Miracle-dz/UniFAR-FTUs huggingface dataset:
SULFIDE OXIDATION OCCURS IN THE ANIMAL TISSUE OF THE GUTLESS CLAM, SOLEMYA REIDI

A gutless clam, Solemya reidi, from sulfide-rich habitats has gills containing symbiotic, chemoautolithotrophic bacteria that are presumed to oxidize sulfide to provide a major energy source for the symbiosis. Sulfide oxidation was studied for S. reidi; activity of gill and foot extracts displayed Michaelis-Menten kinetics and was presumably due to sulfide oxidase enzymes. The activity of S. reidi gill extracts was protease sensitive and heat sensitive and was 10 to 20 times higher than in tissues from bivalves not living in sulfide-rich environments. The site of sulfide oxidation was studied by cytochemistry, 35S-sulfide autoradiography, cell fractionation methods, and by X-ray microanalysis. In gills of S. reidi, the sulfide-oxidizing activity was detected not in the symbiotic bacteria, but within organelles of the gill cells we have named sulfide oxidizing bodies. In foot tissue of S. reidi, sulfide oxidation activity was distributed diffusely throughout the superficial cell layers of the foot. The dis.
the fitness consequences of P element insertion in Drosophila melanogaster

In this study we estimate the frequency at which P -element insertion events, as identified by in situ hybridization, generate lethal and mild viability mutations. The frequency of lethal mutations generated per insertion event was 0·004. Viability dropped an average of 1% per insertion event. Our results indicate that it is deletions and rearrangements resulting from the mobilization of P elements already in place and not the insertions per se that cause the drastic effects on viability and fitness observed in most studies of P–M dysgenesis-derived mutations. Elements of five other families ( I, copia , 412 , B104 , and gypsy ) were not mobilized in these crosses. Finally, we contrast the density of P elements on the X chromosome with the density on the four autosomal arms in a collection of thirty genomes from an African population. The relative number of P elements on the X chromosome is too high to be explained by either a hemizygous selection or a neutrality model. The possible reasons for the failure to detect selection are discussed.
Identification of a hormogonium polysaccharide‐specific gene set conserved in filamentous cyanobacteria

Cyanobacteria comprise a phylum defined by the capacity for oxygenic photosynthesis. Members of this phylum are frequently motile as well. Strains that display gliding or twitching motility across semisolid surfaces are powered by a conserved type IV pilus system (T4P). Among the filamentous, heterocyst‐forming cyanobacteria, motility is usually confined to specialized filaments known as hormogonia, and requires the deposition of an associated hormogonium polysaccharide (HPS). The genes involved in assembly and export of HPS are largely undefined, and it has been hypothesized that HPS exits the outer membrane via an atypical T4P‐driven mechanism. Here, several novel hps loci, primarily encoding glycosyl transferases, are identified. Mutational analysis demonstrates that the majority of these genes are essential for both motility and production of HPS. Notably, most mutant strains accumulate wild‐type cellular levels of the major pilin PilA, but not extracellular PilA, indicating dysregulation of the T4P motors, and, therefore, a regulatory interaction between HPS assembly and T4P activity. A co‐occurrence analysis of Hps orthologs among cyanobacteria identified an extended set of putative Hps proteins comprising most components of a Wzx/Wzy‐type polysaccharide synthesis and export system. This implies that HPS may be secreted through a more canonical pathway, rather than a T4P‐mediated mechanism.
Evolutionary patterns of host utilization by ichneumonoid parasitoids (Hymenoptera: Ichneumonidae and Braconidae)*

The four major biological strategies of ichneumonoid parasitoids, koinobiont and idiobiont, ecto-and endoparasitism, are discussed and the evolutionary radiations of the two families Ichneumonidae and Braconidae compared in an attempt to relate differences in patterns of host utilization to differences in evolutionary history. The most primitive members of both families are idiobiont ectoparasitoids of hosts concealed in plant tissue. Idiobiont ectoparasitic braconids are all still primarily associated with such hosts, but idiobiont ectoparasitic ichneumonids have radiated to attack hosts in other situations, such as in aculeate nests or in cocoons. A shift in emphasis between the behavioural steps, host habitat location and host location, is envisaged as being important in such evolutionary change. Idiobiont endoparasitism is postulated as having arisen amongst ectoparasitoids attacking cocooned hosts, as an adaptation that allows them to exploit pupae and puparia in relatively exposed positions; it is a fairly common strategy in the Ichneumonidae, but virtually unknown in the Braconidae. Koinobiosis is perceived as having evolved in association with hosts which feed in a relatively weakly concealed position, but pupate in a more secluded and safe location. The strategy is advantageous as it allows a parasitoid to oviposit on an easily discoverable host, but to use the host's pupation concealment to complete its own development. The evolution of koinobiosis has allowed parasitoids to exploit hosts that feed in exposed positions, and to attack hosts at a younger and numerically more common stage in the host's life cycle. Koinobiont ectoparasitism is envisaged, in some braconid and ichneumonid groups, to occupy an evolutionary transitional position between idiobiosis and endoparasitic koinobiosis; only in the Ichneumonidae have large radiations of koinobiont ectoparasitoids occurred. Endoparasitic koinobiosis is hypothesized as having arisen in the Braconidae in association with lepidopterous/coleopterous hosts, whilst in the major lineage of endoparasitic koinobiont ichneumonids, this habit is hypothesized as having arisen in association with symphytan hosts. The great majority of braconids are koinobiont endoparasitoids, but only about 50% of the Ichneumonidae have this habit. Very few koinobiont braconids develop as endoparasitoids of hymenopterous hosts, although many endoparasitic ichneumonids attack Hymenoptera. However, lineages of the Braconidae have radiated to exploit adult insects and exopterygote nymphs; ichneumonids do not utilize such hosts.
Impact des altérations du récepteur des androgènes sur les voies de signalisation liées à la différenciation cellulaire et à la progression du cancer de la prostate

La voie de signalisation du recepteur des androgenes (RA) est la principale cible therapeutique des cancers de la prostate metastatiques. Toutefois, l'emergence de variants constitutivement actifs du RA depourvus de leur partie C-terminale conduit a une resistance au traitement. Pendant ma these, j'ai montre que les variants du RA induisent une transition epithelio-mesenchymateuse (EMT) partielle, un phenomene observe lors de la progression tumorale. J'ai ensuite etudie les mecanismes conduisant a cette expression differentielle de marqueurs de l’EMT en me focalisant sur la N-cadherine (CDH2). Le RA entier (AR-FL) et les variants du RA interagissent tous les deux au niveau des elements de reponse aux androgenes dans l'intron1 de CDH2. Cependant, une augmentation du niveau d’acetylation des histones est observee uniquement avec les variants du RA. Mes donnees nous mene a un modele ou l'AR-FL reprimerait l'expression de CDH2 alors que les variants du RA induiraient son expression.
Variation in the reproductive strategy of the sea urchin Sphaerechinus granularis (Echinodermata: Echinoidea) related to food availability

Changes in the reproductive strategy of Sphaerechinus granularis (Echinodermata: Echinoidea) according to food availability were examined by comparing gonadal index changes from two populations with different food conditions. The better nutritional situation was confirmed by a repletion index always higher without significant inverse relationships with the gonadal index. The two populations exhibited a different reproductive strategy during their life cycle. The food limited population showed a delay in reproductive competence, a lower gonadal index and an increase in relative gonadal growth with age. This population showed a seasonal inverse relationship between the consumption index and the gonadal index during the spawning period. A discussion based on the variations in the main life history parameters between the two populations: reproduction, somatic growth, longevity, underlines the plasticity of this species which must maximize its reproductive output in terms of changes in food availability. The adaptive value of this plasticity was observed by the reduction in somatic growth which decreases the energetic cost of maintenance and by the increase in size of the feeding structure (Aristotle's lantern) which improves food acquisition.
Characterization of electrical penetration graphs of the Asian citrus psyllid, Diaphorina citri, in sweet orange seedlings

Detailed information on probing behavior of the Asian citrus psyllid, Diaphorina citri Kuwayama (Hemiptera: Psyllidae), is critical for understanding the transmission process of phloem‐limited bacteria (Candidatus Liberibacter spp.) associated with citrus ‘huanglongbing’ by this vector. In this study, we investigated stylet penetration activities of D. citri on seedlings of Citrus sinensis (L.) Osbeck cv. Pêra (Rutaceae) by using the electrical penetration graph (EPG‐DC system) technique. EPG waveforms were described based on amplitude, frequency, voltage level, and electrical origin of the observed traces during stylet penetration into plant tissues. The main waveforms were correlated with histological observations of salivary sheath termini in plant tissues, to determine the putative location of stylet tips. The behavioral activities were also inferred based on waveform similarities in relation to other Sternorrhyncha, particularly aphids and whiteflies. In addition, we correlated the occurrence of specific waveforms with the acquisition of the phloem‐limited bacterium Ca. Liberibacter asiaticus by D. citri. The occurrence of a G‐like xylem sap ingestion waveform in starved and unstarved psyllids was also compared. By analyzing 8‐h EPGs of adult females, five waveforms were described: (C) salivary sheath secretion and other stylet pathway activities; (D) first contact with phloem (distinct from other waveforms reported for Sternorrhyncha); (E1) putative salivation in phloem sieve tubes; (E2) phloem sap ingestion; and (G) probably xylem sap ingestion. Diaphorina citri initiates a probe with stylet pathway through epidermis and parenchyma (C). Interestingly, no potential drops were observed during the stylet pathway phase, as are usually recorded in aphids and other Sternorrhyncha. Once in C, D. citri shows a higher propensity to return to non‐probing than to start a phloem or xylem phase. Several probes are usually observed before the phloem phase; waveform D is observed upon phloem contact, always immediately followed by E1. After E1, D. citri either returns to pathway activity (C) or starts phloem sap ingestion, which was the longest activity observed.
Agroecology and Politics. How To Get Sustainability? About the Necessity for a Political Agroecology

Agroecological movements are spreading and many local experiences are being carried out. But agroecology still has not developed instruments and approaches to elaborate state and regional strategies, where the political and institutional aspects play a key role. This text contributes to overcoming these oversights by means of a theoretical foundation that demonstrates why agroecology should engage politics. First, we argue that agroecosystems, as socioecological constructions, are produced through power relations. Second, we show the close relationship between agroecosystem dynamics and politics, and, therefore, the crucial role that political agroecology plays in the agroecological transition. Finally, we evaluate the world food system as the context in which agroecological experiences should be developed.
The biology of the malleefowl Leipoa ocellata Gould in the Little Desert area, Australia

Several pairs of malleefowl Leipoa ocellata Gould, 1840, have been studied intensively in a block of natural mallee habitat. The unique observational situation, the result of years of patient and low-impact interactions between the observer and the birds, has provided detailed information on a normally secretive species. The regular mound construction behaviour is described, as is temperature testing and manipulation, copulation, egg laying and hatching.
K+ and Ca2+ Channels Regulate Ca2+ Signaling in Chondrocytes: An Illustrated Review

An improved understanding of fundamental physiological principles and progressive pathophysiological processes in human articular joints (e.g., shoulders, knees, elbows) requires detailed investigations of two principal cell types: synovial fibroblasts and chondrocytes. Our studies, done in the past 8–10 years, have used electrophysiological, Ca2+ imaging, single molecule monitoring, immunocytochemical, and molecular methods to investigate regulation of the resting membrane potential (ER) and intracellular Ca2+ levels in human chondrocytes maintained in 2-D culture. Insights from these published papers are as follows: (1) Chondrocyte preparations express a number of different ion channels that can regulate their ER. (2) Understanding the basis for ER requires knowledge of (a) the presence or absence of ligand (ATP/histamine) stimulation and (b) the extraordinary ionic composition and ionic strength of synovial fluid. (3) In our chondrocyte preparations, at least two types of Ca2+-activated K+ channels are expressed and can significantly hyperpolarize ER. (4) Accounting for changes in ER can provide insights into the functional roles of the ligand-dependent Ca2+ influx through store-operated Ca2+ channels. Some of the findings are illustrated in this review. Our summary diagram suggests that, in chondrocytes, the K+ and Ca2+ channels are linked in a positive feedback loop that can augment Ca2+ influx and therefore regulate lubricant and cytokine secretion and gene transcription.
The Human Y Chromosome Haplogroup Tree: Nomenclature and Phylogeography of Its Major Divisions

▪ Abstract In this review we discuss the recent construction of a highly resolved tree of the nonrecombining portion of the Y chromosome (NRY), and the development of a cladistic nomenclatural system to name the resulting haplogroups. This phylogenetic gene tree comprises 18 major haplogroups that are defined by 48 binary polymorphisms. We also present results from a phylogeographic analysis of NRY haplogroups in a global sample of 2007 males, as well as from a regional study focusing on Siberia (n = 902). We use the following statistical techniques to explicate our presentation: analysis of molecular variance, multidimensional scaling, comparative measures of genetic diversity, and phylogeography-based frequency distributions. Our global results, based on the 18 major haplogroups, are similar to those from previous analyses employing additional markers and support the hypothesis of an African origin of human NRY diversity. Although Africa exhibits greater divergence among haplogroups, Asia contains the l.
Relationship among five populations of Bactrocera dorsalis based on mitochondrial DNA sequences in western Yunnan, China

Genetic variation in the Oriental fruit fly, Bactrocera dorsalis (Hendel), was analysed using five populations from western Yunnan, China, to elucidate the distribution and likely dispersal patterns of this fly. A 503‐bp portion of the mitochondrial cytochrome oxidase gene was sequenced from a minimum of seven individuals from each of five fly populations; 25 haplotypes were observed among 57 individuals in these populations. High genetic diversity within populations was detected. Genetic distances between haplotypes reached 1.2%. Mantel tests did not indicate any isolation because of geographic distance. The Ruili (RL) population was significantly isolated from the others (pairwise Fst ranging from 0.10 to 0.21, and average genetic distances being higher than for all other four population comparisons). RL is geographically separated from the other sites by the Gaoligong Mountains. The Liuku (LK) population had a close genetic relationship with the Lujiangba (LJB) population, suggesting that the LK population probably originated from LJB that is located in the same valley to the south. The Baoshan (BS) and Dali (DL) populations were also geographically isolated from the others, not originating from LJB and RL, where the fly is present year‐round. The north‐south orientation of mountains and valleys in western Yunnan appears to prevent latitudinal gene exchange by dispersing flies and thus divides the five populations into four relatively independent zones, namely BS, DL, LK‐LJB and RL. In addition, air currents that generally flow south to north appear to assist dispersing flies, especially in valleys between the mountain chains.
Managing Coronavirus Disease 2019 Spread With Voluntary Public Health Measures: Sweden as a Case Study for Pandemic Control

Abstract Background The coronavirus disease 19 (COVID-19) pandemic has spread globally, causing extensive illness and mortality. In advance of effective antiviral therapies, countries have applied different public health strategies to control spread and manage healthcare need. Sweden has taken a unique approach of not implementing strict closures, instead urging personal responsibility. We analyze the results of this and other potential strategies for pandemic control in Sweden. Methods We implemented individual-based modeling of COVID-19 spread in Sweden using population, employment, and household data. Epidemiological parameters for COVID-19 were validated on a limited date range; where substantial uncertainties remained, multiple parameters were tested. The effects of different public health strategies were tested over a 160-day period, analyzed for their effects on intensive care unit (ICU) demand and death rate, and compared with Swedish data for April 2020. Results Swedish mortality rates are intermediate between rates for European countries that quickly imposed stringent public health controls and those for countries that acted later. Models most closely reproducing reported mortality data suggest that large portions of the population voluntarily self-isolate. Swedish ICU use rates remained lower than predicted, but a large fraction of deaths occurred in non-ICU patients. This suggests that patient prognosis was considered in ICU admission, reducing healthcare load at a cost of decreased survival in patients not admitted. Conclusions The Swedish COVID-19 strategy has thus far yielded a striking result: mild mandates overlaid with voluntary measures can achieve results highly similar to late-onset stringent mandates. However, this policy causes more healthcare demand and more deaths than early stringent control and depends on continued public will.
STRESS IN FREE-RANGING MAMMALS: INTEGRATING PHYSIOLOGY, ECOLOGY, AND NATURAL HISTORY

Abstract We review developments in the study of stress in free-ranging mammals and summarize the physiological and behavioral components of the stress response. Both the sympathetic nervous system response and the regulation and reactivity of the hypothalamic–pituitary–adrenal (HPA) axis are discussed. In particular, we describe how the activity of the HPA axis at baseline levels follows circadian and circannual rhythms in ways that allow animals to respond to predictable environmental changes, focusing largely on the endpoint of this axis, the glucocorticoid hormones cortisol and corticosterone. Superimposed upon these rhythms are the elevated glucocorticoid levels characteristic of the stress response, which allow an animal to respond to unpredictable social, physical, or environmental challenges. Methods used to explore the stress response in free-ranging mammals are described. Both inter- and intraspecific variation in the stress response as they relate to the environment are discussed. Finally, how the regulation and reactivity of the HPA axis varies by life-history stage and sex in mammals is reviewed, focusing on reproduction and development.
Adaptive Distance-Based Pooling in Convolutional Neural Networks for Audio Event Classification

In the last years, deep convolutional neural networks have become a standard for the development of state-of-the-art audio classification systems, taking the lead over traditional approaches based on feature engineering. While they are capable of achieving human performance under certain scenarios, it has been shown that their accuracy is severely degraded when the systems are tested over noisy or weakly segmented events. Although better generalization could be obtained by increasing the size of the training dataset, e.g. by applying data augmentation techniques, this also leads to longer and more complex training procedures. In this article, we propose a new type of pooling layer aimed at compensating non-relevant information of audio events by applying an adaptive transformation of the convolutional feature maps in the temporal axis. The proposed layer performs a non-linear temporal transformation that follows a uniform distance subsampling criterion on the learned feature space. The experiments conducted over different datasets show significant performance improvements when the proposed layer is added to baseline models, resulting in systems that generalize better to mismatching test conditions and learn more robustly from weakly labeled data.
Distribution and Abundance of American Eels in the White Oak River Estuary, North Carolina

Abstract Apparent widespread declines in abundance of Anguilla rostrata (American eel) have reinforced the need for information regarding its life history and status. We used commercial eel pots and crab (peeler) pots to examine the distribution, condition, and abundance of American eels within the White Oak River estuary, NC, during summers of 2002–2003. Catch of American eels per overnight set was 0.35 (SE = 0.045) in 2002 and 0.49 (SE = 0.044) in 2003. There was not a significant linear relationship between catch per set and depth in 2002 (P = 0.31, depth range 0.9–3.4 m) or 2003 (P = 0.18, depth range 0.6–3.4 m). American eels from the White Oak River were in good condition, based on the slope of a length-weight relationship (3.41) compared to the median slope (3.15) from other systems. Estimates of population density from grid sampling in 2003 (300 mm and larger: 4.0–13.8 per ha) were similar to estimates for the Hudson River estuary, but substantially less than estimates from other (smaller) systems including tidal creeks within estuaries. Density estimates from coastal waters can be used with harvest records to examine whether overfishing has contributed to the recent apparent declines in American eel abundance.