bluuebunny/crossref_metadata_2025_split huggingface dataset:
Human cell structure-driven model construction for predicting protein subcellular location from biological images
Authors: Shao Wei , Liu Mingxia , Zhang Daoqiang 
Published: September 2015

Abstract
Motivation: The systematic study of subcellular location pattern is very important for fully characterizing the human proteome. Nowadays, with the great advances in automated microscopic imaging, accurate bioimage-based classification methods to predict protein subcellular locations are highly desired. All existing models were constructed on the independent parallel hypothesis, where the cellular component classes are positioned independently in a multi-class classification engine. The important structural information of cellular compartments is missed. To deal with this problem for developing more accurate models, we proposed a novel cell structure-driven classifier construction approach (SC-PSorter) by employing the prior biological structural information in the learning model. Specifically, the structural relationship among the cellular components is reflected by a new codeword matrix under the error correcting output coding framework. Then, we construct multiple SC-PSorter-based classifiers corresponding to the columns of the error correcting output coding codeword matrix using a multi-kernel support vector machine classification approach. Finally, we perform the classifier ensemble by combining those multiple SC-PSorter-based classifiers via majority voting.
Results: We evaluate our method on a collection of 1636 immunohistochemistry images from the Human Protein Atlas database. The experimental results show that our method achieves an overall accuracy of 89.0%, which is 6.4% higher than the state-of-the-art method.
Availability and implementation: The dataset and code can be downloaded from https://github.com/shaoweinuaa/.
Contact: dqzhang@nuaa.edu.cn
Supplementary information: Supplementary data are available at Bioinformatics online.
CD30 cell graphs of Hodgkin lymphoma are not scale-free—an image analysis approach
Authors: Schäfer Hendrik , Schäfer Tim , Ackermann Jörg , Dichter Norbert , Döring Claudia , Hartmann Sylvia , Hansmann Martin-Leo , Koch Ina 
Published: September 2015

Abstract
Motivation: Hodgkin lymphoma (HL) is a type of B-cell lymphoma. To diagnose the subtypes, biopsies are taken and immunostained. The slides are scanned to produce high-resolution digital whole slide images (WSI). Pathologists manually inspect the spatial distribution of cells, but little is known on the statistical properties of cell distributions in WSIs. Such properties would give valuable information for the construction of theoretical models that describe the invasion of malignant cells in the lymph node and the intercellular interactions.
Results: In this work, we define and discuss HL cell graphs. We identify CD30+ cells in HL WSIs, bringing together the fields of digital imaging and network analysis. We define special graphs based on the positions of the immunostained cells. We present an automatic analysis of complete WSIs to determine significant morphological and immunohistochemical features of HL cells and their spatial distribution in the lymph node tissue under three different medical conditions: lymphadenitis (LA) and two types of HL. We analyze the vertex degree distributions of CD30 cell graphs and compare them to a null model. CD30 cell graphs show higher vertex degrees than expected by a random unit disk graph, suggesting clustering of the cells. We found that a gamma distribution is suitable to model the vertex degree distributions of CD30 cell graphs, meaning that they are not scale-free. Moreover, we compare the graphs for LA and two subtypes of HL. LA and classical HL showed different vertex degree distributions. The vertex degree distributions of the two HL subtypes NScHL and mixed cellularity HL (MXcHL) were similar.
Availability and implementation: The CellProfiler pipeline used for cell detection is available at https://sourceforge.net/projects/cellgraphs/.
Contact: ina.koch@bioinformatik.uni-frankfurt.de
Supplementary information: Supplementary data are available at Bioinformatics online.
New insights into hepatitis B virus biology and implications for novel antiviral strategies
Authors: Chen Jieliang , Wu Min , Liu Kuancheng , Zhang Wen , Li Yaming , Zhou Xiaohui , Bai Lu , Yuan Zhenghong 
Published: September 2015

AbstractHepatitis B virus (HBV), a small DNA virus with a unique replication mode, can cause chronic hepatitis (CHB), which is characterized by the persistence of the viral covalently closed circular DNA that serves as the template for HBV replication and the production of large amounts of secreted HBV surface antigen (HBsAg) that is present in excess of the levels of infectious virus. Despite the success of currently approved antiviral treatments for CHB patients, including interferon and nucleotide analogs, which suppress HBV replication and reduce the risk of CHB-related liver diseases, these therapies fail to eradicate the virus in most of the patients. With the development of the cell and animal models for HBV study, a better understanding of the HBV life cycle has been achieved and a series of novel antiviral strategies that target different stages of HBV replication have been designed to overcome the viral factors that contribute to HBV persistence. Such basic HBV research advancements and therapeutic developments are the subject of this review.
Model-free Estimation of Tuning Curves and Their Attentional Modulation, Based on Sparse and Noisy Data
Authors: Helmer Markus , Kozyrev Vladislav , Stephan Valeska , Treue Stefan , Geisel Theo , Battaglia Demian 
Published: September 2015

AbstractTuning curves are the functions that relate the responses of sensory neurons to various values within one continuous stimulus dimension (such as the orientation of a bar in the visual domain or the frequency of a tone in the auditory domain). They are commonly determined by fitting a model e.g. a Gaussian or other bell-shaped curves to the measured responses to a small subset of discrete stimuli in the relevant dimension. However, as neuronal responses are irregular and experimental measurements noisy, it is often difficult to determine reliably the appropriate model from the data. We illustrate this general problem by fitting diverse models to representative recordings from area MT in rhesus monkey visual cortex during multiple attentional tasks involving complex composite stimuli. We find that all models can be well-fitted, that the best model generally varies between neurons and that statistical comparisons between neuronal responses across different experimental conditions are affected quantitatively and qualitatively by specific model choices. As a robust alternative to an often arbitrary model selection, we introduce a model-free approach, in which features of interest are extracted directly from the measured response data without the need of fitting any model. In our attentional datasets, we demonstrate that data-driven methods provide descriptions of tuning curve features such as preferred stimulus direction or attentional gain modulations which are in agreement with fit-based approaches when a good fit exists. Furthermore, these methods naturally extend to the frequent cases of uncertain model selection. We show that model-free approaches can identify attentional modulation patterns, such as general alterations of the irregular shape of tuning curves, which cannot be captured by fitting stereotyped conventional models. Finally, by comparing datasets across different conditions, we demonstrate effects of attention that are cell-and even stimulus-specific. Based on these proofs-of-concept, we conclude that our data-driven methods can reliably extract relevant tuning information from neuronal recordings, including cells whose seemingly haphazard response curves defy conventional fitting approaches.
New Methods for Treatment Effect Calibration, with Applications to Non-Inferiority Trials
Authors: Zhang Zhiwei , Nie Lei , Soon Guoxing , Hu Zonghui 
Published: September 2015

Summary
In comparative effectiveness research, it is often of interest to calibrate treatment effect estimates from a clinical trial to a target population that differs from the study population. One important application is an indirect comparison of a new treatment with a placebo control on the basis of two separate randomized clinical trials: a non-inferiority trial comparing the new treatment with an active control and a historical trial comparing the active control with placebo. The available methods for treatment effect calibration include an outcome regression (OR) method based on a regression model for the outcome and a weighting method based on a propensity score (PS) model. This article proposes new methods for treatment effect calibration: one based on a conditional effect (CE) model and two doubly robust (DR) methods. The first DR method involves a PS model and an OR model, is asymptotically valid if either model is correct, and attains the semiparametric information bound if both models are correct. The second DR method involves a PS model, a CE model, and possibly an OR model, is asymptotically valid under the union of the PS and CE models, and attains the semiparametric information bound if all three models are correct. The various methods are compared in a simulation study and applied to recent clinical trials for treating human immunodeficiency virus infection.
Improved integer programming models for simple assembly line balancing and related problems
Authors: Ritt Marcus , Costa Alysson M. 
Published: September 2015

AbstractWe propose a stronger formulation of the precedence constraints and the station limits for the simple assembly line balancing problem. The linear relaxation of the improved integer program theoretically dominates all previous formulations using impulse variables, and produces solutions of significantly better quality in practice. The improved formulation can be used to strengthen related problems with similar restrictions. We demonstrate their effectiveness on the U‐shaped assembly line balancing problem and on the bin packing problem with precedence constraints.
An overview of exact algorithms for the Euclidean Steiner tree problem in n‐space
Authors: Fampa Marcia , Lee Jon , Maculan Nelson 
Published: September 2015

AbstractThe Euclidean Steiner tree problem (ESTP) in is to find a shortest network interconnecting p given points in n‐dimensional Euclidean space. The problem was first described in the plane and an algorithm with very good practical efficiency has been proposed to solve this particular case. The generalization for higher dimensions was proposed in the 19th century, however the numerical solution of the problem remains very challenging when . We give an overview of the exact algorithms presented in the literature for the ESTP when and discuss their common and distinguished features, their advantages and drawbacks, and some possible directions for improvement toward the numerical solution of large instances of the problem.
Sex-Specific Associations of Arsenic Exposure with Global DNA Methylation and Hydroxymethylation in Leukocytes: Results from Two Studies in Bangladesh
Authors: Niedzwiecki Megan M. , Liu Xinhua , Hall Megan N. , Thomas Tiffany , Slavkovich Vesna , Ilievski Vesna , Levy Diane , Alam Shafiul , Siddique Abu B. , Parvez Faruque , Graziano Joseph H. , Gamble Mary V. 
Published: September 2015

Abstract
Background: Depletion of global 5-hydroxymethylcytosine (5-hmC) is observed in human cancers and is strongly implicated in skin cancer development. Although arsenic (As)—a class I human carcinogen linked to skin lesion and cancer risk—is known to be associated with changes in global %5-methylcytosine (%5-mC), its influence on 5-hmC has not been widely studied.
Methods: We evaluated associations of As in drinking water, urine, and blood with global %5-mC and %5-hmC in two studies of Bangladeshi adults: (i) leukocyte DNA in the Nutritional Influences on Arsenic Toxicity study (n = 196; 49% male, 19–66 years); and (ii) peripheral blood mononuclear cell DNA in the Folate and Oxidative Stress study (n = 375; 49% male, 30–63 years).
Results: Overall, As was not associated with global %5-mC or %5-hmC. Sex-specific analyses showed that associations of As exposure with global %5-hmC were positive in males and negative in females (P for interaction &lt; 0.01). Analyses examining interactions by elevated plasma total homocysteine (tHcys), an indicator of B-vitamin deficiency, found that tHcys also modified the association between As and global %5-hmC (P for interaction &lt; 0.10).
Conclusion: In two samples, we observed associations between As exposure and global %5-hmC in blood DNA that were modified by sex and tHcys.
Impact: Our findings suggest that As induces sex-specific changes in 5-hmC, an epigenetic mark that has been associated with cancer. Future research should explore whether altered %5-hmC is a mechanism underlying the sex-specific influences of As on skin lesion and cancer outcomes. Cancer Epidemiol Biomarkers Prev; 24(11); 1748–57. ©2015 AACR.
Pleiotropic Analysis of Cancer Risk Loci on Esophageal Adenocarcinoma Risk
Authors: Lee Eunjung , Stram Daniel O. , Ek Weronica E. , Onstad Lynn E. , MacGregor Stuart , Gharahkhani Puya , Ye Weimin , Lagergren Jesper , Shaheen Nicholas J. , Murray Liam J. , Hardie Laura J. , Gammon Marilie D. , Chow Wong-Ho , Risch Harvey A. , Corley Douglas A. , Levine David M. , Whiteman David C. , Bernstein Leslie , Bird Nigel C. , Vaughan Thomas L. , Wu Anna H. 
Published: September 2015

Abstract
Background: Several cancer-associated loci identified from genome-wide association studies (GWAS) have been associated with risks of multiple cancer sites, suggesting pleiotropic effects. We investigated whether GWAS-identified risk variants for other common cancers are associated with risk of esophageal adenocarcinoma (EA) or its precursor, Barrett's esophagus.
Methods: We examined the associations between risks of EA and Barrett's esophagus and 387 SNPs that have been associated with risks of other cancers, by using genotype imputation data on 2,163 control participants and 3,885 (1,501 EA and 2,384 Barrett's esophagus) case patients from the Barrett's and Esophageal Adenocarcinoma Genetic Susceptibility Study, and investigated effect modification by smoking history, body mass index (BMI), and reflux/heartburn.
Results: After correcting for multiple testing, none of the tested 387 SNPs were statistically significantly associated with risk of EA or Barrett's esophagus. No evidence of effect modification by smoking, BMI, or reflux/heartburn was observed.
Conclusions: Genetic risk variants for common cancers identified from GWAS appear not to be associated with risks of EA or Barrett's esophagus.
Impact: To our knowledge, this is the first investigation of pleiotropic genetic associations with risks of EA and Barrett's esophagus. Cancer Epidemiol Biomarkers Prev; 24(11); 1801–3. ©2015 AACR.
Digoxin Use After Diagnosis of Colorectal Cancer and Survival: A Population-Based Cohort Study
Authors: Karasneh Reema A. , Murray Liam J. , Hughes Carmel M. , Cardwell Chris R. 
Published: September 2015

Abstract
Background: Digoxin has been shown to affect a number of pathways that are of relevance to cancer, and its use has been associated with increased risks of breast and uterus cancer and, more recently, a 40% increase in colorectal cancer risk. These findings raise questions about the safety of digoxin use in colorectal cancer patients, and, therefore, we investigated whether digoxin use after colorectal cancer diagnosis increased the risk of colorectal cancer–specific mortality.
Methods: A cohort of 10,357 colorectal cancer patients newly diagnosed from 1998 to 2009 was identified from English cancer registries and linked to the UK Clinical Practice Research Datalink (to provide digoxin and other prescription records) and to the Office of National Statistics mortality data (to identify 2,724 colorectal cancer–specific deaths). Using time-dependent Cox regression models, unadjusted and adjusted HRs and 95% confidence intervals (CI) were calculated for the association between postdiagnostic exposure to digoxin and colorectal cancer–specific mortality.
Results: Overall, 682 (6%) colorectal cancer patients used digoxin after diagnosis. Digoxin use was associated with a small increase in colorectal cancer–specific mortality before adjustment (HR, 1.25; 95% CI, 1.07–1.46), but after adjustment for confounders, the association was attenuated (adjusted HR, 1.10; 95% CI, 0.91–1.34) and there was no evidence of a dose response.
Conclusions: In this large population-based colorectal cancer cohort, there was little evidence of an increase in colorectal cancer–specific mortality with digoxin use after diagnosis.
Impact: These results provide some reassurance that digoxin use is safe in colorectal cancer patients. Cancer Epidemiol Biomarkers Prev; 24(11); 1804–7. ©2015 AACR.
ЛЕПТОСПІРОЗ, СПРИЧИНЕНИЙ КОМБІНАЦІЄЮ ЗБУДНИКІВ, У ТЕРНОПІЛЬСЬКІЙ ОБЛАСТІ
Authors: Васильєва Н.А. , Кравчук Ю.А. 
Published: September 2015

<p class="MsoBodyTextIndent3" style="margin: 0cm; margin-bottom: .0001pt; text-align: justify; text-indent: 27.0pt; text-autospace: none;"><em style="mso-bidi-font-style: normal;"><span style="font-size: 12.0pt;">На підставі аналізу випадків лептоспірозу у мешканців Тернопільської області, при лабораторному обстеженні яких протягом 1984-2014 рр. виявлені комбінації збудників, встановили, що в останні 10 років частота лептоспірозу-мікст суттєво зросла.</span></em><em style="mso-bidi-font-style: normal;"></em><em style="mso-bidi-font-style: normal;"><span style="font-size: 12.0pt;">Поєднання різних сероварів лептоспір як етіологічний чинник лептоспірозу-мікст підтверджується динамікою титрів антитіл до обох збудників за час спостереження.</span></em><em style="mso-bidi-font-style: normal;"></em><em style="mso-bidi-font-style: normal;"><span style="font-size: 12.0pt;"><span style="mso-spacerun: yes;"> </span>Це може бути однією з особливостей сучасних зоонозів. </span></em></p><p class="MsoBodyTextIndent3" style="margin: 0cm; margin-bottom: .0001pt; text-align: justify; text-indent: 27.0pt; text-autospace: none;"><em style="mso-bidi-font-style: normal;"><span style="font-size: 12.0pt;">Впливу комбінації різних сероварів лептоспір на окремі епідеміологічні (сезонність), клінічні (форма та ступінь тяжкості недуги) особливості, а також гендерний розподіл не виявлено.</span></em></p>
ПОРІВНЯЛЬНИЙ АНАЛІЗ СТАНУ РЕФОРМУВАННЯ СИСТЕМИ ОХОРОНИ ЗДОРОВ’Я В ПІЛОТНИХ РЕГІОНАХ УКРАЇНИ
Authors: ДЗЮБА О.М. , КУЧЕРЕНКО Н.Т. , КАРАМЗІНА Л.А. 
Published: September 2015

<p>Мета: проведення порівняльного аналізу впровадження нових організаційно-правових та фінансово-економічних механізмів у пілотних регіонах (Вінницька, Дніпропетровська області, м. Київ).</p><p>Матеріали і методи. Були використані статистичні дані пілотних регіонів; застосовані економічний, статистичний, методи порівняльного аналізу.</p><p>Результаты. У пілотних регіонах впроваджені нові підходи до організації роботи закладів охорони здоров'я та їх кадрового забезпечення: на базі існуючої мережі закладів створено структуровану за видами медичної допомоги систему медичного обслуговування; організовано роботу центрів первинної медичної допомоги; перепрофільовано заклади охорони здоров'я, що надають вторинну (спеціалізовану) медичну допомогу, з урахуванням інтенсивності її надання; створено центри екстреної медичної допомоги; оптимізовано кадрове забезпечення.</p><p>Висновки. Необхідно запровадити набутий у пілотних регіонах досвід реформування системи охорони здоров’я на національному рівні.</p><p>Ключові слова: пілотні регіони, первинна медична допомога, екстрена медична допомога, вторинна медична допомога, ефективність, якість медичної допомоги.</p>
Outer-Sphere Extraction of Uranyl(VI) from HNO3(aq) to 1-Butyl-3-methylimidazolium Nonafluorobutanesulfonate Ionic Liquid: Towards Decontamination of Uranium Wastes
Authors: Takao Koichiro , Arakawa Kohei , Mori Takahiro , Harada Masayuki , Ikeda Yasuhisa 
Published: September 2015

Abstract
Extraction behavior of U(VI) from an HNO3 aqueous solution to 1-butyl-3-methylimidazolium nonafluorobutanesulfonate ([BMI][NfO]) ionic liquid and recovery of the extracted U(VI) by using H2O2 were investigated. With increasing [HNO3], the distribution ratio of U(VI) tends to decrease (e.g., 4.08 at [HNO3] = 0.01 M, 0.15 at [HNO3] = 1.00 M). Such extraction behavior is mainly governed by [H+], while coordination of NO3− to UO22+ also offers minor contribution to prevent partitioning of U(VI) to [BMI][NfO]. The U(VI) extraction in the current system is exclusively driven by NfO− to form an outer-sphere complex like {[UO2(OH2)5](NfO)4}2−. Addition of 30 wt % H2O2 to [BMI][NfO] containing U(VI) resulted in pale yellow precipitate of [(UO2)(O2)(H2O)2]·2H2O. The recovery efficiency increases with increasing pH of the aqueous layer, and reaches &gt;90% at pH &gt;1.5. This is in line with deprotonation from H2O2 through the precipitation of [(UO2)(O2)(H2O)2]·2H2O, i.e., UO22+ + H2O2 + 4H2O = [(UO2)(O2)(H2O)2]·2H2O (s) + 2H+.
Hyperaccumulation and Mobility of Heavy Metals in Vegetable Crops in India
Authors: J.I. Nirmal Kumar , Soni Hiren , Kumar Rita N. , Bhatt Ira 
Published: September 2015

The heavy metals or trace elements play an important role in the metabolic pathways during the growth and development of plants, when available in appreciable concentration. The heavy metal concentration of Cadmium (Cd), Cobalt (Co), Copper (Cu), Iron (Fe), Nickel (Ni), Lead (Pb) and Zinc (Zn) was analyzed using Inductive Coupled Plasma Analyzer (ICPA) (Perkin-Elmer ICP Optima 3300 RL) in 18 vegetable crop plants and their parts along with their soil, collected from various agricultural fields around Anand province, Gujarat, India. The vegetables crop plants were Anthem (Anthum graveolens), Beat (Brassica oleracea), Bitter Gourd (Momordica charantia), Brinjal (Solanum melongena), Cauliflower (Brassica oleracea var. botrytis), Chilli (Capsicum annum), Coriander (Coriandrum sativum), Fenugreek (Trigonella foenum-graceum), Garlic (Alium sativum), Coccinia indica, Lufa (Luffa acutangula), Lady's Finger (Abelmoschus esculentus), Mint (Mentha piperata), Radish (Raphanus sativum), Spinach (Spinacia oleracea), Tomato (Lycopersicum esculentum), Vetches (Cyamopsis soralioides) and White Gourd (Lagernaria vulgaris). The Accumulation Factor (AF) and Mobility Index (MI) were calculated for assessment of mobility of heavy metals from soil to various plant parts: roots, stems and leaves through different levels: Level 1 (Soil-Roots), Level 2 (Roots-Stems) and Level 3 (Stems-Leaves) in studied vegetable crop plants. The results showed concentration dependent variables of heavy metal levels among vegetable crop plants. The lower and higher concentration gradient alongwith their mobility gradient was also determined. A perusal of data reflects that accumulation gradient of each crop plant component vary according to their nature, properties and podsol climate of a particular crop plant. The data on accumulation and mobility of heavy metals such as Cd, Co, Cu, Fe, Ni, Pb and Zn from soil to leaves through roots and stems, suggested that all the metals were highly mobile. Key words: Vegetable crop plants; Heavy metals; Accumulation factor; Mobility index; etc.The Journal of Agriculture and Environment Vol:10, Jun.2009 page: 34-45