bluuebunny/crossref_metadata_2025_split huggingface dataset:
Co-infections observed in SARS-CoV-2 positive patients using a rapid diagnostic test
Authors: Fontana Carla , Favaro Marco , Minelli Silvia , Bossa Maria Cristina , Altieri Anna 
Published: August 2021

AbstractRapid diagnostic tests are tools of paramount impact both for improving patient care and in antimicrobial management programs. Particularly in the case of respiratory infections, it is of great importance to quickly confirm/exclude the involvement of pathogens, be they bacteria or viruses, while obtaining information about the presence/absence of a genetic target of resistance to modulate antibiotic therapy. In this paper, we present our experiences with the use of the Biofire® FilmArray® Pneumonia Panel Plus (FAPP; bioMérieux; Marcy l’Etoile, France) to assess coinfection in COVID-19 patients. A total of 152 respiratory samples from consecutive patients were examined, and 93 (61%) were found to be FAPP positive, with the detection of bacteria and/or viruses. The patients were 93 males and 59 females with an average age of 65 years who were admitted to our hospital due to moderate/severe acute respiratory symptoms. Among the positive samples were 52 from sputum (SPU) and 41 from bronchoalveolar lavage (BAL). The most representative species was S. aureus (most isolates were mecA positive; 30/44, 62%), followed by gram-negative pathogens such as P. aeruginosa, K. pneumoniae, and A. baumannii. Evidence of a virus was rare. Cultures performed from BAL and SPU samples gave poor results. Most of the discrepant negative cultures were those in which FAPP detected pathogens with a microbial count ≤ 105 CFU/mL. H. influenzae was one of the most common pathogens lost by the conventional method. Despite the potential limitations of FAPP, which detects a defined number of pathogens, its advantages of rapid detection combined with predictive information regarding the antimicrobial resistance of pathogens through the detection of some relevant markers of resistance could be very useful for establishing empirical targeted therapy for the treatment of patients with respiratory failure. In the COVID era, we understand the importance of using antibiotics wisely to curb the phenomenon of antibiotic resistance.
A modified SEIR model to predict the behavior of the early stage in coronavirus and coronavirus-like outbreaks
Authors: Angulo Wilfredo , Ramírez José M. , De Cecchis Dany , Primera Juan , Pacheco Henry , Rodríguez-Román Eduardo 
Published: August 2021

AbstractCOVID-19 is a highly infectious disease that emerged in China at the end of 2019. The COVID-19 pandemic is the first known pandemic caused by a coronavirus, namely, the new and emerging SARS-CoV-2 coronavirus. In the present work, we present simulations of the initial outbreak of this new coronavirus using a modified transmission rate SEIR model that takes into account the impact of government actions and the perception of risk by individuals in reaction to the proportion of fatal cases. The parameters related to these effects were fitted to the number of infected cases in the 33 provinces of China. The data for Hubei Province, the probable site of origin of the current pandemic, were considered as a particular case for the simulation and showed that the theoretical model reproduces the behavior of the data, thus indicating the importance of combining government actions and individual risk perceptions when the proportion of fatal cases is greater than $$4\%$$

4
%

. The results show that the adjusted model reproduces the behavior of the data quite well for some provinces, suggesting that the spread of the disease differs when different actions are evaluated. The proposed model could help to predict outbreaks of viruses with a biological and molecular structure similar to that of SARS-CoV-2.
HDAC1 deregulation promotes neuronal loss and deficit of motor function in stroke pathogenesis
Authors: Chen Jui-Sheng , Wang Hao-Kuang , Hsu Chien-Yu , Su Yu-Ting , Chen Jia-Shing , Liang Cheng-Loong , Hsieh Patrick Ching-Ho , Wu Cheng-Chun , Kwan Aij-Lie 
Published: August 2021

AbstractStroke is a common cause of death worldwide and leads to disability and cognitive dysfunction. Ischemic stroke and hemorrhagic stroke are major categories of stroke, accounting for 68% and 32% of strokes, respectively. Each year, 15 million people experience stroke worldwide, and the stroke incidence is rising. Epigenetic modifications regulate gene transcription and play a major role in stroke. Accordingly, histone deacetylase 1 (HDAC1) participates in DNA damage repair and cell survival. However, the mechanisms underlying the role of HDAC1 in stroke pathogenesis are still controversial. Therefore, we investigated the role of HDAC1 in stroke by using a rat model of endothelin-1-induced brain ischemia. Our results revealed that HDAC1 was deregulated following stroke, and its expressional level and enzymatic activity were decreased. We also used MS-275 to inhibit HDAC1 function in rats exposed to ischemic insult. We found that HDAC1 inhibition promoted the infarct volume, neuronal loss, DNA damage, neuronal apoptosis after stroke, and levels of reactive oxygen species and inflammation cytokines. Additionally, HDAC1 inhibition deteriorated the behavioral outcomes of rats with ischemic insult. Overall, our findings demonstrate that HDAC1 participates in ischemic pathogenesis in the brain and possesses potential for use as a therapeutic target.
Improving event-based progression analysis in glaucomatous visual fields
Authors: Rui Chiara , Montesano Giovanni , Crabb David P. , Brusini Paolo , Chauhan Balwantray C. , Rossetti Luca M. , Fogagnolo Paolo , Giraud Jean-Marie , Fenolland Jean-Rémi , Oddone Francesco 
Published: August 2021

AbstractGlaucoma is a progressive optic neuropathy with characteristic changes to the optic nerve head and the visual field (VF). Detecting progression of VF damage with Standard Automated Perimetry (SAP) is of paramount importance for clinical care. One common approach to detecting progression is to compare each new VF test to a baseline SAP test (event analysis). This comparison is made difficult by the test–retest variability of SAP, which increases with the level of VF damage, and the limited range of measurement, meaning that damage cannot be assessed below a certain level. We performed a prospective international multi-centre data collection of SAP data on 90 eyes from 90 people with glaucoma and different levels of VF damage over a short period of time (6 tests in 60 days). Data were collected using a fundus tracked perimeter (Compass, CenterVue). We used these data (minus the first test) to develop an improved event analysis that accounts for both the change in variability with damage and the lower bound on the measurement imposed by SAP. Using simulations, we show that our approach is more sensitive compared to previously developed methods, especially in the case of advanced glaucoma, while retaining similar specificity.
Genetic polymorphism of 19 autosomal STR loci in the Yi ethnic minority of Liangshan Yi autonomous prefecture from Sichuan province in China
Authors: Cheng Jingliang , Song Binghui , Fu Jiewen , Zheng Xiaoli , He Tao , Fu Junjiang 
Published: August 2021

AbstractThe Yi is one of fifty-six ethnic populations and one of the most ancient ethnic groups in China. The Liangshan Yi Autonomous Prefecture (LYAP) in Sichuan Province has the single largest Yi community in China. To establish a Yi population database in the LYAP of Sichuan in China, a Goldeneye™ DNA Identification System 20A Kit with 19 autosomal STRs (short tandem repeats) was used. As a result, the total discrimination power (TDP) and the cumulative probability of exclusion (CPE) for these STRs in 1016 unrelated individuals were 0.999999999999999999999897 and 0.9999999597, respectively. Totals of 273 alleles for 19 STRs and 8–22 alleles for each locus were found. The allelic frequencies ranged from 0.0005 to 0.5084. The forensic parameter averages of these STRs were as follows: observed heterozygosity (Hobs) of 78.44%, expected heterozygosity (Hexp) of 79.89%, discrimination power (DP) of 92.66%, and probability of exclusion (PE) of 57.68%. Penta E presented the highest levels of Hobs and DP, whereas TPOX showed the lowest Hobs and DP values. Nei’s standard genetic distance matrix among 31 populations found that the nearest genetic distance to the Yi population was the Sichuan Han (0.0056). Altogether, we first reported the forensic parameters and allele frequencies of 19 autosomal STRs of the Yi group in Liangshan. These 19 STR makers could provide highly informative polymorphisms for individual identification, paternity testing and genetic population analyses.
Structural basis of the complementary activity of two ketosynthases in aryl polyene biosynthesis
Authors: Lee Woo Cheol , Choi Sungjae , Jang Ahjin , Yeon Jiwon , Hwang Eunha , Kim Yangmee 
Published: August 2021

AbstractAryl polyenes (APE) are one of the most widespread secondary metabolites among gram-negative bacteria. In Acinetobacter baumannii, strains belonging to the virulent global clone 2 (GC2) mostly contain APE biosynthesis genes; its relevance in elevated pathogenicity is of great interest. APE biosynthesis gene clusters harbor two ketosynthases (KSs): the heterodimeric KS-chain length factor complex, ApeO-ApeC, and the homodimeric ketoacyl-acyl carrier protein synthase I (FabB)-like KS, ApeR. The role of the two KSs in APE biosynthesis is unclear. We determined the crystal structures of the two KSs from a pathogenic A. baumannii strain. ApeO-ApeC and ApeR have similar cavity volumes; however, ApeR has a narrow cavity near the entrance. In vitro assay based on the absorption characteristics of polyene species indicated the generation of fully elongated polyene with only ApeO-ApeC, probably because of the funnel shaped active site cavity. However, adding ApeR to the reaction increases the throughput of APE biosynthesis. Mutagenesis at Tyr135 in the active site cavity of ApeR reduces the activity significantly, which suggests that the stacking of the aryl group between Tyr135 and Phe202 is important for substrate recognition. Therefore, the two KSs function complementarily in the generation of APE to enhance its production.
Postsynthetic treatment of nickel–iron layered double hydroxides for the optimum catalysis of the oxygen evolution reaction
Authors: Tyndall Daire , Jaskaniec Sonia , Shortall Brian , Roy Ahin , Gannon Lee , O’Neill Katie , Browne Michelle P. , Coelho João , McGuinness Cormac , Duesberg Georg S. , Nicolosi Valeria 
Published: August 2021

AbstractNickel–iron-layered double hydroxide (NiFe LDH) platelets with high morphological regularity and submicrometre lateral dimensions were synthesized using a homogeneous precipitation technique for highly efficient catalysis of the oxygen evolution reaction (OER). Considering edge sites are the point of activity, efforts were made to control platelet size within the synthesized dispersions. The goal is to controllably isolate and characterize size-reduced NiFe LDH particles. Synthetic approaches for size control of NiFe LDH platelets have not been transferable based on published work with other LDH materials and for that reason, we instead use postsynthetic treatment techniques to improve edge-site density. In the end, size-reduced NiFe LDH/single-wall carbon nanotube (SWCNT) composites allowed to further reduce the OER overpotential to 237 ± 7 mV (<L> = 0.16 ± 0.01 μm, 20 wt% SWCNT), which is one of the best values reported to date. This approach as well improved the long-term activity of the catalyst in operating conditions.
In situ motions of individual inner-hair-cell stereocilia from stapes stimulation in adult mice
Authors: Wang Yanli , Steele Charles R. , Puria Sunil , Ricci Anthony J. 
Published: August 2021

AbstractIn vertebrate hearing organs, mechanical vibrations are converted to ionic currents through mechanoelectrical-transduction (MET) channels. Concerted stereocilia motion produces an ensemble MET current driving the hair-cell receptor potential. Mammalian cochleae are unique in that the tuning of sensory cells is determined by their mechanical environment and the mode of hair-bundle stimulation that their environment creates. However, little is known about the in situ intra-hair-bundle motions of stereocilia relative to one another, or to their environment. In this study, high-speed imaging allowed the stereocilium and cell-body motions of inner hair cells to be monitored in an ex vivo organ of Corti (OoC) mouse preparation. We have found that the OoC rotates about the base of the inner pillar cell, the hair bundle rotates about its base and lags behind the motion of the apical surface of the cell, and the individual stereocilia move semi-independently within a given hair bundle.
Microbial cell factories: a biotechnology journey across species
Authors: Nikel Pablo I. , Mattanovich Diethard 
Published: August 2021

Abstract
An increasingly large number of microbial species with potential for synthetic biology and metabolic engineering has been introduced over the last few years, adding huge variety to the opportunities of biotechnology. Historically, however, only a handful of microbes have attained the acceptance and widespread use that are needed to fulfil the needs of industrial bioproduction. Synthetic biology is setting out to standardise the methods, parts and platform organisms for bioproduction. These platform organisms, or chassis cells, derive from what has been termed microbial cell factories since the 1990s. In this collection of reviews, 18 microbial cell factories are featured, which belong to one of these three groups: (i) microbes already used before modern biotechnology was introduced; (ii) the first generation of engineered microbes; and (iii) promising new host organisms. The reviews are intended to provide readers with an overview of the current state of methodology and application of these cell factories, and with guidelines of how to use them for bioproduction.
Acquired Brain Injury Survivor Long-Term Cognitive Exercise Engagement Post–Speech Therapy Discharge
Authors: O'Neil-Pirozzi Therese M. 
Published: August 2021

Purpose
The purpose of this article is to promote the viewpoint that speech-language pathologists (SLPs) are well positioned to actively encourage individuals with cognitive-communication disorders following acquired brain injury (ABI) to engage in ongoing, long-term, cognitive exercise post–therapy discharge.

Method
This viewpoint article draws on evidence from the well-researched area of physical exercise, reports findings of early-stage research in the much less studied area of cognitive exercise, and highlights relevant aspects of motivational theory informing exercise participation. Informed by these, an evidence-supported model of cognitive exercise engagement is offered to inform ABI-targeted cognitive wellness empowerment efforts, and a case study illustrates clinical application of the model.

Conclusions
Exercise provides an opportunity to sustain or improve long-term health, function, and quality of life outcomes. It is within SLP scope of practice to collaborate with family members and other caregivers to empower individuals post-ABI, especially those with decreased self-management skills, to engage in long-term computerized and noncomputerized cognitive exercise following SLP therapy discharge. Ongoing research will further inform the evidence supporting the scholarly opinion presented in this viewpoint.
A novel compensation method for impedance measurement when long feeders are involved
Authors: Liu Xin , Feng Zhiyuan , Qi Lei 
Published: August 2021

AbstractBlack‐box modelling for the electrical equipment requires accurate admittance/impedance frequency‐sweep measurements. In some cases, long test leads are required because of the large size of the electrical equipment under test. It would induce unacceptable measurement errors in high frequency band. In order to solve this problem, first, the measurement principle of the impedance analyzer is studied, based on which the factors affecting the measurement accuracy are fully discussed. Second, a novel compensation method for measuring the wide‐band impedance of the large electrical equipment is proposed, in which the long test leads effect and the non‐standard characteristics caused by the extra leads connected to the open/short/50Ω‐load compensation terminals can both be eliminated. Finally, this method is validated by some experiments with 30 m‐long test leads in a frequency band ranging from 40 Hz to 10 MHz.
[α/Fe] traced by H II regions from the CALIFA survey
Authors: Sánchez S. F. , Espinosa-Ponce C. , Carigi L. , Morisset C. , Barrera-Ballesteros J. K. , Walcher C. J. , García-Benito R. , Camps-Fariña A. , Galbany L. 
Published: August 2021

Context. Differential enrichment between α and Fe-peak elements is known to be strongly connected with the shape of the star formation history (SFH), the star formation efficiency (SFE), the inflow and outflow of material, and even the shape of the initial mass function (IMF). However, beyond the Local Group, detailed explorations are mostly limited to early-type galaxies due to the lack of a good proxy for [α/Fe] in late-type ones, limiting our understanding of the chemical enrichment process.
Aims. We intent to extend the explorations of [α/Fe] to late-type galaxies in order to understand the details of the differential enrichment process.
Methods. We compare the gas-phase oxygen abundance with the luminosity-weighted stellar metallicity in an extensive catalogue of ∼25 000 H II regions extracted from the Calar Alto Legacy Integral Field Area (CALIFA) survey, an exploration that uses the integral-field spectroscopy of ∼900 galaxies and covers a wide range of masses and morphologies. This way, we define [O/Fe] as the ratio between both parameters, proposing it as an indirect proxy of the [α/Fe] ratio. This procedure is completely different from the one adopted to estimate [α/Fe] from high-resolution spectroscopic data for stars in our Galaxy.
Results. We illustrate how the [O/Fe] parameter describes the chemical enrichment process in spiral galaxies, finding that: (i) it follows the decreasing pattern with [Fe/H] reported for the [α/Fe] ratio and (ii) its absolute scale depends on the stellar mass and the morphology. We reproduce both patterns using two different chemical evolution models, considering that galaxies with different stellar masses and morphologies present either different SFHs, SFEs, and inflow and outflow rates or a different maximum stellar mass cut for the IMF. We will explore the differential chemical enrichment using this new proxy galaxy by galaxy and region by region in further studies.
Diabetische Retinopathie
Authors: Barth Teresa , Helbig Horst 
Published: August 2021

ZusammenfassungDie diabetische Retinopathie (DR) ist die häufigste Ursache für schwere Sehbehinderung und Erblindung im erwerbstätigen Alter. Eine subjektive Beeinträchtigung des Sehvermögens tritt häufig erst in fortgeschrittenen Stadien der DR ein. Daher sind Screening-Maßnahmen asymptomatischer Patienten und eine stadiengerechte Behandlung essenziell. Dieser Beitrag gibt einen praxisbezogenen Überblick über diagnostische und therapeutische Prinzipien der nicht-proliferativen und proliferativen Form.
Fast-Tracking Health Data Standards Development and Adoption in Real-World Settings: A Pilot Approach
Authors: Dennis Allison F. , White P. Jon , Zayas-Cabán Teresa 
Published: August 2021

Abstract
Background Pilot-testing is important in standards development because it facilitates agile navigation of the gap between needs for and use of standards in real-world settings and can reveal the practicalities of implementation. As the implementation and use of health data standards are usually more complicated than anticipated, the Office of the National Coordinator for Health Information Technology (ONC) routinely oversees and organizes relevant pilot projects.
Objectives This article provides an in-depth look into a sample of ONC's standards-focused pilot projects to (1) inform readers of the complexities of developing, implementing, and advancing standards and (2) guide those seeking to evaluate new standards through pilot projects.
Methods The ONC's approach to conducting pilot projects begins with identifying a clinical care need, research requirement, or policy outcome that is not well supported by existing standards through a landscape review. ONC then selects a testing approach based on the identified need and maturity of relevant standards. Next, ONC identifies use cases and sites to pilot-test the relevant standard. Once complete, ONC publishes a report that informs subsequent projects and standards development.
Results Pilot projects presented here are organized into three categories related to their demonstrated focus and related approach: (1) improving standards for presenting and sharing clinical genetic data, (2) accelerating the development and implementation of new standards, and (3) facilitating clinical data reuse. Each project illustrates the pilot approach from inception to next steps, capturing the role of collaboration among standards development organizations, stakeholders, and end-users to ensure standards are practical and fit for purpose.
Conclusion The ONC approach identifies implementation difficulties prior to broader adoption and use of standards, and provides insight into the steps needed to scale use of standards. The ONC's organization of pilot projects serves as a natural accelerator for building communities of practice, often providing a well-connected beneficiary of lessons learned.
Transformation of Electronic Health Records and Questionnaire Data to OMOP CDM: A Feasibility Study Using SG_T2DM Dataset
Authors: Sathappan Selva Muthu Kumaran , Jeon Young Seok , Dang Trung Kien , Lim Su Chi , Shao Yi-Ming , Tai E Shyong , Feng Mengling 
Published: August 2021

Abstract
Background Diabetes mellitus (DM) is an important public health concern in Singapore and places a massive burden on health care spending. Tackling chronic diseases such as DM requires innovative strategies to integrate patients' data from diverse sources and use scientific discovery to inform clinical practice that can help better manage the disease. The Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM) was chosen as the framework for integrating data with disparate formats.
Objective The study aimed to evaluate the feasibility of converting Singapore based data source, comprising of electronic health records (EHR), cognitive and depression assessment questionnaire data to OMOP CDM standard. Additionally, we also validate whether our OMOP CDM instance is fit for the purpose of research by executing a simple treatment pathways study using Atlas, a graphical user interface tool to conduct analysis on OMOP CDM data as a proof of concept.
Methods We used de-identified EHR, cognitive, and depression assessment questionnaires data from a tertiary care hospital in Singapore to convert it to version 5.3.1 of OMOP CDM standard. We evaluate the OMOP CDM conversion by (1) assessing the mapping coverage (that is the percentage of source terms mapped to OMOP CDM standard); (2) local raw dataset versus CDM dataset analysis; and (3) Implementing Harmonized Intrinsic Data Quality Framework using an open-source R package called Data Quality Dashboard.
Results The content coverage of OMOP CDM vocabularies is more than 90% for clinical data, but only around 11% for questionnaire data. The comparison of characteristics between source and target data returned consistent results and our transformed data did not pass 38 (1.4%) out of 2,622 quality checks.
Conclusion Adoption of OMOP CDM at our site demonstrated that EHR data are feasible for standardization with minimal information loss, whereas challenges remain for standardizing cognitive and depression assessment questionnaire data that requires further work.