Miracle-dz/UniFAR-FTUs huggingface dataset:
Catalogue of Unbalanced Chromosome Aberrations in Man

This special issue should become a vade mecum for any cytogeneticist involved in prenatal diagnosis because it contains such immediately practical and useful information, especially about those relatively rare situations where no individual laboratory can collect enough data to arrive at a firm conclusion about the significance of a finding. I hope that this sort of data will continue to be collected and reported on regularly in the future. The first section gives maternal age specific rates for chromosome aberrations and exhaustively analyses paternal age data. It would have been interesting to have seen the analysis of parental age effects done for male and female trisomy 21 cases separately in view of the findings of Hassold et al (1984), but perhaps this can be done next time. Boue and Gallano give differential risks of an abnormal outcome in pregnancies to parents carrying varied balanced translocations. Translocations ascertained through amniocentesis for other reasons are excluded from these figures and I did wonder whether the elimination of these previously troublefree rearrangements might lead to an overestimation of risk. By sampling error alone some families would be expected to show no adverse outcome despite the risk, but they still form part of the population of outcomes on which risk figures should be based. There is a particularly informative section on de novo structural rearrangements. These cases are among the most difficult on which to give advice and this information will make that job much easier. The section highlights the need for more extended follow up of such cases. Most assessments are made immediately, at birth, and few cases are followed to the time when developmental delay or retardation might be expected to be detectable. It is an indication of the difficulty of assessing mosaicism that three studies of this problem are presented. The Canadian survey produces particularly helpful guidelines for establishing the most effective way of distinguishing between 'true' and pseudomosaicism and in this, and the European study, there are helpful notes about presumptive maternal cell contamination. Again the necessity for 237 full and extended follow up is stressed, without which the long term significance of such aberrations cannot be assessed. For me, this presentation reinforced with hard data impressions gained from a relatively small number of cases. My job is going to be easier because of the broad based information included in this special issue.
Dormancy in two regional cities and its relevance to the growth of Sydney

The dormant cityscape continues to haunt many of our burgeoning, high growth cities. Former port lands, ‘brownfield’ sites and degraded suburban areas persist in these states for what appears to be decades without any apparent revival. Despite the usual forms of planning, zoning and controls they appear to display obstinacy over large time periods that continue to confound local and state planning authorities and leaders. This article studies dormant cityscapes in two regional cities (Newcastle and Townsville) and their revival, to bring a clearer understanding to the nature and dynamics of dormancy. The cityscapes are viewed through a time-lapse, mechanistic view by charting of stimulus events over several decades to identify the often invisible forces at work. The results are discussed in light of a city area in the Sydney Basin (Penrith) and a view of its transformation timeline. The often urgent political reliance on lineal, visible change is shown to confound our view, along with the ‘meta’ use of the economic/demographic lens to view our cities. Missing is a view of not only artefactual indicators but the invisible markers of change. This, along with a mechanistic ‘time-lapse’ view is discussed as a means of enhancing our knowledge of dormancy periods. The study enhances our understanding of dormancy and the historical timelines that they operate under. In this way a revisionist view of this phenomenon informs planners and city leaders to understand dormancy and its revitalization, which goes beyond political urgencies.
DNA‐based species delimitation separates highly divergent populations within morphologically coherent clades of poorly dispersing beetles

We compared species-level entities recovered using distance, tree-based, and DNA-character based methods with morphologically defined species in poorly dispersing lyponiine net-winged beetles. The phylogenetic relationships were investigated using the cytochrome c oxidase 1–2 mtDNA fragment. We identified 31 species using a morphology-based concept and additional candidate species were delimited by the general mixed Yule-coalescent method and barcoding threshold within the morphologically coherent lineages owing to high genetic divergence (up to 10.97% within morphologically defined species, highest density 2.5–6.5%). Genetic divergence was positively correlated with geographical distance: lower in continental China where no apparent dispersal barriers are present (r2 = 0.172, P ≤ 0.001, average increase of genetic distance of 0.32% per 100 km) and much higher in Japan (r2 = 0.490, P ≤ 0.001, 1.81% per 100 km). We hypothesize that low dispersal propensity contributed to the high level of intraspecific, geographically structured divergence. DNA-based methods suggested a high number of morphologically undistinguishable species. The observed patterns agree with the model of neutral evolution. The poor dispersers produce gradually divergent populations across the range of the morphologically coherent lineages. We pose the question of what size of range and level of genetic difference justify formal acceptance of a species without morphological divergence from both the taxonomical and conservation management view points. © 2015 The Linnean Society of London
Analysis of coproporphyrinogen III oxidase in maize : the genes, their expression, and the localization of their products

approved: Carol J. Rivin Coproporphyrinogen III oxidase (CPX) is an enzyme involved in the biosynthesis of tetrapyrroles, catalyzing the oxidative decarboxylation of coproporphyrinogen Ill to protoporphyrinogen IX. In bacteria and yeast this enzyme is cytosolic, in animals it is mitochondrial, and in each it functions to produce heme. However, in all plants investigated, the initial steps of tetrapyrrole production, including those catalyzed by CPX, occur exclusively in the chloroplast stroma. Protoporphyrinogen IX is modified in the plastid envelope to produce chlorophyll and heme, or channeled to the mitochondria for heme production. The maize genome has two CPX-encoding genes: CPX-1 has a putative aminoterminal chloroplast transit peptide, while CPX-2 has an amino-terminal sequence that is more consistent with mitochondrial transit peptides. Both genes are transcribed in all tissues tested but they have distinct expression patterns. The transcription level of cpx-1 is greater than that of cpx-2 in photosynthetic tissues. Neither gene shows light-dependent expression. Redacted for Privacy I have attempted to address the possibility that the two CPX-encoding genes have different roles in maize, and that their products have different cellular locations. One approach was the identification and characterization of cpx mutants to observe whether mutants of cpx-J and cpx-2 have different phenotypes. A transposable element-disrupted cpx-1 allele co-segregates with homozygous dek seed and yellow-lethal seedling phenotypes, consistent with a tetrapyrrole deficiency. In collaboration with Pioneer HiBred Intl. , we identified additional cpx mutants. A plant with a cpx-2 mutant allele appears to develop normally as a homozygote; cpx-1 may complement this deficiency. Another approach was the immunological identification of CPX in protein preparations from isolated chloroplasts and mitochondria. CPX was detected in both the chloroplasts and mitochondria of wild-type plants; however, mitochondrial CPX was not detected in cpx2-578 homozygotes. A third approach was to determine whether the amino-terminal sequence of CPX-2 would mobilize a fusion GFP protein into mitochondria. Maize epidermal cells expressing this construct have mitochondrial-sized foci of GFP localization with some general cytoplasmic background staining. The data supports the theory that CPX1 is chloroplast-localized and participates in tetrapyrrole biosynthesis in that location. CPX-2 is the first mitochondrial-localized CPX enzyme identified in a plant and may function in tetrapyrrole production or the decontamination of excess coproporphyrinogen ffi. ©Copyright by Pascale M Williams September 24, 1999 All Rights Reserved Analysis of Coproporphyrinogen III Oxidase in Maize: the Genes, their Expression, and the Localization of their Products by
The biology of death in Caenorhabditis elegans

The model organism Caenorhabditis elegans has been extensively studied in biogerontology. A putative mechanism of ageing is oxidative damage, but this has been challenged in recent studies. One piece of supporting evidence for the role of molecular damage in C. elegans ageing is the presence of blue fluorescent material within intestinal lysosome related organelles, believed to be lipofuscin. This heterogenous, cross-linked aggregate of oxidatively damaged lipids and proteins that accumulates in an age-dependent fashion in post-mitotic mammalian cells. Lipofuscin can be identified by its fluorescent properties, fluorescing blue under UV light. C. elegans intestinal fluorescence has been equated with lipofuscin based on its similar spectral properties, and its increase in ageing populations. This investigation initially set out to verify this assumption. Individual animals were followed in situ on agar pads and their in vivo fluorescence measured from early adulthood until after death. Intestinal blue fluorescence proved to increase not with age, but instead in a striking burst at death. Such death fluorescence also appeared in young worms when killed, irrespective of age or cause of death. Using NMR-based comparative metabolomics the blue fluorophore was identified as anthranilic acid, derived from tryptophan by kynurenine pathway activity. Death fluorescence is generated within intestinal cells, typically in an anterior to posterior wave, by action of the conserved calpain-cathepsin necrotic cell death pathway, a type of cell death previously only observed during neurodegeneration. Using mutational analysis and in vivo fluorescent reporters, we demonstrate that this wave is propagated by calcium influx. Strikingly, inhibition of systemic necrosis delays stress-induced mortality, demonstrating its role as a driver of organismal death. This first description of the biology of death in C. elegans implies that the passage from life to death entails a regulated, programmed transition that is amenable to analysis.
Pilot Study of PCA3 Quantitative Analysis in Peripheral Blood with Real Time PCR and Non-Contrast Multiparametrics MRI for Prostate Cancer Detection

Prostate cancer is one of major health concerns worldwide. Early detection for prostate cancer is very important since effective treatment is very limited for advanced prostate cancer. Molecular alteration happen prior to any morphological change, and Prostate Cancer Antigen 3 (PCA3) as the most specific marker for prostate cancer had been studied and proved its usefulness in detecting prostate cancer. However, the PCA3 level in peripheral blood remains unclear and only few research focused in the topic. Multiparametric Magnetic Resonance Imaging (mp-MRI) has superiorities in viewing prostate gland, without radiation exposure, also can be used without contrast injection. Early detection should avoid unnecessary medical examinations or interventions that will add up patients’ psychological burden, not to mention health care cost and logistic burdens. This pilot study will quantify PCA3 in blood, and the use of non-contrast mp-MRI for prostate cancer detection. There were 19 patients who met inclusion and exclusion criteria. Evaluation with non-contrast mp-MRI used T2 Weighted Image (T2WI), and Diffusion Weighted Image (DWI). T2WI and DWI image category were based on PI-RADS version 2 criteria, while Apparent Diffusion Coefficient (ADC) value was acquired by defining lesion Region of Interest (ROI) in DWI Sequence. Summation of T2WI and DWI score result in total score. Peripheral blood samples were drawn and analyzed with Real Time Polymerase Chain Reaction (RT-PCR). Distribution table also independent t-test and Mann Whitney test were done, with Receiver Operating Curve (ROC) to find out the cut off value as secondary endpoints.Results revealed that, PCA3 mean level in prostate cancer is 10.996±1.901, mp-MRI median score in prostate cancer is 9 (8:10) with ADC median value is0.542 (0.339:0.768). There is statistically significant difference (p<0.05)in mp-MRI score and ADC value between prostate malignancy and non-malignancy (p=0.005, p=0.022), but there is no significant difference in PCA3 mean level for prostate malignancy and non-malignancy (p=0.851). In conclusion, PCA3 can be quantified from blood sample with mean level in prostate cancer is 10.996±1.901. Total score of non-contrast mp-MRI and ADC value can be used to differentiate prostate malignancy with non malignancy for prostate cancer detection. Further studies with more samples are needed to validate this study.
Detached macrophyte accumulations in surf zones: Significance of macrophyte type and volume in supporting secondary production

Detached macrophytes (sea grass and macroalgae) are transported from more offshore areas and accumulate in large volumes in surf zones, where they are commonly called wrack. In coastal regions in other parts of the world, wrack transported from one habitat to a second habitat can be considered as a "spatial subsidy" for the recipient habitat with significant consequences for community dynamics and food webs. The primary aim of this study was to determine the significance of the different components of wrack (i.e. sea grass and brown, red and green algae) as a direct and indirect food source and habitat for invertebrates and fish in surf zones of south-western Australia. The importance of different volumes of surf zone wrack to determining fish abundance and composition was also investigated. These aims w:ere achieved by examining the food and habitat preference of invertebrates and the habitat preference of fish through laboratory trials and field experiments. Gut content analysis was used to examine the importance of wrack-associated invertebrates as a food source for fish, while stable isotope analysis (carbon, nitrogen and sulfur) and lipid analysis (lipid class and fatty acid composition) were conducted on macrophytes, amphipods and fish to determine the source of nutrients and energy. The composition of surf zone wrack in the region comprises large quantities of seagrass, then brown and red algae, with negligible quantities of green <1;lgae. Allorchestes compressa, the dominant macroinvertebrate in surf zone wrack, showed a preference for consuming brown algae over other macrophyte types. Similarly, stable isotope analysis from some locations and fatty acid analyses indicated that A. compressa assimilates nutrients predominantly from brown algae. The influence of brown algae on secondary production extends to second-order consumers. Allorchestes compressa was the major prey of juveniles of the cobbler Cnidoglanis macrocephalus and the sea trumpeter Pelsartia humeralis, the main fish species in surf zone wrack accumulations in the region. Detached brown algae therefore contributes most to the detached macrophyte amphipod fish trophic pathway in the surf zones, and thus drives secondary production in these regions and provides a crucial link between coastal ecosystems. Detached macrophytes also provide an important, but transient, habitat for invertebrates and fish in south-western Australia. Under laboratory conditions, Allorchestes compressa showed a . strong preference for inhabiting seagrasses over macroalgae,
Summing up the noise

Random fluctuations in genetic networks are inevitable since chemical reactions are probabilistic and many genes, mRNAs and proteins are present in low numbers per cell. Such ‘noise’ affects all life processes and has now been measured directly using green fluorescent protein (GFP). Two studies show that autorepression of replication or transcription suppresses noise and three others4 identify the sources of noise in gene expression – separating the contributions from transcription, translation and the intracellular environment. But they disagree both biologically and mathematically. Here I present a single equation that unifies the mathematical perspectives and resolves the experimental controversies. This connects Biochemical Systems Theory to the fluctuation-dissipation theorem and concepts like susceptibility, time-averaging and disorder.
Methodology of analyzing the InSb semiconductor quantum dots parameters

The investigation of indium antimonide quantum dots has been carried out by the methods of differential normalized tunnel current-voltage characteristics, electron microscopy, particle size analysis and spectral dependence of the absorption coefficient. Qualitatively and quantitatively consistent measurement results were obtained with an error less than 15 %. It is concluded that the analysis of normalized differential tunnel current-voltage characteristics is an effective method of express-analysis that can be used in investigation of quantum-sized objects properties.
Transcriptional responses of tumor cell lines to interferon-alpha

Interferon is an antiviral and antiproliferative cytokine therapeutically applied to treat hepatitis infection and cancer expansion. The beneficial effects of interferon-alpha are dependent on efficient signaling by activation of defined JAK-STAT pathway and the induction of interferon stimulation genes. These genes are translated to proteins with antiviral, antiproliferative, anti-tumor and apoptotic properties. Induction of gene expression is consolidated by binding of interferon activated transcription factors to interferon-specific elements in the promoter of such genes. This interaction is dependent on the accessibility of the chromosomal region given by an open chromatin structure. Some interferon-induced proteins are negatively regulating the signal transduction to avoid overreactions such as triggering senescence and to restore responsiveness to a next round of cytokine stimulation. The response to interferon was characterized using whole-genome gene-expression microarrays. Interferon induced proteins were characterized for their antiproliferative effects by measuring growth in cell culture. These proteins were tagged fluorescently to localize them to cell compartments. Suppressor of cytokine signaling proteins were overexpressed in cancer cell lines and their effect on gene expression was described by genome-wide micro-array analyzes. The epigenetic state in tumor samples was determined, the effect of interferon-alpha on DNA mehtylation was described for one gene and the epigenetic changes documented in embryonic cells defective in a gene involved in DNA damage repair. Our results document antiproliferative action for the interferon-stimulated genes IFI44 and IFITM3. Induction of gene expression can be blocked by overexpression of SOCS1 proteins in cancer cell lines. The epigenetic DNA methylation status is altered in tumor cells and methylation of unique CpG sites can dynamically change during cytokine treatment and may involve a DNA demethylation factor. The interferon-alpha response of cancer cell lines depends on the expression, the inducibility and the epigenetic state of interferon-stimulated genes. The genes studied here are effective in blocking proliferation or signal transduction in interferon-alpha sensitive cell lines. Screening of clinical samples for the expression of these genes or their proteins or determination of the DNA methylation status therein is promising in customization of drug therapy for personalized healthcare.
Distributed consensus of second‐order multiagent systems with nonconvex input constraints

This paper addresses the input constrained consensus of second‐order multiagent systems with nonconvex constraints. A new update law is proposed to make the position states of all agents converge to a common point and the velocities converge to zero, while the input of each agent stays in a certain constraint set. The closed‐loop system is first converted to an equivalent system by taking a novel coordinate transformation. Then, it is proved that the input constrained consensus can be achieved if the graphs jointly have directed spanning trees by using the Metzler matrix theory. Finally, simulations are provided to demonstrate the effectiveness of the proposed algorithm.
COMPARATIVE STUDY OF PRIMARY STABILITY BETWEEN IMMEDIATE PLACED IMPLANTS AND DELAYED IMMEDIATE PLACED IMPLANTS IN MANDIBULAR SINGLE ROOTED TEETH

INTRODUCTION: The timing of implant placement after tooth extraction has been a matter of discussion in dental implant treatment. Primary stability of the implant placed can be measured by the resonance frequency analysis (RFA) which is used to compare the primary stability of immediate and delayed immediate placed implants. OBJECTIVES: This study was designed to compare between primary stability of immediate placed implants and delayed immediate placed implants using resonance frequency analysis device in mandibular single rooted teeth. MATERIALS AND METHODS: Ten patients were selected from Department of Oral and Maxillofacial Surgery, Faculty of Dentistry, Alexandria University divided into two groups, Group A: Five patients indicated for extraction of single rooted teeth had undergone implant placement immediately after tooth extraction (Immediate implant placement). Group B: Five patients indicated for extraction of single rooted teeth had undergone implant placement two weeks after tooth extraction (Delayed immediate implant placement). RESULTS: For group A patients the average mean and standard deviation of the primary stability of the placed implants was 61.75 ± 8.21 ISQ units while for group B patients the average mean and standard deviation of the primary stability of the placed implants was 67.38 ± 11.59 ISQ units. After comparing these results it was shown that the average mean and standard deviation of the primary stability of all cases of group B is greater than the average mean and standard deviation of the primary stability of all cases of group A, which results in a t-value (student t-test) of 0.792 and the p- value of the study was 0.458 which is statistically insignificant. CONCLUSIONS: There is no significant difference between the primary stability of immediately placed implants and delayed immediate placed implants
Inferring community assembly mechanisms from functional diversity patterns: the importance of multiple assembly processes

1. Many studies of community assembly focus on two mechanisms: environmental filtering and competitive interactions. This focus ignores the importance of other assembly processes such as equalizing fitness processes and facilitation. The contribution of different processes to community assembly can be elucidated by examining functional diversity patterns of traits that differ in their contribution to different assembly processes.