Miracle-dz/UniFAR-FTUs huggingface dataset:
iGDP: An integrated genome decontamination pipeline for wild ciliated microeukaryotes

Ciliates are a large group of ubiquitous and highly diverse single‐celled eukaryotes that play an essential role in the functioning of microbial food webs. However, their genomic diversity is far from clear due to the need to develop cultivation methods for most species, so most research is based on wild organisms that almost invariably contain contaminants. Here we establish an integrated Genome Decontamination Pipeline (iGDP) that combines homology search, telomere reads‐assisted and clustering approaches to filter contaminated ciliate genome assemblies from wild specimens. We benchmarked the performance of iGDP using genomic data from a contaminated ciliate culture and the results showed that iGDP could recall 91.9% of the target sequences with 96.9% precision. We also used a synthetic dataset to offer guidelines for the application of iGDP in the removal of various groups of contaminants. Compared with several popular metagenome binning tools, iGDP could show better performance. To further validate the effectiveness of iGDP on real‐world data, we applied it to decontaminate genome assemblies of three wild ciliate specimens and obtained their genomes with high quality comparable to that of previously well‐studied model ciliate genomes. It is anticipated that the newly generated genomes and the established iGDP method will be valuable community resources for detailed studies on ciliate biodiversity, phylogeny, ecology and evolution. The pipeline (https://github.com/GWang2022/iGDP) can be implemented automatically to reduce manual filtering and classification and may be further developed to apply to other microeukaryotes.
Effectiveness of visual and acoustic biofeedback eccentric viewing training in conjunction with home exercises on visual function: a retrospective observational review

ABSTRACT The aim of this study is to evaluate the effectiveness of an eccentric viewing training program that combines biofeedback training using micro-perimetry with home exercises on multiple visual function parameters and to explore potential relationships between post-treatment visual function parameters. A retrospective observational review of 27 participants who underwent the training program was performed. Eligible participants were diagnosed with bilateral central scotomas secondary to age-related macular degeneration. All participants undertook up to 15 visual and acoustic biofeedback training sessions and were required to partake in traditional home exercises between sessions. The biofeedback training was conducted in the better eye using the Macular Integrity Assessment microperimeter (MAIA). Distance and near acuity, contrast sensitivity and fixation stability quantified by the P1 and P2 values and the 63% and 95% bivariate contour ellipse area (BCEA) before and after the rehabilitation program were recorded. Significant improvement was noted post-training for distance visual acuity (t(26) = 4938 p = . 000), near visual acuity (Z = −4.461 p = .000), contrast sensitivity (Z = −3.647 p = .000) and fixation stability for all measures, including P1 (t(26) = −9.490 p = . 000), P2 (t(26) = −7.338 p = 0.000), 63% BCEA (Z = 3.569 p = .000) and 95% BCEA (t(26) = 4.687 p = . 000). Significant medium-to-large correlations were also found between most visual function variables. Visual and acoustic biofeedback in conjunction with home exercises has the potential to improve visual function parameters in patients with age-related macular degeneration and irreversible central vision loss.
Performance of the ITER ICRH system as expected from TOPICA and ANTITER II modelling

The performance on plasma of the antennas of the proposed ITER ICRF system is evaluated by means of the antenna 24 × 24 impedance matrix provided by the TOPICA code and confirmed and interpreted by the semi-analytical code ANTITER II (summarized in an appendix). From this analysis the following system characteristics can be derived: (1) a roughly constant power capability in the entire 40–55 MHz frequency band with the same maximum voltage in the eight feeding lines is obtained for all the considered heating and current drive phasings on account of the broadbanding effect of service stubs. (2) The power capability of the array significantly depends on the distance of the antenna to the separatrix, the density profile in the scrape-off layer (SOL) and on the strap current toroidal and poloidal phasings. The dependence on phasing is stronger for wider SOL. (3) To exceed a radiated power capability of 20 MW per antenna array in the upper part of the frequency band, with a separatrix–wall distance of 17 cm and a conservative short decay plasma edge density profile, the system voltage stand-off must be 45 kV and well chosen combinations of toroidal and poloidal phasing are needed. (4) On account of the plasma gyrotropy and of poloidal magnetic field, special care must be taken in choosing the optimal toroidal current drive and poloidal phasings. The ANTITER II analysis shows furthermore that important coaxial and surface mode excitation can only be expected in the monopole toroidal phasing, that strong wave reflection from a steep density profile significantly reduces the coupling even if the separatrix is closer to the antenna and that the part of the edge density profile having a density lower than the cut-off density pertaining to the considered phasing does not significantly contribute to the coupling.
Different treatment efficacies and T790M acquisition of EGFR‐TKIs on NSCLC patients with variable Del‐19 subtypes of EGFR

EGFR exon 19 deletion (Del‐19) comprises multiple advanced NSCLC subtypes. EGFR‐tyrosine kinase inhibitor (TKI) efficacy and T790M acquisition in various Del‐19 subtypes is unknown. We prospectively collected tissue samples from patients harboring NSCLC with Del‐19 between 2006 and 2020. We evaluated EGFR‐TKI treatment effectiveness among the different Del‐19 subtypes. We collected 1391 NSCLC samples from 892 patients with Del‐19, and the most common subtype was del E746‐A750 (67.5%). 741 patients had taken first‐ or second‐generation EGFR‐TKIs. There were no significant differences in response rates between patients with different Del‐19 subtypes (P = .630). Patients with indel E746 had the longest median PFS (14.6 months), but those with non‐LRE deletions had the shortest PFS (8.9 months; P = .002). For OS analysis, patients with indel E746 also had the longest OS (34.1 months), but those with non‐LRE deletions had the shortest OS (21.1 months; P = .046). Patients with different Del‐19 subtypes showed no significant differences in the T790M acquisition rates (P = .443). Among the 151 patients with acquired T790M who received third‐generation EGFR‐TKIs, the Del‐19 subtype was not associated with different RR and PFS. In vitro cellular viability and activation of the EGFR pathway analysis were consistent with the clinical findings. In conclusion, compared with del E746‐A750, indel E746 was associated with longer PFS and OS, but the non‐LRE subtype was correlated with shorter survival prognosis. There were no significant differences in the acquired T790M rate and treatment effectiveness of subsequent third‐generation EGFR‐TKIs between various Del‐19 subgroups.
Updating the biologically based dose-response model for the nasal carcinogenicity of inhaled formaldehyde in the F344 rat

Abstract Chronic inhalation of formaldehyde by F344 rats causes nasal squamous cell carcinoma (SCC). This outcome is well-characterized: including dose-response and time course data for SCC, mechanistic endpoints, and nasal dosimetry. Conolly et al. (Toxicol. Sci. 75, 432–447, 2003) used these resources to develop a biologically based dose-response (BBDR) model for SCC in F344 rats. This model, scaled up to humans, has informed dose-response conclusions reached by several international regulatory agencies. However, USEPA concluded that uncertainties precluded its use for cancer risk assessment. Here, we describe an updated BBDR model that addresses uncertainties through refined dosimetry modeling, revised analysis of labeling index data, and an extended dataset where both inhaled (exogenous) and endogenous formaldehyde (exogF, endoF) form DNA adducts. Further, since Conolly et al. (ibid) was published, it has become clear that, when controls from all F344 inhalation bioassays are considered, accounting for over 4000 rats, at most one nasal SCC occurred. This low spontaneous incidence constrains possible contribution of endoF to the formation of nasal SCC via DNA reactivity. Further, since both exogF and endoF form DNA adducts, this constraint also applies to exogF. The revised BBDR model therefore drives SCC formation through the cytotoxicity of high concentration exogF. An option for direct mutagenicity associated with DNA adducts is retained to allow estimation of an upper bound on adduct mutagenicity consistent with the lack of a spontaneous SCC incidence. These updates represent an iterative refinement of the 2003 model, incorporating new data and insights to reduce identified model uncertainties.
Clinical efficacy of ultrasound-guided interventional therapy in patients with benign ovarian cysts: a meta-analysis

Abstract This study aimed to explore the clinical efficacy of ultrasound-guided interventional therapy in patients with benign ovarian cysts through meta-analysis. A literature search was performed on PubMed, Web of Science, Embase, CNKI, and WanFang databases to obtain clinical randomized controlled trials on ultrasound-guided interventional therapy for benign ovarian cysts published between 2010 and 2022. A total of 1395 studies were initially retrieved, and finally 12 studies were included for meta-analysis. The results showed that the observation group (ultrasound-guided interventional therapy) had higher treatment effective rate than the control group (conventional laparotomy or laparoscopic cyst resection), but the incidence of adverse reactions was markedly lower. Additionally, the length of hospital stay, intraoperative blood loss, and operation time showed significant lower levels in the observation group. In terms of ovarian function, postoperative luteinizing hormone and follicle-stimulating hormone levels in the observation group were lower than the control group, while oestradiol levels were higher. In conclusion, compared with conventional surgical treatment, ultrasound-guided interventional therapy can significantly improve the clinical effective rate, shorten the hospital stay and reduce intraoperative blood loss. Such therapy can protect ovarian reserve, with high value of clinical promotion. IMPACT STATEMENT What is already known on this subject? Main surgical methods for ovarian cysts consist of laparotomy, laparoscopic surgery, and interventional therapy. What the results of this study add? With the advancement of surgical techniques and instruments, many minimally invasive surgeries have been applied to treat ovarian cysts with good clinical results. However, there is no exact evidence to prove its clinical efficacy. Given the lack in this field, we conducted a meta-analysis of all clinical studies of ultrasound-guided interventional therapy for ovarian cysts to evaluate its efficacy and safety. What the implications are of these findings for clinical practice and/or further research? Compared with conventional laparotomic or laparoscopic cyst resection, ultrasound-guided interventional therapy for ovarian cysts significantly improves the treatment effectiveness, shortens the hospital stay and reduces intraoperative blood loss. This therapy with good clinical efficacy also has advantages of small wound, rapid recovery and less adverse reactions, and can protect ovarian reserve. This safe and effective surgical method for ovarian cysts is worth promoting clinically.
Analysis of participant-reported adverse events following the first dose of inactivated SARS-Cov-2 vaccine (TURKOVAC™) through telephone survey in Türkiye

Abstract Background/Objective(s)/Introduction TURKOVAC™ is a whole-virion inactivated COVID-19 vaccine, which was developed and recently granted emergency use authorization (conditional marketing authorization) in Türkiye. The objective of this study is to assess the spectrum and the distribution of adverse events reported following the administration of the first 150,000 doses as primary and booster vaccine doses in 22 state hospitals of 17 provinces in Türkiye. Patients/Materials and methods In this cohort study, a verbal survey was conducted via telephone calls between 10 January and 17 January 2022, utilizing a structured questionnaire algorithm on a sample group of 20,000 persons on the third- and seventh-days following vaccination. The algorithm consisted of two parts focusing on both systemic and local adverse effects. Other adverse events reported by the participants were also recorded. 6023 people and 5345 people agreed to participate in the telephone survey on the 3rd- and 7th- days of having received the first dose of the vaccine, respectively. Results Thirty-six-point-six percent of the participants on the 3rd day and 22.5% of the participants on the 7th day reported any adverse event following the first dose of the vaccine. On both follow-up days, the most commonly reported (29.7% for Day 3 and 13.1% for Day 7) adverse events were on the injection site. Among the local adverse events, the most frequently reported one was the pain on the injection site (27.9% for Day 3 and 12.4% for Day 7), induration (4.8% for Day 3 and 2.7% for Day 7) and swelling (3.5% for Day 3 and 2.0% for Day 7). Fatigue/weakness (9.6% for Day 3 and 8.3% for Day 7) and headache (7.9% for Day 3 and 8.0% for Day 7) were the most frequent systemic adverse events. Younger age, vaccine dose, and female sex were associated with having any adverse event and pain (on the injection site). Female sex was associated with more swelling (on the injection site), induration (on the injection site), fever, and a higher impact on daily living. Conclusion(s) In this study, we conducted a rapid assessment of adverse events following the first dose of the TURKOVAC vaccine. The vaccine appears to have a good safety profile in the first 7 days following vaccination. Younger age, vaccine dose, and female sex are associated with any adverse event and pain (on the injection site). These results present valuable information for the community and may contribute to increasing vaccine confidence. KEY MESSAGES As a whole-virion inactivated SARS-CoV-2 vaccine, the TURKOVAC™ vaccine, which has a favorable safety profile, can be an alternative to other COVID-19 vaccines including mRNA and viral vector vaccines.
Thrombus Enhancement Sign May Differentiate Embolism From Arteriosclerosis-Related Large Vessel Occlusion

Background and Purpose To evaluate whether the thrombus enhancement sign (TES) can be used to differentiate embolic large vessel occlusion (LVO) from in situ intracranial atherosclerotic stenosis (ICAS)-related LVO in the anterior circulation of patients with acute ischemic stroke (AIS). Methods Patients with LVO in the anterior circulation who underwent both non-contrast computed tomography (CT) and CT angiography and mechanical thrombectomy were retrospectively enrolled. Both embolic LVO (embo-LVO) and in situ ICAS-related LVO (ICAS-LVO) were confirmed by two neurointerventional radiologists after reviewing the medical and imaging data. TES was assessed to predict embo-LVO or ICAS-LVO. The associations between occlusion type and TES, along with clinical and interventional parameters, were investigated using logistic regression analysis and a receiver operating characteristic curve. Results A total of 288 patients with AIS were included and divided into an embo-LVO group (n=235) and an ICAS-LVO group (n=53). TES was identified in 205 (71.2%) patients and was more frequently observed in those with embo-LVO, with a sensitivity of 83.8%, specificity of 84.9%, and area under the curve (AUC) of 0.844. Multivariate analysis showed that TES (odds ratio [OR], 22.2; 95% confidence interval [CI], 9.4–53.8; P<0.001) and atrial fibrillation (OR, 6.6; 95% CI, 2.8–15.8; P<0.001) were independent predictors of embolic occlusion. A predictive model that included both TES and atrial fibrillation yielded a higher diagnostic ability for embo-LVO, with an AUC of 0.899. Conclusion TES is an imaging marker with high predictive value for identifying embo- and ICAS-LVO in AIS and provides guidance for endovascular reperfusion therapy.
Ventilator associated pneumonia in COVID-19 patients: A retrospective cohort study

ABSTRACT Ventilator associated pneumonia in COVID-19 patients: A retrospective cohort study Introduction We aimed to evaluate ventilator-associated pneumonia (VAP) incidence rate, risk factors, and isolated microorganisms in COVID-19 patients as the primary endpoint. Evaluation of VAP-associated intensive care unit (ICU) and hospital mortalities was the secondary endpoint. Materials and Methods Records of patients admitted between March 2020- June 2021 to our pandemic ICU were reviewed and COVID-19 patients with VAP and non-VAP were evaluated retrospectively. Comorbidities, management, length of ICU stay, and outcomes of VAP and non-VAP patients, as well as risk factors for VAP mortality, were identified. Results During the study period, 254 patients were admitted to the ICU. After the exclusion, the data of 208 patients were reviewed. In total, 121 patients required invasive mechanical ventilation, with 78 (64.5%) developing VAP. Length of ICU and hospital stays were longer in VAP patients (p< 0.01 and p< 0.01 respectively). Steroid use was higher in VAP patients, although it was not statistically significant (p= 0.06). APACHE II score (p< 0.01) was higher in non-VAP patients. ICU mortality was high in both groups (VAP 70%, non-VAP 77%). VAP mortality was higher in males (p= 0.03) and in patients who required renal replacement therapy (p= 0.01). Length of ICU stay (p= 0.04), and length of hospital stay (p< 0.01) were both high in VAP survivors. The most common isolated microorganisms were Acinetobacter spp. and Klebsiella spp. in VAP patients and most of them were extensively drug-resistant. Conclusion Critically ill COVID-19 patients who required invasive mechanical ventilation developed VAP frequently. The length of ICU stay was longer in patients who developed VAP and ICU mortality was high in both VAP and non-VAP patients. The length of hospital and ICU stays among VAP survivors were also considerably high which is probably related to the long recovery period of COVID-19. The most frequently isolated microorganisms were Acinetobacter spp. and Klebsiella spp. in VAP patients
The effects of diurnal variability and modality on false memories formation

ABSTRACT The main objective of the current study was to investigate the effect of time of day on visual and auditory, short-term memory (STM), and long-term memory (LTM) distortions using a hybrid Deese-Roediger-McDermott procedure. In Experiment 1, we used semantically related words, whereas in Experiment 2 – words were characterized by phonological similarity. The results showed a relationship between modality and types of stimuli. In STM, more semantic errors were found in the evening for items presented visually and more errors following auditory presentation for phonologically similar words. In LTM, the analysis revealed a higher rate of semantic distortions in the evening hours for auditorily presented words. For words with phonological similarity, we observed more errors in the evening without the effect of modality. The results support the hypothesis that more reliance is placed on elaborative processing in the evening and more on maintenance processing in the morning; however, this is not modality invariant.
Childhood trauma and aggression among Chinese college students: The mediation of self-compassion and moderation of left-behind experience.

OBJECTIVE Previous studies have found that college students with left-behind experience presented high levels of aggression, and childhood trauma may be one of the contributors. This study aimed to examine the relationship between childhood trauma and aggression in Chinese college students, and to explore the mediating role of self-compassion and the moderating role of left-behind experience. METHOD 629 Chinese college students completed the questionnaires at two time points: childhood trauma and self-compassion were assessed at baseline, and aggression was assessed at baseline and 3-month follow-up. RESULTS Among these participants, 391 (62.2%) had left-behind experience. Emotional neglect of college students with left-behind experience in childhood was significantly higher than that of college students without such experience. Childhood trauma predicted aggression after 3 months among college students. Self-compassion mediated the predictive effect of childhood trauma on aggression after controlling for gender, age, only-child status, and family residential status. However, no moderating effect of left-behind experience was found. CONCLUSIONS These findings indicated that childhood trauma is an important predictor of aggression among Chinese college students regardless of their left-behind experience. The reason for the higher aggression of left-behind college students may be that their left-behind situation increased the possibility of childhood trauma. In addition, whether in college students with left-behind experience or without such experience, childhood trauma may increase aggression by reducing the level of self-compassion. Furthermore, interventions incorporating components to improve self-compassion could be effective in decreasing aggression of college students who perceived high childhood trauma. (PsycInfo Database Record (c) 2023 APA, all rights reserved).
Current Practices, Experiences, and Views in Clinical Hypnosis: Findings of an International Survey

ABSTRACT An online survey of 691 clinicians who use hypnosis was conducted in 31 countries to gain a broad real-world picture of current practices, views, and experiences in clinical hypnosis. Among 36 common clinical uses, stress reduction, wellbeing and self-esteem-enhancement, surgery preparations, anxiety interventions, mindfulness facilitation, and labor and childbirth applications were the most frequently rated as highly effective (each by ≥70% of raters) in the clinicians’ own experience. Adverse hypnosis-associated effects had been encountered by 55% of clinicians but were generally short-lived and very rarely judged as serious. The most common hypnosis approaches used were Ericksonian (71%), hypnotic relaxation therapy (55%), and traditional hypnosis (50%). Almost all respondents reported regularly using other therapeutic modalities alongside hypnosis. Among a range of client variables potentially affecting therapy, most clinicians rated hypnotist-client rapport (88%) and client motivation (75%) as very or extremely important factors for successful hypnotherapy. The majority of respondents had conducted hypnosis treatment via teletherapy, and 54% of those estimated it to be as effective as in-person treatment.