bluuebunny/crossref_metadata_2025_split huggingface dataset:
Use of word and graph embedding to measure semantic relatedness between Unified Medical Language System concepts
Authors: Mao Yuqing , Fung Kin Wah 
Published: July 2020

AbstractObjectiveThe study sought to explore the use of deep learning techniques to measure the semantic relatedness between Unified Medical Language System (UMLS) concepts.Materials and MethodsConcept sentence embeddings were generated for UMLS concepts by applying the word embedding models BioWordVec and various flavors of BERT to concept sentences formed by concatenating UMLS terms. Graph embeddings were generated by the graph convolutional networks and 4 knowledge graph embedding models, using graphs built from UMLS hierarchical relations. Semantic relatedness was measured by the cosine between the concepts’ embedding vectors. Performance was compared with 2 traditional path-based (shortest path and Leacock-Chodorow) measurements and the publicly available concept embeddings, cui2vec, generated from large biomedical corpora. The concept sentence embeddings were also evaluated on a word sense disambiguation (WSD) task. Reference standards used included the semantic relatedness and semantic similarity datasets from the University of Minnesota, concept pairs generated from the Standardized MedDRA Queries and the MeSH (Medical Subject Headings) WSD corpus.ResultsSentence embeddings generated by BioWordVec outperformed all other methods used individually in semantic relatedness measurements. Graph convolutional network graph embedding uniformly outperformed path-based measurements and was better than some word embeddings for the Standardized MedDRA Queries dataset. When used together, combined word and graph embedding achieved the best performance in all datasets. For WSD, the enhanced versions of BERT outperformed BioWordVec.ConclusionsWord and graph embedding techniques can be used to harness terms and relations in the UMLS to measure semantic relatedness between concepts. Concept sentence embedding outperforms path-based measurements and cui2vec, and can be further enhanced by combining with graph embedding.
A refined methodology for validation of information models derived from flowsheet data and applied to a genitourinary case
Authors: Westra Bonnie L , Lytle , Kay S , Whittenburg Luann , Adams Mischa , Ali Samira , Furukawa Meg , Hartleben Stephanie , Hook Mary , Johnson Steve , Collins Rossetti Sarah , Settergren Tess (Theresa) 
Published: July 2020

Abstract
Use of electronic health record data is expanding to support quality improvement and research; however, this requires standardization of the data and validation within and across organizations. Information models (IMs) are created to standardize data elements into a logical organization that includes data elements, definitions, data types, values, and relationships. To be generalizable, these models need to be validated across organizations. The purpose of this case report is to describe a refined methodology for validation of flowsheet IMs and apply the revised process to a genitourinary IM created in one organization. The refined IM process, adding evidence and input from experts, produced a clinically relevant and evidence-based model of genitourinary care. The refined IM process provides a foundation for optimizing electronic health records with comparable nurse sensitive data that can add to common data models for continuity of care and ongoing use for quality improvement and research.
Clinical informatics accelerates health system adaptation to the COVID-19 pandemic: examples from Colorado
Authors: Lin Chen-Tan , Bookman Kelly , Sieja Amber , Markley Katie , Altman Richard L , Sippel Jeffrey , Perica Katharine , Reece Lori , Davis Christopher , Horowitz Edward , Pisney Larissa , Sottile Peter D , Kao David , Adrian Bonnie , Szkil Melissa , Griffin Julie , Youngwerth Jeanie , Drew Brendan , Pell Jonathan 
Published: July 2020

Abstract

Objective
Large health systems responding to the coronavirus disease 2019 (COVID-19) pandemic face a broad range of challenges; we describe 14 examples of innovative and effective informatics interventions.

Materials and Methods
A team of 30 physician and 17 nurse informaticists with an electronic health record (EHR) and associated informatics tools.

Results
To meet the demands posed by the influx of patients with COVID-19 into the health system, the team built solutions to accomplish the following goals: 1) train physicians and nurses quickly to manage a potential surge of hospital patients; 2) build and adjust interactive visual pathways to guide decisions; 3) scale up video visits and teach best-practice communication; 4) use tablets and remote monitors to improve in-hospital and posthospital patient connections; 5) allow hundreds of physicians to build rapid consensus; 6) improve the use of advance care planning; 7) keep clinicians aware of patients’ changing COVID-19 status; 8) connect nurses and families in new ways; 9) semi-automate Crisis Standards of Care; and 10) predict future hospitalizations.

Discussion
During the onset of the COVID-19 pandemic, the UCHealth Joint Informatics Group applied a strategy of “practical informatics” to rapidly translate critical leadership decisions into understandable guidance and effective tools for patient care.

Conclusion
Informatics-trained physicians and nurses drew upon their trusted relationships with multiple teams within the organization to create practical solutions for onboarding, clinical decision-making, telehealth, and predictive analytics.
“There’s a problem, now what’s the solution?”: suggestions for technologies to support the menopausal transition from individuals experiencing menopause and healthcare practitioners
Authors: Backonja Uba , Taylor-Swanson Lisa , Miller Andrew D , Jung Se-Hee , Haldar Shefali , Woods Nancy Fugate 
Published: July 2020

Abstract

Objective
To elicit novel ideas for informatics solutions to support individuals through the menopausal transition. (Note: We use “individuals experiencing menopause” and “experiences” rather than “symptoms” when possible to counter typical framing of menopause as a cisgender women’s medical problem.)

Methods
A participatory design study was conducted 2015–2017 in the Western US. Two sessions were held with individuals experiencing menopause recruited from the general public; and 3 sessions with healthcare practitioners (HCPs) including nurses, physicians, and complementary and integrative health (CIH) practitioners were held. Participants designed technologies addressing informational needs and burdensome experiences. HCPs reflected on designs from participants experiencing menopause. Directed content analysis was used to analyze transcripts.

Results
Eight individuals experiencing menopause (n = 4 each session) and 18 HCPs (n = 10 CIH, n = 3 nurses, n = 5 physicians) participated. All participants provided ideas for solution purpose, hardware, software, features and functions, and data types. Individuals experiencing menopause designed technologies to help understand and prevent burdensome menopause experiences. HCPs designed technologies for tracking and facilitating communication. Compared to nurses and physicians, CIH practitioners suggested designs reframing menopause as a positive experience and accounted for the complex lives of individuals experiencing menopause, including stigma; these ideas corresponded to comments made by participants experiencing menopause. Participants from both populations were concerned about data confidentiality and technology accessibility.

Conclusions
Participant generated design ideas included novel ideas and incorporated existing technologies. This study can inform the development of new technologies or repurposing of existing technologies to support individuals through the menopausal transition.
Sensitive Derivative Synchronous and Micellar Enhanced Ecofriendly Spectrofluorimetric Methods for the Determination of Atenolol, Diclofenac, and Triclosan in Drinking Tap Water
Authors: Safwat Nardine , Abdel-Ghany Maha F , Ayad Miriam F 
Published: July 2020

Abstract

Background
Nowadays, emergence of unexpected contaminants in drinking water is a challenging environmental problem facing humanity.

Objective
Two eco-friendly spectrofluorimetric methods were proposed for the determination of three unexpected contaminants in drinking tap water.

Methods
The first method is first derivative synchronous spectrofluorimetric method which was developed for simultaneous determination of atenolol (ATN) and diclofenac (DCF) without prior separation at Δλ = 70 nm and at Δλ = 80 nm for ATN and DCF, respectively. The second method was based on using sodium dodecyl sulfate (SDS) as fluorescent enhancer of triclosan (TCS) native fluorescence. TCS exhibits enhanced fluorescence at λ emission = 600 nm upon excitation at λ excitation = 299.4 nm. Solid phase extraction was carried out in both methods.

Results
Linear calibration curves were obtained in concentration range of (4–3000 ng/mL) for ATN and (4–2000 ng/mL) for DCF, by measuring first derivative signal of fluorescence at 300 nm and 375.2 nm, respectively. TCS exhibits linear range (0.1–1 ng/mL) at 600 nm. Mean percentage recoveries were 101.04 ± 0.571, 99.66 ± 1.443, and 99.73 ± 0.566 for ATN, DCF, and TCS, respectively.

Conclusions
Validation of both methods were performed according to the International Conference on Harmonization guidelines. Results obtained were statistically compared with published methods and no significant differences were found. The proposed methods’ greenness is evaluated using analytical Eco-scale and Green Analytical Procedure Index. A greenness comparison with previously published methods has been performed.

Highlights
Both methods were found to be eco-friendly and were successfully applied for the determination of the emerging contaminants in drinking tap water.
The direct and difference procedures result in similar estimates for amino acid digestibility in feed ingredients fed to growing pigs
Authors: Oliveira Maryane S F , Htoo John K , Stein Hans H 
Published: July 2020

AbstractAn experiment was conducted to test the hypothesis that values for standardized ileal digestibility (SID) of amino acids (AA) in corn, wheat, and wheat middlings obtained using the direct procedure are not different from values obtained using the difference procedure. Sixteen ileal-cannulated barrows (initial BW: 69.5 ± 5.0 kg) were allotted to a replicated 8 × 4 Youden Square design with 8 diets and 4 periods. Each period consisted of 5 d of adaptation to the diet and 2 d of collection of ileal digesta. Four diets were based on soybean meal (SBM), corn, wheat, or wheat middlings as the only AA-containing ingredients. Three additional diets were based on a mixture of SBM and corn, SBM and wheat, or SBM and wheat middlings, and an N-free diet was also used. The apparent ileal digestibility (AID) and the SID of crude protein (CP) and AA for the 4 diets containing SBM, corn, wheat, or wheat middlings as the sole source of AA were calculated using the direct procedure. The AID and SID of CP and AA for the 3 mixed diets containing SBM and corn, wheat, or wheat middlings were also calculated and the contribution of digestible AA from SBM was subtracted from the AID or SID values for the diets. The AID or SID of AA in corn, wheat, and wheat middlings were subsequently calculated by difference. Results indicated that the AID values for a few AA were lower (P &lt; 0.05) if the direct procedure was used instead of the difference procedure, regardless of ingredient. The AID of Trp was greater in corn and wheat middlings, and the SID of Trp in corn and wheat middlings tended to be greater, if the direct procedure rather than the difference procedure was used, but that was not the case for wheat (interaction, P &lt; 0.05 and P &lt; 0.10, respectively). However, for all other indispensable AA, and for most of the dispensable AA, the SID of AA in corn, wheat, and wheat middlings was not different between the difference procedure and the direct procedure. Therefore, values for SID of AA in cereal grains and fiber-rich ingredients may be determined using either the direct or the difference procedure.
Supplemental effects of dietary lysophospholipids in lactation diets on sow performance, milk composition, gut health, and gut-associated microbiome of offspring
Authors: Jang Ki Beom , Purvis Jerry M , Kim Sung Woo 
Published: July 2020

AbstractDietary lysophospholipids (LPL) would influence milk composition of sows, thus positively affect intestinal health of offspring. The objective of this study was to determine effects of dietary LPL fed to lactating sows on performance, milk characteristics, gut health, and gut-associated microbiome of offspring. Sixty pregnant sows were allotted to 2 treatments in a randomized complete block design with parity and BW as blocks on day 110 of gestation. Treatments were CON (no added LPL) and LPL (0.05% LPL; Lipidol-Ultra, Pathway Intermediates, Shrewsbury, UK). Sows were fed 2 kg/d from day 110 of gestation until farrowing and ad libitum after farrowing. Diets were formulated to meet NRC requirement for lactating sows. Colostrum and milk samples from 12 sows per treatment were collected to measure nutrients and immunoglobulins on days 1 and 18 of lactation, respectively. Twelve piglets per treatment (1 piglet per litter) were euthanized on day 18 to collect tissues to measure tumor necrosis factor-α, interleukin-8 (IL-8), malondialdehyde, protein carbonyl, IgA, histomorphology, crypt cell proliferation rate, and microbiota in the jejunum and colon. Data were analyzed using the MIXED procedure of SAS, and the mortality was analyzed using the GLIMMIX procedure of SAS. There was no difference in sow BW, parity, and litter size between treatments on day 0 of lactation. Sows fed LPL had increased (P &lt; 0.05) litter BW gain (53.9 vs. 59.4 kg) and decreased piglet mortality (13.9% vs. 10.6%) on day 18 of lactation. Sows fed LPL had increased (P &lt; 0.05) omega-6:omega-3 (22.1 vs. 23.7) and unsaturated:saturated (1.4 vs. 1.6) fatty acids ratios with increased oleic acid (29.1% vs. 31.4%) and tended to have increased (P = 0.092) IgG (1.14 vs. 1.94 g/L) and linoleic acid (17.7% vs. 18.7%) in the milk on day 18 of lactation. Piglets from sows fed LPL had increased (P &lt; 0.05) IL-8 (184 vs. 245 pg/mg) and crypt cell proliferation rate (39.4% vs. 40.9%) and tended to have increased (P = 0.095) Firmicutes:Bacteroidetes ratio (1.0 vs. 3.5) in the jejunum. In conclusion, sows fed with LPL had milk with increased IgG, oleic acids, and linoleic acids without changes in BW and backfat during lactation. These changes could contribute to improved survivability and intestinal health of piglets by increasing IL-8 concentration, enhancing balance among gut-associated microbiome, and increasing enterocyte proliferation in the jejunum.
A novel site-specific chemical conjugation of IgG antibodies by affinity peptide for immunoassays
Authors: Mori Satoka , Abe Arisa , Ishikawa Naoto , Rafique Abdur , Ito Yuji 
Published: July 2020

AbstractRecently, there has been an increasing interest in site-specific modifications of antibodies used in immunoassays for disease diagnosis and as antibody therapeutics, such as antibody−drug conjugates. Previously, we established a site-specific chemical conjugation system using an IgG-Fc binding chemical conjugation affinity peptide (CCAP). CCAP could be used only for the modification of human IgG owing to the lack of affinity of CCAP to rodent IgG molecules. In this study, novel CCAP reagents are proposed, which can be used for both human and mouse IgG, based on the Staphylococcus aureus protein A domain-derived affinity peptides Z34C and Z33. Compared with the activity of a conventional randomly modified antibody, mouse IgG modified using this method had favourable features in two immunoassays, demonstrating the advantages of the proposed CCAP method in preserving antibody functionality during conjugation.
GTP metabolic reprogramming by IMPDH2: unlocking cancer cells’ fuelling mechanism
Authors: Kofuji Satoshi , Sasaki Atsuo T 
Published: July 2020

AbstractGrowing cells increase multiple biosynthetic processes in response to the high metabolic demands needed to sustain proliferation. The even higher metabolic requirements in the setting of cancer provoke proportionately greater biosynthesis. Underappreciated key aspects of this increased metabolic demand are guanine nucleotides and adaptive mechanisms to regulate their concentration. Using the malignant brain tumour, glioblastoma, as a model, we have demonstrated that one of the rate-limiting enzymes for guanosine triphosphate (GTP) synthesis, inosine monophosphate dehydrogenase-2 (IMPDH2), is increased and IMPDH2 expression is necessary for the activation of de novo GTP biosynthesis. Moreover, increased IMPDH2 enhances RNA polymerase I and III transcription directly linking GTP metabolism to both anabolic capacity as well as nucleolar enlargement historically observed as associated with cancer. In this review, we will review in detail the basis of these new discoveries and, more generally, summarize the current knowledge on the role of GTP metabolism in cancer.
Cd(II)-binding transcriptional regulator interacts with isoniazid and regulates drug susceptibility in mycobacteria
Authors: Yang Min , Jia Shi-Hua , Tao Hui-Ling , Zhu Chen , Jia Wan-Zhong , Hu Li-Hua , Gao Chun-Hui 
Published: July 2020

Abstract
It is urgent to understand the regulatory mechanism of drug resistance in widespread bacterial pathogens. In Mycobacterium tuberculosis, several transcriptional regulators have been found to play essential roles in regulating its drug resistance. In this study, we found that an ArsR family transcription regulator encoded by Rv2642 (CdiR) responds to isoniazid (INH), a widely used anti-tuberculosis (TB) drug. CdiR negatively regulates self and adjacent genes, including arsC (arsenic-transport integral membrane protein ArsC). CdiR directly interacts with INH and Cd(II). The binding of INH and Cd(II) both reduce its DNA-binding activity. Disrupting cdiR increased the drug susceptibility to INH, whereas overexpressing cdiR decreased the susceptibility. Strikingly, overexpressing arsC increased the drug susceptibility as well as cdiR. Additionally, both changes in cdiR and arsC expression caused sensitivity to other drugs such as rifamycin and ethambutol, where the minimal inhibitory concentrations in the cdiR deletion strain were equal to those of the arsC-overexpressing strain, suggesting that the function of CdiR in regulating drug resistance primarily depends on arsC. Furthermore, we found that Cd(II) enhances bacterial resistance to INH in a CdiR-dependent manner. As a conclusion, CdiR has a critical role in directing the interplay between Cd(II) metal ions and drug susceptibility in mycobacteria.
Quasi-oppositional-based Rao algorithms for multi-objective design optimization of selected heat sinks
Authors: Rao R V , Pawar R B 
Published: July 2020

Abstract
In this paper, an endeavor is made to enhance the convergence speed of the recently proposed Rao algorithms. The new upgraded versions of Rao algorithms named as “quasi-oppositional-based Rao algorithms” are proposed in this paper. The quasi-oppositional-based learning is incorporated in the basic Rao algorithms to diversify the searching process of the algorithms. The performance of the proposed algorithms is tested on 51 unconstrained benchmark functions. Also, three multi-objective optimization case studies of different heat sinks such as a single-layered microchannel heat sink (SL-MCHS), a double-layered microchannel heat sink (DL-MCHS), and a plate-fin heat sink (PFHS) are attempted to investigate the effectiveness of the proposed algorithms in solving real-world complex engineering optimization problems. The results obtained using the proposed algorithms are compared with the results obtained using the well-known advanced optimization algorithms such as genetic algorithm (GA), artificial bee colony (ABC), differential evolution (DE), particle swarm optimization (PSO), teaching-learning-based algorithm (TLBO), Jaya algorithm, multi-objective genetic algorithm (MOGA), non-dominated sorting genetic algorithm (NSGA-II), real-coded GA (RCGA), direction-based GA, self-adaptive multi-population (SAMP) Rao algorithms, and basic Rao algorithms. The proposed quasi-oppositional-based Rao algorithms are found superior or competitive to the other optimization algorithms considered.
Verification and Utility in the Arabic Commentaries on the Canon of Medicine: Examples from the Works of Fakhr al-Dīn al-Rāzī (d. 1210) and Ibn al-Nafīs (d. 1288)
Authors: Fancy Nahyan 
Published: July 2020

Abstract
Although over two dozen Arabic commentaries on the Canon of Medicine were composed between the twelfth and fourteenth centuries, historians of medicine have paid scant attention to them. Instead, these commentaries have often been dismissed as being uncritical expositions that further entrenched the dogma of Galenic/Avicennan medical theory. In this article, I shall show that in fact the opposite was the case for at least a subset of the Canon commentaries from this period. Fakhr al-Dīn al-Rāzī developed a new style of verification commentary across his philosophical corpus that he also deployed in his Canon commentary. Even though Fakhr al-Dīn largely adhered to Galenic/Avicennan medical theory, his commitment to verification (taḥqīq) led him to challenge and critically assess many facets of medical theory based on systematic, philosophical investigations. Ibn al-Nafīs, following in Fakhr al-Dīn’s footsteps, undertook a similar, systematic investigation into medical theory in his own Commentary on the Canon. However, in this case, verification led Ibn al-Nafis to challenge and modify several facets of medical theory. Moreover, as a trained, practicing physician, Ibn al-Nafīs also wanted to ensure that his commentary was useful for other practicing physicians. His commentary thus shows how a post-classical physician committed to the principles of verification and utility could employ philosophical argumentation, empirical observations and even occasional experiments to modify key aspects of Galenic/Avicennan medical theory and practice.