gebhart/patrepeval huggingface dataset:
Nanoliter Liquid Metering in Microchannels Using Hydrophobic Patterns (2000)

Nanoliter-sized liquid drops can be accurately metered inside hydrophilic microchannels using a combination of hydrophobic surface treatment and air pressure. The technique involves spontaneously filling the microchannels up to a hydrophobic region and splitting a liquid drop by injecting air through a hydrophobic side channel. The hydrophobic regions are fabricated by using a patterned metal mask on a substrate. The patterned substrate is immersed in an isooctane solution containing 1H,1H,2H,2H-per-fluorodecyltrichlorosilane to form hydrophobic patches on the exposed surface. Stripping the metal mask leaves the hydrophobic patches and restores the hydrophilic substrate surface. Precise and accurate liquid volumes, ranging from 0.5 to 125 nanoliters, have been metered using this technique. Theoretical predictions of the pressure needed to meter drops compare well with the experimental values.
New Developments in Vaccines, Inhibitors of Anthrax Toxins, and Antibiotic Therapeutics for Bacillus anthracis (2011)

Bacillus anthracis, the causative agent responsible for anthrax infections, poses a significant biodefense threat. There is a high mortality rate associated with untreated anthrax infections; specifically, inhalation anthrax is a particularly virulent form of infection with mortality rates close to 100%, even with aggressive treatment. Currently, a vaccine is not available to the general public and few antibiotics have been approved by the FDA for the treatment of inhalation anthrax. With the threat of natural or engineered bacterial resistance to antibiotics and the limited population for whom the current drugs are approved, there is a clear need for more effective treatments against this deadly infection. A comprehensive review of current research in drug discovery is presented in this article, including efforts to improve the purity and stability of vaccines, design inhibitors targeting the anthrax toxins, and identify inhibitors of novel enzyme targets. High resolution structural information for the anthrax toxins and several essential metabolic enzymes has played a significant role in aiding the structure-based design of potent and selective antibiotics.
Propel: A Randomized Trial of Mericitabine Plus Peginterferon Alpha-2a/Ribavirin Therapy in Treatment-NaïVe HCV Genotype 1/4 Patients (2013)

Treatment with mericitabine plus Peg-IFNα-2a/RBV for 8 or 12 weeks provided potent suppression of HCV RNA, was well tolerated, and did not select resistant variants, but did not increase SVR rates, compared to placebo. IFN-free and IFN-containing trials of mericitabine of longer treatment duration are ongoing.
OUTLINE OF A FORWARD-LOOKING MARITIME MOBILE SATELLITE SYSTEM (1978)

The development of the European Maritime Orbital Test Satellite (MAROTS) is reported in order to meet the growing need for more rapid and reliable communications of improved quality between land-based stations and ships at sea. The characteristics of a forward-looking operational maritime mobile-satellite system which would be suitable for the provision of an international world-wide service in the 1980's were also investigated. The system was configured around the MAROTS satellite. An outline of the system is presented.
Use of Lentiviral Vectors for Delivery of Small Interfering RNA (2003)

Silencing of gene expression by small interfering RNAs (siRNAs) is rapidly becoming a powerful tool for genetic analysis of mammalian cells. Although in the original studies expression of siRNA in mammalian cells was achieved via the transfection of double stranded oligonucleotides, subsequent studies described the use of plasmids to achieve long-term and stable expression of siRNA. Recently, several groups have described the use of retroviral vectors for siRNA delivery. However, retroviral vectors require active cell division for gene transfer and also suffer from the problem of gene-silencing. In this report we have modified a commercially available self-inactivating lentiviral vector for the delivery of siRNA into mammalian cells. We demonstrate the ability of this modified vector to efficiently transfer siRNA into HeLa S3 cells and downregulate p53 expression. Our results suggest that lentiviruses are efficient vectors for delivery of siRNA into mammalian cells. Based on the known ability of these vectors to infect both dividing and non-dividing cells and achieve long-term multilineage gene expression, their use as a therapeutic tool for the delivery of siRNA deserves further study.
Systematic floor coverage of unknown environments using rectangular regions and localization certainty (2013)

We address the problem of systematically covering all accessible floor space in an unknown environment by a mobile robot. Our approach uses rectangular regions that are swept across the environment. In the first stage, the robot covers each region using the classic boustrophedon pattern and planning paths to uncovered areas within the region while keeping track of its position uncertainty. The region is then moved sideways to cover the next part of the environment until all accessible space has been visited. In the second stage, the robot revisits the perimeter around the obstacles. We compare our method in terms of total trajectory length to 5 off-line methods including the distance transformation by Zelinsky et al. [1] in a standard test environment as well as in multi-room homes. The presented method has been employed in our Mint cleaning robot [2] for autonomously sweeping and mopping the floors.
Macroporous Membranes with Highly Ordered and Three-Dimensionally Interconnected Spherical Pores (1998)

We have demonstrated the fabrication of highly ordered three-dimensional macroporous membranes with crystalline assemblies of monodispersed mesoscale particles (∼200 nm to ∼10 μm in diameter) as templates. We filled the void spaces among the particles with a UV-curable liquid prepolymer by capillary action. Subsequent solidification of the prepolymer and dissolution of the particles yielded a membrane film consisting of a highly organized and three-dimensionally interconnected framework of spherical pores. The pores are uniform in size, with dimensions defined by the diameter of the particles. The pores are completely exposed on both top and bottom surfaces of the membrane film. In addition to those applications associated with conventional macroporous materials, the macroporous membranes fabricated here are potentially useful as photonic bandgap structures or as supports for the fabrication of diffractive optical sensors due to their specified and highly ordered structures.
Antiepileptics Topiramate and Levetiracetam Alleviate Behavioral Deficits and Reduce Neuropathology in APPswe/PS1dE9 Transgenic Mice (2013)

Therefore, TPM and LEV might have the potential to treat AD effectively in patient care.
Objectvideo forensics: activity-based video indexing and retrieval for physical security applications (2004)

We present an architecture and methodology for high-speed activity-based digital video indexing and retrieval for physical security applications. State of the art computer vision algorithms detect objects in real-time video and determine basic activity information such as object type (human, vehicle, etc.), object trajectory, and interactions with other objects. This information is encoded as a light-weight stream of activity-based meta-data that can be distributed over a network, analysed in real-time to detect security threats, and archived for forensic analyses. To enable flexible forensic analysis, an activity query schema is described that is designed specifically for physical security applications. It is based on a traditional Boolean binary tree approach, but with specific modifications for activity queries. This schema is implemented through an intuitive user interface that enables even unsophisticated users to create complex activity queries. The described mechanism of separating the complex computer vision process from activity queries means that forensic analysis can be achieved at extremely high-speeds - database query time instead of video processing time. Finally a case study is presented concerning the use of this mechanism to optimise the performance of a real-time security system through iterative forensic analysis.
Photonic nanojet calculations in layered radially inhomogeneous micrometer-sized spherical particles (2011)

A photonic nanojet (PNJ) corresponds to the specific highly localized spatial region of electromagnetic near-field distribution in the vicinity of a transparent micrometer-sized particle illuminated by a light wave. Here we consider dielectric spherical composite particles consisting of a core and several concentric shells having different refractive indices. The longitudinal and latitudinal sizes of a PNJ and its peak intensity depending on the optical contrast variation of shells are numerically investigated. We show that by properly changing the refractive indices of neighboring shells, it is possible to manipulate the PNJ shape and, in particular, extend its longitudinal size or increase its peak intensity.
Embryonic mouse lung epithelial progenitor cells co-express immunohistochemical markers of diverse mature cell lineages. (1996)

Developmental expression of marker genes representative of different mature cell types can be used to study differentiation of cell lineages. We used immunohistochemistry to study expression in developing mouse lung of calcitonin gene-related peptide (CGRP), Clara cell 10-KD protein (CC10), and surfactant protein-A (SP-A), markers that are differentially expressed in neuroendocrine cells, Clara cells, and Type II alveolar cells. Two distinct developmental phases were revealed. The earlier phase (embryonic days 13-15; E13-E15) was characterized by CGRP, CC10, and SP-A immunostaining in all epithelial cells of the distal airways, with the three patterns being virtually identical in adjacent sections. The later phase (E16-E18) was characterized by emergence of staining of the differentiated cell types. These expression patterns were recapitulated in serumless organ culture, demonstrating that information necessary to generate both phases of gene expression is present within the lung analage by E11. We conclude that CGRP, CC10, and SP-A are co-expressed in most or all cells of the distal lung epithelium at E13-E15 and later become restricted to different cell lineages. This transient expression in progenitor cells of gene products characteristic of diverse differentiated cell types may reflect an underlying mechanism of gene regulation.
Complete Genome Sequence of a 2019 Novel Coronavirus (SARS-CoV-2) Strain Isolated in Nepal (2020)

A complete genome sequence was obtained for a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strain isolated from an oropharyngeal swab specimen of a Nepalese patient with coronavirus disease 2019 (COVID-19), who had returned to Nepal after traveling to Wuhan, China.
CD4+CD25+ regulatory T cells down-regulate co-stimulatory molecules on antigen-presenting cells (2000)

CD4+CD25+ T cells have been shown to inhibit experimentally induced organ-specific autoimmune disease and depletion of these regulatory T cells from normal mice results in development of such conditions. Furthermore, CD4+CD25+ T cells suppress the IL-2 production and thereby the proliferation of polyclonally activated CD4+CD25- T cells in vitro. The suppression in vitro is independent of secreted factors but requires interactions between CD4+CD25- and CD4+CD25+ T cells and antigen-presenting cells (APC). We have now further investigated the function of CD4+CD25+ T cells in vitro and have focused on their interactions with APC. We found that CD4+CD25+ T cells down-regulated the expression of the co-stimulatory molecules CD80 and CD86 on dendritic cells. The steady-state level of CD80 mRNA was also decreased, while the steady-state level of CD86 mRNA was not, suggesting that distinct mechanisms regulate the expression of these molecules. The down-regulation occurred even in the presence of stimuli that would normally increase the expression of CD80 and CD86 molecules. Thus, down-regulation of co-stimulatory molecules may be an additional effector function of these regulatory T cells.
Toward an Epidemiology and Natural History of SIRS (Systemic Inflammatory Response Syndrome) (1992)

Patients with severe SIRS should not be assumed to have gram-negative infection; furthermore, data derived from studies of patients with gram-negative infection should be applied cautiously to all patients with SIRS. Studies of patients with sepsis or SIRS should include at least a 1-month follow-up if mortality is an end point. More consistent definitions of these disorders should permit more effective comparisons across studies.
Zbtb46 expression distinguishes classical dendritic cells and their committed progenitors from other immune lineages (2012)

Distinguishing dendritic cells (DCs) from other cells of the mononuclear phagocyte system is complicated by the shared expression of cell surface markers such as CD11c. In this study, we identified Zbtb46 (BTBD4) as a transcription factor selectively expressed by classical DCs (cDCs) and their committed progenitors but not by plasmacytoid DCs (pDCs), monocytes, macrophages, or other lymphoid or myeloid lineages. Using homologous recombination, we replaced the first coding exon of Zbtb46 with GFP to inactivate the locus while allowing detection of Zbtb46 expression. GFP expression in Zbtb46gfp/+ mice recapitulated the cDC-specific expression of the native locus, being restricted to cDC precursors (pre-cDCs) and lymphoid organ– and tissue-resident cDCs. GFP+ pre-cDCs had restricted developmental potential, generating cDCs but not pDCs, monocytes, or macrophages. Outside the immune system, Zbtb46 was expressed in committed erythroid progenitors and endothelial cell populations. Zbtb46 overexpression in bone marrow progenitor cells inhibited granulocyte potential and promoted cDC development, and although cDCs developed in Zbtb46gfp/gfp (Zbtb46 deficient) mice, they maintained expression of granulocyte colony-stimulating factor and leukemia inhibitory factor receptors, which are normally down-regulated in cDCs. Thus, Zbtb46 may help enforce cDC identity by restricting responsiveness to non-DC growth factors and may serve as a useful marker to identify rare cDC progenitors and distinguish between cDCs and other mononuclear phagocyte lineages.
X-Ray Structure Determination: A Practical Guide (1989)

PRELIMINARY STAGES. X--Rays. Diffraction of X--Rays. Crystals, Symmetry, and Space Groups. Crystals and Their Properties. Geometric Data Collection. Intensity Data Collection. Data Reduction. Theory of Structure Factors and Fourier Syntheses. Calculation of Structure Factors and Fourier Syntheses. THE PHASE PROBLEM. The Phase Problem. Direct Methods. Patterson Methods. Heavy Atom Methods. Search Methods. Completing the Structure. REFINEMENT AND RESULTS. Refinement of Crystal Structures. Random and Systematic Errors. Derived Results. Ambiguities and Uncertainties. Appendices. Index.
Arthroscopic Single-Row versus Double-Row Suture Anchor Rotator Cuff Repair (2005)

The arthroscopic techniques studied have strong structural properties that approached the reported performance of open repair techniques. Double-row techniques provide a larger footprint width; although not addressed by this study, such a factor may improve the biological quality of repair.
Estimating semantic confidence for spoken dialogue systems (2002)

In order for a spoken dialogue system to carry on a fluent conversation, it must be able to estimate confidence in its interpretation of the input that it is receiving. It must realize when it doesn't understand the user and interact to correct the problem. To this end, most systems have some form of confidence assessment mechanism. These algorithms generally estimate confidence on a word-by-word basis and sometimes use these estimates to accept or reject an utterance as a whole. This paper presents the confidence assessment mechanism developed for the CU Communicator spoken dialogue system. The focus of this mechanism is to assess confidence in the semantic representation extracted from an utterance by the system rather than in the string of words produced by the recognizer. We use a decision tree classifier with features based on acoustic models, language models, word lattice density, parser output and dialogue context. The classification performance is evaluated on a test set from the CU Communicator data. CU Communicator is a telephone based spoken dialogue system for getting information on air travel, hotels and rental cars.
Influence of intranasal immunization with synthetic peptides corresponding to conserved epitopes of M protein on mucosal colonization by group A streptococci (1988)

A major virulence factor of group A streptococci is M protein, a surface-exposed fibrillar molecule of which there exist more than 80 distinct serological types. Antigenic variability resides largely in the amino-terminal region of M protein, whereas the carboxy-terminal half of the molecule is highly conserved among different M serotypes. We sought to determine whether mucosal immunization with conserved epitopes of M protein influences the course of mucosal colonization by group A streptococci in a mouse model. Synthetic peptides corresponding to sequences in the conserved region of M protein were covalently linked to the mucosal adjuvant cholera toxin B subunit. Mice were immunized intranasally with the peptide-cholera toxin B subunit conjugate or with cholera toxin B subunit alone and then challenged intranasally with live streptococci. Pharyngeal colonization by streptococci was measured for up to 15 days postchallenge. Mice immunized with synthetic peptides showed a significant reduction in colonization compared with the control group. The data demonstrate that immunity evoked by conserved portions of M protein influences the outcome of group A streptococcal infection at the nasopharyngeal mucosa in a mouse model.
Convection-enhanced distribution of large molecules in gray matter during interstitial drug infusion (1995)

Many novel experimental therapeutic agents, such as neurotrophic factors, enzymes, biological modifiers, and genetic vectors, do not readily cross the blood-brain barrier. An effective strategy to deliver these compounds to the central nervous system is required for their application in vivo. Under normal physiological conditions, brain interstitial fluid moves by both bulk flow (convection) and diffusion. It has recently been shown that interstitial infusion into the white matter can be used to increase bulk flow, produce interstitial convection, and efficiently and homogeneously deliver drugs to large regions of brain without significant functional or structural damage. In theory, even more uniform distribution is likely in gray matter. In the current study, four experiments were performed to examine if convection-enhanced delivery could be used to achieve regional distribution of large molecules in gray matter. First, the volume and consistency of anatomical distribution of 20 microliters of phaseolus vulgaris-leukoagglutinin (PHA-L; molecular weight (MW) 126 kD) after continuous high-flow microinfusion into the striatum of five rats over 200 minutes were determined using immunocytochemistry and quantified with image analysis. Second, the concentration profile of 14C-albumin (MW 69 kD) infused under identical conditions was determined in four hemispheres using quantitative autoradiography. Third, the volume of distribution after convection-enhanced infusion of 250 or 500 microliters biotinylated dextran (b-dextran, MW 10 kD), delivered over 310 minutes into the caudate and putamen of a rhesus monkey from one (250 microliters) or two (500 microliters) cannulas, was determined using immunocytochemistry and quantified with image analysis. Finally, the ability to target all dopaminergic neurons of the nigrostriatal tract via perfusion of the striatum with subsequent retrograde transport was assessed in three experiments by immunohistochemical analysis of the mesencephalon following a 300-minute infusion of 27 microliters horseradish peroxidase-labeled wheat germ agglutinin (WGA-HRP) into the striatum. Convection-enhanced delivery reproducibly distributed the large-compound PHA-L throughout the rat striatum (the percent volume of the striatum perfused, Vs, was 86% +/- 5%; mean +/- standard deviation) and produced a homogeneous tissue concentration in the perfused region (concentration of 14C-albumin relative to infusate concentration 30% +/- 5%). In the monkey, the infusion widely distributed b-dextran within the striatum using one cannula (caudate and putamen Vs = 76% and 76%) or two cannulas (Vs = 90% and 71%).(ABSTRACT TRUNCATED AT 400 WORDS)
DNA vaccines against mycobacterial diseases (2009)

Bacteria belonging to the genus Mycobacterium can cause several infectious diseases affecting humans and animals. Here, we reviewed the latest advances in the development of DNA vaccines against TB, Buruli ulcer and Johne's disease. Current understanding of the immunity to the respective causative pathogens indicates that the use of DNA vaccines encoding mycobacterial antigens could lead to efficient vaccination strategies. Moreover, characterization of protective mycobacterial antigens has been greatly facilitated by the analysis of immune responses induced after DNA vaccination. In addition, work aiming at optimizing DNA vaccines against mycobacterial diseases and research related to the controversial development of postexposure and therapeutic DNA vaccines are also discussed.
ABCA1 mutation carriers with low high-density lipoprotein cholesterol are characterized by a larger atherosclerotic burden (2012)

Carriers of loss of function ABCA1 mutations display a larger atherosclerotic burden compared with age and sex-matched controls, implying a higher risk for CVD. Further studies are needed to elucidate the full function of ABCA1 in the protection against atherosclerosis. These data support the development of strategies to up-regulate ABCA1 in patients with established CVD.
Effective poxvirus removal by sterile filtration during manufacture of plasma derivatives (2005)

As a consequence of the September 2001 terrorist events, programs to protect against further such acts including potentially the use of biological warfare agents have been launched in the USA and elsewhere. As part of these initiatives, Vaccinia virus was procured for the pre-emptive vaccination of key personnel against smallpox as well as population-wide protection after an eventual exposure. The introduction of this live virus into a population at a relatively large scale represents a theoretical challenge for the safety of the blood supply, and potentially for plasma for fractionation. To strengthen further the demonstration of safety margins for plasma derived products against Vaccinia virus, the capacity of sterile filtration procedures to remove the virus was investigated. An infectivity assay for the Vaccinia virus strain which represents the majority of smallpox vaccine stocks available currently was used to investigate the potential removal of this virus by sterile filtration processes during the manufacture of plasma derivatives. Vaccinia virus behaves as predicted based on its size, i.e., an artificially added virus load is removed about 10,000-fold by the sterile filtration procedures tested. As the current investigation covered a range of different protein concentrations, filter materials and filters from different manufacturers, the results obtained are considered to be widely applicable. The current investigation supports further the high safety margins of plasma derivatives against any potential Vaccinia virus content of plasma for fractionation. As the large size is a general feature of Orthopox viruses, the results would also provide assurance against poxviruses identified more recently, for example, Monkeypox virus.