Chromospherically Active Stars in the RAVE Survey

AbstractWe present a qualitative characterization of activity levels of a large database of ~44,000 candidate RAVE stars (unbiased, magnitude limited medium resolution survey) that show chromospheric emission in the Ca II infrared triplet and this vastly enlarges previously known samples. Our main motivation to study these stars is the anti-correlation of chromospheric activity and stellar ages that could be calibrated using stellar clusters with known ages. Locally linear embedding used for a morphological classification of spectra revealed 53,347 cases with a suggested emission component in the calcium lines. We analyzed a subsample of ~44,000 stars with S/N>20 using a spectral subtraction technique where observed reference spectra of inactive stars were used as templates instead of synthetic ones. Both the equivalent width of the excess emission for each calcium line and their sum is derived for all candidate active stars with no respect to the origin of their emission flux. ~17,800 spectra show a detectable chromospheric flux with at least 2 σ confidence level. The overall distribution of activity levels shows a bimodal shape, with the first peak coinciding with inactive stars and the second with the pre-main-sequence cases.

Download Full-text

Morphological and Ultrastructural Characterization of Hemocytes in an Insect Model, the Hematophagous Dipetalogaster maxima (Hemiptera: Reduviidae)

Insects ◽

10.3390/insects12070640 ◽

2021 ◽

Vol 12 (7) ◽

pp. 640

Author(s):

Natalia R. Moyetta ◽

Fabián O. Ramos ◽

Jimena Leyria ◽

Lilián E. Canavoso ◽

Leonardo L. Fruttero

Keyword(s):

Cell Biology ◽

Cell Types ◽

Transmission Electron ◽

Ultrastructural Characterization ◽

Current Classification ◽

Contrast Microscopy ◽

First Time ◽

Controversial Aspect

Hemocytes, the cells present in the hemolymph of insects and other invertebrates, perform several physiological functions, including innate immunity. The current classification of hemocyte types is based mostly on morphological features; however, divergences have emerged among specialists in triatomines, the insect vectors of Chagas’ disease (Hemiptera: Reduviidae). Here, we have combined technical approaches in order to characterize the hemocytes from fifth instar nymphs of the triatomine Dipetalogaster maxima. Moreover, in this work we describe, for the first time, the ultrastructural features of D. maxima hemocytes. Using phase contrast microscopy of fresh preparations, five hemocyte populations were identified and further characterized by immunofluorescence, flow cytometry and transmission electron microscopy. The plasmatocytes and the granulocytes were the most abundant cell types, although prohemocytes, adipohemocytes and oenocytes were also found. This work sheds light on a controversial aspect of triatomine cell biology and physiology setting the basis for future in-depth studies directed to address hemocyte classification using non-microscopy-based markers.

Download Full-text

Semi-automated regional classification of the style of activity of slow rock-slope deformations using PS InSAR and SqueeSAR velocity data

Landslides ◽

10.1007/s10346-021-01654-0 ◽

2021 ◽

Author(s):

Chiara Crippa ◽

Elena Valbuzzi ◽

Paolo Frattini ◽

Giovanni B. Crosta ◽

Margherita C. Spreafico ◽

...

Keyword(s):

Rock Slope ◽

Progressive Failure ◽

Principal Component ◽

Cost Effective ◽

Displacement Rate ◽

Machine Learning Classification ◽

Management Perspective ◽

Alpine Environments

AbstractLarge slow rock-slope deformations, including deep-seated gravitational slope deformations and large landslides, are widespread in alpine environments. They develop over thousands of years by progressive failure, resulting in slow movements that impact infrastructures and can eventually evolve into catastrophic rockslides. A robust characterization of their style of activity is thus required in a risk management perspective. We combine an original inventory of slow rock-slope deformations with different PS-InSAR and SqueeSAR datasets to develop a novel, semi-automated approach to characterize and classify 208 slow rock-slope deformations in Lombardia (Italian Central Alps) based on their displacement rate, kinematics, heterogeneity and morphometric expression. Through a peak analysis of displacement rate distributions, we characterize the segmentation of mapped landslides and highlight the occurrence of nested sectors with differential activity and displacement rates. Combining 2D decomposition of InSAR velocity vectors and machine learning classification, we develop an automatic approach to characterize the kinematics of each landslide. Then, we sequentially combine principal component and K-medoids cluster analyses to identify groups of slow rock-slope deformations with consistent styles of activity. Our methodology is readily applicable to different landslide datasets and provides an objective and cost-effective support to land planning and the prioritization of local-scale studies aimed at granting safety and infrastructure integrity.

Download Full-text

The Underlying Order Induced by Orthogonality and the Quantum Speed Limit

Quantum Reports ◽

10.3390/quantum3030024 ◽

2021 ◽

Vol 3 (3) ◽

pp. 376-388

Author(s):

Francisco J. Sevilla ◽

Andrea Valdés-Hernández ◽

Alan J. Barrios

Keyword(s):

Energy Spectrum ◽

Energy Distribution ◽

Finite Time ◽

Complete Characterization ◽

Comprehensive Analysis ◽

Orthogonality Condition ◽

Speed Limit ◽

Physical Quantities

We perform a comprehensive analysis of the set of parameters {ri} that provide the energy distribution of pure qutrits that evolve towards a distinguishable state at a finite time τ, when evolving under an arbitrary and time-independent Hamiltonian. The orthogonality condition is exactly solved, revealing a non-trivial interrelation between τ and the energy spectrum and allowing the classification of {ri} into families organized in a 2-simplex, δ2. Furthermore, the states determined by {ri} are likewise analyzed according to their quantum-speed limit. Namely, we construct a map that distinguishes those ris in δ2 correspondent to states whose orthogonality time is limited by the Mandelstam–Tamm bound from those restricted by the Margolus–Levitin one. Our results offer a complete characterization of the physical quantities that become relevant in both the preparation and study of the dynamics of three-level states evolving towards orthogonality.

Download Full-text

Molecular Classification and Tumor Microenvironment Characterization of Gallbladder Cancer by Comprehensive Genomic and Transcriptomic Analysis

Cancers ◽

10.3390/cancers13040733 ◽

2021 ◽

Vol 13 (4) ◽

pp. 733

Author(s):

Nobutaka Ebata ◽

Masashi Fujita ◽

Shota Sasagawa ◽

Kazuhiro Maejima ◽

Yuki Okawa ◽

...

Keyword(s):

Tumor Microenvironment ◽

Gallbladder Cancer ◽

Epithelial To Mesenchymal Transition ◽

Molecular Classification ◽

Mesenchymal Transition ◽

Elevated Expression ◽

Fresh Frozen ◽

Therapeutic Decision Making

Gallbladder cancer (GBC), a rare but lethal disease, is often diagnosed at advanced stages. So far, molecular characterization of GBC is insufficient, and a comprehensive molecular portrait is warranted to uncover new targets and classify GBC. We performed a transcriptome analysis of both coding and non-coding RNAs from 36 GBC fresh-frozen samples. The results were integrated with those of comprehensive mutation profiling based on whole-genome or exome sequencing. The clustering analysis of RNA-seq data facilitated the classification of GBCs into two subclasses, characterized by high or low expression levels of TME (tumor microenvironment) genes. A correlation was observed between gene expression and pathological immunostaining. TME-rich tumors showed significantly poor prognosis and higher recurrence rate than TME-poor tumors. TME-rich tumors showed overexpression of genes involved in epithelial-to-mesenchymal transition (EMT) and inflammation or immune suppression, which was validated by immunostaining. One non-coding RNA, miR125B1, exhibited elevated expression in stroma-rich tumors, and miR125B1 knockout in GBC cell lines decreased its invasion ability and altered the EMT pathway. Mutation profiles revealed TP53 (47%) as the most commonly mutated gene, followed by ELF3 (13%) and ARID1A (11%). Mutations of ARID1A, ERBB3, and the genes related to the TGF-β signaling pathway were enriched in TME-rich tumors. This comprehensive analysis demonstrated that TME, EMT, and TGF-β pathway alterations are the main drivers of GBC and provides a new classification of GBCs that may be useful for therapeutic decision-making.

Download Full-text

High-resolution view of HIV-1 reverse transcriptase initiation complexes and inhibition by NNRTI drugs

Nature Communications ◽

10.1038/s41467-021-22628-9 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Betty Ha ◽

Kevin P. Larsen ◽

Jingji Zhang ◽

Ziao Fu ◽

Elizabeth Montabana ◽

...

Keyword(s):

Reverse Transcriptase ◽

Viral Entry ◽

Reverse Transcription ◽

Molecular Mechanisms ◽

Dissociation Kinetics ◽

Structural Mechanism ◽

Medium Resolution ◽

Kinetics Of ◽

Hiv 1

AbstractReverse transcription of the HIV-1 viral RNA genome (vRNA) is an integral step in virus replication. Upon viral entry, HIV-1 reverse transcriptase (RT) initiates from a host tRNALys3 primer bound to the vRNA genome and is the target of key antivirals, such as non-nucleoside reverse transcriptase inhibitors (NNRTIs). Initiation proceeds slowly with discrete pausing events along the vRNA template. Despite prior medium-resolution structural characterization of reverse transcriptase initiation complexes (RTICs), higher-resolution structures of the RTIC are needed to understand the molecular mechanisms that underlie initiation. Here we report cryo-EM structures of the core RTIC, RTIC–nevirapine, and RTIC–efavirenz complexes at 2.8, 3.1, and 2.9 Å, respectively. In combination with biochemical studies, these data suggest a basis for rapid dissociation kinetics of RT from the vRNA–tRNALys3 initiation complex and reveal a specific structural mechanism of nucleic acid conformational stabilization during initiation. Finally, our results show that NNRTIs inhibit the RTIC and exacerbate discrete pausing during early reverse transcription.

Download Full-text

Practical classification of triple-negative breast cancer: intratumoral heterogeneity, mechanisms of drug resistance, and novel therapies

npj Breast Cancer ◽

10.1038/s41523-020-00197-2 ◽

2020 ◽

Vol 6 (1) ◽

Author(s):

Antonio Marra ◽

Dario Trapani ◽

Giulia Viale ◽

Carmen Criscitiello ◽

Giuseppe Curigliano

Keyword(s):

Breast Cancer ◽

Triple Negative Breast Cancer ◽

Triple Negative ◽

Residual Disease ◽

Therapeutic Approaches ◽

Minimal Residual Disease Monitoring ◽

Anticancer Treatment ◽

Immune Contexture

Abstract Triple-negative breast cancer (TNBC) is not a unique disease, encompassing multiple entities with marked histopathological, transcriptomic and genomic heterogeneity. Despite several efforts, transcriptomic and genomic classifications have remained merely theoretic and most of the patients are being treated with chemotherapy. Driver alterations in potentially targetable genes, including PIK3CA and AKT, have been identified across TNBC subtypes, prompting the implementation of biomarker-driven therapeutic approaches. However, biomarker-based treatments as well as immune checkpoint inhibitor-based immunotherapy have provided contrasting and limited results so far. Accordingly, a better characterization of the genomic and immune contexture underpinning TNBC, as well as the translation of the lessons learnt in the metastatic disease to the early setting would improve patients’ outcomes. The application of multi-omics technologies, biocomputational algorithms, assays for minimal residual disease monitoring and novel clinical trial designs are strongly warranted to pave the way toward personalized anticancer treatment for patients with TNBC.

Download Full-text

A Hybrid Methodology For On-Line Process Monitoring

International Journal of Chemical Reactor Engineering ◽

10.2202/1542-6580.1119 ◽

2004 ◽

Vol 2 (1) ◽

Cited By ~ 1

Author(s):

Rakesh Kumar ◽

Avinash M. Jade ◽

Valadi K. Jayaraman ◽

Bhaskar D. Kulkarni

Keyword(s):

Process Monitoring ◽

Current Practice ◽

Locally Linear Embedding ◽

Support Vector ◽

Nonlinear Dimensionality Reduction ◽

Hybrid Strategy ◽

Vector Machines ◽

On Line ◽

Line Process

A hybrid strategy of using (i) locally linear embedding for nonlinear dimensionality reduction of high dimensional data and (ii) support vector machines for classification of the resultant features is proposed as a robust methodology for process monitoring. Illustrative examples substantiate the methodology vis-à-vis current practice.

Download Full-text

First Characterization of an Archaeal GTP-Dependent Phosphoenolpyruvate Carboxykinase from the Hyperthermophilic Archaeon Thermococcus kodakaraensis KOD1

Journal of Bacteriology ◽

10.1128/jb.186.14.4620-4627.2004 ◽

2004 ◽

Vol 186 (14) ◽

pp. 4620-4627 ◽

Cited By ~ 29

Author(s):

Wakao Fukuda ◽

Toshiaki Fukui ◽

Haruyuki Atomi ◽

Tadayuki Imanaka

Keyword(s):

Binding Sites ◽

Phosphoenolpyruvate Carboxykinase ◽

Cation Binding ◽

Activity Levels ◽

Binding Region ◽

Hyperthermophilic Archaeon ◽

Dependent Activity ◽

Additional Role

ABSTRACT Phosphoenolpyruvate carboxykinase (PCK), which catalyzes the nucleotide-dependent, reversible decarboxylation of oxaloacetate to yield phosphoenolpyruvate and CO2, is one of the important enzymes in the interconversion between C3 and C4 metabolites. This study focused on the first characterization of the enzymatic properties and expression profile of an archaeal PCK from the hyperthermophilic archaeon Thermococcus kodakaraensis (Pck Tk ). Pck Tk showed 30 to 35% identities to GTP-dependent PCKs from mammals and bacteria but was located in a branch distinct from that of the classical enzymes in the phylogenetic tree, together with other archaeal homologs from Pyrococcus and Sulfolobus spp. Several catalytically important regions and residues, found in all known PCKs irrespective of their nucleotide specificities, were conserved in Pck Tk . However, the predicted GTP-binding region was unique compared to those in other GTP-dependent PCKs. The recombinant Pck Tk actually exhibited GTP-dependent activity and was suggested to possess dual cation-binding sites specific for Mn2+ and Mg2+. The enzyme preferred phosphoenolpyruvate formation from oxaloacetate, since the Km value for oxaloacetate was much lower than that for phosphoenolpyruvate. The transcription and activity levels in T. kodakaraensis were higher under gluconeogenic conditions than under glycolytic conditions. These results agreed with the role of Pck Tk in providing phosphoenolpyruvate from oxaloacetate as the first step of gluconeogenesis in this hyperthermophilic archaeon. Additionally, under gluconeogenic conditions, we observed higher expression levels of Pck Tk on pyruvate than on amino acids, implying that it plays an additional role in the recycling of excess phosphoenolpyruvate produced from pyruvate, replacing the function of the anaplerotic phosphoenolpyruvate carboxylase that is missing from this archaeon.

Download Full-text

Characterization of Electroencephalographic Findings at an Electrodiagnostic Unit of a Tertiary Hospital, North-central Nigeria

JOURNAL OF RESEARCH IN BASIC AND CLINICAL SCIENCES ◽

10.46912/jrbcs.94 ◽

2021 ◽

Vol 2 (1) ◽

pp. 49-55

Author(s):

E U Iwuozo ◽

J O Enyikwola ◽

I O Obekpa ◽

O O Ijachi ◽

A A Godwin ◽

...

Keyword(s):

Tertiary Hospital ◽

Seizure Disorder ◽

Cross Sectional ◽

North Central ◽

Younger Age ◽

High Prevalence ◽

Diagnosis And Classification ◽

Age Range

Electroencephalography (EEG) remains an important investigative tool in supporting the diagnosis and classification of various seizure types. We sought to examine and characterize the EEG findings from all patients referred for the procedure. This cross-sectional retrospective study was carried out at an EEG unit in Federal Medical Centre, Makurdi, Benue State, North Central Nigeria from May 2016 to December 2020. Relevant patients' information were extracted and analysed using SPSS version 21. A total of 484 patients were seen over the study period with age range of 1-87 years and median age of 23 years. They comprised of 254 (52.5%) male and 230 (47.5%) female. The psychiatrist and the Physicians/Neurologist referred most of them for EEG, 201 (41.5%) and 124 (25.6%) respectively. The most reported indication for EEG was clinical suspicion of seizure disorder 291 (60.1%), whilst some did not have a clear indication 111 (22.9%). About 417 (86.2%) of our patients had abnormal EEG finding out of which 414 (99.3%) were diagnostic of seizure disorder made up of generalized seizure in 255 (61.6%) and focal seizure in 159 (38.4%). About 237 (48.9%) of them were already on antiepileptic drugs (AEDs) at referral of which 190 (80.2%0 were taking carbamazepine. This study showed a high prevalence of abnormal EEG with most of them diagnostic of seizure disorder especially generalized seizure. They were mostly of younger age group with about half of them already on AEDs at referral, majority of who were sent by the Psychiatrist.

Download Full-text

Soil–landform–plant-community relationships of a periglacial landscape on Potter Peninsula, maritime Antarctica

Solid Earth ◽

10.5194/se-6-583-2015 ◽

2015 ◽

Vol 6 (2) ◽

pp. 583-594 ◽

Cited By ~ 12

Author(s):

E. L. Poelking ◽

C. E. R. Schaefer ◽

E. I. Fernandes Filho ◽

A. M. de Andrade ◽

A. A. Spielmann

Keyword(s):

Climate Change ◽

Plant Communities ◽

Terrestrial Ecosystems ◽

Maritime Antarctica ◽

Climate Change Effects ◽

Ornithogenic Soils ◽

Physical Environmental Factors ◽

Potter Peninsula

Abstract. Integrated studies on the interplay between soils, periglacial geomorphology and plant communities are crucial for the understanding of climate change effects on terrestrial ecosystems of maritime Antarctica, one of the most sensitive areas to global warming. Knowledge on physical environmental factors that influence plant communities can greatly benefit studies on the monitoring of climate change in maritime Antarctica, where new ice-free areas are being constantly exposed, allowing plant growth and organic carbon inputs. The relationship between topography, plant communities and soils was investigated on Potter Peninsula, King George Island, maritime Antarctica. We mapped the occurrence and distribution of plant communities and identified soil–landform–vegetation relationships. The vegetation map was obtained by classification of a QuickBird image, coupled with detailed landform and characterization of 18 soil profiles. The sub-formations were identified and classified, and we also determined the total elemental composition of lichens, mosses and grasses. Plant communities on Potter Peninsula occupy 23% of the ice-free area, at different landscape positions, showing decreasing diversity and biomass from the coastal zone to inland areas where sub-desert conditions prevail. There is a clear dependency between landform and vegetated soils. Soils that have greater moisture or are poorly drained, and with acid to neutral pH, are favourable for moss sub-formations. Saline, organic-matter-rich ornithogenic soils of former penguin rookeries have greater biomass and diversity, with mixed associations of mosses and grasses, while stable felsenmeers and flat rocky cryoplanation surfaces are the preferred sites for Usnea and Himantormia lugubris lichens at the highest surface. Lichens sub-formations cover the largest vegetated area, showing varying associations with mosses.

Download Full-text