bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cloning and characterization of a pectin lyase gene from Colletotrichum lindemuthianumand comparative phylogenetic/structural analyses with genes from phytopathogenic and saprophytic/opportunistic microorganisms
Authors: Lara-Márquez Alicia , Zavala-Páramo María G , López-Romero Everardo , Calderón-Cortés Nancy , López-Gómez Rodolfo , Conejo-Saucedo Ulises , Cano-Camacho Horacio 
Published: December 2011

AbstractBackgroundMicroorganisms produce cell-wall-degrading enzymes as part of their strategies for plant invasion/nutrition. Among these, pectin lyases (PNLs) catalyze the depolymerization of esterified pectin by a β-elimination mechanism. PNLs are grouped together with pectate lyases (PL) in Family 1 of the polysaccharide lyases, as they share a conserved structure in a parallel β-helix. The best-characterized fungal pectin lyases are obtained from saprophytic/opportunistic fungi in the generaAspergillusandPenicilliumand from some pathogens such asColletotrichum gloeosporioides.The organism used in the present study,Colletotrichum lindemuthianum, is a phytopathogenic fungus that can be subdivided into different physiological races with different capacities to infect its host,Phaseolus vulgaris. These include the non-pathogenic and pathogenic strains known as races 0 and 1472, respectively.ResultsHere we report the isolation and sequence analysis of theClpnl2gene, which encodes the pectin lyase 2 ofC. lindemuthianum, and its expression in pathogenic and non-pathogenic races ofC. lindemuthianumgrown on different carbon sources. In addition, we performed a phylogenetic analysis of the deduced amino acid sequence of Clpnl2 based on reported sequences of PNLs from other sources and compared the three-dimensional structure of Clpnl2, as predicted by homology modeling, with those of other organisms. Both analyses revealed an early separation of bacterial pectin lyases from those found in fungi and oomycetes. Furthermore, two groups could be distinguished among the enzymes from fungi and oomycetes: one comprising enzymes from mostly saprophytic/opportunistic fungi and the other formed mainly by enzymes from pathogenic fungi and oomycetes. Clpnl2 was found in the latter group and was grouped together with the pectin lyase fromC. gloeosporioides.ConclusionsTheClpnl2gene ofC. lindemuthianumshares the characteristic elements of genes coding for pectin lyases. A time-course analysis revealed significant differences between the two fungal races in terms of the expression ofClpnl2encoding for pectin lyase 2. According to the results, pectin lyases from bacteria and fungi separated early during evolution. Likewise, the enzymes from fungi and oomycetes diverged in accordance with their differing lifestyles. It is possible that the diversity and nature of the assimilatory carbon substrates processed by these organisms played a determinant role in this phenomenon.
Prevention of falls and fractures in old people by administration of calcium and vitamin d. randomized clinical trial
Authors: López-Torres Hidalgo Jesús ,   ANVITAD Group
Published: December 2011

Abstract

Background
There are many studies that associate vitamin D serum levels in older persons with muscle strength, physical performance and risk of fractures and falls. However, current evidence is insufficient to make a general recommendation for administrating calcium and vitamin D to older persons. The objective of this study is to determine the effectiveness of calcium and vitamin D supplementation in improving musculoskeletal function and decreasing the number of falls in person aged over 65 years.

Methods/Design
Phase III, randomized, double blind, placebo-controlled trial to evaluate the efficacy of already marketed drugs in a new indication. It will be performed at Primary Care doctor visits at several Healthcare Centers in different Spanish Health Areas. A total of 704 non-institutionalized subjects aged 65 years or older will be studied (sample size calculated for a statistical power of 80%, alpha error 0.05, annual incidence of falls 30% and expected reduction of 30% to 20% and expected loss to follow up of 20%). The test drug containing 800 IU of vitamin D and 1000 mg of calcium will be administered daily. The control group will receive a placebo. The subjects will be followed up over two years. The primary variable will be the incidence of spontaneous falls. The secondary variables will include: consequences of the falls (fractures, need for hospitalization), change in calcidiol plasma levels and other analytical determinations (transaminases, PTH, calcium/phosphorous, albumin, creatinine, etc.), change in bone mass by densitometry, change in muscle strength in the dominant hand and change in musculoskeletal strength, risk factors for falls, treatment compliance, adverse effects and socio-demographic data.

Discussion
The following principles have been considered in the development of this Project: the product data are sufficient to ensure that the risks assumed by the study participants are acceptable, the study objectives will probably provide further knowledge on the problem studied and the available information justifies the performance of the study and its possible risk for the participants.
If calcium and vitamin D supplementation is effective in the prevention of falls and fractures in the elderly population, a recommendation may be issued with the aim of preventing some of the consequences of falls that affect quality of life and the ensuing personal, health and social costs.

Trial Registration
ClinicalTrials.gov: NCT01452243

Clinical trial authorized by the Spanish Medicines Agency: EudraCT number 2006-001643-63.
Effects of multi-walled carbon nanotubes (MWCNT) under Neisseria meningitidis transformation process
Authors: Mattos Ives B , Alves Danilo A , Hollanda Luciana M , Ceragiogli Helder J , Baranauskas Vitor , Lancellotti Marcelo 
Published: December 2011

Abstract

Background
This study aimed at verifying the action of multi-walled carbon nanotubes (MWCNT) under the naturally transformable Neisseria meningitidis against two different DNA obtained from isogenic mutants of this microorganism, an important pathogen implicated in the genetic horizontal transfer of DNA, causing the escape of the principal vaccination measured worldwide by the capsular switching process.

Materials and methods
The bacterium receptor strain C2135 was cultivated and had its mutant DNA donor M2 and M6, which received a receptor strain and MWCNT at three different concentrations. The inhibition effect of DNAse on the DNA in contact with nanoparticles was evaluated.

Results
The results indicated an in increase in the transformation capacity of N. meninigtidis in different concentrations of MWCNT when compared with negative control without nanotubes. A final analysis of the interaction between DNA and MWCNT was carried out using Raman Spectroscopy.

Conclusion
These increases in the transformation capacity mediated by MWCNT, in meningococci, indicate the interaction of these particles with the virulence acquisition of these bacteria, as well as with the increase in the vaccination escape process.
Primary clear cell sarcoma of humerus: case report
Authors: Liu Xudong , Zhang Huizhen , Dong Yang 
Published: December 2011

Abstract
We report a case of primary clear cell sarcoma occurring in the humerus. A 20 year old girl was referred to our hospital two years ago with painless swelling of the soft tissue surrounding the proximal right humerus. The conventional radiographic image showed an ill-defined, aggressive, osteolytic lesion associated with a partial cortical defect of the proximal right humerus. Magnetic resonance imaging found an irregularly shaped extraosseous mass extending from the proximal shaft of the right humerus, penetrating through the destroyed bone and invading the biceps brachii. After preoperative chemotherapy, a total tumor resection, internal fixation and bone cement implantation were performed. Histological studies of the resected tumor found that fibrous septa divided into well-defined nests and polygonal and fusiform cells with clear cytoplasm. Immunohistochemical studies demonstrated strong positive cytoplasmic staining with S-100 and scattered positivity with HMB-45. These findings led to a final, definitive diagnosis of clear cell sarcoma of the humerus. After routine postoperative chemotherapy, a 2-year follow-up showed no metastasis. Our findings in this report point out that primary clear cell sarcoma can originate from within the humerus and that limb salvage surgery can obtain a good result.
Integrity of chromatin and replicating DNA in nuclei released from fission yeast by semi-automated grinding in liquid nitrogen
Authors: Givens Robert M , Mesner Larry D , Hamlin Joyce L , Buck Michael J , Huberman Joel A 
Published: December 2011

Abstract

Background
Studies of nuclear function in many organisms, especially those with tough cell walls, are limited by lack of availability of simple, economical methods for large-scale preparation of clean, undamaged nuclei.

Findings
Here we present a useful method for nuclear isolation from the important model organism, the fission yeast, Schizosaccharomyces pombe. To preserve in vivo molecular configurations, we flash-froze the yeast cells in liquid nitrogen. Then we broke their tough cell walls, without damaging their nuclei, by grinding in a precision-controlled motorized mortar-and-pestle apparatus. The cryo-ground cells were resuspended and thawed in a buffer designed to preserve nuclear morphology, and the nuclei were enriched by differential centrifugation. The washed nuclei were free from contaminating nucleases and have proven well-suited as starting material for genome-wide chromatin analysis and for preparation of fragile DNA replication intermediates.

Conclusions
We have developed a simple, reproducible, economical procedure for large-scale preparation of endogenous-nuclease-free, morphologically intact nuclei from fission yeast. With appropriate modifications, this procedure may well prove useful for isolation of nuclei from other organisms with, or without, tough cell walls.
Mortality in people with depressive, anxiety and alcohol use disorders in Finland
Authors: Markkula Niina , Härkänen Tommi , Perälä Jonna , Partti Krista , Peña Sebastián , Koskinen Seppo , Lönnqvist Jouko , Suvisaari Jaana , Saarni Samuli I. 
Published: December 2011

BackgroundMental disorders are associated with increased mortality, but population-based surveys with reliable diagnostic procedures controlling for somatic health status are scarce.AimsTo assess excess mortality associated with depressive, anxiety and alcohol use disorders and the principal causes of death.MethodIn a nationally representative sample of Finns aged 30–70 years, psychiatric disorders were diagnosed with the Composite International Diagnostic Interview. After an 8-year follow-up period, vital status and cause of death of each participant was obtained from national registers.ResultsAfter adjusting for sociodemographic factors, health status and smoking, depressive (hazard ratio (HR) = 1.97) and alcohol use disorders (HR = 1.72) were statistically significantly associated with mortality. Risk of unnatural death was increased among individuals diagnosed with anxiety disorders or alcohol dependence.ConclusionsIndividuals with depressive and alcohol use disorders have an increased mortality risk comparable with many chronic somatic conditions, that is only partly attributable to differences in sociodemographic, somatic health status and hazardous health behaviour.
Magnetic resonance venous velocity mapping during intermittent pneumatic compression of the calf and foot
Authors: Pierce I T , Gatehouse P D , Kalodiki E , Lattimer C , Geroulakos G , Xu X Y , Firmin D N 
Published: December 2011

Objective Assessment and optimization of intermittent pneumatic compression (IPC) devices for prophylaxis of deep vein thrombosis has previously used duplex ultrasound. The aim was to investigate novel magnetic resonance (MR) venous velocity mapping (VM) for IPC research and development. Methods Twelve normal subjects were scanned in the supine position using realtime MR VM with sequential foot and calf IPC (120 mmHg) at 1.5 T. Measurements were taken in the popliteal vein at baseline using both cuffs and each cuff individually recording 60 seconds continuously. Temporal resolution was 310 ms per independent image, at 1 ×1 mm spatial resolution. Results Peak velocity ( Vp) measurements: baseline, Vp = 2.1 cm/second (range = 1.1–3.5); using both compression cuffs, Vp = 41.5 cm/second (18.0–58.1); calf cuff alone, Vp = 40.6 cm/second (18.1–62.2); foot cuff alone, Vp = 7.9 cm/second (4.2–15.3). Flow volume measurements per compression cycle ( F): baseline, F = 2.3 cm3 (0.5–11.4); both compression cuffs, F = 7.1 cm3 (2.5–24.6); calf cuff only, F = 7.1 cm3 (2.4–24.5); foot cuff only, F = 2.6 cm3 (0.9–10.7). The foot cuff contribution was insignificant when combined with the calf cuff ( P < 0.01). The MR venous VM results were similar to those reported elsewhere using ultrasound. Conclusion This novel technique for MR venous VM can measure the realtime variations in venous blood flow during IPC.
Assessment of Deliverability of a Natural Gas Gathering and Production System: Development of an Integrated Reservoir – Surface Model
Authors: Alexis Dennis Arun 
Published: December 2011

Abstract
The present work describes the development of a one-dimensional steady state isothermal reservoir – surface gas pipeline network model. The model was developed by combining reservoir with surface facility description parameters to effectively capture the variations in reservoir flow dynamics with changes in surface network operating conditions. The developed model is an extension of the general pipeline network model where the deliverability from the wells are calculated in addition to the nodal pressures and gas flows in different pipe sections in the system based on a set of operating conditions. Validation of the developed model was done by history matching using field data obtained from a currently operating gas gathering and transportation network located in the Northeastern, United States. After successful validation, the model was used as a diagnostic tool to evaluate ‘what if’ scenarios to identify the pressure and deliverability changes that can happen in the network. Based on the model predictions, recommendations were made to the operator in terms of total production, total sales and fuel consumed by the compressors present in the network. This integrated modeling approach helped in analyzing the system response as a whole and gave a good insight of how the well shut-in pressures used in the model had a significant impact on the deliverability predictions.
Validation Study of Oxford Classification of IgA Nephropathy
Authors: Katafuchi Ritsuko , Ninomiya Toshiharu , Nagata Masaharu , Mitsuiki Koji , Hirakata Hideki 
Published: December 2011

Summary

Background and objectives
The Oxford classification of IgA nephropathy (IgAN) includes mesangial hypercellularity, endocapillary hypercellularity, segmental glomerulosclerosis (S), and tubular atrophy/interstitial fibrosis (T) as prognosticators. The value of extracapillary proliferation (Ex) was not addressed. Because the Oxford classification excludes patients with urinary protein <0.5 g/d and eGFR <30 ml/min per 1.73 m2 at biopsy, the significance of Ex should be confirmed by validation cohorts that include more rapidly progressive cases. We present such a study.

Design, setting, participants, & measurements
The significance of pathologic features for development end-stage renal failure (ESRF) was examined by multivariate analysis in 702 patients with IgAN. The association of Ex with kidney survival was examined by univariate analysis in 416 patients who met the Oxford criteria and 286 who did not, separately.

Results
In a multivariate model, S and T were significantly associated with ESRF. With addition of Ex, not S but Ex was significant for ESRF. In univariate analysis, kidney survival was significantly lower in patients with Ex than in those without, in patients who did not meet the Oxford criteria, but such a difference was not found in patients who met it.

Conclusions
The prognostic significance of Ex was evident in our cohort. It seems that Ex did not emerge from the Oxford classification as a prognosticator because of exclusion of severe cases (eGFR <30 ml/min per 1.73 m2). We suggest that extracapillary proliferation be included in the next version of the Oxford classification of IgAN to widen the scope of the classification.
Low-Molecular-Weight Proteins as Prognostic Markers in Idiopathic Membranous Nephropathy
Authors: van den Brand Jan A.J.G. , Hofstra Julia M. , Wetzels Jack F.M. 
Published: December 2011

Summary

Background
Accurate prediction of prognosis in idiopathic membranous nephropathy (iMN) allows restriction of immunosuppressive therapy to patients at high risk for ESRD. Here we re-evaluate urinary low-molecular-weight proteins as prognostic markers and explore causes of misclassification.

Design, setting, participants, & measurements
In a cohort of 129 patients with serum creatinine concentration <135 μmol/L and proteinuria ≥3.0 g/10 mmol, urinary α1- (uα1m) and β2-microglobulin (uβ2m) excretion rate was determined. Urinary α1m and uβ2m-creatinine ratio was also obtained. We defined progression as a rise in serum creatinine ≥50% or ≥25% and an absolute level ≥135 μmol/L.

Results
Median survival time was 25 months, and 47% of patients showed progression. The area under the receiver operating characteristic curve for uβ2m was 0.81 (95% CI: 0.73 to 0.89). Using a threshold value of 1.0 μg/min, sensitivity and specificity were 73% and 75%, respectively. Similar accuracy was observed for the uβ2m-creatinine ratio with sensitivity and specificity of 75% and 73%, respectively, at a threshold of 1.0 μg/10 mmol creatinine. Similar accuracy was found for uα1m and uα1m-creatinine ratio. Blood Pressure and cholesterol contributed to misclassification. Repeated measurements improved accuracy in patients with persistent proteinuria: the positive predictive value of uβ2m increased from 72% to 89% and the negative predictive value from 76% to 100%.

Conclusions
Urinary excretion of uα2m and uβ2m predict prognosis in iMN. A spot urine sample can be used instead of a timed sample. A repeated measurement after 6 to 12 months increases prognostic accuracy.
Syntaxonomy and Ecology of Black Alder Vegetation in the Southern Part of Central Slovakia
Authors: Slezák Michal , Hrivnák Richard , Petrášová Anna 
Published: December 2011

Syntaxonomy and Ecology of Black Alder Vegetation in the Southern Part of Central Slovakia
The study presents phytosociological and ecological data from azonal black alder forest sites in the southern part of central Slovakia. A data set of 29 relevés was collected by authors in vegetation season 2010 following the standard Braun-Blanquet approach. Numerical classification was performed to delimit the main vegetation types, while statistical analyses were applied to explain the vegetation-environmental relationships. Three associations within two classes were distinguished using a TWINSPAN algorithm. Carici elongatae-Alnetum glutinosae Schwickerath 1933 is an alder carr forest occurring on waterlogged soils in spring fed areas and alluvial zones along rivers. Carici acutiformis-Alnetum glutinosae Scamoni 1933 represents an alder carr forest on habitats with stagnant or slowly flowing water along water courses and artificial water reservoirs. Mesic to humid stands along small brooks are typical for the riparian alder vegetation of Stellario-Alnetum glutinosae Lohmeyer 1957. A detailed description of the floristic and ecological features of these associations is presented. The major environmental gradients affecting variation in species composition of these communities were interpreted as a response of vegetation to soil moisture and nutrient availability regarding the Ellenberg indicator values (moisture and nutrients) and measured variables (total N and C).
A novel adaptation approach for electromagnetic device optimization
Authors: Ouyang Jun , Lowther David 
Published: December 2011

A novel adaptation approach for electromagnetic device optimizationThe ability of case-based reasoning systems to solve new problems mainly depends on their case adaptation knowledge and adaptation strategies. In order to carry out a successful case adaptation in our case-based reasoning system for a low frequency electromagnetic device design, we make use of semantic networks to organize related domain knowledge, and then construct a rule-based inference system which is based on the network. Furthermore, based on the inference system, a novel adaptation algorithm is proposed to derive a new device case from a real-world induction motor case-base with high dimensionality.
Synthesis and characterization of mesoporous silica using new gemini surfactants as templates in neutral pH conditions
Authors: Gui Xia , Xie Anjian , Shen Yuhua , Pan Zhongwen , Sun Song 
Published: December 2011

Abstract
A series of MSU-x wormlike mesoporous silica samples were synthesized using a new type of gemini surfactants [C
n
H2

n

+1N+(CH3)2–CO2–(CH2)4–CO2–N+(CH3)2C
n
H2

n

+1] ·2 Br (n = 12, 14, 16) at circumneutral pH and characterized using Fourier transform infrared spectroscopy, thermo gravimetric analysis, X-ray diffraction, N2 adsorption-desorption and scanning electron microscopy. The MSU-x samples have high surface area and thick pore walls. The pore structure remained after treatment in boiling water for 72 h, which has hardly been reported among mesoporous materials synthesized under mild conditions. The effects of synthesis temperature, aging time and concentration of surfactant on the mesoporous structure were investigated. Based on these, a formation mechanism of mesoporous silica using the new gemini surfactant was proposed.
Corneal Haze Following Disruption of Epithelial Basement Membrane on Ultra-high-resolution OCT Following Femtosecond LASIK
Authors: Vaddavalli Pravin K. , Hurmeric Volkan , Wang Jianhua , Yoo Sonia H. 
Published: December 2011

PURPOSE:
To analyze in vivo structural properties of a case with interface haze that developed after femtosecond laser–assisted LASIK.

METHODS:
Case report.

RESULTS:
A 42-year-old man underwent uncomplicated LASIK. Four months after the surgery he developed regression of his refractive error and interface haze in both eyes. Flap thickness was calculated as 73 μm and 81 μm in the right and left eyes, respectively. A novel ultra-high-resolution spectral domain optical coherence tomography (OCT) system was used to demonstrate in vivo morphology of the cornea. On ultra-high-resolution OCT, haze was demonstrated as increased bright white reflectivity of the flap interface. Areas of focal disruption of the basement membrane and Bowman layer corresponded with the most significant areas of interface haze.

CONCLUSIONS:
Our results support the hypothesis that haze after femtosecond LASIK may be a result of damage to the basement membrane and Bowman layer of the cornea.