bluuebunny/crossref_metadata_2025_split huggingface dataset:
Association rule mining to identify transcription factor interactions in genomic regions
Authors: Ceddia Gaia , Martino Liuba Nausicaa , Parodi Alice , Secchi Piercesare , Campaner Stefano , Masseroli Marco 
Published: August 2019

Abstract

Motivation
Genome regulatory networks have different layers and ways to modulate cellular processes, such as cell differentiation, proliferation, and adaptation to external stimuli. Transcription factors and other chromatin-associated proteins act as combinatorial protein complexes that control gene transcription. Thus, identifying functional interaction networks among these proteins is a fundamental task to understand the genome regulation framework.

Results
We developed a novel approach to infer interactions among transcription factors in user-selected genomic regions, by combining the computation of association rules and of a novel Importance Index on ChIP-seq datasets. The hallmark of our method is the definition of the Importance Index, which provides a relevance measure of the interaction among transcription factors found associated in the computed rules. Examples on synthetic data explain the index use and potential. A straightforward pre-processing pipeline enables the easy extraction of input data for our approach from any set of ChIP-seq experiments. Applications on ENCODE ChIP-seq data prove that our approach can reliably detect interactions between transcription factors, including known interactions that validate our approach.

Availability and implementation
A R/Bioconductor package implementing our association rules and Importance Index-based method is available at http://bioconductor.org/packages/release/bioc/html/TFARM.html.

Supplementary information
Supplementary data are available at Bioinformatics online.
The Function of Amicus Curiae Participation by Legal Scholars: The Al-Bashir Appeal Case at the International Criminal Court as an Illustration
Authors: Mao Xiao 
Published: August 2019

Abstract
In the recent case on non-cooperation of Jordan in the Al-Bashir case, the Appeals Chamber of the International Criminal Court for the first time invited on its initiative amicus curiae submissions by legal scholars. This comment focuses on the role of legal scholars as amici curiae. It argues that based on Martti Koskenniemi’s method on the structure of legal argumentation and analysis of the argumentation structure of several submissions by legal scholars in the Al-Bashir case, the role of legal scholars as amici curiae would better be viewed as grammarians capable of shaping the formulation of arguments of the Court. This view stands contrary to the traditional understanding that the amicus curiae participation can improve the court’s legitimacy by providing a neutral and definite answer to the legal dispute.
Valorization of Red Onion Peels for Quercetin Recovery Using Quercetin-Imprinted Polymer
Authors: Ersoy Şeyda Karaman , Tütem Esma , Başkan Kevser Sözgen , Apak Reşat 
Published: August 2019

Abstract
Quercetin (QC) is one of the most prominent dietary antioxidants present in vegetables/fruits, specifically in onions that rank second in consumption following tomato. QC with proven health benefits is now largely utilized as a nutritional supplement. In this work that aims to isolate QC from red onion peels forming a huge agricultural waste, a QC-molecularly imprinted polymer (QC-MIP) in a molar ratio of 1:4:20 (QC:4-vinylpyridine:ethylene glycol dimethacrylate) was prepared thermally through bulk polymerization. Molecularly imprinted solid phase extraction (MISPE) procedures were applied for the selective pre-concentration and purification of QC from both red onion peel methanolic extract with 58% recovery and from the extract hydrolyzate with 86% recovery. The hydrolysis process increased both the QC amount as expected and the recovery yield due to changing matrix components. The results demonstrated that onion peel can easily and efficiently be converted to a valuable product, QC, using QC-MIP as SPE sorbent.
Pulmonary vein isolation using ablation index vs. CLOSE protocol with a surround flow ablation catheter
Authors: Berte Benjamin , Hilfiker Gabriella , Moccetti Federico , Schefer Thomas , Weberndörfer Vanessa , Cuculi Florim , Toggweiler Stefan , Ruschitzka Frank , Kobza Richard 
Published: August 2019

AbstractAimsPulmonary vein isolation (PVI) using ablation index (AI) incorporates stability, contact force (CF), time, and power. The CLOSE protocol combines AI and ≤6 mm interlesion distance. Safety concerns are raised about surround flow ablation catheters (STSF). To compare safety and effectiveness of an atrial fibrillation (AF) ablation strategy using AI vs. CLOSE protocol using STSF.Methods and resultsFirst cluster was treated using AI and second cluster using CLOSE. Procedural data, safety, and recurrence of any atrial tachycardia (AT) or AF &gt;30 s were collected prospectively. All Classes 1c and III anti-arrhythmic drugs (AAD) were stopped after the blanking period. In total, all 215 consecutive patients [AI: 121 (paroxysmal: n = 97), CLOSE: n = 94 (paroxysmal: n = 74)] were included. Pulmonary vein isolation was reached in all in similar procedure duration (CLOSE: 107 ± 25 vs. AI: 102 ± 24 min; P = 0.1) and similar radiofrequency time (CLOSE: 36 ± 11 vs. AI: 37 ± 8 min; P = 0.4) but first pass isolation was higher in CLOSE vs. AI [left veins: 90% vs. 80%; P &lt; 0.05 and right veins: 84% vs. 73%; P &lt; 0.05]. Twelve-month off-AAD freedom of AF/AT was higher in CLOSE vs. AI [79% (paroxysmal: 85%) vs. 64% (paroxysmal: 68%); P &lt; 0.05]. Only four patients (2%) without recurrence were on AAD during follow-up. Major complications were similar (CLOSE: 2.1% vs. AI: 2.5%; P = 0.87).ConclusionThe CLOSE protocol is more effective than a PVI approach solely using AI, especially in paroxysmal AF. In this off-AAD study, 79% of patients were free from AF/AT during 12-month follow-up. The STSF catheter appears to be safe using conventional CLOSE targets.
Contrasting effects of isocitrate dehydrogenase deletion on fluxes through enzymes of central metabolism in Escherichia coli
Authors: El-Mansi Mansi 
Published: August 2019

ABSTRACT
Flux analysis is central to understanding cellular metabolism and successful manipulation of metabolic fluxes in microbial cell-factories. Isocitrate dehydrogenase (ICDH) deletion conferred contrasting effects on fluxes through substrate-level phosphorylation (SLP) reactions. While significantly increasing flux through pyruvate kinase, it diminishes flux through succinyl CoA synthetase and upregulates phosphotransacetylase (PTA) and acetate kinase (AK). In addition to acetate, the ICDH-less strain excretes pyruvate, citrate and isocitrate. While efflux to acetate excretion by the Escherichia coli parental strain and its ICDH-less derivative is a reflection of high throughput of glycolytic intermediates, excretion of pyruvate is a reflection of high throughput via pyruvate kinase. On the other hand, citrate and isocitrate excretion is a reflection of truncating the Krebs cycle at the level of ICDH. Furthermore, another striking finding is the inability of the ICDH-less cultures to utilize acetate as a source of carbon despite the availability of an adequate supply of extracellular glutamate (for biosynthesis) and elevated levels of AK and PTA (for acetate uptake). This striking observation is now explicable in the light of the newly proposed hypothesis that the expression of the ace operon enzymes is controlled in response to a minimum threshold signal (ATP), which could not be achieved in the ICDH-less strain.
Sea Turtle Population Genomic Discovery: Global and Locus-Specific Signatures of Polymorphism, Selection, and Adaptive Potential
Authors: Chow Julie C , Anderson Paul E , Shedlock Andrew M 
Published: August 2019

AbstractIn the era of genomics, single-nucleotide polymorphisms (SNPs) have become a preferred molecular marker to study signatures of selection and population structure and to enable improved population monitoring and conservation of vulnerable populations. We apply a SNP calling pipeline to assess population differentiation, visualize linkage disequilibrium, and identify loci with sex-specific genotypes of 45 loggerhead sea turtles (Caretta caretta) sampled from the southeastern coast of the United States, including 42 individuals experimentally confirmed for gonadal sex. By performing reference-based SNP calling in independent runs of Stacks, 3,901–6,998 SNPs and up to 30 potentially sex-specific genotypes were identified. Up to 68 pairs of loci were found to be in complete linkage disequilibrium, potentially indicating regions of natural selection and adaptive evolution. This study provides a valuable SNP diagnostic workflow and a large body of new biomarkers for guiding targeted studies of sea turtle genome evolution and for managing legally protected nonmodel iconic species that have high economic and ecological importance but limited genomic resources.
Finite-time stabilization of stochastic coupled systems on networks by feedback control and its application
Authors: Wu Yongbao , Li Wenxue , Feng Jiqiang 
Published: August 2019

Abstract
In this paper, the finite-time stabilization of stochastic coupled systems on networks (SCSNs) is studied. Different from previous research methods, the method used in this paper combines Lyapunov method with graph theory, and some novel sufficient conditions are obtained to ensure finite-time stability for SCSNs. Meanwhile, the convergence time is closely related to topological structure in networks. As a practical application in physics, we address a concrete finite-time stabilization problem of stochastic coupled oscillators through our main results. In addition, a numerical example is presented to illustrate the effectiveness and feasibility of the theoretical results.
Vaccine stockouts and vaccination rate: examination of unique administrative data from Nigeria
Authors: Sato Ryoko 
Published: August 2019

Abstract

Background
Universal access to vaccines is crucial in protecting the population from deadly diseases. This study presents the prevalence of vaccine stockouts in Nigeria and examines the correlation between the vaccine stockouts and vaccine take-up.

Methods
We use the unique administrative data of monthly vaccine stockouts at each health facility in Nigeria. To evaluate the correlation between the stockouts and the vaccine take-up, the administrative data were merged with the Nigeria Demographic and Health Survey conducted in 2013. We used logistic regression for the correlational study.

Results
The prevalence of vaccine stockouts in Nigeria is high: 82.7% between 2012 and 2013. We find a negative correlation between vaccine stockouts and vaccine take-up. However, we observe the differential correlational pattern depending on the regional vaccine coverage, which we consider as the proxy of the level of demand for vaccines.

Conclusions
We find that, while vaccine stockouts are correlated with the low vaccine take-up on average, this negative correlation between stockouts and vaccination rate is observed only in regions with low demand for vaccines. Reducing vaccine stockouts in regions with the low vaccination coverage might be an effective way to increase the overall vaccination rate.
Good Vibrations: Consumer Responses to Technology-Mediated Haptic Feedback
Authors: Hadi Rhonda , Valenzuela Ana 
Published: August 2019

AbstractIndividuals often experience incidental device-delivered haptic feedback (e.g., vibrational alerts accompanying messages on mobile phones and wearables), yet almost no research has examined the psychological and behavioral implications of technology-mediated touch on consumers. Drawing from theories in social psychology and computer science, we explore how device-delivered haptic feedback may have the capability to augment consumer responses to certain consumer-directed communications. Across four studies, we find that haptic alerts accompanying messages can improve consumer performance on related tasks and demonstrate that this effect is driven by an increased sense of social presence in what can otherwise feel like an impersonal technological exchange. These findings provide applied value for mobile marketers and gadget designers, and carry important implications for consumer compliance in health and fitness domains.
Nivolumab plus ipilimumab versus sunitinib in previously untreated advanced renal-cell carcinoma: analysis of Japanese patients in CheckMate 214 with extended follow-up
Authors: Tomita Yoshihiko , Kondo Tsunenori , Kimura Go , Inoue Takamitsu , Wakumoto Yoshiaki , Yao Masahiro , Sugiyama Takayuki , Oya Mototsugu , Fujii Yasuhisa , Obara Wataru , Motzer Robert J , Uemura Hirotsugu 
Published: August 2019

Abstract

Background
Nivolumab plus ipilimumab (NIVO+IPI) demonstrated superior efficacy over sunitinib (SUN) for previously untreated advanced renal cell carcinoma (aRCC) in CheckMate 214, with a manageable safety profile. We report efficacy and safety with extended follow-up amongst Japanese patients.

Methods
CheckMate 214 patients received NIVO (3 mg/kg) plus IPI (1 mg/kg) every 3 weeks for four doses, then NIVO (3 mg/kg) every 2 weeks; or SUN (50 mg) once daily for 4 weeks (6-week cycle). This subgroup analysis assessed overall survival (OS), objective response rate (ORR) and progression-free survival (PFS) per investigator in International Metastatic Renal Cell Carcinoma Database Consortium (IMDC) intermediate/poor-risk and intent-to-treat (ITT) patients and safety (ITT patients).

Results
Of 550 and 546 patients randomized to NIVO+IPI and SUN, 38 and 34, respectively, were Japanese. Of these, 31 (NIVO+IPI) and 29 (SUN) patients were IMDC intermediate/poor-risk. In IMDC intermediate/poor-risk patients with 30 months’ minimum follow-up, there was a delayed trend in OS benefit with NIVO+IPI (hazard ratio [HR] 0.56; 95% confidence interval [CI]: 0.19–1.59; P = 0.2670), and 24-month OS probability favoured NIVO+IPI (84%) versus SUN (76%). The ORR was 39% with NIVO+IPI and 31% with SUN (P = 0.6968). PFS was similar in both treatment arms (HR 1.17; 95% CI: 0.62–2.20; P = 0.6220). Efficacy in ITT patients was similar to IMDC intermediate/poor-risk patients. Grade 3–4 treatment-related adverse event incidence was lower with NIVO+IPI versus SUN (58 versus 91%).

Conclusions
Japanese patients with untreated aRCC in the NIVO+IPI arm had a numerically higher ORR and improved safety profile versus patients in the SUN arm. A delayed OS benefit appears to be emerging with NIVO+IPI. Longer follow-up is needed.
https://clinicaltrials.gov/ct2/show/NCT02231749?term=NCT02231749&rank=1 identifier: NCT02231749.
Prostate-specific antigen bounce after 125I-brachytherapy for prostate cancer is a favorable prognosticator in patients who are biochemical recurrence-free at 4 years and correlates with testosterone
Authors: Nakai Yasushi , Tanaka Nobumichi , Asakawa Isao , Anai Satoshi , Miyake Makito , Morizawa Yosuke , Hori Shunta , Owari Takuya , Fujii Tomomi , Yamaki Kaori , Hasegawa Masatoshi , Fujimoto Kiyohide 
Published: August 2019

Abstract

Background
Because patients with prostate-specific antigen (PSA) bounce do not experience biochemical recurrence (BCR) until PSA bounce occurs, the period until PSA bounce ends can be considered the so-called lead-time bias. Therefore, we evaluated differences in BCR-free rate in prostate cancer patients who were BCR-free 4 years after 125I-brachytherapy alone. Furthermore, we evaluated predictors for PSA bounce and the correlation between testosterone and PSA bounce.

Methods
From 2004 to 2012, 256 patients with prostate adenocarcinoma underwent 125I-brachytherapy alone. PSA and testosterone levels were monitored prior to 125I-brachytherapy, at 1, 3, 6, 12, 18, 24, 30, 36, 42, 48, 54 and 60 months after 125I-brachytherapy and yearly after 5-year follow-up. PSA bounce was defined as ≥0.2 ng/ml increase above the interval PSA nadir, followed by a decrease to nadir or below.

Results
BCR-free rate in patients with PSA bounce (100% 7-year BCR-free rate) was significantly better (P &lt; 0.044) than that in patients without PSA bounce (95.7% 7-year BCR-free rate) in patients who were BCR-free 4 years after 125I-brachytherapy alone (n = 223). Age was the only predictor (odds ratio: 0.93, 95% confidence interval: 0.88–0.98, P = 0.004) for PSA bounce (n = 177). The testosterone level at PSA bounce was significantly higher (P = 0.036) than that at nadir before PSA bounce (87 cases).

Conclusions
Patients with PSA bounce had good BCR-free rate even in patients who were BCR-free 4 years after 125I-brachytherapy alone. Testosterone levels were higher at PSA bounce; increased testosterone levels may be a cause of PSA bounce.
Giving Useful but Not Well-Understood Ideas Their Due
Authors: Omelianchuk Adam 
Published: August 2019

AbstractIn this paper, I introduce the ideas to be discussed in the articles of this journal with reference to an imaginary case involving a pregnant woman declared dead on the basis of neurological criteria. I highlight the fact that although these ideas have proved useful for advancing certain claims in bioethical debates, their implications are not always well understood and may complicate our arguments. The ideas to be discussed are (1) an ethic internal to the profession of medicine; (2) the difference between killing and letting die; (3) the organism as a whole; and (4) the “lives” and interests of the dead.
Is triose phosphate utilization important for understanding photosynthesis?
Authors: Sharkey Thomas D 
Published: August 2019

This article comments on:Fabre D, Yin X, Dingkuhn M, Clément-Vidal A, Roques S, Rouan L, Soutiras A, Luquet D. 2019. Is triose phosphate utilization involved in the feedback inhibition of photosynthesis in rice under conditions of sink limitation? Journal of Experimental Botany 70, 5773–5785.
Causes of Substance Use Disorders
Authors: Daley Dennis C. , Douaihy Antoine 
Published: August 2019

Abstract
SUDs take many forms, and there are many reasons why an individual develops a problem. Substance problems can begin at any time in life. Having an SUD is not a matter of weakness, lack of willpower, or being “bad.” SUDs result from a complex interaction of genetic, psychological, social, and cultural factors. These disorders tend to run in families, so scientists believe a person inherits a predisposition or vulnerability to SUDs that interacts with environmental factors, increasing the risk of developing a problem. SUDs affect people of every age, race, ethnicity, religion, gender, and occupation. Some people develop a problem in early life, while others do so later in life. For some, a SUD develops gradually over years. For others, it happens quickly.
Helping Children Affected by a Parent’s Substance Use Disorder
Authors: Daley Dennis C. , Douaihy Antoine 
Published: August 2019

Abstract
Children of parents with SUDs are at increased risk for alcohol and drug use, behavior problems, school problems, depression and anxiety, and medical problems. Children can appear fine on the outside but suffer quietly on the inside, especially if they keep feelings, fears, and worries bottled up. Not all people, including children, are affected by a parent’s SUD in the same way. Strong connections with school, religious community, adults and mentors (teachers, coaches, relatives, friends), and involvement in meaningful activities (academic, creative, athletic, social) may help offset some of the negative impact of living in a family with an SUD. Many children show resilience and cope with difficult situations, including having a parent with an SUD.
Local and teleconnected temperature effects of afforestation and vegetation greening in China
Authors: Li Yue , Piao Shilong , Chen Anping , Ciais Philippe , Li Laurent Z X 
Published: August 2019

Abstract
Afforestation in China provides carbon sequestration and prevents soil erosion, but its remote impacts on climate in other regions via the coupling of forest energy fluxes with atmospheric circulation are largely unknown. Here, we prescribe inventory-based forest cover change and satellite-observed leaf area index from 1982 to 2011 in a coupled land-atmosphere model to simulate their biophysical climate effects. Both local and global surface air temperatures show a seasonal contrast in response to past vegetation cover expansion over China: a phenomenon we primarily attribute to a variation of seasonality of vegetation greening. A large cooling in spring results in concurrent decreases in geopotential height over China and zonal wind over Mongolia, causing a dipole structure in the upper troposphere over the Arctic. This accounts for ∼58% of simulated spring warming over the Russian Arctic and ∼61% of simulated spring cooling over the Canadian Artic. Our results imply that spring vegetation dynamics in China may affect climate in northern high latitudes.
Comparison of characteristics of children and adolescents with and without a history of abuse assessed in an urgent psychiatric clinic
Authors: Dolp Reinhard , Roberts Nasreen , Groll Dianne 
Published: August 2019

Abstract

Purpose
The objective was 1) to describe the clinical characteristics of children referred for an urgent psychiatric consult with and without, a history of abuse; 2) to study differences in demographic and clinical variables between the groups; and 3) to examine the relationship between different types of abuse and disposition after assessment.

Methods
This is a 2-year retrospective cohort study of all patients aged 12 to 17 years referred to a hospital urgent psychiatric clinic. Patients were divided into two groups, those with a history of abuse and those without. Study variables included demographics, reason for referral, history of emotional, physical, sexual abuse, substance use, bullying victimization, DSM-5 diagnoses, and disposition. The study population was described using means, frequencies, and percentages, while relationships between types of abuse and clinical and demographic variables were assessed using Mann–Whitney U statistics, Spearman correlations, and logistic regression.

Results
The prevalence of any type of abuse was 30.4% (227 of 746 referrals). The abused group were older, more likely to be female, to have a history of substance use, bullying victimization, diagnosis of an externalizing disorder, and more likely to be admitted. Among the abused group, males were significantly more likely to report physical/emotional abuse, and female sexual abuse. There was no difference between different kinds of abuse and final diagnoses.

Conclusions
Almost one-third of children and adolescents referred for urgent psychiatric consultation reported a history of abuse. Awareness of the association between abuse and emergency visits may assist physicians in triaging for urgent psychiatric assessment.
Adsorption of unfolded Cu/Zn superoxide dismutase onto hydrophobic surfaces catalyzes its formation of amyloid fibrils
Authors: Khan Mohammad Ashhar I , Weininger Ulrich , Kjellström Sven , Deep Shashank , Akke Mikael 
Published: August 2019

Abstract
Intracellular aggregates of superoxide dismutase 1 (SOD1) are associated with amyotrophic lateral sclerosis. In vivo, aggregation occurs in a complex and dense molecular environment with chemically heterogeneous surfaces. To investigate how SOD1 fibril formation is affected by surfaces, we used an in vitro model system enabling us to vary the molecular features of both SOD1 and the surfaces, as well as the surface area. We compared fibril formation in hydrophilic and hydrophobic sample wells, as a function of denaturant concentration and extraneous hydrophobic surface area. In the presence of hydrophobic surfaces, SOD1 unfolding promotes fibril nucleation. By contrast, in the presence of hydrophilic surfaces, increasing denaturant concentration retards the onset of fibril formation. We conclude that the mechanism of fibril formation depends on the surrounding surfaces and that the nucleating species might correspond to different conformational states of SOD1 depending on the nature of these surfaces.