Miracle-dz/UniFAR-FTUs huggingface dataset:
Analysis of Cis-acting Regulatory Motifs Involved in Alternative Splicing

ZHAO,SIHUI. Analysis of Cis-acting Regulatory Motifs Involved in Alternative Splicing. (Under the direction of Dr. Steffen Heber). Alternative splicing is an important posttranscriptional process in eukaryotes. It dramatically expands the proteome and contributes essentially to the regulation of gene expression. Cis-acting regulatory motifs play a pivotal role in the regulation of alternative splicing. Many human diseases involved with aberrant (alternative) splicing are caused by mutations of splicing regulatory motifs. However, due to the short, degenerate and contextdependent nature, the prediction of cis-acting splicing motifs is a very challenging task. In this dissertation, we focus on discovery of splicing signals from sequences. This may help to reveal the integrated splicing code and to understand the regulation of gene expression in the resolution of exon level. In chapter one, we review the up-to-date research development in alternative splicing and its regulation, as well as the experimental and computational approaches in genome-wide alternative splicing analysis. We describe a large-scale data analysis experiment to discover AS motifs in chapter two. We applied a computational framework to re-analyze a dataset containing about 2,500 cassette exons and skipping rates for regulatory motifs. The alternative spliced events were clustered by their expression profiles to find co-regulated genes. Rather than using a fixed cutoff as cluster boundary, we used systematic sampling to sample sequence clusters and eliminated redundant motifs predicted from overlapping clusters. We conclude that these predicted motifs may be promising candidates responsible for AS regulation by comparison to known motifs and by positional bias. In chapter three, we describe a new approach to discover short and degenerate AS motifs. We implemented a two-step approach incorporating skipping rates in motif discovery. In the simulation study, we show that this approach is especially suitable to discover short and highly degenerate motifs. Analysis of cassette exons in Central Nervous System tissues produced 15 motifs which are associated with the variation of skipping rates. We discover that Nova and hnRNP A1 binding sites are involved with AS regulation, as well as about ten novel motifs. Moreover, co-operation between predicted motifs are also revealed. In chapter four, we give the present status of SPRED, a database of cis-acting regulatory splicing elements. The motifs in SPRED are compiled from literature. They are all experimentally validated. The web interface is publically accessible and accompanied with query and similarity search tools. The goal of SPRED is to provide a comprehensive motif dictionary to facilitate the research in AS and its regulation. Finally, we give the conclusions in chapter five. We also give the perspective for future study and briefly review the potential challenge. Analysis of Cis-acting Regulatory Motifs Involved in Alternative Splicing
Reconstructing atmospheric changes in Monsoon regions using eolian dust

Mineral dust is generated in continental interiors and exported by winds to ocean basins, providing a sedimentary archive which is one of the few direct indicators we have of atmospheric circulation in the past. This archive can be utilized in regions of dust transport also affected by monsoons to examine how different climate forcing mechanisms impact the monsoon regions over glacialinterglacial, orbital, and millennial timescales. This thesis generates new eolian dust records from two monsoon regions to reconstruct changes in atmospheric circulation in response to forcing by high-latitude insolation and boundary condition change. In Chapters 2 and 3 I use Thxsnormalization to construct high-resolution eolian dust flux records from sedimentary archives downwind from the West African and East Asian Monsoon regions respectively. The West African margin dust records show variability associated with an interplay between Northern Hemisphere summer insolation forcing and North Atlantic cooling. The longest record at ODP Site 658, stretching back to 67 ka, shows evidence for a “Green Sahara” interval from 60-50 ka and a skipped precessional “beat” from 35-20 ka. This record also shows evidence for abrupt increases in dust flux associated with Greenland stadials. The Shatsky Rise record at ODP Site 1208, downwind of East Asian dust sources, shows variability associated with glacial-interglacial boundary conditions over the last 330 ka, exhibiting high dust during glacial times. The record also exhibits variability associated with a Northern Hemisphere summer insolation control at times overriding the glacialinterglacial signal. In Chapter 4 I demonstrate the feasibility of using radiogenic neodymium isotopes (Nd/Nd) at IODP Site U1430 in the Sea of Japan to fingerprint the provenance of eolian material at the core site from Asian dust sources. I then generate a Nd/Nd record from isolated eolian material over the last 200 ka to examine Westerly Jet behavior in the Asian interior, which shows resolvable orbital-scale variability from 200 to 100 ka, and muted variability from 100 to 0 ka. The findings imply a quicker shift of the Westerly Jet to the north of the Tibetan Plateau during times of high Northern Hemisphere summer insolation and a strong Asian monsoon. Thesis Supervisor: David McGee Title: Associate Professor of Paleoclimate
Leading the academy or being led? Hong Kong women academics

This paper provides a new gender-based analysis of survey data collected on Hong Kong academics in 2008. First, it illustrates the gender differences that exist in the Hong Kong academy. Second, it discusses possible explanations for these differences as informed by the data. And third, it offers a novel argument, again informed by the data, for the importance of addressing these differences, particularly with respect to the issue of women and academic leadership.
Thermal alteration of soil organic matter properties: a systematic study to infer response of Sierra Nevada climosequence soils to forest fires

Abstract. Fire is a common ecosystem perturbation that affects many soil properties. As global fire regimes continue to change with climate change, we investigated thermal alteration of soils' physical and chemical properties after they are exposed to a range of temperatures that are expected during prescribed and wildland fires. For this study, we used topsoils collected from a climosequence transect along the western slope of the Sierra Nevada that spans from 210 to 2865 m a.s. l. All the soils we studied were formed on a granitic parent material and had significant differences in soil organic matter (SOM) concentration and mineralogy owing to the effects of climate on soil development. Topsoils (0–5 cm depth) from the Sierra Nevada climosequence were heated in a muffle furnace at six set temperatures that cover the range of major fire intensity classes (150, 250, 350, 450, 550 and 650 °C). We determined the effects of heating temperature on soil aggregate strength, aggregate size distribution, specific surface area (SSA), mineralogy, pH, cation exchange capacity (CEC), and carbon (C) and nitrogen (N) concentrations. With increasing temperature, we found significant reduction of total C, N and CEC. Aggregate strength also decreased with further implications for loss of C protected inside aggregates. Soil pH and SSA increased with temperature. Most of the statistically significant changes (p
Defining the Socially Responsible Leader: Revisiting Issues in Responsible Leadership

We renew an exchange of letters from 2008 regarding the meaning of responsible leadership, which applies to senior executives of firms as they attempt to engage in corporate social responsibility. An interesting aspect to this discussion is that, depending on one’s theoretical perspective, responsible leadership can be defined in multiple, somewhat disparate ways. We use the terms strategist versus integrator to characterize the most common delineation of responsible leader orientations. While the strategist orientation implies the planning and use of corporate social responsibility initiatives for the direct targeting of return on investment, the integrator orientation involves senior leaders’ use of corporate social responsibility to serve the interests of a range of corporate stakeholders. Although a divergence of opinion is expressed in our letters, we concur in our conclusion that more research is necessary to better understand these diverse orientations and their effects on organizations.
A Novel Hybrid MAC Protocol for Basic Safety Message Broadcasting in Vehicular Networks

Basic Safety Messaging plays a crucial role to provide road safety in vehicular ad-hoc networks (VANETs). To avoid potential accidents, vehicles periodically broadcast safety information to neighboring vehicles. However, due to transmission collisions, fading channels and other factors, vehicular networks usually suffer a low packet delivery ratio (PDR) and a large delay, which are intolerant of many safety applications. To tackle these issues, this paper proposes a hybrid medium access control (MAC) protocol for basic safety message (BSM) dissemination based on the framework of Dedicated Short-Range Communication (DSRC). Its partially centralized and partially distributed characteristic not only can effectively suppress the collisions, but keep compatibility with IEEE 802.11p. In addition, the integration of Physical-Layer Network Coding (PNC) and Random Linear Network Coding (RLNC) further strengthens the reliability and efficiency for BSM dissemination. Both the theoretical analysis and comprehensive simulations indicate that, compared with existing schemes, the proposed protocol can significantly improve the PDR by a range of 20% to 300%. Meanwhile, in terms of normalized throughput, it increases by varying percent between 20% and 160% in different scenarios.
U.S. Beliefs about the Causes of Terrorism: An Application of Attribution Theory

This study examined what U.S. residents perceived to be the causes of terrorism and the influence of news media exposure on those beliefs. Examination was guided by Attribution Theory. Data were collected via a nationwide web survey administered in October 2017. Respondents were 444 U.S. adults who listed what they perceived as the causes of terrorism in response to an open-ended survey item. Respondents were more likely to make internal attributions for terrorism than external attributions. Religious beliefs were the most common internal attribution, followed by hatred and mental illness. Hispanics were substantially less likely to make internal attributions than either Whites or Blacks. Respondents with more frequent exposure to terrorism news from local television were less likely to make external attributions than those with less exposure through this medium. More frequent exposure to terrorism news on websites or apps was associated with increased likelihood of making external attributions.
Analysis and Suppression of Induced Voltage Pulsation in DC Winding of Five-Phase Wound-Field Switched Flux Machines

In wound-field (WF) switched flux (SF) (WFSF) machines, the DC winding induced voltage pulsation causes current ripple in the DC winding and challenges the DC power source, and deteriorates the control performance. In this paper, the induced voltage pulsation in DC winding of five-phase WFSF machines is analyzed and its reduction methods are proposed. The cycles per electric period of the open-circuit and armature reaction induced voltage pulsation in DC winding are derived analytically. Modifying the airgap permeance by optimizing the rotor pole arc or chamfering the rotor pole surface, and axial pairing of rotor segments having rotor pole with different arcs are used to suppress the induced voltage pulsation in DC winding, with >90% average torque maintained. Finite element results show that, by optimizing the rotor pole arc, the peak-to-peak value of the induced voltage pulsation in DC winding can be effectively suppressed to 59.59%, 30.67%, 29.99% and 43.35% for the 10-stator-pole five-phase WFSF machines with 8-, 9-, 11- and 12-rotor-pole rotors, respectively. By applying rotor pole surface shaping, the induced voltage pulsation in DC winding peak-to-peak value can be effectively suppressed to 61.76%, 45.47% and 40.21% for the 8-, 9- and 12-rotor-pole machines, respectively, while by applying axial pairing, it can be suppressed to 46.89%, 7.16%, 15.64% and 12.04%, respectively. The 10-stator-pole/12-rotor-pole WFSF machines having the original rotor, optimized rotor, chamfered rotor and axial paired rotor are prototyped and the experiments validate the analytical and finite element results.
Differences between Students' Linguistic Knowledge and Text Production Ability: A Case of the Use of Cohesion as a Resource of Texture in Academic Writing

Assuming cohesion as a non-structural resource of texture in text, the present study analyzed students' academic essays to establish the role of cohesion in creating text. A survey was also conducted to gauge students' beliefs about their ability to use cohesive devices in writing. The results of the text analysis and the survey were then used to identify differences between students' linguistic knowledge and their actual use of the cohesion devices. The results revealed statistically significant relationships between the textual variables of cohesion to the extent that the sample texts had visibly dense texture. The results of the survey variables were also found to be statistically significant. In addition, there were gaps in students' understanding of the concept of cohesive devices and their actual use in the texts. The study recommends explicit teaching of cohesive devices rather than as grammatical entities as well as training in expanding the lexical base of the students to help them achieve discourse competence appropriate to the expectations of the academic discourse community.
Mindful Matching: Ordinal Versus Nominal Attributes

The authors propose a new conceptual basis for predicting when and why consumers match others’ consumption choices. Specifically, they distinguish between ordinal (“ranked”) versus nominal (“unranked”) attributes and propose that consumers are more likely to match others on ordinal than on nominal attributes. Eleven studies involving a range of different ways of operationalizing ordinal versus nominal attributes collectively support this hypothesis. The authors’ conceptualization helps resolve divergent findings in prior literature and provides guidance to managers on how to leverage information about prior customers’ choices and employees’ recommendations to shape and predict future customers’ choices. Furthermore, the authors find process evidence that this effect is driven in part by consumers’ beliefs that a failure to match on ordinal (but not nominal) attributes will lead to social discomfort for one or both parties. Although the primary focus is on food choices, the effects are also demonstrated in other domains, extending the generalizability of the findings and implications for managerial practice and theory. Finally, the conceptual framework offers additional paths for future research.
Non-Tenure Track Faculty Satisfaction: A Self-Determination Model

Full-time non-tenure track faculty, commonly referred to as NTT faculty, are increasingly utilized in higher education and shoulder much of the teaching load within academic institutions. Self-determination theory (SDT) has shown promise as a conceptual frame for characterizing the relationship between environmental support factors and NTT faculty satisfaction. Full-time NTT faculty were sampled nationwide (N = 3,527) to investigate an SDT-based model positing basic psychological needs (i.e., volitional autonomy and relatedness) as mediators between six environmental support indices and NTT faculty satisfaction (i.e., teaching/service and global satisfaction). Structural equation model results showed volitional autonomy and relatedness fully mediated the relationships between the six environmental supports and both indices of faculty satisfaction. Results highlight the utility of basic psychological needs in understanding the relationships between the environment and NTT faculty satisfaction. Implications, future directions, and limitations are also presented.
Limits of Rauzy Graphs of Low-Complexity Words

We consider Benjamini-Schramm limits of Rauzy Graphs of low-complexity words. Low-complexity words are infinite words (over a finite alphabet), for which the number of subwords of length n is bounded by some Kn — examples of such a word include the Thue-Morse word 01101001 . and the Fibonacci word. Rauzy graphs ⇀ R(ω) have the length n subwords of ω as vertices, and the oriented edges between vertices indicate that two words appear immediately adjacent to each other in ω (with overlap); the edges are also equipped with labels, which indicate what “new letter” was appended to the end of the terminal vertex of an edge. In a natural way, the labels of consecutive edges in a Rauzy graph encode subwords of ω. The Benjamini-Schramm limit of a sequence of graphs is a distribution on (possibly infinite) rooted graphs governed by the convergence in distribution of random neighborhoods of the sequence of finite graphs. In the case of Rauzy graphs without edge-labelings, we establish that the Rauzy graphs of aperiodic low-complexity words converge to the line graph in the Benjamini-Schramm sense. In the same case, but for edge-labelled Rauzy graphs, we also prove that that the limit exists when the frequencies of all subwords in the infinite word, ω, are well defined (when the subshift of ω is uniquely ergodic), and we show that the limit can be identified with the unique ergodic measure associated to the subshift generated by the word. The eventually periodic (i.e. finite) cases are also shown. Finally, we show that for non-uniquely ergodic systems, the Benjamini-Schramm limit need not exist —though it can in some instances— and we provide examples to demonstrate the variety of possible behaviors.
Stock markets, banks and economic development: Theory and evidence

This paper discusses the different functions that capital markets and banks have in economic development, and it reviews the debate about marketbased vs. bank-based financial systems. Using data for a sample of 40 countries over the period 1975-98, the paper then shows that variation in both banking sector and stock market development can explain variation in economic growth, but the degree to which a financial system is market- or bank-based cannot explain economic development across countries. This is consistent with the financial services view, which focuses on the services provided rather than the providers of services and which emphasises complementarities between markets and intermediaries.
Program evaluation of integrated primary care in two primary care clinics

Primary care physicians are on the front line of patient intervention, and treat conditions ranging from the physical to the psychological on a daily basis. With their primary training focused on biological issues, physicians may be ill equipped when presented with psychological or mental health problems. The integration of a Behavioral Health Consultant (BHC) into the primary care setting can help to bridge the gap between the physical and the psychological, allowing for a more comprehensive biopsychosocial approach to patient treatment. Two primary care medical clinics have recently collaborated in the establishment of an integrative primary care program utilizing Behavioral Health Consultants. Based on the overall results it was found that brief short-term therapy within the medical setting is an effective method for providing services to patients. The results indicated a significant change and reduction in patients’ perceived level of distress, and significantly improved their global perception of overall wellbeing as well as high levels of both patient and physician satisfaction. Integrated Primary Care iv Table of
Integrated Analysis of Brain Transcriptome Reveals Convergent Molecular Pathways in Autism Spectrum Disorder

Autism spectrum disorder (ASD) is a set of complex neurodevelopmental disorders with etiology that remains elusive. Although there is a mounting body of investigation in different brain regions related to ASD, our knowledge about the common and distinct perturb condition between them is at the threshold of accumulation. In this study, based on protein–protein interactions, post-mortem transcriptome analysis was performed with corpus callosum (CC) and prefrontal cortex (PFC) samples from ASD individuals and controls. Co-expression network analysis revealed that a total of seven (four for CC set, three for PFC set) core dysfunctional modules strongly enriched for known ASD-risk genes. Three quarters of them in CC set (M4, M6, M29) significantly enriched for genes annotated by genetically associated variants in our previous whole genome sequencing data. We further determined transcriptional and post-transcriptional regulation subnetwork for each ASD-correlated module, including 47 pivot transcription factors, 130 pivot miRNAs, and 7 pivot lncRNAs. Moreover, there were significantly more interactions between CC-M4, -M6, and PFC-M2, mainly involved in synaptic functions and neuronal development. Our integrated multifactor analysis of ASD brain transcriptome profile illustrated underlying common and distinct molecular mechanisms and the module crosstalk between CC and PFC, helping to shed light on the molecular neuropathological underlying ASD.
‘Virtuous’ and ‘Vicious’ Circles? Adults’ Participation in Different Types of Training in the UK and Its Association with Wages

The relationship between education, skills and labour market outcomes is becoming an increasingly pressing issue in many countries. In the UK, recent changes in education and skills funding structures and the ongoing consequences of the 2008 recession may have affected participation in training. ‘Virtuous’ and ‘vicious’ circles of learning may exist, whereby access to training is associated with social advantage, and training begets more training. We explore workers’ participation in different types of training and how this is associated with wages using the UK Household Longitudinal Study. Our exploratory findings suggest that those working in lower-level occupations may not only be less likely to undertake training in general, but also less likely to have done types of training associated with wage increases (e.g., to meet occupational standards), and more likely to have done training associated with no or negative changes in wages (e.g., health and safety) compared to those working in higher-level occupations. We suggest that further research is needed to unpack the ‘black box’ of training and its impacts upon different groups of people. We discuss the implications of our findings to help break the ‘vicious’ circles.