gebhart/patrepeval huggingface dataset:
Miniaturized, Ultra-High Throughput Screening of Tyrosine Kinases Using Homogeneous, Competitive Fluorescence Immunoassays (2004)

Assay miniaturization and the implementation of high-density 1,536-microwell screening increase the speed and efficiency of screening and lead discovery. To serve this need, a platform of miniaturizable assay technologies has been assembled for specific biological targets. This platform will enable initiation and completion of uHTS screens in a straightforward and expeditious manner. Although faster primary screening does contribute to a reduction in timelines, the process of assay development can become a bottleneck. Assay technologies that do not require the use of target-specific reagents can reduce the time necessary for assay development. Assays that measure inhibition of tyrosine kinases can be configured in a competitive format where only the enzyme itself is specific to the assay. In this context, several technologies, including time-resolved fluorometry (also known as DELFIA), time-resolved fluorescence resonance energy transfer (also known as LANCE( trade mark )), fluorescence polarization, enzyme fragmentation complementation assay, and confocal laser scanning imaging, were examined. Quality parameters such as assay reproducibility, signal:background ratio, Z factor, and assay sensitivity were compared. Additionally, the relative merits of each of these technologies are assessed in terms of assay miniaturization, ease of development, ultimate screening capability, efficiency, and cost.
Image Restoration for Linear Local Motion-Blur Based on Cepstrum (2012)

This paper presents a real-time restoration method for linear local motion-blur image. for an image in which only the fast moving-object is blurred but the background is clear, the proposed basic strategy is to divide such an image into many sub images firstly and then detect the blurred sub image by the gradient distribution and the maximum of cepstrum. for a blurred sub image, the blur direction and blur length are estimated to calculate the parameters of point spread function (PSF) and Lucy-Richardson deconvolution algorithm is employed to restore this blurred sub image. Using many artificial and real blurred images, the experimental results show that the proposed approach is more accurate and robust than other methods.
Non-Orthogonal Multiple Access via Non-binary Factor Graphs (2023)

In this paper we propose a novel non-orthogonal multiple access (NOMA) scheme via non-binary factor graphs by introducing operations over Galois field GF(q). By utilizing sparse GF(q) spreading, the proposed scheme benefits from an improved diversity of the superimposed symbols and accordingly a lower probability of constellation overlapping. Meanwhile, the coordination with high-order modulation helps to reduce the interference at the receiver, and therefore a better error performance can be expected. Iterative belief-propagation (BP) detection based on log-domain probabilities is derived for the GF(q) NOMA. The upper bounds of maximum likelihood (ML) detection and simulation results in terms of symbol error rate are provided, which demonstrate the superiority of the proposed scheme to its binary counterparts.
Seven-Transmembrane Proteins as Odorant and Chemosensory Receptors (1999)

The olfactory systems of various species solve the challenging problem of general molecular recognition in widely differing ways. Despite this variety, the molecular receptors are invariably G protein-coupled seven-transmembrane proteins, and are encoded by the largest gene families known to exist in a given animal genome. Receptor gene families have been identified in vertebrates and two invertebrate species, the nematode Caenorhabditis elegans and the fruit fly Drosophila melanogaster. The complexity of the odorant receptor repertoire is estimated in mouse and rat at 1000 genes, or 1 percent of the genome, surpassing that of the immunoglobulin and T cell receptor genes combined. Two distinct seven-transmembrane gene families may encode in rodents the chemosensory receptors of the vomeronasal organ, which is specialized in the detection of pheromones. Remarkably, these five receptor families have practically no sequence homology among them. Genetic manipulation experiments in mice imply that vertebrate odorant receptors may fulfill a dual role, also serving as address molecules that guide axons of olfactory sensory neurons to their precise target in the brain.
Neurological update: use of cardiac troponin in patients with stroke (2020)

Cardiac troponin is a specific and sensitive biomarker to identify and quantify myocardial injury. Myocardial injury is frequently detected after acute ischemic stroke and strongly associated with unfavorable outcomes. Concomitant acute coronary syndrome is only one of several possible differential diagnoses that may cause elevation of cardiac troponin after stroke. As a result, there are uncertainties regarding the correct interpretation and optimal management of stroke patients with myocardial injury in clinical practice. Elevation of cardiac troponin may occur as part of a 'Stroke-Heart Syndrome'. The term 'Stroke-Heart Syndrome' subsumes a clinical spectrum of cardiac complications after stroke including cardiac injury, dysfunction, and arrhythmia which may relate to disturbances of autonomic function and the brain-heart axis. In this review, we provide an up-to-date overview about prognostic implications, mechanisms, and management of elevated cardiac troponin levels in patients with acute ischemic stroke.
Synthetic pre-proparathyroid hormone leader sequence inhibits cell-free processing of placental, parathyroid, and pituitary prehormones. (1980)

A chemically synthesized peptide consisting of the NHAerminal precursor-specific leader, or signal, sequence of pre-proparathyroid hormone was used as a molecular probe to investigate the role of the leader sequence in translocation across membranes of polypeptides destined for secretion.When added to a reticulocyte cell-free translation system supplemented with canine pancreatic microsomes that process precursor proteins to their mature -forms, this peptide inhibited in a specific manner the processing of four separate prehormones (bovine pre-proparathyroid hormone, bovine pregrowth hormone, bovine preprolactin, and human preplacental lactogen) to their mature forms.Processing was defined as (a) a reduction in the size of a translation product to ,that of the authentic hormone or prohormone and ( b ) demonstration of resistance of the processed product to limited proteolysis.These criteria are indicative of cleavages of leader sequences from the nascent precursors and the sequestration of the processed products within the microsomes.Several tests supported the specificity of the inhibition by the synthetic precursor-specific peptide.The inhibitory effect of the synthetic peptide was not due to nonspecific disruption of the integrity of the microsomal membranes through detergent-like effects, inasmuch as processed translation products were not released from within microsomes when the peptide was added after the translation reactions were completed.No inhibition of processing was seen when another synthetic peptide consisting of an internal fragment of parathyroid hormone structurally similar in length and hydrophobicity to the precursor-specific peptide was used; inhibition of processing appeared to reside specifically in the leader sequence.These results suggest that microsomal membranes contain specific, saturable recognition elements that function in the membrane-related binding, translocation, and/or cleavage of nascent polypeptides destined for secretion.This synthetic biologically functional peptide of pre-proparathyroid hormone should be useful in the further delineation of the mechanisms involved in the binding of prehormones to, and their translocation across, microsomal membranes, as well as in the identification and isolation of presumed precursor-specific receptors in these membranes.
Hydrogen-bond network and pH sensitivity in human transthyretin (2013)

Transthyretin (TTR) is a tetrameric protein. TTR misfolding and aggregation are associated with human amyloid diseases. Dissociation of the TTR tetramer is believed to be the rate-limiting step in the amyloid fibril formation cascade. Low pH is known to promote dissociation into monomer and the formation of amyloid fibrils. In order to reveal the molecular mechanisms underlying pH sensitivity and structural stabilities of TTR, neutron diffraction studies were conducted using the IBARAKI Biological Crystal Diffractometer with the time-of-flight method. Crystals for the neutron diffraction experiments were grown up to 2.5 mm(3) for four months. The neutron crystal structure solved at 2.0 Å revealed the protonation states of His88 and the detailed hydrogen-bond network depending on the protonation states of His88. This hydrogen-bond network is involved in monomer-monomer and dimer-dimer interactions, suggesting that the double protonation of His88 by acidification breaks the hydrogen-bond network and causes the destabilization of the TTR tetramer. Structural comparison with the X-ray crystal structure at acidic pH identified the three amino acid residues responsible for the pH sensitivity of TTR. Our neutron model provides insights into the molecular stability related to amyloidosis.
Selective Emitter from Structured Diffusion Source Proves its Capability of Industrial Realization (2009)

With the intention to reduce front side recombination in silicon solar cells we developed a robust selective emitter sequence close to the standard manufacturing process. A two-step diffusion utilizing structured phosphorus silicate glass as a dopant source allows the independent optimization of the two emitter regions. Between the metal grid lines, the surface dopant concentration has been reduced significantly which resulted in an open circuit voltage increase of 8 mV. Beneath the front side conductor, the typical kink-and-tail profile with high surface concentration is kept to ensure low contact resistance. Compared to the reference group, fill factor and voltage enhancement add up to 0.15 %abs efficiency gain. Further potential is held in the short circuit current. Twodimensional Sentaurus simulations confirmed that with an optimized surface passivation, the developed doping profiles will result not only in an increased voltage but also in a larger current.
Stackebrandtia nassauensis gen. nov., sp. nov. and emended description of the family Glycomycetaceae (2005)

During the course of a 16S rRNA gene sequence phylogenetic evaluation of putative Glycomyces strains, it was noted that strain NRRL B-16338(T) is phylogenetically nearest to the genus Glycomyces but apparently is not a member of this or any of the other currently described actinomycete genera. The strain was subjected to a polyphasic study using standard methods for chemotaxonomic, morphological and physiological evaluation. The strain exhibited chemotaxonomic characteristics distinct from Glycomyces in spite of having 16S rRNA gene sequence similarity of 92% with the described species of this genus. The whole-cell sugar pattern of NRRL B-16338(T) consisted of ribose and inositol, with traces of arabinose and mannose. The phospholipids observed were phosphatidylglycerol and diphosphatidylglycerol and menaquinones consisting of MK-10(H(4)), MK-10(H(6)), MK-11(H(4)) and MK-11(H(6)). A significant quantity (14.5%) of 17:0 anteiso 2-hydroxy fatty acid was observed in the fatty acid profile of this strain. These characteristics clearly differentiate NRRL B-16338(T) from members of the genus Glycomyces and it is proposed that the strain represents a new genus within the family Glycomycetaceae to be called Stackebrandtia gen. nov. The description of this family is emended to permit its inclusion. It is proposed that the type species of the genus should be named Stackebrandtia nassauensis. The type strain LLR-40K-21(T) (=NRRL B-16338(T)=DSM 44728(T)) was isolated from a soil sample from Nassau, Bahamas.
New thermoplastic elastomers of rubbery polyisobutylene and glassy cyclopolyisoprene segments (1990)

Abstract New thermoplastic elastomers (TPEs) consisting of a central rubbery polyisobutylene (PIB) and glassy outer cyclopolyisoprene (cy‐PIP) segments have been prepared by living carbocationic polymerization by sequential monomer addition. First the homopolymerization of isobutylene (IB) and isoprene (IP) have been investigated. The living polymerization of isobutylene initiated by the p ‐dicumyl methoxy ( p ‐DiCumOMe)/TiCl 4 system in CH 3 Cl/ n ‐C 6 H 14 mixtures at −80°C gave living ⊕PIB⊕ dications of desired molecular weights. The polymerization of IP induced by cumyl acetate (CumOAc)/TiCl 4 or cumyl methyl ether (CumOMe)/TiCl 4 systems in the same solvent at −40°C readily yielded gel‐free off‐white powders comprising trans ‐1,4‐PIP units and cy‐PIP sequences. The polymerization most likely proceeds by trans ‐1,4‐PIP ⊕ cations that undergo inter/intramolecular alkylation and cyclization leading to branched multiblocks. Block copolymers were synthesized by the addition of IP to charges containing ⊕PIB⊕ dications of different molecular weights. Under select conditions pure ( tr ‐1,4‐PIP)‐ b ‐PIB‐ b ‐( tr ‐1,4‐PIP) triblocks with relatively short tr ‐1,4‐PIP sequences have been obtained. Extended reaction times result in multiblocks; most likely ⊕ ( tr ‐1,4‐PIP)‐ b ‐PIB‐ b ‐( tr ‐1,4‐PIP) ⊕ dications induce alkylation and cyclization of PIP sequences. The extent of alkylation can be regulated by the viscosity of the medium (molecular weight and/or concentration of the PIB midblock). The rate of IP incorporation decelerates after an initial fast polymerization; however, it can be accelerated by adding fresh Lewis acid to the system. Although tr ‐1,4‐PIP endblocks of linear triblocks can be completely cyclized by acid treatment to saturated products, multiblocks cannot, probably because of their branched structure. Transmission electron microscopy of multiblocks shows phase separation with PIB (95–70 mol%) the continuous phase ( T g = −73°C) and cy‐PIP blocks (5–30 mol %) the discrete phase. The T g of the cy‐PIP domain is in the range 95–190°C and it is affected by the extent of cyclization and/or the length of the cy‐PIP sequence. The new multiblock TPEs are soluble in organic solvents and can be melt‐processed above ∼ 140°C. A multiblock TPE film containing 15 mol % glassy cy‐PIP block and 85 mol % rubbery PIB block of M̄ n = 55,500 cast from CCl 4 exhibited to MPa tensile strength [120 MPa engineering strength (sigma true)] and 1200% elongation. The completely cyclized linear triblock shows higher T g (≡ 180°C) but, due to its low cy‐PIP content, exhibits unsatisfactory tensile properties.
Elevated estradiol during a hormone simulated pseudopregnancy decreases sleep and increases hypothalamic activation in female Syrian hamsters (2023)

Sleep disruptions are a common occurrence during the peripartum period. While physical and environmental factors associated with pregnancy and newborn care account for some sleep disruptions, there is evidence that peripartum fluctuations in estrogens may independently impact sleep. However, the impact of these large fluctuations in estrogens on peripartum sleep is unclear because it is difficult to tease apart the effects of estrogens on sleep from effects associated with the growth and development of the fetus or parental care. We therefore used a hormone-simulated pseudopregnancy (HSP) in female Syrian hamsters to test the hypothesis that pregnancy-like increases in estradiol decrease sleep in the absence of other factors. Adult female Syrian hamsters were ovariectomized and given daily hormone injections that simulate estradiol levels during early pregnancy, late pregnancy, and the postpartum period. Home cage video recordings were captured at seven timepoints and videos were analyzed for actigraphy. During "late pregnancy," total sleep time and sleep efficiency were decreased in hormone-treated animals during the white light period compared to pretest levels. Likewise, during "late pregnancy," locomotion was increased in the white light period for hormone-treated animals compared to pretest levels. These changes continued into the "postpartum period" for animals who continued to receive estradiol treatment, but not for animals who were withdrawn from estradiol. At the conclusion of the experiment, animals were euthanized and cFos expression was quantified in the ventral lateral preoptic area (VLPO) and lateral hypothalamus (LH). Animals who continued to receive high levels of estradiol during the "postpartum" period had significantly more cFos in the VLPO and LH than animals who were withdrawn from hormones or vehicle controls. Together, these data suggest that increased levels of estradiol during pregnancy are associated with sleep suppression, which may be mediated by increased activation of hypothalamic nuclei.
Conceptual Design of the ElectroMagnetic (EM) Tomography System (1995)

The new EM tomography system was planned for the detailed survey of mineral exploration. EM tomography system consists of surface; transmitter (3-component loop sources) and borehole; receiver (vertical component), and uses frequencies in the 8 - 8,192 Hz range. As the first step of the system development, we conducted model studies using SLDM (3D) developed by Druskin (1994). The phase data of EM tomography is very sensitive to the anomaly and 3-component sources are useful especially for multi-dimensions structure case. Also, these simulation results were used for the system design such as necessary sensitivity of receiver, transmitting moment and so on.
Guided automated learning for query workload re-optimization (2019)

Query optimization is a hallmark of database systems. When an SQL query runs more expensively than is viable or warranted, determination of the performance issues is usually performed manually in consultation with experts through the analysis of query's execution plan (QEP). However, this is an excessively time consuming, human error-prone, and costly process. GALO is a novel system that automates this process. The tool automatically learns recurring problem patterns in query plans over workloads in an offline learning phase, to build a knowledge base of plan-rewrite remedies. It then uses the knowledge base online to re-optimize queries often quite drastically. GALO's knowledge base is built on RDF and SPARQL, W3C graph database standards, which is well suited for manipulating and querying over SQL query plans, which are graphs themselves. GALO acts as a third-tier of re-optimization, after query rewrite and cost-based optimization, as a query plan rewrite . For generality, the context of knowledge base problem patterns, including table and column names, is abstracted with canonical symbol labels. Since the knowledge base is not tied to the context of supplied QEPs, table and column names are matched automatically during the re-optimization phase. Thus, problem patterns learned over a particular query workload can be applied in other query workloads. GALO's knowledge base is also an invaluable tool for database experts to debug query performance issues by tracking to known issues and solutions as well as refining the optimizer with new tuned techniques by the development team. We demonstrate an experimental study of the effectiveness of our techniques over synthetic TPC-DS and real IBM client query workloads.
3D deterministic ray tracing method for massive MIMO channel modelling and parameters extraction (2020)

Geometric stochastic method and deterministic ray tracing method are two common methods of modelling massive multiple‐input multiple‐output (MIMO) channels. The former has high computational efficiency but a large number of input parameters need to be extracted from measurements for different environments. Conversely, the latter is more suitable for a specific environment but consumes a lot of computing costs. In this study, a novel three‐dimensional (3D) deterministic ray tracing method for massive MIMO channel modelling is proposed. The computational efficiency can be improved in two aspects compared with conventional deterministic ray tracing methods. Firstly, substantial intersection tests used in determining the propagation paths of rays are replaced with the adjacency relationships between tetrahedrons. Secondly, the process of ray tracing is independent of the location of a receiving antenna and therefore repeated ray tracing process is unnecessary for different elements of receiving antenna array. The proposed method is also used as a substitute for measurements to extract input parameters for geometric stochastic channel models. The accuracy of the proposed method in massive MIMO channel modelling and parameters extraction is verified by comparing the results with measurements and other existing channel models.
Sexual Dimorphism of Abdominal Aortic Aneurysms (2017)

Sex is the largest nonmodifiable risk factor for the development of abdominal aortic aneurysms (AAAs) in humans and experimental models. Data from several studies consistently demonstrate a higher AAA prevalence in males than in females, contributing to divergent recommendations for AAA screening in men and women. Despite a higher AAA prevalence in males, females have more rapid rates of aneurysm dilation, and aneurysms rupture at smaller sizes. Unfortunately, no therapies have been effective to retard aneurysm dilation in either sex. Results from experimental AAA models indicate a protective role for estrogen in AAA development and progression, while male testosterone has been demonstrated to markedly promote angiotensin II (AngII)‐induced AAAs. Potential mechanisms implicated in sex hormone regulation of AAAs include regulation of inflammation, matrix metalloproteinases, aromatase activity, oxidative stress, stem cells, and transforming growth factor‐beta. In addition to sex hormones, sex chromosomes have been implicated in diseases of the aorta. Turner's syndrome (monosomy X) patients have a high incidence of thoracic aortic rupture. Recent studies indicate a novel approach to define the relative role of sex hormones versus sex chromosomes in experimental AAAs. Further studies are warranted to determine interactions between sex hormones and sex chromosomes in AAA development and progression.
Optimizing the fragmentation and clearance after shock wave lithotripsy (2008)

Tamsulosin can be used to increase clearance, and reduce episodes of ureteric colic and the need for analgesics after shock wave lithotripsy. Shock waves at slow rate improve both the safety and efficacy of shock wave lithotripsy. Percussion, diuresis and inversion augments clearance of lower calyceal fragments.
Cytomegalovirus‐associated cerebral sinus vein thrombosis (2012)

Cytomegalovirus (CMV)-associated thrombosis has been reported many times in the medical literature, and most patients had deep vein thrombosis and/or pulmonary embolism. CMV-associated cerebral sinus vein thrombosis has been reported only twice. We present an immunocompetent patient with CMV-associated cerebral sinus vein thrombosis and no other thrombosis risk factors. This is another example of the pro-thrombotic features of CMV. Physicians should be alert for symptoms and signs of acute CMV infection in patients with thrombosis.