Miracle-dz/UniFAR-FTUs huggingface dataset:
An Algorithm of Curved Path Tracking with Prediction Model for Autonomous Vehicle

The Stanley method is a popular geometric steering controller. However, the Stanley method is not as robust to disturbances. The path tracking of the Stanley method is prone to large deviations in the curved path. In this paper, a predictive method is proposed to improve the curve tracking effect of the Stanley method. The predictive method of curved path tracking not only the relative position of the closest point of the path, but also the direction of the fixation point. Firstly, we use the inertial navigation system of autonomous vehicle to collect waypoints. Considering that the GPS signal is susceptible to environmental disturbances, we use cubic B-spline interpolation to correct the waypoints and get an accurate road map. Secondly, we calculate the position of the preview point by introducing the logarithmic relationship between the vehicle speed and the fixation point. Then, the preview point is used as the target for Stanley path tracking. The results in a variety of environments show the effectiveness of the proposed method.
Kinetic finite element model to optimize sulfur vulcanization: Application to extruded epdm weather-strips

A numerical two-phase approach based on experimental scorch curve data fitting, to predict the optimal exposure time and cure temperature of extruded thick items is applied for the study of a real weather-strip. In the first phase, an existing single equation kinetic model is used to predict the crosslinking density under sulfur vulcanization at variable temperatures. The model requires the calibration of only three kinetic constants. The variation with respect to temperature of such parameters is then evaluated by means of two experimental cure curves performed at two different temperatures. In the second phase, kinetic reaction parameters are implemented in finite element software, to perform thermal analyses on an extruded weather-strip. Once evaluated the final mechanical properties of the item point by point, a set of compression tests is numerically simulated, assuming that the rubber behaves as a Mooney–Rivlin material under the large deformations. Elastic properties of the item are evaluated as a function of the vulcanization degree evaluated in the second phase. It is found that suboptimal vulcanizations result into lower elastic moduli and hence great deformability, sometimes incompatible with real scale engineering applications. POLYM. ENG. SCI., 2013. © 2012 Society of Plastics Engineers
Application of circulating tumor DNA in prospective clinical oncology trials – standardization of preanalytical conditions

Circulating tumor DNA (ctDNA) has emerged as a potential new biomarker with diagnostic, predictive, and prognostic applications for various solid tumor types. Before beginning large prospective clinical trials to prove the added value of utilizing ctDNA in clinical practice, it is essential to investigate the effects of various preanalytical conditions on the quality of cell‐free DNA (cfDNA) in general and of ctDNA in particular in order to optimize and standardize these conditions. Whole blood samples were collected from patients with metastatic cancer bearing a known somatic variant. The following preanalytical conditions were investigated: (a) different time intervals to plasma isolation (1, 24, and 96 h) and (b) different preservatives in blood collection tubes (EDTA, CellSave, and BCT). The quality of cfDNA/ctDNA was assessed by DNA quantification, digital polymerase chain reaction (dPCR) for somatic variant detection and a β‐actin fragmentation assay for DNA contamination from lysed leukocytes. In 11 (69%) of our 16 patients, we were able to detect the known somatic variant in ctDNA. We observed a time‐dependent increase in cfDNA concentrations in EDTA tubes, which was positively correlated with an increase in wild‐type copy numbers and large DNA fragments (> 420 bp). Using different preservatives did not affect somatic variant detection ability, but did stabilize cfDNA concentrations over time. Variant allele frequency was affected by fluctuations in cfDNA concentration only in EDTA tubes at 96 h. Both CellSave and BCT tubes ensured optimal ctDNA quality in plasma processed within 96 h after blood collection for downstream somatic variant detection by dPCR.
molUP: A VMD plugin to handle QM and ONIOM calculations using the gaussian software

The notable advances obtained by computational (bio)chemistry provided its widespread use in many areas of science, in particular, in the study of reaction mechanisms. These studies involve a huge number of complex calculations, which are often carried out using the Gaussian suite of programs. The preparation of input files and the analysis of the output files are not easy tasks and often involve laborious and complex steps. Taking this into account, we developed molUP: a VMD plugin that offers a complete set of tools that enhance the preparation of QM and ONIOM (QM/MM, QM/QM, and QM/QM/MM) calculations. The starting structures for these calculations can be imported from different chemical formats. A set of tools is available to help the user to examine or modify any geometry parameter. This includes the definition of layers in ONIOM calculations, choosing fixed atoms during geometry optimizations, the recalculation or adjustment of the atomic charges, performing SCANs or IRC calculations, etc. molUP also extracts the geometries from the output files as well as the energies of each of them. All of these tasks are performed in an interactive GUI that is extremely helpful for the user. MolUP was developed to be easy to handle by inexperienced users, but simultaneously to be a fast and flexible graphical interface to allow the advanced users to take full advantage of this plugin. The program is available, free of charges, for macOS, Linux, and Windows at the PortoBioComp page https://www.fc. up.pt/PortoBioComp/database/doku.php? id=molup. © 2018 Wiley Periodicals, Inc.
Metabolic Profile of Oral Squamous Carcinoma Cell Lines Relies on a Higher Demand of Lipid Metabolism in Metastatic Cells

Tumor cells are subjected to a broad range of selective pressures. As a result of the imposed stress, subpopulations of surviving cells exhibit individual biochemical phenotypes that reflect metabolic reprograming. The present work aimed at investigating metabolic parameters of cells displaying increasing degrees of metastatic potential. The metabolites present in cell extracts fraction of tongue fibroblasts and of cell lines derived from human tongue squamous cell carcinoma lineages displaying increasing metastatic potential (SCC9 ZsG, LN1 and LN2) were analyzed by 1H NMR (nuclear magnetic resonance) spectroscopy. Living, intact cells were also examined by the non-invasive method of fluorescence lifetime imaging microscopy (FLIM) based on the auto fluorescence of endogenous NADH. The cell lines reproducibly exhibited distinct metabolic profiles confirmed by Partial Least-Square Discriminant Analysis (PLS-DA) of the spectra. Measurement of endogenous free and bound NAD(P)H relative concentrations in the intact cell lines showed that ZsG and LN1 cells displayed high heterogeneity in the energy metabolism, indicating that the cells would oscillate between glycolysis and oxidative metabolism depending on the microenvironment’s composition. However, LN2 cells appeared to have more contributions to the oxidative status, displaying a lower NAD(P)H free/bound ratio. Functional experiments of energy metabolism, mitochondrial physiology, and proliferation assays revealed that all lineages exhibited similar energy features, although resorting to different bioenergetics strategies to face metabolic demands. These differentiated functions may also promote metastasis. We propose that lipid metabolism is related to the increased invasiveness as a result of the accumulation of malonate, methyl malonic acid, n-acetyl and unsaturated fatty acids (CH2)n in parallel with the metastatic potential progression, thus suggesting that the NAD(P)H reflected the lipid catabolic/anabolic pathways.
Visualizing Characters as Images: Understanding Chinese through Internet Usage

In this paper, images generated from pinyin and actual written simplified characters are comprehensively analyzed through Internet and electronic device usage. The study is based on current usage of most frequently used Chinese simplified characters in smart phones, mobile devices and in WWW. Generally a Chinese character carries significant meaning, and evolved over the years through representation of objects in nature, this study focuses on emphasizing understanding a text in the form of limited images. The main focus is to generate optimized image of a sentence or sequence of sentences in the form of images, so that anyone could visualize the meanings without being fluent in Chinese language. In addition, we try to establish, how the individual simplified Chinese characters, carry the meaning in the context of Internet usage, and how they can carry higher meanings through images to readers of non-Chinese. As Chinese characters are usually entered through pinyin, a system of phonetic notation, we have considered pinyin along with radicals and simplified characters.
PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants

With the goal of providing a comprehensive, high-quality resource for both plant transcription factors (TFs) and their regulatory interactions with target genes, we upgraded plant TF database PlantTFDB to version 4.0 (http://planttfdb.cbi.pku.edu.cn/). In the new version, we identified 320 370 TFs from 165 species, presenting a more comprehensive genomic TF repertoires of green plants. Besides updating the pre-existing abundant functional and evolutionary annotation for identified TFs, we generated three new types of annotation which provide more directly clues to investigate functional mechanisms underlying: (i) a set of high-quality, non-redundant TF binding motifs derived from experiments; (ii) multiple types of regulatory elements identified from high-throughput sequencing data; (iii) regulatory interactions curated from literature and inferred by combining TF binding motifs and regulatory elements. In addition, we upgraded previous TF prediction server, and set up four novel tools for regulation prediction and functional enrichment analyses. Finally, we set up a novel companion portal PlantRegMap (http://plantregmap.cbi.pku.edu.cn) for users to access the regulation resource and analysis tools conveniently.
Modelling of the production of ACE inhibitory hydrolysates of horse mackerel using proteases mixtures.

Fish protein hydrolysates from Mediterranean horse mackerel were produced by using a mixture of two commercial endoproteases (i.e. subtilisin and trypsin) at different levels of substrate concentration (2.5 g L(-1), 5 g L(-1), and 7.5 g L(-1) of protein), temperature (40 °C, 47.5 °C, and 55 °C) and percentage of subtilisin in the enzyme mixture (0%, 25%, 50%, 75% and 100%). A crossed mixture process model was employed to predict the degree of hydrolysis (DH) and the ACE inhibitory activity of the final hydrolysates as a function of the experimental factors. Both models were optimized for a maximum DH and ACE inhibition. A maximum DH (17.1%) was predicted at 2.54 g L(-1) of substrate concentration, 40 °C and an enzyme mixture comprising 38.3% of subtilisin and 61.7% of trypsin. Although its proteolytic activity is limited, the presence of trypsin in the enzyme mixture allowed obtaining higher degrees of hydrolysis at low temperatures, which is desirable to minimize thermal deactivation of the proteins. Similarly, a percentage of ACE inhibition above 48% was attained at 2.5 g L(-1) of protein, 40 °C and a 1 : 1 mixture of both proteases. Higher values of ACE inhibition could be attained by increasing both the temperature and the amount of trypsin in the enzyme mixture (e.g. 50% ACE inhibition at 55 °C and 81.5% of trypsin). Finally, those hydrolysates exhibiting the highest levels of ACE inhibition were subjected to simulated gastrointestinal digestion. These assays confirmed the resistance of active fractions against their degradation by digestive enzymes.
Microstructure and Mechanical Properties of Al-Cu-Cr Quasicrystals/Al Matrix Composites Synthesized by Hot-Pressing Technique

Microstructure and mechanical properties of 20% Al-Cu-Cr/Al composites synthesized by hot-pressing technique after annealing, quenching and aging was studied by means of X-ray diffractometer (XRD), scanning electron microscopy (SEM) and transmission electron microscopy (TEM) and uniaxial compressive test. Microstructure of Al-Cu-Cr particles in the composites after hot-pressing is mainly consist of icosahedral quasicrystals and which transformed into decagonal quasicrystals after annealing. Microstructure of matrix in the composites after hot-pressing, annealing, quenching and aging is pure Al, Al + Al2Cu, supersaturated solid solution Al and Al + Al-Cu transition phases respectively. Hardness, fracture strength and the Young’s modulus of the composites are improved by age-hardening.
Stigma gets in my way: Factors affecting client-provider communication regarding childbearing among people living with HIV in Uganda

Introduction Many HIV-affected couples living in sub-Saharan Africa desire to have children, but few quantitative studies have examined support for their childbearing needs. Our study explored client-provider communication about childbearing and safer conception among HIV clients in Uganda. Methods 400 Ugandan HIV clients in committed relationships and with intentions to conceive were surveyed. Knowledge, attitudes and practices related to childbearing, and use of safer conception methods were assessed, including communication with providers about childbearing needs, the correlates of which were examined with bivariate statistics and logistic multivariate analysis. Results 75% of the sample was female; 61% were on antiretroviral therapy; and 61% had HIV-negative or unknown status partners. Nearly all (98%) reported the desire to discuss childbearing intentions with their HIV provider; however, only 44% reported such discussions, the minority (28%) of which was initiated by the provider. Issues discussed with HIV providers included: HIV transmission risk to partner (30%), HIV transmission risk to child (30%), and how to prevent transmission to the child (27%); only 8% discussed safer conception methods. Regression analysis showed that those who had communicated with providers about childbearing were more likely to have been diagnosed with HIV for a longer period [OR (95% CI) = 1.09 (1.03, 1.15)], while greater internalized childbearing stigma was associated with lower odds of this communication [OR (95% CI) = 0.70 (0.49, 0.99)], after controlling for all bivariate correlates and basic demographics. Conclusions Communication between HIV clients and providers about childbearing needs is poor and associated with stigma. Innovations to mitigate stigma among clients as well as training to improve health worker communication and skills related to safer conception counseling is needed.
Data-Based Predictive Control for Wastewater Treatment Process

Wastewater treatment process (WWTP) has long been a challenging industrial issue due to its built-in uncertainties and discontinuous measurement of system states. To solve this problem, in this paper, a data-based predictive control (DPC) strategy, based on the available sensing measurements, is proposed to control the dissolved oxygen (DO) concentration in WWTP. First, a self-organizing fuzzy neural network, which can adjust both the structure and parameters simultaneously, is developed to identify the real-time states of WWTP. Second, an improved nonlinear predictive control method is designed to reduce the online computation complexity by transforming the constrained conditions into an unconstrained nonlinear programming problem. Then, an adaptive second-order Levenberg-Marquardt algorithm is developed to derive the control law of DPC. Third, the theoretical analysis on the stability is also given to confirm the prerequisite of any successful application of DPC. Finally, the proposed DPC strategy is applied to the Benchmark Simulation Model No. 1. Experimental results demonstrate that the control performance of the proposed DPC is better than some existing methods.
Experimental study of inverted L-, T-, and related transmission-line antennas

An ex perimental study is made of inverted L-, T-, and related t rans mis io n-lin e an tennas and of a ll tennas wit h t wo-, t hree-, a nd four-element top loads. The a ppare nt measured impedance is corrected for end e ffect s; the approx imate t heoretical impedances are cal cLl~ lated for very small heig llts for which m easured values cannot be obtained readily. The transmiss ion-line a ntennas stud ied a re shunt -driven wit h one open a nd one closed enc! or wi t h two closed ends.
Immune reconstitution inflammatory syndrome associated with toxoplasmic encephalitis in HIV-infected patients

Objectives: To investigate the incidence and risk factors of immune reconstitution inflammatory syndrome (IRIS) associated with toxoplasmic encephalitis (TE) in patients starting combination antiretroviral therapy (cART). Design: A historical multicenter cohort study. Methods: We included all HIV-infected patients diagnosed with toxoplasmic encephalitis in six Dutch hospitals between 1996 and 2016. Diagnosis of TE–IRIS was made using predefined IRIS criteria. We distinguished paradoxical TE–IRIS (worsening of underlying treated infection) from unmasking TE–IRIS (unmasking of subclinical infection after start of cART). We compared CD4+ cell count, plasma viral load and timing of cART initiation between patients with and without paradoxical TE–IRIS. Results: A total of 211 toxoplasmic encephalitis cases were included. Among 143 cases at risk for paradoxical TE–IRIS, we identified five cases of paradoxical TE–IRIS (3.5%). In six other cases, we could not differentiate paradoxical TE–IRIS from recurrence of disease due to inadequate secondary Toxoplasma prophylaxis. There was no difference in time between start of toxoplasmic encephalitis treatment and cART initiation for patients who did or did not develop paradoxical TE–IRIS (P = 0.50). Within the group of 2228 patients who started cART while having a CD4+ cell count below 200 × 106 cells/l and receiving adequate primary prophylaxis, we identified eight cases of unmasking TE–IRIS (0.36%). Unmasking TE–IRIS could not be differentiated from a newly occurring toxoplasmic encephalitis in six other patients, as they were not receiving adequate primary prophylaxis against Toxoplasma. Conclusion: Unmasking TE–IRIS was rare in this cohort, whereas paradoxical TE–IRIS did occur more often. We found no relationship between the timing of cART initiation and the occurrence of paradoxical TE–IRIS.
The 9-1-1 DNA Clamp Is Required for Immunoglobulin Gene Conversion

ABSTRACT Chicken DT40 cells deficient in the 9-1-1 checkpoint clamp exhibit hypersensitivity to a variety of DNA-damaging agents. Although recent work suggests that, in addition to its role in checkpoint activation, this complex may play a role in homologous recombination and translesion synthesis, the cause of this hypersensitivity has not been studied thoroughly. The immunoglobulin locus of DT40 cells allows monitoring of homologous recombination and translesion synthesis initiated by activation-induced deaminase (AID)-dependent abasic sites. We show that both the RAD9−/− and RAD17−/− mutants exhibit substantially reduced immunoglobulin gene conversion. However, the level of nontemplated immunoglobulin point mutation increased in these mutants, a finding that is reminiscent of the phenotype resulting from the loss of RAD51 paralogs or Brca2. This suggests that the 9-1-1 complex does not play a central role in translesion synthesis in this context. Despite reduced immunoglobulin gene conversion, the RAD9−/− and RAD17−/− cells do not exhibit a prominent defect in double-strand break-induced gene conversion or a sensitivity to camptothecin. This suggests that the roles of Rad9 and Rad17 may be confined to a subset of homologous recombination reactions initiated by replication-stalling lesions rather than those associated with double-strand break repair.
Antenatal reflex DNA screening for trisomy 18 and trisomy 13 in addition to Down’s syndrome

Objective Antenatal reflex DNA screening for Down’s syndrome has a high screening performance. We aimed to determine the performance of trisomy 18 and trisomy 13 reflex DNA screening when added to Down’s syndrome screening. Methods In our modelled screening protocol, women provide two samples: a serum sample for a Combined test and a plasma sample for a possible DNA test. Women with Down’s syndrome, trisomy 18, or trisomy 13 Combined test risks above a single cut-off have a reflex DNA test using the plasma sample, without the need to recall them to collect another sample and provide counselling. Women with a failed DNA test (after a second attempt using a fresh plasma sample) have an Integrated test, and are classified as positive if any of the Down’s syndrome, trisomy 18, or trisomy 13 Integrated test risks are greater than 1 in 25. Results At 1 in 800 term risk cut-offs for Down’s syndrome, trisomy 18, and trisomy 13, an estimated 10% of women are reflexed to DNA screening, yielding a 91% Down’s syndrome detection rate, an 89% trisomy 18 detection rate, and a 79% trisomy 13 detection rate for a 0.05% false-positive rate. At a 1 in 1900 term risk cut-off for Down’s syndrome, trisomy 18, or trisomy 13, an estimated 20% of women are reflexed to DNA screening, and this yields a 94% Down’s syndrome detection rate, a 92% trisomy 18 detection rate, and an 84% trisomy 13 detection rate for a 0.10% false-positive rate. Conclusion Reflex DNA screening for trisomies 18 and 13 can be usefully added to reflex DNA screening for Down’s syndrome.
Elastic-Plastic Stress Analysis and Plastic Zone Propagation in Fibre-Reinforced Thermoplastic Laminates Using Finite Element Method

The results of a study of elastic-plastic stress analysis and plastic zone propagation in a low density polyethylene thermoplastic composite plate subjected to uniform transverse load are presented. Thermoplastic matrix, polyethylene (LDPE), and steel fibres were used to fabricate the composite plates. Yield points and elastic, elastic-plastic and residual stresses are calculated numerically for both symmetric and antisymmetric laminated plates with different ply orientations by using Finite Element Method. First order shear deformation theory was used as an equivalent single-layer laminate theory for small deformations. Contour plots corresponding to 100, 150 and 200 load steps display the expansion of the plastic zone. Mechanical properties of a layer were obtained experimentally.
Nutritional Aspects of Bone Health and Fracture Healing

Introduction Fractures are quite common, especially among the elderly. However, they can increase in prevalence in younger ages too if the bone health is not good. This may happen as a result of bad nutrition. Methods A customized, retrospective review of available literature was performed using the following keywords: bone health, nutrition, and fractures. Results Insufficient intake of certain vitamins, particularly A and D, and other nutrients, such as calcium, may affect bone health or even the time and degree of bone healing in case of fracture. The importance of different nutrients, both dietary and found in food supplements, is discussed concerning bone health and fracture healing. Conclusion A healthy diet with adequate amounts of both macro- and micronutrients is essential, for both decreasing fracture risk and enhancing the healing process after fracture.