gebhart/patrepeval huggingface dataset:
Transport and interaction of nitrogen oxides and NO2 with CO2-HCO3- transporters in pancreatic acini (1994)

Recently, we showed that NO2- increases gap junction (GJ) permeability and synchronizes intracellular Ca2+ concentration oscillations in pancreatic acini (Loessburg et al., J. Biol. Chem. 268: 19769-19775, 1993). NO2- is also an end product of nitric oxide (NO) production and metabolism. Because of the effect of NO2- on GJ permeability and the possible importance of NO2- in NO metabolism and cytotoxicity, we used pancreatic acinar cells and intracellular pH (pHi) measurements to study the interaction of nitrogen oxides and NO2- with cellular proteins. Exposing cells to NO2- resulted in a concentration-dependent cytosolic acidification. The acidification did not require the transport of NO2- and was not mediated by diffusion of HNO2. Because the acidification was prevented by CO2-HCO3- and inhibition of carbonic anhydrase, it is possible that other nitrogen oxides present in a solution containing NO2- enter the cells by diffusion and interact with OH- or H2O to stably acidify the cytosol. NO2- itself is shown to be transported by the HCO3- transporters present in the plasma membrane. Thus manipulation of the cellular Cl- gradient and 4,4'-diisothiocyanostilbene-2,2'-disulfonic acid (DIDS) were used to show Cl-/NO2- exchange, whereas stimulation of external Na(+)-dependent amiloride-insensitive and DIDS-sensitive pHi increase in acidified cells was used to demonstrate a Na(+)-(NO2-)n cotransport. Hence NO2- can be a convenient substitute for HCO3- when studying HCO3- transport in an open system. The studies also show that cellular levels of nitrogen oxides and NO2- can be modulated by the cellular HCO3(-)-buffering system.(ABSTRACT TRUNCATED AT 250 WORDS)
Significance of C4d Banff Scores in Early Protocol Biopsies of Kidney Transplant Recipients with Preformed Donor-Specific Antibodies (DSA) (2010)

The significance of C4d-Banff scores in protocol biopsies of kidney transplant recipients with preformed donor-specific antibodies (DSA) has not been determined. We reviewed 157 protocol biopsies from 80 DSA+ patients obtained at 3 months and 1 year post-transplant. The C4d Banff scores (1,2,3) were associated with significant increments of microcirculation inflammation (MI) at both 3 months and 1 year post-transplant, worse transplant glomerulopathy and higher class II DSA-MFI (p < 0.01). Minimal-C4d had injury intermediate between negative and focal, while focal and diffuse-C4d had the same degree of microvascular injury. A total of 54% of patients had variation of C4d score between 3 months and 1 year post-transplant. Cumulative (3 month + 1 year) C4d scores correlated with long-term renal function worsening (p = 0.006). However, C4d staining was not a sensitive indicator of parenchymal disease, 55% of C4d-negative biopsies having evidence of concomitant MI. Multivariate analysis demonstrated that the presence of MI and class II DSA at 3 months were associated with a fourfold increased risk of progression to chronic antibody-mediated rejection independently of C4d (p < 0.05). In conclusion, the substantial fluctuation of C4d status in the first year post-transplant reflects a dynamic humoral process. However, C4d may not be a sufficiently sensitive indicator of activity, MI and DSA being more robust predictors of bad outcome.
3DTV: Capture, Transmission, and Display of 3D Video (2008)

Art. 585216, 2 S.
Magnetisation density distribution in Mn<sub>1/4</sub>TaS<sub>2</sub>: observation of conduction electron spin polarisation (1983)

The authors have determined the magnetisation density distribution in the ferromagnetic layered compound Mn 1/4 TaS 2 , using the classical polarised neutron technique. These studies show that although the magnetisation is principally localised on the manganese sites, there is a significant spin polarisation of the conduction electrons, extending throughout the unit cell. These measurements thus provide direct evidence of an important interaction between the Ta conduction electrons and the localised moments on the Mn ions, confirming previous speculations based on transport and optical data. Moreover such an interaction suggests an obvious mechanism, the RKKY interaction, for the exchange interaction between the Mn moments. The moment on the Mn sites is depressed, as a result of this interaction, by about 15% compared with that expected for a Mn 2+ d 5 ion. The Mn ions are surrounded by an antiferromagnetically polarised cloud of electrons and the maximum spin density within the TaS 2 layer is about 3% of the maximum spin density on the Mn site. There is no evidence from these experiments that the S atoms play a role in the magnetic Mn-Mn exchange interactions.
<i>In vitro</i> cloning of complex mixtures of DNA on microbeads: Physical separation of differentially expressed cDNAs (2000)

We describe a method for cloning nucleic acid molecules onto the surfaces of 5-micrometer microbeads rather than in biological hosts. A unique tag sequence is attached to each molecule, and the tagged library is amplified. Unique tagging of the molecules is achieved by sampling a small fraction (1%) of a very large repertoire of tag sequences. The resulting library is hybridized to microbeads that each carry approximately 10(6) strands complementary to one of the tags. About 10(5) copies of each molecule are collected on each microbead. Because such clones are segregated on microbeads, they can be operated on simultaneously and then assayed separately. To demonstrate the utility of this approach, we show how to label and extract microbeads bearing clones differentially expressed between two libraries by using a fluorescence-activated cell sorter (FACS). Because no prior information about the cloned molecules is required, this process is obviously useful where sequence databases are incomplete or nonexistent. More importantly, the process also permits the isolation of clones that are expressed only in given tissues or that are differentially expressed between normal and diseased states. Such clones then may be spotted on much more cost-effective, tissue- or disease-directed, low-density planar microarrays.
A REVIEW OF THE PAVEMENT MANAGEMENT SYSTEM OF THE STATE OF LOUISIANA-PHASE I (2008)

Said Ismail, P.E. 1. Associate Professor, Department of Civil Engineering, University of Louisiana at Lafayette, 254J- Madison Hall, Lafayette, LA 70504, Phone: (337) 482-5356, Fax: (337) 482-6688, Email: mxk0940@louisiana.edu 2. Professor, Department of Civil and Environmental Engineering Michigan State University, 3553 Engineering Bldg. E.Lansing, MI 48824-1226,Ph 517) 355-5147, Fax:(517) 432-1827, email: baladi@egr.msu.edu 3. Pavement and Geotechnical Research Administrator, Louisiana Transportation Research Center, 4101 Gourrier Ave, Baton Rouge, LA 70808, Ph: (225) 767-9162, email: doczhang@dotd.la.gov 4. Management Systems Engineer, Louisiana Department of Transportation and Development, Office of Planning and Programming, P.O. Box 94245, Baton Rouge, La 70804, Phone: (225) 242-4547, Fax: (225) 242-4598, e-mail: sismail@dotd.louisiana.gov Word Count Abstract: = 226 Text: = 5,221 Tables: 3 x 250 = 750 Figures: 3 x 250 = 750 References : = 502 Total: = 7,449 Prepared for 87
Prioritizing transcriptional factors in gene regulatory networks with PageRank (2020)

Biological states are controlled by orchestrated transcriptional factors (TFs) within gene regulatory networks. Here we show TFs responsible for the dynamic changes of biological states can be prioritized with temporal PageRank. We further show such TF prioritization can be extended by integrating gene regulatory networks reverse engineered from multi-omics profiles, e.g. gene expression, chromatin accessibility, and chromosome conformation assays, using multiplex PageRank.
Effects of Methylone Pre-Exposure on Fluoxetine-Induced Conditioned Taste Avoidance in Male and Female Sprague-Dawley Rats (2023)

Methylone pre-exposure had no impact on fluoxetine-induced avoidance. These findings suggest that it is unlikely that 5-HT mediates the aversive effects of methylone. The implications of the present results for the mechanisms mediating methylone's aversive effects were discussed. Understanding such mechanisms is important in predictions relevant to drug history and abuse liability as a variety of subject and experiential factors known to affect (reduce) a drug's aversive effects may increase its use and potential for abuse.
The NYU Ultracomputer—designing a MIMD, shared-memory parallel machine (Extended Abstract) (1982)

We present the design for the NYU Ultracomputer, a shared-memory MIMD parallel machine composed of thousands of autonomous processing elements. This machine uses an enhanced message switching network with the geometry of an Omega-network to approximate the ideal behavior of Schwartz's paracomputer model of computation and to implement efficiently the important fetch-and-add synchronization primitive. We outline the hardware that would be required to build a 4096 processor system using 1990's technology. We also discuss system software issues, and present analytic studies of the network performance. Finally, we include a sample of our effort to implement and simulate parallel variants of important scientific programs.
The long and winding road to new porphycenes (2012)

We describe attempts — not always successful — made over the years to improve the efficiency of porphycene synthesis and to produce novel compounds, custom-designed for specific purposes. New porphycenes are reported, some of them obtained rather unexpectedly as by-products of the planned reactions. Structure and energy computations of possible tautomeric forms in porphycenes substituted by one, two, three, and four tert-butyl groups lead to predictions regarding the kinetics and mechanisms of intramolecular double hydrogen transfer. The occurrence of tautomerization in single molecules of tert-butylsubstituted porphycenes is demonstrated by using fluorescence polarization techniques.
The Role of TGA-DTA in the Initial Evaluation of the Solid State Forms for Pharmaceutical New Chemical Entities, Part 1: Evaluation of Pure Forms (2007)

TGA-DTA plays a central role in the strategy outlined for early evaluation of the solid state forms available to pharmaceutical new chemical entities. At this early stage of development, compound and time are typically at a premium, so a successful strategy requires making the best possible use of the materials and time available. In addition, because of time and compound limitations, the goal of a solid state investigation is focused upon early stage objectives rather than development of a complete understanding of all available solid state forms. The TGA-DTA is well suited to addressing these needs.
1/ <i>f</i> noise of Sb-based <i>p</i> -channel HFETs (2008)

The 1/f noise of antimonide-based p-channel HFETs has been measured for the first time. The devices are fabricated with an InAlSb/AlGaSb barrier and a strained In0.41Ga0.59Sb quantum-well channel, yielding a channel hole mobility of 1020 cm2/V s and a sheet density of 1.6×1012 cm−2. The low-frequency noise spectrum in the linear region has a pure 1/f slope with no generation–recombination component. The Hooge parameter, αH, varies between 3×10−4 and 9×10−3 depending on the gate bias.
On the transient behaviour of a laminar rotor–stator cavity (2018)

The unsteady laminar flow between two large rotating disks when one of them is impulsively started is described using the von Kármán similarity analysis to reduce the solution of the Navier–Stokes equations to a set of ordinary differential equations. It is found that the transient phenomenon consists of three distinct phases. Firstly, the development of the Ekman boundary layer, where a quasi-steady Stewartson-type of flow is created. Secondly, angular momentum is initially diffused in the axial direction until the inward radial convection of angular momentum becomes dominating. Thirdly, a Batchelor flow is created once the Bödewadt boundary layer is developed and the entrainment of disk and stator boundary layers are balanced. The dependences of the characteristic dimensionless times on the Reynolds number based on the cavity gap for the second and third stages have been identified numerically and analytically. It is found that the diffusive part of the transient is bypassed if the flow, initially at rest, is perturbed with a small circumferential velocity. The flow and heat transfer transient during a ramp of finite duration has been computed numerically. The integral angular momentum and energy balances of the cavity have been performed in order to understand the energy and momentum budget of the cavity. It is concluded that the spin-up and the spin-down process of a rotor–stator cavity using a quasi-stationary approximation of the fluid, where the time derivatives are neglected, is questionable for realistic gas turbine applications. Finally, the self-similar solution is compared against two-dimensional axisymmetric, steady and unsteady, laminar simulations to assess the limitations and validity of the self-similar analysis. It has been identified that in a closed squared cavity the outer shroud modifies the physics of the transient, but the general conclusions drawn from the one-dimensional model are still valid.
Supplementary Figures S1-S2 from Involvement of the TGF-β and β-Catenin Pathways in Pelvic Lymph Node Metastasis in Early-Stage Cervical Cancer (2023)

Supplementary Figures S1-S2 from Involvement of the TGF-β and β-Catenin Pathways in Pelvic Lymph Node Metastasis in Early-Stage Cervical Cancer
Characteristics of highly stacked quantum dot solar cells fabricated by intermittent deposition of InGaAs (2010)

We report GaAs-based quantum dot (QD) solar cells fabricated by the intermittent deposition of InGaAs using molecular beam epitaxy. We obtained a highly stacked and well-aligned InGaAs/GaAs QD structure of over 100 layers without using a strain compensation technique. The external quantum efficiency of multistacked InGaAs QD solar cells extends the photo-absorption spectra toward a wavelength longer than the GaAs band gap, and the efficiency increases as the number of stacking layers increases. The short-circuit current density of the solar cells increases as the number of InGaAs QD layers increases. Moreover, InGaAs QD solar cells have high open circuit voltage and good cell characteristics even though an interdot spacing is reduced to 3.5 nm. The performance of the QD solar cells indicates that the novel InGaAs QDs facilitate the fabrication of highly stacked QD layers that are suitable for solar cell devices requiring thick QD layers with a minband for sufficient light absorption.
Suppressed blinking in CdTe/CdSe core‐shell quantum dots (2009)

Abstract CdTe/CdSe core‐shell colloidal quantum dots (CQDs) were synthesized by a unique colloidal procedure permitting the growth of spherical structures with the highest emission quantum efficiency (∼90%). The CQDs photoluminescence (PL) intensity shows only minor fluctuations (&lt;10%) in time, revealing a blinking suppression in the CQDs, while the PL of a single CQD shows the occurrence of longer lived (ns) multiexcitons, important for the applications of CQDs also in gain devices. (© 2009 WILEY‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)
Supplementary Figure 1 from Evaluation of Diffusion-Weighted MRI for Pretherapeutic Assessment and Staging of Lymphoma: Results of a Prospective Study in 140 Patients (2023)

&lt;p&gt;PDF file - 388KB, A 63 year-old male patient with a histologically verified MALT lymphoma of the stomach (light blue arrows) and the left parotid gland (light blue arrowheads). The parotid lesion shows only a very faint tracer uptake on 18F-FDG-PET and the fused color-coded PET/CT that was interpreted as physiological muscle uptake by one rater and as mild inflammation of the gland by the other rater. On CE-CT, where the lesion was missed by both raters, the left parotid gland appears only slightly larger than the right gland, and there are some uncharacteristic calcifications. However, no lesion can be delineated. On DWI and fused color-coded DWI-MRI, the lesion shows a very high, clearly abnormally high signal, indicative of strong diffusion restriction (high cellular density). The thickened gastric wall shows no abnormal tracer uptake on PET and PET/CT and is unspecific on CE-CT, whereas it shows an abnormally high signal on DWI and DWI-MRI, in good accordance with the histologically verified lymphoma. Note: the homogeneous high signal of the spleen on DWI(-MRI) is physiological.&lt;/p&gt;
SU‐GG‐T‐446: Dosimetric Characteristics of High Definition Multi‐Leaf Collimator (2008)

Purpose: A new type of high‐definition multi‐leaf collimator (HD 120 MLC, Varian Medical Systems) is being introduced into clinical practice to improve the conformality of stereotactic radiation therapy and radiosurgery. Its leaf width at isocenter is 2.5 mm. The interface and casing are the same as Millennium 120 MLC so it can be easily fit inside the gantry for better clearance and efficiency. This study investigated the dosimetric characteristics of this new micro MLC. Method and Materials: The HD 120 MLC was installed in a Novalis TX dedicated image‐guided SRS/SBRT machine. Beam penumbra (defined between 20–80%) was measured with a scanning radiosurgery diode for various field sizes, depth, and beam energies. Dynamic dosimetric gap and leaf transmission were measured with both low (6 MV and 6 MV SRS) and high energy (15 MV) photon beams. The conformity and step effect were studied with a series of circular beams with various radius. Results: The penumbra of HD 120 MLC was measured to be 0.25 cm for 6 MV at 1.5 cm depth with 2 cm × 2 cm field size. It increases to 0.49 cm for 30 cm × 30 cm field size. For 15 MV at 3 cm depth, the penumbra increases from 0.36 cm at 2 cm × 2 cm to 0.60 at 30 cm × 30 cm. For other field sizes and depth, the penumbra values are listed in Table I. The dynamic dosimetric gap was 0.86 cm for 6 MV and 0.98 mm for 15 MV. The leaf transmission factors were 1.17% for 6 MV and 1.33% for 15 MV. Conclusion: HD 120 MLC provides finer beam penumbra, smaller dynamic dose gap, and lower leaf transmission compared to conventional Millennium MLC, and can thus potentially improve the conformality of SRS/SBRT treatments.
Volumetric Characterization of Microvasculature in Ex Vivo Human Brain Samples By Serial Sectioning Optical Coherence Tomography (2022)

This method provides a viable tool for quantitative characterization of volumetric microvascular network as well as the axonal bundle properties in normal and pathological tissues of the ex vivo human brain.
A fine‐needle aspiration‐based protein signature discriminates benign from malignant breast lesions (2018)

There are increasing demands for informative cancer biomarkers, accessible via minimally invasive procedures, both for initial diagnostics and to follow-up personalized cancer therapy. Fine-needle aspiration (FNA) biopsy provides ready access to relevant tissues; however, the minute sample amounts require sensitive multiplex molecular analysis to achieve clinical utility. We have applied proximity extension assays (PEA) and NanoString (NS) technology for analyses of proteins and of RNA, respectively, in FNA samples. Using samples from patients with breast cancer (BC, n = 25) or benign lesions (n = 33), we demonstrate that these FNA-based molecular analyses (a) can offer high sensitivity and reproducibility, (b) may provide correct diagnosis in shorter time and at a lower cost than current practice, (c) correlate with results from routine analysis (i.e., benchmarking against immunohistochemistry tests for ER, PR, HER2, and Ki67), and (d) may also help identify new markers related to immunotherapy. A specific 11-protein signature, including FGF binding protein 1, decorin, and furin, distinguished all cancer patient samples from all benign lesions in our main cohort and in smaller replication cohort. Due to the minimally traumatic sampling and rich molecular information, this combined proteomics and transcriptomic methodology is promising for diagnostics and evaluation of treatment efficacy in BC.
Towards a Mechanistic Understanding of Factors Controlling the Stereoselectivity of Transketolase (2018)

Abstract A structural model for thiamine‐diphosphate (ThDP)‐dependent transketolase (TK) was developed to analyse the effect of amino acid exchanges on the stereoselectivity of this synthetically important class of enzymes. In this study the carboligation of 3‐hydroxypyruvate as a donor and propanal, as well as pentanal, was studied. Based on literature data and additional mutagenesis studies using E. coli TK, a four‐state model was developed to explain the stereoselectivity of TKs by the relative orientation of donor and acceptor substrates in the active site prior to C−C‐bond formation. To enable a functional comparison of relevant amino acids of TKs from different species, a standard numbering scheme was developed. Using this concept, H26, H261, and F434 were identified as the key residues which mediate stereoselectivity, where two main factors influenced the arrangement of ThDP‐bound donor and acceptor prior to carboligation: the relative orientation of the substrate side chains and the orientation of the acceptor carbonyl group towards the donor hydroxy group. This model provides a first framework to understand the structure‐function relationships of TKs with respect to their stereoselectivity.
Pharmacological Characterisation of Pseudocerastes and Eristicophis Viper Venoms Reveal Anticancer (Melanoma) Properties and a Potentially Novel Mode of Fibrinogenolysis (2021)

Venoms are a rich source of potential lead compounds for drug discovery, and descriptive studies of venom form the first phase of the biodiscovery process. In this study, we investigated the pharmacological potential of crude <i>Pseudocerastes</i> and <i>Eristicophis</i> snake venoms in haematological disorders and cancer treatment. We assessed their antithrombotic potential using fibrinogen thromboelastography, fibrinogen gels with and without protease inhibitors, and colourimetric fibrinolysis assays. These assays indicated that the anticoagulant properties of the venoms are likely induced by the hydrolysis of phospholipids and by selective fibrinogenolysis. Furthermore, while most fibrinogenolysis occurred by the direct activity of snake venom metalloproteases and serine proteases, modest evidence indicated that fibrinogenolytic activity may also be mediated by selective venom phospholipases and an inhibitory venom-derived serine protease. We also found that the <i>Pseudocerastes</i> venoms significantly reduced the viability of human melanoma (MM96L) cells by more than 80%, while it had almost no effect on the healthy neonatal foreskin fibroblasts (NFF) as determined by viability assays. The bioactive properties of these venoms suggest that they contain a number of toxins suitable for downstream pharmacological development as candidates for antithrombotic or anticancer agents.
[Effect of recombinant human p53 adenovirus (Ad-p53) combined with EGFR inhibitor gefitinib on the sensitivity of breast cancer MDA-MB-468 cells]. (2014)

Wild-type p53 may reverse the sensitivity of MDA-MB-468 cells to gefitinib through down-regulation of the PI3K/Akt pathway. The apoptotic activity induced by this combination treatment might be regulated through caspase cascade.