Miracle-dz/UniFAR-FTUs huggingface dataset:
Crossing Methods and Cultivation Conditions for Rapid Production of Segregating Populations in Three Grain Amaranth Species

Grain amaranths (Amaranthus spp.) have been cultivated for thousands of years in Central and South America. Their grains are of high nutritional value, but the low yield needs to be increased by selection of superior genotypes from genetically diverse breeding populations. Amaranths are adapted to harsh conditions and can be cultivated on marginal lands although little is known about their physiology. The development of controlled growing conditions and efficient crossing methods is important for research on and improvement of this ancient crop. Grain amaranth was domesticated in the Americas and is highly self-fertilizing with a large inflorescence consisting of thousands of very small flowers. We evaluated three different crossing methods (open pollination, hot water emasculation and hand emasculation) for their efficiency in amaranth and validated them with genetic markers. We identified cultivation conditions that allow an easy control of flowering time by day length manipulation and achieved flowering times of 4 weeks and generation times of 2 months. All three different crossing methods successfully produced hybrid F1 offspring, but with different success rates. Open pollination had the lowest (10%) and hand emasculation the highest success rate (74%). Hot water emasculation showed an intermediate success rate (26%) with a maximum of 94% success. It is simple to perform and suitable for a more large-scale production of hybrids. We further evaluated 11 single nucleotide polymorphism (SNP) markers and found that they were sufficient to validate all crosses of the genotypes used in this study for intra- and interspecific hybridizations. Despite its very small flowers, crosses in amaranth can be carried out efficiently and evaluated with inexpensive SNP markers. Suitable growth conditions strongly reduce the generation time and allow the control of plant height, flowering time, and seed production. In combination, this enables the rapid production of segregating populations which makes amaranth an attractive model for basic plant research but also facilitates further the improvement of this ancient crop by plant breeding.
STRONG ASSOCIATION BETWEEN INSULIN RESISTANCE WITH URINARY ALBUMIN EXCRETION IN OLDER ADULTS

1. Cross TJ, Antoniades CG, Muiesan P et al. Liver transplantation in patients over 60 and 65 years: An evaluation of long-term outcomes and survival. Liver Transplant 2007;13:1382–1388. 2. Filipponi F, Roncella M, Boggi U et al. Liver transplantation in recipients over 60. Transplant Proc 2001;33:1465–1466. 3. Lipshutz GS, Hiatt J, Ghobrial RM et al. Outcome of liver transplantation in septuagenarians: A single-center experience. Arch Surg 2007;142: 775–781. 4. Garcia CE, Garcia RF, Mayer AD et al. Liver transplantation in patients over sixty years of age. Transplantation 2001;72:679–684. 5. Levy MF, Somasundar PS, Jennings LW et al. The elderly liver transplant recipient: A call for caution. Ann Surg 2001;233:107–113. 6. Bilbao I, Dopazo C, Lazaro JL et al. Our experience in liver transplantation in patients over 65 yr of age. Clin Transplant 2008;22:82–88. 7. Collins BH, Pirsch JD, Becker YT et al. Long-term results of liver transplantation in older patients 60 years of age and older. Transplantation 2000;70: 780–783.
A Potential Role for Pro-Inflammatory Cytokines in the Development of Insulin Resistance in Horses

Summary Insulin resistance is a metabolic condition involving reduced sensitivity of insulin-sensitive tissues to insulin-induced glucose disposal, including adipose tissue, skeletal muscle, and liver. Insulin resistance occurs in overweight and obese horses, and may increase risk for the development of laminitis. The development of insulin resistance is thought to occur in response to increased production of pro-inflammatory cytokines by adipose tissue in obesity, that then have an inhibitory effect on insulin signaling pathways in multiple tissues. This article reviews current knowledge of the involvement of pro-inflammatory cytokines in the development of insulin resistance in horses and uses data from other species to provide context.
Concealed by conspicuousness: distractive prey markings and backgrounds

High-contrast markings, called distractive or dazzle markings, have been suggested to draw and hold the attention of a viewer, thus hindering detection or recognition of revealing prey characteristics, such as the body outline. We tested this hypothesis in a predation experiment with blue tits (Cyanistes caeruleus) and artificial prey. We also tested whether this idea can be extrapolated to the background appearance and whether high-contrast markings in the background would improve prey concealment. We compared search times for a high-contrast range prey (HC-P) and a low-contrast range prey (LC-P) in a high-contrast range background (HC-B) and a low-contrast range background (LC-B). The HC-P was more difficult to detect in both backgrounds, although it did not match the LC-B. Also, both prey types were more difficult to find in the HC-B than in the LC-B, in spite of the mismatch of the LC-P. In addition, the HC-P was more difficult to detect, in both backgrounds, when compared with a generalist prey, not mismatching either background. Thus, we conclude that distractive prey pattern markings and selection of microhabitats with distractive features may provide an effective way to improve camouflage. Importantly, high-contrast markings, both as part of the prey coloration and in the background, can indeed increase prey concealment.
Aminoglycoside binding in the major groove of duplex RNA: the thermodynamic and electrostatic forces that govern recognition.

We use a combination of spectroscopic, calorimetric, viscometric and computer modeling techniques to characterize the binding of the aminoglycoside antibiotic, tobramycin, to the polymeric RNA duplex, poly(rI). poly(rC), which exhibits the characteristic A-type conformation that is conserved among natural and synthetic double-helical RNA sequences. Our results reveal the following significant features: (i) CD-detected binding of tobramycin to poly(rI). poly(rC) reveals an apparent site size of four base-pairs per bound drug molecule; (ii) tobramycin binding enhances the thermal stability of the host poly(rI). poly(rC) duplex, the extent of which decreases upon increasing in Na(+) concentration and/or pH conditions; (iii) the enthalpy of tobramycin- poly(rI). poly(rC) complexation increases with increasing pH conditions, an observation consistent with binding-induced protonation of one or more drug amino groups; (iv) the affinity of tobramycin for poly(rI). poly(rC) is sensitive to both pH and Na(+) concentration, with increases in pH and/or Na(+) concentration resulting in a concomitant reduction in binding affinity. The salt dependence of the tobramycin binding affinity reveals that the drug binds to the host RNA duplex as trication. (v) The thermodynamic driving force for tobramycin- poly(rI). poly(rC) complexation depends on pH conditions. Specifically, at pH< or =6.0, tobramycin binding is entropy driven, but is enthalpy driven at pH > 6.0. (vi) Viscometric data reveal non-intercalative binding properties when tobramycin complexes with poly(rI). poly(rC), consistent with a major groove-directed mode of binding. These data also are consistent with a binding-induced reduction in the apparent molecular length of the host RNA duplex. (vii) Computer modeling studies reveal a tobramycin-poly(rI). poly(rC) complex in which the drug fits snugly at the base of the RNA major groove and is stabilized, at least in part, by an array of hydrogen bonding interactions with both base and backbone atoms of the host RNA. These studies also demonstrate an inability of tobramycin to form a stable low-energy complex with the minor groove of the poly(rI). poly(rC) duplex. In the aggregate, our results suggest that tobramycin-RNA recognition is dictated and controlled by a broad range of factors that include electrostatic interactions, hydrogen bonding interactions, drug protonation reactions, and binding-induced alterations in the structure of the host RNA. These modulatory effects on tobramycin-RNA complexation are discussed in terms of their potential importance for the selective recognition of specific RNA structural motifs, such as asymmetric internal loops or hairpin loop-stem junctions, by aminoglycoside antibiotics and their derivatives.
Bacterial adhesion to solid substrata coated with conditioning films derived from chemical fractions of natural waters

Dissolved organic carbon from seawater and freshwater was separated into hydrophilic-base, hydrophilic-neutral, hydrophilic-acid as well as hydrophobic-base, hydrophobic-neutral, and hydrophobic-acid fractions which were used to form conditioning films on hydrophilic stainless steel and aluminium as well as on hydrophobic polypropylene and perspex. Water contact angles indicated that every conditioning film modified the wettability of clean substrata; the wettability of hydrophobic surfaces was generally increased and that of hydrophilic surfaces decreased. Adhesion results with carbon- and nitrogen-limited phenotypes of the Gram-negative bacterium SW8 suggested that adhesive or abhesive components of conditioning films were not associated with particular chemical fractions. The proportion of conditioning films derived from water fractions which modified the attachment of carbon-limited SW8 on hydrophobic and hydrophilic substrata was 29 and 71 %, respectively. These films generally reduced the number of .
Repeat Procedures Within 30 days in Patients Stented for Malignant Distal Biliary Strictures: Experience of 508 Patients at a Tertiary Referral Center

Background Stent related occlusion and migration remains a problem despite attempts to improve stent design over this time period. Flanged polyethylene plastic stents (FPS) remains the stent of choice in most centers. Early failure of stents placed for malignant extrahepatic biliary strictures (MEBS) has not previously been studied in detail. We set out to determine the incidence and reasons for biliary stent change within 30 days of the index procedure in a large tertiary center population during a period where (FPS) was the sole plastic stent used. Methods Retrospective analysis of endoscopic retrograde cholangiography (ERCP) was undertaken in patients who were stented for presumed or known MEBS between 1993 and 2001. Patients who required repeat stenting within 30 days were identified. Results All 508 patients were stented for MEBS. 5.7% of patients had a total of 34 repeat stenting procedures within 30 days of the index procedure; 27of 29 index stents were plastic, 2 were self-expandable metal stents (SEMS), 20 (3.9%) patients had stent failure as the reason for a stent exchange (plastic stent occlusion n = 15, mean time to stent change 14 ± 8.3 days; metal stent occlusion n = 2, mean time to stent change 24.5 ± 7.8 days; plastic stent migration n = 3, mean time to stent change 25 ± 5.3 days). There was a statistically significant difference in the time to stent change between the occluded plastic stent and migrated plastic stent cases (P = 0.045, 95% CI -21.7 to -0.29). 6 patients spent at least 2 additional days in hospital as a result of stent failure. Conclusions Early stent failure is an uncommon problem, especially in patients with SEMS. Early plastic stent failure appears to occur sooner with stent occlusion than with stent migration. Early stent failure is associated with significant morbidity and bears an economic impact in additional procedures and hospital stay.
Expression of a mutated phospholipase A2 in transgenic Aedes fluviatilis mosquitoes impacts Plasmodium gallinaceum development

The genetic manipulation of mosquito vectors is an alternative strategy in the fight against malaria. It was previously shown that bee venom phospholipase A2 (PLA2) inhibits ookinete invasion of the mosquito midgut although mosquito fitness was reduced. To maintain the PLA2 blocking ability without compromising mosquito biology, we mutated the protein‐coding sequence to inactivate the enzyme while maintaining the protein's structure. DNA encoding the mutated PLA2 (mPLA2) was placed downstream of a mosquito midgut‐specific promoter (Anopheles gambiae peritrophin protein 1 promoter, AgPer1) and this construct used to transform Aedes fluviatilis mosquitoes. Four different transgenic lines were obtained and characterized and all lines significantly inhibited Plasmodium gallinaceum oocyst development (up to 68% fewer oocysts). No fitness cost was observed when this mosquito species expressed the mPLA2.
Tril targets Smad7 for degradation to allow hematopoietic specification in Xenopus embryos

In Xenopus laevis, bone morphogenetic proteins (Bmps) induce expression of the transcription factor Gata2 during gastrulation, and Gata2 is required in both ectodermal and mesodermal cells to enable mesoderm to commit to a hematopoietic fate. Here, we identify tril as a Gata2 target gene that is required in both ectoderm and mesoderm for primitive hematopoiesis to occur. Tril is a transmembrane protein that functions as a co-receptor for Toll-like receptors to mediate innate immune responses in the adult brain, but developmental roles for this molecule have not been identified. We show that Tril function is required both upstream and downstream of Bmp receptor-mediated Smad1 phosphorylation for induction of Bmp target genes. Mechanistically, Tril triggers degradation of the Bmp inhibitor Smad7. Tril-dependent downregulation of Smad7 relieves repression of endogenous Bmp signaling during gastrulation and this enables mesodermal progenitors to commit to a blood fate. Thus, Tril is a novel component of a Bmp-Gata2 positive-feedback loop that plays an essential role in hematopoietic specification. Summary: Tril is a Gata2 target gene that triggers degradation of Smad7 protein during gastrulation, allowing for robust transduction of Bmp signals to enable the commitment of mesoderm to a blood fate.
Using archaeogenomic and computational approaches to unravel the history of local adaptation in crops

Our understanding of the evolution of domestication has changed radically in the past 10 years, from a relatively simplistic rapid origin scenario to a protracted complex process in which plants adapted to the human environment. The adaptation of plants continued as the human environment changed with the expansion of agriculture from its centres of origin. Using archaeogenomics and computational models, we can observe genome evolution directly and understand how plants adapted to the human environment and the regional conditions to which agriculture expanded. We have applied various archaeogenomics approaches as exemplars to study local adaptation of barley to drought resistance at Qasr Ibrim, Egypt. We show the utility of DNA capture, ancient RNA, methylation patterns and DNA from charred remains of archaeobotanical samples from low latitudes where preservation conditions restrict ancient DNA research to within a Holocene timescale. The genomic level of analyses that is now possible, and the complexity of the evolutionary process of local adaptation means that plant studies are set to move to the genome level, and account for the interaction of genes under selection in systems-level approaches. This way we can understand how plants adapted during the expansion of agriculture across many latitudes with rapidity.
Occipital foramina development involves localised regulation of mesenchyme proliferation and is independent of apoptosis

Cranial foramina are holes within the skull, formed during development, allowing entry and exit of blood vessels and nerves. Once formed they must remain open, due to the vital structures they contain, i.e. optic nerves, jugular vein, carotid artery, and other cranial nerves and blood vessels. Understanding cranial foramina development is essential as cranial malformations lead to the stenosis or complete closure of these structures, resulting in blindness, deafness, facial paralysis, raised intracranial pressure and lethality. Here we focus on describing early events in the formation of the jugular, carotid and hypoglossal cranial foramina that form in the mesoderm‐derived, endochondral occipital bones at the base of the embryonic chick skull. Whole‐mount skeletal staining of skulls indicates the appearance of these foramina from HH32/D7.5 onwards. Haematoxylin & eosin staining of sections shows that the intimately associated mesenchyme, neighbouring the contents of these cranial foramina, is initially very dense and gradually becomes sparser as development proceeds. Histological examination also revealed that these foramina initially contain relatively large‐diameter nerves, which later become refined, and are closely associated with the blood vessel, which they also innervate within the confines of the foramina. Interestingly cranial foramina in the base of the skull contain blood vessels lacking smooth muscle actin, which suggests these blood vessels belong to glomus body structures within the foramina. The blood vessel shape also appears to dictate the overall shape of the resulting foramina. We initially hypothesised that cranial foramina development could involve targeted proliferation and local apoptosis to cause ‘mesenchymal clearing’ and the creation of cavities in a mechanism similar to joint cavitation. We find that this is not the case, and propose that a mechanism reliant upon local nerve/blood vessel‐derived restriction of ossification may contribute to foramina formation during cranial development.
Model-based approaches to handling additive noise in reverberant environments

Model-based approaches to handle additive and convolutional noise have been extensively investigated and used. However, the application of these schemes to handling reverberant noise has received less attention. This paper examines the extension of two standard additive/convolutional noise approaches to handling reverberant noise. The first is an extension of vector Taylor series (VTS) compensation, reverberant VTS, where a mismatch function including reverberant noise is used. The second scheme modifies constrained MLLR to allow a wide-span of frames to be taken into account and “projected” into the required dimensionality. To allow additive noise to be handled, both these schemes are combined with standard VTS. The approaches are evaluated and compared on two tasks, MC-WSJ-AV, and a reverberant simulated version of AURORA-4.
Association of Procalcitonin With Acute Pyelonephritis and Renal Scars in Pediatric UTI

BACKGROUND AND OBJECTIVE: Urinary tract infections (UTIs) are common childhood bacterial infections that may involve renal parenchymal infection (acute pyelonephritis [APN]) followed by late scarring. Prompt, high-quality diagnosis of APN and later identification of children with scarring are important for preventing future complications. Examination via dimercaptosuccinic acid scanning is the current clinical gold standard but is not routinely performed. A more accessible assay could therefore prove useful. Our goal was to study procalcitonin as a predictor for both APN and scarring in children with UTI. METHODS: A systematic review and meta-analysis of individual patient data were performed; all data were gathered from children with UTIs who had undergone both procalcitonin measurement and dimercaptosuccinic acid scanning. RESULTS: A total of 1011 patients (APN in 60.6%, late scarring in 25.7%) were included from 18 studies. Procalcitonin as a continuous, class, and binary variable was associated with APN and scarring (P < .001) and demonstrated a significantly higher (P < .05) area under the receiver operating characteristic curve than either C-reactive protein or white blood cell count for both pathologies. Procalcitonin ≥0.5 ng/mL yielded an adjusted odds ratio of 7.9 (95% confidence interval [CI]: 5.8–10.9) with 71% sensitivity (95% CI: 67–74) and 72% specificity (95% CI: 67–76) for APN. Procalcitonin ≥0.5 ng/mL was significantly associated with late scarring (adjusted odds ratio: 3.4 [95% CI: 2.1–5.7]) with 79% sensitivity (95% CI: 71–85) and 50% specificity (95% CI: 45–54). CONCLUSIONS: Procalcitonin was a more robust predictor compared with C-reactive protein or white blood cell count for selectively identifying children who had APN during the early stages of UTI, as well as those with late scarring.
Efficient Pricing of CPPI Using Markov Operators

Constant Proportion Portfolio Insurance (CPPI) is a strategy designed to give participation in a risky asset while protecting the invested capital. Some gap risk due to extreme events is often kept by the issuer of the product: a put option on the CPPI strategy is included in the product. In this paper we present a new method for the pricing of CPPIs and options on CPPIs, which is much faster and more accurate than the usual Monte-Carlo method. Provided the underlying follows a homogeneous process, the path-dependent CPPI strategy is reformulated into a Markov process in one variable, which allows to use efficient linear algebra techniques. Tail events, which are crucial in the pricing are handled smoothly. We incorporate in this framework linear thresholds, profit lock-in, performance coupons. The American exercise of open-ended CPPIs is handled naturally through backward propagation. Finally we use our pricing scheme to study the influence of various features on the gap risk of CPPI strategies.
Object Classification in Semi Structured Enviroment Using Forward-Looking Sonar

The submarine exploration using robots has been increasing in recent years. The automation of tasks such as monitoring, inspection, and underwater maintenance requires the understanding of the robot’s environment. The object recognition in the scene is becoming a critical issue for these systems. On this work, an underwater object classification pipeline applied in acoustic images acquired by Forward-Looking Sonar (FLS) are studied. The object segmentation combines thresholding, connected pixels searching and peak of intensity analyzing techniques. The object descriptor extract intensity and geometric features of the detected objects. A comparison between the Support Vector Machine, K-Nearest Neighbors, and Random Trees classifiers are presented. An open-source tool was developed to annotate and classify the objects and evaluate their classification performance. The proposed method efficiently segments and classifies the structures in the scene using a real dataset acquired by an underwater vehicle in a harbor area. Experimental results demonstrate the robustness and accuracy of the method described in this paper.