gebhart/patrepeval huggingface dataset:
Development of a Novel Multiplex Immunoassay Multi-cruzi for the Serological Confirmation of Chagas Disease (2016)

The results described in this study indicate that the Multi-cruzi improves the serological confirmation of Chagas disease. Moreover the "sum of all antigens" detected by Multi-cruzi could reflect parasitemia level in patients-like PCR signals does-and could serve as an indicator of parasite clearance in longitudinal follow-ups. Validation of this assay is still required on an independent large collection of well characterized samples including typical false-reactive samples such as Leishmaniasis.
Direct Translation of a Protracted Irinotecan Schedule From a Xenograft Model to a Phase I Trial in Children (1999)

This protracted schedule is well tolerated in children. The absence of significant myelosuppression and encouraging clinical responses suggest compellingly that irinotecan be further evaluated in children using the (qd x 5) x 2 schedule, beginning at a dose of 20 mg/m(2). These results imply that data obtained from xenograft models can be effectively integrated into the design of clinical trials.
Acoustic Beamforming for Speaker Diarization of Meetings (2007)

When performing speaker diarization on recordings from meetings, multiple microphones of different qualities are usually available and distributed around the meeting room. Although several approaches have been proposed in recent years to take advantage of multiple microphones, they are either too computationally expensive and not easily scalable or they cannot outperform the simpler case of using the best single microphone. In this paper, the use of classic acoustic beamforming techniques is proposed together with several novel algorithms to create a complete frontend for speaker diarization in the meeting room domain. New techniques we are presenting include blind reference-channel selection, two-step time delay of arrival (TDOA) Viterbi postprocessing, and a dynamic output signal weighting algorithm, together with using such TDOA values in the diarization to complement the acoustic information. Tests on speaker diarization show a 25% relative improvement on the test set compared to using a single most centrally located microphone. Additional experimental results show improvements using these techniques in a speech recognition task.
Epigenetic activation of the MiR-200 family contributes to H19-mediated metastasis suppression in hepatocellular carcinoma (2012)

Although numerous long non-coding RNAs (lncRNAs) have been identified in mammals, many of their biological roles remain to be characterized. Early reports suggest that H19 contributes to carcinogenesis, including hepatocellular carcinoma (HCC). Examination of the Oncomine resource showed that most HCC cases express H19 at a level that is comparable with the liver, with a tendency toward lower expression. This is consistent with our previous microarray data and indicates a more complicated role of H19 in HCC that needs to be characterized. In this study, the expression level of H19 was assessed in different regions of HCC patients' liver samples. Loss- and gain-of-function studies on this lncRNA in the HCC cell lines, SMMC7721 and HCCLM3, were used to characterize its effects on gene expression and to assess its effect on HCC metastasis both in vitro and in vivo. In this study, we show that H19 was underexpressed in intratumoral HCC tissues (T), as compared with peritumoral tissues (L). Additionally, low T/L ratio of H19 predicted poor prognosis. H19 suppressed HCC progression metastasis and the expression of markers of epithelial-to-mesenchymal transition. Furthermore, H19 associated with the protein complex hnRNP U/PCAF/RNAPol II, activating miR-200 family by increasing histone acetylation. The results demonstrate that H19 can alter the miR-200 pathway, thus contributing to mesenchymal-to-epithelial transition and to the suppression of tumor metastasis. These data provide an explanation for the hitherto puzzling literature on the relationship between H19 and cancer, and could suggest the development of combination therapies that target H19 and the miR-200 family.
Phosphate-Mediated Molecular Memory Driven by Two Different Protein Kinases as Information Input Elements (2007)

There is increasing interest in studying molecular-based devices that perform Boolean logic operations whose output state (0 or 1) depends on the input conditions (0/0, 1/0, 0/1, or 1/1). So far, great efforts have been devoted to establish molecular-scaled logic gates activated by chemical, physical, and biological inputs. We herein describe the design and synthesis of a tandem protein kinase substrate peptide acting as a phosphate-mediated molecular memory. The molecular-based memory system is comprised of two different phosphorylatable substrate regions joined in series and a spiropyran derivative at the N-terminus. We also demonstrated three basic "AND", "OR", and "NOR" logic operations on the basis of alterations in the spiropyran-to-merocyanine (SP-to-MC) thermocoloration properties of the spiropyran moiety in the peptide upon kinase-catalyzed phosphorylation. The three logic functions were successfully performed by adding ionic polymers as programming elements with preset thresholds of a signal intensity in a microplate format. Throughout this study, information was recorded on the substrate peptide by protein kinase-catalyzed phosphorylation, stored stably as phosphoesters, read according to the extent of the SP-to-MC thermocoloration, and erased by phosphatase-catalyzed dephosphorylation, resulting in the peptide returning to the initial recordable state. Thus, the proof-of-concept experiments described herein could be used to provide clues for developing practical molecular-based processing and computing.
Design of a Casimir-driven parametric amplifier (2014)

In this paper, we discuss a design for a MEMS parametric amplifier modulated by the Casimir force. We present the theory for such a device and show that it allows for the implementation of a very sensitive voltage measuring technique, where the amplitude of a high quality factor resonator includes a tenth power dependency on an applied DC voltage. This approach opens up a new and powerful measuring modality, applicable to other measurement types.
Determination of the Processing Sites of an Arabidopsis 2S Albumin and Characterization of the Complete Gene Family (1988)

The most abundant isoform of the 2S albumin present in seeds of Arabidopsis thaliana has been sequenced and the corresponding gene isolated. Examination of the protein and DNA sequences allows the determination of the exact proteolytic cleavage sites during posttranslational processing. Like other 2S albumins, that of Arabidopsis is made as a prepropeptide. After removal of the signal peptide, the propeptide is cleaved at four other points, giving two subunits linked by a disulfide bridge(s). Comparison of these cleavage sites with those of 2S albumins of Brassica napus and Bertholletia excelsa suggests that while individual cleavage sites between species are conserved, the four processing sites within a species are not similar, suggesting that up to four different proteases may be involved in processing 2S albumins. The Arabidopsis 2S albumin gene was used to isolate the entire gene family. There are four genes, tightly linked in a tandem array. None of the genes contains an intron. Comparison of the predicted protein sequences shows that only one of the genes can encode the isoform determined by protein analysis to be the most abundant, and therefore this gene is certain to be expressed. It is possible that some or all of the other three genes are also active.
An extended two‐point dixon algorithm for calculating separate water, fat, and B0 images (1997)

A new algorithm is presented that provides separate water, fat, and B0 images utilizing the in-phase and opposed-phase acquisitions of the two-point Dixon (2PD) method. The accuracy of the extended method (E2PD) compares favorably with the three-point Dixon (3PD) method, and the acquisition requires 2/3 the 3PD scan time. Slightly increased mismapping may occur in pixels containing an admixture of water and fat due to reduced SNR in the B0 field map compared with the 3PD method.
Prokaryotic DNA Replication (1992)

The Hippo pathway was initially discovered in Drosophila melanogaster as a key regulator of tissue growth. It is an evolutionarily conserved signaling cascade regulating numerous biological processes, including cell growth and fate decision, organ size ...Read More
Inflammation, Infection, and Pulmonary Function in Infants and Young Children with Cystic Fibrosis (2002)

Our aim was to study the effect of lower airway infection on clinical parameters, pulmonary function tests, and inflammation in clinically stable infants and young children with cystic fibrosis (CF). To accomplish this goal, a prospective cohort of screened CF patients under 4 years of age were studied, using elective anesthesia and intubation for: passive respiratory mechanics (single breath occlusion passive deflation) and lung volumes (nitrogen washout), under neuromuscular blockade; and bronchoalveolar lavage (BAL) of 3 main bronchi for cytology, cytokine interleukin (IL)-8, and quantitative microbiology. There were 22 children studied, with a mean age of 23.2 months (6.7-44 months). A greater relative risk of lower airway pathogens was associated with prior respiratory admission (3.60, 95% confidence interval [CI] 2.87-4.51), history of asthma (1.75, 95% CI 1.52-2.03), and chronic symptoms (1.50, 95% CI 1.23-1.83), especially wheeze (1.88, 95% CI 1.61-2.19). Lower respiratory pathogens (> or = 10 cfu/ml BAL) were found in 14 out of 22, and greater than 10(5) cfu/ml in 8 out of 22 subjects. The level of pathogens in BAL (log10 cfu/ml) explained 78% of the variability in percent neutrophils and 34% of the variability in IL-8 levels. Pathogen level also correlated with pulmonary function tests of specific respiratory system compliance (r -0.49, p = 0.02) and functional residual capacity over total lung capacity (r 0.49, p = 0.03). We conclude that the presence of pathogens in the lower airways correlated with levels of inflammation, respiratory system compliance, and degree of air trapping.
A cover song identification system based on sequences of tonal descriptors (2007)

The present paper corresponds to the extended abstract of a system for cover version identification submitted to the Audio Cover Song task in the context of the Music Information Retrieval Evaluation eXchange (MIREX) 2007. The proposed algorithm extracts sequences of tonal descriptors from audio recordings and uses them to compute a similarity measure between two musical pieces.
Tetracyclines, molecular and clinical aspects (1992)

Journal Article Tetracyclines, molecular and clinical aspects Get access I. Chopra, I. Chopra * aAmerican Cyanamid, Lederle LaboratoriesN. Middletown Road, Pearl River, NY 10965. USA *Corresponding author, current address: Smithkline Beecham Pharmaceuticals, Brockham Park, Betchworth, Surrey RH3 7AJ, UK. Search for other works by this author on: Oxford Academic PubMed Google Scholar P. M. Hawkey, P. M. Hawkey bDepartment of Microbiology, University of LeedsLeeds LS2 9JT Search for other works by this author on: Oxford Academic PubMed Google Scholar M. Hinton M. Hinton cDepartment of Veterinary Medicine, University of BristolLongford House, Longford, Avon, BS18 7DU, UK Search for other works by this author on: Oxford Academic PubMed Google Scholar Journal of Antimicrobial Chemotherapy, Volume 29, Issue 3, March 1992, Pages 245–277, https://doi.org/10.1093/jac/29.3.245 Published: 01 March 1992 Article history Received: 30 July 1991 Accepted: 01 November 1991 Published: 01 March 1992
FK-506-binding protein: three-dimensional structure of the complex with the antagonist L-685,818 (1993)

L-685,818 differs only slightly in structure from the immunosuppressive drug FK-506, and both compounds bind with comparable affinity to the 12-kDa FK-506-binding protein (FKBP12), the major intracellular receptor for the drug. Despite these similarities, L-685,818 is a potent antagonist of both the immunosuppressive and toxic effects of the drug. Here, we present a structural analysis of this problem. Although FK-506 and L-685,818 differ greatly in pharmacology, we have found that the three-dimensional structures of their complexes with FKBP12 are essentially identical. Approximately half of each ligand is in contact with the receptor protein, and half is exposed to solvent; the exposed region includes the two sites where the compounds differ. These results indicate that the profound differences in the pharmacology of these two compounds are not caused by any difference in their interaction with FKBP12. Rather, these effects arise because relatively minor changes in the exposed part of a bound ligand have a strong effect on how FKBP12-ligand complexes interact with calcineurin, their putative intracellular target. In addition, FK-506 complexes with FKBP12 proteins from several species all inhibit mammalian calcineurin. Analysis of the three-dimensional structure of the complex with respect to residues conserved among these proteins suggests a small number of surface residues near the bound ligands that may play a critical role in interactions between the protein-drug complex and calcineurin.
Perforated monolayers: design and synthesis of porous and cohesive monolayers from mercurated calix[n]arenes (1989)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPerforated monolayers: design and synthesis of porous and cohesive monolayers from mercurated calix[n]arenesMichael A. Markowitz, Vaclav Janout, David G. Castner, and Steven L. RegenCite this: J. Am. Chem. Soc. 1989, 111, 21, 8192–8200Publication Date (Print):October 1, 1989Publication History Published online1 May 2002Published inissue 1 October 1989https://pubs.acs.org/doi/10.1021/ja00203a020https://doi.org/10.1021/ja00203a020research-articleACS PublicationsRequest reuse permissionsArticle Views702Altmetric-Citations95LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
An αβ T Cell Receptor Structure at 2.5 Å and Its Orientation in the TCR-MHC Complex (1996)

The central event in the cellular immune response to invading microorganisms is the specific recognition of foreign peptides bound to major histocompatibility complex (MHC) molecules by the alphabeta T cell receptor (TCR). The x-ray structure of the complete extracellular fragment of a glycosylated alphabeta TCR was determined at 2.5 angstroms, and its orientation bound to a class I MHC-peptide (pMHC) complex was elucidated from crystals of the TCR-pMHC complex. The TCR resembles an antibody in the variable Valpha and Vbeta domains but deviates in the constant Calpha domain and in the interdomain pairing of Calpha with Cbeta. Four of seven possible asparagine-linked glycosylation sites have ordered carbohydrate moieties, one of which lies in the Calpha-Cbeta interface. The TCR combining site is relatively flat except for a deep hydrophobic cavity between the hypervariable CDR3s (complementarity-determining regions) of the alpha and beta chains. The 2C TCR covers the class I MHC H-2Kb binding groove so that the Valpha CDRs 1 and 2 are positioned over the amino-terminal region of the bound dEV8 peptide, the Vbeta chain CDRs 1 and 2 are over the carboxyl-terminal region of the peptide, and the Valpha and Vbeta CDR3s straddle the peptide between the helices around the central position of the peptide.
Development of an Adaptive Equalization Algorithm Using Acoustic Energy Density (2009)

Sound pressure equalization of audio signals using digital signal processors has been a subject of ongoing study for many years. The traditional approach is to equalize sound at a point in a listening environment, but because of its specific dependence on the room frequency response between a source and receiver position, this equalization generally causes the spectral response to worsen significantly at other locations in the room. This work presents both a time-invariant and a time-varying implementation of an adaptive acoustic energy density equalization filter for a one-dimensional sound field. Energy density equalization addresses the aforementioned challenge and others that relate to sound equalization. The theory and real-time implementation of time-invariant sound pressure and energy density equalizers designed using the least-squares method are presented, and their performances are compared. An implementation of a time-varying energy density equalizer is also presented. Time-invariant equalization results based on real-time measurements in a plane-wave tube are presented. A sound pressure equalizer results in a nearly flat spectral magnitude at the point of equalization. However, it causes the frequencies corresponding to spatial nulls at that point to be undesirably boosted elsewhere in the sound field, where those nulls do not exist at the same frequencies. An energy density equalization filter identifies and compensates for all resonances and other global spectral effects of the tube and loudspeaker. It does not attempt to equalize the spatially varying frequency nulls caused by local pressure nodes at the point of equalization. An implementation of a time-varying energy density equalizer is also presented. This method uses the filtered-x filter update to adjust the filter coefficients in real-time to adapt to changes in the sound field. Convergence of the filter over time is demonstrated as the closed end of the tube is opened, then closed once again. Thus, the research results demonstrate that an acoustic energy density filter can be used to time-adaptively equalize global spectral anomalies of a loudspeaker and a one-dimensional sound field.
Protrusion of the posterior longitudinal ligament simulating herniated lumbar intervertebral disc. (1968)

Left laminotomy, L4-5, -L5-Sl. Foraminotomy L4-5 Bilateral laminotomy L4-5, 4 yr
Postburn Pancreatitis (1995)

Pancreatitis is a frequent complication after large burn injuries. Patients at high risk for pancreatitis complications should receive surveillance examinations during their acute hospitalization.
Evidence for two functional gal promoters in intact Escherichia coli cells. (1981)

We have used an S1 mapping assay to demonstrate that the mRNA transcripts of the Escherichia coli galactose operon found in intact E. coli cells with a defect in adenylate cyclase or the cyclic AMP receptor protein contain at their 5' end about five nucleotides more than the gal mRNA molecules made in wild type cells. The same difference between gal RNA synthesized in vitro in the absence of cyclic AMP or cyclic AMP receptor protein and gal RNA made in the presence of these factors is detected by this assay. Our results strongly suggest that the same two overlapping promoters, which we previously identified by in vitro transcription of gal DNA fragments, also control the expression of the galactose operon in intact cells. The intracellular levels of cyclic AMP determine which promoter is utilized.
Importance of MHC class 1 α2 and α3 domains in the recognition of self and non-self MHC molecules (1996)

The importance of the species of different domains of class I MHC molecules in peripheral T cell recognition and positive and negative selection was evaluated in a single system. In transgenic mice expressing AAD (containing the alpha1+alpha2 domains of HLA-A2.1 and the alpha3 domain of H-2Dd), the CTL response to influenza peptide M1(58-66) in the context of the alpha1+alpha2 domains of HLA-A2.1 was as strong as the influenza-specific H-2Db-restricted response. However, this strong response was only discernible if the target cell MHC molecule also contained a murine alpha3 domain. In contrast, the response in HLA-A2.1 transgenic mice was about 30-fold weaker, and these CTL were indifferent to the origin of the target molecule alpha3 domain. Further analysis suggested that the major impact of the murine alpha3 domain of the transgene product was to enhance positive selection of a low affinity population of AAD-restricted T cells, presumably through species-specific interaction with CD8. Surprisingly, the response to non-self human class I MHC determinants was not augmented in AAD mice, indicating that the T cells selected are narrowly focused on AAD-related structures. Further analysis indicated that the alphal+alpha2 domains as well as the alpha3 domain influenced the magnitude of the response to non-self human class I MHC determinants, and this effect was mapped to alpha2. We suggest that the alpha2 domains of murine class I molecules contain conserved structural elements that augment the avidity of T cell-class I interactions, and this is particularly important in the recognition of non-self MHC molecules.
Photosensitization of Nanoporous TiO2 Electrodes with InP Quantum Dots (1998)

Quantum dots (QDs) of InP strongly adsorb onto transparent, porous, nanocrystalline TiO2 electrodes prepared by sintering 200−250 Å diameter TiO2 colloidal particles. The interparticle space of the TiO2 electrodes is large enough to permit deep penetration of 65-Å InP QDs into the porous TiO2 film. The absorption of light increases linearly with the thickness of the TiO2 film indicating that the InP QDs are adsorbed homogeneously on the TiO2 surface. We found that large particles adsorb better than smaller ones probably due to less hindrance by the stabilizer. The solid films exhibit strong photoconductivity in the visible region indicating photosensitization of TiO2 by InP QDs. The photocurrent action spectrum of the TiO2/InP QD film at a potential of +1 V is consistent with the absorption spectrum of the InP QDs. A photoelectrochemical cell was formed that consisted of p-type InP QDs loaded on TiO2, which was immersed in a I-/I3- or hydroquinone/quinone acetonitrile solution, and a Pt counter electrode. These photoelectrochemical experiments show that electron transfer from InP QD into TiO2 nanoparticles occurs. p-Type InP/TiO2 electrodes are stable during illumination while n-type photocorrodes in an electrochemical cell.