gebhart/patrepeval huggingface dataset:
Diseases esulting fro Point Mutations (1992)

Summary: A number of mitochondrial DNA (mtDNA) mutations have been identified which cause familial, late onset neuromuscular degenerative diseases. These include missense mutations in most of the mtDNA polypeptide genes as well as base substitutions in several tRNA genes. Missense mutations in the mitochondrial electron-transport genes cause Leber hereditary optic neuropathy. Ten mutations have been associated with this disease, but four at rips 11 178, 3460, 4160 and 15257 appear sufficient in themselves to cause the disease. One missense mutation in the ATPase 6 gene at np 8993 causes a second phenotype, neurogenic muscle weakness, ataxia and retinitis pigmentosum. Transfer RNA mutations have been identified for myoclonic epilepsy and ragged-red fibre disease in the tRNA Ly~ gene at np 8344 and for the mitochondrial encephalomyopathy, lactic acidosis and stroke-like episodes syndrome and for maternal mitochondrial myopathy and cardiomyopathy syndrome in the tRNA Leu~UUR) gene at nps 3234 and 3260, respectively. Deficiencies in mitochondrial oxidative phosphorylation enzymes have been observed in several common neurodegenerative diseases such as Alzheimer and Parkinson diseases. Perhaps mtDNA mutations play a role in these as well. MATERNALLY INHERITED DISEASES A number of hereditary diseases have recently been found to result from point mutations in the mitochondrial DNA (mtDNA). These diseases show maternal transmission, consistent with the maternal inheritance of the mtDNA. However, in contrast to the mtDNA, the phenotypes of the diseases are not strictly maternally inherited, as phenotypes can appear sporadically and disease expression can vary significantly within pedigrees. It is now clear that this is the consequence of a number of other unique aspects of mtDNA genetics.
Design and Synthesis of Inhibitors of Hedgehog Signaling Based on the Alkaloid Cyclopamine (2009)

The synthesis and biological evaluation of structurally simplified, metabolically stable cyclopamine-like Sonic Hedgehog (SHH) signaling inhibitors, i.e., 5, is described in four chemical steps from commercially available steroidal precursors. Biological evaluation of this cyclopamine analogue in two different systems establishes the high potency of 5 as a SHH signaling inhibitor. This approach provides important new lead structures for the development of new cancer chemotherapeutic agents based on the inhibition on SHH signaling.
Exact Tuning of High-Q Optical Microresonators by Use of UV (2006)

In one of several alternative approaches to the design and fabrication of a whispering-gallery optical microresonator of high resonance quality (high Q), the index of refraction of the resonator material and, hence, the resonance frequencies. In this approach, a microresonator structure is prepared by forming it from an ultraviolet-sensitive material. Then the structure is subjected to controlled exposure to UV light while its resonance frequencies are monitored.
Analysis with monoclonal antibodies of the molecular and cellular heterogeneity of human high molecular weight melanoma associated antigen. (1987)

Monoclonal antibodies (MoAbs) 225.28, 657.9, and 902.5 recognizing distinct epitopes of the human high molecular weight melanoma associated antigen (HMW-MAA) were used to investigate the molecular and cellular heterogeneity of the HMW-MAA synthesized by human melanoma cells. Sequential immunodepletion and immunoprecipitation experiments showed that not all HMW-MAA molecules synthesized by a melanoma cell line express the antigenic determinants recognized by the three monoclonal antibodies. The majority of the HMW-MAA molecules expressed the epitope defined by MoAb 657.9 since this monoclonal antibody depleted the melanoma cell lysate of all antigen molecules recognized by the other two monoclonal antibodies. Depletion with MoAb 902.5 resulted in the removal of a large proportion of the HMW-MAA molecules precipitated by MoAb 657.9. The MoAb 225.28 depleted the cell lysate of only a fraction of the HMW-MAA molecules recognized by MoAb 657.9 and 902.5. Two-dimensional gel electrophoresis and peptide mapping analysis did not detect any significant difference among the HMW-MAA immunoprecipitated by the three monoclonal antibodies. The heterogeneity of the epitopes recognized by the three monoclonal antibodies is, at least partly, due to glycosylation of the antigen molecule, since treatment of melanoma cells with glycosidases differentially affects their ability to bind the three anti-HMW-MAA monoclonal antibodies. Fluorescent activated cell sorting analysis of the melanoma cells showed that the heterogeneity exhibited by the HMW-MAA is not due to the presence of different cell clones in the culture but reflects a differential distribution of epitopes on the HMW-MAA expressed on the surface of individual cells. Immunohistochemical staining of surgically removed benign and malignant lesions of melanocytic origin, of normal tissues, and of malignant lesions has shown a differential tissue distribution of the determinants recognized by the three monoclonal antibodies. Staining of melanoma cell lines and of surgically removed melanoma lesions with combinations of the three monoclonal antibodies did not cause any significant change of the percentage of stained cells but markedly increased the intensity of staining. These results indicate that combinations of monoclonal antibodies to distinct determinants of HMW-MAA can markedly increase the sensitivity of immunohistochemical techniques to detect melanoma cells.
Signal-based classical emulation of a universal quantum computer (2015)

In this paper we present a novel approach to emulating a universal quantum computer with a classical system, one that uses a signal of bounded duration and amplitude to represent an arbitrary quantum state. The signal may be of any modality (e.g., acoustic, electromagnetic, etc), but we focus our discussion here on electronic signals. Unitary gate operations are performed using analog electronic circuit devices, such as four-quadrant multipliers, operational amplifiers, and analog filters, although non-unitary operations may be performed as well. In this manner, the Hilbert space structure of the quantum state, as well as a universal set of gate operations, may be fully emulated classically. The required bandwidth scales exponentially with the number of qubits, however, thereby limiting the scalability of the approach, but the intrinsic parallelism, ease of construction, and classical robustness to decoherence may nevertheless lead to capabilities and efficiencies rivaling that of current high performance computers.
CFTR with a partially deleted R domain corrects the cystic fibrosis chloride transport defect in human airway epithelia <i>in vitro</i> and in mouse nasal mucosa <i>in vivo</i> (2002)

In developing gene therapy for cystic fibrosis (CF) airways disease, a transgene encoding a partially deleted CF transmembrane conductance regulator (CFTR) Cl- channel could be of value for vectors such as adeno-associated virus that have a limited packaging capacity. Earlier studies in heterologous cells indicated that the CFTR R (regulatory) domain is predominantly random coil and that parts of the R domain can be deleted without abolishing channel function. Therefore, we designed a series of CFTR variants with shortened R domains (between residues 708 and 835) and expressed them in well-differentiated cultures of CF airway epithelia. All of the variants showed normal targeting to the apical membrane, and for the constructs we tested, biosynthesis was like wild type. Moreover, all constructs generated transepithelial Cl- current in CF epithelia. Comparison of the Cl- transport suggested that the length of the R domain, the presence of phosphorylation sites, and other factors contribute to channel activity. A variant deleting residues 708-759 complemented CF airway epithelia to the same extent as wild-type CFTR and showed no current in the absence of cAMP stimulation. In addition, expression in nasal mucosa of CF mice corrected the Cl- transport defect. These data provide insight into the structure and function of the R domain and identify regions that can be deleted with retention of function. Thus they suggest a strategy for shortening the transgene used in CF gene therapy.
Accurate Prediction Method for Energy Consumption in Automatic Tool Changing Process of Computer Numerical Control Lathe (2019)

In order to achieve accurate prediction of energy consumption in the automatic tool change process of Computer Numerical Control (CNC) lathe and provide a basic model for energy saving optimization of CNC lathe, an accurate prediction method is proposed for energy consumption in the automatic tool changing process for computer numerical control lathe. The method firstly measures the duration of automatic tool changing under multiple sets of rotary cutters by fitting the measured value. The energy consumption of the basic module of the machine tool is obtained by calculating the measured value which is based on the basic module power of the machine tool and the duration of the automatic tool changing. And the steady state energy consumption of the tool changer is obtained by calculating the measured value. By obtaining the energy consumption caused by all the power peaks in the automatic tool changing process of CNC lathe, the transient state energy consumption of the tool changer is got. The whole energy consumption is consisted of the basic module of the machine tool, the steady state of the tool changer and the transient state of the tool changer. Finally, a case study of energy modelling and analysis for a CK6153i CNC lathe finds that the prediction accuracy is above 95%, which indicates that the research can accurately predict the energy consumption of the CNC lathe in the tool changing process.
Leakage Optimization of Labyrinth Seals Using a Navier-Stokes Code (1994)

It has been demonstrated that design optimization of labyrinth seals using the present numerical model is quite beneficial. The results shown include important, but previously unknown effects on the leakage rate, especially that of step height. Further, complete details are given of a very effective seal designed using this technique. Measurements using turbine flow meters revealed that the optimized configuration gives a 60 and 79 percent leakage reduction over the baseline design at laboratory and higher (extrapolated) seal pressure drops, respectively.
SMPL: A Skinned Multi-Person Linear Model (2023)

We present a learned model of human body shape and posedependent shape variation that is more accurate than previous models and is compatible with existing graphics pipelines. Our Skinned Multi-Person Linear model (SMPL) is a skinned vertexbased model that accurately represents a wide variety of body shapes in natural human poses. The parameters of the model are learned from data including the rest pose template, blend weights, pose-dependent blend shapes, identity-dependent blend shapes, and a regressor from vertices to joint locations. Unlike previous models, the pose-dependent blend shapes are a linear function of the elements of the pose rotation matrices. This simple formulation enables training the entire model from a relatively large number of aligned 3D meshes of different people in different poses. We quantitatively evaluate variants of SMPL using linear or dual-quaternion blend skinning and show that both are more accurate than a Blend- SCAPE model trained on the same data. We also extend SMPL to realistically model dynamic soft-tissue deformations. Because it is based on blend skinning, SMPL is compatible with existing rendering engines and we make it available for research purposes.
Graph analytics and storage (2014)

Many Big Data analytics essentially explore the relationship among interconnected entities, which are naturally represented as graphs. However, due to the irregular data access patterns in the graph computations, it remains a fundamental challenge to deliver highly efficient solutions for large scale graph analytics. Such inefficiency restricts the utilization of many graph algorithms in Big Data scenarios. To address the performance issues in large scale graph analytics, we develop a graph processing system called System G, which explores efficient graph data organization for parallel computing architectures. We discuss various graph data organizations and their impact on data locality during graph traversals, which results in various cache performance behavior on processor side. In addition, we analyze data parallelism from architecture's perspective and experimentally show the efficiency for System G based graph analytics. We present experimental results for commodity multicore clusters and IBM PERCS supercomputers to illustrate the performance of System G for large scale graph analytics.
Small‐tip fast recovery imaging using non‐slice‐selective tailored tip‐up pulses and radiofrequency‐spoiling (2012)

Small-tip fast recovery (STFR) imaging is a new steady-state imaging sequence that is a potential alternative to balanced steady-state free precession. Under ideal imaging conditions, STFR may provide comparable signal-to-noise ratio and image contrast as balanced steady-state free precession, but without signal variations due to resonance offset. STFR relies on a tailored "tip-up," or "fast recovery," radiofrequency pulse to align the spins with the longitudinal axis after each data readout segment. The design of the tip-up pulse is based on the acquisition of a separate off-resonance (B0) map. Unfortunately, the design of fast (a few ms) slice- or slab-selective radiofrequency pulses that accurately tailor the excitation pattern to the local B0 inhomogeneity over the entire imaging volume remains a challenging and unsolved problem. We introduce a novel implementation of STFR imaging based on "non-slice-selective" tip-up pulses, which simplifies the radiofrequency pulse design problem significantly. Out-of-slice magnetization pathways are suppressed using radiofrequency-spoiling. Brain images obtained with this technique show excellent gray/white matter contrast, and point to the possibility of rapid steady-state T(2)/T(1) -weighted imaging with intrinsic suppression of cerebrospinal fluid, through-plane vessel signal, and off-resonance artifacts. In the future, we expect STFR imaging to benefit significantly from parallel excitation hardware and high-order gradient shim systems.
Graphene-based Plasmonic Nano-Antenna for Terahertz Band Communication in Nanonetworks (2013)

Nanonetworks, i.e., networks of nano-sized devices, are the enabling technology of long-awaited applications in the biological, industrial and military fields. For the time being, the size and power constraints of nano-devices limit the applicability of classical wireless communication in nanonetworks. Alternatively, nanomaterials can be used to enable electromagnetic (EM) communication among nano-devices. In this paper, a novel graphene-based nano-antenna, which exploits the behavior of Surface Plasmon Polariton (SPP) waves in semi-finite size Graphene Nanoribbons (GNRs), is proposed, modeled and analyzed. First, the conductivity of GNRs is analytically and numerically studied by starting from the Kubo formalism to capture the impact of the electron lateral confinement in GNRs. Second, the propagation of SPP waves in GNRs is analytically and numerically investigated, and the SPP wave vector and propagation length are computed. Finally, the nano-antenna is modeled as a resonant plasmonic cavity, and its frequency response is determined. The results show that, by exploiting the high mode compression factor of SPP waves in GNRs, graphene-based plasmonic nano-antennas are able to operate at much lower frequencies than their metallic counterparts, e.g., the Terahertz Band for a one-micrometer-long ten-nanometers-wide antenna. This result has the potential to enable EM communication in nanonetworks.
Discovery and Structure-Based Optimization of Potent and Selective WD Repeat Domain 5 (WDR5) Inhibitors Containing a Dihydroisoquinolinone Bicyclic Core (2019)

WD repeat domain 5 (WDR5) is a member of the WD40-repeat protein family that plays a critical role in multiple chromatin-centric processes. Overexpression of WDR5 correlates with a poor clinical outcome in many human cancers, and WDR5 itself has emerged as an attractive target for therapy. Most drug-discovery efforts center on the WIN site of WDR5 that is responsible for the recruitment of WDR5 to chromatin. Here, we describe discovery of a novel WDR5 WIN site antagonists containing a dihydroisoquinolinone bicyclic core using a structure-based design. These compounds exhibit picomolar binding affinity and selective concentration-dependent antiproliferative activities in sensitive MLL-fusion cell lines. Furthermore, these WDR5 WIN site binders inhibit proliferation in MYC-driven cancer cells and reduce MYC recruitment to chromatin at MYC/WDR5 co-bound genes. Thus, these molecules are useful probes to study the implication of WDR5 inhibition in cancers and serve as a potential starting point toward the discovery of anti-WDR5 therapeutics.
Rapid Cloning and Heterologous Expression of the Meridamycin Biosynthetic Gene Cluster Using a Versatile <i>Escherichia coli−Streptomyces</i> Artificial Chromosome Vector, pSBAC (2009)

Expression of biosynthetic pathways in heterologous hosts is an emerging approach to expedite production improvement and biosynthetic modification of natural products derived from microbial secondary metabolites. Herein we describe the development of a versatile Escherichia coli-Streptomyces shuttle Bacterial Artificial Chromosomal (BAC) conjugation vector, pSBAC, to facilitate the cloning, genetic manipulation, and heterologous expression of actinomycetes secondary metabolite biosynthetic gene clusters. The utility of pSBAC was demonstrated through the rapid cloning and heterologous expression of one of the largest polyketide synthase (PKS) and nonribosomal peptide synthetase (NRPS) biosynthetic pathways: the meridamycin biosynthesis gene cluster (mer). The entire mer gene cluster ( approximately 90 kb) was captured in a single pSBAC clone through a straightforward restriction enzyme digestion and cloning approach and transferred into Streptomyces lividans. The production of meridamycin (1) in the heterologous host was achieved after replacement of the original promoter with an ermE* promoter and was enhanced by feeding with a biosynthetic precursor. The success of heterologous expression of such a giant gene cluster demonstrates the versatility of BAC cloning technology and paves the road for future exploration of expression of the meridamycin biosynthetic pathway in various hosts, including strains that have been optimized for polyketide production.
Simplified Platform for Microring-Sensing using Wavelength Locking (2013)

We utilize a low-cost, robust method of wavelength locking microring resonators to implement a simplified platform for microring-sensing applications that requires only a single-wavelength laser source and directly maps resonance shifts to DC voltage values.
Evaluation of glass materials by using the line-focus-beam ultrasonic-material-characterization system (2005)

We developed experimental procedures to evaluate glass materials using the line-focus-beam ultrasonic-material-characterization (LFB-UMC) system. We prepared 28 specimens of a commercial borosilicate glass from random lots, and measured the velocities of leaky-surface acoustic waves (LSAWs) and leaky-surface-skimming compressional waves (LSSCWs), VLSAW and VLSSCW, using V(z) curve measurements at 225 MHz and 23 degrees C. The velocities for VLSAW ranged from 3121.83 m/s to 3149.77 m/s, with a maximum deviation of 27.94 m/s. The velocities for VLSSCW ranged from 5547.7 m/s to 5585.0 m/s, with a maximum deviation of 37.3 m/s. To investigate these observed variations in VLSAW and VLSSCW, we measured the bulk acoustic wave (BAW) properties, viz., longitudinal and shear velocities, then the densities and the chemical compositions of 8 of the 28 specimens. The LFB-UMC measurements confirmed that decreases in VLSAW and VLSSCW occur mainly with the B2O3 dopant concentrations, corresponding to the decrease of shear-wave and longitudinal-wave velocities that are caused by the decrease of the stiffness constants c44 and c11, respectively, rather than with decreased densities. The sensitivities are -6.36 x 10(-2) wt%/(m/s) for VLSAW and -4.87 x 10(-2) wt%/(m/s) for VLSSCW. This demonstrates that the LFB-UMC system is effective for evaluating glass materials and controlling production processes, by analyzing variations in chemical composition through the super-accurate velocity measurements of LSAWs and LSSCWs.
Direct GPU/FPGA Communication via PCI Express (2012)

Parallel processing has hit mainstream computing in the form of CPUs, GPUs and FPGAs. While explorations proceed with all three platforms individually and with the CPU-GPU pair, little exploration has been performed with the synergy of GPU-FPGA. This is due in part to the cumbersome nature of communication between the two. This paper presents a mechanism for direct GPU-FPGA communication and characterizes its performance in a full hardware implementation.
Targeted ablation of the vitamin D receptor: An animal model of vitamin D-dependent rickets type II with alopecia (1997)

Vitamin D, the major steroid hormone that controls mineral ion homeostasis, exerts its actions through the vitamin D receptor (VDR). The VDR is expressed in many tissues, including several tissues not thought to play a role in mineral metabolism. Studies in kindreds with VDR mutations (vitamin D-dependent rickets type II, VDDR II) have demonstrated hypocalcemia, hyperparathyroidism, rickets, and osteomalacia. Alopecia, which is not a feature of vitamin D deficiency, is seen in some kindreds. We have generated a mouse model of VDDR II by targeted ablation of the second zinc finger of the VDR DNA-binding domain. Despite known expression of the VDR in fetal life, homozygous mice are phenotypically normal at birth and demonstrate normal survival at least until 6 months. They become hypocalcemic at 21 days of age, at which time their parathyroid hormone (PTH) levels begin to rise. Hyperparathyroidism is accompanied by an increase in the size of the parathyroid gland as well as an increase in PTH mRNA levels. Rickets and osteomalacia are seen by day 35; however, as early as day 15, there is an expansion in the zone of hypertrophic chondrocytes in the growth plate. In contrast to animals made vitamin D deficient by dietary means, and like some patients with VDDR II, these mice develop progressive alopecia from the age of 4 weeks.
Design and Operation of a Waterless PV Soiling Monitoring Station (2018)

ASU-PRL has developed an autonomous, waterless, and wireless soiling monitoring station for photovoltaic (PV) plants. This soiling monitoring station is a 4 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">th</sup> generation design, featuring: two split-cell coupons as sensors coplanar to the PV arrays (two soiled half-cells and two covered clean half-cells), utilizing remote web-monitoring, and capable of providing data for up to 13 different useful ratios. This design employs built-in heat sinks which eliminates the need for temperature correction of the monitored short-circuit current. This paper presents the design and operation of a waterless PV soiling monitoring station and how it differs from currently available soiling monitoring stations on the market as well as a data set obtained from different PV plants located in diverse climates to quantify the operation and methodology.