gebhart/patrepeval huggingface dataset:
Wireless Gigabit Data Telemetry for Large-Scale Neural Recording (2015)

Implantable wireless neural recording from a large ensemble of simultaneously acting neurons is a critical component to thoroughly investigate neural interactions and brain dynamics from freely moving animals. Recent researches have shown the feasibility of simultaneously recording from hundreds of neurons and suggested that the ability of recording a larger number of neurons results in better signal quality. This massive recording inevitably demands a large amount of data transfer. For example, recording 2000 neurons while keeping the signal fidelity ( > 12 bit, > 40 KS/s per neuron) needs approximately a 1-Gb/s data link. Designing a wireless data telemetry system to support such (or higher) data rate while aiming to lower the power consumption of an implantable device imposes a grand challenge on neuroscience community. In this paper, we present a wireless gigabit data telemetry for future large-scale neural recording interface. This telemetry comprises of a pair of low-power gigabit transmitter and receiver operating at 60 GHz, and establishes a short-distance wireless link to transfer the massive amount of neural signals outward from the implanted device. The transmission distance of the received neural signal can be further extended by an externally rendezvous wireless transceiver, which is less power/heat-constraint since it is not at the immediate proximity of the cortex and its radiated signal is not seriously attenuated by the lossy tissue. The gigabit data link has been demonstrated to achieve a high data rate of 6 Gb/s with a bit-error-rate of 10(-12) at a transmission distance of 6 mm, an applicable separation between transmitter and receiver. This high data rate is able to support thousands of recording channels while ensuring a low energy cost per bit of 2.08 pJ/b.
Robust Multi-Resource Allocation with Demand Uncertainties in Cloud Scheduler (2017)

Cloud scheduler manages multi-resources (e.g., CPU, GPU, memory, storage etc.) in cloud platform to improve resource utilization and achieve cost-efficiency for cloud providers. The optimal allocation for multi-resources has become a key technique in cloud computing and attracted more and more researchers' attentions. The existing multi-resource allocation methods are developed based on a condition that the job has constant demands for multi-resources. However, these methods may not apply in a real cloud scheduler due to the dynamic resource demands in jobs' execution. In this paper, we study a robust multi-resource allocation problem with uncertainties brought by varying resource demands. To this end, the cost function is chosen as either of two multi-resource efficiency-fairness metrics called Fairness on Dominant Shares and Generalized Fairness on Jobs, and we model the resource demand uncertainties through three typical models, i.e., scenario demand uncertainty, box demand uncertainty and ellipsoidal demand uncertainty. By solving an optimization problem we get the solution for robust multi-resource allocation with uncertainties for cloud scheduler. The extensive simulations show that the proposed approach can handle the resource demand uncertainties and the cloud scheduler runs in an optimized and robust manner.
Positive-Strand RNA Viruses Infecting the Red Imported Fire Ant,<i>Solenopsis invicta</i> (2011)

The imported fire ants, Solenopsis invicta and S. richteri were introduced into the USA between 1918 and 1945. Since that time, they have expanded their USA range to include some 138 million hectares. Their introduction has had significant economic consequences with costs associated with damage and control efforts estimated at 6 billion dollars annually in the USA. The general consensus of entomologists and myrmecologists is that permanent, sustainable control of these ants in the USA will likely depend on self-sustaining biological control agents. A metagenomics approach successfully resulted in discovery of three viruses infecting S. invicta . Solenopsis invicta virus 1 (SINV-1), SINV-2, and SINV-3 are all positive, single-stranded RNA viruses and represent the first viral discoveries in any ant species. Molecular characterization, host relationships, and potential development and use of SINV-1, SINV-2, and SINV-3 as biopesticides are discussed.
Laser induced fluorescence attenuation spectroscopy: detection of hypoxia (2000)

The development of a new laser-induced fluorescence (LIF) spectroscopy technique for the measurement of the attenuation spectrum of tissue is described. The technique, termed laser-induced fluorescence attenuation spectroscopy (LIFAS), has been applied to study the effects of hypoxia on the in vivo optical properties of renal and myocardial tissue in the 350-600-nm band. Excimer laser (Xe-Cl) is used to excite a small volume of the tissue (rabbit model, N = 20) and induce autofluorescence. The emitted LIF is monitored fiberoptically at two locations that are unevenly displaced about the fluorescing volume. The optical attenuation of the tissue is calculated from the dual LIF measurements by assuming an exponential decay of the fluorescence with distance. The results indicate that hypoxia modulates the attenuation spectrum leading to characteristic changes in its shape. Primarily, the spectral profile becomes more concave between 455 nm and 505 nm and two spectral peaks at about 540 and 580 nm disappear leaving in their place a single peak at about 555 nm. The attenuation spectra of normoxic and hypoxic tissue are used to train partial least squares multivariate model for spectral classification. The model detected acute renal and myocardial hypoxia with an accuracy greater than 90% (range: 90%-96%) and 74% (range: 74%-90%), respectively.
Low-power electromagnetic stimulation of osteotomized rabbit fibulae. A randomized, blinded study. (1994)

The purpose of this study was to determine whether low-power-consuming symmetrical-waveform electromagnetic stimuli could increase the stiffness of fracture sites in a rabbit fibular-osteotomy model. Both active and placebo devices were used in a blinded study protocol. Dose-response studies of pulse amplitude and pulse width were performed by continuous application (twenty-four hours a day) of repetitive (fifteen-hertz), bursted (five-millisecond-long) symmetrical, rectangular electromagnetic stimulus waveforms. The power consumed by these stimuli is approximately one-fifth that consumed by the pulsing electromagnetic field devices that are in current clinical use. Significant increase of callus bending stiffness was produced by pulse widths of five to seven microseconds and pulse amplitudes of fifty to 100 millivolts.
Common allelic variants of cytochrome P4503A4 and their prevalence in different populations (2002)

Marked interindividual variability in expression of CYP3A4 influences the disposition of many endo- and xenobiotics, including the metabolism of steroids, environmental toxins and therapeutically useful drugs. The present study was designed to determine the genetic basis of CYP3A4 variability. We analysed DNA from 82 individuals with known CYP3A4 phenotype including 53 Caucasians and 21 African-American liver donors, seven individuals who were outliers in CYP3A4 metabolism and five individuals in a family of a poor nifedipine metabolizer. In addition, we analysed DNA from the eight person DNA Polymorphism Discovery Resource subset (Coriell Institute) and 89 individuals representing nine ethnic groups. Five non-synonymous mutations in the coding region of CYP3A4 were observed. CYP3A4*14 (T44C) in exon 1 resulted in an L15P change; CYP3A4*15 (G14387A) in exon 6 resulted in a R162Q substitution; CYP3A4*10 (G14422C) in exon 6 resulted in a D174H substitution; CYP3A4*16 (C15721G) in exon 7 resulted in a T185S amino acid substitution; and CYP3A4*12 (C22002T) in exon 11 resulted in a L373F change in the CYP3A4 protein. An additional six single nucleotide polymorphisms (SNPs) in the 5'-UTR, 13 SNPs in the introns and three SNPs in the 3'-UTR were observed. Extensive population differences were observed in the frequencies of various CYP3A4 alleles. None of the 28 CYP3A4 SNPs identified in CYP3A4 phenotyped persons (most individuals being heterozygous for any CYP3A4 variant) was associated with low hepatic CYP3A4 protein expression or low CYP3A4 activity in vivo.
Chemical and topographical patterns combined with solution shear for selective-area deposition of highly-aligned semiconducting carbon nanotubes (2021)

Selective deposition of semiconducting carbon nanotubes (s-CNTs) into densely packed, aligned arrays of individualized s-CNTs is necessary to realize their potential in semiconductor electronics. We report the combination of chemical contrast patterns, topography, and pre-alignment of s-CNTs <i>via</i> shear to achieve selective-area deposition of aligned arrays of s-CNTs. Alternate stripes of surfaces favorable and unfavorable to s-CNT adsorption were patterned with widths varying from 2000 nm down to 100 nm. Addition of topography to the chemical contrast patterns combined with shear enabled the selective-area deposition of arrays of quasi-aligned s-CNTs (∼14°) even in patterns that are wider than the length of individual nanotubes (>500 nm). When the width of the chemical and topographical contrast patterns is less than the length of individual nanotubes (<500 nm), confinement effects become dominant enabling the selective-area deposition of much more tightly aligned s-CNTs (∼7°). At a trench width of 100 nm, we demonstrate the lowest standard deviation in alignment degree of 7.6 ± 0.3° at a deposition shear rate of 4600 s<sup>-1</sup>, while maintaining an individualized s-CNT density greater than 30 CNTs μm<sup>-1</sup>. Chemical contrast alone enables selective-area deposition, but chemical contrast in addition to topography enables more effective selective-area deposition and stronger confinement effects, with the advantage of removal of nanotubes deposited in spurious areas <i>via</i> selective lift-off of the topographical features. These findings provide a methodology that is inherently scalable, and a means to deposit spatially selective, aligned s-CNT arrays for next-generation semiconducting devices.
Galectins-3 and -7, but not Galectin-1, Play a Role in Re-epithelialization of Wounds (2002)

Disorders of wound healing characterized by impaired or delayed re-epithelialization are a serious medical problem. These conditions affect many tissues, are painful, and are difficult to treat. In this study, using cornea as a model, we demonstrate for the first time the importance of carbohydrate-binding proteins galectins-3 and -7 in re-epithelialization of wounds. In two different models of corneal wound healing, re-epithelialization of wounds was significantly slower in galectin-3-deficient (gal3(-/-)) mice compared with wild-type (gal3(+/+)) mice. In contrast, there was no difference in corneal epithelial wound closure rates between galectin-1-deficient and wild-type mice. Quantitation of the bromodeoxyuridine-labeled cells in gal3(+/+) and gal3(-/-) corneas revealed that corneal epithelial cell proliferation rate is not perturbed in gal3(-/-) corneas. Exogenous galectin-3 accelerated re-epithelialization of wounds in gal3(+/+) mice but, surprisingly, not in the gal3(-/-) mice. Gene expression analysis using cDNA microarrays revealed that healing corneas of gal3(-/-) mice contain markedly reduced levels of galectin-7 compared with those of gal3(+/+) mice. More importantly, unlike galectin-3, galectin-7 accelerated re-epithelialization of wounds in both gal3(-/-) and gal3(+/+) mice. In corresponding experiments, recombinant galectin-1 did not stimulate the corneal epithelial wound closure rate. The extent of acceleration of re-epithelialization of wounds with both galectin-3 and galectin-7 was greater than that observed in most of the published studies using growth factors. These findings have broad implications for developing novel therapeutic strategies for treating nonhealing wounds.
Reversibility of biotin-binding by selective modification of tyrosine in avidin (1996)

The tight interaction between the vitamin biotin and the protein avidin is so strong (Ka approximately 10(15) M-1) that conditions which are usually sufficient for protein denaturation fail to dissociate the avidin-biotin complex. In order to form a reversible interaction between the two biomolecules, we have modified the binding-site tyrosine by nitration, thus reducing the pKa of the phenol group which forms a crucial hydrogen bond with the ureido group of biotin. At relatively low pH values (4-5), the resultant modified forms of avidin bind biotin with a very high association constant ( > 10(9) M-1). The modified avidins are thus capable of supporting stable, long-term binding of biotin or biotinylated macro-molecules. The latter molecules can be detached by increasing the pH of the medium or by introduction of excess levels of biotin at neutral pH. These findings demonstrate the importance of a single hydrogen bond for strong biotin binding. The new derivatives of avidin should be useful for applications whereby a reversible interaction between the four biotin-binding sites and biotin is desired, thus increasing the versatility of the avidin-biotin system for biotechnological application.
Equalization Enhancement Approaches for PAM4 Signaling for Next Generation Speeds (2017)

Four-level pulse-amplitude modulation signal (PAM4) is gaining more attention as an alternate coding scheme to binary modulation NRZ (Non Return to Zero) in high speed systems as the signal rate is reduced by half. Transmitter and receiver equalizations continue to play an important role with PAM4 encoding. Even though de-emphasis is a well standardized approach for equalization in NRZ, two enhancement approaches for PAM4 de-emphasis are proposed in the paper. The first enhancement approach is to compensate voltage levels in the de-emphasis process and the second one is to equalize the signal by bit rather than by symbol. Several test cases are presented to show the improvement in eye opening compared to the old approach. The limitations of these two enhancement approaches are also discussed.
Circulating miRNA Biomarkers for Alzheimer's Disease (2013)

A minimally invasive diagnostic assay for early detection of Alzheimer's disease (AD) is required to select optimal patient groups in clinical trials, monitor disease progression and response to treatment, and to better plan patient clinical care. Blood is an attractive source for biomarkers due to minimal discomfort to the patient, encouraging greater compliance in clinical trials and frequent testing. MiRNAs belong to the class of non-coding regulatory RNA molecules of ∼22 nt length and are now recognized to regulate ∼60% of all known genes through post-transcriptional gene silencing (RNAi). They have potential as useful biomarkers for clinical use because of their stability and ease of detection in many tissues, especially blood. Circulating profiles of miRNAs have been shown to discriminate different tumor types, indicate staging and progression of the disease and to be useful as prognostic markers. Recently their role in neurodegenerative diseases, both as diagnostic biomarkers as well as explaining basic disease etiology has come into focus. Here we report the discovery and validation of a unique circulating 7-miRNA signature (hsa-let-7d-5p, hsa-let-7g-5p, hsa-miR-15b-5p, hsa-miR-142-3p, hsa-miR-191-5p, hsa-miR-301a-3p and hsa-miR-545-3p) in plasma, which could distinguish AD patients from normal controls (NC) with >95% accuracy (AUC of 0.953). There was a >2 fold difference for all signature miRNAs between the AD and NC samples, with p-values<0.05. Pathway analysis, taking into account enriched target mRNAs for these signature miRNAs was also carried out, suggesting that the disturbance of multiple enzymatic pathways including lipid metabolism could play a role in AD etiology.
Furilisin:  A Variant of Subtilisin BPN‘ Engineered for Cleaving Tribasic Substrates (1996)

The serine protease, subtilisin BPN', was engineered to cleave proteins after tribasic sequences in a manner that resembles the substrate specificity of furin, one of the mammalian subtilisin homologs that processes prohormones. As a starting point we used a double mutant of subtilisin BPN' (N62D/ G166D) that showed substantial preference for cleaving after sequences having consecutive dibasic residues (namely, at the P1 and P2 substrate positions) [Ballinger et al. (1995) Biochemistry 34, 13312-13319]. Additional specificity for basic residues was engineered at the P4 position by introducing subtilisin-to-furin substitutions at three hydrophobic residues that composed the S4 subsite (Y104, I107, and L126). Initial attempts to incorporate a Y104D or I107E mutation or the Y104D/I107E double mutation into the dibasic specific enzyme failed to generate the processed enzyme. The problem was traced to the inability of the mutant prosubtilisins to process themselves and fold correctly. Replacing the natural processing site sequence (AHAY) with a good furin substrate sequence (RHKR) resulted in expression of the triple subtilisin mutant (N62D/Y104D/G166D) we call "furilisin". Furilisin hydrolyzes synthetic tribasic substrates (succinyl-RAKR-pNA or succinyl-KAKR-pNA) with high catalytic efficiency (kcat/K(m) > 3 x 10(5) M-1 s-1) and discriminates in favor of Arg versus Ala at the P4 position by a factor of 360. The overall specificity change versus the wild-type enzyme was dramatic. For example, succinyl-RAKR-pNA was cleaved approximately 60000 times faster than succinyl-AAPF-pNA, a good substrate for wild-type subtilisin. Similarly, furilisin was inhibited (K1* = 29 nM) by a variant of the turkey ovomucoid third domain inhibitor that contained an engineered furin substrate site (RCKR decreases) [Lu et al. (1993) J. Biol. Chem. 268, 14583-14585] and not by one having a good wild-type subtilisin substrate sequence (ACTL decreases). Interestingly, the extreme changes in substrate specificity resulted from substantial synergy between the engineered subsites. These studies provide a basic example of how to manipulate substrate specificity in a modular fashion, thereby creating an engineered-enzyme that may be useful as a protein processing tool.
Automatic array alignment in data-parallel programs (1993)

Data-parallel languages like Fortran 90 express parallelism in the form of operations on data aggregates such as arrays. Misalignment of the operands of an array operation can reduce program performance on a distributed-memory parallel machine by requiring nonlocal data accesses. Determining array alignments that reduce communication is therefore a key issue in compiling such languages.
Inverse design of microchannel fluid flow networks using Turing pattern dehomogenization (2020)

Abstract Microchannel reactors are critical in biological plus energy-related applications and require meticulous design of hundreds-to-thousands of fluid flow channels. Such systems commonly comprise intricate space-filling microstructures to control the fluid flow distribution for the reaction process. Traditional flow channel design schemes are intuition-based or utilize analytical rule-based optimization strategies that are oversimplified for large-scale domains of arbitrary geometry. Here, a gradient-based optimization method is proposed, where effective porous media and fluid velocity vector design information is exploited and linked to explicit microchannel parameterizations. Reaction-diffusion equations are then utilized to generate space-filling Turing pattern microchannel flow structures from the porous media field. With this computationally efficient and broadly applicable technique, precise control of fluid flow distribution is demonstrated across large numbers (on the order of hundreds) of microchannels.
Improving hearing aid performance in noise (2002)

In Brief Helping hearing aid wearers understand speech in noise is an elusive goal. The authors explain the obstacles that must be overcome and some strategies for doing so.
ReflecTech® Polymer Mirror Film Advancements in Technology and Durability Testing (2011)

One of the most promising developments for lowering the cost of utility scale concentrating solar power (CSP) is the emergence of durable reflective polymer films as an alternative to conventional curved glass mirrors. The broad adoption of wide web polymer film reflectors has been slowed by the lack of long-term weathering data. With the advent of the Ultra Accelerated Weathering System (UAWS), testing and development can proceed at a faster pace, and ReflecTech® Mirror Film has recently exceeded the equivalent terrestrial UV cumulative dosage of 25 years. ReflecTech® Mirror Film was developed through earlier collaborations between ReflecTech, Inc. (a subsidiary of SkyFuel, Inc.) and the National Renewable Energy Laboratory (NREL). More recently, through a Cooperative Research and Development Agreement (CRADA), ReflecTech, Inc. and NREL have developed an abrasion resistant coating (ARC) appropriate for application to polymer based mirror film. This hardcoat was developed to address the need for reflectors that are low in cost, high in performance and durable to mechanical cleaning methods sometimes used in the CSP environment. The combined impact of these two developments has the potential to significantly change the preferred supply choice for solar reflectors in new utility scale CSP projects. ReflecTech® Mirror Film samples prepared with and without the ARC hardcoat were subjected to accelerated exposure conditions more extreme than actual conditions. Both the uncoated and ARC films exhibit excellent weatherability with no loss in reflectance after highly accelerated exposure of over 25 years equivalent terrestrial UV. The ARC coated samples also exhibited outstanding initial abrasion resistance and adhesion to ReflecTech® Mirror Film, properties that were retained after exposure to various accelerated stress conditions including condensation cycling, thermal cycling, water immersion, and accelerated exposure to UV light. ReflecTech® Mirror Film is a commercially available product. The ARC-coated ReflecTech® Mirror Film has been successfully manufactured as a 1.5 m (5 ft) wide roll-to-roll construction in a commercial production environment and after further testing is expected to be commercially available in late 2011.