pwc-archive/papers-with-abstracts huggingface dataset:
Open Source Software Sustainability Models: Initial White Paper from the Informatics Technology for Cancer Research Sustainability and Industry Partnership Work Group
Authors: Y. Ye, R. D. Boyce, M. K. Davis, K. Elliston, C. Davatzikos, A. Fedorov, J. C. Fillion-Robin, I. Foster, J. Gilbertson, M. Heiskanen, J. Klemm, A. Lasso, J. V. Miller, M. Morgan, S. Pieper, B. Raumann, B. Sarachan, G. Savova, J. C. Silverstein, D. Taylor, J. Zelnis, G. Q. Zhang, M. J. Becich
Date: 2019-12-27 00:00:00

The Sustainability and Industry Partnership Work Group (SIP-WG) is a part of the National Cancer Institute Informatics Technology for Cancer Research (ITCR) program. The charter of the SIP-WG is to investigate options of long-term sustainability of open source software (OSS) developed by the ITCR, in part by developing a collection of business model archetypes that can serve as sustainability plans for ITCR OSS development initiatives. The workgroup assembled models from the ITCR program, from other studies, and via engagement of its extensive network of relationships with other organizations (e.g., Chan Zuckerberg Initiative, Open Source Initiative and Software Sustainability Institute). This article reviews existing sustainability models and describes ten OSS use cases disseminated by the SIP-WG and others, and highlights five essential attributes (alignment with unmet scientific needs, dedicated development team, vibrant user community, feasible licensing model, and sustainable financial model) to assist academic software developers in achieving best practice in software sustainability.
Phenotypic Performance of Kambro Crossbreeds of Female Broiler Cobb 500 and Male Pelung Blirik Hitam
Authors: I Wayan Swarautama Mahardhika, Budi Setiadi Daryono
Date: 2020-01-01 00:00:00

This research was conducted to measure the phenotypic performance of Kambro crossbreeds of Pelung Blirik Hitam and Broiler Cobb 500. Based on Body Weight (BT) measurement, Kambro population (n = 17) has an average BT of 1,244.14(..)453.82 grams significant (p <0.01) to F1 Pelung (n = 7) with an average BT of 602.88(..)79.93 grams in 8 weeks period with ad libitum diet of standard feed. Phenotypic performance of Kambro significant to F1 Pelung based on the measurement of linear bodyweight parameter, vitality parameter, PPa-PBe parameter, and phenotype parameter. Kambro has the phenotype combination of parental generation based on the phenotype parameter. PPa parameter was suitable BT estimation model based on non-linear quadratic regression (r = 0.956) with formula 1.84E3(..)3.54E2*x+31.73*x2. Difference between chicken group (p<0.014) was significant to BT and interaction between the group and linear bodyweight parameter was not significant based on Analysis of Covariance. The mortality rate of Kambro was lower than F1 Pelung with the absent of vaccination in a semi-intensive rearing system. As the size of the hybrids population was limited, research findings must be validated with a larger population size of hybrids.
AI and Medicine
Authors: Mihai Nadin
Date: 2019-12-05 00:00:00

Which part of medicine, if any, can and should be entrusted to AI, now or at some moment in the future? That both medicine and AI will continue to change goes without saying.
Improving polyhydroxyalkanoates production in phototrophic mixed cultures by optimizing accumulator reactor operating conditions
Authors: Joana Fradinho, Adrian Oehmen, Maria Reis
Date: 2019-12-02 00:00:00
Tasks: Cultural Vocal Bursts Intensity Prediction

Polyhydroxyalkanoates (PHAs) production with phototrophic mixed cultures (PMCs) has been recently proposed. These cultures can be selected under the permanent presence of carbon and the PHA production can be enhanced in subsequent accumulation steps. To optimize the PHA production in accumulator reactors, this work evaluated the impact of 1) initial acetate concentration, 2) light intensity, 3) removal of residual nitrogen on the culture performance. Results indicate that low acetate concentration (<30CmM) and specific light intensities around 20W/gX are optimal operating conditions that lead to high polyhydroxybutyrate (PHB) storage yields (0.83+-0.07 Cmol-PHB/Cmol-Acet) and specific PHB production rates of 2.21+-0.07 Cmol-PHB/Cmol X d. This rate is three times higher than previously registered in non-optimized accumulation tests and enabled a PHA content increase from 15 to 30% in less than 4h. Also, it was shown for the first time, the capability of a PMC to use a real waste, fermented cheese whey, to produce PHA with a hydroxyvalerate (HV) content of 12%. These results confirm that fermented wastes can be used as substrates for PHA production with PMCs and that the energy levels in sunlight that lead to specific light intensities from 10 to 20W/gX are sufficient to drive phototrophic PHA production processes.
Considerations for Using the Vasculature as a Coordinate System to Map All the Cells in the Human Body
Authors: Griffin M Weber, Yingnan Ju, Katy Börner
Date: 2019-11-08 00:00:00
Tasks: All

Several ongoing international efforts are developing methods of localizing single cells within organs or mapping the entire human body at the single cell level, including the Chan Zuckerberg Initiative's Human Cell Atlas (HCA), and the Knut and Allice Wallenberg Foundation's Human Protein Atlas (HPA), and the National Institutes of Health's Human BioMolecular Atlas Program (HuBMAP). Their goals are to understand cell specialization, interactions, spatial organization in their natural context, and ultimately the function of every cell within the body. In the same way that the Human Genome Project had to assemble sequence data from different people to construct a complete sequence, multiple centers around the world are collecting tissue specimens from a diverse population that varies in age, race, sex, and body size. A challenge will be combining these heterogeneous tissue samples into a 3D reference map that will enable multiscale, multidimensional Google Maps-like exploration of the human body. Key to making alignment of tissue samples work is identifying and using a coordinate system called a Common Coordinate Framework (CCF), which defines the positions, or "addresses", in a reference body, from whole organs down to functional tissue units and individual cells. In this perspective, we examine the concept of a CCF based on the vasculature and describe why it would be an attractive choice for mapping the human body.
Knockdown of human AMPK using the CRISPR-Cas9 genome-editing system
Authors: Adrien Grenier, Pierre Sujobert, Séverine Olivier, Hélène Guermouche, Johanna Mondesir, Olivier Kosmider, Benoit Viollet, Jérôme Tamburini
Date: 2019-11-06 00:00:00
Tasks: Specificity

AMP activated protein kinase (AMPK) is a critical energy sensor, regulating signaling networks involved in pathology including metabolic diseases and cancer. This increasingly recognized role of AMPK has prompted tremendous research efforts to develop new pharmacological AMPK activators. To precisely study the role of AMPK, and the specificity and activity of AMPK activators in cellular models, genetic AMPK inactivating tools are required. We report here methods for genetic inactivation of AMPK $\alpha1/ \alpha2$ catalytic subunits in human cell lines by the CRISPR/Cas9 technology, a recent breakthrough technique for genome editing.
Maize yield under a changing climate: The hidden role of vapor pressure deficit
Authors: Jennifer Hsiao, Abigail L. S. Swann, Soo-Hyung Kim
Date: 2019-10-07 00:00:00
Tasks: Management

Temperatures over the next century are expected to rise to levels detrimental to crop growth and yield. As the atmosphere warms without additional water vapor input, vapor pressure deficit (VPD) increases as well. Increased temperatures and accompanied elevated VPD levels can both lead to negative impacts on crop yield. The independent importance of VPD, however, is often neglected or conflated with that from temperature due to a tight correlation between the two climate factors. We used a coupled process-based crop (MAIZSIM) and soil (2DSOIL) model to gain a mechanistic understanding of the independent roles temperature and VPD play in crop yield projections, as well as their interactions with rising CO2 levels and changing precipitation patterns. We found that by separating out the VPD effect from rising temperatures, VPD increases had a greater negative impact on yield compared to that from warming. The negative impact of these two factors varied with precipitation levels and influenced yield through separate mechanisms. Warmer temperatures caused yield loss mainly through shortening the growing season, while elevated VPD increased water loss and triggered several water stress responses such as reduced photosynthetic rates, lowered leaf area development, and shortened growing season length. Elevated CO2 concentrations partially alleviated yield loss under warming or increased VPD conditions through water savings, but the impact level varied with precipitation levels and was most pronounced under drier conditions. These results demonstrate the key role VPD plays in crop growth and yield, displaying a magnitude of impact comparative to temperature and CO2. A mechanistic understanding of the function of VPD and its relation with other climate factors and management practices is critical to improving crop yield projections under a changing climate.
A Model-Theoretic Approach to Modular Implementation, with Application to Biological Systems
Authors: Leo Marcus
Date: 2019-07-12 00:00:00

We present a method for logical specification of the behavior of a system based on the specification of its components and for representing and specifying the effect of a class of communication "signaling pathways" among them. Variations in the actions and effects (semantics) of the pathways can be seen in the resulting system. We show how to "enrich" the behavior of the original components by exactly what is provided by the signaling pathways. This has the potential to allow a formal proof of a property of the system as a whole, or a formal diagnosis why a system of communicating modules may not satisfy a desired specification, and if and how it can be "fixed." There are five distinct stages in our view: 1. A description of the connections between potential components at the level of which potential modules are connected. 2. Specific choices for those modules 3. An "elaboration" of the connections among different modules to connections among members of those different modules 4. A description of the semantics of those connections (what they actually do) 5. A "padding" of the modules chosen in step 2 to allow for the action of the connections (step 3), as described in step 4. The formalism is completely hierarchical -- in other words, the formalism works equally for the system as a whole, for each of the modules, and for any larger system in which the original system is a component. As it turns out, for whatever reason -- perhaps evolutionary advantage optimization at the right level of abstraction -- many biological systems are hierarchically modular, with the modules communicating via various pathways. Thus, a formalism such as the one presented here could have application to questions in biology.
Scandinavian bed and rise times in the Age of Enlightenment and in the 21st century show similarity, helped by Daylight Saving Time
Authors: José María Martín-Olalla
Date: 2019-09-05 00:00:00

A Letter to the Editor published in the Journal of Sleep Research
Antibacterial and antifungal activity of various extracts of Bacopa monnieri
Authors: Fazlul Mkk, Deepthi Sp, Mohammed Irfan, Farzana Y, Munira B, Nazmulmhm
Date: 2019-09-03 00:00:00
Tasks: Management

Bacopa monnieri was also known as Brahmi. Theses plant has been considered as medicinal plants in Ayurvedic systems for centuries. This present study was carried out to evaluate the antibacterial and antifungal properties of ethanolic, diethyl ether, ethyl acetate, and aqueous extracts of B. monnieri. Agar disc diffusion tests were carried out to determine the antimicrobial effects of ethanolic, diethyl ether, ethyl acetate and aqueous extracts of B. monnieri against Gram-positive (Staphylococcus aureus ATCC 25923), Gram-negative (Escherichia coli ATCC 25922) bacterial strains and antifungal strains (Aspergillus flavus, and Candida albicans). Among the various extracts, diethyl ether extracts of B. monnieri has an antibacterial potency against Staphylococcus aureus (gram positive), and ethyl acetate extract showed effects on E. coli (gram negative) at higher concentrations of 300 microgam mL-1. The ethanolic extract has potent antifungal activity against the fungus (Aspergillus flavus, and Candida albicans) compared to diethyl ether and ethyl acetate-ether. Both extracts (diethyl ether and ethyl acetate) has a minimum antifungal effect while these extracts showed more inhibitory effects on tested bacteria. Inhibitory effects of the aqueous extract were not observed at all concentration (100 microgam mL-1, 200 microgam mL-1and 300 microgam mL-1) against the entire examined bacterial and fungal species. The finding of this study indicates the antibacterial and antifungal activity exhibited by the ethanolic, diethyl ether, and ethyl acetate extract of B. monnieri can be validated to the management of medicinal plant throughout the world.
A New Framework For Spatial Modeling And Synthesis of Genome Sequence
Authors: Salman Mohamadi, Farhang Yeganegi, Hamidreza Amindavar
Date: 2019-08-09 00:00:00

This paper provides a framework in order to statistically model sequences from human genome, which is allowing a formulation to synthesize gene sequences. We start by converting the alphabetic sequence of genome to decimal sequence by Huffman coding. Then, this decimal sequence is decomposed by HP filter into two components, trend and cyclic. Next, a statistical modeling, ARIMA-GARCH, is implemented on trend component exhibiting heteroskedasticity, autoregressive integrated moving average (ARIMA) to capture the linear characteristics of the sequence and later, generalized autoregressive conditional heteroskedasticity (GARCH) is then appropriated for the statistical nonlinearity of genome sequence. This modeling approach synthesizes a given genome sequence regarding to its statistical features. Finally, the PDF of a given sequence is estimated using Gaussian mixture model and based on estimated PDF, we determine a new PDF presenting sequences that counteract statistically the original sequence. Our strategy is performed on several genes as well as HIV nucleotide sequence and corresponding results is presented.
Field models and numerical dosimetry inside an extremely-low-frequency electromagnetic bioreactor: the theoretical link between the electromagnetically induced mechanical forces and the biological mechanisms of the cell tensegrity
Authors: Maria Evelina Mognaschi, Paolo Di Barba, Giovanni Magenes, Andrea Lenzi, Fabio Naro, Lorenzo Fassina
Date: 2019-08-03 00:00:00

We have implemented field models and performed a detailed numerical dosimetry inside our extremely-low-frequency electromagnetic bioreactor which has been successfully used in $\textit{in vitro}$ Biotechnology and Tissue Engineering researches. The numerical dosimetry permitted to map the magnetic induction field (maximum module equal to about 3.3 mT) and to discuss its biological effects in terms of induced electric currents and induced mechanical forces (compression and traction). So, in the frame of the tensegrity-mechanotransduction theory of Ingber, the study of these electromagnetically induced mechanical forces could be, in our opinion, a powerful tool to understand some effects of the electromagnetic stimulation whose mechanisms remain still elusive.
Quantum patterns of genome size variation in angiosperms
Authors: Liaofu Luo, Lirong Zhang
Date: 2018-07-16 00:00:00

The nuclear DNA amount in angiosperms is studied from the eigen-value equation of the genome evolution operator H. The operator H is introduced by physical simulation and it is defined as a function of the genome size N and the derivative with respective to the size. The discontinuity of DNA size distribution and its synergetic occurrence in related angiosperms species are successfully deduced from the solution of the equation. The results agree well with the existing experimental data of Aloe, Clarkia, Nicotiana, Lathyrus, Allium and other genera. It may indicate that the evolutionary constrains on angiosperm genome are essentially of quantum origin.
Mapping the Human Body at Cellular Resolution -- The NIH Common Fund Human BioMolecular Atlas Program
Authors: Michael P Snyder, Shin Lin, Amanda Posgai, Mark Atkinson, Aviv Regev, Jennifer Rood, Orit Rosen, Leslie Gaffney, Anna Hupalowska, Rahul Satija, Nils Gehlenborg, Jay Shendure, Julia Laskin, Pehr Harbury, Nicholas A Nystrom, Ziv Bar-Joseph, Kun Zhang, Katy Börner, Yiing Lin, Richard Conroy, Dena Procaccini, Ananda L Roy, Ajay Pillai, Marishka Brown, Zorina S Galis
Date: 2019-03-18 00:00:00

Transformative technologies are enabling the construction of three dimensional (3D) maps of tissues with unprecedented spatial and molecular resolution. Over the next seven years, the NIH Common Fund Human Biomolecular Atlas Program (HuBMAP) intends to develop a widely accessible framework for comprehensively mapping the human body at single-cell resolution by supporting technology development, data acquisition, and detailed spatial mapping. HuBMAP will integrate its efforts with other funding agencies, programs, consortia, and the biomedical research community at large towards the shared vision of a comprehensive, accessible 3D molecular and cellular atlas of the human body, in health and various disease settings.
Studies on Bone-mass Formation within a Theoretical Model
Authors: Nirmalendu Hui, Biplab Chattopadhyay
Date: 2019-06-03 00:00:00

Bone-mass formation in human is looked at to understand the underlying dynamics with an eye on healing of bone-fracture and non-unions in non-invasive pathways. Three biological cells osteoblasts, osteoclasts and osteocytes are important players in creating new bone or osseous matter in which quite a few hormones, proteins and minerals have indispensable supportive role. Assuming populations of the three mentioned cells as variables, we frame a theoretical model which is represented as a set of time differential equations. These equations imitate the dynamic process of bone matter creation. High value of osteocytes with moderate level values of osteoblast and osteoclast, all at asymptotic scale, imply creation of new bone-matter in our model. The model is studied both analytically and numerically. Some important results are highlighted and relevant predictions are made which could be put to future experimental test.
Effect of E-cigarette Use and Social Network on Smoking Behavior Change: An agent-based model of E-cigarette and Cigarette Interaction
Authors: Yang Qin, Rojiemiahd Edjoc, Nathaniel D Osgood
Date: 2019-05-03 00:00:00

Despite a general reduction in smoking in many areas of the developed world, it remains one of the biggest public health threats. As an alternative to tobacco, the use of electronic cigarettes (ECig) has been increased dramatically over the last decade. ECig use is hypothesized to impact smoking behavior through several pathways, not only as a means of quitting cigarettes and lowering risk of relapse, but also as both an alternative nicotine delivery device to cigarettes, as a visible use of nicotine that can lead to imitative behavior in the form of smoking, and as a gateway nicotine delivery technology that can build high levels of nicotine tolerance and pave the way for initiation of smoking. Evidence regarding the effect of ECig use on smoking behavior change remains inconclusive. To address these challenges, we built an agent-based model (ABM) of smoking and ECig use to examine the effects of ECig use on smoking behavior change. The impact of social network (SN) on the initiation of smoking and ECig use were also explored. Findings from the simulation suggest that the use of ECig generates substantially lower prevalence of current smoker (PCS), which demonstrates the potential for reducing smoking and lowering the risk of relapse. The effects of proximity-based influences within SN increases the prevalence of current ECig user (PCEU). The model also suggests the importance of improved understanding of drivers in cessation and relapse in ECig use, in light of findings that such aspects of behavior change may notably influence smoking behavior change and burden.
Detection of virulence factors and beta-lactamase encoding genes among the clinical isolates of Pseudomonas aeruginosa
Authors: Fazlul Mkk, Najnin A, Farzana Y, Rashid Ma, Deepthi S, Srikumar C, SS Rashid, Nazmul MHM
Date: 2019-02-06 00:00:00

Background: Pseudomonas aeruginosa has emerged as a significant opportunistic bacterial pathogen that causes nosocomial infections in healthcare settings resulting in treatment failure throughout the world. This study was carried out to compare the relatedness between virulence characteristics and \b{eta}-lactamase encoding genes producing Pseudomonas aeruginosa. Methods: A total of 120 P. aeruginosa isolates were obtained from both paediatric and adult patients of Selayang Hospital, Kuala Lumpur, Malaysia. Phenotypic methods were used to detect various virulence factors (Phospholipase, Hemolysin, Gelatinase, DNAse, and Biofilm). All the isolates were evaluated for production of extended spectrum beta-lactamase (ESBL) as well as metallo \b{eta}-lactamase (MBL) by Double-disk synergy test (DDST) and E-test while AmpC \b{eta}-lactamase production was detected by disk antagonism test. Results: In this study, 120 Pseudomonas aeruginosa isolates (20 each from blood, wounds, respiratory secretions, stools, urine, and sputum samples) were studied. Among Pseudomonas aeruginosa isolates, the distribution of virulence factors was positive for hemolysin (48.33%), DNAse (43.33%), phospholipase (40.83%), gelatinase (31.66%) production and biofilm formation (34%) respectively. The prevalence of multiple \b{eta}-lactamase in P. aeruginosa showed 19.16% ESBL, 7.5% MBL and 10.83% AmpC production respectively. Conclusion: A regular surveillance is required to reduce public healt
Measurement of trace elements in five popular medicinal plants using Instrumental Neutron Activation Analysis method (INAA) in Arak, Iran
Authors: Reza Pourimani, Sedigheh Kashian, Ali Asghar Fathivand
Date: 2019-01-05 00:00:00

In this work, the specific mass of twelve elements were determined in five of the most commonly used medicinal plants as Caraway (Carum carvi), Savory (Satureia hortensis), Purslane (Portulaca oleracea), Fenugreek (Trigonella foenum-graecum) and Milk thistle (Silibum marianum) prepared from herbal pharmacies. Multi elemental Instrumental Neutron Activation Analysis (INAA) method was applied to analyze the samples. Tehran research reactor was used as a neutron source and gamma ray spectra registered using high purity germanium (HPGe) detector. Among analyzed samples, highest concentrations of Fe (8789 ppm), Cr (8 ppm) and Na (517 ppm) were found in Caraway. Maximum levels of Mn (95 ppm), Cl (3702 ppm), Ca (18328 ppm) , K (21562 ppm) and V (2.7 ppm) were detected in Savory and Fenugreek contains the lowest concentrations of Fe (195 ppm), Zn (13 ppm), Ca (2243 ppm), Al (99ppm), Mn (26 pm) and Mg (177ppm).
Thermoregulation in mice, rats and humans: An insight into the evolution of human hairlessness
Authors: Bernard J. Feldman
Date: 2018-12-04 00:00:00

The thermoregulation system in animals removes body heat in hot temperatures and retains body heat in cold temperatures. The better the animal removes heat, the worse the animal retains heat and visa versa. It is the balance between these two conflicting goals that determines the mammal's size, heart rate and amount of hair. The rat's loss of tail hair and human's loss of its body hair are responses to these conflicting thermoregulation needs as these animals evolved to larger size over time.