gebhart/patrepeval huggingface dataset:
Correlation Plenoptic Imaging (2016)

Plenoptic imaging is a promising optical modality that simultaneously captures the location and the propagation direction of light in order to enable three-dimensional imaging in a single shot. However, in standard plenoptic imaging systems, the maximum spatial and angular resolutions are fundamentally linked; thereby, the maximum achievable depth of field is inversely proportional to the spatial resolution. We propose to take advantage of the second-order correlation properties of light to overcome this fundamental limitation. In this Letter, we demonstrate that the correlation in both momentum and position of chaotic light leads to the enhanced refocusing power of correlation plenoptic imaging with respect to standard plenoptic imaging.
Fast and robust deblending using Apex Shifted Radon transform (2012)

We present a technique for deblending seismic data acquired with simultaneous shots. We propose the apex shifted Radon transform (ASRT) method to collapse energy from different shots to their apexes or shot locations. The technique is more suited for streamer acquisition, although other uses are possible. The ASRT is implemented via a Stolt migration operator with a high resolution least squares algorithm. The transform collapses all events to their apexes independently of their geometry (offset and azimuth) and does not require the knowledge of shot locations or velocities. It is as fast as a 2D Radon transform and therefore can be applied during acquisition as a preliminary QC.
Minimally Invasive Implantation of a Micropacemaker Into the Pericardial Space (2018)

A novel micropacemaker system allows cardiac pacing without entering the vascular space or surgical exposure of the heart. This pericardial pacemaker system may be an option for a large number of patients currently requiring transvenous pacemakers but is particularly relevant for patients with restricted vascular access, young children, or those with congenital heart disease who require epicardial access.
Use of <i>Bmp1</i>/<i>Tll1</i> Doubly Homozygous Null Mice and Proteomics To Identify and Validate In Vivo Substrates of Bone Morphogenetic Protein 1/Tolloid-Like Metalloproteinases (2003)

Bone morphogenetic protein 1 (BMP-1) and mammalian Tolloid (mTLD), two proteinases encoded by Bmp1, provide procollagen C-proteinase (pCP) activity that converts procollagens I to III into the major fibrous components of mammalian extracellular matrix (ECM). Yet, although Bmp1(-/-) mice have aberrant collagen fibrils, they have residual pCP activity, indicative of genetic redundancy. Mammals possess two additional proteinases structurally similar to BMP-1 and mTLD: the genetically distinct mammalian Tolloid-like 1 (mTLL-1) and mTLL-2. Mice lacking the mTLL-1 gene Tll1 are embryonic lethal but have pCP activity levels similar to those of the wild type, suggesting that mTLL-1 might not be an in vivo pCP. In vitro studies have shown BMP-1 and mTLL-1 capable of cleaving Chordin, an extracellular antagonist of BMP signaling, suggesting that these proteases might also serve to modulate BMP signaling and to coordinate the latter with ECM formation. However, in vivo evidence of roles for BMP-1 and mTLL-1 in BMP signaling in mammals is lacking. To remove functional redundancy obscuring the in vivo functions of BMP-1-related proteases in mammals, we here characterize Bmp1 Tll1 doubly null mouse embryos. Although these appear morphologically indistinguishable from Tll1(-/-) embryos, biochemical analysis of cells derived from doubly null embryos shows functional redundancy removed to an extent enabling us to demonstrate that (i) products of Bmp1 and Tll1 are responsible for in vivo cleavage of Chordin in mammals and (ii) mTLL-1 is an in vivo pCP that provides residual activity observed in Bmp1(-/-) embryos. Removal of functional redundancy also enabled use of Bmp1(-/-) Tll1(-/-) cells in a proteomics approach for identifying novel substrates of Bmp1 and Tll1 products.
The <i>ica</i> Locus of <i>Staphylococcus epidermidis</i> Encodes Production of the Capsular Polysaccharide/Adhesin (1998)

Clinical isolates of coagulase-negative staphylococci often elaborate a biofilm involved in adherence to medical devices and resistance to host defenses. The biofilm contains the capsular polysaccharide/adhesin (PS/A), which mediates cell adherence to biomaterials, and another antigen, termed polysaccharide intercellular adhesin (PIA), which is thought to mediate bacterial accumulation into cellular aggregates. PIA is a polymer of beta-1, 6-linked N-acetyl glucosamine residues with a molecular mass of <30, 000 kDa. We found that recombinant Staphylococcus carnosus and Staphylococcus aureus carrying a plasmid with genes of the ica locus, which was reported to encode the biosynthetic proteins for production of PIA, were also able to synthesize PS/A. PS/A and a chemically and immunologically identical polysaccharide isolated from S. carnosus carrying the ica genes on plasmid pCN27 were found to be high-molecular-mass (>250,000 kDa), acid-stable polymers of beta-1,6-linked glucosamine substituted on the amino group primarily with succinate, although some preparations also contained acetate. Moreover, all recombinant staphylococcal strains with the ica genes had the biologic properties previously attributed to PS/A. ica-positive strains readily formed an in vitro biofilm on plastic, adhered 3- to 10-fold more to catheters during a 30-min assay compared with control strains carrying only the cloning vector, adsorbed out antibodies to PS/A from immune serum, and elaborated a capsule visualized by immunoelectron microscopy with antisera to PS/A. These properties were also seen with PS/A-producing strains of Staphylococcus epidermidis, but not with transposon mutants lacking PS/A. An antiserum raised to PIA contained high-titer antibody to PS/A that was readily adsorbed out by PS/A-positive strains of S. epidermidis and recombinant strains of staphylococci carrying the ica genes. We conclude that the ica locus encodes production of PS/A and that the properties of S. epidermidis associated with initial bacterial adherence, biofilm formation, and intercellular adhesion can be correlated with elaboration of PS/A.
Advanced Cutting Structure Improves PDC Bit Performance in Hard and Abrasive Drilling Environments (2003)

Abstract The performances of PDC bits in hard formations, especially when these formations are also abrasive, still lack effectiveness and consistency. In such applications, the industry has usually resorted to the use of "insert type" roller cone (RC) and impregnated diamond bits (ID) – due primarily to their performance consistencies. Impregnated bits, usually, exhibit the durability characteristics needed to drill long footages in hard and abrasive formations. However, due to their grinding rock removal action, penetration rates (ROP) are typically low, commonly in the (3 – 9 fph) range. These low ROPs experience rapid deteriorations, once argillaceous and/or shale bearing formations are encountered. These conditions reduce the operational efficiency of impregnated bits, driving up drilling costs. From an ROP perspective, roller cone bits perform better (6 – 12 fph) than impregnated bits in hard and abrasive formations. In addition, the ROPs of RC bits experience minimal decay in argillaceous and/or shale bearing formations. However RC bits are commonly tripped on hours and, do not exhibit the longevity needed for hard and abrasive environments. Considering the depths at which such hard and abrasive formations are usually encountered, trips increase operational hours, HSE risk and thus substantially add to drilling cost. Due to their depositional depths, hard and abrasive formations are sometimes encountered in HP/HT environments. This condition often necessitates the use of high mud weights, or BHA's that incorporate high speed drive mechanisms - PDMs or turbo-drills. Such conditions, necessary to improve operational efficiency, further complicate the drilling environment - affecting the ROP and/or durability of all drill bits. This paper discusses an innovative PDC bit, which has specifically been developed to improve operational efficiency in hard and abrasive formations. This new generation PDC bit effectively addresses the ROP limitations of impregnated bits, as well as the footage deficiencies of roller cone bits. In addition, these bits have been developed to be effective, even when hard abrasive formations are drilled with high mud weights and/or with high speed drive mechanisms.
High-spatial-resolution neutron image detector based on wavelength-shifting fiber read out for time-of-flight measurements (2009)

A wavelength-shifting-fiber based neutron image detector with a spatial resolution of less 200 ¿m was developed. The detector had a capability of neutron imaging with a temporal resolution of several ¿s. The detector equipped with a ZnS/ <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">6</sup> LiF scintillator where the scintillation light was read out with individual fibers based on a photon counting method. The fiber-optic tapers (FOTs) were implemented in between the scintillator and the fibers to magnify a neutron image. The prototype detector that equipped with the FOTs exhibited the spatial resolution that was improved by an order better compared that with the original detector. This kind of detector would be a unique and powerful tool for the energy-selective neutron radiography at a pulsed neutron source.
Effect of amino acid substitutions in conserved residues in the leader peptide on biosynthesis of the lantibiotic mutacin II (2001)

The lantibiotic mutacin II, produced by Streptococcus mutans T8, is a ribosomally synthesized peptide antibiotic that contains thioether amino acids such as lanthionine and methyllanthionine as a result of post-translational modifications. The mutacin II leader peptide sequence shares a number of identical amino acid residues with class AII lantibiotic leader peptides. To study the role of these conservative residues in the production of active antimicrobial mutacin, 15 mutations were generated by site-directed mutagenesis. The effects of these substitutions vary from no effect to complete block-out. Mutations G-1A, G-2A, I-4D, and L-7K completely blocked the production of mature mutacin. Other mutations (I-4V, L-7M, E-8D, S-11T/A, V-12I/A, and E-13D) had no detectable effect on mutacin production. The changes of Glu-8 to Lys, Val-12 to Leu, Glu-13 to Lys reduced the mutacin production level to about 75%, 50%, and 10% of the wild-type, respectively. Thus, our data indicated that some of these conserved residues are essential for the mutacin biosynthesis, whereas others are important for optimal biosynthesis rates.
Proteolytic inactivation of human factor VIII procoagulant protein by activated human protein C and its analogy with factor V (1984)

Abstract Purified human factor VIII procoagulant protein (VIII:C) was treated with purified human activated protein C (APC) and the loss of VIII:C activity correlated with proteolysis of the VIII:C polypeptides. APC proteolyzed all VIII:C polypeptides with mol wt = 92,000 or greater, but not the doublet at mol wt = 79–80,000. These results and our previous thrombin activation studies of purified VIII:C, are analogous with similar studies of factor V and form the basis for the following hypothesis: activated VIII:C consists of heavy and light chain polypeptides [mol wt = 92,000 and mol wt = 79–80,000 (or 71–72,000), respectively] which are similar in Mr to the heavy and light chains of activated factor V. Thrombin activates VIII:C and V by generating these polypeptide chains from larger precursors and APC inactivates both molecules by cleavage at a site located in the heavy chain region of activated VIII:C and V.
Synthesis and Structure–Activity Relationship (SAR) of 2-Methyl-4-oxo-3-oxetanylcarbamic Acid Esters, a Class of Potent <i>N</i>-Acylethanolamine Acid Amidase (NAAA) Inhibitors (2013)

N-Acylethanolamine acid amidase (NAAA) is a lysosomal cysteine hydrolase involved in the degradation of saturated and monounsaturated fatty acid ethanolamides (FAEs), a family of endogenous lipid agonists of peroxisome proliferator-activated receptor-α, which include oleoylethanolamide (OEA) and palmitoylethanolamide (PEA). The β-lactone derivatives (S)-N-(2-oxo-3-oxetanyl)-3-phenylpropionamide (2) and (S)-N-(2-oxo-3-oxetanyl)-biphenyl-4-carboxamide (3) inhibit NAAA, prevent FAE hydrolysis in activated inflammatory cells, and reduce tissue reactions to pro-inflammatory stimuli. Recently, our group disclosed ARN077 (4), a potent NAAA inhibitor that is active in vivo by topical administration in rodent models of hyperalgesia and allodynia. In the present study, we investigated the structure-activity relationship (SAR) of threonine-derived β-lactone analogues of compound 4. The main results of this work were an enhancement of the inhibitory potency of β-lactone carbamate derivatives for NAAA and the identification of (4-phenylphenyl)-methyl-N-[(2S,3R)-2-methyl-4-oxo-oxetan-3-yl]carbamate (14q) as the first single-digit nanomolar inhibitor of intracellular NAAA activity (IC50 = 7 nM on both rat NAAA and human NAAA).
A 4-element dual wideband circular Yagi MIMO antenna system with loop excitation (2016)

A 4-element dual-band Circular Yagi based multiple-input-multiple-output (MIMO) antenna system with loop excitation is presented. It has a very wide-bandwidth of 1 GHz in both bands. The lower band covers from 1.45-2.55 GHz while the upper band covers from 3.707-4.71 GHz. This antenna is highly directional with front-to-back ratio (FBR) of 13.8 dB, gain of 6.6 dB and directivity of 7 dB. The proposed antenna shows good MIMO performance in terms of isolation and correlation. It has a minimum isolation of 23 dB across both bands. Due to its geometry configuration, the radiation patterns are orthogonal to each other and hence it has very low correlation coefficient values not exceeding than 0.1338. The size of the single antenna is 78 × 117.5 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> while overall size is 263 × 263 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> .
New Attachment Formation Following Controlled Tissue Regeneration Using Biodegradable Membranes (1988)

The present study evaluated the potential for reestablishment of connective tissue attachment after exclusion of the gingival connective tissue and epithelium during healing after periodontal surgery in a dog model. Buccal mucoperiosteal flaps were elevated in all four premolar regions in two dogs. The buccal bone was reduced to approximately 25% of its original level on 24 roots. Before the elevated flaps were replaced and sutured, membranes were adjusted to cover the exposed root surfaces. On eight surfaces Millipore filters were used and on eight surfaces biodegradable polylactic acid membranes were used. No membranes were placed over the remaining eight root surfaces which served as controls. After two months of healing, the animals were sacrificed and all the roots were subjected to histological analysis. In all of the roots covered with the polylactic acid membrane, newly formed cementum with inserting collagen fibers was observed and covered on the average 46% of the initial defect. Newly formed bone covered 39% of the initial defect. The roots covered by Millipore filters were characterized by significantly less new attachment and bone. In the control roots only minor new attachment was found in the bottom of the defect in some roots. The results suggest that the establishment of a connective tissue attachment is clearly favored by the placement of a polylactic acid membrane to exclude the epithelium and gingival connective tissue during healing.
Indirect-HMM-based hypothesis alignment for combining outputs from machine translation systems (2008)

This paper presents a new hypothesis alignment method for combining outputs of multiple machine translation (MT) systems. An indirect hidden Markov model (IHMM) is proposed to address the synonym matching and word ordering issues in hypothesis alignment. Unlike traditional HMMs whose parameters are trained via maximum likelihood estimation (MLE), the parameters of the IHMM are estimated indirectly from a variety of sources including word semantic similarity, word surface similarity, and a distance-based distortion penalty. The IHMM-based method significantly outperforms the state-of-the-art TER-based alignment model in our experiments on NIST benchmark datasets. Our combined SMT system using the proposed method achieved the best Chinese-to-English translation result in the constrained training track of the 2008 NIST Open MT Evaluation.
Serum chromogranin A: Early detection of hormonal resistance in prostate cancer patients (1998)

We monitored both chromogranin A (CgA) and neuron specific enolase (NSE) in serial serum specimens from 14 patients with prostate cancer (CAP patients) showing resistance to hormonal treatment. Elevated serum CgA was detected in 10 out of these 14 patients (71%) during treatment, and an early appearance of elevated serum CgA was found in 6 of 14 (43%) of these patients when serum tPSA levels were still in the normal range. If patients with radical prostatectomy were not included, the percentage of patients showing an early appearance of elevated serum CgA would have been much higher. Elevated serum CgA levels also were found in patients not subject to hormonal therapy. Serial specimens from two out of three prostate cancer patients, randomly selected, contained elevated serum CgA. Serum NSE was not detectable in any of the serial specimens we studied, suggesting that CgA, not NSE, should be used as a marker for neuroendocrine differentiation. We also compared the serum CgA in random serum specimens between patients with BPH (benign prostate hyperplasia) and with prostate cancer in the concentration range of serum tPSA between 3-15 ng/mL. Although serum CgA concentrations in BPH patients overlapped considerably with those levels in patients with prostate cancer, levels > 100 ng/mL should suggest prostate cancer. The early appearance of elevated serum CgA allows an early change of therapy to be made and can lead to the effective prevention of any further development of metastases.
Design and Evaluation of Artifact-Resistant Finger-Ring Plethysmographic Sensors (2000)

Abstract A miniaturized, telemetric, photoplethysmograph sensor for long-term, continuous monitoring is presented in this paper. The sensor, called a “ring sensor”, is attached to a finger base for monitoring beat-to-beat pulsation, and the data is sent to a host computer via a RF transmitter. An efficient double ring design is developed to lower the influence of external force, acceleration, and ambient light, and to hold the sensor gently and securely on the skin, so that the circulation at the finger may not be obstructed. A prototype ring sensor is designed and built based on the artifact-resistive attachment method. It is verified through experiments that the ring sensor is resistant to interfering forces and acceleration acting on the ring body. Benchmarking tests with FDA-approved photoplethysmograph and EKG reveal that the ring sensor is comparable to those devices in detecting beat-to-beat pulsation despite disturbances.
C. elegans development (1995)

SUMMARY During the development of the C. elegans hermaphrodite, 131 of the 1090 cells generated undergo programmed cell death. Genetic studies have identified mutations in 14 genes that specifically affect this process. These genes define a genetic pathway for programmed cell death in C. elegans. Two genes, ced-3 and ced-4, are required for cells to undergo programmed cell death, while a third gene, ced-9, protects cells that should live from undergoing programmed cell death. The proteins encoded by ced-3 and ced-9 show significant similarity to proteins that affect programmed cell death in vertebrates, suggesting that the molecular cell death pathway in which ced-3, ced-4, and ced-9 act has been conserved between nematodes and vertebrates. 1. THE SETTING The small nematode Caenorhabditis elegans has been widely used over the past two decades to study fundamental problems in developmental biology (Wood 1988). The two characteristics that have contributed most to the widespread use of this organism are its powerful genetics (Brenner 1974) and the simplicity and reproducibility of its develop­ ment. For example, the pattern of cell divisions generating an adult worm from the one-celled zygote is essentially invariant from one animal to the next (Sulston & Horvitz 1977; Kimble & Hirsh 1979; Sulston et al. 1983). During C. elegans development, a number of cells are eliminated, generally shortly after their genera­ tion, by undergoing programmed cell death. The number of cell deaths is high: in hermaphrodites, 131 of the 1090 cells generated die, while in males 147 of the 1178 cells generated die. Like the rest of C. elegans development, these deaths are highly reproducible: the same number of cells die in all individuals, and the time during development at which a given cell dies is constant. Programmed cell death in C. elegans can thus be studied with single-cell resolution.
Leuprolide acetate treatment of adrenocortical disease in ferrets (2001)

Results suggest that leuprolide can be safely used to temporarily eliminate clinical signs and reduce sex hormone concentrations in ferrets with adrenocortical diseases. However, the safety of long-term leuprolide use in ferrets has not been investigated, and the long-term effects of leuprolide in ferrets with nodular adrenal gland hyperplasia or adrenal gland tumors are unknown.
Novel High-Molecular-Weight, R-Type Bacteriocins of Clostridium difficile (2012)

Clostridium difficile causes one of the leading nosocomial infections in developed countries, and therapeutic choices are limited. Some strains of C. difficile produce phage tail-like particles upon induction of the SOS response. These particles have bactericidal activity against other C. difficile strains and can therefore be classified as bacteriocins, similar to the R-type pyocins of Pseudomonas aeruginosa. These R-type bacteriocin particles, which have been purified from different strains, each have a different C. difficile-killing spectrum, with no one bacteriocin killing all C. difficile isolates tested. We have identified the genetic locus of these "diffocins" (open reading frames 1359 to 1376) and have found them to be common among the species. The entire diffocin genetic locus of more than 20 kb was cloned and expressed in Bacillus subtilis, and this resulted in production of bactericidal particles. One of the interesting features of these particles is a very large structural protein of ~200 kDa, the product of gene 1374. This large protein determines the killing spectrum of the particles and is likely the receptor-binding protein. Diffocins may provide an alternate bactericidal agent to prevent or treat infections and to decolonize individuals who are asymptomatic carriers.