bluuebunny/crossref_metadata_2025_split huggingface dataset:
A research plan to define Canada’s first low-risk gambling guidelines
Authors: Currie Shawn R ,   the Low Risk Gambling Guidelines Scientific Working Group, Currie Shawn , Flores-Pajot Marie-Claire , Hodgins David , Nadeau Louise , Paradis Catherine , Robillard Chantal , Young Matthew 
Published: August 2018

AbstractFrom a public health perspective, gambling shares many of the same characteristics as alcohol. Notably, excessive gambling is associated with many physical and emotional health harms, including depression, suicidal ideation, substance use and addiction and greater utilization of health care resources. Gambling also demonstrates a similar ‘dose-response’ relationship as alcohol—the more one gambles, the greater the likelihood of harm. Using the same collaborative, evidence-informed approach that produced Canada’s Low-Risk Alcohol Drinking and Lower Risk Cannabis Use Guidelines, a research team is leading the development of the first national Low-Risk Gambling Guidelines (LRGGs) that will include quantitative thresholds for safe gambling. This paper describes the research methodology and the decision-making process for the project. The guidelines will be derived through secondary analyses of several large population datasets from Canada and other countries, including both cross-sectional and longitudinal data on over 50 000 adults. A scientific committee will pool the results and put forward recommendations for LRGGs to a nationally representative, multi-agency advisory committee for endorsement. To our knowledge, this is the first systematic attempt to generate a workable set of LRGGs from population data. Once validated, the guidelines inform public health policy and prevention initiatives and will be disseminated to addiction professionals, policy makers, regulators, communication experts and the gambling industry. The availability of the LRGGs will help the general public make well-informed decisions about their gambling activities and reduce the harms associated with gambling.
Using natural analogues to investigate the effects of climate change and ocean acidification on Northern ecosystems
Authors: Rastrick Samuel S P , Graham Helen , Azetsu-Scott Kumiko , Calosi Piero , Chierici Melissa , Fransson Agneta , Hop Haakon , Hall-Spencer Jason , Milazzo Marco , Thor Peter , Kutti Tina 
Published: August 2018

AbstractNorthern oceans are in a state of rapid transition. Still, our knowledge of the likely effects of climate change and ocean acidification on key species in the food web, functionally important habitats and the structure of Arctic and sub-Arctic ecosystems is limited and based mainly on short-term laboratory studies on single species. This review discusses how tropical and temperate natural analogues of carbonate chemistry drivers, such as CO2 vents, have been used to further our knowledge of the sensitivity of biological systems to predicted climate change, and thus assess the capacity of different species to show long-term acclimation and adaptation to elevated levels of pCO2. Natural analogues have also provided the means to scale-up from single-species responses to community and ecosystem level responses. However, to date the application of such approaches is limited in high latitude systems. A range of Arctic and sub-Arctic sites, including CO2 vents, methane cold seeps, estuaries, up-welling areas, and polar fronts, that encompass gradients of pH, carbonate saturation state, and alkalinity, are suggested for future high latitude, in-situ ocean acidification research. It is recommended that combinations of monitoring of the chemical oceanography, observational, and experimental (in situ and laboratory) studies of organisms around these natural analogues be used to attain better predictions of the impacts of ocean acidification and climate change on high latitude species and ecosystems.
Genus-One Gromov–Witten Invariants of Quintic Three-folds via MSP Localization
Authors: Chang Huai-Liang , Guo Shuai , Li Wei-Ping , Zhou Jie 
Published: August 2018

Abstract
The moduli stack of Mixed Spin P-fields (MSP) provides an effective algorithm to evaluate all genus Gromov–Witten (GW) invariants of the quintic Calabi–Yau (CY) three-folds. This paper is to apply the algorithm to the genus-one case. We use the localization formula, the proposed algorithm in [ 10, 11], and Zinger’s packaging technique to compute the genus-one GW invariants of the quintic CY three-folds. Our approach to the formula suggests a correspondence between each type of MSP graphs with each physics’ phase: CY, Landau–Ginzburg, or conifold point. In this process, new differential relations among Givental’s I-functions are also discovered.
Pythagoreanism
Authors: Zhmud Leonid 
Published: August 2018

Pythagoreanism is a modern term referring to a multifaceted phenomenon that covered different aspects of the ancient world such as political life, religion, philosophy, and science and existed in only partly overlapping forms. Its originator, Pythagoras of Samos, moved c. 530 bce to Italian Croton, where his followers, the Pythagoreans, organized a political society, whose participants were at the same time encouraged to undertake various intellectual pursuits. Pythagoras’s best attested doctrine is transmigration of the soul, whereas philosophical theories and scientific discoveries ascribed to him are highly disputed. Often he is regarded as a purely religious thinker, though not a single religious figure is known of among his followers. All known ancient Pythagoreans belong to five overlapping categories: politicians, athletes, doctors, natural philosophers, and mathematical scientists. After Pythagoras’s death the Pythagorean societies politically dominated in Croton, Metapontum, Tarentum, and other cities of Southern Italy until the anti-Pythagorean uprising (c. 450), when many Pythagoreans were killed or forced to flee to mainland Greece. The last center of Pythagoreanism in Italy remained in Tarentum, led in 367–361 by Archytas, a successful general and brilliant mathematician. The Pythagorean school created theoretical arithmetic and mathematical harmonics and greatly contributed to natural philosophy, geometry, and astronomy. Its disappearance after 350 bce marked the end of ancient Pythagoreanism. A new form of Pythagoreanism without the Pythagoreans were the pseudo-Pythagorean writings ascribed to Pythagoras and his fictitious family members. The first wave of Pseudo-Pythagorica (late 4th to late 2nd centuries bce) was neither numerous nor popular but since the early 1st century bce it was superseded by the second, more successful wave that was part of the emerging Neopythagoreanism. These treatises written under the names of historical and fictional Pythagoreans and containing Stoic, Platonic, and Aristotelian doctrines aimed to present Pythagoras and his followers as the precursors of Plato and Aristotle. The first Neopythagoreans writing under their own names appeared in the mid-1st century ce and doctrinally belonged to Middle Platonism. The most important representatives of late antique Pythagoreanism were the Neoplatonists Porphyry and especially Iamblichus, who secured its existence until the end of Antiquity.
Vitruvius
Authors: Nichols Marden 
Published: August 2018

Vitruvius is the author of De architectura (c. 20s bce), the only text devoted to architecture that survives from classical antiquity. On the basis of internal evidence, scholars date Vitruvius’s De architectura to c. 27–22 bce. Across ten books of Latin prose dedicated to the emperor Augustus, Vitruvius lays out an ambitious and idiosyncratic vision of architecture. De architectura’s subject matter includes the education of architects and the principles of architecture (Book 1); building materials (Book 2); the construction of temples (Book 3 and Book 4); public buildings (Book 5); houses (Book 6); architectural decor (Book 7); sources of water (Book 8); astronomy, dials, and clocks (Book 9); and machines of war (Book 10). Nothing is securely known about the author, nor is his name attached to any other surviving texts. The readership and influence of De architectura in the ancient world remains mysterious: before Pliny the Elder names Vitruvius as one of the sources for his Naturalis Historia in the 1st century ce, there are no unmistakable signs of Vitruvian influence in Roman literature or architecture. The intelligentsia of the Italian Renaissance, by contrast, poured over De architectura and strenuously attempted to apply its principles, as witnessed by Andrea Palladio’s architectural designs and Leonardo da Vinci’s famous “Vitruvian Man.” For archaeologists, classical art historians, and scholars of ancient science and engineering, Vitruvius remains a unique and precious source, and De architectura holds a place of honor within the academic curriculum of aspiring architects to this day. Nevertheless, ambiguity, inconsistency, and anachronism are but three challenges that dog any interpretation of De architectura as a factual account of Roman engineering, design, or building practices. Likewise, due to the perceived awkwardness and naivety of his prose (as well as his technical subject matter), Vitruvius traditionally has attracted little interest among scholars of classical literature.
Nagisa Oshima
Authors: Cook Ryan 
Published: August 2018

Nagisa Oshima (大島渚/Ōshima Nagisa, b. 1932–d. 2013) is a paradox: one of the most iconic filmmakers in Japanese film history, but one whose body of work is among the most iconoclastic. Oshima was a wayward product of Japan’s postwar studio system. He entered the Shochiku Studio in 1954 after studying law at Kyoto University and cut his professional teeth during the studio golden age, but from his feature directorial debut in 1959 he demonstrated the restlessness and unorthodoxy characteristic of the new youth cinema. His 1960 film Cruel Story of Youth (Seishun zankoku monogatari), along with published editorials denouncing the stagnation of the studio system, assured his position as a representative of the Shochiku New Wave, a group of newly promoted young directors marketed as Japan’s answer to the French New Wave (Oshima later said that he disliked the label). He left Shochiku in 1961 in protest over the shelving of his politically charged 1960 film Night and Fog in Japan (Nihon no yoru to kiri), a striking reflection on student movement factionalism, which was pulled from theaters days after its release. He founded his own production company (Sozosha) the same year, and later worked closely with the Art Theatre Guild, helping forge the path for independent art film production in Japan. He was prolific and provocative during the 1960s: both an influential filmmaker and a public intellectual. But despite his visibility, he resisted auteurist assessment. His body of work includes many bold, perplexing experiments, but generally lacks a consistent signature style. The 1960s theatrical films range from the photo roman–style montages of still photographs and drawn images in Diary of Yunbogi (Yunbogi no nikki) and Band of Ninja (Ninja bugeicho) to the Brechtian theatricality of Death by Hanging (Koshikei), his 1968 international breakthrough film. He made television documentaries, and spent much of his late career as a television commentator and personality. His 1976 French-Japanese coproduction In the Realm of the Senses (Ai no korida) tested the boundaries between the art film and pornography, and was the subject of an obscenity trial in Japan. It also placed him at the international forefront of cinematic modernism. Oshima is known for the reliability of his confrontational posture more than for a recognizable style. He interrogated Japan’s postwar democracy, victim consciousness, and political movements as well as Japan’s relationship to its “others” (notably Koreans), and constantly questioned authority. His post-1970s films, notably Merry Christmas, Mr. Lawrence (Senjo no meri Kurisumasu) and Taboo (Gohatto), provocatively explore historical subjects through the lens of homosociality.
Morphological Differences in the Upper Trapezius Muscle Between Female Office Workers With and Without Trapezius Myalgia: Facts or Fiction?
Authors: De Meulemeester Kayleigh , Calders Patrick , Van Dorpe Jo , De Pauw Robby , Petrovic Mirko , Cagnie Barbara 
Published: August 2018

Abstract

Objective
Work-related trapezius myalgia is a common musculoskeletal disorder in office workers. Prolonged low-level muscle activity during office work may lead to morphological changes in the muscle tissue, causing pain and fatigue. The aim of the present study was to investigate differences in muscle morphology between office workers with and without trapezius myalgia.

Design
Muscle biopsy samples were obtained from the upper trapezius of female office workers with trapezius myalgia (n = 17) and healthy controls (n = 15). Myosin heavy chain immunohistochemistry and Gomori trichrome stainings were performed to identify differences in muscle fiber type proportion, Feret's diameter, and internal nuclear proportion.

Results
The myalgia group showed significantly more type IIA and IIA/IIX fibers and less type I and IIX fibers, compared with the control group (P < 0.001 to P = 0.005). No significant differences were found for Feret's diameter and internal nuclear proportion (P > 0.05). However, a significantly higher Feret's diameter was found for type I fibers, compared with type II fibers in both groups (P < 0.001 to P = 0.002). Several subjects of both groups displayed an internal nuclear proportion of more than 3%.

Conclusions
Female office workers with trapezius myalgia show a different fiber type distribution compared with their healthy colleagues but display no differences in fiber size and internal nuclear proportion.
Molecular features of premenopausal breast cancers in Latin American women: pilot results from the PRECAMA study
Authors: Olivier Magali , Bouaoun Liacine , Villar Stephanie , Robitaille Alexis , Cahais Vincent , Heguy Adriana , Byrnes Graham , Calvez-Kelm Florence Le , Torres-Mejía Gabriela , Alvarado-Cabrero Isabel , Imani-Razavi Fazlollah Shahram , Sánchez Gloria Inés , Jaramillo Roberto , Porras Carolina , Rodriguez Ana Cecilia , Garmendia Maria Luisa , Soto José Luis , Romieu Isabelle , Porter Peggy , Guenthoer Jamie , Rinaldi Sabina ,   on behalf of the PRECAMA team
Published: August 2018

AbstractBackgroundIn Latin America (LA), there is a high incidence rate of breast cancer (BC) in premenopausal women, and the genomic features of these BC remain unknown. Here, we aim to characterize the molecular features of BC in young LA women within the framework of the PRECAMA study, a multicenter population-based case-control study on breast cancer in premenopausal women.MethodsPathological tumor tissues were collected from incident cases from four LA countries. Immunohistochemistry (IHC) was performed centrally for ER, PR, HER2, Ki67, EGFR, CK5/6 and p53 protein markers. Targeted deep sequencing was done on genomic DNA extracted from formalin-fixed paraffin-embedded (FFPE) tumour tissues and their paired blood samples to screen for somatic mutations in eight genes frequently mutated in BC. A subset of samples was analyzed by exome sequencing to identify somatic mutational signatures.ResultsThe majority of cases were positive for ER or PR (168/233; 72%) and there were 21% triple negative (TN) cases, mainly of basal type. Most tumors were positive for Ki67 (189/233; 81%). In 126 sequenced cases,TP53andPIK3CAwere the most frequently mutated genes (32.5% and 21.4%, respectively), followed byAKT1(9.5%).TP53mutations were more frequent in HER2-enriched and TN IHC subtypes, whilePIK3CA/AKT1mutations were more frequent in ER positive tumors, as expected. Interestingly, a higher proportion of G:C>T:A mutations was observed inTP53gene in PRECAMA cases compared to TCGA and METABRIC breast cancer series (27% vs 14%). Exome-wide mutational patterns in 10 TN cases revealed alterations in signaling transduction pathways and major contributions of mutational signatures caused by altered DNA repair pathways.ConclusionsThis pilot results on PRECAMA tumors gives a preview of the molecular features of premenopausal BC in LA. Although, the overall mutation burden was as expected from data in other populations, mutational patterns observed inTP53and exome-wide suggested possible differences in mutagenic processes giving rise to these tumors compared to other populations. Further omics analyses of a larger number of cases in the near future will allow investigating relationships between these molecular features and risk factors.
May the phage be with you? Prophage-like elements in the genomes of Soft Rot Pectobacteriaceae (Pectobacterium spp. and Dickeya spp.)
Authors: Czajkowski Robert 
Published: August 2018

ABSTRACTSoft Rot Pectobacteriaceae (SRP; Pectobacterium spp. and Dickeya spp., formerly known as pectinolytic Erwinia spp.) are necrotrophic bacterial pathogens infecting large number of plant species worldwide including agriculturally-important crops. Regardless of the SRP importance in agriculture, little is known about the bacteriophages infecting Pectobacterium spp. and Dickeya spp. and even less about prophages present in SRP genomes. Prophages are recognized as factors underlying bacterial virulence, genomic diversification and ecological fitness and have association with the novel phenotypic properties of bacterial hosts. Likewise, they are recognized as a driving force of bacterial evolution. The aim of this study was to analyze Pectobacterium spp. and Dickeya spp. complete genome sequences downloaded from GenBank (NCBI) for the presence of prophage sequences following their identification and (comparative) characterization with the main focus on current and upcoming perspectives in that field.
DEBrowser: Interactive Differential Expression Analysis and Visualization Tool for Count Data
Authors: Kucukural Alper , Yukselen Onur , Ozata Deniz M , Moore Melissa J , Garber Manuel 
Published: August 2018

AbstractBackgroundSequencing data has become a standard measure for studying diverse cellular activities. For example, gene expression is accurately measured by RNA sequencing (RNA-Seq) libraries, protein-DNA interactions are captured by chromatin immunoprecipitation sequencing (ChIP-Seq), protein-RNA interactions by crosslinking immunoprecipitation (CLIP-Seq) or RNA immunoprecipitation (RIP-Seq) sequencing, DNA accessibility by assay for transposase-accessible chromatin (ATAC-Seq), and DNase or MNase sequencing libraries. Analysis of these sequencing techniques involve library-specific approaches. However, in all cases, once the sequencing libraries are processed, the result is a count table specifying the estimated number of reads originating from a genomic locus. Differential analysis to determine which loci have different cellular activity under different conditions starts with the count table and iterates through a cycle of data assessment, preparation and analysis. Such iterative approach relies on multiple programs and is therefore a challenge for those without programming skills.ResultsWe developed DEBrowser, as an R bioconductor project, to interactively visualize each step of the differential analysis of count data, without any requirement for programming expertise. The application presents a rich and interactive web based graphical user interface based on R’s shiny infrastructure. We use shiny’s reactive programming interface for a dynamic webpage that responds to user input and integrates its visualization widgets at each stage of the analysis. In this way, every step of the analysis can be displayed in one application that combines many approaches and multiple results. We show DEBrowser’s capabilities by reproducing the analysis of two previously published data sets.ConclusionsDEBrowser is a flexible, intuitive, web-based analysis platform that enables an iterative and interactive analysis of count data without any requirement of programming knowledge.
Reactivated spatial context guides episodic recall
Authors: Herweg Nora A. , Sharan Ashwini D. , Sperling Michael R. , Brandt Armin , Schulze-Bonhage Andreas , Kahana Michael J. 
Published: August 2018

AbstractThe medial temporal lobe (MTL) is known as the locus of spatial coding and episodic memory, but the interaction between these cognitive domains, as well as the extent to which they rely on common neurophysiological mechanisms is poorly understood. Here, we use a hybrid spatial-episodic memory task to determine how spatial information is dynamically reactivated in sub-regions of the MTL and how this reactivation guides recall of episodic information. Our results implicate theta oscillations across the MTL as a common neurophysiological substrate for spatial coding in navigation and episodic recall. We further show that spatial context information is initially retrieved in the hippocampus (HC) and subsequently emerges in the parahippocampal gyrus (PHG). Finally, we demonstrate that hippocampal theta phase modulates parahippocampal gamma amplitude during retrieval of spatial context, suggesting a role for cross frequency coupling in coding and transmitting retrieved spatial information.
Achieving Reversible Ligand-Protein Unbinding with Deep Learning and Molecular Dynamics through RAVE
Authors: Lamim Ribeiro João Marcelo , Tiwary Pratyush 
Published: August 2018

AbstractIn this work we demonstrate how to leverage our recent iterative deep learning–all atom molecular dynamics (MD) technique “Reweighted autoencoded variational Bayes for enhanced sampling (RAVE)” (Ribeiro, Bravo, Wang, Tiwary, J. Chem. Phys. 149, 072301 (2018)) for sampling protein-ligand unbinding mechanisms and calculating absolute binding affinities when plagued with difficult to sample rare events. RAVE iterates between rounds of MD and deep learning, and unlike other enhanced sampling methods, it stands out in simultaneously learning both a low-dimensional physically interpretable reaction coordinate (RC) and associated free energy. Here, we introduce a simple but powerful extension to RAVE which allows learning a position-dependent RC expressed as a superposition of piecewise linear RCs valid in different metastable states. With this approach, we retain the original physical interpretability of a RAVE-derived RC while making it applicable to a wider range of complex systems. We demonstrate how in its multi-dimensional form introduced here, RAVE can efficiently simulate the unbinding of the tightly bound benzene-lysozyme (L99A variant) complex, in all atom-precision and with minimal use of human intuition except for the choice of a larger dictionary of order parameters. These simulations had a 100 % success rate, and took between 3–50 nanoseconds for a process that takes on an average close to few hundred milliseconds, thereby reflecting a seven order of magnitude acceleration relative to straightforward MD. Furthermore, without any time-dependent biasing, the trajectories display clear back–and– forth movement between various metastable intermediates, demonstrating the reliability of the RC and its probability distribution learnt in RAVE. Our binding free energy is in good agreement with other reported simulation results. We thus believe that RAVE, especially in its multi-dimensional variant introduced here, will be a useful tool for simulating the dissociation process of practical biophysical systems with rare events in an automated manner with minimal use of human intuition.