gebhart/patrepeval huggingface dataset:
Regeneration of Tumor-Antigen-Specific Cytotoxic T Lymphocytes from iPSCs Transduced with Exogenous TCR Genes (2020)

In the current adoptive T cell therapy, T cells from a patient are given back to that patient after <i>ex vivo</i> activation, expansion, or genetic manipulation. However, such strategy depends on the quality of the patient's T cells, sometimes leading to treatment failure. It would therefore be ideal to use allogeneic T cells as "off-the-shelf" T cells. To this aim, we have been developing a strategy where potent tumor-antigen-specific cytotoxic T lymphocytes (CTLs) are regenerated from T-cell-derived induced pluripotent stem cells (T-iPSCs). However, certain issues still remain that make it difficult to establish highly potent T-iPSCs: poor reprogramming efficiency of T cells into iPSCs and high variability in the differentiation capability of each T-iPSC clone. To expand the versatility of this approach, we thought of a method to produce iPSCs equivalent to T-iPSCs, namely, iPSCs transduced with exogenous T cell receptor (TCR) genes (TCR-iPSCs). To test this idea, we first cloned TCR genes from WT1-specific CTLs regenerated from T-iPSCs and then established WT1-TCR-iPSCs. We show that the regenerated CTLs from TCR-iPSCs exerted cytotoxic activity comparable to those from T-iPSCs against WT1 peptide-loaded cell line in <i>in vitro</i> model. These results collectively demonstrate the feasibility of the TCR-iPSC strategy.
Synthesis of a novel cyclopropyl phosphonate nucleotide as a phosphate mimic (2021)

The inherent in vivo instability of oligonucleotides presents one of many challenges in the development of RNAi-based therapeutics. Chemical modification to the 5'-terminus serves as an existing paradigm which can make phosphorylated antisense strands less prone to degradation by endogenous enzymes. It has been recently shown that installation of 5'-cyclopropyl phosphonate on the terminus of an oligonucleotide results in greater knockdown of a targeted protein when compared to its unmodified phosphate derivative. In this paper we report the synthesis of a 5'-modified uridine.
Three‐dimensional regional strain computation method with displacement encoding with stimulated echoes (DENSE) in non‐ischemic, non‐valvular dilated cardiomyopathy patients and healthy subjects validated by tagged MRI (2014)

We found agreement between DENSE and tagged MR in patients and volunteers in terms of evaluation of regional strains.
<i>In Vitro</i> Resistance Selection Studies of RLP068/Cl, a New Zn(II) Phthalocyanine Suitable for Antimicrobial Photodynamic Therapy (2009)

Resistance to antimicrobial agents is emerging in a wide variety of nosocomial and community-acquired pathogens. The development of alternative therapies against nosocomial infections caused by clinically relevant pathogens represents a major public health concern. RLP068/Cl is a novel Zn(II) phthalocyanine proposed as a photosensitizer suitable for antimicrobial photodynamic therapy (APDT) for localized infections. Its ability, following activation by light, to induce resistance in three major human pathogens after 20 daily passages was studied. Simultaneously for the same strains, the ability of daily sequential subcultures in subinhibitory concentrations of RLP068/Cl to develop resistant mutants without illumination was evaluated. We demonstrate that 20 consecutive APDT treatments with RLP068/Cl did not result in any resistant mutants and that, in dark conditions, only Staphylococcus aureus strains had increased MICs of RLP068/Cl. However, even in this case, the susceptibility of the mutated bacteria to APDT was not affected by their MIC increase.
Automatic compensation of antenna beam roll-off in SAR images. (2006)

The effects of a non-uniform antenna beam are sometimes visible in Synthetic Aperture Radar (SAR) images. This might be due to near-range operation, wide scenes, or inadequate antenna pointing accuracy. The effects can be mitigated in the SAR image by fitting very a simple model to the illumination profile and compensating the pixel brightness accordingly, in an automated fashion. This is accomplished without a detailed antenna pattern calibration, and allows for drift in the antenna beam alignments.
Wet-etch figuring for precision optical contouring (2003)

Wet-etch figuring utilizes free surface flows driven by surface tension gradients (the Marangoni effect) to confine and stabilize the size and shape of an etchant droplet attached to the underside of a glass surface. This droplet, or wetted zone, is translated on the surface, etching where it contacts and leaving behind no residue, to facilitate an etching-based small-tool figuring process that is free of mechanical and thermal stresses. The optic needs no backing plate, and its back side is free for inspection by optical means. When transmissive optics is figured, the optical thickness between the front and the rear surfaces of the optic is measured interferometrically and used in real time to control the local dwell time of the etchant zone. This truly closed-loop figuring process is robust, environmentally insensitive, and fully automated. It is particularly suited for figuring patterns such as phase plates, corrective elements, and optical flats on very thin (<< 1-mm) substrates that are difficult to figure with traditional abrasive polishing methods.
Nicotianamine aminotransferase activities are correlated to the phytosiderophore secretions under Fe-deficient conditions in Gramineae (1994)

The activities of nicotianamine aminotransferase, one of the enzymes for the biosynthesis of mugineic acid-family phytosiderophores, were examined in six graminaceous species. The enzyme activities were induced by Fe-deficiency treatments in all species tested and had a considerable correlation to the amounts of secreted mugineic acids.
VEGF concentrations in tumor lysates from ovarian cancer patients (2006)

Vascular endothelial growth factor (VEGF) is known to play a key role in the induction of angiogenesis in many tumor types. VEGF is expressed as several isoforms consisting of 121, 165, 189 and 206 amino acids through alternative splicing. Less frequently found isoforms such as VEGF 145 and VEGF 183 were also reported. In addition, VEGF can be processed to shorter forms by proteolysis, for example, VEGF 113 by metalloproteinases and VEGF 110 by plasmin. Previously, an ELISA (VEGF 165‐206 ELISA) for measuring VEGF 165 was described. This ELISA is also expected to detect VEGF 189 and VEGF 206 . We later developed an ELISA (VEGF 121–206 ELISA) which measured recombinant VEGF consisting of amino acids 8–109 of VEGF 165 . Therefore, this ELISA is expected to measure all VEGF isoforms and processed VEGF like VEGF 113 and VEGF 110 . We measured VEGF concentrations in tumor lysates from 256 patients in these ELISAs and obtained a good correlation. The measurable VEGF concentrations determined by VEGF 165–206 and VEGF 121–206 ELISAs were 0.094–74 (median 0.58; n=236) and 0.13–520 (median 4.0; n=228) fmol/mg protein, respectively. In the 164 patients with measurable VEGF concentrations in both assays, VEGF concentrations measured using VEGF 165–206 ELISA was 24±17% of those measured using VEGF 121–206 ELISA. These results indicate that VEGF 121 and possibly processed VEGF fragments may be present at a significant amount in the tumors from ovarian cancer patients.
Design of InGaAs strained quantum-well lasers for high-temperature operation (1992)

The effect of high temperature on the threshold gain and threshold current density of an InGaAs (GaAs based) strained quantum well laser is examined both theoretically and experimentally. It is shown that designing a quantum well laser for low threshold gain through the use of a long laser cavity and/or high reflectivity facet coatings will reduce the temperature induced threshold current increase. This result is related to the nonlinear dependence of quantum well gain and current density on carrier density. The high temperature characteristics of strained InGaAs and GaAs QWs are also compared.
Enzymatic fluorometric assay for tissue cAMP (1994)

cAMP is commonly measured using either immunoassay or high-performance liquid chromatography. The current methods are sensitive but may lack versatility and be expensive; also, radioactivity is potentially harmful to the operator and environment. Given these concerns, we developed a highly sensitive enzymatic fluorometric assay for cAMP. The method consists of five steps: (1) destruction of interfering compounds with apyrase, 5' nucleotidase, adenosine deaminase, and alkaline phosphatase; (2) conversion of cAMP to AMP; (3) conversion of AMP to ATP; (4) amplification of ATP by ATP-ADP cycling; and (5) fluorometric measurement of resultant NADPH. cAMP was measured in male Sprague Dawley rats anesthetized with pentobarbital. Stimulated rats (n = 4) received isoproterenol (16 micrograms/kg, s.q.) and aminophylline (20 mg/kg, s.q.), whereas controls (n = 4) received no additional drug. With the enzymatic fluorometric assay, cAMP content in heart, liver, and kidney (pmol/mg wet wt, mean +/- SEM) was 0.34 +/- 0.03, 0.33 +/- 0.03, and 0.92 +/- 0.11 in the control group and 0.77 +/- 0.10, 0.66 +/- 0.04, and 1.53 +/- 0.12 in the stimulated group, respectively. The total assay duration including sample reading procedure varied at 4.5-9.5 hr, depending on its sensitivity. cAMP from the same samples was measured using a commercially available enzyme immunoassay kit and was found to be very similar to the enzymatic fluorometric assay. We conclude that this new assay is sensitive, safe, versatile, and inexpensive and can be used to measure cAMP in multiple types of tissue, including biopsy samples weighing < 200 micrograms.
Multimodal Emotion Recognition and Sentiment Analysis via Attention Enhanced Recurrent Model (2021)

With the proliferation of user-generated videos in online websites, it becomes particularly important to achieve automatic perception and understanding of human emotion/sentiment from these videos. In this paper, we present our solutions to the MuSe-Wilder and MuSe-Sent sub-challenges in MuSe 2021 Multimodal Sentiment Analysis Challenge. MuSe-Wilder focuses on continuous emotion (i.e., arousal and valence) recognition while the task of MuSe-Sent concentrates on discrete sentiment classification. To this end, we first extract a variety of features from three common modalities (i.e., audio, visual, and text), including both low-level handcrafted features and high-level deep representations from supervised/unsupervised pre-trained models. Then, the long short-term memory recurrent neural network, as well as the self-attention mechanism is employed to model the complex temporal dependencies in the feature sequence. The concordance correlation coefficient (CCC) loss and F1-loss are used to guide continuous regression and discrete classification, respectively. To further boost the model's performance, we adopt late fusion to exploit complementary information from different modalities. Our proposed method achieves CCCs of 0.4117 and 0.6649 for arousal and valence respectively on the test set of MuSe-Wilder, which outperforms the baseline system (i.e., 0.3386 and 0.5974) by a large margin. For MuSe-Sent, F1-scores of 0.3614 and 0.4451 for arousal and valence are obtained, which also outperforms the baseline system significantly (i.e., 0.3512 and 0.3291). With these promising results, we ranked top3 in both sub-challenges.
Curved paper rectification for digital camera document images by shape from parallel geodesics using continuous dynamic programming (2007)

Methods to rectify distortion of digital camera document images of curved papers have become important for camera-based image recognition. In this paper we propose a novel distortion rectification method based on "shape from parallel geodesies." This method considers the following features: parallel lines corresponding to character strings or ruled lines of tables on extended surface become parallel geodesies on a curved paper surface and a smoothly curved paper can be modeled by a ruled surface, that is, a sweep surface of rulings. The projected geodesies and the projected rulings exist in the input image derived from perspective transformation. The presented method extracts the projected geodesies, estimates the projected rulings in the input image, estimates the ruled surface that models the curved paper, and generates the corrected image, in this order. It can estimate the ruled surface model directly by numerical operations of differentiation, integration and matrix inversion without any iterative calculation. We also report on experiments that show the effectiveness of the proposed method.
MEMS direction finding acoustic sensor (2017)

Conventional directional sound sensing systems employ an array of spatially separated microphones to achieve directivity. However, there are insects such as the <i>Ormia ochracea</i> fly that can determine the direction of sound using a miniature hearing organ much smaller than the wavelength of sound it detects. The fly's eardrums are coupled mechanically with a separation of only 0.5 mm and yet have a remarkable sensitivity to the direction of sound. The MEMS based sensor mimicking the fly’s hearing system was fabricated using an SOI substrate with a 25 μm device layer. The sensor consists of two 1.5 mm x1.6 mm wings connected in the middle by a 2.7 mm x 30 μm bridge. The entire structure is connected to the substrate by two torsional legs at the center. The frequency response of the sensor showed two resonance frequencies at approximately 1.1 kHz (rocking) and 1.5 kHz (bending). The resonance at 1.1 kHz is due to rocking of the wings by twisting the legs and the other at 1.5 kHz is due to bending of the bridge. The response of the sensor was probed electronically using comb finger capacitors integrated to the edges of the wings and with the help of an MS3110 chip. A peak output voltage of about 9V/Pa was measured for sound incident normal to the device at the resonance frequency of the bending mode. The bearing of the incident sound under these conditions could be determined to within a few degrees. These findings indicate the potential use of the MEMS sensor to locate sound sources with high accuracy.
Catalyst Systems for Alkene Polymerization Based on Metallocene Complexes and Sterically Hindered Organoaluminates (2003)

The article describes two types of organoaluminate compounds which can serve as cocatalysts for metallocene complexes in alkene polymerization reactions: (a) sterically hindered arylaluminates, oligomeric compounds containing [Al(OPh)−O] units where Ph are aryl groups substituted in the second and the sixth positions with bulky alkyl or aryl groups; and (b) alkylaluminates, compounds containing [Al(OR)−O] units where OR is a heavily sterically hindered alkoxy group. The most effective substituents Ph in the arylaluminates are phenyl groups with two ortho-positioned tert-butyl or phenyl groups. The most effective substituent R in the alkylaluminates is CPh3. These cocatalysts can be produced via two alternative routes: (1) a reaction between an alkylalumoxane and a sterically hindered phenol or an alcohol or (b) two consecutive reactions: first, a reaction between a trialkylaluminum compound and a sterically hindered phenol or an alcohol and, second, a reaction between the product of the first step and water. Oligomeric cocatalyst compositions containing units of two types, organoaluminate and alkylalumoxane, also can serve as cocatalysts for metallocene complexes.
Neural Transplantation of hNT Neurons for Huntington's Disease (1999)

Fetal striatal tissue transplants have been shown to restore motor deficits in rat and monkey models of Huntington's disease (HD). In the present study, using rats with unilateral striatal lesions, we compared fetal striatal tissue transplants to transplants of human NT (hNT) neurons. hNT neurons are terminally differentiated cells derived from the human NTera-2 cell line. In vitro, we have found that purified hNT neurons have a biochemical phenotype similar to that of human fetal striatal tissue. Both hNT neurons and fetal striatal tissue express mRNAs for glutamic acid decarboxylase, choline acetyltransferase, and the D1 and D2 dopamine receptors. Grafts of either hNT neurons or fetal striatal tissue into unilateral quinolinic acid-lesioned rat striatum improved methamphetamine-induced circling behavior. Sham controls showed no changes in methamphetamine-induced circling behavior. In the staircase test for skilled forelimb use, both transplant groups showed partial recovery in skilled use of the paw contralateral to the side of lesion, whereas the control animals showed continued deficits. These findings suggest that transplantation of hNT neurons may be an alternative to transplantation of fetal striatal tissue in the treatment of HD.
A field‐shaping multi‐well avalanche detector for direct conversion amorphous selenium (2012)

This is the first attempt to design a practical direct-conversion amorphous selenium detector with avalanche gain.
Deterministic Design of Ultrahigh Q and Small Mode Volume Photonic Crystal Nanobeam Cavity (2010)

A deterministic design of an ultrahigh Q, subwavelength mode volume, photonic crystal nanobeam cavity, operating at the target frequency, is proposed and experimentally demonstrated. Nonlinear bistability is observed in such nanobeam cavities fabricated in Si at very low pump powers.
Current sensing utilizing heterodyne detection of the Faraday effect in single-mode optical fiber (1986)

A fiber-optic current sensor based on the Faraday effect is described which utilizes laser-diode frequency modulation in order to synthesize a heterodyne-type sensor output. The relative phase of the output carrier is directly modulated by the magnetically induced circular polarization mode-phase delay. Current sensing over three orders of magnitude is demonstrated, and a Verdet constant of <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2.57 \times 10^{-6}</tex> rad/A (at 0.83μm) is reported for the fiber used.
Abstract 1438: Targeting metabolic enzyme with locked nucleic acids in non-small cell lung cancer (2014)

Abstract Despite advances in our knowledge of genetics of cancer and some progress in cancer treatment over the last few decades, lung cancer remains the leading cause of cancer mortality worldwide. Recently cancer metabolomics have been widely applied into cancer research, including of cancer diagnosis and therapy. Our recent work has identified tumor initiating cells (TICs) derived from non-small cell lung cancer (NSCLC) patients and shown that metabolic enzyme glycine decarboxylase (GLDC) is critical for TICs in NSCLC. In the clinic, aberrant activation of GLDC correlates with poorer survival in lung cancer patients. Those findings provide potential diagnostic markers and/or therapeutic target for NSCLC. Locked nucleic acids (LNAs) are novel high-affinity DNA analogs that can be used as genotype-specific drugs. In this study we tested NSCLC patient-derived xenograft tumor growth inhibition by GLDC LNAs antisense oligonucleotides. These LNAs antisense oligonucleotides strongly reduce GLDC protein levels. The osmotic minipumps were filled with GLDC LNAs antisense oligonucleotides at 0.5,1 and 5 mg/kg/day dose and implanted dorsally into tumor-bearing NOD/SCID Il2rγ-/- mice. Tumor growth was inhibited at dosages from 1 mg/kg/day. LNAs antisense oligonucleotides appeared to be non-toxic at dosages of 5 mg/kg/day. Furthermore, we found significant changes of serum metabolomics in lung cancer patients compared to normal donors. Our data show that GLDC LNAs antisense oligonucleotides are potent genotype-specific drugs that can inhibit lung tumor growth in vivo. Note: This abstract was not presented at the meeting. Citation Format: Wen Cai Zhang, Bing Lim. Targeting metabolic enzyme with locked nucleic acids in non-small cell lung cancer. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 1438. doi:10.1158/1538-7445.AM2014-1438
Improved Electrophoresis Cell (1982)

Several proposed modifications are expected to improve performance of a continous-flow electrophoresis cell. Changes would allow better control of buffer flow and would increase resolution by suppressing thermal gradients. Improved electrophoresis device would have high resolution and be easy to operate. Improvements would allow better flow control and heat dissipation.
<title>Dynamic EPD threshold for UBR control</title> (1998)

In many ATM switches, only a limited number of delay priority queues are available at each link. In order to support all five service categories defined in ATM Forum, the UBR and ABR service classes may have to be assigned to the same priority queue. In this paper we address the problem of controlling the resource sharing between UBR and ABR when both share the same FIFO queue in an ATM switch. We achieve the desired bandwidth sharing between these two classes by controlling the amount of buffer each class can occupy. In particular, we use the EDP threshold to control UBR by dropping UBR cells when this threshold is exceeded. We show that the control algorithm proposed in this paper achieves a tight control of the resource allocation between UBR and ABR.
Tumor escape from immune recognition: loss of HLA-A2 melanoma cell surface expression is associated with a complex rearrangement of the short arm of chromosome 6. (1996)

Specific CD8(+) CTL recognition of melanoma requires expression of MHC class I molecules as well as melanoma-associated peptide epitopes. Human melanoma cells may escape immune recognition by a variety of means, including global or allelic down-regulation of MHC class I molecules. Stable MHC class I cell surface expression requires delivery of cytosolic peptides into the endoplasmic reticulum by the peptide transporter molecules TAP1 and TAP2, with peptides subsequently transported to the cell surface in complexes containing MHC class I heavy chain and beta2-microglobulin. We have evaluated a series of mechanisms resulting in MHC class I down-regulation in a human melanoma cell line, Mz18, typed as HLA-A2(+), A3(+), B7(+), B57(+), Cw1(+), and Cw6(+) by genomic PCR analysis. The melanoma cell line Mz18 exhibits a global down-regulation of MHC class I heavy chain transcripts; beta2-microglobulin; the proteasome subunits LMP2/7, involved in generating cytosolic peptide fragments; and the peptide transporter molecules TAP1 and TAP2, involved in peptide transport from the cytosol into the endoplasmic reticulum. IFN-gamma treatment of Mz18 melanoma cells leads to up-regulation of LMP2/7 and TAP1/2, as well as to up-regulation of HLA-B and HLA-C MHC loci alleles, but not HLA-A2 or HLA-A3. Karyotypic analysis and fluorescence in situ hybridization with chromosome 6 and MHC class I-specific probes showed complex rearrangement of one chromosome 6 involving the MHC class I locus on 6p and translocation of 6q to the long arm of chromosome 19. To evaluate the capability of melanoma Mz18 to present tumor-specific peptides to HLA-A2-restricted, melanoma-specific CTLs, we restored HLA-A2 surface expression by retroviral-mediated transfer of functional HLA-A2 cDNA. Melanoma peptides could only be presented and recognized by CTLs if the HLA-A2-transfected Mz18 cell line was first treated with IFN-gamma, thereby restoring LMP2/7 and TAP1/2 expression and function. Because several melanoma antigens recognized by T cells have been reported to be presented by HLA-A2 (MART-1/Melan-A, tyrosinase, gp100, and MAGE-3), the loss of HLA-A2 molecules may represent an important mechanism by which many melanomas evade immune recognition. These findings suggest that patients entering clinical trials for immunotherapy with melanoma vaccines should be carefully examined for tumor cell allelic MHC class I loss and whether such MHC class I antigen down-regulation can be restored by cytokines.