Miracle-dz/UniFAR-FTUs huggingface dataset:
Influence of the composition and structure of modified landscapes on the abundance of two marsupials during the dry season in Chiapas, Mexico

Changes in the landscape due to habitat loss and fragmentation interact with ecological processes of natural populations and define their local abundance. We evaluated the relationship between the abundance of two common marsupials, Didelphis marsupialis (common opossum) and Didelphis virginiana (Virginia opossum), and landscape features under different disturbance levels in two areas of the State of Chiapas: The Highlands and the Central Lowlands. The objective was to identify the effects of changes in landscape on the populations of the marsupials studied. Based on the biological characteristics of D. marsupialis and D. virginiana , we expected a higher abundance of opossums in areas with moderate disturbance. At the same time, we aimed to establish the relationship between landscape composition and the abundance of these two species. We placed 48 Tomahawk traps in sites with three levels of landscape disturbance. Within each disturbance level, landscape structure and composition were determined. The abundance of each species was estimated in terms of the number of specimens captured. A relative abundance index was estimated from the number of specimens captured per trap-night . The influence of disturbance levels, landscape structure, and landscape composition on the abundance of each species was examined by means of multiple regression and generalized lineal models. The mean abundance of Didelphis spp. was higher in the Central Lowlands (5.56 specimens, SD = 4.82). Didelphis marsupialis was captured only in low-disturbance sites, with a mean of 0.56 specimens (SD = 1.04; Figure 2a), while D. virginiana was captured in the three disturbance levels with a mean of 3.56 specimens (SD = 3.88; Figure 2b). The presence of D. marsupialis was influenced by the number of patches (NP; p = 0.003), while the presence of D. virginiana was not associated with the landscape index (Table 2). Our findings suggest that the abundance of D. marsupialis and D. virginiana was not influenced by the disturbance level. However, the abundance of D. marsupialis was related to the number of patches and conserved areas; D. virginiana was unaffected by the landscape attributes evaluated, i. e. composition and configuration, indicating that the Virginia opossum can establish relatively abundant populations in highly disturbed landscapes. This study contributes to the understanding of the effects of landscape changes due to human activities on common species in Mexico.
Seasonality Study of Penaeus vannamei Shrimp Shells from Aquaculture

Chitin and chitosan have nowadays numerous industrial applications in various areas of engineering, but its industrial production and consolidation as a raw material is conditioned by fluctuations in both shrimp seasonality not allowing proper process optimization. One way to bridge this gap would be through the use of shrimp from aquaculture. Thus the present study aims to determine whether the shell from shrimp aquaculture has its characteristics changed over a calendar year. Shells from the processing of Penaeus Vannamei shrimp grown in farm was collected for over an year and characterized for its composition, having determined that the shell has an average of 10% residual moisture, 35% minerals, 35% proteins and 20% of chitin. Additionally, the chitin extracted was characterized for its extrinisic viscosity and degree of acetylation, which were averaged 200cps and 93% respectively. From the results, it was found that there isn’t a significant variation in the composition of the shrimp shells nor the chitin characteristics and is therefore deemed that this source of chitin is suitable to drive chitin and chitosan production industry.
Pre-impoundment stock assessment of two Pimelodidae species caught by small-scale fisheries in the Madeira River (Amazon Basin - Brazil)

The middle stretch of the Madeira River has supported an intensive commercial fishery for several decades. Developed in an area of rapids and waterfalls, this fishery focuses primarily on catfish stocks, mainly pimelodids. Data from fish landings collected in the years immediately prior to the start in operations of two large hydroelectric dams were used to estimate growth and mortality rates for Pirinampus pirinampu (Spix & Agassiz) and Brachyplatystoma platynemum Boulenger. In addition, stock assessment was carried out for both species, and the results used to evaluate the status of the fishery. Mean population parameters were L∞ = 80.85 cm (total length), k = 0.52 year � 1 , / = 3.53, A0.95 = 6 year, M = 0.87, F = 1.41-1.64 and Z = 2.28-2.51 for P. pirinampu ;a nd L∞ = 95.55 cm (total length), k = 0.28 year � 1 , / = 3.40, winter point = 0.41, A0.95 = 11 year, M = 0.55, F = 0.16- 0.35 and Z = 0.71-0.90 for B. platynemum. Yield-per-recruit analysis indicated P. pirinampu was overfished and that the stock of B. platynemum was under-exploited. Moreover, overfishing of the P. pirinampu stock and the effects of fragmentation caused by the construction of the dam should be monitored.
INVESTIGATION AND MASS TRANSPORT MODELING FOR ERH-CHUNG FLOOD WAY WETLAND IN NORTHERN TAIWAN

The Erh-Chung Flood Way wetland is located at the confluence of Tanshui River in northern Taiwan. The present investigation shows that low DO and high heavy metals concentrations in the water column are the two primary water quality problems in the wetland. A one-dimensional mass transport model has been developed to simulate the fate and transport of salinity, suspended solids, and heavy metals (including zinc, copper, and cadmium) in the wetland ecosystem, using the U.S. Environmental Protection Agency’s WASP/EUTRO code. Data collected in the field from Nov. 8, 2002 to April 13, 2003 were utilized to configure and calibrate the models for this wetland ecosystem. Spatial and temporal distributions of salinity were well reproduced by the models. The model also reproduces temporal distributions of the suspended solids and heavy metals concentrations in the water column. A comparison between calculated results and field data shows reasonable agreement. The results of this study can be used for industrial wastewater treatment through the wetland and for river mouth ecosystem.
Deep social neuroscience: the promise and peril of using artificial neural networks to study the social brain

Abstract This review offers an accessible primer to social neuroscientists interested in neural networks. It begins by providing an overview of key concepts in deep learning. It then discusses three ways neural networks can be useful to social neuroscientists: (i) building statistical models to predict behavior from brain activity; (ii) quantifying naturalistic stimuli and social interactions; and (iii) generating cognitive models of social brain function. These applications have the potential to enhance the clinical value of neuroimaging and improve the generalizability of social neuroscience research. We also discuss the significant practical challenges, theoretical limitations and ethical issues faced by deep learning. If the field can successfully navigate these hazards, we believe that artificial neural networks may prove indispensable for the next stage of the field’s development: deep social neuroscience.
Alpha Oscillations and Temporal Binding Windows in Perception—A Critical Review and Best Practice Guidelines

Abstract An intriguing question in cognitive neuroscience is whether alpha oscillations shape how the brain transforms the continuous sensory inputs into distinct percepts. According to the alpha temporal resolution hypothesis, sensory signals arriving within a single alpha cycle are integrated, whereas those in separate cycles are segregated. Consequently, shorter alpha cycles should be associated with smaller temporal binding windows and higher temporal resolution. However, the evidence supporting this hypothesis is contentious, and the neural mechanisms remain unclear. In this review, we first elucidate the alpha temporal resolution hypothesis and the neural circuitries that generate alpha oscillations. We then critically evaluate study designs, experimental paradigms, psychophysics, and neurophysiological analyses that have been employed to investigate the role of alpha frequency in temporal binding. Through the lens of this methodological framework, we then review evidence from between-subject, within-subject, and causal perturbation studies. Our review highlights the inherent interpretational ambiguities posed by previous study designs and experimental paradigms and the extensive variability in analysis choices across studies. We also suggest best practice recommendations that may help to guide future research. To establish a mechanistic role of alpha frequency in temporal parsing, future research is needed that demonstrates its causal effects on the temporal binding window with consistent, experimenter-independent methods.
Ööpäevase invasiivkardioloogilise valveteenistuse osa ägeda koronaarsündroomiga haigete ravi ajakohastamisel

Tartu Ulikooli Kliinikumis on loodud teenistus ageda muokardiinfarktiga ja ebastabiilse stenokardiaga haigete oopaevaringse invasiivkardioloogilise abi osutamiseks. Loodud uksus tagab osale Eesti patsientidest praegu maailmas kasutusel oleva parimate tulemustega infarktiravimeetodi rakendamise ning ravijuhendipohise arstiabi oopaevaringse kattesaadavuse. Eesti Arst 2005; 84 (11): 775–780
A neuroanatomical and cognitive model of impaired social behaviour in frontotemporal dementia.

Impaired social cognition is a core deficit in frontotemporal dementia (FTD). It is most commonly associated with the behavioural-variant of FTD, with atrophy of the orbitofrontal and ventromedial prefrontal cortex. Social cognitive changes are also common in semantic dementia, with atrophy centred on the anterior temporal lobes. The impairment of social behaviour in FTD has typically been attributed to damage to the orbitofrontal cortex and/or temporal poles and/or the uncinate fasciculus that connects them. However, the relative contributions of each region are unresolved. In this Review, we present a unified neurocognitive model of controlled social behaviour that not only explains the observed impairment of social behaviours in FTD, but also assimilates both consistent and potentially contradictory findings from other patient groups, comparative neurology and normative cognitive neuroscience. We propose that impaired social behaviour results from damage to two cognitively- and anatomically-distinct components. The first component is social-semantic knowledge, a part of the general semantic-conceptual system supported by the anterior temporal lobes bilaterally. The second component is social control, supported by the orbitofrontal cortex, medial frontal cortex and ventrolateral frontal cortex, which interacts with social-semantic knowledge to guide and shape social behaviour.
Progressive accumulation of hyperinflammatory NKG2Dlow NK cells in early childhood severe atopic dermatitis

Atopic dermatitis (AD) is a chronic inflammatory skin disease that often precedes the development of food allergy, asthma, and allergic rhinitis. The prevailing paradigm holds that a reduced frequency and function of natural killer (NK) cell contributes to AD pathogenesis, yet the underlying mechanisms and contributions of NK cells to allergic comorbidities remain ill-defined. Here, analysis of circulating NK cells in a longitudinal early life cohort of children with AD revealed a progressive accumulation of NK cells with low expression of the activating receptor NKG2D, which was linked to more severe AD and sensitivity to allergens. This was most notable in children co-sensitized to food and aeroallergens, a risk factor for development of asthma. Individual-level longitudinal analysis in a subset of children revealed coincident reduction of NKG2D on NK cells with acquired or persistent sensitization, and this was associated with impaired skin barrier function assessed by transepidermal water loss. Low expression of NKG2D on NK cells was paradoxically associated with depressed cytolytic function but exaggerated release of the proinflammatory cytokine tumor necrosis factor–α. These observations provide important insights into a potential mechanism underlying the development of allergic comorbidity in early life in children with AD, which involves altered NK cell functional responses, and define an endotype of severe AD. Accumulation of hyperinflammatory NKG2Dlow NK cells in children with atopic dermatitis correlates with disease severity and allergen sensitivity. Editor’s summary Atopic dermatitis (AD) manifests as skin inflammation and is often observed in children that later develop allergies and asthma. To better understand underlying immune mechanisms that contribute to AD, Ochayon et al. characterized the role for natural killer (NK) cells in children. They analyzed NK cells longitudinally in an early life cohort of children with AD and observed that children with more severe AD and allergen sensitivity had a notable accumulation of NK cells with low expression of the activating receptor NKG2D. Further analysis of a subset of children revealed that accumulation of NK cells with decreased NKG2D expression corresponded with allergen sensitization and diminished skin barrier function, and these NK cells showed decreased cytolytic activity but increased TNF-α production. Together, these observations provide critical insights into immune defects driving AD in young children. —Christiana Fogg
Recent statistics shift object representations in parahippocampal cortex

Our representations of the world need to be stable enough to support general knowledge but flexible enough to incorporate new information as our environment changes. How does the human brain manage this stability-plasticity trade-off? We analyzed a large dataset in which participants viewed objects embedded in thousands of natural scenes across many fMRI sessions. Semantic item representations were located by jointly leveraging a voxelwise encoding model to find reliable item representations and a word-embedding model to evaluate semantic content. Within the medial temporal lobe, semantic item representations in hippocampal subfield CA1, parahippocampal cortex, and perirhinal cortex gradually drifted across a period of multiple months. However, rapid plasticity was observed only in parahippocampal cortex, such that item co-occurrence statistics warped item representations within a single session. In conjunction with whole-brain analyses, these results suggest that the brain solves the stability-plasticity trade-off by promoting plasticity in only a subset of semantic regions.
One-step N-terminomics based on isolation of protein N-terminal peptides from LysargiNase digests by tip-based strong cation exchange chromatography

We have developed a one-step isolation method for protein N-terminal peptides from LysargiNase digests by pipette tip-based strong cation exchange (SCX) chromatography. This CHAMP-N (CHromatographic AMplification of Protein N-terminal peptides) method using disposable and parallel-processable SCX tips instead of conventional HPLC SCX columns facilitates simple, sensitive and high-throughput N-terminomic profiling without sacrificing the high identification numbers and selectivity achieved by the HPLC-based method. By applying the CHAMP-N method to HEK293T cells, we identified novel cleavage sites for signal and transit peptides, and non-canonical translation initiation sites. Finally, for proteome-wide terminomics, we present a simple and comprehensive N-and C-terminomics platform employing three different tip-based approaches, including CHAMP-N, in which protease digestion and one-step isolation by tip LC are commonly used to achieve complementary terminome coverages.
Sensory Input Matching Visual Working Memory Guides Internal Prioritization

Adaptive behavior necessitates the prioritization of the most relevant information in the environment (external) and in memory (internal). Internal prioritization is known to guide the selection of external sensory input, but the reverse may also be possible: Does the environment also guide the prioritization of memorized material? Here we addressed whether reappearing sensory input matching visual working memory (VWM) facilitates the prioritization of other non-reappearing memorized items. Participants (total n = 72) memorized three orientations. Crucially some, but not all, items maintained in VWM were made available again in the environment. These reappearing items were task-irrelevant, as they never had to be reproduced later. Experiment 1 showed that the reappearance of all but one memory item benefited accuracy and speed to the same extent as a spatial retro cue. This shows that memory-matching, yet task-irrelevant sensory input facilitates VWM prioritization. What aspects of the reappearing sensory input drive this effect? Experiment 2 demonstrated that prioritization was facilitated most if reappearing items matched VWM content in terms of both location and orientation. Sensory input fully matching VWM is likely processed more efficiently, possibly leading to stronger prioritization of other memory content. We showed the robustness of our findings in Experiment 3. We propose that the link between sensory processing and VWM is bidirectional: internal representations guide the processing of sensory input, which in turn facilitates the prioritization of other VWM content to subserve adaptive behavior.
Mechanical loading modulates AMPK and mTOR signaling in myblasts

Skeletal muscle adaptation to exercise involves various phenotypic changes that enhance metabolic and contractile functions. One key regulator of these adaptive responses is the activation of AMPK, influenced by exercise intensity. However, the mechanistic understanding of AMPK activation during exercise remains incomplete. In this study, we utilized an in vitro model to investigate the effects of mechanical loading on AMPK activation and its interplay with the mTOR signaling pathway. Proteomic analysis of myoblasts subjected to static loading (SL) revealed distinct quantitative protein alterations associated with RNA metabolism, with 10% SL inducing the most pronounced response compared to lower intensity of 5% and 2% as well as control. Additionally, 10% SL suppressed RNA and protein synthesis, while activating AMPK and inhibiting the mTOR pathway. Our RNA sequencing analysis further corroborated these findings, revealing numerous differentially regulated genes and signaling pathways influenced by both AMPK and mTOR. Further examination showed that SL induced changes in mitochondrial biogenesis and the ADP/ATP ratio. These findings provide novel insights into the cellular responses to mechanical loading and shed light on the intricate AMPK-mTOR regulatory network in myoblasts.
Regulatory divergences in dosage compensation cause hybrid male inviability in Caenorhabditis

The genetic basis of Haldane’s rule, such as hybrid male incompatibility in XX systems, has long remained elusive. Here, we found that crosses of Caenorhabditis nigoni males with C. briggsae females result in insufficient expression of Cbr-xol-1, an X-linked master switch responsible for sex determination, consequently activating aberrant dosage compensation in males, and ultimately leading to embryonic inviability. Three compensatory divergences result in comparable xol-1 expression levels between the parental species but lethal Cbr-xol-1 underexpression in hybrid male embryos: 1) a less active Cbr-xol-1 promoter than its C. nigoni ortholog; 2) loss of an X-linked xol-1 paralog in C. briggsae; and 3) pseudogenization of a C. briggsae autosomal repressor of xol-1. Our results define an evolutionary scenario of sexual incompatibility leading to hybrid male inviability.
Homologous recombination deficiency and tumor suppressor heterozygosity mediate resistance to front-line therapy in breast cancer

Germline and somatic variants that drive breast tumorigenesis and therapeutic sensitivity are widely prevalent. The clinical and biologic significance of co-occurring disease-defining germline and somatic events have yet to be defined and exploited. Using multiple, independent clinical cohorts comprising over 4500 patients, we identify that pathogenic RB1 variants are enriched in gBRCA2-associated cancers, and manifest poor outcomes on standard-of-care front-line CDK4/6i plus antiestrogen combinations. We demonstrate gBRCA2-associated cancers commonly give rise to allelic configurations manifesting RB1 heterozygosity and readily lose the second copy through gBRCA2 loss-mediated homologous recombination deficiency (HRD) under the therapeutic pressure of CDK4/6i. The findings unveil a novel therapeutic strategy of targeting the underlying HRD through PARPi prior to CDK4/6i to intercept the deleterious RB1-loss trajectory. The work reveals how germline-somatic driven genomic configurations can shape treatment responses and be exploited in biomarker-directed clinical strategies.
Forecasting Pacific Salmon Production in a Changing Climate: A Review of the 2011–2015 NPAFC Science Plan

In recent decades, the marine production of Asian and North American Pacifi c salmon and steelhead populations has undergone signifi cant variability linked to climate change. Improved forecasts of the abundance and distribution of salmon are needed that will benefi t stock management in all salmon producing countries around the North Pacifi c Rim. The North Pacifi c Anadromous Fish Commission (NPAFC) Science Plan is a long-term comprehensive strategy for international cooperative research. The primary goal of the 2011–2015 Science Plan was to explain and forecast annual variations in Pacifi c salmon production. The plan was developed with an overarching research theme “Forecast of Pacifi c Salmon Production in the Ocean Ecosystems under Changing Climate” and fi ve research topics. This paper describes progress made on each research topic and the overarching theme, much of which was assessed at an international symposium in Kobe, Japan, on May 17–19, 2015. In summary, the reliability of stock identifi cation methods including genetic and otolith mark analyses has improved, enabling better monitoring of stock-specifi c ocean distribution and abundance. Salmon marine survival depends on early marine coastal environments but also on conditions later in life, including winter. Models incorporating fi sh mortality and various environmental factors improve our ability to forecast returns of specifi c salmon stocks. However, limitations on our ability to accurately explain and forecast annual variations in Pacifi c salmon production remain, in part because of uncertainty in the factors responsible for salmon mortality and from the eff ects of climate warming on the marine distribution and abundance of salmon. It is more important than ever to promote cooperative and innovative international research to identify and better understand the ecological mechanisms regulating the distribution and abundance of salmon populations for sustainable salmon and steelhead management.