jimnoneill/paper-to-field-training huggingface dataset:
Transcriptional Regulation of the Chicken Caldesmon Gene

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

Caldesmon, which plays a vital role in the actomyosin system, is distributed in smooth muscle and non-muscle cells, and its isoformal interconversion between a high M(r) form and low M(r) form is a favorable molecular event for studying phenotypic modulation of smooth muscle cells. Genomic analysis reveals two promoters, of which the gizzard-type promoter displays much higher activity than the brain-type promoter. Here, we have characterized transcriptional regulation of the gizzard-type promoter. Transient transfection assays in chick gizzard smooth muscle cells, chick embryo fibroblasts, mouse skeletal muscle cell line (C2C12), and HeLa cells revealed that the promoter activity was high in smooth muscle cells and fibroblasts, but was extremely low in other cells. Cell type-specific promoter activity depended on an element, CArG1, containing a unique CArG box-like motif (CCAAAAAAGG) at -315, while multiple E boxes were not directly involved in this event. Gel shift assays showed the specific interaction between the CArG1 and nuclear protein factors in smooth muscle cells and fibroblasts. These results suggest that the CArG1 is an essential cis-element for cell type-specific expression of caldesmon and that the function of CArG1 might be controlled under phenotypic modulation of smooth muscle cells.
Diversity patterns and host shifts in ectomycorrhizal fungi across an agricultural disturbance gradient in the mid-Zambezi area, Zimbabwe

Field: Agricultural and Biological Sciences (Life Sciences)

Fallowing creates land mosaics characterised by vegetation communities at different stages of succession. Such mosaics are expected to harbour mycorrhizal associations that reflect host species composition and diversity. Ectomycorrhizal fungi are often a neglected group of the ecosystem despite their importance as bioindicators of disturbance. The present study investigated the diversity of ectomycorrhizal fungi and their host associations across a fallow chrono-sequence of 1-14 years in the mid-Zambezi Valley area, Zimbabwe. A total of ten ectomycorrhizal fungaltaxa that included Lactarius gymnocarpus, Lactarius sp., Boletus sp., Thelephora terrestris and Amphinema byssoides were recorded from 13 tree species from six families (Combretaceae, Ebenaceae, Fabaceae, Simaroubaceae, Rhamnaceae and Tiliaceae). The Spearman rank correlation test showed no significant correlation (p=0.002) between fallow age and ectomycorrhizal fungi status of host tree species. The generalised linear model (GLM) showed no significant relationship (p=0.079) among ectomycorrhizal fungi in any tree species and fallow age. The Raup-Crick similarity index indicated that there was an interaction between fallow age and the mycorrhizal status of the tree species, as opposed to host specificity. These results support previously reported low host specificity for ectomycorrhizal fungi among tropical African plant communities. Theyfurther indicate that selective tree felling negatively impacts host specific ectomycorrhizal fungi. The results also indicate that an increase in host tree species does not necessarily lead to increased ectomycorrhizal species diversity, thus implying the influence of other factors. Genetic similarity tests (using Nei and Li similarity coefficients) based on RAPDs and RFLPs showed varying relationships among the collected fungi. PCR-RFLPs confirmed genetic polymorphisms among samples of the recorded taxa. The intra- and inter-specific genetic diversity among the sampled ectomycorrhizal fungi partly explains the low host specificity among the collected ectomycorrhizal fungi and the dominance of a few ectomycorrhizal species in the study area.
Patterns of Neonatal Admission and Outcome in Neonatal Intensive Care Unit of a Tertiary Care Hospital

Field: Medicine (Health Sciences)

Introduction: Analyzing the neonatal admission pattern helps the policymakers to make better strategies for healthcare provider to deliver better service. Objective: To demonstrate the admission pattern and outcome of patients in the Neonatal Intensive Care Unit (NICU) in a tertiary care hospital of Bangladesh. Materials and Methods: This retrospective descriptive study was conducted on all neonates admitted to the NICU of Combined Military Hospital (CMH), Dhaka from January to December 2015. Data were collected from file records of the patients regarding age, gender, mode of delivery, working diagnosis, length of stay in NICU and immediate outcome. Results: A total of 502 neonates were admitted during the study period. Majority of the patients (77.3%) were admitted on the 1st day of life. There were 279(55.6%) males with a male to female ratio 1.2:1. The major cause of admission was prematurity (23.1%) and other leading causes were birth asphyxia (BA)14.9%, infant of a diabetic mother (IDM) 13.5%, neonatal sepsis 12.5%. Most of the neonates (82.7%) were delivered by caesarean section. About 84.1% were discharged after improvement, 65(12.94%) died and 15(3%) were referred to other specialties for further management. Within the first 24 hours of admission, 9.4% deaths occurred and two common causes of neonatal death were preterm (49.18%) and birth asphyxia (23%). Conclusion: Good outcome of a neonate depends on adequate management, monitoring and good nursing care in an intensive care unit. By paying good attention to perinatal services and improving the facilities in the unit, morbidity and mortality in neonates can be reduced. Journal of Armed Forces Medical College Bangladesh Vol.13(2) 2017: 49-53
Exploring Housing Market in Toronto, Ontario: Spatial Hedonic Modeling of Crime Rates, Subway Ridership, Dwelling Density and House Prices

Field: Social Sciences (Social Sciences)

This thesis explores house prices and its relationship to neighborhood characteristics in Toronto, Ontario. In particular, by applying spatial hedonic models at the census tract level, this study examines the association between house prices and three neighborhood characteristics: crime rates, subway ridership and dwelling density. House prices were first explored by cluster analysis at multiple listing service (MLS) district level and results showed a significant spatial clustering of the prices in Toronto. Spatial hedonic models were then conducted on census tract level to examine the role of neighborhood characteristics in explaining the spatial patterns. The spatial mode was applied both across the entire city and separately in three neighborhoods divided by income level. Findings indicate that on the citywide scale, crime rates and dwelling density do not significantly influence house prices, but subway ridership was positively associated with house prices. In the middle-income neighborhood, six types of crime were found to significantly decrease house prices. Densities of all types of dwelling were found to be positively associated with house prices while apartment density decreases house prices in the middle-income neighborhood. Findings from this research can be applied to inform housing and transportation policies, regarding neighborhood improvement, housing affordability and smart growth.
Shakespeare on the Screen: A Selective Filmography

Field: Arts and Humanities (Social Sciences)

This filmography is a reference list of 'complete', straightforward versions of Shakespeare's plays in film, television and videotape form. It specifically excludes free adaptations; film and television programmes containing insets of recorded performance; educational films based on pedagogic manipulations of Shakespeare's texts; material recording rehearsals, workshops, conversations with actors and directors; and all operatic and balletic adaptations. There is much material in all these categories of great potential interest to researchers; this modest compilation should be regarded as the provision of basic information rather than the establishing of a comprehensive reference source.
Relationship between emotional instability and risk of alcohol abuse among adolescents: the moderating role of predisposition to engage in risky behaviors

Field: Psychology (Social Sciences)

There is growing evidence that alcohol abuse among adolescents is a major public health concern. Understanding the risk factors associated with adolescent alcohol misuse is crucial for the development of prevention programs. Our study aimed to examine whether general attitudes toward health risk behaviors (i.e., predisposition to engage in risky behaviors) moderate the association between emotional instability (neuroticism as a stable personality factor) and adolescent alcohol abuse. A population-based sample of 688 Romanian adolescents completed several standardized instruments, including a measure of the current risk of alcohol abuse, the Neuroticism scale from the Big Five Inventory, and a subscale (Health/Safety) from the Risk Behaviors Scale [71]. The risk of alcohol abuse was positively associated with both emotional instability (n = 673; r = 0.345; p < 0.001) and predisposition to engage in risky behaviors (n = 688; r = 0.424; p < 0.001). A positive relationship was also found between emotional instability and the predisposition to engage in risky behaviors (n = 673; r = 0.129; p = 0.001). Hierarchical linear multiple regression analysis provided support for the moderation relationship. In summary, the predisposition to engage in risky behaviors may act as an amplifying factor by increasing the risk associated with emotional instability. Some practical implications for preventive interventions are discussed.
Spread of Pseudomonas fluorescens Due to Contaminated Drinking Water in a Bone Marrow Transplant Unit

Field: Medicine (Health Sciences)

ABSTRACT Pseudomonas infections are an important cause of morbidity and mortality in immunocompromised patients. We present here data for the spread of Pseudomonas fluorescens caused by a contaminated drinking water dispenser in a bone marrow transplant unit. Over a 1-month period we observed a sharp increase in the isolation of P. fluorescens from weekly pharyngeal surveillance swabs. Environmental samples were taken from a variety of water sources throughout the unit. These samples were cultured on cetrimide agar medium, and isolates were epidemiologically characterized by antibiotic susceptibility patterns and molecular typing methods. Nine patients became colonized with P. fluorescens , and six out of the nine developed febrile neutropenia. P. fluorescens was cultured after the filtration of 100 ml of drinking water from one of two stand-alone chiller units supplying cooled bottled water to the bone marrow transplant unit. All other environmental samples were negative. There were no further cases of P. fluorescens colonization after the contaminated dispenser was removed. Molecular typing showed that all P. fluorescens isolates were identical by both random amplification of polymorphic DNA PCR and pulsed-field gel electrophoresis. We recommend that such bottled water supplies not be used in high-risk areas or be subject to regular microbiological monitoring.
Decision enhancement and Improving Business Process Agility

Field: Decision Sciences (Social Sciences)

Achieving Business process agility requires organisations to be able to identify change in their business environment and respond promptly. In addition, they should be able to identify internal and external drivers for improvement. Business Process Management (BPM) suites have thus been developed to support the business process lifecycle by enabling timely changes to be made on process models. However, most BPM suites give little attention to the decision process that takes place when analyzing a business process and deciding on how to improve it. This research therefore proposes to develop a platform (Studio) that will provide an interactive environment to enhance the decision process involved in coming up with alternative solutions on how to improve the business process in response to changes, and identified internal and external drivers for improvement. The design science research method that emphasizes the ‘utility ’ of developed artifacts is followed during this research.
The impact of hydrolyzing and oxidizing agents on chemical composition and digestibility of various high‐fibre forages

Field: Agricultural and Biological Sciences (Life Sciences)

Abstract Urea (U), sodium hypochlorite (H) and sodium chloride (S) alone or combined were applied upon high‐fibre forages ( HFF ) in three experiments. Experiment (Exp) I: tall wheatgrass ( TW ), weeping lovegrass ( WL ), deferred sorghum ( DS ) and barley straw ( BS ) as substrates were untreated (U0) or treated with 4 g 100 g −1 DM (U4), and stored for 45 days. Within each forage, CP and IVDMD were increased by U4 ( p < 0.01). Exp II : TW was treated with U and H: U (as in Exp I) and H (at 0, 0.25, 0.50, 0.75 and 1 g active Cl 100 g −1 DM), alone or combined. The interaction U*H was significant for ADF , ADL and CP . For U4+H0.25 ADF and ADL decreased ( p < 0.01). For U0, ADL was reduced from H.025 through H1.00 ( p < 0.05). U4 increased IVDMD and CP ( p < 0.01). Exp III : oat straw (O) was treated with U0 and U4, H0 and H1, S0 and S4 (4 g S 100 g −1 DM), including all combinations at 3 storage times (T = 10, 20 and 30 days). Interactions U*S*H*T for ADL , U*H*T for NDF and CP and S*H*T for IVDMD ( p < 0.05) were found. ADF was reduced by U4, H1 and S1 ( p < 0.01). The greatest decrease (4.5%) was with U4. Principal components analysis showed U4S4H1 highly related to IVDMD for all T. All treatments had little or no impact on NDF , ADF and ADL content. Lower quality forages had greatest improvements in digestibility and N‐retention.
Emerging infectious diseases and insensible bacillus infectious diseases. Insensible bacillus infectious diseases. ESBL producing strain infection.

Field: Medicine (Health Sciences)

1980年代中頃からヨーロッパで,次いで米国を中心にExtended-spectrum β-lactamase (ESBL)を産生する肺炎桿菌や大腸菌による院内感染症が流行し問題となっている.最近ではわが国においてもESBL産生菌が分離されるようになり,その危険性が問題視されている.しかし,細菌学的立場からすると, ESBL産生菌感染症を治療しうる抗菌薬があり,それらを適正に使用すれば特に恐い感染症というわけではない.流行の背景には, ESBL産生菌を的確に検出できないために適切な抗菌薬の選択が行われなかったことがあると思われる.ここではその診断を中心にESBL産生菌感染症を解説した.
Real input-output energy-switching options

Field: Decision Sciences (Social Sciences)

We provide quasi-analytical solutions to models for real options embedded in flexible energy facilities that have stochastic inputs and outputs with switching costs. We show the facility value and the optimal switching input and output triggers when the possibility for multiple switching between operating and not operating exists. The facility value and optimal shutdown triggers are also calculated when there is only a one-way switch between operating and suspension (which amounts to abandonment). An illustration is provided for a heavy crude oil production field that requires natural gas as an input, with shutdown and restart switching costs. More general applications in the energy field include the operational spark (and dark spark) spread with switching costs. It may be appropriate to extend these models to many manufacturing, distribution and transportation activities.
Bio-nano Science: Better Metrics Would Accelerate Progress

Field: Chemistry (Physical Sciences)

An early step of evaluating a nanomaterial’s potential for biological applications is investigating its interactions with cells and biological fluids. These experiments generate complex data, which are summarized and analyzed through the use of metrics. Choosing appropriate metrics is thus critical to build a foundation for nanomaterial research. Unfortunately, several widely used metrics in the bio-nano scientific literature have significant issues and may not be delivering their intended insight. This perspective will label and discuss three problematic metrics in wide use within the field: Percentage Cell Association, used to measure the interaction strength between a cell and a nanoengineered material; Internalization Factor, used to measure the ability of a cell to internalize a nanoengineered system; and Detected Protein Abundance, used to analyze the composition of proteins that adsorb to a nanoengineered surface. We review the origin of each metric and explain why each fails to deliver the intended insight in the domain of bio-nano experiments. Finally, for each metric, we present alternative metrics that deliver the necessary insight while imposing little (or no) additional experimental burden. We hope that this perspective will increase the use of better metrics, improve reporting, and ultimately aid the transition of bio-nano science to a more quantitative field.
Malignant melanoma of the skin

Field: Medicine (Health Sciences)

Cutaneous malignant melanoma is no longer rare. The incidence in Scotland, 1 Norway 2 and Queensland 3 has doubled in recent years and in Scotland melanoma is now commoner than Hodgkin’s disease. In the UK about 3000 new cases are diagnosed each year. Sun exposure, particularly episodic severe sunburn in those who tan poorly, may be an important causal factor. 4 Malignant melanoma is curable if treated early but usually fatal once it disseminates. All doctors should therefore be able to recognise its clinical features and understand its treatment.
P204 Novel application of artificial intelligence to automate measurement of colonoscopy inspection time

Field: Medicine (Health Sciences)

Introduction

A randomised controlled trial recently demonstrated that adenoma detection rate (ADR) increases as colonoscopy inspection time (CIT) rises from 6 to 13 minutes 1. CIT was defined as withdrawal from caecum to the anal verge with the timer manually stopped during cleaning (washing or suctioning) and polypectomy events. However, CIT measurement cannot be implemented in clinical practice without dedicated staff to pause a timer during these events. Previous work demonstrated artificial intelligences (AI) ability to measure withdrawal time (WT) by detection of caecal landmarks and the anal verge. We aimed to develop convolutional neural networks (CNN) to detect cleaning and polypectomy phases during withdrawal to facilitate automated measurement of CIT.

Methods

Videos of withdrawal were annotated with labels of 'cleaning' (suctioning and washing), 'polypectomy' (injection, polypectomy and inspecting resection margins) and 'inspection time'. Using 98 annotated videos, two ResNet-101 CNNs were developed to detect cleaning (213,936 frames) and polypectomy (56,273 frames) events. The CNNs was then evaluated with 40 consecutive colonoscopy videos from 5 expert (ADR>45%) and 40 videos from 6 non-expert (ADR<30%) endoscopists, with the annotations referenced as the ground truth.

Results

For the test set of 80 procedures, the median WT documented in the endoscopy reporting system (EPIC) was 15.0 minutes (IQR 10.0–23.0), annotated ground truth median CIT was 7.1 minutes (IQR 5.3–9.6), and AI predicted median CIT was 6.9 minutes (IQR 5.1–9.0) with a correlation coefficient (r) of 98.2%. For expert procedures (n=40), these were 16.5 minutes (IQR 11.0–25.3), 7.1 minutes (IQR 5.1–8.6) and 6.9 minutes (IQR 4.9–8.8), respectively. Amongst non-expert procedures (n=40), these were 14.0 minutes (IQR 10.0–22.0), 7.0 minutes (IQR 5.8–10.7) and 7.0 minutes (IQR 5.3–10.2), respectively. The AI system correctly categorised 95% (76/80) of procedures as less or more than 6 minutes CIT.

Conclusions

We have demonstrated the feasibility of AI to differentiate the phases of withdrawal to automate measurement of CIT and the considerable difference in time between CIT and the WT documented in endoscopy reporting system.
Morphological variation of fruits and infrutescences inBiscutellaL. (Cruciferae)

Field: Agricultural and Biological Sciences (Life Sciences)

Abstract The variation of fruits and infrutescences in 51 taxa of the genus Biscutella is reported. The basic structure of the fruit is similar in all species – a stalked strongly compressed indehiscent didymous silicula which breaks from the axis into two one‐seeded loculi at maturity. The peculiar and distinctive nature of the fruit constitutes the most important diagnostic feature for separating the genus from other genera. There is considerable variation in fruit size both within and between some species, e.g. the smallest fruits are found in B. microcarpa where they hardly exceed 2.5 mm × 5.0 mm while in B. megacarpaea they could be as big as 11.0 mm long and 18.5 mm wide. Prominent among species with significant intra‐specific variation are B. lusitanica, B. sempervirens, B. glacialis and B. valentina. The apex of the fruit is notched to varying extents except in B. auriculata where the margins run continuously with the style and the apex is therefore not notched. Style is persistent and contributes to the distinctive appearance of the fruit and the recognition of some species. Other variable characters include the pedicel, margin, valve shape and pubescence. The infrutescence varies from a simple raceme to a much‐branched panicle. The flexuous branches of some taxa constitute an important feature for their preliminary identification. Some of these characters are of value in clarifying the taxonomic relationships among some component taxa.
Geometric properties calculation based on surface representation and its application to ship engineering

Field: Engineering (Physical Sciences)

The geometric properties calculation,related to a ship's waterplane, transverse section,underwater volume,and hold capacity,plays an important role in determining the vessel's static performances.The wet surface area is computed in the resistance and seakeeping performances calculation in order to evaluate and optimize a ship's form.However,for a more precise calculation of a ship's performance,a new algorithm is presented that calculates the 2D or 3D geometric properties based on surface representation.After the represented surface was discretized into quadrangular or triangular elements,the geometric properties of the limited plane,curve surface,and volume were calculated respectively combining the ones of quadrangles,triangles,and generalized prisms.Applying this method,the properties of the sectional area,partial surface area,and volume bounded by analytical surface were calculated based on the non-uniform rational B-spline(NURBS) representation of them with the result coming close to the analytical solution.The related calculation result of a full-scale ship based on this method verifies its feasibility,rationality,and accuracy.