bluuebunny/crossref_metadata_2025_split huggingface dataset:
Availability and price of malaria rapid diagnostic tests in the public and private health sectors in 2011: results from 10 nationally representative cross‐sectional retail surveys
Authors: Poyer Stephen , Shewchuk Tanya , Tougher Sarah , Ye Yazoume ,   The ACTwatch Group, Mann Andrea G. , Willey Barbara A. , Thomson Rebecca , Amuasi John H. , Ren Ruilin , Wamukoya Marilyn , Taylor Mark , Nguah Samuel Blay , Mberu Blessing , Kalolella Admirabilis , Juma Elizabeth , Festo Charles , Johanes Boniface , Diap Graciela , Bruxvoort Katia , Ansong Daniel , Hanson Kara , Arnold Fred , Goodman Catherine 
Published: February 2015

AbstractObjectivesTo describe the state of the public and private malaria diagnostics market shortly after WHO updated its guidelines for testing all suspected malaria cases prior to treatment.MethodsTen nationally representative cross‐sectional cluster surveys were conducted in 2011 among public and private health facilities, community health workers and retail outlets (pharmacies and drug shops) in nine countries (Tanzania mainland and Zanzibar surveyed separately). Eligible outlets had antimalarials in stock on the day of interview or had stocked antimalarials in the past 3 months.ResultsThree thousand four hundred and thirty‐nine rapid diagnostic test (RDT) products from 39 manufacturers were audited among 12 197 outlets interviewed. Availability was typically highest in public health facilities, although availability in these facilities varied greatly across countries, from 15% in Nigeria to >90% in Madagascar and Cambodia. Private for‐profit sector availability was 46% in Cambodia, 20% in Zambia, but low in other countries. Median retail prices for RDTs in the private for‐profit sector ranged from $0.00 in Madagascar to $3.13 in Zambia. The reported number of RDTs used in the 7 days before the survey in public health facilities ranged from 3 (Benin) to 50 (Zambia).ConclusionsEighteen months after WHO updated its case management guidelines, RDT availability remained poor in the private sector in sub‐Saharan Africa. Given the ongoing importance of the private sector as a source of fever treatment, the goal of universal diagnosis will not be achievable under current circumstances. These results constitute national baselines against which progress in scaling‐up diagnostic tests can be assessed.
Characterization and Optimization of a Tensioned Metastable Fluid Nuclear Particle Sensor Using Laser-Based Profilometry
Authors: Hagen Alexander R. , Grimes Thomas F. , Archambault Brian C. , Harris Trevor N. , Taleyarkhan Rusi P. 
Published: February 2015

State-of-the-art neutron detectors lack capabilities required by the fields of homeland security, health physics, and even for direct in-core nuclear power monitoring. A new system being developed at Purdue’s Metastable Fluid and Advanced Research Laboratory in conjunction with S/A Labs, LLC provides capabilities that the state-of-the-art lacks, and simultaneously with beta (β) and gamma (γ) blindness, high (>90% intrinsic) efficiency for neutron/alpha spectroscopy and directionality, simple detection mechanism, and lowered electronic component dependence. This system, the tensioned metastable fluid detector (TMFD), provides these capabilities despite its vastly reduced cost and complexity compared with equivalent present day systems. Fluids may be placed at pressures lower than perfect vacuum (i.e., negative), resulting in tensioned metastable states. These states may be induced by tensioning fluids just as one would tension solids. The TMFD works by cavitation nucleation of bubbles resulting from energy deposited by charged ions or laser photon pile-up heating of fluid molecules, which are placed under sufficiently tensioned (negative) pressure states of metastability. The charged ions may be created from neutron scattering or from energetic charged particles such as alphas, alpha recoils, and fission fragments. A methodology has been created to profile the pressures in these chambers by laser-induced cavitation (LIC) for verification of a multiphysics simulation of the chambers. The methodology and simulation together have led to large efficiency gains in the current acoustically tensioned metastable fluid detector (ATMFD) system. This paper describes in detail the LIC methodology and provides background on the simulation it validates.
Measured Biaxial Residual Stress Maps in a Stainless Steel Weld
Authors: Olson Mitchell D. , Hill Michael R. , Patel Vipul I. , Muránsky Ondrej , Sisneros Thomas 
Published: February 2015

This paper describes a sequence of residual stress measurements made to determine a two-dimensional map of biaxial residual stress in a stainless steel weld. A long stainless steel (316L) plate with an eight-pass groove weld (308L filler) was used. The biaxial stress measurements follow a recently developed approach, comprising a combination of contour method and slitting measurements, with a computation to determine the effects of out-of-plane stress on a thin slice. The measured longitudinal stress is highly tensile in the weld- and heat-affected zone, with a maximum around 450 MPa, and compressive stress toward the transverse edges around −250 MPa. The total transverse stress has a banded profile in the weld with highly tensile stress at the bottom of the plate (y = 0) of 400 MPa, rapidly changing to compressive stress (at y = 5 mm) of −200 MPa, then tensile stress at the weld root (y = 17 mm) and in the weld around 200 MPa, followed by compressive stress at the top of the weld at around −150 MPa. The results of the biaxial map compare well with the results of neutron diffraction measurements and output from a computational weld simulation.
Decreasing
pfmdr1
Copy Number Suggests that Plasmodium falciparum in Western Cambodia Is Regaining
In Vitro
Susceptibility to Mefloquine
Authors: Lim Pharath , Dek Dalin , Try Vorleak , Sreng Sokunthea , Suon Seila , Fairhurst Rick M. 
Published: February 2015

ABSTRACT

Dihydroartemisinin-piperaquine is the current frontline artemisinin combination therapy (ACT) for
Plasmodium falciparum
malaria in Cambodia but is now failing in several western provinces. To investigate artesunate plus mefloquine (AS+MQ) as a replacement ACT, we measured the prevalence of multiple
pfmdr1
copies—a molecular marker for MQ resistance—in 844
P. falciparum
clinical isolates collected in 2008 to 2013. The
pfmdr1
copy number is decreasing in Western Cambodia, suggesting that
P. falciparum
is regaining
in vitro
susceptibility to MQ.
The Transforming Growth Factor β1/Interleukin-31 Pathway Is Upregulated in Patients with Hepatitis B Virus-Related Acute-on-Chronic Liver Failure and Is Associated with Disease Severity and Survival
Authors: Yu Xueping , Guo Ruyi , Ming Desong , Deng Yong , Su Milong , Lin Chengzu , Li Julan , Lin Zhenzhong , Su Zhijun 
Published: February 2015

ABSTRACTThe transforming growth factor β1/interleukin-31 (TGF-β1/IL-31) pathway plays an important role in the process of cell injury and inflammation. The purpose of this work was to explore the role of the TGF-β1/IL-31 pathway in the cytopathic process of hepatitis B virus (HBV)-related acute-on-chronic liver failure (ACLF). The quantitative serum levels of TGF-β1, IL-9, IL-10, IL-17, IL-22, IL-23, IL-31, IL-33, and IL-35 were analyzed among chronic hepatitis B (CHB) patients (n= 17), ACLF patients (n= 18), and normal control (NC) subjects (n= 18). Disease severity in patients with ACLF was assessed using the model for end-stage liver disease (MELD) and Child-Pugh scores. Serum TGF-β1 levels were strongly positively correlated with IL-31 in all subjects, and both of them were positively correlated with IL-17, IL-22, and IL-33. In CHB and ACLF patients, serum levels of TGF-β1 and IL-31 were both increased significantly compared with those in NC subjects and positively correlated with total bilirubin (TBil) and alpha-fetoprotein (AFP) levels. ACLF patients showed the highest levels of TGF-β1 and IL-31, which were positively correlated with Child-Pugh scores. Furthermore, the recovery from the liver injury in CHB was accompanied by decreased TGF-β1 and IL-31 levels. More importantly, serum levels of TGF-β1 and IL-31 were markedly upregulated in ACLF nonsurvivors, and IL-31 displayed the highest sensitivity and specificity (85.7% and 100.0%, respectively) in predicting nonsurvival of ACLF patients. Increasing activity of the TGF-β1/IL-31 pathway is well correlated with the extent of liver injury, disease severity, and nonsurvival of ACLF patients, while reducing activity is detected along the recovery from liver injury in CHB, suggesting its potential role in the pathogenesis of liver injury during chronic HBV infection.
Complete Genome Sequence of Salmonella enterica Serovar Typhimurium Siphophage Shivani
Authors: Piya Denish , Xie Yicheng , Hernandez Morales Adriana C. , Kuty Everett Gabriel F. 
Published: February 2015

ABSTRACT

Here, we describe the complete genome sequence of siphophage Shivani, a T5-like constituent phage in the therapeutic phage cocktail IntestiPhage developed for bacterial gastroenteritis. Shivani was isolated against a foodborne pathogen,
Salmonella enterica
, which is one of the leading causes of gastroenteritis.
Draft Genome Sequence of Pantoea sp. Strain MBLJ3, Isolated in a Laboratory Environmental Control Study
Authors: Zhang Jing , Hung Guo-Chiuan , Lei Haiyan , Li Tianwei , Li Bingjie , Tsai Shien , Lo Shyh-Ching 
Published: February 2015

ABSTRACT
This report describes the draft genome sequence of a newly isolated strain, Pantoea sp. MBLJ3. The genome is 4.8 Mb in size, with a G+C content of 54.27%, and it contains 4,522 protein-coding sequences, 69 tRNA genes, and 5 rRNA genes.
Induction of Caspase-11 by Aspartyl Proteinases of Candida albicans and Implication in Promoting Inflammatory Response
Authors: Gabrielli Elena , Pericolini Eva , Luciano Eugenio , Sabbatini Samuele , Roselletti Elena , Perito Stefano , Kasper Lydia , Hube Bernhard , Vecchiarelli Anna 
Published: February 2015

ABSTRACT

We recently demonstrated that the secreted aspartyl proteinases (Saps), Sap2 and Sap6, of
Candida albicans
have the potential to induce the canonical activation of the NLRP3 inflammasome, leading to the secretion of interleukin-1β (IL-1β) and IL-18 via caspase-1 activation. We also observed that the activation of caspase-1 is partially independent from the NLRP3 activation pathway. In this study, we examined whether Sap2 and Sap6 are also able to activate the noncanonical inflammasome pathway in murine macrophages. Our data show that both Sap2 and Sap6 can activate caspase-11 through type I interferon (IFN) production. Caspase-11 cooperates to activate caspase-1, with a subsequent increase of IL-1β secretion. Endocytosis and internalization of Saps are required for the induction of type I IFN production, which is essential for induction of noncanonical inflammasome activation. Our study indicates a sophisticated interplay between caspase-1 and caspase-11 that connects the canonical and noncanonical pathways of inflammasome activation in response to
C. albicans
Saps.
Anti-APOBEC3G Activity of HIV-1 Vif Protein Is Attenuated in Elite Controllers
Authors: Kikuchi Tadashi , Iwabu Yukie , Tada Takuya , Kawana-Tachikawa Ai , Koga Michiko , Hosoya Noriaki , Nomura Shigeru , Brumme Zabrina L. , Jessen Heiko , Pereyra Florencia , Trocha Alicja , Walker Bruce D. , Iwamoto Aikichi , Tokunaga Kenzo , Miura Toshiyuki 
Published: February 2015

ABSTRACT

HIV-1-infected individuals who control viremia to below the limit of detection without antiviral therapy have been termed elite controllers (EC). Functional attenuation of some HIV-1 proteins has been reported in EC. The HIV-1 accessory protein Vif (virion infectivity factor) enhances viral infectivity through anti-retroviral factor apolipoprotein B mRNA editing enzyme catalytic polypeptide-like 3G (APOBEC3G) degradation; however, little is known regarding Vif function in EC. Here, the anti-APOBEC3G activities of clonal, plasma HIV RNA-derived Vif sequences from 46 EC, 46 noncontrollers (NC), and 44 individuals with acute infection (AI) were compared. Vesicular stomatitis virus glycoprotein (VSV-G)-pseudotyped viruses were generated by cotransfecting 293T cells with expression plasmids encoding patient-derived Vif, human APOBEC3G, VSV-G, and a
vif
/
env
-deficient
luciferase
-reporter HIV-1 proviral DNA clone. Viral stocks were used to infect 293T cells, and Vif anti-APOBEC3G activity was quantified in terms of luciferase signal. On average, the anti-APOBEC3G activities of EC-derived Vif sequences (median log
10
relative light units [RLU], 4.54 [interquartile range {IQR}, 4.30 to 4.66]) were significantly lower than those of sequences derived from NC (4.75 [4.60 to 4.92],
P
< 0.0001) and AI (4.74 [4.62 to 4.94],
P
< 0.0001). Reduced Vif activities were not associated with particular HLA class I alleles expressed by the host. Vif functional motifs were highly conserved in all patient groups. No single viral polymorphism could explain the reduced anti-APOBEC3G activity of EC-derived Vif, suggesting that various combinations of minor polymorphisms may underlie these effects. These results further support the idea of relative attenuation of viral protein function in EC-derived HIV sequences.

IMPORTANCE
HIV-1 elite controllers (EC) are rare individuals who are able to control plasma viremia to undetectable levels without antiretroviral therapy. Understanding the pathogenesis and mechanisms underpinning this rare phenotype may provide important insights for HIV vaccine design. The EC phenotype is associated with beneficial host immunogenetic factors (such as HLA-B*57) as well as with functions of attenuated viral proteins (e.g., Gag, Pol, and Nef). In this study, we demonstrated that HIV-1 Vif sequences isolated from EC display relative impairments in their ability to counteract the APOBEC3G host restriction factor compared to Vif sequences from normal progressors and acutely infected individuals. This result extends the growing body of evidence demonstrating attenuated HIV-1 protein function in EC and, in particular, supports the idea of the relevance of viral factors in contributing to this rare HIV-1 phenotype.
Integrated Microfluidic Card with TaqMan Probes and High-Resolution Melt Analysis To Detect Tuberculosis Drug Resistance Mutations across 10 Genes
Authors: Pholwat Suporn , Liu Jie , Stroup Suzanne , Gratz Jean , Banu Sayera , Rahman S. M. Mazidur , Ferdous Sara Sabrina , Foongladda Suporn , Boonlert Duangjai , Ogarkov Oleg , Zhdanova Svetlana , Kibiki Gibson , Heysell Scott , Houpt Eric 
Published: February 2015

ABSTRACT

Genotypic methods for drug susceptibility testing of
Mycobacterium tuberculosis
are desirable to speed the diagnosis and proper therapy of tuberculosis (TB). However, the numbers of genes and polymorphisms implicated in resistance have proliferated, challenging diagnostic design. We developed a microfluidic TaqMan array card (TAC) that utilizes both sequence-specific probes and high-resolution melt analysis (HRM), providing two layers of detection of mutations. Twenty-seven primer pairs and 40 probes were designed to interrogate 3,200 base pairs of critical regions of the
inhA
,
katG
,
rpoB
,
embB
,
rpsL
,
rrs
,
eis
,
gyrA
,
gyrB
, and
pncA
genes. The method was evaluated on 230 clinical M. tuberculosis isolates from around the world, and it yielded 96.1% accuracy (2,431/2,530) in comparison to that of Sanger sequencing and 87% accuracy in comparison to that of the slow culture-based susceptibility testing. This TAC-HRM method integrates assays for 10 genes to yield fast, comprehensive, and accurate drug susceptibility results for the 9 major antibiotics used to treat TB and could be deployed to improve treatment outcomes.

IMPORTANCE
Multidrug-resistant tuberculosis threatens global tuberculosis control efforts. Optimal therapy utilizes susceptibility test results to guide individualized treatment regimens; however, the susceptibility testing methods in use are technically difficult and slow. We developed an integrated TaqMan array card method with high-resolution melt analysis that interrogates 10 genes to yield a fast, comprehensive, and accurate drug susceptibility result for the 9 major antituberculosis antibiotics.
Sewage Reflects the Microbiomes of Human Populations
Authors: Newton Ryan J. , McLellan Sandra L. , Dila Deborah K. , Vineis Joseph H. , Morrison Hilary G. , Eren A. Murat , Sogin Mitchell L. 
Published: February 2015

ABSTRACT

Molecular characterizations of the gut microbiome from individual human stool samples have identified community patterns that correlate with age, disease, diet, and other human characteristics, but resources for marker gene studies that consider microbiome trends among human populations scale with the number of individuals sampled from each population. As an alternative strategy for sampling populations, we examined whether sewage accurately reflects the microbial community of a mixture of stool samples. We used oligotyping of high-throughput 16S rRNA gene sequence data to compare the bacterial distribution in a stool data set to a sewage influent data set from 71 U.S. cities. On average, only 15% of sewage sample sequence reads were attributed to human fecal origin, but sewage recaptured most (97%) human fecal oligotypes. The most common oligotypes in stool matched the most common and abundant in sewage. After informatically separating sequences of human fecal origin, sewage samples exhibited ~3× greater diversity than stool samples. Comparisons among municipal sewage communities revealed the ubiquitous and abundant occurrence of 27 human fecal oligotypes, representing an apparent core set of organisms in U.S. populations. The fecal community variability among U.S. populations was significantly lower than among individuals. It clustered into three primary community structures distinguished by oligotypes from either:
Bacteroidaceae
,
Prevotellaceae
, or
Lachnospiraceae/Ruminococcaceae
. These distribution patterns reflected human population variation and predicted whether samples represented lean or obese populations with 81 to 89% accuracy. Our findings demonstrate that sewage represents the fecal microbial community of human populations and captures population-level traits of the human microbiome.

IMPORTANCE
The gut microbiota serves important functions in healthy humans. Numerous projects aim to define a healthy gut microbiome and its association with health states. However, financial considerations and privacy concerns limit the number of individuals who can be screened. By analyzing sewage from 71 cities, we demonstrate that geographically distributed U.S. populations share a small set of bacteria whose members represent various common community states within U.S. adults. Cities were differentiated by their sewage bacterial communities, and the community structures were good predictors of a city's estimated level of obesity. Our approach demonstrates the use of sewage as a means to sample the fecal microbiota from millions of people and its potential to elucidate microbiome patterns associated with human demographics.
Peer mentoring for core medical trainees: uptake and impact
Authors: Webb Jessica , Brightwell Alexandra , Sarkar Pamela , Rabbie Roy , Chakravorty Indranil 
Published: February 2015

ABSTRACT

Objective
To assess the uptake and impact of a peer mentoring scheme for core medical trainees on both mentors and mentees.

Method
All second year core medical trainees in the Southwest London Training programme in September 2012 were invited to mentor a first year core medical trainee. In parallel, all first year core medical trainees were invited to be mentored. Both potential mentors and mentees were asked to submit personal statements, to attend a three-session mentoring training programme and to be matched into mentoring pairs. The impact of the mentoring scheme on trainees’ behaviour and outlook was assessed through questionnaires distributed at the start and at the end of the year.

Results
31 of 72 (43%) core medical trainees submitted personal statements and 40 of 72 (56%) attended training sessions. 42 trainees (58%) participated in the scheme (21 mentor/mentee pairs were established). Of the trainees who participated, 23 of 42 (55%) completed the end of year questionnaire. Participating trainees viewed the scheme positively. Reported benefits included changes in their behaviour and acquiring transferable skills that might help them in later career roles, such as an educational supervisor. The end of year questionnaire was sent to all trainees and 10 responded who had not participated. They were asked why they had not participated and their reasons included lack of time, lack of inclination and a desire for more senior mentors. Their suggestions for improvement included more structured sessions to allow the mentor/mentee pairs to meet.

Conclusions
This simple peer mentoring scheme was popular despite busy workloads and benefited all concerned. It is a simple effective way of supporting doctors. More work is needed to improve training for mentors and to improve access to mentoring.
Efficient Audio Filter Using Folded Pipelining Architecture Based on Retiming Using Evolutionary Computation
Authors: Yagain Deepa , Balla Sivanag , Krishna Vijaya 
Published: February 2015

It is important in digital signal processing (DSP) architectures to minimize the silicon area of the integrated circuits. This can be achieved by reducing the number of functional units such as adders and multipliers. In literature, folding technique is used to reduce the functional units by executing multiple algorithm operations on a single functional unit. Register minimization techniques are used to reduce the number of registers in a folded architecture. Retiming is a technique that needs to be performed before applying folding. In this paper, retiming is performed based on nature inspired evolutionary computation method. This technique generates the database of solutions from which best solution can be picked for folding further. As a part of this work, an efficient folded noise removal audio filter prototype is designed as an application example using evolutionary computation-based retiming and folding with register minimization. Folding technique will however increase the number of registers while multiplexing datapath adder and multiplier elements. Register minimization technique is used after folding to reduce the number of registers. After obtaining retimed, folded filter architecture, low level synthesis is performed which involves mapping of datapath adder and multiplier blocks to actual hardware. Various architectures of adders and multipliers are compared in area-power-performance space and depending on the user defined constraint, folded architecture with specific combination of data path elements is mapped on to hardware. A framework is designed in this paper to automate the entire process which reduces the design cycle time. All the designed filters are targeted for ASIC implementation. The results are compared and are provided as part of simulation results.
Carrara Marble: a nomination for ‘Global Heritage Stone Resource’ from Italy
Authors: Primavori P. 
Published: February 2015

Abstract
Carrara Marble, from Italy, probably one of the most famous dimension stones in the collective memory and in ordinary people, is here nominated as a suitable ‘Global Heritage Stone Resource’.
Quarried since pre-Roman times, the Carrara marble is the testimonial of an area/industry that was able – for a variety of reasons not easily repeatable in future stone history – from the dawn of the stone sector, to trigger a flywheel effect on a global scale. Suitable for any environment and cultural context, this versatile marble has been appreciated in almost any field of application – from building to architecture, from fine arts to urban landscape, from funerary art to modern 3D design – probably reaching its highest point in the eternal works of famous sculpturers, artists and architects such as Michelangelo, Donatello, Jacopo Della Quercia, Canova, Bernini, and many others. It is currently excavated in more than 100 quarries, processed almost everywhere and sold all over the world.