gebhart/patrepeval huggingface dataset:
Covariance Estimation in Decomposable Gaussian Graphical Models (2009)

Graphical models are a framework for representing and exploiting prior conditional independence structures within distributions using graphs. In the Gaussian case, these models are directly related to the sparsity of the inverse covariance (concentration) matrix and allow for improved covariance estimation with lower computational complexity. We consider concentration estimation with the mean-squared error (MSE) as the objective, in a special type of model known as decomposable. This model includes, for example, the well known banded structure and other cases encountered in practice. Our first contribution is the derivation and analysis of the minimum variance unbiased estimator (MVUE) in decomposable graphical models. We provide a simple closed form solution to the MVUE and compare it with the classical maximum likelihood estimator (MLE) in terms of performance and complexity. Next, we extend the celebrated Stein's unbiased risk estimate (SURE) to graphical models. Using SURE, we prove that the MSE of the MVUE is always smaller or equal to that of the biased MLE, and that the MVUE itself is dominated by other approaches. In addition, we propose the use of SURE as a constructive mechanism for deriving new covariance estimators. Similarly to the classical MLE, all of our proposed estimators have simple closed form solutions but result in a significant reduction in MSE.
Ancestrally high elastic modulus of gecko setal β-keratin (2007)

Typical bulk adhesives are characterized by soft, tacky materials with elastic moduli well below 1MPa. Geckos possess subdigital adhesives composed mostly of beta-keratin, a relatively stiff material. Biological adhesives like those of geckos have inspired empirical and modelling research which predicts that even stiff materials can be effective adhesives if they take on a fibrillar form. The molecular structure of beta-keratin is highly conserved across birds and reptiles, suggesting that material properties of gecko setae should be similar to that of beta-keratin previously measured in birds, but this has yet to be established. We used a resonance technique to measure elastic bending modulus in two species of gecko from disparate habitats. We found no significant difference in elastic modulus between Gekko gecko (1.6 GPa +/- 0.15s.e.; n=24 setae) and Ptyodactylus hasselquistii (1.4 GPa +/- 0.15s.e.; n=24 setae). If the elastic modulus of setal keratin is conserved across species, it would suggest a design constraint that must be compensated for structurally, and possibly explain the remarkable variation in gecko adhesive morphology.
Local injection of receptor tyrosine kinase inhibitor MAE 87 reduces retinal neovascularization in mice. (2004)

The tyrosine kinase inhibitor MAE 87 may be a promising substance for local treatment of retinal neovascularization. Due to its ability to inhibit not only the VEGF but also the IGF-1 cascade, MAE 87 may prove especially valuable for the treatment of diabetic retinopathy.
Parallel Implementation of OBDD-Based Splitting Surface Search for Power System (2007)

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> Parallel computational structure is helpful for many complicated problems, especially those which can be divided into multiple independent simpler sub-problems. The ordered binary decision diagrams (OBDD)-based splitting surface search algorithm owns this kind of dividability, derived from the associative law of Boolean expression and the dividability of matrix operation. We have implemented the algorithm with the parallel computation structure MPI to save up computing time. Customized verification is available on our interactive illustrative website <emphasis emphasistype="boldital">http://obdd.cfins.au.tsinghua.edu.cn/</emphasis> (login user name: mag, password: 199707). </para>
Noyori–Ikariya catalyst supported on tetra-arylphosphonium salt for asymmetric transfer hydrogenation in water (2015)

An easily prepared, low weight, recyclable supported Noyori–Ikariya catalyst is described. The ruthenium precatalyst provides excellent conversions and high enantioselectivities for the asymmetric transfer hydrogenation of ketones in water.
Experimental Study of Microwave-Induced Discharge and Mechanism Analysis Based on Spectrum Acquisition (2017)

When conductor or semiconductor materials are exposed to microwave radiation in different atmospheres (Ar, He, N <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> , and O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> +N <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> ) intense discharge phenomena are observed. The discharge phenomena, generated when strips of the metals Fe, Al, and Zn or particles of the semiconductor SiC are irradiated with microwaves, are characterized experimentally using spectrum acquisition and analysis. Filamentary discharge is observed in an Ar atmosphere while spark discharge is observed in He, N <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> , and O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> +N <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> atmospheres. The spectral lines of the discharges are concentrated mainly in the visible region, but there are also peaks in the ultraviolet region. The nature of the discharge and the specific details of the spectra are influenced by: 1) the target metal or semiconductor used; 2) the atmosphere; and 3) the microwave field characteristics. The spectra always consist of two parts: one corresponding to the target metal or semiconductor irradiated by the microwaves and the other due to the formation of the high-energy excitation states of atoms, molecules, and ions induced in the gaseous atmosphere. The microwave-induced discharge and the corresponding luminous and plasma effects have potential uses as energy sources in many applications including chemical or photocatalytic enhancement of reactions and the destruction of volatile organic compounds for which preliminary results are encouraging.
Supplementary Figure S6 from Leukemia Cell-Rhabdovirus Vaccine: Personalized Immunotherapy for Acute Lymphoblastic Leukemia (2023)

&lt;p&gt;Supplementary Figure S6 - PDF file 597K, Activated L1210 cells&lt;/p&gt;
The identification of pathogenic yeast strains by electrophoretic analysis of their chromosomes (1990)

Epidemiological studies require characterisation of pathogenic yeasts at and below the species level. The chromosomes of 130 strains of four pathogenic species of the genus Candida, isolated from clinical material, were separated by pulsed field electrophoresis with the clamped homogeneous electric field (CHEF) technique. Each species was characterised by a distinct electrophoretic karyotype (EK). Furthermore, smaller variations of the EK amongst strains belonging to the same species appeared to offer a useful means of strain differentiation. A karyotyping system is proposed for C. albicans. The EKs were assigned to a code of four numbers which designated the number of bands that could be resolved in each of four sets of chromosomes. Morphotypes of the colonies of C. albicans on malt agar plates, which did not correlate with the EK, could provide a complementary means of strain characterisation in epidemiological studies.
Complex Network Information Exchange in Random Wireless Environments (2012)

Abstract : This document summarizes the research performed under AFOSR contract FA9550-08-1-0480, entitled Complex network information exchange in random wireless environments.'' The objective of this project was to develop novel techniques, structures, and algorithms for optimization of complex wireless networks where channels change dynamically and randomly, effecting network performance and reliability. These random dynamics, while challenging for ensuring robust high-performance network operation, also create opportunities that adaptive network control policies can exploit. This is particularly important for advanced military networks operating in rapidly changing, heterogeneous and sometimes hostile environments. A main focus of this research was to develop the new technique of Wireless Network Utility Maximization (WNUM), extending NUM ideas to include network and traffic dynamics. The research also explore optimization of network security protocols that exploit random wireless environments. Finally, compressed sensing and matrix completion ideas were explored to develop low-complexity network control.
Melting, Solidification, and Crystallization of a Thermoplastic Polyurethane as a Function of Hard Segment Content (2019)

Abstract Thermoplastic polyurethanes (TPU) with varying hard segment contents (HSC) are monitored during melting and solidifying (, T max = 220 ° C) by small‐angle and wide‐angle X‐ray scattering (WAXS and SAXS). Hard segments: MDI/BD. Soft segments: PTHF1000. The neat materials are injection‐molded, having small amorphous hard domains (chord length ). Results indicate complexity of morphology changes. For example, crystals are predominantly produced in freshly segregated, sufficiently large hard domains, while the temperature decreases slowly enough. After the thermal treatment, only the materials with HSC &gt;∼ 35% show sharp Bragg peaks and larger hard domains (). When heated, small domains melt, but crystallization in the remaining large domains is not detected. Upon cooling, large agglomerates segregate first, which crystallize immediately. Segregation starts for HSC = 42% at 160 °C and for HSC = 75% at 210 °C. When HSC ≤ 30%, the morphologies before and after are similar, but afterward, many hard blocks are dissolved in the soft phase at the expense of the hard domain fraction. In heating and cooling the melts, multiple homogenization and segregation processes are observed, which are explained by the agglomeration of hard blocks of different lengths in the colloidal fluid.
Time domain deBroglie wave interferometry Time domain deBroglie wave interferometry in a 2D trap (2005)

Time domain deBroglie wave interferometry [Cahn et al, Phys. Rev. Lett. 79, 784] is applied to Rb87 atoms in a 2D linear trap. A standing wave light field is carefully aligned along the guiding direction of the magnetic trapping potential generated by a soft-ferromagnetic 4-foil structure. A sequence of two standing wave pulses is applied to the magnetically trapped atoms. The backscattered light at the revival time is collected and detected via a heterodyning technique. Our interferometer signal shows recoil oscillations that precisely fit the interferometer theory for atoms in free space. We observe decay of the signal on a millisecond time scale, as well as millisecond scale oscillations that suggest a residual variation of the linear trapping potential along the standing wave direction.
Reduced Cathepsin L expression and secretion into the extracellular milieu contribute to lung fibrosis in systemic sclerosis (2022)

Our findings identify CTSL as a protein protective against lung fibrosis via its activation of antifibrotic ES, and whose expression in SSc pLFs and lung tissues is suppressed. Identifying strategies to boost CTSL endogenous levels in SSc patients could serve as a viable therapeutic strategy.
ChemInform Abstract: Mild and Rapid Pd‐Catalyzed Cross‐Coupling with Hydrazine in Continuous Flow: Application to the Synthesis of Functionalized Heterocycles. (2013)

Abstract Continuous flow or batch reactions of the arylhydrazines, formed in the first step, with β‐diketones, benzaldehyde and ketones allows the synthesis of pyrazoles, hydrazones, and indoles.
Crystallization of Sodium Dodecyl Sulfate-Water Micellar Solutions under Linear Cooling (2017)

The crystallization kinetics of sodium dodecyl sulfate (SDS)-water micellar solutions, under linear cooling conditions, were experimentally investigated using optical microscopy, differential scanning calorimetry, and infrared spectroscopy. Cooling rates were systematically varied, from 0.1 to 50 °C min–1, encompassing environmental to near-“isothermal” temperature changes, between 22 and −5 °C, for a reference concentration of 20% SDS-H2O. The cooling rate was shown to determine the dominant crystal morphologies, with platelets and needles predominating at the lowest and highest rates, respectively. The results were rationalized in terms of isothermal crystallization data and the time–temperature cooling profile. Rates 0.1, 5.0, and 10 °C min–1 yield morphologies and kinetics analogous to those of isothermal quenches at the corresponding crystallization temperature window. Nontrivial deviations were observed for intermediate rates (0.5, 1.0 °C min–1), due to commensurate changes in temperature and crystallization mechanism, accompanied by solute depletion. The polythermal metastable zone width was estimated, and the non-isothermal nucleation described by the Nývlt equation, while the Avrami and Kissinger models described overall crystallization kinetics. Our measurements quantify the impact of temperature gradients in the crystallization of ubiquitous SDS micellar solutions, for a range of practically relevant profiles incurred during manufacturing and storage.
Scalable inference of decision tree ensembles: Flexible design for CPU-FPGA platforms (2017)

Decision tree ensembles are commonly used in a wide range of applications and becoming the de facto algorithm for decision tree based classifiers. Different trees in an ensemble can be processed in parallel during tree inference, making them a suitable use case for FPGAs. Large tree ensembles, however, require careful mapping of trees to on-chip memory and management of memory accesses. As a result, existing FPGA solutions suffer from the inability to scale beyond tens of trees and lack the flexibility to support different tree ensembles. In this paper we present an FPGA tree ensemble classifier together with a software driver to efficiently manage the FPGA's memory resources. The classifier architecture efficiently utilizes the FPGA's resources to fit half a million tree nodes in on-chip memory, delivering up to 20× speedup over a 10-threaded CPU implementation when fully processing the tree ensemble on the FPGA. It can also combine the CPU and FPGA to scale to tree ensembles that do not fit in on-chip memory, achieving up to an order of magnitude speedup compared to a pure CPU implementation. In addition, the classifier architecture can be programmed at runtime to process varying tree ensemble sizes.
Epigenetic reprogramming using 5-azacytidine promotes an anti-cancer response in pancreatic adenocarcinoma cells (2018)

Curative management of pancreatic adenocarcinoma is limited because this malignancy remains resistant to most chemotherapeutic drugs. Strategies that reverse epigenetic alterations offer a unique opportunity for cancer cell reprogramming, which is valuable for development of new treatments. The aim of this work was to reprogram pancreatic ductal adenocarcinoma (PDAC) cells toward a less aggressive and drug-responsive phenotype. The process applied is called "epigenetic reprogramming". To evaluate the efficiency of PDAC epigenetic reprogramming, we assessed tumor growth and drug response in PANC-1 cells after exposure to non-cytotoxic doses of the demethylating agent 5-azacytidine (5-AZA). Here, we showed that an epigenetic regimen using 5-AZA promoted an anti-cancer response by inhibiting PDAC tumor growth in vivo after the engraftment of treated cells. Remarkably, the subsequent addition of gemcitabine (GEM) to the 5-AZA-mediated reprogramming resulted in a marked growth inhibition effect in GEM-resistant pancreatic cancer cells. We observed that various characteristic peptides expressed in the pancreas, which included the antiproliferative hormone somatostatin (SST) and the SST receptor 2 (SSTR2), were significantly upregulated in the epigenetically reprogrammed PDAC cells. The inhibitory effect of octreotide (OCT), an SST analog, was tested on PDAC cells and found to be improved after cell reprogramming. Furthermore, we found that SST gene expression restoration following 5-AZA treatment or following knockdown of the DNA methyltransferase (DNMT) 1 enzyme was associated with the reversion of SST epigenetic silencing through regional CpG demethylation. Lastly, we confirmed the efficacy of 5-AZA-based epigenetic reprogramming in vivo using a PDAC tumor growth model. In conclusion, this study demonstrates that epigenetic reprogramming using the demethylating compound 5-AZA shows anti-cancer effects in PANC-1 cells and is potentially attractive for the treatment of solid tumors.
Discovery of a novel set of prostate cancer-related genes associated with the prognostically important TMPRSS2:ERG fusion gene (2008)

5056 Background: Nam et al (BJC 97:1690, 2007) have recently shown that of 165 patients, the subgroup of patients who expressed the TMPRSS2:ERG fusion gene product, had a significantly higher risk of recurrence (58% at 5 yrs) than did patients who lacked the fusion protein (8% at 5 yrs) and was the single most important prognostic factor. We have used the DASL assay to expression profile 502 cancer-related genes in tumors from 145 patients from this study in order to characterize a set of additional genes that correlate with recurrence and that may shed light on novel therapeutic targets. Methods: Patients were drawn from men who underwent radical prostatectomy as the sole treatment for clinically localized PC between 1998 and 2006; at Sunnybrook Health Science Center (Toronto, ON). Most patients had a Gleason score of 7 and the primary endpoint was biochemical recurrence. Total RNA, previously prepared from frozen PC samples, was used in the DASL assay. Labeled PCR products were hybridized to a Sentrix Universal Array which was imaged using a BeadArray Reader. Data was analyzed using BeadStudio, Significance Analysis of Microarrays, Cluster, and Treeview software. Results: RT-PCR results previously classified 73 of the 145 samples as TMPRSS2:ERG gene fusion-positive and 72 as fusion-negative. Of the fusion negative only 4 samples (5.5%) showed recurrence as opposed to 28 of the 73 fusion positive samples which showed recurrence (38.4%). DASL signal intensity supports the RT-PCR results showing an average increase in ERG signal intensity of over 3-fold for samples classified as fusion-positive via RT-PCR versus those classified as fusion-negative. Associated with this bifurcation are 8 other positively regulated genes (MSF, ARHGDIB, PDGFA, HDAC1, THPO, EPHB4, CEACAM1, TRAF4) and 15 negatively regulated genes (LAF4, CD44, FGF12, EPO, IGF1, FGFR4, MAF, TGFB3, FLT1, FGF7, KDR, PTEN, PDGFRA, ETV1, IGF2) with a false discovery rate of 3%. Conclusions: Using the DASL assay on 145 patient samples we have discovered 23 regulated genes that deserve further investigation and may act as therapeutic targets. Four of these genes (CEACAM1, MSF, PDGFA and THPO) are angiogenesis-related and one that is histone acetylase-related suggest immediate therapeutic approaches. No significant financial relationships to disclose.
Single photon HgCdTe avalanche photodiode and integrated detector cooler assemblies for space lidar applications (2018)

A linear mode photon counting HgCdTe avalanche photodiode (APD) focal plane array (FPA) detector was developed for space lidar applications. An integrated detector cooler assembly (IDCA) was manufactured using a miniature Stirling cooler. The HgCdTe APD demonstrated a greater than 60% photon detection efficiency from 0.9 to 4.3 &mu;m wavelength and a dark count rate less than 250,000/s. The IDCA cooled the FPA to 110K from ambient room temperature at a total electrical power of 7 W. The IDCA has passed environmental tests, including vibration, thermal cycling and thermal vacuum tests.
Supplementary Table 1 from Natural Human Plasmacytoid Dendritic Cells Induce Antigen-Specific T-Cell Responses in Melanoma Patients (2023)

&lt;p&gt;Supplementary Table 1 PDF file - 29K, Induration (mm) of the different injection sites in the DTH skin test&lt;/p&gt;
Variable bit-rate video coding for ATM and broadcast applications (1993)

Video data compression algorithms typically produce a bit rate that varies both within the picture and over time. If a constant-bit-rate channel is used to transmit the data, then the picture quality must be varied to avoid buffer overflow and underflow. Variable-bit-rate channels offer the promise of relatively constant image quality, as well as statistical multiplexing between users. However, with variable bit rates, buffer control and timing recovery are much less straightforward than with constant bit rate. Buffer control and policing functions, multiplexing of variable-rate bit streams, and timing recovery are discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Magnetic Resonance Imaging Effects of Interferon Beta-1b in the BENEFIT Study (2007)

Interferon beta-1b treatment had a robust effect on MRI measures, supporting its value as an early intervention in this patient group. This effect was maintained despite including patients who switched from placebo to interferon beta-1b in the active treatment group. Trial Registration clinicaltrials.gov Identifier: NCT00185211.
<title>Modified quantum-well infrared photodetector designs for high-temperature and long-wavelength operation</title> (1992)

A principal concern with the performance of GaAs/AlGaAs multiple quantum well long- wavelength detectors is obtaining high detectivity at relatively high temperatures. We have fabricated GaAs/AlGaAs quantum well infrared photodetectors (QWIPs) with graded barrier regions by varying the aluminum concentration during the barrier growth to improve high temperature performance. The effect of barrier grading has been characterized by the measurement of dark current and responsivity, leading to an evaluation of the temperature dependent detectivity. Detectivity of 2 X 10<SUP>9</SUP> cm(root)Hz/W at 100 K has been measured on graded barrier QWIPs. We also report on the investigation of QWIPs with cut- off wavelengths ((lambda) <SUB>c</SUB>) greater than 12 micrometers . A QWIP with (lambda) <SUB>c</SUB> approximately 13.8 micrometers was grown with peak responsivity (R<SUB>p</SUB>) of 1.2 A/W at 10 K. Both R<SUB>p</SUB> and (lambda) <SUB>c</SUB> were weakly bias dependent. The maximum detectivity of 6 X 10<SUP>12</SUP> cm(root)Hz/W was at 10 K at 11.7 micrometers and (lambda) <SUB>c</SUB> equals 14.5 micrometers .
Arrays of high temperature superconductor Josephson junctions (1993)

The authors present results on parallel, series, and two-dimensional arrays of high-temperature superconductor junctions. The parallel arrays show the expected field dependence of critical current and can function as vortex flow transistors. The series arrays give data about the spread in junction critical currents for the present process. The two-dimensional arrays show many of the phenomena previously observed in low-T/sub c/ technology, such as field frustration of the phase transition, some evidence for superlattice states, and the tentative indications of giant Shapiro steps, showing large-scale cooperative behavior in the device.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>