Miracle-dz/UniFAR-FTUs huggingface dataset:
Filled Skutterudites: from Single to Multiple Filling

This paper shortly reviews our recent work on filled skutterudites, which are considered to be one of the most promising thermoelectric (TE) materials due to their excellent power factors and relatively low thermal conductivities. The filled skutterudite system also provides a platform for studying void filling physics/chemistry in compounds with intrinsic lattice voids. By using ab initio calculations and thermodynamic analysis, our group has made progresses in understanding the filling fraction limit (FFL) for single fillers in CoSb₃, and ultra-high FFLs in a few alkali-metal-filled CoSb₃ have been predicted and then been confirmed experimentally. FFLs in multiple-element-filled CoSb₃ are also investigated and anonymous filling behavior is found in a few specific systems. The calculated and measured FFLs, in both single and multiple-filled CoSb₃ systems, show good accordance so far. The thermal transport properties can be understood qualitatively by a phonon resonance scattering model, and it seems that a scaling rule may exist between the lattice thermal resistivity and the resonance frequency of filler atoms in filled system. Even though a few things become clear now, there are still many unsolved issues that call for further work.
Computational Methods for Protein Identification from Mass Spectrometry Data

Protein identification using mass spectrometry is an indispensable computational tool in the life sciences. A dramatic increase in the use of proteomic strategies to understand the biology of living systems generates an ongoing need for more effective, efficient, and accurate computational methods for protein identification. A wide range of computational methods, each with various implementations, are available to complement different proteomic approaches. A solid knowledge of the range of algorithms available and, more critically, the accuracy and effectiveness of these techniques is essential to ensure as many of the proteins as possible, within any particular experiment, are correctly identified. Here, we undertake a systematic review of the currently available methods and algorithms for interpreting, managing, and analyzing biological data associated with protein identification. We summarize the advances in computational solutions as they have responded to corresponding advances in mass spectrometry hardware. The evolution of scoring algorithms and metrics for automated protein identification are also discussed with a focus on the relative performance of different techniques. We also consider the relative advantages and limitations of different techniques in particular biological contexts. Finally, we present our perspective on future developments in the area of computational protein identification by considering the most recent literature on new and promising approaches to the problem as well as identifying areas yet to be explored and the potential application of methods from other areas of computational biology.
A study on the impact of heuristic initialization functions in a genetic algorithm solving the N-queens problem

In this paper the influence of using heuristic functions to initialize the population of a classic genetic algorithm (GA) applied to the N-Queens Problem (NQP) is analyzed. The aim of this work is to evaluate the impact of the heuristic initialization phase on the results of the classic GA. In order to probe this, several experiments using two different initialization functions have been carried out. In this paper, the well-known NQP has been used as benchmark problem, but the objective of the authors is to contrast the findings of this study with other combinatorial optimization problems.
Inhibition of forkhead box class O family member transcription factors in rheumatoid synovial tissue.

OBJECTIVE Phosphatidylinositol 3-kinase-dependent activation of protein kinase B (PKB) has been observed in rheumatoid arthritis (RA) synovial tissue, and mechanisms that interfere with this process are protective in animal models of arthritis. PKB can regulate cell survival and proliferation via phosphorylation-dependent inactivation of forkhead box class O (FoxO) transcription factors. The present study was undertaken to examine whether FoxO transcription factors are differentially inactivated in RA synovial tissue, and whether this inactivation correlates with laboratory and clinical parameters of disease activity. METHODS The expression and phosphorylation of FoxO family members were assessed in synovial biopsy tissue from 12 patients with RA and 9 patients with inflammatory osteoarthritis (OA), by immunohistochemistry and quantitative computer-assisted image analysis. Immunoblotting was used to assess the interleukin-1beta (IL-1beta)- and tumor necrosis factor alpha (TNFalpha)-induced phosphorylation of FoxO1 and FoxO4 in cultured fibroblast-like synoviocytes (FLS) and macrophages. RESULTS FoxO1, FoxO3a, and FoxO4 were expressed and phosphorylated in synovial tissue from both RA patients and OA patients. In RA synovial tissue, phosphorylation of FoxO1 was observed in both FLS and macrophages, FoxO3a in T lymphocytes, and FoxO4 in macrophages alone. Following stimulation with IL-1beta and TNFalpha, FoxO1 and FoxO4 were phosphorylated in both RA and OA FLS and synovial macrophages, respectively. Inactivation of FoxO4 was significantly enhanced in the RA as compared with the OA synovial sublining. There was a strong negative correlation between inactivation of FoxO4 in RA synovial tissue and increased serum C-reactive protein levels and a raised erythrocyte sedimentation rate in RA patients. CONCLUSION All 3 FoxO family members examined were phosphorylated in both RA and OA synovial tissue; in particular, inactivation of FoxO4 was significantly enhanced in macrophages from RA synovial tissue. Thus, cell-specific inactivation of FoxO family members appears to differentially regulate cell survival and proliferation in the RA synovium.
Spinal anesthesia increases the risk of venous thromboembolism in total arthroplasty

Abstract Clinical guidance on the choice of anesthetic modality vis-à-vis the risk of perioperative venous thromboembolism (VTE) is largely lacking because of a paucity of recent evidence. A comparative effect of general anesthesia and neuraxial blockade on the perioperative incidence of VTE has not been well-investigated. We compared the effects of different types of anesthetic modalities on the risk of VTE after total hip arthroplasty (THA) and total knee arthroplasty (TKA). This is a secondary analysis of the Japanese Study of Prevention and Actual Situation of Venous Thromboembolism after Total Arthroplasty (J-PSVT). Data pertaining to a total of 2162 patients who underwent THA and TKA at 34 hospitals were included in this analysis. We compared the different anesthetic modalities with respect to the incidence of VTE. The composite end-point was asymptomatic/symptomatic deep vein thrombosis detected using scheduled bilateral ultrasonography up to postoperative day (POD) 10 and fatal/non-fatal pulmonary embolism up to POD 10. The study groups were as follows: general anesthesia (n = 646), combined epidural/general anesthesia (n = 1004), epidural anesthesia (n = 87), and spinal anesthesia (n = 425). On multivariate analysis, only spinal anesthesia was associated with a significant increase in the risk of VTE as compared with that associated with general anesthesia. Propensity score-matched analysis for “combined epidural/general anesthesia group” versus “spinal anesthesia group” demonstrated a 48% higher incidence of VTE (relative risk = 1.48, 95% confidence interval [CI] 1.18–1.85) in the latter. Spinal anesthesia was associated with a higher risk of postoperative VTE, as compared with that associated with combined epidural/general anesthesia, in patients undergoing total arthroplasty.
Predicting the buckling Capacity of Steel Cylindrical Shells with Rectangular Stringers under Axial Loading by using Artificial Neural Networks

A parametric study was carried out in order to investigate the buckling capacity of the vertically stiffened cylindrical shells. To this end ANSYS software was used. Cylindrical steel shells with different yield stresses, diameter-to-thickness ratios (D/t) and number of stiffeners were modeled and their buckling capacities were calculated by displacement control nonlinear static analysis. Radial basis function (RBF) neural networks were used to predict the buckling capacity of shells. Herein 70 percent of the results of numerical analyses were used to train the neural network and the remainders were used to test and validate the results of neural networks. Results of this study showed that RBF neural networks are useful tools to predict the buckling capacity of vertically stiffened cylindrical shells. It was also shown that buckling capacities of stiffened shells exponentially vary by distance of adjacent stiffeners (unstiffened length).
Dlx5 Is a Cell Autonomous Regulator of Chondrocyte Hypertrophy in Mice and Functionally Substitutes for Dlx6 during Endochondral Ossification

The axial and appendicular skeleton of vertebrates develops by endochondral ossification, in which skeletogenic tissue is initially cartilaginous and the differentiation of chondrocytes via the hypertrophic pathway precedes the differentiation of osteoblasts and the deposition of a definitive bone matrix. Results from both loss-of-function and misexpression studies have implicated the related homeobox genes Dlx5 and Dlx6 as partially redundant positive regulators of chondrocyte hypertrophy. However, experimental perturbations of Dlx expression have either not been cell type specific or have been done in the context of endogenous Dlx5 expression. Thus, it has not been possible to conclude whether the effects on chondrocyte differentiation are cell autonomous or whether they are mediated by Dlx expression in adjacent tissues, notably the perichondrium. To address this question we first engineered transgenic mice in which Dlx5 expression was specifically restricted to immature and differentiating chondrocytes and not the perichondrium. Col2a1-Dlx5 transgenic embryos and neonates displayed accelerated chondrocyte hypertrophy and mineralization throughout the endochondral skeleton. Furthermore, this transgene specifically rescued defects of chondrocyte differentiation characteristic of the Dlx5/6 null phenotype. Based on these results, we conclude that the role of Dlx5 in the hypertrophic pathway is cell autonomous. We further conclude that Dlx5 and Dlx6 are functionally equivalent in the endochondral skeleton, in that the requirement for Dlx5 and Dlx6 function during chondrocyte hypertrophy can be satisfied with Dlx5 alone.
Middleware support for context-awareness in 4G environments

Context-awareness is a key technology for adaptive software systems. While past and recent research effort investigated the gathering of low-level information, implementation- and domain-driven approaches for context frameworks and conceptual models of context, vertical approaches combining the aspects of modeling, and implementation are still missing. In this paper, we propose a scalable and distributed context service for integrating heterogeneous context sources in large-scale mobile environments based on a layered context model enabling the modeling and support of multiple domain-specific context models. We implemented an adaptive multimedia messaging system on top of a 4G mobile communication testbed which supports the context-dependent selection of codecs and communication modes to validate our approach
Multifunctional hyaluronic acid modified graphene oxide loaded with mitoxantrone for overcoming drug resistance in cancer

Multifunctional nanosheets (HA-GO/Pluronic) with targeted chemo-photothermal properties were successfully developed for controlled delivery of mitoxantrone (MIT) to overcome multidrug resistance (MDR). In vitro release profiles displayed that both an acidic environment and a NIR laser could trigger and accelerate the release of a drug, which ensured nanosheets were stable in blood circulation and released MIT within tumor cells under laser irradiation. HA-GO/Pluronic nanosheets were taken up into MCF-7/ADR cells via receptor-mediated endocytosis, which further facilitated escapement of P-gp efflux. Compared with MIT solution, MIT/HA-GO/Pluronic showed greater cytotoxicity and increase in cellular MIT accumulation in MCF-7/ADR cells. Cell apoptosis and cell cycle arrest studies also revealed that MIT/HA-GO/Pluronic was more potent than MIT/GO/Pluronic and MIT solution. The anticancer efficacy in vivo was evaluated in MCF-7 and MCF-7/ADR-bearing mice, and inhibition of tumors by MIT/HA-GO/Pluronic with NIR laser irradiation was the most effective among all MIT formulations. In summary, the MIT/HA-GO/Pluronic system had striking functions such as P-gp reversible inhibitor and anticancer efficacy, and could present a promising platform for drug-resistant cancer treatment.
Fine mapping and replication of genetic risk loci in primary sclerosing cholangitis

Abstract Background and aims. Primary sclerosing cholangitis (PSC) is a chronic cholestatic liver disease characterized by progressive inflammation and fibrosis of the bile ducts eventually leading to biliary cirrhosis. Recent genetic studies in PSC have identified associations at 2q13, 2q35, 3p21, 4q27, 13q31 and suggestive association at 10p15. The aim of this study was to further characterize and refine the genetic architecture of PSC. Methods. We analyzed previously reported associated SNPs at four of these non-HLA loci and 59 SNPs tagging the IL-2/IL-21 (4q27) and IL2RA (10p15) loci in 992 UK PSC cases and 5162 healthy UK controls. Results. The most associated SNPs identified were rs3197999 (3p21 (MST1), p = 1.9 × 10-6, ORA vs G = 1.28, 95% CI (1.16–1.42)); rs4147359 (10p15 (IL2RA), p = 2.6 × 10-4, ORA vs G = 1.20, 95% CI (1.09–1.33)) and rs12511287 (4q27 (IL-2/IL-21), p = 3.0 × 10-4, ORA vs T = 1.21, 95% CI (1.09–1.35)). In addition, we performed a meta-analysis for selected SNPs using published summary statistics from recent studies. We observed genome-wide significance for rs3197999 (3p21 (MST1), P combined = 3.8 × 10-12) and rs4147359 (10p15 (IL2RA), P combined = 1.5 × 10-8). Conclusion. We have for the first time confirmed the association of PSC with genetic variants at 10p15 (IL2RA) locus at genome-wide significance and replicated the associations at MST1 and IL-2/IL-21 loci in a large homogeneous UK population. These results strongly implicate the role of IL-2/IL2RA pathway in PSC and provide further confirmation of MST1 association.
Secure Sound Classification: Gaussian Mixture Models

We propose secure protocols for Gaussian mixture-based sound recognition. The protocols we describe allow varying levels of security between two collaborating parties. The case we examine consists of one party (Alice) providing data and other party (Bob) providing a recognition algorithm. We show that it is possible to have Bob apply his algorithm on Alice's data in such a way that the data and the recognition results will not be revealed to Bob thereby guaranteeing Alice's data privacy. Likewise we show that it is possible to organize the collaboration so that a reverse engineering of Bob's recognition algorithm cannot be performed by Alice. We show how Gaussian mixtures can be implemented in a secure manner using secure computation primitives implementing simple numerical operations and we demonstrate the process by showing how it can yield identical results to a non-secure computation while maintaining privacy
Environmental Enrichment Increases the GFAP+ Stem Cell Pool and Reverses Hypoxia-Induced Cognitive Deficits in Juvenile Mice

Premature children born with very low birth weight (VLBW) can suffer chronic hypoxic injury as a consequence of abnormal lung development and cardiovascular abnormalities, often leading to grave neurological and behavioral consequences. Emerging evidence suggests that environmental enrichment improves outcome in animal models of adult brain injury and disease; however, little is known about the impact of environmental enrichment following developmental brain injury. Intriguingly, data on socio-demographic factors from longitudinal studies that examined a number of VLBW cohorts suggest that early environment has a substantial impact on neurological and behavioral outcomes. In the current study, we demonstrate that environmental enrichment significantly enhances behavioral and neurobiological recovery from perinatal hypoxic injury. Using a genetic fate-mapping model that allows us to trace the progeny of GFAP+ astroglial cells, we show that hypoxic injury increases the proportion of astroglial cells that attain a neuronal fate. In contrast, environmental enrichment increases the stem cell pool, both through increased stem cell proliferation and stem cell survival. In mice subjected to hypoxia and subsequent enrichment there is an additive effect of both conditions on hippocampal neurogenesis from astroglia, resulting in a robust increase in the number of neurons arising from GFAP+ cells by the time these mice reach full adulthood.
Design of Generalized Analog Network Coding for a Multiple-Access Relay Channel

In this paper, we propose a generalized analog network coding (GANC) scheme for a non-orthogonal multiple-access relay channel (MARC), where two sources transmit their information simultaneously to the destination with the help of a relay. In the GANC scheme, the relay receives interfered signals from the two sources and generates signals to be transmitted with a relay function. We focus on the design of the optimal relay function to achieve the minimum pair-wise error probability (PEP) of the system. Specifically, we first covert the relay function optimization problem to a transformation matrix (TM) design problem by presenting the received complex signals as signal matrices composed of real and imaginary parts. Then, we propose an optimization criteria, i.e., maximizing the minimal squared Euclidean distance (MMSED), to improve the PEP performance, since the PEP is determined by the Euclidean distance of the received constellation at destination. Next, we prove that the MMSED can be equivalently converted to a convex problem by introducing an intermediate matrix. We solve this convex problem by using the Lagrangian method and obtain the closed-form expression of the optimal TM. We further improve the PEP performance by optimizing transmission power of the two sources. Simulation results show that the proposed GANC scheme has a better PEP performance compared to other alternative schemes.
Uncovering Wolbachia Diversity upon Artificial Host Transfer

The common endosymbiotic Wolbachia bacteria influence arthropod hosts in multiple ways. They are mostly recognized for their manipulations of host reproduction, yet, more recent studies demonstrate that Wolbachia also impact host behavior, metabolic pathways and immunity. Besides their biological and evolutionary roles, Wolbachia are new potential biological control agents for pest and vector management. Importantly, Wolbachia-based control strategies require controlled symbiont transfer between host species and predictable outcomes of novel Wolbachia-host associations. Theoretically, this artificial horizontal transfer could inflict genetic changes within transferred Wolbachia populations. This could be facilitated through de novo mutations in the novel recipient host or changes of haplotype frequencies of polymorphic Wolbachia populations when transferred from donor to recipient hosts. Here we show that Wolbachia resident in the European cherry fruit fly, Rhagoletis cerasi, exhibit ancestral and cryptic sequence polymorphism in three symbiont genes, which are exposed upon microinjection into the new hosts Drosophila simulans and Ceratitis capitata. Our analyses of Wolbachia in microinjected D. simulans over 150 generations after microinjection uncovered infections with multiple Wolbachia strains in trans-infected lines that had previously been typed as single infections. This confirms the persistence of low-titer Wolbachia strains in microinjection experiments that had previously escaped standard detection techniques. Our study demonstrates that infections by multiple Wolbachia strains can shift in prevalence after artificial host transfer driven by either stochastic or selective processes. Trans-infection of Wolbachia can claim fitness costs in new hosts and we speculate that these costs may have driven the shifts of Wolbachia strains that we saw in our model system.
Genotyping of Campylobacter jejuni strains from Danish broiler chickens by restriction fragment length polymorphism of the LPS gene cluster

Aims: To apply and evaluate LG (LPS genes) genotyping, which is a genotyping method based on a cluster of genes involved in the synthesis of surface lipopolysaccharides (LPS) in Campylobacter species, for typing of Campylobacter jejuni isolates obtained from Danish broiler chickens. Furthermore, the LG genotyping method was used to study the genetic stability of four C. jejuni strains after gastrointestinal passage through experimentally infected chickens.
The use of the Sensecam to explore daily functioning of older adults with chronic pain

Chronic pain often interferes with daily living. This study aimed to explore day-to-day patterns of functioning and experiences of older adults living with chronic pain. Thirteen older adults (65+ years) living with chronic pain (pain lasting >3 months) took part in the study. Four data collection techniques were used to gather information on various aspects of daily living. Participants were asked to wear a Sensecam, a LifeShirt, as well as complete a daily diary for seven days. Participants also took part in a semi-structured interview. Themes were developed, based on the images, to explain the effect of chronic pain on the participants' functioning. The Sensecam allowed novel data to be gathered increasing knowledge of the daily functioning of older adults living with chronic pain.
Mobisaic: An Information System for a Mobile Wireless Computing Environment

Mobisaic is a World Wide Web information system designed to serve users in a mobile wireless computing environment. Mobisaic extends the Web by allowing documents to both refer and react to potentially changzng contextual information, such as current location in the wireless network. Mobisaic relies on clientside processing of HTML documents that support two new concepts: Dynamic Uniform Resource Locators (URLs) and Active Documents. A dynamic URL is one whose results depend upon the state of the user's mobile context at the time it is resolved, An active document is one that automatically updates its contents in response to changes in a user's mobile context. This paper describes the design of Mobisaic, the mechanism it uses for representing a user's mobile content. and the extensions made to the syntax and function of Uniform Resource Locators and HyperText Markup Language documents to support mobility.
Multicasting in groupware?

While multicast has been studied extensively in many domains such as content streaming and file sharing, there is little research applying it to synchronous collaborations involving shared access to a distributed object. Based on several cases of real-world collaborations involving instant messaging, distributed lectures, and computationally-intensive collaborative game playing, we show that compared to traditional centralized and replicated collaboration architectures, a new bi-architecture collaboration system model with multicasting support can improve response, feedthrough, and task completion times. In addition, we show that to optimize performance, the set of traditionally considered factors, consisting of network delays and transmission costs, must be expanded to include several new factors, such as processing costs, scheduling policies, and think times. In one or more of the real-world collaborations we consider, we show that multicast (a) can increase feedthrough times if processing costs and scheduling policies are not considered and (b) may degrade or improve task completion times depending on the cost of computing the multicast overlay.