Miracle-dz/UniFAR-FTUs huggingface dataset:
Distinguishing between Microbial Habitats Unravels Ecological Complexity in Coral Microbiomes

This study demonstrates that coral tissue or mucus habitats structure the microbiome of corals and that separation of these habitats facilitates identification of consistent microbial associates. Using this approach, we demonstrated that sequences related to “Candidatus Amoebophilus,” recognized intracellular symbionts of amoebae, were highly associated with the tissues of Caribbean corals and possibly endosymbionts of a protistan host within corals, adding a further degree of intricacy to coral holobiont symbioses. Examining specific habitats within complex hosts such as corals is useful for targeting important microbial associations that may otherwise be masked by the sheer microbial diversity associated with all host habitats. ABSTRACT The diverse prokaryotic communities associated with reef-building corals may provide important ecological advantages to their threatened hosts. The consistency of relationships between corals and specific prokaryotes, however, is debated, and the locations where microbially mediated processes occur in the host are not resolved. Here, we examined how the prokaryotic associates of five common Caribbean corals with different evolutionary and ecological traits differ across mucus and tissue habitats. We used physical and chemical separation of coral mucus and tissue and sequencing of partial small-subunit rRNA genes of bacteria and archaea from these samples to demonstrate that coral tissue and mucus harbor unique reservoirs of prokaryotes, with 23 to 49% and 31 to 56% of sequences exclusive to the tissue and mucus habitats, respectively. Across all coral species, we found that 46 tissue- and 22 mucus-specific microbial members consistently associated with the different habitats. Sequences classifying as “Candidatus Amoebophilus,” Bacteroidetes-affiliated intracellular symbionts of amoebae, emerged as previously unrecognized tissue associates of three coral species. This study demonstrates how coral habitat differentiation enables highly resolved examination of ecological interactions between corals and their associated microorganisms and identifies previously unrecognized tissue and mucus associates of Caribbean corals for future targeted study. IMPORTANCE This study demonstrates that coral tissue or mucus habitats structure the microbiome of corals and that separation of these habitats facilitates identification of consistent microbial associates. Using this approach, we demonstrated that sequences related to “Candidatus Amoebophilus,” recognized intracellular symbionts of amoebae, were highly associated with the tissues of Caribbean corals and possibly endosymbionts of a protistan host within corals, adding a further degree of intricacy to coral holobiont symbioses. Examining specific habitats within complex hosts such as corals is useful for targeting important microbial associations that may otherwise be masked by the sheer microbial diversity associated with all host habitats.
Uncontrolled confounding in studies of screening effectiveness: an example of colonoscopy

Objective To estimate the expected magnitude of error produced by uncontrolled confounding from health behaviours in observational medical record-based studies evaluating effectiveness of screening colonoscopy. Methods We used data from the prospective National Institutes of Health American Association of Retired Persons (NIH-AARP) Diet and Health Study to assess the impact of health behaviour related factors (lifestyle, education, and use of non-steroidal anti-inflammatory drugs [NSAID]) on the association between colonoscopy and colorectal cancer (CRC) mortality. We first examined the difference between adjusted and unadjusted results within the cohort data, and then estimated a broader range of likely confounding errors based on the Breslow-Day approach that uses prevalence of confounders among persons with and without exposure, and the rate ratio reflecting the association between these confounders and the outcome of interest. As dietary factors and habits are often inter-correlated, we combined these variables (physical activity, body mass index, waist-to-hip ratio, alcohol consumption, and intakes of red meat, processed meat, fibre, milk, and calcium) into a “healthy lifestyle score” (HLS). Results The estimated error (a ratio of biased-to-true result) attributable to confounding by HLS was 0.959–0.997, indicating less than 5% departure from the true effect of colonoscopy on CRC mortality. The corresponding errors ranged from 0.970 to 0.996 for NSAID, and from 0.974 to 1.006 for education (all ≤3% difference). The results for other CRC screening tests were similar. Conclusion Health behaviour-related confounders, either alone or in combination, seem unlikely to strongly affect the association between colonoscopy and CRC mortality in observational studies of CRC screening.
Privacy Preserving Techniques for Speech Processing

Speech is perhaps the most private form of personal communication but current speech processing techniques are not designed to preserve the privacy of the speaker and require complete access to the speech recording. We propose to develop techniques for speech processing which do preserve privacy. While our proposed methods can be applied to a variety of speech processing problems and also generally to problems in other domains, we focus on the problems of keyword spotting, speaker identification, speaker verification, and speech recognition. Each of these applications involve the two separate but overlapping problems of private classifier evaluation and private classifier release. Towards the former, we study designing privacy preserving protocols using primitives such as homomorphic encryption, oblivious transfer, and blind and permute in the framework of secure multiparty computation (SMC). Towards the latter, we study the differential privacy model, and techniques such as exponential method and sensitivity method for releasing differentially private classifiers trained on private data. We summarize our preliminary work on the subject including techniques such as SMC protocols for eigenvector computation, isolated keyword recognition and differentially private release mechanisms for large margin Gaussian mixture models, and classifiers trained from data belonging to multiple parties. Finally, we discuss the proposed directions of research including techniques such as training differentially private hidden Markov models, and a multiparty framework for differentially private classification by data perturbation, and protocols for applications such as privacy preserving music matching and keyword spotting, speaker verification and identification.
Giant light-induced capacitance enhancements in an unconventional capacitor with two-dimensional hole gas

Capacitance is the ability of a device to store energy in the electric field. Conventional capacitors are composed of two metallic contacts with a dielectric in between arranged in different geometries, the most well-known of them being an parallel plate capacitor with the capacitance value, Cgeo=εrε0A/d, solely dependent on the geometry of the structure and the physical properties of the dielectric. In an unconventional capacitor, however, at least one of the plates is replaced with a two-dimensional electron system (2DES) attained in oxide-semiconductor interfaces [1], quantum wells in III-V material heterojunctions [2, 3]. Distinctive to unconventional capacitors is the capability to control carrier concentration in the non-metallic plates through application of a voltage [4]. Additionally the many body interactions among charge carriers in 2DES are manifested as capacitors in series with the geometrical capacitance of the plates [5] as: 1/Ctot = 1/Cgeo + 1/Ckin+ 1/Cex + 1/Ccorr, (1) oequation where Cex, Ccorr and Ckin represent capacitances due to exchange, correlation and kinetic energies of the 2DES, respectively, and Cgeo and Ctot are the geometrical and total capacitance between the electrodes. Noticeably, Cex and Ccorr can contribute negatively to the total capacitance [4] at critical electron densities in 2DES resulting in a Ctot larger than Cgeo. This capacitance enhancement feature can be utilized as an alternative to high-k dielectric materials to increase gate capacitance in MOS transistors [1]. Moreover transitions from a high-density to a totally depleted 2DES are shown to remarkably improve the performance of the voltage-controlled capacitors based on 2DES [6]. Here we report on design, fabrication and capacitive performance of an interdigitated metal-semiconductor-metal (MSM) photodetector with embedded two-dimensional hole gas (2DHG) achieved in a triangular quantum well in a GaAs/AlGaAs hetero-interface. Capacitance-Voltage (C-V) characteristics obtained through impedance spectroscopy in dark indicate behavior of a switchable capacitor while C-V under 850nm laser light exhibit anomalous features of capacitance enhancement. Light generated carriers that increase the charge density in 2DHG account for arousal of anomalies in C-V characteristics through changing the energetic of the unconventional 2DHG electrode. This device carries a giant light-sensitive capacitance which makes it a good candidate for capacitance-based photodetectors.
Cognitive Function May be a Predictor of Retinopathy Progression in Patients with Type 2 Diabetes

Purpose Microvascular and macrovascular complications of diabetes, such as retinopathy and nephropathy, progress over time and may be associated with cognitive decline. In this article, we aim to gain further insight into the association between cognitive function and retinopathy in type 2 diabetes. Methods and Results In this observational 8-year prospective study of 498 outpatients, demographic and clinical variables were monitored, along with retinopathy, depression, anxiety, and cognitive function. Baseline fundus photographs were available in 477 patients, 240 with no retinopathy, 110 with mild retinopathy, and 127 with moderate/more severe retinopathy. Of the first 2 groups, 279 patients were reevaluated after 8 years, of whom 181 still had no/mild retinopathy and 98 had progressed to more severe stages. On multivariate analysis, retinopathy progression was associated with being insulin-treated (p = 0.036), and worse cognitive function (p = 0.025) at baseline. Conclusions Cognitive function may be an independent predictor of retinopathy progression.
PrefixSummary: A Directory Structure for Selective Probing on Wireless Stream of Heterogeneous XML Data

SUMMARY Wireless broadcasting of heterogeneous XML data has become popular in many applications, where energy-e ﬃ cient processing of user queries at the mobile client is a critical issue. This paper proposes a new index structure for wireless stream of heterogeneous XML data to enhance tuning time performance in processing path queries on the stream. The index called PreﬁxSummary stores for each location path in the XML data the address of a bucket in the stream which contains an XML node satisfying the location path and appearing ﬁrst in the stream. We present algorithms to generate broadcast stream with the proposed index and to process a path query on the stream e ﬃ ciently by exploiting the index. We also suggest a replication scheme of PreﬁxSummary within a broadcast cycle to reduce latency in query processing. By analysis and experiment we show the proposed PreﬁxSummary approach can reduce tuning time for processing path queries signiﬁcantly while it can also achieve reasonable access time performance by means of replication of the index over the broadcast stream.
The Prevalence of Dementia in Warsaw Centenarians: a Population – Based Study**

1Department of Neurodegenerative Disorders Medical Research Centre Polish Academy of Sciences/CSK MSWiA Head of Department: prof. dr hab. med. Maria Barcikowska 2International Institute of Molecular and Cell Biology in Warsaw, Poland Head of Department: prof. dr hab. med. Jacek Kuźnicki 3Department of Clinical Geriatrics, Medical University of Warsaw, Poland Head of Department: prof. dr hab. med. Krzysztof Galus
Dynamic accuracy assessment of data-fusion techniques for wearable, inertial and magnetic based human motion capture

Wearable motion capture systems, based on magneto and inertial sensors are considered a promising technology in the field of human motion capture. Compared to golden standard systems, e.g. based on stereo-photogrammetry, they feature a better portability and usability and are suitable for `out of the lab' data collection. While different applications of human motion capture systems based on magneto and inertial sensors have been explored in literature, few studies have provided insights about the accuracy that can be achieved using data-fusion techniques and even less did that in a rigorous and controlled way. This work focuses on the dynamic absolute accuracy assessment of data-fusion algorithms for orientation tracking under controlled conditions. A 7 DOF robotic arm is used in order to apply controlled angular displacements to the motion capture system, in a range of frequencies that is of interest to human motion capture applications. Preliminary results on absolute accuracy that can be achieved with popular and open-source available fusion algorithms, running on a commercial hardware, are reported.
Lentivirus Vector Gene Expression during ES Cell-Derived Hematopoietic Development In Vitro

ABSTRACT The murine embryonal stem (ES) cell virus (MESV) can express transgenes from the long terminal repeat (LTR) promoter/enhancer in undifferentiated ES cells, but expression is turned off upon differentiation to embryoid bodies (EBs) and hematopoietic cells in vitro. We examined whether a human immunodeficiency virus type 1-based lentivirus vector pseudotyped with the vesicular stomatitis virus G protein (VSV-G) could transduce ES cells efficiently and express the green fluorescent protein (GFP) transgene from an internal phosphoglycerate kinase (PGK) promoter throughout development to hematopoietic cells in vitro. An oncoretrovirus vector containing the MESV LTR and the GFP gene was used for comparison. Fluorescence-activated cell sorting analysis of transduced CCE ES cells showed 99.8 and 86.7% GPF-expressing ES cells in the VSV-G-pseudotyped lentivirus (multiplicity of infection [MOI] = 59)- and oncoretrovirus (MOI = 590)-transduced cells, respectively. Therefore, VSV-G pseudotyping of lentiviral and oncoretrovirus vectors leads to efficient transduction of ES cells. Lentivirus vector integration was verified in the ES cell colonies by Southern blot analysis. When the transduced ES cells were differentiated in vitro, expression from the oncoretrovirus LTR was severely reduced or extinct in day 6 EBs and ES cell-derived hematopoietic colonies. In contrast, many lentivirus-transduced colonies, expressing the GFP gene in the undifferentiated state, continued to express the transgene throughout in vitro development to EBs at day 6, and many continued to express in cells derived from hematopoietic colonies. This experimental system can be used to analyze lentivirus vector design for optimal expression in hematopoietic cells and for gain-of-function experiments during ES cell development in vitro.
The XL-mHG test for gene set enrichment

7 The nonparametric minimum hypergeometric (mHG) test is a popular alternative to Kolmogorov-Smirnov (KS)-type tests for determining gene set enrichment. However, these approaches have not been compared to each other in a quantitative manner. Here, I first perform a simulation study to show that the mHG test is significantly more powerful than the one-sided KS test for detecting gene set enrichment. I then illustrate a shortcoming of the mHG test, which has motivated a semiparametric generalization of the test, termed the XL-mHG test. I describe an improved quadratic-time algorithm for the efficient calculation of exact XL-mHG p-values, as well as a linear-time algorithm for calculating a tighter upper bound for the p-value. Finally, I demonstrate that the XL-mHG test outperforms the one-sided KS test when applied to a reference gene expression study, and discuss general principles for analyzing gene set enrichment using the XL-mHG test. An efficient open-source Python/Cython implementation of the XL-mHG test is provided in the xlmhg package, available from PyPI and GitHub (https://github.com/flo-compbio/xlmhg) under an OSI-approved license. 8
Comparison of the RpoH-Dependent Regulon and General Stress Response in Neisseria gonorrhoeae

ABSTRACT In the gammaproteobacteria the RpoH regulon is often equated with the stress response, as the regulon contains many of the genes that encode what have been termed heat shock proteins that deal with the presence of damaged proteins. However, the betaproteobacteria primarily utilize the HrcA repressor protein to control genes involved in the stress response. We used genome-wide transcriptional profiling to compare the RpoH regulon and stress response of Neisseria gonorrhoeae, a member of the betaproteobacteria. To identify the members of the RpoH regulon, a plasmid-borne copy of the rpoH gene was overexpressed during exponential-phase growth at 37°C. This resulted in increased expression of 12 genes, many of which encode proteins that are involved in the stress response in other species. The putative promoter regions of many of these up-regulated genes contain a consensus RpoH binding site similar to that of Escherichia coli. Thus, it appears that unlike other members of the betaproteobacteria, N. gonorrhoeae utilizes RpoH, and not an HrcA homolog, to regulate the stress response. In N. gonorrhoeae exposed to 42°C for 10 min, we observed a much broader transcriptional response involving 37 differentially expressed genes. Genes that are apparently not part of the RpoH regulon showed increased transcription during heat shock. A total of 13 genes were also down-regulated. From these results we concluded that although RpoH acts as the major regulator of protein homeostasis, N. gonorrhoeae has additional means of responding to temperature stress.
Roa rumsfeldi, a new butterflyfish (Teleostei, Chaetodontidae) from mesophotic coral ecosystems of the Philippines

Abstract A new species of the butterflyfish genus Roa is herein described from the Verde Island Passage in the Philippines, West Pacific Ocean. Roa rumsfeldi sp. n. was found on mesophotic coral ecosystems at Puerto Galera and Batangas, and sampled through technical mixed-gas rebreather diving at 100–130 m depth. This represents the fifth known species of Roa. The main differences between Roa rumsfeldi sp. n. and its congeners are the lower number of pored scales in the lateral line, longer snout, longer caudal peduncle, shorter caudal fin, pelvic fin color (dark first spine vs. white in all other Roa), and genetics (8.4% divergence from its closest relative Roa modesta in the mitochondrial COI gene). Roa spp. are usually seen in pairs, but the two specimens we collected were solitary individuals. We have kept one of the specimens alive in the California Academy of Sciences’ Twilight Zone exhibit for more than one year, where it thrives and is feeding on a variety of dried and fresh food.
l-Selegiline Potentiates the Cellular Poly(ADP-Ribosyl)ation Response to Ionizing Radiation

DNA strand breaks induced by alkylating agents, oxidants, or ionizing radiation trigger the covalent modification of nuclear proteins with poly(ADP-ribose), which is catalyzed for the most part by poly(ADP-ribose) polymerase-1 and plays a role in DNA base-excision repair. Poly(ADP-ribosyl)ation capacity of mononuclear blood cells correlates positively with life span of mammalian species. Here, we show that l-selegiline, an anti-Parkinson drug with neuroprotective activity and life span-extending effect in laboratory animals, can potentiate γ-radiation-induced poly(ADP-ribose) formation in intact cells. COR4 hamster cells were incubated with l-selegiline (50 nM) for various time periods, followed by γ-irradiation (45 Gy). Quantification of cellular poly(ADP-ribose) levels at 10 min after starting the irradiation revealed significant increases (up to 1.8-fold) in cells preincubated with the drug for 8 h to 7 days compared with drug-free irradiated controls. There was no selegiline-induced change in poly(ADP-ribose) levels of unirradiated cells nor in basal or radiation-induced DNA strand breaks, respectively. Surprisingly, poly(ADP-ribose) polymerase-1 protein was down-regulated by l-selegiline treatment. Addition of l-selegiline to purified poly(ADP-ribose) polymerase-1 did not alter enzymatic activity. In conclusion, the results of the present study identify a novel intervention to potentiate the cellular poly(ADP-ribosyl)ation response. We hypothesize that the effect of l-selegiline is due to modulation of accessory proteins regulating poly(ADP-ribose) polymerase-1 activity and that increased cellular poly- (ADP-ribosyl)ation capacity may contribute to the neuroprotective potential and/or life span extension afforded by l-selegiline.
Evaluation of Anti-GERD Activity of Gastro Retentive Drug Delivery System of Itopride Hydrochloride

Abstract The present work describes the formulation and evaluation of the gastroretentive system of Itopride hydrochloride. In this research, we have formulated floating hydrogel-based microspheres employing calcium carbonate (CaCO3) as a gas forming agent dispersed in alginate matrix. In vitro characterizations such as drug content, particle size, and drug release were carried out. GI motility was determined by administration of charcoal meal to rats. Results demonstrated that prepared microspheres were spherical in shape with smooth surface, good loading efficiency, and excellent buoyancy. The gastro retentive dosage form of itiopride demonstrated significant antacid, anti-ulcer, and anti-GERD activity after 12 hours in comparison with the conventional dosage form.
Diagnostic Accuracy of Compression Ultrasonography for the Detection of Asymptomatic Deep Venous Thrombosis in Medical Patients

Summary We assessed the accuracy of venous compression ultrasonography (CUS) for the detection of asymptomatic deep vein thrombosis in 122 consecutive patients, with a mean age of 69 years, who were hospitalised in an internal medicine unit. All included patients had CUS within 48 h of admission. Twelve out of 17 patients with a positive CUS underwent phlebography, as the others withdrew their consent, whereas the remaining 105 patients with a negative serial CUS testing were clinically followed-up at 3 months. We found that CUS had a sensitivity and a specificity of respectively 1 (95% CI, 0.73 to 1) and 1 (95% CI, 0.96 to 1) for the detection of asymptomatic deep vein thrombosis. Kappa-coefficients for intra-observer and inter-observer agreements were respectively 0.88 and 0.56. We concluded that venous compression ultrasonography, performed as described, fulfils requirements of a screening test that could be available for prophylactic clinical trials or epidemiological researches.
The Effect of Message Frame in Anti-Smoking Public Service Announcements on Cognitive Response and Attitude Toward Smoking

This study investigated whether and how message frames in anti-smoking public service announcements (PSAs) affect individuals' cognition and attitude toward smoking. Individuals in a sample of 315 participants were randomly assigned to one of three experimental framing conditions: (a) health consequence, (b) secondhand smoke, and (c) industry manipulation. Each participant viewed four PSAs in a random order within a particular message frame. The study found strong evidence for the application effect in framing. The accessibility effect in framing was found to be conditional on message frame. Individuals' cognition on health consequence of smoking and on industry manipulation predicted their attitude toward smoking, but not cognition on secondhand smoke. The three frames also led to different patterns of affective responses that can be a basis for persuasion. Implications for message framing effect and anti-smoking campaigns were discussed.