gebhart/patrepeval huggingface dataset:
Intratumoral expression levels of <i>PD-L1</i>, <i>GZMA</i>, and <i>HLA-A</i> along with oligoclonal T cell expansion associate with response to nivolumab in metastatic melanoma (2016)

Immune checkpoint inhibitors blocking the interaction between programmed death-1 (PD-1) and PD-1 ligand-1 (PD-L1) are revolutionizing the cancer immunotherapies with durable clinical responses. Although high expression of PD-L1 in tumor tissues has been implicated to correlate with the better response to the anti-PD-1 therapies, this association has been controversial. In this study, to characterize immune microenvironment in tumors, we examined mRNA levels of immune-related genes and characterized T cell repertoire in the tumors of 13 melanoma patients before and after nivolumab treatment. We found that, in addition to the <i>PD-L1</i> (<i>p</i> = 0.03), expression levels of PD-1 ligand-2 (<i>PD-L2</i>), granzyme A (<i>GZMA</i>) and human leukocyte antigen-A (<i>HLA-A</i>) in the pre-treatment tumors were significantly higher (<i>p</i> = 0.04, <i>p</i> = 0.01 and <i>p</i> = 0.006, respectively) in responders (n = 5) than in non-responders (n = 8). With nivolumab treatment, tumors in responders exhibited a substantial increase of <i>CD8</i>, <i>GZMA</i> and perforin 1 (<i>PRF1</i>) expression levels as well as increased ratio of <i>TBX21/GATA3</i>, suggesting dominancy of helper T cell type 1 (Th1) response to type 2 (Th2) response. T cell receptor β (TCR-β) repertoire analysis revealed oligoclonal expansion of tumor-infiltrating T lymphocytes (TILs) in the tumor tissues of the responders. Our findings suggest that melanoma harboring high PD-1 ligands (<i>PD-L1</i> and <i>PD-L2), GZMA</i> and <i>HLA-A</i> expression may respond preferentially to nivolumab treatment, which can enhance Th1-skewed cellular immunity with oligoclonal expansion of TILs.
Fiat Lux: a fluorescent lamp transceiver (2002)

The prevalence of electric discharge illumination has led the authors to consider ways to use discharge lamps for communication. This paper describes an optical transceiver system which transmits by modulating the lamp arc. The prototype power electronic lamp ballast uses a pulse frequency modulation scheme which ensures no perceptible flicker.
Vascular endothelial growth factor enhances macrophage clearance of apoptotic cells (2012)

Efficient clearance of apoptotic cells from the lung by alveolar macrophages is important for the maintenance of tissue structure and function. Lung tissue from humans with emphysema contains increased numbers of apoptotic cells and decreased levels of vascular endothelial growth factor (VEGF). Mice treated with VEGF receptor inhibitors have increased numbers of apoptotic cells and develop emphysema. We hypothesized that VEGF regulates apoptotic cell clearance by alveolar macrophages (AM) via its interaction with VEGF receptor 1 (VEGF R1). Our data show that the uptake of apoptotic cells by murine AMs and human monocyte-derived macrophages is inhibited by depletion of VEGF and that VEGF activates Rac1. Antibody blockade or pharmacological inhibition of VEGF R1 activity also decreased apoptotic cell uptake ex vivo. Conversely, overexpression of VEGF significantly enhanced apoptotic cell uptake by AMs in vivo. These results indicate that VEGF serves a positive regulatory role via its interaction with VEGF R1 to activate Rac1 and enhance AM apoptotic cell clearance.
Comparison of Histidine-Tryptophan Ketoglutarate Solution and University of Wisconsin Solution in Prolonged Cold Preservation of Kidney Allografts (2006)

Although University of Wisconsin (UW) solution is the standard preservation solution for organ transplantation, Histidine-Tryptophan Ketogluatarate (HTK) solution has been increasingly used. This study compared HTK or UW for cold static storage of kidney allografts. In all, 149 renal transplants were performed with cold ischemic times (CI) greater than 16 hr (UW 87, HTK 62) and a subset analysis was performed with CI over 24 hr (HTK 31, UW 38). Data from receiving renal transplant centers focused on delayed graft function (DGF), patient and allograft survival. In CI greater than 16 hr, graft and patient survival were comparable. HTK cohort had lower DGF. In CI greater than 24 hr, there was no difference in patient survival, a trend towards improved graft survival in HTK, and decreased rate of DGF in HTK. This data suggests that UW and HTK have at least similar efficacy in kidney preservation at longer ischemic times.
Highly transparent organic light-emitting diodes with a metallic top electrode: the dual role of a Cs_2CO_3 layer (2011)

Highly transparent organic light-emitting diodes (TrOLEDs) are demonstrated using damage-free top cathodes of Cs2CO3/ Ag capped with ZnS layers. The presence of ultrathin Cs2CO3 layers not only improves the electron injection properties but also makes Ag thin films more continuous and uniform, resulting in ideal top electrodes with low sheet resistance and high transmittance. The combination of the uniform Ag morphology enabled by Cs2CO3 and the optimized thickness of ZnS capping layers results in TrOLEDs that have a peak transmittance as large as 80% with a luminous transmittance of 76.4%. These TrOLEDs exhibit a low turn-on voltage of 2.6V due to injection improvement by the Cs2CO3 layers.
Environmentally friendly mixed tannin/lignin wood resins (2007)

Abstract We obtained lignin‐based wood adhesives satisfying the requirements of relevant international standards for the manufacture of wood particleboard. These were based on two different low‐molecular‐mass lignins. These lignin‐based wood adhesives did not use any formaldehyde in their formulation; formaldehyde was substituted with a nonvolatile nontoxic aldehyde, namely, glyoxal. The last formaldehyde present, contributed by a fortifying synthetic phenol–formaldehyde resin, was also eliminated by the substitution of the phenol–formaldehyde resin with a natural, vegetable polyflavonoid tannin extract to which no aldehyde was added. This substitution brought the total content of natural material up to 80 wt % of the total adhesive. The adhesives yielded good internal bond strength results of the panels, enough to pass relevant international standard specifications for interior‐grade panels. © 2007 Wiley Periodicals, Inc. J Appl Polym Sci, 2008
Phenolic compounds in date palm cultivars sensitive and resistant toFusarium oxysporum (1996)

In date palm (Phoenix dactylifera L.) leaves, the main compounds of the phenolic pool were quercetin and isorhamnetin heterosides, (+)-catechin and (-)-epicatechin. Although previously observed only in date palm fruits, 5-caffeoylshikimic acid (dactylifric acid) and its positional isomers (3-caffeoylshikimic acid and 4-caffeoylshikimic acid) were detected also in the leaves and roots. Quantitative, but not qualitative, differences between cultivars resistant and susceptible toFusarium oxysporum f. sp.albedinis during growth period were observed
Optimizing Main Memory Usage in Modern Computing Systems to Improve Overall System Performance (2016)

Operating Systems use fast, CPU-addressable main memory to maintain an application’s temporary data as anonymous data and to cache copies of persistent data stored in slower block-based storage devices. However, the use of this faster memory comes at a high cost. Therefore, several techniques have been implemented to use main memory more efficiently in the literature. In this dissertation we introduce three distinct approaches to improve overall system performance by optimizing main memory usage. First, DRAM and host-side caching of file system data are used for speeding up virtual machine performance in today’s virtualized data centers. The clustering of VM images that share identical pages, coupled with data deduplication, has the potential to optimize main memory usage, since it provides more opportunity for sharing resources across processes and across different VMs. In our first approach, we study the use of content and semantic similarity metrics and a new algorithm to cluster VM images and place them in hosts where through deduplication we improve main memory usage. Second, while careful VM placement can improve memory usage by eliminating duplicate data, caches in current systems employ complex machinery to manage the cached data. Writing data to a page not present in the file system page cache causes the operating system to synchronously fetch the page into memory, blocking the writing process. In this thesis, we address this limitation with a new approach to managing page writes involving buffering the written data elsewhere in memory and unblocking the writing process immediately. This buffering allows the system to service file writes faster and with less memory resources. In our last approach, we investigate the use of emerging byte-addressable persistent memory technology to extend main memory as a less costly alternative to exclusively using expensive DRAM. We motivate and build a tiered memory system wherein persistent memory and DRAM co-exist and provide improved application performance at lower cost and power consumption with the goal of placing the right data in the right memory tier at the right time. The proposed approach seamlessly performs page migration across memory tiers as access patterns change and/or to handle tier memory pressure.
Genotype associations among seven apolipoprotein B polymorphisms in a population of Orang Asli of western Malaysia. (1997)

Associations among seven apolipoprotein B (APOB) gene polymorphisms [C-T promoter site; Leu-Ala-Leu signal peptide (SP) insertion/deletion; AG C,G site at codon 71; AG A1,D site at codon 591; XbaI site at codon 2488; AG H,I site at codon 3611; and AG T,Z site at codon 4154] were investigated in 195 members of an Orang Asli (aborigine) population from western Malaysia. Frequencies of the rare alleles for all these polymorphisms turned out to be low when compared with European but not Asian populations. The AG H,I site was not polymorphic. The highly polymorphic sites are in linkage disequilibrium among themselves, as shown by their delta values: SP 24,27 and AG C,G, 0.68; SP 24,27 and AG A1,D, 0.71; XbaI and AG C,G, 0.64; XbaI and AG A1,D, 0.57; SP 24,27 and XbaI, 0.48; and AG C,G and AG A1,D, 0.68. Ten unequivocal haplotypes on the basis of six sites (excluding the promoter polymorphism) were observed, and they represent 80% of the sample. The frequency of haplotype SP27,G,A1,X-,I,T, defined by the common homozygotes at all the sites for the APOB gene was 0.7, compared with 0.22 in Europeans. The ancestral haplotype SP27,G,D,X-,I,T was present at low frequency (0.01) in both the Orang Asli and Europeans. A cladogram constructed on the basis of haplotypes in the Orang Asli shows two different lines of evolution and that other haplotypes evolved by subsequent mutations on the ancestral haplotype.
Optimization of missing value imputation using Reinforcement Programming (2015)

Missing value imputation is a crucial and challenging research topic in data mining because the data in real life are often contains missing value. The incorrect way to handle missing value will lead major problem in data mining processing to produce a new knowledge. One technique to solve Missing value imputation is by using machine learning algorithm. In this paper, we will present a new approach for missing data imputation using Reinforcement Programming to deal with incomplete data by filling the incompleteness data with considering exploration and exploitation of its environment to learn the data pattern. The experimental result demonstrates that Reinforcement Programming runs well and has a great result of SSE of new data with assigned value and shows effectiveness computational time than the other five imputation methods used as benchmark.
Protein <i>trans</i> -splicing by a split intein encoded in a split DnaE gene of <i>Synechocystis</i> sp. PCC6803 (1998)

A split intein capable of protein trans-splicing is identified in a DnaE protein of the cyanobacterium Synechocystis sp. strain PCC6803. The N- and C-terminal halves of DnaE (catalytic subunit alpha of DNA polymerase III) are encoded by two separate genes, dnaE-n and dnaE-c, respectively. These two genes are located 745,226 bp apart in the genome and on opposite DNA strands. The dnaE-n product consists of a N-extein sequence followed by a 123-aa intein sequence, whereas the dnaE-c product consists of a 36-aa intein sequence followed by a C-extein sequence. The N- and C-extein sequences together reconstitute a complete DnaE sequence that is interrupted by the intein sequences inside the beta- and tau-binding domains. The two intein sequences together reconstitute a split mini-intein that not only has intein-like sequence features but also exhibited protein trans-splicing activity when tested in Escherichia coli cells.
Ion-bombardment-induced whisker formation on graphite (1983)

The bombardment of surfaces with energetic ions has led to the development of various types of surface topography. In one special case, that of graphite, ion bombardment is responsible for the formation of whiskerlike structures. Whiskers formed under ion bombardment exhibit an initial rapid growth process followed by a slower, diffusion-fed process. The rates of lengthening and thickening during the diffusion-fed process appear to be constant in time. Whisker length increases nonlinearly with beam energy; population density decreases as beam energy increases. Whiskers grow parallel to the ion beam. Their alignment is apparently dominated by the destruction of nonparallel whiskers rather than electric field effects. Simultaneous impurity seeding inhibits whisker formation and can totally suppress formation if sufficient flux is present. A growth model involving stress relief at recrystallization front junctures qualitatively fits many experimental observations.
Algebraic geometrization of the Kuramoto model: Equilibria and stability analysis (2015)

Finding equilibria of the finite size Kuramoto model amounts to solving a nonlinear system of equations, which is an important yet challenging problem. We translate this into an algebraic geometry problem and use numerical methods to find all of the equilibria for various choices of coupling constants K, natural frequencies, and on different graphs. We note that for even modest sizes (N ~ 10-20), the number of equilibria is already more than 100 000. We analyze the stability of each computed equilibrium as well as the configuration of angles. Our exploration of the equilibrium landscape leads to unexpected and possibly surprising results including non-monotonicity in the number of equilibria, a predictable pattern in the indices of equilibria, counter-examples to conjectures, multi-stable equilibrium landscapes, scenarios with only unstable equilibria, and multiple distinct extrema in the stable equilibrium distribution as a function of the number of cycles in the graph.
TriMap: Large-scale Dimensionality Reduction Using Triplets (2019)

We introduce "TriMap"; a dimensionality reduction technique based on triplet constraints, which preserves the global structure of the data better than the other commonly used methods such as t-SNE, LargeVis, and UMAP. To quantify the global accuracy of the embedding, we introduce a score that roughly reflects the relative placement of the clusters rather than the individual points. We empirically show the excellent performance of TriMap on a large variety of datasets in terms of the quality of the embedding as well as the runtime. On our performance benchmarks, TriMap easily scales to millions of points without depleting the memory and clearly outperforms t-SNE, LargeVis, and UMAP in terms of runtime.
Bioregulators for Pest Control (1985)

Agrichemical transport in the phloem is discussed in terms of the physiological, biochemical, and structural bases of assimilate translocation. Specifically, the cellular pathways and mechanisms of phloem loading in source leaves, long distance transport, and phloem unloading in sinks, are used as a framework for examining the biological basis of the systemic mobility of agrichemicals.
Electrochemical Detection of Short DNA Oligomer Hybridization Using the CombiMatrix ElectraSense Microarray Reader (2006)

Abstract A microarray reader named ElectraSense using an electrochemical detection technique has been developed for the CombiMatrix CustomArray 12 544 electrode semiconductor DNA microarray. The detection is based on electrochemical reduction of the enzymatic oxidization product of 3,3′,5,5′‐tetramethylbenzidene (TMB). TMB oxidation is catalyzed by a horseradish peroxidase (HRP) biomarker linked to a DNA target molecule through biotin‐avidin chemistry. Electrochemical signal collection is performed by a computer controlled combinatorial semiconductor addressing instrument. Electrode to electrode switching can be accomplished in hundreds of microseconds and a detection time for each electrode is less than 5 ms. The whole array detection requires less than 60 s. Numerous parameters of the measurement procedure have been optimized and assay performance has been studied and a method for array quality control has been developed. Application of electrochemical detection of Combimatrix microarrays has been demonstrated for DNA detection over 4 orders of magnitude of target concentrations and detection of avian influenza subtype H5N1.
A WAN-Optimized Live Storage Migration Mechanism toward Virtual Machine Evacuation upon Severe Disasters (2013)

Wide-area VM migration is a technology with potential to aid IT services recovery since it can be used to evacuate virtualized servers to safe locations upon a critical disaster. However, the amount of data involved in a wide-area VM migration is substantially larger compared to VM migrations within LAN due to the need to transfer virtualized storage in addition to memory and CPU states. This increase of data makes it challenging to relocate VMs under a limited time window with electrical power. In this paper, we propose a mechanism to improve live storage migration across WAN. The key idea is to reduce the amount of data to be transferred by proactively caching virtual disk blocks to a backup site during regular VM operation. As a result of pre-cached disk blocks, the proposed mechanism can dramatically reduce the amount of data and consequently the time required to live migrate the entire VM state. The mechanism was evaluated using a prototype implementation under different workloads and network conditions, and we confirmed that it dramatically reduces the time to complete a VM live migration. By using the proposed mechanism, it is possible to relocate a VM from Japan to the United States in just under 40 seconds. This relocation would otherwise take over 1500 seconds, demonstrating that the proposed mechanism was able to reduce the migration time by 97.5%.
A comparison of fundamental gate-driver topologies for high frequency applications (2004)

The gate-driver in most power electronic converters is seldom given sufficient attention during the design stage even though it is the circuit exposed to much of the same voltage stresses as the switching devices and yet despite this, is a crucial component to a sound functioning system. At higher switching frequencies, and either low power or high voltage applications, the effect of the gate-driver on the overall converter performance becomes even more pronounced. When considering a gate-driver for a power electronic system, the converter topology, operating conditions and requirements, voltage and current ratings, and switching frequency determines the suitability and applicability of a chosen gate-driver to the application. This paper discusses different gate-drivers, represented by three fundamental gate-driver topologies that are evaluated in terms of suitable operating conditions, construction and losses. These gate-drivers, constructed using two different methods, a hybrid and SMD, also forms part of the evaluation. In addition, some of the issues as switching frequencies keep increasing is also addressed.
A self-organizing map model for spatial and temporal contextual classification (2002)

This paper opens up a new prospect for exploring the Kohonen self-organizing map (SOM) model of multiple SOMs (MSOM, Wan-Fraser, 1994) for spatial and temporal contextual classification of remote sensing (RS) images. Since the model can effectively exploit correlation information within the data in the sense of clustering and autoassociation without parametric models, it can be treated as a unified framework to exploit various correlations as clusters within and among multi-sources and across spectral, spatial, temporal and labeling contexts of images and associated label maps in a recursive manner. It can significantly improve classification accuracy, provided that various spatial and temporal correlations are coded and represented explicitly for compound clustering and autoassociation. The underlying mechanisms for contextual analysis are Markov random field (MRF) and stochastic relaxation by use of recursive neighborhood operators with no parametric models. The capability of the model is demonstrated by a bitemporal TM data experiment.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Ketamine Treatment in Depression: A Systematic Review of Clinical Characteristics Predicting Symptom Improvement (2020)

Ketamine has been shown to be efficacious for the treatment of depression, specifically among individuals who do not respond to first-line treatments. There is still, however, a lack of clarity surrounding the clinical features and response periods across samples that respond to ketamine. This paper systematically reviews published randomized controlled trials that investigate ketamine as an antidepressant intervention in both unipolar and bipolar depression to determine the specific clinical features of the samples across different efficacy periods. Moreover, similarities and differences in clinical characteristics associated with acute versus longer-term drug response are discussed. Similarities across all samples suggest that the population that responds to ketamine's antidepressant effect has experienced chronic, long-term depression, approaching ketamine treatment as a "last resort". Moreover, differences between these groups suggest future research to investigate the potential of stronger efficacy towards depression in the context of bipolar disorder compared to major depression, and in participants who undergo antidepressant washout before ketamine administration. From these findings, suggestions for the future direction of ketamine research for depression are formed.