bluuebunny/crossref_metadata_2025_split huggingface dataset:
Efficient selection of unique and popular oligos for large EST databases
Authors: Zheng Jie , Close Timothy J. , Jiang Tao , Lonardi Stefano 
Published: April 2004

Abstract
Motivation: Expressed sequence tag (EST) databases have grown exponentially in recent years and now represent the largest collection of genetic sequences. An important application of these databases is that they contain information useful for the design of gene-specific oligonucleotides (or simply, oligos) that can be used in PCR primer design, microarray experiments and genomic library screening.
Results: In this paper, we study two complementary problems concerning the selection of short oligos, e.g. 20–50 bases, from a large database of tens of thousands of ESTs: (i) selection of oligos each of which appears (exactly) in one unigene but does not appear (exactly or approximately) in any other unigene and (ii) selection of oligos that appear (exactly or approximately) in many unigenes. The first problem is called the unique oligo problem and has applications in PCR primer and microarray probe designs, and library screening for gene-rich clones. The second is called the popular oligo problem and is also useful in screening genomic libraries. We present an efficient algorithm to identify all unique oligos in the unigenes and an efficient heuristic algorithm to enumerate the most popular oligos. By taking into account the distribution of the frequencies of the words in the unigene database, the algorithms have been engineered carefully to achieve remarkable running times on regular PCs. Each of the algorithms takes only a couple of hours (on a 1.2 GHz CPU, 1 GB RAM machine) to run on a dataset 28 Mb of barley unigenes from the HarvEST database. We present simulation results on the synthetic data and a preliminary analysis of the barley unigene database.
Availability: Available on request from the authors.
A weighted least-squares approach for inferring phylogenies from incomplete distance matrices
Authors: Makarenkov Vladimir , Lapointe François-Joseph 
Published: April 2004

Abstract
Motivation: The problem of phylogenetic inference from datasets including incomplete or uncertain entries is among the most relevant issues in systematic biology. In this paper, we propose a new method for reconstructing phylogenetic trees from partial distance matrices. The new method combines the usage of the four-point condition and the ultrametric inequality with a weighted least-squares approximation to solve the problem of missing entries. It can be applied to infer phylogenies from evolutionary data including some missing or uncertain information, for instance, when observed nucleotide or protein sequences contain gaps or missing entries.
Results: In a number of simulations involving incomplete datasets, the proposed method outperformed the well-known Ultrametric and Additive procedures. Generally, the new method also outperformed all the other competing approaches including Triangle and Fitch which is the most popular least-squares method for reconstructing phylogenies. We illustrate the usefulness of the introduced method by analyzing two well-known phylogenies derived from complete mammalian mtDNA sequences. Some interesting theoretical results concerning the NP-hardness of the ordinary and weighted least-squares fitting of a phylogenetic tree to a partial distance matrix are also established.
Availability: The T-Rex package including this method is freely available for download at http://www.info.uqam.ca/~makarenv/trex.html
MuSiC: a tool for multiple sequence alignment with constraints
Authors: Tsai Yin Te , Huang Yen Pin , Yu Ching Ta , Lu Chin Lung 
Published: April 2004

Abstract
Summary: MuSiC is a web server to perform the constrained alignment of a set of sequences, such that the user-specified residues/nucleotides are aligned with each other. The input of the MuSiC system consists of a set of protein/DNA/RNA sequences and a set of user-specified constraints, each with a fragment of residue/nucleotide that (approximately) appears in all input sequences. The output of MuSiC is a constrained multiple sequence alignment in which the fragments of the input sequences whose residues/nucleotides exhibit a given degree of similarity to a constraint are aligned together. The current MuSiC system is implemented in Java language and can be accessed via a simple web interface.
Availability: http://genome.life.nctu.edu.tw/MUSIC
Drawing phylogenetic trees in LATEX and Microsoft Word
Authors: Savva George , Conn Jenn , Dicks Jo 
Published: April 2004

Abstract
Summary: newicktree is a PSTricks-based LATEX package which enables phylogenetic trees described in the Newick format to be drawn directly into LATEX documents. mswordtree is a macro for producing phylogenetic trees using the drawing elements available in Microsoft Word.
Availability: Both programs are available free from the John Innes Centre's Bioinformatics Research Group website at http://jic-bioinfo.bbsrc.ac.uk/bioinformatics-research/software/index.html.
Supplementary information: A full user-guide for newicktree and installation and usage instructions for mswordtree and available at http://jic-bioinfo.bbsrc.ac.uk/bioinformatics-research/software/index.html
Spot shape modelling and data transformations for microarrays
Authors: Ekstrøm Claus Thorn , Bak Søren , Kristensen Charlotte , Rudemo Mats 
Published: April 2004

Abstract
Motivation: To study lowly expressed genes in microarray experiments, it is useful to increase the photometric gain in the scanning. However, a large gain may cause some pixels for highly expressed genes to become saturated. Spatial statistical models that model spot shapes on the pixel level may be used to infer information about the saturated pixel intensities. Other possible applications for spot shape models include data quality control and accurate determination of spot centres and spot diameters.
Results: Spatial statistical models for spotted microarrays are studied including pixel level transformations and spot shape models. The models are applied to a dataset from 50mer oligonucleotide microarrays with 452 selected Arabidopsis genes. Logarithmic, Box–Cox and inverse hyperbolic sine transformations are compared in combination with four spot shape models: a cylindric plateau shape, an isotropic Gaussian distribution and a difference of two-scaled Gaussian distribution suggested in the literature, as well as a proposed new polynomial-hyperbolic spot shape model. A substantial improvement is obtained for the dataset studied by the polynomial-hyperbolic spot shape model in combination with the Box–Cox transformation. The spatial statistical models are used to correct spot measurements with saturation by extrapolating the censored data.
Availability: Source code for R is available at http://www.matfys.kvl.dk/~ekstrom/spotshapes/
AliasServer: a web server to handle multiple aliases used to refer to proteins
Authors: Iragne Florian , Barré Aurélien , Goffard Nicolas , de Daruvar Antoine 
Published: April 2004

Abstract
Summary: AliasServer provides services that facilitate the assembly of data or datasets that make use of different identifiers for refering to the same protein. This resource relies on a database which contains, for a given organism, a non-redundant list of protein sequences associated with a set of aliases.
Availability: AliasServer is available as an interactive Web server at http://cbi.labri.fr/outils/alias/ and as a web service using a SOAP interface. The complete tool, including sources and data, is available for local installations upon request.
Supplementary information: Technical documentation is available at http://cbi.labri.fr/outils/alias/asdoc.pdf
Cyclic AMP phosphodiesterase activity in human gingival carcinoma
Authors: Spoto Giuseppe , Fioroni Massimiliano , Rubini Corrado , Di Nicola Maurizio , Di Pietrantonio Francesco , Di Matteo Elisabetta , Piattelli Adriano 
Published: April 2004

Background:  The phosphodiesterases (PDEs) are responsible for the hydrolysis of the second messengers, cyclic AMP (cAMP) and cyclic GMP (cGMP), to their corresponding monophosphates with a fundamental role in the transduction of the intracellular signals. At least 11 different enzymatic isoforms have been identified, which are listed according to their specificity or affinity for the substratum, identity of the amino acid sequence, cofactor, and inhibitor sensitivity. Variations in PDE activity have been found in different pathologies, and they have also been correlated to different pathological e/o physiological mechanisms, such as cellular differentiation, apoptosis, and tumor invasivity.Objectives:  In this study, we have evaluated cAMP PDE activity in patients with carcinoma of the gingiva, with the purpose of correlating differences in its development and progression. The same enzymatic activity has been used to evaluate differences between patients with lymph node involvement (group N+), and patients without lymph node involvement (N−).Materials and Methods:  The analysis of PDE activity and the cAMP assay was performed by reverse‐phase HPLC on samples of fresh or frozen gingival tissues. Analysis of cAMP was confirmed with the enzyme‐linked immunoabsorption assay (EIA).Results and Conclusions:  The differences between control and N– groups (P = 0.0433), and between control and N+ groups (P = 0.0156) were statistically significant. PDE3A was also evaluated immunohistochemically in lymph‐node negative and lymph‐node positive cases. The differences between the two groups were statistically significant (P = 0.0397).
Characterization of lymphoid infiltrates in chronic obstructive sialadenitis associated with sialolithiasis
Authors: Teymoortash Afshin , Tiemann Markus , Schrader Carsten , Werner Jochen A. 
Published: April 2004

Background:  Chronic obstructive sialadenitis is characterized by acinar atrophy, lymphocytic infiltrates and progressive fibrosis. The immunological mechanisms involved in the pathogenesis of this disease are, for the most part, unknown. The aim of the present study was to characterize the lymphocytic infiltrates in chronic obstructive sialadenitis associated with sialolithiasis.Methods:  Paraffin‐embedded tissue samples from 23 affected submandibular glands were immunostained for T‐cells (CD3, CD4, CD8), cytotoxic T‐cells (granzyme B), B‐cells (CD20), plasma cells (CD38) and macrophages (Ki‐M1P).Results:  CD4‐positive subsets were the predominant cells, and they were located mainly periductally. Isolated intraepithelial CD8‐positive cytotoxic T‐cells associated with ductal epithelial cell destruction were observed in all cases. B lymphocytes were restricted to lymphoid follicles located periductally and around intralobular ducts. In early stages of the disease, a large number of CD38‐positive plasma cells were distributed diffusely in the periacinar area. With progression of the disease, conspicuous clusters of plasma cells were located especially between atrophic acini adjacent to fibrotic tissue. An intimate relation between the lymphocytic infiltrates and the ductal epithelium, the target of the inflammatory process, was observed.Conclusion:  The composition and distribution of inflammatory cells suggest that intraepithelial infectious agents may be the cause of the inflammatory reaction and the progressive fibrosis in this disease.
Friction melanosis: a clinical, histologic, and ultrastructural study in Jordanian patients
Authors: Al‐Aboosi Mustafa , Abalkhail Ali , Kasim Omer , Al‐Khatib Aymen , Qarqaz Firas , Todd David , Al‐Khidour Munir , Obeidate Fawaz 
Published: April 2004

AbstractBackground  Friction melanosis (FM) is an acquired pigmentary disorder mainly affecting young people. The primary skin regions affected are located over the osseous prominences, especially the clavicular zone and upper back. Our purpose in this study was to report the clinical spectrum, histologic findings, and ultrastructural features of FM in Jordanian patients.Methods  Thirteen patients with FM (10 women and three men) were studied. The patients were seen at Princess Basma Teaching Hospital in north Jordan between 1999 and 2001.Results  Eleven patients presented with asymptomatic, diffuse, brownish patches and two presented with mottled patches on the skin over the trunk bones and limbs. All had a history of rubbing their skin repeatedly with scrub pads (loofah) or bathroom towels. Ten of the 13 cases were studied histologically. Skin biopsies from four patients were examined ultrastructurally. Both histologic and electron microscopic examination of the biopsies from our patients showed a marked increase in melanin and melanin incontinence, with a lack of amyloid in the upper dermis.Conclusions  FM is infrequently seen in north Jordan. We believe that repeated frictional trauma from clothing or scrub pads against the skin overlying the bony protuberances is fundamental in its pathogenesis. Other factors, such as scrub pads made of rough material (loofah), dark skin type, and individual variability, may also play a role in the pathogenesis. We advise patients not to use rough scrub pads during bathing, to avoid rubbing the skin overlying the bony prominences, to avoid rubbing vigorously, and to use a soft cotton pad instead.
Cutaneous sporotrichosis in Bangalore, southern India
Authors: Mohan Nagamani , Jayaseelan Elizabeth , Abraham Anil , Rajendran Srangipani C. , Stephen John , Sharief Shameen , Macaden Ragini 
Published: April 2004

AbstractBackground  Sporotrichosis is a granulomatous infection caused by Sporothrix schenkii. Although world‐wide in distribution, only four cases have been reported from southern India to date.Methods  The medical records of all cases seen at the Department of Dermatology at St John's Medical College Hospital, Bangalore, over the last 15 years were reviewed.Results  A total of seven cases of sporotrichosis were seen in this 15‐year period.Conclusion  Sporotrichosis is considered to occur only sporadically in southern India. Our findings suggest that this may be a result of reporting bias.
Satellite repigmentation after punch grafting
Authors: Agarwal Uma Shankar 
Published: April 2004

AbstractPunch grafting is an established treatment modality for management of localized, nonprogressive vitiligo resistant to conventional therapies.1 In our set up, punch grafting is routinely carried out in focal vitiligo, segmental vitiligo and even in few cases of generalized vitiligo, especially when it is a serious cosmetic problem.2 However, the procedure is adopted only when the disease is stable for a sufficient period. All patients are routinely kept on psoralen tablets and ultraviolet light exposure from sunlight (PUVA sol therapy) after 2–3 weeks of punch grafting. Interestingly, follow up of such patients revealed conspicuous repigmentation in surrounding ungrafted patches in four of the patients (out of 55 follow‐up cases). Herein, this phenomenon has been aptly termed satellite repigmentation (SR). To the best of our knowledge, no other report documenting SR after punch grafting exists in the medical literature. We report the observations of these four patients.
Comparative study of the efficacy of combined cryotherapy and intralesional meglumine antimoniate (Glucantime®) vs. cryotherapy and intralesional meglumine antimoniate (Glucantime®) alone for the treatment of cutaneous leishmaniasis
Authors: Asilian A. , Sadeghinia A. , Faghihi G. , Momeni A. 
Published: April 2004

AbstractBackground  Cutaneous leishmaniasis (CL) is a parasitic disease caused by Leishmania species. There is a need for more effective and less time‐consuming therapeutic methods for this condition.Aim  To evaluate the efficacy of combined cryotherapy and intralesional meglumine antimoniate (MA) (Glucantime®, Specia, Paris, France) for the treatment of CL.Methods  Patients were divided into three groups: Group 1, 100 patients with 149 lesions were treated with cryotherapy plus intralesional MA; Group 2, 200 patients with 230 lesions were treated with cryotherapy; Group 3, 100 patients with 160 lesions were treated with intralesional MA. These groups were followed for 6 months after the end of treatment.Results  The results showed complete cure in 90.9% of cases in Group 1, 57.15% of cases in Group 2, and 55.63% of cases in Group 3. The difference between Group 1 and the other groups was statistically significant (P < 0.05).Conclusions  Combined cryotherapy and intralesional MA is more effective than either cryotherapy or intralesional MA alone for the treatment of CL.
Angiotensin II type 1 receptor mRNA and its protein expression in human pancreatic cancer cell lines
Authors: Jiang Hua , Li Zhao Shen , Xu Guo Ming , Tu Zhen Xing , Gong Yan Fang 
Published: April 2004

OBJECTIVE:  The incidence of pancreatic cancer is increasing in China, and in many patients the surrounding lymphatics have already been invaded and there is blood‐borne metastasis at the time of diagnosis. Additionally, pancreatic cancer is largely refractory to conventional therapies. Therefore, to improve its prognosis, it is important to resolve the problem of its growth. Angiotensin II type 1 receptor (AT1) stimulates the growth and angiogenesis of pancreatic cancer and a selective AT1 antagonist could inhibit these effects. The present study aimed to investigate the expression of AT1 in pancreatic cancer cell lines to provide the theoretical basis for its treatment.METHODS:  The pancreatic cancer cell lines were SW1990, PaTu8988s and PANC‐1. RT‐PCR was used to detect the AT1 mRNA expression, and ABC immunocytochemical staining and SDS‐PAGE were used to detect the expression of AT1 protein.RESULTS:  Both AT1 mRNA and protein were expressed in all three cell lines. The AT1 protein was found on the cell membrane and in the cytoplasm of these cells. The AT1 protein (44 × 103) was also demonstrated by SDS‐PAGE.CONCLUSION:  The results suggest that AT1 plays an important role in the growth of pancreatic cancer and its inhibition may be a therapeutic strategy.
Increased activity of the intestinal mucosal mast cells in rats with multiple organ failure
Authors: Tang Cheng Wei , Lan Cheng , Liu Rui 
Published: April 2004

OBJECTIVE:  This study was undertaken to evaluate the changes in the activity of the intestinal mucosal mast cells (IMMC) in multiple organ failure (MOF).METHODS:  A rat model of MOF was induced by intraperitoneal injection of zymosan. Both the functional alterations and the pathological morphology of essential organs, such as small intestine, liver, kidney and the lungs, were evaluated. The concentrations of histamine and tumor necrosis factor α (TNF‐α) in plasma and small intestinal tissue were detected by fluorimetric assay and enzyme‐linked immunosorbent assay, respectively. The ultrastructural changes of the IMMC from the MOF rats were evaluated by transmission electron microscopy.RESULTS:  Zymosan induced obvious inflammatory morphology and functional impairment in the essential organs of the rats that were indicative of the characteristic changes in MOF. There was a significantly decreased concentration of histamine in the intestinal tissue of the MOF rats when compared with the normal controls (8.67 ± 1.16 vs 11.63 ± 1.97 ng/g protein, P < 0.01), whereas the plasma histamine concentration showed no significant changes. The concentration of TNF‐α was elevated significantly in both the intestinal tissue and plasma of MOF rats. Furthermore, both the increased number and level of degranulation of the IMMC in the gut tissue was marked in MOF rats.CONCLUSION:  The results suggest that the histamine and TNF‐α released from activated IMMC play an important role in the development of MOF.
The human enteric nervous system
Authors: Schemann M. , Neunlist M. 
Published: April 2004

AbstractDecades of work in animal models have demonstrated that the enteric nervous system (ENS) plays a key role in controlling gut functions. Recent advances made it possible to extend such studies to the ENS of man in health and even in disease. Such studies have already provided new insights into the pathophysiology of inflammatory and possibly functional bowel diseases. Studies on human ENS revealed both important similarities and differences between the ENS of man and of experimental animals. Here we summarize the current state of knowledge of the electrophysiology and neurochemistry of the human ENS, including relevant reflex mediated functions in the human gut. Additionally, we review disease associated changes in human ENS properties. Finally, we highlight some research areas that hold special promise in advancing our understanding of the human ENS.
Sensory mechanisms: transmitters, modulators and reflexes
Authors: Raybould H. E. , Cooke H. J. , Christofi F. L. 
Published: April 2004

AbstractThe enteric nervous system in combination with inputs from parasympathetic and sympathetic nerves regulate the contractile, secretory and vasomotor activity of the gastrointestinal track via neural reflexes. Sensory elements which may be present in specialized neurones, enteroendocrine cells or mast cells detect changes in force, chemical composition or even foreign antigens. Sensory elements signal the enteric nervous system to correct these changes by altering contractile activity, secretion and blood flow. Advances have been made in understanding the sensory mechanisms that are involved in 5‐hydroxytryptamine (5‐HT) release from enterochromaffin cells (EC) or a model for EC cells. These advances relate to roles for ATP and its metabolites ADP and adenosine in mechanotransduction and a role for a sodium glucose cotransporter, a SGLT‐like protein, in chemotransduction.
Pharmacology and function of nicotinic acetylcholine and P2X receptors in the enteric nervous system
Authors: Galligan J. J. , North R. A. 
Published: April 2004

AbstractThere are many cell surface receptors expressed by neurones in the enteric nervous system (ENS). Ligand‐gated ion channels are an important class of receptors expressed by enteric neurones. This review will focus on nicotinic acetylcholine receptors (nAChRs) and P2X receptors for ATP, as these receptors contribute to fast synaptic transmission in identified pathways in the ENS. There are multiple subunit proteins that compose nAChRs and P2X receptors in the nervous system. Functional and pharmacological studies indicate that the predominant class of nAChR mediating fast synaptic transmission in enteric neurones is composed of α3 and β4 subunits. P2X receptors mediating fast synaptic excitation are predominately P2X2 homomeric receptors.
Carbon monoxide is an endogenous hyperpolarizing factor in the gastrointestinal tract
Authors: Szurszewski J. H. , Farrugia G. 
Published: April 2004

AbstractIn all mammalian species examined to date, there is a 10 mV or more gradient in resting membrane potential across the wall of the gastric antrum, small intestine and colon, and an even larger gradient along the long axis of the stomach. These voltage gradients, which may be considered biological rheostats, are central to the ability of circular smooth muscle to vary the strength of contraction from weak to propulsive and occluding. In this short review, we consider recent data that support the hypothesis that carbon monoxide generated in interstitial cells of Cajal is a hyperpolarizing factor for circular smooth muscle and the root of the essential voltage gradients.