Miracle-dz/UniFAR-FTUs huggingface dataset:
Microsatellite genotyping of brown crab Cancer pagurus reveals fine scale selection and ‘non-chaotic’ genetic patchiness within a high gene flow system

Title: ABSTRACT: Brown crab, Cancer pagurus , supports one of the most important European fisheries, 11 however, spatial patterns of connectivity and adaptation are largely unknown and difficult to 12 identify due to the species’ life history which entails distinct dispersal characteristics during larval 13 and adult life stages. To address this limitation spatial-temporal genetic structure was assessed, 14 using 8 microsatellite loci, across the majority of the species’ NE Atlantic distribution. Neutral 15 genetic structuring revealed a background of high gene flow throughout the region, with a 16 superimposed pattern of chaotic genetic patchiness (CGP) linked to stochastic recruitment 17 variability. The CGP was geographically patterned, being prevalent among English Channel samples 18 and absent among North Sea samples, suggesting specific biological (e.g. reproductive ecology) and 19 environmental (seascape) drivers. Such recruitment variability may compromise stock resilience and 20 must be considered within spatial management strategies. Another prominent feature was the 21 pronounced differentiation of males sampled within a fjord (Gulmarsfjord) from all other samples, at 22 a single locus exhibiting the effects of divergent selection. Gulmarsfjord females were genetically 23 similar to all other ‘non-fjord’ samples, and exhibited a comparative level of differentiation at the 24 outlier locus from the Gulmarsfjord males. Due to known dispersal differences between the sexes, 25 the pattern within Gulmarsfjord can be explained by the intermingling of allochthonous females with 26 resident, locally adapted, males and demonstrates the occurrence of fine-scale local adaptation in 27 this species. Collectively, the study highlights how considerable intraspecific eco-evolutionary diversification can occur despite high levels of dispersal / gene flow.
Responses of Soybean Dry Matter Production, Phosphorus Accumulation, and Seed Yield to Sowing Time under Relay Intercropping with Maize

Soybean production under maize–soybean relay-intercropping system (MSICS) is vulnerable to shading. A study was initiated to investigate the effects of three sowing-times: ST1, 90; ST2, 70; and ST3, 50 days of co-growth period and two phosphorus-rates: P0, 0; and P60, 60 kg P ha−1 on soybean under MSICS. Results revealed that ST3 significantly increased the photosynthetically active radiations, leaf area index, and photosynthetic rate by 72% and 58%, and 61% and 38%, and 6% and 8%, respectively, at full-flowering and full-pod stage of soybean than ST1. Treatment ST3, increased the total dry-matter (TDM) and the highest TDM was reached at full-seed (R6) stage. Similarly, ST3 considerably increased the dry-matter partitioning to pods and seeds, relative to ST1, soybean under ST3 at R6 had 35% and 30% higher pod and seed dry-matter, respectively. Moreover, ST3 exhibited the maximum seed-yield (mean 1829.5 kg ha−1) for both years of this study. Soybean under ST3 with P60 accumulated 38% higher P, and increased the P content in pods and seeds by 36% and 33%, respectively at R6 than ST1. These results imply that by selecting the appropriate sowing-time and phosphorus-rate for soybean, we can increase the TDM and seed-yield of soybean under MSICS.
Effect of wheat flour protein variations on sensory attributes, texture and staling of Taftoon bread

The quality of flat breads depends in part on the textural properties of breads during storage. These properties are largely affected by flour protein quality and quantity. The present study aimed to examine differences between sensory properties, textural and staling of Tandoori breads made from flours of different quality and different quantities of protein. This was implemented by using three flours with 9.4, 11.5 and 13.5% protein contents and different protein qualities shown by Zeleney sedimentation volume 16.25, 22.75 and 23.25 mL respectively. Bread strips were submitted to uniaxial compression between two parallel plates on an Instron Universal Testing machine, and firmness of the breads was determined. Results indicated the differences in the sensory attributes of breads produced by flours of different protein content and quality, demonstrating that high protein high quality flours are not able to sheet and expand under the high temperature - short time conditions employed in Taftoon bread production and are therefore not suitable for this kind of bread. Results showed that flour with 11.5% protein content, produced bread with better sensory characteristics and acceptable storage time.
Novel Nested Peptide Epitopes Recognized by CD4+ T Cells Induced by HIV-1 Conserved-Region Vaccines

CD4+ T-cell responses play an important role in the immune control of the human immunodeficiency virus type 1 (HIV-1) infection and as such should be efficiently induced by vaccination. It follows that definition of HIV-1-derived peptides recognized by CD4+ T cells in association with HLA class II molecules will guide vaccine development. Here, we have characterized the fine specificity of CD4+ T cells elicited in human recipients of a candidate vaccine delivering conserved regions of HIV-1 proteins designated HIVconsv. The majority of these 19 most immunogenic regions contained novel epitopes, that is, epitopes not listed in the Los Alamos National Laboratory HIV Sequence Database, which were able in vitro to stimulate vaccinees’ CD4+ T cells to proliferate and produce interferon-γ and tumor necrosis factor-α. Accumulation of HLA class II epitopes will eventually accelerate development of HIV-1 prophylactic and therapeutic vaccines.
Some animals are more equal than others: Validation of a new scale to measure how attitudes to animals depend on species and human purpose of use

Globally, many millions of animals are used by humans every year and much of this usage causes public concern. A new scale, devised to measure attitudes to animal use in relation to the purpose of use and species, the Animal Purpose Questionnaire (APQ), was completed by in total 483 participants, 415 British nationals and 68 participants from 39 other countries. The APQ was presented in two survey formats, alongside an established Animal Attitudes Scale (AAS). In both surveys, participants also provided demographic details to provide a context to their attitudes to animals. As might be expected, and consistent with the validity of the new scale, overall scores on the AAS and APQ were highly correlated. However, the APQ provided a more differentiated measure of attitudes to animal use across a variety of settings. The results showed that there was overall higher levels of agreement with the use of animals in medical research and basic science, less endorsement for food production and pest control, and the use of animals for other cultural practices was generally disapproved of, irrespective of species. Participants overall disagreed with the use of rabbits, monkeys, badgers, tree shrews (survey 1), chimpanzees, dogs, dolphins and parrots (survey 2), but were neutral about the use of rats, mice, pigs, octopus, chickens, zebrafish (survey 1), carp, chickens, pigs, pigeons, rabbits and rats (survey 2). Interactions between species and purpose were largely driven by the consideration of using diverse species for food production. In general, females and vegetarians expressed less agreement with the use of animals with some differences by purpose of use. Pet keeping consistently predicted reduced willingness to use animals for basic science (only). The APQ provides a new tool to unpack how public attitudes depend on the intersectionality of demographics, species and purpose of use.
The Moovis® implant for trapeziometacarpal osteoarthritis: results after 2 to 6 years

In this retrospective study we reviewed the outcomes of 46 trapeziometacarpal joint replacements with the Moovis® prosthesis in 46 patients with painful osteoarthritis. The dual mobility design of this prosthesis aims to reduce prosthetic dislocation and subsidence. At follow-up 2 to 6 years (mean 5 years) after operation, pain was reduced from 6 to 0 on a visual analogue scale from 0 to 10. The scores of the Quick Disabilities of the Arm, Shoulder and Hand questionnaire improved significantly. Thumb motion and grip and pinch strength did not differ significantly from the contralateral hand. There were no radiographical signs of implant subsidence or loosening. No implant required revision. Forty-five patients rated the result as excellent or good. We conclude the Moovis® is a reliable and effective implant at short- to mid-term follow-up. Level of evidence: IV
Antiviral activity of sertindole, raloxifene and ibutamoren against transcription and replication-competent Ebola virus-like particles

A chemical library comprising 2,354 drug-like compounds was screened using a transcription and replication-competent virus-like particle (trVLP) system implementing the whole Ebola virus (EBOV) life cycle. Dose-dependent inhibition of Ebola trVLP replication was induced by 15 hit compounds, which primarily target different types of G protein-coupled receptors (GPCRs). Based on the chemical structure, the compounds were divided into three groups, diphenylmethane derivatives, promazine derivatives and chemicals with no conserved skeletons. The third group included sertindole, raloxifene, and ibutamoren showing prominent antiviral effects in cells. They downregulated the expression of viral proteins, including the VP40 matrix protein and the envelope glycoprotein. They also reduced the amount of EBOV-derived tetracistronic minigenome RNA incorporated into progeny trVLPs in the culture supernatant. Particularly, ibutamoren, which is a known agonist of growth hormone secretagogue receptor (GHSR), showed the most promising antiviral activity with a 50% effective concentration of 0.2 μM, a 50% cytotoxic concentration of 42.4 μM, and a selectivity index of 222.8. Here, we suggest a strategy for development of anti-EBOV therapeutics by adopting GHSR agonists as hit compounds.
Travel-Related Typhoid Fever: Narrative Review of the Scientific Literature

Enteric fever is a foodborne infectious disease caused by Salmonella enterica serotypes Typhi and Paratyphi A, B and C. The high incidence in low income countries can increase the risk of disease in travelers coming from high income countries. Pre-travel health advice on hygiene and sanitation practices and vaccines can significantly reduce the risk of acquiring infections. Although the majority of the cases are self-limiting, life-threatening complications can occur. Delayed diagnosis and cases of infections caused by multi-drug resistant strains can complicate the clinical management and affect the prognosis. More international efforts are needed to reduce the burden of disease in low income countries, indirectly reducing the risk of travelers in endemic settings. Surveillance activities can help monitor the epidemiology of cases caused by drug-susceptible and resistant strains.
Aerosol Characteristics and Physico-Chemical Compatibility of Combivent® (Containing Salbutamol and Ipratropium Bromide) Mixed with Three Other Inhalants: Budesonide, Beclomethasone or N-Acetylcysteine

Inhalation therapy with a nebulizer is widely used in chronic respiratory disease. Mixing inhalation solutions/suspensions for simultaneous inhalation is more convenient and might simplify the administration procedure. However, there are no data available to address the in vitro aerosol characteristics and physico-chemical compatibility of Combivent® (containing Salbutamol and Ipratropium bromide) with other inhalation solutions/suspensions. In order to investigate the in vitro aerosol characteristics and physico-chemical compatibility of Combivent® with Budesonide, Beclomethasone, and N-acetylcysteine, the appearance, pH, osmotic pressure, chemical stability, mass median aerodynamic diameter (MMAD), fine particles fraction (FPF), particle size corresponding to X50 (particle size, which accounts for 50% of the total cumulative percentage of volume of all particles), delivery rate, and total delivery of the mixed inhalation solution/suspension were tested. There was no change in the appearance such as a change in color or precipitation formation at room temperature. The pH, osmolality, and chemicals of the mixtures were stable for 24 h after mixing. There were no significant differences between Combivent®, Budesonide, Beclomethasone, N-acetylcysteine, and the mixtures in MMAD, FPF, X50, the delivery rate, and the total delivery. This indicates that the mixtures were physically and chemically compatible. The mixing did not influence the particle size, distribution, or delivery compatibility of the mixtures.
Evaluation of Selected Herbicides on Weed Control Efficiency and Yield of Wheat

Background: Weed control is an important issue for the proper growth of wheat. Objective: The purpose of the present study was to see the effect of selected herbicides on weed infestation behavior in wheat field; to determine the effect of herbicides on growth and development of wheat plants, and to evaluate the effect of herbicides on yield performance of wheat. Methodology: A field experiment was conducted at the Experimental Farm of the Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, Bangladesh during November to May 2011 -2012. Four herbicides were tested at recommended dose alone and also coupled with supplemental hand weeding in wheat crop. In addition, a weedy check (control) was also imposed for treatment comparison. The herbicides were Pendimethalin, Carfentrazone-ethyl + Isoproturon, Carfentrazone-ethyl and 2,4-D. In this way, nine treatment combinations were arranged in the RCBD experiment with three replications. Result: Carfentrazone-ethyl performed the best in terms of weed control efficiency (79.68%), while Pendimethalin performed the worst (52.74%). Carfentrazone-ethyl + Isoproteuron contributed to the highest tillers per unit area (226.3 m -2 ) and the highest total dry matter (1342 g m -2 ). Finally, Carfentrazone-ethyl + Isoproteuron also contributed to the highest grain yield of 3.56 t ha -1 with the highest harvest index of 0.42. Carfentrazone-ethyl + Isoproteuron accompanied by one hand weeding also contributed to statistically identical grain yield of 3.33 t ha -1 . Single ingredient Carfentrazone-ethyl alone and when accompanied with one hand weeding also contributed to statistically identical grain yields of 3.26 t ha -1 and 3.46 t ha -1 , respectively. Conclusion: The study revealed that, combined ingredient herbicide Carfentrazone-ethyl + Isoproteuron as well as Carfentrazone-ethyl alone might used at field level due to their better weed control efficiency, favourable effect on crop growth and development and higher grain yield. Journal of Science Foundation 2014;12(2):27-33 DOI: http://dx.doi. org/10.3329/jsf.v12i2. 27734
Immunopathogenesis of Progressive Scarring Trachoma: Results of a 4-Year Longitudinal Study in Tanzanian Children

Trachoma is initiated during childhood following repeated conjunctival infection with Chlamydia trachomatis, which causes a chronic inflammatory response in some individuals that leads to scarring and in-turning of the eyelids in later life. There is currently no treatment to halt the progression of scarring trachoma due to an incomplete understanding of disease pathogenesis. A cohort study was performed in northern Tanzania in 616 children aged 6 to 10 years at enrollment. Every 3 months for 4 years, children were examined for clinical signs of trachoma, and conjunctival swabs were collected for C. trachomatis detection and to analyze the expression of 46 immunofibrogenic genes. ABSTRACT Trachoma is initiated during childhood following repeated conjunctival infection with Chlamydia trachomatis, which causes a chronic inflammatory response in some individuals that leads to scarring and in-turning of the eyelids in later life. There is currently no treatment to halt the progression of scarring trachoma due to an incomplete understanding of disease pathogenesis. A cohort study was performed in northern Tanzania in 616 children aged 6 to 10 years at enrollment. Every 3 months for 4 years, children were examined for clinical signs of trachoma, and conjunctival swabs were collected for C. trachomatis detection and to analyze the expression of 46 immunofibrogenic genes. Data were analyzed in relation to progressive scarring status between baseline and the final time point. Genes that were significantly associated with scarring progression included those encoding proinflammatory chemokines (CXCL5, CCL20, CXCL13, and CCL18), cytokines (IL23A, IL19, and IL1B), matrix modifiers (MMP12 and SPARCL1), immune regulators (IDO1, SOCS3, and IL10), and a proinflammatory antimicrobial peptide (S100A7). In response to C. trachomatis infection, IL23A and PDGF were significantly upregulated in scarring progressors relative to in nonprogressors. Our findings highlight the importance of innate proinflammatory signals from the epithelium and implicate interleukin 23A (IL-23A)-responsive cells in driving trachomatous scarring, with potential key mechanistic roles for PDGFB, MMP12, and SPARCL1 in orchestrating fibrosis.
Speaking Anxiety in a Kazakhstani Foreign Language Classroom

The present study aimed to contribute to our understanding of foreign language anxiety, in general, and in particular speaking anxiety in Kazakhstani environment. It was the first attempt to fill this gap and reveal more about the speaking anxiety in the Elementary level of Kazakh students group, having considered how anxiety might have affected speaking and overall classroom performance. This study addressed the issue of identifying foreign language speaking anxiety and the major consequences of language speaking anxiety reported by students learning English in the evaluation of the foreign language classroom. Anxiety levels in Kazakh students of English were studied through self-evaluation using a scale adapted from the FLCAS (Foreign Language Classroom Anxiety Scale) developed by E. K. Horwitz, M. B. Horwitz, and Cope (1986). As revealed by the results of this study, English language speaking anxiety does exist among the Kazakh second-year university students who participated in this study. And too, the study revealed that these students have had a number of negative experiences with speaking activities in a foreign language class.
CagA–ASPP2 complex mediates loss of cell polarity and favors H. pylori colonization of human gastric organoids

Significance Infection by the bacterium Helicobacter pylori is the main risk factor for stomach cancer. Strains of H. pylori that produce the virulence factor CagA substantially increase stomach cancer risk compared with strains without CagA. CagA disrupts cell polarity—the specialized asymmetric organization within cells—but the mechanism it uses and its influence on colonization are not fully understood. Using a three-dimensional culture of stomach cells (human gastric organoids) and cell lines, we find that the tumor suppressor ASPP2 is crucial in disruption of cell polarity by CagA during H. pylori infection. Interfering with the CagA–ASPP2 interaction, using small molecules or a specific peptide, blocks loss of cell polarity and reduces bacterial colonization in organoids. The main risk factor for stomach cancer, the third most common cause of cancer death worldwide, is infection with Helicobacter pylori bacterial strains that inject cytotoxin-associated gene A (CagA). As the first described bacterial oncoprotein, CagA causes gastric epithelial cell transformation by promoting an epithelial-to-mesenchymal transition (EMT)-like phenotype that disrupts junctions and enhances motility and invasiveness of the infected cells. However, the mechanism by which CagA disrupts gastric epithelial cell polarity to achieve its oncogenicity is not fully understood. Here we found that the apoptosis-stimulating protein of p53 2 (ASPP2), a host tumor suppressor and an important CagA target, contributes to the survival of cagA-positive H. pylori in the lumen of infected gastric organoids. Mechanistically, the CagA–ASPP2 interaction is a key event that promotes remodeling of the partitioning-defective (PAR) polarity complex and leads to loss of cell polarity of infected cells. Blockade of cagA-positive H. pylori ASPP2 signaling by inhibitors of the EGFR (epidermal growth factor receptor) signaling pathway—identified by a high-content imaging screen—or by a CagA-binding ASPP2 peptide, prevents the loss of cell polarity and decreases the survival of H. pylori in infected organoids. These findings suggest that maintaining the host cell-polarity barrier would reduce the detrimental consequences of infection by pathogenic bacteria, such as H. pylori, that exploit the epithelial mucosal surface to colonize the host environment.
The Neural Inhibition of Learning Increases Asset Market Bubbles: Experimental Evidence

ABSTRACT The authors tested a leading theory of bubble formation, insufficient learning, in a laboratory asset market using a drug, Naltrexone, which inhibits reinforcement learning. We found that asset price bubbles in Naltrexone sessions were larger compared with placebo sessions, averaging 60% higher in amplitude and 77% larger in the deviation from fundamental value in the final 12-period trading round. There was no difference between conditions in understanding of the trading rules, overconfidence, or confusion. Participants on Naltrexone appeared unable to determine appropriate trading strategies as prices changed. The findings indicate that specific neural mechanism of reinforcement learning is involved in the formation of asset market bubbles.
Peripheral Merozoite Surface Proteins Are Targets of Naturally Acquired Immunity against Malaria in both India and Ghana

Development of a successful blood-stage vaccine against Plasmodium falciparum malaria remains a high priority. Immune-epidemiological studies are effective tools for the identification of antigenic targets of naturally acquired immunity (NAI) against malaria. However, differences in study design and methodology may compromise interstudy comparisons. ABSTRACT Development of a successful blood-stage vaccine against Plasmodium falciparum malaria remains a high priority. Immune-epidemiological studies are effective tools for the identification of antigenic targets of naturally acquired immunity (NAI) against malaria. However, differences in study design and methodology may compromise interstudy comparisons. Here, we assessed antibody responses against intact merozoites and a panel of 24 recombinant merozoite antigens in longitudinal cohort studies of Ghanaian (n = 115) and Indian (n = 121) populations using the same reagents and statistical methods. Anti-merozoite antibodies were associated with NAI in both the Indian (hazard ratio [HR] = 0.41, P = 0.020) and the Ghanaian (HR = 0.17, P < 0.001) participants. Of the 24 antigen-specific antibodies quantified, 12 and 8 were found to be protective in India and Ghana, respectively. Using least absolute shrinkage and selection operator (LASSO) regression, a powerful variable subselection technique, we identified subsets of four (MSP6, MSP3.7, MSPDBL2, and Pf12) and five (cMSP33D7, MSP3.3, MSPDBL1, GLURP-R2, and RALP-1) antigens that explained NAI better than the individual antibodies in India (HR = 0.18, P < 0.001) and Ghana (HR = 0.31, P < 0.001), respectively. IgG1 and/or IgG3 subclasses against five antigens from these subsets were associated with protection. Through this comparative study, maintaining uniformity of reagents and methodology, we demonstrate that NAI across diverse geographic regions may result from antibodies to multiple antigenic targets that constitute the peripheral merozoite surface protein complexes.