gebhart/patrepeval huggingface dataset:
Denervation protects limbs from inflammatory arthritis via an impact on the microvasculature (2014)

Two-way communication between the mammalian nervous and immune systems is increasingly recognized and appreciated. An intriguing example of such crosstalk comes from clinical observations dating from the 1930s: Patients who suffer a stroke and then develop rheumatoid arthritis atypically present with arthritis on only one side, the one not afflicted with paralysis. Here we successfully modeled hemiplegia-induced protection from arthritis using the K/BxN serum-transfer system, focused on the effector phase of inflammatory arthritis. Experiments entailing pharmacological inhibitors, genetically deficient mouse strains, and global transcriptome analyses failed to associate the protective effect with a single nerve quality (i.e., with the sympathetic, parasympathetic, or sensory nerves). Instead, there was clear evidence that denervation had a long-term effect on the limb microvasculature: The rapid and joint-localized vascular leak that typically accompanies and promotes serum-transferred arthritis was compromised in denervated limbs. This defect was reflected in the transcriptome of endothelial cells, the expression of several genes impacting vascular leakage or transendothelial cell transmigration being altered in denervated limbs. These findings highlight a previously unappreciated pathway to dissect and eventually target in inflammatory arthritis.
Demo (2012)

The ubiquity of smartphones and their on-board sensing capabilities motivates crowd-sensing, a capability that harnesses the power of crowds to collect sensor data from a large number of mobile phone users. Unlike previous work on wireless sensing, crowd-sensing poses several novel requirements: support for humans-in-the-loop to trigger sensing actions or review results, the need for incentives, as well as privacy and security. Beyond existing crowd-sourcing systems, crowd-sensing exploits sensing and processing capabilities of mobile devices. In this paper, we design and implement Medusa, a novel programming framework for crowd-sensing that satisfies these requirements. Medusa provides high-level abstractions for specifying the steps required to complete a crowd-sensing task, and employs a distributed runtime system that coordinates the execution of these tasks between smartphones and a cluster on the cloud. We have implemented ten crowd-sensing tasks on a prototype of Medusa. We find that Medusa task descriptions are two orders of magnitude smaller than standalone systems required to implement those crowd-sensing tasks, and the runtime has low overhead and is robust to dynamics and resource attacks.
The Discovery of the Nav1.7 Inhibitor GDC-0276 and Development of an Efficient Large-Scale Synthesis (2019)

The voltage-gated ion channel Nav1.7 has been identified as an important mediator of pain signals and has emerged as a promising therapeutic target for the treatment of chronic pain. GDC-0276 is a potent inhibitor of the channel that demonstrated pharmacokinetic properties and pharmacological activity that warranted further exploration in the clinic, progressing to Phase I studies. Following a summary of the key medicinal chemistry discoveries that led to GDC-0276 and its initial synthesis, the process chemistry development that enabled its advancement to clinical studies is described in detail.
Multiple Directional Radiation Patterns, Integrated Antenna for ATSC-TV Indoor Reception (2018)

This paper presents a novel compact, wideband, four directional radiation patterns, antenna. The radiating element topology is inspired from the Annular Slot Antenna (ASA) and printed wideband monopole. The antenna is designed for North American ATSC-TV indoor reception. For an S11<;-6dB, it covers both High-VHF and UHF bands. It presents four relatively uncorrelated patterns. The antenna simulated performances are thoroughly analyzed and validated via measurements.
Accelerating Eulerian Fluid Simulation With Convolutional Networks (2016)

Efficient simulation of the Navier-Stokes equations for fluid flow is a long standing problem in applied mathematics, for which state-of-the-art methods require large compute resources. In this work, we propose a data-driven approach that leverages the approximation power of deep-learning with the precision of standard solvers to obtain fast and highly realistic simulations. Our method solves the incompressible Euler equations using the standard operator splitting method, in which a large sparse linear system with many free parameters must be solved. We use a Convolutional Network with a highly tailored architecture, trained using a novel unsupervised learning framework to solve the linear system. We present real-time 2D and 3D simulations that outperform recently proposed data-driven methods; the obtained results are realistic and show good generalization properties.
Fiber Capacity Limits With Optimized Ring Constellations (2009)

In this letter, we calculate theoretical limits to fiber-optic transport capacity under the constraint of requiring the use of concentric multiring modulation alphabets. Subject to these conditions, we vary ring amplitude ratios and occupation probabilities to determine the capacity-optimized ring constellations. The technique used for fiber transmission calculations accurately captures all fiber nonlinear effects, with the accuracy limited by the noise and signal statistical properties only.
Clinical impact of high-throughput sequencing in patients with advanced cancer: Lessons learned from the Michigan Oncology Sequencing Center. (2015)

11057 Background: The molecular aberrations that drive cancer are diverse and multiple defects are often present. Next generation sequencing permits detection of numerous aberrations within a tumor, which may identify targets for therapy. Methods: From 5/2011-12/2014, 452 patients (pts) underwent comprehensive next generation sequencing (Illumina) of a primary or metastatic tumor at the University of Michigan under an IRB approved protocol. Somatic and germline mutations, copy number alterations, gene fusions, and gene expression findings were reviewed at an institutional tumor board. Clinically actionable alterations were categorized as follows: rationale for use of an investigational targeted agent, rationale for off-label use of therapy approved in another condition, information predictive of treatment efficacy and germline mutations known to confer increased cancer risk. We report subsequent treatment information for the first 200 patients enrolled. Results: Sequencing was successful in 183 samples (92%). Somatic alterations of biological relevance were identified in 176 cases (96%). 100 pts (55%) had potentially actionable results. 79 pts (43%) had alterations providing rationale for use of an investigational targeted therapy and 7 enrolled in a trial informed by results. Somatic alterations provided rationale for off-label use of a drug in 13 cases (7%) and 5 pts received off-label therapy. 22 pts (12%) had alterations predictive of treatment efficacy, prompting treatment change in 3 pts. 5 pts (3%) were found to have germline mutations conferring increased cancer risk. 48 pts (26%) died within 5 months of enrollment. Conclusions: These data demonstrate that comprehensive tumor genome analysis can identify potentially actionable somatic aberrations, indicating this approach is useful as a screening tool for clinical trial participation. Early in the course of the study, many pts died shortly after enrollment. This experience led us to employ this strategy earlier in the therapeutic algorithm.
Zeolithe mit sehr großen Poren als Bindeglied zwischen mikro‐ und mesoporösen Strukturen (2010)

Abstract In diesem Aufsatz wird untersucht, welche Bedingungen für die Synthese von Zeolithen mit niedriger Gerüstdichte und sehr großen Poren erforderlich sind. Korrelationen zwischen der Gerüststabilität und geometrischen und topologischen Deskriptoren werden vorgestellt, wobei vor allem der Einfluss des Synthesemechanismus, des strukturdirigierenden Reagens, der Gerüstatome und der Gelkonzentration betrachtet wird. Ebenfalls diskutiert werden die katalytischen und Adsorptionseigenschaften von Zeolithen mit sehr großen Poren, z. B. dem erst kürzlich entdeckten chiralen mesoporösen ITQ‐37. Schließlich werden Strategien für die gezielte Synthese von Zeolithen mit Porengrößen und ‐formen vorgeschlagen, die diesen bestimmte katalytische und Adsorptionseigenschaften verleihen sollen.
High-Quality CVD SiO[sub 2] Interfacial Layer Prepared by Cyclic Deposition with O[sub 2] Plasma Treatment (2006)

We have developed a new process, cyclic deposition with O 2 plasma treatment C-DOP, to obtain a high-quality interfacial layer IL that can be applied to low-temperature poly-Si thin-film transistors TFTs.The C-DOP process uses sequential deposition followed by O 2 plasma treatment.By increasing radio frequency power during O 2 plasma treatment, the SiO 2 film becomes denser, and the density of the C-DOP-formed SiO 2 becomes close to that of thermal oxide.The amounts of residual impurities, such as OH, H, and C, are decreased by the C-DOP process.We applied the C-DOP process to form a thin IL.It is effective in suppressing the flatband voltage shift V FB due to Fowler-Nordheim negative stress when the IL thickness is more than 5 nm.By applying the C-DOP-formed IL to poly-Si TFTs, drain-current degradation due to drain-avalanche hot-carrier stress is successfully suppressed, and the time to 10% reduction of the drain current is prolonged by 1 order of magnitude.
Surface studies of polymer blends. 2. An ESCA and IR study of poly(methyl methacrylate)/poly(vinyl chloride) homopolymer blends (1989)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSurface studies of polymer blends. 2. An ESCA and IR study of poly(methyl methacrylate)/poly(vinyl chloride) homopolymer blendsJames J. Schmidt, Joseph A. Gardella Jr., and Lawrence Salvati Jr.Cite this: Macromolecules 1989, 22, 12, 4489–4495Publication Date (Print):December 1, 1989Publication History Published online1 May 2002Published inissue 1 December 1989https://doi.org/10.1021/ma00202a019Request reuse permissionsArticle Views690Altmetric-Citations136LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (810 KB) Get e-Alertsclose Get e-Alerts
Temperature-induced collapse of spin dimensionality in magnetic metamaterials (2021)

Spin and spatial dimensionalities are universal concepts, essential for describing both phase transitions and dynamics in magnetic materials. Lately, these ideas have been adopted to describe magnetic properties of metamaterials, replicating the properties of their atomic counterparts as well as exploring properties of ensembles of mesospins belonging to different universality classes. Here, we take the next step when investigating magnetic metamaterials not conforming to the conventional framework of continuous phase transitions. Instead of a continuous decrease in the moment with temperature, discrete steps are possible, resulting in a binary transition in the interactions of the elements. The transition is enabled by nucleation and annihilation of vortex cores, shifting topological charges between the interior and the edges of the elements. Consequently, the mesospins can be viewed as shifting their spin dimensionality, from 2 (XY-like) to 0 (vortices), at the transition. The results provide insight into how dynamics at different length scales couple, which can lead to thermally driven topological transitions in magnetic metamaterials.
Quantitative Analysis of Tryptic Protein Mixtures Using Electrospray Ionization Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (2004)

For the first time, quantitative analysis of tryptic protein mixtures, labeled with Quantification-Using-Enhanced-Signal-Tags (QUEST)-markers, were performed with electrospray ionization and a 9.4 T Fourier Transform Ion Cyclotron Resonance (FTICR) mass spectrometer. Coupling a High-Pressure Liquid Chromatography (HPLC) separation step prior to mass analysis resulted in an increased amount of identified labeled tryptic peptides. The range for the determined intensity ratios of two peptides in a labeled pair was large, but the obtained median intensity ratio correlated very well with the corresponding concentration ratio. This method can be used for observing protein dynamics in a specific cell type, tissue, or in body fluids.
Investigation of Bladder Cancer Cell Response to Cryoablation and Adjunctive Cisplatin Based Cryo/Chemotherapy (2020)

Due to a rising annual incidence of bladder cancer, there is a growing need for development of new strategies for treatment. In 2018, the World Cancer Research Fund and other groups reported that there were ~550,000 new cases worldwide of bladder cancer. It has been further estimated that >200,000 individuals die annually from bladder cancer worldwide. Various treatment options exist. However, many if not all remain suboptimal. While the preferred chemotherapeutic options have changed in the past few years there have been few advances in the bladder cancer medical device field. Cryoablation is now being evaluated as a new option for the treatment of bladder cancer. While several studies have shown cryoablation to be promising for the treatment of bladder cancer, a lack of basic information pertaining to dosing (minimal lethal temperature) necessary to destroy bladder cancer has limited its use as a primary therapeutic option. Concerns with bladder wall perforation and other side effects have also slowed adoption. In an effort to detail the effects of freezing on bladder cancer, two human bladder cancer cell lines, SCaBER and UMUC3, were evaluated <i>in vitro</i>. SCaBER, a basal subtype of muscle invasive bladder cancer, and UMUC3, an intermediate transitional cell carcinoma, are both difficult to treat but are reportedly responsive to most conventional treatments. SCaBER and UMUC3 cells were exposed to a range of freezing temperatures from -10 to -25°C and compared to non-frozen controls. The data show that a single 5 minute freeze to -10°C did not affect cell viability, whereas -15°C and -20°C results in a significant reduction in viability 1 day post freeze to <20%. These populations, however, were able to recover in culture. A complete loss of cell viability was found following a single freeze at -25°C. Application of a repeat (double) freeze resulted in complete cell death at -20°C. In addition to freezing alone, studies investigating the impact of adjunctive low dose (1 μM) cisplatin pre-treatment (30 minutes and 24 hours) in combination with freezing were conducted. The combination of 30 minute cisplatin pre-treatment and mild (-15°C) freezing resulted in complete cell death. This suggests that subclinical doses of cisplatin may be synergistically effective when combined with freezing. In summary, these <i>in vitro</i> results suggest that freezing to temperatures in the range of -20 to 25°C results in a high degree of bladder cancer cell destruction. Further, the data describe a potential combinatorial chemo/cryo therapeutic strategy for the treatment of bladder cancer.
Physical Layer Network Coding with Multiple Antennas (2010)

The two-phase MIMO NC (network coding) scheme can be used to boost the throughput in a two-way relay channel in which nodes are equipped with multiple antennas. The obvious strategy is for the relay node to extract the individual packets from the two end nodes and mix the two packets to form a network-coded packet. In this paper, we propose a new scheme called MIMO PNC (physical network coding), in which the relay extracts the summation and difference of the two end packets and then converts them to the network-coded form. MIMO PNC is a natural combination of the single-antenna PNC scheme and the linear MIMO detection scheme. The advantages of MIMO PNC are many. First, it removes the stringent carrier-phase requirement in single-antenna PNC. Second, it is linear in complexity with respect to the constellation size and the number of simultaneous data streams in MIMO. Simulation shows that MIMO PNC outperforms the straightforward MIMO NC significantly under random Rayleigh fading channel. Based on our analysis, we further conjecture that MIMO PNC outperforms MIMO NC under all possible realizations of the channel.
Modified self-organizing feature map algorithms for efficient digital hardware implementation (1997)

This paper describes two variants of the Kohonen's self-organizing feature map (SOFM) algorithm. Both variants update the weights only after presentation of a group of input vectors. In contrast, in the original algorithm the weights are updated after presentation of every input vector. The main advantage of these variants is to make available a finer grain of parallelism, for implementation on machines with a very large number of processors, without compromising the desired properties of the algorithm. In this work it is proved that, for one-dimensional (1-D) maps and 1-D continuous input and weight spaces, the strictly increasing or decreasing weight configuration forms an absorbing class in both variants, exactly as in the original algorithm. Ordering of the maps and convergence to asymptotic values are also proved, again confirming the theoretical results obtained for the original algorithm. Simulations of a real-world application using two-dimensional (2-D) maps on 12-D speech data are presented to back up the theoretical results and show that the performance of one of the variants is in all respects almost as good as the original algorithm. Finally, the practical utility of the finer parallelism made available is confirmed by the description of a massively parallel hardware system that makes effective use of the best variant.
Scanning near-field photon emission microscopy (2008)

A Scanning Near-field Photon Emission Microscope (SNPEM) for monitoring photon emission sites with a spatial resolution of between 50 to 200 nm is described. A protrusion type probe with a base diameter larger than a wavelength is proposed as a good compromise between resolution and sensitivity. Photon emissions from silicon pn junction and n-MOSFET have been detected with resolution clearly better than the far-field PEM (FFPEM). Features in photon emission distribution smaller than 200 nm were revealed in spite the fact that metal lines prevented the SNPEM probe to reach near-field condition with an actual emission source.
Monolithically integrated low-power phototransceiver incorporating microcavity LEDs and multiquantum well phototransistors (2002)

A densely packed 2D phototransceiver array is an essential element in optical display and image processing applications. However, unlike the requirements of conventional lightwave WDM-based networks, very stringent power handling and dissipation requirements must be met. The pixel size can be limited to 100 /spl mu/m/spl times/100 /spl mu/m in a 100/spl times/100 or larger array. The objective is to detect, amplify and retransmit, possibly at a different wavelength, with input power /spl sim/1-5 /spl mu/W and electrical power consumption not to exceed 500 /spl mu/W. There is therefore a need to develop low-power phototransceivers. 2D arrays of vertical-cavity surface-emitting lasers (VCSELs), operating with ultra-low threshold current, large quantum efficiency, low-beam divergence and very low power dissipation can be used for this application. However, microcavity light emitting diodes (MCLEDs) provide very high wall-plug efficiency, comparable to VCSELs at low current levels (Deppe et al, 1999). The monolithic integration of high-sensitivity heterojunction phototransistors (HPTs) and MCLEDs in a phototransceiver is therefore very attractive for agile sensor technologies. We report here the design and performance characteristics of GaAs based multiquantum well HPT/MCLED low-power phototransceivers which offer the potential of large area uniformity and less sensitivity to temperature variations.
Brain DNA methylomic analysis of frontotemporal lobar degeneration reveals OTUD4 in shared dysregulated signatures across pathological subtypes (2023)

Frontotemporal lobar degeneration (FTLD) is an umbrella term describing the neuropathology of a clinically, genetically and pathologically heterogeneous group of diseases, including frontotemporal dementia (FTD) and progressive supranuclear palsy (PSP). Among the major FTLD pathological subgroups, FTLD with TDP-43 positive inclusions (FTLD-TDP) and FTLD with tau-positive inclusions (FTLD-tau) are the most common, representing about 90% of the cases. Although alterations in DNA methylation have been consistently associated with neurodegenerative diseases, including Alzheimer's disease and Parkinson's disease, little is known for FTLD and its heterogeneous subgroups and subtypes. The main goal of this study was to investigate DNA methylation variation in FTLD-TDP and FTLD-tau. We used frontal cortex genome-wide DNA methylation profiles from three FTLD cohorts (142 FTLD cases and 92 controls), generated using the Illumina 450K or EPIC microarrays. We performed epigenome-wide association studies (EWAS) for each cohort followed by meta-analysis to identify shared differentially methylated loci across FTLD subgroups/subtypes. In addition, we used weighted gene correlation network analysis to identify co-methylation signatures associated with FTLD and other disease-related traits. Wherever possible, we also incorporated relevant gene/protein expression data. After accounting for a conservative Bonferroni multiple testing correction, the EWAS meta-analysis revealed two differentially methylated loci in FTLD, one annotated to OTUD4 (5'UTR-shore) and the other to NFATC1 (gene body-island). Of these loci, OTUD4 showed consistent upregulation of mRNA and protein expression in FTLD. In addition, in the three independent co-methylation networks, OTUD4-containing modules were enriched for EWAS meta-analysis top loci and were strongly associated with the FTLD status. These co-methylation modules were enriched for genes implicated in the ubiquitin system, RNA/stress granule formation and glutamatergic synaptic signalling. Altogether, our findings identified novel FTLD-associated loci, and support a role for DNA methylation as a mechanism involved in the dysregulation of biological processes relevant to FTLD, highlighting novel potential avenues for therapeutic development.