gebhart/patrepeval huggingface dataset:
Evolutionary Potential of (β/α)<sub>8</sub>-Barrels:  Functional Promiscuity Produced by Single Substitutions in the Enolase Superfamily (2003)

The members of the mechanistically diverse, (beta/alpha)(8)-barrel fold-containing enolase superfamily evolved from a common progenitor but catalyze different reactions using a conserved partial reaction. The molecular pathway for natural divergent evolution of function in the superfamily is unknown. We have identified single-site mutants of the (beta/alpha)(8)-barrel domains in both the l-Ala-d/l-Glu epimerase from Escherichia coli (AEE) and the muconate lactonizing enzyme II from Pseudomonas sp. P51 (MLE II) that catalyze the o-succinylbenzoate synthase (OSBS) reaction as well as the wild-type reaction. These enzymes are members of the MLE subgroup of the superfamily, share conserved lysines on opposite sides of their active sites, but catalyze acid- and base-mediated reactions with different mechanisms. A comparison of the structures of AEE and the OSBS from E. coli was used to design the D297G mutant of AEE; the E323G mutant of MLE II was isolated from directed evolution experiments. Although neither wild-type enzyme catalyzes the OSBS reaction, both mutants complement an E. coli OSBS auxotroph and have measurable levels of OSBS activity. The analogous mutations in the D297G mutant of AEE and the E323G mutant of MLE II are each located at the end of the eighth beta-strand of the (beta/alpha)(8)-barrel and alter the ability of AEE and MLE II to bind the substrate of the OSBS reaction. The substitutions relax the substrate specificity, thereby allowing catalysis of the mechanistically diverse OSBS reaction with the assistance of the active site lysines. The generation of functionally promiscuous and mechanistically diverse enzymes via single-amino acid substitutions likely mimics the natural divergent evolution of enzymatic activities and also highlights the utility of the (beta/alpha)(8)-barrel as a scaffold for new function.
Marked Increases in Resting-State MEG Gamma-Band Activity in Combat-Related Mild Traumatic Brain Injury (2019)

Combat-related mild traumatic brain injury (mTBI) is a leading cause of sustained impairments in military service members and veterans. Recent animal studies show that GABA-ergic parvalbumin-positive interneurons are susceptible to brain injury, with damage causing abnormal increases in spontaneous gamma-band (30-80 Hz) activity. We investigated spontaneous gamma activity in individuals with mTBI using high-resolution resting-state magnetoencephalography source imaging. Participants included 25 symptomatic individuals with chronic combat-related blast mTBI and 35 healthy controls with similar combat experiences. Compared with controls, gamma activity was markedly elevated in mTBI participants throughout frontal, parietal, temporal, and occipital cortices, whereas gamma activity was reduced in ventromedial prefrontal cortex. Across groups, greater gamma activity correlated with poorer performances on tests of executive functioning and visuospatial processing. Many neurocognitive associations, however, were partly driven by the higher incidence of mTBI participants with both higher gamma activity and poorer cognition, suggesting that expansive upregulation of gamma has negative repercussions for cognition particularly in mTBI. This is the first human study to demonstrate abnormal resting-state gamma activity in mTBI. These novel findings suggest the possibility that abnormal gamma activities may be a proxy for GABA-ergic interneuron dysfunction and a promising neuroimaging marker of insidious mild head injuries.
Online Learning of Noisy Data (2011)

We study online learning of linear and kernel-based predictors, when individual examples are corrupted by random noise, and both examples and noise type can be chosen adversarially and change over time. We begin with the setting where some auxiliary information on the noise distribution is provided, and we wish to learn predictors with respect to the squared loss. Depending on the auxiliary information, we show how one can learn linear and kernel-based predictors, using just 1 or 2 noisy copies of each example. We then turn to discuss a general setting where virtually nothing is known about the noise distribution, and one wishes to learn with respect to general losses and using linear and kernel-based predictors. We show how this can be achieved using a random, essentially constant number of noisy copies of each example. Allowing multiple copies cannot be avoided: Indeed, we show that the setting becomes impossible when only one noisy copy of each instance can be accessed. To obtain our results we introduce several novel techniques, some of which might be of independent interest.
Sex Steroids and Stem Cell Function (2008)

Gender dimorphisms exist in the pathogenesis of a variety of cardiovascular, cardiopulmonary, neurodegenerative, and endocrine disorders. Estrogens exert immense influence on myocardial remodeling following ischemic insult, partially through paracrine growth hormone production by bone marrow mesenchymal stem cells (MSCs) and endothelial progenitor cells. Estrogens also facilitate the mobilization of endothelial progenitor cells to the ischemic myocardium and enhance neovascularization at the ischemic border zone. Moreover, estrogens limit pathological myocardial remodeling through the inhibitory effects on the proliferation of the cardiac fibroblasts. Androgens also may stimulate endothelial progenitor cell migration from the bone marrow, yet the larger role of androgens in disease pathogenesis is not well characterized. The beneficial effects of sex steroids include alteration of lipid metabolism in preadipocytes, modulation of bone metabolism and skeletal maturation, and prevention of osteoporosis through their effects on osteogenic precursors. In an example of sex steroid-specific effects, neural stem cells exhibit enhanced proliferation in response to estrogens, whereas androgens mediate inhibitory effects on their proliferation. Although stem cells can offer significant therapeutic benefits in various cardiovascular, neurodegenerative, endocrine disorders, and disorders of bone metabolism, a greater understanding of sex hormones on diverse stem cell populations is required to improve their ultimate clinical efficacy. In this review, we focus on the effects of estrogen and testosterone on various stem and progenitor cell types, and their relevant intracellular mechanisms.
STRIATAL GLUTAMATERGIC DYSFUNCTION AND EXTRAPYRAMIDAL MOTOR BEHAVIOR (1996)

Experimental Therapeutics Branch, National Institute of Neurologic Disorders and Stroke, NIH, Bethesda, MD 20892, USA
Effect of long-term implanted nerve cuff electrodes on the electrophysiological properties of human sensory nerves. (1997)

During a long-term implantation (307 days) of a tripolar split cuff electrode around the palmar digital nerve to the radial side of the left index finger, branching off the median nerve in a medullary lesioned C6 patient, the physiological state of the nerve was intensively monitored. The resulting sensory nerve action potential (SNAP) amplitude was recorded, using both near-nerve electrodes and the implanted cuff electrode. The SNAP amplitude declined within 10 days to approximately 50% of the first SNAP cuff amplitude measured on Day 2 after implantation and recovered to the initial amplitude within 3 months. The SNAP amplitude measurements made with near-nerve electrodes were consistent with the cuff results; the SNAP conduction velocity (CV) recorded by the near-nerve electrodes and the cuff electrode was constant during the whole implantation period. This is in agreement with the results from two other patients: one with a cuff implanted around the sural nerve, and the other with a cuff implanted around a branch of the tibial nerve. These results and animals studies show that the cuff electrode is an electrically stable neural-electrical transducer.
The c- <i>myc</i> Insulator Element and Matrix Attachment Regions Definethe c- <i>myc</i> ChromosomalDomain (2003)

Insulator elements and matrix attachment regions are essential for the organization of genetic information within the nucleus. By comparing the pattern of histone modifications at the mouse and human c-myc alleles, we identified an evolutionarily conserved boundary at which the c-myc transcription unit is separated from the flanking condensed chromatin enriched in lysine 9-methylated histone H3. This region harbors the c-myc insulator element (MINE), which contains at least two physically separable, functional activities: enhancer-blocking activity and barrier activity. The enhancer-blocking activity is mediated by CTCF. Chromatin immunoprecipitation assays demonstrate that CTCF is constitutively bound at the insulator and at the promoter region independent of the transcriptional status of c-myc. This result supports an architectural role of CTCF rather than a regulatory role in transcription. An additional higher-order nuclear organization of the c-myc locus is provided by matrix attachment regions (MARs) that define a domain larger than 160 kb. The MARs of the c-myc domain do not act to prevent the association of flanking regions with lysine 9-methylated histones, suggesting that they do not function as barrier elements.
Inductive Logic Programming: Techniques and Applications (1993)

Part 1 Empirical inductive logic programming: introduction empirical ILP systems - an overview LINUS - using attribute-value learners in an ILP framework experiments in learning relations with LINUS ILP as search for program clauses. Part 2 Learning relations from imperfect data: handling imperfect data in ILP using heuristics to handle noise in ILP mFOIL - extending noise-handling in FOIL experiments in learning relations from noisy examples. Part 3 Applications of inductive logic programming: learning rules for early diagnosis of rheumatic diseases finite element mesh design an overview of selected ILP applications.
<title>Use of the wavelet transform for signal detection</title> (1993)

In this paper, the wavelet transform is used for the purpose of noise reduction and signal enhancement in order to aid in the detection of randomly occurring short duration signals in noisy environments with signal to noise ratios of about -30 dB. The noise is characterized as being additive and consists of correlated interference as well as Gaussian noise. Such problems are encountered in many applications, such as health diagnostics (e.g. electrocardiograms, echo-cardiograms and electroencephalograms), underwater acoustics and geophysical applications where a signature signal passes through multiple media. The wavelet transform, with its basis functions localized both in time and frequency, provides the user with a signal representation suitable for detection purposes. Following the introduction, a brief description of the problem with the characteristics of the signal to be detected and the noise that is present in the environment is given. Then, background information on the wavelet transform is presented. Finally, our results obtained by applying the wavelet transform to signal detection are shown.
Long Distance Kinematic Carrier-Phase Ambiguity Resolution Using a Simulated Reference Receiver Network (1997)

partment of Geomatics Engineering where he is responsi-ble for teaching and research related to positioning, navi-gation, and hydrography. He has been involved with GPS developments and applications since 1980. In order to perform the most precise relative positioning using GPS, it is necessary to determine the correct carrier-phase integer ambiguities. Unfortunately, this process be-comes increasingly difficult as the distance between the mobile and reference GPS receivers increases, due to the decorrelation of some of the GPS errors with distance. This results in a practical limit on the distance over which carrier-phase ambiguity resolution can be performed. This is especially limiting in the case of single frequency carrier-phase ambiguity resolution, due to the short wavelength of
[DNA chip analysis of gene expression patterns in poorly-differentiated human stage I lung adenocarcinoma]. (2004)

Many different kinds of genes are possibly involved in the initiation and progression of human lung adenocarcinoma. cDNA chip technique might be a useful method in screening lung cancer implicated genes.
ChemInform Abstract: Stereoselectivity of C(3) Methylation and Aldol Condensation of Camphor and Derivatives. (1991)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Corticospinal Motor Neurons Are Susceptible to Increased ER Stress and Display Profound Degeneration in the Absence of UCHL1 Function (2015)

Corticospinal motor neurons (CSMN) receive, integrate, and relay cerebral cortex's input toward spinal targets to initiate and modulate voluntary movement. CSMN degeneration is central for numerous motor neuron disorders and neurodegenerative diseases. Previously, 5 patients with mutations in the ubiquitin carboxy-terminal hydrolase-L1 (UCHL1) gene were reported to have neurodegeneration and motor neuron dysfunction with upper motor neuron involvement. To investigate the role of UCHL1 on CSMN health and stability, we used both in vivo and in vitro approaches, and took advantage of the Uchl1(nm3419) (UCHL1(-/-)) mice, which lack all UCHL1 function. We report a unique role of UCHL1 in maintaining CSMN viability and cellular integrity. CSMN show early, selective, progressive, and profound cell loss in the absence of UCHL1. CSMN degeneration, evident even at pre-symptomatic stages by disintegration of the apical dendrite and spine loss, is mediated via increased ER stress. These findings bring a novel understanding to the basis of CSMN vulnerability, and suggest UCHL1(-/-) mice as a tool to study CSMN pathology.
Mapping design knowledge from multiple representations (2002)

The requirements and specifications documents which initiate and control design and development projects typically use a variety of formal and informal notational systems. The goal of the research reported is to automatically interpret requirement documents expressed in a variety of notations and to integrate the interpretations in order to support requirements analysis and synthesis from them. Because the source notations include natural language, a form of semantic net called conceptual graphs is adopted as the intermediate knowledge representation for expressing interpretations and integrating them. The focus is to describe the interpretation or mapping of a few requirements notations to conceptual graphs, and to indicate the process of joining these interpretations.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
The effect of adding PTH(1–84) to conventional treatment of hypoparathyroidism: A randomized, placebo-controlled study (2011)

In hypoparathyroidism, plasma parathyroid hormone (PTH) levels are inadequate to maintain plasma calcium concentration within the reference range. On conventional treatment with calcium supplements and active vitamin D analogues, bone turnover is abnormally low, and BMD is markedly increased. We aimed to study the effects of PTH-replacement therapy (PTH-RT) on calcium-phosphate homeostasis and BMD. In a double-blind design, we randomized 62 patients with hypoparathyroidism to daily treatment with PTH(1-84) 100 µg or similar placebo for 24 weeks as add-on therapy to conventional treatment. Compared with placebo, patients on PTH(1-84) reduced their daily dose of calcium and active vitamin D significantly by 75% and 73%, respectively, without developing hypocalcemia. However, hypercalcemia occurred frequently during the downtitration of calcium and active vitamin D. Plasma phosphate and renal calcium and phosphate excretion did not change. Compared with placebo, PTH(1-84) treatment significantly increased plasma levels of bone-specific alkaline phosphatase (+226% ± 36%), osteocalcin (+807% ± 186%), N-terminal propeptide of procollagen 1 (P1NP; +1315% ± 330%), cross-linked C-telopeptide of type 1 collagen (CTX; +1209% ± 459%), and urinary cross-linked N-telopeptide of type 1 collagen (NTX; (+830% ± 165%), whereas BMD decreased at the hip (-1.59% ± 0.57%), lumbar spine (-1.76% ± 1.03%), and whole body (-1.26% ± 0.49%) but not at the forearm. In conclusion, the need for calcium and active vitamin D is reduced significantly during PTH-RT, whereas plasma calcium and phosphate levels are maintained within the physiologic range. In contrast to the effect of PTH(1-84) treatment in patients with osteoporosis, PTH-RT in hypoparathyroidism causes a decrease in BMD. This is most likely due to the marked increased bone turnover. Accordingly, PTH-RT counteracts the state of overmineralized bone and, during long-term treatment, may cause a more physiologic bone metabolism.
An assessment of the efficacy and safety of selenium and cobalt included in an anthelmintic for sheep (1988)

A trial was devised to assess whether the administration of selenium and cobalt together with the anthelmintic mebendazole (Ovitelmin S&C) was safe and could improve the supplies of selenium and cobalt for adult sheep fed a whole grain diet, low in both elements, which produced a steady decrease in blood glutathione peroxidase (GSHPx) and plasma vitamin B12 concentrations. Ovitelmin S&C, when given orally in a single dose as a suspension containing 0.34 mg selenium/ml, and 0.44 mg cobalt/ml (to provide 0.11 mg selenium and 0.15 mg cobalt/kg liveweight) significantly increased the GSHPx activity in blood. After a second dose given 28 days later the rate of change increased from 2.5 to 3.5 u/g haemoglobin/day. The responses in GSHPx were similar for a preparation which contained twice the concentration of selenium. Ovitelmin S&C increased the concentration of vitamin B12 in the plasma by about 1000 pg/ml for four to seven days after each dose and the increases were similar to those observed in sheep treated with an Ovitelmin preparation containing 45 times more cobalt (providing 6.7 mg cobalt/kg liveweight). After 63 days, liver vitamin B12 concentrations were 43 per cent higher in the cobalt treated than in the untreated groups (P less than 0.01) with no differences among the groups given cobalt. Neither adverse reactions nor signs of toxicity followed the administration of Ovitelmin S&C or Ovitelmin containing the higher concentrations of selenium and cobalt.
Dominance of Virus over Host Factors in Cross-Species Activation of Human Cytomegalovirus Early Gene Expression (2001)

Human cytomegalovirus (HCMV) exhibits a highly restricted host range. In this study, we sought to examine the relative significance of host and viral factors in activating early gene expression of the HCMV UL54 (DNA polymerase) promoter in murine cells. Appropriate activation of the UL54 promoter at early times is essential for viral DNA replication. To study how the HCMV UL54 promoter is activated in murine cells, a transgenesis system based on yeast artificial chromosomes (YACs) was established for HCMV. A 178-kb YAC, containing a subgenomic fragment of HCMV encompassing the majority of the unique long (UL) region, was constructed by homologous recombination in yeast. This HCMV YAC backbone is defective for viral growth and lacks the major immediate-early (IE) gene region, thus permitting the analysis of essential cis-acting sequences when complemented in trans. To quantitatively measure the level of gene expression, we generated HCMV YACs containing a luciferase reporter gene inserted downstream of either the UL54 promoter or, as a control for late gene expression, the UL86 promoter, which directs expression of the major capsid protein. To determine the early gene activation pathway, point mutations were introduced into the inverted repeat 1 (IR1) element of the UL54 promoter of the HCMV YAC. In the transgenesis experiments, HCMV YACs and derivatives generated in yeast were introduced into NIH 3T3 murine cells by polyethylene glycol-mediated fusion. We found that infection of YAC, but not plasmid, transgenic lines with HCMV was sufficient to fully recapitulate the UL54 expression program at early times of infection, indicating the importance of remote regulatory elements in influencing regulation of the UL54 promoter. Moreover, YACs containing a mutant IR1 in the UL54 promoter led to reduced ( approximately 30-fold) reporter gene expression levels, indicating that HCMV major IE gene activation of the UL54 promoter is fully permissive in murine cells. In comparison with HCMV, infection of YAC transgenic NIH 3T3 lines with murine cytomegalovirus (MCMV) resulted in lower (more than one order of magnitude) efficiency in activating UL54 early gene expression. MCMV is therefore not able to fully activate HCMV early gene expression, indicating the significance of virus over host determinants in the cross-species activation of key early gene promoters. Finally, these studies show that YAC transgenesis can be a useful tool in functional analysis of viral proteins and control of gene expression for large viral genomes.
Heterogeneity in Epidermal Basal Keratinocytes: Morphological and Functional Correlations (1982)

Two structurally distinct populations of basal keratinocytes, nonserrated and serrated, were observed in cynomolgus monkey and human palm epidermis. Anatomical location, fine structural features, and kinetic properties suggest that nonserrated cells represent a stem cell population and that serrated cells help anchor the epidermis to the dermis.
Peptide Szeto‑Schiller 31 ameliorates doxorubicin‑induced cardiotoxicity by inhibiting the activation of the p38 MAPK signaling pathway (2021)

Oxidative stress serves a key role in doxorubicin (DOX)‑induced cardiotoxicity. The peptide Szeto‑Schiller (SS)31 is an efficacious antioxidant with the capacity to reduce mitochondrial reactive oxygen species (ROS) levels and scavenge free radicals. Although SS31 is involved in the pathophysiological process of various cardiovascular diseases, the role of SS31 in DOX‑induced cardiotoxicity remains unclear. To explore the effects of SS31 in DOX‑induced cardiotoxicity, the present study first constructed DOX‑induced cardiotoxicity models, in which H9c2 cells were incubated with 1 µM DOX for 24 h and C57BL/6 mice were administered DOX (20 mg/kg cumulative dose). The results of various assays in these models demonstrated that SS31 exhibited a cardioprotective effect <i>in vitro</i> and <i>in vivo</i> by attenuating the level of ROS, stabilizing the mitochondrial membrane potential and ameliorating myocardial apoptosis as well as fibrosis following treatment with DOX. Mechanistically, the results of the present study revealed that the p38 MAPK signaling pathway was inhibited by SS31 in DOX‑treated H9c2 cells, which was associated with the cardioprotective function of SS31. In addition, P79350, a selective agonist of p38 MAPK, reversed the protective effects of SS31. Taken together, these results demonstrated the effects of SS31 on ameliorating DOX‑induced cardiotoxicity and indicated its potential as a drug for the treatment of DOX‑induced cardiotoxicity.