gebhart/patrepeval huggingface dataset:
Gate oxide damage: Testing approaches and methodologies (1999)

The main types of gate oxide damage measurement techniques are examined and compared, leading to a selection of “application-specific” damage measurement techniques. Each technique has strengths and weaknesses, so no single measurement can completely characterize damage. Instead, a combination of measurement approaches is needed, each one targeted to provide a piece of the damage puzzle. It is helpful to understand the different damage mechanisms when selecting a measurement technique, so a survey of mechanisms is given. Damage proceeds by either direct exposure of the gate oxide (through ion bombardment or ultraviolet radiation) or by indirect exposure (by charging from a nonuniform plasma or from the presence of high aspect ratio structures on the wafer). The relative importance of each mechanism depends on process technology and other factors. The most useful combination of damage measurement techniques includes surface potential measurement, electrically erasable read-only memory transistors, direct measurement of charging, antenna transistors, and passive voltage contrast. Damage measurements should be calibrated to device performance parameters such as yield or reliability.
Surface-Treated Nanofibers as High Current Yielding Breath Humidity Sensors for Wearable Electronics (2019)

As wearable electronics have gained momentum in the past few years, there is a dire need for smart, responsive, and, most importantly, affordable sensors for biological monitoring. One such noninvasive method to gauge body metabolism is via breath analysis. In a successful attempt to sense and record relative humidity levels (%RH) in nasal and oral breath, this work presents an economical route to fabricate a wearable humidity sensor with high sensitivity and a response time of ∼1 s. The sensor consists of a flexible backbone of electrospun poly(vinylidene fluoride)/reduced graphene oxide (PVDF/rGO) nanofibers which have been selectively sensitized to humidity via surface polymerization of aniline using the inexpensive successive ionic layer adsorption and reaction (SILAR) technique. We report a high sensitivity and a full response range (0–95% RH) supported by a low working voltage and minimalistic circuitry as an attractive feature for integration into wearable electronics. Moreover, as the device sensitivity is adequate even up to 95% RH, it is conducive to detect nasal breath and saturated humidity conditions accurately. As the method utilizes electrospinning, this work involves the preparation of such humidity sensors on a large scale (up to 400 units using 8 mg of rGO) with the benefit of having affordable and cost-effective devices.
Diazo- and azido-functionalized glutaraldehydes as cross-linking reagents and potential fixatives for electron microscopy (1991)

The synthesis of diazo and perfluorophenyl azide (PFPA) functionalized glutaraldehydes 7 and 13a-d as new cross-linking reagents for bioconjugation and potential fixatives for electron microscopy is reported. A key step is the generation of the 1,5-dialdehyde structures by oxidative cleavage of the corresponding cyclopentene epoxide using HIO4 in aqueous tetrahydrofuran. A model reaction between 3-substituted glutaraldehyde 14 and 6-aminohexanoic acid resulted in the formation of pyridinium ion containing products with UV spectra comparable to those observed with glutaraldehyde itself. Thus modification of glutaraldehyde in the 3-position most probably did not significantly change its reactivity with amines under chemical-fixation conditions. Fixation of red blood cells by 7 demonstrates that as a fixative, 7 is comparable to glutaraldehyde.
The influence of graphene addition on the properties of composite membranes RG / PAN and their potential application (2022)

PAN is an inexpensive and popular engineering polymer, which is widely used in membrane techniques: ultrafiltration (UF), nanofiltration (NF), reverse osmosis (RO) and pervaporation (PV). It is characterized by good thermal stability, high thermal conductivity, chemical resistance, solubility in many classic solvents, resistance to UV radiation and good mechanical properties. It can be easily modified both chemically and physically. The paper describes the method of obtaining composite membranes by the phase inversion method of homogeneous dispersion of graphene (RG) in a solution of polyacrylonitrile (PAN) dissolved in N, N-dimethylformamide (DMF). The influence of RG concentration on physicochemical properties, transport and separation properties (removing microplastic), and resistance to fouling of composite was investigated.
In vitro acylation of the transferrin receptor. (1984)

In vitro fatty acylation of the transferrin receptor with [3H]tetradecanoate or [3H]tetradecanoyl-CoA has been demonstrated for isolated sheep reticulocyte plasma membranes. Although less than 5% of the receptor was labeled in vitro, the acylated protein could be readily observed after sodium dodecyl sulfate-gel electrophoresis. The acylated transferrin receptor in the reticulocyte membrane was specifically precipitated with a monoclonal antibody and was absent from mature red cell membranes. Incorporation of fatty acid was dependent on ATP, and fatty acid was 5-10 times less effective as an acyl donor than the acyl-CoA derivative, pointing out the strong potential of this reagent for in vitro acylation of membrane proteins. During in vitro maturation of reticulocytes, the receptor is released in vesicles into the incubation medium. Using reticulocytes labeled with [3H]tetradecanoate, it can be shown that the 3H-labeled receptor is transferred from the cells to the vesicles without loss of acyl groups, suggesting that the vesiculation process does not involve deacylation.
Predictive value of technetium Tc 99m-labeled red blood cell scintigraphy for positive angiogram in massive lower gastrointestinal hemorrhage (1997)

PURPOSE: This study was performed to evaluate whether the time interval from injection of technetium Tc 99m (99mTc)-labeled red blood cells to the time of a radionuclide “blush” (positive scan) can be used to improve the efficacy in predicting a positive angiogram. METHOD: A retrospective review revealed 160 patients who received99mTc-labeled red blood cell scintigraphy for evaluation of massive lower gastrointestinal hemorrhage between 1989 and 1994. Patients were included who demonstrated signs of shock on admission, had an initial decrease in hematocrit of ≥6 percent, or required a minimum transfusion of two units of packed red blood cells. Scanning duration was 90 minutes, with imaging every 2 minutes. Time interval from injection to a positive scan was analyzed to determine predictability of a positive angiography. RESULTS: Of 160 patients, 86 demonstrated positive scans, of whom 47 underwent angiography. These 47 patients were divided into two groups according to scan results. Group 1 (n = 33) had immediate appearance of blush; Group 2 (n = 14) had blush after two minutes. In Group 1, 20 of 33 patients had a positive angiogram, yielding a positive predictive value of 60 percent (P = 0.033). Of the 14 patients with negative angiograms (13 from Group 1, and 1 with a negative scan), 6 had radiographic occlusion of the inferior mesenteric artery and 1 had spasm of the right colic artery, with scans that blushed in the respective distributions. Excluding these seven patients yielded a positive predictive value of 75 percent (P = 0.0072) for angiography. In patients with a delayed blush (Group 2), 13 of 14 had negative angiograms, yielding a negative predictive value of 93 percent (92 percent excluding those with nonvisualization of the inferior mesenteric artery). Twenty of 21 (95 percent) positive angiograms occurred in Group 1 patients. Of the 27 patients with negative angiograms, 13 were Group 2 patients. CONCLUSION: Patients with immediate blush on99mTc-labeled red blood cell scintigraphy required urgent angiography. Patients with delayed blush have low angiographic yields. These data suggest that patients with delayed blush or negative scans may be observed and evaluated with colonoscopy.
ChemInform Abstract: Synthesis and Structure—Activity Relationship Study of Cytotoxic Lupane‐Type 3β‐O‐Monodesmosidic Saponins with an Extended C‐28 Side Chain. (2014)

Abstract Several of the compounds exhibit cyctoxicity against human cancer cell lines.
A bit-parallel, word-parallel, massively parallel associative processor for scientific computing (2002)

A simple but powerful parallel architecture based on the classical associative processor model, which allows bit-parallel computation and communication, is proposed. Complex operations such as multiplication execute in O(m) cycles, as opposed to O(m/sup 2/) for bit-serial machines. This permits very fast processing of floating-point data. A bit-parallel communication network that exploits associative data location independence is presented. It provides the system with a reconfiguration capability, which improves chip yield, as well as fault tolerance. The simplicity of the architecture lends itself to VLSI implementation and hence allows the construction of a bit-parallel, word-parallel, and massively parallel (P/sup 3/) computing system.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
In Vivo Knockdown of the Herpes Simplex Virus 1 Latency-Associated Transcript Reduces Reactivation from Latency (2018)

During herpes simplex virus (HSV) latency, most viral genes are silenced, with the exception of one region of the genome encoding the latency-associated transcript (LAT). This long noncoding RNA was originally described as having a role in enhancing HSV-1 reactivation. However, subsequent evidence showing that the LAT blocked apoptosis and promoted efficient establishment of latency suggested that its effects on reactivation were secondary to establishment. Here, we utilized an adeno-associated virus (AAV) vector to deliver a LAT-targeting hammerhead ribozyme to HSV-1-infected neurons of rabbits after the establishment of HSV-1 latency. The rabbits were then induced to reactivate latent HSV-1. Using this model, we show that decreasing LAT levels in neurons following the establishment of latency reduced the ability of the virus to reactivate. This demonstrates that the HSV-1 LAT RNA has a role in reactivation that is independent of its function in establishment of latency. In addition, these results suggest the potential of AAV vectors expressing LAT-targeting ribozymes as a potential therapy for recurrent HSV disease such as herpes stromal keratitis, a leading cause of infectious blindness.<b>IMPORTANCE</b> Herpes simplex virus (HSV) establishes a lifelong infection and remains dormant (latent) in our nerve cells. Occasionally HSV reactivates to cause disease, with HSV-1 typically causing cold sores whereas HSV-2 is the most common cause of genital herpes. The details of how HSV reactivates are largely unknown. Most of HSV's genes are silent during latency, with the exception of RNAs made from the latency-associated transcript (LAT) region. While viruses that make less LAT do not reactivate efficiently, these viruses also do not establish latency as efficiently. Here we deliver a ribozyme that can degrade the LAT to the nerve cells of latently infected rabbits using a gene therapy vector. We show that this treatment blocks reactivation in the majority of the rabbits. This work shows that the LAT RNA is important for reactivation and suggests the potential of this treatment as a therapy for treating HSV infections.
Localization based on vision using stereo System and SIFT features (2015)

The traditional method uses the GPS signal to determine the location of a vehicle or Mobile Robot, but these methods sometimes fail to determine the exact position of the object especially in urban areas, or inside buildings. It fails to determine the position for multiple reasons such as the multi-fading path, obstacles, rain, and snow which all have an effect on the signal of the GPS. The developed algorithm is intended to get the location of the moving objects by using the computer vision system. The results of the proposed algorithm give higher performance (around 33 second and with a resolution of 10 meters) compared to the other systems on the long trajectory. We use the single camera system to select the suitable features and the stereo camera systems to obtain the locations of the object. It is therefore different from the other methods that are dependent on maps to compare the image features with the features of the map to determine the location of the object.
Crystal structures of the Cid1 poly (U) polymerase reveal the mechanism for UTP selectivity (2012)

Polyuridylation is emerging as a ubiquitous post-translational modification with important roles in multiple aspects of RNA metabolism. These poly (U) tails are added by poly (U) polymerases with homology to poly (A) polymerases; nevertheless, the selection for UTP over ATP remains enigmatic. We report the structures of poly (U) polymerase Cid1 from Schizoscaccharomyces pombe alone and in complex with UTP, CTP, GTP and 3'-dATP. These structures reveal that each of the 4 nt can be accommodated at the active site; however, differences exist that suggest how the polymerase selects UTP over the other nucleotides. Furthermore, we find that Cid1 shares a number of common UTP recognition features with the kinetoplastid terminal uridyltransferases. Kinetic analysis of Cid1's activity for its preferred substrates, UTP and ATP, reveal a clear preference for UTP over ATP. Ultimately, we show that a single histidine in the active site plays a pivotal role for poly (U) activity. Notably, this residue is typically replaced by an asparagine residue in Cid1-family poly (A) polymerases. By mutating this histidine to an asparagine residue in Cid1, we diminished Cid1's activity for UTP addition and improved ATP incorporation, supporting that this residue is important for UTP selectivity.
A Story of Two Streams: Reinforcement Learning Models from Human Behavior and Neuropsychiatry (2019)

Drawing an inspiration from behavioral studies of human decision making, we propose here a more general and flexible parametric framework for reinforcement learning that extends standard Q-learning to a two-stream model for processing positive and negative rewards, and allows to incorporate a wide range of reward-processing biases -- an important component of human decision making which can help us better understand a wide spectrum of multi-agent interactions in complex real-world socioeconomic systems, as well as various neuropsychiatric conditions associated with disruptions in normal reward processing. From the computational perspective, we observe that the proposed Split-QL model and its clinically inspired variants consistently outperform standard Q-Learning and SARSA methods, as well as recently proposed Double Q-Learning approaches, on simulated tasks with particular reward distributions, a real-world dataset capturing human decision-making in gambling tasks, and the Pac-Man game in a lifelong learning setting across different reward stationarities.
Structural templating and growth behavior of copper phthalocyanine thin films deposited on a polycrystalline perylenetetracarboxylic dianhydride layer (2011)

Structural templating and the growth behavior of copper phthalocyanine (CuPc) thin films deposited on a polycrystalline 3,4,9,10-perylenetetracarboxylic dianhydride (PTCDA) layer were examined using x-ray diffraction (XRD) and atomic force microscopy. The templated CuPc films were found to grow on both the (110) and (102) plane of the α-PTCDA layer, indicating the intermolecular π-π interaction is strong enough to induce templating even on the underlying layer which is tilted at an angle of 25° from the substrate surface as well as on the surface-parallel layer. In contrast to the large growth exponent (β) values for other single layer molecular thin films, a significantly small β value of 0.17 ± 0.06 was obtained on the PTCDA/CuPc heterolayer thin film system. The XRD and scaling behavior studies suggest that this relatively slow surface roughening can be rationalized by the lack of surface parallel crystalline ordering at the initial stage of CuPc film growth on the PTCDA layer.
Misalignment-Robust Joint Filter for Cross-Modal Image Pairs (2017)

Although several powerful joint filters for cross-modal image pairs have been proposed, the existing joint filters generate severe artifacts when there are misalignments between a target and a guidance images. Our goal is to generate an artifact-free output image even from the misaligned target and guidance images. We propose a novel misalignment-robust joint filter based on weight-volume-based image composition and joint-filter cost volume. Our proposed method first generates a set of translated guidances. Next, the joint-filter cost volume and a set of filtered images are computed from the target image and the set of the translated guidances. Then, a weight volume is obtained from the joint-filter cost volume while considering a spatial smoothness and a label-sparseness. The final output image is composed by fusing the set of the filtered images with the weight volume for the filtered images. The key is to generate the final output image directly from the set of the filtered images by weighted averaging using the weight volume that is obtained from the joint-filter cost volume. The proposed framework is widely applicable and can involve any kind of joint filter. Experimental results show that the proposed method is effective for various applications including image denosing, image up-sampling, haze removal and depth map interpolation.
Patient-derived pancreas-on-a-chip to model cystic fibrosis-related disorders (2019)

Cystic fibrosis (CF) is a genetic disorder caused by defective CF Transmembrane Conductance Regulator (CFTR) function. Insulin producing pancreatic islets are located in close proximity to the pancreatic duct and there is a possibility of impaired cell-cell signaling between pancreatic ductal epithelial cells (PDECs) and islet cells as causative in CF. To study this possibility, we present an in vitro co-culturing system, pancreas-on-a-chip. Furthermore, we present an efficient method to micro dissect patient-derived human pancreatic ducts from pancreatic remnant cell pellets, followed by the isolation of PDECs. Here we show that defective CFTR function in PDECs directly reduced insulin secretion in islet cells significantly. This uniquely developed pancreatic function monitoring tool will help to study CF-related disorders in vitro, as a system to monitor cell-cell functional interaction of PDECs and pancreatic islets, characterize appropriate therapeutic measures and further our understanding of pancreatic function.
MiR-155-mediated loss of C/EBPβ shifts the TGF-β response from growth inhibition to epithelial-mesenchymal transition, invasion and metastasis in breast cancer (2013)

During breast cancer progression, transforming growth factor-beta (TGF-β) switches from acting as a growth inhibitor to become a major promoter of epithelial-mesenchymal transition (EMT), invasion and metastasis. However, the mechanisms involved in this switch are not clear. We found that loss of CCAAT-enhancer binding protein beta (C/EBPβ), a differentiation factor for the mammary epithelium, was associated with signs of EMT in triple-negative human breast cancer, and in invasive areas of mammary tumors in MMTV-PyMT mice. Using an established model of TGF-β-induced EMT in mouse mammary gland epithelial cells, we discovered that C/EBPβ was repressed during EMT by miR-155, an oncomiR in breast cancer. Depletion of C/EBPβ potentiated the TGF-β response towards EMT, and contributed to evasion of the growth inhibitory response to TGF-β. Furthermore, loss of C/EBPβ enhanced invasion and metastatic dissemination of the mouse mammary tumor cells to the lungs after subcutaneous injection into mice. The mechanism by which loss of C/EBPβ promoted the TGF-β response towards EMT, invasion and metastasis, was traced to a previously uncharacterized role of C/EBPβ as a transcriptional activator of genes encoding the epithelial junction proteins E-cadherin and coxsackie virus and adenovirus receptor. The results identify miR-155-mediated loss of C/EBPβ as a mechanism, which promotes breast cancer progression by shifting the TGF-β response from growth inhibition to EMT, invasion and metastasis.
Highly reliable 1 Mbit ferroelectric memories with newly developed BLT thin films and steady integration schemes (2002)

Highly reliable packaged 1 Mbit ferroelectric memories with 0.35 /spl mu/m CMOS ensuring ten-year retention and imprint at 175/spl deg/C have been successfully developed for the first time. These excellent reliabilities have resulted from newly developed BLT ferroelectric films with superior performance and steady integration schemes free from attacks of process impurities.
220 LENGTH OF DONOR DNA HOMOLOGY TO FACILITATE BI-ALLELIC GENE TARGETING DURING TRANSCRIPTION ACTIVATOR-LIKE EFFECTOR NUCLEASE-MEDIATED GENE TARGETING (2013)

Gene editing techniques are increasing in their availability and ease of use. These techniques are an attractive alternative to conventional gene targeting methods via homologous recombination due to the ease of use and the efficiency of targeting. We have previously produced CMP-N-acetylneuraminic acid hydroxylase (CMAH) knockout (KO) pigs in a Minnesota miniature pig genetic background. These pigs were generated using zinc-finger nucleases (ZFN) in combination with donor DNA containing a total length of homology of 1600 bp (800-bp homology on each arm). A second KO was desired in the CMAH –/– genetic background, GGTA1. We used this opportunity to evaluate the effect of total donor homology on transcription activator-like effector nuclease (TALEN) mediated bi-allelic modification. Donor DNA was designed to symmetrically flank the predicted TALEN cleavage site in GGTA1 and was varied in length of total homology (40, 100, 200, 460, 890, and 1800 bp). The TALEN constructs and donor DNA were introduced into fibroblast cells by a lipid-based transfection method. Each donor DNA was co-transfected with a pair of TALEN constructs. In addition, the TALEN pair alone and the longest donor DNA alone were separately transfected to evaluate error-prone non-homologous end joining (NHEJ) repair or background HR, respectively. Five days post transfection, cells were evaluated for the ablation of the a-1,3 gal epitope, which results from bi-allelic disruption of GGTA1. Lectin IB-4 (FITC labeled) was used to detect the presence/absence of the epitope. If a bi-allelic modification to the GGTA1 gene was accomplished, specific binding of the lectin would not occur; therefore, a lack of FITC was evaluated. Donor DNA alone did not result in detectable bi-allelic conversion of GGTA1. As the length of donor DNA increased, the bi-allelic disruption of GGTA1 increased from 0.5% (no donor DNA) to a maximum of 3% (1800 bp). Inclusion of homologous donor DNA in TALEN transfections facilitates HR that competes with error-free NHEJ. The use of donor DNA with TALEN therefore can provide for increased bi-allelic disruption and predictability in the sequence of the resulting mutation.
Secretome analysis of oral keratinocytes chronically exposed to shisha (2019)

This study serves as a useful resource to understand the effect of chronic shisha smoking on the milieu of secreted proteins of oral cells. In vivo studies are warranted to supplement our in vitro data to elucidate the role of these proteins as early diagnostic biomarkers for oral carcinogenesis among shisha smokers.