Miracle-dz/UniFAR-FTUs huggingface dataset:
Model-measurement consistency and limits of bioaerosol abundance over the continental United States

Abstract. Due to low concentrations and chemical complexity, in situ observations of bioaerosol are geographically and temporally sparse, and this limits the accuracy of current emissions inventories. In this study, we apply a new methodology, including corrections for misidentification of mineral dust, to measurements of single particles over four airborne sampling campaigns to derive vertical profiles of bioaerosol over the continental United States. The new methodology is based on single-particle mass spectrometry (SPMS); it can extend historic datasets to include measurements of bioaerosol, it allows comparisons to other techniques, and it generally agrees with a global aerosol model. In the locations sampled, bioaerosols were at least a factor of 10 less abundant than mineral dust. Below 2 km, bioaerosol concentrations were measured between 6×103 and 2×104 m−3. Between 2 and 8 km, bioaerosol concentrations were between 0 and 2×104 m−3, and above 8 km, bioaerosol concentrations were between 0 and 1×103 m−3. Between 30 % and 80 % of single bioaerosol particles detected were internally mixed with dust. A direct comparison of the SPMS methodology with a co-located wideband integrated bioaerosol sensor (WIB) fluorescence sensor on a mountaintop site showed agreement to within a factor of 3 over the common size range.
SCMAG: A Semisupervised Single-Cell Clustering Method Based on Matrix Aggregation Graph Convolutional Neural Network

Clustering analysis is one of the most important technologies for single-cell data mining. It is widely used in the division of different gene sequences, the identification of functional genes, and the detection of new cell types. Although the traditional unsupervised clustering method does not require label data, the distribution of the original data, the setting of hyperparameters, and other factors all affect the effectiveness of the clustering algorithm. While in some cases the type of some cells is known, it is hoped to achieve high accuracy if the prior information about those cells is utilized sufficiently. In this study, we propose SCMAG (a semisupervised single-cell clustering method based on a matrix aggregation graph convolutional neural network) that takes into full consideration the prior information for single-cell data. To evaluate the performance of the proposed semisupervised clustering method, we test on different single-cell datasets and compare with the current semisupervised clustering algorithm in recognizing cell types on various real scRNA-seq data; the results show that it is a more accurate and significant model.
Identification of protease serine S1 family member 53 as a mitochondrial protein in murine islet beta cells

ABSTRACT The aim of this study was to identify genes that are specifically expressed in pancreatic islet β-cells (hereafter referred to as β-cells). Large-scale complementary DNA-sequencing analysis was performed for 3,429 expressed sequence tags derived from murine MIN6 β-cells, through homology comparisons using the GenBank database. Three individual ESTs were found to code for protease serine S1 family member 53 (Prss53). Prss53 mRNA is processed into both a short and long form, which encode 482 and 552 amino acids, respectively. Transient overexpression of myc-tagged Prss53 in COS-7 cells showed that Prss53 was strongly associated with the luminal surfaces of organellar membranes and that it underwent signal peptide cleavage and N-glycosylation. Immunoelectron microscopy and western blotting revealed that Prss53 localized to mitochondria in MIN6 cells. Short hairpin RNA-mediated Prss53 knockdown resulted in Ppargc1a downregulation and Ucp2 and Glut2 upregulation. JC-1 staining revealed that the mitochondria were depolarized in Prss53-knockdown MIN6 cells; however, no change was observed in glucose-stimulated insulin secretion. Our results suggest that mitochondrial Prss53 expression plays an important role in maintaining the health of β-cells.
Faecal microbiota replacement to eradicate antimicrobial resistant bacteria in the intestinal tract – a systematic review

Supplemental Digital Content is available in the text Purpose of review Antimicrobial resistance is a rising threat to global health and is associated with increased mortality. Intestinal colonisation with multidrug-resistant organisms (MDRO) can precede invasive infection and facilitates spread within communities and hospitals. Novel decolonisation strategies, such as faecal microbiota transplantation (FMT), are being explored. The purpose of this review is to provide an update on how the field of FMT for MDRO decolonisation has developed during the past year and to assess the efficacy of FMT for intestinal MDRO decolonisation. Recent findings Since 2020, seven highly heterogenous, small, nonrandomised cohort studies and five case reports have been published. In line with previous literature, decolonisation rates ranged from 20 to 90% between studies and were slightly higher for carbapenem-resistant Enterobacteriaceae than vancomycin-resistant Enterococcus. Despite moderate decolonisation rates in two studies, a reduction in MDRO bloodstream and urinary tract infections was observed. Summary and implications Although a number of smaller cohort studies show some effect of FMT for MDRO decolonisation, questions remain regarding the true efficacy of FMT (taking spontaneous decolonisation into account), the optimal route of administration, the role of antibiotics pre and post-FMT and the efficacy in different patient populations. The observed decrease in MDRO infections post-FMT warrants further research.
Digital Volumetric Monitoring of Palate Growth in Children With Cleft Lip and Palate

Abstract This study aimed to evaluate longitudinally the volume of the dental arches in children with unilateral cleft lip and palate before and after the rehabilitative plastic surgeries. This is a longitudinal retrospective study was composed by 102 digitized dental casts of children with unilateral complete cleft lip (G1) and cleft lip and palate (G2). The palate volume was evaluated at 3 periods: preoperative (T1), postoperative 1 (T2), and postoperative 2 (T3). The intra- and inter-examiner reliability was analyzed by Wilcoxon test/Dahlberg formula and interclass correlation coefficient, respectively. The intragroup comparison was analyzed by Wilcoxon test and Friedman test followed by post-hoc Dunn test. Mann–Whitney test was applied for the intergroup comparison (α = 5%). G1 had a significant growth at T2 (P = 0.031). G2 demonstrated a positive development at T2, but decreased at T3 (P = 0.003). The intergroup analysis revealed that G2 showed a greater volume at T1 and T2 (P < 0.0001 and P = 0.0024, respectively). T2-T1 exhibited no statistically significant difference (P = 0.262). In conclusion, there was a volumetric increase in the dental arches after cheiloplasty followed by a reduction after palatoplasty. Further investigations are necessary to validate the preliminary results of the present study.
Altered intrinsic default mode network functional connectivity in patients with remitted geriatric depression and amnestic mild cognitive impairment

ABSTRACT Objectives: Patients with geriatric depression exhibit a spectrum of symptoms ranging from mild to severe cognitive impairment which could potentially lead to the development of Alzheimer’s disease (AD). The aim of the study is to assess the alterations of the default mode network (DMN) in remitted geriatric depression (RGD) patients and whether it could serve as an underlying neuropathological mechanism associated with the risk of progression of AD. Design: Cross-sectional study. Participants: A total of 154 participants, comprising 66 RGD subjects (which included 27 patients with comorbid amnestic mild cognitive impairment [aMCI] and 39 without aMCI [RGD]), 45 aMCI subjects without a history of depression (aMCI), and 43 matched healthy comparisons (HC), were recruited. Measurements: All participants completed neuropsychological tests and underwent resting-state functional magnetic resonance imaging (fMRI). Posterior cingulate cortex (PCC)-seeded DMN functional connectivity (FC) along with cognitive function were compared among the four groups, and correlation analyses were conducted. Results: In contrast to HC, RGD, aMCI, and RGD-aMCI subjects showed significant impairment across all domains of cognitive functions except for attention. Furthermore, compared with HC, there was a similar and significant decrease in PCC-seed FC in the bilateral medial superior frontal gyrus (M-SFG) in the RGD, aMCI, and RGD-aMCI groups. Conclusions: The aberrations in rsFC of the DMN were associated with cognitive deficits in RGD patients and might potentially reflect an underlying neuropathological mechanism for the increased risk of developing AD. Therefore, altered connectivity in the DMN could serve as a potential neural marker for the conversion of geriatric depression to AD.
Drug resistance pattern among ART‐naive clients attending an HIV testing and counseling center in Dhaka, Bangladesh

In Bangladesh, antiretroviral therapy (ART) is provided without screening drug resistance‐associated mutations (DRM) among people living with HIV, while DRM might emerge and transmit to the newly infected individual. The present study was aimed to identify DRM among ART‐naive clients from an HIV testing and counseling (HTC) center in the initial stages of ART programs. Randomly selected (n = 64) archived plasma samples were used for the pol gene amplification and sequencing by sanger technology. Recovered sequences (n = 10) were genotyped using HIV genotyping tools of NCBI and analyzed using the Stanford University HIV drug resistance database (hivdb.stanford.edu). Various genotypes with a number of DRM were identified in HTC clients, who belonged to different risk groups based on behavioral data. The drug resistance algorithm showed that all samples were fully resistant to tipranavir/ritonavir drugs except for one intermediate resistance. Despite the small sample size, our understanding from this study warrants an ART policy with a DRM monitoring system for the country.
Orientation selectivity and stimulus vignetting in human visual cortex

Neural selectivity to orientation is one of the simplest and most thoroughly-studied cortical sensory features. Here, we show that a large body of research that purported to measure orientation tuning may have in fact been inadvertently measuring sensitivity to secondorder changes in luminance, a phenomenon we term ‘vignetting'. Using a computational model of neural responses in primary visual cortex (V1), we demonstrate the impact of vignetting on simulated V1 responses. We then used the model to generate a set of predictions, which we confirmed with functional MRI experiments in human observers. Our results demonstrate that stimulus vignetting can wholly determine the orientation selectivity of responses in visual cortex measured at a macroscopic scale, and suggest a reinterpretation of a well-established literature on orientation processing in visual cortex.
Coupling high-throughput mapping with proteomics analysis delineates cis-regulatory elements at high resolution

Abstract Growing evidence suggests that functional cis-regulatory elements (cis-REs) not only exist in epigenetically marked but also in unmarked sites of the human genome. While it is already difficult to identify cis-REs in the epigenetically marked sites, interrogating cis-REs residing within the unmarked sites is even more challenging. Here, we report adapting Reel-seq, an in vitro high-throughput (HTP) technique, to fine-map cis-REs at high resolution over a large region of the human genome in a systematic and continuous manner. Using Reel-seq, as a proof-of-principle, we identified 408 candidate cis-REs by mapping a 58 kb core region on the aging-related CDKN2A/B locus that harbors p16INK4a. By coupling Reel-seq with FREP-MS, a proteomics analysis technique, we characterized two cis-REs, one in an epigenetically marked site and the other in an epigenetically unmarked site. These elements are shown to regulate the p16INK4a expression over an ∼100 kb distance by recruiting the poly(A) binding protein PABPC1 and the transcription factor FOXC2. Downregulation of either PABPC1 or FOXC2 in human endothelial cells (ECs) can induce the p16INK4a-dependent cellular senescence. Thus, we confirmed the utility of Reel-seq and FREP-MS analyses for the systematic identification of cis-REs at high resolution over a large region of the human genome.
The impact of COVID‐19 lockdown on brain metabolism

This study aims to evaluate the impact of French national lockdown of 55 days on brain metabolism of patients with neurological disorders. Whole‐brain voxel‐based PET analysis was used to correlate 18F‐FDG metabolism to the number of days after March 17, 2020 (in 95 patients; mean age: 54.3 years ± 15.7; 59 men), in comparison to the same period in 2019 before the SARS‐CoV‐2 outbreak (in 212 patients; mean age: 59.5 years ± 15.8; 114 men), and to the first 55 days of deconfinement (in 188 patients; mean age: 57.5 years ± 16.5; 93 men). Lockdown duration was negatively correlated to the metabolism of the sensory‐motor cortex with a prevailing effect on the left dominant pyramidal tract and on younger patients, also including the left amygdala, with only partial reversibility after 55 days of deconfinement. Weak overlap was found with the reported pattern of hypometabolism in long COVID (<9%). Restriction of physical activities, and possible related deconditioning, and social isolation may lead to functional disturbances of sensorimotor and emotional brain networks. Of note, this metabolic pattern seems distinct to those reported in long COVID. Further longitudinal studies with longer follow‐up are needed to evaluate clinical consequences and relationships on cognitive and mental health against functional deactivation hypothesis, and to extend these findings to healthy subjects in the context of lockdown.
Three-Dimensional-Printed External Scaffolds Mitigate Loss of Volume and Topography in Engineered Elastic Cartilage Constructs

Objective A major obstacle in the clinical translation of engineered auricular scaffolds is the significant contraction and loss of topography that occur during maturation of the soft collagen-chondrocyte matrix into elastic cartilage. We hypothesized that 3-dimensional-printed, biocompatible scaffolds would “protect” maturing hydrogel constructs from contraction and loss of topography. Design External disc-shaped and “ridged” scaffolds were designed and 3D-printed using polylactic acid (PLA). Acellular type I collagen constructs were cultured in vitro for up to 3 months. Collagen constructs seeded with bovine auricular chondrocytes (BAuCs) were prepared in 3 groups and implanted subcutaneously in vivo for 3 months: preformed discs with (“Scaffolded/S”) or without (“Naked/N”) an external scaffold and discs that were formed within an external scaffold via injection molding (“Injection Molded/SInj”). Results The presence of an external scaffold or use of injection molding methodology did not affect the acellular construct volume or base area loss. In vivo, the presence of an external scaffold significantly improved preservation of volume and base area at 3 months compared to the naked group (P < 0.05). Construct contraction was mitigated even further in the injection molded group, and topography of the ridged constructs was maintained with greater fidelity (P < 0.05). Histology verified the development of mature auricular cartilage in the constructs within external scaffolds after 3 months. Conclusion Custom-designed, 3D-printed, biocompatible external scaffolds significantly mitigate BAuC-seeded construct contraction and maintain complex topography. Further refinement and scaling of this approach in conjunction with construct fabrication utilizing injection molding may aid in the development of full-scale auricular scaffolds.
Nutritional compositions, polyphenolic profiles and antioxidant properties of pigmented rice varieties and adlay seeds enhanced by soaking and germination conditions

Background: Pigmented rice varieties are gaining interest due to their superior nutritional and phenolic properties compared to white rice varieties. With the rising risk of diabetes, cereals with higher protein contents should be consumed with rice. Adlay is one of the underutilized crops with higher protein contents and other functional properties. The germination process is one of the easy and innovative techniques for improving functional properties in seeds. In this study, two pigmented rice varieties and adlay seeds were soaked (24 h) and germinated for 12, 24, 36, and 48 h. The physicochemical properties, polyphenolic profiles, and the antioxidant activities of these samples were evaluated.Results: Purple rice (PR) demonstrated the highest values for polyphenolic contents, with 9 compounds detected for antioxidant activities. There were 6 compounds detected for red rice (RR). The adlay seeds had the least concentrations of phenolic compounds, with 6 compounds and higher nutritional properties identified. New compounds were synthesized. Among the rice samples, 24 h soaking (S24) gave the best results for phenolic and antioxidant properties, with 24 h germination in adlay seeds. 48 h germination yielded better results for the nutritional values in all the samples.Conclusion: The present study demonstrates how the process of soaking is a cheap and less time-consuming process of improving bioactive compounds and antioxidant activities in pigmented rice varieties and adlay seeds. Keywords: polyphenols; antioxidant; pigmented rice; adlay; germination.
Whole‐exome sequencing identified first homozygous frameshift variant in the COLEC10 gene in an Iranian patient causing 3MC syndrome type 3

3MC syndrome type 3 is an autosomal recessive disorder caused by mutations in the COLEC10 gene besides other genes like COLEC11 and MASP1. This disorder is characterized by facial dysmorphism, cleft lip and palate, postnatal growth deficiency, cognitive impairment, hearing loss, craniosynostosis, radioulnar synostosis, genital and vesicorenal anomalies, cardiac anomalies, caudal appendage, and umbilical hernia.
The functional brain networks activated by music listening: A neuroimaging meta-analysis and implications for treatment.

OBJECTIVE Previous behavioral studies show that music listening enhances attention and working memory in both healthy and clinical populations. However, how music listening engages brain functional networks remains elusive due to inconsistent results from previous findings. METHOD A meta-analysis of functional magnetic resonance imaging data using seed-based d mapping (SDM) with permutation of subject images was performed. Studies that presented music listening paradigms to healthy individuals were included. Subgroup analyses were performed to investigate the effects of music genres on brain activation. To examine functional network correlates, voxels that were significantly activated by music listening were overlaid onto cortical, subcortical, and striatal network parcellations. RESULTS Whole-group analysis showed that ventral attention, somatomotor, default, dorsal attention, frontoparietal, and limbic networks significantly coactivated during music listening (familywise error-corrected p < .01). Specifically, music listening activated multiple frontal, temporal, subcortical, and cerebellar regions. Subgroup analyses revealed that classical music, but not songs or simple tunes, activated the limbic network. Meta-regression analysis revealed nonsignificant correlations between years of music training and all brain regions activated during music listening. CONCLUSIONS Music listening bilaterally activated multiple cortical, subcortical, and cerebellar regions encompassing multiple brain networks that were not modulated by music training experience. It is recommended that music listening can be applied to people with neurological disorders to modulate the disordered functional brain networks known to underlie the pathophysiology of these diseases, while future studies may help delineate the effects of music preferences on brain activation patterns among these patients to promote the development of evidence-based medicine. (PsycInfo Database Record (c) 2021 APA, all rights reserved).
Internalised HIV-related stigma associated with physical inactivity in people with HIV and AIDS: A cross-sectional study from Uganda

Aim: The aim of the current study was to explore correlations between continuous physical activity (PA) levels and HIV-related stigma and differences in HIV-related stigma between those who meet versus those who do not meet the international PA recommendation of 150 min of PA per week at moderate intensity. Methods: 295 people living with HIV (PLHIV) (median [interquartile range] age = 37.0 [16.0]; 67.8% [n = 200] female) from central Uganda completed the Internalised AIDS-Related Stigma Scale (IA-RSS), Generalised Anxiety Disorder-7 (GAD-7), the Patient Health Questionnaire-9 (PHQ-9), the Alcohol Use Disorders Identification Test (AUDIT) and the Physical Activity Vital Sign (PAVS). Results: There was a significant correlation between the PAVS and IA-RSS scores correcting for GAD-7, PHQ-9 and AUDIT scores (r = −0.15, p = 0.009). The IA-RSS score was also significantly different between those meeting versus not meeting PA guidelines. Conclusions: Our data demonstrate that higher internalised HIV-related stigma is associated with lower levels of physical activity. The current evidence demonstrates the need to explore whether HIV stigma-reduction interventions could improve physical activity participation and consequently physical and mental health outcomes in PLHIV.
Evaluation of the prognostic ability of serum uric acid for elderly acute coronary syndrome patients with diabetes mellitus: a prospective cohort study

Objective: This study evaluated the prognostic power of serum uric acid (UA) in predicting adverse events in elderly acute coronary syndrome (ACS) patients with diabetes mellitus (DM). Methods: The analysis involved 718 ACS patients >80 years old whose general clinical data and baseline blood biochemical indicators were collected prospectively from January 2006 to December 2012. These patients were classified into two groups based on DM status, and then followed up after discharge. The Kaplan-Meier method was used for major adverse cardiac event (MACE) rates and all-cause mortality. Multivariate Cox regression was performed to analyze the relationship between UA level and long-term clinical prognosis. Receiver operating characteristic (ROC) curves were analyzed to predict the cutoff value of UA in elderly ACS patients with DM. There were 242 and 476 patients in the DM and non-DM (NDM) groups, respectively, and the follow-up time after discharge was 40–120 months (median, 63 months; interquartile range, 51–74 months). Results: The all-cause mortality, cardiac mortality, and MACE rates in both DM and NDM patients were higher than those in the control group (P=0.001). All-cause mortalities, cardiac mortalities, and MACE rates in DM patients with moderate and high UA levels were significantly higher than those in the NDM group (P=0.001). Long-term survival rates decreased significantly with increased UA levels in the ACS groups (P=0.001). UA (odds ratio (OR)=2.106, 95% confidence interval (CI)=1.244–3.568, P=0.006) was found to be an independent risk factor for all-cause mortality and MACE in elderly ACS patients with DM. The cutoff value of UA was 353.6 μmol/L (sensitivity, 67.4%; specificity, 65.7%). Conclusions: Serum UA level is a strong independent predictor of long-term all-cause death and MACE in elderly ACS patients with DM.