Miracle-dz/UniFAR-FTUs huggingface dataset:
Interferon Alpha Induces Establishment of Alphaherpesvirus Latency in Sensory Neurons In Vitro

Background Several alphaherpesviruses, including herpes simplex virus 1 (HSV-1) and pseudorabies virus (PRV), establish lifelong latency in neurons of the trigeminal ganglion (TG). Although it is thought that efficient establishment of alphaherpesvirus latency is based on a subtle interplay between virus, neurons and the immune system, it is not clear which immune components are of major importance for the establishment of latency. Methodology/Principal Findings Here, using an in vitro model that enables a natural route of infection, we show that interferon alpha (IFNalpha) has the previously uncharacterized capacity to induce a quiescent HSV-1 and PRV infection in porcine TG neurons that shows strong similarity to in vivo latency. IFNalpha induced a stably suppressed HSV-1 and PRV infection in TG neurons in vitro. Subsequent treatment of neurons containing stably suppressed virus with forskolin resulted in reactivation of both viruses. HSV and PRV latency in vivo is often accompanied by the expression of latency associated transcripts (LATs). Infection of TG neurons with an HSV-1 mutant expressing LacZ under control of the LAT promoter showed activation of the LAT promoter and RT-PCR analysis confirmed that both HSV-1 and PRV express LATs during latency in vitro. Conclusions/Significance These data represent a unique in vitro model of alphaherpesvirus latency and indicate that IFNalpha may be a driving force in promoting efficient latency establishment.
The association of dietary intake and supplementation of specific polyunsaturated fatty acids with inflammation and functional capacity in chronic obstructive pulmonary disease: a systematic review

Objective:This systematic review sought to identify the association of dietary intake and supplementation of specific polyunsaturated fatty acids with inflammation and function in people with chronic obstructive pulmonary disease (COPD). Data sources:We searched electronic databases including PubMed, CINAHL, MEDLINE, EMBASE, The Cochrane Library, ProQuest Dissertations and Theses, Scopus, Google Scholar, Trove, and WHO International Clinical Trials Registry Platform and reference lists of retrieved articles published prior to August 2014. Inclusion criteria:We considered observational studies that evaluated dietary intake of omega-3 (eicosapentaenoic acid, docosahexaenoic acid or &agr;-linolenic acid) and/or omega-6 fatty acids (&ggr;-linoleic acid or arachidonic acid), and experimental studies that evaluated omega-3 fatty acid supplementation (containing predominantly one or more omega-3 fatty acids) on airway and systemic inflammatory markers and/or functional capacity outcomes in people with COPD-related diagnoses. Data synthesis:Since statistical pooling was not possible, the findings were presented in narrative form including tables and figures to aid in data presentation when appropriate. Results:One 8-week randomized controlled trial conducted in 80 COPD patients in the Netherlands showed polyunsaturated fatty acid supplementation significantly improved exercise capacity compared with the control condition [between-group difference in mean peak workload was 9.7 W (2.5–17.0; P = 0.009); and mean duration was 4.3 min (0.6–7.9; P = 0.023)]. One cross-sectional study conducted in 250 COPD patients in Spain found associations of specific dietary omega-3 fatty acids with inflammation were inconsistent. Conclusions:Limited evidence provides weak support for the use of omega-3 fatty acid supplementation for reducing chronic inflammation and some support for improving functional capacity in COPD patients. There is no consistent evidence showing that low dietary intake of specific omega-3 fatty acids worsens inflammation and/or function. More evidence is required before routinely incorporating this therapy within COPD management plans.
SubtiWiki–a database for the model organism Bacillus subtilis that links pathway, interaction and expression information

Genome annotation and access to information from large-scale experimental approaches at the genome level are essential to improve our understanding of living cells and organisms. This is even more the case for model organisms that are the basis to study pathogens and technologically important species. We have generated SubtiWiki, a database for the Gram-positive model bacterium Bacillus subtilis (http://subtiwiki.uni-goettingen.de/). In addition to the established companion modules of SubtiWiki, SubtiPathways and SubtInteract, we have now created SubtiExpress, a third module, to visualize genome scale transcription data that are of unprecedented quality and density. Today, SubtiWiki is one of the most complete collections of knowledge on a living organism in one single resource.
A novel method to establish microglia‐free astrocyte cultures: Comparison of matrix metalloproteinase expression profiles in pure cultures of astrocytes and microglia

Increased matrix metalloproteinase (MMP) proteolytic activity contributes to the pathogenesis of many neuroinflammatory and neurodegenerative conditions in the CNS. To fully understand this process, it is important to define the MMP expression profile of specific cell types, including the CNS‐resident cells astrocytes and microglia. While previous studies have characterized astrocyte MMP expression by using mixed glial cultures, these results are likely complicated by the presence of contaminating microglia within these cultures. In the current study, we sought to clarify this complexity, by taking a novel approach to prepare pure astrocyte cultures entirely devoid of microglia, by promoting neural stem cell (NSC) differentiation into astrocytes. The MMP expression profile of mixed glial cultures, neurosphere‐derived astrocytes, and pure microglia was characterized by RNase protection assay. This revealed that MMP gene expression is largely cell‐type specific. Astrocytes constitutively expressed MMP‐11, MMP‐14, and MMP‐2 and showed induction of MMP‐3 in response to IL‐1β but did not respond to lipopolysaccharide (LPS). In contrast, microglia constitutively expressed high levels of MMP‐12 and showed strong induction of MMP‐9 and MMP‐14 in response to LPS. Gelatin zymography confirmed that LPS and TNF‐α induced strong expression of MMP‐9 in microglia but not astrocytes. In summary, these studies demonstrate that neurosphere‐derived astrocytes represent an attractive alternative system in which to study astrocyte behavior in vitro. Using this system, we have shown that astrocytes and microglia express distinct sets of MMP genes and that microglia, not astrocytes, are the major source of MMP‐9 in response to LPS or TNF‐α. © 2008 Wiley‐Liss, Inc.
Characterization of the Metabolically Modified Heavy Metal-Resistant Cupriavidus metallidurans Strain MSR33 Generated for Mercury Bioremediation

Background Mercury-polluted environments are often contaminated with other heavy metals. Therefore, bacteria with resistance to several heavy metals may be useful for bioremediation. Cupriavidus metallidurans CH34 is a model heavy metal-resistant bacterium, but possesses a low resistance to mercury compounds. Methodology/Principal Findings To improve inorganic and organic mercury resistance of strain CH34, the IncP-1β plasmid pTP6 that provides novel merB, merG genes and additional other mer genes was introduced into the bacterium by biparental mating. The transconjugant Cupriavidus metallidurans strain MSR33 was genetically and biochemically characterized. Strain MSR33 maintained stably the plasmid pTP6 over 70 generations under non-selective conditions. The organomercurial lyase protein MerB and the mercuric reductase MerA of strain MSR33 were synthesized in presence of Hg2+. The minimum inhibitory concentrations (mM) for strain MSR33 were: Hg2+, 0.12 and CH3Hg+, 0.08. The addition of Hg2+ (0.04 mM) at exponential phase had not an effect on the growth rate of strain MSR33. In contrast, after Hg2+ addition at exponential phase the parental strain CH34 showed an immediate cessation of cell growth. During exposure to Hg2+ no effects in the morphology of MSR33 cells were observed, whereas CH34 cells exposed to Hg2+ showed a fuzzy outer membrane. Bioremediation with strain MSR33 of two mercury-contaminated aqueous solutions was evaluated. Hg2+ (0.10 and 0.15 mM) was completely volatilized by strain MSR33 from the polluted waters in presence of thioglycolate (5 mM) after 2 h. Conclusions/Significance A broad-spectrum mercury-resistant strain MSR33 was generated by incorporation of plasmid pTP6 that was directly isolated from the environment into C. metallidurans CH34. Strain MSR33 is capable to remove mercury from polluted waters. This is the first study to use an IncP-1β plasmid directly isolated from the environment, to generate a novel and stable bacterial strain useful for mercury bioremediation.
Regional measurements of blood flow in experimental RG-2 rat gliomas.

Regional measurements of blood flow (F) were performed in transplanted intracerebral RG-2 rat gliomas using [14C]iodoantipyrine, Kety-Schmidt blood flow equations, and quantitative autoradiography. Twenty-nine intracranial tumors in ten rats were analyzed by location; 18 intraparenchymal, seven meningeal, two third-ventricular, and two fourth-ventricular tumors were studied. For all tumors, averaged mean F was 91 +/- 33 (S.D.) ml/hg/min. In all but one tumor, mean F was intermediate between normal cortex and corpus callosum values. There was moderate regional variation: averaged mean F was lower in tumor center (78 +/- 47 ml/hg/min) than in tumor periphery (93 +/- 30 ml/hg/min). Within individual tumors, F showed moderate variation which correlated to some extent with histological features; a regional F of less than 10 ml/hg/min was observed in only one tumor within an area of necrosis. F in regions of brain immediately surrounding the tumor was higher than in tumor periphery. Blood flow to RG-2 tumors seems unlikely to limit drug delivery any more than to normal brain, and the consistent levels from tumor to tumor and within individual tumors make the RG-2 model an excellent one with which to study drug delivery in experimental brain tumors.
Exploring Brand-Name Drug Mentions on Twitter for Pharmacovigilance

Twitter has been proposed by several studies as a means to track public health trends such as influenza and Ebola outbreaks by analyzing user messages in order to measure different population features and interests. In this work we analyze the number and features of mentions on Twitter of drug brand names in order to explore the potential usefulness of the automated detection of drug side effects and drug-drug interactions on social media platforms such as Twitter. This information can be used for the development of predictive models for drug toxicity, drug-drug interactions or drug resistance. Taking into account the large number of drug brand mentions that we found on Twitter, it is promising as a tool for the detection, understanding and monitoring the way people manage prescribed drugs.
Epilepsy Classification Framework Utilizing Joint Time-Frequency Signal Analysis and Processing

Time Frequency Signal Analysis and Processing (TFSAP) have been proposed in order to analyse the signal in both the time and the frequency domains. Electroencephalography (EEG) as a time-varying frequency signal is an interesting field in which Time Frequency Distribution (TFD) could be used in order to visualize the simultaneous distributions of signal energy in different physiological and pathological brain states. Particularly, epileptic signals due to their great features of seizure activity are introduced as the most attractive research field among researchers. This study outlines an investigation on two main pathologic brain states including, pre-ictal activity and seizure activity compared to normal activity. Pseudo-Wigner -Ville and Choi-William distributions are used in order to visualize the energy content of signals in these states. Different segments of brain electrical activity are analyzed using these distributions. Finally, Renyi’s entropy as an important characteristic which offer insight towards the EEG signal processing has been extracted from TFDs. The results obtained indicate that Renyi’s entropy is a high-quality discriminative feature especially in alpha and delta sub-bands of the EEG signal.
Controlling the deformation in elastic and viscoelastic structures due to temperature and moisture changes using piezoelectric actuators

We study the placement of surface-bonded piezoelectric actuators to control or minimize the deformation due to changes in temperature and moisture content in linear elastic and linear viscoelastic cantilever beams. The effect of unsteady heat and moisture diffusion phenomena on the response characteristics of the elastic and viscoelastic beams, such as displacement, stress, and strain fields, is examined based on which the magnitude of external actuating voltage to minimize deformation is predicted. This is followed by a comparative study of the field variables in cases of actuated and unactuated beams. Finite difference method is used to solve the field equations numerically. The numerical results are corroborated by comparing the results with analytical and experimental results that are available. Relatively smaller magnitude of external actuating voltage is necessary to minimize bending in the viscoelastic structure compared to the elastic structure due to the phenomenon of stress relaxation.
A Turbo Detection and Sphere-Packing-Modulation-Aided Space-Time Coding Scheme

A recently proposed space-time block-coding (STBC) signal-construction method that combines orthogonal design with sphere packing (SP), referred to here as STBC-SP, has shown useful performance improvements over Alamouti's conventional orthogonal design. In this contribution, we demonstrate that the performance of STBC-SP systems can be further improved by concatenating SP-aided modulation with channel coding and performing demapping as well as channel decoding iteratively. We also investigate the convergence behavior of this concatenated scheme with the aid of extrinsic-information-transfer charts. The proposed turbo-detected STBC-SP scheme exhibits a "turbo-cliff" at Eb/N0=2.5 dB and provides Eb/N0 gains of approximately 20.2 and 2.0 dB at a bit error rate of 10 -5 over an equivalent-throughput uncoded STBC-SP scheme and a turbo-detected quadrature phase shift keying (QPSK) modulated STBC scheme, respectively, when communicating over a correlated Rayleigh fading channel.A condensed version of this paper was presented at VTC'04 Fall, LA, USA
Functions of Fasciculation and Elongation Protein Zeta-1 (FEZ1) in the Brain

Fasciculation and elongation protein zeta-1 (FEZ1) is a mammalian ortholog of the Caenorhabditis elegans UNC-76 protein that possesses four coiled-coil domains and a nuclear localization signal. It is mainly expressed in the brain. Suppression of FEZ1 expression in cultured embryonic neurons causes deficiency of neuronal differentiation. Recently, proteomic techniques revealed that FEZ1 interacts with various intracellular partners, such as signaling, motor, and structural proteins. FEZ1 was shown to act as an antiviral factor. The findings reported so far indicate that FEZ1 is associated with neuronal development, neuropathologies, and viral infection. Based on these accumulating evidences, we herein review the biological functions of FEZ1.
Impaired Human Ovarian Follicular Fluid Complement Function in Hereditary Angioedema

We sought and detected functionally active complement in human ovarian follicular fluid obtained during the peri‐ovulatory period. All the functional complement activities tested, including total haemolytic complement, classical pathway activity, alternative pathway activity and C1 inhibitor function were present with values within the normal serum range. Active complement in follicular fluid is relevant for the function of the enzymatic multifactorial mechanism of ovulation. The presence in hereditary angioedema patients of both complement (C1 inhibitor deficiency and chronically consumed complement) and ovarian abnormalities (cystic ovaries), led us to study complement function in the follicular fluid of women of reproductive age affected with hereditary angioedema. In contrast to healthy women, hereditary angioedema patients showed dramatically reduced classical pathway activity and undetectable functional and antigenic C1 inhibitor. C4 was very low, while C3 and B were slightly reduced or within the normal serum range. This complement profile was also detected in patients' sera. Since hereditary angioedema patients often show cystic ovaries (polycystic or multifollicular), the presence of multifollicular ovaries in the two patients studied, along with complement dysfunction, may be relevant. These findings, as well as the normalisation of the ovaries found by us in hereditary angioedema patients and in the patients reported here who were undergoing danazol treatment, and the increase in C1 inhibitor and the improvement of clinical symptoms, suggest a further link between complement and ovarian function.
Phytochemical Properties and Anti-Proliferative Activity of Olea europaea L. Leaf Extracts against Pancreatic Cancer Cells

Olea europaea L. leaves are an agricultural waste product with a high concentration of phenolic compounds; especially oleuropein. Oleuropein has been shown to exhibit anti-proliferative activity against a number of cancer types. However, they have not been tested against pancreatic cancer, the fifth leading cause of cancer related death in Western countries. Therefore, water, 50% ethanol and 50% methanol extracts of Corregiola and Frantoio variety Olea europaea L. leaves were investigated for their total phenolic compounds, total flavonoids and oleuropein content, antioxidant capacity and anti-proliferative activity against MiaPaCa-2 pancreatic cancer cells. The extracts only had slight differences in their phytochemical properties, and at 100 and 200 μg/mL, all decreased the viability of the pancreatic cancer cells relative to controls. At 50 μg/mL, the water extract from the Corregiola leaves exhibited the highest anti-proliferative activity with the effect possibly due to early eluting HPLC peaks. For this reason, olive leaf extracts warrant further investigation into their potential anti-pancreatic cancer benefits.
Integrating family planning into postpartum care through modern quality improvement: experience from Afghanistan

Modern quality improvement approaches enabled hospital staff to analyze barriers and identify solutions for “how” to integrate family planning into postpartum care. Private spaces for postpartum family planning (PPFP) counseling, along with involving husbands and mothers-in-law in counseling, substantially increased the percentage of women receiving PPFP counseling and their preferred method before discharge. Self-reported pregnancy was also significantly lower up to 18 months post-discharge compared with women receiving routine services. Modern quality improvement approaches enabled hospital staff to analyze barriers and identify solutions for “how” to integrate family planning into postpartum care. Private spaces for postpartum family planning (PPFP) counseling, along with involving husbands and mothers-in-law in counseling, substantially increased the percentage of women receiving PPFP counseling and their preferred method before discharge. Self-reported pregnancy was also significantly lower up to 18 months post-discharge compared with women receiving routine services. To address low contraceptive use in Afghanistan, we supported 2 large public maternity hospitals and 3 private hospitals in Kabul to use modern quality improvement (QI) methods to integrate family planning into postpartum care. In 2012, QI teams comprising hospital staff applied root cause analysis to identify barriers to integrated postpartum family planning (PPFP) services and to develop solutions for how to integrate services. Changes made to service provision to address identified barriers included creating a private counseling space near the postpartum ward, providing PPFP counseling training and job aids to staff, and involving husbands and mothers-in-law in counseling in person or via mobile phones. After 10 months, the proportion of postpartum women who received family planning counseling before discharge in the 5 hospitals increased from 36% to 55%, and the proportion of women who received family planning counseling with their husbands rose from 18% to 90%. In addition, the proportion of postpartum women who agreed to use family planning and left the hospital with their preferred method increased from 12% to 95%. Follow-up telephone surveys with a random sample of women who had received PPFP services in the 2 public hospitals and a control group of postpartum women who had received routine hospital services found significant differences in the proportion of women with self-reported pregnancies: 3% vs. 15%, respectively, 6 months after discharge; 6% vs. 22% at 12 months; and 14% vs. 35% at 18 months (P < .001). Applying QI methods helped providers recognize and overcome barriers to integration of family planning and postpartum services by testing changes they deemed feasible.
Habitat and Species Differences in Prevalence and Intensity of Neobenedenia Melleni (Monogenea: Capsalidae) on Sympatric Caribbean Surgeonfishes (Acanthuridae)

Abstract We quantified Neobenedenia melleni from the skin of Caribbean surgeonfishes (Acanthuridae) from June through October 2005 and 2007. Prevalence, or mean intensity of infection, or both, varied significantly among the 3 species, and among sites and between years for the most heavily infected species, blue tang (Acanthurus coeruleus). Among 6 sites sampled, no more than 12% of ocean surgeonfish (Acanthurus bahianus) were infected, compared with 10 to 100% of A. coeruleus. The prevalence of infection among doctorfish (Acanthurus chirurgus), collected at only 1 of the sites, was intermediate between the other 2 species (46%). Mean intensity (range) of infection for the few infected A. bahianus was 1 (1) to 3 (1–8), compared with 1.3 (1–2) to 14.3 (1–59) for A. coeruleus, and 2.5 (1–8) for A. chirurgus. Expected abundance of N. melleni on A. coeruleus from shallow bay sites was greater than for those from non-bay sites. Higher infections on A. coeruleus may be attributable to differences in habitat use, or susceptibility to infection, or both, compared to other species. Among site and between-year differences may be associated with differences in benthic habitat, or water conditions, or both. This system seems ideal for future comparative studies on the relationship between environmental variables and parasites on Caribbean coral reefs.
Skew Dependence of Nanophotonic Devices Based on Optical Near-Field Interactions

We examine the timing dependence of nanophotonic devices based on optical excitation transfer via optical near-field interactions at the nanometer scale. We theoretically analyze the dynamic behavior of a two-input nanophotonic switch composed of three quantum dots based on a density matrix formalism while assuming arrival-time differences, or skew, between the inputs. The analysis reveals that the nanophotonic switch is resistant to a skew longer than the input signal duration, and the tolerance to skew is asymmetric with respect to the two inputs. The skew dependence is also experimentally examined based on near-field spectroscopy of InGaAs quantum dots, showing good agreement with the theory. Elucidating the dynamic properties of nanophotonics, together with the associated spatial and energy dissipation attributes at the nanometer scale, will provide critical insights for novel system architectures.