Miracle-dz/UniFAR-FTUs huggingface dataset:
OP-CBIO190828 1..4

Motivation: The existence of complex subpopulations of miRNA isoforms, or isomiRs, is well established. While many tools exist for investigating isomiR populations, they differ in how they characterize an isomiR, making it difficult to compare results across different tools. Thus, there is a need for a more comprehensive and systematic standard for defining isomiRs. Such a standard would allow investigation of isomiR population structure in progressively more refined sub-populations, permitting the identification of more subtle changes between conditions and leading to an improved understanding of the processes that generate these differences. Results: We developed Jasmine, a software tool that incorporates a hierarchal framework for characterizing isomiR populations. Jasmine is a Java application that can process raw read data in fastq/fasta format, or mapped reads in SAM format to produce a detailed characterization of isomiR populations. Thus, Jasmine can reveal structure not apparent in a standard miRNA-Seq analysis pipeline. Availability and implementation: Jasmine is implemented in Java and R and freely available at bitbucket https://bit bucket.org/bipous/jasmine/src/master/. Contact: simon.rayner@medisin.uio. no Supplementary information: Supplementary data are available at Bioinformatics online.
AN INVESTIGATION OF THE CAUSAL RELATIONSHIP BETWEEN ENERGY CONSUMPTION AND ECONOMIC GROWTH: A CASE STUDY OF VIETNAM

This article investigates the causal links between economic growth and energy consumption in Vietnam by using Vietnam’s updated data in the period of 1984-2016. The error correction mechanism (ECM) is employed to detect the causal relationship in the presence of co-integration between two variables. Applying Granger’s causality test within an error-correction modeling technique, we find long-run bidirectional Granger causality between energy consumption and economic activities. The source of causation in the long-run is found by the significance of the error correction terms in both directions. In the short-run, the unidirectional Granger causality running from energy consumption to economic growth is also observed. The findings provide implications for energy development strategy to ensure the sustainable economic growth in the long term for Vietnam - a rapid developing country in ASEAN region.
Intersectional Invisibility Revisited

Intersectionality theory allows us to examine how systems of power and oppression (e.g., racism, sexism) co-construct each other to create complex and unique forms of systemic harm and injustice. More particularly, intersectional invisibility provides a framework to understanding how Black women, who live at the intersection of racism and sexism, may be harmed when their unique experiences as Black women are not recognized. This study takes a stereotype content approach to explore how group prototypes result in Black women’s intersectional invisibility. Employing a novel stereotypical attribute awareness task administered to more than 1,000 U.S. adults, we build on previous work regarding prototypes and intersectional invisibility. We also advance a differentiation hypothesis positing that the prototypical Black woman and Black man will be less distinct from each other than the prototypical White woman and White man. Respondents differentiated between White men and White women to a greater extent than they differentiated between Black men and Black women. Black women were also rated as being less similar to women in general than were White women. Using nonmetric multidimensional scaling techniques to visualize prototype similarity, we identify racial and gender dimensions in prototype similarity and depict how various group prototypes cluster along these dimensions. We conclude that demographic group prototypes lead to Black women being erased through masculinization and underdistinction from Black men and excluded through overdistinction from women in general. These findings help to explain Black women’s simultaneous victimization by the criminal legal system and neglect from “single-axis” social justice movements.
Sentiment Analysis on Tweets Using Document Embeddings

Sentiment Analysis is one of the primary areas of natural language processing and information retrieval being tackled by researchers to date, and for good reason; the internet. The internet is a mostly untapped source of rich amounts of data that can be used to gauge the opinions of people, in reference to any number of topics. Twitter is one such platform designed for people to voice their opinions in the form of tweets about any topic they desire. My project will set out to investigate the best way to be able to analyse the sentiment of these aforementioned tweets using machine learning techniques. I will be training word vector-based, and paragraph vector-based models on a dataset consisting of 1.6 million tweets, in conjunction with various classifiers in order to find the best performing method in which to obtain the sentiment of tweets.
A Chinese herbal decoction, Danggui Buxue Tang, activates extracellular signal-regulated kinase in cultured T-lymphocytes

Danggui Buxue Tang (DBT) is prepared from Radix Astragali and Radix Angelicae Sinensis. This Chinese herbal decoction has been shown to stimulate the proliferation of T-lymphocytes; however, the action mechanism of this stimulation has not been revealed. In cultured T-lymphocytes, application of DBT markedly induced the cell proliferation, the release of interleukin-2, -6 and -10, as well as the phosphorylation of extracellular signal-regulated kinases (ERK). The pre-treatment of ERK inhibitor blocked the DBT-induced immune responses. In addition, the polysaccharide-enriched fraction of DBT showed marked responses on the cultured T-lymphocytes suggesting the important role of DBT polysaccharide in triggering such immune responses. 2007 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.
Transferring Needs and Operational Experience from Life‐of‐Field to Engineering functions ‐ a case study from the Subsea Industry

This paper investigates how a company in the subsea industry are transferring needs and operational experience from Life‐of‐Fields functions to Engineering functions, to allow for more holistic life cycle design and to improve engineering solutions. The subsea industry is changing, putting more emphasis on total life‐cycle cost. In order to improve their offerings, suppliers within this industry see the need for more effective utilisation of Life‐of‐Field's needs and operational experience. Challenging communication between Life‐of‐field and Engineering affect transference of needs and operational experience, hindering engineering for life cycle. To research this problem, we investigated the operational process and made in‐depth interviews of relevant personnel at both the Engineering and Life‐of‐field functions of a global subsea supplier. We discovered that suboptimal transference of needs and operational experience between the Life‐of‐Field and Engineering functions results in added work, repetitive design issues and operational inefficiencies from project to project. We found an insufficient organisational process, low prioritisation of cross‐functional feedback together with formal tools not fit for purpose to be the predominant causes for ineffective transferring of needs and operational experience between Life‐of‐Field and the other functions. Suggestions for improving the transference of needs and operational experience are presented based on the findings and analysis.
Concerted control approach with leg force as a conductor

In human locomotion, the complex structure of body is controlled such that conceptual models can describe the significant features. This suggests that the interplay of the complex control and musculoskeletal systems projects into a low dimensional space to perform different movements. Such simplification can involve splitting the task into different modular control subproblems (locomotor subfunctions) that can be solved individually. How locomotor subfunctions could be coordinated to generate repeatable and robust motor commands? Establishing internal sensor-motor mappings between different muscles (actuators in robots) similar to reflex-based control, is considered as a novel approach for design and control of assistive devices such as exosuits and exoskeletons. We suggest utilizing the leg force feedback as interplay among environment, body mechanics, and sensory control to synchronize the decoupled subfunctions. We evaluated this approach in push recovery, attenuating ground drop perturbations and by investigating its sensitivity to the reflex gain as the control parameter.
A Study on Fog Computing Environment Mobility and Migration

—Cloud Computing paradigm has reached a high degree of popularity among all kinds of computer users, but it may not be suitable for mobile devices as they need computing power to be as close as possible to data sources in order to reduce delays. This paper focuses on achieving mathematical models for users moving around and proposes an overlay mobility model for Fog Data Centres based on traditional wireless mobility models aimed at better allocating edge computing resources to client demands. Additionally, the focus is also on providing a model as to how the computing assets related to each user follow it through the fog infrastructure so as to minimise the distance to the user according to a Fat-Tree based Data Centre topology.
OPTH_A_255979 1467..1472

Oculoplasty Unit, Ophthalmology Department, Tanta University, Tanta, Egypt Aim: To evaluate the role of anterior segment–optical coherence tomography (AS-OCT) in the diagnosis of punctal stenosis and to compare punctal parameters before and after medical treatment. Patients and Methods: The study was conducted on 40 eyes of 24 patients who had acquired inflammatory punctal stenosis and had persistent epiphora (persistent epiphora group – PEG), and 20 eyes of 10 subjects with normal punctal openings as a control group (control group – CG). We measured the outer punctal diameter (OPD), recorded the visibility of the internal punctum and punctal depth (PD) using AS-OCT, before and 1 month after treatment with preservative free methylprednisolone 5% eye drops. Punctal diameter, tear meniscus height (TMH) and Munk’s score were compared to the control group before and after treatment. Results: The mean OPD of the PEG before treatment (455.5 ± 174 μm) was significantly smaller than that of the CG (590.9 ± 106.6 μm) (P= 0.002). The mean OPD of the PEG significantly increased to 484.6 ± 175.5 μm after treatment (P <0.001). Also, the visibility of vertical canaliculus lumen and PD were restored in 70% of eyes. The TMH was much higher in the PEG than in the CG before treatment (P<0.05). However, after treatment the difference was not statistically significant. Conclusion: AS-OCT parameters were useful in monitoring and measuring the efficacy of medical treatment in relieving punctal edema, which subsequently resulted in reducing the epiphora symptoms.
A Comparative Study for Different Methods used for ECG Denoising

ECG signal recording easily suffers from interferences of the environment, such as patient movement, position of electrodes etc. For primary diagnosis, doctors need noise-free ECG signals. This paper presents a detailed study of denoising ECG signals using several techniques such as morphological filtering, Stationary wavelet transform (SWT) and discrete wavelet Transform (DWT) etc. The results received from various techniques are evaluated through MATLAB and their performance is analyzed using parameters like Signal to Noise Ratio (SNR)
A Low Complexity Algorithm with O ( √ T ) Regret and O (1) Constraint Violations for Online Convex Optimization with Long Term Constraints

This paper considers online convex optimization over a complicated constraint set, which typically consists of multiple functional constraints and a set constraint. The conventional online projection algorithm (Zinkevich, 2003) can be diﬃcult to implement due to the potentially high computation complexity of the projection operation. In this paper, we relax the functional constraints by allowing them to be violated at each round but still requiring them to be satisﬁed in the long term. This type of relaxed online convex optimization (with long term constraints) was ﬁrst considered in Mahdavi et al. (2012). That prior work proposes an algorithm to achieve O ( √ T ) regret and O ( T 3 / 4 ) constraint violations for general problems and another algorithm to achieve an O ( T 2 / 3 ) bound for both regret and constraint violations when the constraint set can be described by a ﬁnite number of linear constraints. A recent extension in Jenatton et al. (2016) can achieve O ( T max { θ, 1 − θ } ) regret and O ( T 1 − θ/ 2 ) constraint violations where θ ∈ (0 , 1). The current paper proposes a new simple algorithm that yields improved performance in comparison to prior works. The new algorithm achieves an O ( √ T ) regret bound with O (1) constraint violations.
Effects of aging on sperm maturation and fertility in mice

AIM: To investigate the effects of aging on sperm maturation and fertility in mice. METHODS: Sperm of caput epididymides and cauda epididymides were obtained from Kunming mice aged 6 months (n=15, as control) and 18 months ( n=15). Sperm parameters including sperm density, viability, motility and nor mal morphological rate were recorded. Sperm of cauda epididymides was observed b y transmission electron microscope. The fertility potential and embryo developme ntal competence were performed by in vitro fertilization and embryo culture. RESULTS: Sperm motility, density and normal morphological rate i n aged mice were lower than those in control (P0.05). The fertilization ra te and embryo developmental rate of aged group were significantly lower than tho se in control (P0.01). CONCLUSION: Aging influences spermatogenesis in testes and sperm maturation in epididymides. Mouse would be served as a good model for male repr oductive aging research.
Cryptosporidium spp'nin Dişkidan Nested PCR ve Carbol Fuchsin Boyama Yöntemi ile Teşhis Edilmesi

ÖZET: Bu çalışma, hastanelere ishal şikayeti ile başvuran 18 çocuk ve yine ishalli 27 buzağı dışkısı olmak üzere, toplam 45 örnek üzerinde yürütülmüştür. Toplanan örneklerin tümü carbol fuchsin boyama ve nested PCR yöntemleri ile Cryptosporidium spp. yönünden taranmıştır. Carbol fuchsin ile yapılan incelemelerde buzağı dışkılarının 3’ünde (%11,2), insan dışkılarının ise 1’inde (%5,6) olmak üzere, 45 örnekten toplam 4’ünde (%8,9) Cryptosporidium spp. ookistlerine rastlanmıştır. Nested PCR ile ise, buzağı dışkılarının 8’inde (%29,7), çocuk dışkılarının 1’inde (%5,6) olmak üzere toplam 9 (%20) örnekte Cryptosporidum spp spesifik amlifikasyonu gösteren bantlar elde edilmiştir. Sonuç olarak, nested PCR yöntemi ile karşılaştırmalı olarak değerlendirildiğinde, carbol fuchsin boyama yöntemi, her ne kadar tanı açısından özgül (%100) olsa da, duyarlılık açısından (%44) yetersiz kalmıştır. Yapılan çalışma, nested PCR yönteminin kuşkulu ishal olgularında, cryptosporidiosis etiyolojisisnin ortaya konması açısından, uygun bir yöntem olduğunu göstermiştir. Anahtar Sözcükler: Cryptosporidiosis, nested PCR, carbol fuchsin, insan, buzağı
Forward Adaptive Dual-Mode Quantizer Based on the First-Degree Spline Approximation and Embedded G.711 Codec

In this paper, we propose a novel model of dual-mode quantizer that combines the restricted and unrestricted forward adaptive piecewise linear scalar quantizers based on the first degree-spline functions, one of them being forward adaptive G.711 quantizer used as the unrestricted one. The analysis presented in the paper can be considered as our further research in the field of dual-mode quantization. In particular, in our novel model we utilize G.711 codec due to the compatibility reasons and we develop one completely novel model of restricted quantizer based on the first-degree spline approximation, which is optimized for the assumed Laplacian source so that to provide a minimal mean-squared error distortion. More-over, unlike previous dual-model quantizer models that processed signals in frame-by-frame manner, our novel model utilizes frame/subframe processing of the signal in order to decrease the total bit rate. The theoretical analysis in a wide dynamic range of input signal variances reveals that the proposed model of quantizer is superior versus the unrestricted G.711 quantizer as well as other similar baselines having the same number of quantization levels. In addition, the results of the experimental analysis performed on the real speech signal show a good agreement with the theoretical ones
A study on effects of antioxidants in micropropagation of Bael (Aegle marmelos L.)

Bael (Aegle marmelos L.) is a rare endangered medicinal plant, requires rapid mass multiplication and germplasm conservation as it has slow growth and expensive cultivation in nature. Multiplication through in vitro technique has problems of culture media browning which delimits its pace of micropropagation. Present investigation was carried out to study effect of different antioxidants on shoot proliferation and callus induction. Antioxidants viz: activated charcoal, ascorbic acid, citric acid and polyvinylpyrollidone were used to control the accumulation of phenolic compounds in the MS medium and enhance the rate of micropropagation were worked out at most responsive level of plant growth regulators. Supplementation of activated charcoal at concentration of 200 mg/l in the MS medium appeared most optimum level for maximum shoot bud proliferation in nodal segment explants followed by 150 mg/l level of activated charcoal. Maximum callus proliferation in leaf explant was observed using polyvinylpyrrolidone at the rate of 6.0 mg/l followed by at 8.0 mg/l polyvinylpyrrolidone with low intensity of browning in the medium. Further, these optimum levels of antioxidants may be utilized in culture media to enhance growth for mass multiplication of Bael.
A Dual Complexity Gradient Theory of Speech Perception

This article proposes a Dual Complexity Gradient theory of speech perception in the brain. The theory unifies a previously proposed phonetic-to-phonological complexity gradient along the ventral auditory processing stream in the temporal lobe with a recently suggested cortical structure complexity gradient. Findings supporting the theory are discussed as well as its predictions.
MAGIC-II’s central pixel system for simultaneous optical and gamma-ray observation

Abstract. The MAGIC telescopes are a system of two imaging atmospheric Cherenkov telescopes designed to observe very-high-energy γ rays. MAGIC utilizes a large reflective surface and photodetectors with ultrafast time response to capture Cherenkov photons. These features, together with the dedicated system installed in the central photomultiplier tube of their camera, so-called central pixel system (CPS), turn MAGIC into a suitable telescope to study high-speed optical astronomy in the millisecond (ms) regime. We report on the status of the CPS currently mounted in the MAGIC-II camera, its performance and calibration to demonstrate the sensitivity of MAGIC-II to ms optical pulses, for both transient and periodic signals, and discuss its potential over several science cases.
SYBR Green I Real time RT-PCR assay for quantitatively detecting the occurrence of Verticillium dahliae of cotton in naturally infested soil.

In order to explore early detection the occurrence of Verticillium dahliae of cotton in naturally infested soil, a SYBR Green I based Real time RT-PCR assay was developed. The positive plasmid included a 342bp PCR product was used as the reference and the specification curve was created on that basis. The specificity, sensitivity and reproducibility of the curve were evaluated and compared with conventional PCR techniques. The result showed that the Real time RT-PCR assay was rapid, highly sensitive and specific. A linear relationship was observed between the amount of input plasmid DNA and cycle threshold (Ct) values over a range of 3.8×10copies/μL to 3.8×10copies/μL, and correlation coefficient was 0.996. PCR amplification efficiency was
Effect of selected Lactic acid bacteria based- starter cultures on development of curds and their antibacterial properties against some enteric pathogens

As many as 77 lactic acid bacterial strains were isolated from various sources. Out of which 10 promising isolated were based on various probiotic and functional traits. They were further subjected for antibacterial activity tested against common enteric human pathogens such as Listeria monocytogenes, Salmonella typhimurium, Escherichia coli and Staphylococcus aureus. Firstly, the pathogens were tested for their growth on de Man Rogosa Sharpe medium over which these isolates were investigated for their antibacterial activity and zone of inhibition was recorded. Thus, these promising 10 isolated showed a good antibacterial activity which further can be utilized for the development of curds using UASD, Dairy milk. They were also checked with curds prepared with standard industrial cultures. Hence, these isolates hold potential to be used as Lactic acid bacterial starter cultures for the development of curds.
Building Teamwork into an Integrated Extension Program: Faculty Perspectives on Area of Expertise Teams

In today's Extension environment of budget cuts and restructuring, the emphasis on building team programs has become greater than ever. We review the Area of Expertise team structure approach that was initiated at Michigan State University for Extension programming in 1994. Goals were to strengthen integration between campus and field staff, between research and Extension, and between disciplines. We provide an update on team-building within this structure and describe two faculty approaches to joining these, now ongoing, teams. Common experiences and lessons learned are highlighted to guide others in the process of joining diverse team environments in an effective way.
Six Major Historical Earthquakes in the Seoul Metropolitan Area during the Joseon Dynasty (1392–1910)

Earthquake records in the historical literature provide valuable information on the seismic hazard potentials for long recurrence times. The Seoul metropolitan area is the center of the economy and infrastructure in South Korea. Six major earthquakes that occurred around the Seoul metropolitan area during the Joseon dynasty in 1392–1910 are analyzed using a probabilistic joint inversion method based on seismic damage records and earthquake-felt reports. The inversion yields sets of event locations and magnitudes with probabilities. The joint inversion method is validated with synthetic and instrumentally observed data sets. The historical earthquakes are found to be located around the Seoul metropolitan area. The magnitudes of the earthquakes range from ML 5.3 to 6.8 at the peak probabilistic locations. These historical earthquakes suggest considerable seismic hazard potentials in the Seoul metropolitan area.