gebhart/patrepeval huggingface dataset:
Effects of megakaryocyte colony-stimulating factor on terminal cytoplasmic maturation of human megakaryocytes. (1987)

Suspensions of enriched human megakaryocytes (MK) devoid of MK progenitors (CFU-MK) undergo complete cytoplasmic maturation in vitro. MK were cultured in the presence of normal human AB serum (NABS) to mimic "normal" development. The rate of maturation was not statistically altered by higher concentrations (10%-20%-30%) of NABS, or by the addition of bovine serum albumin (1.5%-3.0%), but was accelerated in the presence of aplastic anemia serum (AAS). Sera from eight different patients with severe aplastic anemia were effective in accelerating terminal differentiation. MK-CSF, a glycoprotein isolated from AAS, specifically augments MK colony formation by two- to sixfold. Similar doses of MK-CSF were ineffective in altering terminal cytoplasmic maturation. Anti-MK-CSF, a polyclonal antibody prepared against purified MK-CSF, neutralizes the ability of both purified MK-CSF and AAS to promote MK colony formation. However, AAS adsorbed with anti-MK-CSF still retained its ability to accelerate terminal differentiation. Apparently, AAS contains at least two separate humoral factors, which can regulate in vitro human megakaryocytopoiesis: MK-CSF, which stimulates proliferation of the progenitors (CFU-MK), and a maturation factor, which accelerates cytoplasmic maturation of morphologically recognizable megakaryocytes.
Specific C-Receptors for Itch in Human Skin (1997)

In microneurography experiments 56 unmyelinated nerve fibers were studied in the cutaneous branch of the peroneal nerve of healthy volunteers. Units were identified with the "marking" technique as mechanically and heat-responsive (CMH; n = 30), heat-responsive (CH; n = 13), or unresponsive to mechanical and heat stimulation (CMiHi; n = 13). None of the units showed spontaneous activity. These units were tested for responsiveness to iontophoresis of histamine (1 mA, 20 sec) from a small probe (diameter, 6 mm), which induced itch sensations lasting several minutes. Twenty-three units were unresponsive to histamine, and 25 units responded weakly with a few spike discharges after iontophoresis. Eight units, however, responded with sustained discharges to histamine, and their discharge patterns were matching the time course of the itch sensations. All C-units in this group were mechanically insensitive, and five of them were heat-responsive. They had very low conduction velocities of only 0.5 m/sec, on average, which is significantly lower than conduction velocities of the "polymodal" CMH units. This slow conduction velocities attributable to small axon diameters may be one reason why these units have not been encountered in previous studies. Histamine-sensitive C-units had very large innervation territories extending up to a diameter of 85 mm on the lower leg. We conclude that these C-fibers represent a new class of afferent nerve fibers with particularly thin axons but excessive terminal branching. This type of C-fiber probably represents the afferent units long searched for mediating itch sensations.
Comparisons of the Variability of Three Markers of the Human Circadian Pacemaker (2002)

A circadian pacemaker within the central nervous system regulates the approximately 24-h physiologic rhythms in sleep cycles, hormone secretion, and other physiologic functions. Because the pacemaker cannot be examined directly in humans, markers of pacemaker function must be used to study the pacemaker and its response to environmental stimuli. Core body temperature (CBT), plasma cortisol, and plasma melatonin are three marker variables frequently used to estimate the phase of the human pacemaker. Measurements of circadian phase using markers can contain variability due to the circadian pacemaker itself, the intrinsic variability of the marker relative to the pacemaker, the method of analysis of the marker, and the marker assay. For this report, we compared the mathematical variability of a number of methods of identifying circadian phase from CBT, plasma cortisol, and plasma melatonin data collected in a protocol in which pacemaker variability was minimized using low light levels and regular timing of both the light pattern and the rest/activity schedule. We hoped to assess the relative variabilities of the different physiological markers and the analysis methods. Methods were based on the crossing of an absolute threshold, on the crossing of a relative threshold, or on fitting a curve to all data points. All methods of calculating circadian phase from plasma melatonin data were less variable than those calculated using CBT or cortisol data. The standard deviation for the phase estimates using CBT data was 0.78 h, using cortisol data was 0.65 h, and for the eight analysis methods using melatonin data was 0.23 to 0.35 h. While the variability for these markers might be different for other subject populations and/or less stringent study conditions, assessment of the intrinsic variability of the different calculations of circadian phase can be applied to allow inference of the statistical significance of phase and phase shift calculations, as well as estimation of sample size or statistical power for the number of subjects within an experimental protocol.
Assessing EOR Potential from Partitioning Tracer Data (2015)

Abstract In development of mature oil fields using enhanced oil recovery (EOR) techniques, one of the challenges is to quantify remaining oil and to evaluate the potential gain of EOR in pilot studies. One of the proven technologies to estimate remaining amounts of oil is the single-well chemical tracer test (SWCTT). During such push-and-pull tests, oil/water partitioning ester partially hydrolyses to a non-partitioning water tracer. A time-lag in back-production time between the injected ester and the alcohol generated in-situ yields remaining oil saturation (ROS) through a simple relation. A similar time-lag technique is used in partitioning inter-well tracer tests (PITTs), where tracers are injected into injectors and sampled in producers. New and stable, oil-water partitioning tracers suitable for oil reservoir PITTs have been recently developed and field tested (SPE164059), allowing measurement of remaining oil saturation in inter-well regions. This paper reviews methodology to assess oil saturation in both near-well and inter-well regions of an oil reservoir, and highlights the differences and similarities of partitioning near-well and inter-well tracer tests that can be used to evaluate the potential gain from an EOR-operation. SWCTTs and PITTs target different scales of an oil field, as a SWCTT explores the near well zone, up to a few meters, and a PITT explore an inter-well region. In order to assess information on both these scales we propose a systematic procedure for oil saturation measurement, using partitioning tracers. The procedure involves use of PITTs and systematic residence time distribution (RTD) interpretation of tracer production curves to extract information about remaining oil saturation and the distribution of this saturation in an oil field. The procedure is validated using the tracer data recently reported by Viig et al. (SPE164059).
Transforming growth factor-β in critical illness (2005)

From the Department of Surgery, University of Pittsburgh, Pittsburgh, PA. Both authors are supported by a NIAID grant. Dr. Vodovotz has consulted for Immunetrics, Inc. and holds stock and equity interest in the company. He has also received a grant from Pittsburgh Lifesciences Greenhouse to Immunetrics, Inc., and has filed a patent application for an algorithm estimating the outcome of inflammation following injury or infection. Dr. Zamora has no financial interests to disclose.
Preparation and Corrosion Performance of PEO Coating With Low Porosity on Magnesium Alloy AZ91D In Acidic KF System (2011)

A plasma electrolytic oxidation (PEO) ceramic coating F-B-A with excellent compactness was prepared on magnesium alloy AZ91D in acidic KF solution with dihydric phosphate by applying a bi-polar pulse voltage. For comparison, two other coatings F-M and F-M-A were prepared in the same solution with and without addition of dihydric phosphate by applying a mono-polar pulse voltage. The composition and microstructure of the coatings were characterized by XRD, XPS and SEM. While their corrosion performance in 3.5% NaCl solution was examined by potentiodynamic polarization and electrochemical impedance spectroscopy (EIS). Results showed that the F-B-A coating was uniform and compact without fissures on surface, and its porosity was around 4.8%; while the other coatings were loose and porous with porosity around 45.6% and 27.9%, respectively. The F-B-A coating showed a bi-layered microstructure, of which the outer consisted mainly of KMgF3 and MgF2 with seldom MgO, whereas, the inner mainly of MgF2, Mg3 (PO4)2, MgHPO4 and little MgO. The magnesium alloy with F-B-A coating exhibited corrosion resistance about three orders higher than the sample with the F-M coating. EIS tests indicated that this bi-layered coating slowed down the penetration rate of chlorine ions and postponed the initiation of pitting corrosion on substrate.
Synthetic peptides of human lysosomal cathepsin G with potent antipseudomonal activity (1993)

Enzymatically active and inactive (diisopropylfluorophosphate-treated) cathepsin G exerted antibacterial action in vitro against Staphylococcus aureus, whereas only enzymatically active cathepsin G displayed bactericidal action against Pseudomonas aeruginosa. In order to further test the requirement for protease activity for the antipseudomonal action of cathepsin G, synthetic peptides spanning the full-length mature protein were prepared and examined for antibacterial action. Surprisingly, three structurally distinct peptides that correspond to residues 61 to 80, 117 to 136, and 198 to 223 within the full-length protein were found to exert potent antipseudomonal action (> 4.5 logs of killing at 500 micrograms/ml) against P. aeruginosa ATCC 27853 and four mucoid clinical isolates. Only the peptide (CG117-136) corresponding to residues 117 to 136 (117-RPGTLCTVAGWGRVSMRRGT-136) within cathepsin G exerted antibacterial action against the gram-positive pathogen S. aureus. The antipseudomonal action of CG117-136 was rapid and could be inhibited either by increasing concentrations of NaCl or by 0.5 mM MgCl2 plus 0.5 mM CaCl2, and these conditions appeared to reduce binding of the peptide to whole bacteria. Variants of peptide CG117-136 lacking either a hydrophobic N-terminal domain or a positively charged C-terminal domain were found to have significantly less antipseudomonal action than CG117-136. The antibacterial capacity of the all-D-enantiomeric form of peptide CG117-136 was found to be identical to that of the all-L-peptide, suggesting that the mechanism of killing does not require the recognition of a target site possessing a chiral center.
Maintaining Patient Confidentiality When Sharing Medical Data Requires a Symbiotic Relationship Between Technology and Policy (2018)

Often organizations release and receive medical data with all explicit identifiers, such as name, address, phone number, and Social Security number, removed in the incorrect belief that patient confidentiality is maintained because the resulting data look anonymous; however, we show that in most of these cases, the remaining data can be used to re-identify individuals by linking or matching the data to other databases or by looking at unique characteristics found in the fields and records of the database itself. When these less apparent aspects are taken into account, each released record can be made to ambiguously map to many possible people, providing a level of anonymity which the user determines; the greater the number of candidates per record, the more anonymous the data. We examine three general-purpose computer programs for maintaining patient confidentiality when disclosing electronic medical records: the Scrub System which locates personally-identifying information in letters between doctors and notes written by clinicians; the Datafly System which generalizes values based on a profile of the recipient at the time of access; and, the Mu-Argus System which is becoming a European standard for disclosing public use data. Despite the possible effectiveness of these systems, completely anonymous data may not contain sufficient details for all uses, so care must be taken when released data can identify individuals and such care must be enforced by coherent policies and procedures.
Arsenic Trioxide Liposomes: Encapsulation Efficiency and In Vitro Stability (2004)

The use of arsenic-containing compounds in cancer therapy is currently being re-considered, after the recent approval of arsenic trioxide (Trisenox) for the treatment of relapsed promyelocytic leukemia (PML). In an attempt to prepare a carrier system to minimize the toxicity of this drug, the aim of this study is to prepare and characterize liposomes encapsulating arsenic trioxide (ATO). For this, we prepared different types of liposomes entrapping ATO: large multilamellar (MLV), sonicated (SUV) and dried reconstituted vesicles (DRV). The techniques used were: thin film hydration, sonication and the DRV method, respectively. Two lipid compositions were studied for each liposome type, EggPC/Chol (1:1) and DSPC/Chol (1:1). After liposome preparation, drug encapsulation was evaluated by measuring arsenic in liposomes. For this, energy-dispersive X-ray fluorescence spectroscopy or atomic absorption was used. In addition, the retention of the drug in the liposomes was evaluated after incubating the liposomes in buffer at 37 degrees C. The experimental results reveal that encapsulation of ATO in liposomes ranges between 0.003 and 0.506 mol/ mol of lipid, and is highest in the DRV vesicles and lowest in the small unilamellar vesicles, as anticipated. Considering the in vitro stability of ATO-encapsulating liposomes: 1) For the PC/Chol liposomes (DRV and MLV), after 24 hours of incubation, more than 70% (or 90% in some cases) of the initially encapsulated amount of ATO was released. 2) The liposomes composed of DSPC/Chol could retain substantially higher amounts of ATO, especially the DRV liposomes (54% retained after 24 h). 3) In the case of PC/Chol, temperature of incubation has no effect on the ATO release after 24 hours, but affects the rate of ATO release in the MLV liposomes, while for the DSPC/Chol liposomes there is a slight increase (statistically insignificant) of ATO release at higher temperature.
Cloning of the egl gene of Pseudomonas solanacearum and analysis of its role in phytopathogenicity (1988)

The egl gene of Pseudomonas solanacearum was cloned on a cosmid and expressed in Escherichia coli. Restriction endonuclease mapping, transposon mutagenesis, and subclone analysis showed that the egl gene was located on a 2.7-kilobase XhoI-SalI P. solanacearum DNA fragment. Immunoabsorption experiments and sodium dodecyl sulfate-polyacrylamide gel electrophoretic analysis showed that the egl gene encodes the 43-kilodalton endoglucanase that is the major excreted endoglucanase of P. solanacearum. In E. coli, the egl gene appeared to be expressed from its own promoter, but its product was restricted to the cytoplasm. The cloned egl gene was mutagenized with Tn5 and used to specifically mutate the chromosomal egl gene of P. solanacearum by site-directed mutagenesis. The resultant mutant was identical to the wild-type strain in production of extracellular polysaccharide and extracellular polygalacturonase as well as several other excreted proteins but produced at least 200-fold less endoglucanase. This mutant strain was significantly less virulent on tomato than the wild-type strain in plant bioassay experiments. Virulence of the endoglucanase-deficient strain was restored to near wild-type levels by complementation in trans with the cloned egl gene, indicating that the egl gene is important but not absolutely required for pathogenesis.
Fusion to a highly charged proteasomal retargeting sequence increases soluble cytoplasmic expression and efficacy of diverse anti-synuclein intrabodies (2012)

Intrabodies can be powerful reagents to effect modulation of aberrant intracellular proteins that underlie a range of diseases. However, their cytoplasmic solubility can be limiting. We previously reported that overall charge and hydrophilicity can be combined to provide initial estimates of intracellular solubility, and that charge engineering via fusion can alter solubility properties experimentally. Additional studies showed that fusion of a proteasome-targeting PEST motif to the anti-huntingtin intrabody scFv-C4 can degrade mutant huntingtin proteins by directing them to the proteasome, while also increasing the negative charge. We now validate the generality of this approach with intrabodies against α-synuclein (α-syn), an important target in Parkinson disease. In this study, fusion of the PEST sequence to a set of four diverse, poorly soluble anti-α-syn intrabodies (D5E, 10H, D10 scFv, VH14 nanobody) significantly increased steady-state soluble intrabody protein levels in all cases, despite fusion with the PEST proteasomal-targeting signal. Furthermore, adding this PEST motif to the least soluble construct, VH14, significantly enhanced degradation of the target protein, α-syn~GFP. The intrabody-PEST fusion approach thus has dual advantages of potentially solubilizing intrabodies and enhancing their functionality in parallel. Empirical testing of intrabody-PEST fusions is recommended for enhancement of intrabody solubility from diverse sources.
T cell development and activation in Jak3-deficient mice (1998)

Jak3, a member of the Janus family of tyrosine kinases, participates in signaling through cytokine receptors that contain the common gamma-chain, including the receptors for interleukin (IL)-2, IL-4, IL-7, IL-9, and IL-15. Jak3- and gamma c-deficient mice have pleiotropic defects that can be attributed to their inability to respond to multiple specific cytokines. A great deal of recent work has focused on the T cell defects in these mutant mice. Specifically, Jak3- and gamma c-deficient mice have small thymuses revealing a defect in T cell development, and in addition, have functionally unresponsive peripheral T cells with an activated/memory cell phenotype. The thymic defect in these mutant mice strongly resembles that seen in IL-7 and IL-7 receptor knockout mice, suggesting that the lack of IL-7 receptor signaling accounts for this defect in Jak3-/- and gamma c- mice. To characterize this defect further, we have examined the earliest stages of T cell development in adult and fetal Jak3-/- thymuses. These studies identify two discrete developmental defects at the CD4-CD8- stage of T cell maturation. Analyses of peripheral T cells in Jak3-/- and gamma c- mice have also revealed a number of abnormalities. All of the T cells in these mutant mice have an activated phenotype and a large fraction of them are proliferating in vivo. In addition, Jak3-/- and gamma c- T cells are more prone to undergo apoptosis than wild-type T cells. Together, these features account for the decreased IL-2 secretion by in vitro-stimulated Jak3-/- T cells. Overall, many of the lymphoid defects of Jak3- and gamma c-deficient mice can be accounted for by the lack of IL-7R and IL-2R signaling; however, other cytokine systems must also be involved in maintaining peripheral T cell homeostasis.
Measuring MEG closer to the brain: Performance of on-scalp sensor arrays (2016)

Optically-pumped magnetometers (OPMs) have recently reached sensitivity levels required for magnetoencephalography (MEG). OPMs do not need cryogenics and can thus be placed within millimetres from the scalp into an array that adapts to the individual head size and shape, thereby reducing the distance from cortical sources to the sensors. Here, we quantified the improvement in recording MEG with hypothetical on-scalp OPM arrays compared to a 306-channel state-of-the-art SQUID array (102 magnetometers and 204 planar gradiometers). We simulated OPM arrays that measured either normal (nOPM; 102 sensors), tangential (tOPM; 204 sensors), or all components (aOPM; 306 sensors) of the magnetic field. We built forward models based on magnetic resonance images of 10 adult heads; we employed a three-compartment boundary element model and distributed current dipoles evenly across the cortical mantle. Compared to the SQUID magnetometers, nOPM and tOPM yielded 7.5 and 5.3 times higher signal power, while the correlations between the field patterns of source dipoles were reduced by factors of 2.8 and 3.6, respectively. Values of the field-pattern correlations were similar across nOPM, tOPM and SQUID gradiometers. Volume currents reduced the signals of primary currents on average by 10%, 72% and 15% in nOPM, tOPM and SQUID magnetometers, respectively. The information capacities of the OPM arrays were clearly higher than that of the SQUID array. The dipole-localization accuracies of the arrays were similar while the minimum-norm-based point-spread functions were on average 2.4 and 2.5 times more spread for the SQUID array compared to nOPM and tOPM arrays, respectively.
The effects of affinity and valency of an albumin-binding domain (ABD) on the half-life of a single-chain diabody-ABD fusion protein (2010)

Fusion of small recombinant antibody fragments to an albumin-binding domain (ABD) from streptococcal protein G strongly extends their plasma half-life. This ABD binds with nanomolar affinity to human (HSA) and mouse serum albumin (MSA). It was speculated that an increase in albumin-binding affinity should lead to a further increase in half-life. In the present study, we analyzed the effects of affinity and valency of the ABD on the pharmacokinetic properties of a bispecific single-chain diabody (scDb), applied previously to investigate various half-life extension strategies. The scDb is directed against carcinoembryonic antigen (CEA) and CD3 capable of mediating T cell retargeting to tumor cells. Two scDb derivatives with increased (scDb-ABD-H) and decreased (scDb-ABD-L) affinity as well as an scDb molecule fused to two ABD (scDb-ABD(2)) were generated and produced in mammalian cells. The altered binding of these constructs to HSA and MSA was confirmed by ELISA and quartz crystal microbalance measurements. All constructs bound efficiently to CEA and CD3-positive cells and were able to activate T cells in a target cell-dependent manner, although T cell activation was reduced in the presence of serum albumin. All three derivatives showed a strongly increased half-life in mice as compared with scDb. Compared with the wild-type scDb-ABD, the half-life of scDb-ABD-H exhibited a prolonged half-life and scDb-ABD-L a reduced half-life, while the half-life scDb-ABD(2) was almost identical to that of scDb-ABD. However, these changes were only moderate, indicating that the half-life-extending property of the ABD in mice is only weakly influenced by affinity for serum albumin or valency of albumin binding.
Smart vision sensors (2002)

Smart vision sensors represent a niche in machine vision where high performance in terms of frame rates, processing speed, and flexibility is the most essential feature. With the integration of photosensitive devices with processing elements on one and the same substrate it is possible to reach high performance at low complexity and low cost. The MAPP2500 from IVP represents state of the art in this development of CMOS imaging and on-chip processing.