jimnoneill/paper-to-field-training huggingface dataset:
Characterization of Virulence-Related Phenotypes in Candida Species of the CUG Clade

ABSTRACT Candida species cause a variety of mucosal and invasive infections and are, collectively, the most important human fungal pathogens in the developed world. The majority of these infections result from a few related species within the “CUG clade,” so named because they use a nonstandard translation for that codon. Some members of the CUG clade, such as Candida albicans , present significant clinical problems, whereas others, such as Candida ( Meyerozyma ) guilliermondii , are uncommon in patients. The differences in incidence rates are imperfectly correlated with virulence in animal models of infection, but comparative analyses that might provide an explanation for why some species are effective pathogens and others are not have been rare or incomplete. To better understand the phenotypic basis for these differences, we characterized eight CUG clade species— C. albicans , C. dubliniensis , C. tropicalis , C. parapsilosis , Clavispora lusitaniae , M. guilliermondii , Debaryomyces hansenii , and Lodderomyces elongisporus —for host-relevant phenotypes, including nutrient utilization, stress tolerance, morphogenesis, interactions with phagocytes, and biofilm formation. Two species deviated from expectations based on animal studies and human incidence. C. dubliniensis was quite robust, grouping in nearly all assays with the most virulent species, C. albicans and C. tropicalis , whereas C. parapsilosis was substantially less fit than might be expected from its clinical importance. These findings confirm the utility of in vitro measures of virulence and provide insight into the evolution of virulence in the CUG clade.

Topic: Antifungal resistance and susceptibility
Subfield: Infectious Diseases
Field: Medicine
Domain: Health Sciences
Small moments in Spatial Big Data: Calculability, authority and interoperability in everyday mobile mapping

This article considers how Spatial Big Data is situated and produced through embodied spatial experiences as data processes appear and act in small moments on mobile phone applications and other digital spatial technologies. Locating Spatial Big Data in the historical and geographical contexts of Sydney and Hong Kong, it traces how situated knowledges mediate and moderate the rising potency of discourses of cartographic reason and data logics as colonial cartographic imaginations expressed in land divisions and urban planning continue on, in a world that increasingly values models of calculability, interoperability and authority. It draws on ethnographic material gathered through walking interviews in both cities, and in doing so, it argues that by using ethnographic ‘moments’, it is possible to decentre the focus on data processes to consider the critical potential of a politics of everyday experiences that produce and reflect the structures of data logics. Through these ethnographic moments, this article examines how mobile technologies are complicit in the production of Spatial Big Data, and the impact this has on the increasing regimentation and surveillance of modes of being and expression via mobile media. At the same time, it will argue that while spatial calculability has expanded from cartographic reason into data logics, the epistemological universality of Spatial Big Data is constantly being resisted – in moments of experimentation, failure, intuition, memory and desire, the ghosts of the incalculable epistemes, experiences and people, forgotten by the emphasis on calculation, continue to speak.

Topic: Geographic Information Systems Studies
Subfield: Geography, Planning and Development
Field: Social Sciences
Domain: Social Sciences
The Analysis of the Coral Material Testing for the Treatment of Dynamic Compaction of Storage Yard Behind Terminal

Using coral reefs backfill as the foundation can get materials easier,which saves transportation cost,and solves the shortage problem of sand and stone.Because coral reefs backfill loose and porous,property crushability,large compressibility,and its bearing capacity is low,which must be as the foundation to ensure the safety and reliability of foundation.Based on the project of stacking yard for new container berths Port Sudan,through the laboratory test and field test,this paper gets the physical and mechanical indexes before and after the foundation treatment,then analyzes the reinforcement effect of dynamic compaction.

Topic: Geotechnical Engineering and Soil Stabilization
Subfield: Civil and Structural Engineering
Field: Engineering
Domain: Physical Sciences
Demographic Change, Relative Factor Prices, International Capital Flows, and Their Differential Effects on the Welfare of Generations

Demographic change has differential impacts on the welfare of current and future generations. In a simple closed economy, aging -- a relative scarcity of young workers -- increases wages, increasing the welfare of the young. At the same time, population aging will reduce rates of return to capital, thereby reducing the welfare of asset holders who are usually older than the population average. In a global world with pension systems, however, these effects are less straightforward, since international capital flows dampen the factor price changes. Moreover, pay-as-you-go pension systems financed by payroll taxes create a wedge between net and gross wages, and their intergenerational redistribution has important additional effects on the welfare of generations. To quantify these effects, we develop a large-scale multi-country overlapping generations model with uninsurable labor productivity and mortality risk. Due to the predicted relative abundance of the factor capital, the rate of return falls between 2005 and 2050 by roughly 90 basis points. Our simulations indicate that capital flows from rapidly ageing regions to the rest of the world will initially be substantial, but that trends are reversed when households de-cumulate savings. In terms of welfare, our model suggests that young individuals with little assets and currently low labor productivity indeed gain from higher wages associated with population aging. Older, asset-rich households tend to loose because of the predicted decline in real returns to capital.

Topic: Economic Growth and Productivity
Subfield: Economics and Econometrics
Field: Economics, Econometrics and Finance
Domain: Social Sciences
KdV breathers on a cnoidal wave background

Using the Darboux transformation for the Korteweg-de Vries equation, we construct and analyze exact solutions describing the interaction of a solitary wave and a traveling cnoidal wave. Due to their unsteady, wavepacket-like character, these wave patterns are referred to as breathers. Both elevation (bright) and depression (dark) breather solutions are obtained. The nonlinear dispersion relations demonstrate that the bright (dark) breathers propagate faster (slower) than the background cnoidal wave. Two-soliton solutions are obtained in the limit of degeneration of the cnoidal wave. In the small amplitude regime, the dark breathers are accurately approximated by dark soliton solutions of the nonlinear Schrödinger equation. These results provide insight into recent experiments on soliton-dispersive shock wave interactions and soliton gases.

Topic: Gyrotron and Vacuum Electronics Research
Subfield: Atomic and Molecular Physics, and Optics
Field: Physics and Astronomy
Domain: Physical Sciences
Early Childhood Education in Indonesia; A Primary Study on The Beneficiary Family of International Non-Government Organization

This study aimed to examine the prevalence of parental understanding on the Early Childhood Education in the beneficiary family of programs held by the International Non-Government Organization. The research participants were the beneficiary family listed and provided by World Vision Indonesia and Child Fund Indonesia. The research used a quantitative research approach with self-administered survey instruments. The sample used for the present research is the beneficiary of the programmes that had been implemented by INGO, which includes 325 research participants located in Jakarta and Banten. The data collection took place on March 2020 using online media survey, with validity test have been done before the research instruments shared to all the participants. There were nine questions in the survey with nominal data value for every question rated on a 5-point Likert scale and the ratings summed into items corresponding to early childhood education. The analysis of the research instrument was using SPSS series 25 and the all of items being tested were valid with reliability statistic number 896 on Alpha Cronbach scale. The result shown that the child’s education perceiving by the parents falls under the upper-class category with total score 16,341 out of 19,500 perfect score limit.

Topic: Educational Methods and Impacts
Subfield: Education
Field: Social Sciences
Domain: Social Sciences
Six Sigma implementation in a manufacturing unit - a case study

The Six Sigma approach has been increasingly adopted in the manufacturing sector in order to make the process robust to quality variations, thereby, improving the quality and performance. In any manufacturing industry, Shainin Six Sigma methodology is highly adopted because of lesser data collection required for the study. Six Sigma improves the process performance of the critical operational process, leading to better utilisation of resources, decrease in variations and maintaining consistent quality of the process output. The DMAIC approach has been followed here to solve an underlying problem of reducing process variation and the associated high defect rate. This paper describes an application of Six Sigma define, measure, analyse, improve and control (DMAIC) methodology in a manufacturing unit, which provides a framework to identify, quantify and eliminate sources of variation in an operational process to improve the quality. The current investigation focuses on using DMAIC methodology to reduce the rejections in the pasting process during product X manufacturing, resulting in a saving of Rs. 3.96 lakhs per annum

Topic: Quality and Supply Management
Subfield: Management Information Systems
Field: Business, Management and Accounting
Domain: Social Sciences
Unconventional superconductors under a rotating magnetic field. II. Thermal transport

We present a microscopic approach to the calculations of thermal conductivity\nin unconventional superconductors for a wide range of temperatures and magnetic\nfields. Our work employs the non-equilibrium Keldysh formulation of the\nquasiclassical theory. We solve the transport equations using a variation of\nthe Brandt-Pesch-Tewordt (BPT) method, that accounts for the quasiparticle\nscattering on vortices. We focus on the dependence of the thermal conductivity\non the direction of the field with the respect to the nodes of the order\nparameter, and discuss it in the context of experiments aiming to determine the\nshape of the gap from such anisotropy measurements. We consider quasi-two\ndimensional Fermi surfaces with vertical line nodes and use our analysis to\nestablish the location of gap nodes in heavy fermion CeCoIn$_5$ and organic\nsuperconductor $\\kappa$-(BEDT-TTF)$_2$Cu(NCS)$_2$.\n

Topic: Physics of Superconductivity and Magnetism
Subfield: Condensed Matter Physics
Field: Physics and Astronomy
Domain: Physical Sciences
FAKTOR-FAKTOR DETERMINAN STATUS GIZI IBU HAMIL

This paper discusses determinant factors of nutrition of pregnant women. Nutrition problems is a complex issue that is influenced by various factors, but from some intensive programs implemented, it have shown quite encouraging results such as reducing infant and under-five mortality, maternal mortality, and increasing life expectancy. The issue of maternal nutrition has broad implications, both for the mother and fetus. Some research shows a strong correlation between anemia during pregnancy and fetal death, abortion, birth defects, low birth weight, decreased iron stores in children or children born in nutritional anemia. This condition causes the rate of prenatal mortality is still high, including mother’s mortality and morbidity. In addition, the impact may cause bleeding during giving a birth. Bleeding at childbirth is the leading cause (28%) of maternal deaths in Indonesia. Whereby, Indonesian government committed to combat maternal anemia by doing “public nutrition improvement” program with a target prevalence of anemia in the year 2009 by 30%.

Topic: Public Health and Nutrition
Subfield: Pediatrics, Perinatology and Child Health
Field: Medicine
Domain: Health Sciences
Association between growth factors and Sjögren syndrome: A two-sample Mendelian randomization study

Previous observational studies have suggested a link between growth factors and Sjögren syndrome, but a definitive causal relationship has yet to be established. We conducted a two-sample Mendelian randomization (MR) study using summary statistics from the FinnGen study on Sjögren syndrome and various growth factors. Analytical techniques included inverse variance weighted, MR-Egger, weighted median, and weighted mode to explore potential causal links. Our analysis indicated that genetically determined growth factors did not have a causal effect on Sjögren syndrome. The inverse variance weighted method showed nonsignificant associations for various exposures, including epidermal growth factor (odds ratios [OR] = 0.94, P = .720), proheparin-binding EGF-like growth factor (OR = 0.95, P = .621), VEGF sR2 (OR = 1.0, P = .988), FGF7 (OR = 1.08, P = .519), PDGF-AA (OR = 0.87, P = .218), VEGF121 (OR = 0.93, P = .466), TGF-β R II (OR = 1.01, P = .934), and NGFI-A-binding protein 2 (OR = 1.13, P = .264). The MR-Egger, weighted median, and weighted mode methods supported these findings. Our study did not find significant causal associations between genetic levels of the studied growth factors and the onset of Sjögren syndrome. Future research should investigate more detailed genetic interactions and modifiable environmental factors to better understand pathways relevant to the prevention and management of Sjögren syndrome.

Topic: Salivary Gland Disorders and Functions
Subfield: Physiology
Field: Medicine
Domain: Health Sciences
Antioxidant activities and emulsification properties of the new model systems of whey proteins and reduced sugars

The final products formed from the various systems of the Maillard reactions possess different functional properties such as browning intensity, antioxidant activity, and emulsion stability. To study these properties and activities, different systems of whey proteins reaction with glucose and fructose at different concentrations to form a new model system of Maillard reaction products (MRPs) was observed. Results showed that high optical densities (peaks) at 280 and 420 nm indicated the formation of the intermediate stages of MRPs and the formation of advanced MRPs, respectively. Additionally, results showed that these Maillard reaction model systems possessed different antioxidant activities as demonstrated by DPPH and reducing power assays (20 - 93.2% and 40 - 90%, respectively) depending on the type and concentration of sugar, and the incubation time. The whey protein-fructose model system possessed high antioxidant activity (93.2%), and had the highest percentage on the emulsion stability index (75.4%). The whey protein-fructose model systems comprised the highest number of the studied model systems to form MRPs, and had highly powerful antioxidant activity and emulsifying index.

Topic: Advanced Glycation End Products research
Subfield: Clinical Biochemistry
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
Language choice and the construction of knowledge in higher education

This paper looks into how German and international students make use of their respective multilingual repertoires for the construction of academic knowledge. After a short survey of previous research on benefits and problems of English medium instruction for non-native speakers of English two explorative studies carried out at a German university will be presented which highlight the practices / preferences of students for language choice in various types of communication at the university and the underlying motives and assumptions for these choices. Different from previous research, which concentrates mainly on the official teaching-learning discourse in lectures and seminars, these studies focus on the complex interplay of various types of text and discourse typical of university contexts of teaching and learning. The first one deals with note-taking in lectures, the second one is a questionnaire study on preferred language choices in academic contexts of communication. The results suggest that students do not fully exploit their multilingual resources and that their preferred language choices tend to lead to a mere reproduction of knowledge. Therefore suggestions are formulated for a more productive use of students' multilingualism enhancing the depth of processing and the availability of academic knowledge.

Topic: Second Language Learning and Teaching
Subfield: Literature and Literary Theory
Field: Arts and Humanities
Domain: Social Sciences
Review of: "Somatic evolution of Cancer: A new synthesis"

Potential competing interests: No potential competing interests to declare.Bao et al. present an exciting perspective on cancer, supporting the hypothesis that cancer cells reawaken physiological programs/pathways involved in development to facilitate uncontrolled proliferation.Hence, it challenges the traditional idea that perceives cancer as a somatic evolution.The article is interesting and relevant in the field.However, some areas require significant improvement, as mentioned below.1.The authors stated that "the simple view of cancer as accumulation of chance mutations serially or at once which imply that cancer is only bad luck is not compatible with the observed epidemiological patterns ."It is not clear why this is not compatible with epidemiological evidence.2. Authors should consider reducing the introduction to include only the relevant concepts in their manuscript.3. The organization of the article makes it hard to follow.For instance, in the section where the authors discuss the limitations and criticism of existing perspectives on cancer, it may be easy to read to discuss these concepts, their limitations, and criticisms paragraph by paragraph.4. This article states that" a control on cell proliferation is needed at two distinct levels.One is the level of normal healthy tissue maintenance".This should be viewed as developmental regulation that occurs during organismal growth, while wound healing and repair are better perceived as a mechanism evolved to maintain tissue homeostasis.5. This article requires significant grammatical editing.

Topic: Genetics, Bioinformatics, and Biomedical Research
Subfield: Molecular Biology
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
Local ocular surface findings in COVID-19 patients without ocular symptoms

ABSTRACT Purpose: To investigate subjective ocular symptoms and objectively measure tear secretion in patients with a confirmed diagnosis of coronavirus disease-2019 (COVID-19). Methods: In this prospective cross-sectional study, 24 patients who had survived COVID-19 infection and 27 healthy controls were enrolled. Conjunctival impression cytology, the Schirmer test, tear-film break-up time, corneal staining scores were applied to all the participants. Results: No significant difference was noted with regard to the gender and mean age between the two groups (p=0.484 and p=0.599, respectively). The conjunctival impression cytology analysis revealed that the density of the goblet cells was decreased, while the counts of lymphocytes and neutrophils were increased in the COVID-19 group patients when compared with ethe control group patients. When the Nelson classification was applied to the conjunctival impression cytology samples, 25% of the COVID-19 group patients and 14.8% of the control group patients exhibited changes consistent with ≥grade 2. The mean tear-film break-up time, Schirmer test, and corneal staining score results were determined to differ between the COVID-19 and control groups (p=0.02, p&lt;0.001, and p=0.003, respectively). Conclusions: The present study revealed the pathological conjunctival alterations of patients with a confirmed diagnosis of COVID-19, indicating the possibility of the occurrence of pathological ocular surface alterations to even at the end of COVID-19 infection, without the occurrence of any significant clinical ocular manifestations.

Topic: Retinal and Optic Conditions
Subfield: Ophthalmology
Field: Medicine
Domain: Health Sciences
The effect of increased blood pressure on hemispheric lactate and water content during acute cerebral ischaemia in the rat and gerbil.

Infusions of metaraminol and angiotensin were used to test the effect of increased perfusion pressure on tissue metabolism and oedema after induction of regional cerebral ischaemia in the rat and the gerbil. An increase of mean arterial blood pressure of 30-40 mm Hg in the rat over the first 2 hours after diathermy of the middle cerebral artery prevented the 100% rise in hemisphere lactate seen in normotensive control animals. Angiotensin infusion also prevented early hemispheric oedema in this model. In the gerbil, 4 hours after placing a clip on one carotid artery, metaraminol-induced increases in blood pressure had no such protective effect on the metabolic changes or on oedema. When the clip was removed after 3 hours to permit 1 hour of reperfusion, lactate levels returned to normal but the degree of oedema was unchanged. Hypertension in this reperfusion model caused a slight but not statistically significant increase in oedema. The evidence suggests that moderate increases in blood pressure may be protective against the early metabolic sequelae of focal cerebral ischaemia, but there are potential problems with oedema formation. It is argued that a clinical trial should study the potentially beneficial effects of a brief early increase in blood pressure in the acute aftermath of ischaemic stroke.

Topic: Traumatic Brain Injury and Neurovascular Disturbances
Subfield: Neurology
Field: Medicine
Domain: Health Sciences
Taxonomy, Phylogeny, Divergence Time Estimation, and Biogeography of the Family Pseudoplagiostomataceae (Ascomycota, Diaporthales)

Species of Pseudoplagiostomataceae were mainly introduced as endophytes, plant pathogens, or saprobes from various hosts. Based on multi-locus phylogenies from the internal transcribed spacers (ITS), the large subunit of nuclear ribosomal RNA gene (LSU), partial DNA-directed RNA polymerase II subunit two gene (rpb2), the partial translation elongation factor 1-alpha gene (tef1α), and the partial beta-tubulin gene (tub2), in conjunction with morphological characteristics, we describe three new species, viz. Pseudoplagiostoma alsophilae sp. nov., P. bambusae sp. nov., and P. machili sp. nov. Molecular clock analyses on the divergence times of Pseudoplagiostomataceae indicated that the conjoint ancestor of Pseudoplagiostomataceae and Apoharknessiaceae occurred in the Cretaceous period. and had a mean stem age of 104.1 Mya (95% HPD of 86.0–129.0 Mya, 1.0 PP), and most species emerged in the Paleogene and Neogene period. Historical biogeography was reconstructed for Pseudoplagiostomataceae by the RASP software with a S–DEC model, and suggested that Asia, specifically Southeast Asia, was probably the ancestral area.

Topic: Plant Pathogens and Fungal Diseases
Subfield: Cell Biology
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences