gebhart/patrepeval huggingface dataset:
CTLA-4 blockade with ipilimumab increases peripheral CD8+ T cells: Correlation with clinical outcomes. (2010)

2555 Background: Increasing doses of ipilimumab, an antibody to CTLA-4, is associated with a higher likelihood of clinical benefit. Analysis of pharmacodynamic biomarkers shows the magnitude of absolute lymphocyte count (ALC) increase correlates with dose. Identifying the lymphocyte subpopulations specifically increased may further elucidate the mechanism of action of CTLA-4 blockade. In a pooled analysis of four phase II trials (CA184-045, -008, -078, -042), peripheral blood lymphocytes subsets were analyzed from 35 patients (pts) with advanced melanoma treated with ipilimumab at Memorial Sloan-Kettering. Methods: Ipilimumab was administered (10 mg/kg every 3 weeks × 4 doses) and eligible pts continued to receive ipilimumab maintenance therapy every 12 weeks starting at week 24 in the setting of disease control. Under an institutional IRB- approved correlative blood drawing protocol, peripheral blood was obtained at weeks 1 (pre-treatment) and 7 (just before 3rd dose) and lymphocyte counts determined and evaluated for CD8/CD4/CD25+ populations using multiparametric flow cytometry. Response-evaluable pts with lymphocyte subpopulation analysis (n = 35) were classified by clinical activity (complete, partial response, stable disease 24 weeks, or progression of disease). Results: Increases in CD8+ T cells between weeks 1 and 7 were larger than changes in CD4+ or CD4+CD25+ cells. Pts with clinical benefit were noted to have a statistically significant increase in CD8+ T cells (p = 0.0294) but not CD4+ T cells (p = 0.2237) compared with nonclinical benefiters. There was a trend between degree of objective response and absolute change of CD8+ T cells and CD4+ T cells. Changes in CD4+/CD25+ T cells did not correlate with clinical response (p = 0.2912). Conclusions: Increased rate of ALC change during ipilimumab therapy is associated with clinical activity in this retrospective analysis. Specifically, increased CD8+ T cells were associated with improved clinical outcome, while absolute change in CD4+ CD25+ T cells did not appear to differ between the clinical outcome groups. This clinical correlation needs to be confirmed prospectively in trials of CTLA-4 blockade with ipilimumab. Author Disclosure Employment or Leadership Position Consultant or Advisory Role Stock Ownership Honoraria Research Funding Expert Testimony Other Remuneration Bristol-Myers Squibb
Long-Term Culture-Initiating Cell Assay for Mouse Cells (2012)

The long-term culture-initiating cell (LTC-IC) assay is a well-established in vitro assay used to enumerate primitive mouse hematopoietic stem cells (HSCs) and relies on the two cardinal functions of HSCs: ability to self-renew and differentiation capacity. LTC-ICs present in minimally processed and purified cell suspensions and cocultured on a supportive feeder layer are detected by their sustained ability to produce hematopoietic progenitors (colony forming cells) after ≥ 4 weeks in culture. Refinements including the use of a defined stromal cell line, and extending the in vitro culture to 6 weeks allow detection of LTC-IC at similar frequencies to transplantable HSCs quantified using in vivo assays.
Highly-uniform multi-layer ReRAM crossbar circuits (2016)

Resistive switching memories have been identified as an enabling technology for a variety of emerging computing applications, including neuromorphic and logic-in-memory computing. For example, analog tuning of the memory state combined with high integration density of memristors is needed for very compact implementation of synapses, the most numerous devices in artificial neural networks and would be essential for low energy implementations of large-scale neuromorphic circuits. One way to increase effective memristor density is by vertical monolithical integration of memristor crossbar circuits. Previous work on such circuits have focused on their use for digital memory applications. Only limited device statistics was typically reported, not sufficient for understanding prospects for computing applications. Here we report fabrication and detailed characterization results for a bilayer stacked metal-oxide memristor crossbar circuits. The experimental results show excellent uniformity for the memristors in both crossbar layers. Moreover, the utilized low temperature process flow is CMOS compatible and can be extended to multi-layer stacking.
Air Bridge Based Planar Hybrid Technology for Microwave and Millimeterwave Applications (1997)

A new silicon based, planar hybrid technology is being developed to address limitations associated with packaging and interconnections. The approach combines the advantages of both hybrid and monolithic technologies. Microwave transistor chips (e.g. GaAs FETs) are glued with an epoxy resin in openings micromachined in a high resistivity silicon substrate with a vertical precision of better than 2 μm and lateral tolerances less than 10 μm. Air bridge technology and thin film techniques are then used to provide the necessary interconnections. Preliminary results show very promising high frequency properties of this assembly.
TX and RX Front-Ends for 60GHz Band in 90nm Standard Bulk CMOS (2008)

This paper describes the design of a mm-wave power amplifier PA with reliability considerations for hot carrier injection (HCI) degradation. A 60GHz-band single-chip transmitter front- end with an output power of 6dBm for 2.6 Gb/s QPSK modulation and a single-chip receiver front-end are implemented in a standard IV 90 nm CMOS technology.
Association Between Opioid Prescribing Patterns and Opioid Overdose-Related Deaths (2011)

Among patients receiving opioid prescriptions for pain, higher opioid doses were associated with increased risk of opioid overdose death.
Word Embedding-based Context-sensitive Network Flow Payload Anomaly Detection (2021)

Payload anomaly detection can discover malicious behaviors hidden in network packets. It is hard to handle payload due to its various possible characters and complex semantic context, and thus identifying abnormal payload is also a non-trivial task. Prior art only uses the n-gram language model to extract features, which directly leads to ultra-high-dimensional feature space and also fails to capture the context semantics fully. Accordingly, this paper proposes a word embedding-based context-sensitive network flow payload anomaly detection method (termed WECAD). First, WECAD obtains the initial feature representation of the payload through the word embedding-based method. Then, we propose a corpus pruning algorithm, which applies the cosine similarity clustering and frequency distribution to prune inconsequential characters. We only keep the essential characters to reduce the calculation space. Subsequently, we propose a context learning algorithm. It employs the co-occurrence matrix transformation technology and introduces the backward step size to consider the order relationship of essential characters. Comprehensive experiments on real-world intrusion detection datasets validate the effectiveness of our method.
CD40/CD40 Homodimers Are Required for CD40-induced Phosphatidylinositol 3-Kinase-dependent Expression of B7.2 by Human B Lymphocytes (2004)

Preformed CD40/CD40 homodimers were initially observed on human Burkitt lymphoma cell lines, normal B cells, and transitional bladder carcinoma cell lines. However, the nature and the biological relevance of these homodimers have not yet been investigated. In the present study, we demonstrated that Epstein-Barr virus-transformed B cells and CD40-transfected HEK 293 cells constitutively expressed disulfide-linked CD40/CD40 homodimers at low levels. Oligomerization of CD40 leads to a rapid and significant increase in the disulfide-linked CD40/CD40 homodimer formation, a response that could be prevented using a thiol-alkylating agent. Formation of CD40/CD40 homodimers was found to be absolutely required for CD40-mediated activation of phosphatidylinositol 3-kinase, which, in turn regulated B7.2 expression. In contrast, CD40 monomers provided the minimal signal emerging from CD40, activating p38 MAP kinase and inducing homotypic B cell adhesion. CD40/CD40 homodimer formation was totally independent of TRAF1/2/3/5 associations with the threonine at position 254 in the cytoplasmic tail of the CD40 molecules. This finding may be vital to better understanding the molecular mechanisms that govern cell signaling triggered by CD40/CD154 interactions.
Inverse-Design-based Light Via for Multi-Layer Photonic Integration Circuit (2018)

A multi-layer light via for TE-polarized light is proposed based on inverse design. Simulation results show that the insertion loss is 0.55dB at 1550nm, and the device has an ultra-wide 1dB bandwidth of 1451-1712nm.
Seizure frequency reduction after posteromedial hypothalamus deep brain stimulation in drug‐resistant epilepsy associated with intractable aggressive behavior (2015)

In well-selected patients, DBS of the pHyp seems to be a safe and effective procedure for treatment of DRE associated with refractory aggressive behavior. Larger and prospective series are needed to define the pHyp as a target for DRE in different contexts.
Synthesis, Comparative Photosensitizing Efficacy, Human Serum Albumin (Site II) Binding Ability, and Intracellular Localization Characteristics of Novel Benzobacteriochlorins Derived from <i>vic</i>-Dihydroxybacteriochlorins (2003)

In a sequence of reactions, methyl mesopyropheophorbide a, mesochlorin e(6) trimethyl ester, mesochlorin p(6) trimethyl ester, mesopurpurin-18-N-hexylimide methyl ester, and mesopurpurin-18-N-3,5-bis(trifluoromethyl)benzylimide methyl ester were synthesized from chlorophyll-a. These chlorins on reacting with osmium tetraoxide produced the corresponding vic-dihydroxybacteriochlorins. The 8-vinylchlorins obtained by refluxing the related vic-dihydroxybacteriochlorins in o-dichlorobenzene were individually treated with dimethylacetylenedicarboxylate (DMAD) under Diels-Alder reaction conditions. The intermediate adducts on 1,8-diazabicyclo[5.4.0]undec-7-ene (DBU) treatment rearranged to the corresponding stable benzobacteriochlorins, exhibiting the longest wavelength absorption in the range of 737 to 805 nm. In preliminary in vitro (RIF tumor cells) and in vivo screening (C3H/HeJ mice bearing RIF tumors), some of these compounds were found to be quite effective. Under similar treatment conditions (drug dose: 5.0 micromol/kg; light dose: 135 J/cm(2), tumors were exposed to light for 30 min at 24 h postinjection), the benzobacteriochlorins containing N-substituted-imide ring system produced enhanced photosensitizing efficacy with limited skin phototoxicity. These compounds were also found to bind to site II of human serum albumin (HSA). However, no correlation between the binding constant values and photosensitizing efficacy was observed. A competitive intracellular localization study of these novel structures with Rhodamine-123 (a mitochondrial probe) indicated their preferential localization in mitochondria, without producing any specific displacement of (3)H-PK11195 (PBR probe, (3)H-labeled 1-(2-chlorophenyl)-N-methyl-N-(1-methylpropyl)-3-isoquinoline carboxamide). These results suggest that the mitochondrial peripheral benzodiazepine receptor (PBR) is not the cellular binding site for this class of compounds.
Arbitrarily oriented SAW gratings: network model and the coupling-of-modes description (1991)

A network model for surface-acoustic-wave (SAW) structures fabricated along arbitrary and hence nonsymmetric orientations, including natural single-phase unidirectional transducer (NSPUDT) directions, is described. From the predictions of this model for SAW gratings. the frequently used coupling of modes (COM) phenomenological description is evaluated. The network model consists of the usual sequence of mismatched transmission lines with susceptance loading at discontinuities to account for energy storage, plus a new additional reactive element calculated using a perturbation formula, to account for the asymmetry that exists for arbitrary orientations. The circuit elements are determined by geometrical and material parameters. It is demonstrated that the incremental COM description can be derived from the unit-cell-based network model, and analytical formulas quoted in the literature for the COM coefficients are compared with the values calculated from the ABCD network model description. An analytically tractable approximation for the network model is also described, from which rather simple explicit formulas for the COM coefficients that predict their dependence on material parameters and on frequency are derived. The analysis and numerical calculations indicate that these formulas may yield results that are valid over almost 30% relative bandwidths.
Video technique for measuring dynamics of liquid‐liquid dispersion during phase inversion (1994)

Abstract Studies on the dynamics of phase inversion available offer limited information due to the difficulty of following the transient mean and drop‐size distribution. A new technique developed provides such data. A stereo microscope with a very shallow depth of field attached to a video camera gives sharp images of droplets in intensely‐agitated, immiscible liquid dispersions by using a Strobotach pulsing at the camera framing rate. Droplets from 40 μm upward at concentrations up to 70% by volume dispersed phase can be measured accurately. Droplets of continuous organic phase in aqueous drops can be seen. The pictures can be analyzed semiautomatically using a computer and in‐house software to give, using a variety of discretizations, cumulative and frequency distributions to any base and any mean size. Means and distributions are a function of time for phase inversions generated in three ways. The technique gives a powerful tool for understanding fast, complex dispersion processes.
Internal Movement of <i>Erwinia amylovora</i> Through Symptomless Apple Scion Tissues into the Rootstock (1998)

Shoot tips of potted Empire and Golden Delicious trees on the susceptible dwarfing rootstock M.26 in the greenhouse were injected with inoculum containing 5 × 10<sup>9</sup> CFU/ml Erwinia amylovora. At intervals after inoculation, trees were sampled at increments between the shoot tip and the roots by excising stem segments. Segments were ground in phosphate buffer and assayed for the presence of E. amylovora by plating on semi-selective medium and by a polymerase chain reaction (PCR)-based detection method. Eleven days after inoculation, E. amylovora was detected by PCR in symptomless scion tissue >50 cm below the shoot-tip in Empire and Golden Delicious, and in 2-year-old tissue in Golden Delicious. By 21 days, E. amylovora was detected in the M.26 rootstock of Empire trees, and by 41 days in the M.26 rootstock of Golden Delicious. In a similar experiment the following year, Empire trees on M.26 rootstock were inoculated with E. amylovora at early (16 May), mid- (11 June), and late (6 July) phenophase of shoots. Three weeks after inoculation, E. amylovora was detected by PCR from M.26 rootstocks of five of six plants inoculated at the late phenophase, compared to zero of six plants inoculated at the early or mid-phenophase. Late-season fire blight infections of the scion may be particularly hazardous for the health of the rootstock.
A Cross-Cultural Study of Weddings through Media and Ritual: Analyzing Indian and North American Weddings (2006)

The wedding is one of the only rituals or events that many cultures of the world consistently have in common. Weddings are found in almost every society. A wedding can feed consumer appetites and the industry that supports it. Costs for the average United States wedding can range from $26,000 to $35,530 or more (“Cost of Weddings” 2006). The costs of Indian wedding ceremonies vary from $34,000 up to $2 million (Das 2005). Despite this large range the Indian wedding industry averages only $11billion annually while its American counterpart is a whopping $50 billion each year (“Cost of Weddings” 2006, Das 2005). Remarriages constitute 30% of the American wedding industry (Ingram 1999) while in India, remarriage is relatively uncommon. Given the amount of money spent on this cultural ritual, it is reasonable to assert that it carries a great deal of personal, cultural, and social significance. I’m going to contrast and compare Indian and American weddings through an examination of film. This study is similar to Best’s (2000) study of American proms, another related cultural tradition. Specifically I will examine portrayals of wedding ceremonies as presented by both Hollywood and Bollywood films.
Piezoelectricity in tungsten bronze crystals (1994)

The range of piezoelectric properties available in tungsten bronze crystals reviewed includes both longitudinal and shear mode responses. Specific crystal compositions investigated include Sr1-xBaxNb2O6 (SBN), Ba2-xSrxK1-yNayNb5O15 (BSKNN), K3Li2Nb5O15 (KLN), (Ba, Sr)6Ti2Nb8O30 (BSTN), Sr2-x-CaxNaNb5O15 (SCNN), Sr2KNb5O15 (SKN) and Pb1-xBaxNb2O6 (PBN). SBN, SCNN and SKN exhibit large piezoelectric d33 coefficients, while BSKNN, PBN:60 and KLN have large d15 shear coefficients. In La3+ -modified SBN:60, d33 can exceed 1000 pC/N, although its relaxor character increases with increasing La3+ content. The role of dopants in the 12-, 9- and 6-fold coordinated crystallographic sites is described with respect to the relaxor character of SBN crystals. The high piezoelectric and dielectric constants in these single crystals suggest their use in high frequency ultrasonic tomography. Both piezoelectric and electrostrictive options would appear to be available in the bronzes and the very high perfection of the available crystals could permit the generation of composite ultrasonic senders and receivers at scales which would be impossible in conventional polycrystalline piezoelectric ceramics.
Optimized arterial trees supplying hollow organs (2005)

Computer models of arterial trees can be generated from optimization principles using the algorithm of constrained constructive optimization (CCO). Up to now this algorithm could handle only tissue areas of convex shape, without concavities. CCO is now generalized to cope also with non-convex organ shapes, possibly featuring external as well as internal concavities. This allows the modeling of a much larger class of interesting real arterial systems. The concept of a generalized domain-potential was developed to represent arbitrary non-convex shapes mathematically and incorporate them as boundary conditions to optimization. Domain-potentials may be derived from analytical representations as well as from finite element triangulations obtained from organ images. To demonstrate the feasibility of the concept, the optimized growth of an arterial tree model is confined to some part of an elliptical shell, representing the free wall of the left ventricle of the heart.
Mass Spectrometric Imaging of Wheat (<i>Triticum</i> spp.) and Barley (<i>Hordeum vulgare</i> L.) Cultivars: Distribution of Major Cell Wall Polysaccharides According to Their Main Structural Features (2016)

Arabinoxylans (AX) and (1→3),(1→4)-β-glucans (BG) are the main components of cereal cell walls and influence many aspects of their end uses. Important variations in the composition and structure of these polysaccharides have been reported among cereals and cultivars of a given species. In this work, the spatial distribution of AX and BG in the endosperm of mature grains was established for nine wheat varieties and eight barley varieties using enzymatically assisted mass spectrometry imaging (MSI). Important structural features of the AX and BG polymers that were previously shown to influence their physicochemical properties were assessed. Differences in the distribution of AX and BG structures were observed, both within the endosperm of a given cultivar and between wheat and barley cultivars. This study provides a unique picture of the structural heterogeneity of AX and BG polysaccharides at the scale of the whole endosperm in a series of wheat and barley cultivars. Thus, it can participate meaningfully in a strategy aiming at understanding the structure-function relationships of these two polymers.
SAM-T08, HMM-based protein structure prediction (2009)

The SAM-T08 web server is a protein structure prediction server that provides several useful intermediate results in addition to the final predicted 3D structure: three multiple sequence alignments of putative homologs using different iterated search procedures, prediction of local structure features including various backbone and burial properties, calibrated E-values for the significance of template searches of PDB and residue-residue contact predictions. The server has been validated as part of the CASP8 assessment of structure prediction as having good performance across all classes of predictions. The SAM-T08 server is available at http://compbio.soe.ucsc.edu/SAM_T08/T08-query.html.
Cloud resource broker in the optimization of medical image retrieval system: A proposed goal-based request in medical application (2011)

Medical informatics application nowadays combines computer technology and clinical medicine to improve health care, medical education, and medical research. The availability of large amount and ever increasing of medical images produce a big crisis in existing processes for collecting patient's important data which need a great deal of many works to discover, select, and analyze the information. To reduce treatment delay and the errors when retrieving the data, resource broker technology must be bring into this field with providing proper indexing metadata. Existing medical imaging communities are increasingly aware of implementing broker in their technologies. In this paper, we present a solution to improve current medical image retrieval system by introducing goal-based cloud resource broker. Our solution is based on concept of goal which enables users to define required resources and to optimize the use of resources in the cloud. Several contributions have been found from this research where enhanced resources broker by using goal-based request have been proposed to maximize resources allocation within cloud environment and minimizing user involvement in resources discovery.
Elevated Serum Sialic Acid Concentration in NIDDM and Its Relationship to Blood Pressure and Retinopathy (1993)

Total serum sialic acid levels were significantly elevated in a relatively small group of NIDDM patients and were correlated with hypertension and retinopathy. A larger study of circulating sialic acid concentrations as a risk factor for the development or marker of diabetic angiopathy is therefore justified.
Broadband diffraction management and self-collimation of white light in photonic lattices (2006)

We introduce periodic photonic structures where the strength of diffraction can be managed in a very broad frequency range. We show how to design arrays of curved waveguides where light beams experience wavelength-independent normal, anomalous, or zero diffraction. Our results suggest opportunities for efficient self-collimation, focusing, and reshaping of beams produced by white-light and supercontinuum sources. We also predict a possibility of multicolor Talbot effect, which is not possible in free space or conventional photonic lattices.
Design Optimization of Broadband Linear Polarization Converter Using Twisted Nematic Liquid Crystal (2003)

An optimization method was developed for improving the designs of broadband linear polarization converters using a twisted nematic liquid crystal film and two uniaxial compensation films. As compared to the Poincare Sphere approach, our optimization method takes the material dispersions into consideration and results in a broader bandwidth. Such a broadband half-wave film is particularly useful for enhancing the light efficiency of liquid crystal display devices.