gebhart/patrepeval huggingface dataset:
Modification of Cu current collectors for lithium metal batteries – A review (2022)

The energy density of lithium metal batteries (LMBs) could be much higher than that of current graphite anode-based LIBs. When a metallic current collector is used for plating/de-plating of lithium (i.e., anode-free lithium metal batteries (AFLMBs)) energy density could be higher by about 70%. However, LMBs suffer from dendritic lithium growth and formation of an unstable solid-electrolyte interface, which requires careful control to improve the cycling performance and the overall safety. The current collector (CC), typically Cu, plays an important role in lithium nucleation/growth, local current density and Li-ion flux distribution. However, the commonly used planar Cu CC does not work satisfactorily, and as such, modifications of Cu CC, for decreasing the local current density, suppressing the lithium dendrite growth, and improving the Coulombic efficiency (CE), have been widely investigated and reported in the literature. This review systematically summarizes the modification methods for Cu CCs and serves as a guide for rational design of modified Cu CCs with tailored structures and properties. Furthermore, misrepresentation and misinterpretation of data, which are often observed in the literature on this topic, are critically discussed and insights into the key challenges and future directions on this topic are presented.
Expression of Multiple Sclerosis Susceptible Loci Genes May Assist in Diagnostic Decision Making (P6.153) (2014)

OBJECTIVE: To utilize recent findings of large scale Genome Wide Association Studies (GWAS) to develop a blood gene expression based classification tool for Multiple Sclerosis (MS) differential diagnosis. BACKGROUND: Recent GWAS have revealed previously unknown polymorphism in multiple genetic loci that may be of significance for MS susceptibility. We developed a multi-analytical approach to merge statistical evidence of GWAS associations and experimental evidence of gene expression profiles to develop classification tool for MS diagnosis. DESIGN/METHODS: Gene expression analysis (Affimetrix U133A-2 microarrays) was performed on blood samples obtained from 80 relapsing-remitting MS patients (52 females, age 34.8±1.1 years, disease duration 3.6±0.4 years, EDSS 1.8±0.1) and 31 patients with MS-resembling symptoms and white matter brain lesions that don't fulfill MS diagnostic criteria (NonMS, 24 females, age 41.6 ± 2.3 years). Statistical analysis and cross-validation classification algorithm were performed by Partek software. The resulted classifier was validated on independent blood samples from 80 MS patients (55 females, age 37.6±1.2 years, disease duration 5.5±0.6 years, EDSS 2.3±0.1) and 25 NonMS patients (19 females, age 42.3±1.7 years). RESULTS: Candidate classifying biomarkers included 49 gene-transcripts associated with genetic loci contributed to MS susceptibility, as well as 29 differentially expressed genes between MS and NonMS groups in our cohort (p<0.05 after Bonferroni correction). This signature was enriched by genes associated with different mechanisms of immune cell trafficking (p=1.97E-04 to 1.54E-05). The generated 42-genes classifier when tested on the independent validation group of 105 patients, demonstrated correct classification rate of 78.1±4.0 % with sensitivity of 79.0±4.6% and specificity of 76.0±8.5%. CONCLUSIONS: Expression of MS Susceptible Loci genes and genes differentially expressed between MS and Non MS patients may assist in diagnostic decision making. Study Supported by:
Rapid Detection of Live Versus Dead Bacteria (2016)

This paper presents a rapid method of detecting live versus dead pathogenic bacteria. The method combines phage-coated magnetoelastic (ME) biosensors and a wireless planar coil detector, enabling real-time monitoring of the growth and viability of specific bacteria in a nutrient broth. The ME biosensor used in this investigation is composed of a strip-shaped ME resonator (1 mm x 0.2 mm x 30 um) upon which a landscape phage is coated to capture specific bacteria. E2 phage with high binding affinity for Salmonella Typhimurium was used as a model study. The specificity of E2 phage has been reported to be 200 in 10 8 background bacteria. When the binding of Salmonella occurs, the mass of the biosensor increases, which simultaneously results in a decrease in the biosensor's resonant frequency. Monitoring of this mass-induced resonant frequency change allows for the instantaneous detection and quantification of Salmonella . ME biosensors with a pre-determined resonant frequency were first exposed to a low-concentration Salmonella suspension to capture a small but detectable amount of the bacteria on the sensor surface. The wireless coil detector was then used to measure the resonant frequency changes of the biosensors as a function of time in a nutrient broth. Live cells can grow, while dead ones can't, which leads to distinct differences in the resonant frequency changes over time. Hence, this methodology offers direct, real-time detection, quantification, and viability determination of specific bacteria.
The Origin of the Catalytic Activity of a Metal Hydride in CO<sub>2</sub> Reduction (2016)

Abstract Atomic hydrogen on the surface of a metal with high hydrogen solubility is of particular interest for the hydrogenation of carbon dioxide. In a mixture of hydrogen and carbon dioxide, methane was markedly formed on the metal hydride ZrCoH x in the course of the hydrogen desorption and not on the pristine intermetallic. The surface analysis was performed by means of time‐of‐flight secondary ion mass spectroscopy and near‐ambient pressure X‐ray photoelectron spectroscopy, for the in situ analysis. The aim was to elucidate the origin of the catalytic activity of the metal hydride. Since at the initial stage the dissociation of impinging hydrogen molecules is hindered by a high activation barrier of the oxidised surface, the atomic hydrogen flux from the metal hydride is crucial for the reduction of carbon dioxide and surface oxides at interfacial sites.
Synchronous equivalence for embedded systems: a tool for design exploration (1999)

This paper presents a new protocol for parallel and distributed simulation of VLSI systems. It is novel in two aspects: first, it combines optimistic and conservative synchronization methods, allowing processes to self-adapt for maximal utilization of concurrency. Second, it does not require any application-dependent information like lookahead, which in many cases is unknown, zero, or difficult to automatically obtain from a design in a hardware description language. All these features make it very convenient and practical, extending the class of applications to at least all VHDL circuits, including delta cycle. The proposed protocol has been implemented and used for VHDL simulation. Experimental results on several large VHDL circuits (between 1411 and 14704 processes) have shown promising linear speedups. We also observed that the dynamic synchronization, in which processes automatically adapt to optimistic or conservative behavior, follows closely or finds a very good configuration. This protocol may have a string impact for mixed-signal circuit simulation, where digital parts may be optimistic and heavy-state analog parts, conservative.
Synthesis of<i>N</i>-[1-(2-Thienyl)cyclohexyl]piperidine (TCP) Based Irreversible Alkylators of the Phenylcyclidine (PCP) Recognition Site (1991)

Four new thienylcyclohexylamines {N-[1-(4-isothiocyanato/isoselenocyanato-2-thienyl)cyclohexyl]piperidine and 2-[1-(ethylaminocyclohexyl)-4-isothiocyanato/isoselenocyanatothiophene) have been synthesized and examined for their ability to alkylate the MK-801/PCP recognition sites associated with the N-methyl-D-aspartate receptor-ion channel complex.
Two-dimensional fractal metamaterials for applications in THz (2011)

The concept of metamaterials (MTMs) is acknowledged for providing new horizons for controlling electromagnetic radiations thus their use in frequency ranges otherwise difficult to manage (e.g. THz radiation) broadens our possibility to better understand our world as well as opens the path for new applications. THz radiation can be employed for various purposes, among them the study of vibrations in biological molecules, motion of electrons in semiconductors and propagation of acoustic shock waves in crystals. We propose here a new THz fractal MTM design that shows very high transmission in the desired frequency range as well as a clear differentiation between one polarisation and another. Based on theoretical predictions we fabricated and measured a fractal based THz metamaterial that shows more than 60% field transmission at around 1 THz for TE polarized light while the TM waves have almost 80% field transmission peak at 0.6 THz. One of the main characteristics of this design is its tunability by design: by simply changing the length of the fractal elements one can choose the operating frequency window. The modelling, fabrication and characterisation results will be presented in this paper.
Fracture strength of glass, engineering testing methods and estimation of characteristic values (2013)

Glass is a brittle solid with an almost perfectly elastic material behavior at common operation temperatures. Consequently, the strength of glass depends substantially on the surface and edge conditions of the stressed surface. Since glass exhibits brittle fracture at strengths two to three orders of magnitude less than its theoretical modecular bond strength, the knowledge of a reliable value of glass strength is important for designing structural glass elements. The first part of the present paper treats the gasics of fracture mechanics containing short term (i.e. the flaw geometry and depth) and long term (stress corrosion) parameters. In the second part typical engineering testing methods for surface and edge strength are presented. Finally, statistical methods for probability distribution fitting and determination of characteristic values are elucidated.
Chemical and Enzymatic Modification of Chitosan to Produce New Functional Materials with Improved Properties (2019)

Chitin and chitosan are natural biopolymers with applications in different areas. However, to broaden its application area, research is needed to impart new functionality, develop new and better materials and to explore the whole potential of chitin/chitosan derivatives. These derivatives can be made by chemical and enzymatic synthesis. Here, the main classes of chitosan derivatives obtained by using green and sustainable conversion routes and as much as possible using green and/or bio-based chemicals for modification and their potential areas for application are discussed.
Alveolar Epithelial Dynamics in Postpneumonectomy Lung Growth (2013)

The intimate anatomic and functional relationship between epithelial cells and endothelial cells within the alveolus suggests the likelihood of a coordinated response during postpneumonectomy lung growth. To define the population dynamics and potential contribution of alveolar epithelial cells to alveolar angiogenesis, we studied alveolar Type II and I cells during the 21 days after pneumonectomy. Alveolar Type II cells were defined and isolated by flow cytometry using a CD45(-) , MHC class II(+) , phosphine(+) phenotype. These phenotypically defined alveolar Type II cells demonstrated an increase in cell number after pneumonectomy; the increase in cell number preceded the increase in Type I (T1α(+) ) cells. Using a parabiotic wild type/GFP pneumonectomy model, <3% of the Type II cells and 1% of the Type I cells were positive for GFP-a finding consistent with the absence of a blood-borne contribution to alveolar epithelial cells. The CD45(-) , MHC class II(+) , phosphine(+) Type II cells demonstrated the active transcription of angiogenesis-related genes both before and after pneumonectomy. When the Type II cells on Day 7 after pneumonectomy were compared to nonsurgical controls, 10 genes demonstrated significantly increased expression (P<0.05). In contrast to the normal adult Type II cells, there was notable expression of inflammation-associated genes (Ccl2, Cxcl2, Ifng) as well as genes associated with epithelial growth (Ereg, Lep). Together, the data suggest an active contribution of local alveolar Type II cells to alveolar growth.
Fast Quantification Without Conventional Chromatography, The Growing Power of Mass Spectrometry (2020)

Mass spectrometry (MS) in hyphenated techniques is widely accepted as the gold standard quantitative tool in life sciences. However, MS possesses intrinsic analytical capabilities that allow it to be a stand-alone quantitative technique, particularly with current technological advancements. MS has a great potential for simplifying quantitative analysis without the need for tedious chromatographic separation. Its selectivity relies on multistage MS analysis (MS<sup>n</sup>), including tandem mass spectrometry (MS/MS), as well as the ever-growing advancements of high-resolution MS instruments. This perspective describes various analytical platforms that utilize MS as a stand-alone quantitative technique, namely, flow injection analysis (FIA), matrix assisted laser desorption ionization (MALDI), including MALDI-MS imaging and ion mobility, particularly high-field asymmetric waveform ion mobility spectrometry (FAIMS). When MS alone is not capable of providing reliable quantitative data, instead of conventional liquid chromatography (LC)-MS, the use of a guard column (i.e., fast chromatography) may be sufficient for quantification. Although the omission of chromatographic separation simplifies the analytical process, extra procedures may be needed during sample preparation and clean-up to address the issue of matrix effects. The discussion of this manuscript focuses on key parameters underlying the uniqueness of each technique for its application in quantitative analysis without the need for a chromatographic separation. In addition, the potential for each analytical strategy and its challenges are discussed as well as improvements needed to render them as mainstream quantitative analytical tools. Overcoming the hurdles for fully validating a quantitative method will allow MS alone to eventually become an indispensable quantitative tool for clinical and toxicological studies.
Geometric approaches to three-dimensional structural restoration (2016)

Extending “Balanced Cross-Section” structural validation techniques to three dimensions has been an area of active research and development for two decades. Due to the inherent difficulty of the challenge, the resulting tools and methods have had limited practical application. We propose that the advent of so-called “Geological Knowledge-Oriented” earth models makes this traditionally difficult problem more practical. To demonstrate this, we present a practical workflow using one such earth model and discuss how the tool can be used with a natural example. Presentation Date: Tuesday, October 18, 2016 Start Time: 3:45:00 PM Location: 143/149 Presentation Type: ORAL
Heterozygous PINK1 p.G411S mutation increases risk for Parkinson's disease (PD) (2016)

Objective: To investigate the possible disease-association and pathogenic mechanisms of heterozygous PINK1 mutations from a genetic, functional, and structural perspective. Background: It has been postulated that heterozygous mutations in recessive PD genes may increase disease risk. In particular, the PINK1 p.G411S mutation has been reported in families with dominant inheritance patterns, suggesting that it might confer a sizeable disease risk. Methods: We performed a pedigree analysis of seven patients with a heterozygous PINK1 p.G411S mutation with at least one additional affected family member. We screened five case-control series and performed a meta-analysis of previous studies that had examined the variant. For functional cell-based analyses, we used patients skin fibroblast from PINK1 p.G411S or p.Q456X heterozygotes and investigated endogenous protein levels and kinase activity by biochemistry and imaging. For structural analyses, we performed molecular modeling and generated monomeric and dimeric forms of wild type (WT) and mutant PINK1 protein. Using molecular dynamics simulations, we analyzed effects of the p.G411S mutation on WT PINK1 in a heterodimeric complex over time. Results: Our analyses revealed a genetic association of heterozygous PINK1 p.G411S mutation with an increased risk for PD and a possible dominant inheritance with incomplete co-segregation. In patients skin fibroblasts, we establish a dominant negative mode for heterozygous p.G411S mutations under endogenous conditions. While total PINK1 protein levels were similar to controls upon mitochondrial stress, cellular PINK1 kinase activity was significantly reduced in p.G411S heterozygotes compared to WT and importantly to p.Q456X heterozygotes, which resulted in 50% reduction of PINK1 protein levels. Structural analyses supported our hypothesis that the p.G411S mutation can poison PINK1 WT in a heterodimeric complex and thus effectively reduce cellular PINK1 kinase activity. This in turn impairs the protective functions of the PINK1/PARKIN-mediated mitochondrial quality control. Conclusions: Our study uncovers increased disease risk and molecular mechanisms of a particular heterozygous mutation in a recessive PD gene. Based on genetic and clinical evaluation as well as functional and structural characterization, we established PINK1 p.G411S as a rare genetic risk factor with a relatively large effect size conferred by a dominant negative function phenotype.
Identification and Classification of Crowd Activities (2022)

The identification and classification of collective people's activities are gaining momentum as significant themes in machine learning, with many potential applications emerging. The need for representation of collective human behavior is especially crucial in applications such as assessing security conditions and preventing crowd congestion. This paper investigates the capability of deep neural network (DNN) algorithms to achieve our carefully engineered pipeline for crowd analysis. It includes three principal stages that cover crowd analysis challenges. First, individual's detection is represented using the You Only Look Once (YOLO) model for human detection and Kalman filter for multiple human tracking; Second, the density map and crowd counting of a certain location are generated using bounding boxes from a human detector; and Finally, in order to classify normal or abnormal crowds, individual activities are identified with pose estimation. The proposed system successfully achieves designing an effective collective representation of the crowd given the individuals in addition to introducing a significant change of crowd in terms of activities change. Experimental results on MOT20 and SDHA datasets demonstrate that the proposed system is robust and efficient. The framework achieves an improved performance of recognition and detection people with a mean average precision of 99.0%, a real-time speed of 0.6 ms non-maximum suppression (NMS) per image for the SDHA dataset, and 95.3% mean average precision for MOT20 with 1.5 ms NMS per image.
Insertion points of the essential nanoscale science and technology (NST) concepts in the Israeli middle school science and technology curriculum (2018)

Abstract If we wish to integrate modern science such as nanotechnology into the school science curriculum, we need to find the natural insertion point of modern science with the science, technology, engineering and math curriculum. However, integrating nanoscale science and technology (NST) essential concepts into the middle school science curriculum is challenging. The current study was designed to identify the insertion points of the eight NST essential concepts in the middle school science and technology curriculum. Middle school science and technology teachers underwent a course that included all eight NST essential concepts, aiming to help them understand the NST essential concepts in depth. Then, they were asked to identify a natural insertion point in the existing science and technology curriculum for each of the NST essential concepts. To support research validation, two different groups of teachers participated in two sequential stages of the study (the identification stage and the validation stage). The teachers in the identification stage identified the insertion points of all eight NST essential concepts in the subjects of the science and technology curriculum, which reflects the relevance of the NST concepts from the teachers’ perspective in terms of pedagogical level. The majority of the identified insertion points were validated in the second stage. Forty-two insertion points of the NST essential concepts were suggested to be integrated in middle school science and technology curriculum. All the insertion points that were suggested in the identification stage were confirmed in the validation stage. Another 11 new insertion points were added at the validation stage. The connections to the different scientific subjects in the curriculum are as follows: 19 insertion points were suggested by the teachers in the chemistry part of the chemistry curriculum, 12 in the life science, four in the physics-energy, and seven in technology-systems and products. The results present the opportunity to expose middle school students to contemporary science using the existing science and technology curriculum. The study serves as an example of integrating NST concepts into a middle school science curriculum in Israel, but it can be applied in other science curricula worldwide, taking into consideration the topics included in each curriculum.
Synaptotagmin-3 drives AMPA receptor endocytosis, depression of synapse strength, and forgetting (2018)

Forgetting is important. Without it, the relative importance of acquired memories in a changing environment is lost. We discovered that synaptotagmin-3 (Syt3) localizes to postsynaptic endocytic zones and removes AMPA receptors from synaptic plasma membranes in response to stimulation. AMPA receptor internalization, long-term depression (LTD), and decay of long-term potentiation (LTP) of synaptic strength required calcium-sensing by Syt3 and were abolished through Syt3 knockout. In spatial memory tasks, mice in which Syt3 was knocked out learned normally but exhibited a lack of forgetting. Disrupting Syt3:GluA2 binding in a wild-type background mimicked the lack of LTP decay and lack of forgetting, and these effects were occluded in the Syt3 knockout background. Our findings provide evidence for a molecular mechanism in which Syt3 internalizes AMPA receptors to depress synaptic strength and promote forgetting.
All-atom empirical force field for nucleic acids: II. Application to molecular dynamics simulations of DNA and RNA in solution (2000)

Molecular dynamics simulations based on empirical force fields can greatly enhance knowledge of DNA and RNA structure and dynamics in solution. Presented are results on simulations of three DNA sequences and one RNA sequence using the new all-atom CHARMM27 force field for nucleic acids presented in the accompanying manuscript (Foloppe, MacKerell, J Comput Chem, this issue). Data are reported on structural, dynamic, and hydration properties including dihedral angle, sugar puckering, and helicoidal parameter probability distributions. Also presented are calculations of a DNA hexamer in 0 and 75% ethanol starting from both the canonical A and B forms. Analysis of RMS differences with respect to the canonical A and B forms of DNA show a highly anticorrelated behavior indicating that the force field samples the equilibrium between the A and B forms of DNA. Proper stabilization of B form DNA in aqueous solution and A form DNA in 75% ethanol show that this equilibrium can be perturbed by environmental contributions. Success of the force field in reproducing a variety of experimental data for duplex DNA and RNA indicates that it is of general use for computational investigations of nucleic acids as well as nucleic acids in complexes with proteins and lipids. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 105–120, 2000