Miracle-dz/UniFAR-FTUs huggingface dataset:
Multi-locus sequence analysis, taxonomic resolution and biogeography of marine Synechococcus.

Conserved markers such as the 16S rRNA gene do not provide sufficient molecular resolution to identify spatially structured populations of marine Synechococcus, or 'ecotypes' adapted to distinct ecological niches. Multi-locus sequence analysis targeting seven 'core' genes was employed to taxonomically resolve Synechococcus isolates and correlate previous phylogenetic analyses encompassing a range of markers. Despite the recognized importance of lateral gene transfer in shaping the genomes of marine cyanobacteria, multi-locus sequence analysis of more than 120 isolates reflects a clonal population structure of major lineages and subgroups. A single core genome locus, petB, encoding the cytochrome b(6) subunit of the cytochrome b(6) f complex, was selected to expand our understanding of the diversity and ecology of marine Synechococcus populations. Environmental petB sequences cloned from contrasting sites highlight numerous genetically and ecologically distinct clusters, some of which represent novel, environmentally abundant clades without cultured representatives. With a view to scaling ecological analyses, the short sequence, taxonomic resolution and accurate automated alignment of petB is ideally suited to high-throughput and high-resolution sequencing projects to explore links between the ecology, evolution and biology of marine Synechococcus.
Developing a Systematic Design Approach to Tailor Crystal Size Distribution for Mixing-Sensitive Crystallization Processes

The design of crystallization processes becomes more complicated when mixing affects the final crystal product quality (e.g., crystal size distribution and polymorphic form). Such mixing effects are more apparent in antisolvent and reactive crystallizations, which involve the blending of different fluids, and in large-scale crystallizers, where homogeneity cannot be easily achieved. In this paper, we present the use of an integrated algorithm, which couples macromixing and micromixing models with the population balance equation, to model antisolvent crystallization in a stirred vessel and impinging jet crystallizers. The dependency of the crystal size distribution on the mixing speed and scale for a stirred vessel and the effects of jet velocity on the crystal size distribution and polymorphic form for an impinging jet crystallizer are numerically investigated. Eventually, the development of such computational tools would enable us to understand the interactions between hydrodynamics and the kinetics of crystallization in order to develop systematic design methodologies for crystallization processes.
Modeling of molecular mechanisms of cell adhesion.

Cellular adhesion is a process of great importance in biology. We present a simple model of the adhesion process in which the molecular mechanisms involve a receptor, a ligand, and the cytoskeleton of the cell. Based on the energetic consideration of the process, we propose a molecular interpretation of the existing experimental data. The model suggests that the interaction of the receptor and (or) receptor-ligand with the cytoskeleton can have important influence on the formation and strength of the adhesion complex as well as on the subsequent interaction with different ligands. When conformational changes take place during the adhesion process, the characterization of the adhesion bonds based on chemical kinetics alone seems to be incomplete and must be supplemented by parameters, describing the functionality of the complex, i.e., change of the affinity for different ligands, as in the signal transduction, or the strength of the bond, as in the adhesion process.
A Dataset of Gaze Behavior in VR Faithful to Natural Statistics

A Dataset of Gaze Behavior in VR Faithful to Natural Statistics Brendan John Rochester Institute of Technology, 2017 Supervisor: Dr. Reynold Bailey Eye tracking technology is advancing swiftly and many areas of research have begun taking advantage of this. Existing eye trackers project gaze onto a 2D plane, whether it be the display of a head mounted virtual reality (VR) helmet or an image of a real life scene the user is in. This allows us to easily analyze what a viewer is looking at, but limits classification of gaze behaviors from this type of signal. Instead, a system that takes into account head movements within the same space as gaze velocity allows researchers to classify more advanced gaze behaviors such as smooth pursuits and fixations resulting from vestibulo-ocular reflex. For this work data is collected in real world environments where head and gaze movements are recorded over a variety of tasks. The resulting data is then used to construct a distribution of naturally occurring gaze behaviors. This distribution is then used to drive a VR
Population Pharmacokinetics of Tacrolimus in Pediatric Liver Transplantation: Early Posttransplantation Clearance

Background: Tacrolimus is an immunosuppressant with a narrow therapeutic window, with considerable pharmacokinetic variability. Getting sufficient concentrations in pediatric liver transplantation is imperative, but it has proven difficult in the immediate posttransplantation period in particular. A predictive pharmacokinetic model could be the basis for development of a novel initial dose schedule, and therapeutic drug monitoring with Bayesian methodology. Methods: The predictive capacity of 2 previously developed population pharmacokinetic models of tacrolimus in pediatric liver transplant recipients was tested in 20 new patients using Bayesian forecasting. Predictive performance was poor in the immediate posttransplant period with tacrolimus pharmacokinetics changing rapidly. A new population pharmacokinetic model, focusing on the immediate posttransplant period, was subsequently developed in 73 patients. Results: An increase in the apparent clearance of tacrolimus in the first few weeks after transplant was evident. Typical apparent clearance of tacrolimus was 0.148 L·h−1·kg−0.75 immediately after transplantation, increasing to a maximum of 1.37 L·h−1·kg−0.75. Typical apparent distribution volume was 27.2 L/kg. Internal and external validation studies confirmed the predictive capabilities of the developed model. Simulation studies reveal that in 60% of subjects the current initial standard dose without subsequent dosage adjustments overshoot the desired trough concentration range of 10–20 ng/mL. An alternative dosing schedule was developed based on allometric scaling with an initial loading dose followed by a maintenance dose increasing with time. Conclusions: A population pharmacokinetic model for tacrolimus was developed, to better describe the early posttransplantation phase. This model has the potential to aid therapeutic drug monitoring and was also used to suggest a revised dosing scheme in the intended population.
Propionibacterium acnes activates caspase‐1 in human neutrophils

Propionibacterium acnes is a Gram‐positive, slow‐growing, anaerobic bacillus, predominantly found as a commensal on the skin and mucous membranes of adults. It is, however, also considered an opportunistic pathogen; mostly associated with acne vulgaris, but rarely also with severe infections such as infective endocarditis, prosthetic joint infections, and deep sternal wound infections following cardiothoracic surgery. In addition, P. acnes has recently been found in high frequency in prostate tissue from patients with prostatitis and prostate cancer. The NOD‐like receptors (NLR) act as intracellular sensors of microbial components, and a number of various bacteria have been found to induce assembling and activation of NLR‐inflammasomes; leading to a pro‐inflammatory response. The inflammasome‐mediated formation of the pro‐inflammatory cytokines interleukin‐1β (IL‐1β) and IL‐18 involves the auto‐proteolytic maturation of caspase‐1. This study investigated if P. acnes activates inflammasomes. Propionibacterium acnes isolates (n = 29) with diverse origin were used as stimuli for peripheral leukocytes obtained from blood donors (BDs). The activity of inflammasomes was determined by measuring caspase‐1 by flow cytometry and cytokine production by ELISA. A significant amount of caspase‐1 was found in neutrophils upon P. acnes stimulation, whereas only a modest activation was seen in monocytes. The activation was mainly produced by components of the bacterial cell and no exo‐products, because heat‐killed and live bacteria caused high activation of caspase‐1 as well as cytokine production, whereas the bacterial supernatant elicited minor effect. The response among different BDs varied significantly, almost fivefold. In addition, P. acnes of various origins showed considerable variation, however, the commensal isolates showed a stronger response compared with the invasive. In conclusion, although regarded as a harmless commensal of the skin, P. acnes strongly activates the inflammasome of human peripheral neutrophils.
Complement-mediated Opsonization of Invasive Group A Streptococcus pyogenes Strain AP53 Is Regulated by the Bacterial Two-component Cluster of Virulence Responder/Sensor (CovRS) System*

Background: Host complement-mediated opsonophagocytosis is an innate immune response to GAS. Results: Inactivation of the covS component of the covRS system allows GAS to avoid opsonization. Conclusion: Bacterial genes that subvert opsonization of GAS are regulated by the covRS system. Significance: The covRS system regulates complement inhibitor binding to GAS via the products of the fba and enn genes. Group A Streptococcus pyogenes (GAS) strain AP53 is a primary isolate from a patient with necrotizing fasciitis. These AP53 cells contain an inactivating mutation in the sensor component of the cluster of virulence (cov) responder (R)/sensor (S) two-component gene regulatory system (covRS), which enhances the virulence of the primary strain, AP53/covR+S−. However, specific mechanisms by which the covRS system regulates the survival of GAS in humans are incomplete. Here, we show a key role for covRS in the regulation of opsonophagocytosis of AP53 by human neutrophils. AP53/covR+S− cells displayed potent binding of host complement inhibitors of C3 convertase, viz. Factor H (FH) and C4-binding protein (C4BP), which concomitantly led to minimal C3b deposition on AP53 cells, further showing that these plasma protein inhibitors are active on GAS cells. This resulted in weak killing of the bacteria by human neutrophils and a corresponding high death rate of mice after injection of these cells. After targeted allelic alteration of covS− to wild-type covS (covS+), a dramatic loss of FH and C4BP binding to the AP53/covR+S+ cells was observed. This resulted in elevated C3b deposition on AP53/covR+S+ cells, a high level of opsonophagocytosis by human neutrophils, and a very low death rate of mice infected with AP53/covR+S+. We show that covRS is a critical transcriptional regulator of genes directing AP53 killing by neutrophils and regulates the levels of the receptors for FH and C4BP, which we identify as the products of the fba and enn genes, respectively.
Implications of Phytoestrogen Intake for Breast Cancer

Phytoestrogens are a group of plant‐derived substances that are structurally or functionally similar to estradiol. Interest in phytoestrogens has been fueled by epidemiologic data that suggest a decreased risk of breast cancer in women from countries with high phytoestrogen consumption. Women with a history of breast cancer may seek out these “natural” hormones in the belief that they are safe or perhaps even protective against recurrence. Interpretation of research studies regarding phytoestrogen intake and breast cancer risk is hampered by differences in dietary measurement, lack of standardization of supplemental sources, differences in metabolism amongst individuals, and the retrospective nature of much of the research in this area. Data regarding the role of phytoestrogens in breast cancer prevention is conflicting, but suggest early exposure in childhood or early adolescence may be protective. In several placebo‐controlled randomized trials among breast cancer survivors, soy has not been found to decrease menopausal symptoms. There is very little human data on the role of phytoestrogens in preventing breast cancer recurrence, but the few studies conducted do not support a protective role. There is in vivo animal data suggesting the phytoestrogen genistein may interfere with the inhibitive effects of tamoxifen on breast cancer cell growth.
Lysine-specific histone demethylase LSD1 and the dynamic control of chromatin

Abstract The flavin adenine dinucleotide-dependent amine oxidase LSD1 is the first molecularly defined histone demethylase, which specifically demethylates H3K4me1/me2. The enzyme dynamically controls a large variety of biological processes and is associated with protein complexes controlling transcriptional repression and activation. Molecular analysis of the Drosophila LSD1 homolog revealed new insights into the epigenetic control of heterochromatin formation during early embryogenesis, the establishment of transcriptional gene silencing and the epigenetic mechanisms associated with the maintenance of stem cell identity in primordial germline cells. This review summarizes our recent knowledge about the control of enzymatic activity and molecular function of LSD1 enzyme complexes in different model organisms including Schizosaccharomyces pombe, Drosophila and mammals. Finally, new developments in applied cancer research based on molecular analysis of LSD1 in cancer cells are discussed.
One-dimensional resolution improvement of images in time series by genetic algorithm

Several frame images in a time series that can be taken by a TV camera system under specified conditions can be given improved one-dimensional resolution by solving a recurrence formula or by an inverse-filtering method. It appears that one-dimensional resolution improvement is the same as the problem of optimum search satisfying given conditions for the images in a time series. It is known that genetic algorithms are extremely effective in optimum search problems. In this paper, a genetic algorithm is investigated for one-dimensional improvement of the resolution of images in a time series. Some experimental results are presented. Also, it is shown that the proposed method is effective for improvement of the resolution of images in time series with noise. © 2001 Scripta Technica, Syst Comp Jpn, 32(7): 12–19, 2001
IC chip design and synthesis for color matrixing and convolution

An Enhanced ASIC which performs both 3×3 matrix multiplication and 3×3 digital convolution was designed using VHDL. The same chip was compiled and synthesized using Synopsys. The Slack, cell area, power and timing are found by invoking commands in Synopsys. The previous version [1] was implemented on 2 μm CMOS technology which had an operation speed of 14.3 MHz The proposed ASIC is implemented in 0. 12μm CMOS technology. The initial speed was found to be 181 MHz and furthermore enhanced to 307.6 MHz using optimization techniques. The multipliers and adders used in this proposed architecture are pipelined when compared with the previous version [1]. The ASIC has a latency of 7 clock cycles.
Discrete-Time Low-Frequency-Ratio Synchronous-Frame Full-Order Observer for Position Sensorless IPMSM Drives

This paper proposes a complex-vector based discrete-time synchronous-frame full-order observer for position sensorless interior permanent magnet synchronous motor (IPMSM) drives with a low-pulsewidth modulation (PWM) to operating fundamental frequency ratio, a situation common for middle- and high-power applications as well as high-frequency permanent magnet synchronous motor drives. A complex-vector based discrete-time domain zero-order hold equivalent model of IPMSM is developed explicitly incorporating with the stationary frame voltage latch effect of a PWM voltage source inverter. Whereby, a full-order observer is designed and implemented using direct pole assignment in the discrete-time domain to guarantee the stability and dynamic performance with low-frequency ratios. The proposed scheme was verified on a sensorless IPMSM drive. Experimental results confirm both the design methodology and the expected performance attained by the proposed control strategy with low-frequency ratios.
Combined Approach for Lesions Involving the Cerebellopontine Angle and Skull Base: Experience with 30 Cases

This article presents a series of 30 patients who underwent a combination of the subtemporal and posterior fossa approaches for exposure of lesions in the clivus or medial petrous region. This combined supra- and infratentorial approach is divided into three variations with progressively greater petrous bone resection to increase exposure of the clivus and medial petrous region. The approach has been divided into petrous bone resection with preservation of hearing (retrolabyrinthine), greater petrous bone resection with sacrifice of hearing (translabyrinthine), and finally maximum petrous drilling with sacrifice of hearing along with transposition of the facial nerve (transcochlear). Ninety-three percent of the cases returned to their premorbid occupations.
Scheduling residential electric loads for green house gas reductions

Active House is a concept developed by a large collaboration of actors from the automation and power industry and research institutes in Sweden. The frame is the Stockholm City's Royal Seaport city development area which focuses on sustainable development and extensive CO2 reductions. The residential building is called an “Active House” since it has active interaction between the electricity consumer and the utility. The active interaction aims at reducing utilization of electricity production with high CO2 emissions and includes customer-controlled post-shift and reduction of the consumer's electricity loads and local electricity production using Solar PV systems. This paper presents the Active House collaboration, the household incentives to participate and its energy management system used to shift and reduce electric loads, and also discusses the hourly CO2 emission model and some of its simulation results for the Swedish and the United Kingdom power system.
Long-term alcohol use in adolescence and neurocognition: a preliminary study

Background: Despite a large body of evidence of the negative effects of alcohol on cognitive functioning in adults, its effects in adolescence are still unclear. In previous studies, binge drinking in adolescence has been associated with poorer neurocognitive performance with regards attention, working memory, spatial functioning, verbal and visual memory and executive functioning. The aim of this study was to evaluate whether approximately 10 years of alcohol use from adolescence into early adulthood affects cognitive functioning. The participants were 39 subjects with heavy alcohol use measured at three time points over ten years using a shortened version of the Alcohol Use Disorders Identification Test (AUDIT-C) and 32 age-, gender- and education-matched controls. Methods: The participants underwent neuropsychological assessment consisting of measures of intellectual ability, executive functions, and verbal and working memory. In addition, all participants were interviewed using a semi-structured diagnostic psychiatric interview (SCID). Participants were asked about their alcohol use in the previous 12 months using the AUDIT-C at three time points in ten years. Lifetime drug use was also recorded with a questionnaire. Results: No statistically significant differences were found in any particular field of the neuropsychological evaluations. Conclusions: In our study on healthy young adults, no significant differences were found in neuropsychological test results between alcohol users and non-users. Longitudinal studies are warranted to disentangle pre-existing defects from the dose-dependent effects of alcohol on neurodevelopment and to differentiate causes from consequences.
An outbreak of rabbit enteritis: pathological and microbiological findings and possible therapeutic regime

Mortality, averaging about 30% of young born throughout the year, was severest at 5-10 weeks of age, from just before weaning until about 4 weeks after, especially in large litters of 10-11 young. The organism most characteristically associated with enteritis was Escherichia coli. Preliminary experiments suggested that restriction of food decreases the death rate from enteritis among young rabbits.
Suppression of Lysosome Function Induces Autophagy via a Feedback Down-regulation of MTOR Complex 1 (MTORC1) Activity*

Background: Lysosomes are required for autophagic degradation, which can be suppressed by lysosome inhibitors. Results: Inhibition of lysosome function resulted in autophagy activation via down-regulation of MTORC1. Conclusion: Lysosomes can affect autophagy initiation in addition to its role in autophagy degradation. Significance: The finding expands lysosome function to include regulation of autophagy activation and indicates a dual effect of lysosome inhibitors in autophagy. Autophagy can be activated via MTORC1 down-regulation by amino acid deprivation and by certain chemicals such as rapamycin, torin, and niclosamide. Lysosome is the degrading machine for autophagy but has also been linked to MTORC1 activation through the Rag/RRAG GTPase pathway. This association raises the question of whether lysosome can be involved in the initiation of autophagy. Toward this end, we found that niclosamide, an MTORC1 inhibitor, was able to inhibit lysosome degradation and increase lysosomal permeability. Niclosamide was ineffective in inhibiting MTORC1 in cells expressing constitutively activated Rag proteins, suggesting that its inhibitory effects were targeted to the Rag-MTORC1 signaling system. This places niclosamide in the same category of bafilomycin A1 and concanamycin A, inhibitors of the vacuolar H+-ATPase, for its dependence on Rag GTPase in suppression of MTORC1. Surprisingly, classical lysosome inhibitors such as chloroquine, E64D, and pepstatin A were also able to inhibit MTORC1 in a Rag-dependent manner. These lysosome inhibitors were able to activate early autophagy events represented by ATG16L1 and ATG12 puncta formation. Our work established a link between the functional status of the lysosome in general to the Rag-MTORC1 signaling axis and autophagy activation. Thus, the lysosome is not only required for autophagic degradation but also affects autophagy activation. Lysosome inhibitors can have a dual effect in suppressing autophagy degradation and in initiating autophagy.
The Role of AMPK in Metabolic Changes in Pancreatic Cancer Cells through High Protein Diet

The present study investigates the contribution of AMPK response and mTOR (mammalian target of rapamycin) pathways through high protein diet to the pancreas cancer susceptibility. The hypothalamic modulation of the AMPK/ACC and mTOR signaling pathways induce by HPD and are followed by assaying the tumorigenicity. The results demonstrate that AMPK and mTOR cooperated in the hypothalamus during HPD and resulted in reducing AMPK activity, and increasing mTOR activity.
Taste versus the Market: An Extension of Research on the Consumption of Popular Culture

Previous studies of cultural consumption have found a significant but weak relationship between expert judgment (EJ) and popular appeal (PA) and have suggested that this “little taste” phenomenon reflects a mediating role played by ordinary evaluation (OE) in diluting the association between EJ and PA. However, various weaknesses in this work have involved problems with sequential timing, nonindependence of measurements, and contamination by market(ing)-related influences. The present investigation of new data on motion pictures addresses these concerns to show that, when controlling for market success, consumers display aspects of “good taste” via indirect links from EJ to OE to PA.