bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of Raman Lidar Observations of Water Vapor with COSMO-DE Forecasts during COPS 2007
Authors: Herold Christian , Althausen Dietrich , Müller Detlef , Tesche Matthias , Seifert Patric , Engelmann Ronny , Flamant Cyrille , Bhawar Rohini , Di Girolamo Paolo 
Published: June 2011

Abstract
Water vapor measurements with the multiwavelength Raman lidar Backscatter Extinction Lidar-Ratio Temperature Humidity Profiling Apparatus (BERTHA) were performed during the Convective and Orographically-induced Precipitation Study (COPS) in the Black Forest, Germany, from June to August 2007. For quality assurance, profiles of the water vapor mixing ratio measured with BERTHA are compared to simultaneous measurements of a radiosonde and an airborne differential absorption lidar (DIAL) on 31 July 2007. The differences from the radiosonde observations are found to be on average 1.5% and 2.5% in the residual layer and in the free troposphere, respectively. During the two overflights at 1937 and 2018 UTC, the differences from the DIAL results are −2.2% and −3.7% in the residual layer and 2.1% and −2.6% in the free troposphere. After this performance check, short-range forecasts from the German Meteorological Service’s (Deutscher Wetterdienst, DWD) version of the Consortium for Small-Scale Modeling (COSMO-DE) model are compared to the BERTHA measurements for two case studies. Generally, it is found that water vapor mixing ratios from short-range forecasts are on average 7.9% drier than the values measured in the residual layer. In the free troposphere, modeled values are 9.7% drier than the measurements.
The assessment of the performance of balconies using computational fluid dynamics
Authors: Ai ZT , Mak CM , Niu JL , Li ZR 
Published: June 2011

This article presents a numerical study of ventilation performance of balconies using computational fluid dynamics. The pressure coefficients distributed on the opposite walls of a five-storey building model, both with and without balconies, were studied under variation of the wind direction, balcony dimensions and building height. The effect of balconies on the capacity for wind-induced natural ventilation is discussed. The numerical results show good agreement with the experiments of Chand et al. They also indicate that a balcony enhances the cross-ventilation of intermediate floors but weakens that of the ground and top floors, by significantly changing the pressure distribution on the windward wall. Finally, the ventilation performance of a balcony is not greatly affected by variations in its size but is slightly weakened as the height of the building increases. Practical application: This study provides information and guidance in how best to incorporate the use of a balcony in building development at the design stage.
Shear behaviour of polyalkylmethacrylate solutions under thin film lubrication
Authors: Muraki M , Yamashina T 
Published: June 2011

Film-forming properties and traction were determined for the oils containing polyalkylmethacrylates (PAMAs) under a temperature of 40 °C and a rolling speed between 0.001 and 1 m/s with the disc-on-roller tester. Oil film thickness measurements were made under a pure rolling condition and traction measurements were made under the slide/roll ratio of 50 per cent. All the copolymers were synthesized in the base oil by a random copolymerization method. Difference in oil film thickness between polymer solutions became significant under the rolling speed below 0.1 m/s. Among non-functionalized homopolymers, PAMAs with branched alkyl group were superior to those with linear alkyl group in film-forming performance. In functionalized PAMAs, film-forming performance was affected by the functional group as well as the coexisting alkyl group. High-mole-concentration of functional group produced a greater oil film thickness than the corresponding low-mole-concentration PAMAs. This tendency was more marked for high-molecular-weight PAMAs. Among all the polymer solutions, high-molecular-weight PAMA with methyl group as a main component showed the thickest oil film, followed by high-molecular-weight PAMA containing branched alkyl group and dimethylaminoethyl group. In the low speeds of the traction–speed curves, most PAMA solutions showed the effect of friction reduction, whose extent depended upon the type of alkyl group and functional group. It was inferred that the friction behaviour in the partial elastohydrodynamic lubrication (EHL) regime was considerably affected by the friction in the thin film lubrication based on the mutual interaction between polymer molecules.
KIT-D816V–independent oncogenic signaling in neoplastic cells in systemic mastocytosis: role of Lyn and Btk activation and disruption by dasatinib and bosutinib
Authors: Gleixner Karoline V. , Mayerhofer Matthias , Cerny-Reiterer Sabine , Hörmann Gregor , Rix Uwe , Bennett Keiryn L. , Hadzijusufovic Emir , Meyer Renata A. , Pickl Winfried F. , Gotlib Jason , Horny Hans-Peter , Reiter Andreas , Mitterbauer-Hohendanner Gerlinde , Superti-Furga Giulio , Valent Peter 
Published: June 2011

AbstractSystemic mastocytosis (SM) either presents as a malignant neoplasm with short survival or as an indolent disease with normal life expectancy. In both instances, neoplastic mast cells (MCs) harbor D816V-mutated KIT, suggesting that additional oncogenic mechanisms are involved in malignant transformation. We here describe that Lyn and Btk are phosphorylated in a KIT-independent manner in neoplastic MCs in advanced SM and in the MC leukemia cell line HMC-1. Lyn and Btk activation was not only detected in KIT D816V-positive HMC-1.2 cells, but also in the KIT D816V-negative HMC-1.1 subclone. Moreover, KIT D816V did not induce Lyn/Btk activation in Ba/F3 cells, and deactivation of KIT D816V by midostaurin did not alter Lyn/Btk activation. siRNAs against Btk and Lyn were found to block survival in neoplastic MCs and to cooperate with midostaurin in producing growth inhibition. Growth inhibitory effects were also obtained with 2 targeted drugs, dasatinib which blocks KIT, Lyn, and Btk activation in MCs, and bosutinib, a drug that deactivates Lyn and Btk without blocking KIT activity. Together, KIT-independent signaling via Lyn/Btk contributes to growth of neoplastic MCs in advanced SM. Dasatinib and bosutinib disrupt Lyn/Btk-driven oncogenic signaling in neoplastic MC, which may have clinical implications and explain synergistic drug interactions.
IL-7R expression and IL-7 signaling confer a distinct phenotype on developing human B-lineage cells
Authors: Nodland Sonja E. , Berkowska Magdalena A. , Bajer Anna A. , Shah Nisha , de Ridder Dick , van Dongen Jacques J. M. , LeBien Tucker W. , van Zelm Menno C. 
Published: June 2011

AbstractIL-7 is an important cytokine for lymphocyte differentiation. Similar to what occurs in vivo, human CD19+ cells developing in human/murine xenogeneic cultures show differential expression of the IL-7 receptor α (IL-7Rα) chain (CD127). We now describe the relationship between CD127 expression/signaling and Ig gene rearrangement. In the present study, < 10% of CD19+CD127+ and CD19+CD127− populations had complete VDJH rearrangements. IGH locus conformation measurements by 3D FISH revealed that CD127+ and CD127− cells were less contracted than pediatric BM pro-B cells that actively rearrange the IGH locus. Complete IGH rearrangements in CD127+ and CD127− cells had smaller CDR3 lengths and fewer N-nucleotide insertions than pediatric BM B-lineage cells. Despite the paucity of VDJH rearrangements, microarray analysis indicated that CD127+ cells resembled large pre-B cells, which is consistent with their low level of Ig light-chain rearrangements. Unexpectedly, CD127− cells showed extensive Ig light-chain rearrangements in the absence of IGH rearrangements and resembled small pre-B cells. Neutralization of IL-7 in xenogeneic cultures led to an increase in Ig light-chain rearrangements in CD127+ cells, but no change in complete IGH rearrangements. We conclude that IL-7–mediated suppression of premature Ig light-chain rearrangement is the most definitive function yet described for IL-7 in human B-cell development.
Key pathways are frequently mutated in high-risk childhood acute lymphoblastic leukemia: a report from the Children's Oncology Group
Authors: Zhang Jinghui , Mullighan Charles G. , Harvey Richard C. , Wu Gang , Chen Xiang , Edmonson Michael , Buetow Kenneth H. , Carroll William L. , Chen I-Ming , Devidas Meenakshi , Gerhard Daniela S. , Loh Mignon L. , Reaman Gregory H. , Relling Mary V. , Camitta Bruce M. , Bowman W. Paul , Smith Malcolm A. , Willman Cheryl L. , Downing James R. , Hunger Stephen P. 
Published: June 2011

Abstract
We sequenced 120 candidate genes in 187 high-risk childhood B-precursor acute lymphoblastic leukemias, the largest pediatric cancer genome sequencing effort reported to date. Integrated analysis of 179 validated somatic sequence mutations with genome-wide copy number alterations and gene expression profiles revealed a high frequency of recurrent somatic alterations in key signaling pathways, including B-cell development/differentiation (68% of cases), the TP53/RB tumor suppressor pathway (54%), Ras signaling (50%), and Janus kinases (11%). Recurrent mutations were also found in ETV6 (6 cases), TBL1XR1 (3), CREBBP (3), MUC4 (2), ASMTL (2), and ADARB2 (2). The frequency of mutations within the 4 major pathways varied markedly across genetic subtypes. Among 23 leukemias expressing a BCR-ABL1-like gene expression profile, 96% had somatic alterations in B-cell development/differentiation, 57% in JAK, and 52% in both pathways, whereas only 9% had Ras pathway mutations. In contrast, 21 cases defined by a distinct gene expression profile coupled with focal ERG deletion rarely had B-cell development/differentiation or JAK kinase alterations but had a high frequency (62%) of Ras signaling pathway mutations. These data extend the range of genes that are recurrently mutated in high-risk childhood B-precursor acute lymphoblastic leukemia and highlight important new therapeutic targets for selected patient subsets.
FFCA: a feasibility-based method for flux coupling analysis of metabolic networks
Authors: David Laszlo , Marashi Sayed-Amir , Larhlimi Abdelhalim , Mieth Bettina , Bockmayr Alexander 
Published: June 2011

Abstract

Background
Flux coupling analysis (FCA) is a useful method for finding dependencies between fluxes of a metabolic network at steady-state. FCA classifies reactions into subsets (called coupled reaction sets) in which activity of one reaction implies activity of another reaction. Several approaches for FCA have been proposed in the literature.

Results
We introduce a new FCA algorithm, FFCA (Feasibility-based Flux Coupling Analysis), which is based on checking the feasibility of a system of linear inequalities. We show on a set of benchmarks that for genome-scale networks FFCA is faster than other existing FCA methods.

Conclusions
We present FFCA as a new method for flux coupling analysis and prove it to be faster than existing approaches. A corresponding software tool is freely available for non-commercial use at http://www.bioinformatics.org/ffca/.
MotifClick: prediction of cis-regulatory binding sites via merging cliques
Authors: Zhang Shaoqiang , Li Shan , Niu Meng , Pham Phuc T , Su Zhengchang 
Published: June 2011

Abstract

Background
Although dozens of algorithms and tools have been developed to find a set of cis-regulatory binding sites called a motif in a set of intergenic sequences using various approaches, most of these tools focus on identifying binding sites that are significantly different from their background sequences. However, some motifs may have a similar nucleotide distribution to that of their background sequences. Therefore, such binding sites can be missed by these tools.

Results
Here, we present a graph-based polynomial-time algorithm, MotifClick, for the prediction of cis-regulatory binding sites, in particular, those that have a similar nucleotide distribution to that of their background sequences. To find binding sites with length k, we construct a graph using some 2(k-1)-mers in the input sequences as the vertices, and connect two vertices by an edge if the maximum number of matches of the local gapless alignments between the two 2(k-1)-mers is greater than a cutoff value. We identify a motif as a set of similar k-mers from a merged group of maximum cliques associated with some vertices.

Conclusions
When evaluated on both synthetic and real datasets of prokaryotes and eukaryotes, MotifClick outperforms existing leading motif-finding tools for prediction accuracy and balancing the prediction sensitivity and specificity in general. In particular, when the distribution of nucleotides of binding sites is similar to that of their background sequences, MotifClick is more likely to identify the binding sites than the other tools.
NDRG2 inhibits hepatocellular carcinoma adhesion, migration and invasion by regulating CD24 expression
Authors: Zheng Jin , Li Yan , Yang Jiandong , Liu Qiang , Shi Ming , Zhang Rui , Shi Hengjun , Ren Qinyou , Ma Ji , Guo Hang , Tao Yurong , Xue Yan , Jiang Ning , Yao Libo , Liu Wenchao 
Published: June 2011

AbstractBackgroundThe prognosis of most hepatocellular carcinoma (HCC) patients is poor due to the high metastatic rate of the disease. Understanding the molecular mechanisms underlying HCC metastasis is extremely urgent. The role of CD24 and NDRG2 (N-myc downstream-regulated gene 2), a candidate tumor suppressor gene, has not yet been explored in HCC.MethodsThe mRNA and protein expression of CD24 and NDRG2 was analyzed in MHCC97H, Huh7 and L-02 cells. Changes in cell adhesion, migration and invasion were detected by up- or down-regulating NDRG2 by adenovirus or siRNA. The expression pattern of NDRG2 and CD24 in HCC tissues and the relationship between NDRG2 and HCC clinical features was analyzed by immunohistochemical and western blotting analysis.ResultsNDRG2 expression was negatively correlated with malignancy in HCC. NDRG2 exerted anti-tumor activity by regulating CD24, a molecule that mediates cell-cell interaction, tumor proliferation and adhesion. NDRG2 up-regulation decreased CD24 expression and cell adhesion, migration and invasion. By contrast, NDRG2 down-regulation enhanced CD24 expression and cell adhesion, migration and invasion. Immunohistochemical analysis of 50 human HCC clinical specimens showed a strong correlation between NDRG2 down-regulation and CD24 overexpression (P = 0.04). In addition, increased frequency of NDRG2 down-regulation was observed in patients with elevated AFP serum level (P = 0.006), late TNM stage (P = 0.009), poor differentiation grade (P = 0.002), tumor invasion (P = 0.004) and recurrence (P = 0.024).ConclusionsOur findings indicate that NDRG2 and CD24 regulate HCC adhesion, migration and invasion. The expression level of NDRG2 is closely related to the clinical features of HCC. Thus, NDRG2 plays an important physiological role in HCC metastasis.
'The girl with her period is the one to hang her head' Reflections on menstrual management among schoolgirls in rural Kenya
Authors: McMahon Shannon A , Winch Peter J , Caruso Bethany A , Obure Alfredo F , Ogutu Emily A , Ochari Imelda A , Rheingans Richard D 
Published: June 2011

Abstract

Background
The onset of menstruation is a landmark event in the life of a young woman. Yet the complications and challenges that can accompany such an event have been understudied, specifically in resource-poor settings. As interventions aim to improve female attendance in schools, it is important to explore how menstruation is perceived and navigated by girls in the school setting. This research conveys rural Kenyan schoolgirls' perceptions and practices related to menstruation

Methods
Data were collected at six rural schools in the Nyanza Province of Western Kenya. Using focus group discussions, in-depth interviews, and field notes from observations, researchers collected information from 48 primary schoolgirls and nine teachers. Systematic analysis began with a reading of transcripts and debriefing notes, followed by manual coding of the narratives.

Results
Focus group discussions became opportunities for girls to share thoughts on menstruation, instruct one another on management practices and advise one another on coping mechanisms. Girls expressed fear, shame, distraction and confusion as feelings associated with menstruation. These feelings are largely linked to a sense of embarrassment, concerns about being stigmatized by fellow students and, as teachers explained, a perception that the onset of menstruation signals the advent of a girl's sexual status. Among the many methods for managing their periods, girls most frequently said they folded, bunched up or sewed cloth, including cloth from shirts or dresses, scraps of old cloth, or strips of an old blanket. Cloth was reported to frequently leak and cause chafing, which made school attendance difficult particularly as the day progressed. Attitudes and practices of girls toward menstruation have been arranged into personal, environmental and behavioural factors.

Conclusion
Further research on menstrual management options that are practical, sustainable and culturally acceptable must be conducted to inform future programs and policies that aim to empower young girls as they transition into womanhood. Stakeholders working within this and similar contexts must consider systematic mechanisms to explain to young girls what menstruation is and how to manage it. Providing sanitary supplies or guiding girls on how to create supplies serve as critical components for future interventions.
Factors associated with female genital mutilation in Burkina Faso and its policy implications
Authors: Karmaker Bue , Kandala Ngianga-Bakwin , Chung Donna , Clarke Aileen 
Published: June 2011

Abstract

Background
Female genital mutilation (FGM) usually undertaken between the ages of 1-9 years and is widely practised in some part of Africa and by migrants from African countries in other parts of the world. Laws prohibit FGM in almost every country. FGM can cause immediate complications (pain, bleeding and infection) and delayed complications (sexual, obstetric, psychological problems). Several factors have been associated with an increased likelihood of FGM. In Burkina Faso, the prevalence of FGM appears to have increased in recent years.

Methods
We investigated social, demographic and economic factors associated with FGM in Burkina Faso using the 2003 Demographic Health Survey (DHS). The DHS is a nationally representative cross-sectional survey (multistage stratified random sampling of households) of women of reproductive age (15-49 years). Associations between potential risk factors and the prevalence of FGM were explored using χ2 and t-tests and Mann Whitney U-test as appropriate. Logistic regression modelling was used to investigate social, demographic and economic risk factors associated with FGM.

Main outcome measures
i) whether a woman herself had had FGM; ii) whether she had one or more daughters with FGM.

Results
Data were available on 12,049 women. Response rates by region were at least 90%. Women interviewed were representative of the underlying populations of the different regions of Burkina Faso. Seventy seven percent (9267) of the women interviewed had had FGM. 7336 women had a daughter of whom 2216 (30.2%) had a daughter with FGM and 334 (4.5%) said that they intended that their daughter should have it. Univariate analysis showed that age, religion, wealth, ethnicity, literacy, years of education, household affluence, region and who had responsibility for health care decisions in the household had (RHCD) were all significantly related to the two outcomes (p < 0.01). Multivariate analysis stratified by religion mainly confirmed these findings, however, education is significantly associated with a reduced likelihood of FGM only for Christian women.

Conclusions and Policy implications
Factors associated with FGM are varied and complex. Younger women and those from specific groups and religions are less likely to have had FGM. A higher level of education may be protective for women from certain religions. Policies should capitalize on these findings and religious leaders should be involved in continuing programmes of action.
High frequency of chlamydial co-infections in clinically healthy sheep flocks
Authors: Lenzko Hannah , Moog Udo , Henning Klaus , Lederbach Robert , Diller Roland , Menge Christian , Sachse Konrad , Sprague Lisa D 
Published: June 2011

Abstract

Background
The epidemiological situation of ovine chlamydial infections in continental Europe, especially Germany is poorly characterised. Using the German state of Thuringia as a model example, the chlamydial sero- and antigen prevalence was estimated in thirty-two randomly selected sheep flocks with an average abortion rate lower than 1%. Seven vaccinated flocks were reviewed separately.

Results
A wide range of samples from 32 flocks were examined. Assumption of a seroprevalence of 10% (CI 95%) at flock level, revealed that 94% of the tested flocks were serologically positive with ongoing infection (i.e. animals with seroconversion) in nearly half (47%) of the flocks. On the basis of an estimated 25% antigen prevalence (CI 95%), PCR and DNA microarray testing, together with sequencing revealed the presence of chlamydiae in 78% of the flocks. The species most frequently found was Chlamydophila (C.) abortus (50%) followed by C. pecorum (47%) and C. psittaci genotype A (25%). Mixed infections occurred in 25% of the tested flocks. Samples obtained from the vaccinated flocks revealed the presence of C. abortus field samples in 4/7 flocks. C. pecorum was isolated from 2/7 flocks and the presence of seroconversion was determined in 3/7 flocks.

Conclusions
The results imply that chlamydial infections occur frequently in German sheep flocks, even in the absence of elevated abortion rates. The fact that C. pecorum and the potentially zoonotic C. psittaci were found alongside the classical abortifacient agent C. abortus, raise questions about the significance of this reservoir for animal and human health and underline the necessity for regular monitoring. Further studies are needed to identify the possible role of C. psittaci infections in sheep.
Intensity modulated radiotherapy for elderly bladder cancer patients
Authors: Hsieh Chen-Hsi , Chung Shiu-Dong , Chan Pei-Hui , Lai Siu-Kai , Chang Hsiao-Chun , Hsiao Chi-Huang , Wu Le-Jung , Chong Ngot-Swan , Chen Yu-Jen , Wang Li-Ying , Hsieh Yen-Ping , Shueng Pei-Wei 
Published: June 2011

Abstract

Background
To review our experience and evaluate treatment planning using intensity-modulated radiotherapy (IMRT) and helical tomotherapy (HT) for the treatment of elderly patients with bladder cancer.

Methods
From November 2006 through November 2009, we enrolled 19 elderly patients with histologically confirmed bladder cancer, 9 in the IMRT and 10 in the HT group. The patients received 64.8 Gy to the bladder with or without concurrent chemotherapy. Conventional 4-field "box" pelvic radiation therapy (2DRT) plans were generated for comparison.

Results
The median patient age was 80 years old (range, 65-90 years old). The median survival was 21 months (5 to 26 months). The actuarial 2-year overall survival (OS) for the IMRT vs. the HT group was 26.3% vs .37.5%, respectively; the corresponding values for disease-free survival were 58.3% vs. 83.3%, respectively; for locoregional progression-free survival (LRPFS), the values were 87.5% vs. 83.3%, respectively; and for metastases-free survival, the values were 66.7% vs. 60.0%, respectively. The 2-year OS rates for T1, 2 vs. T3, 4 were 66.7% vs. 35.4%, respectively (p = 0.046). The 2-year OS rate was poor for those whose RT completion time greater than 8 weeks when compared with the RT completed within 8 wks (37.9% vs. 0%, p = 0.004).

Conclusion
IMRT and HT provide good LRPFS with tolerable toxicity for elderly patients with invasive bladder cancer. IMRT and HT dosimetry and organ sparing capability were superior to that of 2DRT, and HT provides better sparing ability than IMRT. The T category and the RT completion time influence OS rate.