gebhart/patrepeval huggingface dataset:
Characterization of aromatic- and purine-dependent Salmonella typhimurium: attention, persistence, and ability to induce protective immunity in BALB/c mice (1988)

Stable transposon-generated auxotrophic mutations in aroA, purA, and purE or aroA and purA together were introduced into Salmonella typhimurium strains which were virulent in mice. Strains harboring any of these mutations were attenuated when tested in BALB/c mice. purE strains were less attenuated than aroA or purA strains. Both aroA and purA mutants persisted for several weeks in the livers and spleens of the mice after intravenous infection, although the numbers of viable cells detected at various times after infection differed. aroA strains persisted at a higher level than purA strains and were effective live vaccines given intravenously or orally. purA strains were ineffective as oral vaccines and were poor intravenous vaccines. Strains harboring both aroA and purA mutations together were ineffective vaccines when administered orally or intravenously even though they persisted in the livers and spleens of the mice for long periods after intravenous infection.
ANGIOGENESIS IN THE huPBL-SCID MODEL OF HUMAN TRANSPLANT REJECTION1 (1999)

A significant angiogenesis response was associated with the cell infiltrates in the human skin allografts. The onset of angiogenesis appeared after the initial development of localized infiltrates and preceded the development of microvascular destruction. These findings suggest that alloreactive T cells and/or monocytes mediate the angiogenesis response in skin allografts.
Characterization of a murine model of myocarditis induced by a reactivated coxsackievirus B3. (1994)

A transfection-reactivated Coxsackievirus B3 (rCVB3), from a full-length cDNA clone of Nancy strain, has previously been shown to be as cardiovirulent as the wild-type virus. Myocarditis induced by this genetically defined virus was compared in SWR mice with the traditional Balb/c model. SWR mice inoculated with rCVB3 developed more severe myocarditis but less severe pancreatitis than Balb/c mice. In contrast to the poor general health and frequent mortality of Balb/c mice following CVB3 infection, the body weight of SWR mice was not affected by CVB3 inoculation and no mortality occurred at titres of 10(2)-10(7) plaque forming units (PFU). Typical myocarditis developed in SWR mice 7 days post infection. Myocarditic foci consisting of necrotic myocardial fibres and mononuclear cell infiltrates resolved by day 30, similar to that observed in Balb/c. However, SWR mice were more sensitive to rCVB3-induced myocarditis than were Balb/c mice: mild myocarditis was induced (4/4) by as low as 10(2) PFU of the virus (ID50 < 10(1.5) PFU), and more severe myocarditis was seen at higher PFU of virus in a dose-dependent manner. The SWR model was tested with attenuated variants derived from cardiovirulent rCVB3. The ID50 for myocarditis was 10(7) PFU for a large plaque-size attenuant and 10(6) PFU for a minute plaque-size attenuant, indicating loss of cardiovirulence by a factor of more than 10(4)-10(5). rCVB3-induced SWR mouse is a sensitive and reliable model for myocarditis. It is useful in assessing the cardiovirulence of different CVB3 variants and evaluating the efficacies of anti-viral therapies. It will allow follow-up study after high dose infection with cardiovirulent rCVB3.
Minimizing Probing Cost and Achieving Identifiability in Probe-Based Network Link Monitoring (2011)

Continuously monitoring link performance is important to network diagnosis. In this paper, we address the problem of minimizing the probing cost and achieving identifiability in probe-based network link monitoring. Given a set of links to monitor, our objective is to select the minimum number of probing paths that can uniquely determine all identifiable links and cover all unidentifiable links. We propose an algorithm based on a linear system model to find out all irreducible sets of probing paths that can uniquely determine an identifiable link, and we extend the bipartite model to reflect the relationship between a set of probing paths and an identifiable link. Since our optimization problem is NP-hard, we propose a heuristic-based algorithm to greedily select probing paths. Our method eliminates two types of redundant probing paths, i.e., those that can be replaced by others and those without any contribution to achieving identifiability. Simulations based on real network topologies show that our approach can achieve identifiability with very low probing cost. Compared with prior work, our method is more general and has better performance.
The Assembly of Single-Layer Graphene Oxide and Graphene Using Molecular Templates (2008)

Charged molecular templates were created to direct the placement of single-layer graphite oxide (GO) sheets. The distribution of the GO sheets depended on the surface functionalization, background passivation, pH, and deposition time. Electrostatic attraction guides the templating of the GO sheets and, consequently, templating could be modulated by adjusting the pH of the deposition solution. In contrast to CNT immobilization, we find that the GO sheets do not adhere to the bare Au surface.
Cranking: Combining Rankings Using Conditional Probability Models on Permutations (2002)

A new approach to ensemble learning is introduced that takes ranking rather than classification as fundamental, leading to models on the symmetric group and its cosets. The approach uses a generalization of the Mallows model on permutations to combine multiple input rankings. Applications include the task of combining the output of multiple search engines and multiclass or multilabel classification, where a set of input classifiers is viewed as generating a ranking of class labels. Experiments for both types of applications are presented. 1.
Single-Molecule Detection of Epidermal Growth Factor Receptor Mutations in Plasma by Microfluidics Digital PCR in Non–Small Cell Lung Cancer Patients (2009)

Abstract Purpose: We aim to develop a digital PCR-based method for the quantitative detection of the two common epidermal growth factor receptor (EGFR) mutations (in-frame deletion at exon 19 and L858R at exon 21) in the plasma and tumor tissues of patients suffering from non-small cell lung cancers. These two mutations account for &amp;gt;85% of clinically important EGFR mutations associated with responsiveness to tyrosine kinase inhibitors. Experimental Design: DNA samples were analyzed using a microfluidics system that simultaneously performed 9,180 PCRs at nanoliter scale. A single-mutant DNA molecule in a clinical specimen could be detected and the quantities of mutant and wild-type sequences were precisely determined. Results: Exon 19 deletion and L858R mutation were detectable in 6 (17%) and 9 (26%) of 35 pretreatment plasma samples, respectively. When compared with the sequencing results of the tumor samples, the sensitivity and specificity of plasma EGFR mutation analysis were 92% and 100%, respectively. The plasma concentration of the mutant sequences correlated well with the clinical response. Decreased concentration was observed in all patients with partial or complete clinical remission, whereas persistence of mutation was observed in a patient with cancer progression. In one patient, tyrosine kinase inhibitor was stopped after an initial response and the tumor-associated EGFR mutation reemerged 4 weeks after stopping treatment. Conclusion: The sensitive detection and accurate quantification of low abundance EGFR mutations in tumor tissues and plasma by microfluidics digital PCR would be useful for predicting treatment response, monitoring disease progression and early detection of treatment failure associated with acquired drug resistance.
Proanthocyanidins (condensed tannin) destabilise plant protein foams in a dose dependent manner (1995)

The compressive strength and persistence of protein foams produced from extracts of legume leaves were measured. The presence of foliar proanthocyanidin (PA, condensed tannin) in species such as Onobrychis and Lotus correlated with foams of negligible compressive strength and persistence and also with a reputation for bloat safety in the field. PA purified from forage legume leaves significantly decreased the compressive strength of protein foams produced from purified red clover leaf protein. The decrease in the compressive strength was related to the concentration of added PA in a dose-dependent manner. A ratio of PA to protein of 0.1 reduced the compressive strength by approximately half relative to the strength of the PA-free control. Purified PAS with different chemical structures had similar effects on the compressive strength of protein foams. The significance of these observations to pasture bloat and forage legume improvement is discussed.
How basal are triple‐negative breast cancers? (2008)

The basal molecular subtype of breast cancer (BC) is defined by the mRNA expression pattern of an intrinsic approximately 500-gene set. It is the most homogeneous subtype in transcriptional terms, and one of the most aggressive in prognostic terms. Clinical trials testing new systemic therapeutic strategies have been launched in basal BCs. Although no proof of evidence has yet been reported, basal tumors are currently assimilated to and selected as triple-negative (TN) BCs in these trials because of their frequent immunohistochemical (IHC) negativity for hormone and ERBB2 receptors. Here, we have assessed the degrees of correlation and of homogeneity of the TN phenotype (IHC-based definition) and the basal subtype (gene expression-based definition). We analyzed 172 TN BCs defined by gene expression profile as basal (123 cases) and nonbasal (49 cases). Conversely, 160 tumors were defined as basal by their gene expression profile and included 123 TN and 37 non-TN samples. Uni- and multivariate analyses revealed that TN BCs represent a more heterogeneous group than basal BCs, including basal and nonbasal tumors very different both at the histoclinical and molecular level, notably for mRNA expression of molecules targeted by specific therapies under evaluation in clinical trials. These results call for caution in the interpretation of ongoing trials and selection of patients in future trials. They also warrant the identification of molecular markers for basal BCs more clinically applicable than gene expression profiles.
Proinsulin multi-peptide immunotherapy induces antigen-specific regulatory T cells and limits autoimmunity in a humanized model (2015)

Peptide immunotherapy (PIT) is a targeted therapeutic approach, involving administration of disease-associated peptides, with the aim of restoring antigen-specific immunological tolerance without generalized immunosuppression. In type 1 diabetes, proinsulin is a primary antigen targeted by the autoimmune response, and is therefore a strong candidate for exploitation via PIT in this setting. To elucidate the optimal conditions for proinsulin-based PIT and explore mechanisms of action, we developed a preclinical model of proinsulin autoimmunity in a humanized HLA-DRB1*0401 transgenic HLA-DR4 Tg mouse. Once proinsulin-specific tolerance is broken, HLA-DR4 Tg mice develop autoinflammatory responses, including proinsulin-specific T cell proliferation, interferon (IFN)-γ and autoantibody production. These are preventable and quenchable by pre- and post-induction treatment, respectively, using intradermal proinsulin-PIT injections. Intradermal proinsulin-PIT enhances proliferation of regulatory [forkhead box protein 3 (FoxP3(+))CD25(high) ] CD4 T cells, including those capable of proinsulin-specific regulation, suggesting this as its main mode of action. In contrast, peptide delivered intradermally on the surface of vitamin D3-modulated (tolerogenic) dendritic cells, controls autoimmunity in association with proinsulin-specific IL-10 production, but no change in regulatory CD4 T cells. These studies define a humanized, translational model for in vivo optimization of PIT to control autoimmunity in type 1 diabetes and indicate that dominant mechanisms of action differ according to mode of peptide delivery.
Extraction of membrane proteins by differential solubilization for separation using two‐dimensional gel electrophoresis (1998)

We describe the extraction and enrichment of membrane proteins for separation by two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) after differential solubilization of an Escherichia coli cell lysate. In a simple three-step sequential solubilization protocol applicable for whole cell lysates, membrane proteins are partitioned from other cellular proteins by their insolubility in solutions conventionally used for isoelectric focusing (IEF). As the first step, Tris-base was used to solubilize many cytosolic proteins. The resultant pellet was then subjected to conventional solubilizing solutions (urea, 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate, dithiothreitol, Tris, carrier ampholytes). Following the completion of this step, 89% of the initial E. coli sample mass was solubilized. Finally, the membrane protein rich pellet was partially solubilized using a combination of urea, thiourea, tributyl phosphine and multiple zwitterionic surfactants. Using N-terminal sequence tagging and peptide mass fingerprinting we have identified 11 membrane proteins from this pellet. Two of these outer membrane proteins (Omp), OmpW and OmpX, have previously been known only as an open reading frame in E. coli, while OmpC, OmpT and OmpTOLC have not previously been identified on a 2-D gel. The prefractionation of an entire cell lysate into multiple fractions, based on solubility, results in simplified protein patterns following 2-D PAGE using broad-range pH 3.5-10 immobilized pH gradients (IPGs). Additional advantages of sample prefractionation are that protein identification and gel matching, for database construction, is a more manageable task, the procedure requires no specialized apparatus, and the sequential extraction is conducted in a single centrifuge tube, minimizing protein loss.
HIV particles detected in spermatozoa of patients with AIDS. (1991)

In this paper the Authors describe the presence of HIV particles on and in mature spermatozoa either ejaculated by AIDS patients or incubated in vitro with HIV. Both kinds of spermatozoa have particles localized around the sperm organelles. In the first case, the nucleoid of the virus can be enveloped by a membrane-like coat or be devoid of it and form buddings in the plasma membrane. In the in vitro infected spermatozoa, only membrane enveloped nucleoids are present, and no process of budding can be found. The Authors conclude considering that the spermatozoa of the AIDS patients can be penetrated by the virus particles in different moments of their life, and show the HIV particles in different stages of their cycle: some of them have freshly penetrated the sperm, and are still contained in a membrane-like coat, others are replicated and are budding through the sperm plasma membrane. On the contrary, in vitro infected spermatozoa have only freshly penetrated virus particles, and lack buddings and membrane-free nucleoids. The presence of the HIV virus in spermatozoa is substantiated by labelling with monoclonal or polyclonal anti-HIV antibodies.
Towards In-situ Reservoir Nano-Agents (2008)

To test the future reality of having molecular agents in underground oil and gas reservoirs, an experimental research study was initiated to establish transport boundary conditions for nanoparticles in natural porous media; in this case, carbonate reservoir samples from the proliflc ARAB-D formation. The study used scaled laboratory core ∞ow tests with inert nanoparticle suspensions as a precursor for the injection of traceable nanoparticles into the reservoir. Overall, the experimental study was designed to generate baseline data for the injection response of nanoparticles in a bi-modal carbonate. It worked to correlate the impact on the rock permeability and the particle transport e‐ciency in terms of particle size, concentration, and surface chemistry. This paper details visions, procedures, and results from these tests.
New Constituent from Podocarpus macrophyllus var. macrophyllus Shows Anti-tyrosinase Effect and Regulates Tyrosinase-Related Proteins and mRNA in Human Epidermal Melanocytes (2007)

A new biflavonoid, 2,3-dihydro-4',4'''-di-O-methylamentoflavone (5), and five known compounds, (-)-catechin (1), quercetin (2), 2,3-dihydrosciadopitysin (3), sciadopitysin (4), and isoginkgetin (6), were isolated from Podocarpus macrophyllus var. macrophyllus (Podocarpaceae). These compounds were evaluated their ability to inhibit cellular tyrosinase activity and for their melanin inhibitory activity in human epidermal melanocytes (HEMn). In the melanin synthesis assay, 2,3-dihydro-4',4'''-di-O-methylamentoflavone (5) showed a potent anti-tyrosinase effect with IC(50)=0.098 mM in HEMn. It also significantly decreased both protein and mRNA levels of the tyrosinase-related protein-2 (TRP-2) by Western blot and quantitative real-time PCR (qRT-PCR) analysis. These findings suggest that the new compound, 2,3-dihydro-4',4'''-di-O-methylamentoflavone (5), is the most active component of P. macrophyllus var. macrophyllus in inhibiting pigmentation and that this inhibition is exerted through inhibition of transcription of the genes encoding TRP2.
Reduction of infarct size with coronary venous retroperfusion. (1992)

Coronary venous retroperfusion with PICSO alone and in combination with coronary venous substrate enhancement using L-glutamate significantly decreases ischemic damage during urgent surgical revascularization.
Randomized Phase II Study of Gemcitabine Administered at a Fixed Dose Rate or in Combination With Cisplatin, Docetaxel, or Irinotecan in Patients With Metastatic Pancreatic Cancer: CALGB 89904 (2009)

Gemcitabine/cisplatin, fixed dose rate gemcitabine, gemcitabine/docetaxel, and gemcitabine/irinotecan have similar antitumor activity in metastatic pancreatic cancer. In light of recent negative randomized studies directly comparing several of these regimens with standard gemcitabine, none of these approaches can be recommended for routine use in patients with this disease.
Stability of dried blood spot specimens for detection of human immunodeficiency virus DNA by polymerase chain reaction (1992)

Blood sampling on filter paper has many advantages for the detection of perinatal human immunodeficiency virus (HIV) infection by the polymerase chain reaction (PCR). However, if the method is to be widely used, an assessment of its performance under field conditions is required. To simulate conditions in the field, 50-microliters aliquots of whole blood containing low levels of HIV proviral DNA (4 to 1,024 copies per 100,000 nucleated cells) were spotted onto filter paper; dried; and subjected to heat, humidity, and prolonged storage at room temperature. After exposure, the DNA was recovered and amplified with primers to human leukocyte antigen DQ alpha- and HIV-specific sequences. Treatment at 37 degrees C and 60% humidity for 7 days, storage for 12 weeks at 22 degrees C, and freeze-thawing twice had no adverse effect on PCR reactivity when compared with the results obtained with reference spots stored at -20 degrees C. The lower limits of HIV detection in all tests ranged from 4 to 16 HIV copies per 100,000 cells. Fixation in 70% ethanol improved the amplification of low levels of HIV DNA and reduced biohazard risks. These findings suggest that dried blood spots will provide a powerful new resource for testing for HIV by PCR, especially in remote areas where refrigeration and immediate sample processing are unavailable.
Identification and Characterization of the First Small Molecule Inhibitor of MDMX (2010)

The p53 pathway is disrupted in virtually every human tumor. In approximately 50% of human cancers, the p53 gene is mutated, and in the remaining cancers, the pathway is dysregulated by genetic lesions in other genes that modulate the p53 pathway. One common mechanism for inactivation of the p53 pathway in tumors that express wild-type p53 is increased expression of MDM2 or MDMX. MDM2 and MDMX bind p53 and inhibit its function by distinct nonredundant mechanisms. Small molecule inhibitors and small peptides have been developed that bind MDM2 in the p53-binding pocket and displace the p53 protein, leading to p53-mediated cell cycle exit and apoptosis. To date, peptide inhibitors of MDMX have been developed, but no small molecule inhibitors have been reported. We have developed biochemical and cell-based assays for high throughput screening of chemical libraries to identify MDMX inhibitors and identified the first MDMX inhibitor SJ-172550. This compound binds reversibly to MDMX and effectively kills retinoblastoma cells in which the expression of MDMX is amplified. The effect of SJ-172550 is additive when combined with an MDM2 inhibitor. Results from a series of biochemical and structural modeling studies suggest that SJ-172550 binds the p53-binding pocket of MDMX, thereby displacing p53. This lead compound is a useful chemical scaffold for further optimization of MDMX inhibitors that may eventually be used to treat pediatric cancers and various adult tumors that overexpress MDMX or have similar genetic lesions. When combined with selective MDM2 inhibitors, SJ-172550 may also be useful for treating tumors that express wild-type p53.
Detecting pre-cancerous cells using angle-resolved low coherence interferometry (2004)

Angle-resolved low coherence interferometry is used to detect pre-cancerous basal epithelial cells in intact, unstained animal tissues via quantitative nuclear morphology measurements. Recent results are presented which demonstrate the ability to assess the efficacy of chemopreventive agents.
Articular cartilage repair: Rabbit experiments with a collagen gel-biomatrix and chondrocytes cultured in it (1998)

To repair a full-thickness articular cartilage defect in rabbit knees, we developed a technique of using a collagen gel hardened by cultured allogeneic chondrocytes in it. The gel-chondrocyte composite accumulated an intense metachromatic matrix, and had elasticity and stiffness enough to be shaped easily after 2 weeks' culture in vitro. It was implanted into full-thickness articular cartilage defects. Histologic evaluation was performed up to 6 months after surgery, using a histologic grading scale composed of 5 categories. In the gel-chondrocyte composite implanted group, good repair was observed from as early as 1 day up to 6 months. On the other hand, in the empty control group, no repair was observed 1 day to 2 weeks after the defects were made. At 4 weeks, some repair occurred, but even at 6 months the repair was not good.
Quantum-based automated short answer scoring system (2018)

Answer Scoring is defined as an act of assigning a score to an answer by a human grader. This scoring technique is costly and requires deep logical efforts and it depends on less-than-perfect human assessment. However, the Automated Scoring (AS) System has its importance in providing the student with a score as well as feedback within seconds. This paper describes an AS system in which scores are assigned to essays automatically based upon predefined algorithms. Most of the educational sectors carry out an important examination process, i.e. to examine and assess the capabilities of the student based on his/her given answers. To accomplish this process, the human graders can apply this Automated Answer Scoring system. The paper goes through the existing techniques for automated answer scoring systems and then goes on to explain the newly developed system in which scoring is done by the statistical method adopting and integrating rule-based semantic quantum-based features analysis resulting in more accuracy. It is in a way a hybrid system suitable for short answer type scoring. It also presents the methodology and architecture of AS.