gebhart/patrepeval huggingface dataset:
Logophoricity redefined - the case of Boko (2017)

This paper examines the phenomenon of logophoricity in Boko, a Mande language, and argues that in Boko at least, logophoricity is syntactically defined, contrary to recent claims that it is partially controlled by semantics: In this respect my analysis is an extension of what Culy (1997) postulated in claiming that logophoricity and point of view are distinct phenomena. Boko logophoric domains are broader than what is normally attributed to logophoricity, although limited to the sentence. The hierarchy of logophoric licensing verbs is extended maximally: any context where a pronoun in a lower level structure has an antecedent on a higher level is a logophoric domain. Relative and adverbial clauses are included. Boko reflexive possessive pronouns are interpreted as logophoric and are described here in detail. Their domains include noun phrases, postpositional phrases, simple clauses and complex clauses. In this paper a wide range of Boko examples is presented to illustrate the extent of all its forms, and the non-syntactic definitions logophoricity are shown to be inadequate for Boko.
Protein NMR Spectroscopy: Principles and Practice (1995)

Assical NMR Spectroscopy. Theoretical Description of NMR Spectroscopy. Experimental Aspects of NMR Spectroscopy. Multi-Dimensional NMR Spectroscopy. Relaxation and Dynamic Processes. Experimental 1H NMR Methods. Heteronuclear NMR Experiments. Sequential Assignments and Structure Calculations. Chapter References. Subject Index.
Computational Models of Performance Monitoring and Cognitive Control (2010)

The medial prefrontal cortex (mPFC) has been the subject of intense interest as a locus of cognitive control. Several computational models have been proposed to account for a range of effects, including error detection, conflict monitoring, error likelihood prediction, and numerous other effects observed with single-unit neurophysiology, fMRI, and lesion studies. Here, we review the state of computational models of cognitive control and offer a new theoretical synthesis of the mPFC as signaling response–outcome predictions. This new synthesis has two interacting components. The first component learns to predict the various possible outcomes of a planned action, and the second component detects discrepancies between the actual and intended responses; the detected discrepancies in turn update the outcome predictions. This single construct is consistent with a wide array of performance monitoring effects in mPFC and suggests a unifying account of the cognitive role of medial PFC in performance monitoring.
Prevention and treatment of hepatocellular carcinoma (2004)

Viral hepatitis, by either hepatitis C virus (HCV) or hepatitis B virus (HBV), is the dominant cause of hepatocellular carcinoma (HCC). This is to say that HCC may be prevented by controlling viral infection. Horizontal transmission of HCV has become obsolete owing to the discovery of the virus. Vertical transmission of HBV during delivery has been effectively prevented by vaccination and immunization of neonates. The efficacy of interferon therapy against HCV was recently much improved. We now possess several powerful antiviral drugs against HBV. There has been progress also in the treatment of HCC, and together with advances in diagnostics facilitating HCC detection at an early stage, tumor nodules can often be completely removed either by medical ablation or surgical resection. Nevertheless, recurrence of HCC after apparently curative treatment is extraordinarily frequent, since the remaining liver is still at a particularly high risk of HCC. An effective treatment of HCC should include measures to control de novo carcinogenesis.
naiveBayesCall: An Efficient Model-Based Base-Calling Algorithm for High-Throughput Sequencing (2011)

Immense amounts of raw instrument data (i.e., images of fluorescence) are currently being generated using ultra high-throughput sequencing platforms. An important computational challenge associated with this rapid advancement is to develop efficient algorithms that can extract accurate sequence information from raw data. To address this challenge, we recently introduced a novel model-based base-calling algorithm that is fully parametric and has several advantages over previously proposed methods. Our original algorithm, called BayesCall, significantly reduced the error rate, particularly in the later cycles of a sequencing run, and also produced useful base-specific quality scores with a high discrimination ability. Unfortunately, however, BayesCall is too computationally expensive to be of broad practical use. In this article, we build on our previous model-based approach to devise an efficient base-calling algorithm that is orders of magnitude faster than BayesCall, while still maintaining a comparably high level of accuracy. Our new algorithm is called naive-BayesCall, and it utilizes approximation and optimization methods to achieve scalability. We describe the performance of naiveBayesCall and demonstrate how improved base-calling accuracy may facilitate de novo assembly and SNP detection when the sequence coverage depth is low to moderate.
Generating summaries for large collections of geo-referenced photographs (2006)

We describe a framework for automatically selecting a summary set of photographs from a large collection of geo-referenced photos. The summary algorithm is based on spatial patterns in photo sets, but can be expanded to support social, temporal, as well as textual-topical factors of the photo set. The summary set can be biased by the user, the content of the user's query, and the context in which the query is made. An initial evaluation on a set of geo-referenced photos shows that our algorithm performs well, producing results that are highly rated by users.
Protein secondary structure analyses from circular dichroism spectroscopy: Methods and reference databases (2007)

Circular dichroism (CD) spectroscopy has been a valuable method for the analysis of protein secondary structures for many years. With the advent of synchrotron radiation circular dichroism (SRCD) and improvements in instrumentation for conventional CD, lower wavelength data are obtainable and the information content of the spectra increased. In addition, new computation and bioinformatics methods have been developed and new reference databases have been created, which greatly improve and facilitate the analyses of CD spectra. This article discusses recent developments in the analysis of protein secondary structures, including features of the DICHROWEB analysis webserver.
Imaging and Identification of Phospholipids in Mouse Liver Tissue by Matrix Assisted Laser Desorption Ionization-Fourier Transform Ion Cyclotron Resonance Mass Spectrometry Imaging (2011)

Matrix assisted laser desorption ionization-Fourier transform ion cyclotron resonance mass spectrometry(MALDI-FTICR MS)-based mass spectrometric imaging(MSI) was applied to profile and identify phospholipid molecules in mouse liver tissues,which were cut into tissue sections(7 μm) on a cryostat at-20 ℃ and covered with 7 g/L of alpha-cyano-4-hydroxycinnamicacid(CHCA) as matrix in 50% methanol/0.2 trifluoroacetic acid solution.13 phospholipid compounds,which are classified as 5 different species,phosphatidic acid(PA),phosphatidylcholine(PC),phosphatidylethanolamine(PE),phosphatidylglycerol(PG) and phosphatidylserine(PS),were accurately identified.Their molecular weights are between 700 and 900 Da.The present results indicate that MALDI-FTICR MS-based MSI is a powerful tool to explore the distribution of disease-related molecules and drug metabolites in tissues.
Teletext and viewdata — a comprehensive component solution (1979)

An efficient and low-cost teletext decoder based on l.s.i. i.c.s is essential for the success of broadcast teletext and viewdata. However, other vital peripheral areas, such as teletext remote control, interface with the video circuits, low-cost modem functions, surface acoustic wave (s.a.w.) i.f. filters and so on, are not ignored in a comprehensive component solution from Mullard. Remote control for teletext must have up to 32 commands available together with a very fast action to allow rapid keying of page numbers and must also control all the normal t.v. functions. A system employing infra-red serial data transmission, and which interfaces directly with the teletext decoder, is realised in two low-cost l.s.i. i.c.s. Four l.s.i. i.c.s together with appropriate page memory i.c.s comprise the teletext decoder; three, in m.o.s. technology, carry out the digital functions of data acquisition, display timing and character video generation; the other, a linear bipolar i.c., provides a very efficient data slicer and data clock system which is vital to good off-air teletext performance. The decoder is designed for easy extension for viewdata use. A viewdata extension system based upon the MP8048 microcomputer includes a data-recording facility, optional full-keyboard operation, automatic dialling of several alternative numbers and a comprehensive set of on-screen legends to aid the viewer. A modem unit, designed to meet the British Post Office performance and safety requirements for installation in a t.v. reciever or v.d.u. forms part of the system. The performance of the i.f. amplifier in a t.v. receiver is more critical for the reception of data than t.v. signals and the use of a s.a.w. i.f. filter with excellent amplitude and group-delay response is beneficial to teletext. Feeding decoded data video into the RGB channels of a receiver is greatly simplified by colour decoder i.c.s designed for data insertion, particularly if text inlay into the t.v. picture is required as an option.
Transient introduction of a foreign gene into healing rat patellar ligament. (1996)

We investigated the in vivo introduction of a reporter gene into healing rat patellar ligaments using the hemagglutinating virus of Japan (HVJ)-liposome-mediated gene transfer method. The mid-portion of the medial half of the patellar ligament was cut transversely with a scalpel in 14-wk-old male Wistar rats. A HVJ-liposome suspension containing beta-galactosidase (beta-gal) cDNA was injected directly into the injured site and pooled in the fascial pocket covering the injured site 3 d postoperatively. Thereafter, beta-gal-labeled cells were observed in the wound site accounting for 3% of the wound cells on the first day, 2% on the third, 7% on the seventh, 6% on the 14th, 2% on the 28th, and 0.2% on the 56th day after injection. The beta-gal-labeled cells were initially localized in and adjacent to the wound site, but they were observed spreading into the ligament substance away from the wound on the seventh day after injection. On day 28, beta-gal-labeled cells were observed throughout the length of the ligament substance. With double-labeling for marker antigens for monocyte/macrophage (ED-1) and for collagen I aminopropeptide (pN collagen I), it was revealed that fibroblastic (pN collagen I-positive) cells accounted for 63% and monocyte/macrophage lineage cells for 32% of the beta-gal-labeled cells in the day 7 wound. On day 28, they formed 58 and 35% of the beta-gal-labeled cells in the wound, respectively. Thus, we succeeded in introducing the beta-gal gene into healing rat patellar ligament. Moreover, labeling of the transfected cells made it possible to identify a biological event, namely that the cells in and around the wound site infiltrate into the uninjured ligament substance and come to populate the whole length of the ligament substance as repair progresses. These results suggest that ligament healing may involve not only the repair of the wound site itself but also extensive cellular infiltration of ligament substance adjacent to the wound.
Synthesis of 3‐amino‐2,4(1H,3H)‐quinazolinediones for testing as anticonvulsants (1984)

Abstract A number of 3‐amino‐2,4(1 H ,3 H )‐quinazolinediones were synthesized from o ‐aminobenzoylhydrazines and ethyl chloroformate in pyridine or from 2‐methoxycarbonylphenyl isocyanate and 1,1‐disubstituted hydrazines. Four of the ten compounds screened exhibited anticonvulsant activity in mice.
Pancreatic β Cell-specific Transcription of thepdx-1 Gene (2000)

To identify potential transactivators of pdx-1, we sequenced approximately 4.5 kilobases of the 5' promoter region of the human and chicken homologs, assuming that sequences conserved with the mouse gene would contain critical cis-regulatory elements. The sequences associated with hypersensitive site 1 (HSS1) represented the principal area of homology within which three conserved subdomains were apparent: area I (-2694 to -2561 base pairs (bp)), area II (-2139 to -1958 bp), and area III (-1879 to -1799 bp). The identities between the mouse and chicken/human genes are very high, ranging from 78 to 89%, although only areas I and III are present within this region in chicken. Pancreatic beta cell-selective expression was shown to be controlled by mouse and human area I or area II, but not area III, from an analysis of pdx-1-driven reporter activity in transfected beta- and non-beta cells. Mutational and functional analyses of conserved hepatic nuclear factor 3 (HNF3)-like sites located within area I and area II demonstrated that activation by these regions was mediated by HNF3beta. To determine if a similar regulatory relationship might exist within the context of the endogenous gene, pdx-1 expression was measured in embryonic stem cells in which one or both alleles of HNF3beta were inactivated. pdx-1 mRNA levels induced upon differentiation to embryoid bodies were down-regulated in homozygous null HNF3beta cells. Together, these results suggest that the conserved sequences represented by areas I and II define the binding sites for factors such as HNF3beta, which control islet beta cell-selective expression of the pdx-1 gene.
Clinical implication of 14-3-3 epsilon expression in gastric cancer (2012)

Our results reveal that the reduced 14-3-3ε expression in GC and investigation of 14-3-3ε interaction partners may help to elucidate the carcinogenesis process.
Botulinum Toxin: Mechanisms of Action (2005)

Botulinum toxin (BT) has been perceived as a lethal threat for many centuries. In the early 1980s, this perception completely changed when BT's therapeutic potential suddenly became apparent. We wish to give an overview over BT's mechanisms of action relevant for understanding its therapeutic use. BT's molecular mode of action includes extracellular binding to glycoprotein structures on cholinergic nerve terminals and intracellular blockade of the acetylcholine secretion. BT affects the spinal stretch reflex by blockade of intrafusal muscle fibres with consecutive reduction of Ia/II afferent signals and muscle tone without affecting muscle strength (reflex inhibition). This mechanism allows for antidystonic effects not only caused by target muscle paresis. BT also blocks efferent autonomic fibres to smooth muscles and to exocrine glands. Direct central nervous system effects are not observed, since BT does not cross the blood-brain barrier and since it is inactivated during its retrograde axonal transport. Indirect central nervous system effects include reflex inhibition, normalisation of reciprocal inhibition, intracortical inhibition and somatosensory evoked potentials. Reduction of formalin-induced pain suggests direct analgesic BT effects possibly mediated by blockade of substance P, glutamate and calcitonin gene-related peptide.
New Method To Generate Enzymatically Deficient Clostridium difficile Toxin B as an Antigen for Immunization (2000)

The family of the large clostridial cytotoxins, encompassing Clostridium difficile toxins A and B as well as the lethal and hemorrhagic toxins from Clostridium sordellii, monoglucosylate the Rho GTPases by transferring a glucose moiety from the cosubstrate UDP-glucose. Here we present a new detoxification procedure to block the enzyme activity by treatment with the reactive UDP-2', 3'-dialdehyde to result in alkylation of toxin A and B. Alkylation is likely to occur in the catalytic domain, because the native cosubstrate UDP-glucose completely protected the toxins from inactivation and the alkylated toxin competes with the native toxin at the cell receptor. Alkylated toxins are good antigens resulting in antibodies recognizing only the C-terminally located receptor binding domain, whereas formaldehyde treatment resulted in antibodies recognizing both the receptor binding domain and the catalytic domain, indicating that the catalytic domain is concealed under native conditions. Antibodies against the native catalytic domain (amino acids 1 through 546) and those holotoxin antibodies recognizing the catalytic domain inhibited enzyme activity. However, only antibodies against the receptor binding domain protected intact cells from the cytotoxic activity of toxin B, whereas antibodies against the catalytic domain were protective only when inside the cell.
Ferric uptake regulation protein acts as a repressor, employing iron(II) as a cofactor to bind the operator of an iron transport operon in Escherichia coli (1987)

The Fur (ferric uptake regulation) protein is a negative regulator of the aerobactin operon and of several other siderophore-mediated, high-affinity iron transport systems in Escherichia coli. The purified Fur protein and a plasmid containing a lacZ fusion to the aerobactin operon were used in conjunction with an in vitro coupled transcription/translation system to demonstrate that the Fur protein requires Fe(II) or certain other divalent metals as a cofactor to negatively regulate expression of the aerobactin operon. In a second set of experiments, using a restriction site protection assay, Fur was shown to bind to and block the aerobactin promoter in a metal-dependent fashion. It is concluded that Fur acts as a classical negative repressor that, under in vivo conditions, uses ionic Fe(II) as a corepressor. Our results support the hypothesis [Williams, R.J.P. (1982) FEBS Lett. 140, 3-10] that prokaryotic cells may contain a standing pool of free or loosely bound Fe(II) that is capable of acting in a regulatory capacity.
The Metabolic Pathway Engineering Handbook (2009)

This first volume of the Metabolic Pathway Engineering Handbook provides an overview of metabolic pathway engineering with a look towards the future. It discusses cellular metabolism, including transport processes inside the cell and energy generating reactions, as well as rare metabolic conversions. This volume also explores balances and reaction
Identification of surfactins and iturins produced by potent fungal antagonist, Bacillus subtilis K1 isolated from aerial roots of banyan (Ficus benghalensis) tree using mass spectrometry (2013)

The banyan endophyte, Bacillus subtilis K1, produces a complex mixture of lipopeptides exhibiting potent antifungal activity. These lipopeptides were purified by high-performance liquid chromatography and analyzed using MALDI-TOF-MS as well as liquid chromatography coupled with ESI-MS. A heterogenous mixture of lipopeptides belonging to three different families of cyclic lipopeptides, viz., fengycins, iturins and surfactins, was detected in the cell-free extracellular extract of B. subtilis K1. The detailed mass spectrometric characterization revealed the presence of four variants of iturin A and three variants of iturin C varying in the β-amino fatty acid chain length from C<sub>13</sub> to C<sub>17</sub>. The MS/MS of monovalent alkali metal ion adducts (Na and K) of iturin suggested the Glu<sup>4</sup> as a binding site for metal ion. The LC-ESI-MS/MS analysis of surfactins enabled the identification of seven surfactin variants with the variations in Val/Ile/Leu at position 4 and C<sub>13</sub>-C<sub>17</sub> β-hydroxy fatty acids. This study demonstrates the application of tandem mass spectrometry in identification of closely related lipopeptides from a heterogenous mixture obtained from a natural source. Furthermore, this is the first report of an endophytic bacillus strain co-producing so many variants of surfactins and iturins.
Cysteine proteinase cathepsin L expression correlates closely with the metastatic potential of H-ras-transformed murine fibroblasts. (1987)

A set of H-ras-transfected mouse C3H 10T1/2 cell lines that vary in their experimental and spontaneous metastatic potential has been analysed for the level of expression of the cysteine proteinase cathepsin L, also known as the major excreted protein (MEP). We found a good positive correlation between the extent of ras expression, the metastatic potential, and the amount of the secreted protease in nine independently isolated lines. There was an increased abundance of the MEP mRNA in cells with increased ras expression, suggesting that this gene is under ras control. Expression of glyceraldehyde phosphate dehydrogenase mRNA was also elevated.
Violence Rating Prediction from Movie Scripts (2019)

Violent content in movies can influence viewers’ perception of the society. For example, frequent depictions of certain demographics as perpetrators or victims of abuse can shape stereotyped attitudes. In this work, we propose to characterize aspects of violent content in movies solely from the language used in the scripts. This makes our method applicable to a movie in the earlier stages of content creation even before it is produced. This is complementary to previous works which rely on audio or video post production. Our approach is based on a broad range of features designed to capture lexical, semantic, sentiment and abusive language characteristics. We use these features to learn a vector representation for (1) complete movie, and (2) for an act in the movie. The former representation is used to train a movie-level classification model, and the latter, to train deep-learning sequence classifiers that make use of context. We tested our models on a dataset of 732 Hollywood scripts annotated by experts for violent content. Our performance evaluation suggests that linguistic features are a good indicator for violent content. Furthermore, our ablation studies show that semantic and sentiment features are the most important predictors of violence in this data. To date, we are the first to show the language used in movie scripts is a strong indicator of violent content. This offers novel computational tools to assist in creating awareness of storytelling.