Miracle-dz/UniFAR-FTUs huggingface dataset:
Understanding thermophilic ammonia-oxidizing archaea environments across extreme redox gradients

New understanding of key microbial players in the nitrogen cycle such as the discovery of ammonia-oxidizing archaea (AOA) has sparked a plethora of research aimed at nitrogen cycle processes. Evidence for AOA has been specifically detected in hot springs of Uzon Caldera, Kamchatka Russia. Samples were collected from Orange Thermal Field (OTF) and other thermal fields in Uzon to gain greater understanding of environments in which AOA are found. The geochemistry, microbial communities, mineralogy were examined at OTF from both oxidized and reduced zones. It was hypothesized that crenarchaeol would be more abundant where oxygen and nutrients NH4 + and Cu are more abundant. Instead, a higher abundance of crenarchaeol was observed where smectites were common despite lower Cu and Oxygen levels. Smectites have a greater potential to bind NH4 + and metal cations. It is proposed that in OTF the presence of NH4 -bearing smectites in reduced zones provides a more favorable environment due to the acidity of sediments resulting in greater AOA abundance. INDEX WORDS: ammonia-oxidizing archaea, trace metals, Kamchatka, Uzon Caldera, hot springs, thermophilic ammonia oxidation, redox gradients, expanding-clay UNDERSTANDING THERMOPHILIC AMMONIA-OXIDIZING ARCHAEA ENVIRONMENTS ACROSS EXTREME REDOX GRADIENTS
Lecania cuprea and Micarea pycnidiophora (lichenized Ascomycota) new to Poland

Two lichenized fungi, Lecania cuprea and Micarea pycnidiophora , are reported for the first time from Poland. Lecania cuprea is also recorded as a new lichen species to the Western Beskidy Mts and the Pieniny Mts and M. pycnidiophora is new to the Carpathians. Illustrated descriptions, taxonomic notes, habitat requirements and known distributions for both species are provided.
Breaking the circularity in circular analyses: Simulations and formal treatment of the flattened average approach

There has been considerable debate and concern as to whether there is a replication crisis in the scientific literature. A likely cause of poor replication is the multiple comparisons problem. An important way in which this problem can manifest in the M/EEG context is through post hoc tailoring of analysis windows (a.k.a. regions-of-interest, ROIs) to landmarks in the collected data. Post hoc tailoring of ROIs is used because it allows researchers to adapt to inter-experiment variability and discover novel differences that fall outside of windows defined by prior precedent, thereby reducing Type II errors. However, this approach can dramatically inflate Type I error rates. One way to avoid this problem is to tailor windows according to a contrast that is orthogonal (strictly parametrically orthogonal) to the contrast being tested. A key approach of this kind is to identify windows on a fully flattened average. On the basis of simulations, this approach has been argued to be safe for post hoc tailoring of analysis windows under many conditions. Here, we present further simulations and mathematical proofs to show exactly why the Fully Flattened Average approach is unbiased, providing a formal grounding to the approach, clarifying the limits of its applicability and resolving published misconceptions about the method. We also provide a statistical power analysis, which shows that, in specific contexts, the fully flattened average approach provides higher statistical power than Fieldtrip cluster inference. This suggests that the Fully Flattened Average approach will enable researchers to identify more effects from their data without incurring an inflation of the false positive rate.
Optimization of Phenolic Content, Antioxidant, and Inhibitory Activities of α-Glucosidase and Angiotensin Converting (AC) Enzymes from Zingiber officinale Z.

The optimum extraction conditions of phenolic compounds from ginger were evaluated with respect to antioxidant activity and angiotensin converting enzyme and α-glucosidase inhibitory activities. Free phenolics were extracted under conditions that varied according to extraction time, temperature, and solvent type (water, acetone, and methanol). Acid and base hydrolysis reactions were used to obtain bound phenolic compounds from ginger. The results showed that the type of solvent used and the temperature and time of extraction needed for maximal total phenolic content, antioxidant activity, and angiotensin converting enzyme inhibitory activity differed greatly from solvent conditions and showed the greatest α-glucosidase inhibitory activity. The predominant free phenolics in the methanol extracts included diosmin, thymol, and carvacrol, which varied greatly according to solvent extraction conditions (i.e., time and temperature). Diosmin was the predominant bound phenolic compound of the methanol extracts. The present study findings indicate that differing solvent extraction protocols involving extraction time and temperature for ginger need to be explored to generate specific optimal bioactivities of the extracts, which are related to the pattern of predominant phenolics in those extracts.
Disaggregation of Gendered Differences in Retirement Planning in Urban Ghana

The paper investigates gendered retirement planning, using quantitative and qualitative datasets obtained from formal and informal sector workers [n=442]. The analyses show that the majority of workers (45.4%) opined that women’s retirement preparations are tied to men’s, particularly housewives and married ones, reasoning that men are heads of their households. This includes women’s desire to be and/or live closer to their partners. Whilst women’s preparations may be tied to men’s, men often plan for retirement with the support of their spouses. An extent of independence between men and women regarding retirement planning and different levels of societal responsibilities pertains. These are two independent people with different responsibilities, preferences, needs and reasons. However, women are less likely than men to actively plan for retirement. This is inhibited by women’s low income flows compared to their male counterparts. Yet, women need to institute more plans than men because women most often do not have social security and live relatively longer. Significantly, what prompts women to plan differs from what motivates men. This provides a reinforcement of the importance of considering gender when seeking to understand the variables that predict retirement planning tendencies, and might contribute to successfully attaining financial security.
Involvement of the paired-domain transcription factor Pax6 in the regulation of glucagon gene transcription by insulin

Regulation of gene transcription is an important aspect of insulin's action. However, the mechanisms involved are poorly understood. Insulin inhibits glucagon gene transcription and insulin deficiency is associated with hyperglucagonemia that contributes to hyperglycemia in diabetes mellitus. In the present study transient transfection analysis in a glucagon-producing pancreatic islet cell line was performed, where the activity of an artificial minienhancer consisting of synergizing Pax6 binding sites (G3A) in front of a heterologous promoter, as well as Pax6 activity when assessed using a GAL4/viral E1B system, were inhibited by insulin. This provides evidence that Pax6 can confer negative regulation by insulin in pancreatic islets. Furthermore, Pax6 seems to play a critical role in the insulin responsiveness of the glucagon promoter because the overexpression of the Pax6 paired domain as well as the mutation of the Pax6 binding sites within the glucagon promoter element G1 and G3 markedly reduced basal activity and insulin responsiveness. The expression of GAL4-Pax6 and GAL4-VP16 restored basal activity of the doubly mutated promoter, whereas only GAL4-Pax6 restored also insulin responsiveness. When the potential Pax6 coactivator CBP was fused to the GAL4 DNA-binding domain, the GAL4-CBP activity was inhibited by insulin within the glucagon promoter context but not in front of the viral E1B promoter. Fusing N-, C-terminal and middle parts of CBP with the GAL4 domain only the N- and C-terminal part conferred transcriptional activity and insulin responsiveness. Further mapping of the C-terminal of CBP revealed a single region between amino acids 2040 and 2170 sufficient to confer the negative regulation by insulin. The activity conferred by this region as well as by the N-terminal part of CBP was inhibited by the overexpression of the constitutively active form of PKB, myrPKB. The results of present study suggest that the paired domain transcription factor Pax6 is required for insulin responsiveness of the glucagon promoter. They alsoindicate that the Pax6-interacting coactivator CBP might be involved in this process. It is finally speculated that within the specific context of the glucagon promoter a nucleoprotein complex is being induced with Pax6 and CBP as critical components. Insulin-induced signalling pathways might target this large, glucagon promoter-specific protein complex rather than any single transcriptional factor and therefore act through a IRE-binding factor (IRF)-independent mechanism.
A New Halophilic Species of Eurotium

In 1954, samples of wheat obtained from terminal elevators in several parts of the country were stored in 4 oz prescription bottles with screw caps having rubber liners. The wheats had moisture contents between 13 and 14 per cent, wet weight basis, when placed in the bottles. After about 2 years, mycelium was observed on the embryo surface of many of the seeds. A number of seeds of each of several samples were placed, without prior surface disinfection, on malt agar containing 15 per cent sodium chloride, a medium we frequently have used to isolate Aspergillus restrictus from seeds. After 10 days, the surface of the germs of most seeds was covered with white perithecia. The perithecia developed on the germs of hard red winter wheat from Omaha, Nebraska, soft red winter wheat fromi Marietta, Peinnsylvania, and Chicago, Illinois, and white wheat from Buffalo, New York, and Maumee, Ohio. Several isolates of the fungus were studied in some detail and the fungus appears sufficiently different from known species of Eurotiu1, and Aspcrgillus to warrant description as a new species.
Chikungunya Outbreak in the Republic of the Congo, 2019—Epidemiological, Virological and Entomological Findings of a South-North Multidisciplinary Taskforce Investigation

The Republic of Congo (RoC) declared a chikungunya (CHIK) outbreak on 9 February 2019. We conducted a ONE-Human-Animal HEALTH epidemiological, virological and entomological investigation. Methods: We collected national surveillance and epidemiological data. CHIK diagnosis was based on RT-PCR and CHIKV-specific antibodies. Full CHIKV genome sequences were obtained by Sanger and MinION approaches and Bayesian tree phylogenetic analysis was performed. Mosquito larvae and 215 adult mosquitoes were collected in different villages of Kouilou and Pointe-Noire districts and estimates of Aedes (Ae.) mosquitos’ CHIKV-infectious bites obtained. We found two new CHIKV sequences of the East/Central/South African (ECSA) lineage, clustering with the recent enzootic sub-clade 2, showing the A226V mutation. The RoC 2019 CHIKV strain has two novel mutations, E2-T126M and E2-H351N. Phylogenetic suggests a common origin from 2016 Angola strain, from which it diverged around 1989 (95% HPD 1985–1994). The infectious bite pattern was similar for 2017, 2018 and early 2019. One Ae. albopictus pool was RT-PCR positive. The 2019 RoC CHIKV strain seems to be recently introduced or be endemic in sylvatic cycle. Distinct from the contemporary Indian CHIKV isolates and in contrast to the original Central-African strains (transmitted by Ae. aegypti), it carries the A226V mutation, indicating an independent adaptive mutation in response to vector replacement (Ae. albopictus vs Ae. aegypti).
Genetic and Methylome Variation in Turkish Brachypodium Distachyon Accessions Differentiate Two Geographically Distinct Subpopulations

Brachypodium distachyon (Brachypodium) is a non-domesticated model grass species that can be used to test if variation in genetic sequence or methylation are linked to environmental differences. To assess this, we collected seeds from 12 sites within five climatically distinct regions of Turkey. Seeds from each region were grown under standardized growth conditions in the UK to preserve methylated sequence variation. At six weeks following germination, leaves were sampled and assessed for genomic and DNA methylation variation. In a follow-up experiment, phenomic approaches were used to describe plant growth and drought responses. Genome sequencing and population structure analysis suggested three ancestral clusters across the Mediterranean, two of which were geographically separated in Turkey into coastal and central subpopulations. Phenotypic analyses showed that the coastal subpopulation tended to exhibit relatively delayed flowering and the central, increased drought tolerance as indicated by reduced yellowing. Genome-wide methylation analyses in GpC, CHG and CHH contexts also showed variation which aligned with the separation into coastal and central subpopulations. The climate niche modelling of both subpopulations showed a significant influence from the “Precipitation in the Driest Quarter” on the central subpopulation and “Temperature of the Coldest Month” on the coastal subpopulation. Our work demonstrates genetic diversity and variation in DNA methylation in Turkish accessions of Brachypodium that may be associated with climate variables and the molecular basis of which will feature in ongoing analyses.
Serum Neurofilament Light Chain Levels are Associated with Lower Thalamic Perfusion in Multiple Sclerosis

Both perfusion-weighted imaging (PWI) measures and serum neurofilament light (sNfL) chain levels have been independently associated with disability in multiple sclerosis (MS) patients. This study aimed to determine whether these measures are correlated to each other or independently describe different MS processes. For this purpose, 3T MRI dynamic susceptibility contrast (DSC)–PWI and single-molecule assay (Simoa)-based sNfL methods were utilized when investigating 86 MS patients. The perfusion measures of mean transit time (MTT), cerebral blood volume (CBV), and cerebral blood flow (CBF) were derived for the normal-appearing whole brain (NAWB), the normal-appearing white matter (NAWM), the gray matter (GM), the deep GM (DGM), and the thalamus. The normalized CBV and CBF (nCBV and nCBV) were calculated by dividing by the corresponding NAWM measure. Age- and sex-adjusted linear regression models were used to determine associations between the DSC–PWI and sNfL results. False discovery rate (FDR)-adjusted p-values < 0.05 were considered statistically significant. A greater age and thalamic MTT were independently associated with higher sNfL levels (p < 0.001 and p = 0.011) and explained 36.9% of sNfL level variance. NAWM MTT association with sNfL levels did not survive the FDR correction. In similar models, a lower thalamic nCBF and nCBV were both associated with greater sNfL levels (p < 0.001 and p = 0.022), explaining 37.8% and 44.7% of the variance, respectively. In conclusion, higher sNfL levels were associated with lower thalamic perfusion.
RFLP Mapping of Bph-1 (Brown Planthopper Resistance Gene)in Rice

Restriction fragment length polymorphism (RFLP) analysis was carried out to determine the location on the chromosome and the locus of the resistance gene to brown planthopper, Bph-1, on the linkage Inap of rice, Oryza sativa L. Our results showed that Bph-1 was not located on chromosome 4 but on chromosome 12, that is, Bph-1 was linked at the recombination value of 10.7 % with a RFLP marker XNpb 248 on chromosome 12. Based on the recombination value between Bph-1 and RFLP markers, the arrangement was as follows ; Bph-1 -XNpb 248 -XNpb 336. This is the first report on the tagging of a resistance gene to brown planthopper in rice.
Intraspecies variation in ectotympanic tube length and orientation among humans

Ectotympanic bone morphology is commonly used as a large‐scale phylogenetic indicator across primates. Less well‐understood is the intraspecies variation in this characteristic and the dynamic ways in which it affects and is affected by overall basicranial shape. This study attempts to clarify relationships between the external ear canal and basicranial shape among humans in a sample of archaeological human crania. The ectotympanic length and orientation were hypothesized to correlate with the shape of the cranial base and particularly with shape variables associated with relative brachycephaly. Basicranial shape in 80 computed tomography (CT) scans of adult humans were quantified using landmark coordinate data, with particular emphasis on the cranial base and auditory structures. Scaled ectotympanic lengths were taken from interlandmark distances and then compared to shape variation of the whole basicranium as summarized by procrustes shape variables and principal components analysis (PCA). The length of the ectotympanic bone was correlated with total cranial base variation. Long ectotympanic bones were found to be associated with brachycephalic individuals and less flexed basicrania. Additionally, long ectotympanic bones were found to be more horizontally oriented, as opposed to inferiorly sloped. We suggest that as brachycephaly increases the distance between the otic capsule and the pinna, the ectotympanic bone lengthens in response.
Mortality of New Zealand native frogs in captivity

Three species of New Zealand native frogs (Leiopelma archeyi, L. hochstetteri and L. pakeka) have been held in captivity in various institutions since 2000 as part of a programme to maintain and breed these threatened species. Following the death of a large number of these captive frogs, the Department of Conservation Native Frog Recovery Group decided that an investigation was needed to determine the cause. In this mortality study, we obtained data from captive populations to analyse mortality rates and causes of death for 252 wild-caught Leiopelma spp. These were held in captivity at the University of Canterbury and later transferred to other institutions between 2000 and 2006. Leiopelma archeyi and L. hochstetteri had similar overall average mortality but different yearly mortality patterns, whereas L. pakeka had much lower overall mortality. The major cause of death for L. archeyi and L. hochstetteri was bacterial infection, which was thought to be induced by a combination of husbandry factors, but mainly from oversterilising the substrate. Consequently, Auckland Zoo instigated a change in management, whereby soil was only heated to a temperature and for a length of time that was just sufficient to kill amphibian chytrid. New disease syndromes (skin blisters and muscle deterioration (rhabdomyolysis)) were also detected. Knowledge of disease is an important component of captive husbandry, so that healthy breeding populations can be maintained and we can gain an insight into diseases that may be affecting free-living populations. It is recommended that the staff at each institution undertake a review of all captive mortalities and report back to the Native Frog Recovery Group on an annual basis, so that any husbandry or disease issues that have arisen can be identified quickly.
Centrioles are amplified in cycling progenitors of olfactory sensory neurons

Olfaction in most animals is mediated by neurons bearing cilia that are accessible to the environment. Olfactory sensory neurons (OSNs) in chordates usually have multiple cilia, each with a centriole at its base. OSNs differentiate from stem cells in the olfactory epithelium, and how the epithelium generates cells with many centrioles is not yet understood. We show that centrioles are amplified via centriole rosette formation in both embryonic development and turnover of the olfactory epithelium in adult mice, and rosette-bearing cells often have free centrioles in addition. Cells with amplified centrioles can go on to divide, with centrioles clustered at each pole. Additionally, we found that centrioles are amplified in immediate neuronal precursors (INPs) concomitant with elevation of mRNA for polo-like kinase 4 (Plk4) and SCL/Tal1-interrupting locus gene (Stil), key regulators of centriole duplication. These results support a model in which centriole amplification occurs during a transient state characterized by elevated Plk4 and Stil in early INP cells. These cells then go on to divide at least once to become OSNs, demonstrating that cell division with amplified centrioles, known to be tolerated in disease states, can occur as part of a normal developmental program.
Personalized Medicine Using Cutting Edge Technologies for Genetic Epilepsies

Epilepsy is the most common chronic neurologic disorder in the world, affecting 1-2% of the population. Besides, 30% of epilepsy patients are drug-resistant. Genomic mutations seem to play a key role in its etiology and knowledge of strong effect mutations in protein structures might improve prediction and the development of efficacious drugs to treat epilepsy. Several genetic association studies have been undertaken to examine the effect of a range of candidate genes for resistance. Although, few studies have explored the effect of the mutations into protein structure and biophysics in the epilepsy field. Much work remains to be done, but the plans made for exciting developments will hold therapeutic potential for patients with drug-resistance. In summary, we provide a critical review of the perspectives for the development of individualized medicine for epilepsy based on genetic polymorphisms/mutations in light of core elements such as transcriptomics, structural biology, disease model, pharmacogenomics and pharmacokinetics in a manner to improve the success of trial designs of antiepileptic drugs.
Measuring Effects of Two-Handed Side and Anterior Load Carriage on Thoracic-Pelvic Coordination Using Wearable Gyroscopes

Manual carrying of heavy weight poses a major risk for work-related low back injury. Body-worn inertial sensors present opportunities to study the effects of ambulatory work tasks such as load carriage in more realistic conditions. An immediate effect of load carriage is reflected in altered gait kinematics. To determine the effects of load carriage mode and magnitude on gait parameters using body-worn angular rate gyroscopes, two laboratory experiments (n = 9 and n = 10, respectively) were conducted. Participants performed walk trials at self-selected speeds while carrying hand loads in two modes (two-handed side vs. anterior) at four load levels (empty-handed, 4.5 kg, 9.1 kg, and 13.6 kg). Six measures of postural sway and three measures of thoracic-pelvic coordination were calculated from data recorded by four body-worn gyroscopes for 1517 gait cycles. Results demonstrated that, after adjusting for relative walking speed, thoracic-pelvic sway, and movement coordination particularly in the coronal and transverse planes, characterized by gyroscope-based kinematic gait parameters, are systematically altered by the mode of load carriage and load magnitude. Similar trends were obtained for an anthropometrically homogenous (Expt-1) and diverse (Expt-2) sample after adjusting for individual differences in relative walking speed. Measures of thoracic-pelvic coordination and sway showed trends of significant practical relevance and may provide sufficient information to typify alterations in gait across two-handed side vs. anterior load carriage of different load magnitudes. This study contributes to understanding the effects of manual load carriage on thoracic-pelvic movement and the potential application of body-worn gyroscopes to measuring these gait adaptations in naturalistic work settings.