Miracle-dz/UniFAR-FTUs huggingface dataset:
Modified Protein-Water Interactions in CHARMM36m for Thermodynamics and Kinetics of Proteins in Dilute and Crowded Solutions

Proper balance between protein-protein and protein-water interactions is vital for atomistic molecular dynamics (MD) simulations of globular proteins as well as intrinsically disordered proteins (IDPs). The overestimation of protein-protein interactions tends to make IDPs more compact than those in experiments. Likewise, multiple proteins in crowded solutions are aggregated with each other too strongly. To optimize the balance, Lennard-Jones (LJ) interactions between protein and water are often increased about 10% (with a scaling parameter, λ = 1.1) from the existing force fields. Here, we explore the optimal scaling parameter of protein-water LJ interactions for CHARMM36m in conjunction with the modified TIP3P water model, by performing enhanced sampling MD simulations of several peptides in dilute solutions and conventional MD simulations of globular proteins in dilute and crowded solutions. In our simulations, 10% increase of protein-water LJ interaction for the CHARMM36m cannot maintain stability of a small helical peptide, (AAQAA)3 in a dilute solution and only a small modification of protein-water LJ interaction up to the 3% increase (λ = 1.03) is allowed. The modified protein-water interactions are applicable to other peptides and globular proteins in dilute solutions without changing thermodynamic properties from the original CHARMM36m. However, it has a great impact on the diffusive properties of proteins in crowded solutions, avoiding the formation of too sticky protein-protein interactions.
CT-Diagnosed Sarcopenia and Cardiovascular Biomarkers in Patients Undergoing Transcatheter Aortic Valve Replacement: Is It Possible to Predict Muscle Loss Based on Laboratory Tests?—A Multicentric Retrospective Analysis

Background: Patients with severe aortic valve stenosis (AS) often present with heart failure and sarcopenia. Sarcopenia, described as progressive degradation of skeletal muscle mass, has frequently been implicated as a cause of increased mortality, prolonged hospitalization and generalized poor outcome after transcatheter aortic valve replacement (TAVR). At present, sarcopenia is defined by the European Working Group on Sarcopenia in Older People (EWGSOP) based on clinical examination criteria and radiological imaging. The aim of the present study was to compare patients with Computed Tomography (CT)-diagnosed sarcopenia with regard to the expression of cardiovascular biomarkers in order to obtain additional, laboratory-chemical information. Methods: A total of 179 patients with severe AS were included in this retrospective study. Sarcopenia was determined via CT by measurement of the psoas muscle area (PMA), which was indexed to body surface area (PMAi). According to previous studies, the lowest tertile was defined as sarcopenic. Patients with (59/179) and without sarcopenia (120/179) in the overall cohort were compared by gender-specific cut-offs with regard to the expression of cardiovascular biomarkers such as brain natriuretic peptide (BNP), soluble suppression of tumorigenicity-2 (sST2), growth/differentiation of factor-15 (GDF-15), heart-type fatty-acid binding protein (H-FABP), insulin like growth factor binding protein 2 (IGF-BP2) and soluble urokinase-type plasminogen activator receptor (suPAR). Additionally, binary logistic regression analyses were calculated to detect possible predictors of the presence of sarcopenia. Results: No statistical differences regarding one-year survival could be detected between sarcopenic and non-sarcopenic patients in survival curves (log rank test p = 0.179). In the entire cohort, only BNP and hemoglobin (HB) showed a statistically significant difference, with only HB emerging as a relevant predictor for the presence of sarcopenia after binary logistic regression analysis (p = 0.015). No relevant difference in biomarker expression could be found in the male cohort. Regarding the female cohort, statistically significant differences were found in BNP, HB and hematocrit (HK). In binary logistic regression, however, none of the investigated criteria could be related to sarcopenia. Conclusion: Regardless of gender, patients with imaging-based muscle degradation did not demonstrate significantly different cardiovascular biomarker expression compared to those without it.
Nanoscale Control of Structure and Composition for Nanocrystalline Fe Thin Films Grown by Oblique Angle RF Sputtering

The use of Fe films as multi-element targets in space radiation experiments with high-intensity ultrashort laser pulses requires a surface structure that can enhance the laser energy absorption on target, as well as a low concentration and uniform distribution of light element contaminants within the films. In this paper, (110) preferred orientation nanocrystalline Fe thin films with controlled morphology and composition were grown on (100)-oriented Si substrates by oblique angle RF magnetron sputtering, at room temperature. The evolution of films key-parameters, crucial for space-like radiation experiments with organic material, such as nanostructure, morphology, topography, and elemental composition with varying RF source power, deposition pressure, and target to substrate distance is thoroughly discussed. A selection of complementary techniques was used in order to better understand this interdependence, namely X-ray Diffraction, Atomic Force Microscopy, Scanning and Transmission Electron Microscopy, Energy Dispersive X-ray Spectroscopy and Non-Rutherford Backscattering Spectroscopy. The films featured a nanocrystalline, tilted nanocolumn structure, with crystallite size in the (110)-growth direction in the 15–25 nm range, average island size in the 20–50 nm range, and the degree of polycrystallinity determined mainly by the shortest target-to-substrate distance (10 cm) and highest deposition pressure (10−2 mbar Ar). Oxygen concentration (as impurity) into the bulk of the films as low as 1 at. %, with uniform depth distribution, was achieved for the lowest deposition pressures of (1–3) × 10−3 mbar Ar, combined with highest used values for the RF source power of 125–150 W. The results show that the growth process of the Fe thin film is strongly dependent mainly on the deposition pressure, with the film morphology influenced by nucleation and growth kinetics. Due to better control of film topography and uniform distribution of oxygen, such films can be successfully used as free-standing targets for high repetition rate experiments with high power lasers to produce Fe ion beams with a broad energy spectrum.
Impact of Shunt Resistance on the Performance of Curved Thin-Film Photovoltaic Modules With Series-Connected Solar Cells

Curved photovoltaics (PV) is gaining widespread application in modern energy-efficient infrastructure, wearable electronics, and vehicles. Due to the different orientations of the solar cells in curved PV modules, current mismatch between solar cells is more prevalent in curved PV than conventional flat PV. In this article, we investigated the effect of shunt resistances, which can mitigate current mismatches in series-connected solar cells, on the performance of curved thin-film PV modules. A flexible 85 × 80 mm2 Cu(In,Ga)Se2 mini-module composed of 17 series-connected solar cells on a curved surface was characterized experimentally and theoretically. We found that the short-circuit current of the curved PV module is affected by all the solar cells connected in series and is not simply determined by the current-limiting solar cell. The current-voltage characteristics of a curved PV module are well described by a simple model that includes low shunt resistance. The power generated from normal irradiance decreases with shunt resistance; however, the power for tilted illumination is higher than that of a module without shunt resistance. This indicates that the low shunt resistance can suppress the power loss due to current mismatch. In addition, curved PV modules cause self-shading under highly tilted illumination but curved PV modules with low shunt resistances provide power even when some solar cells are not illuminated. Furthermore, sudden current mismatches in solar cells, which generate detrimentally high reverse biases can be eliminated by the shunt resistance. This confirms the protective effect of the shunt resistance to enhance the durability of curved PV modules.
Urbanization drives adaptive evolution in a Neotropical bird

Abstract Urbanization has dramatic impacts on natural habitats and such changes may potentially drive local adaptation of urban populations. Behavioral change has been specifically shown to facilitate the fast adaptation of birds to changing environments, but few studies have investigated the genetic mechanisms of this process. Such investigations could provide insights into questions about both evolutionary theory and management of urban populations. In this study, we investigated whether local adaptation has occurred in urban populations of a Neotropical bird species, Coereba flaveola, specifically addressing whether observed behavioral adaptations are correlated to genetic signatures of natural selection. To answer this question, we sampled 24 individuals in urban and rural environments, and searched for selected loci through a genome-scan approach based on RADseq genomic data, generated and assembled using a reference genome for the species. We recovered 46 loci as putative selection outliers, and 30 of them were identified as associated with biological processes possibly related to urban adaptation, such as the regulation of energetic metabolism, regulation of genetic expression, and changes in the immunological system. Moreover, genes involved in the development of the nervous system showed signatures of selection, suggesting a link between behavioral and genetic adaptations. Our findings, in conjunction with similar results in previous studies, support the idea that cities provide a similar selective pressure on urban populations and that behavioral plasticity may be enhanced through genetic changes in urban populations.
Aziridination Reactivity of a Manganese(II) Complex with a Bulky Chelating Bis(Alkoxide) Ligand

Treatment of Mn(N(SiMe3)2)2(THF)2 with bulky chelating bis(alkoxide) ligand [1,1′:4′,1′′-terphenyl]-2,2′′-diylbis(diphenylmethanol) (H2[O-terphenyl-O]Ph) formed a seesaw manganese(II) complex Mn[O-terphenyl-O]Ph(THF)2, characterized by structural, spectroscopic, magnetic, and analytical methods. The reactivity of Mn[O-terphenyl-O]Ph(THF)2 with various nitrene precursors was investigated. No reaction was observed between Mn[O-terphenyl-O]Ph(THF)2 and aryl azides. In contrast, the treatment of Mn[O-terphenyl-O]Ph(THF)2 with iminoiodinane PhINTs (Ts = p-toluenesulfonyl) was consistent with the formation of a metal-nitrene complex. In the presence of styrene, the reaction led to the formation of aziridine. Combining varying ratios of styrene and PhINTs in different solvents with 10 mol% of Mn[O-terphenyl-O]Ph(THF)2 at room temperature produced 2-phenylaziridine in up to a 79% yield. Exploration of the reactivity of Mn[O-terphenyl-O]Ph(THF)2 with various olefins revealed (1) moderate aziridination yields for p-substituted styrenes, irrespective of the electronic nature of the substituent; (2) moderate yield for 1,1′-disubstituted α-methylstyrene; (3) no aziridination for aliphatic α-olefins; (4) complex product mixtures for the β-substituted styrenes. DFT calculations suggest that iminoiodinane is oxidatively added upon binding to Mn, and the resulting formal imido intermediate has a high-spin Mn(III) center antiferromagnetically coupled to an imidyl radical. This imidyl radical reacts with styrene to form a sextet intermediate that readily reductively eliminates the formation of a sextet Mn(II) aziridine complex.
Smartphone applications are used for self-management, telerehabilitation, evaluation and data collection in low back pain healthcare: a scoping review

Background: Technological developments have accelerated notably in the field of telecommunications in the last few decades. Smartphone use has grown in providing healthcare for patients with low back pain (LBP), but the literature lacks an analysis of the use of smartphone apps. This scoping review aimed to identify current areas of smartphone apps use for managing LBP. We also aimed to evaluate the current status of the effectiveness or scientific validity of such use and determine perspectives for their potential development. Methods: We searched PubMed, PEDro and Embase for articles published in English up to May 3rd, 2021 that investigated smartphone use for LBP healthcare and their purpose. All types of study design were accepted. Studies concerning telemedicine or telerehabilitation but without use of a smartphone were not included. The same search strategy was performed by two researchers independently and a third researcher validated the synthesis of the included studies. Results: We included 43 articles: randomised controlled trials (RCTs) (n=12), study protocols (n=6), reliability/validity studies (n=6), systematic reviews (n=7), cohort studies (n=4), qualitative studies (n=6), and case series (n=1). The purposes of the smartphone app were for 1) evaluation, 2) telerehabilitation, 3) self-management, and 4) data collection. Self-management was the most-studied use, showing promising results derived from moderate- to good-quality RCTs for patients with chronic LBP and patients after spinal surgery. Promising results exist regarding evaluation and data collection use and contradictory results regarding measurement use. Conclusions: This scoping review revealed a growing scientific literature regarding the use of smartphone apps for LBP patients. The identified purposes point to current scientific status and perspectives for further studies including RCTs and systematic reviews targeting specific usage. Caution should be taken to monitor the impact of smartphone-related compulsive behaviour.
Calcium Overload or Underload? The Effects of Doxorubicin on the Calcium Dynamics in Guinea Pig Hearts

The severe doxorubicin (DOXO) side effect of cardiomyopathy limits it clinical application as an effective anticancer drug. Although Ca2+ overload was postulated as one of the mechanisms for this toxicity, its role was, however, disputable in terms of the contractile dysfunction. In this work, the dynamics of the intracellular Ca2+ signal were optically mapped in a Langendorff guinea pig heart. We found that DOXO treatment: (1) Delayed the activation of the Ca2+ signal. With the reference time set at the peak of the action potential (AP), the time lag between the peak of the Ca2+ signal and AP (Ca-AP-Lag) was significantly prolonged. (2) Slowed down the intracellular Ca2+ releasing and sequestering process. Both the maximum rising (MRV) and falling (MFV) velocity of the Ca2+ signal were decreased. (3) Shortened the duration of the Ca2+ signal in one cycle of Ca2+ oscillation. The duration of the Ca2+ signal at 50% amplitude (CaD50) was significantly shortened. These results suggested a reduced level of intracellular Ca2+ after DOXO treatment. Furthermore, we found that the effect of tachypacing was similar to that of DOXO, and, interestingly, DOXO exerted contradictory effects on the tachypaced hearts: it shortened the Ca-AP-Lag, accelerated the MRV and MFV, and prolonged the CaD50. We, therefore, concluded that DOXO had a different effect on intracellular Ca2+. It caused Ca2+ underload in hearts with sinus rhythm; this might relate to the contractile dysfunction in DOXO cardiomyopathy. It led to Ca2+ overload in the tachypaced hearts, which might contribute to the Ca2+-overload-related toxicity.
Orbit Maneuver of Spinning Tether via Tidal Force

Recently, the spinning tethered system is regarded as a typical and fundamental space structure attracting great interest of the aerospace engineers, and has been discussed primarily for specific space missions in past decades, including on-orbit capture and propellantless orbit transfer etc. The present work studies the dynamical behaviours of a fast spinning tethered binary system under central gravitational field, and derives principles of the basic laws of orbital maneuver. Considering the characteristics of coupled librational and orbital motions, an averaging method is introduced to deal with the slow-fast system equation, thus a definite equivalent model is derived. The general orbit motion is completely determined analytically, including the orbit geometry, periodicity, conversations and moving region etc. Since the possibility of orbit control using tether reaction has been proved by previous studies, special attention is paid to the transportation mode of angular momentum and mechanical energy between the orbit and libration. The effect of tether length change on the orbit shape is verified both in the averaged model and original model. The results show the orbit angular momentum and mechanical energy can be controlled independently, and the operating principles of tether reactions are derived for special modification of orbit shape.
Optimal sampling lattices and trivariate box splines

The Body Centered Cubic (BCC) and Face Centered Cubic (FCC) lattices along with a set of box splines for sampling and reconstruction of trivariate functions are proposed. The BCC lattice is demonstrated to be the optimal choice of a pattern for generic sampling purposes. While the FCC lattice is the second best choice for this purpose, both FCC and BCC lattices significantly outperform the accuracy of the commonly-used Cartesian 3-D lattice. A set of box splines tailored to the geometry of the BCC and FCC lattices are proposed for approximation of trivariate functions on these lattices. Furthermore, for efficient evaluation, the explicit piecewise polynomial representation of the proposed box splines on the BCC lattice are derived. This derivation can be generalized for other box splines to provide efficient evaluation of box splines at arbitrary points. Despite the common assumption on the superior computational performance of tensor-product reconstruction, it is demonstrated that these non-separable box spline-based reconstructions on the BCC and FCC lattices outperform their tensor-product counterparts on the Cartesian lattice. In particular, the box spline-based reconstruction on the BCC lattice is shown to be twice as efficient as the corresponding tensor-product B-spline solution on the Cartesian lattice. Hence, we establish the fact that not only are these non-Cartesian lattices attractive from the sampling-theory aspects, they also allow for efficient and superior reconstruction algorithms.
Processed Food as a Risk Factor for the Development and Perpetuation of Crohn’s Disease—The ENIGMA Study

(1) Background: Developing countries have experienced a rapid recent rise in Inflammatory Bowel Disease (IBD) incidence and emerging evidence suggests processed foods and food additives may predispose one to the development and perpetuation of Crohn’s disease (CD). The aim of this study was to evaluate processed food and food additive intake in CD patients and controls, in Australia (high CD incidence), Hong Kong (intermediate incidence) and mainland China (emerging incidence). (2) Methods: In 274 CD patients (CD), 82 first-degree relatives (FDR), 83 household members (HM) and 92 healthy unrelated controls (HC) from Australia (n = 180), Hong Kong (HK) (n = 160) and mainland China (n = 191) we estimated early life (0–18 years), recent (12 months), and current processed and food additive intake, using validated questionnaires and a 3-day-food diary. (3) Results: Early life processed food intake: Combining all regions, CD were more likely to have consumed soft drinks and fast foods than HM, more likely to have consumed processed fruit and snacks than their FDR, and more likely to have consumed a range of processed foods than HC. HK and China CD patients were more likely to have consumed a range of processed foods than HC. Recent food-additive intake (12-months): Combining all regions, CD patients had significantly higher intakes of aspartame and sucralose, and polysorbate-80, than HC, and more total emulsifiers, artificial sweeteners, and titanium dioxide than FDR and HC. HK and China CD patients had a higher intake of almost all food additives than all controls. Current additive intake (3-days): Australian and HK CD patients had higher total food-additive intake than FDR, and HK CD patients had a higher intake of total food-additives and emulsifiers than HM. (4) Conclusions: CD patients have been exposed to more processed food and food additives than control groups, which may predispose them to CD development and ongoing inflammation.
Design of Ultracompact Content Addressable Memory Exploiting 1T-1MTJ Cell

Content addressable memories (CAMs) are a promising category of computing-in-memory (CiM) elements that can perform highly parallel and efficient search operations for routers, pattern matching, and other data-intensive applications. Various magnetic tunnel junction (MTJ)-based CAM designs have been proposed to realize zero standby power and high-performance search. However, due to the relatively small tunnel magneto-resistance (TMR) ratio, MTJ-based CAMs require extra transistors and differential MTJ branches to distinguish between the parallel and anti-parallel resistance states, resulting in significant area and energy overhead. In this article, we propose a device-circuit co-design approach for an ultracompact CAM design by only exploiting a 1T-1MTJ structure in each cell. We propose a 2-step search scheme to enable the parallel in-memory search operation across the proposed CAM array and demonstrate the sufficient sensing margin of the array in a successful search operation. Evaluation results suggest that our proposed 1T-1MTJ-based CAM design improves $179\times /301\times $ area efficiency compared with the state-of-the-art 15T-4MTJ/20T-6MTJ CAM design. Application benchmarking on hyperdimensional computing (HDC) inference shows a $54.6\times /12.8\times $ speedup compared with GPU/20T-6MTJ CAM-based approaches.