jimnoneill/paper-to-field-training huggingface dataset:
A comparative computational study of the 'rbcL' gene in plants and in the three prokaryotic families-archaea, cyanobacteria and proteobacteria

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

The rbcL (ribulose-1,5-biphosphate carboxylase oxygenase) gene plays a crucial role in carbon fixation. Previous studies shed light on its evolutionary relationship among different Phyla. Here, authors have done a comparative study of rbcL genes among proteobacteria, archaea, cyanobacteria and plants based on their compositional variations (GC%, amino acid frequency, codon usage, etc.). In addition we have checked the mutational pressure on rbcL genes. The results indicate that the rbcL genes of cyanobacteria have a wide range of GC%. On the other hand, those of the proteobacteria have mainly higher GC%. Preferences of some amino acids usages have observed in rbcL genes among all species with an exception of plant. Analysis of RSCU (relative synonymous codon usage) values depicts GC ending codon biasness in proteobacteria, archaea and with few exceptions in cyanobacterial species. On the other hand, AU ending codon biasness has been observed for plants. The correspondence analysis shows the significant difference in codon usage pattern among the selected four groups of species. The ENc (expected effective number of codons) plot implys the choice of rbcL gene codon is constrained only by mutational biasness. Moreover, the rbcL genes’ expression ability, as predicted by CAI (codon adaptation index), is similar for most of the species from different groups.
Coupled Procedure for Elastic Modulus and Damping Ratio Measurement on Pavement Subgrade Structures Using Surface Wave Method

Field: Engineering (Physical Sciences)

Limited financial capability of governments for road rehabilitation in developed countries and technical constraints of laboratory tests in assessing pavement quality highlight the need to develop an innovative technique in pavement evaluation. The performance of the Spectral-Analysis-of-Surface-Wave (SASW) method to evaluate the dynamic parameters on the existing road pavements is presented herein. The aim of this paper is to propose a coupled analyses procedure for calculating elastic modulus and damping ratio of soil subgrade layer in pavement. The dynamic elastic modulus was obtained from the shear wave velocity produced from the inversion of an experimental dispersion curve. To validate the modulus obtained from the SASW method, the falling weight deflectometer (FWD) test was used to determine the subgrade modulus at same sites. In this study, a damping ratio of soil layer was also obtained using attenuation coefficient from the modified Bornitz equation. Good agreements were also obtained between the attenuation coefficients from this study and previous studies. The SASW method is able to characterize adequately the in-situ pavement stiffness which can be potentially developed as an innovative evaluation device.
Infrasound Monitoring in Hawaii

Field: Earth and Planetary Sciences (Physical Sciences)

The infrasound network around Kīlauea, Mauna Loa, and Hualalai Volcanoes is one of the most advanced in the world. The Hawaiian Volcano Observatory (HVO) and the University of Hawaii Infrasound Laboratory (ISLA) maintain a network of infrasound arrays and individual stations to detect hazardous events in Hawaii. The network was designed for natural hazards applications such as volcanic eruptions, severe weather, high surf, and tsunamis. Active open-vent volcanoes such as Kīlauea are particularly good infrasound emitters. We are steadily building a continuous baseline of volcano-acoustic activity, including infrasonic tremor and crater collapses from Halema′uma′u and Pu′u O′o, as well as other natural and anthropogenic infrasound from acoustic sources on-island, offshore, and aloft. New directions include the development and commercialization of ubiquitous sensing platforms for high-density data collection, and the construction of real-time signal identification and early warning systems within the machine learning and big data frameworks. Once field- and stress-tested in Hawaii, the techniques and technologies developed by this collaboration between academia, government, and industry will be exported to other volcanic environments.
Data from Candidate Biomarkers of Response to an Experimental Cancer Drug Identified through a Large-scale RNA Interference Genetic Screen

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

<div>Abstract<p><b>Purpose:</b> A major impediment in the optimal selection of cancer patients for the most effective therapy is the lack of suitable biomarkers that foretell the response of a patient to a given drug. In the present study, we have used large-scale RNA interference–based genetic screens to find candidate biomarkers of resistance to a new acyl sulfonamide derivative, R3200. This compound inhibits the proliferation of tumor cells <i>in vitro</i> and <i>in vivo</i>, but its mechanism of action is unknown.</p><p><b>Experimental Design:</b> We used a large-scale RNA interference genetic screen to identify modulators of the efficacy of R3200. We searched for genes whose suppression in an <i>in vitro</i> cell system could cause resistance to the anticancer effects of R3200.</p><p><b>Results:</b> We report here that knockdown of either <i>RBX1</i> or <i>DDB1</i> causes resistance to the anticancer effects of R3200, raising the possibility that these two genes may have utility as biomarkers of response to this drug in a clinical setting. Interestingly, both RBX1 and DDB1 are part of an E3 ubiquitin ligase complex.</p><p><b>Conclusions:</b> We propose that suppression of the activity of a RBX1 and DDB1-containing E3 ligase complex leads to the stabilization of certain proteins, the increased abundance of which is in turn responsible for resistance to R3200. Moreover, our data suggest that RBX1 and DDB1 could potentially be developed into biomarkers of resistance to acyl sulfonamide–based cancer drugs. This will require clinical validation in a series of patients treated with R3200. (Clin Cancer Res 2009;15(18):5811–9)</p></div>
Simulated Earthquake Tests of R/C Frames

Field: Engineering (Physical Sciences)

The inelastic response of reinforced concrete multistory frames was investigated by subjecting small-scale one-bay three-story reinforced concrete frames to a series of strong base motions simulating one horizontal component of representative earthquake acceleration records. The test results were evaluated from the perspective of analytical methods routinely and economically available to structural-design office: linear dynamic response analysis and static limit analysis based on elasto-plastic response. Linear dynamic analyses provided a good qualitative understanding of the observed inelastic behavior. The observed maximum base shears and overturning moments were much higher than the values predicted by the limit analysis due to strain-hardening of the steel. It is concluded that strain-hardening characteristics of the reinforcing steel must be explicitly considered in the earthquake-resistant design of reinforced concrete structures, especially in relation to design of web reinforcement, foundations, and columns.
Isolating the Effects of Fuel Chemistry on Combustion Phasing in an HCCI Engine and the Potential of Fuel Stratification for Ignition Control

Field: Energy (Physical Sciences)

<div class="htmlview paragraph">An investigation has been conducted to determine the relative magnitude of the various factors that cause changes in combustion phasing (or required intake temperature) with changes in fueling rate in HCCI engines. These factors include: fuel autoignition chemistry and thermodynamic properties (referred to as fuel chemistry), combustion duration, wall temperatures, residuals, and heat/cooling during induction. Based on the insight gained from these results, the potential of fuel stratification to control combustion phasing was also investigated.</div> <div class="htmlview paragraph">The experiments were conducted in a single-cylinder HCCI engine at 1200 rpm using a GDI-type fuel injector. Engine operation was altered in a series of steps to suppress each of the factors affecting combustion phasing with changes in fueling rate, leaving only the effect of fuel chemistry. This involved the use of two novel techniques: 1) alternate-firing operation to remove changes in wall temperature and residuals; and 2) a method for determining the effective intake temperature to remove the effect of heating/cooling during induction.</div> <div class="htmlview paragraph">Three fuels were examined. Iso-octane was found to have only a small change in autoignition chemistry with fueling rate; gasoline had a change just slightly larger than iso-octane; and PRF80 had a large change, due to its significant cool-flame chemistry. Comparison of the data with chemical-kinetic modeling showed that the detailed iso-octane mechanism matches the trends well, but that the detailed PRF mechanism does not. The experimental results indicate that engine management becomes more complicated for fuels with cool-flame chemistry. For PRF80, combustion phasing changes immediately with changes in fueling, whereas sudden changes in fueling have little effect on the combustion phasing for iso-octane or gasoline. However, the results also show that the potential for ignition control by fuel stratification is much larger for PRF80. Stratification significantly and rapidly shifts combustion phasing with PRF80, but not with iso-octane. Charge stratification was also found to be effective for improving combustion efficiency at low-load conditions.</div>
Application of SVM to the Prediction of Water Content in Crude Oil

Field: Engineering (Physical Sciences)

Water content of crude oil has always been an important indicator of evaluating the exploiting capacity of an oil field. Accurate rate of water content will optimize the production and decrease energy consumption. Due to the complicated working condition, large-scale experiments are designed and carried out in the simulation device of multiphase flow. After researching into the non-linear mapping relation between the frequency response of water content and its influencing factors, a prediction model of water content in crude oil about horizontal oil well based on SVM is proposed. The simulation results suggest that the SVM prediction model has higher prediction accuracy and stronger capability of generalization compared with the BP neural network. It will provide a promising theoretical and practical perspective for the explanation and prediction of the data acquired from the oil field.
[Ureaplasma urealyticum and chorioamnionitis].

Field: Medicine (Health Sciences)

160 placentas from a clinical study group of women with pregnancy wastage and a control group were examined histologically and were cultured for Ureaplasma urealyticum. Recovery of Ureaplasma urealyticum was significantly higher in the pathologic group--43 p. cent--versus 21.6 p. cent in the control group, and was associated with chorioamnionitis.
Supercritical Fluid CO2 Extraction and Microcapsule Preparation of Lycium barbarum Residue Oil Rich in Zeaxanthin Dipalmitate

Field: Chemical Engineering (Physical Sciences)

The scope of this investigation aimed at obtaining and stabilizing bioactive products derived from Lycium barbarum seeds and peels, which were the byproducts in the processing of fruit juice. Zeaxanthin dipalmitate is a major carotenoid, comprising approximately 80% of the total carotenoid content in the seeds and peels. The method of obtainment was supercritical fluid CO2 extraction, studying different parameters that affect the oil yield and content of zeaxanthin dipalmitate. The optimized protocol to enact successful supercritical fluid CO2 extraction included optimum extraction pressure of 250 bar, temperature at 60 °C over a time span of 2.0 h, and a CO2 flow of 30 g/min, together with the use of a cosolvent (2% ethanol). The yields of oil and zeaxanthin dipalmitate under these optimal conditions were 17 g/100 g and 0.08 g/100 g, respectively. The unsaturated fatty acids were primarily linoleic acid (C18:2), oleic acid (C18:1), and γ-linolenic acid (C18:3), with their contents being as high as 91.85 ± 0.27% of the total fatty acids. The extract was a red-colored oil that was consequently microencapsulated through spray-drying with octenylsuccinate starch, gum arabic, and maltodextrin (13.5:7.5:3, w/w) as wall materials to circumvent lipid disintegration during storage and add to fruit juice in a dissolved form. The mass ratio of core material and wall material was 4:1. These materials exhibited the highest microencapsulation efficiency (92.83 ± 0.13%), with a moisture content of 1.98 ± 0.05% and solubility of 66.22 ± 0.24%. The peroxide content level within the microencapsulated zeaxanthin dipalmitate-rich oil remained at one part per eight in comparison to the unencapsulated oil, following fast-tracked oxidation at 60 °C for 6 weeks. This indicated the potential oxidation stability properties of microcapsule powders. Consequently, this microencapsulated powder has good prospects for development, and can be utilized for a vast spectrum of consumer health and beauty products.
THE MECHANISM OF THE ANTI-ANDROGENIC THERAPY FOR PROSTATIC CANCER

Field: Medicine (Health Sciences)

Serum total acid phosphatase and serum prostatic acid phosphatase activities of prostatic cancer (21 cases) and the control cases (34 cases) were determined with Bodansky's and Fischman-Lerner's Modification. Histological findings of these prostatic tissues were studied by the needle biopsy and prostatectomy. The relations between variations of serum acid phosphatase activites and the changes of histological findings of these prostatic cancer were analysed. The average value of serum total acid phosphatase activities was 3.39±0.97 B. U., and that of serum prostatic acid phosphatase activities was 2.00±2.18 B. U.. After the antiandrogenic therapy, the total acid phosphatase level decreased to 2.68±0.30 B. U., the prostatic acid phosphatase level decreased to 0.94±0.47 B. U.. In the 7 cases of prostatic cancer which including 4 cases of differentiated adenocarcinoma and 3 cases of undifferentiated carcinoma, before the anti-androgenic therapy in the 4 cases of differentiated adenocarcinoma, the abnomal high levels of total and prostatic acid phoaphatase activities were detected. After the antiandrogenic therapy, the decreasing of these acid phosphatase levels were observed. However, in the 2 cases of undifferentiated carinoma, before anti-androgenic therapy, these acid phosphatase levels were normal. There was no change of total and prostatic acid phosphatase levels by the anti-androgenic therapy. Another cases of undifferentiated carcinoma complicated with extensive metastase had a slightly high acid phosphatase level. In the above cases of differentiated adenocarcinoms, after the anti-androgenic therapy, the remission of clinical symptoms appeared with normalization of total and prostatic acid phosphatase activities and histologically hydropic degeneration of cytoplasma of cancer cells, pyknosis of nuclei, karyorrhexis, karyolysis, necrosis and disappearing of cells, straggling or proliferation of connective tissue were observed. However, in the 2 cases of undifferentiated cancer, after the anti-androgenic therapy, neither improvement of clinical symptoms nor change of acid phosphatase activity were recognized. The histological changes of tumor tissue in these undifferentiated cancer were slight and localized.
On the Abandonment of Coffee Plantations in Jamaica after Emancipation

Field: Arts and Humanities (Social Sciences)

Historians who have studied Jamaican coffee plantations have concluded that plantation production was insignificant after about 1850. I argue that this conclusion is based on an uncritical acceptance of the information contained in one source, a report of the House of Assembly. A critical reading of this document, in its historical context, casts doubt on the conclusion. I further show that many more plantations survived into the 1880s than has been previously recognised. These plantations, although producing a relatively small proportion of Jamaica's coffee, were central to building Jamaica's reputation as a producer of some of the world's best coffee.
Evaluation of Antimicrobial Activity of Zinc Oxide Nanoparticles Against Human Pathogens

Field: Pharmacology, Toxicology and Pharmaceutics (Life Sciences)

Introduction: The purpose of this study was to evaluate the antimicrobial effects of zinc oxide nanoparticles on human bacteria. Methods: The commercially available zinc oxide nanoparticles were purchased. The studied bacteria were purchased as lipophilic ampoules from Iranian Fungal and Bacterial Collection. Finally, the minimum inhibitory concentration and minimum bactericidal concentration were determined by the microdilution method. Results: The results of this study showed that the maximum inhibitory concentration of zinc oxide nanoparticles was 1500 μg/ mL against Staphylococcus aureus and Streptococcus pyogenes. While the minimum inhibitory concentration was 187 μg/mL against Acinetobacter baumannii. The maximum bactericidal concentration (3000 μg/mL) was observed against S. aureus. While the minimum bactericidal concentration was observed against Acinetobacter baumannii. Conclusion: Based on our results, zinc oxide nanoparticles have a good antimicrobial activity against bacteria.
Molecular Detection of Some Virulence Genes Among Streptococcus mutans

Field: Veterinary (Health Sciences)

Abstract Background: Microbes greatly influence oral illnesses. Regulatory mechanisms and bidirectional communication maintain host-mouth bacterial equilibrium throughout life. Objectives: Current study is aimed at the molecular detection of some virulence genes among Streptococcus mutans. Materials and Methods: From November 2022 to March 2023, 100 College of Dentistry, University of Al-Kufa, medical educational clinic patients contributed soft, deep caries lesions. Samples from different media were incubated for 18–24 h at 37°C. S. mutans was found in colony morphology, microscopy, and biochemistry. Results: About 20% of the 100 positive clinical samples were S. mutans . A VITEK 2 automated system examined 64 biochemical GP-ID card S. mutans isolates. It promptly and accurately identified 20 bacterial isolates (94%–99.7%). The 497-bp SM479 gene was amplified by standard polymerase chain reaction (PCR) using all-isolated DNA. All isolates were amplified by standard PCR. The virulence factor gene was found in S. mutans isolates. Unlike an allelic ladder, S. mutans possesses all its virulence genes since all 20 samples have the cnm gene. All twenty S. mutans isolates had PCR-detected 647-bp Cbm genes. All 20 S. mutans isolates had gtfB . The (517 bp) amplicon was found using a gel electrophoresis allelic ladder. Conclusions: The automated VITEK 2 system tested 64 biochemical GP-ID card S. mutans isolates. It quickly and reliably identified 20 bacterial isolates (94%–99.7%). All isolate DNA was used for standard PCR amplification of the SM479 gene. Each previously isolated bacteria was amplified by conventional PCR. Virulence factor gene identification in S. mutans isolates. All 20 samples had cnm , Cbm , and gtfB .
Path integral duality and Planck scale corrections to the primordial spectrum in exponential inflation

Field: Physics and Astronomy (Physical Sciences)

The enormous red-shifting of the modes during the inflationary epoch suggests that physics at the Planck scale may modify the standard, nearly, scale-invariant, primordial, density perturbation spectrum. Under the principle of path-integral duality, the space-time behaves as though it has a minimal length $L_{_{\rm P}}$ (which we shall assume to be of the order of the Planck length), a feature that is expected to arise when the quantum gravitational effects on the matter fields have been taken into account. Using the method of path integral duality, in this work, we evaluate the Planck scale corrections to the spectrum of density perturbations in the case of exponential inflation. We find that the amplitude of the corrections is of the order of $({\cal H}/M_{_{\rm P}})$, where ${\cal H}$ and $M_{_{\rm P}}$ denote the inflationary and the Planck energy scales, respectively. We also find that the corrections turn out to be completely independent of scale. We briefly discuss the implications of our result, and also comment on how it compares with an earlier result.
Associations of Oxidative Stress and Postoperative Outcome in Liver Surgery with an Outlook to Future Potential Therapeutic Options

Field: Medicine (Health Sciences)

Several types of surgical procedures have shown to elicit an inflammatory stress response, leading to substantial cytokine production and formation of oxygen-based or nitrogen-based free radicals. Chronic liver diseases including cancers are almost always characterized by increased oxidative stress, in which hepatic surgery is likely to potentiate at least in the short term and hereby furthermore impair the hepatic redox state. During liver resection, intermittent inflow occlusion is commonly applied to prevent excessive blood loss but resulting ischemia and reperfusion of the liver have been linked to increased oxidative stress, leading to impairment of cell functions and subsequent cell death. In the field of liver transplantation, ischemia/reperfusion injury has extensively been investigated in the last decades and has recently been in the scientific focus again due to increased use of marginal donor organs and new machine perfusion concepts. Therefore, given the intriguing role of oxidative stress in the pathogenesis of numerous diseases and in the perioperative setting, the interest for a therapeutic antioxidative agent has been present for several years. This review is aimed at giving an introduction to oxidative stress in surgical procedures in general and then examines the role of oxidative stress in liver surgery in particular, discussing both transplantation and resection. Results from studies in the animal and human settings are included. Finally, potential therapeutic agents that might be beneficial in reducing the burden of oxidative stress in hepatic diseases and during surgery are presented. While there is compelling evidence from animal models and a limited number of clinical studies showing that oxidative stress plays a major role in both liver resection and transplantation and several recent studies have suggested a potential for antioxidative treatment in chronic liver disease (e.g., steatosis), the search for effective antioxidants in the field of liver surgery is still ongoing.
ADAPTIVE LEADERSHIP: BRIDGING PRACTICES WITH CONTEXT FOR SUSTAINABLE OUTCOMES IN THE NIGERIAN EDUCATION SYSTEM

Field: Social Sciences (Social Sciences)

This paper discussed the role of adaptive leadership in advancing sustainable outcomes within the Nigerian education system. The literature review centered on the usefulness and imperatives of adaptive leadership in strengthening work and partnership ties, enhancing trust and collaboration, and fostering shared commitment and responsibilities toward developing sustainable behaviour in the Nigerian education system. The path-goal theory was adopted in demonstrating the responsibility of the leader in ensuring involvement and in effectively channelling the capacities of institutions toward addressing existing gaps in the curricula and content of tertiary institutions, particularly such concerned with the sustainability behaviour of these institutions; that way enhancing the relevance and value of related institutions within their societies and context. The reviews served is a premise for affirming that adaptive leadership enhances the systemic behaviour of tertiary institutions – increasing learning, collaboration, and receptivity toward change and facilitating sustainable outcomes.