Miracle-dz/UniFAR-FTUs huggingface dataset:
Predictive control of electrophysiological network architecture using direct, single-node neurostimulation in humans

Chronically implantable neurostimulation devices are becoming a clinically viable option for treating patients with neurological disease and psychiatric disorders. Neurostimulation offers the ability to probe and manipulate distributed networks of interacting brain areas in dysfunctional circuits. Here, we use tools from network control theory to examine the dynamic reconfiguration of functionally interacting neuronal ensembles during targeted neurostimulation of cortical and subcortical brain structures. By integrating multi-modal intracranial recordings and diffusion tensor imaging from patients with drug-resistant epilepsy, we test hypothesized structural and functional rules that predict altered patterns of synchronized local field potentials. We demonstrate the ability to predictably reconfigure functional interactions depending on stimulation strength and location. Stimulation of areas with structurally weak connections largely modulates the functional hubness of downstream areas and concurrently propels the brain towards more difficult-to-reach dynamical states. By using focal perturbations to bridge large-scale structure, function, and markers of behavior, our findings suggest that stimulation may be tuned to influence different scales of network interactions driving cognition.
The eldest sibling is the lousiest in an obligate brood-reducer seabird

ABSTRACT Previous studies on vertical transmission of lice on terrestrial birds have shown that the intensity of parasitism can vary within broods in relation to the hatching order of chicks. In species where the hatching order has an important effect on chick survival, lice would benefit from living on the host with the highest survival prospects. In the present work, we test this hypothesis using as model lice from the Imperial Shag, an obligate brood reducer. Our specific aims were to investigate how infestation by Eidmanniella pellucida varies in relation to the age, the order of birth and the hatching date of chicks. We observed that chicks were infested by their parents during their first days of life, mainly by lice in nymphal stage. The first chick to hatch was the most infested. Infestation was also affected by hatching date, increasing as the season progressed, reaching a maximum at the peak of the breeding season and decreasing gradually after that. The age of the chick was unrelated to the intensity of infestation. Our results suggest that lice would prefer the chick that is more likely to survive and highlights the adaptive strategies of lice according to the ecology of their hosts.
NDUFAB1 Protects Heart by Coordinating Mitochondrial Respiratory Complex and Supercomplex Assembly

The impairment of mitochondrial bioenergetics, often coupled with exaggerated reactive oxygen species (ROS) production, is emerging as a common mechanism in diseases of organs with a high demand for energy, such as the heart. Building a more robust cellular powerhouse holds promise for protecting these organs in stressful conditions. Here, we demonstrate that NDUFAB1 (NADH:ubiquinone oxidoreductase subunit AB1), acts as a powerful cardio-protector by enhancing mitochondrial energy biogenesis. In particular, NDUFAB1 coordinates the assembly of respiratory complexes I, II, and III and supercomplexes, conferring greater capacity and efficiency of mitochondrial energy metabolism. Cardiac-specific deletion of Ndufab1 in mice caused progressive dilated cardiomyopathy associated with defective bioenergetics and elevated ROS levels, leading to heart failure and sudden death. In contrast, transgenic overexpression of Ndufab1 effectively enhanced mitochondrial bioenergetics and protected the heart against ischemia-reperfusion injury. Our findings identify NDUFAB1 as a central endogenous regulator of mitochondrial energy and ROS metabolism and thus provide a potential therapeutic target for the treatment of heart failure and other mitochondrial bioenergetics-centered diseases.
Detection, Diversity, and Evolution of Fungal Nitric Oxide Reductases (P450nor)

Members of the Fungi convert nitrate (NO3) and nitrite (NO2) to gaseous nitrous oxide (N2O) (denitrification), but the fungal contributions to N-loss from soil remain uncertain. Cultivation-based methodologies that include antibiotics to selectively assess fungal activities have limitations and complementary molecular approaches to assign denitrification potential to fungi are desirable. Microcosms established with soils from two representative U.S. Midwest agricultural regions produced N2O from added NO3 or NO2 in the presence of antibiotics to inhibit bacteria. Cultivation efforts yielded 214 fungal isolates belonging to at least 15 distinct morphological groups, of which 151 produced N2O from NO2. Novel PCR primers targeting the p450nor gene that encodes the nitric oxide (NO) reductase responsible for N2O production in fungi yielded 26 novel p450nor amplicons from DNA of 37 isolates and 23 amplicons from environmental DNA obtained from two agricultural soils. The sequences shared 54-98% amino acid identity to reference P450nor sequences within the phylum Ascomycota, and expand the known fungal P450nor sequence diversity. p450nor was detected in all fungal isolates that produced N2O from NO2, whereas nirK (encoding the NOforming NO2 reductase) was amplified in only 13-74% of the N2O-forming isolates using two separate nirK primer sets. Collectively, our findings demonstrate the value of p450nor-targeted PCR to complement existing approaches to assess the fungal contributions to denitrification and N2O formation.
Disruptive sexual selection on male body size in the polyphenic black scavenger fly Sepsis thoracica

Males of the fly Sepsis thoracica, which breeds in livestock dung, are either small and black or large and amber. In trying to understand the evolution of this rare phenomenon, we found that large amber males were more successful in obtaining mates, while small black males had greater mating success than males of intermediate size and color. This was mediated by different alternative aggressive mating behaviors that mainly differed in extent.
Exploring the role of GATA2 in normal and malignant haematopoiesis

Haematopoietic stem cells (HSCs) are multipotent stem cells that sustain long-life haematopoiesis. External signals delivered from the bone marrow (BM) niche are crucial for HSC homeostasis, alongside a cell intrinsic transcriptional program driven by transcription factors (TFs). Translocations, epigenetic and genetic mutations altering TF activity, subvert HSC homeostasis leading to the development of preleukaemic stem cells (pre-LSCs) and LSCs that drive the development and maintenance of acute myeloid leukaemia (AML). Gata2, a zinc finger TF expressed in the haematopoietic system, is essential for the generation and survival of HSCs in development, however the requirement for Gata2 in adult HSCs is less clear. Perturbation of GATA2 function by loss of function mutations of the GATA2 gene, gives rise to immunodeficiency syndromes with a high risk of transformation to myelodysplastic syndrome and AML. Conversely, overexpression of GATA2 is observed in approximately 40% of AML patients and has been linked with poor prognosis. However, the precise biological impact of GATA2 expression on AML cell fate, including LSCs, has yet to be interrogated.
Ultramorphology of antennal sensilla of open-nesting honey bees Apis florea F. and Apis dorsata F. (Hymenoptera: Apidae)

Antenna of honey bees is geniculate and has been known to possess a wide variety of sensilla. The sensilla are sensitive to odor, temperature, humidity, air pressure and gustatory stimuli. In the present investigation, ultrastructural study on the antenna of the two open-nesting worker honey bees- Apis florea F. - the dwarf honey bee and A. dorsata F. - the giant honey showed considerable amount of variation in the types and distribution pattern of sensilla in the two species. The antennal form as well as the sensilla arrangement has been suggested to be adapted to the pheromone perception need of regarding a particular species.
Dairy cattle welfare as a result of human-animal relationship – a review

Abstract Despite the various concepts of human-animal relationship, the welfarist approach to this problem is one of the most often considered in theory and used in practice. When dealing with issues related to dairy cattle welfare (DCW), it is necessary to take into account both the reality characteristic for animals used to obtain milk (e.g. the problem of automatic milking of cows) and for slaughter cattle (e.g. slaughter of culled animals). It is not surprising, therefore, that issues related to DCW are the focus of the attention of the public, researchers, breeders as well as the dairy and meat industries. The aim of this article was to possibly most comprehensively cover the above-mentioned issues, although due to its huge scope it was obviously necessary to limit the article to what I think are currently most important issues. That is why in the review I (1) characterized the issues related to the division of human responsibility for DCW; (2) discussed the importance of technology to human-animal relationship; (3) elaborated the matter of stress, emotionality of animals and their cognitive abilities in the aspect of “negative” and “positive” DCW; (4) considered the possibilities of non-invasive assessment of animal welfare in the future and (5) discussed topics related to improving the conditions of the slaughter of animals. In summary, it was proposed paying more attention than has been paid until now, to the assessment of positive DCW in scientific research and breeding practice. I also drew attention to the necessity of reliable information flow on the line of the breeder/milk producer - industry - consumer, as negligence in this area is one of the reasons for public disinformation regarding the level of animal welfare.
The Role of Plant Growth Regulators in the Development of in vitro Flowering, Histology and Ultrastructural Studies in Impatiens balsamina cv. Dwarf Bush

An efficient protocol for in vitro flowering was successfully established for Impatiens balsamina cv Dwarf Bush, an important medicinal plant, through tissue culture techniques. Shoot, stem and petiole explants obtained from 4 week-old aseptic seedlings cultured on MS medium supplemented with different concentrations of plant growth regulator (PGR) were used for in vitro flower induction. Gibberellic acid (GA3), benzylaminopurine (BAP) and kinetin (Kin) treatment singly applied in MS media (pH 5.8), could all stimulate flowering at 23-26 oC with photoperiod of 16 hours light and 8 hours dark. It was observed that shoot explants were more responsive than stem explants in floral formation. Regeneration was achieved via direct organogenesis. For shoot explants, the treatment that induced the highest rate of in vitro flowering (7.30 ± 0.16 flowers per plantlet) was 1.0 mg L-1 GA3. Ultrastructural and histological analysis of in vivo and in vitro flowers were done to discover any somaclonal variation. This research described a simple protocol for rapid in vitro flowering that will be very beneficial for further breeding, cytological and molecular biology research.
Multi-omics approach identifies novel pathogen-derived prognostic biomarkers in patients with Pseudomonas aeruginosa bloodstream infection

Pseudomonas aeruginosa is a human pathogen that causes health-care associated blood stream infections (BSI). Although P. aeruginosa BSI are associated with high mortality rates, the clinical relevance of pathogen-derived prognostic biomarker to identify patients at risk for unfavorable outcome remains largely unexplored. We found novel pathogen-derived prognostic biomarker candidates by applying a multi-omics approach on a multicenter sepsis patient cohort. Multi-level Cox regression was used to investigate the relation between patient characteristics and pathogen features (2298 accessory genes, 1078 core protein levels, 107 parsimony-informative variations in reported virulence factors) with 30-day mortality. Our analysis revealed that presence of the helP gene encoding a putative DEAD-box helicase was independently associated with a fatal outcome (hazard ratio 2.01, p = 0.05). helP is located within a region related to the pathogenicity island PAPI-1 in close proximity to a pil gene cluster, which has been associated with horizontal gene transfer. Besides helP, elevated protein levels of the bacterial flagellum protein FliL (hazard ratio 3.44, p < 0.001) and of a bacterioferritin-like protein (hazard ratio 1.74, p = 0.003) increased the risk of death, while high protein levels of a putative aminotransferase were associated with an improved outcome (hazard ratio 0.12, p < 0.001). The prognostic potential of biomarker candidates and clinical factors was confirmed with different machine learning approaches using training and hold-out datasets. The helP genotype appeared the most attractive biomarker for clinical risk stratification due to its relevant predictive power and ease of detection.
Optimal harvest of age-structured populations of moose Alces alces in a fluctuating environment

We analysed sex- and age-specific harvesting strategies of moose using an age-structured population model that includes density dependence as well as environmental stochasticity. In order to find the strategy that maximises the mean annual yield we simulated the process over a large number of years. The mean annual yield is a function of the three parameters (number of harvested individuals of calves, adult (≥ ½ years old) bulls and adult females) that are involved in the definitions of the strategies. We compare, by numerical maximisation of a function in several variables, two harvest strategies: proportional harvesting, i.e. removal of a certain proportion of individuals in a given age-and sex-class, and threshold harvesting, i.e. all individuals of a given sex- and age-class are harvested when the size of this subpopulation exceeds a certain threshold. In general, proportional harvest gives a smaller mean annual yield than threshold harvesting. The variance in the annual yield is, however, larger for threshold than for proportional harvesting. These differences between the two harvest strategies increase when the annual survival of calves is low, when there is high environmental stochasticity and when there is strong density regulation operating on survival. For both harvest strategies, the optimal harvest strategy involves high harvest of calves and adult bulls, whereas adult females should hardly be harvested.
Biostimulant effects of rhizobacteria on wheat growth and nutrient uptake depend on nitrogen application and plant development

ABSTRACT The capacity of plant growth-promoting rhizobacteria (PGPR) – Bacillus amyloliquefaciens GB03 (BamGB03), B. megaterium SNji (BmeSNji), and Azospirillum brasilense 65B (Abr65B) – to enhance growth and nutrient uptake in wheat was evaluated under different mineral N fertilizer rates, in sterile and non-sterile soils, and at different developmental stages. In gnotobiotic conditions, the three strains significantly increased plant biomass irrespective of the N rates. Under greenhouse conditions using non-sterile soil, growth promotion was generally highest at a moderate N rate, followed by a full N dose, while no significant effect was observed for the inoculants in the absence of N fertilizer. At 50N, plant biomass was most significantly increased in roots (up to +45% with Abr65B) at stem-elongation stage and in the ears (+19–23% according to the strains) at flowering stages. For some nutrients (N, P, Mn, and Cu), the biomass increases in roots and ears were paralleled with reduced nutrient concentrations in the same organs. Nevertheless, growth stimulation resulted in a higher total nutrient uptake and higher nutrient uptake efficiency. Furthermore, Abr65B and BmeSNji counteracted the reduction of root development caused by a high N supply. Therefore, combining PGPR with a proper cultivated system, N rate, and plant stage could enhance their biostimulant effects.
Prediction of protein structure of novel protein (116 kDa) from human sperm membrane

Objective: To predict the protein similarity, biological function and structure of 116 kDa protein that was isolated from human sperm membrane of acrosome by using in silico. Methods: Predictions for 116 kDa protein similarity was done through comparative analysis of its isoelectric point (pI) and molecular weight to the UniProtKB/TrEMBL protein database. The three-dimensional structure of the protein was built using SWISS-MODEL. Results: The 116 kDa protein with pI 4.4 was expected to have similarities with CDH23 proteins that had pI 4.38, thus they likely had similar physical and biochemical properties. The predicted protein had an extracellular N-terminal that likely acted as a receptor, and showed cell recognition characteristic, playing a role in fertilization. Conclusions: The 116 kDa protein isolated from acrosome membrane has similarity on its biophysical character to the CDH23.
Variation in Octopus bimaculatus Verrill, 1883 Diet as Revealed through δ13C and δ15N Stable Isotope Analysis: Potential Indirect Effects of Marine Protected Areas

Abstract: Anthropogenic impacts on marine environments can be far-reaching and variable, and in an effort to mitigate these impacts, marine protected areas (MPAs) have been established globally. Indirect effects of MPAs on marine food webs and consumer behavior can be revealed through the diet of generalist predators, like octopuses, since their diet is a reflection of both preference and prey availability. Octopuses (Octopus bimaculatus Verrill, 1883) and invertebrate prey species were collected around Santa Catalina Island, CA in the summer of 2012, 2013, and 2014, and muscle tissues were analyzed for δ13C and δ15N. The δ13C and δ15N signature of octopuses caught within the MPA area and the non-MPA area were compared within diet space. Estimated contribution of prey species to octopus diet was calculated using a Bayesian mixing model. Octopuses caught in MPA areas had significantly different isotopic signatures than octopuses caught outside MPA areas in 2012 and 2013, but not 2014. Prey contributions to diet were highly variable between areas and years. Bivalves were a consistent contributor to MPA octopus diet, and the large snail Megastrea undosa (W. Wood, 1828) made up a relatively large proportion of the diet of octopuses from all areas and years. Additionally, there were more moray eels, a nocturnal predator outside MPA areas but more diurnal predators inside MPA areas. These results suggest octopus foraging behavior could be influenced by variation in predation risk reveal an indirect impact of diurnal predator recovery in the MPA. To fully understand the impact of anthropogenic change on marine environments, we must assess changes in the entire community and the interactions that drive community function.
Acoustic detection of the critically endangered North Pacific right whale in the northern Bering Sea

DANA L. WRIGHT, University of Washington, Joint Institute for the Study of Atmosphere and Ocean, 3737 Brooklyn Avenue NE, Seattle, Washington 98105, U.S.A. and NOAA NMFS Alaska Fisheries Science Center, Marine Mammal Laboratory, 7600 Sand Point Way NE, Seattle, Washington 98115, U.S.A; CATHERINE L. BERCHOK, JESSICA L. CRANCE, and PHILLIP J. CLAPHAM, NOAA NMFS Alaska Fisheries Science Center, Marine Mammal Laboratory, 7600 Sand Point Way NE, Seattle, Washington 98115, U.S.A.
Determination of Cardinal Temperatures of Flax-leaf Alyssum (Alyssum linifolium) in Response to Salinity, pH, and Drought Stress

Abstract Flax-leaf alyssum (Alyssum linifolium Steph. ex. Willd.) is a winter weed species in irrigated and dryland farming systems of Iran. Experiments were conducted to compare the cardinal temperatures of A. linifolium at different levels of drought, salt concentration, and pH. In all experiments, the dent-like model showed a better fit than the quadratic polynomial model. Alyssum linifolium produced the highest germination rates at pH 7 and a temperature of 20 C in nonstress treatment. Minimum, optimum, and ceiling temperatures in the dent-like model were 4.1 (upper =26.8, lower=10.0) and 35 C, and in the quadratic polynomial model were 3.3, 19.1, and 35.0 C, respectively. At increased salinity and drought potential levels, the minimum temperature increased, while optimum and ceiling temperatures decreased. Seeds could germinate at up to 20 dS m-1 and −1 MPa, respectively, but germination rate and percentage significantly decreased. The seeds of this weed germinated across a wide range of pH values (4 ≤⃒ pH ≥⃒ 8), but the temperature range at which seeds could germinate was reduced. These data serve as guidelines for species-specific propagation protocols and agricultural decision support systems.
Variation in nest characteristics and brooding patterns of female Black-throated Blue Warblers is associated with thermal cues

ABSTRACT Thermal variation poses a problem for nesting birds and can result in reduced offspring growth rates and survival. To increase the thermal stability of the nest, females can adjust nest characteristics and nest attendance in response to changes in environmental conditions. However, it is unclear how and to what extent females modify parental behaviors during various stages of offspring development. We tested the hypothesis that females adjust nest characteristics and brooding patterns in response to thermal variation during the nest-building and nestling stages, respectively. We examined elevational variation in nest location, nest construction, and brooding patterns in the migratory Black-throated Blue Warbler (Setophaga caerulescens) across a 2°C gradient at the Hubbard Brook Experimental Forest, New Hampshire, USA. Density of woody stems at nest sites and nest wall thickness increased from low to high elevation, corresponding to decreasing temperatures, but we found no relationship between weather during nest building and nest characteristics. However, weather during the nestling stage was associated with female brooding patterns: at lower temperatures and with higher rainfall, females spent more time off the nest, which was associated with lower nestling mass near fledging. These results suggest that thermal cues during nest building may be unreliable as predictors of future conditions for developing nestlings and also that females might favor their own self-maintenance and compromise nestling growth under adverse thermal conditions.