gebhart/patrepeval huggingface dataset:
G-Protein-Coupled Receptor Screen Reveals a Role for Chemokine Receptor CCR5 in Suppressing Microglial Neurotoxicity (2008)

G-protein-coupled receptors (GPCRs) form the largest superfamily of membrane proteins, and several GPCRs have been implicated in signaling between neurons and glia to protect neurons from pathological stresses. Here, we have used a screening strategy to investigate GPCRs that are involved in neuronal protection. The real-time PCR was performed using 274 primers targeting nonsensory GPCR mRNAs, which were listed on the database. The cDNAs from control and nerve-injured hypoglossal nuclei of mouse brain were used, and the alterations of PCR products were compared. This screen and the subsequent in situ hybridization screen exhibited six GPCR mRNAs which were prominently and convincingly induced in nerve-injured hypoglossal nuclei. Among these candidates, the chemokine receptor CCR5 was selected, based on the marked induction in CCR5 mRNA in microglia after nerve injury. The mRNA expression of ligands for CCR5, such as regulated on activation normal T-cell expressed and secreted (RANTES/CCL5), MIP-1alpha, and MIP-1beta, were induced in injured motor neurons, indicating that CCR5 and its ligands were expressed in microglia and neurons, respectively, in response to nerve injury. In vitro, lipopolysaccharide (LPS)-induced expression of mRNAs for inflammatory cytokines (IL-1beta, IL-6, and tumor necrosis factor-alpha) and inducible nitric oxide synthase (iNOS) in microglia were all suppressed by RANTES. Those suppressions were not observed in microglia from CCR5 null mice. In addition, nerve injury-induced motor neuron death seen in wild type C56BL/6J mice was accelerated in CCR5 knock-out C57BL/6J. These results may suggest that CCR5-mediated neuron-glia signaling functions to protect neurons by suppressing microglia toxicity.
Primary structure of p19 species of avian sarcoma and leukemia viruses (1985)

The internal structural proteins of avian sarcoma and leukemia viruses are derived from a precursor polypeptide that is the product of the viral gag gene. The N-terminal domain of the precursor gives rise to p19, a protein that interacts with the lipid envelope of the virus and that may also interact with viral RNA. The C terminus of p19 from the Prague C strain of Rous sarcoma virus was previously assigned to a tyrosine residue 175 amino acids from the N terminus. We have used metabolic labeling and carboxypeptidase digestion to show that the C terminus of p19 is actually tyrosine 155. This implies the existence of a sixth gag protein 22 amino acids in length and located between p19 and p10 on the gag precursor. The p19 species of some recombinant avian sarcoma viruses and of the defective endogenous virus derived from the ev-1 locus migrate on sodium dodecyl sulfate-polyacrylamide gel electrophoresis as if they were about 4,000 daltons smaller than p19. We have elucidated the structure of these forms, called p19 beta, by analysis of the proteins and determination of the DNA sequence of the p19 region of the gag gene from ev-1 and ev-2. Esterification of carboxyl groups completely suppressed the differences in migration of p19 and p19 beta. Peptide mapping showed the altered mobility to be determined by sequences in the C-terminal cyanogen bromide fragment of the proteins. We conclude from the DNA sequence that a single glutamate-lysine alteration is responsible for the altered electrophoretic mobility.
PLB (2022)

We present a new, host-based design for link load balancing and report the first experiences of link imbalance in datacenters. Our design, PLB (Protective Load Balancing), builds on transport protocols and ECMP/WCMP to reduce network hotspots. PLB randomly changes the paths of connections that experience congestion, preferring to repath after idle periods to minimize packet reordering. It repaths a connection by changing the IPv6 Flow Label on its packets, which switches include as part of ECMP/WCMP. Across hosts, this action drives down hotspots in the network, and lowers the latency of RPCs.
Moving in a box: Improving spatial orientation in virtual reality using simulated reference frames (2017)

Despite recent advances in virtual reality, locomotion in a virtual environment is still restricted because of spatial disorientation. Previous research has shown the benefits of reference frames in maintaining spatial orientation. Here, we propose using a visually simulated reference frame in virtual reality to provide users with a better sense of direction in landmark-free virtual environments. Visually overlaid rectangular frames simulate different variations of frames of reference. We investigated how two different types of visually simulated reference frames might benefit in a navigational search task through a mixed-method study. Results showed that the presence of a reference frame significantly affects participants' performance in a navigational search task. Though the egocentric frame of reference (simulated CAVE) that translates with the observer did not significantly help, an allocentric frame of reference (a simulated stationary room) significantly improved user performance both in navigational search time and overall travel distance. Our study suggests that adding a variation of the reference frame to virtual reality applications might be a cost-effective solution to enable more effective locomotion in virtual reality.
Warpage prediction of optical media (2003)

Abstract The warpage of injection–compression‐molded optical media, such as compact discs and digital video discs, due to asymmetric cooling during production is predicted. Thermally induced stress is calculated with a nonisothermal compressible flow simulation with a viscoelastic constitutive model. A finite element analysis is formulated with axisymmetric plate elements based on Kirchhoff thin‐plate theory to simulate the warpage of the disc due to the asymmetric thermal stress and gravity after demolding. Simulation results of warpage for compact‐disc‐recordable moldings are compared with experimental observations under different processing conditions, such as the melt temperature, mold temperature, and packing pressure, with an optical grade of polycarbonate. The comparison shows that the simulation well predicts the effects of various processing conditions. Both the simulation and experiment indicate that of the processing conditions, the mold temperature has the greatest effect on warpage. © 2003 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 41: 859–872, 2003
Standardization of Propagation Models: 800 MHz to 100 GHz -- A Historical Perspective (2020)

Propagation models constitute a fundamental building block of wireless communications research. Before we build and operate real systems, we must understand the science of radio propagation, and develop channel models that both reflect the important propagation processes and allow a fair comparison of different systems. In the past five decades, wireless systems have gone through five generations, from supporting voice applications to enhanced mobile broadband. To meet the ever increasing data rate demands of wireless systems, frequency bands covering a wide range from 800 MHz to 100 GHz have been allocated for use. The standardization of these systems started in the early/mid 1980's in Europe by the European Telecommunications Standards Institute with the advent of Global System for Mobile Communications. This motivated the development of the first standardized propagation model by the European Cooperation in Science and Technology (COST) 207 working group. These standardization activities were continued and expanded for the third, fourth, and fifth generations of COST, as well as by the Third Generation Partnership Project, and the International Telecommunication Union. This paper presents a historical overview of the standardized propagation models covering first to fifth-generation systems. In particular, we discuss the evolution and standardization of pathloss models, as well as large and small-scale fading parameters for single antenna and multiple antenna systems. Furthermore, we present insights into the progress of deterministic modelling across the five generations of systems, as well as discuss more advanced modelling components needed for the detailed simulations of millimeter-wave channels. A comprehensive bibliography at the end of the paper will aid the interested reader to dig deeper.
Clinical outcomes of step-synchronized vibration training in patients of Parkinson’s disease with freezing of gait (2019)

OBJECTIVE: To elucidate the effect of step-synchronized vibration training using PDShoe on balance, gait, and quality of life in patients of Parkinson’s disease (PD) with freezing of gait (FOG).MATERIALS AND METHODS: In a pilot study, 17 patients of PD with FOG were recruited for step-synchronized vibration training. The training involved 10 sessions of gait training over 2 weeks. Each session included three 6-min bouts of walking with step-synchronized vibration applied to the second metatarsal head and medial surface of calcaneus. Participants were assessed with the Unified Parkinson’s Disease Rating Scale-III (UPDRS III), Timed Up and Go (TUG) test, Berg Balance Scale (BBS), Timed 10-Meter Walk Test, Freezing of Gait Questionnaire (FOG-Q), Falls Efficacy Scale-International (FES-I), and Parkinson’s Disease Questionnaire-39 (PDQ-39). Measurements were collected pre-intervention, post-intervention, and at a 2-week follow-up. Friedman test followed by Wilcoxon signed-rank test were used for statistical analysis.RESULTS: All participants completed the intervention without any adverse effects. Fifteen participants reported for a follow-up evaluation 2 weeks after intervention. There was statistically significant improvement in UPDRS III (P = 0.044) and significant improvement in TUG test (P = 0.005), BBS (P = 0.026), FES-I (P = 0.041), and PDQ-39 (P = 0.021) scores between pre and follow-up evaluations. No significant changes were seen in FOG-Q and Timed 10-Meter Walk Test.CONCLUSION: Step-synchronized vibration is a novel intervention to improve balance, gait, motor features, and quality of life in patients of PD with FOG. Further research is warranted to confirm the results found in this pilot study.
Broken symmetries and localization lengths in Anderson insulators: Theory and experiment (1990)

Extending a random-matrix theory developed earlier, we show that breaking a basic symmetry in an Anderson insulator (e.g., time-reversal symmetry or spin-rotation symmetry) generically yields a multiplication of the localization length \ensuremath{\xi} by universal factors. Numerical calculations and magnetoconductance measurements in the Mott variable-range-hopping regime confirm that the removal of time-reversal symmetry by a magnetic field yields \ensuremath{\xi}\ensuremath{\rightarrow}2\ensuremath{\xi} in the absence of spin-orbit scattering, and \ensuremath{\xi}\ensuremath{\rightarrow}\ensuremath{\xi}/2 in the presence of spin-orbit coupling.
Cardioinductive Network Guiding Stem Cell Differentiation Revealed by Proteomic Cartography of Tumor Necrosis Factor α-Primed Endodermal Secretome (2007)

In the developing embryo, instructive guidance from the ventral endoderm secures cardiac program induction within the anterolateral mesoderm. Endoderm-guided cardiogenesis, however, has yet to be resolved at the proteome level. Here, through cardiopoietic priming of the endoderm with the reprogramming cytokine tumor necrosis factor alpha (TNFalpha), candidate effectors of embryonic stem cell cardiac differentiation were delineated by comparative proteomics. Differential two-dimensional gel electrophoretic mapping revealed that more than 75% of protein species increased >1.5-fold in the TNFalpha-primed versus unprimed endodermal secretome. Protein spot identification by linear ion trap quadrupole (LTQ) tandem mass spectrometry (MS/MS) and validation by shotgun LTQ-Fourier transform MS/MS following multidimensional chromatography mapped 99 unique proteins from 153 spot assignments. A definitive set of 48 secretome proteins was deduced by iterative bioinformatic screening using algorithms for detection of canonical and noncanonical indices of secretion. Protein-protein interaction analysis, in conjunction with respective expression level changes, revealed a nonstochastic TNFalpha-centric secretome network with a scale-free hierarchical architecture. Cardiovascular development was the primary developmental function of the resolved TNFalpha-anchored network. Functional cooperativity of the derived cardioinductive network was validated through direct application of the TNFalpha-primed secretome on embryonic stem cells, potentiating cardiac commitment and sarcomerogenesis. Conversely, inhibition of primary network hubs negated the procardiogenic effects of TNFalpha priming. Thus, proteomic cartography establishes a systems biology framework for the endodermal secretome network guiding stem cell cardiopoiesis.
L651582: A Novel Antiproliferative and Antimetastasis Agent (1990)

L651582 (Merck Institute for Therapeutic Research, Rahway, NJ) is a novel carboxyamide-amino-imidazole compound originally developed as a coccidiostat (U.S. patent No. 4,590,201). We studied the inhibitory effects of this compound on cancer proliferation, adhesion, and motility in vitro and in vivo in a model of ovarian cancer progression. L651582 reversibly inhibited up to 60% of the autocrine motility factor-stimulated tumor cell motility and tumor cell adhesion to tissue culture plastic. Autocrine motility factor-stimulated phosphoinositide metabolism was reduced significantly by treatment of the cells with 3 microM L651582 (P = .022). Thymidine incorporation and clonogenic growth of A2058 human melanoma, MDA-MB-231 human breast cancer, OVCAR-3 human ovarian cancer, and 5R-transformed rat embryo fibroblast cell lines were inhibited 60%-80% by 1-10 microM L651582. Intraperitoneal injection of OVCAR-3 cells causes malignant ascites, peritoneal carcinomatosis, and serosal and visceral seeding that, if left untreated, are lethal to nude mice. Intraperitoneal L651582 markedly prolonged survival of nude mice heavily laden with ovarian cancer [mean survival time of treated group divided by mean survival time of control group = 220% (P less than .03)]. The apparent mechanism of action of L651582 is via inhibition of the receptor-mediated stimulation of effector enzymes utilizing guanine nucleotide-binding protein signal transduction, which thus makes L651582 a novel anticancer agent. L651582 should be considered for further clinical development.
Automated Detection and Differentiation of Drusen, Exudates, and Cotton-Wool Spots in Digital Color Fundus Photographs for Diabetic Retinopathy Diagnosis (2007)

A machine learning-based, automated system capable of detecting exudates and cotton-wool spots and differentiating them from drusen in color images obtained in community based diabetic patients has been developed and approaches the performance level of retinal experts. If the machine learning can be improved with additional training data sets, it may be useful for detecting clinically important bright lesions, enhancing early diagnosis, and reducing visual loss in patients with diabetes.
Numerical study of magnetoresistance for currents perpendicular to planes in spring ferromagnets (2003)

Magnetoresistance (MR) for currents perpendicular to planes is calculated within the ballistic limit for spring ferromagnets in which an artificial domain wall is formed by the external magnetic fields. We consider two contributions to the MR: one is caused by a twisting of the magnetization and the other is due to a mismatch of the electronic structure between the two ferromagnets comprising the spring ferromagnets. We show that the resulting MR may show a nonmonotonic dependence on the width of the domain walls and can be either positive or negative according to the magnitude of these two contributions. We further show that oscillatory behavior appears in the MR when the soft ferromagnet is sandwiched between hard ferromagnets.
Wide‐Range 2D Lattice Correlation Unveiled for Columnarly Assembled Triphenylene Hexacarboxylic Esters (2012)

Dipole bridge: Liquid-crystalline (LC) triphenylenes (see picture) self-assemble columnarly into a hexagonal geometry with a wide-range 2D lattice correlation, for which distal and proximal dipole–dipole interactions are considered responsible. By virtue of the strong intercolumnar interaction, the LC columns of the triphenylene can spontaneously align homeotropically on the 12 different substrates examined (POM=polarized optical microscopy). Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Active Heating/Cooling Requirements for Divers in Water at Varying Temperatures (2007)

The active heating/cooling requirements to thermally sustain a human subject submerged in 10, 20, 30 and 40 °C water was measured using a system that circulated water through a zoned tubesuit garment. Water at 30 °C was circulated through the garment at a flow rate of about 0.5 L/min to each of six body regions and the outlet temperatures were measured. In addition, skin and core temperature, heat flux, and oxygen consumption was measured. The subject wore either a 6.5 mm or a 3 mm foam neoprene wetsuit. Body temperatures and heat fluxes reached steady state after 30–90 minutes and the immersions lasted 2–4 hours and core and skin temperatures remained within set thermal limits. In both wetsuits there was a linear correlation between the thermal exchange of the tubesuit and water temperature. While in the 6.5 mm wetsuit −214 to 242 W of heating (−) or cooling (+) was necessary in 10 to 40 °C water, respectively. While wearing the 3 mm wetsuit −462 to 342 W was necessary in 10 to 40 °C water, respectively. It was therefore concluded that a subject can be kept in thermal balance and comfort in 10–40 °C water with active heating/cooling.
Laparoscopic right posterior sectionectomy versus laparoscopic right hemihepatectomy for hepatocellular carcinoma in posterior segments: Propensity Score Matching Analysis (2018)

For hepatocellular carcinoma in the posterior segments, laparoscopic right posterior sectionectomy was feasible compared to laparoscopic right hemihepatectomy when performed by experienced laparoscopic surgeons.
Analysis of immune checkpoint blockade biomarkers in elderly patients using large-scale cancer genomics data. (2021)

2543 Background: Immune checkpoint blockade (ICB) immunotherapy in some cases elicits striking patient responses, but its efficacy appears to be dependent on several incompletely understood factors. Most studies of ICB therapies in elderly patients have concluded that they received no reduced benefit or even increased benefit compared to the younger patients analyzed, despite the systemic age-related immune changes that might be expected to produce a less effective immune response, such as loss of the capacity to generate new naive T cells. To understand and apply these results, it is necessary to investigate the relationship of age and the immune tumor microenvironment. Methods: We apply bioinformatics methods to genomic, transcriptomic, and clinical data from 9,523 patients across 31 cancer types from TCGA, 15,557 patients with breast, colon, or head and neck cancers from Caris Life Sciences, and 37,961 patients across 8 cancer types collected by GENIE. From these data we apply multivariate linear models across and within individual tumor types to estimate age-related associations to tumor mutational burden (TMB), T cell receptor diversity (miTCR), differential gene expression (edgeR), pathway enrichment (mSigDB and fgsea), and immune cell type infiltration (Quantiseq and MIXTURE). Results: Our analysis of large-scale molecular and clinical databases associates patient age with changes in several major biomarkers of ICB response. Notably, a robust correlation between increased tumor mutational burden and age was found across three different large cohorts (TCGA, Caris Life Sciences, and GENIE) in most ICB-approved cancer types. In the TCGA data, TMB increased with age pan-cancer (p &lt; 1x10 -16 ) and in 7 of 9 ICB-approved cancer types. These associations were validated in the larger cohort of patient samples in GENIE, which demonstrated correlations between increased TMB levels and patient age in all eight ICB-approved cancer types assayed (Table), as well as in the Caris colorectal (q &lt; 0.001) and breast (q &lt; 0.001) cancer cohorts. Significant associations of age to other biomarkers of ICB response (checkpoint gene expression, immune infiltration, and immune related pathway signaling) will be presented. Conclusions: These results provide context for the efficacy of ICB in elderly patients, highlight potential biomarkers for the treatment of elderly patients with immunotherapies, and strongly suggest the value of large-scale prospective study of elderly cancer patients treated with ICB.[Table: see text]
Absolute quantification of microrna from human and mouse tissue RNA using highly selective isotachophoretic focusing (2010)

We present a novel technique for the quantification of small, non-coding RNA using selective isotachophoretic preconcentration and focusing. Our technique allows for absolute quantification of RNA shorter than 60 nt, in the size range of microRNA (miRNA). Our quantitation is extremely selective, requires only a single dispensing step on a standard chip, and quantifies oligomers <60 nt across five orders of magnitude. We demonstrate the efficacy and accuracy of our assay by quantifying miRNA from total RNA from diverse human and mouse tissues and cultured cells. Selective isotachophoresis (ITP) of miRNA is a unique and powerful method to measure miRNA expression data.