gebhart/patrepeval huggingface dataset:
Learning Stochastic Feedforward Neural Networks (2013)

Multilayer perceptrons (MLPs) or neural networks are popular models used for nonlinear regression and classification tasks. As regressors, MLPs model the conditional distribution of the predictor variables Y given the input variables X. However, this predictive distribution is assumed to be unimodal (e.g. Gaussian). For tasks involving structured prediction, the conditional distribution should be multi-modal, resulting in one-to-many mappings. By using stochastic hidden variables rather than deterministic ones, Sigmoid Belief Nets (SBNs) can induce a rich multimodal distribution in the output space. However, previously proposed learning algorithms for SBNs are not efficient and unsuitable for modeling real-valued data. In this paper, we propose a stochastic feedforward network with hidden layers composed of both deterministic and stochastic variables. A new Generalized EM training procedure using importance sampling allows us to efficiently learn complicated conditional distributions. Our model achieves superior performance on synthetic and facial expressions datasets compared to conditional Restricted Boltzmann Machines and Mixture Density Networks. In addition, the latent features of our model improves classification and can learn to generate colorful textures of objects. 1
Design considerations for 2.5-D and 3-D integration accounting for thermal constraints (2016)

In this paper, we explore the design considerations of two approaches to 2.5-D integration (silicon interposer and bridge-chip) from a thermal perspective and compare to 3-D ICs. Moreover, the impact of die thickness mismatch and die spacing are investigated in 2.5-D systems. We conclude that the die dissipating the largest power should be the thickest in a multi-die package. Larger lateral spacing between dice reduces the temperature at the unrealistic expense of communication power efficiency. Therefore, it is necessary to consider this tradeoff when selecting appropriate die spacing.
Supplementary Table 1 from Common Structural and Epigenetic Changes in the Genome of Castration-Resistant Prostate Cancer (2023)

&lt;p&gt;XLS file - 15K, Candidate Gene List and Copy number:Expression Correlation for Frequently Aberrant Genes.&lt;/p&gt;
In vitro Characterization of a small molecule inhibitor of the alanine serine cysteine transporter ‐1 (SLC7A10) (2013)

NMDA receptor hypofunction is hypothesized to contribute to cognitive deficits associated with schizophrenia. Since direct activation of NMDA receptors is associated with serious adverse effects, modulation of the NMDA co-agonists, glycine or D-serine, represents a viable alternative therapeutic approach. Indeed, clinical trials with glycine and D-serine have shown positive results, although concerns over toxicity related to the high-doses required for efficacy remain. Synaptic concentrations of D-serine and glycine are regulated by the amino acid transporter alanine serine cysteine transporter-1 (asc-1). Inhibition of asc-1 would increase synaptic D-serine and possibly glycine, eliminating the need for high-dose systemic D-serine or glycine treatment. In this manuscript, we characterize Compound 1 (BMS-466442), the first known small molecule inhibitor of asc-1. Compound 1 selectively inhibited asc-1 mediated D-serine uptake with nanomolar potency in multiple cellular systems. Moreover, Compound 1 inhibited asc-1 but was not a competitive substrate for this transporter. Compound 1 is the first reported selective inhibitor of the asc-1 transporter and may provide a new path for the development of asc-1 inhibitors for the treatment of schizophrenia.
A Continuous Flow Polymerase Chain Reactor for DNA Expression Analysis (2006)

The polymerase chain reaction (PCR) has revolutionised molecular biology, and is at the forefront of many current efforts to document and understand human genetic diversity. Recent years has seen a move towards incorporating the PCR technique into a micro Total Analysis System (μTAS) thus exploiting its full potential. Micro scale PCR design offers the opportunity to integrate all functional steps of DNA expression analysis into a miniaturised device allowing for high throughput and reduced analysis times, reduced sample volume requirements and cost efficiency. Consequently, it is desirable to replace the traditional stationary or well based thermal cyclers with continuous flow designs. A continuous flow polymerase chain reaction device consisting of a cylindrical heating core, which is segmented axially into three symmetric heating zones providing the denaturating, annealing and extension phases of the polymerase chain reaction, and a flow through capillary tube which is wound helically around the core has been fabricated and shown to consistently amplify target plasmid DNA samples. At the inlet to the device, PCR samples are segmented into droplets and entrained in an immiscible carrier fluid to eliminate cross contamination between PCR samples. This approach also prevents degradation of the micro-reactor droplets from inhibitory effects posed by the high surface to volume ratios associated with the device. The droplet train is then cycled through the capillary tube with each complete revolution constituting one cycle of the PCR reaction. The results reported in this paper include, initial validation of the spiral cycler design in comparison to an existing commercial PCR platform, and subsequent optimisation of the reaction time and its effects on the devices performance. The spiral thermal cycler has demonstrated successful PCR amplification at the nano scale with stable trains of 30–35nl droplet volumes being processed in an amplification time of 32 minutes. At this level the device offers the potential to process approximately 3500 such droplets in of order one hour.
Design, optimization, and fabrication of mechanical metamaterials for vibration control (2018)

Harsh shock and vibration environments are common in engineering applications. Mechanical metamaterials are showing significant potential as candidates for controlling wave propagation and isolating sensitive structural components, but require proper design of their complex microstructures. In this talk we will present time and frequency-domain strategies for Partial Differential Constrained (PDE)-constrained design optimization of locally resonant elastic/acoustic metamaterials. We will present a variety of notch filter resonators and split ring cylinder/sphere geometries that can be easily optimized for wave control applications, along with fabrication details involving multi-material additive manufacturing. A frequency-domain approach will be presented for band-gap or notch filter materials, and a time-domain strategy for transient shock environments. As the metamaterial structures typically involve concentrated masses and elastic connections, an optimization strategy involving 3D simple shapes will be presented. [Sandia National Laboratories is a multimission laboratory managed and operated by National Technology and Engineering Solutions of Sandia, LLC., a wholly owned subsidiary of Honeywell International, Inc., for the U.S. Department of Energy’s National Nuclear Security Administration. With main facilities in Albuquerque, N.M., and Livermore, C.A., Sandia has major R&amp;D responsibilities in national security, energy and environmental technologies, and economic competitiveness.]
Natural 2,5‐bisaryltetrahydrofuran lignans: Platelet‐activating factor antagonists (1987)

Abstract Lignans are a class of naturally occurring compounds characterized by bonding of two aryl propanoids at the 2‐position. Recently, an increasing significance of the biological activities of these compounds has been recognized. Members of 2,5‐bisaryltetrahydrofuran class of lignans are antagonists of the potent bioactive phospholipid, platelet activating factor (PAF). In this review, a survey of the occurrence, physical properties of all known bisaryltetrahydrofurans and reported biological activities as PAF antagonists is given.
Oxidation-Reduction Photochemistry of Polynuclear Complexes in Solution (1983)

Three classes of polynuclear complexes containing metal-metal bonds possess emissive excited states that undergo oxidation-reduction reactions in solution: the prototypes are Re2Cl2-8(d4·d4), Pt2(P2O5H2)4-4 (d8·d8), and Mo6Cl2-14(d4)6. Two-electron oxidations of Re2Cl2-8 and Pt2(P2O5H2)4-4 have been achieved by one-electron acceptor quenching of the excited complexes in the presence of Cl-, followed by one-electron oxidation of the Cl--trapped mixed-valence species. Two-electron photochemical oxidation-reduction reactions also could occur by excited-state atom transfer pathways, and some encouraging preliminary observations along those lines are reported.
1-Hexene: a renewable C6 platform for full-performance jet and diesel fuels (2013)

A highly efficient and selective process has been developed for the conversion of 1-hexene to jet and diesel fuels. In combination with commercial processes for the dehydration of ethanol and trimerization of ethylene, this work provides a basis for the synthesis of full-performance hydrocarbon fuels from bio-ethanol. Selective oligomerization of 1-hexene with a Cp2ZrCl2/MAO catalyst at ambient temperature and pressure resulted in 100% conversion of 1-hexene with >80% selectivity to a mixture of the dimer and trimer. The hydrogenated dimer had a −20 °C viscosity of only 3.5 mPa s, an exceptionally low freezing point of −77 °C, and a cetane number of 67 suggesting that it has performance characteristics suitable for both jet and diesel fuels. The hydrogenated trimer had a flash point of 128 °C, a cetane number of 92, a 40 °C viscosity of 3.1 mPa s, and a −20 °C viscosity of 24.5 mPa s. These properties suggest that the trimer has applications as a high-performance diesel fuel. In addition to the fuel-range hydrocarbons, heavier oligomers have potential as biolubricants which improves the carbon yield of useful products to near quantitative levels.
Application of the ONVMS model to discriminate challenging UXO targets (2012)

Discrimination of challenging targets, such as small and deep targets in highly cluttered environments, is still an enormous problem for UXO industry. One way to improve target classification is to enhance the sensor hardware, while another way is to fully utilize the data provided by current EMI sensors, by deploying advanced signal processing approaches. To address the latter, our group developed a new ortho-normalized volume magnetic source (ONVMS) technique for representing subsurface targets responses, and for discriminating between UXO and non-UXO targets. The technique has been applied to live-site UXO data sets and demonstrated to be robust and tolerant to noise. In this paper the ONVMS is applied to the data from a small 20 mm projectile, acquired using an advanced, commercially available EMI system “MetalMapper” (MM). The target intrinsic parameters are first extracted from the data using both the ONVMS and simple dipole models, and then analyzed from library matching classification perspective.
Optimal control using state dependent riccati equation (SDRE) for a flexible cable transporter system with arbitrarily varying lengths (2005)

This paper demonstrates a good application of SDRE technology to propose optimal controllers for a flexible transporter system with arbitrarily varying lengths. A model for a flexible cable transporter system with varying cable lengths is developed using Hamilton's principle. Galerkin's method is applied to transform the infinite dimensional system into a set of finite dimensional ordinary differential equations (ODEs) with state-dependent coefficients. Based on this approximate finite dimensional model, a stable optimal controller was proposed based on the SDRE techniques. To ensure the stability with unmodeled dynamics due to the neglecting higher modes, H <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">infin</sub> robust method is used with unmodeled dynamics considered as additive uncertainty. The optimal controller guarantees the asymptotic stability of the closed-loop system and effectively suppresses the longitudinal vibration of cables at the same time. The validity of the proposed controller is verified by numerical simulation
Pinning effect on the phase separation dynamics of thin polymer-dispersed liquid crystals (2005)

The surface pining effects on phase separation dynamics of polymer-dispersed liquid crystals (PDLCs) with thin cell gaps are demonstrated. Comparing various boundary conditions, the inner surfaces of the substrates with or without polyimide layers [but no rubbing] cannot provide enough anchoring force, so in either case the liquid crystal (LC) droplets flow and coalesce to form larger and less uniform droplets. However, if the inner surfaces of the substrates are coated with rubbed polyimide layers with anchoring energy >1x10-4 J/m2, almost all the nucleated LC droplets grow at a fixed position during phase separation. The appearance of the coalescence is not obvious and the formed LC droplets are relatively uniform. The surface anchoring has a significant effect on the morphology of PDLCs.
Catalysis of Protein Disulfide Bond Isomerization in a Homogeneous Substrate (2005)

Protein disulfide isomerase (PDI) catalyzes the rearrangement of nonnative disulfide bonds in the endoplasmic reticulum of eukaryotic cells, a process that often limits the rate at which polypeptide chains fold into a native protein conformation. The mechanism of the reaction catalyzed by PDI is unclear. In assays involving protein substrates, the reaction appears to involve the complete reduction of some or all of its nonnative disulfide bonds followed by oxidation of the resulting dithiols. The substrates in these assays are, however, heterogeneous, which complicates mechanistic analyses. Here, we report the first analysis of disulfide bond isomerization in a homogeneous substrate. Our substrate is based on tachyplesin I, a 17-mer peptide that folds into a beta hairpin stabilized by two disulfide bonds. We describe the chemical synthesis of a variant of tachyplesin I in which its two disulfide bonds are in a nonnative state and side chains near its N and C terminus contain a fluorescence donor (tryptophan) and acceptor (N(epsilon)-dansyllysine). Fluorescence resonance energy transfer from 280 to 465 nm increases by 28-fold upon isomerization of the disulfide bonds into their native state (which has a lower E(o') = -0.313 V than does PDI). We use this continuous assay to analyze catalysis by wild-type human PDI and a variant in which the C-terminal cysteine residue within each Cys-Gly-His-Cys active site is replaced with alanine. We find that wild-type PDI catalyzes the isomerization of the substrate with kcat/K(M) = 1.7 x 10(5) M(-1) s(-1), which is the largest value yet reported for catalysis of disulfide bond isomerization. The variant, which is a poor catalyst of disulfide bond reduction and dithiol oxidation, retains virtually all of the activity of wild-type PDI in catalysis of disulfide bond isomerization. Thus, the C-terminal cysteine residues play an insignificant role in the isomerization of the disulfide bonds in nonnative tachyplesin I. We conclude that catalysis of disulfide bond isomerization by PDI does not necessarily involve a cycle of substrate reduction/oxidation.
40 Gbps WDM Transmission Performance Comparison Between Legacy and Ultra Low Loss G.652 Fibers (2011)

G.652 standard single-mode fiber (SSMF) is today considered as the most efficient solution to transport 40 Gbps and 100 Gbps data traffic over ultra long-haul distances on terrestrial transport networks. In the early 2000s, there was a trend to replace legacy G.652 fibers, which were strongly impaired by polarization mode dispersion (PMD), by G.655 fibers. For economic reasons, incumbent operators decided to keep their legacy G.652 fiber infrastructure, while replacing gradually the most impaired fibers by low PMD G.652 fibers over the links transporting the highest amount of traffic. In this context, we performed in 2009 an experimental evaluation of the performance of a new ultra low loss (ULL) and low PMD G.652 fiber to carry 40 Gbps WDM systems over ultra long-haul distances by using various modulation formats (NRZ-OOK and NRZ-DPSK) and amplification schemes (hybrid Raman-EDFA and EDFA only). We demonstrated record transmission distance of 4400 km at 40 Gbps line rate when NRZ-DPSK was combined with hybrid Raman-EDFA amplification. We complete here this previous study with new results, coming in particular from an extensive experimental and numerical comparison of the transmission performance of this new ULL G.652 fiber with the legacy G.652 fiber, used in the field for 20 years. We demonstrate in particular that this new SMF-28 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">®</sup> ULL optical fiber increases the maximum transmission reach by ~30%, whatever the amplification scheme, when NRZ-DPSK is used.
Kilovolt Tri-Gate GaN Junction HEMTs with High Thermal Stability (2021)

The lack of reports on the high-temperature performance of tri-gate GaN power HEMTs has raised serious concern on their competitiveness. This work demonstrates the first normally-off tri-gate GaN HEMT that can block kilovolts at 150 °C and zero gate bias. The key enabling device design is a new type of tri-gate, the junction tri-gate, which comprises p-n junction wrapping around AlGaN/GaN fins in the gate region. At 150 °C, the GaN tri-gate junction HEMT (Tri-JHEMT) retains strong gate control and stable threshold voltage, while the traditional tri-gate metal-insulator-semiconductor (MIS) HEMTs fabricated on the same wafer shows a large threshold voltage shift and inferior capabilities of voltage blocking. These results show the excellent thermal stability of GaN Tri-JHEMTs and their great potentials for power electronics applications.
Four New Glucosides of Stilbene Oligomers from the Stem of Gnetum gnemonoides (2001)

1Gifu Pharmaceutical University, 5-6-1, Mitahora-higashi, Gifu 502-8585, Japan; 2Gifu Prefectural Institute of Health and Environmental Sciences, 1-1 Naka Fudogaoka, Kakamigahara, Gifu 504-0838, Japan; 3Faculty of Pharmaceutical Sciences, Josai University, 1-1 Keyakidai Sakado, Saitama 350-0295, Japan; 4Botanical Gardens, Koishikawa, Graduate School of Science, The University of Tokyo, 3-7-1 Hakusan, Bunkyo-ku, Tokyo 112-0001, Japan; 5Indinesian Institute of Sciences, Jalan Ir. H. Juanda 13, Bogor 16122, Indonesia
Environmental noise, its types and effects on health (2021)

Noise can be defined as an undesirable sound that pollutes the environment. If noise is continuous and exceeds certain levels, negative effects on health can be observed. In recent years, the impact of environmental noise (road traffic noise, railway traffic noise, air traffic noise and industrial noise) on human health has come under increasingly intense scrutiny. Noise can cause a number of negative effects on health that directly or indirectly affect humans. The occurrence of some certain and harmful health effects drives the onset of others and may contribute to the development of various diseases. Health is not only a state of physical well-being, but also mental well-being. Mental health primarily depends on the quality of life, which can be affected by various environmental factors, such as noise. An important aspect of fighting noise is the most effective protection of the population by avoiding sources of noise and reducing it. This can be achieved by introducing new technical solutions and new technologies, including devices that generate less noise. Another important measure is educating the society and influencing the change of individual and collective behavior, which may contribute to reducing the harmful factor, which is noise in human life, and minimize the resulting negative effects on health.
Kernel Mechanisms for Service Differentiation in Overloaded Web Servers (2001)

The increasing number of Internet users and innovative new services such as e-commerce are placing new demands on Web servers. It is becoming essential for Web servers to provide performance isolation, have fast recovery times, and provide continuous service during overload at least to preferred customers. In this paper, we present the design and implementation of three kernelbased mechanisms that protect Web servers against overload by providing admission control and service differentiation based on connection and application level information. Our basic admission control mechanism, TCP SYN policing, limits the acceptance rate of new requests based on the connection attributes. The second mechanism, prioritized listen queue, supports different service classes by reordering the listen queue based on the priorities of the incoming connections. Third, we present HTTP header-based connection control that uses application-level information such as URLs and cookies to set priorities and rate control policies. We have implemented these mechanisms in AIX 5.0. Through numerous experiments we demonstrate their effectiveness in achieving the desired degree of service di erentiation during overload. We also show that the kernel mechanisms are more ecient and scalable than application level controls implemented in the Web server.
Immunofluorescence measurement in a flow cytometer using low‐power helium—neon laser excitation (1983)

Helium-neon lasers are economical and efficient light sources; their utility in flow cytometry to date has been limited by the lack of fluorescent probes that can be excited at 633 nm. Allophycocyanin (APC), a highly fluorescent phycobiliprotein, can be used as an antibody label and has spectral characteristics suitable for use with He-Ne lasers; we undertook to resolve whether a low-power (7 mW) He-Ne laser could provide sufficient excitation to permit flow cytometric detection of APC-labeled antibodies on cell surfaces. We made an APC conjugate of monoclonal antibody 4F2, which reacts with an antigen abundant on the surfaces of activated human T-lymphocytes; APC-4F2 was used to stain blood mononuclear cells that had been cultured with and without phytohemagglutinin (PHA). Cells so stained were examined in a flow cytometer with orthogonal illumination at 633 nm from a 7 mW He-Ne laser; antibody-bearing cells were detectable by fluorescence emission above 665 nm. Cells from the same cultures were stained with fluorescein-labeled 4F2 antibody and examined in a flow cytometer with argon ion laser excitation at 488 nm. Percentages of antibody-bearing cells determined from APC fluorescence and from fluorescein fluorescence were in good agreement. It thus appears that He-Ne lasers and APC-antibodies are usable for immunofluorescence measurements; the sensitivity attainable with this technique remains to be determined.
Protein Detection by Counting Molecules (2019)

Featured Article: Rissin DM, Kan CW, Campbell TG, Stuart SC, Fournier DR, Song L, et al. Single-molecule enzyme-linked immunosorbent assay detects serum proteins at subfemtomolar concentrations. Nat Biotechnol 2010;28:595–9.3

Proteins are the functional units of life. Berson et al. opened the field of protein measurements with the development of RIAs in the 1950s (1). In 1971, Engvall and Perlmann reported the ELISA (2) that has since been the staple for protein measurements. In 2010, when our article featured here was published, there were 325 proteins detectable in blood, of which 171 were Food and Drug Administration–approved tests of clinical value (3). Most of these proteins are measured using ELISA. When the human genome was sequenced, it was predicted that there should be nearly 4000 proteins in the human bloodstream (4). Where are the missing proteins? ELISA enabled detection down to picomolar concentrations, but this limit of quantification was insufficient to fully access the human blood proteome. The single-molecule array (Simoa) …