gebhart/patrepeval huggingface dataset:
Targeting Adenosine Receptor Signaling in Cancer Immunotherapy (2018)

The immune system plays a major role in the surveillance and control of malignant cells, with the presence of tumor infiltrating lymphocytes (TILs) correlating with better patient prognosis in multiple tumor types. The development of 'checkpoint blockade' and adoptive cellular therapy has revolutionized the landscape of cancer treatment and highlights the potential of utilizing the patient's own immune system to eradicate cancer. One mechanism of tumor-mediated immunosuppression that has gained attention as a potential therapeutic target is the purinergic signaling axis, whereby the production of the purine nucleoside adenosine in the tumor microenvironment can potently suppress T and NK cell function. The production of extracellular adenosine is mediated by the cell surface ectoenzymes CD73, CD39, and CD38 and therapeutic agents have been developed to target these as well as the downstream adenosine receptors (A₁R, A<sub>2A</sub>R, A<sub>2B</sub>R, A₃R) to enhance anti-tumor immune responses. This review will discuss the role of adenosine and adenosine receptor signaling in tumor and immune cells with a focus on their cell-specific function and their potential as targets in cancer immunotherapy.
Continuing evolution of therapy for coronary artery disease. Initial results from the era of coronary angioplasty. (1994)

In this first large-scale, prospective observational treatment comparison of PTCA, CABG, and medicine, we confirmed the previously reported survival advantages for CABG over medical therapy for three-vessel disease and severe two-vessel disease. For less severe CAD, the primary treatment choices are between medicine and PTCA. In these patients, there is a trend for a relative survival advantage with PTCA, although absolute survival differences were modest. In this setting, treatment decisions should be based not only on survival differences but also on symptom relief, quality of life outcomes, and patient preferences.
A comparison of prediction schemes proposed for a new lossless image compression standard (2002)

It has long been realized that the current JPEG standard does not provide state-of-the-art performance in its lossless mode. In view of this, the International Standards Organization (ISO) recently solicited proposals for a new lossless/nearly lossless compression standard for continuous-tone still images. A total of nine proposals were submitted in the summer of 1995. Seven of these used a prediction step for 'decorrelating' the image prior to modelling and encoding. In this paper we investigate the efficacy of the different prediction schemes that were proposed. We also discuss their computational complexity and the price/performance trade-offs that emerge from our study.
High Association of an HL-A Antigen, W27, with Ankylosing Spondylitis (1973)

Abstract The frequencies of 24 HL-A antigens were examined in 40 patients with ankylosing spondylitis, 119 with rheumatoid arthritis, and 66 with gout. No significant deviation from control frequen...
Hydrothermal Liquefaction and Gasification of Nannochloropsis sp. (2010)

We converted the marine microalga Nannochloropsis sp. into a crude bio-oil product and a gaseous product via hydrothermal processing from 200 to 500 °C and a batch holding time of 60 min. A moderate temperature of 350 °C led to the highest bio-oil yield of 43 wt %. We estimate the heating value of the bio-oil to be about 39 MJ kg−1, which is comparable to that of a petroleum crude oil. The H/C and O/C ratios for the bio-oil decreased from 1.73 and 0.12, respectively, for the 200 °C product to 1.04 and 0.05, respectively, for the 500 °C product. Major bio-oil constituents include phenol and its alkylated derivatives, heterocyclic N-containing compounds, long-chain fatty acids, alkanes and alkenes, and derivatives of phytol and cholesterol. CO2 was always the most abundant gas product. H2 was the second most abundant gas at all temperatures other than 500 °C, where its yield was surpassed by that of CH4. The activation energies for gas formation suggest the presence of gas-forming reactions other than steam reforming. Nearly 80% of the carbon and up to 90% of the chemical energy originally present in the microalga can be recovered as either bio-oil or gas products.
Gut Microbiota in Cardiovascular Health and Disease (2017)

Significant interest in recent years has focused on gut microbiota-host interaction because accumulating evidence has revealed that intestinal microbiota play an important role in human health and disease, including cardiovascular diseases. Changes in the composition of gut microbiota associated with disease, referred to as dysbiosis, have been linked to pathologies such as atherosclerosis, hypertension, heart failure, chronic kidney disease, obesity, and type 2 diabetes mellitus. In addition to alterations in gut microbiota composition, the metabolic potential of gut microbiota has been identified as a contributing factor in the development of diseases. Recent studies revealed that gut microbiota can elicit a variety of effects on the host. Indeed, the gut microbiome functions like an endocrine organ, generating bioactive metabolites, that can impact host physiology. Microbiota interact with the host through many pathways, including the trimethylamine/trimethylamine <i>N</i>-oxide pathway, short-chain fatty acids pathway, and primary and secondary bile acids pathways. In addition to these metabolism-dependent pathways, metabolism-independent processes are suggested to also potentially contribute to cardiovascular disease pathogenesis. For example, heart failure-associated splanchnic circulation congestion, bowel wall edema, and impaired intestinal barrier function are thought to result in bacterial translocation, the presence of bacterial products in the systemic circulation and heightened inflammatory state. These are thought to also contribute to further progression of heart failure and atherosclerosis. The purpose of the current review is to highlight the complex interplay between microbiota, their metabolites, and the development and progression of cardiovascular diseases. We will also discuss the roles of gut microbiota in normal physiology and the potential of modulating intestinal microbial inhabitants as novel therapeutic targets.
Endothelial nitric oxide synthase overexpression attenuates congestive heart failure in mice (2003)

Congestive heart failure results in cardiovascular dysfunction and diminished vascular nitric oxide (NO) production. We hypothesized that overexpression of endothelial NO synthase (eNOS) within the endothelium would reduce the extent of contractile dysfunction in a murine model of infarct-induced congestive heart failure. We generated transgenic (TG) mice overexpressing the human eNOS gene. The TG mice displayed significantly enhanced eNOS protein levels and eNOS activity levels (10- to 12-fold greater) in the aorta and the coronary vasculature. Non-TG (NTg) and eNOS TG mice were subjected to permanent left anterior descending coronary artery occlusion and then observed for 1 mo. We assessed cardiac function in vivo by using echocardiography and ultraminiature ventricular pressure catheters. Myocardial infarct size was similar between study groups (approximately 70% of the risk zone). Survival was increased by 43% in the eNOS TG mice compared with NTg (P < 0.05). Fractional shortening and cardiac output were also significantly (P < 0.05) greater in the eNOS TG than in NTg. Interestingly, pulmonary edema was evident only in NTg mice, and no evidence of pulmonary edema was observed in the eNOS TG mice. Thus, targeted overexpression of the eNOS gene within the vascular endothelium in mice attenuates both cardiac and pulmonary dysfunction and dramatically improves survival during severe congestive heart failure.
Catalytic upgrading of levulinic acid to 5-nonanone (2010)

Aqueous solutions of levulinic acid can be catalytically processed, through the intermediate formation of γ-valerolactone (GVL), to an organic liquid stream that spontaneously separates from water, and is enriched in pentanoic acid and 5-nonanone. This organic layer can serve as a source of chemicals or can be upgraded to hydrocarbon fuels.
Evaluation of laser probe performances for measuring cross-coupling in 1-3 piezocomposite arrays (2003)

This paper deals with cross-coupling in 1-3 piezocomposite arrays. Four array configurations are tested. Measurements of surface displacement are performed with a laser interferometer. Experimental results are given with several graphic representation in order to interpret them in terms of cross-coupling mechanisms:temporal displacement profile, time/space and frequency/space cartographies of displacements and dispersion curves of Lamb waves in piezocomposite arrays. Effects of the fluid medium on each of these characteristics are discussed. Effective width of the excited element is determined and all plate modes involved in the mechanical coupling are identified and referenced.
Model building of disulfide bonds in proteins with known three-dimensional structure (1988)

As an aid in the selection of sites in a protein where a disulfide bond might be engineered, a computer program has been developed. The algorithm starts with the generation of C beta positions from the N, C alpha and C atom coordinates available from a three-dimensional model. A first set of residue pairs that might form a disulfide bond is selected on the basis of C beta-C beta distances between residues. Then, for each residue in this set, S gamma positions are generated, which satisfy the requirement that, with ideal values for the C alpha-C beta and C beta-S gamma bond lengths and for the bond angle at C beta, the distance between S gamma of residue 1 and C beta of residue 2 in a pair (determined by the bond angle at S gamma 2) is at, or very close to its ideal value. Usually two acceptable S gamma positions are found for each half cystine, resulting in up to four different conformations for the disulfide bond. Finally, these conformations are subjected to an energy minimization procedure to remove large deviations from ideal geometry and their final energies are calculated. User input determines which final conformations are energetically acceptable. These conformations are written to a file to allow further analysis and e.g. inspection on a computer graphics device.
Building the bridges between QoS and QoE for network control mechanisms (2013)

This last decade has known an explosion of the wireless access connectivity, mostly dominated by Wireless Local Area Networks (WLAN), 3GPP-based cellular networks (3G and 4G), and to a lesser extent by Digital Video Broadcast (DVB) networks. Combined with the emergence of smartphones and tablet PCs, wireless connectivity has changed the users' way to connect to the Internet, where we clearly observe that most of the connection to video platforms (e.g., Youtube, video on demand and IPTV) and social network applications are originated from wireless as well as mobile networks. However, massive accesses to these applications from wireless networks introduce several issues related to the increasing traffic, and the real-time property of some of these applications, which require a guarantee of Quality of Service (QoS) and Quality of Experience (QoE). These issues give rise to several challenges: (i) the need for network operators to have efficient mechanisms and protocols to avoid congestion and to support QoS; (ii) the need for content providers to consider the user context, in terms of bandwidth, user terminal, resolution, etc.), when creating and encoding an audio/video content. In order to address the challenges described above, the novelty of our contributions are in proposing dynamic and adaptive mechanisms to control network functionalities. The adaptive approaches are useful to tackle issues related to: (i) the network dynamics and changes in terms of congestion and contention level; (ii) the wireless channel dynamics and changes in terms of signal quality; (iii) the application dynamics and changes in terms of generated traffic; (iv) the users experience dynamics and changes in terms of QoE degradation/enhancement. Generally speaking, the conducted research work considers the network (or an application in the network) and the network functionality to control as a closed loop system. The objective is to modify (control) the system inputs (e.g., accept or reject a new flow in the network, increase the sleep duration for a wireless station, control congestion, etc.) and monitor the system outputs (e.g., delays, QoE, Queue size, etc.) in order to use these outputs for the next decision epoch of the controlled network mechanism. Our contributions are classified according to the type of monitored variable (system output) used by the network control mechanism. The first class of our research work pertains to QoS/Network centric (e.g. delays, the network load, the queue size of a node, delays, data rate) information, while the second class is based on human centric information by monitoring users' QoE.
Highly parallel, interferometric diffusing wave spectroscopy for monitoring cerebral blood flow dynamics (2018)

Light-scattering methods are widely used in soft matter physics and biomedical optics to probe dynamics in turbid media, such as diffusion in colloids or blood flow in biological tissue. These methods typically rely on fluctuations of coherent light intensity, and therefore cannot accommodate more than a few modes per detector. This limitation has hindered efforts to measure deep tissue blood flow with high speed, since weak diffuse light fluxes, together with low single-mode fiber throughput, result in low photon count rates. To solve this, we introduce multimode fiber (MMF) interferometry to the field of diffuse optics. In doing so, we transform a standard complementary metal-oxide-semiconductor (CMOS) camera into a sensitive detector array for weak light fluxes that probe deep in biological tissue. Specifically, we build a novel CMOS-based, multimode interferometric diffusing wave spectroscopy (iDWS) system and show that it can measure ∼<b>20</b> speckles simultaneously near the shot noise limit, acting essentially as ∼<b>20</b> independent photon-counting channels. We develop a matrix formalism, based on MMF mode field solutions and detector geometry, to predict both coherence and speckle number in iDWS. After validation in liquid phantoms, we demonstrate iDWS pulsatile blood flow measurements at 2.5 cm source-detector separation in the adult human brain in vivo. By achieving highly sensitive and parallel measurements of coherent light fluctuations with a CMOS camera, this work promises to enhance performance and reduce cost of diffuse optical instruments.
Gene selection and classification of microarray data using random forest (2006)

Because of its performance and features, random forest and gene selection using random forest should probably become part of the "standard tool-box" of methods for class prediction and gene selection with microarray data.
Visualization of the Local Insulator-Metal Transition in Pr 0.7 Ca 0.3 MnO 3 (1998)

The light-induced insulator-metal transition in the "colossal magnetoresistance" compound Pr0.7Ca0.3MnO3 is shown to generate a well-localized conducting path while the bulk of the sample remains insulating. The path can be visualized through a change of reflectivity that accompanies the phase transition. Its visibility provides a tool for gaining insight into electronic transport in materials with strong magnetic correlations. For example, a conducting path can be generated or removed at an arbitrary position just because of the presence of another path. Such manipulation may be useful in the construction of optical switches.
Detection of Fetal-derived Paternally Inherited X-Chromosome Polymorphisms in Maternal Plasma (1999)

The recent demonstration of the presence of cell-free fetal DNA in the plasma and serum of pregnant women opens up new possibilities for noninvasive prenatal diagnosis (1)(2)(3)(4)(5). However, many published reports have used Y-chromosomal sequences that are present in a male fetus as a marker (1)(6)(7), an approach that is not applicable to the 50% of pregnancies that involve a female fetus. A marker allowing the positive identification of DNA from a female fetus in maternal plasma would be useful for the investigation of sex-linked genetic disorders and for the extension of studies on pathologies involving fetal DNA abnormalities (7)(8) to pregnancies involving female fetuses. We reason that because the female fetus would have inherited a paternally derived copy of the X-chromosome, short tandem repeat (STR) polymorphisms on this chromosome could potentially be used as a fetus-specific marker for female fetal DNA. In this study, we tested this hypothesis using a panel of STRs on the X-chromosome.

Blood samples from pregnant women were collected into tubes containing EDTA. Plasma was harvested as described previously (9). We studied samples from 25 women with female fetuses as ascertained at delivery. Informed consent was obtained, and the study was approved by the Clinical Research Ethics Committee. In 10 cases, samples were collected during the second trimester (mean gestational age, 18 weeks; range, 16–19 weeks) just before amniocentesis. …
Development of ImmTOR Tolerogenic Nanoparticles for the Mitigation of Anti-drug Antibodies (2020)

The development of anti-drug antibodies (ADAs) is a common cause for treatment failure and hypersensitivity reactions for many biologics. The focus of this review is the development of ImmTOR, a platform technology designed to prevent the formation of ADAs that can be applied broadly across a wide variety of biologics by inducing immunological tolerance with ImmTOR nanoparticles encapsulating rapamycin. The induction of tolerance is antigen-specific and dependent on the incorporation of rapamycin in nanoparticles and the presence of the antigen at the time of administration of ImmTOR. Evidence for the induction of specific immune tolerance vs. general immune suppression is supported by the findings that: (1) ImmTOR induces regulatory T cells specific to the co-administered antigen; (2) tolerance can be transferred by adoptive transfer of splenocytes from treated animals to naïve recipients; (3) the tolerance is durable to subsequent challenge with antigen alone; and (4) animals tolerized to a specific antigen are capable of responding to an unrelated antigen. ImmTOR nanoparticles can be added to new or existing biologics without the need to modify or reformulate the biologic drug. The ability of ImmTOR to mitigate the formation of ADAs has been demonstrated for coagulation factor VIII in a mouse model of hemophilia A, an anti-TNFα monoclonal antibody in a mouse model of inflammatory arthritis, pegylated uricase in hyperuricemic mice and in non-human primates, acid alpha-glucosidase in a mouse model of Pompe disease, recombinant immunotoxin in a mouse model of mesothelioma, and adeno-associated vectors in a model of repeat dosing of gene therapy vectors in mice and in non-human primates. Human proof-of concept for the mitigation of ADAs has been demonstrated with SEL-212, a combination product consisting of ImmTOR + pegadricase, a highly immunogenic enzyme therapy for the treatment of gout. ImmTOR represents a promising approach to preventing the formation of ADAs to a broad range of biologic drugs.
A CONTINUOUS PROCEDURE FOR PREPARATION OF para FUNCTION ALIZED AROMATIC THIOLS USING NEWMAN-KWART CHEMISTRY (2000)

(2000). A CONTINUOUS PROCEDURE FOR PREPARATION OF para FUNCTION ALIZED AROMATIC THIOLS USING NEWMAN-KWART CHEMISTRY. Organic Preparations and Procedures International: Vol. 32, No. 6, pp. 547-555.
ATP Sulfurylase from Higher Plants (1982)

ATP sulfurylase was purified extensively from green cabbage (Brassica capitata L.) leaf. The enzyme appears to be an asymmetric dimer composed of 57,000 dalton subunits. Initial velocity and product inhibition studies of the forward and reverse reactions point to an obligately ordered kinetic mechanism with MgATP adding before MoO42-(or SO4'-). and MgPPi leaving before AMP + MoO42-(or adenosine-5'-phosphosulfate IAPSI).
Structural Analysis of the Contacts Anchoring Moenomycin to Peptidoglycan Glycosyltransferases and Implications for Antibiotic Design (2008)

Peptidoglycan glycosyltransferases (PGTs), enzymes that catalyze the formation of the glycan chains of the bacterial cell wall, have tremendous potential as antibiotic targets. The moenomycins, a potent family of natural product antibiotics, are the only known active site inhibitors of the PGTs and serve as blueprints for the structure-based design of new antibacterials. A 2.8 A structure of a Staphylococcus aureus PGT with moenomycin A bound in the active site appeared recently, potentially providing insight into substrate binding; however, the protein-ligand contacts were not analyzed in detail and the implications of the structure for inhibitor design were not addressed. We report here the 2.3 A structure of a complex of neryl-moenomycin A bound to the PGT domain of Aquifex aeolicus PBP1A. The structure allows us to examine protein-ligand contacts in detail and implies that six conserved active site residues contact the centrally located F-ring phosphoglycerate portion of neryl-moenomycin A. A mutational analysis shows that all six residues play important roles in enzymatic activity. We suggest that small scaffolds that maintain these key contacts will serve as effective PGT inhibitors. To test this hypothesis, we have prepared, via heterologous expression of a subset of moenomycin biosynthetic genes, a novel moenomycin intermediate that maintains these six contacts but does not contain the putative minimal pharmacophore. This compound has comparable biological activity to the previously proposed minimal pharmacophore. The results reported here may facilitate the design of antibiotics targeted against peptidoglycan glycosyltransferases.
A proper model for the partitioning of electrical circuits (1972)

Partitioning algorithms for electrical circuits are often based on the heuristic manipulation of a simple element-to-element interconnection matrix. However, the element-to-element interconnection matrix does not properly represent an electrical interconnection, or “net”, among more than two elements. This paper expands on several aspects of the discrepancy: 1) its source, 2) the circumstances under which it is likely to be significant, and its magnitude for typical circuits, and 3) the comparative difficulty and expense of using a more appropriate representation.
Lactoferrin protects neonatal rats from gut-related systemic infection (2001)

Lactoferrin is a milk protein that reportedly protects infants from gut-related, systemic infection. Proof for this concept is limited and was addressed during in vivo and in vitro studies. Neonatal rats pretreated orally with recombinant human lactoferrin (rh-LF) had less bacteremia and lower disease severity scores (P < 0.001) after intestinal infection with Escherichia coli. Control animals had 1,000-fold more colony-forming units of E. coli per milliliter of blood than treated animals (P < 0.001). Liver cultures from control animals had a twofold increase in bacterial counts compared with cultures from rh-LF-treated pups (P < 0.02). Oral therapy with rh-LF + FeSO(4) did not alter the protective effect. In vitro studies confirmed that rh-LF interacted with the infecting bacterium and rat macrophages. An in vitro assay showed that rh-LF did not kill E. coli, but a combination of rh-LF + lysozyme was microbicidal. In vitro studies showed that rat macrophages released escalating amounts of nitric oxide and tumor necrosis factor-alpha when stimulated with increasing concentrations of rh-LF. The in vitro studies suggest that rh-LF may act with other "natural peptide antibiotics" or may prime macrophages to kill E. coli in vivo.