gebhart/patrepeval huggingface dataset:
Reconstruction of a bacterial isoprenoid biosynthetic pathway in Saccharomyces cerevisiae (2008)

A eukaryotic mevalonate pathway transferred and expressed in Escherichia coli, and a mammalian hydrocortisone biosynthetic pathway rebuilt in Saccharomyces cerevisiae are examples showing that transferring metabolic pathways from one organism to another can have a powerful impact on cell properties. In this study, we reconstructed the E. coli isoprenoid biosynthetic pathway in S. cerevisiae. Genes encoding the seven enzymatic steps of the pathway were cloned and expressed in S. cerevisiae. mRNA from the seven genes was detected, and the pathway was shown able to sustain growth of yeast in conditions of inhibition of its constitutive isoprenoid biosynthetic pathway.
The E670G SNP in the PCSK9 gene is associated with polygenic hypercholesterolemia in men but not in women (2006)

In a European population the E670G SNP in the PCSK9 gene is associated with increased LDL in men but not in women.
Specific associations of fluorescent beta-2-microglobulin with cell surfaces. The affinity of different H-2 and HLA antigens for beta-2-microglobulin. (1988)

We prepared single-labeled FITC derivatives of beta-2-microglobulin (b2m) and examined their interactions with class I MHC Ag H chains on living cells. Human b2m was reacted with FITC under mild conditions and separated by hydroxylapatite chromatography into three peaks containing single labeled derivatives of b2m peaks A, B, and C, and a peak containing the unmodified protein. The three fluorescent derivatives labeled the surfaces of cells bearing class I MHC Ag. The labeling was specific for class I MHC Ag as indicated by failure to label cells in the presence of excess unlabeled b2m and failure to label the HLA-negative cell lines Daudi and 721.221. Mouse cells labeled with fluorescent human b2m were recognized by mAb to the class I MHC Ag and by virus-restricted cytotoxic T lymphocytes, suggesting that labeling with the fluorescent b2m does not significantly alter the structure of class I MHC Ag or impair their ability to present viral antigens to cytotoxic T lymphocytes. We determined the kinetic and equilibrium binding parameters for the fluorescent b2m derivatives associating with the class I H chains of mouse and human cells. Peaks B and C exhibited biphasic binding to the mouse lymphoma cells EL-4(G-CSA-) (Kd1 = 1 x 10(-9) M; K2 = 1.5 to 3.0 x 10(-8) M whereas peak A bound to a small number of low affinity binding sites. In contrast to the biphasic binding observed with EL-4(G-CSA-), only monophasic binding was observed for peak C binding to RDM4 cells. Biphasic binding was also observed with the human B cell line LCL 721. Analysis of a series of LCL 721 class I MHC loss mutants and gene transferents revealed that the heterogeneity in binding is due to differences in the affinity of different class I encoded H chains for b2m.
Mismatch repair deficiency predicts response of solid tumors to PD-1 blockade (2017)

The genomes of cancers deficient in mismatch repair contain exceptionally high numbers of somatic mutations. In a proof-of-concept study, we previously showed that colorectal cancers with mismatch repair deficiency were sensitive to immune checkpoint blockade with antibodies to programmed death receptor-1 (PD-1). We have now expanded this study to evaluate the efficacy of PD-1 blockade in patients with advanced mismatch repair-deficient cancers across 12 different tumor types. Objective radiographic responses were observed in 53% of patients, and complete responses were achieved in 21% of patients. Responses were durable, with median progression-free survival and overall survival still not reached. Functional analysis in a responding patient demonstrated rapid in vivo expansion of neoantigen-specific T cell clones that were reactive to mutant neopeptides found in the tumor. These data support the hypothesis that the large proportion of mutant neoantigens in mismatch repair-deficient cancers make them sensitive to immune checkpoint blockade, regardless of the cancers' tissue of origin.
Is Mycoplasma pneumoniae Associated with Vascular Disease? (2000)

Several studies have postulated a link between infectious agents and atherosclerosis (3, 12). Epidemiological and pathological studies have shown an association between Chlamydia pneumoniae and atherosclerosis (3, 12). C. pneumoniae has been detected in vascular tissues and degenerative heart valves (3, 9). It has been suggested that Mycoplasma pneumoniae might also play a role in the development of atherosclerosis (12). Myocarditis, pericarditis, cerebral stroke, and vasculitis have been previously associated with M. pneumoniae infection (1, 4, 5, 11). M. pneumoniae might be seen as a plausible candidate to play a role in the pathogenesis of atherosclerosis, because it has been related to cardiovascular disease and its ability to induce chronic inflammation (12). Taylor-Robinson and Thomas have postulated that there is a need to investigate the presence of M. pneumoniae in vascular tissues, because there is a similarity in epidemiological behavior and antibiotic susceptibility between M. pneumoniae and C. pneumoniae(12). Furthermore, M. fermentans has been detected in 1 of 19 human arterial specimens that were positive forC. pneumoniae (10), and it has been shown thatM. gallisepticum exhibits tropism for arterial tissue in turkeys (2). However, nothing is known about the presence ofM. pneumoniae in human atherosclerotic vascular tissues. Therefore, we investigated the presence of M. pneumoniae in atherectomy specimens and in degenerative heart valve (DHV) specimens.
Demonstration of a Fourth-Order Pole-Zero Optical Filter Integrated Using CMOS Processes (2007)

We demonstrate a compact fully tunable narrowband fourth-order pole-zero optical filter that is fabricated in a silicon complementary-metal-oxide-semiconductor foundry. The filter is implemented using silicon on oxide channel waveguides and consists of a Mach-Zehnder interferometer with two ring resonator all-pass filters (APFs) on each arm. The filter architecture is based on the sum and difference of the APFs responses. The ring resonators introduce a nonlinear phase response in each arm that allows carving narrow frequency bands out of a broad spectrum. In this paper, we demonstrate a 3-dB filter bandwidth of 1.0 GHz with a stopband rejection of better than 25 dB. The filter free spectral range is 16.5 GHz. Thermooptic phase shifters are used to tune the filter. As silicon has a large thermooptic coefficient compared to silica, the demonstrated filter requires a low tuning power of less than 300 mW. In addition, this filter is compact with dimensions 25 times smaller than the same filter would be if it were made using standard silica on silicon waveguides with a 0.8% step index contrast
MicroMandarin (2011)

Learning a new language is hard, but learning to use it confidently in conversations with native speakers is even harder. From our field research with language learners, with support from Cognitive Psychology and Second Language Acquisition, we argue for the value of contextual microlearning in the many breaks spread across different places and throughout the day. We present a mobile application that supports such microlearning by leveraging the location-based service Foursquare to automatically provide contextually relevant content in the world's major cities. In an evaluation of Mandarin Chinese learning, a four-week, 23-user study spanning Beijing and Shanghai compared this contextual system to a system based on word frequency. Study sessions with the contextual version lasted half as long but occurred in twice as many places as sessions with the frequency version, suggesting a complementary relationship between the two approaches.
The Non-Hodgkin Lymphoma Pathologic Classification Project (1988)

The probability of long-term survival for unselected patients with non-Hodgkin lymphoma can be substantial. Long-term prognosis depends on the histologic subtype of the tumor and the extent of dissemination. The Working Formulation for non-Hodgkin lymphomas is a simple and useful nomenclature for selecting treatment and reporting results. The Ann Arbor staging system is a useful but imperfect prognostic indicator.
Single-dose replicating RNA vaccine induces neutralizing antibodies against SARS-CoV-2 in nonhuman primates (2020)

The ongoing COVID-19 pandemic, caused by infection with SARS-CoV-2, is having a dramatic and deleterious impact on health services and the global economy. Grim public health statistics highlight the need for vaccines that can rapidly confer protection after a single dose and be manufactured using components suitable for scale-up and efficient distribution. In response, we have rapidly developed repRNA-CoV2S, a stable and highly immunogenic vaccine candidate comprised of an RNA replicon formulated with a novel Lipid InOrganic Nanoparticle (LION) designed to enhance vaccine stability, delivery and immunogenicity. We show that intramuscular injection of LION/repRNA-CoV2S elicits robust anti-SARS-CoV-2 spike protein IgG antibody isotypes indicative of a Type 1 T helper response as well as potent T cell responses in mice. Importantly, a single-dose administration in nonhuman primates elicited antibody responses that potently neutralized SARS-CoV-2. These data support further development of LION/repRNA-CoV2S as a vaccine candidate for prophylactic protection from SARS-CoV-2 infection.
Involvement of Hsp90 in Assembly and Nuclear Import of Influenza Virus RNA Polymerase Subunits (2006)

Transcription and replication of the influenza virus RNA genome occur in the nuclei of infected cells through the viral RNA-dependent RNA polymerase consisting of PB1, PB2, and PA. We previously identified a host factor designated RAF-1 (RNA polymerase activating factor 1) that stimulates viral RNA synthesis. RAF-1 is found to be identical to Hsp90. Here, we examined the intracellular localization of Hsp90 and viral RNA polymerase subunits and their molecular interaction. Hsp90 was found to interact with PB2 and PB1, and it was relocalized to the nucleus upon viral infection. We found that the nuclear transport of Hsp90 occurs in cells expressing PB2 alone. The nuclear transport of Hsp90 was in parallel with that of the viral RNA polymerase binary complexes, either PB1 and PB2 or PB1 and PA, as well as with that of PB2 alone. Hsp90 also interacted with the binary RNA polymerase complex PB1-PB2, and it was dissociated from the PB1-PB2 complex upon its association with PA. Furthermore, Hsp90 could form a stable PB1-PB2-Hsp90 complex prior to the formation of a ternary polymerase complex by the assembly of PA in the infected cells. These results suggest that Hsp90 is involved in the assembly and nuclear transport of viral RNA polymerase subunits, possibly as a molecular chaperone for the polymerase subunits prior to the formation of a mature ternary polymerase complex.
Identification of New Genes Involved in the Virulence ofListeria monocytogenesby Signature-Tagged Transposon Mutagenesis (2001)

Listeria monocytogenes is a gram-positive, facultative intracellular pathogen that can cause severe food-born infections in humans and animals. We have adapted signature-tagged transposon mutagenesis to L. monocytogenes to identify new genes involved in virulence in the murine model of infection. We used transposon Tn1545 carried on the integrative vector pAT113. Forty-eight tagged transposons were constructed and used to generate banks of L. monocytogenes mutants. Pools of 48 mutants were assembled, taking one mutant from each bank, injected into mice, and screened for those affected in their multiplication in the brains of infected animals. From 2,000 mutants tested, 18 were attenuated in vivo. The insertions harbored by these mutants led to the identification of 10 distinct loci, 7 of which corresponded to previously unknown genes. The properties of four loci involving putative cell wall components were further studied in vitro and in vivo. The data suggested that these components are involved in bacterial invasion and multiplication in the brain.
Evidence for an impact on the incidence of canine leishmaniasis by the mass use of deltamethrin‐impregnated dog collars in southern Italy (2001)

Dogs are the domestic reservoir of Leishmania infantum Nicolle (Kinetoplastida: Trypanosomatidae), the agent of zoonotic human visceral leishmaniasis. In southern Europe, where canine leishmaniasis (CanL) is widespread due to L. infantum, killing seropositive dogs is considered unacceptable and drug treatment has low efficacy in preventing transmission. We made a field evaluation of the efficacy of deltamethrin dog collars in a CanL focus of southern Italy, Mount Vesuvius area of Campania region, where the vector is Phlebotomus perniciosus Newstead (Diptera: Psychodidae), by assessing their impact on the incidence of CanL in an intervention town, compared to that in dogs of control towns where no collars were fitted. During two consecutive transmission seasons, collars were fitted to 350 (1998) and 354 (1999) dogs from San Sebastiano al Vesuvio (70% of the canine population). Control dogs (371 and 264 in the 2 years, respectively) were from four towns of the same area. Before each transmission season, the CanL seroprevalence in the intervention and control towns was evaluated by cross-sectional surveys and found to be similar (about 15% in 1998 and 10% in 1999, respectively). After each transmission period, incidence rates of seroconversions were determined in adult dogs that were serologically negative before the season under evaluation, and in puppies. After the 1998 season, 2.7% of the dogs in the intervention town seroconverted compared to 5.4% in the control towns (50% protection, P = 0.15). After the 1999 season, 3.5% of collared dogs seroconverted compared to 25.8% of control dogs (86% protection, P < 0.001). The increase in seroconversion rates recorded in control dogs suggests an increase in the Leishmania force of infection in the canine reservoir during the 1999 sandfly season, as supported by the concomitant increase of human cases in control towns and in the whole Campania region. Our results suggest that the impact of mass use of deltamethrin-impregnated dog collars on the incidence of CanL may be negligible during low transmission seasons, or probably in low endemic foci, but can be very strong when the force of transmission is high.
Genomics and the Multifactorial Nature of Human Autoimmune Disease (2011)

This article reviews the many new insights into autoimmune disease brought about through genomic investigations.
Antivascular effects of electrochemotherapy: implications in treatment of bleeding metastases (2010)

Solid tumors of various etiologies can be treated efficiently by electrochemotherapy (ECT), a combined use of electroporation (EP) and chemotherapeutic drugs, such as bleomycin and cisplatin. EP alone and ECT in particular, induce a profound reduction in tumor blood flow, which contributes to the antitumor effect. After EP and ECT, the time course of blood flow changes and follows the same two-phase pattern. The first rapid and short-lived vasoconstriction phase is followed by the second much longer-lived phase resulting from disrupted cytoskeletal structures and a compromised barrier function of the microvascular endothelium. In the case of ECT, however, tumor vascular endothelial cells are also affected by the chemotherapeutic drug, which leads to irrecoverable damage to tumor vessels and to a further decrease in tumor blood flow within hours after application of ECT. Tumor cells surviving the direct effects of ECT are consequently exposed to lack of oxygen and nutrients and are pushed into the secondary cascade of induced cell death. Clinically, the antitumor effectiveness of ECT has been proven extensively in the treatment of melanoma metastases, with 70-80% complete responses. The antivascular effects of ECT were also exploited for palliative treatment of bleeding melanoma metastases, with immediate cessation of bleeding and very good antitumor effectiveness. The antivascular effect of ECT is of utmost importance for translation of ECT into the treatment of deep-seated tumors, especially in well vascularized organs, such as the liver, where it prevents bleeding of the treated area.
Human monocyte chemotactic proteins-2 and -3: structural and functional comparison with MCP-1 (1996)

Structurally, the monocyte chemotactic proteins MCP-1, -2, and -3 form a subfamily of the C-C or beta-chemokines. Like other chemokines, MCPs are produced by a variety of cells on stimulation with cytokines (interleukin-1, tumor necrosis factor-alpha, interferon-gamma), bacterial and viral products or mitogens. MCP-1 levels are enhanced during infection and inflammation, which are characterized by leukocyte infiltration. In vitro, MCPs are chemotactic for a distinct spectrum of target cells and show different specific biological activities depending on the cell type and the chemokine tested. MCP-3 has the broadest range in that it activates monocytes, dendritic cells, lymphocytes, natural killer cells, eosinophils, basophils, and neutrophils. The most sensitive cells to all three MCPs are lymphocytes and monocytes. MCP-1 is a potent basophil activator but does not attract eosinophils, whereas, at higher concentrations, MCP-2 also stimulates both eosinophils and basophils. The signal transduction of MCPs on monocytes involves at least two G protein-linked C-C chemokine receptors: C-C CKR-1 binds MCP-3 and C-C CKR-2 binds MCP-1 and MCP-3 but not MCP-2. Receptor binding leads to enhanced [Ca2+]i for all chemokines except for MCP-2.
A Comparison of Digital Subscriber Line Transmission Systems Employing Different Line Codes (1981)

In this paper the main characteristics and the performance of two systems implemented for two wire digital transmission on subscriber lines are presented. Both systems utilize different time intervals to transmit bursts of bits in the two directions with an information bit rate of 80 kbits/s and a line bit rate in the bursts of 256 kbits/s. One system employing WAL2 as the line code exhibits extreme circuitry simplicity and low power consumption. The other system, which employs CMI as the line code, shows better performance in the presence of line disturbances.
New solution for prolonged myocardial preservation for transplantation. (1998)

The JCT solution is effective (as well as HTK) in preserving the ischemic hearts for up to 12 hours. It is superior to HTK or University of Wisconsin solution at 20 hours of isolated ischemic storage.
Extracellular fluid volume determined by bioelectric impedance and serum albumin in CAPD patients. (1998)

Hypoalbuminaemia is partly dependent on subclinical overhydration in CAPD patients. Serum albumin is negatively correlated with increased extracellular fluid volume and the proportion of Vecf to Vtbw is increased in hypoalbuminaemic patients. Multifrequency bioelectrical impedance is able to identify these abnormalities.
Inherent backbone dynamics fine-tune the functional plasticity of Tudor domains (2021)

Tudor domains are crucial for mediating a diversity of protein-protein or protein-DNA interactions involved in nucleic acid metabolism. Using solution NMR spectroscopy, we assess the comprehensive understanding of the dynamical properties of the respective Tudor domains from four different bacterial (Escherichia coli) proteins UvrD, Mfd, RfaH, and NusG involved in different aspects of bacterial transcription regulation and associated processes. These proteins are benchmarked to the canonical Tudor domain fold from the human SMN protein. The detailed analysis of protein backbone dynamics and subsequent analysis by the Lipari-Szabo model-free approach revealed subtle differences in motions of the amide-bond vector on both pico- to nanosecond and micro- to millisecond timescales. On these timescales, our comparative approach reveals the usefulness of discrete amplitudes of dynamics to discern the different functionalities for Tudor domains exhibiting promiscuous binding, including the metamorphic Tudor domain included in the study.
The role of the thiol/disulfide centers and peptide binding site in the chaperone and anti-chaperone activities of protein disulfide isomerase. (1994)

The complexity of protein folding is often aggravated by the low solubility of the denatured state. The inefficiency of the oxidative refolding of reduced, denatured lysozyme results from a kinetic partitioning of the unfolded protein between pathways leading to aggregation and pathways leading to the native structure. Protein disulfide isomerase (PDI), a resident foldase of the endoplasmic reticulum, catalyzes the in vitro oxidative refolding of reduced, disulfide-containing proteins, including denatured lysozyme. Depending on the concentrations of foldase and denatured substrate and the order in which they are added to initiate folding, PDI can exhibit either a chaperone activity or an anti-chaperone activity (Puig, A., and Gilbert, H. F. (1994) J. Biol. Chem 269, 7764-7771). PDI's chaperone activity leads to quantitative recovery of native lysozyme. Its anti-chaperone activity diverts substrate away from productive folding and facilitates disulfide cross-linking of lysozyme into large, inactive aggregates that specifically incorporate PDI. A mutant PDI (NmCm-PDI), in which both the N- and C-terminal active site cysteines have been changed to serines, loses all chaperone activity and behaves as an anti-chaperone at all substrate and PDI concentrations tested. The dithiol/disulfide sites of PDI are essential for the chaperone activity observed at high PDI concentrations, but they are not required for the anti-chaperone activity found at low PDI concentrations. Inactivation of PDI's peptide/protein binding site by a specific photoaffinity label (Noiva, R., Freedman, R. B., and Lennarz, W. J. (1993) J. Biol. Chem. 268, 19210-19217) inhibits the disulfide isomerase and chaperone activity, but the protein still retains its anti-chaperone activity. In a glutathione redox buffer, lysozyme-PDI aggregates are disulfide cross-linked; however, disulfide cross-linking is not required for aggregate formation or for the incorporation of PDI into the aggregates. Although both the peptide binding site and the catalytic active sites of PDI are required for chaperone and disulfide isomerase activity, neither of these sites are involved in PDI's anti-chaperone activity. PDI's anti-chaperone activity could serve as a quality control device by providing an efficient mechanism to retain misfolded proteins in the endoplasmic reticulum (Marquardt, T., and Helenius, A. (1992) J. Cell. Biol. 117, 505-513).
Weakening of the T7 Promoter-Polymerase Interaction Facilitates Promoter Release (2005)

During transcription initiation, RNA polymerases retain interactions with their promoters until the RNA is extended to 8-13 nucleotides, at which point the polymerase releases the promoter and moves downstream. It has been shown that release of the T7 promoter is inhibited when the T7 RNA polymerase-promoter interaction is strengthened. Here we asked whether release would be facilitated when the T7 promoter-polymerase interaction is weakened by the introduction of promoter mutations known to reduce promoter activity. Using chemical and enzymatic probes to monitor the position of the polymerase as a function of RNA length, we found that promoter mutations upstream of -4 facilitated release of the polymerase from the promoter, but more downstream mutations did not have such effects. We also found that released complexes turn over more slowly than promoter-bound complexes, indicating that retention of promoter interactions contributes to the dissociation of short RNAs during initial transcription.