Miracle-dz/UniFAR-FTUs huggingface dataset:
Analysis of immunological resistance to primary Mycobacterium tuberculosis infection in humans

Background Despite recent advances in diagnosis and treatment, tuberculosis (TB) remains a major infectious disease killer in resource-poor settings. Strategies to prevent Mycobacterium tuberculosis (Mtb) infection are urgently required. By characterising natural protective immunity to Mtb infection we aimed to identify correlates of protection to guide vaccine development and other immune based therapies. Methods Two groups of Mtb-exposed contacts of TB patients were recruited in The Gambia and assessed for Mtb infection status using either tuberculin skin test (TST) reactivity at baseline and 3 months or QuantiFERON (QFT) reactivity at baseline and 6 months. For both groups, converters were defined as having a negative test at baseline and a positive one at follow-up, while those with a negative test at both time-points were defined as non-converters (Mtb resisters). Participants were analysed using RNA-sequencing and plasma Mtb proteome IgA and IgG arrays. Results Several genes were found to be differentially expressed at baseline between the groups prior to any signs of infection by current tests. Modular analysis revealed a distinct B cell gene signature in TST non-converters compared to converters (at q < 10-6, AUC > 0.7), which was only present in the most highly exposed group. Interestingly, when infection status was defined by QFT, enrichment of Type I IFN and antiviral gene signatures was observed. Plasma IgG and IgA antibody reactivity across the entire Mtb proteome showed the best differentiation in individuals with the highest exposure. An AUC of 1.0 (q<10-3) was observed for IgA reactivity to Rv0134 and an AUC of 0.98 for IgA reactivity to both Rv0629c and Rv2188c (all lower in TST non-converters). IgG reactivity to Rv3223c resulted in an AUC of 0.96 (q < 10-4) and was again lower in TST non-converters. The highest AUC for those with lower Mtb exposure were 0.84 (Rv2411c) for IgA and 0.83 (Rv2131c) for IgG. Conclusions These data provide insight into the early protective response to Mtb infection and possible avenues for novel therapeutic strategies to prevent Mtb infection.
Ontogeny of the Human Pancreas

Pancreatic disorders are the most common pathologies in humans worldwide. Detailed information on pancreatic cytoarchitecture, vascularisation, innervation, morphogenesis, and cell differentiation is required for the development of new approaches to the treatment of these diseases. Currently, the majority of studies on pancreas development are performed on experimental animals (mainly rodents). Studies on human pancreatic prenatal development are restricted in number by ethical constraints and some technical difficulties. However, interspecies differences in pancreatic structure and development are considerable. Therefore, data obtained in experiments on animals and cell cultures must be supplemented with information obtained directly from human pancreatic autopsies. In this chapter, we summarise our previous results and the literature data on human pancreatic ontogeny. Special attention has been paid to the endocrine pancreas, which undergoes morphogenetic restructuring during human development. Several forms of structural organisation of the endocrine pancreas (single endocrine cells, small clusters of endocrine cells, mantle, bipolar, and mosaic islets) gradually appear during development. It is important that this restructuring is accompanied by changes in the ratio of pancreatic endocrine cells. The mechanisms of these changes are still unclear. The difficulties in identifying progenitor cells and tracking cell differentiation are the main problems associated with this issue.
REVIEW PAPER ON TREATMENT OF INDUSTRIAL AND DOMESTIC WASTEWATERS USING UASB REACTORS INTEGRATED INTO CONSTRUCTED WETLANDS FOR SUSTAINABLE REUSE

The successful use of anaerobic technologies, especially up-flow sludge blanket (UASB) reactors for the treatment of raw domestic sewage and industrial wastewaters in tropical and subtropical countries opened the opportunity to substitute the aerobic processes with anaerobic reactors in removal of organic matter. Proper management of domestic and industrial wastewaters in developing nations is negligible. Even cost effective integrated green technologies like anaerobic reactor with constructed wetland technologies are not applied. Hence the objective of the present review was to assess the pollutant removal efficiency of the up flow anaerobic sludge blanket (UASB) reactor coupled with a constructed wetland (CW) in treating these wastewaters and their capability to produce quality water for sustainable reuse. To achieve the objectives, the review was organized using reputable journals, articles, and review papers. The interpretation of the result of each document was done using tables, bar graphs, Pie chart and lines. The results were reorganized again by calculating average flow rate, hydraulic loading rate, and percentage removal efficiencies. Most research results revealed that use of UASB-CW integrated treatment system is a promising technology in wastewater treatment and able to complying the effluent discharge standards. Globally, the following abatement efficiencies ranged from 79.2-93.9%, 89.2-92.9%, 87.2-96.3%, 22.6-96.9%, 33-85.9%, and 97.9-99.99% were achieved for Chemical oxygen demand (COD), Biological oxygen demand (BOD), Total suspended solid (TSS), Total Kjeldhal Nitrogen (TKN), Total phosphorus (TP) and fecal Coliforms (FC), respectively using UASB-CW treatment systems. UASB-CW technologies are effectively integrated treatment systems and can be used for resource scarce developing countries. Since, both treatment technologies are cost-effective, easy operation and maintenance and capable of meeting effluent standards. Hence, the indiscriminate disposal of wastewaters and their environmental impacts in Ethiopia can be resolved using these low-cost combined treatment technologies.
Trimethyl chitosan chloride (TMC) as a novel excipient for oral and nasal immunisation against diphtheria

Despite the obvious advantages of mucosal vaccination over invasive injections, degradation of the antigen in the gastro-intestinal tract and/ or low uptake by the mucosal associated lymphoid tissue (MALT) still complicate the introduction of efficient oral or nasal inactivated vaccines. In this study, trimethyl chitosan chloride (TMC) microparticles were prepared according to a precipitation/coacervation method and characterized with respect to morphology, size and antigen [diphtheria toxoid (DT)] loading and release. The stability of the DT-loaded microparticles was studied by determining possible alterations in these parameters over a period of three months. Then DT-specific systemic and mucosal humoral immune responses were measured in mice and rats after oral and nasal vaccination of DT combined with TMC microparticles and co-administered with TMC in solution. In these in vivo studies, the influence of the degree of substitution (DS) of TMC, the administration frequency and the antigen dose were investigated. TMC-20 (DS, 20%) microparticles appeared to be of a suitable size (about 2 μm)for uptake by the M-cells of the Peyer's patches. Up to 80 % of the DT antigen was combined with this microparticulate system and only 7% of the antigen set free during the first 10 min in subsequent release studies. Stability studies showed no alterations in morphology or size, and no additional antigen was released over a period of 13 weeks. In vivo studies in mice demonstrated that DT combined with TMC-20 microparticles induces a strong systemic immune response against the orally administered antigen. An initial in vivo study in rats revealed that both TMC-20 microparticles and TMC-20 in solution are able to enhance the systemic immune response compared to control groups receiving alum-adsorbed DT. Also in nasal vaccination studies in mice, co-administration of TMC-20 solution or combination of DT with TMC-20 microparticles strongly enhances the local and systemic immune response. The degree of substitution of TMC (TMC-20 and TMC-70, respectively) did not influence the formation of local or systemic DT specific antibodies. The local immune response was only significantly enhanced by TMC if the total DT dose was administered on three consecutive days. Dose-response studies revealed that vaccinating at high doses (20 and 40 Lf, respectively) resulted in significantly stronger local and systemic immune responses than low doses (6 Lf). The amount of neutralizing antibodies in mice vaccinated with both TMC formulations was high: the level is considered to be protective in man. In conclusion, TMC microparticles are very promising for oral vaccination against DT. Moreover, both TMC microparticles and TMC in solution are very potent in enhancing the systemic and local immune responses after nasal DT administration.
Proton Pump Inhibitors and Cardiovascular Disease: A Review of Clinical Evidence and Biological Mechanisms

Proton pump inhibitors (PPIs) are amongst the most commonly prescribed medications in the clinical setting. They are commonly used for the treatment of gastroesophageal reflux disease and are readily available over the counter. However, their irrational long term use has been repeatedly discouraged. PPIs are highly lipophilic and may adversely affect multiple physiological pathways of various organs. Over the past few decades, multiple clinical studies have linked PPI use with an increased risk of cardiovascular disease. In this review, we discuss the PPI-induced pathophysiological mechanisms that contribute to cardiovascular disease. Furthermore, we highlight clinical evidence that associates PPI use with an increased risk for various cardiovascular manifestations.
Inhibitors of tumor necrosis factor-a and mechanisms of their action

Tumor necrosis factor (TNF)-α is a proinflammatory cytokine with a role in immunity to pathogens, as well as in the pathogenesis of several autoimmune/inflammatory diseases. Biological drugs targeting this cytokine and inhibiting its effects are designed. Until today, five TNF-α inhibitors are approved: infliximab, adalimumab, golimumab (monoclonal antibodies), certolizumab pegol (pegylated antigen-binding fragment of immunoglobulin), and etanercept [TNF receptor type 2-fragment crystallizable (Fc) of immunoglobulin fusion protein]. Their approved biosimilars are on the market, too. They are mainly used for the treatment of rheumatoid arthritis, inflammatory bowel disease, and psoriasis. Although TNF-α inhibitors are present in clinical practice for more than two decades and are established as an efficacious therapeutics, researchers are still occupied by revealing the complex mechanisms of their action. Namely, in addition to binding and neutralisation of soluble TNF-α, these drugs also bind/block transmembrane form of TNF-α (tmTNF-α), trigger diverse intracellular signals in tmTNF-α positive cells (a process named “reverse signalling”) or, if they have an Fc fragment, mediate killing of tmTNF-α-expressing cells by other immune cells or the complement system. Also, TNF-α inhibitors that contain Fc portion of the IgG antibody may affect Fc receptor-expressing cells and have an effector function quite independent of their TNF-α neutralisation capacity.
The crude glycerin reduces losses fermentative and improves the nutritional value of marandu grass silage in a semiarid region

The ensiling of marandu grass at the recommended time of management results in low dry matter (DM) content and nutritional value, but the addition of crude glycerin can compensate for these deficits if used during ensiling. Thus, the aim of this study was to evaluate the best level of inclusion of crude glycerin that can improve fermentation and the nutritional value of silages prepared with Urochloa brizantha cv. Marandu. The treatments consisted of five levels of inclusion of crude glycerin (0, 7.5, 15, 22.5, 30% of fresh forage) during ensiling of marandu grass with eight replications following the completely randomized design. For the evaluation of ruminal kinetics, four crossbred steers were used, cannulated in the rumen, following a randomized block design in a split plot scheme. For the percentage unit of inclusion of glycerin, there was a linear reduction of 0.34% in gas losses and increase of 0.45% and 0.55% in the recovery of DM (P <0.01) and in the DM content (P <0.01), respectively. The inclusion of up to 22.5% of crude glycerin in the silage of marandu grass is recommended to reduce losses during fermentation and improve the recovery of dry matter and the nutritional value of silage.
Innovation Capabilities and the role of Strategic Intelligence

In rapidly changing environments, innovation allows firms to maintain their market competitiveness. A firm with well-developed innovation capabilities stands a better chance to sustain its competitiveness. Additionally, strategic intelligence practices will also contribute to positive results, as a firm's economic sustainability depends on installed processes to obtain informational elements coming from the external environment to support its decision-making process. In this way, innovation often benefits from intelligence processes, especially when it provides new knowledge, monitors technological trajectories, and expands understanding of the external environment. To survive in a competitive market a firm needs innovation capabilities and strategic intelligence practices, but how are they related? Firms that are proactive in terms of their strategic intelligence practices have more developed innovation capabilities when compared to those reactive ones? This study aims to identify whether firms with activities associated with the strategic intelligence process differ in terms of their innovation capability level, verifying differences when comparing reactive and proactive groups. We analyzed secondary data of 1,331 Brazilian manufacturing firms. From the analysis, we have identified that development, operations and management capabilities are higher in those firms where there are strategic intelligence practices in place.
The first data on fungi and fungus-like organisms in Lake Baikal

The group of aquatic microscopic fungi remains almost unexplored in Lake Baikal. The species composition and functional role of fungi in the ecosystem of the lake are currently unknown. Fungi in aquatic ecosystems play important role is the decomposition of organic residues of various origin, in particular, such hardly biodegradable compounds as lignin and cellulose. They can live in the associations with algae, fishes and invertebrates with positive or negative influence to the hosts. Still there is no good data about isolation, morphological description and taxonomic identification of fungi from Lake Baikal. At the same time the recent publications (using high-throughput sequencing technology) allow us to assume the rather high diversity of fungi and fungi-like organisms in the lake (Kulakova et al., 2016; Yi et al., 2017; Mincheva et al., 2019). This study aimed to obtain the first data of main taxomonic groups of fungi inhabiting in the coastal zone of Lake Baikal.
Enterotoxin and slime gene detection in Staphylococcus coagulase negative isolated from ground beef

Among the meat products, ground beef presents a greater risk of contamination, due to excessive manipulation and greater surface contact. Staphylococcus indicates inadequate hygienic-sanitary conditions of food. Coagulase-negative Staphylococci (CoNS) cover most of the existing staphylococci species and among the virulence factors presented by this group, biofilm production and staphylococcal enterotoxins (SE) are the most prominent. The objective of this study was to detect the presence of enterotoxin and biofilm genes in coagulase-negative Staphylococci isolates obtained from ground beef samples. Twenty four strains of CoNS isolated from fresh bovine meat, phenotypically characterized as biofilm producers, were used. The samples were collected in twenty four commercial establishments (butchers and supermarkets) in Umuarama City from Parana State, Brazil. The CoNS count found was between 1.0 x 10³ and 3.8 x 10 5 CFU/g of food. All 24 samples showed genes belonging to the ica operon , 21 (87.50%) carrying the ica A, ica C and ica D genes and 3 (12.50%) of the ica A and ica D genes. 95.83% (23/24) of the strains were carriers of the sea enterotoxin gene, being 9 (37.5%) only sea , one (4.2%) sea and seb , 7 (29.1%) sea and see and 6 (25.0%) sea , seb and see . One (4.2%) strain did not show any of the enterotoxin genes. The detection of enterotoxin and biofilm genes in CoNS demonstrate the pathogenic potential of this microorganism. The lack of epidemiological data neglects the actual fault of the CoNS in foodborne diseases.
Triple arginines as molecular determinants for pentameric assembly of the intracellular domain of 5-HT3A receptors

Serotonin type 3A receptors (5-HT3ARs) are cation-conducting homo-pentameric ligand-gated ion channels (pLGICs) also known as the Cys-loop superfamily in eukaryotes. 5-HT3Rs are found in the peripheral and central nervous system, and they are targets for drugs used to treat anxiety, drug dependence, schizophrenia, as well as chemotherapy-induced and post-operative nausea and emesis. Decades of research of Cys-loop receptors have identified motifs in both the extracellular and transmembrane domains that mediate pentameric assembly. Those efforts have largely ignored the most diverse domain of these channels, the intracellular domain (ICD). Here we identify molecular determinants inside the ICD for pentameric assembly by first identifying the segments contributing to pentamerization using deletion constructs, and remarkably by making a small number of defined amino acid substitutions. Our work provides direct experimental evidence for the contribution of three arginines, previously implicated in governing the low conductance of 5-HT3ARs, in structural features such as pentameric assembly.
Investigation of Soil Wetting Pattern in Drip Irrigation using LoraWAN Technology

Soil moisture based irrigation was used widely due to its low cost, effectiveness in saving water, and increasing of crop yield. However, soil moisture under drip irrigation varies spatially due to the influences of environmental factors. That means the location of soil moisture sensors can affect the soil moisture levels in a field. Thus, investigation of soil water movement to guide the placement of soil moisture sensors could be an important factor for well-designed soil moisture based irrigation system. To investigate the water movement under drip irrigation, an Internet of Things (IoT) system including soil water potential (SWP) sensors, LoRa (Long Range) communication system, local gateway, and cloud server was developed. 16 SWP sensors were placed in crop root zone at one side of an emitter along with the dripline. With the designed configuration, the data of SWP sensors could be monitored and accessed by end users through internet. The developed IoT system was tested and evaluated functionally, even there was no irrigation event during the period. The results indicated that The SWP sensors could detect the change of SWP and were sensitive enough to respond these changes during a precipitation event. The outcome from this study showed the effectiveness of the LoRaWAN based IoT system in the investigation of water movement in the soil. More experiment will be conducted to measure the soil water movement under drip irrigation in the future.
EFFECTS OF CANOPY STRUCTURE ON GROWTH AND BELOWGROUND/ABOVEGROUND BIOMASS OF SEEDLINGS IN UNEVEN-AGED TROJAN FIR STANDS

Growth and survival of understory seedlings are infl uenced by their interactions with the environmental variables. The understanding of the relationships between stand density, canopy structure, and understory seedlings’ growth help forest managers conduct successful establishment through natural regeneration. In this study, the infl uence of stand basal area (BA) (m2.ha-1), photosynthetically active radiation transmitted through canopy (PART), leaf area index (LAI), height-to-crown base (HCB) and aspect on the root-collar diameter (RCD) (mm) growth, height growth (cm) and belowground/aboveground biomass (g) of seedlings is observed in uneven-aged Trojan fi r stands. Seedling growth and belowground/aboveground biomass models were developed for fi ve growing seasons after germination. PART, aspect and HCB were found to be the most strongly related to RCD and height growth of Trojan fi r seedlings. PART and aspect explained the most variance in belowground/aboveground biomass of the seedlings. The data also showed that the light transmitted through the canopy was the most signifi cant predictor of understory seedlings growth; thus, PART reaching understory can accelerate the development of sub-canopy layers in uneven-aged Trojan fi r stands. Although survival of Trojan fi r seedlings is usually high under canopy, results suggest that complete canopy closure should be avoided even in stands of shade-tolerant species such as Trojan fi r to increase a seedling’s vigor for its successful recruitment into middle and overstory. The fi ndings of this study will be helpful for forest managers to enhance the establishment and recruitment of Trojan fi r seedlings in uneven-aged stands. v.24 n.4 2018
Systematic Analysis of trans and Conjugated Linoleic Acids in the Milk and Meat of Ruminants

Conjugated fatty acids are defined as fatty acids (FA) in which any two double bonds in the molecule are separated by a single carbon-carbon bond (C=C–C=C). The number of possible conjugated fatty acids is considerable since the FA can differ in chain length, position of the conjugated system within the molecule, up to four possible geometric configurations for each positional isomer, and number of additional double bonds in the molecule. In addition to conjugated dienes, some plant oils have conjugated trienes or tetraenes in which there are three and four double bonds each separated by a single carbon-carbon bond (1). In this chapter we will restrict our discussion to the analysis of conjugated dienes derived mainly from ruminant animals. We will use the term conjugated linoleic acid (CLA) even though this term is somewhat restrictive and incorrect (2). For example, 9c11t15c-18:3 is a conjugated fatty acid but is not derived from linoleic acid. All CLA isomers give rise to unique ultraviolet and infrared absorptions, and their chemical properties and chromatographic behaviors are very different from the more common methylene interrupted unsaturated FA. These characteristic properties have been successfully used for their identification and quantification (2). However, it has not been these chemical and chromatographic differences that have distinguished CLA in the past 20 years with the challenges of handling, identification, and completeness of separation, but their unique biological effects. Systematic Analysis of trans and Conjugated Linoleic Acids in the Milk and Meat of Ruminants