bluuebunny/crossref_metadata_2025_split huggingface dataset:
Efficient Infection of a Human B Cell Line with Cell-Free Kaposi's Sarcoma-Associated Herpesvirus
Authors: Dollery Stephen J. , Santiago-Crespo Rey J. , Kardava Lela , Moir Susan , Berger Edward A. 
Published: November 2013

ABSTRACTKaposi's sarcoma-associated herpesvirus (KSHV) is causatively linked to two B cell lymphoproliferative disorders, multicentric Castleman's disease and primary effusion lymphoma. Latently infected B cells are a major KSHV reservoir, and virus activation from tonsillar B cells can result in salivary shedding and virus transmission. Paradoxically, human B cells (primary and continuous) are notoriously refractory to infection, thus posing a major obstacle to the study of KSHV in this cell type. By performing a strategic search of human B cell lymphoma lines, we found that MC116 cells were efficiently infected by cell-free KSHV. Upon exposure to recombinant KSHV.219, enhanced green fluorescent protein reporter expression was detected in 17 to 20% of MC116 cells. Latent-phase transcription and protein synthesis were detected by reverse transcription-PCR and detection of latency-associated nuclear antigen expression, respectively, in cell lysates and individual cells. Selection based on the puromycin resistance gene in KSHV.219 yielded cultures with all cells infected. After repeated passaging of the selected KSHV-infected cells without puromycin, latent KSHV was maintained in a small fraction of cells. Infected MC116 cells could be induced into lytic phase with histone deacetylase inhibitors, as is known for latently infected non-B cell lines, and also selectively by the B cell-specific pathway involving B cell receptor cross-linking. Lytic-phase transition was documented by red fluorescent protein reporter expression, late structural glycoprotein (K8.1A, gH) detection, and infectious KSHV production. MC116 cells were CD27−/CD10+, characteristic of transitional B cells. These findings represent an important step in the establishment of an efficient continuous B cell line model to study the biologically relevant steps of KSHV infection.IMPORTANCEKaposi's sarcoma-associated herpesvirus (KSHV) causes two serious pathologies of B cells, the antibody-producing cells of the immune system. B cells are a major reservoir for KSHV persistence in the body. Paradoxically, in the laboratory, B cells are extremely difficult to infect with KSHV; this problem greatly hinders scientific analysis of B cell infection. We describe our search for and successful identification of a stable human B cell line that can be efficiently infected by KSHV. Upon infection of these cells, the virus goes into a quiet latent phase, a characteristic feature of many herpesvirus infections. The virus can be triggered to enter an active lytic phase by treatments known to stimulate normal B cell functions. These findings suggest that the new B cell line will be a valuable model in which to study KSHV infection of this major target cell type.
A cross-sectional study of factors associated with uptake of vaccination against influenza among older residents in the postpandemic season in Beijing, China
Authors: Zheng Yang , Yang Peng , Wu Shuangsheng , Ma Chunna , Seale Holly , MacIntyre C Raina , Wang Quanyi 
Published: November 2013

ObjectiveAnnually, influenza epidemics are associated with high mortality rates, notably among elderly persons. The aim of the study was to examine the level of influenza vaccine coverage among Chinese residents aged 60 years and older and to examine the demographic, behavioural and lifestyle health factors associated with vaccine receipt.DesignCross-sectional study.SettingBeijing, China.ParticipantsStratified sampling was used to recruit participants for this study. A total of 2578 people aged 60 years and older consented to participate in this study. Questionnaires from 2481 participants were valid and were included in the final analysis.Outcome measuresInfluenza vaccination status and factors associated with vaccination.MethodsIn late 2010, a survey was conducted with residents from three urban and three rural districts in Beijing, China. Multivariate logistic regression was performed to detect the factors associated with influenza vaccination.Results2481 older people (aged ≥60 years) were included in the final analysis. In 2010, 44% had received the annual influenza vaccine. Lower education level, poor health status of the participant, regular taking exercises and considering that vaccine is the best measure for preventing influenza were associated with influenza vaccination coverage.ConclusionsInfluenza vaccine coverage in Beijing still remains suboptimal. Further work needs to be undertaken to ascertain whether the methods used to distribute the vaccine are adequate and whether health professionals are appropriately promoting the vaccine.
Challenges to implementing expanded team models: lessons from a centralised nurse-led cholesterol-lowering programme
Authors: Kadehjian Emily K , Schneider Louise , Greenberg Jeffrey O , Dudley Jessica , Kachalia Allen 
Published: November 2013

BackgroundLowering low-density lipoprotein (LDL) cholesterol in patients with diabetes mellitus (DM) and cardiovascular disease (CVD) is critical to lowering morbidity and mortality. To increase the percentage of patients with DM and CVD at target LDL (<100 mg/dL), we launched an expanded team-based quality improvement programme in which centralised registered nurses (RNs) followed a detailed protocol to adjust cholesterol-lowering medications. Despite the growing use of team-based approaches to improve quality of care, little remains known about how best to implement them.Program evaluationTo share our experiences and lessons from operating a team-based programme, we conducted a retrospective observational analysis of administrative and clinical data on programme performance. We measured: primary care physician (PCP) and patient acceptance of the programme, number of medication adjustments, change in LDL, per cent of patients achieving target, time to LDL target and the efforts required to achieve these goals.ResultsUsing administrative data, we initially identified 374 potential patients for enrolment. Chart review revealed that 203 (54%) were clinically eligible. PCPs agreed to enrol 74% (150/203) of these patients. Thirty-six per cent of PCP-approved patients (54/150) could not be reached via phone and 5.3% (8/150) declined enrolment. Of patients enrolled (n=64), 50% did not complete the programme. Of those enrolled, median LDL decreased by 21 mg/dL and 52% (33/64) achieved the LDL target. Programme RNs spent 12 023 min on programme activities, of which 44.4% (5539) was related to non-enrolled patients.ConclusionsOur adoption of a centralised expanded team-based programme for the management of LDL cholesterol uncovered many barriers to efficiency and success. Even though expanded team programmes may be supported by PCPs, the administrative efforts required to identify, enrol and continually engage eligible patients raise many concerns regarding efficiency and highlight infrastructure changes needed for successful team-based approaches.
The Effect of Pollution Aerosol on Wintertime Orographic Precipitation in the Colorado Rockies Using a Simplified Emissions Scheme to Predict CCN Concentrations
Authors: Letcher Theodore , Cotton William R. 
Published: November 2013

AbstractThe impacts of enhanced CCN concentrations on various cloud and precipitation systems are potentially significant both to the large-scale climate system and local precipitation patterns. Precipitating stable orographic cloud systems are particularly susceptible to increases in CCN as parcel lifetimes within these clouds are typically short compared to clouds of similar depth. As such, even small perturbations to the precipitation efficiency within these clouds can have substantial impacts. In the mountainous regions of the western United States, where water resources are derived primarily from orographic precipitation during the cold season, this effect is of particular interest. The aims of this study are twofold. The first part is focused on the implementation of a simplified aerosol emissions scheme into the Regional Atmospheric Modeling System (RAMS). This scheme uses aerosol output from the Weather Research and Forecast Chemistry model (WRF-Chem) to initialize aerosol sources in RAMS. The second part of this study uses this scheme in the simulation of an orographic snow case that occurred in northwest Colorado during February 2007. The result of this study suggests that atmospheric CCN concentrations can be reasonably simulated using a simplified parameterization of aerosol emissions, despite a lack of explicit secondary aerosol (SA) within the model. Furthermore, the spatial and temporal variations in CCN predicted by this scheme produced a complicated response in the surface distribution of precipitation from the orographic snowstorm, a result not seen in studies where CCN concentrations are set to be horizontally homogenous.
A Search for Chaotic Behavior in Northern Hemisphere Stratospheric Variability
Authors: Badin Gualtiero , Domeisen Daniela I. V. 
Published: November 2013

Abstract
Northern Hemisphere stratospheric variability is investigated with respect to chaotic behavior using time series from three different variables extracted from four different reanalysis products and two numerical model runs with different forcing. The time series show red spectra at all frequencies and the probability distribution functions show persistent deviations from a Gaussian distribution. An exception is given by the numerical model forced with perpetual winter conditions—a case that shows more variability and follows a Gaussian distribution, suggesting that the deviation from Gaussianity found in the observations is due to the transition between summer and winter variability. To search for the presence of a chaotic attractor the correlation dimension and entropy, the Lyapunov spectrum, and the associated Kaplan–Yorke dimension are estimated. A finite value of the dimensions can be computed for each variable and data product, with the correlation dimension ranging between 3.0 and 4.0 and the Kaplan–Yorke dimension between 3.3 and 5.5. The correlation entropy varies between 0.6 and 1.1. The model runs show similar values for the correlation and Lyapunov dimensions for both the seasonally forced run and the perpetual-winter run, suggesting that the structure of a possible chaotic attractor is not determined by the seasonality in the forcing, but must be given by other mechanisms.
Pulmonary artery banding for univentricular heart beyond the neonatal period
Authors: Sasikumar Navaneetha , Ramanan Sowmya , Rema Krishna Manohar Soman , Subramanyan Raghavan , Kumar Raghavannair Suresh , Cherian Kootturathu Mammen 
Published: November 2013

Background It is standard practice to band the pulmonary artery at 2 to 4 weeks of age in patients with univentricular hearts with increased pulmonary blood flow. The behavior of patients banded beyond the neonatal period has not been well elucidated. Patients and methods This was a retrospective chart review of 32 consecutive patients (one neonate) who underwent pulmonary artery banding for functionally univentricular heart. The mean age at banding was 5.7 ± 6.0 months, and 34.4% were over 6-months old. Results Mortality was 15.6%. The mean systolic pulmonary artery pressure decreased from 43.6 ± 9.7 to 29.6 ± 7.0 mm Hg. The mean pre-discharge echocardiographic band gradient was 60.6 ± 13.6 mm Hg (mean systemic systolic pressure 73.7 ± 11.0 mm Hg) and systemic oxygen saturation was 81.7% ± 5.8%. At a mean follow-up period of 44.9 ± 30.0 months, 6 patients were lost to follow-up, 13 had undergone bidirectional Glenn shunt, and 7 had Fontan operations. Pulmonary artery mean pressure was 17.2 ± 4.6 mm Hg at pre-Glenn catheterization. Of the 5 patients who had not undergone further surgery, only one was inoperable. All were in functional class I or II. Conclusion Pulmonary artery banding beyond the neonatal period in suitable patients with univentricular hearts provides reasonable palliation in the intermediate term, with a significant number successfully undergoing Fontan stages.
Trends and practice patterns in the management of thoracic empyema
Authors: Vyas Krishna S , Saha Sibu P , Davenport Daniel L , Ferraris Victor A , Zwischenberger Joseph B 
Published: November 2013

Background This study explored the modern treatment of thoracic empyema. We evaluated outcomes of various operative approaches in both academic and nonacademic institutions. Methods We queried the Society of Thoracic Surgeons National Database for patients undergoing thoracic procedures with a primary diagnosis of empyema between 2009 and 2011. We compared treatment outcomes of patients having procedures at academic ( n = 1101, 28.3%) and nonacademic ( n = 2790, 71.7%) medical centers. Results Empyema treatments recorded in the database included tube thoracostomy ( n = 325, 8.4%), video-assisted thoracic surgery ( n = 1992, 51.2%), and thoracotomy ( n = 1574, 40.5%). Academic centers had higher rates of treatment by thoracostomy (13.8% vs. 6.2%), similar treatment rates of video-assisted thoracic surgery (49.9% vs. 51.7%), and lower rates of thoracotomy (36.3% vs. 42.1%) compared to nonacademic centers ( p < 0.001). Academic centers treated almost twice as many complicated empyemas with fistulas (11.4% vs. 6.5%, p < 0.001). Postoperative length of stay was higher in the academic centers (interquartile range 5–13 vs. 4–11 days, p = 0.001), while mechanical ventilation >48 h was more frequent in the nonacademic centers (7.6% vs. 4.4%, p = 0.013). Conclusion Surgeons in both academic and nonacademic centers use selective surgical approaches for treatment of thoracic empyema, depending on the clinical condition of the patient, with fairly equivalent results across all procedure types.
Aspergillus colonization in patients with bronchogenic carcinoma
Authors: Ali Sana , Malik Abida , Bhargava Rakesh , Shahid Mohammad , Fatima Nazish 
Published: November 2013

Background Aspergillus antigens such as galactomannan antigen, a cell wall polysaccharide, can be detected in patient’s serum or bronchoalveolar lavage. To study the prevalence of Aspergillus infection in patients with bronchogenic carcinoma, we measured galactomannan antigen in serum and bronchoalveolar lavage samples of patients with bronchogenic carcinoma. Methods The study was conducted on 45 bronchogenic carcinoma patients. The diagnosis of lung cancer was confirmed by bronchoscopy, histopathological and radiological examinations. Bronchoalveolar lavage fluid collected from each patient by fiberoptic bronchoscopy was subjected to direct microscopy and culture on Sabouraud’s dextrose agar and Czapek-Dox agar, and Aspergillus galactomannan antigen was measured in serum and bronchoalveolar lavage samples. Results The majority of patients were male (93.3%) in the age group 51–60 years, 88.9% were addicted to gutka chewing, and 82.1% were addicted to smoking. Most patients complained of cough (73%) and shortness of breath (51.1%). Squamous cell carcinoma (64.4%) was the most common malignancy, followed by adenocarcinoma (13.3%). On culture of bronchoalveolar lavage samples, 35.5% showed growth of Aspergillus spp. ( Aspergillus fumigatus in 17.8%, Aspergillus flavus in 13.3%, and Aspergillus niger in 4.4%). Galactomannan antigen was detected in 58.3% of bronchoalveolar lavage samples and 47.2% of serum samples. Conclusions There is a high prevalence of aspergillosis in patients with lung carcinoma, especially among smokers and gutka chewers.
Effects of cranial electrotherapy stimulation on preoperative anxiety, pain and endocrine response
Authors: Lee Se-Hwa , Kim Woon-Young , Lee Chang-Hyung , Min Too-Jae , Lee Yoon-Sook , Kim Jae-Hwan , Park Young-Cheol 
Published: November 2013

Objectives Cranial electrotherapy stimulation (CES) is used as a treatment for depression and anxiety, and as an adjunctive intervention for pain management. This prospective study investigated whether CES could decrease preoperative anxiety, the injection pain of rocuronium, postoperative pain and stress hormone levels. Methods Female patients undergoing thyroidectomy were randomly assigned to two groups, to receive either no pretreatment (control group) or CES pretreatment. Anxiety score, withdrawal response on rocuronium injection, and pain scores at 1, 4, 12 and 24 h post surgery were evaluated. Adrenocorticotrophic hormone (ACTH), cortisol and glucose levels were measured. Patients were blinded to the treatment condition. Results Fifty patients entered the study ( n = 25 per group). Anxiety score and withdrawal responses during rocuronium injection were significantly reduced in the CES group compared with the control group. Pain score was significantly lower in the CES group than in the control group, 1 h and 4 h post surgery. There were no significant differences in ACTH, cortisol and glucose levels. Conclusions CES pretreatment appears to reduce the level of preoperative anxiety, injection pain of rocuronium and postoperative pain. However, CES pretreatment did not affect stress hormone responses.
Emergency diagnosis of upper gastrointestinal bleeding by detection of haemoglobin in nasogastric aspirate
Authors: Colak Sahin , Erdogan Mehmet Ozgur , Sekban Hilal , Afacan Mustafa Ahmet , Uras Ahmet Rıza , Ibrahim Abdullah , Okay Nahide Gizem 
Published: November 2013

Objective To determine the accuracy of the Faecal Occult Blood–Transferrin test (FOB–T; Certest Biotec, San Mateo de Gállego, Spain) for detection of blood in nasogastric aspirate, and its emergency diagnostic value for upper gastrointestinal bleeding (UGIB). Methods Nasogastric aspirate was collected from patients with haematemesis on admission to hospital. Haemoglobin was quantified on admission and after 12 h. FOB–T test was used to assess each nasogastric aspirate sample for the presence of haemoglobin and transferrin. Results Of 64 patients included in the study, 28 (43.8%) were hospitalized for UGIB based on physical examination, haemoglobin level. 24 were confirmed with endoscopy findings. Four were excluded from study due to lack of endoscopic confirmation. The remaining 36 patients had no clinical evidence of UGIB. FOB–T test findings were positive in 26/60 patients, including all 24 patients with UGIB. The FOB–T test had sensitivity 100%, specificity 94.4%, positive predictive value 92.3% and negative predictive value 100% for UGIB. Conclusions A negative FOB–T test may be sufficient to exclude the possibility of UGIB without other diagnostic tests.
Operational effectiveness of blended e-learning program for nursing research ethics
Authors: Cho Kap-Chul , Shin Gisoo 
Published: November 2013

Background: Since 2006, the Korean Ministry of Education, Science and Technology, and the National Research Foundation of Korea have taken the lead in developing an institutional guideline for research ethics. Objectives: The purpose was to identify the effectiveness of the Good Research Practice program, developed on a fund granted by the National Research Foundation of Korea, for nurses and nursing students whose knowledge and perception of research ethics were compared before and after the implementation of the Good Research Practice program. Research design: This study was conducted to compare the levels of knowledge and perception of research ethics in the participants before and after the program was implemented. Participant and research context: The participants included 45 nurses and 69 nursing students from hospitals, colleges of nursing, and the Korean Nurses Association, located in Seoul, Korea. Ethical considerations: This study was approved by the Institutional Research Board in Korea. Findings: Based on the Analysis, Design, Development, Implementation, and Evaluation model, the Good Research Practice program was made up of a total of 30 h of the blended learning both online and off-line. The results of this study showed that there were statistically significant differences in both knowledge and perception of research ethics in nursing students and nurses before and after the program had been implemented. Discussion: The concepts of professional nursing ethics, moral issues, and bioethics were often confused with one another and not clearly defined. Therefore, the concept and scope of bioethics, moral judgment, and overall nursing ethics should be well defined and conceptualized in the future. Conclusions: This study suggested integrating research ethics education in the nursing curriculum as a required course of study for nursing students and as part of the in-service training program for nurses in order to improve research ethics in nursing research in Korea.
A Comprehensive Palliative Care Program at a Tertiary Cancer Center in Jordan
Authors: Shamieh Omar , Hui David 
Published: November 2013

Context: The palliative care program in King Hussein Cancer Center (KHCC) is growing rapidly to serve the needs of patients with cancer and their families. Objective: To describe the KHCC palliative care program and its integration into the oncology care. Methods: Narrative review of our palliative care program. Results: Patients with cancer at KHCC have access to an interprofessional palliative care at different settings. In 2012, the inpatient team saw 400 consultations and 979 referrals and admissions. The outpatient clinic had a total of 1133 patient visits. The home care program provided a total of 1501 visits. Our program is a regional center for education and training and actively conducts research. Conclusion: Our palliative care program may be a model for successful delivery of comprehensive cancer care in the Middle East.
Probabilistic alignment leads to improved accuracy and read coverage for bisulfite sequencing data
Authors: Hong Changjin , Clement Nathan L , Clement Spencer , Hammoud Saher Sue , Carrell Douglas T , Cairns Bradley R , Snell Quinn , Clement Mark J , Johnson William Evan 
Published: November 2013

Abstract

Background
DNA methylation has been linked to many important biological phenomena. Researchers have recently begun to sequence bisulfite treated DNA to determine its pattern of methylation. However, sequencing reads from bisulfite-converted DNA can vary significantly from the reference genome because of incomplete bisulfite conversion, genome variation, sequencing errors, and poor quality bases. Therefore, it is often difficult to align reads to the correct locations in the reference genome. Furthermore, bisulfite sequencing experiments have the additional complexity of having to estimate the DNA methylation levels within the sample.

Results
Here, we present a highly accurate probabilistic algorithm, which is an extension of the Genomic Next-generation Universal MAPper to accommodate bisulfite sequencing data (GNUMAP-bs), that addresses the computational problems associated with aligning bisulfite sequencing data to a reference genome. GNUMAP-bs integrates uncertainty from read and mapping qualities to help resolve the difference between poor quality bases and the ambiguity inherent in bisulfite conversion. We tested GNUMAP-bs and other commonly-used bisulfite alignment methods using both simulated and real bisulfite reads and found that GNUMAP-bs and other dynamic programming methods were more accurate than the more heuristic methods.

Conclusions
The GNUMAP-bs aligner is a highly accurate alignment approach for processing the data from bisulfite sequencing experiments. The GNUMAP-bs algorithm is freely available for download at: http://dna.cs.byu.edu/gnumap. The software runs on multiple threads and multiple processors to increase the alignment speed.