Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification and characterization of hirudin-HN, a new thrombin inhibitor, from the salivary glands of Hirudo nipponia

Transcriptome sequencing data (6.5 Gb) of the salivary glands of the haematophagous leech Hirudo nipponia was obtained by using the BGIseq-500 platform. After identification and analysis, one transcript (Unigene5370) was annotated to hirudin HV3 from Hirudo medicinalis with an e-value of 1e-29 and was named hirudin-HN. This transcript was a new thrombin inhibitor gene belonging to the proteinase inhibitor I14 (hirudin) family. Hirudin-HN, with a 270-bp cDNA, encodes an 89-aa protein containing a 20-aa signal peptide. The mature hirudin-HN protein contains the typical structural characteristics of hirudin, e.g., three conserved disulfide bonds and the PKP and DFxxIP motifs. Proteins (Hir and M-Hir) were obtained via prokaryotic expression, and the mature hirudin-HN protein was shown to have anticoagulant activity and thrombin affinity by using the chromogenic substrate S2238 and surface plasmon resonance (SPR) interaction analysis, respectively. The N-terminal structure of the mature hirudin-HN protein was shown to be important for anticoagulant activity by comparing the activity and thrombin affinity of Hir and M-Hir. The abundances of Hirudin-HN mRNA and protein were higher in the salivary glands of starving animals than in those of feeding or fed leeches. These results provided a foundation for further study on the structure-function relationship of hirudin-HN with thrombin.
Practical algorithms for image compression and surface estimation

Practical Algorithms for Image Compression and Surface Estimation describes three algorithms for image compression and one algorithm for surface estimation that incorporates kriging and parametric cubic splines. Two of the image compression algorithms are innovative extensions of the Run Length Encoding image compression algorithm and the third is an image compression technique based on kriging. In general the modified Run Length Encoding algorithms yield a better compression ratio by a factor of two while retaining fast decompression of the image. The algorithm based on kriging achieves a compression ratio up to 250:1 and is unique in that the compressed image can be viewed directly and resembles a scaled version of the original image. Neither kriging nor parametric cubic splines are new; the theory has existed for many years. The union of the two techniques, however, is unique. The fundamentals of kriging are outlined, three dimensional parametric cubic splines are derived, and finally the union of the two ideas is discussed.
Underutilization of Pre-Exposure Prophylaxis Services Among Transgender and Nonbinary Youth: Findings from Project Moxie and TechStep

Abstract We use quantitative and qualitative data from two ongoing studies to describe pre-exposure prophylaxis (PrEP) awareness, willingness to use PrEP, barriers to facilitators of PrEP uptake, and PrEP use among 15- to 24-year-old transgender and gender nonbinary (TGNB) youth. Most youth were aware of PrEP, but only one participant across both studies reported current use. Uncertainty about willingness to take PrEP may be related to general (e.g., medication cost) and trans-specific (e.g., PrEP–hormone interactions) concerns. Intensified and sustained efforts are needed to engage TGNB youth along the PrEP continuum and the impact of new PrEP administration and dosing options should be examined for TGNB youth.
The CORE Group Partners Project in North East Nigeria: Community Engagement Strategies to Combat Skepticism and Build Trust for Vaccine Acceptance

Abstract. In North East Nigeria, anti-immunization rumors and sentiments have negatively impacted the country’s polio eradication efforts. Since 2014, the CORE Group Partners Project (CGPP) has leveraged local-level strategies to help change prevailing attitudes and behaviors by improving immunization acceptability in some of the most difficult settlements in Nigeria’s states at highest risk for polio. The CGPP’s communication model in Nigeria, in part, emphasizes the need to counter suspicion and address myths and misunderstandings by convening community dialogs and compound meetings, both of which serve as safe spaces for open discussion primarily aimed at addressing non-compliance. In the communities in Kaduna, Katsina, Kano, Borno, and Yobe states located in the CGPP implementation areas, there has been a consistent reduction in the number of missed children and consistent improvement in polio immunization uptake, providing evidence of the effectiveness of the CGPP communication model. The last case of wild poliovirus in Nigeria was detected in August 2016. Since Nigeria has gone more than 3 years without a case of wild poliovirus, the CGPP communication model promises to remain highly relevant in sustaining the community’s awareness about immunizations that will be required to keep the population coverage of polio immunization high and, by extension, the herd immunity required to maintain zero transmission of poliovirus in Nigeria. This article describes the various strategies used to address noncompliance and provides examples of community engagement in Yobe state, which is one of the project’s largest implementation areas.
Detection and identification of Xanthomonas pathotypes associated with citrus diseases using comparative genomics and multiplex PCR

Background In Citrus cultures, three species of Xanthomonas are known to cause distinct diseases. X. citri subsp. citri patothype A, X. fuscans subsp. aurantifolii pathotypes B and C, and X. alfalfae subsp. citrumelonis, are the causative agents of cancrosis A, B, C, and citrus bacterial spots, respectively. Although these species exhibit different levels of virulence and aggressiveness, only limited alternatives are currently available for proper and early detection of these diseases in the fields. The present study aimed to develop a new molecular diagnostic method based on genomic sequences derived from the four species of Xanthomonas. Results Using comparative genomics approaches, primers were synthesized for the identification of the four causative agents of citrus diseases. These primers were validated for their specificity to their target DNA by both conventional and multiplex PCR. Upon evaluation, their sensitivity was found to be 0.02 ng/µl in vitro and 1.5 × 104 CFU ml−1 in infected leaves. Additionally, none of the primers were able to generate amplicons in 19 other genomes of Xanthomonas not associated with Citrus and one species of Xylella, the causal agent of citrus variegated chlorosis (CVC). This denotes strong specificity of the primers for the different species of Xanthomonas investigated in this study. Conclusions We demonstrated that these markers can be used as potential candidates for performing in vivo molecular diagnosis exclusively for citrus-associated Xanthomonas. The bioinformatics pipeline developed in this study to design specific genomic regions is capable of generating specific primers. It is freely available and can be utilized for any other model organism.
Suppression of Wolbachia-mediated male-killing in the butterfly Hypolimnas bolina involves a single genomic region

Background Sex ratio distorting agents (maternally inherited symbionts and meiotically-driving sex chromosomes) are common in insects. When these agents rise to high frequencies they create strong population sex ratio bias and selection then favours mutations that act to restore the rare sex. Despite this strong selection pressure, the evolution of mutations that suppress sex ratio distorting elements appears to be constrained in many cases, where sex-biased populations persist for many generations. This scenario has been observed in the butterfly Hypolimnas bolina, where Wolbachia-mediated male killing endured for 800–1,000 generations across multiple populations before the evolution of suppression. Here we test the hypothesis that this evolutionary lag is the result of suppression being a multilocus trait requiring multiple mutations. Methods We developed genetic markers, based on conservation of synteny, for each H. bolina chromosome and verified coverage using recombinational mapping. We then used a Wolbachia-infected mapping family to assess each chromosome for the presence of loci required for male survival, as determined by the presence of markers in all surviving sons. Results Informative markers were obtained for each of the 31 chromosomes in H. bolina. The only marker that cosegregated with suppression was located on chromosome 25. A genomic region necessary for suppression has previously been located on this chromosome. We therefore conclude that a single genomic region of the H. bolina genome is necessary for male-killing suppression. Discussion The evolutionary lag observed in our system is not caused by a need for changes at multiple genomic locations. The findings favour hypotheses in which either multiple mutations are required within a single genomic region, or the suppressor mutation is a singularly rare event.
Six years of fruit fly surveys in Bangladesh: a new species, 33 new country records and discovery of the highly invasive Bactrocera carambolae (Diptera, Tephritidae)

Abstract We engaged in six years of snap-shot surveys for fruit flies in rural environments and ten protected forest areas of Bangladesh, using traps baited with male lures (cue-lure, methyl eugenol, zingerone). Our work has increased the recorded number of species of Tephritidae in the country from seven to 37. We summarize these surveys and report eight new country occurrence records, and a new species (Zeugodacus madhupuri Leblanc & Doorenweerd, sp. nov.) is described. The highlight among the new records is the discovery, and significant westward range extension, of Bactrocera carambolae Drew & Hancock, a major fruit pest detected in the Chattogram and Sylhet Divisions. We rectify the previously published erroneous record of Bactrocera bogorensis (Hardy), which was based on a misidentification of Zeugodacus diaphorus (Hendel). We also report the occurrence in Bangladesh of nine other Tephritidae, the rearing of three primary fruit fly parasitoids from Zeugodacus, and records of non-target attraction to fruit fly lures.
Investigations of Process Mining Methods to discover Process Models on a Large Public Administration Software

Maintaining large and aging applications in a software house, with heterogeneous technologies, is very challenging. Whereas it is mandatory to continuously enhance user experience and maintain a good quality of service, the real business usage can be difficult to know precisely. To reach this goal, our project is to discover business models from the analysis of "logs". In this paper, we report on existing studies about applying process mining techniques and on our own experience with large datasets generated from daily end-user activities within an existing public services software. Our experiments led us to identify an interesting combination of features making our data hard to process with existing techniques. We conclude by providing perspectives to enable process discovery with such specific data.
Bark tissue transcriptome analyses of inverted Populus yunnanensis cuttings reveal the crucial role of plant hormones in response to inversion

Inverted cuttings of Populus yunnanensis exhibit an interesting growth response to inversion. This response is characterized by enlargement of the stem above the shoot site, while the upright stem shows obvious outward growth below the shoot site. In this study, we examined transcriptome changes in bark tissue at four positions on upright and inverted cuttings of P. yunnanensis: position B, the upper portion of the stem; position C, the lower portion of the stem; position D, the bottom of new growth; and position E, the top of new growth. The results revealed major transcriptomic changes in the stem, especially at position B, but little alteration was observed in the bark tissue of the new shoot. The differentially expressed genes (DEGs) were mainly assigned to four pathways: plant hormone signal transduction, plant-pathogen interaction, mitogen-activated protein kinase (MAPK) signaling pathway-plant, and adenosine triphosphate-binding cassette (ABC) transporters. Most of these DEGs were involved in at least two pathways. The levels of many hormones, such as auxin (IAA), cytokinin (CTK), gibberellins (GAs), ethylene (ET), and brassinosteroids (BRs), underwent large changes in the inverted cuttings. A coexpression network showed that the top 20 hub unigenes at position B in the upright and inverted cutting groups were associated mainly with the BR and ET signaling pathways, respectively. Furthermore, brassinosteroid insensitive 1-associated receptor kinase 1 (BAK1) in the BR pathway and both ethylene response (ETR) and constitutive triple response 1 (CTR1) in the ET pathway were important hubs that interfaced with multiple pathways.
Phylogenetic Classification and the Universal Tree

From comparative analyses of the nucleotide sequences of genes encoding ribosomal RNAs and several proteins, molecular phylogeneticists have constructed a “universal tree of life,” taking it as the basis for a “natural” hierarchical classification of all living things. Although confidence in some of the tree's early branches has recently been shaken, new approaches could still resolve many methodological uncertainties. More challenging is evidence that most archaeal and bacterial genomes (and the inferred ancestral eukaryotic nuclear genome) contain genes from multiple sources. If “chimerism” or “lateral gene transfer” cannot be dismissed as trivial in extent or limited to special categories of genes, then no hierarchical universal classification can be taken as natural. Molecular phylogeneticists will have failed to find the “true tree,” not because their methods are inadequate or because they have chosen the wrong genes, but because the history of life cannot properly be represented as a tree. However, taxonomies based on molecular sequences will remain indispensable, and understanding of the evolutionary process will ultimately be enriched, not impoverished.
Hypereosinophilic syndromes in the precision medicine era: clinical, molecular aspects and therapeutic approaches (targeted therapies)

ABSTRACT Introduction: Hypereosinophilic syndromes are a heterogeneous group of disorders that may be associated with life-threatening organ injury as a result of tissues infiltration by eosinophils. The main goal of therapy is to mitigate eosinophil-mediated organ damage. When possible, therapy should be directed at the underlying etiology. However, even in the absence of any known cause, when organ damage is present, hypereosinophilia must be treated promptly and aggressively to reduce potential morbidity and mortality. Areas covered: Conventional therapies, including corticosteroids, hydroxyurea (hydroxycarbamide) and interferon-alpha, have shown variable efficacy and a non-negligible toxicity emphasizing the need of new therapeutic strategies based on drugs with different mechanisms of action. Expert opinion: Tyrosine kinase inhibitors have a central role among targeted therapies of hypereosinophilic syndromes. Imatinib, initially empirically used based on its activity in chronic myeloid leukemia, achieved preliminary excellent results further confirmed in large series of patients. Third-generation tyrosine kinase inhibitors such as ponatinib, while active in vitro and in vivo in animals, still deserve confirmation in properly designed clinical trials. In addition, clinical investigation on monoclonal antibodies against interleukin-5, interleukin-5Rα, IgE, and CD52 represents a promising area of research.
Yoga-plus exercise mix promotes cognitive, affective, and physical functions in elderly people

ABSTRACT Objectives: Increased attention is being paid to Asian medicine in balanced total health care. We investigated the effects of mixed exercise including yoga (‘Yoga-plus’) among elderly individuals. Methods: A total of 385 subjects (72 males and 313 females, 75.5 ± 8.7 years old) participated in a 12-month (M) exercise program at a health and welfare center, a day service center, and a nursing home. Cognitive, affective, and physical functions, and activities of daily living (ADL), were compared at baseline (0M), 6M and 12M of exercise intervention. Results: Mean scores on the frontal assessment battery, clock drawing test, cube copying test, letter fluency, and category fluency significantly improved after the Yoga-plus intervention, while mini-mental state examination, Hasegawa dementia score-revised, and trail-making test performance were relatively stable. Affective scores on the geriatric depression scale (GDS), apathy scale (AS) and Abe’s behavioral and psychological symptoms of dementia were not significantly affected by exercise therapy, but subgroups with higher baseline GDS (GDS ≥ 5) and AS (AS ≥ 16) scores showed a significant improvement after intervention. One-leg standing time and 3-m timed up and go test performance significantly improved after 12M intervention. Discussion: Yoga-plus improved cognitive, affective, ADL, and physical functions in a local elderly population, particularly among below-baseline individuals, indicating the benefits of dementia prevention among elderly individuals.
Long non‐coding RNAs in cutaneous biology and proliferative skin diseases: Advances and perspectives

Advances in transcriptome sequencing have revealed that the genome fraction largely encodes for thousands of non‐coding RNAs. Long non‐coding RNAs (lncRNAs), which are a class of non–protein‐coding RNAs longer than approximately 200 nucleotides in length, are emerging as key epigenetic regulators of gene expression recently. Intensive studies have characterized their crucial roles in cutaneous biology and diseases. In this review, we address the promotive or suppressive effects of lncRNAs on cutaneous physiological processes. Then, we focus on the pathogenic role of dysfunctional lncRNAs in a variety of proliferative skin diseases. These evidences suggest that lncRNAs have indispensable roles in the processes of skin biology. Additionally, lncRNAs might be promising biomarkers and therapeutic targets for cutaneous disorders.
A highly sensitive molecular structural probe applied to in-situ biosensing of metabolites using PEDOT:PSS.

A large amount of research within organic biosensors is dominated by organic electrochemical transistors (OECTs) that use conducting polymers such as poly(3,4-ethylene dioxythiophene doped with poly(styrenesulfonate) (PEDOT:PSS). Despite the recent advances in OECT-based biosensors, the sensing is solely reliant on the amperometric detection of the bioanalytes. This is typically accompanied by large undesirable parasitic electrical signals from the electroactive components in the electrolyte. Herein, we present the use of in-situ resonance Raman spectroscopy to probe subtle molecular structural changes of PEDOT:PSS associated with its doping level. We demonstrate how such doping level changes of PEDOT:PSS can be used, for the first time, on operational OECTs for sensitive and selective metabolite sensing whilst simultaneously performing amperometric detection of the analyte. We test the sensitivity by molecularly sensing a lowest glucose concentration of 0.02 mM in phosphate buffered saline (PBS) solution. By changing the electrolyte to cell culture media, the selectivity of in-situ resonance Raman spectroscopy is emphasized as it remains unaffected by other electroactive components in the electrolyte. The application of this molecular structural probe highlights the importance of developing biosensing probes that benefit from high sensitivity of the material's structural and electrical properties whilst being complimentary with the electronic methods of detection. This article is protected by copyright. All rights reserved.
Math function based controller applied to electric/hybrid electric vehicle

Hybrid Energy Storage System (HESS) has been implemented for better energy efficiency to Hybrid/Electric Vehicles (HEV/EV), in that the main source is battery and UltraCapacitor (UC) is the auxiliary source. Switching of the energy sources according to the electric vehicle speed also plays an important role, to improve the life of the battery. So designing of the controller is a dynamic factor in case of electric /hybrid electric vehicles. The main objective of this paper is to design a controller for the transition between the sources, battery and Ultracapacitor. Here controller has been designed based on the Math function coding and this can be termed as Math Function Based (MFB) Controller. The controller generates the signals to the converters based on the speed of the motor. The MFB controller mainly designed to work in four modes and for each and every mode separate math function has been created. The overall system has been simulated in MATLAB and plotted the all results with discussions.
Redox-regulation of mitochondrial metabolism through thioredoxin o1 facilitates light induction of photosynthesis

ABSTRACT Despite the well-known biochemistry of the major pathways involved in central carbon and amino acid metabolism, there are still gaps regarding their regulation or regulatory interactions. Recent research demonstrated the physiological significance of the mitochondrial redox machinery, particularly thioredoxin o1 (TRXo1), for proper regulation of the tricarboxylic acid cycle, components of the mitochondrial electron transport chain and photorespiration. These findings imply that TRXo1 regulation contributes to the metabolic acclimation toward changes in the prevailing environmental conditions. Here, we analyzed if TRXo1 is involved in the light induction of photosynthesis. Our results show that the trxo1 mutant activates CO2 assimilation rates to a significantly lower extend than wild type in response to short-term light/dark changes. Metabolite analysis suggests that activation of glycine-to-serine conversion catalyzed through glycine decarboxylase in conjunction with serine hydroxymethyltransferase in trxo1 is slowed down at onset of illumination. We propose that redox regulation via TRXo1 is necessary to allow the rapid induction of mitochondrial steps of the photorespiratory cycle and, in turn, to facilitate light-induction of photosynthesis.
Discrete Event Systems: Modeling, Observation, and Control

This article begins with an introduction to the modeling of discrete event systems, a class of dynamical systems with discrete states and event-driven dynamics. It then focuses on logical discrete event models, primarily automata, and reviews observation and control problems and their solution methodologies. Specifically, it discusses diagnosability and opacity in the context of partially observed discrete event systems. It then discusses supervisory control for both fully and partially observed systems. The emphasis is on presenting fundamental results first, followed by a discussion of current research directions.