gebhart/patrepeval huggingface dataset:
Formation of a novel dihydroxy acid from arachidonic acid by lipoxygenase-catalyzed double oxygenation in rat mononuclear cells and human leukocytes. (1982)

Elicited rat peritoneal mononuclear cells converted arachidonic acid to a new dihydroxy acid, 5(S), 15(S)-dihydroxy-6,13-trans-8,11-cis-eicosatetraenoic acid (5,15-DiHETE). In this system, the amount of 5,15-DiHETE formed was about 20% that of leukotriene B4. The structure of the compound was determined by ultraviolet and mass spectrometric analysis, and comparison to a reference compound prepared by incubation of synthetic 5(R,S)-hydroxy- or hydroperoxy-6-trans-8,11,14-cis-eicosatetraenoic acid (5(R,S)-HETE or HPETE) with soybean lipoxygenase (linoleate:oxygen oxidoreductase, EC 1.13.11.12). Cell incubations performed under an atmosphere of 18O2 demonstrated that both hydroxyl groups in the cell product derived from molecular oxygen and that the oxygen atoms were from different oxygen molecules. Steric analysis indicated that each hydroxyl group had the S-configuration. The structural data thus indicate that 5,15-DiHETE is formed by an enzymatic double oxygenation of arachidonic acid catalyzed by both C-5 and C-15 lipoxygenases. Incubations with with [3H 8]5 (S)-HETE and [3H8]15(S)-HETE revealed that both compounds could be converted to the product. When [3H8]5(S), 15(S)-DiHPETE was added to cells, the majority of the substrate was reduced to 5,15-DiHETE. Leukocytes obtained from three human donors with peripheral blood eosinophilia also synthesized 5,15-DiHETE. Formation of the compound occurred in both eosinophils and neutrophils from these donors.
Angiogenic properties of human immunodeficiency virus type 1 Tat protein. (1995)

Extracellular human immunodeficiency virus type 1 (HIV-1) Tat protein promotes growth of spindle cells derived from AIDS-associated Kaposi sarcoma (AIDS-KS), an angioproliferative disease very frequent in HIV-1-infected individuals. Normal vascular cells, progenitors of AIDS-KS cells, proliferate in response to Tat after exposure to inflammatory cytokines, whose levels are augmented in HIV-1-infected individuals and in KS lesions. Here we show that Tat also promotes AIDS-KS and normal vascular cells to migrate and to degrade the basement membrane and stimulates endothelial cell morphogenesis on a matrix substrate. These effects are obtained at picomolar concentrations of exogenous Tat and are promoted by the treatment of the cells with the same inflammatory cytokines stimulating expression of the receptors for Tat, the integrins alpha 5 beta 1 and alpha v beta 3. Thus, under specific circumstances, Tat has angiogenic properties. As Tat and its receptors are present in AIDS-KS lesions, these data may explain some of the mechanisms by which Tat can induce angiogenesis and cooperate in the development of AIDS-KS.
Production of branched‐chain fatty acids from sterculia oil (1982)

Abstract Methyl sterculate was rearranged by use of 0.5% of rhodium catalyst to isomeric conjugated diene fatty acid methyl esters containing both methylene‐and methyl‐branched isomers. The rearanged products were hydrogenated directly to saturated, methyl‐substituted, branched‐chain fatty acid methyl esters with the methyl substituent at one of the positions formerly occupied by the cyclopropenoid ring. The crude branched‐chain fatty acids from these esters were purified by recrystallization from a mixed solvent of ethanol and water (80:20, v/v) and flash distillation; the product contained about 90% of branched‐chain fatty acids (C 19 :80%, C 18 :10%). Esters of the branched‐chain fatty acid were prepared with 2‐ethylhexyl alcohol or trimethylolpropane, and the characteristic properties of these esters were investigated. The branched‐chain fatty esters appear to have potential utility in lubricants; other uses may be possible.
Temperature insensitive and ultra wideband silica-based dual polarization optical hybrid for coherent receiver with highly symmetrical interferometer design (2011)

To extend the operation wavelength range of dual-polarization optical hybrids (DPOH), we propose a highly symmetrical interferometer design for a polarization beam splitter and an optical hybrid to reduce temperature and wavelength dependence. The design successfully decreases this dependence, and a fabricated DPOH with silica-based planar lightwave circuits provides temperature-insensitive performance with a polarization extinction ratio of over 25 dB and phase errors of less than 3 degrees over the entire C- and L-bands.
Amyloid β-Protein:  Monomer Structure and Early Aggregation States of Aβ42 and Its Pro19Alloform (2005)

The amyloid beta-protein (Abeta) is a seminal neuropathic agent in Alzheimer's disease (AD). Recent evidence points to soluble Abeta oligomers as the probable neurotoxic species. Among the naturally occurring Abeta peptides, the 42-residue form Abeta42 is linked particularly strongly with AD, even though it is produced at approximately 10% of the levels of the more abundant 40-residue form Abeta40. Here, we apply mass spectrometry and ion mobility to the study of Abeta42 and its Pro19 alloform. The Phe19 --> Pro19 substitution blocks fibril formation by [Pro19]Abeta42. Evidence indicates that solution-like structures of Abeta monomers are electrosprayed and characterized. Unfiltered solutions of Abeta42 produce only monomers and large oligomers, whereas [Pro19]Abeta42 solutions produce abundant monomers, dimers, trimers, and tetramers but no large oligomers. When passed through a 10,000 amu filter and immediately sampled, Abeta42 solutions produce monomers, dimers, tetramers, hexamers, and an aggregate of two hexamers that may be the first step in protofibril formation. These results are consistent with recently published photochemical cross-linking data and lend support to recent aggregation mechanisms proposed by Bitan, Teplow, and co-workers [J. Biol. Chem. 2003, 278, 34882-34889].
Preparation of some sulphur-containing polypyrrolic macrocycles. Sulphur extrusion from a meso-thiaphlorin (1970)

The preparation of a meso-thiaphlorin, meso-thiaporphin, and a porphin analogue containing two thiophen rings is described together with several examples of extrusion of sulphur from polypyrrole macrocycles.
Contribution of Seminal Plasma, Sperm Numbers, and Gas Phase to Dilution Effects of Bovine Spermatozoa (1965)

Semen stored at 200 million sperm per milliliter at 5 C survived storage significantly better (P < 0.01) than semen stored at 12.5 million. Both additional seminal plasma and dead sperm significantly depressed livability (P 0.01) in highly diluted samples. However, this difference between dilution rate of storage was eliminated when diIuents were saturated with nitrogen, and a decline in storage life, similar to that exhibited by highly diluted sperm, could be simulated in sperm stored at 300 million per milliliter in a diluent gassed with oxygen. It is concluded that the dilution effects observed are due to availability of 0~ to sperm, and that the protective action of nitrogen saturation lies in the reduction of 02 tension in the diluting media. Field trials showed an advantage for storage at 200, but rediluted to 12.5 million sperm per milliliter immediately before use, compared to storage at 12.5 million sperm per milliliter for semen used on the day after collection (difference 3.1% P ~ 0.025) in an unsaturated diluent, but an advantage of 11.7% (P ~ 0.01) in favor of storage at 12.5 million sperm per milliliter with semen used seven days after collection in a nitrogen-saturated diluent.
Stimulated Raman spectroscopic imaging by microsecond delay-line tuning (2016)

Stimulated Raman scattering (SRS) microscopy is an emerging platform for vibrational imaging of living systems. We present microsecond-scale SRS spectroscopic imaging by temporally tuning two spectrally focused pulses through a resonant delay line. Our platform is able to acquire an SRS spectrum in 42 μs and form a spectral image of 40,000 pixels within 3.3 s. Spectroscopic identification of single bacteria and fungi in blood and 4-D imaging (x–y–z–λ) of intracellular organelles in live C. elegans are demonstrated.
Expression and Immunogenicity of Human Immunodeficiency Virus Type 1 Gag Expressed by a Replication-Competent Rhabdovirus-Based Vaccine Vector (2001)

A replication-competent rhabdovirus-based vector expressing human immunodeficiency virus type 1 (HIV-1) Gag protein was characterized on human cell lines and analyzed for the induction of a cellular immune response in mice. We previously described a rabies virus (RV) vaccine strain-based vector expressing HIV-1 gp160. The recombinant RV was able to induce strong humoral and cellular immune responses against the HIV-1 envelope protein in mice (M. J. Schnell et al., Proc. Natl. Acad. Sci. USA 97:3544-3549, 2000; J. P. McGettigan et al., J. Virol. 75:4430-4434, 2001). Recent research suggests that the HIV-1 Gag protein is another important target for cell-mediated host immune defense. Here we show that HIV-1 Gag can efficiently be expressed by RV on both human and nonhuman cell lines. Infection of HeLa cells with recombinant RV expressing HIV-1 Gag resulted in efficient expression of HIV-1 precursor protein p55 as indicated by both immunostaining and Western blotting. Moreover, HIV-1 p24 antigen capture enzyme-linked immunosorbent assay and electron microscopy showed efficient release of HIV-1 virus-like particles in addition to bullet-shaped RV particles in the supernatants of the infected cells. To initially screen the immunogenicity of this new vaccine vector, BALB/c mice received a single vaccination with the recombinant RV expressing HIV-1 Gag. Immunized mice developed a vigorous CD8(+) cytotoxic T-lymphocyte response against HIV-1 Gag. In addition, 26.8% of CD8(+) T cells from mice immunized with RV expressing HIV-1 Gag produced gamma interferon after challenge with a recombinant vaccinia virus expressing HIV-1 Gag. These results further confirm and extend the potency of RV-based vectors as a potential HIV-1 vaccine.
Development of Small Molecule Chimeras That Recruit AhR E3 Ligase to Target Proteins (2019)

Targeted protein degradation using chimeric small molecules such as proteolysis-targeting chimeras (PROTACs) and specific and nongenetic inhibitors of apoptosis protein [IAP]-dependent protein erasers (SNIPERs) is an emerging modality in drug discovery. Here, we expand the repertoire of E3 ligases capable of ubiquitylating target proteins using this system. By incorporating β-naphthoflavone (β-NF) as a ligand, we developed a novel class of chimeric molecules that recruit the arylhydrocarbon receptor (AhR) E3 ligase complex. β-NF-ATRA, a chimeric degrader directed against cellular retinoic acid binding proteins (CRABPs), induced the AhR-dependent degradation of CRABP-1 and CRABP-2 via the ubiquitin-proteasome pathway. A similar compound ITE-ATRA, in which an alternative AhR ligand was used, also degraded CRABP proteins. Finally, we developed a chimeric compound β-NF-JQ1 that is directed against bromodomain-containing (BRD) proteins using β-NF as an AhR ligand. β-NF-JQ1 induced the interaction of AhR and BRD proteins and displayed effective anticancer activity that correlated with protein knockdown activity. These results demonstrate a novel class of chimeric degrader molecules based on the ability to bring a target protein and an AhR E3 ligase into close proximity.
A retrospective study of neoadjuvant FOLFIRINOX in unresectable or borderline-resectable locally advanced pancreatic adenocarcinoma (2012)

FOLFIRINOX followed by chemoradiotherapy is feasible as neoadjuvant therapy in patients with unresectable LAPC. The R0 resection rate of 44 % in this population is promising. Further studies are warranted.
Authentic GITR Signaling Fails To Induce Tumor Regression unless Foxp3+ Regulatory T Cells Are Depleted (2015)

The glucocorticoid-induced TNFR family-related protein (GITR, TNFRSF18, CD357) is expressed on effector and regulatory T (Treg) cells. Previous studies demonstrated that GITR triggering by anti-GITR mAb enhanced T and B cell-mediated immune responses. GITR-deficient T cells, however, also proliferate more than normal T cells, and this effect is unexplained. Because the activities of mAbs are controlled by their Fc regions, the true effect of GITR signaling needs to be determined by examining its interaction with authentic ligand. Therefore, we generated a pentamerized form of the GITRL extracellular domain (pGITRL) for ligation to GITR and compared its effect on T cells with that of anti-GITR mAb. The pGITRL was more effective than anti-GITR mAb in enhancing the proliferation of effector and regulatory cells in vitro and in vivo. Nonetheless, the growth of MC38 adenocarcinoma cells in vivo was only suppressed for initial 15 d by pGITRL, whereas it was suppressed indefinitely by anti-GITR mAb. Detailed analysis revealed that pGITRL induced extensive proliferation of Foxp3(+)CD4(+) Treg cells and led to the accumulation of activated Treg cells in tumor tissue and draining lymph nodes. Because GITR signaling could not neutralize the suppressive activity of activated Treg cells, pGITRL seems to lose its adjuvant effect when sufficient activated Treg cells have accumulated in the lymph nodes and tumor tissue. Indeed, the antitumor effects of pGITRL were markedly enhanced by depleting CD4(+) cells. These results suggest that GITR signaling has stimulatory effects on effector T cells and inhibitory effects through Treg cells.
Carrier techniques for thin wafer processing (2007)

Three different types of carrier techniques have been investigated and developed: thermal release tapes, solvable thermoplastic glue layer and mobile electrostatic carrier. These carriers were applied for manufacture of ultra-thin RFID chips, 12 µm thin CMOS image sensors and to a new process sequence that enables the formation of solder balls at the front side of an already thinned device wafer. Technical capabilities of different carrier techniques are compared with respect to allowed temperature range, type of bonding and de-bonding mechanism and their compatibility with typical wafer fab processes. Mobile electrostatic carriers were used to perform solder ball bumping at 55 µm thin silicon wafers. The process sequence demonstrates the capability of electrostatic carrier technology to enable thin wafer processing at elevated temperatures.
Coupled GaAs/AlGaAs quantum-well electroabsorption modulators for low-electric-field optical modulation (1989)

Experimental and theoretical studies are presented for exciton transitions in p-i-n GaAs/AlGaAs multiple coupled-quantum-well structures where each quantum well consists of two identical wells with a thin barrier. Electroabsorption and photocurrent studies are carried out to identify how the excitonic peaks respond to transverse electric fields. With a careful choice of the dimensions of the coupled quantum well, it is seen that the lowest heavy-hole exciton peak moves at a rate ∼2.5 faster than in a square well. Thus strong modulation is obtained at much lower electric fields. The nature of the higher-energy transitions is also studied.
On Finding the Maxima of a Set of Vectors (1975)

ASSTRACT. Let U1 , U2, . . . , Ud be totally ordered sets and let V be a set of n d-dimensional vectors In U~ X Us. . X Ud . A partial ordering is defined on V in a natural way The problem of finding all maximal elements of V with respect to the partial ordering ~s considered The computational complexity of the problem is defined to be the number of required comparisons of two components and
Role of Fc–FcγR interactions in the antitumor activity of therapeutic antibodies (2016)

The use of antibody therapy for cancer has steadily increased in recent years and has become standard treatment for numerous tumor types. It is now appreciated that the clinical activity of these antibodies relies upon their specific interactions with Fc receptors in addition to the well‐studied target‐binding region. The interactions mediated by antibody Fc domains can strongly affect the functional outcome of antibody therapy. The Fc portion of an antibody defines its interaction with numerous immune cells and has become an intense area of research as selecting the optimal Fc can greatly enhance the activity as well as mechanism of action of therapeutic antibodies. Recent advances in antibody engineering have enabled the development of antibodies that have altered Fc receptor interactions to take advantage of these findings. Engineering the Fc can fulfill diverse functions such as enhancing effector function for killing of tumor cells or depletion of unwanted immune subsets, enhancing agonist receptor signaling on particular immune cells or eliminating interaction with Fc receptors to avoid cellular depletion or toxicity in normal tissues. This review highlights important data and studies examining the role of Fc–Fc receptor interactions in therapeutic antibodies with a considerations for the future of engineered antibody therapy.
Rule-based anomaly pattern detection for detecting disease outbreaks (2002)

This paper presents an algorithm for performing early detection of disease outbreaks by searching a database of emergency department cases for anomalous patterns. Traditional techniques for anomaly detection are unsatisfactory for this problem because they identify individual data points that are rare due to particular combinations of features. When applied to our scenario, these traditional algorithms discover isolated outliers of particularly strange events, such as someone accidentally shooting their ear, that are not indicative of a new outbreak. Instead, we would like to detect anomalous patterns. These patterns are groups with specific characteristics whose recent pattern of illness is anomalous relative to historical patterns. We propose using a rule-based anomaly detection algorithm that characterizes each anomalous pattern with a rule. The significance of each rule is carefully evaluated using Fisher's Exact Test and a randomization test. Our algorithm is compared against a standard detection algorithm by measuring the number of false positives and the timeliness of detection. Simulated data, produced by a simulator that creates the effects of an epidemic on a city, is used for evaluation. The results indicate that our algorithm has significantly better detection times for common significance thresholds while having a slightly higher false positive rate.
no tail (ntl) is the zebrafish homologue of the mouse T (Brachyury) gene (1994)

The mouse T (Brachyury) gene is required for normal mesoderm development and the extension of the body axis. Recently, two mutant alleles of a zebrafish gene, no tail (ntl), have been isolated (Halpern, M. E., Ho., R. K., Walker, C. and Kimmel, C. B. (1993) Cell 75, 99-111). ntl mutant embryos resemble mouse T/T mutant embryos in that they lack a differentiated notochord and the caudal region of their bodies. We report here that this phenotype is caused by mutation of the zebrafish homologue of the T gene. While ntl embryos express mutant mRNA, they show no nuclear protein product. Later, expression of mRNA in mutants, but not in wild types, is greatly reduced along the dorsal midline where the notochord normally forms. This suggests that the protein is required for maintaining transcription of its own gene.
Sensitive and Specific Real-Time Polymerase Chain Reaction Assays to Accurately Determine Copy Number Variations (CNVs) of Human Complement C4A , C4B , C4-Long , C4-Short , and RCCX Modules: Elucidation of C4 CNVs in 50 Consanguineous Subjects with Defined HLA Genotypes (2007)

Recent comparative genome hybridization studies revealed that hundreds to thousands of human genomic loci can have interindividual copy number variations (CNVs). One of such CNV loci in the HLA codes for the immune effector protein complement component C4. Sensitive, specific, and accurate assays to interrogate the C4 CNV and its associated polymorphisms by using submicrogram quantities of genomic DNA are needed for high throughput epidemiologic studies of C4 CNVs in autoimmune, infectious, and neurological diseases. Quantitative real-time PCR (qPCR) assays were developed using TaqMan chemistry and based on sequences specific for C4A and C4B genes, structural characteristics corresponding to the long and short forms of C4 genes, and the breakpoint region of RP-C4-CYP21-TNX (RCCX) modular duplication. Assignments for gene copy numbers were achieved by relative standard curve methods using cloned C4 genomic DNA covering 6 logs of DNA concentrations for calibrations. The accuracies of test results were cross-confirmed internally in each sample, as the sum of C4A plus C4B equals to the sum of C4L plus C4S or the total copy number of RCCX modules. These qPCR assays were applied to determine C4 CNVs from samples of 50 consanguineous subjects who were mostly homozygous in HLA genotypes. The results revealed eight HLA haplotypes with single C4 genes in monomodular RCCX that are associated with multiple autoimmune and infectious diseases and 32 bimodular, 4 trimodular, and one quadrimodular RCCX. These C4 qPCR assays are proven to be robust, sensitive, and reliable, as they have contributed to the elucidation of C4 CNVs in >1000 human samples with autoimmune and neurological diseases.
High-mobility organic thin-film transistors based on α,α′-didecyloligothiophenes (2003)

We have fabricated organic thin-film transistors and integrated circuits based on the small-molecule organic semiconductors α,α′-didecylquaterthiophene, α,α′-didecylquinquethiophene, and α,α′-didecylsexithiophene. The organic semiconductors were deposited by thermal evaporation, with solution-processed and cross linked poly-4-vinylphenol serving as the gate dielectric layer. We have found that bottom-contact devices based on these materials have better electrical performance than top-contact devices, presumably due to more efficient carrier injection from bottom contacts due to the presence of the relatively long alkyl chains substituted at the α- and ω-positions of the oligothiophene molecules. Bottom-contact transistors have carrier mobility as large as 0.5 cm2/V s and on/off current ratio as large as 105, and ring oscillators fabricated using bottom-contact transistors and α,α′-didecylsexithiophene as the organic active layer have signal propagation delay as low as 30 μs per stage.
Analysis of differential gene expression in human melanocytic tumour lesions by custom made oligonucleotide arrays (2005)

Melanoma is one of the most aggressive types of cancer and resection of the tumour prior to dissemination of tumour cells is still the most effective treatment. Therefore, early diagnosis of melanocytic lesions is important and identification of novel (molecular) markers would be helpful to improve diagnosis. Moreover, better understanding of molecular targets involved in melanocytic tumorigenesis could possibly lead to development of novel interventions. In this study, we used a custom made oligonucleotide array containing 298 genes that were previously found to be differentially expressed in human melanoma cell lines 1F6 (rarely metastasising) and Mel57 (frequently metastasising). We determined differential gene expression in human common nevocellular nevus and melanoma metastasis lesions. By performing nine dye-swap array experiments, using individual as well as pooled melanocytic lesions, a constant differential expression could be detected for 25 genes in eight out of nine or nine out of nine array analyses. For at least nine of these genes, namely THBD, FABP7, H2AFJ, RRAGD, MYADM, HR, CKS2, NCK2 and GDF15, the differential expression found by array analyses could be verified by semiquantitative and/or real-time quantitative RT-PCR. The genes that we identified to be differentially expressed during melanoma progression could be potent targets for diagnostic, prognostic and/or therapeutic interventions.