gebhart/patrepeval huggingface dataset:
Cell‐mediated cytotoxicity for cultured autologous melanoma cells (1979)

Peripheral blood lymphocytes from 32 patients with malignant melanoma were tested for cell-mediated cytotoxicity (CMC) against cultured autologous melanoma cells. Effector cells were prepared from venous blood by defibrination, gel sedimentation, nylon column filtration, and lysis of remaining erythrocytes with NH4Cl. Melanoma cells prelabelled with [3H])proline were used as target cells in a 40-h assay and CMC was evaluated against standards obtained with blood lymphocytes from the least reactive normal donor. Reproducible autologous CMC was detected in 18 of 32 patients in a series of 367 total tests. CMC correlated with tumor volume (5-500 cm3) but not with tumor stage or DNCB reactivity. Preliminary results indicated that autologous CMC was not affected by treatment with DTIC, dexamethasone, intralesional BCG, radiation therapy, or partial surgical excision. Lack of consistent CMC in 14 patients could not be attributed to a measurable decrease in general immune capacity or to increased resistance of the patients' melanoma cells to CMC in general. Fibroblasts were more resistant to CMC than melanoma cells, and therefore of questionable value for defining specificity in direct tests.
A 7T spine array based on electric dipole transmitters (2015)

For imaging of the spine, electric dipole-based transmitters provide an attractive alternative to the traditional loop-based design. Easy integration with existing receive array technology facilitates practical use at high fields.
Optimization of Stacked Vertical Dipoles Above a Ground Plane Using the Genetic Algorithm (1999)

In this paper the Genetic Algorithm (GA) is used to design and optimize a dual-band antenna system covering the UHF and VHF bands. The system contains two stacked vertical wire dipoles, one for each of the bands, above a perfectly-conducting ground plane. Unlike the case of the GA design of a single-band antenna [1, 2], the mutual coupling between the two dipoles introduces some complications in the design of dual-band antennas. Specifically, in the process of broad-banding one dipole by optimizing its loading and matching network for its own frequency band, it becomes necessary to take into account the influence of the second dipole operating in a different frequency band. It is, therefore, essential to carry out the analysis and the synthesis of the entire coupled system concurrently. This paper proposes a design procedure for the dual-band antenna system that makes initial choices for the antenna configuration on the basis of a systematic screening of the potential candidates, and then goes on to apply the GA in conjunction with the Numerical Electromagnetics Code (NEC4) [3] to meet the specifications for the two operating in a simultaneous manner.
Pressure-Induced Superconductivity in (MDT-TS)(AuI2)0.441 [MDT- TS = 5H-2-(1,3-diselenol-2-ylidene)-1,3,4,6-tetrathiapentalene]:  A New Organic Superconductor Possessing an Incommensurate Anion Lattice (2004)

A selenium-containing TTF-type electron donor, MDT-TS [5H-2-(1,3-diselenol-2-ylidene)-1,3,4,6-tetrathiapentalene] was effectively synthesized by a two-step reaction and utilized for electrocrystallization with an AuI2- anion. The resulting salt, (MDT-TS)(AuI2)0.441, has a unique crystal packing, in which the donor subcell and the anion lattice are incommensurate. Although the salt has relatively high conductivity at room temperature (600 S cm-1), it showed a metal−insulator (MI) transition at TMI = 50 K. Application of hydrostatic pressure suppressed the MI transition, and at 11.4 kbar (MDT-TS)(AuI2)0.441 showed a superconducting transition at Tc = 4.7 K.
Learning Efficient Sparse Structures in Speech Recognition (2019)

Recurrent neural networks (RNNs), especially long short-term memories (LSTMs) have been widely used in speech recognition and natural language processing. As the sizes of RNN models grow for better performance, the computation cost and therefore the required hardware resource increase rapidly. We propose an efficient structural sparsity (ESS) learning method for acoustic modeling in speech recognition. ESS aims to generate a model that offers higher execution efficiency while maintaining the accuracy. A three-step training pipeline is developed in our work. First, we apply the group Lasso regularization method during training process and learn a structural sparse model from scratch. Then the learned sparse structures will be fixed and cannot be changed. Finally, we retrain the model and update the nonzero parameters in the model. We applied our ESS method on classic HMM+LSTM model on Kaldi toolkit. The experimental results show that ESS can remove 72.5% weight groups in the weight matrices when slightly increasing the word error rate (WER) 1.1%.
Neurorestorative Effect of Urinary Bladder Matrix-Mediated Neural Stem Cell Transplantation Following Traumatic Brain Injury in Rats (2013)

Traumatic brain injury (TBI) is a leading cause of cell death and disability among young adults and lacks a successful therapeutic strategy. The multiphasic injuries of TBI severely limit the success of conventional pharmacological approaches. Recent successes with transplantation of stem cells in bioactive scaffolds in other injury paradigms provide new hope for the treatment of TBI. In this study, we transplanted neural stem cells (0.5x10(5) cells/µl) cultured in a bioactive scaffold derived from porcine urinary bladder matrix (UBM; 4 injection sites, 2.5µl each) into the rat brain following controlled cortical impact (CCI, velocity, 4.0 m/sec; duration, 0.5 sec; depth, 3.2mm). We evaluated the effectiveness of this strategy to combat the loss of motor, memory and cognitive faculties. Before transplantation, compatibility experiments showed that UBM was able to support extended proliferation and differentiation of neural stem cells. Together with its reported anti-inflammatory properties and rapid degradation characteristics in vivo, UBM emerged to be an ideal scaffold. The transplants reduced neuron/tissue loss and white matter injury, and also significantly ameliorated motor, memory, and cognitive impairments. Furthermore, exposure to UBM alone was sufficient to decrease the loss of sensorimotor skills from TBI (examined 3-28 days post-CCI). However, only UBMs that contained proliferating neural stem cells helped attenuate memory and cognitive impairments (examined 26-28 days post-CCI). In summary, these results demonstrate the therapeutic efficacy of stem cells in bioactive scaffolds against TBI and show promise for translation into future clinical use.
Assessment of fiducial motion in CBCT projections of the abdominal tumor using template matching and sequential stereo triangulation (2022)

Purpose: To assess the fiducial motion in abdominal stereotactic body radiotherapy (SBRT) using the cone-beam computed tomography (CBCT) projections acquired for pre-treatment patient set-up. Materials and Methods: Pre-treatment CBCT projections and anterior-posterior (AP) and lateral (LAT) pair of fluoroscopic sequences of 7 pancreatic and 6 liver SBRT patients with implanted fiducials were analyzed for 49 treatment fractions retrospectively. A tracking algorithm based on template matching and sequential stereo triangulation algorithms was used to track the fiducials in the CBCT projections and the fluoro sequence pairs. We predicted the clinical couch adjustment from CBCT tracking and compared it with the clinical couch decision made during the patient's treatment. Results: In 3D coordinate, the fiducial motion ranges for pancreas cases were 9.90+/-3.52 mm, 10.65+/-5.91 mm, and 10.74+/-6.24 mm for CBCT, AP, and LAT fluoro, respectively, while in the liver, they were 13.93+/-3.39 mm, 11.17+/-3.75 mm, and 11.52+/-4.33 mm, respectively. Prediction of couch adjustment in LAT, SI, and AP coordinates from CBCT tracking agrees with the actual clinical couch correction within 0.92+/-0.74 mm, 1.37+/-1.26 mm, and 0.68+/-0.56 mm for pancreas cases and within 1.12+/-0.96 mm, 1.15+/-0.92 mm and 0.90+/-0.86 mm for liver cases, respectively. Conclusion: Tracking pre-treatment CBCT projections using template matching and sequential stereo triangulation is suitable for assessing fiducial motion and adjusting the patient setup for abdominal SBRT. CBCT can be used for motion modeling, potentially eliminating the need for additional fluoroscopic pair acquisition and thus reducing the imaging dose to the patient and the total treatment time.
Photostable and Proteolysis-Resistant Förster Resonance Energy Transfer-Based Calcium Biosensor (2020)

Molecular sensors from protein engineering offer new methods to sensitively bind to and detect target analytes for a wide range of applications. For example, these sensors can be integrated into probes for implantation, and then yield new and valuable physiological information. Here, a new Förster resonance energy transfer (FRET)-based sensor is integrated with an optical fiber to yield a device measuring free Ca<sup>2+</sup>. This membrane encapsulated optical fiber (MEOF) device is composed of a sensor matrix that fills poly(tetrafluoroethylene) (PTFE) with an engineered troponin C (TnC) protein fused to a pair of FRET fluorophores. The FRET efficiency is modulated upon Ca<sup>2+</sup> ion binding. The probe further comprises a second, size-excluding filter membrane that is synthesized by filling the pores of a PTFE matrix with a poly(ethylene glycol) dimethacrylate (PEGDMA) hydrogel; this design ensures protection from circulating proteases and the foreign body response. The two membranes are stacked and placed on a thin, silica optical fiber for optical excitation and detection. Results show the biosensor responds to changes in Ca<sup>2+</sup> concentration within minutes with a sensitivity ranging from 0.01 to 10 mM Ca<sup>2+</sup>, allowing discrimination of hyper- and hypocalcemia. Furthermore, the system reversibly binds Ca<sup>2+</sup> to allow continuous monitoring. This work paves the way for the use of engineered structure-switching proteins for continuous optical monitoring in a large number of applications.
ChemInform Abstract: Aerobic Asymmetric Dehydrogenative Cross‐Coupling Between Two C(sp3)—H Groups Catalyzed by a Chiral‐at‐Metal Rhodium Complex. (2016)

Abstract Two procedures A) and B) using both the chiral catalyst RHC are applied to the title process.
Additive and solvent effects on samarium diiodide reductions: the effects of water and DMPU (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAdditive and solvent effects on samarium diiodide reductions: the effects of water and DMPUEietsu Hasegawa and Dennis P. CurranCite this: J. Org. Chem. 1993, 58, 18, 5008–5010Publication Date (Print):August 1, 1993Publication History Published online1 May 2002Published inissue 1 August 1993https://pubs.acs.org/doi/10.1021/jo00070a046https://doi.org/10.1021/jo00070a046research-articleACS PublicationsRequest reuse permissionsArticle Views1639Altmetric-Citations186LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Abstract 1777: The characterization of the effects of the strigolactones on the heat shock response (2015)

Abstract Strigolactones (SLs) are a novel class of plant hormones that inhibit the self-renewal of undifferentiated meristem cells in shoots regulating above-ground plant architecture. Data from our lab have shown that SL analogues are able to inhibit the growth and survival of a wide array of cancer-derived cell lines including: prostate, colon, lung, breast and osteosarcoma (U2OS) while minimally affecting cultured normal cells. Treatment of cancer cells with SL analogues leads to the activation of stress-related signaling including p38MAPKs and JNK1/2, as well as the activation of the heat shock master regulator, heat shock transcription factor 1 (HSF1), and heat shock response (HSR) gene expression. We further show that SLs generate reactive oxygen species (ROS) and that SL treatments of cancer cells leads to the activation of GRP78, the master regulator of the unfolded protein response (UPR). To further characterize the relationship between SLs, HSR and UPR, several clones of HSF1 shRNA knockdown, in U2OS cells were generated and are currently being studied. Interestingly, while wild type mouse embryonic fibroblast (MEF) cells are refractory to SLs treatments, we demonstrate that HSF1 knockout in MEFs enhances the sensitivity of the cells to SLs treatments. Taken together, our data suggest that the HSR and UPR are recruited as cell survival mechanisms against the SLs treatments, giving rise to possible future chemotherapeutic combinatorial treatment options. Citation Format: Victor S. Wang, Nu Nu Kyin, Claire Pollock, Hyjoung Lee, Xin Li, Cristina Prandi, Yoram Kapulnik, Hinanit Koltai, Luke Whitesell, Ronit Yarden. The characterization of the effects of the strigolactones on the heat shock response. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 1777. doi:10.1158/1538-7445.AM2015-1777
Accelerated Computational Design of Mixed Protonic and Electronic Conduction for H2Separation through Tailoring Polaron (2017)

The technology of H2 separation is essential for the utilization of hydrogen fuel, which is strongly motivated by the grand challenge of climate change. In particular, SrCeO3 perovskites with mixed protonic and electronic conductivities are promising materials for H2 separation due to negligible oxygen permeability. However, low electronic conductivity of SrCeO3 often limits the overall H2 flux. Yb-doped SrCeO3 has been demonstrated to exhibit excellent performance as H2 separation membranes with high electronic conductivity. Our study reveals the enhancement on electronic conductivity from Yb dopant originates from the polaron mechanism, based on first principles hybrid calculations. Electron polarons on Yb and Ce are mobile, contributing to electronic conductivity in Yb-doped SrCeO3. The insight of the polaron enhancement mechanism will shed light on predicting promising dopants to increase electronic conductivity. Our study demonstrates first principles techniques in accelerating design of mixed conductors.
Accurate Determination of Peptide Phosphorylation Stoichiometry Via Automated Diagonal Capillary Electrophoresis Coupled with Mass Spectrometry: Proof of Principle (2013)

While reversible protein phosphorylation plays an important role in many cellular processes, simple and reliable measurement of the stoichiometry of phosphorylation can be challenging. This measurement is confounded by differences in the ionization efficiency of phosphorylated and unphosphorylated sites during analysis by mass spectrometry. Here, we demonstrate diagonal capillary electrophoresis-mass spectrometry for the accurate determination of this stoichiometry. Diagonal capillary electrophoresis is a two-dimensional separation method that incorporates an immobilized alkaline phosphatase microreactor at the distal end of the first capillary and employs identical electrophoretic separation modes in both dimensions. The first dimension is used to separate a mixture of the phosphorylated and unphosphorylated forms of a peptide. Fractions are parked in the reactor where they undergo complete dephosphorylation. The products are then periodically transferred to the second capillary and analyzed by mass spectrometry (MS). Because the phosphorylated and unphosphorylated forms differ in charge, they are well resolved in the first dimension separation. Because the unphosphorylated and dephosphorylated peptides are identical, there is no bias in ionization efficiency, and phosphorylation stoichiometry can be determined by the ratio of the signal of the two forms. A calibration curve was generated from mixtures of a phosphorylated standard peptide and its unphosphorylated form, prepared in a bovine serum albumin tryptic digest. This proof of principle experiment demonstrated a linear response across nearly 2 orders of magnitude in stoichiometry.
New methods for super-resolution (1993)

This thesis presents a new, non-iterative method for super-resolution which we call the direct method. By exploiting the inherent structure of the discrete signal processing environment, the direct method reduces the discrete super-resolution problem to solving a linear set of equations. The direct method is shown to be closely related to the Gerchberg algorithm for super-resolution. A mathematical justification for early termination of the Gerchberg algorithm is presented and the design of optimal termination schemes is discussed. Another new super-resolution method, which we call the SVD method, is presented. The SVD method is based on the direct method and employs SVD techniques to minimize errors in the solution due to noise and aliasing errors on the known frequency samples. The new SVD method is shown to provide results nearly identical to the optimal solution given by the Gerchberg algorithm, with huge savings in time and computational work.
Novel view synthesis by cascading trilinear tensors (1998)

Presents a new method for synthesizing novel views of a 3D scene from two or three reference images in full correspondence. The core of this work is the use and manipulation of an algebraic entity, termed the "trilinear tensor", that links point correspondences across three images. For a given virtual camera position and orientation, a new trilinear tensor can be computed based on the original tensor of the reference images. The desired view can then be created using this new trilinear tensor and point correspondences across two of the reference images.
Proceedings of the 10th Alcohol Hangover Research Group Meeting in Utrecht, The Netherlands (2020)

The hangover is the most commonly reported negative consequence of alcohol use with several studies reporting the detrimental consequences of hangover on health, economy, and society. Research has emphasized the socioeconomic consequences of experiencing these physical and psychological symptoms in relation to absenteeism, increased risk of having accidents and injuries, and impairment of daily activities, such as job performance and driving a car. During the 10th Alcohol Hangover Research Group meeting, held on 29 April 2018, in Utrecht, The Netherlands, aspects of alcohol hangover were presented with regards to determinants, biological and cognitive consequences and potential treatments. Precursory and posterior factors influencing alcohol hangover, including biological, psychological, behavioral, metabolic aspects, cognitive functioning, and the role of the immune system in the development of alcohol hangover, were presented. In addition, potential preventive measures and treatments of alcohol hangover to reduce the adverse consequences of alcohol consumption and hangover symptoms were discussed. One study revealed that an average of 24% of social and heavy drinkers claimed not to experience hangover symptoms across time. Another study showed that food intake (either healthy or junk food) had no significant impact on next-day hangover severity. Research examining cognitive and psychomotor functioning during hangover revealed impairments in collective problem solving and response inhibition, but not attentional bias towards alcohol-related cues. The alcohol hangover state further significantly impaired driving performance, even for a short commute to work. With regard to the pathology of the alcohol hangover, research was presented that demonstrated increases in saliva cytokine concentrations confirming drinking alcohol and the hangover phase are both associated with an immune response. Other presentations discussed that scientific literature shows that there are no effective hangover treatments available yet. However, although promising, new hangover treatments are currently in development. Taken together, at the 10th Alcohol Hangover Research Group meeting, a comprehensive overview of the causes, consequences, and potential treatments of the alcohol hangover was presented.
Permeabilization of Fungal Hyphae by the Plant Defensin NaD1 Occurs through a Cell Wall-dependent Process (2010)

The antifungal activity of the plant defensin NaD1 involves specific interaction with the fungal cell wall, followed by permeabilization of the plasma membrane and entry of NaD1 into the cytoplasm. Prior to this study, the role of membrane permeabilization in the activity of NaD1, as well as the relevance of cell wall binding, had not been investigated. To address this, the permeabilization of Fusarium oxysporum f. sp. vasinfectum hyphae by NaD1 was investigated and compared with that by other antimicrobial peptides, including the cecropin-melittin hybrid peptide CP-29, the bovine peptide BMAP-28, and the human peptide LL-37, which are believed to act largely through membrane disruption. NaD1 appeared to permeabilize cells via a novel mechanism that required the presence of the fungal cell wall. NaD1 and Bac2A, a linear variant of the bovine peptide bactenecin, were able to enter the cytoplasm of treated hyphae, indicating that cell death is accelerated by interaction with intracellular targets.