bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Association of Work Characteristics With Ovarian Cancer Risk and Mortality
Authors: Trudel-Fitzgerald Claudia , Poole Elizabeth M. , Idahl Annika , Lundin Eva , Sood Anil K. , Kawachi Ichiro , Kubzansky Laura D. , Tworoger Shelley S. 
Published: March 2017

ABSTRACT

Objective
Ovarian cancer (OvCA) is a leading cause of cancer death for women. Depression and social isolation have been associated with a higher OvCA risk and poorer survival, but other forms of chronic psychosocial stress, including work-related characteristics, remain understudied.

Methods
Women from three prospective cohorts (Nurses' Health Study: n = 31,754; Nurses' Health Study II: n = 74,260; Northern Sweden Health and Disease Study: n
nested case–control study = 196) completed a job questionnaire, assessing demand and control at work, social support provided by coworkers and supervisor, and job security. Multivariate Cox and conditional logistic regression models estimated hazard ratios (Nurses' Health Study/Nurses' Health Study II) and odd ratios (Northern Sweden Health and Disease Study) of OvCA risk and mortality among cases. Random coefficient models were used for meta-analyses.

Results
There were 396 OvCA cases and 186 deaths during follow-up. Overall, job strain, strain chronicity, social support, and job security were not significantly associated with OvCA risk (e.g., pooled relative risk [RR]high demand/low control = 1.06, confidence interval [CI] = 0.72–1.55) or mortality (e.g., pooled RRhigh demand/low control = 1.08, CI = 0.64–1.82). When considered individually, compared with low levels, only moderate levels of demand were associated with a reduced OvCA risk (pooled RR = 0.66, CI = 0.49–0.90). Social support provided by the coworker or the supervisor did not moderate the association of job strain with either OvCA risk or overall mortality.

Conclusions
We did not observe clear associations between work characteristics and OvCA incidence or mortality, but further research with diverse populations is warranted.
Chlamydia trachomatis and chlamydia-like bacteria: new enemies of human pregnancies
Authors: Ammerdorffer Anne , Stojanov Miloš , Greub Gilbert , Baud David 
Published: March 2017

Purpose of review
This review provides an update on the roles of Chlamydia trachomatis and the related Waddlia chondrophila and Parachlamydia acanthamoebae in miscarriage, stillbirths and preterm labour in humans. A broad audience, including microbiologist, infectiologists, obstetricians and gynaecologists, should be aware of the potential threat of these Chlamydiales for human reproduction.

Recent findings
Despite increasing laboratory techniques and possibilities to perform diagnostic tests, the cause of miscarriage is only identified in 50% of the cases. Intracellular bacteria, such as C. trachomatis and Chlamydia-related bacteria, are difficult to detect in routine clinical samples and could represent possible agents of miscarriages. C. trachomatis is considered the world largest sexual transmitted bacterial agent and is associated with adverse pregnancy outcome in human. In the last decade Chlamydia-like organisms, such as W. chondrophila and P. acanthamoebae, have also been associated with adverse pregnancy outcomes in human and/or animals.

Summary
We review here the current evidences for a pathogenic role in humans, the diagnostic approaches and possible treatment options of C. trachomatis, W. chondrophila and P. acanthamoebae.
Redefining progressive encephalomyelitis with rigidity and myoclonus after the discovery of antibodies to glycine receptors
Authors: Crisp Sarah J. , Balint Bettina , Vincent Angela 
Published: March 2017

Purpose of review
This review highlights the recent discovery of antibodies to glycine receptor (GlyR-Ab) and discusses the relationship between these antibodies and neurological disorders.

Recent findings
Since the initial description in 2008 of antibodies to glycine receptors (GlyR-Abs) in a patient with progressive encephalomyelitis with rigidity and myoclonus (PERM), these antibodies have been found in PERM and in some patients with a variety of stiff person spectrum (SPS) or related disorders. Patients with GlyR-Abs often improve with aggressive immunotherapy, and antibody titres correlate with disease severity. Around 25% of patients have another autoimmune condition and 10–20% have an underlying malignancy. GlyR-Abs bind to extracellular determinants, are mainly Immunoglobulin G1 subclass and induce GlyR internalization in Human embryonic kidney 293 cells, suggesting pathogenicity. The spectrum of neurological disease associated with GlyR-Abs has not been fully characterized, and lower titres may not be syndrome specific, but GlyR-Abs, like antibodies to other neuronal cell-surface antigens, define immunotherapy-responsive disease and are likely to be pathogenic. This distinguishes them from the glutamic acid decarboxylase antibodies that can also be found at high titres in patients with classical stiff person syndrome which is more often chronic and relatively resistant to immunological treatments.

Summary
Irrespective of the clinical features, GlyR-Abs are helpful in the diagnosis of patients who very often have a subacute, progressive and life-threatening disorder which shows a favourable response to immunotherapy.
Neuromyelitis optica and neuromyelitis optica spectrum disorders
Authors: Marignier Romain , Cobo Calvo Alvaro , Vukusic Sandra 
Published: March 2017

Purpose of review
The discovery of highly specific auto-antibodies directed against the water channel aquaporin 4 was a quantum leap in the definition, classification and management of neuromyelitis optica (NMO). Herein, we propose an update on epidemiological, clinical and therapeutic advances in the field, underlining unmet needs.

Recent findings
Large-scale epidemiological studies have recently provided a more precise evaluation of NMO prevalence and a better stratification regarding ethnicity and sex. New criteria have been proposed for so-called NMO spectrum disorders (NMOSD) and their relevance is currently being assessed. The identification of a new clinical entity associated to antibodies against myelin oligodendrocyte glycoprotein questions the border of NMOSD.

Summary
The concept of NMOSD is opening a new era in clinical practice, allowing an easier and more homogeneous diagnosis and an increase in newly identified cases. This will facilitate clinical studies and support new therapeutic trial. Future researches should focus on the position of seronegative NMOSD and myelin oligodendrocyte glycoprotein-IgG disorders in the field and on promising strategies, including the immune tolerisation approaches, to eventually cure NMO.
Predictive Value of Electrocorticography in Patients With Mesial Temporal Lobe Epilepsy Undergoing Selective Amygdalohippocampectomy
Authors: Herlopian Aline , Shihabuddin Bashir 
Published: March 2017

Purpose:
The utility of intraoperative electrocorticography has been reported in predicting seizure outcome in patients with mesial temporal lobe epilepsy due to mesial temporal sclerosis (MTS) undergoing standard temporal lobectomy. Three studies reported the predictive outcome in patients with MTS undergoing selective amygdalohippocampectomy (sAHE). We evaluate the predictive value of the intraoperative electrocorticography in postoperative outcome in patients with mesial temporal lobe epilepsy secondary to MTS undergoing sAHE.

Methods:
Retrospective analysis of 36 consecutive patients with mesial temporal lobe epilepsy undergoing sAHE between 2001 and 2012. A single neurosurgeon performed the sAHE. Preresection and postresection spikes were recorded in all patients and interpreted by two epileptologists. Long-term postoperative seizure freedom was correlated with intraoperative electrocorticography findings.

Results:
Ten patients had normal brain MRI (G1), whereas 26 had MTS (G2). All patients had MTS on histopathology. Mean duration of postoperative follow-up was 21.3 and 24.4 months for G1 and G2, respectively. In G1, 4/10 (40%) had resolution of spikes after sAHE, with 2/4 (50%) seizure free at last follow-up. Spikes were persistent in 6/10 (60%), with 5/6 (83%) seizure free at last follow-up (P value = 0.5). In G2, 7/26 (27%) had postresection resolution of spikes, with 5/7 (71%) seizure free at last follow-up. Spikes were persistent in 19/26 (73%), with 13/19 (68%) seizure free at last follow-up (P value = 0.62). The difference between the two arms of G1 and G2 was statistically insignificant.

Conclusions:
Postresection intraoperative electrocorticography has limited value in predicting postoperative seizure freedom in patients with mesial temporal lobe epilepsy secondary to MTS undergoing sAHE.
The evolution of transmission mode
Authors: Antonovics Janis , Wilson Anthony J. , Forbes Mark R. , Hauffe Heidi C. , Kallio Eva R. , Leggett Helen C. , Longdon Ben , Okamura Beth , Sait Steven M. , Webster Joanne P. 
Published: March 2017

This article reviews research on the evolutionary mechanisms leading to different transmission modes. Such modes are often under genetic control of the host or the pathogen, and often in conflict with each other via trade-offs. Transmission modes may vary among pathogen strains and among host populations. Evolutionary changes in transmission mode have been inferred through experimental and phylogenetic studies, including changes in transmission associated with host shifts and with evolution of the unusually complex life cycles of many parasites. Understanding the forces that determine the evolution of particular transmission modes presents a fascinating medley of problems for which there is a lack of good data and often a lack of conceptual understanding or appropriate methodologies. Our best information comes from studies that have been focused on the vertical versus horizontal transmission dichotomy. With other kinds of transitions, theoretical approaches combining epidemiology and population genetics are providing guidelines for determining when and how rapidly new transmission modes may evolve, but these are still in need of empirical investigation and application to particular cases. Obtaining such knowledge is a matter of urgency in relation to extant disease threats.This article is part of the themed issue ‘Opening the black box: re-examining the ecology and evolution of parasite transmission’.
Host allometry influences the evolution of parasite host-generalism: theory and meta-analysis
Authors: Walker Josephine G. , Hurford Amy , Cable Jo , Ellison Amy R. , Price Stephen J. , Cressler Clayton E. 
Published: March 2017

Parasites vary widely in the diversity of hosts they infect: some parasite species are specialists—infecting just a single host species, while others are generalists, capable of infecting many. Understanding the factors that drive parasite host-generalism is of basic biological interest, but also directly relevant to predicting disease emergence in new host species, identifying parasites that are likely to have unidentified additional hosts, and assessing transmission risk. Here, we use mathematical models to investigate how variation in host body size and environmental temperature affect the evolution of parasite host-generalism. We predict that parasites are more likely to evolve a generalist strategy when hosts are large-bodied, when variation in host body size is large, and in cooler environments. We then explore these predictions using a newly updated database of over 20 000 fish–macroparasite associations. Within the database we see some evidence supporting these predictions, but also highlight mismatches between theory and data. By combining these two approaches, we establish a theoretical basis for interpreting empirical data on parasites' host specificity and identify key areas for future work that will help untangle the drivers of parasite host-generalism.This article is part of the themed issue ‘Opening the black box: re-examining the ecology and evolution of parasite transmission’.
Contact structure, mobility, environmental impact and behaviour: the importance of social forces to infectious disease dynamics and disease ecology
Authors: Arthur Ronan F. , Gurley Emily S. , Salje Henrik , Bloomfield Laura S. P. , Jones James H. 
Published: March 2017

Human factors, including contact structure, movement, impact on the environment and patterns of behaviour, can have significant influence on the emergence of novel infectious diseases and the transmission and amplification of established ones. As anthropogenic climate change alters natural systems and global economic forces drive land-use and land-cover change, it becomes increasingly important to understand both the ecological and social factors that impact infectious disease outcomes for human populations. While the field of disease ecology explicitly studies the ecological aspects of infectious disease transmission, the effects of the social context on zoonotic pathogen spillover and subsequent human-to-human transmission are comparatively neglected in the literature. The social sciences encompass a variety of disciplines and frameworks for understanding infectious diseases; however, here we focus on four primary areas of social systems that quantitatively and qualitatively contribute to infectious diseases as social–ecological systems. These areas are social mixing and structure, space and mobility, geography and environmental impact, and behaviour and behaviour change. Incorporation of these social factors requires empirical studies for parametrization, phenomena characterization and integrated theoretical modelling of social–ecological interactions. The social–ecological system that dictates infectious disease dynamics is a complex system rich in interacting variables with dynamically significant heterogeneous properties. Future discussions about infectious disease spillover and transmission in human populations need to address the social context that affects particular disease systems by identifying and measuring qualitatively important drivers.This article is part of the themed issue ‘Opening the black box: re-examining the ecology and evolution of parasite transmission’.
Contrasting determinants of mutation rates in germline and soma
Authors: Chen Chen , Qi Hongjian , Shen Yufeng , Pickrell Joseph , Przeworski Molly 
Published: March 2017

AbstractRecent studies of somatic and germline mutations have led to the identification of a number of factors that influence point mutation rates, including CpG methylation, expression levels, replication timing and GC content. Intriguingly, some of the effects appear to differ between soma and germline: in particular, whereas mutation rates have been reported to decrease with expression levels in tumors, no clear effect has been detected in the germline. Distinct approaches were taken to analyze the data, however, so it is hard to know whether these apparent differences are real. To enable a cleaner comparison, we considered a statistical model in which the mutation rate of a coding region is predicted by GC content, expression levels, replication timing, and two histone repressive marks. We applied this model to both a set of germline mutations identified in exomes and to exonic somatic mutations in four types of tumors. Germline and soma share most determinants of mutations; notably, we detected an effect of expression levels on germline mutations as well as on somatic ones. However, whereas in somatic tissues, increased expression levels are associated with greater strand asymmetry anddecreasedmutation rates, in ovaries and testes, increased expression leads to greater strand asymmetry butincreasedmutation rates. This contrast points to differences in damage or repair rates during transcription in soma and germline.
Evaluation and Design of Genome-wide CRISPR/Cas9 Knockout Screens
Authors: Hart Traver , Tong Amy , Chan Katie , Leeuwen Jolanda Van , Seetharaman Ashwin , Aregger Michael , Chandrashekhar Megha , Hustedt Nicole , Seth Sahil , Noonan Avery , Habsid Andrea , Sizova Olga , Nedyalkova Lyudmila , Climie Ryan , Lawson Keith , Sartori Maria Augusta , Alibeh Sabriyeh , Tieu David , Masud Sanna , Mero Patricia , Weiss Alexander , Brown Kevin R. , Usaj Matej , Billmann Maximilian , Rahman Mahfuzur , Constanzo Michael , Myers Chad L. , Andrews Brenda J. , Boone Charles , Durocher Daniel , Moffat Jason 
Published: March 2017

AbstractThe adaptation of CRISPR/Cas9 technology to mammalian cell lines is transforming the study of human functional genomics. Pooled libraries of CRISPR guide RNAs (gRNAs), targeting human protein-coding genes and encoded in viral vectors, have been used to systematically create gene knockouts in a variety of human cancer and immortalized cell lines, in an effort to identify whether these knockouts cause cellular fitness defects. Previous work has shown that CRISPR screens are more sensitive and specific than pooled library shRNA screens in similar assays, but currently there exists significant variability across CRISPR library designs and experimental protocols. In this study, we re-analyze 17 genome-scale knockout screens in human cell lines from three research groups using three different genome-scale gRNA libraries, using the Bayesian Analysis of Gene Essentiality (BAGEL) algorithm to identify essential genes, to refine and expand our previously defined set of human core essential genes, from 360 to 684 genes. We use this expanded set of reference Core Essential Genes (CEG2), plus empirical data from six CRISPR knockout screens, to guide the design of a sequence-optimized gRNA library, the Toronto KnockOut version 3.0 (TKOv3) library. We demonstrate the high effectiveness of the library relative to reference sets of essential and nonessential genes as well as other screens using similar approaches. The optimized TKOv3 library, combined with the CEG2 reference set, provide an efficient, highly optimized platform for performing and assessing gene knockout screens in human cell lines.
Colonization history of the Western Corn Rootworm (Diabrotica virgifera virgifera) in North America: insights from random forest ABC using microsatellite data
Authors: Lombaert Eric , Ciosi Marc , Miller Nicholas J. , Sappington Thomas W. , Blin Aurélie , Guillemaud Thomas 
Published: March 2017

AbstractFirst described from western Kansas, USA, the western corn rootworm,Diabrotica virgifera virgifera, is one of the worst pests of maize. The species is generally thought to be of Mexican origin and to have incidentally followed the expansion of maize cultivation into North America thousands of years ago. However, this hypothesis has never been investigated formally. In this study, the genetic variability of samples collected throughout North America was analysed at 13 microsatellite marker loci to explore precisely the population genetic structure and colonization history ofD. v. virgifera. In particular, we used up-to-date Approximate Bayesian Computation methods based on random forest algorithms to test a Mexican versus a central-USA origin of the species, and to compare various possible timings of colonization. This analysis provided strong evidence that the origin ofD. v. virgiferawas southern (Mexico, or even further south). Surprisingly, we also found that the expansion of the species north of its origin was recent - probably not before 1100 years ago - thus indicating it was not directly associated with the early history of maize expansion out of Mexico, a far more ancient event.
Transformation from independent to integrative coding of multi-object arrangements in human visual cortex
Authors: Kaiser Daniel , Peelen Marius V. 
Published: March 2017

AbstractTo optimize processing, the human visual system utilizes regularities present in naturalistic visual input. One of these regularities is the relative position of objects in a scene (e.g., a sofa in front of a television), with behavioral research showing that regularly positioned objects are easier to perceive and to remember. Here we use fMRI to test how positional regularities are encoded in the visual system. Participants viewed pairs of objects that formed minimalistic two-object scenes (e.g., a “living room” consisting of a sofa and television) presented in their regularly experienced spatial arrangement or in an irregular arrangement (with interchanged positions). Additionally, single objects were presented centrally and in isolation. Multi-voxel activity patterns evoked by the object pairs were modeled as the average of the response patterns evoked by the two single objects forming the pair. In two experiments, this approximation in object-selective cortex was significantly less accurate for the regularly than the irregularly positioned pairs, indicating integration of individual object representations. More detailed analysis revealed a transition from independent to integrative coding along the posterior-anterior axis of the visual cortex, with the independent component (but not the integrative component) being almost perfectly predicted by object selectivity across the visual hierarchy. These results reveal a transitional stage between individual object and multi-object coding in visual cortex, providing a possible neural correlate of efficient processing of regularly positioned objects in natural scenes.
Aggressiveness as a latent personality trait of domestic dogs: testing local independence and measurement invariance
Authors: Goold Conor , Newberry Ruth C. 
Published: March 2017

AbstractStudies of animal personality attempt to uncover underlying or ‘latent’ personality traits that explain broad patterns of behaviour, often by applying latent variable statistical models (e.g. factor analysis) to multivariate data sets. Two integral, but infrequently confirmed, assumptions of latent variable models in animal personality are: i) behavioural variables are independent (i.e. uncorrelated) conditional on the latent personality traits they reflect (local independence), and ii) personality traits are associated with behavioural variables in the same way across individuals or groups of individuals (measurement invariance). We tested these assumptions using observations of aggression in four age classes (4 - 10 months, 10 months - 3 years, 3 - 6 years, over 6 years) of male and female shelter dogs (N = 4,743) in 11 different contexts. A structural equation model supported the hypothesis of two positively correlated personality traits underlying aggression across contexts: aggressiveness towards people and aggressiveness towards dogs (comparative fit index: 0.96; Tucker-Lewis index: 0.95; root mean square error of approximation: 0.03). Aggression across contexts was moderately repeatable (towards people: intraclass correlation coefficient (ICC) = 0.479; towards dogs: ICC = 0.303).However, certain contexts related to aggressiveness towards people (but not dogs) shared significant residual relationships unaccounted for by latent levels of aggressiveness.Furthermore, aggressiveness towards people and dogs in different contexts interacted with sex and age. Thus, sex and age differences in displays of aggression were not simple functions of underlying aggressiveness. Our results illustrate that the robustness of traits in latent variable models must be critically assessed before making conclusions about the effects of, or factors influencing, animal personality. Our findings are of concern because inaccurate ‘aggressive personality’ trait attributions can be costly to dogs, recipients of aggression and society in general.