Miracle-dz/UniFAR-FTUs huggingface dataset:
Identifying the molecular basis for functional divergence of duplicated SOX factors controlling endoderm formation and left-right patterning in zebrafish

Endoderm, one of three primary germ layers of vertebrate embryos, makes major contributions to the respiratory and gastrointestinal tracts and associated organs, including liver and pancreas. Placement and patterning of these organs relies on the left-right organiser – known as Kupffer’s Vesicle (KV) in zebrafish. The transcription factors Sox32 and Sox17 are members of the zebrafish SoxF subfamily. Sox32 and sox17 arose from a duplication of ancestral Sox17 in the teleost lineage. Sox32 induces sox17 expression in the early embryo and is required for the specification of endoderm and KV progenitors. Zebrafish Sox17 is implicated in KV morphogenesis. In mammals, Sox17 is vital for endoderm organ formation and can induce endoderm progenitor identity. Phenotypic evidence therefore suggests functional similarities between zebrafish Sox32 and Sox17 with mammalian SOX17. We sought to explore the functional differences and potential similarities between these proteins in the early zebrafish embryo. Our results indicate that, unlike Sox32, human SOX17 cannot induce endoderm specification in zebrafish. Furthermore, using hybrid protein functional analyses, we show that Sox32 specificity for the endoderm gene regulatory network is linked to evolutionary divergence in its HMG domain from its paralogue Sox17. Additionally, changes in the C-terminal regions of Sox32 and Sox17 underpin their differing target specificity and divergence in mediating differential gene regulatory programmes. Finally, we establish that specific conserved peptides in the C-terminal domain are essential for the role of Sox17 in establishing correct organ asymmetry. Overall, our results provide novel insights into vertebrate endoderm development, left-right patterning, and the evolution of SoxF transcription factor function.
Changes in responses of auditory cortex neurons upon falling asleep and awakening

The neural processes accompanying the process of falling asleep are only partially understood. At the cortical level, previous studies have shed light on aspects of both spontaneous neural activity and sensory responses that change between wakefulness and sleep across species. For example, sleep- related changes in early auditory cortex include reduction in spontaneous firing rates, increases in the occurrence of post-onset silent (OFF) periods, and elevated population synchrony. However, it remains unknown whether changes occur abruptly around behavioral state transitions of sleep onset and awakening. Here, we recorded spontaneous and sound-evoked neuronal spiking activity in early auditory cortex along with polysomnography during thousands of episodes when rats fell asleep or woke up. We found that when falling asleep, stimulus-induced neuronal silent periods (OFF periods), characteristic of non-rapid eye movement (NREM) sleep, increased within few seconds around sleep onset. Moderate reductions in spontaneous firing rate also occurred within seconds. By contrast, an increase in neuronal population synchrony built up gradually over dozens of seconds until reaching maximal levels. Similar effects, but with opposite direction, were observed around awakenings when stimulus-induced silent periods were suppressed within few seconds. The results highlight stimulus- induced neuronal silence as a key indicator of transitions between vigilance states. More generally, these findings emphasize the added value of going beyond monitoring ongoing activity and perturbing the nervous system to reveal its state - an insight that could also help guide development of more sensitive non-invasive monitors of falling asleep in humans.
Hypermigration of macrophages through the concerted action of GRA effectors on NF-κB/p38 signaling and host chromatin accessibility potentiates Toxoplasma dissemination

Mononuclear phagocytes facilitate the dissemination of the obligate intracellular parasite Toxoplasma gondii. Here, we report how a set of secreted parasite effector proteins from dense granule organelles (GRA) orchestrates dendritic cell-like chemotactic and pro-inflammatory activation of parasitized macrophages. These effects enabled efficient dissemination of the type II T. gondii lineage, a highly prevalent genotype in humans. We identify novel functions for effectors GRA15 and GRA24 in promoting CCR7-mediated macrophage chemotaxis by acting on NF-κB and p38 MAPK signaling pathways, respectively, with contributions of GRA16/18 and counter-regulation by effector TEEGR. Further, GRA28 boosted chromatin accessibility and GRA15/24/NF-κB-dependent transcription at the Ccr7 gene locus in primary macrophages. In vivo, adoptively transferred macrophages infected with wild-type T. gondii outcompeted macrophages infected with a GRA15/24 double mutant in migrating to secondary organs in mice. The data show that T. gondii, rather than being passively shuttled, actively promotes its dissemination by inducing a finely regulated pro-migratory state in parasitized human and murine phagocytes via co-operating polymorphic GRA effectors. Importance Intracellular pathogens can hijack cellular functions of infected host cells to their advantage, for example, for intracellular survival and for dissemination. However, how microbes orchestrate the hijacking of complex cellular processes, such as host cell migration, remains poorly understood. As such, the common parasite Toxoplasma gondii actively invades immune cells of humans and other vertebrates and modifies their migratory properties. Here, we show that the concerted action of a number of secreted effector proteins from the parasite, principally GRA15 and GRA24, act on host cell signaling pathways to activate chemotaxis. Further, the protein effector GRA28 selectively acted on chromatin accessibility in the host cell nucleus to selectively boost host gene expression. The joint activities of effectors culminated in pro-migratory signaling within the infected phagocyte. We provide a molecular framework delineating how T. gondii can orchestrate a complex biological phenotype, such as the migratory activation of phagocytes to boost dissemination.
A deterministic, c-di-GMP-dependent genetic program ensures the generation of phenotypically similar, symmetric daughter cells during cytokinesis

Phenotypic heterogeneity in bacteria results from stochastic processes or deterministic genetic programs. These deterministic programs often incorporate the versatile second messenger c-di-GMP, and by deploying c-di-GMP metabolizing enzyme(s) asymmetrically during cell division give rise to daughter cells with different c-di-GMP levels. By contrast, less is known about how phenotypic heterogeneity is kept to a minimum. Here, we identify a deterministic c-di-GMP-dependent genetic program that is hardwired into the cell cycle of Myxococcus xanthus to minimize phenotypic heterogeneity and guarantee the formation of phenotypically similar daughter cells during division. Cells lacking the diguanylate cyclase DmxA have an aberrant motility behaviour. DmxA is recruited to the cell division site and its activity switched on during cytokinesis, resulting in a dramatic but transient increase in the c-di-GMP concentration. During cytokinesis, this c-di-GMP burst ensures the symmetric incorporation and allocation of structural motility proteins and motility regulators at the new cell poles of the two daughters, thereby generating mirror-symmetric, phenotypically similar daughters with correct motility behaviours. These findings suggest a general c-di-GMP-dependent mechanism for minimizing phenotypic heterogeneity, and demonstrate that bacteria by deploying c-di-GMP metabolizing enzymes to distinct subcellular locations ensure the formation of dissimilar or similar daughter cells.
Decoding the Impact of Neighboring Amino Acid on ESI-MS Intensity Output through Deep Learning

Peptide-level quantification using mass spectrometry (MS) is no trivial task as the physicochemical properties affect both response and detectability. The specific amino acid (AA) sequence affects these properties, however the link from sequence to intensity output remains poorly understood. In this work, we explore combinations of amino acid pairs (i.e., dimer motifs) to determine a potential relationship between the local amino acid environment and MS1 intensity. For this purpose, a deep learning (DL) model, consisting of an encoder-decoder with an attention mechanism, was built. The attention mechanism allowed to identify the most relevant motifs. Specific patterns were consistently observed where a bulky/aromatic and hydrophobic AA followed by a cationic AA as well as consecutive bulky/aromatic and hydrophobic AAs were found important for the MS1 intensity. Correlating attention weights to mean MS1 intensities revealed that some important motifs, particularly containing Trp, His, and Cys, were linked with low responding peptides whereas motifs containing Lys and most bulky hydrophobic AAs were often associated with high responding peptides. Moreover, Asn–Gly was associated with low MS1 response. The model could predict MS1 response with a mean average percentage error of ∼11% and a Pearson correlation coefficient of ∼0.68.
Ca2+-driven cytoplasmic backflow secures spindle position in fertilized mouse eggs

Fertilization triggers hours-long Ca2+ oscillations in mammalian eggs, but the effects of repeated Ca2+ surges remain unclear. Here, we investigate spindle dynamics and its relationship with cytoplasmic streaming in fertilized mouse eggs. The spindle, initially parallel to the plasma membrane, rotates vertically, in accordance with previously reported results using artificially activated eggs. Intriguingly, it transiently reverses its rotation direction in synchrony with Ca2+ oscillations, regardless of artificially altered frequency. This effect results from cytoplasmic streaming, initially moving from spindle to egg center, displaying a Ca2+-dependent backflow. Streaming also impacts spindle positioning, balancing spindle rotation and cortical localization maintenance. We provide evidence that Ca2+-dependent cortical myosin II activation causes actomyosin contraction, leading to transient streaming towards non-contracting actin cap regions overlaying chromosomes. Our findings underscore the role of Ca2+ oscillations in maintaining spindle position in fertilized eggs, thereby ensuring highly asymmetric division and preservation of maternal stores in zygotes.
Negative Associations between Minority Stressors and Self-Reported Health Status among Sexual Minority Adults Living in Colombia

Colombia has extensive laws prohibiting discrimination against sexual minority people. However, violence and discrimination toward sexual minorities are still frequent. While a growing body of research shows that sexual minority people experience elevated rates of discrimination and domestic abuse globally, little research has been conducted on these issues affecting sexual minorities in Colombia specifically. Using minority stress theory as a conceptual framework, this paper aims to fill this gap by examining the prevalence of experiencing intimate partner violence (IPV) and witnessed discrimination and the relationship of these stressors to self-reported health among a national sample of sexual minority Colombians. We found that bisexual individuals experienced higher rates of physical and sexual IPV, compared to lesbian and gay individuals. Additionally, sexual minority Colombians who experienced IPV and witnessed discrimination were more likely to report having poorer health, compared to those who had not. We discuss the implications of our findings for future research and clinicians working with sexual minority clients.
What we can ask to hourly temperature recording. Part I: Statistical vs. meteorological meaning of minimum temperature.

When the lowest temperature in 24-hourly time-spans is attributed to the nocturnal minimum, a systematic underestimation of the latter takes place, due to the missing contribution of warm nights that precede colder ones. This study, illustrated over one station, assesses the incidence of such bias in more than 20% of the cases, with a difference of 0.3 °C between the “standard” way of measuring minima, and the one which restricts the search of minima to the early hours of the day. The application of filters on the time band of search of minima is often mandatory for some temperature data processing, including the matching with meteorological and climate models.
Atlantic Connections and Adaptations: Economies, environments and subsistence in lands bordering the North Atlantic

This volume contains a selection of papers from the joint Association for Environmental Archaeology (AEA) and North Atlantic Biocultural Organisation (NABO) meeting held at Glasgow University between 29 and 31 March 2001, as well as extra contributions to the research fields covered in the volume. The papers are arranged in sections related to their geographical area: Atlantic Mainland Scotland, The Scottish Western Isles, The Scottish Northern Isles, and Iceland, as well as a section on contacts across the region entitled North Atlantic Networks. The final section, Looking Fore and Aft, relates to the previous and current research objectives of major international research projects.
A Smooth Muscle Cell-Based Ferroptosis Model to Evaluate Iron-Chelating Molecules for Cardiovascular Disease Treatment

Dysregulation of iron homeostasis causes iron-mediated cell death, recently described as ferroptosis. Ferroptosis is reported in many chronic diseases, such as hepatic cancer, renal, and cardiovascular diseases (heart failure, atherosclerosis). However, there is a notable scarcity of research studies in the existing literature that explore treatments capable of preventing ferroptosis. Additionally, as far as the author is aware, there is currently no established model for studying ferroptosis within cardiovascular cells, which would be essential for assessing metal-chelating molecules with the potential ability to inhibit ferroptosis and their application in the treatment of cardiovascular diseases. In this study, a smooth muscle cell-based ferroptosis model is developed upon the inhibition of the system Xc− transporter by erastin associated or not with Fe(III) overload, and its rescue upon the introduction of well-known iron chelators, deferoxamine and deferiprone. We showed that erastin alone decreased the intracellular concentration of glutathione (GSH) without affecting peroxidized lipid concentrations. Erastin with ferric citrate was able to decrease intracellular GSH and induce lipid peroxidation after overnight incubation. Only deferiprone was able to rescue the cells from ferroptosis by decreasing lipid peroxidation via iron ion chelation in a 3:1 molar ratio.
Carbon Cycle Modeling for Terrestrial Ecosystems

The terrestrial biosphere plays a vital role in global carbon (C) cycling (Prentice et al. 2000; IPCC 2000, 2007). Due to the complexity and heterogeneity of terrestrial ecosystems, however, accurately quantifying terrestrial C cycling and predicting the impacts of global environmental change is immensely challenging. Much effort has been devoted to understanding and quantifying global C cycling through a variety of methods. These include field observation, model simulation, and remote sensing (RS) (Ito and Oikawa 2002). The modeling approach is essential for investigations related to C cycling. It can be applied to all aspects of varying types of research whether local or global or research that integrates empirical information, bridges different spatial scales, or makes predictions. A wide variety of models have been developed, ranging from purely statistical ones to models that simulate basic ecophysiological and demographic processes (Peng 2000). A growing body of research has demonstrated the complementary nature of combining RS and ecosystem modeling for terrestrial C cycling studies (David et al. 2004). Ecosystem process models are important tools used in employing information provided by RS products to quantify C flux and other such key elements. Physiologically based process models applied in a spatially distributed manner can assimilate and effectively integrate a diverse assemblage of environmental data, such as information related to soil, climate, CONTENTS
Automatic extraction of coastline by remote sensing technology based on SVM and auto-selection of training samples

The timely and accurate automatic extraction of coastline from satellite remote sensing imagery is one of the important applications of remote sensing technology and has great significance for management planning of the sea area.Because the spectral characteristics of coastal water are susceptible to regional environment,the traditional method of normalized difference water index(NDWI)threshold segmentation may easily misclassify water as land in the process of separation of land and water,which will seriously affect the accuracy of shoreline extraction.In this paper,on the basis of NDWI model,the authors proposed an automatic coastline extraction method based on classification sample auto-selection and support vector machine(SVM). Firstly,through the NDWI calculation and global threshold segmentation,the initial water distribution information is obtained.And then,the classification samples are selected automatically under the control of NDWI information.Thirdly,the water are separated from the land by using SVM classifier.The last step is to fill small terrestrial water body units and track coastline automatically.The experimental results show that this method can effectively enhance the capability of coastal water identification and improve the accuracy and automation of the coastline extraction from remote sensing imager.
Acquisition Geometry-aware Focal Deblending

The applicability of a deblending method is directly related to acquisition parameters, such as source and detector locations. We formulate focal deblending in two alternative ways. In the first case, the double focal transform is used, which relies on a well-sampled source and detector dimension. In the second case, the single-sided focal transform is used, which does not depend on a well-sampled source dimension. Comparing the deblending results, we find that although the double focal transform is superior, blending noise can be significantly attenuated using the single-sided focal transform, which allows application to more practical acquisition geometries. By combining with shot repetition, the deblending result can be further improved.
Impulsivity and ankylosing spondylitis: Is there a relationship?

Objectives This study aims to evaluate psychological disorders such as impulsivity, alexithymia, depression, and anxiety and to analyze the relationship between psychiatric disorders and disease activity, fatigue and quality of life in ankylosing spondylitis (AS) patients. Patients and methods Between May 2016 and January 2017, a total of 70 AS patients (30 females, 40 males; mean age 42.9±10.5 years; range, 22 to 70 years) and 56 healthy controls (27 females; 29 males; mean age 44.8±13.0 years; range, 21 to 70 years) were included. Demographic characteristic, laboratory analyses, disease activity, quality of life, functionality, fatigue, and psychological disorders were assessed. The Ankylosing Spondylitis Disease Activity Score (ASDAS), Bath Ankylosing Spondylitis Functional Index (BASFI), Bath Ankylosing Spondylitis Metrology Index (BASMI), Nottingham Health Profile (NHP) and Ankylosing Spondylitis Quality of Life (ASQOL), Fatigue Severity Scale (FSS), Beck Depression Inventory (BDI), Beck Anxiety Inventory (BAI), Toronto Alexithymia Scale (TAS-20), Eating Attitude Test (EAT), and Barratt Impulsiveness Scale-11 (BIS-11) were used. Significant predictors for anxiety, depression and impulsiveness were evaluated using multivariate analyses. Results The BDI (13.88±8.99; 9.78±8.34), BAI (14.58±10.02; 10.53±8.99), and non-planning impulsivity (26.00±4.57; 24.28±3.77) scores were higher in the AS group than controls (p=0.01; p=0.01; p=0.02 respectively). Non-planning impulsivity was correlated with fatigue, social isolation, and depression (p=0.03; p=0.01; p=0.01 respectively). Multivariate analyses showed that fatigue scores were positively associated with non- planning impulsiveness. Conclusion Impulsivity may be one of the psychiatric disorders associated with AS, such as the more commonly known anxiety and depression. Fatigue is considered as a critical target for increased impulsivity.
Development of Student Comfort with Various Fabrication Methods in Aerospace and Mechanical Engineering Design Curriculum

Student self-efficacy, or a student’s belief in their ability to perform particular tasks, positively contributes to a number of beneficial student characteristics. The development of student-perceived competence with engineering processes should, therefore, serve as a fundamental goal for engineering curricula. This study seeks to provide further insight into what types of activities contribute to the development of student self-efficacy towards common fabrication methods in aerospace and mechanical engineering, particularly exploring potential differences between the effects of shorter practical assignments and longer design projects. Undergraduate engineering students enrolled in 3 different 200-level design courses in the aerospace and mechanical engineering department at a medium-sized, Midwestern, private university were asked to participate in a survey characterizing their comfort level with and prior exposure to various fabrication methods. The fabrication methods analyzed in this study included additive manufacturing (e.g. 3D printing), basic fabrication methods (e.g. hand tools, drill presses), advanced fabrication methods (e.g. CNC mills/routers, water-jet cutters), and 3D modeling (e.g. SolidWorks). Throughout the semester, students were introduced to these topics in the 3 courses via lectures, short practical, or “hands-on”, assignments that had the students use or perform various fabrication processes, and multi-week design projects. The survey was administered at 3 or 4 different timepoints throughout the semester, dependent upon the course. Appropriate data collection timepoints for each course were determined as coming after the completion of course-specific milestones that exposed students to the different fabrication methods. Aggregate and course-specific data from the survey were used to assess how student comfort with relevant fabrication methods changed throughout the semester. Effects of prior outside exposure to these fabrication methods and gender were also explored. Results showed that student comfort level with each fabrication method generally increased throughout the semester in the 3 courses in response to different assignment types. The greatest increases in comfort were seen from projects that required students to engage with fabrication methods to which they had little previous exposure. In some cases, the comfort levels developed from shorter practical assignments were not statistically different than those from multi-week projects. This study suggests that lectures may be a good introduction to