bluuebunny/crossref_metadata_2025_split huggingface dataset:
Satellite-Derived Tropical Cyclone Intensity in the North Pacific Ocean Using the Deviation-Angle Variance Technique
Authors: Ritchie Elizabeth A. , Wood Kimberly M. , Rodríguez-Herrera Oscar G. , Piñeros Miguel F. , Tyo J. Scott 
Published: December 2013

Abstract
The deviation-angle variance technique (DAV-T), which was introduced in the North Atlantic basin for tropical cyclone (TC) intensity estimation, is adapted for use in the North Pacific Ocean using the “best-track center” application of the DAV. The adaptations include changes in preprocessing for different data sources [Geostationary Operational Environmental Satellite-East (GOES-E) in the Atlantic, stitched GOES-E–Geostationary Operational Environmental Satellite-West (GOES-W) in the eastern North Pacific, and the Multifunctional Transport Satellite (MTSAT) in the western North Pacific], and retraining the algorithm parameters for different basins. Over the 2007–11 period, DAV-T intensity estimation in the western North Pacific results in a root-mean-square intensity error (RMSE, as measured by the maximum sustained surface winds) of 14.3 kt (1 kt ≈ 0.51 m s−1) when compared to the Joint Typhoon Warning Center best track, utilizing all TCs to train and test the algorithm. The RMSE obtained when testing on an individual year and training with the remaining set lies between 12.9 and 15.1 kt. In the eastern North Pacific the DAV-T produces an RMSE of 13.4 kt utilizing all TCs in 2005–11 when compared with the National Hurricane Center best track. The RMSE for individual years lies between 9.4 and 16.9 kt. The complex environment in the western North Pacific led to an extension to the DAV-T that includes two different radii of computation, producing a parametric surface that relates TC axisymmetry to intensity. The overall RMSE is reduced by an average of 1.3 kt in the western North Pacific and 0.8 kt in the eastern North Pacific. These results for the North Pacific are comparable with previously reported results using the DAV for the North Atlantic basin.
Risk factors for contracting watery diarrhoea in Kadoma City, Zimbabwe, 2011: a case control study
Authors: Maponga Brian A , Chirundu Daniel , Gombe Notion T , Tshimanga Mufuta , Shambira Gerald , Takundwa Lucia 
Published: December 2013

Abstract

Background
Kadoma City experienced an increase in watery diarrhoea from 27 cases during week beginning 5th September, to 107 cases during week beginning 26th September 2011. The weekly diarrhoea cases crossed the threshold action line during week beginning 5th September at the children’s clinic in Rimuka Township, and the remaining four clinics reported cases crossing threshold action lines between week beginning 12th September and week beginning 26th September. Eighty-two percent of the cases were children less than 5 years old. We conducted a case controlstudy to determine risk factorsfor contracting watery diarrhoea in children less than 5 years in Kadoma City.

Methods
An unmatched 1:1 case control study was conducted in Ngezi and Rimuka townships in Kadoma City, Zimbabwe. A case was a child less than 5 years old, who developed acute watery diarrhoea between 5th September and 1st October 2011. A control was a child less than 5 years old who stayed in the same township and did not suffer from diarrhoea. A structured questionnaire was administered to caregivers of cases and controls.Laboratory water quality tests and stool test results were reviewed.Epi Info™ statistical software was used to analyse data.

Results
A total of 109 cases and 109 controls were enrolled. Independent protective factors were: having been exclusively breastfed for six months [AOR = 0.44; 95% CI (0.24-0.82)]; using municipal water [AOR = 0.38; 95% CI (0.18-0.80)]; using aqua tablets, [AOR = 0.49; 95% CI (0.26–0.94)] and; storing water in closed containers, [AOR = 0.24; 95% CI (0.07–0.0.83). The only independent risk factor for contracting watery diarrhoea was hand washing in a single bowl, [AOR = 2.89; 95% CI (1.33–6.28)]. Salmonella, Shigella, Rotavirus, and Enteropathogenic Escherichia coli were isolated in the stool specimens. None of the 33 municipal water samples tested showed contamination with Escherichia coli, whilst 23 of 44 (52%) shallow well water samples and 3 of 15(20%) borehole water samples tested were positive for Escherichia coli.

Conclusions
The outbreak resulted from inadequate clean water and use of contaminated water. Evidence from this study was used to guide public health response to the outbreak.
Estimation of glomerular filtration rate from serum creatinine and cystatin C in octogenarians and nonagenarians
Authors: Lopes Marcelo B , Araújo Lara Q , Passos Michelle T , Nishida Sonia K , Kirsztajn Gianna M , Cendoroglo Maysa S , Sesso Ricardo C 
Published: December 2013

Abstract

Background
Equations to estimate GFR have not been well validated in the elderly and may misclassify persons with chronic kidney disease (CKD). We measured GFR and compared the performance of the Modification of Diet in Renal Disease (MDRD), the Chronic Kidney Disease-Epidemiology Collaboration (CKD-Epi) and the Berlin Initiative Study (BIS) equations based on creatinine and/or cystatin C in octogenarians and nonagenarians.

Methods
Using cross-sectional analysis we assessed 95 very elderly persons (mean 85 years) living in the community. GFR was measured by iohexol (mGFR) and compared with estimates using six equations: MDRD, CKD-Epi_creatinine, CKD-Epi_cystatin, CKD-Epi_creatinine-cystatin, BIS_creatinine and BIS_creatinine-cystatin.

Results
Mean mGFR was 55 (range,19–86) ml/min/1.73 m2. Bias was smaller with the CKD-Epi_creatinine-cystatin and the CKD-Epi_creatinine equations (-4.0 and 1.7 ml/min/1.73 m2). Accuracy (percentage of estimates within 30% of mGFR) was greater with the CKD-Epi_creatinine-cystatin, BIS_creatinine-cystatin and BIS_creatinine equations (85%, 83% and 80%, respectively). Among the creatinine-based equations, the BIS_creatinine had the greatest accuracy at mGFR < 60 ml/min/1.73 m2 and the CKD-Epi_creatinine was superior at higher GFRs (79% and 90%, respectively). The CKD-Epi_creatinine-cystatin, BIS_creatinine-cystatin and CKD-Epi_cystatin equations yielded the greatest areas under the receiver operating characteristic curve at GFR threshold = 60 ml/min/1.73 m2 (0.88, 0.88 and 0.87, respectively). In participants classified based on the BIS_creatinine, CKD-Epi_cystatin, or BIS_creatinine-cystatin equations, the CKD-Epi_creatinine-cystatin equation tended to improve CKD classification (net reclassification index: 12.7%, p = 0.18; 6.7%, p = 0.38; and 15.9%; p = 0.08, respectively).

Conclusions
GFR-estimating equations CKD-Epi_creatinine-cystatin and BIS_creatinine-cystatin showed better accuracy than other equations using creatinine or cystatin C alone in very elderly persons. The CKD-Epi_creatinine-cystatin equation appears to be advantageous in CKD classification. If cystatin C is not available, both the BIS_cr equation and the CKD-Epi_cr equation could be used, although at mGFR < 60 ml/min/1.73 m2, the BIS_cr equation seems to be the best alternative.
Fluid overload in hemodialysis patients: a cross-sectional study to determine its association with cardiac biomarkers and nutritional status
Authors: Antlanger Marlies , Hecking Manfred , Haidinger Michael , Werzowa Johannes , Kovarik Johannes J , Paul Gernot , Eigner Manfred , Bonderman Diana , Hörl Walter H , Säemann Marcus D 
Published: December 2013

Abstract

Background
Chronic fluid overload is associated with higher mortality in dialysis patients; however, the link with cardiovascular morbidity has not formally been established and may be influenced by subclinical inflammation. We hypothesized that a relationship exists between fluid overload and [i] cardiovascular laboratory parameter as well as between fluid overload and [ii] inflammatory laboratory parameters. In addition, we aimed to confirm whether volume status correlates with nutritional status.

Methods
We recorded baseline characteristics of 244 hemodialysis patients at three hemodialysis facilities in Vienna (Austria) and determined associations with volume measurements using the body composition monitor (Fresenius/Germany). In one facility comprising 126 patients, we further analyzed cardiovascular, inflammatory and nutritional parameters.

Results
We detected predialysis fluid overload (FO) in 39% of all patients (n = 95) with FO defined as ≥15% of extracellular water (ECW). In this subgroup, the absolute FO was 4.4 +/-1.5 L or 22.9 ± 4.8% of ECW. A sub-analysis of patients from one center showed that FO was negatively associated with body mass index (r = -0.371; p = <0.001), while serum albumin was significantly lower in fluid overloaded patients (p = 0.001). FO was positively associated with D-Dimer (r = 0.316; p = 0.001), troponin T (r = 0.325; p < 0.001), and N-terminal pro-B-type natriuretic peptide (r = 0.436; p < 0.001), but not with investigated inflammatory parameters.

Conclusions
Fluid overload in HD patients was found to be lower in patients with high body mass index, indicating that dry weight was inadequately prescribed and/or difficult to achieve in overweight patients. The association with parameters of cardiovascular compromise and/or damage suggests that fluid overload is a biomarker for cardiovascular risk. Future studies should determine if this applies to patients prior to end-stage renal disease.
Some coincidence point results for generalized "Equation missing"-weakly contractive mappings in ordered G-metric spaces
Authors: Mustafa Zead , Parvaneh Vahid , Abbas Mujahid , Roshan Jamal Rezaei 
Published: December 2013

AbstractThe aim of this paper is to present some coincidence point results for six mappings satisfying the generalized(ψ,φ)-weakly contractive condition in the framework of partially orderedG-metric spaces. To elucidate our results, we present two examples together with an application of a system of integral equations.MSC:47H10, 54H25.
A first-order adjoint and a second-order hybrid method for an energy output least-squares elastography inverse problem of identifying tumor location
Authors: Cahill Nathan D , Jadamba Baasansuren , Khan Akhtar A , Sama Miguel , Winkler Brian C 
Published: December 2013

Abstract
In this paper we investigate the elastography inverse problem of identifying cancerous tumors within the human body. From a mathematical standpoint, the elastography inverse problem consists of identifying the variable Lamé parameter μ in a system of linear elasticity where the underlying object exhibits nearly incompressible behavior. This problem is subsequently posed as an optimization problem using an energy output least-squares (EOLS) functional, but the nonlinearity that arises makes the computation of the EOLS functional’s derivatives challenging. We employ an adjoint method for the computation of the gradient, something shown to be an efficient method in recent studies, and also give a parallelizable hybrid method for the computation of the EOLS functional’s second derivative. Detailed discrete formulas and nontrivial computational examples are provided to show the feasibility of both the adjoint and hybrid approaches. Furthermore, all results are given in the framework of a general saddle point problem allowing easy adaptation to numerous other inverse problems.

MSC:35R30, 65N30.
Identification of broadly neutralizing antibody epitopes in the HIV-1 envelope glycoprotein using evolutionary models
Authors: Lacerda Miguel , Moore Penny L , Ngandu Nobubelo K , Seaman Michael , Gray Elin S , Murrell Ben , Krishnamoorthy Mohan , Nonyane Molati , Madiga Maphuti , Wibmer Constantinos Kurt , Sheward Daniel , Bailer Robert T , Gao Hongmei , Greene Kelli M , Karim Salim S Abdool , Mascola John R , Korber Bette TM , Montefiori David C , Morris Lynn , Williamson Carolyn , Seoighe Cathal ,   the CAVD-NSDP Consortium
Published: December 2013

Abstract

Background
Identification of the epitopes targeted by antibodies that can neutralize diverse HIV-1 strains can provide important clues for the design of a preventative vaccine.

Methods
We have developed a computational approach that can identify key amino acids within the HIV-1 envelope glycoprotein that influence sensitivity to broadly cross-neutralizing antibodies. Given a sequence alignment and neutralization titers for a panel of viruses, the method works by fitting a phylogenetic model that allows the amino acid frequencies at each site to depend on neutralization sensitivities. Sites at which viral evolution influences neutralization sensitivity were identified using Bayes factors (BFs) to compare the fit of this model to that of a null model in which sequences evolved independently of antibody sensitivity. Conformational epitopes were identified with a Metropolis algorithm that searched for a cluster of sites with large Bayes factors on the tertiary structure of the viral envelope.

Results
We applied our method to ID50 neutralization data generated from seven HIV-1 subtype C serum samples with neutralization breadth that had been tested against a multi-clade panel of 225 pseudoviruses for which envelope sequences were also available. For each sample, between two and four sites were identified that were strongly associated with neutralization sensitivity (2ln(BF) > 6), a subset of which were experimentally confirmed using site-directed mutagenesis.

Conclusions
Our results provide strong support for the use of evolutionary models applied to cross-sectional viral neutralization data to identify the epitopes of serum antibodies that confer neutralization breadth.
Common sense: folk wisdom that ethnobiological and ethnomedical research cannot afford to ignore
Authors: Erren Thomas C , Koch Melissa S , Meyer-Rochow V Benno 
Published: December 2013

AbstractCommon sense [CS], especially that of the non-scientist, can have predictive power to identify promising research avenues, as humans anywhere on Earth have always looked for causal links to understand, shape and control the world around them. CS is based on the experience of many individuals and is thus believed to hold some truths. Outcomes predicted by CS are compatible with observations made by whole populations and have survived tests conducted by a plethora of non-scientists. To explore our claim, we provide 4 examples of empirical insights (relevant to probably all ethnic groups on Earth) into causal phenomena predicted by CS: (i) “humans must have a sense of time”, (ii) “at extreme latitudes, more people have the winter blues”, (iii) “sleep is a cure for many ills” and (iv) “social networks affect health and disease”. While CS is fallible, it should not be ignored by science – however improbable or self-evident the causal relationships predicted by CS may appear to be.
Sonoporation as an enhancing method for boron neutron capture therapy for squamous cell carcinomas
Authors: Yamatomo Naofumi , Iwagami Takaki , Kato Itsuro , Masunaga Shin-Ichiro , Sakurai Yoshinori , Iwai Soichi , Nakazawa Mitsuhiro , Ono Koji , Yura Yoshiaki 
Published: December 2013

Abstract

Background
Boron neutron capture therapy (BNCT) is a selective radiotherapy that is dependent on the accumulation of 10B compound in tumors. Low-intensity ultrasound produces a transient pore on cell membranes, sonoporation, which enables extracellular materials to enter cells. The effect of sonoporation on BNCT was examined in oral squamous cell carcinoma (SCC) xenografts in nude mice.

Materials and methods
Tumor-bearing mice were administrated boronophenylalanine (BPA) or boronocaptate sodium (BSH) intraperitoneally. Two hours later, tumors were subjected to sonoporation using microbubbles followed by neutron irradiation.

Results
The 10B concentration was higher in tumors treated with sonoporation than in untreated tumors, although the difference was not significant in BPA. When tumors in mice that received BPA intraperitoneally were treated with sonoporation followed by exposure to thermal neutrons, tumor volume was markedly reduced and the survival rate was prolonged. Such enhancements by sonoporation were not observed in mice treated with BSH-mediated BNCT.

Conclusions
These results indicate that sonoporation enhances the efficiency of BPA-mediated BNCT for oral SCC. Sonoporation may modulate the microlocalization of BPA and BSH in tumors and increase their intracellular levels.
Livin expression is an independent factor in rectal cancer patients with or without preoperative radiotherapy
Authors: Ding Zhen-Yu , Zhang Hong , Adell Gunnar , Olsson Birgit , Sun Xiao-Feng 
Published: December 2013

Abstract

Background
This study was aimed to investigate the expression significance of Livin in relation to radiotherapy (RT), clinicopathological and biological factors of rectal cancer patients.

Methods
This study included 144 primary rectal cancer patients who participated in a Swedish clinical trial of preoperative radiotherapy. Tissue microarray samples from the excised primary rectal cancers, normal mucosa and lymph node metastases were immunostained with Livin antibody. The proliferation of colon cancer cell lines SW620 and RKO was assayed after Livin knock-down.

Results
The expression of Livin was significantly increased from adjacent (P = 0.051) or distant (P = 0.028) normal mucosa to primary tumors. 15.4% (2/13) and 39.7% (52/131) patients with Livin-negative and positive tumors died at 180 months after surgery, and the difference tended to be statistically significant (P = 0.091). In multivariate analyses, the difference achieved statistical significance, independent of TNM stage, local and distant recurrence, grade of differentiation, gender, and age (odds ratio = 5.09, 95% CI: 1.01-25.64, P = 0.048). The in vitro study indicated colon cancer cells with Livin knock-down exhibited decreased proliferation compared with controls after RT.

Conclusions
The expression of Livin was was independently related to survival in rectal cancer patients, suggesting Livin as a useful prognostic factor for rectal cancer patients.
The Bacillus BioBrick Box: generation and evaluation of essential genetic building blocks for standardized work with Bacillus subtilis
Authors: Radeck Jara , Kraft Korinna , Bartels Julia , Cikovic Tamara , Dürr Franziska , Emenegger Jennifer , Kelterborn Simon , Sauer Christopher , Fritz Georg , Gebhard Susanne , Mascher Thorsten 
Published: December 2013

Abstract

Background
Standardized and well-characterized genetic building blocks are a prerequisite for the convenient and reproducible assembly of novel genetic modules and devices. While numerous standardized parts exist for Escherichia coli, such tools are still missing for the Gram-positive model organism Bacillus subtilis. The goal of this study was to develop and thoroughly evaluate such a genetic toolbox.

Results
We developed five BioBrick-compatible integrative B. subtilis vectors by deleting unnecessary parts and removing forbidden restriction sites to allow cloning in BioBrick (RFC10) standard. Three empty backbone vectors with compatible resistance markers and integration sites were generated, allowing the stable chromosomal integration and combination of up to three different devices in one strain. In addition, two integrative reporter vectors, based on the lacZ and luxABCDE cassettes, were BioBrick-adjusted, to enable β-galactosidase and luciferase reporter assays, respectively. Four constitutive and two inducible promoters were thoroughly characterized by quantitative, time-resolved measurements. Together, these promoters cover a range of more than three orders of magnitude in promoter strength, thereby allowing a fine-tuned adjustment of cellular protein amounts. Finally, the Bacillus BioBrick Box also provides five widely used epitope tags (FLAG, His10, cMyc, HA, StrepII), which can be translationally fused N- or C-terminally to any protein of choice.

Conclusion
Our genetic toolbox contains three compatible empty integration vectors, two reporter vectors and a set of six promoters, two of them inducible. Furthermore, five different epitope tags offer convenient protein handling and detection. All parts adhere to the BioBrick standard and hence enable standardized work with B. subtilis. We believe that our well-documented and carefully evaluated Bacillus BioBrick Box represents a very useful genetic tool kit, not only for the iGEM competition but any other BioBrick-based project in B. subtilis.
Similarity and difference in vegetation structure of three desert shrub communities under the same temperate climate but with different microhabitats
Authors: Tao Ye , Zhang Yuan-Ming , Downing Alison 
Published: December 2013

Abstract

Background
Community structure and species composition are closely related to plant diversity and ecosystem stability. To explore the similarity in vegetation structure of shrub communities under the same temperate climate but with different microhabitats, 36, 28 and 13 sampling plots in Ephedra distachya, Seriphidium terrae-albae and Artemisia songarica communities were selected respectively, during the course of three seasons (early spring, summer, autumn) in Gurbantunggut Desert, north-western China. The species composition, abundance, biomass and soil nutrients were investigated. Floristic changes were characterized by similarity and ordination methods.

Results
Two communities, E. distachya and S. terrae-albae, were similar in terms of soil nutrients but differed from the A. songarica community. Soil organic matter, nitrogen and biological soil crusts accounted for the differences of microhabitats. In spring and summer, more plant families, genera and species were recorded in E. distachya and S. terrae-albae communities than in the A. songarica community but in each community, the number of families, genera, species, herbs and life forms showed a consistent trend summer > spring > autumn. There were significant differences in absolute biomass among the three communities, but the ratio of dead biomass to total biomass was consistently 1:4, indicating the constant turnover rate of plant biomass for nutrient cycling. In each community shrubs accounted for the most biomass. Herbaceous biomass was negligible but the herbs contributed the most richness and abundance.

Conclusions
The similarity in response of all three communities to seasonal changes in vegetation structure and biomass allocation demonstrate convergence although divergence is demonstrated in soil characteristics or microhabitats.
A note on transhumant pastoralism in Niti valley, Western Himalaya, India
Authors: Mitra Monideepa , Kumar Amit , Adhikari Bhupendra S , Rawat Gopal S 
Published: December 2013

Abstract
Pastoralism plays an important role in the ecology of alpine habitats and the economy of rural people in some regions of India. The pastoralists move from lower altitudes of the Himalayas to higher alpine regions in summer and return back to lower altitude villages with the onset of autumn. The forested areas along the routes of transhumant pastoralists are affected by anthropogenic pressures, viz. grazing by livestock and tree lopping by the herders for fuelwood. To demarcate such areas and evaluate the effect of anthropogenic disturbances, a preliminary documentation of the routes is needed. Interviews were conducted using semi-structured questionnaires to elucidate the information from herders visiting Niti valley, Western Himalayas. The interviews found that most of these herders had common stopovers following a similar route to the valley from their respective villages. More than 70% of herders made their transit camps at Niti village and adjoining areas. They stay there for a few days and then the majority move on to higher alpine pastures of Geldung. The rest either stay back at alpine areas near Niti or in the alpine areas adjoining Gamsali village. These stopovers are areas which experience maximum anthropogenic pressure during livestock migrations, and the vegetation is the most affected. Documentation of migration routes will help identify such areas of high pressure and develop management plans to minimize the disturbances.