bluuebunny/crossref_metadata_2025 huggingface dataset:
Closantel retinal toxicity: Recovery from severe vision loss after corticosteroid therapy
Authors: Behboudi Hassan , Alizadeh Yousef , Medghalchi Abdolreza , Soltani-moghadam Reza , Azaripour Ebrahim , Moravvej Zahra
Published: July 2022

Purpose

To present a relatively rare case of retinal toxicity and consequent severe vision loss due to Closantel ingestion.

Case report

A 37-year-old female presented with sudden painless decrease vision in both eyes. She had no previous history of medical disease and denied any trauma. The patient had accidentally ingested Closantel a few days prior to presentation. Closantel is a veterinary anti-helminthic drug used mainly in livestock. Best corrected visual acuity (BCVA) at presentation was 20/200 bilaterally. There was no relative afferent pupillary defect (RAPD) and red saturation test was normal. Macular optical coherence tomography (OCT) revealed disruption in the outer retinal layer and ellipsoid zone in both eyes. A diagnosis of retinal toxicity due to Closantel was made and the patient was started on 1 mg/kg oral prednisolone acetate. On the 45th day after presentation, her BCVA had improved to 20/20 bilaterally.

Conclusion

Closantel is a potentially toxic drug causing destruction of the neurosensory retina and visual disturbances. We suggest eye-care personnel awareness regarding the risk of Closantel-induced retinal toxicity and prompt treatment with systemic steroids should be considered.
Progress in the quality of care for newly diagnosed people with HIV in Spain (2004–2019)
Authors: Alejos Belén , Díez Cristina , Galindo María J , López Juan C , Moreno-García Estela , Estrada Vicente , Poveda Eva , Omar Mohamed , Jarrín Inmaculada , Berenguer Juan ,   For CoRIS
Published: July 2022

Background

We monitored the quality of care for newly diagnosed people with HIV (PWH) in Spain, including linkage to care within 1 month of HIV diagnosis (LC-1Mo) and viral suppression within 3 months of HIV diagnosis (VS-3Mo).

Methods

Longitudinal study based on The Cohort of the Spanish AIDS Research Network (CoRIS). We used logistic regression stratified by year of HIV diagnosis (2004–2013 and 2014–2019) to assess differences by sex, country of origin, HIV risk group, age, prior AIDS, HIV Viral Load, and CD4 cell count.

Results

The final analysis included 13,632 PWH: males 85%, men having sex with men (MSM) 61%, median age 35 years. LC-1Mo increased from 42% (95% CI, 38%–46%) in 2004 to 80% (95% CI, 77%−83%) in 2019 ( P < 0.001). Median CD4+ cell counts at ART initiation increased from <250/mm3 in 2004–2005 to >350/mm3 since 2012 ( P < 0.001). The percentage of initial regimens based on integrase strand transfer inhibitors (INSTI) increased from 3% in 2004 to >70% from 2016 onwards ( P < 0.001). VS-3Mo increased from 6% (95% CI, 4%–8%) in 2004 to 45% (95% CI, 41%–49%) in 2019 ( P < 0.001). Worst results for LC-1Mo were found among PWH acquiring HIV by injection drug use and those born in Latin American Countries across all the study period.

Conclusion

Care indicators have improved among newly diagnosed PWH in Spain over the last 15 years. Removal of CD4 cell counts limitations, and probably the increasing use of INSTI-based regimens was decisive for the progress made.
Milder disease trajectory among COVID-19 patients hospitalised with the SARS-CoV-2 Omicron variant compared with the Delta variant in Norway
Authors: Stålcrantz Jeanette , Kristoffersen Anja Bråthen , Bøås Håkon , Veneti Lamprini , Seppälä Elina , Aasand Nina , Hungnes Olav , Kvåle Reidar , Bragstad Karoline , Buanes Eirik Alnes , Whittaker Robert
Published: July 2022

Using individual-level national registry data, we conducted a cohort study to estimate differences in the length of hospital stay, and risk of admission to an intensive care unit and in-hospital death among patients infected with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant, compared with patients infected with Delta variant in Norway. We included 409 (38%) patients infected with Omicron and 666 (62%) infected with Delta who were hospitalised with coronavirus disease 2019 (COVID-19) as the main cause of hospitalisation between 6 December 2021 and 6 February 2022. Omicron patients had a 48% lower risk of intensive care admission (adjusted hazard ratios (aHR): 0.52, 95% confidence interval (CI): 0.34–0.80) and a 56% lower risk of in-hospital death (aHR: 0.44, 95%CI: 0.24–0.79) compared with Delta patients. Omicron patients had a shorter length of stay (with or without ICU stay) compared with Delta patients in the age groups from 18 to 79 years and those who had at least completed their primary vaccination. This supports growing evidence of reduced disease severity among hospitalised Omicron patients compared with Delta patients.
Partition layout inside a muffler integrated with a thermoelectric generator: Multi-physics analysis and optimal design
Authors: Oh Kee Seung , Lee Jin Woo
Published: July 2022

A multi-physics-analysis-based topology optimization (TO) method is proposed to optimally design the internal partition layout of a muffler integrated with a thermoelectric generator (TEG). The basic equations governing the acoustical behavior, heat transfer, and fluid flow in the muffler are introduced, and their interaction is designated for exact numerical analysis in terms of acoustics, heat transfer, and fluid mechanics. To implement density-based TO, one design variable is assigned to each finite element in the design domain, and interpolation functions suitable for each physics phenomenon are employed. In the TO problem formulation, the sum of the squared acoustic pressures at the outlet of the muffler for multi-target frequencies is selected as an objective function to achieve broadband noise attenuation. The temperature of the TEG and the pressure drop are constrained for high energy recovery efficiency and fluid passage, respectively. The optimization problem formulated for the muffler design is solved for various design conditions. Optimal partition layouts are obtained depending on the location and length of the TEG, the upper limit value of the pressure drop, and the number of target frequencies in the same frequency band. The noise attenuation performances of each partition layout are compared, and their expected recovery energies are calculated. One optimal partition layout is discussed in terms of acoustics, heat transfer, and fluid mechanics. The numerical results strongly support the validity of our proposed method for the optimal design of a muffler integrated with a TEG.
Seismic analysis of a I-sectioned steel frame based on an improved time-domain spectral element method
Authors: Wang Dansheng , Chi Jingrong
Published: July 2022

An improved time-domain spectral element method (ITSEM) is developed for seismic analysis of I-sectioned steel structures in this paper. The developed method considers the effect of section type on spectral stiffness using shear correction coefficient. In the calculation process of the time-domain spectral stiffness and mass matrices, the invariant integral operations of the element matrices are extracted and saved in advance. Thus, the global mass and stiffness matrices of the structures can be obtained only by simple addition, subtraction, multiplication and division operations, which greatly improves computational efficiency. Next, the natural frequencies of a I-sectioned beam are computed and compared with the finite element method (FEM) and analytical results to validate the ITSEM. Then, the seismic responses of a ten-story steel frame using ITSEM are obtained and compared with those by FEM, which proves the effectiveness, accuracy and high efficiency of ITSEM in elastic seismic analysis.
Rest in space, Starman! Creative reframing of death metaphors on David Bowie’s mural in London
Authors: Hidalgo-Downing Laura , Pérez-Sobrino Paula
Published: July 2022

This article explores the way in which death metaphors written in the urban mural for David Bowie in London contribute to creatively reframing the artist’s death. While research on death metaphors has focussed on traditional written genres such as obituaries and epitaphs, studies of urban memorials and shrines have focussed on the creation of fandom identities, downplaying the role played by figurativity, creativity and emotional connotation. The present article aims to bridge the gap between these two areas of study by presenting a corpus-based study of 585 items written on the mural for David Bowie. The research questions are: (1) How is Bowie’s death (metaphorically) conceptualised? (2) To what extent are death metaphors in Bowie’s mural creative? and (3) What is the relationship between the metaphorical framing of Bowie’s death and the projection of emotional connotations? The findings of our study reveal that Bowie’s songs emerge as a highly productive metaphorical source domain to understand the artist’s death, in which fans recontextualise lines from Bowie’s lyrics in creative and positive ways.
Sculpting the interpersonal: towards a social semiotic framework for analysing interpersonal meaning in statues
Authors: Bowcher Wendy L , Yameng Liang Jennifer
Published: July 2022

The underlying question of this article is ‘how do statues convey interpersonal meaning?’ To answer this question, the authors briefly critically examine the current social semiotic analytical framework for statues and develop a revised framework for analysing interpersonal meaning in which features from Kress and van Leeuwen’s Reading Images: The Grammar of Visual Design (2006) and selected features from O’Toole’s framework from The Language of Displayed Art (2011) for analysing sculpture are integrated. These features are also extended and/or complemented by incorporating features obtained from research into the fields of gesture, body language and facial expression. Further, in keeping with Systemic Functional Linguistic-inspired research, system networks are used to map out the potential material and semantic (interpersonal) features for figurative statues and to present possible configurations among these features. Although the focus of this article is on interpersonal meaning, it is acknowledged that within a social semiotic approach, there is an interdependency among interpersonal, experiential (representational) and textual (compositional) meanings, and that these configure within a specific context of situation. This interdependency is only briefly attended to in the article itself, but the proposed framework provides a starting point for developing an account of the way that interpersonal features and their realizations in statues may configure with representational and compositional features and their realizations. With the current world focus on statues and their sometimes controversial social meanings, this article offers a timely opportunity for a range of users such as social semioticians or art educators and students to consider, through a systematic analytical framework, the way in which statues may relate interpersonally with viewers, and provides a key step towards accounting for the way that configurations of interpersonal, representational and compositional features may construe contextual tensions in relation to the overall message conveyed by a statue.
A practical review of electroencephalography’s value to consumer research
Authors: McInnes Aaron N , Sung Billy , Hooshmand Reyhane
Published: July 2022

Electroencephalography (EEG) offers insights into the neural responses of consumers to marketing stimuli which can be used to evaluate the effectiveness of such stimuli in directing favorable consumer behavior in real-world settings. This practical review provides guidelines for using EEG in consumer and marketing research. It provides recommendations for how EEG may effectively be employed in neuromarketing in the future. EEG requires careful experimental design, and as such, we outline current recommendations for the collection, processing, analysis, and interpretation of EEG evoked potentials (i.e., event related potentials; ERP) and spectral content (i.e., EEG frequency). By providing an introductory overview of EEG measures in marketing and consumer research, this practical review extends previous literature that is primarily focused on other neuroimaging techniques (e.g., functional magnetic resonance imaging) and other disciplines (e.g., economics and organizational behaviour). Furthermore, by reviewing how EEG has been used throughout psychophysiological and neuromarketing research, we provide recommendations on how EEG can be used to measure marketing-related outcomes. These include processes relating to perception, attention, memory, emotion, and cognitive load, demonstrating the unique value of considering the neural responses captured by EEG in understanding and predicting consumer behavior.
On statistic alignment for domain adaptation in structural health monitoring
Authors: Poole Jack , Gardner Paul , Dervilis Nikolaos , Bull Lawrence , Worden Keith
Published: July 2022

The practical application of structural health monitoring is often limited by the availability of labelled data. Transfer learning – specifically in the form of domain adaptation (DA) – gives rise to the possibility of leveraging information from a population of physical or numerical structures, by inferring a mapping that aligns the feature spaces. Typical DA methods rely on nonparametric distance metrics, which require sufficient data to perform density estimation. In addition, these methods can be prone to performance degradation under class imbalance. To address these issues, statistic alignment (SA) is discussed, with a demonstration of how these methods can be made robust to class imbalance, including a special case of class imbalance called a partial DA scenario. Statistic alignment is demonstrated to facilitate damage localisation with no target labels in a numerical case study, outperforming other state-of-the-art DA methods. It is then shown to be capable of aligning the feature spaces of a real heterogeneous population, the Z24 and KW51 bridges, with only 220 samples used from the KW51 Bridge. Finally, in scenarios where more complex mappings are required for knowledge transfer, SA is shown to be a vital pre-processing tool, increasing the performance of established DA methods.
Donald Trump’s Effect on Who is Considered “Conservative”
Authors: Amira Karyn
Published: July 2022

Conservative intellectuals have expressed concern that Donald Trump has tarnished the conservative brand with his authoritarian-populist rhetoric and style of governing. What exactly is Donald Trump’s effect on this ideological label? In this paper I replicate work showing that members of Congress who have openly supported Trump are seen as more conservative than those who do not openly support him. I then test this relationship experimentally and explore whether a pro (or anti) Trump cue alone drives this perception or whether other perceived, unstated issue positions might influence this result. I find that supporting Trump moves candidates rightward compared to a control group, and this effect is about twice as large as the anti-Trump cue which moves candidates leftward. I also find that candidates who support Trump are more likely to be associated with additional issue-related content, which could affect ideological perception. Roadmaps for extensions are also discussed.
Dual-Energy X-Ray Absorptiometry (DEXA) Evaluation of the Bone Remodeling Effects of a Low-Modulus Composite Hip Stem After 2 Decades of Follow-Up
Authors: Bigach Stephen D. , Kolevar Matthew P. , Moore Rebecca D. , Adavi Pranav , Rimnac Clare M. , Kraay Matthew J.
Published: July 2022

Background: The Epoch FullCoat Hip Stem (Zimmer) was an isoelastic composite femoral stem developed to address stem stiffness concerns. Purpose: We sought to evaluate the long-term bone mineral density (BMD) of a cohort of patients who underwent total hip arthroplasty (THA) using the Epoch isoelastic stem and having more than 2-decade follow-up. Methods: We conducted a retrospective chart review of all patients who were study subjects at our institution in a multicenter prospective trial for the Food and Drug Administration of the Epoch implant in the mid-1990s. Through this, we identified 16 patients who had dual-energy X-ray absorptiometry (DEXA) scans, with which we could determine BMD preoperatively and at 3 points postoperatively. Of these, 5 agreed to participate in the study (the others were deceased, unable or declined to participate, or were lost to follow-up) with mean follow-up of 22 years. These participants underwent clinical and radiographic evaluation consisting of a Harris hip score, anteroposterior (AP) pelvis and AP and lateral hip X-rays, and DEXA evaluation of both hips. BMD in the 7 Gruen zones at last follow-up was compared with immediate postoperative and 2-year follow-up. Results: At last follow-up, all stems were well-fixed with signs of extensive osteointegration. In proximal Gruen zones 1 and 7, patients underwent a decrease in BMD with more modest losses in Gruen zone 1. All patients demonstrated an increase in BMD in zones 2 through 6 at latest follow-up, except for 1 patient in Gruen zone 6. BMD changes were not limited to the first 2 years of follow-up. Conclusion: This small follow-up cohort study found excellent long-term clinical results, no plain radiographic signs of notable stress shielding, and general maintenance of BMD at a follow-up of over 20 years for this isoelastic stem. Long-term bone remodeling after implantation of the isoelastic stem resulted in increased BMD in Gruen zones 2 through 6, suggesting that composite implant designs may still have a role in THA.
Individuals With Mental Illnesses on Probation: The Intersection of Trauma, Race, and Gender
Authors: Givens Ashley , Murray-Lichtman Andrea , Van Deinse Tonya B. , Dallenbach MacKenzie , Cowell Mercier Mariah , Lowder Evan M. , Cuddeback Gary S.
Published: July 2022

Little research exists about PTSD and traumatic experiences among justice-involved individuals with mental illnesses and how those experiences differ by race and gender. We examined traumatic experiences and PTSD among 187 individuals with serious mental illnesses on probation in the United States: 94% of participants experienced a traumatic event, rates of PTSD were highest among Black women ( p < .001), and rates of sexual assault were highest among White women ( p < .001). Justice-involved individuals with mental illnesses have complex needs and an elevated risk of PTSD and exposure to traumatic events, which has implications for probation policy and practice.
Re-Conceptualizing Success: Investigating Specialized Units Responses to the Sexual Trafficking of Female Victim-Survivors
Authors: Ballucci Dale , Stathakis Felicia
Published: July 2022

This paper explores police officers’ experiences working in a specialized human trafficking unit in Canada to identify challenges, strategies, and responses to working with victim-survivors. Analyzing data from semi-structured interviews, we find that officers deploy victim-centered responses reflecting procedural justice outcomes due to their awareness that the criminal justice process often re-victimizes. Officers’ deployment of procedural justice acknowledges the victim-survivor trauma, but also allows them to build a stronger case through evidence gathering, increasing the potential for charges and convictions, also known as distributive justice. We argue that this illustrates that these two approaches to justice are interdependent.
Culture as both a risk and protective factor for vicarious traumatisation in nurses working with refugees: a literature review
Authors: Dodds Hannah , Hunter David J
Published: July 2022

Background

There are an estimated 25.9 million refugees worldwide, who require health services while living in host countries. To effectively treat refugee patients, nurses must document their history which requires hearing about their traumatic journeys. Listening to trauma has been shown to cause vicarious traumatisation.

Aims

To identify the risk and protective factors involved in the development of vicarious traumatisation.

Methods

After searching four databases, nine studies were selected for review. Key words ‘vicarious trauma’, ‘refugee’ and ‘nurse’ formed the search. Articles were appraised using the Critical Appraisal Skills Program and Mixed Methods Appraisal Tool.

Results

Vicarious traumatisation is common amongst nurses working with refugees. Aspects of culture formed the principal risk and protective factors. Differences between cultures made for strained communication while similarities created better understanding. Some cultures provided more resilience than others. Vicarious resilience, a feeling of personal growth resulting from hearing about and helping patients overcome trauma, was also highlighted. The development of vicarious resilience was a protective factor.

Conclusions

Further investigation into how to minimise risk and establish protective factors is required. Some coping recommendations include personal reflection, comprehensive training and better access to counselling.
Intentional Teaching for Risky Play: Practitioner Researchers Move Beyond Their Comfort Zones
Authors: Higginbottom Kate , Newman Linda , West-Sooby Kelly , Wood April
Published: July 2022

Risky play promotes learning for children but can be challenging for adults who may then avoid providing these opportunities for children. Research about educators’ intentional teaching for risky play is limited. The focus of this paper is a project where educators sought to change practice by embedding intentional teaching within children’s risky play. A centre team in Newcastle Australia comprising practitioner researchers with a University Research Mentor used action research to plan, implement and report the research. Positive changes in intentional teaching for risky play were documented. We argue that using action research for risky-play change led to professional gains for educators and strengthened children’s risk-competence using an intentional teaching strategy constructed for risky play. This paper aims to increase awareness of authentic professional learning for educators about intentional teaching and risky play via action research.
Self-Other Agreement in Experience Sampling Measures
Authors: Leikas Sointu , Lönnqvist Jan-Erik
Published: July 2022

Experience sampling methodology (ESM) has provided researchers with a flexible and innovative measurement tool, and the methodology has become increasingly popular in several fields of psychology. Therefore, validity studies on such measures are important. The present study investigated convergent and discriminant validity of ESM measures using peer-ratings as the criteria. We obtained ESM self- and other-ratings of personality states, situation perceptions, and feelings from 344 occasions, from 49 target participants. The results showed that several—but not all—widely used ESM self-ratings have substantial and distinct self-other agreement. We conclude that many ESM self-reports are likely to capture, at least to an extent, target persons’ actual personality states, feelings, and situation perceptions.
Relaxation-weighted 23Na magnetic resonance imaging maps regional patterns of abnormal sodium concentrations in amyotrophic lateral sclerosis
Authors: Müller Hans-Peter , Nagel Armin M. , Keidel Franziska , Wunderlich Arthur , Hübers Annemarie , Gast Lena V. , Ludolph Albert C. , Beer Meinrad , Kassubek Jan
Published: July 2022

Objectives:

Multiparametric magnetic resonance imaging (MRI) is established as a technical instrument for the characterisation of patients with amyotrophic lateral sclerosis (ALS). The contribution of relaxation-weighted sodium (23NaR) MRI remains to be defined. The aim of this study is to apply 23NaR MRI to investigate brain sodium homeostasis and map potential alterations in patients with ALS as compared with healthy controls.

Materials and Methods:

Seventeen patients with ALS (mean age 61.1 ± 11.4 years, m/f = 9/8) and 10 healthy control subjects (mean age 60.3 ± 15.3 years, m/f = 6/4) were examined by 23NaR MRI at 3 T. Regional sodium maps were obtained by the calculation of the weighted difference from two image data sets with different echo times (TE1 = 0.3 ms, TE2 = 25 ms). Voxel-based analysis of the relaxation-weighted maps, together with 23Na concentration maps for comparison, was performed.

Results:

ROI-based analyses of relaxation-weighted brain sodium concentration maps demonstrated increased sodium concentrations in the upper corticospinal tracts and in the frontal lobes in patients with ALS; no differences between ALS patients and controls were found in reference ROIs, where no involvement in ALS-associated neurodegeneration could be anticipated.

Conclusion:

23NaR MRI mapped regional alterations within disease-relevant areas in ALS which correspond to the stages of the central nervous system (CNS) pathology, providing evidence that the technique is a potential biological marker of the cerebral neurodegenerative process in ALS.
The Effect of a Learning Partner Model-Based Program on Spreading Cancer Prevention Knowledge Using Community Health Volunteers in Japan
Authors: Yako-Suketomo Hiroko , Oura Asae , Katayama Kayoko , Saito Kyohei , Ohashi Ken , Navarro Ana M.
Published: July 2022

Objectives:

This study examines the implementation and short-term effects of a Learning Partner Model (LPM)-based educational program on cancer prevention and control information for community health volunteers in Japan.

Methods:

The program was undertaken by 3 local governments in collaboration with a government initiative and offered a 90-min group workshop to community health volunteers. Community health volunteers (primary participants) recruited in turn friend or family members (secondary participants) with whom they were prepared to share the content of the workshop with the help of printed materials received in the workshop. We conducted self-administered paper and pencil questionnaire surveys before, immediately after, and 3 months after the workshop. The t-test, Fisher’s exact test, paired t-test, and McNemar test were used to compare the 2 groups’ demographic characteristics and healthy habits at pretest. Repeated measures ANOVA was used to compare cancer prevention knowledge between groups and over time.

Results:

Of 142 participants, 107 pairs of learning partners (primary and corresponding secondary participant) completed all questionnaires. All primary participants and 37.4% of the secondary participants were women, and 57.9% of the learning partners were spouses. The results showed significantly higher correct answers on the cancer-prevention knowledge questions in the post-workshop and follow-up surveys compared to the pre-workshop survey ( P < .001). The increase in knowledge was observed in all learning-partner groups in all 3 sites.

Conclusion:

The study demonstrates a promising strategy that can be adapted to the health needs of the community beyond cancer prevention and control, building on the efforts of local governments and government health initiatives.
Secukinumab-Induced Lymphocytic Colitis
Authors: Gandu Siva Santosh Kumar , Khan Mohammad Hassaan , Vasikaran Anush , Pandit Sudha
Published: July 2022

Secukinumab an interleukin-17 (IL-17) monoclonal antibody inhibitor is currently approved for the treatment of rheumatological conditions, such as psoriasis and ankylosing spondylitis. Lymphocytic colitis, a phenotype of microscopic colitis, is a long-term inflammatory condition, is characterized by relapsing diarrhea. The specific entity of drug-induced lymphocytic colitis has been discussed with numerous individual cases being reported from around the world. Secukinumab has been linked with exacerbation of and de novo cases of inflammatory bowel disease. However, lymphocytic colitis in association with this drug has not been documented. The management of drug-induced lymphocytic colitis is complicated, as patients frequently exhibit spontaneous remission of symptoms. Removal of the offending agent has shown some benefit; however, some patients continue to exhibit symptoms months after drug cessation and washout. Although our patient’s lymphocytic colitis was benign and responded to the cessation Secukinumab, it is an important diagnosis to consider in patients with new onset relapsing diarrhea treated with biologics.
Comparison of Inlay Cartilage Butterfly and Underlay Temporal Fascia Tympanoplasty
Authors: Lubianca Neto José Faibes , Koerig Schuster Artur , Neves Lubianca João Pedro , Eavey Roland Douglas
Published: July 2022

Objective

To systematically review the results of inlay cartilage butterfly tympanoplasty and standard underlay temporal fascia tympanoplasty for anatomic and functional end points.

Data Sources

PubMed, Embase, MEDLINE, and Virtual Health Library (VHL/Lilacs) databases were searched from inception through April 2, 2021. No restrictions on language, publication year, or publication status were applied.

Review Methods

The meta‐analysis included data from articles that met inclusion criteria and were extracted by 2 authors independently. The PRISMA statement was followed. Risk of Bias 2.0 and Newcastle‐Ottawa Scale were used to assess risk of bias. The primary outcome was tympanic membrane closure rate. The secondary outcome was improvement of the air‐bone gap.

Results

Ten studies were included, 9 cohort studies and 1 randomized clinical trial, with 577 patients. The graft take rate was 82.8% in the butterfly cartilage inlay tympanoplasty group and 85.2% in the temporal fascia underlay tympanoplasty group (relative risk, 1.01; 95% CI, 0.93‐1.11; I2 = 42%, P =. 08). The air‐bone gap reduction ranged from 6.1 to 11.28 in the butterfly cartilage inlay group and from 5.2 to 12.66 in the temporal fascia underlay group, with a mean difference between groups of −2.08 (95% CI, −3.23 to −0.94; I2 = 58%, P =. 04), favoring temporal fascia underlay.

Conclusion

The 2 tympanoplasty techniques analyzed here produced similar results in terms of successful reconstruction of the tympanic membrane and reduction in the air‐bone gap. Neither age nor follow‐up length of time influenced outcomes.
Trauma-informed sentencing in South Australian courts
Authors: McLachlan Katherine J
Published: July 2022

Recently the concepts of ‘compassionate courts’, ‘humane justice’, ‘kindness in court’, and trauma-informed practice have emerged in legal theory and practice in the US, England, Scotland and Australia. This article uses a trauma-informed practice framework to examine how South Australian superior court judges acknowledge defendant trauma in sentencing. Trauma-informed sentencing practice requires that judges realise the presence of trauma, recognise its relevance, respond in a way that is informed by trauma and act to resist re-traumatisation. By using this ‘4Rs’ framework to analyse sentencing remarks of 448 defendants published in 2019, the presence of trauma-informed practice was explored. Analysis indicated that judges realised trauma was present in the lives of many defendants, particularly women and Aboriginal peoples, but did not always overtly recognise a link between trauma and criminal behaviour and were unlikely to refer to a defendant’s trauma history or use trauma-informed principles of practice in their sentencing response. Research findings were presented to judicial officers at a Judicial Development Day in 2021. The article reflects on those discussions as well as the primary research, when making recommendations for future sentencing practice primary for the judiciary, but also for legislators and legal practitioners.
Integer programming for selecting set of informative markers in paternity inference
Authors: Nishiyama Soichiro , Sato Kengo , Tao Ryutaro
Published: July 2022

Background

Parentage information is fundamental to various life sciences. Recent advances in sequencing technologies have made it possible to accurately infer parentage even in non-model species. The optimization of sets of genome-wide markers is valuable for cost-effective applications but requires extremely large amounts of computation, which presses for the development of new efficient algorithms.

Results

Here, for a closed half-sib population, we generalized the process of marker loci selection as a binary integer programming problem. The proposed systematic formulation considered marker localization and the family structure of the potential parental population, resulting in an accurate assignment with a small set of markers. We also proposed an efficient heuristic approach, which effectively improved the number of markers, localization, and tolerance to missing data of the set. Applying this method to the actual genotypes of apple (Malus × domestica) germplasm, we identified a set of 34 SNP markers that distinguished 300 potential parents crossed to a particular cultivar with a greater than 99% accuracy.

Conclusions

We present a novel approach for selecting informative markers based on binary integer programming. Since the data generated by high-throughput sequencing technology far exceeds the requirement for parentage assignment, a combination of the systematic marker selection with targeted SNP genotyping, such as KASP, allows flexibly enlarging the analysis up to a scale that has been unrealistic in various species. The method developed in this study can be directly applied to unsolved large-scale problems in breeding, reproduction, and ecological research, and is expected to lead to novel knowledge in various biological fields. The implementation is available at https://github.com/SoNishiyama/IP-SIMPAT.
getSequenceInfo: a suite of tools allowing to get genome sequence information from public repositories
Authors: Moco Vincent , Cazenave Damien , Garnier Maëlle , Pot Matthieu , Marcelino Isabel , Talarmin Antoine , Guyomard-Rabenirina Stéphanie , Breurec Sébastien , Ferdinand Séverine , Dereeper Alexis , Reynaud Yann , Couvin David
Published: July 2022

Background

Biological sequences are increasing rapidly and exponentially worldwide. Nucleotide sequence databases play an important role in providing meaningful genomic information on a variety of biological organisms.

Results

The getSequenceInfo software tool allows to access sequence information from various public repositories (GenBank, RefSeq, and the European Nucleotide Archive), and is compatible with different operating systems (Linux, MacOS, and Microsoft Windows) in a programmatic way (command line) or as a graphical user interface. getSequenceInfo or gSeqI v1.0 should help users to get some information on queried sequences that could be useful for specific studies (e.g. the country of origin/isolation or the release date of queried sequences). Queries can be made to retrieve sequence data based on a given kingdom and species, or from a given date. This program allows the separation between chromosomes and plasmids (or other genetic elements/components) by arranging each component in a given folder. Some basic statistics are also performed by the program (such as the calculation of GC content for queried assemblies). An empirically designed nucleotide ratio is calculated using nucleotide information in order to tentatively provide a “NucleScore” for studied genome assemblies. Besides the main gSeqI tool, other additional tools have been developed to perform various tasks related to sequence analysis.

Conclusion

The aim of this study is to democratize the use of public repositories in programmatic ways, and to facilitate sequence data analysis in a pedagogical perspective. Output results are available in FASTA, FASTQ, Excel/TSV or HTML formats. The program is freely available at: https://github.com/karubiotools/getSequenceInfo. getSequenceInfo and supplementary tools are partly available through the recently released Galaxy KaruBioNet platform (http://calamar.univ-ag.fr/c3i/galaxy_karubionet.html).
Comparative genomic analysis of the human genome and six bat genomes using unsupervised machine learning: Mb-level CpG and TFBS islands
Authors: Iwasaki Yuki , Ikemura Toshimichi , Wada Kennosuke , Wada Yoshiko , Abe Takashi
Published: July 2022

Background

Emerging infectious disease-causing RNA viruses, such as the SARS-CoV-2 and Ebola viruses, are thought to rely on bats as natural reservoir hosts. Since these zoonotic viruses pose a great threat to humans, it is important to characterize the bat genome from multiple perspectives. Unsupervised machine learning methods for extracting novel information from big sequence data without prior knowledge or particular models are highly desirable for obtaining unexpected insights. We previously established a batch-learning self-organizing map (BLSOM) of the oligonucleotide composition that reveals novel genome characteristics from big sequence data.

Results

In this study, using the oligonucleotide BLSOM, we conducted a comparative genomic study of humans and six bat species. BLSOM is an explainable-type machine learning algorithm that reveals the diagnostic oligonucleotides contributing to sequence clustering (self-organization). When unsupervised machine learning reveals unexpected and/or characteristic features, these features can be studied in more detail via the much simpler and more direct standard distribution map method. Based on this combined strategy, we identified the Mb-level enrichment of CG dinucleotide (Mb-level CpG islands) around the termini of bat long-scaffold sequences. In addition, a class of CG-containing oligonucleotides were enriched in the centromeric and pericentromeric regions of human chromosomes. Oligonucleotides longer than tetranucleotides often represent binding motifs for a wide variety of proteins (e.g., transcription factor binding sequences (TFBSs)). By analyzing the penta- and hexanucleotide composition, we observed the evident enrichment of a wide range of hexanucleotide TFBSs in centromeric and pericentromeric heterochromatin regions on all human chromosomes.

Conclusion

Function of transcription factors (TFs) beyond their known regulation of gene expression (e.g., TF-mediated looping interactions between two different genomic regions) has received wide attention. The Mb-level TFBS and CpG islands are thought to be involved in the large-scale nuclear organization, such as centromere and telomere clustering. TFBSs, which are enriched in centromeric and pericentromeric heterochromatin regions, are thought to play an important role in the formation of nuclear 3D structures. Our machine learning-based analysis will help us to understand the differential features of nuclear 3D structures in the human and bat genomes.
Genomic and proteomic characterization of two strains of Shigella flexneri 2 isolated from infants’ stool samples in Argentina
Authors: Torrez Lamberti Mónica F. , Terán Lucrecia C. , Lopez Fabián E. , de las Mercedes Pescaretti María , Delgado Mónica A.
Published: July 2022

Background

Shigella specie is a globally important intestinal pathogen disseminated all over the world. In this study we analyzed the genome and the proteomic component of two Shigella flexneri 2a clinical isolates, collected from pediatric patients with gastroenteritis of the Northwest region of Argentina (NWA) in two periods of time, with four years of difference. Our goal was to determine putative changes at molecular levels occurred during these four years, that could explain the presence of this Shigella`s serovar as the prevalent pathogen in the population under study.

Results

As previously reported, our findings support the idea of Shigella has a conserved “core” genome, since comparative studies of CI133 and CI172 genomes performed against 80 genomes obtained from the NCBI database, showed that there is a large number of genes shared among all of them. However, we observed that CI133 and CI172 harbors a small number of strain-specific genes, several of them present in mobile genetic elements, supporting the hypothesis that these isolates were established in the population by horizontal acquisition of genes. These differences were also observed at proteomic level, where it was possible to detect the presence of certain secreted proteins in a culture medium that simulates the host environment.

Conclusion

Great similarities were observed between the CI133 and CI172 strains, confirming the high percentage of genes constituting the “core” genome of S. flexneri 2. However, numerous strain specific genes were also determined. The presence of the here identified molecular elements into other strain of our culture collation, is currently used to develop characteristic markers of local pathogens. In addition, the most outstanding result of this study was the first description of a S. flexneri 2 producing Colicin E, as one of the characteristics that allows S. flexneri 2 to persist in the microbial community. These findings could also contribute to clarify the mechanism and the evolution strategy used by this pathogen to specifically colonize, survive, and cause infection within the NWA population.
1,25-dihydroxyvitamin D3 ameliorates lupus nephritis through inhibiting the NF-κB and MAPK signalling pathways in MRL/lpr mice
Authors: Li Xuewei , Liu Jie , Zhao Yingzhe , Xu Ning , Lv E. , Ci Chunzeng , Li Xiangling
Published: July 2022

Background

Lupus nephritis (LN) is a common and serious complication of systemic lupus erythematosus (SLE). However, the aetiology and pathogenesis of LN remain unknown. 1,25-dihydroxyvitamin D3 [1,25-(OH)2-VitD3] is the active form of vitamin D, and it has been shown to perform important functions in inflammatory and immune-related diseases. In this study, we investigated the time-dependent effects of 1,25-dihydroxyvitamin D3 and explored the underlying mechanism in MRL/lpr mice, a well-studied animal model of LN.

Methods

Beginning at 8 weeks of age, 24-h urine samples were collected weekly to measure the levels of protein in the urine. We treated female MRL/lpr mice with 1,25-dihydroxyvitamin D3 (4 μg/kg) or 1% DMSO by intraperitoneal injection twice weekly for 3 weeks beginning at the age of 11 weeks. The mice were separately sacrificed, and serum and kidney samples were collected at the ages of 14, 16, 18, and 20 weeks to measure creatinine (Cr) levels, blood urea nitrogen (BUN) levels, histological damage, immunological marker (A-ds DNA, C1q, C3, IgG, IgM) levels, and inflammatory factor (TNF-α, IL-17, MCP-1) levels. Furthermore, the nuclear factor kappa B (NF-κB) and the mitogen-activated protein kinase (MAPK) signalling pathways were also assessed to elucidate the underlying mechanism.

Results

We found that MRL/lpr mice treated with 1,25-dihydroxyvitamin D3 displayed significantly attenuated LN. VitD3-treated mice exhibited significantly improved renal pathological damage and reduced proteinuria, BUN, SCr, A-ds DNA antibody and immune complex deposition levels (P < 0.05) compared with untreated MRL/lpr mice. Moreover, 1,25-dihydroxyvitamin D3 inhibited the complement cascade, inhibited the release of proinflammatory cytokines, such as TNF-α, IL-17, and MCP-1, and inhibited NF-κB and MAPK activation (P < 0.05).

Conclusion

1,25-dihydroxyvitamin D3 exerts a protective effect against LN by inhibiting the NF-κB and MAPK signalling pathways, providing a potential treatment strategy for LN. Interestingly, the NF-κB and MAPK signalling pathways are time-dependent mediators of LN and may be associated with lupus activity.
Perioperative levetiracetam for seizure prophylaxis in seizure-naive brain tumor patients with focus on neurocognitive functioning
Authors: Konrath Elias , Marhold Franz , Kindler Wolfgang , Scheichel Florian , Popadic Branko , Blauensteiner Katrin , Calabek Bernadette , Freydl Elisabeth , Weber Michael , Ristl Robin , Hainz Katharina , Sherif Camillo , Oberndorfer Stefan
Published: July 2022

Introduction

In seizure-naive brain tumor patients, the efficacy of perioperative prophylactic antiepileptic drug treatment remains controversial. In case of administration, the common preferred drug is levetiracetam (LEV) because of its favorable pharmacological profile. Research to date has not sufficiently determined how LEV affects cognition in the short term, as is the case in the perioperative period. The objective of this prospective study was to examine the neurocognitive functioning of seizure-naive brain tumor patients after receiving LEV perioperatively.

Methods

Fortythree patients with supratentorial brain tumor scheduled for surgery received LEV three days before until six days after surgery as seizure prophylaxis. Cognitive functioning (NeuroCogFX), LEV plasma-levels, hematotoxicity, side-effects, as well as health-related quality of life (HRQoL, Qolie31), were recorded preoperatively before (Baseline) and after onset of LEV (Pre-Op), 4–6 days postoperatively (Post-Op) and 21 days postoperatively (Follow-Up).

Results

No significant changes in cognitive functioning and HRQoL were seen after onset of preoperative LEV. There was a significant improvement of NeuroCogFX total-score at Follow-Up (p = 0.004) compared to Baseline. The overall-score Qolie31 showed simultaneous improvement patterns as cognitive functioning (p < 0.001). The most frequent side effect related to study drug was somnolence (in 28.6% of patients).

Conclusions

A significant improvement of cognitive functioning, as well as an improvement in HRQoL, were detected postoperatively. This is presumably due to the debulking effect of the surgery. Nevertheless, LEV has no detrimental effect on cognitive functioning in the perioperative phase in seizure-naive brain tumor patients.

Trial registration

This study was registered prospectively (Date: 25/11/2015; EudraCT: 2015–003,916-19).
A 15-year retrospective review of urodynamic studies in children at Red Cross War Memorial Children’s Hospital, Cape town, South Africa
Authors: Mosalakatane Thembisile Dintle , McCulloch Mignon , Nourse Peter , Coetzee Ashton , Wright Anne , Raad Jeanette , Lazarus John , Howlett Justin
Published: July 2022

Background

Despite the undeniable diagnostic benefits of urodynamic studies (UDS), their adoption into clinical practice in Africa has been slow. This study aimed to review the use of invasive UDS in children at a tertiary paediatric hospital in South Africa.

Methods

A retrospective analysis of 1108 UDS was conducted. Patient demographic characteristics, primary diagnosis, indication and urodynamic outcomes were reviewed. Presence of urodynamic high-risk features were documented, and a comparison was made between the first study and follow-up study.

Results

This study revealed increasing trends in the use of UDS from 2015. Referrals were from Urology (37.7%), Spinal defects clinic (34.4%), Nephrology (20.8%) and other departments (7.0%). The most common reason for referral was review of medical treatment (36.5%). Spinal dysraphism (58.3%) accounted for the majority of conditions seen. Majority (59.1%) of the patients were receiving more than one type of bladder treatment at the time of their first study, with clean intermittent catheterisation (46.5%) being the most common form of bladder management. 97.5% of studies were performed using transurethral bladder catheterization. Urodynamic diagnosis was neurogenic in 74.0%, anatomical (12.2%), functional (8.8%) and normal (5.0%). There was statistically significant improvement in bladder compliance, detrusor leak point pressure and detrusor sphincter dyssynergia between the first study and a subsequent study following therapeutic intervention.

Conclusions

The unique ability of UDS to demonstrate changes in detrusor pressures, which is a common reason for therapy failure, makes UDS an invaluable tool in the diagnosis and management of children with lower urinary tract dysfunction.