bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rhythm and Beat Perception in Motor Areas of the Brain
Authors: Grahn Jessica A. , Brett Matthew 
Published: May 2007

AbstractWhen we listen to rhythm, we often move spontaneously to the beat. This movement may result from processing of the beat by motor areas. Previous studies have shown that several motor areas respond when attending to rhythms. Here we investigate whether specific motor regions respond to beat in rhythm. We predicted that the basal ganglia and supplementary motor area (SMA) would respond in the presence of a regular beat. To establish what rhythm properties induce a beat, we asked subjects to reproduce different types of rhythmic sequences. Improved reproduction was observed for one rhythm type, which had integer ratio relationships between its intervals and regular perceptual accents. A subsequent functional magnetic resonance imaging study found that these rhythms also elicited higher activity in the basal ganglia and SMA. This finding was consistent across different levels of musical training, although musicians showed activation increases unrelated to rhythm type in the premotor cortex, cerebellum, and SMAs (pre-SMA and SMA). We conclude that, in addition to their role in movement production, the basal ganglia and SMAs may mediate beat perception.
Gene-expression analysis identifies novel RBL2/p130 target genes in endemic Burkitt lymphoma cell lines and primary tumors
Authors: De Falco Giulia , Leucci Eleonora , Lenze Dido , Piccaluga Pier Paolo , Claudio Pier Paolo , Onnis Anna , Cerino Giovanna , Nyagol Joshua , Mwanda Walter , Bellan Cristiana , Hummel Michael , Pileri Stefano , Tosi Piero , Stein Harald , Giordano Antonio , Leoncini Lorenzo 
Published: May 2007

Abstract
Burkitt lymphoma (BL) is a B-cell tumor whose characteristic gene aberration is the translocation t(8;14), which determines c-myc overexpression. Several genetic and epigenetic alterations other than c-myc overexpression have also been described in BL. It has been demonstrated that the RBL2/p130 gene, a member of the retinoblastoma family (pRbs), is mutated in BL cell lines and primary tumors. The aim of this study was to investigate the biologic effect of RBL2/p130 in BL cells and its possible role in lymphomagenesis. Therefore, we reintroduced a functional RBL2/p130 in BL cell lines where this gene was mutated. Our results demonstrated that RBL2/p130-transfected cells regain growth control. This suggests that RBL2/p130 may control the expression of several genes, which may be important for cell growth and viability. Gene-expression analysis revealed a modulation of several genes, including CGRRF1, RGS1, BTG1, TIA1, and PCDHA2, upon RBL2/p130 reintroduction. We then monitored their expression in primary tumors of endemic BL as well, demonstrating that their expression resembled those of the BL cell lines. In conclusion, these data suggest that, as RBL2/p130 modulates the expression of target genes, which are important for cell growth and viability, its inactivation may be relevant for the occurrence of BL.
Using gene expression data and network topology to detect substantial pathways, clusters and switches during oxygen deprivation of Escherichia coli
Authors: Schramm Gunnar , Zapatka Marc , Eils Roland , König Rainer 
Published: May 2007

Abstract

Background
Biochemical investigations over the last decades have elucidated an increasingly complete image of the cellular metabolism. To derive a systems view for the regulation of the metabolism when cells adapt to environmental changes, whole genome gene expression profiles can be analysed. Moreover, utilising a network topology based on gene relationships may facilitate interpreting this vast amount of information, and extracting significant patterns within the networks.

Results
Interpreting expression levels as pixels with grey value intensities and network topology as relationships between pixels, allows for an image-like representation of cellular metabolism. While the topology of a regular image is a lattice grid, biological networks demonstrate scale-free architecture and thus advanced image processing methods such as wavelet transforms cannot directly be applied. In the study reported here, one-dimensional enzyme-enzyme pairs were tracked to reveal sub-graphs of a biological interaction network which showed significant adaptations to a changing environment. As a case study, the response of the hetero-fermentative bacterium E. coli to oxygen deprivation was investigated. With our novel method, we detected, as expected, an up-regulation in the pathways of hexose nutrients up-take and metabolism and formate fermentation. Furthermore, our approach revealed a down-regulation in iron processing as well as the up-regulation of the histidine biosynthesis pathway. The latter may reflect an adaptive response of E. coli against an increasingly acidic environment due to the excretion of acidic products during anaerobic growth in a batch culture.

Conclusion
Based on microarray expression profiling data of prokaryotic cells exposed to fundamental treatment changes, our novel technique proved to extract system changes for a rather broad spectrum of the biochemical network.
Induction of MMP-9 release from human dermal fibroblasts by thrombin: involvement of JAK/STAT3 signaling pathway in MMP-9 release
Authors: Wang Li , Luo Jianmin , He Shaoheng 
Published: May 2007

Abstract

Background
It has been recognized that dermal fibroblasts and matrix metalloproteases (MMP) play crucial roles in wound healing process in skin. Thrombin was found to stimulate IL-8 release from human dermal fibroblasts (HDFs). However, little is known of the effect of thrombin on secretion of MMPs from dermal fibroblasts. In the present study, the influence of thrombin on proMMP-2 and proMMP-9 activity release from primary cultured HDFs, and its potential signaling pathways were investigated.

Results
The results showed that thrombin induced proMMP-9, but not proMMP-2 release from HDFs in a dose dependent manner at 6 h following incubation. Thrombin also upregulated expression of proMMP-9 mRNA in HDFs. Hirudin completely abolished the action of thrombin on HDFs. An agonist peptide of protease-activated receptor-1, SFLLR-NH2 stimulated an enhanced release of proMMP-9 from HDFs. AG490, an inhibitor of STAT3 inhibited basal and thrombin-provoked proMMP-9 release and phosphorylation of STAT3. PD98059, an inhibitor of MAPK and LY294002, an inhibitor PI3K failed to significantly inhibit thrombin induced proMMP-9 release.

Conclusion
Thrombin is a potent stimulus of proMMP-9 release from HDFs. Thrombin induced proMMP-9 release is most likely through activation of PAR-1. JAK/STAT3 signaling pathway is involved in proMMP-9 release from HDFs.
Colon cancer risk and different HRT formulations: a case-control study
Authors: Dinger Jürgen C , Heinemann Lothar AJ , Möhner Sabine , Thai Do Minh , Assmann Anita 
Published: May 2007

Abstract

Background
Most studies have found no increased risk of colon cancer associated with hormone replacement therapy (HRT), or even a decreased risk. But information about the effects of different HRT preparations is lacking.

Methods
A case-control study was performed within Germany in collaboration with regional cancer registries and tumor centers. Up to 5 controls were matched to each case of colon cancer. Conditional logistic regression analysis was applied to estimate crude and adjusted odds ratios (OR) and 95% confidence intervals (95% CI). Stratified analyses were performed to get an impression of the risk associated with different estrogens and progestins.

Results
A total of 354 cases of colon cancer were compared with 1422 matched controls. The adjusted overall risk estimate for colon cancer (ColC) associated with ever-use of HRT was 0.97 (0.71 – 1.32). No clinically relevant trends for ColC risk were observed with increasing duration of HRT use, or increasing time since first or last HRT use in aggregate.
Whereas the overall risk estimates were stable, the numbers in many of the sub-analyses of HRT preparation groups (estrogens and progestins) were too small for conclusions. Nevertheless, if the ColC risk estimates are taken at face value, most seemed to be reduced compared with never-use of HRT, but did not vary much across HRT formulation subgroups. In particular, no substantial difference in ColC risk was observed between HRT-containing conjugated equine estrogens (CEE) or medroxyprogesterone acetate (MPA) and other formulations more common in Europe.

Conclusion
Ever-use of HRT was not associated with an increased risk of colon cancer. In contrary, most risk estimates pointed non-significantly toward a lower ColC risk in HRT ever user. They did not vary markedly among different HRT formulations (estrogens, progestins). However, the small numbers and the overlapping nature of the subgroups suggest cautious interpretation.
A model of blood flow in the mesenteric arterial system
Authors: Mabotuwana Thusitha DS , Cheng Leo K , Pullan Andrew J 
Published: May 2007

Abstract

Background
There are some early clinical indicators of cardiac ischemia, most notably a change in a person's electrocardiogram. Less well understood, but potentially just as dangerous, is ischemia that develops in the gastrointestinal system. Such ischemia is difficult to diagnose without angiography (an invasive and time-consuming procedure) mainly due to the highly unspecific nature of the disease.
Understanding how perfusion is affected during ischemic conditions can be a useful clinical tool which can help clinicians during the diagnosis process. As a first step towards this final goal, a computational model of the gastrointestinal system has been developed and used to simulate realistic blood flow during normal conditions.

Methods
An anatomically and biophysically based model of the major mesenteric arteries has been developed to be used to simulate normal blood flows. The computational mesh used for the simulations has been generated using data from the Visible Human project. The 3D Navier-Stokes equations that govern flow within this mesh have been simplified to an efficient 1D scheme. This scheme, together with a constitutive pressure-radius relationship, has been solved numerically for pressure, vessel radius and velocity for the entire mesenteric arterial network.

Results
The computational model developed shows close agreement with physiologically realistic geometries other researchers have recorded in vivo. Using this model as a framework, results were analyzed for the four distinct phases of the cardiac cycle – diastole, isovolumic contraction, ejection and isovolumic relaxation. Profiles showing the temporally varying pressure and velocity for a periodic input varying between 10.2 kPa (77 mmHg) and 14.6 kPa (110 mmHg) at the abdominal aorta are presented. An analytical solution has been developed to model blood flow in tapering vessels and when compared with the numerical solution, showed excellent agreement.

Conclusion
An anatomically and physiologically realistic computational model of the major mesenteric arteries has been developed for the gastrointestinal system. Using this model, blood flow has been simulated which show physiologically realistic flow profiles.
Ab initio modeling of small proteins by iterative TASSER simulations
Authors: Wu Sitao , Skolnick Jeffrey , Zhang Yang 
Published: May 2007

Abstract

Background

Predicting 3-dimensional protein structures from amino-acid sequences is an important unsolved problem in computational structural biology. The problem becomes relatively easier if close homologous proteins have been solved, as high-resolution models can be built by aligning target sequences to the solved homologous structures. However, for sequences without similar folds in the Protein Data Bank (PDB) library, the models have to be predicted from scratch. Progress in the ab initio structure modeling is slow. The aim of this study was to extend the TASSER (threading/assembly/refinement) method for the ab initio modeling and examine systemically its ability to fold small single-domain proteins.

Results

We developed I-TASSER by iteratively implementing the TASSER method, which is used in the folding test of three benchmarks of small proteins. First, data on 16 small proteins (< 90 residues) were used to generate I-TASSER models, which had an average Cα-root mean square deviation (RMSD) of 3.8Å, with 6 of them having a Cα-RMSD < 2.5Å. The overall result was comparable with the all-atomic ROSETTA simulation, but the central processing unit (CPU) time by I-TASSER was much shorter (150 CPU days vs. 5 CPU hours). Second, data on 20 small proteins (< 120 residues) were used. I-TASSER folded four of them with a Cα-RMSD < 2.5Å. The average Cα-RMSD of the I-TASSER models was 3.9Å, whereas it was 5.9Å using TOUCHSTONE-II software. Finally, 20 non-homologous small proteins (< 120 residues) were taken from the PDB library. An average Cα-RMSD of 3.9Å was obtained for the third benchmark, with seven cases having a Cα-RMSD < 2.5Å.

Conclusion

Our simulation results show that I-TASSER can consistently predict the correct folds and sometimes high-resolution models for small single-domain proteins. Compared with other ab initio modeling methods such as ROSETTA and TOUCHSTONE II, the average performance of I-TASSER is either much better or is similar within a lower computational time. These data, together with the significant performance of automated I-TASSER server (the Zhang-Server) in the 'free modeling' section of the recent Critical Assessment of Structure Prediction (CASP)7 experiment, demonstrate new progresses in automated ab initio model generation. The I-TASSER server is freely available for academic users http://zhang.bioinformatics.ku.edu/I-TASSER.
Expression stability of commonly used reference genes in canine articular connective tissues
Authors: Ayers Duncan , Clements Dylan N , Salway Fiona , Day Philip JR 
Published: May 2007

Abstract

Background
The quantification of gene expression in tissue samples requires the use of reference genes to normalise transcript numbers between different samples. Reference gene stability may vary between different tissues, and between the same tissue in different disease states. We evaluated the stability of 9 reference genes commonly used in human gene expression studies. Real-time reverse transcription PCR and a mathematical algorithm were used to establish which reference genes were most stably expressed in normal and diseased canine articular tissues and two canine cell lines stimulated with lipolysaccaride (LPS).

Results
The optimal reference genes for comparing gene expression data between normal and diseased infrapatella fat pad were RPL13A and YWHAZ (M = 0.56). The ideal reference genes for comparing normal and osteoarthritic (OA) cartilage were RPL13A and SDHA (M = 0.57). The best reference genes for comparing normal and ruptured canine cranial cruciate ligament were B2M and TBP (M = 0.59). The best reference genes for normalising gene expression data from normal and LPS stimulated cell lines were SDHA and YWHAZ (K6) or SDHA and HMBS (DH82), which had expression stability (M) values of 0.05 (K6) and 0.07 (DH82) respectively. The number of reference genes required to reduce pairwise variation (V) to <0.20 was 4 for cell lines, 5 for cartilage, 7 for cranial cruciate ligament and 8 for fat tissue. Reference gene stability was not related to the level of gene expression.

Conclusion
The reference genes demonstrating the most stable expression within each different canine articular tissue were identified, but no single reference gene was identified as having stable expression in all different tissue types. This study underlines the necessity to select reference genes on the basis of tissue and disease specific expression profile evaluation and highlights the requirement for the identification of new reference genes with greater expression stability for use in canine articular tissue gene expression studies.
Dideoxynucleoside HIV reverse transcriptase inhibitors and drug-related hepatotoxicity: a case report
Authors: Lapadula Giuseppe , Izzo Ilaria , Costarelli Silvia , Cologni Giuliana , Bercich Luisa , Casari Salvatore , Gambarotti Marco , Torti Carlo 
Published: May 2007

Abstract
This report regards the case of a 43 year-old HIV-positive woman who developed an episode of serious transaminase elevation during stavudine-including antiretroviral therapy. Diagnostic assessment ruled out hepatitis virus co-infection, alcohol abuse besides other possible causes of liver damage. No signs of lactic acidosis were present. Liver biopsy showed portal inflammatory infiltrate, spotty necrosis, vacuoles of macro- and micro-vesicular steatosis, acidophil and foamy hepatocytes degeneration with organelles clumping, poorly formed Mallory bodies and neutrophil granulocytes attraction (satellitosis). A dramatic improvement in liver function tests occurred when stavudine was discontinued and a new antiretroviral regimen with different nucleoside reverse transcriptase inhibitors was used. The importance of considering hepatotoxicity as an adverse event of HAART including stavudine, even in absence of other signs of mitochondrial toxicity should therefore be underlined. Liver biopsy may provide further important information regarding patients with severe transaminase elevation, for a better understanding of the etiology of liver damage.
Prospective Multicentric Randomized Study Comparing Periareolar and Peritumoral Injection of Radiotracer and Blue Dye for the Detection of Sentinel Lymph Node in Breast Sparing Procedures: FRANSENODE Trial
Authors: Rodier Jean-François , Velten Michel , Wilt Marc , Martel Pierre , Ferron Gwanaël , Vaini-Elies Véronique , Mignotte Hervé , Brémond Alain , Classe Jean-Marc , Dravet François , Routiot Thierry , de Lara Christine Tunon , Avril Antoine , Lorimier Gérard , Fondrinier Eric , Houvenaeghel Gilles , Avigdor Sandrine 
Published: May 2007

Purpose To determine the optimal injection path for blue dye and radiocolloid for sentinel lymph node (SLN) biopsy in early breast cancer. Patients and Methods A prospective randomized multicentric study was initiated to compare the peritumoral (PT) injection site to the periareolar (PA) site in 449 patients. Results The detection rate of axillary SLN by lymphoscintigraphy was significantly higher (P = .03) in the PA group (85.2%) than in the PT group (73.2%). Intraoperative detection rate by blue dye and/or gamma probe was similar (99.11%) in both groups. The rate of SLN detection was somewhat higher in the PA group than in the PT group: 95.6% versus 93.8% with blue dye (P = .24) and 98.2% versus 96.0% by probe (P = .16), respectively. The number of SLNs detected by lymphoscintigraphy and by probe was significantly higher in the PA group than in the PT group, 1.5 versus 1.2 (P = .001) and 1.9 versus 1.7 (P = .02). The blue and hot concordance was 95.6% in the PA group and 91.5% in the PT group (P = .08). The mean ex vivo count of the SLN was significantly higher in the PA group than in the PT group (P < .0001). Conclusion This study strongly validates the PA injection technique given the high detection rate (99.1%) of SLN and the high concordance (95.6%) between blue dye and the radiotracer, as well as higher significant ex and in vivo counts, improving SLN probe detection.
Lung Cancer in the Elderly
Authors: Gridelli Cesare , Langer Corey , Maione Paolo , Rossi Antonio , Schild Steven E. 
Published: May 2007

Purpose Elderly patients often have comorbidities and other characteristics that make the selection of treatment daunting. Methods We have reviewed the available evidence in the literature to gauge the results of therapy for elderly lung cancer patients. Results The beneficial results achieved with adjuvant chemotherapy in the general population with early non–small-cell lung cancer (NSCLC) cannot be automatically extrapolated to the elderly, who are at higher risk of toxicity. Retrospective analyses of combined chemoradiotherapy in locally advanced NSCLC patients suggest equivalent therapeutic benefit for younger and older patients, despite heightened toxicity. There have been no elderly-specific phase III trials for locally advanced NSCLC. For advanced NSCLC, on the basis of evidence-based data, single-agent chemotherapy remains the standard of care for nonselected elderly patients. However, retrospective analyses suggest that the efficacy of platinum-based combination chemotherapy is similar in fit older and younger patients, with increased but acceptable toxicity for elderly patients. In limited-disease small-cell lung cancer (SCLC), sequential chemoradiotherapy is clearly less toxic compared with a standard concurrent approach, but our assessment of treatment is hindered by the absence of prospective elderly-specific trials. Although prophylactic cranial irradiation has emerged as a standard strategy, it should be omitted in patients with cognitive impairment. In extensive SCLC, etoposide in combination with either cisplatin or carboplatin has emerged as standard treatment; hematopoietic support may be necessary. Conclusion With the exception of advanced NSCLC, prospective elderly-specific studies are lacking. Available data suggest that outcomes in the fit elderly mirror results observed in younger patients, although toxicity is generally worse.
Sailing the skies: the improbable aeronautical success of the pterosaurs
Authors: Wilkinson Matthew T. 
Published: May 2007

SUMMARYPterosaur wings bore a striking resemblance to sails, having a bony spar at the leading edge, formed by the forelimb and one enormously elongated digit,and an elastic wing membrane. Such simple wings would be expected to have performed badly due to excessive deformation, membrane flutter and poor control characteristics. Here I discuss how certain anatomical features,specifically a forewing membrane in the inner part of the wing and a system of fibres embedded in the distal part, may have countered these shortcomings. The forewing, supported by the unique pteroid bone, would have reduced the wings'geometric twist, and has been shown in wind tunnel tests to improve membrane stability at low angles of attack and dramatically increase the maximum lift coefficient at high angles of attack. The function of the fibres is poorly understood, but it is suggested that they improved membrane stability and optimised twist nearer the wingtips.