gebhart/patrepeval huggingface dataset:
Response to adversity: molecular control of gene activation following genotoxic stress. (1991)

DNA damage leads to the induction of a variety of genes in mammalian cells. In this article we summarize recent works aimed at examining the specificity of the response and elucidating the molecular mechanisms by which DNA damage effects changes in gene expression. The response to DNA damage is controlled primarily at the level of transcription. Some of the inducible genes are members of the class of "immediate early" genes and encode transcriptional activators. These genes are induced by activators of protein kinase C, and most DNA damage-inducible genes are also activated by phorbol esters. Phorbol ester-response elements within the 5' region of several of these genes have been shown to play a role in mediating their induction in response to DNA damage. However, DNA damage-inducible transcripts that are not sensitive to phorbol esters have also been identified, indicating that there are additional mechanisms involved in such responses. Induction of many of the DNA damage-inducible genes appears to be dependent, at least in part, on protein kinases. These findings demonstrate considerable overlap between signal transduction pathways mediating cellular proliferation and the response to DNA damage.
Differential detection of B virus and rhesus cytomegalovirus in rhesus macaques FN1 (2003)

Non-human primate herpesviruses establish and maintain a lifelong persistent infection in immunocompetent hosts in the absence of clinical signs of disease. A fundamental issue for understanding the natural history of non-human primate herpesviruses is whether the viruses are maintained in a truly latent state or one characterized by a low level of chronic expression. To address this issue, a real-time PCR assay was developed to quantify Cercopithecine herpesvirus type 1 (B virus) DNA in mucosal fluids of rhesus macaques. This assay was rapid, sensitive (10 genome copies) and specific for B virus obtained from multiple species of macaques. The shedding profile of B virus was compared to another endemic herpesvirus, rhesus cytomegalovirus (RhCMV), in colony-reared monkeys. Mucosal swabs or saliva samples were taken daily from two groups of seropositive monkeys undergoing either a stressful relocation (group 1) or daily chair restraint (group 2). B virus DNA was detected in mucosal fluids from four animals relocated during the breeding season (group 1) but not from 10 animals moved at other times of the year. No B virus DNA was detected in any group 2 monkey. In contrast, RhCMV DNA was detected in the majority of animals of both groups 1 and 2. Detection of B virus DNA shedding is a relatively rare event associated with the breeding season, while RhCMV DNA is persistently detected in mucosal fluids of most monkeys.
Identification of a Multifunctional Binding Site on Ubc9p Required for Smt3p Conjugation (2002)

Ubiquitin-like proteins (ub-lps) are conjugated by a conserved enzymatic pathway, involving ATP-dependent activation at the C terminus by an activating enzyme (E1) and formation of a thiolester intermediate with a conjugating enzyme (E2) prior to ligation to the target. Ubc9, the E2 for SUMO, synthesizes polymeric chains in the presence of its E1 and MgATP. To better understand conjugation of ub-lps, we have performed mutational analysis of Saccharomyces cerevisiae Ubc9p, which conjugates the SUMO family member Smt3p. We have identified Ubc9p surfaces involved in thiolester bond and Smt3p-Smt3p chain formation. The residues involved in thiolester bond formation map to a surface we show is the E1 binding site, and E2s for other ub-lps are likely to bind to their E1s at a homologous site. We also find that this same surface binds Smt3p. A mutation that impairs binding to E1 but not Smt3p impairs thiolester bond formation, suggesting that it is the E1 interaction at this site that is crucial. Interestingly, other E2s and their relatives also use this same surface for binding to ubiquitin, E3s, and other proteins, revealing this to be a multipurpose binding site and suggesting that the entire E1-E2-E3 pathway has coevolved for a given ub-lp.
Impact of Azacytidine on the Quality of Life of Patients With Myelodysplastic Syndrome Treated in a Randomized Phase III Trial: A Cancer and Leukemia Group B Study (2002)

Improved quality of life for patients treated with Aza C coupled with significantly greater treatment response and delayed time to transformation to acute myeloid leukemia or death compared with patients on supportive care (P <.001) establishes Aza C as an important treatment option for myelodysplastic syndrome.
High capacity WDM overlay on a passive optical network (1996)

An all-optical passive WDM high capacity overlay on a PON is proposed and experimentally verified, using AWGs and direct detection receivers. The unmodified outside fibre plant and the AWG can be supervised from the CO.
Topical Lomefloxacin 0.3% Twice Daily versus Tobramycin 0.3% in Acute Bacterial Conjunctivitis: A Multicenter Double-Blind Phase III Study (1999)

Both lomefloxacin 0.3% twice daily and tobramycin 0.3% administered 4 times daily were well tolerated and showed a high degree of clinical and microbiological efficacy in the treatment of acute bacterial conjunctivitis. Lomefloxacin caused less resistance than other antibiotics evaluated.
Functional identification of the fatty acid reductase components encoded in the luminescence operon of Vibrio fischeri (1985)

A clone of DNA, obtained from the luminescent bacterium Vibrio fischeri ATCC 7744 and inserted into pBR322, was found to express luminescence in Escherichia coli. Polypeptides involved in biosynthesis of the fatty aldehyde substrate for the light reaction were identified by fatty acid acylation of proteins synthesized in E. coli from the recombinant plasmid. The cloned region was similar to that reported for the V. fischeri MJ1 luminescence system (Engebrecht et al., Cell 32:773-781), except for some differences in endonuclease restriction sites and the requirement of a lower temperature for the expression of light in our cloned system. Fatty acid reductase activity could be detected in extracts of E. coli harboring the recombinant plasmid but not in extracts of the parental V. fischeri strain. Using in vivo labeling with [3H]tetradecanoic acid, we showed that the acylated polypeptides synthesized in the cloned system corresponded to the labeled polypeptides in V. fischeri (34, 42, and 54 kilodaltons) and that they could only be detected after induction of luminescence. These results provide direct evidence that the genes coding for the fatty acid reductase polypeptides are an integral part of the luminescence operon in the V. fischeri luminescence system.
Cone photopigment bleaching abnormalities in diabetes. (1987)

We have used a color-matching technique to obtain estimates of the optical density of cone photopigments as a function of retinal illuminance in patients with insulin-dependent diabetes mellitus (IDDM). We found that the half-bleach illuminance of some patients is abnormally high. That is, it takes more light to bleach an equivalent amount of photopigment in these patients. Since low illuminance color matches for these patients are normal, this implies that these patients have normal amounts of photopigment, but the photopigment is not bleaching normally. This result clearly points to abnormalities in the outer retina of these diabetic patients. The most likely causes of this abnormality are either decreases in the ability of the cones to absorb light, or an increased rate of regeneration of the cone photopigments.
Molecules Mimicking Smad1 Interacting with Hox Stimulate Bone Formation (2004)

Bone morphogenetic proteins (BMPs) induce osteoblast differentiation and bone formation. Smads, a group of functionally and structurally related intracellular effectors, mediate signaling initiated by BMPs and regulate cell definite commitment. Previously, we showed that Smad1 activates osteopontin and osteoprotegerin gene expression by dislodging Hoxc-8 from its DNA binding sites. A domain of Smad1, termed Smad1C, was characterized as interacting with Hoxc-8 and then crippling its DNA-binding ability. Ectopic expression of Smad1C is able to bypass BMP signaling in the induction of osteoblast differentiation and bone formation in vitro. To test the function of Smad1C on osteogenesis in vivo, we generated transgenic mice in which Smad1C expression was induced with doxycycline and localized in bone by using a tetracycline-inducible expression system (Tet-on) modified with a bone-specific gene promoter, type I collagen alpha1. The mice expressing Smad1C showed increased skeletal bone mineral density compared with their littermates. Bone histomorphometric analysis of mouse tibiae showed that Smad1C significantly increases trabecular bone area and length of trabecular surface covered with osteoid and up-regulates bone marker gene (OPN, Cbfa1, Col I alpha1, BSP, ALP) expression in vivo. Moreover, stromal cells isolated from mice expressing Smad1C displayed a higher potential for differentiating into osteoblasts than the other mice. These results indicate that Smad1C mimics BMPs in the induction of osteogenesis in vivo. Most important, using a high throughput screening assay based on mimicking Smad1C's displacement of Hoxc-8 binding to DNA, we identified chemical entities that exhibit bone anabolic activity in cell and bone organ cultures, suggesting the possibility that the compounds may be used as bone anabolic agents to treat bone pathologies.
Natural Killer Cells from Patients with Chronic Rhinosinusitis Have Impaired Effector Functions (2013)

Natural killer (NK) cells are multicompetent lymphocytes of the innate immune system that play a central role in host defense and immune regulation. Although increasing evidence suggests that innate immunity plays a key role in the pathogenesis of chronic rhinosinusitis (CRS), the role of NK cells in CRS has been poorly studied. This study aimed to characterize the peripheral blood NK cells from patients with CRS, and to compare the functions of these cells with those from non-CRS controls. The correlation between NK cell functional activity and prognosis was also assessed. Eighteen CRS patients and 19 healthy non-CRS controls were included. The patients with CRS were classified into two subgroups, namely a treatment-responsive group and recalcitrant group. NK cell degranulation was determined by measuring the cell surface expression of CD107a against 721.221 and K562 cells. Intracytoplasmic cytokine production was determined by flow cytometry. Compared to the controls, the NK cells of CRS group had an impaired ability to degranulate and to produce cytokines such as IFN-γ and TNF-α. The recalcitrant subgroup showed the most severe defects in NK cell effector functions. Moreover, the decreased NK cell functions in patients with CRS were associated with poor prognostic factors such as concomitant asthma and peripheral blood eosinophilia. NK cells, which were originally named for their ability to mediate spontaneous cytotoxicity towards diseased cells including infected cells, may play an important role in regulating the inflammatory process in CRS pathogenesis.
Intranasal Drug Delivery in Neuropsychiatry: Focus on Intranasal Ketamine for Refractory Depression (2015)

Intranasal drug delivery (INDD) systems offer a route to the brain that bypasses problems related to gastrointestinal absorption, first-pass metabolism, and the blood-brain barrier; onset of therapeutic action is rapid, and the inconvenience and discomfort of parenteral administration are avoided. INDD has found several applications in neuropsychiatry, such as to treat migraine, acute and chronic pain, Parkinson disease, disorders of cognition, autism, schizophrenia, social phobia, and depression. INDD has also been used to test experimental drugs, such as peptides, for neuropsychiatric indications; these drugs cannot easily be administered by other routes. This article examines the advantages and applications of INDD in neuropsychiatry; provides examples of test, experimental, and approved INDD treatments; and focuses especially on the potential of intranasal ketamine for the acute and maintenance therapy of refractory depression.
Phase diagram for the collective behavior of limit-cycle oscillators (1990)

We analyze a large dynamical system of limit-cycle oscillators with mean-field coupling and randomly distributed natural frequencies. Depending on the choice of coupling strength and the spread of natural frequencies, the system exhibits frequency locking, amplitude death, and incoherence, as well as novel unsteady behavior characterized by periodic, quasiperiodic, or chaotic evolution of the system's order parameter. The phase boundaries between several of these states are obtained analytically.
A Novel Highly Bioavailable Curcumin Formulation Improves Symptoms and Diagnostic Indicators in Rheumatoid Arthritis Patients: A Randomized, Double-Blind, Placebo-Controlled, Two-Dose, Three-Arm, and Parallel-Group Study (2017)

Rheumatoid arthritis (RA) is an autoimmune, chronic systemic inflammatory disorder. The long-term use of currently available drugs for the treatment of RA has many potential side effects. Natural phytonutrients may serve as alternative strategies for the safe and effective treatment of RA, and curcuminoids have been used in Ayurvedic medicine for the treatment of inflammatory conditions for centuries. In this study, a novel, highly bioavailable form of curcumin in a completely natural turmeric matrix was evaluated for its ability to improve the clinical symptoms of RA. A randomized, double-blind, placebo-controlled, three-arm, parallel-group study was conducted to evaluate the comparative efficacy of two different doses of curcumin with that of a placebo in active RA patients. Twelve patients in each group received placebo, 250 or 500 mg of the curcumin product twice daily for 90 days. The responses of the patients were assessed using the American College of Rheumatology (ACR) response, visual analog scale (VAS), C-reactive protein (CRP), Disease Activity Score 28 (DAS28), erythrocyte sedimentation rate (ESR), and rheumatoid factor (RF) values. RA patients who received the curcumin product at both low and high doses reported statistically significant changes in their clinical symptoms at the end of the study. These observations were confirmed by significant changes in ESR, CPR, and RF values in patients receiving the study product compared to baseline and placebo. The results indicate that this novel curcumin in a turmeric matrix acts as an analgesic and anti-inflammatory agent for the management of RA at a dose as low as 250 mg twice daily as evidenced by significant improvement in the ESR, CRP, VAS, RF, DAS28, and ACR responses compared to placebo. Both doses of the study product were well tolerated and without side effects.
c-myc and c-myb protein degradation: effect of metabolic inhibitors and heat shock. (1988)

The proteins encoded by both viral and cellular forms of the c-myc oncogene have been previously demonstrated to have exceptionally short in vivo half-lives. In this paper we report a comparative study on the parameters affecting turnover of nuclear oncoproteins c-myc, c-myb, and the rapidly metabolized cytoplasmic enzyme ornithine decarboxylase. The degradation of all three proteins required metabolic energy, did not result in production of cleavage intermediates, and did not involve lysosomes or ubiquitin. A five- to eightfold increase in the half-life of c-myc proteins, and a twofold increase in the half-life of c-myb proteins was detected after heat-shock treatment at 46 degrees C. In contrast, heat shock had no effect on the turnover of ornithine decarboxylase. Heat shock also had the effect of increasing the rate of c-myc protein synthesis twofold, whereas c-myb protein synthesis was decreased nearly fourfold. The increased stability and synthesis of c-myc proteins led to an overall increase in the total level of c-myc proteins in response to heat-shock treatment. Furthermore, treatments which reduced c-myc and c-myb protein turnover, such as heat shock and exposure to inhibitors of metabolic energy production, resulted in reduced detergent solubility of both proteins. The recovery from heat shock, as measured by increased turnover and solubility, was energy dependent and considerably more rapid in thermotolerant cells.
PAT1, a new member of the GRAS family, is involved in phytochrome A signal transduction (2000)

Light signaling via the phytochrome A (phyA) photoreceptor controls basic plant developmental processes including de-etiolation and hypocotyl elongation. We have identified a new Arabidopsis mutant, pat (phytochrome A signal transduction)1-1, which shows strongly reduced responses in continuous far-red light. Physiological and molecular data indicate that this mutant is disrupted at an early step of phyA signal transduction. The PAT1 gene encodes a cytoplasmic protein of 490 amino acids with sequence homologies to the plant-specific GRAS regulatory protein family. In the pat1-1 mutant, a T-DNA insertion introduces a premature stop codon, which likely results in the production of a truncated PAT1 protein of 341 amino acids. The semidominant phenotype of this mutant can be recapitulated by overexpression of an appropriately truncated PAT1 gene in the wild type. The results indicate that the truncated PAT1 protein acts in a dominant-negative fashion to inhibit phyA signaling.
Allergy to pistachio: crossre activity between pistachio nut and other Anacardiaceae (1995)

Pistachio nut contains several protein allergens able to trigger type I hypersensitivity reactions. These allergens can be found also in cashew nut and mango seed but not in mango pulp.
Recent developments in shallow-depth electrical and electrostatic prospecting using mobile arrays (1998)

Abstract Application of mobile electrical and electrostatic quadripoles during the past ten years has allowed a considerable increase in the size of the surveyed areas, together with keeping a high spatial resolution and a reduction of the total cost of a survey. Two new developments of towed arrays are illustrated here: (1) a pole-pole array pulled by the operator provides a lightweight solution for mapping large surfaces at a unique given depth of investigation, as shown by the prospection of the Roman-British city of Wroxeter: and (2) a multipole, multidepth system allows a 3-D investigation of the ground resistivity, as illustrated by the experiments undertaken on the test site of Garchy and on the archaeological site of Montbaron (Indre, France).
Killing of non-replicating Mycobacterium tuberculosis by 8-hydroxyquinoline (2010)

This study demonstrates that 8HQ has bactericidal activity of comparable potency against non-replicating and replicating Mtb, a property not observed for anti-infective agents currently approved for treatment of tuberculosis, and a very low FOR. Drugs with these properties are urgently needed to shorten the course of treatment for both active and latent tuberculosis.
Detecting Differential Item Functioning Using Logistic Regression Procedures (1990)

A logistic regression model for characterizing differential item functioning (DIF) between two groups is presented. A distinction is drawn between uniform and nonuniform DIF in terms of the parameters of the model. A statistic for testing the hypothesis of no DIF is developed. Through simulation studies, it is shown that the logistic regression procedure is more powerful than the Mantel‐Haenszel procedure for detecting nonuniform DIF and as powerful in detecting uniform DIF.
A Probabilistic Computing Approach of Attack Graph-Based Nodes in Large-Scale Network (2011)

To protect critical resources in networked environments, it is important to quantify the likelihood of potential multi- step attacks in attack graphs. Aimed at the problems that probabilistic incorrect computing caused by shared dependencies in nodes, a methodology for security risk analysis that is based on the model of attack graphs and the Common Vulnerability Scoring System (CVSS) was presented, and the problem of probabilistic incorrect computing was solved successfully by proposing the probabilistic computing approach of accurate calculation and approximate calculation, While ensuring the accuracy of the probability of attack graph-based nodes, quickly Calculated the probability of each node, which can be adapted to a large-scale network. Reasonableness and effectiveness of proposed method was verified in the simulation. Compared with the related research, our approach can be adapted to a more complex attack graph, and had good scalability.
Resolving the daratumumab interference with blood compatibility testing (2015)

DARA causes panreactivity in vitro by binding to CD38 on reagent RBCs. Treating reagent RBCs with DTT is a robust method to negate the DARA interference, enabling the safe provision of blood to DARA-treated patients. Because DTT denatures Kell antigens, K- units are provided to these patients.
Mechanically Enhancing Planar Lipid Bilayers with a Minimal Actin Cortex (2018)

All cells in all domains of life possess a cytoskeleton that provides mechanical resistance to deformation and general stability to the plasma membrane. Here, we utilize a two-dimensional scaffolding created by actin filaments to convey mechanical support upon relatively fragile planar bilayer membranes (black lipid membranes, BLMs). Robust biomembranes play a critical role in the development of protein nanopore sensor applications and might also prove helpful in ion-channel research. Our investigation utilizes a minimal actin cortex (MAC) that is formed by anchoring actin filaments to lipid membranes via a biotin-streptavidin-biotin bridge. We characterize the joined structure using various modes of optical microscopy, electrophysiology, and applied mechanical stress (including measurements of elastic modulus). Our findings show the resulting structure includes a thin supporting layer of actin. Electrical studies indicate that the integrity of the MAC-bilayer composite remains unchanged over the limits of our tests (i.e., hours to days). The actin filament structure can remain intact for months. Minimalistic layering of the actin support network produces an increase in the apparent elastic modulus of the MAC-derivatized bilayer by >100×, compared to unmodified BLMs. Furthermore, the resistance to applied stress improves with the number of actin layers, which can be cross-linked to arbitrary thicknesses, in principle. The weblike support structure retains the lateral fluidity of the BLM, maintains the high electrical resistance typical of traditional BLMs, enables relatively uninhibited molecular access to the lipid surface from bulk solution, and permits nanopore self-assembly and insertion in the bilayer. These interfacial features are highly desirable for ion-channel and nanopore sensing applications.