Miracle-dz/UniFAR-FTUs huggingface dataset:
Degradation of the repetitive genomic landscape in a close relative of C. elegans

The abundance, diversity, and genomic distribution of repetitive elements is highly variable among species. These patterns are thought to be driven in part by reproductive mode and the interaction of selection and recombination, and recombination rates typically vary by chromosomal position. In the nematode C. elegans, repetitive elements are enriched at chromosome arms and depleted on centers, and this mirrors the chromosomal distributions of other genomic features such as recombination rate. How conserved is this genomic landscape of repeats, and what evolutionary forces maintain it? To address this, we compared the genomic organization of repetitive elements across five Caenorhabditis species with chromosome-level assemblies. As previously reported, repeat content is enriched on chromosome arms in most Caenorhabditis species, and no obvious patterns of repeat content associated with reproductive mode were observed. However, the fig-associated Caenorhabditis inopinata has experienced rampant repetitive element expansion and reveals no association of global repeat content with chromosome position. Patterns of transposable element superfamily-specific distributions reveal this global pattern is driven largely by a few transposable element superfamilies that in C. inopinata have expanded in number and have weak associations with chromosome position. Additionally, 15% of predicted protein-coding genes in C. inopinata align to transposon-related proteins. When these are excluded, C. inopinata has no enrichment of genes in chromosome centers, in contrast to its close relatives who all have such clusters. Forward evolutionary simulations reveal that chromosomal heterogeneity in recombination rate is insufficient for generating structured genomic repetitive landscapes. Instead, heterogeneity in the fitness effects of transposable element insertion is needed to promote heterogeneity in repetitive landscapes. Thus, patterns of gene density along chromosomes are likely drivers of global repetitive landscapes in this group, although other historical or genomic factors are needed to explain the idiosyncrasy of genomic organization of various transposable element taxa within C. inopinata. Taken together, these results highlight the power of comparative genomics and evolutionary simulations in testing hypotheses regarding the causes of genome organization.
Usefulness of a familiarity signal during recognition depends on test format: Neurocognitive evidence for a core assumption of the CLS framework

Familiarity-based discrimination between studied target items and similar foils in yes/no recognition memory tests is relatively poor. According to the complementary learning systems (CLS) framework this is due do a relatively small difference in familiarity strength between these two item classes. The model, however, also predicts that when targets and corresponding similar foils are presented next to each other in a forced-choice corresponding (FCC) test format, familiarity values for targets and foils can be directly compared because in each trial, targets are reliably more familiar than their corresponding foils. In contrast, when forced-choice displays contain non-corresponding foils (FCNC) which are similar to other studied items (but not the target), familiarity should not be diagnostic because familiarity values are not directly comparable (as in yes/no-tasks). We compared ERP old/new effects (ERPs of targets vs. foils) when participants were tested with FCC vs. FCNC displays after having intentionally encoded pictures of objects. As predicted, the mid-frontal old/new effect which is associated with familiarity was significantly larger in FCC compared to FCNC displays. Moreover, the target-foil amplitude difference predicted the accuracy of the recognition judgment in a given trial. This is one of the very few studies which support the assumption of the CLS framework that the test format can influence the diagnosticity of familiarity. Moreover, it implies that the mid-frontal old/new effect does not reflect the mean difference in the familiarity signal itself between studied and non-studied items but reflects the task-adequate assessment of the familiarity signal.
Rapid diversification of alpine bamboos associated with the uplift of the Hengduan Mountains

The Hengduan Mountains (HDM) of southwest China is a biodiversity hotspot and harbours one of the world's richest temperate floras. However, the origin and evolution of its biota remain largely unresolved. Here we explore the impact of mountain uplift on the diversification process of biodiversity in this hotspot using alpine bamboos.
Kinetics of response to ipilimumab (MDX-010) in patients with stage III/IV melanoma

8525 Background: Ipilimumab, a fully human monoclonal antibody that blocks cytotoxic T-lymphocyte antigen-4 (CTLA-4), enhances immune responses to tumor-associated antigens resulting in durable objective responses (OR). This abstract describes the kinetics of response after ipilimumab treatment. Methods: 5 studies (2 complete; 3 ongoing) in 269 treated patients with stage III/IV melanoma were reviewed and analyzed to determine the kinetics and duration of response after ipilimumab. Patients received ipilimumab alone or with dacarbazine, IL-2 or gp100 peptide vaccine. Ipilimumab doses ranged from 0.3–10mg/kg/dose (single or multiple). Complete and partial response (CR, PR), stable and progressive disease (SD, PD) were evaluated. Results: 41 patients (15%) had a confirmed OR at analysis. CR and PR was of late onset in some patients and occurred from ∼10–106 and ∼5–62 weeks (w) post-treatment initiation, respectively. In 28 patients onset of CR or PR occurred after >∼12w of treatment. PD preceded OR (without.
Southern highland papaya (Vasconcellea quercifolia A. St.-Hil.): Do fruit ripening and harvesting time affect seed germination?

In this work, we report the effects of the harvesting time, the stages in fruit ripening and the influence of potassium nitrate in V. quercifolia seed germination. In addition, information about the storage period and light requirements is provided. Fruits were harvested at the beginning and at the end of the fruiting season, and they were classified into five ripening categories. Seed germination was evaluated with two factorial experiments: 1) harvesting time, fruit ripening, and pre-germination treatment; 2) storage and light requirements. The response variables were germination percentage, mean germination time, and seedling vigor. Seeds harvested at the beginning of the season appeared to be less dormant and they were not influenced by fruit ripening or pre-germination treatments. By contrast, seeds harvested at the end of the season were influenced by fruit ripening and pre-germination treatments. Light and seed storage had a positive effect on germination. Mean germination time varied from 12 to 40 days, and vigor index was positively influenced by potassium nitrate. V.quercifolia seeds are photoblastic positive at constant temperatures and their dormancy can be influenced by harvest time, fruit ripening and a storage period.
Root trait responses to drought depend on plant functional group

Drought can strongly modify plant diversity and ecosystem processes. As droughts are expected to intensify in the future, it is important to better understand plant responses to drought. We expect that roots traits constitute an overlooked but powerful predictor of plant responses as roots are in direct contact with the soil environment, taking up nutrients and water. Here, we determine which root traits are sensitive to drought, the magnitude of that response, whether their predictive power and relationships with shoot biomass are affected by drought and whether all these responses depend on plant functional group. To do so, we conducted a glasshouse experiment with 24 plant species grown in pots (10 replicates per species), which represent three different functional groups: grasses, herbs and legumes. All replicates were well watered during the first month and then half of the replicates were kept under drought (30 % water holding capacity (WHC)) with the other half serving as control (kept at 70% WHC). After two months of the treatment, leaf and root traits were measured. Leaf traits had a strong but more uniform response to drought compared to root traits. Root trait response was variable and differed by plant functional group. Most grasses had increased root diameter, specific root surface area (SRSA) while decreased root tissue density (RTD) with drought. Production of thicker roots with a low tissue density could allow grasses to achieve greater nutrient and water acquisition through mycotrophy and would be linked to an increase in the reserve of non-structural carbohydrates needed for osmoregulation. Herbs had decreased SRSA and specific root length (SRL) while increase root carbon allocation. Reduction of root elongation or sacrifice of fine roots would be compensated by an increase in root carbon allocation, which allow herbs to improve water uptake. Legumes did not alter root morphological traits but promote an early flowering in order to scape drought. Our results identify changes in root morphological traits as mechanisms to likely face drought, a response that is species-specific and differed among functional groups.
A functional spiking-neuron model of activity-silent working memory in humans based on calcium-mediated short-term synaptic plasticity

In this paper, we present a functional spiking-neuron model of human working memory (WM). This model combines neural firing for encoding of information with activity-silent maintenance. While it used to be widely assumed that information in WM is maintained through persistent recurrent activity, recent studies have shown that information can be maintained without persistent firing; instead, information can be stored in activity-silent states. A candidate mechanism underlying this type of storage is short-term synaptic plasticity (STSP), by which the strength of connections between neurons rapidly changes to encode new information. To demonstrate that STSP can lead to functional behavior, we integrated STSP by means of calcium-mediated synaptic facilitation in a large-scale spiking-neuron model. The model simulated a recent study that measured behavior and EEG activity of participants in a delayed-response task. In this task, a visual grating had to be maintained in WM, and compared to a subsequent probe. It was demonstrated that WM contents could be decoded from the neural activity elicited by a task-irrelevant stimulus that was displayed during the activity-silent maintenance period. In support of our model, we show that it can perform this task, and that both its behavior as well as its neural representations correspond to the human data. We conclude that information in WM can be effectively maintained in activity-silent states by means of calcium-mediated STSP. Author Summary Mentally maintaining information for short periods of time in working memory is crucial for human adaptive behavior. It was recently shown that the human brain does not only store information through neural firing – as was widely believed – but also maintains information in activity-silent states. Here, we present a detailed neural model of how this could happen in our brain through short-term synaptic plasticity: rapidly adapting the connection strengths between neurons in response to incoming information. By reactivating the adapted network, the stored information can be read out later. We show that our model can perform a working memory task as accurate as human participants can, while using similar mental representations. We conclude that our model is a plausible and effective neural implementation of human working memory.
Lesion of striatal patches disrupts habitual behaviors and increases behavioral variability

Habits are automated behaviors that are insensitive to changes in behavioral outcomes. Habitual responding is thought to be mediated by striatum, with medial striatum guiding goal-directed action and lateral striatum promoting habits. However, interspersed throughout the striatum are neurochemically differing subcompartments known as patches, which are characterized by distinct molecular profiles relative to the surrounding matrix tissue. These structures have been thoroughly characterized neurochemically and anatomically, but little is known regarding their function. Patches have been shown to be selectively activated during inflexible motor stereotypies elicited by stimulants, suggesting that patches may subserve habitual behaviors. To explore this possibility, we utilized transgenic mice (Sepw1 NP67) expressing Cre recombinase in striatal patches to target these neurons for selective ablation with a virus driving Cre-dependent expression of caspase 3. Mice were then trained to press a lever for sucrose rewards on a variable interval schedule to elicit habitual responding. Mice were not impaired on the acquisition of this task, but lesioning striatal patches disrupted behavioral stability across training and lesioned mice utilized a more goal-directed behavioral strategy during training. Similarly, when mice were forced to omit responses to receive sucrose rewards, habitual responding was impaired in lesioned mice. To rule out effects of lesion on motor behaviors, mice were then tested for impairments in motor learning on a rotarod and locomotion in an open field. We found that patch lesions specifically impaired initial performance on the rotarod without modifying locomotor behaviors in open field. This work indicates that patches promote behavioral stability and habitual responding, adding to a growing literature implicating striatal patches in stimulus-response behaviors.
Males’ calls carry information about individual identity and morphological characteristics of the caller in burrowing petrels

Acoustic communication in burrowing petrels has been poorly studied. However, as for many other bird species, acoustic communication seems to play an essential role in social interactions during the breeding season of these seabirds. Bachelor males call from their burrow, likely to attract females, but also when vocally challenged by other males. Calling in the breeding colony exposes petrels to high predation risks and thus it should provide an important benefit. The present study focuses on the informative content of males’ calls in the blue petrel (Halobaena caerulea) and the Antarctic prion (Pachyptila desolata), two monogamous petrel species producing a single egg per year. We tested the hypotheses that acoustic parameters of a male's calls (i) reflect phenotypic characteristics, and (ii) bear an individual vocal signature. To do so, we first tested on both species the relationships between seven morphometric measurements and 11 acoustic parameters using multivariate analyses. Second, we performed a between‐class analysis and calculated the Potential of Individuality Coding (i.e. the ratio between intra‐ and inter‐individual variabilities) for acoustic parameters in both spectral and temporal domains. Results show acoustic parameters (especially energy quartiles, call duration, and syllable or phrase rate) reflect the caller's body size, bill morphology and wing morphology in both species. Considering the seeming pertinence of wing morphology, we suggest wing area may be a more relevant trait to consider than wing length when studying soaring birds. The results support the idea that energy quartiles, phrase rate and call duration also code for individual identity. Information carried by males’ calls might play a role in social interactions, such as burrow defence (e.g. male‐male competition, neighbour‐stranger discrimination) and/or female mate choice.
Aging and the encoding of changes in events: The role of neural activity pattern reinstatement

When encountering unexpected event changes, memories of relevant past experiences must be updated to form new representations. Current models of memory updating propose that people must first generate memory-based predictions to detect and register that features of the environment have changed, then encode the new event features and integrate them with relevant memories of past experiences to form configural memory representations. Each of these steps may be impaired in older adults. Using functional MRI, we investigated these mechanisms in healthy young and older adults. In the scanner, participants first watched a movie depicting everyday activities in a day of an actor’s life. They next watched a second nearly identical movie in which some scenes ended differently. Crucially, before watching the last part of each activity, the second movie stopped, and participants were asked to mentally replay how the activity previously ended. Three days later, participants were asked to recall the activities. Neural activity pattern reinstatement in medial temporal lobe (MTL) during the replay phase of the second movie was associated with detecting changes and with better memory for the original activity features. Reinstatements in posterior medial cortex (PMC) additionally predicted better memory for changed features. Compared to young adults, older adults showed a reduced ability to detect and remember changes and weaker associations between reinstatement and memory performance. These findings suggest that PMC and MTL contribute to change processing by reinstating previous event features, and that older adults are less able to use reinstatement to update memory for changed features.
Brain glycogen decreases during prolonged exercise

Non‐technical summary Energy sources for the brain include not only blood glucose, but also astrocytic glycogen, especially when the blood‐born glucose supply is short (e.g. hypoglycaemia). Although untested, it is hypothesized that during prolonged exercise that induces hypoglycaemia, the resultant hypoglycaemia may cause a decrease in brain glycogen. Here, we tested this hypothesis and provide evidence that brain glycogen decreases during prolonged exercise with hypoglycaemia. Furthermore, in the cortex, we show that the decrease in brain glycogen levels during prolonged exercise is associated with activation of monoamine metabolism, which could be a factor inducing central fatigue. Since the discovery of muscle glycogen depletion as a candidate of peripheral fatigue during prolonged exercise, this is the first study to our knowledge to show that brain glycogen can decrease with prolonged exercise. These findings may provide a clue towards understanding the mechanisms related to central fatigue.
Effects of dietary lysolecithin on growth performance, feed utilization, intestinal morphology and metabolic responses of channel catfish (Ictalurus punctatus)

This study investigated the effects of dietary lysolecithin on growth performance, feed utilization and metabolic responses of channel catfish (Ictalurus punctatus). Fish (initial weight: 14.77 ± 0.45 g) were randomly fed one of five practical diets supplemented with graded levels of lysolecithin (0, 125, 250, 375 and 500 mg/kg) in quadruplicate groups for 10 weeks. Results showed that no significant differences in weight gain, condition factor and viscerosomatic index among all the treatments. Fish fed diet supplemented with 250 mg/kg lysolecithin had significantly decreased feed conversion ratio and significantly increased protein efficiency ratio compared to that fed the control diet. The group with 250 mg/kg of dietary lysolecithin had higher protein and lower lipid contents in the whole body, and lower lipid content in the liver than those in the control group. Groups supplemented with 250–500 mg/kg of dietary lysolecithin had significantly higher gastric and intestinal lipase activities than the control group. Dietary lysolecithin at the level of 250 mg/kg significantly increased the activities of Na⁺, K⁺‐ATPase, alkaline phosphatase, total antioxidative capacity, total superoxide dismutase, glutathione peroxidase and catalase and significantly decreased the content of malondialdehyde compared to the control diet. In conclusion, dietary supplementation of lysolecithin could confer benefits of feed utilization, body composition and antioxidative capacity of channel catfish.
GENDER AND CAREER: FEMALE AND MALE NURSING STUDENTS' PERCEPTIONS OF MALE NURSING ROLE IN TURKEY

Aim. The aim of this study was to determine what female and male undergraduate nursing students think of males in nursing.Method and material. Senior nursing students (n=90) at an undergraduate program in School of Health located in the Northwestern Region of Turkey were included in the study. A questionnaire was used for data collection which received a response rate of 97 %. Results. Close to half of the female nursing students (45.3 %) want to see males as staff nurses while most of the male nursing students wanted to occupy administrative or administrative/instructor positions after graduation. Female and male students’ perceptions about effects of males on image and status of nursing (p
Diversity and antimicrobial resistance of Salmonella isolated from swines feces and carcasses

The aim of this study was to determine the most frequent Salmonella serovars in swine feces in the farm, piggery’s waiting slaughterhouse and after in their carcasses during slaughter, as well as their antimicrobial resistance profiles. Eighty six strains of Salmonella spp. were used, they were previously isolated from three different lots in different collections. The identification of serovars was done by serotyping and the resistance to antimicrobial agents was determined by disc diffusion. A variety of serovars was observed, and the 86 strains were serologically identified as: 28 (32.55%) S. Typhimurium, 20 (23.26%) S. Agona, 17 (19.77%) S. Infantis, 6 (6.98%) S. Panama, and 15 (17.44%) S. Minnesota. The diversity of serovars indicated that different factors influence the infection of finishing pigs and the persistence of microorganisms in the carcass after slaughter of these animals. More than 50% of the isolates were resistant to nine of the 11 tested antibiotics. The drugs that microorganisms had the highest percentages of sensitivity were sulphazotrim and norfloxacin, 22.1% and 14%, respectively. S. Typhimurium serovar was the most isolated, including in the carcasses, and also showed the largest difference in antimicrobial resistance when compared to other serovars. The profile of multidrug resistance observed in this study highlights to the necessity of a judicious observation of antimicrobial resistance in zoonotic foodborne bacteria. de sensibilidade foram o sulfazotrim e a norfloxacina, 22,1% e 14%, respectivamente. S. Typhimurium foi o sorovar mais isolado, inclusive nas carcaças, e também o que demonstrou maior diferença quanto à resistência aos antimicrobianos, quando comparado aos outros sorovares. O perfil de multirresistência observado neste estudo alerta para a necessidade de vigilância e monitoramento sistemático da resistência aos antimicrobianos em bactérias zoonóticas transmitidas pelos alimentos. The technique used for the antimicrobial resistance was the disk diffusion test according to the protocol described by the National Committee for Clinical Laboratory Standards (NCCLS, 2002). The antibiotics used for the test were: amoxicillin 10 μ g, norfloxacin 10 μ g, gentamicin 10 μ g, erythromycin 15 μ g, nalidixic acid 30 μ g, tetracycline 30 μ g and sulfazotrim 25 μ g (Laborclin®); ceftiofur 10 μ g, enrofloxacin 5 μ g and lincomycin 2 μ g (Sensifar®). The strain E. coli ATCC 25922 was used as a control. The plates were incubated at 37 ° C for 18 to 20 hours, and then the sensitivity halos (in millimeters) were measured using a pachymeter and subsequent classification of the microorganism as sensitive, intermediate or resistant to the tested antimicrobial. The antimicrobial resistance profile determined for the different serovars was compared using the Chi-square test with 95% of confidence. The calculations were performed using the Biostat 5.0 program (AYRES, 2007).