Miracle-dz/UniFAR-FTUs huggingface dataset:
Surface-enhanced Raman scattering and biophysics

Surface-enhanced Raman scattering (SERS) is a spectroscopic technique which combines modern laser spectroscopy with the exciting optical properties of metallic nanostructures, resulting in strongly increased Raman signals when molecules are attached to nanometre-sized gold and silver structures. The effect provides the structural information content of Raman spectroscopy together with ultrasensitive detection limits, allowing Raman spectroscopy of single molecules. Since SERS takes place in the local fields of metallic nanostructures, the lateral resolution of the technique is determined by the confinement of the local fields, which can be two orders of magnitude better than the diffraction limit. Moreover, SERS is an analytical technique, which can give information on surface and interface processes. SERS opens up exciting opportunities in the field of biophysical and biomedical spectroscopy, where it provides ultrasensitive detection and characterization of biophysically/biomedically relevant molecules and processes as well as a vibrational spectroscopy with extremely high spatial resolution. The article briefly introduces the SERS effect and reviews contemporary SERS studies in biophysics/biochemistry and in life sciences. Potential and limitations of the technique are briefly discussed.
Positive Display Polarity Is Particularly Advantageous for Small Character Sizes

Objective: To test the display luminance hypothesis of the positive polarity advantage and gain insights for display design, the joint effects of display polarity and character size were assessed with a proofreading task. Background: Studies have shown that dark characters on light background (positive polarity) lead to better legibility than do light characters on dark background (negative polarity), presumably due to the typically higher display luminance of positive polarity presentations. Method: Participants performed a proofreading task with black text on white background or white text on black background. Texts were presented in four character sizes (8, 10, 12, and 14 pt; corresponding to 0.22°, 0.25°, 0.31°, and 0.34° of vertical visual angle). Results: A positive polarity advantage was observed in proofreading performance. Importantly, the positive polarity advantage linearly increased with decreasing character size. Conclusion: The findings are in line with the assumption that the typically higher luminance of positive polarity displays leads to an improved perception of detail. Application: The implications seem important for the design of text on such displays as those of computers, automotive control and entertainment systems, and smartphones that are increasingly used for the consumption of text-based media and communication. The sizes of these displays are limited, and it is tempting to use small font sizes to convey as much information as possible. Especially with small font sizes, negative polarity displays should be avoided.
Brain Volumetric Correlates of Autism Spectrum Disorder Symptoms in Attention Deficit/Hyperactivity Disorder

Autism spectrum disorder (ASD) symptoms frequently occur in subjects with attention deficit/hyperactivity disorder (ADHD). While there is evidence that both ADHD and ASD have differential structural correlates, no study to date has investigated these structural correlates within a framework that robustly accounts for the phenotypic overlap between the two disorders. The presence of ASD symptoms was measured by the parent-reported Children’s Social and Behavioural Questionnaire (CSBQ) in ADHD subjects (n = 180), their unaffected siblings (n = 118) and healthy controls (n = 146). ADHD symptoms were assessed by a structured interview (K-SADS-PL) and the Conners’ ADHD questionnaires. Whole brain T1-weighted MPRAGE images were acquired and the structural MRI correlates of ASD symptom scores were analysed by modelling ASD symptom scores against white matter (WM) and grey matter (GM) volumes using mixed effects models which controlled for ADHD symptom levels. ASD symptoms were significantly elevated in ADHD subjects relative to both controls and unaffected siblings. ASD scores were predicted by the interaction between WM and GM volumes. Increasing ASD score was associated with greater GM volume. Equivocal results from previous structural studies in ADHD and ASD may be due to the fact that comorbidity has not been taken into account in studies to date. The current findings stress the need to account for issues of ASD comorbidity in ADHD.
A Genome-Wide Association Study to Detect QTL for Commercially Important Traits in Swiss Large White Boars

The improvement of meat quality and production traits has high priority in the pork industry. Many of these traits show a low to moderate heritability and are difficult and expensive to measure. Their improvement by targeted breeding programs is challenging and requires knowledge of the genetic and molecular background. For this study we genotyped 192 artificial insemination boars of a commercial line derived from the Swiss Large White breed using the PorcineSNP60 BeadChip with 62,163 evenly spaced SNPs across the pig genome. We obtained 26 estimated breeding values (EBVs) for various traits including exterior, meat quality, reproduction, and production. The subsequent genome-wide association analysis allowed us to identify four QTL with suggestive significance for three of these traits (p-values ranging from 4.99×10−6 to 2.73×10−5). Single QTL for the EBVs pH one hour post mortem (pH1) and carcass length were on pig chromosome (SSC) 14 and SSC 2, respectively. Two QTL for the EBV rear view hind legs were on SSC 10 and SSC 16.
Say Cheese ! Experiences with a Robot

that takes well-composed photographs of people at social events, such as weddings and conference receptions. The robot, Lewis, navigates through the environment, opportunistically taking photographs of people. In this article, we outline the overall architecture of the system and describe how the various components interrelate. We also describe our experiences deploying the robot photographer at a number of real-world events.
Development of superhydrophobic coatings

Ultrarough surfaces with variable architecture were synthesised and examined using a combination of atomic force microscopy, synchrotron small angle X-ray scattering and contact angle goniometry. Using silica nano-particle sol-gel technology, hierarchical superhydrophobic surfaces with water contact angles > 150◦ and hysteresis < 10◦ were fabricated. The addition and subsequent removal of 400 nm latex particles facilitated in carefully controlled, micro-pore formation, resulting in, amongst other things, a transparent superhydrophobic thin film. Varying nanoparticle size from 7 40 nm within the coating, pseudofractal dimension measured using SAXS (Small Angle X-ray Scattering) was shown to be critical in optimising superhydrophobicity. Combined with characterisation using Mie light scattering models, surfaces with RMS roughness < 200 nm and fractal dimension > 2.6 was found to exhibit both superhydrophobicity and optical transparency. The randomly aggregated sol-gel coating presenting an ideal platform to study the wetting of hierarchical rough surfaces similar to those in nature. Using in-situ SAXS measurements, combined with contact angle goniometry, the liquid/solid interface of a superhydrophobic surface at various stages of wetting was directly probed. For the first time, an intermediate wetting state whereby a surface is wetted at the macroscale but unwetted at the nanoscale, was observed in situ. The behaviour of superhydrophobic surfaces in practical applications, icing and marine biofouling, were examined. Superhydrophobic surfaces, due to its de-wetting properties, drastically reduced the adhesion strength of ice formed from liquid water. The coating further acted as an heat insulator, inhibiting frost formation from cold humid air. In marine anti-fouling applications, hierarchical superhydrophobic surfaces show considerable promise in resisting the initial attachment of marine organisms. However, field biofouling experiments suggest that micro-roughness and surface chemistry are dominant factors in antifouling.
Gas sensing in 2D materials

Two-dimensional (2D) layered inorganic nanomaterials have attracted huge attention due to their unique electronic structures, as well as extraordinary physical and chemical properties for use in electronics, optoelectronics, spintronics, catalysts, energy generation and storage, and chemical sensors. Graphene and related layered inorganic analogues have shown great potential for gas-sensing applications because of their large specific surface areas and strong surface activities. This review aims to discuss the latest advancements in the 2D layered inorganic materials for gas sensors. We first elaborate the gas-sensing mechanisms and introduce various types of gas-sensing devices. Then, we describe the basic parameters and influence factors of the gas sensors to further enhance their performance. Moreover, we systematically present the current gas-sensing applications based on graphene, graphene oxide (GO), reduced graphene oxide (rGO), functionalized GO or rGO, transition metal dichalcogenides, layered II.
Intercellular calcium signaling mediated by point-source burst release of ATP

Calcium signaling, manifested as intercellular waves of rising cytosolic calcium, is, in many cell types, the result of calcium-induced secretion of ATP and activation of purinergic receptors. The mechanism by which ATP is released has hitherto not been established. Here, we show by real-time bioluminescence imaging that ATP efflux is not uniform across a field of cells but is restricted to brief, abrupt point-source bursts. The ATP bursts emanate from single cells and manifest the transient opening of nonselective membrane channels, which admits fluorescent indicators of ≤1.5 kDa. These observations challenge the existence of regenerative ATP release, because ATP efflux is finite and restricted to a point source. Transient efflux of cytosolic nucleotides from a subset of cells may represent a conserved pathway for coordinating local activity of electrically nonexcitable cells, because identical patterns of ATP release were identified in human astrocytes, endothelial cells, and bronchial epithelial cells.
The Distribution Pattern of Sediment Archaea Community of the Poyang Lake, the Largest Freshwater Lake in China

Archaea plays an important role in the global geobiochemical circulation of various environments. However, much less is known about the ecological role of archaea in freshwater lake sediments. Thus, investigating the structure and diversity of archaea community is vital to understand the metabolic processes in freshwater lake ecosystems. In this study, sediment physicochemical properties were combined with the results from 16S rRNA clone library-sequencing to examine the sediment archaea diversity and the environmental factors driving the sediment archaea community structures. Seven sites were chosen from Poyang Lake, including two sites from the main lake body and five sites from the inflow river estuaries. Our results revealed high diverse archaea community in the sediment of Poyang Lake, including Bathyarchaeota (45.5%), Euryarchaeota (43.1%), Woesearchaeota (3.6%), Pacearchaeota (1.7%), Thaumarchaeota (1.4%), suspended Lokiarchaeota (0.7%), Aigarchaeota (0.2%), and Unclassified Archaea (3.8%). The archaea community compositions differed among sites, and sediment property had considerable influence on archaea community structures and distribution, especially total organic carbon (TOC) and metal lead (Pb) (p < 0.05). This study provides primary profile of sediment archaea distribution in freshwater lakes and helps to deepen our understanding of lake sediment microbes.
Olig Transcription Factors Are Expressed in Oligodendrocyte and Neuronal Cells in Human Fetal CNS

The transcription factors Olig1 and Olig2 are closely associated with the development of oligodendrocyte (OL) lineage in the vertebrate nervous system, but little is known about their role in the human developing CNS. To test the hypothesis that they contribute to initial OL specification in humans, we studied the expression of Olig1 and Olig2 in human fetuses at 5-24 gestational weeks (GW). Both transcription factors were present in well outlined regions of the ventral neuroepithelium at 5 GW, several weeks before oligodendrogenesis. Spatial differences in the expression of Olig1 and Olig2 along the neuronal axis suggest that they specify different subpopulations of progenitor cells. Olig1 was distributed rostrally, from the basal forebrain to the hindbrain, whereas Olig2 was also found in the ventral spinal cord. Furthermore, at 5 GW, Olig1 was coexpressed with vimentin, and Olig2 was coexpressed with a neuronal marker, microtubule-associated protein 2. With the progression of development at 15 GW, both proteins were present throughout the spinal cord and the ventricular-subventricular zone of the ganglionic eminences, whereas at midgestation (20 GW), they were also expressed in the telencephalic proliferative zones and the emerging white matter. Double-labeling studies revealed that early OL progenitor cells and radial glia expressed Olig1, whereas Olig2 was localized predominantly in mature OLs and a subset of neural progenitor cells and mature neurons. Thus, Olig1 and Olig2 transcription factors in the human CNS are important not only for differentiation of the OL lineage, but they may also have a role in neural cell specification.
Isolating the Epstein-Barr Virus gp350/220 Binding Site on Complement Receptor Type 2 (CR2/CD21)*

Complement receptor type 2 (CR2/CD21) is essential for the attachment of Epstein-Barr virus (EBV) to the surface of B-lymphocytes in an interaction mediated by the viral envelope glycoprotein gp350. The heavily glycosylated structure of EBV gp350 has recently been elucidated by x-ray crystallography, and the CR2 binding site on this protein has been characterized. To identify the corresponding gp350 binding site on CR2, we have undertaken a site-directed mutagenesis study targeting regions of CR2 that have previously been implicated in the binding of CR2 to the C3d/C3dg fragments of complement component C3. Wild-type or mutant forms of CR2 were expressed on K562 cells, and the ability of these CR2-expressing cells to bind gp350 was measured using flow cytometry. Mutations directed toward the two N-terminal extracellular domains of CR2 (SCR1-2) reveal that a large contiguous surface of CR2 SCR1-2 is involved in gp350 binding, including a number of positively charged residues (Arg-13, (Arg-28, (Arg-36, Lys-41, Lys-57, Lys-67, and Arg-83). These data appear to complement the CR2 binding site on gp350, which is characterized by a preponderance of negative charge. In addition to identifying the importance of charge in the formation of a CR2-gp350 complex, we also provide evidence that both SCR1 and SCR2 make contact with gp350. Specifically, two anti-CR2 monoclonal antibodies, designated as monoclonal antibodies 171 and 1048 whose primary epitopes are located within SCR2, inhibit binding of wild-type CR2 to EBV gp350; with regard to SCR1, both K562 cells expressing an S15P mutation and recombinant S15P CR2 proteins exhibit diminished gp350 binding.
Events, Causality and Symmetry —the Next-generation Semantics Section 2: the Scientific Proposal A. State-of-the-art and Objectives

Denotational semantics and domain theory of Scott and Strachey set the standard for semantics of computation. The theory provided a global mathematical setting for sequential computation, and thereby placed programming languages in connection with each other; connected with the mathematical worlds of algebra, topology and logic; and inspired programming languages, type disciplines and methods of reasoning. Despite the many striking successes it has become very clear that many aspects of computation do not fit within the traditional framework of denotational semantics and domain theory. In particular, classical domain theory has not scaled up to the more intricate models used in interactive/distributed computation. Nor has it been as operationally informative as one could hope. How are we to extend the methodology of denotational semantics to the much broader forms of computational processes we need to design, understand and analyze today? How are we to maintain clean algebraic structure and abstraction alongside the operational nature of computation? Here we expand on the Extended Synopsis and describe in more detail the problems with traditional semantics that lead us to seek a next generation of semantics; why this should be an intensional theory, concerned also with the ways values are computed; and how this leads us to seek a comprehensive theory of causal models. As we will see, this is because causal models, such as event structures, have appeared unexpectedly in the role of expressing the ways in which values are computed. But causal models, as they are currently understood and used, have themselves several problems, mainly due to their overly-concrete nature, which has obstructed their expressivity and range of use. A closer examination points to the introduction of a formal treatment of behavioural symmetry as the means to increase expressivity of causal models. The way forward to the next generation of semantics is through the key elements of events, causality and symmetry. Recall the objectives of ECSYM: Objective 1. A comprehensive semantic theory—one which includes that of causal models—together with rich metalanguage(s) and structured operational semantics, extracted from the denotational semantics; Objective 2. New techniques for event-based, causal reasoning, the beginnings of which are suggested by the mathematics; Objective 3. To incorporate quantitative reasoning through enrichment with probability and time—the mathematics and applications suggest a way; Objective 4. To develop application methods, especially where causal models (have the potential to) play a central role, including distributed and parallel computation, and systems biology.
Characterization of a Metabotropic Glutamate Receptor Type 5-Green Fluorescent Protein Chimera (mGluR5–GFP): Pharmacology, Surface Expression, and Differential Effects of Homer-1a and Homer-1c

Metabotropic glutamate receptor 5 (mGluR5) can modulate synaptic transmission by increasing intracellular Ca2+ and it plays a role in several forms of synaptic plasticity. We have constructed a fusion of human mGluR5 and green fluorescent protein (mGluR5-GFP). Expression of mGluR5-GFP in clonal cell lines yielded a functional fluorescent receptor with pharmacological profiles similar to wild-type mGluR5. mGluR5-GFP coimmunoprecipitated with Homer-1c, indicating that addition of GFP to the C-terminal did not prevent Homer binding. Coexpression of wild-type mGluR5 or mGluR5-GFP with Homer 1c, but not Homer-1a, resulted in reduced receptor surface localization and the formation of intracellular clusters. Neither Homer-1a nor Homer-1c had any effect on mGluR1 or mGluR1-GFP distribution. mGluR5-GFP expressed alone or in combination with Homer-1a formed dimers in HEK cells. Coexpression with Homer-1c, however, prevented mGluR5-GFP dimerization. Neither Homer altered the agonist profiles of mGluR5 or mGluR5-GFP. These data indicate that the functional expression of mGluR5 is regulated by Homer-1c and demonstrate that mGluR5-GFP provides a useful tool to study the molecular pharmacology and cell biology of mGluRs in real-time.
Understanding the Role of Reasoning ability in Mathematical Achievement

A theoretical link between reasoning and mathematical abilityhas been supported by some recent empirical evidence. Weargue that some of this evidence is indirect and measureselection may have influenced this relationship. We reportone study in which mathematical ability was measured usinga fluency and a calculation measure (Wood-cock Johnson-III,2001) and reasoning ability was measured using the extendedcognitive reflection test (Toplack, West & Stanovich, 2014)and a belief bias conditional reasoning task. Results from 68undergraduate students suggest that mathematical ability ispredicted by performance on the cognitive reflection test butnot conditional reasoning performance. We discuss theimplications of these findings for research on the link betweenmathematical ability and reasoning skills.
Highlight microdisparity for improved gloss depiction

Human stereo perception of glossy materials is substantially different from the perception of diffuse surfaces: A single point on a diffuse object appears the same for both eyes, whereas it appears different to both eyes on a specular object. As highlights are blurry reflections of light sources they have depth themselves, which is different from the depth of the reflecting surface. We call this difference in depth impression the "highlight disparity". Due to artistic motivation, for technical reasons, or because of incomplete data, highlights often have to be depicted on-surface, without any disparity. However, it has been shown that a lack of disparity decreases the perceived glossiness and authenticity of a material. To remedy this contradiction, our work introduces a technique for depiction of glossy materials, which improves over simple on-surface highlights, and avoids the problems of physical highlights. Our technique is computationally simple, can be easily integrated in an existing (GPU) shading system, and allows for local and interactive artistic control.
Structure–function relationship of the milk fat globule

Purpose of reviewThe complex biochemical composition and physical structure of the milk fat globule (MFG) are presented as a basis for its paradoxical metabolic fate: MFG is a rapid conveyor of energy through its triacylglycerol (TAG) core but contains some low-digestible bioactive complex lipids and proteins, which influence lipid metabolism and contribute to intestinal and systemic health. Recent findingsMFG structure modulates gastrointestinal lipolysis, postprandial lipemia and even the postprandial fate of ingested fatty acids. Proof-of-concept of the nutritional programming induced by early consumption of an emulsion biomimetic of MFG compared with a typical infant formula was published in an animal model (mice). The metabolic response to a high-fat diet during adulthood was improved following neonatal exposure to the biomimetic emulsion. SummaryMFG TAG are tailored with a unique regiodistribution delivering in priority short to medium-chain fatty acids in gastric phase, an important amount of quickly metabolizable oleic acid and protecting palmitic acid in sn-2 position. MFG digestion may not only trigger rapid TAG and chylomicron plasma peaks with fast clearance but also the luminal release of nonhydrolysable bioactive compounds (glycosylated compounds and sphingomyelin), which contribute to intestinal and systemic health by shaping the microbiota and modulating the immune system. These bioactive compounds form self-assembled structures, protect specific micronutrients and lower cholesterol absorption. The health benefits of MFG consumption or of some of its fractions (MFGM) under specific structures are steadily being demonstrated with still much unsolved questions especially for populations with high nutritional needs (e.g. elderly, infants).