Miracle-dz/UniFAR-FTUs huggingface dataset:
Pitting of Transfusion Tracheids in Cupressaceae

The morphology and development of the circular bordered pits on the transfusion tracheids in the leaves of Callitris muelleri are described from light microscopy of semithin sections and SEM studies of cut surfaces. Two parallel bars of thickening develop on the pit border either side of the aperture, and trabecula-like outgrowths develop into the cell lumen from the centre of each bar. These outgrowths are often contorted and may anastomose with the wall or each other. Development is arrested at the barred stage in occasional pits, and both 'barred' and 'trabeculate' pits may occur in the one cell. 'Trabeculate-pitting' occurs in all species of Callitris and Actinostrobus, and was also observed in species of Cupressus and Juniperus. Previous reports of outgrowths on pits in several species of the last two genera suggest that the trabeculate pit is characteristic of both. 'Barred pits' occur in Widdringtonia cupressoides and Catocedrus decurrens. Unadorned circular bordered pits are characteristic of Diselma archeri, and have previously been reported in a range of genera in the family. These three types of pit are considered to represent an evolutionary transformation series in which the last type is plesiomorphic. The occurrence of the apomorphic conditions in both northern and southern hemi- sphere genera does not fit well with the present taxonomy of the family. The probable adaptive significance of the trabeculate pit is discussed.
Autophagy Regulates Fungal Virulence and Sexual Reproduction in Cryptococcus neoformans

Autophagy (macroautophagy) is an evolutionarily conserved degradation pathway involved in bulk degradation of cytoplasmic organelles, old protein, and other macromolecules and nutrient recycling during starvation. Extensive studies on functions of autophagy-related genes have revealed that autophagy plays a role in cell differentiation and pathogenesis of pathogenic fungi. In this study, we identified and characterized 14 core autophagy machinery genes (ATGs) in C. neoformans. To understand the function of autophagy in virulence and fungal development in C. neoformans, we knocked out the 14 ATGs in both α and a mating type strain backgrounds in C. neoformans, respectively, by using biolistic transformation and in vivo homologous recombination. Fungal virulence assay showed that virulence of each atgΔ mutants was attenuated in a murine inhalation systemic-infection model, although virulence factor production was not dramatically impaired in vitro. Fungal mating assays showed that all the 14 ATGs are essential for fungal sexual reproduction as basidiospore production was blocked in bilateral mating between each atgΔ mutants. Fungal nuclei development assay showed that nuclei in the bilateral mating of each atgΔ mutants failed to undergo meiosis after fusion, indicating autophagy is essential for regulating meiosis during mating. Overall, our study showed that autophagy is essential for fungal virulence and sexual reproduction in C. neoformans, which likely represents a conserved novel virulence and sexual reproduction control mechanism that involves the autophagy-mediated proteolysis pathway.
Shiga Toxin-Bearing Microvesicles Exert a Cytotoxic Effect on Recipient Cells Only When the Cells Express the Toxin Receptor

Shiga toxin is the main virulence factor of non-invasive enterohemorrhagic Escherichia coli strains capable of causing hemolytic uremic syndrome. Our group has previously shown that the toxin can reach the kidney within microvesicles where it is taken up by renal cells and the vesicles release their cargo intracellularly, leading to toxin-mediated inhibition of protein synthesis and cell death. The aim of this study was to examine if recipient cells must express the globotriaosylceramide (Gb3) toxin receptor for this to occur, or if Gb3-negative cells are also susceptible after uptake of Gb3-positive and toxin-positive microvesicles. To this end we generated Gb3-positive A4GALT–transfected CHO cells, and a vector control lacking Gb3 (CHO-control cells), and decreased Gb3 synthesis in native HeLa cells by exposing them to the glycosylceramide synthase inhibitor PPMP. We used these cells, and human intestinal DLD-1 cells lacking Gb3, and exposed them to Shiga toxin 2-bearing Gb3-positive microvesicles derived from human blood cells. Results showed that only recipient cells that possessed endogenous Gb3 (CHO-Gb3 transfected and native HeLa cells) exhibited cellular injury, reduced cell metabolism and protein synthesis, after uptake of toxin-positive microvesicles. In Gb3-positive cells the toxin introduced via vesicles followed the retrograde pathway and was inhibited by the retrograde transport blocker Retro-2.1. CHO-control cells, HeLa cells treated with PPMP and DLD-1 cells remained unaffected by toxin-positive microvesicles. We conclude that Shiga toxin-containing microvesicles can be taken up by Gb3-negative cells but the recipient cell must express endogenous Gb3 for the cell to be susceptible to the toxin.
Biological Effects of Population Density in Lower Organisms (Concluded)

I NFORMATION as to the general biology of Drosophila will be found summarized in Sturtevant (I9S.I) and Morgan, Bridges, and Sturtevant (I9 5). Drosophila is ordinarily mentioned as a fruitfly since decaying fruit is its natural food, and large numbers of them always collect seemingly out of nowhere whenever a bit of over-ripe fruit is left exposed in warm weather. Northrop (19I7a) found that they cannot be raised successfully on sterile banana, although decaying banana is an excellent medium. He was unable to raise them on a sterile mixture of pure protein, sugar, salts and fat but the larvae would grow on the kidney, liver, and pancreas tissue from a dog and on the dead bodies of flies themselves. They did quite well on yeast alone while the addition of banana, casein, or sugar to the yeast increased the percentages which were able to develop showing that these substances could be utilized to some degree by the flies as food. Baumberger (I9I9) found that by soaking eggs for io minutes in 85 percent alcohol he could sterilize them so that when they were placed on sterile food they would not inoculate it with yeast, mold, or bacteria. Keeping the medium sterile in this way, he found that Drosophila larvae do not grow well on sterile food but that bacteria and molds may take the place of yeast. A loose symbiosis exists between yeast and Drosophila, the yeast being spread by the flies which depend upon it to synthesize many non-protein nitrogenous compounds into proteins for themselves. Northrop (i9z6b) says, however, that by the proper choice of foods he has been able to raise Drosophila under aseptic conditions in the dark for 230 generations. Drosophila were ordinarily raised in the laboratory on decaying banana and later on banana agar seeded with yeast which was easier to handle. This, however, was a very variable food substance since it depended upon the ripeness and other qualities of the bananas which changed seasonally and could not be well controlled. For his quantitative experimental work, Pearl particularly desired a standard food which could be duplicated in precisely the same fashion at any time. After trying a number of mixtures, Pearl and Penniman (i926) and Pearl, Allen, and Penniman (i926) developed a purely synthetic medium which met the requirements admirably. It is primarily a medium for the growth of yeast which is sprinkled over it in powdered form after it has solidified in the culture bottles. The pH is so regulated as to discourage the growth of bacteria and molds which give trouble particularly at low temperatures. This synthetic medium, called S-ioI, has been used as the standard fly culture medium
Gender-Specific Differences in Patients With Chronic Tinnitus—Baseline Characteristics and Treatment Effects

Whilst some studies have identified gender-specific differences, there is no consensus about gender-specific determinants for prevalence rates or concomitant symptoms of chronic tinnitus such as depression or anxiety. However, gender-associated differences in psychological response profiles and coping strategies may differentially affect tinnitus chronification and treatment success rates. Thus, understanding gender-associated differences may facilitate a more detailed identification of symptom profiles, heighten treatment response rates, and help to create access for vulnerable populations that are potentially less visible in clinical settings. Our research questions are: RQ1: how do male and female tinnitus patients differ regarding tinnitus-related distress, depression severity, and treatment response, RQ2: to what extent are answers to questionnaires administered at baseline associated with gender, and RQ3: which baseline questionnaire items are associated with tinnitus distress, depression, and treatment response, while relating to one gender only? In this work, we present a data analysis workflow to investigate gender-specific differences in N = 1,628 patients with chronic tinnitus (828 female, 800 male) who completed a 7-day multimodal treatment encompassing cognitive behavioral therapy (CBT), physiotherapy, auditory attention training, and information counseling components. For this purpose, we extracted 181 variables from 7 self-report questionnaires on socio-demographics, tinnitus-related distress, tinnitus frequency, loudness, localization, and quality as well as physical and mental health status. Our workflow comprises (i) training machine learning models, (ii) a comprehensive evaluation including hyperparameter optimization, and (iii) post-learning steps to identify predictive variables. We found that female patients reported higher levels of tinnitus-related distress, depression and response to treatment (RQ1). Female patients indicated higher levels of tension, stress, and psychological coping strategies rates. By contrast, male patients reported higher levels of bodily pain associated with chronic tinnitus whilst judging their overall health as better (RQ2). Variables measuring depression, sleep problems, tinnitus frequency, and loudness were associated with tinnitus-related distress in both genders and indicators of mental health and subjective stress were found to be associated with depression in both genders (RQ3). Our results suggest that gender-associated differences in symptomatology and treatment response profiles suggest clinical and conceptual needs for differential diagnostics, case conceptualization and treatment pathways.
Transcutaneous Vagus Nerve Stimulation May Enhance Only Specific Aspects of the Core Executive Functions. A Randomized Crossover Trial

Background Individuals are able to perform goal-directed behaviors thanks to executive functions. According to the neurovisceral integration model, executive functions are upregulated by brain areas such as the prefrontal and cingulate cortices, which are also crucially involved in controlling cardiac vagal activity. An array of neuroimaging studies already showed that these same brain areas are activated by transcutaneous vagus nerve stimulation (tVNS). Despite evidence toward effects of tVNS on specific executive functions such as inhibitory control, there have been no studies investigating what type of inhibition is improved by tVNS by systematically addressing them within the same experiment. Furthermore, the effect of tVNS on another core executive function, cognitive flexibility, has not yet been investigated. Objective We investigated the effects of tVNS on core executive functions such as inhibitory control and cognitive flexibility. Methods Thirty-two participants (nine women, Mage = 23.17) took part in this study. Vagally mediated heart rate variability parameters (root mean square of successive differences, RMSSD, and high frequency, HF) were measured while participants performed four different cognitive tasks that mainly rely on different aspects of both the aforementioned executive functions. Results Despite clear conflict effects in the four tasks, only performance on the task used to measure set-shifting paradigm was improved by tVNS, with switch costs being lower during tVNS than during sham stimulation. Furthermore, HF increased during each of the cognitive flexibility tasks, although HF during tVNS did not differ from HF during sham stimulation. Conclusion The results indicate for the first time (a) that tVNS can increase cognitive flexibility in a set-shifting paradigm, and (b) that tVNS may exert a stronger effect on cognitive flexibility than inhibition. The present study provides only partial evidence for the neurovisceral integration model. Future studies should address further paradigms that demand cognitive flexibility, thus investigating this new hypothesis on the specificity of the tVNS effects on cognitive flexibility.
Estimation of Involuntary Components of Human Arm Impedance in Multi-Joint Movements via Feedback Jerk Isolation

Stable and efficient coordination in physical human-robot interaction requires consideration of human feedback behavior. In unpredictable tasks, where voluntary cognitive feedback is too slow to guarantee desired task execution, the human must rely on involuntary intrinsic and reflexive feedback. The combined effects of these two feedback mechanisms and the inertial characteristics can be summarized in the involuntary impedance components. In this work, we present a method for the estimation of the involuntary impedance components of the human arm in multi-joint movements. We apply force perturbations to evoke feedback jerks that can be isolated using a high pass filter and limit the duration of the estimation interval to guarantee exclusion of voluntary cognitive feedback. Dynamic regressor representation of the rigid body dynamics of the arm and first order Taylor series expansion of the feedback behavior yield a model that is linear in the involuntary impedance components. The constant values of the inertial parameters are estimated in a static posture maintenance task and subsequently inserted to estimate the remaining components in a dynamic movement task. The method is validated with simulated data of a neuromechanical model of the human arm and its performance is compared to established methods from the literature. The results of the validation demonstrate superior estimation performance for moderate movement velocities, and less influence of the variability of the movements. The applicability to real data and the plausibility of the limited estimation interval are successfully demonstrated in an experiment with human participants.
Low Turnover of Soil Bacterial rRNA at Low Temperatures

Ribosomal RNA (rRNA) is used widely to investigate potentially active microorganisms in environmental samples, including soil microorganisms and other microbial communities that are subjected to pronounced seasonal variation in temperature. This raises a question about the turnover of intracellular microbial rRNA at environmentally relevant temperatures. We analyzed the turnover at four temperatures of RNA isolated from soil bacteria amended with 14C-labeled uridine. We found that the half-life of recently produced RNA increased from 4.0 days at 20°C to 15.8 days at 4°C, and 215 days at −4°C, while no degradation was detected at −18°C during a 1-year period. We discuss the implications of the strong temperature dependency of rRNA turnover for interpretation of microbiome data based on rRNA isolated from environmental samples.
Rumen Microbial Responses to Antinutritive Factors in Fodder Trees and Shrub Legumes

Abstract McSweeney, C.S. , Odenyo, A. and Krause, D.O. 2002. Rumen microbial responses to antinutritive factors in fodder trees and shrub legumes. J. Appl. Anim. Res., 21: 181–205. The major limitation to ruminant production in many tropical regions of Africa, Asia and Australia is poor nutrition. Annual growth rates of animals are restricted by the low nitrogen and high fibre content of the native grasses and crop residues that form the basis of the diets in these regions. Supplementation of tropical roughages with fodder trees and shrubs (FTS) is a promising method to alleviate nutrient deficiencies associated with these basal diets. However, FTS often contain toxins and anti-nutritional factors (ANFs) that limit their use as feedstuffs. Selection and breeding for cultivars that are low in toxins/ANFs has not been successful since the presence of these compounds is strongly associated with survival in many tropical environments. A solution to the problem may be the rumen microorganisms from adapted domestic and wild ruminants that have evolved rumen fermentation mechanisms to transform or detoxify some of these plant secondary compounds. This review examines the use in ruminant feeding systems of FTS that contain deleterious secondary compounds; our current understanding of microbial interactions with these secondary compounds, and advances in the use of rumen biotechnology to overcome these limitations.
Age- and sex-specific total mortality impacts of the early weeks of the Covid-19 pandemic in England and Wales: Application of a Bayesian model ensemble to mortality statistics

Background: The Covid-19 pandemic affects mortality directly through infection as well as through changes in the social, environmental and healthcare determinants of health. The impacts on mortality are likely to vary, in both magnitude and timing, by age and sex. Our aim was to estimate the total mortality impacts of the pandemic, by sex, age group and week. Methods: We developed an ensemble of 16 Bayesian models that probabilistically estimate the weekly number of deaths that would be expected had the Covid-19 pandemic not occurred. The models account for seasonality of death rates, medium-long-term trends in death rates, the impact of temperature on death rates, association of death rates in each week on those in preceding week(s), and the impact of bank holidays. We used data from January 2010 through mid-February 2020 (i.e., week starting 15th February 2020) to estimate the parameters of each model, which was then used to predict the number of deaths for subsequent weeks as estimates of death rates if the pandemic had not occurred. We subtracted these estimates from the actual reported number of deaths to measure the total mortality impact of the pandemic. Results: In the week that began on 21st March, the same week that a national lockdown was put in place, there was a >92% probability that there were more deaths in men and women aged [≥]45 years than would occur in the absence of the pandemic; the probability was 100% from the subsequent week. Taken over the entire period from mid-February to 8th May 2020, there were an estimated [~] 49,200 (44,700-53,300) or 43% (37-48) more deaths than would be expected had the pandemic not taken place. 22,900 (19,300-26,100) of these deaths were in females (40% (32-48) higher than if there had not been a pandemic), and 26,300 (23,800-28,700) in males (46% (40-52) higher). The largest number of excess deaths occurred among women aged >85 years (12,400; 9,300-15,300), followed by men aged >85 years (9,600; 7,800-11,300) and 75-84 years (9,000; 7,500-10,300). The cause of death assigned to the majority (37,295) of these excess deaths was Covid-19. There was nonetheless a >99.99% probability that there has been an increase in deaths assigned to other causes in those aged [≥]45 years. However, by the 8th of May, the all-cause excess mortality had become virtually equal to deaths assigned to Covid-19, and non-Covid excess deaths had diminished to close to zero, or possibly become negative, in all age-sex groups. Interpretation: The death toll of Covid-19 pandemic, in middle and older ages, is substantially larger than the number of deaths reported as a result of confirmed infection, and was visible in vital statistics when the national lockdown was put in place. When all-cause mortality is considered, the mortality impact of the pandemic on men and women is more similar than when comparing deaths assigned to Covid-19 as underlying cause of death.
Copepod-Associated Gammaproteobacterial Alkaline Phosphatases in the North Atlantic Subtropical Gyre

Planktonic organisms may provide a niche to associated bacteria in the oligotrophic ocean. Bacterial fitness strategies in association with copepods – abundant planktonic crustaceans – were examined by sampling and incubation experiments in the North Atlantic Subtropical Gyre (NASG). The bacterial metatranscriptome was dominated by Gammaproteobacteria and showed expression of complete bacterial pathways including chemotaxis, cell signaling, and alkaline phosphatase activity. Quantitative PCR and reverse transcriptase qPCR revealed the consistent presence and expression of alkaline phosphatase genes primarily by Vibrio spp. in the copepod association. Copepod-associated bacteria appear to respond to prevailing phosphorus limitation by using alkaline phosphatases to break down organophosphoesters, presumably originating from the copepods. The results suggest that the basin-wide tendency for phosphorus limitation in the North Atlantic Ocean is occurring at microscales in these nitrogen-enriched copepod microenvironments. The bacterial communities and their fitness strategies supported by associations with these abundant mesozooplankton are unique from the surrounding seawater and could have large-scale implications for biogeochemical cycling, marine food web structuring, and copepod and ecosystem health.
The Status of the White-Tailed Hawk in Arizona and Sonora, Mexico

ABSTRACT The white-tailed hawk (Buteo albicaudatus) formerly nested in the American Southwest but no longer appears to do so. We hypothesize that the reason for the absence of this always-scarce species in Arizona and Sonora, Mexico, is the elimination of its grassland habitat caused by cessation of grass fires in the tropic-subtropic regions of these two states. Loss of subtropical grasslands in the Southwest was due to livestock grazing removing fine fuels for grassland fires. When grassland prey sources became scarce due to the reduction in grass cover, nutritional levels were no longer sufficient to allow the white-tailed hawk to successfully engage in nest-building, egg-laying and the rearing of young. These conditions, initiated in the 1880s, have continued through to the present day in both southern Arizona and Sonora.
Amorphous calcium carbonate transforms into calcite during sea urchin larval spicule growth

Sea urchin larvae form an endoskeleton composed of a pair of spicules. For more than a century it has been stated that each spicule comprises a single crystal of the CaCO3 mineral, calcite. We show that an additional mineral phase, amorphous calcium carbonate, is present in the sea urchin larval spicule, and that this inherently unstable mineral transforms into calcite with time. This observation significantly changes our concepts of mineral formation in this well–studied organism.