bluuebunny/crossref_metadata_2025_split huggingface dataset:
Linking Electronic Health Record and Trauma Registry Data: Assessing the Value of Probabilistic Linkage
Authors: Durojaiye Ashimiyu , Puett Lisa , Levin Scott , Toerper Matthew , McGeorge Nicolette , Webster Kristen , Deol Gurmehar , Kharrazi Hadi , Lehmann Harold , Gurses Ayse 
Published: March 2019

Background Electronic health record (EHR) systems contain large volumes of novel heterogeneous data that can be linked to trauma registry data to enable innovative research not possible with either data source alone.
Objective This article describes an approach for linking electronically extracted EHR data to trauma registry data at the institutional level and assesses the value of probabilistic linkage.
Methods Encounter data were independently obtained from the EHR data warehouse (n = 1,632) and the pediatric trauma registry (n = 1,829) at a Level I pediatric trauma center. Deterministic linkage was attempted using nine different combinations of medical record number (MRN), encounter identity (ID) (visit ID), age, gender, and emergency department (ED) arrival date. True matches from the best performing variable combination were used to create a gold standard, which was used to evaluate the performance of each variable combination, and to train a probabilistic algorithm that was separately used to link records unmatched by deterministic linkage and the entire cohort. Additional records that matched probabilistically were investigated via chart review and compared against records that matched deterministically.
Results Deterministic linkage with exact matching on any three of MRN, encounter ID, age, gender, and ED arrival date gave the best yield of 1,276 true matches while an additional probabilistic linkage step following deterministic linkage yielded 110 true matches. These records contained a significantly higher number of boys compared to records that matched deterministically and etiology was attributable to mismatch between MRNs in the two data sets. Probabilistic linkage of the entire cohort yielded 1,363 true matches.
Conclusion The combination of deterministic and an additional probabilistic method represents a robust approach for linking EHR data to trauma registry data. This approach may be generalizable to studies involving other registries and databases.
Leveraging Electronic Dental Record Data to Classify Patients Based on Their Smoking Intensity
Authors: Patel J. , Siddiqui Z. , Krishnan A. , Thyvalikakath T. 
Published: March 2019

Background Smoking is an established risk factor for oral diseases and, therefore, dental clinicians routinely assess and record their patients' detailed smoking status. Researchers have successfully extracted smoking history from electronic health records (EHRs) using text mining methods. However, they could not retrieve patients' smoking intensity due to its limited availability in the EHR. The presence of detailed smoking information in the electronic dental record (EDR) often under a separate section allows retrieving this information with less preprocessing.
Objective To determine patients' detailed smoking status based on smoking intensity from the EDR.
Methods First, the authors created a reference standard of 3,296 unique patients’ smoking histories from the EDR that classified patients based on their smoking intensity. Next, they trained three machine learning classifiers (support vector machine, random forest, and naïve Bayes) using the training set (2,176) and evaluated performances on test set (1,120) using precision (P), recall (R), and F-measure (F). Finally, they applied the best classifier to classify smoking status from an additional 3,114 patients’ smoking histories.
Results Support vector machine performed best to classify patients into smokers, nonsmokers, and unknowns (P, R, F: 98%); intermittent smoker (P: 95%, R: 98%, F: 96%); past smoker (P, R, F: 89%); light smoker (P, R, F: 87%); smokers with unknown intensity (P: 76%, R: 86%, F: 81%), and intermediate smoker (P: 90%, R: 88%, F: 89%). It performed moderately to differentiate heavy smokers (P: 90%, R: 44%, F: 60%). EDR could be a valuable source for obtaining patients’ detailed smoking information.
Conclusion EDR data could serve as a valuable source for obtaining patients' detailed smoking information based on their smoking intensity that may not be readily available in the EHR.
Postoperative Plasma Mitochondrial DNA and Cytokine Profiles of Elderly Patients Undergoing Minimally Invasive Aortic Valve Replacement
Authors: Estevez-Cid Francisco , Serrano-Teruel Maria E. , Fernandez-Rodriguez Fernando , Bouzas-Mosquera Alberto , Fernandez-Moreno Mercedes , Dieguez-Garcia Paula , Cuenca-Castillo Jose J. , Bautista-Hernandez Victor 
Published: March 2019

Introduction Mitochondrial DNA (mtDNA) is gaining increasing interest as a marker of cellular damage and could also act as an inflammatory mediator in cardiopulmonary bypass induced postoperative inflammatory response. Although minimally invasive heart valve surgery reportedly reduces inflammation, the mtDNA and cytokine profile in this context remains unclear.Materials and Methods Here, we report a prospective series of 40 elderly patients with aortic stenosis who underwent bioprosthetic aortic valve replacement (AVR) through upper ministernotomy with either a sutureless (n = 20) or a conventional (n = 20) valve. Primary end points included serial plasma levels of mtDNA (T1: at baseline; T2: 4 hours after surgery; and T3: 24s hour after surgery), cytokines (interleukin-6 [IL-6], tumor necrosis factor-α [TNF-α]), and myocardial necrosis biomarkers (MNBs), whereas secondary end points included clinical and echocardiographic data.Results Significant increases in the postoperative plasma levels (T2) of mtDNA, cytokines, and MNBs were observed in all patients. The postoperative plasma levels of mtDNA, TNF-α, and MNBs showed no significant differences between the treatment groups, although there was a trend toward lower levels in the sutureless group. The decreases in aortic cross-clamp and cardiopulmonary bypass times seen in the sutureless group were associated with significant lower postoperative levels (T2 and T3) of IL-6.Conclusion AVR through upper ministernotomy was associated with a significant increase in postoperative plasma levels of mtDNA and cytokines. There was no difference in the mtDNA levels between the sutureless and conventional valve groups, suggesting a similar level of inflammation in both groups. However, the shorter operation time observed in the sutureless valve group was associated with significantly lower postoperative levels of IL-6, indicating potential clinical benefits.
Avoiding the Unhappy Patient by Building Rapport in the Internet Age
Authors: Kern Eugene , Friedman Oren 
Published: March 2019

AbstractThe dynamics of the doctor–patient relationship has been complicated as more patients seem to expect perfection in this age of selfies and Internet postings. The preoperative patient interview is critical to recognize both body language clues and subtle but apparent red flags to avoid rhinoplasty on potentially unhappy patients. This interview should include routine use of a body dysmorphic disorder screening questionnaire since legions of these patients are undiagnosed prior to surgery and few, if any, are ever satisfied with even an excellent surgical result. These patients need diagnosis and psychological intervention—not surgery. Rapport is critical to patient and surgeon's satisfaction; therefore, it is valuable to practice the ABC's of rapport building: 1) active listening, (2) positive body language, and (3) candor.
Molecular dynamics-guided discovery of an ago-allosteric modulator for GPR40/FFAR1
Authors: Lückmann Michael , Trauelsen Mette , Bentsen Marie A. , Nissen Tinne A. D. , Martins Joao , Fallah Zohreh , Nygaard Mads M. , Papaleo Elena , Lindorff-Larsen Kresten , Schwartz Thue W. , Frimurer Thomas M. 
Published: March 2019

Significance
Structures of G protein-coupled receptors (GPCRs) in complex with ligands mainly provide frozen pictures with little information about the actual molecular mechanism of action of the ligand in the normally highly dynamic receptor. Through computer-based molecular dynamics simulations of a receptor for long-chain fatty acids, free fatty acid receptor 1 (FFAR1), we discover that an unoccupied, solvent-exposed pocket closes on removal of the lipid-like agonist; that is, during a major conformational change of the receptor. Importantly, a compound designed to prevent closure of this previously unrecognized, dynamic pocket was identified through structure-based virtual screening and shown to function as an allosteric agonist for the receptor. The study demonstrates that molecular dynamics simulations can be used in drug discovery to identify different modes of stabilizing specific receptor states.
Volumetric chemical imaging by clearing-enhanced stimulated Raman scattering microscopy
Authors: Wei Mian , Shi Lingyan , Shen Yihui , Zhao Zhilun , Guzman Asja , Kaufman Laura J. , Wei Lu , Min Wei 
Published: March 2019

Significance
Cells form structures and perform functions through intricate 3D tissue organizations. However, due to tissue scattering, coherent Raman microscopy—a powerful method complementary to fluorescence imaging—suffers from limited imaging depth in tissues. Here, we develop a volumetric chemical imaging method with greater than 10-fold depth increase. We formulate a Raman-tailored tissue-clearing recipe and combine it with advanced Raman microscopies. Equipped with the toolbox of volumetric chemical imaging and analyses, we elucidate complex 3D structures, chemical compositions, and metabolic dynamics in diverse tissues including lipid synthesis throughout tumor spheroids, 3D networks of axons, vasculatures, and cell bodies in brain regions, as well as heterogeneous tumor structures and tumor metabolism.
Tree clusters in savannas result from islands of soil moisture
Authors: Rodriguez-Iturbe Ignacio , Chen Zijuan , Staver Ann Carla , Levin Simon Asher 
Published: March 2019

Significance
Patterns of tree clusters in savannas display well-established characteristics that are explained by exogenous dynamics related to hot spots of soil moisture. These characteristics are related to the probability distribution of the cluster sizes and the fractal dimension of the cluster perimeters, both of which have a narrow range of variation regardless of specific climates. Such characteristics match very well those of the hot spots of high soil moisture when accounting for the impact of fire and herbivores.
Glycoconjugate vaccine using a genetically modified O antigen induces protective antibodies toFrancisella tularensis
Authors: Stefanetti Giuseppe , Okan Nihal , Fink Avner , Gardner Erica , Kasper Dennis L. 
Published: March 2019

SignificanceDespite the role of T cell-mediated events in control of intracellular infections, studies from several laboratories have shown that humoral immunity also plays a critical role. An effective glycoconjugate vaccine to preventFrancisella tularensisinfection has many advantages over live-organism vaccines, but protection against pulmonary infection by conjugate vaccines has never been shown. Here, we report a glycoconjugate vaccine that protects against intranasal challenge withF. tularensis. We determined that lipopolysaccharide-specific antibodies induced by a larger sized O antigen exhibit significantly enhanced relative affinity. This observation challenges the paradigm of a direct correlation between the amount of IgG induced by a glycoconjugate and the level of protection conferred, encouraging the development of conjugate vaccines inducing high-affinity antibodies to important pathogens.
The feather, a triumph of natural engineering and multifunctionality.
Authors: Lingham-Soliar T. 
Published: March 2019

Abstract

Structures in nature have evolved over millions of years and, unlike in engineering, are multifunctional. For example, an airplane wing may perform only a single function: lift. This is unlike the bird wing which, besides also producing power, has an ability to detect local updraught information along the entire surface of the wing such as changes in the distribution of pressure that are vital to soaring and energy saving. This chapter demonstrates how multifunctionality of the feather has enabled vital aspects of bird life. Three of these, involving flight, protection and temperature control, are discussed. The feather is a structure central to bird flight and the rachis is the central structure of the feather. Syncytial barbule fibres in the rachis are long continuous strands with intermittent hooked nodes, which contribute with the matrix to form the most effective bonding mechanisms known in nature. The unique microstructure of feathers that has enabled flight has also contributed to a tough outer integument that protects the bird against predators and the environment. Feathers are organized into tracts or pterylae with spaces, the apteria. This system of feather arrangement enables a dense layering of the feathers for mechanical protection without impeding movement. The apteria also help to reduce the total weight of the feathering, which is important for flight. The precise design of the barbule with nodes and hooks is fundamental to the process of thermoregulation in down feathers. The embryonic down feathers of chicks form individual 'clumps' of more or less circular masses that have a tree-like, highly organized self-similar structure, which is crucial to its thermal properties. Each tree-like assemblage comprises a barb and branching barbules, described as primary and secondary structures, attached to the skin by a quill. The whole structure creates a 'fluffiness' that helps to trap the warm air.
The poultry integument in health and disease.
Authors: McMullin P. F. 
Published: March 2019

Abstract

The importance of the integumentary system in commercial poultry encompasses all its functions that are essential to maintaining the health of the bird. Much can be learned about the health condition of the birds in a flock by observation of presence, or absence, and distribution of feathers on the floor in the house, as well as from plumage quality, feather loss and skin condition. Development and colouration of wattles and combs can also be a useful guide to flock health and physiological status. Patterns of skin damage, where present, and plumage loss allow inference of bird behaviour. Close inspection of growing feathers can also provide indications of both physiological and infectious issues during the time that feathers were being formed. The integumentary system of poultry can provide useful information to help to improve management and monitor and control specific diseases, thereby maintaining and improving health, welfare and productivity of farmed poultry. In this chapter, various issues associated with the skin, feather and beak as well as during slaughter process are discussed.
The genetics of contact dermatitis in poultry.
Authors: Kapell D. N. R. G. 
Published: March 2019

Abstract

The prevalence of contact dermatitis traits is an important consideration in modern poultry production, as part of the general focus on leg health and welfare traits. Contact dermatitis is seen as a lesion or discolouration of the skin, potentially accompanied by inflammation or necrosis. Various scoring systems have been developed, often relating ordinal scores to the proportional area affected. Environmental factors have a significant effect on its prevalence, but studies have shown that genetic variation exists for foot pad dermatitis (FPD) in chickens and turkeys and for hock burn in chickens. This review shows genetic parameters for contact dermatitis traits in contemporary chicken and turkey populations in the Aviagen breeding programmes, and their genetic correlations with production traits. FPD is recorded in all Aviagen breeding programmes, with hock burn additionally recorded in the Aviagen chicken breeding programmes. All traits are scored at commercially relevant ages on a four or five point scale (depending on trait/species) through visual inspection by a trained team of scorers. Heritabilities for FPD in chickens range from 21% to 32% and for hock burn from 9% to 23%. Genetic correlations with body weight are generally favourable (FPD) or moderately unfavourable (hock burn). Heritabilities for FPD in turkeys range from 5% to 16%, with low to moderately unfavourable genetic correlations with body weight. Genetic selection to improve contact dermatitis has been incorporated effectively for chickens and turkeys in commercial breeding programmes. The differences in heritability for FPD between the species may be due to fundamental differences of the expression of contact dermatitis, despite similar phenotypes. However, in both species genetic correlations with a production trait were only low to moderately unfavourable or even favourable. In broad breeding goals, where the focus lies simultaneously on welfare traits and production traits, progress can be achieved simultaneously despite potentially antagonistic correlations.
Strengthening the inside: effect of nutrition on gut health and maintenance and its impact on the integument integrity.
Authors: Adedokun S. A. , Olojede O. C. 
Published: March 2019

Abstract

The gastrointestinal tract (GIT) of poultry is equipped to perform several important functions. One of these functions is the protection of the underlying structures of the entire digestive tract and minimization of the translocation of materials that may be inimical to the health of the bird. The GIT also plays an important role in the digestion and absorption of nutrients and houses a vast array of microbiota with the potential to impact gut health. Strengthening the GIT involves early and proper establishment of the gut's physical, microbiological, secretory and immunological components to build strong intestinal barriers against potentially harmful organisms. As such, a strong and healthy gut, characterized by proper intestinal functionality, integrity and immunity, is essential for superior performance and overall well-being of the bird. To meet this goal, timely and balanced nutrition is important and is essential early in the life of the birds. The objective of this chapter is to discuss the impact of nutrition on the health of the GIT of poultry. Nutrition approaches for fostering a healthy gut include the maintenance of a healthy mucous layer throughout the GIT. Research has shown that adequate supply of dietary protein (amino acid) and specific carbohydrates are important for a healthy mucous layer. Also, early nutrition, both in ovo feeding and access to feed within the first 24 h post-hatch, has been shown to quicken the development and the establishment of the GIT and its associated organs. A healthy inside is a reflection of the integrity and functionality of the tight junction proteins that selectively allow the passage of nutrients across the intestinal epithelium layer into the mucosal layer while excluding agents that may be harmful to the bird. Research continues to show that cultivating a healthy microbial population in the GIT is important for the bird to thrive. Feed supplements such as pre- and probiotics have been supplemented to poultry diets for this purpose. However, the total withdrawal of antibiotics from poultry feed creates new challenges as well as more opportunities for cutting-edge research on the best approaches for improving gut health without the use of antibiotics.
Management practices to prevent abnormal feather loss in broiler breeders.
Authors: Tuijl O. A. van 
Published: March 2019

Abstract

This chapter discusses management factors in broiler breeders that can trigger abnormal feathering and unwanted feather damage, such that the birds are unable to maintain good feather cover at all times. Management practices to ensure good feed access include the following. Birds have correct feeder and drinker space. Feed and water are available immediately the lights come on in the morning. Feed distribution time does not exceed 3 min, if necessary filling the system from several locations in order to achieve the correct distribution time. Feed is distributed in the dark, especially during the rearing period and just after moving to the laying house. Spin feeders during rearing help to reduce feather pecking. Because pelleted feed increases the risk of feather pecking unless using spin feeders, a coarse mash is preferred (with added benefits for intestinal health). Feeders and drinkers are correctly distributed in the house and feeders are available in the slatted area of the laying house. At the onset of production, feed quantity is increased sufficiently quickly to match the increase in egg output. Birds have sufficient access to water and have water in their crops 1 h before the lights are turned off. In addition, house environmental factors are important to improve feather cover. Stocking densities higher than recommended will have a detrimental effect on feather quality and increase the risk of feather pecking. By 21 days of age the birds should have access to the whole rearing area of the house. Stimulate feather development by reducing house temperature to 20°C by 28 days of age. Ensure good litter quality for dust bathing to maintain feather condition through proper ventilation. Fluorescent lights at >100 lux will increase the risk of feather pecking, while incandescent lights reduce the risk. Other key management factors to reduce abnormal feather loss are as follows. Do not place too many males in laying house. By 25 weeks there should be no more than 9% males. Ensure that the males and females are at the same level of sexual maturity when they are put together in the laying house to prevent the males damaging the feathers of the females. Coccidiosis or necrotic enteritis must be prevented and, if occurring, treated immediately. Ensure that birds are handled in a calm way during activities such as weighing and vaccination. Prevent mite and/or worm infections and, if found, treat promptly.
Gene editing in livestock: promise, prospects and policy.
Authors: Van Eenennaam A. L. , Young A. E. 
Published: March 2019

Abstract
Although genetically engineered livestock were first introduced in the 1980s, only three biomedical applications (ATryn®, Ruconest®, Kanuma®) and one food animal application (AquAdvantage® salmon) have been brought to market. The initial promise of this technology was hampered by low efficiency, random site integration, public resistance and regulatory hurdles. Gene editing has made it possible to precisely target changes in livestock genomes, overcoming previous challenges. Livestock and poultry editing applications include disease resistance, animal welfare, production traits, animals as bioreactors, xenotransplantation and the development of models for human diseases. The extent to which any of these applications are utilized beyond research laboratories will depend upon regulatory frameworks, uptake by livestock producers and industry, and public acceptance. The 2017 draft US Food and Drug Administration regulatory guidance for gene edited animals, which proposes to regulate 'intentional' genomic alterations introduced by editing as new animal drugs irrespective of product novelty or risk, is at odds with emerging regulations around gene edited plants. Lengthy process-based regulation triggered by human 'intention' rather than novel product risk may dissuade animal genetics companies and breeders from employing gene editing to introduce beneficial genetic alterations into livestock populations, effectively the same fate encountered by genetic engineering in animals. Goal conflicts will likely continue between genetic innovations to address problems like animal disease and welfare and concerns around the use of modern molecular genetics in food animals. The early applications that successfully navigate regulatory hurdles will influence the public discussion around gene edited animals and impact the trajectory of future applications.