gebhart/patrepeval huggingface dataset:
Functional ultrasound imaging of deep visual cortex in awake non-human primates (2019)

Summary Deep regions of the brain are not easily accessible to investigation at the mesoscale level in awake animals or humans. We have recently developed functional Ultrasound (fUS) imaging fUS imaging technique to uncover deep hemodynamic functional responses. Applying fUS imaging on two awake non-human primates performing a passive fixation task, we reconstructed their retinotopic maps down to the deep calcarine and lunate sulci on visual areas (V1, V2 and V3). These maps were acquired in a single hour session with very few stimuli presentation. The spatial resolution of the technology is illustrated by mapping of Ocular Dominance (OD) columns within superficial and deep layers of the primary visual cortex. These acquisitions showed that OD selectivity is mostly present in layer IV but with evidence also in layers II/III and V. The fUS imaging technology therefore provides a new mesoscale approach to map brain activities at high spatiotemporal resolution in awake subjects within the whole depth of the cortex.
Formation of Stable Interphase of Polymer-in-Salt Electrolyte in All-Solid-State Lithium Batteries (2021)

The integration of solid-polymer electrolytes into all-solid-state lithium batteries is highly desirable to overcome the limitations of current battery configurations that have a low energy density and severe safety concerns. Polyacrylonitrile is an appealing matrix for solid-polymer electrolytes; however, the practical utilization of such polymer electrolytes in all-solid-state cells is impeded by inferior ionic conductivity and instability against a lithium-metal anode. In this work, we show that a polymer-in-salt electrolyte based on polyacrylonitrile with a lithium salt as the major component exhibits a wide electrochemically stable window, a high ionic conductivity, and an increased lithium-ion transference number. The growth of dendrites from the lithium-metal anode was suppressed effectively by the polymer-in-salt electrolyte to increase the safety features of the batteries. In addition, we found that a stable interphase was formed between the lithium-metal anode and the polymer-in-salt electrolyte to restrain the uncontrolled parasitic reactions, and we demonstrated an all-solid-state battery configuration with a LiFePO 4 cathode and the polymer-in-salt electrolyte, which exhibited a superior cycling stability and rate capability.
Fascial Tissue Reconstruction Using Acellular Collagen Matrix (2008)

Statement of Purpose: Acellular collagen matrices have been used experimentally and clinically for several applications, including urethra and bladder reconstruction. We investigated the feasibility of using a porcine collagen‐based matrix as an off‐the‐shelf biomaterial for fascial tissue repair in 3 different tissue systems. Methods: Biocompatibility of the acellular matrix derived from porcine bladders was assessed using cell viability, MTT and apoptotic index. The acellular collagen matrices were used as a sling material for the treatment of incontinence, abdominal hernias and penile tunica reconstruction in 24 rabbits. The animals were evaluated up to 3 months after implantation. Results / Discussion: The acellular matrix did not induce significant changes in cell viability, proliferation and apoptotic activity when compared with the controls. All animals survived without any untoward effects. The matrices remained intact at their respective implantation sites and demonstrated the maintenance of fascial tissue function. Histologically, there was only a minimal inflammatory response, which gradually decreased over time. Conclusions: These results show that the acellular collagen matrix derived from porcine bladders is biocompatible, durable and safe for use in vivo.
Expediting the chromatographic analysis of COVID-19 antibody therapeutics with ultra-short columns, retention modeling and automated method development (2022)

The COVID-19 pandemic necessitated the emergency use authorization (EUA) of several new therapeutics and vaccines. Several monoclonal antibodies (mAbs) were among those authorized for use, and they have served a purpose to provide passive immunity and to help minimize dangerous secondary effects in at-risk and hospitalized patients infected with SARS-CoV-2. With an EUA submission, scientific data on a drug candidate is often collected near simultaneously alongside drug development. In such a situation, there is little time to allow misguided method development nor time to wait on traditional turnaround times. We have taken this dilemma as a chance to propose new means to expediting the chromatographic characterization of protein therapeutics. To this end, we have combined the use of automated, systematic modeling and ultrashort LC columns to quickly optimize high throughput RP, IEX, HILIC and SEC separations for two COVID-19-related mAbs. The development and verification of these four complementary analytical methods required only 2 days of experimental work. In the end, one chromatographic analysis can be performed with a sub-2 min run time such that it is feasible to comprehensively characterize a COVID-19 mAb cocktail by 4 different profiling techniques within a 1-hour turnaround time.
Well-defined polyethylene molecular brushes by polyhomologation and ring opening metathesis polymerization (2014)

Well-defined polyethylene molecular brushes were synthesized, for the first time, by combining polyhomologation and ring opening metathesis polymerization (ROMP).
A Hybrid Submodular Optimization Approach to Controlled Islanding with Post-Disturbance Stability Guarantees (2023)

Disturbances may create cascading failures in power systems and lead to widespread blackouts. Controlled islanding is an effective approach to mitigate cascading failures by partitioning the power system into a set of disjoint islands. To retain the stability of the power system following disturbances, the islanding strategy should not only be minimally disruptive, but also guarantee post-disturbance stability. In this paper, we study the problem of synthesizing post-disturbance stability-aware controlled islanding strategies. To ensure post-disturbance stability, our computation of islanding strategies takes load-generation balance and transmission line capacity constraints into consideration, leading to a hybrid optimization problem with both discrete and continuous variables. To mitigate the computational challenge incurred when solving the hybrid optimization program, we propose the concepts of hybrid submodularity and hybrid matroid. We show that the islanding problem is equivalent to a hybrid matroid optimization program, whose objective function is hybrid supermodular. Leveraging the supermodularity property, we develop an efficient local search algorithm and show that the proposed algorithm achieves 1/2-optimality guarantee. We compare our approach with a baseline using mixed-integer linear program on IEEE 118-bus, IEEE 300-bus, ActivSg 500-bus, and Polish 2383-bus systems. Our results show that our approach outperforms the baseline in terms of the total cost incurred during islanding across all test cases. Furthermore, our proposed approach can find an islanding strategy for large-scale test cases such as Polish 2383-bus system, whereas the baseline approach becomes intractable.
S1.03 * GLIOBLASTOMA SUBTYPES DEFINED BY QUANTITATIVE IMAGING MAP TO DIFFERENT CANONICAL SIGNALING PATHWAYS (2014)

We sought to discover subtypes of glioblastoma (GBM) defined by quantitative imaging features and to identify their canonical signaling pathways. Preoperative MR imaging from 121 Stanford patients with de novo, focal, unilateral GBM were analyzed. Two board-certified neuroradiologists and a neurosurgeon reached consensus in delineating Regions-of-Interest (ROIs) around areas of enhancement in each T1 post-contrast MR. We extracted 138 quantitative image features representing signal intensity and morphology of each lesion. We then used Consensus Clustering to define subtypes in the Stanford group. Next, Prediction Analysis for Microarrays (PAM) and the In-Group Proportion (IGP) statistic were used to validate the reproducibility and robustness of our subtype classification in a second cohort of subjects from The Cancer Genome Atlas (TCGA, n = 145). Finally, to map imaging subtypes to particular molecular signaling pathways, we performed Significance Analysis of Microarrays (SAM) on pathway activity estimates derived from analysis of TCGA tumor copy number and RNA sequencing data with the PARADIGM algorithm. Consensus Clustering analysis of the training set identified three clusters whose validity was confirmed in the TCGA cohort (p < 0.0001, p< 0.0001, p = 0.015). Cluster sizes for the TCGA validation cohort (i.e. 45%, 21% and 35%) were similar to those in the Stanford training set (57%, 17% and 26%). Cluster 1 was associated with 49 overexpressed pathways (FDR < 5%) including Wnt, hypoxia, apoptosis, cell proliferation, and angiogenesis signaling pathways while Cluster 2 was characterized by downregulation of these pathways (FDR < 5%). No pathway was significantly associated with Cluster 3. We identified three distinct, robust clusters of focal, unilateral GBM defined by quantitative image signatures. Subtypes identified in a homogeneous Stanford training set were validated in the heterogeneous multi-institutional TCGA data set. Two of our three clusters had significant associations with canonical signaling pathways.
Online aggregation and continuous query support in MapReduce (2010)

MapReduce is a popular framework for data-intensive distributed computing of batch jobs. To simplify fault tolerance, the output of each MapReduce task and job is materialized to disk before it is consumed. In this demonstration, we describe a modified MapReduce architecture that allows data to be pipelined between operators. This extends the MapReduce programming model beyond batch processing, and can reduce completion times and improve system utilization for batch jobs as well. We demonstrate a modified version of the Hadoop MapReduce framework that supports online aggregation, which allows users to see "early returns" from a job as it is being computed. Our Hadoop Online Prototype (HOP) also supports continuous queries, which enable MapReduce programs to be written for applications such as event monitoring and stream processing. HOP retains the fault tolerance properties of Hadoop, and can run unmodified user-defined MapReduce programs.
Pharmacological bypass of NAD + salvage pathway protects neurons from chemotherapy-induced degeneration (2018)

Axon degeneration, a hallmark of chemotherapy-induced peripheral neuropathy (CIPN), is thought to be caused by a loss of the essential metabolite nicotinamide adenine dinucleotide (NAD<sup>+</sup>) via the prodegenerative protein SARM1. Some studies challenge this notion, however, and suggest that an aberrant increase in a direct precursor of NAD<sup>+</sup>, nicotinamide mononucleotide (NMN), rather than loss of NAD<sup>+</sup>, is responsible. In support of this idea, blocking NMN accumulation in neurons by expressing a bacterial NMN deamidase protected axons from degeneration. We hypothesized that protection could similarly be achieved by reducing NMN production pharmacologically. To achieve this, we took advantage of an alternative pathway for NAD<sup>+</sup> generation that goes through the intermediate nicotinic acid mononucleotide (NAMN), rather than NMN. We discovered that nicotinic acid riboside (NAR), a precursor of NAMN, administered in combination with FK866, an inhibitor of the enzyme nicotinamide phosphoribosyltransferase that produces NMN, protected dorsal root ganglion (DRG) axons against vincristine-induced degeneration as well as NMN deamidase. Introducing a different bacterial enzyme that converts NAMN to NMN reversed this protection. Collectively, our data indicate that maintaining NAD<sup>+</sup> is not sufficient to protect DRG neurons from vincristine-induced axon degeneration, and elevating NMN, by itself, is not sufficient to cause degeneration. Nonetheless, the combination of FK866 and NAR, which bypasses NMN formation, may provide a therapeutic strategy for neuroprotection.
<title>Multifunctional photonic devices based on polymeric materials</title> (1999)

A multifunctional polymeric deice capable of performing functions such as electro-optic modulation, optical amplification, and electro-optic switching simultaneously is described. All three modules can be built on a single substrate. A novel polymeric modulator with structure based on 1 X 2 Y-fed directional coupler is demonstrated. The results of preliminary investigations on optical amplifiers are presented.
Electron beam generation and transport for millimeter and THz tubes (2006)

Electron guns and magnetic circuits for high frequency RF sources present unique challenges. As the frequency increases, the size becomes reduced. This becomes a serious problem when feature sizes approach the tolerances that can be achieved with available fabrication and assembly processes. Periodic permanent magnet focusing becomes particularly difficult when the magnets must be enclosed within the tube vacuum. This presentation will describe the challenges and the designs being developed for millimeter and submillimeter wave RF sources.
Enzyme-peeling of Valencia oranges for fresh-cut slices (2006)

In spite of the booming market for fresh cut fruit, fresh cut citrus products have not been successfully commercialized due to technical difficulties in peeling the fruit and concerns over microbial contamination and juice leakage. The USDA and the Florida Department of Citrus have developed processes using enzyme infiltration under vacuum as well as water infusion to facilitate citrus peeling. However, the enzymes (cellulase and/or pectinase) continue their lytic action on the slices after the peeling process, reportedly degrading the slices during storage, and likely contributing to objectionable softening and juice leakage. There is also a perceived fear of microbial contamination in the process of enzyme infiltration or water infusion. The objective of the present study was to investigate low level enzyme concentrations and use of an acid solution (0.1 N HCl) rinse and cold conditioning (2C for 24 hours) to slow down enzymatic activity after peeling of 'Valencia' oranges. In addition, the infiltration system was used to compare two commercial enzymes and water infusion for efficacy of peeling and effect on microbial contamination. Quality factors including juice leakage, firmness, pH, titratable acidity, soluble solids, and surface microbial counts were evaluated over three different harvests. Water infusion resulted in less attractive slices and a tougher texture compared to enzymetreated fruit slices. Microbial counts were highest in water-infused fruit compared to those treated with enzymes or manually peeled, which in both cases were very low. Of the two enzymes tested, Ultrazym resulted in firmer slices and generally less juice leakage, although leakage was minimal for both enzymes within a two-week storage period at the enzyme concentrations used. Juice leakage, however, was not affected by the acid treatment or temperature conditioning.
[Supertransformation of a human lymphoblastoid cell line by chemical carcinogens]. (1983)

We have studied the in vitro malignant progression of human lymphoid cells by the combined effect of genetic, viral and mutagenic factors. A lymphoblastoid cell line immortalized by Epstein-Barr virus was used; it was derived from a patient suffering from ataxia-telangiectasia, a genetic disease linked to a deficiency in DNA repair. Cells were treated by sub-toxic doses of two potent mutagens (carcinogens), NQO (4-nitroquinolein-oxid) and R 7 000 (2-nitro-7-methoxy-naphto-furan). The treated cells showed an increased ability to form colonies in soft agarose, among which some compact colonies appeared, different from the diffuse colonies formed by untreated control cells. Sub-clones derived from these compact colonies differ also from the original cells by their behavior in liquid culture medium, by their increased tumorigenicity in Nude Mice and by their capacity to form nodules on Chicken chorioallantoic membrane. Some of the sub-clones produce non-regressing large tumors in Nude Mice with a cell inoculum lower than that required for Burkitt lymphoma cells while being less invasive than the latter. However, by their morphology, the malignant cells of the sub-clones remain similar to the original lymphoblastoid cells. Thus, such a malignant progression obtained in vitro cannot be considered as identical to that which leads to Burkitt lymphoma in African children.
In vivo isolation of circulating tumor cells in prostate cancer patients by a medical device. (2013)

e22055 Background: CTCs are discussed as a prognostic and stratification biomarker, and may help to assess the treatment efficacy. The aim was to demonstrate proof of concept of in vivo CTC isolation in Prostate cancer patients (PCa). Methods: A medical device (CellCollector) was inserted in a cubital vein for 30 minutes. The interaction of target CTCs with the CellCollector was mediated by antibodies to the epithelial cell adhesion molecule (EpCAM). To confirm binding of CTCs to the wire, immunohistochemical staining against Cytokeratin and CD45 was performed. There were 226 applications of the device in 16 metastasized PCa (PCa-m) with up to 8 wire applications per patient, 24 localized PCa (PCa-l) with up to 3 wire applications per patient as well as 19 men with benign prostate hypertrophy (BPH) and 21 women as control group with only one wire application. CTC counts from 22 PCa patients with 58 applications were directly compared to the CellSearch technology. Results: We obtained in vivo isolation of CTCs in 73 of 98 applications to PCa patients (74.5 %). The sensitivity for metastasized PCa was (86.2%) and for local PCa (57.5%), respectively. Follow up data of one patient with PCa-m: 2009 diagnosed PCa with multiple metastases. 2 years later PSA of 11.2ng/mL and 25 CTCs. After transurethral resection and removal of a brain metastasis, CTCs decreased to 20 cells with no effect on PSA levels. 4 months later we observed 187 CTCs and a PSA level of 76ng/mL, which was correlated with the patient condition. In PCa-l patients we observed prior radical prostatectomy (n=18) and 6 (n=15) and 12 (n=7) months after surgery CTC numbers on average of 18.2, 2.8 and 1.4, respectively. In the direct comparison of the CellCollector and CellSearch we showed detection rates of 65% (13/20) and 20% (4/20). Conclusions: We demonstrate the use of CTCs besides PSA during therapy adjustment in PCa patients In summary the CTC detection rate of the CellCollector in PCa-m and PCa-l in comparison to the CellSearch method increased by 26% and 45%. Further molecular genetic CTC characterization as well as multiple antibody coating at the CellCollector will assume crucial information for therapy decisions. Clinical trial information: ISRCTN10403616.
Novel Point-Like $^{68}{\rm Ge}/^{68}{\rm Ga}$ Radioactive Source With Spherical Positron Absorber (2011)

Purpose: In the conventional techniques for determining the calibration factors of positron emission tomography (PET) scanners, cylindrical water and resin phantoms with radioisotope <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">18</sup> F or <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">68</sup> Ge/ <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">68</sup> Ga are used. In these methods, however, the results depend on attenuation and scatter correction. The purpose of this study is to develop a point-like <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">68</sup> Ge/ <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">68</sup> Ga radioactive source that can be used to determine the calibration factors of PET scanners without the uncertainty of attenuation and scatter correction. Methods: A spherical absorber design was employed to realize a symmetric angular distribution of emitted annihilation photons. A Geant4-based Monte Carlo simulation code was used to compare physics characteristics of point-like sources with various absorber materials. On the basis of this simulation, a point-like <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">68</sup> Ge/ <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">68</sup> Ga source with a spherical aluminum absorber was manufactured. Its radioactivity was calibrated at an accredited national calibration facility. A calibration factor of a clinical PET scanner was then obtained with a point-like source and compared with that obtained by a standard cross-calibration method. Results: The emission probability of 0.511 MeV annihilation photon pairs per positron decay was typically 0.6-0.8. The fraction of background photon pairs was 6-8% in the energy region of 0.4-0.6 MeV. Considering these two figures, lower density materials such as aluminum and pol(ymethyl methacrylate) (PMMA) were preferable. For the aluminum absorber, a diameter of 8 mm was suitable to prevent positrons from escaping. The calibration factor obtained with the point-like source agreed with that obtained by the standard method within 2-3%. Conclusion: A point-like <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">68</sup> Ge/ <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">68</sup> Ga radioactive source was successfully designed, manufactured, and used for determining a calibration factor of a PET scanner. It can be considered a practical tool for calibrating and evaluating the quantitative aspects of PET scanners.
Brain-Derived Neurotrophic Factor Mitigates the Association Between Platelet Dysfunction and Cognitive Impairment (2021)

<b>Background:</b> Platelet hyperactivity is deleterious in coronary artery disease (CAD), requiring lifelong antiplatelet therapy, and is associated with worse cognitive outcomes. Upon activation, platelets release Brain-Derived Neurotrophic Factor (BDNF), a neurotrophin protective against cognitive decline. Given these apparently opposing effects of platelet activation on cognitive health, we investigated whether BDNF levels intercede in the relationship between platelet activation and cognitive function; and whether this relationship is moderated by the presence of CAD. <b>Methods:</b> In this cross-sectional study, 1,280 participants with (<i>n</i> = 673) and without CAD (<i>n</i> = 607) completed the Montreal Cognitive Assessment (MoCA). Plasma BDNF and soluble P-selectin (a marker of platelet activity) levels were assessed using multiplex flow cytometry. <b>Results:</b> In a mediation model, platelet activity was correlated with higher plasma BDNF concentrations (b = 0.53, <i>p</i> < 0.0001). The relationship between sP-selectin and BDNF concentrations was stronger for individuals without CAD (b = 0.71, <i>p</i> < 0.0001) than for CAD participants (b = 0.43, <i>p</i> < 0.0001; <i>p</i> <sub>interaction</sub> <0.0001). Higher BDNF concentrations were associated with higher MoCA scores (b = 0.26, <i>p</i> = 0.03). The overall effect of platelet activity on cognitive performance was non-significant (total effect: b = -0.12, <i>p</i> = 0.13), and became significant when accounting for BDNF as a mediating factor (direct effect: b = -0.26, <i>p</i> = 0.01). This resulted in a positive indirect effect of platelet activity (via BDNF) on MoCA scores (b = 0.14, CI 95% 0.02-0.30), that was smaller in CAD participants than in non-CAD participants [Δ -0.07 (95% CI -0.14 to -0.01)]. <b>Conclusions:</b> BDNF released from activated platelets could be a mitigating factor in a negative association between platelet activity and cognitive function.