gebhart/patrepeval huggingface dataset:
Cold shock domain proteins and glycine-rich RNA-binding proteins from Arabidopsis thaliana can promote the cold adaptation process in Escherichia coli (2006)

Despite the fact that cold shock domain proteins (CSDPs) and glycine-rich RNA-binding proteins (GRPs) have been implicated to play a role during the cold adaptation process, their importance and function in eukaryotes, including plants, are largely unknown. To understand the functional role of plant CSDPs and GRPs in the cold response, two CSDPs (CSDP1 and CSDP2) and three GRPs (GRP2, GRP4 and GRP7) from Arabidopsis thaliana were investigated. Heterologous expression of CSDP1 or GRP7 complemented the cold sensitivity of BX04 mutant Escherichia coli that lack four cold shock proteins (CSPs) and is highly sensitive to cold stress, and resulted in better survival rate than control cells during incubation at low temperature. In contrast, CSDP2 and GRP4 had very little ability. Selective evolution of ligand by exponential enrichment (SELEX) revealed that GRP7 does not recognize specific RNAs but binds preferentially to G-rich RNA sequences. CSDP1 and GRP7 had DNA melting activity, and enhanced RNase activity. In contrast, CSDP2 and GRP4 had no DNA melting activity and did not enhance RNAase activity. Together, these results indicate that CSDPs and GRPs help E.coli grow and survive better during cold shock, and strongly imply that CSDP1 and GRP7 exhibit RNA chaperone activity during the cold adaptation process.
Cre recombinase specificity defined by the <i>tau</i> locus (2004)

We generated a transgenic mouse line (tau::Cre) by targeting the Cre to the tau locus (Mapt). Based on previous reports on the expression of Tau during development, we expected the Cre recombinase to be expressed in a neuron-specific and pan-neuronal manner. However, intercrosses between the tau::Cre and the Cre-activatable reporter animals resulted in offspring with recombination either restricted to the nervous system or throughout the entire conceptus, indicating expression of Tau early in development. The percentage of neuron-specific excision was dependent on the Cre reporter used representing different Cre target sites in the mouse genome. In spite of the observed variability, our data suggest that the tau::Cre mouse line can be used for pan-neuronal recombination of floxed alleles when it is used with caution.
Supersonic Compressor Cascades—An Analysis of the Entrance Region Flow Field Containing Detached Shock Waves (1976)

When the incoming air flow to a supersonic compressor rotor or cascade has a subsonic axial velocity component, a system of shock and Mach waves originates in the blade leading-edge region, propagates upstream of successive blades, and alters the incident flow conditions. The continuity constraint establishes a unique relationship between the incident Mach number and air flow angle. The shocks are detached and curved with blunt leading edged blades thereby violating the assumptions inherent in the classical simple wave analysis of this flow induction process. The current work employs detached shock models and a rotational flow analysis by the method of characteristics to investigate the effects of airfoil leading edge radius and cascade solidity on the unique incidence values and entrance region total pressure losses. The calculated results are compared to simple wave theory for the entrance region and it is shown that the simple wave assumptions lead to appreciable errors when detached shocks are present in the flow field.
Acetylcholine Is an Autocrine or Paracrine Hormone Synthesized and Secreted by Airway Bronchial Epithelial Cells (2004)

The role of acetylcholine (ACh) as a key neurotransmitter in the central and peripheral nervous system is well established. However, the role of ACh may be broader because ACh may also function as an autocrine or paracrine signaling molecule in a variety of nonneuronal tissues. To begin to establish ACh of nonneuronal origin as a paracrine hormone in lung, we have examined neonatal and adult monkey bronchial epithelium for the components involved in nicotinic cholinergic signaling. Using immunohistochemistry and RT-PCR, we have demonstrated in lung bronchial epithelial cells (BECs) expression of choline acetyltransferase, the vesicular ACh transporter, the choline high-affinity transporter, alpha7, alpha4, and beta2 nicotinic ACh receptor (nAChR) subunits, and the nAChR accessory protein lynx1. Confocal microscopy demonstrates that these factors are expressed in epithelial cells and are clearly distinct from neighboring nerve fibers. Confirmation of RNA identity has been confirmed by partial sequence analysis of PCR products and by cDNA cloning. Primary culture of BECs confirms the synthesis and secretion of ACh and the activity of cholinesterases. Thus, ACh meets all the criteria for an autocrine/paracrine hormone in lung bronchial epithelium. The nonneuronal cholinergic signaling pathway in lung provides a potentially important target for cholinergic drugs. This pathway may also explain some of the effects of nicotine on fetal development and also provides additional mechanisms by which smoking affects lung cancer growth and development.
The effect of nanofibre surface amine density and conjugate structure on the adhesion and proliferation of human haematopoietic progenitor cells (2011)

Previous studies have shown that substrate surface chemistry and topography exhibit significant impact on haematopoietic progenitor cell adhesion, proliferation and differentiation. In the present study, the effect of surface amine density and structure of grafted polymer chains on the adhesion and expansion of haematopoietic progenitor cells was investigated. Cryopreserved human umbilical cord blood CD133(+) cells were expanded in cytokine-supplemented medium on ethylenediamine (EDA)- or 2-aminoethyl methacrylate hydrochloride (AEMA)-grafted polyethersulphone (PES) nanofibre scaffolds for 10 days. Although the percentage of CD34(+) cells among the expanded cells increased with the surface amine density, the maximum fold expansion of CD34(+) cells was obtained at a moderate amine density of 20-80 nmol cm(-2). When comparing nanofibre matrices with similar amine densities, but prepared with two different methods, cells cultured on the AEMA-grafted PES nanofibre matrix showed lower fold expansion in terms of total cell number (300 ± 84 fold) and CD34(+) cell number (68 ± 19-fold) in comparison with those cultured on EDA-grafted nanofibres (787 ± 84-fold and 185 ± 84-fold, respectively). These results indicate that the surface amine density and the conjugate structure are important determinants for the preservation of CD34 surface marker and expansion efficiency of CD34(+) cells.
Correction of intensities for preferred orientation in powder diffractometry: application of the March model (1986)

Diffracted intensities from axially symmetric flat-plate or capillary specimens, composed of effectively rod- or disk-shaped crystallites, can be corrected for preferred orientation with a single pole-density profile. A convenient procedure is to approximate this profile with a function whose variable parameters are fit during least-squares structure refinement. Several functions have previously been suggested but without theoretical justification. The present study reviews the derivation of this method and examines its assumptions and applications. The several proposed functions are compared with each other and with the March function which describes the pole-density distribution produced by rigid-body rotation of inequant crystallites (i.e. crystallites with unequal sides) upon axially symmetric volume-conserving compression or expansion. For its basis, ease of use, single variable parameter, direct interpretability and good refinement test results, the March distribution is proposed as an advantageous pole-density profile function for general use.
Differential Effects of Fixed Instructional Ratios on Students' Progress in Reading (1991)

The impact of differential instructional ratios of known/unknown vocabulary words during a drill procedure in reading was investigated. A total of 42 average to low-average children between second and fifth grade participated in the study. Based on the model of Curriculum-based Assessment described by Gickling and Havertape (1981), a flashcard drill intervention was employed that presented known and unknown words under one of four treatment conditions: (a) 90% known to 10% unknown words; (b) 80% known to 20% unknown words; (c) 60% known to 40% unknown words; and (d) 50%o known to 50% unknown words. Pre-and posttest data were obtained on oral reading fluency, comprehension, and reading from grade-level vocabulary word lists. Additionally, bi-weekly CBM reading probes were obtained. Differences across the four conditions were evaluated at the end of an 8-week daily drill intervention. The results tended to provide partial support for Gickling's suggested drill ratios.
Task-oriented design of concentric tube robots using mechanics-based models (2012)

We introduce a method for task-oriented design of concentric tube robots, which are tentacle-like robots with the potential to enable new minimally invasive surgical procedures. Our objective is to create a robot design on a patient-specific and surgery-specific basis to enable the robot to reach multiple clinically relevant sites while avoiding anatomical obstacles. Our method uses a mechanically accurate model of concentric tube robot kinematics that considers a robot's time-varying shape throughout the performance of a task. Our method combines a search over a robot's design space with sampling-based motion planning over its configuration space to compute a design under which the robot can feasibly perform a specified task without damaging surrounding tissues. To accelerate the algorithm, we leverage design coherence, the observation that collision-free configuration spaces of robots of similar designs are similar. If a solution exists, our method is guaranteed, as time is allowed to increase, to find a design and corresponding feasible motion plan. We provide examples illustrating the importance of using mechanically accurate models during design and motion planning and demonstrating our method's effectiveness in a medically motivated simulated scenario involving navigation through the lung.
The viral transcriptional regulatory region upstream of the E6 and E7 genes is a major determinant of the differential immortalization activities of human papillomavirus types 16 and 18 (1991)

The human papillomavirus types 16 (HPV-16) and 18 (HPV-18) can immortalize primary human keratinocytes. The region of the viral genome responsible for this function maps to the E6 and E7 genes and their respective upstream transcriptional regulatory sequences, the long control regions (LCRs). The HPV-18 LCR/E6/E7 is more efficient in this immortalization function than the analogous region of the HPV-16 genome, resembling the difference in the immortalization potentials of the two full-length viral genomes. This study was designed to examine the basis for the difference in HPV-16 and HPV-18 immortalization efficiencies. The E6 and E7 genes of either HPV-16 or HPV-18, when expressed from the same heterologous promoter, immortalized primary human keratinocytes with the same low efficiency, suggesting that the difference in immortalization activities was not due to the different E6 or E7 genes themselves but rather to a difference in the transcriptional regulatory regions upstream of these genes. The analysis of a series of chimeric HPV-16 and HPV-18 LCR/E6/E7 constructs confirmed this observation and further mapped the viral element responsible for the major difference in immortalization efficiency to the transcriptional regulatory region upstream of the E6 and E7 genes.
Finite-cell-gap corrections to the capacitance analysis of liquid crystal displays with periodic interdigital electrodes (2000)

Corrections to the capacitance analysis of liquid crystal displays with periodic interdigital electrodes are presented, accounting for the finite thickness of the liquid crystal (LC) cell gap. Conformal mapping calculations of the corrected equivalent dielectric constant for the LC material and glass substrate are carried out in terms of the aperture ratio, cell gap and LC effective dielectric constant. Departure from the infinite-cell-gap approximation occurs as the gap thickness approaches the electrode width, or the aperture ratio approaches unity. The capacitance–voltage characteristic curve obtained from the conformal mapping calculations is very close to that obtained from the two-dimensional simulations with less than 5% deviation.
Fairness and efficiency in web server protocols (2003)

We consider the problem of designing a preemptive protocol that is both fair and efficient when one is only concerned with the sojourn time of the job and not intermediate results. Our Fair Sojourn Protocol (FSP) is both efficient, in a strong sense (similar to the shortest remaining processing time protocol: SRPT), and fair, in the sense of guaranteeing that it weakly outperforms processor sharing (PS) for every job on any sample path.Our primary motivation is web serving in which the standard protocol is PS, while recent work proposes using SRPT or variants. Our work suggests both a framework in which to evaluate proposed protocols and an attractive new protocol, FSP.
Cleansing Formulations That Respect Skin Barrier Integrity (2012)

Surfactants in skin cleansers interact with the skin in several manners. In addition to the desired benefit of providing skin hygiene, surfactants also extract skin components during cleansing and remain in the stratum corneum (SC) after rinsing. These side effects disrupt SC structure and degrade its barrier properties. Recent applications of vibrational spectroscopy and two-photon microscopy in skin research have provided molecular-level information to facilitate our understanding of the interaction between skin and surfactant. In the arena of commercial skin cleansers, technologies have been developed to produce cleansers that both cleanse and respect skin barrier. The main approach is to minimize surfactant interaction with skin through altering its solution properties. Recently, hydrophobically modified polymers (HMPs) have been introduced to create skin compatible cleansing systems. At the presence of HMP, surfactants assemble into larger, more stable structures. These structures are less likely to penetrate the skin, thereby resulting in less aggressive cleansers and the integrity of the skin barrier is maintained. In this paper, we reviewed our recent findings on surfactant and SC interactions at molecular level and provided an overview of the HM technology for developing cleansers that respect skin barrier.
N-Glucosylation of Cytokinins by Glycosyltransferases of Arabidopsis thaliana (2004)

Cytokinins are plant hormones that can be glucosylated to form O-glucosides and N-glucosides. The glycoconjugates are inactive and are thought to play a role in homeostasis of the hormones. Although O-glucosyltransferases have been identified that recognize cytokinins, the enzymes involved in N-glucosylation have not been identified even though the process has been recognized for many years. This study utilizes a screening strategy in which 105 recombinant glycosyltransferases (UGTs) of Arabidopsis have been analyzed for catalytic activity toward the classical cytokinins: trans-zeatin, dihydrozeatin, N(6)-benzyladenine, N(6)-isopentenyladenine, and kinetin. Five UGTs were identified in the screen. UGT76C1 and UGT76C2 recognized all cytokinins and glucosylated the hormones at the N(7) and N(9) positions. UGT85A1, UGT73C5, and UGT73C1 recognized trans-zeatin and dihydrozeatin, which have an available hydroxyl group for glucosylation and formed the O-glucosides. The biochemical characteristics of the N-glucosyltransferases were analyzed, and highly effective inhibitors of their activities were identified. Constitutive overexpression of UGT76C1 in transgenic Arabidopsis confirmed that the recombinant enzyme functioned in vivo to glucosylate cytokinin applied to the plant. The role of the N-glucosyltransferases in cytokinin metabolism is discussed.
Increased Mortality and Tuberculosis Treatment Failure Rate among Human Immunodeficiency Virus (HIV) Seropositive Compared with HIV Seronegative Patients with Pulmonary Tuberculosis Treated with “Standard” Chemotherapy in Kinshasa, Zaire (1991)

To evaluate their treatment outcomes 170 human immunodeficiency virus (HIV) seropositive and 597 HIV seronegative patients with active pulmonary tuberculosis (TB) treated for 1 yr with "standard" chemotherapy, including streptomycin, isoniazid, and, in most cases, thiacetazone, were traced at completion of therapy. All 582 survivors were invited for reevaluation, and 385 patients, of whom 82 (21.3%) were HIV seropositive, were evaluated. Of those, 325 consenting patients, of whom 67 (20.6%) were HIV seropositive, were followed for 12 months. One year after TB had been diagnosed 47 (31.3%) of the 150 HIV seropositive and 22 (4.4%) of the 501 HIV seronegative patients traced had died (p = 10(-6]. During the subsequent year the mortality of 67 HIV seropositive patients (26.3/100 patient-years) was higher than that of the 303 HIV seronegative patients (2.2/100 patients-years, p = 10(-6]. HIV seropositive patients had a higher overall TB therapy failure rate 24 months after the diagnosis of TB than did HIV seronegative patients (21.1/100 patient-years versus 8.1/100 patient-years, p = 0.002), mainly because their relapse rate of pulmonary TB (18.1/100 patient-years) was higher than that of HIV seronegative patients (6.0/100 patient-years, p = 0.03). Given their higher relapse rate after 1 yr of "standard" chemotherapy, the public health impact of routine maintenance therapy in HIV seropositive patients with pulmonary TB who complete such therapy should be assessed in comparison to the introduction of rifampicin-based short-course antituberculosis chemotherapy in developing countries.
Development and Physical Validation of a Finite Element Model of Total Hip Dislocation (1999)

Component-on-component impingement, followed by levering of the femoral head, is a common mode of dislocation in total hip arthroplasty. While there have been many registry-based studies of dislocation incidence, confounding factors and sources of variability in the clinical domain make it difficult to identify specific parameter influences. A three dimensional nonlinear finite element model has been developed for the purpose of studying the dislocation event, to allow determination of how individual factors such as component design and clinical implantation position affect the propensity for dislocation. Also, a laboratory testing apparatus was constructed to provide physical validation of the computational model. The finite element model correctly predicted the range of motion observed in the physical apparatus to within 1%, and predicted the peak resisting moment to within 2.5%. Under even a light joint load of 200 N, the von Mises stresses developed in the polyethylene insert reached 13 MPa, and the contact stresses rose to as high as 30 MPa. These deleterious elevations occurred not only at the site of neck impingement, but also at the site of head egress from the liner.
Solubility and Diffusion of Hydrogen in Pure Metals and Alloys (2001)

Basic facts are presented of the absorption of hydrogen gas by metals and the diffusion of hydrogen in metals. Specifically considered are crystalline metals without defects and lattice disorder (pure metals), low hydrogen concentrations and the possibility of high hydrogen gas pressures. The first introductory topic is a short presentation of typical phase diagrams of metal hydrogen systems. Then, hydrogen absorption is discussed and shown to be decisively determined by the enthalpy of solution, in particular by its sign which specifies whether absorption is exothermic or endothermic. The formation of high-pressure hydrogen gas bubbles in a metal, which can lead to blistering, is addressed. It is demonstrated that bubble formation will, under realistic conditions, only occur in strongly endothermically hydrogen absorbing metals. The chief aspects of hydrogen diffusion in metals are discussed, especially the large size of the diffusion coefficient and its dependence on lattice structure. It is shown that forces can act on hydrogen in metals, causing a directed hydrogen flux. Such forces arise, for instance, in the presence of stress and temperature gradients and can result in local hydrogen accumulation with potential material failure effects. The final aspect discussed is hydrogen permeation, where the absorption behavior of the hydrogen is found to be in general more decisive on the permeation rate than the value of the diffusion coefficient.
The Extended-focus, Auto-focus and Surface-profiling Techniques of Confocal Microscopy (1988)

Abstract The extended focus and auto-focus techniques of confocal microscopy, which can be used to give greatly increased depth of field, are compared. These methods rely on the use of high numerical apertures, so that the paraxial approximation is found to give inaccurate theoretical image predictions. An improved approximation is discussed and compared with exact high-angle calculations. The confocal surface-profiling technique, which allows non-invasive investigation surface topography is also considered.
A low on-resistance, high-current GaAs power VFET (1995)

We have developed a new fabrication process for GaAs VFETs that results in excellent performance in a 10 A prototype designed for switching in low voltage synchronous rectifier applications. The new fabrication process uses a buried carbon-doped GaAs gate structure for the gate electrodes and an epitaxial overgrowth step. We have demonstrated 10 A devices with 3.5 cm of gate width and 1.5 mohm of on-resistance (specific on-resistance of 84 μohm-cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> ). The device required a 0.5 μm channel etched between 0.5 μm gates placing stringent requirements on the gate side wall etch profile and epitaxial doping uniformity.
A Controlled Study of Psychopathology and Asssociated Symptoms in Tourette Syndrome (2003)

People with GTS who attend clinics have a variety of psychological symptoms that are significantly more severe than controls. Accessory symptoms (e.g. coprophenomena, echophenomena) were also very common in the subject group. Psychological symptoms may occur as part of the disease, a reaction to disability or as a result of ascertainment bias.
Bright Coppertunities: Multinuclear Cu<sup>I</sup> Complexes with N–P Ligands and Their Applications (2014)

Easy come, easy go: the great structural diversity of Cu(I) complexes is an ambivalent trait. Apart from the well-known catalytic properties of Cu(I), a great number of potent luminescent complexes have been found in the last ten years featuring a plethora of structural motifs. The downside of this variety is the undesired formation of other species upon processing. In here, strategies to avoid this behavior are presented: Only one favorable structural unit often exists for multinuclear Cu(I) complexes with bridging ligands. In addition, these complexes exhibit favorable photophysical properties due to cooperative effects of the metal halide core. Furthermore, we demonstrate the broad range of applications of emitting Cu(I) compounds.
The effects of cold-induced brain edema and white-matter ischemia on the somatosensory evoked response (1980)

The electrophysiological effects of cold-lesion edema and white-matter ischemia were studied in cats by reference to the short-latency somatosensory evoked response. The primary cortical waves were found to be considerably delayed following a period of white-matter ischemia; hosever, cold-lesion edema appeared to have no significant effect on the evoked response. The authors conclude that vasogenic edema does not interfere with axonal functioning by an ischemic mechanism.