Miracle-dz/UniFAR-FTUs huggingface dataset:
The Distribution and Origins of Ancient Leprosy

Human leprosy is primarily caused by Mycobacterium leprae, but also by the related ‘M. lepromatosis’. Ancient leprosy can be recognised in archaeological materials by the paleopathology associated with multi-bacillary or lepromatous forms of the disease. Whole M. leprae genomes have been obtained from human skeletons, and diagnostic aDNA fragments have been recovered. The derived M. leprae phylogenies, based on single nucleotide polymorphisms, mirror past human migrations, as M. leprae is usually an obligate pathogen. The detection of M. leprae in historical leprosy cases is assisted by the hydrophobic M. leprae cell envelope, which is composed of unusual lipids that can be used as specific biomarkers. Lipid biomarkers are more stable than aDNA and can be detected directly without amplification. Indigenous human leprosy is extinct in Western Europe, but recently, both M. leprae and ‘M. lepromatosis’ were found in British red squirrels. Leprosy may also be found in ninebanded armadillos (Dasypus novemcinctus) where it can cause a zoonotic human infection. Certain leprosy-like diseases, caused by uncultivable species in cats, for example, may be related to M. leprae. The closest extant relatives of leprosy bacilli are probably members of the M. haemophilum taxon, emerging pathogens with genomic and lipid biomarker similarities.
Diversity and Distribution Patterns of Hard Bottom Polychaete Assemblages in the North Adriatic Sea (Mediterranean)

The knowledge on the hard bottom polychaete assemblages in the Northern Adriatic Sea, a Mediterranean region strongly affected by environmental pressures, is scarce and outdated. The objective of this paper was to update the information on polychaete diversity and depict their patterns of natural spatial variation, in relation to changes in algal coverage at increasing depth. Hard bottom benthos was quantitatively sampled by scraping off the substrate from three stations at Sveti Ivan Island (North Adriatic) at three depths (1.5 m, 5 m and 25 m). Polychaete fauna comprised 107 taxa (the majority of them identified at species level) belonging to 22 families, with the family Syllidae ranking first in terms of number of species, followed by Sabellidae, Nereididae, Eunicidae and Serpulidae. Considering the number of polychaete species and their identity, the present data differed considerably from previous studies carried out in the area. Two alien species, Lepidonotus tenuisetosus, which represented a new record for the Adriatic Sea, and Nereis persica, were recorded. The highest mean abundance, species diversity and internal structural similarity of polychaete assemblages were found at 5 m depth, characterised by complex and heterogeneous algal habitat. The DISTLM forward analysis revealed that the distribution of several algal taxa as well as some algal functional-morphological groups significantly explained the observed distribution patterns of abundance and diversity of polychaete assemblages. The diversity of the North Adriatic hard bottom polychaete fauna is largely underestimated and needs regular updating in order to detect and monitor changes of benthic communities in the area.
Improved Delay-Dependent Stability Criterion for Genetic Regulatory Networks with Interval Time-Varying Delays via New Lyapunov Functionals

In this work, the stability analysis problem of the genetic regulatory networks (GRNs) with interval time-varying delays is presented. In the previous works, the constructions of Lyapunov functional have usually been in simple Lyapunov functional, augmented Lyapunov functional, and multiple integral Lyapunov functional. Therefore, we introduce new Lyapunov functionals expressed in terms of delay product functions. New delay-dependent sufficient conditions for the genetic regulatory networks (GRNs) are established in the terms of linear matrix inequalities (LMIS). In addition, a numerical example is provided to illustrate the effectiveness of the theoretical results.
Global soybean trade - the geopolitics of a bean

Following a collaborative effort and with the support of The UK Research and Innovation Global Challenges Research Fund (UKRI GCRF), the Trade, Development and the Environment Hub -- or simply Trade Hub, https://tradehub.earth/ -- has recently launched the report “Global Soybean Trade – The Geopolitics of a Bean”. Originally cultivated as a traditional staple food in China, soybean today is of the most important global commodities in international trade. The report examines the economics of the ‘soybean miracle’, exploring its complex – and often controversial – implications for people and ecosystems, and analysing how different institutions and stakeholders are addressing the growing sustainability concerns. This publication not only provide a comprehensive review of the existing publications and data, but also highlights some of the open questions that need to be addressed by Trade Hub partners and other stakeholders in order to increase the sustainability of the soybean supply chain, both globally and locally.
KOLMOGOROV CONDITIONALIZERS CAN BE DUTCH BOOKED (IF AND ONLY IF THEY ARE EVIDENTIALLY UNCERTAIN)

Abstract A vexing question in Bayesian epistemology is how an agent should update on evidence which she assigned zero prior credence. Some theorists have suggested that, in such cases, the agent should update by Kolmogorov conditionalization, a norm based on Kolmogorov’s theory of regular conditional distributions. However, it turns out that in some situations, a Kolmogorov conditionalizer will plan to always assign a posterior credence of zero to the evidence she learns. Intuitively, such a plan is irrational and easily Dutch bookable. In this paper, we propose a revised norm, Kolmogorov–Blackwell conditionalization, which avoids this problem. We prove a Dutch book theorem and converse Dutch book theorem for this revised norm, and relate our results to those of Rescorla (2018).
Development of targeted mass spectrometric methods for the quantitation of gluten-specific peptides in foods

Highly purified gluten reference proteins were isolated and extensively characterized by biochemical/analytical methods. 33 Gluten marker peptides in hydrolysed reference protein types were selected and a targeted liquid chromatography-tandem mass-spectrometry method for peptide quantitation was developed. A strategy to convert peptide into protein contents allowed the quantitation of gluten in different food products. Furthermore, a stable isotope dilution analysis to quantitate the immunodominant 33-mer peptide from wheat was developed. The presence in many wheat species and cultivars proved its importance in celiac disease research.
Assessment of Respiratory Bacterial Coinfections Among Severe Acute Respiratory Syndrome Coronavirus 2-Positive Patients Hospitalized in Intensive Care Units Using Conventional Culture and BioFire, FilmArray Pneumonia Panel Plus Assay

Abstract Background Approximately 15% of patients infected by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) present with severe forms of the disease and require hospitalization in intensive care units, which has been associated with high mortality rates. The prevalence of bacterial infections in these patients is not well established, and more data are needed to guide empiric antibiotic therapy and improve patient outcomes. Methods In this prospective multicenter study, we assessed bacterial coinfections identified in culture from 99 French patients infected by SARS-Cov-2 and hospitalized in intensive care units. We concomitantly evaluated an innovative molecular diagnostic technology technique, the BioFire, FilmArray Pneumonia Panel plus (FA-pneumo) assay, to identify these coinfections at an early stage, and its concordance with conventional culture. Results We showed that a bacterial coinfection was detected in 15% of patients based on conventional culture. Staphylococcus aureus and Haemophilus influenzae were the most prevalent pathogens. The sensitivity of FA-pneumo compared with culture was 100%. In contrast, the specificity varied between 88.4% and 100% according to the pathogen, and our results highlighted that 60.5% of bacterial targets reported using this assay were not recovered by culture; 76.9% of discordant results corresponded to bacteria belonging to commensal oral flora and/or reported with ≤105 copies/mL bacterial nucleic acids. Conclusions Based on its excellent sensitivity, the FA-pneumo assay is useful to rule out bacterial coinfections in the context of severe SARS-CoV-2 infection and avoid the inappropriate prescription of antibiotics. However, positive tests should be interpreted carefully, taking into consideration deoxyribonucleic acid bacterial load and all clinical and biological signs.
In the Centre of Attention: How Social Entrepreneurs Influence Organisational Reputation

Abstract To enhance organisational reputation, entrepreneurs are frequently put in the centre of attention. Particularly social entrepreneurs, who combine pro-social and entrepreneurial identities, often represent their organisations. Yet, we know little about how the presentation of a leader influences organisational reputation. Results of a 2 × 2 × 2 pre-registered experiment indicate that a leader-centred communication barely influences the stakeholders’ perceptions. However, stakeholders have a significantly better perception of a social enterprise that presents a leader with salient society-oriented character traits (versus business-oriented character traits). This study contributes to social entrepreneurship and reputation research and reveals new insights for practice.
How Do People Respond to Small Probability Events with Large, Negative Consequences?

We study how people react to small probability events with large negative consequences using the outbreak of the COVID-19 epidemic as a natural experiment. Our analysis is based on a unique administrative data set with anonymized monthly expenditures at the individual level. We find that older consumers reduced their spending by more than younger consumers in a way that mirrors the age dependency in COVID-19 case-fatality rates. This differential expenditure reduction is much more prominent for high-contact goods than for low-contact goods and more pronounced in periods with high COVID-19 cases. Our results are consistent with the hypothesis that people react to the risk of contracting COVID-19 in a way that is consistent with a canonical model of risk taking.
Digestible energy and protein requirements for maintenance and growth of pacu ( Piaractus mesopotamicus ): A factorial approach-based model

: Results of nutrient requirements as determined in dose-response trials are valid only for fish within the same size range of that of experimental model fish. This study used the factorial approach to estimate digestible energy (DE) and digestible protein (DP) requirements for maintenance and growth of pacu ( Piaractus mesopotamicus ). Juvenile pacu (63.5 ± 1.27 g) were stocked in a recirculation system (26.89 ± 0.36 °C) for 58 days, and fed two daily meals. One diet contained 6.96 % lipids (LF) and another 9.98 % lipids (HF), both diets formulated to contain 32 % crude protein, theoretical dietary energy level for maintenance (52.23 kJ DE kg –0.80 d –1 ), in a completely randomized, 2 × 5 factorial experimental design. The apparent digestibility coefficients of energy and protein were 84.66 ± 0.27 % and 89.20 ± 0.61 %, respectively, determined in specific assays for the HF diet, while for the LF diet, the values were 84.52 ± 0.37 % and 89.19 ± 0.16 %, respectively. The analysis of growth and carcass composition data revealed that dietary requirements of digestible energy and protein for maintenance were not influenced by dietary lipid levels; however, requirements of growth digestible energy were higher for fish fed the LF diet (1.39) than for fish fed the HF diet (1.29). The requirement of DP for growth, expressed as g of DP per g of deposited protein, were higher for fish fed the LF diet than for fish fed the HF diet (1.70 vs 1.58).
Consultation-Liaison Psychiatry During COVID-19 Lockdown: A Retrospective Chart Review

The coronavirus disease 2019 (COVID-19) pandemic has caused a major psychosocial impact in the community due to its direct effects and restrictive control strategies, e.g. lockdown. The current pandemic, a highly stressful situation, can predispose not only vulnerable but previously well-adjusted individuals for psychological disorders. A retrospective chart review of consultation-liaison psychiatry (CLP) case records was conducted for one month before and after the start of lockdown. Patients seen during lockdown were relatively younger; t = 1.8, p = 0.074. The most common psychiatric emergency was a suicidal attempt (34.3%) and delirium (35.4%) during and before lockdown, respectively. The probability of the emergency psychiatry presentation for attempted suicide increased significantly during lockdown (odds ratio (OR) 8.0, 95% CI 2.03 to 31.57, p = 0.003). The most common stressors for CLP patients with suicide attempts during lockdown were relationship issues and loss of privacy. It seems that stressors arising due to the current crisis are not only highly severe and multiple but qualitatively different. Further studies with larger sample sizes and from other parts of the country can further improve our understating of the psychological impact of the COVID-19 pandemic in the affected community. Needless to say, higher vigilance in the community for at-risk individuals, availability, and awareness about telemedicine services can play an important role to combat the risk of suicide during the lockdown.
Prognostic subtyping based on estrogen receptor, progesterone receptor, and human epidermal growth factor receptor2 expression in breast cancer cases among north Indian females

Background: Cancer of breast has recently become the leading cancer among women in Kashmir. Worse prognosis of this disease is with the features of higher grade, positivity for Her-2/neu, negativity for ER, PR, and presence of BRCA gene. Thus the receptor status like are a very useful tool for rapid diagnosis, treatment as well as for prognosis of the disease. The objective of the study was to analyze the pattern of expression of hormone receptors which include ER, PR and Her-2/neu in breast cancer cases among Kashmiri females and to find their association with various clinicopathological parameters.Methods: A cross sectional hospital based study done in a tertiary health care centre of Kashmir valley. We selected 102 consecutive breast cancer cases for the period of one year. Cases were sent for biopsy of the tumour lesion and for receptor status analysis.Results: In about 50.9%of cases tumour had spread to T2 stage. There was a significant difference in the tumor stage and the age groups at presentation. The HER 2 status was positive in 85.5% of cases. About 65% were ER positive and 51.9 were PR positive. Only 8 were triple negative and 42 were triple positive for receptors. We did not found any significant relationship between grade, stage of disease and age when compared for receptor status.Conclusions: We found a high percentage being receptor positive tumours which has been found to be a good prognostic sign.
In Vitro Characterization of Multilamellar Fibers with Uniaxially Oriented Electrospun Type I Collagen Scaffolds

Fabrication of an appropriate scaffold is critical in order to recapitulate the architecture and functionality of the native tissue. In this study, we attempted to create favorable collagen fiber alignment and multilamellar with uniaxially oriented layers, using a disc collector by turning mats 90 degrees horizontally at specific times. Different concentrations of rat tail-derived type I collagen (3, 6, 8% w/v) in 1,1,1,3,3,3-hexafluoroisopropanol (HFIP) are used for electrospinning affairs. The 6% w/v collagen at an applied voltage of 20 kV and collector rotation of 2500 rpm was selected to exhibit bead-free homogeneous nanofiber with fiber thickness of 0.14 ± 0.4 µm, maximum thickness of 0.5 ± 0.08 µm, and 60% porosity. Also, scanning electron microscope images of electrospun fibers showed 3D multilamellar scaffold with the goodness of 96.5% ± 0.8 in each aligned uniaxially oriented fiber layer. Cross-linking of collagen fibers with N-(3-dimethylaminopropyl)-N0-ethylcarbodiimide hydrochloride (EDC)/N-hydroxysuccinimide (NHS) reduced the fiber degradation rate and preserved the fiber morphology and alignment. The multilamellar mat showed significant increase in tensile strength and average breaking elongation in comparison with unilamellar mat. In vitro cell culture, using human adipose tissue-derived mesenchymal stem cells (hAT-MSCs) on cross-linked scaffold, showed improvement in cell proliferation, attachment, migration, and intercellular junction with a flattened morphology. Raman spectra revealed the preservation of collagen structure. In addition, Raman spectra of the cell containing scaffold were the same as those of an intact intervertebral disc as a sample to be used in engineering tissues. In conclusion, our results showed that the 3D multilamellar collagen nanofibrous scaffold is more appropriate for the tissues that have multilamellar structure.
Analysis of Efforts to Increase Income Taxes of Social Media Influencers in Endorsement Activities

Technological developments in the era of globalization have brought changes to marketing techniques, by using social media. Marketing through social media is mostly done by influencers because it is easy to do and earns a fairly large income. The purpose of this study is to analyze the efforts made by the Directorate General of Taxes to increase income tax on social media influencers in endorsement activities. This study adopts the positivism paradigm with qualitative methods. The purpose of this research is descriptive. Primary data sources were obtained through in-depth interviews with selected informants. The results showed that the income of social media influencers or arts workers had great taxation potential. The Directorate General of Taxation seeks to increase income tax receipts for influencers by updating the database, disseminating information and conducting surveillance with law enforcement. The Directorate General of Taxes needs to provide confirmation of the tax provisions for programmatic income so as to provide tax treatment similarities with conventional artist activities and close tax gaps that are widely utilized through online activities.
Evaluation of the acoustic emission caused by the chip segmentation frequency during machining of titanium alloy

Abstract This work investigates the relationship between acoustic emission and chip segmentation frequency of Ti-6Al-4V at the external longitudinal turning process. Therefore, several sensors like structure borne sensors, microphones and a force dynamometer have been installed in a vertical turning machine. To induce a change of the segmentation frequency, several experiments with different feed rates have been carried out. From each experiment the acoustic emissions have been recorded and the generated chips have been analyzed. Since the chips get stretched or compressed during the chip formation the change in the length is calculated to get an estimation of the segmentation frequency. The comparison of the spectral analysis of the acoustic emission signals and the chip analysis has shown that both methods show the same tendency. The segmentation frequency decreases with increasing feed.
Soil microbial community structure and enzymatic activity responses to nitrogen management and landscape positions in switchgrass (Panicum virgatum L.)

Switchgrass (Panicum virgatum L.) is usually grown on marginal land for biofuel system, in which nitrogen (N) is an essential management practice, and landscape position is a key topographical factor in impacting the production. However, limited information is available regarding how the N application and landscape positions affect soil microbial communities and enzyme activities under switchgrass. Thus, the specific objective of this study was to evaluate the responses of N rate (high, 112 kg N/ha; medium, 56 kg N/ha; and low, 0 kg N/ha) and landscape positions (shoulder and footslope) on soil biological health under switchgrass field. Data showed that N addition significantly influenced carbon and N fractions. The hot water‐soluble organic carbon (HWC) and nitrogen (HWN) fractions were significantly higher at footslope position than the shoulder position. The amount of total phospholipid fatty acid (PLFA), total bacterial, actinomycetes, gram‐negative and gram‐positive bacteria, total fungi, arbuscular mycorrhizal (AM) fungi, and saprophytes PLFAs were highest with medium and high N rates and footslope position. The N addition increased total PLFAs in N fertilizer treatments, viz. medium (5,946 ng PLFA‐C/g soil) and high N rates (5,871 ng PLFA‐C/g soil). Microbial biomass carbon and nitrogen and enzyme activities (urease, β‐glucosidase, acid phosphatase and arylsulfatase) were significantly enhanced by N fertilization (medium and high N rates) compared to control (low N rates) under footslope position. The urease activity under medium (36.3 µmol N‐NH4+ g−1 soil hr−1) and high N rates (31.4 µmol N‐NH4+ g−1 soil hr−1) was 42.9% and 23.6% higher than low N rates, respectively. This study suggests that the application of medium N rate in footslope position to switchgrass can enhance the soil biological properties and hence can protect the environment from the excessive use of N fertilizer.
Non-Pharmaceutical Interventions for COVID-19: Evidence from Large-Scale Mobility Data in Tokyo

lockdown of Hubei province, large-scale mobility restrictions at the national level, and social distancing. Germany responded with border closures, closures of schools and non-essential businesses, social-distancing requirements, and a ban on public gatherings. India went under lockdown in March, in addition to containment measures including travel restrictions, business closures, and bans on mass gatherings. Brazil announced a temporary ban on foreign air travelers, and most state governors have imposed quarantines to prevent the spread of the virus (IMF 2020).
Effects of lithium on developmental toxicity, teratogenicity and transcriptome in medaka embryos

In this study, we assessed embryonic developmental toxicity and teratogenicity of lithium (Li) on medaka (Oryzias latipes) and predict the molecular mechanisms of their effects using a nanosecond pulsed electric field (nsPEF) technique and bioinformatics analysis. The microscopic observation revealed that the 1 mg/L LiCl treatment causes the most severe deformation effects, such as thrombus, heart hypertrophy, deformation of eyes, and growth retardation to embryos. The RNA-seq analysis identified 2,483 upand down-regulated genes, such as histogenesis and organ growth related genes, in 2 day post-fertilization embryos after treatment with nsPEF and 1 mg/L LiCl. In addition, bioinformatic analyses showed that LiCl affects several aspects of gene ontology, such as molecular functions and cellular components, and some pathways, such as spliceosome, cell cycle, selenocompound metabolism, TGF-β signaling, and RNA degradation. The upregulation of GSK3B (signal transduction and cell growth), BAX (apoptosis), and MAP3K8 (cell death, arrest of cell cycle, and inflammation) genes were also observed in embryos exposed to LiCl. Our results suggest that the incorporation of Li compounds into medaka eggs using nsPEF shows adverse effects to the development and teratogenicity, and that these toxic effects may be affected by the alterations of certain gene expression in medaka embryos.