gebhart/patrepeval huggingface dataset:
Conditional Density Estimation by Penalized Likelihood Model Selection and Applications (2011)

In this technical report, we consider conditional density estimation with a maximum likelihood approach. Under weak assumptions, we obtain a theoretical bound for a Kullback-Leibler type loss for a single model maximum likelihood estimate. We use a penalized model selection technique to select a best model within a collection. We give a general condition on penalty choice that leads to oracle type inequality for the resulting estimate. This construction is applied to two examples of partition-based conditional density models, models in which the conditional density depends only in a piecewise manner from the covariate. The first example relies on classical piecewise polynomial densities while the second uses Gaussian mixtures with varying mixing proportion but same mixture components. We show how this last case is related to an unsupervised segmentation application that has been the source of our motivation to this study.
Energy consumption and conservation in mobile peer-to-peer systems (2006)

Today's mobile devices are growing in number and computational resources. Devices capable of storing gigabytes of digital content are becoming ubiquitous, making them an ideal platform for peer-to-peer content delivery and sharing. However, the always on communication patterns of P2P networks is not a natural fit for energy-constrained mobile devices. In this paper, we perform a detailed study of energy consumption of a structured P2P overlay on a PDA device. Using actual energy measurements, we present energy consumption results for different type of operations in P2P overlays. Based on these observations, we implement an approach to improve energy conservation on P2P protocols and show some promising preliminary results.
Removal of Multi-active-blue Dye from Aqueous Phase using Magnetic Poly-pyrrole Nano-composites: Fixed-bed Adsorption Studies (2016)

The aim of this study was to explore the use of adsorption in the removal of synthetic dyes in water bodies. These dyes pose a serious threat to both aquatic and human lives because of their toxicity and persistence in the environment. There is therefore an urgent need to remove them from water before discharge to the environment. Many of the current dye treatment methods are generally inefficient and expensive; however, adsorption is the most preferred method due to its inherent benefits such as simplicity, ease of operation, low cost and insensitivity to toxic environments. The study evaluated the removal of Multi-Active-Blue (MAB) dye from aqueous solution using poly-pyrrole-magnetitenano-composite (PPy/Fe<sub>3</sub>O<sub>4</sub>) adsorbent in a fixed-bed adsorption column. The influences of initial MAB dye concentration, bed mass and flow rate at the influent stream on the adsorption performance were investigated in an up-flow fashion. Results showed that early breakthrough time (t<sub>b</sub>) was attained at high solution flow rates and dye concentrations and low bed mass. Increasing concentration from 50 to 150mg/L resulted in a decrease in t<sub>b</sub> from 610 to 110 min. Furthermore, at the studied conditions, the highest breakthrough time obtained was 690 min at which 228 bed volumes were processed at 1.45g/L Adsorbent Exhaustion Rate (AER).The adsorber design parameters were calculated by fitting the experimental data to the column adsorption models and based on analysis of linear regression coefficients (R t<sup>b</sup>), it was established that the MAB dye adsorption was described best by Yoon-Nelson model throughout the entire breakthrough profile, while Bohart-Adams model fitted only the initial portion of the profiles. Accordingly, it was concluded that PPy- Fe<sub>3</sub>O<sub>4</sub>nano-composite material is a promising adsorbent for cleaning textile dye polluted water.
Simulation of oxygen uptake and leg joint reaction force during ergometer exercise under altered gravity (2017)

Ergometers are safe devices for patients and elderly individuals, as the exercise intensity can be controlled. Moreover, ergometer exercises, which remove the load from body weight on the leg joint, would better reflect training conditions in locations where the force of gravity is lower than that on Earth, such as the International Space Station or on the surface of Mars. The purpose of this study was not only to validate an ergometer exercise model for measuring oxygen uptake and knee joint reaction force by comparison with experimental results, but also to consider a strategy for electrically stimulating leg joint muscles to modulate them under altered gravity.
Development of an automated steering vehicle based on roadway magnets-a case study of mechatronic system design (1999)

Automated steering control is a crucial element of vehicle automation. The California PATH Program at the University of California at Berkeley has developed one such system using magnetic markers embedded under the roadway for lateral guidance. This system was demonstrated during the August 1997 National Automated Highway System Consortium Feasibility Demonstration, San Diego, CA, without a single failure. Developing a successful demonstration system not only required theoretical understanding of the various control problems involved, but also strong appreciation of all practical issues. In the paper, the comprehensive process of developing such automated steering control system is described. This process consists of control objectives' determination, system structure definition, vehicle dynamics validation, lateral sensing system development, steering actuator design, test track installation, control algorithm development, software/hardware integration, and vehicle testing. The entire process also serves as a good case study for mechatronic system design integrating mechanical components, electronic devices, intelligence, and feedback control to perform vehicle automation functions.
Cell Harvesting Methods Affect Cellular Integrity of Adherent Cells During Apoptosis Detection (2018)

Enzymatic harvesting using 0.25% trypsin instead of mechanical harvesting by rubber scraper caused less damage of cell integrity. Furthermore, the binding buffer used in the apoptosis detection protocol aggravated the existing plasma membrane damage caused by the rubber scraper.
Electroporation-based DNA immunisation: translation to the clinic (2007)

The expectation has been that plasmid DNA vaccines may have use against a wide range of microbial and oncologic targets. However, attempts at their development have been hampered by the inability to achieve high, consistent levels of immunogenicity in large experimental species and humans. Successful development is probably contingent on a delivery method that provides robust, consistent antigen expression and immune responses. Electroporation (EP), a promising approach that dramatically enhances expression of the encoded antigen as well as the potency and immunogenicity of DNA vaccines, could facilitate clinical implementation of DNA vaccination. With the recent development of EP systems that enable safe, tolerable, reproducible and clinically acceptable administration, EP-based DNA vaccination has become a clinical reality. The technology is now being tested for safety and immunogenicity in several Phase I clinical trials.
Molecular phylogeny of Conus chiangi (Azuma, 1972) (Gastropoda: Conidae) (2010)

(Uploaded by Plazi from the Biodiversity Heritage Library) No abstract provided.
Synthesis of Calystegine B2 Analogs by Tandem Tautomerization-Intramolecular Glycosylation of Thioureidosugars (1998)

Ring-modified analogs of calystegine B2, a powerful glycosidase inhibitor of the polyhydroxy-nor-tropane series, have been prepared in one-pot reaction from thiourea-carbohydrate precursors via a tandem tautomerization-intramolecular glycosylation process.
Short-range multi-mode continuous-wave radar for vital sign measurement and imaging (2018)

Short-range compact radar systems are non-invasive sensors that can locate the position and also monitor minute vibrations of the targets. They find wide use in healthcare monitoring, medical imaging, surveillance, industrial, occupancy sensing and gesture sensing applications. In this paper, we present a compact short-range 60 GHz low-power, system integrated radar system which can simultaneously operate several functional modes such as Range-Doppler Imaging, Range-Cross Range Imaging and Doppler interferometric mode without loss of performance. We also present the mechanism and processing to interleave various modes and experimentally validate the performance of the system.
Mutation and copy number discordance in primary versus metastatic colorectal cancer (mCRC). (2014)

3509 Background: Molecular profiling for CRC commonly utilizes formalin-fixed tissue of convenience, which may include tissue obtained from primary or metastatic tumors. While the alterations in KRAShave been shown to have a high degree of concordance, a detailed survey of other commonly mutated genes, copy number variations, and the influence of intervening treatment in CRC has not been conducted. Methods: Primary and metastatic tissue underwent sequencing on a 46 or 50-gene hotspot AmpliSeq panel (IonTorrent) in a CLIA-compliant setting. For a subset of patients, targeted resequencing of a panel of 202 genes by HiSeq 2000 (Illumina) to an average depth of 800 was performed by the MDACC Institute of Personalized Cancer Therapeutics, with single nucleotide variations and copy number called by in-house algorithms. Results: Sequencing was successfully completed on 115 pairs of primary and metastatic tumors (N=107 for 46/50-gene, and N=17 for 202-gene). Forty-six high level amplifications (>4 copies) were found in 28 genes in 11 of 17 pairs, with discordant results in all cases, including discordance in potentially clinically relevant amplifications: HER2, NOTCH1, FLT3, and AURKA. Overall concordance rate for mutations on the 46/50-gene panel was 78%, but varied substantially by gene. APC, TP53, NRAS, and BRAF demonstrated concordance similar to KRAS (89% concordance), while PIK3CA demonstrated a 6.8-fold higher odds of discordance between primary and metastatic site (95% CI of odds ratio (OR) of 2.1 to 22.6, P<0.001). Genes with low prevalence (<10%) such as FGFR3, STK11, and FBXW7 likewise had high levels of discordance (OR 4.4, 95% CI: 1.4 to 14.1, P=0.008). Intervening chemotherapy treatment was associated with a 3.5 fold higher odds of discordance across all genes compared to patients that did not receive therapy between resection of primary and metastatic tumors (95% CI 1.26 to 10.4, P=0.008), including KRAS, TP53, and PIK3CA(OR of 5.2, 3.5, and 3.3 respectively). Conclusions: Rates of discordance between primary and metastases mutations vary substantially by gene and prior treatment in mCRC. Prospective efforts to enrich for biomarkers need to account for tumor site and treatment variability on a gene-by-gene basis.
Molecular Diagnostics of ADPKD Coming of Age (2008)

Ever since the first autosomal dominant polycystic kidney disease (ADPKD) gene was localized to a chromosomal interval ( PKD1 : 16p13.3) in 1985, brave souls have been performing molecular-based diagnostics (1). The enthusiasm was tempered by the discovery of a second gene ( PKD2 : 4q21) and suggestions of a third, with the realization that reliable linkage-based diagnostics required families large enough to determine unequivocally the gene involved (2). Identification of the PKD1 and PKD2 genes in the mid 1990s revived interest, although the large coding region of PKD1 (approximately 13 kb) and reiteration of the genomic region several times elsewhere on chromosome 16 greatly complicated mutation screening (3,4). Consequently, the initial focus was mutations to the single-copy, 3′ region (approximately 20%) of PKD1 , and PKD2 (5,6). It was not until the dawning of the new millennium, after the development of methods for locus-specific amplification of the duplicated part of PKD1 , that comprehensive analysis of both genes was possible (7,8). Even then, indirect methods were used to screen for bp changes—methods that because of the level of precision were not …
PASS: Protein Annotation Surveillance Site for Protein Annotation Using Homologous Clusters, NLP, and Sequence Similarity Networks (2021)

Advances in genome sequencing have accelerated the growth of sequenced genomes but at a cost in the quality of genome annotation. At the same time, computational analysis is widely used for protein annotation, but a dearth of experimental verification has contributed to inaccurate annotation as well as to annotation error propagation. Thus, a tool to help life scientists with accurate protein annotation would be useful. In this work we describe a website we have developed, the Protein Annotation Surveillance Site (PASS), which provides such a tool. This website consists of three major components: a database of homologous clusters of more than eight million protein sequences deduced from the representative genomes of bacteria, archaea, eukarya, and viruses, together with sequence information; a machine-learning software tool which periodically queries the UniprotKB database to determine whether protein function has been experimentally verified; and a query-able webpage where the FASTA headers of sequences from the cluster best matching an input sequence are returned. The user can choose from these sequences to create a sequence similarity network to assist in annotation or else use their expert knowledge to choose an annotation from the cluster sequences. Illustrations demonstrating use of this website are presented.
Environmental Factors Influence the Rate of Human Herpesvirus Type 8 Infection in a Population with High Incidence of Classic Kaposi Sarcoma (2006)

High prevalence of human herpesvirus type 8 (HHV-8) infection has been reported on the island of Sardinia. Among emigrants from Sardinia, rates of HHV-8 infection are lower than they are in Sardinia and are similar to those observed in the local population. Thus, environmental factors seem to play a relevant role in affecting the prevalence of HHV-8 infection.
Performance Impact of NVMe-Over-TCP on HDFS Workloads (2022)

Storage is one of the important components in datacenters. As the data volume rises and the service scale grows, some workloads like database demand increasing amount of storage. While a single server can only host a limited number of disks, distributed file systems (e.g., Hadoop Distributed File System referred to as HDFS) enable accessing disks mounted on the other servers in the cluster, satisfying the storage requirements. On the other side, NVMe-over-Fabric protocols (e.g., NVMe-over-TCP) have been released as a solution on the device level to provide access to remote NVMe disks. Therefore, for those applications developed on top of HDFS, there are at least two choices to make use of the storage resources distributed in datacenters. A concern is whether NVMe-over-TCP will hurt the performance. The evaluation in this paper reveals that the performance degradation NVMe-over-TCP caused on HDFS-based workloads is limited, suggesting NVMe-over-TCP a performant and economical solution in datacenter design to support workloads that needs a lot of storage (such as database applications).
Image Reconstruction using wavelet transform with extended fractional fourier Transform (2014)

Image reconstruction forms the basis of many applications in the fields of medicine, astronomy etc. Historically an image is reconstructed using several methods of which Fourier and wavelet transform methods formed the roots of present day technologies. The reconstructed images possess higher resolution and helps in analyzing the image in more detail. In our thesis we proposed a method where we used fractional Fourier transform in conjunction with wavelet transform to produce the reconstructed image. We employed three wavelets in our thesis namely Haar wavelet, Daubechies wavelet and Coiflet wavelet in order to gain diversity into our results. For the scaling function of each of the three wavelets fractional Fourier transform is applied which gives a new scaling function. A new wavelet function created using the scaling function. Such a wavelet is applied to series of images of various resolutions (256x256, 128x128, 64x64) and is encrypted using DES before transmitting over the channel. The reconstruction is carried out using inverse DES and inverse wavelet Transform to get the reconstructed image. The parameters we used to determine the efficiency of the wavelets are peak signal to noise ratio(PSNR) and Structural similarity Index(SSIM). The results for various images are plotted using box plots. We reached out the conclusions that Daubechies had the better performance compared to other wavelets. Also the performance falls down with the image resolution.
The batch study of Sr2 + sorption by bone char (2008)

Considering the excellent sorption properties of synthetic calcium hydroxyapatite (HAP) towards many divalent cations, the potential application of bone char, the natural source of HAP, for sequestering Sr(2+)ions from aqueous solutions has been studied in batch conditions. Contact time, initial solution pH and initial Sr(2+) concentrations were varied to examine the effect of these process parameters on the amount of Sr(2+) sorbed. The kinetics of Sr(2+) sorption was found to be a 2-step process, with contact time of 24 h required for attaining equilibrium. The sorption isotherm was well fitted with Langmuir and DKR theoretical models. Sorption of Sr(2+) on bone char was found to be a favorable, thermodynamically feasible and spontaneous process, with the maximum sorption capacity of 0.271 mmol/g and sorption energy of 11.09 kJ/mol. The sorption was pH-independent in the initial pH range 4-10, as a result of excellent buffering properties of bone char (constant final pH), while for pH > 10 sorbed amounts of Sr(2+) increased due to attractive electrostatic forces between negatively charged sorbent surface and positively charged metal ions. On the basis of the amount of Ca(2+) released and final pH decrease in respect to the point of zero charge of bone char (pH(PZC)), two possible mechanisms of Sr(2+) sorption were identified: ion-exchange and the formation of complex compounds with HAP and carbon active surface sites. The amounts of Sr(2+) leached from bone char increased with the increase of Ca(2+) content and the decrease of solution pH. In comparison with synthetic HAP, bone char represents a cost-effective alternative for Sr(2+) sequestering.
Sequence Diversity at the Proximal 14q32.1 SERPIN Subcluster: Evidence for Natural Selection Favoring the Pseudogenization of SERPINA2 (2006)

The superfamily of serine protease inhibitors (SERPINs) plays a key role in controlling the activity of proteinases in diverse biological processes. alpha1-antitrypsin (SERPINA1), the most studied member of this family, is encoded by a gene located within the proximal 14q32.1 SERPIN subcluster, together with the highly homologous alpha1-antitrypsin-like sequence (SERPINA2), which was previously proposed to be a pseudogene. Here, we performed a resequencing study encompassing both SERPINA1 and SERPINA2 as well as the adjacent gene coding for corticosteroid-binding globulin (SERPINA6) in samples from Europe and West Africa. In the African sample, we found that a common haplotype carrying a 2-kb deletion in the SERPINA2 gene is associated with remarkable long-range homozygozity as if it was quickly driven to high frequency by natural selection acting on an advantageous variant. An analysis of the HapMap Phase I data for the Yoruba sample confirmed that variation in this subcluster carries a strong signal of positive selection. We also show that the SERPINA2 gene is expressed and probably encodes a functional SERPIN. Finally, comparisons with orthologous sequences in nonhuman primates showed that SERPINA2 is present in some great apes, but in chimpanzees it was lost by a deletion event independent from that observed in humans. In agreement with the "less is more" hypothesis, we propose that loss of SERPINA2 is an ongoing process associated with a selective advantage during recent primate evolution, possibly because of a role in fertility or in host-pathogen interactions.
Chiral spin condensation in a one-dimensional optical lattice (2017)

We study a spinor (two-component) Bose gas confined in a one-dimensional double-valley optical lattice which has a double-well structure in momentum space. Based on field theory analysis, it is found that spinor bosons in the double-valley band may form a spin-charge mixed chiral spin quasicondensate under certain conditions. Our numerical calculations in a concrete $\ensuremath{\pi}$-flux triangular ladder system confirm the robustness of the chiral spin order against interactions and quantum fluctuations. This exotic atomic Bose-Einstein condensate exhibits spatially staggered spin loop currents without any charge dynamics despite the complete absence of spin-orbit coupling in the system, creating an interesting approach to atom spintronics. The entanglement entropy scaling allows us to extract conformal-field-theory central charge and establish the low-energy effective field theory for the chiral spin condensate as a two-component Luttinger liquid. Our predictions should be detectable in atomic experiments through spin-resolved time-of-flight techniques.
EMI sources from mode conversion in a Telco system high-speed SERDES (2010)

Prediction of signal integrity (SI) and electromagnetic interference (EMI) from multilayer circuit boards is an important problem which is of interest to high speed digital system designers. SI and EMI control should be treated as a design problem from the start and it should be given the necessary resources throughout the design process. This can only be accomplished with accurate and effective electrical modeling of the complex interconnection structures. In this paper, electrical modeling methods are described where both differential-mode and common-mode effects and their conversions are accurately captured. Common-mode imbalances degrade the signal integrity margins making the system more susceptible to failure with increased EMI radiation. Simulation models are developed to properly quantify mode conversion mechanisms. A high speed blade system is chosen as a test bench to demonstrate the characterization methodology. The blade chassis is a compact, modular, rack mount scalable server system with support for twelve single-wide server blades. All high-speed communication occurs through a backplane using four sets of redundant fabrics, yielding a total of eight network connections per blade. This architecture allows for communication between any blade server and the chassis management units, the I/O switch modules, the high speed switch modules, and the I/O bridge modules. In the high speed differential serial channel design process it is important to model differential to common mode conversion. In order to minimize the differential insertion loss, increase the signal to noise ratio at the receiver to improve bit-error rate (BER) and minimize EMI, careful analysis of sources of loss, imbalance, and skew within the channel is needed. In this work, we demonstrate the importance of common-mode noise to radiation from a PCB. We then focus on mode conversion due to proximity of transmission lines to plane edges, impedance mismatch, current return path variation, trace loading to due coupling, and AC coupling components. Measured results were shown that highlight the significant variability in mode conversion that can result from the various mechanisms simulated in this study.
Mast cells express IL‐13Rα1: IL‐13 promotes human lung mast cell proliferation and FcɛRI expression (2006)

Human lung mast cell express IL-13Ralpha1 and activation by IL-13 for 5 days increased FcepsilonRI expression and proliferation. Histamine release was not affected by short-term priming with IL-13, but was upregulated by priming for 5 days suggesting that this effect was mediated by the increased FcepsilonRI expression. These data support the view that targeting IL-13 may be beneficial in the treatment of asthma.