Miracle-dz/UniFAR-FTUs huggingface dataset:
Developmental regulation of fear memories by an obesogenic high-saturated fat/high-sugar diet

Background Anxiety and stress-related disorders are strongly linked with obesity and the consumption of obesogenic diets. Paralleling clinical findings, we showed that the consumption of an obesogenic diet during adolescence disrupts the structural integrity of amygdalar and prefrontal cortex circuits underlying emotional responses to stress. These abnormalities were associated with a PTSD-like phenotype, including heightened stress reactivity to predator odor trauma, anxiety-like behaviors, and profound learning deficits. The present follow-up study investigates how an obesogenic diet alters aversion-related associative memories across adolescence. Methods Adolescent Lewis rats were fed for eight weeks with an experimental Western-like high-saturated fat/high-sugar diet (WD, 41% kcal from fat) or a matched control diet (CD, 13% kcal from fat). Acoustic fear-potentiated startle (FPS) responses were assessed longitudinally at weeks 1, 4, and 8 after commencing the diets to determine the effects of the WD on cued fear conditioning, fear extinction learning, and fear extinction retention. Results We found that the rats that consumed the WD exhibited substantial attenuation of fear extinction and fear extinction retention when remote memory was tested. One-week WD consumption was sufficient to induce impairments in fear extinction learning. This phenotype was associated with reduced dopamine receptor 1 mRNA levels in the prefrontal cortex. Interestingly, our reconditioning paradigm revealed that early-acquired fear memories were resistant to the disruptive effects of chronic WD consumption on cued fear learning. Conclusions Our findings demonstrate that consumption of an obesogenic WD during adolescence heightens behavioral vulnerabilities associated with risk for anxiety and stress-related disorders. Given that fear extinction promotes resilience and that fear extinction principles are the foundation of psychological treatments for PTSD, understanding how obesity and obesogenic diets affect the acquisition and expression of fear extinction memories is of tremendous clinical relevance. HIGHLIGHTS Acute WD consumption impairs cued fear extinction learning in a fear-potentiated startle paradigm. WD consumption attenuates fear extinction memory retention WD consumption during adolescence increases acoustic startle responsivity over time Chronic WD consumption decreases dopamine receptor D1 mRNA levels in the prefrontal cortex.
Orexin Neurons Contribute to Central Modulation of Respiratory Drive by Progestins on ex vivo Newborn Rodent Preparations

Dysfunction of central respiratory CO2/H+ chemosensitivity is a pivotal factor that elicits deep hypoventilation in patients suffering from central hypoventilation syndromes. No pharmacological treatment is currently available. The progestin desogestrel has been suggested to allow recovery of respiratory response to CO2/H+ in patients suffering from central hypoventilation, but except the fact that supramedullary regions may be involved, mechanisms are still unknown. Here, we tested in neonates whether orexin systems contribute to desogestrel’s central effects on respiratory function. Using isolated ex vivo central nervous system preparations from newborn rats, we show orexin and almorexant, an antagonist of orexin receptors, supressed strengthening of the increase in respiratory frequency induced by prolonged metabolic acidosis under exposure to etonogestrel, the active metabolite of desogestrel. In parallel, almorexant suppressed the increase and enhanced increase in c-fos expression in respiratory-related brainstem structures induced by etonogestrel. These results suggest orexin signalisation is a key component of acidosis reinforcement of respiratory drive by etonogestrel in neonates. Although stage of development used is different as that for progestin clinical observations, presents results provide clues about conditions under which desogestrel or etonogestrel may enhance ventilation in patients suffering from central hypoventilation syndromes.
A Non-negative Measure Of Feature-specific Information Transfer Between Neural Signals

Quantifying the amount and content of information transfer between neural populations is crucial to understand brain dynamics and cognitive functions. Most data-driven methods exploit the notion of Wiener-Granger causality, a statistical concept based on temporal prediction. Transfer Entropy and Directed Information formalise this notion by means of information theoretical quantities and can capture any (linear and nonlinear) time-lagged conditional dependencies, thus quantifying the amount of information flow between neural signals. Nevertheless, none of these metrics can reveal what type of information is exchanged. To address this issue, we developed a new measure called Feature-specific Information Transfer (FIT) that is able to quantify both the amount and content of information transfer between neuronal signals. We tested the novel metric on simulated data and showed that it successfully captures feature-specific information transfer in different communication scenarios including feedforward communication, external confounding inputs and synergistic interactions. Moreover, the FIT measure displayed sensitivity to modulations in temporal parameters of information transfer and signal-to-noise ratios, and correctly inferred the directionality of transfer between signals. We then tested FIT’s ability to track feature-specific information flow from neurophysiological data. First, we analysed human electroencephalographic data acquired during a face detection task and confirmed current hypotheses suggesting that information about the presence of an eye in a face image flows from the contralateral to the ipsilateral hemisphere with respect to the position of the eye. Second, we analysed multi-unit activity data recorded from thalamus and cortex of rat’s brain, and showed that the FIT measure successfully detected bottom-up information transfer about visual or somatosensory stimuli in the corresponding neural pathway. Third, we analysed cortical high-gamma activity estimated from human magnetoencephalographic data during visuomotor mapping, and confirmed the notion that visuomotor-related information flows from superior parietal to premotor areas. Altogether our work suggests that the FIT measure has the potential to uncover previously hidden feature-specific information transfer from neural data and provide a better understanding of brain communication.
Influence of Silver Nitrate on Somatic Embryogenesis Induction in Arabica Coffee (Coffea arabica L.)

Plant somatic embryogenesis (SE) has been defined as the formation of embryos from a single or group of haploid or somatic cells [1, 2]. Low frequency (LFSE) and high frequency somatic embryogenesis (HFSE) have been described. In the first type, somatic embryos are induced directly from pro-embryogenic cells of explants, while in the second, they originate from embryogenic callus [1]. It has been suggested that in LFSE the origin of somatic embryos is unicellular, whereas in HFSE has been described as unicellular or multicellular [3]. SE is a powerful biotechnological tool used to propagate elite plants or to conserve important genotypes [4]. Moreover, SE offers an efficient in vitro regeneration approach as a fundamental step in plant genetic improvement for studying basic aspects of ontogenesis of somatic embryos [5]. In Coffea spp. , the first studies of SE have been reported at the beginning of 1970 [6]. Since then, a large quantity of LFSE and HFSE protocols have been optimized demonstrating that coffee is not a recalcitrant species for SE [4]. In the LFSE the somatic embryos are obtained faster (approximately 70 days) using only one medium meanwhile in HFSE several media are used and somatic embryo formation takes 9-10 months [4]. Although, in LFSE small number of somatic embryos are obtained (around 10 per explant) compared to hundreds of somatic embryos obtained per gram of embryogenic calli [4], the unicellular origin of somatic embryos in LFSE represents an advantage for the chemical and physical mutagenesis, genetic transformation and genetic editing, since prevents or reduces the appearance of chimeras [7]. In C. arabica and C. canephora many factors (such as genotype, explant type, the physiological state, age and growth conditions of the donor plants, the season of collection, nutrient composition of the medium, the volume of dissolved CO2 or O2 in the culture flask, and plant growth regulators) that affect LFSE induction have been studied [3, 8, 9, 10, 11, 12, 13]. However, few studies reported the effect of silver nitrate on LFSE using leaf explants of C. arabica L. and to the best of our knowledge it has not been analyzed using Caturra and Catuai, which are two economic important producer cultivars in Costa Rica. Since SE is genotype dependent, the culture medium need to be modified for the different genotypes [7]. Therefore, the objective of this study was to determine the influence of the benzyladenine (BAP), indole-3-acetic acid (IAA), and silver nitrate (AgNO3) on low frequency somatic embryogenesis using leaf explants of Coffea arabica L. cultivars Caturra and Catuai.
Prevalence and Antibiotic Susceptibility of Salmonella Strains Isolated from Viscera of Quail (Coturnix coturnix japonica) Breeds in Bingerville Area, Côte d’Ivoire

The control of food products contamination by Salmonella has become essential for the consumer to ensure the safety of these foods. Poultry meat and eggs play an important role as infection risk factors related to Salmonella strains resistant to antibiotics. Quail breeding, which is becoming to be appreciated by the Ivoirian population after chicken meat, may contain Salmonella pathogenic strains. Thus, a preliminary survey in two areas of high quail production (ANNA and SANTAI) in the city of Bingerville (Cote d'Ivoire), allowed collecting 60 viscera of quail for microbiological analysis. The microbiological analysis revealed 25 strains of Salmonella isolated from 11 viscera, resulting in a prevalence rate of 18.33 %. These strains also showed high resistance to Tetracycline (100 %), a relatively average resistance to Nalidixic acid (24 %) and low resistance to Ampicillin (8 %), Ticarcillin (8 %) and Cotrimoxazole (8 %). The presence of antibiotic-resistant strains of Salmonella in quail viscera could constitute a public health problem.
Rest Functional Brain Maturation during the First Year of Life

The first year of life is a key period of brain development, characterized by dramatic structural and functional modifications. Here, we measured rest cerebral blood flow (CBF) modifications throughout babies’ first year of life using arterial spin labeling magnetic resonance imaging sequence in 52 infants, from 3 to 12 months of age. Overall, global rest CBF significantly increased during this age span. In addition, we found marked regional differences in local functional brain maturation. While primary sensorimotor cortices and insula showed early maturation, temporal and prefrontal region presented great rest CBF increase across the first year of life. Moreover, we highlighted a late and remarkably synchronous maturation of the prefrontal and posterior superior temporal cortices. These different patterns of regional cortical rest CBF modifications reflect a timetable of local functional brain maturation and are consistent with baby’s cognitive development within the first year of life.
Cascades frog conservation assessment

Pope, Karen; Brown, Catherine; Hayes, Marc; Green, Gregory; Macfarlane, Diane, tech. coords. 2014. Cascades frog conservation assessment. Gen. Tech. Rep. PSW-GTR-244. Albany, CA: U.S. Department of Agriculture, Forest Service, Pacific Southwest Research Station. 116 p. The Cascades frog (Rana cascadae) is a montane, lentic-breeding amphibian that has become rare in the southern Cascade Range and remains relatively widespread in the Klamath Mountains of northern California. In the southern Cascades, remaining populations occur primarily in meadow habitats where the fungal disease, chytridiomycosis, and habitat desiccation pose threats to persistance. Major risk factors in the Klamath Mountains include introduced fish and chytridiomycosis. Conservation actions are needed for the Cascades frog in California and especially in the southern Cascades. Conservation options include restoration of breeding pools in the southern Cascades, fish removals in the Klamath Mountains, and adaptive methods to help alleviate the effects of chytridiomycosis rangewide.
Structure of molluscan communities in shallow subtidal rocky bottoms of Acapulco, Mexico

The objective of this study was to determine the structure of molluscan communities in shallow subtidal rocky bottoms of Acapulco, Mexico. Thirteen samplings were performed at 8 stations in 2012 (seven samplings), 2014 (four), and 2015 (two). The collection of the mollusks in each station was done at a maximum depth of 5 m for 1 h by 3 divers. A total of 2086 specimens belonging to 89 species, 36 families, and 3 classes of mollusks were identified. Gastropoda was the most diverse and abundant group. Calyptreaidae, Columbellidae, and Muricidae had >5 species, but Pisaniidae, Conidae, Fasciolariidae, and Muricidae had ≥15% of relative abundance. Most species found in this study were recorded in the rocky intertidal zone, and 10 species were restricted to the rocky subtidal zone. The affinity in the composition of the species during 2012-2015 had a low similarity (25%), but we could differentiate natural and anthropogenic effects according to malacological composition. In addition, 46% of the species recorded in this study are commercial fishing resources. We concluded that the rocky subtidal malacological fauna of Acapulco is highly diverse (89 species), and it has remained similar in space and time during this study.
Ampelographic identification of grape varieties grown in Yüksekova (Hakkâri) region.

This study was conducted in 2011-2012 to determine ampelographic characteristics of the grape varieties grown in Yüksekova (Hakkâri) town and villages. Ampelographic characteristics of the varieties were determined based on “Descriptors for Grape” method developed by “International Board for Plant Genetic Resources” (IBPGR). It was determined that 12 grape varieties grown in Yüksekova region belonged to Vitis vinifera L. species. Berry skin color was ‘Green yellow’ in six varieties and ‘dark red’ in the other six varieties. Mean bunch weight of the varieties was “small” in Tırşık and Tritelk varieties, “big” in Besirane, Mirani, Öküzgözü and Reşmıv varieties and “Medium” in the others. The lowest bunch weight (193.50±17,78 g) was observed in Tritelk variety and the heaviest bunch weight (576.30±48.22 g) was observed in Öküzgözü variety. Average yield per grapevine varied between 3.79-6.08 kg, water soluble dry matter content (WSDM) varied between 11-19% and titratable acidity varied between 6,00-16.30 g/l. Flowers of all varieties were “hermaphrodite”.
Systematical analysis reveals the novel function of Cyp2c29 in liver injury

As a severe lethal cancer, hepatocellular carcinoma (HCC) usually originates from chronic liver injury and inflammation, in which the discovery of key genes is important for HCC prevention. Here, we analyzed the time serial (from 0 week to 30 weeks) transcriptome data of liver injury samples in diethylnitrosamine (DEN)-induced HCC mouse model. Through expression and function analyses, we identified that Cyp2c29 was a key gene continuously downregulated during liver injury. Overexpression of Cyp2c29 suppressed the NF-κB activation, proinflammatory cytokine production and hepatocyte proliferation by increasing its production 14,15-epoxyeicosatrienoic acid (14,15-EET). Furthermore, in vivo Cyp2c29 protected against liver inflammation in liver injury mice models by reversing the expression on functions of cell proliferation, metabolism and inflammation including suppressing NF-κB pathway and compensatory proliferation. CYP2C8 and CYP2C9, two human homologs of mouse Cyp2c29, were decreased in human HCC progression and positively correlated with HCC patient survival. Therefore, through systematical analysis and verification, we identified that Cyp2c29 is a novel gene in liver injury and inflammation, which may be a potential biomarker for HCC prevention and prognosis.
Declining abundance of beetles, moths and caddisflies in the Netherlands

Recently, reports of insect declines prompted concerns with respect to the state of insects at a global level. Here, we present the results of longer‐term insect monitoring from two locations in the Netherlands: nature development area De Kaaistoep and nature reserves near Wijster. Based on data from insects attracted to light in De Kaaistoep, macro‐moths (macro‐Lepidoptera), beetles (Coleoptera), and caddisflies (Trichoptera) have declined in the mean number of individuals counted per evening over the period of 1997–2017, with annual rates of decline of 3.8, 5.0 and 9.2%, respectively. Other orders appeared stable [true bugs (Hemiptera: Heteroptera and Auchenorrhyncha) and mayflies (Ephemeroptera)] or had uncertainty in their trend estimate [lacewings (Neuroptera)]. Based on 48 pitfall traps near Wijster, ground beetles (Coleoptera: Carabidae) showed a mean annual decline of 4.3% in total numbers over the period of 1985–2016. Nonetheless, declines appeared stronger after 1995. For macro‐moths, the mean of the trends of individual species was comparable to the annual trend in total numbers. Trends of individual ground beetle species, however, suggest that abundant species performed worse than rare ones. When translated into biomass estimates, our calculations suggest a reduction in total biomass of approximately 61% for macro‐moths as a group and at least 42% for ground beetles, by extrapolation over a period of 27 years. Heavier ground beetles and macro‐moths did not decline more strongly than lighter species, suggesting that heavy species did not contribute disproportionately to biomass decline. Our results broadly echo recent reported trends in insect biomass in Germany and elsewhere.
A gross anatomical and histological study of pancreas in adult Kestrel (Falco tinnunculus)

Fifteen Kestrel were used in this study regardless to their sex. The results study showed that the pancreas of adult Kestrel (Falco tinnunculus) lies under the right side of the peritoneal cavity, and situated between the descending part and ascending part of the duodenum and has pale pinkish to white pinkish colored and consisted of 3 lobes dorsal (lobus pancreatic dorsalis), middle (middle pancreatic lobus) and ventral (lobus pancreatis ventralis) with well-developed interlobar connections made it difficult to distinguish between the 3 lobes. Histologically the pancreas of adult Kestrel (Falco tinnunculus) was covered by very thin layer of connective tissue with mesothelial cells, Connective tissue septa extended from capsule into parenchyma of pancreas dividing it in to many lobules. These septa were very thin and some of them carried blood vessels distributed all over the pancreas. The exocrine portion was constituted from serous acini with pyramidal shaped cells which had dark rounded nucleus in the middle part of the cell. Acidophilic granules found in the apices of cells. Centro acinar cells found as one or two nuclei in the center of the pancreatic acini. The endocrine portion (islets of Langerhans) was formed from clusters of endocrine cells in shape of oval or rounded pale structures with different sizes. The small one has mean diameter of 40.02±0.9 μm while the large one has diameter of 126.3±3.8 μm. Few endocrine cells were seen distributed as single cells among the pancreatic acini.
A revision of the French Trichobranchidae (Polychaeta), with descriptions of nine new species.

Trichobranchidae from French waters are revised based on material available in French marine stations and newly collected specimens. This research is the first part of the "Spaghetti Project" aiming to revise French species of terebellids and trichobranchids. It confirms the absence of the so-called cosmopolitan species Terebellides stroemii from French waters, and describes eight new species of Terebellides: T. bonifi n. sp. , T. ceneresi n. sp. , T. europaea n. sp. , T. gentili n. sp. , T. gralli n. sp. , T. lilasae n. sp. , T. parapari n. sp. and T. resomari n. sp. and one species of Trichobranchus: T. demontaudouini n. sp. using both morphological and molecular tools. An identification key for all European species of Trichobranchidae is provided.
A data-based guide to the North American ecology faculty job market

Every year for three years (2016 to 2018), I tried to identify every single person hired as a tenure track prof in ecology or an allied field (e.g., fish & wildlife) in N. America. I identified a total of 566 hires. I used public sources to compile various data on the new hires and the institutions that hired them (e.g., number of publications, teaching experience, hiring institution Carnegie class). I also compiled data provided by anonymous ecology faculty job seekers on ecoevojobs.net (e.g., number of positions applied for, number of publications, numbers of interviews and offers). And I polled readers of the Dynamic Ecology blog to get information about applicant and search committee behavior (e.g., regarding customization of applications to the hiring institution). These data address some widespread anxieties and misunderstandings about the ecology faculty job market, and also speak to gender diversity and equity in recent ecology faculty hiring. They complement, and in some cases improve on, other sources of information, such as anecdotal personal experiences.
Distinct patterns of thought mediate the link between brain functional connectome and psychological well-being

Ongoing thought patterns constitute important aspects of both healthy and abnormal human cognition. However, the neural mechanisms behind these daily experiences and their contribution to well-being remain a matter of debate. Here, using resting state fMRI and retrospective thought sampling in a large neurotypical cohort (n = 211) we identified two distinct patterns of thought, broadly describing the participants current concerns and future plans, that significantly explained variability in the individual functional connectomes. Consistent with the view that ongoing thoughts are an emergent property of multiple neural systems, network-based analysis highlighted the central importance of both unimodal and transmodal cortices in the generation of these experiences. Importantly, while state-dependent current concerns predicted better psychological health, mediating the effect of functional connectomes; trait-level future plans were related to better social health, yet with no mediatory influence. Collectively, we show that ongoing thoughts can influence the link between brain physiology and well-being.
Assessing cetacean body condition: Is total lipid content in blubber biopsies a useful monitoring tool?

We would like to thank the funders: the Department for Environment Food and Rural Affairs and Marine Scotland, for a number of long‐term monitoring contracts awarded to SMASS, the Sea Mammal Research Unit National Capability Funding from the Natural Environment Research Council (grant no. SMRU 10001), and the Strategic Environmental Research and Development Program (award RC‐2337).