gebhart/patrepeval huggingface dataset:
Cytosolic Alkalinization Increases Stress-activated Protein Kinase/c-Jun NH2-terminal Kinase (SAPK/JNK) Activity and p38 Mitogen-activated Protein Kinase Activity by a Calcium-independent Mechanism (1997)

Stress-activated protein kinases (SAPK) are stimulated by a variety of agents and conditions that also activate the Na+/H+ exchanger (NHE). Activation of the exchanger results in a rapid increase in intracellular pH (pHi), raising the possibility that cytosolic alkalinization may contribute to SAPK activation. This hypothesis was tested by manipulating the pHi of U937 cells using permeant weak bases. Three different bases increased pHi and caused a 4-12-fold increase in SAPK activity with a time course that paralleled intracellular alkalinization. p38, a related stress kinase, was also stimulated by the weak bases. Stimulation of the stress kinases was not accompanied by changes in cytosolic free calcium nor was the activation of SAPK achieved when calcium was elevated by thapsigargin or calcium ionophores. Weak bases not only alter the pH of the cytosol but also alkalinize endomembrane compartments such as endosomes and lysosomes. However, the latter do not appear to mediate the stimulation of SAPK, since neither bafilomycin A1 nor desipramine, agents that neutralize acidic endomembrane compartments, activated the kinase. Because hyperosmolarity acutely activates the NHE, we considered whether the resulting cytosolic alkalinization mediates the activation of SAPK upon cell shrinkage. The addition of amiloride or the omission of Na+, which were verified to inhibit NHE, did not prevent the osmotically induced activation of SAPK. We conclude that cytosolic alkalinization increases the activity of SAPK and p38 by a calcium-independent mechanism that does not involve acidic intracellular organelles. In addition, even though cell shrinkage is accompanied by alkalinization due to the activation of NHE, the increased pHi is not the main cause of the observed stimulation of SAPK upon hyperosmotic challenge.
Localized Soil Management in Fertilizer Injection Zone to Reduce Nitrate Leaching (1998)

Abstract Nitrogen fertilization of row crops in humid regions can result in leaching of NO 3 , which represents an inefficient use of resources and may result in environmental degradation. A localized compaction and doming (LCD) fertilizer injector was developed to alter the physical properties of soil surrounding knife‐injected N. Injection by LCD includes smearing macropores below the injection slot, formation of a localized compacted soil layer over the injected N, and formation of a surface dome to cover the compacted soil layer and the fertilizer band. The LCD injector was tested, along with a conventional knife injector (without a covering disk), to evaluate its effect on leaching by determining NO 3 and Br tracer redistribution after NO 3 fertilizer injection. Chemical distributions were determined by intensive soil sampling to 0.8 m below the soil surface. In a second experiment, corn ( Zea mays L.) yield response to both N injectors was evaluated. Four fertilization rates (67, 112, 157, and 202 kg N ha −1 of UAN [urea‐ammonium nitrate]) were used to define yield response. During seasons when rainfall was below average, neither NO 3 redistribution nor crop yield showed a response to fertilizer injection technique. During a growing season with above‐average rainfall, 26 kg ha −1 more NO 3 and 25 kg ha −1 more Br remained in the top 0.8 m of soil when LCD‐injected. LCD injection increased crop yield approximately 0.48 Mg ha −1 over injection by the conventional knife method during an above‐average rainfall season, indicating that one‐fifth of the conventional knife‐applied N was lost prior to crop uptake during the wet year. These findings suggest that the LCD injector may be effective at reducing leaching losses during growing seasons when rainfall is abundant.
Genetic Susceptibility, HIV Infection, and the Kidney (2007)

In recent years, the sequencing of mammalian and microbial genomes has provided the opportunity to study how genetic variation in the host and pathogen influence the course of infectious disease. In the case of HIV-1 infection, such studies have led to identification of key viral proteins that determine pathogenicity, immune evasion, or drug resistance. In addition, candidate gene association studies have uncovered a large number of host genetic variants that influence the outcome of infection and some organ-specific complications. HIV-associated nephropathy (HIVAN) is a pathologically distinct complication of HIV infection. Interindividual variability in incidence, skewed ethnic distribution, and familial aggregation of HIVAN with other forms of ESRD have suggested genetic susceptibility as a major contributing factor. This article reviews the host genetic factors that influence the course of HIV-1 infection and discusses murine models that have increased the understanding of HIVAN pathogenesis and demonstrated the role of genetic background on determination of disease.
Streptomycin and Misreading of the Genetic Code (1974)

Historical Background In 1961 we accidentally isolated a streptomycin-resistant auxotroph whose arginine requirement could be satisfied by streptomycin (Gorini, Gundersen and Burger 1961). It was shown a few years later (Gorini and Kataja 1964a), using the same streptomycin-resistant parent and by selecting for streptomycin dependence in minimal medium but not in broth, that a class of mutants defective in a number of unrelated metabolic pathways could be easily obtained. The members of this class share the property of “conditional streptomycin dependence (CSD).” It could be shown in extracts that the enzyme normally missing in the mutant was formed during growth in the presence of streptomycin. We suggested that streptomycin might induce mistakes in the transmission of information from DNA to protein, compensating for the effect of the mistake encoded in the mutant DNA. Such a mechanism is analogous to that of “informational suppression” (Gorini 1970), by which the effect of a mutation persists at the level of the gene but is suppressed at the level of translation. However, informational suppression is found to be the consequence of a mutation in one of the molecules involved in the translation process (most commonly in a tRNA), whereas suppression in the case of CSD mutants appeared to depend on the environment, i.e., the presence or absence of streptomycin in the growth medium. We have suggested the designation of “phenotypic suppression” for this streptomycin effect. If streptomycin produces phenotypic suppression by inducing mistakes in translation, then the drug could be expected to induce mistakes...
CD14 Modulates Inflammation-Driven Insulin Resistance (2011)

CD14 modulates adipose tissue inflammatory activity and insulin resistance.
A Clinical Trial of Injectable Testosterone Undecanoate as a Potential Male Contraceptive in Normal Chinese Men<sup>1</sup> (1999)

This is a pilot dose-finding study of spermatogenic suppression using testosterone undecanoate (TU) injections alone in normal Chinese men. Thirty-two healthy men were recruited. Volunteers underwent pretreatment evaluation, then a treatment period in which group I (n = 13) received 500 mg TU, group II (n = 12) received 1000 mg TU, and group III (n = 7) received placebo, respectively, at monthly intervals during the treatment period (or until azoospermia was achieved). Thereafter, they underwent a recovery period until all parameters returned to pretreatment levels. Eleven of 12 volunteers in the 500-mg TU group, and all volunteers in the 1000-mg TU group became azoospermic. Faster suppression of spermatogenesis was achieved in the 1000-mg TU group. Serum testosterone increased significantly in the higher dose group at weeks 8 and 12, but remained within the normal range. Mean serum LH and FSH were profoundly suppressed by both doses to undetectable levels at week 16. TU injections did not cause a significant change in high density lipoprotein cholesterol levels. No serious side-effects were found. We conclude that both dosages of TU can effectively, safely, and reversibly suppress spermatogenesis in normal Chinese men.
Video Image Bandwidth Reduction/Compressions Studies for Remotely Piloted Vehicles. (1976)

A laboratory research and simulation program was conducted to evaluate and demonstrate methods of reducing video bandwidth to improve anti-jam capability of television data links. Four laboratory parametric studies were conducted using a remotely piloted vehicle simulator to establish the relationships between video bandwidth reduction techniques and RPV operator target acquisition performance. Nine bandwidth reduction/compression systems were selected based on the results of the parametric studies and compared to a standard IV baseline system in a laboratory systems simulation. A recommended video bandwidth reduction compression system was selected based on the results of the systems simulation, and a hardware implementation analysis of the recommended system was performed.
Weighted performance index for objective evaluation of border detection methods in dermoscopy images (2010)

Experiments are performed on 55 high-resolution dermoscopy images. Using the union of four sets of dermatologist-drawn borders as the ground truth, weighted metrics of sensitivity, specificity, accuracy, precision, border error and similarity are evaluated. Then, the weighted performance index is constructed and used to optimize the parameters of the hybrid border detection method. The outcome of the optimization process, verified through statistical analysis, yields a higher degree of agreement between automatic borders and the ground truth, compared with using standard metrics only. Finally, the weighted performance index is used to evaluate five recently reported border detection methods.
3D Pose from 3 Corresponding Points Under Weak-Perspective Projection (1992)

Model-based object recognition commonly involves using a minimal set of matched model and image points to compute the pose of a model in image coordinates. This paper discusses how to compute the pose of a model from three corresponding points under ``weak-perspective'''' projection. A new solution to the problem is proposed which, like previous solutions, involves solving a biquadratic equation. Here the biquadratic is motivated geometrically, and its solutions are interpreted graphically. The final equations take a new form, which lead to a simple expression for the image position of any unmatched model point.
<i>Stored Program Controlled Network</i>: Prologue (1982)

The rapid introduction of electronic switching systems with Stored Program Control (SPC) has made possible the interconnection of the control processors by high-speed data links to provide common-channel interoffice signaling (CCIS). Not only does this permit higher-speed, lower-cost, more reliable setup of connections, but also the transfer of packets of information for more flexible call control. The papers in this issue describe the evolution of the SPC network concept since the introduction of CCIS in 1976 and the first new services which will exploit the power of this new network capability.
Meeting the crisis in computer science (1983)

Participants in the 1982 Snowbird Conference reassessed the problems in computer science education and recommended steps for improvement.
Ruthenium(II)-Catalyzed C–H Bond Activation and Functionalization (2012)

International audience
Dissection of complex protein dynamics in human thioredoxin (2007)

We report our direct study of complex protein dynamics in human thioredoxin by dissecting into elementary processes and determining their relevant time scales. By combining site-directed mutagenesis with femtosecond spectroscopy, we have distinguished four partly time-overlapped dynamical processes at the active site of thioredoxin. Using intrinsic tryptophan as a molecular probe and from mutation studies, we ascertained the negligible contribution to solvation by protein sidechains and observed that the hydration dynamics at the active site occur in 0.47-0.67 and 10.8-13.2 ps. With reduced and oxidized states, we determined the electron-transfer quenching dynamics between excited tryptophan and a nearby disulfide bond in 10-17.5 ps for three mutants. A robust dynamical process in 95-114 ps, present in both redox states and all mutants regardless of neighboring charged, polar, and hydrophobic residues around the probe, is attributed to the charge transfer reaction with its adjacent peptide bond. Site-directed mutations also revealed the electronic quenching dynamics by an aspartate residue at a hydrogen bond distance in 275-615 ps. The local rotational dynamics determined by the measurement of anisotropy changes with time unraveled a relatively rigid local configuration but implies that the protein fluctuates on the time scale of longer than nanoseconds. These results elucidate the temporal evolution of hydrating water motions, electron-transfer reactions, and local protein fluctuations at the active site, and show continuously synergistic dynamics of biological function over wide time scales.
Knowledge Base Completion via Coupled Path Ranking (2016)

Knowledge bases (KBs) are often greatly incomplete, necessitating a demand for KB completion. The path ranking algorithm (PRA) is one of the most promising approaches to this task. Previous work on PRA usually follows a single-task learning paradigm, building a prediction model for each relation independently with its own training data. It ignores meaningful associations among certain relations, and might not get enough training data for less frequent relations. This paper proposes a novel multi-task learning framework for PRA, referred to as coupled PRA (CPRA). It first devises an agglomerative clustering strategy to automatically discover relations that are highly correlated to each other, and then employs a multi-task learning strategy to effectively couple the prediction of such relations. As such, CPRA takes into account relation association and enables implicit data sharing among them. We empirically evaluate CPRA on benchmark data created from Freebase. Experimental results show that CPRA can effectively identify coherent clusters in which relations are highly correlated. By further coupling such relations, CPRA significantly outperforms PRA, in terms of both predictive accuracy and model interpretability.
Quantitative evaluation of hepatitis C virus RNA in patients with concurrent human immunodeficiency virus infections (1993)

Quantitation of the hepatitis C virus (HCV) provides a powerful epidemiologic and therapeutic method for the evaluation of infected patients. In this study semiquantitative reverse transcriptase polymerase chain reaction (PCR) is compared with a new branched DNA signal amplification methodology. Samples from HCV-infected patients as well as from human immunodeficiency virus-infected patients were evaluated. Reverse transcriptase PCR correlated well with the branched DNA assay (r = 0.7036, P < 0.05). HCV RNA was found to occur at significantly higher titers (P < 0.05) in patients coinfected with the human immunodeficiency virus compared with titers in those infected with HCV alone. Immune status as defined by the CD4+ count was not associated with the observed difference in viral titer.
Selection for Soluble Proteins via Fusion with Chloramphenicol Acetyltransferase (2003)

The low solubility of a protein is one of the most frequent impediments for its structural and functional analysis and, on a more practical aspect, for its application as an industrial enzyme. The reason for low solubility can lie in low conformational stability (1), in a high number of surface-exposed hydrophobic amino acids (2) or in certain structural features, such as membrane binding regions (3). By changing the amino acid sequence of these proteins, their solubility can be significantly improved (4,5). Hence a general method that can efficiently identify (i.e., select) more soluble protein variants from a large repertoire is very useful in evolving such proteins.
Suramin treatment for chronic active hepatitis B—toxic and ineffective (1987)

Suramin has recently been shown to inhibit the activity of the duck hepatitis B virus DNA polymerase (DHBV DNAp) in vitro. However, we found no demonstrable in vivo suppression of human hepatitis B virus DNA polymerase (HBV DNAp) activity in three male patients with severe chronic active hepatitis. Suramin treatment resulted in prolongation of the prothrombin time in all cases and a rise in bilirubin in two and it may have led to haemorrhage from oesophageal varices in one patient and to hepatic encephalopathy in another. Its use in chronic hepatitis is not recommended.
Physiological and Biochemical Basis of Clinical Liver Function Tests (2012)

Because of the complexity of liver function, one single test does not represent overall liver function. In addition to computed tomography volumetry, quantitative liver function tests should be used to determine whether a safe resection can be performed. Presently, (99m)Tc-mebrofenin hepatobiliary scintigraphy seems to be the most valuable quantitative liver function test, as it can measure multiple aspects of liver function in, specifically, the future remnant liver.
Passy‐muir tracheostomy speaking valve on ventilator‐dependent patients (1993)

Communication for handicapped ventilator-dependent patients is a problem, not only for the patient but also for the healthcare personnel. The inability of these patients to vocalize is a paramount problem in their care. This study evaluates the efficacy of a one-way speaking valve on ventilator-dependent patients and evaluates the resulting effectiveness of their speech. Fifteen ventilator-dependent patients were fitted with the one-way Passy-Muir Tracheostomy Speaking Valve and their communicative skills and ease of vocalization were evaluated. This clinical evaluation was done by the patient, a speech pathologist, two nurses in charge of the patient, and the patient's private physician. No complications were observed in any of the patients. All 15 patients showed marked improvement, not only in speech intelligibility but in speech flow, the elimination of speech hesitancy, and speech time. This ability to communicate enhanced the care given by the healthcare personnel. In conclusion, use of the Passy-Muir Tracheostomy Speaking Valve restored verbal communicative skills of ventilator-dependent patients, facilitated care, and greatly enhanced the mental outlook of these patients without observed complications.
Complementary Roles for Rpn11 and Ubp6 in Deubiquitination and Proteolysis by the Proteasome (2004)

Substrates destined for degradation by the 26 S proteasome are labeled with polyubiquitin chains. These chains can be dismantled by deubiquitinating enzymes (DUBs). A number of reports have identified different DUBs that can hydrolyze ubiquitin from substrates bound to the proteasome. We measured deubiquitination by both isolated lid and base-core particle subcomplexes, suggesting that at least two different DUBs are intrinsic components of 26 S proteasome holoenzymes. In agreement, we find that highly purified proteasomes contain both Rpn11 and Ubp6, situated within the lid and base subcomplexes, respectively. To study their relative contributions, we purified proteasomes from a mutant in the putative metalloprotease domain of Rpn11 and from a ubp6 null. Interestingly, in both preparations we observed slower deubiquitination rates, suggesting that Rpn11 and Ubp6 serve complementary roles. In accord, the double mutant is synthetically lethal. In contrast to WT proteasomes, proteasomes lacking the lid subcomplex or those purified from the rpn11 mutant are less sensitive to metal chelators, supporting the prediction that Rpn11 may be a metalloprotein. Treatment of proteasomes with ubiquitin-aldehyde or with cysteine modifiers also inhibited deubiquitination but simultaneously promoted degradation of a monoubiquitinated substrate along with the ubiquitin tag. Degradation is unique to 26 S proteasome holoenzymes; we could not detect degradation of a ubiquitinated protein by "lidless" proteasomes, although they were competent for deubiquitination. The fascinating observation that a single ubiquitin moiety is sufficient for targeting an otherwise stable substrate to proteasomes exposes how rapid deubiquitination of poorly ubiquitinated substrates may counteract degradation.
Information-theoretically Secure Key insulated encryption: Models, bounds and constructions (2004)

Computer systems are constantly under attack and illegal access is a constant threat which makes security even more critical. A system can be broken into and secret information, e.g. decryption key, may be exposed, resulting in a total break of the system. Recently, a new framework for the protection against such key exposure problem was suggested and was called, Key-Insulated Encryption (KIE). In our paper, we introduce a novel approach to key insulated cryptosystems that offers provable security without computational assumptions. For the model of Information-Theoretically Secure Key-Insulated Encryption (ISKIE), we show lower bounds on required memory sizes of user, trusted device and sender. Our bounds are all tight as our concrete construction of ISKIE achieves all the bounds. We also extend this concept further by adding an extra property so that any pair of users in the system is able to communicate with each other and still have the same security benefits as the existing KIE based on intractability assumptions. We called this, Dynamic and Mutual Key-Insulated Encryption (DMKIE), and concrete implementations of DMKIE will be shown as well. In the end, we discuss the relationship of DMKIE against Key Predistribution Schemes (KPS) and Broadcast Encryption Schemes (BES), that is, we show that DMKIE can be constructed from either KPS or BES.
Large-scale benchmarking reveals false discoveries and count transformation sensitivity in 16S rRNA gene amplicon data analysis methods used in microbiome studies (2016)

Our results, generalizable to datasets from different sequencing platforms, demonstrate how the choice of method considerably affects analysis outcome. Here, we give recommendations for tools that exhibit low false positive rates, have good retrieval power across effect sizes and case/control proportions, and have low sparsity bias. Result output from some commonly used methods should be interpreted with caution. We provide an easily extensible framework for benchmarking of new methods and future microbiome datasets.