bluuebunny/crossref_metadata_2025_split huggingface dataset:
Automatic detection of exonic splicing enhancers (ESEs) using SVMs
Authors: Mersch Britta , Gepperth Alexander , Suhai Sándor , Hotz-Wagenblatt Agnes 
Published: September 2008

Abstract

Background
Exonic splicing enhancers (ESEs) activate nearby splice sites and promote the inclusion (vs. exclusion) of exons in which they reside, while being a binding site for SR proteins. To study the impact of ESEs on alternative splicing it would be useful to have a possibility to detect them in exons. Identifying SR protein-binding sites in human DNA sequences by machine learning techniques is a formidable task, since the exon sequences are also constrained by their functional role in coding for proteins.

Results
The choice of training examples needed for machine learning approaches is difficult since there are only few exact locations of human ESEs described in the literature which could be considered as positive examples. Additionally, it is unclear which sequences are suitable as negative examples. Therefore, we developed a motif-oriented data-extraction method that extracts exon sequences around experimentally or theoretically determined ESE patterns. Positive examples are restricted by heuristics based on known properties of ESEs, e.g. location in the vicinity of a splice site, whereas negative examples are taken in the same way from the middle of long exons. We show that a suitably chosen SVM using optimized sequence kernels (e.g., combined oligo kernel) can extract meaningful properties from these training examples. Once the classifier is trained, every potential ESE sequence can be passed to the SVM for verification. Using SVMs with the combined oligo kernel yields a high accuracy of about 90 percent and well interpretable parameters.

Conclusion
The motif-oriented data-extraction method seems to produce consistent training and test data leading to good classification rates and thus allows verification of potential ESE motifs. The best results were obtained using an SVM with the combined oligo kernel, while oligo kernels with oligomers of a certain length could be used to extract relevant features.
Transcriptional profiling of pea ABR17 mediated changes in gene expression in Arabidopsis thaliana
Authors: Krishnaswamy Sowmya S , Srivastava Sanjeeva , Mohammadi Mohsen , Rahman Muhammad H , Deyholos Michael K , Kav Nat NV 
Published: September 2008

AbstractBackgroundPathogenesis-related proteins belonging to group 10 (PR10) are elevated in response to biotic and abiotic stresses in plants. Previously, we have shown a drastic salinity-induced increase in the levels of ABR17, a member of the PR10 family, in pea. Furthermore, we have also demonstrated that the constitutive expression of peaABR17cDNA inArabidopsis thalianaandBrassica napusenhances their germination and early seedling growth under stress. Although it has been reported that several members of the PR10 family including ABR17 possess RNase activity, the exact mechanism by which the aforementioned characteristics are conferred by ABR17 is unknown at this time. We hypothesized that a study of differences in transcriptome between wild type (WT) andABR17transgenicA. thalianamay shed light on this process.ResultsThe molecular changes brought about by the expression of peaABR17cDNA inA. thalianain the presence or absence of salt stress were investigated using microarrays consisting of 70-mer oligonucleotide probes representing 23,686Arabidopsisgenes. Statistical analysis identified number of genes which were over represented among up- or down-regulated transcripts in the transgenic line. Our results highlight the important roles of many abscisic acid (ABA) and cytokinin (CK) responsive genes inABR17transgenic lines. Although the transcriptional changes followed a general salt response theme in both WT and transgenic seedlings under salt stress, many genes exhibited differential expression patterns when the transgenic and WT lines were compared. These genes include plant defensins, heat shock proteins, other defense related genes, and several transcriptional factors. Our microarray results for selected genes were validated using quantitative real-time PCR.ConclusionTranscriptional analysis inABR17transgenicArabidopsisplants, both under normal and saline conditions, revealed significant changes in abundance of transcripts for many stress responsive genes, as well as those related to plant growth and development. Our results also suggest thatABR17may mediate stress tolerance through the modulation of many ABA- and CK-responsive genes and may further our understanding of the role of ABR17 in mediating plant stress responses.
Fish consumption and its motives in households with versus without self-reported medical history of CVD: A consumer survey from five European countries
Authors: Pieniak Zuzanna , Verbeke Wim , Perez-Cueto Federico , Brunsø Karen , De Henauw Stefaan 
Published: September 2008

Abstract

Background
The purpose of this study was to explore the cross-cultural differences in the frequency of fish intake and in motivations for fish consumption between people from households with (CVD+) or without (CVD-) medical history of cardiovascular disease, using data obtained in five European countries.

Methods
A cross-sectional consumer survey was carried out in November-December 2004 with representative household samples from Belgium, the Netherlands, Denmark, Poland and Spain. The sample consisted of 4,786 respondents, aged 18–84 and who were responsible for food purchasing and cooking in the household.

Results
Individuals from households in the CVD+ group consumed fish more frequently in Belgium and in Denmark as compared to those in the CVD- group. The consumption of fatty fish, which is the main sources of omega-3 PUFA associated with prevention of cardiovascular diseases, was on the same level for the two CVD groups in the majority of the countries, except in Belgium where CVD+ subjects reported to eat fatty fish significantly more frequently than CVD- subjects. All respondents perceived fish as a very healthy and nutritious food product. Only Danish consumers reported a higher subjective and objective knowledge related to nutrition issues about fish. In the other countries, objective knowledge about fish was on a low level, similar for CVD+ as for CVD- subjects, despite a higher claimed use of medical information sources about fish among CVD+ subjects.

Conclusion
Although a number of differences between CVD- and CVD+ subjects with respect to their frequency of fish intake are uncovered, the findings suggest that fish consumption traditions and habits – rather than a medical history of CVD – account for large differences between the countries, particularly in fatty fish consumption. This study exemplifies the need for nutrition education and more effective communication about fish, not only to the people facing chronic diseases, but also to the broader public. European consumers are convinced that eating fish is healthy, but particular emphasis should be made on communicating benefits especially from fatty fish consumption.
Generation and characterization of a human single-chain fragment variable (scFv) antibody against cytosine deaminase from Yeast
Authors: Mallano Alessandra , Zamboni Silvia , Carpinelli Giulia , Santoro Filippo , Flego Michela , Ascione Alessandro , Gellini Mara , Tombesi Marina , Podo Franca , Cianfriglia Maurizio 
Published: September 2008

Abstract

Background
The ability of cytosine deaminase (CD) to convert the antifungal agent 5-fluorocytosine (5-FC) into one of the most potent and largely used anticancer compound such as 5-fluorouracil (5-FU) raised considerable interest in this enzyme to model gene or antibody – directed enzyme-prodrug therapy (GDEPT/ADEPT) aiming to improve the therapeutic ratio (benefit versus toxic side-effects) of cancer chemotherapy. The selection and characterization of a human monoclonal antibody in single chain fragment (scFv) format represents a powerful reagent to allow in in vitro and in vivo detection of CD expression in GDEPT/ADEPT studies.

Results
An enzymatic active recombinant CD from yeast (yCD) was expressed in E. coli system and used as antigen for biopanning approach of the large semi-synthetic ETH-2 antibody phage library. Several scFvs were isolated and specificity towards yCD was confirmed by Western blot and ELISA. Further, biochemical and functional investigations demonstrated that the binding of specific scFv with yCD did not interfere with the activity of the enzyme in converting 5-FC into 5-FU.

Conclusion
The construction of libraries of recombinant antibody fragments that are displayed on the surface of filamentous phage, and the selection of phage antibodies against target antigens, have become an important biotechnological tool in generating new monoclonal antibodies for research and clinical applications. The scFvH5 generated by this method is the first human antibody which is able to detect yCD in routinary laboratory techniques without interfering with its enzymatic function.
Antibody response dynamics to the Plasmodium falciparum conserved vaccine candidate antigen, merozoite surface protein-1 C-terminal 19kD (MSP1-19kD), in Peruvians exposed to hypoendemic malaria transmission
Authors: Torres Katherine J , Clark Eva H , Hernandez Jean N , Soto-Cornejo Katherine E , Gamboa Dionicia , Branch OraLee H 
Published: September 2008

AbstractBackgroundIn high-transmission areas, developing immunity to symptomaticPlasmodium falciparuminfections requires 2–10 years of uninterrupted exposure. Delayed malaria-immunity has been attributed to difficult-to-develop and then short-lived antibody responses.MethodsIn a study area with <0.5P. falciparuminfections/person/year, antibody responses to the MSP1-19kD antigen were evaluated and associations withP. falciparuminfections in children and adults. In months surrounding and during the malaria seasons of 2003–2004, 1,772 participants received ≥6 active visits in one study-year. Community-wide surveys were conducted at the beginning and end of each malaria season, and weekly active visits were completed for randomly-selected individuals each month. There were 79P. falciparuminfections with serum samples collected during and approximately one month before and after infection. Anti-MSP1-19kD IgG levels were measured by ELISA.ResultsThe infection prevalence during February-July was similar in children (0.02–0.12 infections/person/month) and adults (0.03–0.14 infections/person/month) and was negligible in the four-month dry season. In children and adults, the seroprevalence was maintained in the beginning (children = 28.9%, adults = 61.8%) versus ending malaria-season community survey (children = 26.7%, adults = 64.6%). Despite the four-month non-transmission season, the IgG levels inPlasmodium-negative adults were similar toP. falciparum-positive adults. Although children frequently responded upon infection, the transition from a negative/low level before infection to a high level during/after infection was slower in children. Adults and children IgG-positive before infection had reduced symptoms and parasite density.ConclusionIndividuals in low transmission areas can rapidly develop and maintain αMSP1-19kD IgG responses for >4 months, unlike responses reported in high transmission study areas. A greater immune capacity might contribute to the frequent asymptomaticP. falciparuminfections in this Peruvian population.
An increase of cereal intake as an approach to weight reduction in children is effective only when accompanied by nutrition education: a randomized controlled trial
Authors: Rosado Jorge L , del R Arellano María , Montemayor Karina , García Olga P , Caamaño María del C 
Published: September 2008

AbstractBackgroundThe main emphasis of dietary advice for control of obesity has been on reducing dietary fat. Increasing ready to eat cereal (RTEC) consumption could be a strategy to reduce fat intake and increase carbohydrate intake resulting in a diet with lower energy density.Objectives1. To determine if an increase in RTEC intake is an effective strategy to reduce excess body weight and blood lipids in overweight or at risk of overweight children. 2. To determine if a nutrition education program would make a difference on the response to an increase in cereal intake. 3) To determine if increase in RTEC intake alone or with a nutrition education program has an effect on plasma lipid profile.Experimental designOne hundred and forty seven overweight or at risk of overweight children (6–12 y of age) were assigned to one of four different treatments: a. One serving of 33 ± 7 g of RTEC for breakfast; b. one serving of 33 ± 7 g of RTEC for breakfast and another one for dinner; c. one serving of 33 ± 7 g of RTEC for breakfast and a nutrition education program. d. Non intervention, control group. Anthropometry, body composition, physical activity and blood lipids were measured at baseline, before treatments, and 12 weeks after treatments.ResultsAfter 12 weeks of intervention only the children that received 33 ± 7 g of RTEC and nutrition education had significantly lower body weight [-1.01 (-1.69, -0.34) ], p < 0.01], lower BMI [-0.95 (-1.71, -0.20), p < 0.01] and lower total body fat [-0.71 (-1.71, 0.28), p < 0.05] compared with the control group [1.19 (0.39, 1.98), 0.01 (-0.38, 0.41), 0.44 (-0.46, 1.35) respectively]. Plasma triglycerides and VLDL were significantly reduced [-20.74 (-36.44, -5.05), -3.78 (-6.91, -0.64) respectively, p < 0.05] and HDL increased significantly [6.61 (2.15, 11.08), p < 0.01] only in this treatment group. The groups that received 1 or 2 doses of RTEC alone were not significantly different to the control group.ConclusionA strategy to increase RTEC consumption, as a source of carbohydrate, to reduce obesity is effective only when accompanied by nutrition education. The need for education could be extrapolated to other strategies intended for treatment of obesity.Trial RegistrationAustralian New Zealand Clincial Trial Registry. Request no: ACTRN12608000025336
The relationships among endurance performance measures as estimated from VO2PEAK, ventilatory threshold, and electromyographic fatigue threshold: a relationship design
Authors: Graef Jennifer L , Smith Abbie E , Kendall Kristina L , Walter Ashley A , Moon Jordan R , Lockwood Christopher M , Beck Travis W , Cramer Joel T , Stout Jeffrey R 
Published: September 2008

Abstract

Background
The use of surface electromyography has been accepted as a valid, non-invasive measure of neuromuscular fatigue. In particular, the electromyographic fatigue threshold test (EMGFT) is a reliable submaximal tool to identify the onset of fatigue. This study examined the metabolic relationship between VO2PEAK, ventilatory threshold (VT), and the EMGFT, as well as compared the power output at VO2PEAK, VT, and EMGFT.

Methods
Thirty-eight college-aged males (mean ± SD = 22.5 ± 3.5 yrs) performed an incremental test to exhaustion on an electronically-braked cycle ergometer for the determination of VO2PEAK and VT. Each subject also performed a discontinuous incremental cycle ergometer test to determine their EMGFT value, determined from bipolar surface electrodes placed on the longitudinal axis of the vastus lateralis of the right thigh. Subjects completed a total of four, 2-minute work bouts (ranging from 75–325 W). Adequate rest was given between bouts to allow for subjects' heart rate to drop within 10 beats of their resting heart rate. The EMG amplitude was averaged over 10-second intervals and plotted over the 2-minute work bout. The resulting slopes from each successive work bout were used to calculate EMGFT.

Results
Power outputs and VO2 values from each subject's incremental test to exhaustion were regressed. The linear equations were used to compute the VO2 value that corresponded to each fatigue threshold. Two separate one-way repeated measure ANOVAs indicated significant differences (p < 0.05) among metabolic parameters and power outputs. However, the mean metabolic values for VT (1.90 ± 0.50 l·min-1) and EMGFTVO2(1.84 ± 0.53 l·min-1) were not significantly different (p > 0.05) and were highly correlated (r = 0.750). Furthermore, the mean workload at VT was 130.7 ± 37.8 W compared with 134.1 ± 43.5 W at EMGFT (p > 0.05) with a strong correlation between the two variables (r = 0.766).

Conclusion
Metabolic measurements, as well as the power outputs at VT and EMGFT, were strongly correlated. The significant relationship between VT and EMGFT suggests that both procedures may reflect similar physiological factors associated with the onset of fatigue. As a result of these findings, the EMGFT test may provide an attractive alternative to estimating VT.
Allogeneic endometrial regenerative cells: An "Off the shelf solution" for critical limb ischemia?
Authors: Murphy Michael P , Wang Hao , Patel Amit N , Kambhampati Suman , Angle Niren , Chan Kyle , Marleau Annette M , Pyszniak Andrew , Carrier Ewa , Ichim Thomas E , Riordan Neil H 
Published: September 2008

Abstract
Critical limb ischemia (CLI) is an advanced form of peripheral artery disease which is responsible for approximately 100,000 amputations per year in the US. Trials to date have reported clinical improvement and reduced need for amputation in CLI patients receiving autologous bone marrow or mobilized peripheral blood stem cells for stimulation of angiogenesis. While such treatments are currently entering Phase III trials, practical and scientific pitfalls will limit widespread implementation if efficacy is proven. Hurdles to be overcome include: a) reduced angiogenic potential of autologous cells in aged patients with cardiovascular risk factors; b) invasiveness/adverse effects of bone marrow extraction and G-CSF mobilization, respectively; and c) need for on-site cellular manipulation. The Endometrial Regenerative Cell (ERC) is a mesenchymal-like stem cell derived from the menstrual blood that is believed to be associated with endometrial angiogenesis. We discuss the possibility of using allogeneic ERCs as an "off the shelf" treatment for CLI based on the following properties: a) High levels of growth factors and matrix metalloprotease production; b) Ability to inhibits inflammatory responses and lack of immunogenicity; and c) Expandability to great quantities without loss of differentiation ability or karyotypic abnormalities.
ICPD to MDGs: Missing links and common grounds
Authors: Abrejo Farina G , Shaikh Babar T , Saleem Sarah 
Published: September 2008

Abstract
The ICPD agenda of reproductive health was declared as the most comprehensive one, which had actually broadened the spectrum of reproductive health and drove the states to embark upon initiatives to improve reproductive health status of their populations. However, like all other countries, Pakistan also seems to have shifted focus of its policies and programs towards achieving MDGs. As a result, concepts highlighted in the ICPD got dropped eventually. In spite of specific goals on maternal and child mortalities in MDGs and all the investment and policy shift, Pakistan has still one of the highest maternal mortality ratios among developing countries. Lack of synchronized efforts, sector wide approaches, inter-sectoral collaboration, and moreover, the unmet need for family planning, unsafe abortions, low literacy rate and dearth of women empowerment are the main reasons. Being a signatory of both of the international agendas (ICPD and MDGs), Pakistan needed to articulate its policies to keep the balance between the two agendas. There are, however, certainly some common grounds which have been experimented by various countries and we can learn lessons from those best practices. An inter-sectoral cooperation and sector wide approaches would be required to achieve such ambitious goals set out in ICPD-Program of Action while working towards MDGs. There is a need of increasing resource allocation, strengthening primary health care services and emergency obstetric care and motivating the human resource employed in health sector by good governance. These endeavors should lead to formulate evidence based national policies, reproductive health services which are affordable, accessible and culturally acceptable and finally a responsive health system.
Impaired expression of mitochondrial and adipogenic genes in adipose tissue from a patient with acquired partial lipodystrophy (Barraquer-Simons syndrome): a case report
Authors: Guallar Jordi P , Rojas-Garcia Ricardo , Garcia-Arumi Elena , Domingo Joan C , Gallardo Eduardo , Andreu Antoni L , Domingo Pere , Illa Isabel , Giralt Marta , Villarroya Francesc 
Published: September 2008

AbstractIntroductionAcquired partial lipodystrophy or Barraquer-Simons syndrome is a rare form of progressive lipodystrophy. The etiopathogenesis of adipose tissue atrophy in these patients is unknown.Case presentationThis is a case report of a 44-year-old woman with acquired partial lipodystrophy. To obtain insight into the molecular basis of lipoatrophy in acquired partial lipodystrophy, we examined gene expression in adipose tissue from this patient newly diagnosed with acquired partial lipodystrophy. A biopsy of subcutaneous adipose tissue was obtained from the patient, and DNA and RNA were extracted in order to evaluate mitochondrial DNA abundance and mRNA expression levels.ConclusionThe expression of marker genes of adipogenesis and adipocyte metabolism, including the master regulatorPPARγ, was down-regulated in subcutaneous adipose tissue from this patient. Adiponectin mRNA expression was also reduced but leptin mRNA levels were unaltered. Markers of local inflammatory status were unaltered. Expression of genes related to mitochondrial function was reduced despite unaltered levels of mitochondrial DNA. It is concluded that adipogenic and mitochondrial gene expression is impaired in adipose tissue in this patient with acquired partial lipodystrophy.
Sciatica due to extrapelvic heterotopic ossification: A case report
Authors: Panagiotopoulos Elias C , Syggelos Spyros A , Plotas Athanasios , Tsigkas Gregorios , Dimopoulos Panagiotis 
Published: September 2008

Abstract

Introduction
Sciatica is a common problem, usually caused by disc herniation or spinal stenosis. Low back pain is also present in most cases. When sciatica is the unique clinical finding, especially in young patients, extraspinal pathology should be investigated.

Case presentation
We describe a rare case of sciatica in a 32-year-old man, which was developed as a complication of post-traumatic pelvic heterotopic ossification. During the operation, the sciatic nerve was found to be bluish, distorted and compressed in an hourglass fashion around a heterotopic bone mass. The heterotopic bone tissue, 4 cm in diameter, was removed and the patient had fully recovered 3 months after the operation.

Conclusion
In cases of sciatica without back pain, the possibility of direct pressure of the sciatic nerve from cysts, tumours or bone, as in the present case, should be considered.
Primary osteogenic sarcoma of the breast: A case report
Authors: Khan Shabuddin , Griffiths Ewen A , Shah Nigam , Ravi Srinivasan 
Published: September 2008

Abstract

Introduction
Primary osteosarcoma of the breast is a rare malignant tumour. It is typically a poor prognosis tumour, which has some interesting features worthy of discussion. We report a case of primary osteosarcoma of the breast and summarise the previous medical literature to highlight several details of this unusual tumour.

Case presentation
A 66-year-old Caucasian lady presented with painless lump in her right breast. Mammography showed features of fibroadenoma with calcification and fine needle aspiration cytology was reported as showing malignant cells (C5). Wide local excision was performed and histological features were consistent with primary osteosarcoma with predominance of osteoclastic activity. Subsequent completion mastectomy was performed because of suspicion of incomplete excision. She remains disease free 8 years from her initial surgery.