gebhart/patrepeval huggingface dataset:
CONVERSATION ACTS IN TASK‐ORIENTED SPOKEN DIALOGUE (1992)

A linguistic form's compositional, timeless meaning can be surrounded or even contradicted by various social, aesthetic, or analogistic companion meanings. This paper addresses a series of problems in the structure of spoken language discourse, including turn‐taking and grounding . It views these processes as composed of fine‐grained actions, which resemble speech acts both in resulting from a computational mechanism of planning and in having a rich relationship to the specific linguistic features which serve to indicate their presence. The resulting notion of Conversation Acts is more general than speech act theory, encompassing not only the traditional speech acts but turn‐taking, grounding, and higher‐level argumentation acts as well. Furthermore, the traditional speech acts in this scheme become fully joint actions, whose successful performance requires full listener participation. This paper presents a detailed analysis of spoken language dialogue. It shows the role of each class of conversation acts in discourse structure, and discusses how each class can be processed and recognized. Conversation acts, it will be seen, better account for the success of conversation than speech act theory alone. They also provide a pragmatic view of meaning in which the literal/non‐literal distinction is simply irrelevant.
Principles of Vaccination (2015)

Vaccination is an important method for disease control and prevention for horses. This chapter first presents summary tables of the AAEP guidelines for foals and broodmares, and then explains the difference between vaccine efficacy and vaccine effectiveness. In a cohort study, vaccinates (exposed cohort) and non-vaccinates (unexposed cohorts) would be followed forward in time after vaccination, and evaluated for development of disease and other outcomes of interest. If the vaccine is effective against the disease of interest, the incidence of disease will be lower among vaccinates than among unvaccinated horses. The safety of vaccines may be perceived differently than other medical interventions, because vaccines are administered primarily to healthy individuals. Vaccination protocols vary even for horses residing within the same barn. A middle-aged gelding retired from competition that has limited exposure to other horses has a different risk level than a young filly actively engaged in showing.
A DNA target of 30 bp is sufficient for RNA-directed DNA methylation (2000)

In higher plants, RNA-DNA interactions can trigger de novo methylation of genomic sequences via a process that is termed RNA-directed DNA methylation (RdDM). In potato spindle tuber viroid (PSTVd)-infected tobacco plants, this process can potentially lead to methylation of all C residues at symmetrical and nonsymmetrical sites within chromosomal inserts that consist of multimers of the 359-bp-long PSTVd cDNA. Using PSTVd cDNA subfragments, we found that genomic targets with as few as 30 nt of sequence complementarity to the viroid RNA are detected and methylated. Genomic sequencing analyses of genome-integrated 30- and 60-bp-long PSTVd subfragments demonstrated that de novo cytosine methylation is not limited to the canonical CpG, CpNpG sites. Sixty-base-pair-long PSTVd cDNA constructs appeared to be densely methylated in nearly all tobacco leaf cells. With the 30-bp-long PSTVd-specific construct, the proportion of cells displaying dense transgene methylation was significantly reduced, suggesting that a minimal target size of about 30 bp is necessary for RdDM. The methylation patterns observed for two different 60-bp constructs further suggested that the sequence identity of the target may influence the methylation mechanism. Finally, a link between viroid pathogenicity and PSTVd RNA-directed methylation of host sequences is proposed.
A Chronic, Conscious Large Animal Platform to Quantify Therapeutic Effects of Sacral Neuromodulation on Bladder Function (2015)

These data demonstrate the effects of acute sacral neuromodulation on bladder capacity in the conscious sheep. This model represents a useful testing platform for novel sacral neuromodulation concepts such as alternate methods and parameters of therapy delivery.
High-throughput mutate-map-rescue evaluates SHAPE-directed RNA structure and uncovers excited states (2014)

The three-dimensional conformations of noncoding RNAs underpin their biochemical functions but have largely eluded experimental characterization. Here, we report that integrating a classic mutation/rescue strategy with high-throughput chemical mapping enables rapid RNA structure inference with unusually strong validation. We revisit a 16S rRNA domain for which SHAPE (selective 2'-hydroxyl acylation with primer extension) and limited mutational analysis suggested a conformational change between apo- and holo-ribosome conformations. Computational support estimates, data from alternative chemical probes, and mutate-and-map (M(2)) experiments highlight issues of prior methodology and instead give a near-crystallographic secondary structure. Systematic interrogation of single base pairs via a high-throughput mutation/rescue approach then permits incisive validation and refinement of the M(2)-based secondary structure. The data further uncover the functional conformation as an excited state (20 ± 10% population) accessible via a single-nucleotide register shift. These results correct an erroneous SHAPE inference of a ribosomal conformational change, expose critical limitations of conventional structure mapping methods, and illustrate practical steps for more incisively dissecting RNA dynamic structure landscapes.
Long-Term Effects of Botulinum Toxin Injections in Spasmodic Dysphonia (1996)

The purpose was to examine whether physiological changes can be found in laryngeal muscles following repeated treatment with botulinum toxin injections in spasmodic dysphonia. Seven patients whose treatment consisted of multiple unilateral thyroarytenoid injections were examined more than 6 months following their most recent botulinum toxin injection fiberoptic laryngoscopy and electromyography. Comparisons were made between injected and contralateral noninjected muscles' motor unit characteristics, muscle activation patterns, and vocal fold movement characteristics. The results demonstrated that motor unit characteristics differed between injected and noninjected muscles and that these differences were greater in patients less than 12 months since last injection. Motor unit duration differences were reduced and motor unit amplitude and numbers of turns were increased in muscles sampled over 1 year after injection. These results suggest that while the physiologic effects of botulinum toxin are reversible, the reinnervation process continues past 12 months following injection.
Adsorption Mechanism of Carbon Dioxide in Faujasites: Grand Canonical Monte Carlo Simulations and Microcalorimetry Measurements (2005)

Molecular simulations have been coupled with adsorption microcalorimetry measurements in order to understand more deeply the interactions between carbon dioxide and various types of faujasite surfaces. The modeling studies, based on newly derived interatomic potentials for describing the interactions within the whole system, provide isotherms and evolutions of the differential enthalpy of adsorption as a function of coverage for DAY, NaY, and NaLSX which are in very good accordance with those obtained experimentally. The microscopic mechanism of CO2 adsorption was carefully analyzed, with different behaviors proposed, depending on the energetic characteristics of each faujasite surface, which are consistent with the trends observed for the differential enthalpies of adsorption.
SYNTHESIS OF BIARYLS FROM ARYL IODIDES AND ZINC POWDER BY MEANS OF NICKEL CATALYST (1979)

Abstract Nickel species in situ generated from nickel(II) bromide and zinc powder in HMPA catalyzed the formation of biaryls from aryl iodides and zinc powder under mild conditions.
Prostaglandin E2 enhances long-term repopulation but does not permanently alter inherent stem cell competitiveness (2013)

Hematopoietic stem cell (HSC) transplantation is a lifesaving therapy for malignant and nonmalignant hematologic diseases and metabolic disorders. Although successful, hematopoietic transplantation can be hindered by inadequate stem cell number or poor engrafting efficiency. To overcome these deficits, we and others have previously reported the HSC-enhancing ability of a short-term exposure of prostaglandin E2 (PGE2); this strategy has now progressed to phase 1 clinical trials in double cord blood transplantation. To further analyze the short- and long-term effects of HSC exposure to PGE2, we followed the repopulation kinetics of PGE2-treated hematopoietic grafts through 5 serial transplantations and compared inherent long-term competitiveness in a HSC head-to-head secondary transplantation model. Treatment with PGE2 did not result in a long-term increase in HSC competitiveness, lineage bias, or enhanced proliferative potential, demonstrating that pulse exposure to PGE2 results in transient increases in HSC homing and engraftment potential.
X-Chromosome inactivation ratios affect wild-type MeCP2 expression within mosaic Rett syndrome and Mecp2-/+ mouse brain (2004)

Rett syndrome (RTT) is an X-linked neurodevelopmental disorder caused by mutations in MECP2, encoding methyl-CpG-binding protein 2 (MeCP2). The onset of symptoms in RTT is delayed until 6-18 months and 4-6 months in the Mecp2(-/+) mouse model, corresponding to a dynamic and gradual accumulation of MeCP2 expression in individual neurons of the postnatal brain. Because of X chromosome inactivation (XCI), cells within RTT females are mosaic for expression of the heterozygous MECP2 mutation. Using the targeted Mecp2 mouse model, we investigated the effect of Mecp2 mutation on XCI and developmental MeCP2 expression in wild-type (wt)-expressing neurons by quantitative laser scanning cytometry. Mecp2(-/+) female mice exhibited uniform regional distribution of Mecp2 mutant-expressing cells in brain, but unbalanced XCI in the population, favoring expression of the Mecp2 wt allele. Interestingly, MeCP2 expression in Mecp2 wt-expressing cells from Mecp2(-/+) mice was significantly lower than those from Mecp2(+/+) age-matched controls. The negative effect of Mecp2 mutation on wt Mecp2 expression correlated with the percentage of Mecp2 mutant-expressing cells in the cortex. Similar results were observed in two RTT females with identical MECP2 mutations but different XCI ratios. These results demonstrate that Mecp2-mutant neurons affect the development of surrounding neurons in a non-cell-autonomous manner and suggest that environmental influences affect the level of MeCP2 expression in wt neurons. These results help in explaining the role of XCI in the pathogenesis of RTT and have important implications in designing therapies for female RTT patients.
Spatial Weighting for Bag-of-Features (2006)

This paper presents an extension to category classification with bag-of-features, which represents an image as an orderless distribution of features. We propose a method to exploit spatial relations between features by utilizing object boundaries provided during supervised training. We boost the weights of features that agree on the position and shape of the object and suppress the weights of background features, hence the name of our method - "spatial weighting". The proposed representation is thus richer and more robust to background clutter. Experimental results show that our approach improves the results of one of the best current image classification techniques. Furthermore, we propose to apply the spatial model to object localization. Initial results are promising.
Repeating pattern of non-RVD variations in DNA-binding modules enhances TALEN activity (2013)

Transcription activator-like effector (TALE) nuclease (TALEN) is a site-specific nuclease, which can be freely designed and easily constructed. Numerous methods of constructing TALENs harboring different TALE scaffolds and repeat variants have recently been reported. However, the functionalities of structurally different TALENs have not yet been compared. Here, we report on the functional differences among several types of TALENs targeting the same loci. Using HEK293T cell-based single-strand annealing and Cel-I nuclease assays, we found that TALENs with periodically-patterned repeat variants harboring non-repeat-variable di-residue (non-RVD) variations (Platinum TALENs) showed higher activities than TALENs without non-RVD variations. Furthermore, the efficiencies of gene disruption mediated by Platinum TALENs in frogs and rats were significantly higher than in previous reports. This study therefore demonstrated an efficient system for the construction of these highly active Platinum TALENs (Platinum Gate system), which could establish a new standard in TALEN engineering.
Cluster Analysis (1974)

15.3 Analysis Using R Sadly Figure˜15.2 gives no completely convincing verdict on the number of groups we should consider, but using a little imagination ‘little elbows ’ can
Hardware - software co-design of portable functional gastrointestinal stimulator system (2003)

In the recent years, functional electrical stimulation has been applied to restore impaired motility in the gastrointestinal tract. Unlike other methods of electrical stimulation of the gut, microprocessor-controlled, sequential electrical stimulation has been shown to induce peristalsis and enhance emptying in acute canine gastric and colonic models. This study aims at completing the development of a portable microprocessor-based functional stimulator system consisting of a microelectronic stimulator, patient-specific computer-based real-time software and a programming interfacing device. The ultimate goals of the design are to ensure that (1) the portable stimulator can be efficiently utilized in chronic animal experiments; and (2) the device can be further miniaturized into an implantable version. The designed portable stimulator generates four channel sequential bipolar rectangular pulse trains with programmable parameters within the stimulation requirements obtained from a previously developed computer model. Real-time simulation of colonic peristalsis and a case-specific stimulation model were implemented using patient-specific computer-based software. A chronic canine case study confirmed the feasibility of this microprocessor-controlled stimulation method for future clinical applications in humans.
Extendibility of synchrotron radiation lithography to the sub-100 nm region (1996)

This article discusses the resolution of synchrotron radiation lithography in the sub-100 nm region, taking into consideration the mass production of large-scale integrated circuits, under attainable conditions for the x-ray mask, proximity gap, and resist processes. Resolution and exposure latitude for line-and-space patterns are markedly improved by using a mask with a contrast of only 2.5. Resolutions of 90, 80, 70, and 60 nm can be achieved with proximity gaps of 30, 20, 15, and 10 μm if a high-contrast resist and a low-surface tension developer are used. The latitude will be 10% for pattern sizes as small as 70 nm when the proximity gap is narrower than 15 μm. The effects of mask duty [which is defined to be the ratio of the absorber (line) width to the pattern pitch, i.e., duty cycle] on the optimum exposure dose and mask linearity are also evaluated.
Optimizing pKA computation in proteins with pH adapted conformations (2007)

pK(A) in proteins are determined by electrostatic energy computations using a small number of optimized protein conformations derived from crystal structures. In these protein conformations hydrogen positions and geometries of salt bridges on the protein surface were determined self-consistently with the protonation pattern at three pHs (low, ambient, and high). Considering salt bridges at protein surfaces is most relevant, since they open at low and high pH. In the absence of these conformational changes, computed pK(A)(comp) of acidic (basic) groups in salt bridges underestimate (overestimate) experimental pK(A)(exp), dramatically. The pK(A)(comp) for 15 different proteins with 185 known pK(A)(exp) yield an RMSD of 1.12, comparable with two other methods. One of these methods is fully empirical with many adjustable parameters. The other is also based on electrostatic energy computations using many non-optimized side chain conformers but employs larger dielectric constants at short distances of charge pairs that diminish their electrostatic interactions. These empirical corrections that account implicitly for additional conformational flexibility were needed to describe the energetics of salt bridges appropriately. This is not needed in the present approach. The RMSD of the present approach improves if one considers only strongly shifted pK(A)(exp) in contrast to the other methods under these conditions. Our method allows interpreting pK(A)(comp) in terms of pH dependent hydrogen bonding pattern and salt bridge geometries. A web service is provided to perform pK(A) computations.
Hepatitis E virus: identification of type-common epitopes (1991)

Large epidemic outbreaks of enterically transmitted non-A, non-B viral hepatitis (ET-NANBH) have been documented in developing countries. A molecular clone derived from the causative agent, the hepatitis E virus (HEV), has recently been described (G.R. Reyes, M.A. Purdy, J.P. Kim, K.-C. Luk, L.M. Young, K.E. Fry, and D. Bradley, Science 247:1335-1339, 1990). We now report the isolation, by serologic screening, of two cDNA clones derived from a fecal sample collected during a 1986 outbreak of ET-NANBH in Telixtac, Mexico. The cDNA clones encode epitopes that specifically reacted with acute- and convalescent-phase sera collected during five different ET-NANBH epidemics and represent the initial cloning of the Mexico strain of HEV. Recombinant fusion proteins expressed from these clones were also recognized by antibodies from cynomolgus macaques experimentally infected with HEV. The cDNA clones were shown to be derived from HEV by their specific hybridization to the previously recognized full-length genomic RNA transcript of approximately 7.5 kb. In addition, however, subgenomic polyadenylated transcripts of approximately 2.0 and approximately 3.7 kb were also identified in HEV-infected cynomolgus monkey liver. Sequences homologous to the epitope clones were isolated from the Burma strain of the virus, and these demonstrated reactivity comparable to that seen with the Mexico strain epitopes. When compared with the available full-length sequence of the Burma strain of HEV, it was discovered that the cDNA clones were encoded in different open reading frames (ORFs). The comparison between Mexico and Burma HEV strains indicated amino acid homologies of 90.5 and 73.5% for these epitope-encoding clones derived from ORF2 and ORF3, respectively. The identification of these clones not only has provided insight into the expression strategy of HEV but has also resulted in a source of recombinant protein useful in the diagnosis of HEV-induced hepatitis.
Ex-vivo whole blood cultures for predicting cytokine-release syndrome: dependence on target antigen and antibody isotype. (1995)

Ex-vivo whole blood assays have been evaluated for their ability to accurately predict the risk of a first-dose cytokine reaction developing in vivo following therapeutic antibody infusion. Tumour necrosis factor alpha (TNF alpha) release was rapidly detected in cultures incubated with either anti-CD52 antibodies of the human IgG1 or rat IgG2b isotype, and to a lesser extent with a human IgG4 isotype. Endotoxin contamination of the antibodies was not responsive for cytokine release, since polymixin B failed to inhibit cytokine release using concentrations of this antibiotic which neutralized the enhanced cytokine release seen from LPS-spiked antibody. A rat IgG2b antibody to CD45 and a human IgG1 anti-CD3 also induced significant TNF release, however, an aglycosyl anti-CD3 mutant devoid of adverse side-effects in vivo, did not result in cytokine release in vitro. Since the pattern of cytokine release seen following the clinical use of these antibodies was in good agreement with the findings of the ex-vivo whole cultures, this demonstrates the usefulness of this assay to predict cytokine release in vivo.
L-Carnitine Prevents Progression of Non-Alcoholic Steatohepatitis in a Mouse Model with Upregulation of Mitochondrial Pathway (2014)

Non-alcoholic steatohepatitis (NASH) is a severe form of non-alcoholic fatty liver disease characterized by lobular inflammation, hepatocellular ballooning, and fibrosis with an inherent risk for progression to cirrhosis and hepatocellular carcinoma (HCC). Mitochondrial dysfunction appears to play a role in the progression from simple steatosis to NASH. L-carnitine (L-b-hydroxy-g-N-trimethylaminobutyric acid), an essential nutrient that converts fat into energy in mitochondria, has been shown to ameliorate liver damage. The aim of the present study was to explore the preventive and therapeutic effect of L-carnitine in NASH model mice. Eight-week-old male STAM mice, a NASH-cirrhosis-hepatocarcinogenic model, were divided into 3 experimental groups and fed as follows: 1) high-fat diet (HFD) (control group); 2) HFD mixed with 0.28% L-carnitine (L-carnitine group); and 3) HFD mixed with 0.01% α-tocopherol (α-tocopherol group). After 4 or 8 weeks, mice were sacrificed. Blood samples and livers were collected, and hepatic tumors were counted and measured. Livers were subjected to histological study, immunohistochemical staining of 4-hydroxynonenal and ferritin, determination of 8-OHdG levels, mRNA and protein expressions for multiple genes, and metabolomic analysis. The intestinal microbiome was also analyzed. L-carnitine increased hepatic expression of genes related to long-chain fatty acid transport, mitochondrial β-oxidation, and antioxidant enzymes following suppression of hepatic oxidative stress markers and inflammatory cytokines in NASH, and mice treated with L-carnitine developed fewer liver tumors. Although α-tocopherol resulted in NASH improvement in the same manner as L-carnitine, it increased periodontitis-related microbiotic changes and hepatic iron transport-related gene expression and led to less effective for anti-hepatocarcinogenesis. Conclusion: L-carnitine prevents progression of non-alcoholic steatohepatitis in a mouse model by upregulating the mitochondrial β-oxidation and redox system.
Low adiponectin levels are associated with renal cell carcinoma: A case‐control study (2007)

Adiponectin is a novel endogenous insulin sensitizer, secreted by mature adipocytes. Circulating levels of adiponectin are inversely associated with obesity and insulin resistance. Because obesity is a risk factor for renal cell carcinoma (RCC), we hypothesized that low adiponectin levels are associated with RCC. To evaluate this hypothesis, we conducted a case- control study of 70 patients with histologically confirmed RCC and 280 healthy controls matched by gender, age and county of residence. Study subjects were interviewed and blood samples were collected during a 32-month period in Athens, Greece. Serum adiponectin levels were statistically, significantly and inversely associated with RCC when compared with controls (OR=0.76, p=0.05) and this association remained practically unchanged after controlling for BMI; the introduction of waist to hip ratio along with adiponectin in the multiple logistic regression analysis model rendered the association between adiponectin and RCC risk insignificant, indicating that altered levels of adiponectin may mediate the effect of central or intra-abdominal obesity on RCC. Prospective studies as well as studies exploring underlying mechanisms are needed to fully explore the role of adiponectin in predicting future risk of RCC in humans.