bluuebunny/crossref_metadata_2025_split huggingface dataset:
Intensive red blood cell transfusions and risk of alloimmunization
Authors: Zalpuri Saurabh , Middelburg Rutger A. , Schonewille Henk , de Vooght Karen M.K. , le Cessie Saskia , van der Bom Johanna G. , Zwaginga Jaap Jan 
Published: June 2013

BackgroundExposure to allogenic red blood cells (RBCs) may lead to formation of antibodies against nonself‐antigens in transfused patients. While alloimmunization rates are known to increase with the number of transfusions, the transfusion course in patients can vary from receiving multiple units during a single transfusion event or getting them dispersed over a long(er) period. In this study we compared the immunization risk between different transfusion intensities.Study Design and MethodsAn incident new‐user cohort study was conducted among consecutive transfused patients at two university medical centers. All patients who received their first RBC transfusion within the study period from January 2005 to December 2011 were eligible. Intensive transfusions were defined as at least 5, at least 10, and at least 20 RBC units within 48 hours. Alloimmunization hazard ratios (HRs), comparing patients receiving intensive transfusions to patients never receiving intensive transfusions, were estimated.ResultsThe study cohort was composed of 5812 patients who had received a median of 7 (interquartile range, 4‐12) units. RBC alloantibodies were formed by 156 patients. The adjusted Cox regression HRs for alloimmunization, with number of units as the time covariate and adjusted for patient age, sex, and follow‐up time after first transfusion, ranged from 0.8 to 1.2 (95% confidence interval, 0.4‐2.6).ConclusionThe occurrence of RBC alloimmunization in patients receiving intensive transfusions did not differ significantly from patients receiving nonintensive transfusions.
Respiration‐phase‐matched digital tomosynthesis imaging for moving target verification: A feasibility study
Authors: Zhang You , Ren Lei , Ling C. Clifton , Yin Fang‐Fang 
Published: June 2013

Purpose:To develop a respiration‐phase‐matched digital tomosynthesis (DTS) technique to monitor moving targets, and to evaluate its accuracy for various imaging parameters and anatomical characteristics.Methods:Previously developed 3D‐DTS techniques, registering onboard DTS (OB‐DTS, reconstructed from onboard projections) to reference DTS (R‐DTS, reconstructed from DRRs of 3D reference CT), are inadequate to monitor moving targets. The authors’ proposed respiration‐phase‐matched DTS technique registers OB‐DTS to R‐DTS reconstructed from DRRs generated by the same phase images of 4D reference CT as the corresponding onboard projections. To evaluate the improved accuracy of the author's technique, the authors performed thoracic phantom studies using (1) simulation with the 4D digital extended‐cardiac‐torso (XCAT) phantom, and (2) experiments with an anthropomorphic motion phantom. The studies were performed for various: respiratory cycle (RC), scan angle, and fraction of RC contained therein. Also, the authors assessed the accuracy of their technique relative to target size/location, and respiration inconsistencies from the R‐DTS to OB‐DTS.Results:In both simulation and experimental studies, the respiration‐phase‐matched DTS technique is significantly more accurate in determining moving target positions. For 324 different scenarios simulated by XCAT, the respiration‐phase‐matched DTS technique localizes the 3D target position to errors of 1.07 ± 0.57 mm (mean ± S.D.), as compared to (a) 2.58 ± 1.37 and (b) 7.37 ± 4.18 mm, for 3D‐DTS using 3D reference CT of (a) average intensity projection and (b) free‐breathing CT. For 60 scenarios evaluated through experimental study, the uncertainties corresponding to those above are 1.24 ± 0.87, 2.42 ± 1.80, and 5.77 ± 6.45 mm, respectively. For a given scan angle, the accuracy of respiration‐phase‐matched DTS technique is less dependent on RC and the fraction of RC included in the scan. Increasing scan angle improves its accuracy. For different target locations, the targets near the chest wall or in the middle of lung provide higher registration accuracy compared to those near the mediastinum and diaphragm. Larger targets provide higher registration accuracy than small targets. Different respiratory cycle inconsistencies from R‐DTS to OB‐DTS minimally affect the registration accuracy. Increasing the respiratory amplitude inconsistencies will decrease the accuracy.Conclusions:The respiration‐phase‐matched DTS is more accurate and robust in determining moving target positions than 3D‐DTS. It has potential application in pretreatment setup, post‐treatment analysis, and intrafractional target verification.
Performance of the Vitek MS v2.0 System in Distinguishing Streptococcus pneumoniae from Nonpneumococcal Species of the Streptococcus mitis Group
Authors: Branda John A. , Markham Rachelle P. , Garner Cherilyn D. , Rychert Jenna A. , Ferraro Mary Jane 
Published: June 2013

ABSTRACTThe Vitek MS v2.0 matrix-assisted laser desorption ionization–time of flight mass spectrometry system accurately distinguishedStreptococcus pneumoniaefrom nonpneumococcalS. mitisgroup species. Only 1 of 116 nonpneumococcal isolates (<1%) was misidentified asS. pneumoniae. None of 95 pneumococcal isolates was misidentified. This method provides a rapid, simple means of discriminating among these challenging organisms.
Accuracy of Species-Level Identification of Yeast Isolates from Blood Cultures from 10 University Hospitals in South Korea by Use of the Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry-Based Vitek MS System
Authors: Won Eun Jeong , Shin Jong Hee , Lee Kyungwon , Kim Mi-Na , Lee Hye Soo , Park Yeon-Joon , Joo Min Young , Kim Soo Hyun , Shin Myung Geun , Suh Soon Pal , Ryang Dong Wook 
Published: June 2013

ABSTRACT
We assessed the accuracy of yeast bloodstream isolate identification performed over a 1-year period at 10 South Korean hospitals, using the matrix-assisted laser desorption ionization–time of flight (MALDI-TOF)-based Vitek MS system. The overall phenotypic misidentification rate was 3.4% (18/533), with considerable variation between hospitals (0.0% to 19.0%), compared to 1.1% (6/533) for the Vitek MS system.
Two Atypical Cases of Kingella kingae Invasive Infection with Concomitant Human Rhinovirus Infection
Authors: Basmaci Romain , Ilharreborde Brice , Doit Catherine , Presedo Ana , Lorrot Mathie , Alison Marianne , Mazda Keyvan , Bidet Philippe , Bonacorsi Stéphane 
Published: June 2013

ABSTRACT

We describe two atypical cases of
Kingella kingae
infection in children diagnosed by PCR, one case involving a soft tissue abscess and one case a femoral Brodie abscess. Both patients had concomitant human rhinovirus infection.
K. kingae
strains, isolated from an oropharyngeal swab, were characterized by multilocus sequence typing and
rtxA
sequencing.
Distinct Roles of Kaposi's Sarcoma-Associated Herpesvirus-Encoded Viral Interferon Regulatory Factors in Inflammatory Response and Cancer
Authors: Baresova Petra , Pitha Paula M. , Lubyova Barbora 
Published: June 2013

ABSTRACT
Kaposi's sarcoma-associated herpesvirus (KSHV) is the etiologic agent associated with Kaposi's sarcoma (KS), primary effusion lymphoma (PEL), and multicentric Castleman disease (MCD). Similar to other herpesviruses, KSHV has two life cycles, latency and lytic replication. In latency, the KSHV genome persists as a circular episome in the nucleus of the host cell and only a few viral genes are expressed. In this review, we focus on oncogenic, antiapoptotic, and immunomodulating properties of KSHV-encoded homologues of cellular interferon regulatory factors (IRFs)—viral IRF1 (vIRF1) to vIRF4—and their possible role in the KSHV-mediated antiviral response, apoptosis, and oncogenicity.
An Autocrine Loop between TGF-β1 and the Transcription Factor Brachyury Controls the Transition of Human Carcinoma Cells into a Mesenchymal Phenotype
Authors: Larocca Cecilia , Cohen Joseph R. , Fernando Romaine I. , Huang Bruce , Hamilton Duane H. , Palena Claudia 
Published: June 2013

Abstract
The epithelial–mesenchymal transition (EMT) is a process associated with the metastasis of solid tumors as well as with the acquisition of resistance to standard anticancer modalities. A major initiator of EMT in carcinoma cells is TGF-β, which has been shown to induce the expression of several transcription factors ultimately responsible for initiating and maintaining the EMT program. We have previously identified Brachyury, a T-box transcription factor, as an inducer of mesenchymal features in human carcinoma cells. In this study, a potential link between Brachyury and TGF-β signaling has been investigated. The results show for the first time that Brachyury expression is enhanced during TGF-β1–induced EMT in various human cancer cell lines, and that a positive feedback loop is established between Brachyury and TGF-β1 in mesenchymal-like tumor cells. In this context, Brachyury overexpression is shown to promote upregulation of TGF-β1 at the mRNA and protein levels, an effect mediated by activation of the TGF-β1 promoter in the presence of high levels of Brachyury. Furthermore, inhibition of TGF-β1 signaling by a small-molecule inhibitor of TGF-β receptor type I decreases Brachyury expression, induces a mesenchymal-to-epithelial transition, and renders cancer cells more susceptible to chemotherapy. This study thus has implications for the future development of clinical trials using TGF-β inhibitors in combination with other anticancer agents. Mol Cancer Ther; 12(9); 1805–15. ©2013 AACR.
Protease activated receptor 4 limits bacterial growth and lung pathology during late stage Streptococcus pneumoniae induced pneumonia in mice
Authors: van ’t Veer Cornelis , van den Boogaard Florry E. , Nieuwland Rienk , Hoogendijk Arie J. , de Boer Onno J. , Roelofs Joris J. T. H. , der Poll Tom van , de Stoppelaar Sacha F. 
Published: June 2013

Summary
Streptococcus pneumoniae is a common causative pathogen of pneumonia and sepsis. Pneumonia and sepsis are associated with enhanced activation of coagulation, resulting in the production of several host-derived proteases at the primary site of infection and in the circulation. Serine proteases cleave protease activated receptors (PARs), which form a molecular link between coagulation and inflammation. PAR4 is one of four subtypes of PARs and is widely expressed by multiple cell types in the respiratory tract implicated in pulmonary inflammation, by immune cells and by platelets. In mice, mouse (m)PAR4 is the only thrombin receptor expressed by platelets. We here sought to determine the contribution of mPAR4 to the host response during pneumococcal pneumonia. Pneumonia was induced by intranasal inoculation with S. pneumoniae in mPAR4-deficient (par4-/-
) and wild-type mice. Mice were sacrificed after 6, 24 or 48 hours (h). Blood, lungs, liver and spleen were collected for analyses. Ex vivo stimulation assays were performed with S. pneumoniae and mPAR4 activating peptides. At 48 h after infection, higher bacterial loads were found in the lungs and blood of par4-/-
mice (p < 0.05), accompanied by higher histopathology scores and increased cytokine levels (p < 0.05) in the lungs. Ex vivo, co-stimulation with mPAR4 activating peptide enhanced the whole blood cytokine response to S. pneumoniae. Thrombin inhibition resulted in decreased cytokine release after S. pneumoniae stimulation in human whole blood. Our findings suggest that mPAR4 contributes to antibacterial defence during murine pneumococcal pneumonia.
Long-term Survival of Dialysis Patients With Bacterial Endocarditis Undergoing Valvular Replacement Surgery in the United States
Authors: Leither Maxwell D. , Shroff Gautam R. , Ding Shu , Gilbertson David T. , Herzog Charles A. 
Published: June 2013

Background—
Bacterial endocarditis in dialysis patients is associated with high mortality rates. The literature is limited on the long-term outcomes of valvular replacement surgery and the choice of prosthesis in dialysis patients with bacterial endocarditis.

Methods and Results—

Dialysis patients hospitalized for bacterial endocarditis from 2004 to 2007 were studied retrospectively using data from the United States Renal Data System. Long-term survival of patients undergoing valve replacement surgery with tissue or nontissue valves was compared by use of the Kaplan-Meier method. A Cox proportional hazards model was used to identify independent predictors of mortality in patients undergoing valvular replacement surgery. During the study period, 11 156 dialysis patients were hospitalized for bacterial endocarditis and 1267 (11.4%) underwent valvular replacement surgery (tissue valve, 44.3%; nontissue valve, 55.7%). In the valve replacement cohort, 60% were men, 50% were white, 54% were 45 to 64 years of age, and 36% were diabetic. Estimated survival with tissue and nontissue valves at 0.5, 1, 2, and 3 years was 59% and 60%, 48% and 50%, 35% and 37%, and 25% and 30%, respectively (log-rank
P
=0.42). Staphylococcus was the predominant organism (66% of identified organisms). Independent predictors of mortality in patients undergoing valve replacement surgery included older age, diabetes mellitus as the cause of end-stage renal disease, surgery during index hospitalization, staphylococcus as the causative organism, and dysrhythmias as a comorbid condition.

Conclusions—
Valve replacement surgery is appropriate for well-selected dialysis patients with bacterial endocarditis but is associated with high mortality rates. Survival does not differ with tissue or nontissue prosthesis.
Enemy at the Gates: The Phenomenon of Fortifications in Israel Reexamined
Authors: Ben-Ami Doron , Wazana Nili 
Published: June 2013

Abstract
This article addresses the phenomenon of fortifications in Iron Age Israel and tries to portray the specific historical background behind their construction by integrating the archaeological data, the extra-biblical sources and the analysis of the biblical text. Of the two clear stratigraphical phases of fortifications noticed in several Iron Age cities, the latter is more massive and elaborated compared with its predecessor. We propose that the developed phase of fortifications in Israel was created under the Omrides, in a time of economic and political strength, as a response to the expansion policy of Aram Damascus. This analysis offers an explanation to the intriguing absence of any biblical reference to the Assyrians prior to Tiglath-pileser III, and casts a fresh look upon the current debate on the chronology of the Iron Age II. If the elaborate fortification systems were initiated during the first half of the ninth century, the initial phase of the urbanization process, which preceded this developed stage, must have begun in the days prior to the Omride dynasty, namely in the tenth century.
Evaluation of Boundary Layer Depth Estimates at Summit Station, Greenland
Authors: Van Dam B. , Helmig D. , Neff W. , Kramer L. 
Published: June 2013

AbstractBoundary layer conditions in polar regions have been shown to have a significant impact on the levels of trace gases in the lower atmosphere. The ability to properly describe boundary layer characteristics (e.g., stability, depth, and variations on diurnal and seasonal scales) is essential to understanding the processes that control chemical budgets and surface fluxes in these regions. Surface turbulence data measured from 3D sonic anemometers on an 8-m tower at Summit Station, Greenland, were used for estimating boundary layer depths (BLD) in stable to weakly stable conditions. The turbulence-derived BLD estimates were evaluated for June 2010 using direct BLD measurements from an acoustic sounder located approximately 50 m away from the tower. BLDs during this period varied diurnally; minimum values were less than 10 m, and maximum values were greater than 150 m. BLD estimates provided a better comparison with sodar observations during stable conditions. Ozone and nitrogen oxides were also measured at the meteorological tower and investigated for their dependency on boundary layer structure. These analyses, in contrast to observations from South Pole, Antarctica, did not show a clear relation between surface-layer atmospheric trace-gas levels and the stable boundary layer.
The Role of Air–Sea Coupling in Seasonal Prediction of Asia–Pacific Summer Monsoon Rainfall
Authors: Zhu Jieshun , Shukla Jagadish 
Published: June 2013

Abstract
This study examines the role of the air–sea coupled process in the seasonal predictability of Asia–Pacific summer monsoon rainfall by comparing seasonal predictions from two carefully designed model experiments: tier 1 (fully coupled model) and tier 2 (AGCM with prescribed SSTs). In these experiments, an identical AGCM is used in both tier 1 and tier 2 predictions; the daily mean SSTs from tier 1 coupled predictions are prescribed as a boundary condition in tier 2 predictions. Both predictions start in April from 1982 to 2009, with four ensemble members for each case. The model used is the Climate Forecast System, version 2 (CFSv2), the current operational climate prediction model for seasonal-to-interannual prediction at the National Centers for Environmental Prediction (NCEP). Comparisons indicate that tier 2 predictions produce not only higher rainfall biases but also unrealistically high rainfall variations in the tropical western North Pacific (TWNP) and some coastal regions as well. While the prediction skill in terms of anomaly correlations does not present a significant difference between the two types of predictions, the root-mean-square errors (RMSEs) are clearly larger over the above-mentioned regions in the tier 2 prediction. The reduced RMSE skills in the tier 2 predictions are due to the lack of a coupling process in AGCM-alone simulations, which, particularly, results in an unrealistic SST–rainfall relationship over the TWNP region. It is suggested that for a prediction of summer monsoon rainfall over the Asia–Pacific region, it is necessary to use a coupled atmosphere–ocean (tier 1) prediction system.
Profiles of Wind Speed Variances within Nocturnal Low-Level Jets Observed with a Sodar
Authors: Kallistratova Margarita A. , Kouznetsov Rostislav D. , Kramar Valerii F. , Kuznetsov Dmitrii D. 
Published: June 2013

AbstractContinuous sodar measurements of wind profiles have been carried out at the Zvenigorod Scientific Station of the Obukhov Institute of Atmospheric Physics since 2008. The station is located in a slightly inhomogeneous rural area about 45 km west of Moscow, Russia. The data were used to determine the parameters of wind and turbulence within low-level jets in the stable atmospheric boundary layer (ABL). Along with the mean velocity profiles, the profiles of variances of wind speed components from the sodar and the profiles of temperature from a microwave radiometer have been used to quantify turbulence and thermal stratification. Data from two sonic anemometers were used to get the near-surface parameters.The typical standard deviation of the vertical wind component σw within the low-level jet is about 5% of the maximum wind speed in the jet. No noticeable vertical variation of σw across the jets was detected in several earlier sodar campaigns, and it was not found in the present study. An increase in horizontal variances was detected in zones of substantial wind shear, which agrees with earlier published lidar data.Quasi-periodic structures in the sodar return signal, which appear in sodar echograms as braid-shaped patterns, were found to emerge preferably when a substantial increase of wind shear occurs at the top of the stable ABL. The braid patterns in the sodar echograms were not accompanied by any noticeable increase of observed σw, which disagrees with earlier data and indicates that such patterns may originate from various phenomena.
Comparison among nasopharyngeal swab, nasal wash, and oropharyngeal swab for respiratory virus detection in adults with acute pharyngitis
Authors: Li Li , Chen Qiao-Yan , Li Yun-Ying , Wang Yan-Fang , Yang Zi-Feng , Zhong Nan-Shan 
Published: June 2013

Abstract

Background
Acute pharyngitis is frequently seen in primary care. Acute viral pharyngitis may be easily misdiagnosed as acute bacterial pharyngitis. Laboratory-confirmed diagnosis of respiratory viruses is recommended. The purpose of this study was to compare the sensitivities among oropharyngeal swab (OPS), nasopharyngeal swab (NPS), and nasal wash (NW) in adults with acute pharyngitis.

Methods
OPS, NPS, and NW were obtained from each participant with acute pharyngitis. The specimens were tested for 15 respiratory viruses by TaqMan real-time polymerase chain reaction. A sample was considered to be a true positive if any of the specimens was positive. The sensitivities among samples were compared by chi-square test or Fisher’s exact test, as appropriate.

Results
One hundred three triple samples collected consecutively by OPS, NPS, and NW were obtained. In 73 patients, one or more viruses were detected by any of the three methods. Among all viruses, the sensitivity of NPS was significantly higher than that of NW (74% vs. 49%, respectively; p < 0.01) and OPS (74% vs. 49%, respectively; p < 0.01).

Conclusions
Flocked NPS collection may be the most effective alternative to NW and OPS for detection of respiratory viruses in adults with acute pharyngitis using TaqMan real-time polymerase chain reaction.
Bcr-Abl tyrosine kinase inhibitors- current status
Authors: Mughal Anum , Aslam Hafiz Muhammad , Khan Aga Muhammad Hammad , Saleem Shafaq , Umah Ribak , Saleem Maria 
Published: June 2013

Abstract
Bcr-Abl plays a central role in the development of chromosome positive leukaemia. Chronic Myeloid leukaemia occurs due to increase proliferation and resistance to apoptosis by Bcr-Abl positive cells. Imatinib (STI571) is the first drug in the family of Bcr-Abl tyrosine kinase inhibitors while Nilotinib (AMN107) and Dasatinib (BMS-345825) are second generation drugs that are intended to have less resistance and intolerance than imatinib. Ponatinib (AP24534) an orally active Bcr-Abl Tyrosine Kinase Inhibitor and Bafetinib (INNO-406) have efficacy against various point mutations in the Bcr-Abl kinase. 1, 3, 4 thiadiazole derivatives has also displayed moderate inhibitory action on both Abl and Src kinase family. However there are varieties of Bcr-Abl inhibitors but Nilotinib is still the frontline tyrosine kinase inhibitors.