bluuebunny/crossref_metadata_2025_split huggingface dataset:
Meta-GDBP: a high-level stacked regression model to improve anticancer drug response prediction
Authors: Su Ran , Liu Xinyi , Xiao Guobao , Wei Leyi 
Published: February 2019

Abstract
Anticancer drug response prediction plays an important role in personalized medicine. In particular, precisely predicting drug response in specific cancer types and patients is still a challenge problem. Here we propose Meta-GDBP, a novel anticancer drug-response model, which involves two levels. At the first level of Meta-GDBP, we build four optimized base models (BMs) using genetic information, chemical properties and biological context with an ensemble optimization strategy, while at the second level, we construct a weighted model to integrate the four BMs. Notably, the weights of the models are learned upstream, thus the parameter cost is significantly reduced compared to previous methods. We evaluate the Meta-GDBP on Genomics of Drug Sensitivity in Cancer (GDSC) and the Cancer Cell Line Encyclopedia (CCLE) data sets. Benchmarking results demonstrate that compared to other methods, the Meta-GDBP achieves a much higher correlation between the predicted and the observed responses for almost all the drugs. Moreover, we apply the Meta-GDBP to predict the GDSC-missing drug response and use the CCLE-known data to validate the performance. The results show quite a similar tendency between these two response sets. Particularly, we here for the first time introduce a biological context-based frequency matrix (BCFM) to associate the biological context with the drug response. It is encouraging that the proposed BCFM is biologically meaningful and consistent with the reported biological mechanism, further demonstrating its efficacy for predicting drug response. The R implementation for the proposed Meta-GDBP is available at https://github.com/RanSuLab/Meta-GDBP.
Hemisphere and Gender Differences in the Rich-Club Organization of Structural Networks
Authors: Wang Bin , Zhan Qionghui , Yan Ting , Imtiaz Sumaira , Xiang Jie , Niu Yan , Liu Miaomiao , Wang Gongshu , Cao Rui , Li Dandan 
Published: February 2019

AbstractStructural and functional differences in brain hemispheric asymmetry have been well documented between female and male adults. However, potential differences in the connectivity patterns of the rich-club organization of hemispheric structural networks in females and males remain to be determined. In this study, diffusion tensor imaging was used to construct hemispheric structural networks in healthy subjects, and graph theoretical analysis approaches were applied to quantify hemisphere and gender differences in rich-club organization. The results showed that rich-club organization was consistently observed in both hemispheres of female and male adults. Moreover, a reduced level of connectivity was found in the left hemisphere. Notably, rightward asymmetries were mainly observed in feeder and local connections among one hub region and peripheral regions, many of which are implicated in visual processing and spatial attention functions. Additionally, significant gender differences were revealed in the rich-club, feeder, and local connections in rich-club organization. These gender-related hub and peripheral regions are involved in emotional, sensory, and cognitive control functions. The topological changes in rich-club organization provide novel insight into the hemisphere and gender effects on white matter connections and underlie a potential network mechanism of hemisphere- and gender-based differences in visual processing, spatial attention and cognitive control.
Acute Inescapable Stress Rapidly Increases Synaptic Energy Metabolism in Prefrontal Cortex and Alters Working Memory Performance
Authors: Musazzi Laura , Sala Nathalie , Tornese Paolo , Gallivanone Francesca , Belloli Sara , Conte Alessandra , Di Grigoli Giuseppe , Chen Fengua , Ikinci Ayşe , Treccani Giulia , Bazzini Chiara , Castiglioni Isabella , Nyengaard Jens R , Wegener Gregers , Moresco Rosa M , Popoli Maurizio 
Published: February 2019

Abstract
Brain energy metabolism actively regulates synaptic transmission and activity. We have previously shown that acute footshock (FS)-stress induces fast and long-lasting functional and morphological changes at excitatory synapses in prefrontal cortex (PFC). Here, we asked whether FS-stress increased energy metabolism in PFC, and modified related cognitive functions. Using positron emission tomography (PET), we found that FS-stress induced a redistribution of glucose metabolism in the brain, with relative decrease of [18F]FDG uptake in ventro-caudal regions and increase in dorso-rostral ones. Absolute [18F]FDG uptake was inversely correlated with serum corticosterone. Increased specific hexokinase activity was also measured in purified PFC synaptosomes (but not in total extract) of FS-stressed rats, which positively correlated with 2-Deoxy [3H] glucose uptake by synaptosomes. In line with increased synaptic energy demand, using an electron microscopy-based stereological approach, we found that acute stress induced a redistribution of mitochondria at excitatory synapses, together with an increase in their volume. The fast functional and metabolic activation of PFC induced by acute stress, was accompanied by rapid and sustained alterations of working memory performance in delayed response to T-maze test. Taken together, the present data suggest that acute stress increases energy consumption at PFC synaptic terminals and alters working memory.
IBD-associated Colon Cancers Differ in DNA Methylation and Gene Expression Profiles Compared With Sporadic Colon Cancers
Authors: Pekow Joel , Hernandez Kyle , Meckel Katherine , Deng Zifeng , Haider Haider I , Khalil Abdurahman , Zhang Chunling , Talisila Nitya , Siva Shivi , Jasmine Farzana , Li Yan Chun , Rubin David T , Hyman Neil , Bissonnette Marc , Weber Christopher , Kibriya Muhammad G 
Published: February 2019

Abstract

Background and Aims
As ulcerative colitis [UC]-associated colorectal cancer [CRC] and sporadic CRC differ in presentation and molecular features, we sought to evaluate differences in the impact of DNA methylation on gene expression.

Methods
DNA methylation was assessed in 11 UC-CRCs and adjacent tissue and 11 sporadic CRCs and adjacent tissue, using Illumina arrays. RNA sequencing was performed on 10 UC-CRCs and adjacent tissue and eight sporadic CRCs and adjacent tissues. Differences in DNA methylation and transcript expression, as well as their correlation in the same tissues, were assessed. Immunohistochemistry was performed for three proteins, ANPEP, FAM92A1, and STK31, all of which exhibited an inverse correlation between DNA methylation and transcript expression in UC.

Results
Thirty three loci demonstrated differences in DNA methylation between UC-CRC and adjacent tissue. In contrast, there were 4204 differentially methylated loci between sporadic colon cancer and adjacent tissue. Eight hundred eighty six genes as well as 10 long non-coding RNAs [lncRNA] were differentially expressed between UC-CRC and adjacent tissues. Although there were no differentially methylated loci between UC and sporadic CRC, 997 genes and 38 lncRNAs were differentially expressed between UC-CRC and sporadic CRC. In UC, 18 genes demonstrated a negative correlation between DNA methylation and transcript expression. Evaluation of protein expression related to three genes, ANPEP, FAM92A1, and STK31, confirmed down-regulation of ANPEP and up-regulation of STK31 in UC-CRC.

Conclusions
Regulation of transcript expression by DNA methylation involves genes key to colon carcinogenesis and may account for differences in presentation and outcomes between inflammatory bowel disease and sporadic colon cancer.
Effectiveness of individual and group multicomponent interventions for smoking cessation in primary care: a quasi-experimental study
Authors: Suárez-Varela Úbeda Juan Fernando , Rodríguez-Vázquez Sara , Ordóñez Barranco José Antonio , Vega Caldera Gilberto , Pérez Alvárez Pedro Pablo , Buitrago Francisco 
Published: February 2019

Abstract

Background
The efficacy of smoking cessation interventions can be quite diverse in day-to-day clinical practice.

Objective
To analyse the effectiveness in smoking cessation of multicomponent interventions carried out in groups or individually in primary care practices.

Methods
A quasi-experimental, multicentre study of 12-month follow-up of patients treated in multicomponent smoking cessation interventions was carried out in Urban health care centres in Sevilla, Spain. Two hundred and twenty smoking patients, ≥18 years of age, participated either in a multicomponent intervention group (n = 145; mean age 51.7 years; 53.1% women) or in individual interventions (n = 77; mean age 50.5 years; 61.0% women). The abstinence or relapse status was computed from patient self-reports, confirmed by relatives or companions when possible and supplemented by CO-oxymetry tests in 89 patients.

Results
The overall percentage of smoking cessation was 36.9% (37.9% with group and 35.1% with individual intervention, P = 0.398). Patients who quit smoking were younger (48.7 versus 52.9 years old, P < 0.01), with fewer years of smoking (32.9 versus 36.8 years, P < 0.05), with higher education (39.0% versus 25.0%, P < 0.05) and had received pharmacological treatment (91.5% versus 67.9%, P < 0.001). In the multivariate analysis, level of education [odds ratio (OR): 1.995; 95% confidence interval (CI): 1.065–3.735, P < 0.01], group intervention (OR: 1.743; 95% CI: 1.006–3.287, P < 0.05) and drug prescription (OR: 2.368; 95% CI: 1.126–4.980, P < 0.05) were significantly associated with smoking cessation.

Conclusions
Our study found that multicomponent group and individual interventions in primary care were associated with an overall quit rate of smoking of 36.9% at 12-month follow-up, with higher probability of success among patients with higher education and those who received the group intervention and drug treatment.
Posaconazole for the treatment of allergic bronchopulmonary aspergillosis in patients with cystic fibrosis
Authors: Periselneris J , Nwankwo L , Schelenz S , Shah A , Armstrong-James D 
Published: February 2019

Abstract

Objectives
Allergic bronchopulmonary aspergillosis (ABPA) can accelerate lung function decline in patients with cystic fibrosis (CF). Antifungal medication can be used in addition to systemic corticosteroid treatment.

Patients and methods
We evaluated Aspergillus-specific IgE and the use of therapeutic drug monitoring of triazoles in a retrospective analysis of 32 patients.

Results
There was a significant reduction in Aspergillus IgE with posaconazole but not with other triazoles (P = 0.026). Aspergillus IgE levels were inversely correlated with the therapeutic drug level of posaconazole.

Conclusions
These data suggest that posaconazole is better than comparator azoles at decreasing serological response to Aspergillus and that this response was better with therapeutic levels of posaconazole.
Structural VARs and the Monetary Transmission Mechanism in Low-Income African Countries†
Authors: Li Bin Grace , Adam Christopher , Berg Andrew , Montiel Peter , O’Connell Stephen 
Published: February 2019

AbstractStructural Vector Autoregression (SVAR) methods suggest the monetary transmission mechanism may be weak and unreliable in many low-income African countries. But are structural VARs identified via short-run restrictions capable of detecting a transmission mechanism when one exists, under research conditions typical of low-income countries (LICs)? Using a small DSGE as our data-generating process, we assess the impact on VAR-based inference of short data samples, measurement error, high-frequency supply shocks, and other features of the LIC environment. The impact of these features on finite-sample bias appears to be relatively modest when identification is valid—a strong caveat, especially in LICs. Nonetheless many of these features undermine the precision of estimated impulse responses to monetary policy shocks, and cumulatively they suggest that statistically and economically insignificant results can be expected even when the underlying transmission mechanism is strong. These data features not only undermine the efficacy of the SVAR methodology for research and policy-making, but are also severe enough to motivate a continued search for monetary policy rules that are robust to these limitations.
Gastrointestinal Disease in Patients with Common Variable Immunodeficiency: A Retrospective Observational Study
Authors: Khan Rishad , Habbal Mohamad , Scaffidi Michael A , Bukhari Abbas A , Rumman Amir , Al Ghamdi Sarah , Betschel Stephen D , Grover Samir C 
Published: February 2019

Abstract

Background
Gastrointestinal (GI) symptoms are common among patients with common variable immunodeficiency disorder (CVID) yet remain poorly understood.

Aims
The aim of this study was to characterize the demographic, clinical, endoscopic and histologic features of patients with CVID and GI symptoms.

Methods
We conducted a retrospective observational study of all patients with CVID at a large Canadian tertiary care centre between January 2000 and May 2018.

Results
We included 95 patients with CVID. The mean age of patients at the time of CVID diagnosis was 38.2(±16.0). Fifty-three (56%) patients were female. Sixty-four (67%) patients had GI symptoms, with a mean age of onset for GI symptoms of 43.4(±15.1) years. The most common symptoms were bowel movement changes (n = 55 [58%]) and abdominal pain (n = 44 [46%]). Patients with GI symptoms were more likely to have anemia (n = 23 [36%] versus n = 3 [10%], P = 0.0129), iron deficiency (n = 16 [25%] versus n = 2 [7%], P = 0.0481), and have received GI antibiotics (n = 37 [58%] versus n = 0, P &lt; 0.0001) and proton pump inhibitors for reflux (n = 24 [38%] versus n = 3 [10%], P = 0.0067). The most common GI infections were Giardia lamblia (n = 14 [15%]) and Clostridium difficile (n = 4 [4%]). Forty-three (45%) patients with GI symptoms underwent colonoscopy, esophagogastroduodenoscopy or both. The most common findings were inflammation, nodular lymphoid hyperplasia, reduced plasma cells and increased intraepithelial lymphocytes.

Conclusions
This is the largest study on CVID patients in a North American setting. The majority of patients experienced GI symptoms. Future studies should study response to treatment for GI disease among patients with CVID.
Constrained Mutational Sampling of Amino Acids in HIV-1 Protease Evolution
Authors: Boucher Jeffrey I , Whitfield Troy W , Dauphin Ann , Nachum Gily , Hollins Carl , Zeldovich Konstantin B , Swanstrom Ronald , Schiffer Celia A , Luban Jeremy , Bolon Daniel N A 
Published: February 2019

Abstract
The evolution of HIV-1 protein sequences should be governed by a combination of factors including nucleotide mutational probabilities, the genetic code, and fitness. The impact of these factors on protein sequence evolution is interdependent, making it challenging to infer the individual contribution of each factor from phylogenetic analyses alone. We investigated the protein sequence evolution of HIV-1 by determining an experimental fitness landscape of all individual amino acid changes in protease. We compared our experimental results to the frequency of protease variants in a publicly available data set of 32,163 sequenced isolates from drug-naïve individuals. The most common amino acids in sequenced isolates supported robust experimental fitness, indicating that the experimental fitness landscape captured key features of selection acting on protease during viral infections of hosts. Amino acid changes requiring multiple mutations from the likely ancestor were slightly less likely to support robust experimental fitness than single mutations, consistent with the genetic code favoring chemically conservative amino acid changes. Amino acids that were common in sequenced isolates were predominantly accessible by single mutations from the likely protease ancestor. Multiple mutations commonly observed in isolates were accessible by mutational walks with highly fit single mutation intermediates. Our results indicate that the prevalence of multiple-base mutations in HIV-1 protease is strongly influenced by mutational sampling.
Role of the Neurosurgeon in Acute Ischemic Stroke Treatment From Triage to Intensive Care Unit
Authors: Kicielinski Kimberly P , Ogilvy Christopher S 
Published: February 2019

Abstract
As ischemic stroke care advances with more patients eligible for mechanical thrombectomy, so too does the role of the neurosurgeon in these patients. Neurosurgeons are an important member of the team from triage through the intensive care unit. This paper explores current research and insights on the contributions of neurosurgeons in care of acute ischemic stroke patients in the acute setting.
Second primary cancers in long-term survivors of glioblastoma
Authors: Kim Jung-Young , Jackman Jennifer G , Woodring Sarah , McSherry Frances , Herndon James E , Desjardins Annick , Friedman Henry S , Peters Katherine B 
Published: February 2019

Abstract

Background
Overall survival (OS) in glioblastoma (GBM) is poor at an average of 14 to 18 months, and long-term survivors (LTS) of GBM are rare. LTS of GBM, defined as surviving >5 years postdiagnosis, represent only 2% to 10% of all GBM patients. LTS of cancer are at high risk of developing second primary neoplasms. This study looks at occurrences of second primary neoplasms in LTS of GBM.

Methods
Records from adult patients newly diagnosed with GBM between January 1, 1998 and February 8, 2010, were retrospectively reviewed to identify LTS, defined as patients who survived ≥5 years. We focused on the identification of a new diagnosis of cancer occurring at least 2 years after the initial GBM diagnosis.

Results
We identified 155 LTS of GBM, with a median OS of 11.0 years (95% CI: 9.0 to 13.1 years) and a median follow-up of 9.6 years (95% CI: 8.7 to 10.7 years). In this cohort of patients, 13 (8.4%) LTS of GBM developed 17 secondary cancers. Eight could potentially be attributed to previous radiation and chemotherapy (skin cancer in radiation field [n = 4], leukemia [n = 2], low-grade glioma [n = 1], and sarcoma of the scalp [n = 1]). The other 9 cases included melanoma (n = 2), prostate cancer (n = 2), bladder cancer (n = 1), endometrioid adenocarcinoma (n = 1), basal cell carcinoma (n = 1), and renal cell carcinoma (n = 1).

Conclusions
Although second primary cancers are rare in GBM LTS, providers should continue close monitoring with appropriate oncologic care. Moreover, this highlights the need for survivorship care of patients with GBM.
Racial Attitudes in America
Authors: Moberg Sarah Patton , Krysan Maria , Christianson Deanna 
Published: February 2019

ABSTRACTRacial attitudes are multidimensional, and the corresponding picture we get from survey data on racial attitudes is complex. Tracing the results of major national surveys that provide trends over at least 10 years, and with at least three time points (primarily the General Social Survey and the National Election Studies), this article reveals that complexity. Some survey questions show dramatic changes in support of racial equality, while others reveal stagnation or even increasing negativity or disinterest. The article also describes the differences between whites and blacks in patterns and trends. Although compared to some issues, the survey record on racial attitudes is robust and lengthy, we draw attention to important ways in which it is uneven. We conclude by highlighting areas for future research that focus on improved survey measures that will capture more fully the complexity of contemporary public opinion on racial matters.
Group-Based Individualized Comprehensive Core Stability Intervention Improves Balance in Persons With Multiple Sclerosis: A Randomized Controlled Trial
Authors: Arntzen Ellen Christin , Straume Bjørn Kåre , Odeh Francis , Feys Peter , Zanaboni Paolo , Normann Britt 
Published: February 2019

Abstract

Background
Balance and trunk control are often impaired in individuals with multiple sclerosis (MS). Interventions addressing these issues are needed.

Objective
The objective of this study was to compare the immediate and long-term effects of a 6-week individualized, group-based, comprehensive core stability intervention (GroupCoreDIST) with standard care on balance and trunk control in individuals with MS.

Design
This study was a prospective, assessor-masked, randomized controlled trial.

Setting
The GroupCoreDIST intervention was conducted by 6 physical therapists in 6 municipalities in Norway. Standard care included the usual care for individuals with MS in the same municipalities. Assessments at all time points took place at a Norwegian hospital.

Participants
Eighty people with Expanded Disability Status scores of 1 to 6.5 participated in this trial.

Intervention
Randomized, concealed allocation was used to assign the participants to the GroupCoreDIST intervention (n = 40) or to standard care (n = 40). The GroupCoreDIST intervention was conducted with groups of 3 participants (1 group had 4 participants), for 60 minutes 3 times per week.

Measurements
Assessments were undertaken at baseline and at weeks 7, 18, and 30. Outcomes were measured with the Trunk Impairment Scale–Norwegian Version, Mini Balance Evaluation Systems Test, and Patient Global Impression of Change–Balance. Repeated-measures mixed models were used for statistical analysis.

Results
One individual missed all postintervention tests, leaving 79 participants in the intention-to-treat analysis. GroupCoreDIST produced significant between-group effects on the mean difference in the following scores at 7, 18, and 30 weeks: for Trunk Impairment Scale–Norwegian Version, 2.63 points (95% confidence interval [CI] = 1.89–3.38), 1.57 points (95% CI = 0.81–2.33), and 0.95 point (95% CI = 0.19–1.71), respectively; for Mini Balance Evaluation Systems Test, 1.91 points (95% CI = 1.07–2.76), 1.28 points (95% CI = 0.42–2.15), and 0.91 points (95% CI = 0.04–1.77), respectively; and for Patient Global Impression of Change–Balance, 1.21 points (95% CI = 1.66–0.77), 1.02 points (95% CI = 1.48–0.57), and 0.91 points (95% CI = 1.36–0.46), respectively.

Limitations
Groups were not matched for volume of physical therapy.

Conclusions
Six weeks of GroupCoreDIST improved balance and trunk control in the short and long terms compared with standard care in individuals who were ambulant and had MS. The intervention is an effective contribution to physical therapy for this population.
Life below Zero: Bank Lending under Negative Policy Rates
Authors: Heider Florian , Saidi Farzad , Schepens Glenn 
Published: February 2019

AbstractWe show that negative policy rates affect the supply of bank credit in a novel way. Banks are reluctant to pass on negative rates to depositors, which increases the funding cost of high-deposit banks, and reduces their net worth, relative to low-deposit banks. As a consequence, the introduction of negative policy rates by the European Central Bank in mid-2014 leads to more risk-taking and less lending by euro-area banks with a greater reliance on deposit funding. Our results suggest that negative rates are less accommodative and could pose a risk to financial stability, if lending is done by high-deposit banks.Received April 17, 2018; editorial decision September 18, 2018 by Editor Philip Strahan. Authors have furnished an Internet Appendix, which is available on the Oxford University Press Web site next to the link to the final published paper online.