gebhart/patrepeval huggingface dataset:
Macrophage activation of cGAS and TRIM5 distinguish pandemic and non-pandemic HIV (2022)

SUMMARY Pandemic viruses remain a global threat to health and economics but how they adapt to become pandemic remains poorly understood. Here we compare pandemic HIV-1(M) and non-pandemic HIV-(O) and HIV-2 strains finding that non-pandemic HIV replicate poorly in myeloid cell models due to activation of cGAS and TRIM5, and ensuing antiviral responses. We use phylogenetics and viral capsid structural biology to define specific differences between pandemic and non-pandemic HIV capsids and demonstrate that their genetic reversal in HIV-1(M) mutants causes TRIM5, cGAS and innate immune activation. We propose a model in which the parental lineage of pandemic HIV-1(M) has uniquely evolved a dynamic capsid that avoids activation of cGAS and TRIM5 to establish cloaked replication in myeloid cells. The unique adaptations of the pandemic virus lineage suggests a role in effective human-to-human transmissibility and highlight the importance of avoiding innate immune activation during pandemic human-to-human viral transmission.
Liver Support Through Hepatic Tissue Engineering (1993)

Tissue engineering is a relatively new field which brings together several disciplines, including bioengineering, molecular and cellular biology and clinical medicine, with the ultimate goal of producing tissue or organ substitutes. The spectrum of applications of tissue engineering is indeed wide from artificial skin substitutes (Bell et al., 1991) and transplantable cell-polymer matrices (Cima et al., 1991) to bioartificial organs such as the bioartificial liver and bioartificial pancreas (Yarmush et al.,1992a; 1992b; Colton and Avgoustiniatos, 1992). All of these technologies have a number of common aspects, such as (1) the identification of reliable and efficient sources of cells and isolation of cells from tissues, (2) means of culture and preservation of cells, and (3) tissue design.
Sampling Theory: Beyond Bandlimited Systems (2015)

Covering the fundamental mathematical underpinnings together with key principles and applications, this book provides a comprehensive guide to the theory and practice of sampling from an engineering perspective. Beginning with traditional ideas such as uniform sampling in shift-invariant spaces and working through to the more recent fields of compressed sensing and sub-Nyquist sampling, the key concepts are addressed in a unified and coherent way. Emphasis is given to applications in signal processing and communications, as well as hardware considerations, throughout. With 200 worked examples and over 200 end-of-chapter problems, this is an ideal course textbook for senior undergraduate and graduate students. It is also an invaluable reference or self-study guide for engineers and students across industry and academia
Probing ultrafast nano-localized plasmonic fields via XUV light generation (2010)

We present a systematic investigation into the conditions required for the production of XUV light via nanoplasmonic enhanced high harmonic generation in metallic spheroids. Control over the temporal response of the plasmonic fields, and therefore the resulting XUV radiation, is achieved through the nanostructure configuration and the carrier envelope phase of the driving laser pulse. Coupled symmetric structures are shown to produce sufficient localized field enhancement and relatively long exponential plasmon decay times leading to the characteristic high harmonic spectra. In contrast coupled asymmetric structures have a much broader resonance and a highly non-uniform plasmon response in the temporal domain.
Miniaturized UV Fluorescence Collection Optics Integrated with Ion Trap Chips. (2016)

Abstract not provided.
Towards solid batteries operating at ambient temperature: composite polymer electrolytes based on LLZO in a cross-linked PEO matrix (2018)

Possible concerns about the safety of rechargeable lithium metal batteries has postponed their introduction into the smart electronics or automotive industries and have promoted advances in the field of non-flammable solid electrolytes. Among the oxide ceramic super lithium ion conductors, garnet-type Li7La3Zr2O12 (LLZO) has recently attracted much attention because of its relatively high ionic conductivity at room temperature (&gt;10-4 S cm-1), negligible electronic conductivity and absence of harmful decomposition products upon contact with atmospheric moisture. Anyway, processing LLZO in pellets by sintering, results in brittle and more or less porous electrolytes, which often display poor interfacial contact with Li metal electrodes. Moreover, there are some reports of lithium dendrite growth and instability towards the cathode material - especially while processing of the electrode at high temperature - referred to cells assembled with this electrolyte family. To circumvent these problems, recent efforts have been dedicated to the formulation of composite hybrid polymer electrolytes (CPEs), where the ceramic material is embedded in a polymeric matrix. As compared to the pristine components, CPEs are stiff while preserving flexibility, are easily processed, and can be conceived to attain improved ionic conductivity and interfacial contact with the electrodes. In this work, a polymer based matrix containing poly(ethylene oxide) (PEO), lithium bis (trifluoromethylsulphonyl)imide (LiTFSI), tetra(ethylene glycol dimethyl ether) (G4) and a photoinitiator was added with LLZO particles, thoroughly mixed, formed into a film and cross-linked under UV radiation to obtain a composite hybrid electrolyte. This easy procedure allows obtaining self-standing CPEs with desirable properties of flexibility, shape retention upon thermal stress, improved interfacial contact with the electrodes and ionic conductivity suitable for practical application. Lab-scale lithium metal cells assembled with the CPEs and lithium iron phosphate (LFP) cathodes demonstrated specific capacities up to 125 mAh g-1 at 1C rate and could work for hundreds of cycles at ambient temperature.
A Proof-of-Concept Electrochemical Skin Sensor for Simultaneous Measurement of Glial Fibrillary Acidic Protein (GFAP) and Interleukin-6 (IL-6) for Management of Traumatic Brain Injuries (2022)

This work demonstrates the use of a noninvasive, sweat-based dual biomarker electrochemical sensor for continuous, prognostic monitoring of a Traumatic Brain Injury (TBI) with the aim of enhancing patient outcomes and reducing the time to treatment after injury. A multiplexed SWEATSENSER was used for noninvasive continuous monitoring of glial fibrillary acidic protein (GFAP) and Interleukin-6 (IL-6) in a human sweat analog and in human sweat. Electrochemical impedance spectroscopy (EIS) and chronoamperometry (CA) were used to measure the sensor response. The assay chemistry was characterized using Fourier Transform Infrared Spectroscopy (FTIR). The SWEATSENSER was able to detect GFAP and IL-6 in sweat over a dynamic range of 3 log orders for GFAP and 2 log orders for IL-6. The limit of detection (LOD) for GFAP detection in the sweat analog was estimated to be 14 pg/mL using EIS and the LOD for IL-6 was estimated to be 10 pg/mL using EIS. An interference study was performed where the specific signal was significantly higher than the non-specific signal. Finally, the SWEATSENSER was able to distinguish between GFAP and IL-6 in simulated conditions of a TBI in human sweat. This work demonstrates the first proof-of-feasibility of a multiplexed TBI marker combined with cytokine and inflammatory marker detection in passively expressed sweat in a wearable form-factor that can be utilized toward better management of TBIs. This is the first step toward demonstrating a noninvasive enabling technology that can enable baseline tracking of an inflammatory response.
Sulfolipid Deficiency Does Not Affect the Virulence ofMycobacterium tuberculosisH37Rv in Mice and Guinea Pigs (2003)

Lipids that are found only in the cell envelope of pathogenic mycobacteria, such as those containing multiple methyl-branched fatty acids, have long been thought to play a role in pathogenesis. Among these complex lipids, sulfolipids have been the most extensively studied over the last 50 years. The numerous biological effects exhibited by purified sulfolipids on phagocytic cells led to the idea that these molecules are probably important virulence factors facilitating the intracellular survival of Mycobacterium tuberculosis. However, definitive evidence to support this concept has been lacking. The recent construction of an isogenic sulfolipid-deficient mutant of M. tuberculosis H37Rv (Sirakova et al., J. Biol. Chem. 276:16833-16839, 2001) has for the first time provided the opportunity to directly assess the contribution of these complex lipids to pathogenesis. In the present study, we show that against all expectations, sulfolipid deficiency does not significantly affect the replication, persistence, and pathogenicity of M. tuberculosis H37Rv in mice and guinea pigs or in cultured macrophages.
A Pure Population of Ectodermal Cells Derived from Human Embryonic Stem Cells (2007)

Embryonic stem (ES) cells represent a unique cellular model to recapitulate in vitro early steps of embryonic development and an unlimited cellular source in therapy for many diseases, as well as targets for drug discovery and toxicology screens. Although previous studies have reported epidermal differentiation of mouse and human embryonic stem (huES) cells, the heterogeneity of the resulting cell culture impairs the evaluation of differentiated cells for cell therapy. We report here the reproducible isolation of a homogenous ectodermal cell population, IT1, from human ES cells. Like primary cells, IT1 cells remain homogenous over 15 passages, expand up to 60 population doublings, and then die through senescence. Accordingly, IT1 cells display a normal karyotype and a somatic cell cycle kinetics and do not produce teratoma in nude mice. The production of K14-expressing epithelial cells driven by p63 expression strengthens the ectodermal nature of IT1 cells. Since IT1 can be isolated from different huES cell lines, it may provide a ready source of ectodermal progenitors for the development of a toxicology cell model, new-drug-screening strategies, and cell therapy transplantation.
3P-125 G146V mutation in actin inhibits force generation during interaction with skeletal myosin.(Molecular motor,The 47th Annual Meeting of the Biophysical Society of Japan) (2009)

IncorporatedAssociationstator that coiiduLtts protong and the C nng vvhich tunLtions ag the rotor The mechanism oi Lnerg} coupling between proton influx and torquc generation remains
A novel index of infarct morphology predicts the presence of microvascular obstruction in patients with acute myocardial infarction (2012)

Background Microvascular obstruction (MO) has been associated with poor LV remodeling and adverse prognosis. Infarct morphology is related to the presence of MO in that patients with MO generally have larger infarct size (IS) and greater mean infarct transmurality. However, neither index is highly predictive on an individual patient basis. In the current study, we investigated the utility of a novel index of infarct morphology, which reflects the circumferential extent of fully transmural infarction extending to the epicardial surfacethe epicar- dial surface area (EpiSA) of infarctionto predict MO. Methods We studied 302 consecutive patients from 2 centers (Duke and Maastricht University) with first AMI. On contrast-enhanced-CMR, early (2-min post-contrast) and late MO (10-min post-contrast) were defined as hypoenhanced regions within hyperenhanced infarction. Infarct size, mean transmurality, and EpiSA were quanti- fied by manual planimetry of the stack of short-axis views. Results Patients were 58±11 years old (71% male). Prevalence of early and late MO was 64% and 55%, respectively. For the population, IS, mean transmurality, and EpiSA were 14% of LV mass (IQR 7-25%), 74% of infarct sector (IQR 57-86%) and 6% of total LV epicardial-surface-area (IQR 1-13%), respectively. All 3 infarct characteristics were significantly larger in patients with MO (all p 42% of LV (4% of population). However, only a small portion of the population (5%+4%=9%) had infarct size reaching these thresholds, showing that IS had limited discrimi- natory value on an individual patient basis. Similarly, infarct transmurality had limited discriminatory value. In contrast, EpiSA thresholds allowed ruling-in or rul- ing-out MO in a significantly larger percentage of the population (44% for both early and late; p<0.0001 com- pared with IS and transmurality). No patient had MO unless EpiSA was greater than zero. Multivariable analy- sis incorporating clinical, ECG, and CMR data demon- strated that EpiSA was the strongest, independent predictor of early and late MO (p<0.0001 for both). Conclusions The epicardial surface area of infarction, a novel index of infarct morphology, is a stronger predictor of MO than infarct size or mean transmurality. MO does not occur unless infarction extends to the epicardial surface.
Glucose induced genes in bovine aortic smooth muscle cells identified by mRNA differential display (1994)

Hyperglycemia is postulated to cause chronic changes in the vasculature of diabetic patients, suggesting structural or genetic alterations. We have characterized the glucose induced alterations of gene expression in cultured bovine aortic smooth muscle cells using the recently developed mRNA differential display method. After five days of incubation with either 5.5 or 22 mM glucose, RNA preparations were isolated from confluent cells and probed with 10 candidate clones identified after screening up to 3000 mRNA species. Among these, three clones (2A, 2C, 3) showed significant changes in expression by Northern blot analysis. Elevated glucose levels decreased the mRNA expression of clones 2A and 3 to 51 +/- 7% (P < .01) and 59 +/- 10% (P < .05) (mean% of control +/- SEM), respectively. Expression of clone 2C was increased in 22 mM glucose condition to 221 +/- 23% (P < .05). Nucleotide sequence analysis showed that clone 3 had 77% homology to the 3'-noncoding region of human elongation factor 2, a member of the GTPase family which is essential for polypeptide synthesis. Clones 2A and 2C do show no homology to known nucleotide sequences. These results indicate that physiologically attainable high glucose conditions can significantly effect gene expression in aortic smooth muscle cells. Furthermore, mRNA differential display can be used in metabolic studies to identify new genes regulated by nutrients such as glucose.
Lifeline-based global load balancing (2011)

On shared-memory systems, Cilk-style work-stealing has been used to effectively parallelize irregular task-graph based applications such as Unbalanced Tree Search (UTS). There are two main difficulties in extending this approach to distributed memory. In the shared memory approach, thieves (nodes without work) constantly attempt to asynchronously steal work from randomly chosen victims until they find work. In distributed memory, thieves cannot autonomously steal work from a victim without disrupting its execution. When work is sparse, this results in performance degradation. In essence, a direct extension of traditional work-stealing to distributed memory violates the work-first principle underlying work-stealing. Further, thieves spend useless CPU cycles attacking victims that have no work, resulting in system inefficiencies in multi-programmed contexts. Second, it is non-trivial to detect active distributed termination (detect that programs at all nodes are looking for work, hence there is no work). This problem is well-studied and requires careful design for good performance. Unfortunately, in most existing languages/frameworks, application developers are forced to implement their own distributed termination detection.
(Invited) Monolithic Integration of III-V Semiconductors by Selective Area Growth on Si(001) Substrate: Epitaxy Challenges & Applications (2015)

This study relates to the selective area growth (SAG) of III-V semiconductors on Silicon substrates. Both approaches, growth in trenches and NWs bottom-up growth, are considered and discussed. We demonstrated in a first part a high control of the two-step InP buffer growth in STI trench width below 20 nm. First GaAs NWs from production MOVPE tool are also shown in a second part. Finally we conclude with the different applications using III-V semiconductors successfully integrated on Silicon substrates.
Influence of rotor capacitance in on-line rotor ground fault location method for synchronous machines with static excitation (2013)

This paper presents results about the influence of rotor capacitance in the on-line rotor ground fault location method for synchronous machines with static excitation. The location method is based on the measurement of the voltage in a grounding resistance, connected to the neutral of the excitation transformer. Due to the effect of the rotor capacitance to ground on large synchronous generators, it is observed that waveform of the neutral voltage is perturbed, and it causes an error in the fault location in case of defect in the DC side. Firstly, the influence of the fault resistance value and the fault position is evaluated through computer simulations. Then, the impact of the rotor capacitance in the accuracy of the detection and location method is analyzed in case of ground fault, as well as in healthy operating condition.
Flow-Aware Transport of Pseudowires over an MPLS Packet Switched Network (2011)

Where the payload of a pseudowire comprises a number of distinct
flows, it can be desirable to carry those flows over the Equal Cost
Multiple Paths (ECMPs) that exist in the packet switched network. Most
forwarding engines are able to generate a hash of the MPLS label stack
and use this mechanism to balance MPLS flows over ECMPs. This
document describes a method of identifying the flows, or flow groups,
within pseudowires such that Label Switching Routers can balance flows
at a finer granularity than individual pseudowires. The mechanism uses
an additional label in the MPLS label stack. [STANDARDS-TRACK]
Guinea pig plasma kallikrein as a vascular permeability enhancement factor. Its dependence on kinin generation and regulation mechanisms in vivo. (1984)

Plasma kallikrein (mol wt 80,000) was purified from guinea pig plasma, and it caused vascular permeability enhancement when injected into guinea pig skin. The activity had a linear relationship to the logarithm of kallikrein concentrations from 5 X 10(-9) M to 5 X 10(-6) M and was blocked by immunopurified anti-prekallikrein F(ab')2 rabbit antibody and soybean trypsin inhibitor. Carboxypeptidase B(1.7 units), a kinin-destructive enzyme, decreased the permeability activity to 1/20, while SQ 20,881 (10(-6) M), an inhibitor to a kinin-destructive enzyme, augmented the activity 5.4-fold. These results suggested that the permeability activity of kallikrein was performed finally through kinin generation in the skin. The permeability activity was short-lasting, and was completely blocked by a kallikrein inhibitor purified from guinea pig plasma, suggesting the presence of a down-regulation system for the permeability activity in vivo. Prostaglandin E2 (25 ng), a hyperemia inducer in microcirculation, augmented the permeability activity 12-fold, suggesting the presence of an up-regulation system in vivo. Accordingly, it was assumed that kallikrein-kinin system might play a role as a vascular permeability enhancement system in guinea pig skin.
Hybrid linear/quadratic time-frequency attributes (2001)

We present an efficient method for robustly calculating time-frequency attributes of a signal, including instantaneous mean frequency, bandwidth, kurtosis, and other moments. Most current attribute estimation techniques involve a costly intermediate step of computing a (highly oversampled) two-dimensonal (2-D) quadratic time-frequency representation (TFR), which is then collapsed to the one-dimensonal (1-D) attribute. Using the principles of hybrid linear/quadratic time-frequency analysis (time-frequency distribution series), we propose computing attributes as nonlinear combinations of the (slightly oversampled) linear Gabor coefficients of the signal. The method is both computationally efficient and accurate; it performs as well as the best techniques based on adaptive TFRs. To illustrate, we calculate an attribute of a seismic cross section.
Validation of the Korean version of the Trait and State Post-Event Processing Inventory (2021)

사후처리란 사회적 상황이 끝난 뒤 그 상황에서 보였던 자신의 행동과 타인들의 반응을 면밀하게 검토하는 사회불안장애의 특징적인 역기능적 정보처리 과정이다. 이는 인지적 특성인 동시에 상태이기도 하다. 그러나 기존의 사후처리와 관련된 척도들은 특성과 상태를 구분하지 않았다. 본 연구에서는 사후처리 특성 및 상태 척도(Trait and State versions of the Post-Event Processing Inventory)를 타당화 하였다. 2020년 주민등록 인구 통계 기준으로 성별, 연령, 지역을 고려하여 인구비례할당방식으로 참가자를 표집 하였으며, 최종 742명 성인을 대상으로 척도를 실시하였다. 탐색적 요인분석 결과, 한국판 사후처리 특성 및 상태 척도는 원척도의 3요인(빈도, 강도, 자기판단)과는 달리 모두 2요인 구조(역기능적 정보처리-빈도, 일상생활 방해-강도)로 나타났다. 단일 요인과 2요인, 3요인에 대한 확인적 요인분석 결과, 2요인 모델이 가장 적합한 것으로 확인되었다. 한국판 사후처리 특성 및 상태 척도의 신뢰도는 우수하였고 양호한 수렴 및 변별타당도, 증분타당도를 보였다. 본 척도는 사후처리의 특성과 상태를 구분하여 측정할 수 있어 사회불안장애의 임상 및 사후처리 연구 분야에서 유용하게 사용될 수 있을 것이다.
Immunogenicity and Safety of an Inactivated Quadrivalent Influenza Vaccine Candidate: A Phase III Randomized Controlled Trial in Children (2013)

NCT01198756.
Reaktion von 4, 5‐Dihydro‐3‐furancarbonsäure‐alkylestern mit bifunktionellen Stickstoffbasen (1974)

Abstract Die 4,5‐Dihydro‐3‐furancarbonsäure‐alkylester 1a , b reagieren mit Hydrazinen und Amidinen unter Ringöffnung zu den 5‐Pyrazolonen 3a–c bzw. 6‐Pyrimidonen 8a , b . Zwischenprodukte vom Typ der 3‐Furancarboxamide 9a , b werden nur bei der Umsetzung mit Amidinen erhalten. Die Derivate 3a‐c , 8a und b entstehen auch, wenn anstelle 1a, b α‐Hydroxymethylen‐γ‐butyrolacton ( 4b ) eingesetzt wird. Dieses reaktive Lacton 4b setzt sich mit den heterocyclischen Amidinen 7c–g nur zu den 3‐Furancarboxamiden 9c–g um und mit 2‐Thiazolinamin ( 11 ) zu dem Pyrimidonderivat 12 . Brom wird an die CC‐Bindung in 1a, b zu den instabilen Addukten 16a, b addiert, die mit Harnstoffen die Furo[2,3‐d]imidazolidone 19a, b bilden. Die Strukturen dieser Produkte werden durch die spektroskopischen Daten (IR, NMR) gestützt.
A mechanistic model for the enzymic degradation of synthetic biopolymers. (1986)

The degradation pathway of a synthetic biopolymer, poly-N5-(2-hydroxyethyl)-L-glutamine, by papain under physiological conditions, was extensively investigated. The enzymic reaction was found to be rather complex: it progressively slows down, and comes to an end when the degradation fragments are tetrapeptides. In order to account for this phenomenon, a modified Michaelis-Menten kinetic model is proposed, in which Km is assumed to be dependent on the degree of polymerization of the macromolecular substrate, and therefore varies as the degradation reaction proceeds. The new model accurately describes all the experimental data, and allows one to predict the entire course of the reaction. The behaviour of the system considered is interpreted to represent a model of biological recognition at the molecular level.
L‐4: Late‐New Paper: Active‐Matrix Operation of Electrophoretic Devices with Inkjet‐Printed Polymer Thin Film Transistors (2002)

Abstract Active‐matrix operation of an electrophoretic device has been achieved with all‐polymer thin film transistors (TFTs). The source/drain, gate electrodes and gate lines of the TFTs were fabricated by inkjet printing with a conductive polymer, polyethylenedioxythiophene (PEDOT). Electrophoretic material was prepared from TiO 2 particles suspended in dyed solution, and was microencapsulated in polymer membrane spheres. The microcapsules were sandwiched between the polymer active‐matrix array and a counter electrode. The voltage of each pixel was independently changed by switching the printed polymer TFT, and contrast in the electrophoretic material was successfully obtained.