Miracle-dz/UniFAR-FTUs huggingface dataset:
Just keep it simple? Benchmarking the accuracy of taxonomy assignment software in metabarcoding studies

How do you put a name on an unknown piece of DNA? From microbes to mammals, high‐throughput metabarcoding studies provide a more objective view of natural communities, overcoming many of the inherent limitations of traditional field surveys and microscopy‐based observations (Deiner et al., 2017). Taxonomy assignment is one of the most critical aspects of any metabarcoding study, yet this important bioinformatics task is routinely overlooked. Biodiversity surveys and conservation efforts often depend on formal species inventories: the presence (or absence) of species, and the number of individuals reported across space and time. However, computational workflows applied in eukaryotic metabarcoding studies were originally developed for use with bacterial/archaeal data sets, where microbial researchers rely on one conserved locus (nuclear 16S rRNA) and have access to vast databases with good coverage across most prokaryotic lineages – a situation not mirrored in most multicellular taxa. In this issue of Molecular Ecology Resources, Hleap et al. (2021) carry out an extensive benchmarking exercise focused on taxonomy assignment strategies for eukaryotic metabarcoding studies utilizing the mitochondrial Cytochrome C oxidase I marker gene (COI). They assess the performance and accuracy of software tools representing diverse methodological approaches: from “simple” strategies based on sequence similarity and composition, to model‐based phylogenetic and probabilistic classification tools. Contrary to popular assumptions, less complex approaches (BLAST and the QIIME2 feature classifier) consistently outperformed more sophisticated mathematical algorithms and were highly accurate for assigning taxonomy at higher levels (e.g. family). Lower‐level assignments at the genus and species level still pose significant challenge for most existing algorithms, and sparse eukaryotic reference databases further limit software performance. This study illuminates current best practices for metabarcoding taxonomy assignments, and underscores the need for community‐driven efforts to expand taxonomic and geographic representation in reference DNA barcode databases.
Citizen science project characteristics: Connection to participants’ gains in knowledge and skills

Background Biodiversity is being lost rapidly and its conservation is thus one of the most urgent tasks today. For biodiversity conservation to be successful, the public needs to gain an awareness and understanding of biodiversity and its importance. Moreover, species experts are needed who have the skills necessary for identifying and recording biodiversity. Previous research showed that citizen science projects can contribute to educating the public about biodiversity. However, it is still unclear how project characteristics connect to participants’ knowledge and skills and how citizen science projects should be designed if they are to foster participants’ learning. Aim We aimed to investigate specific characteristics of biodiversity citizen science projects that could potentially influence participants’ learning. We explored the following project characteristics from both the project coordinators’ and the participants’ perspectives: information and training provided to participants, social interaction among participants, contact between participants and staff, and feedback and recognition provided to participants. Methods and results In order to examine the extent to which these project characteristics are connected to participants’ gains in knowledge and skills, we conducted a comprehensive study across 48 biodiversity citizen science projects in Europe and Australia. We found that participants’ perceived gains in knowledge and skills were significantly related to the five project characteristics as reported by the participants: information received by the participants, training received by the participants, social interaction among participants, contact between participants and staff, and feedback and recognition received by the participants. Conclusion We conclude that by deliberately designing citizen science projects to include features such as interaction and feedback, these projects could achieve higher learning outcomes for the participants. Thereby, suitable modes of communication between projects and their participants are crucial. We provide specific suggestions for the design of biodiversity citizen science projects and for future research on project characteristics and participant outcomes.
Is 3D laparoscopic off clamp simple enucleation a feasible alternative for clinical T1 renal tumors? Outcomes from a single center experience.

PURPOSE To evaluate the safety of 3D laparoscopic off clamp simple enucleation (SE) of kidney tumors versus standard laparoscopic on-clamp partial nephrectomy (PN) in terms of perioperative, oncological and functional outcomes. METHODS All patients that underwent 3D laparoscopic nephron sparing surgery (NSS) in our department for clinical T1 tumors between January 2019-September 2020 were included. Of the total of 84 patients, 38 (45.24%) underwent SE (SE group) and 46 (54.76%) PN (PN group). Perioperative data was collected and analyzed. Oncological outcomes were evaluated by the positive surgical margin (PSM) rate and follow-up at 6 months after surgery. RESULTS Mean age, gender, tumor size, PADUA score and length of hospital stay were comparable between the two groups. Estimated intraoperative blood loss (284.21 ml vs 151.52 ml, p=0.0001) and hemoglobin drop (p=0.0001) were significantly lower for the PN group. Patients that underwent SE showed a better preservation of renal function (eGFR drop of 4.4 ml/min vs 1.78 ml/min, p=0.75). No significant differences were found regarding the PSM, although the PSM rate was lower in the SE group when compared with the PN group (2.63% vs 4.34%, p= 0.07). CONCLUSION Off-clamp simple enucleation of renal masses is feasible by laparoscopic approach and has produced comparable oncologic outcomes with standard on-clamp partial nephrectomy, with an incremental advantage for the preservation of renal function.
Influence of education level on MMSE and MoCA scores of elderly inpatients

Abstract Objective The purpose of this study was to investigate the influence of education level on MMSE and MoCA scores of elderly inpatients. Method This is a cross-sectional study. A total of 260 elderly inpatients were evaluated by the MMSE and MoCA sequentially. Results The total MMSE scores were highly correlated with the total MoCA scores (r = 0.7629, p < 0.0001), and were correlated with the length of education (r = 0.2723, p < 0.0001). The total MoCA scores were also correlated with the length of education (r = 0.3323, p < 0.0001). Meanwhile, MoCA was also used to reevaluate the elderly inpatients with normal MMSE scores at different education levels. There were no significant differences at different education levels (χ 2=1.351, p = 0.5090). Finally, we analyzed the diagnostic consistency of MMSE and MoCA at different education levels, and the results showed that education level was closely related to the consistency of the diagnoses based on the MMSE and MoCA (χ 2=10.23, p = 0.0368). Conclusions In general, the results of both the MMSE and MoCA were influenced by education level, and this effect was more obvious for the MoCA. However, in the cognitive assessment of elderly patients, the ability to identify impairment with the MoCA is obviously superior to that with the MMSE.
Risk factors for precancerous cervical lesion among women screened for cervical cancer in south Ethiopia: Unmatched case-control study

Background Nearly 90% of deaths from cervical cancer occur in a low resource setting. In Ethiopia, the magnitude of precancerous cervical lesions ranges from 7% to 28%. Precancerous cervical lesions may progress to cervical cancer. Early screening and treatment of precancerous cervical lesions is a cost-effective way to avert the growth of cervical cancer. However, there has been limited research on risk factors for precancerous cervical lesions in Ethiopia. Therefore, this study aimed to identify risk factors for precancerous cervical lesions among women screened for cervical cancer in south Ethiopia. Method A facility-based unmatched case-control study was carried out in five health facilities in south Ethiopia between 8 May to 28 September 2018. Interviewer administered questionnaires were used to collect data from 98 cases and 197 controls. Multivariate logistic regression was employed to identify determinants of precancerous cervical lesions. Results Women aged 30–39 years (AOR = 2.51, 95% CI: 1.03–6.08), monthly income ≤66 (AOR = 3.51, 95% CI: 1.77–6.97), initiation of first sexual intercourse at age less than or equal to 20 (AOR = 2.39, 95% CI: 1.14–5.47), having more than one lifetime sexual partner (AOR = 4.70, 95% CI: 2.02–10.95), having a partner/ husband with more than one lifetime sexual partner (AOR = 2.98, 95% CI: 1.35–6.65) had higher odds of precancerous cervical lesions. Conclusion and recommendation Strategies to prevent precancerous cervical lesions should focus on modification of lifestyle and sexual behaviour. The findings of this study highlight several implications for policymakers: targeting older women for cervical cancer screening, addressing inequalities and education relating to risky sexual behaviour may reduce precancerous cervical lesions. Furthermore, future longitudinal studies are needed to assess the awareness of women about cervical cancer screening.
Depression and anxiety in cardiac rehabilitation: differential associations with changes in exercise capacity and quality of life

ABSTRACT Background Cardiac rehabilitation (CR) has been successful in improving exercise capacity (EC) and quality of life (QoL). However, depression and anxiety are highly prevalent among cardiac patients and might represent risk factors for rehabilitation outcomes. The aim of this study was to investigate the role of depression and anxiety as possible independent risk factors for CR outcomes. Methods The study applied a pre-post-design. The sample comprised N = 3’434 cardiac disease patients taking part in a Swiss inpatient CR center. Variables measured at the beginning (T1) and end of rehabilitation (T2) included depression and anxiety (HADS), EC, and QoL (MacNew). A path analysis was conducted. Results Depression at T1 had a significant negative relationship with improvements in EC and in all aspects of QoL during rehabilitation. Anxiety at T1 was positively related to improvements in EC and in emotional and physical QoL. Improvements in depression during CR were positively related with improvements in all outcomes. Improvements in anxiety showed no significant association with the outcomes. Conclusion Depression and anxiety should be screened for during CR. Depression should be treated due to the negative association found with rehabilitation outcomes. Underlying mechanisms of the positive association of anxiety with rehabilitation outcomes need further investigation.
Do We Hold Males and Females to the Same Standard? A Measurement Invariance Study on the Psychopathy Checklist-Revised

Abstract Psychopathy in females has been understudied. Extant data on gender comparisons using the predominant measure of assessment in clinical practice, the Psychopathy Checklist Revised (PCL-R), points to a potential lack of measurement invariance (MI). If indeed the instrument does not perform equally (well) in both genders, straightforward comparison of psychopathy scores in males and females is unwarranted. Using a sample of female and male forensic patients (N = 110 and N = 147 respectively), we formally tested for MI in a structural equation modeling framework. We found that the PCL-R in its current form does not attain full MI. Four items showed threshold-biases and particularly Factor 2 (the Social Deviance Factor) is gender biased. Based on our findings, it seems reasonable to expect that specific scoring adjustments might go a long way in bringing about more equivalent assessment of psychopathic features in men and women. Only then can we begin to meaningfully compare the genders on the prevalence, structure, and external correlates of psychopathy.
Hospital transmission of borderline oxacillin-resistant Staphylococcus aureus evaluated by whole-genome sequencing

Introduction Staphylococcus aureus is a major cause of hospital infections worldwide. Awareness towards methicillin-resistant S. aureus (MRSA) infections is high but attention towards borderline oxacillin-resistant S. aureus (BORSA) is limited, possibly due to an underestimated clinical relevance, presumption of low incidence and diagnostic limitations. Gap statement BORSA surveillance has not been routinely implemented, and thus consensus with regard to a definition and infection control measures is lacking. Aim Our goals were to investigate the occurrence, molecular characteristics and clinical manifestations of BORSA infections in the hospital setting. Methodology Following an increased incidence in 2016, BORSA cases in 2014/2016 (in our institution) were more specifically evaluated. Medical records were reviewed to investigate epidemiological links, clinical characteristics and outcomes. Resistance and virulence markers were assessed by whole genome sequencing (WGS). Conventional methods: amplified fragment length polymorphism (AFLP) ; multilocus sequence typing (MLST) and multiple locus variable-number tandem repeat analysis (MLVA) were compared with core genome MLST (cgMLST) and whole-genome single nucleotide polymorphism (wgSNP) analysis to confirm genetic clusters. Results From 2009 to 2013, BORSA comprised 0.1 % of all clinical S. aureus strains. In 2016, the incidence was six-fold higher in comparison to the baseline. Whole-genome SNP and cgMLST confirmed two BORSA clusters among patients with dermatological conditions. Patients with BORSA presented with skin infections, and one case developed a severe invasive infection with a fatal outcome. Infection control measures successfully prevented further transmission in both clusters. WGS findings showed that BORSA strains carried multiple resistance and virulence genes with increased pathogenic potential. Conclusion WGS and cgMLST effectively characterized and confirmed BORSA clusters among at-risk patients with clinical manifestations ranging from mild skin infections to life-threatening bacteraemia. Clinical awareness and active monitoring are therefore warranted for the timely implementation of infection control measures to prevent BORSA transmission in high-risk patients.
Influence of Powder Characteristic of ZnO on Antibacterial Activity

The effects of shape, crystallinity and specific surface area of ZnO powder on antibacterial activity were studied by measuring the change in the electrical conductivity with bacterial growth. From the results, it was clarified that the antibacterial activity increased with the increase of powder concentration in the physiological saline. The antibacterial activity against Escherichia coli strongly depended on the specific surface area of the powder; the activity increased with the increase of the surface area, irrespective of the shape and the crystallinity of their powders. In the case of Staphylococcus aureus, however, it was found that there was no difference in the activity according to the characteristic of the powders. The appearance of antibacterial activity was found to be due to the generation of H2O2 from the surface of ZnO powder.
A Longitudinal Exploration of Self-Reported Hearing Loss, Tinnitus, and Posttraumatic Stress Disorder Treatment Outcomes in Australian Veterans

ABSTRACT Objective Tinnitus, hearing loss, and posttraumatic stress disorder (PTSD) are common conditions among veterans. Shared underlying symptoms, such as hypervigilance and heightened sense of threat, may interfere with talk-based psychological treatments. The aim was to investigate the prevalence and risk factors for self-reported tinnitus and hearing loss among Australian treatment-seeking veterans, as well as links with PTSD symptoms and quality of life (QOL) after treatment. Methods Australian veterans participating in hospital-based PTSD treatment (n = 523) completed self-report measures of subjective hearing impairment, service-related factors, PTSD symptoms, and QOL at treatment intake and discharge, as well as 3- and 9-month follow-ups. Univariate analyses of covariance modeled symptom change over time. Results More than half of veterans on PTSD treatment self-reported doctor-diagnosed hearing loss or tinnitus, whereas 43% reported both. However, 75% reported subjective mild to moderate hearing impairment, and only 1% reported severe impairment. Service-related factors, such as longer length of service and exposure to explosions, were risk factors for having any hearing condition. After controlling for intake scores, there were no significant differences on PTSD or QOL outcomes over time between those with and without hearing conditions. Conclusions Although self-reported tinnitus and hearing loss are prevalent among veterans, those with severe hearing impairments are unlikely to be represented in this context. There is a need for psychological treatments that are accessible to patients with severe hearing impairments, which should be examined routinely among military members accessing psychological treatments.
Clinician-driven artificial intelligence in ophthalmology: resources enabling democratization

Purpose of review This article aims to discuss the current state of resources enabling the democratization of artificial intelligence (AI) in ophthalmology Recent findings Open datasets, efficient labeling techniques, code-free automated machine learning (AutoML) and cloud-based platforms for deployment are resources that enable clinicians with scarce resources to drive their own AI projects. Summary Clinicians are the use-case experts who are best suited to drive AI projects tackling patient-relevant outcome measures. Taken together, open datasets, efficient labeling techniques, code-free AutoML and cloud platforms break the barriers for clinician-driven AI. As AI becomes increasingly democratized through such tools, clinicians and patients stand to benefit greatly.
Outcome in Elderly Patients With Cardiogenic Shock Complicating Acute Myocardial Infarction

ABSTRACT Introduction: Despite advances in treatment of patients with cardiogenic shock following acute myocardial infarction (AMICS) in-hospital mortality remains around 50%. Outcome varies among patient subsets and the elderly often have a poor a priori prognosis. We sought to investigate outcome among elderly AMICS patients referred to evaluation and treatment at a tertiary university hospital. Methods: Current analysis was based on the RETROSHOCK registry comprising consecutive AMICS patients admitted to tertiary care. Patients in the registry were individually identified and validated. Results: Of 1,716 admitted patients, 496 (28.9%) patients were ≥75 years old. Older patients were less likely to be admitted directly to a tertiary centre (59.4% vs. 69.9%, P = 0.003), receive mechanical support devices (i.e., Impella® (8.9% vs. 15.0%, P = 0.003), and undergo revascularization attempt (76.8% vs. 90.2%, P < 0.001). Thirty-day survivors ≥75 years were characterized by having higher left ventricular ejection fraction (30.2% ± 12.5% vs. 26.5% ± 11.8%, P = 0.004) and lower arterial lactate (3.2[2.2–5.2] mmol/L vs. 5.5[3.3–8.2] mmol/L, P < 0.001) at admission. In a multivariable analysis of patients ≥75 years, higher age (HR 1.09, 95% CI 1.05–1.14, P < 0.001), higher heart rate (HR 1.01, 95% CI 1.001–1.014, P = 0.03), and higher lactate (HR 1.11, 95% CI 1.07–1.16, P < 0.001) at admission were associated with an increased risk of 30-day mortality. Conclusion: Among patients ≥75 years with AMICS referred for tertiary specialized treatment, 30-day mortality was 73.4%. Survivors were characterized by lower arterial lactate and heart rate at admission.
Altered Dynamic Information Flow through the Cortico-Basal Ganglia Pathways Mediates Parkinson’s Disease Symptoms

Abstract Parkinson’s disease (PD) is a progressive neurodegenerative disorder caused by dopamine deficiency. To elucidate network-level changes through the cortico-basal ganglia pathways in PD, we recorded neuronal activity in PD monkeys treated with 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine. We applied electrical stimulation to the motor cortices and examined responses in the internal (GPi) and external (GPe) segments of the globus pallidus, the output and relay nuclei of the basal ganglia, respectively. In the normal state, cortical stimulation induced a triphasic response composed of early excitation, inhibition, and late excitation in the GPi and GPe. In the PD state, cortically evoked inhibition in the GPi mediated by the cortico-striato-GPi “direct” pathway was largely diminished, whereas late excitation in the GPe mediated by the cortico-striato-GPe-subthalamo (STN)-GPe pathway was elongated. l-DOPA treatment ameliorated PD signs, particularly akinesia/bradykinesia, and normalized cortically evoked responses in both the GPi and GPe. STN blockade by muscimol injection ameliorated the motor deficit and unmasked cortically evoked inhibition in the GPi. These results suggest that information flow through the direct pathway responsible for the initiation of movements is largely reduced in PD and fails to release movements, resulting in akinesia/bradykinesia. Restoration of the information flow through the direct pathway recovers execution of voluntary movements.