bluuebunny/crossref_metadata_2025_split huggingface dataset:
Canonical Hamiltonian ensemble representation of dephasing dynamics and the impact of thermal fluctuations on quantum-to-classical transition
Authors: Chen Hong-Bin , Chen Yueh-Nan 
Published: May 2021

AbstractAn important mathematical tool for studying open quantum system theory, which studies the dynamics of a reduced system, is the completely positive and trace-preserving dynamical linear map parameterized by a special parameter-time. Counter-intuitively, akin to the Fourier transform of a signal in time-sequence to its frequency distribution, the time evolution of a reduced system can also be studied in the frequency domain. A recent proposed idea which studies the representation of dynamical processes in the frequency domain, referred to as canonical Hamiltonian ensemble representation (CHER), proved its capability of characterizing the noncalssical traits of the dynamics. Here we elaborate in detail the theoretical foundation within a unified framework and demonstrate several examples for further studies of its properties. In particular, we find that the thermal fluctuations are clearly manifested in the manner of broadening CHER, and consequently rendering the CHER less nonclassical. We also point out the discrepancy between the notions of nonclassicality and non-Markovianity, show multiple CHERs beyond pure dephasing, and, finally, to support the practical viability, propose an experimental realization based upon the free induction decay measurement of nitrogen-vacancy center in diamond.
A novel thermostable beetle luciferase based cytotoxicity assay
Authors: Choi Sunju , Matta Hittu , Gopalakrishnan Ramakrishnan , Natarajan Venkatesh , Gong Songjie , Jeronimo Alberto , Kuo Wei-Ying , Bravo Bryant , Chaudhary Preet M. 
Published: May 2021

AbstractCytotoxicity assays are essential for the testing and development of novel immunotherapies for the treatment of cancer. We recently described a novel cytotoxicity assay, termed the Matador assay, which was based on marine luciferases and their engineered derivatives. In this study, we describe the development of a new cytotoxicity assay termed ‘Matador-Glo assay’ which takes advantage of a thermostable variant of Click Beetle Luciferase (Luc146-1H2). Matador-Glo assay utilizes Luc146-1H2 and D-luciferin as the luciferase-substrate pair for luminescence detection. The assay involves ectopic over-expression of Luc146-1H2 in the cytosol of target cells of interest. Upon damage to the membrane integrity, the Luc146-1H2 is either released from the dead and dying cells or its activity is preferentially measured in dead and dying cells. We demonstrate that this assay is simple, fast, specific, sensitive, cost-efficient, and not labor-intensive. We further demonstrate that the Matador-Glo assay can be combined with the marine luciferase-based Matador assay to develop a dual luciferase assay for cell death detection. Finally, we demonstrate that the Luc146-1H2 expressing target cells can also be used for in vivo bioluminescence imaging applications.
Sustained release of usnic acid from graphene coatings ensures long term antibiofilm protection
Authors: Pandit Santosh , Rahimi Shadi , Derouiche Abderahmane , Boulaoued Athmane , Mijakovic Ivan 
Published: May 2021

AbstractProtecting surfaces from bacterial colonization and biofilm development is an important challenge for the medical sector, particularly when it comes to biomedical devices and implants that spend longer periods in contact with the human body. A particularly difficult challenge is ensuring long-term protection, which is usually attempted by ensuring sustained release of antibacterial compounds loaded onto various coatings. Graphene have a considerable potential to reversibly interact water insoluble molecules, which makes them promising cargo systems for sustained release of such compounds. In this study, we developed graphene coatings that act as carriers capable of sustained release of usnic acid (UA), and hence enable long-term protection of surfaces against colonization by bacterial pathogens Staphylococcus aureus and Staphylococcus epidermidis. Our coatings exhibited several features that made them particularly effective for antibiofilm protection: (i) UA was successfully integrated with the graphene material, (ii) a steady release of UA was documented, (iii) steady UA release ensured strong inhibition of bacterial biofilm formation. Interestingly, even after the initial burst release of UA, the second phase of steady release was sufficient to block bacterial colonization. Based on these results, we propose that graphene coatings loaded with UA can serve as effective antibiofilm protection of biomedical surfaces.
Interaction among sea urchins in response to food cues
Authors: Sun Jiangnan , Zhao Zihe , Zhao Chong , Yu Yushi , Ding Peng , Ding Jingyun , Yang Mingfang , Chi Xiaomei , Hu Fangyuan , Chang Yaqing 
Published: May 2021

AbstractInteraction among sea urchins remains largely uninvestigated, although the aggregation of sea urchins is common. In the present study, 1, 15 and 30 sea urchins Strongylocentrotus intermedius (11.06 ± 0.99 mm in test diameter) were placed in a 1 m2 circular tank, respectively. Movement behaviors were recorded for 12 min to investigate potential interactions among sea urchins. After the 12-min control period, we added food cues into the tank and recorded the changes in sea urchins’ behaviors. For the first time, we here quantified the interactions among sea urchins in laboratory and found that the interactions varied with food cues and with different densities. The sea urchins dispersed in random directions after being released. There was no significant difference in the movement speed and the displacement of sea urchins among the three density groups (1, 15 and 30 ind/m2). The interaction occurred when sea urchins randomly contacted with the conspecifics and slowed down the movement speed. The speed of sea urchins after physical contacts decreased by an average of 40% in the density of 15 ind/m2 and 17% in the density of 30 ind/m2. This interaction resulted in significantly higher randomness in the movement direction and lower movement linearity in 15 and 30 ind/m2 than in 1 ind/m2. After the introduction of food cues, the movement speed, displacement and dispersal distance of sea urchin groups decreased significantly in all the three densities. The dispersal distance and expansion speed of sea urchins were significantly lower in 30 ind/m2 than those in 15 ind/m2. The present study indicates that the interaction among sea urchins limits the movement of individual sea urchin and provides valuable information into how large groups of sea urchins are stable in places where food is plentiful.
Identification of linear epitopes on the flagellar proteins of Clostridioides difficile
Authors: Razim A. , Pacyga K. , Naporowski P. , Martynowski D. , Szuba A. , Gamian A. , Górska S. 
Published: May 2021

AbstractClostridioides difficile (C. difficile) is an opportunistic anaerobic bacterium that causes severe diseases of the digestive tract of humans and animals. One of the possible methods of preventing C. difficile infection is to develop a vaccine. The most promising candidates for vaccine antigens are the proteins involved in the adhesion phenomena. Among them, the FliC and FliD are considered to be suitable candidates. In this paper, the FliC and FliD protein polypeptide epitopes were mapped in silico and by using PEPSCAN procedure. We identified four promising epitopes: 117QRMRTLS123, 205MSKAG209 of FliC and 226NKVAS230, 306TTKKPKD312 of FliD protein. We showed that 117QRMRTLS123 sequence is not only located in TLR5-binding and activating region, as previously shown, but forms an epitope recognized by C. difficile-infected patients’ antibodies. 205MSKAG209 is a C. difficile-unique, immunogenic sequence that forms an exposed epitope on the polymerized flagella structure which makes it a suitable vaccine antigen. 226NKVAS230 and 306TTKKPKD312 are well exposed and possess potential protective properties according to VaxiJen analysis. Our results open the possibility to use these epitopes as suitable anti-C. difficile vaccine antigens.
Hybrid modeling approach for mode-locked laser diodes with cavity dispersion and nonlinearity
Authors: Cuyvers Stijn , Poelman Stijn , Van Gasse Kasper , Kuyken Bart 
Published: May 2021

AbstractSemiconductor-based mode-locked lasers, integrated sources enabling the generation of coherent ultra-short optical pulses, are important for a wide range of applications, including datacom, optical ranging and spectroscopy. As their performance remains largely unpredictable due to the lack of commercial design tools and the poorly understood mode-locking dynamics, significant research has focused on their modeling. In recent years, traveling-wave models have been favored because they can efficiently incorporate the rich semiconductor physics of the laser. However, thus far such models struggle to include nonlinear and dispersive effects of an extended passive laser cavity, which can play an important role for the temporal and spectral pulse evolution and stability. To overcome these challenges, we developed a hybrid modeling strategy by unifying the traveling-wave modeling technique for the semiconductor laser sections with a split-step Fourier method for the extended passive laser cavity. This paper presents the hybrid modeling concept and exemplifies for the first time the significance of the third order nonlinearity and dispersion of the extended cavity for a 2.6 GHz III–V-on-Silicon mode-locked laser. This modeling approach allows to include a wide range of physical phenomena with low computational complexity, enabling the exploration of novel operating regimes such as chip-scale soliton mode-locking.
Climate drivers of large magnitude snow avalanche years in the U.S. northern Rocky Mountains
Authors: Peitzsch Erich H. , Pederson Gregory T. , Birkeland Karl W. , Hendrikx Jordy , Fagre Daniel B. 
Published: May 2021

AbstractLarge magnitude snow avalanches pose a hazard to humans and infrastructure worldwide. Analyzing the spatiotemporal behavior of avalanches and the contributory climate factors is important for understanding historical variability in climate-avalanche relationships as well as improving avalanche forecasting. We used established dendrochronological methods to develop a long-term (1867–2019) regional avalanche chronology for the Rocky Mountains of northwest Montana using tree-rings from 647 trees exhibiting 2134 avalanche-related growth disturbances. We then used principal component analysis and a generalized linear autoregressive moving average model to examine avalanche-climate relationships. Historically, large magnitude regional avalanche years were characterized by stormy winters with positive snowpack anomalies, with avalanche years over recent decades increasingly influenced by warmer temperatures and a shallow snowpack. The amount of snowpack across the region, represented by the first principal component, is shown to be directly related to avalanche probability. Coincident with warming and regional snowpack reductions, a decline of ~ 14% (~ 2% per decade) in overall large magnitude avalanche probability is apparent through the period 1950–2017. As continued climate warming drives further regional snowpack reductions in the study region our results suggest a decreased probability of regional large magnitude avalanche frequency associated with winters characterized by large snowpacks and a potential increase in large magnitude events driven by warming temperatures and spring precipitation.
Differences in effectiveness and use of laparoscopic surgery in locally advanced colon cancer patients
Authors: Schootman M. , Mutch Matthew , Loux T. , Eberth J. M. , Davidson N. O. 
Published: May 2021

AbstractPatients with locally advanced colon cancer have worse outcomes. Guidelines of various organizations are conflicting about the use of laparoscopic colectomy (LC) in locally advanced colon cancer. We determined whether patient outcomes of LC and open colectomy (OC) for locally advanced (T4) colon cancer are comparable in all colon cancer patients, T4a versus T4b patients, obese versus non-obese patients, and tumors located in the ascending, descending, and transverse colon. We used data from the 2013–2015 American College of Surgeons’ National Surgical Quality Improvement Program. Patients were diagnosed with nonmetastatic pT4 colon cancer, with or without obstruction, and underwent LC (n = 563) or OC (n = 807). We used a composite outcome score (mortality, readmission, re-operation, wound infection, bleeding transfusion, and prolonged postoperative ileus); length of stay; and length of operation. Patients undergoing LC exhibited a composite outcome score that was 9.5% lower (95% CI − 15.4; − 3.5) versus those undergoing OC. LC patients experienced a 11.3% reduction in postoperative ileus (95% CI − 16.0; − 6.5) and an average of 2 days shorter length of stay (95% CI − 2.9; − 1.0). Patients undergoing LC were in the operating room an average of 13.5 min longer (95% CI 1.5; 25.6). We found no evidence for treatment heterogeneity across subgroups (p > 0.05). Patients with locally advanced colon cancer who receive LC had better overall outcomes and shorter lengths of stay compared with OC patients. LC was equally effective in obese/nonobese patients, in T4a/T4b patients, and regardless of the location of the tumor.
The feasibility of Gazefinder under 12 months of age infants
Authors: Fukushima Shuntaro , Takahashi Tomoo , Tsukamoto Kazuki , Matsumura Misaki , Takigawa Ryo , Sakai Yasuo , Maniwa Sokichi , Murphy Lynne , Taketani Takeshi 
Published: May 2021

AbstractEye-tracking to evaluate gaze patterns has developed as an assessment tool for children with autism spectrum disorder (ASD). Gazefinder is one of Eye-tracking devices and few studies have investigated whether it can measure the gaze data of infants under 12 months of age. We conducted a prospective cross-sectional study from April 2019 to March 2020 in a periodic health checkup in Ohchi County, Shimane, Japan. Participants included infants between 4 and 11 months of age who were not suspected the presence of developmental problems. Ninety-three participants’ datapoints were analyzed. The mean age was 6.5 months and mean developmental quotient was 88%. The mean fixation time percentage of all sequences was 81.0% (standard deviation; 4.4), and there was no significant difference in each age group. Infants in all groups showed a significantly higher predilection for eyes than for mouths. There was a positive association of age with human gaze and a negative association with geometric gaze. Moreover, we confirmed that joint attention skills were enhanced in accordance with their growth process. The eye-tracking data were almost corresponding to previous studies’ data of infant with typical development and Gazefinder could be applied to infants starting at 4 months of age.
Infrared light sensors permit rapid recording of wingbeat frequency and bioacoustic species identification of mosquitoes
Authors: Kim Dongmin , DeBriere Terry J. , Cherukumalli Satish , White Gregory S. , Burkett-Cadena Nathan D. 
Published: May 2021

AbstractRecognition and classification of mosquitoes is a critical component of vector-borne disease management. Vector surveillance, based on wingbeat frequency and other parameters, is becoming increasingly important in the development of automated identification systems, but inconsistent data quality and results frequently emerge from different techniques and data processing methods which have not been standardized on wingbeat collection of numerous species. We developed a simple method to detect and record mosquito wingbeat by multi-dimensional optical sensors and collected 21,825 wingbeat files from 29 North American mosquito species. In pairwise comparisons, wingbeat frequency of twenty six species overlapped with at least one other species. No significant differences were observed in wingbeat frequencies between and within individuals of Culex quinquefasciatus over time. This work demonstrates the potential utility of quantifying mosquito wingbeat frequency by infrared light sensors as a component of an automated mosquito identification system. Due to species overlap, wingbeat frequency will need to integrate with other parameters to accurately delineate species in support of efficient mosquito surveillance, an important component of disease intervention.
Inhibition of a nutritional endosymbiont by glyphosate abolishes mutualistic benefit on cuticle synthesis in Oryzaephilus surinamensis
Authors: Kiefer Julian Simon Thilo , Batsukh Suvdanselengee , Bauer Eugen , Hirota Bin , Weiss Benjamin , Wierz Jürgen C. , Fukatsu Takema , Kaltenpoth Martin , Engl Tobias 
Published: May 2021

AbstractGlyphosate is widely used as a herbicide, but recent studies begin to reveal its detrimental side effects on animals by targeting the shikimate pathway of associated gut microorganisms. However, its impact on nutritional endosymbionts in insects remains poorly understood. Here, we sequenced the tiny, shikimate pathway encoding symbiont genome of the sawtoothed grain beetleOryzaephilus surinamensis. Decreased titers of the aromatic amino acid tyrosine in symbiont-depleted beetles underscore the symbionts’ ability to synthesize prephenate as the precursor for host tyrosine synthesis and its importance for cuticle sclerotization and melanization. Glyphosate exposure inhibited symbiont establishment during host development and abolished the mutualistic benefit on cuticle synthesis in adults, which could be partially rescued by dietary tyrosine supplementation. Furthermore, phylogenetic analyses indicate that the shikimate pathways of many nutritional endosymbionts likewise contain a glyphosate sensitive 5-enolpyruvylshikimate-3-phosphate synthase. These findings highlight the importance of symbiont-mediated tyrosine supplementation for cuticle biosynthesis in insects, but also paint an alarming scenario regarding the use of glyphosate in light of recent declines in insect populations.
Coupled oscillations enable rapid temporal recalibration to audiovisual asynchrony
Authors: Lennert Therese , Samiee Soheila , Baillet Sylvain 
Published: May 2021

AbstractThe brain naturally resolves the challenge of integrating auditory and visual signals produced by the same event despite different physical propagation speeds and neural processing latencies. Temporal recalibration manifests in human perception to realign incoming signals across the senses. Recent behavioral studies show it is a fast-acting phenomenon, relying on the most recent exposure to audiovisual asynchrony. Here we show that the physiological mechanism of rapid, context-dependent recalibration builds on interdependent pre-stimulus cortical rhythms in sensory brain regions. Using magnetoencephalography, we demonstrate that individual recalibration behavior is related to subject-specific properties of fast oscillations (>35 Hz) nested within a slower alpha rhythm (8–12 Hz) in auditory cortex. We also show that the asynchrony of a previously presented audiovisual stimulus pair alters the preferred coupling phase of these fast oscillations along the alpha cycle, with a resulting phase-shift amounting to the temporal recalibration observed behaviorally. These findings suggest that cross-frequency coupled oscillations contribute to forming unified percepts across senses.
Accurate absolute free energies for ligand–protein binding based on non-equilibrium approaches
Authors: Gapsys Vytautas , Yildirim Ahmet , Aldeghi Matteo , Khalak Yuriy , van der Spoel David , de Groot Bert L. 
Published: May 2021

AbstractThe accurate calculation of the binding free energy for arbitrary ligand–protein pairs is a considerable challenge in computer-aided drug discovery. Recently, it has been demonstrated that current state-of-the-art molecular dynamics (MD) based methods are capable of making highly accurate predictions. Conventional MD-based approaches rely on the first principles of statistical mechanics and assume equilibrium sampling of the phase space. In the current work we demonstrate that accurate absolute binding free energies (ABFE) can also be obtained via theoretically rigorous non-equilibrium approaches. Our investigation of ligands binding to bromodomains and T4 lysozyme reveals that both equilibrium and non-equilibrium approaches converge to the same results. The non-equilibrium approach achieves the same level of accuracy and convergence as an equilibrium free energy perturbation (FEP) method enhanced by Hamiltonian replica exchange. We also compare uni- and bi-directional non-equilibrium approaches and demonstrate that considering the work distributions from both forward and reverse directions provides substantial accuracy gains. In summary, non-equilibrium ABFE calculations are shown to yield reliable and well-converged estimates of protein–ligand binding affinity.
Structure of a seeded palladium nanoparticle and its dynamics during the hydride phase transformation
Authors: Suzana Ana F. , Wu Longlong , Assefa Tadesse A. , Williams Benjamin P. , Harder Ross , Cha Wonsuk , Kuo Chun-Hong , Tsung Chia-Kuang , Robinson Ian K. 
Published: May 2021

AbstractPalladium absorbs large volumetric quantities of hydrogen at room temperature and ambient pressure, making the palladium hydride system a promising candidate for hydrogen storage. Here, we use Bragg coherent diffraction imaging to map the strain associated with defects in three dimensions before and during the hydride phase transformation of an individual octahedral palladium nanoparticle, synthesized using a seed-mediated approach. The displacement distribution imaging unveils the location of the seed nanoparticle in the final nanocrystal. By comparing our experimental results with a finite-element model, we verify that the seed nanoparticle causes a characteristic displacement distribution of the larger nanocrystal. During the hydrogen exposure, the hydride phase is predominantly formed on one tip of the octahedra, where there is a high number of lower coordinated Pd atoms. Our experimental and theoretical results provide an unambiguous method for future structure optimization of seed-mediated nanoparticle growth and in the design of palladium-based hydrogen storage systems.
The electrochemistry of size dependent graphene via liquid phase exfoliation: capacitance and ionic transport
Authors: Deerattrakul Varisara , Hirunpinyopas Wisit , Pisitpipathsin Nuttapon , Saisopa Thanit , Sawangphruk Montree , Nualchimplee Chakrit , Iamprasertkun Pawin 
Published: May 2021

This work explores the capacitance and ionic transport properties of size dependent graphene (from 100 nm to 1 μm) prepared through the liquid phase exfoliation of graphite in which the size of graphene was finely selected using a multi-step centrifugation technique.