bluuebunny/crossref_metadata_2025_split huggingface dataset:
Accurate identification of fastidious Gram-negative rods: integration of both conventional phenotypic methods and 16S rRNA gene analysis
Authors: de Melo Oliveira Maria G , Abels Susanne , Zbinden Reinhard , Bloemberg Guido V , Zbinden Andrea 
Published: July 2013

AbstractBackgroundAccurate identification of fastidious Gram-negative rods (GNR) by conventional phenotypic characteristics is a challenge for diagnostic microbiology. The aim of this study was to evaluate the use of molecular methods, e.g., 16S rRNA gene sequence analysis for identification of fastidious GNR in the clinical microbiology laboratory.ResultsA total of 158 clinical isolates covering 20 genera and 50 species isolated from 1993 to 2010 were analyzed by comparing biochemical and 16S rRNA gene sequence analysis based identification. 16S rRNA gene homology analysis identified 148/158 (94%) of the isolates to species level, 9/158 (5%) to genus and 1/158 (1%) to family level. Compared to 16S rRNA gene sequencing as reference method, phenotypic identification correctly identified 64/158 (40%) isolates to species level, mainlyAggregatibacter aphrophilus,Cardiobacterium hominis,Eikenella corrodens, Pasteurella multocida, and 21/158 (13%) isolates correctly to genus level, notablyCapnocytophagasp.; 73/158 (47%) of the isolates were not identified or misidentified.ConclusionsWe herein propose an efficient strategy for accurate identification of fastidious GNR in the clinical microbiology laboratory by integrating both conventional phenotypic methods and 16S rRNA gene sequence analysis. We conclude that 16S rRNA gene sequencing is an effective means for identification of fastidious GNR, which are not readily identified by conventional phenotypic methods.
Redox-sensitive DNA binding by homodimeric Methanosarcina acetivorans MsvR is modulated by cysteine residues
Authors: Isom Catherine E , Turner Jessica L , Lessner Daniel J , Karr Elizabeth A 
Published: July 2013

Abstract

Background
Methanoarchaea are among the strictest known anaerobes, yet they can survive exposure to oxygen. The mechanisms by which they sense and respond to oxidizing conditions are unknown. MsvR is a transcription regulatory protein unique to the methanoarchaea. Initially identified and characterized in the methanogen Methanothermobacter thermautotrophicus (Mth), MthMsvR displays differential DNA binding under either oxidizing or reducing conditions. Since MthMsvR regulates a potential oxidative stress operon in M. thermautotrophicus, it was hypothesized that the MsvR family of proteins were redox-sensitive transcription regulators.

Results
An MsvR homologue from the methanogen Methanosarcina acetivorans, MaMsvR, was overexpressed and purified. The two MsvR proteins bound the same DNA sequence motif found upstream of all known MsvR encoding genes, but unlike MthMsvR, MaMsvR did not bind the promoters of select genes involved in the oxidative stress response. Unlike MthMsvR that bound DNA under both non-reducing and reducing conditions, MaMsvR bound DNA only under reducing conditions. MaMsvR appeared as a dimer in gel filtration chromatography analysis and site-directed mutagenesis suggested that conserved cysteine residues within the V4R domain were involved in conformational rearrangements that impact DNA binding.

Conclusions
Results presented herein suggest that homodimeric MaMsvR acts as a transcriptional repressor by binding Ma P
msvR
under non-reducing conditions. Changing redox conditions promote conformational changes that abrogate binding to Ma P
msvR
which likely leads to de-repression.
Staphylococcus aureus colonization of healthy military service members in the United States and Afghanistan
Authors: Vento Todd J , Calvano Tatjana P , Cole David W , Mende Katrin , Rini Elizabeth A , Tully Charla C , Landrum Michael L , Zera Wendy , Guymon Charles H , Yu Xin , Beckius Miriam L , Cheatle Kristelle A , Murray Clinton K 
Published: July 2013

Abstract

Background

Staphylococcus aureus [methicillin-resistant and methicillin-susceptible (MRSA/MSSA)] is a leading cause of infections in military personnel, but there are limited data regarding baseline colonization of individuals while deployed. We conducted a pilot study to screen non-deployed and deployed healthy military service members for MRSA/MSSA colonization at various anatomic sites and assessed isolates for molecular differences.

Methods
Colonization point-prevalence of 101 military personnel in the US and 100 in Afghanistan was determined by swabbing 7 anatomic sites. US-based individuals had received no antibiotics within 30 days, and Afghanistan-deployed personnel were taking doxycycline for malaria prophylaxis. Isolates underwent identification and testing for antimicrobial resistance, virulence factors, and pulsed-field type (PFT).

Results
4 individuals in the US (4 isolates- 3 oropharynx, 1 perirectal) and 4 in Afghanistan (6 isolates- 2 oropharynx, 2 nare, 1 hand, 1 foot) were colonized with MRSA. Among US-based personnel, 3 had USA300 (1 PVL+) and 1 USA700. Among Afghanistan-based personnel, 1 had USA300 (PVL+), 1 USA800 and 2 USA1000. MSSA was present in 40 (71 isolates-25 oropharynx, 15 nare) of the US-based and 32 (65 isolates- 16 oropharynx, 24 nare) of the Afghanistan-based individuals. 56 (79%) US and 41(63%) Afghanistan-based individuals had MSSA isolates recovered from extra-nare sites. The most common MSSA PFTs were USA200 (9 isolates) in the US and USA800 (7 isolates) in Afghanistan. MRSA/MSSA isolates were susceptible to doxycycline in all but 3 personnel (1 US, 2 Afghanistan; all were MSSA isolates that carried tetM).

Conclusion
MRSA and MSSA colonization of military personnel was not associated with deployment status or doxycycline exposure. Higher S. aureus oropharynx colonization rates were observed and may warrant changes in decolonization practices.
Lack of association between Fas rs180082polymorphism and risk of cervical cancer: an update by meta-analysis
Authors: Chen Xu , Mo Wuning , Peng Qiliu , Su Xiandu 
Published: July 2013

Abstract

Background
The Fas rs180082 polymorphism has been reported to be associated with cervical cancer susceptibility, yet the results of these previous results have been inconsistent or controversial. The objective of this study was to explore whether the Fas rs180082 polymorphism confers susceptibility to cervical cancer.

Methods
The relevant studies were identified through a search of PubMed, Excerpta Medica Database (Embase), Elsevier Science Direct and Chinese Biomedical Literature Database (CBM) until July 2012. The association between the Fas rs180082 polymorphism and cervical cancer risk was assessed by odds ratios (ORs) together with their 95% confidence intervals (CIs).

Results
A total of 7 case–control studies were eventually identified. We found no association between Fas rs180082 polymorphism and cervical cancer susceptibility in overall population (G versus A: OR = 1.03, 95% CI = 0.99-1.07, P = 0.197; AG + GG versus AA: OR = 1.04, 95% CI = 0.98-1.09, P = 0.176; GG versus AA + AG: OR = 1.04, 95% CI = 0.84–1.31, P = 0.701). In subgroup analysis, similar results were found in Asian (G versus A: OR = 1.06, 95% CI = 0.97–1.15, P = 0.195; AG + GG versus AA: OR = 1.08, 95% CI = 0.98–1.19, P = 0.176; GG versus AA + AG: OR = 0.97, 95% CI = 0.51–1.84, P = 0.935) and African (G versus A: OR = 1.01, 95% CI = 0.97-1.15, P = 0.195; AG + GG versus AA: OR = 0.99, 95% CI = 0.91–1.07, P = 0.739; GG versus AA + AG: OR = 1.09, 95% CI = 0.94–1.25, P = 0.745).

Conclusion
This meta-analysis has shown that there is a lack of association of the Fas rs180082 polymorphisms with cervical cancer susceptibility. However, larger scale primary studies with the consideration of gene–gene and gene–environment interactions are still required to further evaluate the interaction of Fas rs180082 polymorphism with cervical cancer susceptibility.
Cancer history, bandemia, and serum creatinine are independent mortality predictors in patients with infection-precipitated hyperglycemic crises
Authors: Huang Chien-Cheng , Chou Willy , Lin Hung-Jung , Chen Shih-Chung , Kuo Shu-Chun , Chen Wei-Lung , Chen Jiann-Hwa , Wang Hsien-Yi , Guo How-Ran 
Published: July 2013

Abstract

Background
Infection is the most common precipitating factor and cause of death in patients with hyperglycemic crises. Treating infection-precipitated hyperglycemic crises includes using empiric antibiotics early; correcting dehydration, hyperglycemia, and electrolyte imbalances; and frequent monitoring. Intensive care unit admission, broad-spectrum antibiotics, and even novel therapy for infection may be beneficial for patients with a high risk of mortality. However, these management options are costly and not beneficial for every patient. Selecting high-risk patients who would most likely benefit is more appropriate. We investigated the independent mortality predictors of patients with infection-precipitated hyperglycemic crises to facilitate clinical decision making.

Methods
This study was conducted in a university-affiliated medical center. Consecutive adult patients (> 18 years old) visiting the Emergency Department between January 2004 and December 2010 were enrolled when they met the criteria of an infection-precipitated hyperglycemic crisis. Thirty-day mortality was the primary endpoint.

Results
One hundred forty-two patients were enrolled. The infection source did not predict mortality. The presenting variables that were independently associated with 30-day mortality in a multiple logistic regression model were cancer history (odds ratio [OR], 7.4; 95% confidence interval [CI], 2.4-23.2), bandemia (OR, 7.0; 95% CI, 1.6-30.3), and serum creatinine (OR, 1.4; 95% CI, 1.1-1.8). The common sources of infection were the lower respiratory tract (30.3%), urinary tract (49.3%), skin or soft tissue (12.0%), and intra-abdominal (6.3%).

Conclusions
Cancer history, bandemia, and serum creatinine level are three independent mortality predictors for patients with infection-precipitated hyperglycemic crises. These predictors are both readily available and valuable for physicians making decisions about risk stratification, treatment, and disposition.
Salivary pellicles on titanium and their effect on metabolic activity in Streptococcus oralis
Authors: Dorkhan Marjan , Svensäter Gunnel , Davies Julia R 
Published: July 2013

Abstract

Background
Titanium implants in the oral cavity are covered with a saliva-derived pellicle to which early colonizing microorganisms such as Streptococcus oralis can bind. The protein profiles of salivary pellicles on titanium have not been well characterized and the proteins of importance for binding are thus unknown. Biofilm bacteria exhibit different phenotypes from their planktonic counterparts and contact with salivary proteins may be one factor contributing to the induction of changes in physiology. We have characterized salivary pellicles from titanium surfaces and investigated how contact with uncoated and saliva-coated titanium surfaces affects metabolic activity in adherent cells of S. oralis.

Methods
Salivary pellicles on smooth titanium surfaces were desorbed and these, as well as purified human saliva, were subjected to two-dimensional gel electrophoresis and mass spectroscopy. A parallel plate flow-cell model was used to study binding of a fresh isolate of S. oralis to uncoated and saliva-coated titanium surfaces. Metabolic activity was assessed using the Bac Light CTC Vitality Kit and confocal scanning laser microscopy. Experiments were carried out in triplicate and the results analyzed using Student’s t-test or ANOVA.

Results
Secretory IgA, α-amylase and cystatins were identified as dominant proteins in the salivary pellicles. Selective adsorption of proteins was demonstrated by the enrichment of prolactin-inducible protein and absence of zinc-α2-glycoprotein relative to saliva. Adherence of S. oralis to titanium led to an up-regulation of metabolic activity in the population after 2 hours. In the presence of a salivary pellicle, this effect was enhanced and sustained over the following 22 hour period.

Conclusions
We have shown that adherence to smooth titanium surfaces under flow causes an up-regulation of metabolic activity in the early oral colonizer S. oralis, most likely as part of an adaptation to the biofilm mode of life. The effect was enhanced by a salivary pellicle containing sIgA, α-amylase, cystatins and prolactin-inducible protein which was, for the first time, identified as an abundant component of salivary pellicles on titanium. Further studies are needed to clarify the mechanisms underlying the effect of surface contact on metabolic activity as well as to identify the salivary proteins responsible for enhancing the effect.
A randomized controlled trial investigating the effects of PCSO-524®, a patented oil extract of the New Zealand green lipped mussel (Perna canaliculus), on the behaviour, mood, cognition and neurophysiology of children and adolescents (aged 6–14 years) experiencing clinical and sub-clinical levels of hyperactivity and inattention: study protocol ACTRN12610000978066
Authors: Kean James D , Camfield David , Sarris Jerome , Kras Marni , Silberstein Richard , Scholey Andrew , Stough Con 
Published: July 2013

Abstract

Background
The prevalence rate of attention-deficit/hyperactivity disorder (ADHD) within Western cultures is between 5% and 12%, and is the most common psychiatric illness among school-aged children, with an estimated 50% of these children retaining ADHD symptoms for the rest of their lives. Children with ADHD have lower blood levels of long-chain Poly Unsaturated Fatty Acids (LC PUFAs) compared with children without ADHD, and following PUFA supplementation, have shown improvements in ADHD-related symptoms. One highly promising marine based LC PUFA preparation is the Omega-3-rich Lyprinol/Omega XL which is a natural formulation containing standardised lipid extract of the New Zealand green lipped mussel (Perna canaliculus) known as PCSO-524® which contains a unique combination of free fatty acids, sterol esters, polar lipids and carotenoids. It is this unique combination of marine lipids that may assist in correcting the decreased levels of LC PUFA levels in children with symptoms of ADHD. The compound is a mixture belonging to a lipid group called sterol esters (SE). The fatty acids in the SE fraction are mainly myristic acid, palmitic acid, palmitoleic acid, stearic acid, oleic acid, linoleic acid, eicosapentaenoic acid (EPA), and docosahexaenoic acid (DHA). Lyprinol/Omega XL has previously been shown to contain a potent group of Omega-3 lipids that block the 5 - lipoxygenase metabolic pathway responsible for inflammation in the body.

Methods
A randomized double blind placebo controlled trial will be utilized to assess the effects of 14 weeks administration of Lyprinol/Omega XL versus placebo in 150 children aged 6 to 14 years with high levels of hyperactivity and inattention. Additionally, a range of cognitive, mood and central electrophysiological measures will be undertaken during the 14 week supplementation trial. The primary outcome measure, the Conners’ Parent Rating Scales will be completed initially at baseline, then in weeks 4, 8, 10, 14 and then again at 4 weeks post-administration (week 18). The results will contribute to our understanding of the efficacy of marine based Omega-3 s with high anti-inflammatory actions on inattention and hyperactivity in children aged 6 to 14 years.
Identification of cellular proteome using two-dimensional difference gel electrophoresis in ST cells infected with transmissible gastroenteritis coronavirus
Authors: Zhang Xin , Shi Hong-Yan , Chen Jian-Fei , Shi Da , Lang Hong-Wu , Wang Zhong-Tian , Feng Li 
Published: July 2013

AbstractBackgroundTransmissible gastroenteritis coronavirus (TGEV) is an enteropathogenic coronavirus that causes diarrhea in pigs, which is correlated with high morbidity and mortality in suckling piglets. Information remains limited about the comparative protein expression of host cells in response to TGEV infection. In this study, cellular protein response to TGEV infection in swine testes (ST) cells was analyzed, using the proteomic method of two-dimensional difference gel electrophoresis (2D DIGE) coupled with MALDI-TOF-TOF/MS identification.Results33 differentially expressed protein spots, of which 23 were up-regulated and 10 were down-regulated were identified. All the protein spots were successfully identified. The identified proteins were involved in the regulation of essential processes such as cellular structure and integrity, RNA processing, protein biosynthesis and modification, vesicle transport, signal transduction, and the mitochondrial pathway. Western blot analysis was used to validate the changes of alpha tubulin, keratin 19, and prohibitin during TGEV infection.ConclusionsTo our knowledge, we have performed the first analysis of the proteomic changes in host cell during TGEV infection. 17 altered cellular proteins that differentially expressed in TGEV infection were identified. The present study provides protein-related information that should be useful for understanding the host cell response to TGEV infection and the underlying mechanism of TGEV replication and pathogenicity.
Measurement precision of the disability for back pain scale-by applying Rasch analysis
Authors: Lu Yen-Mou , Wu Yuh-Yih , Hsieh Ching-Lin , Lin Chih-Lung , Hwang Shiuh-Lin , Cheng Kuang-I , Lue Yi-Jing 
Published: July 2013

Abstract

Background
The Oswestry Disability Index (ODI) is widely used for patients with back pain. However, few studies have examined its psychometric properties using modern measurement theory. The purpose of this study was to investigate the psychometric properties of the ODI in patients with back pain using Rasch analysis.

Methods
A total of 408 patients with back pain participated in this cross-sectional study. Patients were recruited from the orthopedic, neurosurgery, rehabilitation departments and pain clinic of two hospitals. Rasch analysis was used to examine the Chinese version of ODI 2.1 for unidimensionality, item difficulty, category function, differential item functioning, and test information.

Results
The fit statistics showed 10 items of the ODI fitted the model’s expectation as a unidimensional scale. The ODI measured the different levels of functional limitation without skewing toward the lower or higher levels of disability. No significant ceiling and floor effects and gaps among the items were found. The reliability was high and the test information curve demonstrated precise dysfunction estimation.

Conclusions
Our results showed that the ODI is a unidimensional questionnaire with high reliability. The ODI can precisely estimate the level of dysfunction, and the item difficulty of the ODI matches the person ability. For clinical application, using logits scores could precisely represent the disability level, and using the item difficulty could help clinicians design progressive programs for patients with back pain.
The characteristics of oviposition and hormonal and gene regulation of ovarian follicle development in Magang geese
Authors: Qin Qingming , Sun Aidong , Guo Rihong , Lei Mingming , Ying Shijia , Shi Zhendan 
Published: July 2013

Abstract

Background
Egg laying in Magang geese is characterized by extended interruption between clutches and lowing laying rate. Both the ovarian follicular development and ovulation characteristics, and the associated endocrine and molecular regulatory mechanisms involved are poorly understood, but could be important for guiding development of molecule aided selection of egg laying performances in geese. This study, therefore, recorded egg-laying characteristics of Magang geese, and the endocrine and molecular regulatory mechanisms of ovarian follicular development, maturation, and ovulation in Magang geese.

Methods
Oviposition, ovarian follicle development, and reproductive hormone and gene expression profiles were observed in a small flock of Magang geese.

Results
Greater than 73% of eggs were laid during the day. The average oviposition interval was 46.8 h (36–55 h). It took approximately 18 days for large white follicles to develop into mature F1 follicles; follicular growth was exponential. LHR expression levels increased from the small to the large mature follicles, but FSHR expression decreased in the granulosa and thecal layers. As the follicles matured, inhibin alpha and inhibin betaA expression increased in the granulosa layer. Activin IR, activin IIRA, activin IIRB, and beta-glycan expressions also increased as the follicles increased in size, but were more abundantly expressed in the thecal than in the granulosa layers. During the oviposition cycle, plasma concentrations of gonadal hormones decreased rapidly, whereas the level of PGFM peaked around ovulation. The profiles of activin, inhibin, follistatin, estradiol, and progesterone leading to ovulation were characterized.

Conclusions
The molecular and endocrine mechanisms that regulate follicular development in Magang geese are similar to those in chickens. Moreover, gonadotropin regulation and interaction between activin, inhibin, and follistatin secretion may govern 3-stage maturation in the final preovulatory follicles in Magang geese. The rapid rebound of post-ovulatory secretions of inhibin and follistatin may inhibit recruitment of new SYF recruitment once a sequence of eggs is started, and may limit the egg clutch size to no more than the number of LYFs present before the first sequence egg.
Analytic Nakagami fading parameter estimation in dependent noise channel using copula
Authors: Gholizadeh Mohammad Hossein , Amindavar Hamidreza , Ritcey James A 
Published: July 2013

Abstract
In this paper, the probability density function (PDF) estimation is introduced in the framework of estimating the Nakagami fading parameter. This approach provides an analytic procedure for finding the fading parameter. Using the copula theory, an accurate PDF estimate is obtained even when the desired signal is corrupted in a noisy environment. In the real world, the noise samples could be highly dependent on the main signal. Copula-based models are a general set of statistical models defined for any multivariate random variable. Thus, they depict the statistical behavior of a received signal including two dependent terms, representative of the desired signal and noise. Previous works in the Nakagami parameter determination have mainly examined estimation based on either a noiseless sample model or an independent trivial noisy one. In this paper, we consider a more comprehensive situation about the noise destruction and our investigation is done in low signal-to-noise ratios. The parametric bootstrap method approves the accuracy of the analytically estimated PDF, and simulation results show that the new estimator has superior performance over conventional estimators.
Development of prophylactic vaccines against HIV-1
Authors: Schiffner Torben , Sattentau Quentin J , Dorrell Lucy 
Published: July 2013

AbstractThe focus of most current HIV-1 vaccine development is on antibody-based approaches. This is because certain antibody responses correlated with protection from HIV-1 acquisition in the RV144 phase III trial, and because a series of potent and broad spectrum neutralizing antibodies have been isolated from infected individuals. Taken together, these two findings suggest ways forward to develop a neutralizing antibody-based vaccine. However, understanding of the correlates of protection from disease in HIV-1 and other infections strongly suggests that we should not ignore CTL-based research. Here we review recent progress in the field and highlight the challenges implicit in HIV-1 vaccine design and some potential solutions.