jimnoneill/paper-to-field-training huggingface dataset:
Determination of azithromycin heteroresistant Campylobacter jejuni in traveler's diarrhea

Field: Immunology and Microbiology (Life Sciences)

Campylobacter is the most common cause of traveler's diarrhea (TD) and human bacterial gastroenteritis. A heteroresistant Campylobacter jejuni (C. jejuni) isolate, identified by microbiological methods and characterized with molecular techniques, was obtained from a traveler in Nepal suffering TD. The presence of atypical colonies within the clear zone of inhibition was the first evidence of an atypical phenotype, leading to additional characterization of this heteroresistant strain. Antimicrobial susceptibility testing (AST) and population analysis profiling (PAP) demonstrated heteroresistance to azithromycin (AZM), a first-line antibiotic treatment for Campylobacter infections. Molecular analysis indicated a point mutation occurred on the 23S rRNA gene at the A2075G transitions, and the number of mutated gene copies was proportional to AZM resistance. Heteroresistant C. jejuni subpopulations from acute TD are likely underestimated, which may lead to treatment failures, as was the case for this patient. The presence of a heteroresistant strain in a high antibiotic environment may select for additional drug resistance and enable distribution into hospital and local communities.
Immune Function and Psychological Factors in Patients With Coronary Heart Disease (I)

Field: Medicine (Health Sciences)

As part of studies on the effects, especially the preventive effects, of exercise and psychological factors on cardiovascular diseases, the association between psychological tendencies and immune response was evaluated in patients with coronary heart disease who were receiving exercise therapy. The Pearson's product-moment correlation coefficients between natural killer (NK) cell activity and various psychological scales were obtained. For the Moudsley Personality Inventory, NK cell activity had a significant positive correlation with the extraversion scale and a significant negative correlation with the neuroticism scale. NK cell activity also had a significant positive correlation with the playful humor scale and a significantly negative correlation with the Self-rating Depression Scale. The positive correlation of NK cell activity with the extraversion scale and the humor scale and its negative correlation with the neuroticism scale suggest an association between a positive-feeling tendency and high NK cell activity. The negative correlations of NK activity with the depression scale and neuroticism scale indicate that decreased or excessive expression of feelings inhibits NK cell activity. Thus, high NK activity appears to be associated with optimal expression of feelings.
Comparative transcriptome to reveal the drought tolerance mechanism in hexaploid <i>Ipomoea trifida</i>

Field: Agricultural and Biological Sciences (Life Sciences)

Hexaploid Ipomoea trifida ( I.trifida ), a wild relative of sweetpotato[ Ipomoea batatas (L.) Lam.], has plentiful superior genes and a variety of anti-adversity characteristics genetically, and used as a distant hybridization materials in sweetpotato breeding. However, insufficient transcriptomic and genomic resources of hexaploid I.trifida are available for understanding the molecular mechanism underlying drought tolerance. In this study, we are the first to report a reference transcriptome using leaf, stem and root tissues under drought-stressed condition from hexaploid I.trifida , which is helpful to generate a large number of transcripts associated with drought tolerance for gene discovery. In this study, a total of 191,231, 226,262, and 171,841 contigs with a mean length of 1,100, 1,038 and 1,106 bp were obtained from the three tissues, respectively. In our assembled sequences, 62.38%, 50.08% and 47.76% of all contigs in the three tissues could be annotated to the nr database. Based on the Gene ontology (GO) analysis, 39,193, 49,997 and 34,887 contigs in leaves, roots and stems could assign with GO terms, and totaled 69 contigs up-regulated expression. In the annotated genes, we identified six transcription factors and two genes involved in drought-stress responses. Furthermore, the gene expression profiles of 15 putative genes associated with drought tolerance were analyzed to verify the reliability of the transcriptome using quantitative real-time PCR (qRT-PCR). These results provide a foundation for understanding the molecular mechanisms underlying drought stress of hexaploid I.trifida , and promoting its further utilization in sweetpotato breeding.
Quantitative consensus of supervised learners for diffuse lung parenchymal HRCT patterns

Field: Computer Science (Physical Sciences)

Automated lung parenchymal classification usually relies on supervised learning of expert chosen regions representative of the visually differentiable HRCT patterns specific to different pathologies (eg. emphysema, ground glass, honey combing, reticular and normal). Considering the elusiveness of a single most discriminating similarity measure, a plurality of weak learners can be combined to improve the machine learnability. Though a number of quantitative combination strategies exist, their efficacy is data and domain dependent. In this paper, we investigate multiple (N=12) quantitative consensus approaches to combine the clusters obtained with multiple (n=33) probability density-based similarity measures. Our study shows that hypergraph based meta-clustering and probabilistic clustering provides optimal expert-metric agreement.
Alan Bullock: historian, social democrat and chairman

Field: Arts and Humanities (Social Sciences)

This study considers the influence on British education (particularly schools) of Alan Bullock, Vice‐Chancellor of Oxford University from 1969 to 1973 and distinguished contemporary historian. It quotes extensively from Bullock’s own writings, including his developing personal views on education, and reflections on his own experiences. Following a brief biographical section, the paper reviews his work as chair of Government committees and advisory bodies, notably the Schools Council and the eponymous ‘Bullock Committee’ to consider all aspects of the teaching of English. These experiences contributed to his increasing disillusion with formal political power structures as a means of bringing about social change. I examine Bullock’s long period as a dominant figure in the administration of the University, and the consequences for schools of the changes which occurred over that time, especially the move towards admissions policies based almost entirely upon academic merit, and towards becoming a leading scientific university. St Catherine’s College, which he founded, played a significant part in these changes. Bullock’s personal views on the need to offer in schools a broader education, which would be attractive to young people searching for values of their own, were developed in his later writings and are briefly summarised. The paper speculates that he would not have been happy with the competitive and measurement‐oriented system of today.
Introduction

Field: Arts and Humanities (Social Sciences)

Portugal is a small nation with a great history. Mariners and missionaries from this little country were in the forefront of European expansion from the fifteenth century onwards and helped establish a colonial enterprise that in its extent and longevity has few rivals in history. Many of the monumental voyages of discovery that thrust European power and influence into exotic and unknown lands were led by courageous Portuguese sailors like Vasco da Gama and Fernão de Magalhães (Magellan), whose attempted circumnavigation of the earth ranks him "as the first navigator of ancient or modern times, and his voyage the greatest single human achievement on the sea."1 Under the banner of Portugal, great ecclesiastical figures such as Saint Francis Xavier (a Spaniard) and Father Manuel da Nóbrega carried European beliefs and culture to the farthest reaches of the globe. During the sixteenth century, Lisbon became one of the world's greatest commercial centers, sharing with Seville the role of principal entrepôt for products brought from the Far East and the recently discovered American continents. Although this splendid era of expansion and commerce lasted less than a century before larger, more advanced European economies surpassed that of Portugal, the country eventually regained a measure of its past glories during the eighteenth century, an age that was certainly gilded, if not golden.KeywordsSmall NationMother CountryArtistic LegacyPast GloryColonial EnterpriseThese keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.
Extrapolation results on variable exponent grand Lebesgue space with Bp(·)$B_{p(\cdot)}$ weights

Field: Mathematics (Physical Sciences)

Abstract In this paper, we study Rubio de Francia extrapolation theorems in the framework of the variable grand Lebesgue spaces with weights. As an application of the extrapolation theorems, we prove the boundedness of the Hardy averaging operator and the fractional Riemann Liouville transform for nonnegative and nonincreasing measurable functions. Some structural properties of the weighted grand Lebesgue spaces with variable exponent are also investigated.
A Multi-Scale Flood Monitoring System Based on Fully Automatic MODIS and TerraSAR-X Processing Chains

Field: Environmental Science (Physical Sciences)

A two-component fully automated flood monitoring system is described and evaluated. This is a result of combining two individual flood services that are currently under development at DLR’s (German Aerospace Center) Center for Satellite based Crisis Information (ZKI) to rapidly support disaster management activities. A first-phase monitoring component of the system systematically detects potential flood events on a continental scale using daily-acquired medium spatial resolution optical data from the Moderate Resolution Imaging Spectroradiometer (MODIS). A threshold set controls the activation of the second-phase crisis component of the system, which derives flood information at higher spatial detail using a Synthetic Aperture Radar (SAR) based satellite mission (TerraSAR-X). The proposed activation procedure finds use in the identification of flood situations in different spatial resolutions and in the time-critical and on demand programming of SAR satellite acquisitions at an early stage of an evolving flood situation. The automated processing chains of the MODIS (MFS) and the TerraSAR-X Flood Service (TFS) include data pre-processing, the computation and adaptation of global auxiliary data, thematic classification, and the subsequent dissemination of flood maps using an interactive web-client. The system is operationally demonstrated and evaluated via the monitoring two recent flood events in Russia 2013 and Albania/Montenegro 2013.
Scale‐Up Production of High‐Quality Reduced Graphene Oxide via Microwave Assistance

Field: Materials Science (Physical Sciences)

Abstract Microwave reduction of graphene oxide (GO) holds significant potential for producing high‐quality reduced graphene oxide (rGO). However, due to the undeciphered underlying mechanism of microwave‐assisted GO reduction, scalable batch preparation using this method has not yet been achieved. Here, high‐quality microwave‐reduced graphene oxide (MrGO) is prepared using a single‐mode cavity (SMC) microwave reactor by modulating the microwave responsiveness of GO precursors. The complete reaction pathway is elucidated via optical emission spectroscopy (OES), revealing that oxygen removal occurs simultaneously with the consumption of carbon radicals, effectively repairing vacancy defects within seconds. Furthermore, an automated microwave system is developed, enabling stable batch production of MrGO with a daily output exceeding 1 kg. LiFePO4 (LFP) cathode coating on the MrGO modified Al foil (LFP‐Al@MrGO) delivers high specific capacities of 188 mAh g −1 at 0.1C, far exceeding LFP‐Al at 25 °C. Even at −25 °C, it still shows a 95.2% capacity retention rate for 1000 cycles. Moreover, the resulting waterborne polyurethane (WPU)/MrGO composite film, with a thickness of 0.35 mm, demonstrates an electromagnetic interference (EMI) shielding effectiveness of 68.8 dB. This study presents a large‐scale, low‐cost, and sustainable MrGO production, providing an efficient potential application in lithium‐ion battery (LIBs) systems and EMI shielding.
Polar Lattices for Lossy Compression

Field: Computer Science (Physical Sciences)

Polar lattices, which are constructed from polar codes, have recently been proved to be able to achieve the capacity of the additive white Gaussian noise (AWGN) channel. In this work, we propose a new construction of polar lattices to solve the dual problem, i.e., achieving the rate-distortion bound of a memoryless Gaussian source, which means that polar lattices can also be good for the lossy compression of continuous sources. The structure of the proposed polar lattices enables us to integrate the post-entropy coding process into the lattice quantizer, which simplifies the quantization process. The overall complexity of encoding and decoding complexity is $O(N \log^2 N)$ for a sub-exponentially decaying excess distortion. Moreover, the nesting structure of polar lattices further provides solutions for some multi-terminal coding problems. The Wyner-Ziv coding problem for a Gaussian source can be solved by an AWGN capacity-achieving polar lattice nested in a rate-distortion bound achieving one, and the Gelfand-Pinsker problem can be solved in a reversed manner.
Progress in snake venom proteomics research

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

The main approaches,the recent achievements and the present problems in snake venomics research were summarized in this paper. In recent years,the elucidation of the panorama of snake venom composition by utilizing high-throughput proteomic approaches has become a hotspot at the field of proteomics research.The protocols for snake venomics studies involve fractionation of the crude venom,followed by proteomic characterization and bioinformatics analysis.Methods for crude venom separation mainly include Two-dimensional gel electrophoresis(2-DE),Gel filtration and RP-HPLC;Proteomic characterization consists of Matrix-assisted laser desorption/ionization mass spectrometry(MALDI-TOF MS),Liquid chromatography and tandem mass spectrometry(LC-MS/MS),Electron spray ionization-tandem mass spectrometry(ESI-MS/MS) and Electron spray ionization-Fourier transform ion cyclotron resonance-mass spectrometry(ESI-FTICR MS);Bioinformatics identification mostly involves BLAST query of peptides interpreted by utilizing Mascot or MS-Fit search engine on protein specific internet sites.Up to now,based on proteomics approaches,venomes from more than one hundred species(subspecies) of fifty-eight Genus among three families(Elapidae,Colubridae and Viperidae) have been studied and more than ten protein families have been identified.These findings will undoubtedly contribute to a deeper understanding of snake venom evolution and diversification,the mechanism of the envenomation and the design of new drugs in search of leading compounds.In the future for snake venomics research,related high-throughput approaches for absolute quantification of snake venome and characterization of identified functional proteins remain to be developed.
A survey on the psychological impact and access to health care of thyroid patients during the first SARS‐COV‐2 lockdown

Field: Medicine (Health Sciences)

Abstract Objective Information on the impact of SARS‐COV‐2 on the daily life of thyroid patients during lockdown is sparse. The main objective was explorative, focusing on how SARS‐COV‐2 affected thyroid patients. Design Cross‐sectional, questionnaire‐based, using an online platform. Patients Patients >18 years with a history of thyroid disease. Measurements Demographic data, psychological impact of SARS‐COV‐2, medical care during the pandemic. Results Valid responses were received from 609 responders. The median age was 50 years, 94% were female and 98.5% were UK residents. The commonest diagnosis was primary hypothyroidism (52.2%). Negative psychological effects following the lockdown were reported by 45.6%–58.7%. Cancellations of appointments with thyroid specialists were reported by 43.8%, although cancellations of thyroid investigations and treatments were relatively infrequent (12.9%–14.1%). Overall satisfaction rates for thyroid services were low (satisfaction score 40.1–42.8 out of 100), but nearly 80% were satisfied with remote consultations. Responder ratings of online information sources about SARS‐COV‐2 and thyroid diseases were lowest for government sites. Unmet needs during lockdown were: more remote access to thyroid specialists, more online information in ‘plain English’, and psychological support. In multivariate analyses, younger age, female gender, history of depression, hyperthyroidism, not having contracted SARS‐COV‐2 and multiple comorbidities were risk factors for a negative psychological impact of lockdown. Conclusions This survey identified a significant negative impact of SARS‐COV‐2 and lockdown on psychological wellbeing, particularly in some groups of patients defined by demographic factors, history of hyperthyroidism and comorbidities. Low satisfaction with healthcare services among thyroid patients was noted, but remote consultations were rated favourably.
Next generation sequencing data in the phylogenetic relationships of the genus Molossus (Chiroptera, Molossidae)

Field: Agricultural and Biological Sciences (Life Sciences)

(Uploaded by Plazi for the Bat Literature Project) The mastiff bat Molossus is a broadly distributed genus within the family Molossidae. Molossus includes groups of species that are either morphologically or genetically very similar, rendering the taxonomy of this genus confusing and unstable. In this paper, we provide inferred phylogenetic relationships of Molossus based on the genotype by sequencing approach from 189 specimens of three species of New World mastiff bats (Molossus, Promops, and Eumops). We also present data on divergent tree topologies produced by alignments using de novo and reference genome approaches and distinct phylogenetic methods (maximum likelihood and coalescent approaches). These data provide the first highly resolved phylogenetic tree for Molossus, not recovered by previous studies using Sanger sequencing. Our dataset brings new insights on relationships among species and show how different approaches might affect phylogenetic resolution and topologies.
An Adaptive Prognostic Approach via Nonlinear Degradation Modeling: Application to Battery Data

Field: Decision Sciences (Social Sciences)

Remaining useful life (RUL) estimation via degradation modeling is considered as one of the most central components in prognostics and health management. Current RUL estimation studies mainly focus on linear stochastic models, and the results under nonlinear models are relatively limited in literature. Even in nonlinear degradation modeling, the estimated RUL is aimed at a population of systems of the same type or depend only on the current degradation observation. In this paper, an adaptive and nonlinear prognostic model is presented to estimate RUL using a system's history of the observed data to date. Specifically, a general nonlinear stochastic process with a time-dependent drift coefficient is first adopted to characterize the dynamics and nonlinearity of the degradation process. In order to render the RUL estimation depending on the degradation history to date, a state-space model is constructed, and Kalman filtering is applied to update one key parameter in the drifting function through treating this parameter as an unobserved state variable. To update the hidden state and other parameters in the state-space model simultaneously and recursively, the expectation maximization algorithm is used in conjunction with Kalman smoother to achieve this aim. The probability density function of the estimated RUL is derived with an explicit form, and some commonly used results under linear models turn out to be its special cases. Finally, the implementation of the presented approach is illustrated by numerical simulations, and an application for estimating the RUL of lithium-ion batteries is used to demonstrate the superiority of the method.
A DNA-binding protein with specificity for pur genes in Escherichia coli.

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

A DNA-binding protein was isolated from Escherichia coli using a procedure designed for selective enrichment of regulatory proteins. In this procedure, a multicopy bacterial plasmid carrying a purE operon was used to sequester and mobilize the putative regulatory protein for pur genes. Purification of the protein from a plasmid-enriched lysate was obtained by precipitation with polyethylene glycol, elution from the precipitate with high salt and fractionation by phosphocellulose, and AMP affinity chromatography. Analysis of DNA binding by nitrocellulose filter assays showed that binding of the protein required the presence of pur genes and was either ATP dependent for some genes (purE, purA) or GTP dependent for others (purF, purI). Plasmid DNA carrying the guaAB operon did not bind the protein.
Regulation of the formation of tumor cell pseudopodia by the Na+/H+ exchanger NHE1

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

ABSTRACT The Na+/H+ exchanger NHE1 is involved in intracellular pH homeostasis and cell volume regulation and accumulates with actin in the lamellipodia of fibroblasts. In order to determine the role of NHE1 following epithelial transformation and the acquisition of motile and invasive properties, we studied NHE1 expression in polarized MDCK cells, Moloney Sarcoma virus (MSV) transformed MDCK cells and an invasive MSV-MDCK cell variant (MSV-MDCK-INV). Expression of NHE1 was significantly increased in MSV-MDCK-INV cells relative to MSV-MDCK and MDCK cells. NHE1 was localized with β-actin to the tips of MSV-MDCK-INV cell pseudopodia by immunofluorescence. Sensitivity of NHE1-mediated 22Na uptake to ethylisopropylamiloride, a specific inhibitor of NHE1, was increased in MSV-MDCK cells relative to MDCK cells. Changes in intracellular pH induced upon EIPA treatment were also of higher magnitude in MSV-MDCK and MSV-MDCK-INV cells compared to wild-type MDCK cells, especially in Hepes-buffered DMEM medium. Inhibition of NHE1 by 50 μM ethylisopropylamiloride induced the disassembly of actin stress fibers and redistribution of the actin cytoskeleton in all cell types. However, in MSV-MDCK-INV cells, the effect of ethylisopropylamiloride treatment was more pronounced and associated with the increased reversible detachment of the cells from the substrate. Videomicroscopy of MSV-MDCK-INV cells revealed that within 20 minutes of addition, ethylisopropylamiloride induced pseudopodial retraction and inhibited cell motility. The ability of ethylisopropylamiloride to prevent nocodazole-induced formation of actin stress fibers in MSV-MDCK cells was more pronounced in Hepes medium relative to NaHCO3 medium, showing that NHE1 can regulate actin stress fiber assembly in transformed MSV-MDCK cells via its intracellular pH regulatory effect. These results implicate NHE1 in the regulation of the actin cytoskeleton dynamics necessary for the adhesion and pseudopodial protrusion of motile, invasive tumor cells.