Miracle-dz/UniFAR-FTUs huggingface dataset:
Evolutionary Dynamics of Pathoadaptation Revealed by Three Independent Acquisitions of the VirB/D4 Type IV Secretion System in Bartonella

The α-proteobacterial genus Bartonella comprises a group of ubiquitous mammalian pathogens that are studied as a model for the evolution of bacterial pathogenesis. Vast abundance of two particular phylogenetic lineages of Bartonella had been linked to enhanced host adaptability enabled by lineage-specific acquisition of a VirB/D4 type IV secretion system (T4SS) and parallel evolution of complex effector repertoires. However, the limited availability of genome sequences from one of those lineages as well as other, remote branches of Bartonella has so far hampered comprehensive understanding of how the VirB/D4 T4SS and its effectors called Beps have shaped Bartonella evolution. Here, we report the discovery of a third repertoire of Beps associated with the VirB/D4 T4SS of B. ancashensis, a novel human pathogen that lacks any signs of host adaptability and is only distantly related to the two species-rich lineages encoding a VirB/D4 T4SS. Furthermore, sequencing of ten new Bartonella isolates from under-sampled lineages enabled combined in silico analyses and wet lab experiments that suggest several parallel layers of functional diversification during evolution of the three Bep repertoires from a single ancestral effector. Our analyses show that the Beps of B. ancashensis share many features with the two other repertoires, but may represent a more ancestral state that has not yet unleashed the adaptive potential of such an effector set. We anticipate that the effectors of B. ancashensis will enable future studies to dissect the evolutionary history of Bartonella effectors and help unraveling the evolutionary forces underlying bacterial host adaptation.
Early vocabulary development in English, Mandarin, and Cantonese : a cross-linguistic study based on Childes

Early language development is an exciting topic in the field of child language acquisition. Only a limited amount of cross-linguistic studies has attempted to investigate the similarities and differences in child language development across different languages. In this thesis, I present a study based on English, Mandarin and Cantonese corpora extracted from the Child Language Data Exchange System (CHILDES, MacWhinney, 2000). I investigated the lexical compositions of certain lexical categories (nouns, verbs, and adjectives) in children and their caregivers’ vocabularies across eight different children age groups ranging from 13 to 60 months. ANOVA, frequency analysis, and cluster analysis were used to analyze the data. The development trajectories of lexical diversity and complexity of children’s speech were also analyzed by two novel techniques: Dmeasure and the Mean Length of Utterances. My research clearly shows that (1) in all the cultures, children’s early language development exhibits roughly similar patterns: an increasing diversity in lexicon and increasingly complicated speech patterns emerge as a function of time, and children’s vocabularies become more similar to those of their parents over time; and (2) culture variations in children’s linguistic input have strong influences on their language output, which is reflected in the noun vs. verb ratio and the varying percentages of nouns, verbs, and adjectives in the total words children are able to speak in the three cultures. I certify that I have read this thesis and find that, in scope and quality, it satisfies the requirements for the degree of Master of Arts.
Increasing cache capacity via critical-words-only cache

Current processors have multiple levels of caches. Choosing the right cache size for each level is critical for performance. The first-level cache (L1) is typically small, in order to match the speed of the processor. The lower level caches, on the other hand, are typically large, in order to reduce capacity misses. However, situations may arise in which the size of a lower level cache cannot be increased beyond a point - for example, recent Intel multi-core processors (including Nehalem and Sandy Bridge) have only 256 kB private L2 caches per core - which adversely affects the performance of benchmarks which have large working set sizes. In this paper, we propose a novel cache design known as the critical-words-only cache (co-cache) for increasing the effective cache capacity. Our approach involves rethinking the notion of cache blocks; instead of storing all the words that belong to a cache block, we only store the critical words, where the critical words are the words that are generally accessed before the others. Our experiments show that with our design a 256 kB L2 performs as well as a 512 kB conventional L2 cache on average.
Mental Contrasting and Goal Commitment: The Mediating Role of Energization

Mentally contrasting a desired future with present reality is a self-regulation strategy that leads to goal commitment in line with a person's expectations of success. One possible mediator variable of these effects is level of energization. In Study 1, energization assessed by physiological measures was found to mediate the effect of mental contrasting on goal commitment. In Study 2, feelings of energization, as assessed by self-report, mediated the effect of mental contrasting on goal commitment as gauged by performance on an acute stress paradigm (giving a talk in front of a camera). Results imply that when expectations of success are high, mental contrasting provides the level of energy needed to commit to realizing desired futures.
Distributed Skyline Retrieval with Low Bandwidth Consumption

We consider skyline computation when the underlying data set is horizontally partitioned onto geographically distant servers that are connected to the Internet. The existing solutions are not suitable for our problem, because they have at least one of the following drawbacks: (1) applicable only to distributed systems adopting vertical partitioning or restricted horizontal partitioning, (2) effective only when each server has limited computing and communication abilities, and (3) optimized only for skyline search in subspaces but inefficient in the full space. This paper proposes an algorithm, called feedback-based distributed skyline (FDS), to support arbitrary horizontal partitioning. FDS aims at minimizing the network bandwidth, measured in the number of tuples transmitted over the network. The core of FDS is a novel feedback-driven mechanism, where the coordinator iteratively transmits certain feedback to each participant. Participants can leverage such information to prune a large amount of local data, which otherwise would need to be sent to the coordinator. Extensive experimentation confirms that FDS significantly outperforms alternative approaches in both effectiveness and progressiveness.
Inference by Reparameterization in Neural Population Codes

Behavioral experiments on humans and animals suggest that the brain performs probabilistic inference to interpret its environment. Here we present a new general-purpose, biologically-plausible neural implementation of approximate inference. The neural network represents uncertainty using Probabilistic Population Codes (PPCs), which are distributed neural representations that naturally encode probability distributions, and support marginalization and evidence integration in a biologically-plausible manner. By connecting multiple PPCs together as a probabilistic graphical model, we represent multivariate probability distributions. Approximate inference in graphical models can be accomplished by message-passing algorithms that disseminate local information throughout the graph. An attractive and often accurate example of such an algorithm is Loopy Belief Propagation (LBP), which uses local marginalization and evidence integration operations to perform approximate inference efficiently even for complex models. Unfortunately, a subtle feature of LBP renders it neurally implausible. However, LBP can be elegantly reformulated as a sequence of Tree-based Reparameterizations (TRP) of the graphical model. We re-express the TRP updates as a nonlinear dynamical system with both fast and slow timescales, and show that this produces a neurally plausible solution. By combining all of these ideas, we show that a network of PPCs can represent multivariate probability distributions and implement the TRP updates to perform probabilistic inference. Simulations with Gaussian graphical models demonstrate that the neural network inference quality is comparable to the direct evaluation of LBP and robust to noise, and thus provides a promising mechanism for general probabilistic inference in the population codes of the brain.
“Reservoir of rage swamps Wall St” The linguistic construction and evaluation of Occupy in international print media

Originating on New York’s Wall Street, the Occupy movement was “an international network of protests against social and economic inequality that began in [September] 2011 in response to the downturn of 2008” ( Thorson et al. 2013 , 427). Whilst there has been research on online activity in relation to Occupy, the scope of linguistic analysis to date has been somewhat narrow. Furthermore, the focus on new media has indirectly led to an absence of analysis of institutionally-endorsed traditional media texts. We adopt a mixed-method approach of corpus analysis and discourse analysis of national newspaper articles to answer questions such as ‘Is Occupy associated with a semantic field of violence and aggression? ’ and ‘Who is represented as having agency? ’ Our results indicate that, in our small corpus of media texts, Occupy and its supporters were predominantly portrayed negatively at the movement’s height; even though protesters are reported to have been peaceful in their majority, the English-speaking media we analysed still aligns them with language suggestive of aggression, conflict and even violence.
Intracerebroventricular Administration of Melanin‐Concentrating Hormone Suppresses Pulsatile Luteinizing Hormone Release in the Female Rat

Melanin‐concentrating hormone (MCH) has been reported to be involved in the regulation of feeding behaviour in rats and mice. Because many neuropeptides that influence ingestive behaviour also regulate reproductive function, the present study was designed to determine if central administration of MCH changes pulsatile secretion of luteinizing hormone (LH) in the rats. Wistar‐Imamichi strain female rats were ovariectomized and implanted with oestradiol to produce a moderate inhibitory feedback effect on LH release. The effects of i.c. v. injections of MCH on LH release were examined in freely moving animals. Blood samples were collected every 6 min for 3 h through an indwelling cannula. After 1 h of sampling, MCH (0.1, 1 or 10 μg/animal) or vehicle (saline) was injected into the third cerebroventricle. Because MCH is also reported to affect the hypothalamo‐pituitary‐adrenal (HPA) axis, which in turn, can influence reproductive function, plasma corticosterone concentrations were determined in the same animals at 30‐min intervals during the first and last hours and every 12 min during the second hour of the 3‐h sampling period. When expressed as per cent changes, mean plasma LH concentrations after MCH administration were significantly lower in the animals injected with all doses of the peptide compared with vehicle‐treated animals; LH pulse frequency was significantly lowered by 1 μg of MCH. Per cent changes in mean plasma corticosterone levels were not significantly affected by MCH administration. These results in oestradiol‐treated ovariectomized rats indicate that central MCH is capable of inhibiting pulsatile LH secretion. We have previously shown that 48‐h fasting suppresses pulsatile LH release in the presence of oestrogen. Take together, these results raise the possibility that MCH could play a role in mediating the suppression of LH secretion during periods of reduced nutrition.
In vitro analysis of factors influencing CYP1A2 expression as potential determinants of interindividual variation

Individual differences in drug metabolism contribute to interindividual variation that characterizes responses to drugs and risk in exposure to foreign chemicals. Large individual differences are found in expression levels of CYP1A2, a major drug‐metabolizing enzyme. Underlying causes for this variation are not well understood. Several factors, including tobacco smoking, consumption of cruciferous vegetables, and sex, have been associated with modulating CYP1A2 expression. To understand factors regulating expression of CYP1A2 in establishing a causal relationship, this study examined effects of cigarette smoke condensate (CSC), indole‐3‐carbinol (I3C), and 17β‐estradiol (estradiol) on CYP1A2 expression in in vitro systems using human liver and lung cells. Treatment with CSC (2–25 μg/mL) significantly increased levels of CYP1A2 in six cell lines examined, in a concentration‐ and time‐dependent manner. Fold changes in expression levels relative to controls varied among cell lines. CYP1A2 enzymatic activity also increased with CSC exposure. Treatment of H1299 and HepB3 cells with dietary agent I3C (50 and 100 μmol/L) increased CYP1A2 expression. In human cell lines H1299 and H1395, treatment with estradiol (10 and 100 nmol/L) significantly reduced expression of CYP1A2. Using ChIP assays, effects of CSC on histone modifications were analyzed. Increases in H3K4me3 and H4K16ac were observed at several segments in the CYP1A2 gene, whereas H3K27me3 decreased, following CSC treatment. These results suggest that CYP1A2 expression is affected epigenetically by CSC. Additional studies will be needed to further establish regulatory mechanisms underlying effects of various environmental, dietary, and endogenous factors on CYP1A2 expression in better predicting individual variation.
Secondhand tobacco smoke in bars and restaurants in Santiago, Chile: evaluation of partial smoking ban legislation in public places

Objective To compare air nicotine concentrations according to the smoking policy selected by bars/restaurants in Santiago, Chile before and after the enactment of partial smoking ban legislation in 2007 (establishments could be smoke free, have segregated (mixed) smoking and non-smoking areas, or allow smoking in all areas). Methods The study measured air nicotine concentrations over 7 days to characterise secondhand smoke exposure in 30 bars/restaurants in 2008. Owner/manager interviews and physical inspections were conducted. Results Median IQR air nicotine concentrations measured in all venues were 4.38 (0.61–13.62) μg/m3. Air nicotine concentrations were higher in bars (median 7.22, IQR 2.48–15.64 μg/m3) compared to restaurants (1.12, 0.15–9.22 μg/m3). By smoking status, nicotine concentrations were higher in smoking venues (13.46, 5.31–16.87 μg/m3), followed by smoking areas in mixed venues (9.22, 5.09–14.90 μg/m3) and non-smoking areas in mixed venues (0.99, 0.19–1.27 μg/m3). Air nicotine concentrations were markedly lower in smoke-free venues (0.12, 0.11–0.46 μg/m3). After adjustment for differences in volume and ventilation, air nicotine concentrations were 3.2, 35.5 and 56.2 times higher in non-smoking areas in mixed venues, smoking areas in mixed venues and smoking venues, respectively, compared to smoke-free venues. Conclusions Exposure to secondhand smoke remains high in bars and restaurants in Santiago, Chile. These findings demonstrate that the partial smoking ban legislation enacted in Chile in 2007 provides no protection to employees working in those venues. Enacting a comprehensive smoke-free legislation which protects all people from exposure to secondhand smoke in all public places and workplaces is urgently needed.
Relationship between Obesity and Depression in the Korean Working Population

This study was conducted to investigate potential relationship between obesity and depression in Korean working population. A total of 8,121 workers, aged 21-75 yr, participated in this nationwide cross-section research. The participants asked to complete a questionnaire regarding the socio-demographic factors and health-related behaviors, height, and weight. To measure degree of depression, the Korean version of the Center for Epidemiologic Studies-Depression scale (CES-D) was used. Chi-square test and multivariate logistic regression analyses were performed to examine the degree of association between obesity and depression. Compared to normal-weight women, overweight women had a lower adjusted odds ratio (OR) for depression (OR=0.65, 95% confidence interval 0.46 to 0.97). Underweight (1.42, 0.83 to 2.44) and obese women (BMI ≥30) had higher ORs for depression (1.47, 0.64 to 3.36), but these were insignificant. Compared to normal-weight men, obese men had higher crude ORs (1.94, 1.03 to 3.62) and adjusted ORs (1.77, 0.89 to 3.53) for depression, while underweight and overweight men showed no significant differences. These findings suggest that being overweight may protect Korean female worker against depression.
Promoting Effects of the Adipokine, Apelin, on Diabetic Nephropathy

Angiogenesis, increased glomerular permeability, and albuminuria are thought to contribute to the progression of diabetic nephropathy (DN). Apelin receptor (APLNR) and the endogenous ligand of APLNR, apelin, induce the sprouting of endothelial cells in an autocrine or paracrine manner, which may be one of the mechanisms of DN. The aim of this study was to investigate the role of apelin in the pathogenesis of DN. Therefore, we observed apelin/APLNR expression in kidneys from patients with type 2 diabetes as well as the correlation between albuminuria and serum apelin in patients with type 2 diabetes. We also measured the proliferating, migrating, and chemotactic effects of apelin on glomerular endothelial cells. To measure the permeability of apelin in glomerular endothelial cells, we used transwells to detect FITC-BSA penetration through monolayered glomerular endothelial cells. The results showed that serum apelin was significantly higher in the patients with type 2 diabetes compared to healthy people (p<0.05, Fig. 1B) and that urinary albumin was positively correlated with serum apelin (R = 0.78, p<0.05). Apelin enhanced the migration, proliferation, and chemotaxis of glomerular endothelial cells in a dose-dependent manner (p<0.05). Apelin also promoted the permeability of glomerular endothelial cells (p<0.05) and upregulated the expression of VEGFR2 and Tie2 in glomerular endothelial cells (p<0.05). These results indicated that upregulated apelin in type 2 diabetes, which may be attributed to increased fat mass, promotes angiogenesis in glomeruli to form abnormal vessels and that enhanced apelin increases permeability via upregulating the expression of VEGFR2 and Tie2 in glomerular endothelial cells.
An urbilaterian origin of the tripartite brain: developmental genetic insights from Drosophila

Studies on expression and function of key developmental control genes suggest that the embryonic vertebrate brain has a tripartite ground plan that consists of a forebrain/midbrain, a hindbrain and an intervening midbrain/hindbrain boundary region, which are characterized by the specific expression of the Otx, Hox and Pax2/5/8 genes, respectively. We show that the embryonic brain of the fruitfly Drosophila melanogaster expresses all three sets of homologous genes in a similar tripartite pattern. Thus, a Pax2/5/8 expression domain is located at the interface of brain-specific otd/Otx2 and unpg/Gbx2 expression domains anterior to Hox expression regions. We identify this territory as the deutocerebral/tritocerebral boundary region in the embryonic Drosophila brain. Mutational inactivation of otd/Otx2 and unpg/Gbx2 result in the loss or misplacement of the brain-specific expression domains of Pax2/5/8 and Hox genes. In addition, otd/Otx2 and unpg/Gbx2 appear to negatively regulate each other at the interface of their brain-specific expression domains. Our studies demonstrate that the deutocerebral/tritocerebral boundary region in the embryonic Drosophila brain displays developmental genetic features similar to those observed for the midbrain/hindbrain boundary region in vertebrate brain development. This suggests that a tripartite organization of the embryonic brain was already established in the last common urbilaterian ancestor of protostomes and deuterostomes.
A New Transmitted Reference Based UWB Receiver

The Transmitted-Reference (TR) signaling scheme, in conjunction with Autocorrelation Receivers (AcR), has received much attention as the low complexity architecture for Ultra Wide Band (UWB) communications system. Due to the usage of the noisy received signal as the correlate tem-plate, the TR scheme suffers performance degradation at low signal-noise ratio (SNR) scenario. However, it enables the low complexity receiver the ability to exploit the dense multipath in the UWB channel. Hence, the TR scheme is superior to the conventional Rake receivers. In this paper, we propose a new TR scheme based UWB Receiver, which is Modify Differential Transmitted Reference (MDTR), to improve the SNR and BER performance of UWB. The corresponding signal frame structure and simulation results are provided and analyzed.
Morphogenetic and developmental functions of the Aspergillus nidulans homologues of the yeast bud site selection proteins Bud4 and Axl2

The yeast bud site selection system represents a paradigm for understanding how fungal cells regulate the formation of a polarity axis. In Saccharomyces cerevisiae, Bud4 and Axl2 are components of the axial bud site marker. To address the possibility that these proteins regulate cellular morphogenesis in filamentous fungi, we have characterized homologues of Bud4 and Axl2 in Aspergillus nidulans. Our results show that Bud4 is involved in septum formation in both hyphae and developing conidiophores. Whereas Axl2 appears to have no obvious role in hyphal growth, it is required for the regulation of phialide morphogenesis during conidiation. In particular, Axl2 localizes to the phialide–spore junction, where it appears to promote the recruitment of septins. Furthermore, the developmental regulators BrlA and AbaA control the expression of Axl2. Additional studies indicate that Axl2 is also involved in the regulation of sexual development, not only in A. nidulans, but also in the phylogenetically unrelated fungus Fusarium graminearum. Our results suggest that Axl2 plays a key role in phialide morphogenesis and/or function during conidiation in the aspergilli.
The virtual ante-room: assessing presence through expectation and surprise

We describe an experiment where subjects entered a virtual replica of the laboratory in which the experiment was taking place. They then moved through a door to a new virtual location and carried out the main experimental task, and then returned to the virtual lab. In the real lab they had learned to search for box-shaped objects and point at a telephone whenever it rang. In the virtual lab, additional colouredboxes were introduced, and although the virtual phone position was not moved, the real phone of which it was a replica was moved. On exit from the virtual to the real laboratory, subjects were asked about their degree of surprise that the additional coloured boxes were not there and that the phone had been moved. This was in the context of an experiment to assess the influence of body movement on presence. This paper reportson the relationship between this surprise factor and the presence reported for the main part of the experiment. It was found that the surprise factor and reported presence were significantly positively correlated, suggesting a new approach towards a behavioural measure of presence.