Miracle-dz/UniFAR-FTUs huggingface dataset:
A Glimpse of the Structural Biology of the Metabolism of Sphingosine-1-Phosphate

As a key sphingolipid metabolite, sphingosine-1-phosphate (S1P) plays crucial roles in vascular and immune systems. It regulates angiogenesis, vascular integrity and homeostasis, allergic responses, and lymphocyte trafficking. S1P is interconverted with sphingosine, which is also derived from the deacylation of ceramide. S1P levels and the ratio to ceramide in cells are tightly regulated by its metabolic pathways. Abnormal S1P production causes the occurrence and progression of numerous severe diseases, such as metabolic syndrome, cancers, autoimmune disorders such as multiple sclerosis, and kidney and cardiovascular diseases. In recent years, huge advances on the structure of S1P metabolic pathways have been accomplished. In this review, we have got a glimpse of S1P metabolism through structural and biochemical studies of: sphingosine kinases, S1P transporters and S1P receptors, and the development of therapeutics targeting S1P signaling. The progress we summarize here could provide fresh perspectives to further the exploration of S1P functions and facilitate the development of therapeutic molecules targeting S1P signaling with improved specificity and therapeutic effects.
Multiscale Legacy Responses of Soil Gas Concentrations to Soil Moisture and Temperature Fluctuations

The sensitivity of soil carbon dynamics to climate change is a major uncertainty in carbon cycle models. Of particular interest is the response of soil biogeochemical cycles to variability in hydroclimatic states and the related quantification of soil memory. Toward this goal, the power spectra of soil hydrologic and biogeochemical states were analyzed using measurements of soil temperature, moisture, oxygen, and carbon dioxide at two sites. Power spectra indicated multiscale power law scaling across subhourly to annual timescales. Precipitation fluctuations were most strongly expressed in the soil biogeochemical signals at monthly to annual timescales. Soil moisture and temperature fluctuations were comparable in strength at one site, while temperature was dominant at the other. The effect of soil hydrologic, thermal, and biogeochemical processes on gas concentration variability was evidenced by low spectral entropy relative to the white noise character of precipitation. A full mass balance model was unable to capture high‐frequency soil temperature influence, indicating a gap in commonly used model assumptions. A linearized model was shown to capture the main features of the observed and modeled gas concentration spectra and demonstrated how the means and variances of soil moisture and temperature interact to produce the gas concentration spectra. Breakpoints in the spectra corresponded to the mean rate of gas efflux, providing a first‐order estimate of the soil biogeochemical integral timescale (∼1 min). These methods can be used to identify biogeochemical system dynamics to develop robust, process‐based soil biogeochemistry models that capture variability in addition to long‐term mean values.
Foreign Language Usage and National and European Identification in the Netherlands

Multilingualism is considered a pathway to European identification but might also undermine national identification. We examine regular foreign language usage and two psychological constructs that can explain the relationship between multilingualism and European and national identification in the Netherlands: greater mental openness and a deprovincialized worldview. Using structural equation modeling, the results of two studies conducted with national Dutch samples show that foreign language usage predicted greater mental openness (cultural in Study 1, and cognitive in Study 2), which then predicted greater European identification. Foreign language usage also predicted greater deprovincialization which, in turn, predicted lower national identification.
Phylogenetic placement and reassessment of Asperisporium pongamiae as Pedrocrousiella pongamiae gen. et comb. nov. (Mycosphaerellaceae)

The leaf spot disease of Pongamia pinnata caused by an asperisporium-like asexual morph, which is usually referred to as Asperisporium pongamiae, is quite common during monsoon seasons in India. Phylogenetic analyses, based on LSU and rpb2 sequence data, and blast searches using ITS sequence data, revealed that this ascomycete forms a lineage within Mycosphaerellaceae distant from all other generic lineages. Pedrocrousiella gen. nov., with P. pongamiae comb. nov., based on Fusicladium pongamiae (≡ A. pongamiae), as type species is introduced for this lineage. This species has been considered the asexual morph of Mycosphaerella pongamiae (≡ Stigmatea pongamiae). However, this connection is unproven and was just based on the occasional association of the two taxa in some collections. Several attempts to induce the formation of a sexual morph in culture failed, therefore the putative connection between these morphs could not be confirmed. Asperisporium pongamiae-pinnatae is reduced to synonymy with P. pongamiae. Asperisporium pongamiae-pinnatae was introduced because of the wrong assumption that F. pongamiae had been described on another host, Pongamia globosa. But Fusicladium pongamiae was actually described in India on Pongamia glabra, which is a synonym of P. pinnata, and hence on the same host as Asperisporium pongamiae-pinnatae. Pedrocrousiella pongamiae clusters in a clade containing Distocercospora, Clypeosphaerella, and “Pseudocercospora” nephrolepidicola, a species which is not congeneric with Pseudocercospora. Phylogenetically, Pedrocrousiella is distant from the Asperisporium s. str. clade (type species A. caricae), which is more closely related to Amycosphaerella, Pseudocercosporella, Distomycovellosiella and Nothopassalora. Citation: Rajeshkumar KC, Braun U, Groenewald JZ, Lad SS, Ashtekar N, Fatima S, Anand G (2021). Phylogenetic placement and reassessment of Asperisporium pongamiae as Pedrocrousiella pongamiae gen. et comb. nov. (Mycosphaerellaceae). Fungal Systematics and Evolution 7: 165–176. doi: 10.3114/fuse.2021. 07.08
Localnet: A Simple Recurrent Neural Network Model for Protein Secondary Structure Prediction Using Local Amino Acid Sequences Only

BackgroundProtein secondary structure prediction (PSSP) is important for protein structure modeling and design. Over the past a few years, deep learning models have shown promising results for PSSP. However, the current good performers for PSSP often require evolutionary information such as multiple sequence alignments and even real protein structures (templates), entire protein sequences, and amino acid property profiles. ResultsIn this study, we used a fixed-size window of adjacent residues and only amino acid sequences, without any evolutionary information, as inputs, and developed a very simple, yet accurate RNN model: LocalNet. The accuracy for three states of secondary structures is as high as 85.15%, indicating that the local amino acid sequence itself contains enough information for PSSP, a well-known classical view. By comparing to other predictors, we also achieve an state-of-art accuracy on dataset of CASP11, CASP12 and CASP13.ConclusionThe well-trained models are expected to have good applications in protein structure modeling and protein design. This model can be downloaded from https://github.com/lake-chao/protein-secondary-structure-prediction.
Data Driven: An Overview and Practical Measures for Organizations

— Data is considered a primary resource for innovation. The existence of a large amount of available data, as well as technological tools capable of explore them, allows companies to extract information that can be used to create and implement new ideas and new projects. To this end, the details regarding the care that organizations should have with data are explored. The difficulties regarding the adoption of data-driven approach and some measures to implement this type of decision-making approach are also discussed. Some examples of data-driven approaches for diverse industries and products are shown. A real example of prediction model for decision making that is based on industrial data is also discussed. This example shows the difficulties in the preparation of data for the building of these models, which confirms that most of the time spent in the construction of predictive models it is due to this step. The use of the data-driven approach allows organizations to obtain superior results in their processes, thus becoming a tremendous competitive advantage and a special strategic factor in a highly competitive market, regardless of the field of
Research on the conductivity of circuit on fabrics based on inkjet printing and electroless deposition technology

Traditional silicon semiconductor substrate based electronic manufacturing has the shortcomings of non-bending, poor biocompatibility, and high cost. Fabric is more suitable for wearable electronic substrate due to its advantages of flexibility, air permeability, and skin-friendliness. We studied the manufacture of the conductive circuit based on inkjet printing and electroless deposition technology and got excellent conductivity and high dimensional accuracy circuit on fabric substrates. Three kinds of commonly used fabric materials cotton, polyester/cotton and polyester are selected to study the key work of surface pre-treatment, inkjet printing circuit pattern, and electroless deposition. The synergetic effect of SU-8 and P4VP (poly-4-vinylpyridine) on fabric ensures that the pattern retains its original size rather than diffusing. The distance between adjacent electric lines is no less than 0.3mm. With the extension of copper deposition time, the copper deposition layer becomes more and more uniform and dense. Sheet resistance reached 0. 01Ω after 2 hours of copper deposition. The performance of all three kinds of fabric is similar. And cotton fabric had the best water lock performance. This technology has great potential for promotion and development in the application of intelligent textiles in the future.
A brief history of quantitative wear analysis with an appeal for a holistic view on dental wear processes

This chapter is a comprehensive overview about the development in the field of quantitative wear analysis during the last 20 years. It focuses on specific interdisciplinary approaches that either introduced new viewpoints or solved technical problems, and in particular guided our projects within the DFG research unit 771 at the University of Hamburg. The scope of our group’s interest facilitates the historical shift from qualitative to quantitative wear analysis. Our research was driven by the urge to gain a deeper understanding of wear, which is much more than just traces, and develop a holistic view of the wear process on diverse materials. We start with a condensed historical review of selected developments, focus on the major debates that have influenced our understanding of tooth wear as a part of oral food processing, and set the context of our work within the larger theoretical framework. We show examples that the field of dental wear analyses is evolving on all scales, and that we are only beginning to comprehend the complex dental wear process as one factor amongst many driving evolution through dental adaptation. In particular, the combined studies based on museum material, in vivo, and in vitro experiments have shed new light on the importance of abrasives in the wear process, but also raised new questions for future research. A brief history of quantitative wear analyses with an appeal for a holistic view on dental wear processes
CAMNet: DeepGait Feature Extraction via Maximum Activated Channel Localization

As the models with fewer operations help realize the performance of intelligent computing systems, we propose a novel deep network for DeepGait feature extraction with less operation for video sensor-based gait representation without dimension decomposition. The DeepGait has been known to have outperformed the hand-crafted representations, such as the frequency-domain feature (FDF), gait energy image (GEI), and gait flow image (GFI), etc. More explicitly, the channel-activated mapping network (CAMNet) is composed of three progressive triplets of convolution, batch normalization, max-pooling layers, and an external max pooling to capture the Spatio-temporal information of multiple frames in one gait period. We conducted experiments to validate the effectiveness of the proposed novel algorithm in terms of cross-view gait recognition in both cooperative and uncooperative settings using the state-of-the-art OU-ISIR multi-view large population OU-MVLP dataset. The OU-MVLP dataset includes 10307 subjects. As a result, we confirmed that the proposed method significantly outperformed state-of-the-art approaches using the same dataset at the rear angles of 180, 195, 210, and 225, in both cooperative and uncooperative settings for verification scenarios.
Comparative Effects of Organic and Conventional Cropping Systems on Trace Elements Contents in Vegetable Brassicaceae: Risk Assessment

Genotypes selected from 3 plant species (Brassica rapa, Eruca vesicaria and Sinapis alba) belonging to the Brassicaceae family were chosen to compare the concentrations of 9 inorganic elements (Cd, Co, Cr, Cu, Fe, Ni, Mn, Pb and Zn) in these varieties, that were grown under both conventional and organic conditions during two agricultural seasons (2018/2019 and 2019/2020) on two different experimental farms (Farm I and Farm II). We found that, together with agriculture practices, the inorganic element concentrations in Brassicas depended on many other factors, including soil characteristics. However, there were no conclusive results indicating a lower heavy metal content or a higher nutritionally beneficial trace elements content in vegetables grown under organic agriculture. Finally, a probabilistic assessment (@Risk) derived from the consumption of 150–200 g of these vegetables showed that organic Brassicas fulfill in comparison with the conventional ones, similar Dietary Reference Intakes (DRI) percentages for Co, Cr, Cu, Fe, Mn and Zn. Regarding heavy metals (Cd, Ni and Pb), we only found slight differences (mainly in the case of Pb) in the Tolerable Intakes (TI) between both cropping systems.
Effect of melatonin supplementation on heat shock proteins expression profile in buffalo calves under summer stress

A study was undertaken to investigate the effect of melatonin supplementation on heat shock proteins (HSPs) (HSP 60, HSP70, HSP 90 and HSP 110) expression profile in buffalo calves under summer stress. Twelve healthy Murrah buffalo male calves of 6 month to 1 year age group were taken for the study. Buffalo calves were divided into control (CG) and treatment (TG) group. In TG, Melatonin (18mg/50 kg BW) was injected subcutaneously, two times at 1st and 20th day. Blood samples were collected on 0th, 7th, 14th, 21st, 28th, 35th and, 42nd days. The relative expression of genes like HSP 60, HSP 70, HSP 90 and HSP 110 was studied in peripheral blood mononuclear cells. Between the groups, the mRNA expression of HSP70, 90 and 110 differed significantly (P
Gas hydrates technologies in the joint concept of geoenergy usage

The paper represents the analysis, which has helped to establish the usage of gas hydrate technologies in the methane conversion. This gas could be obtained in different ways. Possibilities and sources for the gas obtaining have been demonstrated. Use of other environmentally friendly sources to support operation in such systems in terms of joint energy complex has been considered. The necessary kinetic connections to provide operational sustainability of all the constituents have been given. The approach helps evaluate quantitatively the priority of its physicochemical transformations to obtain gas hydrates artificially. It is possible to transport methane at considerable distances when it is solidified. Actually, in this case there is no necessity to build costly compressor stations and pipelines for its transportation to consumers. The approach is extremely important for mining regions as it helps prolong the operating period and working out of the abandoned and off-balance coal reserves. In this case, it is proposed to apply special gasification technologies tending to maximum methane recovery. The proposed solutions give the possibility to define the trends of our further research. They will be highlighted in the following authors’ studies.
Growth Kinetics and Optical Properties of CsPbBr3 Perovskite Nanocrystals

We synthesized CsPbBr3 perovskite nanocrystals (NCs) at different reaction temperatures and tracked their growth kinetics on the basis of their optical properties and estimated size. The energies of the absorption and fluorescence (FL) peaks with increasing reaction temperature for the CsPbBr3 perovskite NCs were tuned within the regions of 2.429–2.570 eV and 2.391–2.469 eV, respectively, depending on size of the NCs (9.9–12.5 nm). The Stokes shifts of CsPbBr3 perovskite NCs with increasing NC size decreased from 101 meV to 38 meV. The full-width at half-maximum of the FL peaks for the CdSe NCs decreased from 150 meV to 90 meV because of the improved size uniformity of the CsPbBr3 perovskite NCs. The energy spacing of CsPbBr3 perovskite NCs synthesized at various reaction temperatures was calculated from Tauc plots; this information is critical for determining the bandgap energy and enables the size of the CsPbBr3 perovskite NCs to be estimated using the effective mass approximation.
Combination of Palbociclib and Erlotinib Exhibits Synergistic Antitumor Effect in Colorectal Cancer Patient-Derived Xenograft (PDX) Models

Background: The heterogenetic nature of colorectal cancer (CRC) constitutes a major challenge for drug development. Simultaneous targeting multiple molecules by combination therapy provides a promising strategy, but it requires identification of more potentially useful targeted agents. Palbociclib, a selective CDK4/6 inhibitor approved for the treatment of HR/ER-positive and HER2-negative breast cancer, exhibited anti-cancer versatility in several types of cancer. In this study, we evaluated its usefulness in the treatment of CRC either by single-agent or combined with a small molecule EGFR inhibitor erlotinib. Methods: The impacts of palbociclib, erlotinib, and their combination on cell proliferation, colony formation, cell cycle, apoptosis, senescence, and ROS accumulation in CRC cells were assessed. Their efficacies were evaluated in CRC patient-derived organoids (PDO) and xenograft (PDX) models.Results: Single-agent palbociclib efficiently inhibited proliferation, suppressed the RB phosphorylation, and caused G1-phase arrest in KRAS/BRAF mutated CRC cell lines. IC50 of all cell lines were below 1 µM. Moreover, it induced ROS accumulation and consequently caused apoptosis and senescence of CRC cells. The addition of erlotinib further aggravated palbociclib-induced anti-proliferation, cell cycle arrest, ROS accumulation, apoptosis, and senescence via blocking multiple critical effectors on RB/PI3K/RAS pathways and such interaction between two agents are synergistic. Finally, both palbociclib and erlotinib demonstrated anti-CRC activities, but only their combination caused statistically meaningful inhibition of tumor growth and prolonged survival with tolerable toxicity in KRAS wildtype/mutated PDX models. Conclusion: Our work demonstrated that the palbociclib and erlotinib combination treatment is a promising therapy for CRC and worthy of further clinical evaluation.
Development of Fluorescence Imaging Technique to Detect Fresh-Cut Food Organic Residue on Processing Equipment Surface

With increasing public demand for ready-to-eat fresh-cut food products, proper sanitation of food-processing equipment surfaces is essential to mitigate potential contamination of these products to ensure safe consumption. This study presents a sanitation monitoring technique using hyperspectral fluorescence images to detect fruit residues on food-processing equipment surfaces. An algorithm to detect residues on the surfaces of 2B-finished and #4-finished stainless-steel, both commonly used in food processing equipment, was developed. Honeydew, orange, apple, and watermelon were selected as representatives since they are mainly used as fresh-cut fruits. Hyperspectral fluorescence images were obtained for stainless steel sheets to which droplets of selected fruit juices at six concentrations were applied and allowed to dry. The most significant wavelengths for detecting juice at each concentration were selected through ANOVA analysis. Algorithms using a single waveband and using a ratio of two wavebands were developed for each sample and for all the samples combined. Results showed that detection accuracies were better for the samples with higher concentrations. The integrated algorithm had a detection accuracy of 100% and above 95%, respectively, for the original juice up to the 1:20 diluted samples and for the more dilute 1:50 to 1:100 samples, respectively. The results of this study establish that using hyperspectral imaging, even a small residual quantity that may exist on the surface of food processing equipment can be detected and that sanitation monitoring and management is possible.
Exercise Capacity Improvements Over Three Months Training: How Can we Relate Medium Term Training Results in A Competitive Roller Skiing Event?

An adapted aerobic – anaerobic training ratio can improve short term VO2max, but can limit long-term improvements aerobic and the anaerobic threshold changes. Twelve (n=12) international competitive male cross-country (G1) and biathlon athletes (G2) with a median age of 23 (21–27) years old were included as study subjects. Two VO2max tests (n=2) were conducted in the study period (93 days), further approached as test 1 (T1) during day 1 and test 2 (T2) during day 93. Several training sessions were conducted over 3.800 km volume. Lack of changes regarding VT1–VT2 group values were obtained between T1–T2 tests. Yet, through an individual approach, both high aerobic (p=0.03, r =0.62, CI95%=0.04 to 0.89) and low aerobic training (p=0.04, r=-0.65, CI95% = -0.90 to -0.03) were correlated with VT in G2. No similar results were obtained in G1 training group (p>0.05). Volume training, unlike early high intensity training, induces changes over the athletes’ exercise capacity. Aerobic training will induce an improved relative oxygen consumption, while both aerobic and anaerobic training can increase peak VO2 value, when implemented during the following 30-60 training days. Received: December 11, 2020