bluuebunny/crossref_metadata_2025_split huggingface dataset:
A report on 10 new patients with heterozygous mutations in the COL11A1 gene and a review of genotype–phenotype correlations in type XI collagenopathies
Authors: Majava Marja , Hoornaert Kristien P. , Bartholdi Deborah , Bouma Mieke C. , Bouman Katelijne , Carrera Marta , Devriendt Koenraad , Hurst Jane , Kitsos George , Niedrist Dunja , Petersen Michael B. , Shears Debbie , Stolte‐Dijkstra Irene , Van Hagen J.M. , Ala‐Kokko Leena , Männikkö Minna , Mortier Geert R. 
Published: January 2007

AbstractA series of 44 unrelated patients in whom COL2A1 screening demonstrated normal results but whose phenotype was nevertheless highly suggestive of either Stickler syndrome (with ocular involvement) or Marshall syndrome were investigated for mutations in the COL11A1 gene. Heterozygous COL11A1 mutations were found in 10 individuals. A splice site alteration (involving introns 47–55) was present in seven cases, with one in intron 50 (c.3816 + 1G > A) occurring in three patients. Two patients had a different deletion, and a missense mutation (Gly1471Asp) was observed in one case. In 4/10 patients the phenotype was classified as Marshall syndrome because of early‐onset severe hearing loss and characteristic facial features. These four patients were all heterozygous for a splice site mutation in intron 50. One of these cases had a type 1 vitreous anomaly despite the presence of a COL11A1 mutation. The remaining 6/10 patients had an overlapping Marshall–Stickler phenotype with less pronounced facial features. None of these had a mutation in the hot spot region of intron 50. © 2007 Wiley‐Liss, Inc.
Whole genome microarray analysis of gene expression in Prader–Willi syndrome
Authors: Bittel Douglas C. , Kibiryeva Nataliya , Sell Susan M. , Strong Theresa V. , Butler Merlin G. 
Published: January 2007

AbstractPrader–Willi syndrome (PWS) is caused by loss of function of paternally expressed genes in the 15q11‐q13 region and a paucity of data exists on transcriptome variation. To further characterize genetic alterations in this classic obesity syndrome using whole genome microarrays to analyze gene expression, microarray and quantitative RT‐PCR analysis were performed using RNA isolated from lymphoblastoid cells from PWS male subjects (four with 15q11‐q13 deletion and three with UPD) and three age and cognition matched nonsyndromic comparison males. Of more than 47,000 probes examined in the microarray, 23,383 were detectable and 323 had significantly different expression in the PWS lymphoblastoid cells relative to comparison cells, 14 of which were related to neurodevelopment and function. As expected, there was no evidence of expression of paternally expressed genes from the 15q11‐q13 region (e.g., SNRPN) in the PWS cells. Alterations in expression of serotonin receptor genes (e.g., HTR2B) and genes involved in eating behavior and obesity (ADIPOR2, MC2R, HCRT, OXTR) were noted. Other genes of interest with reduced expression in PWS subjects included STAR (a key regulator of steroid synthesis) and SAG (an arrestin family member which desensitizes G‐protein‐coupled receptors). Quantitative RT‐PCR for SAG, OXTR, STAR, HCRT, and HTR2B using RNA isolated from their lymphoblastoid cells and available brain tissue (frontal cortex) from separate individuals with PWS and control subjects and normalized to GAPD gene expression levels validated our microarray gene expression data. Our analysis identified previously unappreciated changes in gene expression which may contribute to the clinical manifestations seen in PWS. © 2007 Wiley‐Liss, Inc.
Asymmetrical skull, ptosis, hypertelorism, high nasal bridge, clefting, umbilical anomalies, and skeletal anomalies in sibs: Is Carnevale syndrome a separate entity?
Authors: Al Kaissi Ali , Klaushofer Klaus , Safi Hatem , Chehida Farid Ben , Ghachem Maher Ben , Chaabounni Myriam , Hennekam Raoul C.M. 
Published: January 2007

AbstractA group of syndromes, consisting of Malpuech syndrome, Michels syndrome, Carnevale syndrome, OSA syndrome, and Mingarelli syndrome share the combination of symptoms of highly arched eyebrows, ptosis, and hypertelorism, and vary in other symptoms such as asymmetry of the skull, eyelid, and anterior chamber anomalies, clefting of lip and palate, umbilical anomalies, and growth and cognitive development. It has been suggested that they are in fact part of the same entity. Here, we describe a brother and sister with the same constellation of symptoms, and compare these with the various entities. We conclude that the present patients resemble most patients with Carnevale and Mingarelli syndrome, and the case reported by Guion‐Almeida, and that these patients form together most probably the same entity. We suggest the name Carnevale syndrome as this author described this combination of symptoms for the first time. Malpuech and Michels syndromes are probably separate entities, although they may still be allelic. Pattern of inheritance of Carnevale syndrome is most likely autosomal recessive. © 2007 Wiley‐Liss, Inc.
Synthesis of a Stimuli‐Responsive P‐Chiral Polymer with Chiral Phosphorus Atoms and Azobenzene Moieties in the Main Chain
Authors: Ouchi Yuko , Morisaki Yasuhiro , Ogoshi Tomoki , Chujo Yoshiki 
Published: January 2007

AbstractA reaction of the P‐chiral compound (S,S)‐1,2‐bis(boranato(tert‐butyl)methylphosphino)ethane with an azobenzene derivative gave stimuli‐responsive polymers with P‐chiral phosphines in the main chain. This is the first example of a stimuli‐responsive P‐chiral polymer. The polymer isomerized from the trans to the cis form upon UV irradiation and reverted to the trans form reversibly. The polymer was able to coordinate to platinum, and the resulting polymer complex exhibited the Cotton effect owing to the chirality of the phosphorus atoms. The structure of the P‐chiral polymer obtained could be changed reversibly by light and thermal stimuli, and the polymer chain was induced to rotate helically when complexed with transition metals through the chiral phosphorus atoms.
Integrin‐dependent cell behavior on ECM peptide‐conjugated chitosan membranes
Authors: Mochizuki Mayumi , Yamagata Natsumi , Philp Deborah , Hozumi Kentaro , Watanabe Tadashi , Kikkawa Yamato , Kadoya Yuichi , Kleinman Hynda K. , Nomizu Motoyoshi 
Published: January 2007

AbstractExtracellular matrix (ECM) plays an important role in tissue regeneration by promoting cell adhesion, migration, proliferation, and differentiation. ECM mimetics are of importance for tissue engineering because of their functions as scaffolds for cells. Previously, we developed bioactive laminin‐derived peptide‐conjugated chitosan membranes and demonstrated their cell‐ and peptide‐type specific functions. Here, we conjugated twelve integrin‐binding peptides derived from ECM proteins onto chitosan membranes and examined biological activity. Seven peptide–chitosan membranes promoted human foreskin fibroblast attachment. Additionally, FIB1 (YAVTGRGDSPAS; from fibronectin), A99 (AGTFALRGDNPQG; from laminin α1 chain), EF1zz (ATLQLQEGRLHFXFDLGKGR, X = Nle; from laminin α1 chain), and 531 (GEFYFDLRLKGDKY; from collagen α1 (IV) chain) conjugated chitosan membranes promoted integrin‐dependent cell adhesion. Various integrins, including αv, β1, and β3, were involved in the cell adhesion to the peptide–chitosan membranes. Further, only the FIB1‐ and A99‐chitosan membranes promoted neurite outgrowth with PC12 rat pheochromocytoma cells. These data demonstrate that peptide–chitosan membranes can regulate specific integrin‐mediated cell responses and are useful constructs as ECM mimetics. © 2007 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 88: 122–130, 2007.This article was originally published online as an accepted preprint. The ‘Published Online’ date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com
Disruption of the HIV‐1 protease dimer with interface peptides: Structural studies using NMR spectroscopy combined with [2‐13C]‐Trp selective labeling
Authors: Frutos Silvia , Rodriguez‐Mias Ricard A. , Madurga Sergio , Collinet Bruno , Reboud‐Ravaux Michèle , Ludevid Dolors , Giralt Ernest 
Published: January 2007

AbstractHIV‐1 protease (HIV‐1 PR), which is encoded by retroviruses, is required for the processing of gag and pol polyprotein precursors, hence it is essential for the production of infectious viral particles. In vitro inhibition of the enzyme results in the production of progeny virions that are immature and noninfectious, suggesting its potential as a therapeutic target for AIDS. Although a number of potent protease inhibitor drugs are now available, the onset of resistance to these agents due to mutations in HIV‐1 PR has created an urgent need for new means of HIV‐1 PR inhibition. Whereas enzymes are usually inactivated by blocking of the active site, the structure of dimeric HIV‐1 PR allows an alternative inhibitory mechanism. Since the active site is formed by two half‐enzymes, which are connected by a four‐stranded antiparallel β‐sheet involving the N‐ and C‐ termini of both monomers, enzyme activity can be abolished by reagents targeting the dimer interface in a region relatively free of mutations would interfere with formation or stability of the functional HIV‐1 PR dimer. This strategy has been explored by several groups who targeted the four‐stranded antiparallel β‐sheet that contributes close to 75% of the dimerization energy. Interface peptides corresponding to native monomer N‐ or C‐termini of several of their mimetics demonstrated, mainly on the basis of kinetic analyses, to act as dimerization inhibitors. However, to the best of our knowledge, neither X‐ray crystallography nor NMR structural studies of the enzyme‐inhibitor complex have been performed to date. In this article we report a structural study of the dimerization inhibition of HIV‐1 PR by NMR using selective Trp side chain labeling. © 2007 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 88: 164–173, 2007.This article was originally published online as an accepted preprint. The ‘Published Online’ date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com
Design and implementation of an interdepartmental bioinformatics program across life science curricula
Authors: Miskowski Jennifer A. , Howard David R. , Abler Michael L. , Grunwald Sandra K. 
Published: January 2007

AbstractOver the past 10 years, there has been a technical revolution in the life sciences leading to the emergence of a new discipline called bioinformatics. In response, bioinformatics‐related topics have been incorporated into various undergraduate courses along with the development of new courses solely focused on bioinformatics. This report describes the design and implementation of an interdepartmental bioinformatics program throughout several life science programs. Using elements of the backward curricular design process, nine faculty members from the Biology, Microbiology, and Chemistry Departments at the University of Wisconsin – La Crosse incorporated bioinformatics in a coordinated manner into 10 courses. Key molecular biology concepts were first identified followed by development of bioinformatics exercises that centered on these concepts. An overview of how the program was constructed and implemented and a summary of the exercises that were designed will be presented.
Assessment of a bioinformatics across life science curricula initiative
Authors: Howard David R. , Miskowski Jennifer A. , Grunwald Sandra K. , Abler Michael L. 
Published: January 2007

AbstractAt the University of Wisconsin‐La Crosse, we have undertaken a program to integrate the study of bioinformatics across the undergraduate life science curricula. Our efforts have included incorporating bioinformatics exercises into courses in the biology, microbiology, and chemistry departments, as well as coordinating the efforts of faculty within those departments. Here, we assess student confidence in solving and ability to solve bioinformatics‐related problems. Assessment data show increases in student performance on bioinformatics‐related problems and more confidence in solving such problems with increased exposure to the field of bioinformatics. Additionally, the faculty perceive an increased awareness of the applications of bioinformatics among the students in their courses. The combination of three different assessment tools, a student self‐assessment of learning, a content exam, and faculty survey, was an effective and efficient approach for evaluating this multi‐departmental program.
Surface plasmon resonance label‐free monitoring of antibody antigen interactions in real time
Authors: Kausaite Asta , van Dijk Martijn , Castrop Jan , Ramanaviciene Almira , Baltrus John P. , Acaite Juzefa , Ramanavicius Arunas 
Published: January 2007

AbstractDetection of biologically active compounds is one of the most important topics in molecular biology and biochemistry. One of the most promising detection methods is based on the application of surface plasmon resonance for label‐free detection of biologically active compounds. This method allows one to monitor binding events in real time without labeling. The system can therefore be used to determine both affinity and rate constants for interactions between various types of molecules. Here, we describe the application of a surface plasmon resonance biosensor for label‐free investigation of the interaction between an immobilized antigen bovine serum albumin (BSA) and antibody rabbit anti‐cow albumin IgG1 (anti‐BSA). The formation of a self‐assembled monolayer (SAM) over a gold surface is introduced into this laboratory training protocol as an effective immobilization method, which is very promising in biosensing systems based on detection of affinity interactions. In the next step, covalent attachment via artificially formed amide bonds is applied for the immobilization of proteins on the formed SAM surface. These experiments provide suitable experience for postgraduate students to help them understand immobilization of biologically active materials via SAMs, fundamentals of surface plasmon resonance biosensor applications, and determination of non‐covalent biomolecular interactions. The experiment is designed for master and/or Ph.D. students. In some particular cases, this protocol might be adoptable for bachelor students that already have completed an extended biochemistry program that included a background in immunology.
Accessible NMR experiments studying the hydrodynamics of 15N‐enriched ubiquitin at low fields
Authors: Thompson Laura E. , Rovnyak David 
Published: January 2007

AbstractWe have recently developed and implemented two experiments in biomolecular NMR for an undergraduate‐level biophysical chemistry laboratory with commercially available 15N‐enriched human ubiquitin. These experiments take advantage of 15N direct detection of the NMR signal. The first experiment develops skills in acquiring and interpreting one‐dimensional and two‐dimensional NMR data of an aqueous protein sample (D. Rovnyak, L. E. Thompson (2005) An accessible two‐dimensional solution nuclear magnetic resonance experiment on human ubiquitin, Biochem. Mol. Biol. Educ. 33, 117–122). In the second experiment, discussed here, students examine the overall dynamics of a protein in solution. Students measure spin relaxation times T1 and T2 and use these data to estimate a rotational correlation time, τc, and the diameter of ubiquitin using the Stokes‐Einstein relation. This is a fast and simple experiment, requiring about 1 h of instrument time, and a valuable opportunity to provide a hands‐on experience in studying macromolecular size and dynamics. This experiment is conducted in synchrony with lecture material on hydrodynamics and sedimentation.
Ribosome recycling: An essential process of protein synthesis
Authors: Kiel Michael C. , Kaji Hideko , Kaji Akira 
Published: January 2007

AbstractA preponderance of textbooks outlines cellular protein synthesis (translation) in three basic steps: initiation, elongation, and termination. However, researchers in the field of translation accept that a vital fourth step exists; this fourth step is called ribosome recycling. Ribosome recycling occurs after the nascent polypeptide has been released during the termination step. Despite the release of the polypeptide, ribosomes remain bound to the mRNA and tRNA. It is only during the fourth step of translation that ribosomes are ultimately released from the mRNA, split into subunits, and are free to bind new mRNA, thus the term “ribosome recycling.” This step is essential to the viability of cells. In bacteria, it is catalyzed by two proteins, elongation factor G and ribosome recycling factor, a near perfect structural mimic of tRNA. Eukaryotic organelles such as mitochondria and chloroplasts possess ribosome recycling factor and elongation factor G homologues, but the nature of ribosome recycling in eukaryotic cytoplasm is still under investigation. In this review, the discovery of ribosome recycling and the basic mechanisms involved are discussed so that textbook writers and teachers can include this vital step, which is just as important as the three conventional steps, in sections dealing with protein synthesis.
Functional consistency across two behavioural modalities: fire‐setting and self‐harm in female special hospital patients
Authors: Miller Sarah , Fritzon Katarina 
Published: January 2007

AbstractBackground Fire‐setting and self‐harm behaviours among women in high security special hospitals may be understood using Shye's Action System Theory (AST) in which four functional modes are recognized: ‘adaptive’, ‘expressive’, ‘integrative’, and ‘conservative’.Aims To test for relationships between different forms of fire‐setting and self‐harm behaviours and AST modes among women in special hospital, and for consistency within modes across the two behaviours.Method Clinical case files evidencing both fire‐setting and self‐harm behaviours (n = 50) were analysed for content, focusing on incident characteristics. A total of 29 fire‐setting and 22 self‐harm variables were analysed using Smallest Space Analysis (SSA). Chi‐square and Spearman's rho (ρ) analyses were used to determine functional consistency across behavioural modes.Results Most women showed one predominant AST mode in fire‐setting (n = 39) and self‐harm (n = 35). Significant positive correlations were found between integrative and adaptive modes of functioning. The lack of correlation between conservative and expressive modes reflects the differing behaviours used in each activity. Despite this, significant cross‐tabulations revealed that each woman had parallel fire‐setting and self‐harm styles.Discussion Findings suggest that, for some women, setting fires and self harm fulfil a similar underlying function. Support is given to AST as a way of furthering understanding of damaging behaviours, whether self‐ or other‐inflicted. Copyright © 2007 John Wiley & Sons, Ltd.
Phase II study of low‐dose decitabine in combination with imatinib mesylate in patients with accelerated or myeloid blastic phase of chronic myelogenous leukemia
Authors: Oki Yasuhiro , Kantarjian Hagop M. , Gharibyan Vazganush , Jones Dan , O'Brien Susan , Verstovsek Srdan , Cortes Jorge , Morris Gail M. , Garcia‐Manero Guillermo , Issa Jean‐Pierre J. 
Published: January 2007

AbstractBACKGROUND.Resistance to imatinib is a frequent clinical problem in advanced phase chronic myelogenous leukemia (CML). A Phase II study was performed on low‐dose decitabine, a DNA methyltransferase inhibitor, in combination with imatinib in patients with CML in accelerated phase (AP) and myeloid blastic phase (BP).METHODS.Patients received decitabine 15 mg/m2 intravenously daily, 5 days a week for 2 weeks, and imatinib 600 mg orally daily. Global DNA methylation was measured by long interspersed nucleotide element (LINE) bisulfite/pyrosequencing.RESULTS.Twenty‐eight patients were enrolled (25 with imatinib resistance; 18 in AP, 10 in BP). A total of 91 cycles (median, 2.5 cycles per patient) was administered. Complete hematologic responses, partial hematologic responses, and hematologic improvement were observed in 9 (32%), 1 (4%), and 2 (7%) patients. Major and minor cytogenetic responses were observed in 5 (18%) and 3 (11%) patients. The hematologic response rate was higher in patients without BCR‐ABL kinase mutations (10 of 19, 53%) than in those with mutations (1 of 7, 14%). Median duration of hematologic response was 18 (range, 4 to 107+) weeks. Myelosuppression was the major adverse effect, with neutropenic fever in 9 patients (32%). LINE methylation decreased from 71.6% ± 0.9% (mean ± standard error of the mean) to 60.4% ± 2.0% on Day 5, 60.5% ± 1.8% on Day 12, and returned to 68.8% ± 1.4% at peripheral blood recovery. A decrease in LINE methylation tended to be greater in nonresponders than in responders on Days 5 and 12.CONCLUSIONS.Combination therapy with decitabine and imatinib is well tolerated and active in advanced phase CML without BCR‐ABL kinase mutations. Cancer 2007 © 2007 American Cancer Society.
Updated clinical practice guidelines for the prevention and treatment of mucositis
Authors: Keefe Dorothy M. , Schubert Mark M. , Elting Linda S. , Sonis Stephen T. , Epstein Joel B. , Raber‐Durlacher Judith E. , Migliorati Cesar A. , McGuire Deborah B. , Hutchins Ronald D. , Peterson Douglas E. 
Published: January 2007

AbstractConsiderable progress in research and clinical application has been made since the original guidelines for managing mucositis in cancer patients were published in 2004, and the first active drug for the prevention and treatment of this condition has been approved by the United States Food and Drug Administration and other regulatory agencies in Europe and Australia. These changes necessitate an updated review of the literature and guidelines. Panel members reviewed the biomedical literature on mucositis published in English between January 2002 and May 2005 and reached a consensus based on the criteria of the American Society of Clinical Oncology. Changes in the guidelines included recommendations for the use of palifermin for oral mucositis associated with stem cell transplantation, amifostine for radiation proctitis, and cryotherapy for mucositis associated with high‐dose melphalan. Recommendations against specific practices were introduced: Systemic glutamine was not recommended for the prevention of gastrointestinal mucositis, and sucralfate and antimicrobial lozenges were not recommended for radiation‐induced oral mucositis. Furthermore, new guidelines suggested that granulocyte–macrophage‐colony stimulating factor mouthwashes not be used for oral mucositis prevention in the transplantation population. Advances in mucositis treatment and research have been complemented by an increased rate of publication on mucosal injury in cancer. However, additional and sustained efforts will be required to gain a fuller understanding of the pathobiology, impact on overall patient status, optimal therapeutic strategies, and improved educational programs for health professionals, patients, and caregivers. These efforts are likely to have significant clinical and economic impact on the treatment of cancer patients. Cancer 2007;109:820–31. © 2007 American Cancer Society.