bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of a c0t-1 library enables the targeted identification of minisatellite and satellite families in Beta vulgaris
Authors: Zakrzewski Falk , Wenke Torsten , Holtgräwe Daniela , Weisshaar Bernd , Schmidt Thomas 
Published: January 2010

Abstract

Background
Repetitive DNA is a major fraction of eukaryotic genomes and occurs particularly often in plants. Currently, the sequencing of the sugar beet (Beta vulgaris) genome is under way and knowledge of repetitive DNA sequences is critical for the genome annotation. We generated a c
0
t-1 library, representing highly to moderately repetitive sequences, for the characterization of the major B. vulgaris repeat families. While highly abundant satellites are well-described, minisatellites are only poorly investigated in plants. Therefore, we focused on the identification and characterization of these tandemly repeated sequences.

Results
Analysis of 1763 c
0
t-1 DNA fragments, providing 442 kb sequence data, shows that the satellites pBV and pEV are the most abundant repeat families in the B. vulgaris genome while other previously described repeats show lower copy numbers. We isolated 517 novel repetitive sequences and used this fraction for the identification of minisatellite and novel satellite families. Bioinformatic analysis and Southern hybridization revealed that minisatellites are moderately to highly amplified in B. vulgaris. FISH showed a dispersed localization along most chromosomes clustering in arrays of variable size and number with exclusion and depletion in distinct regions.

Conclusion
The c
0
t-1 library represents major repeat families of the B. vulgaris genome, and analysis of the c
0
t-1 DNA was proven to be an efficient method for identification of minisatellites. We established, so far, the broadest analysis of minisatellites in plants and observed their chromosomal localization providing a background for the annotation of the sugar beet genome and for the understanding of the evolution of minisatellites in plant genomes.
General practitioners' attitudes and preparedness towards Clinical Decision Support in e-Prescribing (CDS-eP) adoption in the West of Ireland: a cross sectional study
Authors: Hor Chee Peng , O'Donnell James M , Murphy Andrew W , O'Brien Timothy , Kropmans Thomas JB 
Published: January 2010

Abstract

Background
Electronic clinical decision support (CDS) is increasingly establishing its role in evidence-based clinical practice. Considerable evidence supports its enhancement of efficiency in e-Prescribing, but some controversy remains. This study evaluated the practicality and identified the perceived benefits of, and barriers to, its future adoption in the West of Ireland.

Methods
This cross sectional study was carried out by means of a 27-part questionnaire sent to 262 registered general practitioners in Counties Galway, Mayo and Roscommon. The survey domains encompassed general information of individual's practice, current use of CDS and the practitioner's attitudes towards adoption of CDS-eP. Descriptive and inferential analyses were performed to analyse the data collected.

Results
The overall response rate was 37%. Nearly 92% of respondents employed electronic medical records in their practice. The majority acknowledged the value of electronic CDS in improving prescribing quality (71%) and reducing prescribing errors (84%). Despite a high degree of unfamiliarity (73%), the practitioners were open to the use of CDS-eP (94%) and willing to invest greater resources for its implementation (62%). Lack of a strategic implementation plan (78%) is the main perceived barrier to the incorporation of CDS-eP into clinical practice, followed by i) lack of financial incentives (70%), ii) lack of standardized product software (61%), iii) high sensitivity of drug-drug interaction or medication allergy markers (46%), iv) concern about overriding physicians' prescribing decisions(44%) and v) lack of convincing evidence on the systems' effectiveness (22%).

Conclusions
Despite favourable attitudes towards the adoption of CDS-eP, multiple perceived barriers impede its incorporation into clinical practice. These merit further exploration, taking into consideration the structure of the Irish primary health care system, before CDS-eP can be recommended for routine clinical use in the West of Ireland.
ASPM-associated stem cell proliferation is involved in malignant progression of gliomas and constitutes an attractive therapeutic target
Authors: Bikeye Sandra-Nadia Ngwabyt , Colin Carole , Marie Yannick , Vampouille Raphaël , Ravassard Philippe , Rousseau Audrey , Boisselier Blandine , Idbaih Ahmed , Calvo Charles Félix , Leuraud Pascal , Lassalle Myriam , El Hallani Soufiane , Delattre Jean-Yves , Sanson Marc 
Published: January 2010

Abstract

Background
ASPM (Abnormal Spindle-like Microcephaly associated) over-expression was recently implicated in the development of malignant gliomas.

Results
To better characterize the involvement of ASPM in gliomas, we investigated the mRNA expression in 175 samples, including 8 WHO Grade II, 75 WHO Grade III and 92 WHO Grade IV tumors. Aspm expression was strongly correlated with tumor grade and increased at recurrence when compared to the initial lesion, whatever the initial grade of the primary tumor. ASPM expression also increased over serial passages in gliomaspheres in vitro and in mouse xenografts in vivo. Lentivirus-mediated shRNA silencing of ASPM resulted in dramatic proliferation arrest and cell death in two different gliomasphere models.

Conclusion
These data suggest that ASPM is involved in the malignant progression of gliomas, possibly through expansion of a cancer stem cell compartment, and is an attractive therapeutic target in glioblastoma multiforme.
Strategies to prevent intraoperative lung injury during cardiopulmonary bypass
Authors: Apostolakis Efstratios E , Koletsis Efstratios N , Baikoussis Nikolaos G , Siminelakis Stavros N , Papadopoulos Georgios S 
Published: January 2010

Abstract
During open heart surgery the influence of a series of factors such as cardiopulmonary bypass (CPB), hypothermia, operation and anaesthesia, as well as medication and transfusion can cause a diffuse trauma in the lungs. This injury leads mostly to a postoperative interstitial pulmonary oedema and abnormal gas exchange. Substantial improvements in all of the above mentioned factors may lead to a better lung function postoperatively. By avoiding CPB, reducing its time, or by minimizing the extracorporeal surface area with the use of miniaturized circuits of CPB, beneficial effects on lung function are reported. In addition, replacement of circuit surface with biocompatible surfaces like heparin-coated, and material-independent sources of blood activation, a better postoperative lung function is observed. Meticulous myocardial protection by using hypothermia and cardioplegia methods during ischemia and reperfusion remain one of the cornerstones of postoperative lung function. The partial restoration of pulmonary artery perfusion during CPB possibly contributes to prevent pulmonary ischemia and lung dysfunction. Using medication such as corticosteroids and aprotinin, which protect the lungs during CPB, and leukocyte depletion filters for operations expected to exceed 90 minutes in CPB-time appear to be protective against the toxic impact of CPB in the lungs. The newer methods of ultrafiltration used to scavenge pro-inflammatory factors seem to be protective for the lung function. In a similar way, reducing the use of cardiotomy suction device, as well as the contact-time between free blood and pericardium, it is expected that the postoperative lung function will be improved.
Prevalence and Correlates of HIV Testing: An Analysis of University Students in Jamaica
Authors: Norman Lisa R , Gebre Yitades 
Published: January 2010

BackgroundPrevention programs often promote HIV testing as one possible strategy of combating the spread of the disease.ObjectiveTo examine levels of HIV testing practices among a large sample of university students and the relationship among HIV testing, sociodemographic variables, and HIV‐related behaviors.MethodsA total of 1252 students were surveyed between June 2001 and February 2002 using a 193‐item questionnaire measuring a variety of HIV‐related knowledge and attitudinal and behavioral items.ResultsHierarchical logistic regression analyses revealed that youths, married persons, persons who had attended an HIV education forum, and those who knew someone with HIV/AIDS were more likely to report a previous HIV test. However, HIV testing was not associated with condom use or number of sex partners.ConclusionThe lack of significant findings between testing and risky sexual behaviors should not negate the importance of HIV testing. Being informed regarding personal HIV serostatus is one of the first steps in self‐protection. Effective messages and programs need to be developed and implemented in Jamaica to promote HIV testing and help persons to adequately assess their level of risk with respect to contracting HIV.
Disease Progression Among Untreated HIV‐Infected Patients in South Ethiopia: Implications for Patient Care
Authors: Jerene Degu , Lindtjørn Bernt 
Published: January 2010

ContextThe natural course of HIV disease progression among resource‐poor patient populations has not been clearly defined.ObjectiveTo describe predictors of HIV disease progression as seen at an outpatient clinic in a resource‐limited setting in rural Ethiopia.DesignThis prospective cohort study included all adult HIV patients who visited an outpatient clinic at Arba Minch hospital in South Ethiopia between January 30, 2003 and April 1, 2004. Clinical and hematologic measurements were done at baseline and every 12 weeks thereafter until the patient was transferred, put on antiretroviral therapy, was lost to follow‐up, or died. Community agents reported patient status every month.SettingA district hospital with basic facilities for HIV testing and patient monitoring.Main Outcome MeasuresDeath, diagnosis of tuberculosis, and change in disease stage.ResultsWe followed 207 patients for a median duration of 19 weeks (range, 0–60 weeks). A total of 132 (64%) of them were in WHO stage III. The overall mortality rate was 46 per 100 person‐years of observation (PYO). Mortality increased with advancing disease stage. Diarrhea, oral thrush, and low total lymphocyte count were significant markers of mortality. The incidence of tuberculosis was 9.9 per 100 PYO. Baseline history of easy fatigability and fever were strongly associated with subsequent development of tuberculosis.ConclusionThe mortality rate and the incidence of tuberculosis in our cohort are among the highest ever reported in sub‐Saharan Africa. We identified oral thrush, diarrhea, and total lymphocyte count as predictors of mortality, and easy fatigability and fever as predictors of tuberculosis. The findings have practical implications for patient care in resource‐limited settings.
Outcomes After Stereotactic Lung Radiotherapy or Wedge Resection for Stage I Non–Small-Cell Lung Cancer
Authors: Grills Inga S. , Mangona Victor S. , Welsh Robert , Chmielewski Gary , McInerney Erika , Martin Shannon , Wloch Jennifer , Ye Hong , Kestin Larry L. 
Published: January 2010

Purpose To compare outcomes between lung stereotactic radiotherapy (SBRT) and wedge resection for stage I non–small-cell lung cancer (NSCLC). Patients and Methods One hundred twenty-four patients with T1-2N0 NSCLC underwent wedge resection (n = 69) or image-guided lung SBRT (n = 58) from February 2003 through August 2008. All were ineligible for anatomic lobectomy; of those receiving SBRT, 95% were medically inoperable, with 5% refusing surgery. Mean forced expiratory volume in 1 second and diffusing capacity of lung for carbon monoxide were 1.39 L and 12.0 mL/min/mmHg for wedge versus 1.31 L and 10.14 mL/min/mmHg for SBRT (P = not significant). Mean Charlson comorbidity index and median age were 3 and 74 years for wedge versus 4 and 78 years for SBRT (P < .01, P = .04). SBRT was volumetrically prescribed as 48 (T1) or 60 (T2) Gy in four to five fractions. Results Median potential follow-up is 2.5 years. At 30 months, no significant differences were identified in regional recurrence (RR), locoregional recurrence (LRR), distant metastasis (DM), or freedom from any failure (FFF) between the two groups (P > .16). SBRT reduced the risk of local recurrence (LR), 4% versus 20% for wedge (P = .07). Overall survival (OS) was higher with wedge but cause-specific survival (CSS) was identical. Results excluding synchronous primaries, nonbiopsied tumors, or pathologic T4 disease (wedge satellite lesion) showed reduced LR (5% v 24%, P = .05), RR (0% v 18%, P = .07), and LRR (5% v 29%, P = .03) with SBRT. There were no differences in DM, FFF, or CSS, but OS was higher with wedge. Conclusion Both lung SBRT and wedge resection are reasonable treatment options for stage I NSCLC patients ineligible for anatomic lobectomy. SBRT reduced LR, RR, and LRR. In this nonrandomized population of patients selected for surgery versus SBRT (medically inoperable) at physician discretion, OS was higher in surgical patients. SBRT and surgery, however, had identical CSS.
Phase II, Randomized Study of Concomitant Chemoradiotherapy Followed by Surgery and Adjuvant Capecitabine Plus Oxaliplatin (CAPOX) Compared With Induction CAPOX Followed by Concomitant Chemoradiotherapy and Surgery in Magnetic Resonance Imaging–Defined, Locally Advanced Rectal Cancer: Grupo Cáncer de Recto 3 Study
Authors: Fernández-Martos Carlos , Pericay Carles , Aparicio Jorge , Salud Antonieta , Safont MariaJose , Massuti Bertomeu , Vera Ruth , Escudero Pilar , Maurel Joan , Marcuello Eugenio , Mengual Jose Luis , Saigi Eugenio , Estevan Rafael , Mira Moises , Polo Sonia , Hernandez Ana , Gallen Manuel , Arias Fernando , Serra Javier , Alonso Vicente 
Published: January 2010

PurposeThe optimal therapeutic sequence of the adjuvant chemotherapy component of preoperative chemoradiotherapy (CRT) for patients with locally advanced rectal cancer is controversial. Induction chemotherapy before preoperative CRT may be associated with better efficacy and compliance.Patients and MethodsA total of 108 patients with locally advanced rectal cancer were randomly assigned to arm A—preoperative CRT with capecitabine, oxaliplatin, and concurrent radiation followed by surgery and four cycles of postoperative adjuvant capecitabine and oxaliplatin (CAPOX)—or arm B—induction CAPOX followed by CRT and surgery. The primary end point was pathologic complete response rate (pCR).ResultsOn an intention-to-treat basis, the pCR for arms A and B were 13.5% (95% CI, 5.6% to 25.8%) and 14.3% (95% CI, 6.4% to 26.2%), respectively. There were no statistically significant differences in other end points, including downstaging, tumor regression, and R0 resection. Overall, chemotherapy treatment exposure was higher in arm B than in arm A for both oxaliplatin (P < .0001) and capecitabine (P < .0001). During CRT, grades 3 to 4 adverse events were similar in both arms but were significantly higher in arm A during postoperative adjuvant CT than with induction CT in arm B. There were three deaths in each arm during the treatment period.ConclusionCompared with postoperative adjuvant CAPOX, induction CAPOX before CRT had similar pCR and complete resection rates. It did achieve more favorable compliance and toxicity profiles. On the basis of these findings, a phase III study to definitively test the induction strategy is warranted.
Field Behavior of a Geogrid Reinforced Soil Retaining Wall with a Wrap-Around Facing
Authors: Yang Guangqing , Ding Junxia , Zhou Qiaoyong , Zhang Baojian 
Published: January 2010

Abstract
The earth pressure and deformation characteristics of a geogrid reinforced soil retaining wall were monitored during and for a period of 1.5 years after construction. Both vertical and lateral soil stresses were recorded with vibrating-wire earth pressure cells, and the reinforcement deformations were measured using flexible displacement sensors. The maximum vertical foundation pressure along the wall’s reinforcements occurred at the center of the reinforcement, gradually decreasing towards the front and back ends. The measured lateral earth pressure within the reinforced soil wall is non-linear along the wall height, and the value is less than the theoretical active lateral earth pressure. The distribution of tensile strain along the reinforcements within the lower portion of the wall has two peak values. The potential failure surface of the wall closely follows the theoretical Coulomb failure surface of an unreinforced backfill.
Recommendations for an ASTM Standardized Test for Determining GIIc of Unidirectional Laminated Polymeric Matrix Composites
Authors: Davidson Barry D. , Teller Sean S. 
Published: January 2010

Abstract
This study was aimed at finalizing the details of a standardized test to determine the Mode II interlaminar fracture toughness of laminated composites. A large number of end-notched flexure tests were performed on glass/epoxy, two graphite/epoxies, and on graphite/bismaleimide specimens. Tests were performed directly from the preimplanted insert as well as from Mode II precracks. Results were combined with those from previous experimental and numerical studies and used to extract recommendations for the proposed standard. A compliance calibration method of data reduction was used. It was found that the results from only two compliance tests, along with the compliance from the fracture toughness test, are sufficient to characterize a specimen’s compliance versus crack length relation. Furthermore, the unloading line and compliance data from the non-precracked toughness test can be used to accurately locate the new crack front, which allows determination of both the non-precracked and precracked toughness from the same specimen. It is shown that accurate and repeatable toughness values are obtained provided that the ratio of crack length to half-span length is 0.6, that compliance tests are performed to a target maximum load corresponding to 0.25 GIIc at each crack length, and that toughness values are only accepted if the actual energy release rate during compliance testing is in-between 15 and 35 % of the computed value of GIIc.
Differenzielle Flachheit: Eine nützliche Methodik auch für lineare SISO-SystemeDifferential Flatness: A Useful Method also for Linear SISO Systems
Authors: Zeitz Michael 
Published: January 2010

Zusammenfassung
Für lineare Systeme ist die differenzielle Flachheit gleichbedeutend mit der Steuerbarkeit und damit einfacher als im nichtlinearen Fall festzustellen. In diesem Beitrag wird für lineare SISO-Systeme gezeigt, wie die differenzielle Flachheit bei der Trajektorienplanung, dem Vorsteuerungs-Entwurf und der Synthese von Folgeregelungen in den Koordinaten der Regelungs-Normalform angewendet wird. In Anbetracht der praktischen Relevanz einer Folgeregelung mit Vorsteuerung und der leichten Vermittelbarkeit der linearen Flachheits-Methodik sprechen viele Argumente für eine Behandlung in der regelungstechnischen Ausbildung.
EOR-2 Is an Obligate Binding Partner of the BTB–Zinc Finger Protein EOR-1 in Caenorhabditis elegans
Authors: Howell Kelly , Arur Swathi , Schedl Tim , Sundaram Meera V 
Published: January 2010

Abstract
BTB-zinc finger transcription factors play many important roles in metazoan development. In these proteins, the BTB domain is critical for dimerization and for recruiting cofactors to target genes. Identification of these cofactors is important for understanding how BTB-zinc finger proteins influence transcription. Here we show that the novel but conserved protein EOR-2 is an obligate binding partner of the BTB-zinc finger protein EOR-1 in Caenorhabditis elegans.EOR-1 and EOR-2 function together to promote multiple Ras/ERK-dependent cell fates during development, and we show that EOR-1 is a robust substrate of ERK in vitro. A point mutation (L81F) in the EOR-1 BTB domain reduces both ERK phosphorylation and EOR-2 binding and eliminates all detectable biological function without affecting EOR-1 expression levels, localization, or dimerization. This point mutation lies near the predicted charged pocket region of the EOR-1 BTB dimer, a region that, in other BTB-zinc finger proteins, has been proposed to interact with corepressors or coactivators. We also show that a conserved zinc finger-like motif in EOR-2 is required for binding to EOR-1, that the interaction between EOR-1 and EOR-2 is direct, and that EOR-2 can bind to the human BTB-zinc finger protein PLZF. We propose that EOR-2 defines a new family of cofactors for BTB-zinc finger transcription factors that may have conserved roles in other organisms.
Improved Activities of CREB Binding Protein, Heterogeneous Nuclear Ribonucleoproteins and Proteasome Following Downregulation of Noncoding hsrω Transcripts Help Suppress Poly(Q) Pathogenesis in Fly Models
Authors: Mallik Moushami , Lakhotia Subhash C 
Published: January 2010

Abstract
Following earlier reports on modulation of poly(Q) toxicity in Drosophila by the developmentally active and stress-inducible noncoding hsrω gene, we investigated possible mediators of this modulation. RNAi-mediated downregulation of the large nuclear hsrω-n transcript, which organizes the nucleoplasmic omega speckles, suppressed the enhancement of poly(Q) toxicity brought about by reduced availability of the heterogeneous nuclear ribonucleoprotein (hnRNP) Hrb87F and of the transcriptional regulator, cAMP response element binding (CREB) binding protein (CBP). Levels of CBP RNA and protein were reciprocally affected by hsrω transcript levels in eye disc cells. Our data suggest that CBP and hnRNPs like Hrb57A and Hrb87F physically interact with each other. In addition, downregulation of hsrω transcripts partially rescued eye damage following compromised proteasome activity, while overexpression of hsrω and/or poly(Q) proteins disrupted the proteasomal activity. Rescue of poly(Q) toxicity by hsrω-RNAi required normal proteasomal function. We suggest that hsrω-RNAi suppresses poly(Q) toxicity by elevating cellular levels of CBP, by enhancing proteasome-mediated clearance of the pathogenic poly(Q) aggregates, and by inhibiting induced apoptosis. The direct and indirect interactions of the hsrω transcripts with a variety of regulatory proteins like hnRNPs, CBP, proteasome, Drosophila inhibitor of apoptosis protein 1 (DIAP1), etc., reinforce the view that the noncoding hsrω RNA functions as a “hub” in cellular networks to maintain homeostasis by coordinating the functional availability of crucial cellular regulatory proteins.