gebhart/patrepeval huggingface dataset:
Determination of critical network interactions: an augmented Boolean pseudo-dynamics approach (2008)

Network theory has established that highly connected nodes in regulatory networks (hubs) show a strong correlation with criticality in network function. Although topological analysis is fully capable of identifying network hubs, it does not provide an objective method for ranking the importance of a particular node by relating its contribution to the overall network response. Towards this end, the authors have developed an augmented Boolean pseudo-dynamics approach to a priori determine the critical network interactions in biological interaction networks. The approach utilises network topology and dynamic state information to determine the set of active pathways. The active pathways are used in conjunction with the key cellular properties of efficiency and robustness, to rank the network interactions based on their importance in the sustenance of network function. To demonstrate the utility of the approach, the authors consider the well characterised guard cell signalling network in plant cells. An integrated analysis of the network revealed the critical mechanisms resulting in stomata closure in the presence and absence of abscisic acid, in excellent agreement with published results.
Arsenic adsorption onto iron-chitosan composite from drinking water (2005)

The entire dissertation/thesis text is included in the research.pdf file; the official abstract appears in the short.pdf file (which also appears in the research.pdf); a non-technical general description, or public abstract, appears in the public.pdf file.
Emotion recognition from audiovisual information (2002)

We report preliminary results on emotion recognition by machine from joint audiovisual input of facial video and speech. The results show potential advantages in using both modalities over either modality alone. The recognition rate for audio alone is about 75% and video alone about 70%. Using audiovisual data we achieved 97% without increasing the number of features. The improvement in performance is accredited to the complementary property between the two modalities. A possible application is in natural human-computer interfaces.
Use of denaturing-gradient gel electrophoresis to study chromium-induced point mutations in human cells. (1994)

A large number of hprt-mutants were obtained by treating human lymphoblast cells (TK6) with 5 microM K2Cr2O7 for 5 hr and selecting by growth in 6-thioguanine. A combination of high fidelity polymerase chain reaction (PCR) and denaturing gradient gel electrophoresis (DGGE) allowed us to measure mutant frequencies as a function of DNA sequence. Chromium(VI) induced four hotspots in a 104 bp domain of hprt exon 3. Substitutions at G:C base pairs were the predominant mutations. One of the chromium-induced hotspots was located at the same position as previously determined hydrogen peroxide and benzo(a)pyrene diol epoxide hotspots.
ChemInform Abstract: Optical Properties of CdS and PbS Clusters Encapsulated in Zeolites. (1987)

Abstract It is demonstrated that CdS and PbS clusters encapsulated in zeolites show dramatic deviations from bulk optical properties.
New interleukin-15 superagonist (IL-15SA) significantly enhances graft-versus-tumor activity (2017)

Interleukin-15 (IL-15) is a potent cytokine that increases CD8+ T and NK cell numbers and function in experimental models. However, obstacles remain in using IL-15 therapeutically, specifically its low potency and short in vivo half-life. To help overcome this, a new IL-15 superagonist complex comprised of an IL-15N72D mutation and IL-15RαSu/Fc fusion (IL-15SA, also known as ALT-803) was developed. IL-15SA exhibits a significantly longer serum half-life and increased in vivo activity against various tumors. Herein, we evaluated the effects of IL-15SA in recipients of allogeneic hematopoietic stem cell transplantation. Weekly administration of IL-15SA to transplant recipients significantly increased the number of CD8+ T cells (specifically CD44+ memory/activated phenotype) and NK cells. Intracellular IFN-γ and TNF-α secretion by CD8+ T cells increased in the IL-15SA-treated group. IL-15SA also upregulated NKG2D expression on CD8+ T cells. Moreover, IL-15SA enhanced proliferation and cytokine secretion of adoptively transferred CFSE-labeled T cells in syngeneic and allogeneic models by specifically stimulating the slowly proliferative and nonproliferative cells into actively proliferating cells.We then evaluated IL-15SA's effects on anti-tumor activity against murine mastocytoma (P815) and murine B cell lymphoma (A20). IL-15SA enhanced graft-versus-tumor (GVT) activity in these tumors following T cell infusion. Interestingly, IL-15 SA administration provided GVT activity against A20 lymphoma cells in the murine donor leukocyte infusion (DLI) model without increasing graft versus host disease. In conclusion, IL-15SA could be a highly potent T- cell lymphoid growth factor and novel immunotherapeutic agent to complement stem cell transplantation and adoptive immunotherapy.
Granulysin: A Novel Host Defense Molecule (2005)

Granulysin is a novel cationic molecule present in the granules of cytotoxic T lymphocytes and natural killer cells. Cytotoxic T lymphocytes have long been associated with graft destruction in transplant rejection. Recent studies implicate granulysin in cell-mediated cytotoxicity, chemoattraction, immune activation and as a potential diagnostic biomarker for transplant rejection.
TAK1 Mitogen-activated Protein Kinase Kinase Kinase Is Activated by Autophosphorylation within Its Activation Loop (2000)

TAK1, a member of the mitogen-activated kinase kinase kinase family, is activated in vivo by various cytokines, including interleukin-1 (IL-1), or when ectopically expressed together with the TAK1-binding protein TAB1. However, this molecular mechanism of activation is not yet understood. We show here that endogenous TAK1 is constitutively associated with TAB1 and phosphorylated following IL-1 stimulation. Furthermore, TAK1 is constitutively phosphorylated when ectopically overexpressed with TAB1. In both cases, dephosphorylation of TAK1 renders it inactive, but it can be reactivated by preincubation with ATP. A mutant of TAK1 that lacks kinase activity is not phosphorylated either following IL-1 treatment or when coexpressed with TAB1, indicating that TAK1 phosphorylation is due to autophosphorylation. Furthermore, mutation to alanine of a conserved serine residue (Ser-192) in the activation loop between kinase domains VII and VIII abolishes both phosphorylation and activation of TAK1. These results suggest that IL-1 and ectopic expression of TAB1 both activate TAK1 via autophosphorylation of Ser-192.
Single Cell Genomics: Advances and Future Perspectives (2014)

Advances in whole-genome and whole-transcriptome amplification have permitted the sequencing of the minute amounts of DNA and RNA present in a single cell, offering a window into the extent and nature of genomic and transcriptomic heterogeneity which occurs in both normal development and disease. Single-cell approaches stand poised to revolutionise our capacity to understand the scale of genomic, epigenomic, and transcriptomic diversity that occurs during the lifetime of an individual organism. Here, we review the major technological and biological breakthroughs achieved, describe the remaining challenges to overcome, and provide a glimpse into the promise of recent and future developments.
The Calcium-Binding Protein SPARC is Secreted by Leydig and Sertoli Cells of the Adult Mouse Testis1 (1989)

In mammals, polypeptides secreted by cells of the testis are believed to influence spermatogenesis and to affect the behavior of the resident somatic cell populations. The 43,000-MW, secreted, calcium-binding glycoprotein SPARC (Secreted Protein, Acidic and Rich in Cysteine) is synthesized by a number of embryonic, fetal, and adult somatic cells and is associated with areas of cellular differentiation, proliferation, and morphological reorganization. Here, we report on the expression of SPARC in the testes of adult mice. By immunohistochemistry, SPARC was observed in the cytoplasm of Leydig cells and of Sertoli cells bearing late-stage, elongate spermatids. Testicular mRNA, translated in vitro, yielded a polypeptide of approximately 42,000 MW that bound anti-SPARC antibodies. Northern blot analysis revealed 2.3 kilobase (kb) SPARC mRNA in the testis, a size comparable to that of SPARC mRNA in nongonadal cells. Western blot assays of proteins separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis revealed an immunoreactive polypeptide of 43,000 MW in purified mouse Sertoli cells and their culture supernatants. Similar assays of testis interstitial fluid revealed 43,000 MW and 30,000 MW immunoreactive polypeptides. By indirect immunofluorescence, purified mouse Leydig cells cultured 24-48 h expressed SPARC in cytoplasmic granules. Cultured Leydig cells incorporated [35S]methionine into a secreted polypeptide of 43,000 MW that was recognized by anti-SPARC antibodies. In metal binding assays, purified SPARC bound Ca2+, Fe2+ and Cu2+. The function of SPARC in testes may be to sequester or transport certain metallic cations. Our recent discovery that SPARC induces changes in shape of certain nongonadal cell types also suggests that this glycoprotein may influence the functions of both Leydig and Sertoli cells by affecting their morphology.
Anthrax Bioterrorism: Lessons Learned and Future Directions (2002)

the United States experienced the worst terrorist attack in its history. As the nation sought to deal with this tragedy, it would face a second wave of terrorism-this time, in the form of a biological attack. The suspicion of anthrax in a patient by an astute infectious disease clinician along with capable clinical and public health laboratory staff in Florida would lead to the discovery that Bacillus anthracis spores had been intentionally distributed through the postal system, causing 22 cases of anthrax, including 5 deaths, and forever changing the realm of public health.
Cell Contact–Dependent Immunosuppression by Cd4+Cd25+Regulatory T Cells Is Mediated by Cell Surface–Bound Transforming Growth Factor β (2001)

CD4(+)CD25(+) T cells have been identified as a population of immunoregulatory T cells, which mediate suppression of CD4(+)CD25(-) T cells by cell-cell contact and not secretion of suppressor cytokines. In this study, we demonstrated that CD4(+)CD25(+) T cells do produce high levels of transforming growth factor (TGF)-beta1 and interleukin (IL)-10 compared with CD4(+)CD25(-) T cells when stimulated by plate-bound anti-CD3 and soluble anti-CD28 and/or IL-2, and secretion of TGF-beta1 (but not other cytokines), is further enhanced by costimulation via cytotoxic T lymphocyte-associated antigen (CTLA)-4. As in prior studies, we found that CD4(+)CD25(+) T cells suppress proliferation of CD4(+)CD25(-) T cells; however, we observed here that such suppression is abolished by the presence of anti-TGF-beta. In addition, we found that CD4(+)CD25(+) T cells suppress B cell immunoglobulin production and that anti-TGF-beta again abolishes such suppression. Finally, we found that stimulated CD4(+)CD25(+) T cells but not CD4(+)CD25(-) T cells express high and persistent levels of TGF-beta1 on the cell surface. This, plus the fact that we could find no evidence that a soluble factor mediates suppression, strongly suggests that CD4(+)CD25(+) T cells exert immunosuppression by a cell-cell interaction involving cell surface TGF-beta1.
MBONE, multicasting tomorrow's Internet (1996)

From the Publisher:
The promise of Web casting, multimedia, streaming video and audio, video conferencing, and multiuser virtual reality (VRML) environments all may soon be realized thanks to something called the MBONE. MBONE: Multicasting Tomorrow's Internet is the complete, authoritative introduction to this exciting new technology. MBONE insiders Kevin Savetz, Neil Randall, and Yves Lepage provide a rare look at the hardware and software you'll need to take advantage of one of the most important Internet innovations since the World Wide Web.
Comparison of intranasal midazolam and sufentanil premedication in pediatric outpatients* (1996)

Both intranasal midazolam and sufentanil provide rapid, safe, and effective sedation in small children before anesthesia for ambulatory surgery. Sufentanil provided somewhat better conditions for induction and emergence. Midazolam causes more nasal irritation during instillation, and sufentanil causes more postoperative nausea and vomiting. Both drugs enabled patients to be separated from their parents with a minimum of distress. Patients in the midazolam group were discharged approximately 40 minutes earlier (p <0.005).
Are aromatase inhibitors effective in endometriosis treatment? (2011)

Until recently, AIs were thought to be an alternative to current medical therapies for endometriosis. However, recent findings question their real utility in clinical practice in the context of this disease. Because there is no strong evidence of their efficacy or benefit compared to other molecules in existing clinical trials, AIs need to be investigated further in well-designed studies to confirm/disprove their hypothetical impact on endometriotic lesions.
Highly sensitive detection of a HER2 12-base pair duplicated insertion mutation in lung cancer using the Eprobe-PCR method (2017)

Somatic mutation in human epidermal growth factor receptor-related 2 gene (HER2) is one of the driver mutations in lung cancer. HER2 mutations are found in about 2% of lung adenocarcinomas (ADCs). Previous reports have been based mainly on diagnostic screening by Sanger sequencing or next-generation sequencing (NGS); however, these methods are time-consuming and complicated. We developed a rapid, simple, sensitive mutation detection assay for detecting HER2 12 base pair-duplicated insertion mutation based on the Eprobe-mediated PCR method (Eprobe-PCR) and validated the sensitivity of this assay system for clinical diagnostics. We examined 635 tumor samples and analyzed HER2 mutations using the Eprobe-PCR method, NGS, and Sanger sequencing. In a serial dilution study, the Eprobe-PCR was able to detect mutant plasmid DNA when its concentration was reduced to 0.1% by mixing with wild-type DNA. We also confirmed amplification of the mutated plasmid DNA with only 10 copies per reaction. In ADCs, Eprobe-PCR detected the HER2 mutation in 2.02% (9/446), while Sanger sequencing detected it in 1.57% (7/446). Eprobe-PCR was able to detect the mutation in two samples that were undetectable by Sanger sequencing. All non-ADC samples were wild-type. There were no discrepancies between frozen and formalin-fixed paraffin-embedded tissues in the nine samples. HER2 mutations detected by NGS data validated the high sensitivity of the method. Therefore, this new technique can lead to precise molecular-targeted therapies.
Cognitive levels and Software Maintenance Sub-tasks. (2009)

This paper describes a case study that was carried out to characterize the behaviour of professional programmers, working on in-vivo software maintenance tasks, in terms of the cognitive levels of Bloom’s taxonomy. Specifically, it evaluates if their behaviour on specific maintenance sub-tasks can be associated with specific cognitive levels of the taxonomy. The findings suggest that some such relationships do exist. Indeed, several of the identified relationships are at the most cognitively-demanding levels of Bloom’s taxonomy. Allied with reports from other research in the domain of software maintenance, these relationships suggest that difficult sub-tasks within software maintenance are difficult, in part, because of the cognitive levels that programmers must work at when undertaking them. Thus, they suggest the nature of the support that should be offered to maintenance programmers involved in these tasks. 1.
Sensitizing antigen-specific CD8+ T cells for accelerated suicide causes immune incompetence (2003)

Death receptor–mediated activation-induced apoptosis of antigen-specific T cells is a major mechanism of peripheral tolerance induction and immune homeostasis. Failure to undergo activation-induced cell death (AICD) is an important underlying cause of many autoimmune diseases. Thus, enhancing the T cell’s own suicide mechanism may provide an efficient therapy for the treatment of autoimmune diseases. Bisindolylmaleimide VIII (Bis VIII), a PKC inhibitor, can sensitize T cells for death receptor–induced apoptosis and thus can inhibit the development of T cell–mediated autoimmune disease in vivo. In this study, we have analyzed the functional consequences of accelerated suicide for a protective CD8+ T cell–mediated immune response. Our data indicate that CD8+ T cells are sensitized by Bis VIII to AICD, both in vitro and in vivo. The sensitizing effect of Bis VIII appears to be mediated by specific downmodulation of the antiapoptotic molecule cellular FLICE-like inhibitory protein (cFLIPL). Importantly, Bis VIII administration during an acute lymphocytic choriomeningitis virus (LCMV) infection causes the depletion of virus-specific CD8+ T cells and subsequently impaired cytotoxicity and virus clearance. We conclude that resistance to death receptor–induced apoptosis is crucial for the efficient induction of a protective immune response, and that Bis VIII–based immunotherapies have to be applied under well-controlled conditions to avoid the induction of immune incompetence and the inability to respond to pathogen infection.
Industrial Polymers, Specialty Polymers, and Their Applications (2008)

�Derived from the fourth edition of the well-known Plastics Technology Handbook, Industrial Polymers, Specialty Polymers, and Their Applications covers a wide range of general and special types of polymers
Top‐Down Fabrication of Semiconductor Nanowires with Alternating Structures along their Longitudinal and Transverse Axes (2005)

The combined use of “top-down” photolithographic techniques and anisotropic etching or electron-beam evaporation provides a versatile approach to fabricate nanowires of III–V semiconductors (e.g., GaAs) with alternating structures along their longitudinal and transverse axes (see Figure). This method can be easily scaled up to produce nanowires in large-scale quantities, and the resultant nanowires have unique optical properties and potential photonic applications. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2421/2005/z500094_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Intravenous Paraquat Poisoning (2009)

Paraquat is a substance that is highly poisonous to humans. Oral ingestion is the most common pathway of poisoning. Intravenous paraquat poisoning is rare and is strongly associated with attempted suicide. The clinical presentations of such a scenario would appear to be quite different from those of oral ingestion. Herein, we present a case of an intravenous drug abuser who injected paraquat in an effort to commit suicide. He received hemoperfusion and intravenous cyclophosphamide treatment and parenteral pulse therapy with methylprednisolone. Nevertheless, he suffered from dyspnea at around 48 hours post-exposure. His condition improved transiently, but he eventually died from severe hypoxia. The findings from our case and those of previously reported cases indicate the grave prognosis and lack of effective management of intravenous paraquat poisoning.
Optically enhancing the small electro-optical effect of a fast-switching liquid-crystal mixture (2000)

The method of optical enhancement by means of intersurface-reflection-excited resonance was applied to a single-pixel device filled with a fast-switching electroclinic mixture M68. A contrast ratio of 6.5: 1, which is sufficient for a spatial light modulator (SLM), has been obtained for an electric-field-induced twist angle of 2.97 deg with an electro-optical response time of 162 ns. Success in a single-pixel device should allow very fast multipixel active-silicon-backplane SLMs to be made in the near future. Using this method, we have observed contrast ratios>5 with a field-induced twist angle>2.5 deg. However, better contrast can be achieved with improved alignment of the material used and device fabrication. The thickness effects of the light modulating layer on the resonant behavior were computer-modeled and are discussed in detail. It was found that considerable change occurs even for a thickness variation of 0.1 ?m. However, the effect is much less for a variation of 0.01 ?m. If SLM fabrication cannot control the thickness better than 0.1 ?m, either computer simulation for known thickness or preliminary measurements are needed.
Key to Understanding InterstitialH2in Si (2002)

A new IR absorption line at 3191.1 cm(-1) has been discovered for the interstitial HD molecule in Si. This new line appears for sample temperatures above approximately 20 K and lies 73.9 cm(-1) below the 3265.0 cm(-1) line previously observed for HD. We attribute the 73.9 cm(-1) energy difference to the rotation of the interstitial HD molecule. The selection rules associated with these two lines are consistent with the puzzling absence of an ortho-para splitting in the IR absorption spectra of H2 and D2 in Si.
Analysis of HIV Type 1 Reverse Transcriptase Expression in a Human Cell Line (1994)

The functional analysis of human immunodeficiency virus type-1 (HIV-1) reverse transcriptase (RT) subunits on transient and constitutive expression, in the absence or presence of the HIV-1 protease (PR) expression, in a human cell line is described. HIV-1 RT is a heterodimer composed of a 51-kDa subunit (p51) and a 66-kDa subunit (p66). Cloning and expression of the RT region of the HIV-1 pol gene in the HT-1080 human fibrosarcoma cell line yielded p66 without any detectable p51 and a low level of RT activity could be measured. Transient expression of PR and RT in cis generated p51 and p66, but when RT and PR were expressed in trans only p66 was produced. Attempts to establish a stable cell line expressing the PR-RT region of the pol gene were hampered by an apparent intolerance of HT-1080 cells to the HIV-1 PR expression. Therefore, to generate p51 independent of PR expression, the 51-kDa subunit was cloned separately. p51 lacked detectable RT activity. Coexpression of p51 and p66 resulted in a dramatic increase in RT activity. Stable HT-1080 cells producing both p51 and p66 exhibited on average a 15-fold increase in RT activity compared to the parental cell line. Immunofluorescence revealed a diffuse cytoplasmic localization of p51 and p66. To date, this is the first example of a human cell line that is constitutively expressing HIV-1 RT in the absence of HIV-1 infection.
A Modular Platform for the Rapid Site-Specific Radiolabeling of Proteins with 18F Exemplified by Quantitative Positron Emission Tomography of Human Epidermal Growth Factor Receptor 2 (2009)

Receptor-specific proteins produced by genetic engineering are attractive as PET imaging agents, but labeling with conventional (18)F-based prosthetic groups is problematic due to long synthesis times, poor radiochemical yields, and low specific activities. Therefore, we developed a modular platform for the rapid preparation of water-soluble prosthetic groups capable of efficiently introducing (18)F into proteins. The utility of this platform is demonstrated by the thiol-specific prosthetic group, [(18)F]FPEGMA, which was used to produce site-specifically (18)F-labeled protein ((18)F-trastuzumab-ThioFab) in 82 min with a total radiochemical yield of 13 +/- 3% and a specific activity of 2.2 +/- 0.2 Ci/micromol. (18)F-trastuzumab-ThioFab retained the biological activity of native protein and was successfully validated in vivo with microPET imaging of Her2 expression in a xenograft tumor-bearing murine model modulated by the Hsp90 inhibitor, 17-(allylamino)-17-demethoxygeldanamycin.