bluuebunny/crossref_metadata_2025_split huggingface dataset:
Topographic variability of the left atrium and pulmonary veins assessed by 3D‐CT predicts the recurrence of atrial fibrillation after catheter ablation
Authors: Kiuchi Kunihiko , Yoshida Akihiro , Takei Asumi , Fukuzawa Koji , Itoh Mitsuaki , Imamura Kimitake , Fujiwara Ryudo , Suzuki Atsushi , Nakanishi Tomoyuki , Yamashita Soichiro , Hirata Ken‐ichi , Kanda Gaku , Okajima Katsunori , Shimane Akira , Yamada Shinichiro , Taniguchi Yasuyo , Yasaka Yoshinori , Kawai Hiroya 
Published: April 2015

AbstractBackgroundCatheter ablation (CA) is an established therapy for atrial fibrillation (AF). However, the assessment of anatomical information and predictors of AF recurrence remain unclear. We investigated the relationship between anatomical information on the left atrium (LA) and pulmonary veins (PVs) from three‐dimensional computed tomography images and the recurrence of AF after CA.MethodsSixty‐seven consecutive AF patients (mean age: 62±10 years, median AF history: 42 (12; 60) months, mean LA size: 41±7 mm, paroxysmal: 56%) underwent CA and were followed for 19±10 months. The segmented surface areas (antral, posterior, septal, and lateral) and dimensions (between the anterior and posterior walls, the right inferior PV and mitral annulus [MA], the right superior PV and MA, the left superior PV and MA, and the mitral isthmus) of the LA were evaluated three dimensionally using the NavX system. The cross‐sectional areas of the PVs were also evaluated.ResultsAfter the follow‐up period, 49 patients (73%) remained free from AF. A multivariate analysis showed that the diameter of the mitral isthmus and cross‐sectional area of the right upper PV were associated with AF recurrence (odds ratio: 1.070, CI: 1.02–1.12, p=0.001; odds ratio: 0.41, CI: 0.21–0.77, p=0.006).ConclusionEnlargement of the mitral isthmus and a smaller right superior PV cross‐sectional area were associated with AF recurrence.
Emerging roles of hypoxia‐inducible factors and reactive oxygen species in cancer and pluripotent stem cells
Authors: Saito Shigeo , Lin Ying‐Chu , Tsai Ming‐Ho , Lin Chang‐Shen , Murayama Yoshinobu , Sato Ryuji , Yokoyama Kazunari K. 
Published: April 2015

AbstractEukaryotic organisms require oxygen homeostasis to maintain proper cellular function for survival. During conditions of low oxygen tension (hypoxia), cells activate the transcription of genes that induce an adaptive response, which supplies oxygen to tissues. Hypoxia and hypoxia‐inducible factors (HIFs) may contribute to the maintenance of putative cancer stem cells, which can continue self‐renewal indefinitely and express stemness genes in hypoxic stress environments (stem cell niches). Reactive oxygen species (ROS) have long been recognized as toxic by‐products of aerobic metabolism that are harmful to living cells, leading to DNA damage, senescence, or cell death. HIFs may promote a cancer stem cell state, whereas the loss of HIFs induces the production of cellular ROS and activation of proteins p53 and p16Ink4a, which lead to tumor cell death and senescence. ROS seem to inhibit HIF regulation in cancer cells. By contrast, controversial data have suggested that hypoxia increases the generation of ROS, which prevents hydroxylation of HIF proteins by inducing their transcription as negative feedback. Moreover, hypoxic conditions enhance the generation of induced pluripotent stem cells (iPSCs). During reprogramming of somatic cells into a PSC state, cells attain a metabolic state typically observed in embryonic stem cells (ESCs). ESCs and iPSCs share similar bioenergetic metabolisms, including decreased mitochondrial number and activity, and induced anaerobic glycolysis. This review discusses the current knowledge regarding the emerging roles of ROS homeostasis in cellular reprogramming and the implications of hypoxic regulation in cancer development.
Diphtheria‐toxin based anti‐human CCR4 immunotoxin for targeting human CCR4+ cells in vivo
Authors: Wang Zhaohui , Wei Min , Zhang Huiping , Chen Hongyuan , Germana Sharon , Huang Christene A. , Madsen Joren C. , Sachs David H. , Wang Zhirui 
Published: April 2015

CC chemokine receptor 4 (CCR4) has attracted much attention as a promising therapeutic drug target for CCR4+ tumor cells and Tregs. CCR4 is expressed on some tumor cells such as T‐cell acute lymphoblastic leukemia (ALL), adult T‐cell leukemia/lymphoma (ATLL), adult peripheral T cell lymphoma (PTCL) and cutaneous T cell lymphoma (CTCL). CCR4 is also expressed on majority of Tregs, mainly effector Tregs. In this study we have successfully developed three versions of diphtheria‐toxin based anti‐human CCR4 immunotoxins (monovalent, bivalent and single‐chain fold‐back diabody). Binding analysis by flow cytometry showed that all three versions of the anti‐human CCR4 immunotoxins bound to the human CCR4+ tumor cell line as well as CCR4+ human PBMC. The bivalent isoform bound stronger than its monovalent counterpart and the single‐chain foldback diabody isoform was the strongest among the three versions. In vitro efficacy analysis demonstrated that the bivalent isoform was 20 fold more potent in inhibiting cellular proliferation and protein synthesis in human CCR4+ tumor cells compared to the monovalent anti‐human CCR4 immunotoxin. The single‐chain fold‐back diabody isoform was 10 fold more potent than its bivalent counterpart and 200 fold more potent than its monovalent counterpart. The in vivo efficacy was assessed using a human CCR4+ tumor‐bearing mouse model. The immunotoxin significantly prolonged the survival of tumor‐bearing NOD/SCID IL‐2 receptor γ−/− (NSG) mice injected with human CCR4+ acute lymphoblastic leukemia cells compared with the control group. This novel anti‐human CCR4 immunotoxin is a promising drug candidate for targeting human CCR4+ tumor cells and Tregs in vivo.
chipPCR: an R package to pre-process raw data of amplification curves
Authors: Rödiger Stefan , Burdukiewicz Michał , Schierack Peter 
Published: April 2015

Abstract
Motivation: Both the quantitative real-time polymerase chain reaction (qPCR) and quantitative isothermal amplification (qIA) are standard methods for nucleic acid quantification. Numerous real-time read-out technologies have been developed. Despite the continuous interest in amplification-based techniques, there are only few tools for pre-processing of amplification data. However, a transparent tool for precise control of raw data is indispensable in several scenarios, for example, during the development of new instruments.
Results: chipPCR is an R package for the pre-processing and quality analysis of raw data of amplification curves. The package takes advantage of R’s S4 object model and offers an extensible environment. chipPCR contains tools for raw data exploration: normalization, baselining, imputation of missing values, a powerful wrapper for amplification curve smoothing and a function to detect the start and end of an amplification curve. The capabilities of the software are enhanced by the implementation of algorithms unavailable in R, such as a 5-point stencil for derivative interpolation. Simulation tools, statistical tests, plots for data quality management, amplification efficiency/quantification cycle calculation, and datasets from qPCR and qIA experiments are part of the package. Core functionalities are integrated in GUIs (web-based and standalone shiny applications), thus streamlining analysis and report generation.
Availability and implementation: http://cran.r-project.org/web/packages/chipPCR. Source code: https://github.com/michbur/chipPCR.
Contact: stefan.roediger@b-tu.de
Supplementary information: Supplementary data are available at Bioinformatics online.
Genome-scale strain designs based on regulatory minimal cut sets
Authors: Mahadevan Radhakrishnan , von Kamp Axel , Klamt Steffen 
Published: April 2015

Abstract
Motivation: Stoichiometric and constraint-based methods of computational strain design have become an important tool for rational metabolic engineering. One of those relies on the concept of constrained minimal cut sets (cMCSs). However, as most other techniques, cMCSs may consider only reaction (or gene) knockouts to achieve a desired phenotype.
Results: We generalize the cMCSs approach to constrained regulatory MCSs (cRegMCSs), where up/downregulation of reaction rates can be combined along with reaction deletions. We show that flux up/downregulations can virtually be treated as cuts allowing their direct integration into the algorithmic framework of cMCSs. Because of vastly enlarged search spaces in genome-scale networks, we developed strategies to (optionally) preselect suitable candidates for flux regulation and novel algorithmic techniques to further enhance efficiency and speed of cMCSs calculation. We illustrate the cRegMCSs approach by a simple example network and apply it then by identifying strain designs for ethanol production in a genome-scale metabolic model of Escherichia coli. The results clearly show that cRegMCSs combining reaction deletions and flux regulations provide a much larger number of suitable strain designs, many of which are significantly smaller relative to cMCSs involving only knockouts. Furthermore, with cRegMCSs, one may also enable the fine tuning of desired behaviours in a narrower range. The new cRegMCSs approach may thus accelerate the implementation of model-based strain designs for the bio-based production of fuels and chemicals.
Availability and implementation: MATLAB code and the examples can be downloaded at http://www.mpi-magdeburg.mpg.de/projects/cna/etcdownloads.html.
Contact: krishna.mahadevan@utoronto.ca or klamt@mpi-magdeburg.mpg.de
Supplementary information: Supplementary data are available at Bioinformatics online.
phylogeo: an R package for geographic analysis and visualization of microbiome data
Authors: Charlop-Powers Zachary , Brady Sean F. 
Published: April 2015

Abstract
Motivation: We have created an R package named phylogeo that provides a set of geographic utilities for sequencing-based microbial ecology studies. Although the geographic location of samples is an important aspect of environmental microbiology, none of the major software packages used in processing microbiome data include utilities that allow users to map and explore the spatial dimension of their data. phylogeo solves this problem by providing a set of plotting and mapping functions that can be used to visualize the geographic distribution of samples, to look at the relatedness of microbiomes using ecological distance, and to map the geographic distribution of particular sequences. By extending the popular phyloseq package and using the same data structures and command formats, phylogeo allows users to easily map and explore the geographic dimensions of their data from the R programming language.
Availability and Implementation: phylogeo is documented and freely available http://zachcp.github.io/phylogeo
Contact: zcharlop@rockefeller.edu
DockStar: a novel ILP-based integrative method for structural modeling of multimolecular protein complexes
Authors: Amir Naama , Cohen Dan , Wolfson Haim J. 
Published: April 2015

Abstract
Motivation: Atomic resolution modeling of large multimolecular assemblies is a key task in Structural Cell Biology. Experimental techniques can provide atomic resolution structures of single proteins and small complexes, or low resolution data of large multimolecular complexes.
Results: We present a novel integrative computational modeling method, which integrates both low and high resolution experimental data. The algorithm accepts as input atomic resolution structures of the individual subunits obtained from X-ray, NMR or homology modeling, and interaction data between the subunits obtained from mass spectrometry. The optimal assembly of the individual subunits is formulated as an Integer Linear Programming task. The method was tested on several representative complexes, both in the bound and unbound cases. It placed correctly most of the subunits of multimolecular complexes of up to 16 subunits and significantly outperformed the CombDock and Haddock multimolecular docking methods.
Availability and implementation: http://bioinfo3d.cs.tau.ac.il/DockStar
Contact: naamaamir@mail.tau.ac.il or wolfson@tau.ac.il
Supplementary information: Supplementary data are available at Bioinformatics online.
Congruences for Fishburn numbers modulo prime powers
Authors: Straub Armin 
Published: April 2015

The Fishburn numbers ξ(n) are defined by the formal power series [Formula: see text] Recently, Andrews and Sellers discovered congruences of the form ξ(pm + j) ≡ 0 modulo p, valid for all m ≥ 0. These congruences have then been complemented and generalized to the case of r-Fishburn numbers by Garvan. In this note, we answer a question of Andrews and Sellers regarding an extension of these congruences to the case of prime powers. We show that, under a certain condition, all these congruences indeed extend to hold modulo prime powers.
Psychological and background correlates of bullying in adolescent residential care
Authors: Sekol Ivana , Farrington David P 
Published: April 2015

Summary This research examined psychological and background correlates of bullying in adolescent residential care. Young people aged 11–21 ( N = 601) from 22 residential institutions in Croatia completed an anonymous self-reported bullying questionnaire, the Basic Empathy Scale, the Rosenberg Self-esteem Scale and the Big Five Personality Inventory. Findings The results demonstrated that both male and female bullies tend to be disagreeable, careless, neurotic, likely to hold attitudes approving of bullying, and likely to bully others in school. Male bullies also tend to be extraverted, lacking in affective empathy, tend to have a history of bullying during their earlier placements, and tend to have been institutionalised for problematic behaviour. It is concluded that bullying is more persistent for males and that psychological and personality factors play a greater role in male bullying than in female bullying. However, both male and female bullies had commonly been school bullies. Applications Bullying in care might be mitigated by: a) avoiding accommodating residents who are prone to victimisation together with older, more experienced residents who manifest antisocial behaviour; b) programmes aimed at changing attitudes approving of bullying; c) techniques for controlling the impulsivity of bullies; and d) empathy enhancement programmes. However, longitudinal research on bullying is needed.
Relocation, portability and social care practice: A scoping review
Authors: White Caroline , Marsland Dave , Manthorpe Jill 
Published: April 2015

Summary The portability of publicly-funded adult social care across local authority boundaries received recent policy attention in England and was addressed in the Care Act 2014. This article presents the findings of a scoping review conducted between July–September 2012 that searched selected journals and online databases for relevant material. The aim of the review was to identify what is known about the experiences of adults entitled to publicly-funded social care who move between local authorities, and the support provided by social workers to those planning to relocate. The review focused specifically on disabled adults and carers, eligible for and in receipt of social care support, who relocate for work or education in England. Findings The review identified little direct research covering experiences of moving between local authorities. However, six specific barriers, challenges and facilitators to relocation were identified; these included the portability of social care support, variations in policy and practice between local authorities, and housing availability. The review concludes that the process of relocation may be complex, challenging, and uncertain, although individuals may experience benefits and positive outcomes. Applications The review outlines areas for good social work practice in supporting people using social care services to relocate. These include: ensuring the provision of information; close working between local authorities and social workers; the development of interim plans to address potential delays in setting up support; proactive and rapid monitoring and reassessment following a move to address potentially changed support needs arising from changed housing circumstances.
Nanoporous Activated Carbons Derived from Agro-Waste Corncob for Enhanced Electrochemical and Sensing Performance
Authors: Adhikari Mandira Pradhananga , Adhikari Rina , Shrestha Rekha Goswami , Rajendran Raja , Adhikari Laxmi , Bairi Partha , Pradhananga Raja Ram , Shrestha Lok Kumar , Ariga Katsuhiko 
Published: April 2015

Abstract
Nanoporous activated carbons (AC) have been prepared from low-cost agro-waste corncob powder by phosphoric acid activation and investigated for their electrochemical supercapacitor and sensing properties. Surface areas and pore volumes are found in the range of 690–1288 m2 g−1 and 0.49–1.64 cm3 g−1, respectively and could be controlled by adjusting the weight ratio of corncob and phosphorous. The corncob-derived AC showed excellent electrochemical performance giving a maximum specific capacitance ca. 340.8 F g−1 at a scan rate of 5 mV s−1. At relatively a high scan rate of 100 mV s−1 the specific capacitance of 133.7 F g−1 was obtained. About 96% capacitance retention rate was achieved even after 1000 cycles demonstrating potential usages of the materials in high-performance supercapacitor electrodes. Furthermore, our AC showed excellent solvent vapor sensing performance with high selectivity for ammonia.
DISSEMINATED HISTOPLASMOSIS IN IMMUNOCOMPETENT INDIVIDUALS- NOT A SO RARE ENTITY
Authors: De Dibyendu , Nath Uttam Kumar 
Published: April 2015

Introduction:Histoplasmosis is a rare fungal disease caused by dimorphic fungi Histoplasma capsulatum. The causative fungus is present in soil, infects through inhalation and manifests in three main types-acute primary, chronic cavitary and progressive disseminated Histoplasmosis. Disseminated Histoplasmosis (DH) is defined as a clinical condition where fungus is present in more than one location. Among the forms of histoplasmosis, DH is the rarest and generally found in immune-compromised individual.Here we are presenting our experiences of the series of cases of Disseminated Histoplasmosis in immune-competent individuals who have been diagnosed in our institute in last 5 years.Materials and methods:This is a single centre retrospective observational study, from May 2009 to April 2014. Only cases with Disseminated Histoplasmosis in otherwise healthy immune-competent individuals were included in the study. The Histoplasmosis is confirmed by either presence of Histoplasma in biopsy specimen from extra-pulmonary organ or by positive growth in fungal cultureResult:Total seven patients met the inclusion criteria. Five out of 7 patients were male. The mean age was 35 years. Five of the 7 patients presented with fever for long duration. Six patients complained of significant weight loss before diagnosis. On examination, one patient had skin nodules, five patients had hepato-splenomegaly, and two patients had lymphadenopathy.The laboratory investigation revealed anaemia in six out of 7 patients, and pancytopenia in 3 patients. Two patients had features of hemophagocytic syndrome in the bone marrow.All of the patient had undergone treatment with conventional amphotericine B deoxy-cholate and azole antifungal. One patient with adrenal involvement died in hospital. The patient with skin nodule had recurrent relapses. The other patients had resolution of symptoms and clinically cured.Conclusion:Disseminated Histoplasmosis is not an uncommon etiology of fever of prolonged duration even in immuno-competent individual, and should be kept as a differential diagnosis. Targeted investigation with early bone marrow biopsy and fungal culture may help in diagnosis of DH. Imaging study to exclude adrenal involvement prevents case fatality in DH. Cytopenia may be due to secondary hemophagocytic syndrome, which improves with anti-fungal therapy. Treatment with either amphotericine B or itraconazole gives excellent outcome, though therapy may have to given for prolonged period in case of relapses.
PROGNOSTIC VALUE OF BRAIN AND ACUTE LEUKEMIA CYTOPLASMIC GENE EXPRESSION IN EGYPTIAN CHILDREN WITH ACUTE MYELOID LEUKEMIA
Authors: Hagag Adel Abd elhaleim 
Published: April 2015

Abstract Background: Acute myeloid leukemia (AML) accounts for 25%-35% of the acute leukemia in children. BAALC (Brain and Acute Leukemia, Cytoplasmic gene) is a recently identified gene on chromosome 8q22.3 that has prognostic significance in AML. The aim of this work was to study the impact of BAALC gene expression on prognosis of AML in Egyptian children. Patients and methods: This study was conducted on 40 patients of newly diagnosed AML who were subjected to the following: Full history taking, clinical examination, laboratory investigations including: complete blood count, LDH, bone marrow aspiration, cytochemistry and immunophenotyping, assessment of BAALC Gene by real time PCR in bone marrow aspirate mononuclear cells before the start of chemotherapy. Results: BAALC gene expression showed positive expression in 24 cases (60%) and negative expression in 16 cases (40%). Patients who showed positive BAALC gene expression included 10 patients achieved complete remission, 8 patients died and 6 relapsed patients, while patients who showed negative expression include 12 patients achieved complete remission, 1 relapsed patient and 3 patients died. There was significant association between BAALC gene expression and FAB classification of patients of AML patientsas positive BAALC expression is predominantly seen in FAB subtypes M1 and M2 compared with negative BAALC gene expression that was found more in M3 and M4 (8 cases with M1, 12 cases with M2, 1 case with M3 and 3 cases with M4 in positive BAALC expression versus 2 cases with M1, 3 cases with M2, 4 cases with M3 and 7 cases with M4 in BAALC gene negative expression group with significant difference regarding FAB subtypes). As regard age, sex, splenomegaly, lymphadenopathy, pallor, purpura, platelets count, WBCs count, and percentage of blast cells in BM, the present study showed no significant association with BAALC. Conclusion: BAALC expression is an important prognostic factor in AML patients and its incorporation into novel risk-adapted therapeutic strategies will improve the currently disappointing cure rate of this group of patients.
Collagen‐Coated Lapatinib‐Loaded Poly(lactic acid) Microspheres for Breast Cancer in Biomedical Applications
Authors: Prabhakar M. N. , Song Jung‐Il , Chowdoji Rao K. 
Published: April 2015

ABSTRACTA novel micro in situ drug loaded with poly(lactic acid) (PLA) microspheres coated with collagen by a simple adsorption technique through the water‐in‐oil emulsion method is introduced to reduce inflammatory responses at the site of implants and enhance the bioactiveness for several applications in the medical field including tissue engineering. The surface modification technique was the current scenario; hence, the protein adsorption principle is used for coating of collagen onto the surface of PLA microspheres. The study was conducted in two steps: (1) Lapatinib drug loaded PLA microspheres were prepared and characterized and (2) the drug‐loaded PLA microspheres were dispersed in a collagen solution, yielding the modified microspheres. The surface morphology of the prepared PLA microspheres was verified by using a scanning electron microscope, and it is concluded that the microspheres are spherical in shape. The PLA microspheres are studied through attenuated total reflectance Fourier transform infrared spectroscopy, and through the differential scanning calorimetry–thermal gravimetric analysis technique it is observed that there is no interaction between polymer and the drug. The in vitro release study of modified PLA microspheres was conducted at pH 7.4, and the results indicated that the adsorption technique can be the simple strategy to coat collagen on the surface of polyester implants to develop the stealth implant in shorter time with low cost technology.