gebhart/patrepeval huggingface dataset:
638 COMMANDER-001: a phase 1/2, first-in-human, multicenter, open label study of SQZ-eAPC-HPV as monotherapy and with pembrolizumab in patients with HPV16+ recurrent, locally advanced, or metastatic solid tumors (trial in progress) (2022)

<h3>Background</h3> Antigen-specific CD8+ T cells are critical for mounting a potent immune response against tumors. Creation of T cell responses requires 3 key signals from antigen presenting cells (APCs): (signal 1) the peptide-MHC complex binding to the T cell receptor, (signal 2) costimulatory molecules that bind to T cell stimulatory domains, and (signal 3) inflammatory cytokines binding to receptors on T cells. To create enhanced APCs (eAPCs) from peripheral blood mononuclear cells (PBMCs), we used the Cell Squeeze® technology to deliver mRNAs encoding HPV16 E6 and E7 antigens (signal 1), CD86 (signal 2), and membrane-bound IL-2 and IL-12 cytokines (signal 3). Co-localizing these signals on the eAPC surface may enable more potent T cell stimulation and limit off-target effects from systemic exposure to signal 2 and 3. SQZ-eAPC-HPV is an improved 2nd generation product, with no HLA restrictions, that builds on the clinical and manufacturing experience with the 1st generation SQZ-PBMC-HPV product. This approach may enable rapid implementation across many tumor types as it facilitates exchange of mRNA to encode for other antigens or T cell activation signals. <h3>Methods</h3> <b>Trial Design:</b> COMMANDER-001 is open for enrollment to patients (pts) with HPV16 driven recurrent, locally advanced, or metastatic solid tumors and includes dose escalation for eAPC monotherapy and in combination with pembrolizumab (pembro) (Part 1), and a lead-in where eAPC is given prior to treatment with pembro (Part 2). Part 1A will assess 3 eAPC monotherapy cohorts using a Bayesian optimal interval design enrolling 3 – 12 pts per cohort. After establishing a safe and tolerable dose (RP2D), Part 1B will assess the RP2D with pembro 200mg q3 weeks (w). Part 2 will explore giving 2 doses of eAPC before the pt receives pembro. Pts will receive eAPC q3w for up to 1 year or until available eAPC is exhausted. Pembro will be given for up to 2 years. Eligible pts will undergo 1 leukapheresis. Manufacturing takes &lt;24 hours and the vein-to-vein time for the 1st dose is expected to be ~1 week. Preconditioning is not required, and the study will be primarily conducted out-patient. <h3>Trial Registration</h3> NCT05357898 <h3>Ethics Approval</h3> The study is registered on clinicaltrials.gov and was approved by the Ethics Board of all institutions listed as recruiting.
The genome and transcriptome of perennial ryegrass mitochondria (2013)

The circular master molecule of the mitochondrial genome from perennial ryegrass presented here constitutes an important tool for future attempts to compare mitochondrial genomes within and between grass species. Our results also demonstrate that mitochondria of perennial ryegrass contain genes crucial for energy production that are well conserved in the mitochondrial genome of monocotyledonous species. The expression analysis gave us first insights into the transcriptome of these mitochondrial genes in perennial ryegrass.
Requirement for CD8 β Chain in Positive Selection of CD8-Lineage T Cells (1994)

CD8 is either an alpha alpha homodimer or an alpha beta heterodimer, although most peripheral CD8-lineage T cells express only the CD8 alpha beta heterodimer. The physiological function of CD8 beta was elucidated with mice that were chimeric for the homozygous disruption of the CD8 beta gene. The CD8 beta-1- T cells developed normally to CD4+CD8+ stage, but did not efficiently differentiate further, which resulted in few peripheral CD8+ T cells. The number of peripheral CD8+ T cells was restored by transfer of an exogenous CD8 beta gene into CD8 beta-deficient T cells. Thus, CD8 beta is necessary for the maturation of CD8+ T cells.
Purification of coagulation factor VIII by immobilized metal affinity chromatography (2014)

Factor VIII (FVIII) is a glycoprotein that plays an essential role in blood coagulation cascade. Purification of plasma-derived coagulation FVIII by direct application of plasma to a chromatographic column is a method of choice. Anion exchange column is a very powerful method because FVIII is strongly adsorbed, resulting in good activity recovery and high purification factor. However, vitamin-K-dependent coagulation factors coelute with FVIII. In the present study, we report the separation of vitamin-K-dependent coagulation proteins from FVIII using immobilized metal affinity chromatography (IMAC) with Cu(2+) as the metal ligand. Plasma was directly loaded to a Q Sepharose Big Beads column, and FVIII was recovered with 65% activity and a purification factor of approximately 50 times. Then, the Q Sepharose eluate was applied to the IMAC-Cu(2+) column, and FVIII was eluted with 200 mM imidazole, with up to 85% recovery of activity. The mass recovery in this fraction was less than 10% of the applied mass of protein. Vitamin-K-dependent proteins elute with imidazole concentrations of lower than 60 mM. Because of the difference in affinity, FVIII could be completely separated from the vitamin-K-dependent proteins in the IMAC column.
Precision measurement of the W boson decay branching fractions in proton-proton collisions at s=13  TeV (2022)

The leptonic and inclusive hadronic decay branching fractions of the W boson are measured using proton-proton collision data collected at ffiffi ffi s p 13 TeV by the CMS experiment at the CERN LHC, corresponding to an integrated luminosity of 35.9 fb -1 . Events characterized by the production of one or two W bosons are selected and categorized based on the multiplicity and flavor of reconstructed leptons, the number of jets, and the number of jets identified as originating from the hadronization of b quarks. A binned maximum likelihood estimate of the W boson branching fractions is performed simultaneously in each event category. The measured branching fractions of the W boson decaying into electron, muon, and tau lepton final states are 10.83 AE 0.10%, 10.94 AE 0.08%, and 10.77 AE 0.21%, respectively, consistent with lepton flavor universality for the weak interaction. The average leptonic and inclusive hadronic decay branching fractions are estimated to be 10.89 AE 0.08% and 67.32 AE 0.23%, respectively. Based on the hadronic branching fraction, three standard model quantities are subsequently derived: the sum of squared elements in the first two rows of the Cabibbo-Kobayashi-Maskawa (CKM) matrix P ij jV ij j 2 1.984 AE 0.021, the CKM element jV cs j 0.967 AE 0.011, and the strong coupling constant at the W boson mass scale, S m 2 W 0.095 AE 0.033.
Compact Built-In Handset MIMO Antenna Using L-Shaped Folded Monopole Antennas (2008)

A compact built-in handset antenna for multiple-input multiple-output (MIMO) system at 2GHz, comprising two elements array of newly proposed L-shaped folded monopole antenna (LFMA), is evaluated under the multipath radio wave propagation environments. By analyzing the fundamental characteristics, mean effective gain (MEG), correlation, and channel capacity, the significant enhancement in the capability, as a handset MIMO antenna under practical use conditions, was confirmed. The performances were also compared to those of an array antenna comprising two planar inversed-F antenna (PIFA) elements in order to verify the effectiveness of the proposed antenna. The results show that the equivalent or improved performances can be realized, by using the proposed LFMA array with a compact size, taking only the volume of 44% of a PIFA array. The LFMA array provides almost the same bandwidth and enhanced isolation compared with a PIFA array, and the sufficiently low correlation and acceptable effective gain are obtained under the multipath radio wave propagation environments. In addition, a greater channel capacity than a PIFA array is achieved especially when the proposed LFMA array is inclined for the display-viewing mode, and moreover, an almost doubled increase in the channel capacity is obtained by using MIMO transmission compared with single-input single-output (SISO). This study also show that the MEG has much effects on the channel capacity, rather than the correlations, for the proposed antenna.
Automated ischemic stroke lesion segmentation from 3D MRI (2022)

Ischemic Stroke Lesion Segmentation challenge (ISLES 2022) offers a platform for researchers to compare their solutions to 3D segmentation of ischemic stroke regions from 3D MRIs. In this work, we describe our solution to ISLES 2022 segmentation task. We re-sample all images to a common resolution, use two input MRI modalities (DWI and ADC) and train SegResNet semantic segmentation network from MONAI. The final submission is an ensemble of 15 models (from 3 runs of 5-fold cross validation). Our solution (team name NVAUTO) achieves the top place in terms of Dice metric (0.824), and overall rank 2 (based on the combined metric ranking).
A Putative Type V Pilus Contributes to Bacteroides thetaiotaomicron Biofilm Formation Capacity (2019)

<i>Bacteroides thetaiotaomicron</i> is a prominent anaerobic member of the healthy human gut microbiota. While the majority of functional studies on <i>B. thetaiotaomicron</i> addressed its impact on the immune system and the utilization of diet polysaccharides, <i>B. thetaiotaomicron</i> biofilm capacity and its contribution to intestinal colonization are still poorly characterized. We tested the natural adhesion of 34 <i>B. thetaiotaomicron</i> isolates and showed that although biofilm capacity is widespread among <i>B. thetaiotaomicron</i> strains, this phenotype is masked or repressed in the widely used reference strain VPI 5482. Using transposon mutagenesis followed by a biofilm positive-selection procedure, we identified VPI 5482 mutants with increased biofilm capacity corresponding to an alteration in the C-terminal region of BT3147, encoded by the <i>BT3148-BT3147</i> locus, which displays homology with Mfa-like type V pili found in many <i>Bacteroidetes</i> We show that BT3147 is exposed on the <i>B. thetaiotaomicron</i> surface and that BT3147-dependent adhesion also requires BT3148, suggesting that BT3148 and BT3147 correspond to the anchor and stalk subunits of a new type V pilus involved in <i>B. thetaiotaomicron</i> adhesion. This study therefore introduces <i>B. thetaiotaomicron</i> as a model to study proteinaceous adhesins and biofilm-related phenotypes in this important intestinal symbiont.<b>IMPORTANCE</b> Although the gut anaerobe <i>Bacteroides thetaiotaomicron</i> is a prominent member of the healthy human gut microbiota, little is known about its capacity to adhere to surfaces and form biofilms. Here, we identify that alteration of a surface-exposed protein corresponding to a type of pili found in many <i>Bacteroidetes</i> increases <i>B. thetaiotaomicron</i> biofilm formation. This study lays the ground for establishing this bacterium as a model organism for <i>in vitro</i> and <i>in vivo</i> studies of biofilm-related phenotypes in gut anaerobes.
Fast iterative physical optics with shadowing (2016)

A fast iterative physical optics (IPO) algorithm for the analysis of scattering from large complex geometries involving multiple scattering and self-shadowing effects is presented. The algorithm comprises two types of nested iterations: reflection ("bounce") iterations and self-shadowing iterations. Both types of iterations involve time consuming surface integrations carrying an O (N <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> ) computational cost (N being the number of quadrature points). The nested iterative formulation is accelerated by using the multilevel non-uniform grid algorithm reducing the computational complexity to O(NlogN). The procedure's applicability to complex geometries and numerical efficiency are demonstrated by comparison to a numerically exact method and to the conventional physical optics.
Experimental Method to Investigate Airflow through Cracked Concrete (2022)

ACI Website Page Not Found. The page may have been updated, moved or deleted. Please also be sure to check your spelling. Options to find your page include on page search, on-line chat, and site navigation.
Wavefront correcting properties of corner-cube arrays (1988)

The performance of corner-cube arrays as pseudophase-conjugation wavefront correctors is investigated theoretically and experimentally. Hollow electroformed arrays and solid plastic arrays of corner-cube retroreflectors have been optically characterized and studied in a pseudophase-conjugate imaging system. The use of a collimating lens is found to improve dramatically the image quality.
Incorporation of Unique Molecular Identifiers (UMIs) into Unique Dual Sample Indexing (UDI) Improves the Accuracy of Quantitative NGS (2020)

The use of Unique Molecular Identifiers has become increasingly popular and offer a multitude of advantages especially when paired with unique dual sample indexing. Two major factors affecting sequencing accuracy are PCR duplication arising from amplification of library molecules and errors introduced during library preparation and actual sequencing on the flow cell. We can account for these factors by incorporating UMIs into library preparation. We incorporate UMIs into UDI adaptors and assess their effect on the accuracy of quantitative sequencing assays. We studied the effectiveness of various computational methods to account for UMIs and remove base-calling errors introduced during sequencing. We analyzed the utility of UMIs for duplicate removal and error correction in low frequency variant detection in genomic sequencing and show that the sensitivity of variant detection is improved with UMI consensus calling. We demonstrate that combining unique dual sample indexing with UMI molecular barcoding further improves data analysis accuracy, especially on patterned flow cells. To test the efficacy of UMIs in RNA-seq we introduced UMI-containing barcoded adaptors into our NEBNext RNA-Seq workflow, optimized across various RNA inputs. Ligation of barcoded adaptors followed by PCR enrichment produced high-quality library and sequencing metrics. Duplication rates significantly differed when utilizing traditional computational approaches to identify duplicates based on mapping position compared to analysis incorporating UMIs. As many as 90% of reads identified as duplicates using read position were determined to in fact originate from unique molecules, increasing the total number of reads available for further analysis. Our approach involves a simple new UMI-containing UDI adaptor design that can also be applied to other sequencing methods and platforms. We conclude that combining unique dual sample indexing with UMI molecular barcoding further improves data accuracy.
Invasion and Persistence ofMycobacterium aviumsubsp.paratuberculosisduring Early Stages of Johne's Disease in Calves (2007)

Infection with Mycobacterium avium subsp. paratuberculosis causes Johne's disease in cattle and is a serious problem for the dairy industry worldwide. Development of models to mimic aspects of Johne's disease remains an elusive goal because of the chronic nature of the disease. In this report, we describe a surgical approach employed to characterize the very early stages of infection of calves with M. avium subsp. paratuberculosis. To our surprise, strains of M. avium subsp. paratuberculosis were able to traverse the intestinal tissues within 1 h of infection in order to colonize distant organs, such as the liver and lymph nodes. Both the ileum and the mesenteric lymph nodes were persistently infected for months following intestinal deposition of M. avium subsp. paratuberculosis despite a lack of fecal shedding of mycobacteria. During the first 9 months of infection, humoral immune responses were not detected. Nonetheless, using flow cytometric analysis, we detected a significant change in the cells participating in the inflammatory responses of infected calves compared to cells in a control animal. Additionally, the levels of cytokines detected in both the ileum and the lymph nodes indicated that there were TH1-type-associated cellular responses but not TH2-type-associated humoral responses. Finally, surgical inoculation of a wild-type strain and a mutant M. avium subsp. paratuberculosis strain (with an inactivated gcpE gene) demonstrated the ability of the model which we developed to differentiate between the wild-type strain and a mutant strain of M. avium subsp. paratuberculosis deficient in tissue colonization and invasion. Overall, novel insights into the early stages of Johne's disease were obtained, and a practical model of mycobacterial invasiveness was developed. A similar approach can be used for other enteric bacteria.
Light-Harvesting Ionic Dendrimer Porphyrins as New Photosensitizers for Photodynamic Therapy (2002)

Photodynamic therapy (PDT) is a promising therapeutic modality for treatment of solid tumors. In this study, third-generation aryl ether dendrimer porphyrins (DPs) with either 32 quaternary ammonium groups (32(+)DPZn) or 32 carboxylic groups (32(-)DPZn) were evaluated as a novel, supramolecular class of photosensitizers for PDT. DPs showed a different cell-association profile depending on the positive or negative charge on the periphery, and both DPs eventually localized in membrane-limited organelles. In contrast, protoporphyrin IX (PIX), which is a hydrophobic and relatively low molecular weight photosensitizer used as a control in this study, diffused through the cytoplasm except the nucleus. Confocal fluorescent imaging using organelle-specific dyes indicated that PIX induced severe photodamage to disrupt membranes and intracellular organelles, including the plasma membrane, mitochondrion, and lysosome. On the other hand, cells treated with DPs kept the characteristic fluorescent pattern of such organelles even after photoirradiation. However, notably 32(+)DPZn achieved remarkably higher (1)O(2)-induced cytotoxicity against LLC cells than PIX. Furthermore, both dendrimer porphyrins had far lower dark toxicity as compared with PIX, demonstrating their highly selective photosensitizing effect in combination with a reduced systemic toxicity.
Electrical spectral technique for measuring cross-phase modulation impact in WDM optical systems (2004)

An electrical spectral technique to correctly evaluate cross-phase modulation behavior in intensity modulation-direct detection systems is proposed. Intrinsic advantages of the technique, in terms of high accuracy, are discussed in comparison with the classical time-domain method, which requires precise receiver noise characterization. Measures have been performed with a pump-and-probe scheme on different standard optical communications fibers (i.e., G.652, G.655). The employed pump has been intensity modulated by a nonreturn-to-zero alternate pattern at different bit rates (from 1 to 10 Gb/s), with 0.8- and 1.6-nm pump-probe wavelength spacing. The experimental results are compared with the time-domain technique when accurate calibration is performed.
Preparation of 2-Oxazolidinones by Intramolecular Nucleophilic Substitution (1997)

Treatment of N-alkoxycarbonyl, N-benzyl protected β-amino alcohols with triphenylphosphine and hexachloroethane in 1,2-dichloroethane induces cyclization to 2-oxazolidinones, which are found by intramolecular attack with inversion of configuration at the secondary alcohol. In contrast, mono N-substituted alkyl carbamates undergo chlorination under the same conditions.
DSD: Dense-Sparse-Dense Training for Deep Neural Networks (2016)

Modern deep neural networks have a large number of parameters, making them very hard to train. We propose DSD, a dense-sparse-dense training flow, for regularizing deep neural networks and achieving better optimization performance. In the first D (Dense) step, we train a dense network to learn connection weights and importance. In the S (Sparse) step, we regularize the network by pruning the unimportant connections with small weights and retraining the network given the sparsity constraint. In the final D (re-Dense) step, we increase the model capacity by removing the sparsity constraint, re-initialize the pruned parameters from zero and retrain the whole dense network. Experiments show that DSD training can improve the performance for a wide range of CNNs, RNNs and LSTMs on the tasks of image classification, caption generation and speech recognition. On ImageNet, DSD improved the Top1 accuracy of GoogLeNet by 1.1%, VGG-16 by 4.3%, ResNet-18 by 1.2% and ResNet-50 by 1.1%, respectively. On the WSJ'93 dataset, DSD improved DeepSpeech and DeepSpeech2 WER by 2.0% and 1.1%. On the Flickr-8K dataset, DSD improved the NeuralTalk BLEU score by over 1.7. DSD is easy to use in practice: at training time, DSD incurs only one extra hyper-parameter: the sparsity ratio in the S step. At testing time, DSD doesn't change the network architecture or incur any inference overhead. The consistent and significant performance gain of DSD experiments shows the inadequacy of the current training methods for finding the best local optimum, while DSD effectively achieves superior optimization performance for finding a better solution. DSD models are available to download at https://songhan.github.io/DSD.