Miracle-dz/UniFAR-FTUs huggingface dataset:
Life history effects on the molecular clock of autosomes and sex chromosomes

Significance Recent estimates of mutation rates obtained by sequencing human pedigrees have challenged conceptions about split times between humans and our closest living relatives. In particular, estimates of human split times from chimpanzees and gorillas based on the new mutation rate estimates are more than twofold shorter than previously believed, seemingly at odds with the fossil record. Here we show that accounting for the effects of sex-specific life histories on mutation rates along the hominid phylogeny largely bridges this apparent gap and leads to more accurate split time estimates. Doing so can also explain other intriguing phylogenetic patterns in hominid and mammalian evolution. One of the foundational results in molecular evolution is that the rate at which neutral substitutions accumulate on a lineage equals the rate at which mutations arise. Traits that affect rates of mutation therefore also affect the phylogenetic “molecular clock. ” We consider the effects of sex-specific generation times and mutation rates in species with two sexes. In particular, we focus on the effects that the age of onset of male puberty and rates of spermatogenesis have likely had in hominids (great apes), considering a model that approximates features of the mutational process in mammals, birds, and some other vertebrates. As we show, this model can account for a number of seemingly disparate observations: notably, the puzzlingly low X-to-autosome ratios of substitution rates in humans and chimpanzees and differences in rates of autosomal substitutions among hominine lineages (i.e., humans, chimpanzees, and gorillas). The model further suggests how to translate pedigree-based estimates of human mutation rates into split times among extant hominoids (apes), given sex-specific life histories. In so doing, it largely bridges the gap reported between estimates of split times based on fossil and molecular evidence, in particular suggesting that the human–chimpanzee split may have occurred as recently as 6.6 Mya. The model also implies that the “generation time effect” should be stronger in short-lived species, explaining why the generation time has a major influence on yearly substitution rates in mammals but only a subtle one in human pedigrees.
What Determines the Level of Short-Selling Activity?

I test several explanations for the short-sale trading for a sample of the NYSE and the Nasdaq stocks during the 1988-2002 period. I find that short-selling activity is positively related to arbitrage opportunities and hedging demand, and negatively related to previous short-term returns. ANOVA analysis shows that the stock option listing is the most dominant variable in explaining the short-selling level. The short-selling level is more positively related to the dummy variables for convertible debt and option listing during the bubble period, suggesting that there was more room for arbitrage opportunity during that volatile period.
Flavonoids and Sesquiterpene Lactones from Artemisia absinthium and Tanacetum parthenium against Schistosoma mansoni Worms

Human schistosomiasis, caused by trematode worms of the genus Schistosoma, is one of the most significant neglected tropical diseases, affecting more than 200 million individuals worldwide and praziquantel is the only available drug to treat this disease. Artemisia absinthium L. and Tanacetum parthenium L. are species popularly used as anthelmintics. We investigated the in vitro schistosomicidal activity of crude extracts of A. absinthium (AA) and T. parthenium (TP) and their isolated compounds. AA and TP, at 200 μg/mL, were active, causing 100% mortality of all adult worms. Chromatographic fractionation of AA leads to isolation of artemetin and hydroxypelenolide, while santin, apigenin, and parthenolide were isolated from TP. Artemetin, hydroxypelenolide, santin, and apigenin, at 100 μM, were inactive against adult worms. Parthenolide (12.5 to 100 μM) caused 100% mortality, tegumental alterations, and reduction of motor activity of all adult worms of S. mansoni, without affecting mammalian cells. Confocal laser scanning microscopy showed tegumental morphological alterations and changes on the numbers of tubercles of S. mansoni worms. This report provides the first evidence for the in vitro activity of parthenolide against adult worms of S. mansoni, opening the route to further schistosomicidal studies with this compound.
Impact of Shorting Vias Placement on Embedded Planar Electromagnetic BandGap Structures Within Multilayer Printed Circuit Boards

This paper investigates the power integrity behavior of planar electromagnetic bandgap (EBG) structures embedded between two solid layers within the stack-up of a multilayer printed circuit board. The bandgap generation and power integrity performance of the embedded EBG can be achieved only by placing vias shorting the solid planes above and below the patterned layer. The vias inhibit the resonances of the cavity made by the two solid planes, ensuring the designed bandgap, as if the planar EBG was laid out on an outer stack-up layer. The impact of the stitching vias' number and location is addressed and the concepts of regular, global, random, or local via placement are introduced.
Mining Code Clustering ( DMCC ) : An Approach Supporting Software Maintenance and Comprehension Technical Report

Problems in software maintenance occur when programs are modified with little understanding of the overall source code organisation and of the full impact of changes. Most software systems are structured as a number of subsystems, consisting of code that collaborates to provide the composed functionality to the program. An important aspect of program understanding is to perceive this subsystem structure. Cluster Analysis can be of use in deriving a meaningful subsystem structure of a program from its source code. The idea is to represent a program as a number of entities, which are grouped in clusters representing subsystems, based on their similarity measured by means of related functionality or data use. Central issues for any clustering-based approach are the specification of program entities and their attributes, similarity metrics, and clustering strategy. We propose here Data Mining Code Clustering (DMCC), an approach for supporting software maintenance and program comprehension that uses input data extracted from a C/C++ program and produces its abstraction as a number of subsystems. New possibilities in the form of weighting rationales and a framework for similarity metrics based on these, and an analysis of these from a novel point of view is a main contribution. The approach was evaluated by implementing a corresponding tool that was used for experimentation with programs of various sizes and languages. Results showed that the approach is useful for deriving accurate subsystem abstraction and identifying interrelationships amongst modules. Factors influencing the feasibility of this approach are identified and directions for improvements are discussed.
Life Experiences that Contributed to the Independence and Success in the Lives of Foster Care Alumni

The purpose of this qualitative study was to determine the factors which helped these foster care alumni to persevere and to succeed. The intent was to provide a framework for equipping youth in foster care more effectively by building on their strengths and the resources available in foster care. The study’s method incorporated the interviewing of ten ethnically diverse individuals who had experienced the foster care system. Based on their insights and the themes which emerged, the WARRIORS Model was created. This acronym represents the key themes derived from the interviews: Wounded, Advocacy, Reality of Belonging, Resources, Inspired to Succeed, Obtain Life Skills, Resilience and Spirituality. A Wounded past was the reality of every participant yet many found purpose and meaning in their Advocacy roles. The Reality of Belonging was vital in each of their lives in addition to accessing Resources for post-high school educational and housing options, both implicating the significance of foster parent involvement. All were Inspired to Succeed both personally and educationally and were receptive to Obtain the Life Skills necessary for their future independence and success. They demonstrated such hopeful countenance and profound Resilience, in addition to accessing and benefitting from their chosen avenues of Spirituality. Finally, while navigating through both the negative and positive aspects of their lives, these youth have revealed the strength of the human spirit which has given them every right to be identified as WARRIORS. The WARRIORS Model can be utilized by clinicians and professionals involved in the systems addressing the needs of youth in foster care and training foster parents. Greater opportunities are needed for youth in foster care to advocate for themselves and others with the hope of gaining a sense of worth as their opinions are valued by the adults claiming to represent them. Finally, further research is needed concerning the spiritual development of youth in foster care and ways in which we can assist in this promising aspect of cultivating resilience as evidenced in this study and other established research. The electronic version of this dissertation can be found at the OhioLink ETD Center, www.ohiolink. edu/etd.
Kinematic modeling of disk galaxies - III. The warped “Spindle” NGC 2685

This is the third of a series of papers in which the structure and kinematics of disk galaxies is studied. By employing direct tilted-ring fits to the data cube as introduced in Paper I, we analyzed the "Spindle" galaxy NGC 2685, previously regarded as a two-ringed polar ring galaxy. Deep HI and optical (i'-band) observations are presented. The HI observations strongly suggest that the gaseous structure of NGC 2685 does not consist of two separate mutually inclined regions, but forms a coherent, extremely warped disk, the appearance of two rings being due to projection effects. By comparing the HI total-intensity maps with the optical image, we demonstrate that at large radii a faint stellar disk is well aligned with the outer HI disk. The shape of the dust lanes obscuring the NE part of the inner stellar body indicates that, also at smaller radii, NGC 2685 possesses a disk containing gas, dust, and stars in which the various constituents are aligned. At smaller radii, this disk is kinematically decoupled from the central stellar body; hence, in the region of the bright, central stellar body, NGC 2685 appears to consist of two disks that share a common center, but have different orientation: a bright stellar lenticular body apparently devoid of dust and gas, and a heavily warped low-surface brightness disk containing stars, gas, and dust. The low-surface-brightness disk changes its orientation gradually and at large radii assumes the orientation of the central stellar S0 disk. Since, according to our analysis, the intrinsic orientation of the low-surface-brightness disk changes through 70 degrees, the gaseous disk is coherent, and is at no radius oriented perpendicularly with respect to the central stellar body, NGC 2685 is not likely to be a classical polar-ring galaxy.
The effects of spatial processing load and collaboration technology on team performance in a simulated C2 environment

Motivation -- To address the effects of spatial processing load and text-based collaborative tools on team performance in command and control environments. Research approach -- Thirty-two people served as paid participants in this study. Teams of two participants competed against a computer opponent in a RoboFlag simulation based on 'capture-the-flag. ' Participants either could or could not see their teammates' simulated vehicles during a trial, and they were restricted to no communication, verbal communication, text-based communication, or verbal and text communication. Findings/design -- Spatial processing load substantially impacted team performance and participants' ratings of workload and situational awareness. Team communication condition influenced workload, situational awareness, and team communications, but did not affect team performance. Take away message -- Results of the current experiment support and extend previous research concerning the effects of collaborative technologies on team performance in C2 environments.
Detection of Primary Malignancy and Metastases with FDG PET/CT in Patients with Cholangiocarcinomas: Lesion-based Comparison with Contrast Enhanced CT

The current National Comprehensive Cancer Network (NCCN) Guidelines consider the role of 2-deoxy-2- 18 F-fluoro-d-glucose positron emission tomography/computer tomography (FDG PET/CT) in the evaluation of cholangiocarcinoma (CCA) as "uncertain," and have recommended contrast enhanced computed tomography (CECT) but not FDG PET/CT as a routine imaging test for CCA workup. We set out to compare the diagnostic performance of FDG PET/CT and CECT in patients with CCA. The retrospective study included patients with CCA who underwent FDG PET/CT and CECT within 2-month interval between 2011 and 2013 in our hospital. Lesion-based comparison was conducted. Final diagnoses were made based on the composite clinical and imaging data with minimal 6-month follow-up. A total of 18 patients with 28-paired tests were included. There is a total of 142 true malignant lesions as revealed by the 6-paired pre-treatment and 22-paired post-treatment tests. On a lesion-based analysis, the sensitivities, specificities, positive predictive values (PPVs), negative predictive values (NPVs), and accuracies of PET/CT and CECT for detection of CCA were 96.5%, 55.5%, 97.2%, 50.0%, 94.1% and 62.2%, 66.7%, 96.7%, 10.0%, 62.5%, respectively. FDG PET/CT detected more intrahepatic malignant and extrahepatic metastases; and had significant higher sensitivity, NPV, and accuracy than CECT, while similar in specificity and PPV. No true positive lesion detected on CECT that was missed on PET/CT, and none of the false negative lesions on PET/CT were detected on CECT. Six patients had paired pretreatment tests, and FDG PET/CT results changed planned management in three patients. Our data suggest that FDG PET/CT detect more primary and metastatic lesions and lead to considerable changes in treatment plan in comparison with CECT.
The development of discontinuous

In this paper, we present an overview of the evolution of the discontin-uous Galerkin methods since their introduction in 1973 by Reed and Hill, in the framework of neutron transport, until their most recent developments. We show how these methods made their way into the main stream of computational uid dynamics and how they are quickly nding use in a wide variety of applications. We review the theoretical and algorithmic aspects of these methods as well as their applications to equations including nonlinear conservation laws, the compressible Navier-Stokes equations, and Hamilton-Jacobi-like equations.
Differential sensitivity of tumor targets to liver macrophage-mediated cytotoxicity.

Liver macrophages activated in vivo with bacterially derived lipopolysaccharide (LPS) display enhanced chemotaxis, phagocytosis, and oxidative metabolism. To determine if LPS also activates these mononuclear phagocytes for tumor cell killing, we compared the cytotoxic activity of macrophages from livers of rats treated with LPS (5 mg/kg, i.v.) with resident Kupffer cells. We found that both macrophage cell types displayed cytotoxicity towards rat N1S1 hepatoma and RBL-1 basophilic leukemia cells. Cytotoxicity of resident and LPS-activated liver macrophages towards these targets increased with cocultivation time, was dependent on the effector:target cell ratio, and appeared to involve extracellular lysis. No direct correlation between macrophage activation and cytotoxicity was observed towards these targets. While liver macrophages from LPS treated rats were more cytotoxic towards N1S1 cells, resident Kupffer cells were more cytotoxic towards RBL-1 cells. In further studies, resident Kupffer cells were also found to display extracellular cytolytic activity towards mouse P815 mastocytoma cells. In contrast, LPS-activated liver macrophage-mediated killing of these targets involved phagocytosis of intact tumor cells, as evidenced by light and electron microscopy and by uptake of 51Cr-labeled cells. These results suggest that cytotoxicity mediated by liver macrophages depends on the type of macrophage and the nature of the tumor cell target. In addition, cytotoxicity towards tumor targets appears to involve at least two different mechanisms including extracellular cytolysis and phagocytosis.
Hydrophobins in the Life Cycle of the Ectomycorrhizal Basidiomycete Tricholoma vaccinum

Hydrophobins—secreted small cysteine-rich, amphipathic proteins—foster interactions of fungal hyphae with hydrophobic surfaces, and are involved in the formation of aerial hyphae. Phylogenetic analyses of Tricholoma vaccinum hydrophobins showed a grouping with hydrophobins of other ectomycorrhizal fungi, which might be a result of co-evolution. Further analyses indicate angiosperms as likely host trees for the last common ancestor of the genus Tricholoma. The nine hydrophobin genes in the T. vaccinum genome were investigated to infer their individual roles in different stages of the life cycle, host interaction, asexual and sexual development, and with respect to different stresses. In aerial mycelium, hyd8 was up-regulated. In silico analysis predicted three packing arrangements, i.e., ring-like, plus-like and sheet-like structure for Hyd8; the first two may assemble to rodlets of hydrophobin covering aerial hyphae, whereas the third is expected to be involved in forming a two-dimensional network of hydrophobins. Metal stress induced hydrophobin gene hyd5. In early steps of mycorrhization, induction of hyd4 and hyd5 by plant root exudates and root volatiles could be shown, followed by hyd5 up-regulation during formation of mantle, Hartig’ net, and rhizomorphs with concomitant repression of hyd8 and hyd9. During fruiting body formation, mainly hyd3, but also hyd8 were induced. Host preference between the compatible host Picea abies and the low compatibility host Pinus sylvestris could be linked to a stronger induction of hyd4 and hyd5 by the preferred host and a stronger repression of hyd8, whereas the repression of hyd9 was comparable between the two hosts.
Reconsidering Fuller’s concerns-based model of teacher development: comparing regular and academic student teachers’ changing concerns

theories as provided by the teacher training, experiences of student teachers during their internships and the practical know-how existing of a sensibility for in Preliminary to check for univariate and multivariate normality, univariate and multivariate outliers, linearity, multicolinearity and singularity and homogeneity of variance-covariance matrices, finding no
Influence of custom-made and prefabricated insoles before and after an intense run

Each time the foot contacts the ground during running there is a rapid deceleration that results in a shock wave that is transmitted from the foot to the head. The fatigue of the musculoskeletal system during running may decrease the ability of the body to absorb those shock waves and increase the risk of injury. Insoles are commonly prescribed to prevent injuries, and both custom-made and prefabricated insoles have been observed to reduce shock accelerations during running. However, no study to date has included a direct comparison of their behaviour measured over the same group of athletes, and therefore great controversy still exists regarding their effectiveness in reducing impact loading during running. The aim of the study was to analyse the acute differences in stride and shock parameters while running on a treadmill with custom-made and prefabricated insoles. Stride parameters (stride length, stride rate) and shock acceleration parameters (head and tibial peak acceleration, shock magnitude, acceleration rate, and shock attenuation) were measured using two triaxial accelerometers in 38 runners at 3.33 m/s before and after a 15-min intense run while using the sock liner of the shoe (control condition), prefabricated insoles and custom-made insoles. No differences in shock accelerations were found between the custom-made and the control insoles. The prefabricated insoles increased the head acceleration rate (post-fatigue, p = 0.029) compared to the control condition. The custom-made reduced tibial (pre-fatigue, p = 0.041) and head acceleration rates (pre-fatigue and post-fatigue, p = 0.01 and p = 0.046) compared to the prefabricated insoles. Neither the stride nor the acceleration parameters were modified as a result of the intense run. In the present study, the acute use of insoles (custom-made, prefabricated) did not reduce shock accelerations compared to the control insoles. Therefore, their effectiveness at protecting against injuries associated with elevated accelerations is not supported and remains unclear.
Hypolipidemic influence of Sargassum subrepandum: mechanism of action.

OBJECTIVES This study aimed to elucidate the role and mode of action of Sargassum subrepandum methanolic extract in management of dyslipidemia in adult female rats. MATERIAL AND METHODS Forty adult female Sprague Dawley rats were assigned into four groups: (1) lean control rats fed on standard diet, (2) dyslipidemia control fed on the atherogenic diet, (3) lean rats orally administered with 100 mg/kg b. wt of Sargassum subrepandum methanolic extract and (4) dyslipidemia rats orally administered with Sargassum subrepandum methanolic extract. Plasma lipid profile, serum MDA, NO, leptin, TNF-alpha and adiponectin levels were demonstrated in the all studied groups. RESULTS The results showed that feeding of rats with athrogenic diet caused significant elevation in plasma cholesterol, triglyceride, LDL, serum MDA, NO, leptin and TNF-alpha levels while, it produced significant decline in plasma HDL and serum adiponectin levels compared with lean control rats. However, treatment of dyslipidemia rats with Sargassum subrepandum methanolic extract induced significant improvement of plasma lipid profile, marked decrease in serum MDA, NO, leptin, TNF-alpha level in concomitant with remarkable increase in serum adiponectin level. CONCLUSIONS These results indicated that Sargassum subrepandum extract plays a vital role in ameliorating dyslipidemia and its complications particularly oxidative stress and implication. This could be attributed to the hypolipidemic effect, antilipidperoxidative activity and antinflammatory property of Sargassum subrepandum methanolic extract.