Miracle-dz/UniFAR-FTUs huggingface dataset:
Importance of the Force Field Choice in Capturing Functionally Relevant Dynamics in the von Willebrand Factor

Whether recent updates and new releases of atomistic force fields can model the structural and dynamical properties of proteins containing both folded and partially disordered domains is still unclear. To address this fundamental question, we tested eight recently released force fields against our set of nuclear magnetic resonance (NMR) observables for a complex and medically relevant system, the major factor VIII binding region on the von Willebrand factor. This biomedically important region comprises both a folded and a partially structured domain. By using an enhanced sampling technique (temperature replica-exchange molecular dynamics simulations), we find that some force fields indeed rise to the challenge and capture the structural and dynamical features of the NMR ensemble and, therefore, are the appropriate choice for simulations of proteins with partially structured domains. What is more, we show that only such force fields can qualitatively capture the effects of a pathogenic mutation on the structural ensemble.
Dynamic Changes of Ascorbic Acid, Phenolics Biosynthesis and Antioxidant Activities in Mung Beans (Vigna radiata) until Maturation

To better understand the regulatory mechanism of phenolics and ascorbic acid accumulation as well as antioxidant activities in mung beans during legume development, the gene expression profiles of 25 key-coding genes in ascorbic acid and phenolics metabolic pathways were analyzed. As well as the dynamitic changes of ascorbic acid, phenolic profiles and antioxidant activities with legume development were studied. The results indicated that gene expression profiles were closely related to the ascorbic acid and phenolics accumulation regularity during legume development. VrVTC2 and VrGME played important roles for ascorbic acid accumulation from 8 to 17 days after flowering (DAF). VrPAL and VrCHS exhibited positive correlations with daidzein and glycitin accumulation, and VrIFS had a strong positive correlation with glycitin biosynthesis. Antioxidant activities dramatically increased during mung bean maturing, which were significantly related to ascorbic acid and phenolics accumulation. Eight days after flowering was the essential stage for ascorbic acid and phenolics biosynthesis in mung beans.
Experimental Investigation of Mechanical Behaviors of Self-Compacting Concrete under Cyclic Direct Tension

Self-compacting concrete (SCC) is increasingly applied in the construction industries due to its advantages of outstanding workability and eco-friendliness. However, few experimental studies on the mechanical behaviors of SCC under cyclic direct tension are available in the literature. In this work, experimental investigations of mechanical behaviors of SCC under cyclic direct tension were conducted. Especially, direct tensile load equipment was developed. It is found that the envelope stress-strain curve under cyclic direct tension is close to that under monotonic direct tension; however, it is different from that in a compressive case. It is also revealed that the ratio of unloading strain to irreversible strain is approximately linearly dependent on unloading strain. The evolutions of energy dissipation for SCC under both cyclic direct tension and compression are similar to those of normally vibrated concrete. In addition, Poisson’s ratio is observed to be nearly 0.21 for SCC. Furthermore, a damage model enabling characterization of the stress-strain curve under both monotonic and cyclic loading was proposed and verified against experimental results. Therefore, the results in this work provide original research material for studying and modelling the mechanical behaviors of SCC under uniaxial cyclic direct tension.
Reliability of cone-beam computed tomography for temporomandibular joint analysis

Objective The aim was to assess the intraobserver and interobserver reliabilities of temporomandibular joint linear measurements and condylar shape classifications performed with cone-beam computed tomography (CBCT). Methods CBCT images of 30 patients were measured at two different time points by two orthodontists using the Dolphin 3D program (n = 60). Anterior, posterior, and superior joint space measurements and sagittal joint morphology classification in the sagittal view and medial and lateral joint space and mediolateral width measurements and coronal joint morphology classification in the coronal view were recorded. Intraclass-interclass correlation coefficients (ICC) and kappa statistics were used to assess intraobserver and interobserver reliability for the measurements and morphology classifications, respectively. Results The ICC values were good for measurements of the posterior joint space by observer I and for measurements of the posterior, medial, and lateral joint spaces by observer II, while the other intraobserver measurements were excellent. Only the mediolateral width measurements showed excellent interobserver ICC values, while the other measurements showed good interobserver ICC values. Intraobserver agreement for the sagittal morphology classifications was moderate (κ = 0.479) and almost perfect (κ = 0.858) for observers I and II, respectively, while the corresponding agreement for the coronal morphology classifications was substantial for both observers. The interobserver agreement values for sagittal and coronal morphology classifications were slight (κ = 0.181) and fair (κ = 0.265), respectively. Conclusions Linear temporomandibular joint measurements were reproducible and reliable in both intraobserver and interobserver evaluations. However, interobserver agreement for assessments of condylar shape was low.
CRISPR screening using an expanded toolkit of autophagy reporters identifies TMEM41B as a novel autophagy factor

The power of forward genetics in yeast is the foundation on which the field of autophagy research firmly stands. Complementary work on autophagy in higher eukaryotes has revealed both the deep conservation of this process, as well as novel mechanisms by which autophagy is regulated in the context of development, immunity, and neuronal homeostasis. The recent emergence of new clustered regularly interspaced palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9)-based technologies has begun facilitating efforts to define novel autophagy factors and pathways by forward genetic screening in mammalian cells. Here, we set out to develop an expanded toolkit of autophagy reporters amenable to CRISPR/Cas9 screening. Genome-wide screening of our reporters in mammalian cells recovered virtually all known autophagy-related (ATG) factors as well as previously uncharacterized factors, including vacuolar protein sorting 37 homolog A (VPS37A), transmembrane protein 251 (TMEM251), amyotrophic lateral sclerosis 2 (ALS2), and TMEM41B. To validate this data set, we used quantitative microscopy and biochemical analyses to show that 1 novel hit, TMEM41B, is required for phagophore maturation. TMEM41B is an integral endoplasmic reticulum (ER) membrane protein distantly related to the established autophagy factor vacuole membrane protein 1 (VMP1), and our data show that these two factors play related, albeit not fully overlapping, roles in autophagosome biogenesis. In sum, our work uncovers new ATG factors, reveals a malleable network of autophagy receptor genetic interactions, and provides a valuable resource (http://crispr.deniclab.com) for further mining of novel autophagy mechanisms.
Political Inequality in the Digital World: The Puzzle of Asian American Political Participation Online

This paper adds to existing literature by reassessing the racial participation gap after placing online activity within the repertoire of minorities’ political actions. Even though Asian Americans are the most resourced in terms of Internet access, I theorize about how individual and structural-level impediments uniquely disadvantage this group from participating in politics online—widening overall participation disparities. Using data from the 2016 National Asian American Survey, I find that while the racial participation gap is similar for Latina/os and African Americans compared to whites, regardless of the activity’s platform either offline or online, disparities magnify solely for Asian Americans when considering digital modes of political behavior. The paper ends by noting how the Internet may contribute to rather than solve issues of political inequality across race and discusses distortions in which political voices are heard or muted offline and online.
Wi-Fi-Based Effortless Indoor Positioning System Using IoT Sensors

Wi-Fi positioning based on fingerprinting has been considered as the most widely used technology in the field of indoor positioning. The fingerprinting database has been used as an essential part of the Wi-Fi positioning system. However, the offline phase of the calibration involves a laborious task of site analysis which involves costs and a waste of time. We offer an indoor positioning system based on the automatic generation of radio maps of the indoor environment. The proposed system does not require any effort and uses Wi-Fi compatible Internet-of-Things (IoT) sensors. Propagation loss parameters are automatically estimated from the online feedback of deployed sensors and the radio maps are updated periodically without any physical intervention. The proposed system leverages the raster maps of an environment with the wall information only, against computationally extensive techniques based on vector maps that require precise information on the length and angles of each wall. Experimental results show that the proposed system has achieved an average accuracy of 2 m, which is comparable to the survey-based Wi-Fi fingerprinting technique.
Effects of Body Condition and Concentrate Proportion of the Ration on Mobilization of Fat Depots and Energetic Condition in Dairy Cows during Early Lactation Based on Ultrasonic Measurements

Simple Summary During early lactation, cows face metabolic challenges. They experience a negative energy balance as energy intake increases more slowly than energy output with milk rises. To compensate for that energy deficit, higher amounts of concentrate are offered. Additionally, cows are able to extract energy from body fat by lipid mobilization. Excessive body fat mobilization, however, leads to metabolic disorders. Therefore, high-conditioned cows are suggested to have a more pronounced lipid mobilization. The intention of the present study was to examine the change of various fat depots during the transition period depending on body condition and energy supply with ultrasonic measurements. Body condition loss after calving usually interpreted as mobilization of subcutaneous adipose tissue was not different between cows with a higher or lower body condition score. However, ultrasonic measurements detected a more pronounced mobilization of subcutaneous adipose tissue in higher conditioned animals. In contrast, inner fat depots were mobilized similarly between cows. Higher concentrate feed proportions led to a less pronounced negative energy balance. A less pronounced negative energy balance would have been expected to decrease lipid mobilization. However, this relation could not be verified in the present study. This demonstrates that sonography-based methods provide a clearer picture of metabolic conditions. Abstract The aim of this study was to evaluate energy metabolism and lipid mobilization via ultrasonic measurements (USM), considering inner fat depots, in lactating dairy cows differing in body condition score (BCS) and fed rations with low (35% at dry matter basis; C35) or high (60% at dry matter basis; C60) concentrate feed proportions postpartum. Sixty pluriparous German Holstein cows were arranged in a 2 × 2 factorial design from d 42 antepartum (relative to calculated calving) until d 120 postpartum. Animals were divided into a group with a lower (initial BCS = 3.1 ± 0.38 SD; BCSL) and a group with a higher (initial BCS = 3.83 ± 0.41 SD; BCSH) BCS. Due to higher dry matter intake C60 groups reached the positive energy balance earlier, whereas C35 groups had a more pronounced negative energy balance. Although this would suggest a more pronounced mobilization of C35 groups the USM revealed no differences between feeding groups. Differences in BCS between both BCS groups remained almost the same over the trial. This was not reflected in ultrasonic data, as lipid mobilization was higher in higher conditioned cows. These findings demonstrate the extended possibilities of USM to depict metabolic processes.
Virulence gene profiles and phylogeny of Shiga toxin-positive Escherichia coli strains isolated from FDA regulated foods during 2010-2017

Illnesses caused by Shiga toxin-producing Escherichia coli (STECs) can be life threatening, such as hemolytic uremic syndrome (HUS). The STECs most frequently identified by USDA’s Microbiological Data Program (MDP) carried toxin gene subtypes stx1a and/or stx2a. Here we describe the genome sequences of 331 STECs isolated from foods regulated by the FDA 2010-2017, determining their genomic identity, serotype, sequence type, virulence potential, and prevalence of antimicrobial resistance. Isolates were selected from the MDP archive, routine food testing by field labs (ORA), food testing by a contract company, and our laboratory (ORS). Only 276 (83%) were confirmed as STECs by in silico analysis. Foods from which STECs were recovered included cilantro (6%), spinach (25%), lettuce (11%), and flour (9%). Phylogenetic analysis using core genome MLST revealed these STEC genomes were highly variable, with some clustering associated with ST types and serotypes. We detected 95 different sequence types (ST); several ST were previously associated with HUS: ST21 and ST29 (O26:H11), ST11 (O157:H7), ST33 (O91:H14), ST17 (O103:H2), and ST16 (O111:H-). in silico virulome analyses showed ~ 51% of these strains were potentially pathogenic [besides stx gene they also carried eae (25%) or 26% subA (26%)]. Virulence gene prevalence was also determined: stx1 only (19%) -variants a and c; stx2 only (66%) – variants a, b, c, d, e, and g; and stx1/sxt2 (15%). Our data form a new WGS database that can be used to support food safety investigations and monitor the recurrence/emergence of E. coli in foods. Importance Shiga toxin-producing Escherichia coli (STECs) are associated with foodborne outbreaks worldwide; however, surveillance has not previously included genomic analyses for phylogenetics, prevalence, or potential virulence. We constructed the first genomic database of isolates from FDA-regulated foods to help monitor the emergence of new pathogenic STECs. Although only ~30 STECs were isolated per year, 50% of these carried markers associated with pathogenesis either a combination of eae plus stx, or subA plus stx. Moreover, those strains also carried virulence genes associated with severe illnesses. Here we showed that WGS enabled comparisons across isolates to establish phylogeny, help in identification of antibiotic resistance by monitoring the presence of antimicrobial resistance genes, and determined the presence of known virulence genes that have been linked with illnesses. Future food safety investigations will benefit from improved source tracking and risk assessments made possible by these analyses and new WGS database.
Image Pattern Recognition using DCT-based Feature Extraction and Genetic Search Feature Selection

Feature selection is a critical task in machine learning that is used for dimensionality reduction of data to enhance the performance of different classification and clustering algorithms. The main challenge of the feature selection problem is its large search space. Different approaches have been adopted to solve the feature selection problem. Meta-heuristic search techniques, including genetic algorithms, have recently gained attention by machine learning community and achieved enhanced performance. A genetic algorithm can generate quality solutions to optimization problems based on genetic operators such as selection, crossover, and mutation. It is an iterative process in which the best candidate solutions are combined to generate even better candidate solutions. The process is repeated until an acceptable solution is achieved or the maximum number of iterations is reached. In this paper, a genetic algorithm is used to search for the optimal subset of relevant features for image classification. Experimental results show that the adopted feature selection technique resulted in enhanced performance of neural networks and logistic regression classifiers using much less number of selected features.
Impact of OM-85 Given during Two Consecutive Years to Children with a History of Recurrent Respiratory Tract Infections: A Retrospective Study

In otherwise healthy infants and young children, respiratory tract infections (RTIs) are extremely common. Clinical data have shown that OM-85 could prevent respiratory recurrences in children. However, further studies are needed to explore the true importance of OM-85 in clinical practice. In addition, an unsolved problem is the efficacy of OM-85 when it is administered for two consecutive years. Moreover, another open question is the safety of OM-85 when co-administered with the influenza vaccine. In order to solve these unanswered issues, 200 children aged three to six years with a history of recurrent RTIs, defined as at least six documented episodes of acute RTI in a single year, who had received OM-85 (Broncho-Vaxom®; OM Pharma, a Vifor Pharma Group Company, Geneva, Switzerland) for two consecutive years (3.5 mg once a day for 10 days for 3 months of each year) were selected and matched based on age, sex, and period of evaluation with children with recurrent RTIs who did not receive OM-85. In the group of children treated with OM-85, the number of patients who did not experience any new episode of RTI, as well as the number of RTIs, wheezing episodes, medical visits, and prescribed antibiotic courses, were significantly lower than that in the group not treated with OM-85. The results were similar in the first and second year of OM-85 administration. A minority of patients showed mild adverse events, and the safety profile was overall good, including in the 49 children who received the influenza vaccination within one month from the beginning of the first cycle of OM-85. Our data suggest that OM-85 can effectively and safely reduce the risk of new infective episodes in children with recurrent RTIs and that a second yearly course of lysate administration can be useful to maintain protection, particularly when the diagnosis of recurrent RTIs is made in younger children for whom it is likely that definitive maturation of the immune system still requires a long time.
Sulfonated Binaphthyl-Containing Poly(arylene ether ketone)s with Rigid Backbone and Excellent Film-Forming Capability for Proton Exchange Membranes

Sterically hindered (S)-1,1′-binaphthyl-2,2′-diol had been successfully copolymerized with 4,4′-sulfonyldiphenol and 4,4′-difluorobenzophenone to yield fibrous poly(arylene ether ketone)s (PAEKs) containing various amounts of binaphthyl unit, which was then selectively and efficiently sulfonated using ClSO3H to yield sulfonated poly(arylene ether ketone)s (SPAEKs) with ion exchange capacities (IECs) ranging from 1.40 to 1.89 mmol·g−1. The chemical structures of the polymers were confirmed by 2D 1H–1H COSY NMR and FT-IR. The thermal properties, water uptake, swelling ratio, proton conductivity, oxidative stability and mechanical properties of SPAEKs were investigated in detail. It was found that the conjugated but non-coplanar structure of binaphthyl unit endorsed excellent solubility and film-forming capability to SPAEKs. The SPAEK-50 with an IEC of 1.89 mmol·g−1 exhibited a proton conductivity of 102 mS·cm−1 at 30 °C, much higher than that of the state-of-the-art Nafion N212 membrane and those of many previously reported aromatic analogs, which may be attributed to the likely large intrinsic free volume of SPAEKs created by the highly twisted chain structures and the desirable microscopic morphology. Along with the remarkable water affinity, thermal stabilities and mechanical properties, the SPAEKs were demonstrated to be promising proton exchange membrane (PEM) candidates for potential membrane separations.
A Dual-Chamber Serial–Parallel Piezoelectric Pump with an Integrated Sensor for Flow Rate Measurement

A new concept of a dual-chamber serial-parallel piezoelectric pump with an integrated sensor (DSPPIS) is presented in this paper. By means of dividing a piezoelectric bimorph into an actuator and a sensor, sensing function is integrated onto the DSPPIS for flow rate measurement. A prototype of the DSPPIS was manufactured and assembled from a finished piezoelectric bimorph. Then, frequency and voltage characteristics were tested to evaluate the performance of the DSPPIS with serial and parallel connection. Experimental results show that the optimal frequency range of DSPPIS can be achieved and determined by itself through monitoring the sensing voltage when driven by a fixed voltage of 150 Vpp and a frequency range of 40–400 Hz. For a fixed frequency of 100 Hz and a voltage range of 50–250 Vpp, both the sensing voltage and output flow rate increase with the increase of driving voltage. It is observed that there is a positive correlation between sensing voltage and output flow rate, which was further fitted by using linear function. The correlation coefficients for the DSPPIS with serial and parallel connection are calculated as 0.9716 and 0.9054, respectively. As a result, the DSPPIS demonstrated in this paper has realized the measurement of flow rate without the additional flow-sensing equipment both in serial and parallel connection.
Histological analysis of ovarium development of Hampala macrolepidota Kuhl & Van Haselt, 1823 from Jatigede Reservoir, West Java

This research was conducted from May to September 2018 at the Biotechnology Laboratory, Faculty of Fisheries and Marine Sciences, University of Padjadjaran. Fish samples were taken from Jatigede Reservoir, Sumedang, West Java. The hampala fish consisted of female hampala barb with gonadal maturity level (GML) IV, GML V, and GML VI. Ovarian histological preparations were made at the Animal Microtechnical Laboratory, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran. This research aimed to determine the stages of ovarian development of hampala barb, and determine the types of spawning. The hampala barb in the Jatigede Reservoir had five stages of oocyte development, namely chromatin nucleolus stage, perinucleolus stage, cortical alveolus stage, vitellogenesis, and oocyte maturation with multi-spawner group synchronous type of ovarian development.