Miracle-dz/UniFAR-FTUs huggingface dataset:
Linking 16S rRNA Gene Classification to amoA Gene Taxonomy Reveals Environmental Distribution of Ammonia-Oxidizing Archaeal Clades in Peatland Soils

The recently established phylogeny of amoA provides a finer resolution than previous studies, allowing clustering of AOA beyond the order level and thus revealing novel clades. While the 16S rRNA gene is mostly appreciated in microbiome studies, this novel phylogeny is in limited use. ABSTRACT A highly resolved taxonomy for ammonia-oxidizing archaea (AOA) based on the alpha subunit of ammonia monooxygenase (amoA) was recently established, which uncovered novel environmental patterns of AOA, challenging previous generalizations. However, many microbiome studies target the 16S rRNA gene as a marker; thus, the usage of this novel taxonomy is currently limited. Here, we exploited the phylogenetic congruence of archaeal amoA and 16S rRNA genes to link 16S rRNA gene classification to the novel amoA taxonomy. We screened publicly available archaeal genomes and contigs for the co-occurring amoA and 16S rRNA genes and constructed a 16S rRNA gene database with the corresponding amoA clade taxonomy. Phylogenetic trees of both marker genes confirmed congruence, enabling the identification of clades. We validated this approach with 16S rRNA gene amplicon data from peatland soils. We succeeded in linking 16S rRNA gene amplicon sequence variants belonging to the class Nitrososphaeria to seven different AOA (amoA) clades, including two of the most frequently detected clades (Nitrososphaerales γ and δ clades) for which no pure culture is currently available. Water status significantly impacted the distribution of the AOA clades as well as the whole AOA community structure, which was correlated with pH, nitrate, and ammonium, consistent with previous clade predictions. Our study emphasizes the need to distinguish among AOA clades with distinct ecophysiologies and environmental preferences, for a better understanding of the ecology of the globally abundant AOA. IMPORTANCE The recently established phylogeny of amoA provides a finer resolution than previous studies, allowing clustering of AOA beyond the order level and thus revealing novel clades. While the 16S rRNA gene is mostly appreciated in microbiome studies, this novel phylogeny is in limited use. Here, we provide an alternative path to identifying AOA with this novel and highly resolved amoA taxonomy by using 16S rRNA gene sequencing data. We constructed a 16S rRNA gene database with the associated amoA clade taxonomy based on their phylogenetic congruence. With this database, we were able to assign 16S rRNA gene amplicons from peatland soils to different AOA clades, with a level of resolution provided previously only by amoA phylogeny. As 16S rRNA gene amplicon sequencing is still widely employed in microbiome studies, our database may have a broad application for interpreting the ecology of globally abundant AOA.
Deep brain stimulation in the subthalamic nucleus for Parkinson’s disease can restore dynamics of striatal networks

Deep brain stimulation (DBS) of the subthalamic nucleus (STN) is highly effective in alleviating movement disability in patients with Parkinson’s disease (PD). However, its therapeutic mechanism of action is unknown. The healthy striatum exhibits rich dynamics resulting from an interaction of beta, gamma and theta oscillations. These rhythms are at the heart of selection, initiation and execution of motor programs, and their loss or exaggeration due to dopamine (DA) depletion in PD is a major source of the behavioral deficits observed in PD patients. Interrupting abnormal rhythms and restoring the interaction of rhythms as observed in the healthy striatum may then be instrumental in the therapeutic action of DBS. We develop a biophysical networked model of a BG pathway to study how abnormal beta oscillations can emerge throughout the BG in PD, and how DBS can restore normal beta, gamma and theta striatal rhythms. Our model incorporates STN projections to the striatum, long known but understudied, that were recently shown to preferentially target fast spiking interneurons (FSI) in the striatum. We find that DBS in STN is able to normalize striatal medium spiny neuron (MSN) activity by recruiting FSI dynamics, and restoring the inhibitory potency of FSIs observed in normal condition. We also find that DBS allows the re-expression of gamma and theta rhythms, thought to be dependent on high DA levels and thus lost in PD, through cortical noise control. Our study shows how BG connectivity can amplify beta oscillations, and delineates the role of DBS in disrupting beta oscillations and providing corrective input to STN efferents to restore healthy striatal dynamics. It also suggests how gamma oscillations can be leveraged to enhance or supplement DBS treatment and improve its effectiveness.
Call Me Back: Examining Provider Biases Through Callback Rates and Responsiveness

We conducted a phone-based field experiment to investigate the callback rate of psychologists. Providers (N = 903) in Los Angeles, California who were selected from a health maintenance organization insurance panel list were left voicemails by actors simulating patients of various backgrounds (i.e., race, gender, clinical diagnosis, and ethnic distinctiveness of name). Findings indicated that 71.5% of providers did not return calls to prospective patients. There were no main effects of race and ethnicity on callback. However, ethnic distinctiveness of name moderated the effects of diagnosis. Providers were more responsive to depressed patients with ethnic names, but less responsive to patients with ethnic names and personality or substance abuse disorders. These findings are important because unresponsive providers and insurance companies that do not provide up-to-date panel listings can act as barriers to care, which can have deleterious consequences for help-seekers. Advocacy recommendations and the importance of cultural competency are highlighted.
Abundant small RNAs in the reproductive tissues of the honey bee, Apis mellifera, are a plausible mechanism for epigenetic inheritance and parental manipulation of gene expression

Polyandrous social insects such as the honey bee are prime candidates for parental manipulation of gene expression in offspring. Although there is good evidence for parent-of-origin effects in honey bees the epigenetic mechanisms that underlie these effects remain a mystery. Small RNA molecules such as miRNAs, piRNAs and siRNAs play important roles in transgenerational epigenetic inheritance and in the regulation of gene expression during development. Here we present the first characterisation of small RNAs present in honey bee reproductive tissues: ovaries, spermatheca, semen, fertilised and unfertilised eggs, and testes. We show that semen contains fewer piRNAs relative to eggs and ovaries, and that piRNAs and miRNAs which map antisense to genes involved in DNA regulation and developmental processes are differentially expressed between tissues. tRNA fragments are highly abundant in semen and have a similar profile to those seen in semen in other animals. Intriguingly we find abundant piRNAs that target the sex determination locus, suggesting that piRNAs may play a role in honey bee sex determination. We conclude that small RNAs play a fundamental role in honey bee gametogenesis and reproduction and provide a plausible mechanism for parent-of origin-effects on gene expression and reproductive physiology.
NORDIC Increases the Sensitivity and Preserves the Spatiotemporal Precision of fMRI Responses

As the neuroimaging field moves towards detecting smaller effects at higher spatial resolutions, and faster sampling rates, there is increased attention given to the deleterious contribution of unstructured, thermal noise. Here, we critically evaluate the performance of a recently developed reconstruction method, termed NORDIC, for suppressing thermal noise using datasets acquired with various field strengths, voxel sizes, sampling rates, and task designs. Following minimal preprocessing, statistical activation (t-values) of NORDIC processed data was compared to the results obtained with alternative denoising methods. Additionally, we examined the consistency of the estimates of task responses at the single-voxel, single run level, using a finite impulse response (FIR) model. To examine the potential impact on effective image resolution, the overall smoothness of the data processed with different methods was estimated. Finally, to determine if NORDIC alters or removes important temporal information, we employed an exhaustive leave-p-out cross validation approach, using FIR task responses to predict held out timeseries, quantified using R2. After NORDIC, the t-values are increased, an improvement comparable to what could be achieved by 1.5 voxels smoothing, and task events are clearly visible and have less cross-run error. These advantages are achieved in the absence of large changes in estimates of spatial smoothness. Cross-validated R2s based on the FIR models show that NORDIC is not measurably distorting the temporal structure of the data and is the best predictor of non-denoised time courses. The results demonstrate that analyzing 1 run of data after NORDIC produces results equivalent to using 2 to 3 original runs and that NORDIC performs equally well across a diverse array of functional imaging protocols. Significance Statement For functional neuroimaging, the increasing availability of higher field strengths and ever higher spatiotemporal resolutions has led to concomitant increase in concerns about the deleterious effects of thermal noise. Historically this noise source was suppressed using methods that reduce spatial precision such as image blurring or averaging over a large number of trials or sessions, which necessitates large data collection efforts. Here, we critically evaluate the performance of a recently developed reconstruction method, termed NORDIC. Across datasets varying in field strength, voxel sizes, sampling rates, and task designs, NORDIC produces substantial gains in data quality. Both conventional t-statistics derived from general linear models and coefficients of determination for predicting unseen data are improved, while avoiding meaningful increases in typical estimates of image smoothness or substantial losses of temporal information.
Gene signature of circulating platelet‐bound neutrophils is associated with poor prognosis in cancer patients

Beyond their critical role in hemostasis, platelets physically interact with neutrophils to form neutrophil-platelet aggregates (NPAs), enhancing neutrophil effector functions during inflammation. NPAs may also promote disease worsening in various inflammatory diseases. However, characterization of NPAs in cancer remains totally unexplored. Using ImageStream®X (ISX) imaging flow cytometer, we were not only allowed able to detect CD15+ CD14− CD36+ ITGA2B+ NPAs in both healthy donors’ (HDs) and cancer patients’ bloods, but we also showed that NPAs result from the binding of platelets preferentially to low-density neutrophils (LDNs) as opposed to normal-density neutrophils (NDNs). By re-analyzing two independent public scRNAseq data of whole blood leukocytes from cancer patients and HDs, we could identify a subset of neutrophils with high platelet gene expression that may correspond to NPAs. Moreover, we showed that cancer patients’ derived NPAs possessed a distinct molecular signature compared with the other neutrophil subsets, independently of platelet genes. Gene ontology (GO) term enrichment analysis of this NPAs-associated neutrophil transcriptomic signature revealed a significant enrichment of neutrophil degranulation, chemotaxis and trans-endothelial migration GO terms. Lastly, using The Cancer Genome Atlas (TCGA), we could show by multivariate Cox analysis that the NPAs-associated neutrophil transcriptomic signature was associated with a worse patient prognosis in several cancer types. These results suggest that neutrophils from NPAs are systemically primed by platelets empowering them with cancer progression capacities once at tumor site. NPAs may therefore hold clinical utility as novel non-invasive blood prognostic biomarker in cancer patients with solid tumors. Novelty and Impact Platelets physically interact with peripheral blood neutrophils to form neutrophil-platelet aggregates (NPAs), known to promote disease worsening in various inflammatory diseases. However, characterization of NPAs in cancer remains totally unexplored. We showed that NPAs-associated neutrophils were a yet-unreported unique subset of circulating neutrophils associated with a worse patient prognosis in several cancer types. NPAs may hold clinical utility as novel non-invasive blood prognostic biomarker in cancer patients with solid tumors.
Scaling Up the Accuracy of Naive-Bayes Classi(cid:12)ers: a Decision-Tree Hybrid

Naive-Bayes induction algorithms were previously shown to be surprisingly accurate on many classi(cid:12)-cation tasks even when the conditional independence assumption on which they are based is violated. However, most studies were done on small databases. We show that in some larger databases, the accuracy of Naive-Bayes does not scale up as well as decision trees. We then propose a new algorithm, NBTree, which induces a hybrid of decision-tree classi(cid:12)ers and Naive-Bayes classi(cid:12)ers: the decision-tree nodes contain uni-variate splits as regular decision-trees, but the leaves contain Naive-Bayesian classi(cid:12)ers. The approach re-tains the interpretability of Naive-Bayes and decision trees, while resulting in classi(cid:12)ers that frequently out-perform both constituents, especially in the larger databases tested.
P300 and Vigilance Level of University Student Under Hot and Humid Condition

The purpose of our study is to contrast the P300 and vigilance indicator in hot and humid condition. Sixteen participants performed this experiment. The participants are university students with nationality Japanese (eight participants) and Indonesia (eight participants). Indonesia participants conducted four experimental conditions: standing position and natural condition (without Air Conditioning and fan), standing position and used a fan, standing position and used Air Conditioning, and sitting position and used Air Conditioning. Japanese participants conducted only one experimental condition (standing position and natural condition (without Air Conditioning and fan). P300 and vigilance indicators were measured before and after the given task. Event-Related Potential (ERP) P300 and Psychomotor Vigilance Task (PVT) were accommodated for P300 and vigilance indicators. According to the measurements, the task performances of the Indonesia participants among interaction between the subjects and the contrasting conditions were significantly different in ERP P300 latency (p<0.05), ERP P300 potential (p<0.05), and mean reaction time of PVT (p<0.05). On standing position and natural conditioning, P300 and PVT were not significantly different by nationality (Indonesia and Japanese students). Results showed that high temperature and humidity in the Japan summer season decreased P300 and vigilance, particularly for natural conditions.
ORAL INVESTIGATIONS Immediate implant placement after maxillary sinus lift using the side window technique: clinical case report Colocação de implante imediato após levantamento de seio maxilar através da técnica de janela lateral: relato de caso clínico

Aim: The aim of this study was to report a maxillary sinus lift surgery associated with the installation of an immediate implant associated with late loading in edge with 3.5 mm in height. Methods: The sinus lift surgery was performed using the lateral window technique, followed by the immediate installation of the implant and subsequent manufacture of a screw-retained single prosthesis. Results: Through the technique of breast lift, it was possible to promote local bone formation in a vertical direction, enabling local dental rehabilitation. Conclusions: Following a solid and meticulous planning, even in crests with less than 5 mm in height, a transcrestal technique can be used predictably with an adequate clinical and radiological outcome, giving patients excellent stability of the grafted material and excellent clinical results.
Pathway profiling of a novel SRC inhibitor, AZD0424, in combination with MEK inhibitors

A more comprehensive understanding of how cells respond to drug intervention, the likely immediate signalling responses and how resistance may develop within different microenvironments allows us anticipate how cells adapt to targeted therapy enabling more informed prediction of rational drug combinations. The non-receptor tyrosine kinase SRC regulates many cellular signalling processes and pharmacological inhibition has long been a target of drug discovery projects for the treatment of cancer. Here we describe the in vitro and in vivo characterisation of the small molecule SRC inhibitor, AZD0424. We show that AZD0424 potently inhibits the phosphorylation of tyrosine-416 of SRC (IC50 ∼ 100 nM) in many cancer cell lines; however inhibition of cell viability, via a G1 cell cycle arrest, was observed only in a sub-set of cancer cell lines in the low (on target) micromolar range. We profiled the changes in intracellular pathway signalling in cancer cells following exposure to AZD0424 and other targeted therapies using Reverse Phase Protein Array analysis. We demonstrate that SRC is activated in response to MEK inhibitor (trametinib or AZD6244)-treatment of KRAS mutant colorectal cell lines (HCT116 and DLD1) and that AZD0424 abrogates this. Cell lines treated with trametinib or AZD6244 in combination with AZD0424 revealed reduction of EGFR, FAK and SRC compensatory activation, and, synergistically inhibits cell viability in vitro. In vivo, trametinib-treatment of mice bearing HCT116 tumours increased phosphorylation of SRC on Tyr416, and when combined with AZD0424, inhibition of tumour growth is greater than trametinib alone. We also demonstrate that drug-induced resistance to trametinib is not re-sensitised by AZD0424 treatment in vitro, likely as a result of multiple compensatory signalling mechanisms; however inhibition of SRC remains an effective way to block invasion of trametinib resistant tumour cells. These data imply that inhibiting SRC may offer a useful addition to MEK inhibitor combination strategies.
BACTERIOLOGICAL PROFILE AND ANTIBIOTIC SUSCEPTIBILITY PATTERN OF LOWER RESPIRATORY TRACT INFECTION IN A TERTIARY HOSPITAL IN NORTH-EAST INDIA

Background: Sputum samples are often sent in the microbiology department for culture and sensitivity as lower respiratory tract infections are frequent among patients. The consequences of increased drug resistance are far reaching since bacterial infection of the lower respiratory tract is a major cause of death from infectious disease. Objective: To determine the commonly encountered bacterial pathogens in sputum samples along with their antibiogram in patients attending RIMS Hospital, Imphal. Materials and Methods: This was a retrospective study conducted on sputum samples sent to the Microbiology Department during July 2015 to June 2016. Sputum samples were subjected to isolation and identification of bacteria by standard technique and subsequently antibiogram was carried out by Kirby-Bauer disc diffusion method. Results: Out of the 523 sputum samples evaluated, 208(39.77%) were culture positive for pathogenic bacteria. Gram negative bacterial isolates (58.94%) were predominant, among which Klebsiella pneumoniae (28.77%) was the major pathogen followed by Staphylococcus aureus (27.35%), Escherichia coli (20.23%), Pseudomonas aeruginosa (6.60%), Coagulase Negative Stapylococcus (5.18%), Streptococcus pyogenes (4.71%), Streptococcus pneumoniae (3.77%), Acinetobacter spp. (1.41%), Enterobacter spp. (1.41%) and Proteus spp. (0.47%). Gram positive organisms showed high susceptibility to vancomycin and gentamicin; while majority of gram negative organisms had high susceptibility to aminoglycosides and carbepenems. Conclusion: Before starting empirical antibiotics on patients with lower respiratory tract infection, it is always advisable to obtain sputum for culture and antibiotic sensitivity test so as to avoid irrational drug usage and emergence of resistant strains.
Longevity of the antimicrobial effect of Silver Diamond Fluoride on cariogenic bacteria in children- A Systematic review

Aim: To critically evaluate the effect of Silver diamine fluoride (SDF) on the bacterial load of cariogenic bacteria in children. Electronic databases were searched from Google Scholar, PubMed, Wiley online library, SciELO, Science Direct, Scopus, Cochrane from 2013 till 15 of August 2020 to list out studies undertaken to evaluate the effect of silver diamine fluoride on cariogenic bacteria in children from 2 to 10 years. Abstracts and subsequently eligible full-text articles were screened. Results: Six hundred sixty-five studies were obtained from all the databases. After a thorough screening, five studies met all the inclusion criteria. Four studies assessed the bacterial load with the microbiological culture method, two studies assessed bacteria with Adenosine triphosphate (ATP) bio-luminometer. Conclusion: Peak antimicrobial action of SDF was appreciated from the 3 -30 day of post-application.
Secondary Plant Metabolites for Sun Protective Cosmetics: From Pre-Selection to Product Formulation

Topical sun protective cosmetics (sunscreens, pre- and post-sun) have been intensively developed and produced to protect human skin against solar irradiation-associated damages/pathologies. Unfortunately, routine cosmetics for sun protection containing synthetic organic and/or physical sunscreens could exert adverse effects towards human organisms and bring undesirable ecological changes. Terrestrial and marine plant species, being exposed to sun light for hundreds of millions of years, have evolved two pro-survival strategies: effective protection against/adaptation to its deleterious effects and the use of solar energy for photosynthesis/photo-biochemical reactions. Secondary plant metabolites (SPM) are primary sensors of solar energy and mediators of its use (photo-sensitisers) or neutralisation (photo-protectors). A similar double photo-protective/photo-sensitising system is built in within human skin. Modern development of toxicologically/ecologically safe yet effective sun-protective cosmetics attempts to pre-select photo-stable and non-phototoxic SPMs that provide broad UVA + UVB sunscreen, free radical scavenging and direct antioxidant defence, endogenous antioxidant rescue, induction of antioxidant enzymes (indirect antioxidant defence), and normalisation of metabolic and immune responses to UVA + UVB. Proper formulation of sun protective cosmetics should assure targeted delivery of photo-active SPMs to definite skin layers to invigorate the built in photo-chemical skin barrier.