gebhart/patrepeval huggingface dataset:
Deletion of RD1 from<i>Mycobacterium tuberculosis</i>Mimics Bacille Calmette‐Guérin Attenuation (2002)

The tuberculosis (TB) vaccine bacille Calmette-Guérin (BCG) is a live attenuated organism, but the mutation responsible for its attenuation has never been defined. Recent genetic studies identified a single DNA region of difference, RD1, which is absent in all BCG strains and present in all Mycobacterium tuberculosis (MTB) strains. The 9 open-reading frames predicted within this 9.5-kb region are of unknown function, although they include the TB-specific immunodominant antigens ESAT-6 and CFP-10. In this study, RD1 was deleted from MTB strain H37Rv, and virulence of H37Rv:DeltaRD1 was assessed after infections of the human macrophage-like cell line THP-1, human peripheral blood monocyte-derived macrophages, and C57BL/6 mice. In each of these systems, the H37Rv:DeltaRD1 strain was strikingly less virulent than MTB and was very similar to BCG controls. Therefore, it was concluded that genes within or controlled by RD1 are essential for MTB virulence and that loss of RD1 was important in BCG attenuation.
Model Reduction of Transfer Functions Using a Dominant Root Method (1990)

Transfer function methods are more efficient for solving long-time transient heat transfer problems than Euler, Crank-Nicolson, or other classical techniques. Transfer functions relate the output of a linear, time-invariant system to a time series of current and past inputs, and past outputs. Inputs are modeled by a continuous, piecewise linear curve. The computational effort required to perform a simulation with transfer functions can be significantly decreased by using the Pade´ approximation and bilinear transformation to determine transfer functions with fewer coefficients. This paper presents a new model reduction method for reducing the number of coefficients in transfer functions that are used to solve heat transfer problems. There are two advantages of this method over the Pade´ approximation and bilinear transformation. First, if the original transfer function is stable, then the reduced transfer function will also be stable. Second, reduced multiple-input single-output transfer functions can be determined by this method.
Redox-Regulation in Cancer Stem Cells (2022)

Cancer stem cells (CSCs) represent a small subset of slowly dividing cells with tumor-initiating ability. They can self-renew and differentiate into all the distinct cell populations within a tumor. CSCs are naturally resistant to chemotherapy or radiotherapy. CSCs, thus, can repopulate a tumor after therapy and are responsible for recurrence of disease. Stemness manifests itself through, among other things, the expression of stem cell markers, the ability to induce sphere formation and tumor growth in vivo, and resistance to chemotherapeutics and irradiation. Stemness is maintained by keeping levels of reactive oxygen species (ROS) low, which is achieved by enhanced activity of antioxidant pathways. Here, cellular sources of ROS, antioxidant pathways employed by CSCs, and underlying mechanisms to overcome resistance are discussed.
Recording, noise, and servo characteristics of patterned thin film media (2000)

In this paper, we present a combined experimental and micromagnetic simulation study of the recording, noise and position error signal characteristics in patterned thin film media. The medium is patterned with a focused ion beam etching technique on typical present thin film disks. It is found the transition noise is completely absent in the patterned thin film media. Comparing with continuous thin film media, the medium noise is reduced to the level of noise at saturation remnant state and is no longer density-dependent. With the elimination of transition noise, the signal-to-medium-noise ratio will be sufficient at very narrow track widths without further reduction of grain size. A slight increase of intergranular exchange coupling will have little impact on medium noise, but enhance thermal magnetic stability of the medium. Down track orientation of the crystalline easy axes will further improve the recording performances. Position error signal patterns in patterned media can be more versatile and significantly more effective and efficient.
Enhancement of Phosphorus Dopant Activation and Diffusion Suppression by Fluorine Co-Implant in Epitaxially Grown Germanium (2012)

This paper aimed to achieve both higher activation level and less diffusion by passivating the vacancies with fluorine (F) implant. The effect of F on P-doped Ge was also demonstrated. In addition, retardation of diffusion by decreased dopant-vacancy pair was indicated, although further experiments were needed with prolonged annealing time to do more detailed analysis.
PROGRESS IN THE DEVELOPMENT OF A TRILEAFLET MECHANICAL HEART VALVE (MHV) (2000)

Progress continues in the development of a trileaflet MHV (Triflo Medical, Inc., Costa Mesa, CA) that does not necessitate anticoagulation therapy. Three versions have been studied in calves: a prototype with delrin leaflets, a similar model, the T1 with pyrolytic carbon leaflets and reduced swing angle from 60° to 50° and the final version, the T2. The T2 was redesigned using flow visualization and computational fluid dynamic (CFD) analysis, in an effort to optimize the valve's hemodynamic characteristics, minimize thrombogenicity and duplicate physiologic valve closing characteristics. All versions have undergone extensive in vitro testing at the Helmholtz Institute, Aachen, Germany. A brief review of design changes and in vitro testing is presented along with the results of ongoing in vivo studies testing versions T1 and T2. In a recently completed study, 14 calves (80 to 100kgs) each received a 29mm T1 valve in the mitral position. Five experiments were ended early because of surgical complications. The intended study duration was 3 months, but 1 experiment was continued for 502 days to investigate the feasibility of in vivo leaflet wear testing. In an ongoing study involving the same calf model, seven model T2 MHVs are being tested in experiments, designed to last 5 to 6 months. Four of these experiments have been completed, 1 of which was terminated at 104 days because of infection. The other 3 are ongoing. In all full-term studies, valve performance was excellent, as evidenced by satisfactory intra-operative echocardiography findings, normal weight gain, activity and good health. In each case, I.V. heparin therapy (100mg/day) was discontinued after 10 days. Hematologically, the full-term calves remained within normal limits. At the end of the experiments, left heart catheterization showed a mean transvalvular pressure gradient of 10.52±2.21 mmHg and insignificant valvular regurgitation at heart rates from 50 to 190 bpm and cardiac outputs from 4 to 20 L/min. Gross examination of explanted valves showed no thrombus deposits. Histopathologic examination of major organs showed no evidence of thromboembolic events. Both the T1 and T2 valves performed well without long-term anticoagulation in the calf MVR model.
Coherent ultrafast spin-dynamics probed in three dimensional topological insulators (2015)

Topological insulators are candidates to open up a novel route in spin based electronics. Different to traditional ferromagnetic materials, where the carrier spin-polarization and magnetization are based on the exchange interaction, the spin properties in topological insulators are based on the coupling of spin- and orbit interaction connected to its momentum. Specific ways to control the spin-polarization with light have been demonstrated: the energy momentum landscape of the Dirac cone provides spin-momentum locking of the charge current and its spin. We investigate a spin-related signal present only during the laser excitation studying real and imaginary part of the complex Kerr angle by disentangling spin and lattice contributions. This coherent signal is only present at the time of the pump-pulses' light field and can be described in terms of a Raman coherence time. The Raman transition involves states at the bottom edge of the conduction band. We demonstrate a coherent femtosecond control of spin-polarization for electronic states at around the Dirac cone.
Identification of Small Ligands Targeting Breast Cancer by In Vivo Screening of Peptide Libraries in Breast Cancer Patients (2000)

Abstract : The purpose of this research is to develop methods of generating tumor specific small peptides that will bind to human cancers. The goal is to develop an in vivo serial selection method of tumor-binding peptides from tumor nodules following intravenous administration of peptide phage to tumor-bearing mice. In particular, following IV infusion of naive phage library, phage collected from a surgically harvested tumor were amplified and readministered to the same tumor-bearing animal. This process was repeated twice so that one naive and two enriched phage samples were administered. It was identified that phage could be successfully recovered from a tumor nodule, amplified and readministered to the same organism. The mice tolerated the serial panning procedure with relatively little toxicity. Phage recovered from the final harvested tumor (3rd pan) were sequenced and amino acid consensus sequences were identified. One of the sequences shared a motif with a reported MMP binding peptide. Based on this work, the Food and Drug Administration has approved a phase I human study utilizing the protocol of the preclinical murine model system. In addition, a clinical study, based on this preclinical work, has been funded by the National Cancer Institute and is now open for accrual.
Production of High Performance Bioinspired Silk Fibers by Straining Flow Spinning (2017)

In the last years, there has been an increasing interest in bioinspired approaches for different applications, including the spinning of high performance silk fibers. Bioinspired spinning is based on the natural spinning system of spiders and worms and requires combining changes in the chemical environment of the proteins with the application of mechanical stresses. Here we present the novel straining flow spinning (SFS) process and prove its ability to produce high performance fibers under mild, environmentally friendly conditions, from aqueous protein dopes. SFS is shown to be an extremely versatile technique which allows controlling a large number of processing parameters. This ample set of parameters allows fine-tuning the microstructure and mechanical behavior of the fibers, which opens the possibility of adapting the fibers to their intended uses.
Nonlinear Optics in AlGaAs on Insulator (2016)

AlGaAs on insulator is a powerful nonlinear platform sporting a high effective nonlinearity and the possibility to fabricate complex designs. We will present low loss waveguides enabling efficient optical signal processing and Kerr comb generation.
Late Na+ current and protracted electrical recovery are critical determinants of the aging myopathy (2015)

The aging myopathy manifests itself with diastolic dysfunction and preserved ejection fraction. We raised the possibility that, in a mouse model of physiological aging, defects in electromechanical properties of cardiomyocytes are important determinants of the diastolic characteristics of the myocardium, independently from changes in structural composition of the muscle and collagen framework. Here we show that an increase in the late Na(+) current (INaL) in aging cardiomyocytes prolongs the action potential (AP) and influences temporal kinetics of Ca(2+) cycling and contractility. These alterations increase force development and passive tension. Inhibition of INaL shortens the AP and corrects dynamics of Ca(2+) transient, cell contraction and relaxation. Similarly, repolarization and diastolic tension of the senescent myocardium are partly restored. Thus, INaL offers inotropic support, but negatively interferes with cellular and ventricular compliance, providing a new perspective of the biology of myocardial aging and the aetiology of the defective cardiac performance in the elderly.
MELAS and <scp>l</scp>‐arginine therapy: pathophysiology of stroke‐like episodes (2010)

Mitochondrial myopathy, encephalopathy, lactic acidosis, and stroke-like episodes (MELAS) is a maternally inherited multisystem mitochondrial disorder. Although many molecular and cellular mechanisms have been discovered leading to mitochondrial cytopathy, the pathogenic mechanism of stroke-like episodes seen in MELAS has not been clarified yet. According to the muscle and brain pathology and vascular physiology, mitochondrial angiopathy, or endothelial dysfunction, were proposed to play an important role for developing stroke-like episodes. Based on a hypothesis of mitochondrial angiopathy theory, we use L-arginine in MELAS patients and report its usefulness. This review aims to give a general idea on the actual knowledge about the possible pathogenic mechanism of stroke-like episodes, including clinical symptoms that lead to stroke-like episodes, muscle, or brain pathology, molecular cellular functions, neuroimagings including MRI, MRS, and SPECT, and the proposed site of action of L-arginine therapy on MELAS patients. Currently, L-arginine therapy may be the most promising for the treatment of stroke-like episodes in MELAS.
<scp>Free‐breathing</scp> high isotropic resolution quantitative susceptibility mapping (<scp>QSM</scp>) of liver using <scp>3D multi‐echo UTE</scp> cones acquisition and respiratory <scp>motion‐resolved</scp> image reconstruction (2023)

Feasibility of free-breathing liver QSM was demonstrated with motion-resolved 3D multi-echo UTE cones MRI, achieving high isotropic resolution currently unachievable in conventional Cartesian MRI.
A SPECTRAL-FILTERING APPROACH TO MUSIC SIGNAL SEPARATION (2004)

The task of separating a mix of several inter-weaving melodies from a mono recording into multiple tracks is attempted by filtering in the spectral domain. The transcribed score is provided in MIDI format a priori. In each time frame a filter is constructed for each instrument in the mix, whose effect is to filter out all harmonics of that instrument from the DFT spectrum. The complication of overlapping harmonics arising from separate notes is discussed and two filter shapes that were found to be fairly successful at separating overlapping harmonics are presented. In comparing the separated audio tracks to the original instrumental parts, signalto-residual ratios (SRR’s) in excess of 20 dB have been achieved. Audio demonstrations are on the internet [1].
Synthesis of New Cyano-Substituted bis-Benzothiazolyl Arylfurans and Arylthiophenes (2003)

The new compounds 2-[4-(6-cyanobenzothiazol-2-yl)phenyl]-5-(6-cyano-benzothiazol-2-yl)furan (6a) and 2-[4-(6-Cyanobenzothiazol-2-yl)phenyl]-5-(6-cyano-benzothiazol-2-yl)thiophene (6b) were synthesized by multi-step reactions from the corresponding 2-furan and 2-thiophene carboxaldehydes (route A), as well as from 2-furan and 2- thiophene carboxylic acids (route B). Route B involves one less step than route A, but the overall yields of the reactions are considerably lower.
Characteristics of a low-profile circular disk DRantenna with very highpermittivity (1995)

The fundamental broadside TM110 mode of an aperture-coupled circular dielectric resonator antenna is studied. By using high-dielectric-constant material, the DR antenna can be made low-profile with a relatively low resonant frequency. The return loss, radiation characteristics, antenna gain and beamwidth of the configuration are measured and discussed.
Segmental Stiffness Achieved by Three Types of Instrumented Fixation for Unstable Lumbar Spondylolytic Motion Segments (2009)

Spondylolysis is a defect in the vertebral pars interarticularis. Its cause may be developmental or due to mechanical etiologies such as trauma. Most childhood and adolescent spondylolisthesis (defined as a slip of one vertebrae relative to another) is associated with spondylolysis of the pars interarticularis at the L5–S1 motion segment.
Environmental Factors Determine Lineage Fate in a Human Model of MLL-AF9 Leukemia. (2007)

Abstract The MLL gene is fused to over 30 different fusion partners by reciprocal translocations in human acute leukemias. Some fusion partners are associated almost exclusively with myeloid or lymphoid leukemias while others are found in both. The degree to which the fusion partner contributes to the lineage of the resulting leukemia remains a matter of controversy. Using a novel model system, we demonstrate that myeloid vs lymphoid differentiation of hematopoietic progenitors transformed by MLL-AF9 can be predictably driven by cytokine combinations in vitro and in vivo. The t(9;11)(p22;q23) MLL-AF9 fusion gene is commonly associated with M5 myeloid leukemia but approximately 5% of MLL-AF9 leukemia is B-lymphoid. Expression of MLL-AF9 in human CD34+ cells enables efficient modeling of acute myeloid, B-lymphoid and biphenotypic leukemia. The lineage of the resulting leukemia can be readily manipulated in vitro (by altering the growth factors) or in vivo (using B-lymphoid-biased NOD/SCID mice or myeloid-biased NOD/SCID that are transgenic for human SCF, GM-CSF and IL-3). The cytokines IL-3, IL-7 and FLT3L appear to exert the major effects on lineage fate determination in vitro. Through limiting dilution and clonality analyses, we find a complex relationship between different leukemia stem cell compartments, with some LSC demonstrating multipotentiality and others showing strict lineage commitment. Data indicate that these differences are primarily due to microenvironment effects, with the identity of the initial cell that is targeted by MLL-AF9 possibly playing a role. These results would argue against a deterministic role for the fusion partner in MLL leukemia. This human-based system should prove useful in addressing the mechanism of lineage promiscuity of MLL leukemias. It also affords us the unique ability to determine the susceptibility of the different LSC to standard chemotherapeutic compounds, in addition to identifying novel therapeutic strategies that may be effective in treating MLL leukemia.
Incorporating organelle correlations into semi-supervised learning for protein subcellular localization prediction (2016)

Supplementary data are available at Bioinformatics online.
Hypothermia reduces ischemia- and stimulation-induced myocardial interstitial norepinephrine and acetylcholine releases (2006)

Although hypothermia is one of the most powerful modulators that can reduce ischemic injury, the effects of hypothermia on the function of the cardiac autonomic nerves in vivo are not well understood. We examined the effects of hypothermia on the myocardial interstitial norepinephrine (NE) and ACh releases in response to acute myocardial ischemia and to efferent sympathetic or vagal nerve stimulation in anesthetized cats. We induced acute myocardial ischemia by coronary artery occlusion. Compared with normothermia (n = 8), hypothermia at 33 degrees C (n = 6) suppressed the ischemia-induced NE release [63 nM (SD 39) vs. 18 nM (SD 25), P < 0.01] and ACh release [11.6 nM (SD 7.6) vs. 2.4 nM (SD 1.3), P < 0.01] in the ischemic region. Under hypothermia, the coronary occlusion increased the ACh level from 0.67 nM (SD 0.44) to 6.0 nM (SD 6.0) (P < 0.05) and decreased the NE level from 0.63 nM (SD 0.19) to 0.40 nM (SD 0.25) (P < 0.05) in the nonischemic region. Hypothermia attenuated the nerve stimulation-induced NE release from 1.05 nM (SD 0.85) to 0.73 nM (SD 0.73) (P < 0.05, n = 6) and ACh release from 10.2 nM (SD 5.1) to 7.1 nM (SD 3.4) (P < 0.05, n = 5). In conclusion, hypothermia attenuated the ischemia-induced NE and ACh releases in the ischemic region. Moreover, hypothermia also attenuated the nerve stimulation-induced NE and ACh releases. The Bezold-Jarisch reflex evoked by the left anterior descending coronary artery occlusion, however, did not appear to be affected under hypothermia.
Semi-automatic cone beam CT segmentation of<i>in vivo</i>pre-clinical subcutaneous tumours provides an efficient non-invasive alternative for tumour volume measurements (2015)

This is the first study evaluating tumour volume assessment of pre-clinical subcutaneous tumours in different anatomical sites using on-board CBCT imaging. We also compared the accuracy of the CBCT method to manual calliper measures, using various volume calculation equations.
Influence of Process Parameters on the Thermophysical Properties of C/C‐SiC (2001)

This paper reports upon the influence of various C-fibers, precursors and annealing process parameters of C/C as well as the microstructure, obtained by pretreating C-fibers, on the thermophysical properties of C/C-SiC. Therefore, C-fabrics were used as received or thermally pretreated and submitted to LSI-processing. Another route is to graphitize the C/C intermediate with subsequent siliconizing [4,5]. Due to the fact that the thermal conductivity (TC) of carbon fibers after graphitization can be higher than that of SiC the dominating contribution to the TC of the composite is expected from the fibers. Because of the pronounced orientation of the fibers in one plane there is a strong anisotropy of the TC parallel and transversal to main fiber orientation, whereby the values parallel to the fibers are by a factor 2 to 3 higher compared to transversal direction [6]. In this paper, only the results of measurements in transversal direction are presented.
Beginning a Special Year for Our Society [From the Editor] (2023)

First, I would like to wish you and your loved ones a nice new year filled with health and happiness. The last few years have been challenging for various reasons: the COVID-19 pandemic, climatic events, and the war in Ukraine, to name a few. It seems impossible to be able to stop the megalomania and madness of some human beings. It also seems difficult to reverse climate changes brought on by habits that we would have to radically change and industrial lobbying focused solely on profits at whatever cost. I fear that based on all of the disasters we have been experiencing, no one sound person can challenge the climate changes taking place around the world.
Upgrading of oxygenated compounds present in aqueous biomass-derived feedstocks over NbO<sub>x</sub>-based catalysts (2017)

Oxygenated organic compounds in biorefinery aqueous effluents are transformed into a mixture of hydrocarbon fuel precursors by using a Nb oxide catalyst.
Apoptosis of Malignant Human B Cells by Ligation of CD20 With Monoclonal Antibodies (1998)

CD20 is a nonglycosylated 33 to 37 kD phosphoprotein involved in B-cell signaling that subserves important functions in the regulation of B-cell proliferation and differentiation. In addition, this B-cell surface antigen has been shown recently to be an effective target for immunotherapy of B-cell malignancies using chimeric (mouse/human) or radiolabeled murine monoclonal anti-CD20 antibodies. In this report we show that extensive crosslinking of CD20 with murine anti-CD20 monoclonal antibodies (MoAbs) in the presence of either goat anti-mouse IgG or Fc receptor (FcR)-expressing cells directly inhibits B-cell proliferation, induces nuclear DNA fragmentation, and leads to cell death by apoptosis. The apoptotic effects of these MoAbs can be inhibited by chelation of extracellular or intracellular Ca2+ by EGTA or Bapta AM, indicating that anti-CD20–mediated apoptosis may be related to changes in Ca2+ concentration. These findings suggest that ligation of CD20 in vivo by anti-CD20 antibodies in the presence of FcR-expressing cells may initiate signal transduction events that induce elevation of [Ca2+]i and lead to apoptosis of malignant B cells, thereby contributing to the impressive tumor regressions observed in mouse models and clinical trials using anti-CD20 MoAbs.