bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fluvial architecture and connectivity of the Williams Fork Formation: use of outcrop analogues for stratigraphic characterization and reservoir modelling
Authors: Pranter Matthew J. , Hewlett Alicia C. , Cole Rex D. , Wang Huabing , Gilman James 
Published: July 2013

Abstract
This study addresses the stratigraphic architecture and connectivity of fluvial sandstones of the Williams Fork Formation through outcrop analysis, and static and dynamic modelling of equivalent reservoirs in the Piceance Basin, Colorado. The Williams Fork Formation is a succession of fluvial channel sandstones, crevasse splays, floodplain mudstones and paludal coals that were deposited by meandering- and braided-river systems within coastal- and alluvial-plain settings.
Three-dimensional (3D) static and dynamic reservoir models that are constrained to both outcrop-derived and subsurface data show how static connectivity is sensitive to sandstone-body type and width, and varies with net to gross ratio. Connectivity analyses of 3D outcrop-based architectural-element models show how relatively wide sandstone bodies enhance connectivity. At Mamm Creek Field, connectivity of sandstones that are pay within the middle Williams Fork Formation is 12–18% higher than for the lower Williams Fork Formation. For highly constrained 3D object-based models of architectural elements, connectivity is only 4% higher when crevasse splays are included as reservoir-quality sandstones. Dynamic simulation results also suggest that the best history match is possible by considering only point bars and channel bars (reservoir-quality sandstones) as pay. Additional research is necessary to determine the impact of crevasse splays on reservoir connectivity.
LINQits
Authors: Chung Eric S. , Davis John D. , Lee Jaewon 
Published: July 2013

We present LINQits, a flexible hardware template that can be mapped onto programmable logic or ASICs in a heterogeneous system-on-chip for a mobile device or server. Unlike fixed-function accelerators, LINQits accelerates a domain-specific query language called LINQ. LINQits does not provide coverage for all possible applications---however, existing applications (re-)written with LINQ in mind benefit extensively from hardware acceleration. Furthermore, the LINQits framework offers a graceful and transparent migration path from software to hardware.
LINQits is prototyped on a 2W heterogeneous SoC called the ZYNQ processor, which combines dual ARM A9 processors with an FPGA on a single die in 28nm silicon technology. Our physical measurements show that LINQits improves energy efficiency by 8.9 to 30.6 times and performance by 10.7 to 38.1 times compared to optimized, multithreaded C programs running on conventional ARM A9 processors.
Will Future Climate Favor More Erratic Wildfires in the Western United States?
Authors: Luo Lifeng , Tang Ying , Zhong Shiyuan , Bian Xindi , Heilman Warren E. 
Published: July 2013

AbstractWildfires that occurred over the western United States during August 2012 were fewer in number but larger in size when compared with all other Augusts in the twenty-first century. This unique characteristic, along with the tremendous property damage and potential loss of life that occur with large wildfires with erratic behavior, raised the question of whether future climate will favor rapid wildfire growth so that similar wildfire activity may become more frequent as climate changes. This study addresses this question by examining differences in the climatological distribution of the Haines index (HI) between the current and projected future climate over the western United States. The HI, ranging from 2 to 6, was designed to characterize dry, unstable air in the lower atmosphere that may contribute to erratic or extreme fire behavior. A shift in HI distribution from low values (2 and 3) to higher values (5 and 6) would indicate an increased risk for rapid wildfire growth and spread. Distributions of Haines index are calculated from simulations of current (1971–2000) and future (2041–70) climate using multiple regional climate models in the North American Regional Climate Change Assessment Program. Despite some differences among the projections, the simulations indicate that there may be not only more days but also more consecutive days with HI ≥ 5 during August in the future. This result suggests that future atmospheric environments will be more conducive to erratic wildfires in the mountainous regions of the western United States.
The value of gadoxetic acid-enhanced and diffusion-weighted MRI for prediction of grading of pancreatic neuroendocrine tumors
Authors: Jang Kyung Mi , Kim Seong Hyun , Lee Soon Jin , Choi Dongil 
Published: July 2013

Background Parenchyma-preserving resection for the treatment of benign pancreatic neuroendocrine tumors (NETs) has been tried, and preoperative prediction of benign pancreatic NET is important. Recently, diffusion-weighted imaging (DWI) of abdomen magnetic resonance imaging (MRI) has been used to characterize benign and malignant tumors and DWI might be helpful in prediction of benign pancreatic NETs. Purpose To evaluate the value of gadoxetic acid-enhanced MRI and DWI in predicting benign pancreatic NETs for determination of parenchyma-preserving resection. Material and Methods Our ethics committee approved this study with a waiver of informed consent given its retrospective design. We searched radiology and pathology databases from November 2010 to July 2012 to identify patients who underwent surgery for pancreatic NETs (<4 cm). Twenty patients in the benign group and 14 patients in the non-benign group were included in this study. Two radiologists analyzed the morphologic features, signal intensity on MR images including DWI ( b = 800), and dynamic enhancement pattern of the tumors with consensus. The tumor-to-parenchyma ratio and tumor apparent diffusion coefficients (ADCs) were quantitatively assessed. Results The benign pancreatic NETs were more often round (7/20, 35%) or ovoid (13/20, 65%) in shape and less hypovascular on the arterial phase (3/20, 15%) than were the non-benign pancreatic NETs (1/14, 7.1% and 5/14, 35.8%; 7/14, 50% respectively; P < 0.05). Main pancreatic duct dilatation by tumors was demonstrated only in non-benign pancreatic NETs (4/14, 28.4%; P = 0.021). ADC values and ratios were significantly different between benign pancreatic NETs (mean, 1.48 × 10−3 mm2/sec, 1.11 ± 0.25, each) and non-benign pancreatic NETs (mean, 1.04 × 10−3 mm2/sec, 0.74 ± 0.13, each) ( P < 0.01). Other qualitative and quantitative analyses between benign and non-benign pancreatic NETs were not significantly different ( P > 0.05). Conclusion Abdominal MRI with DWI may be useful for differentiating benign pancreatic NETs from non-benign pancreatic NETs, which might be helpful for determination of parenchyma-preserving resection.
British Association for Sexual Health and HIV Scottish Investigation 2010–2011: reasons for non-attendance in individuals lost to follow-up for HIV care for more than 12 months in Scotland
Authors: Cullen B L , Codere G , Wallace L A , Baguley S , Clutterbuck DJ 
Published: July 2013

Summary As of 31 March 2011, 6696 HIV diagnoses had ever been reported in Scotland; of these, 1791 individuals had died, 3339 were attending specialist services, but the remainder had defaulted from specialist care; an investigation into their reasons for non-attendance, and the efforts of services to re-engage, was undertaken by British Association for Sexual Health and HIV Scottish branch using a web-based survey questionnaire. Twelve of the 13 Scottish HIV services returned information for 424 of 579 eligible cases; 112 of these 424 individuals were identified as genuine non-attendees. Findings indicate that the epidemiology of these non-attendees is similar to that of the whole Scottish HIV cohort. Three-quarters of individuals failed to attend a booked appointment following their last known attendance and very few attempts to contact non-attending individuals were successful. This survey has refocused attention on those lost to follow-up, while quality of the national data-set has improved, providing a clearer epidemiological picture of people living with HIV in Scotland.
The value of a support group for medical professionals with substance use disorders
Authors: Wile Cheryl , Jenkins Kym 
Published: July 2013

Objective: The objective of this study was to explore how a support group in Victoria, Australia, that has been set up for doctors and medical students with substance use disorders is perceived by group members. Method: Past and present participants were surveyed anonymously regarding their attitudes to the group and its role in their recovery. Results: Respondents overwhelmingly valued the support group, seeing it as an integral and essential part of their recovery and on-going health. Conclusions: It is recommended that such support groups for doctors who have substance use disorders be more widely available in jurisdictions other than Victoria.
Genome-wide upstream motif analysis of Cryptosporidium parvum genes clustered by expression profile
Authors: Oberstaller Jenna , Joseph Sandeep J , Kissinger Jessica C 
Published: July 2013

AbstractBackgroundThere are very few molecular genetic tools available to study the apicomplexan parasiteCryptosporidium parvum. The organism is not amenable to continuousin vitrocultivation or transfection, and purification of intracellular developmental stages in sufficient numbers for most downstream molecular applications is difficult and expensive since animal hosts are required. As such, very little is known about gene regulation inC. parvum.ResultsWe have clustered whole-genome gene expression profiles generated from a previous study of seven post-infection time points of 3,281 genes to identify genes that show similar expression patterns throughout the first 72 hours ofin vitroepithelial cell culture. We used the algorithms MEME, AlignACE and FIRE to identify conserved, overrepresented DNA motifs in the upstream promoter region of genes with similar expression profiles. The most overrepresented motifs were E2F (5′-TGGCGCCA-3′); G-box (5′-G.GGGG-3′); a well-documented ApiAP2 binding motif (5′-TGCAT-3′), and an unknown motif (5′-[A/C] AACTA-3′). We generated a recombinantC. parvumDNA-binding protein domain from a putative ApiAP2 transcription factor [CryptoDB: cgd8_810] and determined its binding specificity using protein-binding microarrays. We demonstrate that cgd8_810 can putatively bind the overrepresented G-box motif, implicating this ApiAP2 in the regulation of many gene clusters.ConclusionSeveral DNA motifs were identified in the upstream sequences of gene clusters that might serve as potentialcis-regulatory elements. These motifs, in concert with protein DNA binding site data, establish for the first time the beginnings of a globalC. parvumgene regulatory map that will contribute to our understanding of the development of this zoonotic parasite.
Surveillance of the prevalence, antibiotic susceptibility, and genotypic characterization of invasive candidiasis in a teaching hospital in China between 2006 to 2011
Authors: Li Fang , Wu Lin , Cao Bin , Zhang Yuyu , Li Xiaoli , Liu Yingmei 
Published: July 2013

Abstract

Background
Invasive candidiasis is an important nosocomial infection associated with high mortality among immunosuppressive or critically ill patients. We described the incidence of invasive candidiasis in our hospital over 6 years and showed the antifungal susceptibility and genotypes of the isolated yeast.

Method
The yeast species were isolated on CHROMagar Candida medium and identified using an yeast identification card, followed by analysis of the D1/D2 domain of 26S rDNA. The susceptibilities of the isolates to flucytosine, amphotericin B, fluconazole, itraconazole, and voriconazole were tested using the ATB FUNGUS 3 system, and that to caspofungin was tested using E-test strips. C. albicans was genotyped using single-strand conformation polymorphism of CAI (Candida albicans I) microsatellite DNA combined with GeneScan data.

Results
From January 2006 to December 2011, a total of 259 isolates of invasive Candida spp. were obtained from 253 patients, among them 6 patients had multiple positive samples. Ninety-one stains were from blood and 168 from sterile fluids, accounting for 6.07% of all pathogens isolated in our hospital. Most of these strains were C. albicans (41.29% in blood/59.06% in sterile body fluids), followed by C. tropicalis (18.06%/25.72%), C. parapsilosis (17.42%/5.43%), C. glabrata (11.61%/3.99%) and other Candida spp. (11.61%/5.80%). Most Candida spp. were isolated from the ICU. The new species-specific CLSI candida MIC breakpoints were applied to these date. Resistance to fluconazole occurred in 6.6% of C. albicans isolates, 10.6% of C. tropicalis isolates and 15.0% of C. glabrata isolates. For the 136 C. albicans isolates, 54 CAI patterns were recognized. The C. albicans strains from blood or sterile body fluids showed no predominant CAI genotypes. C. albicans isolates from different samples from the same patient had the same genotype.

Conclusions
Invasive candidiasis has been commonly encountered in our hospital in the past 6 years, with increasing frequency of non-C. albicans. Resistance to fluconazole was highly predictive of resistance to voriconazole. CAI SSCP genotyping showed that all C. albicans strains were polymorphic. Invasive candidiasis were commonly endogenous infection.
Bone turnover and bone mineral density in HIV-1 infected Chinese taking highly active antiretroviral therapy –a prospective observational study
Authors: Zhang Lixia , Su Yuanbo , Hsieh Evelyn , Xia Weibo , Xie Jing , Han Yang , Cao Ying , Li Yanling , Song Xiaojing , Zhu Ting , Li Taisheng , Yu Wei 
Published: July 2013

Abstract

Background
Low bone mass and high bone turnover have been reported in HIV-infected individuals, both as a consequence of HIV infection itself, as well as from treatment with highly active antiretroviral therapy (HAART). The purpose of this study is to evaluate the impact of HAART on bone mineral density and bone turnover in HIV-1 infected Chinese patients.

Methods
Forty HIV-1 infected patients were enrolled in this study; all patients were followed through 48 weeks, and 17 patients completed 96 weeks. Bone mineral density (BMD), procollagen type 1 N-terminal propeptide (P1NP), collagen type 1 cross-linked C-telopeptide (β-CTX), parathyroid hormone (PTH), and 25-OH vitamin D levels were measured at baseline, 48 and 96 weeks. Baseline measurements were compared with an age-, gender-, and BMI-matched healthy control population.

Results
At baseline, raw BMD in the lumbar spine of HIV-1 infected patients was significantly lower than that of healthy controls (1.138 ± 0.112 g/cm2 vs. 1.195 ± 0.139 g/cm2, p = 0.047). During the first 48 weeks after initiating HAART, BMD of lumbar spine, femoral neck, and total hip decreased significantly in HIV-1 infected patients, with annual percent decline ranging from 1.78-3.28%. However, from week 48 to 96, BMD remained stable. Baseline levels of β-CTX (0.31 ± 0.16 ng/mL vs. 0.42 ± 0.19 ng/mL, p = 0.008) and P1NP (32.96 ± 14.00 ng/mL vs. 55.82 ± 26.87 ng/mL, p = 0.05) were lower in HIV-infected patients compared with controls, respectively. Both β-CTX and P1NP levels increased after onset of HAART until week 48, and remained elevated during the next 48 weeks. 25-OH vitamin D in HIV-infected patients was lower at baseline compared to healthy controls, but this difference was not statistically significant. PTH, however, was higher in HIV patients at baseline, and showed a significant increase throughout the study.

Conclusions
Chinese adults with HIV-1 infection have low bone turnover prior to HAART as well as lower raw BMD of the lumbar spine compared with healthy controls, with further bone loss occurring following the initiation of HAART. The long-term clinical implications of these findings remain unclear at this time.
Germinated brown rice and its bioactives modulate the activity of uterine cells in oophorectomised rats as evidenced by gross cytohistological and immunohistochemical changes
Authors: Muhammad Sani I , Ismail Maznah , Mahmud Rozi B , Salisu Abubakar M , Zakaria Zuki A 
Published: July 2013

Abstract

Background
Germinated brown rice (GBR) is gaining momentum in the area of biomedical research due to its increased use as a nutraceutical for the management of diseases. The effect of GBR on the reproductive organs of oophorectomised rats was studied using the gross, cytological, histological and immunohistochemical changes, with the aim of reducing atrophy and dryness of the genital organs in menopause.

Methods
Experimental rats were divided into eight groups of six rats per group. Groups 1, 2 and 3 (sham-operated (SH), oophorectomised without treatment (OVX) and oophorectomised treated with 0.2 mg/kg oestrogen, respectively) served as the controls. The groups 4,5,6,7 and 8 were treated with 20 mg/kg Remifemin, 200 mg/kg of GBR, ASG, oryzanol and GABA, respectively. All treatments were administered orally, once daily for 8 weeks. Vaginal smear cytology was done at the 7th week on all the rats. The weight and dimensions of the uterus and vagina were determined after sacrifice of the rats. Uterine and vaginal tissues were taken for histology and Immunohistochemical examinations.

Results
GBR and its bioactives treated groups significantly increased the weight and length of both the uterus and the vagina when compared to Oophorectomised non-treated group (OVX-non-treated) (p < 0.05). Significant changes were observed in the ratio of cornified epithelial cells and number of leucocytes in the vaginal cytology between the oophorectomised non-treated and treated groups. There was also an increase in the luminal and glandular epithelial cells activity in the treated compared with the untreated groups histologically. Immunohistochemical staining showed specific proliferating cell nuclear antigen (PCNA) in the luminal and glandular epithelium of the treated groups, which was absent in the OVX-non-treated group. GBR improved the length and weight of the uterus and also increased the number of glandular and luminal cells epithelia of the vagina.

Conclusion
GBR and its bioactives could be a potential alternative in improving reproductive system atrophy, dryness and discomfort during menopause.
Clonidine versus captopril for treatment of postpartum very high blood pressure: study protocol for a randomized controlled trial (CLONCAP)
Authors: Noronha-Neto Carlos , Katz Leila , Coutinho Isabela C , Maia Sabina B , Souza Alex Sandro Rolland , Amorim Melania Maria Ramos 
Published: July 2013

Abstract

Background
The behavior of arterial blood pressure in postpartum of women with hypertension and pregnancy and the best treatment for very high blood pressure in this period still need evidence. The Cochrane systematic review assessing prevention and treatment of postpartum hypertension found only two trials (120 patients) comparing hydralazine with nifedipine and labetalol for the treatment of severe hypertension and did not find enough evidence to know how best to treat women with hypertension after birth. Although studies have demonstrated the effectiveness of treatment with captopril, side effects were reported. Because of these findings, new classes of antihypertensive drugs began to be administered as an alternative therapy. Data on the role of clonidine in this particular group of patients, its effects in the short and long term are still scarce in the literature.

Objectives
To determine the effectiveness of clonidine, compared to captopril, for the treatment of postpartum very high blood pressure in women with hypertension in pregnancy.

Methods/design
The study is a triple blind randomized controlled trial including postpartum women with diagnosis of hypertension in pregnancy presenting very high blood pressure, and exclusion criteria will be presence of heart disease, smoking, use of illicit drugs, any contraindication to the use of captopril or clonidine and inability to receive oral medications.
Eligible patients will be invited to participate and those who agree will be included in the study and receive captopril or clonidine according to a random list of numbers. The subjects will receive the study medication every 20 minutes until blood pressure is over 170 mmHg of systolic blood pressure and 110 mmHg diastolic blood pressure. A maximum of six pills a day for very high blood pressure will be administered. In case of persistent high blood pressure levels, other antihypertensive agents will be used.
During the study the women will be subject to strict control of blood pressure and urine output. This proposal has already obtained approval of the local Institutional Review Board of the coordinating center (IMIP, Recife, Brazil) and of the National Council for Ethics in Research (CONEP) of the Brazilian Ministry of Health.

Trial registration
Clinical Trials Register under the number NCT01761916.
The good, the bad and the dubious: VHELIBS, a validation helper for ligands and binding sites
Authors: Cereto-Massagué Adrià , Ojeda María José , Joosten Robbie P , Valls Cristina , Mulero Miquel , Salvado M Josepa , Arola-Arnal Anna , Arola Lluís , Garcia-Vallvé Santiago , Pujadas Gerard 
Published: July 2013

Abstract

Background
Many Protein Data Bank (PDB) users assume that the deposited structural models are of high quality but forget that these models are derived from the interpretation of experimental data. The accuracy of atom coordinates is not homogeneous between models or throughout the same model. To avoid basing a research project on a flawed model, we present a tool for assessing the quality of ligands and binding sites in crystallographic models from the PDB.

Results
The Validation HElper for LIgands and Binding Sites (VHELIBS) is software that aims to ease the validation of binding site and ligand coordinates for non-crystallographers (i.e., users with little or no crystallography knowledge). Using a convenient graphical user interface, it allows one to check how ligand and binding site coordinates fit to the electron density map. VHELIBS can use models from either the PDB or the PDB_REDO databank of re-refined and re-built crystallographic models. The user can specify threshold values for a series of properties related to the fit of coordinates to electron density (Real Space R, Real Space Correlation Coefficient and average occupancy are used by default). VHELIBS will automatically classify residues and ligands as Good, Dubious or Bad based on the specified limits. The user is also able to visually check the quality of the fit of residues and ligands to the electron density map and reclassify them if needed.

Conclusions
VHELIBS allows inexperienced users to examine the binding site and the ligand coordinates in relation to the experimental data. This is an important step to evaluate models for their fitness for drug discovery purposes such as structure-based pharmacophore development and protein-ligand docking experiments.
Tackling graduate unemployment in North Africa through employment subsidies: A look at the SIVP programme in Tunisia
Authors: Broecke Stijn 
Published: July 2013

Abstract
This paper takes a closer look at Tunisia’s SIVP: an employment subsidy aimed at university graduates and, until recently, the country’s largest active labour market policy. Using a tracer survey of the 2004 graduating cohort, OLS and matching techniques are applied to estimate the relationship between programme participation and the labour market outcomes of participants. Graduates who benefited from the programme appear less likely to be unemployed and considerably more likely to have found a job in the private sector - but this may partly reflect selection into the programme, which is not random.

JEL classification

J08, J20