bluuebunny/crossref_metadata_2025_split huggingface dataset:
MicroRNAs: Control and Loss of Control in Human Physiology and Disease
Authors: Li Min , Marin‐Muller Christian , Bharadwaj Uddalak , Chow Kwong‐Hon , Yao Qizhi , Chen Changyi 
Published: November 2008

AbstractAnalysis of the human genome indicates that a large fraction of the genome sequences are RNAs that do not encode any proteins, also known as non‐coding RNAs. MicroRNAs (miRNAs) are a group of small non‐coding RNA molecules 20–22 nucleotides (nt) in length that are predicted to control the activity of approximately 30% of all protein‐coding genes in mammals. miRNAs play important roles in many diseases, including cancer, cardiovascular disease, and immune disorders. The expression of miRNAs can be regulated by epigenetic modification, DNA copy number change, and genetic mutations. miRNAs can serve as a valuable therapeutic target for a large number of diseases. For miRNAs with oncogenic capabilities, potential therapies include miRNA silencing, antisense blocking, and miRNA modifications. For miRNAs with tumor suppression functions, overexpression of those miRNAs might be a useful strategy to inhibit tumor growth. In this review, we discuss the current progress of miRNA research, regulation of miRNA expression, prediction of miRNA targets, and regulatory role of miRNAs in human physiology and diseases, with a specific focus on miRNAs in pancreatic cancer, liver cancer, colorectal cancer, cardiovascular disease, the immune system, and infectious disease. This review provides valuable information for clinicians and researchers who want to recognize the newest advances in this new field and identify possible lines of investigation in miRNAs as important mediators in human physiology and diseases.
Cu-Doping Effects in CdI2Nanocrystals: The Role of Cu-Agglomerates
Authors: Miah M Idrish 
Published: November 2008

Abstract
Cu-doping effects in CdI2nanocrystals are studied experimentally. We use the photostimulated second harmonic generation (PSSHG) as a tool to investigate the effects. It is found that the PSSHG increases with increasing Cu content up to 0.6% and then decreases due to the formation of the Cu-agglomerates. The PSSHG for the crystal with Cu content higher than 1% reduces to that for the undoped CdI2crystal. The results suggest that a crucial role of the Cu-metallic agglomerates is involved in the processes as responsible for the observed effects.
A solution to limitations of cognitive testing in children with intellectual disabilities: the case of fragile X syndrome
Authors: Hessl David , Nguyen Danh V. , Green Cherie , Chavez Alyssa , Tassone Flora , Hagerman Randi J. , Senturk Damla , Schneider Andrea , Lightbody Amy , Reiss Allan L. , Hall Scott 
Published: November 2008

AbstractIntelligence testing in children with intellectual disabilities (ID) has significant limitations. The normative samples of widely used intelligence tests, such as the Wechsler Intelligence Scales, rarely include an adequate number of subjects with ID needed to provide sensitive measurement in the very low ability range, and they are highly subject to floor effects. The IQ measurement problems in these children prevent characterization of strengths and weaknesses, poorer estimates of cognitive abilities in research applications, and in clinical settings, limited utility for assessment, prognosis estimation, and planning intervention. Here, we examined the sensitivity of the Wechsler Intelligence Scale for Children (WISC-III) in a large sample of children with fragile X syndrome (FXS), the most common cause of inherited ID. The WISC-III was administered to 217 children with FXS (age 6–17 years, 83 girls and 134 boys). Using raw norms data obtained with permission from the Psychological Corporation, we calculated normalized scores representing each participant’s actual deviation from the standardization sample using az-score transformation. To validate this approach, we compared correlations between the new normalized scores versus the usual standard scores with a measure of adaptive behavior (Vineland Adaptive Behavior Scales) and with a genetic measure specific to FXS (FMR1protein or FMRP). The distribution of WISC-III standard scores showed significant skewing with floor effects in a high proportion of participants, especially males (64.9%–94.0% across subtests). With the z-score normalization, the flooring problems were eliminated and scores were normally distributed. Furthermore, we found correlations between cognitive performance and adaptive behavior, and between cognition and FMRP that were very much improved when using these normalized scores in contrast to the usual standardized scores. The results of this study show that meaningful variation in intellectual ability in children with FXS, and probably other populations of children with neurodevelopmental disorders, is obscured by the usual translation of raw scores into standardized scores. A method of raw score transformation may improve the characterization of cognitive functioning in ID populations, especially for research applications.
Proceedings of the Fortieth Meeting of the Agricultural Research
Modellers' Group
Authors: CROMPTON L. A. , WHEELER T. R. 
Published: November 2008

SUMMARYThis group, which is concerned with the applications of mathematics to
agricultural science, was formed in 1970 and has since met at approximately
yearly intervals in London for one-day meetings. The fortieth meeting of the
group, chaired by Dr John Thornley of Henley-on-Thames, UK and the Centre for
Nutrition Modelling, University of Guelph, Canada, was held in the Kohn Centre
at the Royal Society, 6 Carlton House Terrace, London on Friday, 11 April 2008
when the following papers were read.
Predicting the metabolizable energy intake of ruminants using digestibility, ruminal methane production and fermentation data
Authors: McPHEE M. J. , HEGARTY R. S. 
Published: November 2008

SUMMARYObtaining accurate estimates of the metabolizable energy (ME) intake (MEI; MJ/day) of individual grazing ruminants is an important requirement for effective nutritional management and genetic selection of energy efficient ruminants. Diet digestibility and the daily methane production rate (MPR; MJ/day) of ruminants can be closely linked with their MEI, so published data were examined to determine whether MEI could be accurately estimated from digestibility, MPR and other parameters able to be measured on grazing animals. Four modelling approaches were assessed or developed to estimate MEI: (i) a published fixed proportional relationship between the non-metabolizable losses of MPR and urinary energy (UE; MJ/day); (ii) the proportion of energy digestibility (EngDig); (iii) MPR and the ruminal factors that influence the stoichiometric relationships between MPR and MEI; and (iv) the calculated ME arising from rumen fermentation (MEf; MJ/day). Data to develop the models (n=61) were collected across three publications (Paper) where the Paper effect was treated as a random-effect variable. Each of the models (1–4) was challenged with an independent data set (n=19). The inclusion of MEf (P=0·01) to predict MEI [MEI=0·18 (2·03)+3·42 (0·36)×sqrt(MEf) (d.f.=57; residual log likelihood=173·6)] had the lowest mean square error of prediction (MSEP) when challenged with the independent data set; mean bias of −0·42 MJ/day (P<0·05), MSEP=0·68 MJ/day and the bias, slope and random components of the MSEP were, as a proportion, 0·26, 0·13 and 0·61, respectively. None of the models estimated MEI with sufficient accuracy to be useful for identifying individual animals with above average energetic efficiency. A critical limit to any model seeking to estimate MEI from MPR and fermentation traits appears to be the variation between animals and between diets, in the proportion of digested energy which is fermented relative to that which is made available by mammalian digestion, and this is evaluated.
The burden of rotavirus gastroenteritis in children presenting to a paediatric hospital
Authors: INGLIS E. , KESSON A. , NEWALL A. T. , MACARTNEY K. , MacINTYRE C. R. 
Published: November 2008

SUMMARYThe aim of this study was to determine the burden, management and outcomes of rotavirus infection in young children presenting to a tertiary paediatric hospital in Sydney, Australia. All laboratory-confirmed cases of rotavirus in children aged <5 years were identified and medical records reviewed. In 2004, 80 children aged <5 years presented to the hospital with rotavirus gastroenteritis confirmed by stool testing. Infants aged <24 months comprised 75% of cases, with more males than females affected. Most children (86%) acquired rotavirus infection in the community, with a mean length of hospital admission of 2·3 days. There were eight cases of nosocomial infection at a rate of 3/10 000 admissions. The rates of intravenous fluid management (46%) and antibiotic use (28%) were high, reflecting the severity of disease presenting in a hospital setting. These data will help inform the assessment of the recently introduced rotavirus vaccination programme in Australia.
PocketMatch: A new algorithm to compare binding sites in protein structures
Authors: Kalidas Yeturu , Chandra Nagasuma 
Published: November 2008

Abstract
Background:
Recognizing similarities and deriving relationships among protein molecules is a fundamentalrequirement in present-day biology. Similarities can be present at various levels which can be detected through comparison of protein sequences or their structural folds. In some cases similarities obscure at these levels could be present merely in the substructures at their binding sites. Inferring functional similarities between protein molecules by comparing their binding sites is still largely exploratory and not as yet a routine protocol. One ofthe main reasons for this is the limitation in the choice of appropriate analytical tools that can compare binding sites with high sensitivity. To benefit from the enormous amount of structural data that is being rapidly accumulated, it is essential to have high throughput tools that enable large scale binding site comparison.

Results:
Here we present a new algorithm PocketMatch for comparison of binding sites in a frame invariantmanner. Each binding site is represented by 90 lists of sorted distances capturing shape and chemical nature of the site. The sorted arrays are then aligned using an incremental alignment method and scored to obtain PMScores for pairs of sites. A comprehensive sensitivity analysis and an extensive validation of the algorithm have been carried out. Perturbation studies where the geometry of a given site was retained but the residue types were changed randomly, indicated that chance similarities were virtually non-existent. Our analysis also demonstrates that shape information alone is insufficient to discriminate between diverse binding sites, unlesscombined with chemical nature of amino acids.

Conclusions:
A new algorithm has been developed to compare binding sites in accurate, efficient andhigh-throughput manner. Though the representation used is conceptually simplistic, we demonstrate that alongwith the new alignment strategy used, it is sufficient to enable binding comparison with high sensitivity. Novel methodology has also been presented for validating the algorithm for accuracy and sensitivity with respect to geometry and chemical nature of the site. The method is also fast and takes about 1/250th second for one comparison on a single processor. A parallel version on BlueGene has also been implemented.
Surface Modified Ultrathin Polyelectrolyte Nanoreservoir for Delivery of Proteins: Evaluation in Terms of Controlled Release and Biocompatibility
Authors: Gupta Girish Kumar , Jain Vikas , Mishra Prabhat Ranjan 
Published: November 2008

AbstractThe proposed ultrathin polyelectrolyte nanoreservoir (UPN) was fabricated in two combinations by alternate layering of polyelectrolytes poly (allylamine hydrochloride) along with sodium poly (styrene sulfonate) (PAH/PSS)5 and sodium alginate (PAH/SA)5 using porous calcium carbonate as a template using layer-by-layer adsorption technique with the subsequent template removal at low pH. We studied the possibility whether remnant intact nanoreservoir could be suited for encapsulation as well as delivery vehicle for protein such as bovine serum albumin as a model. To tune biocompatibility with biological cells the assembled surface was modified using pluronic (F-68) by adsorption and possible hydrophobic interaction. The prepared system was characterized for surface morphology, size and size distribution, surface charge, layer-by-layer growth due to sequential adsorption and surface modification. The experimental data obtained by Differential Scanning Calorimetry (DSC) and Fourier Transform Infrared Spectroscopy (FTIR) provide evidence for the stepwise surface modification of the films. Further the system was investigated for payload efficiency of proteins, in-vitro release profile, integrity of proteins, cell adhesion and viability against biological cells (murine macrophages cell line J774.1). In both formulations polyelectrolyte composition lead to smooth and spherical nanomatrix, with payload of approx. 72±6% of proteins. Both the systems exhibited biphasic release profile with initial burst release followed by controlled release with overall release of 43.63±4.8% and 44±5.76% in 48h for formulation prepared by combination of (PAH/PSS)5 and (PAH/SA)5 respectively. There was a marked reduction in cell adhesion and improvement in viability upon surface modification. In a nutshell, the proposed system could successfully be used for the delivery of proteins and moreover the system can be tailored to impart desired properties at any stage of layering especially in terms of drug release and to retain the integrity of proteins.
Breaking the habit: a retrospective analysis of desistance factors among formerly problematic heroin users
Authors: BEST DAVID W. , GHUFRAN SAFEENA , DAY ED , RAY RAJASHREE , LOARING JESSICA 
Published: November 2008

AbstractIntroduction and Aims. The aim of this study was to examine heroin careers among former users to assess desistance factors and explanations for sustained abstinence. Design and Methods. The study surveyed 107 former problematic heroin users who have achieved long‐term abstinence about their experiences of achieving and sustaining abstinence. The cohort was recruited opportunistically from three sources, drawing heavily on former users working in the addictions field. Results. On average, the group had heroin careers lasting for just under 10 years, punctuated by an average of 2.6 treatment episodes and 3.1 periods of abstinence, and had been heroin abstinent for an average of 10 years at the time of completing the survey. The most commonly expressed reason for finally achieving abstinence was ‘tired of the lifestyle followed by reasons relating to psychological health. In contrast, when asked to explain how abstinence was sustained, clients quoted both social network factors (moving away from drug‐using friends and support from non‐using friends) and practical factors (accommodation and employment) as well as religious or spiritual factors. Treatment was not mentioned widely either in achieving or sustaining abstinence, in contrast to 12‐Step, which was endorsed widely. Discussion and Conclusions. The study supports a careers perspective for examining heroin careers and indicates that, while achieving abstinence is possible for chronic opiate users, the path to sustained abstinence is complex and often reliant upon external support systems.
Effect of zoledronic acid on oral fibroblasts and epithelial cells: a potential mechanism of bisphosphonate‐associated osteonecrosis
Authors: Scheper Mark A. , Badros Ashraf , Chaisuparat Risa , Cullen Kevin J. , Meiller Timothy F. 
Published: November 2008

SummaryOsteonecrosis of the jaw secondary to bisphosphonate infusion (zoledronic acid‐ZA) is assumed to be a bone disease. This study investigated the effects of ZA on soft tissues using oral mucosal cells as an in vitro model of soft tissue cell death in the pathogenesis of bone necrosis. Human gingival fibroblast and keratinocyte cell lines were exposed to different concentrations of ZA (0·25–3 μmol/l), using 1 μmol/l as the expected baseline concentration. A dose–response effect on apoptosis and cell proliferation [Terminal deoxynucleotidyl transferase‐mediated dUTP‐Biotin End Labelling and Annexin V or Coulter counter and 3‐(4,5‐dimethylthiazol‐2‐yl)‐5‐(3‐carboxymethoxyphenyl)‐2‐(4‐sulfophenyl)‐2H‐tetrazolium), respectively] was observed with increasing ZA concentrations; both reversed using siRNA against caspase 3 or 9. Gene expression analysis using RT2 Profiler polymerase chain reaction Arrays demonstrated the differential expression of multiple genes involved in apoptosis including those that encode TNF, BCL‐2, Caspase, IAP, TRAF and Death Domain families. Western blot analysis confirmed the presence of activated forms of caspase 3 and 9 and underexpression of survivin protein expression. This study demonstrated that low concentrations of ZA rapidly and directly affected the oral mucosal tissues though the induction of a gene‐regulated apoptotic process. These findings support the potential for soft tissue injury as an initiating/potentiating event for osteonecrosis.
Immunoglobulin E antibodies enhance pulmonary inflammation induced by inhalation of a chemical hapten
Authors: Mathias C. B. , Freyschmidt E‐J. , Oettgen H. C. 
Published: November 2008

SummaryBackground
Occupational exposure to chemicals is an important cause of asthma. Recent studies indicate that IgE antibodies enhance sensitization to chemicals in the skin.Objective
We investigated whether IgE might similarly promote the development of airway inflammation following inhalation of a contact sensitizer.Methods
A model of chemical‐induced asthma is described in which introduction of the low‐molecular‐weight compound, trinitrobenzene sulphonic acid (TNBS), via the respiratory tract was used for both sensitization and challenge. The role of IgE antibodies in the immune response to inhaled TNBS in this model was assessed by comparing the responses of wild‐type (WT) and IgE‐deficient (IgE−/−) mice on the BALB/c background. Reconstitution of circulating IgE levels by intravenous injection of IgE antibodies into IgE−/− mice before sensitization was performed to confirm the role of IgE in any differences observed between the responses of WT and IgE−/− mice.Results
Intranasal challenge of TNBS‐sensitized (but not sham‐sensitized control mice) induced intense pulmonary inflammation. Macrophages, eosinophils and lymphocytes, including T, B, natural killer and natural killer T cells, were recruited to the airway and the animals displayed bronchial hyperresponsiveness (BHR) to methacholine. Serum levels of murine mast cell protease‐1 (mMCP‐1) were elevated suggesting mast cell activation. In contrast, the development of airway inflammation, recruitment of lymphocytes, induction of BHR and production of mMCP‐1 were all significantly attenuated in IgE‐deficient mice. Reconstitution of IgE−/− mice with IgE (of unrelated antigen specificity) before sensitization partially restored these features of asthma.Conclusion
Our data indicate that IgE antibodies non‐specifically enhance the development of airway inflammation induced by exposure to chemical antigens.
Feasibility of endoscopic papillectomy in early stage ampulla of Vater cancer
Authors: Woo Sang Myung , Ryu Ji Kon , Lee Sang Hyub , Lee Woo Jin , Hwang Jin Hyok , Yoo Ji Won , Park Joo Kyung , Kang Gyeong Hoon , Kim Yong‐Tae , Yoon Yong Bum 
Published: November 2008

AbstractBackground and Aim:  Although endoscopic papillectomy has been attempted in early stage ampullary cancer (pTis, T1), its curative role and indications remain uncertain. The present study was designed to assess the factors that predict malignancy and lymph node metastasis and to suggest potential indications for endoscopic papillectomy by analyzing clinicopathological data.Methods:  We performed a retrospective analysis of clinical and histopathological data of 216 patients with ampullary cancer between 1991 and 2006.Results:  No tumor in pTis stage had metastasized to lymph nodes and only 9% of tumors in pT1 had metastasized. Tumor size (P = 0.018), depth of invasion (P = 0.021) and venous invasion (P = 0.014) were found to be significantly related to lymph node metastasis. Cases with early stage ampullary cancer of less than 2 cm with a well‐differentiated histology and no angiolymphatic invasion (n = 13) showed no lymph node metastasis and no recurrence during a median follow up of 35.9 months.Conclusion:  Endoscopic papillectomy can be adopted as a viable alternative to surgery in patients with early stage ampullary cancer of less than 2 cm in size and with a well‐differentiated histology. When a resected specimen has a well‐differentiated histology, and there is no resection margin involvement and no angiolymphatic invasion, our findings indicate that subsequent radical surgery is unnecessary.
Treatment of patients with gastric variceal hemorrhage: Endoscopic N‐butyl‐2‐cyanoacrylate injection versus balloon‐occluded retrograde transvenous obliteration
Authors: Hong Cheul Ho , Kim Hong Joo , Park Jung Ho , Park Dong Il , Cho Yong Kyun , Sohn Chong Il , Jeon Woo Kyu , Kim Byung Ik , Hong Hyun Pyo , Shin Jun Ho 
Published: November 2008

AbstractBackground and Aim:  Our study aimed to evaluate the therapeutic results of endoscopic N‐butyl‐2‐cyanoacrylate injection (EBC) and balloon‐occluded retrograde transvenous obliteration (BRTO) in patients with gastric variceal hemorrhage (GVH) and/or high‐risk gastric varices (GV).Methods:  Twenty‐seven patients with GVH and/or high‐risk GV (≥ 5 mm in diameter, those with red spots, and a Child–Pugh grading of B or C liver cirrhosis) who were treated with either EBC or BRTO from April 2005 to December 2007 were included in our study.Results:  EBC or BRTO was initially used for the treatment of GVH in 14 and 13 patients, respectively. Technical success was achieved in all 14 patients (100%) initially treated with EBC, and 10 of 13 patients (76.9%) initially treated with BRTO. Significant rebleeding occurred in 10 patients (71.4%) of the EBC group, and two patients (15.4%) of BRTO group (P < 0.01). Five of six patients (83.3%) treated with rescue BRTO due to rebleeding after initial EBC achieved technical success, and all six patients who were treated with rescue BRTO had no rebleeding during the median follow up of 17 (range: 2–37) months. The cumulative survival rate of the EBC with the BRTO rescue group/BRTO group was significantly higher than the EBC group.Conclusion:  The therapeutic efficacies of EBC and BRTO for the treatment of active GVH and/or high‐risk GV appeared to be similar. However, EBC might be associated with a higher rebleeding rate than BRTO. BRTO could be an effective rescue treatment for patients with GVH after initial treatment of EBC.