gebhart/patrepeval huggingface dataset:
Mechanisms of adhesion among cells from neural tissues of the chick embryo. (1976)

In order to analyze the molecular mechanisms of cell adhesion during development, proteins on the surface of chick embryonic neural cells were compared with proteins released after placing these cells in culture. One of the components released into culture, F1 (molecular weight, Mr 140,000), was derived by proteolytic cleavage of a cell surface precursor with a molecular weight of at least 240,000. Another protein, F2, recovered from culture as a dimer (Mr 1110,000), appeared to be a product of limited proteolytic cleavage of F1. Cells in retinal tissue possessed a surface protein of Mr 150,000 that also appeared to be derived by limited proteolytic cleavage of the cell surface precursor. Antibodies to F2 interacted with determinants on the cell surface protein of Mr 150,000, and specifically prevented homologous and heterologous binding among dissociated retinal and brain cells. In contrast, antibodies to F1 failed to prevent cell-cell adhesion and did not crossreact with F2. These data suggest that the cell surface protein of Mr 150,000 generated by limited proteolysis is involved in adhesion of both retinal and brain cells. Cell-cell binding of both retinal and brain cells varied as a function of developmental age and brain cells acquired their binding properties at an earlier time than retinal cells. Similar results were obtained in experiments on the binding of retinal and brain cells of different ages to nylon fibres coated with antibodies to F2. The results of the molecular and cellular experiments are incorporated in a model for cell adhesion invoking both proteolytic activation and modulation of cell surface ligands.
Studies on the Lipids of Japanese Littleneck, Tapes japonica Deshayes. II. (1967)

The composition of the acetone-insoluble lipids obtained from Japanese Littleneck, Tapes japonica (Deshayes) was studied. The acetone-insoluble lipids were mostly composed of phospholipids. Procedures used for the analysis of the constituents of phospholipids were as follows; silicic acid column chromatography of intact lipids, and paper chromatography of the water-soluble hydrolysis products of phospholipids according to Dawson, were found to be unsatisfactory. Thin-layer chromatography was not able to separate plasmalogens from analogous diacylphospholipids. Two-dimentional thin-layer chromatography according to Owens, which based on the specific hydrolysis of plasmalogens to lysophospholipids in the presence of mercuric chloride spray reagent was effective for the analysis of plasmalogens. By means of this method, phospholipids were separated into individual phospholipid, and lipid phosphorus was determined. The results of the analysis were as follows; phospholipids were rich in ethanolamine phospho-lipids, and these were 23.1% phosphatidyl ethanolamine, 9.2% phosphatidal ethanolamine (ethanolamine plasmalogen), and 17.8% sphingo-ethanolamine. Other phospholipids determined were 19.8% phosphatidyl choline, 10.8% phosphatidyl serine, and 6.0% phosphatidyl inositol.
Fabrication and evaluation of MCVD single-mode fibres with and without central index depression (1982)

A gas phase etching process has been developed to remove the central index depression in the cores of MCVD single-mode preforms. A comparison is made with conventional fibres of the optical loss, spot size and bending sensitivity. The results are in good agreement with the theory.
Genotype and Media Effects on Callus Formation and Regeneration in Barley<sup>1</sup> (1985)

The success of barley ( Hordeum vulgare L.) cell and tissue culture research depends upon reliable callus culture and plant regeneration procedures. The objective of this study was to identify callus‐inducible genotypes, to evaluate media for effectiveness in promoting callus growth, and to identify genotypes capable of regenerating plants. Ninety‐one barley genotypes were evaluated for initiation and maintenance of callus growth. Forty‐five of the genotypes initiated callus, while 46 did not. Callus cultures were maintained by subculturing onto fresh media at monthly intervals. Genotypic variation was noted for longevity and rate of growth of callus cultures. Calli of several genotypes were maintained for more than 2 years. Murashige and Skoog's (MS) media promoted more callus initiation and provided better callus maintenance than media of Blaydes (B), Gamborg et al. (B5), Norstog (N), and Shenk and Hildebrandt (SH). Frequencies of callus initiation were high when either 0.5, 1.0, or 2.0 mg/L of 2,4‐D (2,4‐dichlorophenoxyacetic acid) were added to the media. There were significant genotype ✕ media interactions for callus initiation. Established calli were transferred to differentiation media to promote plant regeneration. Although there were genotypic differences in regeneration, the overall frequency was low (15%). Seventy percent of the regenerated plants were from calli of the cv. Akka and Wisconsin experimental selection X2387‐3.
A Comprehensive Analytical Treatment of Continuum Electrostatics (1996)

An analytical treatment of the continuum model for electrostatic solvation is presented and shown to be in good agreement with numerical finite-difference continuum calculations for the same system. Because the analytic method, called ACE, is relatively fast and yields a pairwise potential from which gradients and second derivatives can be obtained, its use with molecular mechanics/molecular dynamics programs will be possible. For calculating the self-energies of molecules in aqueous solution, a new analytic method is introduced. It is based on a continuum electrostatics model in which charges are defined as Gaussian charge distributions, rather than point charges, and in which the solute interior is described by a continuous density function. The self-energy potential is a pairwise energy function which only depends on charges, interatomic distances, and the effective, solvent-inaccessible volumes of the atoms. The potential is derived by integrating the energy density of the electric field and termed the integrated field (IF) method. A combination of the analytic self-energy potential with the generalized Born equation for charge−charge interactions,1-3 termed analytic continuum electrostatics (ACE) potential, makes possible an analytic treatment of the electrostatic contribution to solvation. The focusing of field lines is included. The IF method is applied to the calculation of self-energies of all charges on a series of small organic compounds and the protein bovine pancreatic trypsin inhibitor (BPTI). The agreement with self-energies as calculated using a finite-difference program is excellent for small molecules and satisfactory for BPTI. Application of the combined ACE potential to the calculation of solvation energies of small compounds shows good agreement with results of finite-difference calculations. The potential on a plane through the protein superoxide dismutase using ACE and a finite-difference program is in good agreement. For the calculation of the solvation energies of small molecules (20 atoms), ACE is more than 3 orders of magnitude faster than the program UHBD91 which was used for all numerical continuum electrostatics calculations; for BPTI, the speedup is more than 2 orders of magnitude.
Ursolic acid triggers calcium-dependent apoptosis in human Daudi cells (2000)

Ursolic acid (UA) is a pentacyclic triterpenoid compound which occurs naturally in a large variety of vegetarian foods, medicinal herbs and plants. In the present study, ursolic acid was found to decrease cell viability in human lymphoma Daudi cells in a dose-dependent manner. UA also induced morphological changes in cells as well as loss of membrane asymmetry, DNA fragmentation and nuclei condensation, indicating that the mechanism by which UA induced cell death was through apoptosis. Treatment with UA increased intracellular Ca2+ levels. Use of Ca2+ channel inhibitors like verapamil blocked this Ca2+ influx and also the triggering of apoptosis. We hypothesized that the binding of UA to glucocorticoid receptors and the Ca2+ currents induced constituted the first steps of apoptosis.
LBNL fiber positioners for wide-field spectroscopy (2008)

A new fiber positioner design has been developed at Lawrence Berkeley National Lab to position hundreds or thousands of optical Fibers on a large-field telescope focal plane. Each fiber is individually actuated within a small cell on the focal plane using an r-θ stage. These fiber positioners are the baseline design for the curved focal plane of the Super IFU Deployable Experiment (SIDE) on the 10.4 m Gran Telescopio Canarias.
DNA-dependent Protein Kinase Protects against Heat-induced Apoptosis (1999)

Purified heat shock transcription factor 1 (HSF1) binds to both the regulatory and catalytic components of the DNA-dependent protein kinase (DNA-PK). This observation suggests that DNA-PK may have a physiological role in the heat shock response. To investigate this possibility, we performed a comparison of cell lines that were deficient in either the Ku protein or the DNA-PK catalytic subunit versus the same cell lines that had been rescued by the introduction of a functional gene. DNA-PK-negative cell lines were up to 10-fold more sensitive to heat-induced apoptosis than matched DNA-PK-positive cell lines. There may be a regulatory interaction between DNA-PK and HSF1 in vivo, because constitutive overexpression of HSF1 sensitized the DNA-PK-positive cells to heat but had no effect in DNA-PK-negative cells. The initial burst of hsp70 mRNA expression was similar in DNA-PK-negative and -positive cell lines, but the DNA-PK-negative cells showed an attenuated rate of mRNA synthesis at later times and, in some cases, lower heat shock protein expression. These findings provide evidence for an antiapoptotic function of DNA-PK that is experimentally separable from its mechanical role in DNA double strand break repair.
QoE-Based Multi-Exposure Fusion in Hierarchical Multivariate Gaussian CRF (2012)

Many state-of-the-art fusion methods, combining details in images taken under different exposures into one well-exposed image, can be found in the literature. However, insufficient study has been conducted to explore how perceptual factors can provide viewers better quality of experience on fused images. We propose two perceptual quality measures: perceived local contrast and color saturation, which are embedded in our novel hierarchical multivariate Gaussian conditional random field model, to illustrate improved performance for multi-exposure fusion. We show that our method generates images with better quality than existing methods for a variety of scenes.
Forced expression of the cyclin B1–CDC2 complex induces proliferation in adult rat cardiomyocytes (2004)

Repair of the mature mammalian myocardium following injury is impaired by the inability of the majority of cardiomyocytes to undergo cell division. We show that overexpression of the cyclin B1-CDC2 (cell division cycle 2 kinase) complex re-initiates cell division in adult cardiomyocytes. Thus strategies targeting the cyclin B1-CDC2 complex might re-initiate cell division in mature cardiomyocytes in vivo and facilitate myocardial regeneration following injury.
Domain-independent local search for linear integer optimization (1998)

Integer and combinatorial optimization problems constitute a major challenge for algorithmics. They arise when a large number of discrete organizational decisions have to be made, subject to constraints and optimization criteria. This thesis describes and investigates new domain-independent local search strategies for linear integer optimization. We introduce WSAT(OIP), an integer local search method which operates on an algebraic problem representation. WSAT(OIP) generalizes Walksat, a successful local search procedure for propositional satisfiability (SAT), to more expressive constraint systems. For this purpose, we introduce over-constrained integer programs (OIPs), a constraint class which is closely related to integer programs. OIP allows for a natural generalization of the principles of SAT local search to integer optimization. Further, it will be shown that OIPs are a special case of integer linear programs and permit combinations with linear programming for bound computation, initialization by rounding, search space reduction, and feasibility testing. The representation is similar enough to integer programs to make use of existing algebraic modeling languages as front-end to a local search solver. To improve performance on realistic problems, WSAT(OIP) incorporates strategies from Tabu Search. We experimentally investigate WSAT(OIP) for a variety of realistic integer optimization problems from the domains of time tabling, sports scheduling, radar surveillance, course assignment, and capacitated production planning. The experimental design examines efficiency, scaling (with increasing problem size and constrainedness), and robustness. The results demonstrate that integer local search can outperform or compete with state-of-the-art integer programming (IP) branch-and-bound and constraint programming (CP) approaches to these problems in finding near-optimal solutions. Key findings of our empirical study include that integer local search is able to solve difficult constraint problems from time-tabling and sports scheduling when cast into a 0-1 representation, which are beyond the scope of IP branch-and-bound strategies and for which devising robust constraint programs is a non-trivial task. For several realistic optimization problems (0-1 integer and finite domain) we show that integer local search exhibits graceful runtime scaling with increasing problem size and constrainedness. It can therefore significantly outperform IP branch-and-bound strategies on large or tightly constrained problems in finding near-optimal solutions. The problems under consideration are mostly beyond the limitations of a previous general-purpose simulated annealing strategy for 0-1 integer programs.
Recoverable user-level mutual exclusion (2002)

Mutual exclusion primitives based on user-level atomic instructions (often called spin locks) have proven to be much more efficient than operating-system semaphores in situations where the contention on the semaphore is low. However, many of these spin lock schemes do not permit registration of ownership to be carried aut atomically with acquisition, potentially leaving the ownership undetermined if a process dies (or makes very slow progress) at a critical point in the registration code. We present an algorithm which can ensure the successful registration of ownership of a spin lock, regardless of where processes fail. Thus, our spin lock implementation is 'recoverable'. The determination of a spin lock's ownership can potentially be used to restore resources protected by the spin lock to consistency and then release the spin lock. Other processes using the lock can then continue to function normally, improving fault resiliency for the application. Our algorithm provides very fast lock acquisition when the acquisition is uncontested (comparable in speed to a simple test-and-set based spin lock), and we prove it works even on the weak memory consistency models implemented by many modern multiprocessor computer systems.
Graphene field effect transistor without an energy gap (2013)

Graphene is a room temperature ballistic electron conductor and also a very good thermal conductor. Thus, it has been regarded as an ideal material for postsilicon electronic applications. A major complication is that the relativistic massless electrons in pristine graphene exhibit unimpeded Klein tunneling penetration through gate potential barriers. Thus, previous efforts to realize a field effect transistor for logic applications have assumed that introduction of a band gap in graphene is a prerequisite. Unfortunately, extrinsic treatments designed to open a band gap seriously degrade device quality, yielding very low mobility and uncontrolled on/off current ratios. To solve this dilemma, we propose a gating mechanism that leads to a hundredfold enhancement in on/off transmittance ratio for normally incident electrons without any band gap engineering. Thus, our saw-shaped geometry gate potential (in place of the conventional bar-shaped geometry) leads to switching to an off state while retaining the ultrahigh electron mobility in the on state. In particular, we report that an on/off transmittance ratio of 130 is achievable for a sawtooth gate with a gate length of 80 nm. Our switching mechanism demonstrates that intrinsic graphene can be used in designing logic devices without serious alteration of the conventional field effect transistor architecture. This suggests a new variable for the optimization of the graphene-based device--geometry of the gate electrode.
Optic nerve injury alters basic fibroblast growth factor localization in the retina and optic tract (1994)

Basic fibroblast growth factor (bFGF) is thought to be a trophic factor for several classes of neurons. Its distribution changes in response to cortical neural injury. We have determined the effect of injury to the optic nerve on localization of bFGF in the rodent retina and visual pathways. Our observations were confirmed by using different antisera and monoclonal antibodies. While photoreceptors normally contain virtually no bFGF, crushing the optic nerve causes a striking increase, over a period of several weeks, in the amount of bFGF in retinal photoreceptors. Since photoreceptors do not synapse directly upon the injured ganglion cells, intermediary cells must participate in the cascade of events that results in the elevated bFGF. In light of the observation that exogenous bFGF protects photoreceptors from photodamage (Faktorovich et al., 1992), this increase in bFGF in photoreceptors may explain, in part, why crushing the optic nerve protects photorecptors against photodamage (Bush and Williams, 1991). Whereas bFGF is constitutively found in glia in the optic nerve, little bFGF is found in glia in the optic tract. However, damage to the optic nerve increases bFGF in astrocytes in the optic tract. This change occurs within days, suggesting that a relatively direct signal may intervene between the injured axon and the adjacent glial cells. Thus, despite the fact that the optic nerve and optic tract are contiguous structures through which axons of retinal ganglion cells project, the glial elements in these structures express distinct properties, because of differences in either glial subclasses or microenvironment.(ABSTRACT TRUNCATED AT 250 WORDS)
Motion deblurring with temporally coded illumination in an LED array microscope (2015)

Motion blur, which results from time-averaging an image over the camera's exposure time, is a common problem in microscopy of moving samples. Here, we demonstrate linear motion deblurring using temporally coded illumination in an LED array microscope. By illuminating moving objects with a well-designed temporal coded sequence that varies during each single camera exposure, the resulting motion blur is invertible and can be computationally removed. This scheme is implemented in an existing LED array microscope, providing benefits of being grayscale, fast, and adaptive, which leads to high-quality deblur performance and a flexible implementation with no moving parts. The proposed method is demonstrated experimentally for fast moving targets in a microfluidic environment.
[Study of photoreflectance in Cd1-xMnxTe/Cd1-yMnyTe superlattices of II - VI diluted magnetic semiconductors]. (1998)

The observation of photoreflectance spectra of Cd1-xMnxTe/Cd1-yMnyTe superlattices was carried out at temperature T = 80K. The samples were grown by molecular beam epitaxy (MBE) technique. The heavy-and light-hole excitonic transition structures 11H, 22H, 33H and 11L were observed and the theoretical calculations, including the strain effects, were performed. By comparison, both agree well.
Cassia angustifolia seed gum as an effective natural coagulant for decolourisation of dye solutions (2002)

Owing to economic advantages in addition to the potential for improved process robustness and to reduce the pollution load on the environment, particularly in water treatment applications in developing countries, an investigation with biodegradable and eco-friendly naturally occurring seed gum as coagulant was undertaken. Naturally occurring Cassia angustifolia (CA) seed gum was evaluated against the chemical coagulant polyaluminium chloride (PAC) for its coagulation ability to remove colour from synthetic dye solutions. Three groups of dyes: Acid Sendula Red, Direct Kahi Green and Reactive Remazol Brilliant Violet were chosen for the case study. For optimum results the variables studied were pH and dosage. CA was found to be a good working substitute alone or in conjunction with a very low dose of PAC for decolourisation of acid and direct, but not for reactive dye solutions. The performance of PAC was better with direct dye and that of CA was better with that of acid dye.
Scattered data interpolation: tests of some methods (1982)

This paper is concerned with the evaluation of methods for scattered data interpolation and some of the results of the tests when applied to a number of methods. The process involves evaluation of the methods in terms of timing, storage, accuracy, visual pleasantness of the surface, and ease of implementation. To indicate the flavor of the type of results obtained, we give a summary table and representative perspective plots of several surfaces.
Poisoning Attacks and Data Sanitization Mitigations for Machine Learning Models in Network Intrusion Detection Systems (2021)

Among many application domains of machine learning in real-world settings, cyber security can benefit from more automated techniques to combat sophisticated adversaries. Modern network intrusion detection systems leverage machine learning models on network logs to proactively detect cyber attacks. However, the risk of adversarial attacks against machine learning used in these cyber settings is not fully explored. In this paper, we investigate poisoning attacks at training time against machine learning models in constrained cyber environments such as network intrusion detection; we also explore mitigations of such attacks based on training data sanitization. We consider the setting of poisoning availability attacks, in which an attacker can insert a set of poisoned samples at training time with the goal of degrading the accuracy of the deployed model. We design a white-box, realizable poisoning attack that reduced the original model accuracy from 95% to less than 50 % by generating mislabeled samples in close vicinity of a selected subset of training points. We also propose a novel Nested Training method as a defense against these attacks. Our defense includes a diversified ensemble of classifiers, each trained on a different subset of the training set. We use the disagreement of the classifiers' predictions as a data sanitization method, and show that an ensemble of 10 SVM classifiers is resilient to a large fraction of poisoning samples, up to 30% of the training data.