gebhart/patrepeval huggingface dataset:
A gene for familial psoriasis susceptibility maps to the distal end of human chromosome 17q (1994)

Psoriasis is a chronic inflammatory dermatosis that affects approximately 2% of the population. A gene for psoriasis susceptibility was localized to the distal region of human chromosome 17q as a result of a genome wide linkage-analysis with polymorphic microsatellites and eight multiply affected psoriasis kindreds. With one large kindred a maximum two-point lod score with D17S784 was 5.70 at 15% recombination. Heterogeneity testing indicated that psoriasis susceptibility in 50% of the families was linked to distal 17q. Susceptibility to psoriasis has repeatedly been found to be associated with HLA-Cw6 and associated HLA alleles. We therefore genotyped the families for loci within and flanking HLA; these included PCR assays for susceptibility alleles. By lod score analysis no evidence of linkage of psoriasis susceptibility to HLA was detected. The distribution of HLA-Cw6 and HLA-Class II alleles showed that HLA-Cw6 was frequent among patients, particularly in 4 of the 5 unlinked families. All affected members of two of these unlinked families carried HLA-Cw6 (empirical P values of 0.027 and 0.004). In 2 other families 4 of 6 and 6 of 7 had HLA-Cw6. In some of these families, an inability to detect linkage to HLA may have been due to the occurrence ofmore » multiple haplotypes carrying the psoriasis associated allele, HLA-Cw6. Contrasting with these findings, we observed a lack of association between HLA-Cw6 and psoriasis in the 3 families in which 17q markers were linked to susceptibility. The ability to detect linkage to 17q confirms that some forms of familial psoriasis are due to molecular defects at a single major genetic locus other than HLA.« less
Emission properties of a defect cavity in a two-dimensional photonic bandgap crystal slab (2000)

A single isolated defect within a two-dimensional photonic crystal semiconductor slab is shown to provide a lithographically tunable doubly degenerate emission resonance within the photonic bandgap, with a measured quality factor (Q) of 80–150, depending on the cavity geometry. Spontaneous emission outside the cavity linewidth is below the measurement limit of our system. Stimulated emission from this photonic crystal defect cavity is demonstrated at room temperature under pulsed optical pumping in spite of the large surface-to-volume ratio of this cavity and the associated large nonradiative surface recombination rate.
Mechanical characterization of a bifunctional Tetronic hydrogel adhesive for soft tissues (2014)

Although a number of tissue adhesives and sealants for surgical use are currently available, attaining a useful balance in high strength, high compliance, and low swelling has proven difficult. Recent studies have demonstrated that a four-arm poly(propylene oxide)-poly(ethylene oxide) block copolymer, Tetronic, can be chemically modified to form a hydrogel tissue adhesive (Cho et al., Acta Biomater 2012;8:2223-2232; Barrett et al., Adv Health Mater 2012;1-11; Balakrishnan, Evaluating mechanical performance of hydrogel-based adhesives for soft tissue applications. Clemson University, All Theses, Paper 1574: Tiger Prints; 2013). Building on the success of these studies, this study explored bifunctionalization of Tetronic with acrylates for chemical crosslinking of the hydrogel and N-hydroxysuccinimide (NHS) for reaction with tissue amines. The adhesive bond strengths of various uni and bifunctional Tetronic blends (T1107 ACR: T1107 ACR/NHS) determined by lap shear testing ranged between 8 and 74 kPa, with the 75:25 (T1107 ACR: T1107 ACR/NHS) blend displaying the highest value. These results indicated that addition of NHS led to improvement of tissue bond strength over acrylation alone. Furthermore, ex vivo pressure tests using the rat bladder demonstrated that the bifunctional Tetronic adhesive exhibited high compliance and maintained pressures under hundreds of filling and emptying cycles. Together, the results of this study provided evidence that the bifunctional Tetronic adhesive with a proper blend ratio may be used to achieve an accurate balance in bulk and tissue bond strengths, as well as the compliance and durability for soft tissue such as the bladder.
Achievement of Energy Focus for Distance-of-Flight Mass Spectrometry with Constant Momentum Acceleration and an Ion Mirror (2007)

Distance-of-flight mass spectrometry (DOF-MS) has not yet been implemented, though it has many potential advantages in a variety of applications. Impeding the implementation of DOF-MS is the development of the required array detectors and working out the equivalents to the focusing methods now used in time-of-flight (TOF) mass analyzers. Ideally, a batch of ions composed of a variety of m/z values, despite initial distributions of space and energy, would be spatially focused at their respective flight distances at the same time. First-order energy focusing, including ion turnaround, is shown to be accomplished by the use of an ion mirror in conjunction with constant momentum acceleration of the initial ion packet. The initial spatial dispersion is maintained throughout the flight path. With zero initial spatial ion spread, energy focusing to achieve resolutions in the tens of thousands is shown to be feasible with ions from the elemental and isotope ratio mass regions through the extremely high m/z range. With moderate spatial spread taken into account, the DOF-MS approach is shown to achieve resolutions competitive with quadrupole and ion trap mass analyzers. Advantages of DOF-MS include all the advantages of TOF-MS plus simpler detector electronics and the improved signal-to-noise ratio and dynamic range afforded by array detection.
Insulin inhibits ATP release from human erythrocytes (2006)

Erythrocytes (RBCs) release ATP via a signal transduction pathway involving both the G protein Gi and increases in cAMP. In non‐erythroid tissue, insulin has been shown to stimulate phosphodiesterase 3 (PDE3) resulting in the hydrolysis of cAMP. Although PDE activity within the RBC has not been fully characterized, incubating human RBCs with a PDE 3 inhibitor, cilostazol (100 μM), increased cAMP in these cells from 1.5±0.1 to 2.0±0.3 pmole (normalized to 5x10 8 RBC/mm 3 , n=12, P<0.05). Here, using mastoparan 7 (MAS 7) to activate Gi, we investigated the hypothesis that insulin reduces cAMP in RBCs and, thereby, decreases ATP release. RBCs from healthy humans were incubated with MAS 7 in the presence or absence of insulin (1 μM). Importantly, insulin alone had no effect on basal levels of cAMP or ATP release. In contrast, ATP release induced by MAS 7 (10 μM) was decreased in the presence of insulin from 1.2±0.2 to 0.78±0.1 μM (normalized to 4x10 5 RBC/mm 3 , n=5, P<0.05). Furthermore, the amount of cAMP in RBCs was decreased in the presence of insulin from 2.9±0.4 to 2.2±0.3 pmole (normalized to 5x10 8 RBC/mm 3 , n=6, P<0.05). These studies support the hypothesis that insulin, by decreasing cAMP accumulation, limits ATP release from RBCs in response to activation of Gi. These findings also suggest that PDE3 activity is present in human RBCs. One interpretation of these results is that increased plasma insulin levels in humans with insulin resistance could be detrimental to the ATP release from RBCs and could contribute to vascular complications in these individuals. Supported by NIH grants HL‐64180 and HL‐51298 and an ADA Innovation Award.
A new co-optimization model for grid scale storage units in energy and frequency regulation markets (2016)

Grid scale storage (GSS) units can participate in day-ahead electricity markets to provide energy and frequency regulation (FR) services to the grid. The uncertainties in real-time FR signal can result in inability of GSS units to provide the FR service according to the market schedule due to their limited energy and power capacities. In this paper, we develop a new co-optimization model that provides the optimal schedule for a GSS unit to maximize its revenue in day-ahead energy and FR markets while fulfilling its commitments with a high confidence level. The uncertainties in the FR signal are captured by defining two pairs of capacity deployment factors. Our model can also include duty cycle-based charging/discharging patterns that GSS units must follow to provide investment deferral services to the grid. Two case studies are presented to evaluate the performance of the proposed method.
Proximity-driven metallopeptide catalysis: Remarkable side-chain scope enables modification of the Fos bZip domain (2011)

Coiled-coil assembly of substrate peptides with dirhodium metallopeptide catalysts enables side-chain modification on the basis of molecular shape. A wide range of amino acids are effectively modified, including the first examples of carboxamide (glutamine and asparagine) modification. The method is used to achieve covalent modification of the c-Fos bZip domain at different residues, depending on the metallopeptide structure. By combining promiscuous catalytic reactivity with specific molecular recognition, this work establishes a general strategy for protein modification on the basis of molecular shape. A broad range of peptide–protein interactions are potentially amenable to this approach.
Tuneable Electromagnetic Bandgap Structures Based on Ba0.25Sr0.75Ti03 Parallel-Plate Varactors on Silicon Coplanar Waveguides (2003)

Experimental performance of Electromagnetic Band Gap (EBG) structures, based on Coplanar Waveguides (CPW) periodically loaded by high-Q-factor ferroelectric varactors is reported. The varactors are made of Ba0.25Sr0.75Ti03 films grown by laser ablation on thick Pt/Au/Pt electrodes. Due to the thick bottom electrodes the varactors have Q-factor larger than 40 at 45 GHz, which is higher in comparison with semiconductor varactors. Up to 30% tuning of the pass band edge is achieved at -20 dB level under 25V DC bias.
Experimental System Prototype of a Portable, Low-Cost, C-Scan Ultrasound Imaging Device (2008)

A system prototype of a future compact, low-cost medical ultrasound device is described and presented with experimental results. The prototype system consists of a 32 x 32 element, fully sampled 2-D transducer array and a printed circuit board (PCB) containing 16 custom "front-end" receive channel integrated circuits (ICs) with analog multiplexing and programmable logic. A PC that included a commercially available data acquisition card is used for data collection and analysis. Beamforming is performed offline using the direct sampled in-phase/quadrature (DSIQ) algorithm. Pulse-echo images obtained with the prototype are presented. Results from this prototype support the feasibility of a low-cost, pocket-sized, C-scan imaging device.
Room Acoustic Response Modeling and Equalization with Linear Predictive Coding and Parametric Filters for Speech and Audio Enhancement (2006)

Room acoustic response modeling is a challenging problem. Typical applications include speech dereverberation and loudspeaker correction. Traditionally, infinite-duration impulse response (IIR) or finite-duration impulse response (FIR) filters have been used for acoustic response modeling and equalization. The IIR filter, also called a parametric filter, has a bell-shaped magnitude response and is characterized by its center frequency, the gain at the center frequency, and a Q factor (which is inversely related to the bandwidth of the filter) and is easily implemented as a cascade for purposes of room response modeling and equalization. In this paper we present a technique for determining the coefficients of a second order IIR using a linear predictive coding (LPC) model, where the poles or roots of a high-order LPC dictate the parameters of the parametric filter. Due to the band interactions between the IIR filters, forming the cascade to model the room response, we also present a technique to optimize the Q values so as to better characterize the room response. An accurate model allows for better equalization, for correcting the loudspeaker and room acoustics for speech/audio enhancement, particularly at low frequencies. Alternatively, this technique can be utilized for speech dereverberation applications where the room responses have been estimated a priori. The advantages of the proposed method is the fast computation of the IIR filter parameters, from to the LPC model, since (i) the LPC model is efficient to compute since it uses the Levinson-Durbin recursion to solve the normal equations that arise from the least squares formulation, and (ii) a reasonably high-order LPC model is able to accurately model the low-frequency room response modes.
Two pathogenicity islands in uropathogenic Escherichia coli J96: cosmid cloning and sample sequencing (1996)

Many of the virulence genes of pathogenic strains of Escherichia coli are carried in large multigene chromosomal segments called pathogenicity islands (PAIs) that are absent from normal fecal and laboratory K-12 strains of this bacterium. We are studying PAIs in order to better understand factors that govern virulence and to assess how such DNA segments are gained or lost during evolution. The isolation and sample sequencing of a set of 11 cosmid clones that cover all of one and much of a second large PAI in the uropathogenic E. coli J96 are described. These PAIs were mapped to the 64- and 94-min regions of the E. coli K-12 chromosome, which differ from the locations of three PAIs identified in other pathogenic E. coli strains. Analysis of the junction sequences with E. coli K-12-like DNAs showed that the insert at 94 min is within the 3' end of a phenylalanine tRNA gene, pheR, and is flanked by a 135-bp imperfect direct repeat. Analysis of the one junction recovered from the insert at 64 min indicated that it lies near another tRNA gene, pheV. To identify possible genes unique to these PAIs, 100 independent subclones of the cosmids were made by PstI digestion and ligation into a pBS+ plasmid and used in one-pass sample DNA sequencing from primer binding sites at the cloning site in the vector DNA. Database searches of the J96 PAI-specific sequences identified numerous instances in which the cloned DNAs shared significant sequence similarities to adhesins, toxins, and other virulence determinants of diverse pathogens. Several likely insertion sequence elements (IS100, IS630, and IS911) and conjugative R1 plasmid and P4 phage genes were also found. We propose that such mobile genetic elements may have facilitated the spread of virulence determinants within PAIs among bacteria.
Conversion of compatible plant–pathogen interactions into incompatible interactions by expression of the <i>Pseudomonas syringae</i> pv. <i>syringae</i> 61 <i>hrmA</i> gene in transgenic tobacco plants (2000)

The hrmA gene from Pseudomonas syringae pv. syringae has previously been shown to confer avirulence on the virulent bacterium P. syringae pv. tabaci in all examined tobacco cultivars. We expressed this gene in tobacco plants under the control of the tobacco Delta0. 3 TobRB7 promoter, which is induced upon nematode infection in tobacco roots (Opperman et al. 1994, Science, 263, 221-223). A basal level of hrmA expression in leaves of transgenic plants activated the expression of pathogenesis-related genes, and the transgenic plants exhibited high levels of resistance to multiple pathogens: tobacco vein mottling virus, tobacco etch virus, black shank fungus Phytophthora parasitica, and wild fire bacterium Pseudomonas syringae pv. tabaci. However, the hrmA transgenic plants were not significantly more resistant to root-knot nematodes. Our results suggest a potential use of controlled low-level expression of bacterial avr genes, such as hrmA, in plants to generate broad-spectrum resistance to bacterial, fungal and viral pathogens.
A new non-invasive approach for early classification of renal rejection types using diffusion-weighted MRI (2016)

Although renal biopsy remains the gold standard for diagnosing the type of renal rejection, it is not preferred due to its invasiveness, recovery time (1-2 weeks), and potential for complications, e.g., bleeding and/or infection. Therefore, there is an urgent need to explore a non-invasive technique that can early classify renal rejection types. In this paper, we develop a computer-aided diagnostic (CAD) system that can classify acute renal transplant rejection (ARTR) types early via the analysis of apparent diffusion coefficients (ADCs) extracted from diffusion-weighted (DW) MRI data acquired at low-(accounting for perfusion) and high-(accounting for diffusion) b-values. The developed framework mainly consists of three steps: (i) data co-alignment using a 3D B-spline-based approach (to handle local deviations due to breathing and heart beat motions) and segmentation of kidney tissue with an evolving geometric (level-set based) deformable model guided by a voxel-wise stochastic speed function, which follows a joint kidney-background Markov-Gibbs random field model accounting for an adaptive kidney shape prior and visual kidney-background appearances of DW-MRI data (image intensities and spatial interactions); (ii) construction of a cumulative empirical distribution of ADC at low and high b-values of the segmented kidney accounting for blood perfusion and water diffusion, respectively, to be our discriminatory ARTR types feature; and (iii) classification of ARTR types (acute tubular necrosis (ATN) anti-body- and T-cell-mediated rejection) based on deep learning of a non-negative constrained stacked autoencoder. Results show that 98% of the subjects were correctly classified in our “leave-one-subject-out” experiments on 39 subjects (namely, 8 out of 8 of the ATN group and 30 out of 31 of the T-cell group). Thus, the proposed approach holds promise as a reliable non-invasive diagnostic tool.
Recent Advances in the Development of HIV-1 Tat-Based Vaccines (2004)

Over the last two decades most of the efforts in HIV vaccine development have been based on the use of the HIV Env with the goal to induce sterilizing immunity. However, as a result of Env variability disappointing results have been obtained in preclinical and phase III clinical trials. Although the objective of a preventive immunity still remains a priority, secondary endpoints (e.g. block of virus replication and disease onset) are being considered at the present as more achievable end-points in HIV vaccine development. This is based on accumulating evidence indicating that low viral load correlates with maintenance of immune functions and slow progression to disease, and that cell-mediated immunity plays a major protective role in the absence of sterilizing immunity. The promising results obtained in non-human primates with a vaccine based on a native Tat protein (B-clade), which is an early regulatory protein key for HIV replication and AIDS pathogenesis, highlights the importance of targeting the virus very early after infection. In particular, the immune response against Tat appears to modify the virus-host interactions at the very beginning of infection, thus containing the depletion of critical immune cells and the progression of infection. Moreover, since Tat targets and induces maturation of dendritic cells, has immunomodulatory activities and drives Th-1 and CTL responses, immunization with Tat may drive or increase these immune responses also against other HIV antigens to support an effective, long-lasting and hopefully even sterilizing antiviral immunity. Finally, Tat B-clade is similarly recognized by sera from individuals infected by different virus clades (A, B, C, D) supporting the concept of a cross-clade vaccine. Therefore, the Tat-vaccine should contain virus replication protecting from disease progression (non-sterilizing immunity) or even favoring an abortive infection. Although only a phase III clinical trial will establish the efficacy of this vaccine strategy, the Tat-vaccine has recently entered preventive and therapeutic phase I clinical testing in Italy to establish safety (primary-end-point) and immunogenicity (secondary end-point) and phase II studies are being prepared.
Integrated photonics using asymmetric twin-waveguide structures (2002)

We demonstrate a number of integrated photonic devices using a twin-waveguide (TG) based technique. The asymmetric TG structure has vertically stacked active and passive waveguides grown in a single epitaxial growth step. All integrated components are defined by post-growth patterning, and tapered mode transformers provide efficient coupling between active and passive sections. Devices made from the same base wafer include single-frequency DBR lasers, semiconductor optical amplifiers and electroabsorption modulators integrated with passive components such as 3 dB couplers, grating sections and Mach-Zehnder interferometers.
Iterative reconstruction for differential phase contrast imaging using spherically symmetric basis functions (2011)

IR algorithms have a wide spectrum of proven advantages in the area of conventional computed tomography. The present work describes for the first time, how a matched forward and back-projection can be implemented for DPCI, which is furthermore free of any heuristics. The newly developed ML reconstruction algorithm for DPCI shows that for the case of sparsely sampled projection data, an improvement in image quality is obtained that is qualitatively comparable to a corresponding situation in conventional x-ray imaging. Based on the proposed operators for forward and back-projection, a large variety of IR algorithms is thus made available for DPCI.
Near Real-Time Return-on-Fracturing-Investment ROFI Optimization for Shale Fracturing by Integrating Anisotropic Acoustic Interpretation, 3D Fracture Modeling, and Neural Networks (2017)

Abstract Current fracturing designs based on 3D fracture modeling have two major issues. First, most current commercial simulators do not account for shale mechanical anisotropy. Second, running fracture simulation coupled with reservoir simulation for the purpose of return-on-fracturing-investment (ROFI) optimization is time consuming, particularly if numerous cases have to be run for parametric study of multiple stimulation treatment parameters including perforating/staging parameters, pumping parameters, proppant and fluid properties, etc. This paper proposes a robust, near real-time workflow with improved prediction of fracture geometry in anisotropic formations for shale fracturing optimization. The workflow has four key steps. The anisotropic models are used to predict an isotropic elastic moduli and closure stress from sonic and density logs. Based on the existence of the Stoneley wave velocity, one can choose Stoneley methods such as ANNIE (Schoenberg et al. 1996) and M-ANNIE 1 (Quirein et al. 2014) or non-Stoneley methods, (Murphy et al. 2015) such as V-reg, M-ANNEI 2, or their combinations. The log interpreted mechanical properties are then input into a 3D fracture simulator to run different cases by varying the treatment parameters. The critical conductivity concept is used to determine the effective propped area (EPA) from the simulation results. Third, input (treatment parameters) and output (EPA) pairs are used to train and validate the neural network (NN) model. Finally, analytical solutions for the linear transient flow regime and boundary dominant flow regime (Wattenbarger et al. 1998) are applied in combination with NN predicted EPA to estimate time-dependent productions and ROFI. Parametric studies can be conducted through NN modeling to investigate the impact of each treatment parameter on the ROFI. Finally, the workflow is applied to optimize one shale example. The results show that the first year ROFI can be improved by 50% after optimizing the perforating and pumping strategy through the workflow.