gebhart/patrepeval huggingface dataset:
Improved transition path sampling methods for simulation of rare events (2008)

The free energy surfaces of a wide variety of systems encountered in physics, chemistry, and biology are characterized by the existence of deep minima separated by numerous barriers. One of the central aims of recent research in computational chemistry and physics has been to determine how transitions occur between deep local minima on rugged free energy landscapes, and transition path sampling (TPS) Monte-Carlo methods have emerged as an effective means for numerical investigation of such transitions. Many of the shortcomings of TPS-like approaches generally stem from their high computational demands. Two new algorithms are presented in this work that improve the efficiency of TPS simulations. The first algorithm uses biased shooting moves to render the sampling of reactive trajectories more efficient. The second algorithm is shown to substantially improve the accuracy of the transition state ensemble by introducing a subset of local transition path simulations in the transition state. The system considered in this work consists of a two-dimensional rough energy surface that is representative of numerous systems encountered in applications. When taken together, these algorithms provide gains in efficiency of over two orders of magnitude when compared to traditional TPS simulations.
The correspondence problem: which brain maps are significantly similar? (2017)

ABSTRACT A critical issue in many neuroimaging studies is the comparison between brain maps. How should we test the hypothesis that two or more brain maps are partially convergent or overlap to a significant extent? This “correspondence problem” affects, for example, the interpretation of comparisons between task-based patterns of functional activation, resting-state networks or modules, and neuroanatomical landmarks. In published work, this problem has been addressed with remarkable variability in terms of methodological approaches and statistical rigor. In this paper, we address the correspondence problem using a spatial permutation framework to generate null models of overlap, by applying random rotations to spherical representations of the cortical surface. We use this approach to derive clusters of cognitive functions that are significantly similar in terms of their functional neuroatomical substrates. In addition, using publicly available data, we formally demonstrate the correspondence between maps of task-based functional activity, resting-state fMRI networks and gyral-based anatomical landmarks. We provide open-access code to implement the methods presented for two commonly-used tools for surface based cortical analysis. This spatial permutation approach constitutes a useful advance over widely-used methods for the comparison of cortical maps, and thereby opens up new possibilities for the integration of diverse neuroimaging data.
Minimum 20 Year Follow-Up of Semi-Constrained Total Ankle Arthroplasty (2017)

Category: Ankle Arthritis Introduction/Purpose: With the introduction of newer generations of total ankle arthroplasty (TAA) constructs, the incidence of TAA in the United States has been increasing. While TAA has emerged as an alternative to ankle arthrodesis for the management of end-stage ankle arthritis, long-term data evaluating clinical outcomes and the survivorship of ankle prostheses is lacking. The purpose of this study was to report the clinical outcomes and radiographic survivorship of a second-generation, semi-constrained titanium and cobalt-chromium total ankle prosthesis at minimum twenty-year follow-up in order to provide a benchmark comparison for future generations of TAA design. Methods: 132 total ankle replacements in 126 patients were performed by a single surgeon between July 1984 and October 1994. Follow-up evaluation consisted of determining revision status, completion of the validated ankle osteoarthritis scale, a short questionnaire, and a review of the available radiographs. All radiographs were evaluated for evidence of progressive radiolucent lines, osteolysis and component subsidence. Results: At minimum twenty-year follow-up, 37 patients were alive, 89 were deceased, and 5 were lost to follow-up. For living patients, average clinical follow up was 25.3 years. Average radiographic follow-up was 21.4 years. Over the minimum 20 year follow-up, 29 ankles were revised (23%). For living patients, 13 ankles were revised (35%). Conclusion: Twenty-three percent of all patients and 35% of living patients required a revision over the minimum 20 year follow up interval. 65% of living patients have retained their prosthesis and 75% of the entire cohort are still functioning with their original ankle replacement or died with the original ankle replacement in place. This study should provide a benchmark for newer designs when they obtain this length of follow-up.
Mesoporous SiO2 thin films containing ZnO photoluminescent nanoparticles. Simultaneous SAXS / WAXS / Ellipsometry investigations (2011)

peer reviewed
Doping Effects on the Properties and Microstructure of Intergrowth Bi 4 Ti 3 O 12 -SrBi 4 Ti 4 O 15 Thin Films (2002)

Abstract Undoped and La-doped intergrowth Bi 4 Ti 3 O 12 -SrBi 4 Ti 4 O 15 thin films were deposited on platinized silicon substrates by a modified metal-organic decomposition (MOD) method. The deposited films were crystallized at about 550-750C in an O 2 atmosphere. The microstructures of the films were investigated using X-ray diffraction and Raman spectroscopy. The ferroelectric and dielectric properties of thin films were measured using an RT66A test system. Compared with the undoped films, when crystallizing under the same temperatures, the XRD patterns of La-doped films present fewer but wider diffraction peaks. Increasing La dopant concentration results in further broadening. However, XRD and Raman spectroscopy studies show that the doping does not lead to a visible distortion of the lattice structure, which implies that La substitutes for either Bi or Sr. The hysteresis measurements show that the doped and undoped thin films have similar coercive field (E c ) and remnant polarization (2P r ). However, the polarization switching time of doped films is much shorter than that of the undoped films irrespective of film thickness. The reversible polarization was found to decrease for BIT-SBTi thin films with thicknesses greater than 210 nm while a maximum reversible polarization was found for La75BIT-SBTI intergrowth films at 280 nm. For a given film thickness, increasing the applied voltages resulted in increased switching times and increased reversible polarization in both cases.
Phase-change Materials in Multifunctional Reconfigurable Metasurfaces (2020)

Metasurfaces, 2D periodic subwavelength electromagnetic resonant structures, enable diverse optical responses in ultrathin geometries. By integrating phase-change materials (PCMs) with optically or thermally tunable material properties into the unit cell geometries, multiple functionalities can be achieved in a single reconfigurable device. However, the extra degrees of freedom offered by PCMs also presents a difficulty, especially since each state of the PCM requires a unique combination of multiple resonances to achieve a desired functionality. To this end, multi-objective optimization algorithms offer the possibility to directly inverse design reconfigurable devices by enabling multiple functionalities to be simultaneously optimized. These devices usually consist of counterintuitively complicated structures that provide novel resonance mechanisms.
Micronetworks by end-linking of polystyrene. 2. Dynamic mechanical behavior and diffusion experiments in the bulk (1989)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMicronetworks by end-linking of polystyrene. 2. Dynamic mechanical behavior and diffusion experiments in the bulkMarkus Antonietti, Karl J. Foelsch, Hans Sillescu, and Tadeusz PakulaCite this: Macromolecules 1989, 22, 6, 2812–2817Publication Date (Print):June 1, 1989Publication History Published online1 May 2002Published inissue 1 June 1989https://pubs.acs.org/doi/10.1021/ma00196a047https://doi.org/10.1021/ma00196a047research-articleACS PublicationsRequest reuse permissionsArticle Views101Altmetric-Citations30LEARN 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
Pharmacological targeting of glutamatergic neurons within the brainstem for weight reduction (2022)

Food intake and body weight are tightly regulated by neurons within specific brain regions, including the brainstem, where acute activation of dorsal raphe nucleus (DRN) glutamatergic neurons expressing the glutamate transporter Vglut3 (DRN<sup>Vglut3</sup>) drive a robust suppression of food intake and enhance locomotion. Activating Vglut3 neurons in DRN suppresses food intake and increases locomotion, suggesting that modulating the activity of these neurons might alter body weight. Here, we show that DRN<sup>Vglut3</sup> neurons project to the lateral hypothalamus (LHA), a canonical feeding center that also reduces food intake. Moreover, chronic DRN<sup>Vglut3</sup> activation reduces weight in both leptin-deficient (ob/ob) and leptin-resistant diet-induced obese (DIO) male mice. Molecular profiling revealed that the orexin 1 receptor (Hcrtr1) is highly enriched in DRN Vglut3 neurons, with limited expression elsewhere in the brain. Finally, an orally bioavailable, highly selective Hcrtr1 antagonist (CVN45502) significantly reduces feeding and body weight in DIO. Hcrtr1 is also co-expressed with Vglut3 in the human DRN, suggesting that there might be a similar effect in human. These results identify a potential therapy for obesity by targeting DRN<sup>Vglut3</sup> neurons while also establishing a general strategy for developing drugs for central nervous system disorders.
Performance of MIMO Rake receivers in WCDMA systems (2004)

The rake receiver is investigated for spatial multiplexing (SM) in wide-band code-division multiple access systems. In general, the SM increases the data rate and the diversity order as well. The appropriate maximum likelihood detector is derived in this paper and it is shown that the diversity order is related to the product of the numbers of receive antennas and taps. With realistic numbers similar diversity orders may be achieved also with reduced complexity detection schemes. Finally, a standard-conformal scrambling technique is proposed to enhance the performance and to equalize it among the full set of orthogonal variable spreading factor (OVSF) sequences used in the third generation cellular system.
Implications of Randomized Link Layers Addresses for IPv6 Address Assignment (2016)

Hosts may assign random link-layer addresses to network interfaces in
an attempt to increase privacy and reduce trackability. Careless
assignment of IPv6 addresses may negate the privacy advantages of
random link-layer addresses. We propose simple solutions to ensure
that IPv6 addresses do change whenever the link layer addresses
change.
A miniaturized acoustic vector sensor with PIN-PMN-PT single crystal cantilever beam accelerometers (2020)

Directional sound detection using vector sensors rather than large hydrophone arrays is highly advantageous for target detection in SONAR. However, developing highly sensitive and compact vector sensors for use in a system whose size is limited has been a challenging issue. In this paper, we describe a miniaturized acoustic vector sensor with piezoelectric single crystal accelerometers for the application in towed line arrays. A mass-loaded cantilever beam accelerometer with a [011] poled PIN-PMN-PT single crystal shows a better signal-to-noise ratio compared to accelerometers with other piezoelectric materials because of its superior piezoelectric properties in the 32 direction. We suggested a sufficiently compact vector sensor by using a cylindrical hydrophone with 10 mm in diameter as a housing of the single crystal accelerometers. Two single crystal accelerometers were orthogonally mounted inside the cylindrical hydrophone to detect direction of sound in the transverse plane of the line array. The receiving voltage sensitivity of the accelerometers and hydrophone was −199 and −196 dB, respectively, at 3 kHz. The directional cardioid beams generated by summing the omnidirectional beam from the hydrophone and the dipole beam from the accelerometers were validated over the entire operating frequency.
Tensile and creep-rupture response of additively manufactured nickel-based superalloy CM247LC (2022)

Tensile and creep rupture properties of crack-free CM247LC alloy, processed via laser powder bed fusion, have been characterised in this work at temperatures up to 1000°C. The subject alloy matches or even exceeds the tensile performance of its directionally solidified counterpart up to 700°C, beyond which both the strength and ductility drop off relatively rapidly with increasing temperature. It was found that the agglomeration of discrete carbides – that essentially pin the grain boundaries – facilitate the nucleation, linking and propagation of microcracks along the adjacent grain boundaries at elevated temperatures. Relatively short-term creep-rupture tests conducted at 800°C show the need for greatly improving the microstructure of this alloy to compete with its directionally solidified or conventionally cast counterparts, especially considering that this material finds extensive application up to ∼950°C in turbomachinery components. Increasing the grain size, incorporating grain boundary engineering concepts and a better understanding of carbide/γ' precipitate evolutionary characteristics can greatly help to improve the material's suboptimal creep response.
Unprecedentedly Low CO2 Transport through Vertically Aligned, Conical Silicon Nanotube Membranes (2020)

Nanotube membranes could show significantly enhanced permeance and selectivity for gas separations. Up until now, studies have primarily focused on applying carbon nanotubes to membranes to achieve ultrafast mass transport. Here, we report the first preparation of silicon nanotube (SiNT) membranes via a template-assisted method and investigate the gas transport behavior through these SiNT membranes using single- and mixed-gas permeation experiments. The SiNT membranes consist of conical cylinder-shaped nanotubes vertically aligned on a porous silicon wafer substrate. The diameter of the SiNT pore mouths are 10 and 30 nm, and the average inner diameter of the tube body is 80 nm. Interestingly, among the gases tested, we found an unprecedentedly low CO<sub>2</sub> permeance through the SiNT membranes in single-gas permeation experiments, exceeding the theoretical Knudsen selectivity toward small gases/CO<sub>2</sub> separation. This behavior was caused by the reduction of CO<sub>2</sub> permeability through the blocking effect of CO<sub>2</sub> adsorbed in the narrow pore channels of the SiNT cone regions, indicating that CO<sub>2</sub> molecules have a high affinity to the native silicon oxide layer (∼2 nm) that is formed on the inner walls of SiNTs. SiNT membranes also exhibited enhanced gas permeance and water flux as compared to classic theoretical models and, as such, may prove useful as a new type of nanotube material for use in membrane applications.
Antibiotic Adjuvants: Diverse Strategies for Controlling Drug‐Resistant Pathogens (2014)

The growing number of bacterial pathogens that are resistant to numerous antibiotics is a cause for concern around the globe. There have been no new broad-spectrum antibiotics developed in the last 40 years, and the drugs we have currently are quickly becoming ineffective. In this article, we explore a range of therapeutic strategies that could be employed in conjunction with antibiotics and may help to prolong the life span of these life-saving drugs. Discussed topics include antiresistance drugs, which are administered to potentiate the effects of current antimicrobials in bacteria where they are no longer (or never were) effective; antivirulence drugs, which are directed against bacterial virulence factors; host-directed therapies, which modulate the host's immune system to facilitate infection clearance; and alternative treatments, which include such therapies as oral rehydration for diarrhea, phage therapy, and probiotics. All of these avenues show promise for the treatment of bacterial infections and should be further investigated to explore their full potential in the face of a postantibiotic era.
Scalable On-Demand Production of Purified Diazomethane Suitable for Sensitive Catalytic Reactions (2020)

We have developed a convenient development-scale reactor (0.44 mol/h) to prepare diazomethane from N-methyl-N-nitroso-p-toluenesulfonamide (MNTS) in ∼80% yield. Diazomethane (CH2N2) made with this reactor is extracted into nitrogen gas from the liquid reaction mixture, effectively removing it from reagents and byproducts that may interfere in subsequent reactions. Vertically oriented tubular reactors were used to produce and consume diazomethane in situ. Key features of this reactor include high productivity and correspondingly low reactor volume (reactor volume/liquid flow rate = 6.5 min) and a commercially available gas/liquid separator equipped with a selectively permeating hydrophilic membrane. The design of the reactor keeps the inventory below 53 mg of CH2N2 during normal operation. The reactor was demonstrated by generating CH2N2 that was used in a connected continuous reactor. We evaluated esterification reactions and a continuous Pd-catalyzed cyclopropanation reaction with the reactor and achieved high conversion with 1.5 and 4.1 equiv of MNTS precursor, respectively.
Wideband in‐phase/quadrature imbalance compensation using finite impulse response filter (2014)

The authors proposed an in‐phase/quadrature (I/Q) imbalance compensation technique for wideband digital receiver applications. An I/Q channel‐based receiver can double the receiver working bandwidth. However, the amplitude/phase imbalance of an imperfect hybrid coupler can generate image signals thus reducing the receiver's instantaneous dynamic range. They developed a finite impulse response filter‐based technique to mitigate deleterious effects because of the amplitude/phase imbalance. Both simulations and experiments were conducted to verify validity of the developed algorithm. The simulation and experiment results show that the proposed imbalance mitigation technique can reduce image signal powers by more than 24 dB or down to noise level. A receiver system level simulation is also conducted to demonstrate the practicality of the proposed imbalance mitigation method.
The Birth-Death-Mutation Process: A New Paradigm for Fat Tailed Distributions (2011)

Fat tailed statistics and power-laws are ubiquitous in many complex systems. Usually the appearance of of a few anomalously successful individuals (bio-species, investors, websites) is interpreted as reflecting some inherent "quality" (fitness, talent, giftedness) as in Darwin's theory of natural selection. Here we adopt the opposite, "neutral", outlook, suggesting that the main factor explaining success is merely luck. The statistics emerging from the neutral birth-death-mutation (BDM) process is shown to fit marvelously many empirical distributions. While previous neutral theories have focused on the power-law tail, our theory economically and accurately explains the entire distribution. We thus suggest the BDM distribution as a standard neutral model: effects of fitness and selection are to be identified by substantial deviations from it.
Teaching GPR in the context of urban geophysics: The IGUaNA project (2020)

Urban and environmental studies (i.e. utility mapping, brownfields, impacted wetlands, archaeology, etc.) provide a clear connection between science and societal issues, and offer opportunities to reach students who would typically not be exposed to geophysics, urban or otherwise. Introducing Geophysics for Urban and Near-Surface Applications (IGUaNA) is developing a series of teaching modules specifically geared to introductory level college student. Curriculum engages students, increases addresses real-life environmental challenges with quantitative approaches, and connects students to relatable societal issues (https://serc.carleton.edu/iguana/index.html). It follows the format of other collaborative efforts, such as InTeGrate and GETSI (serc.carleton.edu), that have been successful in developing and disseminating curricula that meets the needs of educators and addresses key scientific challenges. Here we present a module that employs ground-penetrating radar for utility detection and forensic studies. Students will be able to explain the kinds of man-made features GPR could resolve and method limitations, use GPR data to estimate the depth of buried features. The ultimate goals with these modules are 1) to create interest in geophysics and recruit/retain students at the undergraduate level, and 2) promote early engagement with underrepresented demographics that make up a large portion of the student body.
Assays for Studying the Role of Vitronectin in Bacterial Adhesion and Serum Resistance (2018)

Assays For Studying The Role Of Vitronectin In Bacterial Adhesion And Serum Resistance - Video. JoVE publishes peer-reviewed scientific video protocols to accelerate biological, medical, chemical and physical research. Watch our scientific video articles. JoVE is the world-leading producer and provider of science videos with the mission to improve scientific research, scientific journals, and education. Millions of scientists, educators and students at thousands of universities, colleges, hospitals and biopharmaceutical companies worldwide use JoVE for their research, teaching and learning.
The Murals of the Hall of the Facets in Moscow Kremlin: Returning to Folk Spirit (2014)

Is devoted to the repainting of 16th century murals in the Hall of the Facets in Moscow Kremlin by the Palekh icon­painters Belousovs which was organised on the occasion of the coronation of Alexander III by Georgy Filimonov, a famous archaeologist. While Alexander III considered the “restored” painting as the important element of the celebrations that were to display the idea of sacrosanctity of tsarist autocracy, Filimonov believed that the paintings of the Hall were to contribute to the development of the truly national art in Russia.
Supplementary Table from Development of Highly Effective Anti-Mesothelin hYP218 Chimeric Antigen Receptor T Cells With Increased Tumor Infiltration and Persistence for Treating Solid Tumors (2023)

Supplementary Table from Development of Highly Effective Anti-Mesothelin hYP218 Chimeric Antigen Receptor T Cells With Increased Tumor Infiltration and Persistence for Treating Solid Tumors