Miracle-dz/UniFAR-FTUs huggingface dataset:
Carrying my environment with me in iot-enhanced smart buildings

Smart and intelligent buildings are proposed and heavily studied recently to increase building automation, reduce building operation and electricity costs, and enhance human comfort. With the development of infrastructure, standardization, wireless sensing systems, smart phones, etc, many top-up services that were difficult to realize in traditional buildings can be developed nowadays. In this poster, we show a specific example. We design and implement “Carrying My Environment with Me” (CarryEn). The idea is that for human beings who are adapted to their surrounding environment in a building, e.g., their offices, when they move to other rooms, the configuration of their environment can be carried to next rooms. More importantly, such adjustment should be non-intrusive, i.e., people are not aware of the adjustment. The building management systems (BMS) should control the adjustment. (See Fig. 1) Our design has three components: 1) a smart and open BMS (Internet-of-Things oriented); 2) smart phone based application, and 3) environment adjustment algorithms. IoT-enhanced Building Management System: Our IoT based BMS is designed for general purposes, yet CarryEn can become a specific example for using it. It has two features: 1) smart and wireless; and 2) open. Many new BMS are recently proposed, e.g., sMap [1]. Our design differs from them as we convert the traditional wired BMS into smart and wireless without modification of the upper layer building protocols. Thus, it does not need long time for re-standardization. Our design and real deployment can be found in [3]. We recently extend our BMS to make it open. As such, people can develop top-up apps which can interact with the BMS with public protocols. As an example besides CarryEn, Toshiba can monitor its air-conditioners in different buildings using different BMS. It can become part of cyber-physical search in the future as well. Intrinsically, we solve three problems: 1) a universal ID, 2) public protocols to communicate with the smart BMS, and 3) possible service providers to support the data communication. We choose IPv6 as the IDs. As IPv6 is heavy, we use 6Low-
Optically functional isoxanthopterin crystals in the mirrored eyes of decapod crustaceans

Significance Some aquatic animals use reflectors in their eyes either to form images or to increase photon capture. Guanine is the most widespread molecular component of these reflectors. Here, we show that crystals of isoxanthopterin, a pteridine analog of guanine, form both the image-forming “distal” mirror and the intensity-enhancing tapetum reflector in the compound eyes of some decapod crustaceans. The crystal structure of isoxanthopterin was determined, providing an explanation for why these crystals are so well suited for efficient reflection. Pteridines were previously known only as pigments, and our discovery raises the question of which other organic molecules may be used to form crystals with superior reflective properties either in organisms or in artificial optical devices. The eyes of some aquatic animals form images through reflective optics. Shrimp, lobsters, crayfish, and prawns possess reflecting superposition compound eyes, composed of thousands of square-faceted eye units (ommatidia). Mirrors in the upper part of the eye (the distal mirror) reflect light collected from many ommatidia onto the photosensitive elements of the retina, the rhabdoms. A second reflector, the tapetum, underlying the retina, back-scatters dispersed light onto the rhabdoms. Using microCT and cryo-SEM imaging accompanied by in situ micro–X-ray diffraction and micro-Raman spectroscopy, we investigated the hierarchical organization and materials properties of the reflective systems at high resolution and under close-to-physiological conditions. We show that the distal mirror consists of three or four layers of plate-like nanocrystals. The tapetum is a diffuse reflector composed of hollow nanoparticles constructed from concentric lamellae of crystals. Isoxanthopterin, a pteridine analog of guanine, forms both the reflectors in the distal mirror and in the tapetum. The crystal structure of isoxanthopterin was determined from crystal-structure prediction calculations and verified by comparison with experimental X-ray diffraction. The extended hydrogen-bonded layers of the molecules result in an extremely high calculated refractive index in the H-bonded plane, n = 1.96, which makes isoxanthopterin crystals an ideal reflecting material. The crystal structure of isoxanthopterin, together with a detailed knowledge of the reflector superstructures, provide a rationalization of the reflective optics of the crustacean eye.
THE VISUAL EVOKED POTENTIAL IN MAN

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The divergent mitotic kinesin MKLP2 exhibits atypical structure and mechanochemistry

MKLP2, a kinesin-6, has critical roles during the metaphase-anaphase transition and cytokinesis. Its motor domain contains conserved nucleotide binding motifs, but is divergent in sequence (~35% identity) and size (~40% larger) compared to other kinesins. Using cryo-electron microscopy and biophysical assays, we have undertaken a mechanochemical dissection of the microtubule-bound MKLP2 motor domain during its ATPase cycle, and show that many facets of its mechanism are distinct from other kinesins. While the MKLP2 neck-linker is directed towards the microtubule plus-end in an ATP-like state, it does not fully dock along the motor domain. Furthermore, the footprint of the MKLP2 motor domain on the MT surface is altered compared to motile kinesins, and enhanced by kinesin-6-specific sequences. The conformation of the highly extended loop6 insertion characteristic of kinesin-6s is nucleotide-independent and does not contact the MT surface. Our results emphasize the role of family-specific insertions in modulating kinesin motor function.
Trace Metals in Fish Biominerals as Environmental Indicators: Handheld XRF Analyses

The parts of jawbones and selected teeth (malleolus) of adult marine benthic fish Sparus aurata and Diplodus sargus was collected from different station during east Adriatic coast (Croatia). Biominerals were prepared for three different instrumental analyses: elemental analysis by X-ray Fluorescence (XRF) and inductively coupled plasma spectroscopy (ICP-AES); mineralogical analysis by X-ray diffraction (XRD). The XRF results showed major and traces elements incorporated in the fish teeth. The concentration of zinc (Zn) expressed in mg kg-1 in the enamel - outside part of the malleolus dental surface (teeth crown) varied from 77 up to 1.975 in both fish species. In the root of the same teeth samples of Zn concentration was lower and amounted from 77 - 153 mg kg-1. Contrary, maximal amount of strontium (Sr) was registered in the teeth root from 801 – 1.310 mg kg-1, and in the enamel 476 – 1.104 mg kg-1 respectively. Multivariate statistical analysis based on the Statistica 6.0. PCA has been used to determine differences among elemental composition of the major and trace elements in teeth enamel (crown) and teeth roots, and in examining correlation among incorporated elements and environmental characteristics of the sampling localities.The XRD patterns of both fish jawbones and malleolus teeth showed characteristic hydroxyapatite lines (HAP). The HAP lines of the fish jawbones are broadened and shifted on the higher angles, indicating that mandible and maxilla biominerals are not fully formed and that mineralization of the fish jawbones is a dynamic process that last permanently during organism growth.Selected elements contents Ni, Co, Fe, Cu, and Cr (expressed in mg kg-1) of bulk fishbone samples was determined by ICP-AES analysis. Investigated metals showed higher values in the teeth than in the fish jawbones. The results revealed the distribution of the heavy metals in teeth to be Fe > Cr > Cu > Ni > Co, and in the jaws Fe > Cr > Cu > Ni > Co.The purpose of this study was to investigate the possibility of using XRF for the routine determination of heavy metals in the fish biominerals, in biomonitoring studies and ecological evaluation of the environment. The over-all data obtained indicated that XRF and ICP-AES showed good agreement for the determination of the heavy metals in test samples and that XRF could be used as cost effective method of accurately and precisely determining heavy metals content of the biomineral, while drastically reducing analysis time for initial sample preparation.
HDM2 Promotes NEDDylation of Hepatitis B Virus HBx To Enhance Its Stability and Function

ABSTRACT Hepatitis B virus (HBV)-encoded X protein (HBx) plays a critical role in HBV-related hepatocarcinoma development. In this study, we demonstrate that HBx is specifically modified by NEDD8. We found that E3 ligase HDM2 promotes NEDDylation of HBx to enhance HBx stability by preventing its ubiquitination-mediated degradation. Consistently, analysis of 160 hepatocellular carcinoma patient specimens indicated that the amount of HDM2 protein correlates with HBx protein level. We identified that HBx K91 and K95 as the key HBx NEDDylation sites and observed that the NEDDylation-deficient HBx has shorter half-life. We generated Huh7 cell lines which ectopically express wild-type and NEDDylation-deficient HBx and found that NEDDylation-deficient HBx showed less chromatin localization and less DDB1 binding. Consistently, the expression of HBx-regulated genes (IL-8, MMP9, and YAP) and HBV transcription (the activity of HBV enhancer and the amount of pgRNA transcribed from cccDNA) were significantly higher in cells expressing wild-type (WT) HBx than that in cells expressing mutant HBx. In addition, HBx-expressing cells proliferated faster than control and mutant HBx-expressing cells. We also showed that the ability of WT HBx-expressing cells to form tumors in nude mice was significantly higher than that of mutant HBx-expressing cells. In conclusion, we revealed that E3 ligase HDM2 promotes NEDDylation of HBx to enhance HBx stability and chromatin localization, which in turn favors HBx-dependent transcriptional regulation, cell proliferation, and HBV-driven tumor growth. IMPORTANCE Hepatitis B virus (HBV) HBx protein plays a critical role in viral replication and hepatocarcinogenesis. However, the regulation of HBx stability is not well understood. We found that HBx is modified by NEDD8 and that the HDM2 E3 ligase promotes HBx NEDDylation to enhance HBx stability by inhibiting its ubiquitination. We provide a new evidence to show the positive correlation between HDM2 and HBx in clinical hepatocellular carcinoma (HCC) samples. We also identified the major NEDDylation sites on HBx. Our studies indicate that the defective NEDDylation of HBx negatively affects its ability to activate the transcription of downstream genes and promote cell proliferation and tumor growth in vivo. Taken together, our findings reveal a novel posttranslational modification of HBx by HDM2 which regulates its stability, subcellular localization, and functions. These findings indicate that HDM2 is an important regulator on HBx and a potential diagnosis/therapeutic marker for HBV-associated HCC.
Hepatitis B virus prevalence in rural areas in south-west Chad

In Chad, hepatitis B virus (HBV) is thought to have a high prevalence and is consequently responsible for numerous acute and long-term complications. It is often detected during screening in potential blood donors. However, no general population-based study on the prevalence of hepatitis B has been performed. The aim of this study was to gain an impression of the HBV prevalence in rural areas in south-west Chad. A total of 1309 individuals (745 boys/men, 564 girls/women) with a median age of 15 years (age range, 6–81 years) were screened for the presence of the hepatitis B antigen (HBsAG). We found an overall prevalence of 22.9%. The youngest age group (6–15 years) and the boys/men showed a significantly higher HBsAG prevalence compared to the older groups and the girls/women, respectively (P < 0.01). Vertical infection during birth and horizontal infection by sharing food, water and shelter are believed to be the main sources of infection.
Automatic Detection of Public Development Projects in Large Open Source Ecosystems: An Exploratory Study on GitHub

Hosting over 10 million of software projects, GitHub is one of the most important data sources to study behavior of developers and software projects. However, with the increase of the size of open source datasets, the potential threats to mining these datasets have also grown. As the dataset grows, it becomes gradually unrealistic for human to confirm quality of all samples. Some studies have investigated this problem and provided solutions to avoid threats in sample selection, but some of these solutions (e.g., finding development projects) require human intervention. When the amount of data to be processed increases, these semi-automatic solutions become less useful since the effort in need for human intervention is far beyond affordable. To solve this problem, we investigated the GHTorrent dataset and proposed a method to detect public development projects. The results show that our method can effectively improve the sample selection process in two ways: (1) We provide a simple model to automatically select samples (with 0.827 precision and 0.947 recall); (2) We also offer a complex model to help researchers carefully screen samples (with 63.2% less effort than manually confirming all samples, and can achieve 0.926 precision and 0.959 recall).
Nonbond interactions between graphene nanosheets and polymers: a computational study

Abstract Based on the geometries from molecular dynamics simulations and a package compiled by us, the interactions between graphene nanosheet (GNS) and nine types of flexible polymers have been investigated with force field. Both the van der Waals (vdW) interaction and the electrostatic interaction (EI) for two same polymer chains and between a polymer and a GNS were calculated and compared. The effect of cut-off distance was explored. It was found that the cut-off distance plays a significant role in EI energy, but a less important role in vdW energy when the cut-off distance is over 9.5 Å. The reasonable cut-off distances for EI and vdW interactions for simulation are suggested.
Mechanical Analysis on the New Type of Semi-Rigid Asphalt Pavement Structure Based on Dynamic Parameters

In order to study the dynamic response of the new type of semi-rigid asphalt pavement structure under different speed and continuous variable speed of vehicle,the 3Dfinite element model is built by ABAQUS based on the elastic layered system theory,the dynamic modulus parameters of pavement materials are utilized,and the subroutine UTRACLOAD and DSLOAD are compiled.In addition,mechanical responses of pavement structure calculated by static parameters are compared.And difference of mechanical performance indexes between new semi-rigid and the traditional pavement structure are also analysed.The results show that the vehicle speed has few effects on dynamic responses of pavement structure.Compared to the calculations by static modulus,strain of semi-rigid base layer is reduced and shear stress of asphalt surface course is increased when dynamic modulus is used.Furthermore,the new type of semi-rigid pavement structure can effectively reduce the rutting probability of intersections and improve its resistance to permanent deformation.
Detecting tissue-specific early warning signals for complex diseases based on dynamical network biomarkers: study of type 2 diabetes by cross-tissue analysis

Identifying early warning signals of critical transitions during disease progression is a key to achieving early diagnosis of complex diseases. By exploiting rich information of high-throughput data, a novel model-free method has been developed to detect early warning signals of diseases. Its theoretical foundation is based on dynamical network biomarker (DNB), which is also called as the driver (or leading) network of the disease because components or molecules in DNB actually drive the whole system from one state (e.g. normal state) to another (e.g. disease state). In this article, we first reviewed the concept and main results of DNB theory, and then applied the new method to the analysis of type 2 diabetes mellitus (T2DM). Specifically, based on the temporal-spatial gene expression data of T2DM, we identified tissue-specific DNBs corresponding to the critical transitions occurring in liver, adipose and muscle during T2DM development and progression. Actually, we found that there are two different critical states during T2DM development characterized as responses to insulin resistance and serious inflammation, respectively. Interestingly, a new T2DM-associated function, i.e. steroid hormone biosynthesis, was discovered, and those related genes were significantly dysregulated in liver and adipose at the first critical transition during T2DM deterioration. Moreover, the dysfunction of genes related to responding hormone was also detected in muscle at the similar period. Based on the functional and network analysis on pathogenic molecular mechanism of T2DM, we showed that most of DNB genes, in particular the core ones, tended to be located at the upstream of biological pathways, which implied that DNB genes act as the causal factors rather than the consequence to drive the downstream molecules to change their transcriptional activities. This also validated our theoretical prediction of DNB as the driver network. As shown in this study, DNB can not only signal the emergence of the critical transitions for early diagnosis of diseases, but can also provide the causal network of the transitions for revealing molecular mechanisms of disease initiation and progression at a network level.
Increased RNAi Efficacy in Spodoptera exigua via the Formulation of dsRNA With Guanylated Polymers

Lepidoptera comprise some of the most devastating herbivorous pest insects worldwide. One of the most promising novel pest control strategies is exploiting the RNA interference (RNAi) mechanism to target essential genes for knockdown and incite toxic effects in the target species without harming other organisms in the ecosystem. However, many insects are refractory to oral RNAi, often due to rapid degradation of ingested dsRNA in their digestive system. This is the case for many lepidopteran insects, including the beet armyworm Spodoptera exigua, which is characterized by a very alkaline gut environment (pH > 9.0) and a strong intestinal nucleolytic activity. In this research, guanidine-containing polymers were developed to protect dsRNA against nucleolytic degradation, specifically in high pH environments. First, their ability to protect dsRNA against nucleolytic degradation in gut juice of the beet armyworm S. exigua was investigated ex vivo. Polymers with high guanidine content provided a strong protection against nucleolytic degradation at pH 11, protecting the dsRNA for up to 30 h. Next, cellular uptake of the dsRNA and the polyplexes in lepidopteran CF203 midgut cells was investigated by confocal microscopy, showing that the polymer also enhanced cellular uptake of the dsRNA. Finally, in vivo feeding RNAi bioassays demonstrated that using these guanidine-containing polymer nanoparticles led to an increased RNAi efficiency in S. exigua. Targeting the essential gene chitin synthase B, we observed that the mortality increased to 53% in the polymer-protected dsRNA treatment compared to only 16% with the naked dsRNA and found that polymer-protected dsRNA completely halted the development of the caterpillars. These results show that using guanylated polymers as a formulation strategy can prevent degradation of dsRNA in the alkaline and strongly nucleolytic gut of lepidopteran insects. Furthermore, the polymer also enhances cellular uptake in lepidopteran midgut cells. This new delivery strategy could be of great use in further fundamental research in lepidopterans, using RNAi as a research tool, and could lead to future applications for RNAi-based pest control of lepidopteran insects.
Effectiveness of Mindfulness-based interventions on physiological and psychological complications in adults with diabetes: A systematic review

This systematic review aimed to examine the effectiveness of Mindfulness-based interventions in reducing diabetes-related physiological and psychological symptoms in adults with types 1 and 2 diabetes. Five databases were systematically searched. A total of 11 studies satisfied the inclusion criteria. Mindfulness-based intervention effectiveness for physiological outcomes (glycaemic control and blood pressure) was mixed. Mindfulness-based interventions appear to have psychological benefits reducing depression, anxiety and distress symptoms across several studies. Studies’ short-term follow-up periods may not allow sufficient time to observe physiological changes or illustrate Mindfulness-based interventions’ potential long-term efficacy. More long-term studies that include a consistent, standardised set of outcome measures are required.
Distribution-Based Behavioral Distance for Nondeterministic Fuzzy Transition Systems

Modal logics and behavioral equivalences play an important role in the specification and verification of concurrent systems. In this paper, we first present a new notion of bisimulation for nondeterministic fuzzy transition systems, which is distribution based and coarser than state-based bisimulation appeared in the literature. Then, we define a distribution-based bisimilarity metric as the least fixed point of a suitable monotonic function on a complete lattice, which is a behavioral distance and is a more robust way of formalizing behavioral similarity between states than bisimulations. We also propose an on-the-fly algorithm for computing the bisimilarity metric. Moreover, we present a fuzzy modal logic and provide a sound and complete characterization of the bisimilarity metric. Interestingly, this characterization holds for a class of fuzzy modal logics. In addition, we show the nonexpansiveness of a typical parallel composition operator with respect to the bisimilarity metric, which makes compositional verification possible.
Modeling the chronic lymphocytic leukemia microenvironment in vitro

Abstract Microenvironments within the lymph node and bone marrow promote proliferation and drug resistance in chronic lymphocytic leukemia (CLL). Successful treatment of CLL must therefore target the leukemic cells within these compartments. A better understanding of the interaction between CLL cells and the tumor microenvironment has led to the development of in vitro models that mimic the mechanisms that support leukemic cell survival and proliferation in vivo. Employing these models as part of the pre-clinical evaluation of novel therapeutic agents enables a better approximation of their potential clinical efficacy. In this review we summarize the current literature describing how different aspects of the tumor microenvironment have been modeled in vitro and detail how these models have been employed to study the biology of the disease and potential efficacy of novel therapeutic agents.