gebhart/patrepeval huggingface dataset:
Use of Pressure- and Rate-Transient Techniques for Analyzing Core Permeability Tests for Unconventional Reservoirs: Part 2 (2013)

Abstract Although matrix permeability is an important control on the commercial viability of unconventional reservoirs, there is no consensus on the appropriate way to measure it in the lab. In previous work (Clarkson et al. 2012), we investigated the use of pressure- and rate-transient analysis (PTA/RTA) methods to analyze data obtained from a new core plug analysis procedure designed specifically to extract information (permeability and pore volume) from ultra-low permeability reservoir samples (core plugs). The new approach involved analysis of rate and/or pressure data from the core test analogously to larger-scale well-test/production data. Although this approach offers some advantages over conventional pressure-decay and pulse-decay test analysis procedures, there are some practical issues related to core measurements to support the analysis that need to be addressed. For example, injection or production rate measurements, which are difficult to perform, were required to implement some of the analysis procedures. Further, in the original work, constant injection rates for the injection/falloff portion of the test, and constant flowing pressures for the production portion of the test, were assumed. In this work, we demonstrate that accurate measurement of injection rates is not necessary to obtain an accurate estimate of permeability and that the analysis methods can be applied for variable injection rates and flowback pressures. Several permeability estimates are possible during a single test cycle using the procedures described in this work. Permeability may be estimated from the injection/falloff cycle of the test by 1) identifying the end of transient (linear) flow from derivative techniques combined with the distance of investigation calculation and 2) applying a conventional straight-line analysis of linear flow. Two independent estimates may therefore be obtained, but the latter requires estimation of the injection rate history. Similarly, two permeability estimates may be obtained from the production (flowback) cycle of the test using the distance of investigation and straight-line approaches. Both falloff and production analysis procedures are tested by simulating constant and variable injection rates, and constant and variable flowing pressures, respectively. In some cases, particularly with variable rates/flowing pressures, it may not be possible to obtain permeability from all approaches, making multiple, redundant estimates desirable to avoid a failed core analysis. As with the original test procedure proposed by Clarkson et al. (2012), the unique properties of unconventional reservoirs may be accounted for in the new analysis procedure, such as adsorption and non-Darcy flow (slippage and diffusion), and heterogeneities may be detected and analyzed. We believe this new technique for analyzing core data will considerably improve on current techniques for establishing permeability of unconventional reservoir samples.
Extending 2D object arrangement with pressure-sensitive layering cues (2008)

We demonstrate a pressure-sensitive depth sorting technique that extends standard two-dimensional (2D) manipulation techniques, particularly those used with multi-touch or multi-point controls. We combine this layering operation with a page-folding metaphor for more fluid interaction in applications requiring 2D sorting and layout.
1,3,5-Tris[4-(diphenylamino)phenyl]benzene and its methyl-substituted derivatives as a novel class of amorphous molecular materials (1993)

Novel starburst molecules based on π-electron systems, 1,3,5-tris[4-(diphenylamino)phenyl]benzene and its methyl-substituted derivatives, have been synthesized and found to constitute a new family of amorphous molecular materials with high glass-transition temperatures above 100°C.
Monoclonal antibodies as effective therapeutic agents for solid tumors (2004)

Monoclonal antibodies (mAbs) against growth factors or their receptors have been revealed to be effective therapeutic agents for solid tumors. Trastuzumab (humanized anti-HER2 mAb) is the first mAb approved for the treatment of a solid tumor, metastatic breast cancer. Large-scale phase III clinical trials are now ongoing to further evaluate the additive effects on chemotherapy and the efficacy as a maintenance monotherapy. Another anti-HER2 mAb CH401 that we developed also seems to have good potential. This chimeric mAb completely suppressed the growth of established human tumor xenografts in SCID mice after a single injection. Furthermore, CH401 characteristically showed much stronger induction of apoptosis in HER2-overexpressing gastric cancer cells compared to trastuzumab. Additional targets now being intensively evaluated are epidermal growth factor receptor (EGFR) and vascular endothelial growth factor (VEGF). Both cetuximab (chimeric anti-EGFR mAb) and bevacizumab (humanized anti-VEGF mAb) have recently been shown to be of clinical value for metastatic colorectal cancer. Anti-idiotype mAbs are unique as active immunotherapeutic agents, and survival benefits have been observed in clinical trials for solid tumors.
Challenges in the diagnosis and treatment of pulmonary arterial hypertension (2012)

Advances in the diagnosis and management of pulmonary arterial hypertension (PAH) have resulted in significant improvements in outcomes for patients with this devastating and progressive disease. However, because of the non-specific nature of its symptoms, and the low level of suspicion among clinicians, prompt and accurate diagnosis of PAH as a rare disease remains a challenge. This article explains some of the issues that need to be addressed when faced with a patient with suspected PAH and describes how noninvasive and invasive techniques can be used effectively to ensure an accurate diagnosis. The availability of PAH-specific therapy means that once diagnosed, patients have a much greater chance of survival than they would have had in the past. However, despite improved survival, mortality is still high and, therefore, there is still room for improvement. It is currently recommended that patients with an inadequate clinical response to treatment receive sequential combination therapy; however, supportive data are still scarce. Although there is no clear explanation, these findings may be explained by the design and end-points chosen in clinical trials, the changing population of PAH and a need to improve the management strategy in this disease. Indeed, there is a clear need for randomised controlled studies that investigate whether adopting individualised treatment strategies, including upfront combination therapy, could help to optimise long-term management of patients with PAH.
Relationship of plasma leptin to plasma insulin and adiposity in normal weight and overweight women: effects of dietary fat content and sustained weight loss. (1996)

Leptin, the product of the human homologue of the ob gene, which is defective in the obese (ob/ob) mouse, may be a humoral regulator of human adiposity. Plasma leptin concentrations were measured by RIA in 19 normal weight [body mass index (BMI) = 24.5 +/- 0.6 kg/m2] and 19 overweight to obese (BMI = 34.7 +/- 1.2 kg/m2) nondiabetic postmenopausal women on sequential controlled weight-maintaining diets containing 31%, 23%, and 14% of energy as fat, each for 4-6 weeks. Thereafter, the subjects ate a very low fat diet (< 15%) ad libitum; plasma leptin and insulin concentrations, BMI, percent body fat (%BF), and resting energy expenditure were determined after 6 and 8 months. Absolute and adiposity-corrected plasma leptin levels were higher in overweight/obese women (37.7 +/- 3.5 ng/mL; 1.01 +/- 0.07 ng.mL-1.%BF-1) than in normal weight women (16.9 +/- 2.2 ng/mL; 0.57 +/- 0.06 ng.mL-1.%BF-1, both P < 0.005 vs. obese), but were not different between the 31%, 23%, and 14% fat diets when body weight was stable. Plasma leptin was highly correlated with BMI (r = 0.81, P < 0.0001), %BF (r = 0.80, P < 0.0001), and fasting plasma insulin (r = 0.61, P < 0.0001). After 8 months on the ad libitum low fat diet, the women had lost an average of 6.9 +/- 1.0% of body mass (-2.0 +/- 0.3 kg/m2, P < 0.0001). In 15 subjects who lost more than 7% of body mass (-12.3 +/- 1.0%), plasma leptin concentrations decreased (-9.6 +/- 1.9 ng/mL, P < 0.0005), and the decrease of plasma leptin per change of adiposity (delta leptin/delta %BF) was greater in overweight/obese women (3.6 +/- 0.5) than in normal weight women (0.9 +/- 0.4, P < 0.01 vs. obese). In 18 other subjects who lost less than 7% of body mass (-2.7 +/- 0.6%), plasma leptin was unchanged (+1.4 +/- 1.4 ng/mL). Overall, the change of plasma leptin was significantly correlated with change of BMI (r = 0.43, P < 0.02), the change of %BF (r = 0.49, P < 0.005), the change of resting energy expenditure (r = 0.40, P < 0.02), and with the change of plasma insulin independently of changes of body adiposity (r = 0.45, P < 0.01). We conclude that plasma leptin concentrations are: 1) not affected by dietary fat content per se; 2) highly correlated with BMI, %BF, and plasma insulin in both overweight/obese and normal weight women; 3) decreased in parallel with plasma insulin after sustained weight loss; and 4) decreased more in overweight/obese than in normal weight women.
Cell‐free assays for γ‐secretase activity (2000)

The amyloid b-protein (Ab) deposited in Alzheimer's disease (AD) is a normally secreted proteolytic product of the amyloid b-protein precursor (APP). Generation of Ab from the APP requires two sequential proteolytic events: an initial b-secretase cleavage at the amino terminus of the Ab sequence followed by g-secretase cleavage at the carboxyl terminus of Ab. We describe the development of a robust in vitro assay for g-secretase cleavage by showing de novo Ab production in vitro and establish that this assay monitors authentic gamma-secretase activity by documenting the production of a cognate g-CTF, confirming the size of the Ab produced by mass spectrometry, and inhibiting cleavage in this system with multiple inhibitors that alter g-secretase activity in living cells. Using this assay, we demonstrate that the g-secretase activity 1) is tightly associated with the membrane, 2) can be solubilized, 3) has a pH optimum of 6.8 but is active from pH 6.0 to pH >8.4, and 4) ascertain that activities of the g-40 and g-42 are indeed pharmacologically distinct. These studies should facilitate the purification of the protease or proteases that are responsible for this unusual activity, which is a major therapeutic target for the treatment of AD.
Surface-Initiated Polymerizations in Aqueous Media:  Effect of Initiator Density (2002)

We report the first systematic study of initiator density on surface-initiated polymerizations. We used mixed monolayers comprising of undecanethiol and ω-mercaptoundecyl bromoisobutyrate (1) to initiate the controlled radical polymerization of methyl methacrylate (MMA) and glycidyl methacrylate (GMA) from gold. We found that SAMs composed of 10% and 50% of initiator 1 grow PMMA brushes to approximately 1/10 and 1/2 the thickness of polymer brushes grafted from SAMs comprising 100% 1. We did not find a clear maximum initiator density, beyond which no further increase in polymer brush thickness is observed. We show that the initiator density at the start of the polymerization determines the ultimate “footprint” and hence density of polymer molecules in polymer brushes.
Reversible Effects of Ultrasound on Spinal Reflexes (1962)

<h3>Introduction</h3> This investigation is one of 3 studies<sup>1,2</sup>undertaken so explore the potentialities of high-intensity ultrasound in experimental neurology. Recently there has been increasing interest in this field. Techniques have been developed for producing lesions of constant size and shape at selected sites in the central nervous system.<sup>3-6</sup>Less attention has been paid to the effects of ultrasound on functioning neural circuits. Concurrent studies on the peripheral nerves of frogs<sup>1</sup>and cats<sup>2</sup>show that focused ultrasound will block axonal conduction reversibly or irreversibly, depending upon dosage. The smallest axons, the delta fibers and the C fibers, are most sensitive to irradiation. In these experiments a segment of the cat's spinal cord was irradiated with ultrasound; the effects of the irradiation on the transmission of reflexes through that segment were followed oscillographically, and histological studies were carried out on the irradiated tissue. Spinal reflexes, elicited and recorded
Effectors of Rapid Homeostatic Responses of Endoplasmic Reticulum Cholesterol and 3-Hydroxy-3-methylglutaryl-CoA Reductase (2007)

The cholesterol content of the endoplasmic reticulum (ER) and the activity of 3-hydroxy-3-methylglutaryl-CoA reductase (HMGR) imbedded therein respond homeostatically within minutes to changes in the level of plasma membrane cholesterol. We have now examined the roles of sterol regulatory element-binding protein (SREBP)-dependent gene expression, side chain oxysterol biosynthesis, and cholesterol precursors in the short term regulation of ER cholesterol levels and HMGR activity. We found that SREBP-dependent gene expression is not required for the response to changes in cell cholesterol of either the pool of ER cholesterol or the rate of cholesterol esterification. It was also found that the acute proteolytic inactivation of HMGR triggered by cholesterol loading required the conversion of cholesterol to 27-hydroxycholesterol. High levels of exogenous 24,25-dihydrolanosterol drove the inactivation of HMGR; lanosterol did not. However, purging endogenous 24,25-dihydrolanosterol, lanosterol, and other biosynthetic sterol intermediates by treating cells with NB-598 did not greatly affect either the setting of their ER cholesterol pool or the inactivation of their HMGR. In summary, neither SREBP-regulated genes nor 27-hydroxycholesterol is involved in setting the ER cholesterol pool. On the other hand, 27-hydroxycholesterol, rather than cholesterol itself or biosynthetic precursors of cholesterol, stimulates the rapid inactivation of HMGR in response to high levels of cholesterol.
Electrical Responses and Spontaneous Activity of Human iPS-Derived Neuronal Networks Characterized for 3-month Culture with 4096-Electrode Arrays (2016)

The recent availability of human induced pluripotent stem cells (hiPSCs) holds great promise as a novel source of human-derived neurons for cell and tissue therapies as well as for in vitro drug screenings that might replace the use of animal models. However, there is still a considerable lack of knowledge on the functional properties of hiPSC-derived neuronal networks, thus limiting their application. Here, upon optimization of cell culture protocols, we demonstrate that both spontaneous and evoked electrical spiking activities of these networks can be characterized on-chip by taking advantage of the resolution provided by CMOS multielectrode arrays (CMOS-MEAs). These devices feature a large and closely-spaced array of 4096 simultaneously recording electrodes and multi-site on-chip electrical stimulation. Our results show that networks of human-derived neurons can respond to electrical stimulation with a physiological repertoire of spike waveforms after 3 months of cell culture, a period of time during which the network undergoes the expression of developing patterns of spontaneous spiking activity. To achieve this, we have investigated the impact on the network formation and on the emerging network-wide functional properties induced by different biochemical substrates, i.e., poly-dl-ornithine (PDLO), poly-l-ornithine (PLO), and polyethylenimine (PEI), that were used as adhesion promoters for the cell culture. Interestingly, we found that neuronal networks grown on PDLO coated substrates show significantly higher spontaneous firing activity, reliable responses to low-frequency electrical stimuli, and an appropriate level of PSD-95 that may denote a physiological neuronal maturation profile and synapse stabilization. However, our results also suggest that even 3-month culture might not be sufficient for human-derived neuronal network maturation. Taken together, our results highlight the tight relationship existing between substrate coatings and emerging network properties, i.e., spontaneous activity, responsiveness, synapse formation and maturation. Additionally, our results provide a baseline on the functional properties expressed over 3 months of network development for a commercially available line of hiPSC-derived neurons. This is a first step toward the development of functional pre-clinical assays to test pharmaceutical compounds on human-derived neuronal networks with CMOS-MEAs.
Transcription-coupled changes in nuclear mobility of mammalian cis-regulatory elements (2018)

To achieve guide RNA (gRNA) multiplexing and an efficient delivery of tens of distinct gRNAs into single cells, we developed a molecular assembly strategy termed chimeric array of gRNA oligonucleotides (CARGO). We coupled CARGO with dCas9 (catalytically dead Cas9) imaging to quantitatively measure the movement of enhancers and promoters that undergo differentiation-associated activity changes in live embryonic stem cells. Whereas all examined functional elements exhibited subdiffusive behavior, their relative mobility increased concurrently with transcriptional activation. Furthermore, acute perturbation of RNA polymerase II activity can reverse these activity-linked increases in loci mobility. Through quantitative CARGO-dCas9 imaging, we provide direct measurements of cis-regulatory element dynamics in living cells and distinct cellular and activity states and uncover an intrinsic connection between cis-regulatory element mobility and transcription.
Toll‐like receptors, endogenous ligands, and systemic autoimmune disease (2005)

The critical role of Toll-like receptors (TLRs) as mediators of pathogen recognition by the innate immune system is now firmly established. Such recognition results in the initiation of an inflammatory immune response and subsequent instruction of the adaptive immune system, both of which are designed to rid the host of the invading pathogen. More controversial is the potential role of TLRs in the recognition of endogenous ligands and what effect this might have on the consequent development of autoimmune or other chronic sterile inflammatory disorders. An increasing number of studies implicate TLRs as being involved in the immune response to self-molecules that have in some way been altered from their native state or accumulate in non-physiologic sites or amounts, although questions have been raised about possible contaminants in certain of these studies. In this review, we discuss the evidence for endogenous ligand-TLR interactions with particular emphasis on mammalian chromatin, systemic lupus erythematosus, and atherosclerosis. Overall, the data support the general concept of a role for TLRs in the recognition of endogenous ligands. However, the precise details of the interactions and the extent to which they may contribute to the pathogenesis of human disease remain to be clarified.
Evidence-based pharmacotherapy for personality disorders (2011)

Patients with personality disorders are prescribed psychotropic medications with greater frequency than almost any other diagnostic group. Prescribing practices in these populations are often based on anecdotal evidence rather than rigorous data. Although evidence-based psychotherapy remains an integral part of treatment, Axis II psychopathology is increasingly conceptualized according to neurobiological substrates that correspond to specific psychopharmacological strategies. We summarize the best available evidence regarding medication treatment of personality disordered patients and provide optimal strategies for evidence-based practice. Most available evidence is concentrated around borderline and schizotypal personality disorders, with some additional evidence concerning the treatment of avoidant and antisocial personality disorders. Although maladaptive personality symptoms respond to antidepressants, antipsychotics, mood stabilizers, and other medications, evidence-based pharmacotherapy is most useful in treating circumscribed symptom domains and induces only partial improvement. Most available evidence supports use of medication in reducing impulsivity and aggression, characteristic of borderline and antisocial psychopathology. Efforts have also begun to reduce psychotic-like symptoms and improve cognitive deficits characteristic of schizotypy. Indirect evidence is also provided for psychopharmacological reduction of social anxiety central to avoidant personality disorder. Evidence-based practice requires attention to domains of expected clinical improvement associated with a medication, relative to the potential risks. The development of future rational pharmacotherapy will require increased understanding of the neurobiological underpinnings of personality disorders and their component dimensions. Increasing efforts to translate personality theory and social cognitive neuroscience into increasingly specific neurobiological substrates may provide more effective targets for pharmacotherapy.
IgM AND IgG ALLOANTIBODY RESPONSES TO MHC CLASS I AND II FOLLOWING RAT RENAL ALLOGRAFT REJECTION (1992)

Renal allograft rejection in rats and humans is a potent inducer of alloantibody to donor major histocompatibility complex antigens. Alloantibody in such presensitized recipients can cause hyperacute rejection of subsequent renal allografts. In order to characterize alloantibody production in rats presensitized by renal graft rejection, ACI (RT1a) kidneys were transplanted into untreated fully allogeneic PVG (RT1c) recipients and allowed to reject while one native kidney remained in situ for host survival. Serum samples collected at weekly intervals were analyzed by flow cytometry for IgM and IgG antibody binding to ACI lymphoid target cells. The specificity of alloantibody responses was assessed by (1) differential binding to congenic rat strain target cells expressing only donor class I (PVG.R1) versus both donor class I and II (PVG.1A) antigens, (2) differential binding to unseparated donor lymphoid target cells versus lymphoid target cells depleted of class II MHC antigen-expressing cells, and (3) specific blocking of monoclonal antibodies to donor class I (R2/10P, R2/15S) or class II (F17.23.2) epitopes. Alloantibody responses to both donor class I and II MHC antigens were detected. The initial IgM response to donor class I MHC antigens peaked at the time of rejection, followed by a steady decline to relatively low levels by 4 weeks posttransplantation. The IgM response to donor class II MHC antigens was found to be cyclical with apparent peaks at day 7 and 5-6 weeks. The IgG response to donor class I and class II MHC antigens reached maximum by 5-6 weeks before slowly decreasing. IgM and IgG alloantibody specific for class I and class II MHC antigens could be detected through 19 weeks posttransplantation. The effects on circulating alloantibody of two manipulations, posttransplantation donor specific blood transfusion and allograft removal, were examined in this model. The alloantibody responses to class I MHC antigens were not affected by giving DSBT weekly beginning at day 14 after transplantation. However, posttransplantation DSBT eliminated the second peak of IgM alloantibody to class II MHC antigens seen approximately 5-6 weeks posttransplantation and also decreased circulating IgG specific for class II antigens. Transplantectomy at day 5-7 days after transplantation had no apparent effect on circulating IgM or IgG alloantibody through 7 weeks posttransplantation. These data indicate that in a fully allogeneic rat renal allograft model alloantibody responses are elicited to both class I and II MHC donor antigens, but that the kinetics and regulation of the responses to class I differ from those to class II alloantigens.(ABSTRACT TRUNCATED AT 400 WORDS)