Miracle-dz/UniFAR-FTUs huggingface dataset:
Domain organization and conformational change of dynactin p150

Dynactin is a principal regulator of the minus-end directed microtubule motor dynein. The sidearm of dynactin is essential for binding to microtubules and regulation of dynein activity. Although our understanding of the structure of the dynactin backbone (Arp1 rod) has greatly improved recently, structural details of the sidearm part remain elusive. Here, electron microscopy of individual molecules of the dynactin complex revealed that the sidearm was highly flexible and exhibited diverse morphologies. Utilizing nanogold labeling and deletion mutants, we determined the domain organization of the largest subunit p150 and identified a filamentous structure protruding from the head domain of the sidearm as the coiled-coil 1 (CC1), the dynein-binding domain, in p150. Furthermore, the CC1 protrusion exhibited either a folded or an extended form, suggesting that CC1 works as an extending “arm”. These findings provide clues to understand how dynactin binds to microtubules and regulates dynein.
Genomic profiling of T cell activation reveals dependency of memory T cells on CD28 costimulation

T cell activation is a critical driver of immune response and if uncontrolled, it can result in failure to respond to infection or in excessive inflammation and autoimmunity. CD28 costimulatory pathway is an essential regulator of CD4 T cell responses. To deconvolute how T cell receptor (TCR) and CD28 orchestrate activation of human CD4 T cells we stimulated cells using varying intensities of TCR and CD28 signals followed by gene expression profiling. We demonstrate that T-helper differentiation and cytokine expression are controlled by CD28. Strikingly, cell cycle and cell division are sensitive to CD28 in memory cells, but under TCR control in naive cells, in contrast to the paradigm that memory cells are CD28-independent. Using a combination of chromatin accessibility and enhancer profiling, we observe that IRFs and Blimp-1 (PRDM1) motifs are enriched in naive and memory T cells in response to TCR. In contrast, memory cells initiate AP1 transcriptional regulation only when both TCR and CD28 are engaged, implicating CD28 as an amplifier of transcriptional programmes in memory cells. Lastly, we show that CD28-sensitive genes are enriched in autoimmune disease loci, pointing towards the role of memory cells and the regulation of T cell activation through CD28 in autoimmune disease development. This study provides important insights into the differential role of CD28 in naive and memory T cell responses and offers a new platform for design and interpretation of costimulatory based therapies. One-sentence summary Genomic profiling of CD4 T cell activation reveals a sensitivity switch from TCR in naive to CD28 in memory cells.
Efecto de la temperatura en poblaciones de Dendroctonus frontalis Zimmerman y Dendroctonus mexicanus Hopkins (Coleoptera: Curculionidae: Scolytinae) bajo un escenario de cambio climático en la Sierra Gorda queretana

En México fueron afectadas alrededor de 17,900 ha de bosques de coníferas en 2016 a causa de los brotes de insectos descortezadores. Se ha observado que el aumento en las temperaturas ocasionadas por el cambio climático afecta directamente a los bosques de pino y favorece el desarrollo de insectos plaga. Los gradientes altitudinales generan gradientes climáticos, por lo cual, son buenos modelos de estudio en un contexto de cambio climático. El objetivo del estudio fue determinar el efecto de la temperatura y la abundancia de Dendroctonus frontalis y Dendroctonus mexicanus a lo largo del rango de distribución altitudinal, así como determinar un posible cambio en la abundancia para 2030 bajo un escenario de cambio climático. Los resultados evidenciaron que la mayor abundancia de D. frontalis y D. mexicanus se encuentra en altitudes entre los 1,589 y 1,716 msnm, donde ocurren temperaturas superiores a 16 °C, y en altitudes mayores a los 2,393 msnm la abundancia de ambas especies es menor, correspondiendo a temperaturas menores a 13°C. El escenario A1B de cambio climático predice que la temperatura aumentará del 2015-2016 al año 2030 3.9 °C en promedio.
Calling-Site Preferences of Three Co-occurring Endangered Frog Species on Amami-Oshima Island

Abstract Hotspots of amphibian species diversity typically occur in limited geographical ranges, and critically endangered habitats often contain a large number of endemic amphibian species. In such regions, it is prudent to engage conservation strategies for multiple amphibian species simultaneously. To correctly identify suitable habitats for multiple species, species interactions should be considered in species distribution models. In this study, we adopted a joint species distribution model to determine the abiotic and biotic factors that affect calling-site choice in three endangered co-occurring frog species on Amami-Oshima Island, and examined whether they co-occur more than expected after considering the overlapping preferences in environmental variables. Occurrences of Babina subaspera, Odorrana splendida, and O. amamiensis were assessed by monitoring mating calls using automatic digital voice recorders at 67 sites in 12 streams and explained by 8 environmental variables: water flow volume, temperature, pH, electrical conductivity, ammonium (NH4+-N) concentration, elevation, slope, and forest stand age. The flow volume was negatively associated with occurrences in B. subaspera and O. splendida, but not O. amamiensis. Odorrana splendida occurred more frequently at higher elevations. Babina subaspera and O. splendida showed positive environmental correlations, indicating that they preferred similar environmental conditions, while exhibiting no negative relationships with each other. Our results indicated that B. subaspera and O. splendida do not avoid each other despite potential competition during the tadpole stage. Our results demonstrated that conserving preferable areas for O. splendida would also benefit B. subaspera with no negative species interactions, but not O. amamiensis. Considering species interactions in species distribution models will help us take more effective measures in the conservation of multiple species.
The Role of CAMSAPs and Non-Centrosomal Microtubules in Tissue Injury Response in Caenorhabditis elegans

The microtubule (MT) arrays in mature polarized cells comprise mostly of non-centrosomal MTs; their regulation is poorly understood. Recently, the MT minus end binding proteins CAMSAPs have been shown to be important regulators of non-centrosomal microtubule organization and dynamics. In this dissertation I describe my work on the C. elegans member of the CAMSAP family, PTRN-1, and its roles in the injury responses of two types of tissues, the neurons and the epidermis. First, I found that PTRN-1 is required for axon regeneration. Though PTRN-1 is largely dispensable for normal neuronal development, its proper regulation of neuronal microtubule dynamics is required for axons to regrow after injury. The second part of my work focuses on PTRN-1’s role in epidermal development and wound response by regulating epidermal microtubule stability. Mutations in the gene death associated protein kinase 1 (DAPK1)/dapk-1 results in both hyperactive innate immune response and enhanced wound closure in the epidermis. A genetic suppressor screen of the dapk-1 mutant identified PTRN-1 as a key player in dapk-1 mediated wound phenotypes. Further work uncovered DAPK-1 as a potential novel regulator of PTRN-1’s function in epidermal MT architecture and dynamics. My thesis work reveals new in vivo roles of PTRN-1 in regulating non-centrosomal MTs for normal tissue damage response.
Injectable formulations forming an implant in situ as vehicle of silica microparticles embedding superparamagnetic iron oxide nanoparticles for the local, magnetically mediated hyperthermia treatment of solid tumors

Cette these presente les travaux de developpement de formulations injectables capables de se solidifier in situ, formant ainsi un implant piegeant des microparticules magnetiques en vue du traitement de tumeurs par induction magnetique d'une hyperthermie locale moderee. Nous exposons tout d'abord le contexte physique, biologique et clinique de l'hyperthermie comme traitement anticancereux, particulierement des modalites electromagnetiques. Les performances in vitro et in vivo des materiaux et formulations sont alors presentees. L'objet du chapitre suivant est la caracterisation des proprietes physicochimiques, magnetiques, et chauffantes, dans un champ magnetique alternatif (115 kHz, 9 - 12 mT), des microparticules de silice renfermant des nanoparticules d'oxyde de fer superparamagnetiques (SPIONs) et de deux de leurs formulations: un hydrogel d'alginate de sodium et un organogel de poly(ethylene-co-alcool vinylique) dans le dimethylsulfoxide. Finalement, nous presentons le potentiel therapeutique de 20 minutes d'hyperthermie locale induite apres injection de l'organogel superparamagnetique dans un modele murin sous-cutane de tumeurs necrosantes de colocarcinome humain.
Anti-High Mobility Group Box 1 Neutralizing-Antibody Ameliorates Dextran Sodium Sulfate Colitis in Mice

High mobility group box 1 (HMGB1) is a ubiquitous nuclear protein in mammals. When released into the extracellular space, it acts as a damage-associated molecular pattern. This study investigates whether increased HMGB1 levels are found in the intestinal mucosa of ulcerative colitis (UC) patients, and whether an anti-HMGB1 neutralizing-antibody (HnAb) can inhibit the intestinal inflammation elicited by dextran sulfate sodium (DSS) in mice. Because toll-like receptor 4 (TLR4) is implicated in HMGB1-mediated immune cell activation, DSS colitis was also elicited in TLR4-deficient mice in the presence and absence of HnAb. The expression of HMGB1 in UC patients was examined. HnAb was administered via intraperitoneal injection to TLR4 deficient mice and their wild-type littermates, both being induced to colitis with DSS. Finally, the protective effect of HnAb and TLR4 deficiency were evaluated. In UC patients, HMGB1 was up-regulated in the inflamed colon. When administered during DSS application, HnAb alleviated the severity of colitis with a lower disease activity index, limited histological damages, and reduced production of proinflammatory cytokines. This antibody also limited colonic barrier loss, decreased colonic lamina propria macrophages and partially reversed the DSS treatment-associated dysbiosis. The protective effect of this antibody was enhanced in TLR4-deficient mice in some aspects, indicating that both additional HMGB1-mediated as well as TLR4-mediated inflammatory signaling pathways were involved in the induction of colitis by DSS. HnAb ameliorated colitis via macrophages inhibition and colonic barrier protection. It may therefore be a novel treatment option in colitis.
Near-Infrared Spectroscopy Assessments of Regional Cerebral Oxygen Saturation for the Prediction of Clinical Outcomes in Patients With Cardiac Arrest: A Review of Clinical Impact, Evolution, and Future Directions

Despite three decades of advancements in cardiopulmonary resuscitation (CPR) methods and post-resuscitation care, neurological prognosis remains poor among survivors of out-of-hospital cardiac arrest, and there are no reliable methods for predicting neurological outcomes in patients with cardiac arrest (CA). Adopting more effective methods of neurological monitoring may aid in improving neurological outcomes and optimizing therapeutic interventions for each patient. In the present review, we summarize the development, evolution, and potential application of near-infrared spectroscopy (NIRS) in adults with CA, highlighting the clinical relevance of NIRS brain monitoring as a predictive tool in both pre-hospital and in-hospital settings. Several clinical studies have reported an association between various NIRS oximetry measurements and CA outcomes, suggesting that NIRS monitoring can be integrated into standardized CPR protocols, which may improve outcomes among patients with CA. However, no studies have established acceptable regional cerebral oxygen saturation cut-off values for differentiating patient groups based on return of spontaneous circulation status and neurological outcomes. Furthermore, the point at which resuscitation efforts can be considered futile remains to be determined. Further large-scale randomized controlled trials are required to evaluate the impact of NIRS monitoring on survival and neurological recovery following CA.
Temporal changes in the population structure of Dothistroma septosporum at the site of the first recorded outbreak in Poland

In this study, evolution of the genetic structure of the oldest known population of Dothistroma septosporum in Poland was analysed. Dothistroma needle blight was first recorded in Poland in 1990 in a 5-year-old plantation, meaning the population is relatively young in terms of evolution and genetic development. The preservation of DNA extracts from other studies allowed examination of the genetic variation of the pathogen over the span of a decade with the use of highly sensitive microsatellite markers. A number of evolutionary factors were identified that have shaped the genetic structure of this population over time. First, indications of the founder effect and the impact of selection were observed. Secondly, STRUCTURE analysis provided evidence of the introduction of a new genetic component to the population structure after the pathogen had established. Finally, the impact of the reproductive mode on various components of the Domiarki population was examined, revealing the presence of genetic groups and STRUCTURE clusters with varying levels of sexual recombination. These results demonstrate how well established and genetically robust a new population of a pathogen may become in just a few decades, given favourable conditions, and how new introductions may facilitate this process.
Propagation of orientation selectivity in a spiking network model of layered primary visual cortex

We studied the propagation of orientation selectivity over layers in a model of rodent primary visual cortex in terms of the underlying connectivity. While significant progress has been made in measuring the activity in the different sub-populations as well as the connectivity between those in experiments, a comprehensive theoretical explanation of how network structure and its dynamics are related is still missing. We suggest a model of layered mouse visual cortex by extending the model suggested by Potjans and Diesmann (2014) with thalamic input that has an orientation bias according to Sadeh et al. (2014). We then studied the response properties of the network to such non-homogeneous input. We found that, without further assumptions, the connectivity derived from experimental data leads to layer-specific distributions of orientation selectivity very similar to what has been observed in mouse experiments. Interestingly, the network settles in a dynamical operating point, in which the efficacy of the different projections and their contribution to orientation tuning deviate strongly from the expectations based on the underlying anatomical connectivity. To understand the processes that shape the observed dynamics, it is essential to perform the analysis of the microcircuit on the system level. With that perspective, we find in particular that the difference in tuning of L2/3 and L4 neurons is an immediate, albeit unexpected consequence of the specific network connectivity. Furthermore, we introduce a novel method for predicting the effects of optogenetic stimulation of specific neuronal sub-populations and demonstrate its power in network simulations. Significance Statement Understanding the precise roles of neuronal sub-populations in shaping the activity of neuronal networks is a fundamental objective of neuroscience research. To this end, our work makes three important contributions. First, we show that the experimentally extracted connectivity suffices to explain the degree of selectivity of sub-populations in mouse visual cortex to visual stimulation. Second, we introduce a novel system-level approach for the analysis of input-output relations of recurrent networks, which lead to distinct activity patterns. Third, we present a method for the design of optogenetic experiments that can be used to devise specific stimuli which result in a desired and predictable change of neuronal activity.
Ulva prolifera Extract Alleviates Intestinal Oxidative Stress via Nrf2 Signaling in Weaned Piglets Challenged With Hydrogen Peroxide

Background Ulva prolifera extract contains a variety of functional active substances. Whether these substances had any beneficial effects on the small intestine of weaned piglets under oxidative stress remained unknown. Method We explored the effects of U. prolifera extract on oxidative stress and related mechanisms in weaned piglets and intestinal porcine epithelial cells (IPEC-J2) challenged with hydrogen peroxide. Results U. prolifera extract was found to mainly consist of polyphenols and unsaturated fatty acids. U. prolifera extract increased total antioxidant capacity and superoxide dismutase (SOD) activity, while it decreased malondialdehyde content, in the serum of weaned piglets challenged with hydrogen peroxide. Moreover, U. prolifera extract increased mRNA expression of SOD and catalase, as well as the intestinal expression of nuclear NF-E2-related factor 2 (Nrf2), both in vitro and in vivo. Furthermore, U. prolifera extract decreased reactive oxygen species and improved mitochondrial respiration in IPEC-J2 cells treated with hydrogen peroxide. However, AMPK inhibition did not affect nuclear Nrf2 expression and only partially affected the effects of U. prolifera extract on oxidative stress. Conclusion We suggest that U. prolifera extract alleviates oxidative stress via Nrf2 signaling, but independent of AMPK pathway in weaned piglets challenged with hydrogen peroxide. These results shed new insight into the potential applications of U. prolifera extract as a therapeutic agent for the prevention and treatment of oxidative stress-induced intestinal diseases.
Living Unembodiment: Physicality and Body/Self Discontinuity Among African American Adolescent Girls

: Social conditions shape health and health disparities. However, inquiry and intervention in the social determinants of health all too often rests on thin engagement with customary demographic correlates and predictors rather than robust, empirically and theoretically-informed engagement with health and health disparity as biocultural phenomena – the integrated product of structure, materiality and subjectivity. Within-group variability is neglected. Lived experiences of non-normative status in multiple, mutually informing cultural systems are undertheorized. This paper reports on research addressing these gaps - a study exploring experiences of body/self discontinuity and physical activity engagement among African American adolescent girls. Data suggest that experiences of body/self discontinuity, or unembodiment, are common to membership in multiple, non-normative social categories, vary in degree and quality, and may bear on disposition toward leisure-time physical activity. Unembodiment shows promise as a means of characterizing variability in physical activity engagement within groups evincing low levels of this health behavior. I maintain that I have been a Negro three times—a Negro baby, a Negro girl and a Negro woman. Still, if you have received no clear-cut impression of what the Negro in America is like, then you are in the same place with me. There is no The Negro here. Our lives are so diversified, internal attitudes so varied, appearances and capabilities so different, that there is no possible classification so catholic that it will cover us all, except My people! My people!
Comparative Study of the Effect of Biological Factors on Helminthes Occurrence in Oreochromis niloticus and Tilapia zilli from Lake Manzala, Port Said, Egypt.

Egyptian Academic Journal of Biological Sciences is the official English language journal of the Egyptian Society of Biological Sciences, Department of Entomology, Faculty of Sciences Ain Shams University. The Journal publishes original research papers and reviews from any zoological discipline or from directly allied fields in ecology, behavioral biology, physiology, biochemistry, www.eajbs. eg.net Provided for non-commercial research and education use.
Triiodothyronine and thyroxine changes in yearling sea trout (Salmo trutta L.) during spring

Abstract Triiodothyronine and thyroxine levels and morphological parameters of fish were studied from January to May to evaluate the smoltification of yearling sea trout (Salmo trutta L.) raised in two different rearing systems (recirculating and flow-through) in three different hatcheries in Latvia. Thyroid hormone levels increased from January to May in both rearing systems in fish of different sizes. There was positive correlation between the degree of silvering and fish fork length and thyroid hormone levels, but there was no correlation between condition facor and thyroid hormone levels. Fish reared in recirculating systems were significantly larger (p < 0.05) and exhibited more visible signs of smoltification earlier than those reared in flow-through systems. The thyroid hormone levels and degree of silvering gradually became nearly the same by May in the sea trout from both rearing systems. Changes in thyroid hormone levels or fish size in spring cannot be evaluated separately from other signs to determine smoltification.
Inspecting Morphological Features of Mosquito Wings for Identification with Image Recognition Tools

Mosquitoes are important disease vectors. Different mosquito genera are associated with different diseases at varying levels of specificity. Hence, quick and low-cost methods of identification, even if relatively coarse and to genus level, will be of use in assessing risk and informing mitigation measures. Here we assess the extent to which digital photographs of mosquito wings taken with common cell phone cameras and clip-on lenses can be used to discriminate among mosquito genera when fed into image feature extraction algorithms. Our results show that genera may be distinguished on the basis of features extracted using the SURF algorithm. However, we also found that the naïve features examined here require very standardized photography and that different phone cameras have different signatures that may need to be taken into account.
Homogenization of capillary flow and oxygenation in deeper cortical layers correlates with increased oxygen extraction

Our understanding of how capillary blood flow and oxygen distribute across cortical layers to meet the local metabolic demand is incomplete. We addressed this question by using two-photon imaging of microvascular oxygen partial pressure (PO2) and flow in the whisker barrel cortex in awake mice at rest. Our measurements in layers I-V show that the capillary red-blood-cell flux and oxygenation heterogeneity, and the intracapillary resistance to oxygen delivery, all decrease with depth, reaching a minimum around layer IV, while the depth-dependent oxygen extraction fraction is increased in layer IV, where oxygen demand is presumably the highest. Our findings suggest that homogenization of physiological observables relevant to oxygen transport to tissue is an important part of the microvascular network adaptation to a local brain metabolism increase. These results will inform the biophysical models of layer-specific cerebral oxygen delivery and consumption and improve our understanding of diseases that affect the cerebral microcirculation. IMPACT STATEMENT Homogenization of cortical capillary blood flow and oxygenation underpins an important mechanism, by which the microvascular network adapts to an increase in the local brain oxidative metabolism.