gebhart/patrepeval huggingface dataset:
Ultrastructural localization of alpha-actinin and filamin in cultured cells with the immunogold staining (IGS) method. (1984)

Monospecific antibodies to chicken gizzard actin, alpha-actinin, and filamin have been used to localize these proteins at the ultrastructural level: secondary cultures of 14-d-old chicken embryo lung epithelial cells and chicken heart fibroblasts were briefly lysed with either a 0.5% Triton X-100/0.25% glutaraldehyde mixture, or 0.1% Triton X-100, fixed with 0.5% glutaraldehyde, and further permeabilized with 0.5% Triton X-100, to allow penetration of the gold-conjugated antibodies. After immunogold staining (De Mey, J., M. Moeremans, G. Geuens, R. Nuydens, and M. De Brabander, 1981, Cell Biol. Int. Rep. 5:889-899), the cells were postfixed in glutaraldehyde-tannic acid and further processed for embedding and thin sectioning. This approach enabled us to document the distribution of alpha-actinin and filamin either on the delicate cortical networks of the cell periphery or in the densely bundled stress fibers and polygonal nets. By using antiactin immunogold staining as a control, we were able to demonstrate the applicability of the method to the microfilament system: the label was distributed homogeneously over all areas containing recognizable microfilaments, except within very thick stress fibers, where the marker did not penetrate completely. Although alpha-actinin specific staining was homogeneously localized along loosely-organized microfilaments, it was concentrated in the dense bodies of stress fibers. The antifilamin-specific staining showed a typically spotty or patchy pattern associated with the fine cortical networks and stress fibers. This pattern occurred along all actin filaments, including the dense bodies also marked by anti-alpha-actinin antibodies. The results confirm and extend the data from light microscopic investigations and provide more information on the structural basis of the microfilament system.
Editorial (2011)

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Longitudinal evaluation of dementia of the Alzheimer type (1990)

We administered 3 commonly employed tests of mental status (the Information-Memory-Concentration test [IMC], the Mini-Mental State Examination [MMSE], and the Dementia Rating Scale [DRS]) to 92 patients with probable dementia of the Alzheimer type. The 3 tests were readministered to 55 of the patients (2-year subgroup) approximately 1 year later, and administered a 3rd time to 20 of the patients (3-year subgroup) approximately 2 years after their initial assessment. In all cases, scores on the 3 tests were highly correlated with each other. Examination of the annual rate of change (ARC) in score for the 2-year subgroup revealed an average decline of -3.24 error points on the IMC, 2.81 points on the MMSE, and 11.38 points on the DRS. Of the 3 tests, only the DRS evidenced greater sensitivity to change with increasing dementia severity. In the 3-year subgroup, the ARC between years 1 and 2 was not correlated with ARC between years 2 and 3 for any of the 3 tests. This finding suggests that a patient's rate of progression in 1 year may bear little relationship to future rate of decline.
Euclidean Skeletons of Digital Image and Volume Data in Linear Time by the Integer Medial Axis Transform (2008)

A general algorithm for computing Euclidean skeletons of 2D and 3D data sets in linear time is presented. These skeletons are defined in terms of a new concept, called the integer medial axis (IMA) transform. We prove a number of fundamental properties of the IMA skeleton, and compare these with properties of the CMD (centers of maximal disks) skeleton. Several pruning methods for IMA skeletons are introduced (constant, linear and square-root pruning) and their properties studied. The algorithm for computing the IMA skeleton is based upon the feature transform, using a modification of a linear-time algorithm for Euclidean distance transforms. The skeletonization algorithm has a time complexity which is linear in the number of input points, and can be easily parallelized. We present experimental results for several data sets, looking at skeleton quality, memory usage and computation time, both for 2D images and 3D volumes.
THE INSULATING ENVELOPE (2014)

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Delayed globin synthesis leads to excess heme and the macrocytic anemia of Diamond Blackfan anemia and del(5q) myelodysplastic syndrome (2016)

Diamond Blackfan anemia (DBA) and myelodysplastic syndrome (MDS) with isolated del(5q) are severe macrocytic anemias; although both are associated with impaired ribosome assembly, why the anemia occurs is not known. We cultured marrow cells from DBA (n = 3) and del(5q) MDS (n = 6) patients and determined how heme (a toxic chemical) and globin (a protein) are coordinated. We show that globin translation initiates slowly, whereas heme synthesis proceeds normally. This results in insufficient globin protein, excess heme and excess reactive oxygen species in early erythroid precursors, and CFU-E (colony-forming unit-erythroid)/proerythroblast cell death. The cells that can more rapidly and effectively export heme or can slow heme synthesis preferentially survive and appropriately mature. Consistent with these observations, treatment with 10 μM succinylacetone, a specific inhibitor of heme synthesis, improved the erythroid cell output of DBA and del(5q) MDS marrow cultures by 68 to 95% (P = 0.03 to 0.05), whereas the erythroid cell output of concurrent control marrow cultures decreased by 4 to 13%. Our studies demonstrate that erythropoiesis fails when heme exceeds globin. Our data further suggest that therapies that decrease heme synthesis (or facilitate heme export) could improve the red blood cell production of persons with DBA, del(5q) MDS, and perhaps other macrocytic anemias.
Microcystin‐LR and liver tumor promotion: effects on cytokinesis, ploidy, and apoptosis in cultured hepatocytes (1999)

There is mounting evidence that the cyanobacterial toxins, the microcystins, can act as tumor promoters. However, due to their requirement for active uptake by the cell, there have been few in vitro studies of the mechanism by which this might occur. Most of our understanding of this process has been deduced from experiments using the cell permeant okadaic acid, despite differences in the effects of these toxins. A cell culture system was developed in which nonmitogenically stimulated proliferating primary mouse hepatocytes could be exposed to microcystin-LR and the effects on various cell cycle parameters could be determined. It was found that cytokinesis was stimulated and the rate of apoptosis reduced by picomolar concentrations of microcystin-LR, whereas at higher (nanomolar) concentrations, cytokinesis appeared to be inhibited and cell death was induced. Cell killing was selective at these higher concentrations, favoring retention of a proliferatively active cohort of cells. The differences in effect between okadaic acid and microcystin-LR found by other researchers were confirmed, although in this system the effective concentrations of the toxins were approximately 100-fold lower than those reported previously. The mechanistic implications of these findings with regard to tumor promotion are discussed. ©1999 John Wiley & Sons, Inc. Environ Toxicol 14: 61–75, 1999
Soft tissue elasticity measurement : techniques,instrument and applications (2011)

2010-2011 > Academic research: refereed > Publication in refereed journal
Designing implant surface topography for improved biocompatibility (2013)

Modern approaches to biomaterials aim to instigate a specific tissue response to create truly biocompatible materials. With this in mind, the responses of cells to biomimetic surface topographies have been studied. This review compares the findings and links the results to the processes which occur when cells contact a surface. Topographical features such as grooves and ridges or pits and pillars can have a dramatic effect on the composition of protein layers affecting protein orientation and conformation. It has been demonstrated that these surface properties along with others, such as surface compliance, can significantly impact on specific cell-surface interactions. Design strategies to minimize foreign body reactions should consider the shape, size, spacing and curvature of topographical features. In doing this, it should be possible to control the signals that are relayed to the nucleus and thus gain a degree of control over the cell behavior and ultimately the tissue response.
KTP Optical Parametric Amplifier pumped by High Power Passively Q-switched Microchip Laser. (2005)

We report subnanosecond passively Q-switched 1.57μm laser, based on YAG:Nd/YAG:Cr4+ microchip with intracavity KTP OPA. Pumped by 18W fiber coupled laser diode array, this laser produced 200pJ, 850ps pulses with peak power 235kW.
Otitis Media (1993)

DefinitionsWhen the diagnosis of otitis media has been made on the basis of skilled clinical observation and the tympanic membrane is intact, it is practical to assume that an effusion is present. However, this can be confirmed only by recovery of fluid from the middle ear on tympanocentesis or myringotomy. Several methods will confirm the diagnosis of effusion with the indicated accuracy, as generally reported in the literature (Table 1).Acute Otitis MediaA common error in the diagnosis of otitis media with effusion (OME) is equating an
Evaluation of the Microbiology of Chronic Maxillary Sinusitis (1998)

Chronic paranasal sinusitis is a disease that afflicts a significant percentage of the population and causes considerable long-term morbidity. With the common use of multiple courses of broad-spectrum oral antibiotics to treat this condition, there is a possibility of an alteration in the pathogens that promote a persistence of chronic sinusitis. One hundred seventy-four consecutive patients with a diagnosis of chronic maxillary sinusitis requiring an endoscopic surgical procedure were prospectively evaluated. At the time of surgery, cultures of mucopus in the maxillary sinus were aseptically obtained endoscopically and cultured for aerobes, anaerobes, and fungus. Two hundred seventeen isolates from 174 patients were obtained. Coagulase-negative staphylococci were the most common isolates (36%), followed by Staphylococcus aureus (25%), Streptococcus viridans (8.3%), Corynebacterium (4.6%), and anaerobes (6.4%). Although coagulase-negative Staphylococcus is not considered a pathogen, of the 24 isolates that had sensitivity testing performed, 13 demonstrated resistance to multiple antibiotics, including cephalothin, erythromycin, oxacillin, sulfonamides, and clindamycin. This study demonstrates that aerobic rather than anaerobic bacteria are the more common pathogens in chronic sinusitis. In addition, coagulase-negative Staphylococcus may be a pathogen in the disease process, and sensitivities should be obtained of this isolate for evaluation and possible treatment.
Nucleotide sequence of the heme subunit of flavocytochrome c from the purple phototrophic bacterium, Chromatium vinosum. A 2.6-kilobase pair DNA fragment contains two multiheme cytochromes, a flavoprotein, and a homolog of human ankyrin (1993)

The gene for the cytochrome subunit of Chromatium vinosum flavocytochrome c (sulfide dehydrogenase) was cloned from an EcoRI digest of chromosomal DNA. The mature cytochrome subunit contains 175 amino acid residues and two heme binding sites in agreement with the previously reported amino acid sequence. There is also a signal peptide of 25 residues, which apparently directs the protein to the periplasmic space. There are two open reading frames upstream of the heme subunit gene, which encode a tetraheme cytochrome c and a homolog of human ankyrin. The gene for the flavoprotein subunit of flavocytochrome c is in frame 15 nucleotides downstream of the stop codon for the cytochrome gene. Messenger RNA was isolated from malate grown cells. The transcript is approximately 3 kilobases in size and does not hybridize with a probe containing the tetraheme cytochrome gene and part of the ankyrin homolog gene. The heme subunit and flavoprotein subunit genes thus appear to form an operon. The flavoprotein subunit has a 30-residue signal peptide. The clone ends 95 amino acids into the N-terminal sequence of the mature flavoprotein subunit (which should contain about 400 residues). The apparently periplasmic location of flavocytochrome c has important consequences for the presumed function as a sulfide dehydrogenase, because sulfur, which is the product of oxidation, is stored in the cytoplasm. Our results on the location of the enzyme are incompatible with this function.
Case 37-1975 (1975)

Presentation of Case First admission. An 87-year-old woman was admitted to the hospital because of dermatitis.She was well until 21 months previously, when dryness and scaling of the skin developed. A physician prescribed a fluocinonide ointment, and the skin changes improved. Sixteen months before entry she returned to her physician because of cracking of the skin of the fingers. Fine scaling of the face with minimal erythema was observed. Cellulitis of the leg was treated with clindamycin. Two months before admission she returned because of a rash on the fingers that resembled psoriasis. Scaling of the scalp and . . .
Vacuolar energization: pumps, shunts and stress (1997)

Two H + -pumps may co-reside at the plant vacuolar membrane-the V-PPase and V-ATPase. Elucidation of their transport characteristics by patch clamp electrophysiology has indicated the possibility of distinct physiological roles. The V-ATPase may predominate in vacuolar acidification while the V-PPase may facilitate vacuolar K + accumulation. Little is known of how pump activity is regulated in vivo, but an ATP 4 -regulated vacuolar shunt conductance may help clamp the membrane voltage to permit continued lumenal acidification. Both pumps respond to stress in order to maintain the critical functions of the vacuole. Under chill or hypoxic stress, V-PPase transcript levels and activity can increase to counter the impaired activity of the V-ATPase as ATP levels drop and the latter enzyme dissociates. During salt stress, the subunit composition of the V-ATPase may be modulated and its activity increased to power enhanced vacuolar Na + sequestration.
Overlay Portfolio Management in a Multi-Manager Account (2003)

New portfolio structures are changing the rules of the investment game. Multi-Manager Separate Accounts combine the separate skills of a number of managers in a single account, providing benefits to the investor, the plan sponsor, and the manager. An effective multi-manager account requires what the investment industry is beginning to refer to as Overlay Portfolio Management. We describe the role of the overlay portfolio manager and simulate the value he may add through tax management. We show that an overlay manager is often able to add 0.30% to 0.60% or more each year in net after-tax return. The value we identify creates a compelling proposition for the separate account product industry, especially since significant additional non-quantified benefits also accrue.
Homophily and Latent Attribute Inference: Inferring Latent Attributes of Twitter Users from Neighbors (2021)

In this paper, we extend existing work on latent attribute inference by leveraging the principle of homophily: we evaluate the inference accuracy gained by augmenting the user features with features derived from the Twitter profiles and postings of her friends. We consider three attributes which have varying degrees of assortativity: gender, age, and political affiliation. Our approach yields a significant and robust increase in accuracy for both age and political affiliation, indicating that our approach boosts performance for attributes with moderate to high assortativity. Furthermore, different neighborhood subsets yielded optimal performance for different attributes, suggesting that different subsamples of the user's neighborhood characterize different aspects of the user herself. Finally, inferences using only the features of a user's neighbors outperformed those based on the user's features alone. This suggests that the neighborhood context alone carries substantial information about the user.
Stress Increases Vulnerability to Inflammation in the Rat Prefrontal Cortex (2006)

Inflammation could be involved in some neurodegenerative disorders that accompany signs of inflammation. However, because sensitivity to inflammation is not equal in all brain structures, a direct relationship is not clear. Our aim was to test whether some physiological circumstances, such as stress, could enhance susceptibility to inflammation in the prefrontal cortex (PFC), which shows a relative resistance to inflammation. PFC is important in many brain functions and is a target for some neurodegenerative diseases. We induced an inflammatory process by a single intracortical injection of 2 microg of lipopolysaccharide (LPS), a potent proinflammogen, in nonstressed and stressed rats. We evaluated the effect of our treatment on inflammatory markers, neuronal populations, BDNF expression, and behavior of several mitogen-activated protein (MAP) kinases and the transcription factor cAMP response element-binding protein. Stress strengthens the changes induced by LPS injection: microglial activation and proliferation with an increase in the levels of the proinflammatory cytokine tumor necrosis factor-alpha; loss of cells such as astroglia, seen as loss of glial fibrillary acidic protein immunoreactivity, and neurons, studied by neuronal-specific nuclear protein immunohistochemistry and GAD67 and NMDA receptor 1A mRNAs expression by in situ hybridization. A significant increase in the BDNF mRNA expression and modifications in the levels of MAP kinase phosphorylation were also found. In addition, we observed a protective effect from RU486 [mifepristone (11beta-[p-(dimethylamino)phenyl]-17beta-hydroxy-17-(1-propynyl)estra-4,9-dien-3-one)], a potent inhibitor of the glucocorticoid receptor activation. All of these data show a synergistic effect between inflammation and stress, which could explain the relationship described between stress and some neurodegenerative pathologies.
Listeriolysin O activates mitogen-activated protein kinase in eucaryotic cells (1996)

Infection with Listeria monocytogenes induces the activation of mitogen-activated protein (MAP) kinase in several tissue culture cell lines (P.Tang, I. Rosenshine, and B. B. Finlay, Mol. Biol. Cell 5:455-464, 1994). After various mutants were examined, the bacterial factor responsible for MAP kinase activation was identified as listeriolysin O (LLO). Growth supernatant containing LLO or purified LLO alone can induce MAP kinase tyrosine phosphorylation in HeLa cells. Single-amino-acid mutations in LLO that do not affect its membrane binding capacity but reduce its cytolytic activity also reduced its ability to induce MAP kinase activity in HeLa cells. Streptolysin O, another sulfhydryl-activated hemolysin, and the detergent saponin are also able to activate MAP kinase in target cells. Thus, the increased MAP kinase activity observed in L. monocytogenes-infected cells is most likely a result of the permeabilization of the host cell membrane by LLO and may not be linked with invasion.
MiR-34a, miR-21 and miR-23a as potential biomarkers for coronary artery disease: a pilot microarray study and confirmation in a 32 patient cohort (2015)

The aim of this study was to investigate the expression of circulating microRNAs (miRNAs) in apolipoprotein E (apoE) knockout mice (apoE(-/-)) and to validate the role of these miRNAs in human coronary artery disease (CAD). Pooled plasma from 10 apoE(-/-) mice and 10 healthy C57BL/6 (B6) mice was used to perform the microarray analysis. The results showed that miR-34a, miR-21, miR-23a, miR-30a and miR-106b were differentially expressed in apoE(-/-) mice, and these expression changes were confirmed by real-time quantitative reverse-transcription PCR. Then, miR-34a, miR-21, miR-23a, miR-30a and miR-106b were detected in the plasma of 32 patients with CAD and of 20 healthy controls. Only miR-34a, miR-21 and miR-23a were significantly differentially expressed in the plasma of CAD patients (all P<0.01). In conclusion, miR-34a, miR-21 and miR-23a were elevated in CAD patients, which means that these miRNAs might serve as biomarkers of CAD development and progression.
[Mass spectra of 2-aryl-4-cyanoimidazoles and 2-aryl-4-aminopyrimidines]. (1987)

The EI mass spectra of eight new compounds of 2-aryl-4-ycanoimidazoles and 2-aryl-4-aminopyrimidines were reported and their characteristic fragmentations discussed.
Design of Ferromagnetic Shape Memory Alloy Composites (2004)

Ferromagnetic shape memory alloy (FSMA) composites composed of a ferromagnetic material and a shape memory alloy (SMA) are key material systems for fast-responsive and compact actuators. The function of ferromagnetic material is to induce magnetic force which is then used to induce the stress in the SMA, resulting in the stress-induced marten site transformation (SIM), i.e. change in the Young’s modulus, stiff (austenite) to soft (martensite). This SIM-induced phase change causes larger deformation in the SMA, which is often termed as “superelastic”. This paper discusses a simple model by which the stress and strain field in the FSMA composites subjected to bending and torsion loading are computed with the aim of identifying the optimum geometry of FSMA composites. The results of the present analytical study are utilized to design torque actuator (bending of FSMA composite plate) and spring actuator (torsion of helical FSMA composite spring).
cpSGD: Communication-efficient and differentially-private distributed SGD (2018)

Distributed stochastic gradient descent is an important subroutine in distributed learning. A setting of particular interest is when the clients are mobile devices, where two important concerns are communication efficiency and the privacy of the clients. Several recent works have focused on reducing the communication cost or introducing privacy guarantees, but none of the proposed communication efficient methods are known to be privacy preserving and none of the known privacy mechanisms are known to be communication efficient. To this end, we study algorithms that achieve both communication efficiency and differential privacy. For $d$ variables and $n \approx d$ clients, the proposed method uses $O(\log \log(nd))$ bits of communication per client per coordinate and ensures constant privacy. We also extend and improve previous analysis of the \emph{Binomial mechanism} showing that it achieves nearly the same utility as the Gaussian mechanism, while requiring fewer representation bits, which can be of independent interest.