jimnoneill/paper-to-field-training huggingface dataset:
Developing a bioinformatics pipeline for comparative protein classification analysis

Field: Computer Science (Physical Sciences)

Abstract Background Protein classification is a task of paramount importance in various fields of biology. Despite the great momentum of modern implementation of protein classification, machine learning techniques such as Random Forest and Neural Network could not always be used for several reasons: data collection, unbalanced classification or labelling of the data.As an alternative, I propose the use of a bioinformatics pipeline to search for and classify information from protein databases. Hence, to evaluate the efficiency and accuracy of the pipeline, I focused on the carotenoid biosynthetic genes and developed a filtering approach to retrieve orthologs clusters in two well-studied plants that belong to the Brassicaceae family: Arabidopsis thaliana and Brassica rapa Pekinensis group. The result obtained has been compared with previous studies on carotenoid biosynthetic genes in B. rapa where phylogenetic analysis was conducted. Results The developed bioinformatics pipeline relies on commercial software and multiple databeses including the use of phylogeny, Gene Ontology terms (GOs) and Protein Families (Pfams) at a protein level. Furthermore, the phylogeny is coupled with “population analysis” to evaluate the potential orthologs. All the steps taken together give a final table of potential orthologs. The phylogenetic tree gives a result of 43 putative orthologs conserved in B. rapa Pekinensis group. Different A. thaliana proteins have more than one syntenic ortholog as also shown in a previous finding (Li et al., BMC Genomics 16(1):1–11, 2015). Conclusions This study demonstrates that, when the biological features of proteins of interest are not specific, I can rely on a computational approach in filtering steps for classification purposes. The comparison of the results obtained here for the carotenoid biosynthetic genes with previous research confirmed the accuracy of the developed pipeline which can therefore be applied for filtering different types of datasets.
Precise Charge Density Analysis of PbTiO 3

Field: Materials Science (Physical Sciences)

Precise charge-density distributions of cubic and tetragonal PbTiO 3 have been investigated associated with the ferroelectric phase transition at 763K, by means of the MEM/Rietveld analysis using synchrotron radiation X-ray powder-diffraction data. It has been clearly visualized that cubic PbTiO 3 consists of the three-dimensional covalent network of TiO 6 octahedra and isolated Pb 2+ ions, whereas tetragonal PbTiO 3 forms a layered structure with the two-dimensional covalent network of TiO 5 pyramids, to which Pb atoms are also covalently bonded. These findings on the binding nature of tetragonal PbTiO 3 give good agreement with theoretical predictions by the first-principles calculations.
Motor speech effects in subthalamic deep brain stimulation for Parkinson’s disease

Field: Medicine (Health Sciences)

OBJECTIVE A motor speech disorder or dysarthria commonly arises in patients with Parkinson’s disease (PD). The impact of subthalamic nucleus (STN) deep brain stimulation (DBS) on motor speech and the potential of intraoperative motor speech testing to predict outcomes are unknown. This study examined 1) the types and prevalence of motor speech changes observed with STN DBS and their relation to the preoperative condition, 2) the ability of intraoperative testing to predict postoperative changes in motor speech, and 3) the spatial relationship between stimulation sites producing maximal motor improvement, as measured by the Movement Disorder Society Unified Parkinson’s Disease Rating Scale (MDS-UPDRS), and maximal motor speech deterioration. METHODS Comprehensive preoperative, intraoperative, and postoperative motor speech/dysarthria evaluations were performed in consecutive patients with advanced idiopathic PD who underwent STN DBS surgery in the period from 2011 to 2016. Preoperative type of dysarthria and overall dysarthria severity rating along with intraoperative motor speech testing results were evaluated as predictors of postoperative change. Atlas-independent, fully individualized field modeling was used to identify stimulation sites associated with maximal MDS-UPDRS motor improvement and motor speech deterioration. RESULTS Forty-three patients with PD treated with STN DBS were prospectively studied. Improved MDS-UPDRS motor scores and worsened dysarthria were demonstrated by a subset of patients (16/43). Preoperative dysarthria characteristics did not predict postoperative deterioration. Intraoperative assessment of motor speech strongly predicted postoperative outcomes (OR 4.4, p = 0.02). Sites of maximal MDS-UPDRS motor improvement and worsened dysarthria were distinct. Worsened dysarthria was associated with capsular stimulation, anterior and ventral to the site of maximal MDS-UPDRS motor improvement. CONCLUSIONS The predictive reliability of intraoperative motor speech testing, together with the identification of distinct stimulation sites for motor speech impairment and improved MDS-UPDRS motor function, raise the possibility that DBS lead repositioning or reprogramming could reduce adverse effects on motor speech without impacting MDS-UPDRS motor outcomes in patients undergoing STN DBS.
Improving Surrogate Monitoring Techniques for Suspended Sediment

Field: Environmental Science (Physical Sciences)

The quality of water of our nation’s rivers and streams is important to many vital uses including drinking water treatment, recreation, and the natural environment. Water quality can be severely impacted by the quantity and type of suspended sediment found therein. Because suspended sediment can be associated with many other contaminants that degrade water quality, it is noted as the most common impairment to water quality in the United States. Suspended sediment can cause significant ecological impacts to the chemical and biological characteristics of surface waters. The ability to accurately quantify suspended sediment concentrations at the appropriate time(s) and location(s) is critical in assessing whether streams are meeting their designated beneficial uses and in implementing and evaluating watershed management and mitigation plans and restoration efforts. Currently, new methods for quantifying suspended sediment concentrations use mathematical and statistical techniques to relate turbidity and suspended sediment and have been shown to be affected by several factors, including the size and characteristics of suspended sediment particles. In this research we used turbidity as a surrogate (substitute) for suspended sediment at six locations in the Little Bear River, Utah, U.S.A. We also examined the differences between single-point and width and depth integrated suspended sediment sampling at two sites. This was used to develop a method to account for the differences and improve the resulting estimates of suspended sediment concentrations. Statistical techniques were used to assess—in probabilistic terms—the duration and magnitude of potential water quality criteria exceedance. Findings highlight that among some monitoring locations with wide geographic distances, turbiditysuspended sediment relationships are not site-specific for the more frequent (90th percentile) but lower (NTU) turbidity values. Comparisons of point measures of turbidity and width and depth integrated suspended sediment samples revealed that suspended sediment is homogenous at their respective stream cross sections for 90% and 99% of the time at sites 2 and 6, respectively. The results are applicable to water managers who are charged with the determination of attainment or exceedance of water quality standards.
XPS valence bands of La, Ce and Gd and their aluminium alloys

Field: Physics and Astronomy (Physical Sciences)

The XPS valence band spectra of La, Ce and Gd metal and of their aluminium alloys show the 5d band in La metal at 0.8 eV below the Fermi energy with a width of about 1.5 eV; in Ce and 4f band and 5d band are at 0.5 eV and 1.7 eV below the Fermi energy with widths of 0.7 eV and 1.5 eV respectively. The Gd 5d band is very similar to the La 5d band, while the 4f level is well localized at 8.0 eV below the Fermi energy.
Impact of various types of anti-hail nets on light exposure in orchards and quality parameters of apples– a rewiev

Field: Agricultural and Biological Sciences (Life Sciences)

Abstract The new Common Agricultural Policy (CAP) has been designed to shrink funds that Hungarian agricultural reform will in Nowadays, anti-hail nets are a part of basic equipment in a modern apple orchards. They decrease the risks of apple production and thus allow regular and quality apple harvest. Colours of nets differently obstruct the passing of light through the net, which directly affects some quality parameters of the yield, especially the fruit skin colour. The article includes a brief overview of studies associated with the impact of light exposure under different types of anti-hail nets on quality of apple fruits, as well as investigations which deal with adaptation of various technological measures, such as the use of reflective ground foil. A part of data from the existing literature explains the effect of anti-hail net usage on forming a microclimate under the net, and consequently, its effect on the development and dynamics of diseases and pests.
Uncovering the Ciliogenesis Regulatory Network

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

Ciliopathies comprise disorders associated with aberrant function of essential organelles called cilia. Cilia are found in almost all vertebrate cells, with a subset of this population being motile and/or multiciliated. Over 1,000 proteins have been associated with the ciliary proteome, yet the regulatory circuit controlling the formation of cilia remains lesser known. Our lab has identified transcription factors and coactivators that contribute to the ciliogenesis circuit. Such factors include orphan nuclear receptor Esrrγ and coactivator Ppargc1a/PGC1a. Independently, these factors regulate both mono‐ and multi‐ciliated cells in the early signaling node, ear, and embryonic kidney (pronephros). Absence of these factors results in decreased multiciliated cells, decreased cilia length, and increased unciliated basal bodies. Considering these phenotypic similarities, we hypothesized a cooperative relationship between Esrrγ and Pppargc1a in the context of ciliated cell development. By modelling dual heterozygosity with genetic interaction studies, we found that ppargc1a works synergistically with esrrγa to regulate prostaglandin signaling to support ciliary outgrowth and multiciliated cell fate choice. While previous studies have alluded to the interaction of Esrrγ and Ppargc1a/PGC1a in metabolism, this is the first report of a cooperative effect that is essential for ciliogenesis or lineage decisions in development. This study has far‐reaching implications, as cilia are present in various tissues, and these factors may serve as therapeutic targets for ciliopathic conditions and birth defects.
Chromatographic behaviour of linear DNA molecules of defined size

Field: Chemistry (Physical Sciences)

The aim of our work was to study the chromatographic behaviour of lambda DNA (48.5 kbp) and lambda/HindIII DNA fragments (23.1, 9.4, 6.6, 4.4, 2.3, 2.0, 0.6, 0.1 kbp) using sorbents based on HEMA-co-EDMA. The ion-exchange chromatography (IEC) and gel permeation chromatography (GPC) were used for DNA fragment separations. The resolution of larger lambda/HindIII fragments (23.1 and 9.4 kbp) was insufficient using IEC. In the case of GPC, DNA fragments smaller than 9.4 kbp were not separated from each other and were eluted in the void volume. The order of the separation of relatively large DNA fragments (larger then 9.4 kbp) and lambda DNA molecules was reverse to the order expected for GPC. This is in agreement with the principle of slalom chromatography.
Understanding the complexity of adaptation and effective use in enterprise system implementations

Field: Business, Management and Accounting (Social Sciences)

When organizations want to gain benefits from complex information technology (IT) such as Enterprise Systems (ESs), employees not only need to use the technology, they need to use it effectively. However, few studies have examined the effects of complex IT on employees’ jobs and what it takes for them to adapt towards effectively using it. Specifically, there is little knowledge about the post-adoption phase; the time right after a new ES has been implemented in an organization. Effective use, however, is the prerequisite for organizations to gain any benefits. In this thesis, I build upon a thorough review of the literature on the adoption and use of IT, using a mixed-method approach, grounded in a critical realist philosophy. First, I present the IRR (Inflation-Recession-Recovery), a process theory that explains the outcomes of IT-induced change by an increase in complexity, employees’ adaptation behavior and effective use. The model was developed through a longitudinal case study at a financial services firm over the period of two years. Then, I provide deeper insights on the concepts of adaptation and learning by suggesting, operationalizing, and testing a variance-theoretical research model of social and ambidextrous knowing towards effective use. In sum, I find that structural complexity is an important explanatory factor in employees’ adaptation behavior towards effective use. In turn, adaptation and learning can be well explained by mechanisms of exploration, exploitation and communication in work systems.
Two new Cymatopleura taxa (Bacillariophyta) from Xinjiang, China with slightly twisted frustules

Field: Agricultural and Biological Sciences (Life Sciences)

Two new species of the diatom genus Cymatopleura, Cymatopleura aquastudia and Cymatopleura xinjiangiana, that have torsion about the apical axis of the valves, are reported from Xinjiang Region, China, using light and scanning electron microscopy.The valves of Cymatopleura aquastudia sp.nov.exhibit torsion about the apical axis, are heteropolar, and are slightly constricted at the margin in the middle of the valves.These characters differentiate it from morphologically similar taxa in the genus, e.g. C. solea (Brébisson) W. Smith and C. spiralis Behning in Rauschenbach et Behning.The valves of Cymatopleura xinjiangiana sp.nov.also exhibit torsion about the apical axis, but are small and have curved ridges at both ends and rounded apices that are protracted at the wider ends.These features distinguish C. xinjiangiana from C. cochlea Brun and C. elliptica f. spiralis Boyer.These two new taxa help to demonstrate the unique nature of the freshwater diatom flora from Xinjiang Region, China.
Livelihood and Job Creation

Field: Social Sciences (Social Sciences)

Livelihood and job creation have long \n been critical challenges to disaster recovery. Following the \n Great East Japan Earthquake (GEJE), the Japanese government \n launched an innovative cash-for-work (CFW) project, hiring \n more than 31,700 jobless people to work not only on \n reconstruction, but also on clerical and support work for \n affected people. This allowed it to reach out to women and \n the elderly, vulnerable groups that were traditionally \n excluded from schemes focusing primarily on manual work. \n This report gives findings; lessons; and recommendations for \n developing countries.
Local Volatility Framework

Field: Economics, Econometrics and Finance (Social Sciences)

In derivative pricing and hedging, one of the most crucial components is the volatility smile/skew modelling. This chapter first summarizes the key local volatility stripping formulation, illustrating the inter-relationships among the call option, implied volatility and local volatility. It then describes how to implement the smile/skew with Partial Differential Equation incorporating the local volatilities, and how to deal with discrete dividends. Monte Carlo simulation and pricing in the local volatility framework requires the small step approach. Both Markov terminal mapping and Copula terminal mapping methodology use large step Monte Carlo to avoid the needs of small steps typically required in the local volatility framework. Given an implied volatility surface, a local volatility surface can be easily calculated by using the local volatility stripper. The most likely path concept is useful in the context of obtaining implied volatility from local volatility in the presence of volatility smile/skew.
II. Nationalism In The Middle Ages

Field: Arts and Humanities (Social Sciences)

At an International Historical Congress of some years ago, one speaker explained that, so long as Europe had possessed one Church and one learned language (the Latin), nationalism was suppressed. This dictum received both contradiction and support; but the occasion was unsuited for any but the most superficial discussion. Ever since, however, I have noted passages which seemed to bear upon this important question; and I print them here, with the minimum of comment, by way of assistance to other students who may find time and inclination to pursue the matter further. Professor Marcel Handelsman of Warsaw has surveyed the subject, in brief, with a refinement of philosophical analysis to which I make no pretence. I try to use the term nationalism consistently within my own rough limits, but without attempt at scientific definition. My main object is to present evidence for the reader's judgment, without disguising the direction in which I lean myself: evidence varying a good deal in cogency from case to case, but with variations which any careful reader can estimate. Only thus can one start any really fruitful discussion. The multiplicity of indications collected in this comparatively short time convinces me that these are no more than the merest fraction of that which might be revealed by a concentrated search; but even this fraction may be enough to give a general idea of the whole.
Numerical Study on the Cavitation Characteristics of Micro Automotive Electronic Pumps under Thermodynamic Effect

Field: Engineering (Physical Sciences)

In order to study the influence of thermodynamic effects on the cavitation performance of hydromechanics, the Singhal cavitation model was modified considering the influence of the thermo-dynamic effects, and the modified cavitation model was written into CFX using the CEL language. Numerical simulation of the cavitation full flow field at different temperatures (25 °C, 50 °C and 70 °C) was carried out with the automotive electronic water pump as the research object. The results show that the variation trend of the external characteristic simulation and experimental values is the same at all flow rates, and the calculation accuracy meets the subsequent cavitation demand. With the increase in temperature, the low-pressure area inside the automotive electronic pump’s impeller decreases. NPSHr decreases and the cavitation resistance is enhanced. During the process of no cavitation to cavitation, the maximum pressure pulsation amplitude in the impeller channel gradually increases. The generation and collapse of cavitations cause the change of pressure pulsation in the internal flow field, causing pump vibration.
Introduction. Institution, Culture, And Social Stratification: Towards A Comparative Study Of Chinese Societies

Field: Social Sciences (Social Sciences)

Social stratification research is an intrinsically international and comparative enterprise. Institutional factors are often intertwined with cultural factors. The cultural factors are particularly relevant with respect to education, gender inequality, and family resource distribution, intergenerational relationships, and perceptions of opportunity. Chu, Xie and Yu (2006) modified the theory on the sibship size and educational outcome, and explained the unusual high-order interaction involving sibship size, gender, birth density, and seniority within the context of Taiwan's (Chinese) patriarchal culture, in which families typically favor boys over girls. Over the past decades, mainland China, Hong Kong and Taiwan have been undergoing dramatic economic and social changes. Sociological studies of inequality in China have flourished over the past few decades. More attention has been paid to the unique pattern of inequality shaped by Chinese socialist institutions such as the hukou system that created the rural-urban divide and the danwei segmentation in the urban sector. Keywords: Chinese societies; educational systems; Hong Kong; institutions; social stratification; Taiwan's patriarchal culture
Design of a Cobalt‐Free Maraging Steel with Ultra‐High Strength of 2.3 GPa Through Additive Manufacturing

Field: Materials Science (Physical Sciences)

Abstract Additive manufacturing (AM) is a revolutionary technology that enables the production of components with complex geometries and exceptional properties, which has attracted significant research interest. However, one potential challenge associated with additive manufacturing is its increased susceptibility to cracking resulting from the incorporation of high alloying elements. Furthermore, the formation of brittle Laves phases is frequently observed in cobalt‐containing maraging steels, which significantly compromises the ductility of these materials following heat treatment. Here, we demonstrate that by minimizing the crack susceptibility of the steel and introducing high‐density Ni 3 Ti and NiAl nanoprecipitates with a core‐shell structure, these challenges are simultaneously addressed. The cobalt‐free maraging steel, with a composition of Fe‐18.5Ni‐4.6Mo‐1.5Ti‐0.9Al‐0.05C‐0.01Y, is computationally designed to achieve high crack resistance and martensite start temperature. The alloy exhibits a transition from columnar to equiaxed grains and a uniform elemental distribution after printing. After aging, it achieves exceptional mechanical properties, with a tensile strength of 2.3 GPa and an elongation of 5.7%, making it a more promising alternative to conventional alloys. This study provides a potential avenue toward the design of cost‐effective, high‐performance, and sustainable alloys for additive manufacturing.
Comparing intercultural competence in lower secondary English and French classrooms in Norway: An overview study

Field: Arts and Humanities (Social Sciences)

The purpose of this study is to compare and analyze evidence of intercultural competence across 22 lower secondary English-as-a-second-language and French-as-a-foreign-language classrooms in Norway based on video observations of naturally occurring instruction. We recorded minimum four consecutive lessons in each classroom across two school years, totaling 90 lessons. Research on intercultural competence in second and foreign language classrooms has involved analyses of curricula, textbooks, literary texts in class, and intervention studies, but few scholars have observed naturally occurring instruction. Even fewer studies have used video observations to compare language subjects. This study aims to fill this gap by providing an overview of how intercultural competence is addressed in English and French instruction and identifying similarities and differences between the two subjects. Using the model elaborated in the Reference Framework of Competences for Democratic Culture (RFCDC) as an analytical lens, we found that the model’s area knowledge and critical understanding was most prominent in both subjects and that cultural stereotypes both occurred and were challenged by students across subjects. However, we found more, and more varied, evidence of intercultural competence in the English classrooms, where topics were studied in-depth, whereas the French classes often studied an array of topics more superficially.