jimnoneill/paper-to-field-training huggingface dataset:
An Efficient Genome Fragment Assembling Using GA with Neighborhood Aware Fitness Function

To decode a long genome sequence, shotgun sequencing is the state-of-the-art technique. It needs to properly sequence a very large number, sometimes as large as millions, of short partially readable strings (fragments). Arranging those fragments in correct sequence is known as fragment assembling, which is an NP-problem. Presently used methods require enormous computational cost. In this work, we have shown how our modified genetic algorithm (GA) could solve this problem efficiently. In the proposed GA, the length of the chromosome, which represents the volume of the search space, is reduced with advancing generations, and thereby improves search efficiency. We also introduced a greedy mutation, by swapping nearby fragments using some heuristics, to improve the fitness of chromosomes. We compared results with Parsons’ algorithm which is based on GA too. We used fragments with partial reads on both sides, mimicking fragments in real genome assembling process. In Parsons’ work base-pair array of the whole fragment is known. Even then, we could obtain much better results, and we succeeded in restructuring contigs covering 100% of the genome sequences.

Topic: Genomics and Phylogenetic Studies
Subfield: Molecular Biology
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
Supplementary Methods, Figure Legends 1-2 from Construction and Characterization of a Bispecific Anti-CD20 Antibody with Potent Antitumor Activity against B-Cell Lymphoma

Supplementary Methods, Figure Legends 1-2 from Construction and Characterization of a Bispecific Anti-CD20 Antibody with Potent Antitumor Activity against B-Cell Lymphoma

Topic: Monoclonal and Polyclonal Antibodies Research
Subfield: Radiology, Nuclear Medicine and Imaging
Field: Medicine
Domain: Health Sciences
Characteristics and Performance of RD53A Readout Chip with Small-pixel Silicon Sensors

The luminosity of the Large Hadron Collider (LHC) at CERN will be upgraded by a factor of seven to 7.5 × 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">34</sup> cm" <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> s"', hence boosting the physics potential of its experiments. The increased luminosity leads to a higher rate of proton-proton interactions, in the order of 200 events per bunch crossing and a larger dose and fluence. The CMS experiment will upgrade many of its sub-detectors in order to cope with the new experimental conditions. The current tracking system of the CMS will be fully replaced. New pixel sensor designs with pitches of 50 pm × 50 pm and 100 pm × 25 pm for the phase II upgrade of the CMS Inner Tracker are characterised in order to identify the designs which meet the requirements of the High- Luminosity LHC. The sensors are read out by the new RD53A readout chip which has been developed by the RD53 collaboration, a joint effort of the CMS and ATLAS collaborations. As part of the upgrade programme, the RD53A user community evaluates and characterises the performance of the readout chip when equipped with various sensors types. The studies performed on the RD53A chip within the CMS Inner Tracker upgrade research and development programme are presented in this paper. The studies include charge calibration of the RD53A Linear Frontend using X-ray fluorescence, minimum achievable threshold, crosstalk and efficiency and resolution measurements using particle beams.

Topic: Particle Detector Development and Performance
Subfield: Nuclear and High Energy Physics
Field: Physics and Astronomy
Domain: Physical Sciences
Hemodynamics of Collateral Vasodilatation following Femoral Artery Occlusion in Anesthetized Dogs

Dilatation of collateral blood vessels was studied following occlusion of the femoral artery in anesthetized dogs. This was achieved by measuring pressure and flow in the anterior tibial artery distal to the occlusion and pressure in the femoral artery proximal to the occlusion. Dilatation of the collateral vessels to the anterior tibial artery was estimated by the increase in the conductance of the collaterals from the minimum value measured 8 to 10 seconds following onset of the occlusion. Conductance rose 277 ± 67 (SEM)% during the first 70 seconds following occlusion and an additional 178 ± 66% during the ensuing hour. When the femoral artery was reopened after a 2-minute period of occlusion, the collaterals reconstricted to their preocclusion size in 12 to 14 minutes. Elimination of circulatory reflexes by total spinal anesthesia did not alter the course of collateral vasodilatation. However, when systemic arterial pressure was lowered to approximately 45 mm Hg for 8 minutes prior to occlusion, the collaterals dilated almost completely even before the occlusion was instituted, indicating that tissue ischemia is in some way related to collateral vasodilatation.

Topic: Cardiovascular and exercise physiology
Subfield: Complementary and alternative medicine
Field: Medicine
Domain: Health Sciences
On Collision Avoiding Fixed-Time Flocking with Measurable Diameter to a Cucker–Smale-Type Self-Propelled Particle Model

Dealing with the fixed-time flocking issue is one of the most challenging problems for a Cucker–Smale-type self-propelled particle model. In this article, the fixed-time flocking is established by employing a fixed-time stability theorem when the communication weight function has a positive infimum. Compared with the initial condition-based finite-time stability, an upper bound of the settling time in this paper is merely dependent on the design parameters. Moreover, the size of the final flocking can be estimated by the number of particles and the initial states of the system. In addition, a sufficient condition is formulated to guarantee that all particles do not collide during the process of the flocking. These results can give a reasonable explanation to some flocking phenomena such as bird flocks, fish schools, or human group behaviors. Finally, three numerical examples are granted to display the performance of the obtained results.

Topic: Distributed Control Multi-Agent Systems
Subfield: Computer Networks and Communications
Field: Computer Science
Domain: Physical Sciences
Quantitative intravascular near-infrared fluorescence imaging

Cardiac arrest caused by the rupture of atherosclerotic plaques is one of the main causes of death in the western world. Intravascular near-infrared fluorescence (iNIRF) imaging can be used to detect plaques at high risk of rupture, utilizing a catheter that delivers laser light to excite fluorochromes specific to molecules produced by inflammation and other biological processes associated with plaque formation. One significant feature of iNIRF imaging is its capability to image through blood. However, because of the absorption and scattering of photons caused by red blood cells, fluorescence intensity detected through blood is dependent on the distance between the fluorescent source and the detector, thus preventing quantitative imaging. Moreover, the scattering of photons through blood causes the imaging resolution to degrade as a function of distance, in addition to the blur introduced by the imaging system's point spread function. Here we consider two hybrid approaches whereby structural information of the imaged vessel, acquired from co-registered intravascular ultrasound (IVUS), is employed to correct for variations in the distance between fiber-tip and vessel wall and to improve the imaging resolution.

Topic: Cerebrovascular and Carotid Artery Diseases
Subfield: Pulmonary and Respiratory Medicine
Field: Medicine
Domain: Health Sciences
Identifying small non-coding RNAs as biomarkers for cervical cancer.

e17507 Background: Small non-coding RNAs (sncRNAs) that control post-transcriptional gene expression are attractive candidate molecular targets for cancer screening tests. We evaluated whether sncRNAs expression are markedly different in benign, precancerous, and cancerous cervical tissue. Methods: We examined the expression of six sncRNA species: circular RNAs (circRNAs) microRNAs (miRNAs), piwi-interacting RNA (piRNAs), small nuclear RNA (snRNAs), small nucleolar RNA (snoRNAs), and transfer RNA (tRNA), from archival formalin-fixed paraffin-embedded cervical specimen obtained from 172 women (74 benign, 58 high-grade squamous intraepithelial lesion (HSIL) and 40 invasive cervical cancer). We used DESeq2 to identify differentially expressed sncRNA molecules with adjusted p-value &lt; 0.05 and at least 2-fold up- or down-regulation. Results: Comparing benign to HSIL samples, we foundseveral statistically significant, differentially expressed sncRNAs: 906 circRNAs (*circ_0066810, p=3.76x10 -16 ), 87 miRNAs (*miR-149-5p, p=1.30x10 -14 ), 11 piRNAs (*piR_016945, p=8.32x10 -13 ), 32 snRNAs (*RNU1-17P, p=1.90x10 -10 ), 5 snoRNAs (*SCARNA18, p=1.35x10 -5 ), and 24 tRNA (*tRNA-Glu-TTC-8-1, p=6.45x10 -17 ). Comparing benign to invasive cervical cancer samples, we also foundseveral statistically significant, differentially expressed sncRNAs: 3,192 circRNAs (*circ_0123115, p=7.46x10 -50 ), 325 miRNAs (*miR-7-5p, p=6.72x10 -36 ), 82 piRNAs (*piR-hsa-27513, p=1.44x10 -15 ), 71 snRNAs (*RNU1-20P, p=1.37x10 -45 ), 52 snoRNAs (*SNORD95, p=1.68x10 -23 ), and 68 tRNA (*tRNA-Cys-GCA-9-3, p=1.01x10 -21 ). * Indicates the sncRNA with the smallest p-value, for each specie. Conclusions: Our results identify sncRNAs with potential utility of as diagnostic and prognostic biomarkers, and therapeutic targets for cervical precancer and cancer.

Topic: Cancer-related molecular mechanisms research
Subfield: Cancer Research
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
Genetic relatedness within and between formae speciales of Fusarium oxysporum as measured by DNA-DNA reassociation kinetics.

Genetic relatedness among 18 formae speciales within Fusarium oxysporum was determined on the basis of DNA-DNA reassociation kinetics. DNA homology values were high (more than 95%) between isolates within the same forma specialis, while isolates of different formae speciales showed lower values (63 to 86%) of DNA homology. Comparatively high homology values (90 to 95%) were observed within isolates of different formae speciales causing disease on the Cruciferae or the Cucurbitaceae plants. Isolates of F. oxysporum consistently showed low homology values (36 to 48%) with isolates of F. solani. These results suggest that formae speciales of F. oxysporum can be differentiated genetically from each other, indicating that the reassociation analysis of DNA may be a useful tool in studies involving classification and phylogeny of subspecific taxa in this species.

Topic: Plant Pathogens and Fungal Diseases
Subfield: Cell Biology
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
Écrire et réécrire au cycle 3 : l'effet des mots clés sur la réécriture, avec et sans assistance informatique

Write and rewrite in cycle 3 (8 to 11 years old) : the effect of keywords on rewriting, with and without computer's help. Jacques Crinon, Denis Legros &amp; Brigitte Marin, Coditexte / CNRS-ESA7021 (ParisVIII), IUFM de Créteil. The present study faits within the framework of researches that allowed perfecting a software to help rewriting and to compare rewritings of stories of Personal experience by pupils of cycle 3 whether they benefited or not of computerized help. The pupils of the group that take notes in the computerised database of textual resources rewrite more than the pupils of the group that benefits of textual resources presented on paper. Besides, their additions, more important on the semantic level, belong to the macrostructure of the text. We tried to understand the reasons of these results by analysing the role taken by the access to the resources through keywords. 112 pupils, shared in four groups, have written, then rewritten a story : the textual resources were presented on paper or on a computer ; the consultation was done in a linearly process or with the help of keywords describing these texts' universe. We have compared the number and the «relevance » of the additions made according to the group. The results do not show any quantitative differences between the participants of the groups that used keywords and the others. On the other hand the groups with keywords produce additions less relevant when using paper resources and more relevant when using computer resources. The number of texts available and the possibility for the pupil to find resource texts compatible with the text he is writing seem determining. The presence of keywords allows, on the computer, the efficient circulation through an important corpus. So is the function of the tool underscored : open new possibilites, in a configuration where interact numerous factors.

Topic: French Language Learning Methods
Subfield: Linguistics and Language
Field: Social Sciences
Domain: Social Sciences
The Effect of Corporate Governance and Financial Performance on Dividend Policy

This study aims to examine and analyze the effect of corporate governance and financial performance on dividend policies. The dependent variable is dividend policy and the independent variable is the size of the board of commissioners, independent board of commissioners, managerial ownership, liquidity and profitability. The population of this research is 14 Manufacturing companies listed on the Indonesia Stock Exchange in the period 2015 – 2018. With a total sample size of 56 and this sampling technique uses a purposive sampling method. Testing the hypothesis of this study using multiple linear regression test. The results of this study indicate that the size of the board of commissioners, the board of independent commissioners and profitability affect the dividend policy, managerial ownership and liquidity do not affect the dividend policy

Topic: Financial Analysis and Corporate Governance
Subfield: Accounting
Field: Business, Management and Accounting
Domain: Social Sciences
Linking discoveries, mechanisms, and technologies to develop a clearer perspective on plant long noncoding RNAs

Abstract Long noncoding RNAs (lncRNAs) are a large and diverse class of genes in eukaryotic genomes that contribute to a variety of regulatory processes. Functionally characterized lncRNAs play critical roles in plants, ranging from regulating flowering to controlling lateral root formation. However, findings from the past decade have revealed that thousands of lncRNAs are present in plant transcriptomes, and characterization has lagged far behind identification. In this setting, distinguishing function from noise is challenging. However, the plant community has been at the forefront of discovery in lncRNA biology, providing many functional and mechanistic insights that have increased our understanding of this gene class. In this review, we examine the key discoveries and insights made in plant lncRNA biology over the past two and a half decades. We describe how discoveries made in the pregenomics era have informed efforts to identify and functionally characterize lncRNAs in the subsequent decades. We provide an overview of the functional archetypes into which characterized plant lncRNAs fit and speculate on new avenues of research that may uncover yet more archetypes. Finally, this review discusses the challenges facing the field and some exciting new molecular and computational approaches that may help inform lncRNA comparative and functional analyses.

Topic: Cancer-related molecular mechanisms research
Subfield: Cancer Research
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
Body Image and Functional Loss

<bold>Abstract:</bold> The implications of functional loss following cancer is an area of psychosocial oncology that is rarely ventured. This is especially true in the context of limb and sensory losses, which have important repercussions on the patient’s well-being, namely as the individual is required to reassess and redefine his or her identity in face of these adversities. This chapter explores the implications of these losses via the intersection of the World Health Organization’s International Classification of Functioning, Disability, and Health with key oncological attributes of body image disturbances that seek to render explicit psychological mechanisms underlying impairments, limitations, and restrictions. Emphasizing the use of a standard framework for the assessment of functioning is essential, especially in understudied areas. Through this perspective, further insight is provided for the methodological and biopsychosocial assessment of functioning and body, and implications for clinical inquiry and practice are proposed for the advancement of cancer survivor care.

Topic: Cancer survivorship and care
Subfield: Oncology
Field: Medicine
Domain: Health Sciences
Electrochemical Cascade Cyclization for Selenobenzothiophenes: Synthesis, Photochemistry, and Bioactivity

A mild and highly efficient metal‐ and oxidant‐free electrochemical approach for the synthesis of 3‐selenylated benzothiophene derivatives is described. In this innovative electrochemical cascade cyclization reaction, the selenylated benzothiophene skeletons can be constructed along with the formation of CSe and CS bonds in a single step. Moreover, this electrochemical protocol exhibits good functional group compatibility, paving the way for the construction of diverse selenylated benzothiophene compounds with various functional groups from readily available starting materials under an aerobic reaction condition. Meanwhile, a series of control experiments are carried out, and a reasonable reaction mechanism is proposed. Finally, the scaled‐up reactions are performed, and then the photochemical and bioactive properties of the synthesized compounds are elaborately discussed.

Topic: Organoselenium and organotellurium chemistry
Subfield: Toxicology
Field: Pharmacology, Toxicology and Pharmaceutics
Domain: Life Sciences
Collecting Survey Data during Armed Conflict

Surveys provide crucial information about the social consequences of armed conflict, but armed conflict can shape surveys in ways that limit their value. We use longitudinal survey data from throughout the recent armed conflict in Nepal to investigate the relationship between armed conflict events and survey response. The Chitwan Valley Family Study (CVFS) provides a rare window into survey data collection through intense armed conflict. The CVFS data reveal that with operational strategies tailored to the specific conflict, duration of the panel study is the main determinant of attrition from the study, just as in most longitudinal studies outside of conflict settings. Though minor relative to duration, different dimensions of armed conflict can affect survey response in opposing directions, with bombings in the local area reducing response rates but nationwide political events increasing response rates. This important finding demonstrates that survey data quality may be affected differently by various dimensions of armed conflict. Overall, CVFS response rates remained exceptionally high throughout the conflict. We use the CVFS experience to identify principles likely to produce higher quality surveys during periods of generalized violence and instability.

Topic: Agricultural risk and resilience
Subfield: Soil Science
Field: Agricultural and Biological Sciences
Domain: Life Sciences
Homozygosity for a New Type of<sup>G</sup>γ(<sup>A</sup>γδβ)°-Thalassemia in a Malaysian Male

Hematological and clinical data are presented for a young Malay patient with a homozygous (delta beta)zero-thalassemic condition. His red blood cells contained 100% fetal hemoglobin with alpha and G gamma chains only. Detailed gene mapping defined a large deletion with a 5' end between the Aha III and Apa I sites, some 200-400 bp 5' to the A gamma globin gene and a 3' end beyond sequences 17-18 kb 3' to the beta globin gene. This G gamma (A gamma delta beta)zero-type of thalassemia is different from all the other six types described before. Comparison of the hematological data of this patient with those of homozygotes for either the Sicilian or Spanish types of G gamma A gamma (delta beta)zero-thalassemia showed no differences; all homozygotes have a moderate anemia which is accentuated by the relatively high oxygen affinity of the Hb F containing erythrocytes.

Topic: Hemoglobinopathies and Related Disorders
Subfield: Genetics
Field: Medicine
Domain: Health Sciences
Research on Multi-Source Remote Sensing Image Registration Base on SIFT Algorithm of Window Segmentation

Multi-source remote sensing image registration has important significance, this paper outlines the basic process and common methods of the remote sensing images registration, and the basic principles of SIFT matching algorithm.Then we put forward the SIFT image matching algorithm based on window segmentation and achieve good effect.

Topic: Advanced Image and Video Retrieval Techniques
Subfield: Computer Vision and Pattern Recognition
Field: Computer Science
Domain: Physical Sciences
Unemployment and Inflation: An Assessment of Canadian Macroeconomic Policy

During the decade of the 1970s the Canadian economy was characterized by substantially higher rates of both inflation and unemployment than during the 1960s. This paper reviews some important research in recent years in an attempt to explain this occurrence and draws implications for policy formulation in the 1980s. The predominant view during the 1960s was that an inverse relationship exists between inflation and unemployment, i.e. periods of high inflation tend to be associated with periods of low unemployment and vice versa. The explanation for such an inverse relation between inflation and unemployment is based on three underlying relationships: the rate of price change is directly related to the rate of wage change and other factors; the rate of wage change is directly related to conditions in the labour market and (actual or expected) inflation; and conditions in the labour market are inversely related to the unemployment rate. This inverse relationship between the rate of price (or wage) change and the unemployment rate is called the Phillips curve after A.W. Phillips (1958) who presented striking empirical evidence that such an inverse relationship had existed in the United Kingdom for almost a century. The Phillips curve reflects something that is obvious to those involved in collective bargaining in Canada, i.e that, other things equal, a union can generally achieve a higher wage settlement when the economy is booming than when it is in a recession. The statistical verification of this relationship has proved to be a difficult task, however, and has been the subject of a highly technical statistical debate among researchers.' The conclusion which has emerged

Topic: Canadian Policy and Governance
Subfield: Political Science and International Relations
Field: Social Sciences
Domain: Social Sciences