gebhart/patrepeval huggingface dataset:
Longitudinal distribution of O3 absorption in the lung: gender differences and intersubject variability (1996)

Because the National Ambient Air Quality Standard for ozone (O3) is intended to protect the most sensitive individuals in the general population, it is necessary to identify sources of intersubject variation in the exposure-dose-response cascade. We hypothesize that differences in lung anatomy can modulate exposure-dose relationships between individuals, and this results in differences between their responsiveness to O3 at a fixed exposure condition. During quiet breathing, the conducting airways remove the majority of inhaled O3, so the volume of this region should have an important impact on O3 dose distribution. Employing the bolus inhalation method, we measured the distribution of O3 absorption with respect to penetration volume (Vp), and using the Fowler single-breath N2 washout method, we determined the dead space volume (VD) in the lungs of 10 men and 10 women at a fixed respiratory flow of 250 ml/s. On average, the women absorbed O3 at smaller Vp than the men, and the women had smaller VD than the men. When expressed in terms of Vp/VD, the absorption distribution of the men and women was indistinguishable. Moreover, an interpretation of the O3 distribution in terms of an intrinsic mass transfer parameter (Ka) indicated that differences between the O3 dosimetry in all subjects, whether men or women, could be explained by a unique correlation with anatomic dead space: Ka (in s-1) = 610 VD-105 (in ml). Application of this result to measurements of O3 exposure response indicated that previously reported gender differences may be due to a failure in properly accounting for tissue surface within the conducting airways.
Liquid clathrate formation in ionic liquid–aromatic mixturesElectronic supplementary information (ESI) available: crystallographic information, CCDC 200588–200590. See http://www.rsc.org/suppdata/cc/b2/b212726a/ for crystallographic files in CIF or other electronic format. (2003)

1-Alkyl-3-methylimidazolium containing ionic liquids with hexafluorophosphate, bis(trifyl)imide, tetrafluoroborate, and chloride anions form liquid clathrates when mixed with aromatic hydrocarbons; in the system 1,3-dimethylimidazolium hexafluorophosphate-benzene, the aromatic solute could be trapped in the solid state forming a crystalline 2:1 inclusion compound.
Collagen‐binding motif peptide, a cleavage product of osteopontin, stimulates human neutrophil chemotaxis via pertussis toxin‐sensitive G protein‐mediated signaling (2008)

The collagen-binding motif (CBM) peptide, a cleavage product of osteopontin (OPN), stimulated intracellular calcium increase in human neutrophils. CBM peptide-stimulated calcium was inhibited by pertussis toxin (PTX), suggesting the influence of PTX-sensitive G-proteins. In addition CBM peptide stimulated the chemotactic migration of human neutrophils and human monocytes. CBM peptide-induced neutrophil chemotaxis was completely inhibited by PTX, once again indicating the influence of Gi proteins. CBM peptide was also found to induce mitogen activated protein kinase activation. CBM peptide-induced neutrophil chemotaxis was mediated by p38 kinase as well as an extracellular signal-regulated protein kinase. Taken together, the results suggest that a cleavage product of OPN, CBM peptide, initiates immune responses by inducing neutrophil trafficking via certain PTX-sensitive cell surface receptors.
A resting-state network comparison of combat-related PTSD with combat-exposed and civilian controls (2019)

Resting-state functional connectivity (rsFC) is an emerging means of understanding the neurobiology of combat-related post-traumatic stress disorder (PTSD). However, most rsFC studies to date have limited focus to cognitively related intrinsic connectivity networks (ICNs), have not applied data-driven methodologies or have disregarded the effect of combat exposure. In this study, we predicted that group independent component analysis (GICA) would reveal group-wise differences in rsFC across 50 active duty service members with PTSD, 28 combat-exposed controls (CEC), and 25 civilian controls without trauma exposure (CC). Intranetwork connectivity differences were identified across 11 ICNs, yet combat-exposed groups were indistinguishable in PTSD vs CEC contrasts. Both PTSD and CEC demonstrated anatomically diffuse differences in the Auditory Vigilance and Sensorimotor networks compared to CC. However, intranetwork connectivity in a subset of three regions was associated with PTSD symptom severity among executive (left insula; ventral anterior cingulate) and right Fronto-Parietal (perigenual cingulate) networks. Furthermore, we found that increased temporal synchronization among visuospatial and sensorimotor networks was associated with worse avoidance symptoms in PTSD. Longitudinal neuroimaging studies in combat-exposed cohorts can further parse PTSD-related, combat stress-related or adaptive rsFC changes ensuing from combat.
CYCLIC AMP MEDIATES THE CONCANAVALIN A AGGLUTINABILITY OF MOUSE FIBROBLASTS (1974)

We have devised a quantitative way to measure the agglutination of cells which utilizes the size discrimination feature of an automatic particle counter. With this method we have studied the agglutinability by concanavalin A of 3T3 cells, a mutant of 3T3 cells (3T3cAMP(tcs)) in which cyclic AMP levels fall when the cells are subjected to temperature change or fresh serum, and L929 cells. We find with 3T3cAMP(tcs) cells that low levels of cyclic AMP correlate with increased agglutinability and that high levels of cyclic AMP correlate with decreased agglutinability. Prior treatment of these cells with a cyclic AMP phosphodiesterase inhibitor or Bt(2)cAMP blocks the increase in agglutinability induced by temperature change. When 3T3 cells are treated with fresh serum, their agglutinability also increases although to a much smaller extent than with 3T3cAMP(tcs) cells. Cells change their agglutinability very rapidly. Treatment of L929 cells for 15 min with 1-methyl-3-isobutyl xanthine at 1 mM decreases their agglutinability to the level of normal 3T3 cells. We conclude that in normal and transformed cells the level of cyclic AMP regulates agglutinability.
Diffuse Lymphoplasmacytic Chronic Cholecystitis Is Highly Specific for Extrahepatic Biliary Tract Disease but Does Not Distinguish Between Primary and Secondary Sclerosing Cholangiopathy (2003)

Previous studies of gallbladder pathology in primary sclerosing cholangitis (PSC) have suggested that a distinctive histologic triad ("diffuse lymphoplasmacytic acalculous cholecystitis," composed of diffuse, mucosal-based, dense lymphoplasmacytic infiltrates) is commonly present in gallbladders of patients with PSC and is relatively specific for that disease. However, prior control populations have included only patients with cholecystitis/cholelithiasis and hepatitis, and have not evaluated patients with non-PSC-associated extrahepatic biliary tract disease. We recently observed cases of diffuse lymphoplasmacytic chronic cholecystitis in a subset of patients with biliary tract disease associated with lymphoplasmacytic sclerosing pancreatitis and among patients undergoing Whipple resection for pancreatic head malignancy, suggesting that diffuse lymphoplasmacytic chronic cholecystitis is not specific for PSC. We studied 20 gallbladders from patients with obstructive jaundice due to malignancies of the pancreatic head, duodenum, or ampulla and 5 gallbladders from patients with choledocholithiasis, and compared them with 20 gallbladders from patients with PSC and 20 gallbladders with cholelithiasis. The following histologic features were evaluated: degree of mucosal and deep inflammation, lymphoid nodules, epithelial metaplasia, muscular hypertrophy, Rokitansky-Aschoff sinuses, fibrosis, and cholesterolosis. Gallbladders in malignancy-associated obstructive jaundice were nearly identical to gallbladders in PSC with respect to scores for mucosal inflammation, lymphoid nodules, and frequency of diffuse lymphoplasmacytic chronic cholecystitis (60% vs. 50%, respectively). PSC gallbladders, however, were significantly more likely to contain focal or extensive epithelial metaplasia (P = 0.01). The cholelithiasis control group was characterized by lack of significant mucosal inflammation in the majority of cases (95%) and frequent Rokitansky-Aschoff sinuses, fibrosis, and muscular hypertrophy. Gallbladders in the choledocholithiasis group showed overlapping histologic features with PSC/malignancy-associated obstructive jaundice and cholelithiasis. These results suggest that a pattern of diffuse lymphoplasmacytic chronic cholecystitis is highly specific for extrahepatic biliary tract disease but does not distinguish between primary and secondary cholangiopathies.
Supplemental Figure Legend from Akt Inhibition Enhances Expansion of Potent Tumor-Specific Lymphocytes with Memory Cell Characteristics (2023)

&lt;p&gt;Supplemental Figure Legend. Legend for Supplemental Figures S1-S7.&lt;/p&gt;
Chemical Biology Approaches Confirm MCT4 as the Therapeutic Target of a Cellular Optimized Hit (2023)

Lactic acid transport is a key process maintaining glycolytic flux in tumors. Inhibition of this process will result in glycolytic shutdown, impacting on cell growth and survival and thus has been pursued as a therapeutic approach for cancers. Using a cell-based screen in a MCT4-dependent cell line, we identified and optimized compounds for their ability to inhibit the efflux of intracellular lactic acid with good physical and pharmacokinetic properties. To deconvolute the mechanism of lactic acid efflux inhibition, we have developed three assays to measure cellular target engagement. Specifically, we synthesized a biologically active photoaffinity probe (IC<sub>50</sub> < 10 nM), and using this probe, we demonstrated selective engagement of MCT4 of our parent molecule through a combination of confocal microscopy and in-cell chemoproteomics. As an orthogonal assay, the cellular thermal shift assay (CETSA) confirmed binding to MCT4 in the cellular system. Comparisons of lactic acid efflux potencies in cells with differential expression of MCT family members further confirmed that the optimized compounds inhibit the efflux of lactic acid through the inhibition of MCT4. Taken together, these data demonstrate the power of orthogonal chemical biology methods to determine cellular target engagement, particularly for proteins not readily amenable to traditional biophysical methods.
Exporting and utilizing database interfaces on the web - eScholarship (2006)

Database interfaces define the way database functionality is exported to and utilized by end users, developers and programs. Publishing, integration and service-oriented architectures demand capable interfaces and a higher degree of database functionality utilization in order to realize their potential. In service-oriented architectures, applications need to provide integrated access to the data of multiple sources. Such applications typically support only a restricted set of queries over the schema they export, because the participating information sources contribute limited content and limited access methods. In prior work, these limited access methods have often been specified using a set of parameterized views, with the understanding that the integration system accepts only queries which have an equivalent rewriting using the views. These queries are called feasible. Infeasible queries are rejected without an explanatory feedback. To help a developer, who is building an integration application, avoid a frustrating trial-and-error cycle, I introduced the CLIDE query formulation interface, which extends the QBE-like query builder of Microsoft's SQL Server with a coloring scheme that guides the user toward formulating feasible queries. CLIDE provides guarantees that the suggested query edit actions are complete (i.e. each feasible query can be built by following only suggestions), rapidly convergent (the suggestions are tuned to lead to the closest feasible completions of the query) and suitably summarized (at each interaction step, only a minimal number of actions are suggested). In addition, applications need to publish powerful interfaces to end users who query and browse the underlying information sources. Such interfaces require extensive coding and are expensive to maintain. I developed the QURSED system, which semi-automatically generates web- based query form and report pages for semistructured XML data. QURSED drives the generation of the pages from the XML Schema describing the structure of the underlying data and offers to developers an authoring tool that does not require any coding. The resulting forms and reports encode large sets of parameterized queries and are powerful in the sense that heterogeneity, nesting and optionality are tackled declaratively. The system reduces the cost of developing and maintaining web applications by decoupling the query aspects from the visual ones
Histone Deacetylase Inhibitor, PCI-24781, Induces Growth Inhibition and Apoptosis in Hematopoietic Tumor-Derived Cell Lines and Primary Leukemia Cells. (2006)

Abstract Histone deacetylase (HDAC) inhibitors are a new class of anticancer drugs that have shown promising activity in clinical trials. PCI-24781 (formerly CRA-024781) is a novel, hydroxamic acid-based HDAC inhibitor that is currently under evaluation in phase I clinical trials in patients with refractory solid malignancies and lymphomas. In this study, we show that PCI-24781 inhibits growth and induces apoptosis in a variety of hematopoietic cell lines derived from B-, T- and myeloid malignancies. Growth inhibition and apoptosis were noted at drug concentrations &amp;lt; 0.125 μM and were accompanied by known biochemical markers of HDAC inhibition including histone and tubulin hyperacetylation. PCI-24781 was also found to be active in animal xenograft models of hematopoietic disease displaying favorable drug-like pharmacokinetic and pharmacodynamic profiles, both intravenously and orally. To further establish the potential clinical utility of PCI-24781 in hematologic malignancies, primary leukemia samples were isolated from patients and screened for resistance to PCI-24781 in vitro. Of these 19 leukemia samples (10 acute myelogenous leukemia (AML) and 9 acute lymphocytic leukemia (ALL) some of which were derived from patients who had failed standard therapy), none were resistant to PCI-24781 at 0.5 μM and only 2 (1 AML and 1 ALL) were considered resistant at 50 nM. Gene expression analysis of PCI-24781 activity in these primary samples was consistent with HDAC inhibition and suggested potential downstream mechanisms of action for this compound in leukemia. These results demonstrate that PCI-24781 is active in hematopoietic tumor-derived cell lines in vitro as well as in vivo in preclinical models. Furthermore, the sensitivity of primary leukemic tumors to treatment with PCI-24781 in vitro, coupled with the predicted pharmacokinetics in humans suggests that PCI-24781 could be a valuable agent for the treatment of hematopoietic tumors.
Ultrafast Demagnetization Measurements Using Extreme Ultraviolet Light: Comparison of Electronic and Magnetic Contributions (2012)

Ultrashort pulses of extreme ultraviolet light from high-harmonic generation are a new tool for probing coupled charge, spin, and phonon dynamics with element specificity, attosecond pump-probe synchronization, and time resolution of a few femtoseconds in a tabletop apparatus. In this paper, we address an important question in magneto-optics that has implications for understanding magnetism on the fastest time scales: Is the signal from the transverse magneto-optical Kerr effect at the M 2;3 edges of a magnetic material purely magnetic or is it perturbed by nonmagnetic artifacts? Our measurements demonstrate conclusively that transverse magneto-optical Kerr measurements at the M 2;3 edges sensitively probe the magnetic state, with almost negligible contributions from the transient variation of the refractive index by the nonequilibrium hot-electron distribution. In addition, we compare pump-probe demagnetization dynamics measured by both high harmonics and conventional visible-wavelength magneto-optics and find that the measured demagnetization times are in agreement.
Membrane IgM: Interactions with the cortical cytoskeleton in the human lymphoblastoid cell line WiL2 (1988)

Cell-surface IgM (antigen receptor) sediments with the membrane fraction following osmotic lysis and homogenization of cells of the human lymphoblastoid cell line WiL2. In nonreducing buffers, SDS PAGE analysis of membrane pellets demonstrates that "native" membrane IgM exists as a dimer. In contrast to osmotic lysis, lysis of cells with the nonionic detergent Triton X-100 releases approximately 90% of the membrane-bound IgM into the supernatant; approximately 10% of the IgM pellets with the cytoskeletal fraction on centrifugation. Ligand challenge with either mu-chain-specific antibodies or concanavalin A induces a change in the state of membrane IgM making it refractory to detergent extraction, such that 43% of the IgM pellets during centrifugation. This ligand-induced retention of IgM is significantly diminished by the microfilament-disrupting agent cytochalasin D, whereas pretreatment of cells with sodium azide or colchicine results in no significant change in the percentage of membrane IgM retained by Triton X-100 residues. These results indicate that retention of IgM involves an association with the cortical actin-based cytoskeleton. Investigation of the structural basis for ligand-induced Triton X-100 retention of membrane IgM by using ferritin-conjugated antibodies, myosin subfragment S1, and stereo-imaging electron microscopy has revealed linkages between ligand-receptor (antigen-IgM) complexes and elements of the cortical actin-based cytoskeleton.
A computational framework for disease grading using protein signatures (2016)

In this paper, we propose a novel framework for computational disease stratification based on protein expression tissue images. We extract cellular staining response using color information and create a graph based on morphological features and their spatial distance. This graph is collapsed using a learned dictionary. We then compute the commute time matrix and use it as unique signature per protein and disease grade. We combine protein-based signatures using SVM with an Multiple Kernel Learning approach. We test the proposed framework on a prostate cancer tissue dataset and demonstrate the efficacy of the derived protein signatures for both disease stratification and quantification of the relative importance of each protein.
Defectivity reduction by optimization of 193-nm immersion lithography using an interfaced exposure-track system (2006)

As the integration of semiconductor devices continues, pattern sizes required in lithography get smaller and smaller. To achieve even more scaling down of these patterns without changing the basic infrastructure technology of current cutting-edge 193-nm lithography, 193-nm immersion lithography is being viewed as a powerful technique that can accommodate next-generation mass productions needs. Therefore this technology has been seriously considered and after proof of concept it is currently entering the stage of practical application. In the case of 193-nm immersion lithography, however, because liquid fills the area between the projection optics and the silicon wafer, several causes of concern have been raised - namely, diffusion of moisture into the resist film due to direct resist-water interaction during exposure, dissolution of internal components of the resist into the de-ionized water, and the influence of residual moisture generated during exposure on post-exposure processing. To prevent these unwanted effects, optimization of the three main components of the lithography system: materials, track and scanner, is required. For the materials, 193nm resist formulation improvements specifically for immersion processing have reduced the leaching and the sensitivity to water related defects, further benefits can be seen by the application of protective top coat materials. For the track component, optimization of the processing conditions and immersion specific modules are proven to advance the progress made by the material suppliers. Finally, by optimizing conditions on the 3<sup>rd</sup> generation immersion scanner with the latest hardware configuration, defectivity levels comparable to dry processing can be achieved. In this evaluation, we detail the improvements that can be realized with new immersion specific track rinse modules and formulate a hypothesis for the improvements seen with the rinsing process. Additionally, we show the current status of water induced immersion specific defect reduction using the latest advances in technology.
Diagnosis of parametric path delay faults (2002)

Published research on delay fault testing has largely focused on generating test vector pairs (called delay fault tests) to detect delay faults in a circuit. Little attention has been paid to the diagnosability of delay faults-in the quest for generating tests which can simultaneously detect a delay fault on many paths, one loses the ability to determine which paths caused a chip failure. Since fabrication process perturbations contribute to the occurrence of delay faults, one would also like to determine the likely fabrication process parameter values given that a chip has failed for a set of delay fault tests. We present a framework to detect which parts of the circuit are likely to have caused a chip failure for a set of delay fault tests, and to find the associated fabrication process parameter deviations from their nominal values. This diagnosis is done by using a path sensitization mechanism to find the path delay conditions for which the chip exhibits a delay fault for a subset of the applied tests, followed by a statistical analysis to locate the likely fabrication process parameter value combinations and the parts of the circuit which are likely to have caused the failure. We present results of experiments performed an some ISCAS'89 benchmark circuits, and also relate the slack of a path segment to its probability of contributing to the circuit failure.
Effects of Melatonin on In Vitro Development of Mouse Two-Cell Embryos Cultured in HTF Medium (2010)

Melatonin is capable of improving the developmental capacity of ovine, porcine and bovine embryos in vitro. However, whether melatonin possesses similar benefits to the in vitro mouse embryonic development has yet to be determined. In this study, we assessed the effects of various concentrations of melatonin (10-13 to 10-3 M) on the in-vitro development of mouse embryos cultured in HTF medium for 96 hr; embryos cultured without melatonin were used as control. The in vitro development of mouse two-cell embryos significantly benefited from treatment with melatonin in a concentration-dependent manner. The effects of melatonin on the rates of blastocyst formation, hatching/hatched blastocysts and cell number per blastocyst were bi-phasic; all significantly increased by melatonin at 10-13 to 10-5 M and decreased by melatonin at 10-3 M. Maximal benefit of melatonin on in vitro mouse 2-cell embryo development was achieved at a concentration of 10-9 M. In comparison to control, 10-9 M melatonin increased blastocyst formation rate from 48.08 +/- 5.25% to 82.08 +/- 2.34% (p < 0.05), hatched blastocyst rate from 25.65 +/- 11.79% to 66.47 +/- 4.94% (p < 0.05), and cell number per blastocyst 62.71 +/- 5.97 to 77.91 +/- 10.63 (p < 0.05). Thus, our datas demonstrated firstly that melatonin has beneficial effects on the in vitro development of 2-cell mouse embryos cultured in HTF medium.
Robot-assisted Versus Laparoscopic Surgery for Rectal Cancer (2017)

Robot-assisted surgery in rectal cancer showed TME quality comparable with that of laparoscopic surgery, and it demonstrated similar postoperative morbidity, bowel function recovery, and quality of life.