bluuebunny/crossref_metadata_2025_split huggingface dataset:
Baseline Renal Function among Antiretroviral Therapy-Naive, HIV-Infected Patients in Southeast Nigeria
Authors: Onodugo Obinna D. , Chukwuka Chinwe , Onyedum Cajetan , Ejim Emmanuel , Mbah Anthony , Nkwo Peter , Ugwu George , Ukoma Ubani , Okafor Chinyere , Anyene Chukwujekwu , Nwabueze Emmanuel , Obi Frank , Akabueze Jude , Uche Ikenna , Ekochin Fintan , Nnoruka Edith 
Published: June 2013

Background: Renal insufficiency has been shown to be a significant, independent risk factor for mortality among HIV-infected patients. Unfortunately, little is known about the prevalence and nature of renal impairment in African populations initiating antiretroviral treatment. This study aims to find the prevalence of abnormal renal function among antiretroviral therapy (ART)-naive, HIV-infected patients in the South Eastern geopolitical zone of Nigeria. Method: This is a cross-sectional hospital-based study, involving 300 ART-naive HIV-positive patients, seen over a 1-year period, aged from 18 years and older, presenting to the clinic for the first time. Results: A total of 300 patients were included in the study, 104 (34.7%) males and 196 (65.3%) females. The prevalence of significant renal disease was 24.3% (73 of 300), while 38.3% (115 of 300) had mild renal impairment. Using logistic regression, age, CD4 count, urea, creatinine, and hemoglobin were significantly associated with renal impairment. Conclusion: The authors observed a high prevalence of significant renal impairment among HIV-infected patients at the time of ART initiation.
Identifying Subgroups of Care Providers Participating in a Telehealth Educational Intervention
Authors: Wao Hesborn , Beckstead Jason W. , Beal Jeffrey , Aluoch Marilyn , Skipper Theresa C. , Orrick Joanne J. 
Published: June 2013

Health care providers (HCPs) serving HIV-infected patients, especially in rural and underserved areas, have limited access to continuing medical education. Objective: To identify subgroups of HCPs who might benefit from a telehealth training program focusing on HIV/AIDS care based on HCPs’ objective for attending the training. Methods: Hierarchical cluster analysis combined with thematic analysis identified the subgroups. Results: A total of 56 HCPs attended between 1 and 9 of the 12 sessions conducted (mean ≈ 2, standard deviation = 1.6). Subgroups identified included knowledge (HCPs interested in gaining, increasing, or updating their knowledge in HIV care), learn–expert (HCPs interested in learning, obtaining, or providing expert opinion), and observe–apply–network (HCPs interested in observing the training, applying knowledge gained to practice, and networking). No group differences were found in the participants’ reaction to the session, change in knowledge following the training, and other important characteristics. Conclusion: Methodological contributions of the study are discussed.
Antibiotic therapy in nongastrointestinal MALT lymphoma: a review of the literature
Authors: Kiesewetter Barbara , Raderer Markus 
Published: June 2013

AbstractAlthough antibiotic therapy has been established as the standard of care in patients with gastric mucosa-associated lymphoid tissue (MALT) lymphoma, much less is known about the value of antibiotic therapy in nongastrointestinal (non-GI) MALT lymphomas. A computerized search (Medline) accompanied by a manual search to identify clinical reports on the topic of antibacterial therapy in patients with non-GI MALT lymphomas was performed. The majority of data were available for MALT lymphoma of the ocular adnexa (OAML) including a total of 131 patients in 4 retrospective studies, 3 prospective series (including 81 patients), and 1 case report. Treatment was exclusively targeting Chlamydophila psittaci (CP), using doxycycline in all but 2 studies. The median follow-up for these studies was 25 months, and both CP-positive as well as CP-negative patients responded. Complete remission was achieved in 23 patients (18%), 36 (27%) had a partial remission, 55 (42%) had stable disease, and 8 patients (6%) had progressive disease accounting for an overall response rate of 45%. In the largest study, a better response was suggested in CP-positive patients. By contrast, only scattered reports could be found for other non-GI localizations, allowing no conclusion about the benefit of antibiotic therapy and probably resulting in a publication bias toward positive cases. Based on these results, antibiotic therapy using doxycycline appears to be a reasonable first-line therapy for patients with OAML. Antibiotics, however, remain experimental for the time being in patients with other non-GI MALT lymphomas. Further preclinical studies as well as large-scale therapeutic trials are warranted to define the role of antibiotic therapy in such patients.
Cardiovascular toxicity and titin cross-reactivity of affinity-enhanced T cells in myeloma and melanoma
Authors: Linette Gerald P. , Stadtmauer Edward A. , Maus Marcela V. , Rapoport Aaron P. , Levine Bruce L. , Emery Lyndsey , Litzky Leslie , Bagg Adam , Carreno Beatriz M. , Cimino Patrick J. , Binder-Scholl Gwendolyn K. , Smethurst Dominic P. , Gerry Andrew B. , Pumphrey Nick J. , Bennett Alan D. , Brewer Joanna E. , Dukes Joseph , Harper Jane , Tayton-Martin Helen K. , Jakobsen Bent K. , Hassan Namir J. , Kalos Michael , June Carl H. 
Published: June 2013

Key Points
Engineered T-cell receptors can have redundant recognition of alternative protein motifs, resulting in severe cardiac toxicity. The use of induced pleuripotent stem cells (iPSCs) is a promising approach to identify potential off-target effects of engineered T cells.
SGN-CD33A: a novel CD33-targeting antibody–drug conjugate using a pyrrolobenzodiazepine dimer is active in models of drug-resistant AML
Authors: Kung Sutherland May S. , Walter Roland B. , Jeffrey Scott C. , Burke Patrick J. , Yu Changpu , Kostner Heather , Stone Ivan , Ryan Maureen C. , Sussman Django , Lyon Robert P. , Zeng Weiping , Harrington Kimberly H. , Klussman Kerry , Westendorf Lori , Meyer David , Bernstein Irwin D. , Senter Peter D. , Benjamin Dennis R. , Drachman Jonathan G. , McEarchern Julie A. 
Published: June 2013

Key PointsSGN-CD33A is a novel antibody-drug conjugate, consisting of an engineered anti-CD33 mAb conjugated to a potent DNA cross-linking cytotoxin. SGN-CD33A is highly active in a broad panel of preclinical AML models and, in contrast to GO, is active despite MDR or poor-risk cytogenetics.
FusionQ: a novel approach for gene fusion detection and quantification from paired-end RNA-Seq
Authors: Liu Chenglin , Ma Jinwen , Chang ChungChe , Zhou Xiaobo 
Published: June 2013

Abstract

Background
Gene fusions, which result from abnormal chromosome rearrangements, are a pathogenic factor in cancer development. The emerging RNA-Seq technology enables us to detect gene fusions and profile their features.

Results
In this paper, we proposed a novel fusion detection tool, FusionQ, based on paired-end RNA-Seq data. This tool can detect gene fusions, construct the structures of chimerical transcripts, and estimate their abundances. To confirm the read alignment on both sides of a fusion point, we employed a new approach, “residual sequence extension”, which extended the short segments of the reads by aggregating their overlapping reads. We also proposed a list of filters to control the false-positive rate. In addition, we estimated fusion abundance using the Expectation-Maximization algorithm with sparse optimization, and further adopted it to improve the detection accuracy of the fusion transcripts. Simulation was performed by FusionQ and another two stated-of-art fusion detection tools. FusionQ exceeded the other two in both sensitivity and specificity, especially in low coverage fusion detection. Using paired-end RNA-Seq data from breast cancer cell lines, FusionQ detected both the previously reported and new fusions. FusionQ reported the structures of these fusions and provided their expressions. Some highly expressed fusion genes detected by FusionQ are important biomarkers in breast cancer. The performances of FusionQ on cancel line data still showed better specificity and sensitivity in the comparison with another two tools.

Conclusions
FusionQ is a novel tool for fusion detection and quantification based on RNA-Seq data. It has both good specificity and sensitivity performance. FusionQ is free and available at http://www.wakehealth.edu/CTSB/Software/Software.htm.
bioNerDS: exploring bioinformatics’ database and software use through literature mining
Authors: Duck Geraint , Nenadic Goran , Brass Andy , Robertson David L , Stevens Robert 
Published: June 2013

Abstract

Background
Biology-focused databases and software define bioinformatics and their use is central to computational biology. In such a complex and dynamic field, it is of interest to understand what resources are available, which are used, how much they are used, and for what they are used. While scholarly literature surveys can provide some insights, large-scale computer-based approaches to identify mentions of bioinformatics databases and software from primary literature would automate systematic cataloguing, facilitate the monitoring of usage, and provide the foundations for the recovery of computational methods for analysing biological data, with the long-term aim of identifying best/common practice in different areas of biology.

Results
We have developed bioNerDS, a named entity recogniser for the recovery of bioinformatics databases and software from primary literature. We identify such entities with an F-measure ranging from 63% to 91% at the mention level and 63-78% at the document level, depending on corpus. Not attaining a higher F-measure is mostly due to high ambiguity in resource naming, which is compounded by the on-going introduction of new resources. To demonstrate the software, we applied bioNerDS to full-text articles from BMC Bioinformatics and Genome Biology. General mention patterns reflect the remit of these journals, highlighting BMC Bioinformatics’s emphasis on new tools and Genome Biology’s greater emphasis on data analysis. The data also illustrates some shifts in resource usage: for example, the past decade has seen R and the Gene Ontology join BLAST and GenBank as the main components in bioinformatics processing.

Conclusions
We demonstrate the feasibility of automatically identifying resource names on a large-scale from the scientific literature and show that the generated data can be used for exploration of bioinformatics database and software usage. For example, our results help to investigate the rate of change in resource usage and corroborate the suspicion that a vast majority of resources are created, but rarely (if ever) used thereafter. bioNerDS is available at http://bionerds.sourceforge.net/.
Breed, sex and anatomical location-specific gene expression profiling of the porcine skeletal muscles
Authors: Zhang Jie , Zhou Chaowei , Ma Jideng , Chen Lei , Jiang Anan , Zhu Li , Shuai Surong , Wang Jinyong , Li Mingzhou , Li Xuewei 
Published: June 2013

Abstract

Background
Skeletal muscle is one of the most important economic traits in agricultural animals, especially in pigs. In the modern pig industry, lean type pigs have undergone strong artificial selection for muscle growth, which has led to remarkable phenotypic variations compared with fatty type pigs, making these different breeds an ideal model for comparative studies.

Results
Here, we present comprehensive gene expression profiling for the white (longissimus dorsi muscle) and the red (psoas major muscle) skeletal muscles among male and female fatty Rongchang, feral Tibetan and lean Landrace pigs, using a microarray approach. We identified differentially expressed genes that may be associated the phenotypic differences of porcine muscles among the breeds, between the sexes and the anatomical locations. We also used a clustering method to identify sets of functionally coexpressed genes that are linked to different muscle phenotypes. We showed that, compared with the white muscles, which primarily modulate metabolic processes, the red muscles show a tendency to be a risk factor for inflammation and immune-related disorders.

Conclusions
This analysis presents breed-, sex- and anatomical location-specific gene expression profiles and further identified genes that may be associated with the phenotypic differences in porcine muscles among breeds, between the sexes and the anatomical locations.
ID3 contributes to cerebrospinal fluid seeding and poor prognosis in medulloblastoma
Authors: Phi Ji Hoon , Choi Seung Ah , Lim Sang-Hee , Lee Joongyub , Wang Kyu-Chang , Park Sung-Hye , Kim Seung-Ki 
Published: June 2013

Abstract

Background
The inhibitor of differentiation (ID) genes have been implicated as promoters of tumor progression and metastasis in many human cancers. The current study investigated the expression and functional roles of ID genes in seeding and prognosis of medulloblastoma.

Methods
ID gene expression was screened in human medulloblastoma tissues. Knockdown of ID3 gene was performed in medulloblastoma cells in vitro. The expression of metastasis-related genes after ID3 knockdown was assessed. The effect of ID3 knockdown on tumor seeding was observed in an animal model in vivo. The survival of medulloblastoma patients was plotted according to the ID3 expression levels.

Results
Significantly higher ID3 expression was observed in medulloblastoma with cerebrospinal fluid seeding than tumors without seeding. Knockdown of ID3 decreased proliferation, increased apoptosis, and suppressed the migration of D283 medulloblastoma cells in vitro. In a seeding model of medulloblastoma, ID3 knockdown in vivo with shRNA inhibited the growth of primary tumors, prevented the development of leptomeningeal seeding, and prolonged animal survival. High ID3 expression was associated with shorter survival of medulloblastoma patients, especially in Group 4 medulloblastomas.

Conclusions
High ID3 expression is associated with medullolbastoma seeding and is a poor prognostic factor, especially in patients with Group 4 tumors. ID3 may represent the metastatic/ aggressive phenotype of a subgroup of medulloblastoma.
Inflammatory phenotypes underlying uncontrolled childhood asthma despite inhaled corticosteroid treatment: rationale and design of the PACMAN2 study
Authors: Vijverberg Susanne JH , Koenderman Leo , van Erp Francine C , van der Ent Cornelis K , Postma Dirkje S , Brinkman Paul , Sterk Peter J , Raaijmakers Jan AM , Maitland-van der Zee Anke-Hilse 
Published: June 2013

AbstractBackgroundThe diagnosis of childhood asthma covers a broad spectrum of pathological mechanisms that can lead to similarly presenting clinical symptoms, but may nonetheless require different treatment approaches. Distinct underlying inflammatory patterns are thought to influence responsiveness to standard asthma medication.Methods/designThe purpose of the PACMAN2 study is to identify inflammatory phenotypes that can discriminate uncontrolled childhood asthma from controlled childhood asthma by measures in peripheral blood and exhaled air. PACMAN2 is a nested, case–control follow-up study to the ongoing pharmacy-based “Pharmacogenetics of Asthma medication in Children: Medication with Anti-inflammatory effects” (PACMAN) study. The original PACMAN cohort consists of children aged 4–12 years with reported use of asthma medication. The PACMAN2 study will be conducted within the larger PACMAN cohort, and will focus on detailed phenotyping of a subset of the PACMAN children. The selected participants will be invited to a follow-up visit in a clinical setting at least six months after their baseline visit based on their adherence to usage of inhaled corticosteroids, their asthma symptoms in the past year, and their age (≥ 8 years). During the follow-up visit, current and long-term asthma symptoms, medication use, environmental factors, medication adherence and levels of exhaled nitric oxide will be reassessed. The following measures will also be examined: pulmonary function, exhaled volatile organic compounds, as well as inflammatory markers in peripheral blood and blood plasma. Comparative analysis and cluster-analyses will be used to identify markers that differentiate children with uncontrolled asthma despite their use of inhaled corticosteroids (ICS) (cases) from children whose asthma is controlled by the use of ICS (controls).DiscussionAsthmatic children with distinct inflammatory phenotypes may respond differently to anti-inflammatory therapy. Therefore, by identifying inflammatory phenotypes in children with the PACMAN2 study, we may greatly impact future personalised treatment strategies, uncover new leads for therapeutic targets and improve the design of future clinical studies in the assessment of the efficacy of novel therapeutics.
A patient and physician survey of fibromyalgia across Latin America and Europe
Authors: Clark Patricia , Paiva Eduardo S , Ginovker Anna , Salomón Patricia Arline 
Published: June 2013

Abstract

Background
Patients and physicians from three Latin American (LA) and six European countries were surveyed in order to describe differences in journey to diagnosis, impact, and management of fibromyalgia (FM).

Methods
900 patients (300 LA; 600 Europe) and 1824 physicians (604 LA; 1220 Europe) were surveyed between October-December 2010 (LA) and February-April 2008 (Europe). Patients and physicians (GP or specialists) completed separate questionnaires, on symptoms, impact, and FM management. Interviews were conducted in local languages. Appropriate rating scales were used throughout. Data were analyzed using cross-tabulations and descriptive statistics. Significance was determined at P < 0.05 (indicated by *).

Results
In LA versus Europe, patients reported having FM symptoms for longer (100.8 vs. 83.7* months), and taking longer to be diagnosed (42.3 vs. 31.1* months). FM was characterized by multiple symptoms (11.2 vs. 6.9), but more LA patients reported 14 common symptoms*, and rated pain higher on 11-point scale (8.0 vs. 7.2*). LA patients were taking fewer medications (3.3 vs. 4.0). Patients from both regions found common symptoms very/extremely disruptive to their quality of life, but symptoms impacted daily living and ability to work more significantly in LA. Physicians (GPs or specialists) from LA more often considered problems sleeping*, difficulty concentrating*, anxiety*, depression*, numbness/tingling*, and leg cramps* very/extremely disruptive vs. European physicians. Despite headache, heightened sensitivity to touch, difficulty concentrating, and joint pain being experienced by ≥50% of patients from both regions, <15% of PCPs or specialists considered these typical FM symptoms. Patients also considered 12/14 symptoms more disruptive than PCPs or specialists in the same region. However, a higher proportion of PCPs or specialists considered FM to have a strong/very strong impact on aspects of daily living vs. patients within the same region.

Conclusions
Patient- and physician-rated disease perception and impact was often higher in LA than in Europe. Patient and physician perspective concerning FM impact and disruption were often misaligned within the same region. Our observations may be representative of cultural differences in stoicism, expression, beliefs, and attitudes to pain perception and management. Better understanding of these complexities could help targeted educational/training programs incorporating cultural differences, to improve chronic care.
A quantitative technique to create a femoral tunnel at the averaged center of the anteromedial bundle attachment in anatomic double-bundle anterior cruciate ligament reconstruction
Authors: Kai Shuken , Kondo Eiji , Kitamura Nobuto , Kawaguchi Yasuyuki , Inoue Masayuki , Amis Andrew A , Yasuda Kazunori 
Published: June 2013

AbstractBackgroundIn the anatomic double-bundle ACL reconstruction, 2 femoral tunnel positions are particularly critical to obtain better clinical results. Recently, a few studies have reported quantitative identification methods for posterolateral (PL) bundle reconstruction. Concerning anteromedial (AM) bundle reconstruction, however, no quantitative clinically available methods to insert a guide wire at the center of the direct attachment of the AM mid-substance fibers have been reported to date.MethodsFirst, we determined the center of the femoral attachment of the AM mid-substance fibers using 38 fresh frozen cadaveric knees. Based on this anatomical sub-study, we developed a quantitative clinical technique to insert a guide wire at the averaged center for anatomic double-bundle ACL reconstruction. In the second clinical sub-study with 63 patients who underwent anatomic ACL reconstruction with this quantitative technique, we determined the center of an actually created AM tunnel. Then, we compared the results of the second sub-study with those of the first sub-study to validate the accuracy of the quantitative technique. In both the sub-studies, we determined the center of the anatomical attachment and the tunnel outlet using the “3-dimensional clock” system. The tunnel outlet was evaluated using the “transparent” 3-dimensional computed tomography.ResultsThe averaged center of the direct attachment of the AM bundle midsubstance fibers was located on the cylindrical surface of the femoral intercondylar notch at “10:37” (or “1:23”) o’clock orientation in the distal view and at 5.0-mm from the proximal outlet of the intercondylar notch (POIN) in the lateral view. The AM tunnel actually created in ACL reconstruction was located at “10:41” (or “1:19”) o’clock orientation in the average and at 5.0-mm from the POIN. There was no significant difference between the 2 center locations.ConclusionsThe quantitative technique enabled us to easily create the femoral AM tunnel at the averaged center of the direct attachment of the AM bundle midsubstance fibers with high accuracy. This study reported information on the geometric location of the femoral attachment of the AM bundle and a clinically useful technique for its anatomical reconstruction.
Stem cells in Dentistry: knowledge and attitude of Nigerian Dentists
Authors: Sede Matthew Asizide , Audu Ochuwa , Azodo Clement Chinedu 
Published: June 2013

AbstractBackgroundSeveral controversies exist about the methods of harvesting and eventual utilization of stem cells in Medicine and Dentistry. The objective of the study was to investigate the awareness, attitude and knowledge of the use of stem cells in Dentistry among Nigerian Dentists.MethodsThis descriptive, cross-sectional study was conducted among dentists selected from both private and public health sectors, in some of the major cities in Nigeria.ResultsThe majority of the participants were ≤35 years in age, male, Pentecostal Christians, possessed a postgraduate qualification, had practiced for ≤5 years and were specialists or specializing. In this study, 153(81.0%) of the participants reported awareness about the use of stem cells in dentistry which was significantly associated with qualification and type of practice. Most of the respondents 114 (60.3%) had a poor knowledge of the use of stem cells in Dentistry. This was significantly associated with type of practice and awareness about stem cell use in dentistry but binary logistic regression showed awareness as the only determinant of knowledge. About three-quarters 142 (75.1%) of the participants exhibited positive attitude towards stem cell use. This had a positive non-significant association with knowledge and reported awareness.ConclusionData from this study revealed a high level of awareness, positive attitude to and poor knowledge of the use of stem cells in Dentistry among a cross section of Nigerian Dentists.