gebhart/patrepeval huggingface dataset:
Resonant Dipole-Dipole Energy Transfer Dynamics in a Frozen Rydberg Gas (2014)

The dipole-dipole interaction strongly couples ultracold highly excited atoms, known as Rydberg atoms, and is the dominant mechanism for energy exchange among such atoms on microsecond time scales. I present the results of experiments that investigate this interaction using rubidium atoms excited to Rydberg states with an all-diode laser system. In the first of these, high resolution dipole-dipole interaction spectra for different magnetic sublevels of the 32d5/2 state are collected and analyzed. In the second experiment, ultracold rubidium atoms are implusively excited to coherent superpositions of three closely spaced |mj|sublevels of the 32d5/2 state in a weak electric field. The magnitude of the field sets the energy level spacing between these states, and hence the frequency of the phase dependent oscillations resulting from interference in resonant energy exchange processes. In the third experiment, the dipole-dipole interaction induced resonant energy exchange between columns of ultracold rubidium Rydberg atoms is imaged using a new technique involving selective field ionization with a spatially sensitive ion detector.
Analysis of independent microarray datasets of renal biopsies identifies a robust transcript signature of acute allograft rejection (2008)

Transcriptomics could contribute significantly to the early and specific diagnosis of rejection episodes by defining 'molecular Banff' signatures. Recently, the description of pathogenesis-based transcript sets offered a new opportunity for objective and quantitative diagnosis. Generating high-quality transcript panels is thus critical to define high-performance diagnostic classifier. In this study, a comparative analysis was performed across four different microarray datasets of heterogeneous sample collections from two published clinical datasets and two own datasets including biopsies for clinical indication, and samples from nonhuman primates. We characterized a common transcriptional profile of 70 genes, defined as acute rejection transcript set (ARTS). ARTS expression is significantly up-regulated in all AR samples as compared with stable allografts or healthy kidneys, and strongly correlates with the severity of Banff AR types. Similarly, ARTS were tested as a classifier in a large collection of 143 independent biopsies recently published by the University of Alberta. Results demonstrate that the 'in silico' approach applied in this study is able to identify a robust and reliable molecular signature for AR, supporting a specific and sensitive molecular diagnostic approach for renal transplant monitoring.
Products of bacteriophage T4 genes 32 and 45 improve the accuracy of DNA replication in vitro. (1983)

The six "accessory" proteins of the bacteriophage T4 specified by replication genes 32, 41, 44, 45, 61, and 62 were studied for their ability to enhance the accuracy with which phage T4 DNA polymerase (product of gene 43) replicates synthetic homopolymer duplexes in vitro. Two of these proteins, gene 32-protein (helix-destabilizing protein) and gene 45-protein, inhibited the selection of incorrect, but not correct, precursors, at the growing strand end. Gene 32-protein is shown to enhance replication fidelity by interacting with the DNA, whereas gene 45-protein exerts its fidelity-enhancing effect by interacting with the DNA polymerase. This is the first example to our knowledge of a DNA polymerase's accuracy being altered through interaction with another protein. Possible mechanisms by which gene 32- and gene 45-protein act to enhance replication fidelity are discussed.
Immunoglobulins: Structure, Genetics and Evolution (2004)

The immune system is capable of generating an immense number of different antibody molecules. The nature of the genetic machinery responsible for this diversity has been studied by selective amino acid sequence analysis of homogeneous immunoglobulin light chains (derived from myeloma tumors). The evolution of the immune system has also been examined through chemical studies of normal pooled light chains derived from various mammalian and avian species. These studies place constraints on proposed genetic mechanisms for antibody diversity. The theories, the structural constraints, and the evolutionary implications of these observations are discussed.
Effect of Magnesium Ions and Ethylenediamine Tetra‐acetic Acid on the Activity of Vancomycin against Escherichia coli and Staphylococcus aureus (1967)

SUMMARY When added to logarithmically dividing Encherichia coli , vancomycin caused lysis only when the nutrient medium was deficient in magnesium ions. They did not prevent vancomycin from exerting an inhibitory effect on Staphylococcus aureus growing in the log phase. Ethylenediamine tetra‐acetic acid (EDTA) was less inhibitory to E. coli than to Staph. aureus , but in sub‐bacteriostatic concentrations it potentiated the activity of sub‐inhibitory doses of vancomycin against E. coli. EDTA probably removes some cations in the cell wall, thus facilitating the entry of vancomycin; it does not potentiate the activity of sub‐bacteriostatic doses of vancomycin against Staph. aureus.
Reperfusion recovery after femoral artery ligation and macrophage treatment (n=9). (2015)

&lt;p&gt;A, Representative Laser Doppler images of each group post-operatively and at day 14. B, Treatment with M1, M2a and M2c macrophages increases the reperfusion recovery after 14 days. C, A trend towards an increase in vessel number could be detected in the category ’50-60 µm diameter’ in animals treated with M2a and M2c macrophages.&lt;/p&gt;
Numerical analysis of tiny-focal-spot generation by focusing linearly, circularly, and radially polarized beams through a micro/nanoparticle (2020)

Obtaining a tiny focal spot is desired for super resolution. We do a vectorial numerical analysis of the linearly, circularly, and radidally polarized electromagnetic fields being focused through a dielectric micro/nanoparticle of size comparable to the wavelength. We find tiny focal spots (up to ∼0.05 <i>λ</i><sup>2</sup>) can be obtained behind micro/nanoparticles of various shapes, e.g. spherical, disk-shaped, and cuboid micro/nanoparticles. Furthermore, we also investigate the influence of the misalignment of a real lens system on the tiny focal spots. We find that tiny focal spots can still be generated even though they are distorted due to the misalignment.
Neuronal L-Type Calcium Channels Open Quickly and Are Inhibited Slowly (2005)

Neuronal L-type calcium channels are essential for regulating activity-dependent gene expression, but they are thought to open too slowly to contribute to action potential-dependent calcium entry. A complication of studying native L-type channels is that they represent a minor fraction of the whole-cell calcium current in most neurons. Dihydropyridine antagonists are therefore widely used to establish the contribution of L-type channels to various neuronal processes and to study their underlying biophysical properties. The effectiveness of these antagonists on L-type channels, however, varies with stimulus and channel subtype. Here, we study recombinant neuronal L-type calcium channels, CaV1.2 and CaV1.3. We show that these channels open with fast kinetics and carry substantial calcium entry in response to individual action potential waveforms, contrary to most studies of native L-type currents. Neuronal CaV1.3 L-type channels were as efficient as CaV2.2 N-type channels at supporting calcium entry during action potential-like stimuli. We conclude that the apparent slow activation of native L-type currents and their lack of contribution to single action potentials reflect the state-dependent nature of the dihydropyridine antagonists used to study them, not the underlying properties of L-type channels.
Circulating miRNAs as Biomarkers for Neurodegenerative Disorders (2014)

Neurodegenerative disorders, such as Alzheimer's disease (AD), Parkinson's disease (PD) and frontotemporal dementias (FTD), are considered distinct entities, however, there is increasing evidence of an overlap from the clinical, pathological and genetic points of view. All neurodegenerative diseases are characterized by neuronal loss and death in specific areas of the brain, for example, hippocampus and cortex for AD, midbrain for PD, frontal and temporal lobes for FTD. Loss of neurons is a relatively late event in the progression of neurodegenerative diseases that is typically preceded by other events such as metabolic changes, synaptic dysfunction and loss, neurite retraction, and the appearance of other abnormalities, such as axonal transport defects. The brain's ability to compensate for these dysfunctions occurs over a long period of time and results in late clinical manifestation of symptoms, when successful pharmacological intervention is no longer feasible. Currently, diagnosis of AD, PD and different forms of dementia is based primarily on analysis of the patient's cognitive function. It is therefore important to find non-invasive diagnostic methods useful to detect neurodegenerative diseases during early, preferably asymptomatic stages, when a pharmacological intervention is still possible. Altered expression of microRNAs (miRNAs) in many disease states, including neurodegeneration, and increasing relevance of miRNAs in biofluids in different pathologies has prompted the study of their possible application as neurodegenerative diseases biomarkers in order to identify new therapeutic targets. Here, we review what is known about the role of miRNAs in the pathogenesis of neurodegeneration and the possibilities and challenges of using these small RNA molecules as a signature for neurodegenerative conditions.
Analysis of the Minimum-Norm Least-Squares Estimator and Its Double-Descent Behavior [Lecture Notes] (2023)

Linear regression models have a wide range of applications in statistics, signal processing, and machine learning. In this Lecture Notes column we will examine the performance of the least-squares (LS) estimator with a focus on the case when there are more parameters than training samples, which is often overlooked in textbooks on estimation.
Image noise level estimation by searching for smooth patches with discrete cosine transform (2016)

When denoising an image, noise level is one of the most vital input parameters, because setting wrong noise level affects a result of denoising. Therefore, the noise level must be estimated accurately. In this paper, we propose a new accurate noise level estimation method based on the characteristic of discrete cosine transform (DCT) coefficients. This characteristic is that the high-frequency coefficients of the smooth patches can be assumed to zero. We select smooth patches from a distribution of the standard deviation of high-frequency coefficients in a noisy image, and a distribution function of the standard deviation of high-frequency coefficients in an only noise image. Moreover, we propose a method that the estimated noise level is calculated from high-frequency coefficients in a noisy image. The experiment results with many images demonstrate that the proposed method estimates the noise levels more accurately, in comparison with the conventional methods.
Comparison of the Effects of Propofol and Pentobarbital on Neurologic Outcome and Cerebral Infarct Size after Temporary Focal Ischemia in the Rat (1997)

Background Although propofol is known to have effects on cerebral physiology similar to the barbiturates, a direct comparison of the relative effects of these drugs on outcome from cerebral ischemia has not been performed. The authors postulated that pentobarbital or propofol would yield similar effects on neurologic and histologic outcome from temporary focal ischemia in the rat. Methods Wistar rats were anesthetized with sufficient doses of pentobarbital (n = 20) or propofol (n = 20) to cause electroencephalographic burst suppression. The middle cerebral artery was then occluded for 75 min. Animals were awakened 4-6 h after onset of reperfusion and allowed to recover for 1 week. Neurologic function and infarct size were then assessed. Results Relevant physiologic values were similar between groups during ischemia and early reperfusion. No difference between groups was observed for severity of hemiparesis (P = 0.10). Total cerebral infarct volumes (median +/- quartile deviation) were similar for the two groups (pentobarbital = 190 +/- 36 mm3; propofol = 200 +/- 24 mm3, P = 0.35). Conclusion Neurologic and histologic outcome were similar in pentobarbital or propofol anesthetized rats undergoing temporary focal cerebral ischemia and a 1-week recovery interval.
Optimum pattern derivative synthesis in randomly perturbed linear array (1990)

The concept of pattern derivative is introduced in an optimal sense in a randomly perturbed linear array with equispaced isotropic elements. The effects of the random variations of weights and element positions on the expectations of the first-order derivative of array space-frequency and power responses are analyzed and employed in optimum weight solutions. Without loss of generality, it is assumed that the expected positions of elements are confined to one-dimensional space; the directions of arrivals for the relevant signals are confined to two-dimensional space; and the element positions vary randomly in three-dimensional space. To illustrate the broadband null performance, an optimum point null and an optimum derivative null are combined to produce a deep null in a three-element linear array.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Plasma and acrosomal membrane lipid content of saltwater crocodile spermatozoa (2021)

This study describes the chemical lipid composition of the sperm plasma and acrosomal membranes of the saltwater crocodile Crocodylus porosus with the aim of providing new insights into sperm physiology, particularly that associated with their preservation ex vivo . The specific fatty acid composition of the sperm plasma and acrosomal membranes is documented. The mean (±s.d.) ratio of unsaturated to saturated membrane fatty acids within the plasma membrane was 2.57±0.50, and was determined to be higher than a similar analysis of the lipids found in the acrosomal membrane (0.70±0.10). The saltwater crocodile sperm plasma membrane also contained remarkably high levels of cholesterol (mean (±s.d.) 40.7±4.5 nmol per 106 sperm cells) compared with the spermatozoa of other amniote species that have so far been documented. We suggest that this high cholesterol content could be conferring stability to the crocodile sperm membrane, allowing it to tolerate extreme osmotic fluxes and rapid changes in temperature. Our descriptive analysis now provides those interested in reptile and comparative sperm physiology an improved baseline database for interpreting biochemical changes associated with preservation pathology (e.g. cold shock and cryoinjury), epididymal sperm maturation and capacitation/acrosome reaction.
Identification and Mechanistic Characterization of a Peptide Inhibitor of Glycogen Synthase Kinase (GSK3β) Derived from the Disrupted in Schizophrenia 1 (DISC1) Protein (2020)

Glycogen synthase kinase 3-beta (GSK3β) is a critical regulator of several cellular pathways involved in neurodevelopment and neuroplasticity and as such is a potential focus for the discovery of new neurotherapeutics toward the treatment of neuropsychiatric and neurodegenerative diseases. The majority of efforts to develop inhibitors of GSK3β have been focused on developing small molecule inhibitors that compete with adenosine triphosphate (ATP) through direct interaction with the ATP binding site. This strategy has presented selectivity challenges due to the evolutionary conservation of this domain within the kinome. The disrupted in schizophrenia 1 (DISC1) protein has previously been shown to bind and inhibit GSK3β activity. Here, we report the characterization of a 44-mer peptide derived from human DISC1 (hDISCtide) that is sufficient to both bind and inhibit GSK3β in a noncompetitive mode distinct from classical ATP competitive inhibitors. Based on multiple independent biochemical and biophysical assays, we propose that hDISCtide interacts at two distinct regions of GSK3β: an inhibitory region that partially overlaps with the binding site of FRATide, a well-known GSK3β binding peptide, and a specific binding region that is unique to hDISCtide. Taken together, our findings present a novel avenue for developing a peptide-based selective inhibitor of GSK3β.
Attenuation of insulin secretion by insulin-like growth factor 1 is mediated through activation of phosphodiesterase 3B (1997)

Both insulin and insulin-like growth factor 1 (IGF-1) are known to reduce glucose-dependent insulin secretion from the beta cells of pancreatic islets. In this paper we show that the mechanism by which IGF-1 mediates this effect is in large part through activation of a specific cyclic nucleotide phosphodiesterase, phosphodiesterase 3B (PDE3B). More specifically, in both isolated pancreatic islets and insulin-secreting HIT-T15 cells, IGF-1 inhibits insulin secretion that has been increased by glucose and glucagonlike peptide 1 (GLP-1). Moreover, IGF-1 decreases cAMP levels in parallel to the reduction of insulin secretion. Insulin secretion stimulated by cAMP analogs that activate protein kinase A and also are substrates for PDE3B is also inhibited by IGF-1. However, IGF-1 does not inhibit insulin secretion stimulated by nonhydrolyzable cAMP analogs. In addition, selective inhibitors of PDE3B completely block the ability of IGF-1 to inhibit insulin secretion. Finally, PDE3B activity measured in vitro after immunoprecipitation from cells treated with IGF-1 is higher than the activity from control cells. Taken together with the fact that pancreatic beta cells express little or no insulin receptor but large amounts of IGF-1 receptor, these data strongly suggest a new regulatory feedback loop model for the control of insulin secretion. In this model, increased insulin secretion in vivo will stimulate IGF-1 synthesis by the liver, and the secreted IGF-1 in turn feedback inhibits insulin secretion from the beta cells through an IGF-1 receptor-mediated pathway. This pathway is likely to be particularly important when levels of both glucose and secretagogues such as GLP-1 are elevated.
A Packet Error Rate of AIS Messages Measurement System (2013)

This article discussed a packet error rate of Automatic Identification System messages measurement system. Packet Error Rate is the only verdict conditions of the receive-performance of shipboard AIS, but so far there is no relative equipment. In this paper a measurement scheme is proposed, and there is an arbitrary waveform generator used for generating standard measurement signals and a personal computer used to receive VDM messages via serial port and calculate the packet error rate. Experiments show that this scheme can meet the functional requirement and has some practice value.
PDE10 inhibition increases GluA1 and CREB phosphorylation and improves spatial and recognition memories in a Huntington's disease mouse model (2013)

Huntington's disease (HD) causes motor disturbances, preceded by cognitive impairment, in patients and mouse models. We showed that increased hippocampal cAMP-dependent protein kinase (PKA) signaling disrupts recognition and spatial memories in R6 HD mouse models. However, unchanged levels of hippocampal phosphorylated (p) cAMP-responsive element-binding protein (CREB) suggested unaltered nuclear PKA activity in R6 mice. Here, we extend this finding by showing that nuclear pPKA catalytic subunit (Thr197) and pPKA substrate levels were unaltered in the hippocampus of R6/1 mice. Phosphodiesterases (PDEs) play an important role in the regulation of PKA activity. PDE10A, a cAMP/cGMP dual-substrate PDE, was reported to be restricted to the nuclear region in nonstriatal neurons. Using cell fractionation we confirmed that PDE10A was enriched in nuclear fractions, both in wild-type and R6/1 mice hippocampus, without differences in its levels or intracellular distribution between genotypes. We next investigated whether inhibition of PDE10 with papaverine could improve cognitive function in HD mice. Papaverine treatment improved spatial and object recognition memories in R6/1 mice, and significantly increased pGluA1 and pCREB levels in R6/1 mice hippocampus. Papaverine likely acted through the activation of the PKA pathway as the phosphorylation level of distinct cGMP-dependent kinase (cGK) substrates was not modified in either genotype. Moreover, hippocampal cAMP, but not cGMP, levels were increased after acute papaverine injection. Our results show that inhibition of PDE10 improves cognition in R6 mice, at least in part through increased GluA1 and CREB phosphorylation. Thus, PDE10 might be a good therapeutic target to improve cognitive impairment in HD.
Dorsal Augmentation (2008)

Rhinoplasty surgery is a challenging and demanding area of plastic surgery, partly because a variety of surgical techniques are available to treat the same type of nasal deformity. This is most evident in the treatment of patients requiring dorsal augmentation. Choosing between autogenous, homologous, and alloplastic grafts with the varied options for each can be confusing. The goal of this issue of Seminars in Plastic Surgery is to present a clear and objective review of the current commonly used methods for dorsal augmentation to better enable the rhinoplasty surgeon to choose the most appropriate method for his or her patient.
On building entity recommender systems using user click log and freebase knowledge (2014)

Due to their commercial value, search engines and recommender systems have become two popular research topics in both industry and academia over the past decade. Although these two fields have been actively and extensively studied separately, researchers are beginning to realize the importance of the scenarios at their intersection: providing an integrated search and information discovery user experience. In this paper, we study a novel application, i.e., personalized entity recommendation for search engine users, by utilizing user click log and the knowledge extracted from Freebase.
Analysis of Routing Protocol Performance in Wireless Mesh Networks (2010)

The objective of the paper is to evaluate and compare proactive and reactive routing protocols designed for ad hoc networks and adapted to Wireless Mesh Networks. The analysis of protocol performance is based on the results of multistage simulations made for UDP traffic and TCP traffic, moreover, for both - a normal working network and the network with selfish node injected. We recommend using particular protocols in certain conditions.
A murine monoclonal antibody recognising a single glycoprotein within a human cytomegalovirus virion envelope glycoprotein complex (1985)

Nonionic detergent solubilised polypeptides from highly purified human cytomegalovirus virions were used as immunogens to produce murine monoclonal antibody secreting hybridomas. One monoclonal antibody was shown, by immunoprecipitation followed by SDS-polyacrylamide gel electrophoresis (SDS-PAGE), to precipitate three glycoproteins with molecular weights 52, 95, and 130 (all X 10(3)) and one minor component with a molecular weight of 50 X 10(3). When virion envelope components were first separated by SDS-PAGE and electrophoretically transferred to nitrocellulose membranes, this monoclonal antibody recognised two related components with molecular weights 50 and 52 (both X 10(3)). Immunofluorescence studies suggested that these viral antigens were associated with membrane systems of virus-infected cells and were particularly abundant late in infection.