gebhart/patrepeval huggingface dataset:
Detection of Acidovorax avenae subsp. citrulli in Watermelon Seed Using Immunomagnetic Separation and the Polymerase Chain Reaction (2000)

An immunomagnetic separation and polymerase chain reaction (IMS-PCR)-based assay was developed for detecting Acidovorax avenae subsp. citrulli in watermelon seed. IMS yielded a 10-fold increase in recovery of A. avenae subsp. citrulli over direct spread-plating on King's Medium B; however, the presence of seed debris reduced IMS efficiency. Synthetic oligonucleotide primers were designed based on the 16S rRNA gene of a known A. avenae subsp. citrulli strain and tested for specific DNA amplification by PCR. The primers amplified DNA from all A. avenae subsp. citrulli strains tested but also yielded amplicons with several closely related bacteria. IMS-PCR resulted in a 100-fold increase in A. avenae subsp. citrulli detection sensitivity over direct PCR and was unaffected by PCR inhibitors in watermelon seed. The threshold of A. avenae subsp. citrulli detection for IMS-PCR was 10 CFU/ml in watermelon seed wash, and seedlots with 0.1% infestation were consistently detected. IMS-PCR represents an efficient and sensitive approach to detecting A. avenae subsp. citrulli in watermelon seedlots.
Activation and Partial Proteolysis of Variant Glucocorticoid Receptors, Studied by Two‐Phase Partitioning (1981)

In cultured lines of mouse lymphoma cells, resistant to glucocorticoids is frequently associated with the occurrence of glucocorticoid receptors with an abnormally low affinity (nt-) or an abnormally high affinity (nti) for nuclei and DNA. We have investigated whether the abnormal affinities for DNA are correlated with alterations in charge and surface properties of the receptors, that would be revealed through the partition coefficient in aqueous dextran/poly(ethylene glycol) two-phase systems. We have found that none of the receptor variants is defective in the activation step per se, and that only the nti receptors are abnormal in partition properties. Partial proteolysis of wild-type and nt- receptors with alpha-chymotrypsin produces forms which are indistinguishable from the nti receptors with respect to partition coefficients. Upon alpha-chymotrypsin treatment the wild-type receptors attain DNA-binding properties identical to those of the nti receptors, while the nt- receptors, in spite of some increase in DNA affinity, still bind less firmly to DNA than the alpha-chymotrypsin-treated wild-type receptors. alpha-Chymotrypsin treatment of the various receptor types also produces an increase in the binding to dextran sulphate, but the dextran sulphate affinity is higher and varies less between different receptor types than the DNA affinity. Trypsin-treated receptors were found to be devoid of affinity for DNA and dextran sulphate.
Optimal Charge Control of Plug-In Hybrid Electric Vehicles in Deregulated Electricity Markets (2010)

Plug-in hybrid electric vehicles are a midterm solution to reduce the transportation sector's dependency on oil. However, if implemented in a large scale without control, peak load increases significantly and the grid may be overloaded. Two algorithms to address this problem are proposed and analyzed. Both are based on a forecast of future electricity prices and use dynamic programming to find the economically optimal solution for the vehicle owner. The first optimizes the charging time and energy flows. It reduces daily electricity cost substantially without increasing battery degradation. The latter also takes into account vehicle to grid support as a means of generating additional profits by participating in ancillary service markets. Constraints caused by vehicle utilization as well as technical limitations are taken into account. An analysis, based on data of the California independent system operator, indicates that smart charge timing reduces daily electricity costs for driving from $0.43 to $0.2. Provision of regulating power substantially improves plug-in hybrid electric vehicle economics and the daily profits amount to $1.71, including the cost of driving.
A speech coder based on decomposition of characteristic waveforms (2002)

For low-rate speech coding it is advantageous to represent the speech signal as an evolving characteristic waveform (CW). The CW evolves slowly when the speech signal is clearly voiced and rapidly when the speech signal is clearly unvoiced. The voiced (periodic) and unvoiced (nonperiodic) components of the speech signal can be separated by a simple nonadaptive filter in the CW domain. Because of perceptual effects, a significant increase in coding efficiency is obtained by coding these two components separately. A 2.4 kb/s coder using these principles was developed. In an independent evaluation, the performance of the 2.4 kb/s waveform interpolation (WI) coder was found to be at least equivalent to the 4.8 kb/s FS1016 standard for all of the many tests.
Phosphorylation of Kif26b Promotes Its Polyubiquitination and Subsequent Proteasomal Degradation during Kidney Development (2012)

Kif26b, a member of the kinesin superfamily proteins (KIFs), is essential for kidney development. Kif26b expression is restricted to the metanephric mesenchyme, and its transcription is regulated by a zinc finger transcriptional regulator Sall1. However, the mechanism(s) by which Kif26b protein is regulated remain unknown. Here, we demonstrate phosphorylation and subsequent polyubiquitination of Kif26b in the developing kidney. We find that Kif26b interacts with an E3 ubiquitin ligase, neural precursor cell expressed developmentally down-regulated protein 4 (Nedd4) in developing kidney. Phosphorylation of Kif26b at Thr-1859 and Ser-1962 by the cyclin-dependent kinases (CDKs) enhances the interaction of Kif26b with Nedd4. Nedd4 polyubiquitinates Kif26b and thereby promotes degradation of Kif26b via the ubiquitin-proteasome pathway. Furthermore, Kif26b lacks ATPase activity but does associate with microtubules. Nocodazole treatment not only disrupts the localization of Kif26b to microtubules but also promotes phosphorylation and polyubiquitination of Kif26b. These results suggest that the function of Kif26b is microtubule-based and that Kif26b degradation in the metanephric mesenchyme via the ubiquitin-proteasome pathway may be important for proper kidney development.
Femoral neuropathy following renal transplantation. (1990)

Femoral neuropathy is an uncommon complication that can occur subsequent to a number of abdominal and/or pelvic procedures. The neuropathy is usually evident immediately after the operation, but there may be some delay in diagnosis of the clinical problem. The neuropathy generally resolves completely after a period of time, but in some instances there may be a residual deficit. Four cases of femoral neuropathy are described which developed after operation for renal transplantation.
Homology-directed repair of DNA nicks via pathways distinct from canonical double-strand break repair (2014)

DNA nicks are the most common form of DNA damage, and if unrepaired can give rise to genomic instability. In human cells, nicks are efficiently repaired via the single-strand break repair pathway, but relatively little is known about the fate of nicks not processed by that pathway. Here we show that homology-directed repair (HDR) at nicks occurs via a mechanism distinct from HDR at double-strand breaks (DSBs). HDR at nicks, but not DSBs, is associated with transcription and is eightfold more efficient at a nick on the transcribed strand than at a nick on the nontranscribed strand. HDR at nicks can proceed by a pathway dependent upon canonical HDR factors RAD51 and BRCA2; or by an efficient alternative pathway that uses either ssDNA or nicked dsDNA donors and that is strongly inhibited by RAD51 and BRCA2. Nicks generated by either I-AniI or the CRISPR/Cas9(D10A) nickase are repaired by the alternative HDR pathway with little accompanying mutagenic end-joining, so this pathway may be usefully applied to genome engineering. These results suggest that alternative HDR at nicks may be stimulated in physiological contexts in which canonical RAD51/BRCA2-dependent HDR is compromised or down-regulated, which occurs frequently in tumors.
Thumbs Up or Thumbs Down? Semantic Orientation Applied to Unsupervised Classification of Reviews (2002)

This paper presents a simple unsupervised learning algorithm for classifying reviews as recommended (thumbs up) or not recommended (thumbs down). The classification of a review is predicted by the average semantic orientation of the phrases in the review that contain adjectives or adverbs. A phrase has a positive semantic orientation when it has good associations (e.g., "subtle nuances") and a negative semantic orientation when it has bad associations (e.g., "very cavalier"). In this paper, the semantic orientation of a phrase is calculated as the mutual information between the given phrase and the word "excellent" minus the mutual information between the given phrase and the word "poor". A review is classified as recommended if the average semantic orientation of its phrases is positive. The algorithm achieves an average accuracy of 74% when evaluated on 410 reviews from Epinions, sampled from four different domains (reviews of automobiles, banks, movies, and travel destinations). The accuracy ranges from 84% for automobile reviews to 66% for movie reviews.
Antisense Drug Discovery: Can Cell-Free Screens Speed the Process? (1998)

Many conditions must be satisfied for an antisense drug to function. It must colocalize with its target RNA at a sufficient concentration for a bimolecular reaction to occur, and it must have a structure that favors association with its target. In addition, if the antisense compound is to form Watson-Crick bonds with the target RNA, it must be complementary to sites that are amenable to binding. Unfortunately, the peculiarities that cause certain sites to be especially vulnerable to antisense compounds are undefined, as discussed previously (Branch, 1998). Because vulnerable target sites have no common properties allowing them to be identified by sequence analysis, most target sites and their antisense counterparts are found through a trial and error process in which oligomers--each complementary to a different site in the target RNA--are tested individually to find the one with the greatest specificity and lowest inhibitory concentration (IC50). However, testing antisense molecules one at a time can be a taxing process, and there is great interest in developing cell-free screening methods that can reduce the number of compounds that must be tested in cells and in whole animals. These cell-free screens are designed to generate short lists of target sites that include the ideal site--the site most vulnerable to antisense ablation in vivo. They are based on the unproven assumption that ideal sites have distinctive properties, such as susceptibility to RNase H-mediated cleavage, that allow them to be detected in cell-free assays. This is a review of data emerging from studies using RNase H-based screens and a summary of the challenges confronting these and any similar methods that use naked RNAs as surrogates for intracellular RNAs. It is not yet clear if cell-free screening methods will be effective.
(Triphenyl phosphite)gold(I)-Catalyzed Intermolecular Hydroamination of Alkenes and 1,3-Dienes (2008)

Intermolecular addition of different sulfonamides to alkenes and conjugated dienes can be carried out using a low loading of (triphenyl phosphite)gold(I) chloride and silver triflate as a catalytic mixture. The reaction can be performed under conventional thermal or microwave conditions and at rt in the case of dienes. Terminal alkenes undergo regioselective hydroamination at the internal carbon atom and dienes at the less substituted double bond.
Mesenchymal origin of hepatic stellate cells, submesothelial cells, and perivascular mesenchymal cells during mouse liver development† (2008)

Fetal HSCs, submesothelial cells, and perivascular mesenchymal cells are mesodermal in origin, and ALCAM(+) submesothelial cells may be a precursor for HSCs in developing liver.
The Concise Guide to PHARMACOLOGY 2015/16: G protein‐coupled receptors (2015)

The Concise Guide to PHARMACOLOGY 2015/16 provides concise overviews of the key properties of over 1750 human drug targets with their pharmacology, plus links to an open access knowledgebase of drug targets and their ligands (www.guidetopharmacology.org), which provides more detailed views of target and ligand properties. The full contents can be found at http://onlinelibrary.wiley.com/doi/10.1111/bph.13348/full. G protein-coupled receptors are one of the eight major pharmacological targets into which the Guide is divided, with the others being: ligand-gated ion channels, voltage-gated ion channels, other ion channels, nuclear hormone receptors, catalytic receptors, enzymes and transporters. These are presented with nomenclature guidance and summary information on the best available pharmacological tools, alongside key references and suggestions for further reading. The Concise Guide is published in landscape format in order to facilitate comparison of related targets. It is a condensed version of material contemporary to late 2015, which is presented in greater detail and constantly updated on the website www.guidetopharmacology.org, superseding data presented in the previous Guides to Receptors & Channels and the Concise Guide to PHARMACOLOGY 2013/14. It is produced in conjunction with NC-IUPHAR and provides the official IUPHAR classification and nomenclature for human drug targets, where appropriate. It consolidates information previously curated and displayed separately in IUPHAR-DB and GRAC and provides a permanent, citable, point-in-time record that will survive database updates.
RETRACTED: Methylation Mediated Silencing of MicroRNA-1 Gene and Its Role in Hepatocellular Carcinogenesis (2008)

MicroRNAs (miR) are a class of small ( approximately 21 nucleotide) noncoding RNAs that, in general, negatively regulate gene expression. Some miRs harboring CGIs undergo methylation-mediated silencing, a characteristic of many tumor suppressor genes. To identify such miRs in liver cancer, the miRNA expression profile was analyzed in hepatocellular carcinoma (HCC) cell lines treated with 5-azacytidine (DNA hypomethylating agent) and/or trichostatin A (histone deacetylase inhibitor). The results showed that these epigenetic drugs differentially regulate expression of a few miRs, particularly miR-1-1, in HCC cells. The CGI spanning exon 1 and intron 1 of miR-1-1 was methylated in HCC cell lines and in primary human HCCs but not in matching liver tissues. The miR-1-1 gene was hypomethylated and activated in DNMT1-/- HCT 116 cells but not in DNMT3B null cells, indicating a key role for DNMT1 in its methylation. miR-1 expression was also markedly reduced in primary human hepatocellular carcinomas compared with matching normal liver tissues. Ectopic expression of miR-1 in HCC cells inhibited cell growth and reduced replication potential and clonogenic survival. The expression of FoxP1 and MET harboring three and two miR-1 cognate sites, respectively, in their respective 3'-untranslated regions, was markedly reduced by ectopic miR-1. Up-regulation of several miR-1 targets including FoxP1, MET, and HDAC4 in primary human HCCs and down-regulation of their expression in 5-AzaC-treated HCC cells suggest their role in hepatocarcinogenesis. The inhibition of cell cycle progression and induction of apoptosis after re-expression of miR-1 are some of the mechanisms by which DNA hypomethylating agents suppress hepatocarcinoma cell growth.
Fluidic thrust vectoring for low observable aircraft (2002)

The work presented in this paper deals with the development of a coflow fluidic thrust vectoring system for use on a low observable unmanned air vehicle operating in the subsonic flight regime. Two approximately 1/10 th scale fluidic thrust vectoring demonstrator rigs were designed and built in order to investigate the effect of various geometric variables on thrust vectoring effectiveness. These included secondary gap height, dh, and Coanda surface diameter, ∅. Load measurements were obtained using a six component overhead balance. The thrust vector force, Fz,tv, was made non-dimensional using the thrust force of the nonvectored primary jet, F x , to give a thrust vector coefficient, Cz. Tests were carried out over the mass flow ratio range 0 � m s /m p < 0.13 which corresponded to a momentum flow ratio range of 0 � Ms/Mp < 0.4. A computational investigation for 2D flow was also undertaken primarily to aid in the design of the experimental demonstrator rigs and smoke flow visualisation techniques were used to further investigate the flow characteristics of a non-vectored and a vectored primary jet. The investigation shows that both the experimental and computational results obtained follow a similar trend line. A ‘dead zone’ appears at low mass flow ratios in which no control can be achieved. There then follows a control region in which continuous thrust vector control can be achieved followed by a hypothetical saturation region. The secondary jet blowing rate, the Coanda surface diameter and the primary nozzle to secondary nozzle height ratio are seen to determine whether effective and efficient fluidic thrust vectoring can be achieved. Nomenclature Ap Cross sectional area of primary jet m 2 As Cross sectional area of secondary jet m 2
Obstructive Sleep Apnea Syndrome in Ambulatory Surgical Patients (2002)

Obstructive sleep apnea in the ambulatory surgery setting has become a more significant concern in recent years because its Identification and recognition are a critical part of preoperative patients' risk assessment. The types of surgeries that can be performed on an outpatient basis have increased and include many specialty procedures that previously were performed on an inpatient basis only. Ambulatory surgery has proven to be a cost-effective alternative for patients and physicians; however, patients in this setting often have complex surgical histories. Perioperative nurses must provide a more integrated approach to patient assessment to recognize, identify, plan, and implement a course of safe care for patients with obstructive sleep apnea. Reviewing patients' histories can help nurses identify symptoms of obstructive sleep apnea, allowing them to alert the surgical team of special requirements. Ambulatory patients with identified obstructive sleep apnea will require a planned course of care. Ambulatory care facilities should have a policy in place to ensure that safe care will be provided to patients for the entire perioperative course.
Is Crohn’s disease due to defective immunity? (2006)

The understanding of the pathophysiology of Crohn's disease is currently undergoing a reassessment. The concept of this disease as a primary T cell disorder is being questioned, with a new emphasis on the role of innate immunity in initiating early events and in perpetuating the inflammatory state. Crohn's disease has been proposed instead to result from impaired innate immunity, encompassing the mucosal barrier and cellular elements including neutrophils and macrophages. Recent advances in genetics, functional studies on innate immunity and therapeutic trials on patients with Crohn's disease have lent support to this evolving hypothesis.
Tumor-specific immunogenicity of stress-induced proteins: convergence of two evolutionary pathways of antigen presentation? (1991)

Stress-induced proteins (hsps) elicit tumor-specific immunity to a number of murine tumors. Specificity of this immunity is puzzling in view of the fact that no tumor-specific DNA sequence polymorphisms have been identified in stress-induced genes, nor is there evidence for tumor-specific posttranslational modification of hsps. In this light, the possibility that hsps may not be antigenic per se, but may be carriers of antigenic moieties such as peptides, and may be accessory antigen-presenting molecules, is considered. A model where an hsp molecule such as gp96 acts as an intermediate in presentation of peptides to MHC is discussed and it is suggested that the hsp and MHC antigens are mediators of independent but functionally convergent phylogenetic pathways.
LSTM based Conversation Models (2016)

In this paper, we present a conversational model that incorporates both context and participant role for two-party conversations. Different architectures are explored for integrating participant role and context information into a Long Short-term Memory (LSTM) language model. The conversational model can function as a language model or a language generation model. Experiments on the Ubuntu Dialog Corpus show that our model can capture multiple turn interaction between participants. The proposed method outperforms a traditional LSTM model as measured by language model perplexity and response ranking. Generated responses show characteristic differences between the two participant roles.
Peptidomimetic nitrile warheads as SARS-CoV-2 3CL protease inhibitors (2021)

Tragically, the death toll from the COVID-19 pandemic continues to rise, and with variants being observed around the globe new therapeutics, particularly direct-acting antivirals that are easily administered, are desperately needed. Studies targeting the SARS-CoV-2 3CL protease, which is critical for viral replication, with different peptidomimetics and warheads is an active area of research for development of potential drugs. To date, however, only a few publications have evaluated the nitrile warhead as a viral 3CL protease inhibitor, with only modest activity reported. This article describes our investigation of P3 4-methoxyindole peptidomimetic analogs with select P1 and P2 groups with a nitrile warhead that are potent inhibitors of SARS-CoV-2 3CL protease and demonstrate <i>in vitro</i> SARS-CoV-2 antiviral activity. A selectivity for SARS-CoV-2 3CL protease over human cathepsins B, S and L was also observed with the nitrile warhead, which was superior to that with the aldehyde warhead. A co-crystal structure with SARS-CoV-2 3CL protease and a reversibility study indicate that a reversible, thioimidate adduct is formed when the catalytic sulfur forms a covalent bond with the carbon of the nitrile. This effort also identified efflux as a property limiting antiviral activity of these compounds, and together with the positive attributes described these results provide insight for further drug development of novel nitrile peptidomimetics targeting SARS-CoV-2 3CL protease.
Household projections under the current AIDS pandemic. (2001)

Population and household projections are of crucial importance to both policy makers and researchers who depend on timely and reliable projections to make informed decisions and to produce quality research studies. Currently one of the most problematic areas regarding projections is the demographic impact of the HIV/AIDS epidemic in countries with high prevalence rates i.e. how the epidemic is influencing population and household projections. At the end of the year 2000 36.1 million people were estimated to be living with HIV/AIDS of which 1.4 million were children. 47 per cent of the infected adults were women. 5.3 million people will be newly infected during this year. The pandemic does not spread homogeneously. The number of infections the risk of dying the access to medication and the principal transmission ways vary worldwide and so does the impact of the HIV/AIDS epidemic on population structure and on household formation. In countries where the epidemic is endemic in the general population the impact on the age and gender structure of the population is significant and changes in the social context and behaviour are certain. (excerpt)