gebhart/patrepeval huggingface dataset:
Composition of Points and the Mordell—Weil Problem for Cubic Surfaces (2001)

LetVbe a plane smooth cubic curve over a finitely generated fieldk.The Mordell-Weil theorem for V states that there is a finite subsetP ⠢ V (k)such that the whole V(k) can be obtained fromPby drawing secants and tangents through pairs of previously constructed points and consecutively adding their new intersection points with V. Equivalently, the group of birational transformations of V generated by reflections with respect to k-points is finitely generated. In this paper, elaborating an idea from [M3], we establish a Mordell-Weil type finite generation result for some birationally trivial cubic surfaces W. To the contrary, we prove that the birational automorphism group generated by reflections cannot be finitely generated ifW(k)is infinite.
Hierarchical browsing and search of large image databases (2000)

The advent of large image databases (>10000) has created a need for tools which can search and organize images automatically by their content. This paper focuses on the use of hierarchical tree-structures to both speed-up search-by-query and organize databases for effective browsing. The first part of this paper develops a fast search algorithm based on best-first branch and bound search. This algorithm is designed so that speed and accuracy may be continuously traded-off through the selection of a parameter /spl lambda/. We find that the algorithm is most effective when used to perform an approximate search, where it can typically reduce computation by a factor of 20-40 for accuracies ranging from 80% to 90%. We then present a method for designing a hierarchical browsing environment which we call a similarity pyramid. The similarity pyramid groups similar images together while allowing users to view the database at varying levels of resolution. We show that the similarity pyramid is best constructed using agglomerative (bottom up) clustering methods, and present a fast sparse clustering method which dramatically reduces both memory and computation over conventional methods.
Human to yeast pathway transplantation: cross-species dissection of the adenine de novo pathway regulatory node (2017)

Abstract Pathway transplantation from one organism to another represents a means to a more complete understanding of a biochemical or regulatory process. The purine biosynthesis pathway, a core metabolic function, was transplanted from human to yeast. We replaced the entire Saccharomyces cerevisiae adenine de novo pathway with the cognate human pathway components. A yeast strain was “humanized” for the full pathway by deleting all relevant yeast genes completely and then providing the human pathway in trans using a neochromosome expressing the human protein coding regions under the transcriptional control of their cognate yeast promoters and terminators. The “humanized” yeast strain grows in the absence of adenine, indicating complementation of the yeast pathway by the full set of human proteins. While the strain with the neochromosome is indeed prototrophic, it grows slowly in the absence of adenine. Dissection of the phenotype revealed that the human ortholog of ADE4, PPAT , shows only partial complementation. We have used several strategies to understand this phenotype, that point to PPAT/ADE4 as the central regulatory node. Pathway metabolites are responsible for regulating PPAT’s protein abundance through transcription and proteolysis as well as its enzymatic activity by allosteric regulation in these yeast cells. Extensive phylogenetic analysis of PPATs from diverse organisms hints at adaptations of the enzyme-level regulation to the metabolite levels in the organism. Finally, we isolated specific mutations in PPAT as well as in other genes involved in the purine metabolic network that alleviate incomplete complementation by PPAT and provide further insight into the complex regulation of this critical metabolic pathway.
Managing Tight-binding Receptors for New Separations Technologies (1999)

technologies by gaining control over the properties that militate against such applications. The main advantage of these ligands is in the feats they can accomplish not accessible to ordinary ligands, such as binding in extremely dilute solutions and extracting metal ions from mineralized deposits. Their main limitation is that, as the affinity increases, the rates of binding and dissociation decrease very greatly. Thus the best tight-binding ligands react too slowly to be useful in most known separations and remediation technologies. The subject program aims at solving this basic problem through three specific goals: (1) Make tight-binding ligands that bind fast using the new concept of ''switch-binding'' instead of equilibration. (2) Make tight-binding ligands that dissociate fast using the new concept of ''switch-release''. (3) Develop a ''soil poultice'' as a slow technology for remediation of contaminated soils.
Clinical Decision Support and Closed‐Loop Control for Intensive Care Unit Sedation (2013)

Abstract Critical care patients undergoing surgery require drug administration to regulate physiological variables such as blood pressure, cardiac output, heart rate, and degree of consciousness. The rate of infusion of each administered drug is critical, requiring constant monitoring and frequent adjustments. Patients in the intensive care unit who require mechanical ventilation due to acute respiratory failure also frequently require the administration of sedative agents. Open‐loop control (manual control) by clinical personnel can be tedious, imprecise, time‐consuming, and sometimes of poor quality, depending on the skills and judgment of the clinician. Dynamical system pharmacokinetic and pharmacodynamic modeling and closed‐loop control system design methodologies can significantly advance our understanding of the wide effects of pharmacological agents and anesthetics, as well as advance the state‐of‐the‐art in active control of drug delivery systems for clinical pharmacology. In this paper, we discuss the challenges and opportunities of clinical decision support and closed‐loop control for intensive care unit sedation.
Capacity of MIMO Rician fading channels with transmitter and receiver channel state information (2008)

This paper investigates the capacity of multiple- input multiple-output (MIMO) wireless communication systems when instantaneous channel state information (CSI) is available at both the transmitter and the receiver in a line-of-sight Rician fading environment. Specifically, an infinite series representation for the ergodic capacity of MIMO channels subject to uncorrected Rician fading (URiF) is derived, assuming both transmitter and receiver CSI. The ergodic capacity and its associated outage probability are expressed as a function of a cutoff value capturing the optimal power allocation scheme. Moreover, an equation for evaluating the cutoff value using standard numerical search techniques is derived, along with closed-form expressions for the capacity of the URiF MIMO channel when the so-called eigen-mode channel inversion technique and its truncated variant are implemented. We then provide numerical results showing the effects of Ricianness on the capacity of the eigen-mode optimal power and rate adaptation, and the sub-optimal channel inversion techniques and compare the achievable spectral efficiencies with and without channel knowledge at the transmitter thereby highlighting the capacity gains enabled by channel side information in a Rician fading environment.
A PERCEPTUALLY-INSPIRED 2D VIDEO STABILITY ESTIMATOR (2018)

Video stability is a significant problem for videos captured by handheld or body-worn cameras. An accurate video stability estimation that is consistent with human perception is the basis of effective video stabilization algorithms. It is also useful for comparing different video stabilization algorithms and constructing a benchmark. In this paper, we present a perception-inspired video stability estimator based on 2D image motions. It calculates the fraction of information in each frame that can be perceived by human eyes. Experimental results show that our stability estimator can accurately estimate subjective video stability scores. It requires less time to compute and is more accurate and robust under different scene structures than methods based on 3D motions.
Processing transactions over optimistic atomic broadcast protocols (2003)

Atomic broadcast primitives allow fault-tolerant cooperation between sites in a distributed system. Unfortunately, the delay incurred before a message can be delivered makes it difficult to implement high performance, scalable applications on top of atomic broadcast primitives. A new approach has been proposed which, based on optimistic assumptions about the communication system, reduces the average delay for message delivery. We develop this idea further and present a replicated database architecture that employs the new atomic broadcast primitive in such a way that the coordination phase of the atomic broadcast is fully overlapped with the execution of transactions, providing high performance without relaxing transaction correctness.
Analogs of squalene and oxidosqualene inhibit oxidosqualene cyclase of Trypanosoma cruzi expressed in Saccharomyces cerevisiae (2005)

Recently, a number of inhibitors of the enzyme oxidosqualene cyclase (OSC; EC 5.4.99.7), a key enzyme in sterol biosynthesis, were shown to inhibit in mammalian cells the multiplication of Trypanosoma cruzi, the parasite agent of Chagas' disease. The gene coding for the OSC of T. cruzi has been cloned and expressed in Saccharomyces cerevisiae. The expression in yeast cells could be a safe and easy model for studying the activity and the selectivity of the potential inhibitors of T. cruzi OSC. Using a homogenate of S. cerevisiae cells expressing T. cruzi OSC, we have tested 19 inhibitors: aza, methylidene, vinyl sulfide, and conjugated vinyl sulfide derivatives of oxidosqualene and squalene, selected as representative of different classes of substrate analog inhibitors of OSC. The IC50 values of inhibition (the compound concentration at which the enzyme is inhibited by 50%) are compared with the values obtained using OSC of pig liver and S. cerevisiae. Many inhibitors of pig liver and S. cerevisiae OSC show comparable IC50 for T. cruzi OSC, but some phenylthiovinyl derivatives are 10-100 times more effective on the T. cruzi enzyme than on the pig or S. cerevisiae enzymes. The expression of proteins of pathogenic organisms in yeast seems very promising for preliminary screening of compounds that have potential therapeutic activity.
Cu–SSZ-39, an active and hydrothermally stable catalyst for the selective catalytic reduction of NOx (2012)

A Cu-exchanged SSZ-39 zeolite has been synthesized and tested for the selective catalytic reduction (SCR) of NOx. This material shows an excellent catalytic activity, and most importantly, an extraordinary hydrothermal stability.
Measuring circulating cytokines (1993)

Cytokines, i.e., regulatory proteins derived primarily (but not exclusively) from cells of the immune system, are receiving increasing attention for their influences on physiological processes. This paper outlines several of the unique characteristics of cytokines and discusses the pitfalls encountered when measuring them in biological fluids. At present, each available assay has a combination of advantages and drawbacks; therefore, investigators must be aware of the trade-offs and choose the assay that best addresses their needs. The factors that affect cytokine measurement also influence cytokine activity in vivo; thus they are important from a physiological as well as methodological standpoint. Moreover, the absolute concentration of a single cytokine is probably less important than the balance between that cytokine and its natural antagonists.
Ca2+ and K+ (BK) channels in chick hair cells are clustered and colocalized with apical–basal and tonotopic gradients (2004)

Electrical resonance is a mechanism used by birds and many vertebrates to discriminate between frequencies of sound, and occurs when the intrinsic oscillation in the membrane potential of a specific hair cell corresponds to a specific stimulus sound frequency. This intrinsic oscillation results from an interplay between an inward Ca(2+) current and the resultant activation of a hyperpolarizing Ca(2+)-activated K(+) current. These channels are predicted to lie in close proximity owing to the fast oscillation in membrane potential. The interplay of these channels is widespread in the nervous system, where they perform numerous roles including the control of synaptic release, burst frequency and circadian rhythm generation. Here, we used confocal microscopy to show that these two ion channels are clustered and colocalized in the chick hair cell membrane. The majority of Ca(2+) channels were colocalized while the proportion of colocalized BK channels was markedly less. In addition, we report both an apical-basal gradient of these clusters in individual hair cells, as well as a gradient in the number of clusters between hair cells along the tonotopic axis. These results give physical confirmation of previous predictions. Since the proportion of colocalized channels was a constant function of Ca(2+) channels, and not of BK channels, these results suggest that their colocalization is determined by the former. The molecular mechanisms underpinning their clustering and colocalization are likely to be common to other neuronal cells.
High-Power Coherent Microwave Emission from Magnetic Tunnel Junction Nano-oscillators with Perpendicular Anisotropy (2012)

The excitation of the steady-state precessions of magnetization opens a new way for nanoscale microwave oscillators by exploiting the transfer of spin angular momentum from a spin-polarized current to a ferromagnet, referred to as spin-transfer nano-oscillators (STNOs). For STNOs to be practical, however, their relatively low output power and their relatively large line width must be improved. Here we demonstrate that microwave signals with maximum measured power of 0.28 μW and simultaneously narrow line width of 25 MHz can be generated from CoFeB-MgO-based magnetic tunnel junctions having an in-plane magnetized reference layer and a free layer with strong perpendicular anisotropy. Moreover, the generation efficiency is substantially higher than previously reported STNOs. The results will be of importance for the design of nanoscale alternatives to traditional silicon oscillators used in radio frequency integrated circuits.
A Structure-Activity Relationship Comparison of Imidazodiazepines Binding at Kappa, Mu, and Delta Opioid Receptors and the GABAA Receptor (2020)

Analgesic and anti-inflammatory properties mediated by the κ opioid receptor (KOR) have been reported for oxadiazole imidazodiazepines. Affinities determined by radioligand competition assays of more than seventy imidazodiazepines using cell homogenates from HEK293 cells that overexpress KOR, µ opioid receptor (MOR), and δ opioid receptor (DOR) are presented. Affinities to synaptic, benzodiazepine-sensitive receptors (BZR) were determined with rat brain extract. The highest affinity for KOR was recorded for GL-I-30 (Ki of 27 nM) and G-protein recruitment was observed with an EC<sub>50</sub> of 32 nM. Affinities for MOR and DOR were weak for all compounds. Ester and amide imidazodiazepines were among the most active KOR ligands but also competed with <sup>3</sup>H-flunitrazepam for brain extract binding, which is mediated predominately by gamma aminobutyric acid type A receptors (GABA<sub>A</sub>R) of the α<sub>1-3</sub>β<sub>2-3</sub>γ<sub>1-2</sub> subtypes. Imidazodiazepines with carboxylic acid and primary amide groups did not bind KOR but interacted strongly with GABA<sub>A</sub>Rs. Pyridine substitution reduced KOR affinity. Oxadiazole imidazodiazepines exhibited good KOR binding and interacted weakly with BZR, whereas oxazole imidazodiazepines were more selective towards BZR. Compounds that lack the imidazole moiety, the pendent phenyl, or pyridine substitutions exhibited insignificant KOR affinities. It can be concluded that a subset of imidazodiazepines represents novel KOR ligands with high selectivity among opioid receptors.
Attraction of mosquitoes to primate odours and implications for zoonotic Plasmodium transmission (2019)

Vector-borne diseases often originate from wildlife and can spill over into the human population. One of the most important determinants of vector-borne disease transmission is the host preference of mosquitoes. Mosquitoes with a specialised host preference are guided by body odours to find their hosts in addition to carbon dioxide. Little is known about the role of mosquito host preference in the spillover of pathogenic agents from humans towards animals and vice versa. In the Republic of Congo, the attraction of mosquitoes to primate host odours was determined, as well as their possible role as malaria vectors, using odour-baited traps mimicking the potential hosts of mosquitoes. Most of the mosquito species caught showed a generalistic host preference. Anopheles obscurus was the most abundant Anopheles mosquito, with a generalistic host preference observed from the olfactory response and the detection of various Plasmodium parasites. Interestingly, Culex decens showed a much higher attraction towards chimpanzee odours than to human or cow odours. Human Plasmodium parasites were observed in both human and chimpanzee blood, although not in the Anopheles mosquitoes that were collected. Understanding the role of mosquito host preference for cross-species parasite transmission provides information that will help to determine the risk of spillover of vector-borne diseases.
MECHANISM OF INHIBITION OF PEPSIN BY PEPSTATIN. II (1974)

Pepstatin, a strongly bound inhibitor of acid proteases, does not instantaneously bind to pepsin. The dissociation constant of pepsin-pepstatin complex is 9.7 × 10-11 M using Phe•Gly•His•Phe(NO2)•Phe•Ala•PheOMe as substrate. Difference ultraviolet absorption spectra show conformational change of pepsin in interaction with pepstatin. The bindillg of pepsin with pepstatin is stoicheometric and the normality of pepsin can be easily titrated by pepstain. Pepsin modified by 1, 2-epoxy-3-(p-nitrophenoxy) propane, 2, 3-butanedione, α-diazo-p-bromoacetophenone or p-bromophenacyl bromide shows reduced pepstatin-binding activity.
Ten Years of Sports Health: Authorship Characteristics and Levels of Evidence (2020)

Female authorship in <i>Sports Health</i> surpasses industry standards, and the percentage of high-LOE studies remains remarkably high. <i>Sports Health</i> has stayed true to its multidisciplinary scope, as evidenced by the authors' varying degrees and numerous countries that publish in the journal.
Fragment evolution for GPCRs: the role of secondary binding sites in optimization (2021)

We developed a docking-based fragment evolution approach that extends orthosteric fragments towards a less conserved secondary binding pocket of GPCRs. Evaluating 13 000 extensions for the β<sub>1</sub>- and β<sub>2</sub>-adrenergic receptors we synthesized and tested 112 bitopic molecules. Our results confirmed the positive contribution of the secondary binding pocket to both potency and selectivity optimizations.
New Trends in Anti-Cancer Therapy: Combining Conventional Chemotherapeutics with Novel Immunomodulators (2018)

Cancer is one of the leading causes of death worldwide, and current research has focused on the discovery of novel approaches to effectively treat this disease. Recently, a considerable number of clinical trials have demonstrated the success of immunomodulatory therapies for the treatment of cancer. Monoclonal antibodies can target components of the immune system to either i) agonise co-stimulatory molecules, such as CD137, OX40 and CD40; or ii) inhibit immune checkpoints, such as cytotoxic T-lymphocyte-associated antigen 4 (CTLA-4), programmed cell death-1 (PD-1) and its corresponding ligand PD-L1. Although tumour regression is the outcome for some patients following immunotherapy, many patients still do not respond. Furthermore, chemotherapy has been the standard of care for most cancers, but the immunomodulatory capacity of these drugs has only recently been uncovered. The ability of chemotherapy to modulate the immune system through a variety of mechanisms, including immunogenic cell death (ICD), increased antigen presentation and depletion of regulatory immune cells, highlights the potential for synergism between conventional chemotherapy and novel immunotherapy. In addition, recent pre-clinical trials indicate dipeptidyl peptidase (DPP) enzyme inhibition, an enzyme that can regulate immune cell trafficking to the tumour microenvironment, as a novel cancer therapy. The present review focuses on the current immunological approaches for the treatment of cancer, and summarizes clinical trials in the field of immunotherapy as a single treatment and in combination with chemotherapy.
Development of High Durability Cyan and Magenta Dyes for Ink Jet Printing System (2009)

Water-soluble novel cyan and magenta dyes, which show high ozone-fastness and light-fastness on porous photo media, have been developed for inkjet printing systems. Control of dye energy levels, removal of groups sensitive towards ozone, and acceleration of copper-phthalocyanine complex (CuPc) aggregation were the dominant factors to significantly improve both ozone-fastness and light-fastness. For the development of the CuPc cyan skeleton, alkyl sulfonyl groups, all of which were located at beta positions on the CuPc skeleton, were effective in improving dye fastness. For the development of the magenta skeleton, a combination of aniline-substituted pyridine coupling component and pyrazole diazonium component was an inherently important skeleton to improve dye fastness. Derived from the de-aggregation compounds developed for silver halide photography, we succeeded in developing an anti-bronzing ink additive.
Ensuring effectiveness and reproducibility of inhaled drug treatment (2019)

The guarantee of safety and efficacy of inhaled drug treatment begins with product development measures taken to meet quality standards. The approach of quality by design (QbD) employs a wide range of process and product management and optimization tools. Implementation of statistical experimental design and process control and the application of process analytical technology ensure the greatest possible control over the final product quality and performance in terms of the key determinants of aerodynamic particle size distribution, delivered dose, and uniformity. Additional considerations might include aerosol delivery rate and dissolution. The biopharmaceutical considerations begin with the site of deposition and the rate of drug dissolution that interact with the mechanisms of clearance, which, on a scale of disposition within and between regions of the lungs, consist of absorption and mucociliary and cell-mediated transport. On a cellular scale, biochemical disposition by transporters of by the action of metabolizing enzymes may also contribute to overall disposition. The intrinsic biological variability between patients may be due to disease, age and gender, or within-patient fluctuations in pulmonary function that underlie the effort that can be expended inhaling the aerosolized drug. The confounding of the anatomical and physiological variability with specific drug product may be overcome to some degree by adequate training. The recent emergence of feedback systems and breath control devices will improve outcomes. There is significant current interest in exploring the product and biological factors influencing effective drug delivery with a view to developing an inhaled biopharmaceutical classification system to guide development activity. The challenge of establishing the limits to management of product quality and biopharmaceutical mechanisms that can be achieved to ensure the safety and efficacy of inhaled pharmaceuticals remains.