Miracle-dz/UniFAR-FTUs huggingface dataset:
Evidence of genomic adaptation to climate in Eucalyptus microcarpa: Implications for adaptive potential to projected climate change

Understanding whether populations can adapt in situ or whether interventions are required is of key importance for biodiversity management under climate change. Landscape genomics is becoming an increasingly important and powerful tool for rapid assessments of climate adaptation, especially in long‐lived species such as trees. We investigated climate adaptation in Eucalyptus microcarpa using the DArTseq genomic approach. A combination of FST outlier and environmental association analyses were performed using >4200 genomewide single nucleotide polymorphisms (SNPs) from 26 populations spanning climate gradients in southeastern Australia. Eighty‐one SNPs were identified as putatively adaptive, based on significance in FST outlier tests and significant associations with one or more climate variables related to temperature (70/81), aridity (37/81) or precipitation (35/81). Adaptive SNPs were located on all 11 chromosomes, with no particular region associated with individual climate variables. Climate adaptation appeared to be characterized by subtle shifts in allele frequencies, with no consistent fixed differences identified. Based on these associations, we predict adaptation under projected changes in climate will include a suite of shifts in allele frequencies. Whether this can occur sufficiently rapidly through natural selection within populations, or would benefit from assisted gene migration, requires further evaluation. In some populations, the absence or predicted increases to near fixation of particular adaptive alleles hint at potential limits to adaptive capacity. Together, these results reinforce the importance of standing genetic variation at the geographic level for maintaining species’ evolutionary potential.
Thin saline ice thickness retrieval using time-series C-band polarimetric radar measurements

The application of time-series radar measurements to accurately invert the thickness of saline ice is presented in this study. The authors describe briefly some experimental observations from the United States Army Cold Regions Research and Engineering Laboratory, Hanover, NH, 1993 (CRRELEX'93) campaign of microwave scattering from sea ice. They demonstrate that volume scattering from brine inclusions is an important contribution to the backscatter response of saline ice in this case. From the experimental findings and the thermophysics of ice growth, they develop an inversion algorithm for the ice thickness based on a dynamic electromagnetic scattering model of saline ice. This inversion algorithm uses a parametric estimation approach in which the radiative transfer equation is used as the direct scattering model to calculate the backscattering signatures from ice medium and the Levenberg-Marquardt method is employed to retrieve ice thickness iteratively. Additional information provided by the saline ice thermodynamics is applied to constrain the electromagnetic inverse problem to achieve a reasonably accurate reconstruction. The inversion results using this algorithm and the data from CRRELEX'93 experiment are compared. The accurate thickness retrieval suggests the potential use of this algorithm for retrieving geophysical parameters from satellite remote-sensing data.
A time- and cost-effective strategy to sequence mammalian Y Chromosomes: an application to the de novo assembly of gorilla Y

The mammalian Y Chromosome sequence, critical for studying male fertility and dispersal, is enriched in repeats and palindromes, and thus, is the most difficult component of the genome to assemble. Previously, expensive and labor-intensive BAC-based techniques were used to sequence the Y for a handful of mammalian species. Here, we present a much faster and more affordable strategy for sequencing and assembling mammalian Y Chromosomes of sufficient quality for most comparative genomics analyses and for conservation genetics applications. The strategy combines flow sorting, short- and long-read genome and transcriptome sequencing, and droplet digital PCR with novel and existing computational methods. It can be used to reconstruct sex chromosomes in a heterogametic sex of any species. We applied our strategy to produce a draft of the gorilla Y sequence. The resulting assembly allowed us to refine gene content, evaluate copy number of ampliconic gene families, locate species-specific palindromes, examine the repetitive element content, and produce sequence alignments with human and chimpanzee Y Chromosomes. Our results inform the evolution of the hominine (human, chimpanzee, and gorilla) Y Chromosomes. Surprisingly, we found the gorilla Y Chromosome to be similar to the human Y Chromosome, but not to the chimpanzee Y Chromosome. Moreover, we have utilized the assembled gorilla Y Chromosome sequence to design genetic markers for studying the male-specific dispersal of this endangered species.
Contractions induced by potassium‐free solution and potassium relaxation in vascular smooth muscle of hypertensive and normotensive rats

1 Vascular contractions induced by K+‐free solution and relaxation responses following the return of K+ to the organ bath were studied in mesenteric arterial rings from spontaneously hypertensive rats (SHR) and normotensive Wistar‐Kyoto rats (WKY) with particular focus on the role of vascular adrenergic nerve‐endings and endothelium. 2 In endothelium‐denuded rings the omission of K+ from the incubation medium resulted in gradual contractions, the rate of which was slower in SHR than WKY. Nifedipine (1 μm) inhibited the contractions more effectively in SHR than WKY. 3 Adrenergic denervation in vitro with 6‐hydroxydopamine reduced the contractions induced by the K+‐free medium in endothelium‐denuded rings. The remaining contractions after denervation were markedly greater in SHR than WKY. 4 The presence of intact vascular endothelium attenuated the K+‐free contractions in both strains, the attenuation being smaller in SHR than WKY. NG‐nitro‐l‐arginine methyl ester (l‐NAME, 0.1 mm) and methylene blue (10 μm), but not indomethacin (10 μm), abolished the attenuating effect of endothelium on the K+‐free contractions. l‐Arginine (1 mm) reversed the effect of l‐NAME in WKY but not in SHR. 5 The re‐addition of K+ after full K+‐free contractions dose‐dependently relaxed the rings. The rate of this K+‐induced relaxation was significantly slower in SHR than WKY at all K+ concentrations (0.1–5.9 mm) studied, whether the endothelium or functioning adrenergic nerve‐endings were present or not. Ouabain (1 mm) totally inhibited the K+ relaxation in SHR but only partially in WKY. 6 Vascular smooth muscle contractions induced by high concentrations of potassium were comparable between the strains. The EC50 for noradrenaline‐induced contractions was lower in SHR than WKY, but the maximal forces did not differ significantly. 7 In conclusion, the contractile response in K+‐free solution more clearly differentiates vascular rings from SHR and WKY than the responses induced by the classical contractile agents noradrenaline and high concentrations of potassium. The depressant effect of the presence of intact endothelium on the K+‐free contractions, which was smaller in SHR than WKY, is mediated via the endothelium‐derived relaxing factor. Neurotransmitter release from vascular adrenergic nerve‐endings participates less in the K+‐free contractile response in SHR than WKY. Moreover, the contractile response is more dependent on calcium entry through nifedipine‐sensitive calcium channels in SHR than WKY. The greater K+‐free contractions of denervated endothelium‐denuded rings and the reduced K+ relaxation rate in SHR when compared to WKY suggest increased cell membrane permeability and decreased activity of vascular Na+, K+‐ATPase, respectively, in this type of genetic hypertension.
A Comparison of Hemostatic Changes in Splenectomized and Nonsplenectomized &bgr;-Thalassemia Intermedia Patients

The present study was conducted to compare the coagulation factors between splenectomized and nonsplenectomized thalassemia intermedia (TI) patients as well as a healthy control group. A total of 60 splenectomized and 60 nonsplenectomized TI patients and 60 healthy controls participated in this case-control study. The level of homocysteine, protein C and S, antithrombin III, factors V and VIII, fibrinogen, and D-dimer were measured in all groups. Our results indicated a significant reduction of protein C and S and fibrinogen in TI patients compared with healthy controls (P<0.001), as well as factor V activity (P=0.009). Also a significant elevation of D-dimer (P=0.006) and factor VIII activity (P=0.001) was observed. There was no significant difference considering homocysteine and antithrombin III level among patients and healthy controls. Also our results demonstrated that there was no significant difference considering the homeostatic parameters (except D-dimer activity) between splenectomized and nonsplenectomized TI patients after adjustment for age. In conclusion, reduction of protein C and S, fibrinogen, and factor V activity and elevation of D-dimer levels and factor VIII activity was observed in TI patients compared with healthy controls. It seems that splenectomy has little significant effect on concentration of hemostatic factors except for D-dimer activity.
Determinants of childhood tuberculosis--a case control study among children registered under revised National Tuberculosis Control Programme in a district of South India.

AIM To study the determinants of Tuberculosis (TB) in children between the age group of 0-14 years receiving treatment under Revised National TB Control Programme (RNTCP). METHODS A case (registered under RNTCP) control study was undertaken with 41 cases and 82 controls. RESULTS Factors found to have significance according to binary logistic regression were low-birth weight (LBW) [Odd's ratio = 3.56],Malnutrition [Odd's ratio = 3.96], Passive smoking [Odd's ratio=6.28] and exposure to fire-wood smoke [Odd's ratio = 6.91]. CONCLUSION LBW, malnutrition, passive smoking and fire-wood smoke are the risk factors to be addressed to prevent pediatric TB.
Nerve-independence of limb regeneration in larval Xenopus laevis is correlated to the level of fgf-2 mRNA expression in limb tissues.

In both larval and adult urodele amphibians, limb blastema formation requires the presence of an adequate nerve supply. In previous research, we demonstrated that the hindlimb of early Xenopus laevis larvae formed a regeneration blastema even when denervated, while the denervated limb of late larvae did not. We hypothesized that the nerve-independence was due to the autonomous synthesis of a mitogenic neurotrophic-like factor by undifferentiated limb bud cells. In this paper, we demonstrate that fgf-2 mRNA is present in larval limb tissues and that its level is correlated to the extent of mesenchymal cells populating the limb: in early limbs, fgf-2 mRNA is present at high levels all over the limb, while, in late limbs, the fgf-2 expression is low and detectable only in the distal autopodium. After denervation, fgf-2 mRNA synthesis increases in amputated early limbs but not in amputated late limbs. The implantation of anti-FGF-2 beads into amputated early limbs hardly lowers the mitotic activity of blastema cells. However, FGF-2 beads implanted into the blastema of late limbs prevent the denervation-induced inhibition of mitosis and oppose blastema regression. Our data indicate that FGF-2 is a good candidate for the endogenous mitogenic factor responsible for blastema formation and growth in amputated and denervated early limbs. However, in amputated late limbs, the very limited fgf-2 expression is not sufficient to promote blastema formation in the absence of nerves.
hERG quality control and the long QT syndrome

Long‐QT syndrome type‐2 (LQT2) is characterized by reduced functional expression of the human ether‐à‐go‐go related (hERG) gene product, resulting in impaired cardiac repolarization and predisposition to fatal arrhythmia. Previous studies have implicated abnormal trafficking of misfolded hERG as the primary mechanism of LQT2, with misfolding being caused by mutations in the hERG gene (inherited) or drug treatment (acquired). More generally, environmental and metabolic stresses present a constant challenge to the folding of proteins, including hERG, and must be countered by robust protein quality control (QC) systems. Disposal of partially unfolded yet functional plasma membrane (PM) proteins by protein QC contributes to the loss‐of‐function phenotype in various conformational diseases including cystic fibrosis (CF) and long‐QT syndrome type‐2 (LQT2). The prevalent view has been that the loss of PM expression of hERG is attributed to biosynthetic block by endoplasmic reticulum (ER) QC pathways. However, there is a growing appreciation for protein QC pathways acting at post‐ER cellular compartments, which may contribute to conformational disease pathogenesis. This article will provide a background on the structure and cellular trafficking of hERG as well as inherited and acquired LQT2. We will review previous work on hERG ER QC and introduce the more novel view that there is a significant peripheral QC at the PM and peripheral cellular compartments. Particular attention is drawn to the unique role of the peripheral QC system in acquired LQT2. Understanding the QC process and players may provide targets for therapeutic intervention in dealing with LQT2.
Recent Advances on Fuzzy-Model-Based Nonlinear Networked Control Systems: A Survey

In recent years, the analysis and synthesis of fuzzy-model-based nonlinear networked control systems (NCSs) have received increasing attention from both scientific and industrial communities, and a number of significant results have been proposed. This paper gives a review on recent advances on the analysis and design of fuzzy-model-based nonlinear NCSs with various network-induced limitations such as packet dropouts, time delays, and signal quantization. With these network-induced constraints, the developments on various control and filtering design issues are surveyed in details, and some essential technical difficulties are mentioned. Then, some latest results on event-triggered control and filtering design of fuzzy-model-based nonlinear NCSs are also summarized. Finally, some conclusions are drawn and several potential future research topics are highlighted.
Salivary cortisol to assess the hypothalamic-pituitary-adrenal axis in healthy children under 3 years old.

OBJECTIVE To establish reference concentration intervals for salivary cortisol in healthy children, in the morning and in the afternoon, investigating factors that interfere with the concentration measured and the possibility that circadian rhythms are present. METHODS A controlled observational study was carried out with 91 children aged 45 days to 36 months, selected at random and living in Santo André, state of São Paulo, Brazil. Inclusion criteria were: healthy, well-nourished, free from fever and corticoid use, subdivided by age group (five subsets) at 6-month intervals. Saliva was collected during home visits in the morning and afternoon. Cortisol was radioimmunoassayed with cortisol 3-oxime-bovine albumin antiserum. RESULTS The five subsets exhibited higher cortisol concentration during the morning than in the afternoon (p < 0.001), and this difference passed 30% from 1 year of age onwards. Mean concentrations, in nmol/L, were 557.86 (morning) and 346.36 (afternoon). A negative linear correlation was observed between morning concentrations and hours' sleep and frequency of meals (p < 0.05), and in the afternoon with anthropometric measurements (p < 0.05). CONCLUSIONS Reference values for normal salivary cortisol in healthy children were established. At 45 days it was possible to observe circadian rhythms, which reached maturity at 12 months of life. Sleep and food deprivation increased morning cortisol levels.
Evaluation of Statistical Approaches in Quantitative Nursing Research

The purposes of this study were to (a) develop a tool to assess statistical methods and (b) use the tool to evaluate recently published quantitative research. We rated the statistical approaches used in 152 studies published in the 5 top impact-factor nursing research journals from September 2005 to August 2007. Studies were generally of high quality; 45% scored between 80% and 100%, and 22% achieved a score of 100%. Predictors of high scores were interdisciplinary authorship, a statistician coauthor, and the number of aims. The authors conclude that studies published in high impact-factor nursing journals are statistically sound and provide a solid foundation for evidence-based practice.
Molecular pathophysiology of portal hypertension

Over the past two decades the advances in molecular cell biology have led to significant discoveries about the pathophysiology of portal hypertension (PHT). In particular, great progress has been made in the study of the molecular and cellular mechanisms that regulate the increased intrahepatic vascular resistance (IHVR) in cirrhosis. We now know that the increased IHVR is not irreversible, but that both the structural component caused by fibrosis and the active component caused by hepatic sinusoidal constriction can be, at least partially, reversed. Indeed, it is now apparent that the activation of perisinusoidal hepatic stellate cells, which is a key event mediating the augmented IHVR, is regulated by multiple signal transduction pathways that could be potential therapeutic targets for PHT treatment. Furthermore, the complexity of the molecular physiology of PHT can also be appreciated when one considers the complex signals capable of inducing vasodilatation and hyporesponsiveness to vasoconstrictors in the splanchnic vascular bed, with several vasoactive molecules, controlled at multiple levels, working together to mediate these circulatory abnormalities. Added to the complexity is the occurrence of pathological angiogenesis during the course of disease progression, with recent emphasis given to understanding its molecular machinery and regulation. Although much remains to be learned, with the current availability of reagents and new technologies and the exchange of concepts and data among investigators, our knowledge of the molecular basis of PHT will doubtless continue to grow, accelerating the transfer of knowledge generated by basic research to clinical practice. This will hopefully permit a better future for patients with PHT. (Hepatology 2015;61:1406–1415)
Rectal Prolapse

Rectal prolapse is a condition that usually requires surgical intervention to correct. Abdominal and perineal approaches are well described in the literature. Abdominal approaches have traditionally been reserved for young healthy patients, but this has been challenged by perineal approaches with excellent outcomes. Laparoscopic techniques have been shown to be effective and equivalent to traditional laparotomy techniques.
Climate Change and Tourism in the Arctic Circle

We estimate grid level tourist numbers to Arctic Circle countries under a number of climate change scenarios. At present, the highest tourism volumes are found in Canada and most of the Scandinavian countries. In general, it appears that tourists are attracted to regions with better infrastructure and nicer cities. Under each climate change scenario, Russia sees a significant increase in tourist numbers because Russia is big, its climate is expected to show some improvement and it is relatively close to the growing markets of South and East Asia. A growth in tourist numbers is also projected for Canada and Alaska. While our simulations do not show a re-distribution of tourists within the Arctic under climate change, the volume is likely to increase.
Effects of probiotic bacteria on the bioaccessibility of aflatoxin B1 and ochratoxin A using an in vitro digestion model under fed conditions

In the present study, we aimed at determining the release of aflatoxin B1 (AFB1) and ochratoxin A (OTA) from different food products in the gastro-intestinal tract in the absence and presence of probiotics, a possible adsorbent. The average bioaccessibility of AFB1 and OTA without probiotics was about 90%, and 30%, respectively, depending on several factors, such as food product, contamination level, compound and type of contamination (spiked versus naturally contaminated). The six probiotic bacteria showed varying binding capacity to AFB1 and OTA depending on the bacterial strain, toxin studied, type of food and contamination level. A reduction to a maximum of 37% and 73% as observed for the bioaccessibility of AFB1 and OTA in the presence of probiotic bacteria, respectively. This is the first report on the effect of probiotic bacteria on reducing the fraction of mycotoxins available for absorption in the gastrointestinal tract from different food products.
Prophylactic cranial irradiation or no prophylactic cranial irradiation in metastatic small cell lung cancer: is it a relevant question once again?

Even if chemotherapy is the cornerstone treatment of small cell lung cancer (SCLC), this disease has a particular propensity to recur locally and disseminate in the brain. Hence, there have been several randomized trials assessing the role of thoracic and brain radiotherapy (1). Two individual patient data-based meta-analyses showed that thoracic radiotherapy and prophylactic cranial irradiation (PCI) should be part of the therapeutic strategy (2,3).
Thickness Scaling for ARC Discharges on Electron-Beam-Charged Dielectrics

A study of arc discharges on various thicknesses of electron-beam-charged Mylar, FEP Teflon and Kapton shows that the peak substrate current and the energy dissipated in a load resistor both exhibit maxima at a particular thickness of the order of 50 ¿m, for one set of experiment parameters. The experiments also show that, as thickness increases, this particular thickness is the transition from near-constant to decreasing released charge, and, for Mylar, from decreasing to near-constant arc duration. This transition is interpreted as being caused primarily for thin specimens by punchthrough formation and possibly influenced by the transition from conduction-dominated to emission-dominated charging. Additional low-energy ion exposure is shown to weaken and sometimes eliminate the arc discharges without radically altering the thickness scaling. At low fluxes, the incident ions are focussed into a central spot.
Current Controversies in Rehabilitation After Anterior Cruciate Ligament Reconstruction

Rehabilitation concepts after anterior cruciate ligament (ACL) reconstruction continue to advance rapidly. A review of the recent literature reveals numerous aspects of the rehabilitation program, the subject of investigation, and validation. Areas discussed in this article include the efficacy of functional bracing after ACL reconstruction and perturbation training programs in nonoperative, preoperative and postoperative rehabilitation programs. Also discussed is the need for criteria-based progression through the late stages (return to sports) of the ACL reconstruction rehabilitation.