bluuebunny/crossref_metadata_2025 huggingface dataset:
Calculating cyclotomic polynomials
Authors: Arnold Andrew , Monagan Michael
Published: February 2011

We present three algorithms to calculate

Φ
n

(
z
)

\Phi _n(z)

, the

n

t
h

n_{th}

cyclotomic polynomial. The first algorithm calculates

Φ
n

(
z
)

\Phi _n(z)

by a series of polynomial divisions, which we perform using the fast Fourier transform. The second algorithm calculates

Φ
n

(
z
)

\Phi _n(z)

as a quotient of products of sparse power series. These two algorithms, described in detail in the paper, were used to calculate cyclotomic polynomials of large height and length. In particular, we have found the least

n
n

for which the height of

Φ
n

(
z
)

\Phi _n(z)

is greater than

n
n

,

n
2

n^2

,

n
3

n^3

, and

n
4

n^4

, respectively. The third algorithm, the big prime algorithm, generates the terms of

Φ
n

(
z
)

\Phi _n(z)

sequentially, in a manner which reduces the memory cost. We use the big prime algorithm to find the minimal known height of cyclotomic polynomials of order five. We include these results as well as other examples of cyclotomic polynomials of unusually large height, and bounds on the coefficient of the term of degree

k
k

for all cyclotomic polynomials.
Annotating genes and genomes with DNA sequences extracted from biomedical articles
Authors: Haeussler Maximilian , Gerner Martin , Bergman Casey M.
Published: February 2011

Motivation: Increasing rates of publication and DNA sequencing make the problem of finding relevant articles for a particular gene or genomic region more challenging than ever. Existing text-mining approaches focus on finding gene names or identifiers in English text. These are often not unique and do not identify the exact genomic location of a study.

Results: Here, we report the results of a novel text-mining approach that extracts DNA sequences from biomedical articles and automatically maps them to genomic databases. We find that ∼20% of open access articles in PubMed central (PMC) have extractable DNA sequences that can be accurately mapped to the correct gene (91%) and genome (96%). We illustrate the utility of data extracted by text2genome from more than 150 000 PMC articles for the interpretation of ChIP-seq data and the design of quantitative reverse transcriptase (RT)-PCR experiments.

Conclusion: Our approach links articles to genes and organisms without relying on gene names or identifiers. It also produces genome annotation tracks of the biomedical literature, thereby allowing researchers to use the power of modern genome browsers to access and analyze publications in the context of genomic data.

Availability and implementation: Source code is available under a BSD license from http://sourceforge.net/projects/text2genome/ and results can be browsed and downloaded at http://text2genome.org.

Contact:  maximilianh@gmail.com

Supplementary information:  Supplementary data are available at Bioinformatics online.
Sediment accumulation and bioturbation rates in the deep Northeast Atlantic determined by radiometric techniques
Authors: Carvalho Fernando P. , Oliveira João M. , Soares António M. M.
Published: February 2011

Carvalho, F. P., Oliveira, J. M., and Soares, A. M. M. 2011. Sediment accumulation and bioturbation rates in the deep Northeast Atlantic determined by radiometric techniques. – ICES Journal of Marine Science, 68: . The upper layers of boxcore bottom-sediment samples from the Porcupine Abyssal Plain (five cores) and from the Iberian Abyssal Plain (eight cores) in the Northeast Atlantic were analysed for porosity, grain size, organic carbon, calcium carbonate, and radionuclides. Radiometric ages of sediment layers were determined using 230Th excess (the 230Thexc/232Th ratio method) and 14C radionuclides. Sediment accumulation rates were 0.14 and 3.2 cm kyear−1 at the Porcupine and Iberian Abyssal Plains, respectively. Sediment mixing, determined through 210Pb excess, was in the upper 5–11 cm sediment layer, likely as a result of infauna activity. Biodiffusion coefficients averaged 0.40 ± 0.37 and 1.05 ± 1.02 cm2 year–1 and were not significantly different in the sediments of either abyssal plain. The low rates of sediment accumulation and bioturbation in the abyssal depths of the Northeast Atlantic suggested that immobilization of sediment-reactive man-made radionuclides released near the seafloor will take place very slowly and with limited sediment burial.
New Insights Into the Pathogenesis of Inflammatory Bowel Disease: Transcription Factors Analysis in Bioptic Tissues From Pediatric Patients
Authors: Pierdomenico Maria , Stronati Laura , Costanzo Manuela , Vitali Roberta , Di Nardo Giovanni , Nuti Federica , Oliva Salvatore , Cucchiara Salvatore , Negroni Anna
Published: February 2011

Objectives:

Our work is aimed at identifying ex vivo new transcription factors, potentially involved in the pathogenesis of pediatric inflammatory bowel disease (IBD), by using a microarray approach.

Patients and Methods:

Microarray, including 84 transcription factors, was performed in inflamed and uninflamed mucosal tissues of pediatric patients with Crohn disease (CD) and in healthy controls. Real‐time polymerase chain reaction was used to confirm microarray results on a larger size of CD and patients with ulcerative colitis (UC). Protein expression was evaluated by Western blot assay.

Results:

Microarray assay showed 40 genes differentially regulated in the inflamed mucosa and 17 in the uninflamed mucosa of patients with CD as compared with controls. Real‐time polymerase chain reaction analysis revealed 10 transcripts in CD and 4 in UC, selected among those with higher differences as compared with healthy controls, significantly overexpressed in the inflamed tissues of patients. Moreover, 4 transcripts in CD and 2 in UC were found significantly upregulated in the uninvolved tissue. A further investigation evidenced an increased protein expression of activating transcription factor 3 and hypoxia‐inducible transcription factor‐1α in patients with CD as well as in Caco2 cell line stimulated by cytokines and hypoxia.

Conclusions:

The present study shows an evident upregulation of several transcription factors in the inflamed and uninflamed mucosa of children with IBD, suggesting that the inflammatory process is somehow activated at molecular levels even in the macroscopically normal mucosa of patients. A differential pattern of gene expression between CD and UC indicates distinct molecular mechanisms underlying the pathogenesis of 2 diseases. Finally, activating transcription factor 3 and hypoxia‐inducible transcription factor‐1α are proposed as new transcription factors potentially involved in the onset and maintenance of IBD.
Helicobacter pylori Eradication and Change in Markers of Iron Stores Among Non–iron‐deficient Children in El Paso, Texas: An Etiologic Intervention Study
Authors: Cardenas Victor M , Prieto‐Jimenez Carmen A , Mulla Zuber D , Rivera Jose O , Dominguez Delfina C , Graham David Y , Ortiz Melchor
Published: February 2011

Objectives:

We assessed whether Helicobacter pylori eradication was followed by changes in iron stores among non–iron‐deficient children.

Materials and Methods:

Double‐blind randomized intervention trial on 110 asymptomatic 3‐ to 10‐year‐olds with H pylori infection assigned to any of the following 4 arms: both quadruple eradication and iron supplementation, either quadruple sequential eradication or iron supplementation, or placebo only. Hemoglobin, transferrin saturation, and serum ferritin were measured at baseline and 8 months later to assess changes according to study arm, H pylori infection status at ≥45 days, and cytotoxin‐associated gene product A status.

Results:

Intent‐to‐treat (n = 110) and per‐protocol (n = 90) analyses revealed no differences across study arms in changes of iron stores. However, we found that those who had their infection eradicated had a 3‐fold increased average change from baseline serum ferritin compared with that of children who remained infected (P < 0.05). Eradication of infection by cytotoxin‐associated gene product A negative strains was associated with a larger ferritin increase.

Conclusions:

In this double‐blind randomized trial, the first among non–iron‐deficient, asymptomatic H pylori–infected children living in the contiguous United States, we found no effect of H pylori eradication regarding changes in iron stores. However, those who had their infection eradicated at follow‐up had a significantly larger increase in serum ferritin from baseline.
Hepatitis B virus X protein overcomes all-trans retinoic acid-induced cellular senescence by downregulating levels of p16 and p21 via DNA methylation
Authors: Park Sun-Hye , Jung Jin Kyu , Lim Joo Song , Tiwari Indira , Jang Kyung Lib
Published: February 2011

Despite current molecular evidence suggesting that hepatitis B virus (HBV) X protein (HBx) plays an important role during HBV-mediated hepatocarcinogenesis, the detailed mechanism is still controversial. Here, it was shown that HBx overcomes cellular senescence provoked by all-trans retinoic acid (ATRA) in HepG2 cells, as demonstrated by the impaired induction of irreversible G1 arrest and senescence-associated β-galactosidase activity by ATRA in the presence of HBx. The anti-senescence effect of HBx was also observed in another human hepatoma cell line, Hep3B, but not in Huh-7 cells in which the p16 and p21 proteins are absent. In addition, HBx suppressed ATRA-mediated induction of p16 and p21 in HepG2 cells via promoter hypermethylation, resulting in inactivation of retinoblastoma protein. Furthermore, the ability of HBx to overcome ATRA-induced cellular senescence almost completely disappeared when the levels of p16 and p21 in the HBx-expressing cells became similar to those in the control cells by complementation in the former by exogenous expression, knockdown of their expression in the latter using specific small interfering RNA or treatment with a DNA methylation inhibitor, 5-Aza-2′-deoxycytidine. These results suggest that HBx executes its potential by downregulating levels of p16 and p21 via DNA methylation. As cellular senescence is a tumour-suppression process, the present study provides a new strategy by which HBV promotes hepatocarcinogenesis.
Anti‐platelet therapy: cyclo‐oxygenase inhibition and the use of aspirin with particular regard to dual anti‐platelet therapy
Authors: Warner Timothy D. , Nylander Sven , Whatling Carl
Published: February 2011

Aspirin and P2Y12 antagonists are commonly used anti‐platelet agents. Aspirin produces its effects through inhibition of thromboxane A2 (TXA2) production, while P2Y12 antagonists attenuate the secondary responses to ADP released by activated platelets. The anti‐platelet effects of aspirin and a P2Y12 antagonist are often considered to be separately additive. However, there is evidence of an overlap in effects, in that a high level of P2Y12 receptor inhibition can blunt TXA2 receptor signalling in platelets and reduce platelet production of TXA2. Against this background, the addition of aspirin, particularly at higher doses, could cause significant reductions in the production of prostanoids in other tissues, e.g. prostaglandin I2 from the blood vessel wall. This review summarizes the data from clinical studies in which dose‐dependent effects of aspirin on prostanoid production have been evaluated by both plasma and urinary measures. It also addresses the biology underlying the cardiovascular effects of aspirin and its influences upon prostanoid production throughout the body. The review then considers whether, in the presence of newer, more refined P2Y12 receptor antagonists, aspirin may offer less benefit than might have been predicted from earlier clinical trials using more variable P2Y12 antagonists. The possibility is reflected upon, that when combined with a high level of P2Y12 blockade the net effect of higher doses of aspirin could be removal of anti‐thrombotic and vasodilating prostanoids and so a lessening of the anti‐thrombotic effectiveness of the treatment.
Outcome of children treated with haematopoietic‐stem cell transplantations from donors expressing the rare C77G variant of the PTPRC (CD45) gene
Authors: Samaan Samaan , Guérin‐El Khourouj Valérie , Auboeuf Didier , Peltier Lucas , Pédron Béatrice , Ouachée‐Chardin Marie , Gourgouillon Nadége , Baruchel André , Dalle Jean‐Hugues , Sterkers Ghislaine
Published: February 2011

The uncommon C77G polymorphism of the Protein‐Tyrosine Phosphatase (PTPRC) gene (PTPRC; previously termed CD45) could confer an increased risk of immunopathology. This study compared the outcome of children following human leucocyte antigen‐matched unrelated haematopoïetic‐stem cell transplantations (HSCT) from donors carrying (C77G cases: n = 8) or not (controls: n = 36) the PTPRC C77G polymorphism. Transmission of the PTPRC C77G polymorphism through the graft was suggested by unusual CD45RA phenotype in the donors and/or in the recipients after, but not before HSCT. Restriction‐Fragment Length Polymorphism and sequencing confirmed the polymorphism. Overall survival rates were similar in C77G cases and controls (63% vs. 61%). Acute leukaemia relapse tended to be less frequent in C77G cases (0% vs. 32%; P = 0·09). Among recipients surviving ≥30 d, acute GVHD (aGVHD) ≥ grade 2 tended to be more frequent (100% vs. 58%; P = 0·07) and the rate of steroid‐refractory or –dependant aGVHD higher (67% vs. 28%) in C77G cases. Finally, extensive chronic GVHD tended to occur more frequently (40% vs. 9%) in C77G cases. Recovery of lymphocyte subsets and virus‐specific CD4 was similar in C77G cases and controls while interleukin 2 (IL2)‐responses through CD3 stimulation were higher in C77G cases (P = 0·004). In conclusion, HSCT from PTPRC C77G donors could increase GVHD risk without compromising overall survival. Altered IL2‐responses could be involved in this process.
The use of complementary and alternative medicine among chronic renal failure patients
Authors: Akyol Asiye D , Yildirim Yasemin , Toker Emel , Yavuz Betul
Published: February 2011

Aims and objectives.  The aim of this study is to evaluate the factors affecting the use and frequency of use of complementary and alternative medicine among chronic renal failure patients.

Background.  The use of complementary and alternative medicine in the general population and patients with chronic renal failure has increased significantly. Despite this, there is limited information concerning the use of complementary and alternative medicine among chronic renal failure patients.

Design.  Cross‐sectional survey.

Method.  The research was carried out at the nephrology and internal medicine outpatient clinics. Two hundred and six chronic renal failure patients admitted to the outpatient clinics were included in the study. Mean outcomes measures were the frequency and type of complementary and alternative medicine use, demographic and disease‐related characteristics affecting complementary and alternative medicine use and the reasons for using complementary and alternative medicine. The data were evaluated by Pearson’s chi‐square test and Fisher’s exact test.

Results.  While 2·9% of the patients had been using complementary and alternative medicine before the renal disease occurred, 25·2% of the patients reported that they had at least once used complementary and alternative medicine methods after the renal disease occurred. A significant difference was found between complementary and alternative medicine usage and age, gender, place of living, occupational status and educational background (p < 0·05). While most of the patients using complementary and alternative medicine (78·3%) stated that they used such methods as a cure for their disease, 46·1% used body–mind techniques.

Conclusions.  The results of our study showed that one‐fourth of the chronic renal failure patients were using complementary and alternative medicine, mainly body–mind techniques. In addition, the study proved that most of the patients do not discuss their complementary and alternative medicine usage with their doctors and nurses.

Relevance to clinical practice.  It is essential that nephrology doctors and nurses should ask specific questions about complementary and alternative medicine usage while taking anamnesis on the patients’ disease and nutritional status and that the nephrology team should expand their knowledge on complementary and alternative medicine methods to ensure patient and treatment safety.
The role of health care assistants in supporting district nurses and family carers to deliver palliative care at home: findings from an evaluation project
Authors: Ingleton Christine , Chatwin John , Seymour Jane , Payne Sheila
Published: February 2011

Aims and objectives.  To examine the role of trained health and personal care assistants in supporting district nurses and family carers in providing palliative and end of life care in the community.

Background.  In the UK, there is a policy directive to improve end of life care and to enable greater numbers of people to die at home. This places considerable demands on community nursing services and family carers. In response to this, the Complex and Palliative Continuing Care Service employing generic health and personal care assistants was developed as part of the Marie Curie Delivering Choice Programme in one city in the UK. This paper draws on findings from an independent evaluation of the scheme.

Design.  The wider evaluation used a formative evaluation methodology.

Method.  This paper draws on in‐depth interviews with a range of stakeholders (n = 17), in‐depth interviews with bereaved carers (n = 6) and an analysis of documentation.

Results.  Stakeholders and bereaved carers perceived that the health and personal care assistants made a vital contribution to community palliative care. Careful recruitment, specific training, case management by district nursing with allocation of specific tasks and close ongoing communication were key features which stakeholders indentified. Family carers welcomed the way assistants developed relationships and became familiar and able to meet the care needs of patients. There were some problems reported which related to capacity, work flow and the need for extensive written care plans.

Conclusion.  Employing health care assistants under the supervision of district nurses appears to support patients and family at home during end of life care and contribute to good quality nursing care.

Relevance to clinical practice.  The needs for community‐based palliative and end of life care will increase rapidly over the course of the next 20 years, placing pressure on community nursing services and family carers.
Development and psychometric evaluation of the German version of the Medication Regimen Complexity Index (MRCI‐D)
Authors: Stange Dorit , Kriston Levente , Langebrake Claudia , Cameron Lynda K. , Wollacott John D. , Baehr Michael , Dartsch Dorothee C.
Published: February 2011

Background  Several factors contribute to the complexity of pharmacotherapeutic regimens, like the total number of medications to be taken, the number of dosage units to take at a time, dosage frequency, as well as specific directions concerning the administration. The Medication Regimen Complexity Index (MRCI) is a validated instrument developed in English for the measurement of the complexity of a given pharmacotherapeutic regimen.

Objectives  Translation of the MRCI into German and evaluation of the translated instrument (MRCI‐D) in order to make it more easily accessible for use in German practice and research.

Methods  The process of validation included the translation of the English version to German, back‐translation into English, comparison of the back‐translated and the original versions, pre‐tests, and pilot‐testing of the German version by three raters using 20 medication regimens for inpatients. The subsequent psychometric evaluation included the calculation of inter‐rater and test–retest reliability, as well as the assessment of convergent validity.

Results  The number of medications correlated highly and statistically significantly with the MRCI‐D score (0.91, P < 0.001), indicating sufficient convergent validity of the instrument. Both inter‐rater and test–retest reliability were very high (intraclass correlation coefficients above 0.80 in all cases).

Conclusion  Our results demonstrate that the German version of the MRCI reflects the complexity of therapeutic regimens with similar validity and reliability as the established English version. Thus, it may be a valuable tool to analyse therapeutic regimens in both clinical practice and science.
The use of fentanyl‐patch in dogs undergoing spinal surgery: plasma concentration and analgesic efficacy
Authors: BELLEI E. , RONCADA P. , PISONI L. , JOECHLER M. , ZAGHINI A.
Published: February 2011

Bellei, E., Roncada, P., Pisoni, L., Joechler, M., Zaghini, A. The use of fentanyl‐patch in dogs undergoing spinal surgery: plasma concentrations and analgesic efficacy.J. vet. Pharmacol. Therap.34, 437–441.

Objectives of this study were to evaluate plasma concentrations and analgesic efficacy of fentanyl administered transdermically in dogs undergoing spinal surgery. At the end of the surgery and before awakening, a fentanyl‐patch was applied and was maintainedin situfor 72 h. Blood samples were taken before the application of the patch, at 2, 4, 6, 8, 10, 12, 18, 24, 32, 40, 48, 60, and 72 h after application and then 2, 4, 6, 8, 10, and 12 h after its removal. Before each blood sampling, pain evaluation was carried out using the Glasgow pain score, appropriately modified. Plasma concentrations of fentanyl were determined using a specific immuno‐enzymatic kit. In this study, the minimum analgesic plasma concentration (0.23 ng/mL) required to achieve analgesia in human and considered to apply also for dogs was reached in all animals. No animal showed pain in the range of ‘intense pain’; in two cases, the level of the pain was slight or moderate. No undesired effects were found. Results suggest that the use of transdermic patches could represent a valid aid in pain therapy in small animals; in particular, it contributes to the postoperative well‐being of patients undergoing major surgery.
The role of small intestinal bacterial overgrowth in postgastrectomy patients
Authors: Paik C. N. , Choi M.‐G. , Lim C. H. , Park J. M. , Chung W. C. , Lee K.‐M. , Jun K.‐H. , Song K. Y. , Jeon H. M. , Chin H.‐M. , Park C. H. , Chung I.‐S.
Published: February 2011

Background  Small intestinal bacterial overgrowth (SIBO) is expected in postgastrectomy patients; however, its role has not been clarified. This study was to estimate the prevalence of SIBO and investigate the clinical role of SIBO in postgastrectomy patients.

Methods  This prospective study involved 76 patients who underwent gastrectomy for early gastric cancer with no evidence of recurrence. An H2–CH4 breath test with oral glucose challenge test was performed to diagnose SIBO and dumping syndrome. Sigstad dumping questionnaires, serum glucose, hematocrit and pulse rate were simultaneously monitored for every 30 min for 3 hours.

Key Results  There were significant differences in SIBO between the postgastrectomy patients and controls (77.6%vs 6.7%, P < 0.01). Abdominal fullness or borborygmus during oral glucose load were more common in SIBO‐positive than in negative patients (50.8%vs 17.6%, P = 0.03), and were the independent factors for predicting SIBO in postgastrectomy patients (P = 0.02). The prevalences of dumping syndrome and hypoglycemia after oral glucose were 35 (46.1%) and 19 (25.0%), and were not different between both groups. However, the plasma glucose was significantly lower in SIBO‐positive than in SIBO‐negative patients at 120 and 150 min after oral glucose load (P < 0.05). No significant differences were observed in pulse rate and hematocrit in both groups.

Conclusions & Inferences  SIBO is common among postgastrectomy patients. It appears to be associated with postprandial intestinal symptoms and might aggravate late hypoglycemia. SIBO could be a new therapeutic target for managing intestinal symptoms in postgastrectomy patients.
Flow Cytometric Analysis of TCR Vβ Repertoire in Patients with 22q11.2 Deletion Syndrome
Authors: McLean‐Tooke A. , Barge D. , Spickett G. P. , Gennery A. R.
Published: February 2011

In 22q11.2 deletion patients, the normal decrease in T lymphocyte counts after 1–2 years is blunted such that relatively T lymphocyte numbers increase over early childhood, probably via post‐thymic expansion of peripheral lymphocytes. This may leave less T lymphocyte receptor (TCR) diversity than when derived from naive thymic emigrants. We analysed TCR Vβ repertoire on 27 22q11.2 chromosome deletion patients. No patient had infection at sampling. CD3+CD4+ recent thymic emigrants (RTEs) were identified by CD45RA and CD31 expression. TCR Vβ repertoire was determined using four‐colour flow cytometry. Patients and controls showed significant TCR Vβ family usage differences between CD3+CD4+ and CD3+CD4− T lymphocyte subpopulations. Vβ family abnormalities (±3 SD of controls) were identified in 18/27 (67%) patients and 12/47 (25%) controls. In patients, the magnitude of expansions was increased, with some Vβ families representing 37% of the cells present in the subpopulations. There was a significant increase in frequency of abnormalities in CD3+CD4+ (P < 0.001) and CD3+CD4− T lymphocytes (P < 0.05) in patients. A total of 11/16 patients had an abnormal CD4+CD25Bright TCR Vβ repertoire. There was no difference in expansions/contractions between CD4+CD25Bright and CD4+ T lymphocyte repertoires (P = 0.575) for individual patients but significant differences in expansions/contractions between CD4+CD25Bright and CD8+ T lymphocytes repertoires (P = 0.011). There was bias in Vβ usage between CD3+CD4+ and CD3+CD4− T lymphocyte subsets. A total of 67% patients had TCR Vβ repertoire abnormalities, with a trend towards increased repertoire abnormalities with fewer RTEs, suggesting thymic output plays an important role in TCR repertoire diversity. There was no correlation between skewed repertoire and symptoms of infection or autoimmunity.
Determinants of Experimental Allergic Responses: Interactions Between Allergen Dose, Sex and Age
Authors: Hansen J. S. , Alberg T. , Rasmussen H. , Lovik M. , Nygaard U. C.
Published: February 2011

The prevalence of allergic diseases is influenced by sex and age. Although mouse models are widely used in allergy research, few experimental studies have examined the interaction effects of sex and age on allergy outcomes. Our aim was to investigate the individual and combined effects of sex and age on allergic sensitization and inflammation in two mouse models: an intraperitoneal (i.p.) and an intranasal (i.n.) sensitization model. We also investigated how the allergen immunization dose interacted with age and sex in the i.p. model. Female and male mice were immunized i.p. or i.n. with ovalbumin when 1, 6 or 20 weeks old. In both models, allergen challenges were performed by i.n. delivery. Serum antibodies, draining lymph node cytokine release and airway inflammatory responses were assessed. In the i.p. model, the antibody and cytokine levels and airway inflammation were highly influenced by immunization dose and age. The responses increased with age when using a low immunization dose, but decreased with age when using a high immunization dose. In the i.n. model, antibody production and airway tissue inflammation increased with age. Female compared with male mice generally developed more pronounced antibody and inflammatory responses. Relative to older mice, juvenile mice had augmented airway inflammation to allergen exposures. The study demonstrates that immunization dose, sex and age are highly influential on allergy outcomes. To better mimic different life stages of human allergic airway disease, murine models, therefore, require careful optimization.
Interleukin‐4 Gene Polymorphisms Confer Behçet’s Disease in Turkish Population
Authors: Oral H. B. , Dilek K. , Özçimen A. A. , Taşkapılıoğlu Ö. , Bingöl Ü. , Sarandöl A. , Sarıcaoğlu H. , Yurtkuran M. , Yurtkuran M. A.
Published: February 2011

Several cytokine genes may play crucial roles in host susceptibility to Behçet’s Disease (BD), because the cytokine production capacity varies among individuals and depends on the cytokine gene polymorphisms. The association of the IL‐4 and IL‐4Rα gene polymorphisms with the susceptibility to BD was investigated in this study. DNA samples were obtained from a Turkish population of 97 patients with BD and 76 healthy control subjects. All genotyping (IL‐4 and IL‐4Rα) experiments were performed using PCR sequence‐specific primers. When compared with the healthy controls, the frequency of IL‐4 −1098 TG and −590 CT genotypes was higher in the patients with BD. Analysis of allele frequencies showed that IL‐4 −1098 G and IL‐4 −590 T alleles were more common in the patients with BD when compared with healthy controls. Also, IL‐4 TTC and haplotypes were found to confer BD. Interestingly, we demonstrated that IL‐4Rα gene polymorphism seems to be associated with the Pathergy test positivity in patients with BD. Our data suggest that IL‐4 gene promoter polymorphisms may affect susceptibility to BD and increase risk of developing the disease. However, in order to confirm and assess the association of IL‐4 and IL‐4Rα gene polymorphisms with the BD, large cohort studies are needed.
Distinct evolutionary patterns ofOryza glaberrimadeciphered by genome sequencing and comparative analysis
Authors: Sakai Hiroaki , Ikawa Hiroshi , Tanaka Tsuyoshi , Numa Hisataka , Minami Hiroshi , Fujisawa Masaki , Shibata Michie , Kurita Kanako , Kikuta Ari , Hamada Masao , Kanamori Hiroyuki , Namiki Nobukazu , Wu Jianzhong , Itoh Takeshi , Matsumoto Takashi , Sasaki Takuji
Published: February 2011

Here we present the genomic sequence of the African cultivated rice,Oryza glaberrima, and compare these data with the genome sequence of Asian cultivated rice,Oryza sativa. We obtained gene‐enriched sequences ofO. glaberrimathat correspond to about 25% of the gene regions of theO. sativa(japonica) genome by methylation filtration and subtractive hybridization of repetitive sequences. While patterns of amino acid changes did not differ between the two species in terms of the biochemical properties, genes ofO. glaberrimagenerally showed a larger synonymous–nonsynonymous substitution ratio, suggesting thatO. glaberrimahas undergone a genome‐wide relaxation of purifying selection. We further investigated nucleotide substitutions around splice sites and found that eight genes ofO. sativaexperienced changes at splice sites after the divergence fromO. glaberrima. These changes produced novel introns that partially truncated functional domains, suggesting that these newly emerged introns affect gene function. We also identified 2451 simple sequence repeats (SSRs) from the genomes ofO. glaberrimaandO. sativa. Although tri‐nucleotide repeats were most common among the SSRs and were overrepresented in the protein‐coding sequences, we found that selection against indels of tri‐nucleotide repeats was relatively weak in both African and Asian rice. Our genome‐wide sequencing ofO. glaberrimaand in‐depth analyses provide rice researchers not only with useful genomic resources for future breeding but also with new insights into the genomic evolution of the African and Asian rice species.
A meta‐analysis of Th2 pathway genetic variants and risk for allergic rhinitis
Authors: Bunyavanich Supinda , Shargorodsky Josef , Celedón Juan C.
Published: February 2011

To cite this article: Bunyavanich S, Shargorodsky J, Celedón JC. A meta‐analysis of Th2 pathway genetic variants and risk for allergic rhinitis. Pediatric Allergy Immunology 2011; 22: 378–387.

There is a significant genetic contribution to allergic rhinitis (AR). Genetic association studies for AR have been performed, but varying results make it challenging to decipher the overall potential effect of specific variants. The Th2 pathway plays an important role in the immunological development of AR. We performed meta‐analyses of genetic association studies of variants in Th2 pathway genes and AR. PubMed and Phenopedia were searched by double extraction for original studies on Th2 pathway‐related genetic polymorphisms and their associations with AR. A meta‐analysis was conducted on each genetic polymorphism with data meeting our predetermined selection criteria. Analyses were performed using both fixed and random effects models, with stratification by age group, ethnicity, and AR definition where appropriate. Heterogeneity and publication bias were assessed. Six independent studies analyzing three candidate polymorphisms and involving a total of 1596 cases and 2892 controls met our inclusion criteria. Overall, the A allele of IL13 single nucleotide polymorphism (SNP) rs20541 was associated with increased odds of AR (estimated OR = 1.2; 95% CI 1.1–1.3, p‐value 0.004 in fixed effects model, 95% CI 1.0–1.5, p‐value 0.056 in random effects model). The A allele of rs20541 was associated with increased odds of AR in mixed age groups using both fixed effects and random effects modeling. IL13 SNP rs1800925 and IL4R SNP 1801275 did not demonstrate overall associations with AR. We conclude that there is evidence for an overall association between IL13 SNP rs20541 and increased risk of AR, especially in mixed‐age populations.
Successful pegylated interferon alpha2a monotherapy for hepatitis C virus infection in a transplanted patient who relapsed after the preceding course
Authors: Ichikawa T. , Taura N. , Miyaaki H. , Matsuzaki M. , Eguchi S. , Takatsuki M. , Kanematsu T. , Nakao K.
Published: February 2011

T. Ichikawa, N. Taura, H. Miyaaki, M. Matsuzaki, S. Eguchi, M. Takatsuki, T. Kanematsu, K. Nakao. Successful pegylated interferon alpha2a monotherapy for hepatitis C virus infection in a transplanted patient who relapsed after the preceding course. Transpl Infect Dis 2011: 13: 438–440. All rights reserved
A comparative study of the homologous Lpm‐system allotypes of alpha‐macroglobulins in American mink and Gp‐system allotypes of alpha‐macroglobulin in domestic pig
Authors: Yermolaev V. I. , Mirtskhoulava E. G. , Savina M. A. , Gorelov I. G. , Mitichashvili R. S. , Baranov O. K.
Published: February 2011

This paper summarizes our results with allotyping of alpha‐macroglobulins in pig and the comparative results with their homologs in mink. In p.g, 5 allotypes of α‐macroglobulins, αM1, αM2, αM3AB, αM4, and αM5ab were identified. It was found that αM1, a marker of α‐macroglobulin in pig, is homologous to human α2‐macroglobulin and mink α2‐macroglobulin; αM2‐αM5, the markers of the second isotypic variant of α‐macroglobulin in pig, are homologous to mink Lpm‐macroglobulin (α1M).

The results of the International comparison test (ISABR, 1987–1988) have demonstrated αM1 is new and αM2‐αM5 correspond to the four allotypes of the Gp‐system in pig (Janik et al. 1983). It is concluded that the pig Gp and mink Lpm systems are homologous. Because the studied allotypes belong to α‐macroglobulins, their controlling locus is designated as the AM‐locus. The same designation is suggested for the homologous mink locus (instead of the previous Lpm). The genetic control of 5 allotypes of pig is analysed. The structure of the pig AM‐locus is described in detail, and its organization is compared with the mink homologous locus.

Vergleichende Untersuchung von α‐Makroglobulin Allotypen des Lpm Systems beim Nerz und des Gp‐Systems beim Hausschwein

Diese Veröffentlichung faßt unsere Ergebnisse bezüglich der Allotypen von α‐Makroglobulin des Schweines und die vergleichenden Ergebnisse ihrer Homologe beim Nerz zusammen. Beim Schwein wurden 5 Allotypen des α‐Makroglobulins (αM1, αM2, αM3, αM4 und αM5) identifiziert. Das αM1, ein Marker des α‐Makroglobulins des Schweines, ist homolog zu dem menschlichen α2‐Makroglobulin und dem α2‐Makroglobulin des Nerzes; αM2−αM5, Marker der zweiten isotopischen Variante des α‐Makroglobulin, sind dem Nerz Lpm‐Macroglobulin (α1M) homolog.

Die Ergebnisse des Internationalen Vergleichstestes (ISABR, 1987–1988) hatten demonstriert, daß αM1 neu ist, und daß αM2−αM5 mit den vier Allotypen des Gp‐Systems vergleichbar sind (Janik et al. 1983). Es wird daraus geschlossen, daß Schweine Gp und Nerz Lpm‐System homolog ist. Da die untersuchten Allotypen dem α‐Makroglobulin angehören, wird ihr kontrollierender Locus AM‐Locus genannt. Die gleiche Benennung (statt der vorigen Lpm) wird für den homologen Nerz Locus vorgeschlagen. Die genetische Steuerung der 5 Allotypen des Schweines sind damit auch analysiert, die Struktur des Schweine AM‐Locus beschrieben, und seine Organisation ist mit der homologen des Nerz‐Locus verglichen.
Feed intake, utilization, and the residual component in early‐ and late‐feathering broiler breeder dams
Authors: O'Sullivan N. P. , Dunnington E. A. , Siegel P. B.
Published: February 2011

Feed intake, feed efficiency, and residual feed consumption (RFC) were measured in broiler breeder females for 12 production periods of 28 days each. Experimental variables included 3 feeding regimens, 2 feed consistencies, and 2 sex‐linked feathering genotypes. The habituation of broiler breeders to feed restriction did not inhibit expression of hyperphagia when released to ad libitum feed. Long term obesity, but not short term weight gain, was detrimental to broiler breeder performance. The late‐feathering allele negatively influenced reproductive responses and feed utilization. Inconsistent quality of crumbles was associated with poorer performance both under ad libitum and restricted feeding regimens. There was considerable variation among groups of hens for RFC, associated with different genotypes and husbandry practices, suggesting that measurement of RFC may facilitate development of improved management guidelines.

Futteraufnahme, ‐verwertung und Restfutterverzehr bei früh und spätbefiedernden Mastmutterhennen

Die Messungen erfolgten bei Mastmutterhennen über 12 Produktionsperioden von je 28 Tagen. Versuchsvariable waren 3 Fütterungsmethoden, 2 Futterarten und 2 geschlechtsgekoppelte Befiederungs‐Genotypen. Die Anpassung der Masteltern an die Futterrestriktion hat Hyperphagie bei erneuter ad libitum Fütterung nicht behindert. Langfristiger Fettwuchs, aber nicht kurzfristiger Gewichtszuwachs verschlechterten die Leistung der Mastelterntiere. Das Spätbefiederungsallel hat Reproduktionsleistung und Futterverwertung negativ beeinflußt. Wechselnde Qualität der Futterarten mit schlechterer Leistung sowohl bei ad libitum wie bei restringierter Fütterung verbunden. Es existierte beträchtliche Variabiliät zwischen Hennengruppen hinsichtlich Restfutteraufnahme in Bezug auf unterschiedliche Genotypen und Haltungsmethoden, die vermuten lassen, daß Erhebung der Restfutteraufnahme die Entwicklung verbesserter Management Richtlinien erleichtern würde.
Estimation of genetic parameters for differently recorded fertility data in dairy cattle
Authors: Swalve H. H. , Topf C. , Langholz H.‐J.
Published: February 2011

In the present study data consisting of 244,189 service periods of heifers, first calf cows, and older cows were analyzed. In addition to the fixed effects usually incorporated in models for the analysis of female fertility (herd, year, season, etc.), the data could be differentiated as electronically recorded via a handheld computer or recorded as usual, i. e. handwritten receipts had been issued. The means of the fertility parameters in both data subsets were clearly different. However, this could not be attributed to the recording scheme. Estimates of heritabilities in general were low and in agreement with literature values. Heritability estimates within subsets of the data did not show an effect of the type of recording. Differencies in heritabilities were found between age groups with the highest values for heifers.

Schätzung genetischer Parameter für unterschiedlich erhobene Fruchtbarkeitsdaten beim Milchrind In der vorliegenden Arbeit wurden 244,189 Serviceperioden von Färsen, Erstkalbskühen und älteren Kühen ausgewertet. Zusätzlich zu den fixen Effekten, die üblicherweise in Modellen zur Analyse der weiblichen Fruchtbarkeit enthalten sind (Herden, Jahre, Saison etc.) konnten die Daten differenziert werden in einen Teil, der elektronisch mittels Handheld‐Computer aufgenommen worden war, und einen anderen Teil, welcher auf übliche Weise erhoben worden war, d. h. handgeschriebene Belege waren ausgestellt worden. Die Mittelwerte des Fruchtbarkeitsparameters in den beiden Teildatensätzen waren deutlich verschieden. Dies konnte allerdings nicht auf die Erhebungsart zurückgeführt werden. Schätzwerte für die Heritabilitäten waren allgemein niedrig und in guter Übereinstimmung mit Werten aus der Literatur. Innerhalb der Teildatensätze zeigte sich kein Unterschied in den Heritabilitätsschätzwerten je nach Art der Datenerhebung. Unterschiedliche Heritabilitäten wurden für die verschiedenen Altersgruppen gefunden, wobei die Schätzwerte für Färsen am höchsten waren.
Determination of bovine alpha S1‐casein alleles B and C by allele‐specific polymerase chain reaction
Authors: Schlee P. , Rottmann O.
Published: February 2011

Allele‐specific polymerase chain reaction was used to differentiate alleles B and C of the bovine αS1 casein gene. The method is simple, rapid and reliable. It allows genotyping of animals of any age or sex, so that identification of alleles can be used in cattle breeding.

Bestimmung der bovinen alpha S1‐Kaseinallele B und C mit der allelspezifischen Polymerase‐Kettenreaktion

Zur Unterscheidung der Allele B und C des bovinen αS1‐Kaseingens wurde allel‐spezifische PCR eingesetzt. Die Methode ist einfach, zuverlässig und schnell. Der Genotyp eines Tieres kann unabhängig vom Alter und Geschlecht bestimmt werden, was einen Einsatz in der Rinderzucht ermöglicht.
Effective size of selected populations with overlapping generations
Authors: Nomura T.
Published: February 2011

Genetisch wirksame Populationsgröße bei überlappenden Generationen

Schätzungsgleichungen für die genetisch wirksame Größe selekierter Populationen mit überlappenden Generationen wurde in Form der kumulativen Selektionswirkung auf Geläufigkeiten abgeleitet. Zur Überprüfung der Gleichung wurde eine Monte Carlo Simulation durchgeführt, die eine gute Übereinstimmung zu geschätzten Größen ergab. Aufgrund der abgeleiteten Gleichung werden einige Eigenschaften wirksame Größen selektierte Populationen mit überlappenden Generationen diskutiert.

A prediction equation for the effective size of selected populations with overlapping generations was derived, in terms of the cumulative effect of selection on gene frequency. Monte Carlo simulation was carried out to check the equation. The result showed that there is good agreement between observed and predicted values. Based on the form of the obtained equation, some properties of the effective size of selected populations with overlapping generations were discussed.
Changes in the additive variance of a fitness‐related trait with inbreeding in Tribolium castaneum
Authors: Ruano R. G. , Silvela L. S. , Lopez‐Fanjul C. , Toro M. A.
Published: February 2011

In Tribolium castaneum, a fitness‐related trait was defined as the total weight loss (TWL) of a vial after 21 days, due to the activity of a single pair of parents. TWL showed considerable inbreeding depression and strong heterosis. A significant increase in the heritability of TWL was observed with inbreeding. The results are compatible with the genetic variation of TWL in the base population being generated by segregation of a number of recessive alleles at low frequencies.

Cambio de la varianza aditiva de un componente principal de la eficacia biológica en Tribolium castenum con consanguinidad

Elcarácter “merma” (TWL) se define en Tribolium castaneum como la pérdida de peso que experimenta un pocillo de cristal que contiene medio alimenticioyuna pareja de Padre, debida a la actividad de esa pareja durante 21 días. Es, por tanto, un importante componente de la eficacia biológica. El caracter mostró considerable depresión por consanguinidad, fuerte heterosis en cruzamientosy, además, un significativo incremento de su heredabilidad con el del coeficiente de consanguinidad. Estos resultados son compatibles con que la variación genética del carácter en la población base se debiera a la scgregación de alelos recesivos con bajas frecuencias iniciales.

Änderung der additiv‐genetischen Varianz eines Fitness‐Merkmals bei Inzucht von Tnboleum castaneum

Das Fitness Merkmal wurde als Gewichtsverlust (TWL) eines Zuchtgefäßes mit Elternpaar und ihren Nachkommen in 21 Tagen definiert. TWL zeigte beträchtliche Inzuchtdepression und Heterosis. Durch Inzucht ergab sich eine signifikante Steigerung der additiv‐genetischen Varianz. Die Ergebnisse machen die Annahme wahrscheinlich, daß in der Ausgangsgeneration die genetische Variabilität von TWL durch Spaltung rezessiver Allele geringer Häufigkeit verursacht wurde.
Influence of selection on reaction to stress in mice. IV. Influence of fasting immobilization and exposure to cold on aminotransferases AspAT and AlAT in liver and kidney
Authors: Kołątaj A. , Stępkowska H. , Flak P.
Published: February 2011

The activity of alanine and asparagine aminotransferases in liver and kidney of 6‐week‐old mice, selected for high rates of weight gains, was compared to that in unselected mice. The effect of starvation, immobilization, and cold exposure on their stress reactivity was investigated. The decreases in AspAT and AlAT activity, caused by 24 and 48 h starvation, was higher in liver and kidney in selected mice than in unselected mice, respectively. The increases in AspAT and AlAT activity observed in liver and kidney, after 12 and 48 h immobilization and after cooling (5°C, 12 h), were higher in selected than in unselected mice. The results seem to indicate that mice selected for a high rate of body‐weight gain are less resistant to unfavourable factors in the environment—starvation, immobilization, cold exposure—in comparison with unselected animals.

Einfluss der Selektion auf Stressreaktion bei Mäusen

Bei Mäusen mit hohen Zuwachsraten, sowie bei Kontrolltieren, wurde der Einfluß eines 24 und 48 Stunden langen Fastens auf die Aktivität der Asparagin‐ und Alanin‐Aminotransferasen in der Leber und Niere untersucht. Die gleichen Untersuchungen wurden nach 12 Stunden Immobilisierung und 12 Stunden Unterkühlung (5°C) gemacht.

Nach der Hungerperiode wurde eine stärkere Aktivitätserniederung bei den selektionierten Mäusen im Vergleich zu den Kontrolltieren beobachtet. Im Gegensatz dazu, nach der Immobilisierung und der Unterkühlung, wurde ein signifikanten Anstieg der beiden Enzyme beobachtet, größer in den Geweben der Tiere mit hohen Zuwachsraten.

Die Ergebnisse deuten auf geringere Resistenz der selektionierten Tiere gegenüber Streßfaktoren, im Vergleich zu den Kontrolltieren.