Miracle-dz/UniFAR-FTUs huggingface dataset:
Intercropping durum wheat and chickpea increases nutrient availability and use efficiency under low phosphorus soils

Abstract Intercropping cereals with legumes may achieve high crop yields at reduced input levels. However, few data are available with regards to the ability of the intercropping legumes and cereals to increases nutrient availability and use efficiency under low phosphorus soils. To address this question, chickpea (Cicer arietinum L. cv. Flip 90-13 C) and durum wheat (Triticum turgidum durum L. cv. Simeto), were grown as sole- and inter-crops over two growing seasons 2019 and 2020. The results showed that both the plant biomass and nodulation and, consequently, the amount of P uptake were significantly increased for intercropping than for sole cropping and so more in 2020 compared to 2019. Moreover, grain yield and resource P use efficiency were significantly improved, as indicated by higher land equivalent ratio (LER > 1) in intercropping over sole cropping treatments. Nevertheless, the intercropped chickpea considerably increased the inorganic P availability in durum wheat rhizosphere over two growing seasons. Our findings suggest that intercropping promotes the ability of durum wheat and chickpea to increase rhizosphere nutrient availability and land use efficiency under low-P soils conditions.
First record of Chaetomorpha ligustica (Cladophoraceae, Cladophorales) smothering the seagrass Zostera muelleri in a New Zealand estuary

ABSTRACT The filamentous green alga Chaetomorpha ligustica (Cladophoraceae, Cladophorales) was recorded covering seagrass meadows at Pāuatahanui Inlet, New Zealand. Species of the genus Chaetomorpha are difficult to identify by their morphologically, and the identification of C. ligustica was confirmed by sequencing the 28S rRNA large subunit providing a high level of confidence in the species designation. In November 2019, we found C. ligustica intertwined with Ulva spp. forming dense, heavy and entangled structures. Here we report, for the first time, negative impacts of this species upon meadows of the New Zealand seagrass Zostera muelleri. We observed a significant loss of seagrass cover and evidence of anoxia under C. ligustica mats two weeks from the first sighting. Chaetomorpha ligustica can easily be misidentified in the field. This may lead to over- and under-reporting of species, and we recommend the need for more careful identification of macroalgal blooms in the future and further research on growth requirements and origins of strains.
EchoSensor: Fine-grained Ultrasonic Sensing for Smart Home Intrusion Detection

This article presents the design and implementation of a novel intrusion detection system, called EchoSensor, which leverages speakers and microphones in smart home devices to capture human gait patterns for individual identification. EchoSensor harnesses the speaker to send inaudible acoustic signals (around 20 kHz) and utilizes the microphone to capture the reflected signals. As the reflected signals have unique variations in the Doppler shift respective to the gaits of different people, EchoSensor is able to profile human gait patterns from the generated spectrograms. To mine the gait information, we first propose a two-stage interference cancellation scheme to remove the background noise and environmental interference, followed by a new method to detect the starting point of walking and estimate the gait cycle time. We then perform the fine-grained analysis of the spectrograms to extract a series of features. In the end, machine learning is employed to construct an identifier for individual recognition. We implement the EchoSensor system and deploy it under different household environments to conduct intrusion detection tasks. Extensive experimental results have demonstrated that EchoSensor can achieve the averaged Intruder Gait Detection Rate (IDR) and True Family Member Gait Detection Rate (TFR) of 92.7% and 91.9%, respectively.
The punctate localisation of the yeast sterol transporter Ysp2p is determined by three dimerisation interfaces in its C-terminus

Sterol lipids traffic between intracellular compartments by vesicular and non-vesicular routes. Sterol traffic from the plasma membrane to the endoplasmic reticulum (ER), so-called retrograde traffic, particularly depends on a non-vesicular mechanism, being transported by the ubiquitous family of Lipid transfer proteins Anchored at Membrane contact sites (LAMs, also called GRAMD1/Asters in humans, VASt in plants). LAMs are similar to many lipid transfer proteins in that they localise to membrane contact sites and carry lipids between two organelles. In yeast, the major LAM active at ER-plasma membrane contact sites is Ysp2p, which has a uniquely punctate distribution in the cortical ER. Here, we have comprehensively dissected how Ysp2p achieves its distinctive punctate localisation. We show that the PHGRAM domain of Ysp2p has membrane binding properties similar to its human counterpart GRAMD1B, but that this is not important for punctate localisation of Ysp2p. Instead, all regions necessary for the punctate localisation of Ysp2p at membrane contacts are present in ∼200 residues at the C-terminus of Ysp2p, with a critical region being a small ý-sheet that we predict homodimerises. We also study the role of punctate localisation of Ysp2 in its function in retrograde sterol traffic, and show that function does not require the punctate localisation, but instead requires a polybasic region adjacent to the sterol transfer domain. Finally, to investigate the interaction of the polybasic region with the plasma membrane, we examine contacts populated by the Ysp2 C-terminus by electron tomography, and find that they consist of generic cortical ER.
Climatic and biogeographic processes underlying the diversification of the pantropical and early divergent angiosperm family Annonaceae

Aim Tropical rainforests harbour the richest biodiversity among terrestrial ecosystems, but few studies have addressed underlying processes of species diversification in these ecosystems. We use the pantropical and early divergent flowering plant family Annonaceae as a model system to investigate how abiotic factors such as climate and biogeographic events contribute to the diversification process and lead to its high diversity across a long evolutionary history. Location Tropics and subtropics Taxon Annonaceae Methods A super-matrix was constructed for 835 taxa (34% of Annonaceae species), based on eight chloroplast regions. To understand the patterns of diversification, we reconstructed climatic niche evolution and historical biogeographical events, and tested their association with diversification rates. Results The analysis of temperature-dependent models in Annonaceae lineages provides strong support for the significant influence of global temperature on net diversification and accumulation of species diversity. The pattern of lineage accumulation in the initial radiation is better aligned with the “museum model,” followed by later accumulation consistent with the “recent cradle model” from the late Oligocene to the present. The increase in the diversification rate of the family (around 25 Ma) lags behind the accumulation of niche divergences (around 15 Ma). Biogeographic events are related to only two of the five diversification rate shifts detected. While no direct relationship to shifts in the diversification rate was uncovered, shifts in niche evolution appear to be associated with increasingly seasonal environments. Main Conclusions Global temperature plays a crucial role in driving recent rapid diversification in the Annonaceae. Our study challenges the prevailing assumption of the “museum model” alone and proposes instead a transition from the “museum model” to the “recent cradle model” during the diversification history of the family. However, our findings do not support the direct correlation of any particular climatic niche shifts or historical biogeographical events with shifts in diversification rate. Instead, Annonaceae diversification can lead to later niche divergence as a result of increasing interspecific competition arising from species accumulation. The evolutionary direction of niche shifts furthermore provides insight into the future expansion of Annonaceae into temperate regions. Our results highlight the complexity of the diversification process in taxa with long evolutionary histories, indicating that identifying isolated driving factors is simplistic and inadequate for explaining the observed patterns. Further comprehensive analyses of range evolution are necessary to delve deeper into the interplay among key opportunities, key innovation, and species diversification.
When is noisy state information at the encoder as useless as no information or as good as noise-free state?

For any binary-input channel with perfect state information at the decoder, if the mutual information between the noisy state observation at the encoder and the true channel state is below a positive threshold determined solely by the state distribution, then the capacity is the same as that with no encoder side information. A complementary phenomenon is revealed for a similarly defined quantity.
Identifying small-molecules binding sites in RNA conformational ensembles with SHAMAN

The rational targeting of RNA with small molecules is hampered by our still limited understanding of RNA structural and dynamic properties. Most in silico tools for binding site identification rely on static structures and therefore cannot face the challenges posed by the dynamic nature of RNA molecules. Here, we present SHAMAN, a computational technique to identify potential small-molecule binding sites in RNA structural ensembles. SHAMAN enables exploring the conformational landscape of RNA with atomistic molecular dynamics and at the same time identifying RNA pockets in an efficient way with the aid of probes and enhanced-sampling techniques. In our benchmark composed of large, structured riboswitches as well as small, flexible viral RNAs, SHAMAN successfully identified all the experimentally resolved pockets and ranked them among the most favorite probe hotspots. Overall, SHAMAN sets a solid foundation for future drug design efforts targeting RNA with small molecules, effectively addressing the long-standing challenges in the field.
Full diversity blind space-time block codes

In this paper, we consider the systematic design of a space-time block code for a wireless communication system with multiple transmitter-receiver antennas and flat fading, in which channel state information is completely unknown. From the viewpoint of blind signal processing, we give a necessary and sufficient condition for the unique identification of the MIMO flat fading channel and transmitted signal. Then, we establish some novel unique factorizations for a pair of coprime P-ary and Q-ary Phase Shift Keying (PSK) constellations. With this and currently available coherent space-time block code designs we develop a method to systematically construct full diversity blind nonunitary space-time block codes, as well as unitary codes by just performing the QR decomposition of the non-unitary codes. We prove that under a noise-free environment, our code design can guarantee that the transmitted signals and the channel coefficients are uniquely identified.
EasyFlow: An open source, user friendly cytometry analyzer with graphic user interface (GUI)

Flow cytometry enables quantitative measurements of fluorescence in single cells. The technique was widely used for immunology to identify populations with different surface protein markers. More recently, the usage of flow cytometry has been extended to additional readouts, including intracellular proteins and fluorescent protein transgenes, and is widely utilized to study development, systems biology, microbiology, and many other fields. A common file format (FCS format, defined by International Society for Advancement of Cytometry (ISAC)) has been universally adopted, facilitating data exchange between different machines. A diverse spectrum of software packages have been developed for analysis of flow cytometry data. However, those are either 1) costly proprietary softwares, 2) open source packages with prerequisite installation of R or Python and sometimes require users to have experience in coding or 3) online tools that are limiting for analysis of large data sets. Here we present EasyFlow, an open source flow cytometry analysis GUI based on Matlab or Python, that can be installed and run locally cross-platform-ly (Windows and MacOS), without prerequisite user having previous knowledge on coding. The python version (EasyFlowQ) is also developed on a popular plotting framework (Matplotlib) and modern user interface (UI) toolkit (Qt), allowing more advanced users to customize and keep contributing to the software, as well as its tutorials. Overall, EasyFlow serves as a simple-to-use tool for inexperienced users with little coding experience to use locally, as well as a platform for advanced users to further customize for their own needs.
Multiscale spatial mapping of cell populations across anatomical sites in healthy human skin and basal cell carcinoma

Our understanding of how human skin cells differ according to anatomical site and tumour formation is limited. To address this we have created a multi-scale spatial atlas of healthy skin and basal cell carcinoma (BCC), incorporating in vivo optical coherence tomography, single cell RNA sequencing, spatial global transcriptional profiling and in situ sequencing. Computational spatial deconvolution and projection revealed the localisation of distinct cell populations to specific tissue contexts. Although cell populations were conserved between healthy anatomical sites and in BCC, mesenchymal cell populations including fibroblasts and pericytes retained signatures of developmental origin. Spatial profiling and in silico lineage tracing support a hair follicle origin for BCC and demonstrate that cancer-associated fibroblasts are an expansion of a POSTN+ subpopulation associated with hair follicles in healthy skin. RGS5+ pericytes are also expanded in BCC suggesting a role in vascular remodelling. We propose that the identity of mesenchymal cell populations is regulated by signals emanating from adjacent structures and that these signals are repurposed to promote the expansion of skin cancer stroma. The resource we have created is publicly available in an interactive format for the research community. Significance statement Single cells RNA sequencing has revolutionised cell biology, enabling high resolution analysis of cell types and states within human tissues. Here, we report a comprehensive spatial atlas of adult human skin across different anatomical sites and basal cell carcinoma (BCC) - the most common form of skin cancer - encompassing in vivo optical coherence tomography, single cell RNA sequencing, global spatial transcriptomic profiling and in situ sequencing. In combination these modalities have allowed us to assemble a comprehensive nuclear-resolution atlas of cellular identity in health and disease.
Infant gut bacteriophage strain persistence during the first three years of life

Bacteriophages are key components of gut microbiomes, yet the phage colonization process in the infant gut remains uncertain. Here, we established a large phage sequence database and used strain-resolved analyses to investigate phage succession in infants throughout the first three years of life. Analysis of 819 fecal metagenomes collected from 28 full-term and 24 preterm infants and their mothers revealed that early-life phageome richness increased over time and reached adult-like complexity by age three. Approximately 9% of early phage colonizers, mostly maternally transmitted and infecting Bacteroides, persisted for three years and were more prevalent in full-term than in preterm infants. Although rare, phages with stop codon reassignment were more likely to persist than non-recoded phages and generally displayed an increase in in-frame re-assigned stop codons over three years. Overall, maternal seeding, stop codon reassignment, host CRISPR-Cas locus prevalence, and diverse phage populations contribute to stable viral colonization.
Projective oblique plane structured illumination microscopy

Structured illumination microscopy (SIM) can double the spatial resolution of a fluorescence microscope and video rate live cell imaging in a two-dimensional format has been demonstrated. However, rapid implementations of 2D SIM typically only cover a narrow slice of the sample immediately at the coverslip, with most of the cellular volume out of reach. Here we implement oblique plane structured illumination microscopy (OPSIM) in a projection format to rapidly image an entire cell in a 2D SIM framework. As no mechanical scanning of the sample or objective is involved, this technique has the potential for rapid projection imaging with doubled resolution. We characterize the spatial resolution with fluorescent nanospheres, compare projection and 3D imaging using OPSIM and image mitochondria and ER dynamics across an entire cell at up to 2.7 Hz. To our knowledge, this represents the fastest whole cell SIM imaging to date.
Interaction of PINK1 with nucleotides and kinetin

PINK1 is a ubiquitin kinase that accumulates on damaged mitochondria to trigger mitophagy, and PINK1 loss-of-function mutations cause early onset Parkinson’s disease. Nucleotide analogues such as kinetin triphosphate (KTP) have been suggested to enhance PINK1 activity and may represent a therapeutic strategy for the treatment of Parkinson’s disease. Here, we investigate the interaction of PINK1 with nucleotides, including KTP. We establish a cryo-EM platform exploiting the previously observed dodecamer assembly of Pediculus humanus corporis (Ph) PINK1 to determine PINK1 structures bound to AMP-PNP and ADP, which reveal unexpected conformational changes in the kinase N-lobe to enable PINK1 to form a ubiquitin binding site. Strikingly, we find that KTP is unable to bind PhPINK1 or human (Hs) PINK1 due to a steric clash with the kinase ‘gatekeeper’ residue. Mutation of the gatekeeper to Ala or Gly is required to enable PINK1 to bind and utilise KTP as a phosphate donor in ubiquitin phosphorylation and mitophagy. Indeed, HsPINK1 M318G can be used to conditionally uncouple PINK1 stabilisation and activity on mitochondria.
Purifying selection and adaptive evolution proximate to the zoonosis of SARS-CoV-1 and SARS-CoV-2

Over the past two decades the pace of spillovers from animal viruses to humans has accelerated, with COVID-19 becoming the most deadly zoonotic disease in living memory. Prior to zoonosis, it is conceivable that the virus might largely be subjected to purifying selection, requiring no additional selective changes for successful zoonotic transmission. Alternatively, selective changes occurring in the reservoir species may coincidentally preadapt the virus for human-to-human transmission, facilitating spread upon cross-species exposure. Here we quantify changes in the genomes of SARS-CoV-2 and SARS-CoV-1 proximate to zoonosis to evaluate the selection pressures acting on the viruses. Application of molecular-evolutionary and population-genetic approaches to quantify site-specific selection within both SARS-CoV genomes revealed strong purifying selection across many genes at the time of zoonosis. Even in the viral surface-protein Spike that has been fast-evolving in humans, there is little evidence of positive selection proximate to zoonosis. Nevertheless, in SARS-CoV-2, NSP12, a core protein for viral replication, exhibited a region under adaptive selection proximate to zoonosis. Furthermore, in both SARS-CoV-1 and SARS-CoV-2, regions of adaptive selection proximate to zoonosis were found in ORF7a, a putative Major Histocompatibility Complex modulatory gene. These findings suggest that these replication and immunomodulatory proteins have played a previously underappreciated role in the adaptation of SARS coronaviruses to human hosts.
A New Mathematical Model for Haplotype Inference from Genotypes by Parsimony Criterion

هدیکچ ِلبغه خیبسَلدبّ هبجٌشعا خیبسًَص سا بّ سا يىی بّ لیبغه يمیا زميوّا یزمعا يشمغیس ربيممبیر ُسَمو نمْه ِ لبمغه ِ مث لميلد یربويث ىبهرد ٍ ـيخؾس رد ىآ ىاٍازف یبّدزثربو تمخَه ِمو زمعا يمجلل كازها ٍ زویاشلآ ،زثبید ىَچوّ يىيشًص یبّ رد ىازگؾٍّضد زثبلر ِیارا لذه نشیرَگلا يوازى ٍ زشْث يمبیر یبّ بغه يیا لو یازث زساربو یبّ يملػ یزمعا ُذؽ ِل نمغر ؼٍّضد ىاٍازف یبّ ، ليلد ِث NP-hard ىدَث ِلبغه یارا ِث سبيً ىبٌچوّ لذه ِ ػٍر دَجْث بی ٍ ذیذخ یبّ طبمغوا يلجل یبّ يه خیبسَلدبّ هبجٌشعا یدَؽ يه ىبيث يسٍبفشه یبّربيؼه زحس بّ سا يىی يًَويعربد یدَؽ نْه يیزس بّ ىآ ِملبمه يیا رد ٍ زع ِلبغه ػٍر یزعا ِشفزگ رازل يعرزث درَه ربيؼه يیا بث لو یبّ ِلبغه خیبسَلدبّ هبجٌشعا خیبسًَص سا بّ يًَويعربد ربيؼه بث بّ يه نيغمس يجیزمس ٍ كيلد ِشعد ٍد ِث َؽ ػٍر تلغا ید ِث ار ِلبغه كيلد یبّ هی ررَف ِلبغه ِهبًزث يحمف داذمػا بث یشیر لَهزف يه یذٌث ِلبمه رد ازيخا یذٌٌو مبمً ِث كيلد لذه هی یا HI Base -10 ِلبمغه يمیا یازمث ِ میارا زمّ ِمث اذمشثا ِمو ُذمؽ يه ليىؾس داذػا يیا طبعا زث ار لذه ظذع ٍ ُدزو زظبٌشه دذػ هی خیبسًَص ٍ خیبسَلدبّ ىآرد ِو ذّد یذيل ٍ زيغشه چيّ ُبگیبخ زظبٌشه يوً ليوحس ِلبغه ِث رَگیسٍزشّ یبّ يؽ بث شيً ِلبمه يیا رد یدَؽ َُ خیبسًَص ِث رٍبفشه یا زظبمٌشه یداذمػا بّ هی داذػا يیا طبعا زث ٍ ُدزو ِلبغه ِهبًزث يه ِشخيهآ ٍ يیٍدٍد یبّزيغشه بث یشیر لذمه ،رلایذمجس يمیا ِمديشً رد ینیسبع یبّزيغشه ٍ ِشؽاذً يحف دذػ زيغشه ،ذیذخ نو زس ِث زجغً ی HI Base – 10 ٍ زميغشه چيمّ ذیذخ لذه رد ٍُلاػ ِث یدراد ُبگیبخ زظبٌشه یذيل ُبگیبخ ِث بّزيغشه ٍ دراذً دَخٍ رَگیسَوّ یبّ يه ُداد ؿبقشخا رَگیسٍزشّ یبّ ِمخَس بمث یذًَمؽ ُبگیبخ دبیس داذؼس ِث ُبگیبخ بث ِغیبمه رد رَگیسَوّ یبّ ُداد رد رَگیسٍزشّ یبّ ـخمؾه لذمه يمیا ػسرا يمؼلاٍ یبّ يه یدَؽ
Measurement of Insertion Losses of Aqueous Calcium and Sodium Chloride Solutions in Liquid and Solid Aggregate States in a Coaxial Cell

This paper presents the results of measuring frequency dependences of S-parameters of various aqueous solutions depending on their aggregate state (liquid, solid) in the coaxial cell with regard to temperature. The measurement was performed in the temperature ranges of 0-50°C and -50-0°C, and the frequency ranges of 0.01-12 GHz. It was shown that the values of S-parameters are influenced not only by the dissolved chemical substances, but also by their concentration. To analyze the electrophysical properties of aqueous solutions, the values of the level of losses introduced by them were calculated. It is shown that temperature has a minimal effect on the level of insertion losses when placed inside a coaxial cell for a plastic container, as well as aqueous solutions in the same aggregate state. The frequency dependences of S-parameters of solutions in liquid and solid aggregate states were visualized using the principal component analysis. The relationship between the chemical composition of the solution and its aggregate state was revealed.
Implementation of a ROS Node for Roaming Between APs for an Autonomous Mobile Robot

The wide field of implementation of mobile robotics has increased the need for remote interconnection of a control and visualization station with the robot to monitor the data acquired by the robot’s peripherals, with wireless networks based on the 802.11 protocol being the most optimal for its ease of implementation, bandwidth and operating frequencies. Within these networks, effective service transfer between the Access Points and the robot must be sought so as not to lose communication and for it to send the data in real time by it. For this reason, in this article the implementation of a ROS node that performs the Roaming process based on the intensity of the signal received RSSI from the Access Points of the network is presented. This node runs in parallel to the teleoperated and autonomous operation of the robot. With this node, it was possible to maintain an average link status of 81.15%, signal strength 53.18 dBm, and throughput for the download link of 163.45 Kbps and upload link of 13.45 Mbps, sufficient to maintain a stable interconnection between the control and visualization station and the robot.