gebhart/patrepeval huggingface dataset:
Probing Novel Elements for Protein Splicing in the Yeast Vmal Protozyme: A Study of Replacement Mutagenesis and Intragenic Suppression (1997)

Protein splicing is a compelling chemical reaction in which two proteins are produced posttranslationally from a single precursor polypeptide by excision of the internal protein segment and ligation of the flanking regions. This unique autocatalytic reaction was first discovered in the yeast Vma1p protozyme where the 50-kD site-specific endonuclease (VDE) is excised from the 120-kD precursor containing the N- and G-terminal regions of the catalytic subunit of the vacuolar H(+)-ATPase. In this work, we randomized the conserved valine triplet residues three amino acids upstream of the C-terminal splicing junction in the Vma1 protozyme and found that these site-specific random mutations interfere with normal protein splicing to different extents. Intragenic suppressor analysis has revealed that this particular hydrophobic triplet preceding the C-terminal splicing junction genetically interacts with three hydrophobic residues preceding the N-terminal splicing junction. This is the first evidence showing that the N-terminal portion of the V-ATPase subunit is involved in protein splicing. Our genetic evidence is consistent with a structural model that correctly aligns two parallel beta-strands ascribed to the triplets. This model delineates spatial interactions between the two conserved regions both residing upstream of the splicing junctions.
Identification of Volatile Biomarkers of Gastric Cancer Cells and Ultrasensitive Electrochemical Detection based on Sensing Interface of Au-Ag Alloy coated MWCNTs (2014)

Successful development of novel electrochemical biosensing interface for ultrasensitive detection of volatile biomarkers of gastric cancer cells is a challenging task. Herein we reported to screen out novel volatile biomarkers associated with gastric cancer cells and develop a novel Au-Ag alloy composites-coated MWCNTs as sensing interface for ultrasensitive detection of volatile biomarkers. MGC-803 gastric cancer cells and GES-1 gastric mucous cells were cultured in serum-free media. The sample preparation approaches and HS-SPME conditions were optimized for screening volatile biomarkers. Volatiles emitted from the headspace of the cells/medium culture were identified using GC-MS. The Au-Ag nanoparticles-coated multiwalled carbon nanotubes were prepared as a sensing interface for detection of volatile biomarkers. Results showed that eight different volatile metabolites were screened out between MGC-803 cells and GES-1 cells. Two compounds such as 3-octanone and butanone were specifically present in the headspace of the MGC-803 cells. Three volatiles such as 4-isopropoxybutanol, nonanol and 4-butoxy 1-butanol coexisted in the headspace of both the MGC-803 cells and the GES-1 cells, their concentrations in the headspace of the GES-1cells were markedly higher than those in the MGC-803 cells, three volatiles such as formic acid propyl ester, 1.4-butanediol and 2, 6, 11-trimethyl dodecane solely existed in the headspace of the GES-1 cells. The nanocomposites of MWNTs loaded with Au-Ag nanoparticles were prepared as a electrochemical sensing interface for detection of two volatile biomarkers, cyclic voltammetry studies showed that the fabricated sensor could detect 3-octanone in the range of 0~0.0025% (v/v) and with a detection limitation of 0.3 ppb, could detect butanone in the range of 0 ~ 0.055% (v/v), and with a detection limitation of 0.5 ppb, and exhibited good selectivity. The novel electrochemical biosensor combined with volatile biomarkers of gastric cancer owns great potential in applications such as early diagnosis and the prognosis of gastric cancer in near future.
ChemInform Abstract: SYNTHESIS OF A PROTECTED GLYCOSIDE OF α‐D‐PURPUROSAMINE C BY CYCLOADDITION (1980)

Abstract Aus dem Epoxid (I) erhält man die Spaltprodukte (II), aus denen mit Azid das ungesättigte Derivat (III) zugänglich ist.
Cost-effectiveness analysis per life-year gained based on predictors of response for first-line metastatic colorectal cancer therapy in Spain. (2012)

3601 Background: Economic crisis, increasing prevalence and cost of mCRC management endanger availability of biological therapies for public health systems due to budget limitations. We performed a cost-effectiveness analysis based on markers of response/resistance including biological therapies available in Spain for mCRC. Methods: We aimed to calculate incremental cost-effectiveness ratio (ICER) per life-year gained (LYG) and progression-free year gained based on predictive markers for mCRC. Efficacy data include randomized trials (RT) that guided on-label uses of bevacizumab and cetuximab. Control arms from these trials were used as reference to calculate ICERs. Markers of clinical benefit (biological and radiological) were included in this model. Toxicity as predictor of efficacy was excluded for any therapy. Prices for drugs in Spain were assumed to represent the best-value for each drug including all possibilities to reduce pharmacy costs. For 1st line, median duration of therapy reported by RT was used to calculate the final budget. 70kg and 1.7 m were used as reference for patients dose calculations. If accessible, HR for PFS and OS were used instead of medians. Results: K-Ras status and early response measured by CT at 8 weeks were used as predictors of resistance and increased efficacy for cetuximab-based combinations. We have not identified any predictor marker for other drugs from RT. In this regard, FOLFIRI+cetuximab combination obtained an ICER below the widely-proposed Spanish threshold of 30,000 € per LYG if patients harbored wt K-Ras tumors and evidenced an objective response at 8 weeks. Other ICERs for different schedules were too distant from this limit, they will be presented at the meeting. Multivariate analysis confirmed the robustness of results. Conclusions: 1st line FOLFIRI+cetuximab therapy for wt K-Ras patients that get an objective response measured by CT at 8 weeks is the only cost-effective therapy option for mCRC below usual health-economic thresholds for Spain. Our results are critical to design cost-effectiveness based clinical guidelines for mCRC that will contribute to financial sustainability of public health system in Spain.
Pulmonary irradiation for Kaposiʼs sarcoma in AIDS (1985)

A 26-year-old-old male patient with aids (acquired Immune Deficiency Syndrome) and diffuse Kaposi's sarcoma (KS) infiltration of both lungs received bilateral pulmonary irradiation. The patient received 1,600 rad in 10 treatments to the left lung, followed by a 2-week rest period, followed by 1,800 rad in 10 treatments to the right lung. He tolerated the treatments quite well, and demonstrated symptomatic improvement as well as radiographic improvement. This demonstrates both subjective and objective radioresponsiveness of Kaposi's Sarcoma in AIDS patients, and may be utilized as a consideration for palliative treatment of other patients with AIDS and KS.
A bulk-Si-compatible ultrathin-body SOI technology for sub-100 nm MOSFETs (2003)

A novel method of forming 80 nm gate length ultrathin-body SOI MOSFETs has been presented. Lateral solid-phase epitaxy of a deposited amorphous Si film was used to provide excellent controllability over 20 nm body thickness, resulting in good uniformity of device characteristics. The ultrathin body provides good short channel effect suppression. Further optimization should enable fabrication of high-performance devices using a technology compatible with on-chip bulk devices.
The capsule surrounding primary liver tumors: Wherefrom its prognostic significance? (1990)

Primary liver neoplasms in cirrhotic and non-cirrhotic patients were studied by electron microscopy and immunohistochemical methods for extracellular matrix (ECM) antigens. A capsule of variable thickness was present in many expanding hepatocellular carcinomas, while it was absent in those of small size, and either fragmented or absent in the infiltrating ones. In the capsules of early onset, fibronectin was the most frequent stromal glycoprotein. In the completely formed capsular structures, fibronectin, type-V collagen and laminin were the most common macromolecules seen. No differences were evident in the pattern of ECM macromolecules in the capsules surrounding hepatocellular carcinomas compared with those found in benign lesions, such as hepatocellular adenomas or focal nodular hyperplasia. The possibility is discussed that the capsule could be a result of the following sequence: tissue with expansive (not infiltrative) growth-mechanical compression-ischemic necrosis of surrounding tissues-repair process with ECM deposition.
Functionalized polynorbornene dielectric polymers: Adhesion and mechanical properties (1999)

Within the microelectronics industry, there is an ongoing trend toward miniaturization coupled with higher performance. High glass-transition temperature polynorbornenes exhibit many of the key performance criteria necessary for these demanding applications. However, homopolynorbornene exhibits poor adhesion to common substrate materials, including silicon, silicon dioxide, aluminum, gold, and copper. In addition, this homopolymer is extremely brittle, yielding less than 1% elongation-to-break values. To address these issues, the homopolymer was functionalized to improve adhesive and mechanical properties. Attaching triethoxysilyl groups to the polymer backbone substantially improved the adhesion, but at the cost of increasing the dielectric constant because of the polarity of the functional group. Alkyl groups were also added to the backbone, which decreased the rigidity of the system, and resulted in significantly higher elongation-to-break values and a decrease in residual stress. The addition of an alkyl group slightly decreased the dielectric constant of the polymer as a result of an increase in molar volume. The coefficient of thermal expansion and modulus are also reported for the polynorbornene functionalized with triethoxysilyl groups using a multiple substrate approach. © 1999 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys 37: 3003–3010, 1999
Identifying and Modeling Interactions between Biomass Components during Hydrothermal Liquefaction in Sub-, Near-, and Supercritical Water (2021)

We conducted experiments for the hydrothermal liquefaction (HTL) of binary mixtures of biomass components at 300, 350, and 425 °C and then developed a component-additivity model that accounts for interactions among biomass components during HTL and predicts the oil yields for processing biomass mixtures in sub-, near-, and supercritical water. The experimental work provided new insights about the interactions between different biomass components during HTL. Specifically, the interaction and extent of synergy between soy protein and cellulose was a function of the relative amounts of the two materials. Moreover, alkaline lignin has a stronger synergistic effect when processed with cellulose and starch, whereas dealkaline lignin has a stronger synergistic effect with stearic acid. These differences could not be attributed solely to the influence of pH, so there must be other factors that influence interactions of lignin with other biomass components during HTL. The model predicted 70% of the 141 literature bio-oil yields considered to within 10 wt % and performed better by this metric than did prior component-additivity models. Parameterizing the model at different temperatures and including a composition-dependent interaction between cellulose and protein are at the heart of this improvement.
An NMR‐based metabolomic approach to the analysis of the effects of xenobiotics on endogenous metabolite levels in plants (2004)

High field 1 H NMR spectroscopy has been employed to obtain, in conjunction with chemometric analysis, information regarding fluctuations in endogenous metabolic profiles for Crotalaria cobalticola plant cells following exposure to cobalt chloride. Such ‘metabolomic’ type data analysis is often confounded by experimental, environmental or genetic factors that are not correlated to the classifications of interest and serve only to complicate the extraction of meaningful answers from a dataset. This work demonstrates the application of data filtering to remove extraneous data that result from spectrometer variation rather than being correlated with the classes of interest. Samples were analysed from Crotalaria cobalticola suspension cell culture following exposure to cobalt chloride using 2 spectrometers. Removal of confounding data due to spectrometer variation resulted in clear separation between control and dosed classes. It was then possible to use the model to determine key changes in biochemical status caused as a result of exposure to cobalt. Branched chain amino acids, succinate and secondary metabolite precursors phenylalanine and tyrosine were all higher in the control samples, whilst choline, glutamate, alanine and lactate were higher in the dosed samples.
IN VITRO MODULATION OF HUMAN NEUTROPHIL CHEMOTAXIS BY CIS(Z)‐ AND TRANS(E)‐CLOPENTHIXOL, AND CHLORPROMAZINE (1985)

Phenothiazines have been shown to depress several functions of neutrophils, including chemotaxis. A biphasic effect of chlorpromazine (CPZ) and other phenothiazines on human neutrophil chemotaxis has recently been described. We investigated the effect of the stereo-isomers of clopenthizol, a thioxanthene, and of CPZ on human neutrophil chemotaxis. CPZ, at a concentration of 157 microM, and cis(Z)- or trans(E)-clopenthixol, at 105 microM, decreased cell viability. Cis(Z)- and trans(E)-clopenthixol as well as CPZ exerted a biphasic effect on neutrophil chemotaxis with a maximal enhancement of 57%, 92%, and 119%, respectively, and inhibition at higher concentrations. Enhancement of human neutrophil chemotaxis and possibly of the antibacterial activity of these cells by CPZ and the stereo-isomeric compounds of clopenthixol may have clinical implications especially in immunocompromised hosts. The enhancing effect of trans(E)-clopenthixol is of particular importance as this stereo-isomer of clopenthixol exhibits both antimicrobial and antiplasmodial activity but has no antipsychotic or antihypersecretory effect.
Rare Sulfur-Containing Compounds, Kujounins A1 and A2 and Allium Sulfoxide A1, from Allium fistulosum ‘Kujou’ (2017)

Three sulfur-containing compounds, kujounins A<sub>1</sub> (1) and A<sub>2</sub> (2) and allium sulfoxide A<sub>1</sub> (3), were isolated from the acetone extract of Allium fistulosum 'Kujou'. Their chemical structures were elucidated on the basis of physicochemical evidence, including X-ray crystallographic data. Compounds 1 and 2 possess three rings and an acetal structure and were obtained as complex compounds having disulfide and monosaccharide moieties. On the other hand, compound 3 has a thiolane skeleton derived from allicin. Naturally occurring compounds 1-3 have rare molecular skeletons. This study is the first to determine the absolute configuration of thiolane-type compounds.
Optimal quadratic detection using bilinear time-frequency and time-scale representations (2002)

Bilinear time-frequency representations (TFRs) and time-scale representations (TSRs) are potentially very useful for detecting a nonstationary signal in the presence of nonstationary noise or interference. As quadratic signal representations, they are promising for situations in which the optimal detector is a quadratic function of the observations. All existing time-frequency formulations of quadratic detection either implement classical optimal detectors equivalently in the time-frequency domain, without fully exploiting the structure of the TFR, or attempt to exploit the nonstationary structure of the signal in an ad hoc manner. We identify several important nonstationary quadratic detection scenarios which are "naturally" suited for TFR/TSR-based detectors; that is, in which TFR/TSR-based detectors are both optimal and exploit the many degrees of freedom available in the TFR/TSR. We also derive explicit expressions for the corresponding optimal TFR/TSR kernels. The proposed TFR/TSR detectors are directly applicable to many important radar/sonar detection problems.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
NanoHIV: A Bioinformatics Pipeline for Producing Accurate, Near Full-Length HIV Proviral Genomes Sequenced Using the Oxford Nanopore Technology (2021)

HIV-1 proviral single-genome sequencing by limiting-dilution polymerase chain reaction (PCR) amplification is important for differentiating the sequence-intact from defective proviruses that persist during antiretroviral therapy (ART). Intact proviruses may rebound if ART is interrupted and are the barrier to an HIV cure. Oxford Nanopore Technologies (ONT) sequencing offers a promising, cost-effective approach to the sequencing of long amplicons such as near full-length HIV-1 proviruses, but the high diversity of HIV-1 and the ONT sequencing error render analysis of the generated data difficult. NanoHIV is a new tool that uses an iterative consensus generation approach to construct accurate, near full-length HIV-1 proviral single-genome sequences from ONT data. To validate the approach, single-genome sequences generated using NanoHIV consensus building were compared to Illumina<sup>®</sup> consensus building of the same nine single-genome near full-length amplicons and an average agreement of 99.4% was found between the two sequencing approaches.
Calcitonin Gene-Related Peptide Regulates Expression of Neurokinin1Receptors by Rat Spinal Neurons (2003)

Although neurokinin 1 (NK1) receptors contribute to hyperalgesia, and their expression is increased in the spinal cord during peripheral inflammation, little is known regarding the signaling molecules and the second messenger pathways that they activate in regulating the expression of the NK1 receptor gene. Because the promoter region of the NK1 receptor contains a cAMP response element (CRE), we tested the hypothesis that calcitonin gene-related peptide (CGRP) regulates the expression of NK1 receptors via a pathway involving activation of the transcription factor cAMP response element binding protein (CREB). Experiments were conducted on primary cultures of neonatal rat spinal neurons. Treatment of cultures with CGRP for 8-24 hr increased (125)I-substance P binding on spinal neurons; the increase in binding was preceded by an elevation in NK1 receptor mRNA. The CGRP-induced change in (125)I-substance P binding was concentration-dependent and was inhibited by the antagonist CGRP(8-37). CGRP increased phosphorylated CREB immunoreactivity and CRE-dependent transcription in neurons, indicating the involvement of the transcription factor CREB. Evidence that CGRP increased cAMP levels in spinal neurons and that the protein kinase A inhibitor H89 attenuated CGRP-induced CRE-dependent transcription suggests that the intracellular pathway stimulated by CGRP leads to activation of protein kinase A. Collectively these data define a role for CGRP as a signaling molecule that induces expression of NK1 receptors in spinal neurons. The data provide evidence that a neuropeptide receptor controls gene expression in the CNS and add another dimension to understanding the cotransmission of substance P and CGRP by primary afferent neurons.
The Effect of Schistosoma mansoni Infection on the Response of Mice to Salmonella enteritidis and Listeria monocytogenes (1972)

Journal Article The Effect of Schistosoma mansoni Infection on the Response of Mice to Salmonella enteritidis and Listeria monocytogenes Get access F. M. Collins, F. M. Collins Search for other works by this author on: Oxford Academic PubMed Google Scholar D. L. Boros, D. L. Boros Search for other works by this author on: Oxford Academic PubMed Google Scholar K. S. Warren K. S. Warren Search for other works by this author on: Oxford Academic PubMed Google Scholar The Journal of Infectious Diseases, Volume 125, Issue 3, March 1972, Pages 249–256, https://doi.org/10.1093/infdis/125.3.249 Published: 01 March 1972 Article history Received: 02 June 1971 Revision received: 20 September 1971 Published: 01 March 1972
Monolithic cryogenic preamplifiers based on large gate-area GaAs MESFETs (1995)

Monolithic preamplifiers using large gate-area Gallium-Arsenide Metal-Semiconductor Field-Effect Transistors (GaAs MESFETs) at the input have been designed and fabricated using an ion-implanted GaAs process. Large gate-area is necessary to obtain low series noise. A differential voltage-sensitive preamplifier has at the input two MESFETs with a gate width W=6000 /spl mu/m, it is fully DC coupled, has a large common-mode rejection ratio (CMRR) and dissipates low power at 4 K. Dual current-sensitive preamplifiers using at the input MESFETs with W=24000 /spl mu/m, designed for the readout of noble liquid calorimeters, have been integrated in a single chip. Recent tests with a LAr calorimeter prototype demonstrated strong noise reduction compared to previous state-of-the-art hybrid readout circuits. Radiation damage tests have been performed at cold on the current-sensitive preamplifier chips.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Type IX collagen: A possible function in articular cartilage (1988)

The effect of type IX on in vitro fibrillogenesis of type II collagen indicated that, while not preventing fibrillogenesis, the presence of type IX collagen reduced the size of the type II fibre aggregates. This observation is consistent with the in vivo localisation studies of type IX collagen. Using the immunogold labelling technique, type IX collagen was shown to be located evenly on small fibrils which occur at higher concentration closer to the cell. Therefore type IX collagen may function as a regulator of fibre diameter in articular cartilage.
TRF1 negotiates TTAGGG repeat-associated replication problems by recruiting the BLM helicase and the TPP1/POT1 repressor of ATR signaling (2014)

The semiconservative replication of telomeres is facilitated by the shelterin component TRF1. Without TRF1, replication forks stall in the telomeric repeats, leading to ATR kinase signaling upon S-phase progression, fragile metaphase telomeres that resemble the common fragile sites (CFSs), and the association of sister telomeres. In contrast, TRF1 does not contribute significantly to the end protection functions of shelterin. We addressed the mechanism of TRF1 action using mouse conditional knockouts of BLM, TRF1, TPP1, and Rap1 in combination with expression of TRF1 and TIN2 mutants. The data establish that TRF1 binds BLM to facilitate lagging but not leading strand telomeric DNA synthesis. As the template for lagging strand telomeric DNA synthesis is the TTAGGG repeat strand, TRF1-bound BLM is likely required to remove secondary structures formed by these sequences. In addition, the data establish that TRF1 deploys TIN2 and the TPP1/POT1 heterodimers in shelterin to prevent ATR during telomere replication and repress the accompanying sister telomere associations. Thus, TRF1 uses two distinct mechanisms to promote replication of telomeric DNA and circumvent the consequences of replication stress. These data are relevant to the expression of CFSs and provide insights into TIN2, which is compromised in dyskeratosis congenita (DC) and related disorders.