Miracle-dz/UniFAR-FTUs huggingface dataset:
Interconnected assembly factors regulate the biogenesis of mitoribosomal large subunit

Mitoribosomes synthesize essential proteins encoded in mitochondria. They consist of RNA and protein components, coordinated assembly of which is critical for function. We used mitoribosomes with reduced RNA and increased protein mass from a mammalian parasite Trypanosoma brucei to provide insights into the biogenesis of mitoribosomal large subunit.Structural characterisation of a stable assembly intermediate revealed 16 assembly factors, 10 of which were not previously implicated in biogenesis. Most of the reported factors are also encoded in mammalian genomes. In the structure, the assembly factors form a protein network that spans over 180 Å, shielding the ribosomal RNA surface. The entire central protuberance and L7/L12 stalk are not assembled, and require removal of the factors and remodeling to become functional sites. The conserved mt-RbgA and mt-EngA are bound together in proximity to the peptidyl transferase center. A mitochondrial acyl-carrier protein plays a role in stably docking the L1 stalk that needs to be repositioned during maturation. Together, the extensive network of the assembly factors stabilizes the immature domains and connects between the functionally important regions.
SCARECROW gene function is required for photosynthetic development in maize

C4 photosynthesis in grasses relies on a specialized leaf anatomy. In maize, this ‘Kranz’ leaf anatomy is patterned in part by the duplicated SCARECROW (SCR) genes ZmSCR1 and ZmSCR1h. Here we show that in addition to patterning defects, chlorophyll content and levels of transcripts encoding Golden2-like regulators of chloroplast development are significantly lower in Zmscr1;Zmscr1h mutants than in wild-type. These perturbations are not associated with changes in chloroplast number, size or ultrastructure. However, the maximum rates of carboxylation by ribulose bisphosphate carboxylase/oxygenase (RuBisCO, Vcmax) and phosphoenolpyruvate carboxylase (PEPC, Vpmax) are both reduced, leading to perturbed plant growth. The CO2 compensation point and 13C‰ of Zmscr1;Zmscr1h plants are both normal, indicating that a canonical C4 cycle is operating, albeit at reduced overall capacity. Taken together, our results reveal that the maize SCR genes, either directly or indirectly, play a role in photosynthetic development. Significance statement SCARECROW (SCR) is one of the best studied plant developmental regulators, however, its role in downstream plant physiology is less well-understood. Here, we have demonstrated that SCR is required to establish and/or maintain photosynthetic capacity in maize leaves.
THE EFFECT OF BACTERIOPHAGE T4 AND PB-1 INFECTION WITH TOBRAMYCIN ON THE SURVIVAL OF ESCHERICHIA COLI AND PSEUDOMONAS AERUGINOSA BIOFILMS

section 107). Consistent with fair use as defined in the Copyright Laws, brief quotations from this material are allowed with proper acknowledgement. Use of this material for financial gain without the author's express written permission is not allowed. As the copyright holder of this work I, Lindsey B. Coulter, authorize duplication of this work, in whole or in part, for educational or scholarly purposes only. v ACKNOWLEDGEMENTS I would like to thank my family for their support, my boyfriend, Dustin, for ensuring I wouldn't starve after a late night and making my life with Excel so much easier, Ernie Valenzuela for helping me get my protocol back on the right track, my committee, Dr. McLean and Dr. Rohde, for taking the time to help me through my thesis work, and my committee advisor Dr. Aron for taking the time to answer all my questions. Populations of bacterial cells growing as biofilms demonstrate greater resistance to antibiotics compared to planktonic cells. Consequently, there is renewed interest in bacteriophage therapy as an alternative to antimicrobial chemotherapy. Although phages may be more effective than antibiotics alone in reducing biofilm mass, they are often not able to eradicate the biofilm. The aim of this study was to determine if bacteriophage in combination with an antimicrobial would be more effective in decreasing biofilm mass compared to the use of either antibiotic or phage alone. It was also of interest to determine if the combination of phage and antibiotic could reduce the emergence of either antibiotic or phage resistant mutants. Escherichia coli or Pseudomonas aeruginosa 48 h biofilms were challenged with phage T4 or PB-1, respectively, in combination with tobramycin. At 6 h and 24 h post challenge, total cells, tobramycin resistant cells, and x phage resistant cells were determined. The use of phage in combination with antibiotic resulted in an enhanced reduction of E. coli biofilms compared to either phage or antibiotic alone. The combination of phage and antibiotic resulted in a reduction in P. aeruginosa biofilms compared to phage alone. The combination of phage with antibiotic resulted in a reduced emergence of phage resistant (39% to 99%) and antibiotic resistant (26% to >99%) cells compared to treatment with either phage or antibiotic alone. The study suggests the combination of phage and antibiotic is more effective in reducing both biofilm mass and the emergence of resistance than the use of either phage or antibiotic alone. …
Exploration of Long Non-coding RNAs and Circular RNAs in Porcine Milk Exosomes

RNA in milk exosomes can be absorbed in the mammalian intestinal tract and function in gene expression regulations. Our previous work demonstrated that porcine milk exosomes (PME) contain large amounts of miRNAs and mRNAs. Increasing evidence suggests that long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) are of particular interest, given their key role in diverse biological processes of animals. However, the expression profiles and the potential functions of lncRNAs and circRNAs in PME are still unknown. In the present study, we isolated PME by ultracentrifugation and performed a comprehensive analysis of lncRNA and circRNA in PME by using RNA sequencing. As a result, 2,466 novel lncRNAs, 809 annotated lncRNAs, and 61 circRNAs were identified in PME. The lncRNAs shared similar characteristics with other mammals in terms of length, exon number, and open reading frames. However, lncRNAs showed a higher level compared with mRNAs. Eight lncRNAs and five circRNAs in PME were selected for PCR identification. A functional enrichment analysis on the target genes of lncRNAs indicated that these genes were involved in cellular macromolecule metabolic, RNA metabolic, and immune processes. The circRNAs host genes were enriched in nucleic acid binding and adherence junction. We also evaluated the potential interaction targets between miRNAs and PME lncRNAs or circRNAs, and the results showed that the PME lncRNAs and the circRNAs have a high density of miRNA target sites. The top 20 highly expressed lncRNAs were found to interact with the proliferation-related miRNAs, and the circRNAs potentially targeted many miRNAs that are associated with the intestinal barrier. This study is the first to provide a resource for lncRNA and circRNA research of porcine milk. Moreover, the potential interaction between lncRNA/circRNA and miRNA is revealed. The present study expands our knowledge of non-coding RNAs in milk, and additional research is necessary to confirm their exactly physiological functions.
Short-Term Sensorimotor Deprivation Impacts Feedforward and Feedback Processes of Motor Control

Sensory loss involves irreversible behavioral and neural changes. Paradigms of short-term limb immobilization mimic deprivation of proprioceptive inputs and motor commands, which occur after the loss of limb use. While several studies have shown that short-term immobilization induced motor control impairments, the origin of such modifications is an open question. A Fitts’ pointing task was conducted, and kinematic analyses were performed to assess whether the feedforward and/or feedback processes of motor control were impacted. The Fitts’ pointing task specifically required dealing with spatial and temporal aspects (speed-accuracy trade-off) to be as fast and as accurate as possible. Forty trials were performed on two consecutive days by Control and Immobilized participants who wore a splint on the right arm during this 24 h period. The immobilization modified the motor control in a way that the full spatiotemporal structure of the pointing movements differed: A global slowdown appeared. The acceleration and deceleration phases were both longer, suggesting that immobilization impacted both the early impulse phase based on sensorimotor expectations and the later online correction phase based on feedback use. First, the feedforward control may have been less efficient, probably because the internal model of the immobilized limb would have been incorrectly updated relative to internal and environmental constraints. Second, immobilized participants may have taken more time to correct their movements and precisely reach the target, as the processing of proprioceptive feedback might have been altered.
The first biogeographical map

Unbeknownst to many historians of biology, the first biogeographical map was published in the third edition of the Flore française by Lamarck and Candolle in 1805, the same year in which Humboldt's famous Essai sur la Geographie appeared. Lamarck and Candolle's map marks the beginning of a descriptive or classificatory biogeography focusing on the study of biota rather than on the distributional pathways of taxa. The map is relevant because it heralds the beginning of the creation of biogeographical maps popularized by zoogeographers in the mid‐ to late nineteenth century together with the study of biogeographical regions.
The primary motor cortex prospectively computes the spinal reflex

The spinal reflex transforms sensory signals to generate muscle activity. However, it is unknown how the motor cortex (MCx) takes the spinal reflex into account when performing voluntary limb movements. We simultaneously recorded the activity of the MCx, afferent neurons, and forelimb muscles in behaving monkeys. We decomposed muscle activity into subcomponents explained by the MCx or afferent activity using linear models. Long preceding activity in the MCx, which is responsible for subsequent afferent activity, had the same spatiotemporal contribution to muscle activity as afferent activity, indicating that the MCx drives muscle activity not only by direct descending activation but also by trans-afferent descending activation. Therefore, the MCx implements internal models that prospectively estimate muscle activation via the spinal reflex for precise movement control.
Variation in the Nesting Habits of Clapper Rails in Tidal Marshes of the Northern Gulf of Mexico

Abstract. To document nest survival and habitat differences in the nesting habitats of Clapper Rails (Rallus longirostis) in tidal marshes of the northern Gulf of Mexico, we monitored 76 active nests within the Pascagoula River Marsh Coastal Preserve (a freshwater-dominated estuary) and the Grand Bay National Estuarine Research Reserve (a marine-influenced estuary) in coastal Mississippi from 2005 to 2007. During 2006, we measured the height of each Clapper Rail nest, sampled vegetation at active Clapper Rail nests and at random locations, and measured the distance to the nearest tidally influenced body of water and the average height and density of vegetation. Early in the breeding season, the average nest height was lower at the Pascagoula (36 cm) than at Grand Bay (60 cm), but, as the season progressed, nest height increased at the Pascagoula only. Within both estuaries, Clapper Rail nest sites were more structurally complex than at random locations and were associated with a greater diversity of vegetation. Overall, daily survival rates of Clapper Rail nests were relatively high (0.97–0.99), with the majority of nest loss apparently the result of tidal flooding. Our results suggest that where diverse habitat was available, Clapper Rails varied the height of their nests as a mechanism to avoid nest loss from tidal flooding. Habitat alteration from factors such as sea-level rise and coastal development may lead to lower nest success because of a loss of diverse nesting habitat.
Mapping of stock exchanges: contagion from a new perspective

ABSTRACT This paper addresses the contagion problem between stock exchanges and uses self-organizing maps (SOMs) to develop a two-dimensional map based on five market variables from 48 stock exchanges around the world for the 2000–2012 period. The study addresses markets worldwide that have different levels of economic development. Using five market variables, we group stock exchanges into distinctive clusters and analyze their similarities, differences, and dynamics. The technique applied, artificial neural networks (ANNs), is a non-parametric visualization tool to study the dynamics of the markets worldwide following a non-traditional perspective based on the specific formation of groups and their evolution. Each group is defined by the Euclidean distances between markets. There are certain common features, both economic and geographic, within the migrant and static exchanges, which offer new insights. By applying the standard contagion methodology to the resulting groups, we study the spread of the subprime crisis and find evidence of contagion, as well as a high interdependence between markets for the entire period under consideration.
SOME STUDIES ON BIO-ECOLOGY OF PHEASANT TAILED JACANA, HYDROPHASIANUS CHIRURGUS IN PUNJAB, PAKISTAN

Pheasant Tailed Jacana, Hydrophasianus chirurgus is only beautiful bird maintain its presence in abandoned wetlands of Punjab during summer season.This study was designed to study the population status and its future potentials to estimate the threats and to propose the measures for its conservation if required. Literature suggested sites were selected and schedule of visits month and year wise was developed and sites were visited accordingly, data gathered was analyzed statistically.The population distribution appears, between 298 and 347 highest (83-96) at Marala and lowest (21-57) at Balloki, while density found highest (3/km2) and lowest (0.3/ km2), being the migratory bird March was observed as start of arrival and October was observed as completion of departure from the study areas.Female to male ratio appears 1:0.75 while juvenile to adult ratio observed 1:0.35 are sign of population stability.Physical factors of the habitat such as temperature, pH and phytosociological studies of the habitat distribution and frequency of rooted vegetation species were recorded to understand their association with the species.This shows 32 species distributed in 4 vegetation types within the habitats lies in study areas.The studies on biology of this bird were focused on food and feeding, food consumption which revealed that 56.3% of its food is consists of plant matter and 27.3% on animal matter. Breeding biology studies suggests the clutch size remains between 1-4 eggs, and most of the fertile females laid 2 consecutive clutches to hand over two different males for hatching and chick rearing, incubation calculated of 25-29 days hatchability found around 80%. Defensive responses, egg laying and chick care were observed to understand general behavior of the species. The results of this study suggested that major threats to Pheasant Tailed Jacana are the commercial activities within its habitat and immediate adjacent to them, which could be regulated for its sustainability.
Generation of Realistic Synthetic Validation Healthcare Datasets Using Generative Adversarial Networks.

BACKGROUND Assurance of digital health interventions involves, amongst others, clinical validation, which requires large datasets to test the application in realistic clinical scenarios. Development of such datasets is time consuming and challenging in terms of maintaining patient anonymity and consent. OBJECTIVE The development of synthetic datasets that maintain the statistical properties of the real datasets. METHOD An artificial neural network based, generative adversarial network was implemented and trained, using numerical and categorical variables, including ICD-9 codes from the MIMIC III dataset, to produce a synthetic dataset. RESULTS The synthetic dataset, exhibits a correlation matrix highly similar to the real dataset, good Jaccard similarity and passing the KS test. CONCLUSIONS The proof of concept was successful with the approach being promising for further work.
The Emergence of Chikungunya ECSA Lineage in a Mayaro Endemic Region on the Southern Border of the Amazon Forest

Anthropic changes on the edges of the tropical forests may facilitate the emergence of new viruses from the sylvatic environment and the simultaneous circulation of sylvatic and urban viruses in the human population. In this study, we investigated the presence of arboviruses (arthropod-borne viruses) in the sera of 354 patients, sampled from February 2014 to October 2018 in Sinop city. We sequenced the complete genomes of one chikungunya virus (CHIKV)-positive and one out of the 33 Mayaro virus (MAYV)-positive samples. The CHIKV genome obtained here belongs to the East/Central/South African (ECSA) genotype and the MAYV genome belongs to the L genotype. These genomes clustered with other viral strains from different Brazilian states, but the CHIKV strain circulating in Sinop did not cluster with other genomes from the Mato Grosso state, suggesting that at least two independent introductions of this virus occurred in Mato Grosso. Interestingly, the arrival of CHIKV in Sinop seems to not have caused a surge in human cases in the following years, as observed in the rest of the state, suggesting that cross immunity from MAYV infection might be protecting the population from CHIKV infection. These findings reinforce the need for continued genomic surveillance in order to evaluate how simultaneously circulating alphaviruses infecting the human population will unfold.
Problems of development of resistance to phosphine by insect pests of stored grains1

The FAO global survey of pesticide sensitivity of stored grain pests in 1972–73 showed an overall incidence of phosphine resistance of 9.7% in insect strains from 82 countries, especially in Tribolium spp. and Rhyzopertha dominica. The levels of resistance increased under laboratory selection. Generally, eggs and pupae were found to be more tolerant, and fumigation doses have to be designed with these stages in mind. With increasing worldwide use of phosphine, resistance has become more frequent and occurs at a higher level and in other species (Cryptolestes ferrugineus, Oryzaephilus surinamensis). Studies of fumigation under different conditions in Bangladesh showed that common procedures, without use of sheets, led to chronic underdosing, creating ideal conditions for the selection of resistant strains. Such strains are very likely to be introduced into the EPPO region and established there. While inspection and control procedures in ports could limit this risk, these are costly and impractical. The problem is best tackled at source, by supporting projects aimed at improving the conditions under which grain is stored and fumigated in developing countries.
Nanotoxicology and Nanosafety: Safety-by-Design and Testing at a Glance

This review offers a systematic discussion about nanotoxicology and nanosafety associated with nanomaterials during manufacture and further biomedical applications. A detailed introduction on nanomaterials and their most frequently uses, followed by the critical risk aspects related to regulatory uses and commercialization, is provided. Moreover, the impact of nanotoxicology in research over the last decades is discussed, together with the currently available toxicological methods in cell cultures (in vitro) and in living organisms (in vivo). A special focus is given to inorganic nanoparticles such as titanium dioxide nanoparticles (TiO2NPs) and silver nanoparticles (AgNPs). In vitro and in vivo case studies for the selected nanoparticles are discussed. The final part of this work describes the significance of nano-security for both risk assessment and environmental nanosafety. “Safety-by-Design” is defined as a starting point consisting on the implementation of the principles of drug discovery and development. The concept “Safety-by-Design” appears to be a way to “ensure safety”, but the superficiality and the lack of articulation with which it is treated still raises many doubts. Although the approach of “Safety-by-Design” to the principles of drug development has helped in the assessment of the toxicity of nanomaterials, a combination of scientific efforts is constantly urgent to ensure the consistency of methods and processes. This will ensure that the quality of nanomaterials is controlled and their safe development is promoted. Safety issues are considered strategies for discovering novel toxicological-related mechanisms still needed to be promoted.
Implementation-Independent Representation for Deep Convolutional Neural Networks and Humans in Processing Faces

Deep convolutional neural networks (DCNN) nowadays can match and even outperform human performance in challenging complex tasks. However, it remains unknown whether DCNNs achieve human-like performance through human-like processes; that is, do DCNNs use similar internal representations to achieve the task as humans? Here we applied a reverse-correlation method to reconstruct the internal representations when DCNNs and human observers classified genders of faces. We found that human observers and a DCNN pre-trained for face identification, VGG-Face, showed high similarity between their “classification images” in gender classification, suggesting similar critical information utilized in this task. Further analyses showed that the similarity of the representations was mainly observed at low spatial frequencies, which are critical for gender classification in human studies. Importantly, the prior task experience, which the VGG-Face was pre-trained for processing faces at the subordinate level (i.e., identification) as humans do, seemed necessary for such representational similarity, because AlexNet, a DCNN pre-trained to process objects at the basic level (i.e., categorization), succeeded in gender classification but relied on a completely different representation. In sum, although DCNNs and humans rely on different sets of hardware to process faces, they can use a similar representation, possibly from similar prior task experiences, to achieve the same computation goal. Therefore, our study provides the first empirical evidence supporting the hypothesis of implementation-independent representation.
Recommendations on Recent Proposals for the Classification of Shigellae

A number of recent proposals to change the classification of shigellae were studied by the International Committee on Systematic Bacteriology Subcommittee on the Taxonomy of Enterobacteriaceae, which recommended adoption of the following proposals: (i) subdivision of Shigella flexneri serotype 5 into two subserotypes, 5a and 5b; (ii) reduction of the number of S. flexneri serotype 3 subserotypes from three to two; (iii) that Shigella sp. provisional serotype 2000-53 is not a Shigella, but an Escherichia coli; (iv) that provisional Shigella sp. serotypes 3873-50 and 3341-55 be added to the Shigella serotyping scheme as Shigella dysenteriae serotypes 11 and 12; (v) that provisional Shigella sp. serotypes 2710-54 and 3615-53 be added to the Shigella serotyping scheme as Shigella boydii serotypes 16 and 17; (vi) that Shigella sp. strain E 10163 and similar strains be added to the Shigella serotyping scheme as S. boydii serotype 18; and (vii) that provisional Shigella sp. serotype 1621-54 retain its provisional status pending study of additional strains.