gebhart/patrepeval huggingface dataset:
Mechanisms Regulating Tumor Angiogenesis by 12-Lipoxygenase in Prostate Cancer Cells (2006)

12-Lipoxygenase utilizes arachidonic acid to synthesize 12(S)-hydroperoxyeicosatetraenoic acid, which is converted to the end product 12(S)-hydroxyeicosatetraenoic acid, an eicosanoid that promotes tumorigenesis and metastasis. Increased expression of 12-lipoxygenase has been documented in a number of carcinomas. When overexpressed in human prostate or breast cancer, 12-lipoxygenase promotes tumor angiogenesis and growth in vivo. The present study was undertaken to delineate the mechanisms by which 12-lipoxygenase enhances angiogenesis. Herein we report that nordihydroguaiaretic acid, a pan inhibitor of lipoxygenases and baicalein, a selective inhibitor of 12-lipoxygenase, reduced VEGF expression in human prostate cancer PC-3 cells. Overexpression of 12-lipoxygenase in PC-3 cells resulted in a 3-fold increase in VEGF protein level when compared with vector control cells. An increase in PI 3-kinase activity was found in 12-LOX-transfected PC-3 cells and inhibition of PI 3-kinase by LY294002 significantly reduced VEGF expression. Northern blot and real time PCR analyses revealed an elevated VEGF transcript level in PC-3 cells transfected with a 12-lipoxygenase expression construct. Using a VEGF promoter luciferase construct (-1176/+54), we found a 10-fold increase in VEGF promoter activity in 12-lipoxygenase-transfected PC-3 cells. The region located between -88 and -66 of the VEGF promoter was identified as 12-lipoxygenase responsive using VEGF promoter-based luciferase assays. Further analysis with mutant constructs indicated Sp1 as a transcription factor required for 12-lipoxygenase stimulation of VEGF. Neutralization of VEGF by a function-blocking antibody significantly decreased the ability of 12-lipoxygenase-transfected PC-3 cells to stimulate endothelial cell migration, suggesting VEGF as an important effector for 12-lipoxygenase-mediated stimulation of tumor angiogenesis.
Amino-Acid Sequence of Rabbit Skeletal Tropomyosin and Its Coiled-Coil Structure (1972)

A tentative amino-acid sequence for the COOH-terminal half of rabbit skeletal tropomyosin is reported. These studies confirm our previous conclusions that this tropomyosin consists of several different but similar polypeptide chains. In the sequence, nonpolar residues occur in two series at intervals of seven residues. Amino-acid residues in series I are three residues on the NH(2)-terminal side of, and four residues on the COOH-terminal side of, residues in series II. The presence of occasional charged or ambivalent residues in the positions of series I or II does not lead to a disruption of this long-range pattern. The majority of residues located between the nonpolar residues are charged or polar amino acids. Two highly similar or identical alpha-helices with the reported sequence can be packed together in parallel in a coiled-coil structure. These may be in register or staggered by seven residues or some multiple of it. The observation that groups of small hydrophobic side chains appear to alternate with groups of bulky side chains suggests that a staggered arrangement of the two alpha-helices would maximize the regularity and hydrophobic interactions of the coiled-coil. Model building considerations show that this would occur with a stagger of 14 residues. Such an arrangement could account for the end-to-end aggregation of tropomyosin in solution, and in crystal and tactoid filaments. However, a structure in which the two polypeptides are in register cannot be ruled out.
Afp–Producing Gastric Cancer Associated with Lymphnode Metastasis Mimicking Pancreatic Cancer : A Case Report (2014)

症例は70歳男性．繰り返す胃潰瘍で近医加療中，腹部CT検査にて膵体部に58mm大の腫瘤を指摘され，当院紹介受診となった．潰瘍部より２度の生検が行われたが，いずれも良性の診断であった．血液生化学検査では，CEA14.1ng/ml，CA19-9 45U/ml，AFP 507ng/mlと腫瘍マーカーの上昇を認めた．当院の腹部超音波検査では，膵体部に内部不均一で比較的境界明瞭な等～低エコーの腫瘤として描出された．超音波内視鏡下穿刺吸引生検の結果，低分化腺癌を認めた．膵悪性腫瘍の診断にて膵体尾部切除，リンパ節郭清を行った．術中に胃前庭部に漿膜側へ突出する腫瘍を認めたため，幽門側胃切除術を併施した．術後病理組織診断では，胃はAFP産生腫瘍であり，膵の腫瘤は胃癌の転移リンパ節であった．以上，膵腫瘤が発見契機となったAFP産生胃癌膵周囲リンパ節転移の切除例を経験した．膵腫瘤性病変にAFPの上昇を伴った場合は，胃の十分な精査が肝要と考えられた．
Methane emission rate study in a deep Pocahontas No. 3 coalbed mine in conjunction with drilling degasification holes in the coalbed (1972)

A degasification experiment was conducted in a Pochahontas No. 3 coalbed mine in Virginia. It involved (1) drilling holes in the coalbed in the outside headings of a set of five being developed in virgin area and (2) conducting a methane emission rate study as mining progressed and additional holes were drilled. Degasification from all drill holes except the longest in each of the outside headings and the first three drilled (excluding the in situ pressure hole) was erratic and inconsequential in methane emission rates. The two longest holes liberated 66 and 79 cfm of methane, which is significant for the coalbed, but such quantity lasted a relatively short time; the first three were uniform but low in methane emission.
Towards the human intestinal microbiota phylogenetic core (2009)

The paradox of a host specificity of the human faecal microbiota otherwise acknowledged as characterized by global functionalities conserved between humans led us to explore the existence of a phylogenetic core. We investigated the presence of a set of bacterial molecular species that would be altogether dominant and prevalent within the faecal microbiota of healthy humans. A total of 10 456 non-chimeric bacterial 16S rRNA sequences were obtained after cloning of PCR-amplified rDNA from 17 human faecal DNA samples. Using alignment or tetranucleotide frequency-based methods, 3180 operational taxonomic units (OTUs) were detected. The 16S rRNA sequences mainly belonged to the phyla Firmicutes (79.4%), Bacteroidetes (16.9%), Actinobacteria (2.5%), Proteobacteria (1%) and Verrumicrobia (0.1%). Interestingly, while most of OTUs appeared individual-specific, 2.1% were present in more than 50% of the samples and accounted for 35.8% of the total sequences. These 66 dominant and prevalent OTUs included members of the genera Faecalibacterium, Ruminococcus, Eubacterium, Dorea, Bacteroides, Alistipes and Bifidobacterium. Furthermore, 24 OTUs had cultured type strains representatives which should be subjected to genome sequence with a high degree of priority. Strikingly, 52 of these 66 OTUs were detected in at least three out of four recently published human faecal microbiota data sets, obtained with very different experimental procedures. A statistical model confirmed these OTUs prevalence. Despite the species richness and a high individual specificity, a limited number of OTUs is shared among individuals and might represent the phylogenetic core of the human intestinal microbiota. Its role in human health deserves further study.
Beneficial Effects of Allopurinol on Glutathione Levels and Glutathione Peroxidase Activity in Rat Ischaemic Acute Renal Failure (1996)

The protective effect of allopurinol, an inhibitor of the enzyme, xanthine oxidase, against the renal ischaemia-reperfusion of the rat was investigated. Rats were subjected to renal ischaemia by clamping of the left renal artery and vein for 45 min, and were then reperfused for 24 h; these animals were randomized to receive either saline (n = 10) or allopurinol (n = 10) at a dose of 50 mg/kg bolus intraperitoneally 5 min before reperfusion. The control group comprised seven healthy rats not exposed to ischaemia or reperfusion. The blood urea nitrogen and plasma creatinine levels were increased in the allopurinol group, but the increase was less than that in the placebo group, compared with the controls. The kidney glutathione level was significantly reduced in the placebo group but not in the allopurinol group compared with the controls. The glutathione peroxidase activity in the kidney tissues was reduced more than two-fold in the placebo group compared with the controls, but the reduction in glutathione peroxidase was considerably less in the allopurinol group. Renal tissue lactate dehydrogenase, aspartate amino-transferase, gamma-glutamyl transferase and alkaline phosphatase activities were reduced almost two-fold in the placebo group, but allopurinol treatment maintained these enzyme activities close to the control activities. These results provide evidence that allopurinol treatment may have beneficial effects on antioxidant defences against ischaemia-reperfusion injury of rat kidneys.
Choices Following Antigen Entry: Antibody Formation or Immunologic Tolerance? (1995)

The research briefly summarized here covers 38 years of work in cellular immunology, chiefly devoted to understanding how antigen subserves the antithetical functions of stimulating antibody formation and inducing tolerance. The three interlocking themes running through the work are the development of methods to beat the problem of heterogeneity among lymphocytes by studying single cells and single clones; critical pursuit of antigen-trapping patterns within lymphoid tissues and analysis of consequent cellular events; and construction of models of tolerance that permit the detection of events subtler than direct purging of the B cell repertoire. One of the best features of this adventure has been its international character, the interaction with colleagues in many countries, and the influence that this work, despite its entirely fundamental character, has exerted in the practical world of preventive and clinical medicine.
Design of an Oligonucleotide-Incorporated Nonfouling Surface and Its Application in Electrochemical DNA Sensors for Highly Sensitive and Sequence-Specific Detection of Target DNA (2008)

In this work, we report a novel electrochemical DNA sensor based on a nonfouling monolayer structure self-assembled at gold surfaces. Self-assembled monolayers (SAMs) with oligo(ethylene glycol) (OEG)-terminated thiols are known to be highly protein-resistant and effectively repel nonspecific adsorption. We found that a mixed SAM structure incorporating thiolated oligonucleotides and OEG thiols (SH-DNA/OEG) exhibited the similar non-fouling feature. More importantly, it allowed facile electron transfer across the monolayer and thus was fully compatible with electrochemical detection. On the basis of this SH-DNA/OEG platform, we developed a sandwich-type electrochemical sensor for the sequence-specific detection of DNA targets. This sensor was able to detect as little as 1 pM target DNA even in the presence of complicated biological fluids such as human serum. We also employed this sensor to directly detect a polymerase chain reaction (PCR) amplicon from the genomic DNA of Escherichia coli K12, which led to a very low detect limit of 60 fg (approximately 10 copies).
EagleView: A genome assembly viewer for next-generation sequencing technologies (2008)

The emergence of high-throughput next-generation sequencing technologies (e.g., 454 Life Sciences [Roche], Illumina sequencing [formerly Solexa sequencing]) has dramatically sped up whole-genome de novo sequencing and resequencing. While the low cost of these sequencing technologies provides an unparalleled opportunity for genome-wide polymorphism discovery, the analysis of the new data types and huge data volume poses formidable informatics challenges for base calling, read alignment and genome assembly, polymorphism detection, as well as data visualization. We introduce a new data integration and visualization tool EagleView to facilitate data analyses, visual validation, and hypothesis generation. EagleView can handle a large genome assembly of millions of reads. It supports a compact assembly view, multiple navigation modes, and a pinpoint view of technology-specific trace information. Moreover, EagleView supports viewing coassembly of mixed-type reads from different technologies and supports integrating genome feature annotations into genome assemblies. EagleView has been used in our own lab and by over 100 research labs worldwide for next-generation sequence analyses. The EagleView software is freely available for not-for-profit use at http://bioinformatics.bc.edu/marthlab/EagleView.
Availability in parallel systems: Automatic process restart (1997)

Parallel and clustered architectures are increasingly being used as a foundation for high-capacity servers. At the same time, the availability expectations are also rising rapidly, since the effects of down time become more apparent and have higher economic consequences for larger systems. The use of parallel structures generally implies more hardware and software components. The presence of more and larger components increases the chances that an individual component will fail, and that failure has the potential to hurt the overall availability of the system. This paper discusses the use of “restart techniques” as an important strategy in providing increased availability in a parallel structure. The paper covers a set of functions that have been developed for the S/390® Parallel Sysplex™.
Concepts in the Application of Pneumatic Ventricular Assist Devices for Ischemic Myocardial Injury (1995)

The clinical results of "bridge-to-recovery" from ischemic myocardial injury using pneumatic ventricular assist devices (VADs) have been disappointing, because no significant improvement in the hospital discharge rate (25%) has been observed during the past 10 years. Interestingly, similar results have been reported using the less sophisticated and more widely available centrifugal pumps. It is well recognized that appropriate patient selection and early device implantation are important determinants of patient survival; however, it is less clear why there is a lack of difference in the results between pneumatic VADs and the centrifugal pumps. The reasons for the lack of difference in the results between pneumatic VADs and centrifugal pumps are multifactorial, and to some extent may be due to a conservative approach in the application of the more capable pneumatic VADs. In an effort to provide a more effective approach to the clinical application of pneumatic VADs for bridge-to-recovery, two pneumatic devices (the Jarvik 7-70 total artificial heart and the Symbion acute VAD) were functionally characterized using an in vitro mock circulatory system. The performance under pneumatic VAD asynchronous pumping compared to electrocardiogram synchronous counterpulsation was also evaluated. Based upon the results obtained, a two phase approach was developed. In the initial phase (i.e., the first 12-48 hrs), device output is maximized through asynchronous pumping to rapidly reverse the effects of cardiogenic shock. During the second phase (i.e., after hemodynamic stabilization and early evidence of end-organ recovery), electrocardiogram synchronous counterpulsation is used to focus more specifically on recovery of the heart.(ABSTRACT TRUNCATED AT 250 WORDS)
Thiation reactions of some active carbonyl compounds with sulfur transfer reagents (1987)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThiation reactions of some active carbonyl compounds with sulfur transfer reagentsNai Zhong Huang, M. V. Lakshmikantham, and Michael P. CavaCite this: J. Org. Chem. 1987, 52, 2, 169–172Publication Date (Print):January 1, 1987Publication History Published online1 May 2002Published inissue 1 January 1987https://pubs.acs.org/doi/10.1021/jo00378a001https://doi.org/10.1021/jo00378a001research-articleACS PublicationsRequest reuse permissionsArticle Views1064Altmetric-Citations30LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
A New Approach to Retrain Gait in Stroke Patients Through Body Weight Support and Treadmill Stimulation (1998)

Background and Purpose —A new gait training strategy for patients with stroke proposes to support a percentage of the patient’s body weight while retraining gait on a treadmill. This research project intended to compare the effects of gait training with body weight support (BWS) and with no body weight support (no-BWS) on clinical outcome measures for patients with stroke. Methods —One hundred subjects with stroke were randomized to receive one of two treatments while walking on a treadmill: 50 subjects were trained to walk with up to 40% of their body weight supported by a BWS system with overhead harness (BWS group), and the other 50 subjects were trained to walk bearing full weight on their lower extremities (no-BWS group). Treatment outcomes were assessed on the basis of functional balance, motor recovery, overground walking speed, and overground walking endurance. Results —After a 6-week training period, the BWS group scored significantly higher than the no-BWS group for functional balance ( P =0.001), motor recovery ( P =0.001), overground walking speed ( P =0.029), and overground walking endurance ( P =0.018). The follow-up evaluation, 3 months after training, revealed that the BWS group continued to have significantly higher scores for overground walking speed ( P =0.006) and motor recovery ( P =0.039). Conclusions —Retraining gait in patients with stroke while a percentage of their body weight was supported resulted in better walking abilities than gait training while the patients were bearing their full weight. This novel gait training strategy provides a dynamic and integrative approach for the treatment of gait dysfunction after stroke.
Human Disease-Drug Network Based on Genomic Expression Profiles (2009)

We have automatically generated thousands of disease and drug expression profiles using GEO datasets, and constructed a large scale disease-drug network for effective and efficient drug repositioning as well as drug target/pathway identification.
Substitution of Foreign Protein Sequences into a Chimeric Toxin Composed of Transforming Growth Factor a and Pseudomonas Exotoxin (1991)

TGF alpha-PE40 is a chimeric toxin made by replacing domain Ia of Pseudomonas exotoxin (PE) with transforming growth factor alpha (TGF alpha). We have now replaced a portion of domain Ib of PE with different polypeptides or an extra domain III of PE in transforming growth factor alpha-PE40 and maintained cell killing. Thus, TGF alpha-PE40 can be used to transport foreign protein sequences into the cytosol of cells.
High repetition rate Q-switching performance in transversely diode-pumped Nd doped mixed gadolinium yttrium vanadate bounce laser (2006)

Up to 650kHz high repetition active Q-switching was achieved with a pulse-width of <40ns by using a diode-side-pumped Nd:Gd(x)Y(1-x)VO(4) bounce amplifier. An average output power of 17.5W was obtained at a pump power of 41W. The pulse repetition frequency range of the stable Q-switching operation was adjusted without any loss of the average output power by changing the Gd:Y mixture ratio.
Peripherin and Neurofilament Protein Coexist in Spinal Spheroids of Motor Neuron Disease (1992)

We have compared the immunolocalization of neurofilament protein (NF) with two other neuronal-specific intermediate filament proteins in large spinal axonal swellings (spheroids) of motor neuron disease and controls. All spheroids labeled each of the three different subunits of NF, the low, middle, and high molecular weight polypeptides. In doublelabel immunofluorescence, 300 axonal swellings were immunostained for NF, and 87% of them contained the intermediate protein peripherin. The pattern of immunostaining of NF and peripherin was indistinguishable at a high resolution viewed in 1 microns optical sections by confocal microscopy. A minority of the spheroids contained alpha-internexin, another intermediate protein, but it was weakly immunoreactive. The immunostaining of axonal swellings was similar for all epitopes tested in motor neuron disease and control subjects. The findings suggest that peripherin as well as neurofilament protein are major components of the proliferated intermediate filaments in spheroids.
Prolonged duration local anesthesia from tetrodotoxin-enhanced local anesthetic microspheres (2003)

There is interest in developing prolonged duration local anesthesics. Here we examine whether tetrodotoxin (TTX) can be used to prolong the block from bupivacaine microspheres with and without dexamethasone. Rats received sciatic nerve blocks with 75 mg of microspheres containing 0.05% (w/w) TTX, 50% (w/w) bupivacaine and/or 0.05% (w/w) dexamethasone. 0.1% (w/w) TTX microspheres were also tested. The carrier fluid contained 1:100,000 epinephrine. Nociceptive and motor blockade of the hindpaw were quantified. Nerves and adjacent muscles were harvested 2 weeks after injection for histological assessment by light microscopy. The median nociceptive block duration in hours from the microsphere groups were: bupivacaine=6.2, 0.05% TTX=0, bupivacaine+TTX=35.3, bupivacaine+dexamethasone=31.3, TTX+dexamethasone=8.1, TTX+bupivacaine+dexamethasone=221.7. Some animals receiving particles containing 0.05% TTX had deficits in the uninjected extremity; all animals receiving 0.1% (w/w) TTX particles died. Pockets of particles were associated with localized inflammation, and all samples showed some evidence of myotoxicity in the vicinity of the injection. The nerves themselves appeared intact. In summary, coencapsulation of TTX in controlled release devices containing bupivacaine and dexamethasone resulted in very prolonged nerve blocks. As formulated here, this preparation had a narrow margin of safety. While the myotoxicity appears consistent with the well-known reversible myotoxicity associated with local anesthetics, its long-term significance remains to be established.
Generation and Characterization of Transgenic Mice with the Full-length Human DMD Gene (2007)

We report the generation of mice with an intact and functional copy of the 2.3-megabase human dystrophin gene (hDMD), the largest functional stretch of human DNA thus far integrated into a mouse chromosome. Yeast spheroplasts containing an artificial chromosome with the full-length hDMD gene were fused with mouse embryonic stem cells and were subsequently injected into mouse blastocysts to produce transgenic hDMD mice. Human-specific PCR, Southern blotting, and fluorescent in situ hybridization techniques demonstrated the intactness and stable chromosomal integration of the hDMD gene on mouse chromosome 5. Expression of the transgene was confirmed by RT-PCR and Western blotting. The tissue-specific expression pattern of the different DMD transcripts was maintained. However, the human Dp427p and Dp427m transcripts were expressed at 2-fold higher levels and human Dp427c and Dp260 transcripts were expressed at 2- and 4-fold lower levels than their endogenous counterparts. Ultimate functional proof of the hDMD transgene was obtained by crossing of hDMD mice with dystrophin-deficient mdx mice and dystrophin and utrophin-deficient mdx x Utrn-/- mice. The hDMD transgene rescued the lethal dystrophic phenotype of the mdx x Utrn-/- mice. All signs of muscular dystrophy disappeared in the rescued mice, as demonstrated by histological staining of muscle sections and gene expression profiling experiments. Currently, hDMD mice are extensively used for preclinical testing of sequence-specific therapeutics for the treatment of Duchenne muscular dystrophy. In addition, the hDMD mouse can be used to study the influence of the genomic context on deletion and recombination frequencies, genome stability, and gene expression regulation.