gebhart/patrepeval huggingface dataset:
Critical Role of the Fifth Domain of E-Cadherin for Heterophilic Adhesion with αEβ7, But Not for Homophilic Adhesion (2005)

The integrin alpha(E)beta(7) is expressed on intestinal intraepithelial T lymphocytes and CD8(+) T lymphocytes in inflammatory lesions near epithelial cells. Adhesion between alpha(E)beta(7)(+) T and epithelial cells is mediated by the adhesive interaction of alpha(E)beta(7) and E-cadherin; this interaction plays a key role in the damage of target epithelia. To explore the structure-function relationship of the heterophilic adhesive interaction between E-cadherin and alpha(E)beta(7), we performed cell aggregation assays using L cells transfected with an extracellular domain-deletion mutant of E-cadherin. In homophilic adhesion assays, L cells transfected with wild-type or a domain 5-deficient mutant formed aggregates, whereas transfectants with domain 1-, 2-, 3-, or 4-deficient mutants did not. These results indicate that not only domain 1, but domains 2, 3, and 4 are involved in homophilic adhesion. When alpha(E)beta(7)(+) K562 cells were incubated with L cells expressing the wild type, 23% of the resulting cell aggregates consisted of alpha(E)beta(7)(+) K562 cells. In contrast, the binding of alpha(E)beta(7)(+) K562 cells to L cells expressing a domain 5-deficient mutant was significantly decreased, with alpha(E)beta(7)(+) K562 cells accounting for only 4% of the cell aggregates, while homophilic adhesion was completely preserved. These results suggest that domain 5 is involved in heterophilic adhesion with alpha(E)beta(7), but not in homophilic adhesion, leading to the hypothesis that the fifth domain of E-cadherin may play a critical role in the regulation of heterophilic adhesion to alpha(E)beta(7) and may be a potential target for treatments altering the adhesion of alpha(E)beta(7)(+) T cells to epithelial cells in inflammatory epithelial diseases.
Convergent and Stereodivergent Synthesis of Complex 1-Aza-7-oxabicyclo[2.2.1]heptanes (2011)

A convergent and stereodivergent pathway to highly substituted 1-aza-7-oxabicyclo[2.2.1]heptanes is described. It begins with a coupling reaction involving allylic alcohol, aldehyde, and LiHMDS to produce stereodefined primary homoallylic amines. Subsequent N-oxidation and condensation with formaldehyde or glyoxylate defines a convenient entry to densely functionalized homoallylic nitrones whose intramolecular annulation can be controlled to deliver one of two distinct heterocyclic skeletons, each with ≥20:1 stereoselection. Control of the stereochemistry in these reactions results from both control of the nitrone geometry and selective partitioning of the reaction pathway between direct [3 + 2] cycloaddition and tandem [3,3] rearrangement/[3 + 2] cycloaddition.
R-FCN-3000 at 30fps: Decoupling Detection and Classification (2018)

We propose a modular approach towards large-scale real-time object detection by decoupling objectness detection and classification. We exploit the fact that many object classes are visually similar and share parts. Thus, a universal objectness detector can be learned for class-agnostic object detection followed by fine-grained classification using a (non)linear classifier. Our approach is a modification of the R-FCN architecture to learn shared filters for performing localization across different object classes. We trained a detector for 3000 object classes, called R-FCN-3000, that obtains an mAP of 34.9% on the ImageNet detection dataset. It outperforms YOLO-9000 by 18% while processing 30 images per second. We also show that the objectness learned by R-FCN-3000 generalizes to novel classes and the performance increases with the number of training object classes - supporting the hypothesis that it is possible to learn a universal objectness detector. Code will be made available.
Vessel tree extraction using locally optimal paths (2010)

This paper proposes a method to extract vessel trees by continually extending detected branches with locally optimal paths. Our approach uses a cost function from a multiscale vessel enhancement filter. Optimal paths are selected based on rules that take into account the geometric characteristics of the vessel tree. Experiments were performed on 10 low dose chest CT scans for which the pulmonary vessel trees were extracted. The proposed method is shown to extract a better connected vessel tree and extract more of the small peripheral vessels in comparison to applying a threshold on the output of the vessel enhancement filter.
Optimization of culture conditions for indole-3-pyruvic acid production by <i>Streptomyces griseoflavus</i> (1994)

Thirty strains of actinomycetes were isolated from fertile soils in Egypt on starch–nitrate agar. The isolated organisms were recognized as spore formers with aerial mycelia containing L-DAP (diaminopimelic acid) and glycine. The inability of the vegetative mycelia to fragment into bacillary or coccoid forms and the presence of spores borne on sporophores, placed these organisms in the family Streptomycetaceae. The isolates also proved to be aerobic and Gram positive. The absence of DL-DAP and the presence of L-DAP in their cell hydrolysates, and the production of a wide range of pigments in the aerial and substrate mycelia, assigned these isolates to the genus Streptomyces. The isolated organisms were screened for production of plant growth regulators, and the most active producer of indole-3-pyruvic acid was examined further. Using the described morphological, physiological, and biochemical criteria for identification, this organism was identified as Streptomyces griseoflavus. The optimal culture conditions for maximal production of both cellular and extracellular indole-3-pyruvic acid by S. griseoflavus were investigated and shown to be as follows: a culture medium composed of (g∙100 mL −1 ) NH 4 NO 3 , 0.55; DL-tryptophan, 0.4; NaCl, 0.7; at pH 7 (buffered); with an incubation period of 6 days at 28 °C in the dark and under shaking conditions.Key words: actinomycetes, plant growth regulators, Streptomyces griseoflavus, indole-3-pyruvic acid, culture conditions.
A 12-bit 100-MSps pipelined-SAR ADC with a time-interleaved second-stage (2014)

In this paper, a 12-bit 100-MS/s pipelined-SAR ADC is presented. The design properly selects the resolution of the two pipeline stages and adopts time-interleaving technique to improve the speed. A split-capacitor DAC in 2 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">nd</sup> -satge SAR ADC and a “half gain” residue amplifier minimize the power dissipation. The ADC simulated in a 65-nm CMOS technology achieves an ENOB of 11.2b near the Nyquist input frequency at the sampling rate of 100MS/s. The power consumption is only 8.6mW with the supply voltage of 1.2V and the FoM is 36.6fJ/conv.-step operating at 100MS/s.
Triple S: a new tool for soybean high throughput phenotyping from UAS-based multispectral imagery (2019)

Precise and functional phenotyping is a limiting factor for crop genetic improvement. However, because of its ease of application, imagery-based phenomics represents the next breakthrough for improving the rates of genetic gains in field crops. Currently, crop breeders lack the know-how and computational tools to include such traits in breeding pipelines. A fully automatic user-friendly data management together with a more powerful and accurate interpretation of results should increase the use of field high throughput phenotyping platforms (HTPPs) and, therefore, increasing the efficiency of crop genetic improvement to meet the needs of future generations. The aim of this study is to generate a methodology to high throughput phenotyping based on temporal multispectral imagery (MSI) collected from Unmanned Aerial Systems (UAS) in soybean crops. In this context, ‘Triple S’ (Statistical computing of Segmented Soybean multispectral imagery) is developed as an open-source software tool to statistically analyze the pixel values of soybean end-member and to compute canopy cover area, number and length of soybean rows from georeferenced multispectral images. During the growing season of 2017, a soybean experiment was carried out at the Agronomy Center for Research and Education (ACRE) in West-Lafayette (Indiana, USA). Periodic images were acquired by Parrot Sequoia Multispectral sensor on board senseFly eBee. The results confirm the feasibility of the proposed methodology, providing scalability to a comprehensive analysis of crop extension and affording a constant operational improvement and proactive management.
Quantifying Subjective Quality Evaluations for Mobile Video Watching in a Semi-Living Lab Context (2012)

This paper discusses results from an exploratory study in which Quality of Experience aspects related to mobile video watching were investigated in a semi-living lab setting. More specifically, we zoom in on usage patterns in a natural research context and on the subjective evaluation of high and low-resolution movie trailers that are transferred to a mobile device using two transmission protocols for video (i.e., real-time transport protocol and progressive download using HTTP). User feedback was collected by means of short questionnaires on the mobile device, combined with traditional pen and paper diaries. The subjective evaluations regarding the general technical quality, perceived distortion, fluentness of the video, and loading speed are studied and the influence of the transmission protocol and video resolution on these evaluations is analyzed. Multinomial logistic regression results in a model to estimate the subjective evaluations regarding the perceived distortion and loading speed based on objectively-measured parameters of the video session.
Advances in Pattern Theory (1989)

Pattern theory offers concepts for modelling images and methods for making inferences from observed images. This will be described briefly and illustrated by examples. We shall present limit theorems for the Markov processes on graphs (that are basic to pattern theory) motivated by computational considerations. They will yield approximations that have been exploited to make the inference algorithms computationally feasible. We shall also consider the problem of estimating parameters in the prior measures encountered in pattern theory. These parameters are high dimensional, not automatically identifiable and notoriously difficult to estimate by standard methods. We therefore present a standardization technique for dealing with them and show how, after standardization, the remaining free parameters can be estimated by different methods. The estimation methods are examined in terms of their asymptotic efficiencies.
Special quasirandom structures (1990)

Structural models used in calculations of properties of substitutionally random ${\mathit{A}}_{1\mathrm{\ensuremath{-}}\mathit{x}}$${\mathit{B}}_{\mathit{x}}$ alloys are usually constructed by randomly occupying each of the N sites of a periodic cell by A or B. We show that it is possible to design ``special quasirandom structures'' (SQS's) that mimic for small N (even N=8) the first few, physically most relevant radial correlation functions of a perfectly random structure far better than the standard technique does. We demonstrate the usefulness of these SQS's by calculating optical and thermodynamic properties of a number of semiconductor alloys in the local-density formalism.
Electrochemical and Computational Studies on the Electrocatalytic Effect of Conducting Polymers toward the Redox Reactions of Thiadiazole-Based Thiolate Compounds (2010)

We have studied the electrocatalytic effects of polythiophene-based conducting polymers toward the redox reactions of the dilithium salt of the thiadiazole-based dithiol compound 2,5-dimercapto-1,3,4-thiodiazole (DMcT-2Li) via cyclic voltammetry (CV), rotating-disk electrode voltammetry, and electrochemical impedance spectroscopy (EIS). We have found that the electrocatalytic activity of the conducting polymers is strongly influenced by the potential range over which the polymers are electrically conductive (i.e., window of conductivity), which was tuned by employing different electron-donating groups at the 3- or 3,4-positions of polythiophene (PTh). Both poly(3,4-ethylenedioxythiophene) (PEDOT) and poly(3,4-propylenedioxythiophene) (PProDOT), whose windows of conductivity exhibited a good overlap with the formal potential for the dimerization process of DMcT-2Li; E0′d (−0.54 V versus Ag/Ag+) exhibited electrocatalytic activity toward both the oxidation and reduction processes of DMcT-2Li. On the other hand, PTh, poly(3-methylthiophene) (PMTh), and poly(3,4-dimethoxythiophene) (PDMTh), whose windows of conductivity did not overlap with E0′d, did not exhibit electrocatalytic activity. The standard charge transfer rate constants for the dimerization process of DMcT-2Li at PEDOT, PProDOT, and PDMTh film-modified glassy carbon electrodes (GCEs) were estimated to be 7.4 × 10−4, 3.2 × 10−4, and 6.9 × 10−5 cm/s while the rate constant was 6.3 × 10−5 cm/s at an unmodified GCE. Moreover, EIS studies for PEDOT, PProDOT, and PDMTh film-modified GCEs indicated the smallest charge transfer resistance for a PEDOT film and highest for a PDMTh film at E0′d, indicating that the higher the electrical conductivity of a film at E0′d the higher the electrocatalytic activity toward the redox reactions of DMcT-2Li. These results clearly indicate that in order to accelerate the redox reactions of DMcT-2Li (and likely of other organosulfur compounds) the window of conductivity of a conducting polymer needs to overlap the formal potentials of the organosulfur compounds and, thus, support our previous observations that the electrocatalytic reactions proceed via electron exchange reactions between DMcT-2Li and conducting polymers such as PEDOT. Additional computational results for oligomers of PEDOT, ProDOT, and PDMTh showed that substituents at the 3,4-positions of the thiophene ring influence the window of conductivity via steric and electronic effects. This study provides important insights toward rational design of novel conducting-polymer-based electrocatalysts to enable organosulfur compounds to be of practical use as cathode materials for lithium-ion rechargeable batteries.
Ocular Surface Infection Mediated Molecular Stress Responses: A Review (2022)

Infection mediated ocular surface stress responses are activated as early defense mechanisms in response to host cell damage. Integrated stress responses initiate the host response to different types of infections and modulate the transcription of key genes and translation of proteins. The crosstalk between host and pathogen results in profound alterations in cellular and molecular homeostasis triggering specific stress responses in the infected tissues. The amplitude and variations of such responses are partly responsible for the disease severity and clinical sequelae. Understanding the etiology and pathogenesis of ocular infections is important for early diagnosis and effective treatment. This review considers the molecular status of infection mediated ocular surface stress responses which may shed light on the importance of the host stress-signaling pathways. In this review, we collated literature on the molecular studies of all ocular surface infections and summarize the results from such studies systematically. Identification of important mediators involved in the crosstalk between the stress response and activation of diverse signaling molecules in host ocular surface infection may provide novel molecular targets for maintaining the cellular homeostasis during infection. These targets can be then explored and validated for diagnostic and therapeutic purposes.
Enumerating Alternating Permutations with One Alternating Descent (2013)

Permutations as combinatorial objects will be the basis for this paper. Two of their most basic attributes are ascents and descents. We will examine in this paper a statistic for alternating permutations. Alternating
Crystallization and preliminary X-ray analysis of the N-terminal domain of human thioredoxin-interacting protein (2011)

Thioredoxin-interacting protein (TXNIP) is a negative regulator of thioredoxin and its roles in the pathologies of diabetes and cardiovascular diseases have marked it out as a potential drug target. Expression of TXNIP is robustly induced under various stress conditions such as high glucose, heat shock, UV, H(2)O(2) and mechanical stress amongst others. Elevated levels of TXNIP result in the sequestration and inactivation of thioredoxin, leading to cellular oxidative stress. For some time, this was the only known function of TXNIP; however, more recently the protein has been shown to play a role in regulation of glucose uptake and activation of the inflammasome. Based on the primary sequence, TXNIP is remotely related to β-arrestins, which include the visual arrestins. TXNIP has thus been classified as a member of the α-arrestin family, which to date includes five other members. None of the other α-arrestins are known to interact with thioredoxin, although curiously one has been implicated in glucose uptake. In order to gain insight into the structure-function relationships of the α-arrestin protein family, and particularly that of TXNIP, the N-terminal domain of TXNIP has been crystallized. The crystals belonged to a monoclinic space group and diffracted to 3 Å resolution using synchrotron radiation.
High Voltage GaN Lateral Photoconductive Semiconductor Switches (2017)

High voltage (>4000 V) GaN lateral photoconductive semiconductor switches (PCSSs) were developed and characterized. The epitaxial structure consisted of 1.4 μm of semi-insulating GaN grown on a SiC substrate. Intrinsic mode operation, where above bandgap light is used to trigger the PCSS, results in the highest amount of photocurrent. These PCSSs can also be triggered in extrinsic mode, where sub-bandgap illumination excites carriers from extrinsic defect levels, but this results in a significantly lower photocurrent. Triggering at near bandgap with 10 V applied, the on-state photocurrent is over eight magnitudes higher than the dark off-state leakage, indicating extremely high responsivity. A 293 nm picosecond pulse width laser was used to determine the rise time of the PCSS to be ∼160 ps. Various geometry devices were fabricated, and the low voltage on-state current obeyed a linear trend as a function of perimeter/gap optically while optically gating the PCSS, which is analogous to the width/length of a metal oxide semiconductor field effect transistor. Off-state breakdown voltages >4000 V were achieved and were likely limited by the thickness of the GaN epitaxial layer.
Simple 3D Printed Scaffold‐Removal Method for the Fabrication of Intricate Microfluidic Devices (2015)

<b>An easy and cheap fabrication method for intricate polydimethylsiloxane microfluidic devices</b> is presented. The acrylonitrile butadiene styrene scaffold-removal method uses cheap, off-the-shelf materials and equipment for the fabrication of intricate microfluidic devices. The versatility of the method is proven by the fabrication of 3D multilayer, ship-in-a-bottle, selective heating, sensing, and NMR microfluidic devices. The methodology is coined ESCARGOT: Embedded SCAffold RemovinG Open Technology.
Swimming with stiff legs at low Reynolds number (2015)

Locomotion at low Reynolds number is not possible with cycles of reciprocal motion, an example being the oscillation of a single pair of rigid paddles or legs. Here, I demonstrate the possibility of swimming with two or more pairs of legs. They are assumed to oscillate collectively in a metachronal wave pattern in a minimal model based on slender-body theory for Stokes flow. The model predicts locomotion in the direction of the traveling wave, as commonly observed along the body of free-swimming crustaceans. The displacement of the body and the swimming efficiency depend on the number of legs, the amplitude, and the phase of oscillations. This study shows that paddling legs with distinct orientations and phases offers a simple mechanism for driving flow.
Globus MEDICUS - federation of DICOM medical imaging devices into healthcare Grids. (2007)

The Digital Imaging and Communications in Medicine (DICOM) standard defines Radiology medical device interoperability and image data exchange between modalities, image databases - Picture Archiving and Communication Systems (PACS) - and image review end-points. However the scope of DICOM and PACS technology is currently limited to the trusted and static environment of the hospital. In order to meet the demand for ad-hoc tele-radiology and image guided medical procedures within the global healthcare enterprise, a new technology must provide mobility, security, flexible scale of operations, and rapid responsiveness for DICOM medical devices and subsequently medical image data. Grid technology, an informatics approach to securely federate independently operated computing, storage, and data management resources at the global scale over public networks, meets these core requirements. Here we present an approach to federate DICOM and PACS devices for large-scale medical image workflows within a global healthcare enterprise. The Globus MEDICUS (Medical Imaging and Computing for Unified Information Sharing) project uses the standards-based Globus Toolkit Grid infrastructure to vertically integrate a new service for DICOM devices - the DICOM Grid Interface Service (DGIS). This new service translates between DICOM and Grid operations and thus transparently extends DICOM to Globus based Grid infrastructure. This Grid image workflow paradigm has been designed to provide not only solutions for global image communication, but fault-tolerance and disaster recovery using Grid data replication technology. Actual use-case of 40 MEDICUS Grid connected international hospitals of the Childerns Oncology Group and the Neuroblastoma Cancer Foundation and further clinical applications are discussed. The open-source Globus MEDICU http://dev.globus.org/wiki/Incubator/MEDICUS.
Alternating metabolic pathways in NGF-deprived sympathetic neurons affect caspase-independent death (2003)

Mitochondrial release of cytochrome c in apoptotic cells activates caspases, which execute apoptotic cell death. However, the events themselves that culminate in caspase activation can have deleterious effects because caspase inhibitor-saved cells ultimately die in a caspase-independent manner. To determine what events may underlie this form of cell death, we examined bioenergetic changes in sympathetic neurons deprived of NGF in the presence of a broad-spectrum caspase inhibitor, boc-aspartyl-(OMe)-fluoromethylketone. Here, we report that NGF-deprived, boc-aspartyl-(OMe)-fluoromethylketone-saved neurons rely heavily on glycolysis for ATP generation and for survival. Second, the activity of F0F1 contributes to caspase-independent death, but has only a minor role in the maintenance of mitochondrial membrane potential, which is maintained primarily by electron transport. Third, permeability transition pore inhibition by cyclosporin A attenuates NGF deprivation-induced loss of mitochondrial proteins, suggesting that permeability transition pore opening may have a function in regulating the degradation of mitochondria after cytochrome c release. Identification of changes in caspase inhibitor-saved cells may provide the basis for rational strategies to augment the effectiveness of the therapeutic use of postmitochondrial interventions.