Miracle-dz/UniFAR-FTUs huggingface dataset:
An Integrated Pipeline for de Novo Assembly of Microbial Genomes

Remarkable advances in DNA sequencing technology have created a need for de novo genome assembly methods tailored to work with the new sequencing data types. Many such methods have been published in recent years, but assembling raw sequence data to obtain a draft genome has remained a complex, multi-step process, involving several stages of sequence data cleaning, error correction, assembly, and quality control. Successful application of these steps usually requires intimate knowledge of a diverse set of algorithms and software. We present an assembly pipeline called A5 (Andrew And Aaron's Awesome Assembly pipeline) that simplifies the entire genome assembly process by automating these stages, by integrating several previously published algorithms with new algorithms for quality control and automated assembly parameter selection. We demonstrate that A5 can produce assemblies of quality comparable to a leading assembly algorithm, SOAPdenovo, without any prior knowledge of the particular genome being assembled and without the extensive parameter tuning required by the other assembly algorithm. In particular, the assemblies produced by A5 exhibit 50% or more reduction in broken protein coding sequences relative to SOAPdenovo assemblies. The A5 pipeline can also assemble Illumina sequence data from libraries constructed by the Nextera (transposon-catalyzed) protocol, which have markedly different characteristics to mechanically sheared libraries. Finally, A5 has modest compute requirements, and can assemble a typical bacterial genome on current desktop or laptop computer hardware in under two hours, depending on depth of coverage.
Policing, Race and Racism

Introduction Part 1: Race and police culture, personnel and organisation 1. Recruitment, retention and promotion 2. Culture, training and organisation Part 2: Policing and the public 3. Stop and search 4. Responding to racist incidents 5. Accountability and complaints Part 3: Reconsidering the principles of policing 6. Policing diversity 7. The rise of antiracist policing
Postsynaptic Odorant Concentration Dependent Inhibition Controls Temporal Properties of Spike Responses of Projection Neurons in the Moth Antennal Lobe

Although odorant concentration-response characteristics of olfactory neurons have been widely investigated in a variety of animal species, the effect of odorant concentration on neural processing at circuit level is still poorly understood. Using calcium imaging in the silkmoth (Bombyx mori) pheromone processing circuit of the antennal lobe (AL), we studied the effect of odorant concentration on second-order projection neuron (PN) responses. While PN calcium responses of dendrites showed monotonic increases with odorant concentration, calcium responses of somata showed decreased responses at higher odorant concentrations due to postsynaptic inhibition. Simultaneous calcium imaging and electrophysiology revealed that calcium responses of PN somata but not dendrites reflect spiking activity. Inhibition shortened spike response duration rather than decreasing peak instantaneous spike frequency (ISF). Local interneurons (LNs) that were specifically activated at high odorant concentrations at which PN responses were suppressed are the putative source of inhibition. Our results imply the existence of an intraglomerular mechanism that preserves time resolution in olfactory processing over a wide odorant concentration range.
Improved Pattern Matching to Find DNA Patterns

The process of finding given patterns in DNA sequences is widely used in modern biological sciences. This paper shows an algorithmic improvement for exact pattern matching introducing a new heuristic. For implementation the author created an application that uses three well-known heuristics to ensure the O(n) worst case time, the O(n log sigma (m)/m) average case time and the O(n/m) best case time of searching for an m length pattern in an n length text that use a sigma letter alphabet. This application served as a testbed for the new H4 heuristic. The novelty is in optimization of the direction of text window movement in the preprocessing phase. The idea takes advantages of RAM based searching: usually all the text resides in today's gigabyte memory so the opposite direction of searching window moving requires the same time as the usual. A new function predicts the better moving direction in preprocessing time, based on the unsymmetrical property of pattern. Tests proved that this heuristic may result in fewer jumps and tested characters in the search phase of pattern matching
Robust Exponential Stability and ∞ H Control for Jumping Stochastic Cohen-Grossberg Neural Networks with Mixed Delays

This paper considers robust stability, stabilization and H ∞ control problems for jumping stochastic Cohen-Grossberg neural networks (CGNNs) with delays. A new type of mixed time delays including discrete delays and distributed delays are addressed, which fuses time-varying delays and mode-dependent delays into one whole. A delay-interval dependent control approach is presented to analyze that the closed-loop system is robust mean-square exponential stable and satisfies a prescribed H ∞ performance level based on the Linear matrix inequality (LMI) technique. Moreover, we can get the desired feedback control gain matrix by utilizing the numerically efficient Matlab LMI toolbox. Finally, two numerical examples are given to show the effectiveness of the result.
Modelling Exits from Unemployment in Eastern Germany: A Matching Function Approach

A matching function approach is applied to unemployment exit data from a panel of Eastern German labour office districts since monetary union. With comparable West German data, such a matching function exhibits constant returns, is stable, and can account for at least three-quarters of the variance of exits from unemployment. In contrast, the Eastern German matching function exhibits increasing returns, and vacancies enter the function insignificantly or with incorrect sign. These estimates also differ significantly from those for the Czech Republic, discounting explanations related to the transformation per se . When the effects of special labour market measures introduced since monetary union are accounted for, Eastern German estimates resemble those of the Czech Republic, i.e. they exhibit constant to mildly decreasing returns.
ON THE MECHANISMS OF NEURAL DEVELOPMENT IN THE VENTRAL TELENCEPHALON

To be presented for public examination with the permission of the Faculty of Para a minha família TABLE OF CONTENTS LIST OF ORIGINAL PUBLICATIONS i ABSTRACT ii LIST OF ABBREVIATIONS iv INTRODUCTION 1 1. The development of telencephalon in mouse 1 1.1. Neural development within the telencephalon 2 1.1.1. Neurogenesis and cell migration within the dorsal telencephalon 3 Use of decloaking chamber-based heat-induced epitope retrieval method improves the detection of Olig2-labeled cells in the ventral telencephalon (I) 23 2. NKCC1 regulates cell proliferation in the ventral telencephalon (II) 26 3. GDNF binds to syndecan-3, and promotes the tangential migration of immature interneurons in the ventral telencephalon (III) 29 CONCLUSIONS 32 ACKNOWLEDGEMENTS 33 REFERENCES 34 i LIST OF ORIGINAL PUBLICATIONS This Thesis is based on the following original articles, which are referred to in the text by their Roman numerals: I Magalhães AC and Rivera C. Superior performance of decloaking chamber-based heat-induced epitope retrieval method improves the quantification of Olig2 cells in paraffin-embedded section of embryonic mouse brain (2014) J Neurosci Methods 235: 226–233. II Magalhães AC and Rivera C. In vivo role of NKCC1 in ventral telencephalon cell cycle reentry. Manuscript. III: Planning and performing the experiments, and analyzing the data for figure 6, and contributing to the writing of manuscript (Materials and Methods, Results, and Discussion sections) ii ABSTRACT The time of arrival of interneurons and oligodendrocytes to the neocortex is critical for proper functional brain development. Aberrances in this sequence can be detrimental, and involved in different developmental diseases. Thus, understanding the mechanisms for temporal control of the genesis and migration of neural cells is crucial. In this study we have focused on the ventral telencephalon, a major source of interneurons and oligodendrocytes. We have developed a more sensitive method for detecting and quantifying oligodendrocyte precursor cells, e.g. Olig2. Current immunohistochemistry methods for detection and quantification of this cell type are poor. Optimal immunohistochemistry often requires heat-induced epitope retrieval (HIER) method for improving the staining in paraffin-embedded sections, and therefore helping in quantitative studies. Here, we have developed an immunohistochemistry protocol using the device decloaking chamber for HIER. This method was compared to the microwave oven-based HIER method by studying the labeling of Olig2 marker in paraffin-embedded sections from embryonic mouse brain. We have demonstrated that the decloaking chamber-based HIER method is the most suitable technique for the detection of single Olig2-labeled cells in the ventral telencephalon. This …
MRI evidence for strategic decision-making during resolution of ronoun reference

Pronouns are extraordinarily common in daily language yet little is known about the neural mechanisms that support decisions about pronoun reference. We propose a large-scale neural network for resolving pronoun reference that consists of two components. First, a core language network in peri-Sylvian cortex supports syntactic and semantic resources for interpreting pronoun meaning in sentences. Second, a frontal–parietal network that supports strategic decision-making is recruited to support probabilistic and risk-related components of resolving a pronoun’s referent. In an fMRI study of healthy young adults,
InteractiveMediaMINE at the NTCIR-11 IMine Search Task

The InteractiveMediaMINE team participated in the Task Mine subtask of the NTCIR-11 IMine Search Task. Our framework consists of three steps. First, we extend the query entered by the user in order to optimize the search engine. Second, we extract candidates of tasks from (cid:16)Ya-hoo! Chiebukuro(cid:17) with the extended search query. Here, we use the top 10 pages of the search results. Finally, we calculate the score of the extracted tasks by the words frequency of each sentence; our system outputs tasks in the descending order of the score. This paper describes our approach to solving the Task Mine problem and discusses its results.
High quality workplace training and innovation in highly developed countries

Several studies associate vocational education in general with a strong focus on established technologies and a high firm specificity and therefore expect vocational education not to have positive effects on innovations in firms. However, a specific form of vocational education deviates from this notion and provides firms with new knowledge to generate innovations. Vocational education that a collective of firms organizes (like in Germany and Switzerland) has a governance structure that coordinates collective action in order to define training curricula with joint standards. Firms revise these curricula jointly and thereby diffuse new knowledge to all firms that participate in vocational education by training apprentices. In this paper we describe the governance structure of vocational education and identify four different phases of knowledge diffusion that occurring during the definition of joint training standards: knowledge collection, synthesis, transfer and application. The results of our empirical analysis reveal that participating in collectively organized vocational education by training apprentices has a positive impact on a firm's innovations. We show that collective action of firms can generate a specific form of vocational education that provides innovation-relevant knowledge, diffuses it and thereby has a positive effect on innovation in firms.
Healthy, Educated and Wealthy: Is the Welfare State Really Harmful for Growth?

In this paper, we study how public and private expenditures in health and education affect economic growth by their influence on peoples health, abilities, skills and knowledge. We consider a growth accounting framework in order to test whether welfare expenditures more than offset the efficiency losses caused by distortionary taxation, and whether the effects of public expenditure on economic growth differ from those of private expenditure. Our empirical analysis is based on a panel of 19 OECD countries observed between 1971 and 1998. The results are consistent with the hypothesis that the contribution of welfare expenditures more than compensates for the distortions caused by the tax system; and the estimated positive impact is stronger for health than for education. We also find some evidence that public expenditure influences GDP growth more than private expenditure.
NOISE, CAPM AND THE SIZE AND VALUE EFFECTS

We model a continuous time one factor economy where stock prices are noisy proxies of the informationally efficient values. The pricing error process is modeled as a mean-reverting process; this gives us a well defined notion of over-pricing and under-pricing in the market, and stocks fluctuates between being over-priced and under-priced. We show that in this economy, cap-weighting is a sub-optimal portfolio strategy. A non-cap-weighted portfolio outperforms a cap-weighted portfolio with the same factor exposure. This is because, in a cap-weighting scheme, portfolio weights are driven by market prices; as such, more weights are allocated to overvalued stocks and less weight to undervalued stocks. Following the same intuition, we show that in the cross-section, large cap stocks tend to underperform small cap stocks and high price-to-book stocks (growth stocks) tend to underperform low price-to-book stocks (value stocks). In this economy, if we proxy the hidden risk factor with the market clearing portfolio and regress stock returns against market returns (a CAPM regression), a non-cap-weighted portfolio exhibits significant alpha! However, when we regress the same non-cap-weighted portfolio against market, size and value, the Fama-French style regression exhibits factor loadings on value and size with insignificant alpha. Clearly, value and size are not risk factors in our economy! Value and size shows up in our regressions because the market portfolio is a poorly constructed proxy for the hidden risk factor. The paper contributes to the anomalies literature by showing that mean-reversion in stock returns and the Fama-French size and value effects are driven by the same market defect - pricing noise! This suggests that models, such as disposition effects and information herding, which can generate stock price over-reaction and therefore mean-reversion in stock prices, can also explain the value and size puzzle.
Ideology and Hearings system operations: The perceptions of five participating groups

Recent research related to the children's hearings system Scotland's juvenile 'justice system is limited. This study is an attempt to address this empirical deficiency. It examines the perceptions of members of five participating groups (guidance teachers, social workers, police officers, panel members and reporters) on the structure and practices of the hearings system in three regions of Scotland. The research involved 389 respondents in a questionnaire survey, followed by 45 semi-structured interviews with a selected sub-sample. The study incorporated three research issues. Firstly, the groups' ideological perspectives on juvenile justice and their potential influence on attitudes towards the hearings system, secondly, the groups members' observations on present hearings system operations and thirdly the participants' convictions concerning future practice and structure. The general conclusions drawn from the investigation indicate that support across the five groups exists for the continuation of a welfare based juvenile justice system in Scotland but that differences between groups emerge on the matter of the organisation of that system. Majorities in the police officer, guidance teacher and social worker samples were ideologically opposed to lay decision-makers in juvenile justice and most interviewees from these groups expressed reservations concerning the continuation, in its present form, of the lay panel as the decisionmaking body in the hearings system. Most panel members and reporters in
The Number and Transmission of [PSI +] Prion Seeds (Propagons) in the Yeast Saccharomyces cerevisiae

Background Yeast (Saccharomyces cerevisiae) prions are efficiently propagated and the on-going generation and transmission of prion seeds (propagons) to daughter cells during cell division ensures a high degree of mitotic stability. The reversible inhibition of the molecular chaperone Hsp104p by guanidine hydrochloride (GdnHCl) results in cell division-dependent elimination of yeast prions due to a block in propagon generation and the subsequent dilution out of propagons by cell division. Principal Findings Analysing the kinetics of the GdnHCl-induced elimination of the yeast [PSI+] prion has allowed us to develop novel statistical models that aid our understanding of prion propagation in yeast cells. Here we describe the application of a new stochastic model that allows us to estimate more accurately the mean number of propagons in a [PSI+] cell. To achieve this accuracy we also experimentally determine key cell reproduction parameters and show that the presence of the [PSI+] prion has no impact on these key processes. Additionally, we experimentally determine the proportion of propagons transmitted to a daughter cell and show this reflects the relative cell volume of mother and daughter cells at cell division. Conclusions While propagon generation is an ATP-driven process, the partition of propagons to daughter cells occurs by passive transfer via the distribution of cytoplasm. Furthermore, our new estimates of n0, the number of propagons per cell (500–1000), are some five times higher than our previous estimates and this has important implications for our understanding of the inheritance of the [PSI +] and the spontaneous formation of prion-free cells.
Analysis on flood generation processes by means of a continuous simulation model

Abstract. In the present research, we exploited a continuous hydrological simulation to investigate on key variables responsible of flood peak formation. With this purpose, a distributed hydrological model (DREAM) is used in cascade with a rainfall generator (IRP-Iterated Random Pulse) to simulate a large number of extreme events providing insight into the main controls of flood generation mechanisms. Investigated variables are those used in theoretically derived probability distribution of floods based on the concept of partial contributing area (e.g. Iacobellis and Fiorentino, 2000). The continuous simulation model is used to investigate on the hydrological losses occurring during extreme events, the variability of the source area contributing to the flood peak and its lag-time. Results suggest interesting simplification for the theoretical probability distribution of floods according to the different climatic and geomorfologic environments. The study is applied to two basins located in Southern Italy with different climatic characteristics.
Generation of Anti-Murine ADAMTS13 Antibodies and Their Application in a Mouse Model for Acquired Thrombotic Thrombocytopenic Purpura

Thrombotic thrombocytopenic purpura (TTP) is a life-threatening thrombotic microangiopathy linked to a deficiency in the metalloprotease ADAMTS13. In the current study, a novel mouse model for acquired TTP was generated to facilitate development and validation of new therapies for this disease. Therefore, a large panel (n = 19) of novel anti-mouse ADAMTS13 (mADAMTS13) monoclonal antibodies (mAbs) of mouse origin was generated. Inhibitory anti-mADAMTS13 mAbs were identified using the FRETS-VWF73 assay. Four mAbs strongly inhibited mADAMTS13 activity in vitro (∼68–90% inhibition). Injecting a combination of 2 inhibitory mAbs (13B4 and 14H7, 1.25 mg/kg each) in Adamts13+/+ mice resulted in full inhibition of plasma ADAMTS13 activity (96 ± 4% inhibition, day 1 post injection), leading to the appearance of ultra-large von Willebrand factor (UL-VWF) multimers. Interestingly, the inhibitory anti-mADAMTS13 mAbs 13B4 and 14H7 were ideally suited to induce long-term ADAMTS13 deficiency in Adamts13+/+ mice. A single bolus injection resulted in full ex vivo inhibition for more than 7 days. As expected, the mice with the acquired ADAMTS13 deficiency did not spontaneously develop TTP, despite the accumulation of UL-VWF multimers. In line with the Adamts13-/- mice, TTP-like symptoms could only be induced when an additional trigger (rVWF) was administered. On the other hand, the availability of our panel of anti-mADAMTS13 mAbs allowed us to further develop a sensitive ELISA to detect ADAMTS13 in mouse plasma. In conclusion, a novel acquired TTP mouse model was generated through the development of inhibitory anti-mADAMTS13 mAbs. Consequently, this model provides new opportunities for the development and validation of novel treatments for patients with TTP. In addition, these newly developed inhibitory anti-mADAMTS13 mAbs are of great value to specifically study the role of ADAMTS13 in mouse models of thrombo-inflammatory disease.
Functional Impairment of Central Memory CD4 T Cells Is a Potential Early Prognostic Marker for Changing Viral Load in SHIV-Infected Rhesus Macaques

In HIV infection there is a paucity of literature about the degree of immune dysfunction to potentially correlate and/or predict disease progression relative to CD4+ T cells count or viral load. We assessed functional characteristics of memory T cells subsets as potential prognostic markers for changing viral loads and/or disease progression using the SHIV-infected rhesus macaque model. Relative to long-term non-progressors with low/undetectable viral loads, those with chronic plasma viremia, but clinically healthy, exhibited significantly lower numbers and functional impairment of CD4+ T cells, but not CD8+ T cells, in terms of IL-2 production by central memory subset in response to PMA and ionomycine (PMA+I) stimulation. Highly viremic animals showed impaired cytokine-production by all T cells subsets. These results suggest that functional impairment of CD4+ T cells in general, and of central memory subset in particular, may be a potential indicator/predictor of chronic infection with immune dysfunction, which could be assayed relatively easily using non-specific PMA+I stimulation.