bluuebunny/crossref_metadata_2025_split huggingface dataset:
Newly Diagnosed Primary Gum Lymphoma on FDG PET/CT
Authors: Zhang Jianhua , Fan Yan , Liu Meng , Li Qian , Wang Rongfu 
Published: April 2018

Abstract
An 81-year-old woman presented a 2-month history of left upper gum swelling. Biopsy of the lesion revealed the diffuse large B-cell lymphoma. 18F-FDG PET/CT scan showed the abnormal high uptake at the left upper gum.
Impact of Breast Surgery in Primary Metastasized Breast Cancer
Authors: Fitzal Florian , Bjelic-Radisic Vesna , Knauer Michael , Steger Günther , Hubalek Michael , Balic Marija , Singer Christian , Bartsch Rupert , Schrenk Peter , Soelkner Lidija , Greil Richard , Gnant Michael 
Published: April 2018

Background:
Conflicting evidence exists regarding the value of surgical resection of the primary in stage IV breast cancer patients.

Objective:
The prospective randomized phase III ABCSG-28 POSYTIVE trial evaluated median survival comparing primary surgery followed by systemic therapy to primary systemic therapy in de novo stage IV breast cancer.

Methods:
Between 2011 and 2015, 90 previously untreated stage IV breast cancer patients were randomly assigned to surgical resection of the primary tumor followed by systemic therapy (Arm A) or primary systemic therapy (Arm B) in Austria. Overall survival (OS) was defined as the primary study endpoint.

Results:
The trial was stopped early due to poor recruitment. Ninety patients (45 arm A, 45 arm B) were included; median follow-up was 37.5 months. Patients in the surgery arm had more cT3 breast cancer (22.2% vs 6.7%) and more cN2 staging (15.6% vs 4.4%). Both groups were well balanced with respect to the type of first-line systemic treatment. Median survival in arm A was 34.6 months, versus 54.8 months in the nonsurgery arm [hazard ratio (HR) 0.691, 95% confidence interval (95% CI) 0.358–1.333; P = 0.267]; time to distant progression was 13.9 months in the surgery arm and 29.0 months in the nonsurgery arm (HR 0.598, 95% CI 0.343–1.043; P = 0.0668).

Conclusion:
The prospective phase III trial ABCSG-28 (POSYTIVE) could not demonstrate an OS benefit for surgical resection of the primary in breast cancer patients presenting with de novo stage IV disease.
Evolutionary trade-offs and the structure of polymorphisms
Authors: Sheftel Hila , Szekely Pablo , Mayo Avi , Sella Guy , Alon Uri 
Published: April 2018

Populations of organisms show genetic differences called polymorphisms. Understanding the effects of polymorphisms is important for biology and medicine. Here, we ask which polymorphisms occur at high frequency when organisms evolve under trade-offs between multiple tasks. Multiple tasks present a problem, because it is not possible to be optimal at all tasks simultaneously and hence compromises are necessary. Recent work indicates that trade-offs lead to a simple geometry of phenotypes in the space of traits: phenotypes fall on the Pareto front, which is shaped as a polytope: a line, triangle, tetrahedron etc. The vertices of these polytopes are the optimal phenotypes for a single task. Up to now, work on this Pareto approach has not considered its genetic underpinnings. Here, we address this by asking how the polymorphism structure of a population is affected by evolution under trade-offs. We simulate a multi-task selection scenario, in which the population evolves to the Pareto front: the line segment between two archetypes or the triangle between three archetypes. We find that polymorphisms that become prevalent in the population have pleiotropic phenotypic effects that align with the Pareto front. Similarly, epistatic effects between prevalent polymorphisms are parallel to the front. Alignment with the front occurs also for asexual mating. Alignment is reduced when drift or linkage is strong, and is replaced by a more complex structure in which many perpendicular allele effects cancel out. Aligned polymorphism structure allows mating to produce offspring that stand a good chance of being optimal multi-taskers in at least one of the locales available to the species.This article is part of the theme issue ‘Self-organization in cell biology’.
Self-organization principles of intracellular pattern formation
Authors: Halatek J. , Brauns F. , Frey E. 
Published: April 2018

Dynamic patterning of specific proteins is essential for the spatio-temporal regulation of many important intracellular processes in prokaryotes, eukaryotes and multicellular organisms. The emergence of patterns generated by interactions of diffusing proteins is a paradigmatic example for self-organization. In this article, we review quantitative models for intracellular Min protein patterns inEscherichia coli, Cdc42 polarization inSaccharomyces cerevisiaeand the bipolar PAR protein patterns found inCaenorhabditis elegans. By analysing the molecular processes driving these systems we derive a theoretical perspective on general principles underlying self-organized pattern formation. We argue that intracellular pattern formation is not captured by concepts such as ‘activators’, ‘inhibitors’ or ‘substrate depletion’. Instead, intracellular pattern formation is based on the redistribution of proteins by cytosolic diffusion, and the cycling of proteins between distinct conformational states. Therefore, mass-conserving reaction–diffusion equations provide the most appropriate framework to study intracellular pattern formation. We conclude that directed transport, e.g. cytosolic diffusion along an actively maintained cytosolic gradient, is the key process underlying pattern formation. Thus the basic principle of self-organization is the establishment and maintenance of directed transport by intracellular protein dynamics.This article is part of the theme issue ‘Self-organization in cell biology’.
Fluid flows shaping organism morphology
Authors: Alim Karen 
Published: April 2018

A dynamic self-organized morphology is the hallmark of network-shaped organisms like slime moulds and fungi. Organisms continuously reorganize their flexible, undifferentiated body plans to forage for food. Among these organisms the slime mould
Physarum polycephalum
has emerged as a model to investigate how an organism can self-organize their extensive networks and act as a coordinated whole. Cytoplasmic fluid flows flowing through the tubular networks have been identified as the key driver of morphological dynamics. Inquiring how fluid flows can shape living matter from small to large scales opens up many new avenues for research. This article is part of the theme issue ‘Self-organization in cell biology’.
Ordering of myosin II filaments driven by mechanical forces: experiments and theory
Authors: Dasbiswas Kinjal , Hu Shiqiong , Schnorrer Frank , Safran Samuel A. , Bershadsky Alexander D. 
Published: April 2018

Myosin II filaments form ordered superstructures in both cross-striated muscle and non-muscle cells. In cross-striated muscle, myosin II (thick) filaments, actin (thin) filaments and elastic titin filaments comprise the stereotypical contractile units of muscles called sarcomeres. Linear chains of sarcomeres, called myofibrils, are aligned laterally in registry to form cross-striated muscle cells. The experimentally observed dependence of the registered organization of myofibrils on extracellular matrix elasticity has been proposed to arise from the interactions of sarcomeric contractile elements (considered as force dipoles) through the matrix. Non-muscle cells form small bipolar filaments built of less than 30 myosin II molecules. These filaments are associated in registry forming superstructures (‘stacks’) orthogonal to actin filament bundles. Formation of myosin II filament stacks requires the myosin II ATPase activity and function of the actin filament crosslinking, polymerizing and depolymerizing proteins. We propose that the myosin II filaments embedded into elastic, intervening actin network (IVN) function as force dipoles that interact attractively through the IVN. This is in analogy with the theoretical picture developed for myofibrils where the elastic medium is now the actin cytoskeleton itself. Myosin stack formation in non-muscle cells provides a novel mechanism for the self-organization of the actin cytoskeleton at the level of the entire cell.This article is part of the theme issue ‘Self-organization in cell biology’.
Guided by curvature: shaping cells by coupling curved membrane proteins and cytoskeletal forces
Authors: Gov N. S. 
Published: April 2018

Eukaryote cells have flexible membranes that allow them to have a variety of dynamical shapes. The shapes of the cells serve important biological functions, both for cells within an intact tissue, and during embryogenesis and cellular motility. How cells control their shapes and the structures that they form on their surface has been a subject of intensive biological research, exposing the building blocks that cells use to deform their membranes. These processes have also drawn the interest of theoretical physicists, aiming to develop models based on physics, chemistry and nonlinear dynamics. Such models explore quantitatively different possible mechanisms that the cells can employ to initiate the spontaneous formation of shapes and patterns on their membranes. We review here theoretical work where one such class of mechanisms was investigated: the coupling between curved membrane proteins, and the cytoskeletal forces that they recruit. Theory indicates that this coupling gives rise to a rich variety of membrane shapes and dynamics, while experiments indicate that this mechanism appears to drive many cellular shape changes.
This article is part of the theme issue ‘Self-organization in cell biology’.
Lipid self-assembly and lectin-induced reorganization of the plasma membrane
Authors: Sych Taras , Mély Yves , Römer Winfried 
Published: April 2018

The plasma membrane represents an outstanding example of self-organization in biology. It plays a vital role in protecting the integrity of the cell interior and regulates meticulously the import and export of diverse substances. Its major building blocks are proteins and lipids, which self-assemble to a fluid lipid bilayer driven mainly by hydrophobic forces. Even if the plasma membrane appears—globally speaking—homogeneous at physiological temperatures, the existence of specialized nano- to micrometre-sized domains of raft-type character within cellular and synthetic membrane systems has been reported. It is hypothesized that these domains are the origin of a plethora of cellular processes, such as signalling or vesicular trafficking. This review intends to highlight the driving forces of lipid self-assembly into a bilayer membrane and the formation of small, transient domains within the plasma membrane. The mechanisms of self-assembly depend on several factors, such as the lipid composition of the membrane and the geometry of lipids. Moreover, the dynamics and organization of glycosphingolipids into nanometre-sized clusters will be discussed, also in the context of multivalent lectins, which cluster several glycosphingolipid receptor molecules and thus create an asymmetric stress between the two membrane leaflets, leading to tubular plasma membrane invaginations.
This article is part of the theme issue ‘Self-organization in cell biology’.
Controlling compartmentalization by non-membrane-bound organelles
Authors: Wheeler Richard J. , Hyman Anthony A. 
Published: April 2018

Compartmentalization is a characterizing feature of complexity in cells, used to organize their biochemistry. Membrane-bound organelles are most widely known, but non-membrane-bound liquid organelles also exist. These have recently been shown to form by phase separation of specific types of proteins known as scaffolds. This forms two phases: a condensate that is enriched in scaffold protein separated by a phase boundary from the cytoplasm or nucleoplasm with a low concentration of the scaffold protein. Phase separation is well known for synthetic polymers, but also appears important in cells. Here, we review the properties of proteins important for forming these non-membrane-bound organelles, focusing on the energetically favourable interactions that drive condensation. On this basis we make qualitative predictions about how cells may control compartmentalization by condensates; the partition of specific molecules to a condensate; the control of condensation and dissolution of condensates; and the regulation of condensate nucleation. There are emerging data supporting many of these predictions, although future results may prove incorrect. It appears that many molecules may have the ability to modulate condensate formation, making condensates a potential target for future therapeutics. The emerging properties of condensates are fundamentally unlike the properties of membrane-bound organelles. They have the capacity to rapidly integrate cellular events and act as a new class of sensors for internal and external environments.This article is part of the theme issue ‘Self-organization in cell biology’.
Acute-stress impairs cytoprotective mechanisms through neural inhibition of the insulin pathway
Authors: José De Rosa Maria , Veuthey Tania , Florman Jeremy , Grant Jeff , Blanco Gabriela , Andersen Natalia , Donnelly Jamie , Rayes Diego , Alkema Mark J. 
Published: April 2018

ABSTRACTPersistent activation of the “fight-or-flight” response accelerates aging and increases the susceptibility to disease. We show that repeated induction of the C. elegans flight response inhibits conserved cytoprotective mechanisms. This acute-stress response activates neurons that release tyramine, the invertebrate analog of adrenaline/noradrenaline. Tyramine stimulates the DAF-2/Insulin/IGF-1 pathway and precludes the nuclear translocation of the DAF-16/FOXO transcription factor through the activation of an adrenergic-like receptor TYRA-3 in the intestine. In contrast, environmental long-term stressors, such as heat or oxidative stress, reduce tyramine release allowing the induction of FOXO-dependent cytoprotective genes. These findings demonstrate how a neural stress-hormone signaling provides a state-dependent neural switch between acute and long-term stress responses, and provide mechanistic insights how acute stress impairs cellular defensive systems.One Sentence Summary: The “fight-or-flight” response reduces resistance to environmental challenges.
HMMRATAC: a Hidden Markov ModeleR for ATAC-seq
Authors: Tarbell Evan D. , Liu Tao 
Published: April 2018

ABSTRACTATAC-seq has been widely adopted to identify accessible chromatin regions across the genome. However, current data analysis still utilizes approaches initially designed for ChIP-seq or DNase-seq, without considering the transposase digested DNA fragments that contain additional nucleosome positioning information. We present the first dedicated ATAC-seq analysis tool, a semi-supervised machine learning approach named HMMRATAC. HMMRATAC splits a single ATAC-seq dataset into nucleosome-free and nucleosome-enriched signals, learns the unique chromatin structure around accessible regions, and then predicts accessible regions across the entire genome. We show that HMMRATAC outperforms the popular peak-calling algorithms on published human ATAC-seq datasets. We find that single-end sequenced or size-selected ATAC-seq datasets result in a loss of sensitivity compared to paired-end datasets without size-selection.
Synthetic methanogenic communities reveal differential impact of ecological perturbations on aceto- and hydrogeno-trophic methanogens
Authors: Chen Jing , Wade Matthew , Dolfing Jan , Soyer Orkun S 
Published: April 2018

ABSTRACTSynthetic microbial communities provide reduced microbial ecologies that can be studied under defined conditions. Here, we use this approach to study the interactions underpinning anaerobic digestion communities and involving the key microbial populations of a sulfate reducer (Desulfovibrio vulgaris), and aceto-(Methanosarcina barkeri) and hydrogenotrophic (Methanococcus maripaludis) methanogens. We create all possible mixed culture combinations of these species and analyse the stability and productivity of each system over multiple sub-culturings and under different sulfate levels, mimicking ecological perturbation in the form of strong electron acceptor availability. We find that all three species can co-exist in the absence of sulfate, and that system productivity (in form of methane production from lactate) increases by almost two-fold compared to co-cultures. With increasing sulfate availability, co-existence is perturbed and both methanogenic populations display a diminishing trend. Interestingly, we find that, despite the continued presence of acetate in the system, the acetotrophic methanogens are more readily disrupted by sulfate perturbation. We show that this is due to a shift inM. barkerimetabolism towards increased co-utilisation of hydrogen with acetate, which we verified through experiments on mono cultures and mass balance calculations in co-cultures. We conclude that hydrogen is a key factor for both hydrogeno- and aceto-trophic methanogenesis and can influence these populations differentially under the common ecological perturbation of strong electron acceptor availability. These findings will help engineering of larger synthetic communities for specific applications in biodegradation and understanding complex anaerobic digestion communities found in animal guts, sediments, and bioreactors.
RANKuser
Authors: Singh Abhishek Kumar , Nagwani Naresh Kumar , Pandey Sudhakar 
Published: April 2018

PurposeRecently, with a high volume of users and user’s content in Community Question Answering (CQA) sites, the quality of answers provided by users has raised a big concern. Finding the expert users can be a method to address this problem, which aims to find the suitable users (answerers) who can provide high-quality relevant answers. The purpose of this paper is to find the expert users for the newly posted questions of the CQA sites.Design/methodology/approachIn this paper, a new algorithm, RANKuser, is proposed for identifying the expert users of CQA sites. The proposed RANKuser algorithm consists of three major stages. In the first stage, folksonomy relation between users, tags, and queries is established. User profile attributes, namely, reputation, tags, and badges, are also considered in folksonomy. In the second stage, expertise scores of the user are calculated based on reputation, badges, and tags. Finally, in the third stage, the expert users are identified by extracting topNusers based on expertise score.FindingsIn this work, with the help of proposed ranking algorithm, expert users are identified for newly posted questions. In this paper, comparison of proposed user ranking algorithm (RANKuser) is also performed with other existing ranking algorithms, namely, ML-KNN, rankSVM, LDA, STM CQARank, and EV-based model using performance parameters such as hamming loss, accuracy, average precision, one error,F-measure, and normalized discounted cumulative gain. The proposed ranking method is also compared to the original ranking of CQA sites using the pairedt-test. The experimental results demonstrate the effectiveness of the proposed RANKuser algorithm in comparison with the existing ranking algorithms.Originality/valueThis paper proposes and implements a new algorithm for expert user identification in CQA sites. By utilizing the folksonomy in CQA sites and information of user profile, this algorithm identifies the experts.
The impact of young Chinese employees’ notions of work on conflict management styles
Authors: Meng Yong , Yu Haiyun , Ma Zhenzhong , Yang Zhiyong 
Published: April 2018

PurposeThis study aims to explore the impact of well-educated young Chinese employees’ notions of work on their conflict management styles in the increasingly turbulent workplace to help better manage work-related conflict in the time of transition in China.Design/methodology/approachSelf-administered questionnaires were used to collect data from over 400 young Chinese employees. The data were first factor analyzed to explore the underlying dimensions of contemporary work notions in China’s transition period. Hierarchical regression analysis was then conducted to explore the relationship between dimensions of work notions and conflict management styles.FindingsThe results showed that well-educated young Chinese employees’ notions of work consisted of sense of control, fulfilling and rewarding, holistic concerns, personal growth and development and meaningfulness. The results further indicated that young Chinese employees with strong needs to satisfy individual interests in their work tend to use competitive methods to manage work-related conflicts, employees with strong needs to satisfy group interests in their work prefer to use collaborative methods and those who believe in collective efforts in achieving individual goals through group goals’ obtainment are more likely to use collaborative and compromising approaches.Originality/valueThis study provides a new perspective to manage work-related conflict in the Chinese context. The findings of this study are able to help enrich conflict management theories in China and suggest insightful conflict resolution approaches to work-related conflicts in China’s changing environment. This study also helps bridge the research gap between work notions and conflict management styles. The results of this study can greatly facilitate Chinese companies’ endeavors toward crafting a more innovative workforce and help improve employee performance in China’s transition to industrialization.
Does the quality of academic life mediate the satisfaction, loyalty and recommendation of HEI students?
Authors: Pedro Eugénia de Matos , Alves Helena , Leitão João 
Published: April 2018

PurposeThe purpose of this paper is to identify the effects of students’ satisfaction with services on quality of academic life (QAL), formed by cognitive and affective components; and to assess the mediating effect of QOL components (cognitive and affective) on students’ loyalty and recommendation.Design/methodology/approachBased on 726 respondent students from public higher education institutions (HEIs) in Portugal, this paper uses a partial least squares approach to analyze the impact of satisfaction on emotions and students’ QAL and to assess whether emotions influence recommendation and loyalty.FindingsThe results reveal that satisfaction influences both cognitive and affective components of QAL. The cognitive component has a positive and significant influence on recommendation and loyalty whilst the affective component has no significant effect.Practical implicationsThe results obtained here provide implications for future action to be taken by HEI managers, in order to increase efficiency in the allocation and management of scarce resources. Therefore, when incorporating these results in decision-making processes, attention should be paid to the importance of the influence of satisfaction on QAL’s cognitive and affective components, stressing the importance of the cognitive components associated with learning experiences that play an important role in students’ future decisions in terms of loyalty and recommendation, which, in turn, are pillars of HEI sustainability.Originality/valueThe present study contributes to the literature on HEI management by assessing the influence of satisfaction on two components of QAL separately: cognitive components and affective components. In addition, the causality relationships are analyzed, assessing the emotional nexus, in order to deepen knowledge about the role played by both affective and cognitive components in students’ loyalty and recommendation, which need to be addressed and studied by carrying out new research.