bluuebunny/crossref_metadata_2025_split huggingface dataset:
Response to sunitinib in combination with proton beam radiation in a patient with chondrosarcoma: a case report
Authors: Dallas Jennifer , Imanirad Iman , Rajani Rajiv , Dagan Roi , Subbiah Sukanthini , Gaa Rebecca , Dwarica Wayne A , Ivey Alison M , Zlotecki Robert A , Malyapa Robert , Indelicato Daniel J , Scarborough Mark T , Reith John D , Gibbs C Parker , Dang Long H 
Published: January 2012

Abstract

Introduction
Chondrosarcoma is well-known to be primarily resistant to conventional radiation and chemotherapy.

Case presentation
We present the case of a 32-year-old Caucasian man with clear cell chondrosarcoma who presented with symptomatic recurrence in his pelvis and metastases to his skull and lungs. Our patient underwent systemic therapy with sunitinib and then consolidation with proton beam radiation to his symptomatic site. He achieved complete symptomatic relief with a significantly improved performance status and had an almost complete and durable metabolic response on fluorine-18-fluorodeoxyglucose positron emission tomography.

Conclusions
Our findings have important clinical implications and suggest novel clinical trials for this difficult to treat disease.
A cost-effective and universal strategy for complete prokaryotic genomic sequencing proposed by computer simulation
Authors: Jiang Jingwei , Li Jun , Kwan Hoi Shan , Au Chun Hang , Wan Law Patrick Tik , Li Lei , Kam Kai Man , Lun Ling Julia Mei , Leung Frederick C 
Published: January 2012

Abstract

Background
Pyrosequencing techniques allow scientists to perform prokaryotic genome sequencing to achieve the draft genomic sequences within a few days. However, the assemblies with shotgun sequencing are usually composed of hundreds of contigs. A further multiplex PCR procedure is needed to fill all the gaps and link contigs into complete chromosomal sequence, which is the basis for prokaryotic comparative genomic studies. In this article, we study various pyrosequencing strategies by simulated assembling from 100 prokaryotic genomes.

Findings
Simulation study shows that a single end 454 Jr. run combined with a paired end 454 Jr. run (8 kb library) can produce: 1) ~90% of 100 assemblies with < 10 scaffolds and ~95% of 100 assemblies with < 150 contigs; 2) average contig N50 size is over 331 kb; 3) average single base accuracy is > 99.99%; 4) average false gene duplication rate is < 0.7%; 5) average false gene loss rate is < 0.4%.

Conclusions
A single end 454 Jr. run combined with a paired end 454 Jr. run (8 kb library) is a cost-effective way for prokaryotic whole genome sequencing. This strategy provides solution to produce high quality draft assemblies for most of prokaryotic organisms within days. Due to the small number of assembled scaffolds, the following multiplex PCR procedure (for gap filling) would be easy. As a result, large scale prokaryotic whole genome sequencing projects may be finished within weeks.
HIV‐free survival among nine‐ to 24‐month‐old children born to HIV‐positive mothers in the Rwandan national PMTCT programme: a community‐based household survey
Authors: Ruton Hinda , Mugwaneza Placidie , Shema Nadine , Lyambabaje Alexandre , Bizimana Jean de Dieu , Tsague Landry , Nyankesha Elevanie , Wagner Claire M , Mutabazi Vincent , Nyemazi Jean Pierre , Nsanzimana Sabin , Karema Corine , Binagwaho Agnes 
Published: January 2012

BackgroundOperational effectiveness of large‐scale national programmes for the prevention of mother to child transmission (PMTCT) of HIV in sub‐Saharan Africa remains limited. We report on HIV‐free survival among nine‐ to 24‐month‐old children born to HIV‐positive mothers in the national PMTCT programme in Rwanda.MethodsWe conducted a national representative household survey between February and May 2009. Participants were mothers who had attended antenatal care at least once during their most recent pregnancy, and whose children were aged nine to 24 months. A two‐stage stratified (geographic location of PMTCT site, maternal HIV status during pregnancy) cluster sampling was used to select mother‐infant pairs to be interviewed during household visits. Alive children born from HIV‐positive mothers (HIV‐exposed children) were tested for HIV according to routine HIV testing protocol. We calculated HIV‐free survival at nine to 24 months. We subsequently determined factors associated with mother to child transmission of HIV, child death and HIV‐free survival using logistic regression.ResultsOut of 1448 HIV‐exposed children surveyed, 44 (3.0%) were reported dead by nine months of age. Of the 1340 children alive, 53 (4.0%) tested HIV positive. HIV‐free survival was estimated at 91.9% (95% confidence interval: 90.4‐93.3%) at nine to 24 months. Adjusting for maternal, child and health system factors, being a member of an association of people living with HIV (adjusted odds ratio: 0.7, 95% CI: 0.1‐0.995) improved by 30% HIV‐free survival among children, whereas the maternal use of a highly active antiretroviral therapy (HAART) regimen for PMTCT (aOR: 0.6, 95% CI: 0.3‐1.07) had a borderline effect.ConclusionsHIV‐free survival among HIV‐exposed children aged nine to 24 months is estimated at 91.9% in Rwanda. The national PMTCT programme could achieve greater impact on child survival by ensuring access to HAART for all HIV‐positive pregnant women in need, improving the quality of the programme in rural areas, and strengthening linkages with community‐based support systems, including associations of people living with HIV.
Low doses of esmolol and phenylephrine act as diuretics during intravenous anesthesia
Authors: Li Yu Hong , Zhu Hai Bin , Zheng Xiaozhu , Chen Han Jian , Shao Liang , Hahn Robert G 
Published: January 2012

Abstract
Introduction
The renal clearance of infused crystalloid fluid is very low during anaesthesia and surgery, but experiments in conscious sheep indicate that the renal fluid clearance might approach a normal rate when the adrenergic balance is modified.

Methods
Sixty females (mean age, 32 years) undergoing laparoscopic gynecological surgery were randomized to control group and received only the conventional anesthetic drugs and 20 ml/kg of lactated Ringer's over 30 mins. The others were also given an infusion of 50 μg/kg/min of esmolol (beta1-receptor blocker) or 0.01 μg/kg/min of phenylephrine (alpha1-adrenergic agonist) over 3 hours. The distribution and elimination of infused fluid were studied by volume kinetic analysis based on urinary excretion and blood hemoglobin level.

Results
Both drugs significantly increased urinary excretion while heart rate and arterial pressure remained largely unaffected. The urine flows during non-surgery were 43, 147, and 176 ml in the control, esmolol, and phenylephrine groups, respectively (medians, P < 0.03). When surgery had started the corresponding values were 34, 65 and 61 ml (P < 0.04). At 3 hours, averages of 9%, 20%, and 25% of the infused volume had been excreted in the three groups (P < 0.01). The kinetic analyses indicated that both treatments slowed down the distribution of fluid from the plasma to the interstitial fluid space, thereby preventing hypovolemia.

Conclusions
Esmolol doubled and phenylephrine almost tripled urinary excretion during anesthesia-induced depression of renal fluid clearance.
Dissecting the regulatory architecture of gene expression QTLs
Authors: Gaffney Daniel J , Veyrieras Jean-Baptiste , Degner Jacob F , Pique-Regi Roger , Pai Athma A , Crawford Gregory E , Stephens Matthew , Gilad Yoav , Pritchard Jonathan K 
Published: January 2012

Abstract
Background
Expression quantitative trait loci (eQTLs) are likely to play an important role in the genetics of complex traits; however, their functional basis remains poorly understood. Using the HapMap lymphoblastoid cell lines, we combine 1000 Genomes genotypes and an extensive catalogue of human functional elements to investigate the biological mechanisms that eQTLs perturb.

Results
We use a Bayesian hierarchical model to estimate the enrichment of eQTLs in a wide variety of regulatory annotations. We find that approximately 40% of eQTLs occur in open chromatin, and that they are particularly enriched in transcription factor binding sites, suggesting that many directly impact protein-DNA interactions. Analysis of core promoter regions shows that eQTLs also frequently disrupt some known core promoter motifs but, surprisingly, are not enriched in other well-known motifs such as the TATA box. We also show that information from regulatory annotations alone, when weighted by the hierarchical model, can provide a meaningful ranking of the SNPs that are most likely to drive gene expression variation.

Conclusions
Our study demonstrates how regulatory annotation and the association signal derived from eQTL-mapping can be combined into a single framework. We used this approach to further our understanding of the biology that drives human gene expression variation, and of the putatively causal SNPs that underlie it.
Estrogen Receptor (ER) mRNA and ER-Related Gene Expression in Breast Cancers That Are 1% to 10% ER-Positive by Immunohistochemistry
Authors: Iwamoto Takayuki , Booser Daniel , Valero Vicente , Murray James L. , Koenig Kimberly , Esteva Francisco J. , Ueno Naoto T. , Zhang Jie , Shi Weiwei , Qi Yuan , Matsuoka Junji , Yang Elliana J. , Hortobagyi Gabriel N. , Hatzis Christos , Symmans W. Fraser , Pusztai Lajos 
Published: January 2012

Purpose We examined borderline estrogen receptor (ER) –positive cancers, defined as having 1% to 10% positivity by immunohistochemistry (IHC), to determine whether they show the same global gene-expression pattern and high ESR1 mRNA expression as ER-positive cancers or if they are more similar to ER-negative cancers. Patients and Methods ER status was determined by IHC in 465 primary breast cancers and with the Affymetrix U133A gene chip. We compared expressions of ESR1 mRNA and a 106 probe set ER-associated gene signature score between ER-negative (n = 183), 1% to 9% (n = 25), 10% (n = 6), and more than 10% (n = 251) ER-positive cancers. We also assessed the molecular class by using the PAM50 classifier and plotted survival by ER status. Results Among the 1% to 9%, 10%, and more than 10% ER IHC–positive patients, 24%, 67%, and 92% were also positive by ESR1 mRNA expression. The average ESR1 expression was significantly higher in the ≥ 10% ER-positive cohorts compared with the 1% to 9% or ER-negative cohort. The average ER gene signature scores were similar for the ER-negative and 1% to 9% IHC-positive patients and were significantly lower than in ≥ 10% ER-positive patients. Among the 1% to 9% ER-positive patients, 8% were luminal B and 48% were basal-like; among the 10% ER-positive patients, 50% were luminal. The overall survival rate of 1% to 9% ER-positive patients with cancer was between those of patients in the ≥ 10% ER-positive and ER-negative groups. Conclusion A minority of the 1% to 9% IHC ER–positive tumors show molecular features similar to those of ER-positive, potentially endocrine-sensitive tumors, whereas most show ER-negative, basal-like molecular characteristics. The safest clinical approach may be to use both adjuvant endocrine therapy and chemotherapy in this rare subset of patients.
Sequential Versus Single High-Dose Chemotherapy in Patients With Relapsed or Refractory Germ Cell Tumors: Long-Term Results of a Prospective Randomized Trial
Authors: Lorch Anja , Kleinhans Antje , Kramar Andrew , Kollmannsberger Christian K. , Hartmann Jörg T. , Bokemeyer Carsten , Rick Oliver , Beyer Jörg 
Published: January 2012

Purpose To evaluate the long-term survival rates in patients with relapsed or refractory germ cell tumors (GCTs) after single or sequential high-dose chemotherapy (HDCT). Patients and Methods Between November 1999 and November 2004, 211 patients with relapsed or refractory GCT were randomly assigned to treatment with either one cycle of cisplatin 100 mg/m2, etoposide 375 mg/m2, and ifosfamide 6 g/m2 (VIP) plus three cycles of high-dose carboplatin 1,500 mg/m2 and etoposide 1,500 mg/m2 (CE, arm A) or three cycles of VIP plus one cycle of high-dose carboplatin 2,200 mg/m2, etoposide 1,800 mg/m2, and cyclophosphamide 6,400 mg/m2 (CEC, arm B) followed by autologous stem-cell reinfusion. Long-term progression-free survival (PFS) and overall survival (OS) 6 years after random assignment of the last patient were compared by using the log-rank test. Results Overall, 108 and 103 patients were randomly assigned to arms A and B, respectivelyl. The study was stopped prematurely because of excess treatment-related mortality in arm B (14%) compared with that in arm A (4%; P = .01). As of December 2010, nine (5%) of 211 patients were lost to follow-up; 94 (45%) of 211 are alive and 88 (94%) of 94 patients are progression free. Five-year PFS is 47% (95% CI, 37% to 56%) in arm A and 45% (95% CI, 35% to 55%) in arm B (hazard ratio [HR], 1.16; 95% CI, 0.79 to 1.70; P = .454). Five-year OS is 49% (95% CI, 40% to 59%) in arm A and 39% (95% CI, 30% to 49%) in arm B (HR, 1.42; 95% CI, 0.99 to 2.05; P = .057). Conclusion Patients with relapsed or refractory GCT achieve durable long-term survival after single as well as sequential HDCT. Fewer early deaths related to toxicity translated into superior long-term OS after sequential HDCT.
First Identification of Circulating Prepro–A-Type Natriuretic Peptide (PreproANP) Signal Peptide Fragments in Humans: Initial Assessment as Cardiovascular Biomarkers
Authors: Pemberton Chris J , Siriwardena Maithri , Kleffmann Torsten , Ruygrok Peter , Palmer Suetonia C , Yandle Tim G , Richards A Mark 
Published: January 2012

AbstractBACKGROUNDNew biomarkers are needed to assist clinical decision making in cardiovascular disease. We have recently shown that signal peptides may represent a novel biomarker target in cardiovascular diseases.METHODSWe developed a novel immunoassay for the signal peptide of preproANP (ANPsp) and used it to document cardiac tissue levels of ANPsp in explant human hearts (n = 9), circulating venous concentrations of ANPsp in healthy volunteers (n = 65), temporal ANPsp concentrations in patients with ST-elevation myocardial infarction (STEMI) &lt;4 h after chest pain onset (n = 23), and regional plasma ANPsp concentrations in patients undergoing clinically indicated catheterization (n = 10). We analyzed the structure and sequence of circulating ANPsp by tandem mass spectrometry (MS/MS).RESULTSANPsp levels in human heart tissue were 50–1000 times lower than those of ANP/NT-proANP. ANPsp was detectable in control human plasma at concentrations comparable with ANP itself (approximately 20 ng/L). In STEMI patients, plasma concentrations of ANPsp rose to peak values at 5 h after symptom onset, significantly earlier than myoglobin, creatine kinase-MB, and troponin (P &lt; 0.001). There were significant arteriovenous increases in ANPsp concentrations (P &lt; 0.05) across the heart and kidney; arterial and coronary sinus concentrations of ANPsp both negatively correlated with systolic and mean arterial blood pressures (both P &lt; 0.01). MS/MS verified circulating ANPsp to be preproANP(16–25) and preproANP(18–25).CONCLUSIONSANPsp is a novel circulating natriuretic peptide with potential to act as a cardiovascular biomarker. The rapid increase of plasma ANPsp in STEMI and its significant relationship with blood pressure encourage further study of its potential clinical utility.
Derivation of bond-valence parameters for some cation-oxygen pairs on the basis of empirical relationships between ro
and b
Authors: Krivovichev Sergey V. 
Published: January 2012

Abstract
Relationships between the ro
and b bond-valence parameters are investigated for ideal and distorted coordination polyhedra. For some ranges of the b values, this relationship can be approximated by linear functions, which are used to derive bond-valence parameters for some cation-oxygen pairs (ro
, b [Å]): Cu2+—O (1.679, 0.36), Pb2+—O (1.963, 0.49), Hg2+—O (1.924, 0.38), Bi3+—O (1.990, 0.48), Sb3+—O (1.885, 0.53), Y3+—O (2.028, 0.35), La3+—O (2.086, 0.45), Nd3+—O (2.021, 0.46).
Crystal structure of 1,4-diazoniabicyclo[2.2.2]octane diiodide monohydrate
Authors: Maderlehner Sebastian , Pfitzner Arno 
Published: January 2012

Abstract
1,4-diazoniabicyclo[2.2.2]octane diiodide monohydrate was synthesized by protonation of 1,4-diazabicyclo[2.2.2]octane (DABCO) with an excess of concentrated hydroiodic acid in water. It forms colourless rod-like crystals. At room temperature an orthorhombic unit cell, space group Cmc21, a = 7.781(2) Å, b = 13.010(3) Å, c = 11.610 (2) Å, V = 1175.3(4) Å3, Z = 4, is observed. Both nitrogen atoms bear a proton. The hydrate water ämolecule within the compound is statistically disordered on a site besides a crystallographic mirror plane at room temperature. DSC measurements indicate a phase transition at about –10 °C. A single crystal X-ray diffraction measurement at 123 K reveals a primitive unit cell, space group Pca21, a = 12.8835(2) Å, b = 7.6819(1) Å, c = 11.4392(2) Å, V = 1132.16(3) Å3, Z = 4. The water molecule with its hydrogen atoms is well ordered at this temperature. Two almost linear hydrogen bonds O—H···I are formed. The formation of hydrogen bonds is also detected by IR-spectroscopy with O—H stretching frequencies at -v = 3403 cm–1 and -v = 3354 cm–1, respectively.
Impact of Chronic Diseases on Work Ability in Ageing Firefighters
Authors: Plat Marie‐Christine J , Frings‐Dresen Monique HW , Sluiter Judith K 
Published: January 2012

Impact of Chronic Diseases on Work Ability in Ageing Firefighters: Marie‐Christine J PLAT, et al. Academic Medical Center, University of Amsterdam, Department of Coronel Institute of Occupational Health, The Netherlands—ObjectivesThe aim of this study was to study the impact of chronic diseases on work ability in different age groups of Dutch firefighters.MethodsFirefighters filled out a questionnaire about the presence of nine types of chronic diseases and rated their current work ability (0 unable to10 best ever). The differences in work ability in firefighters in total and in four age groups with and without chronic diseases were calculated with a Fisher's exact test.ResultsOf 276 firefighters 23% reported having a chronic disease, with the rate varying among the age groups between 18 and 41%. Median work ability was 8, varying between 7 and 8 in the age groups. No significant difference was found in work ability for firefighters with and without chronic diseases, independent of the age groups.ConclusionsHaving a chronic disease is not associated with a significantly lower self reported work ability estimate in firefighters.
Effect of Heat Treatment Solution on the Size and Distribution of Gamma Prime (γ´) of Super-alloy INCONEL 738
Authors: Guzmán I. , Garza A. , Garcia F. , Acevedo J. , Méndez R. 
Published: January 2012

ABSTRACTNickel base superalloys, which are gamma prime γ‘(Ni3Al, Ti) precipitation strengthened, is largely responsible for the elevated-temperature strength of the material and the higher resistance to creep deformation. The amount of γ’ depends on the chemical composition and temperature, heat treatment, these alloy are widely used in hot sections of aero-engines, land based turbines, stator parts, nozzle guide vanes, blades and integral wheels, due to its excellent elevated temperature strength and hot corrosion resistance. The γ‘ size decreases not only by the high temperature of heat treatment solution (1120 °C), the cooling environment and cooling rate are important parameter to decrease γ’ size to 0.65 μm. This paper presents the effect of heat treatment solution in base nickel IN 738 superalloy under service conditions, on the size and morphology of the gamma phase γ’ Ni3 (Al, Ti), main phase in the nickel base superalloys. Also shown coarse carbide and precipitates gamma prime size distributed and improve interdentritic spacing in the matrix after heat treatment solution.
Variations in Mechanical Properties of Wood Plates Due Fluctuations on Relative Humidity of Air
Authors: Torres J. A. , De Icaza M. , Boullosa R. R. 
Published: January 2012

ABSTRACTOften, mechanical properties of wood plates are accurately approximated through orthotropic characterization. However, the numerical values may show considerable variations in the case of real wood plates immersed in fluctuant environmental conditions, especially if the relative humidity of air (RH) is changing. Problems arising from the natural variations in RH have been reported on making musical instruments. In this work, the influence of changing RH on the mechanical properties of a guitar’s top plate (clamped on its contour) has been measured. Vibratory responses of the plate were experimentally obtained, through forced vibration, while data were recorded for several RH values, without any alteration in the experimental set-up devices. The six lowest natural frequencies of the structure were extracted from peaks detected in the responses. Natural frequencies depend on mass distribution and mechanical properties of the structure. For the highest sensed RH (67 %), each natural frequency of the plate decreased at least in 11 Hz compared with reference values measured at the lowest sensed RH (53 %). To determine the connection between the shift in natural frequencies and the changes in the wood elastic and shear modulus, a finite element model of the plate was performed. It was useful calculating natural frequencies through simulated modal analyses. Elastic and shear modulus were handled to match simulated results with experimental natural frequencies recorded for a RH=53% level. These elastic moduli must be decreased around 10 % to obtain a similar frequency decrease in the experimental natural frequencies obtained under a RH=67% level. The experimental results show quantitative information on an interaction scarcely researched, that is, the modification on mechanical properties of wood plates induced by RH variations. Sensed changes due this wood-air interaction are responsible of a modification in the behavior of musical instruments, as guitars and violins.
Effect of Microstructure and Mechanical Properties on the Stress Corrosion Cracking Assessment of Type 304 Stainless Steel Using Slow Strain Rate Tests
Authors: Contreras A. , Hernández S. L. , Terres E. , Galvan R. 
Published: January 2012

ABSTRACTThe stress corrosion cracking (SCC) of the commercial austenitic stainless steel type 304 was investigated as function of test temperature, microstructure and mechanical properties in acidic chloride solution (25 wt.%-MgCl2) using slow strain rate tests (SSRT). Susceptibility and mechanism of SCC was investigated using SSRT performed at strain rate of 1 x 10-6 in/s in a glass autoclave containing a magnesium chloride solution at 20, 50 and 80°C. The SCC assessment was carried out in function of the results of time to failure ratio (TFR), elongation ratio (ELR), ultimate tensile strength ratio (UTS-R), strain ratio(eR), yielding strength ratio (YS-R) and stress rupture ratio (SR-R). This assessment was complemented by some scanning electron microscopy (SEM) observations, in order to determine the type of fracture and its features. SSRT results indicate that 304 stainless steel was susceptible to SCC at 50 and 80°C. SCC susceptibility increases as the temperature increase. By the contrary, the mechanical properties decreases with temperature increase. SEM observations showed a ductile type of fracture, indicating that cracks appear to be originated from the pits, increasing the number of cracks as the temperature increases. Corrosion pits are one of the main potential sites for surface crack initiation. The stress concentration in the pits will be the nucleation site for cracks.