Miracle-dz/UniFAR-FTUs huggingface dataset:
Coming of age for COI metabarcoding of whole organism community DNA: Towards bioinformatic harmonisation

Metabarcoding of DNA extracted from community samples of whole organisms (whole organism community DNA, wocDNA) is increasingly being applied to terrestrial, marine and freshwater metazoan communities to provide rapid, accurate and high resolution data for novel molecular ecology research. The growth of this field has been accompanied by considerable development that builds on microbial metabarcoding methods to develop appropriate and efficient sampling and laboratory protocols for whole organism metazoan communities. However, considerably less attention has focused on ensuring bioinformatic methods are adapted and applied comprehensively in wocDNA metabarcoding. In this study we examined over 600 papers and identified 111 studies that performed COI metabarcoding of wocDNA. We then systematically reviewed the bioinformatic methods employed by these papers to identify the state‐of‐the‐art. Our results show that the increasing use of wocDNA COI metabarcoding for metazoan diversity is characterised by a clear absence of bioinformatic harmonisation, and the temporal trends show little change in this situation. The reviewed literature showed (i) high heterogeneity across pipelines, tasks and tools used, (ii) limited or no adaptation of bioinformatic procedures to the nature of the COI fragment, and (iii) a worrying underreporting of tasks, software and parameters. Based upon these findings we propose a set of recommendations that we think the metabarcoding community should consider to ensure that bioinformatic methods are appropriate, comprehensive and comparable. We believe that adhering to these recommendations will improve the long‐term integrative potential of wocDNA COI metabarcoding for biodiversity science.
Effect of feedback type on enhancing subsequent memory: Interaction with initial correctness and confidence level

Abstract Feedback is an important factor to enhance subsequent memory, showing that memory performance increases after the feedback than after the no feedback condition during retrieval practice. However, most studies have provided answers as feedback and only examined memory accuracy. It is unclear whether memory is enhanced over time when other types of feedback (e.g., correct/incorrect) is given. In addition, during retrieval practice, participants' responses differ in correctness and confidence level. To what extent these initial memory features interact with feedback type to influence subsequent memory accuracy and confidence level remains unclear. In this study, to address these questions, participants learned a series of sentences, then during the retrieval practice phase, different types of feedback—feedback with correct/incorrect and answer (CA‐feedback), feedback with answer (A‐feedback), feedback with correct/incorrect (C‐feedback), and no feedback—were given after they performed a cued‐recall test and rated the confidence. After retention intervals of 5 min, 1 day, and 7 days, they took final tests, followed by the confidence rating. The results showed that different types of feedback influenced subsequent memory and forgetting by different mechanisms. The CA‐feedback and A‐feedback enhanced memory performance by correcting initial errors and increasing the confidence of correct trials, but the corrected memory was more easily forgotten from 5 min to 7 days. Compared to A‐feedback, the CA‐feedback maintained the corrected memory after 1 day. The C‐feedback did not correct initial errors but slowed the forgetting rate and reduced the confidence of incorrect trials. This study highlighted the interaction between feedback type and initial memory features (correctness, confidence) to influence subsequent memory performance, including memory accuracy and confidence level.
Optimization of Reservoir Operation using a Bioinspired Metaheuristic Based on the COVID-19 Propagation Model

: Recently, global warming problems with rapid population growth and socio-economic development have intensified the demand for water and increased tensions on water supplies. This research evolves the Multi-Objective Coronavirus Optimization Algorithm (MOCVOA) to obtain operational optimum rules of Voshmgir Dam reservoir under the climate change conditions. The climatic variables downscaled and predicted by the Bias Correction Spatial Disaggregation (BCSD) method of MIROC-ESM model, was introduced into the Extreme Learning Machine (ELM) modelto evaluate the future runoff flowing into the reservoir. The model objective functions included minimizing vulnerability and enhancing reliability indices during baseline and climate change periods. Results revealed that under climate change conditions, the river flow would decrease by 0.17%, increase the temperature up to 2°C and decrease the rainfall by 23.8%, corresponding to the baseline period. Moreover, the extent of vulnerability index variations in the baseline and climate change conditions were also determined as 20-38% and 13-40%, respectively. The reliability index changes under the baseline and climate change conditions obtained were, 57-85% and 40-91%. Therefore, the vulnerability index was also measured at 33% and 30% for baseline and climate change conditions, respectively, with 80% of reliability index. Finally, the comparison of reservoir performance in meeting the water needs of downstream lands at the Pareto point of 80% reliability under both conditions indicated that the reservoir release rate would be more in line with the demand in the climate change conditions.
CT Morphologic Characteristics and Variant Patterns of Interstitial Pulmonary Fibrosis in Systemic Lupus Erythematosus.

Purpose To assess CT features of pulmonary fibrosis in patients with systemic lupus erythematosus (SLE) and to assess the presence of several distinctive patterns of fibrosis associated with connective tissue disease. Materials and Methods A cross-sectional retrospective analysis was performed. An institutional clinical database was queried for the years of 2005-2015 to identify CT examination reports of patients with SLE and fibrotic lung disease, which yielded 50 patients (median age, 49 years; age range, 22-71 years; 46 women). CT examination reports were scored by two subspecialty thoracic radiologists using a standard multilevel semiquantitative system. Readers noted the presence or absence of several recently described CT signs of variant patterns of fibrosis in connective tissue disease (the "anterior upper lobe," "straight-edge," and "exuberant honeycombing" signs), as well as two other morphologic characteristics (an "island-like" appearance of areas of well-defined fibrosis with angular margins surrounded by normal lung and confluent regions of lucent lung destruction). Results The most common CT patterns were characterized as either fibrotic nonspecific interstitial pneumonia (38%, 19 of 50) or variant fibrosis (44%, 22 of 50). CT signs of variant fibrosis were identified by both readers in up to 62% of patients, with good κ agreement (0.44-0.64); the island-like sign (62%) and anterior upper lobe sign (52%) were most commonly observed. Pulmonary function test results showed correlations with several imaging findings but did not show correlations with CT signs of variant fibrosis. Conclusion When present, pulmonary fibrosis in SLE often has a distinctive appearance and may also manifest as several variant fibrotic patterns.Keywords: CT, Lung© RSNA, 2021See also the commentary by White in this issue.
British Society of Gastroenterology guidelines for the management of iron deficiency anaemia in adults

Iron deficiency anaemia (IDA) is a major cause of morbidity and burden of disease worldwide. It can generally be diagnosed by blood testing and remedied by iron replacement therapy (IRT) using the oral or intravenous route. The many causes of iron deficiency include poor dietary intake and malabsorption of dietary iron, as well as a number of significant gastrointestinal (GI) pathologies. Because blood is iron-rich it can result from chronic blood loss, and this is a common mechanism underlying the development of IDA—for example, as a consequence of menstrual or GI blood loss. Approximately a third of men and postmenopausal women presenting with IDA have an underlying pathological abnormality, most commonly in the GI tract. Therefore optimal management of IDA requires IRT in combination with appropriate investigation to establish the underlying cause. Unexplained IDA in all at-risk individuals is an accepted indication for fast-track secondary care referral in the UK because GI malignancies can present in this way, often in the absence of specific symptoms. Bidirectional GI endoscopy is the standard diagnostic approach to examination of the upper and lower GI tract, though radiological scanning is an alternative in some situations for assessing the large bowel. In recurrent or refractory IDA, wireless capsule endoscopy plays an important role in assessment of the small bowel. IDA may present in primary care or across a range of specialties in secondary care, and because of this and the insidious nature of the condition it has not always been optimally managed despite the considerable burden of disease— with investigation sometimes being inappropriate, incorrectly timed or incomplete, and the role of IRT for symptom relief neglected. It is therefore important that contemporary guidelines for the management of IDA are available to all clinicians. This document is a revision of previous British Society of Gastroenterology guidelines, updated in the light of subsequent evidence and developments.
Endoscopic submucosal dissection of high-grade dysplasia recurrence in ulcerative colitis using a multitraction technique

Endoscopic submucosal dissection (ESD) is the gold standard for removing superficial tumor in the digestive tract [1]. Dyplasia in inflammatory bowel disease (IBD) patient is a major concern due to the risk of neoplastic progression. ESD for dysplasia in IBD is feasible, but longterm follow-up data are lacking especially for the management of dysplasia recurrence in an area previously treated by ESD [2–5]. We report the case of a 71-year-old man with a history of long-standing ulcerative colitis who underwent ESD for high-grade dysplasia and focal intramucosal carcinoma in the left colon. The resection was incomplete with dysplasia in the lateral margin. Three years later, recurrence of high-grade dysplasia was detected in the area previously treated (▶Fig. 1). Another ESD was decided upon (▶Video 1). After marking of the lesion and circumferential incision, a new multitraction technique was employed using a device made of three intertwined loops (▶Fig. 2). Each of the loops was attached to an edge of the lesion, then the entire device was attached to the opposite wall, facilitating the exposure of the submucosal area and enabling en bloc resection despite intense fibrosis (▶Fig. 3). We wanted to extend the dissection to the upper pole of the lesion because of the suspicion of a serrated lesion. However, a small perforation was made so we stopped the procedure as the diagnosis was not certain. The defect was closed and the patient discharged the day after without any adverse event. The pathology report confirmed complete en bloc resection of a high-grade dysplasia, with chronic inflammatory changes with focal low-grade dysplasia on the area not removed. Our multidisciplinary team decided on endoscopic surveillance. ESD is feasible in patients with IBD, even in a fibrotic area that has previously been resected, and can be facilitated by a multitraction technique. Patients with dysplasia should always be referred to a center of endoscopic expertise before colectomy is considered.
Effectiveness of Inspiratory Muscle Training on Respiratory Muscle Strength in Patients Undergoing Cardiac Surgeries: A Systematic Review With Meta-Analysis

To determine the effect of inspiratory muscle training (IMT) on pulmonary function, respiratory muscle strength (RMS), and functional capacity in patients undergoing cardiac surgery. The PubMed, PEDro, CINAHL, Web of Science, CENTRAL, and EMBASE databases were searched from inception to June 2020. Randomized controlled trials (RCTs) that evaluated patients who underwent cardiac surgery were included in this review. Meta-analysis performed using a random-effects model showed that the mean difference in forced vital capacity, forced expiratory volume in 1 second, 6-minute walk distance, and RMS was 3.47% (95% confidence interval [CI], 0.57 to 6.36), 5.80% (95% CI, 2.03 to 9.56), 78.05 m (95% CI, 60.92 to 95.18), and 4.8 cmH2O (95% CI, -4.00 to 13.4), respectively. There is strong evidence that IMT improves inspiratory muscle strength, pulmonary function, and functional capacity, and reduces the length of hospital stay in patients undergoing cardiac surgery.
Poststroke Grasp Ability Assessment Using an Intelligent Data Glove Based on Action Research Arm Test: Development, Algorithms, and Experiments

Growing impact of poststroke upper extremity (UE) functional limitations entails newer dimensions in assessment methodologies. This has compelled researchers to think way beyond traditional stroke assessment scales during the out-patient rehabilitation phase. In concurrence with this, sensor-driven quantitative evaluation of poststroke UE functional limitations has become a fertile field of research. Here, we have emphasized an instrumented wearable for systematic monitoring of stroke patients with right-hemiparesis for evaluating their grasp abilities deploying intelligent algorithms. An instrumented glove housing 6 flex sensors, 3 force sensors, and a motion processing unit was developed to administer 19 activities of Action Research Arm Test (ARAT) while experimenting on 20 voluntarily participating subjects. After necessary signal conditioning, meaningful features were extracted, and subsequently the most appropriate ones were selected using the ReliefF algorithm. An optimally tuned support vector classifier was employed to classify patients with different degrees of disability and an accuracy of 92% was achieved supported by a high area under the receiver operating characteristic score. Furthermore, selected features could provide additional information that revealed the causes of grasp limitations. This would assist physicians in planning more effective poststroke rehabilitation strategies. Results of the one-way ANOVA test conducted on actual and predicted ARAT scores of the subjects indicated remarkable prospects of the proposed glove-based method in poststroke grasp ability assessment and rehabilitation.
Maternal egg care enhances hatching success and offspring quality in an oviparous skink.

Maternal egg-caring behavior can often be observed in oviparous scincid lizards. The expression of such behavior is predictably affected by the trade-off between its resultant costs and benefits for mothers and/or offspring, which has been investigated in only a few scincid species. Here, post-ovipositional Plestiodon chinensis females were treated to care for their egg clutches without interference, under simulated predation pressure, or to be care-deprived. Potential maternal costs and offspring benefits associated with egg-caring behavior were then evaluated by measuring changes in maternal body condition, egg mortality, and hatchling performance. Egg-caring behavior caused post-ovipositional females to participate less in outside-nest activity, eat less food, and show relatively poorer body conditions at egg hatching. By contrast, compared with care-deprived females, egg-caring females gained mass slightly faster, and achieved a similar body condition within a few months of hatching. Eggs that were cared for by their mothers were more likely to hatch and produced larger, faster-running and better-growing hatchlings with higher survival than uncared-for eggs. Simulated exposure to a potential predator had no distinct impact on maternal egg-caring behavior expression and offspring performance. These results indicated that marked benefits of offspring viability but minor maternal energy costs might play a decisive role in the occurrence of maternal egg-caring behavior in P. chinensis. This article is protected by copyright. All rights reserved.
Ancestral polymorphisms shape the adaptive radiation of Metrosideros across the Hawaiian Islands

Significance Some of the most spectacular adaptive radiations of plants and animals occur on remote oceanic islands, yet such radiations are preceded by founding events that severely limit genetic variation. How genetically depauperate founder populations give rise to the spectacular phenotypic and ecological diversity characteristic of island adaptive radiations is not known. We generated genomic resources for Hawaiian Metrosideros––a hyper-variable adaptive radiation of woody taxa—for insights into the paradox of remote island radiations. We posit that divergent selection and differential sorting of an unexpectedly rich pool of ancestral variation drove the diversification of lineages. Recurring use of ancient variants from a richer-than-expected gene pool may explain how lineages can diversify to fill countless niches on remote islands. Some of the most spectacular adaptive radiations begin with founder populations on remote islands. How genetically limited founder populations give rise to the striking phenotypic and ecological diversity characteristic of adaptive radiations is a paradox of evolutionary biology. We conducted an evolutionary genomics analysis of genus Metrosideros, a landscape-dominant, incipient adaptive radiation of woody plants that spans a striking range of phenotypes and environments across the Hawaiian Islands. Using nanopore-sequencing, we created a chromosome-level genome assembly for Metrosideros polymorpha var. incana and analyzed whole-genome sequences of 131 individuals from 11 taxa sampled across the islands. Demographic modeling and population genomics analyses suggested that Hawaiian Metrosideros originated from a single colonization event and subsequently spread across the archipelago following the formation of new islands. The evolutionary history of Hawaiian Metrosideros shows evidence of extensive reticulation associated with significant sharing of ancestral variation between taxa and secondarily with admixture. Taking advantage of the highly contiguous genome assembly, we investigated the genomic architecture underlying the adaptive radiation and discovered that divergent selection drove the formation of differentiation outliers in paired taxa representing early stages of speciation/divergence. Analysis of the evolutionary origins of the outlier single nucleotide polymorphisms (SNPs) showed enrichment for ancestral variations under divergent selection. Our findings suggest that Hawaiian Metrosideros possesses an unexpectedly rich pool of ancestral genetic variation, and the reassortment of these variations has fueled the island adaptive radiation.
Platelet-derived extracellular vesicles promote the migration and invasion of rheumatoid arthritis fibroblast-like synoviocytes via CXCR2 signaling

Platelet-derived extracellular vesicles (PEVs), which are generated from the plasma membrane during platelet activation, may be involved in the inflammatory processes of rheumatoid arthritis (RA). The motility of RA fibroblast-like synoviocytes (RA-FLS) plays a key role in the development of synovial inflammation and joint erosion. However, the effects of PEVs on the motility of RA-FLS remain unclear. Thus, the present study aimed to investigate the active contents and potential molecular mechanisms underlying the role of PEVs in regulating the migration and invasion of RA-FLS. The results demonstrated that PEVs contain certain chemokines associated with cell migration and invasion, including C-C motif chemokine ligand 5, C-X-C motif chemokine ligand (CXCL)4 and CXCL7. Furthermore, SB225002, an antagonist of C-X-C motif chemokine receptor 2 (CXCR2; a CXCL7 receptor), partially prevented the migration and invasion of RA-FLS induced by PEVs, suggesting that PEVs may activate a CXCR2-mediated signaling pathway in RA-FLS. In addition, SB225002 antagonized the phosphorylation of IκB and NF-κB in RA-FLS induced by PEVs. Taken together, the results of the present study suggested that PEVs may promote the migration and invasion of RA-FLS by activating the NF-κB pathway mediated by the CXCR2 signaling pathway.
The median effective concentration of propofol with different doses of esketamine during gastrointestinal endoscopy in elderly patients: A randomized controlled trial

Propofol may result in hypotension, bradycardia and loss of protective reflexes, especially in elderly patients, while esketamine, a N‐methyl‐D‐aspartate receptor antagonist, has analgesic, anaesthetic and sympathomimetic properties and is known to cause less cardiorespiratory depression. We hypothesized that esketamine may reduce the median effective concentration (EC50) of propofol and coadministration is less likely to produce hypotension during gastrointestinal endoscopy in elderly patients.
Do patients with well-functioning total hip arthroplasty achieve typical sagittal plane hip kinematics? A proof of concept study

Background: Total hip arthroplasty (THA) patients have been shown to not achieve normal sagittal plane hip kinematics. However, previous studies have only conducted group level analysis and as such lack the sensitivity to highlight whether individual patients do achieve normal hip kinematics. As such this study looked to determine whether some patients with well-functioning THA achieve typical sagittal plane hip kinematics. Methods: Sagittal plane hip kinematics were collected on 11 well-functioning THA patients (Oxford Hip Score = 46 ± 3) and 10 asymptomatic controls using a 3-dimensional motion analysis system during self-paced walking. High-functioning THA patients were identified as those who displayed sagittal plane hip kinematics that were within the variance of the control group on average, and low-functioning patients as those who did not. Results: 5 THA patients were identified as high-functioning, displaying hip kinematics within the variance of the control group. High-functioning THA patients displayed peak hip flexion and extension values more closely aligned to asymptomatic control group than low-functioning patients. However, hip range of motion was comparable between high- and low-functioning total hip arthroplasty patients and reduced compared to controls. Conclusion: The presence of high-functioning THA patients who display comparable sagittal plane hip kinematics to controls suggests these patients do achieve normative function and challenges the conclusions of previous group level analysis. Understanding why some patients achieve better function post-operatively will aid pre- and post-operative practices to maximise functional recovery.