gebhart/patrepeval huggingface dataset:
Pathways linking Aβ and tau pathologies (2010)

Abeta (amyloid beta-peptide) and tau are the main proteins that misfold and accumulate in amyloid plaques and NFTs (neurofibrillary tangles) of Alzheimer's disease and other neurological disorders. Historically, because plaques and NFTs accumulate in diverse cellular compartments, i.e. mainly extracellularly for plaques and intracellularly for NFTs, it was long presumed that the constituent proteins formed these lesions via unrelated pathways. Animal and cell studies over the last decade, however, have provided convincing evidence to show that Abeta can facilitate the development of tau pathology by altering several cell-dependent and -independent mechanisms. In the present article, results are reviewed from several laboratories that show that modulating Abeta pathology can directly affect the development of tau pathology, which has significant implications for the treatment of Alzheimer's disease.
Polygon properties calculated from the vertex neighborhoods (1987)

Calculating properties of polyhedra given only the set of the locations and neighborhoods of the vertices is easy. Possible properties include volume, surface area, and point containment testing. No global topological information at all is explicitly needed (although the complete global topology could be recovered). The neighborhood of the vertex means the directions of the edges and faces on it but not their extents. These vertex-based formulae are dual to the usual formulae that use the faces. They have been implemented and the stability against inconsistent data tested. Alternative data structures and formulae for polyhedron calculation are important since special cases are a function partly of the data structure, and because different methods have different numerical accuracy and error detection properties.
Marinopyrrole A Target Elucidation by Acyl Dye Transfer (2009)

The targeting of marinopyrrole A to actin was identified using a fluorescent dye transfer strategy. The process began by appending a carboxylic acid terminal tag to a phenol in the natural product. The resulting probe was then studied in live cells to verify that it maintained activity comparable to marinopyrrole A. Two-color fluorescence microscopy confirmed that both unlabeled and labeled materials share comparable uptake and subcellular localization in HCT-116 cells. Subsequent immunoprecipitation studies identified actin as a putative target in HCT-116 cells, a result that was validated by mass spectral, affinity, and activity analyses on purified samples of actin. Further data analyses indicated that the dye in the marinopyrrole probe was selectively transferred to a single residue K(115), an event that did not occur with related acyl phenols and reactive labels. In this study, the combination of cell, protein, and amino acid analysis arose from a single sample of material, thereby, suggesting a means to streamline and reduce material requirements involved in mode of action studies.
Synthesis and Properties of Europium Complexes with <i>β</i>-Diketone Ligands for Organic Electroluminescent Devices (1998)

Abstract Europium complexes with new β-diketone ligands with fluorene for organic electroluminescent (EL) devices have been synthesized and their properties examined. The absorption spectra of the complexes were varied by changing the conjugated system of the β-diketone; also, the energy transfer from the host material to the europium complexes and the intramolecular energy transfer have been improved. Concerning the volatility, the thermal properties of the europium complexes were improved by using phenanthroline derivatives. We fabricated organic EL devices using the synthesized complexes, and investigated the luminance of the devices.
Classical and Nonclassical Class I Major Histocompatibility Complex Molecules Exhibit Subtle Conformational Differences That Affect Binding to CD8αα (2000)

The cell surface molecules CD4 and CD8 greatly enhance the sensitivity of T-cell antigen recognition, acting as "co-receptors" by binding to the same major histocompatibility complex (MHC) molecules as the T-cell receptor (TCR). Here we use surface plasmon resonance to study the binding of CD8alphaalpha to class I MHC molecules. CD8alphaalpha bound the classical MHC molecules HLA-A*0201, -A*1101, -B*3501, and -C*0702 with dissociation constants (K(d)) of 90-220 microm, a range of affinities distinctly lower than that of TCR/peptide-MHC interaction. We suggest such affinities apply to most CD8alphaalpha/classical class I MHC interactions and may be optimal for T-cell recognition. In contrast, CD8alphaalpha bound both HLA-A*6801 and B*4801 with a significantly lower affinity (>/=1 mm), consistent with the finding that interactions with these alleles are unable to mediate cell-cell adhesion. Interestingly, CD8alphaalpha bound normally to the nonclassical MHC molecule HLA-G (K(d) approximately 150 microm), but only weakly to the natural killer cell receptor ligand HLA-E (K(d) >/= 1 mm). Site-directed mutagenesis experiments revealed that variation in CD8alphaalpha binding affinity can be explained by amino acid differences within the alpha3 domain. Taken together with crystallographic studies, these results indicate that subtle conformational changes in the solvent exposed alpha3 domain loop (residues 223-229) can account for the differential ability of both classical and nonclassical class I MHC molecules to bind CD8.
Contribution of the Sugar Moiety in the Browning Product between β-Lactoglobulin and Lactose as an Antigenic Determinant (1982)

β-ラクトグロプリンとラクトースの褐変反応物(Lac-β-Lg)中の糖部分がLac-β-Lgの抗原性に寄与しているか否かを知る目的で実験を行なった.β-ラクトログロブリン(β-Lg)と種々の糖,ラクトースと牛血清アルブミン或いは卵アルブミンの褐変反応物を作成し,それら褐変反応物と抗Lac-β-Lg血清の反応性を受動性皮膚アナフィラキシー反応およびその抑制反応により調べた.グルコース,ガラクトース,フラクトースなどの糖とβ-Lgの褐変反応物は,Lac-β-Lgと抗Lac-β-Lg血清の反応を強く阻害したが,Lac-β-Lgのように完全阻害ではなかった.一方,未処理牛血清アルブミンおよび卵アルブミンはそれ自身では抗Lac-β-Lg血清と反応しなかったが,ラクトースとの間で褐変反応物にすることにより反応性を生じた.また,この牛血清アルブミンとラクトースの褐変反応物と抗Lac-β-Lg血清の反応は,S-カルボキシメチル化(SCM)β-Lgを臭化シアン処理して得たペプチドの添加による影響は受けなかったが,SCM Lac-β-Lgを臭化シアン処理して得たペプチドの添加により完全に阻害された.以上の結果より,Lac-β-Lg中の糖部分はLac-β-Lgの抗原性に寄与していることが示された.
Membership privacy (2013)

We introduce a novel privacy framework that we call Membership Privacy. The framework includes positive membership privacy, which prevents the adversary from significantly increasing its ability to conclude that an entity is in the input dataset, and negative membership privacy, which prevents leaking of non-membership. These notions are parameterized by a family of distributions that captures the adversary's prior knowledge. The power and flexibility of the proposed framework lies in the ability to choose different distribution families to instantiate membership privacy. Many privacy notions in the literature are equivalent to membership privacy with interesting distribution families, including differential privacy, differential identifiability, and differential privacy under sampling. Casting these notions into the framework leads to deeper understanding of the strengthes and weaknesses of these notions, as well as their relationships to each other. The framework also provides a principled approach to developing new privacy notions under which better utility can be achieved than what is possible under differential privacy.
Organic Electronics: Universal Route to Impart Orthogonality to Polymer Semiconductors for Sub‐Micrometer Tandem Electronics (Adv. Mater. 28/2019) (2019)

A universal route for manipulating polymer semiconductors physically and chemically orthogonal to the sequential solution coating and etching processes that are involved in conventional photolithography, which is termed an orthogonal polymer semiconductor gel, is demonstrated by Moon Sung Kang, Hojin Lee, Do Hwan Kim, and co-workers in article number 1901400. Ultimately, the proposed strategy is expected to introduce new avenues toward solution-processed, high-resolution, flexible polymer tandem electronics.
Comparison of the Kinetics of Expulsion of Trichostrongylus colubriformis from Previously Uninfected, Reinfected, and Vaccinated Guinea Pigs (1977)

T. L. W. Rothwell, D. A. Griffiths, Comparison of the Kinetics of Expulsion of Trichostrongylus colubriformis from Previously Uninfected, Reinfected, and Vaccinated Guinea Pigs, The Journal of Parasitology, Vol. 63, No. 4 (Aug., 1977), pp. 761-762
104 Development and characterization of human chimeric antigen receptor monocytes (CAR-Mono), a novel cell therapy platform (2021)

<h3>Background</h3> Engineered cell therapies have demonstrated significant clinical activity against hematologic malignancies, but solid tumors remain an intractable challenge. We have previously developed a human chimeric antigen receptor macrophage (CAR-M) platform for adoptive cell therapy and shown potent anti-tumor activity in pre-clinical solid tumor models.<sup>1</sup> CAR-M overcome critical solid tumor challenges such as tumor infiltration, immunosuppression within the tumor microenvironment, lymphocyte exclusion, and target antigen heterogeneity. Currently, CAR-M are generated in a week-long ex-vivo process in which peripheral blood monocytes are differentiated into macrophages prior to genetic manipulation. Here, we demonstrate the production feasibility, phenotype, pharmacokinetics, cellular fate, specificity, and anti-tumor activity of human CD14+ CAR monocytes. <h3>Methods</h3> Using the chimeric adenoviral vector Ad5f35, we engineered primary human CD14+ monocytes to express a CAR targeted against human epidermal growth factor receptor 2 (HER2) (CAR-mono). Using a partially automated approach, we established a process that allowed for same day manufacturing (from Leukopak to cryopreserved CAR-mono cell product). <h3>Results</h3> CAR expression and cell viability exceeded 90%, and cells efficiently differentiated into CAR-expressing macrophages. The adenoviral based gene modification method led to pre-conditioning of CAR-mono cells resulting in a strong M1 phenotype upon differentiation, and potent anti-tumor activity regardless of exposure to GM-CSF, M-CSF, or immunosuppressive factors. Treating CAR-mono cells with GM-CSF and IL-4 resulted in their differentiation to monocyte-derived CAR-DCs, indicating that these cells retain their myeloid differentiation potential. In vivo, CAR-mono treatment induced anti-tumor activity in various HER2+ solid tumor xenograft models. Following intravenous administration, CAR-mono demonstrated the ability to traffic to both GM-CSF < sup >high</sup > and GM-CSF< sup >low</sup >expressing tumors. Notably, CAR-mono showed long-term CAR expression and persistence (>100 days) in both NSG and NSG-S mouse models, demonstrating lasting persistence irrespective of human cytokine support. <h3>Conclusions</h3> The CAR-mono platform allows for a rapid, same-day manufacturing process while maintaining the key characteristics of CAR-M therapy. Ad5f35 engineered human monocytes are primed toward M1 macrophage differentiation and produce a cell population highly similar to our established CAR-M platform. Collectively, these findings provide strong pre-clinical support to advance the CAR-mono platform into clinical testing. <h3>Reference</h3> Klichinsky M, et al. Human chimeric antigen receptor macrophages for cancer immunotherapy. <i>Nature Biotechnology</i> March 2020.
Moving target inference with hierarchical Bayesian models in synthetic aperture radar imagery (2013)

In synthetic aperture radar (SAR), images are formed by focusing the response of stationary objects to a single spatial location. On the other hand, moving targets cause phase errors in the standard formation of SAR images that cause displacement and defocusing effects. SAR imagery also contains significant sources of non-stationary spatially-varying noises, including antenna gain discrepancies, angular scintillation (glints) and complex speckle. In order to account for this intricate phenomenology, this work combines the knowledge of the physical, kinematic, and statistical properties of SAR imaging into a single unified Bayesian structure that simultaneously (a) estimates the nuisance parameters such as clutter distributions and antenna miscalibrations and (b) estimates the target signature required for detection/inference of the target state. Moreover, we provide a Monte Carlo estimate of the posterior distribution for the target state and nuisance parameters that infers the parameters of the model directly from the data, largely eliminating tuning of algorithm parameters. We demonstrate that our algorithm competes at least as well on a synthetic dataset as state-of-the-art algorithms for estimating sparse signals. Finally, performance analysis on a measured dataset demonstrates that the proposed algorithm is robust at detecting/estimating targets over a wide area and performs at least as well as popular algorithms for SAR moving target detection.
El desastre. Cómo responder a un mundo desordenado (2015)

Dada la decreciente hegemonia estadounidense y la falta de un sucesor a la espera para tomar la batuta, es probable que el sistema internacional actual le ceda el paso a un mayor numero de centros de poder que actuan con una creciente autonomia. El orden posterior a la Guerra Fria se esta desmoronando… y se le va a extranar
PENYELIDIKAN AKUIFER BERDASARKAN NILAI RESISTIVITAS DI KAWASAN GAMBUT MENGGUNAKAN METODE GEOLISTRIK KONFIGURASI SCHLUMBERGER DESA JATI MULYO (2023)

Telah dilakukan penelitian dengan menggunakan metode geolistrik konfigurasi Schlumberger yang bertujuan untuk mengetahui keberadaan akuifer baik dari segi kedalaman maupun ketebalan akuifer di Desa Jati Mulyo Kecamatan Dendang Kabupaten Tanjung Jabung Timur, Provinsi Jambi. Pengukuran di lapangan sebanyak 15 titik sounding dengan masing-masing panjang lintasan 400 m, diperoleh jenis batuan dan nilai resistivitas dari hasil pengolahan melalui software IPI2Win sebagai berikut, yaitu top soil dengan nilai resistivitas 20 Ωm sampai 200 Ωm, lempung dengan nilai resistivitas berkisar antara 1 Ωm sampai 15 Ωm, kemudian lempung pasiran yang memiliki nilai resistivitas berkisar antara 15 Ωm sampai 29 Ωm, selanjutnya untuk pasir dengan nilai resistivitas berkisar antara 29 Ωm sampai 100 Ωm, dan kerikil dengan nilai resistivitas besar dari 100 Ωm. Lapisan pasir dan kerikil disini diduga sebagai lapisan yang membawa air (akuifer) secara baik, dikarenakan memiliki nilai porositas dan permeabilitas yang cukup tinggi. Berdasarkan hasil pemodelan 2D yang telah diolah menggunakan software RockWork 15, lapisan yang berpotensi sebagai akuifer berada pada kedalaman 20 m sampai 50 m. Dimana pola akuifer semakin mendalam dan menebal kearah timur laut. Selain itu akuifer juga berada pada kedalaman 75 m sampai 100 m di Barat Daya pemukiman Desa Jati Mulyo. Sehingga untuk ketebalan akuifer di Desa Jati Mulyo berkisar antara 25 m sampai 30 m. Kata kunci : Akuifer; Resistivitas; Schlumberger
Organocatalytic Michael Reaction of Nitroenamine Derivatives with Aldehydes: Short and Efficient Asymmetric Synthesis of (−)‐Oseltamivir (2012)

Abstract Nitroenamine derivatives were used as a new class of Michael acceptors in the organocatalytic Michael reaction of aldehydes. The addition products were obtained in good yields and very good to excellent enantioselectivities. Moreover, a highly efficient, enantioselective, and simple synthesis of (−)‐oseltamivir was accomplished in only five steps: two separate one‐pot operations and one purification step. This procedural simplicity demonstrated the power of the organocatalytic asymmetric Michael reaction of nitroenamine acceptors with aldehydes.
Designing a Smart City Internet of Things Platform with Microservice Architecture (2015)

The Internet of Things (IoT) is being adopted in different application domains and is recognized as one of the key enablers of the Smart City vision. Despite the standardization efforts and wide adoption of Web standards and cloud computing technologies, however, building large-scale Smart City IoT platforms in practice remains challenging. The dynamically changing IoT environment requires these systems to be able to scale and evolve over time adopting new technologies and requirements. In response to the similar challenges in building large-scale distributed applications and platforms on the Web, micro service architecture style has emerged and gained a lot of popularity in the industry in recent years. In this work, we share our early experience of applying the micro service architecture style to design a Smart City IoT platform. Our experience suggests significant benefits provided by this architectural style compared to the more generic Service-Oriented Architecture (SOA) approaches, as well as highlights some of the challenges it introduces.
Generation of intense pulsed electron beams by the pseudospark discharge (1989)

A low-pressure gas discharge is presented as a source of intense pulsed electron beams. The pseudospark discharge emits a short-duration pinched electron beam during the breakdown phase. At voltages of typically 20 kV, approximately 10-20% of the total discharge current appears as the electron-beam current of typically 20 ns in duration. According to the breakdown voltage in the beam, a power density on the order of 10/sup 9/ W/cm/sup 2/ is reached. Thus, this electron beam turns out to be a good tool for material processing, comparable to pulsed high-power lasers. Besides the drilling of holes into metals and insulators, an interesting application is the production of high-temperature superconducting thing YBa/sub 2/Cu/sub 3/O/sub 7-x/ films. The electron beam is used to evaporate material from a stoichiometric 1-2-3 target. Experimental results concerning the propagation behavior in neutral gas, the electron energy distribution, and the interaction with matter are reported.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Development of new photopolymerizable dental sealants (1998)

This paper describes the results obtained in the optimization of the composition of dental sealants in relation to the nature and proportions of monomer mixtures and photoinitiating system employed. The quantification and variation of certain parameters which determine the quality of a dental sealant (such as viscosity and penetrating power, residual double bonds, solubility and absorption, volume shrinkage and certain specific mechanical properties) have resulted in the development of new formulations. The composition which has achieved the best results of all the above properties was that corresponding to the monomer mixture bis-GMA/tri(ethylene glycol) dimethacrylate (TEGDMA) 40/60 wt%, and the photoinitiating system camphorquinone (CQ) with co-initiators N,N,3,5-tetramethyaniline (TMA) or N,N-dimethyl-p-toluidine (DMPT) in the ratio 1:1. The final properties and characteristics of the obtained formulations are superior to those of commercial dental sealants currently in use.
Rapid synthesis of oligodeoxyribonucleotides. V. Further studies in solid phase synthesis of oligodeoxyribonucleotides through phosphotriester intermediates. (1980)

The phosphotriester solid phase method of oligodeoxyribonucleotide synthesis on a polyamide support [M.J. Gait et al. (1980) Nucleic Acids Research 8, 1081-1096] has been applied to purine rich oligodeoxyribonucleotides of 10-12 units. Use of trichloroacetic acid as reagent for removal of terminal dimethoxytrityl groups reduced depurination during chain assembly. Improvements to reaction and isolation conditions for the preparation of monomer and dimer building blocks are also described. The new methods provide a simple, quick and efficient procedure for medium length oligodeoxyribonucleotide synthesis on a scale adequate for most requirements of molecular biology.
Structural basis for compound C inhibition of the human AMP-activated protein kinase α2 subunit kinase domain (2011)

AMP-activated protein kinase (AMPK) is a serine/threonine kinase that functions as a sensor to maintain energy balance at both the cellular and the whole-body levels and is therefore a potential target for drug design against metabolic syndrome, obesity and type 2 diabetes. Here, the crystal structure of the phosphorylated-state mimic T172D mutant kinase domain from the human AMPK α2 subunit is reported in the apo form and in complex with a selective inhibitor, compound C. The AMPK α2 kinase domain exhibits a typical bilobal kinase fold and exists as a monomer in the crystal. Like the wild-type apo form, the T172D mutant apo form adopts the autoinhibited structure of the `DFG-out' conformation, with the Phe residue of the DFG motif anchored within the putative ATP-binding pocket. Compound C binding dramatically alters the conformation of the activation loop, which adopts an intermediate conformation between DFG-out and DFG-in. This induced fit forms a compound-C binding pocket composed of the N-lobe, the C-lobe and the hinge of the kinase domain. The pocket partially overlaps with the putative ATP-binding pocket. These three-dimensional structures will be useful to guide drug discovery.
An investigation in dehazing compressed images and video (2010)

This paper proposes a novel method for single image dehazing that operates at a faster speed than current methods for implementation in video enhancements. We provide a comparison of our proposed dehazing method with current state of the art methods. We then consider the effect of compression by investigating the blocking and ringing artifacts in cases of applying any dehazing method before or after compression. Based on an investigation with the JPEG model, we conclude that the best dehazing performance (with less artifacts) is achieved if the dehazing is applied before compression. Simulations for both JPEG images and H.264 compressed sequences validate our conclusion.
RF coil arrays for MRI applications (2011)

The paper studies several in-house designed RF coil arrays for Low Field Magnetic Resonance Imaging (MRI) Applications. Those planar arrays, operating at around 12.5 MHz, are employed in a low-cost lost-field, 0.3 Tesla, MRI system. Scanned image will be shown.