jimnoneill/paper-to-field-training huggingface dataset:
An investigation of the Ciliary Protein PKHD1 in Cyst development in liver disease: clues to the pathogenesis of Biliary Atresia

Biliary atresia is a common form of paediatric liver disease, with progressive, inflammatory obliteration of the biliary tree, leading to liver failure early in life. Mutations in PKHD1, encoding the ciliary protein fibrocystin, are associated with autosomal recessive polycystic kidney disease (ARPKD), a ciliopathy with clinical features that resemble biliary atresia. The hepatic developmental defects detectable in a significant number of infants with ARPKD are thought to be caused by dysfunction in the structure and function of primary cilia. The pathogenetic mechanism of both disorders is thought to be dysregulation of epithelial cell growth and tubulomorphogenesis. Preliminary investigations uncovered an association of PKHD1 sequence variants in a subset of biliary atresia patients with renal cysts, promoting further investigation to determine the functional role of fibrocystin in epithelial cells from renal and biliary tubules. Immunohistochemical studies, using a monoclonal antibody raised against wildtype fibrocystin, showed that it localises specifically to intrahepatic bile ducts. Absence of fibrocystin staining in end-stage liver tissue reflects ongoing damage to the intrahepatic biliary tree, rather than a phenomenon specific to biliary atresia. Studies utilising the Pkhd1 \\(^{del2/del2}\\) mouse model of ARPKD revealed 17β-estradiol sensitive centrosomal overduplication underlies the dysregulation of epithelial cell growth in renal tubules, however this does not appear to be in synergy with \\(Pkhd1\\) knockdown. Therefore, it remains uncertain whether sequence variants of PKHD1 are associated with biliary atresia.

Topic: Genetic and Kidney Cyst Diseases
Subfield: Genetics
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
MUIR - a language development environment

The concept of a language development environment is introduced and motivated. The key facilities and characteristics of such an environment is described, and a concrete system called Muir is studied. In a language development environment the language definition formalism is central. We introduce a context free grammar definition formalism that emphasizes the hierarchical classification of syntactic domains, and we argue that syntax-directed editing is useful especially when making experiments with new languages. Finally, we discuss how to keep documents consistent with a grammar that is under development.

Topic: Natural Language Processing Techniques
Subfield: Artificial Intelligence
Field: Computer Science
Domain: Physical Sciences
Economic Analysis of Conservation Developments in Western North Carolina

The growth rate in western North Carolina has risen 20% in the past 10 years. This drastic increase has led to an alarming rate of development causing the degradation of many of the natural habitats that are native to western North Carolina. In order to curb some of this degradation development needs to become more sustainable towards the environment. Conservation developments, which are housing developments that place environmental protection as their first priority, are one way to become more sustainable. The economic analysis is done for developers and for society to try and show the economic benefits associated with conservation developments. A cost comparison is done on two different developments, a hedonic pricing model is used to evaluate price premiums and an evaluation of carbon benefits are all used as part of the analysis. \n\nThe results indicate that it is cheaper to build conservation developments and they sell for a 39% price premium. Unfortunately, conservation developments do not gain as much profit as conventional developments due to the difference in housing density. Even with the addition of carbon sequestration values, which are greater in conservation developments, the profits are still less. It is important for conservation developments to be supported in this area since they are much more sensitive to the too often degraded landscape.

Topic: Economic and Environmental Valuation
Subfield: Economics and Econometrics
Field: Economics, Econometrics and Finance
Domain: Social Sciences
What Awful Smell?

Although a rose by any other name might smell as sweet, two people smelling it might not experience that "sweetness" the same way. Different people differ markedly in their perceptions of particular odors: For example, some people think the testosterone derivative androstenone smells pleasantly floral, others think it smells like sweat or urine, and others don’t perceive its scent at all. Keller et al . expressed 335 putative human odorant receptors in a line of human cells that stably expresses accessory factors for odorant receptor expression and identified OR7D4 --which is expressed in nasal epithelium--as encoding the receptor most responsive to androstenone. Searching a SNP database for OR7D4 polymorphisms and sequencing the OR7D4 coding region of 391 individuals enabled the identification of the most common OR7D4 allele and a variant with two amino acid substitutions (R88W and T133M, leading to their respective designation as RT and WM). OR7D4 RT responded to androstenone and the related androstadienone (but not to 64 other odorants), whereas OR7D4 WM failed to respond to any odorants (including androstenone and androstadienone). People who were heterozygous for RT and WM or homozygous for WM were in general less sensitive to these two compounds than people who were homozygous for RT--and tended to have more positive perceptions of these odors. Statistical analysis implicated genetic polymorphisms in OR7D4 in differences in androstenone and androstadienone perception, although they did not fully account for such differences, indicating that odorant receptor function per se contributes to the subjective perception of odor. A. Keller, H. Zhuang, Q. Chi, L. B. Vosshall, H. Matsunami, Genetic variation in a human odorant receptor alters odour perception. Nature 449 , 468-472 (2007). [PubMed]

Topic: Olfactory and Sensory Function Studies
Subfield: Sensory Systems
Field: Neuroscience
Domain: Life Sciences
Sensory evaluation of Extra Virgin Olive Oil (EVOO) extended to include the quality factor "harmony"

Sensory evaluation of olive oil, meaning the official organoleptic assessment of olive oil respectively the "Panel Test" (PT), is based on the standards of the International Olive Council (IOC), as well as on the Regulation (EC) 640/2008 of the European Commission. These regulations lead to the classification of olive oil as "extra virgin" (EVOO), "virgin" (VOO) or "lampant", which however is not sufficient to clearly discriminate between different quality levels within the grade EVOO. The objective of the study at hand was to develop and validate an objective sensory evaluation method for the quality certification of olive oil within the grade EVOO. A new rating system, including a detailed description and evaluation of the complexity and persistence of flavour, was established. First, a comparison between different profile sheets from various olive oil competitions (Ercole Olivario, Premio Biol, Leone D'Oro Mario Solinas Award, among others) and the official profile sheet from the IOC/EC for the panel test (PT) took place. In consecutive steps the basic test procedure from the panel test (PT) then was extended with additional sensory descriptors. Two trained olive oil panels (the German Olive Oil Panel (DOP) and the Swiss Olive Oil Panel (SOP)) were further educated to profile various green and ripe aroma components and to evaluate the complexity of the perceived aroma components and their persistency (descriptor: "harmony/persistency"). This extended methodology was cross-validated over a time period of 3 years between the two panels (DOP/SOP).

Topic: Sensory Analysis and Statistical Methods
Subfield: Food Science
Field: Agricultural and Biological Sciences
Domain: Life Sciences
Which Way to Grow? Startup Internationalization and Innovation in Latin America and Europe

Internationalization and innovation are both critical strategies for growth-oriented startups. Whereas high uncertainty and unique learning challenges in emerging markets such as Latin America make the respective startups set their preference on internationalization, and only thereafter on innovation, in developed markets like Europe internationalization and innovation are more and more regarded as “vicious circle”, reinforcing each other. This suggests that the institutional context of firms shapes the priorities set on innovation and internationalization, and the relationship of the two strategies. In this paper, we investigate potential tradeoffs between internationalization and innovation in Latin America and Europe by having a closer look at the legal business context in a startups home country. Our paper contributes to the literature on international and strategic entrepreneurship and the institutional context startups face in their home countries. Relying on proprietary data of a globally operating European ICT corporation that is listed at the EUROSTOXX 50 index, we analyze the strategic choices between internationalization and innovation in an unbalanced panel of 359 (336) ICT startups and 1,613 (1,422) observations from seven Latin American countries and five European countries during the years 2014-2016. Our findings suggest that the legal business context in a startup’s home country influences the likelihood of startup internationalization.

Topic: Private Equity and Venture Capital
Subfield: Accounting
Field: Business, Management and Accounting
Domain: Social Sciences
Neurotrophin switching in developing sensory neurons

The main aim of this project was to define the neurotrophin survival requirements of sensory neurons during the early stages of their development both in vivo and in vitro. The in vitro survival of neural crest-derived but not placode-derived cranial sensory neurons is promoted by several different neurotrophins early in their development. Neural crest-derived neurons subsequently lose responsiveness to all neurotrophins except NGF. Loss of responsiveness of neural crest-derived sensory neurons to BDNF and NT3 is associated with a marked shift in the dose responses of these neurons to higher neurotrophin concentrations. Analysis of the timing of cell death in the trigeminal ganglia of mouse embryos that are homozygous for null mutations in the TrkA, TrkB and TrkC genes which encode high affinity receptors for NGF, BDNF and NT3 respectively, show that there is an early peak of apoptosis in TrkB and TrkC knockouts which is consistent with the early survival response of trigeminal neurons to BDNF and NT3 in vitro. The elevated peak of apoptosis in TrkA knockouts occurs at the same development stages as in wild type embryos which is consistent with the later response of trigeminal neurons to NGF in vitro. Furthermore, there is a high level of expression of TrkC mRNA in early trigeminal neurons which accords with the early survival response of these neurons to NTS. It is also shown that subsets of trigeminal neurons discriminate between neurotrophins at very high concentrations during the period of cell death, indicating that neurotrophin responses can be far more highly specific than previously thought. Taken together, these results show that neurotrophin switching is a physiologically relevant phenomenon in certain populations of developing sensory neurons.

Topic: Nerve injury and regeneration
Subfield: Cellular and Molecular Neuroscience
Field: Neuroscience
Domain: Life Sciences
Local bounds for stochastic reaction diffusion equations

We prove a priori bounds for solutions of stochastic reaction diffusion equations with super-linear damping in the reaction term. These bounds provide a control on the supremum of solutions on any compact space-time set which only depends on the specific realisation of the noise on a slightly larger set and which holds uniformly over all possible space-time boundary values. This constitutes a space-time version of the so-called 'coming down from infinity' property. Bounds of this type are very useful to control the large scale behaviour of solutions effectively and can be used, for example, to construct solutions on the full space even if the driving noise term has no decay at infinity. Our method shows the interplay of the large scale behaviour, dictated by the non-linearity, and the small scale oscillations, dictated by the rough driving noise. As a by-product we show that there is a close relation between the regularity of the driving noise term and the integrability of solutions.

Topic: Stochastic processes and financial applications
Subfield: Finance
Field: Economics, Econometrics and Finance
Domain: Social Sciences
Conformal deposition of GeTe films with tunable Te composition by atomic layer deposition

Atomic layer deposition (ALD) of chalcogenide amorphous films has attracted attention, thanks to its ability to deposit highly conformal and uniform thin films on three-dimensional structures; these film properties are critical for the development of ultrahigh-density integrated electronic circuits such as nanoscale 3D cross-point memory stacks. Control over the composition of chalcogenide compounds is indispensable for fabricating functional electronic devices. In this work, the authors used trichlorogermane (HGeCl3) and bis(trimethylsilyl)telluride [(Me3Si)2Te] as ALD precursors to develop conformal and uniform germanium telluride (GeTe) films at low temperature (60 °C). The growth of GeTe resulted in moderately Ge rich films independently of the ALD precursor injection time and the use of single or discrete (Me3Si)2Te doses. To achieve control over the GeTe film composition, the authors developed a unique ALD of elemental tellurium (Te) using tellurium ethoxide [Te(OEt)4] and (Me3Si)2Te as precursors. Combining GeTe and elemental Te in an ALD supercycle fashion, they obtained GeTex films with a controllable Te content showing a uniform and conformal morphology on high aspect ratio trench structures. A detailed analysis of the variations in Ge and Te contents upon exposure of GeTex films to Te(OEt)4 revealed that an interfacial replacement of Ge atoms to form volatile Ge(OEt)2 takes place and produces a decrease in Ge and an increase in Te content. The ALD studies of GeTe and Te films described in this work provide a facile route for deposition of GeTe with controllable composition. This material system is important for the development of ovonic threshold switching selectors and phase change memories.

Topic: Phase-change materials and chalcogenides
Subfield: Materials Chemistry
Field: Materials Science
Domain: Physical Sciences
Umbilical cord lesions in early intrauterine fetal demise.

A significantly high number (10.7%) of IUFD in early gestation are associated with umbilical cord abnormalities. Routine assessment of umbilical cords in early pregnancy might help to detect pregnancies at risk.

Topic: Prenatal Screening and Diagnostics
Subfield: Pediatrics, Perinatology and Child Health
Field: Medicine
Domain: Health Sciences
Critical Role of Interdomain Interactions in the Conformational Change and Catalytic Mechanism of Endoplasmic Reticulum Aminopeptidase 1

Endoplasmic reticulum aminopeptidase 1 (ERAP1) is an intracellular enzyme that is important for the generation of antigenic epitopes and major histocompatibility class I-restricted adaptive immune responses. ERAP1 processes a vast variety of different peptides but still shows length and sequence selectivity, although the mechanism behind these properties is poorly understood. X-ray crystallographic analysis has revealed that ERAP1 can assume at least two distinct conformations in which C-terminal domain IV is either proximal or distal to active site domain II. To improve our understanding of the role of this conformational change in the catalytic mechanism of ERAP1, we used site-directed mutagenesis to perturb key salt bridges between domains II and IV. Enzymatic analysis revealed that these mutations, although located away from the catalytic site, greatly reduce the catalytic efficiency and change the allosteric kinetic behavior. The variants were more efficiently activated by small peptides and bound a competitive inhibitor with weaker affinity and faster dissociation kinetics. Molecular dynamics analysis suggested that the mutations affect the conformational distribution of ERAP1, reducing the population of closed states. Small-angle X-ray scattering indicated that both the wild type and the ERAP1 variants are predominantly in an open conformational state in solution. Overall, our findings suggest that electrostatic interactions between domains II and IV in ERAP1 are crucial for driving a conformational change that regulates the structural integrity of the catalytic site. The extent of domain opening in ERAP1 probably underlies its specialization for antigenic peptide precursors and should be taken into account in inhibitor development efforts.

Topic: Peptidase Inhibition and Analysis
Subfield: Oncology
Field: Medicine
Domain: Health Sciences
The Impact of Gamification Marketing Strategies on User Consumption Behavior

In digital transformation, gamification marketing has become a core strategy for companies to stand out in the fierce market competition. Gamification marketing strategies can not only attract users but also enhance brand loyalty. This paper focuses on the target audience of gamification marketing and its influencing factors, and through the SOR psychological model, it deeply explores how these factors affect user behavior. First, this paper deeply explores the characteristics of target users and reveals the differences in motivations and behavior patterns of different user groups in gamification marketing. Then, based on the SOR model, this paper explores the impact of psychological factors such as incentives, stimulation, opportunities, and responses on user engagement and loyalty. Finally, this paper uses Duolingo as an example to explore how its gamification elements, including the points system, level setting, and reward mechanism, cleverly enhance users' learning enthusiasm and encourage them to remain active for a long time. Research shows that by stimulating users' intrinsic motivation and enhancing interactive experience, gamification marketing strategies can deepen the emotional bond between users and brands, thereby promoting the brand's continued growth.

Topic: Technology Adoption and User Behaviour
Subfield: Information Systems and Management
Field: Decision Sciences
Domain: Social Sciences
The rise and retreat of Syriza: an interview with Michalis Spourdalakis

Syriza is the only radical Left party to be elected a national governing party since the worldwide economic crisis began in 2008. In this interview with political theorist Michalis Spourdalakis, a founding member of Syriza, we discuss the unique strategic relationships between social movements and the new radical Left parties such as Syriza, the struggle to maintain the party’s independence amid co-optation into the Greek state and broader European Institutions, and what the Syriza experience can teach us about attempts to transform capitalist states.

Topic: Populism, Right-Wing Movements
Subfield: Political Science and International Relations
Field: Social Sciences
Domain: Social Sciences
Case Study: Farm characteristics and total mixed ration particle size issues on Parmigiano Reggiano farms in northern Italy

A convenience sample of 20 farms in the geographic bounds of the Parmigiano Reggiano cheese producing region of northern Italy were studied. All farms used a TMR feeding system consisting of all dry hay (primarily alfalfa and grass) diets and adhering to the specific limitations of feeds as described by the Parmigiano Reggiano cheese consortium. Farms were visited twice for a survey of general farm characteristics and feeding management practices and collection of feed intake and samples at 0, 8, and 24 h after feeding to measure particle size characteristics of TMR in the feed bunk at each time. Many farms added 1 to 10 L of water per cow to the TMR in an attempt to reduce sorting and enhance intake. Based on particle size analysis it appeared that cows were not sorting diets to any great degree either with or without added water. However, it is likely that adding water to the TMR enabled cows to eat faster, thereby producing less saliva per kilogram of feed, and helped to create a situation for more slug feeding in the warm summer months of this study when the water-added TMR heated due to molding several hours after feeding. There was a positive correlation (r = 0.41) between the amount of added water and the percentage of cows on a farm that had an inversion of milk fat and protein or low fat percentage. Farms using pelleted concentrates also had less milk fat (r = −0.41). Overall there appeared to be no advantage of adding water to reduce TMR sorting on these farms.

Topic: Ruminant Nutrition and Digestive Physiology
Subfield: Agronomy and Crop Science
Field: Agricultural and Biological Sciences
Domain: Life Sciences
Shear Strengthening of Reinforced Concrete Beams Using CFRP Wraps

The need to retrofit existing reinforced concrete (RC) structures have increased over the decades due to corrosion of steel reinforcement inside the concrete, neglect and overuse, and increased loading. Experimental and numerical studies in this research field showed that using fiber-reinforced Polymer (FRP) materials to strengthen RC members in shear, flexure, and column confinement applications is an effective method to retrofit RC structures. This strengthening technology has numerous advantages over conventional steel plating, such as providing high strength-to-weight ratio, versatility, durability, and ease of use to strengthen RC members. The purpose of this paper is to study the effect of strengthening shear deficient RC beams with externally bonded (EB) carbon fiber-reinforced polymer (CFRP) sheets with different wrapping configurations. Two shear strengthening wrapping schemes of CFRP sheets will be investigated; U-Wrapped and completely Wrapped. Although the completely wrapped scheme is more effective, however, due to its limitations, the U-Wrapped scheme became the most commonly used method in shear strengthening of RC structures. The drawback of this strengthening scheme is the premature failure caused by debonding of the CFRP laminates, without utilizing its full strength. The main aim of this study is to compare the performance of a U-Wrapped T-beam with two completely wrapped rectangular beams. The first strengthened rectangular specimen (WBR1) has a depth equivalent to the T-beam’s web height, while the second strengthened rectangular specimen (WBR2) has a depth equivalent to the T-beam’s total depth. In addition, a control T-beam and two rectangular beams were cast and tested as benchmark specimens. The experimental test results showed that the beam strengthened by U-Wrapped CFRP sheets increased the control beam’s shear strength by 114.82%, while the increase in shear capacity of the completely wrapped equivalent WBR1 and WBR2 beams over their control unstrengthened specimens was 69.28% and 201.63%, respectively. In addition, the completely wrapped scheme provided more ductility compared to that of the U-Wrapped T-beam specimen, that failed by CFRP sheets debonding in a brittle manner. Thus, it could be concluded that an ideal way to increase the shear capacity and ductility of RC beams is to completely wrap the beams using CFRP sheets. However, if the completely wrapping scheme is not possible due to geometrical obstructions, U-wrapping scheme could be effective in increasing the shear capacity of RC beams but will fail in a brittle mode by sheet debonding without utilizing its full strength. Anchoring the CFRP U-Wraps could be a viable solution to enhance the performance of strengthened RC beams that should be investigated in future research studies.

Topic: Structural Behavior of Reinforced Concrete
Subfield: Building and Construction
Field: Engineering
Domain: Physical Sciences