bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improved Plaque Assay Identifies a Novel Anti-Chlamydia Ceramide Derivative with Altered Intracellular Localization
Authors: Banhart Sebastian , Saied Essa M. , Martini Andrea , Koch Sophia , Aeberhard Lukas , Madela Kazimierz , Arenz Christoph , Heuer Dagmar 
Published: July 2014

ABSTRACT

Chlamydia trachomatis
is a medically important human pathogen causing different diseases, including trachoma, the leading cause of preventable blindness in developing countries, and sexually transmitted infections that can lead to infertility and ectopic pregnancies. There is no vaccine against
C. trachomatis
at present. Broad-spectrum antibiotics are used as standard therapy to treat the infection but have unwanted side effects, such as inducing persistent or recurring infections and affecting the host microbiome, necessitating the development of novel anti-
Chlamydia
therapies. Here, we describe the establishment of a robust, fast, and simple plaque assay using liquid overlay medium (LOM) for the identification of anti-
Chlamydia
compounds. Using the LOM plaque assay, we identified nitrobenzoxadiazole (NBD)-labeled 1-
O
-methyl-ceramide-C
16
as a compound that efficiently inhibits
C. trachomatis
replication without affecting the viability of the host cell. Further detailed analyses indicate that 1-
O
-methyl-NBD-ceramide-C
16
acts outside the inclusion. Thereby, 1-
O
-methyl-NBD-ceramide-C
16
represents a lead compound for the development of novel anti-
Chlamydia
drugs and furthermore constitutes an agent to illuminate sphingolipid trafficking pathways in
Chlamydia
infections.
Effects of Season and Host Physiological State on the Diversity, Density, and Activity of the Arctic Ground Squirrel Cecal Microbiota
Authors: Stevenson Timothy J. , Duddleston Khrystyne N. , Buck C. Loren 
Published: July 2014

ABSTRACT

We examined the seasonal changes of the cecal microbiota of captive arctic ground squirrels (
Urocitellus parryii
) by measuring microbial diversity and composition, total bacterial density and viability, and short-chain fatty acid concentrations at four sample periods (summer, torpor, interbout arousal, and posthibernation). Abundance of
Firmicutes
was lower, whereas abundances of
Bacteroidetes
,
Verrucomicrobia
, and
Proteobacteria
were higher during torpor and interbout arousal than in summer. Bacterial densities and percentages of live bacteria were significantly higher in summer than during torpor and interbout arousal. Likewise, total short-chain fatty acid concentrations were significantly greater during summer than during torpor and interbout arousal. Concentrations of individual short-chain fatty acids varied across sample periods, with butyrate concentrations higher and acetate concentrations lower during summer than at all other sample periods. Characteristics of the gut community posthibernation were more similar to those during torpor and interbout arousal than to those during summer. However, higher abundances of the genera
Bacteroides
and
Akkermansia
occurred during posthibernation than during interbout arousal and torpor. Collectively, our results clearly demonstrate that seasonal changes in physiology associated with hibernation and activity affect the gut microbial community in the arctic ground squirrel. Importantly, similarities between the gut microbiota of arctic ground squirrels and thirteen-lined ground squirrels suggest the potential for a core microbiota during hibernation.
A Novel Protein, RafX, Is Important for Common Cell Wall Polysaccharide Biosynthesis in Streptococcus pneumoniae: Implications for Bacterial Virulence
Authors: Wu Kaifeng , Huang Jian , Zhang Yanqing , Xu Wenchun , Xu Hongmei , Wang Libin , Cao Ju , Zhang Xuemei , Yin Yibing 
Published: July 2014

ABSTRACT

Teichoic acid (TA), together with peptidoglycan (PG), represents a highly complex glycopolymer that ensures cell wall integrity and has several crucial physiological activities. Through an insertion-deletion mutation strategy, we show that Δ
rafX
mutants are impaired in cell wall covalently attached TA (WTA)-PG biosynthesis, as evidenced by their abnormal banding patterns and reduced amounts of WTA in comparison with wild-type strains. Site-directed mutagenesis revealed an essential role for external loop 4 and some highly conserved amino acid residues in the function of RafX protein. The
rafX
gene was highly conserved in closely related streptococcal species, suggesting an important physiological function in the lifestyle of streptococci. Moreover, a strain D39 Δ
rafX
mutant was impaired in bacterial growth, autolysis, bacterial division, and morphology. We observed that a strain R6 Δ
rafX
mutant was reduced in adhesion relative to the wild-type R6 strain, which was supported by an inhibition assay and a reduced amount of CbpA protein on the Δ
rafX
mutant bacterial cell surface, as shown by flow cytometric analysis. Finally, Δ
rafX
mutants were significantly attenuated in virulence in a murine sepsis model. Together, these findings suggest that RafX contributes to the biosynthesis of WTA, which is essential for full pneumococcal virulence.
Functional Metabolic Map of Faecalibacterium prausnitzii, a Beneficial Human Gut Microbe
Authors: Heinken Almut , Khan M. Tanweer , Paglia Giuseppe , Rodionov Dmitry A. , Harmsen Hermie J. M. , Thiele Ines 
Published: July 2014

ABSTRACT

The human gut microbiota plays a central role in human well-being and disease. In this study, we present an integrated, iterative approach of computational modeling,
in vitro
experiments, metabolomics, and genomic analysis to accelerate the identification of metabolic capabilities for poorly characterized (anaerobic) microorganisms. We demonstrate this approach for the beneficial human gut microbe
Faecalibacterium prausnitzii
strain A2-165. We generated an automated draft reconstruction, which we curated against the limited biochemical data. This reconstruction modeling was used to develop
in silico
and
in vitro
a chemically defined medium (CDM), which was validated experimentally. Subsequent metabolomic analysis of the spent medium for growth on CDM was performed. We refined our metabolic reconstruction according to
in vitro
observed metabolite consumption and secretion and propose improvements to the current genome annotation of
F. prausnitzii
A2-165. We then used the reconstruction to systematically characterize its metabolic properties. Novel carbon source utilization capabilities and inabilities were predicted based on metabolic modeling and validated experimentally. This study resulted in a functional metabolic map of
F. prausnitzii
, which is available for further applications. The presented workflow can be readily extended to other poorly characterized and uncharacterized organisms to yield novel biochemical insights about the target organism.
Localization of Anionic Phospholipids in Escherichia coli Cells
Authors: Oliver Piercen M. , Crooks John A. , Leidl Mathias , Yoon Earl J. , Saghatelian Alan , Weibel Douglas B. 
Published: July 2014

ABSTRACT

Cardiolipin (CL) is an anionic phospholipid with a characteristically large curvature and is of growing interest for two primary reasons: (i) it binds to and regulates many peripheral membrane proteins in bacteria and mitochondria, and (ii) it is distributed asymmetrically in rod-shaped cells and is concentrated at the poles and division septum. Despite the growing number of studies of CL, its function in bacteria remains unknown. 10-
N
-Nonyl acridine orange (NAO) is widely used to image CL in bacteria and mitochondria, as its interaction with CL is reported to produce a characteristic red-shifted fluorescence emission. Using a suite of biophysical techniques, we quantitatively studied the interaction of NAO with anionic phospholipids under physiologically relevant conditions. We found that NAO is promiscuous in its binding and has photophysical properties that are largely insensitive to the structure of diverse anionic phospholipids to which it binds. Being unable to rely solely on NAO to characterize the localization of CL in
Escherichia coli
cells, we instead used quantitative fluorescence microscopy, mass spectrometry, and mutants deficient in specific classes of anionic phospholipids. We found CL and phosphatidylglycerol (PG) concentrated in the polar regions of
E. coli
cell membranes; depletion of CL by genetic approaches increased the concentration of PG at the poles. Previous studies suggested that some CL-binding proteins also have a high affinity for PG and display a pattern of cellular localization that is not influenced by depletion of CL. Framed within the context of these previous experiments, our results suggest that PG may play an essential role in bacterial physiology by maintaining the anionic character of polar membranes.
The effects of designation and volume of neonatal care on mortality and morbidity outcomes of very preterm infants in England: retrospective population-based cohort study
Authors: Watson S I , Arulampalam W , Petrou S , Marlow N , Morgan A S , Draper E S , Santhakumaran S , Modi N ,   On behalf of the Neonatal Data Analysis Unit and the NESCOP Group
Published: July 2014

ObjectiveTo examine the effects of designation and volume of neonatal care at the hospital of birth on mortality and morbidity outcomes in very preterm infants in a managed clinical network setting.DesignA retrospective, population-based analysis of operational clinical data using adjusted logistic regression and instrumental variables (IV) analyses.Setting165 National Health Service neonatal units in England contributing data to the National Neonatal Research Database at the Neonatal Data Analysis Unit and participating in the Neonatal Economic, Staffing and Clinical Outcomes Project.Participants20 554 infants born at <33 weeks completed gestation (17 995 born at 27–32 weeks; 2559 born at <27 weeks), admitted to neonatal care and either discharged or died, over the period 1 January 2009–31 December 2011.InterventionTertiary designation or high-volume neonatal care at the hospital of birth.OutcomesNeonatal mortality, any in-hospital mortality, surgery for necrotising enterocolitis, surgery for retinopathy of prematurity, bronchopulmonary dysplasia and postmenstrual age at discharge.ResultsInfants born at <33 weeks gestation and admitted to a high-volume neonatal unit at the hospital of birth were at reduced odds of neonatal mortality (IV regression odds ratio (OR) 0.70, 95% CI 0.53 to 0.92) and any in-hospital mortality (IV regression OR 0.68, 95% CI 0.54 to 0.85). The effect of volume on any in-hospital mortality was most acute among infants born at <27 weeks gestation (IV regression OR 0.51, 95% CI 0.33 to 0.79). A negative association between tertiary-level unit designation and mortality was also observed with adjusted logistic regression for infants born at <27 weeks gestation.ConclusionsHigh-volume neonatal care provided at the hospital of birth may protect against in-hospital mortality in very preterm infants. Future developments of neonatal services should promote delivery of very preterm infants at hospitals with high-volume neonatal units.
A protocol for a scoping and qualitative study to identify and evaluate indications for damage control surgery and damage control interventions in civilian trauma patients
Authors: Roberts Derek J , Zygun David A , Kirkpatrick Andrew W , Ball Chad G , Faris Peter D , Bobrovitz Niklas , Robertson Helen Lee , Stelfox H Thomas 
Published: July 2014

IntroductionInitial abbreviated surgery with planned reoperation (damage control surgery) is frequently used for major trauma patients to rapidly control haemorrhage while limiting surgical stress. Although damage control surgery may decrease mortality risk among the severely injured, it may also be associated with several complications when inappropriately applied. We seek to scope the literature on trauma damage control surgery, identify its proposed indications, map and clarify their definitions, and examine the content and evidence on which they are based. We also seek to generate a comprehensive list of unique indications to inform an appropriateness rating process.Methods and analysisWe will search 11 electronic bibliographic databases, included article bibliographies and grey literature sources for citations involving civilian trauma patients that proposed one or more indications for damage control surgery or a damage control intervention. Indications will be classified into a predefined conceptual framework and categorised and described using qualitative content analysis. Constant comparative methodology will be used to create, modify and test codes describing principal findings or injuries (eg, bilobar liver injury) and associated decision variables (eg, coagulopathy) that comprise the reported indications. After a unique list of codes have been developed, we will use the organisational system recommended by the RAND/University of California, Los Angeles (RAND-UCLA) Appropriateness Rating Method to group principal findings or injuries into chapters (subdivided by associated decision variables) according to broader clinical findings encountered during surgical practice (eg, major liver injury).Ethics and disseminationThis study will constitute the first step in a multistep research programme aimed at developing appropriate, evidence-informed indications for damage control in civilian trauma patients. With use of an integrated knowledge translation intervention that includes collaboration with surgical practice leaders, this research may allow for development of indications that are more likely to be relevant to and used by surgeons. Ethics approval is not required for this study.
Differences in Short-Term Versus Long-Term Outcomes of Older Black Versus White Patients With Myocardial Infarction
Authors: Mathews Robin , Chen Anita Y. , Thomas Laine , Wang Tracy Y. , Chin Chee Tang , Thomas Kevin L. , Roe Matthew T. , Peterson Eric D. 
Published: July 2014

Background—
Blacks are less likely than whites to receive coronary revascularization and evidence-based therapies after acute myocardial infarction, yet the impact of these differences on long-term outcomes is unknown.

Methods and Results—

We linked Can Rapid Risk Stratification of Unstable Angina Patients Suppress Adverse Outcomes With Early Implementation of American College of Cardiology/American Heart Association Guidelines (CRUSADE) registry data to national Medicare claims, creating a longitudinal record of care and outcomes among 40 500 patients with non–ST-segment–elevation myocardial infarction treated at 446 hospitals to examine mortality and readmission rates (mean follow-up, 2.4 years) among black and white patients. Relative to whites (n=37 384), blacks (n=3116) were more often younger and female; more often had diabetes mellitus and renal failure; and received less aggressive interventions, including cardiac catheterization (60.7% versus 54.0%;
P
<0.001), percutaneous coronary intervention (32.1% versus 23.8%;
P
<0.001), and coronary bypass surgery (9.2% versus 5.7%;
P
<0.001). Although blacks had lower 30-day mortality (9.1% versus 9.9%; adjusted hazard ratio, 0.80; 95% confidence interval, 0.71–0.92), they had higher observed mortality at 1 year (27.9% versus 24.5%;
P
<0.001), although this was not significant after adjustment on long-term follow-up (hazard ratio, 1.00; 95% confidence interval, 0.94–1.07). Black patients also had higher 30-day (23.6% versus 20.0%;
P
<0.001) and 1-year (62.0% versus 54.6%;
P
<0.001) all-cause readmission, but these differences were no longer significant after risk adjustment on 30-day (hazard ratio, 1.02; 95% confidence interval, 0.92–1.13) and long-term (hazard ratio, 1.05; 95% confidence interval, 1.00–1.11) follow-up.

Conclusions—
Although older blacks with an acute myocardial infarction had lower initial mortality rates than whites, this early survival advantage did not persist during long-term follow-up. The reasons for this are multifactorial but may include differences in comorbidities and postdischarge care.
Application Potential of Four Nontraditional Similarity Metrics in Hydrometeorology
Authors: Mo Ruping , Ye Chengzhi , Whitfield Paul H. 
Published: July 2014

AbstractThis paper presents a review and assessment of four nontraditional similarity metrics that can be applied to hydrological and meteorological data. These metrics are 1) the uncentered correlation coefficient, 2) the Hodgkin–Richards index, 3) the Petke index, and 4) the Wang–Bovik index. The first metric has been widely used in hydrometeorology, and the other three have been proposed in other disciplines for similarity analysis. It is demonstrated that these similarity metrics, in their original formulations, either do not actually have the purported advantage over the traditional Pearson correlation coefficient or are not suitable for some hydrometeorological applications. They are reformulated in this study to address these deficiencies. The resulting modified metrics are unitless, bounded, and proportional to the Pearson correlation coefficient, and three of them have the confirmed advantage of explicitly penalizing for differences in the mean and/or in the variance. Two application examples are used to demonstrate the applicability of these similarity metrics in hydrometeorology. A metavalidation model and a graphical tool (Taylor diagram) are used to evaluate the performances of these similarity metrics. In a case study of analog analysis, the Wang–Bovik index stands out as the best metric for simulation of the human perception of similarity between two-dimensional patterns, whereas the modified Petke index and the traditional root-mean-square distance may perform slightly better than the others in the regions with a very large difference between the variances.
Validation of Satellite Rainfall Products for Western Uganda
Authors: Diem Jeremy E. , Hartter Joel , Ryan Sadie J. , Palace Michael W. 
Published: July 2014

AbstractCentral equatorial Africa is deficient in long-term, ground-based measurements of rainfall; therefore, the aim of this study is to assess the accuracy of three high-resolution, satellite-based rainfall products in western Uganda for the 2001–10 period. The three products are African Rainfall Climatology, version 2 (ARC2); African Rainfall Estimation Algorithm, version 2 (RFE2); and 3B42 from the Tropical Rainfall Measuring Mission, version 7 (i.e., 3B42v7). Daily rainfall totals from six gauges were used to assess the accuracy of satellite-based rainfall estimates of rainfall days, daily rainfall totals, 10-day rainfall totals, monthly rainfall totals, and seasonal rainfall totals. The northern stations had a mean annual rainfall total of 1390 mm, while the southern stations had a mean annual rainfall total of 900 mm. 3B42v7 was the only product that did not underestimate boreal-summer rainfall at the northern stations, which had ~3 times as much rainfall during boreal summer than did the southern stations. The three products tended to overestimate rainfall days at all stations and were borderline satisfactory at identifying rainfall days at the northern stations; the products did not perform satisfactorily at the southern stations. At the northern stations, 3B42v7 performed satisfactorily at estimating monthly and seasonal rainfall totals, ARC2 was only satisfactory at estimating seasonal rainfall totals, and RFE2 did not perform satisfactorily at any time step. The satellite products performed worst at the two stations located in rain shadows, and 3B42v7 had substantial overestimates at those stations.
Reconstruction of perineo-scrotal defects from Fournier’s gangrene with the adipofascial anterolateral thigh flap
Authors: Onyekwelu O , Reid A , McGrouther DA 
Published: July 2014

Objective: To present a small case series of a novel solution, using pedicled adipofascial anterolateral thigh (ALT) flaps for skin grafting, for the reconstruction of perineo-scrotal defects following Fournier’s gangrene (a complex surgical problem). Many options are described. We believe that this procedure overcomes the contracture complications of skin grafting alone and that it is a more supple reconstruction in the Western population. Patients: We performed pedicled adipofascial ALT flaps on three patients, for the reconstruction of complex perineo-scrotal wounds with exposed testes, following Fournier’s gangrene. Patients were of male gender, aged 38 – 56 years old and otherwise healthy. The adipofascial ALT flap was raised based on the lateral circumflex femoral artery and was inset with split-thickness skin graft coverage. Results: Study outcomes were time-to-healing and complications. Follow-up was between 6 months to 4 years. At routine outpatient follow-up, all three patients had healed wounds; and at long-term follow-up, all three patients were satisfied with their wound reconstruction. There were no surgical complications. Conclusion: This study demonstrated that the pedicled adipofascial ALT flap is a reliable flap that is straightforward to raise, of an appropriate bulk, and has pliability for the neo-scrotum. The authors recommend this procedure as a good treatment option for reconstructing complex perineo-scrotal wounds following Fournier’s gangrene.
Greater Polar Moment of Inertia at the Tibia in Athletes Who Develop Stress Fractures
Authors: Weidauer Lee A. , Binkley Teresa , Vukovich Matt , Specker Bonny 
Published: July 2014

Background: Several previous investigations have determined potential risk factors for stress fractures in athletes and military personnel. Purpose: To determine factors associated with the development of stress fractures in female athletes. Study Design: Case-control study; Level of evidence, 3. Methods: A total of 88 female athletes (cross-country, n = 29; soccer, n = 15; swimming, n = 9; track and field, n = 14; volleyball, n = 12; and basketball, n = 9) aged 18 to 24 years were recruited to participate in a longitudinal bone study and had their left distal tibia at the 4%, 20%, and 66% sites scanned by peripheral quantitative computed tomography (pQCT). Patients included 23 athletes who developed stress fractures during the following year (cases). Whole body, hip, and spine scans were obtained using dual-energy x-ray absorptiometry (DXA). Analysis of covariance was used to determine differences in bone parameters between cases and controls after adjusting for height, lower leg length, lean mass, fat mass, and sport. Results: No differences were observed between cases and controls in any of the DXA measurements. Cases had significantly greater unadjusted trabecular bone mineral content (BMC), greater polar moment of inertia (PMI) at the 20% site, and greater cortical BMC at the 66% site; however, after adjusting for covariates, the differences became nonsignificant. When analyses were repeated using all individuals who had ever had a stress fracture as cases (n = 31) and after controlling for covariates, periosteal circumference was greater in the cases than the controls (71.1 ± 0.7 vs 69.4 ± 0.5 mm, respectively; P = .04). Conclusion: A history of stress fractures is associated with larger bones. These findings are important because larger bones were previously reported to be protective against fractures and stress fractures, but study findings indicate that may not always be true. One explanation could be that individuals who sustain stress fractures have greater loading that results in greater periosteal circumference but also results in the development of stress fractures.