Miracle-dz/UniFAR-FTUs huggingface dataset:
Phylogenetically Clustered Extinction Risks Do Not Substantially Prune the Tree of Life

Anthropogenic activities have increased the rate of biological extinction many-fold. Recent empirical studies suggest that projected extinction may lead to extensive loss to the Tree of Life, much more than if extinction were random. One suggested cause is that extinction risk is heritable (phylogenetically patterned), such that entire higher groups will be lost. We show here with simulation that phylogenetically clustered extinction risks are necessary but not sufficient for the extensive loss of phylogenetic diversity (PD) compared to random extinction. We simulated Yule trees and evolved extinction risks at various levels of heritability (measured using Pagel's ). At most levels of heritability ( in range of 0 to 10), mean values of extinction risk (range 0.25 to 0.75), tree sizes (64 to 128 tips), tree balance and temporal heterogeneity of diversification rates (Yule and coalescent trees), extinction risks do not substantially increase the loss of PD in these trees when compared to random extinction. The maximum loss of PD (20% above random) was only associated with the combination of extremely excessive values of phylogenetic signal, high mean species' extinction probabilities, and extreme (coalescent) tree shapes. Interestingly, we also observed a decline in the rate of increase in the loss of PD at high phylogenetic clustering of extinction risks. Our results suggest that the interplay between various aspects of tree shape and a predisposition of higher extinction risks in species-poor clades is required to explain the substantial pruning of the Tree of Life.
Reproductive status affects the feeding ecology and social association patterns of female squirrel monkeys (Saimiri collinsi) in an Amazonian rainforest

When making foraging decisions, female primates may follow specific behavioral strategies that reflect their reproductive state. Lactation is considered the most energetically costly phase for females, but we argue that gestation is also energetically expensive for squirrel monkeys. In this study, we examined whether female squirrel monkeys (a seasonally breeding primate) in different reproductive phases showed significant differences in their foraging ecology. We sampled two wild groups of squirrel monkeys (Saimiri collinsi) using the focal animal method, during 12 months (June 2014 to May 2015). During this time, we quantified the effect of reproductive state (mating, gestation, and lactation) and sex (females vs. males) on activity budgets, foraging efficiency, dietary composition, and nearest neighbors. We found significant effects of both sex and reproductive phase on the mean proportion of time spent foraging, resting, traveling, and being social. Females consumed more insects than did males at all times; among females, time spent eating prey and fruit varied according to reproductive state. These data suggest that, due to their life history and seasonal breeding, reproduction is a costly activity for female Saimiri, and not only during lactation. Therefore, adopting the appropriate behavioral strategies is essential to reduce energetic deficits in females.
Walking an unknown street with bounded detour

A polygon with two distinguished vertices, s and g, is called a street if the two boundary chains from s to g are mutually weakly visible. For a mobile robot with onboard vision, a strategy for finding a short path from s to g in a street not known in advance is described, and it is proved that the length of the path created does not exceed 1+3 pi /2 times the length of the shortest path from s to g. Experiments suggest that the strategy is much better than this, as no ratio bigger than 1.8 has yet been observed. This is complemented by a lower bound of 1.41 for the relative detour each strategy can be forced to generate. <<ETX>>
Near-miss maternal morbidity from severe haemorrhage at caesarean section: A process and structure audit of system deficiencies in South Africa.

BACKGROUND A rising caesarean section rate and substandard peri-operative care are believed to be the main reasons for recent increases in maternal deaths from bleeding during and after caesarean section (BDACS) in South Africa (SA). The Donabedian model assumes that clinical outcomes are influenced by healthcare workers and the healthcare system. OBJECTIVES To evaluate near-miss cases from BDACS with regard to health system structure (resources and facilities) and process (patient care). METHODS A cross-sectional prospective study was conducted in greater Johannesburg, SA. Data of women who had near-miss-related BDACS were collected by means of ongoing surveillance at 13 public hospitals. The World Health Organization intervention criteria were used to identify near-miss cases. A comparison of structure and process between the healthcare facilities was conducted. RESULTS Of 20 527 caesarean sections , there were 93 near misses and 7 maternal deaths from BDACS. Dominant risk factors for near misses were previous caesarean section (43.9%), anaemia (25.3%) and pregnancy-induced hypertension (28.6%). Eighteen women were transferred to higher levels of care, and 8 (44.4%) experienced transport delays of >1 hour. The caesarean section decision-to-incision interval (DII) was ≥60 minutes in 77 of 86 women, with an average interval of 4 hours. Structural deficiencies were frequently present in district hospitals, and there were serious delays in ambulance transfer and DIIs at all levels of care. CONCLUSION The majority of the women had risk factors for BDACS. There were major ambulance delays and lack of facilities, mostly in district hospitals. All women required life-saving interventions, but could not access appropriate care timeously. Prevention and management of BDACS require a fully functional health system.
The Extracellular Wall-Bound β-N-Acetylglucosaminidase from Lactobacillus casei Is Involved in the Metabolism of the Human Milk Oligosaccharide Lacto-N-Triose

ABSTRACT Human milk oligosaccharides (HMOs) are considered to play a key role in establishing and maintaining the infant gut microbiota. Lacto-N-triose forms part of both type 1 and type 2 HMOs and also of the glycan moieties of glycoproteins. Upstream of the previously characterized gene cluster involved in lacto-N-biose and galacto-N-biose metabolism from Lactobacillus casei BL23, there are two genes, bnaG and manA, encoding a β-N-acetylglucosaminidase precursor and a mannose-6-phosphate isomerase, respectively. In this work, we show that L. casei is able to grow in the presence of lacto-N-triose as a carbon source. Inactivation of bnaG abolished the growth of L. casei on this oligosaccharide, demonstrating that BnaG is involved in its metabolism. Interestingly, whole cells of a bnaG mutant were totally devoid of β-N-acetylglucosaminidase activity, suggesting that BnaG is an extracellular wall-attached enzyme. In addition to hydrolyzing lacto-N-triose into N-acetylglucosamine and lactose, the purified BnaG enzyme also catalyzed the hydrolysis of 3′-N-acetylglucosaminyl-mannose and 3′-N-acetylgalactosaminyl-galactose. L. casei can be cultured in the presence of 3′-N-acetylglucosaminyl-mannose as a carbon source, but, curiously, the bnaG mutant strain was not impaired in its utilization. These results indicate that the assimilation of 3′-N-acetylglucosaminyl-mannose is independent of BnaG. Enzyme activity and growth analysis with a manA-knockout mutant showed that ManA is involved in the utilization of the mannose moiety of 3′-N-acetylglucosaminyl-mannose. Here we describe the physiological role of a β-N-acetylglucosaminidase in lactobacilli, and it supports the metabolic adaptation of L. casei to the N-acetylglucosaminide-rich gut niche.
Uncovering the Salt Response of Soybean by Unraveling Its Wild and Cultivated Functional Genomes Using Tag Sequencing

Soil salinity has very adverse effects on growth and yield of crop plants. Several salt tolerant wild accessions and cultivars are reported in soybean. Functional genomes of salt tolerant Glycine soja and a salt sensitive genotype of Glycine max were investigated to understand the mechanism of salt tolerance in soybean. For this purpose, four libraries were constructed for Tag sequencing on Illumina platform. We identify around 490 salt responsive genes which included a number of transcription factors, signaling proteins, translation factors and structural genes like transporters, multidrug resistance proteins, antiporters, chaperons, aquaporins etc. The gene expression levels and ratio of up/down-regulated genes was greater in tolerant plants. Translation related genes remained stable or showed slightly higher expression in tolerant plants under salinity stress. Further analyses of sequenced data and the annotations for gene ontology and pathways indicated that soybean adapts to salt stress through ABA biosynthesis and regulation of translation and signal transduction of structural genes. Manipulation of these pathways may mitigate the effect of salt stress thus enhancing salt tolerance.
Autonomous WSN for Lawns Monitoring in Smart Cities

The urban lawns are frequently composed by different grass species to combat some problems of water scarcity and diseases. In order to maintain these lawns, high amount of water is required. Nowadays, smart cities can be understood as a new concept of city that includes, among others, efficient distribution of energy, water, and other resources by using technology. In these cases, the main challenge is to try to estimate the necessary amount of water for irrigation and the phytosanitary uses without wasting water. In this paper, we propose a method to identify the percentage of grass coverage in lawns to deduce the grass productivity and estimate the most accurate quantity of water to ensure a good production of grass. The system is based on a Smart Autonomous Vehicle (SAV) controlled by an Arduino Mega 2560. It also contains an array of 120 colour sensors used to gather the data. The selected colour sensor is a TCS3472. With these sensors, we obtain the RGB histograms of the lawns. For these experiments, we have several lawn parcels of 1.5 x 1 m. From these, a matrix of 150 x 100 RGB values is obtained. After processing the green values of matrix, we have observed a correlation between the level of coverage and these values. The grass coverage is related with values of brightness between 40 and 60 which allow us to classify the lawn as a function of its coverage and the irrigation needs.
Design of high-performance E-band SPDT switch and LNA in 0.13 μm SiGe BiCMOS technology

This paper presents the design of high-performance E-band single-pole double-through (SPDT) switch and low noise amplifier (LNA) as a part of transceiver front-end in an 0.13 μm SiGe BiCMOS technology. The quarter-wave shunt SPDT switch is designed using reverse-saturated SiGe HBTs. The resulting switch exhibits an insertion loss of 2.1 dB, isolation of 26 dB, reflection coefficient better than 18 dB at 75 GHz and provides a bandwidth of more than 35 GHz. The designed switch is integrated with a single-in differential-output (SIDO) low noise amplifier (LNA) and utilized as input matching element of the LNA. The LNA utilizes a common-emitter amplifier at the first stage and a casocode amplifier at the second stage to exploit the advantages of both common-emitter and cascode topologies. The resulting LNA with integrated switch achieves a gain and noise figure(NF) of 26 dB and 6.9 dB, respectively at 75 GHz with a 3 dB bandwidth of 12 GHz. Output referred 1-dB compression point of +5.5 dBm is achieved at 75 GHz. The designed integrated block consumes 45.5 mW of DC power and occupies an area of 720 μm × 580 μm excluding RF pads.
Consolidation of Sand Particles by Aggregates of Calcite Nanoparticles Synthesized by Ureolytic Bacteria under Non-Sterile Conditions

BioCementation technology depends on the consolidation of sand particles by using pure microorganisms (B. pasteurii) under complete sterilization conditions during the cellular growth. In this study, an enrichment culture of ureolytic bacteria was used to precipitate aggregates of calcite in-situ under non-sterile conditions. Those bacteria were enriched in the presence of 3 M urea. Soil sample was collected from agricultural fields in Sakhir, Bahrain. Then they were used to precipitate calcite in-situ and consolidate sand particles in the presence of high concentration of 1 M equimolar urea and calcium ions. Continuous feeding of cells was applied. Optical microscope, SEM, EDS, XRD and XRF examinations revealed that this impure bacterial culture resulted in precipitating aggregates of calcite nanoparticles in spherical arrangement in-situ which consolidate packed sand column. Natural competence between bacteria in the enrichment culture did not affect their ability to precipitate calcite nanoparticles and strengthen the sand without interfering with the hydraulics of the treated sand. Therefore, cost of BioCementation technology can be lowered due to the enrichment of local bacteria under non-sterile conditions.
A FimH inhibitor prevents acute bladder infection and treats chronic cystitis caused by multidrug-resistant uropathogenic Escherichia coli ST131.

BACKGROUND Escherichia coli O25b:H4-ST131 represents a predominant clone of multidrug-resistant uropathogens currently circulating worldwide in hospitals and the community. Urinary tract infections (UTIs) caused by E. coli ST131 are typically associated with limited treatment options and are often recurrent. METHODS Using established mouse models of acute and chronic UTI, we mapped the pathogenic trajectory of the reference E. coli ST131 UTI isolate, strain EC958. RESULTS We demonstrated that E. coli EC958 can invade bladder epithelial cells and form intracellular bacterial communities early during acute UTI. Moreover, E. coli EC958 persisted in the bladder and established chronic UTI. Prophylactic antibiotic administration failed to prevent E. coli EC958-mediated UTI. However, 1 oral dose of a small-molecular-weight compound that inhibits FimH, the type 1 fimbriae adhesin, significantly reduced bacterial colonization of the bladder and prevented acute UTI. Treatment of chronically infected mice with the same FimH inhibitor lowered their bladder bacterial burden by >1000-fold. CONCLUSIONS In this study, we provide novel insight into the pathogenic mechanisms used by the globally disseminated E. coli ST131 clone during acute and chronic UTI and establish the potential of FimH inhibitors as an alternative treatment against multidrug-resistant E. coli.
Sensorimotor integration in chronic stroke: Baseline differences and response to sensory training.

BACKGROUND The integration of somatosensory information from the environment into the motor cortex to inform movement is essential for motor function. As motor deficits commonly persist into the chronic phase of stroke recovery, it is important to understand potential contributing factors to these deficits, as well as their relationship with motor function. To date the impact of chronic stroke on sensorimotor integration has not been thoroughly investigated. OBJECTIVES The current study aimed to comprehensively examine the influence of chronic stroke on sensorimotor integration, and determine whether sensorimotor integration can be modified with an intervention. Further, it determined the relationship between neurophysiological measures of sensorimotor integration and motor deficits post-stroke. METHODS Fourteen individuals with chronic stroke and twelve older healthy controls participated. Motor impairment and function were quantified in individuals with chronic stroke. Baseline neurophysiology was assessed using nerve-based measures (short- and long-latency afferent inhibition, afferent facilitation) and vibration-based measures of sensorimotor integration, which paired vibration with single and paired-pulse TMS techniques. Neurophysiological assessment was performed before and after a vibration-based sensory training paradigm to assess changes within these circuits. RESULTS Vibration-based, but not nerve-based measures of sensorimotor integration were different in individuals with chronic stroke, as compared to older healthy controls, suggesting that stroke differentially impacts integration of specific types of somatosensory information. Sensorimotor integration was behaviourally relevant in that it related to both motor function and impairment post-stroke. Finally, sensory training modulated sensorimotor integration in individuals with chronic stroke and controls. CONCLUSION Sensorimotor integration is differentially impacted by chronic stroke based on the type of afferent feedback. However, both nerve-based and vibration-based measures relate to motor impairment and function in individuals with chronic stroke.
Reduced growth due to belowground sink limitation is not fully explained by reduced photosynthesis

Sink limitation is known to reduce plant growth, but it is not known how plant carbon (C) balance is affected, limiting our ability to predict growth under sink-limited conditions. We manipulated soil volume to impose sink limitation of growth in Eucalyptus tereticornis Sm. seedlings. Seedlings were grown in the field in containers of different sizes and planted flush to the soil alongside freely rooted (Free) seedlings. Container volume negatively affected aboveground growth throughout the experiment, and light saturated rates of leaf photosynthesis were consistently lower in seedlings in containers (-26%) compared with Free seedlings. Significant reductions in photosynthetic capacity in containerized seedlings were related to both reduced leaf nitrogen content and starch accumulation, indicating direct effects of sink limitation on photosynthetic downregulation. After 120 days, harvested biomass of Free seedlings was on average 84% higher than seedlings in containers, but biomass distribution in leaves, stems and roots was not different. However, the reduction in net leaf photosynthesis over the growth period was insufficient to explain the reduction in growth, so that we also observed an apparent reduction in whole-plant C-use efficiency (CUE) between Free seedlings and seedlings in containers. Our results show that sink limitation affects plant growth through feedbacks to both photosynthesis and CUE. Mass balance approaches to predicting plant growth under sink-limited conditions need to incorporate both of these feedbacks.
Relationships between Membrane Binding, Affinity and Cell Internalization Efficacy of a Cell-Penetrating Peptide: Penetratin as a Case Study

Background Penetratin is a positively charged cell-penetrating peptide (CPP) that has the ability to bind negatively charged membrane components, such as glycosaminoglycans and anionic lipids. Whether this primary interaction of penetratin with these cell surface components implies that the peptide will be further internalized is not clear. Methodology Using mass spectrometry, the amount of internalized and membrane bound penetratin remaining after washings, were quantified in three different cell lines: wild type (WT), glycosaminoglycans- (GAGneg) and sialic acid-deficient (SAneg) cells. Additionally, the affinity and kinetics of the interaction of penetratin to membrane models composed of pure lipids and membrane fragments from the referred cell lines was investigated, as well as the thermodynamics of such interactions using plasmon resonance and calorimetry. Principal Findings Penetratin internalized with the same efficacy in the three cell lines at 1 µM, but was better internalized at 10 µM in SAneg>WT>GAGneg. The heat released by the interaction of penetratin with these cells followed the ranking order of internalization efficiency. Penetratin had an affinity of 10 nM for WT cells and µM for SAneg and GAGneg cells and model membrane of phospholipids. The remaining membrane-bound penetratin after cells washings was similar in WT and GAGneg cells, which suggested that these binding sites relied on membrane phospholipids. The interaction of penetratin with carbohydrates was more superficial and reversible while it was stronger with phospholipids, likely because the peptide can intercalate between the fatty acid chains. Conclusion/Significance These results show that accumulation and high-affinity binding of penetratin at the cell-surface do not reflect the internalization efficacy of the peptide. Altogether, these data further support translocation (membrane phospholipids interaction) as being the internalization pathway used by penetratin at low micromolecular concentration, while endocytosis is activated at higher concentration and requires accumulation of the peptide on GAG and GAG clustering.
Polygon Dissections Complexes are Shellable

All dissections of a convex (mn + 2)-gons into (m + 2)-gons are facets of a simplicial complex. This complex is introduced by S. Fomin and A.V. Zelevinsky in [7]. We reprove the result of E. Tzanaki about shellability of such complex by nding a concrete shelling order. Also, we use this shelling order to nd a combinatorial interpretation of h-vector and to describe the generating facets of these complexes.
Bayes Saliency-Based Object Proposal Generator for Nighttime Traffic Images

Object proposal is one of the most key pre-processing steps for nighttime vehicle detection systems in intelligent transportation systems. However, most current object proposal methods are developed on daytime data sets, and these methods demonstrate unsatisfactory results when they are used on nighttime images. Therefore, this paper presents a novel Bayes saliency-based object proposal generator for nighttime RGB traffic images to generate a modest and accurate set of proposals, which are more likely to be vehicles for preceding vehicle detection. First, we propose a new Bayes saliency detection approach in which prior estimation, feature extraction, weight estimation, and Bayes rule are used to compute saliency maps. Then, we propose a simple but effective object proposal generator based on the Bayes saliency map. Multi-scale sliding window, proposal rejecting, scoring, and non-maximum suppression are combined to generate a modest and effective set of proposals. Experimental results demonstrate that our proposed approach generates a modest set of proposals and outperforms some state-of-the-art methods on nighttime images in terms of various evaluation metrics. Furthermore, our proposed object proposal approach can improve the detection performance and the speed of several state-of-the-art vehicle detection approaches.
Conformational Toggling of Yeast Iso-1-Cytochrome c in the Oxidized and Reduced States

To convert cyt c into a peroxidase-like metalloenzyme, the P71H mutant was designed to introduce a distal histidine. Unexpectedly, its peroxidase activity was found even lower than that of the native, and that the axial ligation of heme iron was changed to His71/His18 in the oxidized state, while to Met80/His18 in the reduced state, characterized by UV-visible, circular dichroism, and resonance Raman spectroscopy. To further probe the functional importance of Pro71 in oxidation state dependent conformational changes occurred in cyt c, the solution structures of P71H mutant in both oxidation states were determined. The structures indicate that the half molecule of cyt c (aa 50–102) presents a kind of “zigzag riveting ruler” structure, residues at certain positions of this region such as Pro71, Lys73 can move a big distance by altering the tertiary structure while maintaining the secondary structures. This finding provides a molecular insight into conformational toggling in different oxidation states of cyt c that is principle significance to its biological functions in electron transfer and apoptosis. Structural analysis also reveals that Pro71 functions as a key hydrophobic patch in the folding of the polypeptide of the region (aa 50–102), to prevent heme pocket from the solvent.