Miracle-dz/UniFAR-FTUs huggingface dataset:
The flip side of phospho-signaling: regulation of protein dephosphorylation and the protein phosphatase 2Cs.

Protein phosphorylation is a key signaling mechanism and has myriad effects on protein function. Phosphorylation by protein kinases can be reversed by protein phosphatases, thus allowing dynamic control of protein phosphorylation. While this may suggest a straightforward kinase-phosphatase relationship, plant genomes contain five times more kinases than phosphatases. Here we examine phospho-signaling from a protein phosphatase centered perspective and ask how relatively few phosphatases regulate many phosphorylation sites. The most abundant class of plant phosphatases, the Protein Phosphatase 2Cs (PP2Cs), are surrounded by a web of regulation including inhibitor and activator proteins as well as post-translational modifications that regulate phosphatase activity, control phosphatase stability, or determine the subcellular locations where the phosphatase is present and active. These mechanisms are best established for the Clade A PP2Cs which are key components of stress and Abscisic Acid (ABA) signaling. We also describe other PP2C Clades and illustrate how these phosphatases are highly regulated and involved in a wide range of physiological functions. Together, these examples of multiple layers of phosphatase regulation help explain the unbalanced kinase-phosphatase ratio. Continued use of phosphoproteomics to examine phosphatase targets and phosphatase-kinase relationships will be important for deeper understanding of phosphoproteome regulation.
Knowledge and Awareness of the Health Care Workers about the Hepatitis B Infection and their Vaccination Status in a Newly Started Medical College.

Introduction Healthcare workers (HCWs) are at high risk of hepatitis B virus infection (HBI) and so the present study was carried out to assess the knowledge of HCWs in a tertiary care medical college about HBI and hepatitis B vaccine (HBV). Method After obtaining approval from Institutional Ethics Committee and informed consent from the study participants, HCWs that included teaching faculty, resident doctors, medical students, nurses, laboratory technicians, administrative staff and support staff (ward boys, attendants and sweepers) were administered a validated questionnaire. Descriptive statistics was applied for the categorical variables and the Chi-square test of association was used to assess the statistical significance of variables. Results A total of 300 HCWs were recruited for the study. Although, the overall knowledge amongst all the HCWs was found to be 68%, only 35.3%HCWs knew the transmission risk by needle stick injury (NSI). Similarly, only 40% correctly knew the precautions to be taken for preventing an NSI and 17% for the steps to be taken to disinfect a blood splash. Almost 92.7% (278/300) HCWs were aware about the availability of a vaccine, of which only 41% (1123/300) knew that vaccine will not work in case the patient is already infected. When asked about the steps to be taken in case of an NSI in non-vaccinated HCWs, only 54.7% (164/300) replied about treatment with both immunoglobulin and vaccination. A total of 160 (53.3%) HCWs were found to be vaccinated. The most common reason for not taking vaccination included an improper understanding of HBV and the infection it causes. Conclusion To conclude, the study highlights good knowledge about hepatitis B infection with requirement of more emphasis on the practical aspects of management in a case of NSI/blood splash and can guide to improve the vaccination status and knowledge of HBI amongst HCWs.
Neuraminidase Inhibitors and Hospital Length of Stay: A Meta-analysis of Individual Participant Data to Determine Treatment Effectiveness Among Patients Hospitalized With Nonfatal 2009 Pandemic Influenza A(H1N1) Virus Infection

Abstract Background The effect of neuraminidase inhibitor (NAI) treatment on length of stay (LoS) in patients hospitalized with influenza is unclear. Methods We conducted a one-stage individual participant data (IPD) meta-analysis exploring the association between NAI treatment and LoS in patients hospitalized with 2009 influenza A(H1N1) virus (A[H1N1]pdm09) infection. Using mixed-effects negative binomial regression and adjusting for the propensity to receive NAI, antibiotic, and corticosteroid treatment, we calculated incidence rate ratios (IRRs) and 95% confidence intervals (CIs). Patients with a LoS of <1 day and those who died while hospitalized were excluded. Results We analyzed data on 18 309 patients from 70 clinical centers. After adjustment, NAI treatment initiated at hospitalization was associated with a 19% reduction in the LoS among patients with clinically suspected or laboratory-confirmed influenza A(H1N1)pdm09 infection (IRR, 0.81; 95% CI, .78–.85), compared with later or no initiation of NAI treatment. Similar statistically significant associations were seen in all clinical subgroups. NAI treatment (at any time), compared with no NAI treatment, and NAI treatment initiated <2 days after symptom onset, compared with later or no initiation of NAI treatment, showed mixed patterns of association with the LoS. Conclusions When patients hospitalized with influenza are treated with NAIs, treatment initiated on admission, regardless of time since symptom onset, is associated with a reduced LoS, compared with later or no initiation of treatment.
Comparative genomics groups phages of Negativicutes and classical Firmicutes despite different Gram-staining properties

Negativicutes are Gram-Negative bacteria characterized by two cell membranes, but they are phylogenetically a side-branch of Gram-Positive Firmicutes that contain only a single membrane. We asked whether viruses (phages) infecting Negativicutes were horizontally acquired from Gram-Negative Proteobacteria, given the shared outer cell structure of their bacterial hosts, or if Negativicute phages co-evolved vertically with their hosts and thus resemble Gram-Positive Firmicute prophages. We predicted and characterised 485 prophages from Gram-Negative Firmicute genomes plus 2,977 prophages from other bacterial clades, and we used virome sequence data from 183 human stool samples to provide independent evidence for our predictions. The majority of the identified Negativicute prophages were lambdoids closer related to prophages from other Firmicutes than Proteobacteria by sequence relationship and genome organization (position of the lysis module). Only a single Mu-like candidate prophage and no clear P2-like prophages were identified in Negativicutes, both commonly found in Proteobacteria. Therefore, it is unlikely that Negativicute phages were acquired from Proteobacteria. Sequence-related prophages were identified in two distinct Negativicute orders (Veillonellales and Acidaminococcales) possibly suggesting horizontal cross-order phage infection between human gut commensals. Phages infecting these Negativicute orders occasionally harboured putative antibiotic resistance genes.
Whole-Genome Sequencing Reveals a Prolonged and Persistent Intrahospital Transmission of Corynebacterium striatum, an Emerging Multidrug-Resistant Pathogen

Corynebacterium striatum is an emerging multidrug-resistant (MDR) pathogen that occurs primarily among immunocompromised and chronically ill patients. However, little is known about the genomic diversity of C. striatum, which contributes to its long-term persistence and transmission in hospitals. ABSTRACT Corynebacterium striatum is an emerging multidrug-resistant (MDR) pathogen that occurs primarily among immunocompromised and chronically ill patients. However, little is known about the genomic diversity of C. striatum, which contributes to its long-term persistence and transmission in hospitals. In this study, a total of 192 C. striatum isolates obtained from 14 September 2017 to 29 March 2018 in a hospital in Beijing, China, were analyzed by antimicrobial susceptibility testing and pulsed-field gel electrophoresis (PFGE). Whole-genome sequencing was conducted on 91 isolates. Nearly all isolates (96.3%, 183/190) were MDR. The highest resistance rate was observed for ciprofloxacin (99.0%, 190/192), followed by cefotaxime (90.6%, 174/192) and erythromycin (89.1%, 171/192). PFGE separated the 192 isolates into 79 pulsotypes, and differences in core genome single-nucleotide polymorphisms (SNPs) partitioned the 91 isolates sequenced into four clades. Isolates of the same pulsotype were identical or nearly identical at the genome level, with some exceptions. Two dominant subclones, clade 3a, and clade 4a, were responsible for the hospital-wide dissemination. Genomic analysis further revealed nine resistance genes mobilized by eight unique cassettes. PFGE and whole-genome sequencing revealed that the C. striatum isolates studied were the result mainly of predominant clones spreading in the hospital. C. striatum isolates in the hospital progressively acquired resistance to antimicrobial agents, demonstrating that isolates of C. striatum may adapt rapidly through the acquisition and accumulation of resistance genes and thus evolve into dominant and persistent clones. These insights will be useful for the prevention of C. striatum infection in hospitals.
Predicting treatment dropout among veterans receiving prolonged exposure therapy.

OBJECTIVE To examine whether dropout from prolonged exposure (PE) therapy can be predicted from demographic and outcomes data that would typically be available to clinicians. METHODS Dropout was examined in 2,606 patients treated by clinicians in the U.S. Veterans Health Administration PE Training Program. PE typically consists of 8-15 sessions, with 8 sessions being considered a minimum therapeutic dose for most patients. Logistic regression was used to assess the impact of demographics, depression, trauma history, and PE target trauma on risk for dropout. Growth mixture modeling was used to study how posttraumatic stress disorder symptom patterns during the first 5 treatment encounters predicted dropout. RESULTS In total, 782 patients (30.0%) completed fewer than 8 sessions of PE. Younger veterans were more likely to drop out of PE; odds ratio (OR) per year of age = 0.97, p < . 01. Controlling for other factors, veterans who focused on childhood trauma were less likely to drop out than those focusing on combat trauma (OR = 0.51, p < .05). Dropout was unrelated to symptom course or symptom worsening between sessions. Nevertheless, clinicians attributed dropout to distress or avoidance in 45% of the patients who dropped out, citing other factors in 37% of dropout cases. CONCLUSIONS Treatment dropout was predicted by age but not by initial symptom severity or symptom course early in treatment. Symptom exacerbation was rare and did not increase risk of dropout. Nonetheless, clinicians often attributed dropout to patients not tolerating PE. (PsycINFO Database Record (c) 2019 APA, all rights reserved).
Evaluation of the Adaptation and Fracture Resistance of Three CAD-CAM Resin Ceramics: An In vitro Study.

AIM The internal fit and resistance to fracture of resin ceramics are to be evaluated compared to that of lithium disilicate as the control group. MATERIALS AND METHODS Four groups of 20 crowns each (GC Cerasmart, Vita Enamic, Coltène Brilliant Crios, and e.max CAD) were cemented on identical metal dies. Marginal gaps were measured before cementation and load to fracture was applied after cementation, half of each group was thermodynamically aged (3,000 cycles of 5° to 55° immersion followed by 200,000 cycles of 100 N load), finally the crowns were loaded until fracture in a universal testing machine. Statistical package for social sciences (SPSS) package 23 was used for statistical work. RESULTS Marginal gaps ranged between 68.5 ± 23.8 µm and 87 ± 29.1 µm while occlusal gaps ranged from 220.7 ± 33.3 µm to 275.5 ± 46.5 µm and were not significantly different between groups. Fracture loads ranged from 633.8 ± 127.3 N to 1596.4 ± 497.7 N with lithium disilicate glass ceramics (LDGCs) and Enamic having higher values than resin nano-ceramics (RNCs). The fracture resistance was more related to material than aging and gap value. CONCLUSION The margin adaptation of resin ceramics was comparable to lithium disilicate with no significant difference. Lithium disilicate showed a higher resistance than resin ceramics and there was a higher resistance to fracture for polymer-infiltrated ceramic-network (PICN) than RNCs. CLINICAL SIGNIFICANCE Resin ceramics can have marginal adaptation and fracture resistance within clinical acceptance; therefore, they can be a good chair-side solution achieved in a single appointment session.
Augmentation of EPR Effect and Efficacy of Anticancer Nanomedicine by Carbon Monoxide Generating Agents

One obstacle to the successful delivery of nanodrugs into solid tumors is the heterogeneity of an enhanced permeability and retention (EPR) effect as a result of occluded or embolized tumor blood vessels. Therefore, the augmentation of the EPR effect is critical for satisfactory anticancer nanomedicine. In this study, we focused on one vascular mediator involved in the EPR effect, carbon monoxide (CO), and utilized two CO generating agents, one is an extrinsic CO donor (SMA/CORM2 micelle) and another is an inducer of endogenous CO generation via heme oxygenase-1 (HO-1) induction that is carried out using pegylated hemin. Both agents generated CO selectively in solid tumors, which resulted in an enhanced EPR effect and a two- to three-folds increased tumor accumulation of nanodrugs. An increase in drug accumulation in the normal tissue did not occur with the treatment of CO generators. In vivo imaging also clearly indicated a more intensified fluorescence of macromolecular nanoprobe in solid tumors when combined with these CO generators. Consequently, the combination of CO generators with anticancer nanodrugs resulted in an increased anticancer effect in the different transplanted solid tumor models. These findings strongly warrant the potential application of these CO generators as EPR enhancers in order to enhance tumor detection and therapy using nanodrugs.
Comprehensive Chemical Profiling and Multidirectional Biological Investigation of Two Wild Anthemis Species (Anthemis tinctoria var. Pallida and A. cretica subsp. tenuiloba): Focus on Neuroprotective Effects

Ethyl acetate (EA), methanol (MeOH), and aqueous extracts of aerial parts of Anthemis tinctoria var. pallida (ATP) and A. cretica subsp. tenuiloba (ACT) were investigated for their phenol and flavonoid content, antioxidant, and key enzyme inhibitory potentials. All extracts displayed antiradical effects, with MeOH and aqueous extracts being a superior source of antioxidants. On the other hand, EA and MeOH extracts were potent against AChE and BChE. Enzyme inhibitory effects against tyrosinase and α-glucosidase were observed, as well. We also studied Anthemis extracts in an ex vivo experimental neurotoxicity paradigm. We assayed extract influence on oxidative stress and neurotransmission biomarkers, including lactate dehydrogenase (LDH) and serotonin (5-HT), in isolated rat cortex challenged with K+ 60 mM Krebs-Ringer buffer (excitotoxicity stimulus). An untargeted proteomic analysis was finally performed in order to explore the putative mechanism in the brain. The pharmacological study highlighted the capability of ACT water extract to blunt K+ 60 mM increase in LDH level and 5-HT turnover, and restore physiological activity of specific proteins involved in neuron morphology and neurotransmission, including NEFMs, VAMP-2, and PKCγ, thus further supporting the neuroprotective role of ACT water extract.
Aplicación de modelos de transferencia radiativa para el control operativo del programa BSRN (Baseline Surface Radiation Network) del Centro de Investigación Atmosférica de Izaña

BSRN (Baseline Surface Radiation Network) is a project of the Radiation Panel from the Global Energy and Water Cycle Experiment (GEWEX) under the umbrella of the World Climate Research Programme (WCRP). The objective of the BSRN is to provide, using a high sampling rate (one to three minutes), observations of the best possible quality, for shortwave and longwave surface radiation fluxes. These readings are taken from a small number of selected stations, in contrasting climatic zones, together with collocated surface and upper air meteorological data and other supporting observations. Since March 2009 the Izaña station (IZA in the BSRN notation) belongs to the BSRN network. The IZA is a Global Atmospheric Watch station and it is managed by the Izaña Atmospheric Research Center (IARC), from the Meteorological State Agency of Spain (AEMET). The station is located on Tenerife Island (Spain) and is a high mountain station at 2367 m. above sea level.
Maximum Breaker Height for Design

A re-evaluation of previously published breaking wave data is used to develop a relationship for the maximum breaker height in terms of the depth in which the wave breaks, breaker steepness and the local beach slope. This relationship is used with the breaker travel distance equation of Galvin (3)* to estimate the maximum breaker height to which a coastal structure might be subjected. In addition, the range of depths in which a wave of given height will break is found by examination of the upper bound of observed values of dD/HD . An example problem is presented to illustrate the use of the general maximum breaker height design curves.
Applications de la télédétection infrarouge et visible en océanographie. Etude de la zone de dilution rhodanienne, observations des zones de production dans le Golfe du Lion, et estimation de l'éclairement solaire global en Méditerranée Occidentale

Les travaux ont ete effectues sur le golfe du Lion. Ils presentent des resultats combines de l'interpretation d'images de satellites, obtenues dans l'infrarouge thermique (capteur AVHRR) et dans le domaine visible (capteur CZCS) avec des connaissances historiques et des mesures recueillies simultanement en mer. Ils permettent, d'une part, d'estimer la forte variabilite spatio-temporelle de la zone de dilution rhodanienne, en particulier sous l'influence du vent local et du debit du fleuve, et, d'autre part, d'observer la formation hivernale d'eau profonde dans le golfe du Lion. L'evolution saisonniere des zones de production dans le golfe du Lion est suivie a l'aide d'images de la concentration relative en pigments chlorophylliens et de la temperature de la mer. Le traitement d'images du spectre visible du satellite METEOSAT II permet l'estimation mensuelle de l'eclairement solaire global au niveau de la mer.
OSL dating of an inland dune along the lower River Scheldt near Aard (East Flanders, Belgium)

Abstract The chronostratigraphic position of aeolian dunes in East Flanders (Belgium) has been under debate for decades. Until now, the only available age information consisted of a limited number of radiocarbon dates, which provided indirect sediment deposition chronologies. This paper reports on the first direct determination, by quartz-based single-aliquot optically stimulated luminescence dating, of the time that dune sands were deposited along the Lower River Scheldt in Belgium. The sediments are dated at 12.0±0.9 ka (n = 5), which confirms that the time of inland dune formation in East Flanders dates from the Younger Dryas period and should not be constrained to the Holocene.
The Dominguez Escalante Journal: Their Expedition Through Colorado Utah Arizona and New Mexico in 1776

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Retinoblastoma (RB) in Saudi Arabia- Retrospective Comparative Review of a Registry

Abstract Purpose: Published data regarding retinoblastoma in Saudi Arabia (KSA) is sparse. The study will present comparison of clinical and pathologic features, and evolving patterns of the treatment during 1983-1997 (Early group=EG) to 1998-2012 (Late group=LG) periods from an RB registry representing all Rb cases in KSA.
THE EFFECT OF WAVE REFRACTION OVER DREDGED HOLES

Preliminary results are presented of a study of the beach erosion caused by wave refraction over offshore dredged holes. A mathematical model is used of an idealised sand beach, typical of those on the English Channel and North Sea coasts of Great Britain. Depth and side slopes of dredged area and original water depth before dredging were varied. Beach erosion increased with increasing hole depth and with decreasing original water depth. The effects of side slope and hole depth will be separated in future work, as will the effects of hole shape. Beach erosion due to holes in water depths greater than half the length of "normal" waves, or a fifth of the length of extreme waves, was negligible.
Stellar and Dust Properties of a Complete Sample of Massive Dusty Galaxies at 1 ≤ z ≤ 4 from MAGPHYS Modeling of UltraVISTA DR3 and Herschel Photometry

We investigate the stellar and dust properties of massive (log M*/M⊙ ≥ 10.5) and dusty (AV ≥ 1) galaxies at 1 ≤ z ≤ 4 by modeling their spectral energy distributions (SEDs) obtained from the combination of UltraVISTA DR3 photometry and Herschel PACS-SPIRE data using MAGPHYS. Although the rest-frame U–V versus V–J (UVJ) diagram traces the star formation rates (SFRs) and dust obscuration (AV) well out to z ∼ 3, ∼15%–20% of the sample surprisingly resides in the quiescent region of the UVJ diagram, while ∼50% at 3 < z < 4 falls in the unobscured star-forming region. The median SED of massive dusty galaxies exhibits weaker MIR and UV emission, and redder UV slopes with increasing cosmic time. The IR emission for our sample has a significant contribution (>20%) from dust heated by evolved stellar populations rather than star formation, demonstrating the need for panchromatic SED modeling. The local relation between dust mass and SFR is followed only by a subsample with cooler dust temperatures, while warmer objects have reduced dust masses at a given SFR. Most star-forming galaxies in our sample do not follow local IRX–β relations, though IRX does strongly correlate with AV. Our sample follows local relations, albeit with large scatter, between ISM diagnostics and sSFR. We show that FIR-detected sources represent the extreme of a continuous population of dusty galaxies rather than a fundamentally different population. Finally, using commonly adopted relations to derive SFRs from the combination of the rest-frame UV and the observed 24 μm is found to overestimate the SFR by a factor of 3–5 for the galaxies in our sample.
Random Convolutional Coding for Robust and Straggler Resilient Distributed Matrix Computation

Distributed matrix computations (matrix-vector and matrix-matrix multiplications) are at the heart of several tasks within the machine learning pipeline. However, distributed clusters are well-recognized to suffer from the problem of stragglers (slow or failed nodes). Prior work in this area has presented straggler mitigation strategies based on polynomial evaluation/interpolation. However, such approaches suffer from numerical problems (blow up of round-off errors) owing to the high condition numbers of the corresponding Vandermonde matrices. In this work, we introduce a novel solution approach that relies on embedding distributed matrix computations into the structure of a convolutional code. This simple innovation allows us to develop a provably numerically robust and efficient (fast) solution for distributed matrix-vector and matrix-matrix multiplication.