Miracle-dz/UniFAR-FTUs huggingface dataset:
Spliced leader–based metatranscriptomic analyses lead to recognition of hidden genomic features in dinoflagellates

Environmental transcriptomics (metatranscriptomics) for a specific lineage of eukaryotic microbes (e.g., Dinoflagellata) would be instrumental for unraveling the genetic mechanisms by which these microbes respond to the natural environment, but it has not been exploited because of technical difficulties. Using the recently discovered dinoflagellate mRNA-specific spliced leader as a selective primer, we constructed cDNA libraries (e-cDNAs) from one marine and two freshwater plankton assemblages. Small-scale sequencing of the e-cDNAs revealed functionally diverse transcriptomes proven to be of dinoflagellate origin. A set of dinoflagellate common genes and transcripts of dominant dinoflagellate species were identified. Further analyses of the dataset prompted us to delve into the existing, largely unannotated dinoflagellate EST datasets (DinoEST). Consequently, all four nucleosome core histones, two histone modification proteins, and a nucleosome assembly protein were detected, clearly indicating the presence of nucleosome-like machinery long thought not to exist in dinoflagellates. The isolation of rhodopsin from taxonomically and ecotypically diverse dinoflagellates and its structural similarity and phylogenetic affinity to xanthorhodopsin suggest a common genetic potential in dinoflagellates to use solar energy nonphotosynthetically. Furthermore, we found 55 cytoplasmic ribosomal proteins (RPs) from the e-cDNAs and 24 more from DinoEST, showing that the dinoflagellate phylum possesses all 79 eukaryotic RPs. Our results suggest that a sophisticated eukaryotic molecular machine operates in dinoflagellates that likely encodes many more unsuspected physiological capabilities and, meanwhile, demonstrate that unique spliced leaders are useful for profiling lineage-specific microbial transcriptomes in situ.
Sugar-Sweetened Beverage Taxes in Vermont: Media Framing and Public Perception

This thesis explores the conversation surrounding the recent attempts by the Vermont Legislature to pass a Sugar-Sweetened Beverage tax in the years 2014-2016. We explore the common perceptions expressed by a sample of Vermont residents and also look at how Vermont media outlets portrayed the tax through frames of reference. Framing is a method of emphasizing certain points of an issue. This thesis reports the common opinions of Vermonters, the media framing of the issue, and if there is any relationship between them in two academic journal articles. The first article looks at the common frames used in Vermont media during the 2014-2016 period. Classifying 10 proand anti-tax frames from 30 common arguments, the article analyzes the use of these frames, their prevalence in different news outlets, and their frequency during time periods. The article also looks at sponsors of these frames and measures which frames individuals and organizations are sponsoring. The study finds that anti-tax advocates most often cite economic hindrances as a reason to oppose the tax and pro-tax advocates predominately cite health benefits and economic tax benefits as a reason to support the tax. In the final year, pro-tax advocates sponsored economic benefits more than any other frames and this argument coincided with the statewide discussion of a budget shortfall. The second article measures the relationship between the media portrayal of the Sugar-Sweetened Beverage tax and the opinions of Vermont citizens regarding the tax. By looking at the prevalence of proand anti-tax frames usage in each year, a logistic regression model was built to measure the odds of people favoring tax based off of independent variables, including frames. Vermont residents fluctuated in their opinion of the tax over the years. It was found that in 2015, pro-tax frames made people more likely to support the tax. Democrats were also more likely to support the tax and Republicans were more likely to oppose the tax. This thesis provides insight into the conversation surrounding Sugar-Sweetened Beverage taxes in Vermont. It helps to shed light on the issue, how different groups feel about the issue, and how frames of thought presented through the media can relate to Vermonters’ opinion of the tax.
A change detector for polarimetric SAR data based on the relaxed Wishart distribution

In this paper, we present an unsupervised change detection method for polarimetric synthetic aperture radar (Pol-SAR) images based on the relaxed Wishart distribution. Most polarimetric change detectors assume the Gaussian-based complex Wishart model for multilook covariance matrices, which is only satisfied for homogeneous areas with fully developed speckle and no texture. Liu et al. recently proposed a new change detection algorithm under the multilook product model (MPM) to describe the heterogeneous clutters. The improvement has come at the expense of higher computational cost since the similarity measure is based on more advanced models accounting for texture, and they contain some mathematical special functions that is difficult to evaluate such similarity measures. In this paper, we will demonstrate the ability of the relaxed Wishart distribution for textured change detection analysis. Change results on simulated and real data demonstrate the effectiveness of the algorithm.
Whole-Cell Impedance Analysis for Highly and Poorly Metastatic Cancer Cells

A micro electrical impedance spectroscopy (muEIS) system has been developed and implemented to analyze highly and poorly metastatic head and neck cancer (HNC) cell lines with single-cell resolution. The microsystem has arrays of 16 impedance analysis sites, each of which is capable of capturing a single cell and analyzing its whole-cell electrical impedance spectrum. This muEIS system was used to obtain the electrical impedance spectra of the poorly metastatic HNC cell line 686 LN and the highly metastatic HNC cell line 686 LN-M4e over a frequency range of 40 Hz - 10 MHz. The 686 LN cells had higher impedance phase compared to that of 686 LN-M4e cells at frequencies between 50 kHz and 2 MHz. This result demonstrates that the metastatic state of HNC cells can be distinguished using the developed muEIS system. This system is expected to serve as a powerful tool for future detection and quantification of cancer cells from various tumor stages.
From Theory to Application: Using Simulation to Better Understand Price Determination in a Non-Frictionless Equity Market

This paper focuses on an analytic approach that has received relatively sparse application in the economics/finance literature: simulation. Providing a laboratory-type environment, simulation can generate data that enable a com- plex environment to be assessed in a tractable manner that might not otherwise be readily achievable. These thoughts are illustrated with reference to Grossman and Stiglitz’s (1976) seminal paper on price formation in an equity market. Our simulation results show that, as is not the case in a frictionless market, the dynamic pro- cess of price formation in a non-frictionless market can generate returns that exhibit accentuated short-period volatility, kurtosis, and returns autocorrelations.
Land grabbing, social differentiation, intensified migration and food security in northern Ghana

This paper argues that large-scale land appropriation is displacing subsistence farmers and reworking agrarian social relations in northern Ghana. The recent wave of farmland enclosure has not only resulted in heightened land scarcity, but also fostered a marked social differentiation within farming communities. The dominant form of inequality is an evolving class of landless and near-landless farmers. The majority of households cope with such dynamics by deepening their own self-exploitation in the production process. The fulcrum of this self-exploitation is gendered property rights as part of the conjugal contract, with men exerting a far greater monopoly over land resources than had previously been the case. Due to acute land shortages, women’s rights to use land as wives, mothers and daughters are becoming insecure, as their vegetable plots are being reclassified as male-controlled household fields. The paper further documents the painful choices that landless farmers have to make in order to meet livelihood needs, including highly disciplined, yet low-waged, farm labor work and sharecropping contracts. In these livelihood pathways, there emerge, again, exploitative relations of production, whereby surplus is expropriated from land-dispossessed migrant laborers and concentrated with farm owners. These dynamics produce a ‘simple reproduction squeeze’ for the land-dispossessed. Overall, the paper contributes to the emerging land grabbing literature by showing geographically specific processes of change for large-scale mining operations and gendered differentiated impacts.
Gfer is a critical regulator of HSC proliferation

Hematopoietic stem cells (HSC) are a relatively quiescent pool of cells that perform the arduous task of replacing the short-lived mature cells of the peripheral blood. While a rapid expansion of HSCs under periods of hematological stress is warranted, their enhanced proliferation during homeostasis leads to loss of function. We recently reported that in HSCs, the evolutionarily conserved growth factor erv1-like (Gfer) acts to counter jun activation domain-binding protein 1 (Jab1)-mediated nuclear export and destabilization of the cell cycle inhibitor, p27kip1, by directly binding to and sequestering the COP9 signalosome (CSN) subunit. Through this mechanism, Gfer promotes quiescence and maintains the functional integrity of HSCs. Here, we extend our study to demonstrate an association between Gfer and Ca2+/calmodulin-dependent protein kinase IV (CaMKIV) in the regulation of HSC proliferation. Highly proliferative and functionally deficient Camk4-/- HSCs possess significantly lower levels of Gfer and p27kip1. Ectopic expression of Gfer restores quiescence and elevates p27kip1 expression in Camk4-/- HSCs. These results further substantiate a critical role for Gfer in the restriction of unwarranted proliferation in HSCs through the inhibition of Jab1 and subsequent stabilization and nuclear retention of p27kip1. This Gfer-mediated pro-quiescence mechanism could be therapeutically exploited in the treatment of hematological malignancies associated with elevated Jab1 and reduced p27kip1.
Predictors of longitudinal change in bone mineral density in a cohort of HIV-positive and negative patients

Objective: Although low bone mineral density (BMD) is prevalent in HIV, changes in BMD over time remain unclear. We aimed to compare rates of, and factors associated with, BMD change between HIV-positive and HIV-negative patients. Methods: In a prospective, 3-year cohort, HIV-positive and HIV-negative patients provided annual demographic and clinical data, fasting bloods, and dual x-ray absorptiometry. Using longitudinal mixed models we compared and determined predictors of rate of change in BMD. Results: Of 384 study participants (45.8% HIV positive), 120 contributed two and 264 contributed three BMD measurements. Those with HIV were younger [median interquartile range 39 (34–46) vs. 43 (35–50) years; P = 0.04], more often men (61 vs. 46%; P = 0.003), and less likely Caucasian (61 vs. 82%; P < 0.001). Although BMD was lower in those with HIV, BMD declined in both groups, with nonsignificant between-group difference in rate of BMD change over time. Within the HIV group, starting antiretroviral therapy (ART) within 3 months of enrolment was associated with greater BMD decline at all anatomical sites (all P < 0.001). Age more than 30 years, Caucasian ethnicity, and not being on ART during follow-up were associated with greater decline and higher parathyroid hormone associated with a smaller decline in BMD at the femoral neck. We found no association between BMD change and exposure to tenofovir disoproxil fumarate or protease inhibitors. Conclusion: We observed no difference in rate of BMD decline regardless of HIV status and in HIV-positive patient, having started ART within the previous 3 months was the only factor associated with greater BMD decline at all three sites.
Direct Activation of Mitochondrial Apoptosis Machinery by c-Jun N-terminal Kinase in Adult Cardiac Myocytes*

Although oxidative stress causes activation of c-Jun N-terminal kinase (JNK) and apoptosis in many cell types, how the JNK pathway is connected to the apoptosis pathway is unclear. The molecular mechanism of JNK-mediated apoptosis was investigated in adult rat cardiac myocytes in culture as a model system that is sensitive to oxidative stress. Oxidative stress caused JNK activation, cytochromec release, and apoptosis without new protein synthesis. Oxidative stress-induced apoptosis was abrogated by dominant negative stress-activated protein kinase/extracellular signal-regulated kinase kinase-1 (SEK1)-mediated inhibition of the JNK pathway, whereas activation of the JNK pathway by constitutively active SEK1 was sufficient to cause apoptosis. Inhibition of caspase-9, an apical caspase in the mitochondrial apoptosis pathway, suppressed oxidative stress-induced apoptosis, whereas inhibition of caspase-8 had no effect, indicating that both the JNK pathway and the mitochondrial apoptosis machinery are central to oxidative stress-induced apoptosis. Both JNK and SEK1 localized on mitochondria where JNK was activated by oxidative stress. Furthermore, active JNK caused the release of apoptogenic factors such as cytochrome c from isolated mitochondria in a cell-free assay. These findings indicate that the JNK pathway is a direct activator of mitochondrial death machinery without other cellular components and provide a molecular linkage from oxidative stress to the mitochondrial apoptosis machinery.
Hes1 and Hes5 as Notch effectors in mammalian neuronal differentiation

While the transmembrane protein Notch plays an important role in various aspects of development, and diseases including tumors and neurological disorders, the intracellular pathway of mammalian Notch remains very elusive. To understand the intracellular pathway of mammalian Notch, the role of the bHLH genes Hes1 and Hes5 (mammalian hairy and Enhancer‐of‐split homologues) was examined by retrovirally misexpressing the constitutively active form of Notch (caNotch) in neural precursor cells prepared from wild‐type, Hes1‐null, Hes5‐null and Hes1‐Hes5 double‐null mouse embryos. We found that caNotch, which induced the endogenous Hes1 and Hes5 expression, inhibited neuronal differentiation in the wild‐type, Hes1‐null and Hes5‐null background, but not in the Hes1‐Hes5 double‐null background. These results demonstrate that Hes1 and Hes5 are essential Notch effectors in regulation of mammalian neuronal differentiation.
Training With Virtual Visual Feedback to Alleviate Phantom Limb Pain

Background. Performing phantom movements with visual virtual feedback, or mirror therapy, is a promising treatment avenue to alleviate phantom limb pain. However the effectiveness of this approach appears to vary from one patient to another. Objective. To assess the individual response to training with visual virtual feedback and to explore factors influencing the response to that approach. Methods. Eight male participants with phantom limb pain (PLP) resulting from either a traumatic upper limb amputation or a brachial plexus avulsion participated in this single case multiple baseline study. Training was performed 2 times per week for 8 weeks where a virtual image of a missing limb performing different movements was presented and the participant was asked to follow the movements with his phantom limb. Results. Patients reported an average 38% decrease in background pain on a visual analog scale (VAS), with 5 patients out of 8 reporting a reduction greater than 30%. This decrease in pain was maintained at 4 weeks postintervention in 4 of the 5 participants. No significant relationship was found between the long-term pain relief and the duration of the deafferentation or with the immediate pain relief during exposure to the feedback. Conclusions. These results support the use of training with virtual feedback to alleviate phantom limb pain. Our observations suggest that between-participant differences in the effectiveness of the treatment might be related more to a difference in the susceptibility to the virtual visual feedback, than to factors related to the lesion, such as the duration of the deafferentation.
A Guide to Event Data: Past, Present, and Future

The goal of this paper is to provide a general overview of event data and its importance in the study of political conflict. In doing so, we illustrate how the level of methodological sophistication in the data collection, coding, and analyzing process has progressed from the earliest event-data projects in the 1970s to the most current ones today. Additionally, we highlight ongoing debates in the discipline as well as address key challenges that practitioners of event data will have to overcome to generate increasingly accurate and nuanced analyses in the future.
Parallel ZVS converter with series connected transformers

This paper presents a parallel zero voltage switching (ZVS) dc-dc converter with series connected transformers. In order to increase output power, two transformers connected in series are used in the proposed converter. Two buck-type converters connected in parallel have the same switching devices. The primary windings of series connected transformers can achieve the balanced secondary winding currents. The current doubler rectifiers with ripple current cancellation are connected in parallel at the output side to reduce the current stress of the secondary winding. Thus the current ripple on the output capacitor is reduced and the size of output choke and output capacitor are reduced. Only two switches are used in the proposed circuit instead of four switches in the conventional parallel ZVS converter to achieve zero voltage switching and output current sharing. Therefore, the proposed converter has less power switches. The ZVS turn-on is implemented during the commutation stage of two complementary switches such that the switching losses and thermal stresses on the semiconductors are reduced. Experimental results for a 528W (48V/11A) prototype are presented to prove the theoretical analysis and circuit performance.
LiveSync: a Method for Real Time Video Streaming Synchronization from Independent Sources

This work presents a tool that allows users to synchronize live videos from multiple sources such as YouTube or any other video streaming sources. The proposed approach to proceed the multiple camera video synchronization is based in crowdsourcing techniques, using the power of a crowd of collaborators to synchronize videos, requiring from each user the sync of only a pairs of videos. Additional sync relations are inferred from the known contributions, using transitivity properties and an appropriate structure for this inference, the Dynamic Alignment List.
An Organizational Communication Analysis of a Medium-Sized Newspaper

~n Organizational Communication Analysis of a Medium-Size Newspaper A medium-size newspaper in Central Florida was observed for 8 weeks in the Spring and Summer of 1976 and 58 employees interviewed to determine internal communication patterns and measure attitudes toward the communication system, organization and job related variables. A systems theory of organizations provided basic theoretical assumptions. Since communication activities occur within the framework of internal organization elements such as structure, objectives, leadership style, reward system, technology, intergroup relations, and individual employee characteristics, those elements were described. Communication activities were reported in terms of message purpose, network traversed, method of diffusion and relationships. Findings indicated that the nature and technology of the organization were more important predictors of communication activities than other elements. Messages were primarily task related, diffused both horizontally and vertically over formal and informal networks. The method of diffusion was primarily oral in face to face dyadic or small group situations. Analysis of attitudinal data indicated that communication satisfaction was the most important predictor of organization and job related attitudes. Persons occupying the lowest levels in the organizational hierarchy were the most negative about the communication system and were least involved in it. Persons occupying the upper levels were the most positive about the system and were the most involved in it. A factor analysis of the attitudinal data revealed 14 factors to be considered in future research.
Ventral Striatal Activation During Reward Processing in Psychosis: A Neurofunctional Meta-Analysis.

IMPORTANCE Abnormal reward processing is suggested to underlie the formation of psychotic symptoms, likely driven by elevated ventral striatal (VS) dopamine levels. Functional magnetic resonance imaging studies reveal alterations of VS activity during reward processing in patients with chronic psychosis and first episode of psychosis, as well as individuals at high risk for psychosis, but findings are inconclusive, conflicting, and difficult to subject to meta-analysis without introducing bias because several studies reported that findings were not statistically significant but did not report statistics. OBJECTIVE To assess the differences between patients with schizophrenia spectrum disorders and healthy controls in VS activation during reward processing. DATA SOURCES Web of Knowledge database (incorporating Web of Science and MEDLINE) until July 2015, including references of eligible articles and reviews. STUDY SELECTION Functional magnetic resonance imaging studies comparing VS activity during monetary reward processing between patients with schizophrenia spectrum disorders or clinical or genetic high-risk state for psychosis and healthy controls. DATA EXTRACTION AND SYNTHESIS Statistics and thresholds related to the main outcome measures and potential moderators were independently retrieved by 2 investigators. Effect sizes were analyzed using MetaNSUE, a random-effects method that enables the unbiased inclusion of nonstatistically significant unreported effects. MAIN OUTCOMES AND MEASURES Effect size of the group differences in VS activity, and correlation between VS activity and negative and positive symptom scores in patients. RESULTS The meta-analysis included 23 studies (917 patients) for reward anticipation, 9 studies (358 patients) for reward feedback, and 8 studies (314 patients) for reward prediction error. We found significant bilateral VS hypoactivation during reward anticipation (23 studies, n = 917) in patients compared with healthy controls (left/right Cohen d, -0.50/-0.70; P < .001). Left VS abnormality was more severe in patients with high scores of negative symptoms during reward anticipation (r = -0.41; P < .001). Patients also showed hypoactivation during reward feedback (left/right d, -0.57/-0.56; P < .001). Simulations showed that exclusion of studies with nonstatistically significant unreported effects was associated with a strong bias (d bias = 0.22), whereas estimations using MetaNSUE were unbiased even when statistics were seldom reported (d bias < 0.001). CONCLUSIONS AND RELEVANCE This meta-analysis provides evidence that patients with psychosis demonstrate VS hypoactivation during reward anticipation. The assessment of VS prediction errors seems to be promising, but more studies are needed to draw valid conclusions.