jimnoneill/paper-to-field-training huggingface dataset:
Transport by breaking internal gravity waves on slopes

Field: Earth and Planetary Sciences (Physical Sciences)

We use the results of a direct numerical simulation (DNS) with a particle-tracking model to investigate three-dimensional transport by breaking internal gravity waves on slopes. Onshore transport occurs within an upslope surge of dense fluid after breaking. Offshore transport occurs due to an intrusion of mixed fluid that propagates offshore and resembles an intermediate nepheloid layer (INL). Entrainment of particles into the INL is related to irreversible mixing of the density field during wave breaking. Maximum onshore and offshore transport are calculated as a function of initial particle position, and can be of the order of the initial wave length scale for particles initialized within the breaking region. An effective cross-shore dispersion coefficient is also calculated, and is roughly three orders of magnitude larger than the molecular diffusivity within the breaking region. Particles are transported laterally due to turbulence that develops during wave breaking, and this lateral spreading is quantified with a lateral turbulent diffusivity. Lateral turbulent diffusivity values calculated using particles are elevated by more than one order of magnitude above the molecular diffusivity, and are shown to agree well with turbulent diffusivities estimated using a generic length scale turbulence closure model. Based on a favourable comparison of DNS results with those of a similar two-dimensional case, we use two-dimensional simulations to extend our cross-shore transport results to additional wave amplitude and bathymetric slope conditions.
Trace element characterization and removal from coal and coal wastes

Field: Environmental Science (Physical Sciences)

The FY 1980 research in this program is broken down into four tasks: environmental control technology for trace elements in coal waste drainages, assessment of trace element contamination in coal waste drainages in the Appalachian Region, assessment of trace element contamination and characterization of leaching potential of coal slurry wastes, and assessment of nature and magnitude of trace element contamination in drainages from western coal wastes. These tasks, objectives, and methods are discussed.
Transformation Caused by 3D Modeling and Additive Manufacturing in the Field of Mechanical Engineering

Field: Engineering (Physical Sciences)

This researching material is aiming towards describing the alterations the mechanical engineering industry faced with the development of 3D modeling. As the new technology is applied, it needs time to \nbe adapted to the existing structure, therefore, it changes the arrangement of the system and brings \nnew possibilities as well as questions to the industry. The material covers all the aspects of the affect the \nCAD method brought or will bring, existing issues at hand etc. Even though the potential of 3D modeling \nand its aspects implies the revolutionary possibilities, there is still more to go through before reaching \nthe peak of advantages.
Status of muscle signaling pathways in the early pathogenesis of dystroglycanopathy‐type muscular dystrophy

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

A subset of muscular dystrophies are caused by abnormal glycosylation of α‐dystroglycan. Without its proper sugar structure, α‐dystroglycan binding to extracellular matrix proteins (e.g. laminin, perlecan) is compromised, disrupting the structural integrity of muscle and other tissues. Mutations in the FCMD gene, encoding fukutin, cause severe and milder dystroglycanopathies, Fukuyama congenital muscular dystrophy (FCMD) and limb‐girdle muscular dystrophy type 2M (LGMD 2M), respectively. Using fukutin conditional knockout mice, we have evidence that severe congenital muscular dystrophy phenotypes involve abnormal skeletal muscle development and/or differentiation. We will present a molecular, biochemical and histological approach, screening select muscle signaling pathways in young knockout mice, to identify abnormalities in skeletal muscle development/differentiation. These findings bring new insight to potential mechanisms underlying early disease pathogenesis and severe phenotypic outcomes in dystroglycanopathy‐type congenital muscular dystrophies. This work has been supported by the Muscular Dystrophy Association (Development Grant) and the University of Georgia, College of Pharmacy.
EFFECTS OF HUMIDITY, TEMPERATURE AND CONCENTRATION OF THE NUTRIENT SOLUTION ON FIRMNESS, SHELF LIFE AND FLAVOUR OF SWEET PEPPER FRUITS (CAPSICUM ANNUUM L.)

Field: Agricultural and Biological Sciences (Life Sciences)

ISHS IV International Symposium on Quality of Vegetables EFFECTS OF HUMIDITY, TEMPERATURE AND CONCENTRATION OF THE NUTRIENT SOLUTION ON FIRMNESS, SHELF LIFE AND FLAVOUR OF SWEET PEPPER FRUITS (CAPSICUM ANNUUM L.)
Supplementary Fig 5 from KRT17<sup>high</sup>/CXCL8<sup>+</sup> Tumor Cells Display Both Classical and Basal Features and Regulate Myeloid Infiltration in the Pancreatic Cancer Microenvironment

Field: Medicine (Health Sciences)

<p>CXCL8 and KRT17 tumor epithelial expression trends with worse survival.</p>
HPLC determination of capsaicin and dihydrocapsaicin in pepper straw

Field: Agricultural and Biological Sciences (Life Sciences)

Objective:To determine contents of capsaicin and dihydrocapsaicin in pepper straw of Chaoyue Xinxiang and Fujiao Liuhao according to plant part and harvest time for a basis to expand use of the pepper straw.Methods:The pepper straw was separated into three parts:leaf,branch and trunk,which were dried at 60 ℃,and then were smashed and mixed with methanol abundantly.The contents of capsaicin and dihydrocapsaicin were determined by HPLC.The reliability of method was measured with accuracy,concentration,repeatability,stability and recovery tests.The HPLC method was as follows:Agilent C18 column(4.6 mm × 250 mm,5 μm) was adopted;The mobile phase was methanol-water(85:15) at the flow rate of 1 mL·min-1;The detection wavelength was 280 nm,and the column temperature was 37 ℃.Results:The standard and concentrated curves of capsaicin and dihydrocapsaicin were significantly linear relationship;The RSDs of peak area were 0.13% and 0.08% in continuous injection for five times;RSDs in repeatability tests were 1.7% and 2.7%;RSDs in stability tests were 2.3% and 1.7%,and the recovery rates were 95.8% and 94.3%,respectively.The contents of capsaicin and dihydrocapsaicin among different times and parts were significantly different with interaction effects,and the content in the leaf is higher than those in the branch and trunk(P 0.05).Conclusion:The HPLC method to determine the contents of capsaicin and dihydrocapsaicin is feasible in the present study,and there are higher contents of capsaicin and dihydrocapsaicin in the pepper straw,which may depend on varieties,parts and harvest time.
Winters, Summers, and Destructive Leadership Cultures in Rich Regions

Field: Social Sciences (Social Sciences)

Van de Vliert’s (2009) climato-economic theory of culture proposes that the impact of climatic demands on culture is influenced by wealth resources. In rich regions, much cold and heat in conjunction with relatively little wealth ( undermatching) and little cold and heat in conjunction with relatively much wealth ( overmatching) both are thought to produce less destructive leadership cultures than do approximations of just enough wealth to successfully cope with thermal climate ( optimal matching). Avoiding confounding influences of numerous cross-national differences, we tested this tenet using employee survey data gathered in a sample of 191 Norwegian municipalities. Destructive leadership culture is less prevalent in less wealthy regions with more demanding winters and more demanding summers ( undermatching) and in more wealthy regions with milder winters and milder summers ( overmatching) than in more or less wealthy regions with either more demanding winters and milder summers or more demanding summers and milder winters ( optimal matching). Disconfirmative tests could not obscure or destroy these findings.
Supplementary Tables S1-S5, S7-S8, S10 from Long Noncoding RNA FAM225A Promotes Nasopharyngeal Carcinoma Tumorigenesis and Metastasis by Acting as ceRNA to Sponge miR-590-3p/miR-1275 and Upregulate ITGB3

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

<p>Supplementary Table S1. qPCR primers used in this study Supplementary Table S2. The FAM225A expression level and grouping of samples based on GEO dataset (GSE12452) Supplementary Table S3. Primers used for shRNA plasmid construction Supplementary Table S4. Sequence of miRNA mimic or inhibitor used in this study Supplementary Table S5. Probe sequence of FAM225A in situ hybridization (ISH) Supplementary Table S7. Clinical characteristics of nasopharyngeal carcinoma patients according to the high and low expression of FAM225A. Supplementary Table S8. Univariate and multivariable Cox regression analysis of FAM225A expression level and survival. Supplementary Table S10. Inguinal lymph node metastasis in vivo.</p>
Assessment of mood in aphasia following stroke: validation of the Dynamic Visual Analogue Mood Scales (D-VAMS)

Field: Medicine (Health Sciences)

Objectives: To validate a non-verbal self-report measure of mood – the Dynamic Visual Analogue Mood Scales (D-VAMS) – against the Hospital Anxiety and Depression Scale (HADS) and assess its suitability as an outcome measure or screening measure for depressed mood following stroke. Design: Cross-sectional observational cohort study. Participants: Forty-six stroke survivors (24% with aphasia) recruited from online, from stroke clubs and via an NHS rehabilitation service. Methods: A set of seven bipolar scales was developed enabling users to report mood by modifying facial expression images using a slider. Participants completed a tablet/computer task, reporting their mood on these scales mixed randomly with versions which used only words. The HADS was then completed, followed by a repeat run of the two versions in a different, random sequence. Results: Exploratory factor analysis identified one factor consistent with pleasantness of mood accounting for 80% of the variance. Internal consistency of D-VAMS was high ( α = 0.95), and there was a high correlation between face-only D-VAMS scores and HADS total scores ( r = −0.80, P < 0.001), as well as HADS-D/HADS-A subscale scores ( r = −0.73, P < 0.001; r = −0.71, P < 0.001). D-VAMS showed good sensitivity and specificity against HADS, with means of 85%/77% (sensitivity/specificity) against the HADS-D and 80%/77% against the HADS-A across nine cut-offs. Conclusion: D-VAMS is a valid and reliable measure likely suitable for assessment of depressed mood in aphasia following stroke. Though D-VAMS performed well as a screening measure in this study sample, further study is needed in the acute stage post-stroke.
Depression, depressive symptoms and treatments in women who have recently given birth: UK cohort study

Field: Medicine (Health Sciences)

Objectives To investigate how depression is recognised in the year after child birth and treatment given in clinical practice. Design Cohort study based on UK primary care electronic health records. Setting Primary care. Participants Women who have given live birth between 2000 and 2013. Outcomes Prevalence of postnatal depression, depression diagnoses, depressive symptoms, antidepressant and non-pharmacological treatment within a year after birth. Results Of 206 517 women, 23 623 (11%) had a record of depressive diagnosis or symptoms in the year after delivery and more than one in eight women received antidepressant treatment. Recording and treatment peaked 6–8 weeks after delivery. Initiation of selective serotonin reuptake inhibitors (SSRI) treatment has become earlier in the more recent years. Thus, the initiation rate of SSRI treatment per 100 pregnancies (95% CI) at 8 weeks were 2.6 (2.5 to 2.8) in 2000–2004, increasing to 3.0 (2.9 to 3.1) in 2005–2009 and 3.8 (3.6 to 3.9) in 2010–2013. The overall rate of initiation of SSRI within the year after delivery, however, has not changed noticeably. A third of the women had at least one record suggestive of depression at any time prior to delivery and of these one in four received SSRI treatment in the year after delivery. Younger women were most likely to have records of depression and depressive symptoms. (Relative risk for postnatal depression: age 15–19: 1.92 (1.76 to 2.10), age 20–24: 1.49 (1.39 to 1.59) versus age 30–34). The risk of depression, postnatal depression and depressive symptoms increased with increasing social deprivation. Conclusions More than 1 in 10 women had electronic health records indicating depression diagnoses or depressive symptoms within a year after delivery and more than one in eight women received antidepressant treatment in this period. Women aged below 30 and from the most deprived areas were at highest risk of depression and most likely to receive antidepressant treatment.
Dovecotes in Kayabağ village: an assessment of landscape and architectural characteristics

Field: Arts and Humanities (Social Sciences)

The dovecotes of Kayseri-Gesi stand out as unique examples of indigenous architecture of Anatolia. They are considered significant elements of the rural landscape. The purpose of the construction, the constructional and spatial characteristics peculiar to these dovecotes, make them an important element of global cultural and architectural heritage. Dovecotes that are built upon rocks, with mere building stones provided from the same rocks, look like a shaped form of the topography itself. This is very much to do with the geological features of the Cappadocia Region where Kayseri is located. In terms of construction techniques and spatial organization, the dramatic differences in the dovecotes’ underground and aboveground parts make them even more outstanding. This research is based on the field studies conducted in the dovecotes of Kayabağ. The landscape was studied in all aspects and each dovecote is studied for its placement, topographical interactions, plan and section typologies, materiality and construction techniques. The structural problems stemmed from the geological features and the deterioration caused by external factors are taken into consideration. The study concludes with an overall approach for preservation, sustainability and conservation process of the heritage landscape of Dovecotes [Güvercinlik] of Kayabağ.
Using the SGI Pro64 Open Source Compiler Infra-Structure for Teaching and Research

Field: Computer Science (Physical Sciences)

Modem optimizing compilers are complex programs that require from tens to hundreds of people-years to be developed. Thus professors must use third-party compiler infra-structures to introduce students to compiler optimizations. Until recently only infra-structures developed at universities, research institutes, or by GNU were widely available for teaching. However, in May 2000, SGI made public the source code for Pro64, a highly optimized suite of compilers for the Intel Architecture 64 (IA-64) that is an evolution of the established MIPSPro suite of compilers. The use of a production-level compiler infra-structure for teaching is thus new. In this paper we report our experience using the Pro64 in a graduate compiler optimization class. We paired the study of the Pro64 with the use of IMPACT within Trimaran, and with performance studies conducted with the MIPSPro compilers. The students feedback indicate that they valued working with a state-of-the-art compiler infrastructure and studying open research topics for their class projects.
BIOCONVERSION OF SECONDARY PRODUCTS OF PROCESSING OF GRAIN CEREALS CROPS

Field: Agricultural and Biological Sciences (Life Sciences)

A method has been developed for the production of organic ingredients from secondary products resulting from the high-quality grinding of triticale and wheat into flour, which involves the enzymatic action of amylolytic enzymes to release starch polysaccharides while preserving the native properties of dietary fibers and biologically active substances associated with them. To a large extent, the features of the properties of the obtained ingredients are due to the number and composition of the components of dietary fiber of grain, as well as the morphological features of their structure. It is shown that the viscosity of aqueous colloidal systems at a concentration of soluble dietary fiber of the ingredient 0.5 % increases 11 times; at a concentration of 1.0 % — 30 times, forming a viscous gel-like structure. This allows them to be used for gelling, thickening and stabilization of aquatic food systems. The use of ingredients with a high content of NLP in baking is possible only taking into account their water absorption capacity. A method for the enzymatic modification of secondary products of processing of grain triticale was developed. On the basis of the study of the kinetics and efficiency of the effect of proteolytic and cellulolytic enzyme preparations (EP) and their compositions, optimal conditions for enzymatic modification (the EP dosage is 0.5…0.75 units of PA/g of bran, 0.3…0.4 units of CA/g of bran, the optimum temperature is 40–50 °С, pH is 5.0 and 3.5, the duration of reactions is 1.5 hours) have been determined. The use of cellulolytic EP allowed to increase the amount of reducing substances and soluble protein by 1.5–2.5 times in comparison with the control sample. The biomodified bran obtained using the MEC «Shearzyme 500 L» + «Neutrase 1.5 MG» and «Viscoferm L» + «Distizym Protacid Extra» has a high degree of hydrolysis of non-starch polysaccharides and proteins, is characterized by a certain ratio of high-, medium-, low-molecular peptides and amino acids, has different functional and technological properties. They can be used in the production of a wide range of general-purpose, functional and treatmentand-prophylactic food products.
High processivity polymerases

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

Chimeric proteins comprising a sequence nonspecific single-stranded nucleic-acid-binding domain joined to a catalytic nucleic-acid-modifying domain are provided. Methods comprising contacting a nucleic acid molecule with a chimeric protein, as well as systems comprising a nucleic acid molecule, a chimeric protein, and an aqueous solution are also provided. The joining of sequence nonspecific single-stranded nucleic-acid-binding domain and a catalytic nucleic-acid-modifying domain in chimeric proteins, among other things, may prevent the separation of the two domains due to their weak association and thereby enhances processivity while maintaining fidelity.
In vivo and in vitro studies on the carotenoid cleavage oxygenases from Sphingopyxis alaskensis RB2256 and Plesiocystis pacifica SIR‐1 revealed their substrate specificities and non‐retinal‐forming cleavage activities

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

Carotenoid cleavage oxygenases are nonheme iron enzymes that specifically cleave carbon–carbon double bonds of carotenoids. Their apocarotenoid cleavage products serve as important signaling molecules that are involved in various biological processes. A database search revealed the presence of putative carotenoid cleavage oxygenase genes in the genomes of Sphingopyxis alaskensis RB 2256 and Plesiocystis pacifica SIR ‐1. The four genes sala_1698 , sala_1008 , ppsir1_15490 and ppsir1_17230 were cloned and heterologously expressed in carotenoid‐producing Escherichia coli JM 109 strains. Two of the four encoded proteins exhibited carotenoid cleavage activity. S . alaskensis RB 2256 carotenoid cleavage oxygenase (Sa CCO ), which is encoded by sala_1698 , was shown to cleave acyclic and monocyclic substrates. Coexpression of sala_1698 in carotenoid‐producing E . coli JM 109 strains revealed cleavage activity for lycopene, hydroxylycopene, and dihydroxylycopene. The monocyclic substrate apo‐8′‐carotenal was cleaved in vitro by purified Sa CCO at the 9′/10′ and 11′/12′ double bonds. The second enzyme, P . pacifica SIR ‐1 carotenoid cleavage oxygenase (Pp CCO ), is encoded by ppsir1_15490 . Pp CCO ‐mediated carotenoid cleavage requires the presence of either hydroxy or keto groups. Pp CCO cleaved zeaxanthin, hydroxylycopene, and dihydroxylycopene, and also the C 50 carotenoids decaprenoxanthin, sarprenoxanthin and sarcinaxanthin, in carotenoid‐producing E . coli JM 109 strains. Whole cells of E . coli JM 109 overexpressing ppsir1_15490mut , a mutant of ppsir1_15490 with enhanced gene expression, were applied for the conversion of carotenoids. Analysis of the carotenoid cleavage products revealed a single cleavage site at the 13′/14′ double bond for astaxanthin, and two cleavage sites at the 11′/12′ or 13′/14′ double bond for zeaxanthin, nostoxanthin, and canthaxanthin.
A new path generation method for autonomous in-door and out-door robots

Field: Computer Science (Physical Sciences)

Autonomous robot navigation is an important research field because these robots can solve problems where the human presence is impossible, dangerous, expensive, or uncomfortable. The main problem to be solved for an autonomous robot is that the environment where they have to move safely is usually not or only partially known and possibly even dynamically changing. In such situations universal navigation methods can be advantageous because they can combine the abilities of both the global and local techniques and thus can be used in any environment. In this paper, a new autonomous hybrid navigation method is introduced. The algorithm is composed of visibility graph based global navigation and simple potential field based local navigation parts. It applies a new automated graph generation method which may become necessary if, because of the observed new obstacles, a new path should be generated. The route generated by the introduced technique is quasi optimal. The presented technique offers a universal navigation technique which can successfully be used in all, known, unknown, and dynamically changing environments.