bluuebunny/crossref_metadata_2025_split huggingface dataset:
The peritoneal micromilieu commits B cells to home to body cavities and the small intestine
Authors: Berberich Simon , Förster Reinhold , Pabst Oliver 
Published: February 2007

AbstractThe distinct combination of homing receptors such as selectins, chemokine receptors, and integrins directs the migration of lymphocytes throughout the body. Upon activation lymphocytes irreversibly switch their set of homing receptors, now guiding them to entirely different destinations. Here we report that exposure of naive B cells to the microenvironment of the peritoneal cavity modulates their migration propensities in the absence of antigenic stimulation. B1 and B2 cells isolated from the peritoneal cavity reenter this compartment more efficiently compared with splenic follicular B cells. Moreover, when kept in the peritoneal cavity splenic follicular B cells gain such increased capability to reenter this compartment. These altered migratory capacities are reflected by an up-regulation of the chemokine receptors CXCR4 and CXCR5 and β7 integrin by the peritoneum-experienced splenic B cells, among which CXCR5 is instrumental in directing B cells into the peritoneal cavity. Moreover, intraperitoneal transfer of plasma blasts favors their migration into the small intestine presumably before class switch recombination occurs, demonstrating that a reconfigured transient migration pattern is not restricted to naive cells. In conclusion, these data demonstrate a hitherto unrecognized role for tissue-specific cues, altering the migratory capacity of B1, naive B2, as well as antigen-experienced B2 cells.
msmsEval: tandem mass spectral quality assignment for high-throughput proteomics
Authors: Wong Jason WH , Sullivan Matthew J , Cartwright Hugh M , Cagney Gerard 
Published: February 2007

AbstractBackgroundIn proteomics experiments, database-search programs are the method of choice for protein identification from tandem mass spectra. As amino acid sequence databases grow however, computing resources required for these programs have become prohibitive, particularly in searches for modified proteins. Recently, methods to limit the number of spectra to be searched based on spectral quality have been proposed by different research groups, but rankings of spectral quality have thus far been based on arbitrary cut-off values. In this work, we develop a more readily interpretable spectral quality statistic by providing probability values for the likelihood that spectra will be identifiable.ResultsWe describe an application, msmsEval, that builds on previous work by statistically modeling the spectral quality discriminant function using a Gaussian mixture model. This allows a researcher to filter spectra based on the probability that a spectrum will ultimately be identified by database searching. We show that spectra that are predicted by msmsEval to be of high quality, yet remain unidentified in standard database searches, are candidates for more intensive search strategies. Using a well studied public dataset we also show that a high proportion (83.9%) of the spectra predicted by msmsEval to be of high quality but that elude standard search strategies, are in fact interpretable.ConclusionmsmsEval will be useful for high-throughput proteomics projects and is freely available for download fromhttp://proteomics.ucd.ie/msmseval. Supports Windows, Mac OS X and Linux/Unix operating systems.
PASSIM – an open source software system for managing information in biomedical studies
Authors: Viksna Juris , Celms Edgars , Opmanis Martins , Podnieks Karlis , Rucevskis Peteris , Zarins Andris , Barrett Amy , Neogi Sudeshna Guha , Krestyaninova Maria , McCarthy Mark I , Brazma Alvis , Sarkans Ugis 
Published: February 2007

Abstract

Background
One of the crucial aspects of day-to-day laboratory information management is collection, storage and retrieval of information about research subjects and biomedical samples. An efficient link between sample data and experiment results is absolutely imperative for a successful outcome of a biomedical study. Currently available software solutions are largely limited to large-scale, expensive commercial Laboratory Information Management Systems (LIMS). Acquiring such LIMS indeed can bring laboratory information management to a higher level, but often implies sufficient investment of time, effort and funds, which are not always available. There is a clear need for lightweight open source systems for patient and sample information management.

Results
We present a web-based tool for submission, management and retrieval of sample and research subject data. The system secures confidentiality by separating anonymized sample information from individuals' records. It is simple and generic, and can be customised for various biomedical studies. Information can be both entered and accessed using the same web interface. User groups and their privileges can be defined. The system is open-source and is supplied with an on-line tutorial and necessary documentation. It has proven to be successful in a large international collaborative project.

Conclusion
The presented system closes the gap between the need and the availability of lightweight software solutions for managing information in biomedical studies involving human research subjects.
PLAN: a web platform for automating high-throughput BLAST searches and for managing and mining results
Authors: He Ji , Dai Xinbin , Zhao Xuechun 
Published: February 2007

Abstract

Background
BLAST searches are widely used for sequence alignment. The search results are commonly adopted for various functional and comparative genomics tasks such as annotating unknown sequences, investigating gene models and comparing two sequence sets. Advances in sequencing technologies pose challenges for high-throughput analysis of large-scale sequence data. A number of programs and hardware solutions exist for efficient BLAST searching, but there is a lack of generic software solutions for mining and personalized management of the results. Systematically reviewing the results and identifying information of interest remains tedious and time-consuming.

Results
Personal BLAST Navigator (PLAN) is a versatile web platform that helps users to carry out various personalized pre- and post-BLAST tasks, including: (1) query and target sequence database management, (2) automated high-throughput BLAST searching, (3) indexing and searching of results, (4) filtering results online, (5) managing results of personal interest in favorite categories, (6) automated sequence annotation (such as NCBI NR and ontology-based annotation). PLAN integrates, by default, the Decypher hardware-based BLAST solution provided by Active Motif Inc. with a greatly improved efficiency over conventional BLAST software. BLAST results are visualized by spreadsheets and graphs and are full-text searchable. BLAST results and sequence annotations can be exported, in part or in full, in various formats including Microsoft Excel and FASTA. Sequences and BLAST results are organized in projects, the data publication levels of which are controlled by the registered project owners. In addition, all analytical functions are provided to public users without registration.

Conclusion
PLAN has proved a valuable addition to the community for automated high-throughput BLAST searches, and, more importantly, for knowledge discovery, management and sharing based on sequence alignment results. The PLAN web interface is platform-independent, easily configurable and capable of comprehensive expansion, and user-intuitive. PLAN is freely available to academic users at http://bioinfo.noble.org/plan/. The source code for local deployment is provided under free license. Full support on system utilization, installation, configuration and customization are provided to academic users.
The role of laterally transferred genes in adaptive evolution
Authors: Marri Pradeep Reddy , Hao Weilong , Golding G Brian 
Published: February 2007

Abstract

Background
Bacterial genomes develop new mechanisms to tide them over the imposing conditions they encounter during the course of their evolution. Acquisition of new genes by lateral gene transfer may be one of the dominant ways of adaptation in bacterial genome evolution. Lateral gene transfer provides the bacterial genome with a new set of genes that help it to explore and adapt to new ecological niches.

Methods
A maximum likelihood analysis was done on the five sequenced corynebacterial genomes to model the rates of gene insertions/deletions at various depths of the phylogeny.

Results
The study shows that most of the laterally acquired genes are transient and the inferred rates of gene movement are higher on the external branches of the phylogeny and decrease as the phylogenetic depth increases. The newly acquired genes are under relaxed selection and evolve faster than their older counterparts. Analysis of some of the functionally characterised LGTs in each species has indicated that they may have a possible adaptive role.

Conclusion
The five Corynebacterial genomes sequenced to date have evolved by acquiring between 8 – 14% of their genomes by LGT and some of these genes may have a role in adaptation.
A BAC pooling strategy combined with PCR-based screenings in a large, highly repetitive genome enables integration of the maize genetic and physical maps
Authors: Yim Young-Sun , Moak Patricia , Sanchez-Villeda Hector , Musket Theresa A , Close Pamela , Klein Patricia E , Mullet John E , McMullen Michael D , Fang Zheiwei , Schaeffer Mary L , Gardiner Jack M , Coe Edward H , Davis Georgia L 
Published: February 2007

Abstract

Background
Molecular markers serve three important functions in physical map assembly. First, they provide anchor points to genetic maps facilitating functional genomic studies. Second, they reduce the overlap required for BAC contig assembly from 80 to 50 percent. Finally, they validate assemblies based solely on BAC fingerprints. We employed a six-dimensional BAC pooling strategy in combination with a high-throughput PCR-based screening method to anchor the maize genetic and physical maps.

Results
A total of 110,592 maize BAC clones (~ 6x haploid genome equivalents) were pooled into six different matrices, each containing 48 pools of BAC DNA. The quality of the BAC DNA pools and their utility for identifying BACs containing target genomic sequences was tested using 254 PCR-based STS markers. Five types of PCR-based STS markers were screened to assess potential uses for the BAC pools. An average of 4.68 BAC clones were identified per marker analyzed. These results were integrated with BAC fingerprint data generated by the Arizona Genomics Institute (AGI) and the Arizona Genomics Computational Laboratory (AGCoL) to assemble the BAC contigs using the FingerPrinted Contigs (FPC) software and contribute to the construction and anchoring of the physical map. A total of 234 markers (92.5%) anchored BAC contigs to their genetic map positions. The results can be viewed on the integrated map of maize [1, 2].

Conclusion
This BAC pooling strategy is a rapid, cost effective method for genome assembly and anchoring. The requirement for six replicate positive amplifications makes this a robust method for use in large genomes with high amounts of repetitive DNA such as maize. This strategy can be used to physically map duplicate loci, provide order information for loci in a small genetic interval or with no genetic recombination, and loci with conflicting hybridization-based information.
Factors predictive of alcohol use during pregnancy in three rural states
Authors: Leonardson Gary R , Loudenburg Roland , Struck Judy 
Published: February 2007

Abstract

Background
A substance use screening instrument was used to determine factors predictive of drinking during pregnancy. Alcohol consumption during pregnancy can lead to negative birth outcomes.

Methods
The participants (n = 4,828) for the study were sampled from pregnant women attending prenatal clinics in Montana, South Dakota, and North Dakota. Clinic sites for the administration of the screening instrument were selected in each state, based on geographic and known population characteristics. Univariate and multivariate statistical procedures were used to determine factors predictive of drinking during pregnancy.

Results
Women who drank tended to: be single, be between 21–25 years old, have had fewer children, have had abortions, and be unemployed. Demographic factors that were protective of drinking when pregnant were married and full-time housewife status. Other variables associated with maternal alcohol use were: past sexual abuse, current or past physical abuse, tobacco use, other drug use, lived with substance users, and had mates who were substance users. Other contributing factors for alcohol use included: feeling sad, believing that drinking any amount of alcohol while pregnant was acceptable, had been in treatment, could use treatment now, and were able to hold four or more drinks.

Conclusion
Because drinking rates were high and factors correlated with drinking are known, alcohol screening for this population is essential.
Maintenance treatment with esomeprazole following initial relief of non-steroidal anti-inflammatory drug-associated upper gastrointestinal symptoms: the NASA2 and SPACE2 studies
Authors: Hawkey Christopher J , Talley Nicholas J , Scheiman James M , Jones Roger H , Långström Göran , Næsdal Jorgen , Yeomans Neville D ,   the NASA/SPACE author group
Published: February 2007

Abstract
Non-steroidal anti-inflammatory drugs (NSAIDs), including selective cyclo-oxygenase-2 (COX-2) inhibitors, cause upper gastrointestinal (GI) symptoms that are relieved by treatment with esomeprazole. We assessed esomeprazole for maintaining long-term relief of such symptoms. Six hundred and ten patients with a chronic condition requiring anti-inflammatory therapy who achieved relief of NSAID-associated symptoms of pain, discomfort, or burning in the upper abdomen during two previous studies were enrolled and randomly assigned into two identical, multicentre, parallel-group, placebo-controlled studies of esomeprazole 20 mg or 40 mg treatment (NASA2 [Nexium Anti-inflammatory Symptom Amelioration] and SPACE2 [Symptom Prevention by Acid Control with Esomeprazole] studies; ClinicalTrials.gov identifiers NCT00241514 and NCT00241553, respectively) performed at various rheumatology, gastroenterology, and primary care clinics. Four hundred and twenty-six patients completed the 6-month treatment period. The primary measure was the proportion of patients with relapse of upper GI symptoms, recorded in daily diary cards, after 6 months. Relapse was defined as moderate-to-severe upper GI symptoms (a score of more than or equal to 3 on a 7-grade scale) for 3 days or more in any 7-day period. Esomeprazole was significantly more effective than placebo in maintaining relief of upper GI symptoms throughout 6 months of treatment. Life-table estimates (95% confidence intervals) of the proportion of patients with relapse at 6 months (pooled population) were placebo, 39.1% (32.2% to 46.0%); esomeprazole 20 mg, 29.3% (22.3% to 36.2%) (p = 0.006 versus placebo); and esomeprazole 40 mg, 26.1% (19.4% to 32.9%) (p = 0.001 versus placebo). Patients on either non-selective NSAIDs or selective COX-2 inhibitors appeared to benefit. The frequency of adverse events was similar in the three groups. Esomeprazole maintains relief of NSAID-associated upper GI symptoms in patients taking continuous NSAIDs, including selective COX-2 inhibitors.
The impact of admission diagnosis on gastric emptying in critically ill patients
Authors: Nguyen Nam Q , Ng Mei P , Chapman Marianne , Fraser Robert J , Holloway Richard H 
Published: February 2007

Abstract
Introduction
Disturbed gastric emptying (GE) occurs commonly in critically ill patients. Admission diagnoses are believed to influence the incidence of delayed GE and subsequent feed intolerance. Although patients with burns and head injury are considered to be at greater risk, the true incidence has not been determined by examination of patient groups of sufficient number. This study aimed to evaluate the impact of admission diagnosis on GE in critically ill patients.

Methods
A retrospective review of patient demographics, diagnosis, intensive care unit (ICU) admission details, GE, and enteral feeding was performed on an unselected cohort of 132 mechanically ventilated patients (94 males, 38 females; age 54 ± 1.2 years; admission Acute Physiology and Chronic Health Evaluation II [APACHE II] score of 22 ± 1) who had undergone GE assessment by 13C-octanoic acid breath test. Delayed GE was defined as GE coefficient (GEC) of less than 3.20 and/or gastric half-emptying time (t50) of more than 140 minutes.

Results
Overall, 60% of the patients had delayed GE and a mean GEC of 2.9 ± 0.1 and t50 of 163 ± 7 minutes. On univariate analysis, GE correlated significantly with older age, higher admission APACHE II scores, longer length of stay in ICU prior to GE measurement, higher respiratory rate, higher FiO2 (fraction of inspired oxygen), and higher serum creatinine. After these factors were controlled for, there was a modest relationship between admission diagnosis and GE (r = 0.48; P = 0.02). The highest occurrence of delayed GE was observed in patients with head injuries, burns, multi-system trauma, and sepsis. Delayed GE was least common in patients with myocardial injury and non-gastrointestinal post-operative respiratory failure. Patients with delayed GE received fewer feeds and stayed longer in ICU and hospital compared to those with normal GE.

Conclusion
Admission diagnosis has a modest impact on GE in critically ill patients, even after controlling for factors such as age, illness severity, and medication, which are known to influence this function.
qBase relative quantification framework and software for management and automated analysis of real-time quantitative PCR data
Authors: Hellemans Jan , Mortier Geert , De Paepe Anne , Speleman Frank , Vandesompele Jo 
Published: February 2007

AbstractAlthough quantitative PCR (qPCR) is becoming the method of choice for expression profiling of selected genes, accurate and straightforward processing of the raw measurements remains a major hurdle. Here we outline advanced and universally applicable models for relative quantification and inter-run calibration with proper error propagation along the entire calculation track. These models and algorithms are implemented in qBase, a free program for the management and automated analysis of qPCR data.
Relaxin-induced matrix metalloproteinase-9 expression is associated with activation of the NF-κB pathway in human THP-1 cells
Authors: Ho Teh-Yuan , Yan Wenbo , Bagnell Carol A 
Published: February 2007

AbstractMatrix metalloproteinases (MMPs) and relaxin (RLX) are reported to play an important role in tissue remodeling and wound repair. When macrophages populate wound sites, they secrete biologically active substances, including MMPs. The transcription factor NF-κB is important in MMP gene regulation in macrophage cells. Thus, a monocyte/macrophage cell line, THP-1, was used to study the molecular mechanism of RLX action on MMP-2 and MMP-9 expression. After 24 h incubation with porcine RLX (100 ng/ml), conditioned media (CM) and THP-1 cells were collected. Gelatin zymography demonstrated an increase in pro-MMP-9 activity in response to RLX in CM, and no significant change in pro-MMP-2 expression was observed. Immunoblot analysis also revealed an increase in pro-MMP-9 in CM from RX-treated THP-1 cells. Gel EMSA showed that NF-κB DNA-binding activity was elevated in THP-1 cells treated with RLX for 10 min and reached a peak at 30 min. The NF-κB DNA complex was supershifted using antibodies against NF-κB subunits p50 and p65. Increased expression of the p50 and p65 NF-κB subunits was also detected in THP-1 cells after RLX treatment. Incubation with RLX (90 min) reduced THP-1 expression of the NF-κB inhibitor protein, IκB-α. Using a specific NF-κB inhibitor, pyrrolidine dithiocarmate (PDTC) inhibited nuclear binding of NF-κB. Pre-exposure to PDTC suppressed pro-MMP-9 activity and protein levels in RLX-treated THP-1 cells. In conclusion, these data suggest that RLX-induced tissue remodeling through increasing MMP-9 expression is dependent on NF-κB activation.
Regulation of innate immunity by MAPK dual-specificity phosphatases: knockout models reveal new tricks of old genes
Authors: Salojin Konstantin , Oravecz Tamas 
Published: February 2007

AbstractThroughout evolution, mammals have developed an elaborate network of positive and negative regulatory mechanisms, which provide balance between defensive measures against bacterial and viral pathogens and protective measures against unwarranted destruction of the host by the activated immune system. Kinases and phosphatases encompassing the MAPK pathway are key players in the orderly action of pro- and anti-inflammatory processes, forming numerous promiscuous interactions. Several lines of evidence demonstrate that the phosphorylation and activation status of kinases in the MAPK system has crucial impact on the outcome of downstream events that regulate cytokine production. At least 13 members of the family of dual-specificity phosphatases (DUSP) display unique substrate specificities for MAPKs. Despite the considerable amount of information obtained about the contribution of the different DUSP to MAPK-mediated signaling and innate immunity, the interpretation of available data remains problematic. The in vitro and ex vivo findings are often complicated by functional redundancy of signaling molecules and do not always accurately predict the situation in vivo. Until recently, DUSP research has been hampered by the lack of relevant mammalian knockout (KO) models, which is a powerful tool for delineating in vivo function and redundancy in gene families. This situation changed dramatically over the last year, and this review integrates recent insights into the precise biological role of the DUSP family in innate immunity gained from a comprehensive analysis of mammalian KO models.
Phase III Trial of Ifosfamide With or Without Paclitaxel in Advanced Uterine Carcinosarcoma: A Gynecologic Oncology Group Study
Authors: Homesley Howard D. , Filiaci Virginia , Markman Maurie , Bitterman Pincas , Eaton Lynne , Kilgore Larry C. , Monk Bradley J. , Ueland Frederick R. 
Published: February 2007

Purpose To determine if paclitaxel added to ifosfamide as first-line treatment for advanced uterine carcinosarcoma (CS) improves overall survival (OS), progression-free survival (PFS), response, and toxicity. Patients and Methods Eligible patients had measurable stage III or IV, persistent, or recurrent uterine CS. Random assignment to treatment was between ifosfamide 2.0 g/m2 intravenously (IV) daily for 3 days (arm 1) or ifosfamide 1.6 g/m2 IV daily for 3 days plus paclitaxel 135 mg/m2 by 3-hour infusion day 1 (arm 2). Mesna was administered similarly (both arms); filgrastim began on day 4 (arm 2). Cycles were repeated every 21 days up to eight cycles. Results Of 214 patients enrolled, 179 were eligible (arm 1, 91 patients; arm 2, 88 patients). Arm 2 patients experienced more frequent and severe sensory neuropathy (grade 1 to 4; 8% v 30%). The crude response rate was 29% (arm 1) and 45% (arm 2). The odds of response stratified by performance status were 2.21 greater in arm 2 (P = .017). Median PFS and OS, respectively, for arm 1 compared with arm 2 were 3.6 v 5.8 months and 8.4 v 13.5 months, respectively. There was a 31% decrease in the hazard of death (hazard ratio [HR], 0.69; 95% CI, 0.49 to 0.97; P = .03) and a 29% decrease in the hazard of progression (HR, 0.71; 95% CI, 0.51 to 0.97; P = .03) relative to arm 1 when stratifying by performance status. Conclusion OS was significantly improved in arm 2, and toxicities were as expected and manageable. However, the need for active new agents persists, given that OS remains relatively poor in this disease.