Miracle-dz/UniFAR-FTUs huggingface dataset:
Bioaccumulation of Selected Toxic Heavy Metals in Mastacembelus armatus from Three Rivers of Malakand Division, Pakistan

Hazrat Ali1, 2* and Ezzat Khan1* 1Department of Chemistry, University of Malakand, Chakdara 18800, Dir Lower, Khyber Pakhtunkhwa, Pakistan 2Green and Environmental Chemistry, Ecotoxicology and Ecology Laboratory, Department of Zoology, University of Malakand, Chakdara 18800, Dir Lower, Khyber Pakhtunkhwa, Pakistan Article Information Received 08 July 2017 Revised 24 June 2018 Accepted 27 August 2019 Available online 17 August 2020
The length of the distribution channel as a factor of its efficiency

Distribution network is a system of activities that provide transfer of products between producers and final users. It is also known as distribution channel, marketing channel, distribution chain, distribution pipeline, market chain and trade chain. This network has two or more partners, so it has to be coordinated in the direction of order fulfilment and satisfied demand. As a partnership business network, distribution channels are very important, due to their role in responding to customers’ requests. Distribution channels could provide competitive advantage for all partners along the network, through shorter delivery lead time and higher product availability. Although the main purpose of distribution channels is providing continuous flows of products to customers, they should be designed to fill customer’s demand with minimum total cost. Determining the right number of facilities and proper locations for distribution network is an essential issue for companies involved in the channel. The issue of distribution channel’s length has become more interesting due to the parallel existence of two different trends. On one hand, there is tendency for reducing number of partners, facilities or stages of distribution channels, with the purpose of avoiding extra expenses, but on the other hand there is a necessity to involve more partners in distribution channel, because that is a way for providing greater market share. Configuration of distribution channels depends on many factors. These factors have internal or external character. Therefore, the fact that the distribution of the same products in different countries can be performed completely differently is not surprising at all. In this regard, the aim of this papers is to classify the factors that affect the length of the distribution channel. In addition, the paper will also indicate advantages as well disadvantages of both long and short distribution channels. The goal of the analysis of the factors and the way of designing distribution channels, in terms of its length, is to make an adequate decision for increasing efficiency of the distribution network.
The complete mitochondrial genome of Chinese endemic specie Phascolosoma esculenta (Sipuncula, Phascolosomatidae) from Beibu Bay

Abstract Phascolosoma esculenta is economic important species in the fishery and aquaculture in southeast China. However, whether P. esculenta is conservative endemic specie or a complex of cryptic forms had not been verified yet. Here, we report the complete mitochondrial genome sequence of P. esculenta from Beibu Bay. The mitogenome has 15,494 base pairs and made up of total of 38 genes (13 protein-coding, 23 transfer RNAs, and 2 ribosomal RNAs), and a putative control region. There were only 56 mutations sites within Chinese populations. This study adds second mitogenome of P. esculenta, and will provide useful genetic information for future conservation and exploitation of this economic valuable marine benthic invertebrate.
Not all interactions are positive: testing how antagonistic interactions impact the robustness of plant-pollinator networks

Given ongoing pollinator declines, it is important to understand the dynamics of linked extinctions of plants driven by pollinator extinctions. Topological robustness models focused on this question suggest relatively high robustness of plant species to pollinator species extinctions. Still, existing robustness models typically assume that all interactions in plant-pollinator networks are positive, which is clearly not always the case. For example, many pollinators remove floral resources with-out transferring pollen, or even damage floral structures in the case of nectar robbing. Here we introduce antagonistic interactions into plant-pollinator networks and assess the resilience of plant communities to pollinator species losses. Incorporating antagonistic interactions leads to lower network robustness, i.e. an increased rate of plant species loss (as compared to networks with only mutualistic interactions) in empirical plant-pollinator networks. In conjunction with extinction order, the addition of increasingly antagonistic interactions was idiosyncratic in that it did not always magnify the effects of extinction order across the three networks. These results underscore the importance of considering the full spectrum of interaction outcomes when assessing robustness to coextinctions in plant-pollinator networks, as well as other ecological systems.
Changing Leaf Geometry Provides a Refuge from a Parasitoid for a Leaf Miner

The use of physical barriers is a common defensive strategy in small-sized endophagous arthropods, but this feeding mode often results in tracks being left on host organisms, thus increasing predation risk. Mechanisms of escape from tracking predators are thus particularly important for endophagous arthropods. Leaf miners are herbivorous insects that inhabit the interiors of leaves and produce various forms of tracks on their host plants. Such tracks are called “mines,” and parasitoid wasps, which are the primary enemy of leaf miners, use mines as cues to find host larvae. In the present study, we use the leaf-mining moth Acrocercops transecta (Insecta: Lepidoptera: Gracillariidae), which changes mine forms during larval growth, and its primary parasitoid Aneurobracon philippinensis (Hymenoptera: Braconidae). Larvae of A. transecta make narrow linear mines in the first and second instars, the third instars expand the mines to flat blotch mines, and the fourth and fifth instars construct three-dimensional tentiform blotch mines. A laboratory parasitization experiment showed that successful oviposition rates were significantly lower on tentiform blotch mines than on other mine types. In contrast, all fifth instars that were transplanted into flat blotch mines were oviposited, suggesting that older instars did not deter ovipositing parasitoids and that the lower rates of successful oviposition on tentiform blotch mines were attributable to refuges inside such mines provided by their three-dimensional structure. Field data demonstrated a plateau in parasitism rates in fourth instar larvae, confirming the results of the laboratory experiment. These results indicate that different mine forms affect the viability of endophagous larvae.
Systematic Modeling Approach to Selective Plugging Using In Situ Bacterial Biopolymer Production and Its Potential for Microbial-enhanced Oil Recovery

Abstract This study presents a systematic modeling approach for examining the efficiency of the MEOR process based on in situ selective plugging by bacterial biopolymer production and optimization of the nutrient injection strategy to yield the maximum oil recovery. This study focuses on modeling in situ selective plugging by the bacterial biopolymer dextran that is generated by Leuconostoc mesenteroides. Bacterial growth and dextran generation were described by a stoichiometric equation and kinetic reactions using batch model simulation. Based on the parameters for permeability reduction obtained from the sandpack model, the MEOR process was implemented in a pilot-scale system that included a highly permeable thief zone in a low-permeability reservoir. The base MEOR design yielded a 61.5% improvement of the recovery factor compared to that obtained with waterflooding. The parametric simulations revealed that the recovery efficiency was influenced by the amount of dextran, as well as the distribution of dextran, and thus, the injection strategy is critical for controlling the dextran distribution. By incorporating the results from the sensitivity analysis and optimization to determine the optimal design parameters, a 36.7% improvement of the oil recovery was achieved with the optimized MEOR process in comparison with the base case.
CEB-Map: Visual Localization Error Prediction for Safe Navigation

For safe visual navigation, areas with high localization errors should be concentrated and could be further refined by additional mapping operations. Given an environment map, we propose to predict the visual localization error and hence to either improve the navigation performance or call an additional mapping to refine the built map. Previous work adopts the uncertainty of landmarks for the error prediction. In our work, we take into account both the spatial distribution of visual landmarks and the uncertainty of landmarks. Our main idea is that standing at one place, a good spatial distribution of landmarks means a sufficient enough visible landmarks from all views at that place, i.e., enough landmarks under arbitrary view-direction. Combining the spatial distribution and the uncertainty of landmarks, we propose a new framework to predict the error of visual localization. Furthermore, we show that additional mapping in the area with high predicted error can significantly improve the visual localization precision. Experimental results show that there is a strong relationship between the predicted error and the real error, of which the absolute value of correlation coefficient is between 0.707 to 0.915. We apply our method to conduct an optimal refining policy on the built map and the experimental results show the improved localization precision. Applications on navigation test verify the superiority of our proposed method.
Thyroidal Regulation of Substrate Metabolism in Fasting Northern Elephant Seal Pups; FASTING, Re-defined

Author(s): Martinez, Bridget | Advisor(s): Ortiz, Rudy M | Abstract: To a number of physiological and pathological human conditions, there are a variety of natural animal models that can be studied in an effort to obtain greater knowledge and insight into the progression of the disease, as well as enable more accurate and successful therapeutic strategies. The northern elephant seal, specifically the fasting pups, have been established as a powerful, natural model for a number of human diseases, including the onset and development of insulin resistance. Thyroidal regulation has been implicated to change or be changed during the progression of the disease. Therefore, the aim of this dissertation is to elucidate how the two are regulating one another, and specifically what the contributions of an active thyroidal system are, to the regulation of substrate metabolism, especially lipid. In the first chapter, we demonstrated that despite a prolonged fasting period, northern elephant seal pups do not down-regulate thyroid hormone-mediated events, but rather increase all components that would result in increased cellular metabolism. In the second chapter we showed that fasting duration increases the sensitivity of adipose TH-mediated mechanisms to insulin, some of which may be mediated by increased glucose. The third chapter underscored the physiological relevance of an increased thyroidal status, which very clearly is substantially up-regulated with fasting duration, as the thyroid gland evidently increases its production of thyroid hormones with fasting duration. The fourth chapter reveals the contribution of this perplexing physiological response to fasting and its capacity to not only drive lipid metabolism but also lead the system into a necessary state of insulin resistance. Evolution has led some species to develop unique adaptations to environmental influences and lifestyles that are fascinating, perplexing and, if only understood, bare solutions to widespread health issues. Elephant seals are such a species. Despite prolonged fasting their metabolism neither slows down nor reduces its sensitivity to stimulation, as is common, to avoid resource depletion. Instead we find the opposite. Increased thyroid hormone levels and dynamic response to thyroid gland stimulation reveal how the seals thrive on a fasting-driven body fat diet. These studies have the potential to elucidate new therapeutic targets for hormone treatment of human obesity and related metabolic dysfunctions.
SOCIAL SKILLS DEVELOPMENT FOR PRIMARY SCHOOL STUDENTS WITH MODERATE AND SEVERE MENTAL DISABILITY AT SPECIAL BOARDING SCHOOL

Primary school pupils with moderate and severe mental disabilities characterized by slow and peculiar development of cognitive processes, lack of will, interest and motivation, which makes it difficult to acquire social skills. Often, pupils with mental disabilities also experience autism spectrum disorders characterized by stereotypical behavior, lack of language communication and socialization. Considering the peculiarities of the development of pupils with moderate and severe mental disability and autism spectrum disorders, communication and socialization skills, as well as traffic accident statistics, the social skills of primary school pupils to adhere to the rules of safe behavior on the street and in public transport are becoming more important. There is a question how to stimulate, interest students with moderate and severe mental disability and autism spectrum disorders in a more effective way in promoting the development of this social skill in a special boarding school environment based on the individual needs of students. The aim of the research is theoretically explore the possibilities of developing social skills for primary school pupils with moderate and severe mental disorders and autism spectrum disorders, to develop and test the importance of using interactive social photo stories in promoting social skills safe behavior on the street.
Radiopharmaceuticals and the Ophthalmologist

Introduction Radiopharmaceuticals are not commonly used in ophthalmologist hands, but occasionally used for head and neck cancers [1], especially over the southeastern Asia [2]. With close proximity between the eyes and the sinuses, ophthalmologists sometimes encounter these oncological patients with ocular complaints secondary to orbital invasion of tumor [3]. Here, we outline an ophthalmologist encounter with clinical radiation hazard from such, and patient’s problem with after-life cremation.
Dynamics of living cells in a cytomorphological state space

Significance The cell is where life emerges from nonliving matter. How can we understand the behavior of a complicated, far-from-equilibrium system such as a living cell? By defining a state space for cells and analyzing state transitions, we find that cell behavior can be successfully predicted by an effective potential function, which suggests that although cells are complex nonequilibrium systems, this complexity can be reduced to a simple equilibrium function for predicting cell behavior. Cells are nonequilibrium systems that exchange matter and energy with the environment to sustain their metabolic needs. The nonequilibrium nature of this system presents considerable challenges to developing a general theory describing its behavior; however, when studied at appropriate spatiotemporal scales, the behavior of ensembles of nonequilibrium systems can resemble that of a system at equilibrium. Here we apply this principle to a population of cells within a cytomorphological state space and demonstrate that cellular transition dynamics within this space can be described using equilibrium formalisms. We use this framework to map the effective energy landscape underlying the cytomorphological state space of a population of mouse embryonic fibroblasts (MEFs) and identify topographical nonuniformity in this space, indicating nonuniform occupation of cytomorphological states within an isogenic population. The introduction of exogenous apoptotic agents fundamentally altered this energy landscape, inducing formation of additional energy minima that correlated directly with changes in sensitivity to apoptosis induction. An equilibrium framework allows us to describe the behavior of an ensemble of single cells, suggesting that although cells are complex nonequilibrium systems, the application of formalisms derived from equilibrium thermodynamics can provide insight into the basis of nongenetic heterogeneities within cell populations, as well as the relationship between cytomorphological and functional heterogeneity.
Navigome: Navigating the Human Phenome

We now have access to a sufficient number of genome-wide association studies (GWAS) to cluster phenotypes into genetic-informed categories and to navigate the “phenome” space of human traits. Using a collection of 465 GWAS, we generated genetic correlations, pathways, gene-wise and tissue-wise associations using MAGMA and S-PrediXcan for 465 human traits. Testing 7267 biological pathways, we found that only 898 were significantly associated with any trait. Similarly, out of ~20,000 tested protein-coding genes, 12,311 genes exhibited an association. Based on the genetic correlations between all traits, we constructed a phenome map using t-distributed stochastic neighbor embedding (t-SNE), where each of the 465 traits can be visualized as an individual point. This map reveals well-defined clusters of traits such as education/high longevity, lower longevity, height, body composition, and depression/anxiety/neuroticism. These clusters are enriched in specific groups of pathways, such as lipid pathways in the lower longevity cluster, and neuronal pathways for body composition or education clusters. The map and all other analyses are available in the Navigome web interface (https://phenviz.navigome.com).
Differential Germination Characteristics of Dicamba-Resistant Kochia (Bassia scoparia) Populations in Response to Temperature

Abstract Dicamba-resistant (DR) kochia [Bassia scoparia (L.) A. J. Scott] has been reported in six U.S. states and one Canadian province. To develop effective B. scoparia control tactics, it is necessary to understand the seed germination pattern of DR B. scoparia. The objective of this study was to compare the germination characteristics of DR versus dicamba-susceptible (DS) B. scoparia populations from Montana and Kansas under constant (5 to 35 C) and/or alternating temperatures (5/10 to 30/35 C). DR B. scoparia lines from Montana were generated after three generations of recurrent selection of field-collected populations with dicamba. Seeds of DR or DS lines from Kansas were obtained after one generation of restricted self-pollination. DR B. scoparia lines from both Montana and Kansas had a lower maximum cumulative germination than the DS lines across all temperature treatments. A majority of DR B. scoparia lines from Montana showed a temperature-mediated seed germination response, with a higher thermal requirement (30 to 35 C or 25/30 to 30/35 C) to attain the maximum cumulative germination compared with DS lines. Germination rates at 5 to 30 C were lower for DR versus DS B. scoparia lines from Kansas. All DR lines from Montana took more time than DS lines to initiate germination at 5 and 10 C or 5/10 and 20/25 C. Similarly, there was a delayed onset of germination of the DR versus DS line from Kansas at 5, 10, 15, and 20 C. Furthermore, the DR B. scoparia from both Kansas and Montana had a slower germination pattern relative to the DS B. scoparia. Diversified crop rotations using winter wheat (Triticum aestivum L.), fall-sown cover crops, or early-spring planted crops (e.g., wheat or barley [Hordeum vulgare L.]) that are competitive against lateemerging B. scoparia in conjunction with strategic tillage and late-season weed control tactics should be used to facilitate depletion of DR B. scoparia seedbanks.
Narrow linewidth lasers for use with neutral strontium as a frequency standard

The continual development of precise timing has always pushed technology forward, and the latest generation of clocks uses electronic transitions within cooled atoms as their frequency reference. For atoms where the clock transition is at an optical frequency an ultra stable laser is used to probe the transition; the construction and development of this laser for use with strontium is the subject of this thesis. The system consists of a laser, an optical cavity and the electronics to lock the laser to the optical cavity. The theoretical component of this thesis looked into the possible materials used to make the optical cavity from and how the optical cavity should be supported to minimize the frequency noise of the laser. A compact external cavity diode laser was constructed and shown to have a linewidth of 26 ±15 kHz. To lock and narrow the linewidth of this laser, two ultra stable optical cavity assemblies were constructed with vibration and thermal stabilisation enclosures. To characterise the laser stability a beat measurement was performed between the two stabilised lasers and a beat note linewidth of 1:37 ± 0:28 Hz was measured. The instability of the beat note was measured; an Allan deviation of 2 x10\(^-\)\(^1\)\(^4\) was obtained between averaging times of 0.2 s and 1 s.
Genetic diversity in sesame (Sesamum indicum L.) genotypes under foothill condition of Nagaland

The nature and magnitude of genetic divergence were assessed in 16 sesame genotypes. Based on the relative magnitude of D2 values all the 16 genotypes were grouped in to 5 different clusters. Cluster I had 12 genotypes while remaining clusters II, III, IV and V had one genotype each. The average inter cluster distance was found to be highest between cluster III and IV (79.94) followed by cluster III and V (63.87) and cluster IV and V (62.64) whereas the lowest inter cluster distance was observed between cluster I and II (29.21). The higher inter cluster distance indicated the presence of more diversity among the genotypes included in these clusters. Thus the genotypes of cluster III and IV could be utilized as potential parents and crossing between these genotypes would result in heterotic expression for yield component traits. The relative contribution of different plant characters to the total genetic divergence estimated by D2 analysis indicated that capsule length contributed the maximum (32.5%) towards genetic divergence followed by number of seeds per capsule (30.83%).
EBADIMEX: an empirical Bayes approach to detect joint differential expression and methylation and to classify samples

Abstract DNA methylation and gene expression are interdependent and both implicated in cancer development and progression, with many individual biomarkers discovered. A joint analysis of the two data types can potentially lead to biological insights that are not discoverable with separate analyses. To optimally leverage the joint data for identifying perturbed genes and classifying clinical cancer samples, it is important to accurately model the interactions between the two data types. Here, we present EBADIMEX for jointly identifying differential expression and methylation and classifying samples. The moderated t-test widely used with empirical Bayes priors in current differential expression methods is generalised to a multivariate setting by developing: (1) a moderated Welch t-test for equality of means with unequal variances; (2) a moderated F-test for equality of variances; and (3) a multivariate test for equality of means with equal variances. This leads to parametric models with prior distributions for the parameters, which allow fast evaluation and robust analysis of small data sets. EBADIMEX is demonstrated on simulated data as well as a large breast cancer (BRCA) cohort from TCGA. We show that the use of empirical Bayes priors and moderated tests works particularly well on small data sets.