Miracle-dz/UniFAR-FTUs huggingface dataset:
Genome-Wide Identification and Transcriptomic Analysis of MicroRNAs Across Various Amphioxus Organs Using Deep Sequencing

Amphioxus is the closest living invertebrate proxy of the vertebrate ancestor. Systematic gene identification and expression profile analysis of amphioxus organs is thus important for clarifying the molecular mechanisms of organ function formation and further understanding the evolutionary origin of organs and genes in vertebrates. The precise regulation of microRNAs (miRNAs) is crucial for the functional specification and differentiation of organs. In particular, those miRNAs that are expressed specifically in organs (OSMs) play key roles in organ identity, differentiation, and function. In this study, the genome-wide miRNA transcriptome was analyzed in eight organs of adult amphioxus Branchiostoma belcheri using deep sequencing. A total of 167 known miRNAs and 23 novel miRNAs (named novel_mir), including 139 conserved miRNAs, were discovered, and 79 of these were identified as OSMs. Additionally, analyses of the expression patterns of eight randomly selected known miRNAs demonstrated the accuracy of the miRNA deep sequencing that was used in this study. Furthermore, potentially OSM-regulated genes were predicted for each organ type. Functional enrichment of these predicted targets, as well as further functional analyses of known OSMs, was conducted. We found that the OSMs were potentially to be involved in organ specific functions, such as epidermis development, gonad development, muscle cell development, proteolysis, lipid metabolism and generation of neurons. Moreover, OSMs with non-organ specific functions were detected, and primarily include those related to innate immunity and response to stimuli. These findings provide insights into the regulatory roles of OSMs in various amphioxus organs.
A Projection for the Turkish Economy in 2023 with a Bayesian Approach

Turkish economy has almost experienced a continuous growth process since the first quarter of the year 2002, except for the year 2009 in which the impact of global financial crisis was felt. As a result of this growth period, Turkey has become the 17th largest economy in the world and has set big targets as to join one of the largest 10 economies in the world. In this study, we investigate whether Turkey would be able to meet its 2023 targets or not if the trends and dynamics that have been experienced during the last decade continue. Specifically, we will examine if Turkey’s exports will reach 500 billion US dollars, Turkey’s GDP will reach 2 trillion US dollars, and Turkey’s GDP per capita will reach 25 thousand US dollars. Furthermore, the path that Turkey’s macroeconomic indicators should follow in coming years and the different applicable scenarios in order to reach these 2023 economic targets will be studied. The results of this study show that those 2023 targets will not be met. So if Turkey is serious and insistent on these targets, this study may be a warning to policymakers to take the necessary measures when there is still enough time and opportunity.
Molecular profiling of driver events and tumor-infiltrating lymphocytes in metastatic uveal melanoma

Uveal melanoma (UM) is a rare form of melanoma with a genetics and immunology that is different from skin melanoma. Previous studies have identified genetic driver events of early stage disease when the tumor is confined to the eye. However due to lack of a clinical rationale to biopsy metastatic disease, access to tumor material to perform molecular profiling of metastases has been limited. In this study, we have characterized genomic events in UM metastases using whole-genome sequencing of fresh frozen biopsies from thirty-two patients and profiled the transcriptomes of individual tumor infiltrating lymphocytes in eight patients by single-cell sequencing. We find that 91% of the patients have metastases carrying inactivating events in the tumor suppressor BAP1 and this coincided with somatic alterations in GNAQ, GNA11, CYSLTR2, PLCB4, SF3B1 and/or CDKN2A. Mutational signature analysis revealed a rare subset of tumors with prominent signs of UV damage, associated with outlier mutational burden. We study copy number variations (CNV) and find overrepresented events, some of which were not altered in matched primary eye tumors. A focused siRNA screen identified functionally significant genes of some of the segments recurrently gained. We reintroduced a functional copy of BAP1 into a patient-derived BAP1 deficient tumor cell line and found broad transcriptomic changes of genes associated with subtype distinction and prognosis in primary UM. Lastly, our analysis of the immune microenvironments of metastases revealed a presence of tumor-reactive T cells. However, a majority expressed the immune checkpoint receptors TIM-3, LAG3 and TIGIT, and to a lesser extent PD-1. These results provide an updated view of genomic events represented in metastatic UM and immune interactions in advanced lesions.
Rectus femoris hyperreflexia predicts knee flexion angle in Stiff-Knee gait after stroke

Stiff-knee gait (SKG) after stroke is often accompanied by decreased knee flexion angle during the swing phase. The decreased knee flexion has been hypothesized to originate from excessive quadriceps activation. However, it is unclear whether this activation is due to poor timing or hyperreflexia, both common post-stroke impairments. The goal of this study was to investigate the relation between quadriceps hyperreflexia in post-stroke SKG with knee flexion angle during walking. The rectus femoris (RF) H-reflex was recorded in eleven participants with post-stroke SKG and ten healthy controls during standing and walking during toe-off. In order to separate the effects of poorly timed quadriceps muscle activation from hyperreflexia, healthy individuals voluntarily increased quadriceps activity using RF electromyographic (EMG) biofeedback during standing and pre-swing upon H-reflex stimulation. We observed a negative correlation (R = −0.92, p=0.001) between knee flexion angle and RF H-reflexes in post-stroke SKG. In contrast, H-reflex amplitude in healthy individuals in presence (R = 0.47, p = 0.23) or absence (R = −0.17, p = 0.46) of increased RF activity had no correlation with knee flexion angle. The RF H-reflex amplitude differed between standing and walking in healthy individuals, including when RF activity was increased voluntarily (d = 2.86, p = 0.007), but was not observed post-stroke (d =0.73, p = 0.296). Thus, RF reflex modulation is impaired in post-stroke SKG. Further, RF hyperreflexia, as opposed to overactivity, may play a role in knee flexion kinematics in post-stroke SKG. Interventions targeting self-regulated quadriceps hyperreflexia may be effective in promoting better neural control of the knee joint and thus better quality of walking post-stroke.
The Benefits and Barriers Related to Regular Participation in Physical Activity by African-American Women: Implications for Intervention Development

A common strategy for improving health behaviors is to emphasize the benefits and reduce the barriers to behavior change. This study investigated potential differences in perceived benefits and barriers related to participation in physical activity (PA) between women in pre-maintenance versus the maintenance phase of PA behavior to determine if perceived benefits were greater and perceived barriers lower in women with more extensive and successful PA participation experience. Data were collected from a community-based sample (N = 113) of middle-aged African-American women. The sample was stratified into two groups according to how long they had been regularly engaging in PA (6 months or longer versus less than 6 months). Chi-square analyses were conducted to investigate possible differences between the two groups of women in regard to perceived benefits and barriers associated with PA. Descriptive data showed that nearly all of the benefits and barriers to PA were perceived as being important for a majority of the participants and chi-square and t-test results indicated few significant between-group differences (p < .05) in regard to these perceptions. Additional analyses indicated there was no significant between-group difference (p < .05) for Body Mass Index. The results suggest the benefits and barriers related to PA behavior are already valued and understood by many African-American women. Further, the results do not support the commonly held belief that effective health behavior improvement programming should emphasize the benefits and reduce the barriers related to the behavior. Practitioners should consider focusing on other evidenced based factors proven to promote PA behavior such as counseling regarding social support (e.g., buddy system) and increasing self-efficacy (e.g., goal setting) to initiate and sustain a physically active lifestyle.
Fluid properties and dynamics along the seismogenic plate interface

Fossil structures, such as exhumed accretionary prisms, are the only direct recorders of the fluids wetting the plate interface near the base of the seismo­ genic zone. By studying exhumed accretionary prisms, it is thus possible to determine the physicochemical properties of fluids and the geometry and dynamics of their circulation. We considered here two transects encompass­ ing the brittle­plastic transition (BPT) zone, in the Franco­Italian Alps and the Shimanto Belt in Japan, and compared our data with a broader set of exam­ ples from the literature. On quartz that grew synkinematically at peak burial conditions, we inferred fluid properties indirectly from quartz trace­element concentrations (using cathodoluminescence [CL] imaging) and directly from fluid­inclusion composition and P­ρ­T properties (using Raman and micro­ thermometry). At ~250 °C, quartz grew principally through fracturing and two types of quartz, a CL­brown and a CL­blue, precipitated alternately. At ~350 °C, where plastic deformation and recrystallization is pervasive, only a single, ho­ mogeneously CL­brown quartz is present. The salinity of the fluid in the inclu­ sions shallower than the BPT is consistently of the order or lower than sea­ water, while salinities are very scattered deeper than the BPT and often exceed seawater salinity. The gas dissolved in the fluid is predominantly CH 4 shal­ lower than the BPT, and either CH 4 or CO 2 deeper than the BPT, depending on the nature of the host rock and in particular on the proportion of carbonates. Cathodoluminescence properties, salinity, and nature of the gas all point to a closed­system behavior in rocks deeper than the BPT. In contrast, shallower than the BPT (i.e., at seismogenic depths), textures revealed by CL­imaging evidence the episodic influx of an external fluid, leading to the crystallization of CL­blue quartz. The scale of the circulation leading to the generation of the CL­blue quartz, or its relationship with the seismic cycle, is still unclear. Be­ sides, the fluid pressure recorded in the abundant water­rich fluid inclusions is systematically much lower than the corresponding lithostatic pressure, ir­ respective of the depth domain considered. For inclusions trapped at large depth, the low fluid pressure recorded in the inclusions reflects post­entrap­ ment reequilibration. For inclusions trapped at shallower conditions, typically at seismogenic depths, the low fluid pressure may as well be the result of large fluid pressure drop after earthquakes.
Dynamics Analysis of a Small Training Boat ant Its Optimal Control

This paper describes dynamics analysis of a small training boat and a new type of ship's autopilot not only to keep her course but also to reduce her roll motion. Firstly, statistical analysis through multi-variate auto regressive model is carried out using the real data collected from the sea trial on an actual small training boat Sazanami after the navigational system of the boat was upgraded. It is shown that the roll motion is strongly influenced by the rudder motion and it is suggested that there is a possibility of reducing the roll motion by controlling the rudder order properly. Based on this observation, a new type of ship's autopilot that takes the roll motion into account is designed using the muti-variate modern control theory. Lastly, digital simulations by white noise are carried out in order to evaluate the proposed system and a typical result is demonstrated. As results of simulations, the proposed autopilot had good performance compared with the original data.
Early Protocolized Bedside Ultrasound in Shock: Renal Function Improvements and Other Lessons Learned

Objectives: Rapid assessment and treatment of the critically ill in shock is crucial to survival. The RUSH (Rapid Ultrasound in Shock and Hypotension) exam uses Ultrasound (US) to determine the etiology of undifferentiated shock, but data to demonstrate impact of focused US on clinical outcomes is sparse. This study aimed to assess the clinical impact of early incorporation of the RUSH US exam in the care of patients with new onset shock on a population level. Methods: In this single center randomized control trial, sixty patients were enrolled in the RUSH group and received an early protocolized US exam within the first 24 hours of shock onset, and 65 patients were enrolled in the usual care group. The primary outcome investigated was total hospital length of stay. Secondary outcomes included in-hospital mortality, common markers of morbidity, and resource utilization. Results: There was no difference in the length of stay or resource utilization between the two groups, however the RUSH subjects were more likely to have a lower stage of acute kidney injury by RIFLE staging (p = 0.019). There were non-significant trends towards less total fluid administered, reduced need for new hemodialysis, and fewer ventilator days in the RUSH group. Conclusion: The use of early US in shock patients leads to improvement in renal outcomes which is known to have significant impact on morbidity and mortality. Future studies are required to further investigate additional clinical outcomes impacted by use of an early protocolized US examination for this population.
High-Order Consumption Moments and Asset Pricing

This paper investigates the role of the deviations of individual consumption from per capita consumption in explaining the equity premium. We propose the stochastic discount factor that depends on the moments of the cross-sectional distribution of consumption. Using data from the CEX, we find that not only the mean, as in the representative-agent consumption CAPM, but also the second and third cross-sectional moments of consumption are important determinants of the equity premium. The stochastic discount factor that captures the first three cross-sectional moments of consumption explains the observed mean equity premium with a low (below three) value of risk aversion.
Achieving energy efficiency in government buildings through mandatory policy and program enforcement

Government buildings are responsible for a significant proportion of energy consumption worldwide, for example, in Australia, up to 41.5 PJ energy was consumed by government buildings in 2011–2012. While the newly constructed buildings may be energy efficient, the existing buildings, which account for more than 85% of the total building stock, were built prior to the time when energy rating systems was put in practice and are consequently energy inefficient to a large degree. Reducing the energy consumption in existing government buildings is essential, as it will not only reduce the costs and environmental impacts, but also show governments’ strong commitment towards the reduction of greenhouse gas emission. Furthermore, successful building energy retrofit projects are the showcases to the general public, encouraging other sectors (e.g. commercial) to conduct building retrofits for energy savings. Recognising these benefits, several state governments in Australia have introduced building energy efficiency policies and programs. This paper reviewed the energy efficiency policies/programs in five States in Australia: Victoria, New South Wales, South Australia, Western Australia, and Queensland in terms of respective policies and targets, implementation methods and current progress. The lessons learned from these programs were also discussed. This research revealed that the key factors for a successful government building energy retrofitting program are 1) having a properly enforced energy efficiency mandate with clear energy saving targets, 2) establishing an expert facilitation team and 3) implementing suitable financing and procurement methods.
Adaptation to transposable elements in Drosophila simulans

Transposable elements (TEs) are genomic parasites that proliferate within host genomes, and can also invade new species. The P-element, a DNA-based transposable element, recently invaded two Drosophila species: D. melanogaster in the 20th century, and D. simulans, in the 21st. In both species, lines collected before the invasion are susceptible to ‘hybrid dysgenesis’, a syndrome of abnormal phenotypes that are due to P-element inflicted DNA damage. In D. melanogaster, lines collected after the invasion have evolved a maternally acting mechanism that suppresses the effects of the P-element and therefore hybrid dysgenesis. Extensive work has shown that PIWI-interacting small RNAs (piRNAs) are a key factor suppressing P-element induced hybrid dysgenesis. However, most of these studies were performed using lines collected many generations after the initial P-element invasion. In this thesis, I study lines of D. simulans collected early and late in the invasion of the P-element in that species. Similar to D. melanogaster, late in the invasion D. simulans shows abundant P-element derived piRNAs. Lines collected early in the invasion show substantial variation tolerance to the P-element. Surprisingly, however, these lines show no correlation between tolerance to P- element damage and expression of maternal P-element piRNAs, or other known factors influencing hybrid dysgenesis, suggesting mechanisms contribute to P-element suppression prior to the evolution of piRNA suppression. In addition to that, I identify piRNA-producing loci, piRNA clusters, in D. simulans.
Improving Genomic Selection With Quantitative Trait Loci and Nonadditive Effects Revealed by Empirical Evidence in Maize

Genomic selection (GS), a tool developed for molecular breeding, is used by plant breeders to improve breeding efficacy by shortening the breeding cycle and to facilitate the selection of candidate lines for creating hybrids without phenotyping in various environments. Association and linkage mapping have been widely used to explore and detect candidate genes in order to understand the genetic mechanisms of quantitative traits. In the current study, phenotypic and genotypic data from three experimental populations, including data on six agronomic traits (e.g., plant height, ear height, ear length, ear diameter, grain yield per plant, and hundred-kernel weight), were used to evaluate the effect of trait-relevant markers (TRMs) on prediction accuracy estimation. Integrating information from mapping into a statistical model can efficiently improve prediction performance compared with using stochastically selected markers to perform GS. The prediction accuracy can reach plateau when a total of 500–1,000 TRMs are utilized in GS. The prediction accuracy can be significantly enhanced by including nonadditive effects and TRMs in the GS model when genotypic data with high proportions of heterozygous alleles and complex agronomic traits with high proportion of nonadditive variancein phenotypic variance are used to perform GS. In addition, taking information on population structure into account can slightly improve prediction performance when the genetic relationship between the training and testing sets is influenced by population stratification due to different allele frequencies. In conclusion, GS is a useful approach for prescreening candidate lines, and the empirical evidence provided by the current study for TRMs and nonadditive effects can inform plant breeding and in turn contribute to the improvement of selection efficiency in practical GS-assisted breeding programs.
An effective method for ecosystem‐scale manipulation of bird abundance and species richness

Abstract Manipulation experiments are a cornerstone of ecological research, but can be logistically challenging to execute—particularly when they are intended to isolate the ecological role of large, vagile species, like birds. Despite indirect evidence that birds are influential in many ecosystems, large‐scale, multi‐year bird manipulation experiments are rare. When these studies are conducted, they are typically realized with caged or netted exclosures, an approach that can be expensive, risky for wildlife, and difficult to maintain. In cases where caged exclosures are not appropriate, alternate approaches are needed to allow rigorous empirical studies on the ecological role of birds. Here, we present and validate a method for experimentally increasing the abundance and richness of birds at the scale of entire aquatic ecosystems. Unlike bird exclusion, this approach is experimentally tractable, appealing to land managers, and possible to deploy over large spatial scales. We tested the efficacy of our approach for increasing bird abundance and species richness at 16 central California ponds. Based on bird visitation data obtained by summer camera trapping, our approach significantly increased bird species richness and abundance at manipulated ponds compared to control ponds. Attractant treatments mitigated the negative effects of a major drought on bird species richness and generated a near doubling of bird abundance in the presence of attractants. Treatments had no effect on most mammal species, with the exception of ground squirrels, which increased in abundance in the presence of attractants. These results suggest that attractants are effective in increasing bird abundance and richness. We encourage researchers to consider this approach for experimentally isolating the ecological role of birds in aquatic and open terrestrial ecosystems, especially in cases where cost or logistical constraints preclude the use of caged or netted exclosures.
Estimating Abundance and Life History Characteristics of Threatened Wild Snake River Steelhead Stocks by Using Genetic Stock Identification

Abstract Assessments of threatened wild Snake River steelhead Oncorhynchus mykiss have historically been limited due to a lack of stock-specific information and difficulties in field sampling efforts. We used genetic stock identification (GSI) to estimate the composition of wild adult steelhead migrating past Lower Granite Dam on the Snake River between August 24 and November 25, 2008. Further, we combined genetic data with information on sex, length, age, and run timing to examine for differences in life history or demography among stocks. In total, 1,087 samples collected at the dam were genotyped with 13 standardized steelhead microsatellite loci and a new modified Y-chromosome-specific assay that differentiates sex. A genetic baseline of 66 populations was used to complete GSI of unknown-origin samples from Lower Granite Dam. Large differences in reporting group (stock) contributions were observed for the run as a whole; the Snake River–lower Clearwater River reporting group had the largest single con.
A Generalized SSAR Model and Predictive Distribution with an Application to VaR

The asymmetrical movements between the downward and upward phases of the sample paths of time series have been sometimes observed. By generalizing the SSAR (simultaneous switching autoregressive) models, we introduce a class of nonlinear time series models having the asymmetrical sample paths in the upward and downward phases. We show that the class of generalized SSAR models is useful for estimating the asymmetrical predictive distribution given the present and past information. Applications to the prediction based on the predictive median and the estimation of the VaR (value at risk) in financial risk management are discussed.