gebhart/patrepeval huggingface dataset:
Characterization of Glutamine Deamidation by Long-Length Electrostatic Repulsion-Hydrophilic Interaction Chromatography-Tandem Mass Spectrometry (LERLIC-MS/MS) in Shotgun Proteomics (2016)

Deamidation of glutamine (Gln) residues is a spontaneous or enzymatic process with significant implications in aging and human pathology. Although some methods are available to identify the γ/α-glutamyl products of deamidation, none of these methods allows the characterization of this post-translational modification (PTM) from complex biological samples by shotgun proteomics. Here we present LERLIC-MS/MS, a chromatographic strategy that uses a long (50 cm) anion-exchange capillary column operating in the electrostatic repulsion-hydrophilic interaction mode (ERLIC) and coupled directly to tandem mass spectrometry (MS/MS) for proteome analysis in a single injection. Profiling of soluble extracts of brain tissues by LERLIC-MS/MS distinguished for the first time γ/α-glutamyl isomers of deamidation, encountering a 1.7 γ/α-glutamyl ratio for most Gln deamidation products. A detailed analysis of any deviation from that observed ratio allowed the identification of transglutaminase-mediated γ-glutamyl isomers as intermediate products of transamidation. Furthermore, LERLIC-MS/MS was able to simultaneously separate Gln and asparagine (Asn) deamidation products even for those peptides showing multiple deamidated proteoforms. The characterization of Asn deamidated residues by LERLIC-MS/MS also uncovered novel PIMT (protein L-isoaspartyl methyltransferase) substrate proteins in human brain tissues that deviated from the expected 3:1 isoAsp/Asp ratio. Taken together, our results demonstrate that LERLIC-MS/MS can be used to perform an in-depth study of protein deamidation on a global proteome scale. This new strategy should help to elucidate the biological implications of deamidation in aging and disease conditions.
How to DP-fy ML: A Practical Tutorial to Machine Learning with Differential Privacy (2023)

Machine Learning (ML) models are ubiquitous in real world applications and are a constant focus of research. At the same time, the community has started to realize the importance of protecting the privacy of models' training data.
Gene Mapping by Chromosome Microdissection and Microisolation in the Chicken (1996)

A chromosome microdissection and microisolation technique in combination with filter hybridization was developed for chromosomal localization of cloned chicken genes. The DNA was obtained from microdissected chromosome regions of metaphase spreads. Dissected DNA was amplified by polymerase chain reaction (PCR). The chicken MHC gene located on the nucleolar chromosome and beta-actin gene located on chromosome 2q were chosen as tests for the procedure and then detected by dot blot analysis using amplified chromosomal DNA probed with biotinylated DNA. The study establishes the technique of using chromosome microdissection and microisolation for localization of cloned genes as a complementary or alternative approach to both in situ DNA/chromosome hybridization and fluorescent in situ hybridization.
Angular dependence of isotope enrichment in ultrafast laser ablation plumes (2001)

Summary form only given. It has been observed that isotopic enrichment of light ions occurs in the central portion of laser ablation plumes when such plasmas are formed with ultrafast laser pulses. It was found that the separation of lighter isotopes from heavier isotopes occurs on axis in the expanding plasma plume. The relative independence of the enrichment on axis among different elements and other similarities in the ion distributions have indicated a universality to this effect that lends credence to a possible plasma centrifuge model. In the present work, we examine the angular distribution of isotope enrichments and investigate the dependence on laser parameters and on the atomic-transport mean free path between collisions. The angular dependence is studied as a function of ion energy, ion charge state, and atomic mass.
Laser action in polymeric gain media containing scattering particles (1996)

Optical pumping of polymer sheets containing laser dyes and TiO(2) nanoparticle scatterers results in emissions that exhibit laser behavior with linewidths as low as 4 nm. The input-output characteristics, effects of index matching on the emission, damage thresholds, wavelength stability, and possible applications of these new materials are discussed.
Polycomb complexes in stem cells and embryonic development (2013)

Polycomb group (PcG) proteins are epigenetic modifiers involved in controlling gene repression. Organized within multiprotein complexes, they regulate developmental genes in multiple cell types and tissue contexts, including embryonic and adult stem cells, and are essential for cell fate transitions and proper development. Here, we summarize recent breakthroughs that have revealed the diversity of PcG complexes acting in different cell types and genomic contexts. Intriguingly, it appears that particular PcG proteins have specific functions in embryonic development, in pluripotent stem cells and in reprogramming somatic cells into a pluripotent-like state. Finally, we highlight recent results from analyzing PcG protein functions in multipotent stem cells, such as neural, hematopoietic and epidermal stem cells.
Optimization of Benzoisothiazole dioxide inhibitory activity of the NS5B polymerase of HCV genotype 4 using ligand-steered homological modeling, reaction-driven scaffold-hopping and E-novo workflow (2011)

Infection caused by hepatitis C virus (HCV) is a significant world health problem for which novel therapies are in urgent demand. The virus is highly prevalent in the Middle East and Africa particularly Egypt with more than 90% of infections due to genotype 4. Nonstructural (NS5B) viral proteins have emerged as an attractive target for HCV antivirals discovery. A potent class of inhibitors having benzisothiazole dioxide scaffold has been identified on this target, however they were mainly active on genotype 1 while exhibiting much lowered activity on other genotypes due to the high degree of mutation of its binding site. Based on this fact, we employed a novel strategy to optimize this class on genotype 4. This strategy depends on using a refined ligand-steered homological model of this genotype to study the mutation binding energies of the binding site amino acid residues, the essential features for interaction and provide a structure-based pharmacophore model that can aid optimization. This model was applied on a focused library which was generated using a reaction-driven scaffold-hopping strategy. The hits retrieved were subjected to Enovo pipeline pilot optimization workflow that employs R-group enumeration, core-constrained protein docking using modified CDOCKER and finally ranking of poses using an accurate molecular mechanics generalized Born with surface area method.
Molecular Analysis of an IncF ColV-Like Plasmid Lineage That Carries a Complex Resistance Locus with a Trackable Genetic Signature (2020)

IncF ColV plasmids are important plasmid incompatibility group that are currently restricted to the Enterobacteriaceae. These plasmids carry an important repertoire of virulence-associated genes (VAGs) that contribute to the ability of avian pathogenic <i>Escherichia coli</i> to cause disease in poultry. VAGs found on ColV plasmids have also been linked to urosepsis and meningitis in humans but the mechanisms that elicit these disease conditions are not well understood. Recently we described the sequence of a ColV plasmid pSDJ2009-52F that carried the typical repertoire of VAGs and a complex resistance gene locus flanked by IS<i>26</i>, an insertion element that plays an important role in mobilizing antibiotic resistance genes on plasmids and genomic islands. We recovered complete ColV-like plasmid sequences from public databases that shared >80% sequence identity with pSDJ2009-52F in geographically diverse regions of the world over a 20-year timeframe. Previously we noted that pSDJ2009-52F carries a unique genetic signature in the class 1 integron within the complex resistance locus that was presumably created by the action of IS<i>26</i>. Here we show that most ColV-like plasmids that are closely related to pSDJ2009-52F also carry the same signature. Our studies provide insight into how these signature-bearing plasmids and the mobile genetic elements they carry traffic between <i>E. coli</i> sequence types over large geographic distances.
Zero-v Cellular Honeycomb Flexible Skins for One-Dimensional Wing Morphing (2007)

Morphing aircraft wings require flexible skins that can undergo large strains, have low in-plane stiffness and very high out-of-plane flexural bending stiffness. The large strain capability is especially important for gross morphing applications such as span change where the skins may be required to undergo axial strains of the order of 50% or greater. Low in-plane stiffness allows morphing to be accomplished at a reasonable energy cost while high bending stiffness ensures that skin sections between supports do not suffer from significant out-of-plane deformation under aerodynamic pressure loads. One solution proposed is to use sandwiched skins with flexible face-sheets and cellular cores. The cellular cores can be designed to be high-strain capable, have low axial stiffness and high bending stiffness. For some morphing applications (for example, wing span change or chord or camber change), the required deformation is mostly one-dimensional. In such a case, cellular cores with zero Poisson’s ratios, which do not display contraction (or bulge) perpendicular to the morphing direction are desired. Restraining the Poisson’s contraction (or bulge) of a “conventional” cellular honeycomb results in the effective axial stiffness in the morphing direction increasing by over an order of magnitude. This paper proposes “hybrid” and “accordion” cellular honeycombs, where regular cells (with positive cell angle) and auxetic cells (with negative cell angle) are combined so as to provide large strain capability in one direction (the morphing direction) together with zero Poisson’s ratio. Cellular material theory is extended to allow for the analysis of such hybrid and accordion cellular honeycombs, and the results are validated using the Finite Element code ANSYS. Thereafter, the properties and behavior of the hybrid and accordion zero Poisson’s ratio cellular honeycombs are thoroughly examined vis-a-vis conventional cellular honeycombs which have single cell-type.
Oxygen-tolerant Strain of Chlorella sorokiniana (1969)

An oxygen-tolerant strain (OTS) of Chlorella sorokiniana was isolated by growing and continuously subculturing the oxygen-sensitive strain (OSS) in growth medium bubbled continuously with 95% O(2)-5% CO(2). Under these conditions, 6 to 8 hr were required before the OSS began to grow. The growth rates of the OTS and the OSS were the same when grown in an atmosphere of air-5% CO(2), and the growth rate of the OTS was the same when aerated with 95% O(2)-5% CO(2) and air-5% CO(2). The adaptive process was irreversible since serial transfers of the OTS grown with air-5% CO(2) did not alter the ability of the OTS to grow with 95% O(2)-5% CO(2). Inasmuch as photosynthesis in the OTS and the OSS was inhibited to a similar extent by oxygen and the adaptive process occurred heterotrophically in the absence of photosynthesis, it was concluded that the adaptive process was independent of photosynthesis. Morphological differences between the OTS and the OSS are presented and discussed with respect to the adaptive process.
Thiol-inducible direct fluorescence monitoring of drug release (2012)

A new bifunctional compound NCC, which undergoes thiol-mediated disulfide cleavage after cell entry, produces a red-shifted fluorescent emission in the cytosol and releases free active DNA alkylating agent CLB into the nucleus, and finally leads to DNA damage and cell death.
Corrigendum: Regioselective Preparation of Functionalized exo‐Methylene‐ cyclopentanes and exo‐Methylenepyrrolidines via Silaborative Carbocyclization of 1,6‐Enynes (2011)

In the full paper by Martin Gerdin, Sailendra Kumar Nadakudity, Christin Worch, and Christina Moberg in Issue 14–15, 2010, pp. 2559–2570 (DOI: 10.1002/adsc.201000434), incorrect stereochemical descriptors (E instead of Z) were given for exo-methylenecyclopentanes 16, 18, 20 and 22. The figures show the correct Z-stereochemistry. The authors apologize for this error.
Improved Uniformity of Resistive Switching Behaviors in HfO[sub 2] Thin Films with Embedded Al Layers (2009)

A technical solution is presented to improve the uniformity of -based resistive switching memory by embedding thin Al layers between and electrode layers. Compared with those pure devices, a remarkably improved uniformity of switching parameters such as forming voltages, set voltages, and resistances in high/low states was demonstrated in the devices with embedded Al layers. Al atoms are assumed to diffuse into thin films and are intended to localize oxygen vacancies due to reduced oxygen vacancy formation energy, thus stabilizing the generation of conductive filaments, which helps improve the resistive switching uniformity.
Optical Phase Control of Ultrashort Femtosecond Pulse (1998)

Abstract : When optical pulses achieve durations as short as a few optical cycles, their propagation and nonlinear interaction properties will begin to depend on the phase of the optical waveform relative to its envelope. We have recently demonstrated the feasibility of controlling the relative optical phase of successive pulses from a laser and propose here to study the effect of that control on the pulse formation process itself as well as on other nonlinear optical processes. Phase stabilized Ti:sapphire and Cr:YAG lasers wilt be developed for experiments in two different wavelength regimes.
Double‐Blind, Multicenter Evaluation of Lansoprazole and Amoxicillin Dual Therapy for the Cure of Helicobacter pylori Infection (1996)

Treatment with amoxicillin plus lansoprazole, 30 mg tid, led to cure of H. pylori infection in 67% of patients with active or recently healed duodenal ulcer.
DAMPAK KERUSAKAN LINGKUNGAN AKIBAT AKTIFITAS PEMBANGUNAN PERUMAHAN (Studi Kasus di Perumahan Palaran City Oleh PT.Kusuma Hady Property) (2013)

Pembangunan yang terus bekembang yang terjadi di kota Samarinda sangatlah berpengaruh terhadap kestabilan kondisi lingkungan. Dan perlu diketahui semakin meningkatnya upaya pembangunan akan menyebabkan semakin meningkatnya dampak terhadap lingkungan. Keadaan ini mengindikasikan  diperlukannya upaya pengendalian dampak lingkungan hidup, sehingga resiko kerusakan terhadap lingkungan hidup dapat ditekan sekecil mungkin. pihak pemerintah daerah maupun swasta yang mengelola pembangunan perumahan hendaknya menyediakan sarana untuk mendukung perkembangan pembangunan perumahan penduduk dan menganalisis dampak yang diakibatkan dari pengembangan pembangunan tersebut. Penelitian ini merumuskan masalah mengenai problematika hukum akibat pembangunan perumahan Palaran City oleh PT.Kusuma Hady Property dan upaya pengawasan Pemerintah terhadap kerusakan lingkungan akibat pembangunan perumahan Palaran City. Dengan tujuan untuk mengetahui problematika hukum yang terjadi serta upasa pengawasan pemerintah terhadap kerusakan lingkungan yang terjadi. Dalam pembahasan di uraikan bahwa Kerusakan yang terjadi akibat pembangunan perumahan Palaran City jelas melanggar Undang-undang Nomor 32 Tahun 2009 tentang Perlindungan dan Pengelolaan Lingkungan Hidup pasal 69 ayat (1) huruf (a). PT. Kusuma Hady Property sebagai pihak pengelola perumahan Palaran City telah melakukan kelalaian yang menyebabkan kerusakan di lingkungan sekitar perumahan warga yag letaknya bersebelahan dengan perumahan Palaran City. Secara yuridis hal ini telah di atur oleh Pemerintah Kota Samarinda di dalam Peraturan Daerah Kota Samarinda Nomor 29 tahun 2003 tentang Ketentuan Pengendalian Kegiatan Usaha Yang Mengubah Bentuk Lahan Dalam Wilayah Kota Samarinda Pasal 6 ayat (1). Pemerintah melalui BLH Kota Samarinda melakukan pengawasan terhadap pemulihan kerusakan lingkungan serta ganti rugi kepada warga yang terkena dampak kerusakan lingkungan dan mewajibkan kepada pihak pengelola PT. Kusuma Hady Property untuk melaporkan progresnya ke Badan Lingkungan Hidup Kota Samarinda. Pihak Badan Lingkungan Hidup sebagai mediator melakukan mediasi dengan warga dan PT. Kusuma Hady Property sebagai pihak pengembang perumahan, dan menghasikan kesepakatan yang mewajibkan pihak pengembang Perumahan Palaran City untuk membenahi kerusakan lingkungan yang terjadi serta memberikan dan kompensasi ganti rugi kerusakan bagi warga yang terkena dampak. Kerusakan lingkungan/lahan di rumah warga adalah sebagai dampak yang terjadi akibat pembangunan perumahan Palaran City sebaiknya biasa menjadi perhatian kusus bagi Badan Lingkungan Hidup Kota Samarinda agar lebih memperhatikan kegiatan pembangunan perumahan-perumahan yang terjadi di kota samarinda. Kata kunci : Dampak, Perumahan, Kerusakan Lingkungan.
SIRT1 promotes DNA repair activity and deacetylation of Ku70 (2007)

Human SIRT1 controls various physiological responses including cell fate, stress, and aging, through deacetylation of its specific substrate protein. In processing DNA damage signaling, SIRT1 attenuates a cellular apoptotic response by deacetylation of p53 tumor suppressor. The present study shows that, upon exposure to radiation, SIRT1 could enhance DNA repair capacity and deacetylation of repair protein Ku70. Ectopically over-expressed SIRT1 resulted in the increase of repair of DNA strand breakages produced by radiation. On the other hand, repression of endogenous SIRT1 expression by SIRT1 siRNA led to the decrease of this repair activity, indicating that SIRT1 can regulate DNA repair capacity of cells with DNA strand breaks. In addition, we found that SIRT1 physically complexed with repair protein Ku70, leading to subsequent deacetylation. The dominant-negative SIRT1, a catalytically inactive form, did not induce deacetylation of Ku70 protein as well as increase of DNA repair capacity. These observations suggest that SIRT1 modulates DNA repair activity, which could be regulated by the acetylation status of repair protein Ku70 following DNA damage.
Epidemiological Prevalence of Phenotypical Resistances and Mobilised Colistin Resistance in Avian Commensal and Pathogenic E. coli from Denmark, France, The Netherlands, and the UK (2022)

Colistin has been used for the treatment of non-invasive gastrointestinal infections caused by avian pathogenic E. coli (APEC). The discovery of mobilised colistin resistance (mcr) in E. coli has instigated a One Health approach to minimise colistin use and the spread of resistance. The aim of this study was to compare colistin susceptibility of APECs (collected from Denmark n = 25 and France n = 39) versus commensal E. coli (collected from the Netherlands n = 51 and the UK n = 60), alongside genetic (mcr-1−5) and phenotypic resistance against six other antimicrobial classes (aminoglycosides, cephalosporins, fluoroquinolones, penicillins, sulphonamides/trimethoprim, tetracyclines). Minimum inhibitory concentration (MIC) values were determined using a broth microdilution method (EUCAST guidelines), and phenotypic resistance was determined using disk diffusion. Colistin MIC values of APEC were significantly lower than those for commensals by 1 dilution (p < 0.0001, Anderson-Darling test), and differences in distributions were observed between countries. No isolate carried mcr-1−5. Three phenotypically resistant isolates were identified in 2/62 APEC and 1/111 commensal isolates. Gentamicin or gentamicin−ceftriaxone co-resistance was observed in two of these isolates. This study showed a low prevalence of phenotypic colistin resistance, with no apparent difference in colistin resistance between commensal E. coli strains and APEC strains.
Generative locally linear embedding: A module for manifold unfolding and visualization (2021)

Data often have nonlinear patterns in machine learning. One can unfold the nonlinear manifold of a dataset for low-dimensional visualization and feature extraction. Locally Linear Embedding (LLE) is a nonlinear spectral method for dimensionality reduction and manifold unfolding. It embeds data using the same linear reconstruction weights as in the input space. In this paper, we propose an open source module which not only implements LLE, but also includes implementations of two generative LLE algorithms whose linear reconstruction phases are stochastic. Using this module, one can generate as many manifold unfoldings as desired for data visualization or feature extraction.
CONTRIBUTION OF MODAL AERODYNAMIC DAMPING IN FLUTTER OF SUSPENSION BRIDGES WITH TEMPORARY MASS (1999)

モード毎の空力減衰寄与を解析し, 暴風時質量付加型吊橋のフラッター特性を検討した. その結果, 質量を付加しない状態すなわち従来型吊橋の場合, 鉛直たわみ対称3次モードが, 従来からの基本2モード (鉛直たわみ, ねじれ対称1次モード) に加えて重要となり, それはフラッター発現風速を上昇させること, 質量を付加した暴風時質量付加型吊橋の場合, 質量付加パターンによっては質量を大きくすると却ってフラッター発現風速の低下を招くことがあるが, それはねじれモードを伴った水平たわみモードが誘因となっていること等が明らかにされた.
Illuminant-invariant model-based road segmentation (2008)

Road segmentation is an essential functionality for supporting advanced driver assistance systems (ADAS) such as road following or vehicle detection and tracking. Significant efforts have been made in order to solve this task using vision-based techniques. One of the major challenges of these techniques is dealing with lighting variations, especially shadows. Many of the approaches presented within this field use ad-hoc mechanisms applied after an initial segmentation to recover shadowed road patches. In this paper, we present an innovative method to obtain a road segmentation algorithm robust to extreme shadow conditions. The novelty of the proposal is the use of a shadowless feature space in combination with a model-based region growing algorithm. The former projects the color images such that the shadow effect is greatly attenuated. The latter uses histogram models to label the pixels as belonging to the road or to the background. These models are constructed on a frame by frame basis independently of the road shape to avoid limitations when addressing unstructured roads. The results presented show the validity of our approach.
Expanding Boundaries - Introduction of a Dynamic Interpretation of Building LCA Results: The Case of the Smart Living (Lab) Building in Fribourg, Switzerland – E. Hoxha, T. Jusselme, M. Andersen, E. Rey (2016)

Sustainability, Urban Energy Systems, Spatial Energy Planning, Renewable Energy, Urban Design, Energy Hub, Urban Planning, Renovation Strategy, Sustainable Architectural Design, Building Material, Eco-Efficiency, Material Efficiency Expanding Boundaries