Miracle-dz/UniFAR-FTUs huggingface dataset:
Genome wide analyses of the Escherichia coli primary and secondary transcriptomes

Escherichia coli K12 serves as an important model for studying systems that are important to bacteria in their own right as well as those that are conserved in ‘higher' organisms, which are more difficult and costly to study. Like many model organisms, the genome of K12 has been sequenced, producing a catalogue of protein-coding and stable-RNA genes that enabled study using ‘omic’ approaches. This has led to a rapid expansion of our knowledge of patterns of gene expression and their dependency on growth conditions, cell physiology and individual genes. However, the underlying networks of gene regulation are less well understood, but are known to involve the control of steps in RNA processing and degradation as well as transcription and translation. With this in mind, this thesis describes the development of an approach based on RNA sequencing that produces nucleotide-resolution transcriptome maps that distinguish sites that correspond to RNA processing and steps in degradation from those of transcription initiation, while incorporating all classes of RNA. Comparison with results obtained previously validated the approach, which has been applied already to the study of other bacterial species. Within the E. coli map, many new features were identified, such as previously undetected small RNAs and processing at a site associated with the production of specialised ribosomes, which may ensure the translation of leaderless mRNAs, which were also mapped. The approach also showed the benefit of incorporating steps that can differentiate the 5’ status of transcripts in assigning sites of transcription initiation. RNA sequencing was also used to map sites of cleavage by RNase E, an essential endoribonuclease that is central to both the processing and degradation of RNA in bacteria and plant plastids. This aspect of the thesis has advanced from pilot studies to the point where the ‘code’ that determines one form of substrate recognition by RNase E is beginning to emerge. As a result of this success, equivalent data has been collected for other ribonucleases involved in RNA processing and degradation. Continuing analysis of the primary and secondary transcriptomes, consisting of native, unprocessed transcripts and of transcripts that have been modified from their native form via processing and/or degradation respectively, with the tools presented here promises to broaden and deepen our understanding of an important model organism.
Spatial patterns of root branching and actinorhizal nodulation in Discaria trinervis seedlings

The spatial patterns of root branching (topology) and actinorhizal nodulation of Discaria trinervis seedlings under natural and controlled conditions were analysed. The link, i.e. the root segment between either two branching points, or between a meristem and a branching point, was used as a structural unit of roots. Nodulated field plants displayed a random model of root topology and experimental plants without root symbionts a herringbone model (Fitter, 1991). The occurrence of these different root topologies would suggest that root symbionts influence root model architecture. The frequency distribution of the number of nodules per link on the main roots, for field collected plants, fitted a negative binomial model. Nodules were mainly situated near the main root's proximal end. The position (number of links counted from the main root's proximal end to the root apex) of lateral nodulated roots coincided with the nodulated area of the main root. A nodulation assay showed that the spatial pattern of root nodules was not a consequence of heterogeneous distribution of infective units of Frankia in the soil. The similar pattern of nodule position in field plants and experimental plants suggested that a regulation of nodulation might be also working in plants in their natural environment.
The molecular role of non-canonical Notch signaling via Deltex-1 in high grade glioma

Glioblastoma Multiforme is a WHO grade IV brain tumor with glial characteristics leading to more years of life lost than any other cancer. A better understanding of GBM biology and valid animal models are the two key elements to improved therapeutic results. We found Deltex1, which is part of an alternative Notch pathway, to activate both the PI3K/PKB and the MAPK/ERK pathway and to induce anti-apoptotic Mcl-1. DTX1 over-expression resulted in increased clonogenic and growth potential and also induced cell migration and invasion. Microarray gene expression analysis identified a DTX1-specific transcriptional program related to the changes in phenotype observed. Patients with low DTX1 levels have a favorable prognosis. Therefore, we propose the alternative Notch pathway via DTX1 as an oncogenic factor in glioblastoma. This could partially explain previous findings linking Notch status to prognosis wherein high Notch2 levels correlated with reduced patient survival. We found activated Notch2 in neural stem cells to induce glioma-inducing-cell features including increased proliferation, reduced apoptosis and astrocytic lineage commitment. These observations were found both in vitro and in vivo using a conditional mouse model. Together, these findings indicate an important role for Notch signaling (both canonical and non-canocical) in high grade glioma, offering a potential treatment target. We have also established an in vivo model of GBM which allowed us to analyze the efficacy of novel treatment regimens. Short term treatment of orthotopic xenograft gliomas in nude mice with histone deacetylase inhibitors and 2-deoxy-D-glucose resulted in prolonged survival, reduced tumor growth and induction of cancer cell apoptosis. Therefore, epigenetic reprogramming in combination with energy deprivation was found to have anti-tumor activity in vivo. In an independent project we identified GSK3β as a downstream target of Bmi1. GSK3β maintains a more stem cell like characteristic in GBM cells, potentially also in the glioma inducing cells. Several inhibitors to GSK3β exist and LiCl, which is often used in the clinic, correlates with reduced glioma incidence. Altogether, we believe we have added considerable knowledge on the biology of gliomas thereby helping to characterize the underlying events of gliomagenesis. Furthermore, we have established proof of principle for a novel treatment strategy in vivo.
K-Space Trajectory Design for Reduced MRI Scan Time

The development of compressed sensing (CS) techniques for magnetic resonance imaging (MRI) is enabling a speedup of MRI scanning. To increase the incoherence in the sampling, a random selection of points on the k-space is deployed and a continuous trajectory is obtained by solving a traveling salesman problem (TSP) through these points. A feasible trajectory satisfying the gradient constraints is then obtained by parameterizing it using state-of-the-art methods. In this paper, a constrained convex optimization based method to obtain feasible trajectories is proposed. The method is motivated by the fact that the readout time is proportional to the number of sample points and includes the lengths of the segments of the trajectory in the cost function to obtain variable length trajectories. The proposed method provides a reduction in readout time by more than 50% for random-like trajectories with an improvement of about 1.5 dB in peak signal-to-noise ratio (PSNR) and 0.0762 in structural similarity (SSIM) index on average for a realistic brain phantom MRI image adopting single-shot trajectories.
Survival Analysis of Lung Cancer Patients from TCGA Cohort

Lung cancer is one of the leading causes of death worldwide, accounting for an estimated 2.1 million cases in 2018. To analyze the risk factors behind the lung cancer survival, this paper employs two main models: Kaplan-Meier estimator and Cox proportional hazard model [1]. Also, log-rank test and wald test are utilized to test whether a correlation exists or not, which is discussed in detail in later parts of the paper. The aim is to find out the most influential factors for the survival probability of lung cancer patients. To summarize the results, stage of cancer is always a significant factor for lung cancer survival, and time has to be taken into account when analyzing the survival rate of patients in our data sample, which is from TCGA. Future study on lung cancer is also required to make improvement for the treatment of lung cancer, as our data sample might not represent the overall condition of patients diagnosed with lung cancer; also, more appropriate and advanced models should be employed in order to reflect factors that can affect survival rate of patients with lung cancer in detail.
Bankacılık Endeksi İle Seçilmiş Makroekonomik Faktörler Arasındaki Asimetrik İlişki

Hisse senedinin fiyati gelecekte saglayacagi nakit akisinin iskonto edilmis haline esittir. Iskonto orani ise genellikle piyasa faiz orani (risksiz faiz orani) ve risk primine bagli olarak degismektedir. Ancak hisse senetleri alim satimin yapildigi pazarin etkinlik durumuna gore de degismektedir. Etkin piyasalar hipotezine gore zayif formda etkin piyasalarda piyasaya yansiyan bilgiler fiyatlar uzerinde etkili olabilmektedir. Bu calisma da BIST Bankacilik Endeksine etki etmesi beklenen secilmis makroekonomik degiskenler ile analiz yapilmistir. Analiz donemi 2005/01-2019/12 yillari arasi aylik verilerden olusmaktadir. Calismada degiskenler arasi asimetrik etkiyi belirlemek amaciyla Dogrusal Olmayan Gecikmesi Dagitilmis Oto Regresif Model (NARDL) kullanilmistir. Calismanin sonucunda ise Bankacilik endeksi ile Dolar, Euro ve CDS (pozitif), VIX, Altin ve CDS (negatif) uzun donemli asimetrik bir iliski bulunmustur.
Audio-Based Detection of Explicit Content in Music

We present a novel automatic system for performing explicit content detection directly on the audio signal. Our modular approach uses an audio-to-character recognition model, a keyword spotting model associated with a dictionary of carefully chosen keywords, and a Random Forest classification model for the final decision. To the best of our knowledge, this is the first explicit content detection system based on audio only. We demonstrate the individual relevance of our modules on a set of sub-tasks and compare our approach to a lyrics-informed oracle and an end-to-end naive architecture. The results obtained are encouraging with a F1-score of 67% on a industrial scale explicit content dataset.
EL EFECTO DE LA MOTIVACIÓN SOBRE LA RESILIENCIA Y LA ANSIEDAD DEL DEPORTISTA

Throughout a sports career, a series of traumatic events or sporting failures often occur, which represent a turning point. Therefore, it is necessary to analyze the influence of motivation of the athlete on resilience, and the latter, on their levels of anxiety. This study included 276 volleyball players between the ages of 18 and 31. In this study, several descriptive statistical analyzes were carried out, a reliability analysis of the factors that make up the model and a route analysis that explains the causal relationships between the variables. The indexes of adjustment of the articles of analysis were satisfactory explaining the relationships established between the factors. In conclusion, the self-determined motivation is related to the positive form with the resilience while the less self-determined forms are related to the negative form with it. Likewise, resilience is negatively related to anxiety.
Soil Hg Contamination Impact on Earthworms’ Gut Microbiome

Mercury (Hg) is one of the most toxic heavy metals and is known for its persistence in the environment and potential to accumulate along the food chain. In many terrestrial polluted sites, earthworms are in direct contact with Hg contamination by ingesting large quantities of soil. However, little is known about the impact of Hg soil pollution on earthworms’ gut microbiome. In this study, two incubation experiments involving earthworms in soils from a long-term Hg-polluted site were conducted to assess: (1) the effect of soil Hg contamination on the diversity and structure of microbial communities in earthworm, cast and soil samples; and (2) how the gut microbiome of different digestive track parts of the earthworm responds to soil Hg contamination. The large accumulation of total Hg and methyl-Hg within the earthworm tissues clearly impacted the bacterial and fungal gut community structures, drastically decreasing the relative abundance of the dominating gut bacterial class Mollicutes. Hg-tolerant taxa were found to be taxonomically widespread but consistent along the different parts of the earthworm digestive tract. This study revealed that although Hg might not directly affect the health of macro-organisms in the food-web such as earthworms, their metabolism and legacy in the soil might be impacted through changes in their gut microbiome.
朱鹮（Nipponia nippon）野生种群的现状与保护对策

报道了中国陕西洋县朱鹮野生种群的分布现状，分析了朱鹮的种群动态，如种群数量、出生率和死亡率、年龄结构和性比等．最后叙述了朱鹮种群的保护管理现状，包括种群监测保护、栖息地管理和社区发展战略等．
Community, Diversity, and Marginalization: An Ecological Construction of Immigrant Parenting within the U.S. Neoliberal Home and School Contexts

Abstract Although studies have explored issues related to the partnerships between immigrant families and mainstream schools, tenacious challenges of marginalization within education persist, warranting new frameworks that challenge the present understanding of the immigrant parents’ interactions with the local school. This constructivist grounded theory study analyzed narratives of immigrant families who crossed socio-economic status, cultures, and languages as they parented their children. The findings revealed how the view of community and approach to diversity within the neoliberal climate interacted with the immigrant parents’ pursuit of “becoming American. ” The neoliberal approach to diversity emerged as contentious in the school setting, promoting marginalization and compelling the immigrant parents to seek communities outside of the school. The resulting model summarizes their parenting approach toward school, reflecting individual and collective goals around concepts of community and approach to diversity in the home and school contexts. The discussion of findings is informed by and contributes to Neal and Neal’s networked ecological model, problematizing how schools address community and diversity, suggesting the need for identifying and valuing the networked communities in which immigrant families pursue the goal of “becoming American. ”
Rates and Predictors of Relapse in First-Episode Psychosis: An Australian Cohort Study

Abstract Background Clinical and functional recovery is usually achieved after treatment for a first episode of psychosis (FEP). Unfortunately, subsequent relapse remains common, occurring within a year for approximately 30% of individuals and up to 80% over 5 years. Factors that make relapse more likely in any given individual remain poorly understood. Methods This article presents a naturalistic cohort study of young people (15–24 years old) accessing an early intervention in psychosis service in Melbourne, Australia between January 1, 2011 and December 31, 2016. Demographic and clinical predictors of relapse were collected and analyzed using Cox regression analysis. Results A total of 1220 young people presented with an FEP during the study period; 37.7% (N = 460) experienced at least 1 relapse during their episode of care. Over half of all relapses resulted in an admission to hospital. Non-adherence to medication, substance use, and psychosocial stressors were commonly noted as clinical precipitants of relapse. Significant predictors of relapse (vs no relapse) were a diagnosis of schizophrenia spectrum disorder (adjusted hazard ratio [aHR] = 1.62) or affective psychotic disorder (aHR = 1.37), lifetime amphetamine use (aHR = 1.48), and any substance use during treatment (aHR = 1.63). Conclusion These findings suggest that relapse occurs frequently for young people who have experienced FEP. This is one of the first studies to report that amphetamine use (predominantly illicit methamphetamine) increases the risk of relapse. Clinical services, especially in Australasia, need to consider how best to manage this comorbidity in young people with FEP.
ALK1 SIGNALING IS REQUIRED FOR DIRECTED ENDOTHELIAL CELL MIGRATION IN THE PREVENTION OF ARTERIOVENOUS MALFORMATIONS

ALK1, a TGF-β type I receptor serine/threonine kinase, is critical for proper vascular development. Heterozygous loss of ALK1 results in the vascular disorder, hereditary hemorrhagic telangiectasia type 2 (HHT2), which is characterized by the development of arteriovenous malformations (AVMs) and affects 1:8000 people worldwide. alk1-/- zebrafish develop embryonic lethal AVMs which form via a two-step mechanism. First, loss of alk1 results in an increase in endothelial cell number in cranial arteries, which results in increased vessel caliber. In the second step, normally transient connections between arteries and veins are maintained as an adaptive mechanism to cope with an increased hemodynamic load. Using zebrafish as a tool to study the AVM formation due to loss of Alk1 signaling, I have found that Alk1 is required for directed arterial endothelial cell migration in opposition to blood flow. Embryos lacking alk1 experience a redistribution of cells, with endothelial cells failing to efficiently migrate against the direction of blood flow and accumulating in more distal regions of alk1-dependent arteries. This altered cellular distribution causes an increase in arterial caliber and consequent retention of downstream arteriovenous connections, resulting in fatal AVMs. Notch and ALK1 have been implicated in arterial specification and loss of function of either pathway causes AVMs. Furthermore, ALK1 can cooperate with Notch to upregulate expression of Notch target genes in cultured endothelial cells. These findings have led to the hypothesis that Notch and ALK1 collaboratively program arterial identity and prevent AVMs. I modulated Notch and Alk1 activities in zebrafish embryos and examined effects on Notch target gene expression and vascular morphology. Results demonstrate that control of Notch targets is context-dependent, with gene-specific and region-specific requirements for Notch and Alk1. Although loss of alk1 increases expression of dll4, which encodes a Notch ligand, and enhanced Notch signaling causes AVMs, AVMs in alk1 mutants could neither be phenocopied by Notch activation nor rescued by Notch inhibition. In conclusion, Alk1 is dispensable for acquisition and maintenance of arterial identity, and perturbations in Notch signaling cannot account or AVM development in alk1 mutants.
Fully Convolutional Recurrent Networks for Speech Enhancement

Convolutional recurrent neural networks (CRNs) using convolutional encoder-decoder (CED) structures have shown promising performance for single-channel speech enhancement. These CRNs handle temporal modeling through integrating long short-term memory (LSTM) layers in between convolutional encoder and decoder. However, in such a CRN, the organization of internal representations in feature maps and the focus on local structure of the convolutional mappings has to be discarded for fully-connected LSTM processing. Furthermore, CRNs can be quite restricted concerning the feature space dimension at the input of the LSTM, which, through its fully-connected nature, requires a large amount of trainable parameters. As first novelty, we propose to replace the fully-connected LSTM by a convolutional LSTM (ConvLSTM) and call the resulting network a fully convolutional recurrent network (FCRN). Secondly, since the ConvLSTM retains the structured organization of its input feature maps, we can show that this helps to internally represent the harmonic structure of speech, allowing us to handle high-dimensional input features using less trainable parameters than an LSTM. The proposed FCRN clearly outperforms CRN reference models with similar amounts of trainable parameters in terms of PESQ, STOI, and segmental ∆SNR.
Proteomic and transcriptomic analysis of near-isogenic soybean lines differing in seed protein content

Soybean seeds are a major source of consumable proteins and edible and industrial oils. The overall composition of soybean seeds is determined by complex genetic program and is influenced by the growth environment. Three soybean near-isogenic lines with increased seed protein content were developed from a cross between Evans (low-protein parent) and PI153.296 (high-protein parent). In this study, we sought to identify genes and proteins whose expression is associated with seed composition by evaluating proteomic and transcriptomic data. We applied a high-throughput label-free liquid chromatography tandem mass spectrometry method to analyze proteins from developing seeds of the five soybean lines at 20 days after flowering. More than 800 different proteins were identified in these samples. Three different statistical approaches (a traditional ANOVA based F-test, a permutation test based on the F-statistic, a likelihood ratio test based on a product binomial likelihood (referred to as a Gtest by Zhang et al. 2006)) were evaluated to identify proteins that showed a differential accumulation pattern across the different genotypes of the samples. The G-test identified 35% of the proteins as differentially accumulating, whereas the ANOVA and permutation test did not detect any differentially accumulating proteins. In parallel, the transcriptome of the identical samples were analyzed by using Affymetrix GeneChip Soybean Genome Array. Over
Fuzzy Based AC-DC-AC Converter Controlled Micro Hydro Renewable Power Generation Using Parallel Asynchronous Generators for Remote Areas

A new micro hydro power generation (MHPG) scheme ­ is proposed for supplying loads located at remote areas far away from grid. This paper presents three major contributions for small scale renewable hydro power generation technology. Firstly, the proposed model uses unregulated flow rates for two different generators for generating small scale hydroelectricity which otherwise generally uses constant flow rates. Secondly, a new architecture of converter is designed and implemented for parallel operation of two variable speed generators. Thirdly, a fuzzy PI based converter control is designed for the proposed MHPG system, which is found to perform better than that of conventional PI control based systems. In this, a new architecture of AC-DC-AC converter is used for controlling two parallel operated variable speed Capacitor Excited Asynchronous Generators (CAGs). The two CAGs are considered to be operated at variable speeds as fed by two different variable turbines. The converter system consists of two numbers of two level voltage source converters (VSCs) and one common voltage source inverter (VSI). The control algorithms are appropriately designed so as to manage the variable inputs by converting each of the generated variable ac voltages to dc voltage at a common dc bus. The VSI provides constant voltage and frequency at the load end. This architecture eliminates the problem of synchronization of two variable sources and also optimizes the cost and components required compared to that of system using individual back to back converters for each generating units. The proposed scheme is investigated and analysed to assess the feasibility in terms of its performance and quality of power under different loads such as resistive and inductive loads. Firstly, the switching frequency and modulation index for the converter are determined for giving efficient performance. Finally, the performance of the proposed fuzzy PI controlled converter based MHPG and that of conventional PI controlled converter system is compared and presented. The modeling and the simulation are carried out in MATLAB/Simulink environment.