jimnoneill/paper-to-field-training huggingface dataset:
Abstract 1183: Targeted sequencing of cell-free DNA data enables comprehensive profiling of tumor copy number landscape from blood

Field: Medicine (Health Sciences)

Abstract Background: The evolution of cancer genomes within a single tumor creates mixed cell populations with divergent somatic mutational architectures. Inference of tumor subpopulations has been disproportionately focused on the assessment of somatic point mutations, whereas computational methods targeting copy number alterations (CNA) in targeted sequencing data remain underdeveloped. Methods: Using a large database of clinical cell-free DNA (cfDNA) sequencing data (Guardant Health, CA), we developed a coverage-based probabilistic model to simultaneously normalize molecular coverage, segment the genome, predict copy number alterations, and estimate the tumor content in cfDNA samples, while accounting for mixtures of cell populations. This model was technically validated using tissue fluorescence in situ hybridization (FISH) data and then applied to a unique set of cfDNA sequencing data from &gt;5,000 normal and clinical samples spanning multiple cancer types, where model predictions were compared to the observed allelic frequencies of somatic driver mutations and heterozygous germline SNPs. Results: Technical validation against FISH-derived tissue copy number estimates demonstrated high concordance with model estimates. Analysis of clinical samples demonstrated a wide range of copy number architectures, including prevalent copy number neutral loss-of-heterozygosity, large chromosomal deletions, and high focal amplifications, all of which are not easily detected and/or differentiated with standard sequencing analysis approaches on highly-fragmented cfDNA. Conclusion: Our results show that probabilistic modeling of coverage data generated from targeted cfDNA sequencing can detect and differentiate heterogeneous tumor populations with diverse somatic variations, CNA, and LOH landscape. This method may enable improvements in CNA detection accuracy, sensitivity, and specificity and provides more precise interrogation of tumor fraction and clonal architecture. Citation Format: Catalin Barbacioru, Eric Collisson, Darya Chudova, Justin Odegaard, Richard Lanman, AmirAli Talasaz. Targeted sequencing of cell-free DNA data enables comprehensive profiling of tumor copy number landscape from blood [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1183.
Form and Formalism: The View from Legal Theory

Field: Arts and Humanities (Social Sciences)

Abstract. The article considers Robert Summers' new book ( Summers 2006 ), in the context of Summers' earlier work and the role of form and formalism in other jurisprudential discussions. While accepting the value of a form‐centered approach to studying law, the article questions Summers' claim that his approach is clearly superior to (and not merely complementary with) traditional analytic theories, like those of Hart and Kelsen. The article also suggests that the book's discussion of form in contract and commercial law is somewhat disappointing, given Summers' expertise in this area, and the many difficult form‐related questions that area raises.
The effect of chemotherapy (CT) and external beam radiotherapy (RT) on bone marrow (BM) toxicity of radionuclides in the treatment of bone metastases secondary to breast cancer

Field: Medicine (Health Sciences)

796 Background: Bone metastases are commonly seen in patients with metastatic breast cancer. Radionuclide therapy has been shown to alleviate the pain of bone metastases but may be associated with BM toxicity, particularly thrombocytopenia. Because many patients with breast cancer and bone metastases also receive CT and RT, we examined the effects of these other treatments on the BM of samarium (Sm)-153-EDTMP (Quadramet®). Methods: A retrospective review of patients (pts) with breast cancer and bone metastases who had received Sm-153-EDTMP was undertaken. Dates of CT and RT, as well as CT regimens were noted. Pre-and post-radionuclide platelet (PLT) and WBC counts were compared, as were the percent decreases in these parameters. Results: Forty-eight pts received 79 courses of Sm-153-EDTMP. Twenty-eight pts received 29 different chemotherapy regimens prior to treatment with Sm-153-EDTMP. Pre- and post-treatment data were available for 21 courses of Sm-153-EDTMP in 20 patients who received CT and RT and for 6 courses of Sm-153-EDTMP in 5 patients who received CT alone. For the entire cohort, the mean ± SEM baseline PLT count was 268 ± 12 x 103/μL, the mean nadir PLT count was 160 ± 10 x 103/μL and the mean percent (%) decrease in PLT count was 42%. The mean baseline WBC was 5.8 ± 0.23 x 103/μL, the mean nadir WBC was 3.7 ± 0.18 x 103/μL and the mean % decrease was 33%. The mean % decrease in PLT and WBC counts in patients receiving CT and RT was 45% and 41% respectively and the mean % decrease in PLT and WBC counts in patients receiving CT alone was 27% and 35%, respectively. The lowest nadir PLT count was 29 x 103/μL and the lowest nadir WBC was 1.3 x 103/μL. Median time to nadir was 28 days. Conclusions: Sm-153-EDTMP is well tolerated in patients with breast cancer who also receive CT and RT. BM toxicity is minimal with relatively small changes observed from pre-radionuclide levels of PLTs and WBCs. Author Disclosure Employment or Leadership Consultant or Advisory Stock Ownership Honoraria Research Funding Expert Testimony Other Remuneration Cytogen Corp.
“Tradition” and Ideology in Black Intellectual Life

Field: Arts and Humanities (Social Sciences)

Abstract In 1989 and 1990 at least three new editions of The Souls of Black Folk were published in the United States, and it was excerpted in at least one collection of “African-American Classics.” An earlier wave of reissues had occurred, not surprisingly, during the 1960s, and the introductory essays accompanying editions in the different periods present a revealing contrast. No reference to the double-consciousness passage appears in either Saunders Redding’s introduction to the 1961 Fawcett edition or Nathan Hare’s and Alvin Poussaint’s introductions to the 1968 Signet edition. Nor does John Hope Franklin mention it in his introductory essay to the 1965 Three Negro Classics collection which includes Souls. In a 1989 Penguin edition, however, Donald B. Gibson construes the double-consciousness tension as a central element of Du Bois’s volume.
Glycoprotein IIb/IIIa Antagonist, Murine 7E3 F(ab′)2, and Tissue Plasminogen Activator in Focal Ischemia: Evaluation of Efficacy and Risk of Hemorrhage with Combination Therapy

Field: Medicine (Health Sciences)

Tissue hypoperfusion during cerebral ischemia results from occlusion of large and small vessels. Combination treatment strategies using fibrinolytics to thrombolyse an embolic clot and antiplatelet agents to prevent reocclusion and the formation of new platelet thrombi in the microcirculation may offer advantages over single-agent therapy. The authors report on the effects of tissue plasminogen activator (rt-PA), a glycoprotein (GP) IIb/IIIa receptor antagonist, 7E3 F(ab′) 2 , or a combination of the two agents in a focal embolic model of cerebral ischemia in Wistar rats. Focal ischemia was produced by introducing an autologous thrombus into the right side middle cerebral artery. Forty-six male Wistar rats were randomly divided into 6 groups: control (n = 8), 7E3 F(ab′) 2 (n = 9, 6 mg/kg), rt-PA (n = 9, 10 mg/kg), rt-PA (n = 6, 20 mg/kg), and 7E3 F(ab′) 2 with either 10 mg/kg (n = 10) (low-dose combination) or 20 mg/kg (n = 6) (high-dose combination) rt-PA. Evaluation of neurobehavioral scores, cerebral angiography, bleeding time, and measurement of brain infarction volume were used to determine efficacy. All actively treated groups showed a significant reduction in the infarct volume. Animals treated with 7E3 F(ab′) 2 showed reduced infarction volumes (24.0 ± 5.1%) compared with controls (42.43 ± 5.6%, P < 0.02). Treatment with rt-PA significantly reduced infarction volume (20.7 ± 3.3, = 0.01) at 10 mg/kg and at 20 mg/kg (19.5 ± 8.2%, P < 0.05). Compared with vehicle-treated animals, the low-dose combination (16.4 ± 5.5, P < 0.003) and high-dose combination (23.7 ± 6.2%, P < 0.05) showed significant reduction in infarction volume. Cerebral angiography revealed significantly better recanalization in the combination group (5/6 animals in the high dose and 4/6 in low dose) compared with animals treated with 7E3 F(ab′) 2 (3/10) or rt-PA alone (2/6). Bleeding time significantly increased from 11.25 ± 1.9 minutes in the control group to 17 ± 3.1 minutes in the rt-PA group, 24.5 ± 2.6 minutes in the 7E3 F(ab′) 2 group, 25.7 ± 3.1 minutes in the low-dose combination group, and 32.5 ± 4.7 minutes in the high-dose combination group. The incidence of intercerebral hemorrhage was highest in the high-dose combination group (6 of 6 animals) and lowest in the single treatment with 7E3 F(ab′) 2 alone (1 of 10 animals) ( P < 0.05). Our data show that murine 7E3 F(ab′) 2 alone has therapeutic effects when used after cerebral ischemia. Although this study suggests that higher doses of thrombolytic combined with anti-GPIIb/IIIa therapy may increases the risk of intracranial hemorrhage, the data also support the notion that anti-GPIIb/IIIa agents can safely be combined with low doses of thrombolytic agent to produce significant attenuation of neuronal damage with no increase in the incidence of cerebral hemorrhage.
The impact of animated content on the thinking and behaviour of Algerian children A descriptive-analytical study of YouTube content

Field: Social Sciences (Social Sciences)

Digital screens are among the primary media that play a crucial role in the reproduction of values. These media provide a set of behaviours that children may perceive as models and imitate, as they are unable to filter what they see. However, the content presented in these media, particularly cartoons, can sometimes contradict the traditions of dignity and respect known in Algerian society. This can potentially undermine children's deeply rooted values, behaviours and habits and contribute to the adoption of inappropriate behaviours. This research aims to identify the behaviours portrayed in electronic screens containing animated drawings by analysing the content of the YouTube application. YouTube was chosen because it is one of the most popular websites used by children, offering the latest animated content.
Successful Utilization of Poly-4-Hydroxybutyrate Mesh in High Risk, Complex Abdominal Wall Reconstructions with Photo-Microscopic Analysis.

Field: Medicine (Health Sciences)

Background: Biosynthetic resorbable mesh offers encouraging alternative for reinforcement in complex hernia repairs. This study evaluated outcomes of P4HB, absorbable polymer scaffold, in high-risk patients undergoing complex abdominal hernia repairs. Materials and Methods: This is a retrospective outcomes analysis of a prospectively kept database. Patient/wound characteristics, perioperative findings, short/mid-term outcomes of our cohort were analyzed. Endpoints included hernia recurrences, wound events and any complications. ACS NSQIP online risk calculator was used for each patient to obtain predicted outcomes as virtual matched control group. We also performed a full-thickness abdominal wall biopsy at 14-months post mesh implantation for histologic evaluation. Results: 28 patients with mean age 57 years and mean BMI 31 were analyzed. 21 patients (75%) had preexisting infections. 20 (71%) of patients had class I wounds per CDC classification at time of surgery. However, 19 of these 20 had wound or deep organ/space infections prior to surgery. Repair types included restoration of Linea Alba with retromuscular mesh placement in 23 patients (82%) with 22 of them requiring additional myofascial release. 5 patients (18%) had only mesh placement. Postoperatively, 11 patients (39%) had complications with zero hernia recurrence and zero mesh explantation at maximum of 42 months of follow up. Conclusion: P4HB can be successfully used in high-risk operative fields with no postoperative mesh explantation, despite serious complications such as infected hematomas. Histologic evaluation of the human tissue, 14-months post-implantation of P4HB confirms mesh presence with surrounding dense collagen scaffold formation and minimal inflammatory response.
Cytogenetic responses of birch to stress factors

Field: Agricultural and Biological Sciences (Life Sciences)

The following range of changes in response to anthropogenic stress has been revealed in experimental birch seedlings relative to control: increased mitotic index, the range and frequency of abnormal mitoses, number of cells with persistent nucleoli, and number of cells in prophase. Cells with vacuolated cytoplasm were also observed. The mutagenic pressure on the organisms in the industrial areas of Voronezh demonstrated a trend to increase, which points to their high environmental pollution.
Occurrence Download

Field: Agricultural and Biological Sciences (Life Sciences)

A dataset containing 134 species occurrences available in GBIF matching the query: { "and" : [ "TaxonKey is Cypripedium fasciculatum Kellogg", "HasCoordinate is TRUE" ] } The dataset includes 134 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001411-160118175350007/datasets/export for details. Data from some individual datasets included in this download may be licensed under less restrictive terms.
[Epidemiology of resistance to antituberculosis drugs in Mycobacterium tuberculosis complex strains isolated from adenopathies in Djibouti. Prospective study carried out in 1999].

Field: Medicine (Health Sciences)

Tuberculosis is a major cause of death in the Republic of Djibouti. Tuberculous lymphadenitis represents about 25% of the clinical forms of tuberculosis in this country. Between January 1999 and April 1999, 196 lymph node specimens were consecutively collected from 153 patients living in Djibouti. Testing of susceptibility to the major anti-tuberculosis drugs was performed by the proportion method. Growth of Mycobacterium tuberculosis complex strains was obtained from specimens of 85 patients including 9 with prior treatment. Strains were identified as Mycobacterium tuberculosis in 78 cases, Mycobacterium canetti in 3, Mycobacterium africanum in 3, and Mycobacterium bovis in 1. Prevalence of HIV infection was 15%. Assessment of primary resistance demonstrated that the overall resistance rate, i.e., resistance to 1 or more drugs, was 18 (21.2%). Results showed resistance to isoniazid (H) in 6 cases (7.1%), rifampicin (R) in 3 (3.5%), ethambutol (E) in 1 (1.2%), streptomycin (S) in 13 (15.3%) and pyrazinamide (Z) in 1 (1.2%). Multidrug resistance (MDR) was found in 2 cases (2.4%). Assessment of acquired resistance demonstrated resistance to H in 4 cases (44%), R in 2 (22%), S in 2 (22%), E in 0, Z in 0 and MDR in 1 (11%). These findings were not significantly different from data obtained from sputum samples analysed between 1997 and 2000 or from those described in a study conducted in 1985.
The impact of the ON-S1 standard on railway risk levels in Australia

Field: Social Sciences (Social Sciences)

The objective of this study was to compare risk levels, based on reported railway occurrences, across Australian states. A secondary aim was to use these numbers to assess the impact of a new reporting system, ON-S1, introduced in 2004, on the calculated risk levels. The Australian nationwide standard, ON-S1, defines how to categorize occurrences and their consequences, but it has not been consistently applied in all states. For example, New South Wales and Victoria use broader definitions of 'serious injury' than specified in ON-S1. This paper outlines challenges related to ON-SI's use and the appropriateness of calculating risks based on reported occurrences. Railway occurrence data from five Australian states/territories from 2001 to 2007 were reviewed. Data on fatalities, serious injuries and train kilometres were obtained from the Australian Transport Safety Bureau (ATSB) and The Independent Transport Safety and reliability Regulator's (ITSRR) safety reports. We used these data to calculate an index of Fatalities and Weighted Injuries (FWI), normalized for train kilometres. The results showed that the average annual risk per million train kilometres for the entire period (2001-2007) was highest in New South Wales (FWI 1.28), followed by Victoria (FWI 0.89), South Australia (FWI 0.77), Queensland (FWI 0.34) and Western Australia (FWI 0.26). Following the introduction of ON-S1, the FWI in New South Wales and Victoria doubled from 2004 to 2006. These trends continued into the first half of 2007. The other states showed a stable or decreasing trend. The highest risk appeared to be in the states with the largest populations containing Australia's largest cities. The use of train kilometres to normalize occurrence rates may be inappropriate because this measure does not take into account the number of people travelling on each train. The sharp increase in reported occurrences in New South Wales and Victoria may reflect the misuse of ON-S1, because a similar increase was not observed in the other states. The large difference in risk level between states highlights a need for consistent application of the national reporting regime in Australia to enable valid comparisons of occurrence rates between states. (6 pages)
Predicting 1-H Dead Fuel Moisture Content at Regional Scales Using Machine Learning from Himawari-8 Data

Field: Environmental Science (Physical Sciences)

Dead fuel moisture content (DFMC) is of important significance for estimating and predicting forest wildfire risk, in which 1-h dead fuel is most critical as the easiest fuel to ignite. Current methodologies based on empirical and physical models rely heavily on meteorological data from uneven and sparse stations. In contrast, satellite data become a better choice since its continuous surface observations. Of all satellites, Himawari-8 is the most appropriate data to meet the rapid changes of DFMC throughout the day owing to its high time resolution. Thus, this study explored the application of 1-h DFMC predicting using machine learning from Himawari -8 data. Random forest was selected for the prediction and linear regression was used for comparison. The results showed that random forest has a satisfactory performance with higher R2 (0.53) and lower RMSE (3.15%) than that of linear regression (R2=0.21, RMSE=5.47%). The research suggested that predicting 1-h DFMC at regional scales using machine learning from Himawari -8 data is promising.
Data from An LTR Retrotransposon-Derived Long Noncoding RNA lncMER52A Promotes Hepatocellular Carcinoma Progression by Binding p120-Catenin

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

<div>Abstract<p>Long terminal repeat (LTR) retrotransposons are a major class of transposable elements, accounting for 8.67% of the human genome. LTRs can serve as regulatory sequences and drive transcription of tissue or cancer-specific transcripts. However, the role of these LTR-activated transcripts, especially long non-coding RNAs (lncRNA), in cancer development remains largely unexplored. Here, we identified a novel lncRNA derived from MER52A retrotransposons (lncMER52A) that was exclusively expressed in hepatocellular carcinoma (HCC). HCC patients with higher lncMER52A had advanced TNM stage, less differentiated tumors, and shorter overall survival. LncMER52A promoted invasion and metastasis of HCC cells <i>in vitro</i> and <i>in vivo</i>. Mechanistically, lncMER52A stabilized p120-catenin and triggered the activation of Rho GTPase downstream of p120-catenin. Furthermore, we found that chromatin accessibility was crucial for the expression of lncMER52A. In addition, YY1 transcription factor bound to the cryptic MER52A LTR promoter and drove lncMER52A transcription in HCC. In conclusion, we identified an LTR-activated lncMER52A, which promoted the progression of HCC cells via stabilizing p120-catenin and activating p120-ctn/Rac1/Cdc42 axis. LncMER52A could serve as biomarker and therapeutic target for patients with HCC.</p>Significance:<p>A novel long noncoding RNA lncMER52 modulates cell migration and invasion via posttranslational control of p120-catenin protein stability.</p></div>
Draft Genome Sequence of Komagataeibacter rhaeticus Strain AF1, a High Producer of Cellulose, Isolated from Kombucha Tea

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

ABSTRACT Here, we present the draft genome sequence of Komagatabaeicter rhaeticus strain AF1, which was isolated from Kombucha tea and is capable of producing high levels of cellulose.
Social Robots as the Bride? Understanding the Construction of Gender in a Japanese Social Robot Product

Field: Arts and Humanities (Social Sciences)

This study critically investigates the construction of gender on a Japanese hologram animestyle social robot Azuma Hikari. By applying a mixed method merging the visual semiotic method and heterogeneous engineering approach in software studies, the signs in Azuma Hikari’s anthropomorphized image and the interactivity enabled by the multimedia interface have been analyzed and discussed. The analysis revealed a stereotyped representation of a Japanese “ideal bride” who should be cute, sexy, comforting, good at housework, and subordinated to “Master”-like husband. Moreover, the device interface disciplines users to play the role of “wage earner” in the simulated marriage and reconstructs the gender relations in reality. It suggests the humanization of the objects is often associated with the dehumanization and objectification of the human in reverse.
Evaluation of Some Safety Parameters of Dual Histamine H3 and Sigma-2 Receptor Ligands with Anti-Obesity Potential

Field: Pharmacology, Toxicology and Pharmaceutics (Life Sciences)

Many studies have shown the high efficacy of histamine H3 receptor ligands in preventing weight gain. In addition to evaluating the efficacy of future drug candidates, it is very important to assess their safety profile, which is established through numerous tests and preclinical studies. The purpose of the present study was to evaluate the safety of histamine H3/sigma-2 receptor ligands by assessing their effects on locomotor activity and motor coordination, as well as on the cardiac function, blood pressure, and plasma activity of certain cellular enzymes. The ligands tested at a dose of 10 mg/kg b.w. did not cause changes in locomotor activity (except for KSK-74) and did not affect motor coordination. Significant reductions in blood pressure were observed after the administration of compounds KSK-63, KSK-73, and KSK-74, which seems logically related to the increased effect of histamine. Although the results of in vitro studies suggest that the tested ligands can block the human ether-a-go-go-related gene (hERG) potassium channels, they did not affect cardiac parameters in vivo. It should be noted that repeated administration of the tested compounds prevented an increase in the activity of alanine aminotransferase (AlaT) and gamma-glutamyl transpeptidases (gGT) observed in the control animals fed a palatable diet. The obtained results show that the ligands selected for this research are not only effective in preventing weight gain but also demonstrate safety in relation to the evaluated parameters, allowing the compounds to proceed to the next stages of research.