bluuebunny/crossref_metadata_2025_split huggingface dataset:
Economic Reform and Total Factor Productivity Growth in Indian Manufacturing Industries
Authors: Kim Sangho , Saravanakumar Muthusamy 
Published: January 2012

AbstractA stochastic frontier production function model is applied to Indian manufacturing industries, to decompose the sources of total factor productivity growth into technical progress, technical efficiency, scale efficiency, and allocative efficiency. Empirical results based on data from 2000 to 2006 suggest that increased investment needs time to deliver increased productivity and efficiency, because new technology combined with fresh investment requires higher numbers of skilled workers, better managerial practices and an advanced input mix, all of which generally take time to develop. Thus, the Indian economy must boost technical efficiency by providing skilled workers and high quality managers to further economic reform.
Neuraminidase H275Y and hemagglutinin D222G mutations in a fatal case of 2009 pandemic influenza A (H1N1) virus infection
Authors: DeVries Aaron , Wotton Jason , Lees Christine , Boxrud David , Uyeki Timothy , Lynfield Ruth 
Published: January 2012

Please cite this paper as: DeVries et al. (2012) Neuraminidase H275Y and hemagglutinin D222G mutations in a fatal case of 2009 pandemic influenza A (H1N1) virus infection. Influenza and Other Respiratory Viruses 6(601), e85–e88.Oseltamivir‐resistant 2009 H1N1 influenza virus infections associated with neuraminidase (NA) H275Y have been identified sporadically. Strains possessing the hemagglutinin (HA) D222G mutation have been detected in small numbers of fatal 2009 H1N1 cases. We report the first clinical description of 2009 H1N1 virus infection with both NA‐H275Y and HA‐D222G mutations detected by pyrosequencing of bronchioalveolar lavage fluid obtained on symptom day 19. The 59‐year‐old immunosuppressed patient had multiple conditions conferring higher risk of prolonged viral replication and severe illness and died on symptom day 34. Further investigations are needed to determine the significance of infection with strains possessing NA‐H275Y and HA‐D222G.
Occurrence and Persistence of Bacterial Pathogens and Indicator Organisms in Beach Sand along the California Coast
Authors: Yamahara Kevan M. , Sassoubre Lauren M. , Goodwin Kelly D. , Boehm Alexandria B. 
Published: January 2012

ABSTRACTThis report documents the presence of fecal indicators and bacterial pathogens in sand at 53 California marine beaches using both culture-dependent and -independent (PCR and quantitative PCR [QPCR]) methods. Fecal indicator bacteria were widespread in California beach sand, withEscherichia coliand enterococci detected at 68% and 94% of the beaches surveyed, respectively. Somatic coliphages and aBacteroidaleshuman-specific fecal marker were detected at 43% and 13% of the beaches, respectively. Dry sand samples from almost 30% of the beaches contained at least one of the following pathogens:Salmonellaspp.,Campylobacterspp.,Staphylococcus aureus, and methicillin-resistantStaphylococcus aureus(MRSA), which were detected at 15%, 13%, 14%, and 3% of tested beaches, respectively. Fecal indicators and pathogens were poorly correlated to one another and to land cover. Sands were dry at the time of collection, and those with relatively high moisture tended to have higher concentrations or a more frequent occurrence of both indicators and pathogens. Using culture-dependent assays, fecal indicators decayed faster than pathogens in microcosm experiments using unaltered beach sand seeded with sewage and assessed by culture-dependent assays. The following order of persistence was observed (listed from most to least persistent):Campylobacter>Salmonella> somatic coliphages > enterococci >E. coli> F+phages. In contrast, pathogens decayed faster than fecal indicators in culture-independent assays: enterococci >Bacteroidaleshuman-specific marker >Salmonella>Campylobacter. Microcosm experiments demonstrated that both indicators and pathogens were mobilized by wetting with seawater. Decay rates measured by QPCR were lower than those measured with culture-dependent methods. Enterococcal persistence and possible growth were observed for wetted microcosms relative to unwetted controls.
Unexpected Stability of Bacteroidetes and Firmicutes Communities in Laboratory Biogas Reactors Fed with Different Defined Substrates
Authors: Kampmann K. , Ratering S. , Kramer I. , Schmidt M. , Zerr W. , Schnell S. 
Published: January 2012

ABSTRACT

In the present study, bacterial communities in 200-liter biogas reactors containing liquid manure consecutively fed with casein, starch, and cream were investigated over a period of up to 33 days. A 16S rRNA gene clone library identified
Bacteroidetes
and
Firmicutes
as the most abundant bacterial groups in the starting material, at 58.9% and 30.1% of sequences, respectively. The community development of both groups was monitored by real-time PCR and single-strand conformation polymorphism (SSCP) analysis. The
Firmicutes
and
Bacteroidetes
communities were unexpectedly stable and hardly influenced by batch-feeding events. The continuous feeding of starch led to community shifts that nevertheless contributed to a stable reactor performance. A longer starving period and a change in the pH value resulted in further community shifts within the
Bacteroidetes
but did not influence the
Firmicutes
. Predominant DNA bands from SSCP gels were cloned and sequenced. Sequences related to
Peptococcaceae
,
Cytophagales
, and
Petrimonas sulfuriphila
were found in all samples from all experiments. Real-time PCR demonstrated the abundance of members of the phylum
Bacteroidetes
and also reflected changes in gene copy numbers in conjunction with a changing pH value and acetate accumulation.
Influence of Anaerobiosis and Low Temperature on Bacillus cereus Growth, Metabolism, and Membrane Properties
Authors: de Sarrau Benoît , Clavel Thierry , Clerté Caroline , Carlin Frédéric , Giniès Christian , Nguyen-The Christophe 
Published: January 2012

ABSTRACT

The impact of simultaneous anaerobiosis and low temperature on growth parameters, metabolism, and membrane properties of
Bacillus cereus
ATCC 14579 was studied. No growth was observed under anaerobiosis at 12°C. In bioreactors, growth rates and biomass production were drastically reduced by simultaneous anaerobiosis and low temperature (15°C). The two conditions had a synergistic effect on biomass reduction. In anaerobic cultures, fermentative metabolism was modified by low temperature, with a marked reduction in ethanol production leading to a lower ability to produce NAD
+
. Anaerobiosis reduced unsaturated fatty acids at both low optimal temperatures. In addition, simultaneous anaerobiosis and low temperatures markedly reduced levels of branched-chain fatty acids compared to all other conditions (accounting for 33% of total fatty acids against more 71% for low-temperature aerobiosis, optimal-temperature aerobiosis, and optimal-temperature anaerobiosis). This corresponded to high-melting-temperature lipids and to low-fluidity membranes, as indicated by differential scanning calorimetry, 1,6-diphenyl-1,3,5-hexatriene (DPH) fluorescence anisotropy, and infrared spectroscopy. This is in contrast to requirements for cold adaptation. A link between modification in the synthesis of metabolites of fermentative metabolism and the reduction of branched-chain fatty acids at low temperature under anaerobiosis, through a modification of the oxidizing capacity, is assumed. This link may partly explain the impact of low temperature and anaerobiosis on membrane properties and growth performance.
A Novel Restriction-Modification System Is Responsible for Temperature-Dependent Phage Resistance in Listeria monocytogenes ECII
Authors: Kim Jae-Won , Dutta Vikrant , Elhanafi Driss , Lee Sangmi , Osborne Jason A. , Kathariou Sophia 
Published: January 2012

ABSTRACT

Listeria monocytogenes
epidemic clone II (ECII) strains are unusual in being completely resistant to phage when grown at low temperatures (≤30°C). In the current study we constructed and characterized a
mariner
-based mutant (J46C) of the ECII strain H7550-Cd
S
that lacked temperature-dependent resistance to phage. The transposon was localized in LMOh7858_2753 (open reading frame [ORF] 2753), a member of a 12-ORF genomic island unique to ECII strains. ORF 2753 and ORF 2754 exhibited homologies to restriction endonucleases and methyltransferases associated with type II restriction-modification (RM) systems.
In silico
-based predictions of the recognition site for this putative RM system were supported by resistance of DNA from ECII strains to digestion by BfuI, a type II restriction enzyme specific for GTATCC (N6/5). Similarly to J46C, a mutant harboring an in-frame deletion of ORF 2753 was susceptible to phage regardless of temperature of growth (25°C or 37°C). Genetic complementation restored phage resistance in 25°C-grown cells of ORF 2753 mutants. Reverse transcription (RT) and quantitative real-time PCR data suggested enhanced transcription of ORF 2753 at low temperatures (≤25°C) compared to 37°C. In contrast, available transcriptional data suggested that the putative methyltransferase (ORF 2754) was constitutively expressed at all tested temperatures (4 to 37°C). Thus, temperature-dependent resistance of
L. monocytogenes
ECII to phage is mediated by temperature-dependent expression of the restriction endonuclease associated with a novel RM system (LmoH7) unique to this epidemic clone.
Extensive Manipulation of Caseicins A and B Highlights the Tolerance of These Antimicrobial Peptides to Change
Authors: Norberg Sarah , O'Connor Paula M. , Stanton Catherine , Ross R. Paul , Hill Colin , Fitzgerald Gerald F. , Cotter Paul D. 
Published: January 2012

ABSTRACT

Caseicins A and B are low-molecular-weight antimicrobial peptides which are released by proteolytic digestion of sodium caseinate. Caseicin A (IKHQGLPQE) is a nine-amino-acid cationic peptide, and caseicin B (VLNENLLR) is a neutral eight-amino-acid peptide; both have previously been shown to exhibit antibacterial activity against a number of pathogens, including
Cronobacter sakazakii
. Previously, four variants of each caseicin which differed subtly from their natural counterparts were generated by peptide synthesis. Antimicrobial activity assays revealed that the importance of a number of the residues within the peptides was dependent on the strain being targeted. In this study, this engineering-based approach was expanded through the creation of a larger collection of 26 peptides which are altered in a variety of ways. The investigation highlights the generally greater tolerance of caseicin B to change, the fact that changes have a more detrimental impact on anti-Gram-negative activity, and the surprising number of variants which exhibit enhanced activity against
Staphylococcus aureus
.
Detection of Coxiella burnetii DNA on Small-Ruminant Farms during a Q Fever Outbreak in the Netherlands
Authors: de Bruin A. , van der Plaats R. Q. J. , de Heer L. , Paauwe R. , Schimmer B. , Vellema P. , van Rotterdam B. J. , van Duynhoven Y. T. H. P. 
Published: January 2012

ABSTRACT

During large Q fever outbreaks in the Netherlands between 2007 and 2010, dairy goat farms were implicated as the primary source of human Q fever. The transmission of
Coxiella burnetii
to humans is thought to occur primarily via aerosols, although available data on
C. burnetii
in aerosols and other environmental matrices are limited. During the outbreak of 2009, 19 dairy goat farms and one dairy sheep farm were selected nationwide to investigate the presence of
C. burnetii
DNA in vaginal swabs, manure, surface area swabs, milk unit filters, and aerosols. Four of these farms had a positive status during the
Coxiella burnetii
bulk milk monitoring program in 2009 and additionally reported abortion waves in 2008 or 2009. Eleven farms were reported as having positive bulk milk only, and five selected (control) farms had a bulk milk-negative status in 2009 and no reported Q fever history. Screening by quantitative PCR (qPCR) revealed that on farms with a history of abortions related to
C. burnetii
and, to a lesser extent, on farms positive by bulk milk monitoring, generally higher proportions of positive samples and higher levels of
C. burnetii
DNA within positive samples were observed than on the control farms. The relatively high levels of
C. burnetii
DNA in surface area swabs and aerosols sampled in stables of bulk milk-positive farms, including farms with a Q fever-related abortion history, support the hypothesis that these farms can pose a risk for the transmission of
C. burnetii
to humans.
The Ustilago maydis Nit2 Homolog Regulates Nitrogen Utilization and Is Required for Efficient Induction of Filamentous Growth
Authors: Horst Robin J. , Zeh Christine , Saur Alexandra , Sonnewald Sophia , Sonnewald Uwe , Voll Lars M. 
Published: January 2012

ABSTRACT

Nitrogen catabolite repression (NCR) is a regulatory strategy found in microorganisms that restricts the utilization of complex and unfavored nitrogen sources in the presence of favored nitrogen sources. In fungi, this concept has been best studied in yeasts and filamentous ascomycetes, where the GATA transcription factors Gln3p and Gat1p (in yeasts) and Nit2/AreA (in ascomycetes) constitute the main positive regulators of NCR. The reason why functional Nit2 homologs of some phytopathogenic fungi are required for full virulence in their hosts has remained elusive. We have identified the Nit2 homolog in the basidiomycetous phytopathogen
Ustilago maydis
and show that it is a major, but not the exclusive, positive regulator of nitrogen utilization. By transcriptome analysis of sporidia grown on artificial media devoid of favored nitrogen sources, we show that only a subset of nitrogen-responsive genes are regulated by Nit2, including the Gal4-like transcription factor Ton1 (a target of Nit2). Ustilagic acid biosynthesis is not under the control of Nit2, while nitrogen starvation-induced filamentous growth is largely dependent on functional Nit2.
nit2
deletion mutants show the delayed initiation of filamentous growth on maize leaves and exhibit strongly compromised virulence, demonstrating that Nit2 is required to efficiently initiate the pathogenicity program of
U. maydis
.
Pericallosal artery aneurysm treatment using Y-configuration stent-assisted coil embolization: a report of four cases
Authors: Darkhabani Ziad M , Lazzaro Marc A , Zaidat Osama O 
Published: January 2012

BackgroundPericallosal artery aneurysms at the bifurcation represent a special endovascular technical challenge given their distal location, commonly wide-neck morphology, small parent vessel diameter and potentially high recurrence rate after coiling given the bifurcation location. Y-configuration stent-assisted coil embolization techniques have been reported for the treatment of wide-neck aneurysms located at other vascular bifurcations and only rarely with A2 bifurcation aneurysms.MethodsA neurointerventional database was reviewed for identification of all cases of A2 bifurcation aneurysms that were treated with Y-stent configuration. The authors report clinical, technical and outcome data on four patients with pericallosal aneurysms who were treated with a Y-configuration stent-assisted coil embolization technique.ResultsA Y-configuration stent placement in the anterior cerebral artery/A2 bifurcation was successfully achieved in all four patients without significant technical difficulties. One patient presented with a previously ruptured and partially treated aneurysm and three patients with incidentally found aneurysms. All four patients had a Y-configuration stent placement in one setting. The Y-configuration allowed for complete occlusion of all four aneurysms with no recurrence or arterial occlusion on mean angiographic follow-up of 13.5 months (6–28).ConclusionTreating wide-neck pericallosal artery aneurysms at the bifurcation with Y-configuration stent placement is feasible and effective. This technique may be considered as a therapeutic option for wide-neck aneurysms that pose a difficult technical challenge.
LIFTING FILLING DEHN SPHERES
Authors: VIGARA RUBEN 
Published: January 2012

A Dehn sphere Σ [C. D. Papakyriakopoulos, On Dehn's Lemma and the asphericity of knots, Ann. Math. (2) 66 (1957) 1–26] in a closed 3-manifold M is a sphere immersed in M with only double curve and triple point singularities. The Dehn sphere Σ ⊂ M lifts to M × I, where I is an interval, if there exists an embedded sphere in M × I that projects onto Σ. Every closed 3-manifold has a filling Dehn sphere [J. M. Montesinos-Amilibia, Representing 3-Manifold by Dehn Spheres, Contribuciones Matemáticas: Homenaje a Joaquín Arregui Fernández (Editorial Complutense, 2000), pp. 239–247], i.e. a Dehn sphere that defines a cell decomposition of M. In [R. Vigara, Representación de 3-variedades por esferas de Dehn rellenantes, Ph.D. Thesis, UNED, Madrid (2006)], it is shown that every closed 3-manifold M has a filling Dehn sphere that lifts to M × I. In this paper it is proved that every closed 3-manifold has a filling Dehn sphere that does not lift to M × I. These results solve a question of Roger Fenn.
Downregulation of SMG-1 in HPV-Positive Head and Neck Squamous Cell Carcinoma Due to Promoter Hypermethylation Correlates with Improved Survival
Authors: Gubanova Evgenia , Brown Brandee , Ivanov Sergei V. , Helleday Thomas , Mills Gordon B. , Yarbrough Wendell G. , Issaeva Natalia 
Published: January 2012

Abstract
Purpose: Human papillomavirus (HPV) is linked with a subset of head and neck squamous cell carcinomas (HNSCC). HPV-positive HNSCCs show a better prognosis than HPV-negative HNSCCs, which may be explained by sensitivity of the HPV-positive HNSCCs to ionizing radiation (IR). Although the molecular mechanism behind sensitivity to IR in HPV-positive HNSCCs is unresolved, DNA damage response (DDR) might be a significant determinant of IR sensitivity. An important player in the DDR, SMG-1 (suppressor with morphogenetic effect on genitalia), is a potential tumor suppressor and may therefore be deregulated in cancer. No studies have yet been conducted linking defects in SMG-1 expression with cancer. We investigated whether deregulation of SMG-1 could be responsible for defects in the DDR in oropharyngeal HNSCC.
Experimental Design: Expression and promoter methylation status of SMG-1 were investigated in HNSCCs. To identify a functional link between HPV infection and SMG-1, we transfected the HPV-negative cells with an E6/E7 expression construct. SMG-1 short hairpin RNAs were expressed in HPV-negative cells to estimate survival upon IR.
Results: Forced E6/E7 expression in HPV-negative cells resulted in SMG-1 promoter hypermethylation and decreased SMG-1 expression. Due to promoter hypermethylation, HPV-positive HNSCC cells and tumors express SMG-1 at lower levels than HPV-negative SCCs. Depletion of SMG-1 in HPV-negative HNSCC cells resulted in increased radiation sensitivity, whereas SMG-1 overexpression protected HPV-positive tumor cells from irradiation.
Conclusions: Levels of SMG-1 expression negatively correlated with HPV status in cancer cell lines and tumors. Diminished SMG-1 expression may contribute to the enhanced response to therapy exhibited by HPV-positive HNSCCs. Clin Cancer Res; 18(5); 1257–67. ©2012 AACR.
Antisense inhibition of coagulation factor XI prolongs APTT without increased bleeding risk in cynomolgus monkeys
Authors: Younis Husam S. , Crosby Jeff , Huh Jung-Im , Lee Hong Soo , Rime Soyub , Monia Brett , Henry Scott P. 
Published: January 2012

AbstractA strategy to produce sufficient anticoagulant properties with reduced risk of bleeding may be possible through inhibition of factor XI (FXI), a component of the intrinsic coagulation cascade. The objective of this work was to determine the safety profile of ISIS 416858, a 2′-methoxyethoxy (2′-MOE) antisense oligonucleotide inhibitor of FXI, with focus on assessment of bleeding risk. Cynomolgus monkeys administered ISIS 416858 (4, 8, 12, and 40 mg/kg/wk, subcutaneous) for up to 13 weeks produced a dose-dependent reduction in FXI (mRNA in liver and plasma activity) and a concomitant increase in activated partial thromboplastin time (APTT). ISIS 416858 (20 or 40 mg/kg/wk) reduced plasma FXI activity by 80% at 4 weeks of treatment that resulted in a 33% increase in APTT by 13 weeks with no effects on PT, platelets, or increased bleeding following partial tail amputation or gum and skin laceration. The dose-dependent presence of basophilic granules in multiple tissues in ISIS 416858–treated animals was an expected histologic change for a 2′-MOE antisense oligonucleotide, and no toxicity was attributed to hepatic FXI reduction. Basophilic granules reflect cellular drug uptake and subsequent visualization on hematoxylin staining. These results suggest that ISIS 416858 has an acceptable preclinical safety profile and is a promising clinical candidate to treat thrombotic disease.
Initial bone marrow reticulin fibrosis in polycythemia vera exerts an impact on clinical outcome
Authors: Barbui Tiziano , Thiele Jürgen , Passamonti Francesco , Rumi Elisa , Boveri Emanuela , Randi Maria Luigia , Bertozzi Irene , Marino Filippo , Vannucchi Alessandro M. , Pieri Lisa , Rotunno Giada , Gisslinger Heinz , Gisslinger Bettina , Müllauer Leonhard , Finazzi Guido , Carobbio Alessandra , Gianatti Andrea , Ruggeri Marco , Nichele Ilaria , D'Amore Emanuele , Rambaldi Alessandro , Tefferi Ayalew 
Published: January 2012

Abstract
We examined the prevalence and prognostic relevance of bone marrow reticulin fibrosis in 526 patients with World Health Organization–defined polycythemia vera evaluated at the time of initial diagnosis. Seventy-four patients (14%) displayed mostly grade 1 reticulin fibrosis, with only 2 cases showing higher-grade fibrosis. Presenting clinical and laboratory characteristics, including JAK2V617F allele burden, between patients with and without fibrosis were similar for the most part, with the exception of a higher prevalence of palpable splenomegaly in patients with fibrosis (P < .01). Patients with fibrosis were less prone to experience thrombosis during their clinical course (1.1 vs 2.7 per 100 patient-years; P = .03) and more prone to develop post-polycythemia vera myelofibrosis (2.2 vs 0.8 per 100 patient-years; P = .01). There was no significant difference between the 2 groups in terms of overall or leukemia-free survival. The present study clarifies the incidence, degree, and prognostic relevance of bone marrow fibrosis obtained at time of initial diagnosis of polycythemia vera.
Demand-adapted regulation of early hematopoiesis in infection and inflammation
Authors: Takizawa Hitoshi , Boettcher Steffen , Manz Markus G. 
Published: January 2012

AbstractDuring systemic infection and inflammation, immune effector cells are in high demand and are rapidly consumed at sites of need. Although adaptive immune cells have high proliferative potential, innate immune cells are mostly postmitotic and need to be replenished from bone marrow (BM) hematopoietic stem and progenitor cells. We here review how early hematopoiesis has been shaped to deliver efficient responses to increased need. On the basis of most recent findings, we develop an integrated view of how cytokines, chemokines, as well as conserved pathogen structures, are sensed, leading to divisional activation, proliferation, differentiation, and migration of hematopoietic stem and progenitor cells, all aimed at efficient contribution to immune responses and rapid reestablishment of hematopoietic homeostasis. We also outline how chronic inflammatory processes might impinge on hematopoiesis, potentially fostering hematopoietic stem cell diseases, and, how clinical benefit is and could be achieved by learning from nature.