bluuebunny/crossref_metadata_2025_split huggingface dataset:
Preoperative Resectability Estimates of Nonenhancing Glioma by Neurosurgeons and a Resection Probability Map
Authors: Hendriks Eef J , Idema Sander , Hervey-Jumper Shawn L , Bernat Anne-Laure , Zwinderman Aeilko H , Barkhof Frederik , Vandertop W Peter , Mandonnet Emmanuel , Duffau Hugues , Berger Mitchel S , De Witt Hamer Philip C 
Published: September 2018

Abstract

BACKGROUND
Preoperative interpretation of resectability of diffuse nonenhancing glioma is primarily based on individual surgical expertise.

OBJECTIVE
To compare the accuracy and precision between observed resections and preoperative estimates of neurosurgeons and a resection probability map (RPM). We hypothesize that the RPM estimates is as good as senior neurosurgeons.

METHODS
A total of 234 consecutive patients were included from 2 centers, who had resective surgery with functional mapping between 2006 and 2012 for a supra-tentorial nonenhancing glioma. Extent of resection (EOR) and residual tumor volume (RTV) were segmented and an RPM was constructed in standard brain space. Three junior and three senior neurosurgeons estimated EOR and RTV, blinded for postoperative results. We determined the agreement between the estimates and calculated the diagnostic accuracy of the neurosurgeons and the RPM to predict the observed resections.

RESULTS
Preoperative estimates of resection results by junior and senior neurosurgeons were significantly biased towards overestimation of EOR (4.2% and 11.2%) and underestimation of RTV (4.3 and 9.0 mL), whereas estimates of the RPM were unbiased (−2.6% and −.2 mL, respectively). The limits of agreement were wide for neurosurgeons and for the RPM. The RPM was significantly more accurate in identifying patients in whom an EOR >40% was observed than neurosurgeons.

CONCLUSION
Neurosurgeons estimate preoperative resectability before surgery of a nonenhancing glioma rather accurate–with a small bias–and imprecise–with wide limits of agreement. An RPM provides unbiased resectability estimates, which can be useful for surgical decision-making, planning, and education.
Leadership and Change in Winnipeg’s Smart Policing Initiative
Authors: Catte Ryan , Linden Rick 
Published: September 2018

Abstract
If evidence-based policing is to be successful, we need to know more about how leaders can successfully introduce change into their organizations. This study looks at a Smart Policing Initiative (SPI) implemented by the Winnipeg Police Service. Line officers and management personnel were interviewed to determine how they dealt with the implementation of SPI. We used activity data to determine whether officers actually carried out the activities integral to the SPI programme. The research concludes that there was attitudinal ‘buy-in’ to the programme and that the officers did carry out the proactive policing activities mandated by the programme.
Do Female Officers Improve Law Enforcement Quality? Effects on Crime Reporting and Domestic Violence
Authors: Miller Amalia R , Segal Carmit 
Published: September 2018

AbstractWe study the impact of the integration of women in U.S. policing between the late 1970s and early 1990s on violent crime reporting and domestic violence (DV). Along these two key dimensions, we find that female officers improved police quality. Crime victimization data reveal that as female representation increases among officers in an area, violent crimes against women in that area, and especially DV, are reported to the police at significantly higher rates. There are no such effects for violent crimes against men or from increases in the female share of civilian police employees. Furthermore, increases in female officer shares are followed by significant declines in rates of intimate partner homicide and non-fatal domestic abuse. These effects are all consistent between fixed effects models with controls for economic and policy variables and models that focus exclusively on increases in female police employment driven by externally imposed affirmative action plans following litigation for employment discrimination.
Attribution Bias in Consumer Choice
Authors: Haggag Kareem , Pope Devin G , Bryant-Lees Kinsey B , Bos Maarten W 
Published: September 2018

AbstractWhen judging the value of a good, people may be overly influenced by the state in which they previously consumed it. For example, someone who tries out a new restaurant while very hungry may subsequently rate it as high quality, even if the food is mediocre. We produce a simple framework for this form of attribution bias that embeds a standard model of decision making as a special case. We test for attribution bias across two consumer decisions. First, we conduct an experiment in which we randomly manipulate the thirst of participants prior to consuming a new drink. Second, using data from thousands of amusement park visitors, we explore how pleasant weather during their most recent trip affects their stated and actual likelihood of returning. In both of these domains, we find evidence that people misattribute the influence of a temporary state to a stable quality of the consumption good. We provide evidence against several alternative accounts for our findings and discuss the broader implications of attribution bias in economic decision making.
On the integrability of Birkhoff billiards
Authors: Kaloshin Vadim , Sorrentino Alfonso 
Published: September 2018

In this survey, we provide a concise introduction to convex billiards and describe some recent results, obtained by the authors and collaborators, on the classification of integrable billiards, namely the so-called Birkhoff conjecture.
This article is part of the theme issue ‘Finite dimensional integrable systems: new trends and methods’.
Symplectic invariants for parabolic orbits and cusp singularities of integrable systems
Authors: Bolsinov Alexey , Guglielmi Lorenzo , Kudryavtseva Elena 
Published: September 2018

We discuss normal forms and symplectic invariants of parabolic orbits and cuspidal tori in integrable Hamiltonian systems with two degrees of freedom. Such singularities appear in many integrable systems in geometry and mathematical physics and can be considered as the simplest example of degenerate singularities. We also suggest some new techniques which apparently can be used for studying symplectic invariants of degenerate singularities of more general type.
This article is part of the theme issue ‘Finite dimensional integrable systems: new trends and methods’.
Does voluntary wheel running exist in Neotropical wild mammals?
Authors: Lunteren Peter van , Groenewold Marnix A. , Pozsgai Gabor , Sarvary Joseph 
Published: September 2018

AbstractRunning wheels are frequently used to improve the welfare of captive animals, increase environmental enrichment, and, by doing so, reduce stereotypic behaviors. It is, however, still debated whether or not wheel running itself is a stereotypy. New evidence emerged when Meijer and Robbers (2014, Proc. Royal Soc. B) reported voluntary wheel running of wild animals in the Netherlands. Since stereotypic behaviors are exclusively attributed to captive animals, the occurrence of wheel running in the wild suggests that this behavior is non-stereotypic. Our study explores that same line of investigation, examining whether wild animals will voluntarily use running wheels in a natural area in Paraguay in comparison to the urban and semi-urban settings in the Netherlands. Of the 1857 small mammal visits we recorded, only two occasions showed evidence of what could be considered as wheel running behavior; over hundredfold fewer than previously reported. The potential reasons for the observed difference in wheel running activity, such as different species pool or seasonality, are discussed. The difference, however, is likely to be due to the much lower probability of Neotropical mammals in a remote natural site encountering man-made objects and experiencing urbanization-related behavioral patterns. Additionally, in the light of our findings, we review the definition of wheel running as a stereotypic behavior.
The AP-1 complex regulates AXL expression and determines sensitivity to PI3Kα inhibition in esophagus and head and neck squamous cell carcinoma
Authors: Bdarny Mai , Prasad Manu , Balaban Noa , Ben-Zion Joshua , Dinur Anat Bahat , Grénman Reidar , Cohen Limor , Elkabets Moshe 
Published: September 2018

AbstractAXL overexpression is a common resistance mechanism to anti-cancer therapies, including the resistance to BYL719 (Alpelisib) – the p110α isoform specific inhibitor of phosphoinositide 3-kinase (PI3K) – in esophagus and head and neck squamous cell carcinoma (ESCC, HNSCC respectively). However, the mechanisms underlying AXL overexpression in resistance to BYL719 remain elusive. Here we demonstrated that the AP-1 transcription factors, c-JUN and c-FOS, regulate AXL overexpression in HNSCC and ESCC. The expression of AXL was correlated with that of c-JUN both in HNSCC patients and in HNSCC and ESCC cell lines. Silencing of c-JUN and c-FOS expression in tumor cells downregulated AXL expression and enhanced the sensitivity of human papilloma virus positive (HPVPos) and negative (HPVNeg) tumor cells to BYL719 in vitro. Blocking of the c-JUN N-terminal kinase (JNK) using SP600125 in combination with BYL719 showed a synergistic anti-proliferative effect in vitro, which was accompanied by AXL downregulation and potent inhibition of the mTOR pathway. In vivo, the BYL719-SP600125 drug combination led to the arrest of tumor growth in cell line-derived and patient-derived xenograft models, and in syngeneic head and neck murine cancer models. Collectively, our data suggests that JNK inhibition in combination with anti-PI3K therapy is a new therapeutic strategy that should be tested in HPVPosand HPVNegHNSCC and ESCC patients.
The anaphase-promoting complex regulates the degradation of the inner nuclear membrane protein Mps3 in budding yeast
Authors: Koch Bailey A. , Jin Hui , Tomko Robert J. , Yu Hong-Guo 
Published: September 2018

AbstractThe nucleus is enclosed by the inner nuclear membrane (INM) and the outer nuclear membrane (ONM). While the ONM is continuous with the endoplasmic reticulum (ER), the INM is independent and separates the nucleoplasm from the ER lumen. To maintain INM homeostasis, proteins mislocalized to the INM are degraded by the ER-associated protein degradation (ERAD) pathway. However, the mechanism for turnover of resident INM proteins is less clear. Here we show that the anaphase-promoting complex/cyclosome (APC/C), an E3 ubiquitin ligase, regulates the degradation of Mps3, a conserved integral protein of the INM. Turnover of Mps3 requires the ubiquitin-conjugating enzymes Ubc7 and Ubc6, but not the three known ERAD ubiquitin ligases, Doa10, Hrd1, and the Asi1-Asi3 complex. Using a genetic approach, we have found that Cdh1, a coactivator of APC/C, modulates Mps3 stability. APC/C controls Mps3 degradation through Mps3’s N-terminus, which resides in the nucleoplasm and possesses two putative APC/C-dependent destruction motifs. Accumulation of Mps3 at the INM impairs nuclear morphological changes and cell division. Our findings therefore reveal an unexpected mechanism of APC/C-mediated protein quality control at the INM that coordinates nuclear morphogenesis and cell-cycle progression.
Mian: Interactive Web-Based 16S rRNA Operational Taxonomic Unit Table Data Visualization and Discovery Platform
Authors: Jin Boyang Tom 
Published: September 2018

ABSTRACTIn recent years, there has been strong interest in examining the microbiome and its impact on human health and the environment. By leveraging modern sequencing technologies, investigators can quickly determine the composition of a given microbial sample. At the same time, the same investigations often yield an array of categorical and numerical metadata derived from the sequenced samples such as immunohistochemical measures or locality information. Understanding how the microbiome data is associated with this external metadata is essential in developing targeted treatments for chronic diseases or proposing bacteria-modulated host responses. While many R or Python libraries and command-line tools have been developed for specific analysis purposes, there are still relatively few tools to facilitate open-ended data exploration and hypothesis generation. Here we introduce Mian, an open-source web framework to interactively visualize or run a suite of statistical and feature selection tools on the microbiome to identify important taxonomic groups in the context of any provided categorical or numerical metadata. Visualizations include boxplots, correlation networks, and PCA or NMDS scatterplots. Tools include Fisher’s Exact Test, Boruta feature selection, alpha and beta diversity, and differential and correlational analysis. Mian supports multiple standard representations of the OTU table as input and optionally subsamples the data during the upload process. Users can also filter and aggregate the OTU table at different taxonomic levels and dynamically adjust analysis parameters to see how the visualizations, results, and statistical measures change in real-time. Mian is freely available at: miandata.org
Proteus: an R package for downstream analysis of MaxQuant output
Authors: Gierlinski Marek , Gastaldello Francesco , Cole Chris , Barton Geoffrey J. 
Published: September 2018

AbstractProteus is a package for downstream analysis of MaxQuant evidence data in the R environment. It provides tools for peptide and protein aggregation, quality checks, data exploration and visualisation. Interactive analysis is implemented in the Shiny framework, where individual peptides or protein may be examined in the context of a volcano plot. Proteus performs differential expression analysis with the well-established tool limma, which offers robust treatment of missing data, frequently encountered in label-free mass-spectrometry experiments. We demonstrate on real and simulated data that limma results in improved sensitivity over random imputation combined with a t-test as implemented in the popular package Perseus. Embedding Proteus in R provides access to a wide selection of statistical and graphical tools for further analysis and reproducibility by scripting. Availability and implementation: The open-source R package, including example data and tutorials, is available to install from GitHub (https://github.com/bartongroup/proteus).
Haploinsufficiency of the psychiatric risk gene Cyfip1 causes abnormal postnatal hippocampal neurogenesis through microglial and Arp2/3 mediated actin dependent mechanisms
Authors: Haan Niels , Westacott Laura J , Carter Jenny , Owen Michael J , Gray William P , Hall Jeremy , Wilkinson Lawrence S 
Published: September 2018

AbstractGenetic risk factors can significantly increase chances of developing psychiatric disorders, but the underlying biological processes through which this risk is effected remain largely unknown. Here we show that haploinsufficiency of Cyfip1, a candidate risk gene present in the pathogenic 15q11.2(BP1-BP2) deletion may impact on psychopathology via abnormalities in cell survival and migration of newborn neurons during postnatal hippocampal neurogenesis. We demonstrate that haploinsufficiency of Cyfip1 leads to increased numbers of adult born hippocampal neurons due to reduced apoptosis, without altering proliferation. We confirm this is due to a cell autonomous failure of microglia to induce apoptosis through the secretion of the appropriate factors. Furthermore, we show an abnormal migration of adult-born neurons due to altered Arp2/3 mediated actin dynamics. Together, our findings throw new light on how the genetic risk candidate Cyfip1 may influence the hippocampus, a brain region with strong evidence for involvement in psychopathology.
Intrinsically aggregation-prone proteins form amyloid-like aggregates and contribute to tissue aging in C. elegans
Authors: Huang C. , Wagner-Valladolid S. , Stephens A.D. , Jung R. , Poudel C. , Sinnige T. , Lechler M.C. , Schlörit N. , Laine R.F. , Michel C.H. , Vendruscolo M. , Kaminski C.F. , Kaminski Schierle G.S. , David D.C. 
Published: September 2018

AbstractReduced protein homeostasis and increased protein instability is a common feature of aging. Yet it remains unclear whether protein instability is a cause of aging. In neurodegenerative diseases and amyloidoses, specific proteins self-assemble into amyloid fibrils and accumulate as pathological solid aggregates in a variety of tissues. More recently, widespread protein aggregation has been described during normal aging, in the absence of disease processes. Until now, an extensive characterization of the nature of age-dependent protein aggregation and its consequences for aging has been lacking. Here, we show that age-dependent aggregates are rapidly formed by newly synthesized proteins and contain amyloid-like structures similar to disease-associated protein aggregates. Moreover, we demonstrate that age-dependent protein aggregation accelerates the functional decline of different tissues in C. elegans. Together, these finding reveal that the formation of amyloid aggregates is a generic problem of aging and likely to be an important target for strategies designed to maintain physiological functions in later stages of life.
Proximal perimeter encoding in the rat rostral thalamus
Authors: Matulewicz Pawel , Ulrich Katharina , Islam Md Nurul , Mathiasen Mathias L , Aggleton John P , O’Mara Shane M 
Published: September 2018

AbstractPerimeters are an important part of the environment, delimiting its geometry. Here, we investigated how perimeters (vertical walls; vertical drops) affect neuronal responses in the rostral thalamus (the anteromedial and parataenial nuclei in particular). We found neurons whose firing patterns reflected the presence of walls and drops, irrespective of arena shape. Their firing patterns were stable across multiple sleep-wake cycles and were independent of ambient lighting conditions. Thus, rostral thalamic nuclei may participate in spatial representation by encoding the perimeters of environments.
Automatic interpretation of otoliths using deep learning
Authors: Moen Endre , Handegard Nils Olav , Allken Vaneeda , Albert Ole thomas , Harbitz Alf , Malde Ketil 
Published: September 2018

AbstractThe age structure of a fish population has important implications for recruitment processes and population fluctuations, and is key input to fisheries assessment models. The current method relies on manually reading age from otoliths, and the process is labor intensive and dependent on specialist expertise.Advances in machine learning have recently brought forth methods that have been remarkably successful in a variety of settings, with potential to automate analysis that previously required manual curation. Machine learning models have previously been successfully applied to object recognition and similar image analysis tasks. Here we investigate whether deep learning models can also be used for estimating the age of otoliths from images.We adapt a standard neural network model designed for object recognition to the task of estimating age from otolith images. The model is trained and validated on a large collection of images of Greenland halibut otoliths. We show that the model works well, and that its precision is comparable to and may even surpass that of human experts.Automating this analysis will help to improve consistency, lower cost, and increase scale of age prediction. Similar approaches can likely be used for otoliths from other species as well as for reading fish scales. The method is therefore an important step forward for improving the age structure estimates of fish populations.
Illness, social disadvantage, and sexual risk behavior in adolescence and the transition to adulthood
Authors: Alley Jenna , Owen Rebecca Y. , Wawrzynski Sarah E. , Lasrich Lauren , Ahmmad Zobayer , Utz Rebecca , Adkins Daniel E. 
Published: September 2018

AbstractThis study investigated the influence of illness on sexual risk behavior in adolescence and the transition to adulthood, both directly and through moderation of the impact of social disadvantage. We hypothesized positive effects for social disadvantages and illness on sexual risk behavior, consistent with the development of faster life history strategies among young people facing greater life adversity. Using the first two waves of the National Longitudinal Study of Adolescent Health, we developed a mixed effects multinomial logistic regression model predicting sexual risk behavior in three comparisons, risky nonmonogamous sex vs. 1) safer nonmonogamous sex, 2) monogamous sex, and 3) abstinence, by social characteristics, illness, interactions thereof, and control covariates. Multiple imputation was used to address a modest amount of missing data. Subjects reporting higher levels of illness had lower odds of having safer nonmonogamous sex (OR = 0.84, p < .001), monogamous sex (OR = 0.82, p < .001), and abstinence (OR = 0.74, p < .001) vs. risky nonmonogamous sex, relative to individuals in better health. Illness significantly moderated the sex (OR = 0.88, p < .01), race/ethnicity (e.g., OR = 1.21, p < .001), and childhood SES (OR = 0.94; p < .01) effects for the abstinent vs. risky nonmonogamous sex comparison. Substantive findings were generally robust across waves and in various sensitivity analyses. These findings offer general support for the predictions of life history theory. Illness and various social disadvantages are associated with increased sexual risk behavior in adolescence and the transition to adulthood. Analyses indicate that the buffering effects of several protective social statuses against sexual risk-taking are substantially eroded by illness.
Hox genes limit germ cell formation in the short germ insectGryllus bimaculatus
Authors: Barnett Austen A. , Nakamura Taro , Extavour Cassandra G. 
Published: September 2018

AbstractHox genes are conserved transcription factor-encoding genes that specify the identity of body regions in bilaterally symmetrical animals. In the cricketGryllus bimaculatus, a member of the hemimetabolous insect group Orthoptera, the induction of a subset of mesodermal cells to form the primordial germ cells (PGCs) is restricted to the second through the fourth abdominal segments (A2-A4). In numerous insect species, the Hox genesSex-combs reduced(Scr),Antennapedia(Antp),Ultrabithorax(Ubx) andabdominal-A(abd-A) jointly regulate the identities of middle and posterior body segments, suggesting that these genes may restrict PGC formation to specific abdominal segments inG. bimaculatus. Here we show that all of these Hox genes, either individually or in segment-specific combinations, restrict PGC formation. Our data provides evidence for a segmental Hox code used to regulate the placement of PGC formation, reminiscent of the segmental Hox codes used in other arthropod groups to establish other aspects of segmental identity. These data also provide, to our knowledge, the first evidence for this ancient group of genes in determining PGC placement within the context of axial patterning in any animal studied thus far.