bluuebunny/crossref_metadata_2025_split huggingface dataset:
Do Young Colon Cancer Patients Have Worse Outcomes?
Authors: O’Connell Jessica B. , Maggard Melinda A. , Liu Jerome H. , Etzioni David A. , Livingston Edward H. , Ko Clifford Y. 
Published: May 2004

AbstractPrevious studies on colon cancer have noted rising incidence rates among young individuals and suggest that they may have more aggressive disease and worse 5‐year survivals than their older counterparts. Our study uses a nationwide population‐based cancer registry to analyze colon cancer presentations and outcomes in a young versus an older population. The records of patients with colon carcinoma were obtained from the Surveillance, Epidemiology, and End Results (SEER) national cancer database (1991–1999). Two cohorts based on age at diagnosis (20–40 years, n = 1334 vs. 60–80 years, n = 46,457) were compared for patient and tumor characteristics, treatment, and 5‐year cancer‐specific survival. A multivariate Cox regression was performed to identify predictors of survival. The young group had a higher proportion of black and Hispanic patients than did the older group (p < 0.001). Young patients had less stage I or II disease, more stage III or IV disease (p < 0.001), and worse‐grade (poorly differentiated or anaplastic) tumors (p < 0.001). The 5‐year stage‐specific survival was similar for stage I and III disease (p = NS) but was significantly better for young patients with stage II and IV disease (p < 0.01). Using a nationally representative cancer registry, we found that young colon cancer patients tend to have later‐stage and higher‐grade tumors. However, they have equivalent or better 5‐year cancer‐specific survival compared to older patients. This population‐based finding contradicts prior single‐institution reports.
Galen on Obesity: Etiology, Effects, and Treatment
Authors: Papavramidou Niki S. , Papavramidis Spiros T. , Christopoulou‐Aletra Helen 
Published: May 2004

AbstractOnly a few studies have been conducted to determine the historical background of obesity, and even fewer have focused on specific writers who have made great contributions on the subject. Galen was among the first to establish scientific methods to describe and treat morbid obesity, and a presentation of his ideas is important because of the influence he has exerted even up to modern times. The methodology of the current research was based on detailed study of Galen’s treatises, which concern the nature of obesity, the etiology, the consequences, and the treatment, often in comparison to the writings of other writers from the Hippocratic period up to recent years. Galen stated that obesity results from the surplus of “bad humors” in the body and specifically from a surplus of blood. He specifically described patients’ conditions, both physiologic and practical; he presented side effects; and he introduced methods of treatment that are used even today. Galen also described an illness he called polisarkia, which today we call morbid obesity. According to Galen’s views, we can identify morbid obesity under the description of polisarkia. Galenic physiology and pathology have been proved wrong and have been set aside. Nevertheless, he proposed some treatments for obesity such as diet, exercise, and medications that are still valuable and are nearly the same as what is advocated today.
Development of a fermentation system to model sessile bacterial populations in the human colon
Authors: Probert H. M. , Gibson G. R. 
Published: May 2004

A fermentation system was designed to model the human colonic microflora in vitro. The system provided a framework of mucin beads to encourage the adhesion of bacteria, which was encased within a dialysis membrane. The void between the beads was inoculated with faeces from human donors. Water and metabolites were removed from the fermentation by osmosis using a solution of polyethylene glycol (PEG). The system was concomitantly inoculated alongside a conventional single-stage chemostat. Three fermentations were carried out using inocula from three healthy human donors.Bacterial populations from the chemostat and biofilm system were enumerated using fluorescence in situ hybridization. The culture fluid was also analysed for its short-chain fatty acid (SCFA) content. A higher cell density was achieved in the biofilm fermentation system (taking into account the contribution made by the bead-associated bacteria) as compared with the chemostat, owing to the removal of water and metabolites. Evaluation of the bacterial populations revealed that the biofilm system was able to support two distinct groups of bacteria: bacteria growing in association with the mucin beads and planktonic bacteria in the culture fluid. Furthermore, distinct differences were observed between populations in the biofilm fermenter system and the chemostat, with the former supporting higher populations of clostridia and Escherichia coli. SCFA levels were lower in the biofilm system than in the chemostat, as in the former they were removed via the osmotic effect of the PEG. These experiments demonstrated the potential usefulness of the biofilm system for investigating the complexity of the human colonic microflora and the contribution made by sessile bacterial populations.
Neuronal nitric oxide synthase gene expression in human pituitary tumours: a possible association with somatotroph adenomas and growth hormone‐releasing hormone gene expression
Authors: Ueta Yoichi , Levy Andrew , Powell Michael P. , Lightman Stafford L. , Kinoshita Yoshimasa , Yokota Akira , Shibuya Izumi , Yamashita Hiroshi 
Published: May 2004

OBJECTIVENitric oxide (NO) has been implicated in the control of the secretory response to growth hormone‐releasing hormone (GHRH) and may also modify GH release in response to excitatory aminoacids. Although rat and mouse pituitary cell lines have been shown to express neuronal NO synthase (nNOS), there has until now been no information on nNOS gene expression in human pituitary adenomas. Our objective was to provide such data and correlate the presence of nNOS transcripts with GHRH transcripts.PATIENTSPituitary adenoma tissue was obtained from a random selection of 32 patients with somatotrophadenomas, 16 patients with corticotroph adenomas, 39 patients with endocrinologically inactive adenomas and nine patients with macroprolactinomas undergoing transsphenoidal hypophysectomy.MEASUREMENTSTranscripts for nNOS and GHRH were indentified in frozen tissue sections by in situ hybridization histochemistry using synthetic 35S‐labelled oligodeoxynucleotide probes with 100% homology to the target transcript.RESULTSNeuronal NOS transcripts were identified in one of 16 corticotroph adenomas (6%), one of nine macroprolactinomas (11%), six of 39 endocrinologically inactive adenomas (15%) and 13 of 32 somatotroph adenomas (41%). GHRH transcripts were found in a similar distribution to nNOS transcripts in 10 of the 13 nNOS‐expressing somatotroph adenomas, and in three of the four remaining adenomas from which suitable tissue was available. Cross‐hybridization of the nNOS and GHRH probes to the same target was excluded by including rat brain sections cut through the arcuate nucleus as hybridization controls. Furthermore, two different nNOS oligodeoxynucleotide probes complementary to different regions of the target transcript produced identical results.CONCLUSIONSThese results suggest that there is a close correlation between nNOS gene expression and ‘ectopic’ expression of GHRH in human pituitary tumours, especially somatotroph adenomas. The relevance of these findings from a functional or pathologenic viewpoint remains unclear, but the data again emphasize that it is not just GH secretion that distinguishes somatotroph adenomas from other pituitary tumours.
Intravenous glycerol therapy should not be used in patients with unrecognized fructose‐1,6‐bisphosphatase deficiency
Authors: HASEGAWA YUKIHIRO , KIKAWA YOSHIHARU , MIYAMAOTO JUNKO , SUGIMOTO SHUJI , ADACHI MASANORI , OHURA TOSHIHIRO , MAYUMI MITSUFUMI 
Published: May 2004

Abstract

Background
: In Asian countries, glycerol solution that contains fructose (5%) is often used for management of brain edema. However, glycerol and fructose may cause severe hypoglycemia and metabolic acidosis in patients with fructose‐1,6‐bisphosphatase (FBPase) deficiency, even under stable conditions. The aim of the present study was to determine whether glycerol solution was used for brain edema during acute metabolic decompensation of hypoglycemia and metabolic acidosis in patients with unrecognized FBPase deficiency in Japan and to examine a long‐term prognosis of the patients who had this kind of severe metabolic decompensation with or without glycerol therapy.
Methods
: A retrospective study of 20 children with FBPase deficiency was conducted, based on their medical records.
Results
: Six of the 20 children were given glycerol solution for the presence or possibility of brain edema during acute metabolic decompensation of hypoglycemia and metabolic acidosis; two of the six patients administered with glycerol were given dialysis. In four patients treated with glycerol alone without dialysis, two had no brain edema before glycerol administration but it developed later after the administration. These four patients treated with glycerol alone died or developed severe neurological complications. Fourteen patients who were not treated with glycerol solution had no brain edema and showed good prognosis.
Conclusion
: Glycerol solution, which contains fructose in Asian countries including Japan, should not be used as an osmotic agent for treatment of brain edema in patients who have hypoglycemia and retention‐type metabolic acidosis, until FBPase deficiency is ruled out by measuring blood concentration of lactate.
Analysis of the circumstances at the end of life in children with cancer: A single institution's experience in Japan
Authors: FUJII YUJI , WATANABE CHIEKO , OKADA SHUICHI , INOUE NORIKO , ENDOH AKIRA , YAJIMA SHUHEI , HONGO TERUAKI , OHZEKI TAKEHIKO , SUZUKI ERIKO 
Published: May 2004

Abstract

Background
: With the aim of improving the quality of life of children with cancer, this study presents an analysis of one hospital's experience with terminal care.
Methods
: Between 1994 and 2000, 28 children died after treatment for cancer at Hamamatsu University Hospital. The circumstances of their deaths were analyzed through medical records and interviews with 8 sets of bereaved parents. We compared results of this analysis with our previous data collected from 1978 to 1993.
Results
: Of the 28 children, 11 had leukemia/lymphoma (LL group) and 17 had solid tumors (ST group). Six children (21.4%), all of whom were in the LL group, died of treatment‐related complications. Twenty children (71.4%) died during terminal care: three (27.3%) were in the LL group and 17 (100%) in the ST group. Eleven children (39.3%) received terminal care at home and eight (28.6%) of these died at home. The number of children who received terminal care and died at home had increased in comparison with the previous period. Among problems with terminal care identified by parents were the lack of opportunity for the child to continue with education and an inadequate support system after the child's death.
Conclusions
: Some advances in the quality of life of the children were recognized. However, these advances were extended to a greater percentage of children in the ST group than in the LL group. The psychosocial problems faced by children and their families are now changing for the better.
Analysis of the circumstances at the end of life in children with cancer: Symptoms, suffering and acceptance
Authors: HONGO TERUAKI , WATANABE CHIEKO , OKADA SHUICHI , INOUE NORIKO , YAJIMA SHUHEI , FUJII YUJI , OHZEKI TAKEHIKO 
Published: May 2004

Abstract

Background
: In an effort to improve the quality of life of children with cancer, this study analyzes the signs and symptoms at the end of life in such children. It is hoped that these data will contribute to the development of appropriate programs to address the challenges faced by these children.
Procedure
: Between 1994 and 2000, 28 children died after treatment for cancer at Hamamatsu University Hospital, Japan. The circumstances, signs and symptoms at the end of life of these children were analyzed through their medical records.
Results
: Of the 28 children, the underlying diseases were leukemia/lymphoma (LL group; n=11), brain tumors (BT group; n=7), and other solid tumors (OST group; n=10). Records showed poor appetite (100%), dyspnea (82.1%), pain (75.0%), fatigue (71.4%), nausea/vomiting (57.1%), constipation (46.4%) and diarrhea (21.4%) among these children. Anxiety was reported in 53.6% of the entire group of 28 children; however, no child in the BT group manifested anxiety. However, disturbance of consciousness was reported in all children in the BT group, which was significantly greater than in the other groups. Awareness, fear or acceptance of the imminence of his/her own death as indicated by verbal expression was reported in nine children (32.1%).
Conclusions
: Using the data obtained in the present study, we describe situations faced in the terminal care of children. It is important to address the problems revealed by this analysis in order to achieve improvements in both the physical and psychological care of children with terminal cancer.
Prevention of antibiotic‐associated diarrhea in children by Clostridium butyricum MIYAIRI
Authors: SEKI HIROMI , SHIOHARA MASAAKI , MATSUMURA TADAO , MIYAGAWA NATSUKI , TANAKA MAMORU , KOMIYAMA ATSUSHI , KURATA SUSUMU 
Published: May 2004

Abstract

Background
: Clostridium butyricum MIYAIRI (CBM) is a probiotic bacteria used for anti‐diarrheal medicine in Japan. The preventive effect of CBM was investigated for antibiotic‐associated diarrhea (AAD) in children.
Methods
: One hundred and ten children who suffered from upper respiratory tract infection or gastroenteritis were divided into three groups. Twenty‐seven of the patients received only antibiotics, 38 received CBM from the mid point of the antibiotic treatment and 45 concomitantly received CBM from the beginning of the antibiotic treatment. To examine the effects of CBM on AAD, the changes in intestinal flora were investigated.
Results
: Diarrhea was observed in 59% of the subjects who received only antibiotics, and total fecal anaerobes, especially Bifidobacterium, were remarkably decreased. In contrast, diarrhea in the subjects who received CBM from either the middle or the beginning of the antibiotic therapy was decreased to 5% and 9%, respectively. Concomitant administration of CBM increased anaerobes and prevented the decrease of Bifidobacterium in the subjects who received antibiotics.
Conclusion
: Clostridium butyricum MIYAIRI is effective for both the treatment and the prophylaxis of AAD in children, as it normalizes the intestinal flora disturbed by antibiotics.
HPID: The Human Protein Interaction Database
Authors: Han Kyungsook , Park Byungkyu , Kim Hyongguen , Hong Jinsun , Park Jong 
Published: May 2004

Abstract
Summary: The Human Protein Interaction Database (http://www.hpid.org) was designed (1) to provide human protein interaction information pre-computed from existing structural and experimental data, (2) to predict potential interactions between proteins submitted by users and (3) to provide a depository for new human protein interaction data from users. Two types of interaction are available from the pre-computed data: (1) interactions at the protein superfamily level and (2) those transferred from the interactions of yeast proteins. Interactions at the superfamily level were obtained by locating known structural interactions of the PDB in the SCOP domains and identifying homologs of the domains in the human proteins. Interactions transferred from yeast proteins were obtained by identifying homologs of the yeast proteins in the human proteins. For each human protein in the database and each query submitted by users, the protein superfamilies and yeast proteins assigned to the protein are shown, along with their interacting partners. We have also developed a set of web-based programs so that users can visualize and analyze protein interaction networks in order to explore the networks further.
Availability: http://www.hpid.org
Supplementary information: http://wilab.inha.ac.kr/HPID/Statistics.htm
SIMCOAL 2.0: a program to simulate genomic diversity over large recombining regions in a subdivided population with a complex history
Authors: Laval Guillaume , Excoffier Laurent 
Published: May 2004

Abstract
Summary: We present an extension of the program SIMCOAL, which allows for simulation of the genomic diversity of samples drawn from a set of populations with arbitrary patterns of migrations and complex demographic histories, including bottlenecks and various modes of demographic expansion. The main additions to the previous version include the possibility of arbitrary and heterogeneous recombination rates between adjacent loci and multiple coalescent events per generation, allowing for the simulation of very large samples and recombining genomic regions, together with the simulation of single nucleotide polymorphism data with frequency ascertainment bias.
Availability: http://cmpg.unibe.ch/software/simcoal2/
Supplementary information: http://cmpg.unibe.ch/software/simcoal2/
Identification of DNA regulatory motifs using Bayesian variable selection
Authors: Tadesse Mahlet G. , Vannucci Marina , Liò Pietro 
Published: May 2004

Abstract
Motivation: Understanding the mechanisms that determine gene expression regulation is an important and challenging problem. A common approach consists of identifying DNA-binding sites from a collection of co-regulated genes and their nearby non-coding DNA sequences. Here, we consider a regression model that linearly relates gene expression levels to a sequence matching score of nucleotide patterns. We use Bayesian models and stochastic search techniques to select transcription factor binding site candidates, as an alternative to stepwise regression procedures used by other investigators.
Results: We demonstrate through simulated data the improved performance of the Bayesian variable selection method compared to the stepwise procedure. We then analyze and discuss the results from experiments involving well-studied pathways of Saccharomyces cerevisiae and Schizosaccharomyces pombe. We identify regulatory motifs known to be related to the experimental conditions considered. Some of our selected motifs are also in agreement with recent findings by other researchers. In addition, our results include novel motifs that constitute promising sets for further assessment.
Availability: The Matlab code for implementing the Bayesian variable selection method may be obtained from the corresponding author.
Predicting allergenic proteins using wavelet transform
Authors: Li Kuo-Bin , Issac Praveen , Krishnan Arun 
Published: May 2004

Abstract
Motivation: With many transgenic proteins introduced today, the ability to predict their potential allergenicity has become an important issue. Previous studies were based on either sequence similarity or the protein motifs identified from known allergen databases. The similarity-based approaches, although being able to produce high recalls, usually have low prediction precisions. Previous motif-based approaches have been shown to be able to improve the precisions on cross-validation experiments. In this study, a system that combines the advantages of similarity-based and motif-based prediction is described.
Results: The new prediction system uses a clustering algorithm that groups the known allergenic proteins into clusters. Proteins within each cluster are assumed to carry one or more common motifs. After a multiple sequence alignment, proteins in each cluster go through a wavelet analysis program whereby conserved motifs will be identified. A hidden Markov model (HMM) profile will then be prepared for each identified motif. The allergens that do not appear to carry detectable allergen motifs will be saved in a small database. The allergenicity of an unknown protein may be predicted by comparing it against the HMM profiles, and, if no matching profiles are found, against the small allergen database by BLASTP. Over 70% of recall and over 90% of precision were observed using cross-validation experiments. Using the entire Swiss-Prot as the query, we predicted about 2000 potential allergens.
Availability: The software is available upon request from the authors.
RRE: a tool for the extraction of non-coding regions surrounding annotated genes from genomic datasets
Authors: Lazzarato F. , Franceschinis G. , Botta M. , Cordero F. , Calogero R. A. 
Published: May 2004

Abstract
Summary: RRE allows the extraction of non-coding regions surrounding a coding sequence [i.e. gene upstream region, 5′-untranslated region (5′-UTR), introns, 3′-UTR, downstream region] from annotated genomic datasets available at NCBI.
Availability: RRE parser and web-based interface are accessible at http://www.bioinformatica.unito.it/bioinformatics/rre/rre.html
Genome wide identification and classification of alternative splicing based on EST data
Authors: Gupta S. , Zink D. , Korn B. , Vingron M. , Haas S. A. 
Published: May 2004

Abstract
Motivation: Alternative splicing is currently seen to explain the vast disparity between the number of predicted genes in the human genome and the highly diverse proteome. The mapping of expressed sequences tag (EST) consensus sequences derived from the GeneNest database onto the genome provides an efficient way of predicting exon–intron boundaries, gene structure and alternative splicing events. However, the alternative splicing events are obscured by a large number of putatively artificial exon boundaries arising due to genomic contamination or alignment errors. The current work describes a methodology to associate quality values to the predicted exon–intron boundaries. High quality exon–intron boundaries are used to predict constitutive and alternative splicing ranked by confidence values, aiming to facilitate large-scale analysis of alternative splicing and splicing in general.
Results: Applying the current methodology, constitutive splicing is observed in 33 270 EST clusters, out of which 45% are alternatively spliced. The classification derived from the computed confidence values for 17 of these splice events frequently correlate (15/17) with RT–PCR experiments performed for 40 different tissue samples. As an application of the confidence measure, an evaluation of distribution of alternative splicing revealed that majority of variants correspond to the coding regions of the genes. However, still a significant fraction maps to non-coding regions, thereby indicating a functional relevance of alternative splicing in untranslated regions.
Availability: The predicted alternative splice variants are visualized in the SpliceNest database at http://splicenest.molgen.mpg.de
Supplementary information: For supplementary data, please refer Bioinformatics Online.
Gene-Ontology-based clustering of gene expression data
Authors: Adryan Boris , Schuh Reinhard 
Published: May 2004

Abstract
Summary: The expected correlation between genetic co-regulation and affiliation to a common biological process is not necessarily the case when numerical cluster algorithms are applied to gene expression data. GO-Cluster uses the tree structure of the Gene Ontology database as a framework for numerical clustering, and thus allowing a simple visualization of gene expression data at various levels of the ontology tree.
Availability: The 32-bit Windows application is freely available at http://www.mpibpc.mpg.de/go-cluster/
Supplementary information: A comprehensive software manual, hints for troubleshooting and commented examples are available from the website.