Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular phylogeny of a circum-global, diverse gastropod superfamily (Cerithioidea: Mollusca: Caenogastropoda): pushing the deepest phylogenetic limits of mitochondrial LSU rDNA sequences.

The Cerithioidea is a very diverse group of gastropods with ca. 14 extant families and more than 200 genera occupying, and often dominating, marine, estuarine, and freshwater habitats. While the composition of Cerithioidea is now better understood due to recent anatomical and ultrastructural studies, the phylogenetic relationships among families remain chaotic. Morphology-based studies have provided conflicting views of relationships among families. We generated a phylogeny of cerithioideans based on mitochondrial large subunit rRNA and flanking tRNA gene sequences (total aligned data set 1873 bp). Nucleotide evidence and the presence of a unique pair of tRNA genes (i.e., threonine + glycine) between valine-mtLSU and the mtSSU rRNA gene support conclusions based on ultrastructural data that Vermetidae and Campanilidae are not Cerithioidea, certain anatomical similarities being due to convergent evolution. The molecular phylogeny shows support for the monophyly of the marine families Cerithiidae [corrected], Turritellidae, Batillariidae, Potamididae, and Scaliolidae as currently recognized. The phylogenetic data reveal that freshwater taxa evolved on three separate occasions; however, all three recognized freshwater families (Pleuroceridae, Melanopsidae, and Thiaridae) are polyphyletic. Mitochondrial rDNA sequences provide valuable data for testing the monophyly of cerithioidean [corrected] families and relationships within families, but fail to provide strong evidence for resolving relationships among families. It appears that the deepest phylogenetic limits for resolving caenogastropod relationships is less than about 245--241 mya, based on estimates of divergence derived from the fossil record.
A PHOTOCHEMICAL MID‐ULTRAVIOLET DOSIMETER FOR PRACTICAL USE AS A SUNBURN DOSIMETER

Abstract— A mid‐UV dosimeter has been developed based on the irreversible photochemical conversion of 3′‐[p‐(dimethylamino)‐phenyl] spiro‐[fluorene–9,4′‐oxazolidine]–2′,5′‐dione (1) to p‐dimethylamino‐N‐fluoren‐9‐ylidine aniline (2), carbon monoxide and carbon dioxide. Formulations of 1 in a polycarbonate film matrix are colorless, thermally stable, and undergo photolysis only when exposed to wavelengths of less than 350 nm. The red photoproduct 2 is both thermally and photochemically stable under dosimeter use conditions. The depth of red color developed depends solely on the degree of exposure to mid‐UV radiation. In outdoor studies color intensity steadily developed during an initial 2 h of exposure to noontime Miami June sunshine. Color comparators representing consecutive 15–20 min exposure increments of this sunshine were readily distinguishable from each other by visual inspection. The comparators could be visually matched to colors generated by the dosimeter film formulation, and covered the exposure range of interest for avoidance of sunburn. This photochemical mid‐UV dosimeter is seen to fulfill all the requirements of a practical sunburn dosimeter.
Bridging Data Models and Terminologies to Support Adverse Drug Event Reporting Using EHR Data

Summary Introduction: This article is part of the Focus Theme of Methods of Information in Medicine on “Managing Interoperability and Complexity in Health Systems”. Background: SALUS project aims at building an interoperability platform and a dedicated toolkit to enable secondary use of electronic health records (EHR) data for post marketing drug surveillance. An important component of this toolkit is a drug-related adverse events (AE) reporting system designed to facilitate and accelerate the reporting process using automatic prepopulation mechanisms. Objective: To demonstrate SALUS approach for establishing syntactic and semantic inter-operability for AE reporting. Method: Standard (e.g. HL7 CDA-CCD) and proprietary EHR data models are mapped to the E2B(R2) data model via SALUS Common Information Model. Terminology mapping and terminology reasoning services are designed to ensure the automatic conversion of source EHR terminologies (e.g. ICD-9-CM, ICD-10, LOINC or SNOMED-CT) to the target terminology MedDRA which is expected in AE reporting forms. A validated set of terminology mappings is used to ensure the reliability of the reasoning mechanisms. Results: The percentage of data elements of a standard E2B report that can be completed automatically has been estimated for two pilot sites. In the best scenario (i.e. the avail able fields in the EHR have actually been filled), only 36% (pilot site 1) and 38% (pilot site 2) of E2B data elements remain to be filled manually. In addition, most of these data elements shall not be filled in each report. Conclusion: SALUS platform’s interopera bility solutions enable partial automation of the AE reporting process, which could con tribute to improve current spontaneous reporting practices and reduce under-report ing, which is currently one major obstacle in the process of acquisition of pharmacovigilance data.
Gallic Acid-loaded Cellulose Acetate Electrospun Nanofibers: Thermal Properties, Mechanical Properties, and Drug Release Behavior

The gallic acid-loaded electrospun cellulose acetate fibers were successfully prepared. The fiber containing 2.5% gallic acid was smooth surface but observed drug flake on the surface of the fiber when increasing drug content. The thermal properties, mechanical properties and drug release behavior of the fibers were investigated comparing to the corres-ponding films.
The optical and thermal properties of quantum cascade lasers

The optical and thermal properties of quantum cascade lasers (QCLs) are investigated through the development of comprehensive theoretical models. The optical properties of various multilayer quantum cascade laser waveguides are investigated by solving Maxwell’s equations using a transfer-matrix method. The complex material refractive indices are calculated using a Drude-Lorentz model which takes into account both phonon and plasma contributions to the material properties. A Caughey-Thomas-like mobility model is used to estimate the temperature dependence of the electron mobility which is found to have a significant effect on the optical waveguide properties. The incorporation of this effect leads to better agreement with experimentally measured threshold current densities. In order to investigate the thermal properties of QCLs, a multi-dimensional anisotropic heat diffusion model is developed which includes temperature-dependent material parameters. The model is developed using finite-difference methods in such a way that is can be solved in both the time-domain and in the steady-state. Various heat management techniques were compared in the time-domain in order to extract the heat dissipation time constants. In the steady-state, the model is used to extract the temperature dependence of the cross-plane thermal conductivity of a GaAs-based THz QCL and compare the thermal properties of THz and InP-based mid-infrared QCL optical waveguides. In addition, fully self-consistent scattering rate equation modelling of carrier transport in short-wavelength QCLs is carried out in order to understand the internal carrier dynamics. This knowledge is then used to optimise the device design and the model predicts significant improvements in the performance of the optimised device.
Building flexible groupware through open protocols

This paper presents a technical approach to building flexible groupware applications. Flexibility provides the promise of personalizable groupware, allowing different groups to work with the system in diverse ways which best suit the group’s own needs. An implementation technique called open protocols is described, which is a variation of client/server architectures. Open protocols facilitate the addition of group-specific modules long after the system has been created. Three examples illustrating the use of open protocols are presented: floor control, conference registration, and brainstorming. Finally, a number of issues facing the groupware developer using open protocols are addressed, along with strategies that can help in dealing with these issues.
Mdivi‐1 induced acute changes in the angiogenic profile after ischemia‐reperfusion injury in female mice

The aim of this study is to determine the effects of mitochondrial division inhibitor 1 (Mdivi‐1), the mitochondrial fission inhibitor, on the angiogenic profiles after the ischemia reperfusion injury (IR injury) in female mice. Female mice were treated with Mdivi‐1 inhibitor, 2 days prior, on the day of IR injury and 2 days after IR injury, for a period of 5 days. Both control and treatment groups underwent 30 min of ischemia and 72 h of reperfusion. On the day 3, mice were sacrificed and the ischemic and nonischemic portions of heart tissue were collected. Relative levels of 53 angiogenesis‐related proteins were quantified simultaneously using Angiogenic arrays. Heart function was evaluated before and after 72 h of IR injury. Mdivi‐1 treatment ameliorated IR induced functional deterioration with positive angiogenic profile. The seminal changes include suppression of Matrix metalloproteinase (MMP3), tissue inhibitor of metalloproteases (TIMP1) and chemokine (C‐X‐C motif) ligand 10 (CXCL10) levels and prevention of connexin 43 (Cx43) loss and downregulation in the antioxidant enzyme levels. These changes are correlated with enhanced endothelial progenitor cell marker (cluster of differentiation (CD31), endothelial‐specific receptor tyrosine kinase (Tek), fMS‐like tyrosine kinase 4 (Flt4) and kinase insert domain protein receptor (Kdr)) presence. Our study is the first to report the role of mitochondrial dynamics in regulation of myocardial IR‐induced angiogenic responses. Inhibition of excessive mitochondrial fission after IR injury ameliorated heart dysfunction and conferred positive angiogenic response. In addition, there were improvements in the preservation of Cx43 levels and oxidative stress handling along with suppression of apoptosis activation. The findings will aid in shaping the rational drug development process for the prevention of ischemic heart disease, especially in females.
Performance-Enhancing Methods for Au Film over Nanosphere Surface-Enhanced Raman Scattering Substrate and Melamine Detection Application

A new high-performance surface-enhanced Raman scattering (SERS) substrate with extremely high SERS activity was produced. This SERS substrate combines the advantages of Au film over nanosphere (AuFON) substrate and Ag nanoparticles (AgNPs). A three order enhancement of SERS was observed when Rhodamine 6G (R6G) was used as a probe molecule to compare the SERS effects of the new substrate and commonly used AuFON substrate. These new SERS substrates can detect R6G down to 1 nM. The new substrate was also utilized to detect melamine, and the limit of detection (LOD) is 1 ppb. A linear relationship was also observed between the SERS intensity at Raman peak 682 cm−1 and the logarithm of melamine concentrations ranging from 10 ppm to 1 ppb. This ultrasensitive SERS substrate is a promising tool for detecting trace chemical molecules because of its simple and effective fabrication procedure, high sensitivity and high reproducibility of the SERS effect.
Paradigm Shift in Dendritic Cell-Based Immunotherapy: From in vitro Generated Monocyte-Derived DCs to Naturally Circulating DC Subsets

Dendritic cell (DC)-based immunotherapy employs the patients’ immune system to fight neoplastic lesions spread over the entire body. This makes it an important therapy option for patients suffering from metastatic melanoma, which is often resistant to chemotherapy. However, conventional cellular vaccination approaches, based on monocyte-derived DCs (moDCs), only achieved modest response rates despite continued optimization of various vaccination parameters. In addition, the generation of moDCs requires extensive ex vivo culturing conceivably hampering the immunogenicity of the vaccine. Recent studies, thus, focused on vaccines that make use of primary DCs. Though rare in the blood, these naturally circulating DCs can be readily isolated and activated thereby circumventing lengthy ex vivo culture periods. The first clinical trials not only showed increased survival rates but also the induction of diversified anti-cancer immune responses. Upcoming treatment paradigms aim to include several primary DC subsets in a single vaccine as pre-clinical studies identified synergistic effects between various antigen-presenting cells.
Characterizing light propagation in bone for photodynamic therapy of osteosarcoma

This work aims at characterizing how light propagates through bone in order to efficiently guide treatment of osteosarcoma with photodynamic therapy (PDT). Optical properties of various bone tissues need to be characterized in order to have a working model of light propagation in bone. Bone tissues of particular interest include cortical bone, red and yellow marrow, cancellous bone, and bone cancers themselves. With adequate knowledge of optical properties of osseous tissues, light dosimetry can determine how best to deliver adequate light to achieve phototoxic effects within bone. An optical fiber source-collector pair is used for diffuse reflectance spectroscopic measurements in order to determine the scattering and absorption properties of bone tissues. Native absorbers of interest at visible and near-IR wavelengths include water and oxygenated and deoxygenated hemoglobin. A cylindrically symmetric Monte Carlo model is then used, incorporating these results, in order to predict and guide the delivery of light within bone in order to achieve the desired phototoxic effect in PDT.
Aberrant epidermal differentiation and disrupted ΔNp63/Notch regulatory axis in Ets1 transgenic mice

Summary The transcription factor Ets1 is expressed at low levels in epidermal keratinocytes under physiological conditions, but is over-expressed in cutaneous squamous cell carcinoma (SCC). We previously showed that over-expression of Ets1 in differentiated keratinocytes of the skin leads to significant pro-tumorigenic alterations. Here, we further extend these studies by testing the effects of over-expressing Ets1 in the proliferative basal keratinocytes of the skin, which includes the putative epidermal stem cells. We show that induction of the Ets1 transgene in the basal layer of skin during embryogenesis results in epidermal hyperplasia and impaired differentiation accompanied by attenuated expression of spinous and granular layer markers. A similar hyper-proliferative skin phenotype was observed when the transgene was induced in the basal layer of the skin of adult mice leading to hair loss and open sores. The Ets1-mediated phenotype is accompanied by a variety of changes in gene expression including alterations in Notch signaling, a crucial mediator of normal skin differentiation. Finally, we show that Ets1 disrupts Notch signaling in part via its ability to upregulate &Dgr;Np63, an established transcriptional repressor of several of the Notch receptors. Given the established tumor suppressive role for Notch signaling in skin tumorigenesis, the demonstrated ability of Ets1 to interfere with this signaling pathway may be important in mediating its pro-tumorigenic activities.
AOS: An optimized sandbox method used in behavior-based malware detection

Malware (malicious software) has been widely spread through our computers in the world that many antivirus vendors use signature-based method to detect them. However, the update rate of the virus signature database can never catch up the creation rate of the new malware variants. Using CSS (Crystal Security Sandbox) that monitors the Windows Portable Executable (PE) file execution and generates a sanitized intermediate result for classifying the malware is an emerging research in malware detection. Although the sanitized intermediate result is sufficient to depict the behaviors of malware, it is still a bit too long, too redundant, and too tedious to deal with efficiently. Therefore we compress and sieve the sanitized intermediate result to derive 90% fewer brief expressions which not only reduce the size of data, but also maintain above 93% accuracy rate and less 7 % error rate.
Computational Aspects of cf2 and stage2 Argumentation Semantics

We consider two instantiations of the SCC-recursive schema for argumentation semantics, cf2, using maximal conflict-free sets as base semantics, and stage2, using stage extensions as base semantics. Both of them have been shown to be in general of high complexity. We provide a detailed analysis of possible tractable fragments for these semantics. Moreover we present a labeling based algorithm for computing cf2 extension, which is complexity-sensitive w.r. t. one of the tractable fragments.
A Study of the Passive Gait of a Compass-Like Biped Robot

The focus of this work is a systematic study of the passive gait of a compass-like, planar, biped robot on inclined slopes. The robot is kinematically equivalent to a double pendulum, possessing two kneeless legs with point masses and a third point mass at the "hip" joint. Three parameters, namely, the ground-slope angle and the normalized mass and length of the robot describe its gait. We show that in response to a continuous change in any one of its parame ters, the symmetric and steady stable gait of the unpowered robot gradually evolves through a regime of bifurcations characterized by progressively complicated asymmetric gaits, eventually arriving at an apparently chaotic gait where no two steps are identical. The robot can maintain this gait indefinitely. A necessary (but not sufficient) condition for the stability of such gaits is the contraction of the "phase-fluid" volume. For this frictionless robot, the volume contraction, which we compute, is caused by the dissipative effects of the ground-impact model. In the chaotic regime, the fractal dimension of the robot's strange attractor We present a novel graphical technique based on the first return map that compactly captures the entire evolution of the gait, from symmetry to chaos. Additional passive dissipative elements in the robot joint result in a significant improvement in the stability and the versatility of the gait, and provide a rich repertoire for simple control laws.
POSITRON LIFETIME MEASUREMENTS IN NATURAL RUBBER WITH DIFFERENT FILLERS

Positron annihilation lifetime spectra (PLAS) have been measured for natural rubber polymer with different fillers (Titenium dioxide, Nanosilica and Nanoclay) as a function of filler concentration to investigate how these fillers affect the microstructure of free volume of natural rubber. The lifetime spectra is analyzed by using LT9.0 and the longest lived component(τo-Ps) is attributed to the pick- off annihilation of o-Ps in free volume sites, available mostly in the amorphous region of polymer. On the basis of the τo-Ps values the radii of the free volume holes (Rh) are calculated. The PALS results show that o-Ps lifetime as well as the size of free volume decreases with the increase of filler concentration.
Introduction to the Theory of Computation

From the Publisher: Michael Sipser's philosophy in writing this book is simple: make the subject interesting and relevant, and the students will learn. His emphasis on unifying computer science theory - rather than offering a collection of low-level details - sets the book apart, as do his intuitive explanations. Throughout the book, Sipser - a noted authority on the theory of computation - builds students' knowledge of conceptual tools used in computer science, the aesthetic sense they need to create elegant systems, and the ability to think through problems on their own. INTRODUCTION TO THE THEORY OF COMPUTATION provides a mathematical treatment of computation theory grounded in theorems and proofs. Proofs are presented with a "proof idea" component to reveal the concepts underpinning the formalism. Algorithms are presented using prose instead of pseudocode to focus attention on the algorithms themselves, rather than on specific computational models. Topic coverage, terminology, and order of presentation are traditional for an upper-level course in computer science theory. Users of the Preliminary Edition (now out of print) will be interested to note several new chapters on complexity theory: Chapter 8 on space complexity; Chapter 9 on provable intractability, and Chapter 10 on advanced topics, including approximation algorithms, alternation, interactive proof systems, cryptography, and parallel computing.
PRISM: Concept-preserving Summarization of Top-K Social Image Search Results

Most existing tag-based social image search engines present search results as a ranked list of images, which cannot be consumed by users in a natural and intuitive manner. In this demonstration, we present a novel concept-preserving image search results summarization system called prism. prism exploits both visual features and tags of the search results to generate high quality summary, which not only breaks the results into visually and semantically coherent clusters but it also maximizes the coverage of the original top-k search results. It first constructs a visual similarity graph where the nodes are images in the top-k search results and the edges represent visual similarities between pairs of images. This graph is optimally decomposed and compressed into a set of concept-preserving subgraphs based on a set of summarization criteria. One or more exemplar images from each subgraph is selected to form the exemplar summary of the result set. We demonstrate various innovative features of prism and the promise of superior quality summary construction of social image search results.
Optical amplification at 1525 nm in BaYF 5 : 20% Yb 3+ , 2% Er 3+ nanocrystals doped SU-8 polymer waveguide

We demonstrated optical amplification in BaYF5: 20% Yb3+, 2% Er3+ (BYF) nanocrystals doped polymer waveguide. BYF nanocrystals with an average size of ∼13nm were synthesized by a high-boiling solvent process. Intense 1.53 µm fluorescence was obtained in the nanocrystals under excitation at 980 nm. An optical polymer waveguide was fabricated by using BYF nanocrystals doped SU-8 polymer as the core material. A relative optical gain of ∼10.4 dB at 1525nm was achieved in a 1.1 cm long waveguide for an input signal power of ∼0.09 mW and a pump power of ∼212 mW.
PORCINE REPRODUCTIVE AND RESPIRATORY SYNDROME SUMMARY

Porcine reproductive and respiratory syndrome (PRRS) is characterised by reproductive failure of sows and respiratory problems of piglets and growing pigs. The disease is caused by the PRRS virus, a virus currently classified as a member of the order Nidovirales, family Arteriviridae, genus Arterivirus. The primary target cell of the virus is the alveolar macrophage of the pig. Two major antigenic types of the virus exist, the type 1 (European) and the type 2 (American). The virus is primarily transmitted via infected pigs but also by faeces, urine, semen and fomites.
Decode-and-forward cooperative multicast with space shift keying

In this paper, we consider space-shift keying (SSK) in dual-hop decode-and-forward (DF) cooperative multicast networks, where a source node communicates with multiple destination nodes with the help of relay nodes. We consider a topology consisting of a single source, two relays, and multiple destinations. For such a system, we propose a scheme to select a single relay among the two when SSK is used for transmission on each of the links in the cooperative system. We analyze the end-to-end average bit error probability (ABEP) of this system. For binary SSK, we derive an exact expression for the ABEP in closed-form. Analytical results exactly match the simulation results validating the analysis. For non-binary SSK, we derive an approximate ABEP expression, where the analytical ABEP results closely follow simulation results. We also derive the diversity order of the system through asymptotic ABEP analysis.