Miracle-dz/UniFAR-FTUs huggingface dataset:
CryoEM structure of human CENP-A nucleosome alone and in complex with central domain of human CENP-C

Centromere is a chromosome locus necessary for genetic stability during cell division. Centromere is defined epigenetically, by nucleosome containing histone H3 variant, CENP-A, upon which constitutive centromere-associated network of proteins (CCAN) is built. CENP-C, a member of CCAN, is considered to be a blueprint of centromere. It interacts with several CCAN components and directly bridges CENP-A nucleosomes to kinetochore in mitosis. In this study, we provide new molecular details on structure of CENP-A nucleosome alone and in complex with CENP-C central region (CENP-CCR), main CENP-A binding module of CENP-C. We confirm high-flexibility of DNA ends as intrinsic features of CENP-A-containing nucleosomes independent on DNA sequence it wraps. We establish that, in vitro, two regions of CENP-C (CENP-CCR and CENP-Cmotif), both bind exclusively CENP-A nucleosome, albeit CENP-CCR with a higher affinity due to extended hydrophobic area made of CENP-AV532 and CENP-AV533. Finally, we identify conformational changes on CENP-A nucleosome that occur upon CENP-C binding. Pronounced DNA unwrapping is facilitated by destabilization of H2A N-terminal tail and N-terminal tail of H4 is stabilized in the upward conformation favored for CENP-A specific H4K20 monomethylation. Together, our findings provide foundation for understanding epigenetic basis for centromere formation and functioning.
Comparative RNA-Seq Analysis of Differentially Expressed Genes in the Epididymides of Yak and Cattleyak

Background: Cattleyak are the Fl hybrids between (♀) yak (Bos grunniens) and (♂) cattle (Bos taurus). Cattleyak exhibit higher capability in adaptability to a harsh environment and display much higher performances in production than the yak and cattle. The cattleyak, however, are females fertile but males sterile. All previous studies greatly focused on testes tissues to study the mechanism of male infer-tility in cattleyak. However, so far, no transcriptomic study has been conducted on the epididymides of yak and cattleyak. Objective: Our objective was to perform comparative transcriptome analysis between the epididymides of yak and cattleyak and predict the etiology of male infertility in cattleyak. Methods: We performed comparative transcriptome profiles analysis by mRNA sequencing in the epidi-dymides of yak and cattleyak. Results: In total 3008 differentially expressed genes (DEGs) were identified in cattleyak, out of which 1645 DEGs were up-regulated and 1363 DEGs were down-regulated. Thirteen DEGs were validated by quantitative real-time PCR. DEGs included certain genes that were associated with spermatozoal matura-tion, motility, male fertility, water and ion channels, and beta-defensins. LCN9, SPINT4, CES5A, CD52, CST11, SERPINA1, CTSK, FABP4, CCR5, GRIA2, ENTPD3, LOC523530 and DEFB129, DEFB128, DEFB127, DEFB126, DEFB124, DEFB122A, DEFB122, DEFB119 were all downregu-lated, whereas NRIP1 and TMEM212 among top 30 DEGs were upregulated. Furthermore, protein processing in endoplasmic reticulum pathway was ranked at top-listed three significantly enriched KEGG pathways that as a consequence of abnormal expression of ER-associated genes in the entire ER protein processing pathway might have been disrupted in male cattleyak which resulted in the down-regulation of several important genes. All the DEGs enriched in this pathway were downregulated ex-cept NEF. Conclusion: Taken together, our findings revealed that there were marked differences in the epididymal transcriptomic profiles of yak and cattleyak. The DEGs were involved in spermatozoal maturation, mo-tility, male fertility, water and ion channels, and beta-defensins. Abnormal expression of ER-associated genes in the entire ER protein processing pathway may have disrupted protein processing pathway in male cattleyak resulting in the downregulation of several important genes involved in sperm maturation, motility and defense.
The global loss of net primary production resulting from human-induced soil degradation in drylands

This dataset contains spatially explicit data (maps) on the extent of global human-induced dryland degradation as well as its impact on global Net Primary Production (NPP) at a resolution of 5 arc minutes. Data on extent are in percent-per-gridcell representation, data on NPP losses in percent of potential NPP (from Haberl et al, 2007, PNAS, see below). A layer on the global extent of drylands complements the dataset.
Using Bootstrap Procedures To Assess the Issue of Predictive Bias in College GPA Prediction for Ethnic Groups.

In this paper the bootstrap technique was applied to the evaluation of potential predictive bias for different ethnic groups using the Scholastic Aptitude Test (SAT) and high school ranks to predict college grade point averages (GPAs). Data of three ethnic groups were used; the total number of subjects was close to 5,000. Both conventional statistical-significance testing and the bootstrap procedure were used, and the results from the two approaches compared. For the data analyzed, when one predictor (SAT score) was used for GPA prediction, the two approaches provided somewhat different results. Whin two predictors (SAT score and high school rank) were used, the two approaches provided similar results. Where difference occurred, it was suggested that the results from the bootstrap approach might be more plausible. The paper demonstrated the feasibility of applying the bootstrap technique to the research in the area of predictive bias. Because the bootstrap procedure is more empirically grounded, some problems associated with conventional statistical-significance testing may be avoided. Three tablus and four figures are included. (Contains 32 references.) (Author/SLD) *********************************************************************** Reproductions supplied by EDRS are the best that can be made frowthe original document. *********************************************************************** U.S DEPARMIENT OF EDUCATION Office or Educationsi Research and Improvement EDUCATIONAL RESOURCES INFORMATION CENTER IERICI r/nte document has been reprcduced ss received from the person or organization ougtnattng st 0 Minor changes have been mad* to improve reproduction quality Points ot view Of oprhons stated I n this docir ment do no. necessarily represent official OERI posit.on or policy "PERMISSION TO REPRODUCE THIS MATERIAL HAS BEEN GRANTED BY TO THE EDUCATIONAL RESOURCES INFORMATION CENTER (ERIC) Using Bootstrap Procedures to Assess the Issue of Predictive Bias in College GrA Prediction for Ethnic Groups
A STUDY ON SMART CITY IOT PLATFORM WITH MICRO SERVICE ARCHITECTURE

A smart city uses information and communication technologies (ICT) to enhance quality, performance and interactivity of urban services, to reduce costs and resource consumption and to improve contact between citizens and government. Sectors that have been developing smart city technology include government services, transport and traffic management, energy, health care, water and waste. Smart city applications are developed with the goal of improving the management of urban flows and allowing for real time responses to challenges. A smart city may therefore be more prepared to respond to challenges than one with a simple 'transactional' relationship with its citizens.
Walking and Chewing Gum at the Same Time: Australia's Free Trade Area Strategy

The pursuit of free trade area agreements (FTAs), according to some, does not impede the multilateral trade negotiations process. It is argued to the contrary in the present paper that the FTA approach does impede the multilateral one. Comments are offered on common approaches to the analysis of the impact of FTAs, on the reasons why, despite concerns evident in these comments, the FTA strategy has become so popular, and on ways out of a dilemma of FTA proliferation, or at least ways to avoid the risks associated with it.
3D imaging of colorectal cancer organoids identifies responses to Tankyrase inhibitors

Aberrant activation of the Wnt signalling pathway is required for tumour initiation and survival in the majority of colorectal cancers. The development of inhibitors of Wnt signalling has been the focus of multiple drug discovery programs targeting colorectal cancer and other malignancies associated with aberrant pathway activation. However, progression of new clinical entities targeting the Wnt pathway has been slow. One challenge lies with the limited predictive power of 2D cancer cell lines because they fail to fully recapitulate intratumoural phenotypic heterogeneity. In particular, the relationship between 2D cancer cell biology and cancer stem cell function is poorly understood. By contrast, 3D tumour organoids provide a platform in which complex cell-cell interactions can be studied. However, complex 3D models provide a challenging platform for the quantitative analysis of drug responses of therapies that have differential effects on tumour cell subpopulations. Here, we generated tumour organoids from colorectal cancer patients and tested their responses to inhibitors of Tankyrase (TNKSi) which are known to modulate Wnt signalling. Using compounds with 3 orders of magnitude difference in cellular mechanistic potency together with image-based assays, we demonstrate that morphometric analyses can capture subtle alterations in organoid responses to Wnt inhibitors that are consistent with activity against a cancer stem cell subpopulation. Overall our study highlights the value of phenotypic readouts as a quantitative method to asses drug-induced effects in a relevant preclinical model.
MEASUREMENTS OF RADIOGENIC HEAT PRODUCTION ON BASEMENT SAMPLES FROM SITES 897 AND 9001

Concentrations of radionuclides were measured on six samples each from Sites 897 and 900 of Leg 149 in the Iberia Basin and four samples each from three dredge sites located off Galicia Bank. They are used to calculate radiogenic heat production for rocks located in a rifted, nonvolcanic continental margin setting. Results can be separated into three distinct groups: Galicia dredge samples, primarily from granodiorites (Aav = 1.67 ± 0.31 μW/m); Site 900 samples, primarily from metamorphosed gabbros (Aav = 0.21 + 0.19 μW/m); and Site 897 samples of serpentinized peridotites (Aav < 0.01 μW/m). Values for the Galicia Bank granodiorites are lower than typical granitic values observed in Brittany. Values for Site 900 metamorphosed gabbros are higher than typical values for tholeiitic basalts and similar to values for the lower continental crust. Some reduction is probably caused by radionuclide mobility during weathering. However, it is not possible to distinguish these rocks as lower continental crust, rather than lower oceanic crust, based solely on these values. The low values for the serpentinite samples from Site 897 are consistent with low concentrations in mantle peridotites and additional reduction during hydration. For simple models, heat flow across older rifted margins such as Iberia and Galicia Banks should increase from ocean to continent, in proportion to the increased volume of radionuclides in the continental rocks. These results, therefore, suggest that heat-flow observations over the thinned continental crust of the Galicia Bank Margin should be elevated with respect to measurements on the thinned continental (or oceanic) crust of the Iberia Basin. However, a preliminary comparison between seafloor measurements off Galicia Bank and deeper Leg 149 measurements from Sites 897, 898, and 900 indicate just the reverse. Comparable values for both locations are observed in the oceanic/serpentinite ridge domain, but landward values on transitional crust at Site 900 in the Iberia Basin are 16-23 mW/m higher than values landward of the serpentinite ridge on Galicia Bank.
Isolation, Evaluation and Molecular Identification of Streptomyces Isolates with Antimicrobial Activities

Out of sixteen Streptomyces sp. isolates were isolated from root rhizosphere soil of tomato plants. Four isolates coded; C1, 8SW, 30SW and 11SA were selected as the highest antibiotic productivity. The highest records of the antibiotic productivity were 21 and 25 mm as inhibition zones obtained from the original strains 8SW and 11SA after 10 days using E. coli DH-5α as a tester. The highest records of the antibiotic productivity were 12 mm and 11 mm when used Aspergillus niger and Saccharomyces cerevisiae as testers. Three of the four tested Streptomyces isolates i.e. C1, 8SW and 11SA exhibited highly inhibited (31 mm) of the two fungal plant pathogens. Using RAPD and SRAP marker the clustering of tested isolates were different from each other, RAPD marker could be grouped isolates (C1 and 8SW), (30SW and 11SA) to two clusters. However, SRAP grouped isolates (C1, 8SW and 30SW) in one cluster, however isolate 11SA clustered separately. Based on DNA sequences using 16S rDNA the data showed that isolates C1 and 8SW belonged to Streptomyces albidoflavus andisolates 30SW and 11SA were belonged to Streptomyces bobbili. For more accuracy the isolate C1 aligned with all Streptomyces in gene bank and confirmed in belonged to S. albidoflavus.
Girdin is a component of the lateral polarity protein network restricting cell dissemination

Epithelial cell polarity defects support cancer progression. It is thus crucial to decipher the functional interactions within the polarity protein network. Here we show that Drosophila Girdin and its human ortholog (GIRDIN) sustain the function of crucial lateral polarity proteins by inhibiting the apical kinase aPKC. Loss of GIRDIN expression is also associated with overgrowth of disorganized cell cysts. Moreover, we observed cell dissemination from GIRDIN knockdown cysts and tumorspheres, thereby showing that GIRDIN supports the cohesion of multicellular epithelial structures. Consistent with these observations, alteration of GIRDIN expression is associated with a poor overall survival in subtypes of breast and lung cancers. Overall, we discovered a core mechanism contributing to epithelial cell polarization from flies to humans. Our data also indicate that GIRDIN has the potential to impair the progression of epithelial cancers by preserving cell polarity and restricting cell dissemination.
Annual Meeting of the Cognitive Science Society Title Estimating Correlations and Reliabilities of Implicit and Explicit Tests Using a Latent Variable Approach Permalink

In many fields in psychology implicit tests are used to measure some construct of interest, such as priming measures to test implicit memory and the implicit association test to measure implicit attitudes. In sequence learning, reaction times are regarded as an implicit test of sequence knowledge. The validity and interpretation of implicit tests hinges on its relationship with similar explicit tests. Using different explicit measures, both large associations and dissociations have been reported between measures of sequence knowledge. Part of this inconclusiveness of the results may be due to different reliabilities and sensitivities of the measures being used. In this paper, a latent variable model approach is used to assess differences in reliability and sensitivity of reaction times and online prediction performance in a typical sequence learning task, with the aim of arriving at precise estimates of the correlations between implicit and explicit measures of sequence knowledge.
A New Design for Control Method Based on Hierarchical Deficit Round Robin Scheduler for EPON

With the development of ICT (Information and Communication Technology), how to use EPON for ensuring an effective and fair bandwidth allocation as well as the quality of service has become an important issue. Our research is based on Cousin Fair Hierarchical Deficit Round Robin Dynamic Bandwidth Allocation (CFHDRR DBA), which applies the concepts of hierarchical scheduling to reduce extra actions in information controlling and queue switching and DRR (Deficit Round Robin) to attain the goal of cousin fairness. Our research proposes three additional modules to CFHDDR DBA: (1) an admission control module, which limits the sum weight of QoS-controlled flow; (2) a weight partition module, which isolates the sum weight of other interfering flows from QoS-controlled flows; and (3) the quantum adaptation module, which minimizes the access time of QoS-controlled flows through uantum distribution. With the help of OMNet++ simulation software, this research presents the improvement of CFHDRR by introducing dynamic DDR Quantum. In addition, it proposes admission control and bounded weight to keep the sum of flows within service capacity. The simulation result shows that, while keeping CFHDRR’s fairness, the queuing delay is reduced and the cycle time is effectively controlled so that the packet delay of QoS-controlled flows is minimized and QoS of real-time multimedia in EPON is fairly ensured.
The theory of island biogeography and soundscapes: Species diversity and the organization of acoustic communities

On islands, species richness is reduced and interspecific competition relaxed in relation to the mainland, allowing species to use broader ecological niches. These factors are known to affect diet and morphology, but can also affect communication and acoustic signalling in particular. However, no study has ever compared insular and continental soundscapes to determine to which extent islands present reduced acoustic richness (number of co‐vocalizing species) and fewer constraints for vocalizing species.
Utilising genomics of novel uncultivable Chlamydiae to further understand chlamydial diversity, pathogenesis and evolution

The phylum Chlamydiae comprises a diverse group of obligate intracellular bacteria that share a unique biphasic developmental cycle. While many of these bacteria are considered pathogens of humans and animals, particularly in the well-described Chlamydiaceae family, other more distantly related members can be detected in the environment. The limiting factor to studying these diverse Chlamydia-related bacteria is their requirement to be cultured in a host cell, which for many novel and/or Candidatus species, is lacking. To gain insight into the biology and epidemiology of novel bacteria in the phylum Chlamydiae, my project aimed to develop a culture-independent genome sequencing (CIGS) work-flow to characterise the genomes of novel uncultivated chlamydiae in clinical samples. I addressed these aims by applying our CIGS method to two examples encompassing the taxonomic and biological diversity within the phylum, including (a) novel species in the genus Chlamydia from reptiles; and (b) deeply rooted chlamydiae that had previously been identified infecting fish. ; Submitted in the fulfilment of the requirements of the degree of Doctor of Philosophy, University of the Sunshine Coast, 2018.
Modelling of powder sintering using the discrete element method

This paper presents numerical modelling of powder sintering. The numerical model introduced in this work employs the discrete element method which assumes that material can be modelled by a large assembly of discrete elements (particles) of spherical shape interacting among one another. Modelling of sintering requires introduction of the cohesive interaction among particles representing inter-particle sintering forces. Numerical studies of sintering have been supplemented with experimental studies which provided data for calibration and validation of the model. In the laboratory tests evolution of microstructure and density during sintering have been studied. Comparison of numerical and experimental results shows a good performance of the numerical model developed.
Theta power and theta-gamma coupling support spatial memory retrieval

Hippocampal theta oscillations have been implicated in spatial memory function in both rodents and humans. What is less clear is how hippocampal theta interacts with higher frequency oscillations during spatial memory function, and how this relates to subsequent behaviour. Here we asked ten human epilepsy patients undergoing intracranial EEG recording to perform a desk-top virtual reality spatial memory task, and found that increased theta power in two discrete bands (‘low’ 2-5Hz and ‘high’ 6-9Hz) during cued retrieval was associated with improved task performance. Similarly, increased coupling between ‘low’ theta phase and gamma amplitude during the same period was associated with improved task performance. These results support a role of theta oscillations and theta-gamma phase-amplitude coupling in human spatial memory function.
Multiple components of plant diversity loss determine herbivore phylogenetic diversity in a subtropical forest experiment

Plant diversity loss can alter higher trophic‐level communities via non‐random species interactions, which in turn may cascade to affect key ecosystem functions. These non‐random linkages might be best captured by patterns of phylogenetic diversity, which take into account co‐evolutionary dependencies. However, lack of adequate phylogenetic data of higher trophic levels hampers our mechanistic understanding of biodiversity relationships in species‐rich ecosystems. We used DNA barcoding to generate data on the phylogenetic diversity of lepidopteran caterpillars in a large‐scale forest biodiversity experiment in subtropical China. We analysed how different metrics of lepidopteran phylogenetic diversity (Faith's PD, MPD, MNTD) and taxonomic diversity were influenced by multiple components of tree diversity (taxonomic, functional, phylogenetic). Our data from six sampling periods represent 7,204 mitochondrial cytochrome c oxidase subunit I (COI) sequences of lepidopteran larvae, clustered into 461 molecular operational taxonomic units. Lepidopteran abundance, the effective number of species (irrespective of the focus on rare or common species) and Faith's PD and MPD (reflecting basal evolutionary splits), but not MNTD (reflecting recent evolutionary splits), significantly increased with experimentally manipulated tree species richness. Lepidopteran MNTD decreased with increasing tree MNTD. Path analyses showed that tree phylogenetic and functional diversity explained part, but not all of the effects of tree species richness on lepidopteran diversity. Importantly, tree diversity effects on lepidopteran diversity were to a large extent indirect, operating via changes in lepidopteran abundance. Synthesis. Our study shows that evolutionary dependencies determine the response of herbivore communities to changes in host plant diversity. Incorporating a wider range of diversity metrics both at the level of producers and consumers can thus help to develop a more comprehensive understanding of the functional consequences of biodiversity change across trophic levels. Moreover, the dependence of trophic linkages on herbivore abundances underlines the need to address the consequences of current declines in insect abundances for ecosystem structure and functioning.