Morphology Analysis of Si Island Arrays on Si(001)

The formation of nanometer-scale islands is an important issue for bottom-up-based schemes in novel electronic, optoelectronic and magnetoelectronic devices technology. In this work, we present a detailed atomic force microscopy analysis of Si island arrays grown by molecular beam epitaxy. Recent reports have shown that self-assembled distributions of fourfold pyramid-like islands develop in 5-nm thick Si layers grown at substrate temperatures of 650 and 750°C on HF-prepared Si(001) substrates. Looking for wielding control and understanding the phenomena involved in this surface nanostructuring, we develop and apply a formalism that allows for processing large area AFM topographic images in a shot, obtaining surface orientation maps with specific information on facets population. The procedure reveals some noticeable features of these Si island arrays, e.g. a clear anisotropy of the in-plane local slope distributions. Total island volume analysis also indicates mass transport from the substrate surface to the 3D islands, a process presumably related to the presence of trenches around some of the pyramids. Results are discussed within the framework of similar island arrays in homoepitaxial and heteroepitaxial semiconductor systems

Broad targeting of resistance to apoptosis in cancer

Apoptosis or programmed cell death is natural way of removing aged cells from the body. Most of the anti-cancer therapies trigger apoptosis induction and related cell death networks to eliminate malignant cells. However, in cancer, de-regulated apoptotic signaling, particularly the activation of an anti-apoptotic systems, allows cancer cells to escape this program leading to uncontrolled proliferation resulting in tumor survival, therapeutic resistance and recurrence of cancer. This resistance is a complicated phenomenon that emanates from the interactions of various molecules and signaling pathways. In this comprehensive review we discuss the various factors contributing to apoptosis resistance in cancers. The key resistance targets that are discussed include (1) Bcl-2 and Mcl-1 proteins; (2) autophagy processes; (3) necrosis and necroptosis; (4) heat shock protein signaling; (5) the proteasome pathway; (6) epigenetic mechanisms; and (7) aberrant nuclear export signaling. The shortcomings of current therapeutic modalities are highlighted and a broad spectrum strategy using approaches including (a) gossypol; (b) epigallocatechin-3-gallate; (c) UMI-77 (d) triptolide and (e) selinexor that can be used to overcome cell death resistance is presented. This review provides a roadmap for the design of successful anti-cancer strategies that overcome resistance to apoptosis for better therapeutic outcome in patients with cancer

Large-Scale Evidence for Conservation of NMD Candidature Across Mammals

BACKGROUND: Alternatively-spliced (AS) forms can vary protein function, intracellular localization and post-translational modifications. AS coupled with mRNA nonsense-mediated decay (NMD) can also control the transcript abundance. Here, we have investigated the genome-scale conservation of alternatively-spliced NMD candidates (AS-NMD candidates), in mammals. METHODOLOGY/PRINCIPAL FINDINGS: We mapped>12 million cDNA/EST library transcripts, comprising pooled data from both older and next-generation sequencing techniques, against genomic sequences to annotate AS-NMD candidates generated by in-frame premature termination codons (PTCs), in the human, mouse, rat and cow genomes. In these genomes, we found populations of genes that harbour AS-NMD candidates, varying in number from approximately 149 to 2,051 genes. We discovered that a highly-significant proportion (27%-35%) of AS-NMD candidate genes in mouse, rat and cow, also have human orthologs targeted for NMD. Intron retention was the most abundant type of AS-NMD, ranging from 43% to 67% of genes harbouring an AS-NMD candidate. Groupings of AS-NMD candidate genes either with or without intron retentions also have highly significant AS-NMD conservation, indicating that the trend is not due primarily to conservation of intron retentions. As a subset, the AS-NMD intron retentions are distinguished from non-retained introns by higher GC content, and codon usage similar to the usage in protein-coding sequences. This indicates that most of these alternatively spliced sequences have coded for proteins in the recent evolutionary past. In general, the AS-NMD candidate genes showed a similar pattern of Gene Ontology functional category enrichments in all four species. Genes linked to nucleic-acid interaction and apoptosis, and involved in pathways linked with cancer, were the most common. Finally, we mapped the AS-NMD candidates to mass spectrometry-derived proteomics data, and gathered evidence of truncated polypeptides for at least 10% of all human AS-NMD candidate transcripts. CONCLUSIONS/SIGNIFICANCE: In summary, our analysis provides strong statistical evidence for conservation of functional AS-NMD candidature across Mammalia for a large subset of genes. However, because codon usage of AS-NMD intron retentions is similar to the usage in exons, it is difficult to de-couple conservation of AS-NMD-based regulation from conservation for protein-coding ability, for intron retentions

Disturbed Expression of Splicing Factors in Renal Cancer Affects Alternative Splicing of Apoptosis Regulators, Oncogenes, and Tumor Suppressors

BACKGROUND: Clear cell renal cell carcinoma (ccRCC) is the most common type of renal cancer. One of the processes disturbed in this cancer type is alternative splicing, although phenomena underlying these disturbances remain unknown. Alternative splicing consists of selective removal of introns and joining of residual exons of the primary transcript, to produce mRNA molecules of different sequence. Splicing aberrations may lead to tumoral transformation due to synthesis of impaired splice variants with oncogenic potential. In this paper we hypothesized that disturbed alternative splicing in ccRCC may result from improper expression of splicing factors, mediators of splicing reactions. METHODOLOGY/PRINCIPAL FINDINGS: Using real-time PCR and Western-blot analysis we analyzed expression of seven splicing factors belonging to SR proteins family (SF2/ASF, SC35, SRp20, SRp75, SRp40, SRp55 and 9G8), and one non-SR factor, hnRNP A1 (heterogeneous nuclear ribonucleoprotein A1) in 38 pairs of tumor-control ccRCC samples. Moreover, we analyzed splicing patterns of five genes involved in carcinogenesis and partially regulated by analyzed splicing factors: RON, CEACAM1, Rac1, Caspase-9, and GLI1. CONCLUSIONS/SIGNIFICANCE: We found that the mRNA expression of splicing factors was disturbed in tumors when compared to paired controls, similarly as levels of SF2/ASF and hnRNP A1 proteins. The correlation coefficients between expression levels of specific splicing factors were increased in tumor samples. Moreover, alternative splicing of five analyzed genes was also disturbed in ccRCC samples and splicing pattern of two of them, Caspase-9 and CEACAM1 correlated with expression of SF2/ASF in tumors. We conclude that disturbed expression of splicing factors in ccRCC may possibly lead to impaired alternative splicing of genes regulating tumor growth and this way contribute to the process of carcinogenesis

Assessment of various aspects of using protocols in intensive care units in Plovdiv, Bulgaria

Background: Since 1950 intensive care has become a separate and independent specialty. Significant technological advances have allowed the Intensive Care Unit (ICU)s to be monitored through the centralized work of a multidisciplinary team of specialists. ICUs provide cares at different levels of support. To provide patient access to this highly specialized cares, the “Critical care without walls” or “Intensive Care without Borders” theories have emerged, involving reanimation nurses offering highly specialized care and support. Protocols for nurses have been developed, with the aim of facilitating their day-to-day activities, improving outcomes and safety of patients and all staff. Utilizing this concept, the role of intensive care has rapidly expanded over the past 20 years. Aim of the study: To understand the effectiveness and benefits derived from organisation of the working process. Material and methods: We used documentary and survey methods and analysed the data using the software package SPSS v. 21.0. Graphics were prepared using Microsoft Excel 2013. Numbers from 1 to 5 refer to the answers “no”, “not really”, “cannot judge”, “closer to yes” and “yes”, respectively. Results: Nurses’ performance, as an integral part of multidisciplinary ICU teams, is evidence that mortality and morbidity can be improved thanks to the early recognition of patient deterioration and rapid resuscitation. The better healing process is accomplished by optimising the content and evaluation of the desired results, in association with good doctor practices. Respondents’ opinions about outcomes of protocol use differed significantly between professions in regard to making their job easier, improving patient outcomes, providing consistency in care, and preventing patient harm. Conclusions: A more flexible and standard framework for nurses should be developed to improve quality of care. The rapidly growing lack of ICU nurses in Bulgaria is concerning

Angular Resolved Scattering Measurements as Quality Control Tool for Texture-Etched ZnO:Al Front Contacts

The texture of the transparent front contact is of major importance with respect to the optical performance of a thin-film silicon solar cell. In this study we address the method of angular resolved scattering as a tool to characterize the transparent conductive oxide surface texture. Using variously etched sputter-deposited aluminum doped zinc oxide films correlations between the scattering characteristics of the front contacts and the current generation of different solar cells are investigated. In order to simplify the characterization only discrete angles are used as a fingerprint. Thus, correlations between the front contact scattering and current of a-Si:H and μc- Si:H single junction solar cells as well as a-Si:H/μc-Si:H tandem junction solar cells are established. It is well known that the texture does not only influence the optical performance of the device but also the growth processes of the successive layers. Especially the growth of the μc-Si:H absorber is very sensitive to the front contact texture. Therefore the correlation between the light scattering based texture fingerprint of the front contact and the crystalline volume fraction of the μc-Si-H absorber layer is investigated

Temperature evolution of defects and atomic ordering in Si1−x_{1−x}Gex_{x} islands on Si(001)

The observation of atomic ordering and signatures of defects in self-assembled Ge islands using x-ray diffraction techniques have been previously treated as unrelated subjects. However, mutual understanding can be achieved when both subjects are studied in a common frame. Here, we report on measurements and analysis of both defects and atomic ordering in Si1−xGex islands epitaxially grown on Si(001) substrates as a function of growth temperature. By using x-ray diffraction and mapping around a bulk forbidden reflection, defect sizes, and in-plane spacing between nearby dislocations are extracted and related to the composition of the islands. The results fit well with an independent determination using selective wet chemical etching and atomic force microscopy measurements. Moreover, the temperature dependence of the ordered domain size is discussed. Although both atomic ordering and defect formation take place independently in the system, it is found that the relaxation provided by the onset of defects does not affect the formation of ordered domains, recently pointed out to be stabilized by strain and surface equilibrium on islands facet

Reading the footprints of strained islands

We report on recent advances in the understanding of surface processes occurring during growth and post-growth annealing of strained islands which may find application as self-assembled quantum dots. We investigate the model system SiGe/Si(001) by a new approach based on "reading the footprints" which islands leave on the substrate during their growth and evolution. Such footprints consist of trenches carved in the Si substrate. We distinguish between surface footprints and footprints buried below the islands. The former allow us to discriminate islands which are in the process of growing from those which are shrinking. Islands with steep morphologies grow at the expense of smaller and shallower islands, consistent with the kinetics of anomalous coarsening. While shrinking, islands change their shape according to thermodynamic predictions. Buried footprints are investigated by removing the SiGe epilayer by means of selective wet chemical etching. Their reading shows that: (i) during post-growth annealing islands move laterally because of surface-mediated Si-Ge intermixing; (ii) a tree-ring structure of trenches is created by dislocated islands during their "cyclic" growth. This allows us to distinguish coherent from dislocated islands and to establish whether the latter are the result of island coalescence. (c) 2006 Elsevier Ltd. All rights reserved