Miracle-dz/UniFAR-FTUs huggingface dataset:
Carbon dioxide-dependent signal transduction in mammalian systems

Carbon dioxide (CO2) is a fundamental physiological gas known to profoundly influence the behaviour and health of millions of species within the plant and animal kingdoms in particular. A recent Royal Society meeting on the topic of ‘Carbon dioxide detection in biological systems' was extremely revealing in terms of the multitude of roles that different levels of CO2 play in influencing plants and animals alike. While outstanding research has been performed by leading researchers in the area of plant biology, neuronal sensing, cell signalling, gas transport, inflammation, lung function and clinical medicine, there is still much to be learned about CO2-dependent sensing and signalling. Notably, while several key signal transduction pathways and nodes of activity have been identified in plants and animals respectively, the precise wiring and sensitivity of these pathways to CO2 remains to be fully elucidated. In this article, we will give an overview of the literature relating to CO2-dependent signal transduction in mammalian systems. We will highlight the main signal transduction hubs through which CO2-dependent signalling is elicited with a view to better understanding the complex physiological response to CO2 in mammalian systems. The main topics of discussion in this article relate to how changes in CO2 influence cellular function through modulation of signal transduction networks influenced by pH, mitochondrial function, adenylate cyclase, calcium, transcriptional regulators, the adenosine monophosphate-activated protein kinase pathway and direct CO2-dependent protein modifications. While each of these topics will be discussed independently, there is evidence of significant cross-talk between these signal transduction pathways as they respond to changes in CO2. In considering these core hubs of CO2-dependent signal transduction, we hope to delineate common elements and identify areas in which future research could be best directed.
Prolonged activation of carbon dioxide-sensitive neurons in mosquitoes

Many insects can detect carbon dioxide (CO2) plumes using a conserved receptor made up of members of the gustatory receptor (Gr) family Gr1, Gr2 and Gr3. Mosquitoes are attracted to host animals for blood meals using plumes of CO2 in the exhaled breath using the receptor expressed in the A neuron of the capitate peg sensilla type on the maxillary palps. The receptor is known to also detect several other classes of odorants, including ones emitted from human skin. Here, we discover that a common skin odorant, butyric acid, can cause a phasic activation followed by an unusually prolonged tonic activity after the stimulus is over in the CO2 neurons of mosquitoes. The effect is conserved in both Aedes aegypti and Anopheles gambiae mosquitoes. This raises a question about its role in a mosquito's preference for the skin odour of different individuals. Butyric acid belongs to a small number of odorants known to cause the prolonged activation of the CO2 receptor. A chemical informatic analysis identifies a specific set of physico-chemical features that can be used in a machine learning predictive model for the prolonged activators. Interestingly, this set is different from physico-chemical features selected for activators or inhibitors, indicating that each has a distinct structural basis. The structural understanding opens up an opportunity to find novel ligands to manipulate the CO2 receptor and mosquito behaviour.
A survey on the studies employing machine learning (ML) for enhancing artificial bee colony (ABC) optimization algorithm

Abstract Nature-inspired optimization (NIO) algorithms have gained quite a popularity among the researchers due to their good performance on difficult optimization problems. Recently, machine learning (ML) algorithms dealing with the generation of knowledge automatically from data have been often integrated into NIO algorithms to enhance their performance. One of the widely used popular NIO algorithms is an artificial bee colony (ABC) algorithm mimicking the intelligent foraging behaviour of real honeybees. In order to improve the performance of standard ABC, some hybridization studies of ABC and ML techniques have been performed to introduce more intelligent versions of ABC that can be used for solving the optimization problems arising in ML and other areas. This study presents a survey on the studies combining ABC with ML techniques for enhancing the performance of ABC algorithm and provides a discussion on how ML techniques have been adapted so far and can be employed for improving ABC further. We hope that this study would be very helpful for the researchers dealing with ML and NIO algorithms, particularly ABC.
Knowledge Based database of arm-muscle and activity characterization during load pull exercise using Diagnostic Electromyography (D-EMG) Signal.

Abstract In this paper, Diagnostic Electromyography (D-EMG) signal interpretation of human arm towards characterization of arm-muscle interaction during various arm movements has been discussed. EMG signals from four important arm muscle (i.e., Bicepsbracci, Tricepsbracci, brachioradialis, and lateral deltoids) are recorded clinically during five different arm movements (i.e., Extension of the forearm, flexion of elbow joint, pronation of forearm, shoulder abduction, and Wrist flexor stretch) under load condition (a load of 2 Kg & 4 Kg maintained during experimental arm movement), the recorded D-EMG signals are properly enveloped within a range of 5–100 Hz and quantized within a proper sampling frequency range to produce a knowledge-based database of muscle activity. In addition, correlation of muscle activity and Power spectral density (PSD) analysis has been carried out towards muscle process discriminating during various arm actions.
Reversing extinction in China's Père David's deer

Père David’s deer (Elaphurus davidianus) became extinct in the wild in China in the late 19th century (1), but after reintroduction three decades ago, the population has grown to more than 8000 individuals, with at least 2420 living in the wild in China (2, 3). This species reintroduction is considered one of the most successful stories in the world (4); it provides a watershed example of biodiversity conservation best practices for the upcoming UN Decade on Ecosystem Restoration. However, the species needs continued support to thrive. Heavily endangered as a result of overhunting and habitat loss (1), the last of China’s Père David’s deer had been pillaged by Europeans and sent to zoos across Europe before the Qing Dynasty fell in 1912 (1). In 1985, nearly a century later, 38 deer were donated back to China for re-wilding (5). After the reintroduction of an additional 39 deer from zoos in England in 1986 (6), the population in Dafeng Milu National Nature Reserve grew to 5681 individuals (2). Père David’s deer populations now cover all habitats in which they lived before the species’ extinction in the wild. The conservation of Père David’s deer, however, faces ongoing challenges. The populations within China lack genetic Edited by Jennifer Sills diversity and are therefore susceptible to multiple risks, such as high miscarriage rates, reduced life span, and diseases (4). Wild populations are also limited by environmental constraints, keeping population numbers low and hindering stability. Moreover, there is no master plan for Père David’s deer conservation at the national level and thus no coordinated monitoring platform or guidelines for overcoming inbreeding and environmental obstacles. Finally, there is a lack of international cooperation between researchers in China and abroad. National and international cooperation to strengthen monitoring of Père David’s deer populations and to develop a shared database and germplasm databank between all countries with wild populations would be a major step forward for securing the long-term conservation of this species. Yuanyuan Zhang, Jiade Bai*, Annah Zhu, Ruishan Chen , Dayuan Xue, Zhenyu Zhong, Zhibin Cheng Beijing Biodiversity Conservation Research Center, Beijing, 100076, China. Beijing Milu Ecological Research Center, Beijing, 100076, China. Environmental Policy Group, Wageningen University, 6706 KN Wageningen, Netherlands. East China Normal University, Shanghai 200042, China. College of Life and Environmental Sciences, Minzu University of China, Beijing, 100081, China. *Corresponding author. Email: baijiade234@aliyun.com
Semantic and Physical Properties of Peripheral Vision Are Used for Scene Categorization in Central Vision

Abstract Theories of visual recognition postulate that our ability to understand our visual environment at a glance is based on the extraction of the gist of the visual scene, a first global and rudimentary visual representation. Gist perception would be based on the rapid analysis of low spatial frequencies in the visual signal and would allow a coarse categorization of the scene. We aimed to study whether the low spatial resolution information available in peripheral vision could modulate the processing of visual information presented in central vision. We combined behavioral measures (Experiments 1 and 2) and fMRI measures (Experiment 2). Participants categorized a scene presented in central vision (artificial vs. natural categories) while ignoring another scene, either semantically congruent or incongruent, presented in peripheral vision. The two scenes could either share the same physical properties (similar amplitude spectrum and spatial configuration) or not. Categorization of the central scene was impaired by a semantically incongruent peripheral scene, in particular when the two scenes were physically similar. This semantic interference effect was associated with increased activation of the inferior frontal gyrus. When the two scenes were semantically congruent, the dissimilarity of their physical properties impaired the categorization of the central scene. This effect was associated with increased activation in occipito-temporal areas. In line with the hypothesis of predictive mechanisms involved in visual recognition, results suggest that semantic and physical properties of the information coming from peripheral vision would be automatically used to generate predictions that guide the processing of signal in central vision.
Effect of austenitizing temperatures on the microstructure and mechanical properties of AISI 9254 steel

Abstract In this study, the effect of austenitizing temperatures and low-temperature isothermal heat treatment (below martensite start temperature) on the microstructure and mechanical properties of AISI 9254 high silicon spring steel has been investigated. Experimental studies show that ultra-fine carbide-free bainite, tempered martensite and carbon enriched retained austenite could be observed in isothermally heat-treated samples where the as-received sample consisted of fine pearlite. A high tensile strength of ~2060 MPa, a total elongation of ~8 %, and absorbed energy of 105 J were achieved in a commercial high-Si steel by austempering below the Ms temperature. A good combination of strength and ductility has been obtained in prolonged austempering below the martensite start temperature (225 °C) from an austenitizing temperature of 870 °C.
Analyse des variables temporelles du français spontané

Abstract This second study of the time variables of spoken French unravels the main values of these variables in a forced language activity (the description of cartoons) and compares them with those found in radio interviews. As regards the primary variables, the difference between these two tasks is highly significant. A comparison with English in respect to a similar description task shows a great similarity at the level of the complex variables and the rate of articulation, but a significant difference in the length of the runs and of unfilled pauses. The comparison of the syntactic distribution of unfilled pauses in interviews and in descriptions shows a similarity in the occurrence of pauses at different syntactic positions (in particular finally and medially in sentences), but an increase in the number of pauses and – by about 100% – of their median length. Finally, a very great stability in the classification by order of size of the secondary variables (other hesitation pauses) is noted, which does not prevent these pauses from being distributed differently and two to three times as frequent in the descriptions.
Molecular Evolutionary Dynamics of Energy Limited Microorganisms

Microorganisms have the unique ability to survive extended periods of time in environments with extremely low levels of exploitable energy. To determine the extent that energy limitation affects microbial evolution, we examined the molecular evolutionary dynamics of a phylogenetically diverse set of taxa over the course of 1,000-days. We found that periodic exposure to energy limitation affected the rate of molecular evolution, the accumulation of genetic diversity, and the rate of extinction. We then determined the degree that energy limitation affected the spectrum of mutations as well as the direction of evolution at the gene level. Our results suggest that the initial depletion of energy altered the direction and rate of molecular evolution within each taxon, though after the initial depletion the rate and direction did not substantially change. However, this consistent pattern became diminished when comparisons were performed across phylogenetically distant taxa, suggesting that while the dynamics of molecular evolution under energy limitation are highly generalizable across the microbial tree of life, the targets of adaptation are specific to a given taxon.
A clonal fresh water plants acquires transgenerational stress resistance under recurring copper excess

Although non-genetic inheritance is thought to play an important role in plant ecology and evolution, evidence for adaptive transgenerational plasticity is scarce. Here, we investigated the consequences of copper excess on offspring defences and fitness in the giant duckweed (Spirodela polyrhiza) across multiple asexual generations. We found that exposing large monoclonal populations (>10,000 individuals) for 30 generations to copper excess decreased plant fitness during the first few generations but increased their fitness in consecutive generations under recurring stress when plants were grown for 5 generations under control conditions prior recurring conditions. Similarly, propagating individual plants as single descendants for 5 or 10 generations under copper excess decreased plant fitness when 5 generations and improved plant fitness when 10 generations passed between initial and recurring stress; thus, transgenerational stress responses likely contributed to the observed variations in offspring fitness of long-term copper exposed populations. Fitness benefits under recurring stress were partially associated with avoidance of excessive copper accumulation, which in turn correlated with transgenerationally modified flavonoid concentrations. Taken together, these data demonstrate time-dependent adaptive transgenerational responses under recurring stress, which highlights the importance of non-genetic inheritance for plant ecology and evolution.
Extracellular vesicles induce aggressive phenotype of luminal breast cancer cells by PKM2 phosphorylation

The aerobic glycolysis is a hallmark of cancer glucose metabolism. Several studies have suggested that cancer-derived extracellular vesicles (EVs) can modulate glucose metabolism in adjacent cells and promote disease progression. Here we suggest that EVs originated from cancer cell with highly glycolytic activity can modulate glucose metabolism in the recipient cancer cells with relative low glycolytic activity, and further induce cell proliferation. Two types of breast cancer cell lines with different levels of glycolytic activity, MDA-MB-231 of a claudin low-type breast cancer cell and MCF7 of luminal type breast cancer cell, were selected and co-cultured using indirect co-culture system such as transwell system or microfluidic system. Glucose uptake of the recipient MCF7 cells was markedly increased after co-culture with MDA-MB-231 cells. MCF7 cells after co-culture with MDA-MB-231-tdTomato cells represented multiple tdTomato signal inside the cell, which proved that EVs originated from MDA-MB-231-tdTomato were transferred to MCF7 cell. In addition, serine phosphorylation of PKM2 necessary for tumorigenesis was highly activated, and tyrosine phosphorylation of PKM2 suggesting activated aerobic glycolysis was also increased in the co-cultured MCF7 cells. Proteomic profiling of the co-cultured MCF7 cells revealed the proliferation and dedifferentiation of MCF7 cells, and further confirmed epithelial-mesenchymal transition (EMT), which is a key phenomenon for cancer metastasis. In the transcriptomic analysis, glycolysis increased in co-cultured MCF7 cells, and the component analysis of genes associated with glycolysis revealed that the next major component after cytoplasm was extracellular exosome. Proteomic analysis of EVs revealed that there were important proteins in the EV such as EGFR, ERBB2 and MAPK for phosphorylating PKM2. This phenomenon suggests the potential for aggressive cancer cells to affect other cancer cells through EV mediators.
Speciation across the Earth driven by global cooling in terrestrial orchids

Though climate change has been implicated as a major catalyst of diversification, its effects are thought to be inconsistent and much less pervasive than localised climate or the accumulation of species with time. But, we need focused analyses of highly specious clades to disentangle the consequences of climate change, geography and time. Here, we show that global cooling shapes the biodiversity of terrestrial orchids. Employing a phylogenetic framework of 1,450 species of Orchidoideae, the largest terrestrial orchid subfamily, we find that speciation rate is causally linked with historic global cooling, not time, habitation in the tropics, altitude, variation in chromosome number, or other types of historic climate change. Relative to the gradual accumulation of species with time, models specifying speciation driven by historic global cooling are 328 times more likely. Evidence ratios estimated for 212 other plant and animal groups reveal that the orchidoids represent one of the best-supported cases of temperature-spurred speciation yet reported. Employing >1.4 M georeferenced records, we find that global cooling drove contemporaneous diversification in each of the seven major orchid bioregions of the earth. With current emphasis on understanding and predicting the immediate impacts of global warming, our study provides a clear case study of the longterm impacts of global climate change on biodiversity. Significance statement The staggering biodiversity of angiosperms has been difficult to reconcile with the gradual Darwinian process thought to create it. Changes in climate through the Earth’s history could have instigated this diversification, but perceived variability across clades and geography has restrained generalisation. In this paper, we reconstruct the evolutionary history of a rich terrestrial orchid subfamily favoured by Darwin (Orchidoideae, ~5,000 species), and use >1.4 million georeferenced records to test how and where those orchid species arose. We find that global cooling between the Oligocene and present day spurred an avalanche of speciation in orchidoid assemblages across the Earth. This work resolves the orchidoid phylogeny and provides a clear example of how historic climate change drives global patterns of biodiversity.
LevioSAM: Fast lift-over of alternate reference alignments

Motivation As more population genetics datasets and population-specific references become available, the task of translating (“lifting”) read alignments from one reference coordinate system to another is becoming more common. Existing tools generally require a chain file, whereas VCF files are the more common way to represent variation. Existing tools also do not make effective use of threads, creating a post-alignment bottleneck. Results LevioSAM is a tool for lifting SAM/BAM alignments from one reference to another using a VCF file containing population variants. LevioSAM uses succinct data structures and scales efficiently to many threads. When run downstream of a read aligner, levioSAM completes in less than 13% the time required by an aligner when both are run with 16 threads. Availability https://github.com/alshai/levioSAM Contact tmun1@jhu.edu, langmea@cs.jhu.edu
Architecture of cell–cell junctions in situ reveals a mechanism for bacterial biofilm inhibition

Significance Pseudomonas aeruginosa bacteria form antibiotic-tolerant biofilms that pose significant challenges in clinical settings. Overcoming these challenges requires fundamental insights into how biofilms are formed, combined with innovative strategies to disrupt biofilms. Electron cryotomography in situ data presented here reveal the arrangement of the key P. aeruginosa adhesin CdrA at biofilm cell–cell junctions. Guided by our imaging data, we raised and characterized a CdrA-specific nanobody binder capable of disrupting these cell–cell junctions, thereby increasing the efficacy of antibiotic-mediated bacterial killing in biofilms. Together these data provide a pathway for developing effective alternative bacterial infection treatment strategies. Many bacteria, including the major human pathogen Pseudomonas aeruginosa, are naturally found in multicellular, antibiotic-tolerant biofilm communities, in which cells are embedded in an extracellular matrix of polymeric molecules. Cell–cell interactions within P. aeruginosa biofilms are mediated by CdrA, a large, membrane-associated adhesin present in the extracellular matrix of biofilms, regulated by the cytoplasmic concentration of cyclic diguanylate. Here, using electron cryotomography of focused ion beam–milled specimens, we report the architecture of CdrA molecules in the extracellular matrix of P. aeruginosa biofilms at intact cell–cell junctions. Combining our in situ observations at cell–cell junctions with biochemistry, native mass spectrometry, and cellular imaging, we demonstrate that CdrA forms an extended structure that projects from the outer membrane to tether cells together via polysaccharide binding partners. We go on to show the functional importance of CdrA using custom single-domain antibody (nanobody) binders. Nanobodies targeting the tip of functional cell-surface CdrA molecules could be used to inhibit bacterial biofilm formation or disrupt preexisting biofilms in conjunction with bactericidal antibiotics. These results reveal a functional mechanism for cell–cell interactions within bacterial biofilms and highlight the promise of using inhibitors targeting biofilm cell–cell junctions to prevent or treat problematic, chronic bacterial infections.