Miracle-dz/UniFAR-FTUs huggingface dataset:
Support Measures to Estimate the Reliability of Evolutionary Events Predicted by Reconciliation Methods

The genome content of extant species is derived from that of ancestral genomes, distorted by evolutionary events such as gene duplications, transfers and losses. Reconciliation methods aim at recovering such events and at localizing them in the species history, by comparing gene family trees to species trees. These methods play an important role in studying genome evolution as well as in inferring orthology relationships. A major issue with reconciliation methods is that the reliability of predicted evolutionary events may be questioned for various reasons: Firstly, there may be multiple equally optimal reconciliations for a given species tree–gene tree pair. Secondly, reconciliation methods can be misled by inaccurate gene or species trees. Thirdly, predicted events may fluctuate with method parameters such as the cost or rate of elementary events. For all of these reasons, confidence values for predicted evolutionary events are sorely needed. It was recently suggested that the frequency of each event in the set of all optimal reconciliations could be used as a support measure. We put this proposition to the test here and also consider a variant where the support measure is obtained by additionally accounting for suboptimal reconciliations. Experiments on simulated data show the relevance of event supports computed by both methods, while resorting to suboptimal sampling was shown to be more effective. Unfortunately, we also show that, unlike the majority-rule consensus tree for phylogenies, there is no guarantee that a single reconciliation can contain all events having above 50% support. In this paper, we detail how to rely on the reconciliation graph to efficiently identify the median reconciliation. Such median reconciliation can be found in polynomial time within the potentially exponential set of most parsimonious reconciliations.
Decay of References to Web sites in Articles Published in General Medical Journals: Mainstream vs Small Journals

Summary Background: Over the last decade, Web sites (URLs) have been increasingly cited in scientific articles. However, the contents of the page of interest may change over the time. Objective: To investigate the trend of citation to URLs in five general medical journals since January 2006 to June 2013 and to compare the trends in mainstream journals with small journals. Methods: References of all original articles and review articles published between January 2006 and June 2013 in three regional journals – Archives of Iranian Medicine (AIM), Eastern Mediterranean Health Journal (EMHJ), and Journal of Postgraduate Medical Institute (JPMI) – and two mainstream journals – The Lancet and British Medical Journal (BMJ) – were reviewed. The references were checked to determine the frequency of citation to URLs as well as the rate of accessibility of the URLs cited. Results: A total of 2822 articles was studied. Since January 2006 onward, the number of citations to URLs increased in the journals (doubling time ranged from 4.2 years in EMHJ to 13.9 years in AIM). Overall, the percentage of articles citing at least one URL has increased from 24% in 2006 to 48.5% in 2013. Accessibility to URLs decayed as the references got old (half life ranged from 2.2 years in EMHJ to 5.3 years in BMJ). The ratio of citation to URLs in the studied mainstream journals, as well as the ratio of URLs accessible were significantly (p<0.001) higher than the small medical journals. Conclusion: URLs are increasingly cited, but their contents decay with time. The trend of citing and decaying URLs are different in mainstream journals compared to small medical journals. Decay of URL contents would jeopardize the accuracy of the references and thus, the body of evidence. One way to tackle this important obstacle is to archive URLs permanently. Citation: Habibzadeh P. Decay of references to web sites in articles published in general medical journals: Mainstream vs small journals. Appl Clin Inf 2013; 4: 455–464 http://dx.doi. org/10.4338/ACI-2013-07-RA-0055
Long-Lasting Effects of Human Mesenchymal Stem Cell Systemic Administration on Pain-Like Behaviors, Cellular, and Biomolecular Modifications in Neuropathic Mice

Background: Neuropathic pain (NP) is an incurable disease caused by a primary lesion in the nervous system. NP is a progressive nervous system disease that results from poorly defined neurophysiological and neurochemical changes. Its treatment is very difficult. Current available therapeutic drugs have a generalized nature, sometime acting only on the temporal pain properties rather than targeting the several mechanisms underlying the generation and propagation of pain. Methods: Using biomolecular and immunohistochemical methods, we investigated the effect of the systemic injection of human mesenchymal stem cells (hMSCs) on NP relief. We used the spared nerve injury (SNI) model of NP in the mouse. hMSCs were injected into the tail vein of the mouse. Stem cell injection was performed 4 days after sciatic nerve surgery. Neuropathic mice were monitored every 10 days starting from day 11 until 90 days after surgery. Results: hMSCs were able to reduce pain-like behaviors, such as mechanical allodynia and thermal hyperalgesia, once injected into the tail vein. An anti-nociceptive effect was detectable from day 11 post surgery (7 days post cell injection). hMSCs were mainly able to home in the spinal cord and pre-frontal cortex of neuropathic mice. Injected hMSCs reduced the protein levels of the mouse pro-inflammatory interleukin IL-1β and IL-17 and increased protein levels of the mouse anti-inflammatory interleukin IL-10, and the marker of alternatively activated macrophages CD106 in the spinal cord of SNI mice. Conclusion: As a potential mechanism of action of hMSCs in reducing pain, we suggest that they could exert their beneficial action through a restorative mechanism involving: (i) a cell-to-cell contact activation mechanism, through which spinal cord homed hMSCs are responsible for switching pro-inflammatory macrophages to anti-inflammatory macrophages; (ii) secretion of a broad spectrum of molecules to communicate with other cell types. This study could provide novel findings in MSC pre-clinical biology and their therapeutic potential in regenerative medicine.
The U.S. National Sheep Improvement Program: across-flock genetic evaluations and new trait development.

The U.S. National Sheep Improvement Program (NSIP) began in 1987 to provide within-flock genetic evaluations for the American sheep industry. An evaluation of operating procedures and methodology for NSIP began in 1993 and has resulted in across-flock, multiple-trait EPD for three breeds: Targhee, Suffolk, and Polypay. Traits reported in the across-flock analyses included direct and maternal effects on weaning weight in all breeds, postweaning weight at 120 d in Suffolk and Polypay and at 365 d in Targhee, greasy fleece weight in Targhee and Polypay, and wool fiber diameter in Targhee. Number born per ewe lambing was also evaluated in single-trait analyses for all breeds. Genetic parameters were derived separately for each breed. Important genetic antagonisms include an unfavorable genetic correlation of . 51 between fleece weight and fiber diameter in Targhee and a genetic correlation of -. 55 between direct and maternal effects on weaning weight in Polypay. Estimates of genetic trends between 1987 and 1995 were consistent with perceived breed roles. In Targhee, direct and maternal effects on body weights increased, fiber diameter declined, fleece weight was maintained, and number born declined. In Suffolk, direct effects on body weight increased, but number born and maternal effects on weaning weight did not change. In Polypay, number born and maternal contributions to weaning weight increased, but direct genetic merit for body weight declined. Prospective enhancements to NSIP include methods for genetic evaluation of performance in accelerated lambing and of carcass leanness and development of breeding objectives and selection aids for various production systems.
On selective laser melting of ultra high carbon steel: Effect of scan speed and post heat treatment

Selective laser melting is a laser‐based additive manufacturing process applying layer manufacturing technology and is used to produce dense parts from metallic powders. The application of selective laser melting on carbon steels is still limited due to difficulties arising from carbon content. This experimental investigation aims at gaining an understanding of the application of the process on ultra high carbon steel, which is a special alloy with remarkable structural properties suitable for different industrial applications. The feedstock ultra high carbon steel (2.1% C) powder, 20 μm to 106 μm was prepared by water atomizing technique. This powder was used for the selective laser melting to build specimens 10×10×40 mm in dimensions. To decrease the thermal stresses during layer by layer building, laser scanning was done through 5×5 mm random island patterns while layer thickness was 30 μm. Laser beam diameter, maximum power output, layer thickness and scan speed range were 0.2 mm, 100 W, 30 μm and 50–200 mm/s respectively. The process was done inside high purity nitrogen environment, with less than 0.5% oxygen content. The results illustrate the influence of scan speed from 50 to 200 mm/s on product geometry and dimensions, surface roughness, internal porosity and cracks, microstructure and surface hardness. The effect of post heat treatment by heating and holding for one hour (annealing) at different temperatures of 700°C, 750°C, 950°C is studied. The results indicate that selective laser melting is able to produce near to 95% density of ultra high carbon steel parts with acceptable geometry and surface quality. Porosity cracks, and microstructure formed during the process could be controlled through proper selection of process parameters and post heat treatment. Industrial ultra high carbon steel products can be rapidly fabricated by selective laser melting.
Influences on Adaptive Planning to Reduce Flood Risks among Parishes in South Louisiana

Residents of south Louisiana face a range of increasing, climate-related flood exposure risks that could be reduced through local floodplain management and hazard mitigation planning. A major incentive for community planning to reduce exposure to flood risks is offered by the Community Rating System (CRS) of the National Flood Insurance Program (NFIP). The NFIP encourages local collective action by offering reduced flood insurance premiums for individual policy holders of communities where suggested risk-reducing measures have been implemented. This preliminary analysis examines the extent to which parishes (counties) in southern Louisiana have implemented the suggested policy actions and identifies key factors that account for variation in the implementation of the measures. More measures implemented results in higher CRS scores. Potential influences on scores include socioeconomic attributes of residents, government capacity, average elevation and past flood events. The results of multiple regression analysis indicate that higher CRS scores are associated most closely with higher median housing values. Furthermore, higher scores are found in parishes with more local municipalities that participate in the CRS program. The number of floods in the last five years and the revenue base of the parish does not appear to influence CRS scores. The results shed light on the conditions under which local adaptive planning to mitigate increasing flood risks is more likely to be implemented and offer insights for program administrators, researchers and community stakeholders.
Toll-like receptor 9 mediates invasion and predicts prognosis in squamous cell carcinoma of the mobile tongue.

BACKGROUND Toll-like receptor 9 (TLR9) is a cellular receptor, which recognizes bacterial and host-derived DNA. Stimulation of TLR9 induces cellular invasion via matrix metalloproteinase 13 (MMP-13). The aim of this study was to evaluate the role of TLR9 in invasion of oral tongue squamous cell carcinoma (OTSCC). METHODS The effects of TLR9 ligands on oral squamous cell carcinoma cell lines were studied with invasion and migration assays, as well as in a myoma organotypic model. RESULTS The TLR9 ligand, CpG-ODN, increased invasion and migration in OTSCC lines. These effects were reduced by TLR9 siRNA or inhibition with TLR9 antibodies. Immunohistochemical analysis of tissues from 195 patients with OTSCC revealed that TLR9 was expressed in 181/195 carcinomas. The expression of TLR9 was higher in the malignant cells than in the normal epithelium. High TLR9 expression was associated with high MMP-13 expression and poor differentiation. High TLR9 expression was also identified as an independent predictor of poor prognosis (HR 1.810, 95% CI [1.053-3.112]). CONCLUSION Toll-like receptor 9 mediates OTSCC invasion and migration in vitro and is an independent prognostic factor of OTSCC. Inhibition of TLR9 may be a novel therapeutic opportunity in oral cancer.
Rarefied Transitional Bridging of Blunt Body Aerodynamics

The bridging procedures discussed provide an accurate engineering method for predicting rarefied transitional aerodynamics of spherically-blunted cone entry vehicles. The single-point procedure offers a way to improve the bridging procedures while minimizing the computational effort. However, the accuracy of these procedures ultimately depends on accurate knowledge of the aerodynamics in the free-molecular and continuum limits. The excellent agreement shown for DSMC predictions and bridging relations with the Viking flight data in transitional regime enhance the coincidence in these procedures.
INCREASED EXPRESSION OF BIGLYCAN mRNA IN PRESSURE-OVERLOADED RAT HEART

Biglycan mRNA expression in rat myocardium after abdominal aortic banding with renal ischemia was examined. The Northern blot analysis demonstrated that expression of biglycan mRNA in the pressure-overloaded hearts on days 2, 7, 14 and 28 was 2.88 ± 0.89, 2.32 ± 0.49, 2.17 ± 0.57 and 1.81 ± 0.46-fold higher, respectively, than that in the sham-operated hearts. In situ hybridization showed an increased density of biglycan mRNA signal-positive cells in the pressure-overloaded hearts. The cells with positive signals were spindle-shaped mesenchymal cells in the myocardial interstitium. A marked increase in biglycan mRNA signal expression was also observed in endothelial cells and smooth muscle cells of the thickened myocardial capillary wall. These results demonstrated an increase in biglycan mRNA in the pressure-overloaded heart in mesenchymal cells in the myocardial interstitium, and in endothelial and smooth muscle cells of the capillaries, indicating that biglycan contributes to the ventricular and vascular remodeling in response to pressure overload.
Analysis of Gas6 in Human Platelets and Plasma

Objective—Gas6 is a member of the vitamin K-dependent protein family. Gas6-deficient mice were found to be resistant to thrombosis because of defective platelet function. Mouse Gas6 was demonstrated to be present in platelets and found to be involved in platelet aggregation. The aim of this study was to investigate the presence of Gas6 in human platelets and plasma and determine its role in platelet function. Methods and Results—The presence of Gas6 in human platelets and plasma was analyzed using sensitive immunologic methods. Mass spectrometry and ELISA were used to identify and quantify Gas6 in plasma. Gas6 was demonstrated to be present in human plasma, at a concentration determined to be 13 to 23 ng/mL (0.16 to 0.28 nM). Furthermore, plasma Gas6 levels were found to be lower in patients administered with warfarin. However, Gas6 was undetectable in human platelets. Conclusions—This is the first report to identify and quantify Gas6 in human plasma. However, Gas6 protein was not detected in human platelets, suggesting that any potential platelet-specific function could be because of Gas6 from the circulation. These findings open up new directions regarding the role of Gas6 in normal and pathophysiological situations such as inflammation, autoimmune disease, thrombosis and arteriosclerosis.
Retinal Wave Behavior through Activity-Dependent Refractory Periods

In the developing mammalian visual system, spontaneous retinal ganglion cell (RGC) activity contributes to and drives several aspects of visual system organization. This spontaneous activity takes the form of spreading patches of synchronized bursting that slowly advance across portions of the retina. These patches are non-repeating and tile the retina in minutes. Several transmitter systems are known to be involved, but the basic mechanism underlying wave production is still not well-understood. We present a model for retinal waves that focuses on acetylcholine mediated waves but whose principles are adaptable to other developmental stages. Its assumptions are that a) spontaneous depolarizations of amacrine cells drive wave activity; b) amacrine cells are locally connected, and c) cells receiving more input during their depolarization are subsequently less responsive and have longer periods between spontaneous depolarizations. The resulting model produces waves with non-repeating borders and randomly distributed initiation points. The wave generation mechanism appears to be chaotic and does not require neural noise to produce this wave behavior. Variations in parameter settings allow the model to produce waves that are similar in size, frequency, and velocity to those observed in several species. Our results suggest that retinal wave behavior results from activity-dependent refractory periods and that the average velocity of retinal waves depends on the duration a cell is excitatory: longer periods of excitation result in slower waves. In contrast to previous studies, we find that a single layer of cells is sufficient for wave generation. The principles described here are very general and may be adaptable to the description of spontaneous wave activity in other areas of the nervous system.
Analysis of cytosine-adenine repeats in P1 promoter region of IGF-1 gene in peripheral blood cells and cervical tissue samples of females with cervical intraepithelial lesions and squamous cervical cancer

High oncogenic risk human papillomaviruses (HPVs) are closely associated with cancer of the cervix. However, HPV infection alone may not be sufficient to cause cervical cancer, and other factors or cofactors may have a cumulative effect on the risk of progression from cervical HPV infection to cancer. The present study investigates the cytosine-adenine (CA) repeat polymorphism in the P1 promoter region of the insulin-like growth factor-1 (IGF-1) gene among cervical precancerous and cancer patients and healthy control females. The association between these polymorphisms, tissue and blood serum levels of IGF-1, and cervical cancer risk and progression is evaluated. The material for analysis consisted of blood cells and postoperative tissues from patients diagnosed with low-grade squamous intraepithelial lesions (L-SILs), high-grade squamous intraepithelial lesions (H-SILs) and invasive cervical cancer (ICC). A polymerase chain reaction amplification and the sequencing of DNA were used for the identification of (CA)n repeats in the IGF-1 P1 region and detection of HPV DNA. The blood serum concentration of IGF was determined by enzyme-linked immunosorbent assay. The identification of the IGF-1 protein in the cervical tissues was performed by immunohistochemical analysis. The range of the length of the CA repeats in the study DNA was 11 to 21. However, the most common allele length and genotype in the control and study patients from serum and tissues was 19 CA repeats and a homozygous genotype of CA19/19. Statistically significant differences in the concentration of IGF-1 in the blood serum were observed between H-SILs and controls, only (p=0.047). However, the concentration of IGF-1 in the group of females with CA19/19, CA19<19 and CA19>19 was significantly higher in the group of patients with H-SIL (P=0.041) and ICC (P=0.048) in comparison with the control group. An association was detected between CA repeat length <19 and/or >19, IGF concentration in blood serum and tissues and the development of cervical cancer.
Bilayer Effects of Antimalarial Compounds

Because of the perpetual development of resistance to current therapies for malaria, the Medicines for Malaria Venture developed the Malaria Box to facilitate the drug development process. We tested the 80 most potent compounds from the box for bilayer-mediated effects on membrane protein conformational changes (a measure of likely toxicity) in a gramicidin-based stopped flow fluorescence assay. Among the Malaria Box compounds tested, four compounds altered membrane properties (p< 0.05); MMV007384 stood out as a potent bilayer-perturbing compound that is toxic in many cell-based assays, suggesting that testing for membrane perturbation could help identify toxic compounds. In any case, MMV007384 should be approached with caution, if at all.
Increased Resistance to Biotrophic Pathogens in the Arabidopsis Constitutive Induced Resistance 1 Mutant Is EDS1 and PAD4-Dependent and Modulated by Environmental Temperature

The Arabidopsis constitutive induced resistance 1 (cir1) mutant displays salicylic acid (SA)-dependent constitutive expression of defence genes and enhanced resistance to biotrophic pathogens. To further characterise the role of CIR1 in plant immunity we conducted epistasis analyses with two key components of the SA-signalling branch of the defence network, ENHANCED DISEASE SUSCEPTIBILITY1 (EDS1) and PHYTOALEXIN DEFICIENT4 (PAD4). We demonstrate that the constitutive defence phenotypes of cir1 require both EDS1 and PAD4, indicating that CIR1 lies upstream of the EDS1-PAD4 regulatory node in the immune signalling network. In light of this finding we examined EDS1 expression in cir1 and observed increased protein, but not mRNA levels in this mutant, suggesting that CIR1 might act as a negative regulator of EDS1 via a post-transcriptional mechanism. Finally, as environmental temperature is known to influence the outcome of plant-pathogen interactions, we analysed cir1 plants grown at 18, 22 or 25°C. We found that susceptibility to Pseudomonas syringae pv. tomato (Pst) DC3000 is modulated by temperature in cir1. Greatest resistance to this pathogen (relative to PR-1:LUC control plants) was observed at 18°C, while at 25°C no difference in susceptibility between cir1 and control plants was apparent. The increase in resistance to Pst DC3000 at 18°C correlated with a stunted growth phenotype, suggesting that activation of defence responses may be enhanced at lower temperatures in the cir1 mutant.
Piezoelectric Effect in Human Bones Studied in Nanometer Scale

The piezoelectric effect has been studied in wet and dry human bones using a piezoresponse force microscope (PFM). It allowed to measure piezoelectric response with nanometer scale resolution directly in a collagen matrix and to obtain a piezoresponse image near the Haversian channel. Dielectric response and dc conductivity have been measured. Theoretical calculations taking into account the inhomogeneity of the electric field under the PFM tip apex and its screening in highly conductive bone samples were performed for obtaining the piezoelectric coefficient in the bone collagen.
Parahippocampal gray matter density in panic disorder: a voxel-based morphometric study.

OBJECTIVE The authors examined possible cerebral gray matter abnormalities in patients with panic disorder. METHOD Gray matter concentration in 18 panic disorder outpatients and 18 healthy subjects was compared by using a voxel-based morphometry approach. RESULTS Gray matter density of the left parahippocampal gyrus was significantly lower in patients with panic disorder compared with healthy subjects. CONCLUSIONS This result provides further support for the involvement of the parahippocampal area in the pathophysiology of panic disorder.