gebhart/patrepeval huggingface dataset:
Immunogenicity, Safety, and Anti-Viral Efficacy of a Subunit SARS-CoV-2 Vaccine Candidate in Captive Black-Footed Ferrets (Mustela nigripes) and Their Susceptibility to Viral Challenge (2022)

A preliminary vaccination trial against the emergent pathogen, SARS-CoV-2, was completed in captive black-footed ferrets (Mustela nigripes; BFF) to assess safety, immunogenicity, and anti-viral efficacy. Vaccination and boosting of 15 BFF with purified SARS-CoV-2 S1 subunit protein produced a nearly 150-fold increase in mean antibody titers compared to pre-vaccination titers. Serum antibody responses were highest in young animals, but in all vaccinees, antibody response declined rapidly. Anti-viral activity from vaccinated and unvaccinated BFF was determined in vitro, as well as in vivo with a passive serum transfer study in mice. Transgenic mice that received BFF serum transfers and were subsequently challenged with SARS-CoV-2 had lung viral loads that negatively correlated (p < 0.05) with the BFF serum titer received. Lastly, an experimental challenge study in a small group of BFF was completed to test susceptibility to SARS-CoV-2. Despite viral replication and shedding in the upper respiratory tract for up to 7 days post-challenge, no clinical disease was observed in either vaccinated or naive animals. The lack of morbidity or mortality observed indicates SARS-CoV-2 is unlikely to affect wild BFF populations, but infected captive animals pose a potential risk, albeit low, for humans and other animals.
Fabrication of Fiber Reinforced Metal by Squeeze Casting : Pressurized Infiltration Process of Molten Aluminum to Continuous Glass Fiber Bundle (1984)

The present paper deals with the infiltration length of molten aluminum to a continuous glass fiber bundle for various squeeze conditions. The results show that the infiltrated length is proportional to the squeeze pressure, increases exponentially with an increase in the fiber temperature and does not depend on the ram speed. The empirical infiltration length was in good agreement with the calculated one, based on Darcy's law and a newly proposed infiltration model : molten aluminum infiltrates through the gap accompanied with the formation of a solidified layer on the fiber surface, and finally stops to solidify immediately when the heat quantity of the molten aluminum front is balanced to the released heat to fiber ahead of the front. Thus, a method to predict the infiltrated length for the practical squeeze casting is proposed.
Significance of the expression of the growth factor pleiotrophin in pancreatic cancer patients. (2002)

This study supports the clinical significance of PTN for the malignant progression of pancreatic cancer.
A cortical locus for overlay suppression with broadband stimuli revealed through transcranial direct current stimulation (2013)

Human contrast sensitivity for Gabor targets is largely suppressed when superimposed on a Gabor mask of the same spatial frequency (SF) and orientation (referred to as overlay suppression, OS), with suppression being broadly tuned to orientation (~130° bandwidth) and spatial frequency (~3 octave bandwidth) (Petrov, Carandini, & McKee, 2005). Further, numerous behavioral and neurophysiological experiments have suggested that the suppressive signals leading to OS originate from the initial LGN inputs to V1. However, Kim, Haun, and Essock (2010) have reported anisotropic contrast sensitivity thresholds for differently oriented Gabor targets when masked by broadband noise. Their results suggest a much narrower orientation tuning for OS than would be expected if it originates from initial LGN inputs to V1, and imply that another cortical operation is active when overlay masks are broadband. Here, we sought to explore this notion using transcranial direct current stimulation (tDCS). Since tDCS is only effective at modulating cortical function, we hypothesized that tDCS would influence suppression for OS with broadband stimuli but not for OS with narrowband stimuli which may result from sub-cortical signals. Target stimuli consisted of 8cpd Gabor targets (subtending 0.3°) at one of three orientations (0°, 45°, or 90°). Overlay masks were either identical to the targets (narrowband masks), or consisted of broadband noise patches (20° orientation bandwidth and 2 octaves in SF). All masks were fixed at 0.21 rms contrast; with target contrast controlled by a standard 2IFC staircase procedure (stimulus duration was 150ms). Human participants performed the task foveally with tDCS (anodal and cathodal) and without (i.e., baseline). The results showed that tDCS resulted in a large anisotropic reduction in OS when the masks were broadband, but not when they were narrowband. This supports the hypothesis that OS has a cortical locus when the overlay masks are broadband in SF and orientation. Meeting abstract presented at VSS 2013
Bi-Modal Compositional Network for Feature Disentanglement (2022)

The purpose of Compositional Zero-Shot Learning (CZSL) is to recognise unseen (or new) compositions of known objects (e.g. apple, banana) and its states (e.g. peeled, ripe). The CZSL poses a challenging problem as the visual features of objects and states are often difficult to isolate from their composition in images. Also, the features of a state may have wide variation across different compositions. For example, the state sliced presents different visual features in compositions, sliced potato and sliced bread. Hence, for solving CZSL problem, disentanglement of state and object features is the key challenge that we attempt to address in this paper by introducing Bi-modal Compositional Network (BiComNet). The proposed BiComNet consists of two distinct branches for state and object recognition, which helps in better disentanglement of the state and object features. We also propose a novel loss component to better facilitate the disentanglement of the state and object features. Finally, the proposed BiComNet integrates two different modalities of input data, the visual and word features, to better recognise unseen state-object compositions. Extensive experiments are carried out on the benchmark datasets MIT-States & UT-Zappos50K. Our proposed algorithm outperforms competitive methods in most count.
Difluoromethyl-1,3,4-oxadiazoles are slow-binding substrate analog inhibitors of histone deacetylase 6 with unprecedented isotype selectivity (2022)

Histone deacetylase 6 (HDAC6) is an attractive drug development target because of its role in the immune response, neuropathy, and cancer. Knockout mice develop normally and have no apparent phenotype, suggesting that selective inhibitors should have an excellent therapeutic window. Unfortunately, current HDAC6 inhibitors have only moderate selectivity and may inhibit other HDAC subtypes at high concentrations, potentially leading to side effects. Recently, substituted oxadiazoles have attracted attention as a promising novel HDAC inhibitor chemotype, but their mechanism of action is unknown. Here, we show that compounds containing a difluoromethyl-1,3,4-oxadiazole (DFMO) moiety are potent and single-digit nanomolar inhibitors with an unprecedented greater than 10<sup>4</sup>-fold selectivity for HDAC6 over all other HDAC subtypes. By combining kinetics, X-ray crystallography, and mass spectrometry, we found that DFMO derivatives are slow-binding substrate analogs of HDAC6 that undergo an enzyme-catalyzed ring opening reaction, forming a tight and long-lived enzyme-inhibitor complex. The elucidation of the mechanism of action of DFMO derivatives paves the way for the rational design of highly selective inhibitors of HDAC6 and possibly of other HDAC subtypes as well with potentially important therapeutic implications.
Comet 81P/Wild 2 Under a Microscope (2006)

The Stardust spacecraft collected thousands of particles from comet 81P/Wild 2 and returned them to Earth for laboratory study. The preliminary examination of these samples shows that the nonvolatile portion of the comet is an unequilibrated assortment of materials that have both presolar and solar system origin. The comet contains an abundance of silicate grains that are much larger than predictions of interstellar grain models, and many of these are high-temperature minerals that appear to have formed in the inner regions of the solar nebula. Their presence in a comet proves that the formation of the solar system included mixing on the grandest scales.
Details of included and excluded trials (2011)

<b>Copyright information:</b>Taken from "Effectiveness of polymyxin B-immobilized fiber column in sepsis: a systematic review"http://ccforum.com/content/11/2/R47Critical Care 2007;11(2):R47-R47.Published online 20 Apr 2007PMCID:PMC2206475. MAP, mean arterial pressure; PaO/FiO, arterial partial pressure of oxygen/fraction of inspired oxygen.
An Easy Cell-Free Protein Synthesis System Dependent on the Addition of Crude Escherichia coli tRNA (2000)

The protein-synthesizing S30 extract of Escherichia coli contains tRNA, which limits its applications in cell-free protein synthesis. Here, we show that at least Arg- and Ser-acceptor activities can be removed from a standard S30 extract by treatment with an immobilized RNase A resin. This RNase-treated extract exhibits no protein synthesis activity, but regains it when supplied with crude E. coli tRNA and a small amount of human placental RNase inhibitor. The protein synthesis is dependent on the addition of tRNA in the presence of the RNase inhibitor. Chloramphenicol acetyltransferase was synthesized with this system and found to be active.
Reinforcement Learning Guided Detailed Routing for Custom Circuits (2023)

Detailed routing is the most tedious and complex procedure in design automation and has become a determining factor in layout automation in advanced manufacturing nodes. Despite continuing advances in custom integrated circuit (IC) routing research, industrial custom layout flows remain heavily manual due to the high complexity of the custom IC design problem. Besides conventional design objectives such as wirelength minimization, custom detailed routing must also accommodate additional constraints (e.g., path-matching) across the analog/mixed-signal (AMS) and digital domains, making an already challenging procedure even more so. This paper presents a novel detailed routing framework for custom circuits that leverages deep reinforcement learning to optimize routing patterns while considering custom routing constraints and industrial design rules. Comprehensive post-layout analyses based on industrial designs demonstrate the effectiveness of our framework in dealing with the specified constraints and producing sign-off-quality routing solutions.
Bone marrow stromal cells isolated from the infarcted region of the postischemic brain secrete neuroprotective and angiogenic factors (2009)

Although the therapeutic potential of bone marrow stromal cells (BMSC) has been demonstrated in stroke, there is limited information about the neuroprotective factors secreted by BMSC in the infarcted brain. The objective of this study was to compare the expression of genes for extracellular (EXC) factors produced by BMSC infiltrating brain tissue vs their naïve counterparts. Ischemic stroke was induced in C57BL/6 mice by middle cerebral artery occlusion for 1 h, followed by 24 h reperfusion. BMSC were isolated from H‐2Kb‐tsA58 mice (cells can grow at 33°C), and were administered (i.v.) at 24 h of reperfusion. Infarcted hemispheres were cultured at 33°C for BMSC isolation. Microarray analysis and RT‐PCR were performed to compare gene expression patterns between the BMSC populations in 9 mice. Z‐scoring revealed a robust change in the extracellular region of analyzed cells. Pair‐wise analysis detected 163 extracellular factor genes that were upregulated (≥ 2 fold, P&lt;0.05) between naïve and infiltrated BMSC. Fibroblast growth factors, bone morphogenetic protein, angiopoietins, neural and vascular growth factors were among the expressed genes detected. Our findings indicate that extracellular factors secreted by BMSC infiltrating the postischemic brain may explain the beneficial therapeutic effects of stem cell treatment and reveal potential therapeutic agents for treatment of ischemic stroke. (HL26411)
Differences in the nuclear proteins of normal and malignant liver cells. (1980)

Immunological tests and 2-dimensional gel electrophoresis revealed differences between the nuclear proteins from normal and malignant liver cells. Immunization of rabbits with a nuclear nonhistone protein fraction isolated from normal mouse liver resulted in antisera that in immunofluorescence gave nuclear staining in sections of normal liver, but did not stain nuclei of a transplantable mouse hepatoma. Antisera prepared against a nuclear protein fraction from the hepatoma allowed immunofluorescent staining of hepatoma nuclei but did not stain nuclei from normal liver. Nuclei in liver regeneration after injury caused by administration of carbon tetrachloride stained with antiserum against normal nuclei but not with antisera against hepatoma nuclei. Neither antiserum stained nuclei in fetal liver cells. The presence of differing sets of nuclear proteins in the normal and malignant liver cells was indicated by 2-dimensional gel electrophoresis. Approximately 300 polypeptides were resolved by this technique. Most of these were quantitatively different in the normal and hepatoma nonhistone protein preparations. Several qualitative differences also seemed to be present. Nonhistone proteins from regenerating liver shared some polypeptides with hepatoma that were absent in normal liver. Nuclear proteins characteristic of malignant tissues may provide clues toward the understanding of gene regulation in malignant cells, and some of them could become useful tumor markers.
Articular Cartilage Repair Through Muscle Cell-Based Tissue Engineering (2011)

Abstract : Using the modified preplate technique, we have isolated a population of early myogenic progenitor cells from postnatal skeletal muscle that display stem cell characteristics. We have shown that these muscle-derived stem cells (MDSCs) can differentiate toward myogenic, osteogenic, chondrogenic, neurogenic, and hematopoietic lineages. Specifically, MDSCs cultured in chondrogenic medium can undergo chondrogenic differentiation in vitro, and MDSCs delivered to osteochondral defects display good cell survival and can differentiate into chondrocytes that improve the healing of articular cartilage. We also have observed that bone morphogenetic protein 4 (BMP4) promotes chondrogenic differentiation of MDSCs in vitro and in vivo and that this cytokine can trigger chondrogenic differentiation of other populations of muscle-derived cells, including myoblasts (late myogenic progenitor cells) and fibroblasts. The proposed project will investigate the use of these populations of muscle-derived cells as novel cell sources for articular cartilage repair in osteochondral defects created in nude rats. We will investigate the in vitro chondrogenic potential of various populations of mouse muscle-derived cells (fibroblastic cells and early and late myogenic progenitor cells) expressing BMP4 and determine the regenerative capacity of these cells after implantation in rat articular cartilage defects. We then will explore the relative contributions of these muscle-derived cells long-term proliferation, survival, and self-renewal to their regenerative capacity after transplantation into the cartilage defects (Technical Objective #1). Next, we will determine the contributions of angiogenesis and scar tissue formation to the regenerative capacity of the muscle-derived cells and to the overall quality of the cartilage generated within the treated osteochondral defects (Technical Objective #2).
An Automated Method for the Assessment of Memory and Learning in Larval Zebrafish (2022)

Zebrafish have shown value in translational research for many human diseases, including neuropsychiatric disorders and cognitive dysfunction, with low cost and rapid testing facilitating drug screening and discovery. However, some endpoints, such as associative learning and long-term memory, have relied historically on manual data tracking that slows data acquisition and increases costs. We automated an associative learning/longterm memory test developed by Hinz et al. [1] using a Noldus DanioVision system and EthoVision software to enhance assay throughput and utility for monitoring learning and memory behavior through automated tracking of location and movement of individual fish.
A comparison of the esterification of steroids by rat lecithin:cholesterol acyltransferase and acyl coenzyme A:cholesterol acyltransferase. (1995)

Although fatty acid esters of several steroids have been found in both blood and tissues, their biosynthetic origins are uncertain. For example, the fatty acid esters of delta 5-3 beta-hydroxysteroids pregnenolone and dehydroepiandrosterone (DHEA) are synthesized in tissues by an acyl coenzyme A:acyltransferase. These esters are not secreted, and the circulating esters are formed in blood by lecithin:cholesterol acyltransferase (LCAT). Fatty acid esters of corticosterone (B) and estradiol (E2) are also present in both blood and tissues, but unlike the delta 5-3 beta-hydroxysteroids, their structures are so different from cholesterol that it would not necessarily follow that they are esterified by the same enzyme. We have examined the esterification of the steroids DHEA, B, and E2 in blood and tissue, in comparison to the esterification of cholesterol, using as a model plasma and hepatic microsomes from the rat. All of the steroids were esterified in plasma, but at very different rates: cholesterol > DHEA >> E2 = B. The LCAT inhibitor, 5.5'-dithiobis-(2-nitrobenzoic acid), inhibited the esterification of all of the substrates. DHEA inhibited the esterification of cholesterol, albeit only at high concentration. The fatty acid compositions of the cholesterol and DHEA esters were analyzed, and they were found to be identical, with arachidonate the predominant ester, greater than 60%. In hepatic microsomes, the rate of esterification was different than plasma: cholesterol > E2 > or = DHEA >> B. Although B was esterified in both plasma and hepatic microsomes, the rate was exceedingly slow in both. The acyl coenzyme A:cholesterol acyltransferase inhibitor, N'-(2,4-difluorophenyl)-N-[[4-(2,2-dimethylpropyl)phenyl]- methyl]-N-heptylurea, blocked the esterification of cholesterol almost completely, but surprisingly, it had no effect on the esterification of the other steroids. The fatty acid esters of cholesterol, E2, and DHEA synthesized in the hepatic microsomes were analyzed. The composition of the cholesterol esters from the microsomes was very different than the esters of DHEA and E2. These results show that all of the steroids tested are esterified by LCAT, and consequently that blood LCAT is the probable source of the circulating steroidal esters. Most interesting are the studies of microsomal esterification. It has been presumed that similar to blood, the esterification of steroids in tissues is carried out by the same enzyme that esterifies cholesterol.(ABSTRACT TRUNCATED AT 400 WORDS)
Injectable carbon nanotube-functionalized hydrogel as a tool for cardiac tissue engineering (2022)

Abstract Background/Introduction Heart failure (HF) is an expensive major public health problem in the United States and around the world (1). The current treatments for HF are aimed at reducing symptoms, slowing disease progression, and reducing mortality and not aimed at repairing heart muscle or restoring function. Furthermore, even with these treatments, approximately half of patients with HF will die within 5 years of diagnosis (2). Cardiac transplantation remains the only definitive treatment for those affected with end-stage HF, but availability of donor hearts remains a major limitation (3). Purpose The ability of the adult heart to regenerate cardiomyocytes (CMs) lost after injury is limited, generating interest in developing tissue engineering therapies to avoid progression towards HF. Rigid carbon nanotubes (CNTs) scaffolds have been used to improve CMs viability, proliferation, and maturation (4), but require undesirable invasive surgeries for implantation. To overcome this limitation, we engineered an injectable reverse thermal gel (RTG) functionalized with CNTs (RTG-CNT) that transitions from a liquid-solution to a gel-based matrix shortly after reaching body temperature allowing for a liquid-based delivery rapidly followed by a stable-gel localization (5). Methods and results Here we show experimental evidences the RTG-CNT hydrogel, used as a three-dimensional (3D) niche to culture human induced pluripotent stem cells (hiPSC)-CMs, promotes hiPSC-CMs alignment and elongation with increased Cx43 localization and improved contraction function when compared with traditional two-dimensional (2D) fibronectin controls and plain 3D RTG system without CNTs. Moreover, the short-term (4-week) biocompatibility of the RTG-CNT hydrogel was also assessed in a mouse model (intracardial injection). The results confirmed that the RTG-CNT hydrogel is well tolerated by the cardiac tissue. Conclusion Our results indicated that the injectable RTG-CNT hydrogel has the potential to be used as a minimally invasive tool for cardiac tissue engineering efforts. Funding Acknowledgement Type of funding sources: Other. Main funding source(s): NATIONAL HEART, LUNG, AND BLOOD (NHLBI) INSTITUTE
Comparative Analysis of Non-Isolated and Isolated Type Partial-Power Optimizers for PV-Battery Series Inverter Architecture (2018)

A seamless battery integration with higher power conversion efficiency and lower system power rating can be achieved by adopting the DC-series battery integration topology into a photovoltaic (PV) string inverter system, the PV-battery series inverter. The PV-battery series inverter uses the partial-power processing technique to achieve flexible current control between PV string and battery. In the process of designing the partial-power DC-DC optimizer, different types of DC-DC converters and different size of batteries can be considered, and the system efficiency and the power rating vary based on the system design. This paper presents a comparative analysis of the different type partial-power optimizers for the PV-battery series inverter in residential rooftop applications (<;10kW PV output power, <; 500V DC-bus voltage), in consideration of the DC-DC converter topology. Non-isolated and isolated bidirectional DC-DC converters are considered and selection of battery voltage in each case is made to have the optimized system design. The operation of the designed DC-DC optimizer is verified through controller hardware-in-the-loop test.
Genetically encoded optical activation of DNA recombination in human cells (2016)

We developed two tightly regulated, light-activated Cre recombinase enzymes through site-specific incorporation of two genetically-encoded photocaged amino acids in human cells. Excellent optical off to on switching of DNA recombination was achieved. Furthermore, we demonstrated precise spatial control of Cre recombinase through patterned illumination.
Control of FEL Radiation Properties by Tailoring the Seed Pulses (2018)

Seeded free-electron lasers (FELs) produce intense, ultrashort and fully coherent X-ray pulses. These seeded FEL pulses depend on the initial seed properties. Therefore, controlling the seed laser allows tailoring the FEL radiation for phase-sensitive experiments. In this contribution, we present detailed simulation studies to characterize the FEL process and to predict the operation performance of seeded pulses. In addition, we show experimental data on the temporal characterization of the seeded FEL pulses performed at the sFLASH experiment in Hamburg.