gebhart/patrepeval huggingface dataset:
Antimicrobial Therapy in the Context of the Damage-Response Framework: the Prospect of Optimizing Therapy by Reducing Host Damage (2019)

By design, antimicrobial agents act directly on microbial targets. These drugs aim to eliminate microbes and are remarkably effective against susceptible organisms. Nonetheless, some patients succumb to infectious diseases despite appropriate antimicrobial therapy. Today, with very few exceptions, physicians select antimicrobial therapy based on its activity against the targeted organism without consideration of how the regimen affects patients' immune responses. An important concept to emerge in the past few decades is that immune responses to microbes can be detrimental by enhancing host damage, which can translate into clinical disease. A central tenet of the damage-response framework (DRF) of microbial pathogenesis is that the relevant outcome of host-microbe interaction is the damage that occurs in the host, which can be due to microbial factors, host factors, or both. Given that host damage can make patients sick, reducing it should be a goal of treating infectious diseases. Inflammation and damage that stem from the host response to an infectious disease can increase during therapy with some antimicrobial agents and decrease during therapy with others. When a patient cannot eliminate a microbe with their own immune response, antimicrobial therapy is essential for microbial elimination, and yet it can affect the inflammatory response. In this essay, we discuss antimicrobial therapy in the context of the DRF and propose that consideration of the DRF may help tailor therapy to a patient's need to augment or reduce inflammation.
Electrophoretic Transport of Latex Particles in Lipid Nanotubes (2007)

Lipid vesicles can be connected by membrane nanotubes to build networks with promising bioanalytical properties. Here we characterize electrophoretic transport in such membrane tubes, with a particular eye to how their soft-material nature influences the intratube migration. In the absence of field, the tube radius is 110 +/- 26 nm, and it remains in this range during electrophoresis even though the applied electric field causes a slight decrease in the tube radius (approximately 6-11%). The electrophoretic velocity of the membrane wall (labeled with quantum dots) varies linearly with the field strength. Intratube migration is studied with latex spheres of radii 15, 50, 100, and 250 nm. The largest particle size does not enter the tube at fields strengths lower than 1250 V/m because the energy cost for expanding the tube around the particles is too high. The smaller particles migrate with essentially the same velocity as the membrane at low fields. Above 250 V/cm, the 15 nm particles exhibit an upward deviation from linear behavior and in fact migrate faster than in free solution whereas the 100 nm particles deviate downward. We propose that these nonlinear effects arise because of lipid adsorption to the particles (dominating for 15 nm particles) and a pistonlike compression of the solvent in front of the particles (dominating for 100 nm). As expected from such complexities, existing theories for a sphere migrating in a rigid-wall cylinder cannot explain our velocity results in lipid nanotubes.
A Variable-Spacing, Vacuum-Type Thermionic Diode (1969)

A vacuum-type thermionic diode, designed for student laboratory use, is described which features variable electrode spacing, interchangeable electrodes, and a guard-ring structure. Experiments discussed include a measurement of emitter and collector work junctions, a study of the dependence of space-charge effects on electrode spacing, and field emission studies. Results are generally reproducible and in reasonable agreement with other published data. A space-charge correlation originally developed by Houston and Webster is tested against experimental data for the first time, and a unique measurement of the Schottky parameter at elevated temperature is reported.
TU‐C‐ValB‐04: Margin‐Less Prostate IMRT Plans, Directly Optimized for TCP and NTCP Including Geometric Uncertainties (2006)

Purpose: To account for geometric uncertainties without the use of margins during IMRT planning such that optimal values are obtained for the population averaged TCP and NTCP functions. Methods and materials: A new method of computing cost functions was implemented within the IMRT planning tool Hyperion. Population‐averaged values of biologic score functions (TCP pop and NTCP pop ) are optimized, simulating random errors by blurring the dose, and systematic errors by displacing target and OARs relative to the dose distribution. For 19 prostate (and seminal vesicle) patients, treatment plans for a five beam setup were created, optimising TCP pop while constraining rectum NTCP pop and the maximum dose to the target. Gaussian distributions were used for the systematic and random errors (translations only, no attempt was made to model rotations or deformations). Since geometric uncertainties were accounted for within the cost functions, no CTV to PTV margin was used. For comparison, conventional plans were created using a CTV‐to‐PTV margin (M=2.5Σ+0.7σ) and a Simultaneous Integrated Boost (SIB) technique (68Gy to the above PTV, 78Gy to PTV boost with 5mm margin, 0mm towards rectum). The resulting plans were evaluated using an independent tool that simulates the effects of geometric uncertainties. Results: Compared to conventional plans, our new technique reduced the planned dose to the rectum, while increasing the volume receiving 78Gy. We ensured that TCP pop of the new technique was not smaller than for conventional techniques. The average rectum NTCP pop values were 14% (margin recipe), 8% (SIB), and 4% (new technique), for average TCP pop values of 69%, 70%, and 71%. Conclusions: The computation of TCP and NTCP including knowledge of geometric uncertainties within the inverse IMRT optimization loop is feasible (less than 1 hour optimization time), and results in robust prostate treatment plans with an improved balance between local control and rectum toxicity.
Vaporized H 2 O 2 decontamination against surrogate viruses for the reuse of N95 respirators in the COVID-19 emergency (2020)

Decontamination of N95 respirators has become critical to alleviate PPE shortages for healthcare workers in the current COVID-19 emergency. The factors that are considered for the effective reuse of these masks are the fit, filter efficiency and decontamination/disinfection level both for SARS-CoV-2, which is the causative virus for COVID-19, and for other organisms of concern in the hospital environment such as Staphylococcus aureus or Clostridium difficile. In its guidance entitled ‘Recommendations for Sponsors Requesting EUAs for Decontamination and Bioburden Reduction Systems for Surgical Masks and Respirators During the Coronavirus Disease 2019 (COVID19) Public Health Emergency’ (May 2020)[1], the FDA recommends a 6-log10 reduction in either the most resistant bacterial spores for the system or in a mycobacterium species to authorize the use of a decontamination method of N95 respirators for single or multiple users. While the goal is primarily inactivation against SARS-CoV-2, testing of decontamination methods against the virus may not always be available. For decontamination methods considered for only single users, the recommendation is a 6-log10 reduction in the infective virus concentration of 3 non-enveloped viruses or in the concentration of two Gram (+) and two Gram (-) bacteria. Based on these recommendations, we explored the efficacy of vaporized H2O2 (VHP) treatment of N95 respirators against surrogate viruses covering a wide range of disinfection resistance for emergency decontamination and reuse to alleviate PPE shortages for healthcare workers in the COVID-19 emergency.
Renogram comparison of p-[18F]fluorohippurate with o-[125I]iodohippurate and [99mTc]MAG3 in normal rats (2011)

Compared with [(99m)Tc]MAG3, the renogram parameters of [(18)F]PFH seem to be closer to those obtained from [(125)I]OIH. The quality of the renogram and the images obtained with the dynamic [(18)F]PFH PET study were remarkably better than those obtained with the [(99m)Tc]MAG3 dynamic planar imaging study.
Z-rays (2010)

Arrays are the ubiquitous organization for indexed data. Throughout programming language evolution, implementations have laid out arrays contiguously in memory. This layout is problematic in space and time. It causes heap fragmentation, garbage collection pauses in proportion to array size, and wasted memory for sparse and over-provisioned arrays. Because of array virtualization in managed languages, an array layout that consists of indirection pointers to fixed-size discontiguous memory blocks can mitigate these problems transparently. This design however incurs significant overhead, but is justified when real-time deadlines and space constraints trump performance. This paper proposes z-rays , a discontiguous array design with flexibility and efficiency. A z-ray has a spine with indirection pointers to fixed-size memory blocks called arraylets , and uses five optimizations: (1) inlining the first N array bytes into the spine, (2) lazy allocation, (3) zero compression, (4) fast array copy, and (5) arraylet copy-on-write. Whereas discontiguous arrays in prior work improve responsiveness and space efficiency, z-rays combine time efficiency and flexibility. On average, the best z-ray configuration performs within 12.7% of an unmodified Java Virtual Machine on 19 benchmarks, whereas previous designs have two to three times higher overheads. Furthermore, language implementers can configure z-ray optimizations for various design goals. This combination of performance and flexibility creates a better building block for past and future array optimization.
Caractérisation expérimentale de l'auto-cicatrisation des fissures dans un béton à ultra-hautes performances (2006)

ABSTRACT Self-healing of cracks in an ultra high performance concrete is investigated in this paper. An experimental program is carried out to quantify the phenomenon, which has been mainly highlighted by means of water permeability tests until now. Mechanical behaviour of self-healed concrete under 3 points bending, and acoustic emission analysis of the cracking mechanisms are reported. The mechanical tests demonstrate a recovery of the global stiffness, depending on the time of healing, for beams initially cracked and then self-healed, and a slow improvement of structural strength. The acoustic emission analysis is carried out in order to show the mechanical response of new crystals precipitating in the crack. The microcracking of these crystals during the 3 points bending tests is highlighted.
Zwitterionic Polymerization of Lactide to Cyclic Poly(Lactide) by Using N‐Heterocyclic Carbene Organocatalysts (2007)

Der Ring wird geschlossen: Die zwitterionische Ringöffnungspolymerisation von Lactid in Gegenwart N-heterocyclischer Carbene liefert gut definiertes cyclisches Polylactid (siehe Schema). Die Polymerisation verläuft schnell und resultiert unter außergewöhnlicher Kontrolle des Molekulargewichts und der Polydispersität in hoch reinen makrocyclischen Polymeren. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2001/2007/z604740_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Human Endogenous Retrovirus Expression Is Inversely Associated with Chronic Immune Activation in HIV-1 Infection (2012)

Human endogenous retroviruses (HERV) are remnants of ancestral retroviral infections integrated into the germ line, and constitute approximately 8% of the genome. Several autoimmune disorders, malignancies, and infectious diseases such as HIV-1 are associated with higher HERV expression. The degree to which HERV expression in vivo results in persistent inflammation is not known. We studied the association of immune activation and HERV-K expression in 20 subjects with chronic, untreated progressive HIV-1 infection and 10 HIV-1 negative controls. The mean HERV-K gag and env RNA expression level in the HIV-1 infected cohort was higher than in the control group (p = 0.0003), and was negatively correlated with the frequency of activated CD38+HLA-DR+CD4+ T cells (Rho = -0.61; p = 0.01) and activated CD38+HLA-DR+CD8+ T cells (Rho = -0.51; p = 0.03). Although HIV-infected persons had higher levels of HERV-K RNA expression (as expected), the level of RNA expression was negatively associated with level of T cell activation. The mechanism for this unexpected association remains to be defined.
Compressed Sensing of EEG for Wireless Telemonitoring With Low Energy Consumption and Inexpensive Hardware (2012)

Telemonitoring of electroencephalogram (EEG) through wireless body-area networks is an evolving direction in personalized medicine. Among various constraints in designing such a system, three important constraints are energy consumption, data compression, and device cost. Conventional data compression methodologies, although effective in data compression, consumes significant energy and cannot reduce device cost. Compressed sensing (CS), as an emerging data compression methodology, is promising in catering to these constraints. However, EEG is nonsparse in the time domain and also nonsparse in transformed domains (such as the wavelet domain). Therefore, it is extremely difficult for current CS algorithms to recover EEG with the quality that satisfies the requirements of clinical diagnosis and engineering applications. Recently, block sparse Bayesian learning (BSBL) was proposed as a new method to the CS problem. This study introduces the technique to the telemonitoring of EEG. Experimental results show that its recovery quality is better than state-of-the-art CS algorithms, and sufficient for practical use. These results suggest that BSBL is very promising for telemonitoring of EEG and other nonsparse physiological signals.
Analysis and control of phase-shifted series resonant converter operating in discontinuous mode (2013)

DC-DC series resonant converter operating in Discontinuous Conduction Mode (DCM) offers advantages in terms of low switching losses, high power density, and low control complexity. The low switching loss feature is lost when the converter operation shifts from DCM to Continuous Conduction Mode (CCM). This paper presents an in-depth analysis of such a converter operating in DCM and derives two boundary conditions under which the converter shifts to CCM. The fixed-frequency phase-shifted pulse width modulation is used to adjust the effective duty cycle and regulate the output voltage. Steady state analysis for above resonant frequency operation is also presented in this paper. The derived boundary conditions aid the design of the converter using which DCM operation and hence the soft switching feature is ensured at all operating points. Limits of these boundary conditions are verified using simulation and experimental results on a prototype converter.
A 256kb 6T self-tuning SRAM with extended 0.38V–1.2V operating range using multiple read/write assists and V<inf>MIN</inf> tracking canary sensors (2017)

A closed loop self-tuning 256kb 6T SRAM with 0.38V-1.2V extended operating range using combined read and write assists and canary-based V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">MIN</sub> tracking is presented. 337X and 4.3X power reductions are achieved using multiple assists and V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">MIN</sub> tracking, respectively; combining both saves 1444X in active power and 12.4X in leakage at the 0.38V.
Characterization of Emergent HIV Resistance in Treatment‐Naive Subjects Enrolled in a Vicriviroc Phase 2 Trial (2010)

In this study, only a small proportion of treatment failures were associated with tropism changes or reduced susceptibility to vicriviroc. Genotypic analysis of cloned env sequences revealed no specific mutational pattern associated with reduced susceptibility to vicriviroc, although numerous changes were observed in the variable domain 3 loop and in other regions of gp160.
INTERACTION BETWEEN CYCLOSPORINE AND FLUCONAZOLE IN RENAL ALLOGRAFT RECIPIENTS (1991)

To determine the effect of fluconazole on cyclosporine concentrations, we used a randomized, double-blind, placebo-controlled study design to evaluate 16 stable renal transplant recipients receiving a constant cyclosporine dose. The two groups of patients were given identical capsules of either placebo or fluconazole 200 mg daily for 14 days. Compliance with the protocol was ensured by watching each patient take all the drug doses. Frequent whole-blood cyclosporine trough concentrations, measured by high-performance liquid chromatography, and two area under the blood concentration time curves were determined before and after 14 days of fluconazole or placebo. The results show that cyclosporine trough concentrations, in patients given fluconazole, increased from a mean +/- SD of 27 +/- 16 to 58 +/- 28 ng/ml (P = 0.001) while patients given placebo did not change--35 +/- 26 vs. 37 +/- 35 ng/ml (P = 0.7). Mean cyclosporine AUC increased in the fluconazole patients from 2167 +/- 1039 to 3989 +/- 1675 ng.hr/ml (P = 0.02) while the placebo patients did not change, 3089 +/- 2439 vs. 2954 +/- 2216 ng.hr/ml (P = 0.9). The pre- and post-treatment cyclosporine AUC difference (day 16 minus day 2) for fluconazole vs. placebo was 1822 +/- 1083 vs. -134 +/- 831 ng.hr/ml (P = 0.001). Mean cyclosporine clearance decreased an average of 55% in the fluconazole patients from 1.2 +/- 0.5 to 0.7 +/- 0.4 ml/hr.kg (P = 0.03); the placebo patients did not change--1.4 +/- 1.1 vs. 1.7 +/- 2.3 ml/hr.kg (P = 0.07). During the study period, serum creatinine concentrations did not increase after fluconazole vs. placebo treatment; they were 1.4 +/- 0.3 vs. 1.3 +/- 0.3 mg% (P = 0.8) initially, and 1.4 +/- 0.2 vs. 1.3 +/- 0.3 mg% (P = 0.5) after 14 days. This study indicates that fluconazole 200 mg daily can slowly increase cyclosporine concentrations over two weeks of therapy, approximately doubling the cyclosporine trough concentrations. The management of this interaction requires prospective planning for adjustments in the cyclosporine dosage, guided by cyclosporine concentrations, while transplant recipients are receiving fluconazole.
Glycosidase activities in grapefruit flavedo, albedo and juice vesicles during maturation and senescence (1994)

Glycosidases were extracted from grapefruit ( Citrus paradisi Macf. cv. Ruby Red) flavedo, albedo, and juice vesicles harvested at five periods throughout the season. Flavedo β‐galactosidase activity was high at the September harvest and then significantly declined by November. Thereafter, no further changes occurred in β‐galactosidase activity. Flavedo α‐galactosidase activity was low and unchanged throughout the study. α‐Mannosidase, initially low in flavedo, steadily increased with advanced maturity. Trends in glycosidase activities of albedo were similar but attenuated. Juice vesicle β‐galactosidase did not change through the study period, whereas α‐galactosidase activity decreased 70% after the initial harvest period. α‐Mannosidase was initially high and then decreased to 50% of the original activity. A second peak of activity was measured in March, followed by a second decline. Extractability differences of the glycosidases suggest differences in compartmentation and function. Two isozymes of α‐mannosidase were separated in flavedo and one in juice vesicles, and characteristics were determined at an early and late harvest period. The results suggest that changes in the three glycosidases could be used to further define maturity and senescence in grapefruit.
Salt Effect on Substrate Specificity of a Subtilisin-Like Halophilic Protease (2010)

Enzyme-substrate interaction under the presence of high concentration of salts is of great interest for biotechnology applications and basic enzymology. In our previous work, the salt effect on halophilic subtilase SR5-3 was evaluated with Suc-AAPF-MCA and with the FRET peptide Abz-AAPFSSKQ-EDDnp. It was demonstrated that the magnitude of catalytic activity enhancement was affected by the presence of the prime site residues (Okamoto et al., 2009). In this work, a detailed analysis of the salt effect on SR5-3 protease substrate specificity was performed using chromogenic and coumarin substrates as well as FRET peptides derived from Abz-KLRSSKQ-EDDnp. The followings were demonstrated: 1) Preference of amino acid of SR5-3 protease at the P(3), P(2), P(1), P(1)' or P(2)' position of FRET substrates was almost similar with that of subtilisin. 2) Under the presence of the salts (3M NaCl or 1M Na(2)SO(4)), SR5-3 protease showed higher kcat values, lower Km values and totally 2-6 times higher kcat/Km values compared with those of control for FRET substrates, and salts did not significantly affect the preference of amino acid residues at the primary positions (P1 and P1'), but it affected the preference at the P(2) and P(2)' position. In contrast, for smaller substrates with only non-prime sites, SR5-3 protease showed 20-75 times higher kcat/Km values compared with those of control. These findings are in agreement with the notion that increases in enzyme-substrate interactions in subtilases alter the rate-determining step in peptide hydrolysis.
Supplementary Figure 2 from Human Renal Cancer Cells Express a Novel Membrane-Bound Interleukin-15 that Induces, in Response to the Soluble Interleukin-15 Receptor α Chain, Epithelial-to-Mesenchymal Transition (2023)

Supplementary Figure 2 from Human Renal Cancer Cells Express a Novel Membrane-Bound Interleukin-15 that Induces, in Response to the Soluble Interleukin-15 Receptor α Chain, Epithelial-to-Mesenchymal Transition
rt-me-fMRI: a task and resting state dataset for real-time, multi-echo fMRI methods development and validation (2021)

<ns3:p> A multi-echo fMRI dataset (N=28 healthy participants) with four task-based and two resting state runs was collected, curated and made available to the community. Its main purpose is to advance the development of methods for real-time multi-echo functional magnetic resonance imaging (rt-me-fMRI) analysis with applications in neurofeedback, real-time quality control, and adaptive paradigms, although the variety of experimental task paradigms supports a multitude of use cases. Tasks include finger tapping, emotional face and shape matching, imagined finger tapping and imagined emotion processing. This work provides a detailed description of the full dataset; methods to collect, prepare, standardize and preprocess it; quality control measures; and data validation measures. A web-based application is provided as a supplementary tool with which to interactively explore, visualize and understand the data and its derivative measures: <ns3:ext-link xmlns:ns4="http://www.w3.org/1999/xlink" ext-link-type="uri" ns4:href="https://rt-me-fmri.herokuapp.com/">https://rt-me-fmri.herokuapp.com/</ns3:ext-link> . The dataset itself can be accessed via a data use agreement on DataverseNL at <ns3:ext-link xmlns:ns4="http://www.w3.org/1999/xlink" ext-link-type="uri" ns4:href="https://dataverse.nl/dataverse/rt-me-fmri">https://dataverse.nl/dataverse/rt-me-fmri</ns3:ext-link> . Supporting information and code for reproducibility can be accessed at <ns3:ext-link xmlns:ns4="http://www.w3.org/1999/xlink" ext-link-type="uri" ns4:href="https://github.com/jsheunis/rt-me-fMRI">https://github.com/jsheunis/rt-me-fMRI</ns3:ext-link> . </ns3:p>