gebhart/patrepeval huggingface dataset:
Characterization of a Novel High-Affinity Monoclonal Immunoglobulin G Antibody against the Ricin B Subunit (2006)

There is an urgent need for the development of a passive immunotherapy against the category B select agent ricin, a lethal ribosome-inactivating toxin composed of an enzymatic A subunit (RTA) and a single binding B subunit (RTB). To date, only one monoclonal antibody (MAb), a mouse immunoglobulin G (IgG1) against RTA called R70, has been deemed sufficiently potent in animal models to warrant further testing in humans. In this study, we have identified and characterized MAb 24B11, a murine IgG1 directed against RTB. In a Vero cell cytotoxicity assay, 24B11 was approximately two times more effective at neutralizing ricin than was R70. The equilibrium dissociation constants of 24B11 (KD = 4.2 x 10(-9) M) and R70 (KD = 3.2 x 10(-9) M) were virtually identical, suggesting that the difference in neutralization activity between the two MAbs was not due to differing affinities for the toxin. 24B11 blocked ricin attachment to galactoside receptors on primary mouse splenocytes and on the apical surfaces of human mucosal epithelial cell monolayers. Surprisingly, R70 also effectively interfered with ricin attachment to receptors on cell surfaces. Using a phage-displayed peptide library, we determined that 24B11 binds an epitope on RTB adjacent to, but not within, one of the two galactose binding domains. Finally, we demonstrate that R70 and 24B11, when combined, function synergistically to neutralize ricin in vitro, raising the possibility that these two MAbs could serve as a novel immunotherapeutic in vivo.
Design and Coordination Kinematics of an Insertable Robotic Effectors Platform for Single-Port Access Surgery (2012)

Single port access surgery (SPAS) presents surgeons with added challenges that require new surgical tools and surgical assistance systems with unique capabilities. To address these challenges, we designed and constructed a new insertable robotic end-effectors platform (IREP) for SPAS. The IREP can be inserted through a Ø15 mm trocar into the abdomen and it uses 21 actuated joints for controlling two dexterous arms and a stereo-vision module. Each dexterous arm has a hybrid mechanical architecture comprised of a two-segment continuum robot, a parallelogram mechanism for improved dual-arm triangulation, and a distal wrist for improved dexterity during suturing. The IREP is unique because of the combination of continuum arms with active and passive segments with rigid parallel kinematics mechanisms. This paper presents the clinical motivation, design considerations, kinematics, statics, and mechanical design of the IREP. The kinematics of coordination between the parallelogram mechanisms and the continuum arms is presented using the pseudo-rigid-body model of the beam representing the passive segment of each snake arm. Kinematic and static simulations and preliminary experiment results are presented in support of our design choices.
The Highly Processive DNA Polymerase of Bacteriophage T5 (2004)

The DNA polymerase encoded by bacteriophage T5 has been reported previously to be processive and to catalyze extensive strand displacement synthesis. The enzyme, purified from phage-infected cells, did not require accessory proteins for these activities. Although T5 DNA polymerase shares extensive sequence homology with Escherichia coli DNA polymerase I and T7 DNA polymerase, it contains unique regions of 130 and 71 residues at its N and C termini, respectively. We cloned the gene encoding wild-type T5 DNA polymerase and characterized the overproduced protein. We also examined the effect of N- and C-terminal deletions on processivity and strand displacement synthesis. T5 DNA polymerase lacking its N-terminal 30 residues resembled the wild-type enzyme albeit with a 2-fold reduction in polymerase activity. Deletion of 24 residues at the C terminus resulted in a 30-fold reduction in polymerase activity on primed circular DNA, had dramatically reduced processivity, and was unable to carry out strand displacement synthesis. Deletion of 63 residues at the C terminus resulted in a 20,000-fold reduction in polymerase activity. The 3' to 5' double-stranded DNA exonuclease activity associated with T5 DNA polymerase was reduced by a factor of 5 in the polymerase truncated at the N terminus but was stimulated by a factor of 7 in the polymerase truncated at the C terminus. We propose a model in which the C terminus increases the affinity of the DNA for the polymerase active site, thus increasing processivity and decreasing the accessibility of the DNA to the exonuclease active site.
Computer-Synthesis of an Interference Color Chart of Human Tear Lipid Layer, by a Colorimetric Approach (2003)

A new tear interference color chart was developed in this study, which may be of benefit in converting tear interference color information to data describing the thickness of the tear film lipid layer.
Treatment of Hemophilia A in Utero and Postnatally using Sheep as a Model for Cell and Gene Delivery (2013)

Hemophilia A represents the most common inheritable deficiency of the coagulation proteins. Current state-of- the-art treatment consists of frequent prophylactic infusions of plasma-derived or recombinant FVIII protein to maintain hemostasis, and has greatly increased life expectancy and quality of life for many hemophilia A patients. This treatment approach is, however, far from ideal, due to the need for lifelong intravenous infusions, the high treatment cost, and the fact that it is unavailable to a large percentage of the world's hemophiliacs. There is thus a need for novel treatments that can promise long-term or permanent correction. In contrast to existing protein based therapeutics, gene therapy offers to provide a permanent cure following few, or even a single, treatment. In the present paper, we review ongoing work towards this end, focusing on studies we have performed in a large animal model. Some of the key topics covered in this review include the unique opportunities sheep offer as a model system, the re-establishment and clinical and molecular characterization of a line of sheep with severe hemophilia A, the advantages and feasibility of treating a disease like hemophilia A in utero, and the use of Mesenchymal Stem Cells (MSC) as cellular delivery vehicles for the FVIII gene. The review finishes with a brief discussion of our recent success correcting ovine hemophilia A with a postnatal transplant with gene-modified MSC, and the limitations of this approach that remain to be overcome.
Effect of proteoglycan removal on solute mobility in articular cartilage (1997)

Transport of nutrients, cytokines, pharmacologic agents, and matrix components through articular cartilage is critical for the viability and structural integrity of the tissue. To understand the role of the extracellular matrix in regulating this process, we measured the diffusivity of three uncharged solutes of different molecular size (glucose, MW 180; inulin, MW 5000; dextran, MW 70,000) into intact cartilage and cartilage that had its proteoglycan (PG) component removed. Solute diffusivity was measured by performing transient (nonsteady state) one-dimensional diffusion tests using radiolabelled solutes. Compared to intact cartilage, the diffusivity of glucose was unchanged after PG removal, inulin was unchanged but dextran increased by 1.7 times after 71% PG removal, and both inulin and dextran increased by 1.6 and 2.0 times, respectively, after 93% PG removal. The diffusivities of inulin and dextran were inversely proportional to the PG content. While no change was found in the tissue's bulk fluid content, PG depletion resulted in an increase in fluid content in the upper regions of the tissue and a decrease in the lower regions. These results indicate that in intact tissue small uncharged solutes have free mobility through the inter-molecular and intra-molecular PG volumes, larger molecules have limited intra-molecular mobility, and very large molecules are excluded from the intra-molecular space.
Development of Sniffing Atmospheric Pressure Penning Ionization (2006)

The atmospheric pressure Penning ionization was applied to the analysis of atmospheric-pressure ambient gaseous samples. The metastable rare gas atoms (Rg*) were produced by a negative-mode corona discharge of reagent rare gas (Rg). The rare gas containing Rg* in the discharge cell flowed out into the ion source cell through a nozzle with an inner diameter of 1 mm as a jet stream. The jet stream acts as a gas-jet pump and the pressure of the ion source cell becomes somewhat lower than the atmospheric pressure. The sample gas at ambient atmospheric pressure was sucked into the reduced-pressure ion source cell through the stainless steel tube (10 cm in length, 1 mm in diameter). The sample gases introduced in the ion source cell are ionized by Penning ionization. This technique was found to be applicable to various gaseous samples such as aromatic compounds, oxygen- and nitrogen-containing compounds, etc. However, no ion signal could be detected for aliphatic hydrocarbons. This may be due to the much smaller ionization cross sections for these compounds than N2 and O2 molecules which are introduced into the ion source together with sample gases.
Interleukin-1alpha up-regulation in vivo by a potent carcinogen 7,12-dimethylbenz(a)anthracene (DMBA) and control of DMBA-induced inflammatory responses. (2002)

Tumor-initiating properties of complete carcinogens such as 7,12-dimethylbenz(a)anthracene (DMBA) are well known but not the mechanism of DMBA-mediated tumor promotion. Our hypothesis is that interleukin (IL)-1alpha, an early proinflammatory cytokine that initiates a cascade of other cytokines and growth factors, is up-regulated by DMBA and contributes to inflammation and carcinogenesis. We found that topical exposure of SENCAR mice to a carcinogenic DMBA dose indeed triggers significant increases in mouse skin IL-1alpha and IL-1alpha mRNA. Five DMBA applications (200 nmol each) caused a statistically significant (P = 0.02) increase in serum IL-1alpha, comparable with that induced by 12-O-tetradecanoylphorbol-13-acetate, a potent tumor promoter. IL-1alpha increase in serum was evident 24 h after the first DMBA application, whereas that in skin required five DMBA doses and became statistically significant (P < 0.0003) 48 h later. Skin IL-1alpha enhancement was preceded by a 6-fold up-regulation of IL-1alpha mRNA. A pretreatment with antimurine IL-1alpha antibody (Ab) nearly abolished DMBA-induced IL-1alpha mRNA (P = 0.0001) in skin and substantially decreased IL-1alpha in serum. Infiltration of polymorphonuclear leukocytes into skin was elevated 6-fold (P = 0.002) and >10-fold (P = 0.001) 24 h and 48 h after the fifth DMBA exposure, respectively. A pretreatment with anti-IL-1alpha Ab decreased polymorphonuclear leukocyte infiltration by >65% (P < 0.02), which suggests that this process is at least 65% under IL-1alpha control. Anti-IL-1alpha antibodies had no effect on edema, thus dissociating the two inflammation markers. Injecting anti-IL-1alpha Ab before DMBA applications significantly (P < 0.04) decreased the volume of carcinomas (CAs) in comparison with CAs that arose in mouse skin injected with a nonspecific serum. These results prove that IL-1alpha is induced by a carcinogenic DMBA dose and contributes to DMBA-induced inflammation and volume of CAs, hallmarks of tumor promotion and progression.
Modifiable Risk Factors for Migraine Progression (2006)

Migraine is a chronic-recurrent disorder that progresses in some individuals. Transformed migraine is the result of this progression. Since migraine does not progress in most patients, identifying the risk factors for progression has emerged as a very important public health priority. If risk factors can be identified, that might provide a foundation for more aggressive preventive intervention. Risk factors for progression may be divided into non-remediable (gender, age, race) and remediable categories. In this paper, we focus on several already identified remediable risk factors, including frequency of migraine attacks, obesity, acute medication overuse, caffeine overuse, stressful life events, depression, and sleep disorders. We present the evidence for each risk factor and discuss possible interventions to address them.
The Progress and Promise of Molecular Imaging Probes in Oncologic Drug Development (2005)

As addressed by the recent Food and Drug Administration Critical Path Initiative, tools are urgently needed to increase the speed, efficiency, and cost-effectiveness of drug development for cancer and other diseases. Molecular imaging probes developed based on recent scientific advances have great potential as oncologic drug development tools. Basic science studies using molecular imaging probes can help to identify and characterize disease-specific targets for oncologic drug therapy. Imaging end points, based on these disease-specific biomarkers, hold great promise to better define, stratify, and enrich study groups and to provide direct biological measures of response. Imaging-based biomarkers also have promise for speeding drug evaluation by supplementing or replacing preclinical and clinical pharmacokinetic and pharmacodynamic evaluations, including target interaction and modulation. Such analyses may be particularly valuable in early comparative studies among candidates designed to interact with the same molecular target. Finally, as response biomarkers, imaging end points that characterize tumor vitality, growth, or apoptosis can also serve as early surrogates of therapy success. This article outlines the scientific basis of oncology imaging probes and presents examples of probes that could facilitate progress. The current regulatory opportunities for new and existing probe development and testing are also reviewed, with a focus on recent Food and Drug Administration guidance to facilitate early clinical development of promising probes.
Indolo[3, 2-b]carbazole: a Dietary-Derived Factor That Exhibits Both Antiestrogenic and Estrogenic Activity (1994)

The current focus on the role of dietary and environmental estrogens in human disease should take into account the possible contra-active effects of Ah receptor agonists such as 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), ICZ, I3C, and related compounds that exhibit antiestrogenic activity.
Synthetic gene expression perturbation systems with rapid, tunable, single-gene specificity in yeast (2012)

A general method for the dynamic control of single gene expression in eukaryotes, with no off-target effects, is a long-sought tool for molecular and systems biologists. We engineered two artificial transcription factors (ATFs) that contain Cys(2)His(2) zinc-finger DNA-binding domains of either the mouse transcription factor Zif268 (9 bp of specificity) or a rationally designed array of four zinc fingers (12 bp of specificity). These domains were expressed as fusions to the human estrogen receptor and VP16 activation domain. The ATFs can rapidly induce a single gene driven by a synthetic promoter in response to introduction of an otherwise inert hormone with no detectable off-target effects. In the absence of inducer, the synthetic promoter is inactive and the regulated gene product is not detected. Following addition of inducer, transcripts are induced >50-fold within 15 min. We present a quantitative characterization of these ATFs and provide constructs for making their implementation straightforward. These new tools allow for the elucidation of regulatory network elements dynamically, which we demonstrate with a major metabolic regulator, Gcn4p.
Identification of distinct elements of the stromal microenvironment that control human hematopoietic stem/progenitor cell growth and differentiation. (1998)

Using a novel collection of conditionally immortalized mouse stromal cell clones, we evaluated the role of distinct elements of the hematopoietic microenvironment in supporting and regulating the growth, division, and differentiation of a candidate human stem cell population (CD34+/CD38-). We found functional diversity in the capacity of different stromal cell clones to support the growth of primitive (CD34+/CD38-) and committed (CD34+/CD38+) hematopoietic progenitors and their differentiation into mature hematopoietic cells (CD34-/CD45+). Among the stromal cell clones that supported long-term hematopoiesis, we identified two clones that induced expansion of CD34+ progenitor/stem cells during the first 4 weeks of coculture and that supported the maintenance of this CD34+ population for up to 10 weeks in vitro. However, these two clones appeared to represent two different microenvironments with regard to the signals they provide to the different CD34+ progenitor subpopulations: One stromal clone preserved a pool of undifferentiated, relatively quiescent (CD34+/CD38-) progenitor cells, allowing their differentiation at a low rate into more committed (CD34+/CD38+) progenitors; the other fostered a more extensive and rapid differentiation of all CD34+/CD38- progenitors into CD34+/CD38+ cells, preferentially maintaining this committed population at a higher rate of cell division. These stromal cell clones were also able to support the proliferation and differentiation of CD34+/CD38- cells in conditions in which progenitor-stroma contact was prevented. This collection of stromal cell clones may represent a unique tool for the study of stromal regulators of hematopoiesis as well as for the support of gene transfer into hematopoietic progenitor cells.
Effective blocking of HIV‐1 proteinase activity by characteristic inhibitors of aspartic proteinases (1989)

Inhibitory constants (Ki) between 5 and 35 nM were derived (under different conditions of pH and ionic strength) for the interaction of HIV-1 proteinase with acetyl-pepstatin and H-261, two characteristic inhibitors of aspartic proteinases. Thus this enzyme, essential for replication of the AIDS virus, may be classified unequivocally as belonging to this proteinase family.
Plant protoplasts as genetic tool: selectable markers for developmental studies (1992)

Protoplasts have usually been presented as a methodological tool. Even as such, they make possible an impressive array of applications in plant biology. Here we report on the use of protoplast-derived selectable markers in the study of several disturbed genetic systems with obvious effects on plant development: (1) auxotrophic mutants and the control of amino acid biosynthesis and transport in vegetative and reproductive tissues; (2) introgression of alien genetic information across phylogenetic boundaries by protoplast fusion, a consequence of controlled dedifferentiation-redifferentiation processes and attenuated incompatibility reactions in cultured cells; (3) expression (in)stability of foreign genes in transgenic plants during successive meiotic generations and in crosses between independent transformants.
Localization of epitopes of herpes simplex virus type 1 glycoprotein D (1985)

We previously defined eight groups of monoclonal antibodies which react with distinct epitopes of herpes simplex virus glycoprotein D (gD). One of these, group VII antibody, was shown to react with a type-common continuous epitope within residues 11 to 19 of the mature glycoprotein (residues 36 to 44 of the predicted sequence of gD). In the current investigation, we have localized the sites of binding of two additional antibody groups which recognize continuous epitopes of gD. The use of truncated forms of gD as well as computer predictions of secondary structure and hydrophilicity were instrumental in locating these epitopes and choosing synthetic peptides to mimic their reactivity. Group II antibodies, which are type common, react with an epitope within residues 268 to 287 of the mature glycoprotein (residues 293 to 312 of the predicted sequence). Group V antibodies, which are gD-1 specific, react with an epitope within residues 340 to 356 of the mature protein (residues 365 to 381 of the predicted sequence). Four additional groups of monoclonal antibodies appear to react with discontinuous epitopes of gD-1, since the reactivity of these antibodies was lost when the glycoprotein was denatured by reduction and alkylation. Truncated forms of gD were used to localize these four epitopes to the first 260 amino acids of the mature protein. Competition experiments were used to assess the relative positions of binding of various pairs of monoclonal antibodies. In several cases, when one antibody was bound, there was no interference with the binding of an antibody from another group, indicating that the epitopes were distinct. However, in other cases, there was competition, indicating that these epitopes might share some common amino acids.
Internet traffic classification based on flows' statistical properties with machine learning (2016)

Summary Machine learning has recently entered the area of network traffic classification as an alternative to the deep packet inspection technique. It provides both unsupervised and supervised learning algorithms that are capable to put aside similar types of traffic or recognize Internet protocols based on some training, pre‐labeled samples. The current work proposes a new approach in the area of network traffic classification using machine learning. First, we extract the unidirectional and bidirectional flows from a traffic capture. A flow is a collection of packets that share sender and receiver IP address and port. Second, we select relevant statistical properties of these flows and use an unsupervised learning mechanism to group flows into clusters based on the similarities. Eventually, we use this classification as training input for a supervised learning engine that will have to properly determine the class of new, unseen traffic flows. Copyright © 2016 John Wiley &amp; Sons, Ltd.
The performance of three database storage structures for managing large objects (1992)

This study analyzes the performance of the storage structures and algorithms employed in three experimental database storage systems – EXODUS, Starburst, and EOS – for managing large unstructured general-purpose objects. All three mechanisms are segment-based in that the large object is stored in a sequence of segments, each consisting of physically continuous disk block. To analyze the algorithms we measured object creation time, sequential scan time, storage utilization in the presence of updates, and the I/O cost of random reads, inserts, and deletes.