gebhart/patrepeval huggingface dataset:
Fragmentation landscape of cell-free DNA revealed by deconvolutional analysis of end motifs (2023)

Cell-free DNA (cfDNA) fragmentation is nonrandom, at least partially mediated by various DNA nucleases, forming characteristic cfDNA end motifs. However, there is a paucity of tools for deciphering the relative contributions of cfDNA cleavage patterns related to underlying fragmentation factors. In this study, through non-negative matrix factorization algorithm, we used 256 5' 4-mer end motifs to identify distinct types of cfDNA cleavage patterns, referred to as "founder" end-motif profiles (F-profiles). F-profiles were associated with different DNA nucleases based on whether such patterns were disrupted in nuclease-knockout mouse models. Contributions of individual F-profiles in a cfDNA sample could be determined by deconvolutional analysis. We analyzed 93 murine cfDNA samples of different nuclease-deficient mice and identified six types of F-profiles. F-profiles I, II, and III were linked to deoxyribonuclease 1 like 3 (DNASE1L3), deoxyribonuclease 1 (DNASE1), and DNA fragmentation factor subunit beta (DFFB), respectively. We revealed that 42.9% of plasma cfDNA molecules were attributed to DNASE1L3-mediated fragmentation, whereas 43.4% of urinary cfDNA molecules involved DNASE1-mediated fragmentation. We further demonstrated that the relative contributions of F-profiles were useful to inform pathological states, such as autoimmune disorders and cancer. Among the six F-profiles, the use of F-profile I could inform the human patients with systemic lupus erythematosus. F-profile VI could be used to detect individuals with hepatocellular carcinoma, with an area under the receiver operating characteristic curve of 0.97. F-profile VI was more prominent in patients with nasopharyngeal carcinoma undergoing chemoradiotherapy. We proposed that this profile might be related to oxidative stress.
Development of MAS - a system for pin-pointed muscle force control using a power-assisting device (2007)

This paper proposes a system MAS (muscle assistant system), which controls designated muscle forces by controlling a power-assisting device. MAS estimates muscle force based on posture measured by a motion capture system. The feasibility of the muscle force control for an object muscle is checked based on constrained optimization problem. For realizing the target force, the driving-force of power-assisting device is calculated and controlled. Using this pin-pointed muscle force control method, the effective rehabilitation and sports training is provided.
Fast Two-Stage Vocabulary-Independent Search In Spontaneous Speech (2006)

For efficient organization of speech recordings - meetings, interviews, voice mails, lectures - the ability to search for spoken keywords is an essential capability. In Seide et al. (2004) and Yu et al. (2004), we presented our work on vocabulary-independent search in spontaneous speech. That method involved linear scanning of phonetic lattices, and thus did not scale up to large collections. In this paper, we present a two-stage approach to fast search: first we retrieve segments from an index-like structure that are promising to contain the keyword, then we locate individual keyword occurrences by a detailed linear lattice scan. However, designing an efficient vocabulary-independent indexing structure is non-trivial. We use a "soft" index, similar to Allauzen et al., that provides expected term frequencies (ETF) of query terms. We propose to approximate ETF by M-gram phoneme language models estimated on the lattices (one per segment). Our index stores these language models in an inverted structure. Word spotting experiments on voicemails show that with this two-stage method, we lose under 4% FOM (figure of merit) relative at a 25-times speed-up compared with a full linear search.
USE OF SEISMIC PAVEMENT ANALYZER IN PAVEMENT EVALUATION (1995)

The Seismic Pavement Analyzer (SPA, patent pending) is an instrument designed and constructed to monitor conditions associated with pavement deterioration. It measures such conditions as voids or loss of support under a rigid pavement, moisture infiltration in asphalt concrete pavement, and delamination of overlays. The SPA detects these types of pavement conditions by estimating Young's and shear moduli in the pavement, base, and subgrade from the following wave propagation measurements: (a) impact echo, (b) impulse response, (c) spectral-analysis-of-surface-waves, (d) ultrasonic-surface-wave-velocity, and (e) ultrasonic-body-wave-velocity. The SPA records the pavement response produced by high- and low-frequency pneumatic hammers on five accelerometers and three geophones. A computer controls data acquisition, instrument control. and interpretation: measurements and interpretations are reported in both screen and data base formats. This paper briefly describes the device and summarizes the usefulness of the equipment in pavement evaluation. The results from several field tests are also discussed. The tests conducted so far have produced very promising results. The device is simple to use, and results have been reliable and repeatable.
Synthesis of Isobutyl- <i>C</i> -galactoside (IBCG) as an Isopropylthiogalactoside (IPTG) Substitute for Increased Induction of Protein Expression (2003)

[reaction: see text] Addition of isopropyl-beta-d-thiogalactopyranoside (IPTG) to bacterial cultures is often used to induce expression of plasmid-based genes for the production of recombinant proteins under control of the lac promoter, but a simple method to circumvent the inherent instability of this compound has not been addressed experimentally. Herein we report the first synthesis of isobutyl-C-galactoside (IBCG), the C-glycoside analogue of IPTG, and show that IBCG is superior to IPTG in inducing protein expression over long induction times.
Role of TCL1 and ALL1 in human leukemias and development. (1999)

We have investigated the role of chromosomal translocations in the pathogenesis of human leukemias. The study of T-cell chronic lymphocytic leukemias and T-cell prolymphocytic leukemia has led to the identification of TCL1, a novel gene that is deregulated by translocations, t(14;14)(q11;q32), or inversions, inv(14)(q11;q32.1). Introduction of a human TCL1 gene juxtaposed to the Ick promoter into fertilized mouse eggs resulted in the development of transgenic mice that developed mature T-cell leukemias, indicating that TCL1 is a transforming oncogene. We have also investigated acute leukemias with abnormalities at chromosome 11q23. We have identified a gene, ALL1, that can fuse to many different genes in acute leukemias. We have also shown that ALL1 can fuse with ALL1 in acute myelogenous leukemia. We have proposed that the ALL1 fusion genes may act by a dominant negative mechanism.
Telmisartan in Migraine Prophylaxis: A Randomized, Placebo-Controlled Trial (2009)

We evaluated telmisartan 80 mg for migraine prophylaxis. Migraine patients (n = 95) with three to seven migraine attacks in 3 months were randomized, double-blind to telmisartan or placebo. The primary end-point was the reduction in the number of migraine days (i.e. a day with > or = 1 h of symptoms) between the 4-week baseline period and the last 4 weeks of the 12-week treatment period. A responder was recorded when there was a symptom reduction of > or = 50% in these 4-week baseline and treatment periods. The reduction in migraine days was 1.65 with telmisartan and 1.14 with placebo (P > 0.05). Post hoc analyses adjusting for baseline and centre showed a 38% reduction in migraine days with telmisartan vs. 15% with placebo (P = 0.03), and a borderline significant difference in responders (40% vs. 25%, P = 0.07). The incidence of adverse events was similar between treatments. This study indicates that telmisartan might be effective in migraine prophylaxis.
Novel Cylindrical Magnetic Levitation Stage for Rotation as well as Translation along Axles with High Precisions (2012)

In this paper, a conceptual design and a detailed design of novel cylindrical magnetic levitation stage is introduced. This is came from planar-typed magnetic levitation stage. The proposed stage is composed of cylinder-typed permanent magnet array and semi-cylinder-typed 3 phase winding module. When a proper current is induced at winding module, a magnetic levitation force between the permanent magnet array and winding module is generated. The proposed stage can precisely move the cylinder to rotations and translations as well as levitations with the magnetic levitation force. This advantage is useful to make a nano patterning on the surface of cylindrical specimen by using electron beam lithography under vacuum. Two methods are used to calculate required magnetic levitation forces. The one is 2D FEM analysis, the other is mathematical modeling. This paper shown that results of two methods are similar. An assistant plate is introduced to reduce required currents of winding module for levitations in vacuum. The mathematical model of cylindrical magnetic levitation stage is used for dynamic simulation of magnetic levitations. A lead-lag compensator is used for control of the model. Simulation results shown that the detail designed model of the cylindrical magnetic levitation stage with the assistant plate can be controlled very well.
Partitioning of airway and lung tissue properties: comparison of in situ and open-chest conditions (1995)

The purpose of this study was to investigate under physiological breathing conditions whether airway and lung tissue properties are different in situ and in open-chest conditions. We measured lung input impedance in dogs from 0.2 to 8 Hz with an optimal ventilator waveform at four tidal volumes (VT; from 75 to 450 ml) in intact animals using an esophageal balloon as well as after opening the chest. The lung impedance from both conditions was partitioned into airway and tissue compartments as characterized by airway resistance and inertance (Iaw) and tissue damping (G) and elastance (H) parameters respectively. All parameters except Iaw depended to some extent on VT. The in situ tissue G and H slightly decreased with VT while in the open-chest condition; G decreased and H increased slightly with VT. We found small but significant differences between the mechanical properties of the airway and lung tissues in situ and in open-chest conditions. Over the total population, the G, airway resistance, and Iaw parameters were 13% (not significant), 35% (P < 0.001), and 31% (P < 0.001) smaller, respectively, in situ than in the open-chest condition. However, the H was 15% larger in situ (P < 0.001). Although we cannot completely rule out certain artifacts, these differences most likely reflect real alterations in the lung due to the different configurations and possible differences in the distribution of pleural pressures in the two conditions. The G being smaller and E being larger in situ resulted in hysteresivity (G/H) 36% smaller in situ (P < 0.001).(ABSTRACT TRUNCATED AT 250 WORDS)
A simple IP fast reroute scheme for full coverage (2012)

A major concern in IP networks is to ensure that any topology changes, whether planned or unplanned, do not disrupt network performance. IP Fast Reroute (IP FRR) is a general approach to address this issue, by promptly forwarding an IP packet to a predetermined alternate next hop as soon as the primary next hop to the destination becomes unavailable. Among the numerous IP FRR schemes proposed to date, the simplest ones do not guarantee protection against every component failure, while more sophisticated ones tend to be difficult to implement due to various inherent complexities, such as nontrivial modifications of IP packets or high resource requirements.
Welding for Cryogenic Service (1993)

Abstract Cryogenic temperatures cause many structural alloys to become brittle, which is an unacceptable condition in most structural applications and is rectified by optimizing the weld composition. Although nonmatching weld compositions are most appropriate, differences between the welds and parent material in terms of thermal contraction, corrosion, and other factors must be considered. This article discusses these differences and describes the effect of these factors on the choice of the weld filler metal. It also provides a detailed discussion on the effects of cryogenic services on mechanical properties of the parent metal.
Unifying type checking and property checking for low-level code (2009)

We present a unified approach to type checking and property checking for low-level code. Type checking for low-level code is challenging because type safety often depends on complex, program-specific invariants that are difficult for traditional type checkers to express. Conversely, property checking for low-level code is challenging because it is difficult to write concise specifications that distinguish between locations in an untyped program's heap. We address both problems simultaneously by implementing a type checker for low-level code as part of our property checker. We present a low-level formalization of a C program's heap and its types that can be checked with an SMT solver, and we provide a decision procedure for checking type safety. Our type system is flexible enough to support a combination of nominal and structural subtyping for C, on a per-structure basis. We discuss several case studies that demonstrate the ability of this tool to express and check complex type invariants in low-level C code, including several small Windows device drivers.
Stilbenoid prenyltransferases define key steps in the diversification of peanut phytoalexins (2017)

Defense responses of peanut (<i>Arachis hypogaea</i>) to biotic and abiotic stresses include the synthesis of prenylated stilbenoids. Members of this compound class show several protective activities in human disease studies, and the list of potential therapeutic targets continues to expand. Despite their medical and biological importance, the biosynthetic pathways of prenylated stilbenoids remain to be elucidated, and the genes encoding stilbenoid-specific prenyltransferases have yet to be identified in any plant species. In this study, we combined targeted transcriptomic and metabolomic analyses to discover prenyltransferase genes in elicitor-treated peanut hairy root cultures. Transcripts encoding five enzymes were identified, and two of these were functionally characterized in a transient expression system consisting of <i>Agrobacterium</i>-infiltrated leaves of <i>Nicotiana benthamiana</i> We observed that one of these prenyltransferases, AhR4DT-1, catalyzes a key reaction in the biosynthesis of prenylated stilbenoids, in which resveratrol is prenylated at its C-4 position to form arachidin-2, whereas another, AhR3'DT-1, added the prenyl group to C-3' of resveratrol. Each of these prenyltransferases was highly specific for stilbenoid substrates, and we confirmed their subcellular location in the plastid by fluorescence microscopy. Structural analysis of the prenylated stilbenoids suggested that these two prenyltransferase activities represent the first committed steps in the biosynthesis of a large number of prenylated stilbenoids and their derivatives in peanut. In summary, we have identified five candidate prenyltransferases in peanut and confirmed that two of them are stilbenoid-specific, advancing our understanding of this specialized enzyme family and shedding critical light onto the biosynthesis of bioactive stilbenoids.
Design and Evaluation of an On-Sun Prototype Falling-Particle Cavity Receiver (2014)

Cavity receivers have been an integral part of Concentrated Solar Power (CSP) plants for many years. However, falling solid particle receivers (SPR) which employ a cavity design are only in the beginning stages of on-sun testing and evaluation. A prototype SPR has been developed which will be fully integrated into a complete system to demonstrate the effectiveness of this technology in the CSP sector. The receiver is a rectangular cavity with an aperture on the north side, open bottom (for particle collection), and a slot in the top (particle curtain injection). The solid particles fall from the top of the cavity through the solar flux and are collected after leaving the receiver. There are inherent design challenges with this type of receiver including particle curtain opacity, high wall fluxes, high wall temperatures, and high heat losses. CFD calculations using ANSYS FLUENT were performed to evaluate the effectiveness of the current receiver design. The particle curtain mass flow rate needed to be carefully regulated such that the curtain opacity is high (to intercept as much solar radiation as possible), but also low enough to increase the average particle temperature by 200°C. Wall temperatures were shown to be less than 1200°C when the particle curtain mass flow rate is 2.7 kg/s/m which is critical for the receiver insulation. The size of the cavity was shown to decrease the incident flux on the cavity walls and also reduced the wall temperatures. A thermal efficiency of 92% was achieved, but was obtained with a higher particle mass flow rate resulting in a lower average particle temperature rise. A final prototype receiver design has been completed utilizing the computational evaluation and past CSP project experiences.
Freeze-Dried Sperm Fertilization Leads to Full-Term Development in Rabbits1 (2004)

To date, the laboratory mouse is the only mammal in which freeze-dried spermatozoa have been shown to support full-term development after microinjection into oocytes. Because spermatozoa in mice, unlike in most other mammals, do not contribute centrosomes to zygotes, it is still unknown whether freeze-dried spermatozoa in other mammals are fertile. Rabbit sperm was selected as a model because of its similarity to human sperm (considering the centrosome inheritance pattern). Freeze- drying induces rabbit spermatozoa to undergo dramatic changes, such as immobilization, membrane breaking, and tail fragmentation. Even when considered to be "dead" in the conventional sense, rabbit spermatozoa freeze-dried and stored at ambient temperature for more than 2 yr still have capability comparable to that of fresh spermatozoa to support preimplantation development after injection into oocytes followed by activation. A rabbit kit derived from a freeze-dried spermatozoon was born after transferring 230 sperm-injected oocytes into eight recipients. The results suggest that freeze-drying could be applied to preserve the spermatozoa from most other species, including human. The present study also raises the question of whether rabbit sperm centrosomes survive freeze-drying or are not essential for embryonic development.
Optical Coordinate Transfer Assembly For Precision Boresighting Applications (1989)

Boresighting involves precisely transferring angular coordinates from one point to another. This frequently arises in correlating directional information between systems such as optical telescopes or high-gain microwave antennas that are physically separated by a truss or support. Generally, the separating truss is not rigid to the accuracies required for precise alignment because of thermal, aerodynamic, and vibrational distortions typical of many practical environments. This paper presents a relatively simple concept for optically boresighting between any two points, in three degrees of angular freedom, and independent of the rigid body. Analyses and laboratory investigations indicate that sub-microradian accuracies, data rates exceeding 100 Hz, and dynamic ranges of approximately milliradians are feasible between points separated by over 10 meters.
Development of a repeatedly adjustable intraocular lens (2003)

The mechanically adjustable IOL provides a feasible and promising means of confronting postoperative refractive errors and the changing desires of patients. The viability of this IOL design has been proven, and results suggest that operation of the lens is safe enough to pursue in vivo trials. Evaluation of the biocompatibility of the lens architecture as well as the ultimate goal of noninvasive adjustment using this model are reported in a companion article.
The Sex Specificity of Navigational Strategies in Alzheimer Disease (2007)

Alzheimer disease (AD) is associated with navigational impairments that limit functional independence. We have now examined the role of cognitive and perceptual mechanisms in the navigational impairment of AD to test the hypothesis that men and women with AD may focus on different navigational cues. We conducted navigational, neuropsychologic, and psychophysical testing in men and women from 3 groups: older normal controls, patients with mild cognitive impairment, and patients with AD. Men and women showed parallel declines in navigational capacities from the older normal control, to the mild cognitive impairment, to the AD groups with men and women making similar numbers of errors but different types of errors. There were small sex differences in neuropsychologic and psychophysical performance but large sex differences in how those measures related to navigational capacity: men showed strong links between visual motion processing and navigation. Women showed strong links between verbal capacities and navigation. The findings of these cross-sectional comparisons suggest that there may be sex differences in the progressive navigational decline of AD: men and women who are impaired to the same degree may suffer somewhat different patterns of decline with men relying more on visuospatial processing and women relying more on verbal mediation.
Tumor specific fluorescent contrast agents (2000)

Several dyes are currently used for various biomedical applications due to their biocompatibility and high molar absorptivity. Localization of dyes in tumors may be mediated by several factors such as leaky vasculature and high metabolic activity in proliferating cells. However, these mechanisms of action make it difficult to differentiate inflammation from benign or malignant tumors. In order to enhance their tumor specificity, dyes have been conjugated to biomolecules that target unique factors in various diseased state. However, such large biomolecules can elicit adverse immunogenic reactions in humans, and are often preferentially taken up by the liver. Furthermore, for solid tumors which may rely on diffusion of the biomarkers from the vascular, penetration of large dye conjugates is not favorable. To overcome these problems, we designed and synthesized novel dye-peptide conjugates that are receptor specific. The efficacy of these new fluorescent contrast agents was tested in vivo in well-characterized rat tumor lines. The resulting optical images demonstrate that successful specific tumor targeting was achieved.
Masking of transformed intra-predicted blocks for high quality image and video coding (2014)

Many professional applications for image and video coding require very high levels of quality of the decoded signal. Under these conditions, even state-of-the-art standards such as High Efficiency Video Coding (HEVC) may not provide sufficient compression efficiency. Large values of the residual samples, especially at high frequency components, are difficult to encode and result in high bitrates of the coded signal. A novel scheme for image and video coding is presented in this paper to enhance compression at high quality levels, based on separate transform to the frequency domain of original and prediction signals. Selected frequency components of the prediction signal are discarded by means of appropriate masking patterns prior to the residual computation. The optimal masking pattern is selected for each transformed block and signalled in the bitstream. The approach is shown achieving gains against conventional HEVC under high quality constraints when coding both still images and video sequences.