gebhart/patrepeval huggingface dataset:
Improved image quality of diffusion optical tomography through a deep learning based post-processing method (2023)

Diffusion Optical Tomography (DOT) is an emerging optical imaging modality with the advantages of being low-cost, non-invasive and non-damage-free, it has demonstrated great potential in differentiating benign and malignant breast tumors. However, due to the strong scattering of biological tissues and the limited number of boundary measurements, the DOT image reconstruction is ill-posed and ill-conditioned. Conventional DOT image reconstruction algorithms such as Tikhonov regularization, are easy to implement. Nevertheless, images with poor quality were usually achieved. In this paper, to improve the image quality of DOT, we develop a post-processing reconstruction algorithm based on deep learning. It has a type of U-net architecture, but with the low-quality image obtained with Tikhonov regularization and the acquired multi-wavelength optical signals as the input. Meanwhile, the output of the network is images of chromophores, including HbO, Hb and water. To train the proposed algorithm, we construct a dataset with 15,000 images for training, 6,000 for validation, and 3,900 for testing. Our results demonstrate that it has achieved good reconstruction results for the phantoms with single or double inclusions in terms of PSNR and SSIM. Compared to the Tikhonov regularization, the average PSNR of HbO, Hb and water are improved by 55%, 74% and 71%, respectively, and the average SSIM are improved by 11%, 76%, and 70%, respectively.
Orbital-dependent electric field effect on magnetism in ultrathin cobalt (2020)

Electric field modulations of magnetism in ferromagnetic metals are in general ascribed to the electric field effects on the orbitals. However, a direct observation of the electric-field-induced changes in the orbital states of a ferromagnetic metal is lacking. In this Rapid Communication, we demonstrate that an electric field applied to an ultrathin Co film can change the electron occupations according to the orbitals, combining x-ray absorption and x-ray magnetic circularly dichroism spectroscopies with the sum rules. Under a positive electric field, the ${d}_{xz(yz)}$-occupied states decrease mainly via the modification of orbital hybridizations, while the ${d}_{{z}^{2}}$-occupied state increases. The changes in the ${d}_{xz}$ and ${d}_{yz}$ states dominantly alter the Curie temperature.
Cardiovascular and Metabolic Effects of Adenosine A1-Receptor Agonists in Streptozotocin-Treated Rats (1997)

Because one manifestation of diabetes is an enhancement of the lipolytic process, we evaluated the antilipolytic effects of adenosine A1 agonists in vitro and in vivo in streptozotocin (STZ)-treated diabetic rats. In vitro, we examined the responses to norepinephrine (NE) and adenosine deaminase (ADA), as well as several adenosine A1 agonists, in isolated adipocytes from normal and diabetic rats. Both NE and ADA caused dose-dependent stimulation of lipolysis, elevating glycerol release twofold to threefold over baseline. The sensitivity to both NE and ADA was significantly enhanced in adipocytes from STZ-treated as compared with normal rats. N-5'-ethyl-N(6)(cyclopentyl) adenosine-5'-uronamide (RG14202) was by far the most potent A agonist in inhibiting NE-stimulated lipolysis [50% effective concentration (EC50): 0.014 +/- 0.0008 nM), approximately 1 and 2 log units more potent than N(6)-cyclopentyladenosine (CPA) and N(6)-cyclohexyl-2'-O-methyladenosine (SDZ WAG 994), respectively. In vivo we established a model for evaluating the therapeutic utility of adenosine A1 agonists, emphasizing duration of action. In STZ rats instrumented with telemetry transmitters, the metabolic effects of CPA, RG14202, and SDZ WAG 994 were assessed 6 h after oral administration. Under those conditions, RG14202 and SDZ WAG 994, but not CPA, significantly reduced triglycerides (TRIs) and TRI/free fatty acids (FFAs), respectively. However, all three A1 agonists dose-dependently reduced mean arterial pressure (MAP) and heart rate (HR) concurrently. Thus adenosine A1 agonists can inhibit lipolysis in vitro and in vivo; however, oral administration produces long-lasting beneficial metabolic effects only at doses that also produce a significant bradycardia.
Formula-based software debugging (2016)

Satisfiability modulo theory solvers can help automate the search for the root cause of observable software errors.
Challenges on providing services in a Ubiquitous, Mobile Environment (2006)

In this paper, some challenges for the providing service in a ubiquitous, mobile environment have been described. The first challenge is to provide the performance, the security is the other important challenge where its associations are formed with particular interfaces and the privacy also needed attention in a world that provides ubiquitous services. The design and development of the services brings their own set of challenges. It has to be designed such that they can function effectively in various resources and similarly it development needs careful thought. The other challenges such as novelty, desirability, testing and evaluation are also described in this paper
A 1-V Quasi Rail-to-Rail Operational Amplifier with a Single Input Differential Pair (2007)

A quasi rail-to-rail (VDD -Vdsa, -Vss) operational amplifier with a single differential pair is presented. A new common-mode adapter circuit based on a differential pair structure is proposed. With the common-mode adapter circuit, the common-mode input range is extended; the differential-mode signal is not affected. A two-stage operational amplifier with the proposed common-mode adapter is designed with TSMC 0.18 mum CMOS technology. With a 1 V supply voltage and a 15 pF capacitance load, the simulation shows the DC gain is about 82 dB, unity-gain frequency is about 6 MHz, and the phase margin is about 60deg.
Synchrotron infrared spectroscopy of OH-chondrodite and OH-clinohumite at high pressure (2002)

High-pressure synchrotron infrared (IR) absorption spectra were collected at ambient temperature for OH-chondrodite and OH-clinohumite up to 38 and 29 GPa, respectively, using argon as the pressure-transmitting medium. The crystal structures of both clinohumite and chondrodite are preserved up to the maximum pressure. However, disordering of the silicate framework appears to become more pronounced at high pressure based on significant broadening of the IR bands with increasing pressure. All three OH bands in both structures shift linearly to higher frequency with pressure up to 18 GPa. Above 18 GPa, the variation of OH frequency with pressure remains linear; however, the slopes for the three OH bands are significantly different as a result of different degrees of hydrogen bonding. The IR results are compared to those from recent Raman studies in which water was used as the pressure-transmitting medium.
Formation of PbS Nanowire Pine Trees Driven by Screw Dislocations (2009)

The basic characteristics of nanowire growth driven by screw dislocations were investigated by synthesizing hierarchical lead sulfide (PbS) nanowire "pine trees" using chemical vapor deposition of PbCl(2) and S precursors and systematically observing the effects of various growth parameters, such as hydrogen flow, temperature, pressure, and the growth substrates employed. Statistical surveys showed that the growth rate of the dislocation-driven trunk is about 6 mum/min and that of the vapor-liquid-solid (VLS) driven branch nanowire is about 1.2 mum/min under the typical reaction conditions at 600 degrees C, 900 Torr, and a hydrogen flow rate of 1.5 sccm. The onset of hydrogen flow plus the presence of fresh silicon have been identified as the critical ingredients for generating PbS nanowire trees reproducibly. To explain the experimental findings in the context of classical crystal growth theory, the former is suggested to create a spike in supersaturation of the actual sulfur precursor H(2)S and initiate dislocations with screw components that then propagate anisotropically to form the PbS nanowire trunks. Maintaining suitable hydrogen flow provides a favorable low supersaturation that promotes dislocation-driven trunk nanowire growth and enables the simultaneous VLS nanowire growth of branches. Furthermore, thermodynamic consideration and experiments showed that silicon fortuitously controls the supersaturation by reversibly reacting with H(2)S to form SiS(2) and that SiS(2) can also be a viable precursor for PbS nanowire growth. The key requirements of screw dislocation-driven nanowire growth are summarized. This study provides some general guidelines for further nanowire growth driven by screw dislocations.
Developing a Laser-Based Ionization Approach for Detecting Explosives with Ion Mobility Spectrometry (2008)

Rotationally resolved resonance-enhanced multiphoton ionization (REMPI) spectra of the NO photofragment from nitrobenzene have been observed for the A 2Σ+ − X 2Π (1, 0) transition. These spectra were collected in an atmospheric-pressure nitrogen bath.
COVID-19 patient serum less potently inhibits ACE2-RBD binding for various SARS-CoV-2 RBD mutants (2022)

As global vaccination campaigns against SARS-CoV-2 proceed, there is particular interest in the longevity of immune protection, especially with regard to increasingly infectious virus variants. Neutralizing antibodies (Nabs) targeting the receptor binding domain (RBD) of SARS-CoV-2 are promising correlates of protective immunity and have been successfully used for prevention and therapy. As SARS-CoV-2 variants of concern (VOCs) are known to affect binding to the ACE2 receptor and by extension neutralizing activity, we developed a bead-based multiplex ACE2-RBD inhibition assay (RBDCoV-ACE2) as a highly scalable, time-, cost-, and material-saving alternative to infectious live-virus neutralization tests. By mimicking the interaction between ACE2 and the RBD, this serological multiplex assay allows the simultaneous analysis of ACE2 binding inhibition to the RBDs of all SARS-CoV-2 VOCs and variants of interest (VOIs) in a single well. Following validation against a classical virus neutralization test and comparison of performance against a commercially available assay, we analyzed 266 serum samples from 168 COVID-19 patients of varying severity. ACE2 binding inhibition was reduced for ten out of eleven variants examined compared to wild-type, especially for those displaying the E484K mutation such as VOCs beta and gamma. ACE2 binding inhibition, while highly individualistic, positively correlated with IgG levels. ACE2 binding inhibition also correlated with disease severity up to WHO grade 7, after which it reduced.
Mutations in the phenylalanine hydroxylase gene: methods for their characterization (1994)

Mutations in the phenylalanine hydroxylase (PAH) gene represent the root cause of PAH-deficient hyperphenylalaninemia. To date, more than 160 different mutations have been reported. Single-base substitutions and microdeletions account for the majority of molecular defects. This review provides a brief general introduction to various strategies for detection of PAH mutations, and summarizes our own methodological developments. We have established a method based on PCR in combination with denaturing gradient gel electrophoresis (DGGE) for mutation scanning of the entire coding sequence and all exon/intron boundaries of the PAH. Systematic application of this method to the study of a large number of mutant chromosomes from hyperphenylalaninemic patients demonstrated a 98% diagnostic efficiency and a 100% mutation detection efficiency. We have created compromised PCR and DGGE conditions for simultaneous amplification and simultaneous mutation scanning of all PAH-coding fragments. This technique is convenient in a diagnostic setting and allows "same-day" DNA-based diagnosis of newborns with hyperphenylalaninemia. A further modification of the method allows unambiguous identification of known mutations, circumventing the cumbersome step of nucleotide sequencing.
Above- and Belowground Microclimate of Grow Tubes in an Organic Mulch-incorporated, Raised Bed System for Blueberry (2013)

Grow tubes are well established in forestry and are gaining attention in establishing some woody perennial crops. To date, microclimate descriptions have addressed the aboveground environment, but a mulched raised bed system with organic mulch-incorporated soil requires both the above- and belowground microclimate to be quantified. We measured the microclimate of commercially used, non-ventilated translucent and non-ventilated opaque grow tubes in a model crop of blueberry ( Vaccinium corymbosum L.) grown on sawdust-mulch-covered raised beds formed from sawdust-incorporated tilled soil. The differences in air temperature between tubes and ambient were consistent with those reported in the literature. Air temperature in translucent tubes was up to 19.7 °C higher than ambient. Differences in vapor pressure deficit were largely a function of differences in air temperature between tubes and ambient rather than actual vapor pressure. Stem temperatures were highest outside of the tubes as a result of radiation load. The surface temperature of ambient sawdust mulch (maximum 53 °C) was up to 14 °C above that in the translucent tube and 20 °C above that in the opaque tube. The largest gradients in the bed system were between the loose dry mulch and the soil–mulch interface. The presence of a grow tube did not influence soil temperature or its daily amplitude at 15 cm below the surface—the native tilled soil. Temperatures associated with the opaque tubes were between ambient and those in the translucent tubes. The temperature data indicate that both opaque and translucent unventilated grow tubes should influence shoot and crown growth but may have little influence on root growth in this shallow-rooted plant.
High-level optimization techniques for low-power multiplier design (2003)

While performance and area remain to be two major design goals, power consumption has become a critical concern in today's VLSI system design. Multiplication is a fundamental operation in most arithmetic computing systems. Multipliers have large area, long latency and consume considerable power. Previous work on low-power multipliers focuses on low-level optimizations and has not considered well the arithmetic computation features and application-specific data characteristics. 
At the algorithm and architecture level, this dissertation addresses low-power multiplier design systematically from two aspects: internal efforts considering multiplier architectures and external efforts considering input data characteristics. For internal efforts, we consider recoding optimization for partial product generation, operand representation optimization, and structure optimization of partial product reduction. For external efforts, we consider signal gating to de-activate portions of a full-precision multiplier. Several multiplier types are studied: linear array multipliers, leapfrog array multipliers, left-to-right linear array multipliers, split array multipliers, and tree multipliers. Experiments show that recoding optimization and structure optimization have achieved steady power reduction with reduced delay for both random test data and large-dynamic-range data. Operand representation optimization and signal gating have demonstrated significant power saving for large-dynamic-range data with relatively small overhead.
TowerDefense: Deployment strategies for battling against IP prefix hijacking (2010)

IP prefix hijacking is one of the top security threats targeting today's Internet routing protocol. Several schemes have been proposed to either detect or mitigate prefix hijacking events. However, none of these approaches is adopted and deployed on a large-scale on the Internet for reasons such as scalability, economical practicality, or unrealistic assumptions about the collaborations among ISPs. Thus there are no actionable and deployable solutions for dealing with prefix hijacking. In this paper, we study key issues related to deploying and operating an IP prefix hijacking detection and mitigation system. Our contributions include (i) deployment strategies for hijacking detection and mitigation system (named as TowerDefense): a practical service model for prefix hijacking protection and effective algorithms for selecting agent locations for detecting and mitigating prefix hijacking attacks; and (ii) large scale experiments on PlanetLab and extensive analysis on the performance of TowerDefense.
Dose-intensified ONC201 to exert anti-metastatic efficacy and to promote intra-tumoral recruitment of NK-cells in mice. (2016)

11550 Background: ONC201 is a novel, first-in-class, orally active anti-tumor agent that upregulates the cytotoxic ligand TRAIL and activates an integrated stress response, leading to upregulation of death receptor 5 in bulk tumor and cancer stem cells. ONC201 is being evaluated in multiple clinical trials, where it has demonstrated safety and a preliminary efficacy signal. In the first-in-human trial, patients were dosed every 3 weeks. We investigated dose-intensification of ONC201 to determine whether a higher dose and frequency schedule could impact efficacy with limited toxicity. Methods: HT-29-luciferase, HCT116 p53-null, and MDA-MB-231-luciferase xenografts were treated with ONC201 at doses ranging from 25 mg/kg to 100 mg/kg and frequencies ranging from twice per week to once every 1, 2, 3, or 4 weeks. Results: ONC201 exerted a dose- and schedule-dependent effect on tumor progression in vivo. ONC201 potently suppressed Akt and ERK in a dose- and frequency-dependent manner in vivo, and TRAIL serum levels were impacted by drug frequency. In mouse xenograft models we noted a potent anti-metastatic effect. In culture, ONC201 negatively impacted cancer cell migration and invasion, even in cells that are resistant to ONC201-induced apoptosis. We observed accumulation of CD3+/NK1.1+ cells within ONC201-treated tumors in athymic nude mice, and an upregulation of NK1.1+ cells in C57/BL6 mice without tumor xenografts. The accumulation of CD3+/NK1.1 cells within ONC201-treated tumors appeared more pronounced with dose intensification and is currently being investigated in syngeneic models. Conclusions: These results prompted a phase I dose intensification clinical trial at Fox Chase Cancer Center that is actively enrolling patients. We are evaluating the characteristics and function of the CD3+/NK1.1+ cells and the relationship of their intra-tumoral accumulation to the observed anti-tumor effects of ONC201. Our results present evidence of the unique and potent nature of ONC201 as an anti-tumor agent that demonstrates efficacy, reduces or prevents metastasis, and increases NK cell recruitment to tumors.
Stratified Generalized Procrustes Analysis (2010)

Generalized procrustes analysis computes the best set of transformations that relate matched shape data. In shape analysis the transformations are usually chosen as similarities, while in general statistical data analysis other types of transformation groups such as the affine group may be used. Generalized procrustes analysis has a nonlinear and nonconvex formulation. The classical approach alternates the computation of a so-called reference shape and the computation of transformations relating this reference shape to each shape datum in turn.

We propose the stratified approach to generalized procrustes analysis. It first uses the affine transformation group to analyze the data and then upgrades the solution to the sought after group, whether Euclidean or similarity. We derive a convex formulation for each of these two steps, and efficient practical algorithms that gracefully handle missing data (incomplete shapes).

Extensive experimental results show that our approaches perform well on simulated and real data. In particular our closed-form solution gives very accurate results for generalized procrustes analysis of Euclidean data.
Design of Adiabatic Connections for Ultra-Low-Loss Waveguides (2013)

We propose a variational approach to design adiabatic waveguide connections with minimal intermodal coupling. A design of the “S-bend” of whispering-gallery spiral waveguides is demonstrated with approximately 0.05dB insertion loss.
Laser surgical effects with concentrated solar radiation (2002)

Surgical tissue transformations normally produced with lasers are demonstrated experimentally with highly concentrated sunlight. Our solar surgery prototype decouples the collection and delivery of high-density photon flux: a compact (200 mm) optical system outdoors, with several watts of concentrated solar radiation transported into the operating theater by a flexible, high-transmissivity optical fiber up to 20 m long, at power densities typical of surgical lasers. Measurements of the rates of tissue coagulation, dehydration, and ablation generated with solar surgery on chicken breast are consistent with the corresponding rates produced by common visible and near-infrared surgical lasers. Solar surgery offers an inexpensive alternative to surgical lasers, albeit with limitations on feasible locations and operating periods.
A chemically synthesized peptoid‐based drag‐tag enhances free‐solution DNA sequencing by capillary electrophoresis (2011)

We report a capillary-based DNA sequencing read length of 100 bases in 16 min using end-labeled free-solution conjugate electrophoresis (FSCE) with a monodisperse poly-N-substituted glycine (polypeptoid) as a synthetic drag-tag. FSCE enabled rapid separation of single-stranded (ss) DNA sequencing fragments with single-base resolution without the need for a viscous DNA separation matrix. Protein-based drag-tags previously used for FSCE sequencing, for example, streptavidin, are heterogeneous in molar mass (polydisperse); the resultant band-broadening can make it difficult to obtain the single-base resolution necessary for DNA sequencing. In this study, we synthesized and HPLC-purified a 70mer poly-N-(methoxyethyl)glycine (NMEG) drag-tag with a molar mass of - 11 kDa. The NMEG monomers that comprise this peptoid drag-tag are interesting for bioanalytical applications, because the methoxyethyl side chain's chemical structure is reminiscent of the basic monomer unit of polyethylene glycol, a highly biocompatible commercially available polymer, which, however, is not available in monodisperse preparation at an - 11 kDa molar mass. This is the first report of ssDNA separation and of four-color, base-by-base DNA sequencing by FSCE through the use of a chemically synthesized drag-tag. These results show that high-molar mass, chemically synthesized drag-tags based on the polyNMEG structure, if obtained in monodisperse preparation, would serve as ideal drag-tags and could help FSCE reach the commercially relevant read lengths of 100 bases or more.
Taming vibration demons with flexible couplings (2005)

Unless it is dealt with effectively, torsional vibration can wreck a power transmission system and the pump it is driving. Alan Dean of Renold Hi-Tec Couplings examins the problem and highlights the advantages of of rubber-in-compression couplings in providing a solution.
A quantitative evaluation of rheumatoid arthritic activity with Tc-99m HEDP. (1977)

In an attempt to develop a quantitative method of evaluating rheumatoid arthritic activity, Tc-99m HEDP joint uptake values and joint-to-bone ratios were studied in ten adult rheumatoid arthritic patients and 17 nonarthritic patients. A joint-to-bone activity ratio of 1.8 at the fourth hour after injection (RA Index) discriminated clinically active rheumatoid arthritic joints from control joints with 95% accuracy. Serial studies on five patients during drug trial demonstrated a positive correlation between RA Index and the clinical manifestations of rheumatoid arthritic activity. The RA Index may be a useful quantitative parameter for evaluation of rheumatoid arthritic activity following therapy.