jimnoneill/paper-to-field-training huggingface dataset:
SH1264906.09FU

UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.

Topic: Genetic and Environmental Crop Studies
Subfield: Plant Science
Field: Agricultural and Biological Sciences
Domain: Life Sciences
Expression of coproporphyrinogen oxidase and synthesis of hemoglobin in human erythroleukemia K562 cells

Coproporphyrinogen oxidase (CPOX), the sixth enzyme in the heme‐biosynthetic pathway, catalyzes oxidative decarboxylation of coproporphyrinogen to protoporphyrinogen and is located in the intermembrane space of mitochondria. To clarify the importance of CPOX in the regulation of heme biosynthesis in erythroid cells, we established human erythroleukemia K562 cells stably expressing mouse CPOX. The CPOX cDNA‐transfected cells had sevenfold higher CPOX activity than cells transfected with vector only. Expression of ferrochelatase and heme content in the transfected cells increased slightly compared with the control. When K562 cells overexpressing CPOX were treated with δ‐aminolevulinic acid (ALA), most became benzidine‐positive without induction of the expression of CPOX or ferrochelatase, and the heme content was about twofold higher than that in ALA‐treated control cells. Increases in cellular heme concomitant with a marked induction of the expression of heme‐biosynthetic enzymes, including CPOX, ferrochelatase and erythroid‐specific δ‐aminolevulinic acid synthase, as well as of α‐globin synthesis, were observed when cells were treated with transforming growth factor (TGF)β1. These increases in the transfected cells were twice those in control cells, indicating that overexpression of CPOX enhanced induction of the differentiation of K562 cells mediated by TGFβ1 or ALA. Conversely, the transfection of antisense oligonucleotide to human CPOX mRNA into untreated and TGFβ1‐treated K562 cells led to a decrease in heme production compared with sense oligonucleotide‐transfected cells. These results suggest that CPOX plays an important role in the regulation of heme biosynthesis during erythroid differentiation.

Topic: Porphyrin Metabolism and Disorders
Subfield: Molecular Biology
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
Some nonlinear inverse relations of Bell polynomials via the Lagrange inversion formula

In this paper, by means of the classical Lagrange inversion formula, we establish a general nonlinear inverse relations which is a partial solution to the problem proposed in the paper [J. Wang, Nonlinear inverse relations for the Bell polynomials via the Lagrange inversion formula, J. Integer Seq., Vol. 22 (2019), Article 19.3.8. (https://cs.uwaterloo.ca/journals/JIS/VOL22/Wang/wang53.pdf). As applications of this inverse relation, we not only find a short proof of another nonlinear inverse relation due to Birmajer et al., but also set up a few convolution identities concerning the Mina polynomials.

Topic: Advanced Combinatorial Mathematics
Subfield: Discrete Mathematics and Combinatorics
Field: Mathematics
Domain: Physical Sciences
Convolutional Neural Networks for Automatic Threat Detection in Security X-Ray Images

In this paper we apply Convolutional Neural Networks (CNNs) to the task of automatic threat detection, specifically conventional explosives, in security X-ray scans of passenger baggage. We present the first results of utilizing CNNs for explosives detection, and introduce a dataset, the Passenger Baggage Object Database (PBOD), which can be used by researchers to develop new threat detection algorithms. Using state-of-the-art CNN models and taking advantage of the properties of the Xray scanner, we achieve reliable detection of threats, with the best model achieving an AUC of the ROC of 0.95. We also explore heatmaps as a visualization of the location of the threat.

Topic: Advanced X-ray and CT Imaging
Subfield: Biomedical Engineering
Field: Engineering
Domain: Physical Sciences
De novo Protein Structure Prediction by Coupling Contact With Distance Profile

De novo protein structure prediction is a challenging problem that requires both an accurate energy function and an efficient conformation sampling method. In this study, a de novo structure prediction method, named CoDiFold, is proposed. In CoDiFold, contacts and distance profiles are organically combined into the Rosetta low-resolution energy function to improve the accuracy of energy function. As a result, the correlation between energy and root mean square deviation (RMSD) is improved. In addition, a population-based multi-mutation strategy is designed to balance the exploration and exploitation of conformation space sampling. The average RMSD of the models generated by the proposed protocol is decreased by 49.24 and 45.21 percent in the test set with 43 proteins compared with those of Rosetta and QUARK de novo protocols, respectively. The results also demonstrate that the structures predicted by proposed CoDiFold are comparable to the state-of-the-art methods for the 10 FM targets of CASP13. The source code and executable versions are freely available at http://github.com/iobio-zjut/CoDiFold.

Topic: Protein Structure and Dynamics
Subfield: Molecular Biology
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
Genetic studies on .ALPHA.-amylase isozymes in wheat. III. Intraspecific variation in Aegilops squarrosa and birthplace of hexaploid wheat.

Fifty seven strains of KUSE (Kyoto University Scientific Expedition to The Karakoram and Hindukush) collection and three laboratory strains of Aegilops squarrosa were examined with respect to α-amylase isozymes of germinating seed. Seven zymogram patterns were identified, each of which consisted of a few isozyme bands most probably specified by the genes on chromosome 6D and only one by the gene on chromosome 7D. Among varieties of Ae. Squarrosa, var. typica was most variable, followed by var. strangulata. Variation in α-amylase isozymes, as in the other various characters, was most concentrated in the region of Gorgan, in decreasing order being the regions of Pahlavi, Tabriz and Tehran, and no variation in the other regions. From comparison of the zymograms between tetra- and hexaploid wheat, a particular zymogram pattern of α-amylase, Ams 3 was concluded as the one expected in the D genome donor to the main line of descent of hexaploid wheat. Ams 3 located most predominantly in the region of Gorgan, extending westwards along the south coast of Caspian sea up to Derbent, Caucasus. Therefore, it is most reasonable to consider that birthplace of hexaploid wheat should be extended to the south-east coast-land of Caspian sea from the area including south-west Caspian coast region and Transcaucasus, which the previous authors have indicated. On the other hand, discussion about independent origin of ssp. macha was made in view of the variant zymogram pattern.

Topic: Wheat and Barley Genetics and Pathology
Subfield: Plant Science
Field: Agricultural and Biological Sciences
Domain: Life Sciences
An examination of judicial independence in China

Purpose The purpose of this paper is to consider and evaluate judicial independence in China, through reviewing the value in its presence, assessing its current state in China and evaluating what the future holds for it. Design/methodology/approach The paper reviews the benefits of judicial independence in its support of the rule of law. Following this, an evaluation of the current independence of the judiciary in China is presented. The reforms of the judiciary in the Fourth Plenary Session and the outlook for judicial independence in China are assessed. Findings The paper finds that judicial independence in China cannot be said to exist, being vulnerable to influence from a variety of sources. There is, however, progress observed, and this is expected to continue. Originality/value This paper’s consideration of judicial independence in China and its outlook are framed with discussions of the relationships between judicial independence and the rule of law, and the Chinese state and the rule of law. The paper should thus contribute to discussion of the development trajectory of China in this important facet.

Topic: Judicial and Constitutional Studies
Subfield: Law
Field: Social Sciences
Domain: Social Sciences
Detection of Flares by Decrease in Physical Activity, Collected Using Wearable Activity Trackers in Rheumatoid Arthritis or Axial Spondyloarthritis: An Application of Machine Learning Analyses in Rheumatology

Objective Flares in rheumatoid arthritis (RA) and axial spondyloarthritis (SpA) may influence physical activity. The aim of this study was to assess longitudinally the association between patient‐reported flares and activity‐tracker–provided steps per minute, using machine learning. Methods This prospective observational study (ActConnect) included patients with definite RA or axial SpA. For a 3‐month time period, physical activity was assessed continuously by number of steps/minute, using a consumer grade activity tracker, and flares were self‐assessed weekly. Machine‐learning techniques were applied to the data set. After intrapatient normalization of the physical activity data, multiclass Bayesian methods were used to calculate sensitivities, specificities, and predictive values of the machine‐generated models of physical activity in order to predict patient‐reported flares. Results Overall, 155 patients (1,339 weekly flare assessments and 224,952 hours of physical activity assessments) were analyzed. The mean ± SD age for patients with RA (n = 82) was 48.9 ± 12.6 years and was 41.2 ± 10.3 years for those with axial SpA (n = 73). The mean ± SD disease duration was 10.5 ± 8.8 years for patients with RA and 10.8 ± 9.1 years for those with axial SpA. Fourteen patients with RA (17.1%) and 41 patients with axial SpA (56.2%) were male. Disease was well‐controlled (Disease Activity Score in 28 joints mean ± SD 2.2 ± 1.2; Bath Ankylosing Spondylitis Disease Activity Index score mean ± SD 3.1 ± 2.0), but flares were frequent (22.7% of all weekly assessments). The model generated by machine learning performed well against patient‐reported flares (mean sensitivity 96% [95% confidence interval (95% CI) 94–97%], mean specificity 97% [95% CI 96–97%], mean positive predictive value 91% [95% CI 88–96%], and negative predictive value 99% [95% CI 98–100%]). Sensitivity analyses were confirmatory. Conclusion Although these pilot findings will have to be confirmed, the correct detection of flares by machine‐learning processing of activity tracker data provides a framework for future studies of remote‐control monitoring of disease activity, with great precision and minimal patient burden.

Topic: Rheumatoid Arthritis Research and Therapies
Subfield: Rheumatology
Field: Medicine
Domain: Health Sciences
Impacts of Managerial Characteristics on the Export Performance of Small and Medium-sized Firms: Review and Implications

Previous research on export performance has been criticized for being a mosaic of autonomous endeavors and for a lack of theoretical development. Building upon extant models of export performance, a review and analysis of research on impacts of managerial characteristics on the export performance is developed and theoretical explanations are put forward. It is suggested that a multi-theory approach to explaining export performance is viable. Managerial behavior and perceptions for the SMEs from the review and synthesis of the literature are discussed.

Topic: International Business and FDI
Subfield: Strategy and Management
Field: Business, Management and Accounting
Domain: Social Sciences
Optical spectral transmission to monitor disease activity in arthritis patients: longitudinal follow-up comparison with clinical parameters

Abstract Objective To examine the longitudinal associations of optical spectral transmission (OST) with clinical inflammatory arthritis activity markers in order to investigate its potential in monitoring disease activity. Methods OST measurements were performed in 1312 wrist and finger joints of 60 patients with clinical suspicion of inflammatory activity, within the context of known rheumatic inflammatory diseases at two separate time intervals. In each time point, patients underwent additional clinical and laboratory examinations. The change of OST values was statistically compared with changes in clinical activity parameters like DAS28 and swollen joint counts (SJC). Additionally, the diagnostic performance of OST was assessed in comparison to a historic control group (2508 joints of 114 healthy subjects) using receiver operating characteristics (ROC). The relationships between OST values, clinical and laboratory parameters, as well as patient characteristics, were evaluated through correlation analyses. Results Mean OST scores were significantly higher in the inflammatory arthritis group compared with the control group (P &amp;lt; 0.001). OST correlated significantly with clinical activity markers like DAS28, SJC and TJC in both time points (all; P &amp;lt; 0.05). Longitudinal changes of OST values (ΔOST) were significantly associated with changes in DAS28 (ΔDAS28) (r = 0.377; P = 0.004) and ΔSJC (r = 0.488; P &amp;lt; 0.001) over the same time period. The area under the curve of the baseline receiver operating characteristic curve was 0.781 (95%CI 0.82–0.94). Conclusion OST was able to reliably assess disease activity and correlated longitudinally with arthritis activity markers, showing promising potential during monitoring of inflammatory arthritis.

Topic: Rheumatoid Arthritis Research and Therapies
Subfield: Rheumatology
Field: Medicine
Domain: Health Sciences
Within‐population Y‐linked genetic variation for lifespan in <i>Drosophila melanogaster</i>

Abstract The view that the Y chromosome is of little importance for phenotypic evolution stems from early studies of Drosophila melanogaster . This species’ Y chromosome contains only 13 protein‐coding genes, is almost entirely heterochromatic and is not necessary for male viability. Population genetic theory further suggests that non‐neutral variation can only be maintained at the Y chromosome under special circumstances. Yet, recent studies suggest that the D. melanogaster Y chromosome trans ‐regulates hundreds to thousands of X and autosomal genes. This finding suggests that the Y chromosome may play a far more active role in adaptive evolution than has previously been assumed. To evaluate the potential for the Y chromosome to contribute to phenotypic evolution from standing genetic variation, we test for Y‐linked variation in lifespan within a population of D. melanogaster . Assessing variation for lifespan provides a powerful test because lifespan (i) shows sexual dimorphism, which the Y is primarily predicted to contribute to, (ii) is influenced by many genes, which provides the Y with many potential regulatory targets and (iii) is sensitive to heterochromatin remodelling, a mechanism through which the Y chromosome is believed to regulate gene expression. Our results show a small but significant effect of the Y chromosome and thus suggest that the Y chromosome has the potential to respond to selection from standing genetic variation. Despite its small effect size, Y‐linked variation may still be important, in particular when evolution of sexual dimorphism is genetically constrained elsewhere in the genome.

Topic: Animal Behavior and Reproduction
Subfield: Ecology, Evolution, Behavior and Systematics
Field: Agricultural and Biological Sciences
Domain: Life Sciences
Active pulleys: magnetic resonance imaging of rectus muscle paths in tertiary gazes.

The APH prediction of coordinated anteroposterior shifting of EOM pulleys with gaze is quantitatively supported by changes in EOM path inflections among tertiary-gaze positions. Human rectus pulleys move to shift the ocular rotational axis to attain commutative behavior of the ocular motor plant.

Topic: Ophthalmology and Eye Disorders
Subfield: Pathology and Forensic Medicine
Field: Medicine
Domain: Health Sciences
Efficacy of Mitomycin c in Reducing the Recurrence of Urethral Stricture after Visual Internal Urethrotomy (VIU)

Urethral stricture remains one of the oldest known urologic diseases and also still a common problem with high morbidity.Recurrence rate of VIU is high in different studies ranging from 20% to 60%, the aim of this study was to assess the efficacy of MMC in reducing the recurrence of urethral stricture after VIU.Our consider incorporated 30 patients torment from < 2 cm urethral stricture, starting with might 2018 should november 2019.These patients were randomized under two aggregations; gathering An (study group) incorporated 15 patients who were subjected with intralesional MMC then afterward VIU, What's more one assembly b (control group) incorporated 15 patients who were subjected to VIU best.Utilizing An Cold-knife those urethrotomy might have been performed under immediate dream What's more incisions were aggravated during 12-, 5-, What's more 7 O'clock positions taken after Toward intralesional infusion from claiming MMC.Every one patients were took after dependent upon to 6 months and the stricture repeat rate might have been compared the middle of those two aggregation.Of the aggregate 30 patients, 4 patients clinched alongside gathering a and 3 tolerant On one assembly b were lost should catch up in the initial 2 months Furthermore Subsequently were dropped from the ponder.Those test might have been consequently decreased will 23 patients who were separated under two aggregations.Bunch An (study group) comprised 11 patients who were subjected should intralesional mitomycin c's after VIU.Aggregation b (control group) comprised 12 patients who underwent VIU main.There might have been statistically critical Contrast the middle of 2 bunches in regards will stricture repeat ; 2 patients On one assembly a (18.2%) Furthermore 7 patients On bunch b (58.3%) required repeat (p=0.02).Various intralesional MMC injections Emulating VIU need An possibility with markedly decrease those repeat about urethral stricture.

Topic: Urological Disorders and Treatments
Subfield: Urology
Field: Medicine
Domain: Health Sciences
The bacteriology of perimandibular space infections.

The bacteriology of 21 perimandibular clised-space infections was studied prospectively using optimal bacteriological techniques to collect, transport, and process specimens. There was an average of six microbial species per specimen, including approximately four anaerobes and two aerobes. The predominant aerobes were alpha-hemolytic and non-hemolytic streptococci; the predominant anaerobes were peptostreptococci, Bacteroides melaninogenicus, and Fusobacterium nucleatum. These findings indicate that most perimandibular space infections involve a polymicrobial flora in which anaerobic bacteria are the dominant isolates. Antimicrobial decisions should account for these observations, particularly in cases where cultural data are not available or when anaerobic cultures are not performed with optimal techniques.

Topic: Otolaryngology and Infectious Diseases
Subfield: Infectious Diseases
Field: Medicine
Domain: Health Sciences
The therapeutic impact of [F18]-2-fluordesoxyglucose PET for the staging and monitoring of oral cancer: a comparative study of PET before and after preoperative radiochemotherapy with CT and histologic data

The lack of sensitivity and specificity of conventional imaging techniques based on morphological criteria is responsible for considerable limitations in the staging and surveillance of oral cancer. Therefore, this study investigated the contribution of [F18]-2-fluordesoxyglucose (FDG) positron emission tomography (PET) to tumour management, with special regard to lymph node involvement and therapeutic monitoring after radiotherapy. In this prospective, observational study, 21 patients with advanced oral cancer, predominantly T3/T4, were evaluated. FDG-PET scans before and after preoperative radio(chemo)therapy were performed and standardized uptake values (SUV) were determined for the tumour site and lymph node areas. PET scans were correlated to histological findings after ablative tumour surgery. FDG-PET yielded superior sensitivity and specificity for tumour and lymph node assessment. The effect of radiotherapy was reflected by the metabolic activity of the tumour, which showed a close correlation with the decrease of FDG uptake and histologic tumour regression. PET detected distant metastases and simultaneous tumours. The authors concluded that FDG-PET is a challenging imaging technique with the potential to improve the staging procedure for oral cancer. In the monitoring of metabolic activity of the tumour in the course of radio(chemo)therapy, FDG-PET allowed objective measurement of the treatment response. H. Schliephake

Topic: Head and Neck Cancer Studies
Subfield: Otorhinolaryngology
Field: Medicine
Domain: Health Sciences
First discoveries of colonies of the rare ant species Camponotus tergestinus Müller, 1921 (Hymenoptera: Formicidae) in situ

The rare ant species Camponotus tergestinus Müller, 1921 has so far been reported from few central and southern European localities, but none of its colonies have ever been recorded in situ. In 2016 and 2017, two colonies were found at Lipica (SW Slovenia), the first nesting on Quercus pubescens at the height of 3.2 m, the second on Q. cerris at the height of 2.2 m. Both nests had two entrances each. Numerous visits have been carried out at the site in order to observe both colonies. Based on available data, Camponotus tergestinus is an arboricolous species having a strong association with oaks. Its arboricolous and presumably nocturnal habits could be the main reasons for the paucity of available data. A list of all known localities, retrieved from both published and unpublished records, is also provided.

Topic: Insect and Arachnid Ecology and Behavior
Subfield: Genetics
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences