bluuebunny/crossref_metadata_2025_split huggingface dataset:
Co-expression of adjacent genes in yeast cannot be simply attributed to shared regulatory system
Authors: Tsai Huai-Kuang , Su Cindy PC , Lu Mei-Yeh J , Shih Ching-Hua , Wang Daryi 
Published: October 2007

Abstract

Background
Adjacent gene pairs in the yeast genome have a tendency to express concurrently. Sharing of regulatory elements within the intergenic region of those adjacent gene pairs was often considered the major mechanism responsible for such co-expression. However, it is still in debate to what extent that common transcription factors (TFs) contribute to the co-expression of adjacent genes. In order to resolve the evolutionary aspect of this issue, we investigated the conservation of adjacent pairs in five yeast species. By using the information for TF binding sites in promoter regions available from the MYBS database http://cg1.iis.sinica.edu.tw/~mybs/, the ratios of TF-sharing pairs among all the adjacent pairs in yeast genomes were analyzed. The levels of co-expression in different adjacent patterns were also compared.

Results
Our analyses showed that the proportion of adjacent pairs conserved in five yeast species is relatively low compared to that in the mammalian lineage. The proportion was also low for adjacent gene pairs with shared TFs. Particularly, the statistical analysis suggested that co-expression of adjacent gene pairs was not noticeably associated with the sharing of TFs in these pairs. We further proposed a case of the PAC (polymerase A and C) and RRPE (rRNA processing element) motifs which co-regulate divergent/bidirectional pairs, and found that the shared TFs were not significantly relevant to co-expression of divergent promoters among adjacent genes.

Conclusion
Our findings suggested that the commonly shared cis-regulatory system does not solely contribute to the co-expression of adjacent gene pairs in yeast genome. Therefore we believe that during evolution yeasts have developed a sophisticated regulatory system that integrates both TF-based and non-TF based mechanisms(s) for concurrent regulation of neighboring genes in response to various environmental changes.
Mycobacterium tuberculosis 6-kDa Early Secreted Antigenic Target (ESAT-6) protein downregulates Lipopolysaccharide induced c-myc expression by modulating the Extracellular Signal Regulated Kinases 1/2
Authors: Ganguly Niladri , Giang Pham H , Basu Sandip K , Mir Fayaz Ahmad , Siddiqui Imran , Sharma Pawan 
Published: October 2007

AbstractBackgroundMycobacterium tuberculosis(Mtb) causes death of 2–3 million people every year. The persistence of the pathogenic mycobacteria inside the macrophage occurs through modulation of host cell signaling which allows them, unlike the other non-pathogenic species, to survive inside the host. The secretory proteins ofM. tuberculosishave gained attention in recent years both as vaccine candidates and diagnostic tools; they target the immune system and trigger a putatively protective response; however, they may also be involved in the clinical symptoms of the disease.ResultsOur studies showed that RD-1-encoded secretory protein ESAT-6 is involved in modulation of the mitogen-activated protein (MAP) kinase-signaling pathway inside the macrophage. ESAT-6 induced phosphorylation of extracellular signal-regulated kinases 1/2 (ERK1/2) in the cytoplasm but not in the nucleus, which normally is the case for MAP kinases. ESAT-6 also antagonized LPS-induced ERK1/2 phosphorylation in the nucleus. Stimulation of cells by ESAT-6 along with sodium orthovanadate (a tyrosine phosphatase inhibitor) restored phosphorylation of ERK1/2 in the nucleus, suggesting active dephosphorylation of ERK1/2 by some putative phosphatase(s) in the nucleus. Further, ESAT-6 was found to down regulate the expression of LPS-inducible genec-mycin an ERK1/2-dependent manner.ConclusionThis study showed the effect of secretory proteins ofM. tuberculosisin the modulation of macrophage signaling pathways particularly ERK1/2 MAP kinase pathway. This modulation appears to be achieved by limiting the ERK1/2 activation in the nucleus which ultimately affects the macrophage gene expression. This could be a mechanism by which secretory proteins of Mtb might modulate gene expression inside the macrophages.
Assessment of free light chains in the cerebrospinal fluid of patients with lymphomatous meningitis – a pilot study
Authors: Hildebrandt B , Müller C , Pezzutto A , Daniel PT , Dörken B , Scholz C 
Published: October 2007

Abstract

Background
Lymphomatous meningitis (LM) represents a severe complication of malignant lymphomas. While clinical suspicion is raised by symptoms ranging from mild disturbances of sensation to severe pain or impaired consciousness, the definite diagnosis of LM is often difficult to obtain. Since B-cell lymphomas are clonally restricted to express either kappa or lambda immunoglobulin light chain, we hypothesised that analysis of free light chain (FLC) ratios might facilitate the diagnosis of LM.

Methods
Kappa and lambda FLC were measured using a novel nephelometric assay in cerebrospinal fluid (CSF) and serum from 17 patients. 5/17 suffered from LM as demonstrated by cytology, immunocytology, and/or imaging procedures.

Results
Measurement of FLC concentrations in CSF was achieved for all 17 patients. FLC levels in CSF were lower than serum FLC levels in samples for the same patient obtained at the same time (p < 0.01). CSF and serum FLC concentrations correlated weakly in all patients irrespective of LM status. Significantly more patients with cytopathologically and immunohistochemically proven LM displayed abnormal kappa/lambda FLC ratios in CSF compared to individuals with no LM (p < 0.01).

Conclusion
This is the first report demonstrating that a significant proportion of LM patients display an abnormal kappa/lambda FLC ratio in the CSF.
A systematic approach for testing expression of human full-length proteins in cell-free expression systems
Authors: Langlais Claudia , Guilleaume Birgit , Wermke Nadja , Scheuermann Tina , Ebert Lars , LaBaer Joshua , Korn Bernhard 
Published: October 2007

Abstract

Background
The growing field of proteomics and systems biology is resulting in an ever increasing demand for purified recombinant proteins for structural and functional studies. Here, we show a systematic approach to successfully express a full-length protein of interest by using cell-free and cell-based expression systems.

Results
In a pre-screen, we evaluated the expression of 960 human full-length open reading frames in Escherichia coli (in vivo and in vitro). After analysing the protein expression rate and solubility, we chose a subset of 87 plasmids yielding no protein product in E. coli in vivo. These targets were subjected to a more detailed analysis comparing a prokaryotic cell-free E. coli system with an eukaryotic wheat germ system. In addition, we determined the expression rate, yield and solubility of those proteins. After sequence optimisation for the E. coli in vitro system and generating linear templates for wheat germ expression, the success rate of cell-free protein expression reached 93%.

Conclusion
We have demonstrated that protein expression in cell-free systems is an appropriate technology for the successful expression of soluble full-length proteins. In our study, wheat germ expression using a two compartment system is the method of choice as it shows high solubility and high protein yield.
Misleading pustular plaques of the lower limbs during Crohn's disease: two case reports
Authors: Farhi David , Duriez Paul , Aractingi Selim , Cosnes Jacques , Khosrotehrani Kiarash 
Published: October 2007

Abstract

Background
Extraintestinal manifestations of Crohn's disease may involve the skin, the eyes, the genital mucosa, and the joints. Dermatoses associated with Crohn's disease include neutrophilic dermatoses, erythema nodosum, granulomatous dermatitis, blistering dermatoses, and non-specific skin manifestations. Cutaneous Crohn's disease is characterized by skin non-caseating epithelioid granulomatas with giant cells, remote from the gastrointestinal tract. We report herein two new cases.

Observations
On both patients, differential diagnosis of neutrophilic dermatoses and infectious disease were evoked, and antimicrobial agents were introduced in one of them. Given the atypical presentation, the final diagnosis of cutaneous Crohn's disease could only be made with histological examination. In patient 1, the plaques decreased in size and infiltration by more than 75% after 3 weeks of treatment with bethametasone dipropionate 0.05% cream. In patient 2, the plaques decreased by more than 50% after 6 weeks of treatment with prednisolone (45 mg/day) and azathioprine (100 mg/day).

Discussion
Cutaneous Crohn's disease may present as dusky, erythematous, infiltrated, and ulcerated plaques and nodules. Female-to-male sex ratio is about 2, and the mean age at onset is 35. Recurrently, the hypothesis of a skin mycobacterial or fungal infection greatly delays proper treatment. Rarity of cutaneous Crohn's disease hampers therapeutic assessment in controlled trials. Thus, available literature is limited to case reports and sparse small series, with contradictory results. These reports are subject to publication bias, and no definite evidence-based recommendations can be made on the most adequate therapeutic strategy.
Assessment of Chronic Lymphocytic Leukemia and Small Lymphocytic Lymphoma by Absolute Lymphocyte Counts in 2,126 Patients: 20 Years of Experience at The University of Texas M.D. Anderson Cancer Center
Authors: Tsimberidou Apostolia M. , Wen Sijin , O'Brien Susan , McLaughlin Peter , Wierda William G. , Ferrajoli Alessandra , Faderl Stefan , Manning John , Lerner Susan , Mai Chinh V. , Rodriguez Alma M. , Hess Mark , Do Kim-Anh , Freireich Emil J. , Kantarjian Hagop M. , Medeiros L. Jeffrey , Keating Michael J. 
Published: October 2007

Purpose Chronic lymphocytic leukemia (CLL) and small lymphocytic lymphoma (SLL) are currently considered the same entity, but controversy remains over whether CLL and SLL should be treated similarly. We assessed whether characteristics of patients with CLL and SLL differ in ways other than the absolute lymphocyte count (ALC) and evaluated treatment outcomes and prognostic factors. Methods We searched the electronic database for patients with CLL or SLL who presented to The University of Texas M.D. Anderson Cancer Center (Houston, TX) between 1985 and 2005. We reviewed patient records to determine presenting characteristics, treatment, and clinical outcomes. Cox models using training and validation sets of patients and resampling methods were used to develop a model predicting survival. Results Among 2,126 consecutive CLL/SLL patients, 312 (15%) had ALC less than 5 × 109/L. Patients with ALC less than 5 × 109/L had lower rates of cytogenetic abnormalities (P = .0002) and higher rates of CD38-positive results (P = .0002) and had mutated immunoglobulin heavy-chain variable region gene status (P = .034). Rates of response, survival, and failure-free survival (FFS) were not different among ALC groups. Regimens that included rituximab and a nucleoside analog were associated with superior rates of response and FFS compared with other therapies, irrespective of ALC. Deletion 17p or 6q with or without other cytogenetic abnormalities, age at least 60 years, β2-microglobulin at least 2 mg/L, albumin less than 3.5 g/dL, and creatinine at least 1.6 mg/dL were each found to independently predict shorter survival and formed the basis of a scoring system. Conclusion Patients with CLL or SLL can be treated similarly. A new prognostic score is proposed.
Low-Grade Inflammation, Obesity, and Insulin Resistance in Adolescents
Authors: Herder Christian , Schneitler Sophie , Rathmann Wolfgang , Haastert Burkhard , Schneitler Heiko , Winkler Horst , Bredahl Renate , Hahnloser Erik , Martin Stephan 
Published: October 2007

Abstract
Context: Low-grade inflammation is associated with insulin resistance and precedes the onset of type 2 diabetes mellitus in adults, but there are no comparable data in youth.
Objective: The objective of the study was to characterize the pattern of subclinical immune activation that is associated with indices of obesity and insulin resistance in youth and analyze whether this association is explained by obesity.
Design: This was a cross-sectional study.
Setting: Medical check-up of schoolchildren was conducted by the Public Health Office in Düsseldorf (Germany).
Participants: Participants included 519 adolescents (mean age 15.5 ± 0.8 yr).
Main Outcome Measures: Measures included body mass index (BMI) and waist circumference (WC) as indices of obesity; fasting glucose, insulin, and homeostasis model assessment of insulin resistance; serum concentrations of TNFα, IL-6, IL-8, IL-18, monocyte chemoattractant protein-1, interferon-γ-inducible protein (IP)-10 and adiponectin as immunological variables.
Results: In age-, sex-, and lipid-adjusted analyses, IL-6, IL-18, IP-10, and adiponectin (inversely) were associated with both BMI and WC (all P ≤ 0.002). None of the immune markers was related to glucose, but IL-6, IL-18, and adiponectin (inversely) were associated with insulin and homeostasis model assessment of insulin resistance in age- and sex-adjusted models. Adjustment for BMI or WC indicated that a considerable proportion of these associations may be mediated by obesity.
Conclusions: We found that a differential low-grade immune activation is associated with parameters of obesity in adolescents. Moreover, there is evidence that IL-6, IL-18, IP-10, and adiponectin (inversely) are associated with insulin resistance and that these associations can mainly be attributed to obesity.
A Novel Method for the Deoxygenation of Sulfoxides with the PPh3/Br2/CuBr System
Authors: Bahrami Kiumars , Khodaei Mohammad Mehdi , Khedri Mohammad 
Published: October 2007

Abstract
It was found that the combination of PPh3/Br2/CuBr was an effective promoter for the deoxygenation of sulfoxides and gave the corresponding sulfides in excellent yield in acetonitrile under refluxing conditions. It is worth mentioning that this reagent system is chemoselective, tolerating various functional groups such as carbon–carbon double bond and ketone.
Long saphenous tunnel infiltration with levobupivicaine reduces rescue analgesia requirements following varicose vein surgery: randomized, double-blind, placebo-controlled trial [ISRCTN58431114]
Authors: Walsh S R , Waters C , Hall J , Bakar M , Boyle J , Gaunt M E 
Published: October 2007

Objectives: To determine whether local anaesthetic infiltration of the long saphenous tunnel in patients undergoing unilateral, primary long saphenous stripping and multiple avulsions reduces early postoperative pain and requirement for opiate analgesia. Methods: Patients were randomized to receive either levobupivicaine or an equivalent volume of normal saline infiltrated around the groin incision and along the long saphenous tunnel. Analgesia and linear analogue pain scores at 1, 6 and 24 h postoperatively were recorded. Results: Fourteen patients received local anaesthetic and 13 patients received saline placebo. The anaesthetic group experienced a 22% reduction in pain scores 1 h postoperatively and a 48% reduction at 6 h although this failed to achieve statistical significance. However, the anaesthetic group were less likely to require morphine in recovery (2/14 [14%] versus 8/13 [62%]; P = 0.01). The high morphine requirements in the control group may have reduced the amount of pain those patients recorded on their pain scores and prevented statistical significance from being achieved. Conclusion: In varicose vein surgery, local anaesthetic infiltration to the groin wound and along the full length of the stripper track is associated with reduced postoperative pain and requirements for opiate analgesia.
Assessing the gain in diagnostic performance when two visual inspection methods are combined for cervical cancer prevention
Authors: Muwonge Richard , Walter Stephen D , Wesley Ramani S , Basu Partha , Shastri Surendra S , Thara Somanathan , Mbalawa Charles Gombe , Sankaranarayanan Rengaswamy ,   The IARC Multicentre Study Group on Cervical Cancer Early Detection
Published: October 2007

Objectives: The objectives of this study was to establish whether combined screening with visual inspection with acetic acid (VIA) and Lugol's iodine (VILI) improves detection of cervical intraepithelial neoplasia 2–3 (CIN 2–3) lesions and cancer beyond chance, compared with screening with VIA alone or VILI alone; and to estimate the extra number of false-positive (FP) results per additional disease case found with the combined test, and to estimate the additional costs involved. Setting: Ten cross-sectional studies in Burkina Faso, Congo, Guinea, India, Mali and Niger, between 1999 and 2003. Methods: Using a common protocol, health workers screened 56,147 women aged 25–65 years with VIA and VILI. All women underwent a colposcopy examination and biopsies were taken when necessary. The disease reference standard was histology or negative colposcopy. A positive result on the combined test was defined if either VIA or VILI were positive. The accuracy of the combined test compared with VIA alone or VILI alone was evaluated using likelihood ratios. Results: The estimated sensitivity and specificity were 81.3% and 87.3%, respectively, for VIA; 91.5% and 86.9% for VILI; and 92.9% and 83.5% for the combined test. The ratio of the positive likelihood ratios of the combined test and VIA alone for CIN 2–3 lesions and cancer was 0.88 (95% confidense interval [CI]: 0.86–0.90), favouring use of VIA alone. The ratio of the negative likelihood ratios was 0.40 (95% CI: 0.37–0.47), favouring use of the combined test. Similar results were obtained when the combined test was compared with VILI alone. Assuming equivalent performance of VIA alone and the combined test with a disease prevalence of 2%, there will be about 16.0 (95% CI: 13.6–18.8) additional FPs for each additional true positive (TP) detected if the combined test is used. This number will be 121.1 (95% CI: 75.4–194.6) if VILI is considered as the single test. Conclusions: At the trade-off point between the combined test and VIA alone or VILI alone, given the numbers of additional FP results involved for each additional TP case of disease that were found, it would be more likely that settings already using VIA would advocate combined testing, and for settings using VILI to opt for the single test. The additional costs (per 1000 women) incurred with the combined test would be International &dollar;4117.68 versus either of the tests above.
Comparison of services provided by urban commercial, community-governed and traditional primary care practices in New Zealand
Authors: Hider Phil , Lay-Yee Roy , Crampton Peter , Davis Peter 
Published: October 2007

Objectives: New Zealand has experienced restructuring and reform of primary health care since the 1980s, including the introduction of commercial clinics and increasing numbers of practices run by community-governed organizations. Our aim was to compare commercial, community-governed and traditional practices in five key domains: access; coordination and continuity of care; communication and patient centredness; population health and preventive health; and chronic disease management. Methods: A nationally representative, multistage probability sample of private general practitioners, stratified by geographical location and practice type, was drawn. Representative samples of urban commercial clinics and of practices governed by community organizations were obtained for the same period (2001–02). All doctors were asked to provide data on themselves, their practice, and to report on a 25% sample of patients in two periods of one week. Results: Among the three practice types, commercial clinics differed most in their organization; they charged higher fees and employed more staff, although their doctors were less experienced. Community-governed practices were visited by more people from lower socioeconomic groups. Commercial clinic patients were more likely to be younger and less likely to have an ongoing relationship with the clinic. They frequently attended for self-limiting problems related to injuries or respiratory problems. Investigations, follow-up and referral rates were similar between the three practice types. Treatment rates were higher at traditional and community-governed general practices. Conclusion: Rather than replicating traditional practices, new practice types provide complementary services and established services in innovative ways. The challenge is to achieve an appropriate mix of diverse providers.
Quantifying evidence in forensic authorship analysis
Authors: Grant Tim 
Published: October 2007

The judicial interest in ‘scientific’ evidence has driven recent work to quantify results for forensic linguistic authorship analysis. Through a methodological discussion and a worked example this paper examines the issues which complicate attempts to quantify results in work. The solution suggested to some of the difficulties is a sampling and testing strategy which helps to identify potentially useful, valid and reliable markers of authorship. An important feature of the sampling strategy is that these markers identified as being generally valid and reliable are retested for use in specific authorship analysis cases. The suggested approach for drawing quantified conclusions combines discriminant function analysis and Bayesian likelihood measures. The worked example starts with twenty comparison texts for each of three potential authors and then uses a progressively smaller comparison corpus, reducing to fifteen, ten, five and finally three texts per author. This worked example demonstrates how reducing the amount of data affects the way conclusions can be drawn. With greater numbers of reference texts quantified and safe attributions are shown to be possible, but as the number of reference texts reduces the analysis shows how the conclusion which should be reached is that no attribution can be made. The testing process at no point results in instances of a misattribution.