gebhart/patrepeval huggingface dataset:
Chronic Helminth Infection Induces Alternatively Activated Macrophages Expressing High Levels of CCR5 with Low Interleukin-12 Production and Th2-Biasing Ability (2002)

Helminth infections induce Th2-type biased immune responses. Although the mechanisms involved in this phenomenon are not yet clearly defined, antigen-presenting cells (APC) could play an important role in this process. Here, we have used peritoneal macrophages (F4/80+) recruited at different times after challenge with Taenia crassiceps as APC and tested their ability to regulate Th1/Th2 differentiation. Macrophages from acute infections produced high levels of interleukin-12 (IL-12) and nitric oxide (NO), paralleled with low levels of IL-6 and prostaglandin E(2) (PGE(2)) and with the ability to induce strong antigen-specific CD4+ T-cell proliferation in response to nonrelated antigens. In contrast, macrophages from chronic infections produced higher levels of IL-6 and PGE(2) and had suppressed production of IL-12 and NO, associated with a poor ability to induce antigen-specific proliferation in CD4+ T cells. Failure to induce proliferation was not due to a deficient expression of accessory molecules, since major histocompatibility complex class II, CD40, and B7-2 were up-regulated, together with CD23 and CCR5 as infection progressed. These macrophages from chronic infections were able to bias CD4+ T cells to produce IL-4 but not gamma interferon (IFN-gamma), contrary to macrophages from acute infections. Blockade of B7-2 and IL-6 and inhibition of PGE(2) failed to restore the proliferative response in CD4+ T cells. Furthermore, studies using STAT6(-/-) mice revealed that STAT6-mediated signaling was essential for the expansion of these alternatively activated macrophages. These data demonstrate that helminth infections can induce different macrophage populations that have Th2-biasing properties.
Modified Multiplex PCR Method for Detection of Pyrogenic Exotoxin Genes in Staphylococcal Isolates (2004)

A modified multiplex PCR method for detection of nine Staphylococcus aureus enterotoxin genes (sea, seb, sec, sed, see, seg, seh, sei, and sej) and one form of immunoreactive toxic shock syndrome toxin based on a previously published method (S. R. Monday and G. A. Bohach, J. Clin. Microbiol. 37:3411-3414, 1999) has been developed. The modified PCR protocol seems robust and gives reliable results.
Identification and elimination of an immunodominant T-cell epitope in recombinant immunotoxins based onPseudomonasexotoxin A (2012)

Recombinant immunotoxins (RITs) are chimeric proteins that are being developed for cancer treatment. We have produced RITs that contain PE38, a portion of the bacterial protein Pseudomonas exotoxin A. Because the toxin is bacterial, it often induces neutralizing antibodies, which limit the number of treatment cycles and the effectiveness of the therapy. Because T cells are essential for antibody responses to proteins, we adopted an assay to map the CD4(+) T-cell epitopes in PE38. We incubated peripheral blood mononuclear cells with an immunotoxin to stimulate T-cell expansion, followed by exposure to overlapping peptide fragments of PE38 and an IL-2 ELISpot assay to measure responses. Our observation of T-cell responses in 50 of 50 individuals correlates with the frequency of antibody formation in patients with normal immune systems. We found a single, highly immunodominant epitope in 46% (23/50) of the donors. The immunodominant epitope is DRB1-restricted and was observed in subjects with different HLA alleles, indicating promiscuity. We identified two amino acids that, when deleted or mutated to alanine, eliminated the immunodominant epitope, and we used this information to construct mutant RITs that are highly cytotoxic and do not stimulate T-cell responses in many donors.
A technique for measuring and optimizing modulator extinction ratio (2000)

Summary form only given. As global communication systems rapidly expand and high-speed optical TDM and WDM networks continue to mature, the performance of optical modulators becomes increasingly important. Accurate methods of characterizing and optimizing key parameters, such as the extinction ratio, to levels exceeding 40 dB become necessary. The modulator extinction ratio (ER), defined as the power off-to-on ratio, impacts on communication performance in many ways. It determines the initial distance between logical zero and one power levels. Incomplete ER degrades sensitivity in optically preamplified links and leads to multiple interferometric cross talk, which adversely impacts both TDM and WDM systems. Furthermore, the ER limits the dynamic range of data-rates for variable duty-cycle (VDC) multi-rate optical communications. The author describes a new method for accurately measuring ER using the properties of average power limited (APL) amplifiers that does not require high-speed detection equipment.
Controlled Release of Bevacizumab Through Nanospheres for Extended Treatment of Age-Related Macular Degeneration (2012)

Bevacizumab (Avastin(®)) has been used by ophthalmologists in many countries as an off-label drug for the treatment of wet age-related macular degeneration (AMD). Due to its short half-life necessitating frequent intravitreal injection, a method for sustained delivery is in need. We demonstrated that bevacizumab could be released in a sustained fashion over 90 days from nano- and microspheres fabricated from poly(DL-lactide-co-glycolide) and poly(ethylene glycol)-b-poly(D,L-lactic acid), respectively. The drug release rate could be adjusted by alteration of the drug/polymer ratio. The use of such nano- and microspheres as bevacizumab delivery vehicles may improve the treatment of wet AMD.
LOCAL AND LONG-RANGE SIGNALING PATHWAYS REGULATING PLANT RESPONSES TO NITRATE (2002)

Nitrate is the major source of nitrogen (N) for plants growing in aerobic soils. However, the NO3- ion is also used by plants as a signal to reprogram plant metabolism and to trigger changes in plant architecture. A striking example is the way that a root system can react to a localized source of NO3- by activating the NO3- uptake system and proliferating lateral roots preferentially within the NO3(-)-rich zone. That roots are able to respond autonomously in this fashion implies the existence of local signaling pathways that are sensitive to local changes in the external NO3- concentration. On the other hand, long-range signaling pathways are also needed to modulate these responses according to the plant's N status and to coordinate the allocation of resources between the root and the shoot. This review examines these signaling mechanisms and their interactions with sugar-sensing and hormonal response pathways.
GLYCOBIOLOGY (1988)

The Hippo pathway was initially discovered in Drosophila melanogaster as a key regulator of tissue growth. It is an evolutionarily conserved signaling cascade regulating numerous biological processes, including cell growth and fate decision, organ size ...Read More
Further investigation of a chromosome 15 locus in schizophrenia: Analysis of affected sibpairs from the NIMH genetics initiative (1998)

Linkage of a neurophysiological deficit associated with schizophrenia, i.e., the failure to inhibit the auditory P50 response, was previously reported at chromosome 15q14. The marker with the highest pairwise lod score, D15S1360, was isolated from a yeast artificial chromosome containing a candidate gene, the α7-nicotinic acetylcholine receptor gene. In the present study, this linkage was further investigated in a subset of the NIMH Genetics Initiative schizophrenia families. These families have not been studied neurophysiologically, as were the families in the original report. Therefore, the DSMIII-R diagnosis of schizophrenia was used as the affected phenotype. Twenty families fulfilled the criteria of at least one sibpair concordant for schizophrenia, along with their two parents or another affected relative outside the nuclear family, available for genotyping. Sibpair analysis showed a significant proportion of D15S1360 alleles shared identical-by-descent (0.58; P < 0.0024). The results further support the involvement of this chromosomal locus in the genetic transmission of schizophrenia. Am. J. Med. Genet. (Neuropsychiatr. Genet.) 81:308–312, 1998. © 1998 Wiley-Liss, Inc.
Repurposing Itraconazole as a Treatment for Advanced Prostate Cancer: A Noncomparative Randomized Phase II Trial in Men With Metastatic Castration-Resistant Prostate Cancer (2013)

High-dose itraconazole (600 mg/day) has modest antitumor activity in men with metastatic CRPC that is not mediated by testosterone suppression.
Conformational Antibody Binding to a Native, Cell-Free Expressed GPCR in Block Copolymer Membranes (2014)

G-protein coupled receptors (GPCRs) play a key role in physiological processes and are attractive drug targets. Their biophysical characterization is, however, highly challenging because of their innate instability outside a stabilizing membrane and the difficulty of finding a suitable expression system. We here show the cell-free expression of a GPCR, CXCR4, and its direct embedding in diblock copolymer membranes. The polymer-stabilized CXCR4 is readily immobilized onto biosensor chips for label-free binding analysis. Kinetic characterization using a conformationally sensitive antibody shows the receptor to exist in the correctly folded conformation, showing binding behaviour that is commensurate with heterologously expressed CXCR4.
Ruthenium(II) Complexes of Monodonor Ligands:  Efficient Reagents for Asymmetric Ketone Hydrogenation (2005)

[Chemical reaction: See text] A series of BINOL-derived ligands have been prepared and incorporated into ruthenium(II) complexes containing a diamine ligand. The complexes have proven to be excellent catalysts for the asymmetric hydrogenation of ketones, giving reduction products with enantiomeric excesses of up to 99%.
Zinc finger protein ZBTB20 expression is increased in hepatocellular carcinoma and associated with poor prognosis (2011)

The expression of ZBTB20 is increased in HCC and associated with poor prognosis in patients with HCC, implicating ZBTB20 as a candidate prognostic marker in HCC.
Structure of the novel steroidal antibiotic squalamine determined by two-dimensional NMR spectroscopy (1993)

Squalamine is a novel aminosterol recently isolated from the dogfish shark, Squalus acanthias. This water-soluble steroid exhibits potent antibacterial activity against both gram-negative and gram-positive bacteria. In addition, squalamine is fungicidal and induces osmotic lysis of protozoa. We report here the structural determination of squalamine, 3 beta-N-1-[N(3-[4-aminobutyl])-1,3 diaminopropane]-7 alpha,24 zeta-dihydroxy-5 alpha-cholestane 24-sulfate, which was deduced from the analysis of fast atom bombardment spectra and a series of two-dimensional nuclear magnetic resonance (NMR) spectra. Squalamine is a cationic steroid characterized by a condensation of an anionic bile salt intermediate with the polyamine, spermidine. This molecule is a potential host-defense agent in the shark, and provides insight into a new class of vertebrate antimicrobial molecules.
Helical interactions in homologous pairing and strand exchange driven by RecA protein. (1991)

In a search for mutants that affect genetic recombination, Clark and Margulies (1) discovered the recA gene in Escherichia coli, but subsequently recA mutants were found to be pleiotropic, affecting not only recombination but repair, mutagenesis, phage induction, and cell division (2).Not surprisingly, many years passed before the basis of this complex phenotype was understood.A milestone was the discovery by Roberts et al.(3) that the product of the recA gene catalyzes the cleavage of the X repressor and thereby inactivates it.There followed the discoveries that by proteolytic cleavage RecA protein also catalyzes the inactivation of the cellular LexA repressor, which derepresses more than 20 genes, and the activation of the UmuD protein, which is required for UV-induced mutagenesis (3-6).Especially after the discovery that RecA protein derepresses other genes, it appeared likely that the role of RecA protein in genetic recombination was indirect, via its effect on the expression of those other genes.Experiments on a temperature-sensitive mutant of recA showed that the derepression of other genes was not a sufficient explanation for the role of recA in recombination ( 7), but these experiments could not exclude the possible activation of recombination proteins by cleavage, as for example in the case of UmuD protein whose cleavage activates its role in UV mutagenesis.However, the cloning of the recA gene (8) and the further finding that RecA protein has DNA-dependent ATPase activity (9,lO) led to the discovery that RecA protein also has remarkable recombination activities in vitro (11)(12)(13).Although mutants exist that are proficient in cleavage of LexA repressor and yet are defective in recombination ( 14), the observations on the recombination activities of RecA protein in vitro provide the only compelling evidence that it plays a direct role in recombination, for the reason just described (15-18).
Laser assisted drug delivery: A review of an evolving technology (2014)

Laser assisted drug delivery is an evolving technology with potentially broad clinical applications. Multiple studies demonstrate that laser pretreatment of the skin can increase the permeability and depth of penetration of topically applied drug molecules for both local cutaneous and systemic applications.
Acute Pharyngitis (2001)

The primary care physician needs to identify those patients with acute pharyngitis who require specific antimicrobial therapy and to avoid unnecessary and potentially deleterious treatment in the large majority of patients who have a benign, self-limited infection that is usually viral. In most cases, differentiating between these two types of infection can be accomplished easily if the physician considers the epidemiologic setting, the history, and the physical findings, plus the results of a few readily available laboratory tests. When antimicrobial therapy is required, the safest, narrowest-spectrum, and most cost-effective drugs should be used. Despite agreement on these principles by expert advisory committees, data from national surveys of ambulatory care indicate that antimicrobial agents continue to be prescribed indiscriminately for upper respiratory infections.
Cut to the chase: a review of CD26/dipeptidyl peptidase-4's (DPP4) entanglement in the immune system (2016)

CD26/DPP4 (dipeptidyl peptidase 4/DP4/DPPIV) is a surface T cell activation antigen and has been shown to have DPP4 enzymatic activity, cleaving-off amino-terminal dipeptides with either L-proline or L-alanine at the penultimate position. It plays a major role in glucose metabolism by N-terminal truncation and inactivation of the incretins glucagon-like peptide-1 (GLP) and gastric inhibitory protein (GIP). In 2006, DPP4 inhibitors have been introduced to clinics and have been demonstrated to efficiently enhance the endogenous insulin secretion via prolongation of the half-life of GLP-1 and GIP in patients. However, a large number of studies demonstrate clearly that CD26/DPP4 also plays an integral role in the immune system, particularly in T cell activation. Therefore, inhibition of DPP4 might represent a double-edged sword. Apart from the metabolic benefit, the associated immunological effects of long term DPP4 inhibition on regulatory processes such as T cell homeostasis, maturation and activation are not understood fully at this stage. The current data point to an important role for CD26/DPP4 in maintaining lymphocyte composition and function, T cell activation and co-stimulation, memory T cell generation and thymic emigration patterns during immune-senescence. In rodents, critical immune changes occur at baseline levels as well as after in-vitro and in-vivo challenge. In patients receiving DPP4 inhibitors, evidence of immunological side effects also became apparent. The scope of this review is to recapitulate the role of CD26/DPP4 in the immune system regarding its pharmacological inhibition and T cell-dependent immune regulation.
Silicon Photonic Integrated Circuits for WDM Technology and Optical Switch (2013)

We describe components we developed in addressing several challenges in silicon photonics, including fiber coupling, demultiplexing, and polarization diversity. We then summarize several circuit examples for WDM transmitter / receiver and optical switch.
The human serum paraoxonase/arylesterase polymorphism. (1983)

The heterozygous human serum paraoxonase phenotype can be clearly distinguished from both homozygous phenotypes on the basis of its distinctive ratio of paraoxonase to arylesterase activities. A trimodal distribution of the ratio values was found with 348 individual serum samples, measuring the ratio of paraoxonase activity (with 1 M NaCl in the assay) to arylesterase activity, using phenylacetate. The three modes corresponded to the three paraoxonase phenotypes, A, AB, and B (individual genotypes), and the expected Mendelian segregation of the trait was observed within families. The paraoxonase/arylesterase activity ratio showed codominant inheritance. We have defined the genetic locus determining the aromatic esterase (arylesterase) responsible for the polymorphic paraoxonase activity as esterase-A (ESA) and have designated the two common alleles at this locus by the symbols ESA*A and ESA*B. The frequency of the ESA*A allele was estimated to be .685, and that of the ESA*B allele, 0.315, in a sample population of unrelated Caucasians from the United States. We postulate that a single serum enzyme, with both paraoxonase and arylesterase activity, exists in two different isozymic forms with qualitatively different properties, and that paraoxon is a "discriminating" substrate (having a polymorphic distribution of activity) and phenylacetate is a "nondiscriminating" substrate for the two isozymes. Biochemical evidence for this interpretation includes the cosegregation of the degree of stimulation of paraoxonase activity by salt and paraoxonase/arylesterase activity ratio characteristics; the very high correlation between both the basal (non-salt stimulated) and salt-stimulated paraoxonase activities with arylesterase activity; and the finding that phenylacetate is an inhibitor for paraoxonase activities in both A and B types of enzyme.
In-Ga-Zn-Oxide Semiconductor and Its Transistor Characteristics (2014)

It is revealed that c-axis aligned crystal In-Ga-Zn oxide (CAAC-IGZO) and nanocrystalline IGZO films have high-density crystalline morphologies (5.9−6.3 g/cm3) and are very stable under electron-beam irradiation in transmission electron microscope observation. The electrical properties are suitable for practical use. We attempted to reproduce a previously reported amorphous IGZO film with no ordering. However, we were not able to confirm its existence; rather, we found nanocrystals with a width of 1−3 nm and a thickness of 0.7−0.8 nm. Furthermore, it is apparent that the amorphous-like film has low density (higher than or equal to 5.0 g/cm3 and lower than 5.9 g/cm3), and thus is an unstable material in which nanocrystals change when subjected to electron-beam irradiation. We fabricated field-effect transistors using CAAC-IGZO and examined their switching characteristics. As a result of microfabrication scaling, cutoff frequencies of 2 GHz and 1.5 GHz were obtained when the channel lengths were 60 nm and 100 nm, respectively. Switching characteristics in the order of GHz were obtained by microfabrication scaling with a field effect mobility of 5−10 cm2/V s, which opens new possibilities for oxide semiconductor large-scale integration.
Gender classification with support vector machines (2002)

Support vector machines (SVM) are investigated for visual gender classification with low-resolution "thumbnail" faces (21-by-12 pixels) processed from 1755 images from the FERET face database. The performance of SVM (3.4% error) is shown to be superior to traditional pattern classifiers (linear, quadratic, Fisher linear discriminant, nearest-neighbor) as well as more modern techniques such as radial basis function (RBF) classifiers and large ensemble-RBF networks. SVM also out-performed human test subjects at the same task: in a perception study with 30 human test subjects, ranging in age from mid-20s to mid-40s, the average error rate was found to be 32% for the "thumbnails" and 6.7% with higher resolution images. The difference in performance between low- and high-resolution tests with SVM was only 1%, demonstrating robustness and relative scale invariance for visual classification.
Capillary force in high aspect-ratio micropillar arrays (2009)

High aspect-ratio (HAR) micropillar arrays are important for many applications including, mechanical sensors and actuators, tunable wetting surfaces and substrates for living cell studies. However, due to their mechanical compliance and large surface area, the micropillars are susceptible to deformation due to surface forces, such as adhesive force and capillary force. In this thesis we have explored the capillary force driven mechanical instability of HAR micropillar arrays. We have shown that when a liquid is evaporated off the micropillar arrays, the pillars bend and cluster together due to a much smaller capillary meniscus interaction force while still surrounded by a continuous liquid body, rather than due to often reported Laplace pressure difference because of isolated capillary bridges. We have studied both theoretically and experimentally, the capillary force induced clustering behavior of micropillar arrays as a function of their elastic modulus. To this end, we have developed a modified replica molding process to fabricate a wide range of hydrogel micropillar arrays, whose elastic modulus in the wet state could be tuned by simply varying the hydrogel monomer composition. By minimizing the sum of capillary meniscus interaction energy and bending energy of the pillars in a cluster, we have derived a critical micropillar cluster size, which is inversely proportional to elastic modulus of micropillars. The estimated cluster size as a function of elastic modulus agrees well with our experimental observation. We have also explored the utility of the clustered micropillar arrays as ultrathin whitening layers mimicking the structural whitening mechanism found in some insects in nature. Finally, we have theoretically studied the capillary force induced imbibition of a liquid droplet on a model rough surface consisting of micropillar arrays. Our theoretical model suggests that due to shrinking liquid droplet, the imbibition dynamics does not follow the diffusive Washburn dynamics but progressively becomes slower with time.
Kinetics and Inhibition of Recombinant Human Cystathionine γ-Lyase (1999)

The gene encoding human cystathionine gamma-lyase was cloned from total cellular Hep G2 RNA. Fusion to a T7 promoter allowed expression in Escherichia coli, representing the first mammalian cystathionine gamma-lyase overproduced in a bacterial system. About 90% of the heterologous gene product was insoluble, and renaturation experiments from purified inclusion bodies met with limited success. About 5 mg/liter culture of human cystathionine gamma-lyase could also be extracted from the soluble lysis fraction, employing a three-step native procedure. While the enzyme showed high gamma-lyase activity toward L-cystathionine (Km = 0.5 mM, Vmax = 2.5 units/mg) with an optimum pH of 8.2, no residual cystathionine beta-lyase behavior and only marginal reactivity toward L-cystine and L-cysteine were detected. Inhibition studies were performed with the mechanism-based inactivators propargylglycine, trifluoroalanine, and aminoethoxyvinylglycine. Propargylglycine inactivated human cystathionine gamma-lyase much more strongly than trifluoroalanine, in agreement with the enzyme's preference for C-gamma-S bonds. Aminoethoxyvinylglycine showed slow and tight binding characteristics with a Ki of 10.5 microM, comparable with its effect on cystathionine beta-lyase. The results have important implications for the design of specific inhibitors for transsulfuration components.