bluuebunny/crossref_metadata_2025_split huggingface dataset:
Early diagnosis and critical management of wound botulism in the emergency department: a single center experience and literature review
Authors: Neeki Michael M. , Dong Fanlong , Emond Chuck , Lee Carol , Neeki Arianna S. , Hajjafar Keeyon , Messinger Megan , Anderson Caitlyn O. , Hajjafar Reza , Borger Rodney 
Published: September 2021

Abstract
Background
Clostridium botulinum remains a major threat to a select population of subcutaneous and intramuscular drug users. We conducted a retrospective study of patients who were diagnosed with wound botulism and their clinical presentations to the Emergency Department (ED).

Results
A total of 21 patients met the inclusion criteria and all had a confirmed history of heroin use disorder. Initial presentation to the ED included generalized weakness (n = 20, 95%), difficulty swallowing (n = 15, 71%), and speech/voice problems (n = 14, 79%). Sixteen patients (76%) also presented with visible skin wounds and fifteen (71%) required mechanical ventilation (MV). Patients who presented with dysphagia as well as dysarthria and/or dysphonia were more likely to require a percutaneous endoscopic gastrostomy (PEG) tube. Patients who required MV and PEG tubes were noted to have a longer hospital length of stay (LOS) due to the severity of the disease progression.

Conclusions
Emergency physicians should remain vigilant about early recognition of wound botulism, especially in patients who inject drugs.
Genetic architecture and major genes for backfat thickness in pig lines of diverse genetic backgrounds
Authors: Gozalo-Marcilla Miguel , Buntjer Jaap , Johnsson Martin , Batista Lorena , Diez Federico , Werner Christian R. , Chen Ching-Yi , Gorjanc Gregor , Mellanby Richard J. , Hickey John M. , Ros-Freixedes Roger 
Published: September 2021

AbstractBackgroundBackfat thickness is an important carcass composition trait for pork production and is commonly included in swine breeding programmes. In this paper, we report the results of a large genome-wide association study for backfat thickness using data from eight lines of diverse genetic backgrounds.MethodsData comprised 275,590 pigs from eight lines with diverse genetic backgrounds (breeds included Large White, Landrace, Pietrain, Hampshire, Duroc, and synthetic lines) genotyped and imputed for 71,324 single-nucleotide polymorphisms (SNPs). For each line, we estimated SNP associations using a univariate linear mixed model that accounted for genomic relationships. SNPs with significant associations were identified using a threshold of p < 10–6and used to define genomic regions of interest. The proportion of genetic variance explained by a genomic region was estimated using a ridge regression model.ResultsWe found significant associations with backfat thickness for 264 SNPs across 27 genomic regions. Six genomic regions were detected in three or more lines. The average estimate of the SNP-based heritability was 0.48, with estimates by line ranging from 0.30 to 0.58. The genomic regions jointly explained from 3.2 to 19.5% of the additive genetic variance of backfat thickness within a line. Individual genomic regions explained up to 8.0% of the additive genetic variance of backfat thickness within a line. Some of these 27 genomic regions also explained up to 1.6% of the additive genetic variance in lines for which the genomic region was not statistically significant. We identified 64 candidate genes with annotated functions that can be related to fat metabolism, including well-studied genes such asMC4R,IGF2, andLEPR, and more novel candidate genes such asDHCR7,FGF23,MEDAG,DGKI, andPTN.ConclusionsOur results confirm the polygenic architecture of backfat thickness and the role of genes involved in energy homeostasis, adipogenesis, fatty acid metabolism, and insulin signalling pathways for fat deposition in pigs. The results also suggest that several less well-understood metabolic pathways contribute to backfat development, such as those of phosphate, calcium, and vitamin D homeostasis.
Unveiling the transcriptomic complexity of Miscanthus sinensis using a combination of PacBio long read- and Illumina short read sequencing platforms
Authors: Wang Yongli , Li Xia , Wang Congsheng , Gao Lu , Wu Yanfang , Ni Xingnan , Sun Jianzhong , Jiang Jianxiong 
Published: September 2021

AbstractBackgroundMiscanthus sinensisAndersson is a perennial grass that exhibits remarkable lignocellulose characteristics suitable for sustainable bioenergy production. However, knowledge of the genetic resources of this species is relatively limited, which considerably hampers further work on its biology and genetic improvement.ResultsIn this study, through analyzing the transcriptome of mixed samples of leaves and stems using the latest PacBio Iso-Seq sequencing technology combined with Illumina HiSeq, we report the first full-length transcriptome dataset ofM. sinensiswith a total of 58.21 Gb clean data. An average of 15.75 Gb clean reads of each sample were obtained from the PacBio Iso-Seq system, which doubled the data size (6.68 Gb) obtained from the Illumina HiSeq platform. The integrated analyses of PacBio- and Illumina-based transcriptomic data uncovered 408,801 non-redundant transcripts with an average length of 1,685 bp. Of those, 189,406 transcripts were commonly identified by both methods, 169,149 transcripts with an average length of 619 bp were uniquely identified by Illumina HiSeq, and 51,246 transcripts with an average length of 2,535 bp were uniquely identified by PacBio Iso-Seq. Approximately 96 % of the final combined transcripts were mapped back to theMiscanthusgenome, reflecting the high quality and coverage of our sequencing results. When comparing our data with genomes of four species of Andropogoneae,M. sinensisshowed the closest relationship with sugarcane with up to 93 % mapping ratios, followed by sorghum with up to 80 % mapping ratios, indicating a high conservation of orthologs in these three genomes. Furthermore, 306,228 transcripts were successfully annotated against public databases including cell wall related genes and transcript factor families, thus providing many new insights into gene functions. The PacBio Iso-Seq data also helped identify 3,898 alternative splicing events and 2,963 annotated AS isoforms within 10 function categories.ConclusionsTaken together, the present study provides a rich data set of full-length transcripts that greatly enriches our understanding ofM. sinensistranscriptomic resources, thus facilitating further genetic improvement and molecular studies of theMiscanthusspecies.
Genome sequencing and identification of cellulase genes in Bacillus paralicheniformis strains from the Red Sea
Authors: Fatani Siham , Saito Yoshimoto , Alarawi Mohammed , Gojobori Takashi , Mineta Katsuhiko 
Published: September 2021

AbstractBackgroundCellulolytic microorganisms are considered a key player in the degradation of plant biomass in various environments. These microorganisms can be isolated from various environments, such as soils, the insect gut, the mammalian rumen and oceans. The Red Sea exhibits a unique environment in terms of presenting a high seawater temperature, high salinity, low nutrient levels and high biodiversity. However, there is little information regarding cellulase genes in the Red Sea environment. This study aimed to examine whether the Red Sea can be a resource for the bioprospecting of microbial cellulases by isolating cellulase-producing microorganisms from the Red Sea environment and characterizing cellulase genes.ResultsThree bacterial strains were successfully isolated from the plankton fraction and the surface of seagrass. The isolated strains were identified asBacillus paralicheniformisand showed strong cellulase activity. These results suggested that these three isolates secreted active cellulases. By whole genome sequencing, we found 10 cellulase genes from the three isolates. We compared the expression of these cellulase genes under cellulase-inducing and non-inducing conditions and found that most of the cellulase genes were generally upregulated during cellulolysis in the isolates. Our operon structure analysis also showed that cellulase genes form operons with genes involved in various kinds of cellular reactions, such as protein metabolism, which suggests the existence of crosstalk between cellulolysis and other metabolic pathways in the bacterial isolates. These results suggest that multiple cellulases are playing important roles in cellulolysis.ConclusionsOur study reports the isolation and characterization of cellulase-producing bacteria from the Red Sea. Our whole-genome sequencing classified our three isolates asBacillus paralicheniformis, and we revealed the presence of ten cellulase orthologues in each of three isolates’ genomes. Our comparative expression analysis also identified that most of the cellulase genes were upregulated under the inducing conditions in general. Although cellulases have been roughly classified into three enzyme groups of beta-glucosidase, endo-β-1,4-glucanase and exoglucanase, these findings suggest the importance to consider microbial cellulolysis as a more complex reaction with various kinds of cellulase enzymes.
Carbon starvation of Pseudomonas aeruginosa biofilms selects for dispersal insensitive mutants
Authors: Nair Harikrishnan A. S. , Subramoni Sujatha , Poh Wee Han , Hasnuddin Nabilah Taqiah Binte , Tay Martin , Givskov Michael , Tolker-Nielsen Tim , Kjelleberg Staffan , McDougald Diane , Rice Scott A. 
Published: September 2021

Abstract
Background
Biofilms disperse in response to specific environmental cues, such as reduced oxygen concentration, changes in nutrient concentration and exposure to nitric oxide. Interestingly, biofilms do not completely disperse under these conditions, which is generally attributed to physiological heterogeneity of the biofilm. However, our results suggest that genetic heterogeneity also plays an important role in the non-dispersing population of P. aeruginosa in biofilms after nutrient starvation.

Results
In this study, 12.2% of the biofilm failed to disperse after 4 d of continuous starvation-induced dispersal. Cells were recovered from the dispersal phase as well as the remaining biofilm. For 96 h starved biofilms, rugose small colony variants (RSCV) were found to be present in the biofilm, but were not observed in the dispersal effluent. In contrast, wild type and small colony variants (SCV) were found in high numbers in the dispersal phase. Genome sequencing of these variants showed that most had single nucleotide mutations in genes associated with biofilm formation, e.g. in wspF, pilT, fha1 and aguR. Complementation of those mutations restored starvation-induced dispersal from the biofilms. Because c-di-GMP is linked to biofilm formation and dispersal, we introduced a c-di-GMP reporter into the wild-type P. aeruginosa and monitored green fluorescent protein (GFP) expression before and after starvation-induced dispersal. Post dispersal, the microcolonies were smaller and significantly brighter in GFP intensity, suggesting the relative concentration of c-di-GMP per cell within the microcolonies was also increased. Furthermore, only the RSCV showed increased c-di-GMP, while wild type and SCV were no different from the parental strain.

Conclusions
This suggests that while starvation can induce dispersal from the biofilm, it also results in strong selection for mutants that overproduce c-di-GMP and that fail to disperse in response to the dispersal cue, starvation.
Waitlist management in a pediatric weight management clinic: implementing an orientation session
Authors: Smith Webb A. , Gray Emily , Jones Tamekia L. , Han Joan C. , Burton E. Thomaseo 
Published: September 2021

Abstract
Background
This study evaluates implementation of an orientation session to address a waitlist of more than 2000 referrals to a pediatric weight management clinic in the Mid-South United States.

Methods
An hour-long group-based orientation to the pediatric weight management clinic was implemented to provide information about the structure and expectations of the clinic as well as education on healthy lifestyle recommendations. Families were contacted from the waitlist by telephone and invited to attend an orientation session prior to scheduling a clinic appointment.

Results
Of 2251 patients contacted from the waitlist, 768 scheduled an orientation session, of which 264 (34 %) attended. Of the 264 orientation participants, 246 (93 %) scheduled a clinic appointment. Of those, 193 (79 %) completed a clinic visit. Waitlist times decreased from 297.8 ± 219.4 days prior to implementation of orientation sessions to 104.1 ± 219.4 days after.

Conclusions
Orientation has been an effective and efficient way to triage patient referrals while maximizing attendance in limited clinic slots for patients and families demonstrating interest and motivation. Elements of this approach are likely generalizable to other pediatric clinical settings that must strategically manage a large volume of patient referrals.
Longitudinal trends in malaria testing rates in the face of elimination in eastern Myanmar: a 7-year observational study
Authors: Rae Jade D. , Landier Jordi , Simpson Julie A. , Proux Stéphane , Devine Angela , Maude Richard J. , Thu Aung Myint , Wiladphaingern Jacher , Kajeechiwa Ladda , Thwin May Myo , Tun Saw Win , Nosten François H. 
Published: September 2021

Abstract
Background
Providing at-risk communities with uninterrupted access to early diagnosis and treatment is a key component in reducing malaria transmission and achieving elimination. As programmes approach malaria elimination targets it is critical that each case is tested and treated early, which may present a challenge when the burden of malaria is reduced. In this paper we investigate whether malaria testing rates decline over time and assess the impacts of integrating malaria and non-malaria services on testing rates in the malaria elimination task force (METF) programme in the Kayin state of Myanmar.

Methods
A retrospective analysis was conducted using weekly collected data on testing rates from a network of more than 1200 malaria posts during the period from 2014 to 2020. To determine whether monthly testing rates changed over the years of programme operations, and whether integrating malaria and non-malaria services impacted these testing rates, we fitted negative binomial mixed-effects regression models to aggregate monthly data, accounting for malaria seasonal variation.

Results
In the first year of malaria post operation, testing rates declined, correlating with a decline in attendance by people from outside the malaria post catchment area, but then remained fairly constant (the Rate Ratio (RR) for 2nd versus 1st year open ranged from 0.68 to 0.84 across the four townships included in the analysis, the RR for 3rd to 6th year versus 1st year open were similar, ranging from 0.59–0.78). The implementation of a training programme, which was intended to expand the role of the malaria post workers, had minimal impact on testing rates up to 24 months after training was delivered (RR for integrated versus malaria-only services ranged from 1.00 to 1.07 across METF townships).

Conclusion
Despite the decline in malaria incidence from 2014 to 2020, there has been no decline in the malaria testing rate in the METF programme after the establishment of the complete malaria post network in 2016. While the integration of malaria posts with other health services provides benefits to the population, our evaluation questions the necessity of integrated services in maintaining malaria testing rates in areas approaching elimination of malaria.
Hospitalisation rates differed by city district and ethnicity during the first wave of COVID-19 in Amsterdam, The Netherlands
Authors: Coyer Liza , Wynberg Elke , Buster Marcel , Wijffels Camiel , Prins Maria , Schreijer Anja , van Duijnhoven Yvonne T. H. P. , van Dam Alje P. , van der Lubben Mariken , Leenstra Tjalling 
Published: September 2021

Abstract
Background
It is important to gain insight into the burden of COVID-19 at city district level to develop targeted prevention strategies. We examined COVID-19 related hospitalisations by city district and migration background in the municipality of Amsterdam, the Netherlands.

Methods
We used surveillance data on all PCR-confirmed SARS-CoV-2 hospitalisations in Amsterdam until 31 May 2020, matched to municipal registration data on migration background. We calculated directly standardised (age, sex) rates (DSR) of hospitalisations, as a proxy of COVID-19 burden, per 100,000 population by city district and migration background. We calculated standardised rate differences (RD) and rate ratios (RR) to compare hospitalisations between city districts of varying socio-economic and health status and between migration backgrounds. We evaluated the effects of city district and migration background on hospitalisation after adjusting for age and sex using Poisson regression.

Results
Between 29 February and 31 May 2020, 2326 cases (median age 57 years [IQR = 37–74]) were notified in Amsterdam, of which 596 (25.6%) hospitalisations and 287 (12.3%) deaths. 526/596 (88.2%) hospitalisations could be matched to the registration database. DSR were higher in individuals living in peripheral (South-East/New-West/North) city districts with lower economic and health status, compared to central districts (Centre/West/South/East) (RD = 36.87,95%CI = 25.79–47.96;RR = 1.82,95%CI = 1.65–1.99), and among individuals with a non-Western migration background compared to ethnic-Dutch individuals (RD = 57.05,95%CI = 43.34–70.75; RR = 2.36,95%CI = 2.17–2.54). City district and migration background were independently associated with hospitalisation.

Conclusion
City districts with lower economic and health status and those with a non-Western migration background had the highest burden of COVID-19 during the first wave of COVID-19 in Amsterdam.
Dental students’ preference and perception on intraoral scanning and impression making
Authors: Lam Walter Yu-Hang , Mak Ken Chung-Kan , Maghami Ebrahim , Molinero-Mourelle Pedro 
Published: September 2021

Abstract
Background
To investigate the preference and perception on intraoral scanning and impression making among dental students.

Methods
Final-year dental students from the 2019 and 2020 cohorts were invited to complete an online questionnaire via Google-Form. Their preference on the intraoral-scanning/impression making techniques and their perception on these techniques including the ease of defect identification, ease of infection control, need of chairside support, ease to master the technique as a beginner, efficiency in their hands and ease to handle the scanner software (yes/no) were collected. The results were analysed using McNemar tests and binary logistic regression test. All tests were performed at significance level α = 0.05.

Results
Ninety-seven students participated in this study with a response rate of 96.0 %. Eighty-one students (83.5 %) have tried intraoral scanning on peers. Fifty-three (54.6 %) students preferred intraoral-scanning and were categorized as Pro-scanning group. Forty-four (45.4 %) students either preferred impression-making (n = 21) or not sure (n = 23) were categorized as Others. More than half of students in both groups felt that intraoral-scanning is easier to identify defect, easier in infection control and require less chairside support. Higher proportion of students in the Pro-scanning group felt that intraoral-scanning requires less chairside support, easier to master as a beginner, more efficient in their hands and they can deal well with the scanner software than that in Others (P < 0.05). Regression shown that students preferred a technique that they perceived is more efficient (P = 0.000).

Conclusions
While intraoral scanning has perceived advantages, many students still prefer impression making that works more efficient to them.
Psychometric properties of a clinical reasoning assessment rubric for nursing education
Authors: Lee JuHee , Park Chang Gi , Kim Sung Hae , Bae Juyeon 
Published: September 2021

Abstract
Background
Clinical reasoning is a vital competency for healthcare providers. In 2014, a clinical reasoning assessment rubric (CRAR) composed of analysis, heuristics, inference, information processing, logic, cognition and meta-cognition subdomains was developed for osteopathy students.

Methods
This study was conducted to verify the validity and reliability of the CRAR in nursing education. A total of 202 case vignette assessments completed by 68 students were used for exploratory factor analysis (EFA) and confirmatory factor analysis (CFA). The Cronbach’s α coefficient of the CRAR was calculated.

Results
The content validity indices ranged from 0.57 to 1.0. The EFA resulted in three factors: assessment in nursing, nursing diagnosis and planning, and cognition/meta-cognition in nursing. The CFA supported a 3-factor model. The Cronbach’s α coefficient of the CRAR was 0.94. This study confirmed the content validity, construct validity, and reliability of the CRAR. Therefore, the CRAR is a useful rubric for assessing clinical reasoning in nursing students.

Conclusions
The CRAR is a standardized rubric for assessing clinical reasoning in nurses. This scale will be useful for the development of educational programs for improving clinical reasoning in nursing education.
Socio-demographic, clinical and service use determinants associated with HIV related stigma among people living with HIV/AIDS: a systematic review and meta-analysis
Authors: Armoon Bahram , Higgs Peter , Fleury Marie-Josée , Bayat Amir-Hossien , Moghaddam Ladan Fattah , Bayani Azadeh , Fakhri Yadollah 
Published: September 2021

Abstract
Background
Defining HIV-related stigma (HRS) can be problematic due to structural inequalities, cultural differences, discrimination by health care providers and the limitations of tools measuring stigma for people living with HIV (PLWH). This meta-analysis aimed to determine self-reported HRS and its association with socio-demographic and clinical determinants.

Methods
PubMed, Scopus, Web of Science, PsycInfo, SciELO and Cochrane electronic databases were searched and after reviewing for study duplicates, the full-text of selected articles were assessed for eligibility using Population, Intervention, Comparator, Outcomes criteria. We used fixed and random-effects meta-analysis models to estimate the pooled prevalence, pooled odds ratio (OR) and 95% confidence intervals.

Results
Thirty-one studies containing 10,475 participants met the eligibility criteria. Among the potential risk factors: age > 30 years (OR = 0.93, 95%CI = 0.86, 1), living with a spouse (OR = 0.07, 95%CI = 0.02, 0.17), CD4 count < 200 (OR = 0.5, 95% CI = 0.31, 0.68), medication adherence (OR = 0.96, 95%CI = 0.94, 0.99), poor access to care (OR = 0.79, 95%CI = 0.65, 0.93), time since diagnosis, and accessibility to care (OR = 0.37, 95%CI = 0.11, 0.86) were all significantly associated with self-reported HIV stigma among PWLH.

Conclusion
Stigma is correlated with numerous negative consequences in marginalised populations including PLWH. Considering the negative association that stigma has on HIV prevention and treatment targeted evidence-based stigma reduction interventions are recommended. Interventions that are focused on a particular group, such as healthcare professionals are warranted. Rigorously designed studies with specific and validated outcome measures associated with targeted interventions may help to improve the reduction of HRS for PLWH.