gebhart/patrepeval huggingface dataset:
Antidepressants are a rational complementary therapy for the treatment of Alzheimer's disease (2010)

There is a high prevalence rate (30-50%) of Alzheimer's disease (AD) and depression comorbidity. Depression can be a risk factor for the development of AD or it can be developed secondary to the neurodegenerative process. There are numerous documented diagnosis and treatment challenges for the patients who suffer comorbidity between these two diseases. Meta analysis studies have provided evidence for the safety and efficacy of antidepressants in treatment of depression in AD patients. Preclinical and clinical studies show the positive role of chronic administration of selective serotonin reuptake inhibitor (SSRI) antidepressants in hindering the progression of the AD and improving patient performance. A number of clinical studies suggest a beneficial role of combinatorial therapies that pair antidepressants with FDA approved AD drugs. Preclinical studies also demonstrate a favorable effect of natural antidepressants for AD patients. Based on the preclinical studies there are a number of plausible antidepressants effects that may modulate the progression of AD. These effects include an increase in neurogenesis, improvement in learning and memory, elevation in the levels of neurotrophic factors and pCREB and a reduction of amyloid peptide burden. Based on this preclinical and clinical evidence, antidepressants represent a rational complimentary strategy for the treatment of AD patients with depression comorbidity.
Phorbol ester-induced U-937 differentiation: effects on integrin α5gene transcription (2000)

Lung injury is accompanied by increased deposition of fibronectin (FN) matrices. Activated monocytic cells recruited to sites of lung injury express integrin receptors for FN that mediate their interaction with this matrix. One such integrin, alpha(5)beta(1), mediates many of the biological effects of FN, and its expression may be important for immune cell function at sites of lung injury. Herein, we examine the expression of alpha(5)beta(1) in response to the tumor promoter phorbol 12-myristate 13-acetate (PMA) in the human promonocytic cell line U-937. We demonstrate that PMA enhanced the adherence of U-937 cells to FN by increasing the expression of both the alpha(5)- and beta(1)-subunit mRNAs and the surface expression of the protein. In U-937 cells transfected with an alpha(5) promoter-reporter gene, we found that PMA induced the transcription of the alpha(5) gene by acting on very specific promoter sequences other than activator protein-1 in a protein kinase C-dependent manner. Lipopolysaccharide had a similar effect. Modulation of alpha(5)beta(1) expression may be important for regulation of monocytic cell function in lung inflammation after injury.
Inhibition of Candida albicans adhesiveness to human buccal and vaginal cells by sub-inhibitory concentrations of rilopirox. (1995)

Candida albicans is an opportunistic dimorphic pathogenic yeast which is present on the human mucosal epithelial cell surface. Its adhesion is considered to be an important first step in colonization and in the subsequent symptomatic or asymptomatic infection of buccal or vaginal mucosa. Because the ability to adhere is an important element of the pathogenicity of Candida we investigated in this study the compared effects of sub-inhibitory concentrations (sub-MICs) of rilopirox (CAS 104153-37-9) with those of ciclopirox olamine (CAS 41621-49-2) in inhibiting Candida adhesion to human buccal (BEC) and vaginal cells (VEC). Rilopirox is a new hydroxypyridone antimycotic agent with strong activity, especially against Candida albicans. There was a significant reduction in the mean number of Candida adhering to both buccal and vaginal cells with up to 1/8 MIC rilopirox for buccal and 1/16 MIC for vaginal cells, while for ciclopirox olamine reduction was significant up to 1/16 MIC for buccal and 1/8 MIC for vaginal cells. There were no significant differences in the dose-effect curves for BEC and VEC with either rilopirox and ciclopirox olamine, but on a molar basis, rilopirox was more active than ciclopirox olamine. The present in-vitro results support the developmental concept of an oropharyngeal and vaginal preparation of rilopirox. It can be expected that even sub-inhibitory concentrations of rilopirox exert an important additional effect in the treatment of oral and vaginal candidosis by impairing the pathogenic adhesion process of the fungus.
Development of a multi-electrode array for spinal cord epidural stimulation to facilitate stepping and standing after a complete spinal cord injury in adult rats (2013)

Therefore the high density electrode array allows high spatial resolution and the ability to selectively activate different neural pathways within the lumbosacral region of the spinal cord to facilitate standing and stepping in adult spinal rats and provides the capability to evoke motor potentials and thus a means for assessing connectivity between sensory circuits and specific motor pools and muscles.
Biomarkers for the effects of cannabis and THC in healthy volunteers (2008)

An increasing number of novel therapeutic agents are targeted at cannabinoid receptors. Drug development programmes of new cannabinoid drugs may be facilitated by the identification of useful biomarkers. This systemic literature review aims to assess the usefulness of direct biomarkers for the effects of cannabis and tetrahydrocannabinol (THC) in healthy volunteers. One hundred and sixty-five useful articles were found that investigated the acute effects of cannabis or THC on the central nervous system (CNS) and heart rate in healthy volunteers. Three hundred and eighteen tests (or test variants) were grouped in test clusters and functional domains, to allow their evaluation as a useful biomarker and to study their dose-response effects. Cannabis/THC affected a wide range of CNS domains. In addition to heart rate, subjective effects were the most reliable biomarkers, showing significant responses to cannabis in almost all studies. Some CNS domains showed indications of depression at lower and stimulation at higher doses. Subjective effects and heart rate are currently the most reliable biomarkers to study the effect of cannabis. Cannabis affects most CNS domains, but too many different CNS tests are used to quantify the drug-response relationships reliably. Test standardization, particularly in motor and memory domains, may reveal additional biomarkers.
Neural Induction and Patterning in Mammalian Pluripotent Stem Cells (2011)

Embryonic stem (ES) cells are derived from the inner cell mass (ICM) of blastocyst stage embryos, while induced pluripotent stem (iPS) cells are generated from somatic cells through transient overexpression of defined transcription factors. When transplanted into a preimplantation embryo, ES cells and iPS cells can differentiate into any cell type, including germ cells. Moreover, they can grow in culture indefinitely while maintaining pluripotency. In vitro differentiation of ES cells and iPS cells recapitulates many aspects of in vivo embryogenesis. The acquisition of neural fates (neural induction) in ES cells can be controlled by bone morphogenetic protein (BMP), fibroblast growth factor (FGF), and Wnt signaling, while the production of specific neural cell types (neural patterning) can be controlled by exogenous patterning signals such as Wnt, BMP, Shh, FGF, and retinoic acid. In response to these signals, ES cells can differentiate into a wide range of neural cell types that correlate with their positions along the anterior-posterior and dorsal-ventral axes. ES cell and iPS cell culture systems will provide materials for cell replacement therapy, and can be used as in vitro models for disease and drug testing as well as development. Here we review spatiotemporal control of neural differentiation of mammalian pluripotent stem cells, with a special emphasis on the relationship between in vivo embryogenesis and in vitro ES cell differentiation. Retinal differentiation from ES cells and iPS cells is also outlined.
Improved binding and antitumor activity of a recombinant anti-erbB2 immunotoxin by disulfide stabilization of the Fv fragment (1994)

e23(dsFv)-PE38KDEL is a recombinant immunotoxin composed of the Fv region of anti-erbB2 monoclonal antibody e23 connected to a truncated form of Pseudomonas exotoxin (PE38KDEL), in which the inherently unstable Fv heterodimer (composed of VH and VL) is stabilized by a disulfide bond engineered between structurally conserved framework positions of VH and VL. We have now found that e23(dsFv)-PE38KDEL is considerably more cytotoxic to antigen-positive cell lines than the corresponding single-chain immunotoxin. The basis for the enhanced cytotoxic activity is that the e23 dsFv-immunotoxin binds to erbB2 with greater affinity than the single-chain counterpart. The dsFv-immunotoxin had 4-fold increased binding compared to the scFv and almost identical to the binding affinity of e23 Fab. e23(dsFv)-PE38KDEL was also considerably more stable at 37 degrees C than the single-chain immunotoxin. The therapeutic potential of the disulfide-stabilized immunotoxin was compared with its single-chain counterpart using two animal models of immunodeficient mice bearing subcutaneous tumor xenografts of human gastric tumor N87 cells or human A431 epidermoid carcinoma cells. The antitumor effect of e23(dsFv)-PE38KDEL was significantly better than that of the single-chain immunotoxin. e23(dsFv)-PE38KDEL caused complete regression of tumors at doses which caused no toxic effects in mice, whereas the single-chain immunotoxin did not cause complete regressions at the same doses.
Texture synthesis for digital painting (1984)

The problem of digital painting is considered from a signal processing viewpoint, and is reconsidered as a problem of directed texture synthesis. It is an important characteristic of natural texture that detail may be evident at many scales, and the detail at each scale may have distinct characteristics. A “sparse convolution” procedure for generating random textures with arbitrary spectral content is described. The capability of specifying the texture spectrum (and thus the amount of detail at each scale) is an improvement over stochastic texture synthesis processes which are scalebound or which have a prescribed 1/f spectrum. This spectral texture synthesis procedure provides the basis for a digital paint system which rivals the textural sophistication of traditional artistic media. Applications in terrain synthesis and texturing computer-rendered objects are also shown.
Tracking of User Position and Orientation by Stereo Measurement of Infrared Markers and Orientation Sensing (2004)

A real-time three-dimensional position and orientation tracking system is proposed for use with wearable augmented reality systems. The system combines infrared markers with a head-mounted stereo camera to detect the user's position, and an orientation sensor to measure the orientation of the user's head. An extended Kalman filter is employed to reduce triangulation and orientation error by integrating the signals acquired by multiple sensors. The system is evaluated through a series of experiments, and a navigation system implemented using the proposed scheme is presented. The accuracy of the system is shown to be sufficient to allow annotations and virtual objects to be overlaid on real scenes via a head-mounted display without confusion.
Cdx2 is essential for axial elongation in mouse development (2004)

Inactivation of Cdx2 leads to preimplantation embryonic lethality. Rescue of the implantation defect by tetraploid fusion established that Cdx2 is necessary for trophoblastic development, vasculogenesis in the yolk sac mesoderm, allantoic growth, and chorioallantoic fusion. "Rescued" Cdx2 mutants die at late gastrulation stages because of failure of placental development. Cdx2 is also needed for the completion of the normal process of gastrulation and tail bud elongation. Presegmental paraxial mesoderm is severely restricted in amount and somites posterior to somite 5 are abnormal. The Cdx2 mutation, like mutations impairing Wnt and Fgf signaling, causes posterior truncations and disturbs axial patterning of the embryonic structures, indicated by changes in the Hox expression domains. The gene appears to be important in the integration of the pathways controlling embryonic axial elongation, and anterior-posterior patterning.
Enhanced Survival of the Cyanobacterium Oscillatoria terebriformis in Darkness under Anaerobic Conditions (1987)

Oscillatoria terebriformis, a thermophilic cyanobacterium, maintained viability in darkness under anaerobic conditions by fermenting exogenous glucose or fructose to lactic acid. The time period of survival was greatly extended when the environmental redox potential was lowered by the addition of sodium thioglycolate or titanium(III) citrate. When exposed to aerobic conditions in darkness, many trichomes underwent lysis in 6 h, and death of all cells occurred in 2 to 3 days. The endogenous aerobic respiration rate was high, and the limited dark aerobic survival period appeared to be due to depletion of stored glycogen. Fructose or glucose did not support or increase aerobic respiration in darkness or lengthen aerobic survival time. Enhanced survival of O. terebriformis in darkness under anaerobic, reducing conditions correlates well with the natural nighttime position of this species within sulfide-rich microbial mats associated with hot springs of western North America.
COMPACT PROTON AND CARBON ION SYNCHROTRONS FOR RADIATION THERAPY (2002)

A compact proton and carbon ion synchrotron development program is approved in 2001 to promote the advanced radiation treatment by developing a suitable medical accelerator adopting new technologies. They depend on the high magnetic field to make the ring as small as possible. The maximum proton (carbon ion) energy is 200 MeV (300 MeV/u) with the circumference of 12 m (16m) at the maximum dipole field of 3 T (4 T). Main concerns of this manuscript are the development of a high field magnet with a uniform field distribution and a short high voltage broadband RF cavity. Three dimensional transient field calculations were carried out under the pulse excitation with the rise time of 5 ms and the beam behaviours are also simulated under the sextupole error field in the dipoles. Beam optics and transverse beam stability studies are presented including the lattice design.
Defective transcription of the IL-2 gene is associated with impaired expression of c-Fos, FosB, and JunB in anergic T helper 1 cells (1996)

Anergic CD4+ Th cells do not produce IL-2 when challenged with Ag-pulsed accessory cells because of a transcriptional defect. In this work, we report that these anergic T cells are defective in their ability to up-regulate protein binding and transactivation at two critical IL-2 DNA enhancer elements: NF-AT (nuclear factor of activated T cells; a sequence that binds a heterotrimeric NFATp, Fos, and Jun protein complex) and Activator Protein-1 (AP-1) (that binds Fos and Jun heterodimers). Western blot analysis of nuclear extracts showed that the impaired DNA-protein interactions in anergic T cells were associated with poor expression of the inducible AP-1 family members c-Fos, FosB, and JunB. However, the reduced expression of these proteins was not the result of a global TCR/CD3-signaling defect because CD3 cross-linking induced an equivalent increase in intracellular-free calcium ions, as well as NFATp dephosphorylation, translocation to the nucleus, and DNA binding in both normal and anergic T cells. Thus, defective IL-2 gene transcription appears to be due, at least in part, to a selective block in the expression of the AP-1 Fos and Jun family members in anergic T cells.
Photoluminescence of GaAs single quantum wells confined by short-period all-binary GaAs/AlAs superlattices (1984)

GaAs single quantum well heterostructures (SQWH’s) composed of all-binary AlAs/GaAs heterostructures by using AlAs/GaAs short-period superlattices (SPS) instead of the ternary alloy as cladding layers were grown by molecular beam epitaxy at low substrate temperature. Detailed photoluminescence measurements at 2 K reveal that these SPS confined SQWH’s exhibit superior luminescence properties. They are therefore very attractive for application in new optoelectronic devices. The SPS configuration has a strong effect on the energy of the confined particle transition because of the fully interacting quantum well system.
Acute myeloid leukemia with DNMT3A mutations (2013)

Acute myeloid leukemia (AML), a type of blood cancer, is characterized by an increase in the number of abnormal white blood cells in the bone marrow, frequently causing hematopoietic insufficiency. It is a heterogeneous disease featuring cytogenetic aberrations, recurrent somatic mutations and alterations in gene expression. DNA (cytosine-5-)-methyltransferase 3 alpha (DNMT3A) is closely associated with epigenetic modifications in mammalian development and disease. More recent studies have identified recurrent somatic mutations in DNMT3A in AML, most of which are heterozygous. The DNMT3A R882 codon is a mutational hotspot. The frequency of DNMT3A mutations varies among different countries, but mutations have been found to be associated with cytogenetics, age, white blood cell (WBC) count, prognosis and response of patients to chemotherapy. The normal function of DNMT3A can be disrupted by these mutations, which subsequently results in an abnormality of epigenetic modification. These data suggest that mutations in the DNMT3A gene represent a novel class of mutations in AML with distinct biological and clinical features. Further studies are needed to elucidate the exact molecular mechanism and function of DNMT3A mutations in leukemogenesis.
Mesoporous Carbons With Self-Assembled High-Activity Surfaces (PREPRINT) (2006)

There is great interest in the development of improved mesoporous carbons as sorbents, catalyst supports, capacitors, and electrodes. The optimization of mesoporous carbons typically focuses on the control of pore structure, surface area, and the number and type of surface functional groups. A porous carbon property that is often overlooked is the crystal structure of the carbon in the immediate vicinity of the internal surfaces. This interfacial structure provides the carbon "platform" for subsequent surface treatment and can thus determine the number of potential active sites for functionalization and influence the final polarity, surface charge density, and/or chemisorptive activity of the carbon material.
Noncovalent Monolayer Modification of Graphene Using Pyrene and Cyclodextrin Receptors for Chemical Sensing (2018)

Surprisingly few details have been reported in the literature that help the experimentalist to determine the conditions necessary for the preparation of self-assembled monolayers on graphene with a high surface coverage. With a view to graphene-based sensing arrays and devices and, in particular, in view of graphene-based varactors for gas sensing, graphene was modified in this work by the π–π interaction-driven self-assembly of 10 pyrene and cyclodextrin derivatives from solution. The receptor compounds were pyrene, pyrene derivatives with hydroxyl, carboxyl, ester, ammonium, amino, diethylamino, and boronic acid groups, and perbenzylated α-, β-, and γ-cyclodextrins. Adsorption of these compounds onto graphene was quantified by contact-angle measurements and X-ray photoelectron spectroscopy. Data thus obtained were fitted with the Langmuir adsorption model to determine the equilibrium constants for surface adsorption and the concentrations of self-assembly solutions needed to form dense monolayers on graphene. The equilibrium constants of all pyrene derivatives fell into the range from 103.4 to 104.6 M–1. For the perbenzylated α-, β-, and γ-cyclodextrins, the equilibrium constants are 103.24, 102.97, and 102.95 M–1, respectively. Monolayers of 1-pyrenemethylammonium chloride on graphene were confirmed to be stable under heating to 100 °C in a high vacuum (2 × 10–5 Torr).
Molecular organization of the postsynaptic specialization (2001)

A specific set of molecules including glutamate receptors is targeted to the postsynaptic specialization of excitatory synapses in the brain, gathering in a structure known as the postsynaptic density (PSD). Synaptic targeting of glutamate receptors depends on interactions between the C-terminal tails of receptor subunits and specific PDZ domain-containing scaffold proteins in the PSD. These scaffold proteins assemble a specialized protein complex around each class of glutamate receptor that functions in signal transduction, cytoskeletal anchoring, and trafficking of the receptors. Among the glutamate receptor subtypes, the N-methyl-d-aspartate receptor is relatively stably integrated in the PSD, whereas the alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor moves in and out of the postsynaptic membrane in highly dynamic fashion. The distinctive cell biological behaviors of N-methyl-d-aspartate and alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptors can be explained by their differential interactions with cytoplasmic proteins.
Partial Gene Sequences for the A Subunit of Methyl-Coenzyme M Reductase (mcrI) as a Phylogenetic Tool for the Family Methanosarcinaceae (1995)

Representatives of the family Methanosarcinaceae were analyzed phylogenetically by comparing partial sequences of their methyl-coenzyme M reductase (mcrI) genes. A 490-bp fragment from the A subunit of the gene was selected, amplified by the PCR, cloned, and sequenced for each of 25 strains belonging to the Methanosarcinaceae. The sequences obtained were aligned with the corresponding portions of five previously published sequences, and all of the sequences were compared to determine phylogenetic distances by Fitch distance matrix methods. We prepared analogous trees based on 16S rRNA sequences; these trees corresponded closely to the mcrI trees, although the mcrI sequences of pairs of organisms had 3.01 +/- 0.541 times more changes than the respective pairs of 16S rRNA sequences, suggesting that the mcrI fragment evolved about three times more rapidly than the 16S rRNA gene. The qualitative similarity of the mcrI and 16S rRNA trees suggests that transfer of genetic information between dissimilar organisms has not significantly affected these sequences, although we found inconsistencies between some mcrI distances that we measured and and previously published DNA reassociation data. It is unlikely that multiple mcrI isogenes were present in the organisms that we examined, because we found no major discrepancies in multiple determinations of mcrI sequences from the same organism. Our primers for the PCR also match analogous sites in the previously published mcrII sequences, but all of the sequences that we obtained from members of the Methanosarcinaceae were more closely related to mcrI sequences than to mcrII sequences, suggesting that members of the Methanosarcinaceae do not have distinct mcrII genes.