bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular biomass and MetaTaxogenomic assessment of soil microbial communities as influenced by soil DNA extraction procedure
Authors: Terrat Sébastien , Christen Richard , Dequiedt Samuel , Lelièvre Mélanie , Nowak Virginie , Regnier Tiffanie , Bachar Dipankar , Plassart Pierre , Wincker Patrick , Jolivet Claudy , Bispo Antonio , Lemanceau Philippe , Maron Pierre‐Alain , Mougel Christophe , Ranjard Lionel 
Published: October 2011

SummaryThree soil DNA extraction procedures (homemade protocols and commercial kit) varying in their practicability were applied to contrasting soils to evaluate their efficiency in recovering: (i) soil DNA and (ii) bacterial diversity estimated by 16S rDNA pyrosequencing. Significant differences in DNA yield were systematically observed between tested procedures. For certain soils, 10 times more DNA was recovered with one protocol than with the others. About 15 000 sequences of 16S rDNA were obtained for each sample which were clustered to draw rarefaction curves. These curves, as well as the PCA ordination of community composition based on OTU clustering, did not reveal any significant difference between procedures. Nevertheless, significant differences between procedures were highlighted by the taxonomic identification of sequences obtained at the phylum to genus levels. Depending on the soil, differences in the number of genera detected ranged from 1% to 26% between the most and least efficient procedures, mainly due to a poorer capacity to recover populations belonging to Actinobacteria, Firmicutes or Crenarchaeota. This study enabled us to rank the relative efficiencies of protocols for their recovery of soil molecular microbial biomass and bacterial diversity and to help choosing an appropriate soil DNA extraction procedure adapted to novel sequencing technologies.
Successful resolution of juvenile paradental cysts after marsupialization in five consecutive patients
Authors: Lizio G , Corinaldesi G , Bianchi A , Marchetti C 
Published: October 2011

AbstractBackground:  Juvenile paradental cysts typically occur on the buccal aspect of mandibular first and second molars in children aged 6 to 11 years. The cysts may be treated by enucleation, with or without extraction of the involved teeth, or by marsupialization. This report demonstrates the success of a conservative surgical technique (marsupialization) and good outcomes in five juvenile paradental cyst cases.Methods:  Five patients (two males, three females) with a mean age of 8.4 years, complaining of mandibular buccal swelling around the molars, underwent marsupialization of radiolucent lesions involving partially or fully erupted permanent first molars. Clinical, radiographic and histological characteristics led to diagnoses of juvenile paradental cysts.Results:  The surgical procedures were simple to perform and resulted in complete remission of the lesions with no complications. The mean follow‐up time was 2.8 years. No recurrences were observed, the related teeth developed normally, and complete periodontal healing was achieved.Conclusions:  The surgical marsupialization of juvenile paradental cysts achieved good outcomes without compromising the development of related teeth, and thus may be considered an appropriate treatment for paediatric patients.
Molecular Prevalence ofBartonella,Babesia, and HemotropicMycoplasmasp. in Dogs with Splenic Disease
Authors: Varanat M. , Maggi R.G. , Linder K.E. , Breitschwerdt E.B. 
Published: October 2011

BackgroundAmong diseases that cause splenomegaly in dogs, lymphoid nodular hyperplasia (LNH), splenic hemangiosarcoma (HSA), and fibrohistiocytic nodules (FHN) are common diagnoses. The spleen plays an important role in the immunologic control or elimination of vector‐transmitted, blood‐borne pathogens, includingBartonellasp.,Babesiasp., and hemotropicMycoplasmasp.ObjectiveTo compare the prevalence ofBartonellasp.,Babesiasp., and hemotropicMycoplasmasp.DNAin spleens from dogs withLNH, HSA, andFHN.Materials and MethodsParaffin‐embedded, surgically obtained biopsy tissues fromLNH(N = 50),HSA(N = 50), andFHN(N = 37) were collected from the anatomic pathology archives. Spleens from specific pathogen‐free (SPF) dogs (N = 8) were used as controls.Bartonellasp.,Babesiasp., andMycoplasmasp.DNAwas amplified byPCR, followed byDNAsequencing.ResultsBartonellasp.DNAwas more prevalent inFHN(29.7%) andHSA(26%) as compared toLNH(10%) (P = .019, .0373, respectively) or control spleens (0.0%). The prevalence ofBabesiasp. and hemotropicMycoplasmasp.DNAwas significantly lower thanBartonellasp.DNAinHSA(P = .0005, .006, respectively) andFHN(P = .003, .0004, respectively). There was no statistically significant difference inDNAprevalence among the 3 genera in theLNHgroup.ConclusionsThe higher prevalence ofBartonellasp. inFHNandHSAwarrants future investigations to determine if this bacterium plays a role in the development of these splenic diseases.
Confidence inflation in eyewitnesses: Seeing is not believing
Authors: Douglass Amy Bradfield , Jones Eric E. 
Published: October 2011

Purpose. Confidence inflation in eyewitnesses obscures a useful cue to identification accuracy and affects evaluations of eyewitnesses (e.g., Bradfield & McQuiston, 2004; Jones, Williams, & Brewer, 2008). We examine whether sensitivity to confidence inflation evidence is enhanced by seeing a videotape of the identification procedure.Methods. Participants (N= 131) watched a videotaped trial in which the witness's original confidence statement was presented as part of a previously recorded videotaped identification procedure or read by the witness at trial. In addition, the witness's identification confidence was either consistently high or low at the time of the identification and high at the trial (i.e., it was inflated).Results. Significant interactions demonstrated that confidence inflation evidence factored into judgments of the eyewitness and defendant guilt more strongly in the videotape condition compared with the read condition.Conclusions. The present results support recommendations to collect immediate confidence reports and videotape identification procedures. Using videotape evidence may help innocent defendants convince jurors that the eyewitness's identification is not accurate.
Complete Genome Sequence of the Industrial Strain Ketogulonicigenium vulgare WSH-001
Authors: Liu Liming , Li Yang , Zhang Jing , Zhou Zhemin , Liu Jie , Li Xiaomin , Zhou Jingwen , Du Guocheng , Wang Lei , Chen Jian 
Published: October 2011

ABSTRACT

Ketogulonicigenium vulgare
is an industrial organism commonly used in the vitamin C industry. Here, we report the finished, annotated, and compared 3.28-Mbp high-quality genome sequence of
Ketogulonicigenium vulgare
WSH-001, a 2-keto-
l
-gulonic acid-producing industrial strain stocked in our laboratory.
Genome Sequence of Escherichia coli XH140A, Which Produces
l
-Threonine
Authors: Yang Huilin , Liao Yuling , Wang Bin , Lin Ying , Pan Li 
Published: October 2011

ABSTRACT

Here we report the draft annotated genome sequence of
Escherichia coli
XH140A, which is used to produce
l
-threonine in industry. The genome sequence will allow the characterization of the molecular mechanisms underlying its beneficial properties.
Comparative Performance of Human Papillomavirus DNA Testing Using Novel Sample Collection Methods
Authors: Gage Julia C. , Partridge Edward E. , Rausa Alfio , Gravitt Patti E. , Wacholder Sholom , Schiffman Mark , Scarinci Isabel , Castle Philip E. 
Published: October 2011

ABSTRACT

To explore alternative cervical cancer screening approaches in an underserved population, we compared the performance of human papillomavirus (HPV) DNA assays in combination with different sample collection methods for primary cervical screening in the Mississippi Delta region. Three specimens were collected from women aged 26 to 65 years who were either routinely undergoing screening (
n
= 252) or not (
n
= 191): clinician-collected cervical specimens, clinician-collected cervicovaginal specimens, and self-collected cervicovaginal specimens taken at home. A novel collection device and medium were used for cervicovaginal sampling. Specimens were tested by three HPV DNA assays: hybrid capture 2 (HC2; Qiagen Corp., Gaithersburg, MD), Linear Array (LA; Roche Molecular Systems, Pleasanton, CA), and Amplicor (Roche Molecular Systems, Pleasanton, CA). Liquid-based cytology was performed on cervical specimens. We compared the overall positivity (a proxy for clinical specificity) for any carcinogenic HPV genotype and calculated the agreement across assay and specimen type using McNemar's test for differences in test positivity. Across all three assays there were no significant differences between clinician-collected and self-collected cervicovaginal specimens (
P
> 0.01 for all comparisons). For both cervicovaginal specimens (clinician collected and self-collected), fewer women tested positive by HC2 than by LA or Amplicor (
P
< 0.01 for all comparisons). HC2 had the best agreement between specimens for all assays. HC2 is likely more clinically specific, although possibly less sensitive, than either PCR test. Thus, use of HC2 on cervicovaginal specimens for screening could result in fewer referrals compared to LA and Amplicor.
Sudden Death from Systemic Rotavirus Infection and Detection of Nonstructural Rotavirus Proteins
Authors: Nakano Ineko , Taniguchi Koki , Ishibashi-Ueda Hatsue , Maeno Yoshimasa , Yamamoto Naoki , Yui Akiko , Komoto Satoshi , Wakata Yasushi , Matsubara Tamehito , Ozaki Nozomu 
Published: October 2011

ABSTRACT
A 2.5-year-old girl died suddenly during the course of rotavirus gastroenteritis. The autopsy showed encephalopathy with rotavirus systemic infection. Here, we provide evidence of rotavirus replication in multiple organs. Our findings clarify that rotavirus infection in children can extend beyond the intestinal tract through viremia.
Restricted Enzooticity of Hepatitis E Virus Genotypes 1 to 4 in the United States
Authors: Dong Chen , Meng Jihong , Dai Xing , Liang Jiu-Hong , Feagins Alicia R. , Meng Xiang-Jin , Belfiore Natalia M. , Bradford Carol , Corn Joseph L. , Cray Carolyn , Glass Gregory E. , Gordon Melvin L. , Hesse Richard A. , Montgomery Donald L. , Nicholson William L. , Pilny Anthony A. , Ramamoorthy Sheela , Shaver Douglas D. , Drobeniuc Jan , Purdy Michael A. , Fields Howard A. , Kamili Saleem , Teo Chong-Gee 
Published: October 2011

ABSTRACT

Hepatitis E is recognized as a zoonosis, and swine are known reservoirs, but how broadly enzootic its causative agent, hepatitis E virus (HEV), is remains controversial. To determine the prevalence of HEV infection in animals, a serological assay with capability to detect anti-HEV-antibody across a wide variety of animal species was devised. Recombinant antigens comprising truncated capsid proteins generated from HEV-subgenomic constructs that represent all four viral genotypes were used to capture anti-HEV in the test sample and as an analyte reporter. To facilitate development and validation of the assay, serum samples were assembled from blood donors (
n
= 372), acute hepatitis E patients (
n
= 94), five laboratory animals (rhesus monkey, pig, New Zealand rabbit, Wistar rat, and BALB/c mouse) immunized with HEV antigens, and four pigs experimentally infected with HEV. The assay was then applied to 4,936 sera collected from 35 genera of animals that were wild, feral, domesticated, or otherwise held captive in the United States. Test positivity was determined in 457 samples (9.3%). These originated from: bison (3/65, 4.6%), cattle (174/1,156, 15%), dogs (2/212, 0.9%), Norway rats (2/318, 0.6%), farmed swine (267/648, 41.2%), and feral swine (9/306, 2.9%). Only the porcine samples yielded the highest reactivities. HEV RNA was amplified from one farmed pig and two feral pigs and characterized by nucleotide sequencing to belong to genotype 3. HEV infected farmed swine primarily, and the role of other animals as reservoirs of its zoonotic spread appears to be limited.
Identification and Characterization of an Immunogenic Hybrid Epitope Formed by both HIV gp120 and Human CD4 Proteins
Authors: Lewis George K. , Fouts Timothy R. , Ibrahim Sani , Taylor Brian M. , Salkar Rachita , Guan Yongjun , Kamin-Lewis Roberta , DeVico Anthony L. 
Published: October 2011

ABSTRACTCertain antibodies from HIV-infected humans bind conserved transition state (CD4 induced [CD4i]) domains on the HIV envelope glycoprotein, gp120, and demonstrate extreme dependence on the formation of a gp120-human CD4 receptor complex. The epitopes recognized by these antibodies remain undefined although recent crystallographic studies of the anti-CD4i monoclonal antibody (MAb) 21c suggest that contacts with CD4 as well as gp120 might occur. Here, we explore the possibility of hybrid epitopes that demand the collaboration of both gp120 and CD4 residues to enable antibody reactivity. Analyses with a panel of human anti-CD4i MAbs and gp120-CD4 antigens with specific mutations in predicted binding domains revealed one putative hybrid epitope, defined by the human anti-CD4i MAb 19e. In virological and immunological tests, MAb 19e did not bind native or constrained gp120 except in the presence of CD4. This contrasted with other anti-CD4i MAbs, including MAb 21c, which bound unliganded, full-length gp120 held in a constrained conformation. Conversely, MAb 19e exhibited no specific reactivity with free human CD4. Computational modeling of MAb 19e interactions with gp120-CD4 complexes suggested a distinct binding profile involving antibody heavy chain interactions with CD4 and light chain interactions with gp120. In accordance, targeted mutations in CD4 based on this model specifically reduced MAb 19e interactions with stable gp120-CD4 complexes that retained reactivity with other anti-CD4i MAbs. These data represent a rare instance of an antibody response that is specific to a pathogen-host cell protein interaction and underscore the diversity of immunogenic CD4i epitope structures that exist during natural infection.
Acceptability and response to a postal survey using self-taken samples for HPV vaccine impact monitoring
Authors: Sinka Katy , Lacey Michelle , Robertson Chris , Kavanagh Kim , Cuschieri Kate , Nicholson Donna , Donaghy Martin 
Published: October 2011

ObjectiveTo assess the feasibility and acceptance of a postal survey to measure human papillomavirus (HPV) prevalence and monitor vaccine impact, using self-taken specimens from young women who do not attend their first cervical screening appointment.MethodsFocus groups informed the survey design identifying factors that would influence acceptability. Postal testing kits were sent to a nationally representative sample of unscreened women. Overall response rate, the influence of different specimen types (urine or vaginal swab) and the receipt of a reminder letter on participation were calculated. Specimens were tested anonymously for HPV. Individual test results were not provided.ResultsOf 5500 kits sent, 725 were returned (13.2%). Fifty-two women actively opted out. There was a higher return rate for urine kits (13.7% vs 12%) and from those who received a reminder letter (15.5% vs 12.2%). Response was influenced by deprivation (10.3% in the most deprived quintile vs 16.2% in the least). Overall weighted HPV prevalence was 35.9% (40.0% from swab specimens and 31.9% from urine).ConclusionsSome women were willing to participate in anonymised postal testing. However, the low uptake means that HPV prevalence results are difficult to interpret for ongoing surveillance. Monitoring HPV vaccine impact outwith the cervical screening programme remains challenging.
Palaeoposition of the Seychelles microcontinent in relation to the Deccan Traps and the Plume Generation Zone in Late Cretaceous-Early Palaeogene time
Authors: Ganerød M. , Torsvik T. H. , van Hinsbergen D. J. J. , Gaina C. , Corfu F. , Werner S. , Owen-Smith T. M. , Ashwal L. D. , Webb S. J. , Hendriks B. W. H. 
Published: October 2011

Abstract

The Early Palaeogene magmatic rocks of North and Silhouette Islands in the Seychelles contain clues to the Cenozoic geodynamic puzzle of the Indian Ocean, but have so far lacked precise geochronological data and palaeomagnetic constraints. New
40
Ar/
39
Ar and U–Pb dates demonstrate that these rocks were emplaced during magnetochron C28n; however,
40
Ar/
39
Ar and palaeomagnetic data from Silhouette indicate that this complex experienced a protracted period of cooling. The Seychelles palaeomagnetic pole (57.55°S and 114.22°E; A9512.3°,
N
=14) corresponds to poles of similar ages from the Deccan Traps after being corrected for a clockwise rotation of 29.4°±12.9°. This implies that Seychelles acted as an independent microplate between the Indian and African plates during and possibly after C27r time, confirming recent results based on kinematic studies. Our reconstruction confirms that the eruption of the Deccan Traps, which affected both India and the Seychelles and triggered continental break-up, can be linked to the present active Reunion hotspot, which is being sourced as a deep plume from the Plume Generation Zone.

Supplementary material:

Experimental data are available at
http://www.geolsoc.org.uk/SUP18482
.
Otolaryngologic Manifestations of Antineutrophil Cytoplasmic Antibody–Associated Vasculitis
Authors: Nakamaru Yuji , Takagi Dai , Oridate Nobuhiko , Homma Akihiro , Fukuda Satoshi 
Published: October 2011

Antineutrophil cytoplasmic antibody (ANCA)–associated vasculitis is characterized by systemic necrotizing vasculitis, and patients fall into 2 groups: those with proteinase 3–ANCA and those with myeloperoxidase‐ANCA. As infections are a trigger of ANCA‐associated vasculitis, this disease tends to localize in areas around the upper airway. In this study, the authors compared ear and nasal symptoms between patients with proteinase 3–ANCA and those with myeloperoxidase‐ANCA. We undertook a retrospective case series study of 34 patients diagnosed with ANCA‐associated vasculitis. The otologic symptoms were divided into 3 types: chronic otitis media, secretory otitis media, and sensorineural hearing loss. Chronic otitis media was more common in patients with proteinase 3–ANCA (P =. 001), whereas secretory otitis media was more frequently found in patients with myeloperoxidase‐ANCA (P =. 007). Crust formation (P =. 001), saddle nose (P =. 024), and sinusitis (P =. 001) were more common in patients with proteinase 3–ANCA than in those with myeloperoxidase‐ANCA. Marked differences were observed in the disease spectrum between the 2 ANCA groups.
Pioglitazone improves the cardiovascular profile in patients with uncomplicated systemic lupus erythematosus: a double-blind randomized clinical trial
Authors: Juárez-Rojas JG , Medina-Urrutia AX , Jorge-Galarza E , Caracas-Portilla NA , Posadas-Sánchez R , Cardoso-Saldaña GC , Goycochea-Robles MV , Silveira LH , Lino-Pérez L , Mas-Oliva J , Pérez-Méndez O , Posadas-Romero C 
Published: October 2011

Objective: We studied the effect of pioglitazone on insulin levels, inflammation markers, high-density lipoprotein (HDL) composition and subclasses distribution, in young women with uncomplicated systemic lupus erythematosus (SLE). Methods: This double-blind trial included 30 premenopausal women (30 ±8 years old) with SLE, who were randomized to pioglitazone (30 mg/day) or placebo treatment for 3 months. Plasma and HDL lipids were determined by colorimetric enzymatic assays, insulin by radioimmunometric assay, inflammation by immunonephelometry and HDL size and subclasses distribution by a native 4–30% polyacrylamide gradient gel electrophoresis. Results: Compared with placebo, pioglitazone significantly increased HDL-cholesterol plasma levels (14.2%), reduced fasting insulin plasma levels (23.6%) and the homeostasis model assessment-insulin resistance (31.7%). C-reactive protein (70.9%) and serum amyloid A (34.9%) were also significantly reduced with the pioglitazone use, whereas the HDL particle size was increased (8.80 nm vs. 8.95 nm; p = 0.044) by changes in the distribution of HDL2b, HDL3b, and HDL3c subclasses. The change in HDL size correlated with a rise in free and cholesterol–ester content in the HDL particles. Conclusion: Pioglitazone significantly enhanced insulin sensitivity, reduced inflammation, and modified HDL characteristics, suggesting a potential beneficial effect of this drug in patients with SLE with a risk to develop cardiovascular disease. Trial registration: This trial is registered at ClinicalTrials.gov Protocol Registration System, with the number NCT01322308.
The effect of gender in clinically isolated syndrome (CIS): a meta-analysis
Authors: Dobson Ruth , Ramagopalan Sreeram , Giovannoni Gavin 
Published: October 2011

Background/Objective: A clinically isolated syndrome compatible with demyelination (CIS) is the initial presentation for the majority of people that go on to develop multiple sclerosis (MS). There has previously been little work examining the effect of gender on the development and progression of CIS. Methods: Data from observational studies of CIS were used. In total, 33 suitable studies with 4732 subjects were identified. Results: The overall relative risk (RR) of CIS in females compared with males was 2.12 (95% CI 1.94–2.32). The RR of females developing MS following CIS was 1.20 (95% CI 0.98–1.46) compared with males. Conclusions: These data imply that the gender bias seen in MS is caused by factors acting early in the disease process.
Spousal relationships in which one partner has early cognitive problems
Authors: Prakke Helena M. 
Published: October 2011

The purpose of this literature review was to get an overview about the research on lived experiences of elderly spousal dyads, in which one partner has early cognitive problems. Couples might first experience forgetfulness as something normal for old age. If symptoms become too great, the dyad will go and search for meaning. Through medical assessment the affected spouse will be diagnosed as either non-demented or demented. Both situations are experienced as hard and worrisome. However, if diagnosed with non-dementia, the dyad remains confused about what is going on and how to anticipate the future. In spite of the enormous impact of early cognitive problems on the relationship, both partners are still able to contribute to the quality of it and seem to have few reciprocity issues. How couples are different and what this means for the experience of early cognitive problems remains largely unexplored.
Pleiotropic platelet defects in mice with disrupted FOG1-NuRD interaction
Authors: Wang Yuhuan , Meng Ronghua , Hayes Vincent , Fuentes Rudy , Yu Xiang , Abrams Charles S. , Heijnen Harry F. G. , Blobel Gerd A. , Marks Michael S. , Poncz Mortimer 
Published: October 2011

AbstractUnderstanding platelet biology has been aided by studies of mice with mutations in key megakaryocytic transcription factors. We have shown that point mutations in the GATA1 cofactor FOG1 that disrupt binding to the nucleosome remodeling and deacetylase (NuRD) complex have erythroid and megakaryocyte lineages defects. Mice that are homozygous for a FOG1 point mutation (ki/ki), which ablates FOG1-NuRD interactions, have platelets that display a gray platelet syndrome (GPS)–like macrothrombocytopenia. These platelets have few α-granules and an increased number of lysosomal-like vacuoles on electron microscopy, reminiscent of the platelet in patients with GATA1-related X-linked GPS. Here we further characterized the platelet defect in ki/ki mice. We found markedly deficient levels of P-selectin protein limited to megakaryocytes and platelets. Other α-granule proteins were expressed at normal levels and were appropriately localized to α-granule–like structures. Treatment of ki/ki platelets with thrombin failed to stimulate Akt phosphorylation, resulting in poor granule secretion and platelet aggregation. These studies show that disruption of the GATA1/FOG1/NuRD transcriptional system results in a complex, pleiotropic platelet defect beyond GPS-like macrothrombocytopenia and suggest that this transcriptional complex regulates not only megakaryopoiesis but also α-granule generation and signaling pathways required for granule secretion.