jimnoneill/paper-to-field-training huggingface dataset:
Mining bio-models for synthetic biology design

Field: Computer Science (Physical Sciences)

Engineering of microbes for various applications require lots of prior information. Bio Models database (https://www.ebi.ac.uk/biomodels/) has become a rich resource in which it captures many possible biochemical reactions in a form of mathematical models. It will be extremely useful to be able to mine the models for known reactions whenever someone needs to design a new biological system. The aim of this project is to develop an algorithm to search and mine bio-models. The final product is able to extract relevant information from any bio-model file and present all critical data such as species, parameters, rules, reactions, events and rate equations in a readable manner. Display options are available to the user if he wishes to view the model in its original format (for accuracy checking against the respective annotated PDF file) or translated form. From the derived rate equation results window, users can examine the entire reaction pathway that a species is involved in and easily distinguish if the component is consumed or produced in the respective reactions. Users are also able to search for all reaction pathways between two specified molecules. The algorithm is capable of combining information from two or more bio-models and merging overlapping data. We hope that our work is able to enhance readability and usability for individuals or institutions utilizing bio-models on a large scale in their research.
Quantification of Chemical Composition Distribution of Polyolefin Materials for Improved Accuracy and Speed

Field: Chemical Engineering (Physical Sciences)

Crystallization-based separation techniques are widely used for chemical composition distribution (CCD, also often referred as short chain branching distribution SCBD) measurement in the polyolefin industry, in which CCD is among the most critical structural parameters to define their properties and applications. The desire to improve the sample throughput rate by shortening the analysis time in the current CCD techniques would normally sacrifice measurement accuracy due to the cocrystallization phenomena, in which the polymer chains with similar molecular architectures will cocrystallize or coelute enigmatically in the CCD analysis. Herein, we reported the investigation by exploring various separation packing materials on the cocrystallization phenomena. In comparison with the commercially available Crystallization Elution Fractionation (CEF) technique, an improved technique for CCD measurement (iCCD) was developed using the columns packed with gold-coated nickel substrate or spherical gold particles with or without the dynamic cooling process. With iCCD, it was observed with equivalent cocrystallization degree to the industrial gold standard benchmark Wild-TREF method but with over 70+ times improved sample throughput rate (62 vs 4500 min). The experimental CCD chromatogram for a polyolefin blend similarly assembled to the mathematically constructed result further demonstrated the minimized cocrystallization and measurement accuracy in the iCCD method. In addition, the superior mechanical properties of gold-coated nickel particles enabled the long-term robustness and enhanced measurement precision of the iCCD technique during the repeated thermal treatment cycles and pressure variations.
Intelligent Pollution Mask: a Lifesaving Device

Field: Engineering (Physical Sciences)

Background/objectives: The air pollution level is increasing immensely because of several issues, such as emission of highly inflammable gases from factories, an alarming rise in the use of petrol and diesel vehicles for personal commute, and various other sources that generate smoke; all of this have an seriously harmful impact on human health and are responsible for various diseases. Therefore, the objective of this article is to propose an improved and handy system of mask wearing which will help reduce the hazardous effects of air pollution on human health. Methods/findings: After analysing and comparing several products available in the market, a handy and easy-functioning Adriano-based intelligent pollution mask is proposed. This particular design of mask can detect and filter hazardous air pollutants using various sensors. It can also indicate and communicate the pollution level through an inbuilt app with other mask-wearers, including information about which areas to avoid that have very high air pollution. Improvements/application: Because it can detect and filter out several toxic gasses, this product is can be a great solution for preventing the harmful/dangerous effects of air pollution on the human body and, consequently, preventing diseases resulting from breathing highly polluted and saving many lives.Keywords: Air Pollution, PM2.5, PM10, Air pollutants, Mask
Fas-mediated apoptosis in neuroblastoma requires mitochondrial activation and is inhibited by FLICE inhibitor protein and Bcl-2.

Field: Biochemistry, Genetics and Molecular Biology (Life Sciences)

Fas-mediated apoptosis proceeds though mitochondria-dependent or -independent pathways and is deficient in drug-resistant cells. Neuroblastoma, a common pediatric malignancy, often develops drug-resistance and has a silenced caspase 8 (FLICE) gene, which has been associated with Fas- and drug-resistance. We report that besides caspase 8, which was absent in approximately one-third of 26 neuroblastoma cases in this study, other proteins such as bcl-2 and FLICE-inhibitory protein (FLIP), are equally important in conferring Fas-resistance to neuroblastoma cells. Both bcl-2 and FLIP were frequently expressed in neuroblastoma tissues. Our in vitro studies showed that FLIP was recruited to the death-inducing signaling complex and interfered with the recruitment of caspase 8 in neuroblastoma cells. bcl-2 inhibited the activation of the mitochondria; but it also lowered the free cytoplasmic levels of caspase 8 by binding and sequestering it, thus acting through a novel antiapoptotic mechanism upstream of the mitochondria. In vitro down-regulation of bcl-2 with antisense oligonucleotides allowed the release of cytochrome c from mitochondria and the activation of caspases 8 and 3 upon Fas activation as well as sensitized neuroblastoma cells to Fas-mediated apoptosis. Down-regulation of FLIP had only a modest apoptotic effect because of the coexistent mitochondrial block. However, combined treatment with bcl-2 and FLIP antisense oligonucleotides had a statistically significant synergistic effect reversing Fas-resistance in neuroblastoma cells in vitro. These data indicate that Fas-mediated apoptosis in neuroblastoma cells is mitochondria-dependent and inhibited both at the mitochondrial level and at the level of caspase 8 activation. Thus, gene-targeting therapies for bcl-2 and FLIP may reverse Fas-resistance and prove useful in the treatment of drug-resistant neuroblastomas.
Growth of porous ZnO nanowires by thermal oxidation of ZnS nanowires

Field: Materials Science (Physical Sciences)

The growth of porous ZnO nanowires (NWs) by thermal oxidation of ZnS NWs in air was studied. The ZnS NWs were first synthesized by thermal evaporation of ZnS powder at 1100°C in Ar. On subsequent annealing in air, the ZnS NWs transformed to porous ZnS-ZnO core-shell NWs and porous ZnO NWs at 600-700°C and 700-750°C, respectively. Higher annealing temperature suppressed the formation of porous structure in ZnO NWs. Two factors, the higher formation rate for SO 2 than for ZnO and the incompatible structure at the interface of epitaxial ZnS and ZnO, are beneficial to the formation of porous ZnO NWs from ZnS NWs on annealing in air. The mechanisms for the formation of porous ZnO NWs by thermal oxidation of ZnS NWs in air are discussed.
Atlas of Anatomay

Field: Neuroscience (Life Sciences)

The dopaminergic mechanisms that control reward-motivated behavior are the subject of intense study, but it is yet unclear how, in humans, neural activity in mesolimbic reward-circuitry and its functional neuroimaging correlates are related to dopamine release. To address this question, we obtained functional magnetic resonance imaging (fMRI) measures of reward-related neural activity and [11C]raclopride positron emission tomography measures of dopamine release in the same human participants, while they performed a delayed monetary incentive task. Across the cohort, a positive correlation emerged between neural activity of the substantia nigra/ventral tegmental area (SN/VTA), the main origin of dopaminergic neurotransmission, during reward anticipation and reward-related [11C]raclopride displacement as an index of dopamine release in the ventral striatum, major target of SN/VTA dopamine neurons. Neural activity in the ventral striatum/nucleus accumbens itself also correlated with ventral striatal dopamine release. Additionally, high-reward-related dopamine release was associated with increased activation of limbic structures, such as the amygdala and the hippocampus. The observed correlations of reward-related mesolimbic fMRI activation and dopamine release provide evidence that dopaminergic neurotransmission plays a quantitative role in human mesolimbic reward processing. Moreover, the combined neurochemical and hemodynamic imaging approach used here opens up new perspectives for the investigation of molecular mechanisms underlying human cognition.
Knowledge and the Politics of Innovation

Field: Business, Management and Accounting (Social Sciences)

The chapter discusses the relationship between knowledge management and innovation; specifically, it examines how knowledge in organizations affects the creation of new knowledge and what the implications are for innovation management. The core argument is that in a knowledge-based company, where competition is assessed at the edge of rare expertise and the development of innovations (Boisot, 1998; Drucker, 1993; Sveiby 1997), knowledge, which is always interwoven with power, becomes a precious resource, on the grounds of which struggles are inevitably enacted over its control (Foucault, 1980; Clegg, 1989). To argue this, the chapter brings together two related fields, knowledge management and innovation, which even though in principle they examine similar phenomena, i.e. the creation and sharing of new knowledge, in practice they appear disconnected (Asimakou, 2009b). To support the arguments, two innovation mechanisms in two business groups of a major oil company are discussed. The study used a set of qualitative techniques for data collection (in-depth interview, participant observation, documentary analysis) and a sample of 41 employees, which represented the groups participating in the innovation game (manager, scientists, assistant scientists, administration staff and students). I argue that two mainstream innovation management approaches (the rational planning and the cultural approach) have shaped the understanding and actions of the Business Groups in setting up the innovation mechanisms; however, power struggles at the individual, group and organizational level impacted upon the innovation processes to the extent that the latter became passive ‘technical solutions’.
Relative Impact on GAC Usage Rates of Operating Strategies for Treatment of Contaminated Groundwater

Field: Environmental Science (Physical Sciences)

The former Nebraska Ordnance Plant has groundwater contaminated with a mixture of trichloroethylene (TCE) and the high explosive RDX that is treated in a system of eight granular activated carbon (GAC) contactors. A mathematical model was utilized to simulate alternative operating scenarios along with variable influent concentrations. In this study, blending effluent from parallel columns resulted in the lowest GAC usage rate when the target effluent C∕C0 was >0.3 . Lead-lag operation was best when the target effluent C∕C0 was <0.1 . Only between a target effluent C∕C0 of 0.1 and 0.3 did the percent of the mass transfer zone (MTZ) contained in the column become important. Even then, selection was more sensitive to changes in the target effluent C∕C0 value than the percent of the MTZ contained in the column. Decreasing the TCE influent concentration prior to the GAC treatment system by air stripping may reduce the GAC replacement costs but has significant new capital costs. Because contaminant levels in the extraction wells vary, influent segregation has the potential to reduce GAC usage rates by up to 65% with a relatively low capital expenditure.
STUDY OF DYSLIPIDEMIA IN ASSOCIATION WITH TOTAL ANTIOXIDANT STATUS IN PREECLAMPSIA.

Field: Medicine (Health Sciences)

Introduction: Preeclampsia is a serious complication of the second half of pregnancy that occurs with a frequency of 5-15%. Preeclampsia is an endothelial disease with a major involvement of lipid mediated oxidative damage along with an imbalance between prooxidant production and antioxidant defenses. Aims and objectives: To study the association of dyslipidemia with total antioxidant status in the form of Ferric reducing antioxidant power ( FRAP) in preeclampsia. The present study was carried out for one year on pregnant women attending Materials and methods: Obstetrics department as OP&IP at Narayana Medical College, Nellore.50 normal healthy pregnant women of > 20 weeks gestation were selected as controls.50 diagnosed preeclampsia cases > 20 weeks of gestation and with urine protein creatinine (P/C) ratio more than 0.3 were selected as cases. The cases were further divided into mild and severe. FBS, S. Creatinine, Urine protein and creatinine, Total cholesterol, Triacylglycerol, HDL-C, LDL-C, Uric acid, FRAP were measured. Results: In our study the decrease in (mean±S.D) values of TAS in PE was statistically signicant when compared to controls(586.56 ±109.49 and 534.46 ±97.41,p Value=0.01). Total cholesterol, LDL-C and TAG levels were increased signicantly in comparison to controls(p<0.001). The decrease in HDL-C was not statistically signicant(p=0.71). FRAP correlated negatively with Total cholesterol in our study. The antioxidant levels are inversely Discussion and conclusion: proportional to dyslipidemia. Elevated LDL levels undergo oxidation to form oxidized LDL, which is involved in inammation and free radical generation. In order to counteract the free radicals generated, antioxidant levels decrease. Hence decreased antioxidant status is associated with dyslipidemia, an important cardiovascular risk factor in preeclampsia.
Regular Leisure-Time Physical Activity Is Positively Associated With Happiness Occurrence Among Young Adults In Taiwan

Field: Health Professions (Health Sciences)

Abstract Background: This study aims to examine the relationship between regular leisure-time physical activity (LTPA) and happiness among young adults in Taiwan. Methods: A cross-sectional nationwide study was conducted, and data derived from the National Physical Activity Survey in Taiwan 2020 were reviewed. The participants included 5,611 men and 5,029 women, aged 23 to 44 years. Each participant completed a computer-assisted telephone interviewing with a standardized, structured questionnaire including sociodemographic characteristics, LTPA behavior, self-reported health status, and self-evaluations (comprising height, body weight, and happiness). Results: By using multiple regression, after potential confounders adjustment, we observed that regular LTPA was significantly associated with happiness scores for men ( β = 0.043, p = 0.001) and women ( β = 0.050, p < 0.0001). Furthermore, multiple logistic regression results indicated that with the non-regular LTPA as a baseline, significant associations were observed both for men (odds ratio [OR] = 1.410, 95% CI: 1.173-1.693, p < 0.0001) and women (OR = 1.424, 95% CI: 1.169-1.735, p < 0.0001) at regular LTPA. Conclusions: The current study suggested that regular LTPA, potentially improve the occurrence of happiness among young men. Moreover, this positive effect of regular LTPA was observed for the occurrence of happiness in young women.
Two-Component Regulatory Systems

Field: Biochemistry, Genetics and Molecular Biology (Life Sciences)

Originally characterized for nitrogen regulation (NtrB-NtrC), chemotaxis (CheA-CheY-CheB), osmoregulation (EnvZ-OmpR), and regulation of phosphate uptake (PhoR-PhoB) in Escherichia coli and Salmonella typhimurium, the family of two-component systems has rapidly expanded, and new examples continue to emerge. More than 30 of these regulatory pairs have been identified in both gram-negative and gram-positive bacteria; they control functions ranging from virulence gene expression in Agrobacterium tumefaciens (VirA-VirG), S. typhimurium (PhoQ-PhoP), and Bordetella pertussis (BvgSBvgA) to complex developmental pathways such as sporulation (SpoIIJ-SpoOF-SpoOA) and competence for transformation by exogenous DNA (ComP-ComA and DegS-DegU) in Bacillus subtilis. These pairs are the focus of this chapter. Sequence similarities to other two-component systems suggest the conserved His-189 residue of the DegS protein kinase and Asp-56 residue of the DegU response regulator as likely candidates for the respective phosphorylation sites of the two proteins. A large number of proteins belonging to the histidine protein kinase-response regulator family have been characterized in gram-positive bacteria. It appears that a considerable amount of overlap exists between the different systems controlling postexponential-phase responses in B. subtilis. Thus, DegS-DegU, ComP-ComA, and SpoOA are all involved in controlling competence gene expression, and the SpoOA phosphorelay and DegS-DegU both control protease gene expression.
Study the Inhibitory Effect of Mustard Seed Powder on the Growth of Sclerotium rolfsii

Field: Agricultural and Biological Sciences (Life Sciences)

Groundnut is an important crop in all over the world. The cultivation of groundnut is limited by stem and pod rot
caused by Sclerotium rolfsii. Worldwide the groundnut yield loss due to stem rot is 10 to 25 percent. The fungus, S.
rolfsii has a wide host range. In the present study S. rolfsii was exposed to mustard seed powder (MSP) at different
concentrations (20, 50, 100 and 200 mg) under in vitro conditions. This bioassay was conducted using two types of
methods; (a) Continuously exposing to single MSP and (b) fresh MSP was replenished every 24 hours. Cent per
cent inhibition of S. rolfsii was observed at 100 and 200 mg of MSP in both the methods. But, 50 mg concentration
was also inhibited growth of S. rolfsii up to 93.10% after 72 hours. All results are calculated that MSP has
inhibitory effect against S. rolfsii it may be used as future to reduce soil borne diseases..
Development of a Novel Anti-Erythropoietin-Producing Hepatocellular Receptor B6 Monoclonal Antibody Eb6Mab-3 for Flow Cytometry

Field: Biochemistry, Genetics and Molecular Biology (Life Sciences)

Erythropoietin-producing hepatocellular receptor B6 (EphB6) is a member of the largest Eph subfamily of receptor tyrosine kinases. EphB6 is widely expressed in various tissues and regulates cellular homeostasis by interacting with its membrane-bound ephrin ligands and other receptors. EphB6 is involved in cancer pathology despite lacking kinase activity. Therefore, developing sensitive monoclonal antibodies (mAbs) for EphB6 has been desired for treatment, diagnosis, and further analysis of EphB6. This study established a novel specific and sensitive anti-human EphB6 mAb clone Eb6Mab-3 (mouse IgG1, kappa) by the Cell-Based Immunization and Screening (CBIS) method. In flow cytometry, Eb6Mab-3 demonstrated reactivity with EphB6-overexpressed Chinese hamster ovary-K1 cells (CHO/EphB6) and endogenously EphB6-expressing DLD-1 colorectal cancer cells. Cross-reactivity of Eb6Mab-3 was not observed. Eb6Mab-3 demonstrated a moderate binding affinity (dissociation constant; KD) for CHO/EphB6 (KD: 3.8×10-8 M) and a high binding affinity for DLD-1 (KD: 1.9×10-9 M). Eb6Mab-3 can detect EphB6 protein in CHO/EphB6 lysate in western blot. Therefore, Eb6Mab-3, established by the CBIS method, could be valuable for analyzing the EphB6-associated cellular functions and has potential applications in diagnosis and treatment with specificity and high affinity for cancer cells.
How to Assess Historical Thinking Competencies - An Attempt by the German HiTCH Project -

Field: Arts and Humanities (Social Sciences)

The purpose of this paper is to introduce the HiTCH (Historical Thinking-Competencies in History) project, developed as a tool for assessing historical thinking competencies in Germany. The theoretical origins of the HiTCH project started from Jeismann’s research on historical consciousness in the 1970s. The theory of German historical consciousness was inherited by Pandel and Rüsen, and in the 21st century, it developed into the FUER competency model, which means ‘promotion and development of reflective historical consciousness.’ HiTCH is a large-scale assessment project developed to measure the cultivation of historical thinking competencies oriented towards the FUER model.BR The HiTCH project, which was conducted from 2012 to 2015, produced 15 task blocks and 91 items for each of the four competency areas of the FUER competency model: question competency, method competency, orientation competency, and subject matter competency. In addition, as a derivative study of this project, items to diagnose the narrative competency, deconstruction competency, and the effects of oral history learning were developed. The HiTCH test, which aims to be a “PISA test for history departments,” is currently being used in Germany, Switzerland, Austria, and German-speaking areas of Belgium, and is attracting attention as a model for international historical thinking competency assessment.
Development of a fluorescence-based point detector for biological sensing

Field: Engineering (Physical Sciences)

This paper presents the status of an ongoing development of a point detector for biological warfare agent sensing based on ultraviolet laser-induced fluorescence from single particles in air. The detector will measure the fluorescence spectra of single particles in a sheath flow air beam. The spectral detection part of the system consists of a grating and a photomultiplier tube array with 32 channels, which measure fluorescence spectra in the wavelength band from 300 nm to 650 nm. The detector is designed to measure laser induced fluorescence from single laser pulses and has been tested by measuring fluorescence from simulants of biological warfare agents in aqueous solution. The solutions were excited with laser pulses at the wavelengths of 293 nm and 337 nm. The paper also presents preliminary results on the sheath flow particle injector and time-resolved measurements of fluorescence from biological warfare agent simulants in solution.