bluuebunny/crossref_metadata_2025_split huggingface dataset:
Zionism: A Very Short Introduction
Authors: Stanislawski Michael 
Published: December 2016

Abstract
Zionism: A Very Short Introduction explores the history of Zionism from the origins of modern Jewish nationalism in the 1870s to the present. While situating the history of Zionism within the wider context of Middle Eastern politics, British colonialism, and the policies of the State of Israel since its founding in 1948, this VSI focuses on its internal intellectual history and ideological developments and divides. It illuminates the development of the Zionist ideology from the appearance of Herzl to the Weizmann Era, from the creation of the state of Israel and the Six Day War of 1967 to the rise of the Peace Now movement.
A mass graph-based approach for the identification of modified proteoforms using top-down tandem mass spectra
Authors: Kou Qiang , Wu Si , Tolić Nikola , Paša-Tolić Ljiljana , Liu Yunlong , Liu Xiaowen 
Published: December 2016

Abstract

Motivation
Although proteomics has rapidly developed in the past decade, researchers are still in the early stage of exploring the world of complex proteoforms, which are protein products with various primary structure alterations resulting from gene mutations, alternative splicing, post-translational modifications, and other biological processes. Proteoform identification is essential to mapping proteoforms to their biological functions as well as discovering novel proteoforms and new protein functions. Top-down mass spectrometry is the method of choice for identifying complex proteoforms because it provides a ‘bird's eye view’ of intact proteoforms. The combinatorial explosion of various alterations on a protein may result in billions of possible proteoforms, making proteoform identification a challenging computational problem.

Results
We propose a new data structure, called the mass graph, for efficient representation of proteoforms and design mass graph alignment algorithms. We developed TopMG, a mass graph-based software tool for proteoform identification by top-down mass spectrometry. Experiments on top-down mass spectrometry datasets showed that TopMG outperformed existing methods in identifying complex proteoforms.

Availability and implementation
http://proteomics.informatics.iupui.edu/software/topmg/

Supplementary information
Supplementary data are available at Bioinformatics online.
Defining the clonality of peripheral T cell lymphomas using RNA-seq
Authors: Brown Scott D , Hapgood Greg , Steidl Christian , Weng Andrew P , Savage Kerry J , Holt Robert A 
Published: December 2016

Abstract

Motivation
In T-cell lymphoma, malignant T cells arising from a founding clone share an identical T cell receptor (TCR) and can be identified by the over-representation of this TCR relative to TCRs from the patient’s repertoire of normal T cells. Here, we demonstrate that TCR information extracted from RNA-seq data can provide a higher resolution view of peripheral T cell lymphomas (PTCLs) than that provided by conventional methods.

Results
For 60 subjects with PTCL, flow cytometry/FACS was used to identify and sort aberrant T cell populations from diagnostic lymph node cell suspensions. For samples that did not appear to contain aberrant T cell populations, T helper (TH), T follicular helper (TFH) and cytotoxic T lymphocyte (CTL) subsets were sorted. RNA-seq was performed on sorted T cell populations, and TCR alpha and beta chain sequences were extracted and quantified directly from the RNA-seq data. 96% of the immunophenotypically aberrant samples had a dominant T cell clone readily identifiable by RNA-seq. Of the samples where no aberrant population was found by flow cytometry, 80% had a dominant clone by RNA-seq. This demonstrates the increased sensitivity and diagnostic ability of RNA-seq over flow cytometry and shows that the presence of a normal immunophenotype does not exclude clonality.

Availability and Implementation
R scripts used in the processing of the data are available online at https://www.github.com/scottdbrown/RNAseq-TcellClonality

Supplementary information
Supplementary data are available at Bioinformatics online.
Family Functioning and Mood and Anxiety Symptoms in Adolescents Born Extremely Preterm
Authors: Burnett Alice C. , Lee Katherine J. , Cheong Jeanie L. Y. , De Luca Cinzia R. , Roberts Gehan , Wood Stephen J. , Doyle Lex W. , Anderson Peter J. ,   on behalf of the Victorian Infant Collaborative Study Group
Published: December 2016

ABSTRACT:

Objective:
To (1) compare adolescent- and parent-perceived family functioning between extremely preterm/extremely low birth weight (<28 wk/<1000 g, EP/ELBW) and normal birth weight (>2499 g, NBW) adolescents and (2) determine whether adolescents' or parents' ratings of family functioning were related to concurrent depression and anxiety symptoms in the adolescent and whether these relationships varied by birth group.

Methods:
One hundred ninety-three EP/ELBW and 151 NBW adolescents (aged 15–20 yr) and their parents rated aspects of family functioning on the Family Environment Scale. Adolescents rated current depression and anxiety symptoms on the Center for Epidemiologic Studies Depression Scale-Revised and Beck Anxiety Inventory. Family functioning was compared across the groups using linear regression, and logistic regression was used to assess relationships between family functioning domains and elevated depression and anxiety scores.

Results:
Compared with NBW controls, EP/ELBW adolescents reported similar levels of family Cohesiveness and Expressiveness, but less Conflict, and more Organization and Control. Parent ratings of family functioning were similar between groups except for higher Control scores in EP/ELBW group parents. Poorer family functioning as rated by adolescents, but not parents, was associated with increased depression/anxiety symptoms. These findings were generally consistent across both the EP/ELBW and control groups.

Conclusion:
EP/ELBW adolescents report generally positive family functioning. While adolescents' perceptions of family functioning are associated with concurrent adolescent mental health, parental perceptions of family functioning may not be indicative of adolescents' mental health. Importantly, EP/ELBW adolescents do not appear to be more vulnerable to anxiety/depression in the context of poorly perceived family functioning than their NBW peers.
Donor Screening Experience for Fecal Microbiota Transplantation in Patients With Recurrent C. difficile Infection
Authors: Tariq Raseen , Weatherly Renee , Kammer Patricia , Pardi Darrell S. , Khanna Sahil 
Published: December 2016

Goals:To evaluate our experience with stool donor recruitment, screening, retention, and donor perception for fecal microbiota transplantation (FMT).Background:Multiply recurrentClostridium difficileinfection is being increasingly managed with FMT from donor stools. However, donor selection and recruitment is challenging due to lack of standard evidence-based guidelines, donor exclusion criteria, frequency of screening and donor commitment.Methods:Data on donors screened using institutional guidelines with history, blood and stool testing and their perspectives on donation were analyzed.Results:Overall 42 potential donors (21 known and 21 standard) were prescreened. Of known donors (median age 34 y, 66.6% female), none failed prescreening, blood or stool tests. Twelve standard donors (57%) failed prescreening based on history (depression, diarrhea, autoimmune disease, recent antibiotic exposure, colon polyps, pregnancy). Nine (median age 35 y, 44.4% female) passed blood and stool testing. On repeat screening, 3 were excluded (2-positive stool shiga toxin (asymptomatic), 1-pregnancy). One donor opted out and 5 became long-term donors; 3 have donated >50 times and 2 have donated >25 times. On the basis of donor perception questionnaire, most standard donors were aware of FMT forC. difficileinfection as a treatment option and would not consider 3-monthly blood and stool testing inconvenient.Conclusions:A significant proportion of healthy individuals who volunteered to become a standard donor failed prescreening and were not subjected to blood and stool testing. Repeat testing for asymptomatic donors may be a barrier to donor retention. Universal guidelines are needed to develop strategies to facilitate donor screening.
Cognition in Patients With a Clinical Diagnosis of Parkinson Disease and Scans Without Evidence of Dopaminergic Deficit (SWEDD): 2-Year Follow-Up
Authors: Wyman-Chick Kathryn A. , Martin Phillip K. , Minár Michal , Schroeder Ryan W. 
Published: December 2016

Objective and Background:
More than 10% of patients clinically diagnosed with Parkinson disease demonstrate normal dopamine uptake on dopamine transporter single-photon emission computed tomography (DaTscan), but little is known about how cognitive function differs between patients with dopamine deficiency on DaTscan and patients with scans without evidence of dopaminergic deficit (SWEDD). We compared the cognitive function of these two groups of patients over 2 years.

Methods:
We retrospectively analyzed data obtained from the Parkinson’s Progression Markers Initiative on 309 participants clinically diagnosed with idiopathic Parkinson disease who had scored in the normal range on the Montreal Cognitive Assessment at baseline and had completed 1- and 2-year follow-up visits. We compared the Montreal Cognitive Assessment scores at 1 and 2 years between the 42 participants with SWEDD and the 267 with dopamine deficiency.

Results:
Mean cognitive scores did not differ significantly between groups at 1 year, but at 2 years the participants with SWEDD performed more poorly. At 2 years, 31% of the participants with SWEDD versus 15% of those with dopamine deficiency had statistically reliable cognitive impairment.

Conclusions:
This study provides evidence that some individuals clinically diagnosed with idiopathic Parkinson disease but with SWEDD demonstrate early cognitive decline. The results also suggest that recently diagnosed patients with SWEDD may be at even greater risk for cognitive decline than patients with DaTscan-confirmed early-stage Parkinson disease. While patients with SWEDD likely represent a heterogeneous group of etiologies, our results highlight the need to monitor these patients’ cognitive function over time.
Development of 2-phenylethanol plus acetic acid lures to monitor obliquebanded leafroller (Lepidoptera: Tortricidae) under mating disruption
Authors: Knight A. L. , Judd G. J. R. , Basoalto E. , El-Sayed A. M. 
Published: December 2016

AbstractWe evaluated the effectiveness of 2-phenylethanol (PET) in combination with acetic acid (AA) as a binary lure for monitoring male and female obliquebanded leafroller,Choristoneura rosaceana(Harris). Studies were conducted in apple,Malus domesticaBorkhausen, orchards treated with or without sex pheromone dispensers for mating disruption (MD). Open polypropylene vials, closed membrane cups, and rubber septa loaded with AA and/or PET in varying amounts were first evaluated in a series of trapping experiments. Membrane cups loaded with 800 mg of PET were as effective as 10-mg septa, but longer lasting, and were comparable to the open vials. A membrane cup AA lure was effective in tests, but further work is needed to increase its release rate and extend its activity. Catches of codling moth,Cydia pomonella(L.), andC. rosaceanawere unaffected by combining PET with (E,E)-8,10-dodecadien-1-ol, the sex pheromone of codling moth, pear ester, (E,Z)-2,4-ethyl-decadienoate, and AA lures. Adding (E)-4,8-dimethyl-1,3,7-nonatriene to this blend to enhance codling moth catch, significantly reduced catches ofC. rosaceana.PET+AA was a more attractive binary lure than AA plus phenylacetonitrile (PAN) forC. rosaceana.The addition of PET or PAN to traps already baited with the sex pheromone ofC. rosaceanasignificantly reduced male catches. Traps baited with PET+AA placed in blocks not treated with MD caught significantly fewerC. rosaceanathan traps baited with sex pheromone. In comparison, sex pheromone-baited traps in MD blocks caught ≤ 1 male moth per season which was significantly lower than total moth (> 10) or female moth (≥ 3) catch in these blocks with PET+AA. A high proportion (> 70%) of trapped females were mated in both untreated and MD-treated orchards. Further refinement of this binary, bisexual lure using membrane cup technology may allow the establishment of action thresholds and improve management timings forC. rosaceana.
A simulation-based evaluation of STRUCTURE software for exploring the introduction routes of invasive species
Authors: Lombaert Eric , Guillemaud Thomas , Deleury Emeline 
Published: December 2016

AbstractPopulation genetic methods are widely used to retrace the introduction routes of invasive species. The unsupervised Bayesian clustering algorithm implemented in STRUCTURE is amongst the most frequently use of these methods, but its ability to provide reliable information about introduction routes has never been assessed. We used computer simulations of microsatellite datasets to evaluate the extent to which the clustering results provided by STRUCTURE were misleading for the inference of introduction routes. We focused on the simple case of an invasion scenario involving one native population and two independently introduced populations, because it is the sole scenario with two introduced populations that can be rejected when obtaining a particular clustering with a STRUCTURE analysis atK= 2 (two clusters). Results were classified as “misleading” or “non-misleading”. We then investigated the influence of two demographic parameters (effective size and bottleneck severity) and different numbers of loci on the type and frequency of misleading results. We showed that misleading STRUCTURE results were obtained for 10% of our simulated datasets and at a frequency of up to 37% for some combinations of parameters. Our results highlighted two different categories of misleading output. The first occurs in situations in which the native population has a low level of diversity. In this case, the two introduced populations may be very similar, despite their independent introduction histories. The second category results from convergence issues in STRUCTURE forK= 2, with strong bottleneck severity and/or large numbers of loci resulting in high levels of differentiation between the three populations.
Impact of gray matter signal regression in resting state and language task functional networks
Authors: Herrera Luis C. T. , Castellano Gabriela , Coan Ana C. , Ludwing M. , César C. L. 
Published: December 2016

AbstractA network analysis of the resting state (RS) and language task (LT) of fRMI data sets is presented. Specifically, the analysis compares the impact of the global signal regression of gray matter signal on the graph parameters and community structure derived of functional data. It was found that, without gray matter signal regression (GSR), the group comparison showed no significant changes of the global metrics between the two conditions studied. With gray matter signal regression, significant differences between the global (local) metrics for the conditions were obtained. The mean degree, the clustering coefficient of the network and the mean value of the local efficiency were metrics with significant changes. The community structure of group connectivity matrices was explored for both conditions (RS and LT) and for different preprocessing steps. When gray matter signal regression was performed, small changes of the community structure were observed. Approximately, the same regions were classified in the same communities before and after GSR. This means, that the community structure of the data is weakly affected by this preprocessing step. The modularity index presented significant changes between conditions (RS and LT) and between different preprocessing pipeline.
An empirical model for assessing the effect of ports’ and hinterlands’ characteristics on homeports’ potential
Authors: Niavis Spyros , Vaggelas Georgios 
Published: December 2016

Purpose
The significant benefits associated with cruise tourism have mobilized port industry, as progressively, a large number of ports are developing cruise operations. Although increasing cruise traffic is a major goal for cruise ports, homeporting constitutes a strategic target of the majority of ports due to its greater economic benefits for both the port itself and its hinterland. The establishment of homeport traffic in a cruise port is subjected to a variety of port internal and external factors. Taking these into account, the paper aims at defining elements that affect the potential of a cruise port to become a homeport.

Design/methodology/approach
A sample of 47 Mediterranean ports is selected to form the basis for the implementation of an ordinal regression model which links the likelihood of ports to attract homeport traffic with seven explanatory variables which emerged from relevant literature and are split in the main categories of ports’ and hinterlands’ characteristics. To fit the model into the paper’s data, ports are divided into three categories based on their homeport cruise traffic.

Findings
The results of the empirical model signify that both internal and external factors affect the potential of a port to become a cruise homeport. Concerning the internal factors, adequate infrastructure allowing the facilitation of the last generation of cruise ships and the presence of a private enterprise in ports’ operation seems to foster homeport traffic. Additionally, efficiency in operations seems to be a crucial element. On the other hand, the connectivity of port’s; hinterlands, tourist infrastructure and the level of economic growth are proved to be the hinterlands’ elements which increase the likelihood of a port to attract additional homeport traffic.

Practical implications
The model forms a comprehensive evaluation basis for whether a cruise port should intensify its pursuit of homeport traffic, as the estimated coefficients could support port and local authorities to understand their competitive position against other ports and spot their strengths and weaknesses.

Originality/value
The paper contributes in the research dealing with the identification of crucial elements of homeporting from the port’s point of view. Although, it should be mentioned that previous efforts targeting on revealing the characteristics affecting the homeporting potential of ports mostly have been based on questionnaires and expert judgements or empirical models in which the total – and not the homeport traffic – was used as the dependent variable. With the proposed empirical model, home-porting choice analysis is transferred, on the one hand, from the stated preferences level to the revealed preferences level and, on the other hand, from an indirect to a direct approximation of the issue.
Covariate Balancing through Naturally Occurring Strata
Authors: Alemi Farrokh , ElRafey Amr , Avramovic Ivan 
Published: December 2016

ObjectiveTo provide an alternative to propensity scoring (PS) for the common situation where there are interacting covariates.SettingWe used 1.3 million assessments of residents of the United States Veterans Affairs nursing homes, collected from January 1, 2000, through October 9, 2012.DesignIn stratified covariate balancing (SCB), data are divided into naturally occurring strata, where each stratum is an observed combination of the covariates. Within each stratum, cases with, and controls without, the target event are counted; controls are weighted to be as frequent as cases. This weighting procedure guarantees that covariates, or combination of covariates, are balanced, meaning they occur at the same rate among cases and controls. Finally, impact of the target event is calculated in the weighted data. We compare the performance ofSCB, logistic regression (LR), and propensity scoring (PS) in simulated and real data. We examined the calibration ofSCBandPSin predicting 6‐month mortality from inability to eat, controlling for age, gender, and nine other disabilities for 296,051 residents in Veterans Affairs nursing homes. We also performed a simulation study, where outcomes were randomly generated from treatment, 10 covariates, and increasing number of covariate interactions. The accuracy ofSCB,PS, andLRin recovering the simulated treatment effect was reported.FindingsIn simulated environment, as the number of interactions among the covariates increased,SCBand properly specifiedLRremained accurate but pairwiseLRand pairwisePS, the most common applications of these tools, performed poorly. In real data, application ofSCBwas practical.SCBwas better calibrated than linearPS, the most common method ofPS.ConclusionsIn environments where covariates interact,SCBis practical and more accurate than common methods of applyingLRandPS.
REIT Leverage and Return Performance: Keep Your Eye on the Target
Authors: Giacomini Emanuela , Ling David C. , Naranjo Andy 
Published: December 2016

AbstractThis article examines U.S. REIT leverage decisions and their effects on risk and return. We find that the speed at which REITs close the gap between current debt levels and target leverage levels is 17% annually. REITs that are highly levered relative to the average REIT tend to underperform REITs with less debt in their capital structure. However, REITs that are highly levered relative to their target leverage tend to perform better on a risk‐adjusted basis than under‐levered REITs. Taken together, our results show that REIT leverage has significant return performance effects conditional on deviations from target leverage.
Prospective and Explicit Clinical Validation of the Ottawa Heart Failure Risk Scale, With and Without Use of Quantitative NT‐proBNP
Authors: Stiell Ian G. , Perry Jeffrey J. , Clement Catherine M. , Brison Robert J. , Rowe Brian H. , Aaron Shawn D. , McRae Andrew D. , Borgundvaag Bjug , Calder Lisa A. , Forster Alan J. , Wells George A. 
Published: December 2016

AbstractObjectivesWe previously developed the Ottawa Heart Failure Risk Scale (OHFRS) to assist with disposition decisions for acute heart failure patients in the emergency department (ED). We sought to prospectively evaluate the accuracy, acceptability, and potential impact of OHFRS.MethodsThis prospective observational cohort study was conducted at six tertiary hospital EDs. Patients with acute heart failure were evaluated by ED physicians for the 10 OHFRS criteria and then followed for 30 days. Quantitative NT‐proBNP was measured where feasible. Serious adverse event (SAE) was defined as death within 30 days, admission to monitored unit, intubation, noninvasive ventilation, myocardial infarction, or relapse resulting in hospital admission within 14 days.ResultsWe enrolled 1,100 patients with mean (±SD) age 77.7 (±10.7) years. SAEs occurred in 170 (15.5%) cases (19.4% if admitted and 10.2% if discharged). Compared to actual practice, using an admission threshold of OHFRS score > 1 would have increased sensitivity (71.8% vs. 91.8%) but increased admissions (57.2% vs. 77.6%). For 684 cases with NT‐proBNP values, using a threshold score > 1 would have significantly increased sensitivity (69.8% vs. 95.8%) while increasing admissions (60.8% vs. 88.0%). In only 11.9% of cases did physicians indicate discomfort with use of OHFRS.ConclusionProspective clinical validation found the OHFRS tool to be highly sensitive for SAEs in acute heart failure patients, albeit with an increase in admission rates. When available, NT‐proBNP values further improve sensitivity. With adequate physician training, OHFRS should help improve and standardize admission practices, diminishing both unnecessary admissions for low‐risk patients and unsafe discharge decisions for high‐risk patients.