Miracle-dz/UniFAR-FTUs huggingface dataset:
The complete mitochondrial genome of Haemaphysalis concinna (Ixodida: Ixodidae)

Abstract The complete mitochondrial genome of Haemaphysalis concinna is reported for the first time in this study. Its entire mitogenome is 14,675 bp in length, contained 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and two non-coding regions. Among the 13 protein-coding genes, apart from the nad1, nad4, nad4L, and nad5 gene encoded on the L-strand, the remaining protein-coding genes were encoded on the H-strand. The phylogenetic analysis by Bayesian inference method shows that Amblyomma sphenodonti and H. parva formed one clade, while H. concinna and other species of genus Haemaphysalis formed the other clade, indicating that H. concinna belong to the genus Haemaphysalis.
Characterization of Bacteria Isolated from the Saffron (Crocus sativus L.) Rhizosphere

Abstract One purpose of assessing the soil alive and active community is the identification of beneficial bacteria to use them as biological fertilizers, replacing or supplementing synthetic fertilizers. Such biofertilizers are predicted for the sustainability of agricultural production, especially for low input systems such as saffron fields. The aim of this work was to isolate and identify saffron rhizobacteria and to evaluate their possible effects on saffron growth. During 2013/14, some bacteria were isolated from the rhizosphere of the saffron plantations of different age in Gol village, Birjand, Iran. In total, 12 bacteria species were identified based on phenotypic traits and 16S rDNA sequences analysis. The strains were identified as B. subtilis, B. anthracis, B. cereus, B. megaterium, Bacillus sp. , Paenibacillus, Pseudomonas fluorescens, P. putida, Escherichia coli, Pectobacterium sp. and Pantoea sp. , with the dominant population belonging to the genus Bacillus. In the field study, inoculation of soil with these strains did not affect the leaf dry weight of the cultivated saffron, however, the strains of P. fluorescens increased the leaf area while P. fluorescens, Paenibacillus, Pectobacterium and B. megaterium increased the number of daughter corms and Azotobacter, B. cereus, B. subtilis and B. megaterium increased the corm weight. Our finding revealed that some bacteria present in the soil of perennial saffron plantations have a promising potential for developing as a plant growth promoting rhizobacteria.
Mind your gaps: Overlooking assembly gaps confounds statistical testing in genome analysis

Background The difficulties associated with sequencing and assembling some regions of the DNA sequence result in gaps in the reference genomes that are typically represented as stretches of Ns. Although the presence of assembly gaps causes a slight reduction in the mapping rate in many experimental settings, that does not invalidate the typical statistical testing comparing read count distributions across experimental conditions. However, we hypothesize that not handling assembly gaps in the null model may confound statistical testing of co-localization of genomic features. Results First, we performed a series of explorative analyses to understand whether and how the public genomic tracks intersect the assembly gaps track (hg19). The findings rightly confirm that the genomic regions in public genomic tracks intersect very little with assembly gaps and the intersection was observed only at the beginning and end regions of the assembly gaps rather than covering the whole gap sizes. Further, we simulated a set of query and reference genomic tracks in a way that nullified any dependence between them to test our hypothesis that not avoiding assembly gaps in the null model would result in spurious inflation of statistical significance. We then contrasted the distributions of test statistics and p-values of Monte Carlo simulation-based permutation tests that either avoided or not avoided assembly gaps in the null model when testing for significant co-localization between a pair of query and reference tracks. We observed that the statistical tests that did not account for the assembly gaps in the null model resulted in a distribution of the test statistic that is shifted to the right and a distribu tion of p-values that is shifted to the left (leading to inflated significance). Conclusion Our results shows that not accounting for assembly gaps in statistical testing of co-localization analysis may lead to false positives and over-optimistic findings.
RNA Sequencing, De novo assembly, functional annotation and SSR analysis of the endangered diving beetle Cybister chinensis (= Cybister japonicus) using the Illumina platform

Cybister chinensis Motschulsky, 1854 (synonym Cybister japonicus Sharp, 1873) is a beetle found in ponds and irrigation canals near rice fields regulating the aquatic faunal community through predation. However, due to loss of natural habitats, use of pesticides, and invasion of alien species the beetle is threatened. With lack of understanding at the trophic ecology and genomics level, the conservation study is hindered to a larger extent. In the present study, Illumina HiSeq 4000 platform has been used to unravel the whole‐larval transcriptome of the beetle. A total of 20,129 non‐redundant unigenes were assembled from 67,260,666 clean read sequences. About 18,743 unigenes found a homologous match in any one of the databases like PANM, UniGene, Swiss‐Prot, Clusters of Orthologous Groups (COG), Gene Ontology (GO), KEGG, and InterProScan. While the zinc finger domains topped the unigene hits, about 660 enzymes (2695 sequences) participating in metabolism, environmental information processing, genetic information processing and organismal system pathways were recorded. Furthermore, the HSP70 class, Toll‐like receptors 4, insulin‐receptor substrate, and AMP activated protein kinase showed conspicuous presence in the larval transcriptome. Out of a total of 12,491 unigene sequences examined, 1968 SSRs were detected. Majority of them were dinucleotide repeats with six iterations followed by trinucleotide and tetranucleotide repeats with five and four iterations, respectively. This is the first report of cDNA resources from C. japonicus till date. The data would be crucial for the assessment of the beetle in the wild and making an inventory for utilisation in future genomics and ecological studies.
Association between gray matter atrophy, cerebral hypoperfusion, and cognitive impairment in Alzheimer’s disease

Background Alzheimer’s disease (AD) is one of the most severe neurodegenerative diseases leading to dementia in the elderly. Cerebral atrophy and hypoperfusion are two important pathophysiological characteristics. However, it is still unknown about the area-specific causal pathways between regional gray matter atrophy, cerebral hypoperfusion, and cognitive impairment in AD patients. Method Forty-two qualified AD patients and 49 healthy controls (HC) were recruited in this study. First, we explored voxel-wise inter-group differences in gray matter volume (GMV) and arterial spin labeling (ASL) -derived cerebral blood flow (CBF). Then we explored the voxel-wise associations between GMV and Mini-Mental State Examination (MMSE) score, GMV and CBF, and CBF and MMSE to identify brain targets contributing to cognitive impairment in AD patients. Finally, a mediation analysis was applied to test the causal pathways among atrophied GMV, hypoperfusion, and cognitive impairment in AD. Results Voxel-wise permutation test identified that the left middle temporal gyrus (MTG) had both decreased GMV and CBF in the AD. Moreover, the GMV of this region was positively correlated with MMSE and its CBF, and CBF of this region was also positively correlated with MMSE in AD (p < 0.05, corrected). Finally, mediation analysis revealed that gray matter atrophy of left MTG drives cognitive impairment of AD via the mediation of CBF (proportion of mediation = 55.82%, β = 0.242, 95% confidence interval by bias-corrected and accelerated bootstrap: 0.082 to 0.530). Conclusion Our findings indicated suggested that left MTG is an important hub linking gray matter atrophy, hypoperfusion, and cognitive impairment for AD, and might be a potential treatment target for AD.
Contribution of participatory forest management towards conservation and rehabilitation of dry Afromontane forests and its implications for carbon management in the tropical Southeastern Highlands of Ethiopia

ABSTRACT Participatory forest management (PFM) has been applied as an approach to create a framework for collaborative forest management between local communities and government forestry agencies. This study was designed to assess the contribution of PFM approach in improving forest status in the Southeastern Highlands of Ethiopia. Landsat satellite imageries of four years were used to evaluate the trends and rate of deforestation before and after PFM interventions. Socio-economic data were collected from sample household surveys, key participants, focus group discussions, and field observations. The results showed that there was high rate of deforestation before PFM intervention as forestland has decreased by 19% (2531 ha) between 1990 and 2000. However, after the PFM intervention (2000–2016), the forest cover has increased by 247 ha (2.2%). During this period, net 1016 ha of shrub-lands were converted into forestland owing to significant forest regeneration. In addition, most sampled households (94% and 96% from lower and upper altitudes, respectively) perceived that PFM had significantly contributed to improve forest regeneration in their locality. This study revealed that PFM can serve as a stepping stone for carbon financing mechanisms to reduce greenhouses emission and enhance carbon sinks via forest resources.
Chemical and cellular antioxidant activity of flavone extracts of Labisia pumila before and after in vitro gastrointestinal digestion

Two kinds of flavone extracts were extracted and purified from Labisia pumila (LP). High-performance liquid chromatography (HPLC) analysis was used to determinate the flavones in the extracts, and catechin, glycitin, rutin, naringin, and myricetin were identified in the LP leaf extract (LPL-F) while genistin, naringin, and myricetin were found in the stem extract (LPS-F). Specific flavonol compounds mediated the satisfactory scavenging abilities. The flavone leaf extracts performed better than the stem extracts in chemical antioxidative activities but worse in cellular antioxidative capabilities. The chemical and cellular antioxidative activities were not obviously changed by gastrointestinal digestion but slightly changed at the last 2 hours of intestinal digestion because prolonged exposure to alkaline conditions could destroy the structure of flavonoids. Changes in MDA and GSH content, and enzyme activities of SOD and GSH-Px in human erythrocytes during GI digestion indicated the possible intracellular antioxidant-detoxifying mechanisms were through attenuating AAPH-induced oxidative stress by inhibiting ROS generation, in which stem extracts performed the better.
Resolution of biodiversity and assemblage structure in demersal fisheries surveys: the role of tow duration

Resolution of biodiversity and assemblage structure in demersal fisheries surveys: the role of tow duration M. Moriarty*, A. F. Sell, V. M. Trenkel, C. P. Lynam, F. Burns, E. D. Clarke, S. P. R. Greenstreet, and C. McGonigle Marine Scotland Science, 375 Victoria Road, Aberdeen AB11 9DB, UK Environmental Sciences Research Institute, Ulster University, Cromore Road, Coleraine, BT52 1SA, UK Thünen Institute of Sea Fisheries, Palmaille 9, 22767 Hamburg, Germany Ifremer, Rue de I’lle d’Yeu, BP 21105, 44311 Nantes Cedex 03, France CEFAS, Pakefield Road, Lowestoft, Suffolk NR33 0HT, UK
Evaluation of Patients with Lower Extremity Peripheral Artery Disease by Walking Tests: A Pilot Study

Peripheral arterial disease (PAD) directly affects the quality of life, patients experimenting limited walking ability and disability. The purpose of the current study was to investigate the walking and climbing patterns of patients with lower extremity PAD in relation with several risk factors, applied on Romanian population. A cohort non-randomized design was conducted and all eligible subjects who self-referred for medical care since March 2016 until February 2017 at the Second Surgery Department, County Clinical Emergency Hospital of Cluj-Napoca were included. The eligible patients were older than 18 years, with leg pain and Rutherford grade from I to IV. The following tests were applied to each subject included in the study to investigate the capacity to walk as far as possible in six minute (6 minute walking test), the capacity to climb stairs (climbing stairs test) and the capacity to walk on a treadmill (treadmill test) until the pain occurred. Twenty-four patients with mean age of 65.08±8.53 years were investigated. Almost 81% of patients were with chronic pain, 46% were overweight, and 79% were smokers. The results on applied walking tests were as follows: 279.17±70.58 meters to 6-minutes walking test, 77.50±21.80 stairs and 182.50±73.34 meters on treadmill test. The results of the walking tests significantly correlate with each other (ρ>0.93, p |0.52|, p 0.62, p<0.002). It can be concluded that any of the applied walking test proved reliable instrument, able to identify the patients with most severe PAD.
Beyond emotional intelligence: The new construct of meta-emotional intelligence

Meta-emotional intelligence is a recently developed multidimensional construct that, starting from the original ability model of emotional intelligence, focuses on the cognitive aspects of emotional abilities and on the metacognitive and meta-emotional processes that influence our emotional life. Thus, meta-emotional intelligence is the combination of emotional abilities and meta-emotional dimensions, such as the beliefs about emotions, the self-concept about one's emotional abilities, and the self-evaluation of performance. This article aims to illustrate the theoretical and methodological background of this construct and to describe the IE-ACCME test, an original multi-method tool that has been developed to measure the different variables that compose meta-emotional intelligence. Applications of this construct will be discussed, as well as future directions.
Eurema brigitta (Lepidoptera: Pieridae) – a new record of butterfly for Socotra

Eurema brigitta (Stoll, 1780) (Lepidoptera: Pieridae) is recorded for the first time from the Socotra Island (Yemen). The specimen represents either a wet season form of a subspecies originating from Africa or a form with its usual occurrence in Madagascar, Mascarenes, Aldabra and Comoros. The current number of butterfly species known for Socotra is now 27.
Two components of maintaining developmental competence: microRNA-21 in the maturing oocyte and autophagy induction in the follicular stage ovary

xii CHAPTER 1: INTRODUCTION . 1 CHAPTER 2: LITERATURE REVIEW . 3 Utilization of Pigs in Agriculture . 3 Seasonal Infertility and Heat Stress . 4 Follicular Development . 6 Effects of Heat Stress on the Ovary . 7 Oogenesis and Meiotic Maturation . 9 Effects of Heat Stress on the Oocyte . 11 Autophagy. 12 Pig as a scientific model . 14 MicroRNA biogenesis and RISC . 15 MicroRNA in the oocyte . 19 Role of MicroRNA in Fertilization and Embryo Development . 20 MicroRNA in Embryonic Stem Cells . 21 MicroRNA in Embryo Implantation . 23 Placenta-Specific miRNA . 24 Additional RNA Classes . 25 MicroRNA-21 . 26 Conclusions. 28 Literature Cited. 29 CHAPTER 3: HEAT STRESS INDUCES AUTOPHAGY IN PIG OVARIES DURING FOLLICULAR DEVELOPMENT . 46 Abstract. 47 Introduction. 48 Materials and Methods . 50 Results. 54 Discussion. 57
Predicting natural language descriptions of smells

There has been recent progress in predicting whether common verbal descriptors such as “fishy”, “floral” or “fruity” apply to the smell of odorous molecules. However, the number of descriptors for which such a prediction is possible to date is very small compared to the large number of descriptors that have been suggested for the profiling of smells. We show here that the use of natural language semantic representations on a small set of general olfactory perceptual descriptors allows for the accurate inference of perceptual ratings for mono-molecular odorants over a large and potentially arbitrary set of descriptors. This is a noteworthy approach given that the prevailing view is that human’s capacity to identify or characterize odors by name is poor [1, 2, 3, 4, 5]. Our methods, when combined with a molecule-to-ratings model using chemoinformatic features, also allow for the zero-shot learning inference [6, 7] of perceptual ratings for arbitrary molecules. We successfully applied our semantics-based approach to predict perceptual ratings with an accuracy higher than 0.5 for up to 70 olfactory perceptual descriptors in a well-known dataset, a ten-fold increase in the number of descriptors from previous attempts. Moreover we accurately predict paradigm odors of four common families of molecules with an AUC of up to 0.75. Our approach solves the need for the consuming task of handcrafting domain specific sets of descriptors in olfaction and collecting ratings for large numbers of descriptors and odorants [8, 9, 10, 11] while establishing that the semantic distance between descriptors defines the equivalent of an odorwheel.
From research to health policy: The Noguchi story in the past, present and next 25 years

The Noguchi Memorial Institute for Medical Research (NMIMR) is a semi-autonomous institute of the College of Health Sciences, University of Ghana, Legon. Founded in 1979, the Institute was built with a grant aid from the Government of Japan as a gift to the people of Ghana in memory of the renowned Japanese medical scientist, Dr. Hideyo Noguchi, who died from Yellow fever infection while conducting research on the disease in Ghana. The Institute has a three-pronged mandate to conduct health related research, build human capacity and provide specialized diagnostic and disease monitoring services in support of the Ghana Health Service. Over the past 40 years, the Institute has grown to be a leading biomedical research institute in the African region. It has strong and long-standing collaborations with scientists and institutions in Africa, Japan, Europe, Australia and North America on several projects on diseases of public health importance. The Institute also hosts several regional and national centres such as Regional Influenza laboratory. The Institute’s research activities are relevant to the control and prevention of infectious diseases in Ghana, particularly, HIV/AIDS, Tuberculosis, Buruli ulcer, Polio, Malaria and emerging infectious diseases. The Institute also plays a technical/advisory role to government through collaborations with disease control programmes and has since inception provided the country with needed critical evidence in support of health policy as well as laboratory diagnostic services among others. Going forward, the Institute seeks to expand and consolidate its activities in areas of antimicrobial resistance (AMR), clinical trials, genomic surveillance and academic programs and in the next 25 years, NMIMR hopes to approach every research area using the one health approach.
Inverse Problems and Optimal Power Flow in Active Distribution Networks

During the last decade, distribution networks have experienced essential changes driven by the integration of renewable-energy sources, batteries, electric-vehicle charging stations, etc. This results in not only opportunities, but also operational problems. For example, the renewable power generation and the charging-station power consumption can be very large, leading to line congestion and over-/under-voltage issues. To solve the operational problems, we can develop methods that consist in directly manipulating the power; this is feasible by means of power-electronic devices and local controllers. For example, to address the line congestion and over-/under-voltage issues, we can either perform power curtailment at the energy sources and charging stations, or use batteries and demand response to avoid excessive power. So far, there is a growing number of works on managing distribution networks via direct power manipulation. These works include both the typical ones, such as regulating voltage/frequency by active/reactive power, and the pioneering ones, such as the Commelec that controls distribution networks by multi-agent systems and explicit power setpoints. With the integrated loads/sources and the direct power manipulation, the essence of distribution networks has changed. This gives us the concept of active distribution networks (ADNs). In this thesis, we focus on how to ensure network security and achieve optimality in ADNs. First, we study the AC power-flow problem in generically modelled multi-phase ADNs, which is an inverse problem. It determines whether a target system power injection has a corresponding system electrical state that fulfills the security constraints and might need to be repeatedly solved in real time. For this problem, we apply the fixed-point theory and establish explicit conditions for the existence and uniqueness of the power-flow solution. When the conditions are satisfied, we guarantee the existence of a power-flow solution and analytically specify a domain in which this solution is unique. For this guaranteed solution, we further provide an efficient iterative method to numerically compute it. Second, we take into account that the actual system power injection might be different from the target one, due to improperly modelled system dynamics, reaction delays, and renewable-energy disturbances. As a consequence, it is important to see whether we can ensure that the actual system electrical state always satisfies the security constraints, given that the actual system power injection resides in some known uncertainty set. We refer to this as the admissibility problem, which is another
Entomotoxicity of plant powders against Pulse beetle (Callosobruchus chinensis) on stored mung bean (Vigna radiata)

Experiments were conducted in the biology laboratory of the Department of Entomology, Gomal University, Dera Ismail Khan during 2015 to investigate the efficacy of six different botanicals (Neem, Bakain, Dharek, Turmeric, Tumha and AK), each at six different concentrations (0.5, 1.0, 1.5, 2.0, 2.5 and 3%) for the management of C. chinensis. Fifty gram of sterilized Mung bean grains were treated with these selected plant powders at six different concentrations viz. 3.0, 2.5, 2.0, 1.5, 1.0, 0.5% and data was recorded after 24, 48, 72 hours and 7 days of exposure period. Neem and Turmeric were found to be more effective in all concentrations against pulse beetle as they showed more toxicity against the tested pest. The Neem and Turmeric powders were found comparatively more effective in controlling progeny production of C. chinensis than other tested plant powders. So, it is concluded from the present findings that Neem and Turmeric powders should be incorporated into grain protection practices.