jimnoneill/paper-to-field-training huggingface dataset:
iTerm-PseKNC: a sequence-based tool for predicting bacterial transcriptional terminators

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

Abstract Motivation Transcription termination is an important regulatory step of gene expression. If there is no terminator in gene, transcription could not stop, which will result in abnormal gene expression. Detecting such terminators can determine the operon structure in bacterial organisms and improve genome annotation. Thus, accurate identification of transcriptional terminators is essential and extremely important in the research of transcription regulations. Results In this study, we developed a new predictor called ‘iTerm-PseKNC’ based on support vector machine to identify transcription terminators. The binomial distribution approach was used to pick out the optimal feature subset derived from pseudo k-tuple nucleotide composition (PseKNC). The 5-fold cross-validation test results showed that our proposed method achieved an accuracy of 95%. To further evaluate the generalization ability of ‘iTerm-PseKNC’, the model was examined on independent datasets which are experimentally confirmed Rho-independent terminators in Escherichia coli and Bacillus subtilis genomes. As a result, all the terminators in E. coli and 87.5% of the terminators in B. subtilis were correctly identified, suggesting that the proposed model could become a powerful tool for bacterial terminator recognition. Availability and implementation For the convenience of most of wet-experimental researchers, the web-server for ‘iTerm-PseKNC’ was established at http://lin-group.cn/server/iTerm-PseKNC/, by which users can easily obtain their desired result without the need to go through the detailed mathematical equations involved.
Pliocene Biostratigraphy of California

Field: Earth and Planetary Sciences (Physical Sciences)

Biostratigraphy of Neogene faunas from the Humboldt basin of northern California emphasizes six foraminifera aggregates encountered in the thick clastic sections. Other groups, notably mollusks, are included. Detailed analysis of the chronologic and chorologic relations of the component elements (lineages, faunas, and stratal units) provide a framework for comparison and correlation of clastic sequences of roughly comparable age and thickness from the Los Angeles and Ventura basins. Considerable discussion involves the two primary methods of defining the Pliocene-Pleistocene boundary--Reboul's 1833 concept implying evolutionary changes in fossil faunas gives way to Forbes' 1846 concept of paleoclimatic change reflected by fossil faunas. The writer herein places the boundary 4,000 ft (1,220 m) lower than that cited by Ogle (1953), or Faustman (1964). Paleoecologic interpretations and basin analyses rely on faunal variability and faunal dominance in both foraminiferal and molluscan assemblages. Sediment textures generally reflect basin filling and westward migration of the Humboldt basin shoreline. Turbidite sequences appear to be important, especially in sections containing bathyal assemblages. Upwelling possibly influenced the distribution of some key foraminiferal faunules in northern California. More than 180 species of forams are documented in the systematics and distribution charts, and two species are new and previously undescribed. Important questions are raised concerning the nomenclature of Bulimina subacuminata, Elphidium hughesi, and other species. The use of the generic term Islandiella for certain species of Cassidulina is also questioned. The Neogene bolivinids, mainly Bolivina, Bolivinoides, and Brizalina, are regarded as the most promising for future studies on phylogeny through the extensive use of SEM pictures.
Predictive value of sentinel lymph node imaging and biopsy in early cervical cancers: correlation with scintigraphic uptake patterns and histology

Field: Medicine (Health Sciences)

Aim This study was designed to 1) assess the feasibility, standardization of sentinel lymph node imaging (SLNI) and biopsy in early cervical cancers and also to determine the detection rates. 2) To analyze the SLN uptake pattern and correlate the findings with the histological grades of tumor. Materials and methods 52 early cervical cancer patients underwent same-day 99m Tc sulfur colloid (filtered) SLNI and biopsy with gamma probing. Patients underwent radical hysterectomy, para-aortic and pelvic lymphadenectomy irrespective of sentinel lymph node biopsy (SLNB) findings. We analyzed the colloid transit times, uptake pattern, lymphatic groups involved and histology. Results A total of 203 hot nodes (100% detection rate) were detected and harvested. Study showed 100% sensitivity, specificity, and negative predictive value. Internal iliac nodes were predominantly involved. Lymphatic uptake patterns were graded and correlated with tumor histology (Ki index). Transit time was relatively prolonged in patients with aggressive tumors. Conclusion SLNI and biopsy in early cervical malignancies are feasible with high detection rate. Scintigraphic patterns of nodal uptake were relevant and found to correlate with the tumor histological grades. We found that nonfocal nodal uptake patterns were mainly encountered in patients with tumors having higher Ki index. Immunohistochemistry further facilitated identification of lymph nodal metastases. The visual grading system, implemented in this study provides a good indication of the degree of impairment of lymphatic drainage. Higher visual scintigraphic grade denotes greater lymphatic tumor burden.
Histological and histochemical changes in the liver of gamma-irradiated rats and the possible protective role of Aphanizomenon flos-aquae (AFA)

Field: Pharmacology, Toxicology and Pharmaceutics (Life Sciences)

Exposure to ionizing radiation represents a genuine increasing threat to mankind and our environment. Aphanizomenon flos-aquae (AFA) is a blue-green microalgal species that has antioxidant properties. The Aim of the work: this study aimed to elucidate the possible radioprotective effect of Aphanizomenon flos-aquae (AFA) on the liver of irradiated adult male rats using biochemical parameters, histopathology, and quantitative histochemistry. Material and methods: the current experiment was carried out on 48 adult male albino rats (Rattus rattus). Rats were randomly and equally categorized into four groups: 1) Group C: control rats left without treatment; 2) Group R: rats were exposed to 4Gy of gamma-radiation as a single dose; 3) Group AFA: rats were treated orally with 94.5mg/kg body weight/ day AFA for 3 weeks and 4) Group AFA+R: rats were administrated AFA for one week before and three weeks after irradiation. The experimental rats were sacrificed after 5 and 21 days post-irradiation. Results: exposed to gamma radiation showed many biochemical changes which included a significant increase in serum ALAT, ASAT, ALP activities, and MDA in the liver tissues. Many histopathological and histochemical changes were observed in the liver tissue, such as the corrugated and ruptured endothelial lining of the central vein which contained hemolysed blood cells, numerous vacuolated hepatocytes with increased signs of karyolysis and pyknosis in nuclei of hepatocytes, highly dilated and congested hepatic portal vein, numerous hemorrhagic areas, and distorted bile ducts. Highly increased collagen fibers were also observed after gamma irradiation in the liver tissue. Also, the irradiated group induced a significant increase in amyloid β-protein, while a significant decrease in PAS+ve materials, total protein, and total DNA content were detected. Supplementation with AFA showed a trend toward lowering the incidence of hepatic histopathological and histochemical changes induced by γ-radiation. Conclusion: according to the results obtained in the current study using Aphanizomenon flos- aquae as a natural agent showed a strong radioprotective role.
Evaluierung der Erfolgsfaktoren des EFQM-Modells in der österreichischen Ernährungswirtschaft anhand des Analytischen Hierarchieprozesses

Field: Business, Management and Accounting (Social Sciences)

Numerous companies in the Austrian food industry have already been certified in accordance with the ISO 9000 standards. However, the introduction of a quality management system in a company alone does not guarantee continuous improvement as required by the standard ÖNORM ISO 9001:2000. In order to be successful when introducing and maintaining a quality management system in a company, a number of important factors must be considered. These success factors are derived from the "European Foundation for Quality Management (EFQM) Model for Business Excellence". The purpose of the EFQM Model is to support the internal assessment of the quality management within a company, and it can be regarded as a motor for internal improvement. In particular, for companies planning to introduce a quality management system it is very useful since it tells them which factors have to be taken into account even before they introduce the system. Basically, the EFQM defines a specific weighting of the 9 success factors of the model. The aim of the study is to evaluate the pre-determined weighting of the EFQM success factors for the Austrian food industry.
‘Whatever you say, say nothing’: Teaching public administration in Northern Ireland

Field: Social Sciences (Social Sciences)

This article is a contribution to a special issue of Teaching Public Administration, which offers teachers with many years’ experience the opportunity to reflect on changes over time. The context for this paper is teaching public administration in Northern Ireland, a region of the UK that has a sizeable public sector but a distinctive and unstable structure of governance. The paper begins by summarizing the pedagogic polemic in teaching public administration, how this played out in a devolved region of the UK that has witnessed political conflict, and the influence of this setting on the provision of higher education for public sector officials. It addresses how a regional university has sought to meet the seemingly parochial demands of its students with the wider demands for global outward-facing teaching and research.
Different Effects of 7-nitroindazole and L-NAME Administered Both Individually and Together on the Cardiovascular System of the Rat

Field: Pharmacology, Toxicology and Pharmaceutics (Life Sciences)

We evaluated the effects of NG-nitro-L-arginine methylester (L-NAME) (50 mg/kg/day) and 7-nitroindazole (7NI) (10 mg/kg/day) administered from 10th-16th week of age either individually or together on cardiovascular system of Wistar rats and SHR. Systolic blood pressure (sBP) was measured weekly by the plethysmographic method. For morphological studies, the animals (n=10) were perfused with a fixative (120 mm Hg), and thoracic aorta and carotid and coronary arteries were processed for electron microscopy. For functional investigation (n=10), aortic rings were used in an organ bath. In Wistar rats, L-NAME evoked an increase of sBP; hypertrophy of the heart and arterial walls; an increase in cross-sectional areas (CSA) of endothelial cells (EC), muscle cells (SMC), extracellular matrix (ECM), and a decrease in acetylcholine-induced endothelial-dependent relaxation (EDR). 7NI evoked sBP-independent hypotrophy of the heart and arterial walls, a decrease in CSA of EC and SMC without affecting the CSA of ECM, and a mild decrease in acetylcholine-induced EDR. 7NI and L-NAME administered together evoked lower effect on BP and trophicity of the heart and all arteries, and a similar decrease in acetylcholine-induced EDR compared to L-NAME alone. In SHR, 7NI did not evoke any effect on the studied parameters.
Partition of the Linear Plasmid N15: Interactions of N15 Partition Functions with the sop Locus of the F

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

A locus close to one end of the linear N15 prophage closely resembles the sop operon which governs partition of the F plasmid; the promoter region contains similar operator sites, and the two putative gene products have extensive amino acid identity with the SopA and-B proteins of F. Our aim was to ascertain whether the N15 sop homologue functions in partition, to identify the centromere site, and to examine possible interchange-ability of function with the F Sop system. When expressed at a moderate level, N15 SopA and-B proteins partly stabilize mini-F which lacks its own sop operon but retains the sopC centromere. The stabilization does not depend on increased copy number. Likewise, an N15 mutant with most of its sop operon deleted is partly stabilized by F Sop proteins and fully stabilized by its own. Four inverted repeat sequences similar to those of sopC were located in N15. They are distant from the sop operon and from each other. Two of these were shown to stabilize a mini-F sop deletion mutant when N15 Sop proteins were provided. Provision of the SopA homologue to plasmids with a sopA deletion resulted in further destabilization of the plasmid. The N15 Sop proteins exert effective, but incomplete, repression at the F sop promoter. We conclude that the N15 sop locus determines stable inheritance of the prophage by using dispersed centromere sites. The SopB-centromere and SopA-operator interactions show partial functional overlap between N15 and F. SopA of each plasmid appears to interact with SopB of the other, but in a way that is detrimental to plasmid maintenance.
Figure 65 from: De Mattia W, Reier S, Haring E (2021) Morphological investigation of genital organs and first insights into the phylogeny of the genus Siciliaria Vest, 1867 as a basis for a taxonomic revision (Mollusca, Gastropoda, Clausiliidae). ZooKeys 1077: 1-175. https://doi.org/10.3897/zookeys.1077.67081

Field: Agricultural and Biological Sciences (Life Sciences)

Figure 65 Stigmatica vulcanica vulcanica (Benoit, 1860), Belpasso, Catania 65.1 whole distal genital organs 65.2 internal distal part of genital organs. Cosenza 65.3 whole distal genital organs 65.4 internal distal part of genital organs. Paola 65.5 whole distal genital organs 65.6 internal distal part of genital organs. Stigmatica vulcanica sigridae Nordsieck, 2013, Mendicino, Cosenza 65.7 whole distal genital organs 65.8 internal distal part of genital organs.
Internal gravity waves in a vertically sheared flow

Field: Physics and Astronomy (Physical Sciences)

We investigate the propagation of internal gravity waves in a rotating fluid with horizontal and vertical stratification. The modification of these waves by the presence of a vertically sheared geostrophic current is determined, and the rate of energy exchange between waves and current is estimated and compared to exchange rates of other interaction mechanisms. The effect of boundary conditions on the range of frequencies allowed for wave propagation is also considered. The wave amplitude has horizontal exponential dependence due to the horizontal density variation as well as to exchange of energy with the mean shear flow. The solution also shows a phase difference from surface to bottom. For waves propagating normally to a vertically sheared geostrophic current, the energy exchange mechanism is found to be weak when compared to other exchange mechanisms and is likely to be of little importance in the ocean. The imposition of boundary conditions on the wave solution alters the frequency range over which solutions may exist.
Integrating Target-Triggered Aptamer-Capped HRP@Metal–Organic Frameworks with a Colorimeter Readout for On-Site Sensitive Detection of Antibiotics

Field: Chemistry (Physical Sciences)

Colorimetric analytical strategies exhibit great promise in developing on-site detection methods for antibiotics, while substantial recent research efforts remain problematic due to dissatisfactory sensitivity. Taking this into account, we develop a novel colorimetric sensor for in-field detection of antibiotics by using aptamer (Apt)-capped and horseradish peroxidise (HRP)-embedded zeolitic metal azolate framework-7 (MAF-7) (Apt/HRP@MAF-7) as target recognition and signal transduction, respectively. With the substrate 3,3′,5,5′-tetramethylbenzidine (TMB)-impregnated chip attached on the lid, the assay can be conveniently operated in a tube and reliably quantified by a handheld colorimeter. Hydrophilic MAF-7 can not only prevent HRP aggregation but also enhance HRP activity, which would benefit its detection sensitivity. Besides, the catalytic activity of HRP@MAF-7 can be sealed through assembling with Apt and controllably released based on the bioresponsivity via forming target-Apt complexes. Consequently, a significant color signal can be observed owing to the oxidation of colorless TMB to its blue-green oxidized form oxTMB. As a proof-of-concept, portable detection of streptomycin was favorably achieved with excellent sensitivity, which is superior to most reported methods and commercial kits. The developed strategy affords a new design pattern for developing on-site antibiotics assays and immensely extends the application of enzyme embedded metal–organic framework composites.
“The Root of All Evil” Revisited: My Journey from Heidegger to Cusanus

Field: Arts and Humanities (Social Sciences)

I first examine the context that led me to write 'The Root if all Evil.' A second section rehearses my present understanding of the significance and the inadequacy of Heidegger's fundamental ontology. A third section turns to the way my thinking has evolved, including a brief account of the way it has moved from Heidegger to the 15th century cardinal and philosopher Nicolaus Cusanus. I conclude with some remarks about what I take to be my place in today's philosophy world.
Exploring deep decarbonization pathways for Argentina

Field: Environmental Science (Physical Sciences)

To align near term action with a deep decarbonization objective by 2050, a long term low-greenhouse gas emissions development strategy is needed and involves drastic changes to the energy system and the AFOLU sectors. To help move forward the policy debate in this direction, this paper explores deep decarbonization pathways for the country until 2050 which break with existing more conservative national scenarios. It uses a combined qualitative-quantitative deep decarbonization pathway method based on the complementarity between exploratory storylines and the quantification of pathways based on linked energy-economy models. The built pathways show how deep decarbonization could be reached in Argentina along with other economic development goals and through contrasted possible routes all involving significant changes to the energy and AFOLU sectors. Remarkably, afforestation stands out as a key sectorial measure for reaching DDP. We contrast two alternative DDP Scenarios with a BAU one with specific focus on CO2 emissions, with emphasis on energy sector demand and supply alternatives. Many of the energy initiatives proposed for the BAU scenario were maintained but increased in ambition and many others were incorporated only in these deep decarbonization scenarios. While the HardPath proposes and requires natural gas use-with CO2 capture and storage-the Enlighten scenario proposes replacing it by hydro-nuclear energy. Finally, in none of the DDP scenarios is the export of natural gas proposed as an explicit energy policy objective, since little space is considered in external markets for fossil fuels, within the framework of a global action aimed at decarbonization.
On the History of St. Petersburg School of Probability and Mathematical Statistics: II. Random Processes and Dependent Variables

Field: Mathematics (Physical Sciences)

This is the second paper in a series of reviews devoted to the scientific achievements of the Leningrad and St. Petersburg school of probability and mathematical statistics from 1947 to 2017. This paper is devoted to the works on limit theorems for dependent variables (in particular, Markov chains, sequences with mixing properties, and sequences admitting a martingale approximation) and to various aspects of the theory of random processes. We pay particular attention to Gaussian processes, including isoperimetric inequalities, estimates of the probabilities of small deviations in various norms, and the functional law of the iterated logarithm. We present a brief review and bibliography of the works on approximation of random fields with a parameter of growing dimension and probabilistic models of systems of sticky inelastic particles (including laws of large numbers and estimates for the probabilities of large deviations).
Assessing the essential pre-conditions of an authentic sustainability curriculum

Field: Social Sciences (Social Sciences)

Purpose This study has two aims. It aims to analyse three essential pre-conditions of an authentic sustainability curriculum (ASC). The theoretical analysis involves the definition of authenticity through the learning outcomes (LOs) framework called authentic minimum (AM). This paper also aims to gauge students’ views on economic growth, sustainability and mindfulness. Design/methodology/approach The theoretical aim was accomplished by extensive study of and critical reflections on the relevant literature. The empirical research was qualitative using an online questionnaire as survey instrument consisting of predominantly open-ended questions involving students of two economic faculties. Directed content analysis and nonparametric quantitative methods were used to assess the answers. Findings Viable sustainability goals are in stark contrast with the promotion of sustainable economic growth in sustainable development goals 8 and the reigning neoliberal agenda. The empirical findings provide valuable insights into how undergraduate students view mindfulness, economic growth and aspects of sustainability. Research limitations/implications The empirical research has some obvious limitations that warrant caution in generalizing the results. The authors used a sample of convenience and the base population of the survey consisted only in students of economics in two economic faculties of two Hungarian universities. Practical implications Practical implications of the present paper are many all sharing; however, the need for existential courage on the part of teachers, students and leaders of higher education institutions. Existential courage is required for profound personal transformation, for going against mainstream ideology and the possible confrontations with colleagues, leaders of institutions, students, friends or family members. Originality/value On the theoretical side, the concept of ASC was introduced with AM as its LOs framework. For the first time, an attempt was made to interpret authenticity in sustainability education as an integration of mindfulness, human and environmental ethics and a firm opposition to economic growth and neoliberal ideals. The analysis of qualitative data supported earlier research and also provided unique findings in the examined areas.
Biotechnological Potential of Bacterial Agents in Modern Conditions of Cultivation of Agricultural Crops

Field: Agricultural and Biological Sciences (Life Sciences)

The paper highlights the problem of nitrogen fixation in a biological manner and considers prospects for the use of bacterial agents of an associative nature as an element of biotechnology in practice.Studies of promising domestic bacterial agents, based on associative nitrogen fixers, were carried out on zonal soils (chernozems) in the Rostov Region.The presented materials of scientific studies on preparative forms based on nitrogen-fixing microorganisms showed high performance, which was manifested in the progress of crop yields, and therefore these data can be used in agricultural production.Application of bacterial agents with nitrogenfixing species is profitable, since their cost is not high and the increase in additional crop production fully covers the costs and it cuts down the introduction of mineral nitrogen fertilizers.Nevertheless, it should be noted that the environmental aspect of bacterial agents' application consists in obtaining a clean source of nitrogen by cultivated plants and reduces pollution of the soil, atmosphere and water bodies.