pwc-archive/papers-with-abstracts huggingface dataset:
Antibacterial and antibiofilm activities of a traditional herbal formula against respiratory infection causing bacteria
Authors: H. A Qaralleh, M. O. Al-Limoun, A. Khlaifat, K. M. Khleifat, N. Al-Tawarah, K. Y. Alsharafa, H. A. Abu-Harirah
Date: 2021-01-19 00:00:00

The plants, Althaea officinalis, Tilia cordata and Psidium guaja have been used traditionally to treat respiratory infection symptoms. Flowers of A. officinalis and leaves of T. cordata and P. guaja have been used to treat cough, sore throat, catarrh, oral and pharyngeal mucosa irritation. Therefore, this study was designed to examine the antibacterial and antibiofilm effects of these plants individually as well as in combination, as a formula against respiratory infections causing pathogens. The tested pathogens were Extended Spectrum Beta-Lactamase producing Escherichia coli (ESBL), Beta-Lactamase producing Escherichia coli (BL), Beta-Lactamase producing Klebsiella pneumoniae (BL), Beta-Lactamase producing Pseudomonas aeruginosa (BL), Enterobacter cloacae, and Beta-Lactamase producing Staphylococcus aureus (BL). The tested plants were extracted using ethanol and then fractionated using different polarity solvents (hexane, ethyl acetate and water). Disc diffusion and microdilution (Minimum Inhibitory Concentration) methods were used to evaluate the antibacterial activity while the antibiofilm activity was tested using crystal violet assay. The results showed that A. officinalis and T. cordata extracts and fractions exhibited weak antibacterial activity having MIC values ranged from 6.25 to 12.5 mg/mL. P. guaja exhibited moderate antibacterial activity with MIC values ranged from 6.25 to 1.56 mg/mL. Combination between these plants extracts and fractions in equal proportion provides stronger antibacterial (with MIC values ranged from 6.25 to 0.8 mg/mL) and antibiofilm activities (MBIC50 was 0.2 mg/mL). Therefore, this study provides a valuable scientific knowledge to support the use of plants in combination rather than individually.
Extraction, isolation, structure elucidation and evaluation of toxicity, anti-inflammatory and analgesic activity of Pituranthos scoparius constituents
Authors: Karbab Ahlem
Date: 2021-01-01 00:00:00

The present work aimed to investigate an ethnobotanical survey about Pituranthos scoparius and assess the toxicity, anti-inflammatory (in vitro, and in vivo) potential, in vitro antioxidant, and analgesic effects of stems and roots of Pituranthos scoparius. Furthermore; to isolate and elucidate the chemical constituents of the n-butanol stem extract of P. scoparius (ButE) and determine the toxicity and anti-inflammatory effects of these compounds added to the ButE. Data from an ethnopharmacological study showed that 24.47 % of people used this plant in folk medicine. Four compounds were isolated from ButE. These compounds were characterized by means of NMR and high-resolution mass spectral (HRMS) data.
Effect of administration gamma-amino butyric acid on physiological performance of broiler chicks
Authors: Hasanain N. Ezzat, Ihsan M. Shihab, Samer S. Hameed
Date: 2020-12-16 00:00:00

This experiment was conducted to study the effect of administration {\gamma}-amino butyric acid (GABA) on physiology performance of broiler chicks. The following treatments were used: T1:control treatment, T2: the birds were administration 0.2ml 0.4% GABA solution daily, T3: the birds were administration 0.2ml 0.5% GABA solution daily and T4: the birds were administration 0.2ml 0.6% GABA solution daily. The results of the experiment indicated that there were significant differences for the calculating blood lipids .When calculating blood enzymes, there are significant differences between the treatments
Neuromatch Academy: Teaching Computational Neuroscience with global accessibility
Authors: Tara van Viegen, Athena Akrami, Kate Bonnen, Eric DeWitt, Alexandre Hyafil, Helena Ledmyr, Grace W. Lindsay, Patrick Mineault, John D. Murray, Xaq Pitkow, Aina Puce, Madineh Sedigh-Sarvestani, Carsen Stringer, Titipat Achakulvisut, Elnaz Alikarami, Melvin Selim Atay, Eleanor Batty, Jeffrey C. Erlich, Byron V. Galbraith, Yueqi Guo, Ashley L. Juavinett, Matthew R. Krause, Songting Li, Marius Pachitariu, Elizabeth Straley, Davide Valeriani, Emma Vaughan, Maryam Vaziri-Pashkam, Michael L. Waskom, Gunnar Blohm, Konrad Kording, Paul Schrater, Brad Wyble, Sean Escola, Megan A. K. Peters
Date: 2020-12-15 00:00:00
Tasks: Management

Neuromatch Academy designed and ran a fully online 3-week Computational Neuroscience summer school for 1757 students with 191 teaching assistants working in virtual inverted (or flipped) classrooms and on small group projects. Fourteen languages, active community management, and low cost allowed for an unprecedented level of inclusivity and universal accessibility.
A Mitigation Score for COVID-19
Authors: Jonathan D. Cohen
Date: 2020-12-02 00:00:00

This note describes a simple score to indicate the effectiveness of mitigation against infections of COVID-19 as observed by new case counts. The score includes normalization, making comparisons across jurisdictions possible. The smoothing employed provides robustness in the face of reporting vagaries while retaining salient features of evolution, enabling a clearer picture for decision makers and the public.
Inverted repeats in coronavirus SARS-CoV-2 genome and implications in evolution
Authors: Changchuan Yin, Stephen S. -T. Yau
Date: 2020-11-24 00:00:00
Tasks: Drug Design

The coronavirus disease (COVID-19) pandemic, caused by the coronavirus SARS-CoV-2, has caused 60 millions of infections and 1.38 millions of fatalities. Genomic analysis of SARS-CoV-2 can provide insights on drug design and vaccine development for controlling the pandemic. Inverted repeats in a genome greatly impact the stability of the genome structure and regulate gene expression. Inverted repeats involve cellular evolution and genetic diversity, genome arrangements, and diseases. Here, we investigate the inverted repeats in the coronavirus SARS-CoV-2 genome. We found that SARS-CoV-2 genome has an abundance of inverted repeats. The inverted repeats are mainly located in the gene of the Spike protein. This result suggests the Spike protein gene undergoes recombination events, therefore, is essential for fast evolution. Comparison of the inverted repeat signatures in human and bat coronaviruses suggest that SARS-CoV-2 is mostly related SARS-related coronavirus, SARSr-CoV/RaTG13. The study also reveals that the recent SARS-related coronavirus, SARSr-CoV/RmYN02, has a high amount of inverted repeats in the spike protein gene. Besides, this study demonstrates that the inverted repeat distribution in a genome can be considered as the genomic signature. This study highlights the significance of inverted repeats in the evolution of SARS-CoV-2 and presents the inverted repeats as the genomic signature in genome analysis.
Improved fully automated method for the determination of medium to highly polar pesticides in surface and groundwater and application in two distinct agriculture-impacted areas
Authors: Maria Vittoria Barbieri, Luis Simon Monllor-Alcaraz, Cristina Postigo, Miren Lopez de Alda
Date: 2020-11-23 00:00:00

Water is an essential resource for all living organisms. The continuous and increasing use of pesticides in agricultural and urban activities results in the pollution of water resources and represents an environmental risk. To control and reduce pesticide pollution, reliable multi-residue methods for the detection of these compounds in water are needed. In this context, the present work aimed at providing an analytical method for the simultaneous determination of trace levels of 51 target pesticides in water and applying it to the investigation of target pesticides in two agriculture-impacted areas of interest. The method developed, based on an isotopic dilution approach and on-line solid-phase extraction-liquid chromatography-tandem mass spectrometry, is fast, simple, and to a large extent automated, and allows the analysis of most of the target compounds in compliance with European regulations. Further application of the method to the analysis of selected water samples collected at the lowest stretches of the two largest river basins of Catalonia (NE Spain), Llobregat and Ter, revealed the presence of a wide suite of pesticides, and some of them at concentrations above the water quality standards (irgarol and dichlorvos) or the acceptable method detection limits (methiocarb, imidacloprid, and thiacloprid), in the Llobregat, and much cleaner waters in the Ter River basin. Risk assessment of the pesticide concentrations measured in the Llobregat indicated high risk due to the presence of irgarol, dichlorvos, methiocarb, azinphos ethyl, imidacloprid, and diflufenican (hazard quotient (HQ) values>10), and an only moderate potential risk in the Ter River associated to the occurrence of bentazone and irgarol (HQ>1).
Reliable LC-MS/MS-based method for trace level determination of 50 medium to highly polar pesticide residues in sediments and ecological risk assessment
Authors: Maria Vittoria Barbieri, Cristina Postigo, Simon Monllor-Alcaraz, Damia Barcelo, Miren Lopez de Alda
Date: 2020-11-23 00:00:00

The occurrence of polar pesticides in sediments has not been extensively investigated because of their relatively poor hydrophobicity and apparently less persistence in the environment. However, their continuous release into the aquatic systems calls for the evaluation of their potential accumulation in sediments and the role of this matrix as a potential source of these compounds. Considering this, a method based on pressurized liquid extraction (PLE), extract clean-up by solid phase extraction (SPE) and analyte determination by liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) was developed and validated to analyze 50 relevant (frequently used and/or regulated or found in water) medium to highly polar pesticides in sediments. The method showed good performance regarding accuracy (relative recoveries between 76% and 124%), precision (relative standard deviation values <20%), sensitivity (LODs in the low ng/g for most compounds), linearity (coefficients of determination >0.99), and matrix effects (negligible for all analytes). The use of an isotope dilution approach for quantification ensures results reliability. As a part of the validation process, the method was applied to the analysis of the target pesticides in sediments from the Llobregat River (NE Spain) showing the presence of five of them, namely, terbutryn, dichlorvos, terbuthylazine, diazinon, and irgarol. All 5 pesticides, due to both the concentrations found and their physical-chemical characteristics, demonstrate high potential for bioaccumulation and risk to the aquatic organisms. Additional multidisciplinary studies that investigate pesticides occurrence in the different aquatic compartments and evaluate the potential risks for aquatic ecosystems are required to assess the environmental impact and significance of the presence of pesticides in sediments.
Paradox resolved: The allometric scaling of cancer risk across species
Authors: Christopher P. Kempes, Geoffrey B. West, John W. Pepper
Date: 2020-11-22 00:00:00

Understanding the cross-species behavior of cancer is important for uncovering fundamental mechanisms of carcinogenesis, and for translating results of model systems between species. One of the most famous interspecific considerations of cancer is Peto's paradox, which asserts that organisms with vastly different body mass are expected to have a vastly different degree of cancer risk, a pattern that is not observed empirically. Here we show that this observation is not a paradox at all but follows naturally from the interspecific scaling of metabolic rates across mammalian body size. We connect metabolic allometry to evolutionary models of cancer development in tissues to show that waiting time to cancer scales with body mass in a similar way as normal organism lifespan does. Thus, the expectation across mammals is that lifetime cancer risk is invariant with body mass. Peto's observation is therefore not a paradox, but the natural expectation from interspecific scaling of metabolism and physiology. These allometric patterns have theoretical implications for understanding life span evolution, and practical implications for using smaller animals as model systems for human cancer.
Spectral Kinetic Modeling and Long-term Behavior Assessment of Arthrospira platensis Growth in Photobioreactor under Red (620 nm) Light Illumination
Authors: Bérangère Farges, Céline Laroche, Jean-François Cornet, Claude-Gilles Dussap
Date: 2020-11-07 00:00:00

The ability to cultivate the cyanobacterium Arhtrospira platensis in artificially lightened photobioreactors using high energetic efficiency (quasi-monochromatic) red LED was investigated. In order to reach the same maximal productivities as with the polychromatic lightening control conditions (red + blue, P/2e- = 1.275), the need to work with an optimal range of wavelength around 620 nm was first established on batch and continuous cultures. The long-term physiological and kinetic behavior was then verified in a continuous photobioreactor illuminated only with red (620 nm) LED, showing that the maximum productivities can be maintained over 30 residence times with only minor changes in the pigment content of the cells corresponding to a well-known adaptation mechanism of the photosystems, but without any effect on growth and stoichiometry. For both poly and monochromatic incident light inputs, a predictive spectral knowledge model was proposed and validated for the first time, allowing the calculation of the kinetics and stoichiometry observed in any photobioreactor cultivating A. platensis, or other cyanobacteria if the parameters were updated. It is shown that the photon flux (with a specified wavelength) must be used instead of light energy flux as a relevant control variable for the growth. The experimental and theoretical results obtained in this study demonstrate that it is possible to save the energy consumed by the lightening device of photobioreactors using red LED, the spectral range of which is defined according to the action spectrum of photosynthesis. This appears to be crucial information for applications in which the energy must be rationalized, as it is the case for life support systems in closed environments like a permanent spatial base or a submarine.
A Simple and Reliable Formula for Assessment of Maximum Volumetric Productivities in Photobioreactors
Authors: Jean-François Cornet, Claude-Gilles Dussap
Date: 2020-11-07 00:00:00

This paper establishes and discusses the consistency and the range of applicability of a simple, but general and predictive analytical formula, enabling to easily assess the maximum volumetric biomass growth rates (the productivities) in several kinds of photobioreactors with more or less 15 percents of deviation. Experimental validations are performed on photobioreactors of very different conceptions and designs, cultivating the cyanobacterium Arthrospira platensis, on a wide range of volumes and hemispherical incident light fluxes. The practical usefulness of the proposed formula is demonstrated by the fact that it appears completely independent of the characteristics of the material phase (as the type of reactor, the kind of mixing, the biomass concentration), according to the first principle of thermodynamics and to the Gauss-Ostrogradsky theorem. Its ability to give the maximum (only) kinetic performance of photobioreactors cultivating many different photoautotrophic strains (cyanobacteria, green algae, eukaryotic microalgae) is theoretically discussed but experimental results are reported to a future work of the authors or to any other contribution arising from the scientific community working in the field of photobioreactor engineering and potentially interested by this approach.
Mobile Human Ad Hoc Networks: A Communication Engineering Viewpoint on Interhuman Airborne Pathogen Transmission
Authors: Fatih Gulec, Baris Atakan, Falko Dressler
Date: 2020-11-02 00:00:00
Tasks: Epidemiology

A number of transmission models for airborne pathogens transmission, as required to understand airborne infectious diseases such as COVID-19, have been proposed independently from each other, at different scales, and by researchers from various disciplines. We propose a communication engineering approach that blends different disciplines such as epidemiology, biology, medicine, and fluid dynamics. The aim is to present a unified framework using communication engineering, and to highlight future research directions for modeling the spread of infectious diseases through airborne transmission. We introduce the concept of mobile human ad hoc networks (MoHANETs), which exploits the similarity of airborne transmission-driven human groups with mobile ad hoc networks and uses molecular communication as the enabling paradigm. In the MoHANET architecture, a layered structure is employed where the infectious human emitting pathogen-laden droplets and the exposed human to these droplets are considered as the transmitter and receiver, respectively. Our proof-of-concept results, which we validated using empirical COVID-19 data, clearly demonstrate the ability of our MoHANET architecture to predict the dynamics of infectious diseases by considering the propagation of pathogen-laden droplets, their reception and mobility of humans.
An RNA-Based Theory of Natural Universal Computation
Authors: Hessameddin Akhlaghpour
Date: 2020-08-20 00:00:00

Life is confronted with computation problems in a variety of domains including animal behavior, single-cell behavior, and embryonic development. Yet we currently do not know of a naturally existing biological system that is capable of universal computation, i.e., Turing-equivalent in scope. Generic finite-dimensional dynamical systems (which encompass most models of neural networks, intracellular signaling cascades, and gene regulatory networks) fall short of universal computation, but are assumed to be capable of explaining cognition and development. I present a class of models that bridge two concepts from distant fields: combinatory logic (or, equivalently, lambda calculus) and RNA molecular biology. A set of basic RNA editing rules can make it possible to compute any computable function with identical algorithmic complexity to that of Turing machines. The models do not assume extraordinarily complex molecular machinery or any processes that radically differ from what we already know to occur in cells. Distinct independent enzymes can mediate each of the rules and RNA molecules solve the problem of parenthesis matching through their secondary structure. In the most plausible of these models all of the editing rules can be implemented with merely cleavage and ligation operations at fixed positions relative to predefined motifs. This demonstrates that universal computation is well within the reach of molecular biology. It is therefore reasonable to assume that life has evolved - or possibly began with - a universal computer that yet remains to be discovered. The variety of seemingly unrelated computational problems across many scales can potentially be solved using the same RNA-based computation system. Experimental validation of this theory may immensely impact our understanding of memory, cognition, development, disease, evolution, and the early stages of life.
Estimands in Hematologic Oncology Trials
Authors: Steven Sun, Hans-Jochen Weber, Emily Butler, Kaspar Rufibach, Satrajit Roychoudhury
Date: 2020-10-01 00:00:00

The estimand framework included in the addendum to the ICH E9 guideline facilitates discussions to ensure alignment between the key question of interest, the analysis, and interpretation. Therapeutic knowledge and drug mechanism play a crucial role in determining the strategy and defining the estimand for clinical trial designs. Clinical trials in patients with hematological malignancies often present unique challenges for trial design due to complexity of treatment options and existence of potential curative but highly risky procedures, e.g. stem cell transplant or treatment sequence across different phases (induction, consolidation, maintenance). Here, we illustrate how to apply the estimand framework in hematological clinical trials and how the estimand framework can address potential difficulties in trial result interpretation. This paper is a result of a cross-industry collaboration to connect the International Conference on Harmonisation (ICH) E9 addendum concepts to applications. Three randomized phase 3 trials will be used to consider common challenges including intercurrent events in hematologic oncology trials to illustrate different scientific questions and the consequences of the estimand choice for trial design, data collection, analysis, and interpretation. Template language for describing estimand in both study protocols and statistical analysis plans is suggested for statisticians' reference.
Ribonucleocapsid assembly/packaging signals in the genomes of the coronaviruses SARS-CoV and SARS-CoV-2: Detection, comparison and implications for therapeutic targeting
Authors: Vladimir R. Chechetkin, Vasily V. Lobzin
Date: 2020-07-20 00:00:00

The genomic ssRNA of coronaviruses is packaged within a helical nucleocapsid. Due to transitional symmetry of a helix, weakly specific cooperative interaction between ssRNA and nucleocapsid proteins leads to the natural selection of specific quasi-periodic assembly/packaging signals in the related genomic sequence. Such signals coordinated with the nucleocapsid helical structure were detected and reconstructed in the genomes of the coronaviruses SARS-CoV and SARS-CoV-2. The main period of the signals for both viruses was about 54 nt, that implies 6.75 nt per N protein. The complete coverage of ssRNA genome of length about 30,000 nt by the nucleocapsid would need 4,400 N proteins, that makes them the most abundant among the structural proteins. The repertoires of motifs for SARS-CoV and SARS-CoV-2 were divergent but nearly coincided for different isolates of SARS-CoV-2. We obtained the distributions of assembly/packaging signals over the genomes with non-overlapping windows of width 432 nt. Finally, using the spectral entropy, we compared the load from point mutations and indels during virus age for SARS-CoV and SARS-CoV-2. We found the higher mutational load on SARS-CoV. In this sense, SARS-CoV-2 can be treated as a "newborn" virus. These observations may be helpful in practical medical applications and are of basic interest.
Long range versus short range aerial transmission of SARS-CoV-2
Authors: John E. McCarthy, Myles T. McCarthy, Bob A. Dumas
Date: 2020-08-08 00:00:00

We compare the quantitative risk of infection from short range airborne transmission of SARS-CoV-2 to the long-range risk from aerosol transmission in an enclosed space.