gebhart/patrepeval huggingface dataset:
Therapeutic vaccines as a promising treatment modality against prostate cancer: rationale and recent advances (2014)

Cancer immunotherapy was deemed the medical breakthrough of 2013, in part because it can induce a rapid, durable, self-propagating and adaptable immune response. Specifically in prostate cancer, immunotherapy has emerged as a viable and attractive treatment strategy. To date, therapeutic cancer vaccines and immune checkpoint inhibitors are the two classes of immunotherapy that have demonstrated improvements in overall survival in patients with advanced tumors. The 2010 Food and Drug Administration approval of sipuleucel-T for asymptomatic or minimally symptomatic metastatic prostate cancer set the stage for ongoing phase III trials with the cancer vaccine PSA-TRICOM and the immune checkpoint inhibitor ipilimumab. A class effect of these approved immune-based therapies is a benefit in overall survival without short-term changes in disease progression, apparently due to modulation of tumor growth rate kinetics, in which the activated immune system exerts constant immunologic pressure that slows net tumor growth. A growing body of evidence suggests that the ideal population for clinical trials of cancer vaccines as monotherapy is patients with lower tumor volume and less aggressive disease. Combination strategies include immunotherapy with standard therapies or with other immunotherapies. Here we review emerging data on immunotherapy for patients with prostate cancer.
Resting-State Functional Connectivity Patterns Predict Chinese Word Reading Competency (2012)

Resting-state functional connectivity (RSFC) offers a novel approach to reveal the temporal synchronization of functionally related brain regions. Recent studies have identified several RSFCs whose strength was associated with reading competence in alphabetic languages. In the present study, we examined the role of intrinsic functional relations for reading a non-alphabetic language--Chinese--by correlating RSFC maps of nine Chinese reading-related seed regions and reaction time in the single-character reading task. We found that Chinese reading efficiency was positively correlated with the connection between left inferior occipital gyrus and left superior parietal lobule, between right posterior fusiform gyrus and right superior parietal lobule, and between left inferior temporal gyrus and left inferior parietal lobule. These results could not be attributed to inter-individual differences arising from the peripheral processes of the reading task such as visual input detection and articulation. The observed RSFC-reading correlation relationships are discussed in the framework of Chinese character reading, including visuospatial analyses and semantic/phonological processes.
New approach to correlating overlay and yield (1999)

ABSTRACT Integrated circuit design rules are defined with a given overlay tolerance, but the exact correlation between measured overlayon product wafers and die yield is notoriously difficult to quantify. Interest in better quantifying this relationship is notmerely academic. The ability to shrink the overlay design rule by even a few nanometers would allow more good die to beprinted on every product wafer, providing a substantial economic benefit. Conversely, if the actual distribution of overlayerrors across a wafer is slightly worse than anticipated in the design rules, the resulting shortfall in yield would be difficult toidentify and correct.Traditional linear regression analysis produces poor results for overlay to yield correlation. Product overlay data is usuallyquite limited, necessitating the use of wafer or even lot level averages which obscures the finer details of overlay variation.Statistical fluctuations in other parameters, most notably critical dimensions, and across wafer yield variations due to other
Targeted mRNA degradation by double-stranded RNA in vitro (1999)

Double-stranded RNA (dsRNA) directs gene-specific, post-transcriptional silencing in many organisms, including vertebrates, and has provided a new tool for studying gene function. The biochemical mechanisms underlying this dsRNA interference (RNAi) are unknown. Here we report the development of a cell-free system from syncytial blastoderm Drosophila embryos that recapitulates many of the features of RNAi. The interference observed in this reaction is sequence specific, is promoted by dsRNA but not single-stranded RNA, functions by specific mRNA degradation, and requires a minimum length of dsRNA. Furthermore, preincubation of dsRNA potentiates its activity. These results demonstrate that RNAi can be mediated by sequence-specific processes in soluble reactions.
The dynamics of gene expression of interleukin-19 and interleukin-20 and their receptors in psoriasis (2005)

The increased IL-19 and IL-20 mRNA expression levels in lesional psoriatic skin suggest that these two cytokines play a role in the pathogenesis of psoriasis. An imbalance in the receptor complexes for IL-19 and IL-20 might contribute to their suspected pathogenic effects.
3-D model-based tracking of human upper body movement: a multi-view approach (2002)

In this paper we describe our work on 3-D model-based tracking of unconstrained human upper body movement. Using real image sequences acquired from multiple views, we recover the 3-D body pose at each time instant without the use of markers. The pose-recovery problem is formulated as a search problem and entails finding the pose parameters of a graphical human model for which its synthesized appearance is most similar to the actual appearance of the real human in the multi-view images. We use a decomposition approach and a best-first technique to search through the high dimensional pose parameter space. Chamfer matching is used as a fast similarity measure between synthesized and real edge images. We illustrate our approach on real data acquired simultaneously from three views.
Evaluation of attenuation, immunogenicity and efficacy of a bovine parainfluenza virus type 3 (PIV-3) vaccine and a recombinant chimeric bovine/human PIV-3 vaccine vector in rhesus monkeys (2003)

Restricted replication in the respiratory tract of rhesus monkeys is an intrinsic property of bovine parainfluenza virus type 3 (bPIV-3) strains. This host range phenotype of bPIV-3 has been utilized as a marker to evaluate the attenuation of bPIV-3 vaccines for human use. Two safety, immunogenicity and efficacy studies in primates evaluated and compared three human parainfluenza virus type 3 (hPIV-3) vaccine candidates: biologically derived bPIV-3, a plasmid-derived bPIV-3 (r-bPIV-3) and a chimeric bovine/human PIV-3 (b/hPIV-3). These studies also examined the feasibility of substituting Vero cells, cultured in the presence or absence of foetal bovine serum, for foetal rhesus lung-2 (FRhL-2) cells as the tissue culture substrate for the production of bPIV-3 vaccine. The results demonstrated that (i) Vero cell-produced bPIV-3 was as attenuated, immunogenic and efficacious as bPIV-3 vaccine grown in FRhL-2 cells, (ii) plasmid-derived bPIV-3 was as attenuated, immunogenic and efficacious as the biologically derived bPIV-3 and (iii) the b/hPIV-3 chimera displayed an intermediate attenuation phenotype and protected animals completely from hPIV-3 challenge. These results support the use of bPIV-3 vaccines propagated in Vero cells in human clinical trials and the use of b/hPIV-3 as a virus vaccine vector to express foreign viral antigens.
Synthesis and structure of an extended cluster lead(II) carboxylate, [Pb((CO){sub 9}Co{sub 3}({mu}{sub 3}-CCO{sub 2})){sub 2}]{sub n}. Role of core metals in cluster-derived hydrogenation catalysts (1996)

The reaction of lead acetate with (CO){sub 9}Co{sub 3}({mu}{sub 3}-CCOOH) leads to the formation of [Pb((CO){sub 9}Co{sub 3}({mu}{sub 3}-CCO{sub 2})){sub 2}]{sub n}, I, in high yield. The structure of I exhibits unusual six-coordinate Pb(II) centers with two asymmetrical chelating cluster carboxylates (C{sub 22}Co{sub 6}PbO{sub 22}; triclinic P1; a = 8.119(1), b = 14.346(2), c = 14.660(2) {Angstrom}; {alpha} = 102.18(1), {beta} = 99.01(1), {gamma} = 97.30(1){degrees}; Z = 2). One oxygen of each cluster carboxylate ligand bridges between adjacent lead atoms such that a chainlike extended structure is found in the solid state without the presence of solvent or water. I is converted stepwide on pyrolysis into two metastable forms of solid materials (designated LT and HT), each of which has been characterized spectroscopically. The hydrogenation of 2-butenal as a test reaction shows that the LT catalyst exhibits selectivities similar to previous LT materials derived from other cobalt cluster metal carboxylates and that the HT material is totally inactive. The observed release of the lead core metal under HT activation conditions totally inactivates the catalyst and demonstrates exposure of the core metal in the HT form of these novel catalysts.
Pathogenesis of the Earliest Epithelial Cell Damage Induced by Mepirizole and Cysteamine in the Rat Duodenum (1989)

Mepirizole (200 mg/kg) and cysteamine (100 mg/kg) induced epithelial cell damage in the proximal duodenum of rats within 30 min after s.c. administration. The injury induced was severe 60 min later. Gastric acid secretion determined in intact animals was stimulated by these agents 30 and 60 min later when the intraluminal pH of the duodenum was significantly decreased. Duodenal blood flow was significantly decreased beginning 5 min after administration up to 60 mm. Oral treatment with sodium bicarbonate (300 mg/kg). Cimetidine (100 mg/kg). omeprazole or NC-1300 (gastric proton pump inhibitors. 30 mg/kg) and 16.16-dimethyl prostaglandin E2 (10 μg/kg) protected the epithelium from damage induced by the two duodenal ulcerogens. Epithelial cell damage in the duodenum in response to mepirizole and cysteamine appears to be related to the increased gastric acid secretion followed by lowered intraduodenal pH of the duodenum having decreased blood flow
Controlled Synthesis of Pd–Pt Alloy Hollow Nanostructures with Enhanced Catalytic Activities for Oxygen Reduction (2012)

Pd-Pt alloy nanocrystals (NCs) with hollow structures such as nanocages with porous walls and dendritic hollow structures and Pd@Pt core-shell dendritic NCs could be selectively synthesized by a galvanic replacement method with uniform Pd octahedral and cubic NCs as sacrificial templates. Fine control over the degree of galvanic replacement of Pd with Pt allowed the production of Pd-Pt NCs with distinctly different morphologies. The synthesized hollow NCs exhibited considerably enhanced oxygen reduction activities compared to those of Pd@Pt core-shell NCs and a commercial Pt/C catalyst, and their electrocatalytic activities were highly dependent on their morphologies. The Pd-Pt nanocages prepared from octahedral Pd NC templates exhibited the largest improvement in catalytic performance. We expect that the present work will provide a promising strategy for the development of efficient oxygen reduction electrocatalysts and can also be extended to the preparation of other hybrid or hetero-nanostructures with desirable morphologies and functions.
Ribogenomics: The Science and Knowledge of RNA (2014)

Ribonucleic acid (RNA) deserves not only a dedicated field of biological research - a discipline or branch of knowledge - but also explicit definitions of its roles in cellular processes and molecular mechanisms. Ribogenomics is to study the biology of cellular RNAs, including their origin, biogenesis, structure and function. On the informational track, messenger RNAs (mRNAs) are the major component of ribogenomes, which encode proteins and serve as one of the four major components of the translation machinery and whose expression is regulated at multiple levels by other operational RNAs. On the operational track, there are several diverse types of RNAs - their length distribution is perhaps the most simplistic stratification - involving in major cellular activities, such as chromosomal structure and organization, DNA replication and repair, transcriptional/post-transcriptional regulation, RNA processing and routing, translation and cellular energy/metabolism regulation. An all-out effort exceeding the magnitude of the Human Genome Project is of essence to construct just mammalian transcriptomes in multiple contexts including embryonic development, circadian and seasonal rhythms, defined life-span stages, pathological conditions and anatomy-driven tissue/organ/cell types.
Herpes Simplex Virus Clearance During Purification of a Recombinant Adeno-Associated Virus Serotype 1 Vector (2014)

Gene delivery vectors based on adeno-associated virus (AAV) have potential utility for treatment of many genetic disorders. Current AAV vector manufacturing methods employ helper viruses to deliver functions needed to produce replication-defective recombinant AAV (rAAV) vectors, and clearance of infectious helper virus from the drug substance is essential for ensuring the safety of rAAV-based therapies. We have developed a manufacturing method for the production of rAAV vectors using a recombinant herpes simplex virus type 1 (rHSV) complementation system in suspension baby hamster kidney cells. The manufacturing process includes three primary unit operations, detergent lysis of the cell harvest and two downstream column chromatography steps, which achieve viral clearance. These unit operations inactivate and remove HSV, including replication-competent HSV present at low levels in rHSV helper stocks. Here we report results quantifying the reduction in HSV achieved during rAAV vector purification. Clearance of HSV was at least 6.84 log10 with 1% Triton X-100, 4.34 log10 with CIM Q column chromatography, and 2.86 log10 with AVB affinity chromatography. Combined, these three orthogonal methods achieved clearance of at least 14.04 log10 of HSV. The total input quantity of rHSV in a 100-liter production batch is approximately 1.2×10(12) plaque-forming units (pfu), and after purification, the concentration of residual rHSV in the resulting drug substance of approximately 450 ml would be less than 2.42×10(-5) pfu/ml. A rAAV vector produced using this method was used in a clinical trial in which subjects receive up to 100 intramuscular injections of 1.35 ml each, which would contain a maximum of 3.27×10(-3) pfu of HSV. These results support the safety of rAAV vectors produced using our rHSV complementation method.
Duloxetine Versus Placebo for the Treatment of North American Women With Stress Urinary Incontinence (2003)

These phase 3 data are consistent with phase 2 data and they provide further evidence for the safety and efficacy of duloxetine as a pharmacological agent for the treatment of women with SUI.
ADCC (K‐Cell) Lysis of Human Erythrocytes Sensitized with Rhesus Alloantibodies III. COMPARISON OF IgG ANTI‐D AGGLUTINATING AND LYTIC (ADCC) ACTIVITY AND THE ROLE OF IgG SUBCLASSES (1980)

Conventional manual (enzyme and antiglobulin titres) and AutoAnalyser quantitation of anti-D sera were compared with the ability of the same sera to mediate lysis of Rh(D) positive red cells in an ADCC assay. AutoAnalyser (AA) quantitation correlated significantly with manual titration methods, although there were wide discrepancies between individual sera. The ADCC activity of the anti-D sera did not correlate with any of the conventional assays (AA, enzyme, antiglobulin). There were significant differences between anti-D sera obtained from females immunized during pregnancy and male volunteers immunized by deliberate injection. The female sera contained significantly less anti-D when assessed by AA, yet were significantly more active in ADCC activity at equivalent concentrations. These functional differences in anti-D activity could not be attributed to the absence of IgG subclasses (IgG1 and IgG3) known to induce ADCC. However, there was a relationship between ADCC and IgG1/IgG3 titres in that high ADCC activity was seen where the IgG3 titre was higher than the IgG1 titre. In the male anti-D sera IgG1 titres were greater than or equal to IgG3 titres and ADCC activity was very low.
Modulation of intestinal functions by food substances (1999)

The small intestinal epithelium plays a crucial role in the digestion/modification of food components, absorption of nutrients and recognition of food-derived signals. It also acts as a barrier against unfavourable materials in food. These intestinal functions may be influenced by food substances. In this paper, the effects of various food substances on the intestinal functions, particularly the absorption functions, are discussed. A new assay method, using a monolayer culture system of human intestinal epithelial cells, is applied to examine food-derived substances which could modulate the tight junction (TJ). Capsianoside, a diterpene glycoside from sweet pepper, was isolated and identified as one of the TJ-modulating substances. Those substances can be expected to facilitate the paracellular absorption of small molecular functional substances such as bioactive oligopeptides. The use of a human intestinal cell culture system also enabled us to make a simple screen test for food substances which affect the intestinal transporter functions. Substances which could suppress the activity of intestinal glucose transporters, for example, can be expected to reduce the dietary glucose uptake in the intestinal epithelium and control the blood glucose level. Polyphenolic compounds from plants, including green tea, were found to have such activity. Modulation of the brush border enzymes by food substances is also discussed.
STUDIES OF A MYXOVIRUS RECOVERED FROM PATIENTS WITH INFECTIOUS HEPATITIS (1965)

A virus has been isolated from the serum and urine of patients with infectious hepatitis. This virus is a member of the parinfluenza group. It is serologically distinct from the known members of the group, but apparently is antigenically related to the simian type-2 parainfluenza viruses. A causal relationship between WB virus and infectious hepatitis has not been established.
Systemic Delivery of Recombinant Brain Derived Neurotrophic Factor (BDNF) in the R6/2 Mouse Model of Huntington’s Disease (2013)

Loss of huntingtin-mediated BDNF gene transcription has been shown to occur in HD and thus contribute to the degeneration of the striatum. Several studies have indicated that an increase in BDNF levels is associated with neuroprotection and amelioration of neurological signs in animal models of HD. In a recent study, an increase in BDNF mRNA and protein levels was recorded in mice administered recombinant BDNF peripherally. Chronic, indwelling osmotic mini-pumps containing either recombinant BDNF or saline were surgically placed in R6/2 or wild-type mice from 4 weeks of age until euthanasia. Neurological evaluation (paw clasping, rotarod performance, locomotor activity in an open field) was performed. After transcardial perfusion, histological and immunohistochemical studies were performed. We found that BDNF- treated R6/2 mice survived longer and displayed less severe signs of neurological dysfunction than the vehicle treated ones. Primary outcome measures such as brain volume, striatal atrophy, size and morphology of striatal neurons, neuronal intranuclear inclusions and microglial reaction confirmed a neuroprotective effect of the compound. BDNF was effective in increasing significantly the levels of activated CREB and of BDNF the striatal spiny neurons. Moreover, systemically administered BDNF increased the synthesis of BDNF as demonstrated by RT-PCR, and this might account for the beneficial effects observed in this model.
Input command shaping techniques for robust, high-performance control of flexible structures (1996)

New input command shaping techniques for flexible systems are investigated using convex optimization approaches. These techniques lead to practical timeoptimal prefilters that are robust to modal parameter variations and high frequency unmodelled dynamics. The convex formulation provides a common basis for designing both minimum time prefilters and command input shapers. Further key advantages of the convex approach for complex systems are that it does not require a priori knowledge of the input profile, and it enables much greater flexibility for including additional actuator, performance, and robustness metrics. A simple experiment is used to illustrate that the design method is both systematic and effective.
Identifying authoritative actors in question-answering forums (2008)

We consider the problem of identifying authoritative users in Yahoo! Answers. A common approach is to use link analysis techniques in order to provide a ranked list of users based on their degree of authority. A major problem for such an approach is determining how many users should be chosen as authoritative from a ranked list. To address this problem, we propose a method for automatic identification of authoritative actors. In our approach, we propose to model the authority scores of users as a mixture of gamma distributions. The number of components in the mixture is estimated by the Bayesian Information Criterion (BIC) while the parameters of each component are estimated using the Expectation-Maximization (EM) algorithm. This method allows us to automatically discriminate between authoritative and non-authoritative users. The suitability of our proposal is demonstrated in an empirical study using datasets from Yahoo! Answers.
Autonomous indoor 3D exploration with a micro-aerial vehicle (2012)

In this paper, we propose a stochastic differential equation-based exploration algorithm to enable exploration in three-dimensional indoor environments with a payload constrained micro-aerial vehicle (MAV). We are able to address computation, memory, and sensor limitations by considering only the known occupied space in the current map. We determine regions for further exploration based on the evolution of a stochastic differential equation that simulates the expansion of a system of particles with Newtonian dynamics. The regions of most significant particle expansion correlate to unexplored space. After identifying and processing these regions, the autonomous MAV navigates to these locations to enable fully autonomous exploration. The performance of the approach is demonstrated through numerical simulations and experimental results in single and multi-floor indoor experiments.
Phylogenetic analysis and secondary structure of the Bacillus subtilis bacteriophage RNA required for DNA packaging. (1990)

An unusual RNA molecule encoded by the Bacillus subtilis bacteriophage phi 29 is a structural component of the viral prohead and is required for the ATP-dependent packaging of DNA. Here we report a model of secondary structure for this prohead RNA developed from a phylogenetic analysis of the primary sequences of prohead RNAs of related phages. Twenty-nine phages related to phi 29 were found to produce prohead RNAs. These RNAs were analyzed by their ability to replace phi 29 RNA in in vitro phage assembly, by Northern blot hybridization with a probe complementary to phi 29 RNA, and by partial and complete sequence analyses. These analyses revealed four quite different sequences ranging in length from 161 to 174 residues. The secondary structure deduced from these sequences, in agreement with earlier observations, indicated that prohead RNA is organized into two domains. The larger 5'-domain (Domain I) is composed of 113-117 residues and contains four helices. Three of these helices appear to be organized into a central stem that is interrupted by two unpaired loops and the fourth helix and loop. The smaller 3'-domain (Domain II) is composed of 40-44 residues and consists of two helices. Domains I and II are separated by 8-13 unpaired residues. Nuclease cleavage occurs readily in this single-stranded joining region, and this cleavage allows the subsequent separation of the two RNA domains. The separated Domain I is fully active in DNA packaging in vitro. The functional significance and biological role of Domain II are unknown. The phylogenetic secondary structure model provides a basis for further analysis of the role of this RNA in bacteriophage morphogenesis.