gebhart/patrepeval huggingface dataset:
117 Rapid point-of-care subcutaneous CAR-T from blood draw to injection in 4 hours with modified LV encoding CARs and synthetic driver elements enables efficient CAR-T expansion and tumor regression (2020)

<h3>Background</h3> Adoptive cellular therapy with chimeric antigen receptor (CAR)-T cells has demonstrated remarkable clinical activity in a number of hematologic malignancies, but product chain of custody, individualized manufacturing, preparative chemotherapy, and patient management present technical and logistical hurdles to broader implementation. <h3>Methods</h3> Lentiviral constructs for CARs (either CD19- or CD22-directed) co-expressed with a synthetic driver domain were identified from a &gt;6 × 10 diversity combinatorial library of proliferative elements, transmembrane domains, leucine zippers, and an EGFR epitope screened for cellular expansion in a lymphoreplete model. Modified serum-free-lentiviral manufacturing process was developed to reduce complexity of CAR-T and to introduce CD3-activating elements into the viral envelope allowing activation and transduction of resting lymphocytes from peripheral blood. <h3>Results</h3> Four-hour exposure of as little as 1 ml of blood to the CD3-directed CD19-targeted CAR encoding lentivirus followed by subcutaneous injection in NSG mice bearing CD19+/CD22+ Raji cells resulted in tumor regression (figure 1) and robust CAR-T cell expansion as determined by flow cytometry (figure 2) and qPCR (table 1), with peak levels &gt;10,000 CAR-T cells/µl and less than three CAR copies per genome. In contrast, administration of the same products intravenously failed to support significant CAR-T expansion or control tumor growth (figure 3). Regression of established Raji tumors was also observed in NSG-(KbDb) (IA) animals following SC administration of CD19 or CD22 CARs with driver domains. CAR-T cells contracted in peripheral blood following tumor regression. Regression of Raji tumor from the initial median volume of 151 mm3 throughout 40 days post subcutaneous administration of the LV transduced (at MOI 1 or 5) CD19-directed CAR T product (1M or 5M cells) in the NSG mice <h3>Conclusions</h3> We conclude that through a synthetic subcutaneous lymph node approach with modified lentiviruses and driver domains, rPOC SC may enable CAR-T generation with reduced complexity, while maintaining the ability of CAR-T cells to expand, persist and exert anti-tumor activity. <h3>Ethics Approval</h3> All animal studies were IACUC approved.
Assessment of Body Composition in Dialysis Patients by Arm Bioimpedance Compared to MRI and <sup>40</sup>K Measurements (2009)

This study used multi-frequency bioimpedance spectroscopy (BIS) of the arm and whole body to estimate muscle mass (MM) and subcutaneous adipose tissue (SAT) in 31 hemodialysis (HD) patients comparing these results with magnetic resonance imaging (MRI) and body potassium ((40)K) as gold standards. Total body and arm MM (MM(MRI)) and SAT (SAT(MRI)) were measured by MRI. All measurements were made before dialysis treatment. Regression models with the arm (aBIS) and whole body (wBIS) resistances were established. Correlations between gold standards and the BIS model were high for the arm SAT (r(2) = 0.93, standard error of estimate (SEE) = 3.6 kg), and whole body SAT (r(2) = 0.92, SEE = 3.5 kg), and for arm MM (r(2) = 0.84, SEE = 2.28 kg) and whole body MM (r(2) = 0.86, SEE = 2.28 kg). Total body MM and SAT can be accurately predicted by arm BIS models with advantages of convenience and portability, and it should be useful to assess nutritional status in HD patients.
Amelioration of hepatic fibrosis via Padma Hepaten is associated with altered natural killer T lymphocytes (2009)

Hepatic fibrosis is the end-stage consequence of chronic liver disease, affecting many people worldwide. Unlike the anti-fibrotic effect of natural killer (NK) cells, CD8 and NK T subsets are considered as profibrogenic subsets. Padma Hepaten is a multi-compound herbal preparation derived from Tibetan medicine and has proven efficacy in some clinical trials and tests at the cellular level. In this study, we evaluate the immune efficacy of Padma Hepaten administered intraperitoneally (i.p.) and/or orally in a mice model of hepatic fibrosis. Hepatic fibrosis was induced by 6 weeks of biweekly i.p. carbon tetrachloride (CCl4) injections in male C57Bl6 mice. There were four groups, including naive mice, non-treated fibrotic mice and fibrotic mice treated by Padma Hepaten at weeks 5-6 of fibrosis induction either orally or by i.p. injections. Padma Hepaten was prepared at 10 mg/ml in saline and 250 microl (2.5 mg) were administered four times per week. After week 6, animals were killed. To isolate a Padma Hepaten-associated effect on lymphocytes, splenocytes were harvested from either naive or Padma Hepaten-treated non-fibrotic donors. Isolated splenocytes were therefore reconstituted into two groups of irradiated recipients. Recipients were then administered the same CCl4 regimen. Hepatic fibrosis was determined by sirius red staining of liver sections and by assessment of alpha smooth muscle actin expression compared with beta-actin (both by mRNA as well as the protein liver extract western blotting). Hepatic fibrosis and alanine aminotransferase serum levels were decreased significantly in both Padma Hepaten-treated groups compared with the non-treated fibrotic group. Padma Hepaten treatment was associated with attenuation of lymphocyte subsets in both treated groups. Using a chemiluminescence technique to assess total anti-oxidant capacities (TAC), it was found that both the plasmas and livers of mice treated by CCl4 had significantly higher TAC compared with controls. However, the levels of TAC in animals treated either by CCl4 alone or CCl4 with Padma Hepaten were similar. Adoptive transfer of Padma Hepaten-treated lymphocytes was associated with fibrosis amelioration compared with recipients with naive lymphocytes. CCl4 generates higher levels of anti-oxidant capacities, probably as a response to oxidative stress. Padma Hepaten administration attenuated hepatic fibrogenesis significantly, accompanied by attenuation of lymphocyte but not anti-oxidant capacities.
Deformation Behavior of Fiber-Reinforced Polymer Reinforced Engineered Cementitious Composite (ECC) Flexural Members under Reversed Cyclic Loading Conditions (2003)

Peer Reviewed
DNA-protein interactions in theDrosophila virilismitochondrial chromosome (1984)

The location of proteins on the mitochondrial DNA (mtDNA) of Drosophila virilis was investigeted by Me 3 peoralen photoreaction of mitochondria isoleted from embryos. After photoreaction the mtDNA was purified and the pattern of DNA cross-linking was determined by electron microscopy of the DNA under totally denaturing conditions. The transcribed regions of the mtDNA molecule contained aome uncross-linked regions, but auch regions were infrequent and randomly distributed. In contrast, the A+T-rich region around the origin of replication of the mtDNA was usually protected from psoralen crosslinking. The data were best fit by two protected sites, each approximately 400 base pairs, compared to the four 400 base pair sites observed in the equivalent region of D . melanogester mtDNA [Potter et al. (1980) Proc. Nat. Acsd. Sci. USA 77, 4118−4122]. Thus this region of the mtDNA appears to be involved in a DNA-protein structure that is highly conserved even though the DNA sequence has diverged rapidly relative to protein-coding sequences.
A SARS-CoV-2 variant elicits an antibody response with a shifted immunodominance hierarchy (2021)

Many SARS-CoV-2 variants have mutations at key sites targeted by antibodies. However, it is unknown if antibodies elicited by infection with these variants target the same or different regions of the viral spike as antibodies elicited by earlier viral isolates. Here we compare the specificities of polyclonal antibodies produced by humans infected with early 2020 isolates versus the B.1.351 variant of concern (also known as Beta or 20H/501Y.V2), which contains mutations in multiple key spike epitopes. The serum neutralizing activity of antibodies elicited by infection with both early 2020 viruses and B.1.351 is heavily focused on the spike receptor-binding domain (RBD). However, within the RBD, B.1.351-elicited antibodies are more focused on the "class 3" epitope spanning sites 443 to 452, and neutralization by these antibodies is notably less affected by mutations at residue 484. Our results show that SARS-CoV-2 variants can elicit polyclonal antibodies with different immunodominance hierarchies.
Re-Compose the Image by Evaluating the Crop on More Than Just a Score (2022)

Image re-composition has always been regarded as one of the most important steps during the post-processing of a photo. The quality of an image re-composition mainly depends on a person’s taste in aesthetics, which is not an effortless task for those who have no abundant experience in photography. Besides, while re-composing one image does not require much of a person’s time, it could be quite time-consuming when there are hundreds of images to be recomposed. To solve these problems, we propose a method that automates the process of re-composing an image to the desired aspect ratio. Although there already exist many image re-composition methods, they only provide a score to their predicted best crop but fail to explain why the score is high or low. Conversely, we succeed in designing an explainable method by introducing a novel 10-layer aesthetic score map, which represents how the position of the saliency in the original uncropped image, relative to that of the crop region, contributes to the overall score of the crop, so that the crop is not just represented by a single score. We conducted experiments to show that the proposed score map boosts the performance of our algorithm, which achieves a state-of-the-art performance on both public and our own datasets.
Neural Networks Debunk Phrenology (2007)

Intracortical recordings reveal that distinct regions of the mammalian brain must synchronize their activity to support certain behaviors.
Enhanced computed tomography imaging of breast cancer via phosphatidylserine targeted gold nanoparticles (2019)

Abstract. Breast cancer has one of the highest mortality rates usually due to metastatic development. Mammograms are the current standard of diagnosis; however due to the low sensitivity and high rate of misdiagnosis, patients either experience false positives or negatives leading to overdiagnosis and overtreatment. One of key disadvantages of mammograms is their failed ability to differentiate between a dense breast and a tumor, usually leading to more mammograms and more expensive diagnostic tools. In order to provide a widely available imaging tool, targeted gold nanoparticles have been developed. Gold nanoparticles have been designed with annexin V surface modification to specifically bind phosphatidylserine expressing tumor cells and tumor vasculature. In vitro and in vivo studies showed a significant increase in contrast with targeted nanoparticles. Tumors as small as 4 mm were detectable 4 h post-injection, providing evidence of a promising, sensitive tool for early breast cancer diagnosis.
Inhibition of Transient Gene Expression with Plasmids Encoding Herpes Simplex Virus Type 1 UL55 and Alpha Genes (1991)

Herpes simplex virus type 1 (HSV-1) subgenomic sequences from 0.743 to 0.782 map units have been molecularly cloned as plasmid AT1 and shown to inhibit stable DNA-mediated gene transformation of Ltk- cells with the HSV-1 thymidine kinase (tk) gene. Here it is shown that AT1 also inhibits transient gene expression. Expression from the chloramphenicol acetyltransferase (CAT) gene under the control of either the HSV-1 tk gene or the Rous sarcoma virus (RSV) promoter was inhibited when cotransfected into Ltk- and CV-1 cells with equimolar amounts of AT1. AT1 was subcloned as three overlapping plasmids called AT1a, alpha 27 and AT1b. The alpha 27 plasmid encodes the HSV-1 immediate early gene, alpha 27; AT1a possesses sequences that specify an open reading frame in HSV-1 strain KOS used in these studies, although the significance of this open reading frame is unknown; AT1b possesses the sequences for UL55 and UL56, also genes for which no function has been reported. No single subclone or pair of subclones demonstrated significant inhibition of transient gene expression. Cotransfection of all three subclones did result in inhibition of RSV-CAT gene expression, suggesting that information from each subclone is necessary. One of the three subclones, alpha 27, contains the HSV-1 immediate early gene, alpha 27, so the possibility that other immediate early genes could substitute for alpha 27 was tested. Inhibition of RSV-CAT gene expression was also achieved by cotransfection of AT1a and AT1b with either an alpha 0- or alpha 4-containing plasmid, suggesting that the role of the alpha 27-containing plasmid can be replaced by other alpha genes with trans-regulating capability. Finally, AT1a and AT1b linker insertion mutants have been constructed and used to study the role these plasmids play in mediating inhibition. These results suggest that AT1 contains HSV-1 functions in addition to that of alpha 27 that interfere with gene expression.
Myocardial Infarction Is Coupled with the Activation of Cyclins and Cyclin-Dependent Kinases in Myocytes (1996)

To determine whether the molecular components implicated in the regulation of the cell cycle are activated in myocytes after infarction, the expression of cyclins E, A, and B and the levels of their associated kinase activity were measured at 1 and 7 days following surgery. The quantity of cdk2 and cdc2 and the level of their kinase activity were also determined. Myocardial infarction was characterized by an increase in cyclins E, A, and B and cdc2 proteins in the surviving myocytes at 1 and 7 days. Cyclin E, A, and B and cdk2 and cdc2 kinase activity also increased. The quantity of cyclins E and A and the level of cyclin E-associated kinase activity in myocytes after infarction were comparable with those measured in neonatal myocytes. Moreover, cdc2 protein and cdc2 kinase activity in myocytes reached levels after infarction which were similar to those in neonatal myocytes. Thus, myocytes react to myocardial infarction by activating cyclins and cyclin-dependent kinases which may be coupled with the regeneration of muscle mass and recovery of ventricular function.
Simulation of the vortex dynamics in a real pinning landscape of YBa$_2$Cu$_3$O$_{7-δ}$ coated conductors (2015)

The ability of high-temperature superconductors (HTSs) to carry very large currents with almost no dissipation makes them irreplaceable for high-power applications. The development and further improvement of HTS-based cables requires an in-depth understanding of the superconducting vortex dynamics in presence of complex pinning landscapes. We present a critical current analysis of a real HTS sample in a magnetic field by combining state-of-the-art large-scale Ginzburg-Landau simulations with reconstructive three-dimensional scanning transmission electron microscopy tomography of the pinning landscape in Dy-doped YBa$_2$Cu$_3$O$_{7-δ}$. This methodology provides a unique look at the vortex dynamics in the presence of a complex pinning landscape, responsible for the high current-carrying capacity characteristic of commercial HTS wires. Our method demonstrates very good functional and quantitative agreement of the critical current between simulation and experiment, providing a new predictive tool for HTS wires design.
Von Willebrand factor contaminating porcine factor VIII concentrate (Hyate: C) causes platelet aggregation (1986)

Severe thrombocytopenia has been reported to occur in some patients treated with a polyelectrolyte-fractionated porcine factor VIII concentrate (Hyate:C) (Kernoff et al, 1984; Gatti & Mannucci, 1984). We report here that Hyate:C induces aggregation of platelet-rich plasma in vitro accompanied by ATP release and thromboxane B2 formation, and is inhibited by EDTA and prostaglandin E1. Hyate:C induced platelet aggregation is affected by monoclonal antibodies anti-glycoprotein Ib or anti-glycoprotein IIb/IIIa and suppressed by polyclonal anti-porcine von Willebrand factor antiserum. We conclude that the aggregating ability of Hyate:C is due to porcine von Willebrand factor present in the concentrate. The occasional thrombocytopenia described after Hyate:C infusions probably results from the interaction between platelets and the porcine von Willebrand factor contaminating the concentrate.
Variability effects on the V<inf>T</inf> distribution of nanoscale NAND Flash memories (2010)

This work investigates the variability effects on the threshold voltage distribution of deca-nanometer NAND Flash memories. Different sources of variability have been considered, evaluating their impact on the neutral, programmed and erased distributions. A compact model that is able to account for the variability effects on the array performance and reliability is presented and used. Monte Carlo simulations have been employed to analyze the contributions of variability when technology nodes scale down and to compare the intrinsic variability with the electron injection statistical fluctuations. A good agreement with experimental data is reached, opening the application of the proposed methodology to investigate the reliability impact of variability on future technology nodes.
A multi-agent Q-Learning-based framework for achieving fairness in HTTP Adaptive Streaming (2014)

HTTP Adaptive Streaming (HAS) is quickly becoming the de facto standard for Over-The-Top video streaming. In HAS, each video is temporally segmented and stored in different quality levels. Quality selection heuristics, deployed at the video player, allow dynamically requesting the most appropriate quality level based on the current network conditions. Today's heuristics are deterministic and static, and thus not able to perform well under highly dynamic network conditions. Moreover, in a multi-client scenario, issues concerning fairness among clients arise, meaning that different clients negatively influence each other as they compete for the same bandwidth. In this article, we propose a Reinforcement Learning-based quality selection algorithm able to achieve fairness in a multi-client setting. A key element of this approach is a coordination proxy in charge of facilitating the coordination among clients. The strength of this approach is three-fold. First, the algorithm is able to learn and adapt its policy depending on network conditions, unlike current HAS heuristics. Second, fairness is achieved without explicit communication among agents and thus no significant overhead is introduced into the network. Third, no modifications to the standard HAS architecture are required. By evaluating this novel approach through simulations, under mutable network conditions and in several multi-client scenarios, we are able to show how the proposed approach can improve system fairness up to 60% compared to current HAS heuristics.
Structural and electronic characteristics of Cu(In,Ga)Se2 thin films sputtered from quaternary targets (2012)

Although the advantages of sputter deposition for large area, uniform deposition are well known, it has long been believed that sputtering Cu(In,Ga)Se <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> (CIGS) from a quaternary sputtering target yields films with morphological and electronic properties that make them unsuitable for use in high-efficiency photovoltaic devices. Recent work, however, has demonstrated that this deposition method can produce dense, polycrystalline, highly oriented films with the desired stoichiometry. Devices built with these films exhibit efficiencies >10%. While effective parameters for target composition and deposition conditions have been achieved, variation from these conditions can result in a wide array of morphologies, even while composition remains near that of stoichiometric CIGS. In this paper, we review the broad range of structural and electronic properties that result from various sets of target compositions and deposition conditions. Films deposited under some conditions are similar in important respects - their composition, a dense structure composed of ∼1 µm sized grains, and the presence of a MoSe <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> layer - to those of evaporated CIGS. We discuss how these results point towards the possibility of higher-efficiency sputtered CIGS.
Inter- and Intrasite Correlations of Large-Scale Parameters from Macrocellular Measurements at 1800 MHz (2007)

The inter- and intrasite correlation properties of shadow fading and power-weighted angle spread at both the mobile station and the base station are studied utilizing narrowband multisite MIMO measurements in the 1800 MHz band. The influence of the distance between two base stations on the correlation is studied in an urban environment. Measurements have been conducted for two different situations: widely separated as well as closely located base stations. Novel results regarding the correlation of the power-weighted angle spread between base station sites with different separations are presented. Furthermore, the measurements and analysis presented herein confirm the autocorrelation and cross-correlation properties of the shadow fading and the angle spread that have been observed in previous studies.
Effects of integrating maternity VR-based situated learning into professional training on students’ learning performances (2022)

Educators have recognized the importance of providing a realistic learning environment which helps learners to not only comprehend learning content, but also to link the content to practical problems. Such an environment can hence foster problem-solving skills in nursing training. However, when learners interact in a virtual environment with rich learning resources, they might encounter difficulties if there is a lack of proper guidance, clinical sense, or a well thought-out instructional design process. Hence, this work developed a maternity VR-based situated learning system (MVR-SLS) based on the experiential learning theory to support professional courses in obstetrics. A quasi-experiment was conducted to verify the impacts of this method on learners' learning achievement, OSCE (Objective Structured Clinical Examination) competency, problem solving skills, learning engagement, and teaching effectiveness. The experimental results indicate that the new method improved learners' learning achievement, OSCE competency, problem-solving ability, and recognition of learning engagement. Moreover, the learners who learned with the new method showed more active learning behaviors compared to the learners in the control group. Findings of the present study offer concrete suggestions for implementing effective virtual reality (VR)-based learning strategies for medical and nursing textbooks.
Room-temperature direct bandgap electroluminesence from Ge-on-Si light-emitting diodes (2009)

We report what we believe to be the first demonstration of direct bandgap electroluminescence (EL) from Ge/Si heterojunction light-emitting diodes (LEDs) at room temperature. In-plane biaxial tensile strain is used to engineer the band structure of Ge to enhance the direct gap luminescence efficiency by increasing the injected electron population in the direct Gamma valley. Room-temperature EL is observed at the direct gap energy from a Ge/Si p-i-n diode exhibiting the same characteristics of the direct gap photoluminescence of Ge. The integral direct gap EL intensity increases superlinearly with electrical current owing to an indirect valley filling effect. These results indicate a promising future of tensile-strained Ge-on-Si for electrically pumped, monolithically integrated light emitters on Si.