Miracle-dz/UniFAR-FTUs huggingface dataset:
Conserved Residue Asn-145 in the C-Terminal Heptad Repeat Region of HIV-1 gp41 is Critical for Viral Fusion and Regulates the Antiviral Activity of Fusion Inhibitors

Entry of HIV-1 into target cells is mediated by its envelope (Env) glycoprotein composed of the receptor binding subunit gp120 and the fusion protein gp41. Refolding of the gp41 N- and C-terminal heptad repeats (NHR and CHR) into a six-helix bundle (6-HB) conformation drives the viral and cellular membranes in close apposition and generates huge amounts of energy to overcome the kinetic barrier leading to membrane fusion. In this study, we focused on characterizing the structural and functional properties of a single Asn-145 residue, which locates at the middle CHR site of gp41 and is extremely conserved among all the HIV-1, HIV-2, and simian immunodeficiency virus (SIV) isolates. By mutational analysis, we found that Asn-145 plays critical roles for Env-mediated cell-cell fusion and HIV-1 entry. As determined by circular dichroism (CD) spectroscopy and isothermal titration calorimetry (ITC), the substitution of Asn-145 with alanine (N145A) severely impaired the interactions between the NHR and CHR helices. Asn-145 was also verified to be important for the antiviral activity of CHR-derived peptide fusion inhibitors and served as a turn-point for the inhibitory potency. Intriguingly, Asn-145 could regulate the functionality of the M-T hook structure at the N-terminus of the inhibitors and displayed comparable activities with the C-terminal IDL anchor. Crystallographic studies further demonstrated the importance of Asn-145-mediated interhelical and intrahelical interactions in the 6-HB structure. Combined, the present results have provided valuable information for the structure-function relationship of HIV-1 gp41 and the structure-activity relationship of gp41-dependent fusion inhibitors.
Navigated non-contact fluorescence tomography

A non-contact approach for diffuse optical tomography (DOT) has been developed for on-demand image updates using surgical navigation technology. A stereoscopic optical tracker provides real-time localization of reflective spheres mounted to a laser diode and near-infrared camera. Standard camera calibration is combined with tracking data to determine the intrinsic camera parameters (focal length, principal point and non-linear lens distortion) and the tracker-to-camera transform. Tracker-to-laser calibration is performed using images of laser beam intersection with a tracked calibration surface. Source and detector positions for a finite-element DOT implementation are projected onto the boundary elements of the tissue mesh by finding ray-triangle intersections. A multi-stage model converts camera counts to surface flux by accounting for lens aperture settings, fluorescence filter transmittance, photodetector quantum efficiency, photon energy, exposure time, readout offset and camera gain. The image-guidance framework was applied to an in-house optical tomography system configured for indocyanine green (ICG) fluorescence. Mean target registration errors for camera and laser calibration were less than 1 mm. Surface flux measurements of total reflectance and fluorescence in Intralipid-based fluorescence phantoms (0–2 μg ml−1) had mean errors of 3.1% and 4.4%, respectively, relative to diffusion theory predictions. Spatially-resolved reflectance measurements in a calibrated optical phantom agreed with theory for radial distances up to 25 mm from the laser source. Inverse fluorescence reconstructions of a sub-surface fluorescence target confirmed the localization accuracy (average target centroid error of 0.44 mm). This translational research system is under investigation for clinical applications in head and neck surgery, including oral cavity tumor resection, lymph node mapping and free-flap perforator assessment.
Quantum Chemical Modeling of the Photoinduced Activity of Multichromophoric Biosystems

Multichromophoric biosystems represent a broad family with very diverse members, ranging from light-harvesting pigment–protein complexes to nucleic acids. The former are designed to capture, harvest, efficiently transport, and transform energy from sunlight for photosynthesis, while the latter should dissipate the absorbed radiation as quickly as possible to prevent photodamages and corruption of the carried genetic information. Because of the unique electronic and structural characteristics, the modeling of their photoinduced activity is a real challenge. Numerous approaches have been devised building on the theoretical development achieved for single chromophores and on model Hamiltonians that capture the essential features of the system. Still, a question remains: is a general strategy for the accurate modeling of multichromophoric systems possible? By using a quantum chemical point of view, here we review the advancements developed so far highlighting differences and similarities with the single chromophore treatment. Finally, we outline the important limitations and challenges that still need to be tackled to reach a complete and accurate picture of their photoinduced properties and dynamics.
Detection & Removal of Cracks in Digitized Paintings Based on Image Processing

This paper presents of crack detection & removal techniques in digitized paintings. It is also used as a nondestructive tool for the actual restoration. The user must select an area on each crack that to be restored. The cracks are identified and detected by Gabor which is an integrated methodology for removal of cracks. First, we filter the selected crack image using 8 differently oriented Gabor filters. We describe an orientationbased feature extraction method to represent a crack network from sets of local orientation features. The resultant features are used for crack filling with median filter and weighted median filter. The methodology has been shown to perform very well on digitized paintings suffering from cracks.
Reinforcement of Polylactic Acid for Fused Deposition Modeling Process with Nano Particles Treated Bamboo Powder

The focus of this report was to understand the tensile properties and dynamic mechanical properties of bamboo powder (BP) reinforced polylactic acid (PLA) composite filaments which were treated with nano calcium carbonate (CaCO3), cellulose nanofibers (CNF), and micro-crystalline cellulose (MCC) using impregnation modification technology. The storage modulus (E’) of nano CaCO3-BP/PLA, MCC-BP/PLA, and CNF-BP/PLA composite filaments increased compared with BP/PLA composite filaments before the glass transition temperature Tg. When the temperature was above Tg, the reinforcement effect of nano CaCO3, MCC, and CNF gradually became less apparent. The loss modulus (E’’) and loss factor (tan δmax) of the nano CaCO3-BP/PLA, MCC-BP/PLA, and CNF-BP/PLA composite filaments was higher than that of BP/PLA composite filaments produced by the “one-step” method. The tensile strength (TS) results showed a similar trend. Compared with the control samples, the TS of nano CaCO3-BP/PLA, MCC-BP/PLA, and CNF-BP/PLA composite filaments produced by the “one-step” method (and the “two-step” method) increased by 40.33% (and 10.10%), 32.35% (and −8.61%), and 12.32% (and −12.85%), respectively. The TS of nano CaCO3-BP/PLA, MCC-BP/PLA, and CNF-BP/PLA composite filaments produced by the “one-step” method was slightly higher than those produced by the “two-step” method. The elongation at break (EAB) of BP/PLA composite filaments was higher than that of BP/PLA samples treated with nano CaCO3, MCC, or CNF. The PLA and modified BP were readily accessible through a simple mixing process. The rheological investigation of such mixtures showed that nano CaCO3, CNF, and MCC have different effects on the processability and rheological properties of composites.
Anisotropic Vibration Tactile Model and Human Factor Analysis for a Piezoelectric Tactile Feedback Device

Tactile feedback technology has important development prospects in interactive technology. In order to enrich the tactile sense of haptic devices under simple control, a piezoelectric haptic feedback device is proposed. The piezoelectric tactile feedback device can realize tactile changes in different excitation voltage amplitudes, different excitation frequencies, and different directions through the ciliary body structure. The principle of the anisotropic vibration of the ciliary body structure was analyzed here, and a tactile model was established. The equivalent friction coefficient under full-coverage and local-coverage of the skin of the touch beam was deduced and solved. The effect of system parameters on the friction coefficient was analyzed. The results showed that in the full-coverage, the tactile effect is mainly affected by the proportion of the same directional ciliary bodies and the excitation frequency. The larger the proportion of the same direction ciliary body is, the smaller the coefficient of friction is. The larger the excitation frequency is, the greater the coefficient of friction is. In the local-coverage, the tactile effect is mainly affected by the touch position and voltage amplitude. When changing the touch pressure, it has a certain effect on the change of touch, but it is relatively weak. The experiment on the sliding friction of a cantilever touch beam and the experiment of human factor were conducted. The experimental results of the sliding friction experiment are basically consistent with the theoretical calculations. In the human factor experiment, the effects of haptic regulation are mainly affected by voltage or structure of the ciliary bodies.
Food Consumption in Adolescents and Young Adults: Age-Specific Socio-Economic and Cultural Disparities (Belgian Food Consumption Survey 2014)

A key issue in nutritional public health policies is to take into account social disparities behind health inequalities. The transition from adolescence toward adulthood is a critical period regarding changes in health behaviors. This study aimed to determine how consumption of four emblematic food groups (two to favor and two to limit) differed according to socio-economic and cultural characteristics of adolescents and young adults living in Belgium. Two non-consecutive 24-h dietary recalls were carried out in a nationally representative sample of 10–39 year old subjects (n = 1505) included in the Belgian food consumption survey 2014. Weighted daily mean consumption of “fruits and vegetables”, “whole grain bread and cereals”, “refined starchy food”, and “sugary sweetened beverages” (SSB) was calculated and explored in multivariable linear regressions stratified into four age groups. After adjustment, 10–13 year old adolescents living in less educated households daily consumed lower amounts of “fruits and vegetables” (adjusted mean: 165.6 g/day (95% CI: 125.3–206.0)) and “whole grain bread and cereals” (40.4 g/day (22.9–58.0)), and higher amounts of SSB (309.7 g/day (131.3–488.1) than adolescents of same ages living in more educated households (220.2 g/day (179.8–260.7); 59.0 g/day (40.3–77.8); and 157.8 g/day (1.7–314.0), respectively). The same trends were observed in older groups, along with strong consumption disparities according to region of residency, country of birth, and occupation, with specificities according to age. Our findings suggest the need to better explore such disparities by stage of transition to adulthood, and to adapt nutritional health programs.
Comparative Analysis of the PIN Auxin Transporter Gene Family in Different Plant Species: A Focus on Structural and Expression Profiling of PINs in Solanum tuberosum

Plant growth and morphogenesis largely benefit from cell elongation and expansion and are normally regulated by environmental stimuli and endogenous hormones. Auxin, as one of the most significant plant growth regulators, controls various phases of plant growth and development. The PIN-FORMED (PIN) gene family of trans-membrane proteins considered as auxin efflux carriers plays a pivotal role in polar auxin transport and then mediates the growth of different plant tissues. In this study, the phylogenetic relationship and structural compositions of the PIN gene family in 19 plant species covering plant major lineages from algae to angiosperms were identified and analyzed by employing multiple bioinformatics methods. A total of 155 PIN genes were identified in these species and found that representative of the PIN gene family in algae came into existence and rapidly expanded in angiosperms (seed plants). The phylogenetic analysis indicated that the PIN proteins could be divided into 14 distinct clades, and the origin of PIN proteins could be traced back to the common ancestor of green algae. The structural analysis revealed that two putative types (canonical and noncanonical PINs) existed among the PIN proteins according to the length and the composition of the hydrophilic domain of the protein. The expression analysis of the PIN genes exhibited inordinate responsiveness to auxin (IAA) and ABA both in shoots and roots of Solanum tuberosum. While the majority of the StPINs were up-regulated in shoot and down-regulated in root by the two hormones. The majority of PIN genes had one or more putative auxin responses and ABA-inducible response elements in their promoter regions, respectively, implying that these phytohormones regulated the expression of StPIN genes. Our study emphasized the origin and expansion of the PIN gene family and aimed at providing useful insights for further structural and functional exploration of the PIN gene family in the future.
Neuronal loss without amyloid‐β deposits in the thalamus and hippocampus in the late period after middle cerebral artery occlusion in cynomolgus monkeys

Conflicting evidence exists regarding whether focal cerebral infarction contributes to cerebral amyloid‐β (Aβ) deposition, as observed in Alzheimer's disease. In this study, we aimed to evaluate the presence of Aβ deposits in the ipsilateral thalamus and hippocampus 12 months post‐stroke in non‐human primates, whose brains are structurally and functionally similar to that of humans. Four young male cynomolgus monkeys were subjected to unilateral permanent middle cerebral artery occlusion (MCAO), and another four sham‐operated monkeys served as controls. All monkeys underwent magnetic resonance imaging examination on post‐operative day 7 to assess the location and size of the infarction. The numbers of neurons, astrocytes, microglia and the Aβ load in the non‐affected thalamus and hippocampus ipsilaterally remote from infarct foci were examined immunohistochemically at sacrifice 12 months after operation. Thioflavin S and Congo Red stainings were used to identify amyloid deposits. Multiple Aβ antibodies recognizing both the N‐terminal and C‐terminal epitopes of Aβ peptides were used to avoid antibody cross‐reactivity. Aβ levels in cerebrospinal fluid (CSF) and plasma were examined using enzyme‐linked immunosorbent assay. The initial infarct was restricted to the left temporal, parietal, insular cortex and the subcortical white matter, while the thalamus and hippocampus remained intact. Of note, there were fewer neurons and more glia in the ipsilateral thalamus and hippocampus in the MCAO group at 12 months post‐stroke compared to the control group (all P < 0.05). However, there was no sign of extracellular Aβ plaques in the thalamus or hippocampus. No statistically significant difference was found in CSF or plasma levels of Aβ40, Aβ42 or the Aβ40/Aβ42 ratio between the two groups (P > 0.05). These results suggest that significant secondary neuronal loss and reactive gliosis occur in the non‐affected thalamus and hippocampus without Aβ deposits in the late period after MCAO in non‐human primates.
Use of Repeated Group Measurements with Drop Out Animals for Variance Component Estimation and Genetic Evaluation: A Simulation Study

The efficiency of feed utilization plays an important role in animal breeding. However, measuring feed intake (FI) is costly on an individual basis under practical conditions. Using group measurements to model FI could be practically feasible and cost-effective. The objectives of this study were to develop a random regression model based on repeated group measurements with consideration of missing phenotypes caused by drop out animals. Focus is on variance components (VC) estimation and genetic evaluation, and to investigate the effect of group composition on VC estimation and genetic evaluation using simulated datasets. Data were simulated based on individual FI in a pig population. Each individual had measurement on FI at 6 different time points, reflecting 6 different weeks during the test period. The simulated phenotypes consisted of additive genetic, permanent environment, and random residual effects. Additive genetic and permanent environmental effects were both simulated and modeled by first order Legendre polynomials. Three grouping scenarios based on genetic relationships among the group members were investigated: (1) medium within and across pen genetic relationship; (2) high within group relationship; (3) low within group relationship. To investigate the effect of the drop out animals during test period, a proportion (15%) of animals with individual phenotypes was set as the drop out animals, and two drop out scenarios within each grouping scenario were assessed: (1) animals were randomly dropped out; (2) animals with lower phenotypes were dropped out based on the ranking at each time point. The results show that using group measurements yielded similar VCs estimates but with larger SDs compared with the corresponding scenario of using individual measurements. Compared to scenarios without drop out, similar VC estimates were observed when animals were dropped out randomly, whereas reduced VC estimates were observed when animals were dropped out by the ranking of phenotypes. Different grouping scenarios produced similar VC estimates. Compared to scenarios without drop out, there were no loss of accuracies of genetic evaluation for drop out scenarios. However, dropping out animals by the ranking of phenotypes produced larger bias of estimated breeding values compared to the scenario without dropped out animals and scenario of dropping out animals by random. In conclusion, with an optimized group structure, the developed model can properly handle group measurements with drop out animals, and can achieve comparable accuracy of genetic evaluation for traits measured at the group level.
Home Energy Management System Incorporating Heat Pump Using Real Measured Data †

The demand for electricity has been rising significantly over the past years and it is expected to rise further in the coming years due to economic and societal development. Smart grid technology is being developed in order to meet the rising electricity requirement. In order for the smart grid to perform its full functions, the Energy Management Systems (EMSs), especially Home Energy Management Systems (HEMS) are essential. It is necessary to understand the energy demand of the loads and the energy supply either from the national grid or from renewable energy technologies. To facilitate the Demand Side Management (DSM), Heat Pumps (HP) and air conditioning systems are often utilised for heating and cooling in residential houses due to their high-efficiency power output and low CO2 emissions. This paper presents a program for a HEMS using a Particle Swarm Optimisation (PSO) algorithm. A HP is used as the load and the aim of the optimisation program is to minimise the operational cost, i.e., the cost of electricity, while maintaining end-user comfort levels. This paper also details an indoor thermal model for temperature update in the heat pump control program. Real measured data from the UK Government’s Renewable Heat Premium Payment (RHPP) scheme was utilised to generate characteristic curves and equations that can represent the data. This paper compares different PSO variants with standard PSO and the unscheduled case calculated from the data for five winter days in 2019. Among all chosen algorithms, the Crossover Subswarm PSO (CSPSO) achieved an average saving of 25.61% compared with the cost calculated from the measured data with a short search time of 1576 ms for each subswarm. It is clear from this work that there is significant scope to reduce the cost of operating a HP while maintaining end user comfort levels.
Debonding Detection and Monitoring for CFRP Reinforced Concrete Beams Using Pizeoceramic Sensors

The bonding status between Carbon Fiber Reinforced Polymer (CFRP) and concrete is one of the key issues for the safety of CFPR-reinforced structures, thus it is of great importance to detect the debonding as early as possible. Instead of detecting the debonding which is artificially set at the very beginning, this paper investigates the feasibility of using low-cost piezoceramic sensors to detect and monitor the debonding of CFRP-reinforced concrete beams in situ. For existing debonding detection, a concrete beam reinforced with CFRP sheet was loaded through the three-point bending test till failure to induce debonding between CFRP sheet and the concrete substrate, and piezoceramic sensors were used to detect the existing debonding by analyzing the receiving ultrasonic waves. In addition, the debonding detection results were further compared with and verified by the vision-based strain testing results. For in-situ debonding monitoring, 10 piezoceramic sensors were used as an array to track the wave transmission changes during the loading process of a CFRP-reinforced concrete beam, and the debonding development process was successfully monitored. The test results show that the low-cost piezoceramic sensors are very effective to generate and receive ultrasonic waves, and are capable of detecting the existing debonding and monitoring of the in-situ debonding process as well.
Comparação paralela exata de sequências biológicas em plataformas híbridas de alto desempenho

Once a new biological sequence is discovered, its functional and structural characteristics must be established. In order to do that, the newly discovered sequence is compared against other sequences, looking for similarities. Sequence comparison is, therefore, one of the most basic operations in Bioinformatics. The most accurate algorithm to execute pairwise comparisons is the one proposed by Smith-Waterman (SW), which is based on dynamic programming, with quadratic time and space complexity. This can easily lead to very high execution times and huge memory requirements. Parallel processing can be used to produce results faster, reducing significantly the time needed to obtain results with the SW algorithm. There are many parallel versions of SW in the literature, which run in multicores, GPUs, Field-Programmable Gate Arrays (FPGAs) and CellBEs. Even though there are some versions of SW that run on hybrid platforms composed of GPUs and multicores, they assign work in a fixed way, based on the theoretical performance of the processing units or in the results obtained by some benchmarks. This MsC Dissertation proposes and evaluates a flexible and optimized strategy to run Smith-Waterman applications in hybrid platforms composed of GPUs and multicores with SIMD extensions. Our strategy provides multiple task allocation policies and the user can choose the one which is more appropriate to his/her problem. We also propose a workload adjustment mechanism that tackles situations that arise when slow nodes receive the last tasks. The results obtained comparing query sequences to 5 public genomic databases in a platform composed of 4 GPUs and 2 multicores show that we are able to reduce the execution time with hybrid platforms, when compared to the GPU-only solution. We also show that our workload adjustment technique can provide significant performance gains in our target platform.