bluuebunny/crossref_metadata_2025_split huggingface dataset:
The influence and changes in the dosages of concomitantly used psychotropic drugs associated with the discontinuation of donepezil in severe Alzheimer’s disease with behavioral and psychological symptoms on dementia: a preliminary open-label trial
Authors: Suzuki Hidenobu , Inoue Yuichi , Mikami Katsunaka , Gen Keishi 
Published: October 2013

Objective: We investigated the influence on behavioral and psychological symptoms on dementia (BPSD) and the changes in the dosages of concomitant psychotropic drugs associated with the discontinuation of donepezil in patients with severe Alzheimer’s disease (AD) who developed BPSD during donepezil therapy. Methods: The subjects were 44 inpatients who had been diagnosed with AD according to the Diagnostic and Statistical Manual of Mental Disorders IV (DSM-IV). The outcome measures assessed were BPSD and cognitive function. BPSD was assessed using the Neuropsychiatric Inventory (NPI) and cognitive function was assessed using the Mini Mental Examination (MMSE). The changes in the dosages of concomitant psychotropic drugs were also assessed. Results: Significant decreases were found in the donepezil treatment discontinuation group in the following NPI total score and two NPI subscales (agitation and irritability), but no significant differences were seen between the donepezil treatment discontinuation group and the control group. Furthermore, the mean changes from baseline in the risperidone equivalent dose and the diazepam equivalent dose were hardly changed in the donepezil treatment discontinuation group. Conclusion: The results of this study suggest that the discontinuation of donepezil treatment in patients with AD with BPSD may afford superior efficacy and may make it possible to not increase the dosage of other psychotropic drugs.
Impact of allele-level HLA matching on outcomes after myeloablative single unit umbilical cord blood transplantation for hematologic malignancy
Authors: Eapen Mary , Klein John P. , Ruggeri Annalisa , Spellman Stephen , Lee Stephanie J. , Anasetti Claudio , Arcese William , Barker Juliet N. , Baxter-Lowe Lee Ann , Brown Maria , Fernandez-Vina Marcelo A. , Freeman John , He Wensheng , Iori Anna Paola , Horowitz Mary M. , Locatelli Franco , Marino Susana , Maiers Martin , Michel Gerard , Sanz Guillermo F. , Gluckman Eliane , Rocha Vanderson 
Published: October 2013

Key PointsEfficacy of transplanting allele-level HLA-matched cord blood units.
Clinical and laboratory predictive markers for acute dengue infection
Authors: Ho Tzong-Shiann , Wang Shih-Min , Lin Yee-Shin , Liu Ching-Chuan 
Published: October 2013

Abstract

Background
Early diagnosis of dengue virus infection during the febrile stage is essential for adjusting appropriate management. This study is to identify the predictive markers of clinical and laboratory findings in the acute stage of dengue infection during a major outbreak of dengue virus type 1 that occurred in southern Taiwan during 2007. A retrospective, hospital-based study was conducted at a university hospital in southern Taiwan from January to December, 2007. Patient who was reported for clinically suspected dengue infection was enrolled. Laboratory-positive dengue cases are confirmed by enzyme-linked immunosorbent assay of specific dengue IgM, fourfold increase of dengue-specific IgG titers in convalescent serum, or by reverse transcription-polymerase chain reaction (RT-PCR) of dengue virus.

Results
The suspected dengue cases consist of 100 children (≤ 18 years) and 481 adults. Among the 581 patients, 67 (67%) children and 309 (64.2%) adults were laboratory-confirmed. Patients who had laboratory indeterminate were excluded. Most cases were uncomplicated and 3.8% of children and 2.9% of adults developed dengue hemorrhagic fever or dengue shock syndrome (DHF/DSS). The overall mortality rate in those with DHF/DSS was 7.1%, and the average duration of hospitalization was 20 days. The most common symptoms/signs at admission were myalgia (46.8%), petechiae (36.9%) and nausea/vomiting (33.5%). The most notable laboratory findings included leukopenia (2966 ± 1896/cmm), thrombocytopenia (102 ± 45 × 103/cmm), prolonged activated partial thromboplastin time (aPTT) (45 ± 10 s), and elevated serum levels of aminotransferase (AST, 166 ± 208 U/L; ALT, 82 ± 103 U/L) and low C - reactive protein (CRP) (6 ± 11 mg/L). Based on the clinical features for predicting laboratory-confirmed dengue infection, the sensitivities of typical rash, myalgia, and positive tourniquet test are 59.2%, 46.8%, and 34.2%, while the specificities for above features are 75.4%, 53.5% and 100%, respectively. The positive predictive value (PPV) for combination of leukopenia, thrombocytopenia (< 150 × 103/cmm), elevated aminotransferase (AST/ALT > 1.5) and low CRP (< 20 mg/L) is 89.5%, while the negative predictive value is 37.4%. Furthermore, the PPV of the combination was increased to 93.1% by adding prolonged aPTT (>38 secs).

Conclusions
Leukopenia, thrombocytopenia, elevated aminotransferases, low CRP and prolonged aPTT, were useful predictive markers for early diagnosis of dengue infection during a large outbreak in southern Taiwan.
A new model for the biodegradation kinetics of oil droplets: application to the Deepwater Horizon oil spill in the Gulf of Mexico
Authors: Vilcáez Javier , Li Li , Hubbard Susan S 
Published: October 2013

Abstract
Oil biodegradation by native bacteria is one of the most important natural processes that can attenuate the environmental impacts of marine oil spills. Existing models for oil biodegradation kinetics are mostly for dissolved oil. This work developed a new mathematical model for the biodegradation of oil droplets and applied the model to estimate the time scale for oil biodegradation under conditions relevant to the Deepwater Horizon oil spill in the Gulf of Mexico. In the model, oil is composed of droplets of various sizes following the gamma function distribution. Each oil droplet shrinks during the microbe-mediated degradation at the oil-water interface. Using our developed model, we find that the degradation of oil droplets typically goes through two stages. The first stage is characterized by microbial activity unlimited by oil-water interface with higher biodegradation rates than that of the dissolved oil. The second stage is governed by the availability of the oil-water interface, which results in much slower rates than that of soluble oil. As a result, compared to that of the dissolved oil, the degradation of oil droplets typically starts faster and then quickly slows down, ultimately reaching a smaller percentage of degraded oil in longer time. The availability of the water-oil interface plays a key role in determining the rates and extent of degradation. We find that several parameters control biodegradation rates, including size distribution of oil droplets, initial microbial concentrations, initial oil concentration and composition. Under conditions relevant to the Deepwater Horizon spill, we find that the size distribution of oil droplets (mean and coefficient of variance) is the most important parameter because it determines the availability of the oil-water interface. Smaller oil droplets with larger variance leads to faster and larger extent of degradation. The developed model will be useful for evaluating transport and fate of spilled oil, different remediation strategies, and risk assessment.
Comprehensive discovery and characterization of small RNAs in Corynebacterium glutamicumATCC 13032
Authors: Mentz Almut , Neshat Armin , Pfeifer-Sancar Katharina , Pühler Alfred , Rückert Christian , Kalinowski Jörn 
Published: October 2013

Abstract

Background
Recent discoveries on bacterial transcriptomes gave evidence that small RNAs (sRNAs) have important regulatory roles in prokaryotic cells. Modern high-throughput sequencing approaches (RNA-Seq) enable the most detailed view on transcriptomes offering an unmatched comprehensiveness and single-base resolution. Whole transcriptome data obtained by RNA-Seq can be used to detect and characterize all transcript species, including small RNAs. Here, we describe an RNA-Seq approach for comprehensive detection and characterization of small RNAs from Corynebacterium glutamicum, an actinobacterium of high industrial relevance and model organism for medically important Corynebacterianeae, such as C. diphtheriae and Mycobacterium tuberculosis.

Results
In our RNA-Seq approach, total RNA from C. glutamicum ATCC 13032 was prepared from cultures grown in minimal medium at exponential growth or challenged by physical (heat shock, cold shock) or by chemical stresses (diamide, H2O2, NaCl) at this time point. Total RNA samples were pooled and sequencing libraries were prepared from the isolated small RNA fraction. High throughput short read sequencing and mapping yielded over 800 sRNA genes. By determining their 5′- and 3′-ends and inspection of their locations, these potential sRNA genes were classified into UTRs of mRNAs (316), cis-antisense sRNAs (543), and trans-encoded sRNAs (262). For 77 of trans-encoded sRNAs significant sequence and secondary structure conservation was found by a computational approach using a whole genome alignment with the closely related species C. efficiens YS-314 and C. diphtheriae NCTC 13129. Three selected trans-encoded sRNAs were characterized by Northern blot analysis and stress-specific transcript patterns were found.

Conclusions
The study showed comparable numbers of sRNAs known from genome-wide surveys in other bacteria. In detail, our results give deep insight into the comprehensive equipment of sRNAs in C. glutamicum and provide a sound basis for further studies concerning the functions of these sRNAs.
Global regulatory architecture of human, mouse and rat tissue transcriptomes
Authors: Prasad Ajay , Kumar Suchitra Suresh , Dessimoz Christophe , Bleuler Stefan , Laule Oliver , Hruz Tomas , Gruissem Wilhelm , Zimmermann Philip 
Published: October 2013

Abstract

Background
Predicting molecular responses in human by extrapolating results from model organisms requires a precise understanding of the architecture and regulation of biological mechanisms across species.

Results
Here, we present a large-scale comparative analysis of organ and tissue transcriptomes involving the three mammalian species human, mouse and rat. To this end, we created a unique, highly standardized compendium of tissue expression. Representative tissue specific datasets were aggregated from more than 33,900 Affymetrix expression microarrays. For each organism, we created two expression datasets covering over 55 distinct tissue types with curated data from two independent microarray platforms. Principal component analysis (PCA) revealed that the tissue-specific architecture of transcriptomes is highly conserved between human, mouse and rat. Moreover, tissues with related biological function clustered tightly together, even if the underlying data originated from different labs and experimental settings. Overall, the expression variance caused by tissue type was approximately 10 times higher than the variance caused by perturbations or diseases, except for a subset of cancers and chemicals. Pairs of gene orthologs exhibited higher expression correlation between mouse and rat than with human. Finally, we show evidence that tissue expression profiles, if combined with sequence similarity, can improve the correct assignment of functionally related homologs across species.

Conclusion
The results demonstrate that tissue-specific regulation is the main determinant of transcriptome composition and is highly conserved across mammalian species.
Genomic diversity and adaptation of Salmonella enterica serovar Typhimurium from analysis of six genomes of different phage types
Authors: Pang Stanley , Octavia Sophie , Feng Lu , Liu Bin , Reeves Peter R , Lan Ruiting , Wang Lei 
Published: October 2013

Abstract

Background

Salmonella enterica serovar Typhimurium (or simply Typhimurium) is the most common serovar in both human infections and farm animals in Australia and many other countries. Typhimurium is a broad host range serovar but has also evolved into host-adapted variants (i.e. isolated from a particular host such as pigeons). Six Typhimurium strains of different phage types (defined by patterns of susceptibility to lysis by a set of bacteriophages) were analysed using Illumina high-throughput genome sequencing.

Results
Variations between strains were mainly due to single nucleotide polymorphisms (SNPs) with an average of 611 SNPs per strain, ranging from 391 SNPs to 922 SNPs. There were seven insertions/deletions (indels) involving whole or partial gene deletions, four inactivation events due to IS200 insertion and 15 pseudogenes due to early termination. Four of these inactivated or deleted genes may be virulence related. Nine prophage or prophage remnants were identified in the six strains. Gifsy-1, Gifsy-2 and the sopE2 and sspH2 phage remnants were present in all six genomes while Fels-1, Fels-2, ST64B, ST104 and CP4-57 were variably present. Four strains carried the 90-kb plasmid pSLT which contains several known virulence genes. However, two strains were found to lack the plasmid. In addition, one strain had a novel plasmid similar to Typhi strain CT18 plasmid pHCM2.

Conclusion
The genome data suggest that variations between strains were mainly due to accumulation of SNPs, some of which resulted in gene inactivation. Unique genetic elements that were common between host-adapted phage types were not found. This study advanced our understanding on the evolution and adaptation of Typhimurium at genomic level.
Accurate measurement of gene copy number for human alpha-defensin DEFA1A3
Authors: Khan Fayeza F , Carpenter Danielle , Mitchell Laura , Mansouri Omniah , Black Holly A , Tyson Jess , Armour John AL 
Published: October 2013

Abstract

Background
Multi-allelic copy number variants include examples of extensive variation between individuals in the copy number of important genes, most notably genes involved in immune function. The definition of this variation, and analysis of its impact on function, has been hampered by the technical difficulty of large-scale but accurate typing of genomic copy number. The copy-variable alpha-defensin locus DEFA1A3 on human chromosome 8 commonly varies between 4 and 10 copies per diploid genome, and presents considerable challenges for accurate high-throughput typing.

Results
In this study, we developed two paralogue ratio tests and three allelic ratio measurements that, in combination, provide an accurate and scalable method for measurement of DEFA1A3 gene number. We combined information from different measurements in a maximum-likelihood framework which suggests that most samples can be assigned to an integer copy number with high confidence, and applied it to typing 589 unrelated European DNA samples. Typing the members of three-generation pedigrees provided further reassurance that correct integer copy numbers had been assigned. Our results have allowed us to discover that the SNP rs4300027 is strongly associated with DEFA1A3 gene copy number in European samples.

Conclusions
We have developed an accurate and robust method for measurement of DEFA1A3 copy number. Interrogation of rs4300027 and associated SNPs in Genome-Wide Association Study SNP data provides no evidence that alpha-defensin copy number is a strong risk factor for phenotypes such as Crohn’s disease, type I diabetes, HIV progression and multiple sclerosis.
Surveillance of ischemic heart disease should include physician billing claims: population-based evidence from administrative health data across seven Canadian provinces
Authors: Robitaille Cynthia , Bancej Christina , Dai Sulan , Tu Karen , Rasali Drona , Blais Claudia , Plante Céline , Smith Mark , Svenson Lawrence W , Reimer Kim , Casey Jill , Puchtinger Rolf , Johansen Helen , Gurevich Yana , Waters Chris , Lix Lisa M , Quan Hude 
Published: October 2013

Abstract

Background
Canadian provinces and territories routinely collect health information for administrative purposes. This study used Canadian medical and hospital administrative data for population-based surveillance of diagnosed ischemic heart disease (IHD).

Methods
Hospital discharge abstracts and physician billing claims data from seven provinces were analyzed to estimate prevalence and incidence of IHD using three validated algorithms: a) one hospital discharge abstract with an IHD diagnosis or procedure code (1H); b) 1H or at least three physician claims within a one-year period (1H3P) and c) 1H or at least two physician claims within a one-year period (1H2P). Crude and age-standardized prevalence and incidence rates were calculated for Canadian adults aged 20 +.

Results
IHD prevalence and incidence varied by province, were consistently higher among males than females, and increased with age. Prevalence and incidence were lower using the 1H method compared to using the 1H2P or 1H3P methods in all provinces studied for all age groups. For instance, in 2006/07, crude prevalence by province ranged from 3.4%-5.5% (1H), from 4.9%-7.7% (1H3P) and from 6.0%-9.2% (1H2P). Similarly, crude incidence by province ranged from 3.7-5.9 per 1,000 (1H), from 5.0-6.9 per 1,000 (1H3P) and from 6.1-7.9 per 1,000 (1H2P).

Conclusions
Study findings show that incidence and prevalence of diagnosed IHD will be underestimated by as much as 50% using inpatient data alone. The addition of physician claims data are needed to better assess the burden of IHD in Canada.
The protective effect of VSL#3 on intestinal permeability in a rat model of alcoholic intestinal injury
Authors: Chang Bing , Sang Lixuan , wang Ying , Tong Jing , Zhang Dai , Wang Bingyuan 
Published: October 2013

Abstract

Background
This study aimed to investigate the mechanism of the probiotic VSL#3 in acute alcoholic intestinal injury, and evaluate the effect of VSL#3, glutamine,VSL#3+glutamine and heat-killed VSL#3 therapy in a rat model.

Methods
Six- to eight-week-old male wild-type rats were divided into seven groups. To establish the acute alcohol liver disease model, rats received three doses of corn starch dissolved in PBS/40% alcohol administered intra-gastrically every 12 hours. Treatment groups received an intra-gastric dose of VSL#3, Glutamine, heat-killed VSL#3, or VSL#3+Glutamine 30 minutes prior to alcohol administration. The placebo group was treated with PBS prior to alcohol administration. TNFα and endotoxin in plasma was measured by ELISA and Tachypleus Ameboctye Lysate assays, and electron microscopy, Western blotting, and reverse transcription polymerase chain reaction were used to identify the mechanisms of VSL#3 in the regulation of epithelial permeability.

Results
First, compared with control group, endotoxin and TNFα in alcohol group was obviously high. At the same time, in VSL#3 group,the expression of endotoxin and TNFα obviously lower than the alcohol group. And the trends of the expression of tight junction proteins in these groups were reversed with the change of endotoxin and TNFα. Second, compared the groups of VSL#3 with glutamine,VSL#3+glutamine and heat-killed VSL#3,we found that both VSL#3 and heat-killed VSL#3, glutamine were as effective as VSL#3+glutamine in the treatment of acute alcohol liver disease, the expression of endotoxin and TNFα were lower than the alcohol group, and tight junction proteins were higher than the alcohol group whereas the expression of tight junction proteins were higher in VSL#3 + glutamine group than either agent alone, but have no significant difference.

Conclusion
We conclude that VSL#3 treatment can regulate the ecological balance of the gut microflora, preventing passage of endotoxin and other bacterial products from the gut lumen into the portal circulation and down-regulating the expression of TNFα, which could otherwise down-regulate the expression of tight junction proteins and increase epithelial permeability.
Time to blood culture positivity as a predictor of clinical outcome in patients with Candida albicansbloodstream infection
Authors: Nunes Cintia Zoya , Marra Alexandre R , Edmond Michael B , da Silva Victor Elivane , Pereira Carlos Alberto Pires 
Published: October 2013

Abstract

Background
Few studies have assessed the time to blood culture positivity as a predictor of clinical outcome in fungal bloodstream infections (BSIs). The purpose of this study was to evaluate the time to positivity (TTP) of blood cultures in patients with Candida albicans BSIs and to assess its impact on clinical outcome.

Methods
A historical cohort study with 89 adults patients with C. albicans BSIs. TTP was defined as the time between the start of incubation and the time that the automated alert signal indicating growth in the culture bottle sounded.

Results
Patients with BSIs and TTPs of culture of ≤36 h (n=39) and >36 h (n=50) were compared. Septic shock occurred in 46.2% of patients with TTPs of ≤36 h and in 40.0% of patients with TTP of >36 h (p=0.56). A central venous catheter source was more common with a BSI TTP of ≤36 h (p=0.04). Univariate analyis revealed that APACHE II score≥20 at BSI onset, the development of at least one organ system failure (respiratory, cardiovascular, renal, hematologic, or hepatic), SOFA at BSI onset, SAPS II at BSI onset, and time to positivity were associated with death. By using logistic regression analysis, the only independent predictor of death was time to positivity (1.04; 95% CI, 1.0-1.1, p=0.035), with the chance of the patient with C. albicans BSI dying increasing 4.0% every hour prior to culture positivity.

Conclusion
A longer time to positivity was associated with a higher mortality for Candida albicans BSIs; therefore, initiating empiric treatment with antifungals may improve outcomes.
Computer-assisted counting of retinal cells by automatic segmentation after TV denoising
Authors: Bredies Kristian , Wagner Marcus , Schubert Christian , Ahnelt Peter 
Published: October 2013

Abstract

Background
Quantitative evaluation of mosaics of photoreceptors and neurons is essential in studies on development, aging and degeneration of the retina. Manual counting of samples is a time consuming procedure while attempts to automatization are subject to various restrictions from biological and preparation variability leading to both over- and underestimation of cell numbers. Here we present an adaptive algorithm to overcome many of these problems.
Digital micrographs were obtained from cone photoreceptor mosaics visualized by anti-opsin immuno-cytochemistry in retinal wholemounts from a variety of mammalian species including primates. Segmentation of photoreceptors (from background, debris, blood vessels, other cell types) was performed by a procedure based on Rudin-Osher-Fatemi total variation (TV) denoising. Once 3 parameters are manually adjusted based on a sample, similarly structured images can be batch processed. The module is implemented in MATLAB and fully documented online.

Results
The object recognition procedure was tested on samples with a typical range of signal and background variations. We obtained results with error ratios of less than 10% in 16 of 18 samples and a mean error of less than 6% compared to manual counts.

Conclusions
The presented method provides a traceable module for automated acquisition of retinal cell density data. Remaining errors, including addition of background items, splitting or merging of objects might be further reduced by introduction of additional parameters. The module may be integrated into extended environments with features such as 3D-acquisition and recognition.