gebhart/patrepeval huggingface dataset:
Metal-Assisted and Microwave-Accelerated Decrystallization of Pseudo-Tophus in Synthetic Human Joint Models (2019)

In this paper, we tested a hypothesis that the metal-assisted and microwave-accelerated decrystallization (MAMAD) technique, based on the combined use of low-power medical microwave heating (MWH) and gold nanoparticles (Au NPs), can be used to decrystallize laboratory-prepared monosodium urate monohydrate crystal aggregate (pseudo-tophus) placed in three-dimensional (3D) synthetic human joint models. To simulate a potential treatment of chronic tophaceous gout using the MAMAD technique, we used three different 3D synthetic human joint models and assessed the percent mass reduction (PMR, i.e., decrystallization) of pseudo-tophus and microwave-induced synthetic skin patch damage after MAMAD sessions (a MAMAD session = 120 s of MWH in the presence of Au NPs). Our three synthetic joint models are: Model 1: Application of seven MAMAD sessions in a closed synthetic joint with a pseudo-bursa containing a pseudo-tophus submerged in a solution of 20 nm Au NPs followed by dehydration of pseudo-tophus after each MAMAD session to assess PMR. Model 2: Application of seven MAMAD sessions in a closed or open synthetic joint with a pseudo-bursa containing a pseudo-tophus submerged in a solution of Au NPs followed by intermittent dehydration of pseudo-tophus after seven MAMAD sessions to assess PMR. Model 3: Application of 18 MAMAD sessions in a rotated closed synthetic joint (three sides are heated separately) with a pseudo-bursa containing a pseudo-tophus submerged in a solution of Au NPs followed by dehydration after every three MAMAD sessions to assess PMR. After a single MAMAD session, pseudo-tophus exposed to MWH and Au NPs had an average PMR of 8.30% (up to an overall PMR of 15%), and microwave-induced damage to the synthetic skin can be controlled by the use of a sacrificial skin sample and by adjusting the duration and the number of the MAMAD sessions. Computational electromagnetic simulations predict a 10% absorption of electric field by the pseudo-tophus placed in the synthetic joint models, which led us to conclude that a medical microwave source with higher power than 20 W can potentially be used with the MAMAD technique.
Highly Effective Detection of Human Papillomavirus 16 and 18 DNA by a Testing Algorithm Combining Broad-Spectrum and Type-Specific PCR (2006)

The use of a single broad-spectrum human papillomavirus (HPV) DNA-based PCR test may fail to detect lower concentrations of HPV DNA due to competition between different genotypes in mixed infections. To improve HPV detection by PCR, broad-spectrum and type-specific (TS) PCRs were combined, with a focus on HPV-16 and HPV-18. Cervical and cervicovaginal cell samples were obtained from 1,113 healthy women (age range, 15 to 25 years) participating in an HPV-16/HPV-18 candidate vaccine efficacy trial. These samples were tested by a broad-spectrum SPF(10) PCR-DNA enzyme immunoassay, followed by a primer SPF(10)-based line probe assay (SPF(10) LiPA), and HPV-16- and HPV-18-TS PCRs. The results for the majority of the HPV-16/18 SPF(10) LiPA-positive samples were confirmed by TS-PCR (kappa values, 0.775 for HPV-16 and 0.785 for HPV-18). However, TS PCR revealed additional positive samples among those that contained other HPV genotypes due to competition. Conversely, SPF(10) LiPA identified HPV-16 or -18 in samples that remained negative by TS PCR as a result of sampling variation. Analysis of follow-up samples from more than 1,000 women confirmed that the combination of SPF(10)-LiPA with additional HPV-16- and HPV-18-TS PCR diminishes the rate of false-negative diagnosis. The combination of broad-spectrum and TS PCRs resulted in a novel testing algorithm. This combination of assays is more accurate than either method alone, and the novel algorithm offers a highly accurate and effective method for the analysis of HPV infections.
A New Presumed Commit Optimization for Two Phase Commit (1993)

The Cambridge laboratory became operational in 1988 and is located at One Kendall Square, near MIT. CRL engages in computing research to extend the state of the computing art in areas likely to be important to Digital and its customers in future years. CRL’s main focus is applications technology; that is, the creation of knowledge and tools useful for the preparation of important classes of applications. CRL Technical Reports can be ordered by electronic mail. To receive instructions, send a message to one of the following addresses, with the word help in the Subject line:
Mesoporous Silica as Nanoreactors to Prepare Gd‐Encapsulated Carbon Dots of Controllable Sizes and Magnetic Properties (2016)

Gd‐encapsulated carbonaceous dots (Gd@C‐dots) hold great potential in clinical applications as a novel type of T 1 contrast agent for magnetic resonance imaging (MRI). However, current synthetic methods require multiple purification steps due to poor size control, making them unsuitable for high throughput. Herein, a novel, mesoporous silica nanoparticle (MSN)‐templated method for the size‐controlled synthesis of Gd@C‐dots is reported. Briefly, MSNs nanoreactors of different pore sizes are loaded with Gd precursors. Upon calcination, carbon layers are grown around the Gd cations. The spatial restraint of the silica cavity facilitates size control of the produced Gd@C‐dots. Specifically, using 3, 7, and 11 nm MSNs as templates allows the synthesis of 3.0, 7.4, and 9.6 nm Gd@C‐dots, respectively. A significant size impact on the magnetic and optical properties of the nanoparticles is shown, with the smallest Gd@C‐dots showing the highest r 1 relaxivity (10 mM −1 s −1 ) and fluorescence quantum yield (30.2%). The 3.0‐nm Gd@C‐dots were then conjugated with a tumor‐targeting ligand, c(RGDyK), and injected into U87MG xenograft tumor models. Good tumor targeting was observed in T 1 ‐weighted MRI images; whereby the unbound nanoparticles were efficiently excreted through renal clearance, avoiding long‐term toxicity to the host.
Non-linear temperature-dependent curvature of a Phase Change Composite Bimorph beam (2017)

Bimorph films curl in response to temperature. The degree of curvature typically varies linearly with temperature and in proportion to the difference in thermal expansion of the individual layers. In many applications, such as controlling a thermostat, this gentle linear behavior is acceptable. In other cases, such as opening or closing a valve or latching a deployable column into place, an abrupt motion at a fixed temperature is preferred. To achieve this non-linear motion, we describe the fabrication and performance of a new bilayer structure we call 'Phase Change Composite Bimorph (PCBM)'. In a PCBM, one layer in the bimorph is a composite containing small inclusions of phase change materials. When the inclusions melt, their large (generally positive and >1%) expansion coefficient induces a strong, reversible step function jump in bimorph curvature. The measured jump amplitude and thermal response is consistent with theory.
Cloning and Nucleotide Sequence of the <i>gyrB</i> Gene of <i>Vibrio parahaemolyticus</i> and Its Application in Detection of This Pathogen in Shrimp (1998)

Because biochemical testing and 16S rRNA sequence analysis have proven inadequate for the differentiation of Vibrio parahaemolyticus from closely related species, we employed the gyrase B gene (gyrB) as a molecular diagnostic probe. The gyrB genes of V. parahaemolyticus and closely related Vibrio alginolyticus were cloned and sequenced. Oligonucleotide PCR primers were designed for the amplification of a 285-bp fragment from within gyrB specific for V. parahaemolyticus. These primers recognized 117 of 117 reference and wild-type V. parahaemolyticus strains, whereas amplification did not occur when 90 strains of 37 other Vibrio species or 60 strains representing 34 different nonvibrio species were tested. In 100-microliter PCR mixtures, the lower detection limits were 5 CFU for live cells and 4 pg for purified DNA. The possible application of gyrB primers for the routine identification of V. parahaemolyticus in food was examined. We developed and tested a procedure for the specific detection of the target organism in shrimp consisting of an 18-h preenrichment followed by PCR amplification of the 285-bp V. parahaemolyticus-specific fragment. This method enabled us to detect an initial inoculum of 1.5 CFU of V. parahaemolyticus cells per g of shrimp homogenate. By this approach, we were able to detect V. parahaemolyticus in all of 27 shrimp samples artificially inoculated with this bacterium. We present here a rapid, reliable, and sensitive protocol for the detection of V. parahaemolyticus in shrimp.
Detection and Spatial Mapping of Mercury Contamination in Water Samples Using a Smart-Phone (2014)

Detection of environmental contamination such as trace-level toxic heavy metal ions mostly relies on bulky and costly analytical instruments. However, a considerable global need exists for portable, rapid, specific, sensitive, and cost-effective detection techniques that can be used in resource-limited and field settings. Here we introduce a smart-phone-based hand-held platform that allows the quantification of mercury(II) ions in water samples with parts per billion (ppb) level of sensitivity. For this task, we created an integrated opto-mechanical attachment to the built-in camera module of a smart-phone to digitally quantify mercury concentration using a plasmonic gold nanoparticle (Au NP) and aptamer based colorimetric transmission assay that is implemented in disposable test tubes. With this smart-phone attachment that weighs <40 g, we quantified mercury(II) ion concentration in water samples by using a two-color ratiometric method employing light-emitting diodes (LEDs) at 523 and 625 nm, where a custom-developed smart application was utilized to process each acquired transmission image on the same phone to achieve a limit of detection of ∼ 3.5 ppb. Using this smart-phone-based detection platform, we generated a mercury contamination map by measuring water samples at over 50 locations in California (USA), taken from city tap water sources, rivers, lakes, and beaches. With its cost-effective design, field-portability, and wireless data connectivity, this sensitive and specific heavy metal detection platform running on cellphones could be rather useful for distributed sensing, tracking, and sharing of water contamination information as a function of both space and time.
MPTG: a portable test generator for cache-coherent multiprocessors (2002)

Cache-coherent multiprocessors are typically verified by extensive simulation with randomly generated testcases. With this methodology, certain aspects of test coverage can be measured using monitors that record the occurrence of specific events during simulation. If certain events do not occur sufficiently often, the designer must somehow bias the random test generator or write hand-written testcases to improve coverage of the desired event. This is usually a labor-intensive process that is made worse by frequent changes in design specifications and the high cost of simulating large multiprocessor models. This paper describes MPTG (MultiProcessor Test Generator): a portable test generator that automates much of this labor-intensive component of the simulation process. MPTG does this by deterministically generating sets of testcases that are guaranteed to cause specific events to happen. For example, with a single, compact test specification it is possible to generate a set of tests that exercise all transaction types and current cache state combinations at a particular cache in the system. Alternatively, it is easy to generate a set of tests that exercise all two-way races that can occur at a particular cache. Test generation at this level of detail requires the incorporation of a system-wide coherence protocol within the test generator, which can make it difficult to port the test generator to different systems. Portability is achieved in MPTG by breaking the test generator into two parts: a generic test generation engine and a system-specific set of protocol tables.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
160-Gb/s Bidirectional Parallel Optical Transceiver Module for Board-Level Interconnects Using a Single-Chip CMOS IC (2007)

We report here on the design, fabrication and high-speed performance of a novel parallel optical module with sixteen 10-Gb/s transmitter and receiver channels for a 160-Gb/s bidirectional aggregate data rate. The module utilizes a single-chip CMOS optical transceiver containing both transmitter and receiver circuits. 16-channel high-speed photodiode (PD) and VCSEL arrays are flip-chip attached to the low-power CMOS IC. The substrate emitting/illuminated VCSEL and PD arrays operate at 985 nm and include collimating lenses integrated into the backside of the substrate. The IC-OE assembly is then flip-chip attached to a high density organic package forming the transceiver optical module. The exclusive use of flip-chip packaging for both the IC-to-optoelectronic (OE) devices and for the IC-to-organic package minimizes the module footprint and associated packaging parasitics. The OE-on-IC assembly achieves a high area efficiency of 9.4 Gb/s/mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> (Schow et al., 2007). The complete organic carrier transceiver package provides a low-cost, low-profile module similar to a conventional chip-carrier that can be directly surface mounted to a circuit board using a conventional BGA solder process. SLC transceiver modules with transmitter and receiver OE-IC arrays were assembled and characterized. Operation of all 16 transmitters in the transceiver module was demonstrated at data rates >10 Gb/s. Similarly, all 16 receiver channels operated error-free at >10 Gb/s. The receiver eye-diagrams were generated using a second transceiver source and therefore constitute a full transceiver optical link.
Process Studies on the Conversion of Methanol to Gasoline (1978)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTProcess Studies on the Conversion of Methanol to GasolineClarence D. Chang, James C. W. Kuo, William H. Lang, Solomon M. Jacob, John J. Wise, and Anthony J. SilvestriCite this: Ind. Eng. Chem. Process Des. Dev. 1978, 17, 3, 255–260Publication Date (Print):July 1, 1978Publication History Published online1 May 2002Published inissue 1 July 1978https://pubs.acs.org/doi/10.1021/i260067a008https://doi.org/10.1021/i260067a008research-articleACS PublicationsRequest reuse permissionsArticle Views1955Altmetric-Citations122LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access options Get e-Alerts
I-V characteristics and formation of single Josephson junction using the intrinsic layer in Bi-2223 thin films (1998)

Intrinsic Josephson junctions prepared in bulk materials were fabricate in thin films. We selected Bi-2223 instead of often sued Bi-2212 as the superconducting materials in which insulating and superconducting layers are stacked along c- axis. Single crystal fragments having its high crystallinity and flat surfaces were chose carefully among many grains in thin films and Mesa structures were formed by photolithographic technique. Superconducting gap structure and branching structure peculiar to stacked S-I-S junctions were clearly observed on current-voltage characteristics. On the structure stacked by plural intrinsic junctions, the interaction between different intrinsic junctions clearly appeared in decrease of values of Josephson critical current with increasing the number of junctions in the resistive state, and collective switching was observed. The Ic decrease leading to the collective behavior was explained by taking it effective heat diffusion into account. With reducing the number of the junctions, the gap value, which is suppressed by heat generation, increased. This response of the quasi-particle current was evaluated using a single intrinsic junction and confirmed to be able to explained by assuming d-symmetry for the superconducting order parameter without the term of the gap suppression.
A low-cost intrinsically low-distortion EDFA design for AM-CATV applications with a wide input power and wavelength range (1995)

We present a 980 nm pumped low-cost EDFA design for AM-CATV applications with intrinsic low distortion and noise-figure over a wide input power and wavelength range by using an optimized Erbium Doped Fibre.
[Rapid diagnosis of gram-negative bacteriuria with endotoxin-specific chromogenic test]. (1989)

Limulus amebocyte lysate test is a simple, yet sensitive laboratory method for detecting endotoxin. Although the specificity of the test was questioned, we recently solved this problem by removing a (1----3)-beta-D-glucan-sensitive factor G from the lysate (Endospecy, Seikagaku Kogyo Co., Ltd, Tokyo). In this study, we have established a method for the determination of endotoxin urine in using Endospecy. An aliquot of 0.2 ml of Endospecy dissolved in 4.4 ml of 0.1 mol/l Tris-HCl buffer (pH 8.0) was added to 5 microliter of urine sample. The mixture was incubated at 37 degrees C for 30 min. After diazo-coupling, absorbance was measured at 545 nm. The standard curve using Escherichia coli 0111: B4 endotoxin showed a good linearity. The addition-recovery test of various endotoxins showed nearly 100% recovery. Normal urine contained less than 60 pg/ml of endotoxin. Urine from patients with Gram-negative bacteriuria showed definitely high values, whereas urines infected either with Gram-positive bacteria or with fungi all showed nearly normal values. This method will be useful as a rapid and reliable test for the diagnosis of urinary tract infection with Gram-negative bacteria.
Comparative Analysis of the Capsid Structures of AAVrh.10, AAVrh.39, and AAV8 (2019)

Adeno-associated viruses (AAVs) from clade E are often used as vectors in gene delivery applications. This clade includes rhesus isolate 10 (AAVrh.10) and 39 (AAVrh.39) which, unlike representative AAV8, are capable of crossing the blood-brain barrier (BBB), thereby enabling the delivery of therapeutic genes to the central nervous system. Here, the capsid structures of AAV8, AAVrh.10 and AAVrh.39 have been determined by cryo-electron microscopy and three-dimensional image reconstruction to 3.08-, 2.75-, and 3.39-Å resolution, respectively, to enable a direct structural comparison. AAVrh.10 and AAVrh.39 are 98% identical in amino acid sequence but only ∼93.5% identical to AAV8. However, the capsid structures of all three viruses are similar, with only minor differences observed in the previously described surface variable regions, suggesting that specific residues S269 and N472, absent in AAV8, may confer the ability to cross the BBB in AAVrh.10 and AAVrh.39. Head-to-head comparison of empty and genome-containing particles showed DNA ordered in the previously described nucleotide-binding pocket, supporting the suggested role of this pocket in DNA packaging for the <i>Dependoparvovirus</i> The structural characterization of these viruses provides a platform for future vector engineering efforts toward improved gene delivery success with respect to specific tissue targeting, transduction efficiency, antigenicity, or receptor retargeting.<b>IMPORTANCE</b> Recombinant adeno-associated virus vectors (rAAVs), based on AAV8 and AAVrh.10, have been utilized in multiple clinical trials to treat different monogenetic diseases. The closely related AAVrh.39 has also shown promise <i>in vivo</i> As recently attained for other AAV biologics, e.g., Luxturna and Zolgensma, based on AAV2 and AAV9, respectively, the vectors in this study will likely gain U.S. Food and Drug Administration approval for commercialization in the near future. This study characterized the capsid structures of these clinical vectors at atomic resolution using cryo-electron microscopy and image reconstruction for comparative analysis. The analysis suggested two key residues, S269 and N472, as determinants of BBB crossing for AAVrh.10 and AAVrh.39, a feature utilized for central nervous system delivery of therapeutic genes. The structure information thus provides a platform for engineering to improve receptor retargeting or tissue specificity. These are important challenges in the field that need attention. Capsid structure information also provides knowledge potentially applicable for regulatory product approval.
Low noise low cost ultra wideband N-push VCO (2005)

The coexistence of second and third generation wireless system requires multi-mode, multi-band and multistandard mobile communication systems, therefore, requiring a wideband source that may replace narrow band VCO modules by a single low noise wideband VCO. The coupled N-Push oscillator integrated with the phase detector design approach demonstrated in this work can satisfy the need for the present demand for low cost, low noise, power efficient, wide tuning range, compact size, and amenable for integration in chip form. The measured phase noise is better than –118 dBc/Hz at 100 kHz offset over the tuning range (1-3 GHz/3-6 GHz), and to our knowledge, this is the highest tuning band of operation using Push-Push topology with discrete components so far reported.
On the architectural considerations of the FISSION (Flexible Interconnection of Scalable Systems Integrated using Optical Networks) framework for data-centers (2013)

We have proposed the FISSION (Flexible Interconnection of Scalable Systems Integrated using Optical Networks) architecture for data-centers in [1]. The Fission architecture comprises of the creation of sectors that comprise of server systems and switches are backplane wired up using optical buses. These optical buses deploy ultra-dense wavelength division multiplexing (UDWDM). A modified Carrier Ethernet system provides protocol connectivity within the data-center that scales to support beyond a million servers. We delve into the architectural and protocol aspects of the Fission concept, particularly focusing on its scalability, working, wavelength-assignment and protection issues. The working of the Fission concept is further explained through numerical results achieved through rigorous simulation.
Fresnel lens sidewall design for imaging optics (2015)

We developed a ray tracing simulation tool for imaging systems including a Fresnel lens with a quasi-arbitrary sidewall structure. One issue with Fresnel lens is that noise in the image plane can appear from rays passing through or reflected at its sidewalls. One way to reduce it is to modify the orientation of the sidewalls so that rays will not reach the image plane. To find the best sidewall orientations, we developed a method where locally, a sidewall can freely be oriented. We could then derive the best modulation scheme for each Fresnel lens sidewall. In the case of a single imaging Fresnel lens, relative parasite noise intensity could mostly be prevented. To experimentally check our method, snapshot images were taken with single Fresnel lenses and a single spherical lens. No noticeable differences in image quality could be observed using a standard C-MOS camera. However, parasite noise could experimentally be detected with a Fresnel lens prototype when using a very high-dynamic range C-MOS camera.