Miracle-dz/UniFAR-FTUs huggingface dataset:
DNA polymerase IV primarily operates outside of DNA replication forks in Escherichia coli

In Escherichia coli, damage to the chromosomal DNA induces the SOS response, setting in motion a series of different DNA repair and damage tolerance pathways. DNA polymerase IV (pol IV) is one of three specialised DNA polymerases called into action during the SOS response to help cells tolerate certain types of DNA damage. The canonical view in the field is that pol IV primarily acts at replisomes that have stalled on the damaged DNA template. However, the results of several studies indicate that pol IV also acts on other substrates, including single-stranded DNA gaps left behind replisomes that re-initiate replication downstream of a lesion, stalled transcription complexes and recombination intermediates. In this study, we use single-molecule time-lapse microscopy to directly visualize fluorescently labelled pol IV in live cells. We treat cells with the DNA-damaging antibiotic ciprofloxacin, Methylmethane sulfonate (MMS) or ultraviolet light and measure changes in pol IV concentrations and cellular locations through time. We observe that only 5–10% of foci induced by DNA damage form close to replisomes, suggesting that pol IV predominantly carries out non-replisomal functions. The minority of foci that do form close to replisomes exhibit a broad distribution of colocalisation distances, consistent with a significant proportion of pol IV molecules carrying out postreplicative TLS in gaps behind the replisome. Interestingly, the proportion of pol IV foci that form close to replisomes drops dramatically in the period 90–180 min after treatment, despite pol IV concentrations remaining relatively constant. In an SOS-constitutive mutant that expresses high levels of pol IV, few foci are observed in the absence of damage, indicating that within cells access of pol IV to DNA is dependent on the presence of damage, as opposed to concentration-driven competition for binding sites.
Dynamic partitioning to mitigate stuck-at faults in emerging memories

Emerging non-volatile memories have many advantages over conventional memory. Unfortunately, many are susceptible to write endurance challenges, resulting in stuck-at faults. Existing mitigation methods statically partition and invert data within a block containing such faults (partition-and-flip) to ensure data is written to match stuck-at cells such that they may remain in service. Unfortunately, these schemes have limited fault tolerance capabilities and require the assumption that their auxiliary bits are fault free. We propose a dynamic partitioning scheme that improves the number of tolerated stuck-at faults and simultaneously protects auxiliary bits. Dynamic partitioning can significantly improve the fault tolerance over existing static partitioning approaches with an equal number of auxiliary bits. Moreover, it can often still improve fault tolerance while reducing the number of auxiliary bits. Compared to flip-N-write and Aegis, a leading mitigation scheme, dynamic partitioning can achieve 7–72% and 5–53 x lower write error rates, respectively, for the same capacity overhead with a stuck-at-fault rate of 10−3.
Mechanism of Macrophage-Derived Chemokine/CCL22 Production by HaCaT Keratinocytes

Background CC chemokine ligand 17 (CCL17) and CCL22 are the functional ligands for CCR4. We previously reported that inhibitors of nuclear factor-kappa B and p38 mitogen-activated protein kinase (p38 MAPK), but not of extracellular signal-related kinase (ERK), inhibited tumor necrosis factor (TNF)-α- and interferon (IFN)-γ-induced production of CCL17 by the human keratinocyte cell line, HaCaT. Further, an inhibitor of epidermal growth factor receptor (EGFR) enhanced the CCL17 production by these keratinocytes. Objective To identify the mechanism underlying CCL22 production by HaCaT cells. Methods We investigated the signal transduction pathways by which TNF-α and IFN-γ stimulate HaCaT cells to produce CCL22 by adding various inhibitors. Results TNF-α- and IFN-γ-induced CCL22 production was inhibited by PD98059, PD153035, Bay 11-7085, SB202190, c-Jun N-terminal kinase (JNK) inhibitor II, and Janus kinase (JAK) inhibitor 1. Conclusion Our results indicate that CCL22 production in HaCaT cells is dependent on ERK, EGFR, p38 MAPK, JNK, and JAK and is mediated by different signal pathways from those regulating CCL17 production. Altogether, our previous and present results suggest that EGFR activation represses CCL17 but enhances CCL22 production by these cells.
Micromechanical properties of a laser-induced iron oxide–aluminum matrix composite coating

A laser-based technique was used to deposit Fe_3O_4 on A319Al, producing an Fe_3O_4/Al reaction composite coating. Scanning Auger microscopy indicated a reaction between oxide particles and aluminum-forming Fe–Al intermetallic compounds, Al_2O_3, and various intermediate reaction products. Analysis of the coating region, fractured in vacuo , indicated substantial toughness of the material due to extremely refined microstructure with finely distributed oxide and intermetallic particles and strong interfacial bonding between particles and the matrix. Mechanical properties of the coating were evaluated by nanoindentation techniques employing both Berkovich and cube-corner indenters. Hardness and elastic modulus values were found to be uniform at 1.24 and 76 GPa, respectively. No radial cracking was observed for either the Berkovich or cube-corner indenters. These results indicate that the laser-induced rapidly solidified composite material is tough and fracture resistant.
Double casting prototyping with a thermal aging step for fabrication of 3D microstructures in poly(dimethylsiloxane)

The paper describes a cheap and accessible technique of a poly(dimethylsiloxane) (PDMS) master treatment by thermal aging as a step of double casting microfabrication process. Three-dimensional PDMS microstructures could have been achieved using this technique. It was proved, that thermal aging changes nanotopology of a PDMS surface and thus enhances efficiency of double casting prototyping. The thermally aged PDMS master could have been used for multiple and correct replication of over 98% of the fabricated microstructures. Moreover, lack of chemical modification preserved the biocompatibility of PDMS devices. The fabricated microstructures were successfully utilized for 3D cell culture.
Development and Test of a New Cryostat Module for the Injector of the S-Dalinac*

The present injector of the superconducting Darmstadt electron linear accelerator S-DALINAC provides an electron beam of up to 10 MeV kinetic energy and up to 60 A current in continuous wave operation. A new cryostat module has been constructed to replace the actual one in order to provide higher beam energies of up to 14 MeV and currents of up to 250 A for nuclear resonance fluorescence experiments at the Darmstadt High Intensity Photon Setup (DHIPS). As before two 20-cell superconducting microwave cavities will be operated at an acceleration frequency of 3 GHz in a liquid helium bath at 2 K. For the injector upgrade two new elliptical 20-cell niobium cavities were manufactured and in addition a third spare one. The rf power is transferred to the cavities by newly developed waveguide-transition line and input couplers. The module was assembled for a first test and cooled down to 4 and 2 K outside the accelerator. This test was successful and confirmed the rf properties of the newly designed waveguide power couplers.
Dose-finding designs for cumulative toxicities using multiple constraints

&NA; This article addresses the concern regarding late‐onset dose‐limiting toxicities (DLT), moderate toxicities below the threshold of a DLT and cumulative toxicities that may lead to a DLT, which are mostly disregarded or handled in an ad hoc manner when determining the maximum tolerated dose (MTD) in dose‐finding cancer clinical trials. An extension of the Time‐to‐Event Continual Reassessment Method (TITE‐CRM) which allows for the specification of toxicity constraints on both DLT and moderate toxicities, and can account for partial information is proposed. The method is illustrated in the context of an Erlotinib dose‐finding trial with low DLT rates, but a significant number of moderate toxicities leading to treatment discontinuation in later cycles. Based on simulations, our method performs well at selecting the dose level that satisfies both the DLT and moderate‐toxicity constraints. Moreover, it has similar probability of correct selection compared to the TITE‐CRM when the true MTD based on DLT only and the true MTD based on grade 2 or higher toxicities alone coincide, but reduces the probability of recommending a dose above the MTD.
Gene Expression in Experimental Aortic Coarctation and Repair: Candidate Genes for Therapeutic Intervention?

Coarctation of the aorta (CoA) is a constriction of the proximal descending thoracic aorta and is one of the most common congenital cardiovascular defects. Treatments for CoA improve life expectancy, but morbidity persists, particularly due to the development of chronic hypertension (HTN). Identifying the mechanisms of morbidity is difficult in humans due to confounding variables such as age at repair, follow-up duration, coarctation severity and concurrent anomalies. We previously developed an experimental model that replicates aortic pathology in humans with CoA without these confounding variables, and mimics correction at various times using dissolvable suture. Here we present the most comprehensive description of differentially expressed genes (DEGs) to date from the pathology of CoA, which were obtained using this model. Aortic samples (n=4/group) from the ascending aorta that experiences elevated blood pressure (BP) from induction of CoA, and restoration of normal BP after its correction, were analyzed by gene expression microarray, and enriched genes were converted to human orthologues. 51 DEGs with >6 fold-change (FC) were used to determine enriched Gene Ontology terms, altered pathways, and association with National Library of Medicine Medical Subject Headers (MeSH) IDs for HTN, cardiovascular disease (CVD) and CoA. The results generated 18 pathways, 4 of which (cell cycle, immune system, hemostasis and metabolism) were shared with MeSH ID’s for HTN and CVD, and individual genes were associated with the CoA MeSH ID. A thorough literature search further uncovered association with contractile, cytoskeletal and regulatory proteins related to excitation-contraction coupling and metabolism that may explain the structural and functional changes observed in our experimental model, and ultimately help to unravel the mechanisms responsible for persistent morbidity after treatment for CoA.
Simulating the effects of phosphorus limitation in the Mississippi and Atchafalaya River plumes

Abstract. The continental shelf of the northern Gulf of Mexico receives high dissolved inorganic nitrogen and phosphorus loads from the Mississippi and Atchafalaya rivers. The nutrient load results in high primary production in the river plumes and contributes to the development of hypoxia on the Louisiana shelf in summer. While phytoplankton growth is considered to be typically nitrogen-limited in marine waters, phosphorus limitation has been observed in this region during periods of peak river discharge in spring and early summer. Here we investigate the presence, spatio-temporal distribution and implications of phosphorus limitation in the plume region using a circulation model of the northern Gulf of Mexico coupled to a multi-nutrient ecosystem model. Results from a 7-yr simulation (2001–2007) compare well with several sources of observations and suggest that phosphorus limitation develops every year between the Mississippi and Atchafalaya deltas. Model simulations show that phosphorus limitation results in a delay and westward shift of a fraction of river-stimulated primary production. The consequence is a reduced flux of particulate organic matter to the sediment near the Mississippi delta, but slightly enhanced fluxes west of Atchafalaya Bay. Simulations with altered river phosphate concentrations (±50%) show that significant variation in the spatial extent of phosphorus limitation (±40% in July) results from changes in phosphate load.
Forest or meadow: the consequences of habitat for the condition of female arctic ground squirrels (Urocitellus parryii plesius)

Body condition of animals influences the likelihood of surviving harsh environmental conditions, successfully reproducing, and resisting disease. The sum of these individual components of fitness, in turn, have consequences for the growth and persistence of wildlife populations. Here we compared the body mass and condition of adult female arctic ground squirrels (Urocitellus parryii plesius (Osgood, 1900)), an obligate hibernator, in source and sink habitats. We tested the hypothesis that adult females would be in poorer condition in the boreal forest than in adjacent meadows. We found that, during spring, postpartum females in forests weighed less (405 ± 7 vs. 437 ± 11 g; mean ± SE) and were in poorer condition (mean (±SE) residual of mass over structural size = −11.0 ± 10.2 vs. 20.5 ± 6.1 g) compared with females in meadow-source habitat. However, by the onset of entrance into hibernation in August, forest squirrels had reached parity with meadow squirrels and no difference was found in mass (519 ± 13 v.
Cell behaviour on micropatterned substrata: limits of extracellular matrix geometry for spreading and adhesion

Cell adhesion, spreading and migration require the dynamic formation and dispersal of contacts with the extracellular matrix (ECM). In vivo, the number, availability and distribution of ECM binding sites dictate the shape of a cell and determine its mobility. To analyse the geometrical limits of ECM binding sites required for cell attachment and spreading, we used microcontact printing to produce regular patterns of ECM protein dots of defined size separated by nonadhesive regions. Cells cultured on these substrata adhere to and spread on ECM regions as small as 0.1 μm2, when spacing between dots is less than 5 μm. Spacing of 5-25 μm induces a cell to adapt its shape to the ECM pattern. The ability to spread and migrate on dots ≥1 μm2 ceases when the dot separation is ≥30 μm. The extent of cell spreading is directly correlated to the total substratum coverage with ECM-proteins, but irrespective of the geometrical pattern. An optimal spreading extent is reached at a surface coating above 15%. Knowledge of these geometrical limits is essential for an understanding of cell adhesion and migration, and for the design of artificial surfaces that optimally interact with cells in a living tissue.
Rapid Gene Expression Changes in Peripheral Blood Lymphocytes upon Practice of a Comprehensive Yoga Program

One of the most common integrative medicine (IM) modalities is yoga and related practices. Previous work has shown that yoga may improve wellness in healthy people and have benefits for patients. However, the mechanisms of how yoga may positively affect the mind-body system are largely unknown. Here we have assessed possible rapid changes in global gene expression profiles in the peripheral blood mononuclear cells (PBMCs) in healthy people that practiced either a comprehensive yoga program or a control regimen. The experimental sessions included gentle yoga postures, breathing exercises, and meditation (Sudarshan Kriya and Related Practices – SK&P) compared with a control regimen of a nature walk and listening to relaxing music. We show that the SK&P program has a rapid and significantly greater effect on gene expression in PBMCs compared with the control regimen. These data suggest that yoga and related practices result in rapid gene expression alterations which may be the basis for their longer term cell biological and higher level health effects.
Functional Genome Mining for Metabolites Encoded by Large Gene Clusters through Heterologous Expression of a Whole-Genome Bacterial Artificial Chromosome Library in Streptomyces spp

ABSTRACT Genome sequencing projects in the last decade revealed numerous cryptic biosynthetic pathways for unknown secondary metabolites in microbes, revitalizing drug discovery from microbial metabolites by approaches called genome mining. In this work, we developed a heterologous expression and functional screening approach for genome mining from genomic bacterial artificial chromosome (BAC) libraries in Streptomyces spp. We demonstrate mining from a strain of Streptomyces rochei, which is known to produce streptothricins and borrelidin, by expressing its BAC library in the surrogate host Streptomyces lividans SBT5, and screening for antimicrobial activity. In addition to the successful capture of the streptothricin and borrelidin biosynthetic gene clusters, we discovered two novel linear lipopeptides and their corresponding biosynthetic gene cluster, as well as a novel cryptic gene cluster for an unknown antibiotic from S. rochei. This high-throughput functional genome mining approach can be easily applied to other streptomycetes, and it is very suitable for the large-scale screening of genomic BAC libraries for bioactive natural products and the corresponding biosynthetic pathways. IMPORTANCE Microbial genomes encode numerous cryptic biosynthetic gene clusters for unknown small metabolites with potential biological activities. Several genome mining approaches have been developed to activate and bring these cryptic metabolites to biological tests for future drug discovery. Previous sequence-guided procedures relied on bioinformatic analysis to predict potentially interesting biosynthetic gene clusters. In this study, we describe an efficient approach based on heterologous expression and functional screening of a whole-genome library for the mining of bioactive metabolites from Streptomyces. The usefulness of this function-driven approach was demonstrated by the capture of four large biosynthetic gene clusters for metabolites of various chemical types, including streptothricins, borrelidin, two novel lipopeptides, and one unknown antibiotic from Streptomyces rochei Sal35. The transfer, expression, and screening of the library were all performed in a high-throughput way, so that this approach is scalable and adaptable to industrial automation for next-generation antibiotic discovery.
The Influence of Requirements in Software Model Development in an Industrial Environment

Textual description of requirements is a specification technique that is widely used in industry, where time is key for success. How requirements are specified textually greatly depends on human factors. In order to study how requirements processing is affected by the level of detail in textual descriptions, this paper compares enriched textual requirements specifications with non-enriched ones. To do this, we have conducted an experiment in industry with 19 engineers of CAF (Construcciones y Auxiliares de Ferrocarril), which is a supplier of railway solutions. The experiment is a crossover design that analyzes efficiency, effectiveness, and perceived difficulty starting from a written specification of requirements that subjects must process in order to build software models. The results show that effectiveness and efficiency for enriched requirements are better, while non-enriched requirements are slightly more difficult to deal with. Therefore, even though enriched requirements require more time to be specified, the results are more successfully when using them.
Illness perceptions and coping determine quality of life in COPD patients

Background A key goal of chronic obstructive pulmonary disease (COPD) care is to improve patients’ quality of life (QoL). For outcomes such as QoL, illness perceptions and coping are important determinants. Aim The primary aim was to assess the associations between illness perceptions, coping and QoL in COPD patients. A secondary aim was to compare illness perceptions and coping of patients with reference values derived from the literature. Patients and methods A total of 100 patients were included in the study. Patients were asked to complete the Brief Illness Perception Questionnaire (B-IPQ), the Utrecht Proactive Coping Competence scale (UPCC), and a QoL item. Correlations and linear regression models were used to analyze the data. Student’s t-tests were used to compare patients with COPD with reference values derived from the literature. Results Patients with better understanding of COPD utilized more proactive coping strategies (P=0.04). A more intense emotional response to COPD was related to less proactive coping (P=0.02). Patients who reported using more proactive coping techniques also reported to have a better QoL (P<0.01). Illness perceptions were also related to QoL: more positive illness perceptions were related to a better QoL (all P<0.05). Patients with COPD reported more negative illness perceptions than people with a common cold or patients with asthma (all P<0.01), but reported similar perceptions compared with patients with diabetes. Conclusion Patients with COPD reported a moderate QoL, but appeared to be proficient in proactive coping. Illness perceptions, coping, and QoL were all associated with each other. Patients reported more strongly affected illness perceptions compared to people with a cold and patients with asthma. We postulate that a self-management intervention targeting patients’ illness perceptions leads to improved QoL.
Hepatocellular toxicity of oxalicumone A via oxidative stress injury and mitochondrial dysfunction in healthy human liver cells

The marine-derived oxalicumone A (POA) has been demonstrated as a potent anti-tumor bioactive agent for a variety of human carcinoma, but to the best of our knowledge, remains to be evaluated in healthy liver cells. As many drugs distribute preferentially in the liver, the present study aimed to investigate the effects of POA on apoptosis, oxidative stress and mitochondrial function in L-02 healthy liver cells. A Cell-Counting kit-8 assay demonstrated that POA inhibits the proliferation of L-02 cells in a dose- and time-dependent manner. Furthermore, POA induced apoptosis by increasing the percentage of cells in early apoptosis and the sub-G1 cell cycle, along with causing S-phase arrest in L-02 cells. Additionally, POA activated caspase 3, increased the protein expression levels of Fas ligand and B-cell lymphoma X-associated protein, and decreased the expression of the anti-apoptotic protein B-cell lymphoma 2. POA additionally reduced the content of GSH and the activity of superoxide dismutase, elevated malondialdehyde and nitric oxide levels, increased reactive oxygen species production and the levels of alanine aminotransferase and aspartate aminotransferase, which suggested that POA induced lipid peroxidation injury in L-02 cells and that oxidative stress serves an important role. Furthermore, POA caused alternations of mitochondrial function, including an abrupt depletion of adenosine triphosphate synthesis, mitochondrial permeability transition pore opening and depletion of mitochondrial membrane potential in L-02 cells. These data suggested that POA exerts cytotoxicity, at least in part, by inducing oxidative stress, mitochondrial dysfunction, and eventually apoptosis. Changes in mitochondrial function and oxidative stress by POA may therefore be critical in POA-induced toxicity in L-02 cells.