Miracle-dz/UniFAR-FTUs huggingface dataset:
Plasmodium-specific atypical memory B cells are not part of the long-lived memory response

A subset of atypical memory B cells accumulates in malaria and several infections, autoimmune disorders and aging in both humans and mice. It has been suggested these cells are exhausted long-lived memory B cells, and their accumulation may contribute to poor acquisition of long-lasting immunity to certain chronic infections, such as malaria and HIV. Here, we generated an immunoglobulin heavy chain knock-in mouse with a BCR that recognizes MSP1 of the rodent malaria parasite, Plasmodium chabaudi. In combination with a mosquito-initiated P. chabaudi infection, we show that Plasmodium-specific atypical memory B cells are short-lived and disappear upon natural resolution of chronic infection. These cells show features of activation, proliferation, DNA replication, and plasmablasts. Our data demonstrate that Plasmodium-specific atypical memory B cells are not a subset of long-lived memory B cells, but rather short-lived activated cells, and part of a physiologic ongoing B-cell response.
The Impact of Human Error in the Use of Agricultural Tractors: A Case Study Research in Vineyard Cultivation in Italy

Recently, standards and regulations concerning occupational safety have become more and more rigorous. Nevertheless, the number of accidents and victims has not decreased significantly, as reported by official statistics. In Italy, the agricultural sector is certainly one of the most affected by this situation, especially taking into account the occurrence of serious injuries and fatalities related to the use of tractors. The main reasons for such a situation can be ascribed to the peculiarities of agricultural operations. Therefore, when analyzing the root causes of agricultural accidents, a user-centered approach is needed in order to make the development of health and safety interventions easier and more effective. Based on this, the present paper proposes a practical case study research focused on integrating the factor of human error into the risk assessment procedures of agricultural activities in vineyard cultivation. Such an approach allowed us to consider the impact of human error—while performing work activities (e.g., the use of a tractor)—on hazards and related hazardous events in a thorough manner. The proposed approach represents a novelty in the sector of the safety assessment of agricultural activities, providing a first valuable basis for further analysis and implementation by researchers and practitioners.
Distribution of Fim A Genotypes among Porphyromonas Gingivalis associated with Chronic Periodontitis in Al-Najaf Al-Ashraf City

This research aims to detect the prevalence of fim A genotypes I, Ib, II, III, IV and V among Porphyromonas gingivalis related with periodontitis. Amplification of 16S rRNA gene showed that out of 150 DNA samples that extracted from subgingival plaque specimens of patients with chronic periodontitis only 40 DNA specimens were belonged to P. gingivalis and DNA sequencing demonstrated 98% homologous with P. gingivalis strain CP38 16S rRNA gene, partial sequence. fimA type IV gene was the most predominance with 27.5% followed by fimA type III with12.5% while fimA type II show up with the lowest percentage (5%) while fimA type Ib was not identified. This finding denoted that P. gingivalis that possess fimA type IV was the most importance pathogens associated with chronic periodontitis Keywords: P. gingivalis, Fim A genotypes, Periodontitis.
Human Amniotic Mesenchymal Stem Cells Exhibit Similar Immunosuppressive Ability with Bone Marrow Mesenchymal Stem Cells and Possess a Higher Proliferation Activity and Clearer Stem Cell Properties in vitro

Objectives: Human bone marrow mesenchymal stem cells (hBMSCs) have been used for the prevention and treatment of acute graft-versus-host disease (aGVHD) in post-hematopoietic stem cell transplant patients. In this study, we compared the biological characteristics and immunosuppressive activity of human amniotic mesenchymal stem cells (hAMSCs) and hBMSCs to provide experimental evidence for the potential use of hAMSCs for treating aGVHD, thus solving the problem of insufficient hBMSCs sources. Methods: HAMSCs were isolated by enzymatic digestion. hBMSCs were isolated using Ficoll-Hypaque density gradients. The biological characteristics of both stem cell types were compared by morphological analysis, analysis of cell growth, cell cycle profiling, immunophenotyping, and immunofluorescence assays. An in vitro co-culture of MSCs and peripheral blood mononuclear cells (PBMCs) was performed and lymphocyte proliferation measured using the Cell Counting Kit-8(CCK-8) assay. IFN-γ production was determined in the co-culture supernatant using enzyme linked immunosorbent assay (ELISA). Results: Both hAMSCs and hBMSCs had fibroblast-like morphology. hAMSCs could be maintained for at least 15 culture passages, but hBMSCs started to show signs of aging and remarkably reduced proliferation at 6-7 passages. There was no significant difference in the proportion of cells in G2/M phase between hAMSCs and hBMSCs (P>0.05). Immunophenotyping revealed positive expression of CD105, CD90, and CD73 and negative expression of CD34, CD45, CD11b, CD19, and HLA-DR on the surface of both hAMSCs and hBMSCs. hAMSCs were positive for Oct-3/4, but hBMSCs were not. Both hAMSCs and hBMSCs expressed vimentin. PHA-stimulated PBMCs proliferation was inhibited by hAMSCs and hBMSCs. This inhibition was stronger, as the proportion of MSCs increased. There were not significant differences between the inhibitory effects of the two MSCs types on PBMCs proliferation (P>0.05). Interferon-γ (IFN-γ) production was lower when PBMCs were co-cultured with either hAMSCs or hBMSCs than when they were cultured alone (P 0.05). Conclusion: The results of this study demonstrated that hAMSCs have higher proliferation activity and clearer stem cell properties than hBMSCs. Both hAMSCs and hBMSCs were able to suppress the proliferation of allogeneic peripheral blood lymphocytes and reduce IFN-γ secretion stimulated by PHA in vitro.
Limonene attenuates methylglyoxal-induced dysfunction in MC3T3-E1 osteoblastic cells

ABSTRACT Limonene is a common natural terpene with powerful antioxidative properties. This study investigated the effects of limonene, a terpene found in citrus fruits, on the function of the murine pre-osteoblast cell line, MC3T3-E1 cells. The results showed that limonene treatment significantly elevated collagen synthesis, alkaline phosphatase activity, osteocalcin synthesis, and mineralization in osteoblastic cells. Methylglyoxal (MG), a highly reactive dicarbonyl metabolite, is a major precursor of advanced glycation end products, which are involved in the pathogenesis of diabetic osteopathy. We therefore investigated the effects of limonene on MG-induced cytotoxicity. Pre-treatment of MC3T3-E1 cells with limonene prevented MG-induced cell death and apoptosis. Limonene also reduced MG-triggered endoplasmic reticulum (ER) stress, as indicated by decreases in the levels of the ER-localized transmembrane signal transducers ATF-6 and IRE1. Furthermore, limonene treatment significantly reduced MG-induced autophagic activity and reactive oxygen species release. These results suggest that limonene may prevent the development of diabetic osteopathy.
Climber Diversity across Vegetational Landscape of North-Eastern Uttar Pradesh, India

The composition and diversity of climbers among grassland, wasteland and forest vegetations was examined with respect to their woodiness, climbing mode and circumnutation pattern across the vegetational landscape of north-eastern Uttar Pradesh during 2011-2015. A total of 111 climbers, constituting 63 lianas and 48 vine species, under 35 families, were recorded. The forest and wasteland vegetation were quite similar in regard with climber diversity. Family Convolvulaceae included a maximum of 19 climbers. Majority of twining climbers showed right-handed twining. The wasteland vegetation was most suitable and quite similar to forest habitat for vines as well as for lianas. The right handed circumnutation was the dominant pattern among the twiners of the region. Local climbing flora provides considerable natural resource to the region. They often create special micro-habitats and increase the complexity of the ecosystem.
Distractor inhibition contributes to retroactive attentional orienting within working memory: Evidence by lateralized event-related parameters of the EEG

Shifts of attention within mental representations based on retroactive cues (retro-cues) facilitate performance in working memory tasks. It was suggested that this retro-cue benefit is related to the concentration of working memory resources on a subset of representations, thereby improving storage and retrieval at the cost of non-cued items. However, the attentional mechanisms underlying this updating of working memory representations remain unknown. Here, we present EEG data for distinguishing between target enhancement and distractor suppression processes in the context of retroactive attentional orienting. Therefore, we used a working memory paradigm with retro-cues indicating a shift of attention to either a lateralized or non-lateralized item. Posterior and anterior asymmetries in the event-related potential suggested a contribution of both target enhancement and distractor suppression to retroactive attentional selection. Following this stage of selection, there was an increase of posterior alpha power contralateral compared to ipsilateral to the irrelevant item when a non-lateralized mental representation was cued. No comparable asymmetry was revealed when a lateralized item had to be selected. This suggests that the inhibition of the non-cued information is an important feature of attentional orienting within working memory. The current results thus enable a first impression on the interplay of attentional sub-processes in the context of retroactive cuing.
The population genetics of spatial sorting

Recently it has been claimed that natural selection has a “shy younger sibling” called spatial sorting. Spatial sorting is the process whereby variation in dispersal ability is sorted along density clines and will, in nature, often be a transient phenomenon. Spatial sorting is, however, persistent on invasion fronts, where its effect cannot be ignored, causing rapid evolution of traits related to dispersal. While spatial sorting is described in several elegant models, these models require a high level of mathematical sophistication and are not accessible to most evolutionary biologists or their students. Here we incorporate spatial sorting into the classic haploid and diploid models of natural selection. We show that spatial sorting can be conceptualized precisely as selection operating through space rather than (as with natural selection) time, and that genotypes can be viewed as having both spatial and temporal aspects of fitness. The resultant model is strikingly similar to the classic models of natural selection. This similarity renders the model easy to understand (and to teach), but also suggests that many established theoretical results around natural selection will apply equally to spatial sorting.
Effects of Foraging Enrichment on the Behaviour of Parrots

The purpose of this study was to enrich parrot enclosures by creating foraging opportunities appropriate for the species and to investigate the possible preference for a variable versus a constant food supply. The foraging device comprised of a length of wood (2×0.08×0.08m) with 50 holes (0.02m diameter x 0,02m depth) drilled into one face. Food was placed in the holes of the foraging device in one of two distributions: ‘constant’, one food item in every hole (total = 50 food items) or ‘variable’, 5 food items in 10 of the holes (total = 50 food items). The holes were then covered with starch paper. During the enrichment period the parrots spent significantly more time allopreening than in the baseline or post-enrichment periods. The results also provide some evidence of contrafreeloading in parrots, but no preference for a variable over a constant food source. The study shows that providing extra foraging opportunities for parrots is a useful form of enrichment.
Supplemental Information: Cortical reliability amid noise and chaos

It is possible that the amount of internally generated variability in terms of divergence depends not just on the dynamical state of the model circuit but also on its size. We have previously shown that increasing the size of the model beyond the size described above does not alter the observed dynamical states1. At this size, dendritic trees and thus the afferent connections of neurons in the lateral center of the microcircuit are fully located within the microcircuit. However, a large fraction of their recurrent connections with neurons in the surrounding tissue are with neurons beyond the periphery of the microcircuit. Since these neurons were not included in the simulations, large portions of synaptic input to peripheral neurons were missing. To quantify the effect of this additional input on variability in the microcircuit, we surrounded the original microcircuit with six additional microcircuits, simulating a much larger mesocircuit, providing missing synaptic input to the neurons at the periphery of the microcircuit (Fig. 2b1, blue and grey). Connectivity in this mesocircuit was homogeneous, both within and between the individual microcircuits. When we compared the divergence of membrane potentials between microand mesocircuit simulations, we found that membrane potentials diverged slightly faster in the mesocircuit, although the time courses of divergence followed similar trends (Fig. 2b2). The mean difference in rV(t) was always below 0.06, and the steady state difference below 0.03. Considering the difference at 10-20 ms (which we found to be a good predictor of the relative order of differences at any time), we found this difference to increase towards the periphery of the microcircuit (Fig. 2b3). This suggests that additional direct synaptic input onto a neuron increases variability, but has only a weak effect on indirectly connected neurons. Thus, at the scale of the microcircuit, the amount of internally generated variability is nearly saturated, albeit underestimated for neurons at the periphery.
A review of genetic polymorphisms in the receptors for gonadotropic and sex hormones in polycystic ovary syndrome

Polycystic ovary syndrome is a complex, heterogeneous disease that affects 510% of reproductive-aged women. It is characterized by clinical or biochemical hyperandrogenism, oligo-anovulation, and polycystic ovary morphology. Instigating endocrine findings include aberrantly rapid gonadotropin-releasing hormone pulsatile secretion, elevated luteinizing hormone, sub-optimal levels of follicle-stimulating hormone, and hyperandrogenism. Metabolic symptoms are also present including hyperinsulinemia, insulin resistance, and dyslipidemia. These endocrine and metabolic findings are also accompanied by ovarian dysfunction and improper folliculogenesis. Because aberrant functioning of the hypothalamic-pituitary-gonadal axis is central to the pathophysiology of polycystic ovary syndrome, it is beneficial to examine it for abnormalities. Polycystic ovary syndrome has been shown to have both genetic and environmental components. Its strong genetic component has been demonstrated in twin studies, family association studies, candidate gene studies, and genome-wide association studies. Previous genome-wide association studies have found many candidate genes including those for DENND1A (differentially expressed in normal and neoplastic cells domain containing 1A), THADA (thyroid adenoma-associated protein), FSHR (folliclestimulating hormone receptor), and LHR (luteinizing hormone receptor). This, together
Temporal Dynamics of the Origin and Domestication of Sweet Potato and Implications for Dispersal to Polynesia

In a study focussed on the origin of Ipomoea batatas (L.) Lam. (the sweet potato) and its close relatives [1], the authors claimed that a specimen of sweet potato collected by Banks and Solander in 1769 in Polynesia was distinct and along with some other varieties had levels of genetic variation of more than 100,000 years. This timeframe, along with several other lines of evidence, was interpreted, by the authors, as questioning human-mediated transport of the sweet potato to Polynesia within the last 1,000 years. This aspect of the paper received widespread media coverage as well as a number of critical remarks, and correspondence. The criticism questioned whether claims in the paper were justified. Here, three authors from the paper take the opportunity to fully explain the reasoning for calling into question the need to invoke human mediated transport of the sweet potato to Polynesia.
A simple centrifugation protocol for metagenomic studies increases mitochondrial DNA yield by two orders of magnitude

DNA (meta)barcoding is applied to study biodiversity and is available for standardized biodiversity assessments. However, it suffers from PCR bias, which can lead to the loss of specific taxa. PCR‐free techniques such as shotgun metagenomics are therefore thought to be more suited for biodiversity assessments, but are currently limited by incomplete reference libraries. The technique of “mitogenome‐skimming” or “mitogenomics,” in which complete mitochondrial genomes are sequenced, is ideal to bridge the techniques of (meta)barcoding and metagenomics. However, without the enrichment of mitochondria, roughly 99% of all sequencing reads are of non‐mitochondrial origin and mostly useless for common applications, e.g. species identification. Here, we present a simple centrifugation protocol that leads to an average 140‐fold enrichment of mitochondrial DNA. By sequencing six ‘mock’‐communities—comprising the freshwater taxa Corbicula fluminea, Gammarus roeselii and Hydropsyche exocellata each—we recovered whole mitochondrial genomes of these species and the acanthocephalan endoparasite Pomphorhynchus laevis. The enrichment protocol will speed up building reference libraries for whole mitochondrial genomes, as dozens of species can be sequenced on a single MiSeq run. Subsequently, it will also allow biodiversity assessments, using mitogenomics at greatly reduced costs in comparison to mitogenomic approaches without prior enrichment for mitochondria.
Specificity of Molecular Responses to Erk1/2 and Mkk1/2 Inhibitors in Melanoma Cells

Skin cancer is the most commonly diagnosed cancer in the U.S. and 75% of skin cancer related deaths are due to malignant melanoma, a cancer originating in melanin producing melanocytes. The RAF/MKK/ERK signaling cascade is constitutively activated in over 90% of melanomas and 52% of tumors contain BRAF V600E/K oncogenic driver mutations. Although small molecule inhibitors specifically targeting mutant BRAF V600E/K and the downstream kinases MKK1/2 have been successful in clinical settings, resistance invariably develops. In preclinical studies, inhibitors of ERK1/2 can overcome resistance to BRAF V600E/K and MKK1/2 inhibitors, making them promising alternative pathway inhibitors for the treatment of melanoma. However, the specificity of molecular responses to ERK1/2 inhibitors remains unknown. In this thesis, I use SILAC-based phosphoproteomics to quantify molecular responses to the clinically available MKK1/2 inhibitor, trametinib, and the ERK1/2 inhibitors, SCH772984, GDC0994 and Vertex-11e in WM239a human metastatic melanoma cells. I observed significant responses in approximately 5% of all phosphosites identified. Significantly regulated phosphosites showed a high degree of overlap between all inhibitors, suggesting that the pathway functions linearly with relatively little evidence for branchpoints that lead to bifurcation upstream of ERK1/2. I also observe phosphosites responsive to only one of four MKK1/2 or ERK1/2 inhibitors. For example, trametinib shows an ability to block activating phosphorylation sites on p38α MAPK, which are not shared by ERK1/2 inhibitors SCH772984 and GDC0994, the MKK1/2 inhibitor selumetinib, or the BRAF V600E/K inhibitor, vemurafenib. Trametinib
Assessment of external egg characteristics and production indices of the dual purpose French guinea fowl under semi-arid conditions in Nigeria.

A total of fifty one (51) dual purpose French guinea hens were managed intensively on deep litter under the semi-arid weather condition. Data were collected on external egg measurements and daily egg production during the first phase of production before the birds exhibited broodiness. Data were analyzed to measure egg production indices. The average egg length (5.16 ± 0.02 cm), egg width (4.01 ± 0.01), egg shape index (77.82 ± 0.18%) and egg weigh (53.63 ± 0.15 g.) were obtained. There was a significant (P<0.01) correlation between egg weight and egg length (0.879), egg weight and egg width (0.676), egg length and egg width (0.712) and between egg width and egg shape index (0.322). Negative correlations were observed between egg weight and egg shape index (-0.314), egg length and egg shape index (-0.434). The average daily egg, hen day production and hen house production were 26.71 ± 0.35 eggs, 51.39 ± 0.65% and 50.40 ± 2.24% respectively. The mean weekly egg number, hen day rate and hen house production reach their peaks at the third week of production, 46.57 ± 0.78 eggs and 87.87 ± 1.48% and 87.87 ± 1.48%, respectively. Mean weekly egg number and hen day rate begin to decline at week five, eight, nine, twelve, thirteen and fourteen but hen house production decreases from the peak immediately at week four of lay and continued steadily up to week fourteen.
Establishment of EBV latency in nasopharyngeal tumor epithelial cells by in vivo cell-mediated transfer infection

Epstein-Barr virus (EBV) is a herpesvirus associated with approximately 1% of tumors worldwide. Although EBV is consistently detected in nasopharyngeal carcinoma(NPC) biopsy, it is hardly detected in normal nasopharyngeal epithelium. The mechanism how virus establishes latent infection in tumor epithelial cells, including the source of virus and the route of entry, has not been fully elucidated largely due to the lack of appropriate in vivo models. We herein aim to investigate the potential route that epithelial cells are infected with EBV. To this end, we established in vivo model system by injection of cell-free EBV or EBV producer line Akata cells together with EBV negative NPC line HONE-1 cells. Akin to in vitro infections, we presented the first in vivo evidence that cell-mediated transfer infection via Akata cells was much more efficient than cell-free virus. These cells then expressed the EBV latency-associated small RNA EBERs, but not lytic antigens, such as BZLF1. However, when cells were inoculated at separate sites, EBV producer line Akata cell failed to demonstrate the ability of migrating from distant location to interact with HONE-1 cell to establish latent infection. In conclusion, cell-cell contact is critical for in vivo EBV infection of nasopharyngeal epithelial cells. *Correspondence to: Hironori Yoshiyama, Department of Microbiology, Shimane University Faculty of Medicine, Japan, Tel: +81 853-23-2111; E-mail: yosiyama@med.shimane-u.ac. jp Fenggang Yu, Department of Otolaryngology-Head and Neck Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Tel: (65) 6772 5309; Fax: (65) 6775 3820; E-mail: entyf@nus.edu. sg