Miracle-dz/UniFAR-FTUs huggingface dataset:
Quorum Sensing Gene Regulation by LuxR/HapR Master Regulators in Vibrios

ABSTRACT The coordination of group behaviors in bacteria is accomplished via the cell-cell signaling process called quorum sensing. Vibrios have historically been models for studying bacterial communication due to the diverse and remarkable behaviors controlled by quorum sensing in these bacteria, including bioluminescence, type III and type VI secretion, biofilm formation, and motility. Here, we discuss the Vibrio LuxR/HapR family of proteins, the master global transcription factors that direct downstream gene expression in response to changes in cell density. These proteins are structurally similar to TetR transcription factors but exhibit distinct biochemical and genetic features from TetR that determine their regulatory influence on the quorum sensing gene network. We review here the gene groups regulated by LuxR/HapR and quorum sensing and explore the targets that are common and unique among Vibrio species.
Network-Coded Multiple Access with Higher-Order Modulations

This paper presents the first network-coded multiple access (NCMA) system operated on higher- order modulations beyond BPSK. NCMA allows multiple nodes to transmit simultaneously to an access point (AP) to boost throughput of wireless local area networks (WLAN): the key idea is to jointly exploit multiuser decoding (MUD) and physical-layer network coding (PNC). High- order modulations are commonly adopted in WLAN systems when the signal-to-noise ratio (SNR) is medium or high. However, direct generalization of the existing NCMA decoding algorithm, originally designed for BPSK, to higher-order modulations will lead to huge performance degradation. We find that the throughput degradation is caused by the relative phase offset between received signals from different nodes. To circumvent the throughput degradation, this paper investigates an NCMA system with multiple receive antennas at the AP, referred to as MIMO-NCMA. We have implemented MIMO-NCMA on software-defined radios. Our experimental results show that, at SNR of 10dB, the throughput of MIMO-NCMA outperforms single-antenna NCMA and conventional distributed MIMO-MUD, respectively. We believe that MIMO-NCMA throughput can be further improved with modulations beyond QPSK (e.g., 64-QAM).
Time course and robustness of ERP object and face differences Centre for Cognitive Neuroimaging

Conflicting results have been reported about the earliest “true” ERP differences related to face processing, with the bulk of the literature focusing on the signal in the first 200 ms after stimulus onset. Part of the discrepancy might be explained by uncontrolled low-level differences between images used to assess the timing of face processing. In the present experiment, we used a set of faces, houses, and noise textures with identical amplitude spectra to equate energy in each spatial frequency band. The timing of face processing was evaluated using face–house and face–noise contrasts, as well as upright-inverted stimulus contrasts. ERP differences were evaluated systematically at all electrodes, across subjects, and in each subject individually, using trimmed means and bootstrap tests. Different strategies were employed to assess the robustness of ERP differential activities in individual subjects and group comparisons. We report results showing that the most conspicuous and reliable effects were systematically observed in the N170 latency range, starting at about 130–150 ms after stimulus onset.
Biogeosciences Coupling of heterotrophic bacteria to phytoplankton bloom development at different p CO 2 levels : a mesocosm study

The predicted rise in anthropogenic CO 2 emissions will increase CO2 concentrations and decrease seawater pH in the upper ocean. Recent studies have revealed effects of pCO2 induced changes in seawater chemistry on a variety of marine life forms, in particular calcifying organisms. To test whether the predicted increase in pCO2 will directly or indirectly (via changes in phytoplankton dynamics) affect abundance, activities, and community composition of heterotrophic bacteria during phytoplankton bloom development, we have aerated mesocosms with CO2 to obtain triplicates with three different partial pressures of CO 2 (pCO2): 350μatm (1×CO2), 700μatm (2×CO2) and 1050μatm (3×CO2). The development of a phytoplankton bloom was initiated by the addition of nitrate and phosphate. In accordance to an elevated carbon to nitrogen drawdown at increasing pCO2, bacterial production (BPP) of free-living and attached bacteria as well as cellspecific BPP (csBPP) of attached bacteria were related to the C:N ratio of suspended matter. These relationships significantly differed among treatments. However, bacterial abundance and activities were not statistically different among treatments. Solely community structure of free-living bacteria changed withpCO2 whereas that of attached bacteria seemed to be independent of pCO2 but tightly coupled to phytoplankton bloom development. Our findings imply that changes inpCO2, although reflected by changes in commuCorrespondence to: H. -P. Grossart (hgrossart@igb-berlin.de) nity structure of free-living bacteria, do not directly affect bacterial activity. Furthermore, bacterial activity and dynamics of heterotrophic bacteria, especially of attached bacteria, were tightly correlated to phytoplankton development and, hence, may also potentially depend on changes in pCO2.
Rutting analysis of 100 mm diameter polypropylene modified asphalt specimens using gyratory and Marshall compactors

Compaction technique used in Marshall design does not model the process of actual rolling procedures on site exactly. Carrying out laboratory compaction of dense bituminous mixtures with Superpave gyratory compactors is a more realistic way of simulating actual compaction. In this study, mechanical differences of reference and polypropylene modified asphalt mixtures were compared using Superpave gyratory and Marshall compaction methods by carrying out repeated creep tests utilising universal testing machine. In addition, there is no standard Superpave design procedure for 100 mm diameter samples till date. The other purpose of this study is to propose new standards for the compaction and testing procedures of these 100 mm specimens. Indeed, extensive studies have shown that the design gyration number should be 40 for reference and 33 for polypropylene modified specimens under medium traffic conditions for the similar and specific type of aggregate sources, bitumen, aggregate gradation, mix proportioning, modification technique and laboratory conditions. Moreover, it was shown that, the asphalt samples produced by Superpave gyratory compactor were much resistant to destructive rutting effects than the asphalt specimens prepared by Marshall design.
An interlaboratory study of TEX86 and BIT analysis of sediments, extracts, and standard mixtures

Two commonly used proxies based on the distribution of glycerol dialkyl glycerol tetraethers (GDGTs) are the TEX86 (TetraEther indeX of 86 carbon atoms) paleothermometer for sea surface temperature reconstructions and the BIT (Branched Isoprenoid Tetraether) index for reconstructing soil organic matter input to the ocean. An initial round‐robin study of two sediment extracts, in which 15 laboratories participated, showed relatively consistent TEX86 values (reproducibility ±3–4°C when translated to temperature) but a large spread in BIT measurements (reproducibility ±0.41 on a scale of 0–1). Here we report results of a second round‐robin study with 35 laboratories in which three sediments, one sediment extract, and two mixtures of pure, isolated GDGTs were analyzed. The results for TEX86 and BIT index showed improvement compared to the previous round‐robin study. The reproducibility, indicating interlaboratory variation, of TEX86 values ranged from 1.3 to 3.0°C when translated to temperature. These results are similar to those of other temperature proxies used in paleoceanography. Comparison of the results obtained from one of the three sediments showed that TEX86 and BIT indices are not significantly affected by interlaboratory differences in sediment extraction techniques. BIT values of the sediments and extracts were at the extremes of the index with values close to 0 or 1, and showed good reproducibility (ranging from 0.013 to 0.042). However, the measured BIT values for the two GDGT mixtures, with known molar ratios of crenarchaeol and branched GDGTs, had intermediate BIT values and showed poor reproducibility and a large overestimation of the “true” (i.e., molar‐based) BIT index. The latter is likely due to, among other factors, the higher mass spectrometric response of branched GDGTs compared to crenarchaeol, which also varies among mass spectrometers. Correction for this different mass spectrometric response showed a considerable improvement in the reproducibility of BIT index measurements among laboratories, as well as a substantially improved estimation of molar‐based BIT values. This suggests that standard mixtures should be used in order to obtain consistent, and molar‐based, BIT values.
The effectiveness of realistic replication strategies on quality of availability for peer-to-peer systems

We take an availability-centric view on quality of service (QoS) and propose a model and mechanisms for studying the effectiveness of realistic replication schemes on availability QoS for peer-to-peer (P2P) systems. We especially tackle the dynamic replica placement (RP) problem where our focus is on choosing dynamically the number and location of replicas while (1) meeting different availability QoS requirements for all individual peers and (2) taking the intermittent connectivity of peers explicitly into account. We model P2P systems as a dynamic stochastic graph in which the nodes go up and down depending on their assigned up probability. We develop some simple heuristic algorithms for solving the RP problem, which are fully distributed and adaptive. Through an event-driven simulation study we compare and evaluate the achieved availability QoS of the proposed RP algorithms. Simulation results show that (1) even simple heuristics can achieve reasonably high availability QoS, and (2) satisfying availability QoS requires more replicas than for only increasing the hit rate.
Retinal Never Fiber Layer Thickness In Chronic Renal Failure: Analysis By Optical Coherence Tomography

Purpose: To analyze the retinal nerve fiber layer thickness (RNFL) in CKD patients by means of optical coherence tomography, ascertaining mean overall RNFL and mean RNFL in the nasal, temporal, superior, and inferior quadrants and comparing these measurements to those obtained from a control group. Methods: This was a prospective, analytical, cross-sectional case-control study. The study sample comprised 22 eyes from 11 patients and 33 eyes from 17 patients in the case and control groups respectively. RNFLT was measured with a model 3000 OCT unit (Stratus OCT-3â„¢, Carl Zeiss Meditec Inc., Dublin, CA). The fast RNFL protocol was used, which consists of three consecutive 3.4-mm-diameter circular scans centered on the optic nerve. Measured parameters included overall mean RNFL and mean RNFL at the temporal (316â€“45Â°), superior (46â€“135Â°), nasal (136â€“225Â°), and inferior (226â€“315Â°) quadrants. The Mann-Whitney U was employed to assess possible between-group differences in mean overall RNFL and RNFL at the superior, temporal, nasal, and inferior quadrants. The null hypothesis was rejected when p-values were smaller than the set significance level of <0.05. Results: Mean RNFL overall and at the superior, nasal, and inferior quadrants was greater in the control group, and that no significant between-group differences were detected in RNFL at the temporal quadrant. Conclusion: Mean retinal nerve fiber thickness was significantly lower in the group of patients with CRF than in the control group. Ischemia resulting from uremia may explain the overestimation of cases of glaucomatous optic neuropathy. Keywords: Chronic Kidney Failure, Uremia, Optical Coherence Tomography, Retina
Combined erythropoietin and iron therapy for anaemic patients undergoing transcatheter aortic valve implantation: the EPICURE randomised clinical trial.

AIMS The aim of this study was to evaluate, in anaemic patients, the efficacy of erythropoietin (EPO) in reducing red cell (RC) transfusion rates post TAVI. METHODS AND RESULTS This was a randomised double-blind trial. Patients with severe symptomatic aortic stenosis and concomitant anaemia with an indication for TAVI were randomised (1:1) to receive two weight-based doses of EPO (darbepoetin alfa)+iron or placebo at days 10 (±4 days) and 1 (±1 day) pre TAVI. The primary outcome was the rate of RC transfusions at 30 days. A total of 100 patients (mean age 81±7 years, male 49%) were included: 48 patients received EPO (+iron) and 52 patients received placebo. Baseline characteristics and procedural findings were well balanced between groups except for baseline haemoglobin levels, which were lower in those patients receiving EPO (10.7±1.2 vs. 11.3±1.1 g/dl, p=0.01). The rate of 30-day RC transfusion was similar in both groups (27.1 vs. 25.0% in the EPO and placebo groups, respectively; adjusted odds ratio 1.05, 95% CI: 0.42-2.64, p=0.92), and no differences were observed in the number of RC units per transfused patient (1 [1-3] vs. 2 [1-2] in the EPO and placebo groups, respectively, adjusted p=0.99). Rates of 30-day mortality, stroke, new-onset atrial fibrillation, acute kidney injury, and troponin peak were also similar between groups (p>0.20 for all). CONCLUSIONS EPO (+iron) administration failed to reduce RC transfusion rates or the per-patient number of transfusion units in anaemic patients undergoing TAVI.
MYC and hsa-miRNA-423-5p as biomarkers in nasopharyngeal carcinoma revealed by miRNA-mRNA-pathway network integrated analysis

The present study was performed to identify the dysregulated microRNAs (miRNAs/miRs) and mRNAs, and enriched pathways involved in nasopharyngeal carcinoma (NPC) through the establishment of an miRNA-mRNA-pathways network. mRNA and miRNA expression profiles were collected from the European Molecular Biology Laboratory-European Bioinformatics Institute. Differentially expressed genes and differentially expressed miRNA were selectively screened using the metaDE package. Following prediction of the risk genes and pathway pairs involved in NPC, an miRNA-mRNA-pathway network was constructed by merging the miRNA-mRNA pairs, the mRNA-pathway pairs and the mRNA-mRNA pairs. The miRNA and mRNA biomarkers, as well as the functional pathway pairs, were identified in the network analysis, based on the topological properties of nodes in the network. Additionally, 10-fold cross-validation was performed to evaluate the performance of the selected risk genes and their corresponding miRNA in NPC by calculating the area under the curve (AUC). In total, 99 upregulated and 841 downregulated genes, and 192 upregulated and 26 downregulated miRNAs were identified. The miRNA-mRNA-pathway network was established using 403 miRNA-mRNA pairs, including 40 miRNAs and 302 risk genes, as well as 22 prominent pathway pairs. Network analysis demonstrated that v-myc avian myelocytomatosis viral oncogene homolog (MYC) and hsa-miR-423-5p were the mRNA and miRNA signatures for NPC, respectively. The AUC of these biomarkers for NPC was 0.7568 and 0.7798, respectively. Additionally, the focal adhesion pair pathway in cancer was identified to be associated with NPC. MYC and hsa-miR-423-5p have been identified to be critical biomarkers in NPC as revealed by miRNA-mRNA-pathway network integrated analysis, suggesting a direction for further research into the diagnosis and treatment of NPC.
CSOLNP: Numerical Optimization Engine for Solving Non-linearly Constrained Problems

We introduce the optimizer CSOLNP, which is a C++ implementation of the R package RSOLNP (Ghalanos & Theussl, 2012, Rsolnp: General non-linear optimization using augmented Lagrange multiplier method. R package version, 1) alongside some improvements. CSOLNP solves non-linearly constrained optimization problems using a Sequential Quadratic Programming (SQP) algorithm. CSOLNP, NPSOL (a very popular implementation of SQP method in FORTRAN (Gill et al., 1986, User's guide for NPSOL (version 4.0): A Fortran package for nonlinear programming (No. SOL-86-2). Stanford, CA: Stanford University Systems Optimization Laboratory), and SLSQP (another SQP implementation available as part of the NLOPT collection (Johnson, 2014, The NLopt nonlinear-optimization package. Retrieved from http://ab-initio.mit.edu/nlopt)) are three optimizers available in OpenMx package. These optimizers are compared in terms of runtimes, final objective values, and memory consumption. A Monte Carlo analysis of the performance of the optimizers was performed on ordinal and continuous models with five variables and one or two factors. While the relative difference between the objective values is less than 0.5%, CSOLNP is in general faster than NPSOL and SLSQP for ordinal analysis. As for continuous data, none of the optimizers performs consistently faster than the others. In terms of memory usage, we used Valgrind's heap profiler tool, called Massif, on one-factor threshold models. CSOLNP and NPSOL consume the same amount of memory, while SLSQP uses 71 MB more memory than the other two optimizers.
Simple Preoperative Patient‐Reported Factors Predict Adverse Outcome After Elective Cranial Neurosurgery

BACKGROUND Patient‐reported preoperative factors hold promise in improving the prediction of postoperative adverse events, but they have been poorly studied. OBJECTIVE To study the role of patient‐reported factors in the preoperative risk stratification of elective craniotomy patients. METHODS A prospective, unselected cohort of 322 adult patients underwent elective craniotomy in Helsinki, Finland. We preoperatively recorded the American Society of Anesthesiologists (ASA) score, Helsinki ASA score, and 3 questionnaire‐based patient‐reported factors including overall health status, ability to climb 2 flights of stairs, and cognitive function (Test Your Memory test). Outcome measures comprised in‐hospital major and overall morbidity. Receiver‐operating characteristic curves served to calculate area under the curve (AUC) values for a composite score of patient‐reported factors and both ASA scores with regard to outcomes. RESULTS In‐hospital major and overall morbidity rate was 15.2%. Only preoperatively diminished cognitive function remained a significant predictor of major morbidity after multivariable logistic regression analysis (P < .001, odds ratio 1.1, confidence interval 1.0‐1.1). A composite score of our 3 patient‐reported factors had a higher AUC (0.675) for major morbidity than original ASA score (0.543) or Helsinki ASA score (0.572). In elderly patients, the composite score had an AUC of 0.726 for major morbidity. CONCLUSION Preoperative patient‐reported factors had higher sensitivity for detecting major morbidity compared to the ASA scores in this study. Particularly, the simple composite score seems to predict adverse outcomes in elective cranial surgery surprisingly well, especially in the elderly. These results are interesting and worth confirming in other centers.
Structures of the prefusion form of measles virus fusion protein in complex with inhibitors

Significance Measles remains a major cause of childhood morbidity and mortality worldwide, and no licensed therapeutic agents are currently available. Measles virus (MeV) sometimes invades the central nervous system (CNS), causing neurodegenerative diseases several months/years after acute infection. Recently, MeV-induced encephalitis among human immunodeficiency virus (HIV)-infected children has become a great concern in high–HIV-prevalence countries. The tropism of MeV for the CNS is mediated by hyperfusogenic mutations in the MeV fusion (F) protein. Here we show the crystal structures of MeV-F alone and bound to inhibitors. The structures and accompanying cell-based fusion assays with inhibitors provide insight into the molecular mechanism for the inhibition of MeV-mediated fusion, which would help us conquer MeV-induced neurodegenerative diseases. Measles virus (MeV), a major cause of childhood morbidity and mortality, is highly immunotropic and one of the most contagious pathogens. MeV may establish, albeit rarely, persistent infection in the central nervous system, causing fatal and intractable neurodegenerative diseases such as subacute sclerosing panencephalitis and measles inclusion body encephalitis. Recent studies have suggested that particular substitutions in the MeV fusion (F) protein are involved in the pathogenesis by destabilizing the F protein and endowing it with hyperfusogenicity. Here we show the crystal structures of the prefusion MeV-F alone and in complex with the small compound AS-48 or a fusion inhibitor peptide. Notably, these independently developed inhibitors bind the same hydrophobic pocket located at the region connecting the head and stalk of MeV-F, where a number of substitutions in MeV isolates from neurodegenerative diseases are also localized. Since these inhibitors could suppress membrane fusion mediated by most of the hyperfusogenic MeV-F mutants, the development of more effective inhibitors based on the structures may be warranted to treat MeV-induced neurodegenerative diseases.
Diagnostic performance of cardiac imaging methods to diagnose ischaemia-causing coronary artery disease when directly compared with fractional flow reserve as a reference standard: a meta-analysis

Aims The aim of this study was to determine the diagnostic performance of single-photon emission computed tomography (SPECT), stress echocardiography (SE), invasive coronary angiography (ICA), coronary computed tomography angiography (CCTA), fractional flow reserve (FFR) derived from CCTA (FFRCT), and cardiac magnetic resonance (MRI) imaging when directly compared with an FFR reference standard. Method and results PubMed and Web of Knowledge were searched for investigations published between 1 January 2002 and 28 February 2015. Studies performing FFR in at least 75% of coronary vessels for the diagnosis of ischaemic coronary artery disease (CAD) were included. Twenty-three articles reporting on 3788 patients and 5323 vessels were identified. Meta-analysis was performed for pooled sensitivity, specificity, likelihood ratios (LR), diagnostic odds ratio, and summary receiver operating characteristic curves. In contrast to ICA, CCTA, and FFRCT reports, studies evaluating SPECT, SE, and MRI were largely retrospective, single-centre and with generally smaller study samples. On a per-patient basis, the sensitivity of CCTA (90%, 95% CI: 86–93), FFRCT (90%, 95% CI: 85–93), and MRI (90%, 95% CI: 75–97) were higher than for SPECT (70%, 95% CI: 59–80), SE (77%, 95% CI: 61–88), and ICA (69%, 95% CI: 65–75). The highest and lowest per-patient specificity was observed for MRI (94%, 95% CI: 79–99) and for CCTA (39%, 95% CI: 34–44), respectively. Similar specificities were noted for SPECT (78%, 95% CI: 68–87), SE (75%, 95% CI: 63–85), FFRCT (71%, 95% CI: 65–75%), and ICA (67%, 95% CI: 63–71). On a per-vessel basis, the highest sensitivity was for CCTA (pooled sensitivity, 91%: 88–93), MRI (91%: 84–95), and FFRCT (83%, 78–87), with lower sensitivities for ICA (71%, 69–74), and SPECT (57%: 49–64). Per-vessel specificity was highest for MRI (85%, 79–89), FFRCT (78%: 78–81), and SPECT (75%: 69–80), whereas ICA (66%: 64–68) and CCTA (58%: 55–61) yielded a lower specificity. Conclusions In this meta-analysis comparing cardiac imaging methods directly to FFR, MRI had the highest performance for diagnosis of ischaemia-causing CAD, with lower performance for SPECT and SE. Anatomic methods of CCTA and ICA yielded lower specificity, with functional assessment of coronary atherosclerosis by SE, SPECT, and FFRCT improving accuracy.