jimnoneill/paper-to-field-training huggingface dataset:
Mining genome traits that determine the different gut colonization potential of Lactobacillus and Bifidobacterium species

Although the beneficial effects of probiotics are likely to be associated with their ability to colonize the gut, little is known about the characteristics of good colonizers. In a systematic analysis of the comparative genomics, we tried to elucidate the genomic contents that account for the distinct host adaptability patterns of Lactobacillus and Bifidobacterium species. The Bifidobacterium species, with species-level phylogenetic structures affected by recombination among strains, broad mucin-foraging activity, and dietary-fibre-degrading ability, represented niche conservatism and tended to be host-adapted. The Lactobacillus species stretched across three lifestyles, namely free-living, nomadic and host-adapted, as characterized by the variations of bacterial occurrence time, guanine–cytosine (GC) content and genome size, evolution event frequency, and the presence of human-adapted bacterial genes. The numbers and activity of host-adapted factors, such as bile salt hydrolase and intestinal tissue-anchored elements, were distinctly distributed among the three lifestyles. The strains of the three lifestyles could be separated with such a collection of colonization-related genomic content (genes, genome size and GC content). Thus, our work provided valuable information for rational selection and gut engraftment prediction of probiotics. Here, we have found many interesting predictive results for bacterial gut fitness, which will be validated in vitro and in vivo .

Topic: Probiotics and Fermented Foods
Subfield: Food Science
Field: Agricultural and Biological Sciences
Domain: Life Sciences
Thalesian Lessons: Mad Astronomers in British Fiction of the Long Eighteenth Century

Taking its cue from the representation of astronomy in Book Three of Gulliver's Travels and versions of Thales of Miletus' stargazing accident circulating in eighteenth-century England, this essay examines 'mad' astronomers in fictions of the long eighteenth century. In Margaret Cavendish's The Blazing World, Swift's Voyage to Laputa, Charlotte Lennox's The Female Quixote, Dr Johnson's Rasselas, and Mary Shelley's The Last Man, it explores the links that stargazers establish between reason, represented by the practice of astronomy as a 'pure' observational science, and the imagination, represented by madness and fiction. Either overly cerebral or motivated by the most basic drives, fictional astronomers hold up for consideration various kinds of madness that offer insight into the developing relationship between science and the imagination, and in particular the legitimacy and dangers of fictionalizing.

Topic: History of Science and Medicine
Subfield: History and Philosophy of Science
Field: Arts and Humanities
Domain: Social Sciences
Janthinobacterium aestuarii sp. nov., a novel violacein-producing bacterium isolated from the Tidal Basin in Washington, D.C., USA

Strain TB1-E2-13 T was isolated from water collected from the Tidal Basin in Washington, D.C., USA, due to the bright purple colour of its colonies, and was taxonomically evaluated with a polyphasic approach. Comparison of a partial 16S rRNA gene sequence found that strain TB1-E2-13 T was most similar to species in the Janthinobacterium genus. For more precise taxonomic inference, a phylogenomic analysis was conducted and indicated that strain TB1-E2-13 T was most closely related to Janthinobacterium lividum , ‘ Janthinobacterium kumbetense ’, Janthinobacterium rivuli and Janthinobacterium violaceinigrum . Analyses of genomic indices found that pairwise comparisons between strain TB1-E2-13 T and other members of the Janthinobacterium genus returned values below the threshold of species novelty. Based on a polyphasic characterization and identifying differences in genomic and taxonomic data, strain TB1-E2-13 T represents a novel species, for which the name Janthinobacterium aestuarii sp. nov. is proposed. The type strain is TB1-E2-13 T (=ATCC TSD-339 T =JCM 36076 T ).

Topic: Microbial Metabolism and Applications
Subfield: Biotechnology
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
Assessing the sensitivity of consumption expenditure to inflation sentiment in post-communist economies

The aim of this article is to examine the influence of inflation sentiment on aggregate consumption. The study adds to the existing literature by i) emphasising the role of inflation perceptions and expectations in determining consumption patterns, ii) using structural VAR methodology that has not yet been applied in consumer studies, iii) employing an extensive dataset of eight individual post-communist countries (Czech Republic, Estonia, Hungary, Lithuania, Poland, Romania, Slovakia and Slovenia). Using innovation analysis it is shown that the theoretically expected conclusions are valid: consumers instantaneously decrease their consumption expenditure in response to shocks in perceived inflation, while their reaction to shocks in near-term inflation expectations is an abrupt (but temporary) consumption boost.

Topic: Market Dynamics and Volatility
Subfield: Economics and Econometrics
Field: Economics, Econometrics and Finance
Domain: Social Sciences
[Use of rapid electrochemical methods for detection of bacteriuria in kidney transplant patients].

A total of 1299 urine samples from kidney-transplant patients were tested for bacteriuria using the electrochemical rapid procedure. For germ counts of more than 10(5)/ml the registration rate was 97.6% after incubation for 1 hour and 100% after 2 h, providing the patients were not under the influence of antibiotics at the time of examination. Bacteria inhibitors in the urine delayed the reaction so that an incubation period of 2-3 hours was necessary. The electrochemical rapid procedure proved to be unsuitable in cases where small quantities of germs are expected to be discharged.

Topic: Metabolism and Genetic Disorders
Subfield: Clinical Biochemistry
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
An engineering approach to knowledge acquisition by the interactive analysis of dictionary definitions

It has long been recognised that everyday dictionaries are a potential source of lexical and world knowledge of the type required by many Natural Language Processing (NLP) systems. This research presents a semi-automated approach to the extraction of rich semantic relationships from dictionary definitions. The definitions are taken from the recently published "Cambridge International Dictionary of English" (CIDE). The thesis illustrates how many of the innovative features of CIDE can be exploited during the knowledge acquisition process. The approach introduced in this thesis uses the LOLITA NLP system to extract and represent semantic relationships, along with a human operator to resolve the different forms of ambiguity which exist within dictionary definitions. Such a strategy combines the strengths of both participants in the acquisition process: automated procedures provide consistency in the construction of complex and inter-related semantic relationships, while the human participant can use his or her knowledge to determine the correct interpretation of a definition. This semi-automated strategy eliminates the weakness of many existing approaches because it guarantees feasibility and correctness: feasibility is ensured by exploiting LOLITA's existing NLP capabilities so that humans with minimal linguistic training can resolve the ambiguities within dictionary definitions; and correctness is ensured because incorrectly interpreted definitions can be manually eliminated. The feasibility and correctness of the solution is supported by the results of an evaluation which is presented in detail in the thesis.

Topic: Natural Language Processing Techniques
Subfield: Artificial Intelligence
Field: Computer Science
Domain: Physical Sciences
An Integrated Assessment Metamodel for Developing Adaptation Pathways for Sustainable Water Management in the Lower Rhine Delta

Water management is increasingly challenged by pressures from population&#13;\ngrowth, sea level rise and potential climate change. Moreover, these developments&#13;\nare highly uncertain and change over time. The challenge is to develop&#13;\nstrategies that are either robust - insensitive to the future - or flexible enough to&#13;\nadapt to changing conditions. Adaptation is not only determined by what is known&#13;\nor anticipated at present, but also by what will be experienced and learned while&#13;\nthe future unfolds, and by policy responses to social and water events. As a result,&#13;\nan adaptation pathway emerges. Exploring adaptation pathways into the future will&#13;\nprovide indispensable support to decisionmaking in achieving sustainable water&#13;\nmanagement. For a structured exploration of the various adaptation pathways, we&#13;\nare developing a computational model of the Rhine Delta in the Netherlands. With&#13;\nthis model, we will simulate an evolvement of the system wherein pressures influence&#13;\nthe water system state, and impacts on flood risk and water services such as&#13;\nagriculture and nature, which may then trigger a policy response. The result of this&#13;\ndynamic simulation is an adaptation pathway. The model should run fast enough&#13;\nto calculate many 100-year transient scenarios, representing the dominant processes&#13;\nand natural variability, and be able to implement various policy options. To&#13;\nenable such dynamic modelling we are developing an Integrated Assessment&#13;\nMetaModel (IAMM) using the technique of metamodelling. Metamodels are simple&#13;\naggregated models that approximate the behaviour of complex and detailed models.&#13;\nThe IAMM is simple in terms of process and spatial information, but complex&#13;\nin terms of time-series and policy response. The challenge is to capture enough&#13;\ndetail and process information ensuring an adequate model behavior for policy&#13;\nanalysis. We present the concept and describe for which situations - policy options&#13;\nand effects - the model can be used to support decisionmaking under uncertainty.

Topic: Complex Systems and Decision Making
Subfield: Management Science and Operations Research
Field: Decision Sciences
Domain: Social Sciences
A Broker-agent Based Computational Model in the Embedded Internet Systems

In company with the development of chips and the trends of Internet mobilization and personalization,embedded Internet system is concerned by more and more researchers. According to characteristics of embedded system, this paper presents a Browser-Broker/Agent/Server (B-A) computational model which tries to minimize data transmission volume, saves the limited bandwidth and improves the response time by applying static/dynamic cache management, page compression and protocol reduction. The experimental result proves the idea.

Topic: Mobile Agent-Based Network Management
Subfield: Computer Networks and Communications
Field: Computer Science
Domain: Physical Sciences
Optimal Kernel Parameters of Smooth-WindowedWigner-Ville Distribution for Power Quality Analysis

Bilinear time-frequency distributions (TFDs) are developed to represent time-varying signal jointly in time frequency
representation (TFR). The TFDs offer a good time and frequency resolution, are appropriate to analyze power quality signals that
consist of magnitude variation and multiple frequencies. However, the TFD suffers from cross-terms interferences because of their
bilinear structures. In this paper, smooth-windowed Wigner-Ville distribution (SWWVD) is used to analyze power quality signals. The
power quality signals are swell, sag, interruption, harmonic, interharmonic and transient. To get an accurate TFR, the parameters of
the separable kernel are estimated from the signal. A set of performance measures are defined and used to compare the TFR for
various kernel parameters.

Topic: Power Quality and Harmonics
Subfield: Electrical and Electronic Engineering
Field: Engineering
Domain: Physical Sciences
ANALISIS SOAL UJIAN AKHIR SEMESTER PADA MATA PELAJARAN IPA BERDASARKAN DIMENSI PROSES KOGNITIF TAKSONOMI ANDERSON DANKEMAMPUAN BERPIKIR KRITISDI SMP NEGERI 1 NUNUKAN SELATAN

The final exam is a summative evaluation applied by schools to measure student’s cognitive learning outcomes which are usually given in the form of tests. The analysis of each test item is expected to be useful to make improvements and refinement of the items that have been tested on students. The type of research is a qualitative descriptive study. The sample in this study were all manuscripts of final exam questions for natural science subjects of VII, VIII, and IX grades Negeri 1 Nunukan Selatan on 2018 Academic Year. Data collection is done by means of documentation and interviews. Data were analyzed according to operational verbs in the dimensions of Anderson's Taxonomy cognitive process and aspects of critical thinking skills. The results showed that (1) the distribution of the cognitive process dimensions of Anderson's Taxonomy in the questions was not evenly distributed, the questions were dominated by the dimensions of cognitive processes at levels C1, C2 and C3. The percentage of cognitive dimensions in VII grade namely C1 gained 44%, C2 gained 44% and C3 gained 12%. The VIII grade namely C1 gained 20%, C2 gained 46.7%, C3 gained 26.7% and C4 gained 6.7%. The IX grade namely C1 gained 2.8%, C2 gained 25.7%, C3 gained 42.8%, and C4 gained 28.5%; (2) the distribution of critical thinking skills aspects in the questions is also not evenly distributed, the questions are dominated in aspects 1 and aspect 2. The percentage of critical thinking skills aspects in VII grade is A1 gained 44% and A2 gained 56%. The VIII grade is A1 gained 46.7%, A2 gained 43.3% and A3 gained 10%. The IX grade is A1 gained 5.7%, A2 gained 48.5%, A3 gained 40% and A5 gained 5.7%. Keywords: Question, Cognitive, Anderson’s Taxonomy, Critical thinkingANALISIS SOAL UJIAN AKHIR SEMESTER PADA MATA PELAJARAN IPA BERDASARKAN DIMENSI PROSES KOGNITIF TAKSONOMI ANDERSON DANKEMAMPUAN BERPIKIR KRITISDI SMP NEGERI 1 NUNUKAN SELATAN

Topic: Education and Critical Thinking Development
Subfield: Education
Field: Social Sciences
Domain: Social Sciences
A novel multi-stage ensemble model with enhanced outlier adaptation for credit scoring

Nine datasets from the UC Irvine (UCI) machine learning repository, i.e., the Australian, Japanese, German (Asuncion &amp; Newman, 2007), Taiwan (Yeh &amp; Lien, 2009) and Polish credit datasets (Zięba et al., 2016) were adopted for the current study. The Polish credit datasets contain five datasets distinguished five classification cases that depend on the forecasting period (e.g., the Polish 1, the Polish 2, the Polish 3, the Polish 4 and the Polish 5). AER credit dataset (Greene, 2003), which is a credit card dataset for econometric analysis. Creator dataset, which is published in 2019 by a Chinese digital government services provider named Creator Information Technology Co., Ltd[1]. The Creator dataset contains the property rights, financial statements, and basic company information of 35960 Chinese companies. <br> [1] http://www.chinacreator.com/cn/

Topic: Financial Distress and Bankruptcy Prediction
Subfield: Accounting
Field: Business, Management and Accounting
Domain: Social Sciences
CCDC 140720: Experimental Crystal Structure Determination

An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

Topic: X-ray Diffraction in Crystallography
Subfield: Materials Chemistry
Field: Materials Science
Domain: Physical Sciences
Food: A Sensuous Matter of the Everyday : A sensorial exploration of material and bounded natures of mundane food practices

This thesis examines everyday food practices such as sensed by seven households in the city ofStockholm, Sweden. By sensuously exploring the acts of acquiring, preparing, cooking, eating,and wasting food, I analyze how food is a matter of olfactory, gustatory, auditory, tactile, andvisual significance, as much as matter per se. More specifically, I address relational andbounded aspects of food, looking at how ambient surroundings, presences of material andimmaterial factors, sensuously influence everyday experiences of food. Intrigued by the at onceinter-, extra-, and re-corporeal matters of food, I analytically position myself alongside Latour,Ingold, Douglas, and Bennett. In entertaining their theoretical lines of thoughts, using them asanalytical springboards, this thesis explores socio-material dimensions of food practices, as wellas corporeal dynamics of human-material encounters. Methodologically carried out by meansof sensuous ethnography, following Pink’s notion of participatory practice, I have during tenweeks of fieldwork—in people’s homes and in their frequented grocery stores—engaged mysenses to experientially sense the world of food, such as lived by them. In our conjoint sensorialexploration, taken-for-granted mundane understandings of what food constitutes and whatconstitutes it, have emerged as domestically diverse, bounded to sensuous perceptionsderivative of the past, carried out in the presents, and cor(po)related to the future. By surveyingsituated meanings of what is smelled when savored, tasted when flavored, seen when looked,and felt when touched, simultaneously as accounting for nonhuman matters salient to coursesof actions, the thesis remarks context-sensorial-imbued figurations of everyday food.

Topic: Culinary Culture and Tourism
Subfield: Food Science
Field: Agricultural and Biological Sciences
Domain: Life Sciences
Advances in Radio Science Iterative least squares method for global positioning system

Abstract. The efficient implementation of positioning algo-rithms is investigated for Global Positioning System (GPS). In order to do the positioning, the pseudoranges between the receiver and the satellites are required. The most commonly used algorithm for position computation from pseudoranges is non-linear Least Squares (LS) method. Linearization is done to convert the non-linear system of equations into an iterative procedure, which requires the solution of a linear system of equations in each iteration, i.e. linear LS method is applied iteratively. CORDIC-based approximate rotations are used while computing the QR decomposition for solv-ing the LS problem in each iteration. By choosing accu-racy of the approximation, e.g. with a chosen number of optimal CORDIC angles per rotation, the LS computation can be simplified. The accuracy of the positioning results is compared for various numbers of required iterations and various approximation accuracies using real GPS data. The results show that very coarse approximations are sufficient for reasonable positioning accuracy. Therefore, the presented method reduces the computational complexity significantly and is highly suited for hardware implementation.

Topic: GNSS positioning and interference
Subfield: Aerospace Engineering
Field: Engineering
Domain: Physical Sciences
An Experimental Study of Silicate-Polymer Gel Systems to Seal Shallow Water Flow and Lost Circulation Zones in Top Hole Drilling

Placement of silicate based gel systems is one of the oldest methods to seal such undesired zones. For this study, sodium-silicate based gel system is investigated experimentally. This gel system is deliberately delayed multi-component system mixed as a uniform liquid at the surface but desired to form strong gel where it is placed in the well. The experimentally analyzed system is composed of distilled water, sodiumsilicate solution, polymer solution, lost circulation materials, weighting agent and organic initiator. In this study, effect of these components on gel time, gel quality and gel strength at room temperature is investigated as a function of their concentration. To be able to compare gelation time of different compositions, gel time tests were performed by following the developed method in this study. Observation codes were defined to be able to compare the gel qualities of different compositions. For gel time and quality tests, sodium-silicate (SS) concentrations from 3.5% to 15% were studied and the concentrations between 7.5% and 10% were found as optimum. Gel time is getting higher as silicate-initiator ratio (SIR) increases for these optimum concentrations. It was also determined that, addition of polymers reduces the gel time and increases the elasticity of the resulting gels. Long term gelation process was investigated by monitoring turbidity (NTU) of the mixtures and plotting NTU versus time curves. Viscosity development curves obtained from rotational viscometer at various constant shear rates indicated reduced gelation times with increasing shear rate. Furthermore, by using modified High-Pressure, High-Temperature filter press cell, it was determined that, addition of lost circulation materials increases the extrusion pressure.

Topic: Drilling and Well Engineering
Subfield: Ocean Engineering
Field: Engineering
Domain: Physical Sciences
Objectives Should Dictate Methods in Managing Stream Habitat for Fish

Objectives are desired future results of management. Effective planning of stream habitat management begins with broad, long-term objectives, such as 'good fishing' and 'health of stream and riparian ecosystems,' which provide indefinite but fundamental guidance. Following from these is a continuum of intermediate and specific objectives, which are subordinate and contribute to attainment of the broad objectives. In habitat management, as in other fields, losing sight of (or never developing) broad objectives is common, often because of overorientation toward methods. Selection of methods should derive from objectives, not the other way around. Specific objectives, hence methods, while being consistent with broad objectives, should also be based on the fundamentals of ecology and physical science, on needs of the target species and of the ecosystem's full biotic community, on character of the specific stream and riparian area, and on values held by fishers. Fish abundance, angler satisfaction, and ecosystem health can probably be maximized and balanced with each other by promoting the physical and biological features and processes that occur and operate most often in nature - the stream attributes to which fish are adapted. As programs progress, objectives and methods can be improved. Objectives should be limited in number and mutually compatible, but a full range of objectives helps prioritize management phases and keeps managers aware of related parts of larger ecosystems; it is important to protect and restore floodplains and riparian zones before working on the channel. Channel stabilization is an objective that may often have been carried too far.

Topic: Fish Ecology and Management Studies
Subfield: Nature and Landscape Conservation
Field: Environmental Science
Domain: Physical Sciences