bluuebunny/crossref_metadata_2025_split huggingface dataset:
Surgical Site Infection in a Tertiary Neonatal Surgery Centre
Authors: Woldemicael Adiam , Bradley Sarah , Pardy Caroline , Richards Justin , Trerotoli Paolo , Giuliani Stefano 
Published: March 2018

Introduction Surgical site infection (SSI) is a key performance indicator to assess the quality of surgical care. Incidence and risk factors for SSI in neonatal surgery are lacking in the literature.
Aim To define the incidence of SSI and possible risk factors in a tertiary neonatal surgery centre.
Materials and Methods This is a prospective cohort study of all the neonates who underwent abdominal and thoracic surgery between March 2012 and October 2016. The variables analyzed were gender, gestational age, birth weight, age at surgery, preoperative stay in neonatal intensive care unit, type of surgery, length of stay, and microorganisms isolated from the wounds. Statistical analysis was done with chi-square, Student's t- or Mann–Whitney U-tests. A logistic regression model was used to evaluate determinants of risk for SSI; variables were analyzed both with univariate and multivariate models. For the length of hospital stay, a logistic regression model was performed with independent variables.
Results A total of 244 neonates underwent 319 surgical procedures. The overall incidence of SSIs was 43/319 (13.5%). The only statistical differences between neonates with and without SSI were preoperative stay (<4 days vs. ≥4 days, p < 0.01) and length of hospital stay (<30 days vs. ≥30 days, p < 0.01). A pre-operative stay longer than 4 days was associated with almost three times increased risk of SSI (odds ratio [OR] 2.96, 95% confidence interval [CI] 1.05–8.34, p = 0.0407). Gastrointestinal procedures were associated with more than ten times the risk of SSI compared with other procedures (OR 10.17, 95% CI 3.82–27.10, p < 0.0001). Gastroschisis closure and necrotizing enterocolitis (NEC) laparotomies had the highest incidence SSI (54% and 62%, respectively). The risk of longer length of hospital stay after SSI was more than three times higher (OR = 3.36, 95%CI 1.63–6.94, p = 0.001).
Conclusion This is the first article benchmarking the incidence of SSI in neonatal surgery in the United Kingdom. A preoperative stay ≥4 days and gastrointestinal procedures were independent risk factors for SSI. More research is needed to develop strategies to reduce SSI in selected neonatal procedures.
Future cities: moving from technical to human needs
Authors: Caprotti Federico 
Published: March 2018

AbstractThe article argues for a foregrounding of human needs at the heart of urban societal futures. While economic, technical and environmental imperatives are understandably the focus of policymaking and governance arrangements at national and supra-national scales, defining and targeting priorities in the ‘ordinary’ city is key. The argument is that it is now time to place basic human needs (as enshrined both in international agreements and in the more prosaic conditions of specific cities) at the centre of thinking and planning for future cities. The piece therefore proposes that plans for urban futures start from an elaboration of contextually sensitive as well as internationally negotiated needs rather than from macro-scale and potentially ephemeral visions of glittering technological future metropoles.
LSD1 activates a lethal prostate cancer gene network independently of its demethylase function
Authors: Sehrawat Archana , Gao Lina , Wang Yuliang , Bankhead Armand , McWeeney Shannon K. , King Carly J. , Schwartzman Jacob , Urrutia Joshua , Bisson William H. , Coleman Daniel J. , Joshi Sunil K. , Kim Dae-Hwan , Sampson David A. , Weinmann Sheila , Kallakury Bhaskar V. S. , Berry Deborah L. , Haque Reina , Van Den Eeden Stephen K. , Sharma Sunil , Bearss Jared , Beer Tomasz M. , Thomas George V. , Heiser Laura M. , Alumkal Joshi J. 
Published: March 2018

Significance
Medical castration or interference with androgen receptor (AR) function is the principal treatment for advanced prostate cancer. However, progression is universal, and therapies following the emergence of castration resistance do not offer durable control of the disease. Lysine-specific demethylase 1 (LSD1) is an important regulator of gene expression, including in cancer. Here, we show that LSD1 is highly expressed in tumors of patients with lethal castration-resistant prostate cancer (CRPC) and that LSD1 promotes AR-independent survival in CRPC cells in a noncanonical, demethylase-independent manner. We determined that the drug SP-2509 acts as an allosteric inhibitor of LSD1–blocking demethylase-independent functions. Our demonstration of tumor suppression with this inhibitor in CRPC preclinical models provides the rationale for clinical trials with LSD1 inhibitors.
Dependence of the evolution of carbon dynamics in the northern permafrost region on the trajectory of climate change
Authors: McGuire A. David , Lawrence David M. , Koven Charles , Clein Joy S. , Burke Eleanor , Chen Guangsheng , Jafarov Elchin , MacDougall Andrew H. , Marchenko Sergey , Nicolsky Dmitry , Peng Shushi , Rinke Annette , Ciais Philippe , Gouttevin Isabelle , Hayes Daniel J. , Ji Duoying , Krinner Gerhard , Moore John C. , Romanovsky Vladimir , Schädel Christina , Schaefer Kevin , Schuur Edward A. G. , Zhuang Qianlai 
Published: March 2018

Significance
We applied regional and global-scale biogeochemical models that coupled thaw depth with soil carbon exposure to evaluate the dependence of the evolution of future carbon storage in the northern permafrost region on the trajectory of climate change. Our analysis indicates that the northern permafrost region could act as a net sink for carbon under more aggressive climate change mitigation pathways. Under less aggressive pathways, the region would likely act as a source of soil carbon to the atmosphere, but substantial net losses would not occur until after 2100. These results suggest that effective mitigation efforts during the remainder of this century could attenuate the negative consequences of the permafrost carbon–climate feedback.
An Inclusive History for a Divided World?
Authors: Frolova-Walker Marina 
Published: March 2018

ABSTRACTThe article discusses various historiographical problems created by Soviet music and, more broadly, music under the so-called ‘totalitarian’ regimes for the conventional modernism-driven narrative of the twentieth century. It reviews a number of existing challenges to the dominant narrative within musicology and related fields such as art and architectural history, and it proposes ways in which we can move forward. In conclusion, the author considers the new challenges to the breaking down of cold-war barriers, not only in a historical sense, but also today, in the midst of a new cold war.
‘Che soave zeffiretto’ and the Structure of Act 3 of Le nozze di Figaro
Authors: Woodfield Ian 
Published: March 2018

ABSTRACT‘Che soave zeffiretto’, the letter duettino sung by the Countess and Susanna in Le nozze di Figaro, has achieved iconic status as a perfect example of the transcendental beauty of Mozart's music. An examination of the extant sources suggests that the composer and his librettist regarded it as a key moment in the opera: the crux of a developing relationship between the two women. A late change of plan over its location led to a reconfiguration of Act 3, resulting in the minor inconsistencies that Robert Moberly and Christopher Raeburn sought to explain in their celebrated double-casting hypothesis. The various versions of the text and a complete continuity draft of the score reveal the meticulous craftsmanship that went into its creation, in particular the development of its comedic potential as a vaudeville.
SimPhospho: a software tool enabling confident phosphosite assignment
Authors: Suni Veronika , Suomi Tomi , Tsubosaka Tomoya , Imanishi Susumu Y , Elo Laura L , Corthals Garry L 
Published: March 2018

Abstract

Motivation
Mass spectrometry combined with enrichment strategies for phosphorylated peptides has been successfully employed for two decades to identify sites of phosphorylation. However, unambiguous phosphosite assignment is considered challenging. Given that site-specific phosphorylation events function as different molecular switches, validation of phosphorylation sites is of utmost importance. In our earlier study we developed a method based on simulated phosphopeptide spectral libraries, which enables highly sensitive and accurate phosphosite assignments. To promote more widespread use of this method, we here introduce a software implementation with improved usability and performance.

Results
We present SimPhospho, a fast and user-friendly tool for accurate simulation of phosphopeptide tandem mass spectra. Simulated phosphopeptide spectral libraries are used to validate and supplement database search results, with a goal to improve reliable phosphoproteome identification and reporting. The presented program can be easily used together with the Trans-Proteomic Pipeline and integrated in a phosphoproteomics data analysis workflow.

Availability and implementation
SimPhospho is open source and it is available for Windows, Linux and Mac operating systems. The software and its user’s manual with detailed description of data analysis as well as test data can be found at https://sourceforge.net/projects/simphospho/.

Supplementary information
Supplementary data are available at Bioinformatics online.
Integrating long-range connectivity information into de Bruijn graphs
Authors: Turner Isaac , Garimella Kiran V , Iqbal Zamin , McVean Gil 
Published: March 2018

Abstract

Motivation
The de Bruijn graph is a simple and efficient data structure that is used in many areas of sequence analysis including genome assembly, read error correction and variant calling. The data structure has a single parameter k, is straightforward to implement and is tractable for large genomes with high sequencing depth. It also enables representation of multiple samples simultaneously to facilitate comparison. However, unlike the string graph, a de Bruijn graph does not retain long range information that is inherent in the read data. For this reason, applications that rely on de Bruijn graphs can produce sub-optimal results given their input data.

Results
We present a novel assembly graph data structure: the Linked de Bruijn Graph (LdBG). Constructed by adding annotations on top of a de Bruijn graph, it stores long range connectivity information through the graph. We show that with error-free data it is possible to losslessly store and recover sequence from a Linked de Bruijn graph. With assembly simulations we demonstrate that the LdBG data structure outperforms both our de Bruijn graph and the String Graph Assembler (SGA). Finally we apply the LdBG to Klebsiella pneumoniae short read data to make large (12 kbp) variant calls, which we validate using PacBio sequencing data, and to characterize the genomic context of drug-resistance genes.

Availability and implementation
Linked de Bruijn Graphs and associated algorithms are implemented as part of McCortex, which is available under the MIT license at https://github.com/mcveanlab/mccortex.

Supplementary information
Supplementary data are available at Bioinformatics online.
ONETOOL for the analysis of family-based big data
Authors: Song Yeunjoo E , Lee Sungyoung , Park Kyungtaek , Elston Robert C , Yang Hyeon-Jong , Won Sungho 
Published: March 2018

Abstract

Motivation
Despite the need for separate tools to analyze family-based data, there are only a handful of tools optimized for family-based big data compared to the number of tools available for analyzing population-based data.

Results
ONETOOL implements the properties of well-known existing family data analysis tools and recently developed methods in a computationally efficient manner, and so is suitable for analyzing the vast amount of variant data available from sequencing family members, providing a rich choice of analysis methods for big data on families.

Availability and implementation
ONETOOL is freely available from http://healthstat.snu.ac.kr/software/onetool/.

Supplementary information
Supplementary data are available at Bioinformatics online.
So Close and Yet So Irritating: Negative Relations and Implications for Well-being by Age and Closeness
Authors: Birditt Kira S , Sherman Carey W , Polenick Courtney A , Becker Lucia , Webster Noah J , Ajrouch Kristine J , Antonucci Toni C 
Published: March 2018

Abstract

Objectives
Negative social relationships are associated with poor health, chronic illness, and mortality. Yet, we know little about the dynamics of negative aspects of relationships within individual’s closest relationships over time, how those experiences vary by age, and the implications of those relationships for well-being.

Method
A total of 592 participants (ages 25–97; M = 57.5; 63.3% women) from the Social Relations Study completed monthly web surveys for up to 12 months. Each month they reported negative relationship quality with their three closest network members and multiple dimensions of well-being (positive affect, negative affect, self-rated health, and sleep quality).

Results
Multilevel models revealed older individuals reported less negativity in their relationships than younger people, but fewer age differences in the closest tie. Greater negative relationship quality predicted poor well-being (i.e., greater negative affect, sleep problems). Links between negative relations and well-being were less strong among older individuals; especially in the closest ties.

Discussion
Results were partially consistent with the strength and vulnerability integration (SAVI) model, which proposes fewer age-related improvements in emotion regulation when individuals are unable to avoid tensions. Despite feeling just as negative as younger individuals, older individuals may be more resilient to tensions in their closest relationships.
Change of Polarization for Moduli of Sheaves on Surfaces as Bridgeland Wall-crossing
Authors: Bertram Aaron , Martinez Cristian 
Published: March 2018

Abstract
We prove that the “Thaddeus flips” of L-twisted sheaves constructed by Matsuki and Wentworth explaining the change of polarization for Gieseker semistable sheaves on a surface can be obtained via Bridgeland wall-crossing. Similarly, we realize the change of polarization for moduli spaces of one-dimensional Gieseker semistable sheaves on a surface by varying a family of stability conditions.
Isocitrate Dehydrogenase Mutations in Low-Grade Gliomas Correlate With Prolonged Overall Survival in Older Patients
Authors: Jones Pamela S , Carroll Kate T , Koch Matthew , DiCesare Jasmine A T , Reitz Kara , Frosch Matthew , Barker Fred G , Cahill Daniel P , Curry William T 
Published: March 2018

Abstract

BACKGROUND
Older age has been associated with worse outcomes in low-grade gliomas (LGGs). Given their rarity in the older population, determining optimal treatment plans and patient outcomes remains difficult.

OBJECTIVE
To retrospectively study LGG survival outcomes in an older population stratified by molecular genetic profiles.

METHODS
We included patients age ≥40 yr with pathologically confirmed World Health Organization grade II gliomas treated at a single institution between 1995 and 2015. We collected tumor genomic information when available.

RESULTS
Median overall survival for the entire group (n = 111, median age 51 yr, range 40-77 yr) was 15.75 yr with 5- and 10-yr survival rates of 84.3% and 67.7%, respectively. On univariate analysis, patients with isocitrate dehydrogenase (IDH) mutation had significantly increased survival compared to IDH wildtype (hazard ratio [HR] 0.17 [0.07-0.45], P < .001). Older age, seizure at presentation, larger tumor size, IDH wildtype, biopsy only, chemotherapy, and radiation were significantly associated with shorter survival based on univariate analyses. In patients with known IDH status (n = 73), bivariate analysis of IDH mutation status and age showed only IDH status significantly influenced overall survival (HR 0.22 [0.07-0.68], P = .008). Greater surgical resection was predictive of survival, although extent of resection significantly correlated with IDH mutation status (odds ratio 7.5; P < .001).

CONCLUSION
We show that genomic alterations in LGG patients ≥40 occur at high rates like the younger population and predict a similar survival advantage. Maximizing surgical resection may have survival benefit, although feasibility of resection is often linked to IDH status. Given the importance of molecular genetics, a redefinition of prognostic factors associated with these tumors is likely to emerge.
Disentangling social interactions and environmental drivers in multi-individual wildlife tracking data
Authors: Calabrese Justin M. , Fleming Christen H. , Fagan William F. , Rimmler Martin , Kaczensky Petra , Bewick Sharon , Leimgruber Peter , Mueller Thomas 
Published: March 2018

While many animal species exhibit strong conspecific interactions, movement analyses of wildlife tracking datasets still largely focus on single individuals. Multi-individual wildlife tracking studies provide new opportunities to explore how individuals move relative to one another, but such datasets are frequently too sparse for the detailed, acceleration-based analytical methods typically employed in collective motion studies. Here, we address the methodological gap between wildlife tracking data and collective motion by developing a general method for quantifying movement correlation from sparsely sampled data. Unlike most existing techniques for studying the non-independence of individual movements with wildlife tracking data, our approach is derived from an analytically tractable stochastic model of correlated movement. Our approach partitions correlation into a deterministic tendency to move in the same direction termed ‘drift correlation’ and a stochastic component called ‘diffusive correlation’. These components suggest the mechanisms that coordinate movements, with drift correlation indicating external influences, and diffusive correlation pointing to social interactions. We use two case studies to highlight the ability of our approach both to quantify correlated movements in tracking data and to suggest the mechanisms that generate the correlation. First, we use an abrupt change in movement correlation to pinpoint the onset of spring migration in barren-ground caribou. Second, we show how spatial proximity mediates intermittently correlated movements among khulans in the Gobi desert. We conclude by discussing the linkages of our approach to the theory of collective motion.This article is part of the theme issue 'Collective movement ecology'.
Collective animal navigation and migratory culture: from theoretical models to empirical evidence
Authors: Berdahl Andrew M. , Kao Albert B. , Flack Andrea , Westley Peter A. H. , Codling Edward A. , Couzin Iain D. , Dell Anthony I. , Biro Dora 
Published: March 2018

Animals often travel in groups, and their navigational decisions can be influenced by social interactions. Both theory and empirical observations suggest that such collective navigation can result in individuals improving their ability to find their way and could be one of the key benefits of sociality for these species. Here, we provide an overview of the potential mechanisms underlying collective navigation, review the known, and supposed, empirical evidence for such behaviour and highlight interesting directions for future research. We further explore how both social and collective learning during group navigation could lead to the accumulation of knowledge at the population level, resulting in the emergence of migratory culture.This article is part of the theme issue ‘Collective movement ecology’.
From single steps to mass migration: the problem of scale in the movement ecology of the Serengeti wildebeest
Authors: Torney Colin J. , Hopcraft J. Grant C. , Morrison Thomas A. , Couzin Iain D. , Levin Simon A. 
Published: March 2018

A central question in ecology is how to link processes that occur over different scales. The daily interactions of individual organisms ultimately determine community dynamics, population fluctuations and the functioning of entire ecosystems. Observations of these multiscale ecological processes are constrained by various technological, biological or logistical issues, and there are often vast discrepancies between the scale at which observation is possible and the scale of the question of interest. Animal movement is characterized by processes that act over multiple spatial and temporal scales. Second-by-second decisions accumulate to produce annual movement patterns. Individuals influence, and are influenced by, collective movement decisions, which then govern the spatial distribution of populations and the connectivity of meta-populations. While the field of movement ecology is experiencing unprecedented growth in the availability of movement data, there remain challenges in integrating observations with questions of ecological interest. In this article, we present the major challenges of addressing these issues within the context of the Serengeti wildebeest migration, a keystone ecological phenomena that crosses multiple scales of space, time and biological complexity.
This article is part of the theme issue 'Collective movement ecology'.
Migration in the Anthropocene: how collective navigation, environmental system and taxonomy shape the vulnerability of migratory species
Authors: Hardesty-Moore Molly , Deinet Stefanie , Freeman Robin , Titcomb Georgia C. , Dillon Erin M. , Stears Keenan , Klope Maggie , Bui An , Orr Devyn , Young Hillary S. , Miller-ter Kuile Ana , Hughey Lacey F. , McCauley Douglas J. 
Published: March 2018

Recent increases in human disturbance pose significant threats to migratory species using collective movement strategies. Key threats to migrants may differ depending on behavioural traits (e.g. collective navigation), taxonomy and the environmental system (i.e. freshwater, marine or terrestrial) associated with migration. We quantitatively assess how collective navigation, taxonomic membership and environmental system impact species' vulnerability by (i) evaluating population change in migratory and non-migratory bird, mammal and fish species using the Living Planet Database (LPD), (ii) analysing the role of collective navigation and environmental system on migrant extinction risk using International Union for Conservation of Nature (IUCN) classifications and (iii) compiling literature on geographical range change of migratory species. Likelihood of population decrease differed by taxonomic group: migratory birds were more likely to experience annual declines than non-migrants, while mammals displayed the opposite pattern. Within migratory species in IUCN, we observed that collective navigation and environmental system were important predictors of extinction risk for fishes and birds, but not for mammals, which had overall higher extinction risk than other taxa. We found high phylogenetic relatedness among collectively navigating species, which could have obscured its importance in determining extinction risk. Overall, outputs from these analyses can help guide strategic interventions to conserve the most vulnerable migrations.This article is part of the theme issue ‘Collective movement ecology'.