gebhart/patrepeval huggingface dataset:
Overexpression of JAK2 mRNA in Chronic Myeloproliferative Disease and Its Implication on Mutation Testing and Biology of Disease. (2007)

Abstract The V617F point mutation in the JAK2 gene is considered the most important molecular abnormality that characterizes patients with non-chronic myeloid leukemia (CML)-myeloproliferative disease (MPD). While it is well-documented that the V617F mutation leads to continuous activation of the JAK2-STAT5 pathway, the levels of JAK2 mRNA expression is not well defined in myeloproliferative diseases. We quantified the levels total JAK2 mRNA as well as V617F mutant mRNA in the plasma of patients with non-CML MPD using RT/PCR, and compared the results with clinical findings and disease behavior. Patients with non-CML MPD (n = 175) had significantly higher levels (P &lt;0.0001) of JAK2 mRNA (median, 1843 pg/ul) than patients with CML (median, 71.53 pg/ul) and normal controls (median, 34.34 pg/ul). In contrast, there was no significant difference (P = 0.15) in DNA levels (copies of JAK2 DNA/ul plasma) between CML patients and non-CML MPD patients. There was no significant difference in JAK2 mRNA levels in the MPD group between patients with or without the V617F mutation. There was no significant difference in JAK2 mRNA levels between patients with polycythemia vera, essential thrombocythemia, or agnogenic myeloid metaplasia, or unclassified MPD (P = 0.09). Survival data was available for only 68 patients; JAK2 mRNA levels in these patients did not correlate with overall survival. In contrast, mutant (V617F) JAK2 mRNA levels in the plasma correlated negatively with overall survival in continuous fashion (P = 0.04) when all patients (with and without the mutation) were considered, as well as when only patients with the mutation were considered (P = 0.03). In contrast, when we quantified levels of mutant JAK2 DNA, 4 of the 68 patients who showed mutation using RNA were negative for the V617F mutation by DNA analysis, and the levels of mutant JAK2 DNA did not correlate with survival. This data suggests that JAK2 mRNA is overexpressed in all patients with non-CML MPD, and levels of mutant JAK2 mRNA may correlate with clinical behavior. Furthermore, when testing for JAK2 mutation, RNA rather than DNA should be used.
Ultra-open acoustic metamaterial silencer based on Fano-like interference (2019)

Recently, with advances in acoustic metamaterial science, the possibility of sound attenuation using subwavelength structures, while maintaining permeability to air, has been demonstrated. However, the ongoing challenge addressed herein is the fact that among such air-permeable structures to date, the open area represents only small fraction of the overall area of the material. In the presented paper in order to address this challenge, we first demonstrate that a transversely placed bilayer medium with large degrees of contrast in the layers' acoustic properties exhibits an asymmetric transmission, similar to the Fano-like interference phenomenon. Next, we utilize this design methodology and propose a deep-subwavelength acoustic metasurface unit cell comprising nearly 60% open area for air passage, while serving as a high-performance selective sound silencer. Finally, the proposed unit-cell performance is validated experimentally, demonstrating a reduction in the transmitted acoustic energy of up to 94%. This ultra-open metamaterial design, leveraging a Fano-like interference, enables high-performance sound silencing in a design featuring a large degree of open area, which may find utility in applications in which highly efficient, air-permeable sound silencers are required, such as smart sound barriers, fan or engine noise reduction, among others.
Hypocatalasemic Fibroblasts Accumulate Hydrogen Peroxide and Display Age‐Associated Pathologies (2005)

Human epidemiological studies point to an association of hypocatalasemia and an increased risk of age-related disease. Unfortunately, the cellular and molecular manifestations of hypocatalasemia are only poorly understood. In this analysis, we have extensively characterized hypocatalasemic human fibroblasts and report that they amass hydrogen peroxide and are oxidatively damaged. Protein and DNA alike are affected, as are functioning and biogenesis of peroxisomes - the subcellular organelles which normally house catalase. Despite these pathologies and their relative inability to grow, the cells do not appear to be intrinsically senescent. With the goal of restoring oxidative balance and perhaps reversing some of the accumulated damage to critical cellular components, we transduced hypocatalasemic fibroblasts with a form of catalase specifically designed to efficiently traffic to peroxisomes. We show the strategy is extremely effective, with dramatic reductions seen in cellular hydrogen peroxide levels. Future longitudinal studies aimed at examining the effects of a more continuous and long-term protein therapy may now commence.
Carbocyclic analogs of 5-substituted uracil nucleosides. Synthesis and antiviral activity (1983)

Carbocyclic analogues of 3'-deoxyuridines, 3'-deoxyuridines, and uridines with substituents at position 5 of the uracil moiety were prepared by direct halogenation (5-bromo and 5-iodo groups) and by displacement of the 5-bromo group by amino and substituted-amino groups. The analogue of 5-(hydroxymethyl)uridine was prepared via reaction of the isopropylidene derivative of the uridine analogue with paraformaldehyde. The carbocyclic analogues of thymidine and of 5-bromo-, 5-iodo-, and 5-(methylamino)-2'-deoxyuridine were highly active in vitro against herpes simplex virus, types 1 and 2. The corresponding analogues of 5-substituted 3'-deoxyuridines and of 5-substituted uridines were not active in this assay.
Retinal blood flow measurement by circumpapillary Fourier domain Doppler optical coherence tomography (2008)

We present in vivo human total retinal blood flow measurements using Doppler Fourier domain optical coherence tomography (OCT). The scan pattern consisted of two concentric circles around the optic nerve head, transecting all retinal branch arteries and veins. The relative positions of each blood vessel in the two OCT conic cross sections were measured and used to determine the angle between the OCT beam and the vessel. The measured angle and the Doppler shift profile were used to compute blood flow in the blood vessel. The flows in the branch veins was summed to give the total retinal blood flow at one time point. Each measurement of total retinal blood flow was completed within 2 s and averaged. The total retinal venous flow was measured in one eye each of two volunteers. The results were 52.90+/-2.75 and 45.23+/-3.18 microlmin, respectively. Volumetric flow rate positively correlated with vessel diameter. This new technique may be useful in the diagnosis and treatment of optic nerve and retinal diseases that are associated with poor blood flow, such as glaucoma and diabetic retinopathy.
Liquid-phase-epitaxial growth of Inp/InGaAsP/InGaAs buried-structure avalanche photodiodes (1984)

An InP/InGaAsP/InGaAs avalanche photodiode with an effective guard-ring structure has been successfully fabricated. The diode has a planar structure with an n-InP layer buried by n−-InP in the multiplication region The structure has been grown on a (111)A-oriented InP substrate by two-step growth of liquid-phase epitaxy. Prior to the second growth of n−-InP a meltback technique was used to reduce dark current.
The E2 Glycoprotein of Classical Swine Fever Virus Is a Virulence Determinant in Swine (2005)

To identify genetic determinants of classical swine fever virus (CSFV) virulence and host range, chimeras of the highly pathogenic Brescia strain and the attenuated vaccine strain CS were constructed and evaluated for viral virulence in swine. Upon initial screening, only chimeras 138.8v and 337.14v, the only chimeras containing the E2 glycoprotein of CS, were attenuated in swine despite exhibiting unaltered growth characteristics in primary porcine macrophage cell cultures. Additional viral chimeras were constructed to confirm the role of E2 in virulence. Chimeric virus 319.1v, which contained only the CS E2 glycoprotein in the Brescia background, was markedly attenuated in pigs, exhibiting significantly decreased virus replication in tonsils, a transient viremia, limited generalization of infection, and decreased virus shedding. Chimeras encoding all Brescia structural proteins in a CS genetic background remained attenuated, indicating that additional mutations outside the structural region are important for CS vaccine virus attenuation. These results demonstrate that CS E2 alone is sufficient for attenuating Brescia, indicating a significant role for the CSFV E2 glycoprotein in swine virulence.
Providing QoS guarantees in packet switches (2003)

The continuous growth in the demand for diversified quality-of-service (QoS) guarantees in broadband networks introduces new challenges in the design of next-generation packet switches. Packet scheduling is the most critical function involved in the provision of individual bandwidth and delay guarantees to the switched flows. Most of the scheduling techniques proposed so far assume the presence in the switch of a single contention point, residing in front of the outgoing links. Such an assumption is not consistent with many popular switch architectures, which typically have multiple contention points, located in both ingress and egress port cards, as well as in the fabric itself. We define a distributed scheduling architecture to provide differentiated QoS guarantees to individual traffic flows in a switch with multiple contention points. Our scheduling architecture is simple to implement, since it keeps per-flow scheduling confined to the port cards, and is suitable for applications in QoS frameworks for both IP and ATM networks.
Crimp-Imbalanced Protective (Crimp) Fabrics (2010)

This report documents research that was conducted to explore the unique concept of using crimp imbalance, which is a simple architectural modification achieved during the weaving process, as a potential mechanism to enhance fragmentation and ballistic protection levels of single-ply woven fabrics. It is shown in this report that crimp imbalance (1) can substantially influence the energy-absorption levels of single-ply fabrics for select fragment simulating projectile (FSP) velocities and friction coefficients; (2) can be tailored to controllably delay stress-wave propagations among yarn directions; and (3) can minimize reflections at the yarn crossover regions. This research, which used numerical models of single ply, plain-woven fabric, demonstrated that deviations in crimp contents can have significant effects on energy absorptions and projectile residual velocities; in short, optimal levels of crimp imbalance may exist for a specific ballistic threat type.
Immobilization of DNA Probes onto Gold Surface and its Application to Fully Electric Detection of DNA Hybridization using Field-Effect Transistor Sensor (2006)

A field-effect transistor (FET) sensor with a gold sensing electrode (extended-gate FET sensor), on which DNA probes can be immobilized via an Au–S bond, was designed. A method of controlling the surface density of DNA probes immobilized on the gold electrode was developed using a competitive reaction between DNA probes and alkanethiols. The immobilized DNA probes were characterized using voltammetry and a single-base extension reaction combined with bioluminescence detection. The relationship between DNA probe density and hybridization efficiency was clarified, and it was found that the optimum density for FET sensors was about 2.6×1012 molecules/cm2. The fully electric detection of hybridized target DNA (about 7 fmol) was achieved by the extended-gate FET sensor with the above DNA probe density. In addition, the surface potential in proportion to the density of both single-stranded DNA and double-stranded DNA immobilized on the gold electrode was successfully obtained using the extended-gate FET sensor.
Primate animal models and titered inocula for the study of human hepatitis A, hepatitis B, and non-A, non-B hepatitis. (1983)

Although many primate species have been inoculated with the agents of human hepatitis A, B, and non-A, non-B, only a small number of species have been shown to be susceptible, and only the chimpanzee (Pan troglodytes) has been shown to be reproducibly susceptible to all three types of human hepatitis. Infectious inocula containing each agent have been identified in different laboratories and the end-point titers of infectivity determined, in most cases by inoculation of chimpanzees. These inocula and the nonhuman primate models have permitted investigators to study the inactivation of these agents and to evaluate passive and active immunization against the agents.
Evolutionarily Divergent Type II Protein Arginine Methyltransferase in <i>Trypanosoma brucei</i> (2007)

ABSTRACT Protein arginine methylation is a posttranslational modification that impacts cellular functions, such as RNA processing, transcription, DNA repair, and signal transduction. The majority of our knowledge regarding arginine methylation derives from studies of yeast and mammals. Here, we describe a protein arginine N -methyltransferase (PRMT), TbPRMT5, from the early-branching eukaryote Trypanosoma brucei . TbPRMT5 shares the greatest sequence similarity with PRMT5 and Skb1 type II enzymes from humans and Schizosaccharomyces pombe , respectively, although it is significantly divergent at the amino acid level from its mammalian and yeast counterparts. Recombinant TbPRMT5 displays broad substrate specificity in vitro, including methylation of a mitochondrial-gene-regulatory protein, RBP16. TbPRMT5 catalyzes the formation of ω- N G -monomethylarginine and symmetric ω- N G , N G ′ -dimethylarginine and does not require trypanosome cofactors for this activity. These data establish that type II PRMTs evolved early in the eukaryotic lineage. In vivo, TbPRMT5 is constitutively expressed in the bloodstream form and procyclic-form (insect host) life stages of the parasite and localizes to the cytoplasm. Genetic disruption via RNA interference in procyclic-form trypanosomes indicates that TbPRMT5 is not essential for growth in this life cycle stage. TbPRMT5-TAP ectopically expressed in procyclic-form trypanosomes is present in high-molecular-weight complexes and associates with an RG domain-containing DEAD box protein related to yeast Ded1 and two kinetoplastid-specific proteins. Thus, TbPRMT5 is likely to be involved in novel methylation-regulated functions in trypanosomes, some of which may include RNA processing and/or translation.
Prevalent hypertension and stroke in the Sleep Heart Health Study: association with an ECG-derived spectrographic marker of cardiopulmonary coupling. (2009)

An ECG-derived spectrographic marker related to low frequency cardiopulmonary coupling is associated with greater sleep apnea severity. Whether this biomarker is solely a sign of more severe disease or whether it reflects primary alterations in sleep apnea pathophysiology (which may either cause or result from sleep apnea) is unknown. This ECG-based spectral marker is associated with a higher prevalence of hypertension and stroke.
Purification and characterization of a tissue plasminogen activator-inhibitor complex from human umbilical vein endothelial cell conditioned medium (1987)

Tissue plasminogen activator-inhibitor complexes were purified from the conditioned medium of human umbilical vein endothelial cells by affinity chromatography followed by gel filtration. It was found that a single complex was isolated which can exist in two distinct interconvertible conformations. These may be separated by electrophoresis into a form with a 105,000 apparent molecular weight and a form with an 88,000 apparent molecular weight. The particular conformation which predominates may be altered by changing the pH at which preparations are incubated or by including dithiothreitol in incubation buffers. Plasminogen activator enzymatic activity may be partially recovered from purified complexes by incubation in the presence of fibrin. Incubation in 1.5 M NH4OH results in the dissociation of the complex into two major polypeptides of 67 and 40 kilodaltons (kDa). The 40-kDa protein was isolated by gel filtration high-pressure liquid chromatography. N-Terminal amino acid analysis of this protein revealed three distinct sequences. Two of these were nearly identical and matched the N-terminal sequence recently reported for the native plasminogen activator inhibitor from endothelial cells. The third sequence exactly matched an internal portion of the same protein. The results suggest that the internal sequence is located at the site where the inhibitor is cleaved by tissue plasminogen activator.
Impedance & Admittance-Based Coordination Control Strategies for Robotic Lower Limb Prostheses (2014)

This article presents and compares two different control systems for a powered knee and ankle prosthesis for transfemoral amputees, which were constructed to provide the user a safe, intuitive, and well-coordinated interaction with the prosthesis. The piecewise-passive impedance (PPI) controller utilizes only impedance-like behaviors, while the second – a hybrid impedance-admittance (HIA) controller – utilizes both impedance-like and admittance-like behaviors in a hybrid approach. The HIA approach maintains many of the desirable characteristics of the PPI controller while also reducing the number of selectable control parameters. The HIA approach essentially incorporates the PPI control structure during the early and middle stance phases of gait, and a trajectory tracking control approach in terminal stance and swing. These controllers were implemented on a powered knee and ankle prosthesis and tested in walking trials by a transfemoral amputee. Data from these trials indicate that both controllers achieve comparable performance with respect to healthy subject data, despite some substantial structural differences between the two.
Fabrications and Mechanical Properties of Sintered SiC Fiber-Bonded Ceramics. (2000)

A sintered SiC fiber-bonded ceramic was synthesized by hot-pressing the plied sheets of an amorphous Si-Al-C-O fiber. Here we describe the microscopic structure and mechanical properties of the two-directional sintered SiC fiber-bonded ceramic synthesized from three kinds of starting fiber with different concentration of excess carbon and oxygen and different fiber diameter. The desirable sintered SiC fiber-bonded ceramic has been found to show a perfectly close-packed structure of the hexagonal columnar fibers with a very thin interfacial carbon layer. Furthermore, the interior of the fiber element was composed of sintered β-SiC crystal without an obvious second phase at the grain boundary and its triple points. Its mechanical properties at high temperatures are closely relate to the microscopic structure. The strength and the fracture behavior are strongly dominated by the uniformity of the interfacial carbon layer and a densified structure of the fiber element. A reduction in the excess carbon and oxygen included in the starting fiber resulted in the improved mechanical strength of the fiber-bonded-ceramic. Furthermore, it was found the highest four-point bending strength (-500MPa) could be obtained by the use of a thinner starting fiber (8μm) with low concentration of carbon and oxygen. It was concluded from these facts that the improvement in mechanical strength was strongly related to the formation of the uniform interfacial carbon layer and the most densified structure of the fiber element.
Identification, characterization, and mapping of a mouse homolog of the gene mutated in Nijmegen breakage syndrome (1999)

The rare autosomal recessive disorder Nijmegen breakage syndrome (NBS) results from mutations in the NBS1 gene on human chromosome 8q21. A mouse homolog of the NBS1 gene was isolated and its nucleotide sequence determined. Somatic cell hybrid analysis and fluorescence in situ hybridization were used to map this gene, Nbn, to mouse chromosome band 4A. Northern blotting revealed comparable levels of Nbn transcripts in most tissues in the mouse. However, transcripts were elevated 10-20 fold in the testes, consistent with a possible role for the product of the Nbn gene in meiotic recombination.
Ultrasound applicators with internal water-cooling for high-powered interstitial thermal therapy (2000)

Internal water-cooling of direct-coupled ultrasound (US) applicators for interstitial thermal therapy (hyperthermia and coagulative thermal therapy) was investigated. Implantable applicators were constructed using tubular US sources (360 angular acoustic emittance, approximately 7 MHz) of 10 mm length and 1.5, 1.8, 2.2, and 2.5 mm outer diameter (OD). Directional applicators were also constructed using 2.2 mm OD tubes sectored to provide active acoustic sectors of 90 degrees and 200 degrees. A water-cooling mechanism was integrated within the inner lumen of the applicator to remove heat from the inner transducer surface. High levels of convective heat transfer (2100-3800 W/m2K) were measured for practical water flow rates of 20-80 mL/min. Comparative acoustic measurements demonstrated that internal water-cooling did not significantly degrade the acoustic intensity or beam distribution of the US transducers. Water-cooling allowed substantially higher levels of applied electrical power (> 45 W) than previous designs (with air-cooling or no cooling), without detriment to the applicators. High-temperature heating trials performed with these applicators in vivo (porcine liver and thigh muscle) and in vitro (bovine liver) showed improved thermal penetration and coagulation. Radial depth of coagulation from the applicator surface ranged from 12 to 20 mm for 1-5 min of sonication with 28-W applied power. Higher powers (41 W) demonstrated increased coagulation depths (approximately 9 mm) at shorter times (15 s). Thermal lesion dimensions (angular and axial expanse) produced with directional applicators were controlled and directed, and corresponded to the active zone of the transducer. These characteristic lesion shapes were also generally unchanged with different sonication times and power, and were found to be consistent with previous coagulation studies using air-cooled applicators. The implementation of water-cooling is a significant advance for the application of ultrasound interstitial thermal therapy (USITT), providing greater treatment volumes, shorter treatment times, and the potential for treatment of highly perfused tissue with shaped lesions.
Fabrication of Sintered Annular Fuel Pellet for HANARO Irradiation Test (2010)

The fabrication method of an annular pellet with highly precise diametric tolerances, same dimensions, and various sintered densities has been investigated. To examine the in-pile densification and swelling of the annular pellet, 5 different types of annular pellet were prepared for a HANARO irradiation test. In order to obtain annular fuel pellets with the same dimensions and various sintered densities, we control the green density of an annular compact, the sintering temperatures, and the sintering time. For a diametric tolerance control, we have introduced a new compaction process that combines the usual double-acting pressing and cold isostatic pressing. Annular fuel pellets with the same dimensions and various sintered densities were fabricated successfully, and all the pellets satisfied the pellet specification of the HANARO irradiation test. Sintered annular pellets show an excellent inner diametric tolerance of less than ±12 μm without an inner surface grinding.