bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of the Drug-O-Matic Automated Dispensing System
Authors: Maliekal James 
Published: April 2023

Objective To compare the time savings and accuracy rates of a manual dispensing system with the Drug-O-Matic (DOM), an automated tablet and capsule counter. Design In part one, phase A of this two-part study, a time trial measured the time of the prescription-filling process using the manual method. In part one, phase B, a time trial measured the time of that process using the DOM system. Part two of the study measured the accuracy of the DOM. Results The DOM requires 9 hours 42 minutes less per day than does the manual system. However, its accuracy causes some concern because we found a 14 percent discrepancy rate in terms of over- and underfills. Conclusions Our initial experience with the DOM suggests significant time-savings potential compared with the manual method of prescription filling, and our institutional goal is to translate the time saved into other activities that will allow us to function as a free-standing pharmacy. A concern is the DOM's 14 percent discrepancy rate. Further studies are needed to confirm or challenge our initial findings.
Cost of Inappropriate Use of Ciprofloxacin in Ambulatory Care
Authors: Koo Ji. M. , Renner Edward D. 
Published: April 2023

Objective To determine the incidence of inappropriate ciprofloxacin use and the resulting cost thereof in ambulatory care. Design Retrospective cost analysis. Setting Ambulatory care clinic of a Department of Veterans Affairs Medical Center. Patients One hundred thirty-seven ambulatory patients prescribed ciprofloxacin during March, April, and May 1992. Forty-six patient charts were available for review. Main Outcome Measure Indications for ciprofloxacin use were determined from chart review. Results Chart review of 46 of the 137 patients prescribed ciprofloxacin during the three-month study period indicated that only 8 (17 percent) had infections that were appropriately treated with this antibiotic. If 550 patients had received ciprofloxacin that year (figure extrapolated from the three-month totals), the cost of prescribing would have been $29,260. This study indicates that $20,500 per year could be saved by prescribing equally efficacious oral antibiotics. Conclusions Restricting ciprofloxacin use to its proven indications in the ambulatory setting may result in considerable cost savings to medical centers.
Two simple methods to improve the accuracy of the genomic selection methodology
Authors: Montesinos-López Osval A. , Kismiantini  , Montesinos-López Abelardo 
Published: April 2023

Abstract
Background
Genomic selection (GS) is revolutionizing plant and animal breeding. However, still its practical implementation is challenging since it is affected by many factors that when they are not under control make this methodology not effective. Also, due to the fact that it is formulated as a regression problem in general has low sensitivity to select the best candidate individuals since a top percentage is selected according to a ranking of predicted breeding values.

Results
For this reason, in this paper we propose two methods to improve the prediction accuracy of this methodology. One of the methods consist in reformulating the GS (nowadays formulated as a regression problem) methodology as a binary classification problem. The other consists only in a postprocessing step that adjust the threshold used for classification of the lines predicted in its original scale (continues scale) to guarantee similar sensitivity and specificity. The postprocessing method is applied for the resulting predictions after obtaining the predictions using the conventional regression model. Both methods assume that we defined with anticipation a threshold, to divide the training data as top lines and not top lines, and this threshold can be decided in terms of a quantile (for example 80%, 90%, etc.) or as the average (or maximum) of the performance of the checks.
In the reformulation method it is required to label as one those lines in the training set that are equal or larger than the specified threshold and as zero otherwise. Then we train a binary classification model with the conventional inputs, but using the binary response variable in place of the continuous response variable. The training of the binary classification should be done to guarantee a more similar sensitivity and specificity, to guarantee a reasonable probability of classification of the top lines.

Conclusions
We evaluated the proposed models in seven data sets and we found that the two proposed methods outperformed by large margin the conventional regression model (by 402.9% in terms of sensitivity, by 110.04% in terms of F1 score and by 70.96% in terms of Kappa coefficient, with the postprocessing methods). However, between the two proposed methods the postprocessing method was better than the reformulation as binary classification model. The simple postprocessing method to improve the accuracy of the conventional genomic regression models avoid the need to reformulate the conventional regression models as binary classification models with similar or better performance, that significantly improve the selection of the top best candidate lines. In general both proposed methods are simple and can easily be adopted for use in practical breeding programs, with the guarantee that will improve significantly the selection of the top best candidates lines.
The mitochondrial genome of the diploid oat Avena longiglumis
Authors: Liu Qing , Yuan Hongyu , Xu Jiaxin , Cui Dongli , Xiong Gui , Schwarzacher Trude , Heslop-Harrison John Seymour 
Published: April 2023

Abstract
Background
Avena longiglumis Durieu (2n = 2x = 14) is a wild relative of cultivated oat (Avena sativa, 2n = 6x = 42) with good agronomic and nutritional traits. The plant mitochondrial genome has a complex organization and carries genetic traits of value in exploiting genetic resources, not least male sterility alleles used to generate F1 hybrid seeds. Therefore, we aim to complement the chromosomal-level nuclear and chloroplast genome assemblies of A. longiglumis with the complete assembly of the mitochondrial genome (mitogenome) based on Illumina and ONT long reads, comparing its structure with Poaceae species.

Results
The complete mitochondrial genome of A. longiglumis can be represented by one master circular genome being 548,445 bp long with a GC content of 44.05%. It can be represented by linear or circular DNA molecules (isoforms or contigs), with multiple alternative configurations mediated by long (4,100–31,235 bp) and medium (144–792 bp) size repeats. Thirty-five unique protein-coding genes, three unique rRNA genes, and 11 unique tRNA genes are identified. The mitogenome is rich in duplications (up to 233 kb long) and multiple tandem or simple sequence repeats, together accounting for more than 42.5% of the total length. We identify homologous sequences between the mitochondrial, plastid and nuclear genomes, including the exchange of eight plastid-derived tRNA genes, and nuclear-derived retroelement fragments. At least 85% of the mitogenome is duplicated in the A. longiglumis nuclear genome. We identify 269 RNA editing sites in mitochondrial protein-coding genes including stop codons truncating ccmFC transcripts.

Conclusions
Comparative analysis with Poaceae species reveals the dynamic and ongoing evolutionary changes in mitochondrial genome structure and gene content. The complete mitochondrial genome of A. longiglumis completes the last link of the oat reference genome and lays the foundation for oat breeding and exploiting the biodiversity in the genus.
Protocol optimization and assessment of genotypic response for inbred line development through doubled haploid production in maize
Authors: Kaur Harjot , Kyum Mohammed , Sandhu Surinder , Singh Gagandeep , Sharma Priti 
Published: April 2023

Abstract
Background
Doubled haploid technology offers the fastest route of inbred line development by rapidly fixing the desirable combinations in a single year. However, the differential response of haploid induction to genetic background of maternal lines accompanied with low induction rate and high mortality rate due to artificial chromosomal doubling of haploid seedlings creates hindrance in doubled haploid production on a commercial scale under tropical conditions. To speed up the hybrid breeding programme in sub-tropical maize, efforts are reported here to optimize the protocol for efficient production of fixed lines using haploid inducers. The second-generation haploid inducers i.e. CIM2GTAILs obtained from CIMMYT, Mexico were used for haploid induction in 13 F1s of diverse backgrounds. For standardization of chromosomal doubling protocol, various concentrations of colchicine and two seedling growth stages were used to determine the extent of chromosomal doubling and survival rate of doubled haploid plants.

Results
A high mean haploid induction rate is obtained from CIM2GTAIL P2 (10%) as compared to CIM2GTAIL P1 (7.46%). Out of four treatments, CIMMYT reported protocol of chromosome doubling in tropical maize comprising combination of 0.07% colchicine and 0.1% DMSO at V2 stage is highly effective for acquiring doubled haploid plants in sub-tropical adapted maize with high survival rate of 52.7%. However, increasing the colchicine concentration from 0.07 to 0.1% led to high mortality rate.

Conclusion
According to the findings, the haploid induction rate, survival rate and overall success rate varied depending upon the genotype of the inducer and the source population along with the concentrations of chemical used. The optimized protocol developed using CIMMYT haploid inducer CIM2GTAIL P2 for efficient doubled haploid production will not only fasten the breeding programme but will also reduce the production cost of doubled haploid with great efficiency in sub-tropical maize.
Delivery of index-linked HIV testing for children: learnings from a qualitative process evaluation of the B-GAP study in Zimbabwe
Authors: Dringus Stefanie , Davis Katherine , Simms Victoria , Bernays Sarah , Redzo Nicol , Bandason Tsitsi , Chikodzore Rudo , Sibanda Edwin , Webb Karen , Ncube Getrude , Kranzer Katharina , Ferrand Rashida A. , Dziva Chikwari Chido 
Published: April 2023

Abstract
Background
Index-linked HIV testing for children, whereby HIV testing is offered to children of individuals living with HIV, has the potential to identify children living with undiagnosed HIV. The “Bridging the Gap in HIV Testing and Care for Children in Zimbabwe” (B-GAP) study implemented and evaluated the provision of index-linked HIV testing for children aged 2–18 years in Zimbabwe. We conducted a process evaluation to understand the considerations for programmatic delivery and scale-up of this strategy.

Methods
We used implementation documentation to explore experiences of the field teams and project manager who delivered the index-linked testing program, and to describe barriers and facilitators to index-linked testing from their perspectives. Qualitative data were drawn from weekly logs maintained by the field teams, monthly project meeting minutes, the project coordinator’s incident reports and WhatsApp group chats between the study team and the coordinator. Data from each of the sources was analysed thematically and synthesised to inform the scale-up of this intervention.

Results
Five main themes were identified related to the implementation of the intervention: (1) there was reduced clinic attendance of potentially eligible indexes due to community-based differentiated HIV care delivery and collection of HIV treatment by proxy individuals; (2) some indexes reported that they did not live in the same household as their children, reflecting the high levels of community mobility; (3) there were also thought to be some instances of ‘soft refusal’; (4) further, delivery of HIV testing was limited by difficulties faced by indexes in attending health facilities with their children for clinic-based testing, stigma around community-based testing, and the lack of familiarity of indexes with caregiver provided oral HIV testing; (5) and finally, test kit stockouts and inadequate staffing also constrained delivery of index-linked HIV testing.

Conclusions
There was attrition along the index-linked HIV testing cascade of children. While challenges remain at all levels of implementation, programmatic adaptations of index-linked HIV testing approaches to suit patterns of clinic attendance and household structures may strengthen implementation of this strategy. Our findings highlight the need to tailor index-linked HIV testing to subpopulations and contexts to maximise its effectiveness.
Viral reactivations and co-infections in COVID-19 patients: a systematic review
Authors: Kim Jenny Yeon Hee , Ragusa Martin , Tortosa Fernando , Torres Ana , Gresh Lionel , Méndez-Rico Jairo Andres , Alvarez-Moreno Carlos Arturo , Lisboa Thiago Costa , Valderrama-Beltrán Sandra Liliana , Aldighieri Sylvain , Reveiz Ludovic 
Published: April 2023

Abstract
Background
Viral reactivations and co-infections have been reported among COVID-19 patients. However, studies on the clinical outcomes of different viral reactivations and co-infections are currently in limit. Thus, the primary purpose of this review is to perform an overarching investigation on the cases of latent virus reactivation and co-infection in COVID-19 patients to build collective evidence contributing to improving patient health. The aim of the study was to conduct a literature review to compare the patient characteristics and outcomes of reactivations and co-infections of different viruses.

Methods
Our population of interest included confirmed COVID-19 patients who were diagnosed with a viral infection either concurrently or following their COVID-19 diagnosis. We extracted the relevant literature through a systematic search using the key terms in the online databases including the EMBASE, MEDLINE, Latin American Caribbean Health Sciences Literature (LILACS), from inception onwards up to June 2022. The authors independently extracted data from eligible studies and assessed the risk of bias using the Consensus-based Clinical Case Reporting (CARE) guidelines and the Newcastle–Ottawa Scale (NOS). Main patient characteristics, frequency of each manifestation, and diagnostic criteria used in studies were summarized in tables.

Results
In total, 53 articles were included in this review. We identified 40 reactivation studies, 8 coinfection studies, and 5 studies where concomitant infection in COVID-19 patients was not distinguished as either reactivation or coinfection. Data were extracted for 12 viruses including IAV, IBV, EBV, CMV, VZV, HHV-1, HHV-2, HHV-6, HHV-7, HHV-8, HBV, and Parvovirus B19. EBV, HHV-1, and CMV were most frequently observed within the reactivation cohort, whereas IAV and EBV within the coinfection cohort. In both reactivation and coinfection groups, patients reported cardiovascular disease, diabetes, and immunosuppression as comorbidities, acute kidney injury as complication, and lymphopenia and elevated D-dimer and CRP levels from blood tests. Common pharmaceutical interventions in two groups included steroids and antivirals.

Conclusion
Overall, these findings expand our knowledge on the characteristics of COVID-19 patients with viral reactivations and co-infections. Our experience with current review indicates a need for further investigations on virus reactivation and coinfection among COVID-19 patients.
Factors associated with negative conversion of viral RNA in hospitalized children infected with SARS-CoV-2 Omicron variant in Shanghai, China: a retrospective analysis
Authors: Yang Yan , You Yannan , Liu Yazun , Geng Lina , Huang Lirong , Zhou Huan , Piao Xiang , Liu Xiao , Wu Mingyun , Wang Yajuan , Zhou Lili , Wang Peng , Shen Shiping , Hu Mingge , Han Zhaopeng , Xue Zheng 
Published: April 2023

Abstract
Objectives
This study aimed to identify the related risk factors and potential predictors of SARS-CoV-2 RNA negative conversion by describing the dynamics of viral shedding in infected children admitted to two hospitals from Shanghai during the Omicron variant outbreak.

Methods
This retrospective cohort included laboratory-confirmed cases of SARS-CoV-2 infection from Shanghai between March 28 and May 31, 2022. Clinical characteristics, personal vaccination, and household vaccination rates were collected through electronic health records and telephone interviews.

Results
A total of 603 paediatric patients confirmed to have COVID-19 were included in this study. Both univariate and multivariate analyses were performed to filter independent factors for the duration to viral RNA negative conversion. Data on the redetection of SARS-CoV-2 in the patients after they showed negative results on the RT‒PCR test (intermittent negative status) were also analysed. The median duration of virus shedding was 12 (interquartile range, IQR: 10–14) days. The severity of clinical outcome, personal vaccination-2doses, household vaccination rates, and abnormal defecation were factors indecently affecting negative conversion of SARS-CoV-2 RNA, suggesting that patients who had abnormal defecation or with more severe conditions would have delayed virological clearance, while patients who previously had 2 doses of vaccination or had higher household vaccination rates would have accelerated virological clearance. Loss of appetite (odds ratio (OR): 5.343; 95% CI: 3.307–8.632) and abnormal defecation (OR: 2.840; 95% CI: 1.736–4.645) were significantly associated with intermittent negative status.

Conclusion
These findings could provide clues for the early identification of paediatric patients with prolonged viral shedding and could enrich the evidence for the development of prevention and control strategies, especially vaccination policies for children and adolescents.
Risk factors of stillbirths in four district hospitals on Pemba Island, Tanzania: a prospective cohort study
Authors: Skytte Tine Bruhn , Holm-Hansen Charlotte Carina , Ali Said Mouhammed , Ame Shaali , Molenaar Jil , Greisen Gorm , Poulsen Anja , Sorensen Jette Led , Lund Stine 
Published: April 2023

Abstract
Background
More than 2 million third-trimester stillbirths occur yearly, most of them in low- and middle-income countries. Data on stillbirths in these countries are rarely collected systematically. This study investigated the stillbirth rate and risk factors associated with stillbirth in four district hospitals in Pemba Island, Tanzania.

Methods
A prospective cohort study was completed between the 13th of September and the 29th of November 2019. All singleton births were eligible for inclusion. Events and history during pregnancy and indicators for adherence to guidelines were analysed in a logistic regression model that identified odds ratios [OR] with a 95% confidence interval [95% CI].

Results
A stillbirth rate of 22 per 1000 total births in the cohort was identified; 35.5% were intrapartum stillbirths (total number of stillbirths in the cohort, n = 31). Risk factors for stillbirth were breech or cephalic malpresentation (OR 17.67, CI 7.5-41.64), decreased or no foetal movements (OR 2.6, CI 1.13–5.98), caesarean section [CS] (OR 5.19, CI 2.32–11.62), previous CS (OR 2.63, CI 1.05–6.59), preeclampsia (OR 21.54, CI 5.28–87.8), premature rupture of membranes or rupture of membranes 18 h before birth (OR 2.5, CI 1.06–5.94) and meconium stained amniotic fluid (OR 12.03, CI 5.23–27.67). Blood pressure was not routinely measured, and 25% of women with stillbirths with no registered foetal heart rate [FHR] at admission underwent CS.

Conclusions
The stillbirth rate in this cohort was 22 per 1000 total births and did not fulfil the Every Newborn Action Plan’s goal of 12 stillbirths per 1000 total births in 2030. Awareness of risk factors associated with stillbirth, preventive interventions and improved adherence to clinical guidelines during labour, and hence improved quality of care, are needed to decrease the stillbirth rate in resource-limited settings.
Down-regulation of ERAP1 mRNA expression in non-small cell lung cancer
Authors: Wagner Marta , Sobczyński Maciej , Jasek Monika , Pawełczyk Konrad , Porębska Irena , Kuśnierczyk Piotr , Wiśniewski Andrzej 
Published: April 2023

Abstract
Background
ERAP1 is a major aminopeptidase that serves as an editor of the peptide repertoire by trimming N-terminal residues of antigenic peptides, creating a pool of peptides with the optimal length for MHC-I binding. As an important component of the antigen processing and presenting machinery – APM, ERAP1 is frequently down-regulated in many cancers. Since ERAP1 expression has not yet been thoroughly investigated in non-small cell lung cancer (NSCLC), we decided to analyze ERAP1 mRNA levels in tissues collected from NSCLC patients.

Methods
Using real-time qPCR, we evaluated ERAP1 mRNA expression in samples of tumor and adjacent non-tumor tissue (serving as control tissue) from 61 NSCLC patients.

Results
We observed a significantly lower level of ERAP1 mRNA expression in tumor tissue (MedTumor = 0.75) in comparison to non-tumor tissue (MedNon-tumor = 1.1), p = 0.008. One of the five tested polymorphisms, namely rs26653, turned out to be significantly associated with ERAP1 expression in non-tumor tissue (difference [d] = 0.59 CI95% (0.14;1.05), p = 0.0086), but not in tumor tissue.
The levels of ERAP1 mRNA expression did not affect the overall survival of NSCLC patients, either in the case of the tumor (p = 0.788) or in non-tumor (p = 0.298) tissue.
We did not detect any association between mRNA ERAP1 expression level in normal tissue and: (i) age at diagnosis (p = 0.8386), (ii) patient’s sex (p = 0.3616), (iii) histological type of cancer (p = 0.7580) and (iv) clinical stage of NSCLC (p = 0.7549). Furthermore, in the case of tumor tissue none of the abovementioned clinical parameters were associated with ERAP1 expression (p = 0.76).

Conclusion
Down-regulation of ERAP1 mRNA observed in NSCLC tissue may be related to tumor immune evasion strategy. The rs26653 polymorphism can be considered an expression quantitative trait locus (eQTL) associated with ERAP1 expression in normal lung tissue.