gebhart/patrepeval huggingface dataset:
Endoscopic augmentation of gastroesophageal junction using a full-thickness endoscopic suturing device (2018)

<b>Background and study aims </b> This preliminary study was conducted to determine the feasibility and safety of endoscopic augmentation of the gastroesophageal junction (GEJ) using the Apollo OverStitch endoscopic suturing system in patients with gastroesophageal reflux disease (GERD) symptoms. <b>Patients and methods </b> Endoscopic augmentation of GEJ was performed on 10 consecutive patients and the data were analyzed retrospectively. Using a double-channel gastroscope affixed to the endoscopic suturing platform, interrupted sutures were placed on the gastric side of the GEJ in 2 layers in order to create a narrowed and elongated GEJ. <b>Results </b> Technical success was achieved in all patients, including those with a history of previous antireflux procedures (n = 7) and those with a hiatal hernia (n = 6). The median follow-up duration was 5 mo (range: 2 - 12). The median pre-procedure GERD-Health Related Quality of Life Questionnaire improved from 20 (range: 11 - 45) to a post-procedure score of 6 (range: 3 - 25) ( <i>P</i> = 0.001). The median duration of GERD symptom improvement after the procedure was 1 mo (range: 0.5 - 4). Adverse events were limited to 1 patient who developed nausea and vomiting, which was self-limited. <b>Conclusions</b> The use of a novel endoscopic suturing technique for the treatment of GERD is feasible and safe. The procedure resulted in short-term GERD symptom improvement. Further prospective studies using refined techniques are currently underway to improve durability and to prove efficacy.
Analytical drain current models for AlGaAs/GaAs MODFET's including subthreshold conduction (1993)

Analytical models for self-aligned-gate AlGaAs/GaAs MODFET's that predict static current-voltage characteristics continuously from below to above threshold are presented. The characteristic equations are derived from fundamental device analysis and contain no nonphysical fitting parameters. They are closed-form and describe device behavior explicitly in terms of terminal voltages. The model equations are amenable to modification for incorporating short-channel effects both in the subthreshold and above-threshold operating regimes. Comparisons of model predictions with data from numerical models are presented. In addition to retaining the physical basis of MODFET operation, the models, due to their relative simplicity, promise digital circuit design, analysis, and simulations with accuracy, ease, and efficiency.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Gene Expression Changes Induced by a Recombinant E1<sup>–</sup>/E3<sup>–</sup> Adenovirus Type 5 Vector in Human Mammary Epithelial Cells (2005)

Our study provides insight into the host transcriptional response following transduction of an adenoviral vector into mammary epithelial cells.
A three dimensional in vitro glial scar model to investigate the local strain effects from micromotion around neural implants (2017)

Glial scar formation remains a significant barrier to the long term success of neural probes. Micromotion coupled with mechanical mismatch between the probe and tissue is believed to be a key driver of the inflammatory response. In vitro glial scar models present an intermediate step prior to conventional in vivo histology experiments as they enable cell-device interactions to be tested on a shorter timescale, with the ability to conduct broader biochemical assays. No established in vitro models have incorporated methods to assess device performance with respect to mechanical factors. In this study, we describe an in vitro glial scar model that combines high-precision linear actuators to simulate axial micromotion around neural implants with a 3D primary neural cell culture in a collagen gel. Strain field measurements were conducted to visualize the local displacement within the gel in response to micromotion. Primary brain cell cultures were found to be mechanically responsive to micromotion after one week in culture. Astrocytes, as determined by immunohistochemical staining, were found to have significantly increased in cell areas and perimeters in response to micromotion compared to static control wells. These results demonstrate the importance of micromotion when considering the chronic response to neural implants. Going forward, this model provides advantages over existing in vitro models as it will enable critical mechanical design factors of neural implants to be evaluated prior to in vivo testing.
Cellular Effects of Reversed Amidines on Trypanosoma cruzi (2007)

Aromatic diamidines represent a class of DNA minor groove-binding ligands that exhibit high levels of antiparasitic activity. Since the chemotherapy for Chagas' disease is still an unsolved problem and previous reports on diamidines and related analogues show that they have high levels of activity against Trypanosoma cruzi infection both in vitro and in vivo, our present aim was to evaluate the cellular effects in vitro of three reversed amidines (DB889, DB702, and DB786) and one diguanidine (DB711) against both amastigotes and bloodstream trypomastigotes of T. cruzi, the etiological agent of Chagas' disease. Our data show that the reversed amidines have higher levels of activity than the diguanidine, with the order of trypanocidal activities being as follows: DB889 > DB702 > DB786 > DB711. Transmission electron microscopy analysis showed that the reversed amidines induced many alterations in the nuclear morphology, swelling of the endoplasmic reticulum and Golgi structures, and consistent damage in the mitochondria and kinetoplasts of the parasites. Interestingly, in trypomastigotes treated with the reversed amidine DB889, multiple axoneme structures (flagellar microtubules) were noted. Flow cytometry analysis confirmed that the treated parasites presented an important loss of the mitochondrial membrane potential, as revealed by a decrease in rhodamine 123 fluorescence. Our results show that the reversed amidines have promising activities against the relevant mammalian forms of T. cruzi and display high trypanocidal effects at very low doses. This is especially the case for DB889, which merits further in vivo evaluation.
Initiators of the Type Mo(NAr)(CHR‘)(OR‘ ‘)2 for the Controlled Polymerization of Diethyldipropargylmalonate (2006)

The reaction between Mo(NAr)(trans-CHCHCHMe)[OCMe(CF3)2]2(quin) (Ar = 2,6-i-Pr2-C6H3; quin = quinuclidine) and lithium tert-butoxide yields Mo(NAr)(trans-CHCHCHMe)(O-t-Bu)2(quin) (1). The achiral,syn isomer could be isolated and was shown in an X-ray study to be a trigonal bipyramid in which quinuclidine is coordinated trans to a syn butenylidene group. A base-free species (2) that contains a five-membered ring as part of a trienylidene unit could be obtained by treating Mo(NAr)(CHCMe2R)[OCMe(CF3)2]2 (R = Me, Ph) with diethyl 3-(2-methylprop-1-enyl)-4-vinylcyclopent-3-ene-1,1-dicarboxylate (B) in pentane. The tert-butoxide analogue of 2 (3) was obtained straightforwardly and was shown in an X-ray study to be the syn alkylidene isomer. The reaction between 1-methylidene-5,5-bis(carboxyethyl)cyclohex-1-ene and Mo(NAr)(CHCMe3)[OCMe(CF3)2]2 gave Mo(NAr)[1-methylidene-5,5-bis(carboxyethyl)cyclohex-1-ene)][OCMe(CF3)2]2 (5a), which could be treated with LiO-t-Bu to yield an analogous tert-butoxide species (5b). An X-ray structure of a sample of 5b that retained 2 equiv of LiOCMe(CF3)2 showed it to be a dimeric species in which two Mo complexes were joined through a Li4O4 heterocubane-type structure binding to one ester oxygen in each of the Mo species. Reactions between diethyldipropargylmalonate (DEDPM) and 1, 3, or 5b showed initiation to be smooth with kp/ki values less than 1 and to yield oligomers that were consistent with formation of polymers that contain largely five-membered rings. All reactions can be followed by proton NMR spectra of the alkylidene proton region, and all appear to be living polymerizations under the conditions employed. A Wittig-like reaction between diethyl 3-formyl-4-(2-methylprop-1-enyl)cyclopent-3-ene-1,1-dicarboxylate (A) and 2 yielded a symmetric pentaene (C) as an ivory-colored solid. The heptaene (D) and the nonaene (E) could be isolated from reactions between 1 equiv of DEDPM and 3 in CH2Cl2 in the presence of 1 equiv of quinuclidine at −30 °C followed by quenching with aldehyde A.
Correction-Helical Structures of Poly(D-L-peptides). A Conformational Energy Analysis (1978)

ADVERTISEMENT RETURN TO ISSUEPREVArticleCorrection-Helical Structures of Poly(D-L-peptides). A Conformational Energy AnalysisF. Colonna-Cesari, S. Premilat, F. Heitz, G. Spach, and B. LotzCite this: Macromolecules 1978, 11, 2, 438Publication Date (Print):March 1, 1978Publication History Published online1 May 2002Published inissue 1 March 1978https://pubs.acs.org/doi/10.1021/ma60062a034https://doi.org/10.1021/ma60062a034research-articleACS PublicationsRequest reuse permissionsArticle Views23Altmetric-Citations-LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Influence of Ion Solvation on the Properties of Electrolyte Solutions B (2018)

It is widely appreciated that the addition of salts to water leads to significant changes in the thermodynamic and dynamic properties of these aqueous solutions that have great significance in biology and manufacturing applications. However, no theoretical framework currently exists that describes these property changes in an internally consistent fashion. In previous work, we developed a coarse-grained model of electrolyte solutions capable of reproducing basic trends on how salts influence the viscosity and water diffusion coefficient. The present work explores the predictions of this model for basic thermodynamic properties of electrolyte solutions, namely, the density, isothermal compressibility, and surface tension. On the basis of our model, we find that ion-specific effects on thermodynamics properties, and by extension the dynamics of electrolyte solutions, derive primarily from ion solvation.
An Algorithm for Risk Stratification of Preterm Infants (2017)

Preterm infants have a higher incidence of lifethreatening events including apnea (cessation of breathing), bradycardia (slowing of heart rate) and hypoxemia (oxygen de-saturation). In Neonatal Intensive Care Units, clinicians face a demanding task of assessing the risk of these infants based on their physiological signals. In this study, we propose an algorithm of heart rate dynamics that could potentially be employed for risk stratification of preterm infants.
Modulation of membrane receptor endocytosis by chemical effectors of membrane fluidity (1985)

Several chemical effectors were used to induce changes in spleen B cell membrane fluidity. Membrane fluidity was monitored by fluorescence polarization analysis of the hydrophobic probe 1,6-diphenyl-1,3,5-hexatriene (DPH) and cell viability was checked not to be affected by the treatments. Membrane immunoglobulin (Ig) endocytosis by the living B cells with modified or unmodified membranes was quantitatively measured by flow cytometry, using a previously described method (Métézeau et al., 1982, 1984). The kinetics of endocytosis of membrane Ig was not affected by chemical effectors increasing membrane fluidity. On the contrary, increasing membrane microviscosity resulted in the slowing down and eventually the blocking of membrane Ig endocytosis. It is suggested that a step depending on membrane microviscosity is involved in the process of endocytosis; this step may become rate limiting when membranes are artificially rendered or naturally become (i.e. for pathological or particularly differentiated cells) more viscous.
IDDF2020-ABS-0068 3D model reconstruction of the whole stomach from standard endoscope video (2020)

<h3>Background</h3> Endoscopy is a common clinical practice to evaluate gastrointestinal diseases. Although endoscopy assesses gastrointestinal mucosal surface, it cannot evaluate the shape and volume of gastrointestinal organs and localization of the lesion. The accurate localization of a malignant lesion within the global view of the stomach is crucial for gastric surgeons to make a clinical decision of the operative procedure. Further, the shape of gastrointestinal organs possibly associates with some abdominal symptoms or disorders. Structure from Motion (SfM) is a method to recover 3D scene structure and camera motion from multiple images. SfM may be applied to endoscopy in order to reconstruct the shape of gastrointestinal organs. We aimed to reconstruct the 3D model of the whole stomach from standard endoscopic video image using SfM. <h3>Methods</h3> Seven participants underwent gastroscopy under sedation for screening upper gastrointestinal diseases. The endoscope video was captured using a standard endoscope system. The video data was saved as an AVI format in 30 frames per second with full HD resolution. All endoscopic video was converted to RGB frames. The red channel of the extracted RGB frames were put to the SfM, where feature extraction, matching, pose estimation, and feature points triangulation were performed to generate a sparse 3D point cloud. Poisson surface reconstructed was performed to construct a 3D mesh model of the stomach. Finally, the texture of the endoscopic images was applied to the generated 3D mesh model to add more visual detail. <h3>Results</h3> Most 3D point clouds were extracted from the red channel of the endoscopic images with the indigo carmine dye (figure 1). 3D meshes and texture representation resembling the whole shape of a stomach were generated from the cloud model (figure 2). Gastric ulcer lesion was clearly localized and reconstructed in one subject. <h3>Conclusions</h3> Our study found that 3D reconstruction of the whole stomach can be achieved from a standard endoscopic video image using SfM. Furthermore, gastric ulcer lesion was also localized and reconstructed in 3D reconstruction model. Our future work will be focused on the clinical significance of our proposed method. We will try to evaluate the clinical usefulness of this method for the patients undergone surgery for early gastric cancers.
Evolution of optical phonons in epitaxial Ge1−ySny structures (2020)

Abstract We report polarized Raman scattering results of Ge 1− y Sn y ( 0 ≤ y ≤ 0.09 ) epitaxial layers grown on Ge‐buffered Si substrates. Polarized Raman spectra from the sample surfaces revealed strong Ge–Ge longitudinal optical (LO) phonon responses. The Ge–Ge LO(z) phonon wavenumber decreased systematically as the Sn content increased. Linear fitting results of the Ge–Ge LO(z) phonon wavenumber shifts as a function of Sn content suggested that a partial strain relaxation occurred in the Ge 1− y Sn y layers. Spatially resolved Raman mapping measurements from the cross section of a Ge 0.938 Sn 0.062 samplev showed that the peak wavenumber of the Ge–Ge transverse optical phonon decreased gradually toward the top surface, providing direct evidence that the residual built‐in strain initially formed at the Ge 0.938 Sn 0.062 /Ge interface tended to relax gradually along the growth direction. Further, a hydrogen inductively coupled plasma treatment induced a greater homogeneous strain profile in the Ge 0.938 Sn 0.062 layer.
[superscript 15]N-[superscript 15]N Proton Assisted Recoupling in Magic Angle Spinning NMR (2009)

We describe a new magic angle spinning (MAS) NMR experiment for obtaining [superscript 15]N−[superscript 15]N correlation spectra. The approach yields direct information about the secondary and tertiary structure of proteins, including identification of α-helical stretches and interstrand connectivity in antiparallel β-sheets, which are of major interest for structural studies of membrane proteins and amyloid fibrils. The method, [superscript 15]N−[superscript 15]N proton assisted recoupling (PAR), relies on a second-order mechanism, third spin assisted recoupling (TSAR), used previously in the context of [superscript 15]N−[superscript 13]C and [superscript 13]C−[superscript 13]C polarization transfer schemes. In comparison to [superscript 15]N−[superscript 15]N proton-driven spin diffusion experiments, the PAR technique accelerates polarization transfer between [superscript 15]N’s by a factor of ~10[superscript 2]−10[superscript 3] and is furthermore applicable over the entire range of currently available MAS frequencies (10−70 kHz).
An extended triangulation to the Marching Cubes 33 algorithm (2019)

The Marching Cubes algorithm is arguably the most popular isosurface extraction algorithm. Since its inception, two problems have lingered, namely, triangle quality and topology correctness. Although there is an extensive literature to solve them, topology correctness is achieved in detriment of triangle quality and vice versa. In this paper, we present an extended version of the Marching Cubes 33 algorithm (a variation of the Marching Cubes algorithm which guarantees topological correctness), called Extended Marching Cubes 33. In the proposed algorithm, the grid vertex are labeled with “+,” “ −,” and “=,” according to the relationship between its scalar field value and the isovalue. The inclusion of the “=” grid vertex label naturally avoids degenerate triangles. As an application of our method, we use the proposed triangulation to improve the quality of the triangles in the generated mesh while preserving its topology as much as possible.
The Power and Challenges of Transformative I/O (2012)

Extracting high data bandwidth and metadata rates from parallel file systems is notoriously difficult. User workloads almost never achieve the performance of synthetic benchmarks. The reason for this is that real-world applications are not as well-aligned, well-tuned, or consistent as are synthetic benchmarks. There are at least three possible ways to address this challenge: modification of the real-world workloads, modification of the underlying parallel file systems, or reorganization of the real-world workloads using Tran formative middleware. In this paper, we demonstrate that Tran formative middleware is applicable across a large set of high performance computing workloads and is portable across the three major parallel file systems in use today. We also demonstrate that our transformative middleware layer is capable of improving the write, read, and metadata performance of I/O workloads by up to 150x, 10x, and 17x respectively, on workloads with processor counts of up to 65,536.
Proteomic Screening Method for Phosphopeptide Motif Binding Proteins Using Peptide Libraries (2011)

Phosphopeptide binding domains mediate the directed and localized assembly of protein complexes essential to intracellular kinase signaling. To identify phosphopeptide binding proteins, we developed a proteomic screening method using immobilized partially degenerate phosphopeptide mixtures combined with SILAC and microcapillary LC-MS/MS. The method was used to identify proteins that specifically bound to phosphorylated peptide library affinity matrices, including pTyr, and the motifs pSer/pThr-Pro, pSer/pThr-X-X-X-pSer/pThr, pSer/pThr-Glu/Asp, or pSer/pThr-pSer/pThr in degenerate sequence contexts. Heavy and light SILAC lysates were applied to columns containing these phosphorylated and nonphosphorylated (control) peptide libraries respectively, and bound proteins were eluted, combined, digested, and analyzed by LC-MS/MS using a hybrid quadrupole-TOF mass spectrometer. Heavy/light peptide ion ratios were calculated, and peptides that yielded ratios greater than ∼3:1 were considered as being from potential phosphopeptide binding proteins since this ratio represents the lowest ratio from a known positive control. Many of those identified were known phosphopeptide-binding proteins, including the SH2 domain containing p85 subunit of PI3K bound to pTyr, 14-3-3 bound to pSer/pThr-Asp/Glu, polo-box domain containing PLK1 and Pin1 bound to pSer/pThr-Pro, and pyruvate kinase M2 binding to pTyr. Approximately half of the hits identified by the peptide library screens were novel. Protein domain enrichment analysis revealed that most pTyr hits contain SH2 domains, as expected, and to a lesser extent SH3, C1, STAT, Tyr phosphatase, Pkinase, C2, and PH domains; however, pSer/pThr motifs did not reveal enriched domains across hits.
Empirical Characterization of Mobility of Multi-Device Internet Users (2020)

Understanding the mobility of humans and their devices is a fundamental problem in mobile computing. While there has been much work on empirical analysis of human mobility using mobile device data, prior work has largely assumed devices to be independent and has not considered the implications of modern Internet users owning multiple mobile devices that exhibit correlated mobility patterns. Also, prior work has analyzed mobility at the spatial scale of the underlying mobile dataset and has not analyzed mobility characteristics at different spatial scales and its implications on system design. In this paper, we empirically analyze the mobility of modern Internet users owning multiple devices at multiple spatial scales using a large campus WiFi dataset. First, our results show that mobility of multiple devices belonging to a user needs to be analyzed and modeled as a group, rather than independently, and that there are substantial differences in the correlations exhibited by device trajectories across users that also need to be considered. Second, our analysis shows that the mobility of users shows different characteristics at different spatial scales such as within and across buildings. Third, we demonstrate the implications of these results by presenting generative models that highlight the importance of considering the spatial scale of mobility as well as multi-device mobility. More broadly, our empirical results point to the need for new modeling research to fully capture the nuances of mobility of modern multi-device users.
Blind Bandwidth Extension of Speech based on LPCNet (2020)

A blind bandwidth extension is presented which improves the perceived quality of 4 kHz speech by artificially extending the speech's frequency range to 8 kHz. Based on the source-filter model of the human speech production, the speech signal is decomposed into spectral envelope and excitation signal and each of them is extrapolated separately. With this decomposition, good perceptual quality can be achieved while keeping the computational complexity low. The focus of this work is in the generation of an excitation signal with and autoregressive model that calculates a distribution for each audio sample conditioned on previous samples. This is achieved with a deep neural network following the architecture of LPCNet [1].A listening test shows that it significantly improves the perceived quality of bandlimited speech. The system has an algorithmic delay of 30 ms and can be applied in state-of-the-art speech and audio codecs.