bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reproducibility and quantitation of amplicon sequencing-based detection
Authors: Zhou Jizhong , Wu Liyou , Deng Ye , Zhi Xiaoyang , Jiang Yi-Huei , Tu Qichao , Xie Jianping , Van Nostrand Joy D , He Zhili , Yang Yunfeng 
Published: February 2011

Abstract
To determine the reproducibility and quantitation of the amplicon sequencing-based detection approach for analyzing microbial community structure, a total of 24 microbial communities from a long-term global change experimental site were examined. Genomic DNA obtained from each community was used to amplify 16S rRNA genes with two or three barcode tags as technical replicates in the presence of a small quantity (0.1% wt/wt) of genomic DNA from Shewanella oneidensis MR-1 as the control. The technical reproducibility of the amplicon sequencing-based detection approach is quite low, with an average operational taxonomic unit (OTU) overlap of 17.2%±2.3% between two technical replicates, and 8.2%±2.3% among three technical replicates, which is most likely due to problems associated with random sampling processes. Such variations in technical replicates could have substantial effects on estimating β-diversity but less on α-diversity. A high variation was also observed in the control across different samples (for example, 66.7-fold for the forward primer), suggesting that the amplicon sequencing-based detection approach could not be quantitative. In addition, various strategies were examined to improve the comparability of amplicon sequencing data, such as increasing biological replicates, and removing singleton sequences and less-representative OTUs across biological replicates. Finally, as expected, various statistical analyses with preprocessed experimental data revealed clear differences in the composition and structure of microbial communities between warming and non-warming, or between clipping and non-clipping. Taken together, these results suggest that amplicon sequencing-based detection is useful in analyzing microbial community structure even though it is not reproducible and quantitative. However, great caution should be taken in experimental design and data interpretation when the amplicon sequencing-based detection approach is used for quantitative analysis of the β-diversity of microbial communities.
Development Planning in Iran: A Historical Survey
Authors: Daftary Farhad 
Published: February 2011

By the time the Fifth Development Plan was adopted in 1973, Iran had already experienced more than three decades of governmental efforts towards economic development. These efforts first started in the early 1920s and culminated, in the postwar period, in the country's First Development Plan. Before discussing the second and subsequent plans, it will be useful to review the main features of the initial efforts at planning in Iran.The development policies of the government during the reign of Reza Shah (1925-1941) did not constitute development planning as the term has come to be understood in the postwar economic literature. The prewar policies were restricted to partial investment programs for the public sector only, with little consideration concerning the activities of the private sector. Furthermore, even the public sector programs did not reflect any explicitly defined set of policy objectives.
The prevalence of alcohol use disorders among night‐time weekend drivers
Authors: Furr‐Holden C. Debra , Voas Robert B. , Lacey John , Romano Eduardo , Jones Kristina 
Published: February 2011

ABSTRACTAims  The objective of this study was to establish the extent of alcohol use disorders (AUDs) among drivers at risk for alcohol‐related crashes. The prevalence of drivers with AUDs on US roads on weekend evenings when alcohol‐related crashes are most frequent is unknown. This study will inform laws and programs designed to reduce alcohol‐involved crashes.Design  Interviews using a 15‐item AUD questionnaire with a stratified random sample of non‐commercial drivers at 60 primary sampling locations in the 48 contiguous states on Fridays and Saturdays between 10 p.m. and 3 a.m. from July to November 2007.Setting  Off‐road locations into which a police officer directed a random selection of motorist passing the site.Participants  A total of 4614 drivers of non‐commercial vehicles.Measurements  AUDs, including heavy drinking, alcohol abuse, and alcohol dependence.Findings  Of the participating drivers, 73.7% were current drinkers (reported drinking in the last year). Among those drinkers, 14% were classifiable either as dependent drinkers or as abusive drinkers based on self‐reports of drinking. Another 10% of the drivers were classified as heavy drinkers. Nearly half of the drivers in the survey who had blood alcohol concentrations (BACs) at or higher than the 0.08 g per deciliter legal limit fell into one of those three AUD categories.Conclusions  Survey data suggest that the majority of high‐blood alcohol concentration drivers on US roads show no clinical signs of an alcohol use disorder, but they are categorized as heavy drinkers. This suggests that environmental programs directed at reducing heavy drinking and brief behavioral interventions aimed at reducing episodes of excessive consumption have promise for reducing alcohol‐related crashes.
Germination and emergence of Ambrosia artemisiifolia L. under changing environmental conditions in China
Authors: SANG WEIGUO , LIU XINYAN , AXMACHER JAN C. 
Published: February 2011

AbstractLaboratory and greenhouse studies were conducted to determine the effects of key environmental factors on germination and seedling emergence of the invasive weed Ambrosia artemisiifolia L. (common ragweed) collected from Mudanjiang (temperate climate), Nanjing (temperate–subtropical) and Nanchang (subtropical) in China. Germination of seeds occurred at temperatures ranging from 5 to 40°C, under both a 12‐h photoperiod and continuous darkness. Germination success exceeded 48% in solutions with pH values between 4 and 12, with maximum rates occurring in distilled water at pH 5.57. Germination was greatly reduced in solutions with osmotic potentials below −0.8 MPa. Accordingly, the final germination ratio exceeded 69% at <200 mmol/L NaCl, but only reached 8% at 400 mmol/L NaCl. Emergence was greater than 75% at burial seed depths of 1–4 cm; no seedlings emerged from a soil depth of 8 cm. Seeds collected from Mudanjiang, Nanjing and Nanchang had very similar germination traits, with the main differences occurring in relation to temperature. The great germination success of common ragweed over highly variable conditions throughout its Chinese distribution range explains its successful large‐scale invasion.
Induction of Immune Tolerance in Asthmatic Mice by Vaccination with DNA Encoding an Allergen–Cytotoxic T Lymphocyte-Associated Antigen 4 Combination
Authors: Zhang Fang , Huang Gang , Hu Bo , Song Yong , Shi Yi 
Published: February 2011

ABSTRACTAllergen-specific immunotherapy is a potential treatment for allergic diseases. We constructed an allergen–cytotoxic T lymphocyte-associated antigen 4 (CTLA-4)-encoding DNA vaccine, administered it directly to antigen-presenting cells (APCs), and investigated its ability and mechanisms to ameliorate allergic airway inflammation in an asthmatic mouse model. An allergen-CTLA-4 DNA plasmid (OVA-CTLA-4-pcDNA3.1) encoding an ovalbumin (OVA) and the mouse CTLA-4 extracellular domain was constructed and transfected into COS-7 cells to obtain the fusion protein OVA-CTLA-4, which was able to bind the B7 ligand on dendritic cells (DCs), and induced CD25+Foxp3+regulatory T (Treg) cells by the coculture of naive CD4+T cells with DCsin vitro. In an animal study, BALB/c mice were sensitized and challenged with OVA to establish the asthmatic model. Vaccination with a high dose of OVA-CTLA-4-pcDNA3.1significantly decreased interleukin-4 (IL-4) and IL-5 levels and eosinophil counts and prevented OVA-induced reduction of the gamma interferon level in the bronchoalveolar lavage fluid. In addition, these mice suffered less severe airway inflammation and had lower levels of OVA-specific IgE and IgG1 titers in serum. Also, high-dose OVA-CTLA-4-pcDNA3.1vaccination inhibited the development of airway hyperreactivity and prevented OVA-induced reduction of the percentages of Foxp3+Treg cells in the spleen. Our results indicate that a high dose of allergen-CTLA-4-encoding DNA vaccine was more effective in preventing an allergen-induced Th2-skewed immune response through the induction of Treg cells and may be a new alternative therapy for asthma.
Efficacy of the Canine Influenza Virus H3N8 Vaccine To Decrease Severity of Clinical Disease after Cochallenge with Canine Influenza Virus and Streptococcus equi subsp. zooepidemicus
Authors: Larson Laurie J. , Henningson Jamie , Sharp Patricia , Thiel Bliss , Deshpande Muralidhar S. , Davis Tamara , Jayappa Huchappa , Wasmoen Terri , Lakshmanan Nallakannu , Schultz Ronald D. 
Published: February 2011

ABSTRACTSince first emerging in the North American canine population in 2004, canine influenza virus (CIV) subtype H3N8 has shown horizontal transmission among dogs, with a high level of adaptation to this species. The severity of disease is variable, and coinfection by other respiratory pathogens is an important factor in the degree of morbidity and mortality. The first influenza vaccine for dogs, an inactivated vaccine containing CIV subtype H3N8, was conditionally approved by the U.S. Department of Agriculture (USDA) for licensure in May 2009 and fully licensed in June 2010. This study evaluates the efficacy of this vaccine to reduce the severity of illness in dogs cochallenged with virulent CIV andStreptococcus equisubsp.zooepidemicus.
Evaluation of Fluoromycobacteriophages for Detecting Drug Resistance in Mycobacterium tuberculosis
Authors: Rondón Liliana , Piuri Mariana , Jacobs William R. , de Waard Jacobus , Hatfull Graham F. , Takiff Howard E. 
Published: February 2011

ABSTRACT

We tested a new method for detecting drug-resistant strains of
Mycobacterium tuberculosis
that uses a TM4 mycobacteriophage phAE87::
hsp60-EGFP
(
EGFP
-phage) engineered to contain the gene encoding enhanced green fluorescent protein (EGFP). After promising results in preliminary studies, the
EGFP
-phage was used to detect isoniazid (INH), rifampin (RIF), and streptomycin (STR) resistance in 155 strains of
M. tuberculosis
, and the results were compared to the resazurin microplate technique, with the proportion method serving as the reference standard. The resazurin technique yielded sensitivities of 94% for INH and RIF and 98% for STR and specificities of 97% for INH, 95% for RIF, and 98% for STR. The sensitivity of
EGFP
-phage was 94% for all three antibiotics, with specificities of 90% for INH, 93% for RIF, and 95% for STR. The
EGFP
-phage results were available in 2 days for RIF and STR and in 3 days for INH, with an estimated cost of ∼2$ to test the three antibiotics. Using a more stringent criterion for resistance improved the specificity of the
EGFP
-phage for INH and RIF without affecting the sensitivity. In preliminary studies, the
EGFP
-phage could also effectively detect resistance to the fluoroquinolones. The
EGFP
-phage method has the potential to be a valuable rapid and economic screen for detecting drug-resistant tuberculosis if the procedure can be simplified, if it can be adapted to clinical material, and if its sensitivity can be improved.
Role of Helicobacter Species in Chinese Patients with Inflammatory Bowel Disease
Authors: Zhang Shenghong , Zhong Bihui , Chao Kang , Xiao Yingliang , Cui Yi , Gao Xiang , Chen Baili , He Yao , Hu Pinjin , Chen Minhu , Mitchell Hazel M. 
Published: February 2011

ABSTRACT

Based on 16S rRNA gene PCR, no significant difference was observed in rates of detection of
Helicobacter
species in intestinal biopsy specimens from 160 Chinese inflammatory bowel disease (IBD) patients (10%) and 80 controls (6.3%). By using a [
13
C]urea breath test, the
H. pylori
infection rate in 208 Chinese IBD patients (19.7%) was found to be significantly lower than that in 416 controls (48.8%).
Clinical Isolates of Trichomonas vaginalis Concurrently Infected by Strains of Up to Four Trichomonasvirus Species (Family Totiviridae)
Authors: Goodman Russell P. , Freret Taylor S. , Kula Tomasz , Geller Alexander M. , Talkington Megan W. T. , Tang-Fernandez Vanessa , Suciu Olimpia , Demidenko Aleksander A. , Ghabrial Said A. , Beach David H. , Singh Bibhuti N. , Fichorova Raina N. , Nibert Max L. 
Published: February 2011

ABSTRACT

Trichomonas vaginalis
, which causes the most common nonviral sexually transmitted disease worldwide, is itself commonly infected by nonsegmented double-stranded RNA (dsRNA) viruses from the genus
Trichomonasvirus
, family
Totiviridae
. To date, cDNA sequences of one or more strains of each of three trichomonasvirus species have been reported, and gel electrophoresis showing several different dsRNA molecules obtained from a few
T. vaginalis
isolates has suggested that more than one virus strain might concurrently infect the same parasite cell. Here, we report the complete cDNA sequences of 3 trichomonasvirus strains, one from each of the 3 known species, infecting a single, agar-cloned clinical isolate of
T. vaginalis
, confirming the natural capacity for concurrent (in this case, triple) infections in this system. We furthermore report the complete cDNA sequences of 11 additional trichomonasvirus strains, from 4 other clinical isolates of
T. vaginalis
. These additional strains represent the three known trichomonasvirus species, as well as a newly identified fourth species. Moreover, 2 of these other
T. vaginalis
isolates are concurrently infected by strains of all 4 trichomonasvirus species (i.e., quadruple infections). In sum, the full-length cDNA sequences of these 14 new trichomonasviruses greatly expand the existing data set for members of this genus and substantiate our understanding of their genome organizations, protein-coding and replication signals, diversity, and phylogenetics. The complexity of this virus-host system is greater than has been previously well recognized and suggests a number of important questions relating to the pathogenesis and disease outcomes of
T. vaginalis
infections of the human genital mucosa.
A Tryptophan-Rich Motif in the Human Parainfluenza Virus Type 2 V Protein Is Critical for the Blockade of Toll-Like Receptor 7 (TLR7)- and TLR9-Dependent Signaling
Authors: Kitagawa Yoshinori , Yamaguchi Mayu , Zhou Min , Komatsu Takayuki , Nishio Machiko , Sugiyama Tsuyoshi , Takeuchi Kenji , Itoh Masae , Gotoh Bin 
Published: February 2011

ABSTRACT

Plasmacytoid dendritic cells (pDCs) do not produce alpha interferon (IFN-α) unless viruses cause a systemic infection or overcome the first-line defense provided by conventional DCs and macrophages. We show here that even paramyxoviruses, whose infections are restricted to the respiratory tract, have a V protein able to prevent Toll-like receptor 7 (TLR7)- and TLR9-dependent IFN-α induction specific to pDCs. Mutational analysis of human parainfluenza virus type 2 demonstrates that the second Trp residue of the Trp-rich motif (Trp-X
3
-Trp-X
9
-Trp) in the C-terminal domain unique to V, a determinant for IRF7 binding, is critical for the blockade of TLR7/9-dependent signaling.
TRIM22 Inhibits HIV-1 Transcription Independently of Its E3 Ubiquitin Ligase Activity, Tat, and NF-κB-Responsive Long Terminal Repeat Elements
Authors: Kajaste-Rudnitski Anna , Marelli Sara S. , Pultrone Cinzia , Pertel Thomas , Uchil Pradeep D. , Mechti Nadir , Mothes Walther , Poli Guido , Luban Jeremy , Vicenzi Elisa 
Published: February 2011

ABSTRACTPrevious studies identified clones of the U937 promonocytic cell line that were either permissive or nonpermissive for human immunodeficiency virus type 1 (HIV-1) replication. These clones were investigated further in the search for host restriction factors that could explain their differential capacity to support HIV-1 replication. Among known HIV-1 restriction factors screened,tripartitemotif-containing protein 22 (TRIM22) was the only factor constitutively expressed in nonpermissive and absent in permissive U937 cells. Stable TRIM22 knockdown (KD) rescued HIV-1 long-terminal-repeat (LTR)-driven transcription in KD-nonpermissive cells to the levels observed in permissive cells. Conversely, transduction-mediated expression of TRIM22 in permissive cells reduced LTR-driven luciferase expression by ∼7-fold, supporting a negative role of TRIM22 in HIV-1 transcription. This finding was further confirmed in the human T cell line A3.01 expressing TRIM22. Moreover, overexpression of TRIM22 in 293T cells significantly impaired basal and phorbol myristate acetate-ionomycin-induced HIV-1 LTR-driven gene expression, whereas inhibition of tumor necrosis factor alpha-induced viral transcription was a consequence of lower basal expression. In agreement, TRIM22 equally inhibited an LTR construct lacking the tandem NF-κB binding sites. In addition, TRIM22 did not affect Tat-mediated LTR transactivation. Finally, these effects were independent of TRIM22 E3 ubiquitin-ligase activity. In the context of replication-competent virus, significantly higher levels of HIV-1 production were observed in KD-nonpermissive versus control nonpermissive U937 cells after infection. In contrast, lower peak levels of HIV-1 replication characterized U937 and A3.01 cells expressing TRIM22 versus their control transduced counterpart. Thus, nuclear TRIM22 significantly impairs HIV-1 replication, likely by interfering with Tat- and NF-κB-independent LTR-driven transcription.
Evaluation of human papillomavirus testing for squamous cell carcinoma of the tonsil in clinical practice
Authors: Thavaraj Selvam , Stokes Angela , Guerra Eliete , Bible Jon , Halligan Eugene , Long Anna , Okpokam Atuora , Sloan Philip , Odell Edward , Robinson Max 
Published: February 2011

BackgroundOncogenic human papillomavirus (HPV)-associated oropharyngeal squamous cell carcinoma (SCC) is a subtype of head-and-neck cancer with a distinct clinical and prognostic profile. While there are calls to undertake HPV testing for oropharyngeal SCCs within the diagnostic setting and for clinical trials, there are currently no internationally accepted standards.Methods142 tonsil SCCs were tested using p16 immunohistochemistry (IHC), high-risk HPV DNA in situ hybridisation (ISH) and HPV DNA polymerase chain reaction (PCR; GP5+/6+ primers).ResultsThere were high levels of agreement between pathologists for p16 IHC and HPV ISH scoring; however, around 10% of HPV ISH cases showed some interobserver discrepancy that was resolved by slide review. The combination of p16 IHC and HPV ISH classified 53% of the samples as HPV-positive, whereas the combination of p16 IHC and HPV PCR classified 61% of the samples as HPV-positive. By employing a three-tiered, staged algorithm (p16 IHC/HPV ISH/HPV PCR), the authors were able to classify 98% of the cases as either HPV-positive (p16 IHC+/HPV DNA+; 62%) or HPV-negative (p16 IHC−/HPV DNA−; 35%).ConclusionsThe current study suggests that using a combination of p16 IHC/HPV ISH/HPV PCR, in a three-tiered, staged algorithm, in conjunction with consensus reporting of HPV ISH, leads to less equivocal molecular classification. In order to ensure consistent reporting of this emerging disease, it is increasingly important for the head-and-neck oncology community to define the minimum requirements for assigning a diagnosis of ‘HPV-related’ oropharyngeal SCC in order to inform prognosis and for stratification in clinical trials.
Enhancing tectonic and provenance information from detrital zircon studies: assessing terrane-scale sampling and grain-scale characterization
Authors: Hietpas Jack , Samson Scott , Moecher David , Chakraborty Suvankar 
Published: February 2011

Abstract:
Determining detrital zircon U–Pb ages has become the method of choice for single- mineral-based provenance studies focused on the identification of potential source regions of siliciclastic sediments. Advances in microanalytical methods have significantly accelerated the acquisition rate of U–Pb ages, thus allowing for more statistically significant zircon age datasets to be acquired than previously. However, several studies have demonstrated limitations of relying solely on detrital zircon as a provenance proxy. To further assess the utility of this provenance indicator we measured U–Pb ages of detrital zircon derived from modern sediment collected from the French Broad River and its tributaries that drain portions of the Appalachian Orogen in southeastern USA. The results demonstrate that significant detrital zircon age variations occur along the length of the river. The age variations suggest that characterization of entire sedimentary formations by analysis of single samples may be misleading and that a multiple-sample approach is required. In addition, by incorporating high-magnification cathodoluminescence images with Th/U for each detrital grain, a more robust interpretation can be made regarding zircon source.

Supplementary material:

Global positioning system coordinates for each sampling location and complete zircon data are available at
http:/www.geolsoc.org.uk/SUP18445
.
Late Cretaceous to Recent deformation related to inherited structures and subsequent compression within the Persian Gulf: a 2D seismic case study
Authors: Burberry C.M. , Jackson C.A.-L. , Cosgrove J.W. 
Published: February 2011

Abstract:
The Persian Gulf is part of an asymmetric foreland basin related to the Zagros Orogen. Few published studies of this basin and associated onshore areas include seismic reflection data. We present a seismic-stratigraphic interpretation based on marine 2D seismic data, which reveals the presence of two types of compressional structures within the basin: (1) faulted domes related to salt movement and the offshore trace of a NNE–SSW-trending dextral basement fault (the Kazerun Fault); (2) long-wavelength (16 km), low-amplitude (60 ms two-way travel time) folds relating to the advancing deformation front associated with the orogen. Thinning of age-constrained stratal units across structures related to the offshore trace of the Kazerun Fault implies a distinct pulse of uplift on this fault during the Maastrichtian. The geometry of growth strata across other intra-basin structures suggests a second, later stage of deformation, which began in the Middle Miocene. Thickening and folding of post-Middle Miocene stratal units towards the NE (i.e. towards the Zagros Orogen) is interpreted to reflect rapid loading, subsidence and compression related to southwestwards advance of the orogen. The results of this study have implications for the interaction between pre-existing structures and later compressional events both within the Persian Gulf and elsewhere.
Sedimentation in deep-sea lobe-elements: implications for the origin of thickening-upward sequences
Authors: Macdonald Heather A. , Peakall Jeff , Wignall Paul B. , Best Jim 
Published: February 2011

Abstract:
The frequency and origin of thickening-upward packages in the sediments of deep-sea environments has been a topic of much recent debate. Excellent bed-scale exposures in the Carboniferous Ross Formation, western Ireland, allow single surfaces to be traced laterally and the detailed architecture of whole packages to be evaluated using multiple vertical logs. The deposits comprise architectural elements including bed-sets, lobe-elements and composite lobes, with the lobe-elements being arranged in thickening-upward depositional packages. Results show that these packages are the result of the progradation of each lobe-element, whereby each package records a vertical trend from distal to proximal deposits accompanied by an increasing frequency of megaflutes and ultimately the development of broad erosional surfaces. We propose a six-stage model for lobe-element evolution that documents successive phases of deposition, sediment bypass, erosion and lobe abandonment. This new model provides a mechanism for lobe-element switching and explains the development of thickening-upward successions. This allows the re-examination of existing process models for these sedimentary packages in deep-sea sediments.