gebhart/patrepeval huggingface dataset:
Soluble CD16 binds peripheral blood mononuclear cells and inhibits pokeweed-mitogen-induced responses (1993)

Human neutrophils express two types of low affinity receptors for IgG, Fc gamma RII or CD32 and Fc gamma RIIIB or CD16. Human serum contains soluble CD16 (sCD16), which is produced by proteolysis of neutrophil Fc gamma RIIIB, the cleavage site being located close to the cell surface. In order to assess the functional roles of sCD16, we have produced, in eukaryotic cells, a recombinant sCD16 containing the extracellular region of Fc gamma RIIIB. Purified sCD16, of molecular mass of 48 kD, bound human IgG1 and IgG3 but not IgG2, IgG4, or F(ab')2. It inhibited, in a time and dose-dependent fashion, proliferation and IgM and IgG production of human peripheral blood mononuclear cells (PBMC) stimulated by pokeweed mitogen (PWM) in vitro. FACS analysis showed that biotinylated sCD16 bound specifically to a fraction (35%) of PBMC, which corresponds to monocytes and to subsets of B and T lymphocytes. Moreover, sCD16 did not modify the staining of PBMC by FITC-coupled PWM. Thus, the biologic function(s) of sCD16 on PWM-induced responses are exerted through direct and specific interaction(s) with mononuclear blood cells and not with PWM. In conclusion, neutrophils may play a regulatory role on immune responses via the production of soluble forms of CD16 with cell-binding and antiproliferative capacities.
Characterization of the MLO gene family in Rosaceae and gene expression analysis in Malus domestica (2014)

Genomic tools available for Rosaceae were exploited in order to characterize the MLO gene family. Candidate MLO susceptibility genes were identified. In follow-up studies it can be investigated whether silencing or a loss-of-function mutations in one or more of these candidate genes leads to PM resistance.
Endothelial barrier dysfunction and oxidative stress: roles for nitric oxide? (1997)

Endothelial dysfunction has an important role to play in the pathophysiology of human vascular disease. The maintenance of barrier function is critical to the role of vascular endothelium in cardiovascular haemostasis and this function can be compromised by inflammatory mediators, cytokines or oxidants. Under conditions of oxidative stress a variety of reactive oxygen species (ROS) may be generated, which increase the permeability of the endothelial monolayer to fluid, macromolecules and inflammatory cells. The endothelium-derived nitric oxide radical (NO), whose physiological actions include effects on vascular smooth muscle, is normally inactivated by the superoxide radical anion. While large amounts of NO have cytotoxic potential, it is now becoming clear that combinations of NO with ROS can produce either cytotoxic or cytoprotective effects, depending on the relative amounts of each which are present in the target cell or its environment at a particular time. The contribution of NO to oxidant-mediated endothelial barrier dysfunction can be assessed in vitro in endothelial monolayers grown on porous membrane supports. In this model, using hydrogen peroxide (H2O2) as the oxidant, H2O2-induced losses of barrier function can be enhanced or partially offset by NO donor drugs, depending on the concentration of NO donor used. Furthermore, the injurious or cytoprotective effects of these agents appear to be determined by the quantity of NO generated. Since NO is administered clinically by inhalation in conditions such as pulmonary hypertension or the adult respiratory distress syndrome, which are themselves associated with generation of ROS, it is likely that low concentrations of NO may protect the pulmonary vascular endothelium while high concentrations might be expected to combine with ROS to yield intermediates capable of causing further endothelial injury or loss of barrier function.
No Fuss Distance Metric Learning Using Proxies (2017)

We address the problem of distance metric learning (DML), defined as learning a distance consistent with a notion of semantic similarity. Traditionally, for this problem supervision is expressed in the form of sets of points that follow an ordinal relationship - an anchor point x is similar to a set of positive points Y , and dissimilar to a set of negative points Z, and a loss defined over these distances is minimized. While the specifics of the optimization differ, in this work we collectively call this type of supervision Triplets and all methods that follow this pattern Triplet-Based methods. These methods are challenging to optimize. A main issue is the need for finding informative triplets, which is usually achieved by a variety of tricks such as increasing the batch size, hard or semi-hard triplet mining, etc. Even with these tricks, the convergence rate of such methods is slow. In this paper we propose to optimize the triplet loss on a different space of triplets, consisting of an anchor data point and similar and dissimilar proxy points which are learned as well. These proxies approximate the original data points, so that a triplet loss over the proxies is a tight upper bound of the original loss. This proxy-based loss is empirically better behaved. As a result, the proxy-loss improves on state-of-art results for three standard zero-shot learning datasets, by up to 15% points, while converging three times as fast as other triplet-based losses.
Concurrent Use of Oral Contraceptives With Antidepressants for Premenstrual Syndromes (2001)

Freeman, Ellen W. PhD; Rickels, Karl MD; Sondheimer, Steven J. MD; Polansky, Marcia ScD Author Information
Water diffusion and exchange as they influence contrast enhancement (1997)

The contrast-enhanced magnetic resonance imaging (MRI) signal is rarely a direct measure of contrast concentration; rather it depends on the effect that the contrast agent has on the tissue water magnetization. To correctly interpret such studies, an understanding of the effects of water movement on the magnetic resonance (MR) signal is critical. In this review, we discuss how water diffusion within biological compartments and water exchange between these compartments affect MR signal enhancement and therefore our ability to extract physiologic information. The two primary ways by which contrast agents affect water magnetization are discussed: (1) direct relaxivity and (2) indirect susceptibility effects. For relaxivity agents, for which T1 effects usually dominate, the theory of relaxation enhancement is presented, along with a review of the relevant physiologic time constants for water movement affecting this relaxation enhancement. Experimental issues that impact accurate measurement of the relaxation enhancement are discussed. Finally, the impact of these effects on extracting physiologic information is presented. Susceptibility effects depend on the size and shape of the contrast agent, the size and shape of the compartment in which it resides, as well as the characteristics of the water movement through the resulting magnetic field inhomogeneity. Therefore, modeling of this effect is complex and is the subject of active study. However, since susceptibility effects can be much stronger than relaxivity effects in certain situations, they may be useful even without full quantitation.
Convex relaxations and linear approximation for optimal power flow in multiphase radial networks (2014)

Distribution networks are usually multiphase and radial. To facilitate power flow computation and optimization, two semidefinite programming (SDP) relaxations of the optimal power flow problem and a linear approximation of the power flow are proposed. We prove that the first SDP relaxation is exact if and only if the second one is exact. Case studies show that the second SDP relaxation is numerically exact and that the linear approximation obtains voltages within 0.0016 per unit of their true values for the IEEE 13, 34, 37, 123-bus networks and a real-world 2065-bus network.
Selective Internal Radiation Therapy with SIR-Spheres ® in Patients with Nonresectable Liver Tumors (2005)

Our initial experience confirms that SIRT is a promising local therapeutic approach in patients with nonresectable liver tumors which is feasible and has an acceptable toxicity profile. Prospective data on comparing this treatment alone or in combination with other modalities are needed to answer whether long-term survival in this unfavorable stage of disease can be markedly improved.
Clozapine and weight gain. (1994)

Treatment with clozapine is associated with a high incidence of substantial weight gain, posing a potential long-term health risk. Studies are needed of the underlying mechanisms of weight gain, as well as the treatment for this side effect.
Maternal Antibody-Mediated Protection Against Gastroenteritis Due to Rotavirus in Newborn Mice is Dependent on Both Serotype and Titer of Antibody (1985)

In order to evaluate the role of passively acquired, rotavirus-specific antibodies in protection against diarrhea, we inoculated mouse dams with rotaviruses of various serotypes, and their newborns were orally challenged with a primate rotavirus (simian SA-11). Dams were immunized by using a regimen that included repeated inoculations administered either orally or intraperitoneally with adjuvant. The serum antibody response detected in dams by radioimmunoassay and plaque-reduction neutralization after parenteral immunization was approximately 15-fold and 80-fold greater, respectively, than that found after oral "hyperimmunization." Parenteral immunization with rotavirus serotypes either homotypic or heterotypic to the challenge virus protected suckling mice against diarrhea; protection was closely correlated with the in vitro neutralizing activity of maternal serum against the challenge virus. Oral immunization with only rotavirus strains homotypic to the challenge virus afforded protection; the lower immune response after oral immunization with rotaviruses heterotypic to the challenge virus resulted in a titer of neutralizing antibody to the challenge virus below the protective threshold. From our current studies it appears that antibody-mediated passive protection against rotavirus challenge is dependent on both serotype and titer of antibody.
The Protein-Protein Interface Evolution Acts in a Similar Way to Antibody Affinity Maturation (2009)

Understanding the evolutionary mechanism that acts at the interfaces of protein-protein complexes is a fundamental issue with high interest for delineating the macromolecular complexes and networks responsible for regulation and complexity in biological systems. To investigate whether the evolution of protein-protein interface acts in a similar way as antibody affinity maturation, we incorporated evolutionary information derived from antibody affinity maturation with common simulation techniques to evaluate prediction success rates of the computational method in affinity improvement in four different systems: antibody-receptor, antibody-peptide, receptor-membrane ligand, and receptor-soluble ligand. It was interesting to find that the same evolutionary information could improve the prediction success rates in all the four protein-protein complexes with an exceptional high accuracy (>57%). One of the most striking findings in our present study is that not only in the antibody-combining site but in other protein-protein interfaces almost all of the affinity-enhancing mutations are located at the germline hotspot sequences (RGYW or WA), indicating that DNA hot spot mechanisms may be widely used in the evolution of protein-protein interfaces. Our data suggest that the evolution of distinct protein-protein interfaces may use the same basic strategy under selection pressure to maintain interactions. Additionally, our data indicate that classical simulation techniques incorporating the evolutionary information derived from in vivo antibody affinity maturation can be utilized as a powerful tool to improve the binding affinity of protein-protein complex with a high accuracy.
Abstract LB-185: A PSMA-directed natural killer cell approach for prostate cancer immunotherapy (2017)

Abstract Prostate Cancer (PCa) is the third leading cause of cancer mortality in men in the United States. Locally advanced or metastatic PCa is clinically managed with androgen deprivation therapy (ADT), androgen receptor antagonists, and/or taxane chemotherapy. While initially effective, patients eventually develop resistance, leading to onset of a lethal castration-resistant disease state for which no curative interventions currently exist. Cell-based immunotherapy—which is centered on infusion of modified, tumor-directed immune cells intended to drive a more potent anti-tumor response—could potentially provide a new approach to treating advanced PCa. In this study, we describe the modification of an allogeneic, immortalized human natural killer cell line, NK-92, with a chimeric antigen receptor (CAR) directed against prostate-specific membrane antigen (PSMA), a cell-surface antigen expressed by most prostate tumors. We observed that both unmodified and CAR-bearing NK-92 cells display potent cytolytic activity against the majority of PCa cell lines tested in vitro. Expression of PSMA on PCa cell lines affected the activity of CAR-modified, but not unmodified, NK-92. Combination of NK-92 immunotherapy with ADT and taxanes is also discussed, as well as ongoing in vivo preclinical modeling. Overall, CAR-modified NK-92 cells show promise as a novel immunotherapeutic agent for the treatment of PCa. Citation Format: Lucas J. Brand, Alexander B. Zaslavsky, Ganesh S. Palapattu, Karen E. Knudsen. A PSMA-directed natural killer cell approach for prostate cancer immunotherapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr LB-185. doi:10.1158/1538-7445.AM2017-LB-185
Open pulled straw (OPS) vitrification: A new way to reduce cryoinjuries of bovine ova and embryos (1998)

Although cryopreservation of certain mammalian embryos is now a routine procedure, considerable differences of efficiency exist depending on stage, species and origin (in vivo or in vitro produced). Factors that are suspected to cause most of these differences are the amount of the intracellular lipid droplets and the different microtubular structure leading to chilling injury as well as the volume/surface ratio influencing the penetration of cryoprotectants. A new approach, the Open Pulled Straw (OPS) method, which renders very high cooling and warming rates (over 20,000 degrees C/min) and short contact with concentrated cryoprotective additives (less than 30 sec over -180 degrees C) offers a possibility to circumvent chilling injury and to decrease toxic and osmotic damage. In this paper we report the vitrification by the OPS method of in vitro produced bovine embryos at various stages of development. Embryos cryopreserved from Day 3 to Day 7 (Day 0 = day of fertilization) exhibited development into blastocysts at rates equivalent to those of control embryos; even those cryopreserved on Day 1 or 2 exhibited only somewhat reduced survival. Eighty-one percent of Day 8 hatched blastocysts also survived the procedure. The method was also successfully used for bovine oocytes; of 184 vitrified oocytes, 25% developed into blastocysts after fertilization and culture for 7 days. Pregnancies were achieved following transfer after vitrification at both the oocyte and blastocyst stage. The OPS vitrification offers a new way to solve basic problems of reproductive cryobiology and may have practical impact on animal biotechnology and human assisted reproduction.
Pointer analysis for multithreaded programs (1999)

This paper presents a novel interprocedural, flow-sensitive, and context-sensitive pointer analysis algorithm for multithreaded programs that may concurrently update shared pointers. For each pointer and each program point, the algorithm computes a conservative approximation of the memory locations to which that pointer may point. The algorithm correctly handles a full range of constructs in multithreaded programs, including recursive functions, function pointers, structures, arrays, nested structures and arrays, pointer arithmetic, casts between pointer variables of different types, heap and stack allocated memory, shared global variables, and thread-private global variables.We have implemented the algorithm in the SUIF compiler system and used the implementation to analyze a sizable set of multithreaded programs written in the Cilk multithreaded programming language. Our experimental results show that the analysis has good precision and converges quickly for our set of Cilk programs.
Bacterial and fungal killing by iontophoresis with long-lived electrodes (1991)

Iontophoresis with gold, carbon, and platinum electrodes was shown to effectively reduce or eliminate gram-positive, gram-negative, and Candida albicans inocula in synthetic urine. Platinum and gold electrodes were more effective than carbon electrodes, but platinum showed the best longevity and may reduce or eliminate microbial colonization of catheters.
Towards a fast, high specific and reliable discrimination of bacteria on strain level by means of SERS in a microfluidic device (2011)

The interest in a fast, high specific and reliable detection method for bacteria identification is increasing. We will show that the application of vibrational spectroscopy is feasible for the validation of bacteria in microfluidic devices. For this purpose, reproducible and specific spectral pattern as well as the establishment of large databases are essential for statistical analysis. Therefore, short recording times are beneficial concerning the time aspect of fast identification. We will demonstrate that the requirements can be fulfilled by measuring ultrasonic busted bacteria by means of microfluidic lab-on-a-chip based SERS. With the applied sample preparation, high specificity and reproducibility of the spectra are achieved. Taking advantage of the SERS enhancement, the spectral recording time is reduced to 1 s and a database of 11,200 spectra is established for a model system E. coli including nine different strains. The validation of the bacteria on strain level is achieved accomplishing SVM accuracies of 92%. Within this contribution the potential of our approach of bacterial identification for future application is discussed, focusing on the time-benefit and the combination with other microfluidic applications.
Microtubule‐associated Protein Tau, Paired Helical Filaments, and Phosphorylationa (1993)

This paper summarizes our recent studies on microtubule-associated protein tau and its pathological state resembling that of the paired helical filaments of Alzheimer's disease. The Alzheimer-like state of tau protein can be identified and analyzed in terms of certain phosphorylation sites and phosphorylation-dependent antibody epitopes. It can be induced by protein kinases which tend to phosphorylate serine or threonine residues followed by a proline; this includes mitogen-activated protein kinase (MAPK) and glycogen-synthase kinase 3 (GSK-3). Both of these are tightly associated with microtubules as well as with paired helical filaments. Structurally, tau appears as a rod-like molecule; it tends to self-associate into dimers whose monomers are antiparallel. Constructs of truncated tau made up of antiparallel dimers of the microtubule binding domain can be assembled into paired helical filaments in vitro.
Unique inflammatory RNA profiles of microglia in Creutzfeldt–Jakob disease (2003)

Previous studies in Creutzfeldt-Jakob disease (CJD) have shown that myeloid cells in the periphery as well as derivative microglial cells in the brain are infectious. Microglia can show an activated phenotype before prion protein (PrP) pathology is detectable in brain, and isolated infectious microglia contain very little PrP. To find whether a set of inflammatory genes are significantly induced or suppressed with infection, we analyzed RNA from isolated microglia with relevant cDNA arrays, and identified approximately 30 transcripts not previously examined in any transmissible spongiform encephalopathy. This CJD expression profile contrasted with that of uninfected microglia exposed to prototypic inflammatory stimuli such as lipopolysaccharide and IFN-gamma, as well as PrP amyloid. These findings underscore inflammatory pathways evoked by the infectious agent in brain. Transcript profiles unique for CJD microglia and other myeloid cells provide opportunities for more sensitive preclinical diagnoses of infectious and noninfectious neurodegenerative diseases.
Rapid in situ detection of alkaloids in plant tissue under ambient conditions using desorption electrospray ionization (2005)

Desorption electrospray ionization (DESI) mass spectrometry is applied to the in situ detection of alkaloids in the tissue of poison hemlock (Conium maculatum), jimsonweed (Datura stramonium) and deadly nightshade (Atropa belladonna). The experiment is carried out by electrospraying micro-droplets of solvent onto native or freshly-cut plant tissue surfaces. No sample preparation is required and the mass spectra are recorded under ambient conditions, in times of a few seconds. The impact of the sprayed droplets on the surface produces gaseous ions from organic compounds originally present in the plant tissue. The effects of operating parameters, including the electrospray high voltage, heated capillary temperature, the solvent infusion rate and the carrier gas pressure on analytical performance are evaluated and optimized. Different types of plant material are analyzed including seeds, stems, leaves, roots and flowers. All the previously reported alkaloids have been detected in C. maculatum, while fifteen out of nineteen known alkaloids for D. stramonium and the principal alkaloids of A. belladonna were also identified. All identifications were confirmed by tandem mass spectrometry. Results obtained show similar mass spectra, number of alkaloids, and signal intensities to those obtained when extraction and separation processes are performed prior to mass spectrometric analysis. Evidence is provided that DESI ionization occurs by both a gas-phase ionization process and by a droplet pick-up mechanism. Quantitative precision of DESI is compared with conventional electrospray ionization mass spectrometry (after sample workup) and the RSD values for the same set of 25 dicotyledonous C. maculatum seeds (one half of each seed analyzed by ESI and the other by DESI) are 9.8% and 5.2%, respectively.
Bacterial Expression and Characterization of Recombinant Biologically Active Anti-Tyrosine Kinase Receptor Antibody Forms (1998)

Homomeric and heteromeric interactions among cell-surface tyrosine kinase receptors belonging to the ErbB family lead to intracellular signaling cascades which are involved in cell activation, cytoskeletal interactions, and cellular transformation leading to neoplasia. Monoclonal antibodies which specifically bind to p185neu or epidermal growth factor receptor (EGFR), such as 7.16.4 and 225, respectively, can elicit tumor growth-inhibitory effects on transformed cells which overexpress either or both of these receptors. In order to better understand these receptor-receptor and receptor-antibody interactions and to gain insights that may be useful in the production and design of an antibody-based anticancer therapeutic, novel small recombinant 7.16.4 and 225 single-chain Fv fragments (scFv) were constructed, expressed, and characterized. We showed that these recombinant antibody fragments, which retain binding affinity, can be produced and purified from bacterial cell lysates. Our analyses further demonstrate that fusion of a 61 amino-acid dimerization domain with 7.16.4 and 225 scFv (7.16.4hth and 225hth) is sufficient to restore biological activity to these recombinant proteins.