gebhart/patrepeval huggingface dataset:
African origin of human-specific polymorphic Alu insertions. (1994)

Alu elements are a family of interspersed repeats that have mobilized throughout primate genomes by retroposition from a few "master" genes. Among the 500,000 Alu elements in the human genome are members of the human-specific subfamily that are not fixed in the human species; that is, not all chromosomes carry an Alu element at a particular locus. Four such polymorphic human-specific Alu insertions were analyzed by a rapid, PCR-based assay that uses primers that flank the insertion point to determine genotypes based on the presence or absence of the Alu element. These four polymorphic Alu insertions were shown to be absent from the genomes of a number of nonhuman primates, consistent with their arising as human genetic polymorphisms sometime after the human/African ape divergence. Analysis of 664 unrelated individuals from 16 population groups from around the world revealed substantial levels of variation within population groups and significant genetic differentiation among groups. No significant associations were found among the four loci, consistent with their location on different chromosomes. A maximum-likelihood tree of population relationships showed four major groupings consisting of Africa, Europe, Asia/Americas, and Australia/New Guinea, which is concordant with similar trees based on other loci. A particularly useful feature of the polymorphic Alu insertions is that the ancestral state is known to be the absence of the Alu element, and the presence of the Alu element at a particular chromosomal site reflects a single, unique event in human evolution. A hypothetical ancestral group can then be included in the tree analysis, with the frequency of each insertion set to zero. The ancestral group connected to the maximum-likelihood tree within the African branch, which suggests an African origin of these polymorphic Alu insertions. These data are concordant with other diverse data sets, which lends further support to the recent African origin hypothesis for modern humans. Polymorphic Alu insertions represent a source of genetic variation for studying human population structure and evolution.
A fundamental study of regional chemotherapy given by intraarterial infusion with concomitant hemodialysis and hemoperfusion. (1981)

In the intraarterial infusion of anticancer drugs, the majority of systemic side effects are caused by the systemic circulation of the infused drug. If the extraregional infusate could be removed by hemodialysis (HD) or direct hemoperfusion (DHP), side effects in the intraarterial infusion therapies could be mitigated and regional administration of anticancer drugs in large doses would than be possible. To substantiate this postulate, the authors carried out in vivo experiments using mongrel dogs, and obtained the results evidencing removal of extra regional anticancer drugs by HD and DHP. The maximum mitomycin C clearance of HD was 35.7 ml per min, whereas that of DHP was 119.7 ml per min. The results show the usefulness of concomitant use of HD or DHP in the intraarterial infusion of anticancer drugs via internal iliac artery in the treatment of cancer of the urinary bladder.
Synthesis of Diazatricyclic Core of Madangamines from <i>cis</i>-Perhydroisoquinolines (2007)

Synthesis of the tricyclic core of madangamine alkaloids has been achieved in a 10-step sequence starting from a 4-(aminomethyl)anisole derivative. A Birch reduction and acylation with cyanoacetic acid followed by an intramolecular Michael process renders a polyfunctionalized cis-perhydroisoquinoline. A diastereoselective allylation and reduction of amide, nitrile, and ketone groups leads to a bicyclic alcohol, which undergoes aminocyclization through the nosyl derivative to the diazatricyclic ring.
Bio-based Large Tablet Controlled-Release Urea: Synthesis, Characterization, and Controlled-Released Mechanisms (2018)

To improve nitrogen (N) use efficiency and minimize environmental pollution caused by fertilizer overuse, novel bio-based large tablet controlled-release urea (LTCRU) was prepared using bio-based coating materials to coat large tablet urea (LTU) derived from urea prills (U). Nano fumed silica (NFS) was added to the bio-based coating materials to improve the slow-release properties. The surface area of the LTU and U was measured by three-dimensional scanning. In comparison to U, LTU had a smaller surface area/weight ratio, which can reduce the coating materials. Scanning electron microscopy analysis showed that the addition of NFS in bio-based coating materials reduced the porosity of the coating shells of LTCRUs and, thus, enhanced the N release longevity of the controlled-released fertilizer. Dependent upon the pores on the coating shells of LTCRU, two N release patterns were revealed. Because of the good release characteristics, the novel LTCRU shows great potential to support sustainable agricultural production.
A DNA polymorphism adjacent to the human apolipoprotein CII gene. (1983)

We have used a cDNA clone for human apolipoprotein CII (apo CII) to detect a common DNA polymorphism with the enzyme TaqI. This polymorphism is probably caused by a single base change approximately 2000 base-pairs from the 3' end of the structural gene. In the normal population (n = 90) the frequency of the less common allele is approximately 0.44. No significant differences were observed in the allele frequency in individuals with type IIa, IIb, III, IV and V lipoprotein patterns. There does not seem to be any population association between the TaqI polymorphism and factors that predispose an individual to hyperlipidaemia.
Fracture Permeability of Gas Shale: Effects of Roughness, Fracture Offset, Proppant, and Effective Stress (2010)

Abstract Domestic gas shale production is made economic through new completion practices which include horizontal wells and multiple hydraulic fractures. The performance of these fractures is improved through the injection of proppant. Success has largely been based on empiricism through field experiments. We attempt to remove some uncertainty in this empiricism through a series of laboratory controlled experiments. We have measured the permeability of fractured rock as a function of effective stress, proppant, proppant distribution and fracture offset. Our findings indicate that fracture offset is as effective as propping a fracture; both increase initial permeabilities more than 1000 fold over initial fracture values. However, the pressure dependence of the propped fracture is stronger, i.e. the permeability is reduced more per increment of pressure than the offset fractures. Neither obeys the simple cubic pressure dependence law proposed by Walsh. A simple monolayer of proppant is as effective as a fairway distribution of proppant in enhancing permeability. Initial fracture permeability is dependent on surface roughness, quantified as root mean square asperity heights. Pressure dependence of permeability of these fractured surfaces does obey the Walsh permeability models. SEM observations of surfaces and proppant suggest a new approach to proppant design.
Spectra of Quantized Signals (1948)

Signals which are quantized both in time of occurrence and in magnitude are in fact quite old in the communications art. Printing telegraph is an outstanding example. Here, time is divided into equal divisions, and the number of magnitudes to be distinguished in any one interval is usually no more than two, corresponding to the closed or open positions of a sending switch. It is only in recent years, however, that the development of high speed electronic devices has progressed sufficiently to enable quantizing techniques to be applied to rapidly changing signals such as produced by speech, music, or television. Quantizing of time, or time division, has found application as a means of multiplexing telephone channels. <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sup> The method consists of connecting the different channels to the line in sequence by fast moving switches synchronized at the transmitting and receiving ends. In this way a transmission medium capable of handling a much wider band of frequencies than required for one telephone channel can be used simultaneously by a group of channels without mutual interference. The plan is the same as that used in multiplex telegraphy. The difference is that ordinary rotating machinery suffices at the relatively low speeds employed by the latter, while the high speeds needed for time division multiplex telephony can be realized only by practically inertialess electron streams. Also the widths of frequency band required for multiplex telephony are enormously greater than needed for the telegraph, and in fact have become technically feasible only with the development of wide-band radio and cable transmission systems. As far as any one channel is concerned the result is the same as in telegraphy, namely that signals are received at discrete or quantized times. In the limiting case when many channels are sent the speech voltage from one channel is practically constant during the brief switch closure and, in effect, we can send only one magnitude for each contact or quantum of time. The more familiar word “sampling” will be used here interchangeably with the rather formidable term “quantizing of time”.
Application of statistical physics to heartbeat diagnosis (1999)

We present several recent studies based on statistical physics concepts that can be used as diagnostic tools for heart failure. We describe the scaling exponent characterizing the long-range correlations in heartbeat time series as well as the multifractal features recently discovered in heartbeat rhythm. It is found that both features, the long-range correlations and the multifractility, are weaker in cases of heart failure.
Clinical results of implantation of the Chirila keratoprosthesis in rabbits (1998)

<h3>ABSTRACT</h3> SARS-CoV-2 has infected more than 400 million people around the globe and caused millions of deaths. Since its identification in November 2021, Omicron, a highly transmissible variant, has become the dominant variant in most countries. Omicron’s highly mutated spike protein, the main target of vaccine development, significantly compromises the immune protection from current vaccination. We develop an mRNA vaccine (S<sub>Omicron</sub>-6P) based on an Omicron-specific sequence. In mice, S<sub>Omicron</sub>-6P shows superior neutralizing antibodies inducing abilities to a clinically approved inactivated virus vaccine, a clinically approved protein subunit vaccine, and an mRNA vaccine (S<sub>WT</sub>-2P) with the same sequence of BNT162b2 RNA. Significantly, S<sub>Omicron</sub>-6P induces a 14.4∼27.7-fold and a 28.3∼50.3-fold increase of neutralizing activity against the pseudovirus of Omicron and authentic Omicron compared to S<sub>WT</sub>-2P, respectively. In addition, two doses S<sub>Omicron</sub>-6P significantly protects Syrian hamsters against challenge with SARS-CoV-2 Omicron variant and elicits high titers of nAbs in a dose-dependent manner in macaques. Our results suggest that S<sub>Omicron</sub>-6P offers advantages over current vaccines, and it will be helpful for those with weak immunity.
Picture Processing for the 4:2:2 Digital Videotape Recorder (1985)

Digital videotape recording has been researched for more than ten years. This article analyzes the results from more than five generations of experimental hardware in terms of the fundamental tape format parameters and the signal processing required to achieve optimum performance from those parameters. Most researchers agree on the major elements of the track dimensions. The next issue to be decided is the recorded data structure. Practical experience and theoretical analysis are combined to explain the advantages of various approaches.
Brain tissue classification of magnetic resonance images using partial volume modeling (2000)

This paper presents a fully automatic three-dimensional classification of brain tissues for Magnetic Resonance (MR) images. An MR image volume may be composed of a mixture of several tissue types due to partial volume effects. Therefore, we consider that in a brain dataset there are not only the three main types of brain tissue: gray matter, white matter, and cerebro spinal fluid, called pure classes, but also mixtures, called mixclasses. A statistical model of the mixtures is proposed and studied by means of simulations. It is shown that it can be approximated by a Gaussian function under some conditions. The D'Agostino-Pearson normality test is used to assess the risk alpha of the approximation. In order to classify a brain into three types of brain tissue and deal with the problem of partial volume effects, the proposed algorithm uses two steps: 1) segmentation of the brain into pure and mixclasses using the mixture model; 2) reclassification of the mixclasses into the pure classes using knowledge about the obtained pure classes. Both steps use Markov random field (MRF) models. The multifractal dimension, describing the topology of the brain, is added to the MRFs to improve discrimination of the mixclasses. The algorithm is evaluated using both simulated images and real MR images with different T1-weighted acquisition sequences.
Thermal stability of MnBi magnetic materials (2014)

MnBi has attracted much attention in recent years due to its potential as a rare-earth-free permanent magnet material. It is unique because its coercivity increases with increasing temperature, which makes it a good hard phase material for exchange coupling nanocomposite magnets. MnBi phase is difficult to obtain, partly because the reaction between Mn and Bi is peritectic, and partly because Mn reacts readily with oxygen. MnO formation is irreversible and harmful to magnet performance. In this paper, we report our efforts toward developing MnBi permanent magnets. To date, high purity MnBi (>90%) can be routinely produced in large quantities. The produced powder exhibits 74.6 emu g(-1) saturation magnetization at room temperature with 9 T applied field. After proper alignment, the maximum energy product (BH)max of the powder reached 11.9 MGOe, and that of the sintered bulk magnet reached 7.8 MGOe at room temperature. A comprehensive study of thermal stability shows that MnBi powder is stable up to 473 K in air.
Embedded Mixed-Integer Quadratic optimization Using the OSQP Solver (2018)

We present a novel branch-and-bound solver for mixed-integer quadratic programs (MIQPs) that efficiently exploits the first-order OSQP solver for the quadratic program (QP) sub-problems. Our algorithm is very robust, requires no dynamic memory allocation and is division-free once an initial factorization is computed. Thus, it suitable for embedded applications with low computing power. Moreover, it does not require any assumption on the problem data such as strict convexity of the objective function. We exploit factorization caching and warm-starting to reduce the computational cost of QP relaxations during branch-and-bound and over repeated solutions of parametric MIQPs such as those arising in embedded control, portfolio optimization, and machine learning. Numerical examples show that our method, using a simple high-level Python implementation interfaced with the OSQP solver, is competitive with established commercial solvers.
Design of close-to-capacity constrained codes for multi-level optical recording (2009)

We report a new method for designing (M,d, k) constrained codes for use in multi-level optical recording channels. The method allow us to design practical codes, which have simple encoder tables and decoders having fixed window length. The codes presented here for the d = 1 and d = 2 cases, achieve higher storage densities than previously reported codes, and come within 0.3 - 0.7% of capacity.
Using Hardware Isolated Execution Environments for Securing Systems (2015)

With the rapid proliferation of malware attacks on the Internet, malware detection and analysis play a critical role in crafting effective defenses. Advanced malware detection and analysis rely on virtualization and emulation technologies to introspect the malware in an isolated environment and analyze malicious activities by instrumenting code execution. Virtual Machine Introspection (VMI) systems have been widely adopted for malware detection and analysis. VMI systems use hypervisor technology to create an isolated execution environment for system introspection and to expose malicious activity. However, recent malware can detect the presence of virtualization or corrupt the hypervisor state and thus avoid detection and debugging.
U- and W-shaped diffusion profiles of gold in silicon (1986)

The diffusion of Au in dislocation-free Si was investigated at 1473K by means of neutron-activation analysis combined with mechanical sectioning. In most wafers the diffusion profiled were U-shaped, as known from previous studies of this kind performed at lower temperatures. In these wafers the Au concentration in the profile centres measured after 45 min diffusion anneals decrease inversely proportional to the wafer thicknesses in accordance with the so-called kick-out diffusion model. This model is confirmed further by the good agreement of the contribution by self-interstitials to the self-diffusion coefficient at 1473K calculated from the present Au-diffusion data with directly measured values of the Si self-diffusion coefficient. In some Au-diffused Si wafers W-shaped penetration profiles were found. From spreading-resistance, preferential-etching, and X-ray topography studies it is concluded that the Au-concentration peaks occurring in the interior of these specimens are located at faulted dislocation loops formed during the in-diffusion of Au. An electron-microscopy analysis showed that the stacking faults are of extrinsic nature. Presumably they were formed by agglomeration of self-interstitials produced in supersaturation via the kick-out diffusion mechanism.
Autogenous production of a hemopoietic growth factor, persisting-cell-stimulating factor, as a mechanism for transformation of bone marrow-derived cells. (1983)

Lines of hemopoietic progenitor cells can be grown for prolonged or indefinite periods in vitro in the presence of a specific growth factor produced by activated T lymphocytes, persisting (P)-cell-stimulating factor (PSF). From such a PSF-dependent line, we report the emergence of variants that had concomitantly acquired both the capacity for autonomous growth in the absence of exogenous PSF and the capacity for the autogenous production of PSF. The link between these two new properties was strengthened by the demonstration that the variant lines absorbed PSF and, in some culture conditions, responded to exogenous PSF. Thus when variant cells were plated at low density in 1-ml agar cultures, cloning efficiency and colony size were enhanced by supplementation with sources of PSF, including medium conditioned by concanavalin A-stimulated normal spleen cells, T-cell tumors and T-cell hybridomas, and, importantly, medium conditioned by the autonomous P-cell lines themselves. In contrast to the parental line, the autonomous clones tested formed progressively growing tumors in vivo. It is proposed that the myelomonocytic leukemia WEHI-3B that produces PSF arose from a neutrophil-macrophage progenitor through acquisition of the capacity for the autogenous production of PSF and that the autogenous production of PSF may play a similar role in a range of proliferative disorders both of the blood and of other tissues containing components derived from the bone marrow.
Effect of Intestinal Microflora on the Survival Time of Mice Exposed to Lethal Whole-Body γ Irradiation (1981)

Masaharu Onoue, Kazumi Uchida, Teruo Yokokura, Tokutaro Takahashi, Masahiko Mutai, Effect of Intestinal Microflora on the Survival Time of Mice Exposed to Lethal Whole-Body γ Irradiation, Radiation Research, Vol. 88, No. 3 (Dec., 1981), pp. 533-541
Switchable Deep Network for Pedestrian Detection (2014)

In this paper, we propose a Switchable Deep Network (SDN) for pedestrian detection. The SDN automatically learns hierarchical features, salience maps, and mixture representations of different body parts. Pedestrian detection faces the challenges of background clutter and large variations of pedestrian appearance due to pose and viewpoint changes and other factors. One of our key contributions is to propose a Switchable Restricted Boltzmann Machine (SRBM) to explicitly model the complex mixture of visual variations at multiple levels. At the feature levels, it automatically estimates saliency maps for each test sample in order to separate background clutters from discriminative regions for pedestrian detection. At the part and body levels, it is able to infer the most appropriate template for the mixture models of each part and the whole body. We have devised a new generative algorithm to effectively pretrain the SDN and then fine-tune it with back-propagation. Our approach is evaluated on the Caltech and ETH datasets and achieves the state-of-the-art detection performance.
Equalization Architectures for High Speed ADC-Based Serial I/O Receivers (2016)

The growth in worldwide network traﬃc due to the rise of cloud computing and wireless video consumption has required servers and routers to support increased serial I/O data rates over legacy channels with signiﬁcant frequency-dependent attenuation. For these high-loss channel applications, ADC-based high-speed links are being considered due to their ability to enable powerful digital signal processing (DSP) algorithms for equalization and symbol detection. Relative to mixed-signal equalizers, digital implementations oﬀer robustness to process, voltage and temperature (PVT) variations, are easier to reconﬁgure, and can leverage CMOS technology scaling in a straight-forward manner. Despite these advantages, ADC-based receivers are generally more complex and have higher power consumption relative to mixed-signal receivers. The ensuing digital equalization can also consume a signiﬁcant amount of power which is comparable to the ADC contribution. Novel techniques to reduce complexity and improve power eﬃciency, both for the ADC and the subsequent digital equalization, are necessary.\n\nThis dissertation presents eﬃcient modeling and implementation approaches for ADC-based serial I/O receivers. A statistical modeling framework is developed, which is able to capture ADC related errors, including quantization noise, INL/DNL errors and time interleaving mismatch errors. A novel 10GS/s hybrid ADC-based receiver, which combines both embedded and digital equalization, is then presented. Leveraging a time-interleaved asynchronous successive approximation ADC architecture, a new structure for 3-tap embedded FFE inside the ADC with low power/area overhead is used. In addition, a dynamically-enabled digital 4-tap FFE + 3-tap DFE equalizer architecture is introduced, which uses reliable symbol detection to achieve remarkable savings in the digital equalization power. Measurement results over several FR4 channels verify the accuracy of the modeling approach and the eﬀectiveness of the proposed receiver. The comparison of the fabricated prototype against state-of-the-art ADC-based receivers shows the ability of the proposed archi-tecture to compensate for the highest loss channel, while achieving the best power eﬃciency among other works.