gebhart/patrepeval huggingface dataset:
MicroRNA-26a Regulates Pathological and Physiological Angiogenesis by Targeting BMP/SMAD1 Signaling (2013)

These findings establish miR-26a as a regulator of bone morphogenic protein/SMAD1-mediated EC angiogenic responses, and that manipulating miR-26a expression could provide a new target for rapid angiogenic therapy in ischemic disease states.
Three-dimensional laser printing of macro-scale glass objects at a micro-scale resolution (2020)

Femtosecond laser-induced chemical etching (FLICE) has proved itself a powerful approach when attempting to fabricate three-dimensional (3D) microstructures in glass, whereas maintaining a high spatial resolution in fabricating samples of great heights/thicknesses is challenging due to the diffraction nature of light waves. Here, we demonstrate the fabrication of macro-scale 3D glass objects of large heights up to ~3.8 cm with a well-balanced lateral and longitudinal resolution of ~20 μm using the FLICE. Moreover, a freeform hand printed with embedded blood vessel system has been produced. The remarkable accomplishments are achieved by revealing an unexplored regime in the interaction of ultrafast laser pulses with fused silica, which gives rise to depth-insensitive focusing of the laser pulses and polarization-independent selective etching inside fused silica. We examine the difference in the plasma dynamics between interactions of picosecond and femtosecond laser pulses with fused silica glass.
Diterpenes from <i>Cryptomeria japonica</i> Inhibit Androgen Receptor Transcriptional Activity in Prostate Cancer Cells (2007)

We identified eight diterpenes from Cryptomeria japonica (Taxodiaceae), which inhibit the activity of the androgen receptor (AR) in human prostate cancer (PCa) 22Rv1-derived 103E cells. The compounds 6,12-dihydroxyabieta-5,8,11,13-tetraen-7-one ( 2), sugiol ( 3), ferruginol ( 4), and 5-epixanthoperol ( 7) have near 100 % AR inhibition efficacy at concentrations of 10, 5, 25, and 25 microM, respectively. Because these compounds have very similar structures, analysis of their differential activity may aid in the design of inhibitors for PCa treatment.
Alternative modes for optical trapping and manipulation using counter-propagating shaped beams (2011)

Counter-propagating beams have enabled the first stable three-dimensional optical trapping of microparticles and this procedure has been enhanced and developed over the years to achieve independent and interactive manipulation of multiple particles. In this work, we analyse counter-propagating shaped-beam traps that depart from the conventional geometry based on symmetric, coaxial counter-propagating beams. We show that projecting shaped beams with separation distances previously considered axially unstable can, in fact, enhance the axial and transverse trapping stiffnesses. We also show that deviating from using perfectly counter-propagating beams to use oblique beams can improve the axial stability of the traps and improve the axial trapping stiffness. These alternative geometries can be particularly useful for handling larger particles. These results hint at a rich potential for light shaping for optical trapping and manipulation using patterned counter-propagating beams, which still remains to be fully tapped.
Structural Requirements of Histone Deacetylase Inhibitors: SAHA Analogs Modified on the Hydroxamic Acid (2016)

Histone deacetylase (HDAC) proteins have emerged as targets for anti-cancer therapeutics, with several inhibitors used in the clinic, including suberoylanilide hydroxamic acid (SAHA, vorinostat). Because SAHA and many other inhibitors target all or most of the 11 human HDAC proteins, the creation of selective inhibitors has been studied intensely. Recently, inhibitors selective for HDAC1 and HDAC2 were reported where selectivity was attributed to interactions between substituents on the metal binding moiety of the inhibitor and residues in the 14-Å internal cavity of the HDAC enzyme structure. Based on this earlier work, we synthesized and tested SAHA analogs with substituents on the hydroxamic acid metal binding moiety. The N-substituted SAHA analogs displayed reduced potency and solubility, but greater selectivity, compared to SAHA. Docking studies suggested that the N-substituent accesses the 14-Å internal cavity to impart preferential inhibition of HDAC1. These studies with N-substituted SAHA analogs are consistent with the strategy exploiting the 14-Å internal cavity of HDAC proteins to create HDAC1/2 selective inhibitors.
<i>Mcr</i>I: a novel class‐II restriction endonuclease from <i>Micrococcus cryophilus</i> recognizing 5'‐CGRY/CG‐3' (1990)

A new class-II restriction endonuclease, McrI, with a novel sequence specificity as isolated from the Gram-positive eubacterium Micrococcus cryophilus. McrI recognizes the palindromic hexanucleotide sequence. [sequence: see text] The novel enzyme in the presence of Mg2(+)-ions cleaves specifically both strands as indicated by the arrows. The staggered cuts generate 3'-protruding ends with single-stranded 5'-RY-3' dinucleotide extensions. The McrI recognition sequence was deduced from mapping data on DNAs of bacteriophages theta X174RF and M13mp18RF characterized by one and four cleavage sites, respectively. The cut positions within both strands of the recognition sequence were determined in sequencing experiments by analyzing hydrolysis of phosphodiester bonds within a polylinker region of M13mp18RF DNA containing an additional McrI recognition site including treatment with T4 DNA polymerase. The novel enzyme may be a useful tool for cloning experiments by completion of the enzymes EclXI (5'-C/GGCCG-3'), NotI (5'-GC/GGCCGC-3'), PvuI (5'-CGAT/CG-3') as well as EaeI (5'-Y/GGCCR-3') and XhoII (5'-Y/GATCR-3') characterized by partly identical sequence specificities.
Single step process for epitaxial lateral overgrowth of GaN on SiC and sapphire substrates (1999)

Using flow modulation organometallic vapor phase epitaxy, a process has been developed which produces epitaxial lateral overgrowth of GaN-base materials directly on SiC and sapphire substrates patterned with silicon nitride. The key feature of this single step process is the use of a high temperature AlGaN nucleation layer which wets the exposed substrate surface, without significant nucleation on the mask. This eliminates the need for regrowth while producing smooth growth surfaces in the window opening as well as over the mask. Subsequent GaN deposition results in relatively defect free materials grown laterally over the mask. Using arrays of stripe windows aligned parallel to the 〈11_00〉 crystal direction, the epitaxial films completely planarize after roughly 5 microns of growth. Defect densities estimated from atomic force micrographs indicate a reduction from mid 108 to 105 cm−2 in regions over the window and over the mask, respectively. This process represents a significant simplification over currently used regrowth methods for obtaining low defect density laterally overgrown GaN materials.
Functional Analysis of Lymphoblast and Cybrid Mitochondria Containing the 3460, 11778, or 14484 Leber's Hereditary Optic Neuropathy Mitochondrial DNA Mutation (2000)

Leber's hereditary optic neuropathy (LHON) is a form of blindness caused by mitochondrial DNA (mtDNA) mutations in complex I genes. We report an extensive biochemical analysis of the mitochondrial defects in lymphoblasts and transmitochondrial cybrids harboring the three most common LHON mutations: 3460A, 11778A, and 14484C. Respiration studies revealed that the 3460A mutation reduced the maximal respiration rate 20-28%, the 11778A mutation 30-36%, and the 14484C mutation 10-15%. The respiration defects of the 3460A and 11778A mutations transferred in cybrid experiments linking these defects to the mtDNA. Complex I enzymatic assays revealed that the 3460A mutation resulted in a 79% reduction in specific activity and the 11778A mutation resulted in a 20% reduction, while the 14484C mutation did not affect the complex I activity. The enzyme defect of the 3460A mutation transferred with the mtDNA in cybrids. Overall, these data support the conclusion that the 3460A and 11778A mutants result in complex I defects and that the 14484C mutation causes a much milder biochemical defect. These studies represent the first direct comparison of oxidative phosphorylation defects among all of the primary LHON mtDNA mutations, thus permitting insight into the underlying pathophysiological mechanism of the disease.
A gravity balancing leg orthosis for robotic rehabilitation (2004)

A number of methods can be found in the literature to gravity balance a machine. In this paper we use hybrid method to achieve gravity balancing. Hybrid method employs a mechanism to locate center of mass of the robot in conjunction with springs. This method is used to develop a rehabilitation device, which compensates the effect of gravity on a human leg. For a quantitative evaluation of the performance of the device, electromyograph data of the muscles involved in the motion of leg were collected and analyzed. This data showed that the machine could be used for gravity balancing of the leg and could be potentially used for rehabilitation of patients.
Primary data deduplication-large scale study and system design (2012)

We present a large scale study of primary data deduplication and use the findings to drive the design of a new primary data deduplication system implemented in the Windows Server 2012 operating system. File data was analyzed from 15 globally distributed file servers hosting data for over 2000 users in a large multinational corporation. The findings are used to arrive at a chunking and compression approach which maximizes deduplication savings while minimizing the generated metadata and producing a uniform chunk size distribution. Scaling of deduplication processing with data size is achieved using a RAM frugal chunk hash index and data partitioning – so that memory, CPU, and disk seek resources remain available to fulfill the primary workload of serving IO. We present the architecture of a new primary data deduplication system and evaluate the deduplication performance and chunking aspects of the system. 1
Measurement accuracy analysis of photocarrier radiometric determination of electronic transport parameters of silicon wafers (2004)

Simulations are performed to investigate the accuracy of the simultaneous determination of the electronic transport properties (the carrier lifetime, the carrier diffusion coefficient, and the front and rear surface recombination velocities) of silicon wafers by means of the photocarrier radiometry (PCR) technique through fitting frequency-scan data to a rigorous model via a multi-parameter fitting process. The uncertainties of the fitted parameter values are analyzed by calculating the dependence of the square variance including both amplitude and phase variances on the electronic transport properties. Simulation results show that the ability of the PCR to accurately determine carrier lifetimes gradually decreases for lifetimes longer than roughly 100 microseconds. In case the carrier diffusion coefficient is previously known, the carrier lifetime and front surface recombination velocity can be determined with uncertainties approximately ±20% or less. Experiments with an ion-implanted silicon wafer were performed and the carrier lifetime and front surface recombination velocity were determined with estimated uncertainties approximately ±30% and ±15%, respectively.
A full degree-of-freedom photonic crystal spatial light modulator (2022)

Harnessing the full complexity of optical fields requires complete control of all degrees-of-freedom within a region of space and time -- an open goal for present-day spatial light modulators (SLMs), active metasurfaces, and optical phased arrays. Here, we solve this challenge with a programmable photonic crystal cavity array enabled by four key advances: (i) near-unity vertical coupling to high-finesse microcavities through inverse design, (ii) scalable fabrication by optimized, 300 mm full-wafer processing, (iii) picometer-precision resonance alignment using automated, closed-loop "holographic trimming", and (iv) out-of-plane cavity control via a high-speed micro-LED array. Combining each, we demonstrate near-complete spatiotemporal control of a 64-resonator, two-dimensional SLM with nanosecond- and femtojoule-order switching. Simultaneously operating wavelength-scale modes near the space- and time-bandwidth limits, this work opens a new regime of programmability at the fundamental limits of multimode optical control.
Antifungal Resistance of <i>Candida glabrata</i> Vaginal Isolates and Development of a Quantitative Reverse Transcription-PCR-Based Azole Susceptibility Assay (2008)

A multiplex quantitative reverse transcription-PCR assay was developed to detect azole resistance in Candida glabrata, an important opportunistic pathogen that develops resistance rapidly. Resistance was defined as a >or=3-fold increase in CDR1 expression by this assay, which proved to be 100% sensitive and 95% specific in comparison to the gold standard broth microdilution assay.
Design, Synthesis, and SAR of C-3 Benzoic Acid, C-17 Triterpenoid Derivatives. Identification of the HIV-1 Maturation Inhibitor 4-((1<i>R</i>,3a<i>S</i>,5a<i>R</i>,5b<i>R</i>,7a<i>R</i>,11a<i>S</i>,11b<i>R</i>,13a<i>R</i>,13b<i>R</i>)-3a-((2-(1,1-Dioxidothiomorpholino)ethyl)amino)-5a,5b,8,8,11a-pentamethyl-1-(prop-1-en-2-yl)-2,3,3a,4,5,5a,5b,6,7,7a,8,11,11a,11b,12,13,13a,13b-octadecahydro-1<i>H</i>-cyclopenta[<i>a</i>]chrysen-9-yl)benzoic Acid (GSK3532795, BMS-955176) (2018)

GSK3532795, formerly known as BMS-955176 (1), is a potent, orally active, second-generation HIV-1 maturation inhibitor (MI) that advanced through phase IIb clinical trials. The careful design, selection, and evaluation of substituents appended to the C-3 and C-17 positions of the natural product betulinic acid (3) was critical in attaining a molecule with the desired virological and pharmacokinetic profile. Herein, we highlight the key insights made in the discovery program and detail the evolution of the structure-activity relationships (SARs) that led to the design of the specific C-17 amine moiety in 1. These modifications ultimately enabled the discovery of 1 as a second-generation MI that combines broad coverage of polymorphic viruses (EC<sub>50</sub> <15 nM toward a panel of common polymorphisms representative of 96.5% HIV-1 subtype B virus) with a favorable pharmacokinetic profile in preclinical species.
Selection of Parity Check Equations For the Iterative Message-Passing Detection of M-Sequences (2017)

We consider the joint detection and decoding of m-sequences. The receiver has to decide whether an m-sequence is received and possibly to decode its initial state. To do so, it implements an iterative message-passing decoding algorithm that operates on a parity check matrix, built upon a number of reference parity-check equations satisfied by the m-sequence. This matrix concatenates several elementary parity check matrices which are derived from reference equations. Unlike the conventional decoding case, the detection problem imposes to consider false alarms that may occur when the decoder is only fed with noise. While absorbing sets are known to be responsible for the error floor phenomenon of iterative message-passing decoders, we show that they may have a beneficial effect on the detection performance, in that they may prevent the decoder to produce false alarms. We further compute the number of hybrid cycles of length six and eight in the Tanner graph of the decoder and use the minimization of this number as criterion to derive an algorithm for selecting the reference parity check equations. This algorithm was found to be efficient for minimizing the probability of false alarm and decreases also the probability of wrong detection in the very small SNR region. This has been achieved at the cost of a reduction of the probability of correct detection.
Cold Vapor Generation beyond the Input Solar Energy Limit (2018)

100% efficiency is the ultimate goal for all energy harvesting and conversion applications. However, no energy conversion process is reported to reach this ideal limit before. Here, an example with near perfect energy conversion efficiency in the process of solar vapor generation below room temperature is reported. Remarkably, when the operational temperature of the system is below that of the surroundings (i.e., under low density solar illumination), the total vapor generation rate is higher than the upper limit that can be produced by the input solar energy because of extra energy taken from the warmer environment. Experimental results are provided to validate this intriguing strategy under 1 sun illumination. The best measured rate is ≈2.20 kg m<sup>-2</sup> h<sup>-1</sup> under 1 sun illumination, well beyond its corresponding upper limit of 1.68 kg m<sup>-2</sup> h<sup>-1</sup> and is even faster than the one reported by other systems under 2 sun illumination.
On-demand weighing of single dry biological particles over a 5-order-of-magnitude dynamic range (2014)

We report a simple and highly versatile system to select and weigh individual dry biological particles. The system is composed of a microtweezer to pick and place individual particles and a cantilever-based resonator to weigh them. The system can weigh entities that vary from a red blood cell (~10(-11) g) to the eye-brain complex of an insect (~10(-6) g), covering a 5-order-of-magnitude mass range. Due to its versatility and ease of use, this weighing method is highly compatible with established laboratory practices. The system can provide complementary mass information for a wide variety of individual particles imaged using scanning electron microscopy and determine comparative weights of individual biological entities that are attached to microparticles as well as weigh fractions of individual biological entities that have been subjected to focused ion beam milling.
Three-dimensional woven forming technology and equipment (2015)

To meet requirements of high performance and light weight of parts in equipment, automobile and mechanical industries, etc. coupled with problems during weaving such as simple structure, small size, complex process, low machine automation, poor fiber volume fraction of products, high void fraction of resin impregnation and difficulty of making large and complex structure, a new weaving method for three-dimensional hybrid woven with composite material is provided. Fibers are weaved to structures along with a digital guide template controlled by computer and parts are formed after resin being impregnated from outside to inside. Fabric of three-dimensional hybrid woven method based on the board, method of resin impregnation from outside to inside of three-dimensional hybrid woven fabricated part, and development of test platform for three-dimensional hybrid woven parts and fabric test for typical parts are mainly studied. This new forming technology improves flexibility and operability in forming process of large parts, and has great academic value, active meaning in science study and good foreground in engineering applications.
Layered Representations for Recognizing Office Activity (2002)

We present the use of layered probabilistic representations using Hidden Markov Models for performing sensing, learning, and inference at multiple levels of temporal granularity. We describe the use of the representation in a system that diagnoses states of a user’s activity based on real-time streams of evidence from video, acoustic, and computer interactions. We review the representation, present an implementation, and report on experiments with the layered representation in an office-awareness application.
Subtyping of renal cortical neoplasms in fine needle aspiration biopsies using a decision tree based on genomic alterations detected by fluorescence <i>in situ</i> hybridization (2014)

The present study suggests that a novel FISH assay developed by us has a role to play in assisting in the yield and accuracy of diagnosis of renal cortical neoplasms in needle biopsies in particular, and can help guide the clinical management of patients with SRMs that were non-diagnostic by histology.
Staged induction of HIV-1 glycan–dependent broadly neutralizing antibodies (2017)

A preventive HIV-1 vaccine should induce HIV-1-specific broadly neutralizing antibodies (bnAbs). However, bnAbs generally require high levels of somatic hypermutation (SHM) to acquire breadth, and current vaccine strategies have not been successful in inducing bnAbs. Because bnAbs directed against a glycosylated site adjacent to the third variable loop (V3) of the HIV-1 envelope protein require limited SHM, the V3-glycan epitope is an attractive vaccine target. By studying the cooperation among multiple V3-glycan B cell lineages and their coevolution with autologous virus throughout 5 years of infection, we identify key events in the ontogeny of a V3-glycan bnAb. Two autologous neutralizing antibody lineages selected for virus escape mutations and consequently allowed initiation and affinity maturation of a V3-glycan bnAb lineage. The nucleotide substitution required to initiate the bnAb lineage occurred at a low-probability site for activation-induced cytidine deaminase activity. Cooperation of B cell lineages and an improbable mutation critical for bnAb activity defined the necessary events leading to breadth in this V3-glycan bnAb lineage. These findings may, in part, explain why initiation of V3-glycan bnAbs is rare, and suggest an immunization strategy for inducing similar V3-glycan bnAbs.
Development of a multivariate statistical algorithm to analyze human cervical tissue fluorescence spectra acquired in vivo (1996)

The multivariate statistical algorithm based on both types of spectral inputs at 337 nm excitation has a similar sensitivity and significantly improved specificity relative to colposcopy in expert hands.
Large-area Silicon-FilmTM manufacturing (1996)

In three years, AstroPower’s Silicon‐FilmTM program has grown from a laboratory batch process making 100 cm2 solar cells to a continuous manufacturing process used to fabricate a 20 kW array of modules made with 240 cm2 cells. Under the PVMaT‐2A program AstroPower has established a Silicon‐FilmTM sheet production capacity of 4.5 MW/year. Significant advances were made in sheet production, device fabrication, and device and module efficiency. In developing a low‐cost process, the focus has been on limiting the consumption of high quality silicon, reducing sawing requirements, and utilizing a high yield continuous manufacturing technology. Key device results include the verification of a 2.9 watt solar cell using the 240 cm2 substrate (12.2%) and 7.9 watt solar cell on a 676 cm2 substrate (11.7%). AstroPower’s manufacturing plans include a sheet production capability of 20 MW/year over the next three years. Initial production runs were used to successfully fabricate and install a nominal 20 kW array for the PVUSA program.