gebhart/patrepeval huggingface dataset:
Projection lithography patterned high-resolution quantum dots/thiol-ene photo-polymer pixels for color down conversion (2019)

Pixelated color converters are envisioned to achieve full-color high-resolution display through down conversion of blue/ultraviolet(UV) micro-LEDs. Quantum dots (QDs) are promising narrow-band converters of high quantum efficiency and brightness enabling saturated colors with wide color gamut in displays. Here we demonstrate high-resolution pixelated red and green QDs/thiol-ene photo-polymer converters (single pixel down to 6 µm; converters array of 21 µm pixel, 30 µm pitch and sub 10 µm thickness) patterned through projection lithography. QDs capped with amine surface group are uniformly dispersed in thiol-ene photo-polymer matrix at high concentrations (up to 100 mg/mL), which reduces aggregation and improves conversion efficiency by 0.5-1 times compared to drop-cast QDs. Color cross-talk is also reduced through patterning light blocking walls between converter pixels.
Hyperglucagonemia Mitigates the Effect of Metformin on Glucose Production in Prediabetes (2018)

(Cell Reports 15, 1394–1400; May 17, 2016) In the originally published version of this article, the labels “Placebo” and “Metformin” were mistakenly switched in Table S2, which displayed plasma concentrations of amino acids. We have corrected this error as well as the following additional errors, which we would like to bring to the attention of the readers:1.The third bullet point within the Highlights now reads “…metformin increases glucogenic amino acids …” rather than “… metformin decreases glucogenic amino acids …”2.The last sentence of the In Brief blurb now reads “… increased glucagon and glucogenic precursors” rather than “increased glucagon and decreased glucogenic precursors” (the word “decreased” was removed).3.In paragraph 6, line 21 of page 1396, the text now reads “... including decreased metabolites of the urea pathway …” rather than “including elevated metabolites of the urea pathway”4.In paragraph 6, line 26 of page 1396, the text now reads “... revealed an increase in glucogenic AAs” rather than “... revealed a decline in glucogenic AAs” Although amino acid metabolites are not the primary outcome of the work described in this paper and these errors do not alter the main conclusions outlined therein, the authors regret the errors. Hyperglucagonemia Mitigates the Effect of Metformin on Glucose Production in PrediabetesKonopka et al.Cell ReportsMay 5, 2016In BriefUsing a randomized, double-blinded, placebo-controlled, crossover study design in prediabetic individuals, Konopka et al. show that metformin improves fasting and postprandial glycemia without inhibiting glucagon-stimulated glucose production as reported in preclinical studies. During metformin therapy, increased glucagon and glucogenic precursors may maintain glucose production to prevent hypoglycemia. Full-Text PDF Open Access
Evolution of Rhizaria: new insights from phylogenomic analysis of uncultivated protists (2010)

Our study provides new insights into the evolution of Rhizaria based on phylogenomic analyses of ESTs from three groups of previously under-sampled protists. It was enabled through the application of a recently developed method of transcriptome analysis, requiring very small amount of starting material. Our study illustrates the potential of this method to elucidate the early evolution of eukaryotes by providing large amount of data for uncultivable free-living and parasitic protists.
Cloning, Sequencing, Heterologous Expression, and Mechanistic Analysis of A-74528 Biosynthesis (2010)

A-74528 is a recently discovered natural product of Streptomyces sp. SANK 61196 that inhibits 2',5'-oligoadenylate phosphodiesterase (2'-PDE), a key regulatory enzyme of the interferon pathway. Inhibition of 2'-PDE by A-74528 reduces viral replication, and therefore shows promise as a new type of antiviral drug. The complete A-74528 gene cluster, comprising 29 open reading frames, was cloned and sequenced, and shown to possess a type II polyketide synthase (PKS) at its core. Its identity was confirmed by analysis of a mutant generated by targeted disruption of a PKS gene, and by functional expression in a heterologous Streptomyces host. Remarkably, it showed exceptional end-to-end sequence identity to the gene cluster responsible for biosynthesis of fredericamycin A, a structurally unrelated antitumor antibiotic with a distinct mode of action. Whereas the fredericamycin producing strain, Streptomyces griseus, produced undetectable quantities of A-74528, the A-74528 gene cluster was capable of producing both antibiotics. The biosynthetic roles of three genes, including one that represents the only qualitative difference between the two gene clusters, were investigated by targeted gene disruption. The implications for the evolution of antibiotics with different biological activities from the same gene cluster are discussed.
Clavaspirin, an antibacterial and haemolytic peptide from Styela clava. (2001)

We cloned the precursor of a novel peptide from a cDNA library prepared from pharyngeal tissues of the tunicate, Styela clava. Its sequence predicted a histidine-rich, amidated 23-residue peptide (FLRF(IG)SVIHGIGHLVHHIGVAL-NH2) that we named clavaspirin. A synthetic clavaspirin was prepared and it was found that it killed Gram-positive and Gram-negative bacteria, permeabilized the outer and inner membranes of Escherichia coli, lysed phosphatidylglycerol (POPG) liposomes, and was potently haemolytic towards human and bovine erythrocytes. Each of these activities was performed more effectively at an acidic pH. Circular dichroism measurements of synthetic clavaspirin revealed a largely alpha-helical structure and polarized and residue-specific FTIR spectrometry showed that its association with phospholipid membranes was influenced by pH. Peptides such as clavaspirin may equip tunicate haemocytes to mediate cytotoxicity and participate in antimicrobial defence.
Glial Reaction in Parkinsons Diseases: Inflammatory Activation Signaling of Glia as a Potential Therapeutic Target (2007)

Although the main cause of many neurodegenerative diseases is unknown, the glial reaction is considered to be a consequence of neuronal cell death in Alzheimers disease, Parkinsons disease, and Huntingtons disease. In Parkinsons disease, postmortem examination and experimental animal models exposed to neurotoxin reveals a dramatic loss of dopaminergic neurons in the substantia nigra associated with a massive astrogliosis and the presence of activated microglial cells. These glial cells can release deleterious compounds such as proinflammatory prostaglandins and cytokines, which may act by stimulating reactive oxygen species in glial cells, or which may exert a more direct effect on dopaminergic neurons by activating receptors that contain death domains involved in neuronal apoptosis. The anti-inflammatory drugs and the tetracycline derivative minocycline have been shown to reduce glial activation and protect the substantia nigra in an animal model of the disease. Inhibition of the glial reaction and the inflammatory processes may thus represent a therapeutic target to reduce neuronal degeneration in Parkinsons disease. Elucidation of molecular mechanisms underlying intracellular signal transductions of glial activation will provide promising means of controlling neuroinflammation and the subsequent neurodegeneration.
Analysis of three contention protocols in distributed real-time systems (1990)

The probability of a station/node failing to deliver packets before their deadlines, called the probability of dynamic failure, P/sub dyn/, and the in -bounded delivery time, which is defined as the time period between the arrival of a packet and its delivery with probability greater than 1- in , are important performance parameters for the communication subsystems of a distributed real-time system. The parameters are derived and are used to evaluate the token passing protocol, the token ring scheduling protocol, and the P/sub i/-persistent protocol and a priority-based variation thereof. The communication subsystem equipped with different contention protocols as embedded Markov chains is modeled. The probability distributions of the access delay are then derived, from which P/sub dyn/ and T/sub in / can be calculated. Using P/sub dyn/ and I/sub in / as indices, the performances of these contention protocols are evaluated and compared over a wide range of traffic.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Automatic protocol field inference for deeper protocol understanding (2015)

Security tools have evolved dramatically in the recent years to combat the increasingly complex nature of attacks, but to be effective these tools need to be configured by experts that understand network protocols thoroughly. In this paper we present FieldHunter, which automatically extracts fields and infers their types; providing this much needed information to the security experts for keeping pace with the increasing rate of new network applications and their underlying protocols. FieldHunter relies on collecting application messages from multiple sessions and then applying statistical correlations is able to infer the types of the fields. These statistical correlations can be between different messages or other associations with meta-data such as message length, client or server IPs. Our system is designed to extract and infer fields from both binary and textual protocols. We evaluated FieldHunter on real network traffic collected in ISP networks from three different continents. FieldHunter was able to extract security relevant fields and infer their nature for well documented network protocols (such as DNS and MSNP) as well as protocols for which the specifications are not publicly available (such as SopCast) and from malware such as (Ramnit).
Turbulent Boundary Layer Inner-Outer Interactions (1993)

A summary of work performed to study the interactions between the inner and outer regions of a turbulent boundary layer is presented. The interactions were studied by observing the response of the boundary layer to different perturbations. The inner region was modified by adding surface roughness, and the outer region suppressed using LEBU's. Velocity measurements were made with a three component LDV, a scanning LDV, and an X-type hot-film probe. The scanning LDV was developed to obtain continuous time history measurements of instantaneous velocity profiles down to y+ = 10. Details of the structure of bursts, sweeps, and shear layers over smooth and rough walls were determined using conditional sampling with simultaneous measurements from a detector probe and a mapping probe. This allowed the mapping of the complete three-dimensional structure of the three-component velocity field for these structures. Both single point detection, using quadrant and VITA techniques, and a unique spatially coherent structure detection technique were used. The spatial detection technique developed in this project takes advantage of the two- dimensional velocity field information obtained from the scanning LDV. Scanning laser doppler velocimeter, Burst, Sweep, Shear layer large scale structure,
Intermittent pneumatic compression for prevention of pulmonary thromboembolism after gynecologic surgery (2005)

Preventive measures, including intermittent pneumatic compression, should be taken to avoid postoperative pulmonary thromboembolism in the gynecology field.
USC Rocket Propulsion Laboratory: Experiences Modeling a Composite Combustion Chamber (2012)

The University of Southern California Rocket Propulsion Laboratory is developing a single stage sounding rocket capable of delivering a small electronics payload past the Karman line at 100 km altitude. In order to launch the rocket, the FAA requires extensive ight quali cation testing and analysis of the vehicle. This development and quali cation process includes a full scale static ring of the solid fuel booster to verify propulsion performance and design integrity. The single stage solid motor design incorporates an entirely carbon composite combustion chamber. This unique design is necessary to meet weight requirements on the rocket, but introduces complexities in the structural analysis. The combustion chamber structure is a very long carbon composite tube, the ends of which are sealed with aluminum pressure bulkheads retained with steel dowel pins. Though successfully demonstrated in subscale static and ight testing, this motor case design experienced catastrophic failures during consecutive static rings of ight-scale hardware. Post ight accident investigation was performed in order to identify the root cause failure of these static rings. A high delity model of the thrust chamber accounting for the continuously varying directional properties was built using the Abaqus Uni ed Finite Element Analysis (FEA). The cause of the failure of the rst live ring was determined to be the direct result of loads applied by the thrust stand retention methods. The second livering failed as a result of a buckling failure of the thrust stand. The numerical simulation exonerated the ight motor case design and provided insight into how to x the thrust stand for future testing. Additionally, it a orded the student team the rationale to move forward with the development of ight hardware and the seeking of ight opportunities despite testing anomalies.
Buried InGaP/GaAs grating distributed feedback laser with AlGaAs cladding (2009)

We report on a DFB laser technology for GaAs based lasers. Such a structure is normally problematic to achieve due to overgrowth on Al containing layers. Our technique is to use an InGaP/GaAs grating layer in conjunction with AlGaAs cladding layers, where the AlGaAs is never exposed to air. Due to the high refractive index contrast of InGaP/GaAs, the grating layer is ~450 nm from the active layer, which helps in minimising any deleterious effects of the re-growth process on laser performance. The initial structure was grown by MOVPE process. The epitaxial structure was designed by modelling confinement factors in a commercial refractive index mode solver.
On the Reliable Identification of Plant Sequences Containing a Polyadenylation Site (2007)

It is a challenging task to predict with high reliability whether plant genomic sequences contain a polyadenylation (polyA) site or not. In this paper, we solve the task by means of a systematic machine-learning procedure applied on a dataset of 1000 Arabidopsis thaliana sequences flanking polyA sites. Our procedure consists of three steps. In the first step, we extract informative features from the sequences using the highly informative k-mer windows approach. Experiments with five classifiers show that the best performance is approximately 83%. In the second step, we improve performance to 95% by reducing the number of features using linear discriminant analysis, followed by applying the linear discriminant classifier. In the third step, we apply the transductive confidence machines approach and the receiver operating characteristic isometrics approach. The resulting two classifiers enable presetting any desired performance by dealing carefully with sequences for which it is unclear whether they contain polyA sites or not. For example, in our case study, we obtain 99% performance by leaving 26% of the sequences unclassified, and 100% performance by leaving 40% of the sequences unclassified. This is clearly useful for experimental verification of putative polyA sites in the laboratory. The novel methods in our machine-learning procedure should find applications in several areas of bioinformatics.
ChemInform Abstract: New Routes to Synthesizing an Ordered Perovskite CaCu3Fe2Sb2O12 and Its Magnetic Structure by Neutron Powder Diffraction. (2014)

Abstract A high‐quality A,B‐site‐ordered double perovskite CaCu 3 Fe 2 Sb 2 O 12 is prepared at ambient pressure by two routes, a wet‐chemical procedure involving a mixture of CuO, Fe(NO 3 ) 3.9 H 2 O, Ca(NO 3 ) 2 , and Sb 2 O 3 in citric acid and few HNO 3 which is slowly evaporated and decomposed at 550 °C followed by a complex heating schedule (≈92% yield) and, secondly, by activating an oxide mixture of CuO, Fe 2 O 3 , Sb 2 O 3 , and CaCO 3 by ball milling also followed by a complex heating schedule in which the amorphous material recrystallizes at &lt; 820 °C (perovskite phase yield of 97%).
A Pilot Study of Anti-CTLA4 Antibody Ipilimumab in Patients with Synovial Sarcoma (2013)

Background. Patients with recurrent synovial sarcomas have few options for systemic therapy. Since they express large amounts of endogenous CT (cancer testis) antigens such as NY-ESO-1, we investigated the clinical activity of single agent anti-CTLA4 antibody ipilimumab in patients with advanced or metastatic synovial sarcoma. Methods. A Simon two-stage phase II design was used to determine if there was sufficient activity to pursue further. The primary endpoint was tumor response rate by RECIST 1.0. Patients were treated with ipilimumab 3 mg/kg intravenously every 3 weeks for three cycles and then restaged. Retreatment was possible for patients receiving an extra three-week break from therapy. Sera and peripheral blood mononuclear cells were collected before and during therapy to assess NY-ESO-1-specific immunity. Results. Six patients were enrolled and received 1-3 cycles of ipilimumab. All patients showed clinical or radiological evidence of disease progression after no more than three cycles of therapy, for a RECIST response rate of 0%. The study was stopped for slow accrual, lack of activity, and lack of immune response. There was no evidence of clinically significant either serologic or delayed type hypersensitivity responses to NY-ESO-1 before or after therapy. Conclusion. Despite high expression of CT antigens by synovial sarcomas of patients treated in this study, there was neither clinical benefit nor evidence of anti-CT antigen serological responses. Assessment of the ability of synovial sarcoma cell lines to present cancer-germ cell antigens may be useful in determining the reason for the observed lack of immunological or clinical activity.
Estimation of the chemical potential of chain molecules by simulation (1992)

A novel method is presented for the calculation of the chemical potential of molecules with articulated structure by molecular simulation. The method, based on a biased sampling of phase space, is applied here to systems of linear alkanes represented by methylene pseudoatoms connected by rigid bonds at fixed angles. The results of our biased-sampling scheme are compared to those of other available methods (when they can provide results) for calculation of the chemical potential of dense systems.
Developing Seeds of Arabidopsis Store Different Minerals in Two Types of Vacuoles and in the Endoplasmic Reticulum (2002)

Mineral-accumulating compartments in developing seeds of Arabidopsis were studied using high-pressure-frozen/freeze-substituted samples. Developing seeds store minerals in three locations: in the protein storage vacuoles of the embryo, and transiently in the endoplasmic reticulum (ER) and vacuolar compartments of the chalazal endosperm. Energy dispersive x-ray spectroscopy and enzyme treatments suggest that the minerals are stored as phytic acid (myo-inositol-1,2,3,4,5,6-hexakisphosphate) salts in all three compartments, although they differ in cation composition. Whereas embryo globoids contain Mg, K, and Ca as cations, the chalazal ER deposits show high levels of Mn, and the chalazal vacuolar deposits show high levels of Zn. The appearance of the first Zn-phytate crystals coincides with the formation of network-like extensions of the chalazal vacuoles. The core of these networks consists of a branched network of tubular ER membranes, which are separated from the delineating tonoplast membranes by a layer of cytosolic material. Degradation of the networks starts with the loss of the cytosol and is followed by the retraction of the ER, generating a network of collapsed tonoplast membranes that are resorbed. Studies of fertilized fis2 seeds, which hyperaccumulate Zn-phytate crystals in the chalazal vacuolar compartments, suggest that only the intact network is active in mineral sequestration. Mineral determination analysis and structural observations showed that Zn and Mn are mobilized from the endosperm to the embryo at different developmental stages. Thus, Zn appears to be removed from the endosperm at the late globular stage, and Mn stores appear to be removed at the late bent-cotyledon stage of embryo development. The disappearance of the Mn-phytate from the endosperm coincides with the accumulation of two major Mn binding proteins in the embryo, the 33-kD protein from the oxygen-evolving complex of photosystem II and the Mn superoxide dismutase. The possible functions of transient heavy metal storage in the chalazal endosperm are discussed. A model showing how phytic acid, a potentially cytotoxic molecule, is transported from its site of synthesis, the ER, to the different mineral storage sites is presented.
34.2: Field Sequential LC Barrier for a Full Resolution Auto‐stereoscopic 3D Display (2011)

Abstract In this paper, we have developed 15.6 inch auto‐stereoscopic 3D display with a field sequential LC parallax barrier which shows the full resolution image of the panel even in the 3D mode. By field sequential switching of a barrier and an image panel, we can compensate the loss of the resolution in the LC barrier type 3D display. We also investigated the field sequential switching effect on the performance of the LC parallax barrier type 3D display.
High speed observation of ultrafast machining dynamics (2008)

We demonstrate simultaneous drilling and coaxial depth imaging of holes in stainless steel at axial rates of 46 kHz. Depth measurement with 6 mum resolution is performed using the machining beam via Fourier-domain interferometry.
Detachable Object Detection: Segmentation and Depth Ordering From\n Short-Baseline Video (2011)

We describe an approach for segmenting an image into regions that correspond\nto surfaces in the scene that are partially surrounded by the medium. It\nintegrates both appearance and motion statistics into a cost functional, that\nis seeded with occluded regions and minimized efficiently by solving a linear\nprogramming problem. Where a short observation time is insufficient to\ndetermine whether the object is detachable, the results of the minimization can\nbe used to seed a more costly optimization based on a longer sequence of video\ndata. The result is an entirely unsupervised scheme to detect and segment an\narbitrary and unknown number of objects. We test our scheme to highlight the\npotential, as well as limitations, of our approach.\n