Miracle-dz/UniFAR-FTUs huggingface dataset:
Cryo-electron Tomography Reveals the Roles of FliY in Helicobacter pylori Flagellar Motor Assembly

Helicobacter pylori is the major risk factor related with gastric diseases. Flagellar motor is one of the most important virulence factors in H. pylori. ABSTRACT Helicobacter pylori plays a causative role in gastric diseases. The pathogenicity of H. pylori depends on its ability to colonize the stomach guided by motility. FliY is a unique flagellar motor switch component coexisting with the classical FliG, FliM, and FliN switch proteins in some bacteria and has been shown to be essential for flagellation. However, the functional importance of FliY in H. pylori flagellar motor assembly is not well understood. Here, we applied cryo-electron tomography and subtomogram averaging to analyze the in situ structures of flagellar motors from wild-type strain, fliY-null mutant and complementation mutants expressing the N-terminal or C-terminal domain of FliY. Loss of full-length FliY or its C-terminal domain interrupted the formation of an intact C ring and soluble export apparatus, as well as the hook and flagellar filaments. Complementation with FliY C-terminal domain restored all these missing components of flagellar motor. Taken together, these results provide structural insights into the roles of FliY, especially its C-terminal domain in flagellar motor assembly in H. pylori. IMPORTANCE Helicobacter pylori is the major risk factor related with gastric diseases. Flagellar motor is one of the most important virulence factors in H. pylori. However, the assembly mechanism of H. pylori flagellar motor is not fully understood yet. Previous report mainly described the overall structures of flagellum but had not focused on its specific components. Here, we focus on H. pylori flagellar C-ring protein FliY. We directly visualize the flagellar structures of H. pylori wild-type and FliY N-/C-terminal complementary strains by cryo-electron tomography and subtomogram averaging. Our results show that deletion of FliY or its C-terminal domain causes the loss of C ring, whereas deletion of FliY N-terminal does not affect C-ring assembly and flagellar structures. Our results provide direct evidence that C-ring protein FliY, especially its C-terminal domain, plays an indispensable role in H. pylori motor assembly and flagellar formation. This study will deepen our understanding about H. pylori pathogenesis.
Efficacy and safety of colchicine treatment in patients with COVID‐19: A prospective, multicenter, randomized clinical trial

Colchicine has shown clinical benefits in the management of COVID‐19 via its anti‐inflammatory effect. However, the exact role of colchicine in COVID‐19 patients is unknown. The current clinical trial was performed on 202 patients with moderate to severe COVID‐19. Patients were randomly assigned in a 1:1 ratio to receive up to a 3‐day course of 0.5 mg colchicine followed by a 12‐day course of 1 mg colchicine in combination with standard care or a 15‐day course of standard care. Among 202 randomized patients, 153 completed the study and received colchicine/standard care or continued standard care (M age, 54.72 [SD, 15.03] years; 93 [63.1%] men). On day 14, patients in the colchicine/standard care group had significantly higher odds of a better clinical status distribution on chest CT evaluation (p = .048). Based on NYHA classification, the percentage change of dyspnea on day 14 between groups was statistically significant (p = .026), indicating a mean of 31.94% change in the intervention group when compared with 19.95% in the control group. According to this study, colchicine can improve clinical outcomes and reduce pulmonary infiltration in COVID‐19 patients if contraindications and precautions are considered and it is prescribed at the right time and in appropriate cases.
A randomized, adaptive design, double-blind, 3-arm, parallel study assessing the pharmacokinetics and safety of AVT02, a high-concentration (100 mg/mL) Adalimumab biosimilar, in healthy adult subjects (ALVOPAD FIRST)

ABSTRACT Background This study (ALVOPAD FIRST) assessed bioequivalence, safety, and immunogenicity of AVT02, an adalimumab biosimilar, compared with reference product adalimumab (EU- and US-approved Humira®). Methods Healthy subjects (N = 392) were randomized 1:1:1 to receive one 40 mg dose of AVT02, EU-reference product, or US-reference product subcutaneously. An interim analysis was planned when ~30 subjects per arm had completed the study, to optimize final sample size. The primary PK parameters were Cmax, AUC0-t, and AUC0-inf. Bioequivalence was demonstrated if the 90% confidence intervals (CI) for the ratio of geometric means for the primary pharmacokinetic (PK) parameters were all contained within the prespecified margins of 80% and 125%. Safety and immunogenicity were assessed until Day 64. Results The 90% CI for the ratio of geometric means for the primary PK parameters, based on Fisher’s Combination test analysis, were all contained within the prespecified bioequivalence margins of 80% and 125%, supporting the demonstration of bioequivalence between AVT02 and both EU- and US-reference product. The safety and immunogenicity profiles were comparable across all three treatment arms. Conclusion PK bioequivalence was supported between AVT02, US-licensed- and EU-approved-reference product adalimumab. Similar safety and immunogenicity were also demonstrated. Trial Registration The trial is registered at ClinicalTrials.gov (CT.gov identifier: NCT03849313).
Custom-Built Operant Conditioning Setup for Calcium Imaging and Cognitive Testing in Freely Moving Mice

Visual Abstract Operant chambers are widely used in animal research to study cognition, motivation, and learning processes. Paired with the rapidly developing technologies for brain imaging and manipulations of brain activity, operant conditioning chambers are a powerful tool for neuroscience research. The behavioral testing and imaging setups that are commercially available are often quite costly. Here, we present a custom-built operant chamber that can be constructed in a few days by an unexperienced user with relatively inexpensive, widely available materials. The advantages of our operant setup compared with other open-source and closed-source solutions are its relatively low cost, its support of complex behavioral tasks, its user-friendly setup, and its validated functionality with video imaging of behavior and calcium imaging using the UCLA Miniscope. Using this setup, we replicate our previously published findings showing that mice exposed to social defeat stress in adolescence have inhibitory control impairments in the Go/No-Go task when they reach adulthood. We also present calcium imaging data of medial prefrontal cortex (mPFC) neuronal activity acquired during Go/No-Go testing in freely moving mice and show that neuronal population activity increases from day 1 to day 14 of the task. We propose that our operant chamber is a cheaper alternative to its commercially available counterparts and offers a better balance between versatility and user-friendly setup than other open-source alternatives.
GBA and APOE Impact Cognitive Decline in Parkinson’s Disease: A 10-Year Population-Based Study

Common genetic variance in apolipoprotein E (APOE), β‐glucocerebrosidase (GBA), microtubule‐associated protein tau (MAPT), and α‐synuclein (SNCA) has been linked to cognitive decline in Parkinson's disease (PD), although studies have yielded mixed results.
2022 American College of Rheumatology/European Alliance of Associations for Rheumatology classification criteria for granulomatosis with polyangiitis

Objective To develop and validate revised classification criteria for granulomatosis with polyangiitis (GPA). Methods Patients with vasculitis or comparator diseases were recruited into an international cohort. The study proceeded in five phases: (1) identification of candidate criteria items using consensus methodology, (2) prospective collection of candidate items present at the time of diagnosis, (3) data-driven reduction of the number of candidate items, (4) expert panel review of cases to define the reference diagnosis and (5) derivation of a points-based risk score for disease classification in a development set using least absolute shrinkage and selection operator logistic regression, with subsequent validation of performance characteristics in an independent set of cases and comparators. Results The development set for GPA consisted of 578 cases of GPA and 652 comparators. The validation set consisted of an additional 146 cases of GPA and 161 comparators. From 91 candidate items, regression analysis identified 26 items for GPA, 10 of which were retained. The final criteria and their weights were as follows: bloody nasal discharge, nasal crusting or sino-nasal congestion (+3); cartilaginous involvement (+2); conductive or sensorineural hearing loss (+1); cytoplasmic antineutrophil cytoplasmic antibody (ANCA) or anti-proteinase 3 ANCA positivity (+5); pulmonary nodules, mass or cavitation on chest imaging (+2); granuloma or giant cells on biopsy (+2); inflammation or consolidation of the nasal/paranasal sinuses on imaging (+1); pauci-immune glomerulonephritis (+1); perinuclear ANCA or antimyeloperoxidase ANCA positivity (−1); and eosinophil count ≥1×109 /L (−4). After excluding mimics of vasculitis, a patient with a diagnosis of small- or medium-vessel vasculitis could be classified as having GPA if the cumulative score was ≥5 points. When these criteria were tested in the validation data set, the sensitivity was 93% (95% CI 87% to 96%) and the specificity was 94% (95% CI 89% to 97%). Conclusion The 2022 American College of Rheumatology/European Alliance of Associations for Rheumatology classification criteria for GPA demonstrate strong performance characteristics and are validated for use in research.
Impact of the HeartMate 3 continuous-flow left ventricular assist device in patients with small body size

Abstract OBJECTIVES Limited data are available for use of the HeartMate 3 (HM 3) left ventricular assist device in patients with a small body surface area (BSA). Because the HM 3 is currently the sole device available worldwide, we conducted a single-centre retrospective study of patients with a small BSA (<1.5 m2) who underwent HM 3 implantation to better understand the operative and postoperative management. METHODS This study enrolled 64 consecutive patients who had undergone HM 3 implantation from August 2018 to July 2021. The patients were divided into 2 groups based on their BSA before the operation: BSA of <1.5 m2 (small BSA group, n = 18) and BSA of ≥1.5 m2 (regular BSA group, n = 46). The primary study endpoint was survival free of events such as disabling stroke and pump failure. The secondary endpoint was the frequency of adverse events. RESULTS The average BSA was 1.38 m2 in the small BSA group. The overall event-free survival rate at 12 months was 100% and 86.7% in the small BSA group and regular BSA group, respectively, and no significant difference was found between the 2 groups (log-rank P = 0.2). The number of cumulative adverse events of death, stroke of any severity, driveline infection, pump infection, ventricular arrhythmia, gastrointestinal Haemorrhage and pump failure was similar between the 2 groups. CONCLUSIONS The HM 3 was safely implanted in patients with a small BSA, and postoperative outcomes were acceptable regardless of BSA. However, further research is needed to confirm the indications for HM 3 implantation in even smaller patients.
MR and fluorescence imaging of gadobutrol‐induced optical clearing of red fluorescent protein signal in an in vivo cancer model

Multimodality registration of optical and MR images in the same tissue volume in vivo may be enabled by MR contrast agents with an optical clearing (OC) effect. The goals of this study were to (a) investigate the effects of clinical MR contrast agent gadobutrol (GB) and its combinations as a potential OC agent assisting in fluorescence intensity (FI) imaging in vivo and (b) evaluate MRI as a tool for imaging of topical or systemic application of GB for the purpose of OC. Subcutaneous tumor xenografts expressing red fluorescent marker protein were used as disease models. MRI was performed at 1 T 1H MRI using T1‐weighted 3D gradient‐echo (T1w‐3D GRE) sequences to measure time‐dependent MR signal intensity changes by region of interest analysis after image segmentation. Topical application of 1.0 M or 0.7 M GB‐containing OC mixture with water and dimethyl sulfoxide showed similar 30–40% increases of tumor FI during the initial 15 min. Afterwards, the OC effect of GB on FI and tumor/background FI ratio showed a decrease over time in the case of 1.0 M GB, unlike the 0.7 M GB mixture, which resulted in a steady increase of FI and tumor/background ratio for 15–60 min. The use of T1w‐3D GRE MR pulse sequences showed that concentrated 1.0 M GB resulted in MR signal loss of the skin due to high magnetic susceptibility and that signal loss coincided with the OC effect. Intravenous injection of 0.3 mmol GB/kg resulted in a rapid but transient 40% increase of FI of the tumors. Overall, 1 T MRI enabled tracking of GB‐containing OC compositions on the skin surface and tumor tissue, supporting the observation of a time‐dependent FI increase in vivo.
Emotional maltreatment and neglect impact neural activation upon exclusion in early and mid-adolescence: An event-related fMRI study

Abstract Child maltreatment gives rise to atypical patterns of social functioning with peers which might be particularly pronounced in early adolescence when peer influence typically peaks. Yet, few neuroimaging studies in adolescents use peer interaction paradigms to parse neural correlates of distinct maltreatment exposures. This fMRI study examines effects of abuse, neglect, and emotional maltreatment (EM) among 98 youth (n = 58 maltreated; n = 40 matched controls) using an event-related Cyberball paradigm affording assessment of both social exclusion and inclusion across early and mid-adolescence (≤13.5 years, n = 50; >13.5 years, n = 48). Younger adolescents showed increased activation to social exclusion versus inclusion in regions implicated in mentalizing (e.g., superior temporal gyrus). Individual exposure-specific analyses suggested that neglect and EM coincided with less reduction of activation to social exclusion relative to inclusion in the dorsal anterior cingulate cortex/pre-supplementary motor area (dACC/pre-SMA) among younger versus older adolescents. Integrative follow-up analyses showed that EM accounted for this dACC/pre-SMA activation pattern over and above other exposures. Moreover, age-independent results within respective exposure groups revealed that greater magnitude of neglect predicted blunted exclusion-related activity in the parahippocampal gyrus, while EM predicted increased activation to social exclusion in the precuneus/posterior cingulate cortex.
Hostility Toward Baby Boomers on TikTok

Abstract Background and Objectives The recent entry of the hashtag #OkBoomer into social media vernacular underscores the collective frustration of younger people with a group whose views they find increasingly incompatible with theirs. Most social media analyses in gerontology focus on the content on Twitter and Facebook, with content on TikTok virtually unexplored. Given the burgeoning popularity of TikTok among younger people, we assess the content of TikTok videos with the hashtags #OkBoomer or #Boomer to distill the undercurrents of hostility expressed by younger people toward Baby Boomers. Research Design and Methods We collated TikTok videos (N = 332) with the hashtags #OkBoomer or #Boomer, which received over 5.4 billion views. Both inductive and deductive approaches guided the qualitative content analysis of the videos. Results Five themes emerged. Most videos (79%) described “Negative Encounters with Baby Boomers” (Theme 1); 58% were about “Conflicting Values/Beliefs between Baby Boomers and Younger People” (Theme 2); 39% were about “Baby Boomers Antagonizing Younger Generations” (Theme 3); 22% of the videos made references to the “Karen Meme” (Theme 4); and 7% bemoaned the existence of a “Wealth Gap” between Baby Boomers and younger people (Theme 5). Discussion and Implications Findings reveal that the usage of the hashtags #OkBoomer and #Boomer is highly nuanced, at times explicitly ageist, and at others, emblematic of a phenomenon far more complex than ageism. There is a need to leverage social media as a space to foster interaction between older and younger people. Society is ultimately well served by intergenerational interaction.
Two new triterpenoid saponins from the flowers of Albizia lebbeck

Abstract The chemical investigation of the fresh flowers of Albizia lebbeck (L.) Benth. (Fabaceae, Mimosoideae) led to the isolation of two new echinocystic acid saponins. They were isolated by using chromatographic methods and their structures were elucidated by detailed 1H and 13C NMR spectral data including 2 D-NMR (COSY, HSQC, HMBC and APT) spectroscopic techniques, high-resolution electrospray ionization mass spectrometry (HRESIMS) and acid hydrolysis. Their structures were established as 16-hydroxy-3-[[O-β-D-xylopyranosyl-(1→2)-O-α-L-arabinopyranosyl-(1→6)-2-(acetylamino)-2-deoxy-β-D-glucopyranosyl]oxy]-(3β,16α)-olean-12-en-28-oic acid O-6-deoxy-α-L-mannopyranosyl-(1→4)-O-6-deoxy-α-L-mannopyranosyl-(1→2)-β-D-glucopyranosyl ester (1) and 16-hydroxy-3-[[O-β-D-xylopyranosyl-(1→2)-O-α-L-arabinopyranosyl-(1→6)-2-(acetylamino)-2-deoxy-β-D-glucopyranosyl]oxy]-(3β,16α)-olean-12-en-28-oic acid 6-O-[(2S,3R,4R)-tetrahydro-3-hydroxy-4-(hydroxymethyl)-2-furanyl]-β-D-glucopyranosyl ester (2). Additionally, the permeability property and the capacity of interaction with biological membranes of compounds 1 and 2 were investigated. Graphical Abstract
AFP-Mask: Anchor-Free Polyp Instance Segmentation in Colonoscopy

Colorectal cancer (CRC) is a common and lethal disease. Globally, CRC is the third most commonly diagnosed cancer in males and the second in females. The most effective way to prevent CRC is through using colonoscopy to identify and remove precancerous growths at an early stage. The detection and removal of colorectal polyps have been found to be associated with a reduction in mortality from colorectal cancer. However, the false negative rate of polyp detection during colonoscopy is often high even for experienced physicians. With recent advances in deep learning based object detection techniques, automated polyp detection shows great potential in helping physicians reduce false positive rate during colonoscopy. In this paper, we propose a novel anchor-free instance segmentation framework that can localize polyps and produce the corresponding instance level masks without using predefined anchor boxes. Our framework consists of two branches: (a) an object detection branch that performs classification and localization, (b) a mask generation branch that produces instance level masks. Instead of predicting a two-dimensional mask directly, we encode it into a compact representation vector, which allows us to incorporate instance segmentation with one-stage bounding-box detectors in a simple yet effective way. Moreover, our proposed encoding method can be trained jointly with object detector. Our experiment results show that our framework achieves a precision of 99.36% and a recall of 96.44% on public datasets, outperforming existing anchor-free instance segmentation methods by at least 2.8% in mIoU on our private dataset.
Ferroptosis: regulation by competition between NRF2 and BACH1 and propagation of the death signal

Ferroptosis is triggered by a chain of intracellular labile iron‐dependent peroxidation of cell membrane phospholipids. Ferroptosis is important not only as a cause of ischaemic and neurodegenerative diseases but also as a mechanism of cancer suppression, and a better understanding of its regulatory mechanism is required. It has become clear that ferroptosis is finely controlled by two oxidative stress‐responsive transcription factors, NRF2 (NF‐E2‐related factor 2) and BACH1 (BTB and CNC homology 1). NRF2 and BACH1 inhibit and promote ferroptosis, respectively, by activating or suppressing the expression of genes in the major regulatory pathways of ferroptosis: intracellular labile iron metabolism, the GSH (glutathione) ‐GPX4 (glutathione peroxidase 4) pathway and the FSP1 (ferroptosis suppressor protein 1)‐CoQ (coenzyme Q) pathway. In addition to this, NRF2 and BACH1 control ferroptosis through the regulation of lipid metabolism and cell differentiation. This multifaceted regulation of ferroptosis by NRF2 and BACH1 is considered to have been acquired during the evolution of multicellular organisms, allowing the utilization of ferroptosis for maintaining homeostasis, including cancer suppression. In terms of cell–cell interaction, it has been revealed that ferroptosis has the property of propagating to surrounding cells along with lipid peroxidation. The regulation of ferroptosis by NRF2 and BACH1 and the propagation phenomenon could be used to realize anticancer cell therapy in the future. In this review, these points will be summarized and discussed.
FAdV-4 without Fiber-2 Is a Highly Attenuated and Protective Vaccine Candidate

Among all serotypes of fowl adenovirus, serotypes FAdV-1, FAdV-4, and FAdV-10 are unique members with two fiber genes (fiber-1 and fiber-2). Recent studies reveal that Fiber-1, not Fiber-2, directly triggers viral infection of FAdV-4, whereas Fiber-2, but not Fiber-1, has been identified as the major virulence determiner and an efficient protective immunogen for subunit vaccines. ABSTRACT Hepatitis-hydropericardium syndrome (HHS) caused by the highly pathogenic fowl adenovirus serotype 4 (FAdV-4) has resulted in huge economic losses to the poultry industry globally. The fiber-2 gene, as a major virulence determiner, is also an important vaccine target against FAdV-4. In this study, we used a CRISPR/Cas9-based homology-dependent recombinant technique to replace the fiber-2 gene with egfp and generate a novel recombinant virus, designated FAdV4-EGFP-rF2. Although FAdV4-EGFP-rF2 showed low replication ability compared to the wild-type FAdV-4 in LMH cells, FAdV4-EGFP-rF2 could effectively replicate in LMH-F2 cells with the expression of Fiber-2. Moreover, FAdV4-EGFP-rF2 was not only highly attenuated in chickens, but also could provide efficient protection against a lethal challenge of FAdV-4. Moreover, FAdV4-EGFP-rF2 without fiber-2 could induce neutralizing antibodies at the same level as FA4-EGFP with fiber-2. These results clearly demonstrate that although fiber-2 affects the viral replication and pathogenesis of FAdV-4, it is not necessary for virus replication and induction of neutralizing antibodies; these findings provide novel insights into the roles of fiber-2 and highlight fiber-2 as an insertion site for generating live-attenuated FAdV-4 vaccines against FAdV-4 and other pathogens. IMPORTANCE Among all serotypes of fowl adenovirus, serotypes FAdV-1, FAdV-4, and FAdV-10 are unique members with two fiber genes (fiber-1 and fiber-2). Recent studies reveal that Fiber-1, not Fiber-2, directly triggers viral infection of FAdV-4, whereas Fiber-2, but not Fiber-1, has been identified as the major virulence determiner and an efficient protective immunogen for subunit vaccines. Here, we replaced fiber-2 with egfp to generate a novel recombinant virus, designated FAdV4-EGFP-rF2. In vitro and in vivo studies on FAdV4-EGFP-rF2 revealed that fiber-2 was not necessary for either virus replication or efficient protection for FAdV-4; these results not only provide a novel live-attenuated vaccine candidate against HHS, but also give new ideas for generating a FAdV-4 based vaccine vector against other pathogens.