gebhart/patrepeval huggingface dataset:
Topical Bixin Confers NRF2-Dependent Protection Against Photodamage and Hair Graying in Mouse Skin (2018)

Environmental exposure to solar ultraviolet (UV) radiation causes acute photodamage, premature aging, and skin cancer, attributable to UV-induced genotoxic, oxidative, and inflammatory stress. The transcription factor NRF2 [nuclear factor erythroid 2 (E2)-related factor 2] is the master regulator of the cellular antioxidant response protecting skin against various environmental stressors including UV radiation and electrophilic pollutants. NRF2 in epidermal keratinocytes can be activated using natural chemopreventive compounds such as the apocarotenoid bixin, an FDA-approved food additive and cosmetic ingredient from the seeds of the achiote tree (<i>Bixa orellana</i>). Here, we tested the feasibility of topical use of bixin for NRF2-dependent skin photoprotection in two genetically modified mouse models [SKH1 and C57BL/6J (<i>Nrf2<sup>+/+</sup></i> versus <i>Nrf2<sup>-/-</sup></i> )]. First, we observed that a bixin formulation optimized for topical NRF2 activation suppresses acute UV-induced photodamage in <i>Nrf2<sup>+/+</sup></i> but not <i>Nrf2<sup>-/-</sup></i> SKH1 mice, a photoprotective effect indicated by reduced epidermal hyperproliferation and oxidative DNA damage. Secondly, it was demonstrated that topical bixin suppresses PUVA (psoralen + UVA)-induced hair graying in <i>Nrf2<sup>+/+</sup></i> but not <i>Nrf2<sup>-/-</sup></i> C57BL/6J mice. Collectively, this research provides the first <i>in vivo</i> evidence that topical application of bixin can protect against UV-induced photodamage and PUVA-induced loss of hair pigmentation through NRF2 activation. Topical NRF2 activation using bixin may represent a novel strategy for human skin photoprotection, potentially complementing conventional sunscreen-based approaches.
Minimizing Nonsubmodular Functions with Graph Cuts-A Review (2007)

Optimization techniques based on graph cuts have become a standard tool for many vision applications. These techniques allow to minimize efficiently certain energy functions corresponding to pairwise Markov Random Fields (MRFs). Currently, there is an accepted view within the computer vision community that graph cuts can only be used for optimizing a limited class of MRF energies (e.g., submodular functions). In this survey, we review some results that show that graph cuts can be applied to a much larger class of energy functions (in particular, nonsubmodular functions). While these results are well-known in the optimization community, to our knowledge they were not used in the context of computer vision and MRF optimization. We demonstrate the relevance of these results to vision on the problem of binary texture restoration.
Formal Performance Guarantees for Behavior-Based Localization Missions (2016)

Localization and mapping algorithms can allow a robot to navigate well in an unknown environment. However, whether such algorithms enhance any specific robot mission is currently a matter for empirical validation. In this paper we apply our MissionLab/VIPARS mission design and verification approach to an autonomous robot mission that uses probabilistic localization software. Two approaches to modeling probabilistic localization for verification are presented: a high-level approach, and a sample-based approach which allows run-time code to be embedded in verification. Verification and experimental validation results are presented for two different missions, each using each method, demonstrating the accuracy of verification, and both are compared with verification of an odometry-only mission, to show the mission-specific benefit of localization.
Yonsei nomogram: A predictive model of new‐onset chronic kidney disease after on‐clamp partial nephrectomy in patients with T1 renal tumors (2018)

We developed a novel nomogram for predicting the 5-year chronic kidney disease-free survival probability after on-clamp partial nephrectomy. This model might have an important role in partial nephrectomy decision-making and follow-up plan after surgery. External validation of our nomogram in a larger cohort of patients should be considered.
Supplementary Table 1, Figures 1-5 from A Bispecific Antibody-IFNα2b Immunocytokine Targeting CD20 and HLA-DR Is Highly Toxic to Human Lymphoma and Multiple Myeloma Cells (2023)

Supplementary Table 1, Figures 1-5 from A Bispecific Antibody-IFNα2b Immunocytokine Targeting CD20 and HLA-DR Is Highly Toxic to Human Lymphoma and Multiple Myeloma Cells
Characterization and manipulation of foamy virus membrane interactions (2012)

Foamy viruses (FVs), a unique type of retroviruses, are characterized by several unusual features in their replication strategy. FVs, common to all non-human primates and several other species, display an extremely broad tropism in vitro. Basically, all mammalian cells and species examined, but also cells of amphibian or bird origin, are permissive to FV glycoprotein (Env)-mediated capsid release into the cytoplasm. The nature of the broadly expressed, and potentially evolutionary conserved, FV entry receptor molecule(s) is poorly characterized. Although recent data indicate that proteoglycans serve as an important factor for FV Env-mediated target cell attachment, additional uncharacterized molecules appear to be essential for the pH-dependent fusion of viral and cellular lipid membranes after endocytic uptake of virions. Furthermore, FVs show a very special assembly strategy. Unlike other retroviruses, the FV capsid precursor protein (Gag) undergoes only very limited proteolytic processing during assembly. This results in an immature morphology of capsids found in released FV virions. In addition, the FV Gag protein appears to lack a functional membrane-targeting signal. As a consequence, FVs utilize a specific interaction between capsid and cognate viral glycoprotein for initiation of thebudding process. Genetic fusion of heterologous targeting domains for plasma but not endosomal membranes to FV Gag enables glycoprotein-independent particle egress. However, this is at the expense of normal capsid morphogenesis and infectivity. The low-level Gag precursor processing and the requirement for a reversible, artificial Gag membrane association for effective pseudotyping of FV capsids by heterologous glycoproteins strongly suggest that FVs require a transient interaction of capsids with cellular membranes for viral replication. Under natural condition, this appears to be achieved by the lack of a membrane-targeting function of the FV Gag protein and the accomplishment of capsid membrane attachment through an unusual specific interaction with the cognate glycoprotein.
Supplementary Figures Legend from Single Nucleotide Polymorphism–Based Genome-Wide Chromosome Copy Change, Loss of Heterozygosity, and Aneuploidy in Barrett's Esophagus Neoplastic Progression (2023)

Supplementary Figures Legend from Single Nucleotide Polymorphism–Based Genome-Wide Chromosome Copy Change, Loss of Heterozygosity, and Aneuploidy in Barrett's Esophagus Neoplastic Progression
Program analysis using random interpretation (2005)

This dissertation describes a new program analysis technique called random interpretation that uses the power of randomization to verify and discover program properties. Random interpretation is inspired by, and combines the strengths of, the two complementary techniques for program analysis: random testing and abstract interpretation. Random testing is simple and finds real bugs in programs, but cannot prove absence of bugs. Abstract interpretation, on the other hand, is a class of sound and deterministic program analyses that find all bugs, but also report spurious bugs (false positives). Often these analyses are complicated and have long running time. In this dissertation, we describe few random interpretation based program analyses that are more efficient as well as simpler than their deterministic counterparts that had been state-of-the-art for almost 30 years. We then show how to extend these intra-procedural analyses to an inter-procedural setting, and how to combine these analyses. We also discuss our experience experimenting with some of these algorithms.
Proton Gradient-Dependent Transport of p-Glucocoumaryl Alcohol in Differentiating Xylem of Woody Plants (2019)

Lignin is a cell wall component of vascular plants crucial for survival in terrestrial environments. While p-hydroxyphenyl lignin is minor, it is considered to be localised in the outermost part of the cell wall providing strong adhesion between cells, which determines cell shape. Transport of the lignin precursor from the cytosol to the cell wall is critical to regulate temporal and spatial lignin deposition; however, little information on the transport step is available. Here, we report transport activity of p-glucocoumaryl alcohol, a precursor of p-hydroxyphenyl lignin, in a broad-leaved tree (hybrid poplar, Populus sieboldii × P. grandidentata) and a coniferous tree (Japanese cypress, Chamaecyparis obtusa). Membrane vesicles of both trees were prepared from differentiating xylem with vigorous lignification and used for transport assays. Several inhibition assays indicated that not ABC transporters but the proton gradient and V-ATPase are involved in p-glucocoumaryl alcohol transport depending on ATP. These results support the hypothesis that p-glucocoumaryl alcohol is loaded into the secretory vesicles and delivered to the cell wall by exocytosis. Furthermore, this transport mechanism was common in both poplar and Japanese cypress, strongly suggesting that p-glucocoumaryl alcohol transport in the differentiating xylem is conserved within woody plants.
Petrophysical, geochemical, and hydrological evidence for extensive fracture-mediated fluid and heat transport in the Alpine Fault's hanging-wall damage zone (2021)

© 2017. American Geophysical Union. All Rights Reserved. Fault rock assemblages reflect interaction between deformation, stress, temperature, fluid, and chemical regimes on distinct spatial and temporal scales at various positions in the crust. Here we interpret measurements made in the hanging-wall of the Alpine Fault during the second stage of the Deep Fault Drilling Project (DFDP-2). We present observational evidence for extensive fracturing and high hanging-wall hydraulic conductivity (∼10−9 to 10−7 m/s, corresponding to permeability of ∼10−16 to 10−14 m2) extending several hundred meters from the fault's principal slip zone. Mud losses, gas chemistry anomalies, and petrophysical data indicate that a subset of fractures intersected by the borehole are capable of transmitting fluid volumes of several cubic meters on time scales of hours. DFDP-2 observations and other data suggest that this hydrogeologically active portion of the fault zone in the hanging-wall is several kilometers wide in the uppermost crust. This finding is consistent with numerical models of earthquake rupture and off-fault damage. We conclude that the mechanically and hydrogeologically active part of the Alpine Fault is a more dynamic and extensive feature than commonly described in models based on exhumed faults. We propose that the hydrogeologically active damage zone of the Alpine Fault and other large active faults in areas of high topographic relief can be subdivided into an inner zone in which damage is controlled principally by earthquake rupture processes and an outer zone in which damage reflects coseismic shaking, strain accumulation and release on interseismic timescales, and inherited fracturing related to exhumation.
Freezing Dilute Ceramic/Camphene Slurry for Ultra‐High Porosity Ceramics with Completely Interconnected Pore Networks (2006)

Highly porous alumina ceramics with completely interconnected pore channels were fabricated by freezing dilute alumina/camphene slurries with solid loadings ranging from 5 to 20 vol%. This method fundamentally made full use of the three‐dimensional camphene dendritic network for producing interconnected pore channels and the concentrated alumina powder network for achieving dense alumina walls. Firstly, alumina/camphene slurries were prepared at 60°C using ball milling and then cast into molds at 20°C. After subliming the frozen camphene, the samples were sintered at 1400°C for 5 h. This method enabled us to freeze very dilute ceramic slurries with a low solid loading of ≤20 vol% without the collapse of the sample after sintering. As the initial solid loading decreased from 20 to 5 vol%, the porosity linearly increased from 66% to 90% with an increase in the pore size, while completely interconnected pore networks were obtained in all cases. In addition, the free surfaces of the alumina walls showed full densification after sintering even at a low temperature of 1400°C, while some pores were present in the inner regions of the alumina walls.
Exomes and transcriptomes to reveal actionable findings in patients with negative-targeted panel sequencing. (2020)

3562 Background: Next generation sequencing targeted panels increasingly inform clinical decisions, but may miss actionable findings detectable by whole exome sequencing (WES) and RNA-seq. There has been no direct comparison of WES plus RNA-seq against targeted panel sequencing to determine its added utility. To address this, we performed WES and RNA-seq analysis in a cohort of 100 patients with no actionable findings on prior panel sequencing. Methods: Ontario-wide Cancer Targeted Nucleic Acid Evaluation (OCTANE; NCT02906943) has sequenced 2,106 patients using a 161-gene Oncomine or 555-gene Hi5 panel. 100 patients (98 Hi5, 2 Oncomine) were chosen for further sequencing. Tumor (100x coverage) and normal (50x) exomes and tumor transcriptomes were sequenced on Illumina HiSeq2500 or NextSeq550. Interpretation included knowledgebase annotation (e.g. OncoKB, CIViC), mutation signatures, homologous recombination deficiency (HRD) scores, gene expression, and pathway analysis. Findings were deemed “actionable” if they could directly inform management or trial eligibility. Results: WES and RNA-seq identified one or more novel actionable findings in 38 patients. Of these, the main actionable finding was tumor mutation burden (TMB), mutation signature, or HRD score in 19 (50%), a copy number variant in 16 (42%), a fusion in 2 (5%), and a point mutation in 1 (2.6%). WES identified a MALAT1-GLI1 fusion in a cancer of unknown primary (CUP) whose transcriptome was consistent with gastric cancer, together suggesting the diagnosis of a rare gastroblastoma. To date, two cases have received exome-supported targeted therapy: (1) a metastatic high grade serous ovarian cancer, HRD-high, treated with olaparib then cisplatin for a combined 15 months, and (2) a metastatic neuroendocrine rectal tumor with RICTOR amplification treated with everolimus starting in Dec 2016 until last follow-up in Sep 2019. Of 62 patients with no actionable finding, expanded sequencing identified one or more known cancer drivers in 25 (40%): 17 CNVs, 3 fusions, and 5 point mutations or indels. In 16 patients, an oncogenic variant found on panel was not captured by WES, and may represent artifacts, germline mutations, or subclonal/localized variants. Conclusions: WES and RNA-seq expanded detection of actionable biomarkers and oncogenic mutations, especially CNV, TMB/signatures, and HRD. Two cases have undergone exome-supported targeted treatment. We performed the first WES of a rare gastroblastoma, originally a CUP but reclassified by expanded fusion detection and RNA-seq.
Controlling light using mesoscale magnetic textures (2020)

We have explored the use of a magneto-optical diffraction grating, in the form of a YIG (Y<sub>3</sub>Fe<sub>5</sub>O<sub>12</sub>) continuous film, as a mean of controlling light with mesoscale magnetic textures. The existence of a periodicity for the out-of-plane magnetic component opens up the possibility of using the film as a magneto-optical diffraction grating. For incident light linearly-polarized along the stripe direction, the Faraday rotation yields a polarization profile of the transmitted light characterized by a uniform distribution along the direction parallel to the stripes and a periodic phase-reversal texture along the corresponding orthogonal direction. The interference pattern resulting from the latter gives rise to magnetic Bragg peaks, in good agreement with the Fourier transform of the real-space magnetic domain texture recorded with Kerr microscopy. These results highlight the potential of controlling the scattering of light by employing and tailoring meso-scale magnetic textures.
High-radix interconnection networks (2008)

Over the past twenty years, the pin bandwidth available to a chip has increased by approximately an order of magnitude every five years—a rate very similar to Moore's Law. This increasing pin bandwidth can be effectively utilized by creating high-radix routers with large number of skinny ports instead of low-radix routers with fat ports. The use of high-radix routers leads to lower cost and better performance, but high-radix networks present many difficult challenges. This thesis explores challenges in scaling to high-radix routers, including topology, routing, and router microarchitecture.
Topology is a critical aspect of any interconnection network as it sets performance bounds and determines the cost of the network. This thesis presents a cost-efficient high-radix topology referred to as the flattened butterfly topology which exploits the availability of high-radix routers. Compared to a folded-Clos topology, the flattened butterfly provides approximately 2× reduction in cost per performance on balanced traffic while maintaining the same cost per performance on adversarial traffic pattern. Given the topology, routing determines the path between the source and its destination. Proper routing is required to exploit the path diversity available in a high-radix network and we discuss the advantages of using adaptive routing in high-radix networks as well as how non-minimal routing is critical to properly exploiting the flattened butterfly topology.
Conventional microarchitectures do not scale to high radix since the complexity of the allocators in the routers scale quadratically with the radix. This thesis presents a hierarchical router organization that results in a distributed, complexity-effective microarchitecture and maintains high performance. As a case study, the implementation of this microarchitecture in the Cray YARC router with 64 ports will also be presented.
With the recent increase in the number of cores on a single-chip, the on-chip interconnection network that connects the on-chip cores and memory together will become more critical in determining the overall performance and cost of the entire chip. In the last part of this thesis, we expand the use of high-radix routers to on-chip networks and show how high-radix routers and the flattened butterfly topology can be mapped to on-chip networks.
Recent progress in the development of antagonists to the chemokine receptors CCR3 and CCR4 (2014)

Pharmaceutical companies have expended a considerable amount of money and effort to identify potent inhibitors of CCR3 and CCR4 for the treatment of asthma and atopic diseases. Although a variety of compounds have been described and several have progressed into the clinic, none have so far made it as approved drugs. There are, however, novel approaches such as mogamulizumab, a monoclonal antibody to CCR4 currently is in clinical trials for cancer and ASM8, an antisense nucleotide to CCR3, which is in Phase II clinical trials for asthma that might still prove to be successful new therapeutics.
The organic redox transistor for neuromorphic computing (2023)

Inspired by the in-memory computing architectures of biological systems, neuromorphic computing using crossbar arrays of artificial synapses based on non-volatile memory (NVM) devices with variable conductances has emerged as a new paradigm to enable massively parallel and ultra-low power computing hardware for data centric applications. Although inference has been demonstrated successfully using crossbars based on a variety of NMV technologies, efficient learning and scaling to large arrays (>10<sup>6</sup> elements) remains a challenge due to the synaptic elements' non-ideal electrical characteristics which degrades ANN accuracy. A further challenge is that in the conductive state memristors draw large currents >μA resulting in significant voltage drops in the interconnect wires and increased probability of failure in scaled arrays. We suggest the organic polymer redox transistor (RT) is an alternate approach that could solve many of these challenges, enabling both inference and parallel outer product updates, as recently demonstrated by Fuller et al. An RT consists of redox-active channel and gate electrodes in contact with a liquid or solid electrolyte. lon insertion through the electrolyte controls the channel electronic conductivity, while electron transfer through an external circuit maintains overall charge neutrality. Unlike a rechargeable battery, in the RT the voltage built-up across the electrolyte is kept to a minimum (typically <100 mV) by using the same material for the gate and channel. Elimination of the voltage offset simplifies integration of the RT into programmable arrays by enabling the use of various selectors. RTs based on inorganic and organic materials have been recently demonstrated with conductance tuning occurring at potentials of just a few mV and hundreds to thousands of linearly and symmetrically programmable conductance states, enabling near ideal accuracy in neural network simulations. Introduced in the 1980's, redox transistors with metallic gate electrodes and organic channel materials, also known as organic electrochemical transistors (OECTs), have been explored for a variety of applications such as chem- and bio-sensing, neural interfaces, and low cost printed circuits. A typical channel material for OECTs is the conducting polymer poly(3,4-ethylenedioxythiophene) doped with poly(styrene sulfonate) (PEDOT:PSS). PEDOT is a p-type semiconducting polymer with mobile positively charged polarons that hop chain-to-chain.
Hybrid Physical Layer Security for Passive RFID Communication (2020)

Thanks to its low cost, small weight and energy efficiency, passive radio frequency identification (RFID) backscatter communications systems have attracted a lot of attention in several application fields. However, such devices have limited computational capabilities and resources which makes them unable to incorporate traditional security protocols and are there-fore vulnerable to several types of attacks including cloning and counterfeiting. Therefore, in this paper, a novel hybrid RFID tags identification and malicious devices detection system is proposed by exploiting the estimated tags locations and manufacturing imperfections. In particular, an iterative approach is proposed to estimate the minimum power response at each frequency of the tag in addition to its location. The conducted simulation results show the efficiency of this technique in detecting all the malicious tags and classify the legitimate ones under different network configurations.
Application of pattern recognition techniques in ultrasound tissue characterization (2003)

An approach to the application of pattern recognition techniques is described by presenting examples of the tissue characterization from an ultrasound image. A Bayesian classifier is used to determine the feasibility of classifying tissue types and determining some properties of various feature spaces. An application of an unsupervised clustering technique that leads to more inherent properties of the features is described. A hypothesis-testing criterion is described and used to detect focal disease. The results to date are judged promising for tissue characterization of the liver and other abdominal organs.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>