gebhart/patrepeval huggingface dataset:
A Common Variant on Chromosome 9p21 Affects the Risk of Myocardial Infarction (2007)

The investigators, recognizing that coronary artery disease (CAD), including acute myocardial infarction (MI), is the leading cause of death worldwide, carried out a genome-wide associational study on Icelandic patients with MI. Initially more than 300,000 single nucleotide polymorphisms (SNPs) were examined for any association with MI. Ultimately, the study enrolled 4587 cases and 12,769 controls. The strongest association with MI was noted with 3 correlated SNPs, all located within a 190-kb linkage disequilibrium block on chromosome 9p21. The association with MI was replicated in case-control sample sets of persons of European descent from 3 US cities. The identified variant was adjacent to the tumor suppressor genes CDKN2A and CDKN2B. It was associated with MI at a high level of significance (P = 1.2 × 10−20). The proteins encoded by these genes have a key role in regulating cell proliferation, cell senescence, and apoptosis—all important features of atherogenesis. Approximately 21% of individuals in the study population are homozygous for the variant, and it is estimated that their risk of having MI is 1.64-fold greater than for noncarriers. The risk is 2.02-fold greater for early-onset cases. The population-attributable risk was estimated as 21% for MI in general and 31% for early-onset cases. This is the first common variant found to consistently confer a substantial risk of MI, defined as an odds ratio exceeding 1.20, in multiple case-control groups of European descent. The variant poses a substantial risk from a public health viewpoint, but it explains only a small part of familial clustering of the disease and would not yield high linkage scores. The implication is that other susceptibility variants are as yet unidentified. In addition to MI, there is reason to believe that the present variant might increase the risk of CAD in general. Just how genetic variants influence the pathogenesis of MI remains to be clarified.
Heart rate-based window segmentation improves accuracy of classifying posttraumatic stress disorder using heart rate variability measures (2017)

These results demonstrate our segmentation approach improves the classification of PTSD from HR and HRV measures, and suggest the potential for tracking PTSD illness severity via objective physiological monitoring. Future studies should prospectively evaluate if classifier output changes significantly with worsening or effective treatment of PTSD.
Magnetic Nanobeads as Potential Contrast Agents for Magnetic Resonance Imaging (2013)

Metal-oxo clusters have been used as building blocks to form hybrid nanomaterials and evaluated as potential MRI contrast agents. We have synthesized a biocompatible copolymer based on a water stable, nontoxic, mixed-metal-oxo cluster, Mn8Fe4O12(L)16(H2O)4, where L is acetate or vinyl benzoic acid, and styrene. The cluster alone was screened by NMR for relaxivity and was found to be a promising T2 contrast agent, with r1 = 2.3 mM(-1) s(-1) and r2 = 29.5 mM(-1) s(-1). Initial cell studies on two human prostate cancer cell lines, DU-145 and LNCap, reveal that the cluster has low cytotoxicity and may be potentially used in vivo. The metal-oxo cluster Mn8Fe4(VBA)16 (VBA = vinyl benzoic acid) can be copolymerized with styrene under miniemulsion conditions. Miniemulsion allows for the formation of nanometer-sized paramagnetic beads (~80 nm diameter), which were also evaluated as a contrast agent for MRI. These highly monodispersed, hybrid nanoparticles have enhanced properties, with the option for surface functionalization, making them a promising tool for biomedicine. Interestingly, both relaxivity measurements and MRI studies show that embedding the Mn8Fe4 core within a polymer matrix decreases r2 effects with little effect on r1, resulting in a positive T1 contrast enhancement.
Tracking fish motion and behavior with acoustic flow (2006)

Fish populations in the New Jersey continental shelf have been continuously monitored over thousands of square kilometers using acoustic waveguide remote sensing techniques [Makris et al., ‘‘Fish population and behavior revealed by instantaneous continental-shelf-scale imaging,’’ Science 311, 660–663 (2006)]. Here, we explore the approaches for tracking both large shoals and smaller isolated fish groups over space and time from images of fish population density. One method uses density thresholds to segment coherent population centers and track their centroids. These data are then used to compute differential velocities between population centers and to determine the rate at which information may be transmitted across a population center. We also examine the possibility of applying optical flow concepts from machine vision [Horn, B. Robot Vision, MIT Press, 1986], as a global approach for estimating fish velocity at every pixel in the fish density image. The analogous acoustic flow is computed based on changes in acoustic intensity over space and time. Acoustic flow automatically tracks fish motion within a school or shoal and migration across fish bridges connecting shoals segments. We also investigate the possibility of using acoustic flow for navigating the ocean environment and correcting for errors in charting acoustic returns, for instance caused by array-heading sensor.
RDO cost modeling for low-complexity HEVC intra coding (2016)

High efficiency video coding (HEVC) is the newest international standard for video compression, providing improved coding performance that achieves compression ratios up to 50% higher than those obtained with H.264/AVC. However, this improvement comes at the expense of high computational complexity and coding time. In this paper, we propose a novel method for fast and low-complexity intra HEVC mode decision based on rate-distortion optimization (RDO) cost modeling, which permits the exclusion of non-promising candidates from the RDO processing. To achieve even more complexity reduction, an additional rough most probable modes examination is coupled with the main algorithm. Experimental results show that the proposed algorithms reduce the encoding time by 41.8% on average, with a negligible quality loss of 0.058 dB (BD-PSNR) for all-intra scenarios, as compared to the HEVC reference implementation, the HM 15.0.
Rapid measurement of single-molecule conductance (2008)

A new device for measuring the conductance values of single-molecule junctions which are covalently bound to two electrodes is presented. The system works by repeatedly bringing two electrodes into and out of contact in a solution of molecules while measuring the current between the two electrodes during withdrawal. When molecules connect the two electrodes, steps occur in the current transient, and a statistical analysis provides the most probable conductance value for a single-molecule junction. This system provides an order of magnitude increase in speed over previous devices used for single-molecule conductance measurements, and the applicability of this tool is demonstrated in array based measurements as well as in biologically relevant samples where the conductances of single amino acid residues are measured.
A new imaging science phantom for performance evaluation of ultrasonic imaging systems (2002)

We have developed a phantom manufactured with thin film techniques that enables precise placement of sub-resolvable "digital scatterers" on an acoustically transparent supporting medium within the scan plane of an ultrasound system. This technique permits formation of sophisticated test targets commonly used in imaging science. These phantoms can reveal the combined influence of all the stages in the imaging chain, as well as demonstrate imaging phenomenon that are difficult or not feasible to evaluate with conventional ultrasound phantoms. Use of half-tone mask techniques permit the specification of placement, pattern and statistical distribution of these "digital scatterers" necessary to produce images with definable gray scale characteristics. We have also been able to produce controlled stimulus sources for Doppler and color flow Doppler evaluation.
Highly Potent and Subtype Selective Ligands Derived by<i>N</i>-Methyl Scan of a Somatostatin Antagonist (2001)

The search for synthetic peptide analogues of somatostatin (SRIF) which exhibit selective affinities for the five known receptor subtypes (sst1-5) has generated a large number of potent agonists. Some of these agonists display good subtype selectivities and affinities for the subtypes 1, 2, 3, and 5, including analogues created by N-methyl amino acid substitutions in a standard octapeptide analogue format. We have now extended this peptide backbone N-methylation approach to a potent somatostatin receptor antagonist series using the antagonist Cpa-cyclo(DCys-Pal-DTrp-Lys-Thr-Cys)-Nal-NH2 9 reported from this laboratory as the lead structure. Synthetic analogues were tested for their ability to inhibit somatostatin-stimulated GH release from rat pituitary cells in culture and to displace 125I-labeled somatostatin from CHO cells transfected with the five known human somatostatin receptors. Several interesting observations resulted from the study. N-Methylation at the Lys(9) residue (5) increased the rat GH release inhibitory potency nearly 4-fold to 0.73 nM but resulted in little change in the binding affinity for human type 2 receptor. This analogue also had a high affinity of 5.98 nM for sst5 receptor (compared to 1.4 nM for somatostatin itself) and is the first antagonist analogue to be reported with high affinity for sst5. It also had high potency on in vitro inhibition of sst5 mediated intracellular calcium mobilization. These results were considered surprising, since the Lys(9) residue has long been considered to constitute the active center of somatostatin, important both for receptor binding and activation, and suggests important conformational differences between D-Cys(9) somatostatin antagonists and normal agonist structures. More modifications were carried out on this analogue with the aim of improving antagonist potency and/or specificity. Tyr(7) substitution of 5 resulted in an analogue, which had the highest affinity in the series for hsst2 (K(I) 5.51 nM) and an extraordinarily low IC50 of 0.53 nM in the rat pituitary cell assay. However, this analogue lost considerable affinity for sst5 relative to analogue 5. Analogue 16 with DTrp(12) at C-terminus had the highest affinity for hsst2, however, the IC50 in the rat GH release assay was only 11.6 nM. Replacement of Lys(9) in 9 with Dab(9) gave 11 which displayed high binding affinity for sst3, and it was also quite selective for that receptor. Both the sst3 and sst5 antagonists should be of value in assigning the physiological roles to type 3 and 5 receptor, respectively.
A Fault Location Algorithm for Two-End Series-Compensated Double-Circuit Transmission Lines Using the Distributed Parameter Line Model (2017)

A new fault location algorithm for two-end series-compensated double-circuit transmission lines utilizing unsynchronized two-terminal current phasors and local voltage phasors is presented in this paper. The distributed parameter line model is adopted to take into account the shunt capacitance of the lines. The mutual coupling between the parallel lines in the zero-sequence network is also considered. The boundary conditions under different fault types are used to derive the fault location formulation. The developed algorithm directly uses the local voltage phasors on the line side of series compensation (SC) and metal oxide varistor (MOV). However, when potential transformers are not installed on the line side of SC and MOVs for the local terminal, these measurements can be calculated from the local terminal bus voltage and currents by estimating the voltages across the SC and MOVs. MATLAB SimPowerSystems is used to generate cases under diverse fault conditions to evaluating accuracy. The simulation results show that the proposed algorithm is qualified for practical implementation.
Macrophage stimulating protein: purification, partial amino acid sequence, and cellular activity. (1991)

Macrophage stimulating protein (MSP) was purified to homogeneity from human blood plasma by selection of biologically active fractions obtained by sequential immunoaffinity and high pressure liquid ion exchange chromatography. By sodium dodecyl sulfate-polyacrylamide gel electrophoresis the molecular mass of MSP was 70 kilodaltons (kD); under reducing conditions two gel bands were seen, at 47 and 22 kD. The disulfide-linked two-chain structure of MSP was confirmed by separation of reduced and alkylated MSP chains. A computer search comparison of six partial sequences of MSP digests showed that MSP has not been recorded in data banks of protein sequences. Two MSP fragments had greater than 80% identity in overlaps of 12-16 residues to sequences in the protein family that includes human prothrombin, plasminogen, and hepatocyte growth factor. The concentration of purified MSP required for half-maximal biological activity was the order of 10(-10) M. In addition to making mouse resident peritoneal macrophages responses to chemoattractants, MSP caused the appearance of long cytoplasmic processes and pinocytic vesicles in freshly plated macrophages. MSP also caused phagocytosis via the C3b receptor, CR1. Whereas resident peritoneal macrophages bind but do not ingest sheep erythrocytes opsonized with IgM anti-Forssman antibody and mouse C3b, addition of MSP caused ingestion. Thus, MSP causes direct or indirect activation of two receptors of the mouse resident peritoneal macrophage, CR1 and the C5a receptor.
Macroscopic Kelvin Probe for contactless corrosion assessment of structures buried in soil (2016)

A pioneering application of a Kelvin Probe (KP) sensor for surface potential mapping of soil and cementitious soil fill to assess corrosion of embedded steel reinforcement is presented. The KP potential measurements were rapid, stable and adequately reproducible, for constructing surface maps to serve for corrosion assessments without any disturbance of the surface. Results are promising for mobile deployment. The KP successfully operated under dynamic conditions representative of a cathodic protection installation, showing capability for electrochemical diagnostic operations. Operation of a dual sensor array was demonstrated as well.
Structured outlier models for robust dictionary learning (2015)

Robust dictionary learning algorithms seek to learn a dictionary while being robust to the presence of outliers in the training set. Often, the elements of the training set have an underlying structure due to, for example, their spatial relation or their similarity. When outliers are present as elements of the training set, they often inherit the underlying structure of the training set. This work capitalizes on such structure, encoded as an undirected graph connecting elements of the training set, and on sparsity-aware outlier modeling tools to develop robust dictionary learning algorithms. Not only do these algorithms yield a robust dictionary, but they also identify the outliers in the training set. Computationally efficient algorithms based on block coordinate descent and proximal gradient methods are developed.
Cellular signaling and gene expression profiles evoked by a bivalent macrocyclic peptide that serves as an artificial MET receptor agonist (2018)

Non-native ligands for growth factor receptors that are generated by chemical synthesis are applicable to therapeutics. However, non-native ligands often regulate cellular signaling and biological responses in a different manner than native ligands. Generation of surrogate ligands comparable to native ligands is a challenging need. Here we investigated changes in signal transduction and gene expression evoked by a bivalent macrocyclic peptide (aMD5-PEG11) capable of high-affinity binding to the MET/hepatocyte growth factor (HGF) receptor. Binding of aMD5-PEG11 to the MET extracellular region was abolished by deletion of the IPT3-IPT4 domain, indicating the involvement of IPT3-IPT4 in the binding of aMD5-PEG11 to the MET receptor. aMD5-PEG11 induced dimerization and activation of the MET receptor and promoted cell migration that was comparable to induction of these activities by HGF. Signal activation profiles indicated that aMD5-PEG11 induced phosphorylation of intracellular signaling molecules, with a similar intensity and time dependency as HGF. In 3-D culture, aMD5-PEG11 as well as HGF induced epithelial tubulogenesis and up-regulated the same sets of functionally classified genes involved in multicellular organism development. Thus, a non-native surrogate ligand that consisted of a bivalent macrocyclic peptide can serve as an artificial MET receptor agonist that functionally substitutes for the native ligand, HGF.
Guiding of optical laser pulses in fast capillary discharge plasma columns (2003)

We report the generation and characterization of plasma waveguides in a highly ionized Ar plasma created by a fast capillary discharge. Their results are of interest for the efficient longitudinal laser excitation of collisional soft x-ray lasers. A discharge-driven hydrodynamic compression guides progressively lower order modes through a plasma with increasing density and degree of ionization. The mode structure and guiding properties were investigated using near and far field imaging, and transmission measurements. The lowest order mode (FWHM diameter ~ 50 um) is guided with an energy transmission of ~ 75% over a 5.5 cm long plasma a fraction of a ns before the discharge plasma column reaches the conditions for lasing in Ne-like Ar. The rapid expansion of the highly ionized plasma column after the pinch forms a significantly more leaky and absorbent waveguide.
Cell Balancing Scheme with Series Coupling of Multiple Primary Windings for Hybrid Electric Vehicle Lithium-Ion Battery Cells (2007)

Charge equalization scheme for HEV lithium-ion battery system is proposed in this paper, where all the primary windings with in parallel bi-directional switches are coupled in series to provide the equalizing energy from the whole battery string to the specific under charged cells. Moreover, to realize minimized size of equalization circuit employing the proposed cell balancing scheme, the optimal power rating design rule according to equalization time and SOC distribution of imbalance is proposed. A prototype of HEV lithium-ion battery system of four cells shows the outstanding charge equalization performance while maintaining greatly reduced size of cell balancing circuit.
Scheduling of Single-Arm Cluster Tools for an Atomic Layer Deposition Process With Residency Time Constraints (2016)

In semiconductor manufacturing, there are wafer fabrication processes with wafer revisiting. Some of them must meet wafer residency time constraints. Taking atomic layer deposition (ALD) as a typical wafer revisiting process, this paper studies the challenging scheduling problem of single-arm cluster tools for the ALD process with wafer residency time constraints. It is found that there are only several scheduling strategies that are applicable to this problem and one needs to apply each of them to decide whether a feasible schedule can be found or not. This work, for each applicable strategy, performs the schedulability analysis and derives the schedulability conditions for such tools for the first time. It proposes scheduling algorithms to obtain an optimal schedule efficiently if such conditions are met. It finally gives illustrative examples to show the application of the proposed concepts and approach.
A Genomic Algorithm for the Molecular Classification of Common Renal Cortical Neoplasms: Development and Validation (2014)

In a clinical diagnostic setting the implementation of genome based molecular classification could serve as an ancillary assay to assist in the histological classification of common renal neoplasms.
Scintillator manufacture at Fermilab (1998)

A decade of research into plastic scintillation materials at Fermilab is reviewed. Early work with plastic optical fiber fabrication is revisited and recent experiments with large-scale commercial methods for production of bulk scintillator are discussed. Costs for various forms of scintillator are examined and new development goals including cost reduction methods and quality improvement techniques are suggested.
Using Light Backscatter at 980 nm to Determine Curd Moisture Content at Various Milk Fat and Gel Firmness Levels in Cheese-making (2008)

Curd moisture control plays a fundamental role in determining the quality of the final cheese. A large field of view (LFV) light backscatter sensor at 980 nm was used as a rapid on-line method for monitoring curd moisture content changes during syneresis. Improving the control of curd moisture content during the cheese-making process may enhance product consistency and reduce the overall production cost. The objective of this study was to evaluate the influence of two experimental variables (i.e. fat and gel firmness at cutting) using light backscatter at 980 nm on syneresis and curd moisture content prediction. An experiment was conducted in which whole milk was recombined at three fat levels, clotted under constant conditions and the milk gel was cut at three gel firmness levels. The curd-whey mixture was stirred in the vat after gel cutting and the syneresis process was monitored using the LFV sensor which was installed in the cheese vat wall.
Surgical navigation using audio feedback. (1997)

Current medical visualization technology intended for positional guidance in surgical applications may only ever have limited utility in the operating room due to the preexisting visual requirements of surgical practice. Additionally, visual systems impose limits as a result of their high latency, poor image resolution, problems with stereopsis and physical strain upon the user. Audio technology is relatively unexamined in the broad range of available methodologies for medical devices. The potential to translate surgical instrument position into audio feedback presents a novel solution to the human factors and engineering problems faced by visual display technology because audio technology employs a rich and as yet unburdened sensory modality. We describe an experimental system we have developed for investigating this new interface design approach using commercially available hardware.