Miracle-dz/UniFAR-FTUs huggingface dataset:
Global Analysis of Gene Expression and Identification of Modules in Echinacea purpurea Using Systems Biology Approach

Co-expression analysis is a useful tool to analysis data and detection of genes that act in the same pathway or biological process. Echinacea purpurea is one of the most important medicinal plant of the Asteraceae family that is known as antioxidative and antiviral agent. Despite medicinal importance of E. purpurea, very few reports are available for metabolic mechanisms in this plant. With the aim to elucidate the gene expression profiling and identification of modules in E. purpurea, we performed a systems biology analysis on publicly available transcriptome data. Gene ontology and KEGG pathway enrichment analysis revealed that the unigenes were highly related to the cellular process, primary metabolic process, carbon metabolism and biosynthesis of antibiotics. The coexpression networks divided genes into multiple modules. Of these, module M2 associated with secondary metabolic process. Moreover, a total of 47 transcription factor families such as bHLH, bZIP, C2H2, MYB and WRKY in modules were identified. These findings can provide an overall picture for better understanding the gene expression patterns and common transcriptional mechanisms in E. purpurea.
Improved growth of hydroponically-grown rough lemon (Citrus jambhiri Lush) seedlings treated with kelp and vermi extracts

A substantial number of South African citrus trees are rooted on rough lemon rootstocks. In order to ensure the successful establishment of a high percentage of young citrus trees, it is necessary to ensure that farmers are provided with young vigorous nursery trees that have a large and healthy root system. Vermicast extracts (VE) and liquid extracts from the giant seaweed, Ecklonia maxima (EM), have been used on various crops over the past decades to promote plant growth and development. It is widely reported that plant growth, seedling vigour, water-use efficiency and nutrient-uptake of these crops improves with EM and VE treatments, thereby reducing excessive fertiliser applications. With the improved uptake of nutrients such as nitrogen (N), which is the main component of chloroplasts and proteins involved in the Calvin cycle, it is likely that the application of EM and VE to plants could lead to an improvement in the photosynthetic capacity of plants. The benefits from applications of EM and VE have been attributed to the presence of plant growth regulators/hormones (PGRs) such as auxins and cytokinins. Since seaweed extracts are manufactured using different methods, some of which may include the use of elevated temperatures, acid and/or alkaline hydrolysis of plant material,
The neglected biliary mucus and its phosphatidylcholine content: a putative player in pathogenesis of primary cholangitis—a narrative review article

Primary sclerosing cholangitis (PSC) is a rare progressive cholangitis resulting in cirrhosis and cholangiocellular carcinoma. The pathogenesis is unclear and an effective medical therapy is not available. It is highly associated to ulcerative colitis for which recently a disturbance of the tight junction (TJ) barrier has been claimed as etiologic feature. Genetic mouse models with intestinal TJ disruption showed a defective transport of phosphatidylcholine (PC) to intestinal mucus. Consequently, an ulcerative colitis phenotype developed. In the present study we evaluate whether there is also a paracellular transport of PC through TJ to the apical side of cholangiocytes. As in ulcerative colitis, a TJ defect could lead to deficient PC in biliary mucus. It would impair the protective barrier against aggressive bile acids in bile. Indeed with polarized biliary tumor cells a vectorial transport of PC from basal to luminal side was demonstrated using a transwell culture system. PC was not taken up by the cells but moved paracellularly via TJ to the apical side driven by luminal HCO3− generated by the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) and the anion exchange protein 2 (AE2). If such a TJ-mediated PC translocation to the apical surface of cholangiocytes could be disrupted in a genetic mouse model, a PSC phenotype would be expected. With such an experimental model functional operative therapies can be evaluated. We propose that disruption of TJ mediated paracellular transport of PC to the apical side of cholangiocytes could lead to biliary mucus PC depletion. This may be a pathogenetic factor for development of PSC.
Techniques to deal with imbalanced data in multi-class problems: A review of existing methods

Imbalanced learning is one of the most challenging classification problems in the field of machine learning and has been receiving increased attention over the years due to the necessity of handling real world information which is usually skewed. This effect occurs when one of the classes has a bigger number of examples compared to the rest. When we attempt to classify data in said conditions, machine learning algorithms will be able to correctly identify the majority class examples but will most likely fail when attempting to identify minority class examples, which often end up representing the most valuable information. Several surveys were published in the last few years about approaches to solve the problem. Adding to this issue, when we have a multi-class scenario where the examples to be classified can fall into more than two classes, the accuracy of applied techniques plummets due to their inability to deal with the issue. In the latest years, various techniques were proposed to deal with the matter, and they usually do so by converting the problem into subsets of two-class problems that can be solved by common classifiers. This process is called class decomposition. However, recent studies show that it can cause class overlapping and loss of valuable information. In this study, we address the topic first, by identifying algorithms that deal with multi-class imbalance without using class decomposition and categorizing them based on their approach. Then, we proceed to benchmark the two latest state-of-the-art ensemble algorithms, MBBR and SOUPBagging against each other and see how they perform in 9 real life datasets. The results showcase their ability to handle multi-class imbalance with high accuracy for classifying skewed data. Lastly, a possible future direction in the field is briefly discussed.
Neuronal Activity in the Posterior Cingulate Cortex Signals Environmental Information and Predicts Behavioral Variability during Trapline Foraging

Animals engage in routine behavior to efficiently navigate their environments. This routine behavior may be influenced by the state of the environment, such as the location and size of rewards. The neural circuits tracking environmental information and how that information impacts decisions to deviate from routines remain unexplored. To investigate the representation of environmental information during routine foraging, we recorded the activity of single neurons in posterior cingulate cortex (PCC) in 2 male monkeys searching through an array of targets in which the location of rewards was unknown. Outside the laboratory, people and animals solve such traveling salesman problems by following routine traplines that connect nearest-neighbor locations. In our task, monkeys also deployed traplining routines; but as the environment became better known, they deviate from them despite the reduction in foraging efficiency. While foraging, PCC neurons tracked environmental information but not reward and predicted variability in the pattern of choices. Together, these findings suggest that PCC may mediate the influence of information on variability in choice behavior. SIGNIFICANCE STATEMENT Many animals seek information to better guide their decisions and update behavioral routines. In our study, subjects visually searched through a set of targets on every trial to gather two rewards. Greater amounts of information about the distribution of rewards predicted less variability in choice patterns, whereas smaller amounts predicted greater variability. We recorded from the posterior cingulate cortex, an area implicated in the coding of reward and uncertainty, and discovered that these neurons signaled the expected information about the distribution of rewards instead of signaling expected rewards. The activity in these cells also predicted the amount of variability in choice behavior. These findings suggest that the posterior cingulate helps direct the search for information to augment routines.
Sexual selection, phenotypic plasticity and female reproductive output

In a rapidly changing environment, does sexual selection on males elevate a population's reproductive output? If so, does phenotypic plasticity enhance or diminish any such effect? We outline two routes by which sexual selection can influence the reproductive output of a population: a genetic correlation between male sexual competitiveness and female lifetime reproductive success; and direct effects of males on females' breeding success. We then discuss how phenotypic plasticity of sexually selected male traits and/or female responses (e.g. plasticity in mate choice), as the environment changes, might influence how sexual selection affects a population's reproductive output. Two key points emerge. First, condition-dependent expression of male sexual traits makes it likely that sexual selection increases female fitness if reproductively successful males disproportionately transfer genes that are under natural selection in both sexes, such as genes for foraging efficiency. Condition-dependence is a form of phenotypic plasticity if some of the variation in net resource acquisition and assimilation is attributable to the environment rather than solely genetic in origin. Second, the optimal allocation of resources into different condition-dependent traits depends on their marginal fitness gains. As male condition improves, this can therefore increase or, though rarely highlighted, actually decrease the expression of sexually selected traits. It is therefore crucial to understand how condition determines male allocation of resources to different sexually selected traits that vary in their immediate effects on female reproductive output (e.g. ornaments versus coercive behaviour). In addition, changes in the distribution of condition among males as the environment shifts could reduce phenotypic variance in certain male traits, thereby reducing the strength of sexual selection imposed by females. Studies of adaptive evolution under rapid environmental change should consider the possibility that phenotypic plasticity of sexually selected male traits, even if it elevates male fitness, could have a negative effect on female reproductive output, thereby increasing the risk of population extinction. This article is part of the theme issue ‘The role of plasticity in phenotypic adaptation to rapid environmental change’.
Deep Learning Techniques for Traffic Flow Prediction in Intelligent Transportation System: A Survey

Intelligent Transportation System (ITS) intends to provide progressive services linking different modes of transportation and related service system. Road transportation is one of the major and complex entity of the traffic management system. Traffic flow prediction (TFP) contributessignificantrole inpredicting various parameters for road transportation thatgenerates stochastic and nonlineardata through sensors. Traffic flow is demarcated as the average number of vehicles present in a specific region given the historical flow data.Accurate forecasting of macroscopic parameters such as volume, density, speed and flowof traffic can improve the efficiency of traffic management system.In order to predict traffic flow, spatial and temporal traffic features act as a raw data input for the predicting models. Most of the shallow models are incapable to reveal bothspatiotemporal information in big data. Deep neural networks (DNNs) have recently highlighted the potentiality of capturing andextracting important features for various application frommassive dataset.Our work depictsthe current state-of-the-art deep learning techniques (DL) and itsinspirations in TFP incorporating various contextual factorssuch as construction zones, weather conditions, special events, traffic incidents, weekdays and holidays apart from spatiotemporalfeatures for predicting the flow.Finally, provides open challengesyet to be exploredfurther for enhancing deep learning techniques and approachesin forecasting accurate flow.
StormGraph: A graph-based algorithm for quantitative clustering analysis of diverse single-molecule localization microscopy data

Clustering of proteins is crucial for many cellular processes and can be imaged at nanoscale resolution using single-molecule localization microscopy (SMLM). Ideally, molecular clustering in regions of interest (ROIs) from SMLM images would be assessed using computational methods that are robust to sample and experimental heterogeneity, account for uncertainties in localization data, can analyze both 2D and 3D data, and have practical computational requirements in terms of time and hardware. While analyzing surface protein clustering on B lymphocytes using SMLM, we encountered limitations with existing cluster analysis methods. This inspired us to develop StormGraph, an algorithm using graph theory and community detection to identify clusters in heterogeneous sets of 2D and 3D SMLM data while accounting for localization uncertainties. StormGraph generates both multi-level and single-level clusterings and can quantify cluster overlap for two-color SMLM data. Importantly, StormGraph automatically determines scale-dependent thresholds from the data using scale-independent input parameters. This makes identical choices of input parameter values suitable for disparate ROIs, eliminating the need to tune parameters for different ROIs in heterogeneous SMLM datasets. We show that StormGraph outperforms existing algorithms at analyzing heterogeneous sets of simulated SMLM ROIs where ground-truth clusters are known. Applying StormGraph to real SMLM data in 2D, we reveal that B-cell antigen receptors (BCRs) reside in a heterogeneous combination of small and large clusters following stimulation, which suggests for the first time that two conflicting models of BCR activation are not mutually exclusive. We also demonstrate application of StormGraph to real two-color and 3D SMLM data.
Assessment of Iodine Deficiency in Pregnant Women and Neonates in the Capital Territory of Pakistan

One of the major nutritional problems in Pakistan is the deficiency of iodine in different groups of population, e.g., pregnant women and neonates. The neonates and their expectant mothers have been significant target groups of the population to be studied for the deficiency of iodine. The objective of the present research work was to evaluate the status of iodine deficiency in neonates and their mothers in Islamabad, Pakistan. A hospital based study was carried out on two hundred sixty one pregnant women and one hundred twenty five neonates of these women, to find out iodine level among these samples. Fifty healthy and non pregnant women were used as control in the maternity and gynecological unit of the hospitals of Islamabad. The status of iodine of the pregnant and non-pregnant women was assessed by catalytic reduction method. Thyroid function was assessed by determining the concentration of TSH in the cord blood of neonates using radioimmunoassay technique, in the environmental laboratory of the Chemical and Materials Engineering Department at Pakistan Institute of Engineering and Applied Sciences (PIEAS) Islamabad. Ninety-four percent pregnant women and ninety-eight percent non-pregnant women exhibited urinary iodine concentration (UIC) between 20 µg/L to 99 µg/L respectively. It indicates that there was severe to mild iodine deficiency in population of study area. The median values of urinary iodine concentrations in the pregnant women and control group were 30.37 µg/L and 19.08 µg/L respectively. Statistically it was found that there was a significant (p 0.05) difference in the concentration of urinary iodide between the pregnant women of different age groups. An overall 57.14% neonates exhibited TSH levels >5 mIU/L. From these results, it is concluded that the pregnant women had moderate iodine deficiency while their neonates had severe iodine deficiency. Keeping in view these results it is suggested that the practice of iodized salt utilization could be continued, and it is recommended that the screening of neonates or TSH levels should be compulsory in the iodine deficient areas.
Climate niche conservatism and complex topography illuminate the cryptic diversification of Asian shrew‐like moles

The drivers of extraordinary species diversity and endemism in biodiversity hotspots remain elusive. To identify such drivers, it is necessary to understand the origin of allopatric cryptic diversity that formed as an important part of the biodiversity in low‐latitude montane areas. Here, we test hypotheses regarding the patterns and processes that underlie the diversity of Asian shrew‐like moles (Uropsilus, Uropsilinae, Talpidae), which exhibit strikingly high cryptic diversity. Specifically, we test the hypotheses that niche conservatism and complex topography explain the largely cryptic diversification of these small montane mammals.
Pengaruh Risk Based Capital, Premium Growth Dan Beban Klaim Terhadap Profitabilitas (studi Kasus Pada Perusahaan Asuransi Jiwa Yang Terdaftar Di Otoritas Jasa Keuangan Tahun 2013-2018)

ABSTRAK Penelitian ini bertujuan untuk mengetahui pengaruh risk based capital, premium growth dan beban klaim terhadap profitabilitas pada Perusahaan Asuransi Jiwa yang terdaftar di Otoritas Jasa Keuangan tahun 2013-2018. Alat ukur yang digunakan yaitu risk based capital menggunakan rasio risk based capital, premium growth menggunakan rasio premium growth, beban klaim menggunakan rasio beban klaim dan profitabilitas menggunakan rasio return on asset. Populasi yang dalam penelitian ini yaitu Perusahaan Asuransi Jiwa yang terdaftar di Otoritas Jasa Keuangan tahun 2013-2018. Penelitian ini memiliki 15 sample dan periode penelitian selama 6 tahun yang menghasilkan 90 data dengan cara teknik purposive sampling. Hasil penelitian ini menunjukan bahwa secara simultan risk based capital, premium growth dan beban klaim berpengaruh signifikan terhadap profitabilitas. Secara parsial, risk based capital dan premium growth berpengaruh positif signifikan terhadap profitabilitas, dan beban klaim berpengaruh negative signifikan terhadap profitabilitas. Kata Kunci : Risk Based Capital, Premium Growth, Beban Klaim, Profitabilitas
An Insight into Online Shopping Behaviour among Young Adults in Malaysia

In twenty-first century, online shopping becomes increasingly popular as more people starts to shop online using their smart phones and internet. Online shopping is a process of buying and selling of products and services through internet. The purpose of this paper is to examine online shopping behaviour among young adults in Malaysia. This paper investigates four variables that influence young adults online shopping behaviour namely convenience, customers satisfaction, persived and price level. A survey has been conducted by distributing google form questionnaires through WhatsApps applications.The collected data was analised using both frequencies and multiple regression analyses. The empirical findings of this study shows that convenience, customers satisfaction and price level positively influence the online shopping behaviour among adults. In contrast, persived risk has a negative effect with regards to online shopping. Among the four variables, convenience, persived risk and price level were found to be significant while consumer satisfaction was not.
Anthelmintic resistance in naturally infected sheep flocks of Cuddalore district, Tamil nadu

Anthelmintic resistance against commonly used anthelmintics (ivermectin, levamisole, and fenbendazole) was studied in naturally occurring gastrointestinal (GI) nematodes in adult sheep flocks of Cuddalore district, Tamil Nadu by using Faecal egg count reduction tests (FECRT) and also to determine the efficiency of anthelminitics (fenbendazole, levamisole and ivermectin) used for treatment against nematode parasites. The results of the present study revealed high levels of anthelminitic resistance to Fenbendazole treated sheep flocks in Cuddalore district with the reduction of 50 89 per cent, whereas, a low resistant to Levamisole with the faecal egg reduction of 93 95 per cent. Ivermectin was found to be effective in controlling nematodes in all the sheep farms. The posttreatment (fenbendazole and levamisole) larval culture revealed the presence of Haemonchus contortus larvae.
Analysis and Synthesis of Novel Inhibitors of MMPs and other Biological Targets

i Acknowledgements . i i Table of Figures . iv Chapter 1: Introduction . 1 2.1 Overview of Proteinases . 2 2.2 Matr ix Metal loproteinases . 3 2.2.1 Structure and Function . 4 2.3 Regulation of MMPs . 6 2.3. 1 Transcriptional . 7 2.3. 2 Post-transcriptional . 8 Secretion and Activation . 8 Inhibition . 9 Other Post-transcriptional Regulation . 10 2.4 MMPs in Disease . 11 2.4. 1 MMPs roles in non-malignant diseases . 12 2.4. 2 MMPs roles in malignant diseases . 13 Chapter Summary . 13 Chapter 3: Experimental . 16 Compound 2: 3-amino-3-phenylpropanoic acid or Beta-phenylalanine . 17 Compound 3: 3-amino-3-phenylpropanoic acid methyl ester or Betaphenylalanine methyl ester . 18 Compound 4: methyl 3-[3-(benzyloxy)-2-[(tertbutoxycarbonyl) amino]propanamido]-3-phenylpropanoate . 19 Compound 5: methyl 3-[2-amino-3-(benzyloxy)propanamido]-3phenylpropanoate . 20 Compound 6: methyl 3-[3-(benzyloxy)-2-(5-phenylpentanamido) propanamido]-3-phenylpropanoate . 21 Compound 7: 3-[3-(benzyloxy)-2-(5-phenylpentanamido) propanamido]3-phenylpropanoic acid . 22 Chapter 4: Results and Discussion . 23 Chapter 5: Conclusion . 26 References . 28 Appendices . 32 Appendix A: NMR Data . 32
Role of Arterial Wall Antioxidant Defense in Beneficial Effects of Exercise on Atherosclerosis in Mice

The mechanism(s) by which exercise reduces atherogenic risk remains unknown. This study tested the hypothesis that sustained exercise-induced oxidative stress may increase antioxidant defense in the arterial wall. Acute exercise induced an increase in antibodies to oxidatively modified proteins and catalase in the aortic walls of normal mice compared with sedentary control mice. In male atherogenic diet-fed low density lipoprotein (LDL) receptor-deficient mice, exercise lowered plasma cholesterol (15%) and decreased atherosclerotic lesions by 40% compared with values in sedentary control mice, with a concomitant increase in arterial catalase and endothelial NO synthase. Because these mice lack the LDL receptor, the results indicate that the LDL receptor might not be responsible for the exercise-induced lowering of plasma cholesterol. Vitamin E supplementation to exercising LDL receptor-deficient mice did not reduce atherosclerotic lesion formation significantly as opposed to lesion formation in untreated .
Reception Analysis of Androgyny According to College Student

Androgini's presence began to be known through the style of dress displayed by celebrity on Instagram, Jovi Adhiguna. The purpose of this study was to find out how the audience's understanding and acceptance of the style of androgynous dress worn by Jovi Adhiguna in his personal Instagram account used reception analysis theory. This research is a qualitative research by conducting interviews with four informants from among students with different socio-cultural backgrounds. The data obtained were then analyzed using the Stuart Hall reception analysis method. The results of this study indicate that there are diverse meanings of the audience in interpreting the style of androgyny of Jovi Adhiguna based on their experience and social and cultural background.