bluuebunny/crossref_metadata_2025_split huggingface dataset:
Intestinal Dysbiosis and Depletion of Butyrogenic Bacteria in Clostridium difficile Infection and Nosocomial Diarrhea
Authors: Antharam Vijay C. , Li Eric C. , Ishmael Arif , Sharma Anuj , Mai Volker , Rand Kenneth H. , Wang Gary P. 
Published: June 2013

ABSTRACT

Clostridium difficile
infection (CDI) causes nearly half a million cases of diarrhea and colitis in the United States each year. Although the importance of the gut microbiota in
C. difficile
pathogenesis is well recognized, components of the human gut flora critical for colonization resistance are not known. Culture-independent high-density Roche 454 pyrosequencing was used to survey the distal gut microbiota for 39 individuals with CDI, 36 subjects with
C. difficile
-negative nosocomial diarrhea (CDN), and 40 healthy control subjects. A total of 526,071 partial 16S rRNA sequence reads of the V1 to V3 regions were aligned with 16S databases, identifying 3,531 bacterial phylotypes from 115 fecal samples. Genomic analysis revealed significant alterations of organism lineages in both the CDI and CDN groups, which were accompanied by marked decreases in microbial diversity and species richness driven primarily by a paucity of phylotypes within the
Firmicutes
phylum. Normally abundant gut commensal organisms, including the
Ruminococcaceae
and
Lachnospiraceae
families and butyrate-producing C2 to C4 anaerobic fermenters, were significantly depleted in the CDI and CDN groups. These data demonstrate associations between the depletion of
Ruminococcaceae
,
Lachnospiraceae
, and butyrogenic bacteria in the gut microbiota and nosocomial diarrhea, including
C. difficile
infection. Mechanistic studies focusing on the functional roles of these organisms in diarrheal diseases and resistance against
C. difficile
colonization are warranted.
PCR for Detection of Herpes Simplex Virus in Cerebrospinal Fluid: Alternative Acceptance Criteria for Diagnostic Workup
Authors: López Roa Paula , Alonso Roberto , de Egea Viviana , Usubillaga Rafael , Muñoz Patricia , Bouza Emilio 
Published: June 2013

ABSTRACT

The determination of herpes simplex virus (HSV) infection using a PCR assay is one of the most commonly requested tests for analysis of cerebrospinal fluid (CSF), although only a very low proportion of results are positive. A previously reported study showed that selecting only those CSF samples with >5 leukocytes/mm
3
or a protein level of >50 mg/dl was adequate for the diagnostic workup. The aim of the present study was to assess the reliability of alternative acceptance criteria based on elevated CSF white blood cell counts (>10 cells/mm
3
). We analyzed all requests for HSV PCR received between January 2008 and December 2011. CSF samples were accepted for analysis if they had >10 cells/mm
3
or if the sample was from an immunocompromised patient or a child aged <2 years. In order to evaluate our selection criteria, we identified those CSF samples with a leukocyte count of 5 to 10 cells/mm
3
or protein levels of >50 mg/dl in order to test them for HSV type 1 and 2 (HSV-1 and HSV-2) DNA. During the study period, 466 CSF samples were submitted to the microbiology laboratory for HSV PCR. Of these, 268 (57.5%) were rejected, and 198 (42.5%) were tested according to our routine criteria. Of the tested samples, 11 (5.5%) were positive for HSV DNA (7 for HSV-1 and 4 for HSV-2). Of the 268 rejected specimens, 74 met the criteria of >5 cells/mm
3
and/or protein levels of >50 mg/dl. Of these, 70 (94.6%) were available for analysis. None of the samples yielded a positive HSV PCR result. Acceptance criteria based on CSF leukocyte counts, host immune status, and age can help to streamline the application of HSV PCR without reducing sensitivity.
Multiplex 5′ Nuclease Quantitative Real-Time PCR for Clinical Diagnosis of Malaria and Species-Level Identification and Epidemiologic Evaluation of Malaria-Causing Parasites, Including Plasmodium knowlesi
Authors: Reller Megan E. , Chen Wan Hsin , Dalton Justin , Lichay Marguerite A. , Dumler J. Stephen 
Published: June 2013

ABSTRACT

Molecular diagnosis of malaria offers many potential advantages over microscopy, including identification of malaria to the species level in an era with few experienced microscopists. We developed high-throughput multiplex 5′ nuclease quantitative PCR (qPCR) assays, with the potential to support large studies, to specifically identify
Plasmodium falciparum
,
P. vivax
,
P. ovale
,
P. malariae
, and
P. knowlesi
. We compared qPCR to microscopy and confirmed discordant results with an alternative target PCR assay. The assays specifically detected 1 to 6 parasites/μl of blood. The clinical sensitivities (95% confidence intervals [CIs]) of the 4-plex assay to detect microscopically confirmed malaria were 95.8% (88.3 to 99.1%) for
P. falciparum
, 89.5% (75.2 to 97.1%) for
P. vivax
, 94.1% (71.3 to 99.9%) for
P. ovale
, and 100% (66.4 to 100%) for
P. malariae
. The specificities (95% CIs) were 98.6% (92.4 to 100%) for
P. falciparum
, 99% (84.8 to 100%) for
P. vivax
, 98.4% (94.4 to 99.8%) for
P. ovale
, and 99.3% (95.9 to 100%) for
P. malariae
. The clinical specificity for samples without malaria was 100%. The clinical sensitivity of the 5-plex assay for confirmed
P. knowlesi
malaria was 100% (95% CI, 69.2 to 100%), and the clinical specificity was 100% (95% CI, 87.2 to 100%). Coded retesting and testing with an alternative target PCR assay showed improved sensitivity and specificity of multiplex qPCR versus microscopy. Additionally, 91.7% (11/12) of the samples with uncertain species by microscopy were identified to the species level identically by both our multiplex qPCR assay and the alternative target PCR assay, including 9
P. falciparum
infections. Multiplex qPCR can rapidly and simultaneously identify all 5
Plasmodium
species known to cause malaria in humans, and it offers an alternative or adjunct to microscopy for clinical diagnosis as well as a needed high-throughput tool for research.
Blind Evaluation of the Microwave-Accelerated Metal-Enhanced Fluorescence Ultrarapid and Sensitive Chlamydia trachomatis Test by Use of Clinical Samples
Authors: Melendez Johan H. , Huppert Jill S. , Jett-Goheen Mary , Hesse Elizabeth A. , Quinn Nicole , Gaydos Charlotte A. , Geddes Chris D. 
Published: June 2013

ABSTRACT

Accurate point-of-care (POC) diagnostic tests for
Chlamydia trachomatis
infection are urgently needed for the rapid treatment of patients. In a blind comparative study, we evaluated microwave-accelerated metal-enhanced fluorescence (MAMEF) assays for ultrafast and sensitive detection of
C. trachomatis
DNA from vaginal swabs. The results of two distinct MAMEF assays were compared to those of nucleic acid amplification tests (NAATs). The first assay targeted the
C. trachomatis
16S rRNA gene, and the second assay targeted the
C. trachomatis
cryptic plasmid. Using pure
C. trachomatis
, the MAMEF assays detected as few as 10 inclusion-forming units/ml of
C. trachomatis
in less than 9 min, including DNA extraction and detection. A total of 257 dry vaginal swabs from 245 female adolescents aged 14 to 22 years were analyzed. Swabs were eluted with water, the solutions were lysed to release and to fragment genomic DNA, and MAMEF-based DNA detection was performed. The prevalence of
C. trachomatis
by NAATs was 17.5%. Of the 45 samples that were
C. trachomatis
positive and the 212 samples that were
C. trachomatis
negative by NAATs, 33/45 and 197/212 were correctly identified by the MAMEF assays if both assays were required to be positive (sensitivity, 73.3%; specificity, 92.9%). Using the plasmid-based assay alone, 37/45
C. trachomatis
-positive and 197/212
C. trachomatis
-negative samples were detected (sensitivity, 82.2%; specificity, 92.9%). Using the 16S rRNA assay alone, 34/45
C. trachomatis
-positive and 197/212
C. trachomatis
-negative samples were detected (sensitivity, 75.5%; specificity, 92.9%). The overall rates of agreement with NAAT results for the individual 16S rRNA and cryptic plasmid assays were 89.5% and 91.0%, respectively. Given the sensitivity, specificity, and rapid detection of the plasmid-based assay, the plasmid-based MAMEF assay appears to be suited for clinical POC testing.
Glycoproteins gE and gI Are Required for Efficient KIF1A-Dependent Anterograde Axonal Transport of Alphaherpesvirus Particles in Neurons
Authors: Kratchmarov Radomir , Kramer Tal , Greco Todd M. , Taylor Matthew P. , Ch'ng Toh Hean , Cristea Ileana M. , Enquist Lynn W. 
Published: June 2013

ABSTRACT
Alphaherpesviruses, including pseudorabies virus (PRV), spread directionally within the nervous systems of their mammalian hosts. Three viral membrane proteins are required for efficient anterograde-directed spread of infection in neurons, including Us9 and a heterodimer composed of the glycoproteins gE and gI. We previously demonstrated that the kinesin-3 motor KIF1A mediates anterograde-directed transport of viral particles in axons of cultured peripheral nervous system (PNS) neurons. The PRV Us9 protein copurifies with KIF1A, recruiting the motor to transport vesicles, but at least one unidentified additional viral protein is necessary for this interaction. Here we show that gE/gI are required for efficient anterograde transport of viral particles in axons by mediating the interaction between Us9 and KIF1A. In the absence of gE/gI, viral particles containing green fluorescent protein (GFP)-tagged Us9 are assembled in the cell body but are not sorted efficiently into axons. Importantly, we found that gE/gI are necessary for efficient copurification of KIF1A with Us9, especially at early times after infection. We also constructed a PRV recombinant that expresses a functional gE-GFP fusion protein and used affinity purification coupled with mass spectrometry to identify gE-interacting proteins. Several viral and host proteins were found to associate with gE-GFP. Importantly, both gI and Us9, but not KIF1A, copurified with gE-GFP. We propose that gE/gI are required for efficient KIF1A-mediated anterograde transport of viral particles because they indirectly facilitate or stabilize the interaction between Us9 and KIF1A.
Quantifying fracture density and connectivity of fractured chalk reservoirs from core samples: implications for fluid flow
Authors: Sagi D. A. , Arnhild M. , Karlo J. F. 
Published: June 2013

Abstract
Fractured carbonate reservoirs, characterized by high structural porosity/permeability, are of great economic importance because in such systems a single well can access large volumes of easily migrating hydrocarbons. Therefore, the accurate quantification of fracture density and connectivity values within a reservoir can be an important input for reservoir models and field development plans. However, a large number of the fractures that are present in a field are smaller than the resolution of most industry standards methods. In this paper we use two independent methods to quantify small-scale fracture density and connectivity, such as two-dimensional image analysis of slabbed cores and rubble-size measurements.
Cyclin G1 Expands Liver Tumor-Initiating Cells by Sox2 Induction via Akt/mTOR Signaling
Authors: Wen Wen , Han Tao , Chen Cheng , Huang Lei , Sun Wen , Wang Xue , Chen Shu-Zhen , Xiang Dai-Min , Tang Liang , Cao Dan , Feng Gen-Sheng , Wu Meng-Chao , Ding Jin , Wang Hong-Yang 
Published: June 2013

Abstract
Recurrence and chemoresistance of liver cancer has been attributed to the existence of liver tumor-initiating cells (T-ICs). It is important to decipher the molecular mechanism for acquisition of drug resistance and to design combinatorial therapeutic strategies. Cyclin G1 has been shown to play a pivotal role in initiation and metastasis of hepatocellular carcinoma. In this study, we found that enhanced cyclin G1 expression was associated with drug resistance of hepatoma cells and higher recurrence rate in hepatocellular carcinoma patients. Expression of cyclin G1 was elevated in liver T-ICs and closely correlated with the expression of liver T-IC markers. Forced cyclin G1 expression remarkably enhanced self-renewal and tumorigenicity of hepatoma cells. Cyclin G1 overexpression dramatically upregulated the expression of Sox2 both in vitro and in vivo, which was impaired by chemical inhibitors of Akt/mTOR signaling. Furthermore, blockade of Akt/mTOR signaling or interference of Sox2 expression suppressed cyclin G1–enhanced self-renewal, chemoresistance, and tumorigenicity of hepatoma cells, indicating that cyclin G1 expands liver T-ICs through Sox2 induction via Akt/mTOR signaling pathway. These results suggest that cyclin G1–induced liver T-IC expansion contributes to the recurrence and chemoresistance of hepatoma, and cyclin G1 may be a promising biomarker for individualized therapy of hepatocellular carcinoma patients. Mol Cancer Ther; 12(9); 1796–804. ©2013 AACR.
Learning Minimally Invasive Mitral Valve Surgery
Authors: Holzhey David M. , Seeburger Joerg , Misfeld Martin , Borger Michael A. , Mohr Friedrich W. 
Published: June 2013

Background—
Learning curves are vigorously discussed and viewed as a negative aspect of adopting new procedures. However, very few publications have methodically examined learning curves in cardiac surgery, which could lead to a better understanding and a more meaningful discussion of their consequences. The purpose of this study was to assess the learning process involved in the performance of minimally invasive surgery of the mitral valve using data from a large, single-center experience.

Methods and Results—
All mitral (including tricuspid, or atrial fibrillation ablation) operations performed over a 17-year period through a right lateral mini-thoracotomy with peripheral cannulation for cardiopulmonary bypass (n=3907) were analyzed. Data were obtained from a prospective database. Individual learning curves for operation time and complication rates (using sequential probability cumulative sum failure analysis) and average results were calculated. A total of 3895 operations by 17 surgeons performing their first minimally invasive surgery of the mitral valve operation at our institution could be evaluated. The typical number of operations to overcome the learning curve was between 75 and 125. Furthermore, >1 such operation per week was necessary to maintain good results. Individual learning curves varied markedly, proving the need for good monitoring or mentoring in the initial phase.

Conclusions—
A true learning curve exists for minimally invasive surgery of the mitral valve. Although the number of operations required to overcome the learning curve is substantial, marked variation exists between individual surgeons. Such information could be very helpful in structuring future training and maintenance of competence programs for this kind of surgery.
Zygoidy, a new nomenclatural concept
Authors: DUBOIS Alain 
Published: June 2013

In zoological taxonomy, unambiguous and universal designation of a given taxon at a given rank in a given classification requires to establish its valid nomen and the correct spelling of the latter. Consequently, a need to resolve the situations of conflict that may exist between available nomina and spellings arises. These situations of nomenclatural conflict are here designated as zygoidy. They are of three kinds: zygonymy (conflicts of omonymy or synonymy between nomina for validity), zygography (conflicts of parography between spellings for correctness) and zygophory (conflicts of airetophory between onomatophore designations for validity). The resolution of these conflicts relies on several basic Principles already formulated in the Code (the Principles of Homonymy, Priority and “First-Reviser”, here renamed “Airesy”), as well as additional ones not yet recognized in this text: the Principles of Zygoidy, Proedry, Nomography and Sozoidy. A detailed analysis of these ituations is provided. It allows to identify in which cases and under which conditions these Principles apply. This omplete inventory of possible situations and solutions will be of great usefulness for a forecoming utomatisation and computerization of the Rules of the Code in forthcoming databases and Web applications.
Implementation of an Urban Parameterization Scheme into the Regional Climate Model COSMO-CLM
Authors: Trusilova Kristina , Früh Barbara , Brienen Susanne , Walter Andreas , Masson Valéry , Pigeon Grégoire , Becker Paul 
Published: June 2013

AbstractAs the nonhydrostatic regional model of the Consortium for Small-Scale Modelling in Climate Mode (COSMO-CLM) is increasingly employed for studying the effects of urbanization on the environment, the authors extend its surface-layer parameterization by the Town Energy Budget (TEB) parameterization using the “tile approach” for a single urban class. The new implementation COSMO-CLM+TEB is used for a 1-yr reanalysis-driven simulation over Europe at a spatial resolution of 0.11° (~12 km) and over the area of Berlin at a spatial resolution of 0.025° (~2.8 km) for evaluating the new coupled model. The results on the coarse spatial resolution of 0.11° show that the standard and the new models provide 2-m temperature and daily precipitation fields that differ only slightly by from −0.1 to +0.2 K per season and ±0.1 mm day−1, respectively, with very similar statistical distributions. This indicates only a negligibly small effect of the urban parameterization on the model's climatology. Therefore, it is suggested that an urban parameterization may be omitted in model simulations on this scale. On the spatial resolution of 0.025° the model COSMO-CLM+TEB is able to better represent the magnitude of the urban heat island in Berlin than the standard model COSMO-CLM. This finding shows the importance of using the parameterization for urban land in the model simulations on fine spatial scales. It is also suggested that models could benefit from resolving multiple urban land use classes to better simulate the spatial variability of urban temperatures for large metropolitan areas on spatial scales below ~3 km.
Airborne Flux Measurements of BVOCs above Californian Oak Forests: Experimental Investigation of Surface and Entrainment Fluxes, OH Densities, and Damköhler Numbers
Authors: Karl T. , Misztal P. K. , Jonsson H. H. , Shertz S. , Goldstein A. H. , Guenther A. B. 
Published: June 2013

Abstract
Airborne flux measurements of isoprene were performed over the Californian oak belts surrounding the Central Valley. The authors demonstrate for the first time 1) the feasibility of airborne eddy covariance measurements of reactive biogenic volatile organic compounds; 2) the effect of chemistry on the vertical transport of reactive species, such as isoprene; and 3) the applicability of wavelet analysis to estimate regional fluxes of biogenic volatile organic compounds. These flux measurements demonstrate that instrumentation operating at slower response times (e.g., 1–5 s) can still be used to determine eddy covariance fluxes in the mixed layer above land, where typical length scales of 0.5–3 km were observed. Flux divergence of isoprene measured in the planetary boundary layer (PBL) is indicative of OH densities in the range of 4–7 × 106 molecules per cubic centimeter and allows extrapolation of airborne fluxes to the surface with Damköhler numbers (ratio between the mixing time scale and the chemical time scale) in the range of 0.3–0.9. Most of the isoprene is oxidized in the PBL with entrainment fluxes of about 10% compared to the corresponding surface fluxes. Entrainment velocities of 1–10 cm s−1 were measured. The authors present implications for parameterizing PBL schemes of reactive species in regional and global models.
Clozapine and agranulocytosis: re-assessing the risks
Authors: Drew Leslie 
Published: June 2013

Objective: The aim of the study was to estimate the maximum incidence of agranulocytosis which clozapine would have caused between 2006 and 2010 had there been no blood monitoring system; and to determine the number of clozapine-associated cases of agranulocytosis and related deaths recorded between 1993 and 2011. Method: Records associating clozapine use with white blood cell deficiency (WBCD), in the Therapeutic Goods Administration’s Case Line Listing of adverse drug reactions, were examined. The figure of 11,000 was used as the population on clozapine each year from 2006–2010. Results: Between 2006 and 2010 there were 209 cases of clozapine-associated WBCD recorded, probably caused by clozapine in 141 cases. WBCD caused by clozapine could have progressed to agranulocytosis if clozapine had not been withdrawn. The risk of WBCD/agranulocytosis decreased with increasing duration of clozapine use. Between 1993 and 2011 there were 141 recorded cases of agranulocytosis, and four deaths, from clozapine-associated WBDC. Conclusions: During 2006–2010, without any monitoring system, the maximum annual incidence of agranulocytosis caused by clozapine would have been 0.26%. The risks of agranulocytosis, and related deaths, decreased with length of time on clozapine. During 1993–2011 141 cases of agranulocytosis, with four deaths, were recorded in association with clozapine use. The monitoring system could have successfully prevented relatively few deaths.
Hallux Metatarsophalangeal Joint Arthrodesis With a Hybrid Locking Plate and a Plantar Neutralization Screw
Authors: Doty Jesse , Coughlin Michael , Hirose Christopher , Kemp Travis 
Published: June 2013

Background: Many techniques have been described for arthrodesis of the first metatarsophalangeal (MTP) joint. The purpose of this study was to determine the results of fixation using a low-profile dorsal titanium plate with locking screws in the phalanx, nonlocking screws in the metatarsal, and a plantar neutralization screw. Methods: Forty-nine consecutive patients (51 feet) underwent a first MTP joint arthrodesis during an enrollment period of 1 year from October 2010 to November, 2011. All patients were evaluated preoperatively for primary pathology, pain, function, radiographic findings, AOFAS scores, and physical exam findings. First MTP joint arthrodesis was performed with a precontoured dorsal titanium plate with preset valgus and dorsiflexion after the joint surfaces were prepared with dome-shaped power reamers to achieve congruous cancellous bone surfaces. At a minimum of 1-year follow-up, patients returned for postoperative evaluation of pain, function, radiographic findings, satisfaction, AOFAS scores, and physical exam findings. Results: Forty-six of 49 (48 feet) patients returned for final follow-up examination at least 12 months after operative intervention. Forty-one patients (89%) reported good to excellent results. Visual analog pain scores improved from an average of 6.6 preoperatively to an average of 1.6 postoperatively ( t = −9.3339, df = 45, P < .001). Functional capacity scores improved from a preoperative mean of 2.5 to a postoperative mean of 1.4 ( t = −5.2648, df = 46, P < .001). AOFAS hallux MTP joint scores improved from a preoperative mean of 45 to a postoperative mean of 77 ( t = 9.9498, df = 46, P < .003). Eighteen of 48 great toes (38%) had preoperative pronation whereas, 2 of 48 great toes (4%) had postoperative pronation. Eleven of 46 patients (24%) were unable to perform preoperative toe rise, and 8 of 46 (17%) were unable to perform postoperative toe rise. Twenty-five of 46 patients (54%) had gait improvement, while 19 patients (44%) had no change in gait, and 2 patients (4%) had gait deterioration. The mean preoperative hallux valgus angle of 27 degrees improved to a mean postoperative angle of 13 degrees ( t = −6.1982, df = 46, P < .001). The mean preoperative 1-2 intermetatarsal angle of 12 degrees improved to a mean postoperative angle of 9 degrees ( t = −5.2614, df = 46, P < .001). There was 1 delayed union (2%) and 1 nonunion (2%). Conclusion: Our outcome scores indicate that first MTP joint arthrodesis with a precontoured dorsal titanium plate with locking screws in the phalanx and nonlocking screws in the first metatarsal is both reliable and reproducible with a very high bony union rate. Level of Evidence: Level IV, prospective case series.