jimnoneill/paper-to-field-training huggingface dataset:
DNA in situ sensitivity to denaturation: a new parameter for flow cytometry of normal human colonic epithelium and colon carcinoma.

Field: Medicine (Health Sciences)

Modal DNA (ploidy) and sensitivity of DNA in situ to denaturation by acid have been analyzed by flow cytometry of 10 colorectal adenomas and 35 adenocarcinomas; 39 normal mucosa samples served as controls. A new method was developed to denature DNA in chromatin of the freshly isolated, intact, and unfixed individual cell nuclei from surgically resected material. The sensitivity of DNA denaturation (T alpha) was assayed by metachromatic staining with acridine orange and calculated as a ratio of the alpha t index of the tumor sample to the alpha t index of normal mucosa; the alpha t index is that fraction of DNA, following treatment at pH 1.4, that stains metachromatically with acridine orange at pH 2.6. All adenomas were diploid and in nine of 10 the T alpha value was close to 1.00, indicating no difference from control specimens in DNA sensitivity to denaturation. Forty-nine% of adenocarcinomas were aneuploid. Forty-six% of adenocarcinomas differed from normal in sensitivity of DNA to denaturation; the T alpha value was lower than 0.90 indicating that chromatin of the tumor cells was more resistant to denaturation than control cells. There was no correlation between sensitivity to denaturation of DNA and incidence of aneuploidy. However, there was a correlation between T alpha and the pathologically determined stage of disease. There was increased resistance to denaturation in 58% of tumors classified as Dukes' C/D stage, in 36% of tumors classified as Dukes' B, and in 20% classified as Dukes' A stage of the disease. Statistical analysis of these results revealed significant differences between distributions of T alpha in noninvasive (Adenomas and Dukes' A) versus invasive (Dukes' B and C/D) tumors with level of significance at P = 0.02. The data suggest that acid denaturation of DNA in situ may be a valuable adjunct in assessing the biology of colon cancer. The molecular basis for this phenomenon is discussed.
Sleep apnea detection directly from unprocessed ECG through singular spectrum decomposition

Field: Computer Science (Physical Sciences)

ECG-based detection of sleep apnea is generally based on heart rate related indices. Computation of these indices requires an ECG record to be pre-processed and the R-peak locations to be estimated. This study proposes a novel method to detect minute-by-minute sleep apnea episodes directly from an unprocessed ECG through singular spectrum decomposition (SSD). Given an ECG record, SSD was applied to non-overlapping segments and the dominant frequency (DF) of the component in the frequency range 0.02-0.5 Hz was estimated. Each segment was binary classified based on the corresponding DF (1, if DF larger than a defined threshold, 0 otherwise). For every minute, the sum of the corresponding binary values was then used to classify that minute as normal or apnea. Validation was based on the learning set of the Apnea-ECG Database. Two segment lengths, 10s and 20s, were tested, and K-fold cross-validation was used to determine the optimal values for threshold and sum, and for performance analysis. The 20s segment-based analysis proved to be more reliable and provided a sensitivity and a specificity of 67% and 52%, respectively. Although performance of the proposed model is still unsatisfactory, the preliminary results reported in this study suggest that detection of sleep apnea directly from unprocessed ECG may be possible.
Molecular diagnosis of human papilloma virus (HPV) genotypes in women with genital warts in Mosul / Iraq

Field: Medicine (Health Sciences)

Human Papillomavirus (HPV) belongs to the Papillomaviridae family and can contribute to Cervical Cancer (CC). The present study aimed to investigate the genotypic distribution and prevalence of HPV using Phosphate Buffered Saline (PBS) embedded tissue, a cervical swab and a cervical brush in Viral transport medium (VTM) from women with different genital warts with no other disease in Mosul City/ Iraq. A total of 150 samples collected from women with genital warts infections were analyzed. A sequencing analysis of the amplified HPV L1 gene was made and compared with that of the National Center for Biotechnology Information (NCBI). The existence of HPV nucleic acid DNA was examined in all samples by Polymerase Chain Reaction (PCR) using MY09/MY11 and GP+5/GP+6 primers, and then HPV genotypes were identified in Macrogen (Macrogen Co., Seoul, Korea) BioEdit (version 7.2.5.0). From 150 (cervical swab, brush, and tissue) patients with genital warts, the distribution of HPV genotype frequency in females with vaginal warts was 127 patients (84.6%), 10 patients (8%) with High-Risk (HR-HPV) serotypes (4%) of each HPV (16 and 45), while the rest 117 patients (92%) with Low-Risk (LR-HPV) included 60.5% HPV11, 20.5% HPV6 and 11.% HPV10. For the first time in Mosul, Iraq, the study used PBS-embedded tissue from patients with various anogenital lesions to examine the prevalence and genotypic distribution of HPV.
Evaluation of effectiveness of photosensitizers used in laser endodontics disinfection: A systematic review

Field: Dentistry (Health Sciences)

Abstract Photo‐activated disinfection using photosensitizers has been proposed as an adjunct to conventional endodontic therapy for additional disinfection and improved treatment outcomes. This systematic review aims to investigate the effectiveness of photosensitizers used in laser endodontics disinfection. A comprehensive literature search is conducted to identify in vitro and in vivo studies involving photo‐activated disinfection in endodontic treatment. Publications are selected based on predetermined eligibility criteria. From 121 articles, 34 met the inclusion criteria, comprising eight polymicrobial and 26 bacteria‐specific studies. A total of 10 photosensitizers were investigated, including methylene blue, tolonium chloride, polyethylenimine and chlorin (e6), phenothia zinium, chitosan, rose bengal, malachite green, indocyanine green, chlorine p6 and curcumin. Photo‐activated disinfection using tolonium chloride or methylene blue can be an effective adjunct to conventional root canal therapy. More studies are needed to assess the performance of newer photosensitizers to optimize photo‐activated disinfection of the complex root canal space.
Clinical Characteristics, Diagnostic Approach and Outcome of Thyroid Incidental Findings vs. Clinically Overt Thyroid Nodules: An Observational Single-Centre Study.

Field: Medicine (Health Sciences)

Context: Thyroid nodules are common and can present as clinically overt nodules (visible, palpable or symptomatic nodules) and so-called incidentalomas (coincidental findings on imaging techniques). The majority are benign but recognizing clinically relevant nodules remains a challenge. Current Dutch guidelines recommend to refrain from additional diagnostic testing in incidentalomas other than FDG-PET-incidentalomas, unless there are suspicious clinical and/or sonographic features. However, there is no consensus on the further approach and no "real-life" data on the outcome of such an approach. Objective: To compare clinical characteristics, diagnostic approaches and clinical outcome between patients referred with thyroid incidentalomas and non-incidentalomas at one academic referral thyroid clinic. Methods: Clinical and demographical characteristics, diagnostic and therapeutic approaches and outcome were retrospectively obtained from the files of all patients newly referred because of thyroid incidentalomas or non-incidentalomas to our institution (between March 2011 and January 2017). Subsequently, the data were compared between both groups. Results: In total, 351 patients (64.3%) were referred because of non-incidentalomas and 195 (35.7%) because of incidentalomas. Incidentalomas were smaller (48.7% <2 cm) than non-incidentalomas (23.4% <2 cm). Furthermore, incidentalomas were less often symptomatic (15.9 vs. 42.7% p < 0.001). Fine-needle aspiration was performed in a similar percentage of the patients in the two groups (62.6% of incidentalomas vs. 69.8% in non-incidentaloma, p = 0.08). Significantly less malignancies were found among incidentalomas compared to non-incidentalomas (5.1% vs. 11.1%, p = 0.019). Moreover, significantly more malignancies occurred in PET-incidentalomas than non-PET-incidentalomas (11.8% vs. 2.8%, p = 0.023). In fact, the proportion of malignancies in PET-incidentalomas and non-incidentalomas was similar (11.8% vs. 11.1%, p = 0.895). Stability or decrease in size was observed in 96.5% of nodules receiving ultrasound follow-up. Conclusions: Patients with small asymptomatic thyroid incidentalomas represent an important proportion of the patients referred for additional diagnostic evaluation. The risk of malignancy in these patients is lower than in those with symptomatic palpable lesions, particularly in the patients with incidentalomas discovered on CT, MRI or US. Our findings support the current recommendations from the Dutch guidelines to not indiscriminately perform additional analysis and treatment on all incidentalomas, but prioritize this to FDG-PET-incidentalomas and clinically relevant non-PET-incidentalomas. Moreover, US features can further refine the selection of the patients who require immediate FNAC and/or surgery.
Abstract 2900: Phylogenetic classification, structural evolution, and functional divergence of the Ras superfamily of GTPases as tracked by the Conserved Domain Database (CDD)..

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

Abstract The Conserved Domain Database (CDD, http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml) is part of NCBI's Entrez query and retrieval system and is a collection of annotated multiple sequence alignment (MSA) models representing ancient conserved protein domains, basic units of protein function and protein evolution.These MSA models are available as position specific score matrices (PSSMs) for fast identification of conserved domains in protein sequences via Reverse Position Specific -BLAST (RPS-BLAST), a variation of the commonly used PSI-BLAST. The domain models can be viewed and examined interactively using NCBI's CDTree/Cn3D software applications. Conserved functional annotations such as key catalytic and ligand-binding sites are displayed on protein structures sharing significant homology to the query, thereby inferring the underlying mechanism(s) of the protein domain family. Here, we present the current, functionally annotated, evolutionary classification of the Ras GTPase superfamily, including the circularly permuted Ras-like domain, and its downstream effectors such as RasGAP and RasGEF. Using CDTree/Cn3D tools, subfamilies in diverse organisms were inferred from the MSAs, phylogenetic trees, and domain architectures of the Ras superfamily. Furthermore, several subfamilies comprising of only uncharacterized protein sequences have their functions annotated by inference from the molecular and cellular functions of known related proteins having 3D structure, and based on the available literature. We demonstrate the utility of CDTree/Cn3D in studying molecular evolution of protein domain families, and in accelerating the pace of biological discovery by enabling researchers to obtain valuable clues regarding as-yet-unidentified molecular properties and mechanisms. CDTree/Cn3D software is freely available for download via the CDD website. Citation Format: James S. Song, Narmada Thanki, Myra K. Derbyshire, Marc Gwadz, Noreen R. Gonzales, Aron Marchler-Bauer, Stephen H. Bryant. Phylogenetic classification, structural evolution, and functional divergence of the Ras superfamily of GTPases as tracked by the Conserved Domain Database (CDD). [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 2900. doi:10.1158/1538-7445.AM2013-2900
CNO Cycle Burning in Ultra-low Metallicity Solar Mass Stars

Field: Physics and Astronomy (Physical Sciences)

Abstract We use the 1D stellar evolution code MESA to run select models at one solar mass at near zero metallicity to examine the effect of a lack of catalysts for CNO burning on the evolution of these models. We find that for metallicities below 10 −10 Z ⊙ a loop occurs on the HR diagram as the star evolves off the main sequence, corresponding to the onset of significant CNO burning in the core of the star. This feature is visible in the Kippenhahn diagram as a period where the core becomes convective while the burning takes place. During this loop, the degeneracy of the core is lifted as CNO burning produces around 3.7% of the total nuclear energy.
Geysering in Rapidly Filling Storm-Water Tunnels

Field: Engineering (Physical Sciences)

Events that are referred to as geysers have been observed in storm-water or combined sewer systems and are associated with jets of water rising through manholes to a considerable distance above the ground surface. Visual observations suggest that air may be a significant component of the jet. The mechanisms of geyser occurrence have been previously assumed to originate in inertial oscillations that force water up through vertical ventilation shafts. Recent laboratory investigations indicate that geyser formation is associated with the release of trapped air pockets through partially filled vertical shafts. Pressure data from a storm-water tunnel subject to infrequent geyser events is presented to indicate that measured piezometric heads adjacent to the ventilation shaft never increase to levels approaching the ground surface during a geyser event suggesting that air interactions must be an important part of the process. It is concluded that system design to avoid geyser formation must include the consideration of trapped air within the tunnel system.
Working capital management and firm performance in China

Field: Business, Management and Accounting (Social Sciences)

Purpose The purpose of this paper is to examine the relationship between working capital management (WCM) and firm performance in the context of the Chinese economy. Specifically, it investigates the effects of ownership structures as an internal factor and of institutional environments (IE) as an external factor shaping this relationship. Design/methodology/approach The study applies two-way fixed effect regression models to a sample of Chinese listed manufacturing firms for the period of 2010 to 2017. WCM is measured by cash conversion cycles (CCC); profitability is measured by core profit ratios; ownership structures are classified based on state-owned enterprises (SOEs) and non-SOEs; and IEs are measured from dimensions of factor markets (FM) and legal systems (LS). Findings First, the results show a negative relationship between CCC and firm performance. Second, the negative relationship between CCC and profitability is significant for non-SOEs but not for SOEs. Third, both the FM and LS strengthen the negative association between CCC and profitability. Fourth, the moderating effect of FMs and LSs is evident for non-SOEs only. The results hold when using alternative measures of WCM and profitability and while controlling for additional variables. Originality/value The current study shows that while WCM has a significant effect on the profitability of Chinese firms, such an effect greatly depends on the ownership structures and IE involved. The results thus offer important implications in helping the Chinese government create better IEs and in allowing manufacturing firms to improve upon their WCM practices.
The Neotropical Mailed Catfishes of the Genera Lamontichthys P. de Miranda Ribeiro, 1939 and Pterosturiosma N. gen.,

Field: Agricultural and Biological Sciences (Life Sciences)

Descriptions and illustrations are given of four species of mailed catfishes belonging to the subfamily Loricariinae, tribe Harttiini. Two species are assigned to Lamontichthys P. de Miranda Ribeiro, 1939: Lamontichthys filamentosus (La Monte, 1935) (type-species, of which Harttia filamentissima C. H. Eigenmann & Allen, 1942, is provisionally considered a junior synonym), based on a total of thirteen specimens, including all type-specimens, from Brazil, Bolivia, Peru, and Ecuador (all from tributaries of the Rio Amazonas system), and Lamontichthys stibaros n. sp., based on two specimens from Ecuador, sympatric with the former species.
[Exploration on the fulminating plague in Bianjing in 1232 and the climatic factors].

Field: Medicine (Health Sciences)

The plague occurred in Bianjing in 1232 was a serious event in the history of Chinese epidemic. It lasted for over 50 days, with a death toll of over 900,000. It is speculated that this is a mass epidemic of pneumonic plague and the pathogen was carried by the Mongolian Army when attacking Bianjing. At that time, the plague spread in Mongolian Army camp and finally involved the suburbs of Bianjing. After the army withdrawal, when Bianjing residents and soldiers went out of the city to collect foods and were unfortunately infected, and thus this dangerous infectious disease was transmitted into the city from the suburbs. Soon, the plague broke out and became epidemic in Bianjing during the 27-day period of 5 May-1 June, because of the cold snap rushed upon Bianjing on 1 June, the unusual weather was the motive for the mass epidemic of the plague. By then, it was popularly recognized as "exogenous cold damage". At present, facing the global climatologic changes, it is of great practical significance to explore the rich materials of plague and the climatic records accumulated in Chinese medicine.
Mucosal vaccination of mice with recombinant Schistosoma japonicum GST-CA induced the immune protection against the challenge infection

Field: Medicine (Health Sciences)

To test the immune protection against challenge infection in mice vaccinated intranasally with recombinant schistosoma japonicum (S j) GST-cytosal aminopeptidese (rSjGST-CA) Mice for experiment of rSjGST-CA were divided into 4 groups each with 11 mice They were immunized intranasally with CTB,rSjGST26+CTB,rSjGST-CA+CTB respectively PBS was used intranasally as control groups The mice were challenged with 40±1 S j cercariae per mouse 2 week after the third vaccination Forty-five days later,mice were killed and perfused,and the adult worms and eggs were counted Serum and saliva samples were collected before the first immunization and the challenge infection IgA and IgG in sera and slgA in salvia were detected by ELISA Results showed that the level of IgA and IgG in sera and slgA in salvia of mice increased after immunization The worm reduction rate and the egg reduction rate were 2 87%,29 62%,31 55% and 10 5%,45 00%,63 34% respectively Collectively a partialy immune protection against schistosoma japonicum infection was induced by intranasal vaccination with rSjGST-CA
Study on Cooperative Games in Electric Vehicle Charging Market on Account of Shapley Distribution Model

Field: Decision Sciences (Social Sciences)

This thesis applies the thought of cooperative game and studies on the best mode of cooperation and benefit distribution in the charging market in supply chain. Firstly by researching the relationship between the unit cost and the number of charging pile construction, the thesis concludes that grid, gas station and car park three party will participate at the same time. Then, with the data of Beijing charging market, it makes specific accounting of five unions of profit model, and finds out the best program in which the three-party union could be established. Finally, it uses classic Shapley method, getting the distribution models of enterprise union.
The Sorediate Punctelia Species With lecanoric Acid in Europe

Field: Agricultural and Biological Sciences (Life Sciences)

Abstract A revision is presented of the sorediate, lecanoric acid-containing Punctelia species occurring in Europe. Two species are common in western andcentral Europe, viz. Punctelia subrudecta s. str. and Punctelia ulophylla comb. nov.They differ in several morphological characters, most notably in the colour andpruinosity of the margin. Both species occur sympatrically, often together on onetree. A third species, Punctelia perreticulata , is known in Europe only from the Mediterranean.
202 ABLATION OF HEPATITIS C VIRUS REPLICON USING SMALL INTERFERING RIBONUCLEIC ACID.

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

The aim of this study was to characterize an adenovirus vector containing the gene for a small interfering RNA (siRNA) targeting the 59-untranslated region (UTR) of the hepatitis C virus (HCV) transcript. Viral production of AdSi73 was upscaled in human embryonic kidney (HEK) 293 cells, and virus particles were purified by a double cesium chloride centrifugation gradient and dialysis. Viral titer was determined by optical density measurement, and the presence of the siRNA gene was confirmed by polymerase chain reaction using sequence-specific primers. Cell cytotoxicity of AdSi73 was assayed in human hepatoma 7 (Huh-7) cells using the Trypan Blue Exclusion method to determine nontoxic titers of virus. AdSi73 was then infected in varying concentration at nontoxic levels into 5/15 replicon cell line stably expressing HCV replicon and grown in selection media supplemented with geneticin (G418) to select for cells expressing the HCV replicon. Twenty-four hours after infection, cells were fixed in acetone, and cells were immunostained for the viral protein NS3. The results of immunstaining showed a dose-dependent inhibition of NS3 expression. The findings of these studies demonstrated that the AdSi73 virus could be purified in a significant quantity and retain the siRNA gene. The data further showed that nontoxic levels of adenovirus could be infected into cells to elicit an inhibition of HCV protein expression. The findings of the current studies implicate that siRNA targeting the 59-UTR could provide a novel mechanism for treatment of HCV infection.
Comic Parrhêsia and the Paradoxes of Repression

Field: Arts and Humanities (Social Sciences)

Comic satirists such as Aristophanes thrive on the tension that arises from their need to ridicule prominent figures of contemporary society and the possibility that this ridicule will cause genuine offense. The history of satire is full of complaints by authors that they work in a dangerous profession, and that their detractors fail to appreciate their high-minded, often explicitly didactic intentions. In such moments, satirists attempt to leave the impression that those who try to repress their freedom to mock and abuse are unwelcome obstacles to their enterprise. It is precisely such allegations of risk and danger, however, that make for effective satire and allow satirists to present themselves as comically “heroic” in the first place. And if satire requires a fraught, antagonistic relationship between author and target, we cannot trust the satirist’s account of the relationship or accept the claim that the alleged oppression is unwelcome. This study begins with such conundra in Aristophanes, and examines comparative evidence from other periods and literary forms, including Homer’s Thersites, Horace, Socrates and Lenny Bruce. Disciplines Arts and Humanities | Classics Comments Rosen, R. M. (2013). Comic Parrhesiaand the Paradoxes of Repression. In Olson, S. D. (Ed.), Ancient Comedy and Reception: Essays in Honor of Jeffrey Henderson (pp. 13-28). Walter de Gruyter. DOI (Chapter): 10.1515/ 9781614511250.13 This book chapter is available at ScholarlyCommons: http://repository.upenn.edu/classics_papers/37