bluuebunny/crossref_metadata_2025_split huggingface dataset:
Community profiling and quantification of putative autotrophic thaumarchaeal communities in environmental samples
Authors: Offre Pierre , Nicol Graeme W. , Prosser James I. 
Published: October 2010

SummaryGrowth of thaumarchaea with ammonia as a sole energy source has been demonstrated but their mode(s) of carbon metabolism remain uncertain, with evidence for autotrophy, heterotrophy and mixotrophy. Understanding the role played by autotrophy in thaumarchaeal growth strategies has been hindered by the lack of an adequate marker gene and PCR primers. The aim of this study was to develop PCR‐based approaches to determine the prevalence of autotrophy associated with thaumarchaea. Primer pairs were designed specifically targeting hcd genes, encoding putative 4‐hydroxybutyryl‐CoA dehydratase, a key functional enzyme in thaumarchaeal autotrophy. Phylogenetic analysis of hcd gene sequences amplified from soils and sediments indicated the existence of environment‐specific sequence clusters and hcd abundance in soil was 105–106 g−1 soil, as assessed by quantitative PCR. Abundance and diversity of hcd genes were also determined in soil microcosms incubated with and without acetylene, a known inhibitor of nitrification. Nitrification was accompanied by increases in hcd gene abundance and in the relative abundance of two bands in denaturing gradient gel electrophoresis profiles. Nitrification, growth and community changes were inhibited by acetylene and the findings are consistent with active autotrophic ammonia oxidation by archaea in soil.
Case of cavitary pulmonary endometriosis with catamenial hemoptysis
Authors: Ohshio Y , Asakura S , Ichinose M 
Published: October 2010

AbstractA 32‐year‐old woman was admitted to our department with recurrent hemoptysis coincident with the onset of her menses. Chest computed tomography revealed a cyst in the left S4 area of the lung and, during the menses, ill‐defined opacity with blood oozing from the cyst. Pelvic magnetic resonance imaging revealed adenomyomatosis uteri and endometriosis of the right ovary. Bronchoscopic washing was carried out at the left B4, but no endometrial tissue was obtained. The patient refused hormone therapy, so left S4+5 segmentectomy was carried out thoracoscopically. The histopathological examination of the resected specimen revealed typical findings of endometrial tissue. The postoperative course was favorable with no further episodes of hemoptysis.
Through which layer, between the gallbladder and the liver, does the deep branch of the cystic artery run?
Authors: Honda G , Iwasaki KI , Matsumura H , Kurata M , Matsumoto H , Horiguchi S , Katoh I 
Published: October 2010

AbstractIntroduction: During laparoscopic cholecystectomy, an enlarged field of vision increases safety and precision, but surgeons often encounter bleeding that can cause difficulties. It is important to prevent and control arterial bleeding from Calot's triangle and the liver bed that results from injury to the deep branch of the cystic artery (DBCA). However, no previous reports have mentioned the layer between the gallbladder and liver through which the DBCA runs.Materials and Surgical Technique: To determine this layer, we investigated the histological findings from consecutive thin‐slice (3 mm) blocks in six cases (three cadavers and three patients who underwent extended cholecystectomy).Results: The subserosal layer of the gallbladder wall can be divided into an inner (ss‐i) layer, which consists of abundant vasculature and some fibrous tissue, and an outer (ss‐o) layer, which consists of abundant fat tissue. DBCA runs through the ss‐o layer, far from the ss‐i layer in Calot's triangle, and runs toward the gallbladder body and ramifies into several branches that flow into the ss‐i layer.Discussion: If the gallbladder is dissected in the layer close to the ss‐i layer, as in our standardized procedure, the subbranches of DBCA are transected at the border of the ss‐i layer, and most of the DBCA is left within the ss‐o layer in Calot's triangle and the liver bed. Knowledge of the anatomy of DBCA is useful to avoid and stop bleeding from the deep part of Calot's triangle and the liver bed.
Sequence analysis of the S gene region in HBV DNA from patients positive for both HBsAg and HBsAb tests
Authors: Wang Lei , Liu Hua , Ning Xiaoxiao , Gao Feng 
Published: October 2010

Aims:  To study the characteristics of mutation in the amino acids coded by the S gene region in the HBV DNA sequence and to comprehensively explore and analyze the cause of the double positive result phenomena in both HBsAg and HBsAb tests.Methods:  Specimens collected from 43 cases of chronic hepatitis B patients with positive results for both HBsAg and HBsAb tests were used as the experimental group; specimens collected from 43 cases randomly picked from all patients with chronic hepatitis B with a single positive result for HBsAg test were used as the control group. In HBV DNA, the S gene region was amplified and sequenced. Amino acid sequences were grouped, and mutations were analyzed based on the sequencing results.Results:  The patients were infected with HBV of the genotype B and C and those who with genotype C show more mutations than genotype B carriers. Compared with the control group, the experimental group had a marked increase in S gene amino acid mutations; a higher amino acid mutation rate was observed in the first loop (aa124–137) of the a‐determinant (aa124–147) and there was a statistical difference (genotype B: 2.68% vs. 0.00%, P = 0.041; genotype C: 7.14% vs. 2.01%, P < 0.001).Conclusion:  The first loop in a‐determinant of S gene sequence possesses a large numbers of mutated amino acids, leading to changes of antigenicity and simultaneous positive results in both HBsAg and HBsAb tests finally.
Combined pre‐S deletion and core promoter mutations related to hepatocellular carcinoma: A nested case‐control study in China
Authors: Qu Li‐Shuai , Liu Tao‐Tao , Jin Fei , Guo Yan‐Mei , Chen Tao‐Yang , Ni Zheng‐Pin , Shen Xi‐Zhong 
Published: October 2010

Aim:  To investigate the roles of biomedical factors, hepatitis B virus (HBV) DNA levels, genotypes, and specific viral mutation patterns on the progression of hepatocellular carcinoma (HCC) in Qidong, China.Methods:  A total of 2387 males (aged 20–65 years) who were seropositive for the hepatitis B surface antigen (HBsAg), but had not been diagnosed with HCC, were recruited to a community‐based HCC screening study from August, 1996. Evaluation of virological parameters at recruitment was determined for 196 HCC patients during 10 years of follow‐up and 323 controls.Results:  After adjustment for age at recruitment, history of cigarette smoking and alcohol consumption, alanine aminotransferase (ALT) elevation, alpha‐fetoprotein (AFP) levels >20 ng/mL, hepatitis B e antigen positive, HBV DNA levels ≥4.00 log10 copies/mL, pre‐S deletion, T1653 mutation, T1762/A1764 double mutations, and T1766 and/or A1768 mutations were associated with subsequent risk of HCC. A significant biological gradient of HCC risk by HBV DNA levels from less than 2.69 log10 copies/mL to 6.00 log10 copies/mL or greater was observed. HBV with a complex mutation combination pattern (pre‐S deletion, T1762/A1764 double mutations, and T1766 and/or A1768 mutations) rather than a single mutation was associated with the development of HCC. The longitudinal observation demonstrated a gradual combination of pre‐S deletion, T1762/A1764 double mutations, and T1766 and/or A1768 mutations during the development of HCC.Conclusions:  AFP levels >20 ng/mL, high HBV DNA levels, pre‐S deletion, and T1762/A1764 double mutations at recruitment were independent risk factors of HCC. Combination of pre‐S deletion and core promoter mutations increased the risk of HCC.
Organic anion transporter 1B1 (SLCO1B1) polymorphism and gallstone formation: High incidence of Exon4 CA genotype in female patients in North India
Authors: Srivastava Anshika , Srivastava Anvesha , Srivastava Neena , Choudhuri Gourdas , Mittal Balraj 
Published: October 2010

Aim:  Gallstone disease is an important cause of abdominal morbidity Organic anion transport protein 1B1 (OATP1B1) (encoded by SLCO1B1) is a major transporter protein for bile salt uptake in enterohepatic circulation of bile salts. Disturbance in this pathway can decrease relative concentration of bile salts in gallbladder and may lead to formation of gallstones. We investigated role of SLCO1B1 polymorphisms [(Exon4 C > A (Pro155Thr; rs11045819) and Ex6 + 40T > C (Val174Ala; rs4149056)] in conferring interindividual susceptibility to gallstone disease.Methods:  A total of 173 healthy controls and 226 gallstone patients (USG positive) were recruited. Genotyping was done by using standard polymerase chain reaction restriction fragment length polymorphism (PCR‐RFLP) method.Results:  The observed control frequencies of both polymorphisms of SLCO1B1 gene [(Exon4 C > A (Pro155Thr; rs11045819) and Ex6 + 40T > C (Val174Ala; rs4149056)] were in agreement with Hardy‐Weinberg equilibrium. The frequency CA genotype and A allele of Exon4 C > A polymorphism was higher in gallstones patients (12.4% and 6.2%) as compared to controls (5.2% and 2.6%) which was statistically significant [(P = 0.029; OR = 2.31; 95% CI = 1.1–5.0); (P = 0.034; OR = 2.22; 95% CI = 1.1–4.8)], respectively). However, distribution of genotypes and alleles of Ex6 + 40T > C polymorphism was almost similar between gallstone patients and controls. Haplotype analysis showed frequency of A,T haplotype consisting of was significantly higher in gallstone patients as compared to controls and was imposing risk for the disease (P = 0.036; OR = 2.34; 95% CI = 1.0–5.1).Conclusion:  These results suggest that SLCO1B1 Exon4 C > A polymorphism confers increased risk for gallstone disease in North Indian population.
Computational Prediction of Type III and IV Secreted Effectors in Gram-Negative Bacteria
Authors: McDermott Jason E. , Corrigan Abigail , Peterson Elena , Oehmen Christopher , Niemann George , Cambronne Eric D. , Sharp Danna , Adkins Joshua N. , Samudrala Ram , Heffron Fred 
Published: October 2010

ABSTRACTIn this review, we provide an overview of the methods employed in four recent studies that described novel methods for computational prediction of secreted effectors from type III and IV secretion systems in Gram-negative bacteria. We present the results of these studies in terms of performance at accurately predicting secreted effectors and similarities found between secretion signals that may reflect biologically relevant features for recognition. We discuss the Web-based tools for secreted effector prediction described in these studies and announce the availability of our tool, the SIEVE server (http://www.sysbep.org/sieve). Finally, we assess the accuracies of the three type III effector prediction methods on a small set of proteins not known prior to the development of these tools that we recently discovered and validated using both experimental and computational approaches. Our comparison shows that all methods use similar approaches and, in general, arrive at similar conclusions. We discuss the possibility of an order-dependent motif in the secretion signal, which was a point of disagreement in the studies. Our results show that there may be classes of effectors in which the signal has a loosely defined motif and others in which secretion is dependent only on compositional biases. Computational prediction of secreted effectors from protein sequences represents an important step toward better understanding the interaction between pathogens and hosts.
Discovery of Novel Secreted Virulence Factors from
Salmonella enterica
Serovar Typhimurium by Proteomic Analysis of Culture Supernatants
Authors: Niemann George S. , Brown Roslyn N. , Gustin Jean K. , Stufkens Afke , Shaikh-Kidwai Afshan S. , Li Jie , McDermott Jason E. , Brewer Heather M. , Schepmoes Athena , Smith Richard D. , Adkins Joshua N. , Heffron Fred 
Published: October 2010

ABSTRACT

Salmonella enterica
serovar Typhimurium is a leading cause of acute gastroenteritis throughout the world. This pathogen has two type III secretion systems (TTSS) encoded in
Salmonella
pathogenicity islands 1 and 2 (SPI-1 and SPI-2) that deliver virulence factors (effectors) to the host cell cytoplasm and are required for virulence. While many effectors have been identified and at least partially characterized, the full repertoire of effectors has not been catalogued. In this proteomic study, we identified effector proteins secreted into defined minimal medium designed to induce expression of the SPI-2 TTSS and its effectors. We compared the secretomes of the parent strain to those of strains missing essential (
ssaK
::
cat
) or regulatory (Δ
ssaL
) components of the SPI-2 TTSS. We identified 20 known SPI-2 effectors. Excluding the translocon components SseBCD, all SPI-2 effectors were biased for identification in the Δ
ssaL
mutant, substantiating the regulatory role of SsaL in TTS. To identify novel effector proteins, we coupled our secretome data with a machine learning algorithm (SIEVE,
S
VM-based
i
dentification and
e
valuation of
v
irulence
e
ffectors) and selected 12 candidate proteins for further characterization. Using CyaA′ reporter fusions, we identified six novel type III effectors and two additional proteins that were secreted into J774 macrophages independently of a TTSS. To assess their roles in virulence, we constructed nonpolar deletions and performed a competitive index analysis from intraperitoneally infected 129/SvJ mice. Six mutants were significantly attenuated for spleen colonization. Our results also suggest that non-type III secretion mechanisms are required for full
Salmonella
virulence.
Myeloperoxidase Selectively Binds and Selectively Kills Microbes
Authors: Allen Robert C. , Stephens Jackson T. 
Published: October 2010

ABSTRACTMyeloperoxidase (MPO) is reported to selectively bind to bacteria. The present study provides direct evidence of MPO binding selectivity and tests the relationship of selective binding to selective killing. The microbicidal effectiveness of H2O2and of OCl−was compared to that of MPO plus H2O2. Synergistic microbicidal action was investigated by combiningStreptococcus sanguinis, a H2O2-producing microbe showing low MPO binding, with high-MPO-bindingEscherichia coli,Staphylococcus aureus, orPseudomonas aeruginosawithout exogenous H2O2, with and without MPO, and with and without erythrocytes (red blood cells [RBCs]). Selectivity of MPO microbicidal action was conventionally measured as the MPO MIC and minimal bactericidal concentration (MBC) for 82 bacteria includingE. coli,P. aeruginosa,S. aureus,Enterococcus faecalis,Streptococcus pyogenes,Streptococcus agalactiae, and viridans streptococci. Both H2O2and OCl−destroyed RBCs at submicrobicidal concentrations. Nanomolar concentrations of MPO increased H2O2microbicidal action 1,000-fold. Streptococci plus MPO produced potent synergistic microbicidal action against all microbes tested, and RBCs caused only a small decrease in potency without erythrocyte damage. MPO directly killed H2O2-producingS. pyogenesbut was ineffective against non-H2O2-producingE. faecalis. The MPO MICs and MBCs forE. coli,P. aeruginosa, andS. aureuswere significantly lower than those forE. faecalis.The streptococcal studies showed much higher MIC/MBC results, but such testing required lysed horse blood-supplemented medium, thus preventing valid comparison of these results to those for the other microbes.E. faecalisMPO binding is reportedly weak compared to binding ofE. coli,P. aeruginosa, andS. aureusbut strong compared to binding of streptococci. Selective MPO binding results in selective killing.
Multicentric Castleman's disease with abundant IgG4-positive cells: a clinical and pathological analysis of six cases
Authors: Sato Yasuharu , Kojima Masaru , Takata Katsuyoshi , Morito Toshiaki , Mizobuchi Kohichi , Tanaka Takehiro , Inoue Dai , Shiomi Hideyuki , Iwao Haruka , Yoshino Tadashi 
Published: October 2010

BackgroundDifferentiation between multicentric Castleman's disease and systemic immunoglobulin (Ig) G4-related lymphadenopathy is sometimes difficult. It has been suggested that measurement of the IgG4-/IgG-positive cell ratio is useful for the differential diagnosis of the two diseases. However, the authors present a detailed report of six patients with multicentric Castleman's disease with abundant IgG4-positive cells (IgG4-/IgG-positive cell ratio, >40%).ResultsIn the present series, the patients showed systemic lymphadenopathy, polyclonal hypergammaglobulinaemia and elevated serum interleukin-6 (IL-6) and C-reactive protein levels. Further, anaemia, hypoalbuminaemia, hypocholesterolaemia and thrombocytosis were observed. These findings were consistent with those of multicentric Castleman's disease. Although five patients showed elevated serum IgG4 levels, only two patients showed an increased serum IgG4/IgG ratio. However, the two patients showed highly elevated serum IgG4 levels, but the serum IgG4/IgG ratios were, although increased, not very high. Also, a patient with increased serum IgG4/IgG ratio showed a good response to antihuman IL-6 receptor monoclonal antibody (tocilizumab). Histologically, the germinal centres were mostly small and regressive, and frequently penetrated by hyalinised blood vessels, and there was no eosinophil infiltration. These findings were different from those of IgG4-related lymphadenopathy.ConclusionsThe authors conclude that multicentric Castleman's disease sometimes occurs with abundant IgG4-positive cells and elevated serum IgG4 levels. Therefore, the two diseases cannot be differentially diagnosed by immunohistochemical staining alone. Laboratory findings, especially IL-6 level, C-reactive protein level and platelet count, are important for the differential diagnosis of the two diseases.
Development of retrospective quantitative and qualitative job-exposure matrices for exposures at a beryllium processing facility
Authors: Couch James R , Petersen Martin , Rice Carol , Schubauer-Berigan Mary K 
Published: October 2010

ObjectivesTo construct a job-exposure matrix (JEM) for an Ohio beryllium processing facility between 1953 and 2006 and to evaluate temporal changes in airborne beryllium exposures.MethodsQuantitative area- and breathing-zone-based exposure measurements of airborne beryllium were made between 1953 and 2006 and used by plant personnel to estimate daily weighted average (DWA) exposure concentrations for sampled departments and operations. These DWA measurements were used to create a JEM with 18 exposure metrics, which was linked to the plant cohort consisting of 18 568 unique job, department and year combinations. The exposure metrics ranged from quantitative metrics (annual arithmetic/geometric average DWA exposures, maximum DWA and peak exposures) to descriptive qualitative metrics (chemical beryllium species and physical form) to qualitative assignment of exposure to other risk factors (yes/no). Twelve collapsed job titles with long-term consistent industrial hygiene samples were evaluated using regression analysis for time trends in DWA estimates.ResultsAnnual arithmetic mean DWA estimates (overall plant-wide exposures including administration, non-production, and production estimates) for the data by decade ranged from a high of 1.39 μg/m3in the 1950s to a low of 0.33 μg/m3in the 2000s. Of the 12 jobs evaluated for temporal trend, the average arithmetic DWA mean was 2.46 μg/m3and the average geometric mean DWA was 1.53 μg/m3. After the DWA calculations were log-transformed, 11 of the 12 had a statistically significant (p<0.05) decrease in reported exposure over time.ConclusionsThe constructed JEM successfully differentiated beryllium exposures across jobs and over time. This is the only quantitative JEM containing exposure estimates (average and peak) for the entire plant history.
Forecasting Click-Through Rates Based on Sponsored Search Advertiser Bids and Intermediate Variable Regression
Authors: Gluhovsky Ilya 
Published: October 2010

To participate in sponsored search online advertising, an advertiser bids on a set of keywords relevant to his/her product or service. When one of these keywords matches a user search string, the ad is then considered for display among sponsored search results. Advertisers compete for positions in which their ads appear, as higher slots typically result in more user clicks. All existing position allocating mechanisms charge more per click for a higher slot. Therefore, an advertiser must decide whether to bid high and receive more, but more expensive, clicks.
In this work, we propose a novel methodology for building forecasting landscapes relating an individual advertiser bid to the expected click-through rate and/or the expected daily click volume. Displaying such landscapes is currently offered as a service to advertisers by all major search engine providers. Such landscapes are expected to be instrumental in helping the advertisers devise their bidding strategies.

We propose a
triply
monotone regression methodology. We start by applying the current state-of-the-art monotone regression solution. We then propose to condition on the ad position and to estimate the bid-position and position-click effects separately. While the latter translates into a standard monotone regression problem, we devise a novel solution to the former based on approximate maximum likelihood. We show that our proposal significantly outperforms the standard monotone regression solution, while the latter similarly improves upon routinely used ad-hoc methods.

Last, we discuss other e-commerce applications of the proposed intermediate variable regression methodology.
I know you think it's too late
Authors: Dement Linda , Rizzo Maria 
Published: October 2010

“I Know You Think It's Too Late” is an installation across three computers that takes a systems theory approach in considering human impulses to violence. A struggling spinning hairball, pulsing blood drops. and jittering swathes of fat respond to each other and to the user. These gruesome remnants of violent acts form a system that can snowball out of control or be tempered by a user's activity.
The more a user interacts with one computer, the less that substance builds up on the other two. The less a computer is used, the more its substance builds up on the other two. If no one interacts with any of the computers, the build up of fat, hair, and blood escalates and compounds, and the system can go into runaway growth (a positive feedback system). A user's interaction brings the system back into balanced stability (a negative feedback system).
This gives voice to a strange distributed entity that inhabits and grows from the detritus of violent death.