gebhart/patrepeval huggingface dataset:
Glutamatergic Mechanisms in Schizophrenia (2002)

Schizophrenia is a chronic, severely disabling brain disorder with symptomatic onset in early adulthood. Typical antipsychotic medications that block dopamine D2 receptors are most effective in treating the psychosis but have limited effects on the negative symptoms and cognitive impairments. Considerable research has demonstrated that noncompetitive NMDA receptor antagonists, the dissociative anaesthetic like phencyclidine and ketamine, reproduce the cardinal symptomatic features of schizophrenia. Postmortem studies reveal variable alterations in glutamate receptors and their modulators in schizophrenia. Several clinical trials indicate agents that enhance NMDA receptor function via the glycine modulatory site reduce negative and variably improve cognitive function in schizophrenics receiving typical antipsychotics. Thus, hypofunction of a subpopulation of cortico-limbic NMDA receptors may participate in the pathophysiology of schizophrenia.
The Neurobiology of Consolidations, Or, How Stable is the Engram? (2004)

Consolidation is the progressive postacquisition stabilization of long-term memory. The term is commonly used to refer to two types of processes: synaptic consolidation, which is accomplished within the first minutes to hours after learning and occurs in all memory systems studied so far; and system consolidation, which takes much longer, and in which memories that are initially dependent upon the hippocampus undergo reorganization and may become hippocampal-independent. The textbook account of consolidation is that for any item in memory, consolidation starts and ends just once. Recently, a heated debate has been revitalized on whether this is indeed the case, or, alternatively, whether memories become labile and must undergo some form of renewed consolidation every time they are activated. This debate focuses attention on fundamental issues concerning the nature of the memory trace, its maturation, persistence, retrievability, and modifiability.
Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina) (2008)

Trichoderma reesei is the main industrial source of cellulases and hemicellulases used to depolymerize biomass to simple sugars that are converted to chemical intermediates and biofuels, such as ethanol. We assembled 89 scaffolds (sets of ordered and oriented contigs) to generate 34 Mbp of nearly contiguous T. reesei genome sequence comprising 9,129 predicted gene models. Unexpectedly, considering the industrial utility and effectiveness of the carbohydrate-active enzymes of T. reesei, its genome encodes fewer cellulases and hemicellulases than any other sequenced fungus able to hydrolyze plant cell wall polysaccharides. Many T. reesei genes encoding carbohydrate-active enzymes are distributed nonrandomly in clusters that lie between regions of synteny with other Sordariomycetes. Numerous genes encoding biosynthetic pathways for secondary metabolites may promote survival of T. reesei in its competitive soil habitat, but genome analysis provided little mechanistic insight into its extraordinary capacity for protein secretion. Our analysis, coupled with the genome sequence data, provides a roadmap for constructing enhanced T. reesei strains for industrial applications such as biofuel production.
N-Oxidation of Epothilone A–C and O-Acyl Rearrangement to C-19- and C-21-Substituted Epothilones (1999)

A bothersome side reaction in the last step of a total synthesis of epothilone led to the formation of the thiazol-N-oxide 1. Obtained from epothilones prepared by fermentation, these biologically active N-oxides allow the extremely short synthesis of the highly active epothilones 2 with modified side chains by an O-acyl rearrangement.
Evidence of Limited Contributions for Intratumoral Steroidogenesis in Prostate Cancer (2010)

Androgen-deprivation therapy for prostate cancer (PC) eventually leads to castration-resistant PC (CRPC). Intratumoral androgen production might contribute to tumor progression despite suppressed serum androgen concentrations. In the present study, we investigated whether PC or CRPC tissue may be capable of intratumoral androgen synthesis. Steroidogenic enzyme mRNAs were quantified in hormonally manipulated human PC cell lines and xenografts as well as in human samples of normal prostate, locally confined and advanced PC, local nonmetastatic CRPC, and lymph node metastases. Overall, the majority of samples showed low or absent mRNA expression of steroidogenic enzymes required for de novo steroid synthesis. Simultaneous but low expression of the enzymes CYP17A1 and HSD3B1, essential for the synthesis of androgens from pregnenolone, could be detected in 19 of 88 patient samples. Of 19 CRPC tissues examined, only 5 samples expressed both enzymes. Enzymes that convert androstenedione to testosterone (AKR1C3) and testosterone to dihydrotestosterone (DHT; SRD5A1) were abundantly expressed. AKR1C3 expression was negatively regulated by androgens in the experimental models and was increased in CRPC samples. Expression of SRD5A1 was upregulated in locally advanced cancer, CRPC, and lymph node metastases. We concluded that intratumoral steroid biosynthesis contributes less than circulating adrenal androgens, implying that blocking androgen production and its intraprostatic conversion into DHT, such as via CYP17A1 inhibition, may represent favorable therapeutic options in patients with CRPC.
Characterization of the image-derived carotid artery input function using independent component analysis for the quantitation of [18F] fluorodeoxyglucose positron emission tomography images (2007)

We previously developed a noninvasive technique for the quantification of fluorodeoxyglucose (FDG) positron emission tomography (PET) images using an image-derived input function obtained from a manually drawn carotid artery region. Here, we investigate the use of independent component analysis (ICA) for more objective identification of the carotid artery and surrounding tissue regions. Using FDG PET data from 22 subjects, ICA was applied to an easily defined cubical region including the carotid artery and neighboring tissue. Carotid artery and tissue time activity curves and three venous samples were used to generate spillover and partial volume-corrected input functions and to calculate the parametric images of the cerebral metabolic rate for glucose (CMRgl). Different from a blood-sampling-free ICA approach, the results from our ICA approach are numerically well matched to those based on the arterial blood sampled input function. In fact, the ICA-derived input functions and CMRgl measurements were not only highly correlated (correlation coefficients >0.99) to, but also highly comparable (regression slopes between 0.92 and 1.09), with those generated using arterial blood sampling. Moreover, the reliability of the ICA-derived input function remained high despite variations in the location and size of the cubical region. The ICA procedure makes it possible to quantify FDG PET images in an objective and reproducible manner.
Treatment with α-Galactosylceramide Attenuates the Development of Bleomycin-Induced Pulmonary Fibrosis (2004)

Pulmonary fibrosis is an end-stage disorder for which efficacious therapeutic options are not readily available. Although its pathogenesis is poorly understood, pulmonary fibrosis occurs as a result of various inflammations. NKT cells modulate inflammation because of their ability to produce large amounts of cytokines by stimulation with their glycolipid ligand. In the present study, we investigated the effects of alpha-galactosylceramide (alpha-GalCer), a selective NKT cell ligand, on the development of bleomycin-induced pulmonary fibrosis. Treatment of mice with alpha-GalCer prolonged their survival under bleomycin administration by attenuating the development of pulmonary fibrosis. The protective effects of alpha-GalCer were associated with an increase in the pulmonary level of IFN-gamma and a decrease in the pulmonary level of fibrogenic cytokines such as TGF-beta and connective tissue growth factor. The initial pulmonary inflammation caused by bleomycin was also attenuated by alpha-GalCer with the reduction of the macrophage inflammatory protein-2 level. The protective effects of alpha-GalCer were markedly reduced in mice lacking NKT cells or as a result of treatment with anti-IFN-gamma Ab. These results suggest that alpha-GalCer suppresses bleomycin-induced acute pulmonary inflammation and thus attenuates the development of pulmonary fibrosis possibly by regulating several cytokine levels.
Blue Electroluminescence in Thin Films of Azomethin-Zinc Complexes (1993)

Organic electroluminescent (EL) cells with azomethin-zinc complexes as an emitting layer showed bright blue emission. A cell structure of [indium-tin-oxide (ITO)/hole transport layer/emitting layer/MgIn] was employed. The color was blue, and emission peaks were 458∼470 nm. High luminance exceeding 1000 cd/m 2 was obtained for the first time with an EL cell using a complex emitting material. The azomethin-zinc complexes exhibited good electron transport, as indicated by the high luminance obtained in two-layer EL cells.
Topography of Oxytocin and Vasopressin Neurons in the Forebrain of <i>Equus caballus:</i>Further Support of Proposed Evolutionary Relationships for Proopiomelanocortin, Oxytocin and Vasopressin Neurons (1989)

The present study describes the topography of immunoreactive (ir) oxytocin (OXY) and vasopressin (AVP) neurons in the forebrain of Equus caballus and the coexistence of ir proopiomelanocortin (POMC)-derived peptides in the same cells. These data are compared to those for other mammalian species and the possible significance of species variations is considered. As expected, magnocellular neurons of the equine hypothalamus, which contain ir OXY or AVP, have prominent discernible projections to the neurohypophysis. Further, as in other mammalian species, the field of ir OXY perikarya generally extends rostral and dorsal to groups of ir AVP cell bodies, and caudal projections from OXY neurons appear to be more numerous than ir AVP projections to the brainstem and/or spinal cord. Interestingly, however, the brain of E. caballus also contains: (1) perikarya staining for OXY in the arcuate nucleus, (2) ir AVP and OXY cell bodies in the suprachiasmatic nucleus, and (3) neurons in the supraoptic and paraventricular nuclei that stained for beta-endorphin but not for other posttranslational products of POMC or dynorphin. These results give further credence to the proposal that there is an evolutionary relationship between OXY-, AVP- and POMC-producing hypothalamic neurons. Whether or not species differences in peptide coexistence reflect functional differences in neuronal populations or species differences in residual genomic expression by these neuroendocrine cells warrants further investigation.
Sequence-Selective Interaction of the Minor-Groove Interstrand Cross-Linking Agent SJG-136 with Naked and Cellular DNA:  Footprinting and Enzyme Inhibition Studies (2005)

SJG-136 (3) is a novel pyrrolobenzodiazepine (PBD) dimer that is predicted from molecular models to bind in the minor groove of DNA and to form sequence-selective interstrand cross-links at 5'-Pu-GATC-Py-3' (Pu = purine; Py = pyrimidine) sites through covalent bonding between each PBD unit and guanines on opposing strands. Footprinting studies have confirmed that high-affinity adducts do form at 5'-G-GATC-C-3' sequences and that these can inhibit RNA polymerase in a sequence-selective manner. At higher concentrations of SJG-136, bands that migrate more slowly than one of the 5'-G-GATC-C-3' footprint sites show significantly reduced intensity, concomitant with the appearance of higher molecular weight material near the gel origin. This phenomenon is attributed to interstrand cross-linking at the 5'-G-GATC-C-3' site and is the first report of DNA footprinting being used to detect interstrand cross-linked adducts. The control dimer GD113 (4), of similar structure to SJG-136 but unable to cross-link DNA due to its C7/C7'-linkage rather than C8/C8'-linkage, neither produces footprints with the same DNA sequence nor blocks transcription at comparable concentrations. In addition to the two high-affinity 5'-G-GATC-C-3' footprints on the MS2 DNA sequence, other SJG-136 adducts of lower affinity are observed that can still block transcription but with lower efficiency. All these sites contain the 5'-GXXC-3' motif (where XX includes AG, TA, GC, CT, TT, GG, and TC) and represent less-favored cross-link sites. In time-course experiments, SJG-136 blocks transcription if incubated with a double-stranded DNA template before the transcription components are added; addition after transcription is initiated fails to elicit blockage. Single-strand ligation PCR studies on a sequence from the c-jun gene show that SJG-136 binds to 5'-GAAC-3'/5'-GTTC-3' (preferred) or 5'-GAGC-3'/5'-GCTC-3' sequences. Significantly, adducts are obtained at the same sequences following extraction of DNA from drug-treated K562 cells, confirming that the agent reaches the cellular genome and interacts with the DNA in a sequence-selective fashion. Finally, SJG-136 efficiently inhibits the action of restriction endonuclease BglII, which has a 5'-A-GATC-T-3' motif at its cleavage site.
Selective oxidation of methanol to methyl formate on catalysts of Au–Ag alloy nanoparticles supported on titania under UV irradiation (2014)

Au–Ag alloy nanoparticles on titania exhibit superior photocatalytic performance in selective oxidation of methanol to methyl formate.
Potential use of ipatropium bromide for the treatment of clozapine-induced hypersalivation: a preliminary report (2000)

Sialorrhea is reported by 31% of patients taking clozapine. Anticholinergic agents and adrenergic agonists are used for its treatment based on empirical evidence. In the present study, 10 patients who failed to respond to anticholinergic or adrenergic agents received intranasal ipatropium bromide (IPB) to minimize anticholinergic systemic absorption. Intranasal IPB was given to 10 patients for clozapine-induced sialorrhea who failed to respond to benztropine or clonidine. Pre-, post- and 6 month follow-up values were recorded on a single-item, 5-point Hypersalivation Rating Scale. The sign test was used for statistical comparison (P < 0.05). Eight patient reported initial improvement in sialorrhea values. Two patients reported no change and two patients discontinued IPB. At 6 months, six patients maintained improvement. Side-effects for IPB were minor. A significant trend was observed in the values pre- and post-treatment with IPB (P < 0.004). Improvement was maintained at 6 month follow-up (P < 0.008). This case series demonstrates the possible utility of intranasal IPB for clozapine-induced sialorrhea. Intranasal IPB lacks significant systemic anticholinergic effects when prescribed along with clozapine. This study shows only qualitative differences in salivation values and large controlled-comparative trials are needed.
Functional Outcome of Knee Articular Cartilage Repair in Adolescent Athletes (2005)

Treatment of full-thickness articular injuries of the knee in adolescent athletes with autologous chondrocyte transplantation yields a high rate of functional success at a mean follow-up of 47 months. The rate of return to demanding athletic activities is higher in cases in which the preoperative duration of symptoms is 12 months or less.
Decoding spoken words using local field potentials recorded from the cortical surface (2010)

Pathological conditions such as amyotrophic lateral sclerosis or damage to the brainstem can leave patients severely paralyzed but fully aware, in a condition known as 'locked-in syndrome'. Communication in this state is often reduced to selecting individual letters or words by arduous residual movements. More intuitive and rapid communication may be restored by directly interfacing with language areas of the cerebral cortex. We used a grid of closely spaced, nonpenetrating micro-electrodes to record local field potentials (LFPs) from the surface of face motor cortex and Wernicke's area. From these LFPs we were successful in classifying a small set of words on a trial-by-trial basis at levels well above chance. We found that the pattern of electrodes with the highest accuracy changed for each word, which supports the idea that closely spaced micro-electrodes are capable of capturing neural signals from independent neural processing assemblies. These results further support using cortical surface potentials (electrocorticography) in brain-computer interfaces. These results also show that LFPs recorded from the cortical surface (micro-electrocorticography) of language areas can be used to classify speech-related cortical rhythms and potentially restore communication to locked-in patients.
Text Summarization Techniques: A Brief Survey (2017)

In recent years, there has been a explosion in the amount of text data from a variety of sources. This volume of text is an invaluable source of information and knowledge which needs to be effectively summarized to be useful. Text summarization is the task of shortening a text document into a condensed version keeping all the important information and content of the original document. In this review, the main approaches to automatic text summarization are described. We review the different processes for summarization and describe the effectiveness and shortcomings of the different methods.
Calcein-Acetyoxymethyl Cytotoxicity Assay: Standardization of a Method Allowing Additional Analyses on Recovered Effector Cells and Supernatants (2001)

Cytotoxicity assays provide an in vitro evaluation of the lytic activity of NK and T cells against tumors or transformed cells. However, none of these methods allow the recovery of cells or supernatants after the assay. We standardized a microcytotoxicity test using calcein-acetoxymethyl (calcein-AM) dye that requires very small quantities of cells while maintaining the same sensitivity as the traditional (51)Cr assay. The assay is applicable to resting as well as activated human effector cells and uses different targets such as human cell lines that are adherent or growing in suspension and resistant or sensitive. The most important feature of the method is the possibility of recovering cells and supernatants for additional analyses such as phenotyping and evaluation of soluble factors.
A rhesus monkey model of respiratory syncytial virus infection (2002)

Respiratory syncytial virus (RSV) is a major cause of lower respiratory tract disease in infants and young children worldwide. To date, there is no single animal model that adequately reproduces all human disease states. Here, we have developed a model of experimental infection with human RSV in infant Rhesus macaques. Infected animals demonstrated mild clinical disease including increased respiratory rates, fever and adventitious lung sounds. While more severe disease was not observed, preliminary virological and histopathological findings are promising. It is anticipated that with further optimization, this model will provide a useful system with which to study disease due to RSV infection and evaluate candidate vaccines.
Structure of Moloney murine leukemia viral DNA: nucleotide sequence of the 5' long terminal repeat and adjacent cellular sequences. (1980)

Some unintegrated and all integrated forms of murine leukemia viral DNA contain long terminal repeats (LTRs). The entire nucleotide sequence of the LTR and adjacent cellular sequences at the 5' end of a cloned integrated proviral DNA obtained from BALB/Mo mouse has been determined. It was compared to the nucleotide sequence of the LTR at the 3' end. The results indicate: (i) a direct 517-nucleotide repeat at the 5' and 3' termini; (ii) 145 nucleotides out of 517 nucleotides represent sequences between the 5'-CAP nucleotide and 3' end of the primer tRNA (strong-stop DNA); (iii) an 11-nucleotide inverted repeat is present at the ends of the 5'-LTR and a total of 17 out of 21 nucleotides at the termini are inverted repeats; (iv) sequences CAATAAAAG (at positions -24 to -31) and CAATAAAC (at positions +46 to +53) resembling the hypothetical DNA-dependent RNA polymerase II promoter site can be identified in the 5'-LTR; (v) the sequence GAAA appears to be repeated on both sides of the junction of viral and cellular sequences; and (vi) in analogy with the bacterial transposons, the presence of an inverted repeat sequence at the termini of 5'-LTR suggests that M-MLV also has the integration properties of a transposon.
Photonic Band Gap Architectures for Holographic Lithography (2004)

Using symmetry considerations, we identify three families of large photonic band-gap (PBG) architectures defined by the isointensity surfaces of four beam laser interference. For particular choices of beam intensities, directions, and polarizations, we obtain a diamondlike crystal, a novel body-centered cubic architecture, and a simple cubic structure with PBG to center frequency ratios of 25%, 21%, and 11%, respectively, when the isointensity surface defines a silicon (dielectric constant of 11.9) to air boundary.
Scalable Biofabrication of Tissue Spheroids for Organ Printing (2013)

Organ printing technology or robotic additive biofabrication of 3D functional tissue and organ constructs is based on using tissue spheroids as building blocks. In order to bioprint human organs it is necessary to develop technology for scalable production of millions tissue spheroids. Ideally, these tissue spheroids must have standard size and shape suitable for bioprinting process. The scalable biofabrication of large volume of standard size tissue spheroids could be achieved only by maximal employment of robotics and automation technologies. The three main competing groups of emerging tissue spheroid biofabrication technologies include: i) modified handing drop method, 2) molded non-adhesive hydrogel technology and iii) digital microfluidic technologies. The comparative analysis of emerging scalable tissue spheroid biofabrication technologies has been performed. Our data indicates that all these technologies have potential for robotization and automation. The molded non-adhesive hydrogel technologies provide best outcome for standardization of tissue spheroid size. The microfluidics technology has strong advantage in accelerating of tissue spheroids biofabrication (theoretically, up to 10 000 droplets per second). New emerging approaches for biofabrication tissue spheroid using nanopatterned biomimetic surface and technologies for tissue spheroid encapsulation and functionalization will be also presented. The tissue spheroid biofabrication technologies are still evolving and represent hot area in biofabrication research. Moreover, these technologies are already subject of ongoing commercialization. Thus, it is safe to predict that scalable robotic tissue spheroid biofabricators must be integrated parts of organ biofabrication line.