gebhart/patrepeval huggingface dataset:
Photoaffinity Labeling of Tumor Promoter-Binding Protein (CN-TPBP) and Preparation of Affinity Sorbent Gels. (1997)

Cytosolic-nuclear tumor promoter-specific binding protein (CN-TPBP) was photoaffinity-labeled with a specific ligand, 3beta,5alpha-dihydroxycholestan-6-one (YS-64). Analysis by ODS-HPLC of peptide fragments obtained from the labeled CN-TPBP by trypsinization indicated the existence of a single specifically labeled site. Affinity gels for the purification of CN-TPBP were then prepared. As ligands for the affinity gels, 12-O-tetradecanoylphorbol 13-acetate (TPA), a typical phorbol-type tumor promoter, and benzolactam-V8-310 (BL-V8-310), a structural/biological mimic of teleocidin-class tumor promoters, were adopted. The use of these gels afforded a protein that showed a single band of 58 kDa on SDS-PAGE.
Deep learning to predict Pulmonary Tuberculosis from Lung Posterior Chest Radiographs (2023)

Tuberculosis is one of the most dangerous health conditions on the globe. As it affects thehuman body, tuberculosis is an infectious illness. According to the World Health Organization, roughly1.7 million individuals get TB throughout their lifetimes. Pakistan ranks fifth among high-burdennations and is responsible for 61% of the TB burden within the WHO Eastern Mediterranean Region.Various methods and procedures exist for the early identification of TB. However, all methods andtechniques have their limits. Most currently known approaches for detecting TB rely on model-basedlung segmentation. The primary purpose of the proposed study is to identify pulmonary TB utilisingchest X-ray (Poster Anterior) lung pictures processed using image processing and machine learningmethods. The recommended study introduces a unique model segmentation strategy for TB identification.For classification, CNN and Google Net. Other systems based on deep learning are used. Thebest accuracy attained by the suggested method utilising Google Net on merged datasets was 89.58percent. The recommended study will aid in the detection and accurate diagnosis of TB.
WITHDRAWN: Enhancement of efficiency of single walled carbon nanotubes-n-type silicon solar cells using molybdenum disulfide (2019)

This article has been withdrawn at the request of the author, on the basis of the need to add extra data related to the research work. The Publisher apologizes for any inconvenience this may cause. The Publisher apologizes for any inconvenience this may cause. The full Elsevier Policy on Article Withdrawal can be found at https://www.elsevier.com/about/our-business/policies/article-withdrawal
962: Highly Efficient Therapeutic Gene Delivery for Bladder Cancers by Intravesically Administered Replication-Competent Retroviral Vectors (2004)

You have accessJournal of UrologyDiscussed Poster, Monday, May 10, 2004, 1:00 - 5:00 pm1 Apr 2004962: Highly Efficient Therapeutic Gene Delivery for Bladder Cancers by Intravesically Administered Replication-Competent Retroviral Vectors Eiji Kikuchi, Silvia Menendez, Makoto Ohori, Carlos Cardon-Carda, Christopher R. Logg, Noriyuki Kasahara, and Bernard H. Bochner Eiji KikuchiEiji Kikuchi More articles by this author , Silvia MenendezSilvia Menendez More articles by this author , Makoto OhoriMakoto Ohori More articles by this author , Carlos Cardon-CardaCarlos Cardon-Carda More articles by this author , Christopher R. LoggChristopher R. Logg More articles by this author , Noriyuki KasaharaNoriyuki Kasahara More articles by this author , and Bernard H. BochnerBernard H. Bochner More articles by this author View All Author Informationhttps://doi.org/10.1016/S0022-5347(18)38199-0AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail "962: Highly Efficient Therapeutic Gene Delivery for Bladder Cancers by Intravesically Administered Replication-Competent Retroviral Vectors." The Journal of Urology, 171(4S), p. 255 © 2016 by American Urological AssociationFiguresReferencesRelatedDetails Volume 171Issue 4SApril 2004Page: 255 Advertisement Copyright & Permissions© 2016 by American Urological AssociationMetricsAuthor Information Eiji Kikuchi More articles by this author Silvia Menendez More articles by this author Makoto Ohori More articles by this author Carlos Cardon-Carda More articles by this author Christopher R. Logg More articles by this author Noriyuki Kasahara More articles by this author Bernard H. Bochner More articles by this author Expand All Advertisement PDF DownloadLoading ...
Influence of Dominant Electrical Brainwaves on Learning Performance (2009)

Abstract: In this work, we developed a new approach to predict learning performance regarding a group, by analyzing his brain activity during a two-day experiment. In fact, we recruited 21 participants and asked them to read multiple texts in the first day and to answer questions about these texts on the second day. In our experiment we recorded for every learner the amplitude of the six main frequency bands and we computed the rate of the dominant brainwave vector per second. The other factor that we register is the variation of this rate during the two days of the experiment. The combination of these factors was used to predict the learner performance of the 21 participants and permitted us to predict the learning performance with 76 % of accuracy.
In Vitro Activation of a Nonproductive Immunoglobulin Allele by a Single Base Pair Insertion (1994)

We have shown that one of the alleles in a hybridoma was nonproductive because the sequence in the N region of the heavy chain caused it to be out of frame and to terminate prematurely. This allele became productive, and the gamma 1 heavy chain that it encoded was secreted when an adenosine was inserted to produce an open reading frame. This event occurred at a very low frequency following mutagenesis of the cultured cells. This result suggests that similar sorts of events must occur in vivo when both productive and nonproductive alleles undergo frequent mutations and that new genes may be expressed in hybridomas as they are being subcloned.
Cluster analysis of WIBS single-particle bioaerosol data (2013)

Abstract. Hierarchical agglomerative cluster analysis was performed on single-particle multi-spatial data sets comprising optical diameter, asymmetry and three different fluorescence measurements, gathered using two dual Wideband Integrated Bioaerosol Sensors (WIBSs). The technique is demonstrated on measurements of various fluorescent and non-fluorescent polystyrene latex spheres (PSL) before being applied to two separate contemporaneous ambient WIBS data sets recorded in a forest site in Colorado, USA, as part of the BEACHON-RoMBAS project. Cluster analysis results between both data sets are consistent. Clusters are tentatively interpreted by comparison of concentration time series and cluster average measurement values to the published literature (of which there is a paucity) to represent the following: non-fluorescent accumulation mode aerosol; bacterial agglomerates; and fungal spores. To our knowledge, this is the first time cluster analysis has been applied to long-term online primary biological aerosol particle (PBAP) measurements. The novel application of this clustering technique provides a means for routinely reducing WIBS data to discrete concentration time series which are more easily interpretable, without the need for any a priori assumptions concerning the expected aerosol types. It can reduce the level of subjectivity compared to the more standard analysis approaches, which are typically performed by simple inspection of various ensemble data products. It also has the advantage of potentially resolving less populous or subtly different particle types. This technique is likely to become more robust in the future as fluorescence-based aerosol instrumentation measurement precision, dynamic range and the number of available metrics are improved.
Defects in a Noncentrosymmetric Lemellar Block Copolymer Blend (2005)

Here we report results from a defect study on the noncentrosymmetric (NCS) lamellar blend of an ABCD tetrablock copolymer and an AD diblock copolymer. The block copolymers used were polystyrene-block-polybutadiene-block-polyisoprene-block-polycyclohexadiene and polystyrene-block-polycyclohexadiene. Coexisting tetrablock-rich mixed centrosymmetric (CS) and NCS lamellar morphologies were seen in TEM, as predicted by the mean-field theory. NCS grain boundary defects similar to those in CS lamellar systems were observed as well as new defects unique to NCS layered systems, such as chain polarity reversals and kink bands with dilation or compression of the layers. In addition to morphology observations, geometrical and energetic calculations were performed on several new NCS defects, which are in good agreement with experimental results.
Demonstrations on the scattering of ultrasound by turbulence in water (1989)

A beam of monochromatic sound incident on a turbulent velocity field (produced by a submerged water jet) is scattered by the velocity fluctuations in the flow. Angular measurements of the Doppler shift and spectral broadening in the received frequency spectrum of the scattered sound intensity help to characterize the mean flow and rms velocities of the turbulent field, respectively. Scattered spectra are displayed for comparison in the cases where the incident beam is generated by a point source, a plane circular array, and a focused spherical array transducer. Results are shown in an arrangement where the focused beam scans across the width of the jet. Scattering theories are briefly mentioned in light of spectral broadening results.
Triangulation (2011)

Die Triangulation ist ein Messverfahren zur Abstandsmessung. Dabei wird mit einem Laser oder einer Laserdiode ein kleiner Fleck auf der Oberfläche erzeugt, deren Entfernung man bestimmen möchte. Unter einem definierten Winkel wird der Fleck auf einen Detektor abgebildet. Je nach Abstand zwischen Sensor und Oberfläche verändert sich die Geometrie des Dreiecks aus Laser, Oberfläche und Detektor. Damit ändert sich auch die Position des abgebildeten Flecks auf dem Detektor. Aus der Position kann schließlich auf den Abstand zurückgerechnet werden.
Allocation of periodic task modules with precedence and deadline constraints in distributed real-time systems (1997)

This paper addresses the problem of allocating (assigning and scheduling) periodic task modules to processing nodes in distributed real-time systems subject to task precedence and timing constraints. Using the branch-and-bound technique, a module allocation scheme is proposed to find an "optimal" allocation that maximizes the probability of meeting task deadlines. The task system within a planning cycle is first modeled with a task flow graph which describes computation and communication modules, as well as the precedence constraints among them. To incorporate both timing and logical correctness into module allocation, the probability of meeting task deadlines is used as the objective function. The module allocation scheme is then applied to find an optimal allocation of task modules in a distributed system. The timing aspects embedded in the objective: function drive the scheme not only to assign task modules to processing nodes, but also to use a module scheduling algorithm (with polynomial time complexity) for scheduling all modules assigned to each node, so that all tasks maybe completed in time. In order to speed up the branch-and-bound process and to reduce the computational complexity, a dominance relation is derived. Several numerical examples are presented to demonstrate the effectiveness and practicality of the proposed scheme.
A Novel Framework for DTCO: Fast and Automatic Routability Assessment with Machine Learning for Sub-3nm Technology Options (2021)

We report, for the first time, block-level area scaling that is reversed from cell-level scaling in cell height 400 unique standard-cell architectures are studied, combining cell height (CH, 80~150nm), contacted poly pitch (CPP, 39~57nm), metal pitch (MP, 16~30nm) and use/non-use of buried power rails (BPR). Cell- and design-level routability assessments are performed to obtain routability index (a.k.a. K th ) and utilization of designs. CH <120nm with four available tracks increases block-level area due to routing difficulty, showing diminishing return from further pushing of ground rules. BPR improves block-level scaling with CH <120nm, but benefit slows down with CH <100nm. A 1:2 gear ratio (MP:CPP) improves block-level area compared to a 2:3 ratio. This DTCO flow is automated, and the ML-based prediction expedites the process.
Biological Safety Assessment of Docosahexaenoic Acid Supplementation in a Randomized Clinical Trial for X-Linked Retinitis Pigmentosa (2003)

Long-term docosahexaenoic acid supplementation to patients with XLRP was associated with no identifiable safety risks in this 4-year clinical trial.
Conformational preferences of Leu-enkephalin in reverse micelles as membrane-mimicking environment (1997)

Enkephalin represents one of the bioactive peptide molecules most extensively investigated both in solution and in the crystal state. Depending upon the environment chosen for such studies, three main conformational states were identified for this flexible, linear pentapeptide—i.e., an extended conformation, a single-bend, and a double-bend structure. Since CD and Fourier transform ir (FTIR) spectra of Leu-enkephalin solubilized in negatively charged reverse micelles of bis (2-ethylhexyl)sulfosuccinate sodium salt/isooctane/water were supportive of a restricted conformational space of the aromatic side chains and of a bended type fold, we have analyzed by nmr the conformational preferences of Leu-enkephalin in reverse micelles using a synthetic [13C, 15N]-backbone-labeled sample. The overall conformation derived from nuclear Overhauser effect spectroscopy (NOESY) and 15N-filtered rotating frame NOESY (ROESY) spectra and by distance geometry calculations is a double-bend fold of the backbone that is comparable to one of the known x-ray structures. Thereby the tyrosine side chain is inserted into the hydrophobic core of the reverse micelles in a restrained conformational space as well evidenced by NOEs between the aromatic ring protons and the surfactant. The proximity of the aromatic rings of tyrosine and phenylalanine indicate a preferred structure consistent with the postulated conformation of the opioid peptide in the δ-receptor-bound state. These results confirm the interesting and promising properties of reverse micelles as membrane mimetica. © 1997 John Wiley & Sons, Inc. Biopoly 41: 591–606, 1997
Clinical and biochemical analysis of the ageing tear film (2019)

Distinct differences in tear film composition between the two age groups were observed. Parallels in terms of clinical symptoms which reflected a biochemical response (and vice versa) were found, but specific correlations between clinical measurements and biomarkers for individual subjects were not observed.
Dynamic Light Scattering Near the Smectic A—Smectic C Phase Transition in Thin Planar Cells (1996)

Abstract Using the quasielastic light scattering we have studied the order parameter dynamics close to the SmA-SmC* phase transition in thin cells of ferroelectric liquid crystals, with planar boundary conditions. As a result of confinement, the bulk soft mode splits into two modes, whereas from the thickness dependence of the relaxation rate of the phase mode we measure the diffusion coefficients. The appearance of the chevron structure is manifested in the temperature dependence of the relaxation rate of the phase mode.
Evaluation of glioblastoma tumor microenvironment after treatment with pembrolizumab. (2020)

2559 Background: Neoadjuvant pembrolizumab improved outcome of patients with recurrent Glioblastoma (GBM) in two early phase clinical trials. However, several large phase II/III studies in patients with newly diagnosed and recurrent GBM failed to demonstrate a therapeutic benefit of anti-PD-1 therapy. Therefore, identification of biomarkers of response is crucial for appropriate patient selection and further clinical development of anti-PD-1 therapy. We reported the outcome of our window-of-opportunity clinical trial of neoadjuvant pembrolizumab in 15 patients with recurrent GBM, demonstrating rare CD8+ T cells and abundant of CD68+ macrophages in GBM tissue after 3 weeks of anti-PD-1 treatment (NCT02337686). In the current study, we compared tumor infiltrating lymphocyte (TIL) and PD-L1 scores, known biomarkers of response to anti-PD-1 therapy in other cancers, in pre-trial vs. on-trial tumor tissue and associated these markers with survival. Methods: We determined TIL score (morphological assessment of the presence or absence of TILs, 0-3) and PD-L1 H score (defined as [1*1+ %]+[2*2+ %]+[3*3+ %], 0-200) and correlated these with survival. The Wilcoxon signed rank test was used to compare levels of PD-L1 H or TIL scores between pre-trial and on-trial specimens. The Cox proportional hazards models were used to assess associations between correlative markers and progression free survival or overall survival (OS). Results: The on-trial TIL level (median: 3) was significantly higher than the pre-trial TIL level (median: 1) (p = 0.031). However the difference between pre-trial and on-trial PD-L1 levels was not statistically significant (p &gt; 0.9). Patients whose on-trial PD-L1 H score was ≥ 3 trended toward a longer OS than those with a PD-L1 H score &lt; 3 (HR [95% CI] = 0.225 [0.043, 1.183]) (p = 0.0782). Conclusions: Although GBM tissue lacks abundant T cells, treatment with pembrolizumab increases trafficking of T cells to the tumor microenvironment, which is necessary but not sufficient to induce an effector T-cell response. Elevated PD-L1 expression may be a biomarker of response to anti-PD1 therapy in GBM, which needs confirmation in larger studies. Further genomic, transcriptomic, and methylation profiling of the pre-trial and on-trial tissues is ongoing. Clinical trial information: NCT02337686 .
SHIP1 Intrinsically Regulates NK Cell Signaling and Education, Resulting in Tolerance of an MHC Class I–Mismatched Bone Marrow Graft in Mice (2015)

NK cells are an important component of host immune defense against malignancy and infection. NK cells are educated by MHC class I ligands to ensure self-tolerance while also promoting lytic competency against altered self and damaged self targets. However, the intracellular molecular events that culminate in tolerance and functional competency of educated NK cells remain undefined. Mice with germline deficiency in SHIP1 were shown to have a defective NK cell compartment. However, SHIP1 is expressed in all hematopoietic lineages, and consequently several hematolymphoid phenotypes have already been identified in certain cell types that are the result of SHIP1 deficiency in cells in separate and distinct lineages, that is, cell-extrinsic phenotypes. Thus, it was previously impossible to determine the NK cell-intrinsic role of SHIP1. In the present study, through the creation of an NK cell-specific deletion mouse model of SHIP1, we show that SHIP1 plays a profound NK lineage-intrinsic role in NK cell homeostasis, development, education, and cytokine production. Moreover, we show SHIP1 expression by NK cells is required for in vivo-mismatched bone marrow allograft rejection as well as for NK memory responses to hapten.
Simulation of Bubbles and Liquid Films (2006)

Liquid and gas interactions often contain bubbles surrounded by thin liquid films. Simulation of these liquid films is challenging since they quickly become thinner than the grid resolution, which leads to premature bursting or merging of the bubbles. We prevent this thinning process by applying a disjoining force to the film, obtaining bubbles that last much longer without bursting or merging. The surface tension on the liquid film is the next diffuculty. Since the level set is not differentiable at the center of the thin liquid film, the curvature computed from the level set gradient is noisy, and the thin liquid film ruptures quickly. To prevent this, we compute the surface tension from the local isosurface, obtaining long-lasting liquid films. However, since bubbles stay longer without bursting or merging, the volume loss of each bubble is noticeable. To solve this problem, we modify the pressure projection to produce a velocity field whose divergence is controlled by the proportional and integral feedback. This allows us to preserve the volume or, if desired, to inflate or deflate the bubbles. In addition to premature bursting and volume change, another difficulty is the complicated liquid surface, which increases memory and computational costs. To reduce storage requirement, we collocate the velocity and pressure to simplify the octree mesh. To reduce the computational complexity of the pressure projection, we use a multigrid method.
Synthesis, Luminescence and Nonlinear Optical Properties of Homoleptic Tetracyanamidogermanates <i>ARE</i>[Ge(CN<sub>2</sub>)<sub>4</sub>] (<i>A</i> = K, Cs, and <i>RE</i> = La, Ce, Pr, Nd, Sm, Eu, Gd) (2017)

Two new series of tetracyanamidogermanates were prepared by solid‐state reaction of appropriate amounts of RE F 3 ( RE = rare earth), A 2 [GeF 6 ] ( A = alkaline), and Li 2 (CN 2 ) in evacuated silica tubes. Powder X‐ray diffraction patterns of crystalline samples of K RE [Ge(CN 2 ) 4 ] and Cs RE [Ge(CN 2 ) 4 ] were indexed isotypically to K RE [Si(CN 2 ) 4 ] and Rb RE [Ge(CN 2 ) 4 ], respectively. Luminescence properties of Ce 3+ , Eu 3+ , and Tb 3+ doped compounds and non‐linear optical properties (NLO) of K RE [Ge(CN 2 ) 4 ] are reported.
SarA plays a predominant role in controlling the production of extracellular proteases in the diverse clinical isolates of<i>Staphylococcus aureus</i>LAC and UAMS-1 (2020)

Using DNA affinity chromatography we demonstrate that the <i>S. aureus</i> regulatory proteins MgrA, Rot, SarA, and SarS bind DNA baits derived from the promoter regions associated with the genes encoding aureolysin, ScpAB, SspABC, and SplA-F. Three of four baits also bound SarR and SarZ, the exception in both cases being the ScpAB-associated bait. Using the USA300, methicillin-resistant strain LAC and the USA200, methicillin-sensitive strain UAMS-1, we generated mutations in the genes encoding each of these proteins alone and in combination with <i>sarA</i> and examined the impact on protease production, the accumulation of high molecular weight proteins, and biofilm formation. These studies confirmed that multiple regulatory loci are involved in limiting protease production to a degree that impacts all of these phenotypes, but also demonstrate that <i>sarA</i> plays a predominant role in this regard. Using <i>sarA</i> mutants unable to produce individual proteases alone and in combination with each other, we also demonstrate that the increased production of aureolysin and ScpA is particularly important in defining the biofilm-deficient phenotype of LAC and UAMS-1 <i>sarA</i> mutants, while aureolysin alone plays a key role in defining the reduced accumulation of alpha toxin and overall cytotoxicity as assessed using both osteoblasts and osteoclasts.
Automatic estimation of left ventricular dysfunction from echocardiogram videos (2009)

Echocardiography is often used to diagnose cardiac diseases related to regional and valvular motion abnormalities. Due to the low resolution of the imaging modality, the choice of viewpoint and mode, and the experience of the sonographers, there is a large variance in the estimation of important diagnostic measurements such as ejection fraction. In this paper, we develop an automatic algorithm to estimate diagnostic measurements from raw echocardiogram video sequences. Specifically, we locate and track the left ventricular region over a heart cycle using active shape models. We also present efficient ventricular localization in video sequences by automatically detecting and propagating echocardiographer annotations. Results on a large database of cardiac echo videos demonstrate the use of our method for the prediction of left ventricular dysfunction.