Miracle-dz/UniFAR-FTUs huggingface dataset:
Evolutionary conservation and divergence of the segmentation process in arthropods

A fundamental characteristic of the arthropod body plan is its organization in metameric units along the anterior–posterior axis. The segmental organization is laid down during early embryogenesis. Our view on arthropod segmentation is still strongly influenced by the huge amount of data available from the fruit fly Drosophila melanogaster (the Drosophila paradigm). However, the simultaneous formation of the segments in Drosophila is a derived mode of segmentation. Successive terminal addition of segments from a posteriorly localized presegmental zone is the ancestral mode of arthropod segmentation. This review focuses on the evolutionary conservation and divergence of the genetic mechanisms of segmentation within arthropods. The more downstream levels of the segmentation gene network (e.g., segment polarity genes) appear to be more conserved than the more upstream levels (gap genes, Notch/Delta signaling). Surprisingly, the basally branched arthropod groups also show similarities to mechanisms used in vertebrate somitogenesis. Furthermore, it has become clear that the activation of pair rule gene orthologs is a key step in the segmentation of all arthropods. Important findings of conserved and diverged aspects of segmentation from the last few years now allow us to draw an evolutionary scenario on how the mechanisms of segmentation could have evolved and led to the present mechanisms seen in various insect groups including dipterans like Drosophila. Developmental Dynamics 236:1379–1391, 2007. © 2007 Wiley‐Liss, Inc.
DFT Studies on cis-1,4-Polymerization of Dienes Catalyzed by a Cationic Rare-Earth Metal Complex Bearing an Ancillary PNP Ligand

Dnsity functional theory (DFT) calculations have been carried out for the highly selective cis-1,4-polymerization of butadiene catalyzed by a cationic rare-earth metal complex bearing an ancillary PNP ligand. It has been found that the chain initiation and propagation of butadiene polymerization occurs via the favorable cis-1,4-insertion route. The trans-1,4 and 1,2-insertion are unfavorable both kinetically and thermodynamically. The chain growth follows the π-allyl-insertion mechanism. The analyses of energy decomposition of transition states indicate that the likelihood of rival insertion pathways is predominantly controlled by the interaction energy of butadiene with a metal center and the deformation energy of butadiene moiety. The electronic factor of the central metal has a decisive influence on the cis- vs. trans-insertion and the regioselectivity (cis-1,4- vs. cis-1,2-insertion) is mainly determined by steric hindrance. Tetrahydrofuran (THF) coordination made monomer insertion less favorable compared with THF-free case and had more noticeable impact on the trans-monomer insertion compared with the cis case. During the chain propagation, cis-insertion of monomer facilitates THF de-coordination and the THF molecule could therefore dissociate from the central metal.
Identification of Histone Mutants That Are Defective for Transcription-Coupled Nucleosome Occupancy

ABSTRACT Our previous studies of Saccharomyces cerevisiae described a gene repression mechanism where the transcription of intergenic noncoding DNA (ncDNA) (SRG1) assembles nucleosomes across the promoter of the adjacent SER3 gene that interfere with the binding of transcription factors. To investigate the role of histones in this mechanism, we screened a comprehensive library of histone H3 and H4 mutants for those that derepress SER3. We identified mutations altering eight histone residues (H3 residues V46, R49, V117, Q120, and K122 and H4 residues R36, I46, and S47) that strongly increase SER3 expression without reducing the transcription of the intergenic SRG1 ncDNA. We detected reduced nucleosome occupancy across SRG1 in these mutants to degrees that correlate well with the level of SER3 derepression. The histone chromatin immunoprecipitation experiments on several other genes suggest that the loss of nucleosomes in these mutants is specific to highly transcribed regions. Interestingly, two of these histone mutants, H3 R49A and H3 V46A, reduce Set2-dependent methylation of lysine 36 of histone H3 and allow transcription initiation from cryptic intragenic promoters. Taken together, our data identify a new class of histone mutants that is defective for transcription-dependent nucleosome occupancy.
Effect of Age on Anthropometric and Physical Performance Measures in Professional Baseball Players

Abstract Mangine, GT, Hoffman, JR, Fragala, MS, Vazquez, J, Krause, MC, Gillett, J, and Pichardo, N. Effect of age on anthropometric and physical performance measures in professional baseball players. J Strength Cond Res 27(2): 375–381, 2013—The purpose of this study was to investigate age-related changes in anthropometric and performance variables in professional baseball players. Baseball players (n = 1,157) from several professional baseball organizations were categorized into 7 cohorts based upon age. All adolescent athletes were categorized as age group 1 (AG1), whereas the next 5 groups (AG2–AG6) consisted of players 20–22, 23–25, 26–28, 29–31, and 31–34 years, respectively. The final group (AG7) comprised athletes ≥35 years. All performance assessments were part of the athlete's normal preseason training camp testing routine. Field assessments were used to analyze lower-body power, speed, agility, grip strength, and body composition. The players were heaviest between the ages of 29 and 31 (AG5), and their body mass in that age group was 10.1% (p = 0.004) greater than that of AG1. A 7.0% increase (p = 0.000) in lean body mass occurred between AG1 and AG5. No differences in 10-yd sprint times or agility were seen across any age group or position. A 2.0 seconds (p = 0.001) slower run time for the 300-yd shuttle was seen between AG4 and AG5 for all positions combined. Elevations in grip strength were seen at AG4 compared with AG1 (p = 0.001) and AG2 (p = 0.007) for all positions combined. No other differences were noted. Lower-body power was increased for all positions combined from AG1 to AG3 (p = 0.007). This pattern was similar to that observed in position players, but a 12.4% decrease (p = 0.024) in VJMP was seen between AG7 and AG5 in pitchers. Results of this study indicate that lower-body power is maintained in baseball players until the age of 29–31, whereas speed, agility, and grip strength are maintained in players able to play past the age of 35 years. Age-related differences observed in this study suggest that athletes focus on their strength and conditioning programs to extend the length of their professional careers.
Immediate anti‐tumor necrosis factor‐α (etanercept) therapy enhances axonal regeneration after sciatic nerve crush

Peripheral nerve regeneration begins immediately after injury. Understanding the mechanisms by which early modulators of axonal degeneration regulate neurite outgrowth may affect the development of new strategies to promote nerve repair. Tumor necrosis factor‐α (TNF‐α) plays a crucial role in the initiation of degenerative cascades after peripheral nerve injury. Here we demonstrate using real‐time Taqman quantitative RT‐PCR that, during the time course (days 1–60) of sciatic nerve crush, TNF‐α mRNA expression is induced at 1 day and returned to baseline at 5 days after injury in nerve and the corresponding dorsal root ganglia (DRG). Immediate therapy with the TNF‐α antagonist etanercept (fusion protein of TNFRII and human IgG), administered systemically (i.p.) and locally (epineurially) after nerve crush injury, enhanced the rate of axonal regeneration, as determined by nerve pinch test and increased number of characteristic clusters of regenerating nerve fibers distal to nerve crush segments. These fibers were immunoreactive for growth associated protein‐43 (GAP‐43) and etanercept, detected by anti‐human IgG immunofluorescence. Increased GAP‐43 expression was found in the injured nerve and in the corresponding DRG and ventral spinal cord after systemic etanercept compared with vehicle treatments. This study established that immediate therapy with TNF‐α antagonist supports axonal regeneration after peripheral nerve injury. © 2009 Wiley‐Liss, Inc.
Probing glucocorticoid‐dependent osteogenesis in rat and chick cells in vitro by specific blockade of osteoblastic differentiation with progesterone and RU38486

Glucocorticoids and sex‐steroids can modulate osteogenesis in vivo and in vitro. Although the effects of glucocorticoids on bone cells in vitro have been described in detail, the role of sex‐steroids is not as well defined. We examined whether sex‐steroids influence bone metabolism indirectly by regulating glucocorticoid effects on bone. Interactions of the sex‐steroid progesterone or its analog RU38486 with the glucocorticoid dexamethasone (dex) were studied in functional assays of osteogenesis. Three osteoblastic models were evaluated:(1) the rat bone marrow stromal cell (RBMC) nodule system; (2) the chick periosteal osteogenesis (CPO) model; and (3) ROS 17/2.8 cells. RU38486, progesterone, and unlabelled dex competitively inhibited 3H‐dex uptake by ROS 17/2.8 cells as well as its (3H‐dex) binding to cytosol preps.
Active Learning with the CyberCIEGE Video Game

Hands-on exercises promote active learning where student experience reinforces material presented in lectures or reading assignments [1]. Drawing the student into a meaningful context where student decisions have clear consequences strengthens the learning experience and thus improves the potential for internalization of knowledge. The CyberCIEGE video game was designed to confront students with computer security decision points within an environment that encourages experimentation, failure and reflection. The game includes over twenty scenarios that address a range of computer and network security concepts. CyberCIEGE is extensible through use of a scenario development language that allows instructors to create and customize game scenarios. The Naval Postgraduate School uses the game in our Introduction to Computer Security course, and it has been used by hundreds of educational institutions worldwide. The game's tools allow ongoing experimentation with the student's learning experience. Student assessment is facilitated by log generation, collection and analysis. These logs help the game's developers identify areas within scenarios that may be confusing or may require additional player feedback. Ongoing development is focused on ultimately adapting the game and its student assessment functions for deployment in a broader range of formal education environments.
Parents' needs following identification of childhood hearing loss.

PURPOSE Appropriate support for families of children diagnosed with hearing impairment may have a direct impact on the success of early hearing detection and intervention programs in reducing the negative effects of permanent hearing loss. We conducted a qualitative study to explore parents' needs after learning of their child's hearing loss to better understand the important components of service delivery from families' perspectives. METHOD Semistructured interviews were conducted with 17 families (21 parents) of preschool children in 4 centers in Ontario, Canada. Parents of children identified by neonatal screening as well as those identified through traditional referral routes participated. We asked parents to share their perceptions of the strengths and gaps in the care system. RESULTS Although the majority of parents were satisfied with the range and quality of audiology and therapy services available, they identified gaps in the areas of service coordination, availability of information, and the integration of social service and parent support into the system. Access to audiology services appears to have been facilitated for children who were systematically screened. CONCLUSIONS The findings provide insights into the services most valued by families. These findings highlight the importance of eliciting parents' perspectives in designing optimal care models for children and families.
Biophysical studies on bone cement composites based on polyester fumarate

Polypropylene fumarate (PPF) as unsaturated linear polyester crosslinked with three different monomers namely N-vinyl pyrrolidone (NVP), methyl methacrylate (MMA), and a mixture of NVP/MMA (1 : 1 weight ratio) were prepared. The chemical structure of the PPF was characterized by means of 1H-NMR, FTIR, as well as GPC. The mixture of PPF resin with the crosslinking monomers filled with (60, 65, and 70 wt %) of gypsum were also prepared as bone cement composites. The dielectric measurements carried out on these prepared samples at frequency range from 100 Hz–100 kHz indicate that the permittivity e′ and dielectric loss e″ follow the order NVP > NVP/MMA > MMA. Both parameters were found to decrease by increasing the percentage of gypsum. According to Frohlich and Havriliak Nagami functions, the relaxation times obtained could be attributed, respectively, to Maxwell-Wagner effect and to the relaxation process related to carboxyl, hydroxyl, and ester functions associated with main chain. The latter relaxation time was found to increase by increasing gypsum content, whereas the electrical conductivity was found to decrease. The mechanical data of the investigated samples containing 60 wt % gypsum is characterized by the best properties and the behavior of the composites follows the order found in the case of dielectric properties (NVP > NVP/MMA > MMA). Formation of carbonate apatite of composite samples loaded with 60 wt % gypsum after immersing the samples for 4 weeks in simulated body fluid (SBF) was confirmed by the dielectric measurements and FTIR spectroscopy. In addition, the weight loss and the mechanical properties for such systems were also studied. © 2009 Wiley Periodicals, Inc. J Appl Polym Sci, 2010
How mutualisms arise in phytoplankton communities: building eco‐evolutionary principles for aquatic microbes

Abstract Extensive sampling and metagenomics analyses of plankton communities across all aquatic environments are beginning to provide insights into the ecology of microbial communities. In particular, the importance of metabolic exchanges that provide a foundation for ecological interactions between microorganisms has emerged as a key factor in forging such communities. Here we show how both studies of environmental samples and physiological experimentation in the laboratory with defined microbial co‐cultures are being used to decipher the metabolic and molecular underpinnings of such exchanges. In addition, we explain how metabolic modelling may be used to conduct investigations in reverse, deducing novel molecular exchanges from analysis of large‐scale data sets, which can identify persistently co‐occurring species. Finally, we consider how knowledge of microbial community ecology can be built into evolutionary theories tailored to these species’ unique lifestyles. We propose a novel model for the evolution of metabolic auxotrophy in microorganisms that arises as a result of symbiosis, termed the Foraging‐to‐Farming hypothesis. The model has testable predictions, fits several known examples of mutualism in the aquatic world, and sheds light on how interactions, which cement dependencies within communities of microorganisms, might be initiated.
Troponin I and echocardiography in patients with systemic sclerosis and matched population controls

Objectives: Cardiac manifestations in systemic sclerosis (SSc) are associated with poor prognosis. Few studies have investigated cardiac troponins in SSc. We studied the relationships between echocardiographic abnormalities, cardiac biomarkers, and disease manifestations in a population-based cohort of patients with SSc and controls. Method: The study comprised 110 patients with SSc and 105 age- and sex-matched population-based controls. We examined ventricular function, heart valves, and estimated pulmonary arterial pressure (ePAP) by echocardiography in all participants. Disease characteristics, manifest ischaemic heart disease (IHD), and measurements of N-terminal prohormone brain natriuretic peptide (NT-proBNP) and high-sensitivity cardiac troponin I (hs-cTnI) were tabulated. Results: NT-proBNP and hs-cTnI levels were higher in SSc patients than controls. Both NT-proBNP and hs-cTnI were associated with the presence of echocardiographic abnormalities. Forty-four SSc patients and 23 control subjects had abnormal echocardiograms (p = 0.002). As a group, SSc patients had lower (but normal) left ventricular ejection fraction (LVEF, p = 0.02), more regional hypokinesia (p = 0.02), and more valve regurgitations (p = 0.01) than controls. Thirteen patients and four controls had manifest IHD. Decreased right ventricular (RV) function (n = 7) and elevated ePAP (n = 15) were exclusively detected among SSc patients. Conclusions: Both NTproBNP and hs-cTnI were associated with echocardiographic abnormalities, which were more prevalent in SSc patients than in controls. Our results thus suggest that hs-cTnI could be a potential cardiac biomarker in SSc. Low RV function and signs of pulmonary hypertension (PH) were uniquely found in the SSc group. SSc patients had more valve regurgitation than controls, an observation that warrants more clinical attention.
Catastrophic Interference is Eliminated in Pretrained Networks

When modeling strictly sequential experimental memory tasks, such as serial list learning, connectionist networks appear to experience excessive retroactive interference, known as catastrophic interference (McCloskey & Cohen,1989; Ratcliff, 1990). The main cause of this interference is overlap among representations at the hidden unit layer (French, 1991; Hetherington,1991; Murre, 1992). This can be alleviated by constraining the number of hidden units allocated to representing each item, thus reducing overlap and interference (French, 1991; Kruschke, 1992). When human subjects perform a laboratory memory experiment, they arrive with a wealth of prior knowledge that is relevant to performing the task. If a network is given the benefit of relevant prior knowledge, the representation of new items is constrained naturally, so that a sequential task involving novel items can be performed with little interference. Three laboratory memory experiments (ABA free recall, serial list, and ABA paired-associate learning) are used to show that little or no interference is found in networks that have been pretrained with a simple and relevant knowledge base. Thus, catastrophic interference is eliminated when critical aspects of simulations are made to be more analogous to the corresponding human situation.
Influence of Climate and Economic Variables on the Aggregated Supply of a Wild Edible Fungi (Lactarius deliciosus)

A mycological supply function of wild edible fungi is determined by a set of forest and economic variables, among which climate variables stand out. Focusing on wild mushroom picking with commercial value (Lactarius deliciosus (L.) Gray) as an example, the main objective of this paper is to obtain empirical evidence about the impact of meteorological and economic variables on the mushroom supply. A multidisciplinary vector error correction (VEC) model for mushroom supply is estimated. Coefficients for the Error Correction Term (ECT) are all significant, at the 0.01 significance level, both in the model for prices and for collected mushrooms. The value of the ECT coefficient in the equation for prices is -0.086 (t-value: -9.321), and for the collected mushroom equation is 0.499 (t-value: 3.913). The impact of precipitation on price changes is -0.104 (t-value: -1.66), and the impact of temperature on mushroom harvest picking is 0.605 (t-value: 3.07). We find that including climate factors to explain mushroom supply considerably strengthens the explanatory power of the model, and in some cases greatly changes the results.
Muscle force during an acute exacerbation in hospitalised patients with COPD and its relationship with CXCL8 and IGF-I

Background: Chronic obstructive pulmonary disease (COPD) is often associated with peripheral muscle weakness, which is caused by several factors. Acute exacerbations may contribute, but their impact on muscle force remains unclear. Correlations between peripheral muscle force and inflammatory and anabolic markers have never been studied in COPD. The effect of an acute exacerbation on quadriceps peak torque (QPT) was therefore studied in hospitalised patients, and the aforementioned correlations were examined in hospitalised and in stable patients. Methods: Lung function, respiratory and peripheral muscle force, and inflammatory and anabolic markers were assessed in hospitalised patients on days 3 and 8 of the hospital admission and 90 days later. The results on day 3 (n=34) were compared with those in clinically stable outpatients (n=13) and sedentary healthy elderly subjects (n=10). Results: Hospitalised patients had lowest mean (SD) QPT (66 (22)% predicted) and highest median (IQR) levels of systemic interleukin-8 (CXCL8, 6.1 (4.5 to 8.3) pg/ml). Insulin-like growth factor I (IGF-I) tended to be higher in healthy elderly subjects (p=0.09). QPT declined between days 3 and 8 in hospital (mean −5% predicted (95% CI −22 to 8)) and partially recovered 90 days after admission to hospital (mean 6% predicted (95% CI −1 to 23)). QPT was negatively correlated with CXCL8 and positively correlated with IGF-I and lung transfer factor in hospitalised and in stable patients. Conclusions: Peripheral muscle weakness is enhanced during an acute exacerbation of COPD. CXCL8 and IGF-I may be involved in the development of peripheral muscle weakness in hospitalised and in stable patients with COPD.
Analyzing Mosquito (Diptera: Culicidae) Diversity in Pakistan by DNA Barcoding

Background Although they are important disease vectors mosquito biodiversity in Pakistan is poorly known. Recent epidemics of dengue fever have revealed the need for more detailed understanding of the diversity and distributions of mosquito species in this region. DNA barcoding improves the accuracy of mosquito inventories because morphological differences between many species are subtle, leading to misidentifications. Methodology/Principal Findings Sequence variation in the barcode region of the mitochondrial COI gene was used to identify mosquito species, reveal genetic diversity, and map the distribution of the dengue-vector species in Pakistan. Analysis of 1684 mosquitoes from 491 sites in Punjab and Khyber Pakhtunkhwa during 2010–2013 revealed 32 species with the assemblage dominated by Culex quinquefasciatus (61% of the collection). The genus Aedes (Stegomyia) comprised 15% of the specimens, and was represented by six taxa with the two dengue vector species, Ae. albopictus and Ae. aegypti, dominant and broadly distributed. Anopheles made up another 6% of the catch with An. subpictus dominating. Barcode sequence divergence in conspecific specimens ranged from 0–2.4%, while congeneric species showed from 2.3–17.8% divergence. A global haplotype analysis of disease-vectors showed the presence of multiple haplotypes, although a single haplotype of each dengue-vector species was dominant in most countries. Geographic distribution of Ae. aegypti and Ae. albopictus showed the later species was dominant and found in both rural and urban environments. Conclusions As the first DNA-based analysis of mosquitoes in Pakistan, this study has begun the construction of a barcode reference library for the mosquitoes of this region. Levels of genetic diversity varied among species. Because of its capacity to differentiate species, even those with subtle morphological differences, DNA barcoding aids accurate tracking of vector populations.