bluuebunny/crossref_metadata_2025_split huggingface dataset:
Utilization of TREC and KREC quantification for the monitoring of early T- and B-cell neogenesis in adult patients after allogeneic hematopoietic stem cell transplantation
Authors: Mensen Angela , Ochs Christoph , Stroux Andrea , Wittenbecher Friedrich , Szyska Martin , Imberti Luisa , Fillatreau Simon , Uharek Lutz , Arnold Renate , Dörken Bernd , Thiel Andreas , Scheibenbogen Carmen , Na Il-Kang 
Published: August 2013

AbstractBackgroundAfter hematopoietic stem cell transplantation (HSCT) T- and B-cell reconstitution from primary lymphoid organs are a prerequisite for an effective early lymphocyte reconstitution and a long-term survival for adult patients suffering from acute leukemia. Here, we asked whether quantification of T cell receptor excision circle, (TREC) and kappa-deleting recombination excision circle (KREC) before and within six month after allogeneic HSCT could be used to measure the thymic and bone marrow outputs in such patients.MethodsWe used a duplex real time PCR assay to quantify the absolute copy counts of TREC and KREC, and correlated the data with absolute cell counts of CD3+CD4+T-cell and CD19+B-cell subsets determined by flow cytometry, respectively.ResultsBy comparing two recently proposed naïve T cell subsets, CD31+naive and CD31-naive T cells, we found a better correlation for the CD31+subset with TREC level post alloHSCT, in line with the assumption that it contained T cells recently derived from the thymus, indicating that TREC levels reflected real thymicde novoproduction. Transitional as well as naïve B cells highly correlated with KREC levels, which suggested an association of KREC levels with ongoing bone marrow B cell output. CD45RO+memory T cells and CD27+memory B cells were significantly less correlated with TREC and KREC recovery, respectively.ConclusionWe conclude that simultaneous TREC/ KREC quantification is as a suitable and practicable method to monitor thymic and bone marrow output post alloHSCT in adult patients diagnosed with acute leukemia.
Flotillin-2 is associated with breast cancer progression and poor survival outcomes
Authors: Wang Xi , Yang Qi , Guo Ling , Li Xing-Hua , Zhao Xiao-Hui , Song Li-Bing , Lin Huan-Xin 
Published: August 2013

Abstract

Background
Flotillin-2 (FLOT2) has been implicated in several signaling pathways in tumor cells. Our study aimed to investigate the expression pattern and clinicopathological significance of FLOT2 in patients with breast cancer.

Methods
The expression level of FLOT2 in normal breast epithelial cells, breast cancer cell lines, and four breast cancer biopsies paired with adjacent noncancerous tissues were quantified using real-time RT-PCR and Western blotting. FLOT2 protein expression was analyzed in 171 archived paraffin-embedded breast cancer samples using immunohistochemistry (IHC). Statistical analyses were performed to evaluate the clinicopathological significance of FLOT2 expression.

Results
FLOT2 was significantly upregulated in breast cancer cell lines and tissue samples compared with normal cells and adjacent noncancerous breast tissues, respectively. IHC analysis revealed high expression levels of FLOT2 in 82 of 171 (48.0%) breast cancer specimens. Statistical analysis revealed that FLOT2 expression was significantly correlated with clinical stage (P < 0.001), T classification (P < 0.001), M classification (P < 0.001), histological differentiation (P = 0.005) and ErbB2 expression (P = 0.003). Patients with higher levels of FLOT2 expression had a shorter overall survival duration than patients with lower FLOT2 expression levels. Multivariate analysis suggested that FLOT2 expression was an independent prognostic marker for survival in patients with breast cancer.

Conclusions
The current results demonstrated that high FLOT2 protein expression was associated with poor outcomes in patients with breast cancer. FLOT2 could be used as a prognostic biomarker for breast cancer progression.
Joint-specific changes in locomotor complexity in the absence of muscle atrophy following incomplete spinal cord injury
Authors: Hillen Brian K , Yamaguchi Gary T , Abbas James J , Jung Ranu 
Published: August 2013

Abstract

Background
Following incomplete spinal cord injury (iSCI), descending drive is impaired, possibly leading to a decrease in the complexity of gait. To test the hypothesis that iSCI impairs gait coordination and decreases locomotor complexity, we collected 3D joint angle kinematics and muscle parameters of rats with a sham or an incomplete spinal cord injury.

Methods
12 adult, female, Long-Evans rats, 6 sham and 6 mild-moderate T8 iSCI, were tested 4 weeks following injury. The Basso Beattie Bresnahan locomotor score was used to verify injury severity. Animals had reflective markers placed on the bony prominences of their limb joints and were filmed in 3D while walking on a treadmill. Joint angles and segment motion were analyzed quantitatively, and complexity of joint angle trajectory and overall gait were calculated using permutation entropy and principal component analysis, respectively. Following treadmill testing, the animals were euthanized and hindlimb muscles removed. Excised muscles were tested for mass, density, fiber length, pennation angle, and relaxed sarcomere length.

Results
Muscle parameters were similar between groups with no evidence of muscle atrophy. The animals showed overextension of the ankle, which was compensated for by a decreased range of motion at the knee. Left-right coordination was altered, leading to left and right knee movements that are entirely out of phase, with one joint moving while the other is stationary. Movement patterns remained symmetric. Permutation entropy measures indicated changes in complexity on a joint specific basis, with the largest changes at the ankle. No significant difference was seen using principal component analysis. Rats were able to achieve stable weight bearing locomotion at reasonable speeds on the treadmill despite these deficiencies.

Conclusions
Decrease in supraspinal control following iSCI causes a loss of complexity of ankle kinematics. This loss can be entirely due to loss of supraspinal control in the absence of muscle atrophy and may be quantified using permutation entropy. Joint-specific differences in kinematic complexity may be attributed to different sources of motor control. This work indicates the importance of the ankle for rehabilitation interventions following spinal cord injury.
SETX mutations are a frequent genetic cause of juvenile and adult onset cerebellar ataxia with neuropathy and elevated serum alpha-fetoprotein
Authors: Nanetti Lorenzo , Cavalieri Simona , Pensato Viviana , Erbetta Alessandra , Pareyson Davide , Panzeri Marta , Zorzi Giovanna , Antozzi Carlo , Moroni Isabella , Gellera Cinzia , Brusco Alfredo , Mariotti Caterina 
Published: August 2013

AbstractObjectives/backgroundAtaxia with oculomotor apraxia defines a group of genetically distinct recessive ataxias including ataxia-telangectasia (A-T,ATMgene), ataxia with oculomotor apraxia type 1 (AOA1,APTXgene) and type 2 (AOA2,SETXgene). Although, a few unique clinical features differentiate each of these forms, the patients also share common clinical signs, such as the presence of cerebellar atrophy, sensorimotor axonal neuropathy, and elevated alpha-fetoprotein (AFP) serum level.Materials and methodsWe selected 22 Italian patients from 21 families, presenting progressive cerebellar ataxia, axonal neuropathy, and elevated serum AFP. We screened the coding regions ofATM,APTXandSETXgenes for point mutations by direct sequencing or DHPLC, and searched genomic rearrangements inSETXby MLPA analysis. In selected cases, quantification of ATM and senataxin proteins was performed by Western blot. Clinical, neurophysiological, and neuroimaging data were collected.ResultsThirteen patients (12 families) carriedSETXmutations (AOA2, 57%), two were mutated inATM(A-T), and three inAPTX(AOA1). In three remaining patients, we could not find pathogenic mutations, and in one case we found, in homozygosis, theSETXp.K992R polymorphism (population frequency 1-2%). In AOA2 cases, we identified 14 novel and three reportedSETXmutations. Signs at onset were gait ataxia and facial dyskinesia, and the age ranged between 11 and 18 years. None had obvious oculomotor apraxia at the latest examination (age 14–45 years). The patient carrying the p.K992RSETXpolymorphism had a phenotype similar to that of the diagnosed AOA2 patients, while the other three undiagnosed subjects had a very late onset and a few distinguishing clinical features.Discussion and conclusionsWe describe a large series of 13 AOA2 Italian patients. The phenotype was consistent with previous descriptions of AOA2, except for a higher frequency of strabism, and for the absence of oculomotor apraxia. In our survey ~60% of juvenile-to-adult cases with cerebellar ataxia, sensorimotor neuropathy and increased AFP are due to mutations in theSETXgene, and a smaller percentage toAPTXandATMgene mutations.
Successful pregnancy in each half uterus cavity of the septate uterus after transferring three embryos in one half-cavity: a case report
Authors: Guo Xiaoqiao , Sun Xiaofang , Xu Haiyan , Si Shasha , Yu Bolan , Liu Jianqiao 
Published: August 2013

Abstract
The incidence of Müllerian duct anomalies in women is rare, associating with urinary tract anomalies such as horseshoe or pelvic kidney, renal agenesis, duplication of the collecting system, or ectopic uterus. Septate uterus is one type of congenital uterine anomalies, in which there is a septum from the fundus to the cervix. Currently, it is believed that hysteroscopic metroplasty is a leading choice for patients if their recurrent spontaneous abortion is resulted from septate uterus. But, some people refuse to have a surgery, and successfully delivery. In this case report, we report a successful pregnancy with two gestational sacs, one in each half-cavity, in a woman with septate uterus after transfer of three embryos into one half–cavity. Finally, the women gave birth to two healthy babies in our hospital.
Compassion fatigue, burnout and compassion satisfaction among family physicians in the Negev area - a cross-sectional study
Authors: El-bar Nurit , Levy Amalia , Wald Hedy S , Biderman Aya 
Published: August 2013

Abstract

Background
Compassion fatigue among health care professionals has gained interest over the past decade. Compassion fatigue, as well as burnout, has been associated with depersonalization and suboptimal patient care. Professional caregivers in general are exposed to the risk of compassion fatigue (CF), burnout (BO) and low levels of compassion satisfaction (CS). While CF has been studied in health care professionals, few publications address its incidence among family physicians, specifically. The objectives of this study were to assess the prevalence and severity of CF among family practitioners (FPs) in the Negev (Israel’s southern region), evaluating the correlations between CF, BO and CS and their relations with socio-demographic variables and work related characteristics.

Methods
Self-report anonymous Compassion Satisfaction and Fatigue Test questionnaires (CSFT) measuring CF, BO, and CS were distributed among 194 family physicians at Clalit Health Services clinics in the Negev between July 2007 and April 2008. Correlations between CF, BO and CS were assessed. Multivariable logistic regression models with backward elimination were constructed.

Results
128 (66%) physicians responded. 46.1% of respondents scored extremely high and high for CF, 21.1% scored low for CS and 9.4% scored high for BO. Strong correlations were found between BO and CF (r = 0.769, p < 0.001), and between BO and CS (r = −0.241, p = 0.006), but no correlation was found between CS and CF. The logistic regression model showed that the only factor associated with a significantly increased risk for CF was former immigration to Israel. Increased risk for BO was associated with female gender, history of personal trauma and lack of academic affiliation. Higher CS was associated with holding management positions and teaching residents.

Conclusions and policy recommendations
Family physicians in the Negev are at high risk for CF, with the potential for CF- associated patient dissatisfaction, compromised patient safety and increased medical error. We propose creation of a CF educational and early intervention treatment program for family physicians and other health care professionals. Such programs would train facilitators of physician well-being and resiliency building. We also recommend analyzing contributing variables and organizational factors related to higher CF. Policy recommendations include integrating such programs within required risk management continuing medical education.
mPUMA: a computational approach to microbiota analysis by de novo assembly of operational taxonomic units based on protein-coding barcode sequences
Authors: Links Matthew G , Chaban Bonnie , Hemmingsen Sean M , Muirhead Kevin , Hill Janet E 
Published: August 2013

Abstract

Background
Formation of operational taxonomic units (OTU) is a common approach to data aggregation in microbial ecology studies based on amplification and sequencing of individual gene targets. The de novo assembly of OTU sequences has been recently demonstrated as an alternative to widely used clustering methods, providing robust information from experimental data alone, without any reliance on an external reference database.

Results
Here we introduce mPUMA (microbial Profiling Using Metagenomic Assembly, http://mpuma.sourceforge.net), a software package for identification and analysis of protein-coding barcode sequence data. It was developed originally for Cpn 60 universal target sequences (also known as Gro EL or Hsp 60). Using an unattended process that is independent of external reference sequences, mPUMA forms OTUs by DNA sequence assembly and is capable of tracking OTU abundance. mPUMA processes microbial profiles both in terms of the direct DNA sequence as well as in the translated amino acid sequence for protein coding barcodes. By forming OTUs and calculating abundance through an assembly approach, mPUMA is capable of generating inputs for several popular microbiota analysis tools. Using SFF data from sequencing of a synthetic community of Cpn 60 sequences derived from the human vaginal microbiome, we demonstrate that mPUMA can faithfully reconstruct all expected OTU sequences and produce compositional profiles consistent with actual community structure.

Conclusions
mPUMA enables analysis of microbial communities while empowering the discovery of novel organisms through OTU assembly.
Novel xylanases from Simplicillium obclavatum MTCC 9604: comparative analysis of production, purification and characterization of enzyme from submerged and solid state fermentation
Authors: Roy Saugata , Dutta Tanmay , Sarkar Tuhin Subhra , Ghosh Sanjay 
Published: August 2013

Abstract
The production of extracellular xylanase by a newly isolated fungus Simplicillium obclavatum MTCC 9604 was studied in solid-state and submerged fermentation. Multiple xylanases and endoglucanases were produced by the strain during growth on wheat bran in solid state fermentation (SSF). A single xylanase isoform was found to be produced by the same fungus under submerged fermentation (SF) using wheat bran as sole carbon source. Enzyme activity, stability and the protein yield were much higher in SSF than SF. The two dimensional zymogram of the crude enzyme indicated the presence of six isoforms with different pI values starting from pH 3–10. The optimum temperature and pH for the partially purified xylanase activity were 50°C and pH 5.0 respectively; xylanase enzymes exhibited remarkable stability over a broad pH range and the temperature range of 30-60°C which has great potential to be used in biofuels, animal feed and food industry applications.
Oxygen doping of HTSC and resistive switching in HTSC-based heterostructures
Authors: Tulina Natalia A , Borisenko Ivan Yu , Ivanov Andrey A , Ionov Andrey M , Shmytko Ivan M 
Published: August 2013

Abstract
The studies of the bipolar resistive switching effect in thin film heterojunctions (YBa2Cu3O7−δ
/Ag) and (Nd 2−x
Ce
x
CuO4−y
/Ag) have exhibited the role of oxygen as a doping element in hole- and electron-doped HTSC compounds.
Agent-based modeling and simulation of emergent behavior in air transportation
Authors: Bouarfa Soufiane , Blom Henk AP , Curran Richard , Everdij Mariken HC 
Published: August 2013

Abstract

Purpose
Commercial aviation is feasible thanks to the complex socio-technical air transportation system, which involves interactions between human operators, technical systems, and procedures. In view of the expected growth in commercial aviation, significant changes in this socio-technical system are in development both in the USA and Europe. Such a complex socio-technical system may generate various types of emergent behavior, which may range from simple emergence, through weak emergence, up to strong emergence. The purpose of this paper is to demonstrate that agent-based modeling and simulation allows identifying changed and novel rare emergent behavior in this complex socio-technical system.

Methods
An agent based model of a specific operation at an airport has been developed. The specific operation considered is the controlled crossing by a taxiing aircraft of a runway that is in use for controlled departures. The agent-based model includes all relevant human and technical agents, such as the aircraft, the pilots, the controllers and the decision support systems involved. This agent-based model is used to conduct rare event Monte Carlo (MC) simulations.

Results
The MC simulation results obtained confirm that agent based modeling and simulation of a socio-technical air transportation system allows to identify rare emergent behavior that was not identified through earlier, non-agent-based simulations, including human-in-the-loop simulations of the same operation. A typical example of such emergent behavior is the finding that alerting systems do not really reduce the safety risk.

Conclusions
Agent based MC simulations of commercial aviation operations has been demonstrated as a viable way to be evaluated regarding rare emergent behaviour. This rare emergent behaviour could not have been found through the more traditional simulation approaches.
Degradation of neutrophil extracellular traps co-varies with disease activity in patients with systemic lupus erythematosus
Authors: Leffler Jonatan , Gullstrand Birgitta , Jönsen Andreas , Nilsson Jan-Åke , Martin Myriam , Blom Anna M , Bengtsson Anders A 
Published: August 2013

Abstract
Introduction
The ability to degrade neutrophil extracellular traps (NETs) is reduced in a subset of patients with systemic lupus erythematosus (SLE). NETs consist of chromatin covered with antimicrobial enzymes and are normally degraded by DNase-I, an enzyme which is known to have reduced activity in SLE. Decreased ability to degrade NETs is associated with disease activity. In the current study we investigated how the ability of serum from SLE patients to degrade NETs varies during the course of SLE as well as what impact this may have for the clinical phenotype of SLE.

Methods
Serum from 69 patients with SLE, included in a prospective study, was taken every 60 days for a median of 784 days. The ability of serum to degrade NETs was determined and associated with clinical parameters occurring before and at the time of sampling, as well as after sampling by using conditional logistic regression.

Results
As many as 41% of all patients in the study showed decreased ability to degrade NETs at least once, but with a median of 20% of all time points. Decreased degradation was associated with manifestations of glomerulonephritis as well as low complement levels and elevated levels of antibodies directed against histones and DNA. Furthermore, the odds ratio for the patient to develop alopecia and fever after an episode of decreased NETs degradation was increased by four to five times compared to normal.

Conclusions
Decreased degradation of NETs is associated with clinical manifestations in SLE and may contribute to disease pathogenesis. Potential therapeutics restoring the ability to degrade NETs could be beneficial for certain patients with SLE.
HIF-1α/GPER signaling mediates the expression of VEGF induced by hypoxia in breast cancer associated fibroblasts (CAFs)
Authors: De Francesco Ernestina Marianna , Lappano Rosamaria , Santolla Maria Francesca , Marsico Stefania , Caruso Arnaldo , Maggiolini Marcello 
Published: August 2013

Abstract
Introduction
Carcinoma-associated fibroblasts (CAFs) play a pivotal role in cancer progression by contributing to invasion, metastasis and angiogenesis. Solid tumors possess a unique microenvironment characterized by local hypoxia, which induces gene expression changes and biological features leading to poor outcomes. Hypoxia Inducible Factor 1 (HIF-1) is the main transcription factor that mediates the cell response to hypoxia through different mechanisms that include the regulation of genes strongly associated with cancer aggressiveness. Among the HIF-1 target genes, the G-protein estrogen receptor (GPER) exerts a stimulatory role in diverse types of cancer cells and in CAFs.

Methods
We evaluated the regulation and function of the key angiogenic mediator vascular endothelial growth factor (VEGF) in CAFs exposed to hypoxia. Gene expression studies, Western blotting analysis and immunofluorescence experiments were performed in CAFs and breast cancer cells in the presence of cobalt chloride (CoCl2) or cultured under low oxygen tension (2% O2), in order to analyze the involvement of the HIF-1α/GPER signaling in the biological responses to hypoxia. We also explored the role of the HIF-1α/GPER transduction pathway in functional assays like tube formation in human umbilical vein endothelial cells (HUVECs) and cell migration in CAFs.

Results
We first determined that hypoxia induces the expression of HIF-1α and GPER in CAFs, then we ascertained that the HIF-1α/GPER signaling is involved in the regulation of VEGF expression in breast cancer cells and in CAFs exposed to hypoxia. We also assessed by ChIP assay that HIF-1α and GPER are both recruited to the VEGF promoter sequence and required for VEGF promoter stimulation upon hypoxic condition. As a biological counterpart of these findings, conditioned medium from hypoxic CAFs promoted tube formation in HUVECs in a HIF-1α/GPER dependent manner. The functional cooperation between HIF-1α and GPER in CAFs was also evidenced in the hypoxia-induced cell migration, which involved a further target of the HIF-1α/GPER signaling like connective tissue growth factor (CTGF).

Conclusions
The present results provide novel insight into the role elicited by the HIF-1α/GPER transduction pathway in CAFs towards the hypoxia-dependent tumor angiogenesis. Our findings further extend the molecular mechanisms through which the tumor microenvironment may contribute to cancer progression.
Effect of Dopants Pr and La on the Catalytic Activity of Cerium Oxide for Soot Oxidation
Authors: Harada Koichiro , Oishi Tetsuya , Hamamoto Seiji , Ishihara Tatsumi 
Published: August 2013

Abstract
Effects of rare earth or transition metal doping on the activity of CeO2 to particulate matter oxidation were investigated, and it was found that a Ce–Pr–La–O mixed oxide demonstrates the lowest ignition temperature of carbon, as low as 550 K. Oxygen-temperature-programmed desorption measurements suggested that the amount of O2 desorbed from CeO2 increases with the substitution of Pr, and furthermore, La doping reduces the desorption temperature of the lattice oxygen. Even in the absence of oxygen, carbon oxidation occurs on Ce–Pr–La–O, and the ignition temperature of carbon is almost the same as the desorption temperature of the lattice oxygen. Doping of La and Pr into CeO2 has a positive impact on carbon oxidation because of this decreased desorption temperature of the lattice oxygen.