Miracle-dz/UniFAR-FTUs huggingface dataset:
Single Cell Analysis: From Technology to Biology and Medicine

Single-cell analysis heralds a new era that allows “omics” analysis, notably genomics, transcriptomics, epigenomics and proteomics at the single-cell level. It enables the identification of the minor subpopulations that may play a critical role in a biological process of a population of cells, which conventionally are regarded as homogeneous. It provides an ultra-sensitive tool to clarify specific molecular mechanisms and pathways and reveal the nature of cell heterogeneity. It also facilitates the clinical investigation of patients when a very low quantity or a single cell is available for analysis, such as noninvasive prenatal diagnosis and cancer screening, and genetic evaluation for in vitro fertilization. Within a few short years, single-cell analysis, especially whole genomic sequencing and transcriptomic sequencing, is becoming robust and broadly accessible, although not yet a routine practice. Here, with single cell RNA-seq emphasized, an overview of the discipline, progresses, and prospects of single-cell analysis and its applications in biology and medicine are given with a series of logic and theoretical considerations.
Sustained NF-κB Activation and Inhibition in β-Cells Have Minimal Effects on Function and Islet Transplant Outcomes

The activation of the transcription factor NF-κB leads to changes in expression of many genes in pancreatic β-cells. However, the role of NF-κB activation in islet transplantation has not been fully elucidated. The aim of the present study was to investigate whether the state of NF-κB activation would influence the outcome of islet transplantation. Transgenic mice expressing a dominant active IKKβ (constitutively active) or a non-degradable form of IκBα (constitutive inhibition) under control of the rat insulin promoter were generated. Islets from these mice were transplanted into streptozotocin diabetic mice in suboptimal numbers. Further, the effects of salicylate (an inhibitor of NF-κB) treatment of normal islets prior to transplantation, and the effects of salicylate administration to mice prior to and after islet implantation were evaluated. Transplantation outcomes were not affected using islets expressing a non-degradable form of IκBα when compared to wild type controls. However, the transplantation outcomes using islets isolated from mice expressing a constitutively active mutant of NF-κB were marginally worse, although no aberrations of islet function in vitro could be detected. Salicylate treatment of normal islets or mice had no effect on transplantation outcome. The current study draws attention to the complexities of NF-κB in pancreatic beta cells by suggesting that they can adapt with normal or near normal function to both chronic activation and inhibition of this important transcription factor.
Towards a spatio-chromatic standard observer for detection

The aim of the ColorFest is to extend the original ModelFest (http://vision.arc.nasa.gov/modelfest/) experiments to build a spatio-chromatic standard observer for the detection of static coloured images. The two major issues that need to be addressed are (1) the contrast sensitivity functions for the three chromatic mechanisms and (2) how the output of these channels is combined. We measured detection thresholds for stimuli modulated along different colour directions and for a wide range of spatial frequencies. The three main directions (an achromatic direction, a nominally isoluminant red-green direction, and the tritanopic confusion line) and four intermediate colour directions were used. These intermediate directions were the vector sums of the thresholds along the main directions. We evaluate two models. Detection performance is described by a linear transformation C defining the chromatic tuning and a diagonal matrix S reflecting the sensitivity of the chromatic mechanisms for a particular spatial frequency. The output of the three chromatic mechanisms is combined according to a Minkowski metric (General Separable Model), or according to a Euclidean Distance measure (Ellipsoidal Separable Model). For all three observers the ellipsoidal model fits as well as the general separable model. Estimating the chromatic tuning improves the model fit for one observer.
Moral Injury, Self-Compassion, and Mental Health

Military veterans are exposed to unique stressors (e.g., combat) that can precipitate the onset of various mental health problems. Morally compromising combat experiences have recently gained empirical and clinical attention, following the increased rates of mental health problems observed in Afghanistan and Iraq veterans. The current investigation aimed to assess the relationship between these morally compromising experiences and various mental health outcomes. Further, it examined the potential protective role of self-compassion in these relationships. Specifically, moderation analyses were conducted to evaluate the interaction between exposure to and intensity of morally compromising experiences and self-compassion on various mental health outcomes. Study findings indicate that self-compassion significantly moderated the relationship between morally compromising experiences and posttraumatic stress disorder (PTSD), depression severity, and deliberate selfharm severity, but not substance misuse. These results highlight the potential clinical utility of self-compassion in military mental health, particularly in the context of morally compromising experiences.
Leucon (Crymoleucon) rossi , a new species (Crustacea: Cumacea: Leuconidae) from the shelf waters of the Ross Sea (Antarctica), with a key to the genus Leucon south of 60°S

A new leuconid cumacean, Leucon (Crymoleucon) rossi n. sp. , is described from depths of 84 to 458 m in the Ross Sea off the Victoria Land coast. Leucon rossi n. sp. is distinguished from other members of the genus by a combination of characters including 1) a blunt, horizontally directed pseudorostrum without a distinctly protruding siphon; 2) strongly developed antennal notch; 3) entire dorsomedian margin of carapace appearing serrate, armed with 14 to 19 anteriorly curved spines in female (up to 21 in subadult males); 4) a small, but distinct, spine behind the frontal lobe; and 5) the uropodal peduncle slightly shorter than the exopod. After Leucon antarcticus Zimmer, 1907, L. rossi was the second most frequently occurring cumacean in the samples collected off Victoria Land. Statistical analyses showed significant differences in the proportion of carapace length and height of adult (all incubating in the present study) and immature females compared to immature males; no adult males were available for study.
The effect of stock prices on the demand for money market mutual funds

During the 1990s, households have sharply increased the share of their portfolios held in equities and mutual funds and sharply reduced the share held in bank accounts. We show that this reallocation has substantially increased the impact of financial-market developments on the demand for money. Specifically, both increases and decreases in the Wilshire 5000 have boosted the demand for money funds during the 1990s, although they had little effect on money funds during the 1980s. The estimated effects in the 1990s are generally statistically significant and economically important.
DISTANCE, GROWTH FACTOR, AND DARK ENERGY CONSTRAINTS FROM PHOTOMETRIC BARYON ACOUSTIC OSCILLATION AND WEAK LENSING MEASUREMENTS

Baryon acoustic oscillations (BAOs) and weak lensing (WL) are complementary probes of cosmology. We explore the distance and growth factor measurements from photometric BAO and WL techniques, and investigate the roles of the distance and growth factor in constraining dark energy. We find for WL that the growth factor has a great impact on dark energy constraints, but is much less powerful than the distance. Dark energy constraints from WL are concentrated in considerably fewer distance eigenmodes than those from BAO, with the largest contributions from modes that are sensitive to the absolute distance. Both techniques have some well-determined distance eigenmodes that are not very sensitive to the dark energy equation-of-state parameters w0 and wa, suggesting that they can accommodate additional parameters for dark energy and for the control of systematic uncertainties. A joint analysis of BAO and WL is far more powerful than either technique alone, and the resulting constraints on the distance and growth factor will be useful for distinguishing dark energy and modified gravity models. The Large Synoptic Survey Telescope (LSST) will yield both WL and angular BAO over a sample of several billion galaxies. Joint LSST BAO and WL can yield 0.5% level precision on ten comoving distances evenly spaced in log(1 + z) between redshift 0.3 and 3 with cosmic microwave background priors from Planck. In addition, since the angular diameter distance, which directly affects the observables, is linked to the comoving distance solely by the curvature radius in the Friedmann–Robertson–Walker metric solution, the LSST can achieve a pure metric constraint of 0.017 on the mean curvature parameter Ωk of the universe simultaneously with the constraints on the comoving distances.
Early adolescents' perceptions and attitudes towards gender representations in video games

This study investigated adolescents’ perception and attitudes towards gender representation in video game covers, and the degree to which these depictions may influence their notions on gender and identification. Seventeen participants ranging from ages 12 and 13 participated in semi-structured interviews to explore this topic. This study’s conceptual framework encompassed social cognitive theory, gender schema theory, and cultivation theory. Findings suggest that gender representation in video games does influence the majority of participants’ notions of gender. However, there are differences between how males and females’ approach, interpret, and respond to this type of media. Findings also showcased that evidence of implicit bias was detected in both male and female participants, demonstrated through inconsistencies in their responses. Finally, the findings revealed a significant lack of identification from the majority of participants with video game characters, as many participants were able to clearly distinguish between simulated and real-life experiences.
Validity issues in the application of selected qualitative social research methods

This paper investigated the validity concerns in the application of Focus Group Discussions (FGDs) and One-on-one Qualitative Interviews as forms of qualitative social research methods with the objective of unraveling the validity concerns embedded in their application.In order to reach this objective, theeffectiveness of qualitative social research methods – FGDs and One-on-one Qualitative Interviews– is put on the line by empirically comparing and contrasting data from two FGD sessions and one-on-one interviews to ascertain the consistency in terms of data retrieved from participants using these two data collection methods. The study is guided by the hypothesis that data obtained via FGDs may be influenced by groupthink rather than individual participant’s perspectives. A critical scrutiny of the data that emanated from the two organized FGDs departed quite significantly from the data that was elicited from the one-on-one qualitative interviews. The difference in responses confirms that FGDs are not fully insulated from the shackles of groupthink. It is recommended, among others,that though FGD can stand unilaterally as a research methodology for non-sensitive topics with no direct personal implications forparticipants; researchers should be encouraged to adopt FGD in league with other methods in a form of triangulation or mixed methodological approach for amore quality data, bearing in mind the central role occupied by data in the social scientific research process.Key Words: Focus Group Discussion, One-on-One Qualitative Interview, Social Research Methodology, Qualitative Data, and Groupthink.
Immunity of the Saccharomyces cerevisiae SSY5 mRNA to nonsense-mediated mRNA decay

The nonsense-mediated mRNA decay (NMD) pathway is a specialized pathway that triggers the rapid degradation of select mRNAs. Initially, identified as a pathway that degrades mRNAs with premature termination codons, NMD is now recognized as a pathway that also regulates some natural mRNAs. Since natural mRNAs do not typically contain premature termination codons, these mRNAs contain features that target them to NMD. In Saccharomyces cerevisiae mRNAs with atypically long 3′-UTRs are usually degraded by NMD, however in some conditions a constitutively expressed SSY5 mRNA with multiple NMD targeting signals including an atypically long 3′-UTR is an exception. We investigated the features of the SSY5 mRNAs that confer immunity to NMD. We found that the SSY5 mRNA 3′-UTRs are sufficient to target NMD insensitive mRNA to the pathway. Replacing the SSY5 3′-UTRs with the cyc1-512 3′-UTRs, known to target mRNAs to NMD or with the CYC1 3′-UTR, known not to target mRNAs to NMD, resulted in production of SSY5 mRNAs that were regulated by NMD. These observations suggest that the SSY5 mRNAs require sequences both within the 5′-UTR and/or ORF as well as the 3′-UTR to escape decay by NMD.
Small signal analyses and hardware implementation of a buck-boost converter for renewable energy applications

In this study small signal analyses of a buck boost converter for a renewable energy applications is performed and hardware implementation is realized. State equations are solved for different study conditions and transfer function of uncontrolled system is obtained for stability analyses. Experimental hardware of buck boost converter realized with a MOSFET driver circuit which is designed for high frequency, high voltage and high current implementations. Experimental studies and results are given in the paper. The results show that hardware implementation of the system is accomplished.
Prediction of social bookmarking based on a behavior transition model

We propose an algorithm to predict users' future bookmarking using social bookmarking data. It is a problem that primitive collaborative filtering cannot exactly catch users' preferences in social bookmarkings containing enormous items (URLs) because in many cases user's adoption data is sparse. There can be various influences on bookmarking such as effects from the environment and changes in user preference. We use temporal sequence among the bookmarking-users to represent word-of-mouth and among the bookmarked-URLs to represent user's interest, and model each sequential order as a continuous-time Markov chain. This idea comes from diffusion of innovation theory. A transition probability from a state (user/URL) to another state is defined by the transition rate calculated from the time taken for the transition. We predicted user's preferences through a combination of estimating the most likely transition between users using URLs as input and between URLs using users as input. We conducted evaluation experiments with a social bookmarking service in Japan called Hatena bookmark. The proposed algorithm predicts users' preferences with higher accuracy than collaborative filtering or simple transition models based on either user or URL.
Dynamic Web-Page Generation in Resource-Constrained Environments The Kertasarie Server Pages

Today, many embedded systems are equipped with network interfaces. Thus, Web based management and administration are often required in such embedded systems. General approaches, which are widely available, fail to work on those resource constrained devices. Yet, there exists a necessity to support rapid development for dynamically generated pages. In this contribution we present a framework that will be usable on many embedded systems and also helps the Web developer to simplify the document structure.
Request Window: an Approach to Improve Throughput of RDBMS-based Data Integration System by Utilizing Data Sharing Across Concurrent Distributed Queries

This paper focuses on the problem of improving distributed query throughput of the RDBMS-based data integration system that has to inherit the query execution model of the underlying RDBMS: execute each query independently and utilize a global buffer pool mechanism to provide disk page sharing across concurrent query execution processes. However, this model is not suitable for processing concurrent distributed queries because the foundation, the memory-disk hierarchy, does not exist for data provided by remote sources. Therefore, the query engine cannot exploit any data sharing so that each process will have to interact with data sources independently: issue data requests and fetch data over the network. This paper presents Request Window, a novel DQP mechanism that can detect and employ data sharing opportunities across concurrent distributed queries. By combining multiple similar data requests issued to the same data source to a common data request, Request Window allows concurrent query executing processes to share the common result data. With the benefits of reduced source burdens and data transfers, the throughput of query engine can be significantly improved. This paper also introduces the IGNITE system, an extended PostgreSQL with DQP support. Our experimental results show that Request Window makes IGNITE achieve a 1.7x speedup over a commercial data integration system when running a workload of distributed TPC-H queries.
Admixture Fine-Mapping in African Americans Implicates XAF1 as a Possible Sarcoidosis Risk Gene

Sarcoidosis is a complex, multi-organ granulomatous disease with a likely genetic component. West African ancestry confers a higher risk for sarcoidosis than European ancestry. Admixture mapping provides the most direct method to locate genes that underlie such ethnic variation in disease risk. We sought to identify genetic risk variants within four previously-identified ancestry-associated regions—6p24.3–p12.1, 17p13.3–13.1, 2p13.3–q12.1, and 6q23.3–q25.2—in a sample of 2,727 African Americans. We used logistic regression fit by generalized estimating equations and the MIX score statistic to determine which variants within ancestry-associated regions were associated with risk and responsible for the admixture signal. Fine mapping was performed by imputation, based on a previous genome-wide association study; significant variants were validated by direct genotyping. Within the 6p24.3–p12.1 locus, the most significant ancestry-adjusted SNP was rs74318745 (p = 9.4*10−11), an intronic SNP within the HLA-DRA gene that did not solely explain the admixture signal, indicating the presence of more than a single risk variant within this well-established sarcoidosis risk region. The locus on chromosome 17p13.3–13.1 revealed a novel sarcoidosis risk SNP, rs6502976 (p = 9.5*10−6), within intron 5 of the gene X-linked Inhibitor of Apoptosis Associated Factor 1 (XAF1) that accounted for the majority of the admixture linkage signal. Immunohistochemical expression studies demonstrated lack of expression of XAF1 and a corresponding high level of expression of its downstream target, X-linked Inhibitor of Apoptosis (XIAP) in sarcoidosis granulomas. In conclusion, ancestry and association fine mapping revealed a novel sarcoidosis susceptibility gene, XAF1, which has not been identified by previous genome-wide association studies. Based on the known biology of the XIAP/XAF1 apoptosis pathway and the differential expression patterns of XAF1 and XIAP in sarcoidosis granulomas, we suggest that this pathway may play a role in the maintenance of sarcoidosis granulomas.
Preliminary Evaluation of Inter-Oraganizational Information Systems and Relationships

It is agreed that good communication systems between organisations increase customer satisfaction and relationship behaviour. However, less is known about the details of how information is used to manage relationships. Theories that have been found have either been tested on non-perishable goods or on small case studies. This paper presents a preliminary evaluation of some aspects of Storer (2001) model of inter-organizational information feedback systems (IOIS) and relationships. Specifically whether patterns of information sharing between organisations can be explained by relationship and environmental variables. A case study was conducted of 32 dyadic pairs of organisations (64 respondents) involving perishable products (green life plants). A Rasch analysis of the types of information exchanged variables showed there was a consistent order of information sharing and that an interval scale of information sharing could be calculated. All respondents had similar information sharing patterns. Factor analysis of relationship variables resulted in three reliable factors – ‘trust’, ‘responsiveness’, and ‘satisfaction and commitment’. Factor analysis of environmental variables also resulted in three reliable factors – ‘relationship predictability’, ‘uncertainty’, and ‘dependence and influence’. Two variables did not load well onto these factors and were used separately in further analysis (‘difficulty in replacement’ and ‘loyalty remain with them despite alternatives’). Regression analysis was conducted to determine if information sharing patterns could be predicted by environmental and relationship variables and factors. However, it did not explain a great deal of the variance in the information sharing patterns (adjusted R = 0.13) and the only significant predictor factor was the perceived responsiveness of the other party. It is concluded that future research needs to be undertaken to see if the results will hold for a larger sample size. In addition, it may be that the other variables in the IOIFS also need to be analysed and modelled with the relationship and environmental variables as originally hypothesised by Storer (2001).
On Accelerating the Global Literacy Transition by Annababette Wils (Research and Assessment Systems for Sustainability Program Discussion Paper 2002-18)

Literacy has been defined as one of the primary goals of the sustainable development. Two of the UN’s millennium goals pertain to education. This paper examines the importance of literacy to sustainability, the speed with which literacy spreads in a country, and identifies factors, which can accelerate the literacy transition. This paper suggests that most countries in the world are either in the process of an education transition to full literacy, and perhaps to universal full primary and secondary education achievements for all adults, or have finished this transition. A significant number of countries is far from completion. The work presented here shows that the transition has a general, sigmoid pattern. A statistical analysis shows 2/3 of countries is on a time path lasting 55-100 years for the transition from 10 to 90 percent adult literacy (the remainder is on a longer path). As literacy is an important skill in the modern world, it is important that we find ways to move slower countries, particularly those in the early stages of the transition, towards the 3 generation path. This paper presents data on the education transition, identifies factors that accelerate the literacy transition and explores the fastest possible transition with a simulation model. The global literacy transition pattern – 130 countries’ literacy by birth cohort grouped together to form the transition pattern. Source: World Bank Development Indicators 2001. 0 10 20 30 40 50 60 70 80 90 100 -2 5 -2 0 -1 5 -1 0 -5 0 5 10 15 20 25 30 35 40 45 50 55 60 65 70 75 80 85 90 95 10 0 10 5 11 0 11 5 12 0 12 5 Estimated years since 10% literacy Ad ul t f em al e lit er ac y