bluuebunny/crossref_metadata_2025 huggingface dataset:
New eco-friendly quantum dots absorb infrared light and boost solar cell efficiency
Authors: Cockbill Louisa
Published: August 2018

Novel type II Cu 2 GeS 3 /InP core/shell quantum dots have been synthesized with tailored band gap alignment for optimal red shift absorption and electron injection rate.
Conformational changes in Arp2/3 complex induced by ATP, WASp-VCA, and actin filaments
Authors: Espinoza-Sanchez Sofia , Metskas Lauren Ann , Chou Steven Z. , Rhoades Elizabeth , Pollard Thomas D.
Published: August 2018

Significance

Arp2/3 complex consists of actin-related proteins 2 and 3 with five other subunits. It forms actin filament branches under the regulation of ATP, actin monomers, actin filaments, and a nucleation-promoting factor (NPF). Here we used fluorescence spectroscopy and EM to characterize conformational changes in Arp2/3 complex along the pathway of actin filament branch formation. ATP binding to Arp2/3 complex causes small local changes in Arp2 and Arp3. NPF binding causes a larger conformational change that moves Arp2 closer to Arp3 and favors binding to the side of an actin filament, which allows further rearrangement of the subunits in the complex and growth of the new branch.
Neurobehavioral correlates of obesity are largely heritable
Authors: Vainik Uku , Baker Travis E. , Dadar Mahsa , Zeighami Yashar , Michaud Andréanne , Zhang Yu , García Alanis José C. , Misic Bratislav , Collins D. Louis , Dagher Alain
Published: August 2018

Significance

Obesity is a widespread heritable health condition. Evidence from psychology, cognitive neuroscience, and genetics has proposed links between obesity and the brain. The current study tested whether the heritable variance in body mass index (BMI) is explained by brain and behavioral factors in a large brain imaging cohort that included multiple related individuals. We found that the heritable variance in BMI had genetic correlations 0.25–0.45 with cognitive tests, cortical thickness, and regional brain volume. In particular, BMI was associated with frontal lobe asymmetry and differences in temporal-parietal perceptual systems. Further, we found genetic overlap between certain brain and behavioral factors. In summary, the genetic vulnerability to BMI is expressed in the brain. This may inform intervention strategies.
Forecast accuracy hardly improves with method complexity when completing cohort fertility
Authors: Bohk-Ewald Christina , Li Peng , Myrskylä Mikko
Published: August 2018

Significance

Information on cohort fertility is critical for the understanding of population dynamics, but only in historical settings can it be calculated without forecasting. Several forecasting methods exist, but their strengths and weaknesses have not been evaluated. Relying on the Human Fertility Database, the largest high-quality fertility dataset to date, and the globally representative United Nations World Population Prospects, we present an assessment of all major methods that complete cohort fertility. This analysis is crucial to advance the understanding of benefits and drawbacks of state-of-the-art methods. We analyze forecast accuracy and uncertainty quantification, identify methodological breakthroughs, and uncover unresolved issues. This study constitutes an evaluation benchmark for cohort fertility forecasting and may inspire establishment of similar evaluation benchmarks in related fields.
Architecture of cell–cell adhesion mediated by sidekicks
Authors: Tang Hua , Chang Haishuang , Dong Yue , Guo Luqiang , Shi Xiangyi , Wu Yichun , Huang Ying , He Yongning
Published: August 2018

Significance

Cell adhesion is important for the survival of living organisms and is mediated by the adhesion molecules that bridge the membranes of adjacent cells. Cell adhesion molecules usually have long flexible ectodomains, and their structures have been studied extensively in the past decades. However, due to technical limitations, how these long molecules are assembled between membranes and what are the mechanisms of forming cell adhesion interfaces have not been well understood. Here, we combine electron microscopy with other biophysical methods to investigate the structure of cell–cell adhesion mediated by Sdk molecules and generate three-dimensional views of the adhesion interfaces in situ, thus revealing the architecture and the potential mechanism of Sdk-mediated cell adhesion at molecular level.
Exposure to opposing views on social media can increase political polarization
Authors: Bail Christopher A. , Argyle Lisa P. , Brown Taylor W. , Bumpus John P. , Chen Haohan , Hunzaker M. B. Fallin , Lee Jaemin , Mann Marcus , Merhout Friedolin , Volfovsky Alexander
Published: August 2018

Significance

Social media sites are often blamed for exacerbating political polarization by creating “echo chambers” that prevent people from being exposed to information that contradicts their preexisting beliefs. We conducted a field experiment that offered a large group of Democrats and Republicans financial compensation to follow bots that retweeted messages by elected officials and opinion leaders with opposing political views. Republican participants expressed substantially more conservative views after following a liberal Twitter bot, whereas Democrats’ attitudes became slightly more liberal after following a conservative Twitter bot—although this effect was not statistically significant. Despite several limitations, this study has important implications for the emerging field of computational social science and ongoing efforts to reduce political polarization online.
Rapid growth of organic aerosol nanoparticles over a wide tropospheric temperature range
Authors: Stolzenburg Dominik , Fischer Lukas , Vogel Alexander L. , Heinritzi Martin , Schervish Meredith , Simon Mario , Wagner Andrea C. , Dada Lubna , Ahonen Lauri R. , Amorim Antonio , Baccarini Andrea , Bauer Paulus S. , Baumgartner Bernhard , Bergen Anton , Bianchi Federico , Breitenlechner Martin , Brilke Sophia , Buenrostro Mazon Stephany , Chen Dexian , Dias António , Draper Danielle C. , Duplissy Jonathan , El Haddad Imad , Finkenzeller Henning , Frege Carla , Fuchs Claudia , Garmash Olga , Gordon Hamish , He Xucheng , Helm Johanna , Hofbauer Victoria , Hoyle Christopher R. , Kim Changhyuk , Kirkby Jasper , Kontkanen Jenni , Kürten Andreas , Lampilahti Janne , Lawler Michael , Lehtipalo Katrianne , Leiminger Markus , Mai Huajun , Mathot Serge , Mentler Bernhard , Molteni Ugo , Nie Wei , Nieminen Tuomo , Nowak John B. , Ojdanic Andrea , Onnela Antti , Passananti Monica , Petäjä Tuukka , Quéléver Lauriane L. J. , Rissanen Matti P. , Sarnela Nina , Schallhart Simon , Tauber Christian , Tomé António , Wagner Robert , Wang Mingyi , Weitz Lena , Wimmer Daniela , Xiao Mao , Yan Chao , Ye Penglin , Zha Qiaozhi , Baltensperger Urs , Curtius Joachim , Dommen Josef , Flagan Richard C. , Kulmala Markku , Smith James N. , Worsnop Douglas R. , Hansel Armin , Donahue Neil M. , Winkler Paul M.
Published: August 2018

Significance

Aerosol particles can form and grow by gas-to-particle conversion and eventually act as seeds for cloud droplets, influencing global climate. Volatile organic compounds emitted from plants are oxidized in the atmosphere, and the resulting products drive particle growth. We measure particle growth by oxidized biogenic vapors with a well-controlled laboratory setup over a wide range of tropospheric temperatures. While higher temperatures lead to increased reaction rates and concentrations of highly oxidized molecules, lower temperatures allow additional, but less oxidized, species to condense. We measure rapid growth over the full temperature range of our study, indicating that organics play an important role in aerosol growth throughout the troposphere. Our finding will help to sharpen the predictions of global aerosol models.
Molecular strategy for blocking isopeptide bond formation in nascent pilin proteins
Authors: Rivas-Pardo Jaime Andrés , Badilla Carmen L. , Tapia-Rojo Rafael , Alonso-Caballero Álvaro , Fernández Julio M.
Published: August 2018

Significance

At the onset of an infection, gram-positive bacteria adhere to host cells through their pili, filamentous structures built by hundreds of repeats of pilin proteins. These proteins can withstand large mechanical challenges without unfolding, remaining anchored to the host and resisting cleavage by proteases and oxygen radicals present in the targeted tissues. The key structural component that gives pilins mechanical resilience are internal isopeptide bonds, strategically placed so that pilins become inextensible structures. We target this bond by designing a blocking peptide that interferes with its formation during folding. We demonstrate that peptide-modified pilins lack mechanical stability and extend at low forces. We propose this strategy as a rational design of mechanical antibiotics, targeting the Achilles heel of bacterial adhesion.
Physical foundations of biological complexity
Authors: Wolf Yuri I. , Katsnelson Mikhail I. , Koonin Eugene V.
Published: August 2018

Significance

Living organisms are characterized by a degree of hierarchical complexity that appears to be inaccessible to even the most complex inanimate objects. Routes and patterns of the evolution of complexity are poorly understood. We propose a general conceptual framework for emergence of complexity through competing interactions and frustrated states similar to those that yield patterns in striped glasses and cause self-organized criticality. We show that biological evolution is replete with competing interactions and frustration that, in particular, drive major transitions in evolution. The key distinction between biological and nonbiological systems seems to be the existence of long-term digital memory and phenotype-to-genotype feedback in living matter.
BRAF/MAPK and GSK3 signaling converges to control MITF nuclear export
Authors: Ngeow Kao Chin , Friedrichsen Hans J. , Li Linxin , Zeng Zhiqiang , Andrews Sarah , Volpon Laurent , Brunsdon Hannah , Berridge Georgina , Picaud Sarah , Fischer Roman , Lisle Richard , Knapp Stefan , Filippakopoulos Panagis , Knowles Helen , Steingrímsson Eiríkur , Borden Katherine L. B. , Patton E. Elizabeth , Goding Colin R.
Published: August 2018

Significance

Signaling pathways ultimately exert their influence on cell behavior by regulating the activity of transcription factors that drive gene expression programs associated with specific cell phenotypes. How transcription factors integrate the outputs from multiple independent signaling events to coordinate cell behavior is a key issue. Here, we identify a regulated nuclear export signal in the lineage survival oncogene and cell fate-determining factor MITF. The regulated export signal integrates the outputs from the MAPK signaling pathway with those regulating GSK3 that play key roles in development and disease. The regulation of MITF nuclear export provides a means by which these key signaling pathways tune MITF activity that, in turn, controls cell identity in development and disease.
Circular DNA tumor viruses make circular RNAs
Authors: Toptan Tuna , Abere Bizunesh , Nalesnik Michael A. , Swerdlow Steven H. , Ranganathan Sarangarajan , Lee Nara , Shair Kathy H. , Moore Patrick S. , Chang Yuan
Published: August 2018

Significance

Circular RNAs (circRNAs) play critical physiologic functions, but it is not known whether human DNA viruses express circRNAs. We surveyed Epstein−Barr virus (EBV) and Kaposi’s sarcoma herpesvirus (KSHV) tumors and cell lines, and found specific circRNAs expressed from both viruses. EBV circular BamHI A rightward transcripts (circBARTs) were expressed in all EBV tumor latency forms, including all EBV-infected posttransplant lymphoproliferative disease tumors tested, whereas EBV circBHLF1 and circLMP2 were more variably expressed. KSHV expressed circvIRF4 constitutively in primary effusion lymphoma cell lines, while the polyadenylated nuclear locus promiscuously generated variable, inducible, and bidirectional circRNAs. Tumor virus circRNAs can be long-lived, unique tumor biomarkers that may also open new research opportunities into understanding how these viruses cause cancer.
Uniform regularity for the incompressible Navier-Stokes system with variable density and Navier boundary conditions
Authors: Xu Xin
Published: August 2018

We investigate the uniform regularity for the nonhomogeneous incompressible Navier-Stokes system with Navier boundary conditions and the inviscid limit to the Euler system. It is shown that there exists a unique strong solution of the Navier-Stokes equations in an interval of time that is uniform with respect to the viscosity parameter. The uniform estimate in conormal Sobolev spaces is established. Based on the uniform estimate, we show the convergence of the viscous solutions to the inviscid ones in

L
∞

(
[
0
,
T
]
×
Ω
)

L^\infty ([0,T]\times \Omega )

. This improves the result obtained by Ferreira et al. [SIAM J. Math. Anal. Vol. 45, No. 4, (2013), pp. 2576-2595], where

L
∞

(
[
0
,
T
]
,

L
2

(
Ω
)
)

L^\infty ([0,T],L^2(\Omega ))

convergence was proved.
Protease target prediction via matrix factorization
Authors: Marini Simone , Vitali Francesca , Rampazzi Sara , Demartini Andrea , Akutsu Tatsuya
Published: August 2018

Motivation

Protein cleavage is an important cellular event, involved in a myriad of processes, from apoptosis to immune response. Bioinformatics provides in silico tools, such as machine learning-based models, to guide the discovery of targets for the proteases responsible for protein cleavage. State-of-the-art models have a scope limited to specific protease families (such as Caspases), and do not explicitly include biological or medical knowledge (such as the hierarchical protein domain similarity or gene–gene interactions). To fill this gap, we present a novel approach for protease target prediction based on data integration.

Results

By representing protease-protein target information in the form of relational matrices, we design a model (i) that is general and not limited to a single protease family, and (b) leverages on the available knowledge, managing extremely sparse data from heterogeneous data sources, including primary sequence, pathways, domains and interactions. When compared with other algorithms on test data, our approach provides a better performance even for models specifically focusing on a single protease family.

Availability and implementation

https://gitlab.com/smarini/MaDDA/ (Matlab code and utilized data.)

Supplementary information

Supplementary data are available at Bioinformatics online.
Pharmacokinetics, Safety, and Efficacy of an Allometric Miltefosine Regimen for the Treatment of Visceral Leishmaniasis in Eastern African Children: An Open-label, Phase II Clinical Trial
Authors: Mbui Jane , Olobo Joseph , Omollo Raymond , Solomos Alexandra , Kip Anke E , Kirigi George , Sagaki Patrick , Kimutai Robert , Were Lilian , Omollo Truphosa , Egondi Thaddaeus W , Wasunna Monique , Alvar Jorge , Dorlo Thomas P C , Alves Fabiana
Published: August 2018

Background

Convenient, safe, and effective treatments for visceral leishmaniasis in Eastern African children are lacking. Miltefosine, the only oral treatment, failed to achieve adequate efficacy, particularly in children, in whom linear dosing (2.5 mg/kg/day for 28 days) resulted in a 59% cure rate, with lower systemic exposure than in adults.

Methods

We conducted a Phase II trial in 30 children with visceral leishmaniasis, aged 4–12 years, to test whether 28 days of allometric miltefosine dosing safely achieves a higher systemic exposure than linear dosing.

Results

Miltefosine accumulated during treatment. Median areas under the concentration time curve from days 0–210 and plasma maximum concentration values were slightly higher than those reported previously for children on linear dosing, but not dose-proportionally. Miltefosine exposure at the start of treatment was increased, with higher median plasma concentrations on day 7 (5.88 versus 2.67 μg/mL). Concentration-time curves were less variable, avoiding the low levels of exposure observed with linear dosing. The 210-day cure rate was 90% (95% confidence interval, 73–98%), similar to that previously described in adults. There were 19 treatment-related adverse events (AEs), but none caused treatment discontinuation. There were 2 serious AEs: both were unrelated to treatment and both patients were fully recovered.

Conclusions

Allometric miltefosine dosing achieved increased and less-variable exposure than linear dosing, though not reaching the expected exposure levels. The new dosing regimen safely increased the efficacy of miltefosine for Eastern African children with visceral leishmaniasis. Further development of miltefosine should adopt allometric dosing in pediatric patients.

Clinical Trials Registration

NCT02431143.
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

From 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

Northern 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

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.
Mental Causation
Authors: Donaldson John
Published: August 2018

Mental causation occurs when mental entities cause other mental and physical entities: seeings causing believings, itches causing scratchings, headaches causing eye twitches, and so on. The term “mental causation” is most often used to refer to the problem of mental causation, which is really a collection of problems with each possessing its own character and tradition of debate. The problem of mental causation began in earnest with an objection to Cartesian dualism raised by Princess Elizabeth of Bohemia (how can immaterial minds causally interact with material bodies?) and still persists via a series of different objections raised against various views including non-reductive physicalism, anomalous monism, and psychological externalism. What unites the different problems of mental causation is their attempt to address a question of this general form: is model x of the non-causal mental-physical relationship (e.g., non-reductive physicalism) consistent with there being mental causation? A negative answer is usually taken to constitute a fatal objection to model x, but not always. There have been two major avenues of inquiry since Elizabeth’s original objection began the debate: (a) what theories of causation can tell us about the consistency of model x with mental causation; or (b) what theories about the non-causal mental-physical relationship can tell us about the consistency of model x with mental causation. Nearly every contribution in the literature on the problem of mental causation can be understood as belonging in either category (a) or (b), or as containing distinguishable elements which so belong. The most important discussions about mental causation have taken place over the last few decades, hence this entry will focus largely on work conducted in that period. Mental causation is also discussed in other areas of philosophy, such as political philosophy or ethics, but this entry will be primarily concerned with the metaphysical and philosophy of mind literature.
Sex versus Gender
Authors: Conte Jill
Published: August 2018

In the late 1960s and early 1970s, a conceptual distinction between “sex” and “gender” arose in the clinical literature on human psychosexual development. Sex came to signify the biological or bodily component of difference, that is, male and female. Gender, on the other hand, came to signify the social or cultural component of difference, that is, masculine and feminine. This sex/gender distinction, as it is often called, was heartily embraced by many feminists of the day who sought to account for differences between the sexes as well as explain and remediate women’s second-class status in society. The establishment of gender as a distinctly “social” concept appealed to feminists because it opened up an intellectual and political space—a space beyond biological determinism—for inquiry into the causes of “male domination” and “female subordination” that were not essential, universal, or fixed. In this space, social change was possible; gender relations could be reconfigured. To that end, the sex/gender distinction became, by and large, paradigmatic in feminist thought and social science, and from it grew a burgeoning body of gender theory loosely characterized as the social construction of gender. Intersectional, post-structural, postmodern, and queer schools of thought produced new insights and advanced theory in ways that posed challenges to the viability and utility of gender as a concept as well as to the sex/gender paradigm. The ensuing debates were highly productive, ushering in a new era of social theory on the body that centered corporeality and embodiment and that sought to deconstruct binary thinking. As thinking on sex/gender evolved, the conceptual split was no longer understood as a simple separation between the biological and the social. Feminist and queer scholars problematized the distinction, reformulating it as an interlocking set of relationships: the sex/gender/sexuality system. Interdisciplinary gender scholars, including prominent feminist scientists, began theorizing the complex interrelationship between sex and gender with greater sophistication in an attempt to more firmly discredit biological determinist approaches to the study of difference based on sex, gender, or sexuality. Advancing theory, research, and praxis has not only deepened understanding about a wider variety of identities, experiences, and practices around sex, gender, and sexuality but has also won greater recognition in the early 21st century for them. This multiplicity of sexes, genders, and sexualities has brought with it unique methodological concerns in the social sciences, which represent a new frontier of research and activism in gender and sexuality studies.
The Finance Film
Authors: Parvulescu Constantin
Published: August 2018

Cinematic representation of finance, financiers and financialization goes back to the early days of cinema in both Europe and the United States. Banks and stock markets, together with their growing power as well as the effects of speculation and securitization on everyday lives, have been the object of documentary and feature film reflection under all political regimes of the 20th and 21st centuries, including capitalist, Bolshevik, communist, socialist, and fascist. A staple of Soviet cinema montage is the intercutting between images of manual labor and speculation to suggest exploitation—as in Vsevolod Pudovkin’s The End of St. Petersburg (1927), which contrasts hectic activity on the stock market with the trench warfare fought by the Russian commoner during World War I. The German communist interwar documentary classic Kuhle Wampe (1932) with its indicative subtitle “To Whom Does the World Belong?” was made as a response to the 1929–1934 world economic crisis. Nazi anti-Semitic propaganda films feature evil bankers corrupting the honest way of life of gentiles. American capitalism’s Hollywood also reacted early. Buster Keaton’s first feature film lead role was of a blue-blood broker in The Saphead (1920), while D. W. Griffith presented stock exchange speculation in a one-reeler as early as 1909 (A Corner in Wheat). As the American film industry developed, several other such films were produced, marking landmark moments in humanity’s affair with capitalism in the 20th century. The Grapes of Wrath (1940) served as a paean to the Great Depression (1929–1939); It’s a Wonderful Life (1946) testified to the start of the postwar economic boom; Wall Street (1987) heralded the era of deregulation, while American Psycho (2000) marked the rise of the yuppie. After 2008, countless features and documentaries engaged in explaining the derivative and subprime mortgage scams that led to the crash and the subsequent Big Bailout of 2008, which engendered the Great Recession (2008–2014). With its roots in literature (the finance novel) and the visual arts, recent film production has put finance and financialization on the map of academic film research and legitimized the use of the concept of finance film and of its subdivision, the Wall Street film. The finance film has served scholars in their efforts to investigate the representation of finance-related economic and social situations on film and write its history as well as academics delving into the industry’s ethos, political influence, organization, emotional culture, and sustainability. This article is thus interdisciplinary. For reasons of space and relevance, however, it is limited to materials written in English that analyze European and North American productions.
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.
Ecosystem Ecology
Authors: Moore J.C.
Published: August 2018

Ecosystem ecology is a branch of study and thinking within the ecological sciences that focuses on the ecosystem—a dynamic network of interactions of organisms and their environment—and the importance of these interactions to the organisms and earth system processes. The discipline represents one of two different epistemological approaches within ecology that emerged in the 20th century: a species-centric community-based approach, and a process-centric ecosystem-based approach. Both approaches study the ways in which species interact among themselves and their environment, share a common language, and share a common set of principles. The community-based approach focuses on how species’ distributions and abundances are shaped by their resource needs and tolerances to environmental conditions, and by their interactions with other species. The ecosystem-based approach represents a significant departure in that it considers both the resource needs and tolerances of species and their interactions with other species, but also factors in the contributions that species make to earth system processes (e.g., biogeochemical cycles, climate). The two perspectives are not as mutually exclusive as the phrasing of the approaches suggests, but rather offer different approaches to how we view the environment and communities and the factors that regulate them. In the 21st century, modern ecosystem science includes the influences that humans have as part of ecological communities and as drivers of change in ecological communities. This linkage within the ecosystem perspective of biology affecting the physical environment, and the recent developments that include the social and human dimensions, has positioned the approach as a critical one in understanding the relationship among global processes and the services that ecosystems provide to human well-being that is embodied in the emerging science of sustainability.
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

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

Background

In 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.

Methods

Pathological 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.

Results

The 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.

Conclusions

This 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

Soft 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

Background

Sequencing 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.

Results

We 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.

Conclusions

DEBrowser 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

The 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.