Miracle-dz/UniFAR-FTUs huggingface dataset:
Studying differential isomiRs in high-throughput sequencing data identifies miRNA end-reads as a novel, putative miRNA degradation product

With the advancement of deep-sequencing technologies, it has become clear that individual miRNAs show varying degrees of heterogeneity in the expressed mature sequence. Recent evidence has suggested isomiR variants may be biologically relevant, and that small sequence variations can affect e.g. miRNA stability and RISC loading. The goal of this work was to investigate and characterize such isomiRs to determine whether isomiRs of the same miRNA show biologically relevant differences. The work can further be divided into two sub-studies. I first present a support-vector machine classifier for predicting expression changes for isomiRs in Ago2-knockout cells. The classifier is constructed from miRNA sequence features, and is trained and tested using the observed read data for individual isomiRs, thus handling the possibility that highly similar isomiRs can experience different expression changes. The classifier is not successful, suggesting expression changes in Ago2-knockout is determined by other factors. I also look more closely at whether there are isomiR variants that experience significantly different expression changes, but find no strong evidence of this. Working with the Ago2-knockout sequencing data, a second line of work was set off from the discovery of a group of short ∼ 10 nt reads that align to the 3’ end of mature miRNAs. I initially searched for such reads with the goal of finding products of Ago2 cleavage, but interestingly the reads are found in both wildtype and Ago2-knockout samples. I present an analysis of these reads and their corresponding miRNAs, and suggest they are produced by a previously undescribed regulated miRNA degradation process. In light of this, I also study the project data for isomiRs with non-templated 3’ A/U-tails, which previously has been reported to affect miRNA degradation. I find both Aand U-tailing is common in the studied samples, but find neither a strong correlation nor a lack of overlap between miRNAs targeted by 3’ tailing and miRNAs with corresponding short 3’-aligning reads.
Destruction complex dynamics: Wnt/β-catenin signaling alters Axin-GSK3β interactions in vivo

ABSTRACT The central regulator of the Wnt/β-catenin pathway is the Axin/APC/GSK3β destruction complex (DC), which, under unstimulated conditions, targets cytoplasmic β-catenin for degradation. How Wnt activation inhibits the DC to permit β-catenin-dependent signaling remains controversial, in part because the DC and its regulation have never been observed in vivo. Using bimolecular fluorescence complementation (BiFC) methods, we have now analyzed the activity of the DC under near-physiological conditions in Drosophila. By focusing on well-established patterns of Wnt/Wg signaling in the developing Drosophila wing, we have defined the sequence of events by which activated Wnt receptors induce a conformational change within the DC, resulting in modified Axin-GSK3β interactions that prevent β-catenin degradation. Surprisingly, the nucleus is surrounded by active DCs, which principally control the degradation of β-catenin and thereby nuclear access. These DCs are inactivated and removed upon Wnt signal transduction. These results suggest a novel mechanistic model for dynamic Wnt signal transduction in vivo. Summary: Distinct conformations for active and inactivated destruction complex, the central regulator in the Wnt/β-catenin pathway, are identified in vivo using bimolecular fluorescence complementation.
policy? What's the problem with teenage parents? And what's the problem with

Public discourse in Britain sees teenage motherhood as a pernicious social problem where mothers, their children and society generally will all suffer. Fathers are seen as feckless. This is reflected in New Labour’s teenage pregnancy strategy, which understands teenage parents as victims of ignorance, mis-information, and low expectations. But a review of the research evidence finds that the age at which pregnancy occurs has little effect on social outcomes. Many teenage mothers describe how motherhood makes them feel stronger, and marks a change for the better. Many fathers seek to remain connected with their children. For both, parenting seems to provide an impetus to take up education, training and employment. Teenage parenting may be more of an opportunity than a catastrophe, and often makes sense in the life worlds inhabited by young mothers. The paper ends by asking how we can explain this yawning gulf between the experience of teenage parenting and policy, and concludes that this largely rests on assumptions of rational choice, in turn creating a ‘rationality mistake’.
Small Interference RNA Targeting Connexin-43 Improves Motor Function and Limits Astrogliosis After Juvenile Traumatic Brain Injury

Juvenile traumatic brain injury (jTBI) is the leading cause of death and disability for children and adolescents worldwide, but there are no pharmacological treatments available. Aquaporin 4 (AQP4), an astrocytic perivascular protein, is increased after jTBI, and inhibition of its expression with small interference RNA mitigates edema formation and reduces the number of reactive astrocytes after jTBI. Due to the physical proximity of AQP4 and gap junctions, coregulation of AQP4 and connexin 43 (Cx43) expressions, and the possibility of water diffusion via gap junctions, we decided to address the potential role of astrocytic gap junctions in jTBI pathophysiology. We evaluated the role of Cx43 in the spread of the secondary injuries via the astrocyte network, such as edema formation associated with blood–brain barrier dysfunctions, astrogliosis, and behavioral outcome. We observed that Cx43 was altered after jTBI with increased expression in the perilesional cortex and in the hippocampus at several days post injury. In a second set of experiments, cortical injection of small interference RNA against Cx43 decreased Cx43 protein expression, improved motor function recovery, and decreased astrogliosis but did not result in differences in edema formation as measured via T2-weighted imaging or diffusion-weighted imaging at 1 day or 3 days. Based on our findings, we can speculate that while decreasing Cx43 has beneficial roles, it likely does not contribute to the spread of edema early after jTBI.
RF MEMS ohmic switches for matrix configurations

Two different topologies of radio frequency micro-electro-mechanical system (RF MEMS) series ohmic switches (cantilever and clamped–clamped beams) in coplanar waveguide (CPW) configuration have been characterized by means of DC, environmental, and RF measurements. In particular, on-wafer checks have been followed by RF test after vibration, thermal shocks, and temperature cycles. The devices have been manufactured on high resistivity silicon substrates, as building blocks to be implemented in different single-pole 4-throw (SP4 T), double-pole double-throw (DPDT) configurations, and then integrated in Low Temperature Co-fired Ceramics (LTCC) technology for the realization of large-order Clos 3D networks.
Streptomyces sp. MUM273b: A mangrove‐derived potential source for antioxidant and UVB radiation protectants

Microbial natural products serve as a good source for antioxidants. The mangrove‐derived Streptomyces bacteria have been evidenced to produce antioxidative compounds. This study reports the isolation of Streptomyces sp. MUM273b from mangrove soil that may serve as a promising source of antioxidants and UV‐protective agents. Identification and characterization methods determine that strain MUM273b belongs to the genus Streptomyces. The MUM273b extract exhibits antioxidant activities, including DPPH, ABTS, and superoxide radical scavenging activities and also metal‐chelating activity. The MUM273b extract was also shown to inhibit the production of malondialdehyde in metal‐induced lipid peroxidation. Strong correlation between the antioxidant activities and the total phenolic content of MUM273b extract was shown. In addition, MUM273b extract exhibited cytoprotective effect on the UVB‐induced cell death in HaCaT keratinocytes. Gas chromatography–mass spectrometry analysis detected phenolics, pyrrole, pyrazine, ester, and cyclic dipeptides in MUM273b extract. In summary, Streptomyces MUM273b extract portrays an exciting avenue for future antioxidative drugs and cosmeceuticals development.
Outcome of Botulinum Toxin‐A intraprostatic injection for benign prostatic hyperplasia induced lower urinary tract symptoms: A prospective multicenter study

Our aim was to determine the factors predicting the outcome of intraprostatic injection of Botulinum Toxin‐A (BTX‐A) in the treatment of benign prostatic hyperplasia (BPH)‐induced lower urinary tract symptoms (LUTS) and to evaluate its efficacy and safety.
A review on degradation modelling and its engineering applications

Degradation modeling is an effective approach for reliability assessment, remaining useful life prediction, maintenance planning, and prognostics health management. Degradation models are usually developed based on degradation data and/or prior understandings of physics behind degradation processes of products or systems. Further, the effects of environmental or operational conditions on degradation processes and the knowledge about the dependency between degradation processes help improve the explanatory capabilities of degradation models. This paper presents a comprehensive review of existing degradation modeling approaches commonly used in engineering applications. To assist practitioners in understanding the concept of degradation modelling, the existing methods are classified into two broad categories: the data-driven approach and physics-based modelling approach. By systematically reviewing these approaches, we highlight their merits, useful applications and limitations. Finally, we provide a summary and indicate several future research challenges in this important area of reliability engineering.
Multiple Optimal Reconciliations Under the Duplication-Loss-Coalescence Model

Gene trees can differ from species trees due to a variety of biological phenomena, the most prevalent being gene duplication, horizontal gene transfer, gene loss, and coalescence. To explain topological incongruence between the two trees, researchers apply reconciliation methods, often relying on a maximum parsimony framework. However, while several studies have investigated the space of maximum parsimony reconciliations (MPRs) under the duplication-loss and duplication-transfer-loss models, the space of MPRs under the duplication-loss-coalescence (DLC) model remains poorly understood. To address this problem, we present new algorithms for computing the size of MPR space under the DLC model and sampling from this space uniformly at random. Our algorithms are efficient in practice, with runtime polynomial in the size of the species and gene tree when the number of genes that map to any given species is fixed, thus proving that the MPR problem is fixed-parameter tractable. We have applied our methods to a biological data set of 16 fungal species to provide the first key insights in the space of MPRs under the DLC model. Our results show that a plurality reconciliation, and underlying events, are likely to be representative of MPR space.
Mitochondrial Damage and Mitochondria-Targeted Antioxidant Protection in LPS-Induced Acute Kidney Injury

Induced and frequently unwanted alterations in the mitochondrial structure and functions are a key component of the pathological cascade in many kidney pathologies, including those associated with acute damage. One of the principal pathogenic elements causing mitochondrial dysfunction in Acute Kidney Injury (AKI) is oxidative stress. After ischemia and nephrotoxic action of drugs, sepsis and systemic inflammation are the most frequent causes of AKI. As the kidney suffers from oxidative stress during sepsis, one of the most promising approaches to alleviate such damaging consequences is the use of antioxidants. Considering administration of lipopolysaccharide (LPS) as a model of sepsis, we demonstrate that the mitochondria of neonatal renal tissue are severely affected by LPS-induced AKI, with pathological ultrastructural changes observed in both the mitochondria of the renal tubular epithelium and the vascular endothelium. Upon mitochondrial damage, we evaluated the effect of the mitochondria-targeted antioxidant plastoquinol decylrhodamine 19 (SkQR1) on the development of acute renal failure in newborn rats associated with systemic inflammation induced by the administration of LPS. We found that SkQR1 administration 3 h before LPS led to decreased urinal expression of the AKI marker neutrophil gelatinase-associated lipocalin 2 (NGAL), in addition to a decrease in urea and creatinine levels in the blood. Additionally, an observed impairment of proliferative activity in the neonatal kidney caused by LPS treatment was also prevented by the treatment of rat pups with SkQR1. Thus, one of the key events for renal tissue damage in neonatal sepsis is an alteration in the structure and function of the mitochondria and the mitochondria-targeted antioxidant SkQR1 is an effective nephroprotective agent, which protects the neonatal kidney from sepsis-induced AKI.
Electrospun ZnO / Bi 2 O 3 Nanofibers with Enhanced Photocatalytic Activity

ZnO/Bi 2 O 3 nanofibers were synthesized by a simple electrospinning method and both the UV and visible light responsive photocatalytic properties were studied by the decolorization of RhB dye. Thermogravimetric analysis/differential thermal analysis (TGA-DTA), X-ray diffraction (XRD), scanning electron microscope (SEM), and UV-vis diffuse reflectance spectra (DRS) were employed to study the structure, morphology, and optical properties of the ZnO/Bi 2 O 3 nanofibers, respectively. The relationship between the ZnO/Bi 2 O 3 ratio and photocatalytic activity was also studied, and the composite with a molar ratio of 23 : 1 demonstrated the best activity under both excitations. The photocatalytic mechanisms for the composite fibers can be described as the direct photocatalysis under UV excitation and photosensitation for visible light irradiation. The enhanced photocatalytic activities can be ascribed to the effective electron-hole pairs separation that leads to the promoted photocatalytic efficiency.
TTL Proteins Scaffold Brassinosteroid Signaling Components at the Plasma Membrane to Optimize Signal Transduction in Arabidopsis

Plant-specific TTL proteins function as positive regulators of BR responses likely by bringing together signaling components at the plasma membrane. Brassinosteroids (BRs) form a group of steroidal hormones essential for plant growth, development, and stress responses. BRs are perceived extracellularly by plasma membrane receptor-like kinases that activate an interconnected signal transduction cascade, leading to the transcriptional regulation of BR-responsive genes. TETRATRICOPEPTIDE THIOREDOXIN-LIKE (TTL) genes are specific for land plants, and their encoded proteins are defined by the presence of protein–protein interaction motives, that is, an intrinsic disordered region at the N terminus, six tetratricopeptide repeat domains, and a C terminus with homology to thioredoxins. TTL proteins thus likely mediate the assembly of multiprotein complexes. Phenotypic, molecular, and genetic analyses show that TTL proteins are positive regulators of BR signaling in Arabidopsis (Arabidopsis thaliana). TTL3 directly interacts with a constitutively active BRASSINOSTEROID INSENSITIVE1 (BRI1) receptor kinase, BRI1-SUPPRESSOR1 phosphatase, and the BRASSINAZOLE RESISTANT1 transcription factor and associates with BR-SIGNALING KINASE1, BRASSINOSTEROID INSENSITIVE2 kinases, but not with BRI1-ASSOCIATED KINASE1. A functional TTL3-green fluorescent protein (GFP) shows dual cytoplasmic plasma membrane localization. Depleting the endogenous BR content reduces plasma membrane localization of TTL3-GFP, while increasing BR content causes its plasma membrane relocalization, where it strengthens the association of BR signaling components. Our results reveal that TTL proteins promote BR responses and suggest that TTL proteins may function as scaffold proteins by bringing together cytoplasmic and plasma membrane BR signaling components.
HFRECCA : A New Sentence Clustering Technique For Text Mining

Clustering is the process of grouping or aggregating of data items. Sentence clustering mainly used in variety of applications such as classify and categorization of documents, automatic summary generation, organizing the documents, etc. In text processing, sentence clustering plays a vital role this is used in text mining activities. Size of the clusters may change from one cluster to another. The traditional clustering algorithms have some problems in clustering the input dataset. The problems such as, instability of clusters, complexity and sensitivity. To overcome the drawbacks of these clustering algorithms, this paper proposes a algorithm called Hierarchical Fuzzy Relational Eigenvector Centrality-based Clustering Algorithm (HFRECCA) is extension of FRECCA which is used for the clustering of sentences. Contents present in text documents contain hierarchical structure and there are many terms present in the documents which are related to more than one theme hence HFRECCA will be useful algorithm for natural language documents.
The practice and challenges of e-Government in Nigeria in the 21st century

This paper investigates the state of the present condition of e-government commitment in Nigeria. It also, examines the difficulties encountered in the implementation process.Layne and Lee (2001) “Stages of growth theory” was adopted to explain the position of Nigeria in the implementation and the challenges it faced on e-government.To do this,this paper used secondary data as a source to collect different articles and report.This paper finds that while e-government is present in Nigeria, it is still in its initial stage.Not only have that, the environment lacked many prerequisites for the survival and continued maintenance of e-governance due to many factors such as inadequate electricity, technical expertise etcetera.It is therefore suggested that both the government and the stakeholders should take it up as a challenge to find quick and lasting solutions to them. There must also be political will and government should have its administrative staff retrained in IT to properly manage the facilities and infrastructure necessary for e-government.
Pre- and Perinatal Characteristics Associated with Apgar Scores in a Review and in a New Study of Dutch Twins

Abstract A literature review was carried out to identify pre and perinatal characteristics associated with variation in Apgar scores in population-based studies. The parameters identified in the literature search were included in the classical twin design study to estimate effects of pre and perinatal factors shared and nonshared by twins and to test for a contribution of genetic factors in 1- and 5-min Apgar scores in a large sample of Dutch monozygotic (MZ) and dizygotic (DZ) twins. The sample included MZ and DZ twins (N = 5181 pairs) recruited by the Netherlands Twin Register shortly after birth, with data on prenatal characteristics and Apgar scores at first and/or fifth minutes. The ordinal regression and structural equation modeling were used to analyze the effects of characteristics identified in the literature review and to estimate genetic and nongenetic variance components. The literature review identified 63 papers. Consistent with the review, we observed statistically significant effects of birth order, zygosity and gestational age (GA) for 1- and 5-min Apgar scores of both twins. Apgar scores are higher in first-born versus second-born twins and DZ first-born versus MZ first-born twins. Birth weight had an effect on the 5-min Apgar of the first born. Fetal presentation and mode of delivery had different effects on Apgar scores of first- and second-born twins. Parental characteristics and chorionicity did not have significant main effects on Apgar scores. The MZ twins’ Apgar correlations equaled the DZ Apgar correlations. Our analyses suggest that individual differences in 1- and 5-min Apgar scores are attributable to shared and nonshared pre and perinatal factors, but not to genotypic factors of the newborns. The main predictors of Apgar scores are birth order, zygosity, GA, birth weight, mode of delivery and fetal presentation.
Timing synchronization in string quartet performance: a preliminary study

This work presents a preliminary study of timing synchro- nization phenomena in string quartet performance. Accurate timing in- formation extracted from real recordings is used to compare timing de- viations in solo and ensemble performance when executing a simple mu- sical passage. Multi-modal data is acquired from real performance and processed towards obtaining note-level segmentation of recorded perfor- mances. From such segmentation, a series of timing deviation analyses are carried out at two dierent temporal levels, focusing on the explo- ration of significant dierences between solo and ensemble performances. This paper briefly introduces, via an initial exploratory study, the exper- imental framework on which further, more complete analyses are to be carried out with the aim of observing and describing certain synchro- nization phenomena taking place in ensemble music making.
Peptide TNIIIA2 Derived from Tenascin-C Contributes to Malignant Progression in Colitis-Associated Colorectal Cancer via β1-Integrin Activation in Fibroblasts

Inflammatory bowel diseases increase the risk of colorectal cancer and colitis-associated colorectal cancer (CAC). Tenascin-C, a matricellular protein, is highly expressed in inflammatory bowel diseases, especially colorectal cancer. However, the role of tenascin-C in the development of CAC is not yet fully understood. We previously showed that a peptide derived from tenascin-C, peptide TNIIIA2, induces potent and sustained activation of β1-integrin. Moreover, we recently reported that peptide TNIIIA2 promotes invasion and metastasis in colon cancer cells. Here, we show the pathological relevance of TNIIIA2-related functional site for the development of CAC. First, expression of the TNIIIA2-containing TNC peptides/fragments was detected in dysplastic lesions of an azoxymethane/dextran sodium sulfate (AOM/DSS) mouse model. In vitro experiments demonstrated that conditioned medium from peptide TNIIIA2-stimulated human WI-38 fibroblasts induced malignant transformation in preneoplastic epithelial HaCaT cells. Indeed, these pro-proliferative effects stimulated by peptide TNIIIA2 were abrogated by peptide FNIII14, which has the ability to inactivate β1-integrin. Importantly, peptide FNIII14 was capable of suppressing polyp formation in the AOM/DSS model. Therefore, tenascin-C-derived peptide TNIIIA2 may contribute to the formation of CAC via activation of stromal fibroblasts based on β1-integrin activation. Peptide FNIII14 could represent a potential prophylactic treatment for CAC.
Transitional Justice Comes of Age: Enduring Lessons and Challenges

The study and practice of transitional justice analyzes policy choices made by regimes emerging from armed conflict and/or authoritarian rule with regard to accountability for past abuses, stability, reform, and democratization. Transitional justice emerged as a policy problem and subject of study during political transitions from dictatorships in the late 1970s in Southern European countries such as Greece and Spain, and, more recently, evolved dramatically with the transitions in Latin America and Eastern Europe in countries ranging from Argentina and Guatemala to Poland and Lithuania.1 Most literature on the subject starts with a discussion of states emerging from authoritarian rule, civil