Investigating ripple pattern formation and damage profiles in Si and Ge induced by 100 keV Ar+ ion beam: a comparative study.

Desired modifications of surfaces at the nanoscale may be achieved using energetic ion beams. In the present work, a complete study of self-assembled ripple pattern fabrication on Si and Ge by 100 keV Ar+ ion beam bombardment is discussed. The irradiation was performed in the ion fluence range of ≈3 × 1017 to 9 × 1017 ions/cm2 and at an incident angle of θ ≈ 60° with respect to the surface normal. The investigation focuses on topographical studies of pattern formation using atomic force microscopy, and induced damage profiles inside Si and Ge by Rutherford backscattering spectrometry and transmission electron microscopy. The ripple wavelength was found to scale with ion fluence, and energetic ions created more defects inside Si as compared to that of Ge. Although earlier reports suggested that Ge is resistant to structural changes upon Ar+ ion irradiation, in the present case, a ripple pattern is observed on both Si and Ge. The irradiated Si and Ge targets clearly show visible damage peaks between channel numbers (1000-1100) for Si and (1500-1600) for Ge. The clustering of defects leads to a subsequent increase of the damage peak in irradiated samples (for an ion fluence of ≈9 × 1017 ions/cm2) compared to that in unirradiated samples.

Novel human-derived EML4-ALK fusion cell lines identify ribonucleotide reductase RRM2 as a target of activated ALK in NSCLC.

INTRODUCTION: Echinoderm microtubule-associated protein-like 4 (EML4)-Anaplastic Lymphoma Kinase (ALK) rearrangements occur in 3% to 7% of lung adenocarcinomas and are targets for treatment with tyrosine kinase inhibitors (TKIs). Here we have developed three novel EML4-ALK-positive patient-derived Non-Small-Cell-Lung-Cancer (NSCLC) cancer cell lines, CUTO8 (variant 1), CUTO9 (variant 1) and CUTO29 (variant 3) and included a fourth ALK-positive cell line YU1077 (variant 3) to study ALK-positive signaling and responses. Variants 1 and 3 are the most common EML4-ALK variants expressed in ALK-positive NSCLC, and currently cell lines representing these EML4-ALK variants are limited. MATERIALS AND METHODS: Resazurin assay was performed to evaluate cell viability. Protein levels were determined using western blotting. RNA sequencing was performed in all four cell lines to identify differentially expressed genes. Whole-genome sequencing was performed to determine the presence of EML4-ALK fusion and ALK tyrosine kinase inhibitor resistance mutations. RESULTS: In this study, we have confirmed expression of the corresponding ALK fusion protein and assessed their sensitivity to a range of ALK tyrosine kinase inhibitors. These patient derived cell lines exhibit differential sensitivity to lorlatinib, brigatinib and alectinib, with EML4-ALK variant 3 containing cell lines exhibiting increased sensitivity to lorlatinib and brigatinib as compared to alectinib. These cell lines were further characterized by whole genome sequencing and RNA-seq analysis that identified the ribonucleotide reductase regulatory subunit 2 (RRM2) as a downstream and potential therapeutic target in ALK-positive NSCLC. CONCLUSION: We provide a characterization of four novel EML4-ALK-positive NSCLC cell lines, highlighting genomic heterogeneity and differential responses to ALK TKI treatment. The RNA-Seq characterization of ALK-positive NSCLC CUTO8, CUTO9, CUTO29 and YU1077 cell lines reported here, has been compiled in an interactive ShinyApp resource for public data exploration (https://ccgg.ugent.be/shiny/nsclc_rrm2_2022/).

Signature of strong localization and crossover conduction processes in doped ZnO thin films: synergetic effect of doping fraction and dense electronic excitations.

GaxZn1-xO thin films with varying Ga fraction within the solubility limit were irradiated with high-energy heavy ions to induce electronic excitations. The films show good transmittance in the visible region and a reduction of about 20% in transmittance was observed for irradiated films at higher ion fluences. The Urbach energy was estimated and showed an augmenting response upon increase in doping fraction and ion irradiation, this divulges an enhancement of localized states in the bandgap or disorder in the films. The evolution of such localized states plays a vital role in charge transport and thus the temperature dependent electrical conductivity of irradiated thin films was studied to elucidate the dominant conduction mechanisms. The detailed analysis unfolds that in the high-temperature regime (180 K

Reversible hydrogen control of antiferromagnetic anisotropy in α-Fe2O3.

Antiferromagnetic insulators are a ubiquitous class of magnetic materials, holding the promise of low-dissipation spin-based computing devices that can display ultra-fast switching and are robust against stray fields. However, their imperviousness to magnetic fields also makes them difficult to control in a reversible and scalable manner. Here we demonstrate a novel proof-of-principle ionic approach to control the spin reorientation (Morin) transition reversibly in the common antiferromagnetic insulator α-Fe2O3 (haematite) - now an emerging spintronic material that hosts topological antiferromagnetic spin-textures and long magnon-diffusion lengths. We use a low-temperature catalytic-spillover process involving the post-growth incorporation or removal of hydrogen from α-Fe2O3 thin films. Hydrogenation drives pronounced changes in its magnetic anisotropy, Néel vector orientation and canted magnetism via electron injection and local distortions. We explain these effects with a detailed magnetic anisotropy model and first-principles calculations. Tailoring our work for future applications, we demonstrate reversible control of the room-temperature spin-state by doping/expelling hydrogen in Rh-substituted α-Fe2O3.

Nano-scale depth-varying recrystallization of oblique Ar+ sputtered Si(111) layers.

Silicon, the workhorse of semiconductor industry, is being exploited for various functional applications in numerous fields of nanotechnology. In this paper, we report the fabrication of depth controllable amorphous silicon (a-Si) layers under 80 keV Ar+ ion sputtering at off-normal ion incidences of 30°, 40° and 50° and crystallization of these amorphous Si(111) layers under thermal annealing. We find that the irradiated samples were not fully amorphized even for the lowest oblique incidence of 30°. Sputtering at off-normal incidences induces depth controllable surface amorphization in Si(111). Annealing at temperature of 1,073 K is characterized by formation of depth-varying buried amorphous layer due to defect recrystallization and damage recovery. Some remnant tensile stress has been observed for recrystallized samples even for lowest oblique incidence. The correlation of amorphization and stress due to sputtering induced by oblique incidence has been discussed systematically. The possible mechanism of recrystallization is discussed in terms of vacancies produced in sputtering dominated regime and their migration during annealing treatment. Our results reveal that with appropriate selection of oblique ion beam sputtering parameters, depth controllable surface amorphization and recrystallization may be fine-tuned to achieve co-existing amorphous and crystalline phases, playing a crucial role in fabrication of substrates for IC industry.

Role of Ni substitution on structural, magnetic and electronic properties of epitaxial CoCr2O4 spinel thin films.

Cubic spinel CoCr2O4 has recently attained attention due to its multiferroic properties. However, the Co site substitution effect on the structural and magnetic properties has rarely been studied in thin film form. In this work, the structural and magnetic properties of Co1-x Ni x Cr2O4 (x= 0, 0.5) epitaxial thin films deposited on MgAl2O4 (100) and MgO (100) substrates to manipulate the nature of strain in the films using pulsed laser deposition (PLD) technique are presented. The epitaxial nature of the films was manifested through x-ray diffraction (XRD), reciprocal space mapping (RSM) and Rutherford backscattering spectrometry (RBS) measurements. Raman measurements revealed a disappearance of characteristic A 1 g and F 2 g modes of the CoCr2O4 with increase in the Ni content. Atomic force microscopy (AFM) and field emission scanning electron microscopy (FE-SEM) studies show a modification of the surface morphology upon Ni substitution. Magnetic measurements disclose that the ferrimagnetic Curie temperature (T C) of the CoCr2O4 in thin film grown on MgAl2O4 (100) and MgO (100) substrates were found to be 100.6 ± 0.5 K and 93.8 ± 0.2 K, respectively. With Ni substitution the T C values were found to be enhanced to 104.5 ± 0.4 K for MgAl2O4 (100) and 108.5 ± 0.6 K for MgO (100) substrates. X-ray photoelectron spectroscopy (XPS) suggests Cr3+ oxidation states in the films, while Co ions are present in a mixed Co2+/Co3+ oxidation state. The substitution of Ni at Co site significantly modifies the line shape of the core level as well as the valence band. Ni ions are also found to be in a mixed 2+/3+ oxidation state. O 1s core level display asymmetry related to possible defects like oxygen vacancies in the films.

Self-assembled nano-dots structures on Si(111) surfaces by oblique angle sputter-deposition.

Controlled surface modification and nano-dots structures over Si(111) surfaces have been produced by oblique angle sputter deposition of 80 keV Ar+ beam. Temporal parameters such as self-assemble, tunability of size and density of fabricated nano-dots exhibit distinct fluence dependence. Crystalline to amorphous (c/a) phase transition for sputter deposited Si(111) surfaces has been observed. RBS/C reveals the non-linear response of damage distribution with Ar ion fluence. Compositional alterations like degree of amorphization, damage distribution and depth profiling of Ar in these nano-structured surfaces has been correlated with the morphological and structural findings. The underlying self-organization mechanism relies in ion beam sputtering induced erosion and re-deposition of Si atoms thereby leading to mass transport inside the amorphous layers. Such nano-structured Si(111) surfaces could be applied as key engineering substrates for surface reconstruction, optoelectronic devices, data storage devices, recording media and photovoltaic applications.

On the spectroscopic examination of printed documents by using a field emission scanning electron microscope with energy-dispersive X-ray spectroscopy (FE-SEM-EDS) and chemometric methods: application in forensic science.

The detection of computer-generated document forgeries has always been a challenging task for forensic document examiners (FDE). With the aim to support the examination processes, Schottky field emission scanning electron microscopy with energy-dispersive X-ray spectroscopy (FE-SEM-EDS) is explored as a recent tool to analyze black toners obtained from laser printers and photocopier machines. Forty samples each from the laser printer and photocopier machines are procured and studied for morphological features, elemental profile, and multivariate analysis. The acquired SEM images and spectra are evaluated to discriminate and classify the toners having a different source of origin. Multivariate analysis is applied to develop a model of classification to successfully classify the printed documents on the basis of the similarities and differences in their composition. Hierarchical cluster analysis (HCA) discriminates the printouts in the forms of groups based on their chemical composition. The laser printer and the photocopier printed documents are grouped into 11 and eight clusters, respectively, based on their elemental composition. Cross-validation is further conducted to assess the capabilities of developed principal component analysis (PCA) and linear discriminant analysis (LDA) models for the examination of printouts from unknown origin. Graphical abstract.

Physiological stress responses in wild Asian elephants Elephas maximus in a human-dominated landscape in the Western Ghats, southern India.

Increasing anthropogenic pressures on forests, especially in the tropical regions of the world, have restricted several large mammalian species such as the Asian elephant to fragmented habitats within human-dominated landscapes. In this study, we assessed the effects of an anthropogenic landscape and its associated conflict with humans on the physiological stress responses displayed by Asian elephants in the Anamalai Hills of the Western Ghats mountains in south India. We have quantified faecal glucocorticoid metabolite (FGM) concentrations in focal individual elephants within and across herds, inhabiting both anthropogenic and natural habitats, and evaluated their physiological responses to different socio-ecological situations between November 2013 and April 2014. Physiological stress responses varied significantly among the tested elephant age- and sex categories but not across different types of social organisation. Adults generally showed higher FGM concentrations, even in the absence of stressors, than did any other age category. Males also appeared to have higher stress responses than did females. Although there was no significant variation in mean stress levels between elephants on the plateau in the absence of human interactions and those in adjacent, relatively undisturbed forest habitats, FGM concentrations increased significantly for adult and subadult individuals as well as for calves following drives, during which elephants were driven off aggressively by people. Our study emphasises the general importance of understanding individual variation in physiology and behaviour within a population of a seriously threatened mammalian species, the Asian elephant, and specifically highlights the need for long-term monitoring of the stress physiology and behavioural responses of individual elephants across both human-dominated and natural landscapes. Such studies would not only provide comprehensive insights into the adaptive biology of elephants in changing ecological regimes but also aid in the development of effective management and conservation strategies for endangered populations of the species.

The ALK inhibitor PF-06463922 is effective as a single agent in neuroblastoma driven by expression of ALK and MYCN.

The first-in-class inhibitor of ALK, c-MET and ROS1, crizotinib (Xalkori), has shown remarkable clinical efficacy in treatment of ALK-positive non-small cell lung cancer. However, in neuroblastoma, activating mutations in the ALK kinase domain are typically refractory to crizotinib treatment, highlighting the need for more potent inhibitors. The next-generation ALK inhibitor PF-06463922 is predicted to exhibit increased affinity for ALK mutants prevalent in neuroblastoma. We examined PF-06463922 activity in ALK-driven neuroblastoma models in vitro and in vivo In vitro kinase assays and cell-based experiments examining ALK mutations of increasing potency show that PF-06463922 is an effective inhibitor of ALK with greater activity towards ALK neuroblastoma mutants. In contrast to crizotinib, single agent administration of PF-06463922 caused dramatic tumor inhibition in both subcutaneous and orthotopic xenografts as well as a mouse model of high-risk neuroblastoma driven by Th-ALK(F1174L)/MYCN Taken together, our results suggest PF-06463922 is a potent inhibitor of crizotinib-resistant ALK mutations, and highlights an important new treatment option for neuroblastoma patients.

The 34,XY1,der(13) chromosome constitution with loss of Y2 is associated with unilateral testicular hypoplasia in the endangered Indian blackbuck antelope (Antilope cervicapra).

The present study is the first report of unilateral testicular hypoplasia in 3 of 15 (20%) Indian blackbuck antelopes (Antilope cervicapra). Interestingly, the condition was restricted to only the right testis in all cases. Cytogenetic analysis revealed chromosomal aneuploidy in the affected individuals which had a 34,XY(1),der(13) karyotype with loss of the acrocentric (autosomal) Y(2) and an aberrant chromosome 13. We further determined that the semen output and the circulating testosterone levels were markedly low in the males with hypoplastic testes as compared to fertile males.

Conservation of wild animals by assisted reproduction and molecular marker technology.

Wild animals are an integral component of the ecosystem. Their decimation due to abrupt natural calamities or due to gradual human intervention would be disastrous to the ecosystem and would alter the balance in nature between various biotic components. Such an imbalance could have an adverse effect on the ecosystem. Therefore, there is an urgent need to put an end to the ever increasing list of endangered species by undertaking both in situ and ex situ conservation using tools of modern biology, to ascertain the degree of genetic variation and reproductive competence in these animals. This review highlights the development and use of molecular markers such as microsatellites, minisatellites, mitochondrial control region, cytochrome b and MHC loci to assess the genetic variation in various Indian wild animals such as the lion, tiger, leopard and deer. The review also presents data on the semen profile of the big cats of India. Reproductive technologies such as cryopreservation of semen and artificial insemination in big cats are also highlighted.

The demography of the lion-tailed macaque (Macaca silenus) in rain forest fragments in the Anamalai Hills, South India.

We examined demographic consequences of habitat fragmentation in the lion-tailed macaque in the Anamalai Hills in southern Western Ghats. The parameters examined were group size, age/sex composition, and birth rate, in relation to various habitat parameters. Demographic parameters were estimated for 11 groups in 8 rain forest fragments, during January to May 1996. Area, tree density, canopy cover, canopy height, and tree basal area were estimated for these fragments. As fragment area decreased, there was a decline in birth rate and proportion of immatures in the group, and an increase in the number of adult males, and the variability in group size and adult sex ratios. A similar pattern was also observed with decreasing values of other habitat variables. Differences in the founder population size and age structure, demographic randomness, and history of poaching have caused greater variability in group size and adult sex ratios in the small fragments. The lack of dispersal in the small fragments is another reason for the high variability.