bluuebunny/crossref_metadata_2025_split huggingface dataset:
Real-Time PCR and Sequencing Assays for Rapid Detection and Identification of Avian Schistosomes in Environmental Samples
Authors: Jothikumar Narayanan , Mull Bonnie J. , Brant Sara V. , Loker Eric S. , Collinson Jeremy , Secor W. Evan , Hill Vincent R. 
Published: April 2015

ABSTRACT

Cercarial dermatitis, also known as swimmer's itch, is an allergenic skin reaction followed by intense itching caused by schistosome cercariae penetrating human skin. Cercarial dermatitis outbreaks occur globally and are frequently associated with freshwater lakes and are occasionally associated with marine or estuarine waters where birds reside year-round or where migratory birds reside. In this study, a broadly reactive TaqMan assay targeting 18S rRNA gene (ribosomal DNA [rDNA]) sequences that was based on a genetically diverse panel of schistosome isolates representing 13 genera and 20 species (the 18S rDNA TaqMan assay) was developed. A PCR assay was also developed to amplify a 28S rDNA region for subsequent sequencing to identify schistosomes. When applied to surface water samples seeded with
Schistosoma mansoni
cercariae, the 18S rDNA TaqMan assay enabled detection at a level of 5
S. mansoni
cercariae in 100 liters of lake water. The 18S rDNA TaqMan and 28S rDNA PCR sequencing assays were also applied to 100-liter water samples collected from lakes in Nebraska and Wisconsin where there were reported dermatitis outbreaks. Avian schistosome DNA was detected in 11 of 34 lake water samples using the TaqMan assay. Further 28S rDNA sequence analysis of positive samples confirmed the presence of avian schistosome DNA and provided a preliminary identification of the avian schistosomes in 10 of the 11 samples. These data indicate that the broadly schistosome-reactive TaqMan assay can be effective for rapid screening of large-volume water samples for detection of avian schistosomes, thereby facilitating timely response actions to mitigate or prevent dermatitis outbreaks. Additionally, samples positive by the 18S rDNA TaqMan assay can be further assayed using the 28S rDNA sequencing assay to both confirm the presence of schistosomes and contribute to their identification.
Functional Characterization of Corynebacterium alkanolyticum β-Xylosidase and Xyloside ABC Transporter in Corynebacterium glutamicum
Authors: Watanabe Akira , Hiraga Kazumi , Suda Masako , Yukawa Hideaki , Inui Masayuki 
Published: April 2015

ABSTRACT

The
Corynebacterium alkanolyticum
xylEFGD
gene cluster comprises the
xylD
gene that encodes an intracellular β-xylosidase next to the
xylEFG
operon encoding a substrate-binding protein and two membrane permease proteins of a xyloside ABC transporter. Cloning of the cluster revealed a recombinant β-xylosidase of moderately high activity (turnover for
p
-nitrophenyl-β-
d
-xylopyranoside of 111 ± 4 s
−1
), weak α-
l
-arabinofuranosidase activity (turnover for
p
-nitrophenyl-α-
l
-arabinofuranoside of 5 ± 1 s
−1
), and high tolerance to product inhibition (

K
i

for xylose of 67.6 ± 2.6 mM). Heterologous expression of the entire cluster under the control of the strong constitutive
tac
promoter in the
Corynebacterium glutamicum
xylose-fermenting strain X1 enabled the resultant strain X1EFGD to rapidly utilize not only xylooligosaccharides but also arabino-xylooligosaccharides. The ability to utilize arabino-xylooligosaccharides depended on
cgR
_
2369
, a gene encoding a multitask ATP-binding protein. Heterologous expression of the contiguous
xylD
gene in strain X1 led to strain X1D with 10-fold greater β-xylosidase activity than strain X1EFGD, albeit with a total loss of arabino-xylooligosaccharide utilization ability and only half the ability to utilize xylooligosaccharides. The findings suggest some inherent ability of
C. glutamicum
to take up xylooligosaccharides, an ability that is enhanced by in the presence of a functional
xylEFG
-encoded xyloside ABC transporter. The finding that
xylEFG
imparts nonnative ability to take up arabino-xylooligosaccharides should be useful in constructing industrial strains with efficient fermentation of arabinoxylan, a major component of lignocellulosic biomass hydrolysates.
Abundance and Distribution of Dimethylsulfoniopropionate Degradation Genes and the Corresponding Bacterial Community Structure at Dimethyl Sulfide Hot Spots in the Tropical and Subtropical Pacific Ocean
Authors: Cui Yingshun , Suzuki Shotaro , Omori Yuko , Wong Shu-Kuan , Ijichi Minoru , Kaneko Ryo , Kameyama Sohiko , Tanimoto Hiroshi , Hamasaki Koji 
Published: April 2015

ABSTRACT

Dimethylsulfoniopropionate (DMSP) is mainly produced by marine phytoplankton but is released into the microbial food web and degraded by marine bacteria to dimethyl sulfide (DMS) and other products. To reveal the abundance and distribution of bacterial DMSP degradation genes and the corresponding bacterial communities in relation to DMS and DMSP concentrations in seawater, we collected surface seawater samples from DMS hot spot sites during a cruise across the Pacific Ocean. We analyzed the genes encoding DMSP lyase (
dddP
) and DMSP demethylase (
dmdA
), which are responsible for the transformation of DMSP to DMS and DMSP assimilation, respectively. The averaged abundance (±standard deviation) of these DMSP degradation genes relative to that of the 16S rRNA genes was 33% ± 12%. The abundances of these genes showed large spatial variations.
dddP
genes showed more variation in abundances than
dmdA
genes. Multidimensional analysis based on the abundances of DMSP degradation genes and environmental factors revealed that the distribution pattern of these genes was influenced by chlorophyll
a
concentrations and temperatures.
dddP
genes,
dmdA
subclade C/2 genes, and
dmdA
subclade D genes exhibited significant correlations with the marine
Roseobacter
clade, SAR11 subgroup Ib, and SAR11 subgroup Ia, respectively. SAR11 subgroups Ia and Ib, which possessed
dmdA
genes, were suggested to be the main potential DMSP consumers. The
Roseobacter
clade members possessing
dddP
genes in oligotrophic subtropical regions were possible DMS producers. These results suggest that DMSP degradation genes are abundant and widely distributed in the surface seawater and that the marine bacteria possessing these genes influence the degradation of DMSP and regulate the emissions of DMS in subtropical gyres of the Pacific Ocean.
A Glycosylation Mutant of Trypanosoma brucei Links Social Motility Defects
In Vitro
to Impaired Colonization of Tsetse Flies
In Vivo
Authors: Imhof Simon , Vu Xuan Lan , Bütikofer Peter , Roditi Isabel 
Published: April 2015

ABSTRACT

Transmission of African trypanosomes by tsetse flies requires that the parasites migrate out of the midgut lumen and colonize the ectoperitrophic space. Early procyclic culture forms correspond to trypanosomes in the lumen; on agarose plates they exhibit social motility, migrating
en masse
as radial projections from an inoculation site. We show that an
Rft1
−/−
mutant needs to reach a greater threshold number before migration begins, and that it forms fewer projections than its wild-type parent. The mutant is also up to 4 times less efficient at establishing midgut infections. Ectopic expression of
Rft1
rescues social motility defects and restores the ability to colonize the fly. These results are consistent with social motility reflecting movement to the ectoperitrophic space, implicate N-glycans in the signaling cascades for migration
in vivo
and
in vitro
, and provide the first evidence that parasite-parasite interactions determine the success of transmission by the insect host.
Nationwide registry-based ecological analysis of Q fever incidence and pregnancy outcome during an outbreak in the Netherlands
Authors: de Lange Marit M A , Hukkelhoven Chantal W P M , Munster Janna M , Schneeberger Peter M , van der Hoek Wim 
Published: April 2015

ObjectiveWhether areas affected by Q fever during a large outbreak (2008–2010) had higher rates of adverse pregnancy outcomes than areas not affected by Q fever.DesignNationwide registry-based ecological study.SettingPregnant women in areas affected and not affected by Q fever in the Netherlands, 2003–2004 and 2008–2010.ParticipantsIndex group (N=58 737): pregnant women in 307 areas with more than two Q fever notifications. Reference group (N=310 635): pregnant women in 921 areas without Q fever notifications. As a baseline, pregnant women in index and reference areas in the years 2003–2004 were also included in the reference group to estimate the effect of Q fever in 2008–2010, and not the already existing differences before the outbreak.Main outcome measuresPreterm delivery, small for gestational age, perinatal mortality.ResultsIn 2008–2010, there was no association between residing in a Q fever-affected area and both preterm delivery (adjusted OR 1.01 (95% CI 0.94 to 1.08)), and perinatal mortality (adjusted OR 0.87 (95% CI 0.72 to 1.05)). In contrast, we found a weak significant association between residing in a Q fever-affected area in 2008–2010 and small for gestational age (adjusted OR 1.06 (95% CI 1.01 to 1.12)), with a population-attributable fraction of 0.70% (95% CI 0.07% to 1.34%). We observed no dose–response relation for this outcome with increasing Q fever notifications, and we did not find a stronger association for women who were in their first trimester of pregnancy during the months of high human Q fever incidence.ConclusionsThis study found a weak association between residing in a Q fever-affected area and the pregnancy outcome small for gestational age. Early detection of infection would require mass screening of pregnant women; this does not seem to be justified considering these results, and the uncertainties about its efficacy and the adverse effects of antibiotic treatment.
Preventing device-associated infections in US hospitals: national surveys from 2005 to 2013
Authors: Krein Sarah L , Fowler Karen E , Ratz David , Meddings Jennifer , Saint Sanjay 
Published: April 2015

BackgroundNumerous initiatives have focused on reducing device-associated infections, contributing to an overall decrease in infections nationwide. To better understand factors associated with this decline, we assessed the use of key practices to prevent device-associated infections by US acute care hospitals from 2005 to 2013.MethodsWe mailed surveys to infection preventionists at a national random sample of ∼600 US acute care hospitals in 2005, 2009 and 2013. Our survey asked about the use of practices to prevent the 3 most common device-associated infections: central line-associated bloodstream infection (CLABSI), ventilator-associated pneumonia (VAP) and catheter-associated urinary tract infection (CAUTI). Using sample weights, we estimated the per cent of hospitals reporting regular use (a score of 4 or 5 on a scale from 1 (never use) to 5 (always use)) of prevention practices from 2005 to 2013.ResultsThe response rate was about 70% in all 3 periods. Use of most recommended prevention practices increased significantly over time. Among those showing the greatest increase were use of an antimicrobial dressing for preventing CLABSI (25–78%, p<0.001), use of an antimicrobial mouth rinse for preventing VAP (41–79%, p<0.001) and use of catheter removal prompts for preventing CAUTI (9–53%, p<0.001). Likewise, a significant increase in facility-wide surveillance was found for all three infections. Practices for which little change was observed included use of antimicrobial catheters to prevent either CLABSI or CAUTI.ConclusionsUS hospitals have responded to the call to reduce infection by increasing use of key recommended practices. Vigilance is needed to ensure sustained improvement and additional strategies may still be required, given an apparent continuing lag in CAUTI prevention efforts.
Preoperative serum-gamma-glutamyltransferase (GGT) does not represent an independent prognostic factor in a European cohort of patients with non-metastatic renal cell carcinoma
Authors: Dalpiaz Orietta , Pichler Martin , Mrsic Edvin , Reitz Daniel , Krieger Daniel , Venturino Luca , Bezan Angelika , Stojakovic Tatjana , Pummer Karl , Zigeuner Richard , Hutterer Georg C 
Published: April 2015

AimsIncreasing evidence suggests that the serum-gamma-glutamyltransferase (GGT) might correlate with tumour development and growth rates in various human cancer types. Thus, we decided to investigate the potential prognostic impact of the preoperatively assessed serum-GGT in a European cohort of patients with non-metastatic renal cell carcinoma (RCC).MethodsClinicopathological data from 700 consecutive patients with non-metastatic RCC, operated between 2000 and 2010 at a single tertiary academic centre, were evaluated retrospectively. Preoperative serum-GGT was assessed 1 day before surgery. Patients were categorised using a serum-GGT cut-off value of 40 U/L according to a calculation by receiver operating curve analysis. Patients’ cancer-specific survival (CSS), metastasis-free survival (MFS), as well as overall survival (OS) were assessed using the Kaplan-Meier method and Cox proportional models.ResultsIn univariate analysis, an elevated preoperative serum-GGT level (<40 U/L vs ≥40 U/L) was statistically significantly associated with a shorter MFS (HR=1.517, 95% CI 1.047 to 2.197, p=0.027). In multivariate analyses, pathological T-Stage (pT-1 vs pT-2–4, HR=2.065, 95% CI 1.665 to 2.560), tumour grade (G-1+G-2 vs G-3+G-4, HR=1.671, 95% CI 1.261 to 2.213), as well as the presence of histological tumour necrosis (No vs Yes, HR=2.031, 95% CI 1.355 to 3.046) were independent predictors of MFS in patients with RCC, whereas the preoperative serum-GGT failed to reach independent predictor status (<40 U/L vs ≥40 U/L, HR=1.156, 95% CI 0.791 to 1.690). No prognostic role for GGT in OS or CSS could be identified.ConclusionsIn the cohort studied, patients with an elevated (≥40 U/L) preoperative serum-GGT had a subsequently shorter MFS only in univariate analysis. In contrast to previous studies, our data failed to demonstrate preoperatively assessed serum-GGT as an independent prognostic factor in patients with non-metastatic RCC.
Photographic art in exam rooms may reduce white coat hypertension
Authors: Harper Michael B , Kanayama-Trivedi Stacy , Caldito Gloria , Montgomery David , Mayeaux EJ , DelRosso Lourdes M 
Published: April 2015

IntroductionBlood pressure (BP) elevation in medical office settings in patients who are normotensive in nonmedical settings is an effect known as ‘white coat hypertension’. This phenomenon is thought to be due to situational anxiety caused by the experience of visiting a doctor and the anxiety-inducing nature of the medical office. Our study was designed to determine if carefully selected photographic art could counter the anxiety that causes white coat hypertension and lead to lower BP recordings in some patients.Methods117 adults, non-pregnant patients from the Louisiana State University Health Sciences Center Family Medicine Resident Clinic participated in this study. After the triage nurse measured the BP, the patients were randomly placed in either an exam room with standard medical posters (control room) or in an exam room with photographic art (photo room). The BP was measured in the exam room. After the medical visit, the patients switched rooms and the BP was measured a third time. The patients were asked to fill out a questionnaire to identify room preference.ResultsOn average, the BP obtained in the control rooms was higher than that obtained in the photo rooms. There was a statistically significant difference between the mean arterial pressure, systolic BP and diastolic BP between the control room and the photo room.ConclusionsLandscape photographic art may have the beneficial effect of reducing BP in medical office examination rooms.
Three-dimensional printing of anatomically accurate, patient specific intracranial aneurysm models
Authors: Anderson Jeff R , Thompson Walker L , Alkattan Abdulaziz K , Diaz Orlando , Klucznik Richard , Zhang Yi J , Britz Gavin W , Grossman Robert G , Karmonik Christof 
Published: April 2015

ObjectiveTo develop and validate a method for creating realistic, patient specific replicas of cerebral aneurysms by means of fused deposition modeling.MethodsThe luminal boundaries of 10 cerebral aneurysms, together with adjacent proximal and distal sections of the parent artery, were segmented based on DSA images, and corresponding virtual three-dimensional (3D) surface reconstructions were created. From these, polylactic acid and MakerBot Flexible Filament replicas of each aneurysm were created by means of fused deposition modeling. The accuracy of the replicas was assessed by quantifying statistical significance in the variations of their inner dimensions relative to 3D DSA images. Feasibility for using these replicas as flow phantoms in combination with phase contrast MRI was demonstrated.Results3D printed aneurysm models were created for all 10 subjects. Good agreement was seen between the models and the source anatomy. Aneurysm diameter measurements of the printed models and source images correlated well (r=0.999; p<0.001), with no statistically significant group difference (p=0.4) or observed bias. The SDs of the measurements were 0.5 mm and 0.2 mm for source images and 3D models, respectively. 3D printed models could be imaged with flow via MRI.ConclusionsThe 3D printed aneurysm models presented were accurate and were able to be produced inhouse. These models can be used for previously cited applications, but their anatomical accuracy also enables their use as MRI flow phantoms for comparison with ongoing studies of computational fluid dynamics. Proof of principle imaging experiments confirm MRI flow phantom utility.
Systematic Screening Identifies Dual PI3K and mTOR Inhibition as a Conserved Therapeutic Vulnerability in Osteosarcoma
Authors: Gupte Ankita , Baker Emma K. , Wan Soo-San , Stewart Elizabeth , Loh Amos , Shelat Anang A. , Gould Cathryn M. , Chalk Alistair M. , Taylor Scott , Lackovic Kurt , Karlström Åsa , Mutsaers Anthony J. , Desai Jayesh , Madhamshettiwar Piyush B. , Zannettino Andrew C.W. , Burns Chris , Huang David C.S. , Dyer Michael A. , Simpson Kaylene J. , Walkley Carl R. 
Published: April 2015

Abstract
Purpose: Osteosarcoma is the most common cancer of bone occurring mostly in teenagers. Despite rapid advances in our knowledge of the genetics and cell biology of osteosarcoma, significant improvements in patient survival have not been observed. The identification of effective therapeutics has been largely empirically based. The identification of new therapies and therapeutic targets are urgently needed to enable improved outcomes for osteosarcoma patients.
Experimental Design: We have used genetically engineered murine models of human osteosarcoma in a systematic, genome-wide screen to identify new candidate therapeutic targets. We performed a genome-wide siRNA screen, with or without doxorubicin. In parallel, a screen of therapeutically relevant small molecules was conducted on primary murine– and primary human osteosarcoma–derived cell cultures. All results were validated across independent cell cultures and across human and mouse osteosarcoma.
Results: The results from the genetic and chemical screens significantly overlapped, with a profound enrichment of pathways regulated by PI3K and mTOR pathways. Drugs that concurrently target both PI3K and mTOR were effective at inducing apoptosis in primary osteosarcoma cell cultures in vitro in both human and mouse osteosarcoma, whereas specific PI3K or mTOR inhibitors were not effective. The results were confirmed with siRNA and small molecule approaches. Rationale combinations of specific PI3K and mTOR inhibitors could recapitulate the effect on osteosarcoma cell cultures.
Conclusions: The approaches described here have identified dual inhibition of the PI3K–mTOR pathway as a sensitive, druggable target in osteosarcoma, and provide rationale for translational studies with these agents. Clin Cancer Res; 21(14); 3216–29. ©2015 AACR.
Transição em infraestruturas urbanas de controle pluvial: uma estratégia paisagística de adaptação às mudanças climáticas
Authors: Moura Newton Celio Becker , Pellegrino Paulo Renato Mesquita , Martins José Rodolfo Scarati 
Published: April 2015

<p>Projeções em modelos climáticos globais quanto às emissões de gases de efeito estufa apontam um aumento na intensidade e frequência dos eventos extremos de chuva, que, associado ao crescimento urbano e à expansão das superfícies impermeáveis, deverá gerar impactos sem precedentes sobre a infraestrutura de drenagem. Diante desse cenário, as cidades têm a oportunidade de realizar uma transição infraestrutural ao adotar técnicas de Melhores Práticas de Manejo (MPM) das águas de chuva como solução mais sustentável, resiliente e integrada à paisagem urbana. Este estudo apresenta uma comparação qualiquantitativa entre reservatórios de detenção e MPM dos escoamentos como estratégias de controle pluvial. Considerando uma microbacia urbana na Região Metropolitana de São Paulo (RMSP), onde foram instalados dois reservatórios com volume de detenção total de 19.200 m3, distribuíram-se elementos de<br />biorretenção e passeios porosos nas vias públicas localizadas na área de contribuição da bacia. O volume de retenção das técnicas propostas como tratamento dos espaços abertos públicos corresponde a 42% da capacidade de detenção dos reservatórios. Confirma-se, então, a viabilidade das MPM como alternativas para adaptação das cidades às mudanças climáticas, desde que levadas em conta as especificidades ambientais e paisagísticas locais no desenho desses elementos como forma de garantir a sua eficiência. </p>