gebhart/patrepeval huggingface dataset:
An Isolated Rat Liver Model for the Evaluation of Thermal Techniques to Quantify Perfusion (1984)

An isolated, thermally regulated, perfused rat liver model system is presented. The model was developed to evaluate thermal methods to quantify perfusion in small volumes of tissue. The surgically isolated rat liver is perfused with an isothermal oxygenated Krebs-Ringer bicarbonate buffer solution via the cannulated portal vein. A constant-pressure head variable-resistance scheme is utilized to control the total flow to the liver. Total flow is quantified by hepatic vein collection. The spatial distribution of perfusion within the liver is determined using two independent methods. In the first method, radio-labelled microspheres are injected into the portal vein, and the regional flow distribution is determined from the relative radioactivity of each section of tissue. In the second method, the tissue is thermally perturbed, and the time constant of the tissue temperature recovery is measured. The regional distribution is determined from the relative time constants of each section of tissue. Both methods require the measurement of total liver flow to determine the absolute perfusion at each point. Results obtained by the two methods were well correlated (0.973). The rat liver system offers a stable, controllable, and measurable perfusion model for the evaluation of new perfusion measurement techniques.
Superresolution HRR ATR with high definition vector imaging (2001)

A new 1-D template-based automatic target recognition (ATR) algorithm is developed and tested on high range resolution (HRR) profiles formed from synthetic aperture radar (SAR) images of targets taken from the Moving and Stationary Target Acquisition and Recognition (MSTAR) data set. In this work, a superresolution technique known as High Definition Vector Imaging (HDVI) is applied to the HRR profiles before the profiles are passed through ATR classification. The new I-D ATR system using HDVI demonstrates significantly improved target recognition compared with previous I-D ATR systems that use conventional image processing techniques. This improvement in target recognition is quantified by improvement in probability of correct classification (PCC). More importantly, the application of HDVI to HRR profiles helps to maintain the same ATR performance with reduced radar resource requirements.
The Healing Effects of Autologous Platelet Gel on Acute Human Skin Wounds (2007)

clinicaltrials.gov Identifier: NCT00199992.
Putative Precursors of Vasopressin, Oxytocin, and Neurophysins in the Rat Hypothalamus* (1981)

The biosynthesis of [arginine8]vasopressin (AVP) and oxytocin (OT) was studied, and the results obtained have been compared with a study of their associated neurophysins (NP), AVP-NP and OT-NP. Rat hypothalamic extracts obtained at acid pH were subjected to Sephadex G-75 gel filtration chromatography and sodium dodecyl sulfate (SDS)-polyacrylamide gel electrophoresis (PAGE). Fractions of gel chromatography effluent and extract of SDS-PAGE gel slices were subjected to RIA for immunoreactive precursors of AVP, AVP-NP, OT, and OT-NP using specific antisera fro each molecule. Tritiated bovine serum albumin, ovalbumin, and cytochrome c were used as internal standards during gel filtration chromatography and SDS-PAGE. Molecular weight estimates obtained for precursors of AVP were more than 70K, 31K, 13K, 5K, and less than 5K (AVP) by G-75 chromatography and more than 70K, 39K, 15K, and less than 5K (AVP) by SDS-PAGE. Molecular weight estimates obtained for precursors of AVP-NP were more than 70K, 35K, 24K, and 12K (AVP-NP) by G-75 chromatography and 19K and 10K (AVP-NP) by SDS-PAGE. Molecular weight estimates of OT were more than 70K, 35K, 19K, 8K, and less than 5K (OT) by G-75 chromatography and 60K, 35K, 19K, 9K, and less than 5K (OT) by SDS-PAGE. Precursors of OT-NP were estimated to be more than 70K, 17-18K, and 10K (OT-NP) by G-75 chromatography and 28K, 18K and 10K (Ot-NP) by SDS-PAGE. These studies show that there are small differences in precursor processing among AVP, AVP-NP, and OT, OT-NP, but allow for the existence of common precursors for AVP and AVP-NP and for OT and OT-NP.
Engineered Exosomes for Delivery of Therapeutic siRNAs to Neurons (2018)

Extracellular vesicles (EVs), exosomes and microvesicles, transfer endogenous RNAs between neurons over short and long distances. We have explored EVs for siRNA delivery to brain. (1) We optimized siRNA chemical modifications and siRNA conjugation to lipids for EV-mediated delivery. (2) We developed a GMP-compatible, scalable method to manufacture active EVs in bulk. (3) We characterized lipid and protein content of EVs in detail. (4) We established how protein and lipid composition relates to siRNA delivering activity of EVs, and we reverse engineered natural exosomes (small EVs) into artificial exosomes based on these data. We established that cholesterol-conjugated siRNAs passively associate to EV membrane and can be productively delivered to target neurons. We extensively characterized this loading process and optimized exosome-to-siRNA ratios for loading. We found that chemical stabilization of 5'-phosphate with 5'-E-vinylphosphonate and chemical stabilization of all nucleotides with 2'-O-methyl and 2'-fluoro increases the accumulation of siRNA and the level of mRNA silencing in target cells. Therefore, we recommend using fully modified siRNAs for lipid-mediated loading to EVs. Later, we identified that α-tocopherol-succinate (vitamin E) conjugation to siRNA increases productive loading to exosomes compared to originally described cholesterol. Low EV yield has been a rate-limiting factor in preclinical development of the EV technology. We developed a scalable EV manufacturing process based on three-dimensional, xenofree culture of mesenchymal stem cells and concentration of EVs from conditioned media using tangential flow filtration. This process yields exosomes more efficient at siRNA delivery than exosomes isolated via differential ultracentrifugation from two-dimensional cultures of the same cells. In-depth characterization of EV content is required for quality control of EV preparations as well as understanding composition–activity relationship of EVs. We have generated mass-spectrometry data on more than 3000 proteins and more than 2000 lipid species detected in exosomes (small EVs) and microvesicles (large EVs) isolated from five different producer cells: two cell lines (U87 and Huh7) and three mesenchymal stem cell types (derived from bone marrow, adipose tissue and umbilical cord Wharton’s jelly). These data represent an indispensable resource for the community. Furthermore, relating composition change to activity change of EVs isolated from cells upon serum deprivation allowed us to identify essential components of siRNA-delivering exosomes. Based on these data we reverse engineered natural exosomes into artificial exosomes consisting of dioleoyl-phosphatidylcholine, cholesterol, dilysocardiolipin, Rab7, AHSG and Desmoplakin. These artificial exosomes reproduced efficient siRNA delivery of natural exosomes both in vitro and in vivo. Artificial exosomes may facilitate manufacturing, quality control and cargo loading challenge that currently impede the therapeutic EV field.
Palantir: Early Detection of Development Conflicts Arising from Parallel Code Changes (2011)

The earlier a conflict is detected, the easier it is to resolve-this is the main precept of workspace awareness. Workspace awareness seeks to provide users with information of relevant ongoing parallel changes occurring in private workspaces, thereby enabling the early detection and resolution of potential conflicts. The key approach is to unobtrusively inform developers of potential conflicts arising because of concurrent changes to the same file and dependency violations in ongoing parallel work. This paper describes our research goals, approach, and implementation of workspace awareness through Palantír and includes a comprehensive evaluation involving two laboratory experiments. We present both quantitative and qualitative results from the experiments, which demonstrate that the use of Palantír, as compared to not using Palantír 1) leads to both earlier detection and earlier resolution of a larger number of conflicts, 2) leaves fewer conflicts unresolved in the code base that was ultimately checked in, and 3) involves reasonable overhead. Furthermore, we report on interesting changes in users' behavior, especially how conflict resolution strategies changed among Palantír users.
Enhanced photocoagulation with catheter-based diffusing optical device (2012)

A novel balloon catheter-based diffusing optical device was designed and evaluated to assist in treating excessive menstrual bleeding. A synthetic fused-silica fiber was micro-machined precisely to create scattering segments on a 25 mm long fiber tip for uniform light distribution. A visible wavelength (λ=532 nm) was used to specifically target the endometrium due to the high vascularity of the uterine wall. Optical simulation presented 30% wider distribution of photons along with approximately 40% higher irradiance induced by addition of a glass cap to the diffuser tip. Incorporation of the optical diffuser with a polyurethane balloon catheter considerably enhanced coagulation depth and area (i.e., 3.5 mm and 18.9 cm2 at 1 min irradiation) in tissue in vitro. The prototype device demonstrated the coagulation necrosis of 2.8±1.2 mm (n=18) and no thermal damage to myometrium in in vivo caprine models. A prototype 5 cm long balloon catheter-assisted optical diffuser was also evaluated with a cadaveric human uterus to confirm the coagulative response of the uterine tissue as well as to identify the further design improvement and clinical applicability. The proposed catheter-based diffusing optical device can be a feasible therapeutic tool to photocoagulate endometrial cell layers in an efficient and safe manner.
Secretion, blood levels and cutaneous expression of <scp>TL</scp>1A in psoriasis patients (2015)

TL1A is a TNF-like cytokine which has been shown to co-stimulate TH1 and TH17 responses during chronic inflammation. The expression of this novel cytokine has been investigated in inflammatory disorders like rheumatoid arthritis and inflammatory bowel disease, but little is known about expression and induction in psoriasis. Indeed, the pathogenesis in psoriasis is still not fully understood and it is speculated that cytokines other than TNF-α are important in subsets of patients. Also, for patients with severe disease that are treated with systemic anti-TNF-α blockade, novel candidates to be used as disease and response biomarkers are of high interest. Here, we demonstrate TL1A expression in biopsies from psoriatic lesions. Also, we investigated spontaneous and induced TL1A secretion from PBMCs and blood levels from a cohort of psoriasis patients. Here, increased spontaneous secretion from PBMCs was observed as compared to healthy controls and a small subset of patients had highly elevated TL1A in the blood. Interestingly, activation of PBMCs with various cytokines showed a decreased sensitivity for TL1A activation in psoriasis patients compared to healthy controls.TL1A levels in blood and biopsies could not be correlated with disease activity with this patient cohort. Thus, additional large-scale studies are warranted to investigate TL1A as a biomarker.
Differential binding of c-Myc and Max to nucleosomal DNA. (1994)

The ability of a transcription factor to function in vivo must be determined in part by its ability to bind to its recognition site in chromatin. We have used Max and derivatives of c-Myc to characterize the effect of changes of dimerization partner on binding to nucleosomal DNA templates. We find that homo- and heterodimeric complexes of these proteins bind to the CACGTG sequence in free DNA with similar affinities. Although Max homodimers bind to nucleosomes, truncated c-Myc homodimers do not. Surprisingly, modifying the c-Myc dimerization interface or changing its dimerization partner to Max enables nucleosomal DNA binding. Thus, changes in dimer structure or dimerization efficiency can have significant effects on nucleosome binding that are not predicted from their affinity for free DNA. We conclude that domains other than the basic region per se influence the ability of a transcription factor to bind to nucleosomal DNA and that changes of dimerization partner can directly affect the ability of a factor to occupy nucleosomal binding sites.
RAPID AND EFFICIENT SYNTHESIS OF 2-[3-CYANO-4-(2-ARYLIDEN)-5, 5-DIMETHYL-5<i>H</i>-FURAN-2-YLIDENE]-MALONONITRILE UNDER FOCUSED MICROWAVE IRRADIATION (2001)

New biological potential furan-2-ylidenemalononitriles (IIIa-j) were synthetised efficiently by one-pot condensation under focused microwave from starting and easy available compounds.
Time-frequency formulation and design of nonstationary Wiener filters (2002)

The nonstationary Wiener filter (WF) is the optimum linear system for estimating a nonstationary signal contaminated by nonstationary noise. We propose a time-frequency (TF) formulation of nonstationary WFs for the practically important case of underspread processes. This TF formulation extends the spectral representation of stationary WFs to the nonstationary case, and it allows an approximate TF design of nonstationary WFs. For underspread processes, the performance obtained with the approximate TF design is close to that of the exact WF.
Telemonitoring Physiological Parameters of a Patient from a Distance by Near Field Communication Mobile (2014)

Mobile phones and wireless sensors become popular in telemonitoring field for disease that is persistent or otherwise long-lasting in its effects. Common chronic diseases include arthritis, asthma, cancer, COPD, diabetes and AIDS. To manage the communication between cell phone and wireless sensor combination of Bluetooth and Near Field Communication is required which is easy to use wireless communication interface for the last few centimeters. This technique will be a useful for non technical person also after set up. Telemonitoring is a convenient way for patients to avoid travel and to perform some of the more basic work of healthcare for themselves. This technology is easy to use just by touching the items.
Case History: Comparison of linear regression and a probabilistic neural network to predict porosity from 3-D seismic attributes in Lower Brushy Canyon channeled sandstones, southeast New Mexico (2001)

Abstract The Lower Brushy Canyon Formation of the Delaware Basin, New Mexico, consists of a series of overlying sand-filled channels and associated fans separated by laterally extensive organic siltstone and carbonate interbeds. This laterally and vertically complex geology creates the need for precise interwell estimation of reservoir properties. In this paper we integrate wireline log and 3-D seismic data to directly predict porosity in the area of an existing oil field in southeast New Mexico. The 3-D seismic data were used to interpret the location of major stratigraphic markers between wells, and these seismic horizons were used to constrain a time window for a volume-based attribute analysis. Stepwise regression and crossvalidation were used to combine seismic attributes to predict porosity in wells where the porosity was known from the well logs. The results of a linear regression porosity model showed good correlation (r2 = 0.74) between seven seismic attributes and the observed porosity logs at 11 wells in the study area, but the porosity volume created from the regression model did not display the known geologic features. A probabilistic neural network was then trained to look for a nonlinear relationship between the input data (the seven attributes) and the observed porosity at the 11 wells. The correlation was better (r2 = 0.82), but the biggest improvement over the linear regression model came in the more geologically realistic predicted porosity distribution.
Effect of dietary water intake on urinary output, specific gravity and relative supersaturation for calcium oxalate and struvite in the cat (2011)

It has been reported that daily fluid intake influences urinary dilution, and consequently the risk of urolithiasis in human subjects and dogs. The aim of the present study was to investigate the role of dietary moisture on urinary parameters in healthy adult cats by comparing nutritionally standardised diets, varying only in moisture content. A total of six cats were fed a complete dry food (6.3 % moisture) hydrated to 25.4, 53.2 and 73.3 % moisture for 3 weeks in a randomised block cross-over design. Urinary specific gravity (SG), urine volume, water drunk and total fluid intake were measured daily; relative supersaturation (RSS) for calcium oxalate (CaOx) and struvite was calculated using the SUPERSAT computer program. Cats fed the 73.3 % moisture diet produced urine with a significantly lower SG (P < 0.001) compared with diets containing 53.2 % moisture or lower. Mean RSS for CaOx was approaching the undersaturated zone (1.14 (sem 0.21); P = 0.001) for cats fed the diet with 73.3 % moisture and significantly lower than the 6.3 % moisture diet (CaOx RSS 2.29 (sem 0.21)). The effect of diet on struvite RSS was less clear, with no significant difference between treatment groups. Total fluid intake was significantly increased (P < 0.001) in the 73.3 % moisture diet (144.7 (SEM 5.2) ml, or 30 ml/kg body weight per d) compared with the 6.3 % (103.4 (SEM 5.3) ml), 25.4 % (98.6 (SEM 5.3) ml) and 53.3 % (104.7 (SEM 5.3) ml) moisture diets, despite voluntary water intake decreasing as dietary moisture intake increased. Cats fed the 73.3 % moisture diet had a higher total daily fluid intake resulting in a more dilute urine with a lower risk of CaOx when compared with the lower-moisture diets.
Parallel architectures for 3-step hierarchical search block-matching algorithm (1994)

The paper describes fully pipelined parallel architectures for the 3-step hierarchical search block-matching algorithm, a fast motion estimation algorithm for video coding. The advantage of this algorithm was completely utilized by use of intelligent data arrangement and memory configuration. Techniques for reducing interconnections and external memory accesses were also developed. Because of their low costs, high speeds, and low memory bandwidth requirements, the proposed 3-PE, 9-PE, and 27-PE architectures provide efficient solutions for real-time motion estimations required by video applications of various data rates, from low bit-rate video to HDTV systems.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Anionic salts and dietary 25-hydroxyvitamin D stimulate calcium availability in steers (2012)

The influence of feeds containing varying dietary cation-anion differences (DCADs) with and without supplements of 25-hydroxyvitamin D (25(OH)D) on urine pH and excretion of macro minerals was determined in fistulated crossbred steers (mean live weight 315 ± 45 kg). A basal forage diet comprising lucerne hay and wheat chaff was used, to which varying quantities of MgCl(2) or K(2)CO(3) were added to achieve four levels of DCAD: -300, 50, 150 or 250 mEq/kg dry matter (DM). Steers were allocated to one of six treatments, one treatment for each diet and a further treatment for both the 50 and 150 mEq/kg DCAD diets, which were supplemented with 25(OH)D at a rate of 3 mg/steer per day. Urine pH from steers offered the diets comprising DCADs of 50, 150 and 250 mEq/kg ranging from 8.3 to 8.8. In treatments not containing 25(OH)D with DCADs of 50 to 250 mEq/kg, there were no significant differences in urine pH or Ca excretion. However, steers offered the diet with a DCAD of -300 mEq/kg DM produced urine with a significantly lower pH (6.5 to 7.5). Daily output of Ca in urine was also significantly higher from steers given this diet. Supplementation with 25(OH)D significantly increased urinary Ca excretion from steers offered diets of DCADs 50 and 150 mEq/kg DM. Estimates of daily urinary Ca excretion, calculated using the ratio of creatinine to Ca in 'spot' urine samples, were less variable than those based on total collection (residual mean square of 0.54 and 0.63, respectively).
Dynamic, site-specific interaction of hypoxia-inducible factor-1alpha with the von Hippel-Lindau tumor suppressor protein. (2001)

Hypoxia-inducible factor (HIF)-1alpha is a transcription factor that plays a critical role in regulating genes involved in erythropoiesis and angiogenesis. Recent evidence indicates that the von Hippel-Lindau tumor suppressor protein (VHL) is part of a ubiquitin ligase complex that promotes the degradation of HIF-1alpha under normoxic conditions. Under hypoxic conditions, HIF-1alpha is markedly stabilized. A critical issue in understanding the hypoxic response is the identification of hypoxia-regulated steps. We show here that hypoxia and cobalt treatment modulate the capacity of a HIF-1alpha fragment comprising residues 531-652 to coimmunoprecipitate with VHL. Hypoxia and cobalt both significantly diminish the interaction, and furthermore, normoxia treatment after hypoxia rapidly normalizes it. This HIF-1alpha fragment confers hypoxia and cobalt inducibility on a heterologous protein. Significantly, contained within this fragment is a short 27-residue sequence that behaves identically in all respects noted above. Finally, evidence is provided to show that cobalt and hypoxia both induce a posttranslational modification (or loss of one) in HIF-1alpha that affects its binding to VHL. We propose that dynamic, site-specific interaction of HIF-1alpha with VHL provides one mechanism by which HIF-1alpha can be regulated.
Nuclear Reassembly Excludes Large Macromolecules (1987)

Interphase nucleus and cytoplasm are distinct compartments, whose soluble macromolecular contents mix when the nuclear envelope disassembles at mitosis. To determine how their interphase identities are reestablished, fibroblasts were loaded with fluorescent dextrans and then allowed to divide. Large dextrans (molecular weight of 40,000 or more) were excluded from condensed mitotic chromosomes and from newly formed, postmitotic interphase nuclei. Therefore, postmitotic reassembly of the nucleus as a compartment distinct from cytoplasm occurs by exclusion not only of organelles but also of soluble macromolecules. This might occur by exclusion of macromolecules from condensed chromatin throughout mitosis and completion of nuclear envelope assembly before nuclear expansion.