bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modified signal-to-noise: a new simple and practical gene filtering approach based on the concept of projective adaptive resonance theory (PART) filtering method
Authors: Takahashi Hiro , Honda Hiroyuki 
Published: April 2006

Abstract
Summary: Considering the recent advances in and the benefits of DNA microarray technologies, many gene filtering approaches have been employed for the diagnosis and prognosis of diseases. In our previous study, we developed a new filtering method, namely, the projective adaptive resonance theory (PART) filtering method. This method was effective in subclass discrimination. In the PART algorithm, the genes with a low variance in gene expression in either class, not both classes, were selected as important genes for modeling. Based on this concept, we developed novel simple filtering methods such as modified signal-to-noise (S2N′) in the present study. The discrimination model constructed using these methods showed higher accuracy with higher reproducibility as compared with many conventional filtering methods, including the t-test, S2N, NSC and SAM. The reproducibility of prediction was evaluated based on the correlation between the sets of U-test p-values on randomly divided datasets. With respect to leukemia, lymphoma and breast cancer, the correlation was high; a difference of &gt;0.13 was obtained by the constructed model by using &lt;50 genes selected by S2N′. Improvement was higher in the smaller genes and such higher correlation was observed when t-test, NSC and SAM were used. These results suggest that these modified methods, such as S2N′, have high potential to function as new methods for marker gene selection in cancer diagnosis using DNA microarray data.
Availability: Software is available upon request.
Contact: honda@nubio.nagoya-ac.jp
Supplementary information: Supplementary data are available at Bioinformatics online.
Craniofacial, Craniocervical, and Pharyngeal Morphology in Bilateral Cleft Lip and Palate and Obstructive Sleep Apnea Patients
Authors: Oosterkamp Barbara C. M. , Remmelink Hendrik J. , Pruim Gerard J. , Hoekema Aarnoud , Dijkstra Pieter U. 
Published: April 2006

Objective: The aim of this study was to analyze craniofacial, craniocervical, and pharyngeal morphology in surgically treated bilateral cleft lip and palate (BCLP) men, untreated men with obstructive sleep apnea (OSA), and a reference group of men. Subjects and methods: Lateral cephalograms were obtained of 27 male BCLP patients (mean age 29.0 ± 8.3 years), 27 untreated male OSA patients (mean age 38.6 ± 5.3 years), and 27 male controls serving as a reference group (mean age 30.8 ± 9.2 years). Tracings were made, and 26 variables representing craniofacial, craniocervical, and pharyngeal dimensions were obtained using Viewbox 3.1.1.6. software. The groups were compared using a one-way analysis of variance. Results: Craniofacial, craniocervical, and pharyngeal morphology of BCLP and OSA patients was similar except for a significantly more retrusive maxilla in the BCLP group. Compared to the reference group, the BCLP and OSA groups had significantly larger craniocervical angulations, smaller depth of the oropharynx at the tip of the velum, and a more inferiorly positioned hyoid bone. Significantly larger vertical dimensions were found in the BCLP group compared to the reference group. Conclusions: Craniofacial, craniocervical, and pharyngeal morphology of BCLP and OSA patients demonstrate substantial similarities except for a significantly more retrusive maxilla in the BCLP group. It is suggested that airway obstruction and postural adaptation to the obstruction may possibly be related to the aberrant craniofacial, craniocervical, and pharyngeal morphology in OSA and in BCLP patients.
Republic of South Africa v. Grootboom. Case No. CCT 11/00. 2000 (11) BCLR 1169 and Minister of Health v. Treatment Action Campaign. Case No. CCT 8/02
Authors: Caron David D. , Fitzpatrick Joan , Slye Ron C. 
Published: April 2006

Republic of South Africa v. Grootboom. Case No. CCT 11/00. 2000 (11) BCLR 1169. Constitutional Court of South Africa, October 4, 2000.Minister of Health v. Treatment Action Campaign. Case No. CCT 8/02. At <http://www.concourt.gov.za>.Constitutional Court of South Africa, July 5, 2002.Two cases decided by the Constitutional Court of South Africa in 2000 and 2002 implement several economic, social, and cultural rights guaranteed by the Constitution of South Africa. The decisions illuminate the role in such reasoning of human rights treaties to which South Africa is a state party or a signatory. They also analyze General Comment No. 3 of die UN Committee on Economic, Social and Cultural Rights (Committee). These cases, Republic of South Africa v. Grootboom, decided October 4,2000, and Minister of Health v. Treatment Action Campaign, decided July 5, 2002, illuminate questions concerning both die jusdciability of economic, social, and cultural rights—at least as incorporated into Soudi Africa's Bill of Rights, sections 7 through 39 of its Constitution—and the concept of “minimum core obligations” as developed by the Committee.
Exploiting indirect neighbours and topological weight to predict protein function from protein–protein interactions
Authors: Chua Hon Nian , Sung Wing-Kin , Wong Limsoon 
Published: April 2006

Abstract
Motivation: Most approaches in predicting protein function from protein–protein interaction data utilize the observation that a protein often share functions with proteins that interacts with it (its level-1 neighbours). However, proteins that interact with the same proteins (i.e. level-2 neighbours) may also have a greater likelihood of sharing similar physical or biochemical characteristics. We speculate that functional similarity between a protein and its neighbours from the two different levels arise from two distinct forms of functional association, and a protein is likely to share functions with its level-1 and/or level-2 neighbours. We are interested in finding out how significant is functional association between level-2 neighbours and how they can be exploited for protein function prediction.
Results: We made a statistical study on recent interaction data and observed that functional association between level-2 neighbours is clearly observable. A substantial number of proteins are observed to share functions with level-2 neighbours but not with level-1 neighbours. We develop an algorithm that predicts the functions of a protein in two steps: (1) assign a weight to each of its level-1 and level-2 neighbours by estimating its functional similarity with the protein using the local topology of the interaction network as well as the reliability of experimental sources and (2) scoring each function based on its weighted frequency in these neighbours. Using leave-one-out cross validation, we compare the performance of our method against that of several other existing approaches and show that our method performs relatively well.
Contact: g0306417@nus.edu.sg
Molecular complexes at a glance: automated generation of two-dimensional complex diagrams
Authors: Stierand Katrin , Maaß Patrick C. , Rarey Matthias 
Published: April 2006

AbstractMotivation: In this paper a new algorithmic approach is presented, which automatically generates structure diagrams of molecular complexes. A complex diagram contains the ligand, the amino acids of the protein interacting with the ligand and the hydrophilic interactions schematized as dashed lines between the corresponding atoms. The algorithm is based on a combinatorial optimization strategy which solves parts of the layout problem non-heuristically. The depicted molecules are represented as structure diagrams according to the chemical nomenclature. Due to the frequent usage of complex diagrams in the scientific literature as well as in text books dealing with structural biology, biochemistry and medicinal chemistry, the new algorithm is a key element for computer applications in these areas.Results: The method was implemented in the new software tool PoseView. It was tested on a representative dataset containing 305 protein–ligand complexes in total from the Brookhaven Protein Data Bank. PoseView was able to find collision-free layouts for more than three quarters of all complexes. In the following the layout generation algorithm is presented and, additional to the statistical results, representative test cases demonstrating the challenges of the layout generation will be discussed.Availability: The method is available as a webservice atContact: rarey@zbh.uni-hamburg.de
The ILC’s Articles on Responsibility of States for Internationally Wrongful Acts: A Retrospect
Authors: Crawford James 
Published: April 2006

The development of the articles on state responsibility of the International Law Commission (ILC) has been described elsewhere, in particular in the ILC’s Yearbook. The phases of development of the first (1955-1996) andsecond (1998-2001) readings are well enough known, and there is little point in repeating this material. Whatever the trials and longueurs of their production, the articles with their commentaries now exist and may be assessed as a whole.The first reading was the product of decades of work under successive special rapporteurs (Roberto Ago, Willem Riphagen, and Gaetano Arangio-Ruiz). The second readingwas equally a collective process and many members contributed to the final result. As I was formally responsible for shaping the work on second reading, I may not be the best person to comment on the outcome. Anything less than a full-scale defense of the text will be seen as an unauthorized retreat, and if the text cannot defend itself with the aid of the commentaries, it is too late for individuals to make up for any deficiencies.
Compliance With Final Judgments of the International Court of Justice Since 1987
Authors: Paulson Colter 
Published: April 2006

Commentators on the International Court of Justice (ICJ) note that cases of noncompliance with final judgments are very rare. The ICJ registrar Philippe Couvreur, however, recognized that compliance is often hard to determine because judgments are varied, declarations may not reflect actual conduct, effects may only become apparent long after the judgment is given, and the legal or political situation may substantially change after the judgment. In this vein, Judge Jennings asked:The judgments of the Court are binding in law, but do they, in fact, resolve the matter? More work needs to be done here. It is ironic that the Court's business up to the delivery of judgment is published in lavish detail, but it is not at all easy to find out what happened afterwards.
Impact of Active Versus Usual Algorithmic Titration of Basal Insulin and Point-of-Care Versus Laboratory Measurement of HbA1c on Glycemic Control in Patients With Type 2 Diabetes
Authors: Kennedy Laurence , Herman William H. , Strange Poul , Harris Anthony ,   for the GOAL A1C Team
Published: April 2006

OBJECTIVE—The objective of this study was to assess the impact of active versus usual monitoring of algorithmic insulin titration and point-of-care (POC) versus laboratory HbA1c (A1C) measurement on glycemic control in primary care.
RESEARCH DESIGN AND METHODS—The Glycemic Optimization with Algorithms and Labs at Point of Care (GOAL A1C) study was a 24-week, randomized, parallel-group, four-arm, open-label study of 7,893 adults with type 2 diabetes uncontrolled by oral antidiabetic agents and requiring insulin. Patients were randomly assigned by investigators from 2,164 sites in the U.S. to insulin glargine with either 1) usual (no unsolicited contact between visits) insulin titration using a simple algorithm with laboratory A1C testing, 2) usual titration with POC A1C testing, 3) active (weekly monitored) titration with laboratory A1C testing, or 4) active titration with POC A1C testing. Outcome measures included a change in A1C and fasting self-monitoring of blood glucose (SMBG) levels, percentage of patients achieving A1C &lt;7.0%, and hypoglycemia frequency.
RESULTS—Significant A1C and SMBG reductions were observed in all arms (P &lt; 0.0001). Compared with usual insulin titration, active titration achieved greater A1C reduction (1.5 vs. 1.3%; P &lt; 0.0001), SMBG reduction (88 vs. 79 mg/dl; P &lt; 0.0001), and proportion of patients achieving A1C &lt;7.0% (38 vs. 30%; P &lt; 0.0001). Among patients receiving active titration, POC A1C testing was associated with an increase in the proportion achieving an A1C &lt;7.0% (41% for POC vs. 36% for laboratory; P &lt; 0.0001). Hypoglycemia rates were low (usual vs. active groups: 3.7 vs. 6.0 all confirmed episodes/patient-year [P &lt; 0.001]; 0.09 vs. 0.14 severe episodes/patient-year [NS]).
CONCLUSIONS—In a predominantly primary care setting, addition of insulin glargine using a simple algorithm achieved significant improvements in glycemic control in patients with type 2 diabetes in all four study arms. Active titration resulted in significant incremental improvements in glycemic control, and, among patients receiving active titration, POC A1C testing resulted in a greater portion achieving A1C &lt;7.0%.
Long-Term Effects of Ranirestat (AS-3201) on Peripheral Nerve Function in Patients With Diabetic Sensorimotor Polyneuropathy
Authors: Bril Vera , Buchanan Robert A. ,   the Ranirestat Study Group*
Published: April 2006

OBJECTIVES—We aimed to determine whether ranirestat, an aldose reductase inhibitor, maintains the improved nerve function observed in patients with diabetic sensorimotor polyneuropathy (DSP) after completing a 12-week nerve biopsy study.
RESEARCH DESIGN AND METHODS—Patients with mild to moderate DSP, as determined by the presence of sural nerve responses, were enrolled in a double-blind, placebo-controlled biopsy trial and randomized to placebo or 5 or 20 mg/day ranirestat for 12 weeks. Patients completing this biopsy study were offered a 48-week extension at the same ranirestat dose or at 5 mg/day ranirestat if they were originally treated with placebo. Electrophysiological tests, the Toronto Clinical Neuropathy Score, and vibration perception thresholds (VPTs) were performed at entry and at 12 (end of the biopsy study) and 60 (end of the 48-week extension) weeks.
RESULTS—Peroneal motor nerve conduction velocity (NCV) improved in the 20-mg/day group following 60 weeks of treatment. Sural and median sensory NCV improved after both 12 and 60 weeks of treatment with 20 mg/day. VPT improved after 60 weeks of treatment with 20 mg/day. Ranirestat was well tolerated with no difference in adverse events between the 5- and 20-mg/day groups.
CONCLUSIONS—Twenty milligrams ranirestat per day improves NCV and VPT following 60 weeks of administration. The improved sensory nerve function observed after 12 weeks of therapy was maintained at 60 weeks, and improved motor nerve function was observed at 60 weeks.
Population genetic structure of crimson snapper Lutjanus erythropterus in East Asia, revealed by analysis of the mitochondrial control region
Authors: Zhang Junbin , Cai Zeping , Huang Liangmin 
Published: April 2006

AbstractThe population genetic structure of the crimson snapper Lutjanus erythropterus in East Asia was examined with a 427-bp hypervariable portion of the mtDNA control region. A total of 262 samples were collected and 75 haplotypes were obtained. Neutrality tests (Tajima's and Fu's) suggested that Lutjanus erythropterus in East Asia had experienced a bottleneck followed by population expansion since the late Pleistocene. Despite the low phylogeographic structures in mtDNA haplotypes, a hierarchical examination of populations in 11 localities from four geographical regions using analysis of molecular variance (AMOVA) indicated significant genetic differentiation among regions (ΦCT = 0.08564, p < 0.01). Limited gene flow between the eastern region (including a locality in the western Pacific Ocean and two localities in the East Sea) and three geographic regions of the South China Sea largely contributed to the genetic subdivision. However, comparisons among three geographic regions of the South China Sea showed little to no genetic difference. Populations of Lutjanus erythropterus in East Asia are inferred to be divided into two major groups: an eastern group, including populations of the western Pacific Ocean and the East Sea, and a South China Sea group, consisting of populations from northern Malaysia to South China. The results suggest that fishery management should reflect the genetic differentiation and diversity in East Asia.
Inhibition of Brassinosteroid Biosynthesis by Either a dwarf4 Mutation or a Brassinosteroid Biosynthesis Inhibitor Rescues Defects in Tropic Responses of Hypocotyls in the Arabidopsis Mutant nonphototropic hypocotyl 4
Authors: Nakamoto Daisuke , Ikeura Akimitsu , Asami Tadao , Yamamoto Kotaro T. 
Published: April 2006

Abstract
The nonphototropic hypocotyl 4 (nph4)/auxin response factor 7 (arf7) mutant of Arabidopsis (Arabidopsis thaliana) is insensitive to auxin and has defects in hypocotyl tropism, hook formation, differential leaf growth, and lateral root formation. To understand an auxin-signaling pathway through NPH4, we carried out screening of suppressor mutants of nph4-103 and obtained a dwarf suppressor mutant, suppressor of nph4 (snp2). snp2 had short hypocotyls in the dark condition and dark green and round leaves, short petioles, and more lateral shoots than the wild type in the light condition. The snp2 phenotypes were rescued by adding brassinolide to the growth medium in both light and dark conditions. Genetic mapping, sequence analysis, and a complementation test indicated that snp2 was a weak allele of DWARF4 (DWF4), which functions in brassinosteroid (BR) biosynthesis. snp2, which was renamed dwf4-101, exhibited photo- and gravitropisms of hypocotyls similar to those of the wild type with a slightly faster response in gravitropism. dwf4-101 almost completely suppressed defects in both tropisms of nph4-103 hypocotyls and completely suppressed hyponastic growth of nph4-103 leaves. Treatment with brassinazole, an inhibitor of BR biosynthesis, also partially rescued the tropic defects in nph4-103. Hypocotyls of nph4-103 were auxin insensitive, whereas hypocotyls of dwf4-101 were more sensitive than those of the wild type. dwf4-101 nph4-103 hypocotyls were as sensitive as those of dwf4-101. Auxin inducibility of massugu 2 (MSG2)/IAA19 gene expression was reduced in nph4-103. mRNA level of MSG2 was reduced in dwf4-101 and dwf4-101 nph4-103, but both mutants exhibited greater auxin inducibility of MSG2 than the wild type. Taken together, dwf4-101 was epistatic to nph4-103. These results strongly suggest that BR deficiency suppresses nph4-103 defects in tropic responses of hypocotyls and differential growth of leaves and that BR negatively regulates tropic responses.
Sequence-Level Analysis of the Diploidization Process in the TriplicatedFLOWERING LOCUS CRegion ofBrassica rapa
Authors: Yang Tae-Jin , Kim Jung Sun , Kwon Soo-Jin , Lim Ki-Byung , Choi Beom-Soon , Kim Jin-A , Jin Mina , Park Jee Young , Lim Myung-Ho , Kim Ho-Il , Lim Yong Pyo , Kang Jason Jongho , Hong Jin-Han , Kim Chang-Bae , Bhak Jong , Bancroft Ian , Park Beom-Seok 
Published: April 2006

AbstractStrong evidence exists for polyploidy having occurred during the evolution of the tribe Brassiceae. We show evidence for the dynamic and ongoing diploidization process by comparative analysis of the sequences of four paralogous Brassica rapa BAC clones and the homologous 124-kb segment of Arabidopsis thaliana chromosome 5. We estimated the times since divergence of the paralogous and homologous lineages. The three paralogous subgenomes of B. rapa triplicated 13 to 17 million years ago (MYA), very soon after the Arabidopsis and Brassica divergence occurred at 17 to 18 MYA. In addition, a pair of BACs represents a more recent segmental duplication, which occurred ∼0.8 MYA, and provides an exception to the general expectation of three paralogous segments within the B. rapa genome. The Brassica genome segments show extensive interspersed gene loss relative to the inferred structure of the ancestral genome, whereas the Arabidopsis genome segment appears little changed. Representatives of all 32 genes in the Arabidopsis genome segment are represented in Brassica, but the hexaploid complement of 96 has been reduced to 54 in the three subgenomes, with compression of the genomic region lengths they occupy to between 52 and 110 kb. The gene content of the recently duplicated B. rapa genome segments is identical, but intergenic sequences differ.
Human Rights in 2002: The Annual Sessions of the UN Commission on Human Rights and the Economic and Social Council
Authors: Dennis Michael J. 
Published: April 2006

The fifty-eighth session of the United Nations Commission on Human Rights opened with the United States in an observer seat for the first time ever. The Commission ultimately adopted ninety-two resolutions and eighteen decisions, thirty-nine of which were adopted by roll-call vote. Subsequently, at its July 2002 session, the Economic and Social Council (ECOSOC, the parent body of the Commission) approved nearly all of the Commission's decisions by similar votes. The United States was also reelected to the Commission for its fiftyninth session during a separate ECOSOC meeting.The debate during the Commission's deliberations was more chaotic and fractious than in prior years, reflecting the membership of an increased number of repressive governments that sought to block international scrutiny of their human rights practices.
A Single Factor Underlies the Metabolic Syndrome
Authors: Pladevall Manel , Singal Bonita , Williams L. Keoki , Brotons Carlos , Guyer Heidi , Sadurni Josep , Falces Carles , Serrano-Rios Manuel , Gabriel Rafael , Shaw Jonathan E. , Zimmet Paul Z. , Haffner Steven 
Published: April 2006

OBJECTIVE—Confirmatory factor analysis (CFA) was used to test the hypothesis that the components of the metabolic syndrome are manifestations of a single common factor.
RESEARCH DESIGN AND METHODS—Three different datasets were used to test and validate the model. The Spanish and Mauritian studies included 207 men and 203 women and 1,411 men and 1,650 women, respectively. A third analytical dataset including 847 men was obtained from a previously published CFA of a U.S. population. The one-factor model included the metabolic syndrome core components (central obesity, insulin resistance, blood pressure, and lipid measurements). We also tested an expanded one-factor model that included uric acid and leptin levels. Finally, we used CFA to compare the goodness of fit of one-factor models with the fit of two previously published four-factor models.
RESULTS—The simplest one-factor model showed the best goodness-of-fit indexes (comparative fit index 1, root mean-square error of approximation 0.00). Comparisons of one-factor with four-factor models in the three datasets favored the one-factor model structure. The selection of variables to represent the different metabolic syndrome components and model specification explained why previous exploratory and confirmatory factor analysis, respectively, failed to identify a single factor for the metabolic syndrome.
CONCLUSIONS—These analyses support the current clinical definition of the metabolic syndrome, as well as the existence of a single factor that links all of the core components.