gebhart/patrepeval huggingface dataset:
Computer‐extracted features of nuclear morphology in hematoxylin and eosin images distinguish stage II and IV colon tumors (2022)

We assessed the utility of quantitative features of colon cancer nuclei, extracted from digitized hematoxylin and eosin-stained whole slide images (WSIs), to distinguish between stage II and stage IV colon cancers. Our discovery cohort comprised 100 stage II and stage IV colon cancer cases sourced from the University Hospitals Cleveland Medical Center (UHCMC). We performed initial (independent) model validation on 51 (143) stage II and 79 (54) stage IV colon cancer cases from UHCMC (The Cancer Genome Atlas's Colon Adenocarcinoma, TCGA-COAD, cohort). Our approach comprised the following steps: (1) a fully convolutional deep neural network with VGG-18 architecture was trained to locate cancer on WSIs; (2) another deep-learning model based on Mask-RCNN with Resnet-50 architecture was used to segment all nuclei from within the identified cancer region; (3) a total of 26 641 quantitative morphometric features pertaining to nuclear shape, size, and texture were extracted from within and outside tumor nuclei; (4) a random forest classifier was trained to distinguish between stage II and stage IV colon cancers using the five most discriminatory features selected by the Wilcoxon rank-sum test. Our trained classifier using these top five features yielded an AUC of 0.81 and 0.78, respectively, on the held-out cases in the UHCMC and TCGA validation sets. For 197 TCGA-COAD cases, the Cox proportional hazards model yielded a hazard ratio of 2.20 (95% CI 1.24-3.88) with a concordance index of 0.71, using only the top five features for risk stratification of overall survival. The Kaplan-Meier estimate also showed statistically significant separation between the low-risk and high-risk patients, with a log-rank P value of 0.0097. Finally, unsupervised clustering of the top five features revealed that stage IV colon cancers with peritoneal spread were morphologically more similar to stage II colon cancers with no long-term metastases than to stage IV colon cancers with hematogenous spread. © 2022 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
Vichy Thermal Spring Water (VTSW), a cosmetic ingredient of potential interest in the frame of skin ageing exposome: an in vitro study (2018)

This work suggests that VTSW could be considered as an ingredient of potential interest to address some of the deleterious effects of skin ageing exposome.
Faculty Opinions recommendation of Small Maf proteins (MafF, MafG, MafK): History, structure and function. (2017)

The small Maf proteins (sMafs) are basic region leucine zipper (bZIP)-type transcription factors.The basic region of the Maf family is unique among the bZIP factors, and it contributes to the distinct DNA-binding mode of this class of proteins.MafF, MafG and MafK are the three vertebrate sMafs, and no functional differences have been observed among them in terms of their bZIP structures.sMafs form homodimers by themselves, and they form heterodimers with cap 'n' collar (CNC) proteins (p45 NF-E2, Nrf1, Nrf2, and Nrf3) and also with Bach proteins (Bach1 and Bach2).Because CNC and Bach proteins cannot bind to DNA as monomers, sMafs are indispensable partners that are required by CNC and Bach proteins to exert their functions.sMafs lack the transcriptional activation domain; hence, their homodimers act as transcriptional repressors.In contrast, sMafs participate in transcriptional activation or repression depending on their heterodimeric partner molecules and context.Mouse genetic analyses have revealed that various biological pathways are under the regulation of CNC-sMaf heterodimers.In this review, we summarize the history and current progress of sMaf studies in relation to their partners.
Point spread function model for microscopic image deconvolution in digital holographic microscopy (2003)

A simple model is proposed in order to evaluate the complex amplitude point spread function (intensity and phase) of a microscope objective. The model is based on the Fresnel diffraction theory and takes also into account the possible optical aberrations. Experimental evaluation of this amplitude point spread function has been carried out by using a holographic set-up and 60 nanometers gold spheres as punctual objects. The measured values are then compared with the theoretical predicted model.
Optimization of Phase-Change Material–Elastomer Composite and Integration in Kirigami-Inspired Voxel-Based Actuators (2021)

Phase-change material-elastomer composite (PCMEC) actuators are composed of a soft elastomer matrix embedding a phase-change fluid, typically ethanol, in microbubbles. When increasing the temperature, the phase change in each bubble induces a macroscopic expansion of the matrix. This class of actuators is promising for soft robotic applications because of their high energy density and actuation strain, and their low cost and easy manufacturing. However, several limitations must be addressed, such as the high actuation temperature and slow actuation speed. Moreover, the lack of a consistent design approach limits the possibility to build PCMEC-based soft robots able to achieve complex tasks. In this work, a new approach to manufacture PCMEC actuators with different fluid-elastomer combinations without altering the quality of the samples is proposed. The influence of the phase-change fluid and the elastomer on free elongation and bending is investigated. We demonstrate that choosing an appropriate fluid increases the actuation strain and speed, and decreases the actuation temperature compared with ethanol, allowing PCMECs to be used in close contact with the human body. Similarly, by using different elastomer materials, the actuator stiffness can be modified, and the experimental results showed that the curvature is roughly proportional to the inverse of Young's modulus of the pure matrix. To demonstrate the potential of the optimized PCMECs, a kirigami-inspired voxel-based design approach is proposed. PCMEC cubes are molded and reinforced externally by paper. Cuts in the paper induce anisotropy into the structure. Elementary voxels deforming according to the basic kinematics (bending, torsion, elongation, compression and shear) are presented. The combination of these voxels into modular and reconfigurable structures could open new possibilities towards the design of flexible robots able to perform complex tasks.
Rarity of Anti-Na+/I−Symporter (NIS) Antibody with Iodide Uptake Inhibiting Activity in Autoimmune Thyroid Diseases (AITD) (2000)

The search for antibody against the Na+/I- symporter (NIS) has seen conflicting results over the years. Prior to cloning of NIS, Raspe et al found iodide uptake inhibiting sera were rare in autoimmune thyroid diseases (AITD) while post-cloning, others reported the presence of antibody in 12-15% of Hashimoto's thyroiditis (HT) and 30-84% of Graves' disease (GD). To evaluate the role of NIS as a potential antigen in AITD, a stable COS 7 cell line expressing high level of functional hNIS was established which allowed the screening of large number of sera for iodide uptake inhibiting activity in a 96-well plate format. Five hundred and fourteen serum samples taken from normal subjects and patients with AITD, non-autoimmune thyroid diseases, and non-thyroid autoimmune diseases were assayed for presence of iodide uptake inhibiting activity. Under the influence of these sera, iodide uptake showed a normal frequency distribution and diminution of uptake 2 SDs below the mean of controls was observed with 14 sera. Among these, 7 that were available for further study were re-evaluated after dialysis and/or Ig G extraction. All 7 sera lost their iodide uptake inhibiting activity, indicating that the effects were not antibody mediated and unknown serum factors had been responsible. In conclusion, contrary to previous results, the present study indicates that antibodies capable of modulating NIS activity are rare in AITD.
Reclassification of Streptomyces caeruleus as a synonym of Actinoalloteichus cyanogriseus and reclassification of Streptomyces spheroides and Streptomyces laceyi as later synonyms of Streptomyces niveus (2008)

Previous studies have proposed that Streptomyces caeruleus is an earlier heterotypic synonym for Streptomyces niveus and Streptomyces spheroides. In this study, phylogenetic analysis of the almost complete 16S rRNA gene sequences of the Streptomyces caeruleus type strains NBRC 13344T, JCM 4014T and NRRL B-2194T revealed that S. caeruleus was closely related to Actinoalloteichus cyanogriseus and not to S. niveus, S. spheroides or any other species of the genus Streptomyces. Moreover, the diagnostic cell-wall diamino acid was found to be meso-diaminopimelic acid in S. caeruleus and DNA–DNA hybridization studies revealed that S. caeruleus NBRC 13344T was a member of the same species as A. cyanogriseus NBRC 14455T. Based on these chemotaxonomic and phylogenetic data, it is proposed that Streptomyces caeruleus ( Baldacci 1944 ) Pridham et al. 1958 be reclassified as a heterotypic synonym of Actinalloteichus cyanogriseus Tamura et al. 2000 . Furthermore, based on phylogenetic, morphological and MALDI-TOF MS analyses, it is proposed that the species Streptomyces laceyi Manfio et al. 2004 and Streptomyces spheroides Wallick et al. 1956 are reclassified as later heterotypic synonyms of Streptomyces niveus Smith et al. 1956 .
Dynamics of Microbeams under Multi-Frequency Excitations (2017)

This paper presents an investigation of the dynamics of microbeams under multiple harmonic electrostatic excitation frequencies. First, the response of a cantilever microbeam to two alternating current (AC) source excitation is examined. We show by simulations the response of the microbeam at primary resonance (near the fundamental natural frequency) and at secondary resonances (near half, superharmonic, and twice, subharmonic, the fundamental natural frequency). A multimode Galerkin method combined with the Euler-Bernoulli beam equation, accounting for the nonlinear electrostatic force, has been used to develop a reduced order model. The response of the cantilever microbeam to three AC source excitation is also investigated and shown as a promising technique to enhance the bandwidth of resonators. Finally, an experimental study of a clamped-clamped microbeam is conducted, demonstrating the multi-frequency excitation resonances using two, three, and four AC sources.
Interactions of α-, β-, and θ-Defensins with Influenza A Virus and Surfactant Protein D (2009)

We have reported that the alpha-defensins human neutrophil peptides (HNP)-1 and HNP-2 neutralize and aggregate influenza A virus (IAV) and promote uptake of IAV by neutrophils. These alpha-defensins were also shown to bind to surfactant protein (SP)-D and reduce its antiviral activity. In this study, we examined retrocyclin (RC)1 and RC2, humanized versions of the antiviral theta-defensins found in the leukocytes of certain nonhuman primates. RC1 was just as effective as HNP-1-3 in neutralizing IAV, and RC2 and RC101 (an analog of RC1) were more effective. In contrast, human beta-defensins (HBDs) showed less neutralizing activity. Human defensins 5 and 6 (mainly produced by intestinal Paneth cells) had viral neutralizing activity similar to HNP-1-3. Like HNP-1-3, RCs induced viral aggregation and promoted the uptake of IAV by neutrophils. We used surface plasmon resonance to evaluate binding of defensins to SP-D. HBDs, HD6, and HNP-4 bound minimally to SP-D. HNP-1-3 and RCs bound SP-D with high affinity; however, unlike HNP-1 and HNP-2, RCs did not inhibit SP-D antiviral activity. HBDs also did not inhibit antiviral activity of SP-D. Given their strong neutralizing activity and compatibility with SP-D, RCs may provide attractive prototypes for designing therapeutics that can prevent or treat respiratory infections caused by IAV.
o-Acetamidophenylboronate esters stabilized toward hydrolysis by an intramolecular oxygen-boron interaction: potential linkers for selective bioconjugation via vicinal diol moieties of carbohydrates (1991)

The synthesis and properties of o-acetamidophenylboronic acid 8 and the corresponding 1,2-diol cyclic boronates 13 and 16 are reported. The presence of an O-B interaction in 8 and 13 has been established by 11B and 1H NMR spectroscopy. The O-B interaction stabilizes boronate 13 toward hydrolysis and accelerates esterification of acid 8 in contrast to the non-ortho-substituted boronate 10 and acid 3. The enhanced stability of o-acetamidophenylboronate esters toward hydrolysis suggests their application as vicinal diol protecting groups in carbohydrate synthesis. Through the incorporation of an amino group as a second site for a coupling reaction (e.g. via isothiocyanate 22), o-acetamidophenylboronic acids may serve as novel agents for bioconjugation reactions involving carbohydrate moieties.
New underwater acoustic tank facility at Georgia Tech (2002)

A large underwater acoustic tank facility located in the Woodruff School of Mechanical Engineering at Georgia Tech has recently been completed. The facility includes a rectangular concrete water tank 25 feet deep, 25 feet wide, and 34 feet long containing around 160,000 gallons of water. There are three computer-controlled positioners: an x-y-z-θ positioner and a z-θ positioner mounted on carriages and a bottom mounted rotator. The facility has a large rectangular nearfield array which can be used either as a receiver or a transmitter. A single vertical nearfield line array can be translated by the x-y positioner to synthesize a cylindrical nearfield receiving array. The rectangular nearfield transmitting array and the synthesized cylindrical receiving array were designed to be used with the bottom mounted rotator to measure the true farfield bistatic target strength of any target up to one meter in length as a function of the target aspect angle. Such measurements can be done from 2 kHz to over 10 kHz. The tank is being used for transducer development, materials, and flow noise studies in addition to structural acoustics. Several available multichannel data acquisition systems will be described. [Work supported, in part, by a DURIP grant from ONR.]
Adjustable transfer function optical filter for microwave applications (2011)

All-optical techniques for microwave and radio frequency (RF) signal processing has attracted considerable attention in recent years. An important optical component in these all-optical signal processing techniques is the optical filter. Tunable optical filters with a variety of transfer functions have been proposed. However, adjustability of the optical filter transfer function is required to provide an extra degree of control. This adjustability of the shape of the transfer function has not been addressed adequately in the literature. In this paper, we report on the theoretical basis for an all-fiber based adjustable transfer function optical filter. In particular, we model the optical filter using FO-circuit transfer matrices and Jones matrices to fully describe the state of polarization changes of the optical signals through the optical filter. The filter is based on an all fiber Michelson Gires-Turnois interferometer (MGTI). The Gires-Turnois resonators (GTRs) required for the formation of the MGTI are realized by pairs of fiber-loop mirrors (FLMs) in the two arms of the Michelson interferometer. The optical reflectivity of the GTRs is control via adjustment of the polarization in the fiber loop mirrors. We show that arbitrary transfer functions can be realized by adjusting the reflectivity of the FLMs as well as the cavity length of the fiber based GTRs.
Fast Diagnosis With Sensors of Uncertain Quality (2008)

This correspondence presents an approach to the detection and isolation of component failures in large-scale systems. In the case of sensors that report at rates of 1 Hz or less, the algorithm can be considered real time. The input is a set of observed test results from multiple sensors, and the algorithm's main task is to deal with sensor errors. The sensors are assumed to be of threshold test (pass/fail) type, but to be vulnerable to noise, in that occasionally true failures are missed, and likewise, there can be false alarms. These errors are further assumed to be independent conditioned on the system's diagnostic state. Their probabilities, of missed detection and of false alarm, are not known a priori and must be estimated (ideally along with the accuracies of these estimates) online, within the inference engine. Further, recognizing a practical concern in most real systems, a sparsely instantiated observation vector must not be a problem. The key ingredients to our solution include the multiple-hypothesis tracking philosophy to complexity management, a Beta prior distribution on the sensor errors, and a quickest detection overlay to detect changes in these error rates when the prior is violated. We provide results illustrating performance in terms of both computational needs and error rate, and show its application both as a filter (i.e., used to "clean" sensor reports) and as a standalone state estimator.
A high performance cement for solidification of spent ion-exchange resin (1993)

A high performance cement has been developed to improve ion-exchange resin embedding in cement-based materials. The cement mainly consists of slag cement, reinforcing carbon fiber and natural zeolite. The fiber allowed waste loading to be increased from 25 to 60kg-dry resin/200 liters. The zeolite, whose main constituent was clinoptilolite, reduced cesium leachability from the waste form to about 1/10. Laboratory- and full-scale experiments were performed to estimate properties of the waste form, using simulated spent ion-exchange resin. Emphasis was laid on such long-term properties as radiation stability and water resistance.
Contribution of Acute-Phase Proteins and Cardiovascular Risk Factors to Erythrocyte Aggregation in Normolipidemic and Hyperlipidemic Individuals (1998)

This study suggests that acute-phase proteins such as IgG, Hp, AGP and Alb influence significantly and in an independent way the level of RBC aggregation. The close association between RBC aggregation and cardiovascular risk factors further strengthens its clinical importance.
AGC simulator for price-based operation. II. Case study results (1997)

For pt.I see ibid., vol.12, no.2, p.527-32 (1997). This paper deals with an automatic generation control (AGC) problem in a deregulated industry. Through the passage of new public utility regulatory policies, the Federal Energy Regulatory Commission (FERC) encourages an open market system for price based operation. The FERC has issued a notice of proposed rulemaking seeking comments on various ancillary services. One of these ancillary services is load following. Part I describes the simulation models and software implementation of load following contracts in the new environment, and also developed a framework for new market structure to understand AGC implementation in the price-based operation. This paper reviews the case studies to show the modifications required of conventional AGC software for the new environment. Three sets of case study results are reported. The first and second case studies illustrate how to simulate bilateral and poolco based transactions respectively in the new market place. The third case study considers various (bilateral and poolco based) contracts existing simultaneously in the system. The simulation results illustrate that the tie-line flows due to increased number of various contracts will tend to cancel among each other.
Disordered Network State in Hydrated Block-Copolymer Surfactants (2006)

Hydration of poly(butadiene-b-ethylene oxide) diblock copolymers leads to various ordered and disordered phases, analogous to the aqueous phase behavior of surfactants and lipids. Small-angle x-ray scattering measurements corroborated by cryogenic scanning electron microscopy imaging reveal a random network (N) morphology at polymer compositions and water content intermediate to those associated with ordered cylinders (H1) and lamellae (L). This sequence of self-assembled structures is strikingly similar to the phase behavior of certain water-oil-surfactant microemulsions.
Fibrin Sealant Improves Hemostasis in Peripheral Vascular Surgery: A Randomized Prospective Trial (2003)

FS achieved more rapid hemostasis than traditional techniques in this peripheral vascular procedure. FS use appeared to be safe for this procedure.
Rayleigh Limit (2016)

This document contains recommendations for terminology in mass spectrometry. Development of standard terms dates back to 1974 when the IUPAC Commission on Analytical Nomenclature issued recommendations on mass spectrometry terms and definitions. In 1978, the IUPAC Commission on Molecular Structure and Spectroscopy updated and extended the recommendations and made further recommendations regarding symbols, acronyms, and abbreviations. The IUPAC Physical Chemistry Division Commission on Molecular Structure and Spectroscopy’s Subcommittee on Mass Spectroscopy revised the recommended terms in 1991 and appended terms relating to vacuum technology. Some additional terms related to tandem mass spectrometry were added in 1993 and accelerator mass spectrometry in 1994. Owing to the rapid expansion of the field in the intervening years, particularly in mass spectrometry of biomolecules, a further revision of the recommendations has become necessary. This document contains a comprehensive revision of mass spectrometry terminology that represents the current consensus of the mass spectrometry community.
High performance dynamic lock-free hash tables and list-based sets (2002)

Lock-free (non-blocking) shared data structures promise more robust performance and reliability than conventional lock-based implementations. However, all prior lock-free algorithms for sets and hash tables suffer from serious drawbacks that prevent or limit their use in practice. These drawbacks include size inflexibility, dependence on atomic primitives not supported on any current processor architecture, and dependence on highly-inefficient or blocking memory management techniques.Building on the results of prior researchers, this paper presents the first CAS-based lock-free list-based set algorithm that is compatible with all lock-free memory management methods. We use it as a building block of an algorithm for lock-free hash tables. In addition to being lock-free, the new algorithm is dynamic, linearizable, and space-efficient.Our experimental results show that the new algorithm outperforms the best known lock-free as well as lock-based hash table implementations by significant margins, and indicate that it is the algorithm of choice for implementing shared hash tables.
An improved implicit finite‐difference scheme for boundary‐layer flows (1992)

Abstract The paper presents a modification to two well‐known non‐iterative implicit finite‐difference schemes for confined and unconfined boundary‐layer‐type flows. The modification aims at improving the accuracy of these schemes by reducing the adverse effect of linearization, which is inherent in both of them. Using the present improved scheme, the same level of accuracy of the results could be obtained with large mesh sizes in the flow direction (coarse grid). The modification is done by adding a local iterative procedure at each computational step in the flow (marching) direction. As an example, to demonstrate the proposed modification, the simple case of developing forced convection in the entry region of concentric annuli has been considered. The results are presented, which prove the applicability of the proposed modification and show its effect on the obtained accuracy and on the required computer time.