability and their fit to the developmental phases as well as the target populations’ realities and needs. This article aims to discuss children’s and young people’s health literacy by elaborating and exploring childhood and youth as life phases with unique characteristics from multidisciplinary perspectives. Drawing on theories and findings from developmental studies, sociology and socialization research, health literacy in childhood and youth is discussed along five ‘D’ dimensions: (i) disease patterns and health perspectives, (ii) demographic patterns, (iii) developmental change, (iv) dependency and (v) democracy. The unique particularities of children and young people relevant for health literacy include their disease and health-risk profiles, their vulnerability to demographic factors, their social role and status, and their right to participation. Inter- and intra-generational relationships and an unequal distribution of power can either promote or hinder children and young people’s health literacy development and their opportunities for participating in health-related decision making. Specifying what is called the ‘contextual’ and ‘relational’ dimension of health literacy for the target group requires considering their personal attributes and agency as contextually embedded and interrelated. Taking these considerations into account can help to move towards a more tailored and holistic approach to health literacy of children and young people.
Static Scaling and the Evolution of Extreme Canine Size in a Saber-Toothed Cat (Smilodon fatalis)
Authors: O’Brien D M
Published: May 2019

The canines of saber-toothed cats are a classic example of an extreme morphology, yet important questions pertaining to their evolution remain unanswered. Recent analyses suggest these structures functioned as tools of intrasexual combat where trait size acts as both a weapon of battle and signal of competitive ability. However, classic skeletal reconstructions suggest saber-tooth canines evolved as specialized hunting tools. Either scenario could have led to the evolution of extreme canine size and distinguishing between these hypotheses is therefore difficult. This is made more challenging by the fact that natural observation of saber-toothed cats is impossible, and biologists must rely on measures of static morphology to study the patterns of selection that favored extreme canine size. Here I analyze the static intraspecific scaling relationship between canine size and body size in the saber-toothed cat, Smilodon fatalis, to determine whether or not extreme canine size functioned as a sexually selected signal. I review the literature surrounding the evolution of sexually selected signals and the methods recently established by O’Brien et al. (2018), show how static scaling relationships can be useful, reliable tools for inferring patterns of selection, especially in fossil organisms, and provide evidence that extreme canine size in saber-toothed cats was not the product of selection for effective sexual signals, but instead evolved as either a pure intrasexually selected weapon or a hunting tool.
Competition, self-organization, and social scaling—accounting for the observed distributions of Tobin’s q
Authors: dos Santos Paulo L , Scharfenaker Ellis
Published: May 2019

We develop a systemic, information-theoretic model of competitive capital-market functioning that can account for the observed statistical regularities in cross-sectional distributions of the logarithm of Tobin’s q for US non-financial corporations since 1962. The model considers capital markets as a self-organizing system driven by competitive interactions among investors and corporate managers. The persistent pattern of organization we observe in those distributions is primarily defined by the efforts of corporate managers to appropriate arbitrage capital gains defined by heterogeneity across individual measures of the logarithm of Tobin’s q. Competition ensures the structures of security prices shaped by those efforts reflect an aggregate tradeoff between the gross returns and costs they pose to corporate managers. The distributions are also influenced by the endogenous, competitive formation of the opportunity cost of capital corporations face, which is conditioned by what investors come to expect to be a typical or general expected rate of return on assets across all corporations. In addition to offering an economic account of what we observe, the resulting framework defines new conceptualizations and aggregate measures of the informational and allocative performance of capital markets. Those suggest the performance of US capital markets has deteriorated since the 1980s.
A mathematical model of HIV dynamics treated with a population of gene-edited haematopoietic progenitor cells exhibiting threshold phenomenon
Authors: Ratti Vardayani , Nanda Seema , Eszterhas Susan K , Howell Alexandra L , Wallace Dorothy I
Published: May 2019

The use of gene-editing technology has the potential to excise the CCR5 gene from haematopoietic progenitor cells, rendering their differentiated CD4-positive (CD4+) T cell descendants HIV resistant. In this manuscript, we describe the development of a mathematical model to mimic the therapeutic potential of gene editing of haematopoietic progenitor cells to produce a class of HIV-resistant CD4+ T cells. We define the requirements for the permanent suppression of viral infection using gene editing as a novel therapeutic approach. We develop non-linear ordinary differential equation models to replicate HIV production in an infected host, incorporating the most appropriate aspects found in the many existing clinical models of HIV infection, and extend this model to include compartments representing HIV-resistant immune cells. Through an analysis of model equilibria and stability and computation of $R_0$ for both treated and untreated infections, we show that the proposed therapy has the potential to suppress HIV infection indefinitely and return CD4+ T cell counts to normal levels. A computational study for this treatment shows the potential for a successful ‘functional cure’ of HIV. A sensitivity analysis illustrates the consistency of numerical results with theoretical results and highlights the parameters requiring better biological justification. Simulations of varying level production of HIV-resistant CD4+ T cells and varying immune enhancements as the result of these indicate a clear threshold response of the model and a range of treatment parameters resulting in a return to normal CD4+ T cell counts.
Immunogenicity, Lot Consistency, and Extended Safety of rVSVΔG-ZEBOV-GP Vaccine: A Phase 3 Randomized, Double-Blind, Placebo-Controlled Study in Healthy Adults
Authors: Halperin Scott A , Das Rituparna , Onorato Matthew T , Liu Kenneth , Martin Jason , Grant-Klein Rebecca J , Nichols Rick , Coller Beth-Ann , Helmond Frans A , Simon Jakub K
Published: May 2019

Background

This double-blind study assessed immunogenicity, lot consistency, and safety of recombinant vesicular stomatitis virus-Zaire Ebola virus envelope glycoprotein vaccine (rVSVΔG-ZEBOV-GP).

Methods

Healthy adults (N = 1197) were randomized 2:2:2:2:1 to receive 1 of 3 consistency lots of rVSVΔG-ZEBOV-GP (2 × 107 plaque-forming units [pfu]), high-dose 1 × 108 pfu, or placebo. Antibody responses pre-/postvaccination (28 days, 6 months; in a subset [n = 566], months 12, 18, and 24) were measured. post hoc analysis of risk factors associated with arthritis following vaccination was performed.

Results

ZEBOV-GP enzyme-linked immunosorbent assay (ELISA) geometric mean titers (GMTs) increased postvaccination in all rVSVΔG-ZEBOV-GP groups by 28 days (>58-fold) and persisted through 24 months. The 3 manufacturing lots demonstrated equivalent immunogenicity at 28 days. Neutralizing antibody GMTs increased by 28 days in all rVSVΔG-ZEBOV-GP groups, peaking at 18 months with no decrease through 24 months. At 28 days, ≥94% of vaccine recipients seroresponded (ZEBOV-GP ELISA, ≥2-fold increase, titer ≥200 EU/mL), with responses persisting at 24 months in ≥91%. Female sex and a history of arthritis were identified as potential risk factors for the development of arthritis postvaccination.

Conclusions

Immune responses to rVSVΔG-ZEBOV-GP persisted to 24 months. Immunogenicity and safety results support continued rVSVΔG-ZEBOV-GP development.

Clinical Trials Registration

NCT02503202.
Serial monitoring of isavuconazole blood levels during prolonged antifungal therapy
Authors: Furfaro E , Signori A , Di Grazia C , Dominietto A , Raiola A M , Aquino S , Ghiggi C , Ghiso A , Ungaro R , Angelucci E , Viscoli C , Mikulska M
Published: May 2019

Background

Isavuconazole is the newest triazole antifungal approved for the treatment of invasive aspergillosis (IA) and invasive mucormycosis in adult patients.

Objectives

To characterize the assessment of the blood levels of isavuconazole and their association with efficacy and toxicity.

Methods

From January 2017 to May 2018, blood samples obtained from patients receiving isavuconazole were analysed for therapeutic drug monitoring. Factors influencing the blood concentrations of isavuconazole, such as weight, length of treatment, route of administration and results of selected liver function tests, were analysed in univariate and multivariate models. The receiver operating characteristic (ROC) curve was analysed to detect the best cut-off for isavuconazole toxicity.

Results

A total of 264 isavuconazole blood concentrations in 19 patients were analysed. The median value of isavuconazole concentration in all patients during the first 30 days of therapy was 3.69 mg/L (range 0.64–8.13 mg/L). A linear increase of 0.032 mg/L (range 0.023–0.041 mg/L) for each day of treatment (P = 0.002) was observed. In multivariate analysis the association between the length of treatment and higher levels of isavuconazole (P < 0.001) and higher serum GGT and lower isavuconazole levels (P = 0.001) was confirmed. Adverse events, mainly gastrointestinal, were reported in six patients (31.6%). Based on time-dependent and fixed-time ROC curve analysis, 4.87 mg/L and 5.13 mg/L, respectively, were the identified thresholds for toxicity.

Conclusions

Isavuconazole was efficacious and well tolerated. Side effects, mainly gastrointestinal, were associated with prolonged administration and high serum levels.
Identifying vulnerable older adult populations by contextualizing geriatric syndrome information in clinical notes of electronic health records
Authors: Chen Tao , Dredze Mark , Weiner Jonathan P , Kharrazi Hadi
Published: May 2019

Objective

Geriatric syndromes such as functional disability and lack of social support are often not encoded in electronic health records (EHRs), thus obscuring the identification of vulnerable older adults in need of additional medical and social services. In this study, we automatically identify vulnerable older adult patients with geriatric syndrome based on clinical notes extracted from an EHR system, and demonstrate how contextual information can improve the process.

Materials and Methods

We propose a novel end-to-end neural architecture to identify sentences that contain geriatric syndromes. Our model learns a representation of the sentence and augments it with contextual information: surrounding sentences, the entire clinical document, and the diagnosis codes associated with the document. We trained our system on annotated notes from 85 patients, tuned the model on another 50 patients, and evaluated its performance on the rest, 50 patients.

Results

Contextual information improved classification, with the most effective context coming from the surrounding sentences. At sentence level, our best performing model achieved a micro-F1 of 0.605, significantly outperforming context-free baselines. At patient level, our best model achieved a micro-F1 of 0.843.

Discussion

Our solution can be used to expand the identification of vulnerable older adults with geriatric syndromes. Since functional and social factors are often not captured by diagnosis codes in EHRs, the automatic identification of the geriatric syndrome can reduce disparities by ensuring consistent care across the older adult population.

Conclusion

EHR free-text can be used to identify vulnerable older adults with a range of geriatric syndromes.
Effect of Sex and Air Temperature on the Flight Capacity of Bradysia odoriphaga (Diptera: Sciaridae)
Authors: Hu Jing-rong , Xie Chao , Shi Cai-hua , Wang Shao-li , Wu Qing-jun , Li Chuan-ren , Zhang You-jun
Published: May 2019

Bradysia odoriphaga Yang & Zhang (Diptera: Sciaridae) is an important pest of Chinese chives. Information on the effects of biotic and abiotic factors on the flight performance of B. odoriphaga is crucial for understanding the pest’s ability to disperse and migrate. In this study, the effects of sex and air temperature on the flight performance of B. odoriphaga imagoes were assessed by tethering individual imagoes to computerized flight mills for a 10-h experiment. The results showed that the percentage of imagoes that flew a particular distance gradually decreased as flight distance increased. The percentage of imagoes was significantly higher for males than females when the flight distance was <300 m. Sex and air temperature significantly affected average flight time (which ranged from 14.6 to 68.3 min) and average flight distance (which ranged from 10.4 to 107.2 m), but did not significantly affect average flight speed (which ranged from 3.8 to 6.4 m/min). For both females and males, the average flight distance and flight time were shortest at 18°C and longest at 22°C; the interaction between air temperature and sex was not significant. The results suggest that B. odoriphaga has a poor potential for long-distance migration. These findings will be helpful for developing forecasting and management systems for B. odoriphaga.
The Interplay between ‘Abhyudaya’ and ‘Niḥśreyasa’ in Vaiśeṣika System
Authors: Moise Ionut
Published: May 2019

In the second half of the first millennium AD, Vaiśeṣika system undergoes a process of synthesis, articulated by the development of the doctrine of dharma under which umbrella, two contrasting views on ‘salvation’ abhyudaya (possibly Vedic) and niḥśreyasa (Upaniṣadic) come to be explained as implying each other. The doctrine of salvation in Vaiśeṣika is a static state, devoid of change, and is indeed defined with niḥśreyasa (mokṣa), but because it is determined by a particular dharma as Candrānanda says [Vaiśeṣikasūtras with Candrānanda’s Vṛtti (VSc) 6.2.11; VSc 1.1.2], it comes to be seen as not exclusively removed from the necessity of action, be it ethical or karmic, which are so much the domain of abhyudaya (VSc 1.1.2; 1.1.6). It seems that the system’s soteriology expands as to include not only the renouncer’s acts, but also worldly ones, hence abhyudaya becomes preliminary to niḥśreyasa.
The First Molecular and Phenotypic Characterization of the Invasive Population of Aedes albopictus (Diptera: Culicidae) from the Central Balkans
Authors: Gojković Nemanja , Ludoški Jasmina , Krtinić Bosiljka , Milankov Vesna
Published: May 2019

Aedes (Stegomya) albopictus (Skuse 1984), the Asian tiger mosquito, represents the most invasive and one of the medically most important mosquito vectors. Although native to South East Asia, the species has recently spread globally, and was registered in the city of Novi Sad (Serbia, Central Balkans) in August 2018. We characterized the invasive population using phenotypic (wing size and shape) and molecular (nuclear, internal transcribed spacer 2- ITS2, and mitochondrial, cytochrome c oxidase subunit I- COI) markers. The results of phenotypic analyses indicated that the Serbian population could be differentiated from the native (Thailand) and invasive (Hawaii and Florida) populations due to restricted gene flow, founder effect, and supposed different strain origin. The Serbian population showed genetic homogeneity, indicative of a small founder number (bottleneck invasion model). Despite the incorporation of ITS2 GenBank sequences into the data set, neither spatial (Geneland) nor nonspatial (BAPS) genetic structuring analyses helped infer the Serbian population origin. However, the comparison of the retrieved COI haplotype with previously characterized mitogenomes indicated a temperate strain origin, capable of overwintering. Such findings suggest that the newly registered Ae. albopictus population could be able to establish itself since previous studies outlined Novi Sad as a suitable area.
Smoking, Alcohol, and Biliary Tract Cancer Risk: A Pooling Project of 26 Prospective Studies
Authors: McGee Emma E , Jackson Sarah S , Petrick Jessica L , Van Dyke Alison L , Adami Hans-Olov , Albanes Demetrius , Andreotti Gabriella , Beane-Freeman Laura E , Berrington de Gonzalez Amy , Buring Julie E , Chan Andrew T , Chen Yu , Fraser Gary E , Freedman Neal D , Gao Yu-Tang , Gapstur Susan M , Gaziano J Michael , Giles Graham G , Grant Eric J , Grodstein Francine , Hartge Patricia , Jenab Mazda , Kitahara Cari M , Knutsen Synnove F , Koh Woon-Puay , Larsson Susanna C , Lee I-Min , Liao Linda M , Luo Juhua , Milne Roger L , Monroe Kristine R , Neuhouser Marian L , O’Brien Katie M , Peters Ulrike , Poynter Jenny N , Purdue Mark P , Robien Kim , Sandler Dale P , Sawada Norie , Schairer Catherine , Sesso Howard D , Simon Tracey G , Sinha Rashmi , Stolzenberg-Solomon Rachael , Tsugane Shoichiro , Wang Renwei , Weiderpass Elisabete , Weinstein Stephanie J , White Emily , Wolk Alicja , Yuan Jian-Min , Zeleniuch-Jacquotte Anne , Zhang Xuehong , Zhu Bin , McGlynn Katherine A , Campbell Peter T , Koshiol Jill
Published: May 2019

Background

Tobacco and alcohol are well-established risk factors for numerous cancers, yet their relationship to biliary tract cancers remains unclear.

Methods

We pooled data from 26 prospective studies to evaluate associations of cigarette smoking and alcohol consumption with biliary tract cancer risk. Study-specific hazard ratios (HRs) and 95% confidence intervals (CIs) for associations with smoking and alcohol consumption were calculated. Random-effects meta-analysis produced summary estimates. All statistical tests were two-sided.

Results

Over a period of 38 369 156 person-years of follow-up, 1391 gallbladder, 758 intrahepatic bile duct, 1208 extrahepatic bile duct, and 623 ampulla of Vater cancer cases were identified. Ever, former, and current smoking were associated with increased extrahepatic bile duct and ampulla of Vater cancers risk (eg, current vs never smokers HR = 1.69, 95% CI = 1.34 to 2.13 and 2.22, 95% CI = 1.69 to 2.92, respectively), with dose-response effects for smoking pack-years, duration, and intensity (all Ptrend < .01). Current smoking and smoking intensity were also associated with intrahepatic bile duct cancer (eg, >40 cigarettes per day vs never smokers HR = 2.15, 95 % CI = 1.15 to 4.00; Ptrend = .001). No convincing association was observed between smoking and gallbladder cancer. Alcohol consumption was only associated with intrahepatic bile duct cancer, with increased risk for individuals consuming five or more vs zero drinks per day (HR = 2.35, 95%CI = 1.46 to 3.78; Ptrend = .04). There was evidence of statistical heterogeneity among several cancer sites, particularly between gallbladder cancer and the other biliary tract cancers.

Conclusions

Smoking appears to increase the risk of developing all biliary tract cancers except gallbladder cancer. Alcohol may increase the risk of intrahepatic bile duct cancer. Findings highlight etiologic heterogeneity across the biliary tract.
Plugging the holes—new Canadian and US regulations to reduce upstream methane emissions
Authors: Ingelson Allan
Published: May 2019

In the USA and Canada where most of global shale oil and gas development has occurred, due to concerns about climate change the national governments have adopted new regulations to further significantly reduce national methane emissions from the upstream oil and gas industry. The 2016 US Environmental Protection Agency emissions standards and 2018 Canadian methane regulations build on decades old oil and gas conservation schemes to further reduce the volume of methane that is released from facility equipment leaks and venting. In Canada, venting methane at new oil and gas well sites is now prohibited. Operators are required to capture and use a much larger volume of natural gas than in the past. A negotiated settlement of the first US emissions reduction enforcement action was reached in April 2018. The facility operator agreed to pay a civil penalty of US $610,000 and spend a minimum of $2 million to install new technology at its facilities to further reduce methane emissions. The creative settlement agreement contains a comprehensive set of conditions to provide for a reduction in upstream industry emissions.
Current approaches to measure nitric oxide in plants
Authors: Vishwakarma Abhaypratap , Wany Aakanksha , Pandey Sonika , Bulle Mallesham , Kumari Aprajita , Kishorekumar Reddy , Igamberdiev Abir U , Mur Luis A J , Gupta Kapuganti Jagadis
Published: May 2019

Nitric oxide (NO) is now established as an important signalling molecule in plants where it influences growth, development, and responses to stress. Despite extensive research, the most appropriate methods to measure and localize these signalling radicals are debated and still need investigation. Many confounding factors such as the presence of other reactive intermediates, scavenging enzymes, and compartmentation influence how accurately each can be measured. Further, these signalling radicals have short half-lives ranging from seconds to minutes based on the cellular redox condition. Hence, it is necessary to use sensitive and specific methods in order to understand the contribution of each signalling molecule to various biological processes. In this review, we summarize the current knowledge on NO measurement in plant samples, via various methods. We also discuss advantages, limitations, and wider applications of each method.
S-Alk(en)ylcysteine sulfoxides in the genus Allium: proposed biosynthesis, chemical conversion, and bioactivities
Authors: Yoshimoto Naoko , Saito Kazuki
Published: May 2019

S-Alk(en)ylcysteine sulfoxides are sulfur-containing natural products characteristic of the genus Allium. Both the flavor and medicinal properties of Allium plants are attributed to a wide variety of sulfur-containing compounds that are generated from S-alk(en)ylcysteine sulfoxides. Previous radiotracer experiments proposed that S-alk(en)ylcysteine sulfoxides are biosynthesized from glutathione. The recent identification of γ-glutamyl transpeptidases and a flavin-containing S-oxygenase involved in the biosynthesis of S-allylcysteine sulfoxide (alliin) in garlic (Allium sativum) provided insights into the reaction order of deglutamylation and S-oxygenation together with the localization of the biosynthesis, although the rest of the enzymes in the pathway still await discovery. In intact plants, S-alk(en)ylcysteine sulfoxides are stored in the cytosol of storage mesophyll cells. During tissue damage, the vacuolar enzyme alliinase contacts and hydrolyzes S-alk(en)ylcysteine sulfoxides to produce the corresponding sulfenic acids, which are further converted into various sulfur-containing bioactive compounds mainly via spontaneous reactions. The formed sulfur-containing compounds exhibit bioactivities related to pathogen defense, the prevention and alleviation of cancer and cardiovascular diseases, and neuroprotection. This review summarizes the current understanding of the occurrence, biosynthesis, and alliinase-triggered chemical conversion of S-alk(en)ylcysteine sulfoxides in Allium plants as well as the impact of S-alk(en)ylcysteine sulfoxides and their derivatives on medicinal, food, and agricultural sciences.
Gene expression changes in human bronchial epithelial cells (BEAS-2B) and human pulmonary alveolar epithelial cells (HPAEpiC) after interaction with Cladosporium sphaerospermum
Authors: Lo Sing Gee , Wong Shew Fung , Mak Joon Wah , Choo Khi Khi , Ng Kee Peng
Published: May 2019

Cladosporium is one of the most abundant spore. Fungi of this genus can cause respiratory allergy and intrabronchial lesion. We studied the differential expression of host genes after the interaction of Cladosporium sphaerospermum conidia with Human Bronchial Epithelial Cells (BEAS-2B) and Human Pulmonary Alveolar Epithelial Cells (HPAEpiC). C. sphaerospermum conidia were harvested and co-cultured with BEAS-2B cells or HPAEpiC cells for 48 hours respectively. This culture duration was chosen as it was associated with high germination rate. RNA was extracted from two biological replicates per treatment. RNA of BEAS-2B cells was used to assess changes in gene expression using AffymetrixGeneChip® Human Transcriptome Array 2.0. After co-culture with Cladosporium spores, 68 individual genes were found differentially expressed (P ≤ 0.05) and up-regulated ≥ 1.5 folds while 75 genes were found differentially expressed at ≤ −1.5 folds compared with controls. Reverse transcription and qPCR were performed on the RNA collected from both BEAS-2B cells and HPAEpiC cells to validate the microarray results with 7 genes. Based on the findings, infected pulmonary epithelial cells exhibited an increase in cell death-related genes and genes associated with innate immunity.
Characterizing stellar parameters from high-resolution spectra of main sequence cool stars. I. The G2V–K2V stars
Authors: Kulenthirarajah Logithan , Donati Jean-François , Hussain Gaitee , Morin Julien , Allard France
Published: May 2019

The goal of the present study is to construct, test, and validate a high-resolution synthetic spectral library using PHOENIX model atmospheres and develop a reliable tool to estimate stellar parameters from high-resolution optical and/or near-infrared spectra of M dwarfs. We report here the preliminary results of tests characterizing main sequence G–K stars from high-resolution spectra. We anchored the atomic line-list using the stellar standards Sun, ξ Boo A, and ϵ Eri to ensure the synthetic spectra computed with PHOENIX reproduce their observed counterparts. These stars were chosen because their parameters are very well characterized, and on which the absolute accuracy of our method depends on.

We successfully estimated the stellar parameters with associated error bars for 17 stars. Using a pseudo Monte Carlo statistical analysis, we present overall improved uncertainties on the stellar parameters compared to those in the literature (on average 9 K, 0.014 dex, and 0.008 dex for the effective temperature, the surface gravity, and the metallicity, respectively). Our estimated stellar parameters are also in good agreement with values found in the literature.
Solving the γ-ray radiative transfer equation for supernovae
Authors: Wilk Kevin D , Hillier D John , Dessart Luc
Published: May 2019

We present a new relativistic radiative transfer code for γ-rays of energy less than 5 MeV in supernova (SN) ejecta. This code computes the opacities, the prompt emissivity (i.e. decay), and the scattering emissivity, and solves for the intensity in the co-moving frame. Because of the large expansion velocities of SN ejecta, we ignore redistribution effects associated with thermal motions. The energy deposition is calculated from the energy removed from the radiation field by scattering or photoelectric absorption. This new code yields comparable results to an independent Monte Carlo code. However, both yield non-trivial differences with the results from a pure absorption treatment of γ-ray transport. A synthetic observer’s frame spectrum is also produced from the co-moving frame intensity. At early times when the optical depth to γ-rays is large, the synthetic spectrum shows asymmetric line profiles with redshifted absorption as seen in SN 2014J. This new code is integrated within cmfgen and allows for an accurate and fast computation of the decay energy deposition in SN ejecta.
Constraints on magnetospheric radio emission from Y dwarfs
Authors: Kao Melodie M , Hallinan Gregg , Pineda J Sebastian
Published: May 2019

As a pilot study of magnetism in Y dwarfs, we have observed the three known infrared variable Y dwarfs WISE J085510.83−071442.5, WISE J140518.40+553421.4, and WISEP J173835.53+273258.9 with the NSF’s Karl G. Jansky Very Large Array in the 4–8 GHz frequency range. The aim was to investigate the presence of non-bursting quiescent radio emission as a proxy for highly circularly polarized radio emission associated with large-scale auroral currents. Measurements of magnetic fields on Y dwarfs may be possible by observing auroral radio emission, and such measurements are essential for constraining fully convective magnetic dynamo models. We do not detect any pulsed or quiescent radio emission, down to rms noise levels of 7.2 µJy for WISE J085510.83−071442.5, 2.2 µJy for WISE J140518.40+553421.4, and 3.2 µJy for WISEP J173835.53+273258.9. The fractional detection rate of radio emission from T dwarfs is ∼10 per cent suggesting that a much larger sample of deep observations of Y dwarfs is needed to rule out radio emission in the Y dwarf population. We discuss a framework that uses an empirical relationship between the auroral tracer Hα emission and quiescent radio emission to identify brown-dwarf auroral candidates. Finally, we discuss the implications that Y dwarf radio detections and non-detections can have for developing a picture of brown dwarf magnetism and auroral activity.
2StrucCompare: a webserver for visualizing small but noteworthy differences between protein tertiary structures through interrogation of the secondary structure content
Authors: Drew Elliot D , Janes Robert W
Published: May 2019

2StrucCompare is a webserver whose primary aim is to visualize subtle but functionally important differences between two related protein structures, either of the same protein or related homologues, with similar or functionally different tertiary structures. At the heart of the package is identifying and visualizing differences between conformations at the secondary structure and at the residue level, such as contact differences or side chain conformational differences found between two protein chains. The protein secondary structures are determined according to four established methods (DSSP, STRIDE, P-SEA and STICKS), and as each employs different assignment strategies, small conformational differences between the two structures can give rise to paired residues being denoted as having different secondary structure features with the different methods. 2StrucCompare captures both the large and more subtle differences found between structures, enabling visualization of these differences that could be key to an understanding of a proteins’ function.

2StrucCompare is freely accessible at http://2struccompare.cryst.bbk.ac.uk/index.php
On the 2-head of the colored Jones polynomial for pretzel knots
Authors: Beirne Paul
Published: May 2019

In this paper, we prove a formula for the 2-head of the colored Jones polynomial for an infinite family of pretzel knots. Following Hall, the proof utilizes skein-theoretic techniques and a careful examination of higher order stability properties for coefficients of the colored Jones polynomial.
Comparison of disease activity measures in early psoriatic arthritis in usual care
Authors: Wervers Kim , Luime Jolanda J , Tchetverikov Ilja , Gerards Andreas H , Kok Marc R , Appels Cathelijne W Y , van der Graaff Wiebo L , van Groenendael Johannes H L M , Korswagen Lindy-Anne , Veris-van Dieren Josien J , Hazes Johanna M W , Vis Marijn ,   for CICERO
Published: May 2019

Objectives

To compare responsiveness and longitudinal validity of Disease Activity Score 28 (DAS28), Disease Activity index for PSoriatic Arthritis (DAPSA), Composite Psoriatic Disease Activity Index (CPDAI), Psoriatic ArthritiS Disease Activity Score (PASDAS), GRAppa Composite scorE (GRACE) and Minimal Disease Activity (MDA) in usual care PsA patients, within 1 year after diagnosis.

Methods

Data collected in the Dutch southwest early PsA cohort (DEPAR) were used. Responsiveness was assessed using effect size (ES), standardized response mean (SRM), and discrimination between different general health states. Longitudinal validity was tested using mixed models with outcomes health-related quality of life (HRQOL), productivity and disability.

Results

Responsiveness was highest for PASDAS, with ES 1.00 and SRM 0.95, lowest for DAPSA, with ES 0.73 and SRM 0.71, and in between for DAS28, CPDAI and GRACE. Differences in general health were best discriminated with PASDAS and GRACE. Patients reporting stable or worsening general health could not be distinguished by DAS28 or CPDAI. Discrimination was better using DAPSA, but worse than when using PASDAS and GRACE. Longitudinal evolvement of HRQOL and productivity had the highest association with low disease activity according to GRACE, followed by PASDAS, MDA, DAPSA, DAS28, with the lowest association for CPDAI.

Conclusion

PASDAS and GRACE were superior with respect to responsiveness, and together with MDA best related to longitudinal evolvement of HRQOL, productivity and disability. Responsiveness and longitudinal validity of most outcomes were inferior for DAS28, DAPSA and CPDAI. As alternatives to the continuous measure DAPSA, use of PASDAS or GRACE should be considered.
Low delta and high alpha power are associated with better conflict control and working memory in high mindfulness, low anxiety individuals
Authors: Jaiswal Satish , Tsai Shao-Yang , Juan Chi-Hung , Muggleton Neil G , Liang Wei-Kuang
Published: May 2019

Working memory capacity (WMC) can predict conflict control ability. Measures of both abilities are impaired by anxiety, which is often inversely linked with mindfulness. It has been shown that a combination of high mindfulness and low anxiety is associated with better conflict control and WMC. The current study explored the electrophysiology related to such behavioral differences. Two experimental groups, one with high mindfulness and low anxiety (HMLA) and one with low mindfulness and high anxiety (LMHA), performed a color Stroop task and a change detection task, both with simultaneous electroencephalogram (EEG) recording. An advanced EEG analytical approach, Hilbert–Huang transform (HHT) analysis, was employed. This is regarded as a robust method to analyze non-linear and non-stationary signals. Lower delta activity at posterior temporal and occipital regions was seen in the HMLA group for the Stroop conflict conditions and might be generally associated with higher accuracy in this group and indicative of higher attentiveness. Higher accuracy rates and WMC were seen in the HMLA group and might be specifically associated with the higher alpha activity observed in prefrontal cortex, fronto-central and centro-parietal regions in this group. Future studies should explore how mindfulness and anxiety can independently affect these cognitive functions and their associated neurophysiology.
The Carceral Creep: Gender-Based Violence, Race, and the Expansion of the Punitive State, 1973–1983
Authors: Kim Mimi E
Published: May 2019

The development of the feminist anti-domestic violence movement in the United States illustrates the trajectory from a social movement field devoid of carceral involvement to one fully occupied by the agents of crime control. Countering a narrative that often begins with the Violence against Women Act of 1994, this study demonstrates how the roots of carceral feminism extend back to the movement’s first decade from 1973 to 1983. This study analyzes data from 60 social movement leaders. The pluralist coalition resulting from a successful lawsuit against the Oakland Police Department, the creation of the victim witness program in San Francisco, and the development of the Community Coordinated Response in Duluth, Minnesota, represent mechanisms of engagement with law enforcement tied to innovative organizational forms. The process called the “carceral creep” describes how early social movement successes against an initially unresponsive criminal justice system evolved into collaborative relationships that altered the autonomy and constitution of initial social movement organizations. The creation of new organizational forms and their replication contributed to today’s carceral feminism. These developments were accompanied by persisting gender, race, and class tropes used to justify pro-criminalization strategies and obfuscate impacts on marginalized communities.
Abdominal Surgical Site Infection Incidence and Risk Factors in a Mexican Population
Authors: Guzmán-García Crystell , Flores-Barrientos Oscar I. , Juárez-Rojop Isela E. , Robledo-Pascual Julio C. , Baños-González Manuel A. , Tovilla-Záratee Carlos A. , Hernández-Díaz Yazmín , González-Castro Thelma B.
Published: May 2019

OBJECTIVE:

To investigate possible predictors and prevalence of surgical site infections (SSIs) in a group of Mexican patients who underwent open abdominal surgery.

METHODS:

This retrospective study included all patients (N = 755) who underwent elective or emergency open abdominal surgeries from October 2011 to March 2012.

MAIN OUTCOME MEASURE:

Sociodemographic and clinical characteristics were collected through preoperative and postoperative examinations by the infection surveillance team. The relationship among variables (age, gender, body mass index, comorbidities, smoking habit, antimicrobial prophylaxis, hair removal, American Society of Anesthesiologists classification, type of operation, duration of operation, and SSI classification) was analyzed by odds ratio and χ
2 tests.

MAIN RESULTS:

Of the 755 patients, 91 (12%) suffered from SSI. Several variables were associated with SSI: American Society of Anesthesiologists classification (P = .001) and receiving preoperative prophylactic antimicrobials (P < .0001), among other factors. Isolated pathogens were mostly enterobacteria (60%).

CONCLUSIONS:

Surveillance plays an important role in the control and prevention of SSI. Providers must implement appropriate procedures to reduce SSI after abdominal surgery.