gebhart/patrepeval huggingface dataset:
Bi-directional signaling for dynamic TDD with decentralized beamforming (2015)

This paper introduces a novel bi-directional signaling scheme for decentralized beamformer design to maximize the weighted sum rate (WSR) of multi-cell multi-user multiple-input multiple-output dynamic time division duplexing (TDD) system. In particular, the base stations are assumed to be either in uplink or downlink state based on the instantaneous traffic demand. The WSR maximization problem is solved via the corresponding weighted sum mean-squared error (MSE) minimization problem. An iterative algorithm is proposed with the bi-directional signaling embedded into the TDD frame structure. A detailed signaling architecture is proposed to facilitate channel estimation, exchanging the user beamformers and the user MSE weight matrices among the coordinating nodes. The proposed coordinated system is compared with the uncoordinated system while taking into account the overhead originated from bi-directional signaling. Finally, a periodic beamformer re-initialization strategy is introduced, which enhances the beamformer convergence rate and the system performance in a time-correlated fading environment. The proposed coordinated system provides significant performance gain in an interference limited environment.
ChemInform Abstract: Sol‐Gel Encapsulated Light‐Transducing Protein Phycoerythrin: A New Biomaterial (1996)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Vacuum-sealed silicon micromachined pressure sensors (1998)

Considerable progress in silicon pressure sensors has been made in recent years. This paper discusses three types of vacuum-sealed silicon micromachined pressure sensors that represent the present state of the art in this important area. The devices are a capacitive vacuum sensor, a surface-micromachined microdiaphragm pressure sensor, and a resonant pressure sensor. Vacuum sealing for these devices is accomplished using anodic bonding, films deposited using low-pressure chemical vapor deposition, and thermal out-diffusion of hydrogen, respectively. These sensors emphasize high sensitivity, small size, and excellent stability, respectively. The silicon-diaphragm vacuum sensor uses electrostatic force balancing to achieve a wide pressure measurement range.
Compound A influences gene regulation of the Dexamethasone-activated glucocorticoid receptor by alternative cofactor recruitment (2017)

The glucocorticoid receptor (GR) is a transcription factor of which the underlying gene regulatory mechanisms are complex and incompletely understood. The non-steroidal anti-inflammatory Compound A (CpdA), a selective GR modulating compound in various cell models, has been shown to favour GR-mediated gene repression but not GR-mediated gene activation. Shifting balances towards only a particular subset of GR gene regulatory events may be of benefit in the treatment of inflammatory diseases. We present evidence to support that the combination of CpdA with Dexamethasone (DEX), a classic steroidal GR ligand, can shape GR function towards a unique gene regulatory profile in a cell type-dependent manner. The molecular basis hereof is a changed GR phosphorylation status concomitant with a change in the GR cofactor recruitment profile. We subsequently identified and confirmed the orphan nuclear receptor SHP as a coregulator that is specifically enriched at GR when CpdA and DEX are combined. Combining CpdA with DEX not only leads to stronger suppression of pro-inflammatory gene expression, but also enhanced anti-inflammatory GR target gene expression in epithelial cells, making ligand combination strategies in future a potentially attractive alternative manner of skewing and fine-tuning GR effects towards an improved therapeutic benefit.
NeuroSoL: Automated classification of neurons using the sorted Laplacian of a graph (2017)

One of the most exciting open problems in biological image analysis is the categorization of neurons based on observed morphology. Complex arborization patterns, varied orientations, different sizes, nonidentical alignments of local branches act as barriers to a systematic and quantitative analysis of neurons. This open problem demands a refined approach to capture salient and robust, global and local features to compare digitally-traced 3D neuron atlases. We propose NeuroSoL to consolidate global as well as local morphological and geometrical features by leveraging a specialized graph framework. Specifically, without imposing any restriction on the structure and connectivity, we use fully-sorted and mixed-sorted Laplacians of the neuron graph and the corresponding complementary graph. For meaningful clustering of neurons, we also develop a similarity metric after retrieving optimal local alignment between the feature descriptors of two neurons. Results on neuron datasets show the efficacy of our approach over state-of-the-art techniques.
DNA Synthesis in Human Fibroblasts: Stimulation by Insulin and by Nonsuppressible Insulin-like Activity (NSILA-S) (1974)

The effects of acid-soluble nonsuppressible insulin-like activity (NSILA-S) and insulin on DNA synthesis by cultured human fibroblasts have been compared. NSILA-S and insulin, like serum, stimulated [3H]thymidine incorporation into DNA after an 8- to 10-hour lag, reaching maximum levels after 16 to 20 hr. Insulin was effective only at high concentrations, 0.02 μg/ml or greater, whereas NSILA-S was active at concentrations that have been reported in human serum. Combined addition of maximally effective concentrations of insulin and NSILA-S failed to give additive stimulation, suggesting that the two polypeptides act by a common mechanism. In contrast, combined addition of insulin and serum, or NSILA-S and serum, gave additive responses.
The genomic substrate for adaptive radiation in African cichlid fish (2014)

Cichlid fishes are famous for large, diverse and replicated adaptive radiations in the Great Lakes of East Africa. To understand the molecular mechanisms underlying cichlid phenotypic diversity, we sequenced the genomes and transcriptomes of five lineages of African cichlids: the Nile tilapia (Oreochromis niloticus), an ancestral lineage with low diversity; and four members of the East African lineage: Neolamprologus brichardi/pulcher (older radiation, Lake Tanganyika), Metriaclima zebra (recent radiation, Lake Malawi), Pundamilia nyererei (very recent radiation, Lake Victoria), and Astatotilapia burtoni (riverine species around Lake Tanganyika). We found an excess of gene duplications in the East African lineage compared to tilapia and other teleosts, an abundance of non-coding element divergence, accelerated coding sequence evolution, expression divergence associated with transposable element insertions, and regulation by novel microRNAs. In addition, we analysed sequence data from sixty individuals representing six closely related species from Lake Victoria, and show genome-wide diversifying selection on coding and regulatory variants, some of which were recruited from ancient polymorphisms. We conclude that a number of molecular mechanisms shaped East African cichlid genomes, and that amassing of standing variation during periods of relaxed purifying selection may have been important in facilitating subsequent evolutionary diversification.
Nontrivial link overlap distribution in three-dimensional Ising spin glasses (2007)

We investigate the distributions of the link overlap, $P(Q)$, in three-dimensional Ising spin glasses. We use clustering methodology to identify a set of pairs of states from different Gibbs states and calculate its contribution to $P(Q)$. We find that the distribution over this set does not become trivial as the system size increases.
Differences in the level of expression of class I major histocompatibility complex proteins on thymic epithelial and dendritic cells influence the decision of immature thymocytes between positive and negative selection (1998)

Both positive and negative selection of immature T cells rely on engagement of their antigen-specific receptors (TCR) by peptide in association with proteins encoded in the major histocompatibility complex (MHC) protein. The decision made between these two outcomes seems to be determined by the number of TCR engaged by peptide-MHC complexes. It has been unclear how such a mechanism can be reconciled with evidence that positive and negative selection occur in different thymic compartments and are mediated by different antigen-presenting cells (APCs). In this study we demonstrate that the level of class I MHC protein is 10-fold higher on thymic dendritic cells, which mediate the negative selection of immature T cells, than on thymic epithelial cells, which mediate for positive selection. We also demonstrate that as little as a 3-fold increase in the level of a particular cognate peptide-MHC ligand is sufficient to result in negative rather than positive selection. The results suggest that quantitative differences in the level of expression of class I MHC proteins on thymic epithelial and dendritic cells contribute to the opposing roles these cells play in forming the repertoire of mature class I MHC restricted (CD8+) T cells.
P556 The effect of multiple doses of upadacitinib 45 mg on the pharmacokinetics of cytochrome P450 substrates in healthy adult subjects (2022)

Abstract Background Upadacitinib is a selective Janus kinase 1 inhibitor, which is approved for treatment of several inflammatory diseases. Upadacitinib 45 mg QD dose was evaluated for induction treatment in ulcerative colitis Phase 3 studies and is currently being evaluated in Crohn’s disease Phase 3 studies. A prior clinical study demonstrated that upadacitinib 30 mg QD dose resulted in no clinically relevant effects on plasma exposures of sensitive probe substrates for cytochrome P450 (CYP) enzymes. The objective of this study was to evaluate the effect of repeated doses of upadacitinib 45 mg on the pharmacokinetics of sensitive probe substrates of CYP enzymes in healthy adult subjects. Methods This was an open-label, multiple-dose, two-period study using the modified Cooperstown 5 + 1 cocktail drugs (midazolam [CYP3A], caffeine [CYP1A2], warfarin + vitamin K [CYP2C9], omeprazole [CYP2C19], and dextromethorphan [CYP2D6]). Twenty healthy adults received single oral doses of the cocktail drugs without upadacitinib in Period 1, followed by daily dosing of upadacitinib 45 mg for 16 days and administration of the cocktail drugs on Day 11 (for midazolam) and Day 12 (rest of substrates) in Period 2. A washout period of 6 days separated each Period. Serial blood samples and 12-hour urine samples (for dextromethorphan and dextrorphan) were collected. Pharmacokinetic parameters were estimated using noncompartmental analysis and repeated-measures analyses were performed for the natural logarithms of Cmax and AUC to assess the effect of upadacitinib on the probe substrates. Results The ratio (90% confidence interval) of area under the plasma concentration-time curve from time 0 to infinity (AUCinf) central values when the cocktail drugs were administered with upadacitinib 45 mg relative to when administered alone were 0.76 (0.69–0.83) for midazolam, 1.04 (0.95–1.13) for caffeine, 1.12 (1.05–1.20) for S-warfarin, 1.35 (1.18–1.54) for dextromethorphan, and 0.98 (0.85–1.13) for omeprazole. The 5-hydroxy-omeprazole to omeprazole plasma AUC ratio was unchanged (90% confidence interval within the no effect limits of 0.8 to 1.25). Conclusion Administration of daily upadacitinib 45 mg doses resulted in a limited effect on midazolam (CYP3A) and dextromethorphan (CYP2D6) exposures and had no relevant effects on the sensitive probe substrates for CYP1A2, CYP2C9 and CYP2C19. These limited effects are not expected to be clinically relevant or necessitate dose adjustment of CYP3A or CYP2D6 substrates. These results are consistent with a previous drug interaction evaluation for upadacitinib 30 mg and support lack of relevant effects of upadacitinib on drugs metabolized by CYP enzymes.
A Case Report of Diffuse Alveolar Hemorrhage Coexisting With Immunoglobulin A (IgA) Nephropathy (2022)

Immunoglobulin A (IgA) nephropathy is the most common cause of primary glomerulonephritis worldwide. IgA vasculitis (formerly known as Henoch-Schonlein purpura) typically presents with IgA nephropathy on renal biopsy in addition to extrarenal symptoms like purpura, abdominal pain, and arthritis. Diffuse alveolar hemorrhage (DAH) is the most common pulmonary complication, but this is rarely seen. In this case report, we describe a 35-year-old male with chronic untreated hepatitis B infection who presented with pulmonary-renal syndrome. He was found to have clinical findings of DAH and concomitant IgA nephropathy on renal biopsy, without having any other typical manifestations of IgA vasculitis. This shows that IgA nephropathy should be considered in the differential diagnosis of DAH and emphasizes the importance of a renal biopsy in patients presenting with pulmonary-renal syndrome.
A fap5 Allele for Elevated Palmitate in Soybean (2000)

Soybean [ Glycine max (L.) Merr.] oil with elevated palmitate content may be useful for producing plastic fats without hydrogenation. The mutant line A27, with ≈160 g kg −1 palmitate, was developed by treatment of seeds of ‘Kenwood’ with ethyl methanesulfonate. The objective of this study was to determine the genetic control of elevated palmitate content in A27. A27 was crossed to Kenwood and to lines possessing the fap1 , fap2‐b , fap3 , fap4 , or fap6 alleles for altered palmitate. Analysis of the F 1 , F 2 , and F 3 generations indicated that A27 had an allele for elevated palmitate at a single locus, designated fap5 , that exhibited additive gene action with Fap5 and mutant alleles for altered palmitate content. The fap5 locus was independent of the fap1 , fap3 , fap4 , and fap6 loci, but closely linked to the fap2‐b locus.
Nanospectroscopy of single quantum dots with local strain control using a phase-change mask (2017)

Herein, we describe a new technique that allows high-sensitivity near-field imaging spectroscopic analysis of individual quantum constituents in semiconductors. This method employs an optical mask composed of a phase-change material (PCM) and operates at optical telecommunication wavelengths. Superior collection efficiency and spatial resolution are achieved by using an amorphous nanoaperture as a result of the extreme optical contrast between the PCM in amorphous and crystalline phases at visible wavelengths and the good near-infrared transparency of this material. Fine tuning of quantum dot (QD) emission levels via localized strain as a result of the increase in volume of the PCM upon amorphization has also been demonstrated. Both red and blue shifts of the energy levels were predicted to occur beneath the flat and edge regions of the amorphous mask, respectively, using finite element simulations. The viability of localized strain tuning as an approach to nanospectroscopy employing phase changes was confirmed by measurements of the photoluminescence of individual InAs/InP QDs. In addition, the emission levels of two neighboring QDs were matched based on modifying the shift magnitudes and directions via careful adjustment of the indenter size and position.
From microbial genomics to meta-genomics (1997)

Modern microbial genomics is best exemplified by determination of the complete nucleotide sequences of whole genomes. To date, the sequences of at least 11 nuclear genomes have been completed, with many more in progress. Most are microbial, with exceptions such as the eukaryotic genome Saccharomyces cerevisiae. Genomics, while built upon foundations laid in the era of classical genetics, has grown by leaps and bounds because of three significant technological advances: 1) high-throughput sequencing and automation technology, 2) sophisticated bioinformatics and sequence analysis tools, and 3) microarray or “chip” technology for expression, resequencing, and polymorphism analysis. These technological advances have made it possible to generate massive amounts of nucleotide sequence data from a series of random, overlapping, and redundant clones and to assemble these data into contiguous sequences, with the final goal of elucidating complete gene structure at single nucleotide resolution. In the immediate future, linear genomics will be replaced by functional genomics and pathogens compared on an evolutionary scale. Drug Dev. Res. 41:180–192, 1997. © 1997 Wiley-Liss, Inc.
The prognosis of CALM-AF10-positive adult T-cell acute lymphoblastic leukemias depends on the stage of maturation arrest (2013)

CALM-AF10 (also known as PICALM-MLLT10) is the commonest fusion protein in T-cell acute lymphoblastic leukemia, but its prognostic impact remains unclear. Molecular screening at diagnosis identified CALM-AF10 in 30/431 (7%) patients with T-cell acute lymphoblastic leukemia aged 16 years and over and in 15/234 (6%) of those aged up to 15 years. Adult CALM-AF10-positive patients were predominantly (72%) negative for surface (s)CD3/T-cell receptor, whereas children were predominantly (67%) positive for T-cell receptor. Among 22 adult CALM-AF10-positive patients treated according to the LALA94/GRAALL03-05 protocols, the poor prognosis for event-free survival (P=0.0017) and overall survival (P=0.0014) was restricted to the 15 T-cell receptor-negative cases. Among CALM-AF10-positive, T-cell receptor-negative patients, 82% had an early T-cell precursor phenotype, reported to be of poor prognosis in pediatric T-cell acute lymphoblastic leukemia. Early T-cell precursor acute lymphoblastic leukemia corresponded to 22% of adult LALA94/GRAALL03-05 T-cell acute lymphoblastic leukemias, but had no prognostic impact per se. CALM-AF10 fusion within early T-cell precursor acute lymphoblastic leukemia (21%) did, however, identify a group with a poor prognosis with regards to event-free survival (P=0.04). CALM-AF10 therefore identifies a poor prognostic group within sCD3/T-cell receptor negative adult T-cell acute lymphoblastic leukemias and is over-represented within early T-cell precursor acute lymphoblastic leukemias, in which it identifies patients in whom treatment is likely to fail. Its prognosis and overlap with early T-cell precursor acute lymphoblastic leukemia in pediatric T-cell acute lymphoblastic leukemia merits analysis. The clinical trial GRAALL was registered at Clinical Trials.gov number NCT00327678.
KGI: An Integrated Framework for Knowledge Intensive Language Tasks (2022)

Md Faisal Mahbub Chowdhury, Michael Glass, Gaetano Rossiello, Alfio Gliozzo, Nandana Mihindukulasooriya. Proceedings of the 2022 Conference on Empirical Methods in Natural Language Processing: System Demonstrations. 2022.
Supplementary Figure 1 from Antibody Targeting GRP78 Enhances the Efficacy of Radiation Therapy in Human Glioblastoma and Non–Small Cell Lung Cancer Cell Lines and Tumor Models (2023)

&lt;p&gt;Treatment with antibody against GRP78 does not reduce proliferation and colony formation in normal cell lines.&lt;/p&gt;
Herpes simplex virus type I infection of the CNS induces major histocompatibility complex antigen expression on rat microglia (1990)

Rats were infected with herpes simplex virus type I (HSV-1) by corneal scarification. The spread of virus in the brain, the infiltration of leucocytes into infected areas, and the expression of major histocompatibility complex (MHC) glycoproteins by brain cells were assessed as a function of time by immunohistochemistry. Virus moved along neuronal pathways, achieving widespread distribution in the brain by days 8-10 when the illness appeared most severe. Granulocytes, T-lymphocytes, and monocytes infiltrated the tissue matrix at sites of infection. Microglial cells were induced to express MHC class I and class II glycoproteins. Reactive microglia near the sites of infection most vigorously expressed such glycoproteins. At the peak of the infection they were detectable on microglia throughout the brain, including areas apparently separated from active infection. Evidence of viral antigens, as well as microglial MHC expression, had largely disappeared by day 30. Neurons, astrocytes, and oligodendroglial cells failed to express MHC antigens.
Faculty Opinions recommendation of Affinity profiling of the cellular kinome for the nucleotide cofactors ATP, ADP, and GTP. (2013)

Most kinase inhibitor drugs target the binding site of the nucleotide cosubstrate ATP. The high intracellular concentration of ATP can strongly affect inhibitor potency and selectivity depending on the affinity of the target kinase for ATP. Here we used a defined chemoproteomics system based on competition-binding assays in cell extracts from Jurkat and SK-MEL-28 cells with immobilized ATP mimetics (kinobeads). This system enabled us to assess the affinities of more than 200 kinases for the cellular nucleotide cofactors ATP, ADP, and GTP and the effects of the divalent metal ions Mg(2+) and Mn(2+). The affinity values determined in this system were largely consistent across the two cell lines, indicating no major dependence on kinase expression levels. Kinase-ATP affinities range from low micromolar to millimolar, which has profound consequences for the prediction of cellular effects from inhibitor selectivity profiles. Only a small number of kinases including CK2, MEK, and BRAF exhibited affinity for GTP. This extensive and consistent data set of kinase-nucleotide affinities, determined for native enzymes under defined experimental conditions, will represent a useful resource for kinase drug discovery. PMID: 23215245
Ion Desorption from TiO<sub>2</sub>(110) by Low Energy Positron Impact (2017)

We have observed positron-stimulated ion desorption from a TiO 2 (110) surface. H + and O + ions were desorbed at incident positron energies above the desorption thresholds for electron impact. However, only O + ions were detected at energies below those thresholds. These results suggest that by surface ionization positron annihilation as well as by positron impact leads to the O + ion desorption. By contrast, it is likely that the H + ions are not desorbed by positron annihilation, but rather by impact ionization.
Relationship between Acropora millepora juvenile fluorescence and composition of newly established Symbiodinium assemblage (2018)

Abstract Coral-dinoflagellate symbiosis is the key biological interaction enabling existence of modern-type coral reefs, but the mechanisms regulating initial host–symbiont attraction, recognition and symbiont proliferation thus far remain largely unclear. A common reef-building coral, Acropora millepora , displays conspicuous fluorescent polymorphism during all phases of its life cycle, due to the differential expression of fluorescent proteins (FPs) of the green fluorescent protein family. In this study, we examine whether fluorescent variation in young coral juveniles exposed to natural sediments is associated with the uptake of disparate Symbiodinium assemblages determined using ITS-2 deep sequencing. We found that Symbiodinium assemblages varied significantly when redness values varied, specifically in regards to abundances of clades A and C. Whether fluorescence was quantified as a categorical or continuous trait, clade A was found at higher abundances in redder juveniles. These preliminary results suggest juvenile fluorescence may be associated with Symbiodinium uptake, potentially acting as either as an attractant to ecologically specific types or as a mechanism to modulate the internal light environment to control Symbiodinium physiology within the host.