Miracle-dz/UniFAR-FTUs huggingface dataset:
An Anatomical Site and Genetic-Based Prognostic Model for Patients With Nuclear Protein in Testis (NUT) Midline Carcinoma: Analysis of 124 Patients

Abstract Background NUT midline carcinoma, renamed NUT carcinoma (NC), is an aggressive squamous cancer defined by rearrangement of the NUTM1 gene. Although a subset of patients can be cured, for the majority of patients the prognosis is grim. We sought to classify patients into risk groups based on molecular and clinicopathologic factors at the time of diagnosis. Methods Clinicopathologic variables and survival outcomes were extracted for a total of 141 NC patients from the NUT midline carcinoma Registry using questionnaires and medical records. Translocation type was identified by molecular analyses. Survival tree regression analysis was performed to determine risk factors associated with overall survival (OS). Results For 141 patients, the median age at diagnosis was 23.6 years. Fifty-one percent had thoracic origin compared with 49% nonthoracic sites (41% head and neck, 6% bone or soft tissue, 1% other). The median OS was 6.5 months (95% confidence interval [CI] = 5.8 to 9.1 months). Most patients had the BRD4-NUTM1 fusion (78%), followed by BRD3-NUTM1 (15%) and NSD3-NUTM1 (6%). Survival tree regression identified three statistically distinct risk groups among 124 patients classified by anatomical site and genetics: group A is nonthoracic primary, BRD3-, or NSD3-NUT (n = 12, median OS = 36.5 months, 95% CI = 12.5 to not reported months); group B is nonthoracic primary, BRD4-NUT (n = 45, median OS = 10 months, 95% CI = 7 to 14.6 months); and group C is thoracic primary (n = 67, median OS = 4.4 months, 95% CI = 3.5 to 5.6 months). Only groups A and B had long-term (≥3 years, n = 12) survivors. Conclusions We identify three risk groups defined by anatomic site and NUT fusion type. Nonthoracic primary with non-BRD4-NUT fusion confers the best prognosis, followed by nonthoracic primary with BRD4-NUT. Thoracic NC patients, regardless of the NUT fusion, have the worst survival.
Polycyclic aromatic hydrocarbon internal dose, oxidative stress, inflammation and asthma exacerbation in asthmatic adults and children in Baltimore City

Background: Asthma is a common chronic inflammatory respiratory disease that disproportionately affects children and African Americans residing in urban, low socioeconomic status communities. Polycyclic aromatic hydrocarbons (PAH) are products of incomplete combustion of organic materials and are found in gas phase, and on fine and ultrafine particulate matter (PM). In vitro, animal and human studies have shown PAHs to be associated with increased oxidative stress, allergen-mediated inflammatory responses and asthma exacerbation. Methods: In this study, we examined whether internal dose of PAHs (urinary 1-OHPG) was associated with early effect biomarkers of oxidative stress, inflammation, and asthma-related symptoms in the DISCOVER/Asthma-Diet study (children with asthma in Baltimore) and the Nasal Challenge to Indoor Particulate Matter study (adults with atopic asthma in Baltimore). Results: We found that children spending time in homes with low air nicotine concentrations showed inverse associations between time spent indoors and urinary 1OHPG concentrations. In addition, time spent outdoors was independently associated with increased 1-OHPG in boys. Atopy modulated the associations between urinary 1OHPG and peripheral blood eosinophils and neutrophils, with significantly stronger positive associations among atopic asthmatic children compared to non-atopic asthmatic children. Children with high urinary 1-OHPG concentrations were also at an increased risk for nighttime waking due to asthma symptoms and nighttime rescue medication use. We also found that GSTM1 genotype modified the associations between 1-OHPG and urinary isoprostane and serum and peripheral blood inflammatory biomarkers in adult
Ecology and applications of benthic foraminifera

In this volume John Murray investigates the ecological processes that control the distribution, abundance, and species diversity of benthic foraminifera in environments ranging from marsh to the deepest ocean. To interpret the fossil record it is necessary to have an understanding of the ecology of modern foraminifera and the processes operating after death leading to burial and fossilisation. This book presents the ecological background required to explain how fossil forms are used in dating rocks and reconstructing past environmental features including changes of sea level. It demonstrates how living foraminifera can be used to monitor modern-day environmental change. Ecology and Applications of Benthic Foraminifera presents a comprehensive and global coverage of the subject using all the available literature. It is supported by a website hosting a large database of additional ecological information (www.cambridge.org/0521828392) and will form an important reference for academic researchers and graduate students in Earth and Environmental Sciences.
Produtividade, qualidade fisiológica e composição química de sementes de crambe em diferentes doses de fósforo

O crambe e uma brassica com alto teor de oleo utilizada para producao de biodiesel e que tem despertado interesse pelo ciclo curto e baixo custo de producao. Porem, existem duvidas quanto a sua resposta a adubacao fosfatada. O objetivo deste trabalho foi avaliar o efeito de diferentes doses de fosforo sobre a produtividade, a qualidade fisiologica, a composicao quimica e o teor de oleo de sementes de crambe. Os tratamentos foram constituidos de cinco doses de fosforo (0, 25, 50, 75 e 100 kg ha-1) aplicados na semeadura. Nao houve interferencia do fosforo sobre a composicao mineral e o teor de oleo das sementes de crambe que apresentaram as seguintes medias: 30,11 de N; 7,46 de P; 7,35 de K; 10,06 de Ca; 6,58 de Mg e 8,98 g kg-1 de S; 36,25 de Cu; 169,40 de Fe; 36,75 de Mn, 73,60 mg kg-1 de Zn e 30,22% de oleo. Concluiu-se que a produtividade de crambe aumenta com doses de fosforo de ate 100 kg ha-1, porem o seu uso nao afeta a porcentagem de sobrevivencia de plantas, a fitomassa seca, a massa de mil sementes, a qualidade fisiologica, a composicao quimica e o teor de oleo da semente.
N-フェニルスルホニル-2-クロロイソニコチン酸アミドのイネいもち病に対する作用特性

N-フェニルスルホニル-2-クロロイソニコチン酸アミド (NPSI) はイネいもち病に対し治療効果には乏しかったが, 50cm2ポット当り有効成分量2. 2mg以上の水面施用で高い防除効果を示し, 効果は4週間以上持続した. NPSIのイネいもち病菌に対する直接の抗菌力は非常に弱く, これによって防除効果は説明できなかった. NPSI処理イネ葉上に生ずるイネいもち病病斑については小型の褐色病斑の全病斑数に対する割合が無処理の25. 5%から45. 7%へ高まった. NPSI処理イネにイネいもち病菌を接種するとイネ葉のパーオキシダーゼ活性が無処理-接種イネに比し, 接種1日後で1. 53倍, 3日後で1. 73倍, 7日後で1. 56倍に増大した. さらにNPSIの防除効果はアブシジン酸50ppmの茎葉散布で低下した. 以上よりNPSIはイネ体のイネいもち病に対する抵抗反応に関わって防除効果を発揮すると考えられた.
N‐[6‐(Hydroxy­methyl)pyridin‐2‐yl]‐2,2‐dimethyl­propanamide

In the title compound, C11H16N2O2, inversion-related mol­ecules form an O—H⋯O and N—H⋯O hydrogen-bonded dimer. The hydrogen bonds generate rings of motifs R_{2}^{1}(6) and R_{2}^{2}(10). Weak π–π interactions between the dimers stabilize the crystal packing.
Influence of temperature on pathogenicity of some entomopathogenic nematode isolates (Steinernema spp.) from Japan screened for ability to control some noctuid moth larvae

Nematodes belonging to the genera Steinernema Travassos, 1927 and Heterorhabditis Poinar, 1976 are called “entomopathogenic nematodes (EPNs)”. As EPNs have outstanding beneficial traits such as high pathogenicity against insects, durable survivability and host-searching ability of the infective third-stage juvenile, reproduction on artificial medium, symbiotic association with entomopathogenic bacteria, and so on (Gaugler, 2002), scientific and commercial interests in EPNs discovered numerous geographic isolates (Hominick, 2002), are still searching for new species/isolates, are developing mass-production and formulation technologies and creating commercial insecticide products composed of EPNs for pest management (Georgis et al., 2006; Kaya et al., 2006). In Japan, a series of intensive research projects for the practical utilization of the EPNs, especially an introduced species, S. carpocapsae (Weiser, 1955), were conducted from the 80s to the 90s (Ishibashi, 1992) and two introduced nematode insecticide products composed of S. carpocapsae and S. glaseri (Steiner, 1929) are being utilized in Japan nowadays. Especially an introduced nematode insecticide product composed of S. carpocapsae is widely being applied to turfgrass, vegetables, fruit trees, flowers, ornamental plants, and so on (JPPNET, 2009). On the contrary, although more than ten steinernematid species have been recorded from Japan (Mamiya and Ogura, 1990; Mamiya et al., 1995; 2001; Phan et al., 2006; Stock et al., 1998; Yoshida, 2003; 2004; 2007; Yoshida et al., 1998), so far only S. kushidai Mamiya, 1988 has been applied to control white grubs mainly in golf course turfgrass and sweet potato fields (Ando, 1995; Ogura and Oya, 1992; Oya and Kamiwada, 1990; Suzuki et al., 2000). Temperature conditions have a significant impact on infectivity of EPNs and low and high temperatures usually restrict the use of the EPNs (Griffin, 1993). For example, S. carpocapsae is generally recommended to be used at ambient temperatures between 20 and 30°C with the efficacy declining at temperatures below 15°C and above 35°C (Fujiie, 1998). The lethal effect of S. kushidai also declined on the third instar larvae of Anomala cuprea (Hope, 1839) at 10, 15 and 35°C (Fujiie et al., 1995). When examining the efficacy of EPNs against insects, it is important to monitor the temperature range at which the tested EPNs demonNematological Research Vol. 40 No. 2 December, 2010
Agrupamiento de genotipos de la colección nacional de trigo en base a genes de interés agronómico

En la busqueda de diversidad para incluir en los programas de mejoramiento es de gran importancia el estudio de la coleccion nacional de trigo como fuente donadora de genes y con base en el comportamiento genotipico y fenotipico de sus accesiones detectar las asociaciones de importancia entre ambos caracteres, asi como agrupar individuos con fondos genetico similares para caracteristicas de interes agronomico como tolerancia a royas, gluteninas, altura, vernalizacion. Para evaluar los caracteres fenotipicos, el ensayo se establecio en Nanacamilpa, Tlaxcala y Roque, Guanajuato, durante dos ciclos en cada localidad, otono- invierno 2010-2011 y 2011-2012 en Roque, y primavera- verano 2011 y 2012 en Nanacamilpa. Para las variables genotipicas se usaron 16 marcadores moleculares asociados a diferentes caracteristicas de interes en trigo, para royas: Lr68, Lr34, Lr46 y Sr2; gluteninas: Glu-A1b, Glu-B1al y Glu-D1; altura de planta: Rht-B1 y Rht-D1; fotoperiodo: Ppd-D1a; vernalizacion: Vrn-A1, Vrn-B1 y Vrv-D1a; dureza del endospermo: PinA-D1a y PinB-D1a; y contenido de amilosa: GBSS. Las medias de los caracteres fenotipicos se conjuntaron con los resultados de los marcadores y se analizaron mediante un analisis de conglomerados, usando la metodologia de Ward (1963). Se formaron 12 grupos de los cuales, las variedades del grupo 5 fueron las mas precoces con un ciclo medio a floracion y madurez de 74.8 y 118.6 dds respectivamente. Las variedades mas tardias estan comprendidas en el grupo 6 (sin alelos Ppd-D1) con una diferencia de hasta 14.3 dias en el ciclo a madurez. En general los grupos 3, 4 y 12 poseen variedades con caracteristicas deseables (precocidad, resistencia a enfermedades y genes asociados a la calidad industrial).
Interleukin-3 supports expansion of long-term multilineage repopulating activity after multiple stem cell divisions in vitro

Although long-term repopulating hematopoietic stem cells (HSC) can self-renew and expand extensively in vivo, most efforts at expanding HSC in vitro have proved unsuccessful and have frequently resulted in compromised rather than improved HSC grafts. This has triggered the search for the optimal combination of cytokines for HSC expansion. Through such studies, c-kit ligand (KL), flt3 ligand (FL), thrombopoietin, and IL-11 have emerged as likely positive regulators of HSC self-renewal. In contrast, numerous studies have implicated a unique and potent negative regulatory role of IL-3, suggesting perhaps distinct regulation of HSC fate by different cytokines. However, the interpretations of these findings are complicated by the fact that different cytokines might target distinct subpopulations within the HSC compartment and by the lack of evidence for HSC undergoing self-renewal. Here, in the presence of KL+FL+megakaryocyte growth and development factor (MGDF), which recruits virtually all Lin(-)Sca-1(+)kit(+) bone marrow cells into proliferation and promotes their self-renewal under serum-free conditions, IL-3 and IL-11 revealed an indistinguishable ability to further enhance proliferation. Surprisingly, and similar to IL-11, IL-3 supported KL+FL+MGDF-induced expansion of multilineage, long-term reconstituting activity in primary and secondary recipients. Furthermore, high-resolution cell division tracking demonstrated that all HSC underwent a minimum of 5 cell divisions, suggesting that long-term repopulating HSC are not compromised by IL-3 stimulation after multiple cell divisions. In striking contrast, the ex vivo expansion of murine HSC in fetal calf serum-containing medium resulted in extensive loss of reconstituting activity, an effect further facilitated by the presence of IL-3. (Blood. 2000;96:1748-1755)
Desarrollo floral del maíz in vitro durante la inducción y multiplicación de brotes

El cultivo in vitro para la induccion floral presenta una ventaja por la facilidad de aplicar diversos estimulos que induzcan o inhiban este fenomeno sin involucrar factores ambientales (Scorza, 1982). Los altos rendimientos en maiz como en muchos cultivos depende principalmente del numero de granos producidos por planta y se ha observado que el numero de mazorcas esta determinado por reguladores de crecimiento endogenos (Leal-Leon et al., 2002). Durante la organogenesis directa del maiz in vitro obtenida a partir de la base del coleoptilo se generan estructuras reproductivas femeninas de manera precoz, lo cual es un problema en la induccion y multiplicacion in vitro de brotes de maiz debido a la competencia por la asimilacion de los componentes del medio de cultivo (Iracheta et al., 2003). En el Colegio de Postgraduados en Ciencias Agricolas, en 2006 se estudio la funcion de las fitohormonas en el desarrollo floral de lineas de maiz en la induccion y multiplicacion de brotes probando diferentes citocininas en diferentes dosis y en combinacion con dos dosis de acido indol acetico. Las lineas evaluadas difirieron en su capacidad morfogenica, siendo las lineas de maiz L13 y L14 las que mostraron la mayor capacidad de induccion de brotes. La iniciacion floral se detecto entre 10 y 15 d a partir de la siembra de explantes. El desarrollo de inflorescencias femeninas dependio del tipo de citocininas (de mayor a menor respuesta): BAP > KIN > TDZ. Con ZEA y 2iPA solo se inducen y multiplican brotes vegetativos.
Organogenesis of the kidney

Preface 1. Ontogenesis of the vertebrate excretory system 2. Experimental methods to study kidney development 3. Morphogenetic tissue interactions in the kidney 4. Experimental tubulogenesis 5. Vascularization of the nephron 6. Concluding remarks References Author index Subject index.
Evolution of a Shelly Beach Ridge System over the Last Decades in a Hypertidal Open-coast Embayment (Western Mont-Saint-Michel Bay, NW France)

ABSTRACT Tessier, B. ; Poirier, C. ; Weill, P.; Dezileau, L. ; Rieux, A. ; Mouazé, D. ; Fournier, J., and Bonnot-Courtois, C. , 2019. Evolution of a shelly beach ridge system over the last decades in a hypertidal open-coast embayment (western Mont-Saint-Michel Bay, NW France). In: Castelle, B. and Chaumillon, E. (eds.), Coastal Evolution under Climate Change along the Tropical Overseas and Temperate Metropolitan France. Journal of Coastal Research, Special Issue No. 88, pp. 77–88. Coconut Creek (Florida), ISSN 0749-0208. The behavior of the shelly beach ridge system forming a more or less continuous barrier lying along the southern coast of the hypertidal Mont-Saint-Michel bay (NW France) is examined using a set of various data including aerial photographs since 1947, sediment cores collected in back-barrier salt marshes, ground penetrating radar profiles, and differential digital elevation models (DEMs). The latter shows that since the middle of the 20th century, the tidal flats extending in front of the ridge system experience erosion and accretion that alternate spatially according to cross-shore corridors. The shelly ridges are better developed on line with the erosional bands. The reasons for this erosion/accretion compartment pattern are not totally elucidated. It probably results from the combined influence of shellfish farms, tidal channels and reef present on the tidal flats on wave and current dynamics. At the decadal to pluri-decadal scale, the shelly beach ridge system behavior as well as its internal organization can partly be related to the fluctuations of hydrodynamic conditions controlled by the 18.6 years nodal tidal cycle. Periods of intense landward migration alternate with periods of relative stability during the peak and the trough of the cycle respectively. This general scheme is complicated due to variations in storm wave dynamics. The most morphogenic events happen potentially during coinciding nodal cycle peaks and enhanced storminess. Such conditions actually occurred around 1995-2000, resulting in the most prominent washover fan deposit preserved within the back-barrier infilling successions. These sediment successions evidence as well that no beach ridge system older than the 19th century is preserved in front of the Medieval dike built during the 11th century on a relict beach ridge, and on which the present-day system is backed. We suggest that the enhanced storminess conditions of the Little Ice Age provoked the reworking of beach ridges formed between the 11th and 19th centuries. Changes in quantity and type of mollusk shells, related to the shellfish farming development during the 20th century are also thought to have had positive consequences on the barrier building and stability.
Molecular Architecture of Genetically-Tractable GABA Synapses in C. elegans

Inhibitory synapses represent a minority of the total chemical synapses in the mammalian brain, yet proper tuning of inhibition is fundamental to shape neuronal network properties. The neurotransmitter γ-aminobutyric acid (GABA) mediates rapid synaptic inhibition by the activation of the type A GABA receptor (GABAAR), a pentameric chloride channel that governs major inhibitory neuronal transduction in the nervous system. Impaired GABA transmission leads to a variety of neuropsychiatric diseases, including schizophrenia, autism, epilepsy or anxiety. From an evolutionary perspective, GABAAR shows remarkable conservations, and are found in all eukaryotic clades and even in bacteria and archaea. Specifically, bona fide GABAARs are found in the nematode Caenorhabditis elegans. Because of the anatomical simplicity of the nervous system and its amenability to genetic manipulations, C. elegans provide a powerful system to investigate the molecular and cellular biology of GABA synapses. In this mini review article, we will introduce the structure of the C. elegans GABAergic system and describe recent advances that have identified novel proteins controlling the localization of GABAARs at synapses. In particular, Ce-Punctin/MADD-4 is an evolutionarily-conserved extracellular matrix protein that behaves as an anterograde synaptic organizer to instruct the excitatory or inhibitory identity of postsynaptic domains.
Millimeter-Level Plant Disease Detection From Aerial Photographs via Deep Learning and Crowdsourced Data

Computer vision models that can recognize plant diseases in the field would be valuable tools for disease management and resistance breeding. Generating enough data to train these models is difficult, however, since only trained experts can accurately identify symptoms. In this study, we describe and implement a two-step method for generating a large amount of high-quality training data with minimal expert input. First, experts located symptoms of northern leaf blight (NLB) in field images taken by unmanned aerial vehicles (UAVs), annotating them quickly at low resolution. Second, non-experts were asked to draw polygons around the identified diseased areas, producing high-resolution ground truths that were automatically screened based on agreement between multiple workers. We then used these crowdsourced data to train a convolutional neural network (CNN), feeding the output into a conditional random field (CRF) to segment images into lesion and non-lesion regions with accuracy of 0.9979 and F1 score of 0.7153. The CNN trained on crowdsourced data showed greatly improved spatial resolution compared to one trained on expert-generated data, despite using only one fifth as many expert annotations. The final model was able to accurately delineate lesions down to the millimeter level from UAV-collected images, the finest scale of aerial plant disease detection achieved to date. The two-step approach to generating training data is a promising method to streamline deep learning approaches for plant disease detection, and for complex plant phenotyping tasks in general.
Iron Sulfide Nanoparticles Embedded Into a Nitrogen and Sulfur Co-doped Carbon Sphere as a Highly Active Oxygen Reduction Electrocatalyst

The unique micro/mesoporous spherical nanostructure composed of non-noble metal nanoparticles encapsulated within a heteroatom-doped carbon matrix provides great advantages for constructing advanced non-precious oxygen reduction (ORR) electrocatalysts. Herein, a promising oxygen electrocatalyst comprising iron sulfide (Fe1−xS) nanoparticles embedded into a nitrogen and sulfur co-doped carbon sphere (Fe1−xS/NS-CS) is successfully explored through a simple and fast polymerization between methylolmelamines (MMA) and ammonium ferric citrate (AFC) as well as a high-temperature vulcanization process. Moreover, the proposed polymerization reaction can be finished completely within a very short time, which is useful for large-scale manufacturing. Impressively, the developed Fe1−xS/NS-MCS catalyst demonstrates outstanding ORR catalytic activity in terms of a more positive onset and half-wave potential as well, as much a better methanol tolerance and stability, in comparison with that of Pt/C benchmarked catalyst. The remarkable ORR electrocatalytic properties are strongly associated with the favorable characteristic spherical N, the S co-doped porous graphitic carbon nanoskeleton incorporated with the Fe1−xS nanoparticle-encapsulation structure.
BDNF Val66Met Positive Players Demonstrate Diffusion Tensor Imaging Consistent With Impaired Myelination Associated With High Levels of Soccer Heading: Indication of a Potential Gene-Environment Interaction Mechanism

The purpose of this study was to examine the potential effect modifying role of the BDNF Val66Met polymorphism on the association of soccer heading with white matter microstructure. We studied 312 players enrolled in the ongoing Einstein Soccer Study, a longitudinal study of amateur soccer player in New York City and surrounding areas. At enrollment and 2 years later, total heading in the prior 12 months (12-mo.) was estimated using an established self-report instrument and diffusion tensor imaging (DTI) was performed. Generalized Estimating Equations (GEE) logistic regression models were employed to test effect modification by the BDNF Val66Met polymorphism on the association between 12-mo. heading exposure and DTI. We identified a significant interaction of 12-mo heading*BDNF Val66Met genotype on the presence of low Radial Diffusivity, a DTI marker associated with myelination. Only Met (+) players demonstrated significantly reduced odds of low RD [OR (95 % CI): −2.36 (−3.53, −1.19)] associated with the highest vs. lowest quartile of 12-mo heading exposure. BDNF Val66Met (+) soccer players with long-term exposure to high levels of heading exhibit less low Radial Diffusivity, suggesting impaired re-myelination may be a substrate of the previously reported association between heading and poor functional outcomes in soccer players.