Miracle-dz/UniFAR-FTUs huggingface dataset:
Production of polyhydroxyalkanoate from high cell density fermentations using palm oil and waste animal fats as carbon feedstocks and their recovery with non-halogenated solvents

1 Zusammenfassung . 3 Aim of Thesis . 5 Structure of thesis . 5 CHAPTER I . 7 Introduction . 7 Bioplastics . 7 Ralstonia eutropha relevance for production of polyhydroxyalkanoate . 14 PHA recovery . 19 Biodegradation of PHA . 21 Global production of biopolymers . 23 References . 25 CHAPTER II . 37 Growth conditions for hydrophobic carbon sources . 37 Goal of Chapter II . 37 Introduction . 37 Materials and methods . 38 Results . 40 Discussion . 44 References . 45 CHAPTER III . 47 Selection of P(HB-co-HHx) production strain . 47 Goal of Chapter III . 47 Introduction . 47 Materials and methods . 48 Results . 50 Discussion . 54 References . 57 CHAPTER IV . 61 Development of a high cell density fermentation for PHA production from palm oil with Ralstonia eutropha . 61 Goal of Chapter IV . 6
Single Cell Observations Show Persister Cells Wake Based on Ribosome Content

Since persister cells survive antibiotic treatments through dormancy and resuscitate to reconstitute infections, it is imperative to determine the rate at which these cells revive. Using two sets of Escherichia coli persister cells, those arising naturally at low levels and those generated at high levels by ceasing transcription via rifampicin pretreatment (shown to be bona fide persisters through seven sets of experiments), we used microscopy of single cells to determine that persisters have low levels of antibiotic-corrupting proteins and that their resuscitation is heterogeneous and includes cells that grow immediately. In all, five phenotypes were found for persister cell resuscitation: (i) immediate division, (ii) immediate elongation followed by division, (iii) immediate elongation but no division, (iv) delayed elongation/division, and (v) no growth. In addition, once cell division begins, the growth rate is that of exponential cells. Critically, the greater the ribosome content, the faster the persister cells resuscitate.
A Machine-Learning Based Approach for Extracting Logical Structure of a Styled Document

A styled document is a document that contains diverse decorating functions such as different font, colors, tables and images generally authored in a word processor (e.g., MS-WORD, Open Office). Compared to a plain-text document, a styled document enables a human to easily recognize a logical structure such as section, subsection and contents of a document. However, it is difficult for a computer to recognize the structure if a writer does not explicitly specify a type of an element by using the styling functions of a word processor. It is one of the obstacles to enhance document version management systems because they currently manage the document with a file as a unit, not the document elements as a management unit. This paper proposes a machine learning based approach to analyzing the logical structure of a styled document composing of sections, subsections and contents. We first suggest a feature vector for characterizing document elements from a styled document, composing of eight features such as font size, indentation and period, each of which is a frequently discovered item in a styled document. Then, we trained machine learning classifiers such as Random Forest and Support Vector Machine using the suggested feature vector. The trained classifiers are used to automatically identify logical structure of a styled document. Our experiment obtained 92.78% of precision and 94.02% of recall for analyzing the logical structure of 50 styled documents.
Whole-genome sequencing analysis of human bocavirus detected in South Korea

Abstract Human bocaviruses (HBoVs) have been detected in human gastrointestinal infections worldwide. In 2005, HBoV was also discovered in infants and children with infections of the lower respiratory tract. Recently, several genotypes of this parvovirus, including HBoV genotype 2 (HBoV2), genotype 3 (HBoV3) and genotype 4 (HBoV4), were discovered and found to be closely related to HBoV. HBoV2 was first detected in stool samples from children in Pakistan, followed by detection in other countries. HBoV3 was detected in Australia and HBoV4 was identified in stool samples from Nigeria, Tunisia and the USA. Recently, HBoV infection has been on the rise throughout the world, particularly in countries neighbouring South Korea; however, there have been very few studies on Korean strains. In this study, we characterised the whole genome and determined the phylogenetic position of CUK-BC20, a new clinical HBoV strain isolated in South Korea. The CUK-BC20 genome of 5184 nucleotides (nt) contains three open-reading frames (ORFs). The genotype of CUK-BC20 is HBoV2, and 98.77% of its nt sequence is identical with those of other HBoVs, namely Rus-Nsc10-N386. Especially, the ORF3 amino acid sequences from positions 212–213 and 454 corresponding to a variable region (VR)1 and VR5, respectively, showed genotype-specific substitutions that distinguished the four HBoV genotypes. As the first whole-genome sequence analysis of HBoV in South Korea, this information will provide a valuable reference for the detection of recombination, tracking of epidemics and development of diagnosis methods for HBoV.
Scene flow estimation by growing correspondence seeds

A simple seed growing algorithm for estimating scene flow in a stereo setup is presented. Two calibrated and synchronized cameras observe a scene and output a sequence of image pairs. The algorithm simultaneously computes a disparity map between the image pairs and optical flow maps between consecutive images. This, together with calibration data, is an equivalent representation of the 3D scene flow, i.e. a 3D velocity vector is associated with each reconstructed point. The proposed method starts from correspondence seeds and propagates these correspondences to their neighborhood. It is accurate for complex scenes with large motions and produces temporally-coherent stereo disparity and optical flow results. The algorithm is fast due to inherent search space reduction. An explicit comparison with recent methods of spatiotemporal stereo and variational optical and scene flow is provided.
Phylogenetic Patterns of Geographical and Ecological Diversification in the Subgenus Drosophila

Colonisation of new geographic regions and/or of new ecological resources can result in rapid species diversification into the new ecological niches available. Members of the subgenus Drosophila are distributed across the globe and show a large diversity of ecological niches. Furthermore, taxonomic classification of Drosophila includes the rank radiation, which refers to closely related species groups. Nevertheless, it has never been tested if these taxonomic radiations correspond to evolutionary radiations. Here we present a study of the patterns of diversification of Drosophila to test for increased diversification rates in relation to the geographic and ecological diversification processes. For this, we have estimated and dated a phylogeny of 218 species belonging to the major species groups of the subgenus. The obtained phylogenies are largely consistent with previous studies and indicate that the major groups appeared during the Oligocene/Miocene transition or early Miocene, characterized by a trend of climate warming with brief periods of glaciation. Ancestral reconstruction of geographic ranges and ecological resource use suggest at least two dispersals to the Neotropics from the ancestral Asiatic tropical disribution, and several transitions to specialized ecological resource use (mycophagous and cactophilic). Colonisation of new geographic regions and/or of new ecological resources can result in rapid species diversification into the new ecological niches available. However, diversification analyses show no significant support for adaptive radiations as a result of geographic dispersal or ecological resource shift. Also, cactophily has not resulted in an increase in the diversification rate of the repleta and related groups. It is thus concluded that the taxonomic radiations do not correspond to adaptive radiations.
Fatigue damage characterisation of MarBN steel for high temperature flexible operating conditions

This article is concerned with the high temperature low cycle fatigue behaviour of a new nano-strengthened martensitic-ferritic steel, MarBN. A range of strain-controlled, low cycle fatigue tests are presented on MarBN at 600 ℃ and 650 ℃, and compared with previously published data for a current state-of-the-art material, P91 steel, including microstructural analysis of the fracture mechanisms. A modified Chaboche damage law, incorporating Coffin–Manson life prediction, is implemented within a hyperbolic sine unified cyclic viscoplastic constitutive model. Calibration and validation of the model with respect to the effects of strain-rate and strain-range is performed based on an optimisation procedure for identification of the material parameters. The cyclic viscoplasticity model with damage successfully predicts fatigue damage evolution and life in the cyclically softening materials, MarBN and P91.
Job Satisfaction among Health-Care Staff in Township Health Centers in Rural China: Results from a Latent Class Analysis

Background: The lower job satisfaction of health-care staff will lead to more brain drain, worse work performance, and poorer health-care outcomes. The aim of this study was to identify patterns of job satisfaction among health-care staff in rural China, and to investigate the association between the latent clusters and health-care staff’s personal and professional features; Methods: We selected 12 items of five-point Likert scale questions to measure job satisfaction. A latent-class analysis was performed to identify subgroups based on the items of job satisfaction; Results: Four latent classes of job satisfaction were identified: 8.9% had high job satisfaction, belonging to “satisfied class”; 38.2% had low job satisfaction, named as “unsatisfied class”; 30.5% were categorized into “unsatisfied class with the exception of interpersonal relationships”; 22.4% were identified as “pseudo-satisfied class”, only satisfied with management-oriented items. Low job satisfaction was associated with specialty, training opportunity, and income inequality. Conclusions: The minority of health-care staff belong to the “satisfied class”. Three among four subgroups are not satisfied with income, benefit, training, and career development. Targeting policy interventions should be implemented to improve the items of job satisfaction based on the patterns and health-care staff’s features.
Development and validation of a HPLC method for the determination of aldicarb, aldicarb sulfoxide and aldicarb sulfone in liquid samples from anaerobic reactors

This study describes the development and validation of a high-performance liquid chromatography (HPLC) method for detecting aldicarb and its residues in liquid samples without pretreatment. The HPLC system was equipped with a C-18 column and the mobile phase was composed of a mixture of water and acetonitrile using a linear gradient elution. The UV detector was utilized at 210 nm. Methomyl was used as an internal standard. Water and synthetic medium were used as solvents. The method was linear from 0.49-15.0 mg L-1 (r2 > 0.9985), 0.1-5.0 mg L-1 (r2 > 0.9974) and 0.1-5.0 mg L-1 (r2 > 0.9987) for aldicarb, aldicarb sulfoxide and aldicarb sulfone, respectively. The linearity of the method was confirmed by the ANOVA F-test through adjustment of the linear model, validity of the regression and efficiency of the regression tests. The limit of detection in water and synthetic medium were of 0.391/0.440 mg L-1, 0.069/0.192 mg L-1 and 0.033/0.068 mg L-1 for aldicarb, aldicarb sulfoxide and aldicarb sulfone, respectively. Total time of analysis was of 22 min. In the application of the method, the aldicarb degradation in horizontal-flow anaerobic immobilized biomass (HAIB) reactor was evaluated under different conditions (methanogenic, sulfidogenic and denitrifying).
Wolbachia-Mediated Antibacterial Protection and Immune Gene Regulation in Drosophila

The outcome of microbial infection of insects is dependent not only on interactions between the host and pathogen, but also on the interactions between microbes that co-infect the host. Recently the maternally inherited endosymbiotic bacteria Wolbachia has been shown to protect insects from a range of microbial and eukaryotic pathogens. Mosquitoes experimentally infected with Wolbachia have upregulated immune responses and are protected from a number of pathogens including viruses, bacteria, Plasmodium and filarial nematodes. It has been hypothesised that immune upregulation underpins Wolbachia-mediated protection. Drosophila is a strong model for understanding host-Wolbachia-pathogen interactions. Wolbachia-mediated antiviral protection in Drosophila has been demonstrated for a number of different Wolbachia strains. In this study we investigate whether Wolbachia-infected flies are also protected against pathogenic bacteria. Drosophila simulans lines infected with five different Wolbachia strains were challenged with the pathogenic bacteria Pseudomonas aeruginosa PA01, Serratia marcescens and Erwinia carotovora and mortality compared to paired lines without Wolbachia. No difference in mortality was observed in the flies with or without Wolbachia. Similarly no antibacterial protection was observed for D. melanogaster infected with Wolbachia. Interestingly, D. melanogaster Oregon RC flies which are naturally infected with Wolbachia showed no upregulation of the antibacterial immune genes TepIV, Defensin, Diptericin B, PGRP-SD, Cecropin A1 and Attacin D compared to paired flies without Wolbachia. Taken together these results indicate that Wolbachia-mediated antibacterial protection is not ubiquitous in insects and furthermore that the mechanisms of antibacterial and antiviral protection are independent. We suggest that the immune priming and antibacterial protection observed in Wolbachia-infected mosquitoes may be a consequence of the recent artificial introduction of the symbiont into insects that normally do not carry Wolbachia and that antibacterial protection is unlikely to be found in insects carrying long-term Wolbachia infections.
Private cloud and media privacy in social networks

Privacy rules imposed by social networks (SNs) impose several restrictions to user privacy. Though they usually offer the user some control to limit access to his own data, the social network may share uploaded data with other partners and marketing companies. Pictures and videos may have a second life, even after being deleted by the user, and consequently storage and access must take place in the user home domain or facilities managed by the user, following an end to end approach. We propose to combine the usage of private clouds, specialized in media contents, in cooperation with SNs, offering the user complete control over his data, while benefiting from the SNs visibility to announce and spread the data. To achieve transparency, we propose a plug-in system to embed links as annotations in reduced media replacement uploaded in the SN. These links point to the real resource stored in the private cloud, now under complete user control. We perform validation tests which show important improvements in uploading time and user experience.
CO{sub 2} laser beam welding of magnesium-based alloys

Magnesium has gained increased attention in recent years as a structural metal--especially in the automotive industry--necessitating the development of welding techniques qualified for this new application. Lasers are known to be an excellent tool for joining metals. This paper presents results of recent investigations on the weldability of several cast and wrought magnesium-based alloys. Plates with a thickness of 2.5--8 mm were butt joint welded with and without filler metal using a 2.5-kW CO{sub 2} laser. The investigations showed that magnesium alloys can be easily laser welded in similar and dissimilar joints. The beam characteristics of the laser leads to small welds and a deep penetration depth. Crackfree welds exhibiting low porosity and good surface finish can be achieved with appropriate process parameters. Generally, the laser welding leads to either no change or a small increase in hardness in the fusion zone (FZ) and in the heat-affected zone (HAZ) relative to the base metal. Less promising results were obtained for the cast alloy QE22, in which cracking in the age-hardened condition and a significant decrease in hardness occurred. Laser welded die cast alloys showed an extremely high level of porosity in the weld.
From skin to spontaneous lysis: A case of spontaneous tumor lysis syndrome in metastatic melanoma

Tumor lysis syndrome is a life-threatening complication that often occurs after administration of cytotoxic therapy, but rarely occurs spontaneously without chemotherapy. This vignette describes a 59-year-old male with known extensive metastatic melanoma who presented to the hospital with spontaneous tumor lysis syndrome. Most spontaneous tumor lysis cases occur in patients with acute leukemias and aggressive lymphomas; however, this rare case depicts a patient with melanoma developing tumor lysis before the administration of chemotherapy.
First report on a novel Nigrospora sphaerica isolated from Catharanthus roseus plant with anticarcinogenic properties

This paper reports on the vinca alkaloid produced by a novel Nigrospora sphaerica isolated from Catharanthus roseus. Through liquid chromatography–mass spectrometry (LCMS), only the crude mycelia extract of this fungus was positive for determination of vinblastine. This vinca alkaloid was then purified by using high‐performance liquid chromatography (HPLC) and tested for cytotoxicity activity using MTT assays. The breast cell line cancer (MDA‐MB 231) was treated with a purified vinblastine which was intracellulary produced by N. sphaerica. The purified vinblastine from extracted leaf of C. roseus was used as a standard comparison. A positive result with a value of half maximal inhibitory concentration (IC50) of > 32 μg ml−1 was observed compared with standard (IC50) of 350 μg ml−1 only. It showed that a vinblastine produced by N. sphaerica has a high cytotoxicity activity even though the concentration of vinblastine produced by this endophytic fungus was only 0.868 μg ml−1.
XIST RNA paints the inactive X chromosome at interphase: evidence for a novel RNA involved in nuclear/chromosome structure

The XIST gene is implicated in X chromosome inactivation, yet the RNA contains no apparent open reading frame. An accumulation of XIST RNA is observed near its site of transcription, the inactive X chromosome (Xi). A series of molecular cytogenetic studies comparing properties of XIST RNA to other protein coding RNAs, support a critical distinction for XIST RNA; XIST does not concentrate at Xi simply because it is transcribed and processed there. Most notably, morphometric and 3-D analysis reveals that XIST RNA and Xi are coincident in 2- and 3-D space; hence, the XIST RNA essentially paints Xi. Several results indicate that the XIST RNA accumulation has two components, a minor one associated with transcription and processing, and a spliced major component, which stably associates with Xi. Upon transcriptional inhibition the major spliced component remains in the nucleus and often encircles the extra-prominent heterochromatic Barr body. The continually transcribed XIST gene and its polyadenylated RNA consistently localize to a nuclear region devoid of splicing factor/poly A RNA rich domains. XIST RNA remains with the nuclear matrix fraction after removal of chromosomal DNA. XIST RNA is released from its association with Xi during mitosis, but shows a unique highly particulate distribution. Collective results indicate that XIST RNA may be an architectural element of the interphase chromosome territory, possibly a component of nonchromatin nuclear structure that specifically associates with Xi. XIST RNA is a novel nuclear RNA which potentially provides a specific precedent for RNA involvement in nuclear structure and cis-limited gene regulation via higher-order chromatin packaging.
3D mapping of airway wall thickening in asthma with MSCT: a level set approach

Assessing the airway wall thickness in multi slice computed tomography (MSCT) as image marker for airway disease phenotyping such asthma and COPD is a current trend and challenge for the scientific community working in lung imaging. This paper addresses the same problem from a different point of view: considering the expected wall thickness-to-lumen-radius ratio for a normal subject as known and constant throughout the whole airway tree, the aim is to build up a 3D map of airway wall regions of larger thickness and to define an overall score able to highlight a pathological status. In this respect, the local dimension (caliber) of the previously segmented airway lumen is obtained on each point by exploiting the granulometry morphological operator. A level set function is defined based on this caliber information and on the expected wall thickness ratio, which allows obtaining a good estimate of the airway wall throughout all segmented lumen generations. Next, the vascular (or mediastinal dense tissue) contact regions are automatically detected and excluded from analysis. For the remaining airway wall border points, the real wall thickness is estimated based on the tissue density analysis in the airway radial direction; thick wall points are highlighted on a 3D representation of the airways and several quantification scores are defined. The proposed approach is fully automatic and was evaluated (proof of concept) on a patient selection coming from different databases including mild, severe asthmatics and normal cases. This preliminary evaluation confirms the discriminative power of the proposed approach regarding different phenotypes and is currently extending to larger cohorts.
Quality-Aware Energy Optimization in Wireless Video Communication With Multipath TCP

The advancements in wireless communication technologies prompt the bandwidth aggregation for mobile video delivery over heterogeneous access networks. Multipath TCP (MPTCP) is the transport protocol recommended by IETF for concurrent data transmission to multihomed terminals. However, it still remains challenging to deliver user-satisfied video services with the existing MPTCP schemes because of the contradiction between energy consumption and received video quality in mobile devices. To enable the energy-efficient and quality-guaranteed video streaming, this paper presents an energy-distortion-aware MPTCP (EDAM) solution. First, we develop an analytical framework to characterize the energy-distortion tradeoff for multipath video transmission over heterogeneous wireless networks. Second, we propose a video flow rate allocation algorithm to minimize the energy consumption while achieving target video quality based on utility maximization theory. The performance of the proposed EDAM is evaluated through both experiments in real wireless networks and extensive emulations in exata. Experimental results show that EDAM exhibits performance advantages over existing MPTCP schemes in energy conservation and video quality.