jimnoneill/paper-to-field-training huggingface dataset:
Is tissue still the issue in detecting molecular alterations in lung cancer?

ABSTRACT Molecular biomarker testing of advanced‐stage NSCLC is now considered standard of care and part of the diagnostic algorithm to identify subsets of patients for molecular‐targeted treatment. Tumour tissue biopsy is essential for an accurate initial diagnosis, determination of the histological subtype and for molecular testing. With the increasing use of small biopsies and cytological specimens for diagnosis and the need to identify an increasing number of predictive biomarkers, proper management of the limited amount of sampling materials available is important. Many patients with advanced NSCLC do not have enough tissue for molecular testing and/or do not have a biopsy‐amenable lesion and/or do not want to go through a repeat biopsy given the potential risks. Molecular testing can be difficult or impossible if the sparse material from very small biopsy specimens has already been exhausted for routine diagnostic purposes. A limited diagnostic workup is recommended to preserve sufficient tissue for biomarker testing. In addition, tumour biopsies are limited by tumour heterogeneity, particularly in the setting of disease resistance, and thus may yield false‐negative results. Hence, there have been considerable efforts to determine if liquid biopsy in which molecular alterations can be non‐invasively identified in plasma cell‐free ctDNA, a potential surrogate for the entire tumour genome, can overcome the issues with tissue biopsies and replace the need for the latter.

Topic: Cancer Genomics and Diagnostics
Subfield: Cancer Research
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
Fundus Autofluorescence Imaging in Age-Related Macular Degeneration

Fundus autofluorescence (FAF) is a noninvasive imaging technology that provides information on the distribution of lipofuscin within the retinal pigment epithelial cells. Progressive accumulation of lipofuscin within retinal pigment epithelial cells is involved in the pathogenesis of age-related macular degeneration (AMD). Fundus autofluorescence imaging using a confocal scanning laser ophthalmoscope is a useful technique to identify high-risk characteristics in patients with nonexudative AMD. It gives also some valuable knowledge and clues in differantial diagnosis of exudative age-related macular degeneration. This review comprises an introduction to fundus autofluorescence, a review of FAF imaging in AMD, and the recent classification of geographic atrophy (GA) and early AMD phenotypes by the Fundus Autofluorescence in Age-related Macular Degeneration Study. The association of phenotype and atrophy progression and choroidal neovascularization development are also summarized.

Topic: Retinal Diseases and Treatments
Subfield: Ophthalmology
Field: Medicine
Domain: Health Sciences
Acute Megakaryoblastic Leukemia: A Case Report

Acute megakaryoblastic leukemia (M7) is described as the systemic and rapidly progressive proliferation of megakaryoblasts, atypical megakaryocytes and their undifferentiated precursors. It was an unusal and rare reported in the literature. Here we presented a case of M7 associated with myelofibrosis. The diagnosis of M7 was confirmed by positive immunocytochemical staining with a monoclonal antibody (HP1-1D) specific for glycoprotein IIb/IIIa antigen of platelet and megakaryocyte.

Topic: Chronic Myeloid Leukemia Treatments
Subfield: Hematology
Field: Medicine
Domain: Health Sciences
Labisia pumila var. alata Extract Induces Apoptosis Cell Death by Inhibiting the Activity of Oestrogen Receptors in MCF-7 Breast Cancer Cells

Labisia pumila var. alata (LP) is an herbaceous shrub commonly used by women to promote health and vitality, alleviate postmenopausal symptoms, and enhance libido. Research indicates that LP possesses significant oestrogenic and antiproliferative properties towards breast cancer; however, the specific mechanisms involved remain unclear. We investigate the oestrogenic effects of LP in inducing apoptosis in human breast adenocarcinoma (MCF-7) cells and the mechanisms underlying this process. Docking analysis reveals that the phytoestrogens in LP can bind to oestrogen receptors (ER), specifically ERα and ERβ. MTT assays demonstrate that LP has a dose- and time-dependent antiproliferative effect on MCF-7 cells. Furthermore, the antiproliferative activity of LP on MCF-7 cells is inhibited by Fulvestrant, indicating that its effects are mediated through oestrogen receptors. Flow cytometry analysis shows that the antiproliferative effect of LP results from the induction of apoptosis in MCF-7 cells. The activation of caspase 3, along with caspase 8 and caspase 9, suggests that LP triggers apoptosis through both intrinsic and extrinsic pathways. The findings regarding the aqueous extract of LP and its impact on the proliferative activity of MCF-7 cells may have significant therapeutic and preventive implications for future drug development, particularly in the context of breast cancer.

Topic: Estrogen and related hormone effects
Subfield: Genetics
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
Research of electromagnetic shielding within buildings near transmission line based on FEM

In recent years, the impact of electromagnetic radiation on the lives and environment of urban residents is becoming increasingly apparent. And in the meantime the rapidly growing requirement of people's life quality makes that the electromagnetic environmental problem near high voltage transmission lines is gathering more and more concern. Based on the study of the Finite Element Method, and through simulating and analyzing the electromagnetic character and electromagnetic shielding within building near extra high voltage transmission line, this paper makes use of the Control Variable Method to comprehensively study all the factors that may have an influence on shielding effectiveness. Finally, it puts forward practical, feasible and effective approaches of the electromagnetic shielding scheme selection.

Topic: Electromagnetic Simulation and Numerical Methods
Subfield: Electrical and Electronic Engineering
Field: Engineering
Domain: Physical Sciences
MODELLING THE INACTIVATION BY PEF OF LACTOBACILLUS PLANTARUM IN AN ORANGE JUICE-MILK BEVERAGE

ISHS III International Symposium on Applications of Modelling as an Innovative Technology in the Agri-Food Chain; MODEL-IT MODELLING THE INACTIVATION BY PEF OF LACTOBACILLUS PLANTARUM IN AN ORANGE JUICE-MILK BEVERAGE

Topic: Botanical Research and Applications
Subfield: Food Science
Field: Agricultural and Biological Sciences
Domain: Life Sciences
Genetics of Diabetic Retinopathy

Abstract Diabetic retinopathy (DR) is a common, vision‐threatening microvascular complication of diabetes mellitus (DM). Early epidemiologic studies revealed a potential heritable component as differences in disease risk persisted between ethnic groups even when controlling for common diabetes risk factors. These insights spawned sib‐pair genetic linkage analyses which confirmed a genetic component to DR risk. Insights from large genome wide association studies (GWAS) have identified numerous single nucleotide polymorphisms (SNPs) associated with DR risk, but these largely could not be replicated in other studies or across ethnic groups. Whole‐exome sequencing (WES) is an emerging technology better positioned than GWAS to identify rare variants conferring risk of DR among diabetic patients. Although the multifactorial, polygenic nature of DR complicates the search for significant genetic risk variants, advances in sequencing technology with large patient cohorts may provide novel actionable insights to improve care for DR patients. Key Concepts Diabetic retinopathy is the most common microvascular complication of diabetes mellitus. Diabetic retinopathy is a leading cause of blindness worldwide. Early epidemiologic studies suggested a strong heritable component to risk of diabetic retinopathy. Genome wide association studies have demonstrated many weak genetic associations with risk of developing diabetic retinopathy but are difficult to reproduce across ethnic groups. Whole exome sequencing is a newer technology that provides more detailed analysis of rare genetic variants and has revealed several diabetic retinopathy risk variants. Epigenetics and pharmacogenomics are emerging areas of research that may guide future personalised therapies for diabetic retinopathy. Diabetes mellitus and diabetic retinopathy are heterogeneous disorders with multifactorial causes, including environmental and genetic factors.

Topic: Retinal Diseases and Treatments
Subfield: Ophthalmology
Field: Medicine
Domain: Health Sciences
CCDC 2011130: Experimental Crystal Structure Determination

An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

Topic: Crystallization and Solubility Studies
Subfield: Materials Chemistry
Field: Materials Science
Domain: Physical Sciences
Fistula Between Bowel and Urinary Tract

No AccessJournal of Urology1 Jul 1960Fistula Between Bowel and Urinary Tract Willard E. Goodwin, Chester C. Winter, and Roderick D. Turner Willard E. GoodwinWillard E. Goodwin More articles by this author , Chester C. WinterChester C. Winter More articles by this author , and Roderick D. TurnerRoderick D. Turner More articles by this author View All Author Informationhttps://doi.org/10.1016/S0022-5347(17)65494-6AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail © 1960 by The American Urological Association Education and Research, Inc.FiguresReferencesRelatedDetailsCited byKrompier A, Howard R, Macewen A, Natoli C and Wear J (2018) Vesicocolonic Fistulas in DiverticulitisJournal of Urology, VOL. 115, NO. 6, (664-666), Online publication date: 1-Jun-1976.Brust R and Morgan A (2018) Renocolic Fistula Secondary to Carcinoma of the ColonJournal of Urology, VOL. 111, NO. 4, (439-440), Online publication date: 1-Apr-1974.Bissada N, Cole A and Fried F (2018) Reno-Alimentary Fistula: An Unusual Urological ProblemJournal of Urology, VOL. 110, NO. 3, (273-276), Online publication date: 1-Sep-1973.Flaster S and Bush I (2018) Ureteroileal Fistula: Report of a Case Complicated by Increased Chloride Reabsorption from the Ileal SegmentJournal of Urology, VOL. 109, NO. 4, (589-591), Online publication date: 1-Apr-1973.Scardino P and Lippitt W (2018) Vesical Intestinal FistulaJournal of Urology, VOL. 99, NO. 6, (752-754), Online publication date: 1-Jun-1968.Ehrenfeld W, Sack M, Shorofsky M and Fine A (2018) Cutaneous Nephrogastric Fistula: Case ReportJournal of Urology, VOL. 97, NO. 1, (33-35), Online publication date: 1-Jan-1967.Wise H and Shimada T (2018) Pyeloduodenal Fistula: A Case ReportJournal of Urology, VOL. 97, NO. 6, (987-989), Online publication date: 1-Jun-1967.Gibbons R and Schmidt J (2018) Reno-Colic and Reno-Colic-Cutaneous Fistula: Report of 3 CasesJournal of Urology, VOL. 94, NO. 5, (520-527), Online publication date: 1-Nov-1965. Volume 84Issue 1July 1960Page: 95-105 Advertisement Copyright & Permissions© 1960 by The American Urological Association Education and Research, Inc.MetricsAuthor Information Willard E. Goodwin More articles by this author Chester C. Winter More articles by this author Roderick D. Turner More articles by this author Expand All Advertisement PDF downloadLoading ...

Topic: Diverticular Disease and Complications
Subfield: Surgery
Field: Medicine
Domain: Health Sciences
Data from &lt;i&gt;GSTP1&lt;/i&gt; Promoter Haplotypes Affect DNA Methylation Levels and Promoter Activity in Breast Carcinomas

&lt;div&gt;Abstract&lt;p&gt;The CpG island spanning the transcription start of the glutathione &lt;i&gt;S&lt;/i&gt;-transferase P1 becomes methylated in a variety of human cancers including breast cancer. To study the effect of sequence variation on hypermethylation of the &lt;i&gt;GSTP1&lt;/i&gt; promoter, we analyzed the genetic and epigenetic variability in 90 tumors from patients with locally advanced breast cancer. High-resolution quantitative analysis revealed large variability in the DNA methylation levels. Lack of methylation was more often observed in the basal and normal-like estrogen receptor (ER)-negative tumors, and methylated &lt;i&gt;GSTP1&lt;/i&gt; was associated with better overall survival (&lt;i&gt;P&lt;/i&gt; = 0.00063). Studies of the genetic variation identified 14 different haplotypes. The distribution of methylation levels of tumors homozygous for the most frequent haplotype was significantly different from other haplotype combinations (&lt;i&gt;P&lt;/i&gt; = 0.011), the difference being more pronounced in ER-positive (&lt;i&gt;P&lt;/i&gt; = 0.005) and progesterone receptor–positive (&lt;i&gt;P&lt;/i&gt; = 0.008) tumors. Regression modeling identified the ER status and haplotype as the main determinants of DNA methylation variability. We identified a putative c-Myb response element (MRE) that was present in one of two minimal promoter haplotypes. &lt;i&gt;In vitro&lt;/i&gt; analysis showed that c-Myb binds to the MRE, but binding was weakened by the two polymorphisms. Transient cotransfections in luminal-type and basal-like breast cancer cell lines confirmed cell-specific differential binding of c-Myb to the polymorphic sites, leading to a change in the expression from the &lt;i&gt;GSTP1&lt;/i&gt; promoter &lt;i&gt;in vivo. GSTP1&lt;/i&gt; expression was moderately but significantly (&lt;i&gt;P&lt;/i&gt; = 0.01) reduced after siRNA-mediated knockdown of c-Myb. Our results indicate that haplotype structure of a promoter is important for the extent of DNA methylation. [Cancer Res 2008;68(14):5562–71]&lt;/p&gt;&lt;/div&gt;

Topic: Epigenetics and DNA Methylation
Subfield: Molecular Biology
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
Preventive effect of FK143, a 5alpha-reductase inhibitor, on chemical hepatocarcinogenesis in rats.

The incidence of hepatocellular carcinoma (HCC) is more prevalent in males than in females. 5alpha-Dihydrotestosterone is the most potent form of androgen and is converted from testosterone by 5alpha-reductase. The antitumor effect of a 5alpha-reductase inhibitor (FK143) was evaluated in a rat chemical hepatocarcinogenesis model (Solt-Farber). Male Fischer 344 rats were used in three groups: (a) control group; (b) low-dose FK143 (FKL) group (20 ppm FK143); and (c) high-dose FK143 (FKH) group (200 ppm FK143). The numbers of both glutathione S-transferase placental form-positive foci (P < 0.05) and hyperplastic nodules (HNs; P < 0.01) in the liver were significantly lower in the FKL group than in the control group. The numbers (P < 0.05) and tumor volume (P < 0.01) of HCCs per liver were significantly lower in the FKL group when compared with the control group. All HCCs were well differentiated in the FKL group, whereas 38% and 36% of HCCs were moderate to poorly differentiated in the control group and the FKH group, respectively. The proliferating cell nuclear antigen labeling index:apoptotic index ratios of enzyme-altered foci, HNs, and HCCs were significantly lower in the FKL group than in the control group. Serum 5alpha-dihydrotestosterone was significantly lower in both the FKL and FKH groups. However, a high dose of FK143 (200 ppm) provided no protection against hepatocarcinogenesis, and the level of serum testosterone was elevated in this group when compared with that in the control group. The low dose of FK143 significantly suppressed the formation of enzyme-altered foci, HNs, and HCCs in rat hepatocarcinogenesis. This may indicate that 5alpha-dihydrotestosterone enhances hepatocarcinogenesis. We conclude that an optimal dose of FK143 may have a suppressive effect on hepatocarcinogenesis.

Topic: Hormonal Regulation and Hypertension
Subfield: Endocrinology, Diabetes and Metabolism
Field: Medicine
Domain: Health Sciences
A New Heuristic Reinforcement Learning for Container Relocation Problem

Abstract Many research efforts on reinforcement learning (RL) is dedicated to solving challenging combinatorial optimization problems, including the container relocation problem (CRP) arising from maritime industry. In CRP, large and heavy containers are stacked on top of each other, those above the target container should be relocated elsewhere before retrieving it. This problem, which minimizes the number of relocations in the retrieval process, is NP-hard, while existing RL studies do not provide satisfactory results yet. We study the structure of CRP problem and design a new heuristic RL framework. On a set of commonly used examples, our RL demonstrates a performance almost equivalent to the most famous results.

Topic: Maritime Ports and Logistics
Subfield: Industrial and Manufacturing Engineering
Field: Engineering
Domain: Physical Sciences
Quantification of medicinally valuable weeds in oil palm plantations of Kerala.

The medicinally valuable weeds naturally growing in young, medium and mature plantations of oil palm were identified and quantified by stratified random sampling technique. Quantification of plants was done in comparison with that in the open condition. Chrysopogon aciculatus Trin. dominates in all the four strata. Naregamia alata Wight & Arn. is another dominant species in mature plantation. Hemidesmus indicus R. Br. occurs frequently in all the four strata. Another frequently occurring species in young oil palm plantation is Elephantopus scaber Linn, and in medium plantations is Chromolaena odorata King & Robinson. Phyllanthus amarus Schum.& Thonn. is very frequent in medium plantation and open condition. Holostemma adakodien Schult occurs frequently in mature plantation. Young oil palm plantation and open condition were found to be the most similar strata whereas mature plantation and open condition were the most dissimilar strata in vegetation pair-wise analysis. Medium oil palm plantation was found to have high concentration of dominance. Species diversity was the highest in mature oil palm plantation. Species evenness was maximum in open condition.

Topic: Biological Control of Invasive Species
Subfield: Insect Science
Field: Agricultural and Biological Sciences
Domain: Life Sciences
Financial Determinants of Corporate Governance Disclosure: Portuguese Evidence

The present study analyses the financial determinants of the level of corporate governance disclosure (CGD) across a large sample of Portuguese firms, listed in the Euronext Lisbon index, in the period between 2005 and 2011. An index, using data drawn from firms’ annual reports regarding corporate governance, was constructed based on content analysis to measure CGD levels. An ordinal logistic model was formulated to explore the financial determinants of information disclosure. The present study’s main findings suggest that firm size and growth opportunities had a significant and positive influence on CGD while financial leverage negatively affected the latter. Finally, no relationship was observed between CGD and financial performance.

Topic: Auditing, Earnings Management, Governance
Subfield: Accounting
Field: Business, Management and Accounting
Domain: Social Sciences
Deciphering the invasive history of a bacterial crop pathogen in the Southern Indian Ocean islands: insights from historical herbarium specimens

Crop pathogens have been a threat to human kind since the birth of agriculture. However, little is known on the evolutionary processes and ecological factors that underlie their emergence and success, and explain epidemics. Insular ecosystems are especially vulnerable to exotic disease invasions and thus provide a model of particular interest. Nowadays, our understanding of plant pathogens and the diseases they cause greatly beneﬁts from molecular genetics and genomics. In this context, herbarium collections are an enormous source of dated, identiﬁed and preserved DNA material that can be used in comparative genomic and phylogeographic studies to elucidate the emergence and evolutionary his-tory of pathogens. In this study, we reconstructed the genomes of 6 historical strains of the Citrus phytopathogen Xanthomonas citri pv. citri ( Xcc) obtained from infected herbarium specimens. We designed a speciﬁc extraction protocol suited for bacterial ancient DNA (aDNA) from herbarium spec-imens, and showed the authenticity of our historical samples by assessing DNA damage patterns. We then compared the historical strains to a large set of modern genomes to reconstruct their phylogenetic relationship and estimate several evolutionary parameters at the scale of the Southern Indian Ocean (SIO) islands, using Bayesian tip-calibration inferences. Our results ﬁrst conﬁrm that Xcc originated in Asia and subsequently spread to the rest of the world, including the SIO islands. We dated the arrival of Xcc in the SIO area to the mid-19th century and hypothesize that it was linked to human migrations following the abolishment of slavery. By analysing the phylogenetic structure of SIO Xcc we suggest that the introduction of the disease happened ﬁrst in La R´eunion and Mauritius, from which it spread to all other SIO islands. Finally, our results also include the ﬁrst estimation of a mutation rate for a plant pathogenic bacterium. Our study shows the great potential hidden in herbarium collections to bring light on the evolutionary dynamics that drive pathogens invasion at the scale of the Southern Indian Ocean islands, ultimately helping us to better control current and future crop epidemics.

Topic: Plant Pathogenic Bacteria Studies
Subfield: Plant Science
Field: Agricultural and Biological Sciences
Domain: Life Sciences
Additional file 6: of Maternal care in Acanthosomatinae (Insecta: Heteroptera: Acanthosomatidae)—correlated evolution with morphological change

Format: nexus. Title: Data matrix for parsimonious reconstruction of the two traits (maternal care and Pendegrast’s organ) on 53 species, including species with missing data. (NEX 20 kb)

Topic: Coleoptera Taxonomy and Distribution
Subfield: Ecology, Evolution, Behavior and Systematics
Field: Agricultural and Biological Sciences
Domain: Life Sciences
Hipparchia hermione

Hipparchia hermione (Linnaeus, 1764) Papilio hermione Linnaeus, 1764: 281. FIRST RECORD FOR THE VALDIERI AREA. — Turati & Verity (1911). CHOROTYPE. — CS European. ECOLOGY. — Subnemoral, lowland-upper montane, thermophilous, xerophilous. EDIT PROJECT SAMPLING. — Natural reserve Juniperus phoenicea, dry grassland 878 m, VII.2008, CS.

Topic: Lepidoptera: Biology and Taxonomy
Subfield: Genetics
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences