Miracle-dz/UniFAR-FTUs huggingface dataset:
AB-DeepLabv3+: An Encoder-Decoder Method with Attention Mechanism for Polyp Segmentation

A polyp is an abnormal growth that can occur in the colon and can be a precursor to colorectal cancer. Colorectal cancer can be diagnosed and treated earlier when polyps are detected and segmented accurately in medical images. The use of deep learning models for medical image segmentation has shown promising results in recent years. This paper presents a polyp segmentation using the modified version of Deeplabv3+ with an attention mechanism called AB-DeepLabv3+. An attention mechanism enhances the discriminatory power of the network by highlighting informative regions of the input image. In the evaluation of the AB-DeepLabv3+ on the publicly available Kvasir-SEG dataset, it achieved state-of-the-art performance with an overall Dice coefficient of 0.98 and an intersection over union of 0.96. The results demonstrated that the AB-DeepLabv3+ provides accurate and efficient polyp segmentation in colonoscopy images.
Intracranial Haemorrhage Detection Based on Deep Learning Using CT Images

Intracranial haemorrhage (ICH) is a medical condition that can have life-threatening consequences if it is not promptly diagnosed and treated. Diagnostic tools for medical imaging, such computed tomography (CT) scans, can help identify ICH. In this study, we investigated the application of deep learning methods to CT scan images used for ICH diagnosis. In particular, the authors made use of the Block Matching 3D (BM3D) algorithm for image pre-processing, the Densenet121 neural network design, and the Hough Transformation for image transformation. The objective was to create a model that could correctly identify and categorize ICH in CT scan pictures. The region of interest (ROI) in the CT scan pictures was then located and extracted using the Hough Transformation approach. Overall, the findings of this study show the potential of deep learning methods to support ICH diagnosis from CT scan pictures. The suggested approach was highly accurate and has the potential to help radiologists identify ICH.
Warming Early Earth and Mars

Life on Earth is thought to have started about 4 billion years ago, yet the sun's luminosity at that stage of its evolution would have been 25 to 30% lower than today. This primordial solar luminosity would have been insufficient to heat the Earth enough to allow water to be in its liquid phase and so enable the formation of life, a dilemma that has been called the early faint sun paradox. In his Perspective, Kasting reviews the background to this paradox and comments on the results of Sagan and Chyba in the same issue, which are presented as a resolution to the dilemma. Sagan and Chyba ([p. 1217][1]) suggest that absorption of solar ultraviolet radiation by high-altitude organic particulates may have permitted sufficient ammonia concentration in the early atmosphere to allow greenhouse warming of the Earth. Kasting comments on this suggestion and discusses its implications. [1]: http://www.sciencemag. org/cgi/content/short/276/5316/1217
Nuclear lamin A-associated proteins are required for centromere assembly

Many Lamin A-associated proteins (LAAP’s) that are key constituents of the nuclear envelope (NE), assemble at the “core” domains of chromosomes during NE reformation and mitotic exit. However, the identity and function of the chromosomal core domains remain ill-defined. Here, we show that a distinct section of the core domain overlaps with the centromeres/kinetochores of chromosomes during mitotic telophase. The core domain can thus be demarcated into a kinetochore proximal core (KPC) on one side of the segregated chromosomes and the kinetochore distal core (KDC) on the opposite side, close to the central spindle. We next tested if centromere assembly is connected to NE re-formation. We find that centromere assembly is markedly perturbed after inhibiting the function of LMNA and the core-localized LAAPs, BANF1 and Emerin. We also find that the LAAPs exhibit multiple biochemical interactions with the centromere and inner kinetochore proteins. Consistent with this, normal mitotic progression and chromosome segregation was severely impeded after inhibiting LAAP function. Intriguingly, the inhibition of centromere function also interferes with the assembly of LAAP components at the core domain, suggesting a mutual dependence of LAAP and centromeres for their assembly at the core domains. Finally, we find that the localization of key proteins involved in the centromeric loading of CENP-A, including the Mis18 complex and HJURP were markedly affected in LAAP-inhibited cells. Our evidence points to a model where LAAP assembly at the core domain serves a key function in loading new copies of centromeric proteins during or immediately after mitotic exit.
Minimal epistatic networks from integrated sequence and mutational protein data

Predicting the functional effects of mutations to a wild-type protein sequence is a major computational challenge. We introduce here a computationally efficient procedure to identify the few, most informative epistatic links between residues in a protein, integrating sequence data and functional measurements with mutational scans. Our approach shows performances comparable to state-of-the-art deep networks, while requiring much less parameters and being hence much more interpretable. The selected network links mostly focus on the protein functional sites, adapt to the in vitro or in vivo function experimentally tested, and are not necessary related to structural contacts.
iPSC-based modeling of helicase deficiency reveals impaired cell proliferation and increased apoptosis after NK cell lineage commitment

Cell proliferation is a ubiquitous process required for organismal development and homeostasis. However, individuals with partial loss-of-function variants in DNA replicative helicase components often present with immunodeficiency due to specific loss of natural killer (NK) cells. Such lineage-specific disease phenotypes raise questions on how the proliferation is regulated in cell type-specific manner. We aimed to understand NK cell-specific proliferative dynamics and vulnerability to impaired helicase function using iPSCs from individuals with NK cell deficiency (NKD) due to hereditary compound heterozygous GINS4 variants. We observed and characterized heterogeneous cell populations that arise during the iPSC differentiation along with NK cells. While overall cell proliferation decreased with differentiation, early NK cell precursors showed a short burst of cell proliferation. GINS4 deficiency induced replication stress in these early NK cell precursors, which are poised for apoptosis, and ultimately recapitulate the NKD phenotype.
Evidence About Hydrate and Solid Water in the Martian Surface From the

The Mariner Mars 6 and 7 infrared spectrometer spectra of Mars include a broad absorption near 3 μ that can be ascribed to water of hydration in the surface minerals and/or ice. Laboratory experiments show that an increase in either form of condensed phase water is accompanied by a decreased intensity ratio R1 = I(3.10 μ)/I(2.20 μ). Evidence for the presence of ice is provided by the intensity ratio R2 = I(2.90 μ)/I(3.10 μ) since R2 is below unity for silicate hydrates and exceeds unity for ice. Near the Martian equator both the surface temperature and R1depend inversely upon brightness at 2.2 μ: a doubling of B(2.2 μ) is accompanied by a 19° temperature drop and a 30% drop in R1. BothR1 and R2 depend upon latitude: R1 is low near the equator and at latitudes more southerly than 50°S, whereas R1 is high in between. These data show that condensed phase water is present throughout the observed surface of Mars, the brighter areas near the equator (and north of it) and the regions south of 50°S being the most hydrated. All three variables, B(2.2), R1, and R2, change dramatically and in concert in a 5° latitude range at the polar cap edge. The characteristic spectral signature of ice can be discerned as well, indicating that ice is forming in this region, most likely on the planetary surface.
Historia vegetal reciente en Patagonia occidental. Análisis palinológico de Laguna Cea (45°40'S, 72°14'W), Coyhaique, Chile

A palynological analysis was performed on the sedimentary cover of Laguna Cea, located in the subbasin of the Simpson River in the Coyhaique region of southern Chile. The pollen record shows a landscape evolution from a woodland-type ecosystem covered by Nothofagaceae (Nothofagus antarctica/N. dombeyi) to a meadow-type ecosystem in which low brush such as calafate (Berberidaceae), herbaceous layers such as different types of grasses (Poaceae), and hydrophilic vegetation such as marsh plants (Cyperaceae) may be found. This structural change in vegetation occurred approximately 120 years before present (BP) and coincided with the middle of the XIX Century, the epoch which marks the beginning of colonial settlements and the consequent clearing and livestock grazing. The palynological record supports the occurrence of fire through charcoal
Calcineurin-dependent contributions to fitness in the opportunistic pathogen Candida glabrata

ABSTRACT The protein phosphatase calcineurin is vital for the virulence of the opportunistic fungal pathogen Candida glabrata. The host-induced stresses that activate calcineurin signaling are unknown, as are the targets of calcineurin relevant to virulence. To potentially shed light on these processes, millions of transposon insertion mutants throughout the genome of C. glabrata were profiled en masse for fitness defects in the presence of FK506, a specific inhibitor of calcineurin. Eighty-seven specific gene deficiencies depended on calcineurin signaling for full viability in vitro both in wild-type and pdr1∆ null strains lacking pleiotropic drug resistance. Three genes involved in cell wall biosynthesis (FKS1, DCW1, FLC1) possess co-essential paralogs whose expression depended on calcineurin and Crz1 in response to micafungin, a clinical antifungal that interferes with cell wall biogenesis. Interestingly, 80% of the FK506-sensitive mutants were deficient in different aspects of vesicular trafficking, such as endocytosis, exocytosis, sorting, and biogenesis of secretory proteins in the endoplasmic reticulum (ER). In response to the experimental antifungal manogepix that blocks GPI-anchor biosynthesis in the ER, calcineurin signaling increased and strongly prevented cell death independent of Crz1, one of its major targets. Comparisons between manogepix, micafungin, and the ER-stressing tunicamycin reveal a correlation between the degree of calcineurin signaling and the degree of cell survival. These findings suggest that calcineurin plays major roles in mitigating stresses of vesicular trafficking. Such stresses may arise during host infection and in response to antifungal therapies. IMPORTANCE Calcineurin plays critical roles in the virulence of most pathogenic fungi. This study sheds light on those roles in the opportunistic pathogen Candida glabrata using a genome-wide analysis in vitro. The findings could lead to antifungal developments that also avoid immunosuppression. Calcineurin plays critical roles in the virulence of most pathogenic fungi. This study sheds light on those roles in the opportunistic pathogen Candida glabrata using a genome-wide analysis in vitro. The findings could lead to antifungal developments that also avoid immunosuppression.
Identification and Analysis of Emotions from the Text for Stress Detection

An emotion is an integral part of human behavior. It helps to identify whether a person is happy, sad, angry, scared, stressed, etc. Every emotion makes a positive or negative impact on the health of a person. Among various forms of emotions, Stress is an important one that causes a high impact on the mental health of the people of different ages. This paper tries to identify and analyze the emotions that result in stress. Due to the rise in the use of internet and social media, huge data in the form of text, facial expressions, speech, etc. are available and can be used to detect emotions and stress. This paper identifies a total of eighteen different emotions for stress detection. Out of eighteen, three emotions, i.e., anger, fear, grief or sadness, have been widely used by most of the researchers. The next stage is to identify stress-inducing emotions from the text data. This paper applies a machine learning algorithm called Complement Naïve Bayes and a deep learning algorithm called Bidirectional Long Short-Term Memory (Bi-LSTM) with GloVe word embedding technique for emotion detection from the text which results in an accuracy of 88.40% and 89% respectively. The proposed algorithms are compared with the existing algorithms and proved to perform better than the existing ones.
Neuroplasticity of speech-in-noise processing in older adults assessed by functional near-infrared spectroscopy (fNIRS)

Functional near-infrared spectroscopy (fNIRS), a non-invasive optical neuroimaging technique that is portable and acoustically silent, has become a promising tool for evaluating auditory brain functions in hearing- vulnerable individuals. This study, for the first time, used fNIRS to evaluate neuroplasticity of speech-in-noise processing in older adults. Ten older adults, most of whom had moderate-to-mild hearing loss, participated in a 4-week speech-in-noise training. Their speech-in-noise performances and fNIRS brain responses to speech (auditory sentences in noise), non-speech (spectrally-rotated speech in noise) and visual (flashing chequerboards) stimuli were evaluated pre- (T0) and post-training (immediately after training, T1; and after a 4-week retention, T2). Behaviourally, speech-in-noise performances were improved after retention (T2 vs. T0) but not immediately after training (T1 vs. T0). Neurally, we intriguingly found brain responses to speech vs. non-speech decreased significantly in the left auditory cortex after retention (T2 vs. T0 and T2 vs. T1) for which we interpret as suppressed processing of background noise during speech listening alongside the significant behavioural improvements. Meanwhile, functional connectivity within and between multiple regions of temporal, parietal and frontal lobes was significantly enhanced in the speech condition after retention (T2 vs. T0). We also found neural changes before the emergence significant behavioural improvements. Compared to pre-training, responses to speech vs. non-speech in the left frontal/prefrontal cortex were decreased significantly both immediately after training (T1 vs. T0) and retention (T2 vs. T0), reflecting possible alleviation of listening efforts. Finally, connectivity was significantly decreased between auditory and higher-level non-auditory (parietal and frontal) cortices in response to visual stimuli immediately after training (T1 vs. T0), indicating decreased cross-modal takeover of speech-related regions during visual processing. The results thus showed that neuroplasticity can be observed not only at the same time, but also before behavioural changes in speech-in- noise perception. To our knowledge, this is the first fNIRS study to evaluate speech-based auditory neuroplasticity in older adults. It thus provides important implications for current research by illustrating the promises of detecting neuroplasticity using fNIRS in hearing-vulnerable individuals.
Numerical and analytical modeling of advective travel times in realistic three‐dimensional fracture networks

Travel time distributions obtained from advective transport in multiple realizations of realistic discrete fracture network simulations are analyzed using the truncated one‐sided stable distribution, which has previously been shown to generalize both the advection‐dispersion solution as well as one‐sided stable distributions. Using this model, it is shown that the Fickian assumption inherent in the advection‐dispersion equation generally fails, despite the first two moments of travel time essentially scaling linearly with distance. It is also observed that the equally probable realizations drawn from the ensemble can produce a wide range of behavior under the current configuration, such that Fickian conditions are almost obtained in some cases for increasing scales. On the basis of a small‐scale calibration against particle breakthrough, the model is then shown to successfully predict limiting bounds of transport for a one order of magnitude increase in scale. Correlation in particle velocity is explicitly shown to be significant for scales close to the characteristic Lagrangian segment length. The network configuration is obtained from extensive site characterization data at the Laxemar region in Sweden and represents a block‐scale domain of reasonably sparse background fractures.
Estimates of Site Effectsin the Garhwal Himalaya

Three-component digital datafrom a 12-station seismological network in the Garhwal Himalaya have been used estimate the site effectsfrom S-wave componentsof eight local earthquakes and microtremors. These earthquakes (2.0 ≤ ML≤2.92) have been occurred at epicentral distances between 100 km to 200 km from the center of the network with focal depths ranging from 2.5 km to 22.7 km. S-wave spectral ratios were computed from 273 waveforms in frequency range from 1 to 12 Hz considering PRT as a reference site. H/V spectral ratios in frequency range from 1 Hz to 25 Hz have been estimated from 117 samples of microtremors with duration ranging from 30 seconds to 280 seconds. From S–wave spectral ratios, higher amplifications have been brought out at sites located nearest to the epicenters of the earthquakes as compared to sites located away from the epicenters. Almost similar frequency dependent trends in the S-wave site amplifications in the radial and transverse components have been brought out at the majority of sites.High amplificationaround 10 Hz at CHN site seems to be due to topographic effect as the site is located on 2244 m high mountain peak. At most of the sites, the vertical components show consistently low site amplifications as compared to horizontal components particularly at frequencies above 4 Hz to 5 Hz. H/V spectral ratios from the microtremorsof morning hours have showndominant broad peaks between 3 Hz and 4 Hz at CNT, PRT, NTT and RAJ sites, whereas at all sites microtremors recorded in the afternoon show maximum peaks between 2 Hz and 4 Hz, and beyond 4 Hz the amplifications decreases. An interesting feature at NTT and AYR sites, is a sharp peak embedded in a broad peak around 4 Hz. This response seems to be due to the vibrations generated by the operation of turbines which are within the radius of 2 km to 3 km from the sites.
De novo sequencing of the transcriptome of Fargesia macclureana (Poaceae) reveals regulators of the �oral transition and ecological adaptations to high altitude

Background: Fargesia macclureana (Poaceae) is a woody bamboo species found on the Qinghai–Tibet Plateau (QTP) approximately 2,000 ~ 3,800 m above sea level. It rarely blossoms in the QTP, but it �owered 20 days after growing in our lab, which is in a low-altitude area outside the QTP. To date, little is known regarding the molecular mechanism of bamboo �owering, and no studies of �owering have been conducted on wild bamboo plants growing in extreme environments. Here, we report the �rst de novo transcriptome sequence for F. macclureana to investigate the putative mechanisms underlying the �owering time control used by F. macclureana to adapt to its environment. Results: Illumina deep sequencing of the F. macclureana transcriptome generated 140.94 Gb of data, assembled into 99,056 unigenes. A comprehensive analysis of the broadly, speci�cally and differentially expressed unigenes (BEUs, SEUs and DEUs) indicated that they were mostly involved in metabolism and signal transduction, as well as DNA repair and plant-pathogen interactions, which may be of adaptive importance. In addition, comparison analysis between non-owering and �owering tissues revealed that expressions of FmFT and FmHd3a, two putative F. macclureana orthologs, were differently regulated in NF-vs F-leaves, and carbohydrate metabolism and signal transduction were two major KEGG pathways that DEUs were enriched in. Finally, we detected 9,296 simple sequence repeats (SSRs) that may be useful for further molecular marker-assisted breeding. Conclusions: F. macclureana may have evolved speci�c reproductive strategies for owering-related pathways in response to photoperiodic cues to ensure long vegetation growing period. Our �ndings will provide new insights to future investigations into the mechanisms of �owering time control and adaptive evolution in plants growing at high altitudes.
PanEffect: A pan-genome visualization tool for variant effects in maize

Understanding the effects of genetic variants is crucial for accurately predicting traits and phenotypic outcomes. Recent advances have utilized protein language models to score all possible missense variant effects at the proteome level for a single genome, but a reliable tool is needed to explore these effects at the pan-genome level. To address this gap, we introduce a new tool called PanEffect. We implemented PanEffect at MaizeGDB to enable a comprehensive examination of the potential effects of coding variants across 51 maize genomes. The tool allows users to visualize over 550 million possible amino acid substitutions in the B73 maize reference genome and also to observe the effects of the 2.3 million natural variations in the maize pan-genome. Each variant effect score, calculated from the Evolutionary Scale Modeling (ESM) protein language model, shows the log-likelihood ratio difference between B73 and all variants in the pan-genome. These scores are shown using heatmaps spanning benign outcomes to strong phenotypic consequences. Additionally, PanEffect displays secondary structures and functional domains along with the variant effects, offering additional functional and structural context. Using PanEffect, researchers now have a platform to explore protein variants and identify genetic targets for crop enhancement. Availability and implementation: The PanEffect code is freely available on GitHub (https://github.com/Maize-Genetics-and-Genomics-Database/PanEffect). A maize implementation of PanEffect and underlying datasets are available at MaizeGDB (https://www.maizegdb.org/effect/maize/).
Diagnosis of Thyroid Nodule Based on Multi-Scale Se-Segnet and Resnet50

Thyroid nodule is a common chronic endocrine system disease, which may deteriorate into thyroid cancer without treatment. However, due to the distribution of many blood vessels, nerves and organs near the thyroid, the clarity of ultrasonic image is poor, and human eye recognition has great limitations.We propose a method for thyroid nodule diagnosis based on multi-scale Se-SegNet network and ResNet50. We improved and optimized the SegNet as the main backbone, and constructed a multi-scale Se-SegNet network to segment thyroid ultrasonography. Then we used ResNet50 to classify the segmented images and get the diagnosis results. The accuracy of the multi-scale Se-SegNet image segmentation model is 0.959. The accuracy of classification results was 0.967. This paper proposes a new diagnostic scheme for thyroid nodule, which can diagnose thyroid nodule quickly and accurately. The experimental results show that it has higher diagnostic accuracy than the traditional scheme.