gebhart/patrepeval huggingface dataset:
Identification and characterization of dppA, an Escherichia coli gene encoding a periplasmic dipeptide transport protein (1991)

We describe the isolation and analysis of an Escherichia coli gene, dppA, and its role in dipeptide transport. dppA maps near min 79 and encodes a protein (DppA) that has regions of amino acid similarity with a peptide-binding protein from Salmonella typhimurium (OppA). Like OppA, DppA is found in the periplasmic space and thus is most likely a dipeptide-binding protein. Insertional inactivation of dppA results in the inability of a proline auxotroph to utilize Pro-Gly as a proline source. dppA-dependent Pro-Gly utilization does not require any of the three major proline transport systems, demonstrating that DppA is not simply a dipeptidase. An in vivo competition assay was used to show that DppA is probably involved in the transport of dipeptides other than Pro-Gly. Transcription of dppA is repressed by the presence of casamino acids, suggesting that the cell alters its dipeptide transport capabilities in response to an environmental signal.
Treatment of Autoimmune Diabetes and Insulitis in NOD Mice With Heat Shock Protein 60 Peptide p277 (1995)

We recently showed that a peptide of the M(r) 60,000 heat shock protein molecule, designated peptide p277, is a target of T-cells in autoimmune diabetes in NOD mice. Indeed, the p277 peptide could be used as a therapeutic agent to arrest the autoimmune process even after it was far advanced. The present study was done to document the effects of p277 therapy on inflammation of the islets and on T-cell responsiveness to p277. Groups of female NOD mice of various ages up to 17 weeks were treated with a single inoculation of p277 given before or after the onset of overt hyperglycemia. We now report that fragments of p277 can affect diabetes but that optimal therapy requires the whole peptide. The positive response to p277 was dependent on administration of a threshold dose of peptide. Therapy was accompanied by the regression of intra-islet inflammation and the reappearance of histologically normal islets. Successful peptide therapy was associated with downregulation of T-cell immunity to p277. Adoptive transfer experiments demonstrated that the spleen cells of p277-treated mice were no longer diabetogenic and also could suppress the diabetogenic potential of cotransferred spleen cells of untreated female NOD mice. These results indicate that specific treatment of diabetes with a defined peptide can reprogram the autoimmune response.
Obstructive sleep apnea syndrome detection based on ballistocardiogram via machine learning approach (2019)

Obstructive sleep apnea (OSA) is a common sleep-related respiratory disease that affects people's health, especially in the elderly. In the traditional PSG-based OSA detection, people's sleep may be disturbed, meanwhile the electrode slices are easily to fall off. In this paper, we study a sleep apnea detection method based on non-contact mattress, which can detect OSA accurately without disturbing sleep. Piezoelectric ceramics sensors are used to capture pressure changes in the chest and abdomen of the human body. Then heart rate and respiratory rate are extracted from impulse waveforms and respiratory waveforms that converted by filtering and processing of the pressure signals. Finally, the Heart Rate Variability (HRV) is obtained by processing the obtained heartbeat signals. The features of the heartbeat interval signal and the respiratory signal are extracted over a fixed length of time, wherein a classification model is used to predict whether sleep apnea will occur during this time interval. Model fusion technology is adopted to improve the detection accuracy of sleep apnea. Results show that the proposed algorithm can be used as an effective method to detect OSA.
Thermostabilization of the Bacillus circulansxylanase by the introduction of disulfide bonds (1994)

The thermostability of the 20 396 Da Bacillus circulans xylanase was increased by the introduction of both intra- and intermolecular disulfide bridges by site-directed mutagenesis. Based on the 3-D structure of the enzyme, sites were chosen where favourable geometry for a bridge existed; in one case, to obtain favourable geometry additional mutations around the cysteine sites were designed by computer modelling. The disulfide bonds introduced into the xylanase were mostly buried and, in the absence of protein denaturants, relatively insensitive to reduction by dithiothreitol. The mutant proteins were examined for residual enzymatic activity after various thermal treatments, and were assayed for enzymatic activity at elevated temperatures to assess their productivity. We have examined one of these mutants by X-ray crystallography. All of the disulfide bond designs tested increased the thermostability of the B. circulans xylanase, but not all enhanced the activity of the enzyme at elevated temperatures.
LGeDBMS: a small DBMS for embedded system with flash memory (2006)

The ever-increasing requirement of high performance and huge capacity memories of emerging consumer electronics appliances, such as mobile phone, digital camera, MP3, PMP, PDA, etc., has led to the widespread adaptation of flash memory as main data storages, respectively. As a result, managing the data on ash memory has been gaining in significant to satisfy the requirement of mobile embedded applications. However, the read/write/erase behaviors of flash memory are radically different than that of magnetic disks which make traditional database technology irrelevant. In this paper, we introduce LGeDBMS, a scale-downed DBMS engine designed for ash memory and its application. Finally, we demonstrate a PIM(Personal Information Management) application on a mobile phone using LGeDBMS.
Ca3AlAs3 – ein intermetallisches Analogon zu den Kettensilicaten (1981)

Ketten aus AlAs 4 ‐Tetraedern wurden in der intermetallischen Verbindung Ca 3 AlAs 3 nachgewiesen. Damit ließ sich erstmals zeigen, daß solche Kettenverbände auch in Zintl‐Phasen – und nicht nur in Silicaten und Polyphosphaten – vorkommen.
Dendritic Core−Shell Macromolecules Soluble in Supercritical Carbon Dioxide (2006)

Supercritical carbon dioxide has found strong interest as a reaction medium recently.1,2 As an alternative to organic solvents, compressed carbon dioxide is toxicologically harmless, nonflammable, inexpensive, and environmentally benign.3 Its accessible critical temperature and pressure (Tc ) 31 °C, Pc ) 7.38 MPa, Fc ) 0.468 g cm-3)4 and the possibility of tuning the solvent-specific properties between the ones of liquid and gas are very attractive.
Effect of inhibition of Na+/Ca2+ exchanger at the time of myocardial reperfusion on hypercontracture and cell death (2002)

These results are consistent with the hypothesis that during initial reperfusion NCX activity results in net reverse mode operation contributing to Ca(2+) overload, hypercontracture and cell death, and that NCX inhibition during this phase is beneficial. Beyond this phase, NCX inhibition may impair forward mode-dependent Ca(2+) extrusion and be detrimental. These findings may help in the design of therapeutic strategies against lethal reperfusion injury, with NCX as the target.
Individually Addressable Conducting Polymer Nanowires Array (2004)

A facile technique for fabrication of individually addressable, conducting polymer nanowire arrays of controlled dimension, high aspect ratio, and site-specific positioning using electrodeposition between electrodes in channels created on semiconducting and insulating surfaces that can be easily scaled up is reported. In addition, the ability to create “arrays” of conducting polymer nanowires of same or different materials on the same chip has been demonstrated. The fidelity, quality, and electrical properties of single polypyrrole and polyaniline nanowires have been examined by SEM and I−V characteristics. Dendrite-free conducting polymer nanowires completely confined within the channels with full dimension control were observed. I−V characteristic of such nanowires show the ohmic nature of the contact with Au electrode.
Broad Immunogenicity of a Multigene, Multiclade HIV‐1 DNA Vaccine Boosted with Heterologous HIV‐1 Recombinant Modified Vaccinia Virus Ankara (2008)

International Standard Randomised Controlled Trial number: ISRCTN32604572 .
Design and validation of a synthetic VH repertoire with tailored diversity for protein recognition (2006)

Previous studies have indicated differences in the specificity-determining residues (SDRs) of antibodies that recognize haptens, peptides, or proteins. Here, we designed a V(H) repertoire based on the human scaffold 3-23/J(H)4 and diversification of high and medium-usage SDRs of anti-protein and anti-peptide antibodies. The repertoire was synthesized by overlapping polymerase chain reaction (PCR) and combined with the V(L) chain of the anti-hen egg-white lysozyme (HEL) antibody D1.3. The resulting chimeric single-chain Fv fragments (scFvs) phage-displayed library was panned in HEL-coated immunotubes. After two rounds of selection under non-stringent conditions, that is, trypsinization after 2 h of incubation at room temperature, 63 of 167 clones analyzed (38%) were found to express scFvs specific to HEL. Twenty clones were characterized by DNA sequencing resulting in 10 unique scFvs. Interestingly, the panel of unique scFvs was highly diverse, with V(H) sequences differing in 16 of the 17 positions variegated in the repertoire. Thus, diverse chemico-physical and structural solutions were selected from the library, even when the V(H) repertoire was constrained by the V(L) chain of D1.3 to yield binders against a definite region of HEL surface. The more often selected scFvs, namely H6-1 and B7-1, which differed in eight SDRs, showed levels of expression in E. coli TG1 strain, 6 and 10 times higher than the parental D1.3 Fv fragment, respectively. Dissociation constants (K(Ds)) measured in the BIAcore were 11 and 6.6 nM for H6-1 and B7-1, respectively. These values compared well to the K(D) of 4.7 nM measured for D1.3, indicating that the V(H) repertoire here designed is a valuable source of diverse, well-expressed and high affinity V(H) domains.
Inhibition of Akt signaling promotes the generation of superior tumor-reactive T cells for adoptive immunotherapy (2014)

Effective T-cell therapy against cancer is dependent on the formation of long-lived, stem cell-like T cells with the ability to self-renew and differentiate into potent effector cells. Here, we investigated the in vivo existence of stem cell-like antigen-specific T cells in allogeneic stem cell transplantation (allo-SCT) patients and their ex vivo generation for additive treatment posttransplant. Early after allo-SCT, CD8+ stem cell memory T cells targeting minor histocompatibility antigens (MiHAs) expressed by recipient tumor cells were not detectable, emphasizing the need for improved additive MiHA-specific T-cell therapy. Importantly, MiHA-specific CD8+ T cells with an early CCR7+CD62L+CD45RO+CD27+CD28+CD95+ memory-like phenotype and gene signature could be expanded from naive precursors by inhibiting Akt signaling during ex vivo priming and expansion. This resulted in a MiHA-specific CD8+ T-cell population containing a high proportion of stem cell-like T cells compared with terminal differentiated effector T cells in control cultures. Importantly, these Akt-inhibited MiHA-specific CD8+ T cells showed a superior expansion capacity in vitro and in immunodeficient mice and induced a superior antitumor effect in intrafemural multiple myeloma-bearing mice. These findings provide a rationale for clinical exploitation of ex vivo-generated Akt-inhibited MiHA-specific CD8+ T cells in additive immunotherapy to prevent or treat relapse in allo-SCT patients.
Photocontrolled Nanoparticle Delivery Systems for Biomedical Applications (2014)

"Smart" stimuli-responsive nanomaterials are becoming popular as targeted delivery systems because they allow the use of internal or external stimuli to achieve spatial or temporal control over the delivery process. Among the stimuli that have been used, light is of special interest because it is not only noninvasive but also controllable both spatially and temporally, thus allowing unprecedented control over the delivery of bioactive molecules such as nucleic acids, proteins, drugs, etc. This is particularly advantageous for biomedical applications where specificity and selectivity are highly desired. Several strategies have evolved under the umbrella of light based delivery systems and can be classified into three main groups. The first strategy involves "caging" of the bioactive molecule using photolabile groups, loading these caged molecules onto a carrier and then "uncaging" or activating them at the targeted site upon irradiation with light of a particular wavelength. The second strategy makes use of nanocarriers that themselves are made photoresponsive either through modification with photosensitive groups or through the attachment of photolinkers on the carrier surface. These nanoparticles upon irradiation dissociate, releasing the cargo encapsulated within, or the photolinkers attaching the cargo to the surface get cleaved, resulting in release. The third approach makes use of the surface plasmon resonance of noble metal based nanoparticles. Upon irradiation with light at the plasmon resonant frequency, the resulting thermal or nonthermal field enhancement effects facilitate the release of bioactive molecules loaded onto the nanoparticles. In addition, other materials, certain metal sulfides, graphene oxide, etc., also exhibit photothermal transduction that can be exploited for targeted delivery. These approaches, though effective, are constrained by their predominant use of UV or visible light to which most photolabile groups are sensitive. Near infrared (NIR) excitation is preferred because NIR light is safer and can penetrate deeper in biological tissues. However, most photolabile groups cannot be excited by NIR light directly. So light conversion from NIR to UV/visible is required. Nanomaterials that display upconversion or two-photon-excitation properties have been developed that can serve as nanotransducers, converting NIR to UV/visible light to which the aforementioned photoresponsive moieties are sensitive. This Account will review the existing light-based nanoparticle delivery systems, their applications, the limitations they face, and the technologies that have emerged in an effort to overcome these limitations.
The Cellular Inhibitor of the PKR Protein Kinase, P58IPK, Is an Influenza Virus-activated Co-chaperone That Modulates Heat Shock Protein 70 Activity (1999)

P58(IPK), a member of the tetratricopeptide repeat and J-domain protein families, was first recognized for its ability to inhibit the double-stranded RNA-activated protein kinase, PKR. PKR is part of the interferon-induced host defense against viral infection, and down-regulates translation initiation via phosphorylation of eukaryotic initiation factor 2 on the alpha-subunit. P58(IPK) is activated in response to infection by influenza virus, and inhibits PKR through direct protein-protein interaction. Previously, we demonstrated that the molecular chaperone heat shock protein 40 (hsp40) was a negative regulator of P58(IPK). We could now report that influenza virus activates the P58(IPK) pathway by promoting the dissociation of hsp40 from P58(IPK) during infection. We also found that the P58(IPK)-hsp40 association was disrupted during recovery from heat shock, which suggested a regulatory role for P58(IPK) in the absence of virus infection. The PKR pathway is even more complex as we show in this report that the molecular chaperone, hsp/Hsc70, was a component of a trimeric complex with hsp40 and P58(IPK). Moreover, like other J-domain proteins, P58(IPK) stimulated the ATPase activity of Hsc70. Taken together, our data suggest that P58(IPK) is a co-chaperone, possibly directing hsp/Hsc70 to refold, and thus inhibit kinase function.
Systemic Effects of Periodontitis: Epidemiology of Periodontal Disease and Cardiovascular Disease (2005)

There have been 42 published studies describing associations between oral conditions and cardiovascular diseases. In the absence of randomized controlled trials, the 16 longitudinal studies represent the highest level of evidence available. However, two databases produced eight of the 16 studies. There also is extensive variability in definitions of the oral exposure that include salivary flow, reported periodontal disease, number of teeth, oral organisms, antibodies to oral organisms, Total Dental Index, Community Periodontal Index of Treatment Needs, plaque scores, probing depth, attachment loss, and bone level. Variability also exists in the cardiovascular outcomes that include atherosclerosis measures and events, such as hospitalization for coronary heart disease (CHD), chronic CHD, fatal CHD, total stroke, ischemic stroke, and revascularization procedures. One of the criticisms of this research is that the exposure has not been represented by measures of infection. To begin to address this concern, we present new data showing that patterns of high and low levels of eight periodontal pathogens and antibody levels against those organisms are related to clinical periodontal disease as well as other characteristics of the individuals, such as age, race, gender, diabetic status, atherosclerosis, and CHD. As others before us, we conclude that the cumulative evidence presented above supports, but does not prove, a causal association between periodontal infection and atherosclerotic cardiovascular disease or its sequelae. A number of legitimate concerns have arisen about the nature of the relationship and, indeed, the appropriate definitions for periodontal disease when it is thought to be an exposure for systemic diseases. There is still much work needed to identify which aspects of the exposure are related to which aspects of the outcome. Principal component analyses illustrate the complexity of the interactions among risk factors, exposures, and outcomes. These analyses provide an initial clustering that describes and suggests the presence of specific syndromes.
HOT SAX: Efficiently Finding the Most Unusual Time Series Subsequence (2006)

In this work, we introduce the new problem of finding time series discords. Time series discords are subsequences of a longer time series that are maximally different to all the rest of the time series subsequences. They thus capture the sense of the most unusual subsequence within a time series. Time series discords have many uses for data mining, including improving the quality of clustering, data cleaning, summarization, and anomaly detection. Discords are particularly attractive as anomaly detectors because they only require one intuitive parameter (the length of the subsequence) unlike most anomaly detection algorithms that typically require many parameters. We evaluate our work with a comprehensive set of experiments. In particular, we demonstrate the utility of discords with objective experiments on domains as diverse as Space Shuttle telemetry monitoring, medicine, surveillance, and industry, and we demonstrate the effectiveness of our discord discovery algorithm with more than one million experiments, on 82 different datasets from diverse domains.
Vibrational mode effects, scattering dynamics, and energy disposal in reaction of C2H+2 with methane (1995)

The effects of collision energy and mode-selective vibrational excitation on the reaction of C2H+2 with CH4 and CD4 have been measured, along with the corresponding product velocity distributions. Two distinct reaction mechanisms are active in the energy range below 5 eV. At low energies, a long-lived C3H+6 complex forms efficiently, then decomposes primarily to C3H+5+H and C3H+4+H2. The RRKM lifetime of this complex is estimated to range between ∼10 ns and ∼10 ps over the experimental energy range, and this is sufficient time to allow substantial H-atom scrambling. Complex formation is strongly inhibited by collision energy, weakly inhibited by CC stretching, and enhanced by bending excitation. Competing with the complex-mediated mechanism is a direct H-atom abstraction reaction, producing C2H+3+CH3 with little atom scrambling. This reaction is shown to have a ∼150 meV activation barrier and is strongly enhanced by collision energy, becoming the dominant channel above 0.4 eV. CC stretching provides a weaker enhancement than collision energy, while bending enhances the reaction ∼10 times more efficiently. As collision energies increase, the C2H+3 product is increasingly forward scattered with an increasing fraction of the available energy going into recoil. Energy put into reactant vibration mostly is retained as internal energy of the products. Over the collision energy range from 0.4 to 2.8 eV, the collision time in the direct reaction varies from ≥1.3 ps to ≤70 fs.
Statistical considerations for enumeration of circulating tumor cells (2007)

Elimination of the errors made in the identification of tumor cells isolated from 7.5 ml of blood could potentially reduce the CTC threshold for the identification of patients with a poor prognosis from the current value of five CTCs to one CTC per 7.5 ml of blood.
Increased Secretion of Atrial and Brain Natriuretic Peptides during Acute Myocardial Ischaemia Induced by Dynamic Exercise in Patients with Angina Pectoris (1995)

1. This study was conducted to assess the role of artrial and brain natriuretic peptides during acute myocardial ischaemia associated with dynamic exercise. 2. Study subjects consisted of 35 angiographically proven patients with angina pectoris and 35 angiographically normal control subjects. All subjects underwent 201Tl dynamic exercise testing. The presence and localization of the exercise-induced acute myocardial perfusion defect were assessed by 201Tl single-photon emission computed tomography. The severity score was calculated using the early image for quantitative assessment of the acute myocardial perfusion defect. 3. Plasma levels of atrial natriuretic peptide increased from 21.3 +/- 3.8 to 72.2 +/- 26.7 pg/ml (P < 0.01) in the angina pectoris group, and increased from 19.4 +/- 2.4 to 36.4 +/- 17.4 pg/ml (P < 0.01) in the control group during dynamic exercise. Plasma levels of brain natriuretic peptide increased from 2.8 +/- 0.8 to 6.9 +/- 2.6 pg/ml (P < 0.01) in the angina pectoris group, but did not change significantly in the control group (from 2.7 +/- 0.7 to 2.9 +/- 1.0 pg/ml) during dynamic exercise. At peak exercise, plasma levels of these natriuretic peptides in the angina pectoris group were significantly higher than those in the control group (P < 0.01). 4. At peak exercise, there were correlations between the plasma level of atrial natriuretic peptide and heart rate in both the angina pectoris and control groups (P < 0.01, r = 0.46; P < 0.01, r = 0.51, respectively), but no significant correlations between the plasma level of brain natriuretic peptide and heart rate in either group. The plasma levels of these peptides at peak exercise correlated well with the severity score in the angina pectoris group (atrial natriuretic peptide, r = 0.71, P < 0.01; brain natriuretic peptide, r = 0.69, P < 0.01).
Digital Diffractive Optics: An Introduction to Planar Diffractive Optics and Related Technology (2000)

Introduction: From Diffraction to Diffractive Optics. Design and Simulation of Diffractive Optical Elements. DOE Fabrication and Replication Techniques. CAD/CAM Tools for DOEs. DOE Fabrication Tolerancing Analysis. DOE Mask Layout Generation. System-Oriented DOE Designs: Examples. Conclusion. Index.