Miracle-dz/UniFAR-FTUs huggingface dataset:
In silico Analysis for Functional Predicition of Salmonella typhi Gene in Human Infection through Threading Model

via transferring an effector protein into host cells through type III secretion system. This effector protein starts interfering various host mechanisms which helps in bacterial survival. Antibiotics activate the immune system against infection but sometimes bacteria develop resistance by modulating its mechanism. The present study was carried out to explore an uncharacterized gene which may be involved in infection enhancement. YejF gene was selected from transcriptomic data analysis and its function prediction was done by in silico studies with the help of similarity in structure of YejF model to their homologs. This study revealed that YejF protein is a part of transporter family which is enrolled in probably transferring the effector protein into human cells
Towards a System of Distributional National Accounts: Methods and Global Inequality Estimates from WID.world

This paper briefly presents the methodology of Distributional National Accounts (DINA), which distributes total national income and total wealth among all individual residents. With DINA, we can estimate inequality statistics and growth by income and wealth groups that are consistent with aggregate growth from National Accounts. This methodology has been recently applied to a number of countries, and the data produced are available from WID.world. The paper summarizes the initial empirical findings. We observe rising top income and wealth shares in nearly all countries in recent decades, but the magnitude of the increase varies substantially, thereby suggesting that different country-specific institutions and policies matter. We combine countries' statistics to estimate global inequality since 1980. Global inequality has increased since 1980 in spite of the catching up of large emerging countries like China and India. This has been driven by the income growth of top world earners.
Effects of Banco de la Republica’s Communication on the Yield Curve

We analyze the effect on the yield curve of Banco de la Republica’s communication through two specific outlets, the minutes of the monetary policy meetings and the inflation reports during the period 2011-Q2 to 2018-Q4. We extract numeric information from the inflation reports’ fan charts, and narrative information -using Latent Dirichlet Allocation, a computational linguistics tool- from the text of both outlets. We use an event-study approach to analyze the impact on four specific maturities: one-year spot, three-year forward, five-year forward and five-year ahead five-year forward rates. We find no evidence that numeric information has any effect on market yields. Regarding narrative variables we find that (i) for the inflation report, there is a significant effect on just two yields (one-year spot and five-year forward), and (ii) for the minute, there is a significant effect on all yields. We believe that these results may be explained by the publication lag of the inflation report during the period of analysis. **** RESUMEN: Analizamos el efecto, sobre la curva de rendimientos, de la comunicacion del Banco de la Republica mediante dos tipos de documentos, las minutas de las reuniones de politica monetaria y los informes de politica monetaria (anteriormente informes sobre inflacion) durante el periodo 2011-II a 2018-IV. Extraemos informacion numerica de los fan charts publicados en los informes de politica monetaria e informacion narrativa –usando Latent Dirichlet Allocation, una herramienta de linguistica computacional- tanto de las minutas como de los informes. Mediante la metodologia de estudio de eventos analizamos el impacto sobre cuatro diferentes tasas: spot a un ano, forward a 3 anos, forward a 5 anos y forward a 5 anos, dentro de 5 anos. No encontramos evidencia de que la informacion numerica tenga algun efecto sobre estas tasas. Con respecto a las variables narrativas encontramos que (i) para los informes de politica, hay un efecto significativo solo sobre dos de las tasas (spot a un ano y forward a 5 anos) y (ii) para las minutas hay un efecto significativo sobre las cuatro tasas. Creemos que estos resultados pueden explicarse por el rezago de publicacion que tenia el informe de politica monetaria durante el periodo analizado.
Increased Aerosol Extinction Efficiency Hinders Visibility Improvement in Eastern China

Though China has witnessed substantial particular matter pollution mitigation owing to the strict emission control in recent years, the frequency of haze events with low visibility is not improved as much as expected, especially in cold seasons. Here, 6‐year wintertime observations, satellite retrievals, a thermodynamic model, and theoretical calculation were integrated to better understand the complex influence of aerosol chemical composition and hygroscopic behaviors on visibility impairment. We found that the proportion of nitrate in aerosol mass concentration increased by approximately 10% from 2013 to 2018. Such a transition in aerosol chemical compositions together with increasing ambient humidity in past years jointly enhanced aerosol extinction efficiency, and the elevated proportion of nitrate played an increasingly critical role after 2017. The increased aerosol extinction efficiency is responsible for the less improved visibility despite large decrease in aerosol mass concentrations in eastern China.
The development and application of molecular tools for the diagnosis of foot-and-mouth disease in field and low-resource laboratory settings

The requirements for prompt diagnosis of foot-and-mouth disease (FMD) during outbreaks, and the need to establish robust laboratory testing capacity within FMD-endemic countries, have motivated the development of point-of-care tests (POCTs) to support current diagnostic strategies. Despite numerous publications detailing the design of platforms and assays for this purpose, the majority have only been evaluated in laboratory settings, using protocols incompatible for use in challenging environments. To address this gap, this thesis describes the development of an end-to-end molecular toolbox for the detection and characterisation of FMD virus (FMDV) RNA in decentralised settings. A critical review and multiway comparison of seven assay formats and 11 sample preparation methods revealed that reverse transcription loop-mediated isothermal amplification (RT-LAMP) and real-time reverse transcription PCR (rRT-PCR) POCT-formats exhibited comparable analytical and diagnostic sensitivity to their laboratory-based equivalents. Additionally, reagent lyophilisation provided a solution for cold chain and storage considerations, whilst not compromising assay performance. Both assays were compatible with simple sample preparation methods, removing the requirement for nucleic acid extraction. For example, dilution of samples in nuclease-free water enabled FMDV RNA to be detected in multiple sample types (epithelial tissue suspensions, serum, oesophageal-pharyngeal fluid and lesion swabs), from as early as one day post infection. Notably, when the robust field-ready protocols were deployed into challenging low-resource laboratory and field-settings within East Africa, POCT results (rRT-PCR = 144; RT-LAMP = 145) were consistent with clinical observations and a reference rRT-PCR, with FMDV detected from acutely infected as well as convalescent cattle. Furthermore, transitioning of East Africa-specific FMDV-typing rRT-PCR assays (for serotypes O, A, Southern African Territories [SAT] 1 and SAT 2) into a multiplex POCT-format enabled rapid identification of FMDV serotype in situ, confirming active outbreaks of both O and A. This thesis also describes the development of GoPrime, a novel real-time PCR (rPCR) primer/probe validation tool. By parameterising GoPrime with experimental data, collected to investigate the effects of primer/probe-template mismatches on cycle threshold and limit of detection, it was possible to quantitatively predict the performance of rPCR assays in silico. The work of this thesis supports the deployment of molecular POCTs into non-specialised, resource-limited and challenging settings for simple, highly sensitive and rapid detection and/or characterisation of FMDV.
Propidium monoazide-denaturing gradient gel electrophoresis (PMA-DGGE) assay for the characterization of viable diatoms in marine sediments

Molecular-based community profiles often overestimate species richness and diversity as they are incapable of distinguishing DNA signals derived from extracellular or moribund sources from that of viable organisms. Propidium monoazide (PMA), a double stranded DNA-binding dye, was used to selectively isolate the genetic signature of viable diatoms from marine cultures and environmental samples. Upon optimization of photoactivation time using a 600-W halogen lamp, PMA concentrations, and number of treatments, the compromised genetic signals from heat-killed samples, visualized by denaturing gradient gel electrophoresis, were either greatly reduced or removed entirely while those derived from intact, viable samples remained relatively unaffected. Subsequent tests illustrated that bands associated with extracellular and moribund DNA were removed from combinations of viable and nonviable cells initially derived from two sedimentary diatom isolates. In addition, viable and nonviable samples of Skeletonema marinoi that were spiked into fresh deposit-feeder (Balanoglossus aurantiacus) faecal-coil sediments demonstrated the effectiveness of the assay within an environmental matrix. Thus, we propose the use of PMA as a quick and necessary addition to any protocol relying on genetic profiles to discern changes in viable benthic diatom community structure.
A Theory of Proxy Advice when Investors Have Social Goals

This paper develops a theory of the proxy advice market when some investors have nonpecuniary goals such as environmental sustainability and protection of human rights. We assume advisory firms choose their scale of production, price, and “slant” of advice to attract investors with heterogenous preferences over returns and social goals. When the market for advice is small, the industry equilibrium consists of small “boutique” firms that provide a wide array of types of advice, and voting outcomes reflect the distribution of investor preferences. When the market is large, the industry reduces to a single advisory firm using a platform technology, the firm’s advice is slanted toward the preferences of funds with non-value-maximizing goals, and voting outcomes overrepresent the preferences of activist funds. We discuss normative principles for assessing proxy advice when value maximization is not the sole objective of investors.
Experimental and numerical study on the cracking characteristics of repetitive electrohydraulic discharge shock waves

The application of repetitive electrohydraulic shock waves (EHSs) is a developing underwater discharge technology; however, its cracking characteristics on rock under different loading modes are rarely studied. In this paper, an experimental platform of electrohydraulic discharge is built, and test results show that repetitive EHSs can cause obvious macroscopic cracks on samples. A fitting method is proposed for the time-domain waveform of the EHS. The mechanism of the EHS cracking process (liquid–solid interface transmission process, cracking process in rock) is analyzed, and the cracking criterion and fracture zone range of a single EHS on rock are given. In addition, PFC3D simulation is used to establish a three-dimensional numerical model of the test sample under the experimental conditions, and the development characteristics of the damage shape and crack density inside the rock under the action of repetitive EHSs are deeply analyzed. Under different repetitive loading modes with the same loading total energy, the simulation results show the following cracking characteristics: in single-level mode, the crack density is mainly related to the energy of the single loading. The higher the single-loading energy, the more conducive it is to the growth of the number of main cracks, but it will form a crushing zone to cause energy loss; lower single-loading energy is more favorable to the length of main cracks. In the multi-level loading mode, the degraded loading mode has a higher crack density than the upgraded loading mode. Compared to the single-level loading mode, the multi-level loading mode can effectively promote the development of the number and length of main cracks, and effectively reduce the range of the crushing zone. This paper provides theoretical and simulation guidance for the research and application of repetitive EHSs.
Optimization of Nutrient Media of in Vitro Propagation for Some Cherry Rootstocks (Prunus Cerasus)

The most important species of which have origin many populations, land-races and local varieties: wild cherry, wild pears, wild almond, wild medlar, etc. This study was focused in many important rootstocks of P. avium x P canascens - Gisela 6, P.avium x P. pseudocerasus - Colt (nano), P. mahaleb x P.avium (Maxma), P. Mahaleb and cultivar Prunus avium L. (Cerasus avium L. var. sativa Ser., P. cerasus): Bigarreau Hatif. Are used two important media in the micro propagation of the horticultural species above, MS (Murashige & Skoog) and LP (Quoirin & Lepoivre). Nutrients of MS media have affected with sensible changes compare with LP media, in the explants proliferation for differentiations of the buds, shoots and leafs. Inoculation of explants in LP media, results with lower result on the qualitative indicators of the research. Average growing of the shoots on the MS media, resulted 10.1 mm while on the LP media was 6.0 mm. Average number of leafs 2.47 on the MS media, while on the media LP was 1.34 leaf. In the statistic analyses for the min and max, in all the cases it has predominance of the MS media. Intensity of the growing has cv (coefficient of variation) = 63% and on the MS media results 1.88 highest of LP media. Keywords: Murashige & Skoog, Quoirin & Lepoivre, buds, leafs, shoots.
Studies of Inter-and Intra-Molecular Coordination in Cytoplasmic Dynein

Author(s): DeWitt, Mark Alan | Advisor(s): Yildiz, Ahmet | Abstract: Cytoplasmic dynein is one of the principle motors in eukaryotic cells, responsible for most microtubule (MT) minus end-directed motility and force generation processes, including vesicular and organelle transport, and mitotic spindle MT organization. Despite being essential to the maintanence of cellular structure in higher eukaryotes, many aspects of dynein's stepping mechanism have remained enigmatic. In this Dissertation, I directly observe several fundamental aspects of dynein's mechanism, and build a strong framework for future studies. I outline in detail the methods for the fluorescent tracking of motor proteins, including advanced two-color and super-resolution techniques. To study cytoplasmic dynein, I developed a two-color fluorescent tracking assay to simultaneously measure the positions of both heads of the motor while it walks along the MT. The results of this experiment clearly show that dynein steps through a unique mechanism: the heads remain widely separated, and do not appear to coordinate with each other to a significant extent. However, the leading head is less likely to take a step at large inter-head separations, indicating some degree of residual coordination remains. I hypothesized that tension along the linker connecting the two heads is the source of this coordination. Using a high-speed two-color assay, I examined the motility of a homodimeric dynein with a flexible linker between the two heads that decreases inter-molecular tension. Despite this alteration, this homodimer has identical stepping and overall motility properties to wild-type dynein, but has reduced coordination, indicating that coordination is dispensable to motility. Coordination could be achieved by gating one of the heads. I investigated gating using a heterodimeric dynein with a wild-type head and an inactive, tightly-bound head. In this heterodimer, we find that the WT head is gated when widely separated from its inactive partner, but becomes un-gated when immediately behind it, indicating that the gating is caused by extension-dependent changes in linker tension as predicted. I next I turned from inter- to intra-molecular communication. Dynein has six distinct AAA subdomains on its motor head, of which only two AAA1 and AAA3, are essential to robust motility. By reducing MT affinity with added salt, I found that AAA3 is required for robust MT release, and that MT release in turn promotes hydrolysis at AAA1. To investigate coordination between AAA1 and AAA3, I analyzed motility in the presence of a slowly-hydrolyzable ATP analog, ATPγS. I found that ATPγS selectively inhibits the AAA3 site. In the presence of saturating analog, the motor can still take long runs of fast motility, indicating that the hydrolysis cycle of AAA3 is much shorter than AAA1. These results show that AAA1 and AAA3 do not coordinate. Instead, AAA3 acts as a "switch" that controls AAA1-directed release from the MT.
Exploring the Relationship between Customer Loyalty and Financial Performance of Banks: Customer Open Innovation Perspective

In the age of technology, continuous innovation is the ultimate motto of the financial sector to attract customers. Firms in the financial sector must be innovative in terms of service quality and operational performance to obtain customer loyalty and gain financial stability. A dearth of studies on customer loyalty and financial performance of Islamic Banks motivated the authors to examine the relationship between customer loyalty and financial performance. The study also explores whether the service qualities have any impact on customer loyalty. The study uses both primary and secondary data to conclude the research objectives. A survey of 356 questionnaires was carried out among the customers of the selected Islamic banks of Bangladesh to gather information regarding customer service quality and customer loyalty, while financial performance data were attained from the annual reports. Moreover, the study follows the SERVQUAL model’s five dimensions (tangibles, empathy, assurance, reliability, and responsiveness) to determine the service quality of Bangladeshi Islamic Banks. Rigorous statistical techniques, including exploratory factor analysis, reliability testing, and regression analysis were used to investigate the hypothesis. The study empirically documents a positively significant impact of service quality (tangibles, empathy, reliability, and responsiveness) on customer loyalty, while assurance shows an insignificant relationship. Furthermore, the study does not find any significant relationship between customer loyalty and the financial performance of Bangladeshi Islamic Banks. The findings of the study profoundly denote that the financial performance of Bangladeshi Islamic Banks mostly depends on many other financial and non-financial factors, rather than customer loyalty.
Active site alanine substitutions can convert deubiquitinating enzymes into avid ubiquitin-binding domains

A common strategy for studying the biological role of deubiquitinating enzymes (DUBs) in different pathways is to study the effects of replacing the wild type DUB with a catalytically inactive mutant in cells. We report here that a commonly studied DUB mutation, in which the catalytic cysteine is replaced with alanine, can dramatically increase the affinity of some DUBs for ubiquitin. Overexpression of these tight-binding mutants thus has the potential to sequester cellular pools of monoubiquitin and ubiquitin chains. As a result, cells expressing these mutants may display unpredictable dominant negative physiological effects that are not related to loss of DUB activity. The structure of the SAGA DUB module bound to free ubiquitin reveals the structural basis for the 30-fold higher affinity of Ubp8C146A for ubiquitin. We show that an alternative option, substituting the active site cysteine with arginine, can inactivate DUBs while also decreasing the affinity for ubiquitin.
SDFMUCR: Software-defined and fuzzy-based multi-hop unequal cluster routing

Recently, wireless sensor networks play an important role in our life. Researchers give more and more attention to the design of the routing algorithm. Cluster routing is the most popular routing protocol in wireless sensor networks. However, hotspot problem always exists. Unequal cluster routing is an effective method to solve this problem. In these protocols, nodes closer to base station have the smaller cluster size than other sensor nodes. It will reduce the relay pressure of the node which is near to the base station. The development of the software-defined network optimizes the performance of wireless sensor networks. In this article, we propose a software-defined and fuzzy-based multi-hop unequal cluster routing protocol. It adopts three methods to make the routing protocol outstanding. First, it uses a novel software-defined network architecture to reduce computation overhead and energy overhead in sensor nodes. Then, the fuzzy logic–based intracluster and intercluster routing is designed to balance energy consumption. Finally, residual energy–based rotating scheme is proposed to reduce most of the control overhead. According to the simulation results, the proposed protocol balances and reduces the energy consumption, extends the lifetime, and reduces the control overhead and latency of the network.
Differential Responses of Food Web Properties to Opposite Assembly Rules and Species Richness

Trophic niches condition the energetic performance of species within food webs providing a vital link between food web assembly, species diversity, and functioning of ecosystems. Our understanding of this important link is, however, limited by the lack of empirical tools that can be easily applied to compare entire food webs at regional scales. By comparison, with different a priori synthetic models defined according to specific assembly rules (i.e., purely random, limiting similarity, and niche filtering), we demonstrate that a set of food web properties (trophic richness, evenness, and divergence) are controlled by ecological processes. We further demonstrate that although both limiting similarity and niche filtering are statistically significant assembly processes shaping our studied lake food webs, their relative importance is richness-dependent, and contextual to the specific food web property under consideration. Our results have both important theoretical and practical implications. Theoretically, the observed richness-dependent variation on food web properties contradicts the common criticism on food web theory that food web properties are roughly scale-invariant. Practically, these properties can help avoiding spurious conclusions, while providing useful information for multiple food web niche spaces supporting the ecosystem functioning.