jimnoneill/paper-to-field-training huggingface dataset:
P066 DNA methylation differences and methylation quantitative trait loci in primary sclerosing cholangitis and IgG4-related sclerosing cholangitis

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

Primary sclerosing cholangitis (PSC) and IgG4-related sclerosing cholangitis (IgG4-SC) are fibro-inflammatory conditions of the liver and biliary tree, driven by a complex interplay of genetic, environmental, and immunologic factors. Epigenetic studies sit at the interface between genes and the environment. In previous work we have defined replicable alterations in new-onset adult (Ventham et al, Nat Commun 2016;7:13507) and paediatric inflammatory bowel disease (Adams et al, Inflamm Bowel Dis 2014;20:1784). We have now assayed methylomes of patients with PSC and IgG4-SC to ascertain epigenetic signatures that may provide insight into pathogenesis and novel biomarkers, and compared these with the methylome of ulcerative colitis (UC) and healthy controls (HC). DNA methylation profiling in whole blood and genotyping was performed in 70 PSC, 56 IgG4-SC, 66 UC, and 88 HC samples, with Infinium MethylationEPIC and Global Screening arrays (Illumina). UC patients were selected to match the clinical characteristics (extent, activity) of the PSC-UC cohort. Analysis was performed with R (v4.0.3). DNA methylation data was processed with Minfi, batch effects were treated with ComBat and associations were tested using limma. Genotyping was analysed with Plink (v1.9) and meQTLs with linear models in R. Statistical significance was determined using the Holm method. Compared to HC, 31 probes showed significant methylation differences in PSC, and 13 in IgG4-SC, with 8 probes shared between conditions. In separate subanalyses of PSC-UC and PSC without IBD (n=13) we found 25 significant probes in PSC-UC (6 not found in combined PSC) and 4 significant probes in PSC without IBD, of which only one was shared with PSC-UC. Analysis of the epigenetic clock did not show any age acceleration in PSC or IgG4-SC compared to healthy controls. Genotyping data revealed a strong signal in the HLA region in PSC, not observed in the other groups, though no findings were significant genome-wide as this study was underpowered as a GWAS. However, meQTLs in PSC were also strong in the HLA region with 19/40 significant findings in 4 clusters (HLA-DRB1, BTNL2, CSNK2B, and SFTA2). There was no overlap with the 36 significant meQTLs found in IgG4-SC. Of the significant disease-associated methylation differences PYY, involved in gut mobility and pancreatic secretion, and Interferon receptor subunit IFNAR1 stand out as targets for further investigation. This study provides a novel description of whole-blood methylomes in PSC and IgG4-SC, and correlations with genetic variants. Future studies are needed to establish relationships with gene expression, and outcome measures. Selected significant disease-associated methylation changes in PSC, IgG4-SC, and UC. P values are unadjusted, – denotes non-significance after Holm correction for multiple testing.
Mental health effects from urban bed bug infestation ( Cimex lectularius L.): a cross-sectional study

Field: Medicine (Health Sciences)

Objective To assess whether bed bug infestation was linked to sleep disturbances and symptoms of anxiety and depression. Design Exploratory cross-sectional study. Setting Convenience sample of tenants recruited in apartment complexes from Montreal, Canada. Participants 39 bed bug-exposed tenants were compared with 52 unexposed tenants. Main outcome measures The effect of bed bug-exposed tenants on sleep disturbances, anxiety and depression symptoms measured using the Pittsburgh Sleep Quality Index, 5th subscale, Generalised Anxiety Disorder 7-item scale and Patient Health Questionnaire, 9-item, respectively. Results In adjusted models, bed bug infestation was strongly associated with measured anxiety symptoms (OR (95% CI)=4.8 (1.5 to 14.7)) and sleep disturbance (OR (95% CI)=5.0 (1.3–18.8)). There was a trend to report more symptoms of depression in the bed bug-infested group, although this finding was not statistically significant ((OR (95% CI)=2.5(0.8 to 7.3)). Conclusions These results suggest that individuals exposed to bed bug infestations are at risk of experiencing sleep disturbance and of developing symptoms of anxiety and possibly depression. Greater clinical awareness of this problem is needed in order for patients to receive appropriate mental healthcare. These findings highlight the need for undertaking of deeper inquiry, as well as greater collaboration between medical professionals, public health and community stakeholders.
Fabrication and Characterization of Through-Substrate Interconnects

Field: Engineering (Physical Sciences)

We developed a through-substrate copper-damascene interconnect technology in silicon with minimal impedance. Via impedance was extracted using parameter measurements at 50 GHz that were matched to simple circuit models. The extracted impedance shows resistances ≤ 1 Ω, record-low inductance for aspect ratios > 4, and sidewall capacitance that approaches the theoretical value. For an aspect ratio of 10 (10 in diameter and 100 high), the through-substrate via has an average inductance of 36 pH at 10 GHz, resistance of 0.6 at 1 GHz, and sidewall capacitance of 0.3 pF.
Elevated limb-bud and heart development (LBH) expression indicates poor prognosis and promotes gastric cancer cell proliferation and invasion via upregulating Integrin/FAK/Akt pathway

Field: Medicine (Health Sciences)

The limb-bud and heart development (LBH) gene is a highly conserved, tissue-specific transcription cofactor in vertebrates that regulates multiple key genes in embryonic development. The role of LBH in various cancer types is still controversial, and its specific role and molecular mechanism in the oncogenesis of gastric cancer (GC) remains largely unexplored. In the present study, the prognostic significance and clinicopathological characteristics of LBH in GC was determined. The LBH mRNA expression was first investigated in four independent public datasets (TCGA-STAD, GSE15459, GSE29272, and GSE62254) and then validated with our samples at the protein level. LBH was overexpressed at both the mRNA and protein levels in cancer compared with normal tissues. High LBH expression was correlated with advanced T, N, and M stages. Kaplan–Meier analysis and log-rank test indicated that higher LBH expression was statistically correlated with shorter overall survival (OS) in the public datasets and our study samples. Univariate and multivariate Cox regression analysis showed that LBH was an independent prognostic biomarker for survival in TCGA-STAD, GSE15459, GSE62254 cohorts, and our GC patients. In vitro experiments showed that knockdown of LBH can significantly inhibit the proliferation and invasion of HGC-27 cells, while overexpression of LBH can significantly enhance the proliferation and invasion of BGC-823 cells. Gene Set Enrichment Analysis (GSEA), Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomics (KEGG) indicated that high LBH expression is associated with the PI3K-Akt pathway, focal adhesion, and extracellular matrix (ECM)-receptor interaction. Western blot analysis showed that knockdown of LBH significantly inhibited the expression of integrin α5, integrin β1, p-FAK, and p-Akt. Therefore, results from the present study indicate that LBH is a potential independent prognostic biomarker and promotes proliferation and invasion of GC cells by activating the integrin/FAK/Akt pathway.
Sertularia echinocarpa Allman, 1888, an unexpected new species of Staurotheca Allman, 1888 (Cnidaria; Hydrozoa; Sertulariidae)

Field: Agricultural and Biological Sciences (Life Sciences)

The holotype of Sertularia echinocarpa Allman has been examined, re-described and figured to determine its actual systematic position. The species actually belongs to the genus Staurotheca, raising the number of known species for this genus to 25.
Application of transcriptomics concentration-response modeling for prioritization of contaminants detected in tributaries of the North American Great Lakes

Field: Environmental Science (Physical Sciences)

Abstract As part of the Great Lakes Restoration Initiative, chemical monitoring and surveillance efforts have detected approximately 330 chemicals in surface water of Great Lakes tributaries. There were 140 chemicals for which no empirical toxicity data were available. The aim of this study was to generate transcriptomic points of departure (tPODs) for 10 of these compounds and demonstrate how they could be applied in a screening-level prioritization. Organisms representing three trophic levels of the aquatic food web (Pimephales promelas, Daphnia magna, and Raphidocelis subcapitata) were exposed for 24 hr to a half-log dilution series of nominal exposure concentrations typically ranging from 66.7–0.021 µM of each chemical. In addition to observations of apical effects (e.g., survival and morphology), whole body transcriptomic responses (tPODs) to each chemical were evaluated with targeted analysis using TempO-seq for P. promelas and D. magna and nontargeted RNA-seq for R. subcapitata. The tPODs ranged from 0.18–10.8 µM for P. promelas and 0.32–29 µM for D. magna, with the most potent of the chemicals tested being fipronil carboxamide for both species. For R. subcapitata, the tPODs ranged from 0.04–1.77 µM, with gabapentin as the most potent chemical tested. Empirically derived tPODs from these data-poor chemicals were compared with concentrations detected in the Great Lakes basin. Environmental concentrations were less than the tPODs except for R. subcapitata and 3,4-dichlorophenyl isocyanate. Similarly, tPODs from previously tested data-rich chemicals were compared with environmental concentrations, in which case tPODs from several chemicals overlapped environmental concentrations. This work demonstrates the potential utility of emerging ecological high-throughput transcriptomics assays to support screening and prioritization of data-poor environmental contaminants.
Concentric Left Ventricular Hypertrophy Geometry Predicts Cardiovascular Events After Renal Transplantation

Field: Medicine (Health Sciences)

Background and Objectives Chronic kidney disease population, even after kidney transplant, is at higher risk of cardiovascular events. The aim of the study is to evaluate the relationship between pre-transplant echocardiographic assessment of left ventricular abnormalities and post-transplant cardiovascular events occurrence. Study Design and Setting, Participants and Measurements: Retrospective cohorts observational study, including 231 consecutive kidney transplant patients from Bellvitge University Hospital between 2010 and 2013 accounting with echocardiographic evaluation up to one year before kidney transplant. Patients were classified depending on its left ventricle morphology and mass into four categories (concentric hypertrophy, eccentric hypertrophy, concentric remodeling and normal geometry). Left ventricle mass was indexed to body surface area. Clinical and analytical data was also gathered. The primary outcome was a composite of cardiovascular events (congestive heart failure, acute coronary syndrome, cardiac sudden death, ictus and aortic aneurism rupture). Renal outcomes, and cardiac and overall mortality was also recorded. Results Using the classical definition of LVH, our study found a prevalence of 71 % for LVH in patients screened for waiting list inclusion, similar to previously described prevalence of LVH in dialysis patients. The mean LVMI in our patients was higher compared to general population, indicating the need for other echocardiographic findings to define cardiovascular risk. Of note mean LVMI was 130,43 ± 42,27 g/m2. 164 (71,6%) patients accomplished the previously described left ventricular hypertrophy criteria. 44 patients (18.2 %) were classified as normal geometry, 22 patients (9.6 %) patients as concentric remodeling, 86 patients (37.6 %) as concentric hypertrophy, and 79 patients (34.6 %) as eccentric hypertrophy. LVMI was higher in concentric group compared to all others groups (p. < 0.001 compared to each other group). Figure 1 shows mean left ventricular mass index among geometry groups. Table 1 shows basal population characteristics according geometric pattern At kaplan mayer analysis, patients with concentric pattern had lower cardiovascular free events survival compared with others group (Log Rank 0.002-see Figure 2) At cox regression logistic analysis concentric hypertrophy increases the risk of cardiovascular events comparing to the rest of geometric patterns (HR 2.753 CI 1.368-5.542 p=0.005). Every g/m2 increase on left ventricular mass (compared to the mean of our population) represents a 1.08 fold risk for cardiovascular events (HR 1.08 1.002-1.014 p value 0.005).Conclusions left ventricular geometry is a simple and useful parameter to stratify patients after kidney transplant by risk of cardiovascular events as earlier as from pre-transplant evaluation.
Investigating the challenges and opportunities for sustainable waterfront development in Jeddah City

Field: Environmental Science (Physical Sciences)

Abstract The research paper discusses the challenges and opportunities surrounding sustainable waterfront development in Jeddah City, Saudi Arabia. The city faces several challenges such as inadequate infrastructure and hasty urbanization, but its strategic location, cultural heritage, and economic potential provide opportunities for sustainable development. The paper presents a comprehensive literature review of successful case studies from other cities and regions to identify the best practices and innovative methods for sustainable waterfront development in Jeddah City. The paper recommends green infrastructure, public–private partnerships and community-based planning and design to promote sustainable waterfront development. The paper emphasizes the need for an integrated and coordinated approach to waterfront development that focuses on enhancing resilience, preserving cultural heritage and promoting social equity. The paper suggests that further research is necessary to better understand the challenges and opportunities for sustainable waterfront development in Jeddah City. The areas that require attention include stakeholder engagement, the impact of climate change and the potential for alternative financing mechanisms. The findings of this research paper can guide policy makers, planners, developers and community leaders to make informed decisions toward sustainable waterfront development in Jeddah City.
Normal and anomalous densities in Bose–Einstein condensates with optical lattices

Field: Physics and Astronomy (Physical Sciences)

We study the quantum phase transition from the superfluid to the Mott insulator state in two- and three-dimensional Bose–Einstein condensate with optical lattices using Bose–Hubbard Hamiltonian within the generalized Hatree–Fock–Bogoliubov approximation. The behavior of the depletion and the anomalous fraction has been investigated in the Mott insulator phase. We found that at T = 0, these quantities become significant in two and three dimensions. It is shown also that the dimensionality of the lattice enhances the anomalous density.
Soil erosion hazard assessment using the RUSLE model for the Taung Watershed of Ramotswa Agricultural District in Botswana

Field: Environmental Science (Physical Sciences)

The Revised Universal Soil Loss Equation (RUSLE) model integrated with Remote Sensing (RS) and Geographical Information Systems (GIS) was positively validated to spatially assess soil erosion risk in the Taung Watershed of Ramotswa Agricultural District during the period 2000 – 2020. The estimated annual soil erosion averaged 12.04 and 12.74 t/ha/year in 2000 and 2020, respectively. The Land Use/Land Cover (LULC) and soil type were found to be key determinants of high soil erosion hazard when using RUSLE. The soil erosion assessment tools enabled prioritization of high erosion prone areas in the study area for soil conservation planning and watershed management.
“Write a Word, Get a Third”

Field: Social Sciences (Social Sciences)

This article examines the doubly uncertain work environment of professional songwriters: They are affected by wider events in the music industry, and their immediate work context is a team setting where the distribution of tasks varies from one project to the next. Interviews reveal that songwriters pursue professional interests by enhancing cooperation, rather than engaging in defensive tactics. The author identifies two conventions: equal authorship and professional conciliation. Such conventions elucidate how rewards are managed in a team context of task variation and underscore the mutually constitutive relationship between conflict and cooperation within postbureaucratic forms of organizing.
Pipes, profits and peace: toward a feminist political economy of gas during war

Field: Social Sciences (Social Sciences)

Neoliberal reforms instituted at the behest of International Financial Institutions (IFIs) during conflict are both unchallenged and commonplace. In Ukraine, the IFIs have prescribed radical economic restructuring amid the war in Donbas. One of the most notable reform programs has been the liberalization of the gas market. This article offers a critical, global feminist political economy framework that seeks to understand the gendered impact of radical energy liberalization on Ukrainians during the war in Donbas. The aim of this article is to highlight the fundamentally gendered aspects of such economic restructuring and demonstrate how it has catalyzed further insecurity, inequality, and instability during war. The article argues that more critical, feminist political economy research is needed to understand and critique both economic reforms during war and orthodox energy policy.
Alpha-fetoprotein concentrations measured by radioimmunoassay in diagnosing and excluding hepatocellular carcinoma.

Field: Medicine (Health Sciences)

Serum alpha-fetoprotein (AFP) concentrations were estimated by sensitive radioimmunoassay in 30 patients with cirrhosis complicated by hepatocellular carcinoma and in 100 patients with cirrhosis in whom malignancy was excluded. Twenty-nine of the 30 patients with hepatocellular carcinoma had concentrations above 10 IU/ml (10.5 ng/ml) (median 3500 IU/ml (3675 ng/ml)), whereas only one of the 100 patients with cirrhosis and no tumour development had a raised concentration. Eleven out of 20 patients in whom hepatocellular carcinoma had developed in an apparently normal liver had raised AFP concentrations. In this group the differential diagnosis is usually secondary carcinoma, and three of 50 such patients had AFP concentrations above 10 IU/ml. Noting raised AFP concentrations is thus of considerable value both in detecting and in excluding hepatocellular carcinoma in cirrhosis, for in this case such concentrations gave only 1% false-positive and 3% false-negative results. They are less useful, however, in distinguishing between primary tumours arising in patients without cirrhosis and secondary hepatic deposits, giving 6% false-positive and 45% false-negative results.
The Culture of Piracy, 1580–1630: English Literature and Seaborne Crime

Field: Arts and Humanities (Social Sciences)

Listening to what she terms 'unruly pirate voices' in early modern English literature, in this study Claire Jowitt offers an original and compelling analysis of the cultural meanings of 'piracy'. By examining the often marginal figure of the pirate (and also the sometimes hard-to-distinguish privateer) Jowitt shows how flexibly these figures served to comment on English nationalism, international relations, and contemporary politics. She considers the ways in which piracy can, sometimes in surprising and resourceful ways, overlap and connect with, rather than simply challenge, some of the foundations underpinning Renaissance orthodoxies-absolutism, patriarchy, hierarchy of birth, and the superiority of Europeans and the Christian religion over other peoples and belief systems. Jowitt's discussion ranges over a variety of generic forms including public drama, broadsheets and ballads, prose romance, travel writing, and poetry from the fifty-year period stretching across the reigns of three English monarchs: Elizabeth Tudor, and James and Charles Stuart. Among the early modern writers whose works are analyzed are Heywood, Hakluyt, Shakespeare, Sidney, and Wroth; and among the multifaceted historical figures discussed are Francis Drake, John Ward, Henry Mainwaring, Purser and Clinton. What she calls the 'semantics of piracy' introduces a rich symbolic vein in which these figures, operating across different cultural registers and appealing to audiences in multiple ways, represent and reflect many changing discourses, political and artistic, in early modern England. The first book-length study to look at the cultural impact of Renaissance piracy, The Culture of Piracy, 1580-1630 underlines how the figure of the Renaissance pirate was not only sensational, but also culturally significant. Despite its transgressive nature, piracy also comes to be seen as one of the key mechanisms which served to connect peoples and regions during this period.
COMPARISON OF SCREENING TESTS FOR METALLO-BETA-LACTAMASE PRODUCING GRAM NEGATIVE BACTERIA

Field: Immunology and Microbiology (Life Sciences)

BACKGROUND:The wide spread dissemination of metallo-beta-lactamase (MBL) resistance to carbapenem antibiotics, such as Imipenem (IMP) and other antibiotics, among gram negative pathogens have become a global concern.The present study is to evaluate various screening tests to determine Metallobetalactamase production.OBJECTIVES: 1)To determine the frequency of metallo-beta-lactamases among Imipenem and ceftazidime resistant isolates 2)To evaluate four phenotypic tests for detection of metallo-beta-lactamase. MATERIALS AND METHODS: A total of 48 clinical isolates from various samples showing resistance to imepenem and ceftazidime were screened for MBL production by 4 different methods 1)Imepenem with Ethylene-Diamine-Tetra-Acetic acid ( EDTA) combined disc test,2)EDTA disc potentiation test with imepenem,3) EDTA disc potentiation test with ceftazidime and 4)ceftazidime with EDTA combined disc test, and compared .RESULTS: In the present study, Of the 48 isolates tested, 34(70.83%)were positive for MBL production by at least one of the methods used.Pseudomonas aeruginosa was the predominant organism producing MBL 18(52.94%)followed by Klebsiella pneumoniae 4(11.76%).EDTA disc potentiation test with imepenem was the most sensitive method 28(82.35%).CONCLUSION: In the present study, Imepenem with EDTA, both combined and double disc potentiation tests were more effective than ceftazidime with EDTA.Though there are several screening methods recommended for detection of MBL production, no single test when used alone is specific for these enzymes.
Human factors influencing the reliability and safety of vehicles, Kenya case study

Field: Engineering (Physical Sciences)

This paper investigates how human decisions and actions in maintenance practices influence the reliability and safety of vehicles in the Kenyan transportation sector. It specifically addresses several human factors that play a crucial role in influencing the reliability and safety of vehicles. Neglecting the manufacturer's recommended maintenance schedule, employing inadequately skilled maintenance personnel, utilizing substandard replacement parts, and exhibiting poor driving habits emerge as key contributors to the compromised reliability and safety within the country's road transportation sector. The research underscores the substantial implications of these human factors, shedding light on their profound influence on the overall condition and security of vehicles in the Kenyan transportation landscape. This paper aims to contribute valuable insights for improving maintenance practices and fostering a safer and more reliable environment within the country's transportation sector, ultimately promoting enhanced safety standards and operational efficiency.