gebhart/patrepeval huggingface dataset:
Role of the early secretory pathway in SARS-CoV-2 infection (2020)

Similar to other RNA viruses, SARS-CoV-2 must (1) enter a target/host cell, (2) reprogram it to ensure its replication, (3) exit the host cell, and (4) repeat this cycle for exponential growth. During the exit step, the virus hijacks the sophisticated machineries that host cells employ to correctly fold, assemble, and transport proteins along the exocytic pathway. Therefore, secretory pathway-mediated assemblage and excretion of infective particles represent appealing targets to reduce the efficacy of virus biogenesis, if not to block it completely. Here, we analyze and discuss the contribution of the molecular machines operating in the early secretory pathway in the biogenesis of SARS-CoV-2 and their relevance for potential antiviral targeting. The fact that these molecular machines are conserved throughout evolution, together with the redundancy and tissue specificity of their components, provides opportunities in the search for unique proteins essential for SARS-CoV-2 biology that could also be targeted with therapeutic objectives. Finally, we provide an overview of recent evidence implicating proteins of the early secretory pathway as potential antiviral targets with effective therapeutic applications.
Compiler Algorithms for Synchronization (1987)

Translating program loops into a parallel form is one of the most important transformations performed by concurrentizing compilers. This transformation often requires the insertion of synchronization instructions within the body of the concurrent loop. Several loop synchronization techniques are presented first. Compiler algorithms to generate synchronization instructions for singly-nested loops are then discussed. Finally, a technique for the elimination of redundant synchronization instructions is presented.
[Hemodynamic effects of renal interoreceptor and afferent nerve stimulation in rabbit]. (1990)

Hemodynamic effects of renal mechano- and chemoreceptor activation and afferent renal nerve stimulation were observed in 39 anesthetized rabbits. The mean arterial pressure (MAP) and heart rate (HR) were decreased following elevation of ureteral pressure (13-22 mmHg), and retrograde perfusion of NaCl (1.0 mol/L) or KCl (0.15 mol/L) into pelvis via ureter route. The decrease in MAP was enhanced by sinoaortic denervation. HR, MAP, mesentery arterial perfusion pressure (MPP), hindlimb arterial perfusion pressure (HLPP), left ventricular pressure (LVP), left ventricular dp/dtmax (LV dp/dtmax), cardiac output (CO) and total peripheral resistance (TPR) were decreased during electrical stimulation of afferent renal nerve. By sinoaortic denervation, the aforementioned hemodynamic parameters, except HR, CO and TPR, were reduced more markedly by electric stimulation of afferent renal nerves. Therefore it appears that sinoaortic depressor reflex plays a buffer role in the cardiovascular responses to the stimulation of afferent renal nerves.
Towards developing effective Continence Management through wetness alert diaper: Experiences, lessons learned, challenges and future directions (2010)

Incontinence is one of the major healthcare issues in everyday nursing care especially for frail elderly and patients with dementia (PWD) in nursing homes. Urinary incontinence and diaper use are prevalent in PWD due to decline in intellect and physical activities. They may lie in soiled diapers for
Cycle-slip resilient carrier phase estimation for polarization multiplexed 16-QAM systems (2012)

A cycle-slip resilient pilot-aided carrier phase estimation that achieves 4000km transmission is proposed for 16-QAM systems. We demonstrate that fast phase transition induced by ASE and nonlinear distortions are the main reasons of cycle-slips.
Growth and yield of chia (Salvia hispanica L.) in the Mediterranean and desert climates of Chile (2016)

Chia (Salvia hispanica L.) is a species with seeds that have high essential fatty acid content, which has encouraged increased crop production worldwide. However, the expansion of chia is limited because it is a photoperiodsensitive plant adapted to areas without cold. The objective of the present study was to determine the effect of different climatic conditions on the growth, grain yield and oil production of chia under irrigation in three geographic areas of Chile: Valle de Azapa (1830' S lat) with a coastal desert climate, normal desert climate in Canchones (2026' S lat), and Las Cruces (3330' S lat) with dry Mediterranean climate with marine influence, and two chia phenotypes: white and dark. Results indicated that desert conditions in the Valle de Azapa (VA) and Canchones (CH) provided better conditions for plant growth; the highest yield (> 2900 kg ha -1 ) and oil production (> 550 L ha -1 ). In Las Cruces (LC), at higher latitude, low temperatures present beginning in April coincided with the reproductive stage, affecting yield which was no more than 129 kg ha -1 ; thus this zone is not recommendable for chia cultivation. This study also determined an 11.8 h day length threshold for the beginning of flowering; when plants are exposed to shorter days flower initiation is more precocious, but when day length is not adequate plants only begin to flower when they have accumulated 600-700 C d.
Oxygen Consumption Can Regulate the Growth of Tumors, a New Perspective on the Warburg Effect (2009)

We interpret these findings to show that non-oncogenic genetic changes that alter mitochondrial metabolism can regulate tumor growth through modulation of the consumption of oxygen, which appears to be a rate limiting substrate for tumor proliferation.
Three New Cholinesterase-Inhibiting cis-Clerodane Diterpenoids from Otostegia limbata (2005)

Three new tricyclic cis-clerodane type diterpenoids trivially named as limbatolide A (1), limbatolide B (2) and limbatolide C (3) have been isolated from the roots of Otostegia limbata along with two known compounds; oleanic acid and beta-sitosterol. The structure elucidation of the new compounds was based primarily on two-dimensional (2D) NMR techniques. Compounds 1-3 displayed inhibitory potential in a concentration-dependent manner against acetylcholinesterase (AChE; EC 3.1.1.7) and butyrylcholinesterase (BChE; EC 3.1.1.8) enzymes, respectively.
Ethane-1,2- and Propane-1,3-disulfonic Acids and Anhydrides (1945)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTEthane-1,2- and Propane-1,3-disulfonic Acids and AnhydridesS. M. McElvain, Arthur Jelinek, and Kurt RorigCite this: J. Am. Chem. Soc. 1945, 67, 9, 1578–1581Publication Date (Print):September 1, 1945Publication History Published online1 May 2002Published inissue 1 September 1945https://pubs.acs.org/doi/10.1021/ja01225a053https://doi.org/10.1021/ja01225a053research-articleACS PublicationsRequest reuse permissionsArticle Views453Altmetric-Citations17LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Silver Plating (1941)

Electroplating silver on other metals is over a hundred years old. One of the first baths proposed was the cyanide bath which, with slight modifications, is the standard silver bath today. Both the potassium silver cyanide and the sodium silver cyanide bath are in commercial use today. Aside from the higher cost of the potassium salts, the potassium bath is the preferred one. The brightening agent used in most plants is carbon disulfide, proposed many years ago. A relatively new silver cyanide bath, which is gaining in popularity, is that containing from 11 to 15% of potassium nitrate. As pointed out by the authors, this has many advantages over the older cyanide baths. Full operating details, based on best modern silver plating practice, are detailed and discussed.
Tubulin‐tyrosine ligase catalyzes covalent binding of 3‐fluoro‐tyrosine to tubulin: kinetic and [<sup>19</sup>F]NMR studies (1995)

The use of 3-fluoro-tyrosine as an alternative substrate for the enzyme tubulin:tyrosine ligase which catalyzes the incorporation of tyrosine into the alpha-tubulin subunit was investigated. The incorporation of tyrosine into tubulin was inhibited competitively by 3-fluoro-tyrosine with an apparent Ki of approximately 25 microM. The affinity for this analog was similar to that of tyrosine, confirming that the hydrogen at position 3 of the aromatic ring is not essential for the reaction catalyzed by TTLase. The incorporation of 3-fluoro-tyrosine into the C-terminus of the alpha-tubulin subunit was demonstrated through [19F]NMR spectroscopy. The 3-fluoro-tyrosine signal at -58.6 ppm (trifluoroacetic acid as external standard), with a bandwidth of 24.7 Hz presented a chemical shift of 0.75 ppm upfield and an enlargement in the bandwidth (30.5 Hz) when incorporated into tubulin. These results strongly suggest that this amino acid is exposed to the solvent in tubulin. Tubulin covalently labeled with 3-fluoro-tyrosine was competent to polymerize into microtubules. The use of fluorinated tubulin in [19F]NMR spectroscopy for studying questions concerning protein conformation and interactions will be discussed.
Topology and Design of Wide-Band 3D Metamaterials made of Periodically Loaded Transmission Line Arrays (2005)

We propose a new topology for realizing artificial microwave materials that exhibit a negative refractive index over a wide frequency band. These metamaterials consist of a three-dimensional transmission line mesh that is loaded with reactive series and shunt elements to create negative permittivity and permeability. The cubic-cell transmission line host network is a physical realization of the 3D distributed node TLM lattice which has the same low-frequency properties as the FDTD Yee scheme. This paper describes the topology, the theory, the design, and possible realizations of such a metamaterial. Its wave properties are validated by full-wave simulations using the time domain electromagnetic field simulation tool MEFiSTo-3D Pro.
The effect of iron and transferrin on the killing of Escherichia coli in fresh serum. (1971)

Iron in excess of the binding capacity of transferrin allows Escherichia coli to grow in fresh serum. This appears to be due to two mechanisms. Firstly iron stimulates growth as it is an essential metabolite which is not available to E. coli in serum. Secondly, it interferes with bacterial killing, a process normally mediated by natural antibody and complement.
A novel zinc‐binding motif found in two ubiquitous deaminase families (1994)

Two families of deaminases, one specific for cytidine, the other for deoxycytidylate, are shown to possess a novel zinc-binding motif, here designated ZBS. We have (1) identified the protein members of these 2 families, (2) carried out sequence analyses that allow specification of this zinc-binding motif, and (3) determined signature sequences that will allow identification of additional members of these families as their sequences become available.
Decontaminating Biological Sludge for Agricultural Use (1985)

A biological oxidation process called bacterial leaching was used to remove heavy metals from anaerobically digested sewage sludge. The purpose was to decontaminate the sludge so that it could be utilized on agricultural land. The leaching process was found to be affected by pH, aeration and temperature. At α pH of 4, an aeration rate of 100 cm3 of air per litre of sludge per minute and a temperature of 25°C, the following metal removal efficiencies were observed: cadmium, 80 - 85% ; copper, 66 - 80% ; nickel, 70 - 78% and zinc, 84 - 90%. No significant removal was observed for lead. In addition to removing heavy metals, bacterial leaching preserves the soil conditioning and fertilizing properties of the sludge. According to Ontario guidelines, the sludge used in this study was initially not acceptable for use on agricultural lands. However, after bacterial leaching, all criteria for the application of sludge to agricultural lands were easily met.
Biomass degrading enzymes from anaerobic rumen fungi. (1995)

Obligately anaerobic fungi are part of the natural microflora of the alimentary tract of many herbivorous mammals. They produce a complete set of polysaccharide hydrolytic enzymes which efficiently degrade plant cell-walls. This article summarizes the present work on biomass degrading enzymes with special emphasis on their cellulases, xylanases, and esterases from both monocentric and polycentric anaerobic fungi. The possibility of the cellulosome or xylanosome-like high molecular mass complexes in the fungi are also discussed.
Developmental Phenotype of a Membrane Only Estrogen Receptor α (MOER) Mouse (2008)

Estrogen receptors (ERs) alpha and beta exist as nuclear, cytoplasmic, and membrane cellular pools in a wide variety of organs. The relative contributions of each ERalpha pool to in vivo phenotypes resulting from estrogen signaling have not been determined. To address this, we generated a transgenic mouse expressing only a functional E domain of ERalpha at the plasma membrane (MOER). Cells isolated from many organs showed membrane only localized E domain of ERalpha and no other receptor pools. Liver cells from MOER and wild type mice responded to 17-beta-estradiol (E2) with comparable activation of ERK and phosphatidylinositol 3-kinase, not seen in cells from ERalphaKO mice. Mating the MOER female mice with proven male wild type breeders produced no pregnancies because the uterus and vagina of the MOER female mice were extremely atrophic. Ovaries of MOER and homozygous Strasbourg ERalphaKO mice showed multiple hemorrhagic cysts and no corpus luteum, and the mammary gland development in both MOER and ERalphaKO mice was rudimentary. Despite elevated serum E2 levels, serum LH was not suppressed, and prolactin levels were low in MOER mice. MOER and Strasbourg female mice showed plentiful abdominal visceral and other depots of fat and increased body weight compared to wild type mice despite comparable food consumption. These results provide strong evidence that the normal development and adult functions of important organs in female mice requires nuclear ERalpha and is not rescued by membrane ERalpha domain expression alone.
Hardware and software implementation for an auto-calibrated measurement system (2004)

In this paper we present the mixed hardware and software implementation of an auto-calibrated measurement system. The use of an analog programmable circuit (FPAA) as a sensor's conditioning interface, allows a full benefit of its reconfigurable aspect, to carry out self-test and self-adjustment routines, in order to calibrate the measurement chain. The proposed software calibration method permits a successive correction and linearization of the whole measurement system transfer function, using a few number of calibration data. The proposed auto-calibration method can be used for different sensors types, and allows considerable cost reduction of their exploitation and calibration.
Laser action on the 342-nm molecular iodine band (1975)

A new laser operating on the 342-nm band of I2 is reported. Electron-beam-excited mixtures of argon with CF3I and HI produced this I2 laser. The excited state of this laser is probably formed by ion recombination reactions, and a plausible mechanism is given.
Stabilization of Aspergillus awamori glucoamylase by proline substitution and combining stabilizing mutations (1998)

To stabilize Aspergillus awamori glucoamylase (GA), three proline substitution mutations were constructed. When expressed in Saccharomyces cerevisiae, Ser30-->Pro (S30P) stabilized the enzyme without decreased activity, whereas Asp345-->Pro (D345P) did not significantly alter and Glu408-->Pro (E408P) greatly decreased enzyme thermostability. The S30P mutation was combined with two previously identified stabilizing mutations: Gly137-->Ala, and Asn20-->Cys/Ala27-->Cys (which creates a disulfide bond between positions 20 and 27). The combined mutants demonstrated cumulative stabilization as shown by decreased irreversible thermoinactivation rates between 65 and 80 degrees C. Additionally, two of the combined mutants outperformed wild-type GA in high-temperature (65 degrees C) saccharifications of DE 10 maltodextrin and were more active than the wild-type enzyme when assayed using maltose as substrate.
Malaria Parasite-Synthesized Heme Is Essential in the Mosquito and Liver Stages and Complements Host Heme in the Blood Stages of Infection (2013)

Heme metabolism is central to malaria parasite biology. The parasite acquires heme from host hemoglobin in the intraerythrocytic stages and stores it as hemozoin to prevent free heme toxicity. The parasite can also synthesize heme de novo, and all the enzymes in the pathway are characterized. To study the role of the dual heme sources in malaria parasite growth and development, we knocked out the first enzyme, δ-aminolevulinate synthase (ALAS), and the last enzyme, ferrochelatase (FC), in the heme-biosynthetic pathway of Plasmodium berghei (Pb). The wild-type and knockout (KO) parasites had similar intraerythrocytic growth patterns in mice. We carried out in vitro radiolabeling of heme in Pb-infected mouse reticulocytes and Plasmodium falciparum-infected human RBCs using [4-(14)C] aminolevulinic acid (ALA). We found that the parasites incorporated both host hemoglobin-heme and parasite-synthesized heme into hemozoin and mitochondrial cytochromes. The similar fates of the two heme sources suggest that they may serve as backup mechanisms to provide heme in the intraerythrocytic stages. Nevertheless, the de novo pathway is absolutely essential for parasite development in the mosquito and liver stages. PbKO parasites formed drastically reduced oocysts and did not form sporozoites in the salivary glands. Oocyst production in PbALASKO parasites recovered when mosquitoes received an ALA supplement. PbALASKO sporozoites could infect mice only when the mice received an ALA supplement. Our results indicate the potential for new therapeutic interventions targeting the heme-biosynthetic pathway in the parasite during the mosquito and liver stages.
Hamilton‐Jacobi Method for Mechanical Systems on Time Scales (2018)

This paper presents the Hamilton‐Jacobi method for integrating the equations of motion of mechanical systems on time scales. We give the criterion and four basic forms of canonical transformation on time scales. Also, various examples are given to illustrate the role played by a generating function in the canonical transformation. By choosing an appropriate generating function, we construct the Hamilton‐Jacobi equation on time scales and prove the Jacobi theorem on time scales. An example for an Emden‐Fowler type equation is discussed to show the application of the method.
The relational database layout to store ontology knowledge base (2012)

The Semantic Web has been recognized as the next generation web which aims at the automation, integration and reuse of data across different web applications. To realize the Semantic Web, the W3C has adopted standards and tools such as the Resource Description Framework (RDF) and Web Ontology Language (OWL). With the development of the Semantic Web, OWL ontology became a W3C recommended mechanism and state-of-the-art technology toward the ideal Semantic Web. Most semantic web applications developed for such an environment require the management of large amounts of semantic data which are stored in semantic models. This requirement has motivated the design of specialized repositories in order to store and manipulate semantic models. However, semantic repositories still have problems related to hierarchical relations in that OWL data cannot be directly represented by a relation table i.e. `a single table'. In this paper, we propose a new relational database layout to store an OWL knowledge base by considering the hierarchical relations.
Structure of mutagen nucleic acid complexes in solution. Proton chemical shifts in 9-aminoacridine complexes with dG-dC, dC-dG, and dA-dT-dG-dC-dA-dT (1978)

The influence of self-complementary oligodeoxynucleotides on the chemical shifts of protons of the mutagenic acridine dye 9-aminoacridine has been measured. Upfield shifts indicative of intercalative binding are found in the cases of dG-dC, dC-dG, and dA-dT-dG-dC-dA-dT but not in dA-dT. Geometries for the complexes that are compatibile with the chemical-shift data and the X-ray structure of the complex between ri5C-rG and 9-aminoacridine determined by Sakore et al. [Sakore, T.D., Jain, S.C., Tsai, C., and Sobell, H.M. (1977), Proc. Natl. Acad. Sci. U.S.A. 74, 188--192] can be identified using recent theoretical estimates of shifts induced by nucleotide bases.
A differential geometry approach for biomedical image processing (2002)

We show in this paper how simple considerations about bio-arrays images lead to a peak segmentation allowing the genes activity analysis. Bio-arrays images have a particular structure and the aim of the paper is to present a mathematical method allowing their automatic processing. The differential geometry approach used here can be also employed for other types of images presenting grey level peaks corresponding to a functional activity or to a chemical concentration. The mathematical method is based on elementary techniques of differential geometry and dynamical systems theory and provides a simple efficient algorithm when the peaks to segment are isolated.
BOLD MRI of human tumor oxygenation during carbogen breathing (2001)

An MRI method is described for demonstrating improved oxygenation of human tumors and normal tissues during carbogen inhalation (95% O2, 5% CO2). T2*-weighted gradient-echo imaging was performed before, during, and after carbogen breathing in 47 tumor patients and 13 male volunteers. Analysis of artifacts and signal intensity was performed. Thirty-six successful tumor examinations were obtained. Twenty showed significant whole-tumor signal increases (mean 21.0%, range 6.5-82.4%), and one decreased (-26.5 +/- 8.0%). Patterns of signal change were heterogeneous in responding tumors. Five of 13 normal prostate glands (four volunteers and nine patients with nonprostatic tumors) showed significant enhancement (mean 11.4%, range 8.4-14.0%). An increase in brain signal was seen in 11 of 13 assessable patients (mean 8.0 +/- 3.7%, range 5.0-11.7%). T2*-weighted tumor MRI during carbogen breathing is possible in humans. High failure rates occurred due to respiratory distress. Significant enhancement was seen in 56%, suggesting improved tissue oxygenation and blood flow, which could identify these patients as more likely to benefit from carbogen radiosensitization.