gebhart/patrepeval huggingface dataset:
DNA torsion as a feedback mediator of transcription and chromatin dynamics (2014)

The double helical structure of DNA lends itself to topological constraints. Many DNA-based processes alter the topological state of DNA, generating torsional stress, which is efficiently relieved by topoisomerases. Maintaining this topological balance is crucial to cell survival, as excessive torsional strain risks DNA damage. Here, we review the mechanisms that generate and modulate DNA torsion within the cell. In particular, we discuss how transcription-generated torsional stress affects Pol II kinetics and chromatin dynamics, highlighting an emerging role of DNA torsion as a feedback mediator of torsion-generating processes.
The pseudospectral method; comparisons with finite differences for the elastic wave equation (1987)

Abstract The pseudospectral (or Fourier) method has been used recently by several investigators for forward seismic modeling. The method is introduced here in two different ways: as a limit of finite differences of increasing orders, and by trigonometric interpolation. An argument based on spectral analysis of a model equation shows that the pseudospectral method (for the accuracies and integration times typical of forward elastic seismic modeling) may require, in each space dimension, as little as a quarter the number of grid points compared to a fourth-order finite-difference scheme and one-sixteenth the number of points as a second-order finite-difference scheme. For the total number of points in two dimensions, these factors become 1/16 and 1/256, respectively; in three dimensions, they become 1/64 and 1/4 096, respectively.In a series of test calculations on the two-dimensional elastic wave equation, only minor degradations are found in cases with variable coefficients and discontinuous interfaces.
NMR imaging of cell phone radiation absorption in brain tissue (2012)

A method is described for measuring absorbed electromagnetic energy radiated from cell phone antennae into ex vivo brain tissue. NMR images the 3D thermal dynamics inside ex vivo bovine brain tissue and equivalent gel under exposure to power and irradiation time-varying radio frequency (RF) fields. The absorbed RF energy in brain tissue converts into Joule heat and affects the nuclear magnetic shielding and the Larmor precession. The resultant temperature increase is measured by the resonance frequency shift of hydrogen protons in brain tissue. This proposed application of NMR thermometry offers sufficient spatial and temporal resolution to characterize the hot spots from absorbed cell phone radiation in aqueous media and biological tissues. Specific absorption rate measurements averaged over 1 mg and 10 s in the brain tissue cover the total absorption volume. Reference measurements with fiber optic temperature sensors confirm the accuracy of the NMR thermometry.
Fast timing closure by interconnect criticality driven delay relaxation (2005)

Due to decreasing transistor sizes and increasing clock frequency, interconnect delay is a dominant factor in achieving timing closure in deep sub-micron designs. Techniques like wire pipelining and retiming can manage delay of timing critical wires. The latency of the system, however, limits the total pipelining in the design. New techniques are, thus, needed at synthesis stage to consider the effect of critical wires in the design. In this work, we propose a novel intuitive algorithm, critical edge reduction (CER) algorithm, which produces a maximal delay budgeting solution under fixed latency while minimizing the number of critical wires. We also present an in-depth analysis of trade-off between maximum budgeting and critical edge minimization. We implemented our design flow using a set of MediaBench data paths on Xilinx VirtexE FPGA devices. Using our algorithm, the Xilinx Place and Route tool achieved timing closure, on average, 2.8 times faster than using maximum budgeting. The resulting average clock period using CER algorithm outperforms the one using maximum budgeting by 6%.
HDL-S1P: cardiovascular functions, disease-associated alterations, and therapeutic applications (2015)

Sphingosine-1-phosphate (S1P) is a bioactive sphingolipid contained in High-density lipoproteins (HDL) and has drawn considerable attention in the lipoprotein field as numerous studies have demonstrated its contribution to several functions inherent to HDL. Some of them are partly and some entirely due to the S1P contained in HDL (HDL-S1P). Despite the presence of over 1000 different lipids in HDL, S1P stands out as it possesses its own cell surface receptors through which it exercises key physiological functions. Most of the S1P in human plasma is associated with HDL, and the amount of HDL-S1P influences the quality and quantity of HDL-dependent functions. The main binding partner of S1P in HDL is apolipoprotein M but others may also exist particularly under conditions of acute S1P elevations. HDL not only exercise functions through their S1P content but have also an impact on genuine S1P signaling by influencing S1P bioactivity and receptor presentation. HDL-S1P content is altered in human diseases such as atherosclerosis, coronary artery disease, myocardial infarction, renal insufficiency and diabetes mellitus. Low HDL-S1P has also been linked to impaired HDL functions associated with these disorders. Although the pathophysiological and molecular reasons for such disease-associated shifts in HDL-S1P are little understood, there have been successful approaches to circumvent their adverse implications by pharmacologically increasing HDL-S1P as means to improve HDL function. This mini-review will cover the current understanding of the contribution of HDL-S1P to physiological HDL function, its alteration in disease and ways for its restoration to correct HDL dysfunction.
ΙKΕΤΙΔΕΣ (2010)

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Compact high repetition rate magnetically switched transverse, electric, atmospheric CO2 laser (1990)

A corona preionized compact transverse, electric, atmospheric CO2 laser providing an average optical output of 18 W from a 4.6-cm3 discharge volume is reported. The laser was driven at pulse rates up to 1 kHz by an all solid-state exciter circuit which has produced&gt;109 pulses.
Robotic based thermoplastic fibre placement process (2002)

Carbon fibre reinforced composites offer excellent specific stiffness and strength and are therefore interesting for rotating machinery applications. The main disadvantage of high performance composites is the manufacturing process which is labor intensive and thus slow and expensive. The thermoplastic fibre placement process overcomes these difficulties due to its high degree of automation. During the process, an impregnated thermoplastic tape is heated up and then consolidated in-situ under pressure. This process has been implemented on a 6-axis robot in our laboratory and on a 3-axis robotic workcell at the ABB motor factory in Switzerland. This workcell is used to wind overhang bandages for motors.
Cytokine Profile in Children During the First 3 Months after the Diagnosis of Type 1 Diabetes (2004)

Type 1 diabetes is an autoimmune disease with an inflammatory process directed against the beta cells in pancreas. This investigation aimed at studying the immune response during the first 3 months after the diagnosis of type 1 diabetes, with focus on the balance of T-helper 1 (Th1)- and Th2-like cytokines, produced spontaneously and in response to relevant autoantigens. Peripheral blood mononuclear cells (PBMCs) were collected from type 1 diabetic children (10-17 years) at 5, 20, 35 and 90 days after diagnosis. Expression of interferon-gamma (IFN-gamma) and interleukin-4 (IL-4) mRNA were detected by real-time reverse transcriptase polymerase chain reaction and IFN-gamma, IL-10 and IL-13 by enzyme-linked immunosorbent assay in cell supernatant after stimulation with a glutamic acid decarboxylase 65 (GAD(65))-peptide [amino acid (a.a.) 247-279], insulin, the ABBOS-peptide (a.a. 152-169), phytohaemagglutinin and keyhole limpet haemocyanin. Spontaneous and antigen-induced expression and secretion of cytokines were low at the diagnosis of type 1 diabetes. During the first month, after diagnosis, the GAD(65)-peptide caused an increased ratio of IFN-gamma/IL-4 mRNA expression (P < 0.05) and increased secretion of IFN-gamma (P = 0.07). Expression of IFN-gamma mRNA did also increase from stimulation with insulin (P < 0.05), even though cytokine secretion remained low. Thus, duration after diagnosis as well as metabolic state should be carefully considered both in studies of the pathogenesis of type 1 diabetes and in immune intervention studies at onset.
Design of 4.48–5.89 GHz LC-VCO in 65 nm RF CMOS Technology (2014)

This paper describes a 4.48 GHz–5.89 GHz LC voltage-controlled oscillator (LC-VCO) as a key component in RF transceivers. The circuit is fully designed in TSMC’s 65 nm radio-frequency complimentary metal-oxide-semiconductor technology process. The LC-VCO uses the structure of only one couple of NMOS differential negative resistances, tank circuit which consists of an optimal on-chip spiral inductor with switched capacitor and varactor arrays. The proposed design accomplishes wide tuning range frequency by using 6-bit switch capacitor array in addition to linearly varying MOS varactors. A switched current source block is used to improve the performance of the LC-VCO. The oscillator has a wide tuning range, between 4.48 GHz and 5.89 GHz. The LC-VCO dissipates 15.96 mW from a voltage supply of 1.8 V, whereas its phase noise is -124.1 dBc/Hz at 1 MHz offset of a at 5.89 GHz carrier. DOI: http://dx.doi.org/10.5755/j01.eee.20.2.6383
Coulomb peak shifts under terahertz-wave irradiation in carbon nanotube single-electron transistors (2007)

The authors have studied the effect of terahertz irradiation on single-electron transistors (SETs) based on single-wall carbon nanotubes, and have observed that the radiation generates Coulomb peak shifts. Time-resolved measurements of the terahertz response have revealed that the peak-shift signal has very long time constants, measured in seconds, and that the time trace of the signal after the terahertz irradiation is turned off deviates from a single-exponential curve. These experimental results suggest that the terahertz irradiation causes a charging process in trap states in the close vicinity of the SET, leading to a change in its effective gate voltage.
Feasibility study on a slot array in the millimeter-wave band based on a conformal waveguide (2015)

A novel antenna array with over 120 degree coverage in the azimuth plane based on a conformal waveguide is proposed. The 8×8 element array with directivity gain of 15.7dBi at 79GHz is designed and confirmed that the side lobe level by using switching method can be suppressed over 5dB compared to a linear array with 8 branch.
Galectin-3 Precipitates as a Pentamer with Synthetic Multivalent Carbohydrates and Forms Heterogeneous Cross-linked Complexes (2004)

Galectin-3 is unique among the galectin family of animal lectins in its biological activities and structure. Most members of the galectin family including galectin-1 possess apoptotic activities, whereas galectin-3 possesses anti-apoptotic activity. Galectin-3 is also the only chimera type galectin and consists of a nonlectin N-terminal domain and a C-terminal carbohydrate-binding domain. Recent sedimentation equilibrium and velocity studies show that murine galectin-3 is a monomer in the absence and presence of LacNAc, a monovalent sugar. However, quantitative precipitation studies in the present report indicate that galectin-3 precipitates as a pentamer with a series of divalent pentasaccharides with terminal LacNAc residues. Furthermore, the kinetics of precipitation are fast, on the order of seconds. This indicates that although the majority of galectin-3 in solution is a monomer, a rapid equilibrium exists between the monomer and a small percentage of pentamer. The latter, in turn, precipitates with the divalent oligosaccharides, resulting in rapid conversion of monomer to pentamer by mass action equilibria. Mixed quantitative precipitation experiments and electron microscopy suggest that galectin-3 forms heterogenous, disorganized cross-linking complexes with the multivalent carbohydrates. This contrasts with galectin-1 and many plant lectins that form homogeneous, organized cross-linked complexes. The results are discussed in terms of the biological properties of galectin-3.
The Angiotensin-Converting Enzyme Inhibitor Captopril Inhibits Poly(Adp-Ribose) Polymerase Activation and Exerts Beneficial Effects in an Ovine Model of Burn and Smoke Injury (2011)

We investigated the effect of the angiotensin-converting enzyme (ACE) inhibitor captopril in a clinically relevant ovine model of smoke and burn injury, with special reference to oxidative stress and activation of poly(ADP-ribose) polymerase, in the lung and in circulating leukocytes. Female, adult sheep (28-40 kg) were divided into three groups. After tracheostomy and under deep anesthesia, both vehicle-control-treated (n = 5) and captopril-treated (20 mg/kg per day, i.v., starting 0.5 h before the injury) (n = 5) groups were subjected to 2 × 20%, third-degree burn injury and were insufflated with 48 breaths of cotton smoke. A sham group not receiving burn/smoke was also studied (n = 5). Animals were mechanically ventilated and fluid resuscitated for 24 h in the awake state. Burn and smoke injury resulted in an upregulation of ACE in the lung, evidenced by immunohistochemical determination and Western blotting. Burn and smoke injury resulted in pulmonary dysfunction, as well as systemic hemodynamic alterations. Captopril treatment of burn and smoke animals improved PaO2/FiO2 ratio and pulmonary shunt fraction and reduced the degree of lung edema. There was a marked increase in PAR levels in circulating leukocytes after burn/smoke injury, which was significantly decreased by captopril. The pulmonary level of ACE and the elevated pulmonary levels of transforming growth factor β in response to burn and smoke injury were significantly decreased by captopril treatment. Our results suggest that the ACE inhibitor captopril exerts beneficial effects on the pulmonary function in burn/smoke injury. The effects of the ACE inhibitor may be related to the prevention of reactive oxygen species-induced poly(ADP-ribose)polymerase overactivation. Angiotensin-converting enzyme inhibition may also exert additional beneficial effects by inhibiting the expression of the profibrotic mediator transforming growth factor β.
A Combined Nucleic Acid and Protein Analysis in Friedreich Ataxia: Implications for Diagnosis, Pathogenesis and Clinical Trial Design (2011)

We report the first explorative study on combined frataxin and mRNA levels in PBMCs from a cohort of FRDA patients, carriers and healthy individuals. Lateral-flow immunoassay differentiated cFA and pFA patients from controls, whereas determination of mRNA in q-PCR was sensitive and specific only in cFA.
Upregulation of DF3, in Association with ICAM-1 and MHC Class II by IFN-γ in Short-Term Human Mammary Carcinoma Cell Cultures (1996)

This study was designed to determine whether in vitro exposure of isolated short-term human primary and metastatic breast tumor cell cultures to interferon-gamma (IFN-gamma) could enhance expression of the breast tumor associated DF3 antigen in association with the intercellular adhesion molecule 1 (ICAM-1) and MHC class II molecules. Cell cultures were established from primary solid tumors and metastatic cells as previously described (Sgagias et al., 1995). Data show that recombinant human IFN-gamma treatment, in vitro, dramatically increased the breast tumor associated DF3 antigen, in association with ICAM-1, and MHC class II antigens in primary breast cancer cell cultures. All primary breast tumor cell cultures constitutively expressed high levels of HLA-class I antigen. Metastatic breast cancer cell cultures expressed high levels of DF3 and recombinant human IFN-gamma treatment, in vitro, upregulated ICAM-1 and MHC class II antigens before and after passage of the metastatic cells through the nude mouse. Metastatic breast cancer cells similar to primary breast cancer cells constitutively expressed high levels of MHC class I antigens. In addition, three LAK cell lines significantly lysed the primary and the metastatic breast tumor cell cultures to the same degree before and after passage of the metastatic cancer cells through the nude mouse. These data indicate the upregulation of the breast tumor associated DF3 antigen in vitro after IFN-gamma treatment and its persistence in vivo, after passage of the metastatic breast cancer cells through the nude mouse. The ability of IFN-gamma to upregulate the breast tumor associated DF3 antigen in association with the ICAM-1 and HLA class II antigens may play an important role in eliciting an immune response which may contribute to the immunodiagnosis, and immunotherapy of breast cancer.
Regulation of the Immune Response: Production of a Soluble Suppressor by Immune Spleen Cells in Vitro (1975)

The addition of ovalbumin-immune spleen cells (Ova ISC) to sheep erythrocytes-immune spleen cells (SRBC ISC) in Mishell-Dutton-type cultures resulted in a dramatic reduction of PFC to SRBC and was dependent upon the addition of soluble Ova at low concentrations of Ova ISC. The suppressing cells in the Ova ISC were shown to be irradiation sensitive, depleted by anti-theta antiserum and complement treatment, and did not absorb to glass bead columns. Ova ISC-induced inhibition also occurred in culture chambers across a cell-impermeable membrane and a soluble inhibitor was recovered in chambers opposite the Ova ISC. This suppressor factor was sensitive to trypsin treatment and to heating at 80 degrees C, but not to 70 degrees C, for 30 min. The molecular weight, as determined by sucrose gradient analysis, was between 55,000 and 60,000 daltons. This suppressor factor appears to be distinct from a T-cell "helper" factor which was found to be sensitive to heating at 70 degrees C for 30 min. We propose that this suppressor factor participates in the termination of most immunologic responses and is responsible for the antigenic competition phenomenon.
Enforcing reference and object immutability in Java (2008)

Immutability information is useful in many software engineering tasks, such as modeling, verification, optimization, and refactoring. Furthermore, undesired mutation or side-effect are hard to detect and debug. This paper describes a javac plug-in that enables programmers to write immutability annotations in a Java program to detect and prevent bugs.
Ultrasound Gene Therapy: On the Road from Concept to Reality (2001)

The promise of gene therapy lies in the potential to ameliorate or cure conditions that are resistant to conventional therapeutic approaches. Progress in vascular and all other fields of gene therapy has been hampered by concerns over the safety and practicality of recombinant viral vectors and the inefficiency of current nonviral transfection techniques. This review summarizes the increasing evidence that exposure of eukaryotic cells to relatively modest intensity ultrasound, within the range emitted by diagnostic transducers, either alone or in combination with other nonviral techniques, can enhance transgene expression by up to several orders of magnitude over naked DNA alone. In combination with the flexibility and excellent clinical safety profile of therapeutic and diagnostic ultrasound, these data suggest that ultrasound-assisted gene delivery has great promise as a novel approach to improve the efficiency of many forms of nonviral gene delivery.
Morphology and pore control in carbon materials via templating (2011)

Carbonization of the precursors by using various templates (template carbonization) was reviewed as the process to control morphology of the carbon and pore structure in the carbon. Prospects are discussed for the processes using various templates and comparison among the processes for pore structure control is presented.
Increased brain white matter diffusivity in normal adult aging: Relationship to anisotropy and partial voluming (2003)

Diffusion tensor imaging (DTI) was used to examine 1) age-related changes in genu, splenium, and centrum semiovale white matter diffusivity in 64 healthy men and women (age 23-85 years); 2) the relationship between diffusivity (trace) and fractional anisotropy (FA) across and within individuals; and 3) the role of macrostructural and microstructural partial voluming effects on the DTI metrics. Regional differences were greater in FA (approximately 43%) than in trace (approximately 16%). Depending on the region of interest, trace increased with age (r = 0.24 to 0.58) and FA decreased with age (r = -0.29 to -0.79). FA was inversely correlated with trace, even when controlling for age. Histogram analysis of trace and FA following systematic expansion and dilation of the white matter regions demonstrated greater susceptibility of FA than trace to error arising from macrostructural partial voluming, i.e., erroneous inclusion of primarily nonwhite-matter voxels. Three-phase ellipsoid shape analysis revealed that after morphometric erosion the spherical component remained greater in older than younger subjects in the splenium and centrum, suggesting that age-related reduction in FA arises from intravoxel increased interstitial fluid. Reducing the size of the white matter samples to control for macrostructural partial voluming attenuated but did not negate effects, indicating that observed changes in white matter with aging can reflect real microstructural alterations rather than sampling artifact. Morphological dilation of white matter regions of interest resulting in purposeful inclusion of non-white matter pixels significantly reduced mean FA, suggesting that reports of FA values below 0.25 in healthy adults may reflect partial voluming rather than actual changes in white matter coherence.
Vehicle and Pedestrian Detection in eSafety Applications (2009)

Abstract—This paper describes a target detection system on road environments based on Support Vec-tor Machine (SVM) and monocular vision. The fi-nal goal is to provide pedestrian-to-car and car-to-car time gap. The challenge is to use a single camera as input, in order to achieve a low cost final system that meets the requirements needed to undertake serial production in automotive industry. The basic fea-ture of the detected objects are first located in the image using vision and then combined with a SVM-based classifier. An intelligent learning approach is proposed in order to better deal with objects vari-ability, illumination conditions, partial occlusions and rotations. A large database containing thousands of object examples has been created for learning pur-poses. The classifier is trained using SVM in order to be able to classify pedestrians, cars and trucks. In the paper, we present and discuss the results achieved up to date in real traffic conditions.
Calibration of axial length measurements with the Zeiss IOLMaster (2005)

The quality of the axial length readings of the IOLMaster was influenced by the SNR value. However, with proper SNR evaluation and recalibration of the PCI measurements, it is possible to achieve consistent PCI readings with little variation between preoperative and postoperative measurements. These results are promising for a higher accuracy of the IOL power calculation.