Miracle-dz/UniFAR-FTUs huggingface dataset:
Optimization, Constraint, and History in the Evolution of Eyes

Several features of the evolution of eyes and photoreceptors are examined in an effort to explore the relative roles of adaptation and historical and developmental constraints. Optical design shows clear evidence of adaptation, which is some respects approaches optima predictable from physics. The primate fovea, on the other hand, illustrates how adaptation can be channeled by developmental heritage. The primary structure of opsins reveal multiple evolutionary lineages within both Drosophila and humans. The pigments of vertebrate rods comprise a subset of opsins whose evolutionary relationships map onto the phylogeny of the parent species. The evolutionary reasons for why most rod pigments absord maximally at 500 ± 10 nm are obscure, as there is no convincing explanation based on adaptation alone. Rods are appropriately distinguished from cones on the basis of which opsin gene is expressed. This criterion is likely to be in conflict with other difinitions in phyletic lines (e.g., geckos, snakes) that have long diurnal of noctural histories accompanied by loss of one or more opsin genes, followed by a secondary adaptation to life in a different photic environment. Color vision-a generalizable perception associated with the spectral composition of light-is usefully distinguished from wavelength-specific behaviors. The latter are also based on multiple visual pigments and more that one spectral class of receptors but cannot be altered by learning. The distinction is particularly forceful in bees, which exhibit both kinds of behavior. The evolution of primate color vision has been shaped by historical factors involving an extensive period of early mammalian nocturnality. Birds, by contrast, have more elaborate cones and a richer set of visual pigments. Avian color space can be represented in a tetrahedron.
A polymorphism in the alpha2a-adrenoceptor gene and endurance athlete status.

PURPOSE In a case control study, we examined the allelic frequencies and genotype distributions of two restricted fragment length polymorphisms (RFLP) in the alpha-2A-adrenoceptor gene (ADRA2A) and beta-2-adrenoceptor gene (ADRB2) among elite endurance athletes (EEA) and sedentary controls (SC). METHODS The EEA group included 148 Caucasian male subjects recruited on the basis that they had a VO2max > 74 mL O2 x kg(-1) x min(-1). The SC group comprised 149 unrelated sedentary male subjects, all Caucasians, from the Quebec Family Study. After digestion with the restriction enzymes Dra I (ADRA2A) and Ban I (ADRB2), Southern blotting and hybridization techniques were used to detect the mutations in the two ADR genes, which are encoded on chromosomes 10 (q24-26) and 5 (q31-32), respectively. RESULTS For the Dra I ADRA2A RFLP, we observed a significant difference in genotype distributions between the two groups (P = 0.037). A higher frequency of the 6.7-kb allele was observed in the EEA group compared with the SC group (P = 0.013). No statistically significant difference was found between groups for the Ban I ADRB2 polymorphic site. Genotype frequencies for both genes in both groups were in Hardy-Weinberg equilibrium. CONCLUSIONS In summary, we found evidence that ADRA2A gene variability detected with Dra I is weakly associated with elite endurance athlete status, and we conclude that genetic variation in the ADRA2A gene or a locus in close proximity may play a role in being able to sustain the endurance training regimen necessary to attain a high level of maximal aerobic power.
Video Analysis of Anterior Cruciate Ligament Injury

Background Most anterior cruciate ligament research is limited to variables at the knee joint and is performed in the laboratory setting, often with subjects postinjury. There is a paucity of information on the position of the hip and ankle during noncontact anterior cruciate ligament injury. Hypothesis When landing after maneuvers, athletes with anterior cruciate ligament injury (subjects) show a more flatfooted profile and more hip flexion than uninjured athletes (controls). Study Design Case control study; Level of evidence, 3. Methods Data from 29 videos of subjects were compared with data from 27 videos of controls performing similar maneuvers. Joint angles were analyzed in 5 sequential frames in sagittal or coronal planes, starting with initial ground-foot contact. Hip, knee, and ankle joint angles were measured in each sequence in the sagittal plane and hip and knee angles in the coronal plane with computer software. The portion of the foot first touching the ground and the number of sequences required for complete foot-ground contact were assessed. Significance was set at P <. 05. Results In sagittal views, controls first contacted the ground with the forefoot; subjects had first ground contact with the hindfoot or entirely flatfooted, attained the flatfoot position significantly sooner, had significantly less plantar-flexed ankle angles at initial contact, and had a significantly larger mean hip flexion angle at the first 3 frames. In coronal views, no significant differences in knee abduction (initial contact) or hip abduction angle were found between groups; knee abduction was relatively unchanged in controls but progressed in subjects. Conclusion Initial ground contact flatfooted or with the hindfoot, knee abduction and increased hip flexion may be risk factors for anterior cruciate ligament injury.
Music for the ageing brain: Cognitive, emotional, social, and neural benefits of musical leisure activities in stroke and dementia

Music engages an extensive network of auditory, cognitive, motor, and emotional processing regions in the brain. Coupled with the fact that the emotional and cognitive impact of music is often well preserved in ageing and dementia, music is a powerful tool in the care and rehabilitation of many ageing-related neurological diseases. In addition to formal music therapy, there has been a growing interest in self- or caregiver-implemented musical leisure activities or hobbies as a widely applicable means to support psychological wellbeing in ageing and in neurological rehabilitation. This article reviews the currently existing evidence on the cognitive, emotional, and neural benefits of musical leisure activities in normal ageing as well as in the rehabilitation and care of two of the most common and ageing-related neurological diseases: stroke and dementia.
Environmental Niche Equivalency versus Conservatism: Quantitative Approaches to Niche Evolution

Abstract Environmental niche models, which are generated by combining species occurrence data with environmental GIS data layers, are increasingly used to answer fundamental questions about niche evolution, speciation, and the accumulation of ecological diversity within clades. The question of whether environmental niches are conserved over evolutionary time scales has attracted considerable attention, but often produced conflicting conclusions. This conflict, however, may result from differences in how niche similarity is measured and the specific null hypothesis being tested. We develop new methods for quantifying niche overlap that rely on a traditional ecological measure and a metric from mathematical statistics. We reexamine a classic study of niche conservatism between sister species in several groups of Mexican animals, and, for the first time, address alternative definitions of “niche conservatism” within a single framework using consistent methods. As expected, we find that environmental niches of sister species are more similar than expected under three distinct null hypotheses, but that they are rarely identical. We demonstrate how our measures can be used in phylogenetic comparative analyses by reexamining niche divergence in an adaptive radiation of Cuban anoles. Our results show that environmental niche overlap is closely tied to geographic overlap, but not to phylogenetic distances, suggesting that niche conservatism has not constrained local communities in this group to consist of closely related species. We suggest various randomization tests that may prove useful in other areas of ecology and evolutionary biology.
DNA hypermethylation of extracellular matrix-related genes in human periodontal fibroblasts induced by stimulation for a prolonged period with lipopolysaccharide derived from Porphyromonas gingivalis.

OBJECTIVES AND BACKGROUND The involvement of DNA methylation in periodontal disease is not clear. Lipopolysaccharide (LPS) derived from Porphyromonas gingivalis is involved in the progression of periodontal disease. We recently developed an in vitro model of LPS infection in human periodontal fibroblast cells (HPdLFs) for a prolonged period. In this study, we examined genome-wide analysis of DNA methylation in HPdLFs stimulated with LPS derived from P. gingivalis for a prolonged period. We noted the hypermethylation of extracellular matrix (ECM)-related genes and examined whether hypermethylation affected their transcription levels. MATERIAL AND METHODS HPdLFs were grown in Dulbecco's modified Eagle's medium containing 10% fetal bovine serum. The culture was repeated, alternating 3 d with LPS derived from P. gingivalis and 3 d without LPS for 1 mo. Untreated samples were used as controls. DNA was analyzed using the human CpG island microarray. Quantitative methylation-specific polymerase chain reaction was carried out to confirm reproducibility of the microarray data. The expression levels of mRNA of the selected ECM-related genes from the data were analyzed by quantitative reverse transcription-polymerase chain reaction. RESULTS We found 25 ECM-related genes with hypermethylation at the CpG island of the promoter region, which exhibited a fourfold greater hypermethylation than controls. Among these genes, hypermethylation of nine ECM-related genes, FANK1, COL4A1-A2, 12A1 and 15A1, LAMA5 and B1, MMP25, POMT1 and EMILIN3, induced a significantly downregulated expression of their mRNA. CONCLUSION These results indicate that LPS derived from P. gingivalis may cause DNA hypermethylation of some ECM-related genes followed by downregulated expression of their transcriptional levels.
Neuron-Specific Enolase as a Marker for Acute Ischemic Stroke: A Systematic Review

Background: To date, most work delineating the usefulness of neuron-specific enolase (NSE) as a marker for acute ischemic stroke has been inconclusive. This study had the following objectives: (1) to determine whether serum concentrations of NSE correlate with time of onset of stroke symptoms, volume of infarcted tissue, stroke severity, functional outcome, or length of hospital stay; (2) to determine whether serial measurements of NSE levels are useful markers for ongoing brain ischemia, and (3) to determine whether NSE levels at various time intervals are significantly higher in patients with stroke than in controls. Methods: All abstracts and published full reports identified as potentially relevant by the literature search were independently assessed for inclusion in the review by each reviewer. Twelve studies (including 597 patients) satisfied the entry criteria for this qualitative analysis. Results: In 4 studies, time of onset of stroke symptoms was compared with time of first detectable NSE levels, which ranged from 4 to 8 h after stroke onset. In 7 studies, NSE levels increased with increased size of stroke, but in 2 studies there was no correlation. In the 2 studies that compared stroke severity with NSE levels, high NSE levels generally indicated worse outcome, but at low NSE levels the results were equivocal. In 7 studies, functional outcome at hospital dismissal and follow-up was compared with NSE levels; in 4, there was no correlation. Conclusions: The serum level of NSE does seem to be higher in stroke patients than in controls, and it does appear to correlate with volume of infarcted tissue. However, it does not appear to correlate with functional outcome, and its relationship to stroke severity is unclear. This may be explained at least in part by the disparity in sampling times because the NSE level has been shown to peak after 24 h in most studies. Hence, the more delayed the sampling, the greater the correlation with stroke severity.
Consanguinity associated with increased risk for bipolar I disorder in Egypt

We aimed to contrast rates of consanguinity among patients with bipolar I disorder (BP1) and controls in a population with customary consanguineous marriages (i.e., marriage between related individuals). Consanguinity increases risk for numerous monogenic and polygenic diseases. Whether the risk for BP1 increases with consanguinity has not been investigated systematically. Two independent studies were conducted in Egypt: (1) Case–control study 93 patients with BP1, 90 screened adult control individuals, and available parents. The inbreeding coefficient/consanguinity rate was estimated in two ways: using 64 DNA polymorphisms (“DNA‐based” rate); and from family history data (“self report”); (2) Epidemiological survey: total of 1,584 individuals were screened, from whom self‐reported consanguinity data were obtained for identified BP1 cases (n = 35) and 150 randomly selected, unaffected control individuals. DNA‐based consanguinity rates showed significant case–control differences (P = 0.0039). Self‐reported consanguinity rates were also elevated among BP1 patients in both samples (Study #1 OR = 2.66, 95% confidence intervals, CI: 1.34, 5.29; Study #2: OR = 4.64, 95% CI: 2.01, 10.34). In conclusion, two independent, systematic studies indicate increased consanguinity among Egyptian BP1 patients in the Nile delta region. Self‐reported estimates of consanguinity are bolstered by DNA‐based estimates, and both show significant case–control differences for BP1. © 2009 Wiley‐Liss, Inc.
Value Based Scheduling for Oversubscribed Power-Constrained Homogeneous HPC Systems

Power-aware scheduling has become a critical research thrust for deploying exascale High Performance Computing (HPC) systems with limited power budget. Time-varying pricing of electricity with respect to the market demand and dynamic HPC workloads can lead to unpredictable operational cost, which complicates the scheduling decisions further. For an oversubscribed HPC system, value based scheduling heuristics have been shown to be a more productive option for scheduling time-constrained tasks over priority and deadline based heuristics. However, oversubscribed HPC systems have higher probability of exceeding the power constraints. Earlier studies on value based heuristics do not take power constraints into account during scheduling decisions. In this study, we propose a methodology for deriving task-specific power-execution time models. These models are derived by interpolating the execution time and power consumption measurements over a configuration space parameterized with pairs of dynamic voltage frequency scaling and forced idleness values. We then propose two power-aware value based heuristics, which utilize those models for power capping the nodes and making resource allocation decisions in an oversubscribed homogeneous HPC system. We compare their performance with traditional value based heuristics under a defined power constraint on a real system using different synthetic traces of scientific computing routines. We show that, as power constraints become tighter, the proposed heuristics significantly outperform earlier heuristics in terms of value earning of the HPC system. We also compare the task completion percentage of proposed heuristics and relate the completion percentage with value earnings of the heuristics.
Partisan Dynamics in Presidential Primaries and Campaign Divisiveness

Observers have noted that the Republican and Democratic primaries differ substantially, with Republicans typically having an easier time selecting their nominee. Previous research has suggested that this may be attributable to Republican Party homogeneity and delegate allocation rules that winnow candidates faster, but there is little empirical evidence on how these factors influence the primary process. Rather than predicting overall vote share or the nominee, I examine the temporal dynamics of each party’s primary campaigns. I show that Republican candidates are over-rewarded for winning elections, while Democrats are rewarded for performing well overall. The result is that late in the campaign, Republicans are much more likely to exit as compared with Democrats, and there is little evidence that these dynamics have changed over time. I conclude that the Republican Party produces systematically shorter and less divisive primaries as a result of its faster and more efficient winnowing process.
Modulation of the Xanthine Oxidase/Xanthine Dehydrogenase Ratio by Reaction of Malondialdehyde with NH2-Groups

The potential of xanthine oxidoreductase to generate oxygen radicals depends on the ratio of xanthine dehydrogenase and xanthine oxidase. Previous studies showed that the lipid peroxidation products, malondialdehyde and 4-hydroxynonenal have different effects on xanthine oxidoreductase activity. These results suggest that the activity of xanthine oxidase, but not xanthine dehydrogenase, is influenced by NH2-group modulation. We therefore investigated the influence of malondialdehyde on xanthine oxidoreductase. Malondialdehyde reacted with NH2-groups to form Schiff bases, and this reaction was associated with inhibition of xanthine oxidase; SH-groups were not affected. Malondialdehyde had no influence on the xanthine dehydrogenase activity. The inhibited xanthine oxidase was converted to an active xanthine dehydrogenase by dithiothreitol treatment. These experiments indicate the importance of NH2-groups for xanthine oxidase but not for xanthine dehydrogenase activity. Beside the well known regulation of the xanthine dehydrogenase/xanthine oxidase ratio by the redox status of SH-groups, substances reacting with NH2-groups of the xanthine oxidoreductase are also able to change the xanthine dehydrogenase/xanthine oxidase activity ratio, thereby influencing the potential to generate oxygen radicals by xanthine oxidoreductase.
Pharmacologic Prophylaxis for Venous Thromboembolism Among Patients With Total Joint Replacement: An Electronic Medical Records Study

Patients who have total hip (THR) or knee (TKR) replacement have an elevated risk of venous thromboembolism (VTE). The American College of Chest Physicians guidelines recommend prophylactic anticoagulation. The aim of the study was to examine pharmacologic prophylaxis against VTE among patients with THR or TKR and to assess demographic and clinical correlates related to VTE prophylaxis. Using 15 years of data (1995–2009) from an electronic medical record system for an inner-city public hospital in the United States, we examined pharmacologic prophylaxis against VTE and associated factors in patients after THR (n = 242) and TKR (n = 317). Before the early 2000s, aspirin was the most common prophylaxis agent (THR, 61% and TKR, 65%), and 26% of patients with THR and 19% of patients with TKR did not receive prophylaxis. Enoxaparin use has increased since 2000, and warfarin is now the most common prophylaxis agent (THR, 70% and TKR, 61%). After controlling for time period, factors associated with prophylaxis pattern included obesity, hip fracture, and the surgeon's number of years in practice. VTE prophylaxis medications in patients with total joint replacement have changed over 15 years, in trends generally consistent with the evolution of guidelines. Obesity, history of hip fracture, and physician's experience are associated with the prescription of VTE prophylaxis medications.
Gene fusions with lacZ by duplication insertion in the radioresistant bacterium Deinococcus radiodurans

Deinococcus radiodurans is the most-studied species of a eubacterial family characterized by extreme resistance to DNA damage. We have focused on developing molecular biological techniques to investigate the genetics of this organism. We report construction of lacZ gene fusions by a method involving both in vitro splicing and the natural transformation of D. radiodurans. Numerous fusion strains were identified by expression of beta-galactosidase. Among these fusion strains, several were inducible by exposure to the DNA-damaging agent mitomycin C, and four of the inducible fusion constructs were cloned in Escherichia coli. Hybridization studies indicate that one of the damage-inducible genes contains a sequence reiterated throughout the D. radiodurans chromosome. Survival measurements show that two of the fusion strains have increased sensitivity to mitomycin C, suggesting that the fusions within these strains inactivate repair functions.
Intervention Program to Improve Executive Functions and Enhance Planning Abilities of Patients With Mild Neurocognitive Disorder.

PURPOSE The aim of this study was to examine the effects of an intervention program to improve executive functions and enhance the planning abilities of patients with mild neurocognitive disorder. DESIGN A pilot intervention study. METHODS Ten inpatients performed an intervention program based on Lezak's conceptual model that teaches task-specific routines. The program consisted of six training sessions presented over a 2-week period. Neuropsychological assessments were performed pre- and postintervention. FINDINGS The postintervention scores of the Behavioral Assessment of Dysexecutive Syndrome Total Profile and two subtests were significantly higher than the preintervention scores. The instrumental Activities of Daily Living Scale and the Visual Analog Scale were significantly improved. CONCLUSION This intervention program leads to improvement in the executive function of planning ability and promotes independence and self-confidence in patients with mild neurocognitive disorder. CLINICAL RELEVANCE Clinicians should consider the program in terms of improving the executive dysfunction, and the process of planning and the process of actual practice are important.
The Influence of On-site Professional Development on Teacher Practice

The purpose of this research was to explore how on-site professional development (PD) addresses the goal of improved teacher practice. It was conducted within the context of a national educational reform in Australia. This reform, implemented from 2009 to 2012/13, was a National Partnership Agreement (NPA) with the Commonwealth Government that included the Smarter Schools National Partnerships (SSNP). This research was a multi-site case study of five Catholic primary schools that implemented on-site PD for four years as part of a system response to a reform agenda. Learning on-site was a change in practice for teachers that involved the establishment of professional learning communities (PLCs) and the appointment in each school of an additional school leader entitled a ‘Teacher Educator’ (TE). The interpretative paradigm of research, through the lens of symbolic interactionism and the epistemology of constructionism, was adopted to guide and inform the study. A multi-site case study methodology was chosen as the five schools constituted a single case on multiple sites that shared the phenomenon of interest, i.e., on-site PD (Huberman & Miles, 2002). The data gathering methods were semi-structured interviews, group interviews and a pre-interview self-reflection tool. Findings emerged through qualitative data analysis that utilised the Constant Comparative Method (Merriam, 1998). The major research question was: How does on-site professional development influence teacher practice? Findings from this research indicate that on-site PD influenced teacher practice in certain ways. First, underpinning the approach to changing teacher practice was collaboration. School leaders shared the instructional leadership role and worked collaboratively with teachers, primarily in classrooms, to demonstrate how teaching practice could change. The influence of system leaders on teacher practice was a secondary process mediated by school leaders. Due to a perceived lack of strategic direction, teacher consultation, or involvement in schools throughout the reform, system leaders were not seen as having a positive influence on teacher practice. Second, the structure of the in-situ