jimnoneill/paper-to-field-training huggingface dataset:
Abstract P2-03-11: Genomic pattern of breast carcinomas carrying mutations of non-BRCA homologous recombination genes

Field: Medicine (Health Sciences)

Abstract Background BRCA1 and BRCA2 are involved in the homologous recombination (HR) double-strand DNA break repair and genomic patterns of breast tumors with defective BRCA are characterized by increased genomic instability. The pre-clinical and clinical studies show that tumors with defective BRCA or other HR genes can response to platinum and PARP inhibitors. However, the genomic pattern of tumors carrying mutations of non-BRCA HR genes are not investigated. Methods Genomic patterns of breast carcinomas were performed by comparative genomic hybridization (CGH) array containing 60000 probes covering the whole genome with an average spacing of 40kb. The frequency of gains and losses for each regions detected by probes was calculated by ratio thresholds of 0.25 and -0.25, respectively. Large-scale genomic structural aberration was defined as the region of gains and losses of at least 10Mb. We analyzed the difference of large-scale aberration, including numbers, length and specific regions, between tumors with BRCA mutation (mtBRCA), non-BRCA HR mutation (mtHR) and wild type. Results We examined 41 breast carcinomas, including 15 cases with BRCA mutations, 14 with non-BRCA HR gene mutations and 12 without mutations (control). The 14 non-BRCA HR gene were 1 ATM, 1 BRIP1, 1 BARD1, 1 FANCA, 2 FANCB, 1 FANCI, 1 PALB2, 2 RAD50, 2 RAD51C and 2 RAD51D. The number and length of large-scale genomic structural aberration of mtBRCA tumors were significantly higher than wild type tumors (number p=0.005; length p=0.005), indicating CGH can distinguish the mtBRCA from control tumors. We then checked the mtHR tumors, which also revealed significantly increased number and longer length of structural aberrations compared to wild type tumors (number p=0.035; length p=0.022), but were not different from mtBRCA tumors (number p=0.204; length p=0.425). Among the specific regions on chromosomes, mtBRCA and mtHR tumors contained similar genomic aberration regions but different from wild type tumors. The most frequent aberration regions of mtBRCA and mtHR tumors are chromosome 6p22.1-p25, 6q21-q27, 8q11.1-q24, 11p11.2-p14.1, 11q, 12p and 19p, which are less revealed in the wild type (all p value &lt;0.05). Conclusions Our study demonstrated a direct evidence that increased genomic instability were the common characteristics of mtBRCA and non-BRCA mtHR tumors. In addition, we identify the specific genomic patterns of mtBRCA and mtHR tumors, which can be a biomarker indicating HR deficiency and response to platinum and PARP inhibitors. Citation Format: Lin P-H, Kuo W-H, Wang M-Y, Lo C, Lin C-H, Lu Y-S, Chiu C-F, Huang C-S. Genomic pattern of breast carcinomas carrying mutations of non-BRCA homologous recombination genes [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P2-03-11.
Predicting wildfire vulnerability using logistic regression and artificial neural networks: a case study in Brazil’s Federal District

Field: Environmental Science (Physical Sciences)

Predicting the spatial distribution of wildfires is an important step towards proper wildfire management. In this work, we applied two data-mining models commonly used to predict fire occurrence – logistic regression (LR) and an artificial neural network (ANN) – to Brazil’s Federal District, located inside the Brazilian Cerrado. We used Landsat-based burned area products to generate the dependent variable, and nine different anthropogenic and environmental factors as explanatory variables. The models were optimised via feature selection for best area under receiver operating characteristic curve (AUC) and then validated with real burn area data. The models had similar performance, but the ANN model showed better AUC (0.77) and accuracy values when evaluating exclusively non-burned areas (73.39%), whereas it had worse accuracy overall (66.55%) when classifying burned areas, in which LR performed better (65.24%). Moreover, we compared the contribution of each variable to the models, adding some insight into the main causes of wildfires in the region. The main driving aspects of the burned area distribution were land-use type and elevation. The results showed good performance for both models tested. These studies are still scarce despite the importance of the Brazilian savanna.
Flight-initiating interneurons in the locust

Field: Neuroscience (Life Sciences)

We have used intracellular recording and staining techniques to investigate the cellular mechanisms for the initiation and maintenance of flight in the locust, Locusta migratoria. In particular, we examined the properties of a small group of interneurons in the mesothoracic ganglion. We refer to these interneurons as 404 neurons. Their structure has been described, in a closely related species, by Watson and Burrows (21). Using a preparation in which intracellular recordings could be made from the main neurite of a 404 neuron during the generation of flight activity, we observed that the 404 neurons discharged tonically throughout flight episodes elicited by a constant wind stimulus on the head and by a sudden dimming of the lights. Their discharge rate was linearly related to the frequency of the flight activity. Depolarization of individual 404 neurons often initiated flight activity in quiescent preparations, and the application of hyperpolarizing currents during a flight episode either slowed or stopped flight activity. Hyperpolarizing currents also prevented the initiation of flight activity in some preparations. Individual 404 neurons were not always necessary for the generation of flight activity, since flight activity sometimes persisted when all spiking in a 404 neuron was prevented by the application of a hyperpolarizing current. We conclude that the 404 neurons function to initiate and maintain flight activity in response to wind stimulation of the head, but we have not yet established that they are the only thoracic neurons with this function. The 404 neurons discharged with a high-frequency burst at the time of triggering of a kick. Since the motor program for a jump is similar to that for a kick, the 404 neurons may also be involved in linking the initiation of flight activity to the jump. None of our data indicate that the 404 neurons receive input from the central rhythm generator. Thus the neuronal circuitry for flight appears to be hierarchically organized with at least one distinct neuronal system providing a tonic drive to initiate and maintain activity in the system that patterns activity in flight motoneurons.
Aerodynamic modeling and scale-up of a low NO{sub x} oil burner

Field: Engineering (Physical Sciences)

Results of computational and experimental studies in support of the design of a low NO{sub x} oil burner are presented. Radial density stratification is utilized in the Radially Stratified Flame Core (RSFC) burner to reduce the air-fuel mixing in the flame`s near burner flow field and increase the fuel-rich zone residence time in order to reduce NO{sub x} emissions. In the course of the modeling, relationships were established between flow field and flame characteristics in search of an optimal flow pattern leading to low emissions without excessive flame length. The optimal flow pattern was dominated by two internal recirculating zones (IRZ), both produced by the rotating burner air flow. The key burner variables are the radial distributions of the axial and tangential components of the burner air velocity, the fuel spray angle and droplet size distribution. The trends of the modeling data are compared with those of experimental data obtained in full scale tests.
Isolation and biochemical characterization of tyrosinase-rich GERL and coated vesicle in melanin synthesizing cells

Field: Biochemistry, Genetics and Molecular Biology (Life Sciences)

The site of condensation and activation of tyrosinase prior to melanosome melanogenesis has been investigated using subcellular fractionation and enzymic analysis of so-called Golgi apparatus of melanoma cells. Two different functional units have been found in the so-called Golgi fraction, the tyrosinase-rich GERL-coated vesicle unit and the TPPase-rich Golgi unit. The tyrosinase-rich unit consists of a tubular structure with a cisternal portion corresponding to the three-dimensional structural characteristics of GERL, and spheroid vesicles, corresponding to the currently accepted criteria for coated vesicles. This fact suggests, in agreement with electron microscopic observations, that the GERL-coated vesicle unit is a specialized portion of smooth endoplasmic reticulum having the function of activating and condensing the tyrosinase synthesized by ribosomes.
C-21- and 6-hydroxylation of progesterone by rabbit liver subcellular fractions

Field: Biochemistry, Genetics and Molecular Biology (Life Sciences)

In vitro C-21-hydroxylation of [ 3 H]progesterone (P) has been demonstrated for the first time with rabbit liver microsomes and mitochondria. Deoxycorticosterone (DOC) was rigorously characterized as a metabolite of both mitochondrial and microsomal metabolism, whereas 6α-hydroxy DOC and 6α-hydroxy P were only identified as microsomal metabolites. 6β-Hydroxy metabolites were also detected but were of less quantitative significance. Formation of 6α-hydroxy P and 6α-hydroxy DOC increased steadily between 5 and 120 min of incubation with the microsomal fraction, whereas DOC increased up to 30 min of incubation and then declined. Maximal yield of DOC was 25.9 and 22.5 pmol/mg protein with the mitochondrial and microsomal fractions, respectively.
Acute ischaemic stroke

Field: Medicine (Health Sciences)

Stroke is the third most common cause of death worldwide. About 80% of strokes are ischaemic. The only reliable way of distinguishing cerebral infarction from haemorrhage is with neuroimaging, most commonly CT scanning in the UK. The last decade has produced a number of RCTs clarifying former areas of management uncertainty. Three interventions have been shown to be beneficial in acute stroke: admission to a stroke unit; early aspirin; and intravenous thrombolysis. Aspirin and stroke service admission should be available to all patients, thrombolysis is of benefit to a select minority of patients. Accurate diagnosis, investigation, and management of physiological variables such as BP, temperature, glycaemia, and oxygen saturation should improve outcome. Multiprofessional guidelines exist and, when used with education, audit, and other areas of clinical governance, improve the basic standards of care. The National Sentinel Audits of Stroke have repeatedly shown that care is suboptimal. Secondary prevention with anti-platelet drugs (or warfarin in the case of atrial fibrillation), statins, and antihypertensive drugs, reduce recurrent strokes and other vascular events. Patients with 70–99% stenosis of the ipsilateral carotid bulb or internal carotid artery may benefit from early carotid endarterectomy.
NOTE ON THE GENUS APOTOMUS ILLIGER WITH DESCRIPTION OF A NEW SPECIES FROM CHINA (COLEOPTERA:CARABIDAE)

Field: Agricultural and Biological Sciences (Life Sciences)

Apotomus Illiger ranges in Asia,Europe,Africa and Australia,containing fourteen species.One species, Apotomus atripennis Motschulsky,was recorded in Hubei Province of China.One species of the genus is described as new to science in this paper.The type specimen is deposited in the Insect Collections of South China Agricultural University,Guangzhou.
Molecular characterization of Aspergillus flavus strains isolated from animal feeds

Field: Immunology and Microbiology (Life Sciences)

Animal feeds are targets of contamination by aflatoxin producing fungi such as Aspergillus flavus. It is the most prevalent and producer of AFB1, a potent mutagen and carcinogen in humans and animals. The recent molecular and phenotypic data demonstrated existence of different genetic lineages within this species. In this study, we used a combination of morphological and molecular methods to characterize isolated fungal specimens. Figures and tables: 1-Phenotypic characterization of A. flavus isolates grown on A flavus/parasiticus agar (AFPA) medium. 2-Analysis of PCR products of the five Aspergillus flavus isolates. 3-PCR/RFLP analysis of fungal amplicons. 4-Aspergillus flavus isolates identity from NBCI blast. 5-Genbank accession numbers of the Aspergillus flavus isolates. 6-Alignment of aflR-aflS(J) intergenic spacer region sequences in A. flavus isolates and reference strains. 7-Maximum Likelihood tree showing the phylogenetic relationships between the examined Aspergillus flavus strains and reference strains, based on aflR/aflS(J) intergenic sequence.
Learning to Set the Reserve Price Optimally in Laboratory First Price Auctions

Field: Economics, Econometrics and Finance (Social Sciences)

We analyze choices of sellers, each setting a reserve price in a laboratory first price auction with automated equilibrium bidding. Subjects are allowed to gain experience for a fixed period of time prior to making a single payoff-relevant choice. Behavior of more experienced sellers was consistent with benchmark theory: average reserve price for these sellers was independent of the number of bidders and equaled the predicted level. Less experienced sellers however deviated from the theoretical benchmark: on average, they tended to shade reserve price below the predicted level and positively relate it to the number of bidders.
LHD ICRF-DC45 #177566.1

Field: Physics and Astronomy (Physical Sciences)

Ion Cyclotron Range of Frequencies (ICRF) heating system to launch fast waves (Ion Cyclotron Range of Frequencies (ICRF) waves) to heat plasma particles by wave-particle interaction. Raw data are forward and reflected power and voltage of transmission lines, 3.5 U/L and 4.5 U/L.
A Computational Study of the Fluid Particles Distribution in an Helicopter Wake

Field: Engineering (Physical Sciences)

This paper presents a Computational Fluid Dynamics (CFD) study of droplet spray dispersal in the wake of a Mi-2 helicopter up to 600 m downstream. The Reynolds-averaged Navier-Stokes (RANS) equation use a Lagrangian (droplet phase) and Eulerian (fluid phase) procedure to predict the droplet trajectories trough the turbulent aircraft wake. The methods described have the potential to improve current models for aerial spraying and help in the development of new spraying procedure. In this study, models are developed for the sprays released from atomizers mounted on a helicopter. A parametric study of the aircraft model examines the effects of crosswinds on the helicopter's vortex structures and the resulting droplet trajectories. The study shows, that such influence is underestimated in the current models. A comparison of our results with those obtained with AGricultural DISPersal (AGDISP) is also presented.
GENETIC VARIABILITY IN GREEK HONEY BEE (A. mellifera L.) POPULATIONS USING GEOMETRIC MORPHOMETRICS ANALYSIS

Field: Agricultural and Biological Sciences (Life Sciences)

ABSTRACT. The genetic variability of 37 honey bee populations of Greece was studied, using geometric morphometrics analysis, on a sample of 798 honey bees collected from 105 different apiaries. The geometric morphometrics analysis was based on coordinates of 19 landmarks located at vein intersections of the left wing. Statistical analysis of measurements, using MS Excel and Matlab packages, showed high hybridization between the Greek honey bee populations, probably due to beekeeping manipulations (migratory beekeeping and commercial breeding), represented with the standarized wings ’ shapes and revealed from the centroid size of the wings ’ shapes appearance. This estimation is confirmed in the UPGMC dendrogram, where all populations are mixed with the exception of Ikaria and Antikythira populations. Minor inter-population variability was detected only in Karpathos, Kos, Ikaria, Antikythira and Astypalaia islands populations. Samples from Crete island appear to be of a mixed origin, a result that it is in coincidence with a previous study based on mtDNA analysis (Harizanis and Bouga, 2003). Our results are in disagreement with Ruttner’s (1988) morphometrics analysis and partly in disagreement with a preliminary study of ours (Hatjina et al., 2002), where we found that the populations from Rodos, Astypalaia and Ikaria were clearly differentiated from the rest ones and formed a distant group. Geometric morphometrics analysis can be very powerful in exploring intra-specific variation at the population level and it is largely employed in evolutionary studies concerning honey bees in Greece, combined with other approaches such as classical morphometrics and molecular markers.
SH1094155.09FU

Field: Agricultural and Biological Sciences (Life Sciences)

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.
Spontaneous Heteromerization of Gammaretrovirus Envelope Proteins: a Possible Novel Mechanism of Retrovirus Restriction

Field: Biochemistry, Genetics and Molecular Biology (Life Sciences)

ABSTRACT The env gene of gammaretroviruses encodes a glycoprotein conserved among diverse retroviruses, except for the domains involved in receptor binding. Here we show that pairs of gammaretrovirus envelope proteins (from Friend virus and GALV or xenotropic viruses) assemble into heteromers when coexpressed. This assembly results in a strong inhibition of infectivity. An unrelated envelope protein does not assemble in heteromers with the gammaretrovirus glycoproteins tested and does not affect their infectivity, demonstrating the specificity of the mechanism we describe. We propose that the numerous copies of endogenous retroviral env genes conserved within mammalian genomes act as restriction factors against infectious retroviruses.
Comparison of genomic structures in the serovar 1/2a Listeria monocytogenes isolated from meats and listeriosis patients in Japan.

Field: Immunology and Microbiology (Life Sciences)

Foodborne disease by Listeria monocytogenes, serovar 1/2a has recently been reported in many countries. Although contamination by this bacteria is also known to be gradually spreading among the marketed foods of Japan, there is little information on relation between listeriosis and food contamination. In the present study, the characteristics of the genomic structures of serovar 1/2a were compared among the isolates from marketed meats and listeriosis patients. Several isolates from meats purchased at the same shop on different days had the same genomic structure, and prolonged contamination was suggested by the conditions in the shop. Genomic structures of one strain isolated from meat were identical to those of two isolates from a patient. Another isolate was obtained from meats purchased at two different shops, and this isolate was also identical to that of the isolates from another patient. These findings suggest that the isolates from meat may have caused the listeriosis in the patients, and that the strains may have somehow traveled between the shops.
Triacylglycerol Composition of Coffee Beans (Coffea canephora P.) by Reversed Phase High-Performance Liquid Chromatography and Positive Electrospray Tandem Mass Spectroscopy

Field: Agricultural and Biological Sciences (Life Sciences)

The triacylglycerol (TAG) composition of coffee beans (Coffea canephora P.) was determined by reversed phase liquid chromatography−mass spectrometry and tandem mass spectrometry. The TAGs were separated on a Microsorb RP C-18 column in series with a Supelcosil RP C-18 column using isocratic elution with acetonitrile/2-propanol/hexane (v/v/v, 57:38:5) as the mobile phase at a flow rate of 1 mL/min for 100 min. Under these conditions, 13 TAGs were identified (elution order): trilinoleyl-glycerol (LLL, 11.76%), dilinolenoyl-palmitoyl-glycerol (PLnLn, 2.94%), dilinoleyl-oleyl-glycerol (OLL, 7.77%), dilinoleyl-palmitoyl-glycerol (PLL, 25.90%), dipalmitoyl-linolenoyl-glycerol (PPLn, 1.66%), dioleoyl-linoleyl-glycerol (OOL, 1.68%), dilinoleyl-stearyl-glycerol (SLL, 8.28%), palmitoyl-oleyl-linoleyl-glycerol (POL, 8.76%), dipalmitoyl-linoleyl-glycerol (PPL, 13.74%), dilinoleyl-arachidyl-glycerol (ALL, 3.51%), trioleoyl-glycerol (OOO, 2.33%), palmitoyl -linoleyl-stearyl -glycerol (PLS, 8.73%), and distearoyl-linolenonyl-glycerol (SSLn, 2.91%). The relative composition (%) was obtained directly from the data system with the photodiode array detector. Keywords: Coffea canephora P.; coffee beans; triacylglycerols; LC-MS; LC-MS/MS; coffee oil; lipids
Attitudes, decision-making processes, and preferences regarding preconception carrier screening among Hutterites in Manitoba

Field: Social Sciences (Social Sciences)

In response to the increased prevalence of certain autosomal recessive conditions in the Hutterite population, a targeted carrier screening panel is under development at the Health Sciences Centre in Winnipeg, MB. Research on the implementation of other population-based carrier screening tests has shown that to be viewed as acceptable and valuable by the community offered screening, the test itself as well as related education and genetic counselling should be tailored. Tailoring requires an understanding of the perspectives of the target population regarding the benefits, risks, and utility of screening as well as their cultural practices and beliefs that might influence those perspectives. Little is known about the attitudes of Hutterites toward comprehensive carrier screening, how they would use the results, or what their preferences would be regarding provision of such a test. This cross-sectional exploratory study used a convergent mixed methods design to answer these questions, consisting of a chart review, survey, and semi-structured interviews. Surveys were completed by 95 Hutterites and 13 of these also participated in an interview. Results showed that there is considerable support for carrier screening among Manitoban Hutterites but the sentiment is not universal. Many feel that carrier screening has the potential to be helpful to families and communities, but that it may also lead to an unintended loss of social cohesion through an increase in stigma or changes to cultural practices. Individuals need to consider both individual and community factors when making decisions related to carrier screening. Most respondents who expressed interest in carrier screening would alter their family planning after receiving a high-risk result, but an individual’s life stage and life experiences modified this pattern. The results of this study illustrate that the provision of carrier screening can be tailored to the Hutterite community in many ways including at an organizational, educational, and counselling level. Successful implementation of the recommendations provided will help to ensure Hutterites in Manitoba have access to tailored and culturally sensitive care.