Miracle-dz/UniFAR-FTUs huggingface dataset:
High‐resolution transcription maps reveal the widespread impact of roadblock termination in yeast

Transcription termination delimits transcription units but also plays important roles in limiting pervasive transcription. We have previously shown that transcription termination occurs when elongating RNA polymerase II (RNAPII) collides with the DNA‐bound general transcription factor Reb1. We demonstrate here that many different DNA‐binding proteins can induce termination by a similar roadblock (RB) mechanism. We generated high‐resolution transcription maps by the direct detection of RNAPII upon nuclear depletion of two essential RB factors or when the canonical termination pathways for coding and non‐coding RNAs are defective. We show that RB termination occurs genomewide and functions independently of (and redundantly with) the main transcription termination pathways. We provide evidence that transcriptional readthrough at canonical terminators is a significant source of pervasive transcription, which is controlled to a large extent by RB termination. Finally, we demonstrate the occurrence of RB termination around centromeres and tRNA genes, which we suggest shields these regions from RNAPII to preserve their functional integrity.
A Proteome-wide Domain-centric Perspective on Protein Phosphorylation

Phosphorylation is a widespread post-translational modification that modulates the function of a large number of proteins. Here we show that a significant proportion of all the domains in the human proteome is significantly enriched or depleted in phosphorylation events. A substantial improvement in phosphosites prediction is achieved by leveraging this observation, which has not been tapped by existing methods. Phosphorylation sites are often not shared between multiple occurrences of the same domain in the proteome, even when the phosphoacceptor residue is conserved. This is partly because of different functional constraints acting on the same domain in different protein contexts. Moreover, by augmenting domain alignments with structural information, we were able to provide direct evidence that phosphosites in protein-protein interfaces need not be positionally conserved, likely because they can modulate interactions simply by sitting in the same general surface area.
Development of a new human-like head robot WE-4

The authors have been developing human-like head robots in order to develop new head mechanisms and functions for a humanoid robot that has the ability to communicate naturally with a human by expressing human-like emotion. We were able to simulate four sensations (the visual, auditory, cutaneous and olfactory sensations) of a human five senses by developing WE-3 (W_aseda E_ye No.3_) series since 1995. However, the robot system of WE-3 has become too complex and big from added improvements. Therefore, in 2002, we developed a new human-like head robot WE-4 (W_aseda E_ye No. 4_). We newly added a waist to WE-4, and realized emotional expression with not only the face, but also the upper-half part of the robot body. Also, WE-4 is smaller and lighter from revisions in mechanisms of the robot head In this paper we describe the mechanical features of the human-like head robot WE-4.
Exploring the use of technology pathways to access health information by Australian university students: a multi-dimensional approach

Objective: Mobile wireless communication technologies (MWCT) and social media (SM) networks create pathways for accessing widely available information that are favoured particularly by younger generations. The purpose of this study was to explore the way university students use these communication technologies to access health information. Method: Participants (n = 696), who were recruited via an email invitation, completed an online self-reported survey that collected multi-dimensional data consisting of quantitative, qualitative and spatial statistics. Results: The results indicate that technology was used extensively to search for health information and resulted in positive changes in participants’ behaviours; however they perceived lack of reliability of the information as a pressing issue. Conclusion: The results suggest that appealing, persuasive and reliable MWCT and SM can be used extensively to promote health amongst Australian youth.
Microtubules are involved in anterior-posterior axis formation in C. elegans embryos

Microtubules deliver positional signals and are required for establishing polarity in many different organisms and cell types. In Caenorhabditis elegans embryos, posterior polarity is induced by an unknown centrosome-dependent signal. Whether microtubules are involved in this signaling process has been the subject of controversy. Although early studies supported such an involvement (O'Connell, K.F., K.N. Maxwell, and J.G. White. 2000. Dev. Biol. 222:55–70; Wallenfang, M.R., and G. Seydoux. 2000. Nature. 408:89–92; Hamill, D.R., A.F. Severson, J.C. Carter, and B. Bowerman. 2002. Dev. Cell. 3:673–684), recent work involving RNA interference knockdown of tubulin led to the conclusion that centrosomes induce polarity independently of microtubules (Cowan, C.R., and A.A. Hyman. 2004. Nature. 431:92–96; Sonneville, R., and P. Gonczy. 2004. Development. 131: 3527–3543). In this study, we investigate the consequences of tubulin knockdown on polarity signaling. We find that tubulin depletion delays polarity induction relative to wild type and that polarity only occurs when a small, late-growing microtubule aster is visible at the centrosome. We also show that the process of a normal meiosis produces a microtubule-dependent polarity signal and that the relative levels of anterior and posterior PAR (partitioning defective) polarity proteins influence the response to polarity signaling. Our results support a role for microtubules in the induction of embryonic polarity in C. elegans.
Collaborative representation of Grassmann manifold projection metric for robust multi-spectral face recognition

Spectral face recognition is gaining importance as the information from different bands can lead to robust face representation that are presentation (a.k.a, spoofing) attack resistant. However, the key challenge here is to process the high dimensional spatio-spectral data to extract and represent the reliable data while discarding redundant data information for processing. In this work, we present a new approach to represent the spectral images in a holistic manner by employing the well-known Projection Metric Learning (PML) in Grassmann manifold such that the redundant information from the spectral data is discarded while retaining significant information. The approach is adopted to learn discriminative information from an high dimensional spectral dataset. Further, we propose an extension using collaborative representation of learnt projection metrics for improving the classification accuracy of spectral data. With the extensive set of experiments conducted on a relatively large scale extended-spectral face image database (6048 images) of 168 subjects, we demonstrate the applicability of the proposed framework. The obtained results indicates highest accuracy by achieving a Rank-1 recognition rate of 98.21% in classifying the spectral face images.
Tunable Photoluminescence via Thermally Evaporated ZnS Ultra Thin Films

ZnS thin films have been deposited by thermal evaporation at various deposition rates. By controlling the deposition rate, the position of the maximum in the photoluminescence spectra could be easily tuned from 2.9 to 2.0 eV, which produced a corresponding change in the emission color. The optical and morphological characteristics of the ZnS thin films were measured. The photoluminescence spectra had broad peaks, suggesting a distribution of ZnS nanocrystallites dimensions. Nanocrystallites dimensions were in the range of 1 nm to 3 nm via TEM analyses. The changes in optical properties were potentially attributable to the lattice defects of ZnS crystals, including Schottky defects and the substation of sulfur atoms by oxygen atoms. The color of the resulting light emission was obtained by controlling the deposition rate of ZnS.
Analysis of Fresnel Zone Plates Focusing Dependence on Operating Frequency

The focusing properties of Fresnel Zone Plates (FZPs) against frequency are analyzed in this work. It is shown that the FZP focal length depends almost linearly on the operating frequency. Focal depth and focal distortion are also considered, establishing a limit on the frequency span at which the operating frequency can be shifted. An underwater FZP ultrasound focusing system is demonstrated, and experimental results agree with the theoretical analysis and simulations.
Role of Defects in Swelling and Creep of Irradiated SiC

Silicon carbide is a promising cladding material because of its high strength and relatively good corrosion resistance. However, SiC is brittle and therefore SiC-based components need to be carefully designed to avoid cracking and failure by fracture. In design of SiC-based composites for nuclear reactor applications it is essential to take into account how mechanical properties are affected by radiation and temperature, or in other words, what strains and stresses develop in this material due to environmental conditions. While thermal strains in SiC can be predicted using classical theories, radiation-induced strains are much less understood. In particular, it is critical to correctly account for radiation swelling and radiation creep, which contribute significantly to dimensional instability of SiC under radiation. Swelling typically increases logarithmically with radiation dose and saturates at relatively low doses (damage levels of a few dpa). Consequently, swelling-induced stresses are likely to develop within a few months of operation of a reactor. Radiation-induced volume swelling in SiC can be as high as 2%, which is significantly higher than the cracking strain of 0.1% in SiC. Swelling-induced strains will lead to enormous stresses and fracture, unless these stresses can be relaxed via some other mechanism. An effective way tomore » achieve stress relaxation is via radiation creep. Although it has been hypothesized that both radiation swelling and radiation creep are driven by formation of defect clusters, existing models for swelling and creep in SiC are limited by the lack of understanding of specific defects that form due to radiation in the range of temperatures relevant to fuel cladding in light water reactors (LWRs) (<1000°C). For example, defects that can be detected with traditional transmission electron microscopy (TEM) techniques account only for 10-45% of the swelling measured in irradiated SiC. Here, we have undertaken an integrated experimental and modeling effort to discover the previously invisible defects in irradiated SiC and to determine the contributions of these defects to radiation swelling. Knowledge of the most stable defect structures and the rate controlling processes during defect evolution is essential for development of predictive models for swelling and creep as a function of temperature and radiation dose. This research has been enabled by state-of-the-art imaging techniques, such as the aberration corrected scanning transmission electron microscopy (STEM) (FEI TITAN) closely coupled with multi-scale models of stable defect clusters and their evolution. « less
Reporting on Internationalization of Operations, GLOBOP: Design and Management of Global Supply Chains

The research project entitled Design and Management of Global Supply Chains (GLOBOP) focuses on the specific model configuration stages with productive multi location and new productive implantations, which affect the design of productive and logistic systems, and the associated supplier network design. This research project aims to offer a methodological and technical solution for those companies that have begun an internationalization process in recent years (late movers).
AN ASSESSMENT OF SOIL EXTRACTION METHODS FOR PREDICTING THE SILICON REQUIREMENT OF SUGARCANE

Crop and sucrose loss from Eldana saccharina Walker (Lepidoptera: Pyralidae) damage still ranks as being the most important factor limiting productivity in the South African sugar industry. Recent studies at the South African Sugarcane Research Institute (SASRI) have emphasised the important role of applied silicon (Si) in improving the resistance of sugarcane to eldana infestation, especially in the more susceptible varieties such as N26 and N30. Available results from trials have indicated that the silicon requirement of sugarcane is predominantly a function of soil type, and properties such as soil pH, texture, organic matter and plant available silicon. This paper documents the results of recent glasshouse and laboratory studies of six published soil test procedures to determine the soil extractant that showed the best correlation with silicon uptake and prediction of a yield response to applied Si in sugarcane.
Microbiome-based companion diagnostics: no longer science fiction?

In the last decade, our knowledge on the role of the gut microbiome in health and disease has greatly increased, accompanied by an unseen hype around both its diagnostic and therapeutic potential. Yet, one application area of the microbiome has thus far remained understudied: its role as guidance for therapeutic decisions, treatment monitoring and prediction of response. In this issue of Gut , Mondot et al 1 investigate to what extent the microbiome can both inform us on as well as contribute to treatment outcome in resection surgery for Crohn's disease (CD). Although often the only resort next to dilatation,2 this intervention is not curative, with first-year endoscopic recurrence rates at 28–93% and frequent necessity of reoperation.3 As such, there is an important need for effective postoperative maintenance strategies and predictions for postoperative outcome. In a longitudinal study of both the faecal and mucosa-adherent microbiota in 20 patients undergoing resection surgery, Mondot et al describe the microbial groups recolonising the intestinal lining around the anastomosis and show different trajectories in recurring patients versus those in remission; the latter were found to exhibit …
Housing Booms, Manufacturing Decline, and Labor Market Outcomes

We study the extent to which manufacturing decline and local housing booms contributed to changes in labor market outcomes during the 2000s, focusing primarily on the distributional consequences across geographical areas and demographic groups. Using a local labor markets design, we estimate that manufacturing decline significantly reduced employment between 2000 and 2006, while local housing booms increased employment by roughly the same magnitude. The effects of manufacturing decline persist through 2012, but we find no persistent employment effects of local housing booms, likely because housing booms were associated with subsequent busts of similar magnitude. These results suggest that housing booms “masked” negative employment growth that would have otherwise occurred earlier in the absence of the booms. This “masking” occurred both within and between cities and demographic groups. For example, manufacturing decline disproportionately affected older men without a college education, while the housing boom disproportionately affected younger men and women, as well as immigrants. Applying our local labor market estimates to the national labor market, we find that roughly 40 percent of the reduction in employment during the 2000s can be attributed to manufacturing decline and that these negative effects would have appeared in aggregate employment statistics earlier had it not been for the large, temporary increases in housing demand.
An Arrhythmia Susceptibility Gene in Caenorhabditis elegans*

kcne are evolutionarily conserved genes that encode accessory subunits of voltage-gated K+ (Kv) channels. Missense mutations in kcne1, kcne2, and kcne3 are linked to congenital and acquired channelopathies in Homo sapiens. Here we show an unique example of conservation of kcne activities at genetic, physiological, functional, and pathophysiological level in Caenorhabditis elegans. Thus, mps-4 is the homologue of kcne1 that operates in human heart and inner ear. Like its KCNE relatives, MPS-4 assembles with a Kv channel, EXP-2, to form a complex that controls pharyngeal muscle contractility. MPS-4 modulates EXP-2 function in a similar fashion as KCNE proteins endow human channels. When defective, MPS-4, can induce abnormal repolarization by mechanisms that resemble the way KCNE proteins are thought to provoke arrhythmia in human heart. Mutation of a conserved aspartate residue associated with human disease (MPS-4-D74N) alters the functional attributes of the C. elegans current. Taken together these data underscore a significant conservation of KCNE activities in different pumps. This implies that C. elegans can develop into a system to study the molecular and genetic basis of KCNE-mediated muscle contractility and disease states.
Mitochondrial metabolic function assessed in vivo and in vitro

Purpose of reviewMitochondrial content and function vary across species, tissue types, and lifespan. Alterations in skeletal muscle mitochondrial function have been reported to occur in aging and in many other pathological conditions. This review focuses on the state of the art in-vivo and in-vitro methodologies for assessment of muscle mitochondrial function. Recent findingsClassic studies of isolated mitochondria have measured function from maximal respiratory capacity. These fundamental methods have recently been substantially improved and novel approaches to assess mitochondrial functions in vitro have emerged. Noninvasive methods based on magnetic resonance spectroscopy and near-infrared spectroscopy permit in-vivo assessment of mitochondrial function and are rapidly becoming more accessible to many investigators. Moreover, it is now possible to gather information on regulation of mitochondrial content by measuring the in-vivo synthesis rate of individual mitochondrial proteins. SummaryHigh-resolution respirometry has emerged as a powerful tool for in-vitro measurements of mitochondrial function in isolated mitochondria and permeabilized fibers. Direct measurements of adenosine triphosphate production are possible by bioluminescence. Mechanistic data provided by these methods is further complimented by in-vivo assessment using magnetic resonance spectroscopy and near-infrared spectroscopy and the translational rate of gene transcripts.
Facing the challenge of mammalian neural microcircuits: Taking a few breaths may help.

Breathing in mammals is a seemingly straightforward behavior controlled by the brain. A brainstem nucleus called the preBötzinger Complex sits at the core of the neural circuit generating respiratory rhythm. Despite the discovery of this microcircuit almost 25 years ago, the mechanisms controlling breathing remain elusive. Given the apparent simplicity and well-defined nature of regulatory breathing behavior, the identification of much of the circuitry, and the ability to study breathing in vitro as well as in vivo, many neuroscientists and physiologists are surprised that respiratory rhythm generation is still not well-understood. Our view is that conventional rhythmogenic mechanisms involving pacemakers, inhibition, or bursting are problematic and that simplifying assumptions commonly made for many vertebrate neural circuits ignore consequential detail. We propose that novel emergent mechanisms govern generation of respiratory rhythm. That a mammalian function as basic as rhythm generation arises from complex and dynamic molecular, synaptic, and neuronal interactions within a diverse neural microcircuit highlights the challenges in understanding neural control of mammalian behaviors, many (considerably) more elaborate than breathing. We suggest that the neural circuit controlling breathing is inimitably tractable and may inspire general strategies for elucidating other neural microcircuits. This article is protected by copyright. All rights reserved.
p16INK4a Expression in Cervical Lesions Correlates with Histologic Grading - a Tertiary Level Medical Facility Based Retrospective Study

p16INK4a is a tumor-suppressor protein and cyclin-dependent kinase (cdk) inhibitor that blocks cdk4- and cdk6-mediated pRb phosphorylation to inhibit E2F-dependent transcription and cell-cycle progression. Because the E7 protein of high-risk HPVs inactivates pRB, the resulting overexpression of p16INK4a may be a good marker for infection with high risk HPV types. Immunostaining of p16INK4a allows precise identification of even small CIN or cervical cancer lesions in biopsy sections and can help reduce inter-observer variation in the histopathological interpretation of cervical biopsy specimens. The aims of the present study were to evaluate the expression of p16 INK4a in cervical biopsies and to compare the grade of cervical neoplasia with intensity of staining. The study covered 110 cervical biopsy tissue blocks over a period of 2 years, (85 cases of CIN of varying grade and invasive cervical cancers and 25 of non-neoplastic lesions). Immunostaining with p16INK4a antibodies followed standard operating procedures. The results showed an increasing trend for p16INK4a immunoreactivity from benign to higher grade lesions. Out of 25 cases of non dysplasia (15 cervicitis &10 immature squamous metaplasia), 8%(2/25) showed P16INK4a expression (grade 1). Among low grade lesions like CIN1, 32% (8/25) cases demonstrated P16INK4a expression (grade 1). Some 52.3% (11/21) of CIN2 cases proved positive. The intensity of p16INK4a expression in CIN 2 was grade 1 in 33%, grade 2 in 14% and grade 3 in 4.7% of cases. All the CIN3 lesions and cervical squamous cell carcinomas exhibited grade 3 anti p16INK4a antibody staining. The association of p16INK4a expression with histologic grade of cervical pathology was highly significant (χ2-value:51.81, p<0.0001). The staining intensity increase with higher grade disease was also statistically significant (χ2-value :133.95, p<0.0001).
Research of local outlier mining algorithm based on spark

Cluster-based outlier mining algorithm is one of the impotent local outlier mining algorithms, but there are many problems in it. In this paper, we propose an algorithm named CFLDOF to optimize the LDOF algorithm by pruning the dataset with clustering feature trees, then the parallel design of CFLDOF is given, and use the Spark platform to set up improved parallelization algorithm, finally, a comparative experiment is carried out, it is verified that CFLDOF reduces the time complexity, the accuracy is similar to the LDOF.