gebhart/patrepeval huggingface dataset:
In Vitro and In Vivo Chemical Labeling of Ribosomal Proteins: A Quantitative Comparison (2012)

Thioimidates have emerged as reagents for probing the protein structure, folding, and interactions under physiological conditions. The same properties that give thioimidates biological relevance make these molecules ideal candidates for use in vivo. Through labeling of ribosomal proteins, we have quantified the in vivo and in vitro reactivity of two thioimidates: S-methylthioacetimidate (SMTA) and a novel, charge-carrying analogue, S-sulfethylthioacetimidate (SSETA). In vitro experiments demonstrate that both amidinating reagents can probe the protein structure. Under comparable in vivo conditions, SMTA is found to be membrane-permeable while SSETA is not. The use of mass spectrometry with permeant and impermeant thioimidates promises insights into the membrane topology and protein structure in the native environment.
Design, preparation, and characterization of hydrogen bonded supramolecular aggregates based on the cyanuric acid‐melamine lattice (1994)

Abstract Molecular self‐assembly is described as a strategy for synthesizing large hydrogen‐bonded supramolecular aggregates that are based on the planar lattice formed of equimolar portions of cyanuric acid and melamine. The aggregates described in this paper contain four to ten individual molecules, are stabilized by networks of 18 to 54 hydrogen bonds, and have molecular weights in the range 2.7 to 6.5 kDa. Each of these aggregates has been characterized using 1 H NMR. spectroscopy, gel permeation chromatography, and vapor pressure osmometry. Physical‐organic chemistry is used to (i) improve our criteria for the design of self‐assembling structures and (ii) develop techniques for characterizing non‐covalently bound aggregates in organic solution.
Robust magnetotelluric inversion (2014)

Author Posting. © The Author(s), 2014. This article is posted here by permission of The Royal Astronomical Society for personal use, not for redistribution. The definitive version was published in Geophysical Journal International 196 (2014): 1365-1374, doi:10.1093/gji/ggt484.
Stereochemistry and mechanism of an acid-catalyzed 1,2-phospho group migration: evidence for pseudorotation in the reaction of a phosphoric monoester (1982)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTStereochemistry and mechanism of an acid-catalyzed 1,2-phospho group migration: evidence for pseudorotation in the reaction of a phosphoric monoesterStephen L. Buchwald, Diana H. Pliura, and Jeremy R. KnowlesCite this: J. Am. Chem. Soc. 1982, 104, 3, 845–847Publication Date (Print):February 1, 1982Publication History Published online1 May 2002Published inissue 1 February 1982https://pubs.acs.org/doi/10.1021/ja00367a033https://doi.org/10.1021/ja00367a033research-articleACS PublicationsRequest reuse permissionsArticle Views224Altmetric-Citations16LEARN 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
3.4-Inch Quarter High Definition Flexible Active Matrix Organic Light Emitting Display with Oxide Thin Film Transistor (2011)

In this paper, we report a 3.4-in. flexible active matrix organic light emitting display (AMOLED) display with remarkably high definition (quarter high definition: QHD) in which oxide thin film transistors (TFTs) are used. We have developed a transfer technology in which a TFT array formed on a glass substrate is separated from the substrate by physical force and then attached to a flexible plastic substrate. Unlike a normal process in which a TFT array is directly fabricated on a thin plastic substrate, our transfer technology permits a high integration of high performance TFTs, such as low-temperature polycrystalline silicon TFTs (LTPS TFTs) and oxide TFTs, on a plastic substrate, because a flat, rigid, and thermally-stable glass substrate can be used in the TFT fabrication process in our transfer technology. As a result, this technology realized an oxide TFT array for an AMOLED on a plastic substrate. Furthermore, in order to achieve a high-definition AMOLED, color filters were incorporated in the TFT array and a white organic light-emitting diode (OLED) was combined. One of the features of this device is that the whole body of the device can be bent freely because a source driver and a gate driver can be integrated on the substrate due to the high mobility of an oxide TFT. This feature means “true” flexibility.
Abstract 044: Ddah-1 And Adma Regulate Proximal Tubular Fluid Reabsorption: Comparison Of Pharmacological Blockade Of Ddah-1 With Gene Knockdown (2014)

Background: Proximal tubule (PT) fluid reabsorption (Jv) is diminished by knockout of NOS-I or III. ADMA is an endogenous inhibitor of NOS, but its effects on tubular function are unknown. ADMA is degradated by DDAH whose type 1 isoform (DDAH-1) is richly expressed in the PT. SNIPs of DDAH-1 predict the decline of GFR in chronic kidney disease (CKD). Hypothesis: that DDAH-1 metabolizes ADMA in the PT thereby reducing its plasma concentration and enhancing Jv. Methods: Jv was measured in anesthetized rats and mice in S2 segments of the PT by direct in vivo micropuncture and microperfusion of artificial tubular fluid (ATF). Results: Addition of L-257 (10 -4 M; DDAH-1 inhibitor) vs vehicle to ATF perfusing the PT of rats for 10 mins did not affect Jv (3.4 ± 0.20 vs 3.1±0.39 nl/min/mm). However, a bolus i.v. injection (60mg/kg) of L-257 2hrs before and 10 mins of PT perfusion significantly (P&lt; 0.005) reduced Jv by 33% to 2.3±0.17 nl/min/mm and increased plasma ADMA (systemic Veh: 0.46 ± 0.030 vs. systemic L-257: 0.67 ± 0.029 μmol/l; P &lt; 0.0001) without changing SDMA. Microperfusion of ADMA (10 -4 M) or L-NAME (10 -4 M) in rats both reduced Jv significantly by &gt;40% to 2.0±0.24 and 1.8±0.22 nl/min/mm, respectively (P&lt;0.05). An IV 1 ml bolus of saline containing Transit and siRNA targeted to DDAH-1 (hydrodynamic in vivo gene silencing in mice) three days later reduced Jv significantly by 36% compared to scrambled siRNA (2.2 ± 0.16 vs 1.4 ± 0.26 nl/min/mm; P&lt;0.05). Surprisingly, PT cell-specific DDAH-1 knockdown in mice did not affect Jv significantly compared to wild type (PTC-D1WT: 1.7 ± 0.21 vs PTC-D1KO: 2.0 ± 0.15). Conclusions: PT fluid reabsorption is regulated by ADMA and its tubular metabolism by DDAH-1. The two-hour delay for L-257 to diminish Jv likely was required for accumulation of sufficient tubular ADMA to impair PT reabsorption. Whereas systemic DDAH-1 gene knockdown in mice was as effective as systemic DDAH-1 blockade with L-257 in rats in reducing Jv in the PT, lifelong deletion of PT DDAH-1 was ineffective, suggesting robust adaptive mechanisms that restore PT reabsorption. Thus, L-257 is a novel regulator of PT function. SNIPs that alter DDAH-1 in the PT may change tubular function and thereby contribute to CKD progression.
Improving Melanoma Classification by Integrating Genetic and Morphologic Features (2008)

Refined morphological classification of primary melanomas can be used to improve existing melanoma classifications by forming subgroups that are genetically more homogeneous and likely to differ in important clinical variables such as outcome and pattern of metastasis. We expect this information to improve classification and facilitate stratification for therapy as well as retrospective analysis of existing trial data.
Highly efficient room temperature spin injection in a metal-insulator-semiconductor light emitting diode (2002)

We demonstrate highly efficient spin injection at low and room temperature in an AlGaAs/GaAs semiconductor heterostructure from a CoFe/AlOx tunnel spin injector. We use a double-step oxide deposition for the fabrication of a pinhole-free AlOx tunnel barrier. The measurements of the circular polarization of the electroluminescence in the Oblique Hanle Effect geometry reveal injected spin polarizations of at least 24% at 80K and 12% at room temperature.
WE-D-BRB-01: Fragile Proteins and the Origins of Cancer (2015)

Discoveries in cancer research are impacting patients through development of new therapeutics and better diagnostic tools. However, there is still a lack of understanding about heterogeneity in patient response to these therapeutics, optimizing therapeutic dosing schedules, or predicting complex metastatic patterns due to the complexity of the disease. Heterogeneity of patient response to treatment stems from the intricate interactions with the microenvironment, and distant organs and other environmental pressures including low oxygen, high acidity, and toxic drugs. To deconvolute some of this complexity physical scientists are using intricate tools to improve cancer diagnosis and predict drug resistance. Also to predict tumor growth and response to therapeutics, computational scientists are developing mathematical tools that link physical sciences or evolutionary sciences approaches with experimental and clinical data. These models yield predictions based on initial parameters obtained from patient clinical data, such as noninvasive imaging. This session will highlight the utilization of these mathematical and physical tools to predict patient response to treatment options, predict the optimal drug dosing schedule, and improve cancer diagnosis. This approach could be further enhanced by developing tools and models to chart the progress of stressed, aging tissue towards the progression to uncontrolled cell growth and mutational meltdown even before the diagnosis. Learning Objectives: 1. To learn about treatment response heterogeneity 2. To learn about tumor evolutionary capabilities 3. To learn about mathematical tools that link physical sciences with experimental and clinical data
N‐Carboxyanhydride Polymerization of Glycopolypeptides That Activate Antigen‐Presenting Cells through Dectin‐1 and Dectin‐2 (2018)

Abstract The C‐type lectins dectin‐1 and dectin‐2 contribute to innate immunity against microbial pathogens by recognizing their foreign glycan structures. These receptors are promising targets for vaccine development and cancer immunotherapy. However, currently available agonists are heterogeneous glycoconjugates and polysaccharides from natural sources. Herein, we designed and synthesized the first chemically defined ligands for dectin‐1 and dectin‐2. They comprised glycopolypeptides bearing mono‐, di‐, and trisaccharides and were built through polymerization of glycosylated N ‐carboxyanhydrides. Through this approach, we achieved glycopolypeptides with high molecular weights and low dispersities. We identified structures that elicit a pro‐inflammatory response through dectin‐1 or dectin‐2 in antigen‐presenting cells. With their native proteinaceous backbones and natural glycosidic linkages, these agonists are attractive for translational applications.
Lignin–Chitosan Gel Polymer Electrolytes for Stable Zn Electrodeposition (2023)

Electrochemical energy storage technologies offer means to transition toward a decarbonized society and carbon neutrality by 2050. Compared to conventional lithium-ion batteries, aqueous zinc-ion chemistries do not require scarce materials or toxic and flammable organic-based electrolytes to function, making them favorable contenders in the scenario of intensifying climate change and supply chain crisis. However, environmentally benign and bio-based materials are needed to substitute fossil-based battery materials. Accordingly, this work taps into the possibilities of lignin together with chitosan to form gel polymer electrolytes (GPEs) for zinc-ion chemistries. A simple fabrication process enabling free-standing sodium lignosulfonate–chitosan and micellar lignosulfonate–kraft lignin–chitosan GPEs with diameters exceeding 80 mm is developed. The GPEs combine tensile strength with ductility, reaching Young’s moduli of 55 ± 4 to 940 ± 63 MPa and elongations at break of 14.1 ± 0.2 to 43.9 ± 21.1%. Competitive ionic conductivities ranging from 3.8 to 18.6 mS cm–1 and electrochemical stability windows of up to +2.2 V vs Zn2+/Zn were observed. Given the improved interfacial adhesion of the GPEs with metallic Zn promoted by the anionic groups of the lignosulfonate, a stable cycling of the Zn anode is obtained. As a result, GPEs can operate at 5000 μA cm–2 with no short-circuit and Coulombic efficiencies above 99.7%, outperforming conventional separator–liquid electrolyte configurations such as the glass microfiber separator soaked into 2 M ZnSO4 aqueous electrolyte, which short-circuits after 100 μA cm–2. This work demonstrates the potential of underutilized biorefinery side-streams and marine waste as electrolytes in the battery field, opening new alternatives in the sustainable energy storage landscape beyond LIBs.
On a model of indexability and its bounds for range queries (2002)

We develop a theoretical framework to characterize the hardness of indexing data sets on block-access memory devices like hard disks. We define an indexing workload by a data set and a set of potential queries. For a workload, we can construct an indexing scheme, which is a collection of fixed-sized subsets of the data. We identify two measures of efficiency for an indexing scheme on a workload: storage redundancy, r (how many times each item in the data set is stored), and access overhead, A (how many times more blocks than necessary does a query retrieve).For many interesting families of workloads, there exists a trade-off between storage redundancy and access overhead. Given a desired access overhead A , there is a minimum redundancy that any indexing scheme must exhibit. We prove a lower-bound theorem for deriving the minimum redundancy. By applying this theorem, we show interesting upper and lower bounds and trade-offs between A and r in the case of multidimensional range queries and set queries.
Transplantation of Embryonic Neural Stem/Precursor Cells Overexpressing BM88/Cend1 Enhances the Generation of Neuronal Cells in the Injured Mouse Cortex (2009)

The intrinsic inability of the central nervous system to efficiently repair traumatic injuries renders transplantation of neural stem/precursor cells (NPCs) a promising approach towards repair of brain lesions. In this study, NPCs derived from embryonic day 14.5 mouse cortex were genetically modified via transduction with a lentiviral vector to overexpress the neuronal lineage-specific regulator BM88/Cend1 that coordinates cell cycle exit and differentiation of neuronal precursors. BM88/Cend1-overexpressing NPCs exhibiting enhanced differentiation into neurons in vitro were transplanted in a mouse model of acute cortical injury and analyzed in comparison with control NPCs. Immunohistochemical analysis revealed that a smaller proportion of BM88/Cend1-overexpressing NPCs, as compared with control NPCs, expressed the neural stem cell marker nestin 1 day after transplantation, while the percentage of nestin-positive cells was significantly reduced thereafter in both types of cells, being almost extinct 1 week post-grafting. Both types of cells did not proliferate up to 4 weeks in vivo, thus minimizing the risk of tumorigenesis. In comparison with control NPCs, Cend1-overexpressing NPCs generated more neurons and less glial cells 1 month after transplantation in the lesioned cortex whereas the majority of graft-derived neurons were identified as GABAergic interneurons. Furthermore, transplantation of Cend1-overexpressing NPCs resulted in a marked reduction of astrogliosis around the lesioned area as compared to grafts of control NPCs. Our results suggest that transplantation of Cend1-overexpressing NPCs exerts beneficial effects on tissue regeneration by enhancing the number of generated neurons and restricting the formation of astroglial scar, in a mouse model of cortical brain injury.
The ETS transcription factor ETV6 constrains the transcriptional activity of EWS–FLI to promote Ewing sarcoma (2023)

Transcription factors (TFs) are frequently mutated in cancer. Paediatric cancers exhibit few mutations genome-wide but frequently harbour sentinel mutations that affect TFs, which provides a context to precisely study the transcriptional circuits that support mutant TF-driven oncogenesis. A broadly relevant mechanism that has garnered intense focus involves the ability of mutant TFs to hijack wild-type lineage-specific TFs in self-reinforcing transcriptional circuits. However, it is not known whether this specific type of circuitry is equally crucial in all mutant TF-driven cancers. Here we describe an alternative yet central transcriptional mechanism that promotes Ewing sarcoma, wherein constraint, rather than reinforcement, of the activity of the fusion TF EWS-FLI supports cancer growth. We discover that ETV6 is a crucial TF dependency that is specific to this disease because it, counter-intuitively, represses the transcriptional output of EWS-FLI. This work discovers a previously undescribed transcriptional mechanism that promotes cancer.
Advanced receiver architectures and I/Q signal processing (2004)

The evolution of wireless communications receivers from the traditional superheterodyne architecture to more advanced structures with better integrability is largely based on the concept of complex or I/Q signals. In this paper, we discuss the role of I/Q signal processing in different receivers, with emphasis on I/Q imbalance effects. Also the use of adaptive DSP algorithms for I/Q imbalance compensation in different receiver structures is analyzed, and some measurement-based results concerning the performance of these techniques with practical analog front-ends are presented.
Simulation-Based Evaluation and Optimization of Control Strategies in Buildings (2018)

Over the last several years, a great amount of research work has been focused on the development of model predictive control techniques for the indoor climate control of buildings, but, despite the promising results, this technology is still not adopted by the industry. One of the main reasons for this is the increased cost associated with the development and calibration (or identification) of mathematical models of special structure used for predicting future states of the building. We propose a methodology to overcome this obstacle by replacing these hand-engineered mathematical models with a thermal simulation model of the building developed using detailed thermal simulation engines such as EnergyPlus. As designing better controllers requires interacting with the simulation model, a central part of our methodology is the control improvement (or optimisation) module, facilitating two simulation-based control improvement methodologies: one based in multi-criteria decision analysis methods and the other based on state-space identification of dynamical systems using Gaussian process models and reinforcement learning. We evaluate the proposed methodology in a set of simulation-based experiments using the thermal simulation model of a real building located in Portugal. Our results indicate that the proposed methodology could be a viable alternative to model predictive control-based supervisory control in buildings.
Quantum Energy Regression using Scattering Transforms (2015)

We present a novel approach to the regression of quantum mechanical energies based on a scattering transform of an intermediate electron density representation. A scattering transform is a deep convolution network computed with a cascade of multiscale wavelet transforms. It possesses appropriate invariant and stability properties for quantum energy regression. This new framework removes fundamental limitations of Coulomb matrix based energy regressions, and numerical experiments give state-of-the-art accuracy over planar molecules.
The role of gender in association between inhibition capacities and risky decision making (2018)

These findings do not support the hypothesis that risky decisions are due to impaired inhibitory control. Further studies are needed to identify the cognitive mechanisms involved in the tendency to make risky decisions.
1348. A Novel Host-Protein Signature Comprising TRAIL, IP-10 and CRP Differentiates Bacterial from Viral Infection in COPD Patients with Suspected Lower Respiratory Tract Infection (2021)

Abstract Background Identifying infectious etiology is often challenging, yet essential for patient management, including antibiotic use. Studies have shown that a host signature comprising TNF-related apoptosis induced ligand (TRAIL), interferon gamma induced protein-10 (IP-10) and C-reactive protein (CRP) accurately differentiates bacterial from viral infection with negative predictive value &amp;gt;98%. Performance data was lacking in chronic obstructive pulmonary disease (COPD) patients with suspected lower respiratory tract infection (LRTI). Methods Adults aged &amp;gt;18 years with suspected LRTI were prospectively recruited at 3 medical centers (OBSERVER; grant #684589; NCT003011515). Reference standard infection etiology was adjudicated by 3 independent experts based on clinical, laboratory, microbiological, radiological and follow-up data. Host signature generates a bacterial likelihood score (0-100), providing three results: viral (0-35), equivocal (35-65) and bacterial (65-100). Experts were blinded to the signature result. Results Out of 583 adults recruited with suspected LRTI, 422 met infectious criteria, of whom 48 had a recorded history of COPD. 19 cases were adjudicated by the experts as bacterial, 14 as viral and 15 were indeterminate (Figure 1). The mean age was 68.2 years (standard deviation 12.3); 33 (68.8%) presented after two or more days of symptoms and 38 (79.2%) were hospitalized for a median of 6 days. 15 (31.2%) were female. For the patients adjudicated bacterial or viral labels (n=33), the discharge diagnoses were: COPD exacerbation, 12 cases (36.4%); pneumonia, 12 cases (36.4%) (3.0%); acute bronchitis, 2 cases (6.1%); upper RTI ,1 case; unspecified viral infection 1 case (3.0%); or other, 5 cases (15.2%). Host signature correctly classified all 19 bacterial cases and 8 of the viral cases, providing accurate etiology labels for 27/33 COPD patients with reference standard labels (81.8%). The remaining 6 viral cases received equivocal scores (18.2%). COPD patient enrollment and etiology labels in the Observer study Conclusion Host signature accurately differentiates between bacterial and viral infections in patients with COPD history, supporting potential to improve management among these patients frequently admitted for RTIs. Disclosures Michal Stein, MeMed (Employee) Meital Paz, MD, MeMed (Employee) Tanya Gottlieb, PhD, MeMed (Employee, Shareholder) Eran Barash, MA, MeMed (Employee) Roy Navon, MSc, MeMed (Employee, Shareholder) Einat Moscoviz, BSc+ MBA, MeMed (Employee) Tahel Ilan Ber, MD, MeMed (Employee, Shareholder) Liran Shani, MD, MeMed (Employee) Olga Boico, PhD, MeMed (Employee) Einav Simon, PhD, MeMed (Employee, Shareholder) Noa Avni, PhD, MeMed (Employee) Kfir Oved, MD, PhD, MeMed (Board Member, Employee, Shareholder) Eran Eden, PhD, MeMed (Board Member, Employee, Shareholder)