bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hon-yaku: a biology-driven Bayesian methodology for identifying translation initiation sites in prokaryotes
Authors: Makita Yuko , de Hoon Michiel JL , Danchin Antoine 
Published: February 2007

Abstract

Background
Computational prediction methods are currently used to identify genes in prokaryote genomes. However, identification of the correct translation initiation sites remains a difficult task. Accurate translation initiation sites (TISs) are important not only for the annotation of unknown proteins but also for the prediction of operons, promoters, and small non-coding RNA genes, as this typically makes use of the intergenic distance. A further problem is that most existing methods are optimized for Escherichia coli data sets; applying these methods to newly sequenced bacterial genomes may not result in an equivalent level of accuracy.

Results
Based on a biological representation of the translation process, we applied Bayesian statistics to create a score function for predicting translation initiation sites. In contrast to existing programs, our combination of methods uses supervised learning to optimally use the set of known translation initiation sites. We combined the Ribosome Binding Site (RBS) sequence, the distance between the translation initiation site and the RBS sequence, the base composition of the start codon, the nucleotide composition (A-rich sequences) following start codons, and the expected distribution of the protein length in a Bayesian scoring function. To further increase the prediction accuracy, we also took into account the operon orientation. The outcome of the procedure achieved a prediction accuracy of 93.2% in 858 E. coli genes from the EcoGene data set and 92.7% accuracy in a data set of 1243 Bacillus subtilis 'non-y' genes. We confirmed the performance in the GC-rich Gamma-Proteobacteria Herminiimonas arsenicoxydans, Pseudomonas aeruginosa, and Burkholderia pseudomallei K96243.

Conclusion
Hon-yaku, being based on a careful choice of elements important in translation, improved the prediction accuracy in B. subtilis data sets and other bacteria except for E. coli. We believe that most remaining mispredictions are due to atypical ribosomal binding sequences used in specific translation control processes, or likely errors in the training data sets.
FlowerPower: clustering proteins into domain architecture classes for phylogenomic inference of protein function
Authors: Krishnamurthy Nandini , Brown Duncan , Sjölander Kimmen 
Published: February 2007

Abstract

Background
Function prediction by transfer of annotation from the top database hit in a homology search has been shown to be prone to systematic error. Phylogenomic analysis reduces these errors by inferring protein function within the evolutionary context of the entire family. However, accuracy of function prediction for multi-domain proteins depends on all members having the same overall domain structure. By contrast, most common homolog detection methods are optimized for retrieving local homologs, and do not address this requirement.

Results
We present FlowerPower, a novel clustering algorithm designed for the identification of global homologs as a precursor to structural phylogenomic analysis. Similar to methods such as PSIBLAST, FlowerPower employs an iterative approach to clustering sequences. However, rather than using a single HMM or profile to expand the cluster, FlowerPower identifies subfamilies using the SCI-PHY algorithm and then selects and aligns new homologs using subfamily hidden Markov models. FlowerPower is shown to outperform BLAST, PSI-BLAST and the UCSC SAM-Target 2K methods at discrimination between proteins in the same domain architecture class and those having different overall domain structures.

Conclusion
Structural phylogenomic analysis enables biologists to avoid the systematic errors associated with annotation transfer; clustering sequences based on sharing the same domain architecture is a critical first step in this process. FlowerPower is shown to consistently identify homologous sequences having the same domain architecture as the query.

Availability
FlowerPower is available as a webserver at http://phylogenomics.berkeley.edu/flowerpower/.
Alterated integrin expression in lichen planopilaris
Authors: d'Ovidio Roberto , Sgarra Concetta , Conserva Anna , Angelotti Umberto Filippo , Erriquez Roberta , Foti Caterina 
Published: February 2007

Abstract

Background
Lichen planopilaris (LPP) is an inflammatory disease characterized by a lymphomononuclear infiltrate surrounding the isthmus and infundibulum of the hair follicle of the scalp, that evolves into atrophic/scarring alopecia. In the active phase of the disease hairs are easily plucked with anagen-like hair-roots. In this study we focused on the expression of integrins and basement membrane components of the hair follicle in active LPP lesions.

Methods
Scalp biopsies were taken in 10 patients with LPP and in 5 normal controls. Using monoclonal antibodies against α3β1 and α6β4 integrins we showed the expression of these integrins and of the basement membrane components of the hair follicle in active LPP lesions and in healthy scalp skin.

Results
In the LPP involved areas, α3β1 was distributed in a pericellular pattern, the α6 subunit was present with a basolateral distribution while the β4 subunit showed discontinuous expression at the basal pole and occasionally, basolateral staining of the hair follicle. Conclusion: An altered distribution of the integrins in active LPP lesions can explain the phenomenon of easy pulling-out of the hair with a "gelatinous" root-sheath.
Dual roles of the transmembrane protein p23/TMP21 in the modulation of amyloid precursor protein metabolism
Authors: Vetrivel Kulandaivelu S , Gong Ping , Bowen James W , Cheng Haipeng , Chen Ying , Carter Meghan , Nguyen Phuong D , Placanica Lisa , Wieland Felix T , Li Yue-Ming , Kounnas Maria Z , Thinakaran Gopal 
Published: February 2007

Abstract

Background
Alzheimer's disease (AD) is characterized by cerebral deposition of β-amyloid (Aβ) peptides. Aβ is released from ectodomain cleaved amyloid precursor protein (APP) via intramembranous proteolysis by γ-secretase, a complex consisting of presenilin and a few other proteins. p23/TMP21, a member of the p24 family type I transmembrane proteins, was recently identified as a presenilin complex component capable of modulating γ-secretase cleavage. The p24 family proteins form oligomeric complexes and regulate vesicular trafficking in the early secretory pathway, but their role in APP trafficking has not been investigated.

Results
Here, we report that siRNA-mediated depletion of p23 in N2a neuroblastoma and HeLa cells produces concomitant knockdown of additional p24 family proteins and increases secretion of sAPP. Furthermore, intact cell and cell-free Aβ production increases following p23 knockdown, similar to data reported earlier using HEK293 cells. However, we find that p23 is not present in mature γ-secretase complexes isolated using an active-site γ-secretase inhibitor. Depletion of p23 and expression of a familial AD-linked PS1 mutant have additive effects on Aβ42 production. Knockdown of p23 expression confers biosynthetic stability to nascent APP, allowing its efficient maturation and surface accumulation. Moreover, immunoisolation analyses show decrease in co-residence of APP and the APP adaptor Mint3. Thus, multiple lines of evidence indicate that p23 function influences APP trafficking and sAPP release independent of its reported role in γ-secretase modulation.

Conclusion
These data assign significance to p24 family proteins in regulating APP trafficking in the continuum of bidirectional transport between the ER and Golgi, and ascribe new relevance to the regulation of early trafficking in AD pathogenesis.
Protein, iron, and meat consumption and risk for rheumatoid arthritis: a prospective cohort study
Authors: Benito-Garcia Elizabeth , Feskanich Diane , Hu Frank B , Mandl Lisa A , Karlson Elizabeth W 
Published: February 2007

Abstract
A recent prospective study showed that higher consumption of red meat and total protein was associated with increased risk for inflammatory polyarthritis. We therefore prospectively examined the relationship between diet (in particular, protein, iron, and corresponding food sources) and incident rheumatoid arthritis (RA) among 82,063 women in the Nurses' Health Study. From 1980 to 2002, 546 incident cases of RA were confirmed by a connective tissue disease screening questionnaire and medical record review for American College of Rheumatology criteria for RA. Diet was assessed at baseline in 1980 and five additional times during follow up. We conducted Cox proportional hazards analyses to calculate the rate ratio of RA associated with intakes of protein (total, animal, and vegetable) and iron (total, dietary, from supplements, and heme iron) and their primary food sources, adjusting for age, smoking, body mass index, and reproductive factors. The multivariate models revealed no association between RA and any measure of protein or iron intake. In comparisons of highest with lowest quintiles of intake, the rate ratio for total protein was 1.17 (95% confidence interval 0.89–1.54; P for trend = 0.11) and for total iron it was 1.04 (95% confidence interval 0.77–1.41; P for trend = 0.82). Red meat, poultry, and fish were also not associated with RA risk. We were unable to confirm that there is an association between protein or meat and risk for RA in this large female cohort. Iron was also not associated with RA in this cohort.
Dipeptidyl peptidase 8/9-like activity in human leukocytes
Authors: Maes Marie-Berthe , Dubois Véronique , Brandt Inger , Lambeir Anne-Marie , Van der Veken Pieter , Augustyns Koen , Cheng Jonathan D , Chen Xin , Scharpé Simon , De Meester Ingrid 
Published: February 2007

AbstractThe proline-specific dipeptidyl peptidases (DPPs) are emerging as a protease family with important roles in the regulation of signaling by peptide hormones. Inhibitors of DPPs have an intriguing, therapeutic potential, with clinical efficacy seen in patients with diabetes. Until now, only recombinant forms of DPP8 and DPP9 have been characterized. Their enzymatic activities have not been demonstrated in or purified from any natural source. Using several selective DPP inhibitors, we show that DPP activity, attributable to DPP8/9 is present in human PBMC. All leukocyte types tested (lymphocytes, monocytes, Jurkat, and U937 cells) were shown to contain similar DPP8/9-specific activities, and DPPII- and DPPIV-specific activities varied considerably. The results were confirmed by DPPIV/CD26 immunocapture experiments. Subcellular fractionation localized the preponderance of DPP8/9 activity to the cytosol and DPPIV in the membrane fractions. Using Jurkat cell cytosol as a source, a 30-fold, enriched DPP preparation was obtained, which had enzymatic characteristics closely related to the ones of DPP8 and/or -9, including inhibition by allo-Ile-isoindoline and affinity for immobilized Lys-isoindoline.
Circulating 25-Hydroxyvitamin D Levels Predict Survival in Early-Stage Non–Small-Cell Lung Cancer Patients
Authors: Zhou Wei , Heist Rebecca S. , Liu Geoffrey , Asomaning Kofi , Neuberg Donna S. , Hollis Bruce W. , Wain John C. , Lynch Thomas J. , Giovannucci Edward , Su Li , Christiani David C. 
Published: February 2007

Purpose Our previous analyses suggested that surgery in the summertime with higher vitamin D intake is associated with improved survival in patients with early-stage non–small-cell lung cancer (NSCLC). We further investigated the results of circulating 25-hydroxyvitamin D (25[OH]D) levels on overall survival (OS) and recurrence-free survival (RFS) in NSCLC patients. Patients and Methods Among 447 patients with early-stage NSCLC, data were analyzed using Cox proportional hazards models, adjusting for age, sex, stage, smoking, and treatment. Results The median follow-up time was 72 months (range, 0.2 to 141), with 161 recurrences and 234 deaths. For OS, the adjusted hazard ratio (AHR) was 0.74 (95% CI, 0.50 to 1.10; Ptrend = .07) for the highest versus lowest quartile of 25(OH)D levels. Stratified by stage, a strong association was observed among stage IB-IIB patients (AHR, 0.45; 95% CI, 0.24 to 0.82; Ptrend = .002), but not among stage IA patients (AHR, 1.10; 95% CI, 0.62 to 1.96; Ptrend = .53). Similar effects of 25(OH)D levels were observed among the 309 patients with dietary information (AHR, 0.74; 95% CI, 0.46 to 1.17; Ptrend = .19). For the joint effects of 25(OH)D level and vitamin D intake, the combined high 25(OH)D levels and high vitamin D intake (by median) were associated with better survival than the combined low 25(OH)D levels and low vitamin D intake (AHR, 0.64; 95% CI, 0.42 to 0.98; Ptrend = .06). Again, stronger associations were observed among stage IB-IIB than IA patients. Similar effects of 25(OH)D levels and vitamin D intake were observed for RFS. Conclusion Vitamin D may be associated with improved survival of patients with early-stage NSCLC, particularly among stage IB-IIB patients.
An Investigation on Time-Interval Optimisation of Traffic Noise Measurement
Authors: Abbaspour Madjid , Golmohammadi Rostam , Nassiri Parvin , Mahjub Hossien 
Published: February 2007

Noise is one of the most important sources of pollution in metropolitan areas, it causes discomfort for urban residents and hampers the efficiency of the work force. Currently, there is an urgent need to conduct basic studies on this issue in order to attain a mathematical model for prediction of traffic noise levels in the major cities of Iran. This article is the result of research conducted in the city of Hamadan in 2005 with the ultimate objective of setting up a traffic noise model based on the traffic conditions of Iranian cities. For this study, main access roads of Hamadan city were divided in 64 segments and after careful considerations, 94 measuring stations were assigned to them. For the optimisation of noise measurement intervals in each station and the determination of background noise impact on the main traffic noise, 30 stations with the specifications of the target stations were randomly selected at the pilot stage. In all the pilot stations, the background sound pressure level (SPLb), Leq, SPLmax, L10 were measured simultaneously in 10, 30 and 60 minute intervals (in random non-holiday days at random hours). The measurements were made 3 meters away from the road side. Pilot results indicated that the mean equivalent sound pressure levels at the measuring stations in 10, 30 and 60 minute intervals were 70.76±2.11 dBA, 30 minutes 70.88±2.19 dBA, and 60 minutes 70.93±2.13dBA respectively. The mean background sound pressure level at the stations was 60.77±5.04 dBA. The results of the traffic noise measurements at the research stations through the comparison of mean values (Variance Analysis) indicated that there is no meaningful deviation between the Leq in the above-mentioned time intervals (10, 30 and 60 minutes) in the hourly measurements (P= 0.998). In the pilot phase, it was determined that the background noise level did not impose a considerable impact on the main traffic noise and it was possible to make 10-minute interval measurements to forecast the 30-minute and 60-minute interval equivalent levels. Therefore in the main phase of study with the utilisation of the 10-minute interval results collected from each of the 94 stations, a total of 282 measurements including 2 daily-hour and one nightly-hour measurements were conducted. The final results revealed that the average Leq in all stations was 69.04±4.25 dBA, the average speed of vehicles was 44.57±11.46 km/hr and average traffic load was 1231.9±910.2 V/hr. Moreover, the results indicated that the Leq in the studied roads were exceeding the allowable levels of urban noise pollution and there was a meaningful deviation between equivalent levels during a 24-hour period, traffic load and various vehicle speeds (P= 0.003).
Cloning: National and International Law
Authors: Kuppuswamy Chamundeeswari 
Published: February 2007

AbstractGovernance of cloning is a controversial national and international issue. It has occupied the time of legislatures across different countries and even the United Nations General Assembly. Despite attempts at obtaining clarity and coherence in rules governing human reproductive and therapeutic cloning, many countries have adopted a vague and uncertain policy. This is in the nature of the issue under consideration, given that rapid advancements in science and technology can quickly make laws redundant. As law increasingly moves in to regulate private matters of citizens, it takes a big risk, in terms of becoming outdated soon and being poorly enforced. This article delves into the laws and policies of a cross section of countries in an attempt to succinctly present the state of the law in cloning research and other allied areas. This is followed by an international public law approach to governance of cloning, in the light of the 2005 declaration on human cloning.
Editorial
Authors: Spranger Tade M 
Published: February 2007

AbstractInter- and supranational law knows many examples of specific biotech regulations. The Convention on Biological Diversity with its so-called Biosafety Protocol deals with the access to and use of genetic resources as well as security issues like labelling of living modified organisms. The Council of Europe's Convention on Human Rights and Biomedicine, which is also completed by several Additional Protocols, aims at setting basic standards for biomedical research, especially in the field of patient's rights. The UNESCO contributed (legally non binding) Declarations on the Human Genome and Human Genetic Data. The European Union and the Andean Community established legal frameworks for selected areas of biomedicine and gene technology. However, despite the need for uniform standards in this field, international law does not form a coherent set of norms. According to
From ethical advice to legal regulation: History and practise of Research Ethics Committees in Germany
Authors: Fuchs Michael , Heyer Martin , Berbuir Alexander 
Published: February 2007

AbstractSince many years the Federal Republic of Germany has an extensive system of ethics committees responsible for reviewing research projects on human subjects. The legal context of their work is complex and can only be understood from a perspective that takes into account the federalism enshrined in the German Constitution, with its division of functions between the federal government (
The Sex-Determining Locus in the Tiger Pufferfish,Takifugu rubripes
Authors: Kikuchi Kiyoshi , Kai Wataru , Hosokawa Ayumi , Mizuno Naoki , Suetake Hiroaki , Asahina Kiyoshi , Suzuki Yuzuru 
Published: February 2007

AbstractThe tiger pufferfish (fugu), Takifugu rubripes, is a model fish that has had its genome entirely sequenced. By performing genomewide linkage analyses, we show that the sex of fugu is determined by a single chromosomal region on linkage group 19 in an XX–XY system.
Ssh4, Rcr2 and Rcr1 Affect Plasma Membrane Transporter Activity in Saccharomyces cerevisiae
Authors: Kota Jhansi , Melin-Larsson Monika , Ljungdahl Per O , Forsberg Hanna 
Published: February 2007

Abstract
Nutrient uptake in the yeast Saccharomyces cerevisiae is a highly regulated process. Cells adjust levels of nutrient transporters within the plasma membrane at multiple stages of the secretory and endosomal pathways. In the absence of the ER-membrane-localized chaperone Shr3, amino acid permeases (AAP) inefficiently fold and are largely retained in the ER. Consequently, shr3 null mutants exhibit greatly reduced rates of amino acid uptake due to lower levels of AAPs in their plasma membranes. To further our understanding of mechanisms affecting AAP localization, we identified SSH4 and RCR2 as high-copy suppressors of shr3 null mutations. The overexpression of SSH4, RCR2, or the RCR2 homolog RCR1 increases steady-state AAP levels, whereas the genetic inactivation of these genes reduces steady-state AAP levels. Additionally, the overexpression of any of these suppressor genes exerts a positive effect on phosphate and uracil uptake systems. Ssh4 and Rcr2 primarily localize to structures associated with the vacuole; however, Rcr2 also localizes to endosome-like vesicles. Our findings are consistent with a model in which Ssh4, Rcr2, and presumably Rcr1, function within the endosome–vacuole trafficking pathway, where they affect events that determine whether plasma membrane proteins are degraded or routed to the plasma membrane.
Highly Variable Patterns of Linkage Disequilibrium in Multiple Soybean Populations
Authors: Hyten David L , Choi Ik-Young , Song Qijian , Shoemaker Randy C , Nelson Randall L , Costa Jose M , Specht James E , Cregan Perry B 
Published: February 2007

AbstractProspects for utilizing whole-genome association analysis in autogamous plant populations appear promising due to the reported high levels of linkage disequilibrium (LD). To determine the optimal strategies for implementing association analysis in soybean (Glycine max L. Merr.), we analyzed the structure of LD in three regions of the genome varying in length from 336 to 574 kb. This analysis was conducted in four distinct groups of soybean germplasm: 26 accessions of the wild ancestor of soybean (Glycine soja Seib. et Zucc.); 52 Asian G. max Landraces, the immediate results of domestication from G. soja; 17 Asian Landrace introductions that became the ancestors of North American (N. Am.) cultivars, and 25 Elite Cultivars from N. Am. In G. soja, LD did not extend past 100 kb; however, in the three cultivated G. max groups, LD extended from 90 to 574 kb, likely due to the impacts of domestication and increased self-fertilization. The three genomic regions were highly variable relative to the extent of LD within the three cultivated soybean populations. G. soja appears to be ideal for fine mapping of genes, but due to the highly variable levels of LD in the Landraces and the Elite Cultivars, whole-genome association analysis in soybean may be more difficult than first anticipated.
XI.—Notes on Spanish Sources of Molière
Authors: Morley S. Griswold 
Published: February 2007

The object of this article is to call attention to certain cases of close resemblance between passages in Molière's plays and others taken from Spanish literature or connected with it. Except in details where credit is duly given to the discoverer, none of these cases has ever before been noted, to my knowledge.It is seldom possible to decide categorically whether or no these parallels are genuine instances of borrowing by Molière, or merely coincidences of thought and expression. Therefore I am content usually to leave the judgment to the reader, after putting the facts before him.
The Use of the Conditional Perfect for the Conditional Present in Italian
Authors: Goggio Charles 
Published: February 2007

Characteristic of the Italian Language is the modern use of the conditional perfect instead of the present. This interchange of tenses is not permitted by either of her two living sister languages, French and Spanish. Nor does English admit such constructions: we are not allowed to say, for example, “He said he should have done it tomorrow,” but must say, “He said he would do it tomorrow.” In Italian on the other hand, there are numerous examples of this construction as the following quotations will illustrate:“Ma se avessi alcuno luogo di fuori, in nel qual fusse persona che tu fidare te ne potessi, io direi che tu la Pippa quine mandassi, et aresti fuggito il pericolo tuo e quello della tua donna, che la dei piu amare che te.” Sercambi.