Izmir Institute of Technology

Using first-principles plane-wave calculations, we investigate two-dimensional (2D) honeycomb structure of group-IV elements and their binary compounds as well as the compounds of group III-V elements. Based on structure optimization and phonon-mode calculations, we determine that 22 different honeycomb materials are stable and correspond to local minima on the Born-Oppenheimer surface. We also find that all the binary compounds containing one of the first row elements, B, C, or N have planar stable structures. On the other hand, in the honeycomb structures of Si, Ge, and other binary compounds the alternating atoms of hexagons are buckled since the stability is maintained by puckering. For those honeycomb materials which were found stable, we calculated optimized structures, cohesive energies, phonon modes, electronic-band structures, effective cation and anion charges, and some elastic constants. The band gaps calculated within density functional theory using local density approximation are corrected by $G{W}_{0}$ method. Si and Ge in honeycomb structure are semimetal and have linear band crossing at the Fermi level which attributes massless Fermion character to charge carriers as in graphene. However, all binary compounds are found to be semiconductor with band gaps depending on the constituent atoms. We present a method to reveal elastic constants of 2D honeycomb structures from the strain energy and calculate the Poisson's ratio as well as in-plane stiffness values. Preliminary results show that the nearly lattice matched heterostructures of these compounds can offer alternatives for nanoscale electronic devices. Similar to those of the three-dimensional group-IV and group III-V compound semiconductors, one deduces interesting correlations among the calculated properties of present honeycomb structures.

Flow cytometry is a sophisticated instrument measuring multiple physical characteristics of a single cell such as size and granularity simultaneously as the cell flows in suspension through a measuring device. Its working depends on the light scattering features of the cells under investigation, which may be derived from dyes or monoclonal antibodies targeting either extracellular molecules located on the surface or intracellular molecules inside the cell. This approach makes flow cytometry a powerful tool for detailed analysis of complex populations in a short period of time. This review covers the general principles and selected applications of flow cytometry such as immunophenotyping of peripheral blood cells, analysis of apoptosis and detection of cytokines. Additionally, this report provides a basic understanding of flow cytometry technology essential for all users as well as the methods used to analyze and interpret the data. Moreover, recent progresses in flow cytometry have been discussed in order to give an opinion about the future importance of this technology.

Compact solid-state sources of terahertz (THz) radiation are being sought for sensing, imaging, and spectroscopy applications across the physical and biological sciences. We demonstrate that coherent continuous-wave THz radiation of sizable power can be extracted from intrinsic Josephson junctions in the layered high-temperature superconductor Bi2Sr2CaCu2O8. In analogy to a laser cavity, the excitation of an electromagnetic cavity resonance inside the sample generates a macroscopic coherent state in which a large number of junctions are synchronized to oscillate in phase. The emission power is found to increase as the square of the number of junctions reaching values of 0.5 microwatt at frequencies up to 0.85 THz, and persists up to approximately 50 kelvin. These results should stimulate the development of superconducting compact sources of THz radiation.

Abstract The grand challenges of contemporary fundamental physics—dark matter, dark energy, vacuum energy, inflation and early universe cosmology, singularities and the hierarchy problem—all involve gravity as a key component. And of all gravitational phenomena, black holes stand out in their elegant simplicity, while harbouring some of the most remarkable predictions of General Relativity: event horizons, singularities and ergoregions. The hitherto invisible landscape of the gravitational Universe is being unveiled before our eyes: the historical direct detection of gravitational waves by the LIGO-Virgo collaboration marks the dawn of a new era of scientific exploration. Gravitational-wave astronomy will allow us to test models of black hole formation, growth and evolution, as well as models of gravitational-wave generation and propagation. It will provide evidence for event horizons and ergoregions, test the theory of General Relativity itself, and may reveal the existence of new fundamental fields. The synthesis of these results has the potential to radically reshape our understanding of the cosmos and of the laws of Nature. The purpose of this work is to present a concise, yet comprehensive overview of the state of the art in the relevant fields of research, summarize important open problems, and lay out a roadmap for future progress. This write-up is an initiative taken within the framework of the European Action on ‘Black holes, Gravitational waves and Fundamental Physics’.

Cell viability is defined as the number of healthy cells in a sample and proliferation of cells is a vital indicator for understanding the mechanisms in action of certain genes, proteins and pathways involved cell survival or death after exposing to toxic agents. Generally, methods used to determine viability are also common for the detection of cell proliferation. Cell cytotoxicity and proliferation assays are generally used for drug screening to detect whether the test molecules have effects on cell proliferation or display direct cytotoxic effects. Regardless of the type of cell-based assay being used, it is important to know how many viable cells are remaining at the end of the experiment. There are a variety of assay methods based on various cell functions such as enzyme activity, cell membrane permeability, cell adherence, ATP production, co-enzyme production, and nucleotide uptake activity. These methods could be basically classified into different categories: (I) dye exclusion methods such as trypan blue dye exclusion assay, (II) methods based on metabolic activity, (III) ATP assay, (IV) sulforhodamine B assay, (V) protease viability marker assay, (VI) clonogenic cell survival assay, (VII) DNA synthesis cell proliferation assays and (V) raman micro-spectroscopy. In order to choose the optimal viability assay, the cell type, applied culture conditions, and the specific questions being asked should be considered in detail. This particular review aims to provide an overview of common cell proliferation and cytotoxicity assays together with their own advantages and disadvantages, their methodologies, comparisons and intended purposes.

The antibacterial activity and antioxidant effect of the compounds α-terpineol, linalool, eucalyptol and α-pinene obtained from essential oils (EOs), against pathogenic and spoilage forming bacteria were determined. The antibacterial activities of these compounds were observed in vitro on four Gram-negative and three Gram-positive strains. S. putrefaciens was the most resistant bacteria to all tested components, with MIC values of 2% or higher, whereas E. coli O157:H7 was the most sensitive strain among the tested bacteria. Eucalyptol extended the lag phase of S. Typhimurium, E. coli O157:H7 and S. aureus at the concentrations of 0.7%, 0.6% and 1%, respectively. In vitro cell growth experiments showed the tested compounds had toxic effects on all bacterial species with different level of potency. Synergistic and additive effects were observed at least one dose pair of combination against S. Typhimurium, E. coli O157:H7 and S. aureus, however antagonistic effects were not found in these combinations. The results of this first study are encouraging for further investigations on mechanisms of antimicrobial activity of these EO components.

The machine learning field, which can be briefly defined as enabling computers make successful predictions using past experiences, has exhibited an impressive development recently with the help of the rapid increase in the storage capacity and processing power of computers. Together with many other disciplines, machine learning methods have been widely employed in bioinformatics. The difficulties and cost of biological analyses have led to the development of sophisticated machine learning approaches for this application area. In this chapter, we first review the fundamental concepts of machine learning such as feature assessment, unsupervised versus supervised learning and types of classification. Then, we point out the main issues of designing machine learning experiments and their performance evaluation. Finally, we introduce some supervised learning methods.

Iron is an essential element for human life since it participates in many functions in the human body, including oxygen transport, immunity, cell division and differentiation, and energy metabolism. Iron homeostasis is mainly controlled by intestinal absorption because iron does not have active excretory mechanisms for humans. Thus, efficient intestinal iron bioavailability is essential to reduce the risk of iron deficiency anemia. There are two forms of iron, heme and nonheme, found in foods. The average daily dietary iron intake is 10 to 15 mg in humans since only 1 to 2 mg is absorbed through the intestinal system. Nutrient-nutrient interactions may play a role in dietary intestinal iron absorption. Dietary inhibitors such as calcium, phytates, polyphenols and enhancers such as ascorbic acid and proteins mainly influence iron bioavailability. Numerous studies have been carried out for years to enhance iron bioavailability and combat iron deficiency. In addition to traditional methods, innovative techniques are being developed day by day to enhance iron bioavailability. This review will provide information about iron bioavailability, factors affecting absorption, iron deficiency, and recent studies on improving iron bioavailability.

In nature, adaptive coloration has been effectively utilized for concealment and signaling. Various biological mechanisms have evolved to tune the reflectivity for visible and ultraviolet light. These examples inspire many artificial systems for mimicking adaptive coloration to match the visual appearance to their surroundings. Thermal camouflage, however, has been an outstanding challenge which requires an ability to control the emitted thermal radiation from the surface. Here we report a new class of active thermal surfaces capable of efficient real-time electrical-control of thermal emission over the full infrared (IR) spectrum without changing the temperature of the surface. Our approach relies on electro-modulation of IR absorptivity and emissivity of multilayer graphene via reversible intercalation of nonvolatile ionic liquids. The demonstrated devices are light (30 g/m2), thin (<50 μm), and ultraflexible, which can conformably coat their environment. In addition, by combining active thermal surfaces with a feedback mechanism, we demonstrate realization of an adaptive thermal camouflage system which can reconfigure its thermal appearance and blend itself with the varying thermal background in a few seconds. Furthermore, we show that these devices can disguise hot objects as cold and cold ones as hot in a thermal imaging system. We anticipate that, the electrical control of thermal radiation would impact on a variety of new technologies ranging from adaptive IR optics to heat management for outer space applications.

Chemotherapy is the main strategy for the treatment of cancer. However, the main problem limiting the success of chemotherapy is the development of multidrug resistance. The resistance can be intrinsic or acquired. The resistance phenotype is associated with the tumor cells that gain a cross-resistance to a large range of drugs that are structurally and functionally different. Multidrug resistance arises via many unrelated mechanisms, such as overexpression of energy-dependent efflux proteins, decrease in uptake of the agents, increase or alteration in drug targets, modification of cell cycle checkpoints, inactivation of the agents, compartmentalization of the agents, inhibition of apoptosis and aberrant bioactive sphingolipid metabolism. Exact elucidation of resistance mechanisms and molecular and biochemical approaches to overcome multidrug resistance have been a major goal in cancer research. This review comprises the mechanisms guiding multidrug resistance in cancer chemotherapy and also touches on approaches for reversing the resistance.

BACKGROUND: Solanum pimpinellifolium has high breeding potential for fruit quality traits and has been used as a donor in tomato breeding programs. Unlocking the genetic potential of S. pimpinellifolium requires high-throughput polymorphism identification protocols for QTL mapping and introgression of favourable alleles into cultivated tomato by both positive and background selection. RESULTS: In this study we identified SNP loci using a genotyping by sequencing (GBS) approach in an IBL mapping population derived from the cross between a high yielding fresh market tomato and S. pimpinellifolium (LA1589) as the recurrent and donor parents, respectively. A total of 120,983,088 reads were generated by the Illumina HiSeq next-generation sequencing platform. From these reads 448,539 sequence tags were generated. A majority of the sequence tags (84.4%) were uniquely aligned to the tomato genome. A total of 3.125 unique SNP loci were identified as a result of tag alignment to the genome assembly and were used in QTL analysis of 11 fruit quality traits. As a result, 37 QTLs were identified. S. pimpinellifolium contributed favourable alleles for 16 QTLs (43.2%), thus confirming the high breeding potential of this wild species. CONCLUSIONS: The present work introduced a set of SNPs at sufficiently high density for QTL mapping in populations derived from S. pimpinellifolium (LA1589). Moreover, this study demonstrated the high efficiency of the GBS approach for SNP identification, genotyping and QTL mapping in an interspecific tomato population.

Focal adhesions (FAs) are specialized adhesive structures which serve as cellular communication units between cells and the surrounding extracellular matrix. FAs are involved in signal transduction and actin cytoskeleton organization. FAs mediate cell adhesion, which is a critical phenomenon in cancer research. Since cells can form many and micrometer scale FAs, their quantitative analysis demands well-optimized image analysis approaches [1Berginski M.E. Vitriol E.A. Hahn K.M. Gomez S.M. High-resolution quantification of focal adhesion spatiotemporal dynamics in living cells.PLoS One. 2011; 6 (PubMed PMID: 21779367. Pubmed Central PMCID: Pmc3136503 (Epub 2011/07/23)): e22025Crossref PubMed Scopus (125) Google Scholar, 2Lamers E. van Horssen R. te Riet J. van Delft F.C. Luttge R. Walboomers X.F. et al.The influence of nanoscale topographical cues on initial osteoblast morphology and migration.Eur. Cells Mater. 2010; 20 (PubMed PMID: 21061239 (Epub 2010/11/10)): 329-343Crossref PubMed Scopus (124) Google Scholar, 3Zamir E. Katz B.Z. Aota S. Yamada K.M. Geiger B. Kam Z. Molecular diversity of cell-matrix adhesions.J. Cell Sci. 1999; 112 (PubMed PMID: 10318759 (Epub 1999/05/13)): 1655-1669Crossref PubMed Google Scholar]. Here, we have optimized the analysis of FAs of MDA-MB-231 breast cancer cells. The optimization is based on proper processing of immunofluorescence images of vinculin, which is one of the markers of FAs. All image processing steps are carried out using the ImageJ software, which is freely available and in the public domain. The advantages of our method are:•The analysis steps are simplified by combining different plugins of the ImageJ program.•FAs are better detected with minimal false negatives due to optimized processing of fluorescent images.•This approach can be applied to quantify a variety of fluorescent images comprising focal and/or localized signals within a high background such as FAs, one of the many complex signaling structures in a cell.

All‐solid‐state Li‐ion batteries based on Li 7 La 3 Zr 2 O 12 (LLZO) garnet structures require novel electrode assembly strategies to guarantee a proper Li + transfer at the electrode–electrolyte interfaces. Here, first stable cell performances are reported for Li‐garnet, c‐Li 6.25 Al 0.25 La 3 Zr 2 O 12 , all‐solid‐state batteries running safely with a full ceramics setup, exemplified with the anode material Li 4 Ti 5 O 12 . Novel strategies to design an enhanced Li + transfer at the electrode–electrolyte interface using an interface‐engineered all‐solid‐state battery cell based on a porous garnet electrolyte interface structure, in which the electrode material is intimately embedded, are presented. The results presented here show for the first time that all‐solid‐state Li‐ion batteries with LLZO electrolytes can be reversibly charge–discharge cycled also in the low potential ranges (≈1.5 V) for combinations with a ceramic anode material. Through a model experiment, the interface between the electrode and electrolyte constituents is systematically modified revealing that the interface engineering helps to improve delivered capacities and cycling properties of the all‐solid‐state Li‐ion batteries based on garnet‐type cubic LLZO structures.

Visual tracking has attracted a significant attention in the last few decades. The recent surge in the number of publications on tracking-related problems have made it almost impossible to follow the developments in the field. One of the reasons is that there is a lack of commonly accepted annotated data-sets and standardized evaluation protocols that would allow objective comparison of different tracking methods. To address this issue, the Visual Object Tracking (VOT) workshop was organized in conjunction with ICCV2013. Researchers from academia as well as industry were invited to participate in the first VOT2013 challenge which aimed at single-object visual trackers that do not apply pre-learned models of object appearance (model-free). Presented here is the VOT2013 benchmark dataset for evaluation of single-object visual trackers as well as the results obtained by the trackers competing in the challenge. In contrast to related attempts in tracker benchmarking, the dataset is labeled per-frame by visual attributes that indicate occlusion, illumination change, motion change, size change and camera motion, offering a more systematic comparison of the trackers. Furthermore, we have designed an automated system for performing and evaluating the experiments. We present the evaluation protocol of the VOT2013 challenge and the results of a comparison of 27 trackers on the benchmark dataset. The dataset, the evaluation tools and the tracker rankings are publicly available from the challenge website (http://votchallenge.net).

High quality indium tin oxide (ITO) thin films were grown without oxygen by both dc and RF magnetron sputtering techniques on glass substrates. The effects of substrate temperature, film thickness and sputtering method on the structural, electrical and optical properties of the as-grown films were investigated. The results showed that the substrate temperature had substantial effects on the film properties, in particular on the crystallization and resistivity. When the substrate temperature was increased to 150 °C, crystallization in the (2 2 2) plane started appearing for both dc and RF sputtered films. We additionally found that with further increments of substrate temperature, the preferred crystallization orientation changed differently for dc and RF sputtered films. Optical transmission in the visible region for a film thickness of 70 nm was found to be above 85%. The bandgap was calculated to be about 3.64 eV for the substrate temperature of 150 °C for a 70 nm thick film. The value of the bandgap increased with respect to the increment in film thickness as well as substrate temperature. We also measured the temperature dependence of the resistivity and Hall coefficient of the films, and calculated the carrier concentration and Hall mobility. Very low room temperature resistivities for dc and RF magnetron sputtered grown films of about 1.28 × 10 −4 Ω cm and 1.29 × 10 −4 Ω cm, respectively, were obtained.

Abstract The measurement of the luminosity recorded by the CMS detector installed at LHC interaction point 5, using proton–proton collisions at $$\sqrt{s}=13\,{\text {TeV}} $$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mrow> <mml:msqrt> <mml:mi>s</mml:mi> </mml:msqrt> <mml:mo>=</mml:mo> <mml:mn>13</mml:mn> <mml:mspace/> <mml:mtext>TeV</mml:mtext> </mml:mrow> </mml:math> in 2015 and 2016, is reported. The absolute luminosity scale is measured for individual bunch crossings using beam-separation scans (the van der Meer method), with a relative precision of 1.3 and 1.0% in 2015 and 2016, respectively. The dominant sources of uncertainty are related to residual differences between the measured beam positions and the ones provided by the operational settings of the LHC magnets, the factorizability of the proton bunch spatial density functions in the coordinates transverse to the beam direction, and the modeling of the effect of electromagnetic interactions among protons in the colliding bunches. When applying the van der Meer calibration to the entire run periods, the integrated luminosities when CMS was fully operational are 2.27 and 36.3 $$\,\text {fb}^{-1}$$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mrow> <mml:mspace/> <mml:msup> <mml:mtext>fb</mml:mtext> <mml:mrow> <mml:mo>-</mml:mo> <mml:mn>1</mml:mn> </mml:mrow> </mml:msup> </mml:mrow> </mml:math> in 2015 and 2016, with a relative precision of 1.6 and 1.2%, respectively. These are among the most precise luminosity measurements at bunched-beam hadron colliders.

Two-dimensional (2D) Janus materials are a new class of materials with unique physical, chemical, and quantum properties. The name “Janus” originates from the ancient Roman god which has two faces, one looking to the future while the other facing the past. Janus has been used to describe special types of materials which have two faces at the nanoscale. This unique atomic arrangement has been shown to present rather exotic properties with applications in biology, chemistry, energy conversion, and quantum sciences. This review article aims to offer a comprehensive review of the emergent quantum properties of Janus materials. The review starts by introducing 0D Janus nanoparticles and 1D Janus nanotubes, and highlights their difference from classical ones. The design principles, synthesis, and the properties of graphene-based and chalcogenide-based Janus layers are then discussed. A particular emphasis is given to colossal built-in potential in 2D Janus layers and resulting quantum phenomena such as Rashba splitting, skyrmionics, excitonics, and 2D magnetic ordering. More recent theoretical predictions are discussed in 2D Janus superlattices when Janus layers are stacked onto each other. Finally, we discuss the tunable quantum properties and newly predicted 2D Janus layers waiting to be experimentally realized. The review serves as a complete summary of the 2D Janus library and predicted quantum properties in 2D Janus layers and their superlattices.

We report on the discovery of stellar occultations, observed with Kepler, which recur periodically at 15.685 hr intervals, but which vary in depth from a maximum of 1.3% to a minimum that can be less than 0.2%. The star that is apparently being occulted is KIC 12557548, a V = 16 mag K dwarf with T_eff, s ≃ 4400 K. The out-of-occultation behavior shows no evidence for ellipsoidal light variations, indicating that the mass of the orbiting object is less than ~3 M_J (for an orbital period of 15.7 hr). Because the eclipse depths are highly variable, they cannot be due solely to transits of a single planet with a fixed size. We discuss but dismiss a scenario involving a binary giant planet whose mutual orbit plane precesses, bringing one of the planets into and out of a grazing transit. This scenario seems ruled out by the dynamical instability that would result from such a configuration. We also briefly consider an eclipsing binary, possibly containing an accretion disk, that either orbits KIC 12557548 in a hierarchical triple configuration or is nearby on the sky, but we find such a scenario inadequate to reproduce the observations. The much more likely explanation—but one which still requires more quantitative development—involves macroscopic particles escaping the atmosphere of a slowly disintegrating planet not much larger than Mercury in size. The particles could take the form of micron-sized pyroxene or aluminum oxide dust grains. The planetary surface is hot enough to sublimate and create a high-Z atmosphere; this atmosphere may be loaded with dust via cloud condensation or explosive volcanism. Atmospheric gas escapes the planet via a Parker-type thermal wind, dragging dust grains with it. We infer a mass-loss rate from the observations of order 1 M_⊕ Gyr^(–1), with a dust-to-gas ratio possibly of order unity. For our fiducial 0.1 M_⊕ planet (twice the mass of Mercury), the evaporation timescale may be ~0.2 Gyr. Smaller mass planets are disfavored because they evaporate still more quickly, as are larger mass planets because they have surface gravities too strong to sustain outflows with the requisite mass-loss rates. The occultation profile evinces an ingress-egress asymmetry that could reflect a comet-like dust tail trailing the planet; we present simulations of such a tail.

Estrogens and progesterones are major drivers of breast development but also promote carcinogenesis in this organ. Yet, their respective roles and the mechanisms underlying their action in the human breast are unclear. Receptor activator of nuclear factor κB ligand (RANKL) has been identified as a pivotal paracrine mediator of progesterone function in mouse mammary gland development and mammary carcinogenesis. Whether the factor has the same role in humans is of clinical interest because an inhibitor for RANKL, denosumab, is already used for the treatment of bone disease and might benefit breast cancer patients. We show that progesterone receptor (PR) signaling failed to induce RANKL in PR(+) breast cancer cell lines and in dissociated, cultured breast epithelial cells. In clinical specimens from healthy donors and intact breast tissue microstructures, hormone response was maintained and RANKL expression was under progesterone control, which increased RNA stability. RANKL was sufficient to trigger cell proliferation and was required for progesterone-induced proliferation. The findings were validated in vivo where RANKL protein expression in the breast epithelium correlated with serum progesterone levels and the protein was expressed in a subset of luminal cells that express PR. Thus, important hormonal control mechanisms are conserved across species, making RANKL a potential target in breast cancer treatment and prevention.

Bacterial wilt, caused by strains belonging to the Ralstonia solanacearum species complex, inflicts severe economic losses in many crops worldwide. Host resistance remains the most effective control strategy against this disease. However, wilt resistance is often overcome due to the considerable variation among pathogen strains. To help breeders circumvent this problem, we assembled a worldwide collection of 30 accessions of tomato, eggplant and pepper (Core-TEP), most of which are commonly used as sources of resistance to R. solanacearum or for mapping quantitative trait loci. The Core-TEP lines were challenged with a core collection of 12 pathogen strains (Core-Rs2) representing the phylogenetic diversity of R. solanacearum. We observed six interaction phenotypes, from highly susceptible to highly resistant. Intermediate phenotypes resulted from the plants' ability to tolerate latent infections (i.e., bacterial colonization of vascular elements with limited or no wilting). The Core-Rs2 strains partitioned into three pathotypes on pepper accessions, five on tomato, and six on eggplant. A "pathoprofile" concept was developed to characterize the strain clusters, which displayed six virulence patterns on the whole set of Core-TEP host accessions. Neither pathotypes nor pathoprofiles were phylotype specific. Pathoprofiles with high aggressiveness were mainly found in strains from phylotypes I, IIB, and III. One pathoprofile included a strain that overcame almost all resistance sources.