gebhart/patrepeval huggingface dataset:
Effects of pristine or contaminated polyethylene microplastics on zebrafish development (2022)

The presence of microplastics in the aquatic ecosystem represents a major issue for the environment and human health. The capacity of organic pollutants to adsorb onto microplastic particles raises additional concerns, as it creates a new route for toxic compounds to enter the food web. Current knowledge on the impact of pristine and/or contaminated microplastics on aquatic organisms remains insufficient, and we provide here new insights by evaluating their biological effects in zebrafish (Danio rerio). Zebrafish larvae were raised in ZEB316 stand-alone housing systems and chronically exposed throughout their development to polyethylene particles of 20-27 μm, pristine (MP) or spiked with benzo[α]pyrene (MP-BaP), supplemented at 1% w/w in the fish diet. While they had no effect at 30 days post-fertilization (dpf), MP and MP-BaP affected growth parameters at 90 and 360 dpf. Relative fecundity, egg morphology, and yolk area were also impaired in zebrafish fed MP-BaP. Zebrafish exposed to experimental diets exhibited an increased incidence of skeletal deformities at 30 dpf as well as an impaired development of caudal fin/scales, and a decreased bone quality at 90 dpf. An intergenerational bone formation impairment was also observed in the offspring of parents exposed to MP or MP-BaP through a reduction of the opercular bone in 6 dpf larvae. Beside a clear effect on bone development, histological analysis of the gut revealed a reduced number of goblet cells in zebrafish fed MP-BaP diet, a sign of intestinal inflammation. Finally, exposure of larvae to MP-BaP up-regulated the expression of genes associated with the BaP response pathway, while negatively impacting the expression of genes involved in oxidative stress. Altogether, these data suggest that long-term exposure to pristine/contaminated microplastics not only jeopardizes fish growth, reproduction performance, and skeletal health, but also causes intergenerational effects.
SENESCENCE-DERIVED PROTEIN BIOMARKERS DURING AGING AND OSTEOARTHRITIS (2022)

Abstract Aging is a complex biological process associated with progressive loss of physiological function and susceptibility to several diseases, such as cancer and neurodegeneration. As senescence burden increases with aging and becomes a risk factor for many age-related diseases we are specifically interested in senescence-derived aging signatures. We use cutting-edge proteomic workflows to investigate both the senescence-associated secretory phenotype (SASP) in tissue cultures. We are subsequently examining exosome proteins as well as lipid cargo in plasma from human young (20–26 yrs) and old cohorts and old (60–66 yrs) individuals. We will also present current work assessing senescence markers in cartilage and bone targeting underlying mechanisms and options for intervention for osteoarthritis. Overall, our focus is specifically directed towards senescence-derived biomarkers of aging.
Stochastic Frequency Masking to Improve Super-Resolution and Denoising\n Networks (2020)

Super-resolution and denoising are ill-posed yet fundamental image\nrestoration tasks. In blind settings, the degradation kernel or the noise level\nare unknown. This makes restoration even more challenging, notably for\nlearning-based methods, as they tend to overfit to the degradation seen during\ntraining. We present an analysis, in the frequency domain, of\ndegradation-kernel overfitting in super-resolution and introduce a conditional\nlearning perspective that extends to both super-resolution and denoising.\nBuilding on our formulation, we propose a stochastic frequency masking of\nimages used in training to regularize the networks and address the overfitting\nproblem. Our technique improves state-of-the-art methods on blind\nsuper-resolution with different synthetic kernels, real super-resolution, blind\nGaussian denoising, and real-image denoising.\n
Conversion Reaction in the Binder-Free Anode for Fast-Charging Li-Ion Batteries Based on WO<sub>3</sub> Nanorods (2020)

The development of lithium-ion batteries (LIBs) with high-energy densities faces challenges to meet the ever-growing market demands. Tungsten oxide (WO3) with high theoretical capacity and low cost is a potential replacement for conventional graphite anodes, whose low reversible capacity limits the energy densities of existing LIBs. However, large volumetric changes during the cycling result in the degradation of WO3-based electrodes. Hence, we integrated an anode based on vertically aligned WO3 nanorods with a current collector. The controlled geometry of binder-free anodes minimized volumetric expansion effects and conferred high mechanical stability proven by stable cycling performance up to a rate of 3 C without disintegration. Ex situ X-ray diffraction and electron microscopy analyses supported by theoretical calculations revealed the appearance of the intermediate active phases during conversion reaction.
KCa3.1 Channel-Blockade Attenuates Airway Pathophysiology in a Sheep Model of Chronic Asthma (2013)

These findings suggest that K(Ca)3.1-activity contributes to allergen-induced airway responses, inflammation and vascular remodelling in a sheep model of asthma, and that inhibition of K(Ca)3.1 may be an effective strategy for blocking allergen-induced airway inflammation and hyperresponsiveness in humans.
Development of an integrated automated retinal surgical laser system. (1996)

Diabetes is a serious disease that affects millions of people world wide. One of the many complications that may result from this disease is an eye disorder called diabetic retinopathy. This side effect is characterized by the leaching of fluid, mainly blood, into the retinal tissue ultimately killing the rods and cones in the area. Scientists have discovered that by occulating and destroying some of the capillaries near the infected area, further damage may be limited and further vision loss prevented. This procedure is performed on the retina by using a Continuous Wave argon laser to place a pattern of lesions that kill the rods, cones, and underlying capillaries. The "Computer Aided Laser Optics System for Ophthalmic Surgery" or CALOSOS is a system that fully integrates the placement of therapeutic retinal lesions through computer control. To date, two different sub-systems have been used to achieve the desired accuracy needed including lesion placement and depth; an all-digital system and a hybrid analog/digital system. The current tracking system that precisely controls the laser uses a wide-angle lens camera to view the whole retina. The difficulty lies in the fact that the only way to control the depth of the lesion is to measure the central reflectance. The goal of this research is to establish that there is a linear relationship between the reflectance of the lesion and the depth of the lesion when this wide-angle lens is used.
Cine Flow Measurements using Phase-Contrast bSSFP at 0.75 Tesla (2023)

The use of balanced steady-state free precession sequences (bSSFP) is an approach to compensate for the signal-to-noise ratio (SNR) loss at lower-field systems (&amp;lt;1T). Low field MRI systems are cheaper, lighter, and less prone to system imperfections than regular 1.5-3T systems, used in clinical practice. In this work, the feasibility and accuracy of velocity encoding using phase-contrast balanced SSFP (PC-bSSFP) is demonstrated and tested on a clinical 3T MRI system ramped down to 0.75T. Phantom and in-vivo results are compared to a standard 2D spoiled gradient echo phase-contrast sequence (PC-GRE).
1813-P: Coadministration of a GLP-1/Glucagon Receptor Agonist with an FXR Agonist and ACC Inhibitor Reverses Nonalcoholic Steatohepatitis (NASH) in Diet-Induced and Biopsy-Confirmed Mice (2020)

Combination approaches for the treatment of NASH are being actively pursued. We examined the effects of administration of a dual GLP-1 and glucagon receptor agonist (GLP-1:GCG, 0.015 mg/kg, s.c., q.d.) alone and combined with an FXR agonist (cilofexor, CILO; 30 mg/kg) and/or an acetyl-CoA carboxylase inhibitor (firsocostat analog, ACCi; 5 mg/kg, both p.o., q.d) on NASH endpoints in the AMLN diet-induced and biopsy-confirmed DIO-NASH mouse (n=15-16/group). After 12 weeks of treatment, GLP-1:GCG reduced body weight 15%, being slightly greater in the GLP-1:GCG + CILO group (22%). Liver triglyceride was reduced by GLP-1:GCG (by 76% vs. vehicle, p&amp;lt;0.001). Addition of CILO, ACCi or both to GLP-1:GCG further reduced liver lipid (by 82%, 88% and 91%, respectively). Histopathological pre-to-post NAFLD activity score (NAS) was reduced in 7/16 (44%) of vehicle controls and in all mice (100%) in the GLP-1:GCG-containing groups. In vehicle controls, 0/16 mice had a final NAS of 0-1 whereas this increased to 5/15 mice (33%) with GLP-1:GCG, and was not significantly improved by addition of CILO (7/15, 47%) or ACCi (6/16, 38%). Triple therapy increased number of mice with NAS of 0-1 to 11/16 (69%). GLP-1:GCG was associated with 1/15 mice (7%) improving pre-to-post fibrosis stage which was not altered by addition of CILO or ACCi, but increased to 7/16 (44%) with triple therapy. Collagen-1a and α-SMA immunoreactivity (% area) revealed no significant effect of GLP-1:GCG for collagen (5.7%), but reduction in α-SMA (1.4%, p&amp;lt;0.001) vs. vehicle (6.8% and 4.9%, respectively). Triple therapy reduced both collagen and α-SMA area (3.8% and 1.5%, respectively, both p&amp;lt;0.001 vs. vehicle). In conclusion, GLP-1:GCG effectively reduced hepatic lipid and the addition of an FXR agonist and ACC inhibitor further improved pre-to-post NAS and fibrosis stage in DIO-NASH mice, supporting development of combination approaches for NASH. Disclosure J.L. Trevaskis: Employee; Self; Gilead Sciences, Inc. J. Norlin: Employee; Self; Novo Nordisk A/S. Stock/Shareholder; Self; Novo Nordisk A/S. D.A. Miranda: None. J.G. Bates: Employee; Self; Gilead Sciences, Inc. N.E. Zois: Employee; Self; Gubra. S. Veidal: None. M. Feigh: None. M. Latta: Employee; Self; Novo Nordisk A/S.
Developability of triangle meshes (2018)

Developable surfaces are those that can be made by smoothly bending flat pieces without stretching or shearing. We introduce a definition of developability for triangle meshes which exactly captures two key properties of smooth developable surfaces, namely flattenability and presence of straight ruling lines. This definition provides a starting point for algorithms in developable surface modeling---we consider a variational approach that drives a given mesh toward developable pieces separated by regular seam curves. Computation amounts to gradient descent on an energy with support in the vertex star, without the need to explicitly cluster patches or identify seams. We briefly explore applications to developable design and manufacturing.
Author response: Forniceal deep brain stimulation induces gene expression and splicing changes that promote neurogenesis and plasticity (2018)

Forniceal deep brain stimulation is a promising treatment for several neuropsychiatric disorders as it upregulates synaptic and neurogenesis-associated genes, normalizes genes misregulated in Rett syndrome mice, and regulates genes altered in intellectual disability and major depression.
Ginga-NCL (2009)

Multimedia applications for DTV systems can take profit of multiple exhibition devices to enrich the set of supported interactive applications. New applications in which viewers can cooperate besides being able to have its own navigation space without disturbing their neighbors in a common environment will now be possible. The NCL language allows developing such applications following a hierarchical model supported by its presentation environment called Ginga-NCL, by using a set of components in charge of orchestrating the several devices used in the presentation. This paper presents the mentioned support provided by the reference implementation of the Ginga-NCL middleware, stressing its architecture and illustrating the new possibilities opened by the multi-device applications.
Inflammation-Induced Oxidative Stress Mediates Gene Fusion Formation in Prostate Cancer (2016)

Approximately 50% of prostate cancers are associated with gene fusions of the androgen-regulated gene TMPRSS2 to the oncogenic erythroblast transformation-specific (ETS) transcription factor ERG. The three-dimensional proximity of TMPRSS2 and ERG genes, in combination with DNA breaks, facilitates the formation of TMPRSS2-ERG gene fusions. However, the origins of DNA breaks that underlie gene fusion formation in prostate cancers are far from clear. We demonstrate a role for inflammation-induced oxidative stress in the formation of DNA breaks leading to recurrent TMPRSS2-ERG gene fusions. The transcriptional status and epigenetic features of the target genes influence this effect. Importantly, inflammation-induced de novo genomic rearrangements are blocked by homologous recombination (HR) and promoted by non-homologous end-joining (NHEJ) pathways. In conjunction with the association of proliferative inflammatory atrophy (PIA) with human prostate cancer, our results support a working model in which recurrent genomic rearrangements induced by inflammatory stimuli lead to the development of prostate cancer.
Factor Analysis of Seattle Fine Particles (2004)

Ambient particulate matter ≤2.5 μm in aerodynamic diameter (PM2.5) samples were collected at a centrally located urban monitoring site in Seattle, WA on Wednesdays and Saturdays using Interagency Monitoring of Protected Visual Environments (IMPROVE) samplers. Particulate carbon was analyzed using the thermal optical reflectance method that divides carbon into four organic carbon (OC), pyrolyzed organic carbon (OP), and three elemental carbon (EC) fractions. A total of 384 samples that were analyzed for 36 species were collected between March 1996 and February 2000. These data were analyzed with the standard factor analysis model using the Multilinear Engine (ME). Eleven sources were identified: sulfate-rich secondary aerosol (26%), diesel emissions (22%), wood smoke (16%), gasoline vehicle (10%), aged sea salt (8%), airborne soil (7%), nitrate-rich secondary aerosol (5%), sea salt (4%), oil combustion (3%), paper mill (2%), and ferrous metal processing (1%). The use of ME provided enhanced source separations, including the nitrate-rich aerosol source and two industrial sources that were not deduced in a previous PMF2 solution. Conditional probability functions using surface wind data and resolved source contributions aid in the identifications of local sources. Potential source contribution function analysis tentatively shows southern Washington State, along the Canadian border, and southwestern British Colombia, Canada as the possible source areas and pathways that give rise to the high contribution of the sulfate-rich secondary aerosol.
Oncolytic Alphaherpesvirus and Myeloid-Tropic Cytomegalovirus Cooperatively Enhance Systemic Antitumor Responses (2023)

Abstract Oncolytic virotherapy aims to activate host antitumor immunity, but the effectiveness of current intratumoral herpes-simplex virus (HSV) based monotherapy is limited. Here, to boost the potency of cancer cell targeting α-herpesviruses derived from HSV or Varicella-Zoster Virus (VZV), we coinjected them with myeloid cell-tropic β-herpesviruses derived from cytomegalovirus (CMV) which can powerfully modulate immune responses. Co-administered CMV was shown to promote intratumoral replication of HSV, increase local release of pro-inflammatory cytokines, inhibit adaptive antiviral immune responses, enhance systemic antitumor responses, and lead to superior control of both injected and contralateral tumors. CMV-encoded myeloid-tropic genes, NK evasins (i.e. the vMHC-I homolog), and the m02-m16 region (involved in downregulating classical MHC-I) were implicated in enhancing antitumor activities. CMV is a promising adjuvant to reshape and enhance the antitumor immune responses following α-herpesvirus therapy.
Prevalence and causes of vision loss in South-east Asia and Oceania in 2015: magnitude, temporal trends and projections (2018)

In both regions, the main challenges for eye care come from cataract which remains the main cause of blindness with uncorrected refractive error the main cause of MSVI. The trend between 1990 and 2015 is for a lower prevalence of blindness and MSVI in both regions.
Electron cyclotron current drive under neutral beam injection on HL-2M (2022)

Abstract Based on OMFIT framework and HL-2M parameters, this paper comprehensively considers the changes in plasma density, temperature, and other transport quantities caused by the interaction of neutral beam injection (NBI) and electron cyclotron wave (ECW) with plasma. The changes in the Shafranov shift of the plasma magnetic surface center are also evaluated. Theoretically, the influence of NBI on the deposition location and current drive efficiency of the ECW is studied. According to the findings, NBI affected the position location and efficiency of the electron cyclotron current drive (ECCD) deposited on both high field side (HFS) and low field side (LFS). NBI can relocate the ECW power deposition location to the core and increase the current drive efficiency when the ECW power is deposited on the LFS. When the NBI power increases to 7 MW, the ECCD deposition location can shift to the core by roughly 0.15 normalized small radii, and the current drive efficiency can be improved by 1.3 times. Moreover, as NBI power increases, the radial region where the dimensionless current drive efficiency equals to zero gets closer to the plasma edge. When ECW power is deposited on the HFS paraxial, increasing NBI power causes the ECW deposition location to move toward the plasma edge, thus lowering current drive efficiency. This trend is caused by an increase in NBI power, which can increase the Shafranov shift of the plasma center, increase the electron density, and change the electron temperature. These studies hold great significance for achieving more effective current drive and controlling the plasma current profile and neoclassical tearing mode instability.
46: Population Pharmacokinetic Evaluation of Cefepime in Critically Ill Adults (2020)

Barreto, Erin1; Scheetz, Marc2; Bjergum, Matthew1; Mara, Kristin1; Vollmer, Kathryn3; Meade, Laurie1; Fogelson, Lindsay1; Gajic, Ognjen4; Jannetto, Paul1; OHoro, John5; Reid, Joel1; Rule, Andrew1 Author Information
Sweep-based Spectrum Sensing Method for Interference-Aware Cognitive Automotive Radar (2020)

The ongoing automation of driving functions in cars leads to a massive growth in the number of automotive radar sensors, and thus to more radar interference. An approach for actively mitigating interference between automotive radars is the interference-aware cognitive radar (IACR). One major challenge for IACR is, however, sensing of a large spectral band (e.g. 77-81 GHz) potentially available for radar operation. In this paper, we present a cost-efficient spectrum sensing method based on linear sweeping over a wide spectral band. The signal resulting from the sweep is lowpass filtered prior to sampling, which allows a significant bandwidth reduction down to few tens of MHz. In the digital domain, the captured signal is pulse-compressed with a bank of matched filters. The output image of the time-frequency space provides a basis for identification of interference-free regions and a subsequent adaptation for the next measurement cycle. The performance of the proposed approach is studied in simulation and demonstrated with a prototype. The results indicate the feasibility of such spectrum sensing module for automotive radar both in terms of performance and cost.
Multi-label Prediction in Time Series Data using Deep Neural Networks (2019)

This paper addresses a multi-label predictive fault classification problem for multidimensional time-series data. While fault (event) detection problems have been thoroughly studied in literature, most of the state-of-the-art techniques can’t reliably predict faults (events) over a desired future horizon. In the most general setting of these types of problems, one or more samples of data across multiple time series can be assigned several concurrent fault labels from a finite, known set and the task is to predict the possibility of fault occurrence over a desired time horizon. This type of problem is usually accompanied by strong class imbalances where some classes are represented by only a few samples. Importantly, in many applications of the problem such as fault prediction and predictive maintenance, it is exactly these rare classes that are of most interest. To address the problem, this paper proposes a general approach that utilizes a multi-label recurrent neural network with a new cost function that accentuates learning in the imbalanced classes. The proposed algorithm is tested on two public benchmark datasets: an industrial plant dataset from the PHM Society Data Challenge, and a human activity recognition dataset. The results are compared with state-ofthe-art techniques for time-series classification and evaluation is performed using the F1-score, precision and recall.
Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry Analysis of Poly(para-phenyleneethynylene)s (2005)

Abstract For the first time, MALDI-TOF MS was utilized for the determination of the structures of four partially soluble poly(p-phenyleneethynylene)s (PPEs) used to disperse single-walled carbon nanotubes in polymers. The spectra obtained indicated that the synthesis of the PPEs resulted in the formation of a co-oligomer with two different repeat groups. Various methods were employed to obtain an optimum spectrum. The evaporation-grinding sample preparation method (E-G method) combined with dithranol as matrix and KTFA as cationizing agent appeared to be the best method for obtaining a MALDI-TOF MS spectrum. AgTFA was the most effective cationizing agent for one sample that contained a high carbon-to-oxygen ratio.
Supplementary Methods, Table, and Legends from Targeting Adenosine in BRAF-Mutant Melanoma Reduces Tumor Growth and Metastasis (2023)

&lt;p&gt;This file contains Supplementary experimental Procedures, Supplementary Figure Legends, and Table S1. Table S1. Changes to patient CD73 expression following BRAF targeted therapy.&lt;/p&gt;