Miracle-dz/UniFAR-FTUs huggingface dataset:
Analysis of protein kinases regulating the Trypanosoma brucei cell cycle

Trypanosoma brucei spp. are protozoan parasites that cause Human African Trypanosomiasis in humans, and Nagana in cattle. These diseases are mostly fatal if left untreated and there is an urgent need for safe, effective drugs that can be easily administered. T. brucei has a complex cell cycle, the regulation of which appears to be divergent compared to other model eukaryotes. This implies that the regulators of the T. brucei cell cycle could be exploited as a source of novel drug targets. One such cell cycle regulator of interest is T. brucei polo-like kinase (TbPLK), a serine/threonine protein kinase thought to diverge from its canonical functions in eukaryotic mitosis and be mainly involved in the duplication of the parasite’s cytoskeletal structures. This study sought to investigate how the activity and localisation of TbPLK is regulated in procyclic form (PCF) and bloodstream form (BSF) parasites. A second aim of this study was to identify novel protein kinases (PKs) which regulate the T. brucei cell cycle by screening part of a kinome-wide RNA interference (RNAi) library of BSF cell lines, that has recently been established (Jones et al. 2014). The cell lines had already been assessed for proliferation defects upon RNAi induction by using an Alamar blue viability assay. In this study, the cell lines which displayed proliferation defects were further screened for cell cycle defects using growth curves and DAPI staining, to identify as yet uncharacterised protein kinases required for T. brucei cell cycle regulation. 50 PKs had been shown to be required for viability in vitro and were screened for potential cell cycle roles. Of these, 25 were identified as potential cell cycle regulators, 15 of which were detected for the first time. The majority of the hits were deemed to be involved in either just cytokinesis, or cytokinesis in combination with kinetoplast duplication or mitosis, with surprisingly few in G1/S. Knockdown of a number of these putative cell cycle PKs induced cell death signifying their potential as drug targets. Indeed, one of the hits, CLK1, was genetically validated as a potential drug target in a mouse model. The identification of these putative cell cycle kinases has also provided valuable starting points by which the signalling pathways that regulate the cell division cycle of these parasitic organisms can be elucidated.
Emotion recognition model based on the Dempster–Shafer evidence theory

Abstract. Automatic emotion recognition for video clips has become a popular area of research in recent years. Previous studies have explored emotion recognition methods through monomodal approaches, such as voice, text, facial expression, and physiological information. We focus on the complementarity of the information and construct an automatic emotion recognition model based on deep learning technology and multimodal fusion strategy. In this model, visual features, audio features, and text features are extracted from the video clips. A decision-level fusion strategy, based on the theory of evidence, is proposed to fuse the multiple classification results. To solve the problem of evidence conflict in evidence theory, we study a compatibility algorithm designed to correct conflicting evidence based on the similarity matrix of the evidence. This approach is shown to improve the accuracy of emotion recognition.
Predicting firm-level volatility in the United States: the role of monetary policy uncertainty

This paper provides novel evidence for the predictive power of monetary policy uncertainty (MPU) over stock return volatility at the firm level based on a dataset constructed from 9,458 U.S. firms. Our findings show that monetary policy uncertainty contains significant predictive information over realized and implied volatilities at both the firm- and industry-level, with higher policy uncertainty predicting higher volatility in subsequent periods. While the strongest possible volatility effect is observed in the case of Retail Trade, we observe opposite results for Mining with high policy uncertainty predicting lower volatility in this sector. We argue that the dual nature of the underlying commodity for Mining companies, both as a consumption and investment asset, drives the negative effect of policy uncertainty on volatility in this sector. Nevertheless, the findings highlight the predictive information captured by monetary policy actions on the idiosyncratic component of equity market volatility.
Disturbance of Ego-Boundary Enaction in Schizophrenia

Abstract:The psychopathology of schizophrenic conditions is today often characterized merely in diverse and disjunctive symptomatic terms. Classically, however, what was understood to underpin and unify such diverse symptoms was a disturbance to the 'self' or 'ego,' especially in that ego's boundaries. As psychoanalytic and phenomenological theories have become less influential in psychiatry, concepts like 'self' or 'ego,' 'self-other distinction' or 'ego boundary,' have become less popular as psychopathological organizers, with the result that the very idea of distinctively 'schizophrenic' conditions has itself also appeared to want for validity. Yet within the philosophy of psychology, enactivism provides a new naturalistic framework for understanding the emergence and maintenance of the self-other distinction. This framework considers the distinction neither as something constituted a priori, nor as something showing up within experience, but rather as a continuously enacted achievement. The contention of this article is that an enactivist perspective provides us with the apparatus to retheorize the conception of ego boundaries, contribute to the reunification of the 'schizophrenia' concept, and inform the provision of therapies targeted at the schizophrenic diathesis itself.
The role of preMBT transcription in Xenopus development

In most organisms, control of the developmental program involves a regulated transition from maternally supplied mRNAs and proteins to newly synthesized zygotically encoded factors. This phenomena, known as the maternal to zygotic transition (MZT), is observed in a wide range of embryos in the animal and plant kingdoms; in chordates, the MZT typically occurs during midblastula stages, and therefore is often referred to as the midblastula transition (MBT). Early development of most organisms is exclusively maternally controlled, and the zygotic genome of the embryo remains transcriptionally silent until after the MBT, when the transition to zygotic control culminates. Recent work in a number of organisms has identified several genes that are activated prior to the MBT, but whether precocious expression of specific mRNAs is important for later development has not been examined in detail. In this work, I characterize the role of a maternal transcription factor in preMBT transcription, and identify a developmentally significant function for the expression of specific transcripts before the MBT. I identify a class of protein coding transcripts activated before the MBT by the maternal T-box factor VegT, all of which are components of an established transcriptional regulatory network required for mesendoderm induction in Xenopus laevis, including the Nodal related ligands xnr5, xnr6, and derrière and the transcription factors bix4, and sox17α. Phosphorylated Smad2, a hallmark of active Nodal signaling, is present before the MBT and preMBT transcription of xnr5 and xnr6 is required for this activation. Furthermore, preMBT activation of the Nodal pathway is essential for mesendodermal gene expression and patterning of the embryo. Together, this work demonstrates that regulated transcription before the MBT is important for the establishment of dorsal mesoderm and the development of the embryo. Degree Type Dissertation Degree Name Doctor of Philosophy (PhD) Graduate Group Cell & Molecular Biology First Advisor Peter S. Klein
Extensive gaps and biases in our knowledge of a well‐known fauna: implications for integrating biological traits into macroecology

Aim Ecologists seeking to describe patterns at ever larger scales require compilations of data on the global abundance and distribution of species. Comparable compilations of biological data are needed to elucidate the mechanisms behind these patterns, but have received far less attention. We assess the availability of biological data across an entire assemblage: the well-documented demersal marine fauna of the United Kingdom. We also test whether data availability for a species depends on its taxonomic group, maximum body size, the number of times it has been recorded in a global biogeographic database, or its commercial and conservation importance.
A review of Canadian Arctic killer whale (Orcinus orca) ecology

The killer whale (Orcinus orca (Linnaeus, 1758)) is a widely distributed marine predator with a broad ecological niche at the species level with evidence of specialization and narrow ecological niches among populations. Their occurrence in Canadian Arctic waters is limited by sea ice and it has been suggested that climate warming, which has caused increases in the area of ice-free water and duration of the ice-free season, has led to an increased killer whale presence during the open-water period. In this review, we summarize our knowledge of Canadian Arctic killer whale demographics and ecology, synthesizing published and previously unpublished information in a single document. More specifically, we summarize our knowledge of killer whale population size and trends, distribution and seasonality (including results from recent satellite-tracking studies), feeding ecology, and threats, and identify research priorities in the Canadian Arctic. Despite increased research efforts during the past decade, our demographic and ecological knowledge remains incomplete. An improved ecological understanding is necessary for effective management of killer whales and their prey, species of ecological, economic, and cultural importance to Canadian Inuit and the marine ecosystem. This knowledge will allow us to better understand the ecological consequences of a changing Arctic climate.
Risk Profile, Secure Bond, and Bond Rating in Banking Industry

The research aimed to assess the impact of the Risk Profile on the banking industry bond ratings in Indonesia Stock Exchange (IDX) and have a rating for bonds at PT PEFINDO. Sampleswere selected by purposive sampling method. The population were banks listed on the Indonesia Stock Exchange in 2015-2018. The population was 44 banks and 16 banks were selected as samples. The analysis a used descriptive statistics and Partial Least Square (PLS) for testing structural and structural models. The results show that Non-Performing Loan (NPL)and Loan to Deposit Ratio (LDR) directly have a significant direct positive effect on bond ratings, and security directly do not have a significant effect on bond ratings, security strengthen risk relationships credit with a bond rating. However, security weakens the relationship between liquidity risk and the bond rating. The variables indicate that these variables can explain the bond rating of 44,4% while the remaining 55,6% is influenced by other variables not contained in the research model.
Antioxidant capability and potableness of fresh cloudy wheat beer stored at different temperatures

To investigate the sensory evolution and antioxidant capacities and their correlation with related indices of fresh cloudy wheat beer (FCWB), the beer was stored at different temperatures and analysed during an 18-day storage period. A fresh balance of aroma, taste and mouthfeel was maintained for 9days at 5°C, 6 days at 10 and 15°C, or 3 days at 20°C. With extension of storage, the colour and the thiobarbituric acid (TBA) value of the FCWB increased remarkably, while the turbidity decreased remarkably. Colour, turbidity and the TBA value were significantly influenced by storage temperature. The ferric reducing antioxidant power (FRAP), 2,2-diphenyl-1-picrylhydrazyl (DPPH) and superoxide anion (O2 · –) scavenging activities declined, and the storage temperature significantly influenced the FRAP and the DPPH radical scavenging activities in sequence, except for the O2 · – scavenging activities of the FCWB. In addition, colour and turbidity remarkably influenced the FRAP, O2 · –and DPPH scavenging activities. It was suggested that the FCWB had an admirable antioxidant capacity under the potableness conditions (9 days at 5°C, 6 days at 10 and 15°C, or 3 days at 20°C). Copyright © 2013 The Institute of Brewing & Distilling
The effects of Urtica dioica L. ethanolic extract against urinary calculi in rats

Nephrolithiasis is common urological problem and stone formation has multiple underlying pathogenetic factors. We investigated the possible preventive and therapeutic effects of Urtica dioica ethanol extract (UD) on ethylene glycol-induced nephrolithiasis model in rats. Sprague-Dawley rats were divided into four groups (n = 10). The control group was given normal drinking water for 8 weeks and was administered vehicle by gastric gavage. Stone formation was induced by adding 0.75% ethylene glycol (EG) to their drinking water. UD (700 mg/kg) was given orally for 8 weeks to the preventive group and for last 4 weeks to the treatment group, respectively. At the end of the experiment, urine, blood samples and kidney tissues were obtained. In 24-hour urine samples, calcium and citrate levels were decreased and oxalate levels were increased in EG group whereas UD treatment groups reversed these parameters back to control levels. In addition, serum levels of creatinine and urea were increased in EG group, while UD significantly reduced these parameters. Malondialdehyde, 8-hydroxydeoxyguanosine and tumor necrosis alpha levels, and caspase3 and N-acetyl-β-glucosaminidase activities were elevated in EG group and showed a decrease in UD treated groups. Glutathione level was decreased in EG group, whereas it was increased in UD preventive group. Histological examination showed an improvement in UD treated groups. Our results suggest that UD is effective both in prevention and treatment for kidney stones. The mechanism underlying this effect may be the antioxidant effect of UD and the effect on the concentration of stone-forming components in the urine.
Fluctuating asymmetry is a function of population isolation in island lizards

We measured the level of fluctuating asymmetry (FA) in head shape, head scalation and femoral pores in two lizard species (Podarcis bocagei and Podarcis hispanica) from 13 islands and 15 mainland localities in the Ria de Arosa archipelago of north-western Spain. Given the recent geological history of the region, the degree of isolation to which lizard populations have been subjected can be ordered along a spatio-temporal gradient, yielding the following hypotheses to be tested: FA will be higher (1) in island populations than in mainland populations; (2) on remote islands than on islands close to the mainland; (3) on small islands than on large islands. Molecular genetic data suggest that P. hispanica is autochthonous in the Ria de Arosa, whereas P. bocagei is a more recent arrival. Therefore, we predict also (4) a higher level of FA in P. hispanica than in P. bocagei. Statistically significant results were obtained for head-shape asymmetry, supporting the second and the fourth hypotheses. With an overall meristic asymmetry index, none of the hypotheses were corroborated, whereas for certain independent meristic traits, the first, the third and the fourth hypotheses were partially supported. Both head shape and meristic traits constitute precise measures of FA, but FA is more convincingly expressed in head shape and in single meristic traits than in overall meristic traits asymmetry. We conclude that FA reflects population isolation and may be a good indicator of developmental instability. It seems worthwhile to test for FA in a landlocked system under environmental and genetic stress, for the purpose of conservation biological assessments.
Groundwater Release on Early Mars: Utilizing Models and Proposed Evidence for Groundwater Release to Estimate the Required Climate and Subsurface Water Budget

It has been proposed that groundwater was released onto the early martian surface in several locations, including Meridiani Planum, NE Hellas, Terra Sirenum, the northern lowlands, and Gale crater. We assume that groundwater was released in a manner similar to a groundwater‐fed lake on Earth and then use a combination of a global climate model and mathematical relationships to place lower limit estimates on the early climate and subsurface water inventory that are required for groundwater release to occur at all of these locations. We find that the minimum required conditions are global mean annual temperature >284 K and a subsurface water inventory >496 m global equivalent layer. Additionally, thermal models predict that if such warm conditions occurred from punctuated heating in an otherwise “cold and icy” climate, the warm conditions must have persisted for thousands of years in order to remove the cryosphere and permit groundwater release.
LRRK2 genetics and expression in the Parkinsonian brain

Mutations in LRRK2 have been established as a common genetic cause of Parkinson’s disease (PD). Variation in gene expression of PARK loci has previously been demonstrated in PD pathogenesis, although it has not been described in detail for LRRK2 expression in the human brain. This study further elucidates the role of LRRK2 in development of PD by describing an investigation into the role of LRRK2 genetics and expression in the human brain. The G2019S mutation is a common LRRK2 mutation that exhibits a clinical and pathological phenotype indistinguishable from idiopathic PD. Thus, the study of G2019S mutation is a recurrent theme. The frequency of G2019S was estimated in unaffected subjects that lived or shared a cultural heritage to the predicted founding populations of the mutation, and was found not to be common in these populations. Morphological analysis revealed a ubiquitous expression for LRRK2 mRNA and protein in the human brain. In-situ hybridisation data suggests that LRRK2 mRNA is present as a low copy number mRNA in the human brain. A semi-quantitative analysis of LRRK2 immunohistochemistry revealed extensive regional variation in the LRRK2 protein levels, although the weakest immunoreactivity was consistently identified in the nigrostriatal dopamine region. No difference was observed in the morphological localisation of LRRK2 mRNA and protein in unaffected, IPD or G2019S positive PD subjects. Dysregulation of LRRK2 mRNA expression and the effects of cis- acting genetic variation on these levels were demonstrated. A widespread decrease of LRRK2 mRNA was observed in IPD and G2019S positive PD subjects in comparison to unaffected controls. Furthermore, non-coding genetic variation was also demonstrated to have an effect on the LRRK2 transcriptional activity in PD subjects. Collectively, these findings suggest that LRRK2 has an important physiological role, and a dysregulation in its levels could affect auxiliary mechanisms that contribute to PD pathogenesis. This data also supports the possibility of a shared mechanism contributing to the identical phenotype of IPD and G2019S linked PD.
Hydrochemical and Quality Assessment of Groundwater Resources in Al-Madinah City, Western Saudi Arabia

Fifty-four groundwater samples were collected from Hamra Alasad in Al-Madinah City. The chemical and microbial characteristics of the samples were analyzed and compared with their respective standards. The results revealed that 90.7% of the samples showed higher amounts of NO3. However, 59.3% of the samples were found unfit for irrigation purposes due to a high salinity hazard. Most of the groundwater samples were highly saline, yet no sodicity hazards were anticipated as predicted by sodium adsorption ratio (SAR). Generally, the soluble cations and anions, dissolved salts, boron, and NO3− exceeded the maximum permissible limits for drinking water in most of the samples; however, Pb, Cd, As, Zn, Cu, Ni, Co, Fe, Mn, and Cr were within the permissible limits. Furthermore, 42.6%, 24.1%, 18.5%, 14.8%, 1.9%, and 37.0% of the samples were infected by a total coliforms group, fecal coliform, Escherichia coli, Staphylococcus sp. , Salmonella sp. , and Shigilla sp. , respectively. The water quality index revealed that 3.7% of the samples were good for drinking (class II), and 9.3% were very poor (class IV). The remaining samples were unfit for drinking (class V) due to high salinity and/or microbial contamination. Durov and Piper diagrams revealed that the majority of water samples were of the calcium sulfate–chloride type. Overall, 87% of water samples were inappropriate for drinking purposes, while 77.8% were unsuitable for irrigation.
DEA Performance Measurements in Cotton Production of Harran Plain, Turkey: A Single and Double Bootstrap Truncated Regression Approaches

A single and a double bootstrap of data envelopment analysis examines Harran Plain cotton farming in Turkey. The single bootstrap technique was employed to derive the bias-corrected efficiency values under both constant returns to scale (CRS) and versus variable returns to scale (VRS) technologies while discriminating between the two technologies using a smoothed bootstrap test statistic. Results indicated that the farms operated under VRS technology. Given that VRS technology prevailed across Harran Plain cotton farmers sampled, we then determined factors affecting the bias-corrected technical efficiencies using the double bootstrap technique. Another important finding in the single bootstrap analysis is that cotton farmers in the region have a U-shaped technical efficiency based on the input and output scale. Thus, small-scale farmers tend to use their resources more efficiently in cotton farming than that of both medium- and large-scale farmers. Interestingly, the medium-scale farmers with resource inefficiency are at the forefront of the other two types of farmers (i.e., small-scale and large-scale) on the Harran Plain in Turkey. The results also showed that most of the farm and farmer specific as well as economic factors play a significant role in explaining the technical efficiency values.
TLSM: Tiered Log-Structured Merge-Tree Utilizing Non-Volatile Memory

Log-Structured Merge-tree (LSM-tree) organizes write-friendly and hierarchical structure, which leads to inevitable disk I/O from data compaction occuring between layers. Previous research tried to reduce write bottlenecks of LSM-tree by using non-volatile memory (NVM) to LSM-tree, but write amplification on compaction does not resolved. In this paper, we present tiered LSM (TLSM), a persistent LSM-based key-value database tiering NVM, which is regarded as fast storage device. Our design aims to exploit multi-layered LSM system utilizing NVM and reduce redundant cost on compaction. We address 4 key points: (1) analysis of disk I/O overhead on current LSM-tree, (2) novel design of TLSM preserving the concept of LSM-tree and utilizing NVM, (3) persistent and byte-addressable data compaction minimizing disk write, and (4) tiering policy for increasing usability to TLSM. To implement TLSM-tree, we extended LevelDB, which is a simple LSM-based key-value store. On micro-benchmark DB Bench, the write and read latencies of TLSM are improved up to 34% and 57%, respectively, compared to those of LevelDB-NVM. In evaluation of YCSB, TLSM also reduces the write and read latencies of existing LevelDB up to 25%, 33%, respectively. Furthermore, frequency of write stall and total amount of data write are reduced significantly in TLSM.