bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Physalis peruviana leaf transcriptome: assembly, annotation and gene model prediction
Authors: Garzón-Martínez Gina A , Zhu Z Iris , Landsman David , Barrero Luz S , Mariño-Ramírez Leonardo 
Published: April 2012

Abstract

Background

Physalis peruviana commonly known as Cape gooseberry is a member of the Solanaceae family that has an increasing popularity due to its nutritional and medicinal values. A broad range of genomic tools is available for other Solanaceae, including tomato and potato. However, limited genomic resources are currently available for Cape gooseberry.

Results
We report the generation of a total of 652,614 P. peruviana Expressed Sequence Tags (ESTs), using 454 GS FLX Titanium technology. ESTs, with an average length of 371 bp, were obtained from a normalized leaf cDNA library prepared using a Colombian commercial variety. De novo assembling was performed to generate a collection of 24,014 isotigs and 110,921 singletons, with an average length of 1,638 bp and 354 bp, respectively. Functional annotation was performed using NCBI’s BLAST tools and Blast2GO, which identified putative functions for 21,191 assembled sequences, including gene families involved in all the major biological processes and molecular functions as well as defense response and amino acid metabolism pathways. Gene model predictions in P. peruviana were obtained by using the genomes of Solanum lycopersicum (tomato) and Solanum tuberosum (potato). We predict 9,436 P. peruviana sequences with multiple-exon models and conserved intron positions with respect to the potato and tomato genomes. Additionally, to study species diversity we developed 5,971 SSR markers from assembled ESTs.

Conclusions
We present the first comprehensive analysis of the Physalis peruviana leaf transcriptome, which will provide valuable resources for development of genetic tools in the species. Assembled transcripts with gene models could serve as potential candidates for marker discovery with a variety of applications including: functional diversity, conservation and improvement to increase productivity and fruit quality. P. peruviana was estimated to be phylogenetically branched out before the divergence of five other Solanaceae family members, S. lycopersicum, S. tuberosum, Capsicum spp, S. melongena and Petunia spp.
Age – related treatment strategy and long-term outcome in acute myocardial infarction patients in the PCI era
Authors: Kala Petr , Kanovsky Jan , Rokyta Richard , Smid Michal , Pospisil Jan , Knot Jiri , Rohac Filip , Poloczek Martin , Ondrus Tomas , Holicka Maria , Spinar Jindrich , Jarkovsky Jiri , Dusek Ladislav 
Published: April 2012

Abstract

Background
Older age, as a factor we cannot affect, is consistently one of the main negative prognostic values in patients with acute myocardial infarction. One of the most powerful factors that improves outcomes in patients with acute coronary syndromes is the revascularization preferably performed by percutaneous coronary intervention. No data is currently available for the role of age in large groups of consecutive patients with PCI as the nearly sole method of revascularization in AMI patients. The aim of this study was to analyze age-related differences in treatment strategies, results of PCI procedures and both in-hospital and long-term outcomes of consecutive patients with acute myocardial infarction.

Methods
Retrospective multicenter analysis of 3814 consecutive acute myocardial infarction patients divided into two groups according to age (1800 patients ≤ 65 years and 2014 patients > 65 years). Significantly more older patients had a history of diabetes mellitus and previous myocardial infarctions.

Results
The older population had a significantly lower rate of coronary angiographies (1726; 95.9% vs. 1860; 92.4%, p < 0.0001), PCI (1541; 85.6% vs. 1505; 74.7%, p < 0.001), achievement of optimal final TIMI flow 3 (1434; 79.7% vs. 1343; 66.7%, p < 0.001) and higher rate of unsuccessful reperfusion with final TIMI flow 0-1 (46; 2.6% vs. 78; 3.9%, p = 0.022). A total of 217 patients (5.7%) died during hospitalization, significantly more often in the older population (46; 2.6% vs. 171; 8.5%, p < 0.001). The long-term mortality (data for 2847 patients from 2 centers) was higher in the older population as well (5 years survival: 86.1% vs. 59.8%). Though not significantly different and in contrast with PCI, the presence of diabetes mellitus, previous MI, final TIMI flow and LAD, as the infarct-related artery, had relatively lower impact on the older patients. Severe heart failure on admission (Killip III-IV) was associated with the worst prognosis in the whole group of patients, though its significance was higher in the youngers (HR 6.04 vs. 3.14, p = 0.051 for Killip III and 12.24 vs. 5.65, p = 0.030 for Killip IV). We clearly demonstrated age as a strong discriminator for the whole population of AMI patients.

Conclusions
In a consecutive AMI population, the older group (>65 years) was associated with a less pronounced impact of risk factors on long-term outcome. To ascertain the coronary anatomy by coronary angiography and proceed to PCI if suitable regardless of age is crucial in all patients, though the primary success rate of PCI in the older age is lower. Age, when viewed as a risk factor, was a dominant discriminating factor in all patients.
Accuracy and precision of variance components in occupational posture recordings: a simulation study of different data collection strategies
Authors: Liv Per , Mathiassen Svend Erik , Svendsen Susanne Wulff 
Published: April 2012

AbstractBackgroundInformation on exposure variability, expressed as exposure variance components, is of vital use in occupational epidemiology, including informed risk control and efficient study design. While accurate and precise estimates of the variance components are desirable in such cases, very little research has been devoted to understanding the performance of data sampling strategies designed specifically to determine the size and structure of exposure variability. The aim of this study was to investigate the accuracy and precision of estimators of between-subjects, between-days and within-day variance components obtained by sampling strategies differing with respect to number of subjects, total sampling time per subject, number of days per subject and the size of individual sampling periods.MethodsMinute-by-minute values ofaverage elevation,percentage time above 90°andpercentage time below 15°were calculated in a data set consisting of measurements of right upper arm elevation during four full shifts from each of 23 car mechanics. Based on this parent data, bootstrapping was used to simulate sampling with 80 different combinations of the number of subjects (10, 20), total sampling time per subject (60, 120, 240, 480 minutes), number of days per subject (2, 4), and size of sampling periods (blocks) within days (1, 15, 60, 240 minutes). Accuracy (absence of bias) and precision (prediction intervals) of the variance component estimators were assessed for each simulated sampling strategy.ResultsSampling in small blocks within days resulted in essentially unbiased variance components. For a specific total sampling time per subject, and in particular if this time was small, increasing the block size resulted in an increasing bias, primarily of the between-days and the within-days variance components. Prediction intervals were in general wide, and even more so at larger block sizes. Distributing sampling time across more days gave in general more precise variance component estimates, but also reduced accuracy in some cases.ConclusionsVariance components estimated from small samples of exposure data within working days may be both inaccurate and imprecise, in particular if sampling is laid out in large consecutive time blocks. In order to estimate variance components with a satisfying accuracy and precision, for instance for arriving at trustworthy power calculations in a planned intervention study, larger samples of data will be required than for estimating an exposure mean value with a corresponding certainty.
Myocardial strains from 3D displacement encoded magnetic resonance imaging
Authors: Kindberg Katarina , Haraldsson Henrik , Sigfridsson Andreas , Engvall Jan , Ingels Neil B , Ebbers Tino , Karlsson Matts 
Published: April 2012

Abstract

Background
The ability to measure and quantify myocardial motion and deformation provides a useful tool to assist in the diagnosis, prognosis and management of heart disease. The recent development of magnetic resonance imaging methods, such as harmonic phase analysis of tagging and displacement encoding with stimulated echoes (DENSE), make detailed non-invasive 3D kinematic analyses of human myocardium possible in the clinic and for research purposes. A robust analysis method is required, however.

Methods
We propose to estimate strain using a polynomial function which produces local models of the displacement field obtained with DENSE. Given a specific polynomial order, the model is obtained as the least squares fit of the acquired displacement field. These local models are subsequently used to produce estimates of the full strain tensor.

Results
The proposed method is evaluated on a numerical phantom as well as in vivo on a healthy human heart. The evaluation showed that the proposed method produced accurate results and showed low sensitivity to noise in the numerical phantom. The method was also demonstrated in vivo by assessment of the full strain tensor and to resolve transmural strain variations.

Conclusions
Strain estimation within a 3D myocardial volume based on polynomial functions yields accurate and robust results when validated on an analytical model. The polynomial field is capable of resolving the measured material positions from the in vivo data, and the obtained in vivo strains values agree with previously reported myocardial strains in normal human hearts.
Carnitine palmitoyltransferase 1A (CPT1A): a transcriptional target of PAX3-FKHR and mediates PAX3-FKHR–dependent motility in alveolar rhabdomyosarcoma cells
Authors: Liu Lingling , Wang Yong-Dong , Wu Jing , Cui Jimmy , Chen Taosheng 
Published: April 2012

Abstract

Background
Alveolar rhabdomyosarcoma (ARMS) has a high propensity to metastasize, leading to its aggressiveness and a poor survival rate among those with the disease. More than 80% of aggressive ARMSs harbor a PAX3-FKHR fusion transcription factor, which regulates cell migration and promotes metastasis, most likely by regulating the fusion protein’s transcriptional targets. Therefore, identifying druggable transcription targets of PAX3-FKHR that are also downstream effectors of PAX3-FKHR–mediated cell migration and metastasis may lead to novel therapeutic approaches for treating ARMS.

Methods
To identify genes whose expression is directly affected by the level of PAX3-FKHR in an ARMS cellular-context, we first developed an ARMS cell line in which PAX3-FKHR is stably down-regulated, and showed that stably downregulating PAX3-FKHR in ARMS cells significantly decreased the cells’ motility. We used microarray analysis to identify genes whose expression level decreased when PAX3-FKHR was downregulated. We used mutational analysis, promoter reporter assays, and electrophoretic mobility shift assays to determine whether PAX3-FKHR binds to the promoter region of the target gene. We used siRNA and pharmacologic inhibitor to downregulate the target gene of PAX3-FKHR and investigated the effect of such downregulation on cell motility.

Results
We found that when PAX3-FKHR was downregulated, the expression of carnitine palmitoyltransferase 1A (CPT1A) decreased. We showed that PAX3-FKHR binds to a paired-domain binding-site in the CPT1A promoter region, indicating that CPT1A is a novel transcriptional target of PAX3-FKHR. Furthermore, downregulating CPT1A decreased cell motility in ARMS cells, indicating that CPT1A is a downstream effector of PAX3-FKHR–mediated cell migration and metastasis.

Conclusions
Taken together, we have identified CPT1A as a novel transcriptional target of PAX3-FKHR and revealed the novel function of CPT1A in promoting cell motility. CPT1A may represent a novel therapeutic target for the treatment of ARMS.
Assessment of the effect of insecticide-treated nets and indoor residual spraying for malaria control in three rural kebeles of Adami Tulu District, South Central Ethiopia
Authors: Bekele Damtew , Belyhun Yeshambel , Petros Beyene , Deressa Wakgari 
Published: April 2012

Abstract

Background
In the Adami Tulu District, indoor residual spraying (IRS) and insecticide-treated nets (ITNs) has been the main tool used to control malaria. The purpose of this study was to assess the effect of IRS and ITNs control strategies in Aneno Shisho kebele (lowest administrative unit of Ethiopia) compared with Kamo Gerbi (supplied ITN only) and Jela Aluto (no IRS and ITNs), with regards to the prevalence of malaria and mosquito density.

Methods
Cross-sectional surveys were conducted after heavy rains (October/November, 2006) and during the sporadic rains (April, 2007) in the three kebeles of Adami Tulu District. Malaria infection was measured by means of thick and thin film. Monthly collection of adult mosquitoes from October-December 2006 and April-May 2007 and sporozoite enzyme-linked immunosorbent assay (ELISA) on the collected mosquitoes were detected. Data related to the knowledge of mode of malaria transmission and its control measures were collected. Data collected on parasitological and knowledge, attitude and practice (KAP) surveys were managed and analysed using a statistical computer program SPSS version 13.0. A P-value <0.05 was considered to be statistically significant.

Results
The overall prevalence of malaria was 8.6% in Jela Aluto, 4.4% in Kamo Gerbi and 1.3% in Aneno Shisho in the two season surveys. The vector, Anopheles gambiae s.l., Anopheles pharoensis and Anopheles coustani were recorded. However, sporozoite ELISA on mosquito collections detected no infection. The difference in overall malaria prevalence and mosquito density between the three kebeles was significant (P<0.05).

Conclusions
The present study has provided some evidence for the success of ITNs/IRS combined malaria control measures in Aneno Shisho kebele in Adami Tulu District. Therefore, the combined ITNs/IRS malaria control measures must be expanded to cover all kebeles in the District of Ethiopia.
Lymph-node ratio is an independent prognostic factor in patients with stage III colorectal cancer: a retrospective study from the Middle East
Authors: Elias Elias , Mukherji Deborah , Faraj Walid , Khalife Mohammad , Dimassi Hani , Eloubeidi Mohamad , Hattoum Hasan , Abou-Alfa Ghassan K , Saleh Ahmad , Shamseddine Ali 
Published: April 2012

Abstract

Background
In this retrospective study, we evaluated the prognostic effect of positive lymph-node ratio (pLNR) on patients with stage III colorectal cancer (CRC). Our paper is the first analysis, to our knowledge, to deal with such data from the Middle East.

Methods
We analyzed the clinicopathological data of 535 patients diagnosed with colorectal cancer at our institution between 1983 and 2003. The 164 patients diagnosed with stage III disease were divided into two categories based on lymph-node ratio (LNR) being the ratio of positive lymph nodes over total lymph nodes dissected: LNR ≤0.4 and LNR >0.4. We used Kaplan-Meier and Cox proportional hazard models to evaluate the prognostic effect of pLNR.

Results
The 10-year survival rate for the patients with stage IIIA, IIIB and IIIC cancers were 76%, 56% and 0% respectively (P = 0.014). Using pLNR of 0.4 as the cutoff point was found to yield clinically and significant results, with a significant difference in the outcomes of patients with pLNR ≤0.4 compared to those with pLNR >0.4 (hazard ratio = 5.25, 95% confidence interval = 1.2 to 22.1, P = 0.02).

Conclusion
The ratio-based staging (pLNR) of CRC is a more accurate and clinically useful prognostic method than the number of positive LNs resected or the total number of LNs retrieved for predicting the course of patients with stage III CRC.
Skp2 expression unfavorably impacts survival in resectable esophageal squamous cell carcinoma
Authors: Liang Yi , Hou Xue , Cui Qian , Kang Tie-Bang , Fu Jian-Hua , Zhang Lan-Jun , Luo Rong-Zhen , He Jie-Hua , Zeng Yi-Xin , Yang Hao-Xian 
Published: April 2012

Abstract

Background
The correlation of S-phase kinase–associated protein 2 (Skp2) with metastasis and prognosis in esophageal squamous cell carcinoma (ESCC) is controversial. The purpose of this study was to explore whether there was a correlation between the expression of Skp2 evaluated by immunohistochemistry and the clinical outcome of patients with operable ESCC, and to further determine the possible mechanism of the impact of Skp2 on survival.

Methods
Tissue microarrays that included 157 surgically resected ESCC specimens was successfully generated for immunohistochemical evaluation. The clinical/prognostic significance of Skp2 expression was analyzed. Kaplan-Meier analysis was used to compare the postoperative survival between groups. The prognostic impact of clinicopathologic variables and Skp2 expression was evaluated using a Cox proportional hazards model. A cell proliferation assay and a colony formation assay were performed in ESCC cell lines to determine the function of Skp2 on the progression of ESCC in vitro.

Results
Skp2 expression correlated closely with the T category (p = 0.035) and the pathological tumor-node-metastasis (TNM) stage (p = 0.027). High expression of Skp2 was associated with poor overall survival in resectable ESCC (p = 0.01). The multivariate Cox regression analysis demonstrated that pathological T category, pathological N category, cell differentiation, and negative Skp2 expression were independent factors for better overall survival. In vitro assays of ESCC cell lines demonstrated that Skp2 promoted the proliferative and colony-forming capacity of ESCCs.

Conclusions
Negative Skp2 expression in primary resected ESCC is an independent factor for better survival. Skp2 may play a pro-proliferative role in ESCC cells.
Proteomic analysis of HIV-1 Nef cellular binding partners reveals a role for exocyst complex proteins in mediating enhancement of intercellular nanotube formation
Authors: Mukerji Joya , Olivieri Kevin C , Misra Vikas , Agopian Kristin A , Gabuzda Dana 
Published: April 2012

Abstract

Background
HIV-1 Nef protein contributes to pathogenesis via multiple functions that include enhancement of viral replication and infectivity, alteration of intracellular trafficking, and modulation of cellular signaling pathways. Nef stimulates formation of tunneling nanotubes and virological synapses, and is transferred to bystander cells via these intercellular contacts and secreted microvesicles. Nef associates with and activates Pak2, a kinase that regulates T-cell signaling and actin cytoskeleton dynamics, but how Nef promotes nanotube formation is unknown.

Results
To identify Nef binding partners involved in Pak2-association dependent Nef functions, we employed tandem mass spectrometry analysis of Nef immunocomplexes from Jurkat cells expressing wild-type Nef or Nef mutants defective for the ability to associate with Pak2 (F85L, F89H, H191F and A72P, A75P in NL4-3). We report that wild-type, but not mutant Nef, was associated with 5 components of the exocyst complex (EXOC1, EXOC2, EXOC3, EXOC4, and EXOC6), an octameric complex that tethers vesicles at the plasma membrane, regulates polarized exocytosis, and recruits membranes and proteins required for nanotube formation. Additionally, Pak2 kinase was associated exclusively with wild-type Nef. Association of EXOC1, EXOC2, EXOC3, and EXOC4 with wild-type, but not mutant Nef, was verified by co-immunoprecipitation assays in Jurkat cells. Furthermore, shRNA-mediated depletion of EXOC2 in Jurkat cells abrogated Nef-mediated enhancement of nanotube formation. Using bioinformatic tools, we visualized protein interaction networks that reveal functional linkages between Nef, the exocyst complex, and the cellular endocytic and exocytic trafficking machinery.

Conclusions
Exocyst complex proteins are likely a key effector of Nef-mediated enhancement of nanotube formation, and possibly microvesicle secretion. Linkages revealed between Nef and the exocyst complex suggest a new paradigm of exocyst involvement in polarized targeting for intercellular transfer of viral proteins and viruses.
Hemodynamic effects of peri-operative statin therapy in on-pump cardiac surgery patients
Authors: Hinz Jose , Gehoff Philipp , Schotola Hanna , Hosseini Morteza Tavakkoli , Didilis Vassilios N , Jebran Ahmad Fawad , Gehoff Anastasia , Wiese Christoph H , Schulz Egbert Godehard , Schoendube Friedrich Albert , Popov Aron Frederik 
Published: April 2012

Abstract

Background
Peri-operative statin therapy in cardiac surgery cases is reported to reduce the rate of mortality, stroke, postoperative atrial fibrillation, and systemic inflammation. Systemic inflammation could affect the hemodynamic parameters and stability. We set out to study the effect of statin therapy on perioperative hemodynamic parameters and its clinical outcome.

Methods
In a single center study from 2006 to 2007, peri-operative hemodynamic parameters of 478 patients, who underwent cardiac surgery with cardiopulmonary bypass, were measured. Patients were divided into those who received perioperative statin therapy (n = 276; statin group) and those who did not receive statin therapy (n = 202; no-statin group). The two groups were compared together using Kolmogorov-Smirnov-Test, Fisher’s-Exact-Test, and Student’s-T-test. A p value < 0.05 was considered as significant.

Results
There was no significant difference in the preoperative risk factors. Onset of postoperative atrial fibrillation was not affected by statin therapy. Extended hemodynamic measurements revealed no significant difference between the two groups, apart from Systemic Vascular Resistance Index (SVRI) . The no-statin group had a significantly higher SVRI (882 ± 206 vs. 1050 ± 501 dyn s/cm5/m2, p = 0.022). Inotropic support was the same in both groups and no significant difference in the mortality rate was noticed. Also, hemodynamic parameters were not affected by different types and doses of statins.

Conclusions
Perioperative statin therapy for patients undergoing on-pump coronary bypass grafting or valvular surgery, does not affect the hemodynamic parameters and its clinical outcome.