Miracle-dz/UniFAR-FTUs huggingface dataset:
groE mutants of Escherichia coli are defective in umuDC-dependent UV mutagenesis

Overexpression of the SOS-inducible umuDC operon of Escherichia coli results in the inability of these cells to grow at 30 degrees C. Mutations in several heat shock genes suppress this cold sensitivity. Suppression of umuD+C+-dependent cold sensitivity appears to occur by two different mechanisms. We show that mutations in lon and dnaK heat shock genes suppress cold sensitivity in a lexA-dependent manner. In contrast, mutations in groES, groEL, and rpoH heat shock genes suppress cold sensitivity regardless of the transcriptional regulation of the umuDC genes. We have also found that mutations in groES and groEL genes are defective in umuDC-dependent UV mutagenesis. This defect can be suppressed by increased expression of the umuDC operon. The mechanism by which groE mutations affect umuDC gene product function may be related to the stability of the UmuC protein, since the half-life of this protein is shortened because of mutations at the groE locus.
Secreted aspartic proteases of Candida albicans activate the NLRP3 inflammasome

In a recent report, we demonstrated that distinct members of the secreted aspartic protease (Sap) family of Candida albicans are able to induce secretion of proinflammatory cytokines by human monocytes, independently of their proteolytic activity and specific pH optima. In particular, C. albicans Sap2 and Sap6 potently induced IL‐1β, TNF‐α, and IL‐6 production. Here, we demonstrate that Sap2 and Sap6 proteins trigger IL‐1β and IL‐18 production through inflammasome activation. This occurs via NLRP3 and caspase‐1 activation, which cleaves pro‐IL‐1β into secreted bioactive IL‐1β, a cytokine that was induced by Saps in monocytes, in monocyte‐derived macrophages and in dendritic cells. Downregulation of NLRP3 by RNA interference strongly reduced the secretion of bioactive IL‐1β. Inflammasome activation required Sap internalization via a clathrin‐dependent mechanism, intracellular induction of K+ efflux, and ROS production. Inflammasome activation of monocytes induced by Sap2 and Sap6 differed from that induced by LPS‐ATP in several aspects. Our data reveal novel immunoregulatory mechanisms of C. albicans and suggest that Saps contribute to the pathogenesis of candidiasis by fostering rather than evading host immunity.
Calpain-dependent Proteolytic Cleavage of the p35 Cyclin-dependent Kinase 5 Activator to p25*

Cyclin-dependent kinase 5 (CDK5) is a unique CDK, the activity of which can be detected in postmitotic neurons. To date, CDK5 purified from mammalian brains has always been associated with a truncated form of the 35-kDa major brain specific activator (p35, also known as nck5a) of CDK5, known as p25. In this study, we report that p35 can be cleaved to p25 both in vitro and in vivo by calpain. In a rat brain extract, p35 was cleaved to p25 by incubation with Ca2+. This cleavage was inhibited by a calpain inhibitor peptide derived from calpastatin and was ablated by separating the p35·CDK5 from calpain by centrifugation. The p35 recovered in the pellet after centrifugation could then be cleaved to p25 by purified calpain. Cleavage of p35 was also induced in primary cultured neurons by treatment with a Ca2+ ionophore and Ca2+ and inhibited by calpain inhibitor I. The cleavage changed the solubility of the CDK5 active complex from the particulate fraction to the soluble fraction but did not affect the histone H1 kinase activity. Increased cleavage was detected in cultured neurons undergoing cell death, suggesting a role of the cleavage in neuronal cell death.
Endogenous and exogenous glucocorticoids have different roles in modulating endotoxin lethality in D-galactosamine-sensitized mice

Endotoxin sensitivity and dexamethasone protection have been assessed in mice that were adrenalectomized and also treated with D-galactosamine at the time of endotoxin challenge. Our data establish that adrenalectomy did not detectably alter the magnitude of the increased sensitivity induced by D-galactosamine alone. Furthermore, protection provided by acute exogenous glucocorticoid treatment was still demonstrable in these mice and was not influenced by chronic experimentally induced glucocorticoid deficiency. Our data confirm that the adrenalectomized mouse model of endotoxin lethality is characterized by increased sensitivity to endotoxin and establish that the magnitude of this sensitizing effect is more than 100-fold. We also show for the first time that adrenalectomy causes an appreciable kinetic shift in the endotoxic crisis and that dexamethasone, given at the time of endotoxin challenge, will significantly reverse the increased sensitivity to lethality. Our results indicate that the protective effects of corticosteroids may involve important chronic as well as acute responses. In particular, we conclude that endogenous glucocorticoid need not always increase host resistance to endotoxin, nor does such a circumstance eliminate the possibility for exogenous glucocorticoid-mediated protective effects.
UNCERTAINTIES IN THE RELATIONSHIP BETWEEN HYPERSPECTRAL DATA AND LEAF NITROGEN CONTENT

REFERENCES 1. Ollinger, S.V. et al. (2008). Canopy nitrogen, carbon assimilation, and albedo in temperate and boreal forests: Functional relations and potential climate feedbacks. Proc. Natl. Acad. of Sci., 105, 19336-19341 2. Smith, M.L. , & Martin, M.E. (2001). A plot-based method for rapid estimation of forest canopy chemistry. Can. J. of For. Res., 31, 549-555 3. Schull MA (2010) Application of spectral invariants for monitoring forest across multiple scales. PhD Thesis. Department of Geography and Environment, Boston University, November 2nd, 2010, 137 pp., http://library.bu. edu/search/X. 4. Diner D, et al., Early results from Ground MSPI and AirMSPI, MISR Data Users Science Symposium, Dec. 2010 5. Grant et al.,(1993) Polarized and Specular Reflectance Variation with Leaf Surface-Features. Physiol Plantarum 88(1):1-9 ACKNOWLEDGEMENTS
Isolation, genetic mapping, and characterization of Escherichia coli K-12 mutants lacking gamma-glutamyltranspeptidase

Escherichia coli K-12 mutants lacking gamma-glutamyltranspeptidase (EC 2.3.2.2) were isolated after mutagenesis of cells with ethyl methanesulfonate. They lost the enzyme activity to different extents. The mutations of two mutants that had lost the enzyme activity completely were mapped at 76 min of the E. coli K-12 linkage map. These mutations made the cells neither nutrient requiring nor cold sensitive. The mutants leaked much more glutathione into the medium than the wild type. We propose the symbol ggt for these mutations.
Estudio de sistemas planetarios de periodo corto alrededor de estrellas gigantes

To date, more than 800 exoplanets have been detected, most of them by the radial velocity (RV) technique. In order to achieve high enough RV precision, the stellar spectrum of the host star has to contain thousands of narrow absoprtion lines, which restricts this method mainly to FGK main-sequence stars (M . 1.3M⊙). However, after the main-sequence, earlier spectral type stars (A and early F) expand, hence becoming cooler and rotate slower than their former main-sequence progenitors (Schrijver & Pols 1993), hence presenting a spectrum containing thousands of narrow absorption lines. Therefore, evolved stars present an ideal case where we can use the RV technique to search for planets orbiting intermediate-mass (1.3.M/M⊙. 3.0) stars and to investigate the effect of the post-MS star-planet interactions. During the last decade, several exoplanets were detected around post-MS stars, revealing different properties than those orbiting solar-type stars. In particular, the semimajor axis distribution shows a lack of planets orbiting interior to 0.6 AU, which has been interpreted as the observational evidence of the engulfment of planets due to tidal decay (e.g. Villaver & Livio 2009). However, the effect of the stellar mass is also playing a role, which might be in part responsible for this observational result (Johnson et al. 2007). In this dissertation a large RV study of 166 giant stars is presented. The main goal of this survey is to search for giant planets in close-in orbits, and to determine whether the effect of the stellar evolution is responsible for the observed lack of short period orbit planets around post-MS stars. During this project, three massive giant planets were detected, all of them having orbital distances greater than 0.57 AU, around first ascending giant branch stars. With the current statistics for these kind of objects, is not possible to dissentangle the effect of the stellar mass from the stellar evolution, thus there is still no conclusive evidence in favor of the afore mentioned mechanism.
An Outlook on the Unlicensed Operation Aspects of NR

The standardization of 5G New Radio (NR) has started and addresses a wide range of use-cases. The 5G application demands include among others, very high data rates, support for huge number of low-power devices and mission critical communication. NR design supports operation in both traditional licensed frequency spectrum bands as well as unlicensed frequencies. In this paper, we present some of the design aspects and architectural details of NR to support spectrum sharing in the unlicensed spectrum. Moreover, we present system level simulation results showing the NR spectrum sharing capabilities while complying with the regulatory requirements.
Limit Orders, Depth, and Volatility: Evidence from the Stock Exchange of Hong Kong

We investigate the role of limit orders in the liquidity provision in a pure order-driven market. Results show that market depth rises subsequent to an increase in transitory volatility, and transitory volatility declines subsequent to an increase in market depth. We also examine how transitory volatility affects the mix between limit orders and market orders. When transitory volatility arises from the ask (bid) side, investors will submit more limit sell (buy) orders than market sell (buy) orders. This result is consistent with the existence of limit-order traders who enter the market and place orders when liquidity is needed. Copyright The American Finance Association 2001.
Construction of Varicella-Zoster Virus Recombinants from Parent Oka Cosmids and Demonstration that ORF65 Protein Is Dispensable for Infection of Human Skin and T Cells in the SCID-hu Mouse Model

ABSTRACT We generated an ORF65 deletion mutant by using a cosmid system constructed from the genome of a low-passage clinical isolate (P-Oka). Using the SCID-hu mouse model, we demonstrated that the ORF65 protein is dispensable for viral replication in skin and T cells, which are critical host cell targets during primary varicella-zoster virus infection.
Using Hierarchical Graph Maps to Explain Collaborative Filtering Recommendations

The explanation of and justification for recommendation results are important objectives in recommender systems because such explanations and justifications strongly influence the user's trust in the system. Traditional justification methods are based on textual explanations, which can be inadequate for analysis, comprehension, and decision making on the part of the user. In this paper, we present a method that generates tree graphs that contain the following information: the recommended items, the items that have appeared most often in the recommendation process, the relative importance of the items, and the relationships that exist among the items. The trees obtained in the experiments show (1) the greater novelty of user‐to‐user results, (2) the overspecialization inherent in the item‐to‐item approach, and (3) the equilibrium obtained by employing hybrid user‐to‐user/item‐to‐item collaborative filtering. The proposed method presents the possibility of extending recommendation result justifications to groups of users and facilitates the explanation of large numbers of recommended items.
Harmonic impedance measurement on submarine cable

The lumped equivalent circuit parameters and distributed parameters of a line at high frequency are a little different from those at power frequency, because of distribution effects. The paper derives the formulas to get the lumped equivalent circuit parameters and distributed parameters from open circuit and short circuit harmonic impedance, and the actual measurement was carried out on a three phases of 500kV single-core submarine cables. The line parameters at harmonic frequency are also calculated and compared with the actual measurement. Some phenomena is expecting further exploration.
Visual and auditory presentation, presentation rate, and short-term memory in children.

Lists of six digits were presented either auditorially or visually at rates of 1, 2 or 3 digits/sec to groups of 7-, 8-, 9- and 10-year-old girls. Immediate recall improved with age under all conditions, but the recall of visually presented slow lists improved with age at a steeper rate than did the recall of visually presented fast lists or of auditorially presented lists. The results are related to the findings of previous studies on STM as a function of presentation rate, and in particular to the hypothesis that when slow rates give superior recall as compared with fast, it is because subjects can more fluently read and rehearse the items at the time of perception.
Regeneration in zebrafish lateral line neuromasts: Expression of the neural progenitor cell marker sox2 and proliferation‐dependent and‐independent mechanisms of hair cell renewal

Mechanosensory hair cells are essential for audition in vertebrates, and in many species, have the capacity for regeneration when damaged. Regeneration is robust in the fish lateral line system as new hair cells can reappear after damage induced by waterborne aminoglycoside antibiotics, platinum‐based drugs, and heavy metals. Here, we characterize the loss and reappearance of lateral line hair cells induced in zebrafish larvae treated with copper sulfate using diverse molecular markers. Transgenic fish that express green fluorescent protein in different cell types in the lateral line system have allowed us to follow the regeneration of hair cells after different damage protocols. We show that conditions that damage only differentiated hair cells lead to reappearance of new hair cells within 24 h from nondividing precursors, whereas harsher conditions are followed by a longer recovery period that is accompanied by extensive cell division. In order to characterize the cell population that gives rise to new hair cells, we describe the expression of a neural stem cell marker in neuromasts. The zebrafish sox2 gene is strongly expressed in neuromast progenitor cells, including those of the migrating lateral line primordium, the accessory cells that underlie the hair cells in neuromasts, and in interneuromastic cells that give rise to new neuromasts. Moreover, we find that most of the cells that proliferate within the neuromast during regeneration express this marker. Thus, our results describe the dynamics of hair cell regeneration in zebrafish and suggest the existence of at least two mechanisms for recovery of these cells in neuromasts. © 2007 Wiley Periodicals, Inc. Develop Neurobiol, 2007
Interactive Visualization and Content Analysis of Instant Messaging Networks

In this paper, we present our efforts towards allowing users to query and reflect upon their instant messaging histories. The problem is important since the volume of chat data is increasing at a significant rate, and traditional text based retrieval does not capture the social conventions in such systems, allowing no space for insightful exploration. In this work, we develop an analysis and interactive visualization framework, to provide insight to the user. In addition to the traditional text retrieval features like dominant concepts and their frequency, we propose to extract novel features specific to instant messaging domain like, usage of emoticons, use of exaggerations and emphasis words, number of foreign language words. These features are used to determine the key aspects of communication (a) between two users, (b) between a user and different categories/groups of people like friends, family, colleagues etc. Finally we develop two novel exploratory schemes to explore an archive of a group of users to help the users reflect on the nature of the communication (concepts, network temporal evolution, and communication density).
US Air Force Behavioral Health Optimization Program: team members’ satisfaction and barriers to care

Background. Research has shown significant contribution of integrated behavioural health care; however, less is known about the perceptions of primary care providers towards behavioural health professionals. Objective. The current study examined barriers to care and satisfaction with integrated behavioural health care from the perspective of primary care team members. Design. This study utilized archival data from 42 treatment facilities as part of ongoing program evaluation of the Air Force Medical Service’s Behavioral Health Optimization Program. Setting. This study was conducted in a large managed health care organization for active duty military and their families, with specific clinic settings that varied considerably in regards to geographic location, population diversity and size of patient empanelment. Study participants. De-identified archival data on 534 primary care team members were examined. Results. Team members at larger facilities rated access and acuity concerns as greater barriers than those from smaller facilities (t(533) = 2.57, P < 0.05). Primary Care Managers (PCMs) not only identified more barriers to integrated care (&bgr; = −0.07, P < 0.01) but also found services more helpful to the primary care team (t(362.52) = 1.97, P = 0.05). Barriers to care negatively impacted perceived helpfulness of integrated care services for patients (&bgr; = −0.12, P < 0.01) and team members, particularly among non-PCMs (&bgr; = −0.11, P < 0.01). Conclusions. Findings highlight the potential benefits of targeted training that differs in facilities of larger empanelment and is mindful of team members’ individual roles in a Patient Centered Medical Home. In particular, although generally few barriers were perceived, given the impact these barriers have on perception of care, efforts should be made to decrease perceived barriers to integrated behavioural health care among non-PCM team members.
Probability reconstruction based on graph distance neighbor network for visualizing data

In the era of information exploration, it is an urgent need to process and analyze high-dimensional data sets which may contain thousands of dimensions. If high-dimensional data can be unfolded in a two or three-dimensional map, we can intuitively learn about the main structure of the data, which will greatly benefit data exploration and pattern discovery. The visualization technique which aims to reveal the low-dimensional manifold embedded in the high-dimensional data can complete the challenging task above. This paper introduces a new visualization algorithm called probability reconstruction based on graph distance neighbor network (PR-GDNN). The PR-GDNN algorithm uses the graph distance to construct a neighbor network, then performs the probability reconstruction inferred from the neighborhood relationship, and finally minimizes the Kullback-Leibler divergence. Under these operations, the PR-GDNN algorithm has a better performance than the classical embedding algorithms in revealing the structure of data, especially keeping the local structure. The qualitative and quantitative comparisons on three standard data sets demonstrate the superiority of the proposed algorithm.
Identification of grass-associated and toluene-degrading diazotrophs, Azoarcus spp., by analyses of partial 16S ribosomal DNA sequences

The genus Azoarcus includes nitrogen-fixing, grass-associated strains as well as denitrying toluene degraders. In order to identify and group members of the genus Azoarcus, phylogenetic analysis based on partial sequences of 16S rRNA genes (16S rDNAs) is proposed. 16S rRNA-targeted PCR using specific primers to exclude amplification in the majority of other members of the beta subclass of the class Proteobacteria was combined with direct sequencing of the PCR products. Tree inference from comparisons of 446-bp rDNA fragments yielded similar results for the three known Azoarcus spp. sequences and for analysis of the complete 16S rDNA sequence. These three species formed a phylogenetically coherent group with representatives of two other Azoarcus species which were subjected to 16S rRNA sequencing in this study. This group was related to Rhodocyclus purpureus and Thauera selenatis. New isolates and also sequences of so far uncultured bacteria from roots of Kallar grass were assigned to the genus Azoarcus as well. Also, strains degrading monoaromatic hydrocarbons anaerobically in the presence of nitrate clustered within this genus, albeit not with grass-associated isolates. All representative members of the five species harboring rhizospheric bacteria were able to form N2O from nitrate and showed anaerobic growth on malic acid with nitrate but not on toluene. In order to visualize different Azoarcus spp. by whole-cell in situ hybridizations, we generated 16S rRNA-targeted, fluorescent probes by in vitro transcription directly from PCR products which spanned the variable region V2. Hybridization was species specific for Azoarcus communis and Azoarcus indigens. (ABSTRACT TRUNCATED AT 250 WORDS)
Pharmacokinetics and pharmacodynamics of propofol and fentanyl in patients undergoing abdominal aortic surgery – a study of pharmacodynamic drug–drug interactions

Propofol is routinely combined with opioid analgesics to ensure adequate anesthesia during surgery. The aim of the study was to assess the effect of fentanyl on the hypnotic effect of propofol and the possible clinical implications of this interaction. The pharmacokinetic/pharmacodynamic (PK/PD) data were obtained from 11 patients undergoing abdominal aortic surgery, classified as ASA III. Propofol was administered by a target‐controlled infusion system. Fentanyl 2–3 µg/kg was given whenever insufficient analgesia occurred. The bispectral index (BIS) was used to monitor the depth of anesthesia. A population PK/PD analysis with a non‐linear mixed‐effect model (NONMEM 7.2 software) was conducted. Two‐compartment models satisfactorily described the PK of propofol and fentanyl. The delay of the anesthetic effect in relation to PK was described by the effect compartment. The BIS was linked to propofol and fentanyl effect‐site concentrations through an additive Emax model. Context‐sensitive decrement times (CSDT) determined from the final model were used to assess the influence of fentanyl on the recovery after anesthesia. The population PK/PD model was successfully developed to describe simultaneously the time course and variability of propofol and fentanyl concentrations and BIS. Additive propofol–fentanyl interactions were observed and quantitated. The duration of the fentanyl infusion had minimal effect on CSDT when it was shorter than the duration of the propofol infusion. If the fentanyl infusion was longer than the propofol infusion, an almost two‐fold increase in CSDT occurred. Additional doses of fentanyl administered after the cessation of the propofol infusion result in lower BIS values, and can prolong the time of recovery from anesthesia. Copyright © 2016 John Wiley & Sons, Ltd.