gebhart/patrepeval huggingface dataset:
Progress and Prospects on Vaccine Development against SARS-CoV-2 (2020)

In December 2019, the outbreak of pneumonia caused by a novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has led to a serious pandemic in China and other countries worldwide. So far, more than 460,000 confirmed cases were diagnosed in nearly 190 countries, causing globally over 20,000 deaths. Currently, the epidemic is still spreading and there is no effective means to prevent the infection. Vaccines are proved to be the most effective and economical means to prevent and control infectious diseases. Several countries, companies, and institutions announced their programs and progress on vaccine development against the virus. While most of the vaccines are under design and preparation, there are some that have entered efficacy evaluation in animals and initial clinical trials. This review mainly focused on the progress and our prospects on field of vaccine development against SARS-CoV-2.
Prime-Boost Immunization Schedules Based on Influenza Virus and Vaccinia Virus Vectors Potentiate Cellular Immune Responses against Human Immunodeficiency Virus Env Protein Systemically and in the Genitorectal Draining Lymph Nodes (2003)

Vaccines that elicit systemic and mucosal immune responses should be the choice to control human immunodeficiency virus (HIV) infections. We have previously shown that prime-boost immunizations with influenza virus Env and vaccinia virus (VV) WR Env recombinants induced an enhanced systemic CD8(+) T-cell response against HIV-1 Env antigen. In this report, we analyzed in BALB/c mice after priming with influenza virus Env the ability of two VV recombinants expressing HIV-1 Env B (VV WR Env and the highly attenuated modified VV Ankara [MVA] Env) to boost cellular immune responses in the spleen and in the lymph nodes draining the genital and rectal tracts. Groups of mice were primed by the intranasal route with 10(4) PFU of influenza virus Env and boosted 14 days later by the intraperitoneal or intranasal route with 10(7) PFU of MVA Env or VV WR Env, while the control group received two immunizations with influenza virus Env. We found that the combined immunization (Flu/VV) increased more than 60 times the number of gamma interferon-specific CD8(+) T cells compared to the Flu/Flu scheme. Significantly, boosting with MVA Env by the intraperitoneal route induced a response 1.25 or 2.5 times (spleen or genital lymph nodes) higher with respect to that found after the boost with VV WR Env. Mice with an enhanced CD8(+) T-cell response also had an increased Th1/Th2 ratio, evaluated by the cytokine pattern secreted following in vitro restimulation with gp160 protein and by the specific immunoglobulin G2a (IgG2a)/IgG1 ratio in serum. By the intranasal route recombinant WR Env booster gave a more efficient immune response (10 and 1.3 times in spleen and genital lymph nodes, respectively) than recombinant MVA Env. However, the scheme influenza virus Env/MVA Env increased four times the response in the spleen, giving a low but significant response in the genital lymph nodes compared with a single intranasal immunization with MVA Env. These results demonstrate that the combination Flu/MVA in prime-booster immunization regimens is an effective vaccination approach to generate cellular immune responses to HIV antigens at sites critical for protective responses.
Nucleotide sequence analysis of genome segment A of infectious bursal disease virus (1990)

The nucleotide sequence of genome segment A cDNA of the STC strain of infectious bursal disease virus (IBDV) was determined and compared with sequences of the homologous genome segment of the 002-73 strain of IBDV and the Jasper strain of infectious pancreatic necrosis virus (IPNV). The STC-IBDV genome segment A was determined to be 3262 base pairs (bp), which is close to the estimated total length of 3300 bp for genome segment A in IBDV, although there is no proof that it is the real length of this genome segment. The STC-IBDV genome segment A contains two major overlapping open reading frames (ORFs). The large ORF of 3036 bp predicts a polyprotein of Mr 109,358, whereas the small ORF is 435 bp and predicts a protein of Mr 16,550 in STC-IBDV. STC-IBDV and 002-73-IBDV polyproteins are closely related (97.4% amino acid homology). Most of the amino acid mismatches are in VP2 sequences, mainly within the area of the conformation-dependent epitope. Comparison with the Jasper-IPNV polyprotein reveals levels of amino acid sequence homology of about 40% in VP2, 32% in VP3 and 21% in VP4. Within the VP2 molecule the conformation-dependent epitope area is again the least homologous, but the heterogeneity is more conspicuous than between the two IBDV strains, which is not surprising since IBDV and IPNV are serologically unrelated. The small ORF proteins have about 88% amino acid sequence homology between STC-IBDV and 002-73-IBDV, and 30% between each IBDV strain and Jasper-IPNV. There is no homology at all in the non-coding regions of IBDV and IPNV. These comparative sequence data will be useful for subgrouping the Birnaviridae family.
Memory loss in old rats is associated with brain mitochondrial decay and RNA/DNA oxidation: Partial reversal by feeding acetyl- l -carnitine and/or R -α-lipoic acid (2002)

Accumulation of oxidative damage to mitochondria, protein, and nucleic acid in the brain may lead to neuronal and cognitive dysfunction. The effects on cognitive function, brain mitochondrial structure, and biomarkers of oxidative damage were studied after feeding old rats two mitochondrial metabolites, acetyl-l-carnitine (ALCAR) [0.5% or 0.2% (wt/vol) in drinking water], and/or R-alpha-lipoic acid (LA) [0.2% or 0.1% (wt/wt) in diet]. Spatial memory was assessed by using the Morris water maze; temporal memory was tested by using the peak procedure (a time-discrimination procedure). Dietary supplementation with ALCAR and/or LA improved memory, the combination being the most effective for two different tests of spatial memory (P < 0.05; P < 0.01) and for temporal memory (P < 0.05). Immunohistochemical analysis showed that oxidative damage to nucleic acids (8-hydroxyguanosine and 8-hydroxy-2'-deoxyguanosine) increased with age in the hippocampus, a region important for memory. Oxidative damage to nucleic acids occurred predominantly in RNA. Dietary administration of ALCAR and/or LA significantly reduced the extent of oxidized RNA, the combination being the most effective. Electron microscopic studies in the hippocampus showed that ALCAR and/or LA reversed age-associated mitochondrial structural decay. These results suggest that feeding ALCAR and LA to old rats improves performance on memory tasks by lowering oxidative damage and improving mitochondrial function.
The effect of cigarette smoking on the development of AIDS in HIV-1-seropositive individuals (1993)

Cigarette smoking by HIV-1-seropositive individuals is associated with a more rapid development of AIDS and should be discouraged.
The Vaginal Microbiota: What Have We Learned after a Decade of Molecular Characterization? (2014)

We conducted a systematic review of the Medline database (U.S. National Library of Medicine, National Institutes of Health, Bethesda, MD, U.S.A) to determine if consistent molecular vaginal microbiota (VMB) composition patterns can be discerned after a decade of molecular testing, and to evaluate demographic, behavioral and clinical determinants of VMB compositions. Studies were eligible when published between 1 January 2008 and 15 November 2013, and if at least one molecular technique (sequencing, PCR, DNA fingerprinting, or DNA hybridization) was used to characterize the VMB. Sixty three eligible studies were identified. These studies have now conclusively shown that lactobacilli-dominated VMB are associated with a healthy vaginal micro-environment and that bacterial vaginosis (BV) is best described as a polybacterial dysbiosis. The extent of dysbiosis correlates well with Nugent score and vaginal pH but not with the other Amsel criteria. Lactobacillus crispatus is more beneficial than L. iners. Longitudinal studies have shown that a L. crispatus-dominated VMB is more likely to shift to a L. iners-dominated or mixed lactobacilli VMB than to full dysbiosis. Data on VMB determinants are scarce and inconsistent, but dysbiosis is consistently associated with HIV, human papillomavirus (HPV), and Trichomonas vaginalis infection. In contrast, vaginal colonization with Candida spp. is more common in women with a lactobacilli-dominated VMB than in women with dysbiosis. Cervicovaginal mucosal immune responses to molecular VMB compositions have not yet been properly characterized. Molecular techniques have now become more affordable, and we make a case for incorporating them into larger epidemiological studies to address knowledge gaps in etiology and pathogenesis of dysbiosis, associations of different dysbiotic states with clinical outcomes, and to evaluate interventions aimed at restoring and maintaining a lactobacilli-dominated VMB.
Classification of primary headaches (2004)

Given the range of disorders that produce headache, a systematic approach to classification and diagnosis is an essential prelude to clinical management. For the last 15 years, the diagnostic criteria of the International Headache Society (IHS) have been the accepted standard. The second edition of The International Classification of Headache Disorders (January 2004) reflects our improved understanding of some disorders and the identification of new disorders. Neurologists who treat headache should become familiar with the revised criteria. Like its predecessor, the second edition of the IHS classification separates headache into primary and secondary disorders. The four categories of primary headaches include migraine, tension-type headache, cluster headache and other trigeminal autonomic cephalalgias, and other primary headaches. There are eight categories of secondary headache. Important changes in the second edition include a restructuring of these criteria for migraine, a new subclassification of tension-type headache, introduction of the concept of trigeminal autonomic cephalalgias, and addition of previously unclassified primary headaches. Several disorders were eliminated or reclassified. In this article, the authors present an overview of the revised IHS classification, highlighting the primary headache disorders and their diagnostic criteria. They conclude by presenting an approach to headache diagnosis based upon these criteria.
Inkjet Printing Approach to Fabrication of Non-sintered Dielectric Films and 3D Structures (2010)

With the current explosive growth of information communication technologies, it is required to realize 3D system integration of hetero-materials such as organic and inorganic materials with multi-functionality based on information-, nano-, bio, and energy technology. The direct-writing by the inkjet printing has significant attention since it is feasible to pattern and fabricate fine features directly from design or image file. In this presentation, we have formulated ceramic suspension inks (Al2O3 and BaTiO3) and synthesized Ag conductive ink to print dielectric films and 3D circuitry such as metal-insulator-metal (MIM) capacitors and metal-via-metal interconnects. Inkjet-printed dielectric films were prepared without high temperature sintering process. Instead, a polymer resin was infiltrated through the inkjet-printed ceramic films and cured at 280&#xB0;C. Since our goal is to fabricate non-sintered ceramic films, it is preferred that the inkjet-printed ceramic films should have a high packing density of more than 60%. High packing density leads to the inkjet-printed worth better electrical and mechanical properties. Roughly about 40% of micro-voids inside the inkjet-printed ceramic films were filled with the resin. The dielectric property measurement of the inkjet-printed Al2O3-resin hybrid films indicated that dielectric constant and dielectric loss are 6 and 0.003, respectively at 1 MHz In the case of inkjet-printed BaTiO3-resin films, their dielectric constant and dielectric loss at 1MHz are 75 and 0.009, respectively. And we could fabricate all inkjet-printed embedded capacitor having MIM structure and daisy structure having metal-via-metal interconnection for 3D integration. The MIM capacitor consisted of 4 hybrid films that was placed Al2O3-Ag-BaTiO3-Ag hybrid layers in order from below. In daisy structure case, the conductor patterns of lower and upper layer were built up each other with the Al2O3 films, and micro via was formed by laser drilling process then filled with Ag paste for interconnection between the conductor patterns.
Quasilinear simulation of auroral kilometric radiation by a relativistic Fokker-Planck code (1991)

An intense terrestrial radiation called the auroral kilometric radiation (AKR) is believed to be generated by cyclotron maser instability. We study a quasilinear evolution of this instability by means of a two-dimensional relativistic Fokker-Planck code which treats waves and distributions self-consistently, including radiation loss and electron source and sink. We compare the distributions and wave amplitude with spacecraft observations to elucidate physical processes involved. 3 refs., 1 fig.
Localized and Sustained Delivery of Silencing RNA from Macroscopic Biopolymer Hydrogels (2009)

The ability to silence the expression of specific genes at a particular location of the body would provide a powerful new therapeutic tool for treatment of diseases such as cancer or for use in regenerative medicine. RNA interference (RNAi) is a gene silencing mechanism where specific mRNA molecules that are complementary to short interfering RNA (siRNA) are degraded, thus inhibiting gene expression at the post-transcriptional level. However, the use of siRNA has not yet realized its full clinical potential due to degradation in vivo, the difficulty retaining siRNA at the site of interest, and the relatively short-term effect it has on rapidly dividing cells. In this work a new paradigm is presented that will allow for the localized delivery of siRNA that is controlled and sustained over time, thus allowing cells at the site of interest to be directly exposed to a gradual release of bioactive siRNA. To accomplish this, three different types of macroscopic, degradable biomaterial hydrogel scaffolds were employed: calcium crosslinked alginate, photocrosslinked alginate, and collagen. Differing rates of release from these hydrogels were achieved, and the ability of the released siRNA to knock down the expression of GFP in cells that constitutively express this protein was shown. Furthermore, the ability to encapsulate cells within these materials and achieve sustained gene silencing of these incorporated cells was demonstrated. These biopolymer hydrogels are injectable and, therefore, can be delivered in a minimally invasive manner, and they can serve as delivery vehicles for both siRNA and transplanted cell populations.
Enzyme-Free Nucleic Acid Logic Circuits (2006)

Biological organisms perform complex information processing and control tasks using sophisticated biochemical circuits, yet the engineering of such circuits remains ineffective compared with that of electronic circuits. To systematically create complex yet reliable circuits, electrical engineers use digital logic, wherein gates and subcircuits are composed modularly and signal restoration prevents signal degradation. We report the design and experimental implementation of DNA-based digital logic circuits. We demonstrate AND, OR, and NOT gates, signal restoration, amplification, feedback, and cascading. Gate design and circuit construction is modular. The gates use single-stranded nucleic acids as inputs and outputs, and the mechanism relies exclusively on sequence recognition and strand displacement. Biological nucleic acids such as microRNAs can serve as inputs, suggesting applications in biotechnology and bioengineering.
PROTECTIVE EFFECT OF CTLA4Ig SECRETED BY TRANSGENIC FETAL PANCREAS ALLOGRAFTS1 (2000)

Sustained local secretion of CTLA4Ig from transgenic grafts in combination with transient systemic CD4 T-cell depletion can enhance allograft acceptance.
In vitro transposition of transposon Tn3. (1990)

Transposition of the ampicillin-resistant transposon Tn3 was reproduced in vitro using the Escherichia coli cell extract. In this cell-free system, we used plasmid DNA carrying mini-Tn3 as donor and phage lambda DNA as target and assayed for ampicillin-resistance transducing phages formed by cointegration of these DNA molecules. Ampicillin-resistance transducing phages, which were obtained by in vitro packaging of lambda DNA after the in vitro transposition reaction, were formed only in the presence of Tn3 transposase. The reaction required mini-Tn3 with the proper sequence and orientation of the terminal inverted repeats of Tn3. The reaction also required DNA synthesis but not RNA synthesis by E. coli RNA polymerase.
Best Practices for Shale Core Handling: Transportation, Sampling and Storage for Conduction of Analyses (2020)

Drill core shale samples are critical for palaeoenvironmental studies and potential hydrocarbon reservoirs. They need to be preserved carefully to maximise their retention of reservoir condition properties. However, they are susceptible to alteration due to cooling and depressurisation during retrieval to the surface, resulting in volume expansion and formation of desiccation and micro fractures. This leads to inconsistent measurements of different critical attributes, such as porosity and permeability. Best practices for core handling start during retrieval while extracting from the barrel, followed by correct procedures for transportation and storage. Appropriate preservation measures should be adopted depending on the objectives of the scientific investigation and core coherency, with respect to consolidation and weathering. It is particularly desirable to maintain a constant temperature of 1 to 4 °C and a consistent relative humidity of &gt;75% to minimise any micro fracturing and internal moisture movement in the core. While core re-sampling, it should be ensured that there is no further core compaction, especially while using a hand corer.
Characterization of a human monoclonal immunoglobulin M (IgM) antibody (IgMBEN) specific for Vi capsular polysaccharide of Salmonella typhi (1995)

A search for human monoclonal antibodies to protective antigens of bacteria revealed an immunoglobulin M lambda chain [IgM(lambda); designated IgMBEN] reactive with the Vi capsular polysaccharide of Salmonella typhi. Vi, a linear homopolymer of alpha(1-->4)GalApNAc that is O acetylated at C-3, is a licensed vaccine for typhoid fever. Immunologic properties of IgMBEN were compared to those of burro globulin prepared by intravenous injections of S. typhi (B339-340). IgMBEN and B339-340 yielded identical precipitin lines with Vi by double immunodiffusion. IgMBEN and B339-340 produced similar precipitation results with Vi and its derivatives prepared by de-O-acetylation, carboxyl reduction, and removal or replacement of the N-acetyl at C-2 with O-acetyl. B339-340 yielded maximal precipitation with Vi (0.41 mg of antibody per ml with 1.4 micrograms of Vi); next was carboxyl-reduced, O-acetylated Vi, which precipitated 0.325 mg of antibody per ml with 2.5 micrograms of Vi. IgMBEN yielded maximal precipitation with de-O-acetylated, carboxyl-reduced Vi (approximately 11.0 mg of antibody per ml with approximately 1.3 micrograms of antigen); next were de-O-acetylated Vi (9.89 mg/ml) and Vi (9.19 mg/ml). The precipitin curves and equivalence points of these three antigens were similar. Pneumococcus type 1, which contains GalApNAc, did not precipitate with Vi or its derivatives. These slight differences in specificity between IgMBEN and B339-340 were related to our proposed structure of Vi. We plan to use IgMBEN as a reference for measurement of vaccine-induced Vi antibodies.
Relating web characteristics with link based web page ranking (2001)

In the last years, several techniques based in link analysis have been proposed and used in search engines to rank Web pages. As links are generated by humans, link based ranking seems to give better results than traditional automatic techniques such as word based ranking. However, no studies have been done about their real impact. In this paper we extend global page ranking techniques to Web site ranking, and do a first experimental analysis of link ranking regarding the structure and dynamics of the Web.
Absence of modulation of CD4+CD25high regulatory T cells in CTCL patients treated with bexarotene (2009)

Cutaneous T-cell lymphoma (CTCL) are a heterogeneous group of lymphoproliferative disorders, characterized by the infiltration of the epidermis by mature and activated malignant CD4+ T-lymphocytes. Retinoids such as retinoic acid and synthetic analogues have long been used alone or in combination with other therapies for CTCL. Bexarotene, the first synthetic highly selective RXR retinoid, was approved for the treatment of all stages of CTCL in patients refractory to at least one systemic therapy. Recently, six cases in which the initiation of bexarotene therapy for CTCL was associated with the progression of internal disease despite improvement of cutaneous signs and symptoms were reported. Moreover, it has been established that retinoids promote the generation of CD4+ Foxp3+ regulatory T cells, raising the question of an induction of regulatory T-cells by bexarotene. The aim of this work was to determine if bexarotene induces an increase of functional regulatory T cells which could play a role in the development of secondary extra-cutaneous lymphomas. Regulatory T cells were studied both in cutaneous biopsy specimens using an immunohistochemical analysis of CD4, CD25 and Foxp3 and in blood where proportion and functionality of circulating CD4+CD25(high) T-cells were determined. The study was performed in 10 patients [five patients with Sézary syndrome (SS) and five mycosis fungoïdes (MF)], treated for 6 months with bexarotene. Four healthy donors were used as controls for phenotypic and functional analysis on PBL. We found that the frequency of CD4+CD25(high) Treg cells was not significantly different before starting bexarotene and after 6 months of treatment in CTCL patients. However, we observed that the frequency of CD4+CD25(high) Treg cells before the beginning of the treatment was significantly increased compared to healthy donors. In addition, functional assays demonstrated that Foxp3 expressing CD4+CD25(high) T-cells were capable of suppressing autologous CD4 + CD25- T-cell proliferation. In the present work, we detected the presence of functional circulating CD4+CD25(high) Foxp3+ regulatory T-cells in CTCL patients, with an increased frequency compared to healthy donors. The treatment with bexarotene does not seem to affect the regulatory T-cell compartment.