gebhart/patrepeval huggingface dataset:
Human immunoglobulin G antibody response to the major gonococcal iron-regulated protein (1987)

In humans, gonococcal infection occurs in environments limited with respect to free iron. Neisseria gonorrhoeae produces increased quantities of iron-regulated membrane proteins when grown under in vitro conditions which restrict the availability of free iron. Using sodium dodecyl sulfate-polyacrylamide gel electrophoresis and Western blot (immunoblot) techniques, we studied the reactivity of specific antibodies to the 37-kilodalton (kDa) major iron-regulated protein (MIRP) of gonococci grown under iron-limiting conditions. Antibodies reactive with the 37-kDa MIRP were distinguished from those reactive with protein I by using purified 37-kDa MIRP or gonococcal protein preparations. Acute-phase sera from patients with disseminated gonococcal infection (DGI) reacted strongly to both the 37-kDa MIRP and protein I. Acute sera from nine patients with uncomplicated gonorrhea did not exhibit strong reactivity with the 37-kDa MIRP and were indistinguishable from five control sera. When compared with acute-phase sera, convalescent-phase sera from patients with DGI failed to demonstrate increased reactivity, whereas convalescent-phase sera from one of nine patients with uncomplicated gonorrhea developed reactivity to the 37-kDa MIRP. These data indicate that (i) the 37-kDa MIRP is expressed and antigenic in vivo and (ii) humans with DGI consistently develop a systemic antibody response to the 37-kDa MIRP.
Conditionally Cycle-Free Generalized Tanner Graphs: Theory and Application to High-Rate Serially Concatenated Codes (2006)

Generalized Tanner graphs have been implicitly studied by a number of authors under the rubric of generalized parity-check matrices. This work considers the conditioning of binary hidden variables in such models in order to break all cycles and thus derive optimal soft-in soft-out (SISO) decoding algorithms. Conditionally cycle-free generalized Tanner graphs are shown to imply optimal SISO decoding algorithms for the first order Reed-Muller codes and their duals - the extended Hamming codes - which are substantially less complex than conventional bit-level trellis decoding. The study of low-complexity optimal SISO decoding algorithms for the family of extended Hamming codes is practically motivated. Specifically, it is shown that exended Hamming codes offer an attractive alternative to high-rate convolutional codes in terms of both performance and complexity for use in very high-rate, very low-floor, serially concatenated coding schemes.
An effective data structure for a 3D printing slicer API (2016)

3D printing slicer is the essential part of additive manufacturing. While the algorithms and technology of slicing is mostly independent from characteristics of 3D printer hardware, the machine code is much closer and related to them. So someone who wants to build up his own machine-code generator will need a generic and effective slicing API. There is, however, no such a slicing API for this purpose. In this paper, we propose an effective data structure of such a slicer API and define the elements in the structure. So the machine-code generator can be plug-in-able to the slicing API and the adaptation process for each 3D printer will be simpler and effective.
<title>Optical Doppler tomography for noninvasive imaging of in-vivo blood flow</title> (1997)

We report the development of an optical technique for noninvasive in vivo imaging of tissue structure and blood flow dynamics with high spatial resolution (2 - 15 micrometer) in biological systems. The technique is based on coherence optical Doppler tomography (ODT), which combines Doppler velocimetry with optical coherence tomography to measure blood flow velocity at discrete spatial locations. The exceptionally high resolution of ODT allows noninvasive in vivo imaging of both blood microcirculation and tissue structures surrounding the vessel, which has significance for biomedical research and clinical applications. Tomographic velocity imaging of in vivo blood flow in a rat mesentery is demonstrated.
Deep Learning MR Imaging–based Attenuation Correction for PET/MR Imaging (2017)

Purpose To develop and evaluate the feasibility of deep learning approaches for magnetic resonance (MR) imaging-based attenuation correction (AC) (termed deep MRAC) in brain positron emission tomography (PET)/MR imaging. Materials and Methods A PET/MR imaging AC pipeline was built by using a deep learning approach to generate pseudo computed tomographic (CT) scans from MR images. A deep convolutional auto-encoder network was trained to identify air, bone, and soft tissue in volumetric head MR images coregistered to CT data for training. A set of 30 retrospective three-dimensional T1-weighted head images was used to train the model, which was then evaluated in 10 patients by comparing the generated pseudo CT scan to an acquired CT scan. A prospective study was carried out for utilizing simultaneous PET/MR imaging for five subjects by using the proposed approach. Analysis of covariance and paired-sample t tests were used for statistical analysis to compare PET reconstruction error with deep MRAC and two existing MR imaging-based AC approaches with CT-based AC. Results Deep MRAC provides an accurate pseudo CT scan with a mean Dice coefficient of 0.971 ± 0.005 for air, 0.936 ± 0.011 for soft tissue, and 0.803 ± 0.021 for bone. Furthermore, deep MRAC provides good PET results, with average errors of less than 1% in most brain regions. Significantly lower PET reconstruction errors were realized with deep MRAC (-0.7% ± 1.1) compared with Dixon-based soft-tissue and air segmentation (-5.8% ± 3.1) and anatomic CT-based template registration (-4.8% ± 2.2). Conclusion The authors developed an automated approach that allows generation of discrete-valued pseudo CT scans (soft tissue, bone, and air) from a single high-spatial-resolution diagnostic-quality three-dimensional MR image and evaluated it in brain PET/MR imaging. This deep learning approach for MR imaging-based AC provided reduced PET reconstruction error relative to a CT-based standard within the brain compared with current MR imaging-based AC approaches. <sup>©</sup> RSNA, 2017 Online supplemental material is available for this article.
Effect of Inlet Flow Angle on Gas Turbine Blade Tip Film Cooling (2009)

The influence of incidence angle on film-cooling effectiveness is studied for a cutback squealer blade tip. Three incidence angles are investigated −0 deg at design condition and ±5 deg at off-design conditions. Based on mass transfer analogy, the film-cooling effectiveness is measured with pressure sensitive paint techniques. The film-cooling effectiveness distribution on the pressure side near tip region, squealer cavity floor, and squealer rim tip is presented for the three incidence angles at varying blowing ratios. The average blowing ratio is controlled to be 0.5, 1.0, 1.5, and 2.0. One row of shaped holes is provided along the pressure side just below the tip; two rows of cylindrical film-cooling holes are arranged on the blade tip in such a way that one row is offset to the suction side profile and the other row is along the camber line. The pressure side squealer rim wall is cut near the trailing edge to allow the accumulated coolant in the cavity to escape and cool the tip trailing edge. The internal coolant-supply passages of the squealer tipped blade are modeled similar to those in the GE-E3 rotor blade. Test is done in a five-blade linear cascade in a blow-down facility with a tip gap clearance of 1.5% of the blade span. The Mach number and turbulence intensity level at the cascade inlet were 0.23 and 9.7%, respectively. It is observed that the incidence angle affects the coolant jet direction on the pressure side near tip region and the blade tip. The film-cooling effectiveness distribution is also altered. The peak of laterally averaged effectiveness is shifted upstream or downstream depending on the off-design incidence angle. The film cooling effectiveness inside the tip cavity can increase by 25% with the positive incidence angle. However, in general, the overall area-averaged film-cooling effectiveness is not significantly changed by the incidence angles in the range of study.
Isomorphic behavior of poly(aryl ether ketone) blends (1987)

Abstract Blends of various poly(aryl ether ketones) have been found to exhibit a range of miscibility and isomorphic behavior. This range is dependent on molecular weight; however, for poly(aryl ether ketones) with number‐average molecular weight of 20,000, this range is about ±25% difference in ketone content. All miscible blends exhibit isomorphism, and all immiscible blends exhibit no evidence of isomorphism. The dependence of the glass transition temperature T g versus composition exhibits a minimum deviation from linearity whereas the melting temperature T m versus composition exhibits a pronounced maximum deviation from linear behavior. The crystalline melting point versus composition for isomorphic blends is considerably different than for random copolymers with isomorphic units. Homopolymers and random copolymers exhibit a melting point that is a linear function of ketone content (increasing ketone content increases T m ). For blends, the melting point is essentially the same as that of the higher melting constituent until high levels of the lower melting constituent are present. The observed melting point versus composition behavior will be interpreted using classical theory to calculate the components of the liquid and crystalline phase compositions. As a miscible blend is cooled from the melt, essentially pure component of the highest melting point crystallizes out of solution, as predicted by calculated solid‐liquid phase diagrams. This occurs until the crystallization is complete owing to spherulitic impingement. At high concentrations of the lower melting constituent, lower melting points will be observed because the highest melting constituent will be depleted before the crystallization is complete. In many miscible blends involving addition of an amorphous polymer to a crystalline polymer, the degree of crystallinity of the crystalline polymer has been shown to increase. On the basis of evidence presented here, it is hypothesized that dilution by a miscible, amorphous polymer allows for a higher level of crystallinity.
Simulation vector generation from HDL descriptions for observability-enhanced statement coverage (1999)

Article Free Access Share on Simulation vector generation from HDL descriptions for observability-enhanced statement coverage Authors: Farzan Fallah Fujitsu Labs. of America, Inc., Sunnyvale, CA Fujitsu Labs. of America, Inc., Sunnyvale, CAView Profile , Pranav Ashar CCRL, NEC USA, Princeton CCRL, NEC USA, PrincetonView Profile , Srinivas Devadas Laboratory for Computer Science, MIT, Cambridge Laboratory for Computer Science, MIT, CambridgeView Profile Authors Info & Claims DAC '99: Proceedings of the 36th annual ACM/IEEE Design Automation ConferenceJune 1999 Pages 666–671https://doi.org/10.1145/309847.310023Published:01 June 1999Publication History 27citation257DownloadsMetricsTotal Citations27Total Downloads257Last 12 Months12Last 6 weeks5 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
Preparation and characterization of triple shape memory composite foams (2014)

Foams prepared from shape memory polymers (SMPs) offer the potential for low density materials that can be triggered to deploy with a large volume change, unlike their solid counterparts that do so at near-constant volume. While examples of shape memory foams have been reported in the past, they have been limited to dual SMPs: those polymers featuring one switching transition between an arbitrarily programmed shape and a single permanent shape established by constituent crosslinks. Meanwhile, advances by SMP researchers have led to several approaches toward triple- or multi-shape polymers that feature more than one switching phase and thus a multitude of temporary shapes allowing for a complex sequence of shape deployments. Here, we report the design, preparation, and characterization of a triple shape memory polymeric foam that is open cell in nature and features a two phase, crosslinked SMP with a glass transition temperature of one phase at a temperature lower than a melting transition of the second phase. The soft materials were observed to feature high fidelity, repeatable triple shape behavior, characterized in compression and demonstrated for complex deployment by fixing a combination of foam compression and bending. We further explored the wettability of the foams, revealing composition-dependent behavior favorable for future work in biomedical investigations.
Prospective clinical testing and experimental validation of the Pediatric Sepsis Biomarker Risk Model (2019)

Sepsis remains a major public health problem with no major therapeutic advances over the last several decades. The clinical and biological heterogeneity of sepsis have limited success of potential new therapies. Accordingly, there is considerable interest in developing a precision medicine approach to inform more rational development, testing, and targeting of new therapies. We previously developed the Pediatric Sepsis Biomarker Risk Model (PERSEVERE) to estimate mortality risk and proposed its use as a prognostic enrichment tool in sepsis clinical trials; prognostic enrichment selects patients based on mortality risk independent of treatment. Here, we show that PERSEVERE has excellent performance in a diverse cohort of children with septic shock with potential for use as a predictive enrichment strategy; predictive enrichment selects patients based on likely response to treatment. We demonstrate that the PERSEVERE biomarkers are reliably associated with mortality in mice challenged with experimental sepsis, thus providing an opportunity to test precision medicine strategies in the preclinical setting. Using this model, we tested two clinically feasible therapeutic strategies, guided by the PERSEVERE-based enrichment, and found that mice identified as high risk for mortality had a greater bacterial burden and could be rescued by higher doses of antibiotics. The association between higher pathogen burden and higher mortality risk was corroborated among critically ill children with septic shock. This bedside to bench to bedside approach provides proof of principle for PERSEVERE-guided application of precision medicine in sepsis.
Aluminum Chloride Catalyzed Intramolecular Cyclization and Allylsilylation of Diallylsilanes (1997)

Reactions of diallylsilanes with allyltrimethylsilane in the presence of aluminum chloride as a catalyst resulted in intramolecularly cyclized allylsilylation products of trans- and cis-3-allyl-1,1-dimethyl-5-((trialkylsilyl)methyl)-1-silacyclohexanes in good yields. The reaction proceeded faster and gave better yields with the incorporation of chlorotrimethylsilane in the aluminum chloride catalyst.
A multiplexed separation of iron oxide nanocrystals using variable magnetic fields (2011)

The size-dependent magnetic properties of nanocrystals are exploited in a separation process that distinguishes particles based on their diameter. By varying the magnetic field strength, four populations of magnetic materials were isolated from a mixture. This separation is most effective for nanocrystals with diameters between 4 and 16 nm.
High Performance Clean Fracturing Fluid Using a New Tri-Cationic Surfactant (2018)

In order to improve the heat resistance of current clean fracturing fluids, a novel cationic surfactant (VES-T), composed of three single-chains and a spacer group, was designed and synthesized as thickener for the fluids. Various performances of such VES-T fluid in the presence of NaSal were evaluated carefully. Study of the rheological properties demonstrated that the fluids with varying concentrations (3⁻5 wt %) of VES-T have excellent thermal stabilities under ultra-high temperatures ranging from 140 to 180 °C. Until now, this is the highest temperature that the VES fracturing fluid could bear. The VES-T/NaSal fluid exhibited good viscoelasticity and proppant-suspending capability, which was attributed to the three-dimensional network formed by entangled wormlike micelles. Furthermore, the VES fracturing fluids can be completely gel broken by standard brines within 2 h. Thus, the VES-T synthesized in this work has a good prospect for utilization during the development of ultra-high temperature reservoirs.
Tissue Engineering: A Modular Strategy to Engineer Complex Tissues and Organs (Adv. Sci. 5/2018) (2018)

In article number 1700402, Eben Alsberg and co-workers report the engineering of tri-tissue tracheas using a scaffold-free approach that allows for the integration of structural cartilage rings, prevascular blood vessel networks, and epithelial cells into a single construct. Neotracheas of various dimensions, including human size, are formed via cellular self-assembly. Prevascular tracheas are subcutaneously implanted into mice and demonstrate anastamosis with and perfusion by host vasculature.
In-place decomposition for robustness in FPGA (2010)

The programmable logic block (PLB) in a modern FPGA features a built-in carry chain (or adder) and a decomposable LUT, where such an LUT may be decomposed into two or more smaller LUTs. Leveraging decomposable LUTs and underutilized carry chains, we propose to decompose a logic function in a PLB into two subfunctions and to combine the subfunctions via a carry chain to make the circuit more robust against single-event upsets(SEUs). Note that such decomposition can be implemented using the decomposable LUT and carry chain in the original PLB without changing the PLB-level placement and routing. Therefore, it is an in-place decomposition (IPD) with no area and timing overhead at the PLB level and has an ideal design closure between logic and physical syntheses. For 10 largest combinational MCNC benchmark circuits with a conservative 20% utilization rate for carry chain, IPD improves MTTF (mean time to failure) by 1.43 and 2.70 times respectively, for PLBs similar to those in Xilinx Virtex-5 and Altera Stratix-IV.
Development of retroviral vectors for gene transfer to airway epithelia. (2000)

Retroviral vectors offer several potential advantages for attaining persistent expression of a therapeutic gene in airway epithelia for diseases such as cystic fibrosis. However, several problems have limited their application. Developments in vector production and the advent of lentiviral vectors have increased the investigation of recombinant retrovirus for gene transfer to airway epithelia. In addition, an improved understanding of some of the barriers limiting gene transfer has led to increased transduction efficiencies. The development of novel vector formulations and the use of new envelope pseudotypes are examples of recent findings that are leading to advances in this field.
Eigennews: Generating and delivering personalized news video (2013)

Next-generation news video consumption will be more personalized, device agnostic, and pooled from many different sources. The EigenNews system provides each viewer with a personalized newscast filled with stories that matter most to them. While personalized text-based news services already exist, personalized video news streams are still a critically missing technology. Our system records multiple channels, segments each news stream into individual stories, discovers links between the stories themselves and links between the stories and online articles, and generates a personalized playlist for each user. The dynamic mixing and aggregation of broadcast news videos from multiple sources greatly enriches the news watching experience by providing more comprehensive coverage and varying perspectives. Over time, the website collects click and view histories and uses this information to continuously optimize the personalization.
Design, fabrication, and testing of a novel end-to-end vascular coupling system (2014)

Microvascular anastomosis is common and necessary during reconstructive and free tissue transfer surgeries. Traditional hand suturing techniques are time consuming, subject to human error, and require complex instruments. Prior attempts including staples, ring-pin devices, cuffing devices, and clips were either more cumbersome, were unable to maintain a tight seal, or did not work for both arteries and veins. To provide a more efficient and reliable vessel anastomosis, a pin-free vascular coupling system that can be used for both arteries and veins was designed and manufactured. A set of corresponding instruments were developed to facilitate the anastomosis process. Both bench testing and ex vivo testing were performed to evaluate the operating abilities of the vascular coupling system. Preliminary studies were performed on cadaver pigs.
Toward Waveform Nonlinear Optics Using Multimillijoule Sub-Cycle Waveform Synthesizers (2015)

Waveform nonlinear optics aims to study and control the nonlinear interactions of matter with extremely short optical waveforms custom-tailored within a single cycle of light. Different technological routes to generate such multimillijoule sub-optical-cycle waveforms are currently pursued, opening up unprecedented opportunities in attoscience and strong-field physics. Here, we discuss the experimental schemes, introduce the technological challenges, and present our experimental results on high-energy sub-cycle optical waveform synthesis based on (1) parametric amplification and (2) induced-phase modulation in a two-color-driven gas-filled hollow-core fiber compressor. More specifically, for (1), we demonstrate a carrier-envelope-phase (CEP)-stable, multimillijoule three-channel parametric waveform synthesizer generating a >2-octave-wide spectrum (0.52-2.4 μm). After two amplification stages, the combined 125-μJ output supports 1.9-fs FWHM waveforms; energy scaling to >2 mJ is achieved after three amplification stages. FROG pulse characterization of all three second-stage outputs demonstrates the feasibility to recompress all three channels simultaneously close to the Fourier limit and shows the flexibility of our intricate dispersion management scheme for different experimental situations. For (2), we generate CEP-stable 1.7-mJ waveforms covering 365-930 nm (measured at 1% of the peak intensity) obtained from induced-phase modulation in a two-color-driven gas-filled hollow-core fiber. Using custom-designed double-chirped mirrors and a UV spatial light modulator will permit compression close to the 0.9-fs FWHM transform limit. These novel sources will become versatile tools for controlling strong-field interactions in matter and for attosecond pump-probe spectroscopy using VIS/IR and XUV/soft-X-ray pulses.
Fabrication Technology of Ferroelectric Memories (1998)

Two types of ferroelectric memories have been proposed. One is a 1 transistor and 1 capacitor (1T1C) type and another is an FET (field effect transistor) type. The fabrication technique for fabrication ferroelectric capacitors on polycrystalline Si (poly-Si) was very effective for high density 1T1C ferroelectric memory and metal-ferroelectric-metal-insulator-semiconductor (MFMIS) FET with stable properties. MFMIS FET is one type of FET ferroelectric memory which we proposed. To obtain good ferroelectric capacitors on poly-Si, we used Ir based materials as electrodes of the capacitors. By using Ir based electrodes, the characteristics of Pb(Zi,Ti)O 3 (PZT) capacitors on poly-Si were equivalent to those on SiO 2 . Moreover, the PZT capacitors with Ir based electrodes showed dramatic improvement in fatigue and imprint properties.