Miracle-dz/UniFAR-FTUs huggingface dataset:
Invasive pulmonary aspergillosis in critically ill patients with severe COVID-19 pneumonia: Results from the prospective AspCOVID-19 study

Background: Superinfections, including invasive pulmonary aspergillosis (IPA), are well-known complications of critically ill patients with severe viral pneumonia. Aim of this study was to evaluate the incidence, risk factors and outcome of IPA in critically ill patients with severe COVID-19 pneumonia. Methods: We prospectively screened 32 critically ill patients with severe COVID-19 pneumonia for a time period of 28 days using a standardized study protocol for oberservation of developement of COVID-19 associated invasive pulmonary aspergillosis (CAPA). We collected laboratory, microbiological, virological and clinical parameters at defined timepoints in combination with galactomannan-antigen-detection from bronchial aspirates. We used logistic regression analyses to assess if COVID-19 was independently associated with IPA and compared it with matched controls. Findings: CAPA was diagnosed at a median of 4 days after ICU admission in 11/32 (34%) of critically ill patients with severe COVID-19 pneumonia as compared to 8% in the control cohort. In the COVID-19 cohort, mean age, APACHE II score and ICU mortality were higher in patients with CAPA than in patients without CAPA (36% versus 9.5%; p<0.001). ICU stay (21 versus 17 days; p=0.340) and days of mechanical ventilation (20 versus 15 days; p=0.570) were not different between both groups. In regression analysis COVID-19 and APACHE II score were independently associated with IPA. Interpretation: CAPA is highly prevalent and associated with a high mortality rate. COVID-19 is independently associated with invasive pulmonary aspergillosis. A standardized screening and diagnostic approach as presented in our study can help to identify affected patients at an early stage.
Dietary cholesterol drives fatty liver-associated liver cancer by modulating gut microbiota and metabolites

Objective Non-alcoholic fatty liver disease (NAFLD)-associated hepatocellular carcinoma (HCC) is an increasing healthcare burden worldwide. We examined the role of dietary cholesterol in driving NAFLD–HCC through modulating gut microbiota and its metabolites. Design High-fat/high-cholesterol (HFHC), high-fat/low-cholesterol or normal chow diet was fed to C57BL/6 male littermates for 14 months. Cholesterol-lowering drug atorvastatin was administered to HFHC-fed mice. Germ-free mice were transplanted with stools from mice fed different diets to determine the direct role of cholesterol modulated-microbiota in NAFLD–HCC. Gut microbiota was analysed by 16S rRNA sequencing and serum metabolites by liquid chromatography–mass spectrometry (LC–MS) metabolomic analysis. Faecal microbial compositions were examined in 59 hypercholesterolemia patients and 39 healthy controls. Results High dietary cholesterol led to the sequential progression of steatosis, steatohepatitis, fibrosis and eventually HCC in mice, concomitant with insulin resistance. Cholesterol-induced NAFLD–HCC formation was associated with gut microbiota dysbiosis. The microbiota composition clustered distinctly along stages of steatosis, steatohepatitis and HCC. Mucispirillum, Desulfovibrio, Anaerotruncus and Desulfovibrionaceae increased sequentially; while Bifidobacterium and Bacteroides were depleted in HFHC-fed mice, which was corroborated in human hypercholesteremia patients. Dietary cholesterol induced gut bacterial metabolites alteration including increased taurocholic acid and decreased 3-indolepropionic acid. Germ-free mice gavaged with stools from mice fed HFHC manifested hepatic lipid accumulation, inflammation and cell proliferation. Moreover, atorvastatin restored cholesterol-induced gut microbiota dysbiosis and completely prevented NAFLD–HCC development. Conclusions Dietary cholesterol drives NAFLD–HCC formation by inducing alteration of gut microbiota and metabolites in mice. Cholesterol inhibitory therapy and gut microbiota manipulation may be effective strategies for NAFLD–HCC prevention.
Frontera: The Evolution of Leadership Computing at the National Science Foundation

As part of the NSF’s cyberinfrastructure vision for a robust mix of high capability and capacity HPC systems, Frontera represents the most recent evolution of trans-petascale resources available to all open science research projects in the U.S. Debuting as the fifth largest supercomputer in the world, Frontera represents a robust and well-balanced HPC system designed to enable large-scale, productive science on day one of operations. The system provides a primary compute capability of nearly 39PF, delivered completely via more than 8,000 dual-socket servers with conventional Intel 8280 (“Cascade Lake”) processors. A unique configuration of both desktop GPUs and advanced floating units from NVIDIA enables both machine learning and scientific workloads, and the system delivers nearly 2TB/s of total filesystem bandwidth with 55 PB of usable Lustre disk-based storage and 3PB of all flash Lustre storage. A Mellanox InfiniBand (IB) interconnect provides very low latency with 100Gbps to each node, and 200Gbps between switches in a fat tree topology with minimal oversubscription for efficient communication, even in jobs that use the full system with complex communication patterns. The system hardware is complemented by a robust set of software services, including Application Programmer Interfaces (APIs) to support an evolving user base that increasingly demands productive access via science gateways and automated workflows, as well as a first-of-its-kind partnership with the three major cloud service providers to create a bridge between “traditional” HPC and the cloud infrastructure upon which research increasingly depends.
Phylogeography of the widespread marine invader Microcosmus squamiger (Ascidiacea) reveals high genetic diversity of introduced populations and non‐independent colonizations

The spread of non‐indigenous species into new marine habitats represents an increasing threat to global diversity. Genetic techniques provide basic understanding of the invasion processes. The ascidian Microcosmus squamiger is considered to be native to Australia, having been spread worldwide via transoceanic vessels. It has successfully invaded artificial and natural habitats where it has become a pest. We studied phylogeography and genetic structure of 12 M. squamiger populations, including samples from its native range (Australia) and introduced populations from the Indian, Pacific, and Atlantic oceans, as well as the Mediterranean Sea. We amplified 574 bp of the mitochondrial COI gene in 258 individuals and found a total of 52 haplotypes. A haplotype tree revealed two main groups of haplotypes. The relative frequency of each group of haplotypes, multidimensional scaling, and analysis of molecular variance showed important differences between the western Australia localities and the remaining ones (eastern Australia and introduced populations). Furthermore, we found that the colonization of the different areas by M. squamiger has not occurred independently, as many introduced populations shared some low frequency alleles. A nested clade analysis showed a global pattern of restricted gene flow with isolation by distance, although we found episodes of long‐distance dispersal in some clades. A contiguous range expansion was detected between Australian populations. We conclude that M. squamiger is native to Australia and has most likely expanded its range of distribution sequentially through worldwide shipping, especially from the harbours of the more populated eastern Australia. In introduced populations, we found a high genetic diversity which suggests enhanced invasive potential. Consequently, there is a need to control this species, as it outcompetes local biota and is an economic threat.
Selective extinction against redundant species buffers functional diversity

The extinction of species can destabilize ecological processes. A way to assess the ecological consequences of species loss is by examining changes in functional diversity. The preservation of functional diversity depends on the range of ecological roles performed by species, or functional richness, and the number of species per role, or functional redundancy. However, current knowledge is based on short timescales and an understanding of how functional diversity responds to long-term biodiversity dynamics has been limited by the availability of deep-time, trait-based data. Here, we compile an exceptional trait dataset of fossil molluscs from a 23-million-year interval in the Caribbean Sea (34 011 records, 4422 species) and develop a novel Bayesian model of multi-trait-dependent diversification to reconstruct mollusc (i) diversity dynamics, (ii) changes in functional diversity, and (iii) extinction selectivity over the last 23 Myr. Our results identify high diversification between 23–5 Mya, leading to increases in both functional richness and redundancy. Conversely, over the last three million years, a period of high extinction rates resulted in the loss of 49% of species but only 3% of functional richness. Extinction rates were significantly higher in small, functionally redundant species suggesting that competition mediated the response of species to environmental change. Taken together, our results identify long-term diversification and selective extinction against redundant species that allowed functional diversity to grow over time, ultimately buffering the ecological functions of biological communities against extinction.
Woven EndoBridge (WEB) device in the treatment of ruptured aneurysms

Background Wide-necked bifurcation aneurysms (WNBAs) present unique challenges for endovascular treatment. The Woven EndoBridge (WEB) device is an intrasaccular braided device, recently approved by the FDA for treatment of WNBAs. While treatment of intracranial aneurysms with the WEB device has been shown to yield an adequate occlusion rate of 85% at 1 year, few data have been published for patients with ruptured aneurysms. Objective To present a multi-institutional series depicting the safety and efficacy of using the WEB device as the primary treatment modality in ruptured intracranial aneurysms. Methods A multi-institutional retrospective analysis was conducted, assessing patients presenting with aneurysmal subarachnoid hemorrhage treated with the WEB between January 2014 and April 2020. Baseline demographics, aneurysm characteristics, adverse events, and long-term outcomes (occlusion, re-treatment, functional status) were collected. A descriptive analysis was performed, and variables potentially associated with aneurysm recurrence or re-treatment were assessed. Results Forty-eight patients were included. Anterior communicating artery aneurysms were the most common (35.4%) location for treatment, followed by middle cerebral artery (20.8%) and basilar apex (16.7%). Procedural success was noted in 95.8% of patients, and clinically significant periprocedural adverse events occurred in 12.5%. After a median follow-up of 5.5 months, 54.2% of patients had follow-up angiographic imaging. Complete occlusion was seen in 61.5% of cases with adequate occlusion in 92.3%. Re-treatment was required in only 4.2% of patients during the study period. Tobacco use was significantly higher in patients with aneurysm recurrence (88.9% vs 35.7%; p=0.012). No other characteristics were associated with recurrence/re-treatment. At 30 days, 81.1% were functionally independent (modified Rankin Scale score ≤2). Conclusion Treatment of acutely ruptured aneurysms with the WEB device demonstrates both safety and efficacy on par with rates of conventional treatment strategies.
Interaction of Estradiol and Endoplasmic Reticulum Stress in the Development of Esophageal Carcinoma

Gender differences in esophageal cancer patients indicate that estradiol may have antitumor effects on esophageal cancer. The initiation of endoplasmic reticulum stress (ERS) can induce apoptosis in esophageal cancer cells. However, it is still unknown whether estradiol inhibits the development of esophageal cancer by activating ERS pathway. In this study, the gender difference in the development of esophageal cancer was observed by analyzing clinical data and the experimental tumor xenografts in mice. Meanwhile, we investigated the mechanism of ERS in estradiol-mediated inhibition of esophageal cancer using esophageal squamous cell carcinoma cell line EC109. The proportion of male patients with esophageal cancer was significantly higher than female patients. Meanwhile, male patients were prone to have adventitial invasion. The weight of transplanted tumors in female mice was significantly smaller than that in male mice. In vitro experiments showed estradiol inhibits the viability and migration of EC109 cells by increasing the expression of ERS-related proteins, whereas ERS inhibitor 4-PBA abolished the effects of estradiol. In conclusion, our data demonstrate that sex difference exists in the occurrence of esophageal cancer. Estradiol can inhibit the viability and migration of esophageal cancer cells through the activation of ERS, providing a novel insight for esophageal cancer development, treatment, and prevention.
A Cephalometric Study of Soft Tissue Norms in Yemeni Adults

Background: Evaluating patient’s soft tissue profile is one of the most imperative components for orthodontic diagnosis and treatment planning. Objectives: The purpose of this study was to determine the soft-tissue cephalometric standards for Yemeni adults. Methods: The material composed of the lateral cephalometric radiographs of one hundred ninety-four Yemeni adults (105 females and 89 males) aged between 18 and 25 years, selected from dental students in Sana’a University. Each film was traced and analyzed using variable linear and angular measurement. Results: Statistical significant differences were reported among genders in Hangle and N’-Pr-Pg’, whereas, N’-Sn-Pg’, nasolabial and mentolabial angles showed no significant differences. Conclusions: The results of Yemeni cephalometric analyses showed ethnic differences in soft tissue findings. Considering the soft tissues pattern of each population will guarantee improved results of treatment to establish the best possible facial harmony.
The effects of recursive communication dynamics on belief updating

Many social interactions are characterized by dynamic interplay, such that individuals exert reciprocal influence over each other's behaviours and beliefs. The present study investigated how the dynamics of reciprocal influence affect individual beliefs in a social context, over and above the information communicated in an interaction. To this end, we developed a simple social decision-making paradigm in which two people are asked to make perceptual judgments while receiving information about each other's decisions. In a Static condition, information about the partner only conveyed their initial, independent judgment. However, in a Dynamic condition, each individual saw the evolving belief of their partner as they learnt about and responded to the individual's own judgment. The results indicated that in both conditions, the majority of confidence adjustments were characterized by an abrupt change followed by smaller adjustments around an equilibrium, and that participants' confidence was used to arbitrate conflict (although deviating from Bayesian norm). Crucially, recursive interaction had systematic effects on belief change relative to the static baseline, magnifying confidence change when partners agreed and reducing confidence change when they disagreed. These findings indicate that during dynamic interactions—often a characteristic of real-life and online social contexts—information is collectively transformed rather than acted upon by individuals in isolation. Consequently, the output of social events is not only influenced by what the dyad knows but also by predictable recursive and self-reinforcing dynamics.
Ocular Examinations and Investigation of Intraocular Pressure, Tear Production, Central Corneal Thickness, and Corneal Touch Threshold in a Captive Flock of Atlantic Puffins (Fratercula arctica)

Abstract: Ocular examinations were completed on a group of 10 Atlantic puffins (Fratercula arctica), 5 males and 5 females that ranged in age from 8 months to older than 30 years. The exams consisted of intraocular pressure/rebound tonometry, tear production/phenol red thread test, central corneal thickness/ultrasound pachymetry, and corneal sensitivity/esthesiometry. On ocular examination, there were no corneal abnormalities observed. Bilateral cataracts were diagnosed in 8 puffins, 6 of which were considered incipient, focal subcapsular opacities. One bird had hypermature cataracts and was removed from the study and excluded from data analysis; the other birds had no evidence of ophthalmic pathology that would interfere with diagnostic results (n = 9). All results for 9 birds were included in the study, with the exception of 1 puffin's tear production, which was too low for accurate assessment and was excluded from data analysis. There were no significant differences between right and left eye measurements for intraocular pressure, corneal thickness, and corneal sensitivity. The median intraocular pressure for both eyes (OU) was 13 mm Hg with an interquartile range [IQR] of 12–15 mm Hg. The median corneal thickness OU was 241 µm, IQR 233–248 µm. The median corneal sensitivity OU was 1.13 cm, IQR 0.81–1.50 cm. There was a significant difference between right and left eye measurements for tear production (right eye median, 7.5 mm/15 s, IQR 6.5–9.3 mm/15 s; and left eye median, 5.0 mm/15 s, IQR 4.0–7.3 mm/15 s) (P= .03), with the right eye producing more tears than the left. However, 1 puffin was determined to be an outlier, and when removed, there was no longer a significant difference (OU median, 7.0 mm/15 s, IQR 4.6–8.0 mm/15 s) (P = .38). There was no significant difference between sex and intraocular pressure, tear production, and corneal sensitivity. However, there was a significant difference between sex and corneal thickness (P = .02), with males (left eye median, 249 µm, IQR 241–249 µm) having thicker corneas than females (left eye median, 236 µm, 234–238 µm). Although sample size precluded statistical testing, there appeared to be an association between opacities and increasing age. There were no associations between age and intraocular pressure, tear production, or corneal thickness. There was a moderate correlation between age and corneal sensitivity, with older birds showing decreased corneal sensitivity (r = –0.57). Although the sample size of 9 birds was small, these findings provide preliminary ranges for ocular parameters of Atlantic puffins.
Diet Influences the Oral Microbiota of Infants during the First Six Months of Life

Oral bacteria and fungi contribute to oral health and establishment of the distal gastrointestinal tract microbiota; however, the impact of diet on the oral microbiota of infants is under‐investigated. We aimed to characterize the influence of feeding method (exclusive human milk [HM], formula [FF], HM + FF [mixed], and solid foods) on oral bacterial and fungal communities in vaginally delivered infants during the first 6 mo of life. Infant (N=12) feeding records and tongue and cheek swabs were collected within 24 hr of birth, and at 2, 4, and 6 mo of age. DNA was extracted, sequenced on an Illumina MiSeq, and analyzed with QIIME 1.8 and SAS. Bacterial diversity was lowest in HM and highest in FF and solid food fed infants (p<0.01). Principal coordinates analysis (PCoA) of UniFrac distances between samples based on their 97% OTU composition and abundances indicated that bacterial communities were impacted by feeding method (p<0.005). Infants fed HM or mixed diets had reduced relative abundances of Bacteroidetes while solid foods increased Fusobacteria (p<0.05). Infants had greater proportions of Proteobacteria at birth compared to other time points (p<0.05). Among genera, Streptococcus predominated in all infants, with the highest proportions in HM or mixed diets. Compared to HM, the relative abundances of Prevotella were increased with FF (p=0.01) and solid foods (p=0.02). Fungal communities were not impacted by diet. Five infants had detectable levels of fungi within 24 hr of birth, 4 at 2 mo, 9 at 4 mo, and 10 at 6 mo. These novel findings demonstrate that the oral microbiota of infants differs depending on dietary composition during the first 6 mo of life. Funded by Hatch Project #ILLU‐971‐350.
Weed Hosts of Root-Knot Nematodes in Tomato Fields

Root-knot nematodes (Meloidogyne spp.) are one of the three most economically damaging genera of plant parasitic nema- todes on horticultural and field crops. Root-knot nematodes are distributed worldwide, and are obligate parasites of the roots of thousands of plant species. All major field crops, vegetable crops, turf, ornamentals, legumes and weeds are susceptible to one or more of the root-knot species. In this study, nineteen weed species were found to be hosts for Meloidogyne incognita, M. javanica, M. arenaria race 2, and M. hapla in tomato fields in Khorasan Province, Iran. Egg mass production and galling differed (p < 0.05) among these weed species: Amaranthus blitoides, Portulaca oleracea, Polygonum aviculare, Convolvulus arvensis, Cyperus rotundus, Plantago lanceolatum, Rumex acetosa, Solanum nigrum, Datura stramonium, Acroptilon repens, Alcea rosa, Alhaji camelorum, Chenopodium album, Echinochla crusgalli, Hibiscus trionum, Kochia scoparia, Malva rotundifolia, Setaria viridis, Lactuca serriola. The species P. oleracea, A. blioides, S. nigrum, P. lanceolatum, Ch. album, and C. arvensis are major threats to the natural ecosystem in the Iranian province of Khorasan. A. blitoides collected from tomato fields was a good host for 4 Meloidogyne species. C. arvensis, as an important weed, was a distin- guished appropriate host for M. hapla, M. incognita, M. javanica. S. nigrum and Ch. album were good hosts for M. hapla, M. javanica, M. incognita race 1, and M. arenaria race 3. In this survey, we reported E. crusgalli as a new host of M. javanica and C. rotundus was a good host for M. arenaria and M. incognita. S. nigrum was also reported as a new host of M. hapla. R. acetosella was reported as a host of M. arenaria. M. incognita was recently described as a new species infecting D. stramonium worldwide.