bluuebunny/crossref_metadata_2025_split huggingface dataset:
CRISPR Cas12a‐based “sweet” biosensor coupled with personal glucose meter readout for the point‐of‐care testing of Salmonella
Authors: Zhou Chi , Huang Di , Wang Ziyi , Shen Peijie , Wang Pu , Xu Zhinan 
Published: August 2022

AbstractSalmonella is a pathogen that comes from different animal‐originated foods and poses a significant threat to human health. The present detection methods for Salmonella are time‐consuming and labor‐intensive and requires skilled workers and specialized instruments. In this study, the conservative invA was selected as the target gene, and a quantitative detection method for Salmonella with wide availability and user‐friendliness was established based on CRISPR Cas12a and a personal glucose meter (PGM). The indirect signal transformation from the original target DNA to the final glucose signal was achieved through RAA, CRISPR Cas12a reaction, enzymic reaction, and glucose signal reading by a PGM (accu‐chek type from Roche). This PGMs‐CRISPR assay showed a detection sensitivity of Salmonella as low as 5 colony‐forming units (CFU)/reaction in either pure culture or artificially contaminated food samples and exhibited specificity between Salmonella isolates and non‐Salmonella isolates. Furthermore, quantitative detection of Salmonella in spiked milk samples was also achieved within the range from 1 to 1 × 103 CFU/reaction. Subsequently, the correlation and consistency between the PGMs‐CRISPR assay and quantitative polymerase chain reaction (qPCR) in detection of Salmonella in spiked milk samples were achieved. Therefore, a highly sensitive, portable, quantitative, and user‐friendly detection method based on CRISPR Cas12a and PGMs was developed in this study for Salmonella detection and identification.Practical ApplicationA sensitive, rapid, user‐friendly, and quantitative detection method based on CRISPR Cas12a for Salmonella in food has been developed in this study, which is of great significance to food safety supervision and management.
Beef quality, biochemical attributes, and descriptive sensory scores of gluteus medius, biceps femoris, and tensor fasciae latae muscles subjected to combined tumbling and postmortem aging
Authors: Tuell Jacob R. , Nondorf Mariah J. , Abdelhaseib Maha , Setyabrata Derico , Barker Samantha , Legako Jerrad F. , Kim Yuan H. Brad 
Published: August 2022

This study assessed how fresh beef tumbling without brine inclusion combined with aging would affect quality, biochemical attributes, and descriptive sensory scores of sirloin muscles. Paired gluteus medius (GM), biceps femoris (BF), and tensor fasciae latae (TFL) muscles from beef carcasses (n = 16) at 5 days postmortem were assigned to 0 or 120 min of tumbling, after which sections were aged 0 or 10 days. Tumbled GM (p < 0.001) and TFL (p < 0.01) muscles had increased objective tenderness compared to respective controls. Greater cook and initial purge losses were induced in all muscles with tumbling (p < 0.05), while thawing loss and purge loss with aging were similar (p > 0.05). Fragmentation of myofibrils was increased with tumbling and aging main effects (p < 0.001), although degradation of troponin T and desmin were primarily affected by aging only. In general, neither tumbling nor aging affected properties of collagen. Trained panelists assessed muscles aged 10 days for descriptive sensory scores including tenderness (myofibrillar, connective tissue, and overall), flavor (beef flavor identity, bloody/serumy, fat‐like, liver‐like, oxidized, umami, metallic, and sour), and juiciness (overall). Tumbled GM had greater myofibrillar tenderness than the control group (p < 0.05). Most sensory scores were unaffected by tumbling; however, tumbling increased oxidized and liver‐like flavors of GM and TFL, respectively, as well as decreased overall juiciness of BF (p < 0.05). These findings indicate tumbling combined with postmortem aging can improve tenderness of certain sirloin muscles like GM, although some impairments to flavor and juiciness could also occur.Practical ApplicationThe findings of this study are applicable to the beef industry to develop postharvest strategies to ensure sufficient tenderization of fresh beef sirloin muscles is achieved. However, the effectiveness of this process would differ between individual cuts, and minimizing possible impairments to flavor and juiciness would be critical.
Improvement of fitness and biocontrol properties of Pseudomonas putida via an extracellular heme peroxidase
Authors: Santamaría‐Hernando Saray , De Bruyne Lieselotte , Höfte Monica , Ramos‐González María‐Isabel 
Published: August 2022

AbstractThe extracellular 373‐kDa PehA heme peroxidase of Pseudomonas putida KT2440 has two enzymatic domains which depend on heme cofactor for their peroxidase activity. A null pehA mutant was generated to examine the impact of PehA in rhizosphere colonization competence and the induction of plant systemic resistance (ISR). This mutant was not markedly hampered in colonization efficiency. However, increase in pehA dosage enhanced colonization fitness about 30 fold in the root and 900 fold in the root apex. In vitro assays with purified His‐tagged enzymatic domains of PehA indicated that heme‐dependent peroxidase activity was required for the enhancement of root tip colonization. Evaluation of live/dead cells confirmed that overexpression of pehA had a positive effect on bacterial cell viability. Following root colonization of rice plants by KT2440 strain, the incidence of rice blast caused by Magnaporthe oryzae was reduced by 65% and the severity of this disease was also diminished in comparison to non‐treated plants. An increase in the pehA dosage was also beneficial for the control of rice blast as compared with gene inactivation. The results suggest that PehA helps P. putida to cope with the plant‐imposed oxidative stress leading to enhanced colonization ability and concomitant ISR‐elicitation.
Extracting abundance information from DNA‐based data
Authors: Luo Mingjie , Ji Yinqiu , Warton David , Yu Douglas W. 
Published: August 2022

AbstractThe accurate extraction of species‐abundance information from DNA‐based data (metabarcoding, metagenomics) could contribute usefully to diet analysis and food‐web reconstruction, the inference of species interactions, the modelling of population dynamics and species distributions, the biomonitoring of environmental state and change, and the inference of false positives and negatives. However, multiple sources of bias and noise in sampling and processing combine to inject error into DNA‐based data sets. To understand how to extract abundance information, it is useful to distinguish two concepts. (i) Within‐sample across‐species quantification describes relative species abundances in one sample. (ii) Across‐sample within‐species quantification describes how the abundance of each individual species varies from sample to sample, such as over a time series, an environmental gradient or different experimental treatments. First, we review the literature on methods to recover across‐species abundance information (by removing what we call “species pipeline biases”) and within‐species abundance information (by removing what we call “pipeline noise”). We argue that many ecological questions can be answered with just within‐species quantification, and we therefore demonstrate how to use a “DNA spike‐in” to correct for pipeline noise and recover within‐species abundance information. We also introduce a model‐based estimator that can be used on data sets without a physical spike‐in to approximate and correct for pipeline noise.
Positional errors in species distribution modelling are not overcome by the coarser grains of analysis
Authors: Gábor Lukáš , Jetz Walter , Lu Muyang , Rocchini Duccio , Cord Anna , Malavasi Marco , Zarzo‐Arias Alejandra , Barták Vojtěch , Moudrý Vítězslav 
Published: August 2022

Abstract

The performance of species distribution models (SDMs) is known to be affected by analysis grain and positional error of species occurrences. Coarsening of the analysis grain has been suggested to compensate for positional errors. Nevertheless, this way of dealing with positional errors has never been thoroughly tested. With increasing use of fine‐scale environmental data in SDMs, it is important to test this assumption. Models using fine‐scale environmental data are more likely to be negatively affected by positional error as the inaccurate occurrences might easier end up in unsuitable environment. This can result in inappropriate conservation actions.

Here, we examined the trade‐offs between positional error and analysis grain and provide recommendations for best practice. We generated narrow niche virtual species using environmental variables derived from LiDAR point clouds at 5 × 5 m fine‐scale. We simulated the positional error in the range of 5 m to 99 m and evaluated the effects of several spatial grains in the range of 5 m to 500 m. In total, we assessed 49 combinations of positional accuracy and analysis grain. We used three modelling techniques (MaxEnt, BRT and GLM) and evaluated their discrimination ability, niche overlap with virtual species and change in realized niche.

We found that model performance decreased with increasing positional error in species occurrences and coarsening of the analysis grain. Most importantly, we showed that coarsening the analysis grain to compensate for positional error did not improve model performance. Our results reject coarsening of the analysis grain as a solution to address the negative effects of positional error on model performance.

We recommend fitting models with the finest possible analysis grain and as close to the response grain as possible even when available species occurrences suffer from positional errors. If there are significant positional errors in species occurrences, users are unlikely to benefit from making additional efforts to obtain higher resolution environmental data unless they also minimize the positional errors of species occurrences. Our findings are also applicable to coarse analysis grain, especially for fragmented habitats, and for species with narrow niche breadth.
Optimizing an existing prediction model for quality of life one‐year post‐intensive care unit: An exploratory analysis
Authors: de Jonge Manon , Wubben Nina , van Kaam Christiaan R. , Frenzel Tim , Hoedemaekers Cornelia W. E. , Ambrogioni Luca , van der Hoeven Johannes G. , van den Boogaard Mark , Zegers Marieke 
Published: August 2022

AbstractBackgroundThis study aimed to improve the PREPARE model, an existing linear regression prediction model for long‐term quality of life (QoL) of intensive care unit (ICU) survivors by incorporating additional ICU data from patients' electronic health record (EHR) and bedside monitors.MethodsThe 1308 adult ICU patients, aged ≥16, admitted between July 2016 and January 2019 were included. Several regression‐based machine learning models were fitted on a combination of patient‐reported data and expert‐selected EHR variables and bedside monitor data to predict change in QoL 1 year after ICU admission. Predictive performance was compared to a five‐feature linear regression prediction model using only 24‐hour data (R2 = 0.54, mean square error (MSE) = 0.031, mean absolute error (MAE) = 0.128).ResultsThe 67.9% of the included ICU survivors was male and the median age was 65.0 [IQR: 57.0–71.0]. Median length of stay (LOS) was 1 day [IQR 1.0–2.0]. The incorporation of the additional data pertaining to the entire ICU stay did not improve the predictive performance of the original linear regression model. The best performing machine learning model used seven features (R2 = 0.52, MSE = 0.032, MAE = 0.125). Pre‐ICU QoL, the presence of a cerebro vascular accident (CVA) upon admission and the highest temperature measured during the ICU stay were the most important contributors to predictive performance. Pre‐ICU QoL's contribution to predictive performance far exceeded that of the other predictors.ConclusionPre‐ICU QoL was by far the most important predictor for change in QoL 1 year after ICU admission. The incorporation of the numerous additional features pertaining to the entire ICU stay did not improve predictive performance although the patients' LOS was relatively short.
Postoperative pain in a prospectively assessed surgical short‐stay cohort: A subgroup analysis
Authors: Lappalainen Emma , Ruohoaho Ulla‐Maija , Kokki Hannu , Aaltomaa Sirpa , Anttila Maarit , Gissler Mika , Kokki Merja 
Published: August 2022

AbstractBackgroundThere is sparse information about postoperative pain after short stay surgery. We explored the incidence of immediate postoperative pain and its relationship with persistent pain or opioid use 2 weeks after surgery.MethodsThis was a subgroup analysis of prospective and controlled data from adult patients (n = 931) who underwent short‐stay surgery in a tertiary care hospital. Data comprised patient demographics, surgical category, pain scores and analgesic management during the recovery unit stay, before discharge on the postoperative morning after surgery and again 2 weeks after surgery.ResultsHalf of the patients had severe dynamic pain in the recovery unit. It was commonest after orthopaedic (70% of patients), followed by gynaecological (54%), gastrointestinal (51%) and spine surgery (49%). Multimodal pain management was used for most patients (n = 811, 87%) with opioid use predominant. The median oxycodone dose during short‐stay was the highest after orthopaedic surgery (39 mg). The first individual dynamic pain score after surgery was associated with follow‐up pain score at rest (OR = 1.37), dynamic pain (OR = 1.35) and pain interference (OR = 1.34) at 2 weeks after surgery. Maximum dynamic pain reported in the recovery unit was associated with pain at rest (OR = 1.56), dynamic pain (OR = 1.65) and pain interference (OR = 1.45) at 2 weeks after surgery. Pain scores at 2 weeks were highest and analgesic use greatest in those patients who underwent spinal surgery.ConclusionsIntense postoperative pain remains common after short‐stay surgery in some surgical categories including orthopaedic surgery and is associated with a greater likelihood of pain at 2 weeks.
Risk of serious adverse events associated with non‐steroidal anti‐inflammatory drugs in orthopaedic surgery. A protocol for a systematic review
Authors: Leth Morten Fiil , Bukhari Shaheer , Laursen Christina Cleveland Westerdahl , Larsen Mia Esta , Tornøe Anders Schou , Jakobsen Janus Christian , Maagaard Mathias , Mathiesen Ole 
Published: August 2022

AbstractBackgroundPostoperative pain is a common condition following orthopaedic surgeries and causes prolonged hospitalisation, delayed rehabilitation and hamper the quality of life. Non‐steroidal anti‐inflammatory drugs (NSAIDs) are effective analgesics and anti‐inflammatory mediators in the treatment of postoperative pain. The association of NSAIDs with serious adverse events may however keep some clinicians and clinical decision makers from using NSAIDs perioperatively. The evidence regarding the risks of serious adverse events following perioperative use of NSAIDs in orthopaedic surgery is sparse and needs to be assessed in a systematic review. This is a protocol for a systematic review that aims to identify the risks of serious adverse events from perioperative use of NSAIDs in orthopaedic patients.MethodsOur methodology is based on the Preferred Reporting Items for Systematic Review and Meta‐Analysis Protocols and the eight‐step assessment procedure suggested by Jakobsen and colleagues. We wish to assess if NSAIDs versus placebo, usual care or no intervention, will influence the risks of serious adverse events in patients undergoing orthopaedic surgery. We will include all randomised trials assessing the use of NSAIDs perioperatively. To identify trials we will search the Medical Literature Analysis and Retrieval System Online, Excerpta Medica database, Cochrane Central Register, Science Citation Index Expanded on Web of Science and BIOSIS. Two authors will screen the literature and extract data. We will use the ‘Risk of Bias 2 tool’ to assess trials. Extracted data will be analysed using RStudio and Trial Sequential Analysis. We will create a ‘Summary of Findings’ table in which we will present our primary and secondary outcomes. We will assess the quality of evidence using Grading of Recommendations Assessment, Development and Evaluation (GRADE).DiscussionThis systematic review can potentially aid clinicians and clinical decision makers in the use of NSAIDs for treatment of postoperative pain following orthopaedic surgeries.
Fluid management of emergency department patients with sepsis—A survey of fluid resuscitation practices
Authors: Jessen Marie Kristine , Simonsen Birgitte Y. , Thomsen Marie‐Louise H. , Andersen Lars W. , Kolsen‐Petersen Jens Aage , Kirkegaard Hans 
Published: August 2022

AbstractBackgroundFluid administration and resuscitation of patients with sepsis admitted through emergency departments (ED) remains a challenge, and evidence is sparse especially in sepsis patients without shock. We aimed to investigate emergency medicine physicians' and nurses' perceptions, self‐reported decision‐making and daily behavior, and challenges in fluid administration of ED sepsis patients.MethodsWe developed and conducted a multicenter, web‐based, cross‐sectional survey focusing on fluid administration to ED patients with sepsis sent to all nurses and physicians from the five EDs in the Central Denmark Region. The survey consisted of three sections: (1) baseline information; (2) perceptions of fluid administration and daily practice; and (3) clinical scenarios about fluid administration. The survey was performed from February to June, 2021.ResultsIn total, 138 of 246 physicians (56%) and 382 of 595 nurses (64%) responded to the survey. Of total, 94% of physicians and 97% of nurses regarded fluid as an important part of sepsis treatment. Of total, 80% of physicians and 61% of nurses faced challenges regarding fluid administration in the ED, and decisions were usually based on clinical judgment. The most common challenge was the lack of guidelines for fluid administration. Of total, 96% agreed that they would like to learn more about fluid administration, and 53% requested research in fluid administration of patients with sepsis. For a normotensive patient with sepsis, 46% of physicians and 44% of nurses administered 1000 ml fluid in the first hour. Of total, 95% of physicians and 89% of nurses preferred to administer ≥1000 ml within an hour if the patients' blood pressure was 95/60 at admission. There was marked variability in responses. Blood pressure was the most commonly used trigger for fluid administration. Respondents preferred to administer less fluid if the patient in the scenario had known renal impairment or heart failure. Normal saline was the preferred fluid.ConclusionFluid administration is regarded as an important but challenging aspect of sepsis management. Responses to scenarios revealed variability in fluid volumes. Blood pressure was the most used trigger. ED nurses and physicians request evidence‐based guidelines to improve fluid administration.
Quantification of noradrenergic‐, dopaminergic‐, and tectal‐neurons during aging in the short‐lived killifish Nothobranchius furzeri
Authors: Bagnoli Sara , Fronte Baldassare , Bibbiani Carlo , Terzibasi Tozzini Eva , Cellerino Alessandro 
Published: August 2022

AbstractParkinson's disease (PD) is characterized by phosphorylation and aggregation of the protein α‐Synuclein and ensuing neuronal death progressing from the noradrenergic locus coeruleus to midbrain dopaminergic neurons. In 2019, Matsui and colleagues reported a spontaneous age‐dependent degeneration of dopaminergic neurons and an even greater neurodegeneration of the noradrenergic neurons in the short‐lived killifish Nothobranchius furzeri. Given the great possible relevance of a spontaneous model for PD, we assessed neurodegeneration of noradrenergic and dopaminergic neurons in two further laboratory strains of N. furzeri. We implemented, for the first time in N. furzeri, a whole‐brain clarification technique and proceeded to entire 3D nuclei reconstruction to quantify total cell numbers in two different stains of N. furzeri. In both strains, we observed that age‐dependent neurodegeneration is limited to the locus coeruleus and does not involve the posterior tuberculum. We also applied 3D counting to the optic tectum, an area of active adult neurogenesis, and detected an increase of neurons with age. Our results confirm age‐dependent neurodegeneration of noradrenergic neurons, a condition reminiscent of the presymptomatic stage of PD indicating that N. furzeri could be used in the future to identify modifying factors for age‐dependent neurodegeneration and open the intriguing possibility that natural genetic variation may influence the susceptibility of dopaminergic neurons.
Economic impacts of food safety incidents in a modern supply chain: E. coli in the romaine lettuce industry
Authors: Spalding Ashley , Goodhue Rachael E. , Kiesel Kristin , Sexton Richard J. 
Published: August 2022

AbstractFood‐safety incidents disrupt impacted markets, cause destruction of edible product, shake consumer confidence, and impose economic losses upon participants across the implicated supply chain. Despite the prevalence of such incidents, we know surprisingly little about their supply chain impacts, especially in modern produce markets where contracts may impede the diffusion of price impacts through the supply chain. The November 2018 E. coli incident for romaine lettuce in Central California roiled North American produce markets throughout the fall of 2018 and well into 2019. Our study of the economic impacts of this incident benefited from access to disaggregate information on prices and sales for romaine and substitute leafy greens at all stages of the supply chain, enabling us to overcome data limitations that have impeded prior studies. We decompose impacts from the incident into price and quantity components. Romaine growers were largely protected from damage due to fixed‐price provisions in grower‐processor contracts. Economic losses were incurred mostly by romaine shippers and processors, and grocery retailers who pulled saleable product from the supply chain and lost sales during and well after the incident due to reduced consumer demand. We estimate that the total societal loss from the incident was in the range of $276–$343 million. Widespread and long‐lasting impacts from a food‐safety incident demonstrate the economic benefit of industries adopting mandatory food‐safety standards and improved traceability to minimize the occurrence and impacts of such incidents.
Phantom Counterfactuals
Authors: Slough Tara 
Published: August 2022

AbstractResearchers often seek to identify the effects of a treatment on a sequence of behaviors, such as whether citizens register to vote and whether they then cast ballots. I show that average treatment effects (ATEs) are only identified until the first behavior (registering to vote) that affects the set of possible subsequent actions (voting). When one action changes the set of possible subsequent actions, it creates ‘phantom counterfactuals,’ or undefined potential outcomes, which render ATEs unidentified. I show that applied theory allows researchers to diagnose phantom counterfactuals, which helps to recognize unidentified ATEs and focus instead on other estimands that are identified. I illustrate this approach using a stylized model of crime reporting, showing how different theories generate different sets of identified estimands while holding constant an experimental design. I thereby establish the necessity of applied theory for causal identification in empirical research with sequential behavioral outcomes.