gebhart/patrepeval huggingface dataset:
Development of Emulsion Type New Vehicle for Soft Gelatin Capsule. I. Selection of Surfactants for Development of New Vehicle and Its Physicochemical Properties. (1998)

Screening of surfactants was carried out to develop an oil in water (o/w) emulsion type new vehicle for a soft gelatin capsule (SGC), using polyethyleneglycol 400 (PEG 400) as hydrophilic phase and medium chain triglyceride (Miglyol 810), propyleneglycol dicaprylate (Sefsol 228) or soybean oil as hydrophobic phase (PEG 400: hydrophobic phase: surfactant = 87:10:3) and by means of simple homogenization. Polyoxyethylene (20) cetylether (BC-20TX), which can form homogeneous and viscous white gels using the above hydrophilic and hydrophobic phase combination, was selected as a model surfactant for developing the new vehicle. Using Miglyol 810 as hydrophobic phase, a model new vehicle formulation (PEG 400:water:Miglyol 810: BC-20TX = 77:10:10:3) was prepared, and its physicochemical properties were evaluated. The particle size distribution of the new vehicle, after diluting about 3000 times with water, ranged from about 0.5 to 50 microns. Furthermore, the new vehicle had thixotropic property at room temperature (about 25 degrees C) and temperature-dependent gel-sol transforming property with the transformation temperature of about 37 degrees C. These properties meet the requirement for encapsulation of the new vehicle in SGC and suggest that it can be expected to form the o/w emulsion state in the aqueous environment in the stomach. The rheological properties would also make it advantageous for use in other dosage forms such as suppository, cataplasm or liniment.
Investigating User Confidence for Uncertainty Presentation in Predictive Decision Making (2015)

Machine Learning (ML) based decision support systems are often like a black box to non-expert users. Here user's confidence becomes critical for effective decision making and maintaining trust in the system. We find that user confidence varies significantly depending on supplementary material presented on screen. We investigate change in user confidence (in the context of ML based decision making) by varying level of uncertainty presented (in an online water-pipe failure prediction case study) and find that all 26 subjects rated higher uncertainty task to be most difficult and had lowest user confidence in predictive decisions of the same. This agrees with our expectation that increased uncertainty would reduce user confidence in predictive decision making. However, ML-researchers subgroup reported being most confident when uncertainty with known probability was presented, whereas other subgroups (viz. general staff and non-ML researchers) appeared most confident when uncertainty was not at all presented. This is an original research to improve understanding of user's decision making confidence with respect to uncertainty presented in machine learning context.
Conversational gaze mechanisms for humanlike robots (2012)

During conversations, speakers employ a number of verbal and nonverbal mechanisms to establish who participates in the conversation, when, and in what capacity. Gaze cues and mechanisms are particularly instrumental in establishing the participant roles of interlocutors, managing speaker turns, and signaling discourse structure. If humanlike robots are to have fluent conversations with people, they will need to use these gaze mechanisms effectively. The current work investigates people's use of key conversational gaze mechanisms, how they might be designed for and implemented in humanlike robots, and whether these signals effectively shape human-robot conversations. We focus particularly on whether humanlike gaze mechanisms might help robots signal different participant roles, manage turn-exchanges, and shape how interlocutors perceive the robot and the conversation. The evaluation of these mechanisms involved 36 trials of three-party human-robot conversations. In these trials, the robot used gaze mechanisms to signal to its conversational partners their roles either of two addressees, an addressee and a bystander, or an addressee and a nonparticipant. Results showed that participants conformed to these intended roles 97% of the time. Their conversational roles affected their rapport with the robot, feelings of groupness with their conversational partners, and attention to the task.
The molecular virology of coronaviruses (2020)

Few human pathogens have been the focus of as much concentrated worldwide attention as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the cause of COVID-19. Its emergence into the human population and ensuing pandemic came on the heels of severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV), two other highly pathogenic coronavirus spillovers, which collectively have reshaped our view of a virus family previously associated primarily with the common cold. It has placed intense pressure on the collective scientific community to develop therapeutics and vaccines, whose engineering relies on a detailed understanding of coronavirus biology. Here, we present the molecular virology of coronavirus infection, including its entry into cells, its remarkably sophisticated gene expression and replication mechanisms, its extensive remodeling of the intracellular environment, and its multifaceted immune evasion strategies. We highlight aspects of the viral life cycle that may be amenable to antiviral targeting as well as key features of its biology that await discovery.
Epidermal Growth Factor in the Topical Treatment of Herpetic Corneal Ulcers (1994)

The tolerability and efficacy of epidermal growth factor (EGF) in the topical treatment of herpetic corneal ulcers in addition to topical acyclovir have been evaluated in a double-blind, placebo-controlled, randomized study in two groups of patients. The time required for complete reepithelialization of the cornea was recorded, and the data obtained were analyzed statistically. In the EGF group, the reepithelialization was significantly faster than in the control group. Tolerability of EGF was always excellent. These results indicate that EGF is safe and effective in reducing the healing time of herpetic corneal ulcers.
Modelling and predictive control of an olive oil mill (2001)

This paper describes the modelling and predictive control of the extraction process in an olive oil mill. The work is focused on the thermal part of the process, where the raw material is prepared for the mechanical separation. The paper shows the development of a model based upon first principles combined with experimental results and validated with real data. Different control strategies have been tested under simulation, showing that good performance can be obtained by the use of a predictive controller that takes into account the measurable disturbances that appear in the process. Constraints in actuators are also included in the control strategy.
Efficient video decoding on GPUs by point based rendering (2006)

To accelerate computation intensive video decoding tasks, we present a novel framework to offload most decoding operations to current GPUs. Our method is based on rendering graphics points and suitable for block-based video standards. By representing video blocks as graphics points, we achieve great flexibility and high parallelism to utilize the GPU's pipelined stream processing architecture. The computational resources within texture units and blending units are also exploited to facilitate computations. We propose a high performance implementation of IDCT on GPUs, which efficiently excludes most zero-value coefficients to save the bandwidth and the computations. Compared with the existing quad-based representation, our point based implementation of MC greatly reduces data transfer and redundancy. We have demonstrated the efficiency of our proposed framework by a MPEG-2 decoder. Our results indicate a significant improvement over prior CPU and GPU solutions.
Cloning, sequencing, and expression of the gene encoding a large S-layer-associated endoxylanase from Thermoanaerobacterium sp. strain JW/SL-YS 485 in Escherichia coli (1996)

The gene (xynA) encoding a surface-exposed, S-layer-associated endoxylanase from Thermoanaerobacterium sp. strain JW/SL-YS 485 was cloned and expressed in Escherichia coli. A 3.8-kb fragment was amplified from chromosomal DNA by using primers directed against conserved sequences of endoxylanases isolated from other thermophilic bacteria. This PCR product was used as a probe in Southern hybridizations to identify a 4.6-kb EcoRI fragment containing the complete xynA gene. This fragment was cloned into E. coli, and recombinant clones expressed significant levels of xylanase activity. The purified recombinant protein had an estimated molecular mass (150 kDa), temperature maximum (80 degrees C), pH optimum (pH 6.3), and isoelectric point (pH 4.5) that were similar to those of the endoxylanase isolated from strain JW/SL-YS 485. The entire insert was sequenced and analysis revealed a 4,044-bp open reading frame encoding a protein containing 1,348 amino acid residues (estimated molecular mass of 148 kDa).xynA was preceded by a putative promoter at -35 (TTAAT) and -10 (TATATT) and a potential ribosome binding site (AGGGAG) and was expressed constitutively in E. coli. The deduced amino acid sequence showed 30 to 96% similarity to sequences of family F beta-glycanases. A putative 32-amino-acid signal peptide was identified, and the C-terminal end of the protein contained three repeating sequences 59, 64, and 57 amino acids) that showed 46 to 68% similarity to repeating sequences at the N-terminal end of S-layer and S-layer-associated proteins from other gram-positive bacteria. These repeats could permit an interaction of the enzyme with the S-layer and tether it to the cell surface.
Phylogenetic Analysis of Nonthermophilic Members of the Kingdom <i>Crenarchaeota</i> and Their Diversity and Abundance in Soils (1998)

Within the last several years, molecular techniques have uncovered numerous 16S rRNA gene (rDNA) sequences which represent a unique and globally distributed lineage of the kingdom Crenarchaeota that is phylogenetically distinct from currently characterized crenarchaeotal species. rDNA sequences of members of this novel crenarchaeotal group have been recovered from low- to moderate-temperature environments (-1.5 to 32 degreesC), in contrast to the high-temperature environments (temperature, >80 degreesC) required for growth of the currently recognized crenarchaeotal species. We determined the diversity and abundance of the nonthermophilic members of the Crenarchaeota in soil samples taken from cultivated and uncultivated fields located at the Kellogg Biological Station's Long-Term Ecological Research site (Hickory Corners, Mich.). Clones were generated from 16S rDNA that was amplified by using broad-specificity archaeal PCR primers. Twelve crenarchaeotal sequences were identified, and the phylogenetic relationships between these sequences and previously described crenarchaeotal 16S rDNA sequences were determined. Phylogenetic analyses included nonthermophilic crenarchaeotal sequences found in public databases and revealed that the nonthermophilic Crenarchaeota group is composed of at least four distinct phylogenetic clusters. A 16S rRNA-targeted oligonucleotide probe specific for all known nonthermophilic crenarchaeotal sequences was designed and used to determine their abundance in soil samples. The nonthermophilic Crenarchaeota accounted for as much as 1.42% +/- 0.42% of the 16S rRNA in the soils analyzed.
Induction of systemic lupus erythematosus syndrome in BALB/c mice by immunization with active chromatin. (2004)

The active chromatin-induced SLE-like mouse model was similar to idiopathic SLE in human.
Accurate calculation of the density of proteins (2000)

On the basis of theoretical calculations, Andersson & Hovmöller have recently suggested that the long-established value of 1.35 g cm(-3) for the mean density of proteins should be revised to 1.22 g cm(-3) [Andersson & Hovmöller (2000), Acta Cryst. D56, 789-790]. To substantiate their assertion, these authors used the Voronoi algorithm to calculate the mean atomic volume for 30 representative protein structures. The Voronoi procedure requires that atoms of interest be bounded on all sides by other atoms. Volume calculations for surface atoms that are not surrounded or are only sparsely surrounded by other atoms either are not possible or may be unreliable. In an attempt to circumvent this problem, Andersson & Hovmöller rejected atoms with calculated volumes that were indeterminate or were greater than 50 A(3). In the present study, it is shown that this criterion is not sufficiently restrictive to ensure accurate volume determinations. When only strictly buried atoms are included in the volume calculations using the Voronoi algorithm, the mean density is found to be 1.47 +/- 0.05 g cm(-3). In addition, an alternate procedure based on the Connolly algorithm that permits all protein atoms to be included in volume calculations gives 1.43 +/- 0.03 g cm(-3) for the mean density of the same set of proteins. The latter two calculated values are mutually consistent and are in better agreement with the experimental value.
DO CCTV USERS REALLY PREFER NEGATIVE POLARITY? ARMD PATIENTS ACTUAL USE OF LOW VISION DEVICES. (2001)

Monday, December 10, 2001. Posters: Academy Information, Public Health, Ocular Disease, Low Vision, Cornea and Contact Lenses: PDF Only
On the use of anthropometry in the invariant analysis of human actions (2004)

We propose a novel approach to matching human actions using semantic correspondence between human bodies with an eye towards invariant analysis of activity. The correspondences are used to provide geometric constraints between multiple anatomical landmarks (e.g. hands, shoulders and feet) to match actions performed from different viewpoints and in different environments. The fact that the human body has certain anthropometric proportion allows innovative use of the machinery of epipolar geometry to provide constraints to accurately analyze actions performed by different people leading to some interesting results. Temporally invariant matching is performed, using non-linear time warping, to ensure that similar actions performed at different rates are accurately matched as well. Thus, the proposed algorithm guarantees that both temporal and view invariance is maintained in matching. We demonstrate the versatility of our algorithm in a number of challenging sequences and applications.
Arp2/3 complex requires hydrolyzable ATP for nucleation of new actin filaments (2001)

The Arp2/3 complex, a seven-subunit protein complex containing two actin-related proteins, Arp2 and Arp3, initiates formation of actin filament networks in response to intracellular signals. The molecular mechanism of filament nucleation, however, is not well understood. Arp2 and Arp3 are predicted to bind ATP via a highly conserved nucleotide-binding domain found in all members of the actin superfamily and to form a heterodimer than mimics a conventional actin dimer. We show here that adenosine nucleotides bind with micromolar affinity to both Arp2 and Arp3 and that hydrolyzable ATP is required for actin nucleation activity. Binding of N-WASP WA increases the affinity of both Arp2 and Arp3 for ATP but does not alter the stoichiometry of nucleotides bound in the presence of saturating concentrations of ATP. The Arp2/3 complex bound to ADP or the nonhydrolyzable ATP analogue AMP-PNP cannot nucleate actin filaments, but addition of the phosphate analogue BeF 3 partially restores activity to the ADP–Arp2/3 complex. Bound nucleotide also regulates the affinity of the Arp2/3 complex for its upstream activators N-WASP and ActA. We propose that the active nucleating form of the Arp2/3 complex is the ADP-P i intermediate in the ATPase cycle and that the ATPase activity of the Arp2/3 complex controls both nucleation of new filaments and release of the Arp2/3 complex from membrane-associated activators.
Gene Therapy of Huntington’s Disease (1998)

A triplet repeat mutation in a gene (ITIS) on chromosome 4 p16.3 (1,2),resulting in a protein with an expanded polyglutamine tract causes Huntington’s disease (HD). The neuroscience and clinical community now faces the formidable challenge of using this information to develop a treatment against this fatal disease. This chapter reviews the recent literature pertaining to HD and presents an overview of possible intervention strategies against the disease’s neurodegenerative process, discussed in detail elsewhere (3,4). Our discussion focuses on four biological levels at which therapies could be devised. Examples are given of how novel therapies could be devised for HD in the near future, including interference with RNA splicing, blockade of the deleterious protein’ s effect, or physiological intervention by pharmacological tools or neural transplants. Finally, the status of existing gene transfer strategies and the problems highlighted by clinical gene therapy trials are outlined.
Genomic profiling and efficacy of anti-EGFR therapy in appendiceal adenocarcinoma. (2016)

4102 Background: Metastatic appendiceal adenocarcinoma (AAC) is a heterogenous disease and a large proportion of patients present with diffuse metastases in the peritoneal cavity. Cytotoxic and targeted therapies are typically extrapolated from colorectal adenocarcinoma (CRC), however, the efficacy is not well studied. Herein we investigated the genetic profiles of these tumors in an effort to identify molecular characteristics and potentially actionable mutations, as well as the response to anti-EGFR therapy in RAS/BRAF wild type (wt) AAC. Methods: We identified patients (pts) with ACC treated at MSKCC from 2002 to 2016 who had undergone molecular profiling, either by next generation sequencing using our MSK-IMPACT platform, or by MALDI-TOF mass spectroscopy genotyping (Sequenom). MSK-IMPACT tumors and matched normal samples were analyzed on a 410 gene panel. Sequenom provided an 8 gene panel including KRAS, NRAS, BRAF, and PIK3CA. Via an IRB approved waiver, we collected tumor histology and evaluated those who were RAS/RAF wt and were treated with anti-EGFR therapy. Results: To date, we identified a total 109 AAC patients, of whom 60 had Sequenom testing and 49 had MSK-IMPACT. Among pts analyzed with MSK-IMPACT, 34 had mucinous adenocarcinoma, 6 adenocarcinoma, 9 adenocarcinoma ex goblet cell carcinoid. In total 194 alterations were identified with a median 3.9 alterations/patient (range 0-10). Alterations were seen most commonly in KRAS (57%), GNAS (33%), TP53 (29%), and SMAD4 (6%). Potentially treatable alterations were present in 12% of patients and included BRAF V600E (1), MTOR (2), ERBB2 (1) and NTRK(2). Of the total 109 pts, 51 (47%) were RAS/BRAF wt. Of those, 12 evaluable patients received anti-EGFR therapy with either panitumumab or cetuximab. There were no responders. Conclusions: Mutational sequencing in AAC indicates that 12% have mutations in genes such as BRAF V600E, MTOR, ERBB2 and NTRK with the potential to expand investigational options. Additionally, in RAS/BRAF wt pts, panitumumab/cetuximab does not appear to have therapeutic efficacy comparable to historic controls in RAS/RAF wt CRC.
Cationic surfactant mediated hybridization and hydrophobization of DNA molecules at the liquid/liquid interface and their phase transfer (2001)

Hybridization of complementary oligonucleotides mediated by a cationic surfactant at the water/hexane interface leads to hydrophobic, double-helical DNA which may be readily phase transferred to the organic phase and cast into thin films on solid substrates.
Estimation of ambient radiation temperature for emissivity-corrected thermography (2005)

A non-contact method for the measurement of emissivity, and emissivity-corrected temperatures has been developed, where the ambient radiation-temperature is changed in a discontinuous way. When the ambient radiation-temperature is changed quickly, so that the surface temperature of the object can be assumed to be unchanged, the radiometer output before, and immediately after that change can be expressed as two simultaneous equations. The temperature and emissivity of the surface can be derived by solving these equations when the ambient radiation-temperatures are known. In previous studies, one or two hoods were used to provide the ambient radiation-temperature. However, there was a problem in controlling the ambient radiation-temperature. A new method is introduced where two reference plates coated with paints of different emissivities are placed in the field of view of the infrared camera. Eight simultaneous equations were derived from regions of the plates, and the ambient radiation-temperatures before and after the change were obtained by solving these equations. The validity of this method was confirmed by experiment. This method will eliminate the need to use hoods as in the previous report, and will simplify the equipment needed.
The Recent Advances on Molecular Biology of Newcastle Disease Virus (2002)

This review foused on Newcastle Disease Virus (NDV) on genemic structure, structure protein and their function, the essence of pathogenesis, molecular diagnosis, and its vaccine research.
Primary structure of guinea pig apolipoprotein E (1990)

Journal Article Primary structure of guinea pig apolipoprotein E Get access Guy Matsushima, Guy Matsushima 1Departments of Pathology, Biochemistry, The University of ChicagoChicago, IL 60637, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Godfrey S. Getz, Godfrey S. Getz 1Departments of Pathology, Biochemistry, The University of ChicagoChicago, IL 60637, USA2Departments of Molecular Biology, The University of ChicagoChicago, IL 60637, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Stephen C. Meredith Stephen C. Meredith 1Departments of Pathology, Biochemistry, The University of ChicagoChicago, IL 60637, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 18, Issue 1, 11 January 1990, Page 202, https://doi.org/10.1093/nar/18.1.202 Published: 11 January 1990 Article history Received: 25 September 1989 Published: 11 January 1990
Autoantibodies in infectious mononucleosis have specificity for the glycine-alanine repeating region of the Epstein-Barr virus nuclear antigen. (1987)

Viruses have been postulated to be involved in the induction of autoantibodies by: autoimmunization with tissue proteins released by virally induced tissue damage; immunization with virally encoded antigens bearing molecular similarities to normal tissue proteins; or nonspecific (polyclonal) B cell stimulation by the infection. Infectious mononucleosis (IM) is an experiment of nature that provides the opportunity for examining these possibilities. We show here that IgM antibodies produced in this disease react with at least nine normal tissue proteins, in addition to the virally encoded Epstein-Barr nuclear antigen (EBNA-1). The antibodies are generated to configurations in the glycine-alanine repeat region of EBNA-1 and are crossreactive with the normal tissue proteins through similar configurations, as demonstrated by the effectiveness of a synthetic glycine-alanine peptide in inhibiting the reactions. The antibodies are absent in preillness sera and gradually disappear over a period of months after illness, being replaced by IgG anti-EBNA-1 antibodies that do not crossreact with the normal tissue proteins but that are still inhibited by the glycine-alanine peptide. These findings are most easily explained by either a molecular mimicry model of IgM autoantibody production or by the polyclonal activation of a germline gene for a crossreactive antibody. It also indicates a selection of highly specific, non-crossreactive anti-EBNA-1 antibodies during IgM to IgG isotype switching.