Miracle-dz/UniFAR-FTUs huggingface dataset:
Estimating a binary character's effect on speciation and extinction.

Determining whether speciation and extinction rates depend on the state of a particular character has been of long-standing interest to evolutionary biologists. To assess the effect of a character on diversification rates using likelihood methods requires that we be able to calculate the probability that a group of extant species would have evolved as observed, given a particular model of the character's effect. Here we describe how to calculate this probability for a phylogenetic tree and a two-state (binary) character under a simple model of evolution (the "BiSSE" model, binary-state speciation and extinction). The model involves six parameters, specifying two speciation rates (rate when the lineage is in state 0; rate when in state 1), two extinction rates (when in state 0; when in state 1), and two rates of character state change (from 0 to 1, and from 1 to 0). Using these probability calculations, we can do maximum likelihood inference to estimate the model's parameters and perform hypothesis tests (e.g., is the rate of speciation elevated for one character state over the other? ). We demonstrate the application of the method using simulated data with known parameter values.
Stable nuclear expression of ATP8 and ATP6 genes rescues a mtDNA Complex V null mutant

We explore the possibility of re-engineering mitochondrial genes and expressing them from the nucleus as an approach to rescue defects arising from mitochondrial DNA mutations. We have used a patient cybrid cell line with a single point mutation in the overlap region of the ATP8 and ATP6 genes of the human mitochondrial genome. These cells are null for the ATP8 protein, have significantly lowered ATP6 protein levels and no Complex V function. Nuclear expression of only the ATP8 gene with the ATP5G1 mitochondrial targeting sequence appended restored viability on Krebs cycle substrates and ATP synthesis capabilities but, failed to restore ATP hydrolysis and was insensitive to various inhibitors of oxidative phosphorylation. Co-expressing both ATP8 and ATP6 genes under similar conditions resulted in stable protein expression leading to successful integration into Complex V of the oxidative phosphorylation machinery. Tests for ATP hydrolysis / synthesis, oxygen consumption, glycolytic metabolism and viability all indicate a significant functional rescue of the mutant phenotype (including re-assembly of Complex V) following stable co-expression of ATP8 and ATP6. Thus, we report the stable allotopic expression, import and function of two mitochondria encoded genes, ATP8 and ATP6, resulting in simultaneous rescue of the loss of both mitochondrial proteins.
Divergence of AMP Deaminase in the Ice Worm Mesenchytraeus solifugus (Annelida, Clitellata, Enchytraeidae)

Glacier ice worms, Mesenchytraeus solifugus and related species, are the largest glacially obligate metazoans. As one component of cold temperature adaptation, ice worms maintain atypically high energy levels in an apparent mechanism to offset cold temperature-induced lethargy and death. To explore this observation at a mechanistic level, we considered the putative contribution of 5′ adenosine monophosphate deaminase (AMPD), a key regulator of energy metabolism in eukaryotes. We cloned cDNAs encoding ice worm AMPD, generating a fragment encoding 543 amino acids that included a short N-terminal region and complete C-terminal catalytic domain. The predicted ice worm AMPD amino acid sequence displayed conservation with homologues from other mesophilic eukaryotes with notable exceptions. In particular, an ice worm-specific K188E substitution proximal to the AMP binding site likely alters the architecture of the active site and negatively affects the enzyme's activity. Paradoxically, this would contribute to elevated intracellular ATP levels, which appears to be a signature of cold adapted taxa.
Synergistic effects of micro-/nano-fillers on conductive and electromagnetic shielding properties of polypropylene nanocomposites

ABSTRACT This study presents the synergistic effects of graphene nanosheets (GNSs) and carbon fibers (CFs) additions on the electrical and electromagnetic shielding properties of GNS/CF/polypropylene (PP) composites. These composites were fabricated by the melt blending of different ratios of GNSs and CFs (20:0, 15:5, 10:10, 5:15 and 0:20 wt/wt%) into a PP polymer matrix using a Brabender mixer. Besides, the chemical and crystalline structures and the thermal stability of the resultant GNS/CF/PP composites were characterized by Fourier transform infrared (FT-IR) spectroscopy, X-ray diffraction (XRD) and thermogravimetric analysis (TGA). FT-IR and XRD showed that with the addition of GNSs content, transmittances at 1373.4 cm−1 and 1454.4 cm−1 became smaller and the characteristic peak at 26.82° became stronger. TGA showed that the GNS/CF/PP composite can be used at high temperature below 456°C. Blending 10 wt% CFs and 10 wt% GNSs into the PP polymer resulted in excellent conductivity (0.397 S/cm), which indicated the occurrence of the critical percolation threshold phenomenon, and also reached the maximum electromagnetic shielding effectiveness (EMSE) of 20 dB at 1.28–2.00 GHz. Laminated with five layers of composites, its EMSE achieved 25–38 dB at 0.3–3.0 GHz, corresponding to blocking of 94.38–98.74% electromagnetic waves.
Buckled Germanene Formation on Pt(111)

Germanene, a 2D honeycomb lattice analogous to graphene, is fabricated on a Pt(111) surface. It exhibits a buckled configuration with a (3 × 3) superlattice coinciding with the substrate's (√19 × √19) superstructure. Covalent bonds exist throughout the germanene layer. The resulting high-quality germanene enables researchers to explore the fundamentals of germanene and its potential applications.
Surface Modification of Polymer Substrates for Biomedical Applications

While polymers are widely utilized materials in the biomedical industry, they are rarely used in an unmodified state. Some kind of a surface treatment is often necessary to achieve properties suitable for specific applications. There are multiple methods of surface treatment, each with their own pros and cons, such as plasma and laser treatment, UV lamp modification, etching, grafting, metallization, ion sputtering and others. An appropriate treatment can change the physico-chemical properties of the surface of a polymer in a way that makes it attractive for a variety of biological compounds, or, on the contrary, makes the polymer exhibit antibacterial or cytotoxic properties, thus making the polymer usable in a variety of biomedical applications. This review examines four popular methods of polymer surface modification: laser treatment, ion implantation, plasma treatment and nanoparticle grafting. Surface treatment-induced changes of the physico-chemical properties, morphology, chemical composition and biocompatibility of a variety of polymer substrates are studied. Relevant biological methods are used to determine the influence of various surface treatments and grafting processes on the biocompatibility of the new surfaces—mammalian cell adhesion and proliferation is studied as well as other potential applications of the surface-treated polymer substrates in the biomedical industry.
Rapid Estimation of Fruit Starch and Soluble Sugar Concentrations in Kiwifruit

Experiments investigating kiwifruit [Actinidia deliciosa (A. Chev) C.F. Liang et A.R. Ferguson var. deliciosa] maturation were undertaken requiring the determination of total soluble sugar (TSS) and starch concentrations in numerous fruit samples. The phenol-sulfuric acid assay was judged to be a convenient method for determining TSS from tissue extracts and gave results similar to those obtained by high-pressure liquid chromatography. The starch procedure adopted involved gelatinizing fruit tissue using hot water and a thermostable a-amylase (Termamyl); hydrolizing starch using amyloglucosidase; and determining glucose using glucose oxidase [. ]
Polarimetric features analysis of oil spills in C-band and L-band SAR images

Compared with single-polarization synthetic aperture radar (SAR), full-polarization SAR can not only collect the echo intensity of backscattered from the sea surface, but also can collect the phase information. For oil spill detection, polarimetric SAR has more advantages. Features extraction is a crucial step for oil spill discrimination. In this paper, eight kinds of polarimetric features, such as the polarimetric entropy, average scatter angle and so on, have been investigated to analyze the capability of the polarimetric features to observe an oil spill at C-band and L-band, and to identify the most powerful multi-polarimetric SAR descriptors for oil spill detection. And a systematic comparison of the eight multi-polarization features is provided. Here, the analysis is conducted on the quad-pol SAR images acquired by the SIR-C/X-SAR. The experiment results show that the pedestal height and the parameter P perform better than the other polarimetric features at C-band.
Effect of sampling on the estimation of the apparent coefficient of diffusion in MRI

The Apparent Diffusion Coefficient (ADC) is a quantitative measure derived from MRI that is able to asses the amount of diffusion within living tissues. It is employed to characterize different diseases and to evaluate response to therapy. For ADC estimation, the diffusion signal needs to be sampled using a small number of values, presenting distortions due to the aliasing and windowing effect. In this work we theoretically study these effects and propose some new robust estimators for ADC based on the Fourier Transform of the signal.
Large-scale cluster-based retrieval experiments on Turkish texts

We present cluster-based retrieval (CBR) experiments on the largest available Turkish document collection. Our experiments evaluate retrieval effectiveness and efficiency on both an automatically generated clustering structure and a manual classification of documents. In particular, we compare CBR effectiveness with full-text search (FS) and evaluate several implementation alternatives for CBR. Our findings reveal that CBR yields comparable effectiveness figures with FS. Furthermore, by using a specifically tailored cluster-skipping inverted index we significantly improve in-memory query processing efficiency of CBR in comparison to other traditional CBR techniques and even FS.
Reasoning About Object Systems in VTLoE

VTLoE (Variable Type Logic of Effects) is a logic for reasoning about imperative functional programs inspired by the variable type systems of Feferman. The underlying programming language, λmk, extends the call-by-value lambda calculus with primitives for arithmetic, pairing, branching, and reference cells (mutable data). In VTLoE one can reason about program equivalence and termination, input/output relations, program contexts, and inductively (and co-inductively) define data structures. In this paper we present a refinement of VTLoE. We then introduce a notion of object specification and establish formal principles for reasoning about object systems within VTLoE. Objects are self-contained entities with local state. The local state of an object can only be changed by action of that object in response to a message. In λmk objects are represented as closures with mutable data bound to local variables. A semantic principle called simulation induction was introduced in our earlier work as a means of establishing equivalence relations between streams, object behaviors, and other potentially infinite structures. These are formulated in VTLoE using the class apparatus. The use of these principles is illustrated by validating a variety of basic tranformation rules.
Identification of Human Faces Using Orthogonal Locality Preserving Projections

This paper presents a technique for identification of human faces using an algorithm based on Orthogonal Locality Preserving Projections (OLPP). It differs from Principal Component Analysis (PCA) and Linear Discriminant Analysis (LDA), which preserves the Euclidean structure of face space. Locality Preserving Projections (LPP) finds an embedding that preserves local information, and obtains a face subspace that best detects the essential manifold structure. Locality Preserving Projections (LPP) is non-orthogonal, and this makes it difficult to reconstruct the data. This problem is overcome by using Orthogonal Locality Preserving Projection method which produces orthogonal basis functions and can have more locality preserving power than LPP. Since the locality preserving power is potentially related to the discriminating power, the OLPP is expected to have more discriminating power than LPP. This approach, builds an adjacency graph which best reflects the geometry of the face manifold and the class relationship between various points. The projection is then obtained by preserving such graph structure which forms the Orthogonal Laplacianface. In this way, the unwanted variations resulting from changes in lighting, facial expression and poses are reduced.
A Methodology for Modeling and Simulation of Saturated Cores Fault Current Limiters

Inductive fault current limiters, such as saturated cores topology, have been considered as an enabling technology for the advent of modern power grids. Thereby, several full-scale prototypes have been developed in recent years aiming, e.g., supporting increased penetration of dispersed generation, mostly from renewable sources. For the advent of these devices and technology, the development of straightforward design tools that allow simulating them in electrical power grids with different voltage ratings and characteristics is required. In this paper, a methodology for simulating the behavior of saturated cores limiters is presented as an alternative to techniques based on finite elements methods (FEM), thereby dramatically reducing computation time. This methodology is based on characteristic parameters of those limiters and is compared with FEM simulations. Experimental measurements in a laboratory scale prototype are also carried out to validate the proposed methodology.
Endocytic Sorting of Lipid Analogues Differing Solely in the Chemistry of Their Hydrophobic Tails

To understand the mechanisms for endocytic sorting of lipids, we investigated the trafficking of three lipid-mimetic dialkylindocarbocyanine (DiI) derivatives, DiIC16(3) (1,1′-dihexadecyl-3,3,3′,3′-tetramethylindocarbocyanine perchlorate), DiIC12(3) (1,1′- didodecyl-3,3,3′,3′-tetramethylindocarbocyanine perchlorate), and FAST DiI (1,1′-dilinoleyl-3,3,3′,3′-tetramethylindocarbocyanine perchlorate), in CHO cells by quantitative fluorescence microscopy. All three DiIs have the same head group, but differ in their alkyl tail length or unsaturation; these differences are expected to affect their distribution in membrane domains of varying fluidity or curvature. All three DiIs initially enter sorting endosomes containing endocytosed transferrin. DiIC16(3), with two long 16-carbon saturated tails is then delivered to late endosomes, whereas FAST DiI, with two cis double bonds in each tail, and DiIC12(3), with saturated but shorter (12-carbon) tails, are mainly found in the endocytic recycling compartment. We also find that DiOC16(3) (3,3′- dihexadecyloxacarbocyanine perchlorate) and FAST DiO (3,3′-dilinoleyloxacarbocyanine perchlorate) behave similarly to their DiI counterparts. Furthermore, whereas a phosphatidylcholine analogue with a BODIPY (4,4-difluoro-4-bora-3a,4a-diaza-s-indacene) fluorophore attached at the end of a 5-carbon acyl chain is delivered efficiently to the endocytic recycling compartment, a significant fraction of another derivative with BODIPY attached to a 12-carbon acyl chain entered late endosomes. Our results thus suggest that endocytic organelles can sort membrane components efficiently based on their preference for association with domains of varying characteristics.
Slow Conduction and Flutter Following Atrial Fibrillation Ablation: Proarrhythmia or Unmasking Effect of RadiofrequencyApplication?

Few fields in cardiology are evolving as rapidly as catheter ablation of atrial fibrillation (AF). Transvenous ablation of AF was first described by Haissaguerre et al. more than 10 years ago.1 They reported on a patient with incessant AF episodes who was cured following linear ablation in the right atrium. After this, various designs for linear ablation were proposed both in the right and left atrium, but with little or moderate success.2-4 Focal ablation was first reported as the ablation of a rapidly discharging focus with fibrillatory conduction to the atria5,6 and, later, as the ablation of atrial ectopy triggering AF.7,8 Ablation was initially aimed at the ectopic focus, usually well within the pulmonary veins, which gave rise to a new complication, pulmonary vein stenosis. This, together with the frequent lack of ectopy during the procedure, was responsible for changing the ablation approach from focal radiofrequency application to multiple sequential radiofrequency application, which was first aimed at pulmonary vein electrical disconnection9 and, subsequently, to pulmonary vein linear encirclement.10 Both these latter approaches have been associated with another singular complication, left atrial tachycardia (LAT). 11-17 In this issue of the Journal, Shah et al. report a series of 15 patients with reentrant LAT following AF ablation that in some cases was successfully ablated by focal radiofrequency application.18 Their report provides original information that is relevant when trying to understand the mechanisms and pathogenesis of these arrhythmias.
Biosafety: Guidelines for Working with Pathogenic and Infectious Microorganisms

This unit, in conjunction with local and national guidelines and regulations, provides the basic biosafety information needed to perform the procedures detailed in this manual. Topics discussed include routine precautions when working with biohazards, disinfectants, disposal of biohazards, biosafety levels (as established by the U.S. National Institutes of Health, and the Centers for Disease Control and Prevention), animal facilities, and clinical laboratories. In addition, resources for more information are provided in the Literature Cited and Key References sections and in URLs given text and within the Internet Resources section.
CYTOKINE AND MATRIX METALLOPROTEINASE EXPRESSION IN PIGMENTED VILLONODUIAR SYNOVITIS MAY MEDIATE BONE AND CARTIIAGE DESTRUCTION

Background: Pigmented villonodular synovitis (PVNS) is characterized by hypervascular prolif-erative synovium containing multinucleated giant cells, macrophages, and hemosiderin. The destruction of articular cartilage and erosion of periarticular bone is thought to be mediated by matrix metalloproteinases (MMPs). Expression of MMPs in some tumors appears to be stimulated through local production of cytokines, and several specific cytokines (INFa, IIL-1, and IL-6) play an impor-tant role in the stimulation of osteoclastic bone resorption. The role of cytokine secretion and regu-lation of MMP production in PVNS has not been investigated. Design: In the present study, ten specimens from eight patients (ages 19 to 80) were evaluated histologically according to a modified Mirra classification and immunohistochemically (IHC) for the expression of MMP-9 (92 kDa gelatinase B), tumor necrosis factor alpha (TNFa), interleukin 1-Li (IL-1tB), and interleukin 6 (IL-6). con-firmed Results: All specimens, regardless of location (six knees, one ankle, one subtalar joint), showed diffuse and intense immunoreactivity for the giant synovial cells, and less in-Departments
Robust Formation and Maintenance of Continuous Stratified Cortical Neuroepithelium by Laminin-Containing Matrix in Mouse ES Cell Culture

In the mammalian cortex, the dorsal telencephalon exhibits a characteristic stratified structure. We previously reported that three-dimensional (3D) culture of mouse ES cells (mESCs) can efficiently generate cortical neuroepithelium (NE) and layer-specific cortical neurons. However, the cortical NE generated in this mESC culture was structurally unstable and broke into small neural rosettes by culture day 7, suggesting that some factors for reinforcing the structural integrity were missing. Here we report substantial supporting effects of the extracellular matrix (ECM) protein laminin on the continuous formation of properly polarized cortical NE in floating aggregate culture of mESCs. The addition of purified laminin and entactin (a laminin-associated protein), even at low concentrations, stabilized the formation of continuous cortical NE as well as the maintenance of basement membrane and prevented rosette formation. Treatment with the neutralizing ß1-integrin antibody impaired the continuous NE formation. The stabilized cortical NE exhibited typical interkinetic nuclear migration of cortical progenitors, as seen in the embryonic cortex. The laminin-treated cortical NE maintained a continuous structure even on culture days 12 and 15, and contained ventricular, basal-progenitor, cortical-plate and Cajal-Retzius cell layers. The cortical NE in this culture was flanked by cortical hem-like tissue. Furthermore, when Shh was added, ventral telencephalic structures such as lateral ganglionic eminence–like tissue formed in the region adjacent to the cortical NE. Thus, our results indicate that laminin-entactin ECM promotes the formation of structurally stable telencephalic tissues in 3D ESC culture, and supports the morphogenetic recapitulation of cortical development.
Preparation, scratch adhesion and anti-corrosion performance of TiO2-MgO-BHA coating on Ti6Al4V implant by plasma electrolytic oxidation technique

Abstract Bovine hydroxyapatite (BHA) (from cortical bone), was selected as the main electrolyte for plasma electrolytic oxidation (PEO) on Ti6Al4V implant. The prepared PEO coatings were examined by X-ray diffraction, field emission scanning electron microscope and energy-dispersive X-ray spectroscopy. The surface roughness, adhesion strength, wettability, surface energy and corrosion behaviour of the film were also investigated. The results show that the oxide layer (26 μm) formation on the Ti6Al4V was rough and porous. The micro-pores were filled with anatase TiO2, cubic MgO and hexagonal BHA particles. The porous structures and the compound particles were mainly composed of Mg, O, Ca, P, Ti, Na and Al. Unlike previous coatings produced from calcium and phosphorus inorganic solutions, the coating formation from a newly developed bovine bone-derived HA electrolyte revealed an additional MgO phase in the coating layer. Moreover, higher amount of single phase hexagonal crystalline BHA phase with a Ca/P ratio of 1.1 was achieved with a single PEO process. A film-to-substrate adhesion strength of 1862.24 mN and scratch hardness of about 4.1 GPa was achieved from this method. The TiO2/MgO/BHA film exhibited better wettability, higher surface energy and superior corrosion resistance compared to the bare Ti6Al4V substrate.
Idea navigation: structured browsing for unstructured text

Traditional interfaces for information access do not fully support queries that rely on semantic relationships between terms. To better support such queries, we introduce a system that automatically extracts subject-verb-object concepts from unstructured text documents and dynamically presents them to the user as navigable refinements. This approach, which we call "idea navigation," makes subject-verb-object querying as simple as selecting successive refinements. It also supports exploratory search by providing a view of the most common ideas in the current result set. First-time users of a prototype system successfully used idea navigation to solve realistic search tasks, demonstrating its effectiveness.