Miracle-dz/UniFAR-FTUs huggingface dataset:
Defective Tobamovirus Movement Protein Lacking Wild-Type Phosphorylation Sites Can Be Complemented by Substitutions Found in Revertants

ABSTRACT We reported previously that the movement protein (MP) of tomato mosaic tobamovirus is phosphorylated, and we proposed that MP phosphorylation is important for viral pathogenesis. Experimental data indicated that phosphorylation enhances the stability of MP in vivo and enables the protein to assume the correct intracellular location to perform its function. A mutant virus designated 37A238A was constructed; this virus lacked two serine residues within the MP, which prevented its phosphorylation. In the present study, we inoculated plants with the 37A238A mutant, and as expected, it was unable to produce local lesions on the leaves. However, after an extended period, we found that lesions did occur, which were due to revertant viruses. Several revertants were isolated, and the genetic changes in their MPs were examined together with any changes in their in vivo characteristics. We found that reversion to virulence was associated first with increased MP stability in infected cells and second with a shift in MP intracellular localization over time. In one case, the revertant MP was not phosphorylated in vivo, but it was functional.
MATRIX-ASSISTED LASER DESORPTION IONIZATION-TIME OF FLIGHT MASS SPECTROMETRY FOR THE IDENTIFICATION OF BACTERIA AND YEASTS IN A CLINICAL MICROBIOLOGICAL LABORATORY: A REVIEW

Abstract Recently, MALDI-TOF MS devices designed for use in clinical laboratories have been commercially introduced in various large centres worldwide. All published studies conclude that MALDI-TOF MS can be implemented easily for routine identification of bacteria and yeasts in a clinical microbiological laboratory. Although all data show that MALDI-TOF MS correctly identifies the great majority of isolates processed routinely, it cannot yet identify every such isolate. Until today, MALDI-TOF MS is inappropriate for the identification of Shigella species, pneumococci and viridans streptococci. Database upgrades and sample enrichment are essential elements to refine the MALDI-TOF MS technique, allowing the method to increase its power. For the identification of a significant proportion of yeasts, an extraction method prior to analysis in the mass spectrometer is mandatory to obtain appropriate spectra. Because of the low marginal costs, and the extreme speed of MALDI-TOF MS, the technique can improve laboratory efficiency when used early in identification protocols. Lengthier, more labour-intensive, and costlier techniques can be reserved for the minority of isolates not identified with high confidence by MALDI-TOF MS. MALDI-TOF MS also has the potential to directly identify pathogens in biological fluids, such as urine samples and blood cultures. For this application however, further well-designed prospective studies are warranted. The potential for identification at the serotype or strain level, and antibiotic resistance profiling within minutes make MALDI-TOF mass spectrometry an ongoing revolution in the clinical microbiology laboratory.
Priming of the Neutrophil Respiratory Burst Involves p38 Mitogen-activated Protein Kinase-dependent Exocytosis of Flavocytochrome b 558-containing Granules*

The respiratory burst of human neutrophils is primed by a number of pro-inflammatory stimuli, including tumor necrosis factor-α (TNFα) and lipopolysaccharide (LPS); however, the mechanism of priming remains unknown. LPS has been shown previously to increase membrane expression of flavocytochromeb 558, a component of the NADPH oxidase. This study shows that TNFα also increases membrane expression of flavocytochrome b 558. Mitogen-activated protein kinase (MAPK) modules have been implicated in the action of priming agents. Pharmacologic inhibitors of MAPKs, SB203580 and PD098059, revealed that priming of the respiratory burst and up-regulation of flavocytochrome b 558 are dependent on p38 MAPK but not on extracellular-signal regulated kinase (ERK). TNFα and LPS primed respiratory burst activity and increased membrane expression of CD35 and CD66b, specific markers of secretory vesicles and specific granules that contain flavocytochrome b 558, with similar time courses and concentration dependences. These processes also required p38 MAPK but were independent of ERK. TNFα failed to prime respiratory burst activity or to increase membrane CD35 expression in enucleated neutrophil cytoplasts. These data suggest that one mechanism by which TNFα and LPS prime neutrophil respiratory burst activity is by increasing membrane expression of flavocytochromeb 558 through exocytosis of intracellular granules in a process regulated by p38 MAPK.
The role of extracellular signal‐regulated protein kinase in transcriptional regulation of the hypoxia marker carbonic anhydrase IX

In the present study, we investigated the role of the extracellular signal‐regulated protein kinase (ERK) in regulation of the hypoxia marker, carbonic anhydrase IX (CAIX). U0126, a specific inhibitor of MEK1/2, downregulated CAIX expression induced by true hypoxia and cell density. CA9 promoter activity was similarly affected. Mapping of the U0126 effect revealed that both critical elements within the CA9 promoter, the hypoxia response element and the juxtaposed SP1‐binding PR1, were inhibited. This confirmed that ERK signaling modulates CA9 promoter activity via its effects on hypoxia inducible factor‐1 (HIF‐1) and SP1. Further analysis of the U0126 effect on HIF‐1‐dependent transcription in MCF‐7 cells identified p300, a transcriptional co‐activator of HIF‐1, as the target of ERK. Constitutively increased ERK activity in isogenic fibrosarcoma cell lines did not cause increased cell density‐dependent CAIX expression/CA9 promoter activity. In HeLa cells, an inverse correlation between cell density‐induced CAIX expression and ERK activation was observed: sparse cultures did not express CAIX and displayed high ERK activation, whereas CAIX expression in dense cultures was associated with low ERK activation. Collectively, our data do not support any quantitative relationship between ERK activation and CAIX expression. Thus, although ERK signaling is required for optimal CAIX expression, our data are consistent with a model in which constitutive basal ERK activity plays an auxiliary role in CA9 promoter transactivation by modulating activity of the transcription factor SP1 and the transcriptional co‐activator p300. © 2005 Wiley‐Liss, Inc.
Factions, Local Accountability, and Long-Term Development: County-Level Evidence from a Chinese Province

This paper investigates, both theoretically and empirically, the role of factional competition and local accountability in explaining the enormous but puzzling county-level variations in development performance in Fujian province of China. When the Communist armies took over Fujian from the Nationalist control circa 1949, Communist cadres from two different army factions were assigned as county leaders. For decades the Fujian Provincial Standing Committee of the Communist Party had been dominated by members from one particular faction, which we refer as the strong faction. Counties also differed in whether there was local guerrilla presence prior to the Communist takeover. The model predicts that county leaders from the strong faction were less likely to pursue policies friendly to local development, because their political survival relied more on their loyalty to the provincial leader than on the grassroots support from local residents. In contrast, the political survival of county leaders from the weak faction was based more on local grassroots support, which could be best secured if these leaders focused on local development. In addition, the local guerrilla presence in the county further improved the development performance either because it intensified local accountability of the county leader, or because it better facilitated the provision of local public goods beneficial to development. The paper finds consistent and robust evidence supporting these assumptions; being affiliated with weak factions and having local accountability are both associated with sizable long-term benefits in terms of growth, education, private-sector development, and survival in the Great Famine. The paper also finds that being affiliated with the strong faction and adopting pro-local policies are associated with higher likelihood of political survival. The empirical findings here suggest that factional competition contributes to efficiency in non-democratic countries, and that local accountability is a key ingredient for balanced development.
Ovariectomy vs. Hypofunction: Their Effects on Rat Mandibular Bone

Previous studies have suggested that the mandible may be more influenced by mechanical loading than by circulating hormone levels. We tested the hypothesis that hypofunction has a greater influence than ovariectomy on mandibular bone. Two-month-old rats were ovariectomized (OVX) or had maxillary molars removed from one side to induce unilateral mandibular hypofunction. Control animals remained untreated. After 5 months, animals were killed, and bones were assessed by micro-tomography (μCT), quantitative back-scattered electron analysis in an SEM (qBSE-SEM), and light microscopy. Mineralization density was reduced in calvarial, maxillary, and mandibular alveolar bone following OVX, yet was increased in lingual mandibular alveolar bone of the hypo-function animals compared with controls. OVX caused a reduction in osteocyte density in alveolar bone, while hypofunction showed an increase compared with controls. Hypofunction led to alveolar bone becoming more highly mineralized and more cellular, while ovariectomy caused a reduction in both mineralization density and osteocyte numbers.
Effect of Systolic Cardiac Function on Passive Leg Raising for Predicting Fluid Responsiveness: A Prospective Observational Study

Background: Passive leg raising (PLR) represents a “self-volume expansion (VE)” that could predict fluid responsiveness, but the influence of systolic cardiac function on PLR has seldom been reported. This study aimed to investigate whether systolic cardiac function, estimated by the global ejection fraction (GEF) from transpulmonary-thermodilution, could influence the diagnostic value of PLR. Methods: This prospective, observational study was carried out in the surgical Intensive Care Unit of the First Affiliated Hospital of Sun Yat-sen University from December 2013 to July 2015. Seventy-eight mechanically ventilated patients considered for VE were prospectively included and divided into a low-GEF (<20%) and a near-normal-GEF (≥20%) group. Within each group, baseline hemodynamics, after PLR and after VE (250 ml 5% albumin over 30 min), were recorded. PLR-induced hemodynamic changes (PLR-&Dgr;) were calculated. Fluid responders were defined by a 15% increase of stroke volume (SV) after VE. Results: Twenty-five out of 38 patients were responders in the GEF <20% group, compared to 26 out of 40 patients in the GEF ≥20% group. The thresholds of PLR-&Dgr;SV and PLR-&Dgr; cardiac output (PLR-&Dgr;CO) for predicting fluid responsiveness were higher in the GEF ≥20% group than in the GEF <20% group (&Dgr;SV: 12% vs. 8%; &Dgr;CO: 7% vs. 6%), with increased sensitivity (&Dgr;SV: 92% vs. 92%; &Dgr;CO: 81% vs. 80%) and specificity (&Dgr;SV: 86% vs. 70%; &Dgr;CO: 86% vs. 77%), respectively. PLR-&Dgr; heart rate could predict fluid responsiveness in the GEF ≥20% group with a threshold value of −5% (sensitivity 65%, specificity 93%) but could not in the GEF <20% group. The pressure index changes were poor predictors. Conclusions: In the critically ill patients on mechanical ventilation, the diagnostic value of PLR for predicting fluid responsiveness depends on cardiac systolic function. Thus, cardiac systolic function must be considered when using PLR. Trial Registration: Chinese Clinical Trial Register, ChiCTR-OCH-13004027; http://www.chictr. org.cn/showproj.aspx? proj=5540.
Selective Activation of p38 Mitogen-activated Protein (MAP) Kinase Isoforms by the MAP Kinase Kinases MKK3 and MKK6*

The cellular response to treatment with proinflammatory cytokines or exposure to environmental stress is mediated, in part, by the p38 group of mitogen-activated protein (MAP) kinases. We report the molecular cloning of a novel isoform of p38 MAP kinase, p38β2. This p38 MAP kinase, like p38α, is inhibited by the pyridinyl imidazole drug SB203580. The p38 MAP kinase kinase MKK6 is identified as a common activator of p38α, p38β2, and p38γ MAP kinase isoforms, while MKK3 activates only p38α and p38γ MAP kinase isoforms. The MKK3 and MKK6 signal transduction pathways are therefore coupled to distinct, but overlapping, groups of p38 MAP kinases.
A survey on Data Analytic Platforms for Internet of Things

Due to wide availability of programmable, off-the-shelf sensors and advancements in Radio Frequency Identification Technologies as well as Wireless Sensor Networks, the Internet of Things (IoT) is making our lives smarter than ever before. The abundant growth in sensors triggers the spontaneous generation of IoT data at colossal scale which is referred to as big data. Processing, analyzing this data in a secure, timely and efficient manner has become the sine qua non for the successful working of IoT paradigm and thereby emanating the need of Data Analytic Platforms in IoT based smart systems. The data analytic platform performs analytics over massive data and provides crucial baseline for decision and planning in the IoT sphere. The fully matured cloud computing technology best fit the scenario of IoT and big data analytics offering powerful resources to carry out analytical and management tasks. The paper focuses on various big data analytic platforms for IoT in cloud computing domain.
Multi-parameter actuation of a neutrally stable shell: a flexible gear-less motor

We have designed and tested experimentally a morphing structure consisting of a neutrally stable thin cylindrical shell driven by a multi-parameter piezoelectric actuation. The shell is obtained by plastically deforming an initially flat copper disc, so as to induce large isotropic and almost uniform inelastic curvatures. Following the plastic deformation, in a perfectly isotropic system, the shell is theoretically neutrally stable, having a continuous set of stable cylindrical shapes corresponding to the rotation of the axis of maximal curvature. Small imperfections render the actual structure bistable, giving preferred orientations. A three-parameter piezoelectric actuation, exerted through micro-fibre-composite actuators, allows us to add a small perturbation to the plastic inelastic curvature and to control the direction of maximal curvature. This actuation law is designed through a geometrical analogy based on a fully nonlinear inextensible uniform-curvature shell model. We report on the fabrication, identification and experimental testing of a prototype and demonstrate the effectiveness of the piezoelectric actuators in controlling its shape. The resulting motion is an apparent rotation of the shell, controlled by the voltages as in a ‘gear-less motor’, which is, in reality, a precession of the axis of principal curvature.
Induction of axon growth arrest without growth cone collapse through the N‐terminal region of four‐transmembrane glycoprotein M6a

During development, axons elongate vigorously, carefully controlling their speed, to connect with their targets. In general, rapid axon growth is correlated with active growth cones driven by dynamic actin filaments. For example, when the actin‐driven tip is collapsed by repulsive guidance molecules, axon growth is severely impaired. In this study, we report that axon growth can be suppressed, without destroying the actin‐based structure or motility of the growth cones, when antibodies bind to the four‐transmembrane glycoprotein M6a concentrated on the growth cone edge. Surprisingly, M6a‐deficient axons grow actively but are not growth suppressed by the antibodies, arguing for an inductive action of the antibody. The binding of antibodies clusters and displaces M6a protein from the growth cone edge membrane, suggesting that the spatial rearrangement of this protein might underlie the unique growth cone behavior triggered by the antibodies. Molecular dissection of M6a suggested involvement for the N‐terminal intracellular domain in this antibody‐induced growth cone arrest. © 2011 Wiley Periodicals, Inc. Develop Neurobiol 71: 733–746, 2011
GM1 stabilizes expression of NMDA receptor subunit 1 in the ischemic hemisphere of MCAo/reperfusion rat.

OBJECTIVE To determine the protective effect of monosialoganglionside (GM1) and evaluate the influence of GM1 on expression of N-methyl-D-aspartate receptor subunit 1 (NMDAR1) in Sprague-Dawley (SD) rats with focal cerebral ischemia-reperfusion (I/R). METHODS Left middle cerebral artery (MCA) was occluded by an intraluminal suture for 1 h and the brain was reperfused for 72 h in SD rats when infarct volume was measured, GM1 (10 mg/kg) was given ip (intraperitoneally) at 5 min (group A), 1 h (group B) and 2 h (group C) after MCA occlusion (MCAo). Expression of NMDAR1 was detected by Western blot at various time after reperfusion (4 h, 6 h, 24 h, 48 h and 72 h) in ischemic hemispheres of the rats with or without GM1 administered. RESULTS (1) Adjusted relative infarct volumes of groups A and B were significantly smaller than that of group C and the control group (P<0.01 and P<0.05, respectively). (2) Expression level of NMDAR1 was temporally high at 6 h after reperfusion, and dipped below the normal level at 72 h after reperfusion. GM1 at 5 min after MCAo significantly suppressed the expression of NMDAR1 at 6 h after reperfusion (P<0.05 vs the control). At 72 h after reperfusion, the NMDAR1 expression level of rats treated with GM1 administered (at 5 min or 2 h after MCAo) was significantly higher than that of the control (P<0.05). CONCLUSION GM1 can time-dependently reduce infarct volume in rats with focal cerebral I/R partly through stabilizing the expression of NMDAR1.
Chronic high glucose induced INS‐1β cell mitochondrial dysfunction: A comparative mitochondrial proteome with SILAC

As glucose‐stimulated insulin secretion of pancreatic β cell is triggered and promoted by the metabolic messengers derived from mitochondria, mitochondria take a central stage in the normal function of β cells. β cells in diabetics were chronically exposed to hyperglycemia stimulation, which have been reported to exert deleterious effects on β‐cell mitochondria. However, the mechanism of the toxic effects of hyperglycemia on β‐cell mitochondria was not clear. In this study, we characterized the biological functional changes of rat INS‐1β cells and their mitochondria with chronic exposure to hyperglycemia and created a research model of chronic hyperglycemia‐induced dysfunctional β cells with damaged mitochondria. Then, SILAC‐based quantitative proteomic approach was used to compare the mitochondrial protein expression from high glucose treated INS‐1β cells and control cells. The expression of some mitochondrial proteins was found with significant changes. Functional classification revealed most of these proteins were related with oxidative phosphorylation, mitochondrial protein biosynthesis, substances metabolism, transport, and cell death. These results presented some useful information about the effect of glucotoxicity on the β‐cell mitochondria.
Privacy-preserving recommendations in context-aware mobile environments

Purpose This paper aims to address privacy concerns that arise from the use of mobile recommender systems when processing contextual information relating to the user. Mobile recommender systems aim to solve the information overload problem by recommending products or services to users of Web services on mobile devices, such as smartphones or tablets, at any given point in time and in any possible location. They use recommendation methods, such as collaborative filtering or content-based filtering and use a considerable amount of contextual information to provide relevant recommendations. However, because of privacy concerns, users are not willing to provide the required personal information that would allow their views to be recorded and make these systems usable. Design/methodology/approach This work is focused on user privacy by providing a method for context privacy-preservation and privacy protection at user interface level. Thus, a set of algorithms that are part of the method has been designed with privacy protection in mind, which is done by using realistic dummy parameter creation. To demonstrate the applicability of the method, a relevant context-aware data set has been used to run performance and usability tests. Findings The proposed method has been experimentally evaluated using performance and usability evaluation tests and is shown that with a small decrease in terms of performance, user privacy can be protected. Originality/value This is a novel research paper that proposed a method for protecting the privacy of mobile recommender systems users when context parameters are used.
Validating Machine Learning Algorithms for Twitter Data Against Established Measures of Suicidality

Background One of the leading causes of death in the United States (US) is suicide and new methods of assessment are needed to track its risk in real time. Objective Our objective is to validate the use of machine learning algorithms for Twitter data against empirically validated measures of suicidality in the US population. Methods Using a machine learning algorithm, the Twitter feeds of 135 Mechanical Turk (MTurk) participants were compared with validated, self-report measures of suicide risk. Results Our findings show that people who are at high suicidal risk can be easily differentiated from those who are not by machine learning algorithms, which accurately identify the clinically significant suicidal rate in 92% of cases (sensitivity: 53%, specificity: 97%, positive predictive value: 75%, negative predictive value: 93%). Conclusions Machine learning algorithms are efficient in differentiating people who are at a suicidal risk from those who are not. Evidence for suicidality can be measured in nonclinical populations using social media data.
Family history influences the early onset of hepatocellular carcinoma.

AIM To evaluate the relationship between a positive family history of primary liver cancer and hepatocellular carcinoma (HCC) development in Korean HCC patients. METHODS We studied a total of 2242 patients diagnosed with HCC between January 1990 and July 2008, whose family history of primary liver cancer was clearly described in the medical records. RESULTS Of the 2242 patients, 165 (7.4%) had a positive family history of HCC and 2077 (92.6%) did not. The male to female ratio was 3.6:1, and the major causes of HCC were chronic hepatitis B virus (HBV) infection in 75.1%, chronic hepatitis C virus infection in 13.2% and alcohol in 3.1%. The median ages at diagnosis in the positive- and negative-history groups were 52 years (range: 29-79 years) and 57 years (range: 18-89 years), respectively (P < 0.0001). Furthermore, among 1713 HCC patients with HBV infection, the number of patients under 45 years of age out of 136 patients with positive family history was 26 (19.1%), whereas those out of 1577 patients with negative family history was 197 (12.5%), suggesting that a positive family history may be associated with earlier development of HCC in the Korean population (P = 0.0028). CONCLUSION More intensive surveillance maybe recommended to those with a positive family history of HCC for earlier diagnosis and proper management especially when HBV infection is present.