gebhart/patrepeval huggingface dataset:
Hierarchical buffered routing tree generation (2002)

This paper presents a solution to the problem of performance-driven buffered routing tree generation for very large scale integrated circuits. Using a novel bottom-up construction algorithm and a local neighborhood search strategy, our polynomial time algorithm finds the optimum solution in an exponential-size solution subspace. The final output is a buffered rectilinear Steiner routing tree that connects the driver of a net to its sink nodes. The two variants of the problem, i.e. maximizing the required time at the driver subject to a maximum total area constraint and minimizing the total area subject to a minimum required time at the driver constraint, are handled by propagating three-dimensional solution curves during the construction phase. Experimental results demonstrate the effectiveness of our algorithm compared to other techniques.
Immunoglobulin heavy chain gene organization in mice: analysis of a myeloma genomic clone containing variable and alpha constant regions. (1979)

We have isolated a myeloma genomic DNA clone containing the variable and constant regions of a mouse alpha chain. Restriction enzyme analyses and electron microscopic R loop mapping have demonstrated that the variable region is separated from the constant region by 6.8 kilobases of intervening DNA. In addition, two intervening DNA sequences of 100--200 bases separate the constant region into three approximately equal units. These intervening sequences may separate each of the segments coding for the three constant region domains of the alpha heavy chain. Southern blot analysis of embryo and myeloma DNA suggests that DNA rearrangement of heavy chain variable and constant regions occurs during the differentiation of antibody-producing cells.
Long-Term Growth Hormone Therapy Changes the Natural History of Body Composition and Motor Function in Children with Prader-Willi Syndrome (2010)

hGH treatment in children with PWS, begun prior to 2 yr of age, improves body composition, motor function, height, and lipid profiles. The magnitude of these effects suggests that long-term hGH therapy favorably alters the natural history of PWS to an extent that exceeds risks and justifies consideration for initiation during infancy.
You'll Never Be Paged in This Town Again (2003)

Critical illness in pandemic 2009 influenza A (H1N1) was associated with patients under age 65, with obesity, underlying diseases, and pregnancy. Persistently increased CRP and lower counts of T lymphocytes were associated with unfavorable prognosis. The patients with higher BMI and secondary fungal infection had higher fatal risks. Oseltamivir treatments at early stage would probably reduce mortality.
Compositional Analysis and Quantification of Heparin and Heparan Sulfate by Electrospray Ionization Ion Trap Mass Spectrometry (2003)

A new method using a combination of electrospray ionization mass spectrometry (ESI-MS) and tandem mass spectrometry (MSn) was developed for the identification and quantitative analysis of eight heparan sulfate (HS)- and heparin-derived delta-disaccharides obtained by enzymatic depolymerization. The compositional analysis of nonisomeric disaccharide constituents of heparin/HS was achieved from full-scan MS1 spectra using an internal standard and a calculated response factor for each disaccharide. Diagnostic product ions from MSn spectra of isomeric disaccharides were used for the quantitative analysis of the relative amounts of each of the isomers in mixtures. The protocol was validated using several quality control samples and showed satisfactory accuracy and precision. The analysis is rapid, accurate, and uses no purification or separation steps prior to analysis by MS, thus reducing sample consumption and analysis time of traditional methods. Using this quantitative analysis procedure, percentages of disaccharide compositions for heparins from porcine and bovine intestinal mucosa and heparan sulfate from bovine kidney were determined.
A -Acting DNA Element Located between TATA Box and Transcription Initiation Site Is Critical in Response to Regulatory Sequences in Human Angiotensinogen Gene (1996)

The promoter of the human angiotensinogen (hAG) gene functioned in its own core promoter context but not when replaced with simian virus 40 (SV40) core promoter, suggesting the presence of a transcriptionally important cis-acting sequence. Electrophoretic mobility shift assays demonstrated that a ubiquitously expressed nuclear factor, AGCF1, bound to AGCE1 (hAG core promoter element 1; positions -25 to -1) located between the TATA box and transcription initiation site. Substitution mutation in AGCE1 which disrupted AGCF1 binding affected the promoter activity more severely than a nonsense mutation of the hAG TATA sequences did. When AGCE1 was placed at the downstream of SV40 core promoter, the responsiveness to hAG upstream region was significantly restored. Furthermore, mutation and in vivo competition experiments suggested that AGCF1 acts as a critical regulator of hAG transcription by mediating the activity of the hAG upstream and downstream enhancer elements. DNase I footprinting and UV cross-linking analyses showed that AGCF1 with apparent molecular masses of 31, 33, and 43 kDa as the components protected the region from -26 to -9 which partially overlapped with the TATA box consensus sequences. These findings indicate that AGCE1 in addition to the TATA box plays a key role in mediating the hAG regulatory elements.
Treatment of metastatic colorectal carcinoma with 5-FU, mitomycin, vincristine, and methotrexate. (1984)

Fifty-three patients with advanced metastatic colorectal carcinoma were treated every 4-5 weeks with a chemotherapeutic regimen consisting of 5-FU (300 mg/m2 iv on Days 1-5), mitomycin (10 mg/m2 iv on Day 1 only [repeated every other course]), vincristine (0.75 mg/m2 on Days 1 and 5), and methotrexate (8.0 mg/m2 iv on Days 1 and 5). The overall response rate was 43.4%, with three patients (5.7%) achieving complete response (mean duration, 13.3 months) and 20 patients (37.7%) achieving partial response (mean duration, 6.3 months). Stable disease was not considered to be a response category in this report. The mean overall response duration was 7.8 months. The observed mean survival duration in responders was 15.2 months and in nonresponders was 8.9 months (P less than or equal to 0.01). Hematologic and subjective toxic effects are discussed.
Semisynthetic enzymes: characterization of isomeric flavopapains with widely different catalytic efficiencies (1984)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSemisynthetic enzymes: characterization of isomeric flavopapains with widely different catalytic efficienciesJames T. Slama, Czestaw Radziejewski, SubbaRao Oruganti, and E. T. KaiserCite this: J. Am. Chem. Soc. 1984, 106, 22, 6778–6785Publication Date (Print):October 1, 1984Publication History Published online1 May 2002Published inissue 1 October 1984https://pubs.acs.org/doi/10.1021/ja00334a053https://doi.org/10.1021/ja00334a053research-articleACS PublicationsRequest reuse permissionsArticle Views308Altmetric-Citations35LEARN 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
Development of Human Single-Chain Antibodies to the Transferrin Receptor that Effectively Antagonize the Growth of Leukemias and Lymphomas (2010)

The major route of iron uptake by cells occurs through transferrin receptor (TfR)-mediated endocytosis of diferric-charged plasma transferrin (holo-Tf). In this work, we pursued TfR antibodies as potential cancer therapeutics, characterizing human single-chain variable antibody fragments (scFv) specific for the human TfR isolated from a phage display library. We hypothesized that many of these antibodies would function as ligand mimetics because scFvs from the library were selected for binding and internalization into living cells. In support of this hypothesis, the anti-TfR scFvs identified were antagonists of TfR binding to holo-Tf, particularly two of the most potent antibodies, 3TF12 and 3GH7, which blocked the in vitro proliferation of a number of hematopoietic cancer cell lines. We optimized this activity of 3TF12 and 3GH7 by engineering 55-kDa bivalent antibody formats, namely, F12CH and H7CH, which could block cell proliferation with an IC(50) of 0.1 microg/mL. We found that the mechanism of the scFv antibody cytotoxicity was unique compared with cytotoxic anti-TfR monoclonal antibodies that have been described, causing cell surface upregulation of TfR along with the inhibition of holo-Tf cell uptake and induction of cell death. In a nude mouse model of erythroleukemia, administration of F12CH reduced tumor growth. Together, our findings define a new class of fully human anti-TfR antibodies suitable for immunotherapy against tumors whose proliferation relies on high levels of TfR and iron uptake, such as acute lymphoid and myeloid leukemias.
Introns in UTRs: Why we should stop ignoring them (2012)

Although introns in 5'- and 3'-untranslated regions (UTRs) are found in many protein coding genes, rarely are they considered distinctive entities with specific functions. Indeed, mammalian transcripts with 3'-UTR introns are often assumed nonfunctional because they are subject to elimination by nonsense-mediated decay (NMD). Nonetheless, recent findings indicate that 5'- and 3'-UTR intron status is of significant functional consequence for the regulation of mammalian genes. Therefore these features should be ignored no longer.
Bacillus subtilis Spores Germinate in the Chicken Gastrointestinal Tract (2008)

A number of poultry probiotics contain bacterial spores. In this study, orally administered spores of Bacillus subtilis germinated in the gastrointestinal (GI) tracts of chicks. Furthermore, 20 h after spores were administered, vegetative cells outnumbered spores throughout the GI tract. This demonstrates that spore-based probiotics may function in this host through metabolically active mechanisms.
High-Performance High- T c Superconducting Wires (2006)

We demonstrated short segments of a superconducting wire that meets or exceeds performance requirements for many large-scale applications of high-temperature superconducting materials, especially those requiring a high supercurrent and/or a high engineering critical current density in applied magnetic fields. The performance requirements for these varied applications were met in 3-micrometer-thick YBa2Cu3O(7-delta) films epitaxially grown via pulsed laser ablation on rolling assisted biaxially textured substrates. Enhancements of the critical current in self-field as well as excellent retention of this current in high applied magnetic fields were achieved in the thick films via incorporation of a periodic array of extended columnar defects, composed of self-aligned nanodots of nonsuperconducting material extending through the entire thickness of the film. These columnar defects are highly effective in pinning the superconducting vortices or flux lines, thereby resulting in the substantially enhanced performance of this wire.
The PI3K/Akt signaling pathway regulates the expression of Hsp70, which critically contributes to Hsp90-chaperone function and tumor cell survival in multiple myeloma (2012)

Despite therapeutic advances multiple myeloma remains largely incurable, and novel therapeutic concepts are needed. The Hsp90-chaperone is a reasonable therapeutic target, because it maintains oncogenic signaling of multiple deregulated pathways. However, in contrast to promising preclinical results, only limited clinical efficacy has been achieved through pharmacological Hsp90 inhibition. Because Hsp70 has been described to interact functionally with the Hsp90-complex, we analyzed the suitability of Hsp72 and Hsp73 as potential additional target sites. Expression of Hsp72 and Hsp73 in myeloma cells was analyzed by immunohistochemical staining and western blotting. Short interfering RNA-mediated knockdown or pharmacological inhibition of Hsp72 and Hsp73 was performed to evaluate the role of these proteins in myeloma cell survival and for Hsp90-chaperone function. Furthermore, the role of PI3K-dependent signaling in constitutive and inducible Hsp70 expression was investigated using short interfering RNA-mediated and pharmacological PI3K inhibition. Hsp72 and Hsp73 were frequently overexpressed in multiple myeloma. Knockdown of Hsp72 and/or Hsp73 or treatment with VER-155008 induced apoptosis of myeloma cells. Hsp72/Hsp73 inhibition decreased protein levels of Hsp90-chaperone clients affecting multiple oncogenic signaling pathways, and acted synergistically with the Hsp90 inhibitor NVP-AUY922 in the induction of death of myeloma cells. Inhibition of the PI3K/Akt/GSK3β pathway with short interfering RNA or PI103 decreased expression of the heat shock transcription factor 1 and down-regulated constitutive and inducible Hsp70 expression. Treatment of myeloma cells with a combination of NVP-AUY922 and PI103 resulted in additive to synergistic cytotoxicity. In conclusion, Hsp72 and Hsp73 sustain Hsp90-chaperone function and critically contribute to the survival of myeloma cells. Translation of Hsp70 inhibition into the clinic is therefore highly desirable. Treatment with PI3K inhibitors might represent an alternative therapeutic strategy to target Hsp70.
Lack of protection following immunisation with H. pylori outer membrane vesicles highlights antigenic differences between H. felis and H. pylori (1998)

Helicobacter pylori-induced inflammation is associated with the development of gastritis, peptic ulcer disease and gastric cancer in humans. Immunisation against this bacterium would ultimately have a major impact on H. pylori-related disease, notably global gastric cancer rates. To date, several potential H. pylori vaccine candidates have been identified. In this study, the Helicobacter felis/murine model was used to assess the immunogenicity of a previously undescribed H. pylori outer membrane vesicle fraction in immune protection.
Soluble interleukin-6 receptor triggers osteoclast formation by interleukin 6. (1993)

It has been reported that soluble interleukin (IL)-6 receptor (sIL-6R) is detected in the serum of healthy individuals and its level is increased in patients with multiple myeloma and human immunodeficiency virus infection. Although several reports have suggested that sIL-6R potentiates IL-6 action, its physiological role remains unclear. In this study, we examined the role of sIL-6R on osteoclast formation by IL-6, using a coculture of mouse osteoblasts and bone marrow cells. Neither recombinant mouse IL-6 (mIL-6) nor mouse sIL-6R (smIL-6R) induced osteoclast-like multinucleated cell (MNC) formation when they were added separately. In contrast, simultaneous treatment with mIL-6 and smIL-6R strikingly induced MNC formation. These MNCs satisfied major criteria of authentic osteoclasts, such as tartrate-resistant acid phosphatase (TRAP) activity, calcitonin receptors, and pit formation on dentine slices. The MNC formation induced by mIL-6 and smIL-6R was dose-dependently inhibited by adding monoclonal anti-mouse IL-6R antibody (MR16-1). It is likely that osteoblasts and osteoclast progenitors are capable of transducing a signal from a complex of IL-6 and sIL-6R through gp130, even though they may have no or a very small number of IL-6Rs. Factors such as IL-11, oncostatin M, and leukemia inhibitory factor, which are known to exert their functions through gp130 (the signal-transducing chain of IL-6R), also induced MNC formation in our coculture system. These results suggest that increased circulating or locally produced sIL-6R induces osteoclast formation in the presence of IL-6 mediated by a mechanism involving gp130. This may play an important physiological or pathological role in conditions associated with increased osteoclastic bone resorption.
Studies on anti-von Willebrand factor (vWF) monoclonal antibody NMC-4, which inhibits both ristocetin- and botrocetin-induced vWF binding to platelet glycoprotein Ib (1991)

Anti-von Willebrand factor (vWF) monoclonal antibody NMC-4 completely inhibited vWF binding to platelet glycoprotein (GP) lb induced by either ristocetin or botrocetin at an IgG concentration of approximately 10 micrograms/mL, and also blocked binding of asialo-vWF to GP lb. NMC-4 coupled beads isolated a 97-Kd fragment (Fr) from a whole tryptic digest of vWF. The N-terminal sequencing of the nonreduced 97-Kd Fr, in combination with amino acid analysis, showed it to be a homodimer of residues 449 through 728 of the constituent subunit. Present data, together with the results obtained from previous studies, confirm the existence of one or three possible inter-subunit disulfide bonds between cysteine residues 459, 462, and 464. NMC-4 bound to reduced vWF Fr(s) more weakly than to nonreduced Fr(s), but it did not react with Fr III-T2 of vWF, a disulfide-linked twin heterodimer of residues 273 through 511 and 674 through 728 (Marti et al, Biochemistry 26:8099, 1987). Fr III-T2 completely inhibited ristocetin-induced vWF binding at a concentration of 100 mumol/L but had no effect on botrocetin-induced binding. In addition, both the N- and C-terminal polypeptides, residues 449 through 549 and 674 through 728, generated by subdigestion of the 52/48-Kd Fr (Fujimura et al, J Biol Chem 261:381, 1986), inhibited preferentially ristocetin-induced vWF binding without affecting to botrocetin-induced vWF binding. These findings suggest that amino acid residues 512 through 673 of the vWF subunit are involved in botrocetin-induced vWF binding.
Structures and Transitions in Lipid Monolayers at the Air-Water Interface (1991)

Machine learning (ML) is transforming all areas of science. The complex and time-consuming calculations in molecular simulations are particularly suitable for an ML revolution and have already been profoundly affected by the application of existing ML ...Read More
Synthetic matrix metalloproteinase inhibitors inhibit growth of established breast cancer osteolytic lesions and prolong survival in mice. (2002)

The present study suggests the potential of synthetic MMP inhibitors as intervention or prevention treatments of breast cancer-induced osteolysis.
High-efficiency formation of influenza virus transfectants (1991)

cDNA-derived RNAs were introduced into the genomes of influenza viruses by using an improved ribonucleoprotein (RNP) transfection protocol. Up to 10(5) viral transfectants with a novel neuraminidase gene could be obtained by using a 35-mm dish (10(6) cells) for RNP transfection. In addition to genes coding for surface proteins (hemagglutinin and neuraminidase), we also exchanged a gene coding for nonsurface proteins. The cDNA-derived influenza A/PR/8/34 virus NS gene was introduced into a temperature-sensitive mutant with a defect in this gene. We suggest that the term influenza virus transfectant be used for those viruses which are made by RNP transfection with cDNA-derived RNA.
Template-based Geometric Transformations of a Functionally Enriched DMU into FE Assembly Models (2014)

Computer-Aided Design and Applications is an international journal on the applications of CAD and CAM. It publishes papers in the general domain of CAD plus in emerging fields like bio-CAD, nano-CAD, soft-CAD, garment-CAD, PLM, PDM, CAD data mining, CAD and the internet, CAD education, genetic algorithms and CAD engines. The journal is aimed at all developers and users of CAD technology to ptovide CAD solutions for various stages of design and manufacturing. The journal publishes all about Computer-Aided Design and Computer-Aided technologies.
Increase of regulatory T cells in the peripheral blood of cancer patients. (2003)

Thus, we provide evidence of an increased pool of CD4(+)CD25(+) regulatory T cells in the peripheral blood of cancer patients with potent immunosuppressive features. These findings should be considered for the design of immunomodulatory therapies such as dendritic cell vaccination.
Placebo Response in Randomized Controlled Trials of Antidepressants for Pediatric Major Depressive Disorder (2008)

The recent shift toward large multisite trials of antidepressant medications for pediatric major depression may be contributing to an increasing incidence of response to placebo. Pharmacotherapy studies of pediatric depression that carefully recruit patients with at least moderately severe depression may be more informative and efficient than many trials conducted to date. Such studies should have sufficient power to determine whether age moderates medication and placebo response.
Separation, purification and properties of β-lactamase I and β-lactamase II from Bacillus cereus 569/H/9 (1974)

1. A procedure was devised which is suitable for the isolation of beta-lactamase I and beta-lactamase II from Bacillus cereus 569/H/9 on a large scale. After adsorption on to Celite both enzymes were eluted in good yield and separated by chromatography on Sephadex CM-50. 2. beta-Lactamase I was separated into three main components by isoelectric focusing and into two components by chromatography. 3. The Zn(2+)-requiring beta-lactamase II obtained by this procedure had a lower molecular weight (22000) than beta-lactamase I (28000) and also differed from the latter in containing one cysteine residue. 4. The beta-lactamase II contained no carbohydrate, but showed the thermostability of the enzyme isolated earlier as a protein-carbohydrate complex. 5. Amino acid analyses and tryptic-digest ;maps' indicate that some degree of homology between beta-lactamase I and beta-lactamase II is possible, but that beta-lactamase I is not composed of the entire sequence of beta-lactamase II together with an additional peptide fragment. 6. A 6-methylpenicillin and a 7-methylcephalosporin showed much lower affinities for both enzymes than did penicillins and cephalosporins themselves.