jimnoneill/paper-to-field-training huggingface dataset:
Complete mitochondrial genome revealed different taxonomic assignment of the fungus Pleurocordyceps sinensis (Hypocreales, Ascomycota)

Abstract The complete mitochondrial (mt) genome of Pleurocordyceps sinensis , a fungus originally isolated from Ophiocordyceps sinensis was sequenced, and assembled as a single circular DNA of 31,841 bp. The mt genome encoded 15 conserved proteins ( rps3 , cox1 , cox2 , cox3 , cob , atp6 , atp8 , atp9 , nad1 , nad2 , nad3 , nad4 , nad4L , nad5 and nad6 ), 2 rRNA ( rnl and rns ) and 25 tRNA, as well as 10 additional non-conserved open reading frames. Comparative analyses showed that mt genomes within the order Hypocreales encoded same number and synteny of conserved protein coding genes despite an obvious size variation among this group of fungi. Phylogenetic analyses using 14 conserved protein sequences revealed that this fungus may not belong to the current designated family Ophiocordycipitaceae but is more closely related to the species of Clavicipitaceae . The mt genome presented herein would aid to clarify the phylogenetic position of species of Polycephalomyces s. l. and also gave valuable information on reconstructing the evolutionary history of clavicipitaceous fungi.

Topic: Fungal Biology and Applications
Subfield: Pharmacology
Field: Medicine
Domain: Health Sciences
The Palaeoproterozoic Komatiite-Picrite Association of Finnish Lapland

The large range of chemical variation within intimately associated highly magnesian volcanic rocks in the Palaeoprolerozoic Central Lapland Greenstone Belt prompted the construction of a new classification scheme for MgO-rich volcanic rocks, based on an [Al2O3] vs [TiO2] diagram where the axes are the Al2O3 and TiO2 contents (in mole proportions) of the rocks projected from the olivine composition. This diagram places the Lapland rocks in the fields of Ti-enriched komatiites and picrites. Komatiitic rocks are depleted in both light and heavy rare earth elements (LREE and HREE) relative to middle REE (MREE) and possess relatively high TiO2 even in the most LREE-depleted varieties, whereas picritic rocks approach geochemically Hawaiian picrites. Seven clinopyroxene and whole-rock pairs analysed for Sm-Nd isotopes yield an average age of 2056 25 Ma for the komatiites. Uncontaminated komatiites and picrites have similar positive Nd values (+ 4) indicating generation from a mantle source with a long-term depletion in LREE relative to MREE. Geochemical characteristics of the komatiite-picrite association, including REE and Nb/Y-Zr/Y systematics, indicate chemical heterogeneities in the source region, which seem to have been created by complex depletion and enrichment processes shortly before or related to a dynamic melting process. The high MgO contents of the rocks coupled with chemical similarity between the Lapland and Hawaiian picrites supports a mantle plume model for their genesis. Nevertheless, the geotectonic evolution appears to have proceeded without significant regional uplift shortly before volcanism.

Topic: Geological and Geochemical Analysis
Subfield: Geophysics
Field: Earth and Planetary Sciences
Domain: Physical Sciences
Application of artificial intelligence techniques to addressing and mitigating biotic stress in paddy crop: A review

Agriculture provides basic livelihood for a large section of world's population. It is the oldest economic activity in India, with two third of Indian population involved in crop production. India is second largest producer of rice and biggest exporter globally, with rice which is most common staple crop consumed in country. However, there are several challenges for paddy production including small production yield, soil quality, seed quality, huge volume of water needed and biotic stress. Of these, biotic stress drastically affects yield and susceptibility to other diseases in paddy production. It is caused by pathogens such as bacteria, viruses, fungi, nematodes, all of which severely affect growth and productivity of paddy crop. To mitigate these challenges, infected crops are identified, detected, classified, categorized, and prevented according to their respective suffering disease by using conventional methods which are not effective and efficient for growth of paddy crop. Thus, use of artificial intelligence (AI) and a smart agriculture-based Internet of Things (IoT) platform could be effective for detecting the biotic stresses in very less time or online mode. For this, deep learning, and convolutional neural networks (CNN) multi-structured layer approach were used for diagnosing disease in rice plants. Different models and classifiers of CNN were used for detecting disease by processing high-spectral images and using logistic and mathematical formulation methods for classification of biotic paddy crop stresses. Continuous monitoring of stages of infection in paddy crop can be achieved using real-time data. Thus, use of AI has made diagnosing paddy crop diseases much easier and more efficient.

Topic: Smart Agriculture and AI
Subfield: Plant Science
Field: Agricultural and Biological Sciences
Domain: Life Sciences
The decline in state funding of public higher education in the United States: competing budget priorities and state variations

State and national policy makers for 150 years have promoted public access to higher education, supported through state tax funds and more recently through federal direct appropriations and tax expenditures. In the past 3 decades, state tax funding of higher education has declined, resulting in increased reliance on tuition and reduced college affordability, thereby raising barriers to access. There are also vast differences in how well states fund higher education, with some providing more generous tax funds and others steadily providing less. Higher education researchers have conducted ongoing inquiry regarding factors that may influence the level of state legislative support for higher education. These include institutional, political, economic, cultural, demographical, and fiscal factors. Several have pointed to what appears to be an inverse relationship between state funding of higher education and state funding of Medicaid. This study employs regression analyses of a 20-year, 50-state panel of data (1992-2011), considering the changes in budget share devoted to higher education, Medicaid, K-12 Public Education, and Corrections. During that 20-year period, higher education's share declined in 33 states, Medicaid's increased in 44 states, and 28 states experienced both a decrease in higher education's share and an increase in Medicaid's. Also considered were political party control of states, and changes in Gross State Product. The analysis tries to determine if increases in Medicaid's share is contributing to a decline in the share for higher education, and whether the share for each budget category explains state funding variations. A fixed effects regression model, taking into account both the differences within (across time) and between (across states), determined that 85% of the variation in the error term is due to the wide cross-sectional state differences. This calls into question much of the prior research that relied on ordinary least squares regression models, and did not account for what Zhu called "cross-unit heterogeneity". These findings indicate that additional research is needed, both quantitative (considering groupings of states rather than all 50 states), and interpretive case studies to elicit more insights and research questions that will yield more definitive answers about budgetary tradeoffs between higher education funding and other budgetary categories.

Topic: Hermeneutics and Narrative Identity
Subfield: Philosophy
Field: Arts and Humanities
Domain: Social Sciences
[Surgery for Wolff-Parkinson-White syndrome in the first year of life].

A case of surgical treatment for reentrant atrioventricular tachycardia in a 7 months old child is reported. Episodes of tachycardia were repetitive and long-lasting, often leading to signs of hemodynamic impairement, and were not controlled by antiarrhythmic drugs. The electrophysiologic study showed a circus-movement tachycardia utilizing a concealed accessory pathway located at the anterior septal aspect of tricuspid anulus. The child underwent successful surgical treatment by the endocardial technique. Few minutes after weaning from extracorporeal circulation, developed T wave inversion followed by acute right ventricular dysfunction and ventricular fibrillation. Others ischemic like episodes, maybe as a result of coronary artery spasm, occurring in the next 6 hours were successfully treated with isosorbide dinitrate. At 18 months follow-up, the child is free of tachycardia and has normal atrioventricular conduction.

Topic: Cardiac Arrhythmias and Treatments
Subfield: Cardiology and Cardiovascular Medicine
Field: Medicine
Domain: Health Sciences
[Genetic parameter estimation for inosine-5-monophosphate and intramuscular fat contents and other meat quality traits in chicken muscle].

The genetic parameters for some important flavor traits like inosine-5'-monophosphate (IMP) and intramuscular fat (IMF) contents in breast meat were estimated using a MTDFREML procedure on 1063 male, 90-day-old, purebred Beijing-You meat-type chicks (BJY). The result showed that the heritability of IMP and IMF contents in BJY breast meat was moderate or low (h2=0.23, 0.10), whereas these parameters were higher for abdominal fat weight (AFW), breast meat yield (BMY), ratio of BMY to carcass weight (BMR), leg muscle yield (LMY), body weight (BW), comb weight(CW) and comb weight percentage (CWB) (h2=0.56-0.79). The heritability of abdominal fat percentage (AFP), leg meat yield (LMY), testicle weight (TW) and testicle weight percentage (TWP) were 0.24, 0.32, 0.39 and 0.35, respectively. IMP exhibited low phenotypic correlations with BMY, LMY and SFT and no significant phenotypic correlations with other traits. IMF, to some extent, exhibited positive phenotypic correlation with BW, AFP, SFT and FSW (rP=0.11-0.33). In terms of genetic correlation, IMP was moderately or significantly negatively correlated with BW and CWP (rA=-0.38,-0.62), and a high level of positive correlation was observed with BMY (rA=0.57). Moreover, IMF was highly correlated with BW and AFW (rA=0.75,0.66), and moderately correlated with AFP and CWP (rA=0.32, 0.40). A low level of positive correlation was observed between IMP and IMF (rA =0.27). We propose that IMP and IMF contents in chicken meat could be increased with selection through line-breeding.

Topic: Cancer-related molecular mechanisms research
Subfield: Cancer Research
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
Building Genetic Competence Through Partnerships and Interactive Models

Background: Nurses are increasingly using genetic-directed therapies in routine care, but evidence indicates that nurse educators lack knowledge about basic genetic concepts and related clinical implications. Educators are the key to preparing future nurses for effective practice in the genomic era, and creative approaches are needed for faculty development. Method: Nurse educators in academic and clinical settings partnered with science educators who use sophisticated DNA, RNA, and protein models to explore ways to teach abstract genetic concepts. Results: Hands-on learning enabled the workshop participants to understand how transcription of gene mutations leads to the translation of defective proteins responsible for specific diseases. Participants found using the models helped clarified complex concepts that occur at the cellular level. Conclusion: Partnerships with science educators can address gaps in nurse educators' knowledge about genetics and introduce creative teaching strategies. [ J Nurs Educ. 2016;55(5):300–303.]

Topic: Science Education and Perceptions
Subfield: Developmental and Educational Psychology
Field: Psychology
Domain: Social Sciences
Simultaneous targeting of HSV-1 with two gRNAs completely impairs virus replication.

&lt;p&gt;&lt;b&gt;a)&lt;/b&gt; Vero cells were transduced with the indicated single or double gRNAs and subsequently infected with HSV-1-eGFP at an MOI of 0.5. Cells were analyzed for eGFP-expression by flow cytometry at 1, 2, and 3 dpi to assess the percentage of virus-infected cells. &lt;b&gt;b)&lt;/b&gt; Similar experiment as in a) but now performed in human MRC5 cells and at an MOI of 0.005, as MRC5 cells are more susceptible to HSV-1 infection. Cells were analyzed for eGFP-expression by flow cytometry at 1 dpi and 3 dpi to assess the percentage of successfully infected cells. &lt;b&gt;c)&lt;/b&gt; Supernatants from b) were subjected to plaque assays to quantify the infectious HSV-1 titer produced by gRNA-expressing MRC5 cells that had been infected with HSV-1-eGFP three days earlier. Plaques were scored if visible by eye. &lt;b&gt;d)&lt;/b&gt; Plaques from c) obtained after infection of cells with HSV-1 harvested from control or anti-&lt;i&gt;UL8&lt;/i&gt; gRNA-expressing MRC5-cells were analyzed by light-microscopy. Whereas large plaques (‘P’) are observed in infected cells not carrying any gRNAs, virus harvested from UL8 gRNA- expressing cells induced microplaques. In double gRNA-treated cells, no signs of infection were observed. For all bar diagrams, measurements of triplicate experiments are presented + STD.&lt;/p&gt;

Topic: Herpesvirus Infections and Treatments
Subfield: Epidemiology
Field: Medicine
Domain: Health Sciences
A Scheme's Synchronization of Chua Chaotic System with Oscillating Parameters under the Impulsive Control

Most Chaotic synchronization control methods have some flaws which increase the security risks of the communication system. Attacker can reconstruct the chaotic system or estimate parameters by using the information of the chaotic system which can be obtained by analyzing the control signal. Therefore we propose a schemepsilas synchronization of Chua chaotic system with oscillating parameters under the impulsive control. In this paper, we proved that two systems can get synchronized without control signal transmitting.

Topic: Chaos control and synchronization
Subfield: Statistical and Nonlinear Physics
Field: Physics and Astronomy
Domain: Physical Sciences
Clinical Significance of Molecular Diagnostic Tools for Bacterial Bloodstream Infections: A Systematic Review

Bacterial bloodstream infection (bBSI) represents any form of invasiveness of the blood circulatory system caused by bacteria and can lead to death among critically ill patients. Thus, there is a need for rapid and accurate diagnosis and treatment of patients with septicemia. So far, different molecular diagnostic tools have been developed. The majority of these tools focus on amplification based techniques such as polymerase chain reaction (PCR) which allows the detection of nucleic acids (both DNA and small RNAs) that are specific to bacterial species and sequencing or nucleic acid hybridization that allows the detection of bacteria in order to reduce delay of appropriate antibiotic therapy. However, there is still a need to improve sensitivity of most molecular techniques to enhance their accuracy and allow exact and on time antibiotic therapy treatment. In this regard, we conducted a systematic review of the existing studies conducted in molecular diagnosis of bBSIs, with the main aim of reporting on clinical significance and benefits of molecular diagnosis to patients. We searched both Google Scholar and PubMed. In total, eighteen reviewed papers indicate that shift from conventional diagnostic methods to molecular tools is needed and would lead to accurate diagnosis and treatment of bBSI.

Topic: Bacterial Identification and Susceptibility Testing
Subfield: Clinical Biochemistry
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
[Development of fluorescence imaging based assay for screening compounds with anti-migration activity].

In the present study, A fluorescent imaging-based high-throughput screening method was developed for identifying anti-migratory compounds with 96-well Transwell plates. The correlation, precision and stability of this method were examined and the incubation time of dye Hoechst 33342 in addition to migration time was optimized. In addition, The inhibitory activity of anti-cancer drug paclitaxel on tumor cell migration was assayed and an IC50 value of 0.717 micromol x L(-1) was obtained. Using this method, 24 components from Rhizoma Alismatis were screened and one component with anti-migration activity was found. These results show that the new proposed method with good precision, stability and linear range has the potential to assay the inhibitory activity of anticancer compounds.

Topic: Flavonoids in Medical Research
Subfield: Pharmacology
Field: Medicine
Domain: Health Sciences
Fenomena kehujanan di Semenanjung Malaysia berdasarkan indeks kerpasan piawai (Peninsular Malaysia rainfall phenomenon based on standard precipitation index)

Kajian ini bertujuan mengenal pasti pola taburan kehujanan di Semenanjung Malaysia menggunakan Indeks Kerpasan Piawai bagi skala masa yang berbeza iaitu sebulan, enam bulan dan dua belas bulan. Data kajian adalah data hujan harian dari 75 stesen tadahan hujan yang merangkumi empat zon iaitu Barat Laut, Barat, Barat Daya dan Timur untuk 33 tahun; 1975 – 2007. Hasil kajian mendapati nilai serakan bagi frekuensi keberlakuan keadaan basah/kering bertambah dengan peningkatan skala masa. Kajian pemboleh ubah berkaitan iaitu tempoh, keparahan dan selang ketibaan mendapati wujud peningkatan dalam nilai-nilai maksimum, purata dan sisihan piawai di setiap zon dengan bertambahnya skala masa yang digunakan. Seterusnya, zon Barat Daya secara konsisten mengalami tempoh keadaan basah yang lebih lama berbanding tempoh keadaan kering manakala zon Barat pula menghasilkan nilai sisihan piawai yang paling tinggi berbanding dengan zon lain untuk kesemua pemboleh ubah kajian kecuali intensiti.

Topic: Economic Growth and Fiscal Policies
Subfield: Economics and Econometrics
Field: Economics, Econometrics and Finance
Domain: Social Sciences
Bilingualism caught in a net. A new approach to understanding the complexity of bilingual experience

The growing importance of research on bilingualism in psychology and neuroscience motivates the need for a psychometric model that can be used to understand and quantify this phenomenon. This research is the first to meet this need. We re-analyzed two datasets (N = 171 and N = 112) from relatively young adult language-unbalanced bilinguals and asked whether bilingualism is best described by the factor structure or by the network structure. The factor and network models were established on one dataset and then validated on the other dataset in a fully confirmatory manner. The network model provided the best fit to the data. This implies that bilingualism should be conceptualized as an emergent phenomenon arising from direct and idiosyncratic dependencies among the history of language acquisition, diverse language skills, and language-use practices. These dependencies can be reduced to neither a single universal quotient nor to some more general factors. Additional in-depth network analyses showed that the subjective perception of proficiency along with language entropy and language mixing were the most central indices of bilingualism, thus indicating that these measures can be especially sensitive to variation in the overall bilingual experience. Overall, this work highlights the great potential of psychometric network modeling to gain a more accurate description and understanding of complex (psycho)linguistic and cognitive phenomena.

Topic: Mental Health Research Topics
Subfield: Experimental and Cognitive Psychology
Field: Psychology
Domain: Social Sciences
Social Realities of Loss and Suffering Following Mastectomy

This article draws on personal accounts of women’s thoughts and feelings following mastectomy. The analysis of the material obtained in multiple, focused interviews has revealed two major themes in these accounts: on the one hand, the loss of bodily symmetry (one of the basic cultural criteria of physical beauty) was deeply felt; and on the other, peace of mind (a characteristic of psychological beauty) was permanently disturbed by the fear of the recurrence of cancer and the possibility of death. While the asymmetrical body is a potentially (socially) visible problem of presentation and representation, the fear of recurrence is a fear of the workings of the body that are not visible and not knowable. A woman who has had a breast removed will concern herself, usually in isolation, with her secret unpredictable interior. This fear will be her very own preoccupation, not only because in our society death and disease are deemed threatening and ugly – but also because the uncertainty of the health-status of a woman following mastectomy is socially (as well as medically) veiled by discourse which assumes that she is ‘well’. Though a woman may feel well, she fears that her body may not be well; yet her fear is necessarily silenced through both social denial and incongruity with experience. The article explores in some detail the nature of the stress that inevitably results in this ill-understood, complex situation.

Topic: Body Image and Dysmorphia Studies
Subfield: Clinical Psychology
Field: Psychology
Domain: Social Sciences
MECHANIZATION STUDY OF THE U. S. NAVY MARINE ENGINEERING LABORATORY LIBRARY, ANNAPOLIS, MARYLAND

Computer mechanization at the U.S. Navy Marine Engineering Laboratory (MEL) Library presently consists of production of a journal listing on an IBM 1401 computer from punched cards. When the computer file of information on reports is expanded, it will be the data base for bibliographic searches and retrieval of information. This data base will be maintained and processed by the Information Storage Package, a series of computer programs developed by the Applied Physics Laboratory of Johns Hopkins University. The MEL Library feels that, while the Information Storage Package is useful, a universally accepted information system would be more beneficial for all aspects of library mechanization; with such a system, centralized cataloging might become feasible.

Topic: Hermeneutics and Narrative Identity
Subfield: Philosophy
Field: Arts and Humanities
Domain: Social Sciences
HIV Prevalence and Correlates of Receptive Needle Sharing Among Injection Drug Users in the Mexican-U.S. Border City of Tijuanat

Abstract-Injection drug use is a growing but understudied problem in Tijuana, a city situated on the northwestern Mexico-U.S border. The authors studied factors associated with receptive needle sharing in an effort to inform prevention activities. In 2003, street-recruited injection drug users (IDUs) in Tijuana underwent interviews on injection risk behaviors and rapid HIV antibody tests. Logistic regression was used to identify correlates of receptive needle sharing at the last injection episode. Of 402 IDUs, 87.6 % were male; the median age was 34. HIV prevalence was 4.01 % (95%Cl:

Topic: HIV, Drug Use, Sexual Risk
Subfield: Epidemiology
Field: Medicine
Domain: Health Sciences