gebhart/patrepeval huggingface dataset:
Viral Vector Mediated Overexpression of Human <i>α</i>-Synuclein in the Nigrostriatal Dopaminergic Neurons: A New Model for Parkinson's Disease (2005)

Parkinson's disease is predominantly a dopamine deficiency syndrome, which is produced in the brain by the loss of cells located in a small area in the ventral midbrain called the substantia nigra. Complete unilateral dopamine lesions, based on the administration of toxic substances (ie, 6-hydroxy-dopamine in rats and 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine in mice and primates) have been extremely useful in testing strategies of replacement. For example, the functional and biochemical impact of the transplanted ventral mesencephalic dopaminergic progenitors has been characterized to a large extent, using the complete lesion model in rats. Over the last decade, however, studies addressing the ability of neurotrophic factors to protect injured dopamine cells prompted researchers to make available partial and progressive lesion models to allow a window of opportunity to interfere the disease progression. Recent findings relating alpha-synuclein with Parkinson's disease pathology have opened new possibilities to develop alternative models based on the overexpression of this protein using recombinant adeno-associated viral vectors, which is valuable not only for helping to better understand its involvement in the disease process, but also to more closely resemble the neurodegeneration found in Parkinson's disease.
Advanced Multitenant Hadoop in Smart Open Data Platform (2017)

Nowadays, there has been an immense amount of data coming from various devices sensors, social networks and IoT services. Among these data, open data is playing more and more important role in practice. Many individuals and organizations collect a broad range of different types of data in order to perform their analytic tasks. However, the current open data platforms still have many limitations. Among the drawbacks, data management, an important process of analytic service development, needs to be improved significantly. The main reason is that the emergence of massive data explosion coming from various sources has been making the process become more and more complicated and costly. Therefore, we propose here a system related to the field of data management to allow multitenant users to find and access easily their desired data as well as metadata. It also helps improve the performance of platform.
High-resolution cryo-EM structure of the human 80S ribosome (2017)

Chemical modifications of human ribosomal RNA (rRNA) are introduced during biogenesis and have been implicated in the dysregulation of protein synthesis, as is found in cancer and other diseases. However, their role in this phenomenon is unknown. Here we visualize more than 130 individual rRNA modifications in the three-dimensional structure of the human ribosome, explaining their structural and functional roles. In addition to a small number of universally conserved sites, we identify many eukaryote- or human-specific modifications and unique sites that form an extended shell in comparison to bacterial ribosomes, and which stabilize the RNA. Several of the modifications are associated with the binding sites of three ribosome-targeting antibiotics, or are associated with degenerate states in cancer, such as keto alkylations on nucleotide bases reminiscent of specialized ribosomes. This high-resolution structure of the human 80S ribosome paves the way towards understanding the role of epigenetic rRNA modifications in human diseases and suggests new possibilities for designing selective inhibitors and therapeutic drugs.
CCXCIV.—Researches in the menthone series. Part III. Optically inactive menthylamines (1926)

J. Read, A. M. R. Cook and M. I. Shannon, J. Chem. Soc., 1926, 129, 2223 DOI: 10.1039/JR9262902223
Nuclear-mitochondrial DNA segments resemble paternally inherited mitochondrial DNA in humans (2020)

Several strands of evidence question the dogma that human mitochondrial DNA (mtDNA) is inherited exclusively down the maternal line, most recently in three families where several individuals harbored a 'heteroplasmic haplotype' consistent with biparental transmission. Here we report a similar genetic signature in 7 of 11,035 trios, with allelic fractions of 5-25%, implying biparental inheritance of mtDNA in 0.06% of offspring. However, analysing the nuclear whole genome sequence, we observe likely large rare or unique nuclear-mitochondrial DNA segments (mega-NUMTs) transmitted from the father in all 7 families. Independently detecting mega-NUMTs in 0.13% of fathers, we see autosomal transmission of the haplotype. Finally, we show the haplotype allele fraction can be explained by complex concatenated mtDNA-derived sequences rearranged within the nuclear genome. We conclude that rare cryptic mega-NUMTs can resemble paternally mtDNA heteroplasmy, but find no evidence of paternal transmission of mtDNA in humans.
Kinetics of ethylene polymerization initiated by free radicals (1962)

Abstract Ethylene polymerization can be carried out under milder conditions than heretofore because of the development of peroxydicarbonate catalysts. This simplifies study of polymerization kinetics. Diethyl peroxydicarbonate undergoes first‐order decomposition in tert ‐butyl alcohol with an energy of activation of 33 kcal./mole, and a half‐life of 1.5 hr. at 60°C. The rate of decomposition, 1.3 × 10 −4 sec. −1 , does not change in the presence of polymerizing ethylene. The rate of polymerization can be followed by pressure change. But, because the concentration of ethylene in tert ‐butyl alcohol as a function of pressure is not known accurately, it is better to measure polymerization rate by isolating the polymer. A mathematical relationship was developed between initiator decomposition and polymer formation. It is based on a conventional free‐radical polymerization mechanism and is supported by the experimental data. Polymer molecular weight is independent of initiator concentration and increases only slightly with duration of polymerization. The effects of reaction variables of molecular weight are explained by normal free‐radical transfer reactions. The polymer contains ethyl carbonate groups from homolytic scission of diethyl peroxydicarbonate, and it exhibits the same absorption bands in the infrared as does ethyl n ‐octyl carbonate. These bands disappear on saponification and are not present in polyethylene made with other peroxide catalysts.
LILY BREEDING RESEARCH IN THE NETHERLANDS. (1996)

At the Centre for Plant Breeding and Reproduction Research (CPRO-DLO) in Wageningen lily breeding research in the Netherlands is concentrated. To this end sources of germplasm (genetic material) are maintained in a lily species and cultivar collection. Research is done on long term storage of this collection by use of low temperature and minimal growth conditions in vitro. Main themes of our breeding research are breeding for resistance (to Fusarium oxysporum, Pythium and virus diseases), breeding for quality traits (flower longevity lily; forcing ability; bulbgrowth of Lilium longiflorum), interspecific hybridization and genetic modification. A molecular marker system using RAPD's is developed in lily to link Fusarium resistance with molecular markers and to construct a genetic map of lily. A system for in vitro pollination, fertilization and embryo rescue has been developed for lily. By combining pollination techniques to overcome prefertilization barriers with in vitro methods to overcome postfertilization barriers, wide interspecific crosses could be made more efficiently. This resulted into a range of new interspecific hybrids, which have led to completely new hybrid groups in the lily assortment. To overcome F1-sterility of interspecific hybrids, owing to lack of chromosome pairing during meiosis, colchicine and oryzalin are used for the induction of mitotic tetraploids. Interspecific crosses at tetraploid level between complex hybrids of L. longiflorum, L. henryi, L. candidum, Asiatic and Oriental hybrid lilies have been made. To develop efficient methods for breeding at tetraploid level, meiotic polyploidization is investigated. Procedures of genetic modification of lily are developed in several directions. At the University of Leiden, for the introduction of virus resistances a transformation technique is in development by particle bombardment on bulb-scale explants. An approach followed by CPRO-DLO is pollen transformation: isolated pollen bombarded with particles coated with DNA containing the kanamycin resistance gene and the B-glucuronidase gene are used to obtain transgenic plants. Other biotechnological techniques are based on protoplast regeneration for either somatic hybridization or direct DNA transfer and microspore culture for the induction of haploidy.
Kinetic Analysis of NodST Sulfotransferase Using an Electrospray Ionization Mass Spectrometry Assay (2002)

A novel and efficient enzyme kinetics assay using electrospray ionization mass spectrometry was developed and applied to the bacterial carbohydrate sulfotransferase (NodST). NodST catalyzes the sulfuryl group transfer from 3'-phosphoadenosine 5'-phosphosulfate (PAPS) to chitobiose, generating 3'-phosphoadenosine 5'-phosphate (PAP) and chitobiose-6-OSO(3)(-) as products. Traditional spectrophotometric assays are not applicable to the NodST system since no shift in absorption accompanies sulfuryl group transfer. Alternative assays have employed thin-layer chromatography, but this procedure is time-consuming and requires radioactive materials. The ESI-MS assay presented herein requires no chromophoric substrate or product, and the analysis time is very short. The ESI-MS assay is used to determine NodST kinetic parameters, including K(M), V(max), and K(i) (for PAP). In addition, the mode of inhibition for PAP was rapidly determined. The results were in excellent agreement with those obtained from previous assays, verifying the accuracy and reliability of the ESI-MS assay. This unique technique is currently being used to investigate the enzymatic mechanism of NodST and to identify sulfotransferase inhibitors.
An efficient second-order projection method for viscous incompressible flow (1991)

In this paper we describe a second-order projection method for the time-dependent, incompressible Navier-Stokes equations. The method is a second-order fractional step scheme in which one first solves diffusion-convection equations to determine intermediate velocities which are then projected onto the space of divergence-free vector fields. The diffusion-convection step uses a specialized second-order Godunov method for differencing the nonlinear convective terms that is conservative and free-stream preserving and provides a robust treatment of the nonlinearities at high Reynolds number. The projection is based on cell-centered centered difference approximations to divergence and gradient operators with the resulting linear system solved using a multigrid relaxation scheme. We apply the method to vortex spindown in a box to validate the numerical convergence of the method and to measure its overall performance.
Design of Continuous-Time <inline-formula> <tex-math notation="LaTeX">$\Delta \Sigma $</tex-math> </inline-formula> Modulators With Dual Switched-Capacitor Return-to-Zero DACs (2016)

Single-bit continuous-time sigma-delta modulators (CTDSMs) are overly sensitive to clock jitter when a non-return-to-zero (NRZ) feedback DAC is used. One way of addressing this problem is to use a DAC with an exponentially decaying pulse shape, realized using a switched capacitor (SC). Existing variants of the SC feedback DAC degrade linearity due to the high peak-to-average ratio of the feedback waveform and severely compromise the alias rejection of the modulator around multiples of the sampling frequency. We introduce the dual switched-capacitor return-to-zero (Dual-SCRZ) DAC, which combines the low clock jitter sensitivity of a switched-capacitor DAC with the low peak-to-average ratio characteristic of NRZ feedback. Further, this DAC preserves the implicit anti-aliasing feature of the CTDSMs around all odd multiples of the sampling frequency. A single-bit CTDSMs that uses the Dual-SCRZ technique and opamp-assistance to improve linearity and reduce jitter sensitivity achieves 91/85.1/83 dB DR/SNR/SNDR in a 2 MHz bandwidth. Operating at 256 MHz in a 0.18 μm CMOS process, the modulator dissipates 14.8 mW from a 1.8 V supply.
Regulation Of Transposition In Bacteria (1990)

Cells organize many of their biochemical reactions in non-membrane compartments. Recent evidence has shown that many of these compartments are liquids that form by phase separation from the cytoplasm. Here we discuss the basic physical concepts necessary ...Read More
Specification-Based Intrusion Detection in WLANs (2006)

Wireless networking technologies based on the IEEE 802.11 series of standards fail to authenticate management frames and network card addresses and suffer from serious vulnerabilities that may lead to denial of service, session hijacking, and address masquerading attacks. In this paper, we describe and implement a specification-based intrusion detection system for IEEE 802.11 wireless infrastructure networks, which not only provides attack detection, but also implements policy compliance monitoring. The specification used by our intrusion detection system is derived from network protocol state transition models and site security policy constraints. We also perform an experimental and comparative analysis of the technique to assess its effectiveness. The results indicate that the approach is superior at successfully detecting a greater variety of attacks than other existing approaches
The role and regulation of programmed cell death in plant-pathogen interactions (2004)

It is commonly known that animal pathogens often target and suppress programmed cell death (pcd) pathway components to manipulate their hosts. In contrast, plant pathogens often trigger pcd. In cases in which plant pcd accompanies disease resistance, an event called the hypersensitive response, the plant surveillance system has learned to detect pathogen-secreted molecules in order to mount a defence response. In plants without genetic disease resistance, these secreted molecules serve as virulence factors that act through largely unknown mechanisms. Recent studies suggest that plant bacterial pathogens also secrete antiapoptotic proteins to promote their virulence. In contrast, a number of fungal pathogens secrete pcd-promoting molecules that are critical virulence factors. Here, we review recent progress in determining the role and regulation of plant pcd responses that accompany both resistance and susceptible interactions. We also review progress in discerning the mechanisms by which plant pcd occurs during these different interactions.
A laboratory system for element specific hyperspectral X-ray imaging (2012)

X-ray tomography is a ubiquitous tool used, for example, in medical diagnosis, explosives detection or to check structural integrity of complex engineered components. Conventional tomographic images are formed by measuring many transmitted X-rays and later mathematically reconstructing the object, however the structural and chemical information carried by scattered X-rays of different wavelengths is not utilised in any way. We show how a very simple; laboratory-based; high energy X-ray system can capture these scattered X-rays to deliver 3D images with structural or chemical information in each voxel. This type of imaging can be used to separate and identify chemical species in bulk objects with no special sample preparation. We demonstrate the capability of hyperspectral imaging by examining an electronic device where we can clearly distinguish the atomic composition of the circuit board components in both fluorescence and transmission geometries. We are not only able to obtain attenuation contrast but also to image chemical variations in the object, potentially opening up a very wide range of applications from security to medical diagnostics.
Definitive Endoderm from Embryonic Stem Cells (2006)

Evaluation of: D'Amour KA, Agulnick AD, Eliazer S, Kelly OG, Kroon E, Baetge EE. Efficient differentiation of human embryonic stem cells to definitive endoderm. Nat. Biotechnol. 23(12), 1534–1541(2005) [1] and Yasunaga M, Tada S, Torikai-Nishikawa S et al. Induction and monitoring of definitive and visceral endoderm differentiation of mouse ES cells. Nat. Biotechnol. 23(12),1542–1550 (2005) [2].
A 286 MHz 64-bit floating point multiplier with enhanced CG operation (2002)

High speed floating point (FP) multipliers are essential for high speed calculation systems because increasingly large numbers of FP multiplications must be carried out in various applications such as scientific calculation and computer graphics (CG). CG, in particular, requires enormous amount of FP multiplications to obtain high quality images required for multimedia systems. To realize high speed, the critical path delay must be minimized. In this paper, we discuss a method to shorten the delay time of the critical path. Then we present an FP multiplier design based on the method. A special function for CG is also implemented without increasing the critical path delay. Finally, we show the fabrication and test results of the FP multiplier.
Anomaly pattern detection in categorical datasets (2008)

We propose a new method for detecting patterns of anomalies in categorical datasets. We assume that anomalies are generated by some underlying process which affects only a particular subset of the data. Our method consists of two steps: we first use a "local anomaly detector" to identify individual records with anomalous attribute values, and then detect patterns where the number of anomalous records is higher than expected. Given the set of anomalies flagged by the local anomaly detector, we search over all subsets of the data defined by any set of fixed values of a subset of the attributes, in order to detect self-similar patterns of anomalies. We wish to detect any such subset of the test data which displays a significant increase in anomalous activity as compared to the normal behavior of the system (as indicated by the training data). We perform significance testing to determine if the number of anomalies in any subset of the test data is significantly higher than expected, and propose an efficient algorithm to perform this test over all such subsets of the data. We show that this algorithm is able to accurately detect anomalous patterns in real-world hospital, container shipping and network intrusion data.
Evidence of an inhibitory restraint of seizure activity in humans (2012)

The location and trajectory of seizure activity is of great importance, yet our ability to map such activity remains primitive. Recently, the development of multi-electrode arrays for use in humans has provided new levels of temporal and spatial resolution for recording seizures. Here, we show that there is a sharp delineation between areas showing intense, hypersynchronous firing indicative of recruitment to the seizure, and adjacent territories where there is only low-level, unstructured firing. Thus, there is a core territory of recruited neurons and a surrounding 'ictal penumbra'. The defining feature of the 'ictal penumbra' is the contrast between the large amplitude EEG signals and the low-level firing there. Our human recordings bear striking similarities with animal studies of an inhibitory restraint, indicating that they can be readily understood in terms of this mechanism. These findings have important implications for how we localize seizure activity and map its spread.
Destruction and reorganization of the receptor membrane in labellar chemosensory cells of the blowfly. Long-lasting latent action of colchicine. (1986)

Electron micrographs of sections of the labellar chemosensilla of the blowfly, Phormia regina, showed that treatment with sodium deoxycholate (DOC; 7.2 mM for 2 min) destroyed the distal processes of the receptors from up to 10 microns from the tip of the sensillum, but these processes regenerated almost completely within 0.5 h. However, when DOC treatment was preceded by colchicine treatment (25 mM for 2 min), greater than 10 h was required for complete regeneration. Sugar receptor responses supported these findings and disclosed a more detailed time course of regeneration after DOC treatment: without colchicine pretreatment, the destroyed distal process completely regenerated in 0.3-1.0 h, but with pretreatment, regeneration began at 3 h and reached the chemosensillar tip at 8 h at the earliest. Hardly any depression of the response was observed for 8 h after treatment with colchicine alone, but a transient depression was detected at 12 h. Based on these results, the role of microtubules in the maintenance of the receptor membrane is discussed.
Mauvaise utilisation des aérosol-doseurs par les asthmatiques (1980)

The purpose of this study was to determine in a population of asthmatics, the number of patients who correctly used the pressurized aerosols (bronchodilator drugs or steroids) spontaneously, or after training sessions. 115 asthmatics (in- or outpatients, 14-70 years old) were asked to use their inhaler in the presence of an observer. The inhalation technique was considered correct when (1) the puff release was coordinated with a deep inspiration and (2) when the inspiration was followed by a few seconds' breath-holding. The patients were divided into two groups: a trained group of 46 patients who were observed for 1 month or more after the two above-mentioned maneuvres had been demonstrated to them by a physician and the need for correct use strongly emphasized. The other group (the untrained group) comprised 69 patients who were presumably using their inhalers according to the manufacturer's instructions: (1) expiration; (2) inspiration and actuation, and (3) apnea. In the trained group 52% of the patients were classified by the observer as correct users, as compared to 28% in the untrained group. The results were not influenced by sex. age or occupational differences. These observations suggest that a majority of asthmatics probably derived incomplete benefit from the use of pressurized aerosols. Although training apparently results in a more efficient use of the canisters, this study shows that training sessions must be repeated, and the results checked at regular intervals by a member of the medical staff. In subjects who repeatedly fail to achieve a correct inhalation technique the drug should be given by another route.
Rate control using enhanced frame complexity measure for H.264 video (2004)

Bit rate control is an important issue for wireless and Internet video streaming. The paper presents a revised rate control scheme based on an improved frame complexity measure. Rate control adopted by both MPEG-4 VM18 and H.264/AVC uses a quadratic rate-distortion (R-D) model that determines quantization parameters (QPs). The classical quadratic R-D model is suitable for MPEG-4, but it performs poorly for H.264/AVC because one of the important parameters, mean absolute difference (MAD), is predicted through a linear model, whereas the MAD used in MPEG-4 VM18 is the actual MAD. Inaccurately predicted MAD results in the wrong QP and consequently degrades rate distortion optimization (RDO) performance in H.264/AVC. To overcome the limitation of the existing rate control schemes, we introduce an enhanced linear model for predicting MAD, utilizing some knowledge of current frame complexity. Moreover, we propose a more accurate frame complexity measure, namely, normalized MAD, to replace the current use of MAD parameters. Normalized MAD has a stronger correlation with optimally allocated bits than that of the predicted MAD. Finally, a dynamic bit allocation scheme among basic units is implemented. Extensive simulation results show that our method, with inexpensive added computational complexity, improves the average peak signal-to-noise ratio (PSNR) considerably, by up to 1.2 dB, and reduces PSNR variances significantly, by up to 63%.