Miracle-dz/UniFAR-FTUs huggingface dataset:
Position control of a robotic manipulator using neural network and a simple vision system

This paper describes a new approach for approximating the inverse kinematics of a manipulator using a RBFN (Radial Basis Function Network). In fact, there are several traditional methods based on the known geometry of the manipulator to calculate the relationship between the joint variable space and the world coordinate space. However, these traditional methods are impractical if the manipulator geometry cannot be determined, in a robot-vision system for example. Therefore, a neural network with its inherent learning ability can be an effective alternative solution for the inverse kinematics problem. In this paper, a training solution using the strict interpolation method and the LMS (Least Mean Square) algorithm is presented in a two phase training procedure. The strict interpolation method with regularly-spaced-position training patterns in the workspace can produce an appropriate approximation of the inverse kinematic function. However, this solution has the main difficulty in how to collect accurate training patterns whose inputs are selected at pre-defined positions in the workspace. Additionally, the LMS algorithm can improve the approximate function iteratively through on-line training with arbitrary position patterns. A training approach combining two mentioned techniques can be applied for the inverse kinematics problem even with an inaccurate training set. It consists of two steps, firstly producing an inaccurate inverse kinematic approximation by strict interpolation (reflecting the situation that the initial setup and application environments are different) and then re-correcting the network through on-line training by the LMS. The advantages of both training methods can deal with the difficulty of collecting training patterns for practical applications. To verify the performance of the proposed approach, a practical experiment has been performed using a Mitsubishi PA10-6CE manipulator observed by a webcam. All application programmes, such as robot servo control, neural network, and image processing were written in C/C++ and run in a real robotic system. The experimental results prove that the proposed approach is effective.
Evaluation of antimalarial drugs usage according to WHO prescribing indicators in a tertiary health facility in Maiduguri, Northeastern Nigeria

Background: The high morbidity and mortality associated with malaria especially in sub-Saharan Africa such as Nigeria calls for prompt preventive and curative measures including adherence to standard treatment guideline. Aim: To assess the level of adherence with the five defined WHO prescribing key indicators. Methods: This was a retrospective evaluation of the performance of antimalarial drugs prescribing practice among clinicians from January to December 2014. It was done through a set of drug prescribing indicators developed by WHO and the International Network of Rational Use of Drugs (INRUD). Results: Of the 385 patients prescription randomly generated from the record of 12,477 patients in this descriptive study, a total of 143 (37.1%) had antimalarial prescription(s) with no gender variation. The evaluation of the studied antimalarial drug prescriptions through defined WHO prescribing indicators revealed an average number of drugs per encounter of 3.9, with 37.4% of the prescriptions written in generic names. All the antimalarial drugs were prescribed from the National Drug Formulary, with injectable form constituting 4.7%. Conclusion: This study shows suboptimal compliance with WHO prescribing indicators with respect to average number of antimalarial per encounter and prescription in generic names. The proportion of antimalarials prescription in injectable form falls within the WHO acceptable limit of ≤10%. All antimalarial drug prescriptions in this study were from essential drug list. We, therefore, recommend rational antimalarial drug prescription in conformity with WHO/INRUD core drug prescribing indicators.
Supplementing Maturation Medium With Insulin Growth Factor I and Vitrification-Warming Solutions With Reduced Glutathione Enhances Survival Rates and Development Ability of in vitro Matured Vitrified-Warmed Pig Oocytes

The present study sought to determine whether in vitro maturation (IVM) of pig oocytes in a medium supplemented with insulin growth factor-I (IGF-I) and subsequent vitrification with or without reduced glutathione (GSH) affect their quality and developmental competence, and the expression of genes involved in antioxidant, apoptotic and stress responses. In Experiment 1, cumulus-oocyte complexes were matured in the absence or presence of IGF-I (100 ng·mL−1) and then vitrified-warmed with or without 2 mM of GSH. Maturation rate was evaluated before vitrification, and oocyte viability, DNA fragmentation and relative transcript abundances of BCL-2-associated X protein (BAX), BCL2-like1 (BCL2L1), heat shock protein 70 (HSPA1A), glutathione peroxidase 1 (GPX1) and superoxide dismutase 1 (SOD1) genes were assessed in fresh and vitrified-warmed oocytes. In Experiment 2, fresh and vitrified-warmed oocytes were in vitro fertilized and their developmental competence determined. Whereas the addition of IGF-I to maturation medium had no effect on oocyte maturation, it caused an increase in the survival rate of vitrified-warmed oocytes. This effect was accompanied by a concomitant augment in the relative transcript abundance of HSPA1A and a decrease of BAX. Furthermore, the addition of GSH to vitrification-warming media increased survival rates at post-warming. Likewise, the action of GSH was concomitant with an increase in the relative abundance of GPX1 and a decrease of BAX transcript. Blastocyst rates of vitrified-warmed oocytes did not differ from their fresh counterparts when IGF-I and GSH were combined. In conclusion, supplementing maturation medium with 100 ng·mL−1 IGF-I and vitrification-warming solutions with 2 mM GSH improves the quality and cryotolerance of IVM pig oocytes, through a mechanism that involves BAX, GPX1 and HSPA1A expression.
Acute Kidney Injury in Nephrotic Syndrome

Nephrotic syndrome (NS) is one of the commonest kidney diseases seen in childhood and is characterized by a relapsing remitting course. Various complications have been reported in children with NS, including infections, thromboembolism, hypovolemia, and acute kidney injury (AKI). There is often a modest decrease in renal function in patients with active proteinuria due to decreased glomerular permeability that improves when they go into remission. However, more pronounced AKI in NS is multifactorial in origin. It is most often secondary to hypovolemia, nephrotoxic medications, and infections, although other reasons may also be seen. Recent years have seen an increase in the incidence of AKI in NS. There is limited data on the correlation between AKI in pediatric NS and long-term outcomes. A better understanding of this increasingly common condition will help improve patient outcomes.
Normal Ribosomal Biogenesis but Shortened Protein Synthetic Response to Acute Eccentric Resistance Exercise in Old Skeletal Muscle

Anabolic resistance to feeding in aged muscle is well-characterized; however, whether old skeletal muscle is intrinsically resistant to acute mechanical loading is less clear. The aim of this study was to determine the impact of aging on muscle protein synthesis (MPS), ribosome biogenesis, and protein breakdown in skeletal muscle following a single bout of resistance exercise. Adult male F344/BN rats aged 10 (Adult) and 30 (Old) months underwent unilateral maximal eccentric contractions of the hindlimb. Precursor rRNA increased early post-exercise (6–18 h), preceding elevations in ribosomal mass at 48 h in Adult and Old; there were no age-related differences in these responses. MPS increased early post-exercise in both Adult and Old; however, at 48 h of recovery, MPS returned to baseline in Old but not Adult. This abbreviated protein synthesis response in Old was associated with decreased levels of IRS1 protein and increased BiP, CHOP and eIF2α levels. Other than these responses, anabolic signaling was similar in Adult and Old muscle in the acute recovery phase. Basal proteasome activity was lower in Old, and resistance exercise did not increase the activity of either the ATP-dependent or independent proteasome, or autophagy (Cathepsin L activity) in either Adult or Old muscle. We conclude that MPS and ribosome biogenesis in response to maximal resistance exercise in old skeletal muscle are initially intact; however, the MPS response is abbreviated in Old, which may be the result of ER stress and/or blunted exercise-induced potentiation of the MPS response to feeding.
Understanding the SO2 Degassing Budget of Mt Etna's Paroxysms: First Clues From the December 2015 Sequence

The persistent open-vent activity of Mt. Etna volcano, in Sicily, is frequently punctuated by some of the most spectacular paroxysmal basaltic explosions in nature. Although magmatic gas is unquestionably the driver of these events, direct measurements of a paroxysm’s gas flux budget have remained challenging and limited in number, to date. A particularly violent paroxysmal sequence took place on Etna on December 2015, intermittently involving four of its summit craters, especially the Voragine (VOR) that had previously displayed no activity for several years. Here, we characterize the volcano’s SO2 degassing budget prior to, during and after this paroxysmal sequence, using ground-based (UV-Camera) and satellite (OMI) observations, complemented with thermal (thermal cameras and MODIS) measurements from both ground and space. We make use of the high spatial resolution of UV-cameras to resolve SO2 emissions from the erupting VOR crater for the first time, and to characterize temporal switches in degassing activity from VOR to the nearby New Southeast Crater (NSEC). Our data show that onset of paroxysmal activity on December 3-5 was marked by visible escalation in VOR SO2 fluxes (4700-8900 tons/day), in satellite-derived thermal emissions (2000 MW vs. ~2-11 MW July-November 2015 average), and in OMI-derived daily SO2 masses (5.4±0.7 to 10.0±1.3 kilotonnes, kt; 0.5 kt was the average in the pre-eruptive period). Switch in volcanic activity from VOR to NSEC on December 6 was detected by increasing SO2 fluxes at the NSEC crater (up to 3460±350 tons/day), and by decaying SO2 emissions at VOR, until activity termination on December 19. Taken together, our observations infer the total degassed SO2 mass for the entire VOR paroxysmal sequence at 21,000±2730 t, corresponding to complete degassing of ~1.9±0.3 Mm3 of magma, or significantly less than the measured erupted magma volumes (5.1-12 Mm3). From this mismatch, we propose that a sizeable fraction of the erupted magma during the paroxysms was stored and degassed in the volcano’s shallow plumbing system well before eruption.
Long Term Diversity and Distribution of Non-photosynthetic Cyanobacteria in Peri-Alpine Lakes

The phylum Cyanobacteria comprises a non-photosynthetic lineage. The diversity and distribution of non-photosynthetic cyanobacteria (NCY) across aquatic environments are currently unknown, including their ecology. Here, we report about composition and phylogenetic diversity of two clades of NCY in ten lakes of the European peri-Alpine region, over the past ∼100 years. Using 16S rDNA sequences obtained from dated sediment cores, we found almost equal proportion of taxa assigned to Melainabacteria and the deepest-branching group Sericytochromatia (ML635J-21) (63 total detected taxa). The topology of our reconstructed phylogenies reflected evolutionary relationships expected from previous work, that is, a clear separation between the deepest branching Sericytochromatia, the Melainabacteria, and the photosynthetic cyanobacteria clades. While different lakes harbored distinct NCY communities, the diversity of NCY assemblages within and between lakes (alpha and beta diversity) did not significantly change over the last century. This is in contrast with what was previously reported for photosynthetic cyanobacteria. Unchanged community phylogenetic similarity over geographic distance indicated no dispersal limitation of NCY at the regional scale. Our results solicit studies linking in-lake environmental factors to the composition of these microorganisms’ communities, whose assembly appeared not to have been influenced by large-scale anthropogenic environmental changes. This is the first attempt to study the diversity and distribution of NCY taxa across temperate lakes. It provides a first step towards understanding their distribution and ecological function in pelagic aquatic habitats, where these organisms seem to be prevalent.
The Precursor Hypothesis of Sponge Kleptocnidism: Development of Nematocysts in Haliclona cnidata sp. nov. (Porifera, Demospongiae, Haplosclerida)

Marine sponges thrive in benthic environments despite intense spatial competition and predator pressure. The sessile filter feeders usually compensate their lack of physical defense and behavioral escape by a high level of bioactivity. In the stinging black sponge (Haliclona cnidata sp. nov.), these chemical defense mechanisms are complemented by ‘cellular weapons’ – functional nematocysts likely acquired from cnidarians (kleptocnidism). Whereas kleptocnidism might be facilitated by a close contact with cnidarian donors, preliminary investigations suggest that the stinging black sponge sustains nematocysts even if kept apart from cnidarians. As the underlying mechanisms causing this phenomenon remain unknown, the development of its nematocysts was studied in both presence and absence of potential cnidarian donors. First, we compared inherent nematocysts of adult sponge individuals with foreign nematocysts of co-cultivated cnidarians to identify potential donors. Second, we experimentally assessed the donor independent and donor dependent development of inherent and foreign nematocysts within cultures of sponge cell aggregates (SCAs). The inherent nematocysts comprised two specific types that both differed from those of the eight co-cultivated cnidarians. Specifically, we showed that the number of sponge-inherent nematocysts increased in SCAs over time in the absence of potential donors. Numbers of supplied foreign nematocysts, however, did not increase in the SCAs. We conclude that the observed increase of inherent kleptocnidae nematocysts is due to the maturation of nematocyst precursor cells. Given these findings, we here propose the precursor hypothesis of sponge kleptocnidism. Accordingly, nematocyst precursors or immature nematocyte-nematocyst complexes might be initially acquired by sponges through filtration, maintained in sponge tissues, and nurtured to fully functioning nematocyte-nematocyst complexes. The underlying evolutionary processes are likely facilitated by bacteria derived secondary metabolites and photosynthetically active dinoflagellates. Due to a simple body plan and the in vitro proliferation capacity of sponge cells, Haliclona cnidata sp. nov. may serve as a novel evolutionary model system to further assess fundamental research questions regarding kleptocnidism. This study not only sheds new light on kleptocnidism in sponges, it also calls for a holobiontic view at defense mechanisms that involves the actual sponge, cnidarian nematocysts, dinoflagellate endosymbionts, and a complex microbial community.
The Histopathological Correlation with Clinical and Endoscopic Evidence in Patients with Barrett'S Esophagus

Barrett’s esophagus (BE) is a condition in which the normal squamous epithelium of the esophagus is replaced with metaplastic intestinal-type epithelium. Many factors that appear to be risk factors for the presence of BE include obesity, the presence of hiatal hernia, and interestingly, the absence of Helicobacter pylori infection. The diagnosis of Barrett’s esophagus is made by endoscopy and confirmed by histology The aim of this study was to determine the histological correlation with clinical end endoscopical appearance in this patients with BE. Methods: 58 patients with endoscopically diagnosed and histopathologically verified BE were included in this prospective study. We analysed predictive factors such as: age, sex, obesity, alcohol consumption and smoking, reflux symptom duration in this patients, prevalence of short and long segment of BE, and the presence of hiatal hernia. After endoscopic examination of these patients, the presence of BE was verified with histopathological examination to determine the correlation between the endoscope diagnosis and histopathologic outcome in patients with BE. Results: Among 58 subjects, 35 (60%) were males and 23 (40%) were females, with mean age of 50.4 ±3.28 years. Obesity was present in 32/58 patients (55.2%). 39 patients from 58 patients were smokers (67.2%). Symptom duration in these patients was approximately 8.9±1.90 years. From total number of patients, 35 were with short segment (60.3%), the rest (23 patients) were with long segment of Barrett’s esophagus (39.7%). Hiatal hernia was present in 64% of patients, 40 of 58 patients diagnosed with Barrett’s esophagus (69%) also had hiatal hernia, of which 32/40 (80%) were with LSBE, and 8/40 patients (20%) were with SSBE. Conclusions: The important risk factors for appearance of BE in GERD patients were male sex, middle age, obesity, hiatal hernia, smoking and alcohol consumption. The prevalence of infection with H. Pylori in patients with BE was lower and this may predict a protective role of this microorganism. Diagnostic accuracy of Barrett’s esophagus is significantly greater in patients with LSBE than in those with SSBE (94.3% vs 43.5%) and p <0.05).
iVikodak—A Platform and Standard Workflow for Inferring, Analyzing, Comparing, and Visualizing the Functional Potential of Microbial Communities

Background: The objectives of any metagenomic study typically include identification of resident microbes and their relative proportions (taxonomic analysis), profiling functional diversity (functional analysis), and comparing the identified microbes and functions with available metadata (comparative metagenomics). Given the advantage of cost-effectiveness and convenient data-size, amplicon-based sequencing has remained the technology of choice for exploring phylogenetic diversity of an environment. A recent school of thought, employing the existing genome annotation information for inferring functional capacity of an identified microbiome community, has given a promising alternative to Whole Genome Shotgun sequencing for functional analysis. Although a handful of tools are currently available for function inference, their scope, functionality and utility has essentially remained limited. Need for a comprehensive framework that expands upon the existing scope and enables a standardized workflow for function inference, analysis, and visualization, is therefore felt. Methods: We present iVikodak, a multi-modular web-platform that hosts a logically inter-connected repertoire of functional inference and analysis tools, coupled with a comprehensive visualization interface. iVikodak is equipped with microbial co-inhabitance pattern driven published algorithms along with multiple updated databases of various curated microbe-function maps. It also features an advanced task management and result sharing system through introduction of personalized and portable dashboards. Results: In addition to inferring functions from 16S rRNA gene data, iVikodak enables (a) an in-depth analysis of specific functions of interest (b) identification of microbes contributing to various functions (c) microbial interaction patterns through function-driven correlation networks, and (d) simultaneous functional comparison between multiple microbial communities. We have bench-marked iVikodak through multiple case studies and comparisons with existing state of art. We also introduce the concept of a public repository which provides a first of its kind community-driven framework for scientific data analytics, collaboration and sharing in this area of microbiome research. Conclusion: Developed using modern design and task management practices, iVikodak provides a multi-modular, yet inter-operable, one-stop framework, that intends to simplify the entire approach toward inferred function analysis. It is anticipated to serve as a significant value addition to the existing space of functional metagenomics. iVikodak web-server may be freely accessed at https://web.rniapps. net/iVikodak/.
Comparative Evaluation of Microbiota Engraftment Following Fecal Microbiota Transfer in Mice Models: Age, Kinetic and Microbial Status Matter

The intestinal microbiota and its functions are intricately interwoven with host physiology. Colonizing rodents with donor microbiota provides insights into host-microbiota interactions characterization and the understanding of disease physiopathology. However, a better assessment of inoculation methods and recipient mouse models is needed. Here, we compare the engraftment at short and long term of genetically obese mice microbiota in germ-free (GF) mice and juvenile and adult specific pathogen free (SPF) mice. We also tested the effects of initial microbiota depletion before microbiota transfer. In the present work, donor microbiota engraftment was better in juvenile SPF mice than in adult SPF mice. In juvenile mice, initial microbiota depletion using laxatives or antibiotics improved donor microbiota engraftment 9 weeks but not 3 weeks after microbiota transfer. Microbiota-depleted juvenile mice performed better than GF mice 3 weeks after the microbiota transfer. However, 9 weeks after transfer, colonized GF mice microbiota had the lowest Unifrac distance to the donor microbiota. Colonized GF mice were also characterized by a chronic alteration in intestinal absorptive function. With these collective results, we show that the use of juvenile mice subjected to initial microbiota depletion constitutes a valid alternative to GF mice in microbiota transfer studies.
Distribution of ExPEC Virulence Factors, blaCTX-M, fosA3, and mcr-1 in Escherichia coli Isolated From Commercialized Chicken Carcasses

Pathogenic Escherichia coli found in humans and poultry carcasses harbor similar virulence and resistance genes. The present study aimed to analyze the distribution of extraintestinal pathogenic E. coli (ExPEC) virulence factors (VF), blaCTX−M groups, fosA3, and mcr-1 genes in E. coli isolated from commercialized chicken carcasses in southern Brazil and to evaluate their pathogenic risk. A total of 409 E. coli strains were isolated and characterized for genes encoding virulence factors described in ExPEC. Results of antimicrobial susceptibility testing confirmed that the strains were resistant to β-lactams, fosfomycin, colistin, and others resistance groups. The highest prevalence of VFs was observed in isolates belonging to the CTX-M groups, especially the CTX-M-2 group, when compared to those in other susceptible strains or strains with different mechanisms of resistance. Furthermore, ESBL strains were found to be 1.40 times more likely to contain three to five ExPEC virulence genes than non-ESBL strains. Our findings revealed the successful conjugation between ESBL-producing E. coli isolated from chicken carcass and the E. coli recipient strain J53, which suggested that genetic determinants encoding CTX-M enzymes may have originated from animals and could be transmitted to humans via food chain. In summary, chicken meat is a potential reservoir of MDR E. coli strains harboring resistance and virulence genes that could pose serious risks to human public health.