gebhart/patrepeval huggingface dataset:
Use of the Parodi Anti-Embolism System in Carotid Stenting: Italian Trial Results (2002)

Purpose: To investigate the safety and efficacy of the Parodi anti-embolism system (PAES) in establishing flow reversal in the internal carotid artery (ICA) as a means of protecting against embolic phenomena during carotid stenting. Methods: Seven centers participated in a nonrandomized, prospective trial of carotid angioplasty and stenting under PAES protection in 30 patients (22 men; mean age 72 years, range 49–88) with 15 symptomatic (&gt;70%) and 15 asymptomatic (&gt;80%) stenotic ICAs. Safety was defined as achieving sufficient brain oxygenation during flow reversal as determined by level of awareness and motor control. The presence of new or enhanced neurological deficits and death were endpoints. Performance was based on angiographic evidence of successful retrograde flow. Results: The PAES was positioned in all 30 patients, but technical error and access-related difficulties prevented establishment of reversed flow in 2. Among the 28 (93%) patients treated under PAES protection, 1 patient developed aphasia after flow reversal, necessitating balloon deflation between subsequent stages of the procedure. Three other adverse events included 1 case of bradycardia and 2 cases of hypotension, with dysarthria and facial paresis in one and temporary loss of consciousness in the other. All events resolved with appropriate therapy, and there was no change from baseline in the neurological status or brain scans at 24 hours. There were no strokes or neurological deficits at 30 days. Conclusions: The PAES appears to be a safe and effective means of providing protection from embolic complications during carotid stenting.
P63 gene mutations and human developmental syndromes (2002)

The P63 gene is a recently discovered member of the p53 family. While P53 is ubiquitously expressed, p63 is expressed specifically in embryonic ectoderm and in the basal regenerative layers of epithelial tissues in the adult. Complete abrogation of P63 gene function in an animal model points to the relevance of P63 for the proper development of ectodermally derived tissues. The p63 knockout mouse dies at birth and has truncation of the limbs, as well as absence of epidermis, prostate, breast, and urothelial tissues, apparently reflecting ectodermal stem cell loss. A number of dominant human syndromes have been mapped to chromosome 3q27 and ultimately to mutations in the p63 gene. These syndromes have abnormal limb development and/or ectodermal dysplasia and include ectrodactyly, ectodermal dysplasia, clefting syndrome; ankyloblepharon, ectodermal dysplasia, clefting syndrome; acro-dermato-ungual-lacrimal-tooth syndrome; limb-mammary syndrome; as well as nonsyndromic split hand/foot malformation. The pattern of heterozygous mutations is distinct for each of these syndromes. Consistent with this syndrome-specific mutational pattern, the functional consequences of mutations on the p63 proteins also vary, invoking dominant-negative and gain-of-function mechanisms rather than a simple loss of function.
Evaluating treatment protocols to prevent antibiotic resistance (1997)

The spread of bacteria resistant to antimicrobial agents calls for population-wide treatment strategies to delay or reverse the trend toward antibiotic resistance. Here we propose new criteria for the evaluation of the population-wide effects of treatment protocols for directly transmitted bacterial infections and discuss different usage patterns for single and multiple antibiotic therapy. A mathematical model suggests that the long-term benefit of single drug treatment from introduction of the antibiotic until a high frequency of resistance precludes its use is almost independent of the pattern of antibiotic use. When more than one antibiotic is employed, sequential use of different antibiotics in the population ("cycling") is always inferior to treatment strategies where, at any given time, equal fractions of the population receive different antibiotics. However, treatment of all patients with a combination of antibiotics is in most cases the optimal treatment strategy.
Recombination in theompAGene but Not theomcBGene ofChlamydiaContributes to Serovar-Specific Differences in Tissue Tropism, Immune Surveillance, and Persistence of the Organism (2001)

Sequences of the major outer membrane protein (MOMP) gene (ompA) and the outer membrane complex B protein gene (omcB) from Chlamydia trachomatis, Chlamydia pneumoniae, and Chlamydia psittaci were analyzed for evidence of intragenic recombination and for linkage equilibrium. The Sawyer runs test, compatibility matrices, and index of association analyses provided substantial evidence that there has been a history of intragenic recombination at ompA including one instance of interspecies recombination between the C. trachomatis mouse pneumonitis strain and the C. pneumoniae horse N16 strain. Although none of these methods detected intragenic recombination within omcB, differences in divergence reported in earlier studies suggested that there has been intergenic recombination involving omcB, and the analyses presented in this study are consistent with this. For C. trachomatis, index-of-association analyses suggested a higher degree of recombination for C class than for B class strains and a higher degree of recombination in the downstream half of ompA. In concordance with these findings, many significant breakpoints were found in variable segments 3 and 4 of MOMP for the recombinant strains D/B120, G/UW-57, E/Bour, and LGV-98 identified in this study. We provide examples of how genetic diversity generated by repeated recombination in these regions may be associated with evasion of immune surveillance, serovar-specific differences in tissue tropism, and persistence.
Software defined batteries (2015)

Different battery chemistries perform better on different axes, such as energy density, cost, peak power, recharge time, longevity, and efficiency. Mobile system designers are constrained by existing technology, and are forced to select a single chemistry that best meets their diverse needs, thereby compromising other desirable features. In this paper, we present a new hardware-software system, called Software Defined Battery (SDB), which allows system designers to integrate batteries of different chemistries. SDB exposes APIs to the operating system which control the amount of charge flowing in and out of each battery, enabling it to dynamically trade one battery property for another depending on Application And/Or User Needs. Using microbenchmarks from our prototype SDB implementation, and through detailed simulations, we demonstrate that it is possible to combine batteries which individually excel along different axes to deliver an enhanced collective performance when compared to traditional battery packs.
Switching a spin valve back and forth by current-induced domain wall motion (2003)

We have studied the current-induced displacement of a domain wall (DW) in the permalloy (Py) layer of a Co/Cu/Py spin valve structure at zero and very small applied field. The displacement is in opposite direction for opposite dc currents, and the current density required to move DW is only of the order of 106 A/cm2. For H=3 Oe, a back and forth DW motion between two stable positions is observed. We also discuss the effect of an applied field on the DW motion.
3D intensity and phase imaging from light field measurements in an LED array microscope (2015)

Realizing high resolution across large volumes is challenging for 3D imaging techniques with high-speed acquisition. Here, we describe a new method for 3D intensity and phase recovery from 4D light field measurements, achieving enhanced resolution via Fourier ptychography. Starting from geometric optics light field refocusing, we incorporate phase retrieval and correct diffraction artifacts. Further, we incorporate dark-field images to achieve lateral resolution beyond the diffraction limit of the objective (5× larger NA) and axial resolution better than the depth of field, using a low-magnification objective with a large field of view. Our iterative reconstruction algorithm uses a multislice coherent model to estimate the 3D complex transmittance function of the sample at multiple depths, without any weak or single-scattering approximations. Data are captured by an LED array microscope with computational illumination, which enables rapid scanning of angles for fast acquisition. We demonstrate the method with thick biological samples in a modified commercial microscope, indicating the technique’s versatility for a wide range of applications.
Connection-monitor & connection-breaker: A novel approach for prevention and detection of high survivable ransomwares (2015)

Ransomwares have become a growing threat in recent years, and this situation continues to worsen. It rose awareness on a particular class of malwares which extort a ransom in exchange for a captive asset. Most widespread ransomwares make an intensive use of data encryption. Basically, they encrypt various files on victim's hard drives, removable drives and mapped network shares before asking for a ransom to get the files decrypted. In this paper, at first we propose a comprehensive ransomware taxonomy. Then, based on this taxonomy and according to a principal feature which we discovered in high survivable ransomwares (HSR) in the key exchange protocol step, we present a novel approach for detecting high survivable ransomwares and preventing them from encrypting victim's data. Experimental evaluation demonstrates that our framework can detect variants of recent dangerous ransomwares.
Design of a Wireless Assisted Pedestrian Dead Reckoning System—The NavMote Experience (2005)

In this paper, we combine inertial sensing and sensor network technology to create a pedestrian dead reckoning system. The core of the system is a lightweight sensor-and-wireless-embedded device called NavMote that is carried by a pedestrian. The NavMote gathers information about pedestrian motion from an integrated magnetic compass and accelerometers. When the NavMote comes within range of a sensor network (composed of NetMotes), it downloads the compressed data to the network. The network relays the data via a RelayMote to an information center where the data are processed into an estimate of the pedestrian trajectory based on a dead reckoning algorithm. System details including the NavMote hardware/software, sensor network middleware services, and the dead reckoning algorithm are provided. In particular, simple but effective step detection and step length estimation methods are implemented in order to reduce computation, memory, and communication requirements on the Motes. Static and dynamic calibrations of the compass data are crucial to compensate the heading errors. The dead reckoning performance is further enhanced by wireless telemetry and map matching. Extensive testing results show that satisfactory tracking performance with relatively long operational time is achieved. The paper also serves as a brief survey on pedestrian navigation systems, sensors, and techniques.
In Vivo Site-Specific DNA Methylation with a Designed Sequence-Enabled DNA Methylase (2007)

Covalent modification of DNA, such as cytosine methylation, can induce heritable gene silencing. If epigenetic modifications can be specifically targeted, new approaches to transcriptional therapy should result. To address this challenge we sought to design methyltransferases that would act only at a desired site by adapting the sequence-enabled assembly strategy. Our split DNA methylase performed site-specific CpG methylation in living cells without any background methylation when appropriately assembled at the target site. This is the first successful application of the sequence-enable enzyme reassembly approach in vivo. This split-enzyme reassembly strategy will allow creation of programmable zinc finger methylases that act at any specific CpG site in the mammalian genome. Programmable methylases should orchestrate heritable gene silencing and should find application in DNA tagging approaches and in nanotechnology.
Chaperone Probes and Bead-Based Enhancement To Improve the Direct Detection of mRNA Using Silicon Photonic Sensor Arrays (2012)

Herein, we describe the utility of chaperone probes and a bead-based signal enhancement strategy for the analysis of full length mRNA transcripts using arrays of silicon photonic microring resonators. Changes in the local refractive index near microring sensors associated with biomolecular binding events are transduced as a shift in the resonant wavelength supported by the cavity, enabling the sensitive analysis of numerous analytes of interest. We employ the sensing platform for both the direct and bead-enhanced detection of three different mRNA transcripts, achieving a dynamic range spanning over 4 orders of magnitude and demonstrating expression profiling capabilities in total RNA extracts from the HL-60 cell line. Small, dual-use DNA chaperone molecules were developed and found to both enhance the binding kinetics of mRNA transcripts by disrupting complex secondary structure and serve as sequence-specific linkers for subsequent bead amplification. Importantly, this approach does not require amplification of the mRNA transcript, thereby allowing for simplified analyses that do not require expensive enzymatic reagents or temperature ramping capabilities associated with RT-PCR-based methods.
Changes in Distance Running Kinematics with Fatigue (1991)

This study investigated changes in kinematics with fatigue during intercollegiate competition, a noncompetitive track run, and a constant speed treadmill run. To account for changes in kinematics resulting from speed differences, regression equations for each individual generated from nonfatigue data were used to predict rested kinematics for speeds matching those of the fatigue conditions. A factor analysis procedure grouped 29 kinematic variables into sets of independent factors, and both factor variables and individual variables were analyzed for changes with fatigue, which were minimal. Only one significant difference was found in the factor variables between nonfatigue and fatigue states. Comparisons of specific kinematic variables showed a significant increase in step length with fatigue, an increased maximal knee flexion angle during swing, and an increased maximal thigh angle during hip flexion. While fatigue did not result in marked changes in kinematics for the group as a whole, changes for individuals were at times large.
Critical issues in dengue vaccine development (2011)

Dengue is a unique and complex disease; developing a dengue vaccine has proven equally complex. In this review, the authors discuss issues that will prove to be critical to the success or failure of the dengue vaccine development effort.
In vivo inhibition of angiogenesis and growth of the human U-87 malignant glial tumor by treatment with an antibody against basic fibroblast growth factor (1995)

The effectiveness of in vivo suppression of neovascularization and growth of malignant glial tumors by in situ administration of an antibody directed against basic fibroblast growth factor (bFGF), a strong mitogen for cells of mesodermal origin, was tested. One hundred fifty congenitally athymic nude rats (han rnu/rnu) were implanted intracerebrally with U-87MG tumor cells, known constitutive producers of bFGF. The animals were randomly assigned to six groups of 25 animals each. Animals were treated by in situ application of saline (Group F), control antibody (Group D), or polyclonal anti-bFGF antibody (Group B). In additional groups a putative effect on tumor growth caused by the treatment application device itself (between growth control Groups A and E), and the effect of heat-inactivated tumor cells (negative control Group C) were tested. After 3 weeks of treatment, tumor progression and degree of neovascularization were morphometrically recorded. In the untreated Groups A and E massive tumor growth was recorded, consisting of 19.9% +/- 0.4% and 27.1% +/- 0.5%, respectively, of the total brain cross-sectional area. In Group C, no tumor growth occurred. In control Groups D and F tumor progression consisted of 18.6% +/- 0.4% and 18.5% +/- 0.4%, respectively, of the total brain cross-sectional area; whereas in the anti-bFGF treated Group B, significantly smaller tumor masses measuring 7.2% +/- 0.1% were recorded. New blood vessels were located both peritumorally and intratumorally and defined as numerical density and area fraction (number/area and area/area). Significantly more new blood vessels were found in Groups A, D, E, and F, ranging from 41,380/mm2 +/- 464/mm2 to 53,442/mm2 +/- 150/mm2 peritumorally and 51,846/mm2 +/- 495/mm2 to 64,660/mm2 +/- 183/mm2 intratumorally than in the anti-bFGF treated Group B, which numbered 8220/mm2 +/- 225/mm2 peritumorally and 16,554/mm2 +/- 236/mm2 intratumorally. The authors conclude that treatment with anti-bFGF antibody is effective in inhibiting tumor-induced angiogenesis and correlated tumor progression. However, owing to the character of the experimental system used, one cannot exclude the possibility that application of the specific anti-bFGF antibody also counteracts device-induced neovascularization. The authors suggest that combined surgical excision and adjuvant immunotherapy of tumors such as glioblastoma and other malignant brain tumors that express bFGF might prevent tumor recurrence.
Molecular analysis of the amy gene locus of Thermoanaerobacterium thermosulfurigenes EM1 encoding starch-degrading enzymes and a binding protein-dependent maltose transport system (1996)

A gene of Thermoanaerobacterium thermosulfurigenes EM1 encoding a protein with similarity to the maltose-binding protein of Escherichia coli was cloned and sequenced. It was located in the amy gene region of the chromosome downstream of the pullulanase-encoding amyB gene and upstream of amyDC, encoding membrane components of an ABC transport system, and the alpha-amylase gene amyA. The gene was designated amyE. Analysis of mRNA by Northern (RNA) blotting revealed that expression of the amy gene region is repressed during growth on glucose. Maximum levels of mRNA were detected with maltose as a substrate. An operon which was transcribed in the order amyBEDC was identified. However, an additional transcription start point was found in front of amyE. The amyA gene represented a monocistronic operon. Putative -35 and -10 promoter sites were deduced from the three transcription start sites of the amy gene region, and possible regulatory regions mediating induction by maltose and catabolite repression by glucose were identified by sequence analysis and comparison. The biochemical characterization of maltose uptake in T. thermosulfurigenes EM1 revealed two transport systems with Km values of 7 microM (high affinity) and 400 microM (low affinity). We conclude that the high-affinity system, which is specific for maltose and maltotriose, is a binding-protein-dependent transporter encoded by amyEDC. The gene for the putative ATP-binding protein has not yet been identified, and in contrast to similar systems in other bacteria, it is not located in the immediate vicinity of the chromosome.
In situ control of the catalyst efficiency in chemical vapor deposition of vertically aligned carbon nanotubes on predeposited metal catalyst films (2004)

Premature termination of growth, presumably because of catalyst deactivation, is an undesirable side effect of chemical vapor deposition of vertically aligned carbon nanotubes on predeposited metal catalyst films. The addition of ferrocene, an effective precursor for in situ Fe formation, was found to enhance carbon nanotube growth rates and extend growth to 3.25 mm thick carbon nanotube films. Ferrocene was introduced into the gas stream by thermal evaporation concurrently with acetylene using a specially constructed source. The key factor facilitating the growth of thick carbon nanotube films was the independent and precise control of the ferrocene amount in the feedstock. The carbon nanotube films were characterized by scanning and transmission electron microscopy, and Raman spectroscopy. The temperature dependence of the carbon nanotube growth with ferrocene exhibits a steep drop at high substrate temperatures and a loss of vertical alignment at 900 °C. The negative temperature coefficient of the growth rate suggests that the reaction mechanism of vertically aligned carbon nanotube growth is governed by a heterogeneous intermediate step.
New developments of the IMPAX small-volume automated crystallization system (1994)

Recent developments of the IMPAX system for automated crystallization are presented. A five-channel microtip has been introduced into the system thereby providing an extra degree of freedom for carrying out experiments. A new mouse-driven program for screening has been introduced, which creates a much wider scope for designing and executing screens covering new conditions of crystallization. The hardware has been adapted so that the system can also be used to set up vapour-diffusion trials. A simple design of a vapour-diffusion vessel, suitable for sitting drops of 2-15 microl, using smaller reservoir volumes (up to 100 microl), facilitates large-scale systematic trials.
Effects of nanoparticle deposition on surface wettability influencing boiling heat transfer in nanofluids (2006)

Buildup of a porous layer of nanoparticles on the heated surface occurs upon boiling of nanofluids containing alumina, zirconia, or silica nanoparticles. This layer significantly improves the surface wettability, as shown by a reduction of the static contact angle on the nanofluid-boiled surfaces compared with the pure-water-boiled surfaces. The contact angle reduction is attributed to changes in surface energy and surface morphology brought about by the presence of the nanoparticle layer. The high surface wettability can plausibly explain the boiling critical heat flux enhancement in nanofluids.
Crystallization of a Deglycosylated T Cell Receptor (TCR) Complexed with an Anti-TCR Fab Fragment (1996)

A strategy to overexpress T cell receptors (TCRs) in Lec3.2.8.1 cells has been developed using the "Velcro" leucine zipper sequence to facilitate alpha-beta pairing. Upon secretion in culture media, the VSV-8-specific/H2-Kb-restricted N15 TCR could be readily immunopurified using the anti-leucine zipper monoclonal antibody 2H11, with a yield of 5-10 mg/liter. Mass spectrometry analysis revealed that all attached glycans were GlcNAc2-Man5. Following Superdex 200 gel filtration to remove aggregates, wild-type N15 or N15(s), a C183S variant lacking the unpaired cysteine at amino acid residue 183 in the Cbeta domain, was thrombin-cleaved and endoglycosidase H-digested, and the two derivatives were termed iN15DeltaH and N15(s)DeltaH, respectively, and sized by Superdex 75 chromatography to high purity. N-terminal and C-terminal microsequencing analysis showed the expected unique termini of N15 alpha and beta subunits. Nevertheless, neither protein crystallized under a wide range of conditions. Subsequently, we produced a Fab fragment of the murine TCR Cbeta-specific hamster monoclonal antibody H57 and complexed the Fab fragment with iN15DeltaH and N15(s)DeltaH. Both N15(s)DeltaH-Fab[H57] and iN15DeltaH-Fab[H57] complexes crystallize, with the former diffracting to 2.8-A resolution. These findings show that neither intact glycans nor the conserved and partially exposed Cys-183 is required for protein stability. Furthermore, our results suggest that the H57 Fab fragment aids in the crystallization of TCRs by altering their molecular surface and/or stabilizing inherent conformational mobility.