jimnoneill/paper-to-field-training huggingface dataset:
The early development and application of FTIR difference spectroscopy to membrane proteins: A personal perspective

Field: Chemistry (Physical Sciences)

Membrane proteins facilitate some of the most important cellular processes including energy conversion, ion transport and signal transduction.While conventional infrared absorption provides information about membrane protein secondary structure, a major challenge is to develop a dynamic picture of the functioning of membrane proteins at the molecular level.The introduction of FTIR difference spectroscopy around 1980 to study structural changes in membrane proteins along with a number of associated techniques including protein isotope labeling, site-directed mutagenesis, polarization dichroism, attenuated total reflection and time-resolved spectroscopy have led to significant progress towards this goal.It is now possible to routinely detect conformational changes of individual amino acid residues, backbone peptides, binding ligands, chromophores and even internal water molecules under physiological conditions with time-resolution down to nanoseconds.The advent of ultrafast pulsed-IR lasers has pushed this time-resolution down to femtoseconds.The early development of FTIR difference spectroscopy as applied to membrane proteins with special focus on bacteriorhodopsin is reviewed from a personal perspective.
Salvia officinalis L. extract and its new food antioxidant formulations induce apoptosis through mitochondrial/ caspase pathway in leukemia L1210 cells

Field: Pharmacology, Toxicology and Pharmaceutics (Life Sciences)

ABSTRACT Salvia officinalis, L. (Lamiaceae) is one of the most widespread herbal species used in the area of human health and in the foodprocessing industry. Salvia and its extracts are known to be a rich source of antioxidants. As shown previously, the crude ethanolic extract of salvia (SE) exerts lower anti-oxidative properties in lard compared to the new salvia food formulations No. 1 (SF1; 32% of SE + 68% of the emulsifier Dimodan S-T) and No. 2 (SF2; 32% of SE + 68% of the emulsifier Topcithin 50). The aim of the present study was to investigate and compare the effects of the SE and its food formulations SF1 and SF2 on the toxicity and/or proliferation of L1210 leukemia cells. We found that SE and both SF1 and SF2 demonstrated different concentration- and time-dependent cytotoxic/antiproliferative cellular effects already within the first 24 h of the treatment. However, SE was nearly 10 times more effective than the new salvia food formulations SF1 and SF2. We investigated partially also the molecular mechanisms lying behind the action of SE, SF1 and SF2 induced apoptosis in our cell model. We found an apparent involvement of the mitochondrial/caspase-dependent pathway in the described processes. Nevertheless, further investigation is needed before salvia extract and its new antioxidant formulations can be included among the potential food antioxidants with protective properties against cancer.
Changes in gastric mucosal microbiota in gastric carcinogenesis: a systematic review protocol

Field: Medicine (Health Sciences)

Introduction The human stomach is a complex and diverse microbial ecosystem. Consecutive alternations of gastric microbiota occur in gastric carcinogenesis, while the changing pattern during this process remains controversial across studies. We aim to identify the changes in the diversity and composition of gastric mucosal microbiota in gastric tumorigenesis. Methods and analysis We will search through PubMed, EMBASE and Cochrane databases, as well as conference proceedings and references of review articles for observational articles reporting either the relative abundance of bacteria at the phylum or genus level or at least one of the alpha diversity indexes respectively and clearly in both gastric cancer and non-cancer groups. Selection of studies and data extraction will be performed independently by two researchers. Disagreements will be resolved through discussion. Risk of bias will be assessed using the modified Newcastle-Ottawa Scale. Quantitative analyses will be performed using a random effects model, where the effect measurement will be expressed as the MD. Ethics and dissemination Ethical approval for this systematic review is not required, as the study is based exclusively on published documents and will not include any individual data. Findings of this study are expected to be disseminated through peer-reviewed journals or conference proceedings. PROSPERO registration number CRD42020206973.
Comparison of Combustion and Gasification for Energy Recovery from Residual Woody Biomass

Field: Energy (Physical Sciences)

More than half of global electrical and thermal energy is generated by fossil fuels, around 63% in 2019. This is one of the main causes of greenhouse gas (GHG) emissions, responsible for the increase of the atmospheric average temperature above the reference level. Combined heat and power (CHP) generation from biomass may contribute to increasing renewable energy generation and reducing GHGs emissions, pursuing the goals of the European Union green deal 2021. In the present study, CHP generation potentiality, efficiencies, and environmental impact are compared numerically by using Aspen Plus V8.8 software between the thermal treatment of combustion and gasification integrated with a gas turbine system of residual woody biomass. The gas turbine is powered by the exhausts of biomass combustion in the first configuration, and by the exhausts of syngas combustion in the second one. Modeling of cogeneration through biomass combustion and gasification is developed based on the available literature data, founding a good agreement with the experimental campaign. Wood combustion is more advantageous in terms of cogeneration efficiencies (around 40% higher), whereas gasification emits lower GHGs.
Computational Design of an Iron Catalyst for Olefin Metathesis

Field: Chemistry (Physical Sciences)

Olefin metathesis is a versatile reaction in synthetic chemistry. The use of iron compounds as olefin metathesis catalysts has attracted interest but has not succeeded because most Fe complexes catalyze cyclopropanation reactions preferentially to cycloreversion, which is a key step in the metathesis reaction cycle. In the present study, we performed density functional theory calculations to study the catalytic effect of ancillary pincer ligands in an Fe organometallic catalyst for olefin metathesis. We show here that the partial atomic charge on Fe in the metallocyclobutane intermediate is a descriptor for the tendency of the Fe complex to favor olefin metathesis over cyclopropanation. The results suggest that the pincer ligands can decrease the partial atomic charge on the Fe ion and that decreasing this charge can make the desired cycloreversion reaction more energetically favorable than the cyclopropanation side reaction. In this way, we found that the Fe carbene stabilized by N-heterocyclic dicarbene ligands (Fe(C–N–C)(=CHCH3), where C–N–C denotes 2,6-bis(methylimidazol-2-ylidene)pyridine), is a potential candidate for catalyzing the olefin metathesis reaction. We then calculated the whole catalytic cycle for the propylene metathesis reaction catalyzed by the Fe(C–N–C) carbene, and the results indicate that the cyclopropanation reaction is disfavored by ~4 kcal/mol. We verified the stability of the proposed Fe(C–N–C) catalyst by considering two possible deformation pathways: the transformation of the carbene ligand to a coordinated alkene molecule and the formation of a hydride carbyne intermediate followed by the insertion of a propylene molecule. We found that neither deformation pathway is energetically favorable. Finally we propose a viable route to synthesize the Fe(C–N–C) carbene complex by utilizing the already available Fe(N<sub>2</sub>)<sub>2</sub> complex stabilized by an N-heterocyclic dicarbene ligand.
Modelling Travel Behaviour in Multi-modal Networks

Field: Decision Sciences (Social Sciences)

Multi-modal transport is seen as a promising approach to solve modern mobility problems, including recurrent congestion, deteriorating accessibility of city centers, and negative impacts on the environment. This monograph presents a thesis that models travel behavior in multi-modal networks in cities in The Netherlands. The author establishes a theoretical framework of multi-modal travel behavior, identifying specific features of multi-modal trips and defining terminology. The research included setting up and conducting a large data collection among train travelers, developing and applying an algorithm suitable to generate an objective choice set for multi-modal transport networks, analyzing reported chosen and non-chosen alternatives and the availability of multi-modal trip alternatives, and estimating advanced choice models for train trips. The author concludes that most travelers do not even mention other alternatives than the one they used. Expected differences in sizes of reported subjective choice sets between types of trips could no be found. In urbanized corridors, train users have a large number of multi-modal trip alternatives available. Shares of private mode transport are high at home-ends as well as activity-ends of trips, and walking is the dominant private mode.
LHD TESPEL #54613.1

Field: Physics and Astronomy (Physical Sciences)

Tracer-Encapsulated Solid Pellet(TESPEL) is a double-layered impurity pellet, which basically consists of polystyrene polymer (-CH(C6H5)CH2-) as an outer shell and tracer particles as a core. TESPEL can be utilized for various physics-oriented experiments, e.g. impurity injection for the perturbative impurity transport, induction of a cold pulse propagation.
RNAs on the Go: Extracellular Transfer in Insects with Promising Prospects for Pest Management

Field: Agricultural and Biological Sciences (Life Sciences)

RNA-mediated pathways form an important regulatory layer of myriad biological processes. In the last decade, the potential of RNA molecules to contribute to the control of agricultural pests has not been disregarded, specifically via the RNA interference (RNAi) mechanism. In fact, several proofs-of-concept have been made in this scope. Furthermore, a novel research field regarding extracellular RNAs and RNA-based intercellular/interorganismal communication is booming. In this article, we review key discoveries concerning extracellular RNAs in insects, insect RNA-based cell-to-cell communication, and plant–insect transfer of RNA. In addition, we overview the molecular mechanisms implicated in this form of communication and discuss future biotechnological prospects, namely from the insect pest-control perspective.
Data presentation, interpretation, and communication

Field: Agricultural and Biological Sciences (Life Sciences)

A phosphorus decision support system (PDSS) has been developed to diagnose P deficiency and predict P fertilizer requirements for Ultisols and Oxisols. Uncertainty analysis has indicated that a major source of uncertainty in prediction was the value of the buffer coefficient (BC, the increase in extractable P per m-fit of applied P). In the current implementation of PDSS, BC is predicted using an equation that relates BC with soil clay content. We compared PDSS estimates of BC with those obtained by regressing extracted Mehlich 1 P values against amounts of P applied to soil, (a) in field experiments at crop harvest and one year after P addition, and (b) in laboratory wet-to-dry incubations with 1:1 soil:P solution mixture. In the field, P amounts were added to upland rice-soybean rotations at 0 to 236 mg P dm-3 at Matalom and 0 to 166 at Siniloan, Philippines, and at 0 to 275 at Sitiung, Indonesia, sites in the IRRI Long Term P Experiment (LTPE) network. In the laboratory, P rates of 0 to 272 mg P dm-3 were added and the soil dried at 30 C for 10 days. The PDSS estimates of BC were 0.22 at Matalom (35% clay), 0.10 at Siniloan (54% clay) and 0.07 at Sitiung (63% clay). The field BC values decreased over time as expected from 0.25 at crop harvest to 0.14 after one year at Matalom and from 0.21 to 0.11 at Siniloan but remained unchanged at 0.09 and 0.11 at Sitiung. The laboratory estimates were similar for soil sampled at different times and were close to the one-year field estimates with values averaging 0.16 at Matalom, 0.07 at Siniloan and 0.12 at Sitiung. These estimates, however, differed somewhat from both field estimates at crop harvest and PDSS predictions. While PDSS predictions were generally in the range of the field and laboratory estimates, there was a lack of consistency in the rankings in tiffs limited range of sites and clay content. A much larger set of sites and comparisons would be needed to further refine the prediction of BC.
ADMET Polymers Containing Precisely Spaced Pendant Boronic Acids and Esters

Field: Chemistry (Physical Sciences)

Precise aryl boronic ester- and acid-containing polymers have been synthesized via acyclic diene metathesis. High-molecular weight phenyl boronic acid polymers were synthesized. Cross-linked phenyl boronic acid polymers were also synthesized and demonstrate a unique crystallization behavior not usually seen in cross-linked polymers.
On the radiation from unbaffled pistons and their dipole equivalent

Field: Physics and Astronomy (Physical Sciences)

The radiation efficiency from simple vibrating planar surfaces is often used as a basis to describe the sound radiation from more complex structures, having important applications in various fields of acoustics. The low-frequency radiation efficiency of a baffled piston can easily be represented by a simple monopole source. Notably, the equivalent source strength is dependent on the piston surface area. However, the unbaffled case presents additional difficulties as the so-called ``edge effects'' significantly alter the piston radiation impedance. Consequently, a low-frequency equivalence between dipoles and an unbaffled pistons is not as straight forward, since not only the piston area but also its shape will have an effect on the radiated sound. In this work, the search for a simple and generic, equivalence between dipoles and unbaffled pistons is pursued. A finite element model is used to calculate the radiation efficiency from unbaffled pistons with the same surface area but different shapes. A broad set of results indicate that the ``edge effects'' can be accurately represented by a simple term dependent on the piston compactness (ratio of area to perimeter). Effectively, pistons with smaller area to perimeter ratio will be less efficient radiators. Such term allows the definition of an equivalent dipole source strength that approximates the low-frequency behavior of an unbaffled piston of arbitrary shape.
Effect of GGBFS and GSS on the properties of mortar

Field: Engineering (Physical Sciences)

Industrial wastes are generally considered as a major source of environmental problems in the world. Land disposal that is a partial solution for this problem causes secondary pollution problems and extra costs. For this reason, more efficient solutions such as alternative recovery options need to be investigated. In this respect, cement and concrete industry could be an important consumer of industrial by-products or solid wastes. Fly ash (FA), blast-furnace slag (BFS), and silica fume (SF) are currently used in cement and concrete industry. In Europe, every year, nearly 12 million tons of steel slags (SS) get generated. Today about 65% of the produced SS is used on qualified fields of application. But the remaining 35% of the slag are still dumped (Motz & Geiseler 2001). On the other hand, it is generally agreed that Portland cement clinker production is expensive and ecologically harmful. For this reason, various studies have investigated about usage of slags in cement production. However most of these studies concerns mostly one type of slag that is mainly GGBFS. Especially, a combination ofGGBFS and GSS as Portland clinker substitution has not yet been reported in the literature.
Library Advocacy Through Twitter: A Social Media Analysis of #savelibraries and #getESEAright

Field: Social Sciences (Social Sciences)

Advocacy groups of all types use social media to reach their constituents. However, are messages of library advocacy disseminated through social media reaching those who can become allies in the quest to save libraries? How far reaching are library advocacy messages? This study addresses the use of Twitter for library advocacy. A review of the literature outlining social network analysis and the use of Twitter for advocacy, procedures for using NodeXL (a software package for social media analysis), and a taxonomy of Twitter conversations are provided.
Organizing Independent Activity in EFL Teaching in Ethnically Diverse Classrooms at the University of the Coal Mining Region

Field: Social Sciences (Social Sciences)

Training of highly qualified specialists is a significant factor for the consistent progress in any branch of economics. Kemerovo State University provides training of specialists for the coal mining region in Russia. Nowadays, the University tends to increase the proportion of foreign students as well. Most of these are students from neighboring countries, such as Tajikistan, Uzbekistan, Kyrgyzstan, Kazakhstan, where raw materials industries, including mining, are developed. Taking into account the multi-ethnic diversity of students at Kemerovo State University, we analyzed the experience and determined the worthwhile forms of organizing independent activity in EFL teaching. Among the forms of independent activity, we introduced independent reading, preparing thematic presentations, written tasks based on video content, and writing thematic essays. Organizing independent work in the educational process, which involves a large number of multinational groups of students, we took into account the following conditions. We considered such particular qualities of contemporary students as their general need in flexible learning environment as well as in self-expression; we took into account their interest in new knowledge and motivation for self- improvement, and at the same time, lack of desire for completing reproductive types of tasks, along with fragmented thinking.
Muscle Splitting Augmentation Mastopexy: A l3-year Analysis and Outcome of Primary and Secondary Procedures

Field: Medicine (Health Sciences)

Background: The muscle splitting technique is a submuscular pocket used for augmentation mammoplasty. Its use and results following primary and secondary procedures are presented. Methods: A retrospective study that analyzed complication and revision rates following primary and secondary mastopexy with augmentation in a muscle splitting pocket performed between April 2007 and March 2020 was carried out. Data were divided into two groups: primary and secondary single-stage mastopexies with augmentation. Results: A total of 169 patients had a primary procedure and 49 had secondary procedures. The mean ages of patients in the primary and secondary were 32.3 ± 9.89 and 38.2 ± 9.63 years, respectively. Five (3.0%) patients had periprosthetic or wound infections in the primary group when compared with 0% in secondary surgery group. Wound breakdown was seen in 13 (7.7%) patients with a primary procedure compared with one patient (2%) with a secondary procedure. One patient had partial nipple loss and another had total nipple loss in the primary group (1.2%) when compared with one patient (2.0%) who had partial nipple loss in the secondary group. Revision surgeries were carried out in 16 (10.1%) of the primary procedures compared with five (10.2%) of the secondary procedures. Conclusion: Even though there was a higher prevalence of complications in the primary procedures group than in the secondary procedures group, the overall complications following muscle splitting mastopexy with augmentation are within an acceptable range.
Identification and validation of genes involved in pyroptosis of LPS and D-GALN induced acute liver injury

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

Abstract

Pyroptosis plays an important role in the development of acute liver failure (ALF). In this study, we aimed to identify and validate important pyroptosis-related genes in ALF by bioinformatics analysis. The pyroptosis-related genes involved in the differential expression of ALF were identified using the gene expression comprehensive database (GEO) and the mRNA expression profile dataset GSE217659 provided by R software. The Gene Ontology (GO) enrichment analysis and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were performed for the differentially expressed related genes.Further screened the module genes by WGCNA and identified four genes (Gzmb, Mefv, Gbp 2 and Casp 4), which could be used as potential diagnostic biomarkers for ALF. Subsequently, the hub gene was modeled using nomogram to assess whether the model was good.
A generalized quantile estimator under censoring

Field: Mathematics (Physical Sciences)

Based on right-censored data from a lifetime distribution F0 a smooth alternative to the product-limit estimator as a nonparametric quantile estimator of a population quantile is proposed; The estimator is a "generalized product-limit quantile" obtained by averaging appropriate subsample product-limit quantiles over all subsamples of a fixed size. Under the random censorship model and some conditions on Fop it is shown that the estimator is consistent and has the same asymptotic normal distribution as the product-limit quantile estimator. A small Monte Carlo simulation study shows that there exist some values of the subsample size for which the estimator performs better than the product-limit quantile estimator in the sense of estimated mean squared errors.
Dielectric Properties of Ionic Liquids: Achievements So Far and Challenges Remaining

Field: Chemistry (Physical Sciences)

The static dielectric constant of an ionic liquid is not measurable by conventional methods because the samples are largely short-circuited by their intrinsic electrical conductance. It is, however, possible to determine this quantity by recording the frequency-dependent dielectric dispersion curve in the microwave regime, followed by extrapolation to quasi-static conditions. This review compiles the information on static dielectric constants available from such experiments, and discusses trends in the cation and anion dependence. The results classify most aprotic ionic liquids as moderately polar solvents with dielectric constants of the order of ϵ = 10–12; protic ionic liquids, however, exhibit much higher values.
Tracheal contraction and relaxation initiated by lung and somatic afferents in dogs

Field: Neuroscience (Life Sciences)

Capsaicin injected into the right heart of dogs causes reflex bronchoconstriction by stimulating pulmonary C-fibers, but injected into the left heart it is said to have little effect even though it stimulates bronchial C-fibers, which are known to cause contraction of airway smooth muscle. Attempting to resolve this apparent contradiction, we recorded smooth muscle tension in an innervated tracheal segment in anesthetized dogs and examined the reflex effects of injecting capsaicin intravascularly at different sites. Right atrial injection of capsaicin (10 micrograms/kg) caused tracheal contraction, as did bronchial arterial injection (0.15–5.0 micrograms); left atrial injection (10 micrograms/kg), however, caused relaxation or slight contraction, or a combination of the two. Contraction but not relaxation was abolished by cutting or cooling (0 degree C) the cervical vagus nerves. Femoral arterial injection (10–100 micrograms) caused tracheal relaxation, which was abolished by cutting hindlimb nerves. We conclude that both pulmonary and bronchial C-fibers evoke tracheal contraction, but when capsaicin is injected into the left atrium any effects of stimulating bronchial C-fibers are masked by the reflex action of somatic afferents, which cause tracheal relaxation.