gebhart/patrepeval huggingface dataset:
Python for Scientific Computing (2007)

Python is an excellent "steering" language for scientific codes written in other languages. However, with additional basic tools, Python transforms into a high-level language suited for scientific and engineering code that's often fast enough to be immediately useful but also flexible enough to be sped up with additional extensions.
Immunological Detection of Conformational Neoepitopes Associated with the Serpin Activity of Plasminogen Activator Inhibitor Type-2 (1998)

The physiological roles of plasminogen activator inhibitor-2 (PAI-2) are not yet well understood. Kinetic studies suggest a role in the regulation of plasminogen activator-driven proteolysis in many cell types. This study describes a monoclonal antibody (2H5), which uniquely recognizes neoepitope determinants on PAI-2 appearing after thermodynamic relaxation of the molecule. Enzyme-linked immunosorbent assays and native polyacrylamide gel electrophoresis immunoblotting confirmed the specificity of 2H5 for urokinase type plasminogen activator.PAI-2 complexes. Examination of the affinity of 2H5 for complexes formed between PAI-2 and a synthetic 14-mer reactive site loop peptide, PAI-2 treated with tissue plasminogen activator, or thrombin suggests that the 2H5 epitope is determined exclusively by sequences found only on PAI-2 following proteolytic cleavage of the Arg380-Thr381 bond and insertion of the reactive site loop into beta-sheet A. Peptides lacking both the P13 (Glu368) and P14 (Thr367) residues did not induce a conformational change or affect the inhibitory activity of PAI-2, indicating that one or both of these residues are critical for PAI-2 function. To our knowledge, this is the first description of a monoclonal antibody that can distinguish conformational changes in PAI-2 related specifically to its potential biological function(s).
Deformable Filter Convolution for Point Cloud Reasoning (2019)

Point clouds are the native output of many real-world 3D sensors. To borrow the success of 2D convolutional network architectures, a majority of popular 3D perception models voxelize the points, which can result in a loss of local geometric details that cannot be recovered. In this paper, we propose a novel learnable convolution layer for processing 3D point cloud data directly. Instead of discretizing points into fixed voxels, we deform our learnable 3D filters to match with the point cloud shape. We propose to combine voxelized backbone networks with our deformable filter layer at 1) the network input stream and 2) the output prediction layers to enhance point level reasoning. We obtain state-of-the-art results on LiDAR semantic segmentation and producing a significant gain in performance on LiDAR object detection.
Slider Air Bearing Design Enhancements for High Speed Flexible Disk Recording (2005)

The current effort was motivated largely by the fact that computing and communication platforms are becoming more portable and mobile with increased demands for both speed and disk storage. This work makes use of an asymmetric opposed slider arrangement to provide both static and dynamic improvements to the recording head air bearing interface for high speed flexible disk applications. The combination of a longitudinally slotted rail opposed by an uninterrupted rail that functions as a noncontact hydrodynamic pressure pad causes the disk to deflect at the submicron level over critical areas of the slider interface. This allows the required static minimum flying height to be focused over the recording transducer while higher clearances are positioned elsewhere, resulting in minimized exposure to contact between slider and disk. The high stiffness and low flying height of the air film at the recording element together with the low stiffness and high flying height of the opposing air film provides a noncontact air bearing interface that is especially immune to mechanical shock. A computer code called FLEXTRAN was developed that provides both static and dynamic numerical solutions of the air bearing interface composed of two opposed gimbal mounted sliders loaded against a high speed flexible disk. Simulations of the asymmetric opposed slider configuration are presented and compared with those of other slider air bearing designs.
Accuracy and risk of malignancy for diagnostic categories in urine cytology at a large tertiary institution (2014)

The findings suggest that atypia favoring malignancy is being appropriately flagged. However, further definition of the atypical category is needed to increase specificity with a better qualitative or quantitative morphological algorithm. This study provides a risk of malignancy for each category for benchmarking and clinical triage. The data suggest that follow-up should include at least 4 consecutive urine specimens over a period of 22.2 months.
A Multi-element Proportional Counter for Radiation Protection Measurements (1989)

A detector incorporating about 300 individual counting volumes is described, and the results of performance tests are reported. The device can be employed for a direct measurement of the dose equivalent in an unspecified radiation field on the basis of the lineal energy spectrum in 1-micron diameter tissue regions. It is substantially smaller than a conventional tissue equivalent proportional counter yielding the same counting rate and may be useful for measurements in phantoms.
Experimental Study of Plasmoids (1957)

A plasma source can be used to project ionized matter across a magnetic field. The configuration of plasma observed when an electromagnetic braking action is produced by the presence of low-pressure gas (\ensuremath{\sim}1 \ensuremath{\mu}) in the vacuum chamber provides an insight into the manner in which magnetic-field lines can be dragged and twisted. By firing several sources simultaneously, it is possible to simulate in geometrical form the production of spiral galaxies and barred spirals.
Wetting and energetics in nanoparticle etching of graphene (2010)

Molten metallic nanoparticles have recently been used to construct graphene nanostructures with crystallographic edges. The mechanism by which this happens, however, remains unclear. Here, we present a simple model that explains how a droplet can etch graphene. Two factors possibly contribute to this process: a difference between the equilibrium wettability of graphene and the substrate that supports it, or the large surface energy associated with the graphene edge. We calculate the etching velocities due to either of these factors and make testable predictions for evaluating the significance of each in graphene etching. This model is general and can be applied to other materials systems as well. As an example, we show how our model can be used to extend a current theory of droplet motion on binary semiconductor surfaces.
Conotruncal anomaly face syndrome is associated with a deletion within chromosome 22q11. (1993)

The conotruncal anomaly face syndrome was described in a Japanese publication in 1976 and comprises dysmorphic facial appearance and outflow tract defects of the heart. The authors subsequently noted similarities to Shprintzen syndrome and DiGeorge syndrome. Chromosome analysis in five cases did not show a deletion at high resolution, but fluorescent in situ hybridisation using probe DO832 showed a deletion within chromosome 22q11 in all cases.
A new focusing method for nondestructive evaluation by surface acoustic wave (1984)

The focalization of surface acoustic wave on piezoelectric substrates has been largely studied. It is of great interest, in the nondestructive testing area, to use focused surface acoustic waves to monitor defects like cracks which are hardly detected by acoustic bulk waves. In this paper, a new method for nondestructive testing is reported, which uses cylindrically focused surface acoustic beams. This allows for an increase in sensitivity in the detection mode and in spatial resolution in the imaging mode. Using a very simple geometrical model, the resolution and conversion efficiency of the system are estimated.
Wetting of ceramic particulates with liquid aluminum alloys (1987)

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Materials Science and Engineering, 1987.
A minimal solution to the autocalibration of radial distortion (2007)

Epipolar geometry and relative camera pose computation are examples of tasks which can be formulated as minimal problems and solved from a minimal number of image points. Finding the solution leads to solving systems of algebraic equations. Often, these systems are not trivial and therefore special algorithms have to be designed to achieve numerical robustness and computational efficiency. In this paper we provide a solution to the problem of estimating radial distortion and epipolar geometry from eight correspondences in two images. Unlike previous algorithms, which were able to solve the problem from nine correspondences only, we enforce the determinant of the fundamental matrix be zero. This leads to a system of eight quadratic and one cubic equation in nine variables. We simplify this system by eliminating six of these variables. Then, we solve the system by finding eigenvectors of an action matrix of a suitably chosen polynomial. We show how to construct the action matrix without computing complete Grobner basis, which provides an efficient and robust solver. The quality of the solver is demonstrated on synthetic and real data.
Optimal multi-paragraph text segmentation by dynamic programming (1998)

There exist several methods of calculating a similarity curve, or a sequence of similarity values, representing the lexical cohesion of successive text constituents, e.g., paragraphs. Methods for deciding the locations of fragment boundaries are, however, scarce. We propose a fragmentation method based on dynamic programming. The method is theoretically sound and guaranteed to provide an optimal splitting on the basis of a similarity curve, a preferred fragment length, and a cost function defined. The method is especially useful when control on fragment size is of importance.
Bovine Brain Endothelial Cells Express Tight Junctions and Monoamine Oxidase Activity in Long‐Term Culture (1989)

The passage of substances across the blood-brain barrier is regulated by cerebral capillaries which possess certain distinctly different morphological and enzymatic properties compared to capillaries of other organs. Investigations of the functional characteristics of brain capillaries have been facilitated by the use of cultured brain endothelial cells, but in most studies a number of characteristics of the in vivo system are lost. To provide an in vitro system for studies of brain capillary functions, we developed a method of isolating and producing a large number of bovine brain capillary endothelial cells. These cells, absolutely free of pericyte contamination, are subcultured, at the split ratio of 1:20 (20-fold increase of the cultured surface), with no apparent changes in cell morphology up to the fiftieth generation (10 passages). Retention of endothelial-specific characteristics (factor VIII-related antigen, angiotensin-converting enzyme, and nonthrombogenic surface) is shown for brain capillary-derived endothelial cells up to passage 10, even after frozen storage at passage 3. Furthermore, we showed that bovine brain capillary endothelial cells retain, up to the fiftieth generation, some of the characteristics of the blood-brain barrier: occurrence of tight junctions, paucity of pinocytotic vesicles, and monoamine oxidase activity.
Backyard Anthropology and Community-Based Environmental Protection: Lessons from the SFAA Environmental Anthropology Project (2001)

This issue of Practicing Anthropology communicates some lessons emerging from a unique praxis project that attempted to strengthen the meaning and presence of environmental anthropology in U.S. communities. We include articles authored by some of the SfAA Environmental Anthropology Project interns and fellows. David Driscoll's work in South Florida on The Brownfields/Eastward Ho! Project involved developing and testing a participatory approach to environmental risk and brownfields redevelopment planning in an urban neighborhood, and advising public officials on methodologies for profiling and assessing the range of communities affected by brownfields issues. Johnelle Lamarque's internship with Philadelphia residents and property owners involved documenting their awareness of lead hazards and assessing the efficacy of existing lead hazards outreach. Her work demonstrates how cultural values are embedded in outreach materials, suggesting that environmental health information may be communicated in ways that discourage behavioral change. John Stone's fellowship involved demonstrating the utility of Risk Perception Mapping (RPM) to planning staff at the Great Lakes Commission by developing case study data in ways that demonstrated RPM methodology and planning process contributions. Aaron Scrol's fellowship with the Lower Elwha Tribe supported tribal efforts to define and shape political mechanisms that protect the reservation community water system. And, Kreg Ettenger worked with the Haudensaunee Environmental Task Force and the Tuscarora Nation Nations to support efforts to produce culturally relevant information about source water threats and protection needs.
An Anti-HIV-1 V3 Loop Antibody Fully Protects Cross-Clade and Elicits T-Cell Immunity in Macaques Mucosally Challenged with an R5 Clade C SHIV (2011)

Neutralizing antibodies have been shown to protect macaques against SHIV challenge. However, genetically diverse HIV-1 clades have evolved, and a key question left unanswered is whether neutralizing antibodies can confer cross-clade protection in vivo. The novel human monoclonal antibody HGN194 was isolated from an individual infected with an HIV-1 clade AG recombinant circulating recombinant form (CRF). HGN194 targets an epitope in the third hypervariable loop (V3) of HIV-1 gp120 and neutralizes a range of relatively neutralization-sensitive and resistant viruses. We evaluated the potential of HGN194 to protect infant rhesus monkeys against a SHIV encoding a primary CCR5-tropic HIV-1 clade C envelope. After high-dose mucosal challenge, all untreated controls became highly viremic while all HGN194-treated animals (50 mg/kg) were completely protected. When HGN194 was given at 1 mg/kg, one out of two monkeys remained aviremic, whereas the other had delayed, lower peak viremia. Interestingly, all protected monkeys given high-dose HGN194 developed Gag-specific proliferative responses of both CD4+ and CD8+ T cells. To test whether generation of the latter involved cryptic infection, we ablated CD8+ cells after HGN194 clearance. No viremia was detected in any protected monkeys, thus ruling out virus reservoirs. Thus, induction of CD8 T-cell immunity may have resulted from transient "Hit and Run" infection or cross priming via Ag-Ab-mediated cross-presentation. Together, our data identified the HGN194 epitope as protective and provide proof-of-concept that this anti-V3 loop mAb can prevent infection with sterilizing immunity after challenge with virus of a different clade, implying that V3 is a potential vaccine target.
A Global Interactome Map of the Dengue Virus NS1 Identifies Virus Restriction and Dependency Host Factors (2017)

Dengue virus (DENV) infections cause the most prevalent mosquito-borne viral disease worldwide, for which no therapies are available. DENV encodes seven non-structural (NS) proteins that co-assemble and recruit poorly characterized host factors to form the DENV replication complex essential for viral infection. Here, we provide a global proteomic analysis of the human host factors that interact with the DENV NS1 protein. Combined with a functional RNAi screen, this study reveals a comprehensive network of host cellular processes involved in DENV infection and identifies DENV host restriction and dependency factors. We highlight an important role of RACK1 and the chaperonin TRiC (CCT) and oligosaccharyltransferase (OST) complexes during DENV replication. We further show that the OST complex mediates NS1 and NS4B glycosylation, and pharmacological inhibition of its N-glycosylation function strongly impairs DENV infection. In conclusion, our study provides a global interactome of the DENV NS1 and identifies host factors targetable for antiviral therapies.
A Phase II dose ranging, double‐blind, placebo‐controlled study of alicaforsen enema in subjects with acute exacerbation of mild to moderate left‐sided ulcerative colitis (2006)

Alicaforsen enema was safe and well tolerated at all doses studied. The durability of the response to alicaforsen enema treatment may suggests a disease-modifying effect.
Generalized transduction of serotype 1/2 and serotype 4b strains of <i>Listeria monocytogenes</i> (2000)

This is the first report of generalized transduction in the gram-positive, food-borne pathogen Listeria monocytogenes. Bacteriophages were isolated from the environment and from lysogens, or were obtained from other laboratories. Of the 59 bacteriophages tested, 34 proved to be capable of transduction. We exploited the ability of L. monocytogenes to grow at room temperature and isolated bacteriophages that were incapable of growth at 37 degrees C. Transductions at this temperature therefore eliminated transductant killing and lysogeny, as did inclusion of citrate and the use of a low multiplicity of infection. Transducing bacteriophages were found for each of the well-characterized L. monocytogenes strains: EGD, 10403, Mack (serotype1/2a), L028 (serotype 1/2c), Scott A (serotype 4b) and strains from the Jalisco and Halifax, Nova Scotia outbreaks (serotype 4b). P35 (phiLMUP35) is a particularly useful generalized transducing bacteriophage with a wide host range (75% of all serotype 1/2 strains tested). Its disadvantages are that it is small and transduction is relatively infrequent. U153(phiCU-SI153/95) is larger than P35 and transduction frequency increased 100-fold, but it has a very narrow host range. We demonstrated interstrain transduction and used transduction to test linkage between transposon insertions and mutant phenotypes in a variety of strains.
Polyethylene encapsulatin of nitrate salt wastes: Waste form stability, process scale-up, and economics (1991)

A polyethylene encapsulation system for treatment of low-level radioactive, hazardous, and mixed wastes has been developed at Brookhaven National Laboratory. Polyethylene has several advantages compared with conventional solidification/stabilization materials such as hydraulic cements. Waste can be encapsulated with greater efficiency and with better waste form performance than is possible with hydraulic cement. The properties of polyethylene relevant to its long-term durability in storage and disposal environments are reviewed. Response to specific potential failure mechanisms including biodegradation, radiation, chemical attack, flammability, environmental stress cracking, and photodegradation are examined. These data are supported by results from extensive waste form performance testing including compressive yield strength, water immersion, thermal cycling, leachability of radioactive and hazardous species, irradiation, biodegradation, and flammability. The bench-scale process has been successfully tested for application with a number of specific problem'' waste streams. Quality assurance and performance testing of the resulting waste form confirmed scale-up feasibility. Use of this system at Rocky Flats Plant can result in over 70% fewer drums processed and shipped for disposal, compared with optimal cement formulations. Based on the current Rocky Flats production of nitrate salt per year, polyethylene encapsulation can yield an estimated annual savings between $1.5 million and $2.7 million, compared with conventional hydraulic cement systems. 72 refs., 23 figs., 16 tabs.
Ventricular Slices of Adult Mouse Hearts - a new Multicellular In Vitro Model for Electrophysiological Studies (2006)

Adult murine ventricular slices are electrophysiologically intact and respond physiologically to cardioactive drugs. Thus, they provide a new multicellular in vitro model of adult cardiac tissue suitable for electrophysiological investigations, which in future could be used to study the functional integration of stem cells transplanted in infarcted hearts in vivo.
Evidence for human T cell lymphoma-leukemia virus infection of family members of human T cell lymphoma-leukemia virus positive T cell leukemia-lymphoma patients. (1983)

Sera of family members of patients from the United States, the Caribbean, and Japan, with human T cell lymphoma-leukemia virus (HTLV) associated T cell malignancies, possess HTLV-specific antibodies directed against internal structural components of HTLV, p24 and p19. The prevalence of antibodies to HTLV is greater in family members than in random healthy donors, which supports the infectious nature of HTLV and its association with particular aggressive T cell malignancies. Expression of HTLV p24 and p19 has also been observed in cultured T cells of some healthy relatives, and intact virus particles have been released from cells of one possibly pre-leukemic family member.
Design of an anthropomorphic robot head for studying autonomous development and learning (2004)

We describe the design of an anthropomorphic robot head intended as a research platform for studying autonomously learning active vision systems. The robot head closely mimics the major degrees of freedom of the human neck/eye apparatus and allows a number of facial expressions. We show that our robot head can shift its direction of gaze at speeds which come close to that of human saccades. Since our design only makes use of low cost consumer grade components, it paves the way for widespread use of anthropomorphic robot heads in science, education, health-care, and entertainment.
The Apolipoprotein L1 (APOL1) Gene and Nondiabetic Nephropathy in African Americans (2010)

Mapping by admixture linkage disequilibrium (LD) detected strong association between nonmuscle myosin heavy chain 9 gene (MYH9) variants on chromosome 22 and nondiabetic nephropathy in African Americans. MYH9-related variants were posited to be the probable, but not necessarily the definitive, causal variants as a result of impressive statistical evidence of association, renal expression, and a role in autosomal dominant MYH9 disorders characterized by progressive glomerulosclerosis (Epstein and Fechtner syndromes). Dense mapping within MYH9 revealed striking LD patterns and racial variation in risk allele frequencies, suggesting population genetic factors such as selection may be operative in this region. Genovese and colleagues examined large chromosomal regions adjacent to MYH9 using genome-wide association methods and non-HapMap single nucleotide polymorphisms identified in Yoruba from the 1000 Genomes project. Statistically stronger associations were detected between two independent sequence variants in the Apolipoprotein L1 gene (APOL1) and nondiabetic nephropathy in African Americans, with odds ratios of 10.5 in idiopathic FSGS and 7.3 in hypertension-attributed ESRD. These kidney disease risk variants likely rose to high frequency in Africa because they confer resistance to trypanosomal infection and protect from African sleeping sickness. Risk variants in MYH9 and APOL1 are in strong LD, and the genetic risk that was previously attributed to MYH9 may reside, in part or in whole, in APOL1, although more complex models of risk cannot be excluded. This association likely explains racial disparities in nondiabetic nephropathy as a result of the high prevalence of risk alleles in individuals of African ancestry.