jimnoneill/paper-to-field-training huggingface dataset:
Data from Reconstructing Complex Cancer Evolutionary Histories from Multiple Bulk DNA Samples Using Pairtree

&lt;div&gt;Abstract&lt;p&gt;Cancers are composed of genetically distinct subpopulations of malignant cells. DNA-sequencing data can be used to determine the somatic point mutations specific to each population and build clone trees describing the evolutionary relationships between them. These clone trees can reveal critical points in disease development and inform treatment. Pairtree is a new method that constructs more accurate and detailed clone trees than previously possible using variant allele frequency data from one or more bulk cancer samples. It does so by first building a Pairs Tensor that captures the evolutionary relationships between pairs of subpopulations, and then it uses these relations to constrain clone trees and infer violations of the infinite sites assumption. Pairtree can accurately build clone trees using up to 100 samples per cancer that contain 30 or more subclonal populations. On 14 B-progenitor acute lymphoblastic leukemias, Pairtree replicates or improves upon expert-derived clone tree reconstructions.&lt;/p&gt;Significance:&lt;p&gt;Clone trees illustrate the evolutionary history of a cancer and can provide insights into how the disease changed through time (e.g., between diagnosis and relapse). Pairtree uses DNA-sequencing data from many samples of the same cancer to build more detailed and accurate clone trees than previously possible.&lt;/p&gt;&lt;p&gt;&lt;i&gt;&lt;a href="https://aacrjournals.org/bloodcancerdiscov/article/doi/10.1158/2643-3230.BCD-22-0036" target="_blank"&gt;See related commentary by Miller, p. 176&lt;/a&gt;.&lt;/i&gt;&lt;/p&gt;&lt;p&gt;&lt;i&gt;&lt;a href="https://aacrjournals.org/bloodcancerdiscov/article/doi/10.1158/2643-3230.BCD-3-3-ITI" target="_blank"&gt;This article is highlighted in the In This Issue feature, p. 171&lt;/a&gt;.&lt;/i&gt;&lt;/p&gt;&lt;/div&gt;

Topic: Cancer Genomics and Diagnostics
Subfield: Cancer Research
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
Distal Realignment of the Patellar Tendon to Correct Abnormal Patellar Tracking

Between January 1980 and January 1994, 31 knees required distal realignment of the extensor mechanism to treat lateral patellar subluxation that could not be corrected with lateral patellar release and vastus medialis advancement during total knee arthroplasty. Fifteen had a preoperative valgus angle of more than 12 degrees, and 16 were undergoing revision total knee arthroplasty. Ten knees had a modified Roux-Goldthwait procedure, 18 had medial tibial tubercle transfer, and three had medial transfer of the medial 1/2 of the patellar tendon. The length of followup ranged from 2 to 16 years. No late patellar subluxations or dislocations have occurred in any of these cases. Three cases of medial tibial tubercle transfer had hematomas develop, with two requiring surgical evacuation; one of these developed a late infection. No fractures or displacements of the tubercle fragment have occurred. No significant patellar complications have occurred in those patients who underwent the modified Roux-Goldthwait procedure or the medial transfer of the medial 1/2 of the patellar tendon. One year after surgery, the mean knee flexion was 113 degrees, four knees had a flexion contracture of 5 degrees, and none had a quadriceps lag.

Topic: Tendon Structure and Treatment
Subfield: Orthopedics and Sports Medicine
Field: Medicine
Domain: Health Sciences
Corporate Philanthropy Affecting Consumer Patronage Behavior: The Effect of Reciprocity and the Moderating Roles of Vicarious Licensing and Strategic Fit

This study investigates the manner in which corporate philanthropy affects consumer patronage toward a brand. In so doing, we propose reciprocity as a key mechanism, which manifests the effect of corporate philanthropy on patronage behavior, and examine how vicarious licensing and strategic fit would mitigate the relationship between reciprocity and patronage behavior. The results indicate that reciprocity significantly increases one’s intention to participate in the philanthropic activities that a company supports and the intention to purchase its products. Vicarious licensing is found to lessen the effects of reciprocity on participation intention and purchasing intention. Strategic fit strengthens the path from participation intention to purchasing intention.

Topic: Environmental Sustainability in Business
Subfield: Marketing
Field: Business, Management and Accounting
Domain: Social Sciences
Finite-Dynamic Model for Infinite Media: Corrected Solution of Viscous Boundary Efficiency

This paper presents the corrected development of viscous boundary efficiency initially proposed by Lysmer and Kuhlemeyer. The expressions of the energy ratio are given, in accordance with the original numerical results, and confirm the authors' recommendations to minimize the reflected energy of body waves that impinge on the artificial boundary.

Topic: Elasticity and Wave Propagation
Subfield: Mechanics of Materials
Field: Engineering
Domain: Physical Sciences
Ryle, Gilbert (1900–76)

Alongside Wittgenstein and Austin, Ryle was one of the dominant figures in that middle period of twentieth-century English language philosophy which became known as ‘Linguistic Analysis’. His views in philosophy of mind led to his being described as a ‘logical behaviourist’ and his major work in that area, The Concept of Mind (1949), both by reason of its style and content, has become one of the modern classics of philosophy. In it Ryle attacked what he calls ‘Cartesian dualism’ or the myth of ‘the Ghost in the Machine’, arguing that philosophical troubles over the nature of mind and its relation with the body arose from a ‘category mistake’ which led erroneously to treating statements about mental phenomena in the same way as those about physical phenomena. For Ryle, to do something was not to perform two separate actions - one mental, one physical - but to behave in a certain way. Much of Ryle’s work had a similar theme: philosophical confusion arose through the assimilation or misapplication of categorically different terms, and could only be cleared up by a careful analysis of the logic and use of language. He later became preoccupied with the nature of reflective thinking, since this stood as an example of an activity which seemed to evade the behaviouristic analysis that he recommended. Ryle was also a considerable Plato scholar, though his work in this area has been less influential.

Topic: Classical Philosophy and Thought
Subfield: Philosophy
Field: Arts and Humanities
Domain: Social Sciences
Synthesis, physico-chemical properties and potential applications of colloidal gel particles

Four new N-isopropylacrylamide (NIPAM) based particles have been synthesized and characterized. The first experimental chapter reports that fluorescent poly(Nisopropylacrylamide-co-5% vinyl cinnamate) microgels were deposited on different solid surfaces to produce new environmental responsive surfaces. The mass of microgel particles deposited on glass pre-treated with acid, glass pre-treated with base, quartz, stainless steel, gold and Teflon at 25°C and 60°C was determined using fluorescence spectroscopy. The factors affecting the adsorption/desorption of the microgel particles were also investigated. The study shows that the solid surface charge is the most significant factor, followed by that of surface roughness and temperature; meanwhile, the hydrophobicity/hydrophilicity of the surface was the least significant.&#13;\n&#13;\nFluorescent temperature/pH responsive p(NIPAM-co-5% acrylic acid)-rhodamine B particles were studied. The results confirm the attachment of rhodamine B to the microgel particles. The long chains attached to the particles caused the particles to be poly-dispersed which suggests non-uniformity of particle size and behavior.&#13;\n&#13;\nFluorescent temperature/pH responsive poly(N-isopropylacrylamide-co-5% lucifer yellow) (p(NIPAM-co-5% LY)) microgel particles were tested for toxicity. The particles were negatively charged, mono-dispersed and were approximately 250 nm in diameter at 15°C. The toxicity of different concentrations of p(NIPAM-co-5% LY), p(NIPAM) and NIPAM monomer was tested on two cell lines (HeLa and Vero). The results show that the two particles maintain cell viability over 80% (for both cell lines HeLa and Vero) up to a concentration of 3 mg/mL while NIPAM monomer showed a cell viability of over 80% at a concentration equal to or less than 0.3 mg/mL.&#13;\n&#13;\nThe fourth experimental chapter explores the opportunity of using microgel particles as an emulsifier. p(NIPAM-co-5% acrylic acid)-hexenol particles with both hydrophilic and hydrophobic groups in their molecular structure were used to stabilize two emulsions (tricaprylin-in-water and hexadecane-in-water). The stability of the emulsions increased with increasing the concentration of the microgel. For the tricaprylin-in-water emulsion, a concentration of 0.3% w/v of the novel microgel particles managed to stabilize the emulsion for a week. In case of the hexadecane emulsion in water, 0.45% w/v microgel particles could show an increase in the emulsion stability and a decrease in the creaming.

Topic: Hydrogels: synthesis, properties, applications
Subfield: Molecular Medicine
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
Lips Contour Detection and Tracking Using Watershed Region-Based Active Contour Model and Modified $H_{\infty}$

In this paper, a region-based active contour model (ACM) with local information using watershed segmentation is proposed for lips contour detection. Compared to the ACM with global energy terms, the proposed system provides a more precise lips contour convergence under the circumstances where the lips are difficult to distinguish using global statistics. Furthermore, since the ACM is sensitive to the initial contour position, a modified H∞ based on Lyapunov stability theory is proposed to provide better tracking of the subsequent lips feature points as the ACM initialization. The integration of the proposed ACM and modified H∞ has revealed an improvement of the overall lips contour detection.

Topic: Speech and Audio Processing
Subfield: Signal Processing
Field: Computer Science
Domain: Physical Sciences
Talker familiarity effects on speech-in-speech perception

Talker familiarity can facilitate the extraction of linguistic content from speech signals embedded in broadband noise; however, relatively little research has investigated the impact of talker familiarity with competing speech in the background. This study explores the effects of familiarity with the target or competing talker in speech-in-speech perception. Listeners were first familiarized with and trained to identify three female voices. They then completed a sentence recognition task in the presence of 1-talker babble. Familiarity with either the target or background talker was manipulated in separate conditions. Results revealed significantly better sentence recognition for familiar relative to unfamiliar target talkers in the presence of an unfamiliar background talker; however, sentence recognition with an unfamiliar target talker did not differ depending on background talker familiarity. Thus, while listeners were able to capitalize on familiarity with a talker’s voice to aid target speech recognition, familiarity with the competing talker was neither facilitative nor inhibitory. This suggests that the influence of talker familiarity is limited to the actively attended stream. This stands in contrast to other aspects of the unattended stream which have been shown to exert an influence on speech-in-speech recognition including language and semantic content of the background speech.

Topic: Speech and Audio Processing
Subfield: Signal Processing
Field: Computer Science
Domain: Physical Sciences
CRITICAL ROLE OF NEPHRON DOSING: GENDER DIFFERENCE IN OUTCOME FOR RECIPIENTS OF FEMALE LIVE DONOR KIDNEY TRANSPLANTS.

Achille, Marie A; Chantale Fortin, Marie; Soos, John; Fugère, Jo-Ann; Pâquet, Michel Author Information

Topic: Organ Donation and Transplantation
Subfield: Public Health, Environmental and Occupational Health
Field: Medicine
Domain: Health Sciences
Ever-bearing strawberry culture using a new aeroponic system with dry-fog spray fertigation during the summer

A new spray fertigation system (dry-fog hydroponics) was developed for establishing ever-bearing strawberry (Fragaria × ananassa Duch. 'Summer ruby') production during the summer. Dry-fog hydroponics is an aeroponic technique that sprays a very fine foggy nutrient solution with an average droplet diameter of less than 10 μm into the root zone. The roots extend into the chamber filled with dry-fog of the liquid fertilizer and absorb water and nutrients from the dry-fog that fills the rhizosphere. This aeroponic system needs less water than any other hydroponic technique and keeps rhizosphere temperature lower than air temperature owing to the release of latent heat by dry-fog evaporation and adiabatic expansion of solution from the exhaust nozzle. Runner seedlings of strawberry plants were cultivated with dry-fog aeroponic system from early June to December in a greenhouse, and the growth, flower bud formation, fruit quality, photosynthetic rates as well as the contents of chlorophyll and total soluble protein in leaves were compared with those of plants cultivated by drip fertigation with palm shell medium as a control. Rhizosphere and the crown temperatures of dry-fog aeroponics were reduced by approximately 3-5°C throughout the day compared with control and were maintained below 25°C during the late summer. Although ever-bearing strawberry plants are insensitive to high temperature under long day conditions from a viewpoint of flower initiation, low temperature, especially the crown part of shoot base, is considered important for inducing flowering. For dry-fog aeroponics, the number of inflorescences and °Brix of fruits significantly increased but the number of runners and vegetative growth significantly decreased compared with control. Photosynthetic rates of leaves grown with dry-fog aeroponics increased compared to those of the control under both light and CO2 limited and saturated measurement conditions. In addition, leaf chlorophyll and total soluble protein contents significantly increased in dry-fog aeroponics compared with the control. From these findings, we suggested that dry-fog aeroponics is a usable new hydroponics for raising ever-bearing strawberry plants during the summer by maintaining rhizosphere temperature low, and thus suitable for shifting their growth phase from vegetative to reproductive.

Topic: Berry genetics and cultivation research
Subfield: Plant Science
Field: Agricultural and Biological Sciences
Domain: Life Sciences
Acquired hemophilia A resolution in a hepatitis C virus/human immunodeficiency virus–coinfected patient with cure of hepatitis C by direct‐acting antiviral agents

1Assistance Publique-Hôpitaux de Paris, Hôpital européen Georges Pompidou, Service d'Hématologie biologiqueParisFrance 2INSERM UMR-S970Centre de Recherche Cardiovasculaire de ParisParisFrance 3Sorbonne Paris Cité, Université Paris DescartesParisFrance 4Assistance Publique-Hôpitaux de Paris, Hôpital européen Georges Pompidou, Service d'Immunologie cliniqueParisFrance *ADDRESS CORRESPONDENCE AND REPRINT REQUESTS TO:Laetitia Mauge, M.D.Hématologie Biologique, Hôpital Européen Georges Pompidou20 rue Leblanc75015 Paris, FranceE‐mail: [email protected]Tel: +33‐156093905

Topic: Hemophilia Treatment and Research
Subfield: Hematology
Field: Medicine
Domain: Health Sciences
Portraits of Exemplary Literacy Practices: The Arizona Initiative for Children.

This booklet presents portraits of 10 Literacy Sites selected by the Arizona Department of Education, sites where the entire school was involved in the Arizona Literacy Initiative for Children. An introductory section of the booklet discusses the Initiative, which was established to promote early experiences in reading and writing that would motivate students and build better literacy skills in the kindergarten through third grade public school population through an integration of the language arts. Sections of the booklet are: (1) Weaving Writing, Speaking, Reading, Listening into Literacy; (2) Using Literacy for Purposeful Learning; (3) Making Literacy Meaningful; (4) Supporting Literacy through School Culture. An appendix lists the 10 sites. (RS) *********************************************************************** Reproductions supplied by EDRS are the best that can be made from the original document. *********************************************************************** . . ,114,PrkAar.ii.Y., -4

Topic: Education and Technology Integration
Subfield: Education
Field: Social Sciences
Domain: Social Sciences
Pharaonic Circumcision Under Patriarchy and Breast Augmentation Under Phallocentric Capitalism

In this article, the author discusses the similarities and differences between Pharaonic circumcision and reinfibulation and breast augmentation under systems of male dominance and female subordination. Despite the medical problems associated with each, women choose to be reinfibulated or have breast implants. There are systemic reasons associated with male dominance—in the case of reinfibulation, patriarchy and polygamy, and in the case of breast augmentation, institutional interests and phallocentrism—that impinge on women's “choice” of these procedures.

Topic: Female Genital Mutilation/Cutting Issues
Subfield: Public Health, Environmental and Occupational Health
Field: Medicine
Domain: Health Sciences
Deficiency of centromere-associated protein Slk19 causes premature nuclear migration and loss of centromeric elasticity

The cohesin complex prevents premature segregation of duplicated chromosomes by providing resistance to the pole-ward pull by spindle microtubules. The centromeric region (or sister kinetochores) bears the majority of this force and undergoes transient separation prior to anaphase, indicative of its elastic nature. A cysteine protease, separase, cleaves the cohesin subunit Scc1 and dissolves cohesion between sister chromatids, initiating their separation. Separase also cleaves the kinetochore protein Slk19 during anaphase. Slk19 has been implicated in stabilization of the mitotic spindle and regulation of mitotic exit, but it is not known what role it plays at the kinetochores. We show that during pre-anaphase arrest, the spindle in slk19Δ cells is excessively dynamic and the nuclei move into mother-daughter junction prematurely. As a result, the chromatin mass undergoes partial division that requires neither anaphase promoting complex (APC) activity nor Scc1 cleavage. Partial division of the chromatin mass is accompanied by the loss of the centromeric region's ability to resist pole-ward pull by the spindle. Slk19 physically associates with Scc1 and this association appears necessary for efficient cleavage of Slk19 by separase. Our results suggest that Slk19 participates in regulating nuclear migration and, in conjunction with cohesin complex, may be involved in the maintenance of centromeric tensile strength to resist the pole-ward pull.

Topic: Microtubule and mitosis dynamics
Subfield: Cell Biology
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
SH1051747.09FU

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: Wheat and Barley Genetics and Pathology
Subfield: Plant Science
Field: Agricultural and Biological Sciences
Domain: Life Sciences
Application of Organic Chemical Spectroscopic Techniques to Study the Organic Chemical Structure of Coal in Solid State and in Solubilised (Extract) Form

Centre for Energy Studies, Indian Institute of Technology Delhi, New Delhi-110 016<br> <em>Manuscript received 28 December 1987, accepted 13 January 1988</em> With the ultimate depletion of oil, dependence on coal for the oil supplies will increase. No real breakthrough in developing the cheaper and convenient coal conver­sion technologies can be made without clearly understanding the organic chemical structure of coal. Most of the spectroscopic and chromatographic techniques developed to work on solutions can not be applied on coal as it is relatively insoluble in generally available solvents. Spectroscopic techniques, such as FTIR, solid state <sup>12</sup>C nmr, esr and mass spectroscopy can be applied on solid coal. Solubilisation (extractability) of coal in generally available organic solvents (such as chloroform) can be enhanced through depolymerisation (phenolation), reduction, alkaline degradation and acety­lation of coal. Solubilisation of coal through these reactions affords the application of spectral techniques. Studies have been reported on Assam coal. Pyrolysis and hydro-pyrolysis of Godavari coal yield predominantly aliphatic and aromatic tars, respec­tively. Spectral studies of coal tars reveal some information on the organic chemical structure of coal. A combination of spectroscopic studies of coal extracts and coal tars obtained would help in the studies of the organic chemical structure of coal macromolecules.

Topic: Coal and Coke Industries Research
Subfield: Fuel Technology
Field: Energy
Domain: Physical Sciences
Black–white wage differentials: duration and probability unemployment effects in a multiple of sample selection bias model

The extent to which probability and duration of unemployment affect the black--white wage differentials is examined in this paper. The paper simultaneously incorporates in the wage equation the multiple sample selection bias that occurs as a result of individuals’ propensity to be in the labor force, and the firm’s hiring decisions. The results reveal a substantial contribution of the duration of unemployment variable to the black--white wage differential, but a small portion of the differential is explained by the probability of unemployment. The results also indicate a sizeable difference between the contribution of the duration of unemployment variable to the male’s wage differentials (26%) and to the female’s (35%). The study finds that an individual’s labor force decision as well as a firm’s hiring decision are important in the wage determination process and that failure to account for the sample selectivity bias due to these two decisions will result in either underestimating or overestimating the wage differentials between black and white workers. At the macro level, the results seem to suggest that promotion of racial wage equality should be associated with policies that will minimize blacks’ incidence of unemployment and duration of unemployment spells.

Topic: Labor market dynamics and wage inequality
Subfield: Economics and Econometrics
Field: Economics, Econometrics and Finance
Domain: Social Sciences