bluuebunny/crossref_metadata_2025_split huggingface dataset:
Differences in characteristics between healthcare-associated and community-acquired infection in community-onset Klebsiella pneumoniae bloodstream infection in Korea
Authors: Jung Younghee , Lee Myung Jin , Sin Hye-Yun , Kim Nak-Hyun , Hwang Jeong-Hwan , Park Jinyong , Choe Pyoeng Gyun , Park Wan Beom , Kim Eu Suk , Park Sang-Won , Park Kyoung Un , Kim Hong Bin , Kim Nam-Joong , Kim Eui-Chong , Song Kyoung-Ho , Oh Myoung-don 
Published: October 2012

Abstract

Background
Healthcare-associated (HCA) infection has emerged as a new epidemiological category. The aim of this study was to evaluate the impact of HCA infection on mortality in community-onset Klebsiella pneumoniae bloodstream infection (KpBSI).

Methods
We conducted a retrospective study in two tertiary-care hospitals over a 6-year period. All adult patients with KpBSI within 48 hours of admission were enrolled. We compared the clinical characteristics of HCA and community-acquired (CA) infection, and analyzed risk factors for mortality in patients with community-onset KpBSI.

Results
Of 553 patients with community-onset KpBSI, 313 (57%) were classified as HCA- KpBSI and 240 (43%) as CA-KpBSI. In patients with HCA-KpBSI, the severity of the underlying diseases was higher than in patients with CA-KpBSI. Overall the most common site of infection was the pancreatobiliary tract. Liver abscess was more common in CA-KpBSI, whereas peritonitis and primary bacteremia were more common in HCA-KpBSI. Isolates not susceptible to extended-spectrum cephalosporin were more common in HCA- KpBSI than in CA-KpBSI (9% [29/313] vs. 3% [8/240]; p = 0.006). Overall 30-day mortality rate was significantly higher in HCA-KpBSI than in CA-KpBSI (22% [70/313] vs. 11% [27/240]; p = 0.001). In multivariate analysis, high Charlson’s weighted index of co-morbidity, high Pitt bacteremia score, neutropenia, polymicrobial infection and inappropriate empirical antimicrobial therapy were significant risk factors for 30-day mortality.

Conclusions
HCA-KpBSI in community-onset KpBSI has distinctive characteristics and has a poorer prognosis than CA-KpBSI, but HCA infection was not an independent risk factor for 30-day mortality.
Epoetin administrated after cardiac surgery: effects on renal function and inflammation in a randomized controlled study
Authors: de Seigneux Sophie , Ponte Belen , Weiss Lucien , Pugin Jérôme , Romand Jacques André , Martin Pierre-Yves , Saudan Patrick 
Published: October 2012

Abstract

Background
Experimentally, erythropoietin (EPO) has nephroprotective as well as immunomodulatory properties when administered after ischemic renal injury. We tested the hypothesis that different doses of recombinant human EPO administered to patients after cardiac surgery would minimize kidney lesions and the systemic inflammatory response, thereby decreasing acute kidney injury (AKI) incidence.

Methods
In this double-blinded randomized control study, 80 patients admitted to the ICU post-cardiac surgery were randomized by computer to receive intravenously isotonic saline (n = 40) versus α-Epoetin (n = 40): either 40000 IU (n = 20) or 20000 IU (n = 20). The study lasted one year. The primary outcome was the change in urinary NGAL concentration from baseline and 48 h after EPO injection. Creatinine, cystatine C and urinary NGAL levels were measured on the day of randomization and 2–4 days after EPO injection. To assess acute inflammatory response, serum cytokines (IL6 and IL8) were measured at randomization and four days after r-HuEPO injection. Patients and care-takers were blinded for the assignment.

Results
No patient was excluded after randomization. Patient groups did not differ in terms of age, gender, comorbidities and renal function at randomization. The rate of AKI assessed by AKIN criteria was 22.5% in our population. EPO treatment did not significantly modify the difference in uNGAl between 48 hours and randomization compared to placebo [2.5 ng/ml (−17.3; 22.5) vs 0.7 ng/ml (−31.77; 25.15), p = 0.77] and the incidence of AKI was similar. Inflammatory cytokines levels were not influenced by EPO treatment. Mortality and hospital stays were similar between the groups and no adverse event was recorded.

Conclusion
In this randomized-controlled trial, α-Epoetin administrated after cardiac surgery, although safe, demonstrated neither nephroprotective nor anti-inflammatory properties.

Trial registration number
NCT00676234
High DMBT1 concentrations in breast milk correlate with increased risk of infection in preterm and term neonates
Authors: Ronellenfitsch Sebastian , Weiß Christel , Frommhold David , Koch Lutz , Mollenhauer Jan , Poeschl Johannes , Müller Hanna 
Published: October 2012

Abstract

Background
Human milk contains immune molecules involved in the protection of newborns against infections. We analyzed the concentration of Deleted in Malignant Brain Tumors 1 (DMBT1), a protein with functions in innate immunity, in breast milk.

Methods
DMBT1 was detected in breast milk by Western blotting and its concentration was quantified by ELISA in 95 breast milk samples collected from mothers of preterm and term neonates during the first four weeks after delivery. Possible effects of maternal or neonatal parameters were analyzed by different statistical tests.

Results
The mean DMBT1 concentration (± standard error of the mean) in the tested milk samples was 2.48 ± 0.26 μg/mL (range: 0.112 μg/mL to 17.984 μg/mL) and represented 0.0087% of the total protein content. The comparison between the newborns with infection and the newborns without infection revealed significantly higher DMBT1 concentrations in breast milk in the group with infection (6.72 ± 2.53 μg/mL versus 2.20 ± 0.35 μg/mL (P = 0.031)). Neither maternal nor neonatal parameters showed a correlation with the milk DMBT1 levels.

Conclusions
DMBT1 is a component of breast milk after birth and is up-regulated in the breast milk from mothers with newborns suffering from neonatal infection. Thus, breast milk DMBT1 may be part of the innate immunity similar to secretory IgA.
Fiber optic micro sensor for the measurement of tendon forces
Authors: Behrmann Gregory P , Hidler Joseph , Mirotznik Mark S 
Published: October 2012

Abstract
A fiber optic sensor developed for the measurement of tendon forces was designed, numerically modeled, fabricated, and experimentally evaluated. The sensor incorporated fiber Bragg gratings and micro-fabricated stainless steel housings. A fiber Bragg grating is an optical device that is spectrally sensitive to axial strain. Stainless steel housings were designed to convert radial forces applied to the housing into axial forces that could be sensed by the fiber Bragg grating. The metal housings were fabricated by several methods including laser micromachining, swaging, and hydroforming. Designs are presented that allow for simultaneous temperature and force measurements as well as for simultaneous resolution of multi-axis forces.
The sensor was experimentally evaluated by hydrostatic loading and in vitro testing. A commercial hydraulic burst tester was used to provide uniform pressures on the sensor in order to establish the linearity, repeatability, and accuracy characteristics of the sensor. The in vitro experiments were performed in excised tendon and in a dynamic gait simulator to simulate biological conditions. In both experimental conditions, the sensor was found to be a sensitive and reliable method for acquiring minimally invasive measurements of soft tissue forces. Our results suggest that this sensor will prove useful in a variety of biomechanical measurements.
A validation of ground ambulance pre-hospital times modeled using geographic information systems
Authors: Patel Alka B , Waters Nigel M , Blanchard Ian E , Doig Christopher J , Ghali William A 
Published: October 2012

Abstract

Background
Evaluating geographic access to health services often requires determining the patient travel time to a specified service. For urgent care, many research studies have modeled patient pre-hospital time by ground emergency medical services (EMS) using geographic information systems (GIS). The purpose of this study was to determine if the modeling assumptions proposed through prior United States (US) studies are valid in a non-US context, and to use the resulting information to provide revised recommendations for modeling travel time using GIS in the absence of actual EMS trip data.

Methods
The study sample contained all emergency adult patient trips within the Calgary area for 2006. Each record included four components of pre-hospital time (activation, response, on-scene and transport interval). The actual activation and on-scene intervals were compared with those used in published models. The transport interval was calculated within GIS using the Network Analyst extension of Esri ArcGIS 10.0 and the response interval was derived using previously established methods. These GIS derived transport and response intervals were compared with the actual times using descriptive methods. We used the information acquired through the analysis of the EMS trip data to create an updated model that could be used to estimate travel time in the absence of actual EMS trip records.

Results
There were 29,765 complete EMS records for scene locations inside the city and 529 outside. The actual median on-scene intervals were longer than the average previously reported by 7–8 minutes. Actual EMS pre-hospital times across our study area were significantly higher than the estimated times modeled using GIS and the original travel time assumptions. Our updated model, although still underestimating the total pre-hospital time, more accurately represents the true pre-hospital time in our study area.

Conclusions
The widespread use of generalized EMS pre-hospital time assumptions based on US data may not be appropriate in a non-US context. The preference for researchers should be to use actual EMS trip records from the proposed research study area. In the absence of EMS trip data researchers should determine which modeling assumptions more accurately reflect the EMS protocols across their study area.
Increased conductance of individual self-assembled GeSi quantum dots by inter-dot coupling studied by conductive atomic force microscopy
Authors: Zhang Yifei , Ye Fengfeng , Lin Jianhui , Jiang Zuimin , Yang Xinju 
Published: October 2012

Abstract
The conductive properties of individual self-assembled GeSi quantum dots (QDs) are investigated by conductive atomic force microscopy on single-layer (SL) and bi-layer (BL) GeSi QDs with different dot densities at room temperature. By comparing their average currents, it is found that the BL and high-density QDs are more conductive than the SL and low-density QDs with similar sizes, respectively, indicating the existence of both vertical and lateral couplings between GeSi QDs at room temperature. On the other hand, the average current of the BL QDs increases much faster with the bias voltage than that of the SL QDs does. Our results suggest that the QDs’ conductive properties can be greatly regulated by the coupling effects and bias voltages, which are valuable for potential applications.
Co-circulation of two genotypes of dengue virus serotype 3 in Guangzhou, China, 2009
Authors: Jiang Tao , Yu Xue-Dong , Hong Wen-Xin , Zhou Wei-Ze , Yu Man , Deng Yong-Qiang , Zhu Shun-Ya , Qin E-De , Wang Jian , Qin Cheng-Feng , Zhang Fu-Chun 
Published: October 2012

Abstract
Dengue is emerging as the most important mosquito borne viral disease in the world. In mainland China, sporadic and large outbreaks of dengue illness caused by the four serotypes of dengue virus (DENV-1 to DENV-4) have been well documented. Guangdong province is the major affected area in China, and DENV-1 has dominantly circulated in Guangdong for a long time. In this study, a family cluster of DENV-3 infection in Guangzhou was described. Three cases were diagnosed as dengue fever based on clinical manifestation, serological and RT-PCR assays. Two DENV-3 strains were isolated in C6/36 cells and the complete genome sequences were determined. Phylogenetic analysis revealed that the new DENV-3 isolates from the family cluster were grouped within genotype III. Considering the fact that several DENV-3 strains within genotype V were also identified in Guangzhou in 2009, at least two genotypes of DENV-3 co-circulated in Guangzhou. Careful investigation and virological analysis should be warranted in the future.
NLRP1 polymorphisms in patients with asbestos-associated mesothelioma
Authors: Girardelli Martina , Maestri Iva , Rinaldi Rosa R , Tognon Mauro , Boldorini Renzo , Bovenzi Massimo , Crovella Sergio , Comar Manola 
Published: October 2012

Abstract

Background
An increasing incidence of malignant mesothelioma (MM) cases in patients with low levels of asbestos exposure suggests the interference of alternative cofactors. SV40 infection was detected, as co-morbidity factor, only in 22% of asbestos-MM patients from a North-Eastern Italy area. An additional mechanism of injury related to asbestos exposure in MM development has been recently associated to inflammatory responses, principally driven by interleukin (IL)-1 beta (ß) activated within the inflammasome complex.

NLRP3 inflammosome has been described as the intracellular sensor for asbestos able to induce inflammasome activation and IL-1ß secretion while NLRP1 is expressed in lung epithelial cells and alveolar macrophages and contributes to the immune response and to survival/apoptosis balance. This study proposes to evaluate the impact of known NLRP3 and NLRP1 polymorphisms in the individual susceptibility to asbestos-induced mesothelioma in subjects from a hyperendemic area for MM.

Methods
134 Italian patients with diagnosis of mesothelioma due (MMAE, n=69) or not (MMAF, n=65) to asbestos, 256 healthy Italian blood donors and 101 Italian healthy subjects exposed to asbestos (HCAE) were genotyped for NLRP1 (rs2670660 and rs12150220) and NLRP3 (rs35829419 and rs10754558) polymorphisms.

Results
While NLRP3 SNPs were not associated to mesothelioma, the NLRP1 rs12150220 allele T was significantly more frequent in MMAE (0.55) than in HCAE (0.41) (p=0.011; OR=1.79) suggesting a predisponent effect of this allele on the development of mesothelioma. This effect was amplified when the NLRP1 rs2670660 allele was combined with the NLRP1 rs12150220 allele (p=0.004; OR=0.52).

Conclusion
Although NLRP3 SNPs was not involved in mesothelioma predisposition, these data proposed NLRP1 as a novel factor possibly involved in the development of mesothelioma.
Cerebral venous sinus thrombosis presenting with diplopia in pregnancy: a case report
Authors: Munira Yusoff , Sakinah Zakariah , Zunaina Embong 
Published: October 2012

Abstract

Introduction
Cerebral venous sinus thrombosis is a rare condition. The most frequent symptoms and signs are headache, focal seizures with or without secondary generalization, unilateral or bilateral paresis and papilledema. We report a case of transverse sinus and superior sagittal sinus thrombosis that presented with diplopia in a pregnant woman.

Case presentation
A 34-year-old Malay woman, gravida 3 para 2 at 8 weeks of pregnancy, was admitted for hyperemesis gravidarum, presented with sudden onset of diplopia, blurring of vision and headache. A magnetic resonance scan of her brain showed the presence of cerebral edema with no space occupying lesion, but magnetic resonance venography ultimately revealed right transverse sinus and superior sagittal sinus thrombosis. The patient was treated with anticoagulation for 1 year, after which the patient recovered fully.

Conclusion
Due to its diverse and varied neurological presentation, cerebral venous sinus thrombosis should be considered in almost any brain syndrome.
Systematically characterizing and prioritizing chemosensitivity related gene based on Gene Ontology and protein interaction network
Authors: Chen Xin , Jiang Wei , Wang Qianghu , Huang Teng , Wang Peng , Li Yan , Chen Xiaowen , Lv Yingli , Li Xia 
Published: October 2012

AbstractBackgroundThe identification of genes that predict in vitro cellular chemosensitivity of cancer cells is of great importance. Chemosensitivity related genes (CRGs) have been widely utilized to guide clinical and cancer chemotherapy decisions. In addition, CRGs potentially share functional characteristics and network features in protein interaction networks (PPIN).MethodsIn this study, we proposed a method to identify CRGs based on Gene Ontology (GO) and PPIN. Firstly, we documented 150 pairs of drug-CCRG (curated chemosensitivity related gene) from 492 published papers. Secondly, we characterized CCRGs from the perspective of GO and PPIN. Thirdly, we prioritized CRGs based on CCRGs’ GO and network characteristics. Lastly, we evaluated the performance of the proposed method.ResultsWe found that CCRG enriched GO terms were most often related to chemosensitivity and exhibited higher similarity scores compared to randomly selected genes. Moreover, CCRGs played key roles in maintaining the connectivity and controlling the information flow of PPINs. We then prioritized CRGs using CCRG enriched GO terms and CCRG network characteristics in order to obtain a database of predicted drug-CRGs that included 53 CRGs, 32 of which have been reported to affect susceptibility to drugs. Our proposed method identifies a greater number of drug-CCRGs, and drug-CCRGs are much more significantly enriched in predicted drug-CRGs, compared to a method based on the correlation of gene expression and drug activity. The mean area under ROC curve (AUC) for our method is 65.2%, whereas that for the traditional method is 55.2%.ConclusionsOur method not only identifies CRGs with expression patterns strongly correlated with drug activity, but also identifies CRGs in which expression is weakly correlated with drug activity. This study provides the framework for the identification of signatures that predict in vitro cellular chemosensitivity and offers a valuable database for pharmacogenomics research.
Molecular mapping of the Pi2/9 allelic gene Pi2-2 conferring broad-spectrum resistance to Magnaporthe oryzae in the rice cultivar Jefferson
Authors: Jiang Nan , Li Zhiqiang , Wu Jun , Wang Yue , Wu Liqun , Wang Suhua , Wang Dan , Wen Ting , Liang Yi , Sun Pingyong , Liu Jinling , Dai Liangying , Wang Zhilong , Wang Chao , Luo Meizhong , Liu Xionglun , Wang Guo-Liang 
Published: October 2012

Abstract

Background
Utilization of broad-spectrum resistance (R) genes is an effective and economical strategy to control the fungal pathogen Magnaporthe oryzae, the causal agent of the rice blast disease. Among the cloned blast resistance genes, Pi9, Pi2 and Piz-t confer broad-spectrum resistance to diverse M. oryzae isolates and were isolated from the Pi2/9 locus on chromosome 6. Identification and isolation of additional R genes with different resistance spectra from this locus will provide novel genetic resources for better control of this important rice disease.

Results
In this study, we identified a dominant R gene, Pi2-2, at the Pi2/9 locus from Jefferson, an elite U.S. rice cultivar, through genetic and physical mapping. Inoculation tests showed that Jefferson has different resistant specificities to M. oryzae isolates compared rice lines with the Pi9, Pi2 and Piz-t genes. Fine mapping delimited Pi2-2 to a 270-kb interval between the markers AP5659-3 and RM19817, and this interval contains three nucleotide-binding site-leucine-rich repeat (NBS-LRR) genes in the Nipponbare genome. Five bacterial artificial chromosome (BAC) clones spanning the region were identified, and a BAC contig covering the Pi2-2 locus was constructed.

Conclusions
We identified a new allelic gene at the Pi2/9 locus and fine-mapped the gene within a 270-kb region. Our results provide essential information for the isolation of the Pi2-2 gene and tightly linked DNA markers for rice blast resistance breeding.
Metformin overdose causes platelet mitochondrial dysfunction in humans
Authors: Protti Alessandro , Lecchi Anna , Fortunato Francesco , Artoni Andrea , Greppi Noemi , Vecchio Sarah , Fagiolari Gigliola , Moggio Maurizio , Comi Giacomo Pietro , Mistraletti Giovanni , Lanticina Barbara , Faraldi Loredana , Gattinoni Luciano 
Published: October 2012

Abstract
Introduction
We have recently demonstrated that metformin intoxication causes mitochondrial dysfunction in several porcine tissues, including platelets. The aim of the present work was to clarify whether it also causes mitochondrial dysfunction (and secondary lactate overproduction) in human platelets, in vitro and ex vivo.

Methods
Human platelets were incubated for 72 hours with saline or increasing doses of metformin (in vitro experiments). Lactate production, respiratory chain complex activities (spectrophotometry), mitochondrial membrane potential (flow-cytometry after staining with JC-1) and oxygen consumption (Clark-type electrode) were then measured. Platelets were also obtained from ten patients with lactic acidosis (arterial pH 6.97 ± 0.18 and lactate 16 ± 7 mmol/L) due to accidental metformin intoxication (serum drug level 32 ± 14 mg/L) and ten healthy volunteers of similar sex and age. Respiratory chain complex activities were measured as above (ex vivo experiments).

Results
In vitro, metformin dose-dependently increased lactate production (P < 0.001), decreased respiratory chain complex I activity (P = 0.009), mitochondrial membrane potential (P = 0.003) and oxygen consumption (P < 0.001) of human platelets. Ex vivo, platelets taken from intoxicated patients had significantly lower complex I (P = 0.045) and complex IV (P < 0.001) activity compared to controls.

Conclusions
Depending on dose, metformin can cause mitochondrial dysfunction and lactate overproduction in human platelets in vitro and, possibly, in vivo.

Trial registration
NCT%2000942123.
BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions
Authors: Hansen Kasper D , Langmead Benjamin , Irizarry Rafael A 
Published: October 2012

AbstractDNA methylation is an important epigenetic modification involved in gene regulation, which can now be measured using whole-genome bisulfite sequencing. However, cost, complexity of the data, and lack of comprehensive analytical tools are major challenges that keep this technology from becoming widely applied. Here we present BSmooth, an alignment, quality control and analysis pipeline that provides accurate and precise results even with low coverage data, appropriately handling biological replicates. BSmooth is open source software, and can be downloaded from http://rafalab.jhsph.edu/bsmooth.
H2A.Z landscapes and dual modifications in pluripotent and multipotent stem cells underlie complex genome regulatory functions
Authors: Ku Manching , Jaffe Jacob D , Koche Richard P , Rheinbay Esther , Endoh Mitsuhiro , Koseki Haruhiko , Carr Steven A , Bernstein Bradley E 
Published: October 2012

Abstract
Background
The histone variant H2A.Z has been implicated in nucleosome exchange, transcriptional activation and Polycomb repression. However, the relationships among these seemingly disparate functions remain obscure.

Results
We mapped H2A.Z genome-wide in mammalian ES cells and neural progenitors. H2A.Z is deposited promiscuously at promoters and enhancers, and correlates strongly with H3K4 methylation. Accordingly, H2A.Z is present at poised promoters with bivalent chromatin and at active promoters with H3K4 methylation, but is absent from stably repressed promoters that are specifically enriched for H3K27 trimethylation. We also characterized post-translational modification states of H2A.Z, including a novel species dually-modified by ubiquitination and acetylation that is enriched at bivalent chromatin.

Conclusions
Our findings associate H2A.Z with functionally distinct genomic elements, and suggest that post-translational modifications may reconcile its contrasting locations and roles.