Miracle-dz/UniFAR-FTUs huggingface dataset:
Outcomes of Universal Preprocedure Coronavirus Disease 2019 Testing Before Endoscopy in a Tertiary Care Center in New York City

This is a PDF file of an article that has undergone enhancements after acceptance, such as the addition of a cover page and metadata, and formatting for readability, but it is not yet the definitive version of record. This version will undergo additional copyediting, typesetting and review before it is published in its final form, but we are providing this version to give early visibility of the article. Please note that, during the production process, errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.
THE FUNCTIONAL MORPHOLOGY OF THE PUTATIVE INJECTING APPARATUS OF SPELEONECTES TANUMEKES (REMIPEDIA)

Abstract Ever since the first individuals of the class Remipedia were discovered, it has been suggested that these animals are capable of injecting their prey with a venomous or digestive substance using the fang on their maxillules. In this study, we investigate the functional morphology of the putative injecting apparatus of Speleonectes tanumekes. Serial sectioning of specimens shows a pair of well-developed glands in the anterior part of the trunk. Spatial interpretations of serial sections suggest that extensions of the glandular cells collectively continue as ducts that lead to the distal segments of the maxillules where a complex of apodemal muscles, associated with a bulbous reservoir, serve to facilitate injection. Different components of the supposedly injectable substance appear to be separated throughout the apparatus.
Spatial and temporal variation in patch occupancy and population density in a model system of an arctic Collembola species assemblage

We employed an experimental model system to investigate the mechanisms underlying patterns of patch occupancy and population density in a high arctic assemblage of Collembola species inhabiting a sedge tussock landscape on Svalbard. The replicate model systems consisted of 5 cores of the tussocks (habitat patches) imbedded in a barren matrix. Four of the patches were open so that animals could migrate between them, while there was one closed patch per system to test the effect of migration on extinction rate. There were model systems of two types: one with long and one with short inter-patch distances to test the effect of patch isolation on colonisation and extinction rates. Each of the four most common collembolan species at the field site were introduced to two open patches per system (source patches), with the other two functioning as colonisation patches for the species. The experiment was run in an ecotrone over three identical, simulated arctic summers separated by winters of 3 weeks. Six replicates of systems with short and long inter-patch distances were sampled at the end of each summer. The species varied markedly in their performance in both open arenas and closed patches, indicating differential responses to patch humidity, consistent with their differential distribution along the moisture gradient in the field site. The extinction – colonisation dynamics differed markedly between species as predicted from our field studies. This could partly be ascribed to differential dispersal and colonisation ability, but also to different tolerance to spatially variable patch quality and/or tendency for aggregative behaviour. Three of the species exhibited dynamics that superficially resemble what could be expected from classical metapopulation dynamics. However, there was a striking discrepancy between what would be expected from the effect of migration on the extinction rate of isolated patches (in particular closed patches) and the observed rates. Thus, metapopulation processes, such as stochastic colonisation and extinction events due to demographic stochasticity, were relatively unimportant compared to other sources of spatial variability among which subtle differences in patch quality are probably most important. We discuss the value of combining field studies with model system experiments, in particular when habitat quality cannot easily be measured in the field. However, our field and laboratory studies also emphasise the need for a thorough knowledge of species-specific life history traits for making biologically sound interpretations based on both observational and experimental data.
Methylome-wide analysis reveals epigenetic marks associated with resistance to tuberculosis in HIV-infected individuals from East Africa

Background: Tuberculosis (TB) is the most deadly infectious disease globally and highly prevalent in the developing world, especially sub-Saharan Africa. Even though a third of humans are exposed to Myocbacterium tuberculosis (Mtb), most infected immunocompetent individuals do not develop active TB. In contrast, for individuals infected with both TB and the human immunodeficiency virus (HIV), the risk of active disease is 10% or more per year. Previously, we identified in a genome-wide association study a region on chromosome 5 that was associated with resistance to TB. This region included epigenetic marks that could influence gene regulation so we hypothesized that HIV-infected individuals exposed to Mtb, who remain disease free, carry epigenetic changes that strongly protect them from active TB. To test this hypothesis, we conducted a methylome-wide study in HIV-infected, TB-exposed cohorts from Uganda and Tanzania. Results: In 221 HIV-infected adults from Uganda and Tanzania, we identified 3 regions of interest that included markers that were differentially methylated between TB cases and LTBI controls, that also included methylation QTLs and associated SNPs: chromosome 1 (RNF220, p=4x10-5), chromosome 2 (between COPS8 and COL6A3 genes, p=2.7x10-5), and chromosome 5 (CEP72, p=1.3x10-5). These methylation results colocalized with associated SNPs, methylation QTLs, and methylation x SNP interaction effects. These markers were in regions with regulatory markers for cells involved in TB immunity and/or lung. Conclusion: Epigenetic regulation is a potential biologic factor underlying resistance to TB in immunocompromised individuals that can act in conjunction with genetic variants.
Prescribed Fire Has a Greater Impact on Artificial Nest Predation Than a Recent Bison Re-introduction in Illinois Tallgrass Prairie

Abstract. Grazing differentially affects both the abundance and breeding success of grassland birds (e.g., due to differences in bird species' preferences for sparse or dense vegetation structure, nest predator response to grazing, and/or trampling of nests). Coupled with prescribed fire, grazing impacts can be compounded by pyric herbivory—the preference of grazers to choose newly-burned sites in which to graze. The purpose of this study was to determine how a recent re-introduction of American bison (Bison bison) coupled with prescribed fire may impact grassland bird nests. Artificial nests were used to determine if grazing and fire impacted nest success, total mammalian depredation, and depredation by the most common nest predator, mice (Peromyscus spp.). Artificial nests were placed in sites with and without bison before (2014) and after bison re-introduction (2015–2018); sites had fire return intervals from 1–2 y. We found the re-introduction of bison had a negligible influence on nest success and total mammalian depredation. However, nest success was lower in burned sites compared to unburned sites. The decrease in nest success correlated with an increase in total proportion of depredation events in burned sites compared to unburned sites. In addition, the proportion of Peromyscus spp. depredation events was marginally higher in burned sites compared to unburned sites. Although predation by Peromyscus increased after bison re-introduction, prescribed fire differences drove this change. Our results suggest prescribed fire may increase nest predation of artificial nests, indicating a possible impact on ground-nesting grassland birds. In contrast, bison had a negligible impact on artificial nest success in the first 4 y following their re-introduction.
Modeling the integrated management of giant foxtail in corn–soybean

Abstract The objectives of this study were to use a computer simulation model to predict the influence of herbicides and mechanical treatments on giant foxtail population dynamics, annualized net return (ANR), and the giant foxtail economic optimum threshold (EOT) in a corn–soybean rotation over 20 yr. Mechanical treatments were interrow cultivation in corn and rotary hoe in soybean. Herbicides at full (1 ×) and half (½ ×) rates applied alone reduced giant foxtail seedbank 95% within 4 and 8 yr, respectively. Predicted seedbank dynamics had more variability when managed with herbicides at ½ × than at 1 × rates applied alone. Mechanical treatments integrated with herbicide at ½ × rates resulted in giant foxtail seedbank and variability similar to herbicides at 1 × rates applied alone. ANR was maximized when herbicides were applied between ⅜ × and 9/16 × rates applied alone. As initial giant foxtail density increased from 100 to 10,000 seeds m−2, the herbicide rate that maximized ANR increased. Economic optimum thresholds (EOTs) did not vary when herbicides were applied at different rates, but integrating mechanical treatment with herbicides increased the EOT from 0.1 to 0.7 seedlings m−2. Sensitivity analysis determined that giant foxtail seedbank demographics, seedling survival, and seed production per plant had the most influence on model predictions. Model sensitivity varied little between 1 × and ½ × rates. Integrating herbicides and mechanical treatment decreased the sensitivity of the model to perturbations in parameter estimates. Herbicides at reduced rates were more profitable over the long term than 1 × rates, but risk of herbicide failure increased as rate decreased. Integration of herbicides applied at reduced rates with mechanical treatments increased ANR and minimized the risk of herbicide failure compared to herbicides applied at 1 × rates alone. Nomenclature: Corn, Zea mays L. ; giant foxtail, Setaria faberi Herrm. SETFA; soybean, Glycine max (L.) Merr.
Complete Genome Sequences and Methylome Analyses of Cutibacterium acnes subsp. acnes Strains DSM 16379 and DSM 1897T

Cutibacterium acnes is a member of the normal human skin microbiome. However, it is also associated with skin disorders and persistent infections of orthopedic implants. Here, we announce complete genome sequences and methylomes of the C. acnes subsp. acnes strains DSM 1897T and DSM 16379 together with their active restriction-modification systems. ABSTRACT Cutibacterium acnes is a member of the normal human skin microbiome. However, it is also associated with skin disorders and persistent infections of orthopedic implants. Here, we announce complete genome sequences and methylomes of the C. acnes subsp. acnes strains DSM 1897T and DSM 16379 together with their active restriction-modification systems.
TOWARDS ESTABLISHING A MODERN BASELINE FOR PALEOPATHOLOGY: TRACE-PRODUCING PARASITES IN A BIVALVE HOST

Abstract One hundred one individuals of Protothaca staminea were live-collected from Argyle Lagoon (sand/mud substrate) and Argyle Creek (gravel/sand substrate), San Juan Island, Washington and examined for trace-producing parasite infestation. Eighty-six percent of individuals contained at least one parasite-induced trace. Trematode-induced pits and blisters were identified on 62% of individual clams. Spionid-induced mudblisters and u-shaped borings were identified on 50% and 29% of individuals, respectively. Trematode and spionid parasites were not selective between the left and right valve when infesting the host. Epifaunal clams from Argyle Creek were significantly smaller than their infaunal counterparts from Argyle Lagoon. This size discrepancy between environments may be related to the reduction of growth rates triggered by environmental stress or parasitism, increased susceptibility to durophagous predators, differences in hydrodynamics, or the comparison of different cohorts. Spionid mudblister-infested clams from Argyle Creek are significantly smaller than noninfested clams from the same environment. This suggests that substrate-induced epifaunality and parasite-induced shell weakening reduced the bivalves’ defenses against durophagous predators. These results suggest that parasites may negatively affect the survival of infested bivalves. The frequent occurrence of trematode and spionid trace-producing parasites in modern bivalve populations suggests that these traces are common in the fossil record, making the systems amenable to study in deep time.
Effects of Long-term Use of Polyphenols on the Absorption and Tissue Distribution of Orally Administered Metformin and Atenolol in Rats

Aim: To evaluate the effect of long-term use of silibinin, epigallocatechin (ECGC), quercetin and rutin on the absorption and tissue distribution of metformin and atenolol. Materials and Methods: Thirty male rats were used, allocated into 5 groups and treated as follow: 1st group treated with olive oil and served as control; the other 4 groups were treated with either silibinin, EPGC, quercetin or rutin, administered orally as oily solutions for 30 days. At day 30, a 300mg/kg metformin and 50mg/kg atenolol were administered orally; 3.0 hrs later, the animals were sacrificed and blood samples, tissues of brain, kidney and liver were obtained for evaluation of the drugs level. Results: The polyphenols increased both serum and tissue levels of metformin compared with controls. This effect was relatively varied according to the structural differences among flavonoids. Conclusion: Long-term use of supraphysiological doses of flavonoids increase absorption of Zn, Cu and Fe and their tissue availability in brain, kidney and liver; this effect seems to be different with variations in structural features.
A New Euharamiyidan Mammaliaform from the Lower Cretaceous of Yakutia, Russia

Euharamiyida represent [Euharamiyida plural] a clade of Mesozoic mammaliaforms with gliriform-like dentition and a dental formula of 1–2.0. 2.2/1.0. 1.2. By having a high triangular last premolar, on.
Impact of Meteorological factors and population size on the transmission of Micro-size respiratory droplets based Coronavirus: A brief study of highly infected cities in Pakistan

Ongoing Coronavirus epidemic (COVID-19) identified first in Wuhan, China posed huge impact on public health and economy around the globe. Both cough and sneeze based droplets or aerosols encapsulated COVID-19 particles are responsible for air borne transmission of this virus and caused unexpected escalation and high mortality worldwide. Current study intends to investigate correlation of COVID-19 epidemic with meteorological parameters particularly, temperature, rainfall, humidity, and wind speed along with population size. Data set of COVID-19 for highly infected cities of Pakistan was collected from the official website of National Institute of health (NIH). Spearman rank (rs) correlation coefficient test employed for data analysis revealed significant correlation between temperature minimum (TM), temperature average (TA), wind speed (WS) and population size (PS) with COVID-19 pandemic. Furthermore, receiver operating characteristics (ROC) curve was used to analyze the sensitivity of TA, WS, and PS on transmission rate of COVID-19 in selected cities of Pakistan. The results obtained for sensitivity and specificity analysis for all selected parameters signifies sensitivity and direct correlation of COVID-19 transmission with temperature variation, WS and PS. Positive correlation and strong association of PS parameter with COVID-19 pandemic suggested need of more strict actions and control measures for highly populated cities. These findings will be helpful for health regulatory authorities and policymakers to take specific measures to combat COVID-19 epidemic in Pakistan.
The Role of an IL-10/Hyaluronan Axis in Dermal Wound Healing

Scar formation is the typical endpoint of postnatal dermal wound healing, which affects more than 100 million individuals annually. Not only do scars cause a functional burden by reducing the biomechanical strength of skin at the site of injury, but they also significantly increase healthcare costs and impose psychosocial challenges. Though the mechanisms that dictate how dermal wounds heal are still not completely understood, they are regulated by extracellular matrix (ECM) remodeling, neovascularization, and inflammatory responses. The cytokine interleukin (IL)-10 has emerged as a key mediator of the pro- to anti-inflammatory transition that counters collagen deposition in scarring. In parallel, the high molecular weight (HMW) glycosaminoglycan hyaluronan (HA) is present in the ECM and acts in concert with IL-10 to block pro-inflammatory signals and attenuate fibrotic responses. Notably, high concentrations of both IL-10 and HMW HA are produced in early gestational fetal skin, which heals scarlessly. Since fibroblasts are responsible for collagen deposition, it is critical to determine how the concerted actions of IL-10 and HA drive their function to potentially control fibrogenesis. Beyond their independent actions, an auto-regulatory IL-10/HA axis may exist to modulate the magnitude of CD4+ effector T lymphocyte activation and enhance T regulatory cell function in order to reduce scarring. This review underscores the pathophysiological impact of the IL-10/HA axis as a multifaceted molecular mechanism to direct primary cell responders and regulators toward either regenerative dermal tissue repair or scarring.
CFTR Depletion Confers Hypersusceptibility to Mycobacterium fortuitum in a Zebrafish Model

The Mycobacterium fortuitum complex comprises several closely related species, causing pulmonary and extra-pulmonary infections. However, there is very limited knowledge about the disease pathogenesis involved in M. fortuitum infections, particularly due to the lack of suitable animal models. Using the zebrafish model, we show that embryos are susceptible to M. fortuitum infection in a dose-dependent manner. Furthermore, zebrafish embryos form granulomas from as early as 2 days post-infection, recapitulating critical aspects of mycobacterial pathogenesis observed in other pathogenic species. The formation of extracellular cords in infected embryos highlights a previously unknown pathogenic feature of M. fortuitum. The formation of large corded structures occurs also during in vitro growth, suggesting that this is not a host-adapted stress mechanism deployed during infection. Moreover, transient macrophage depletion led to rapid embryo death with increased extracellular cords, indicating that macrophages are essential determinants of M. fortuitum infection control. Importantly, morpholino depletion of the cystic fibrosis transmembrane conductance regulator (cftr) significantly increased embryo death, bacterial burden, bacterial cords and abscesses. There was a noticeable decrease in the number of cftr-deficient infected embryos with granulomas as compared to infected controls, suggesting that loss of CFTR leads to impaired host immune responses and confers hypersusceptiblity to M. fortuitum infection. Overall, these findings highlight the application of the zebrafish embryo to study M. fortuitum and emphasizes previously unexplored aspects of disease pathogenesis of this significant mycobacterial species.
Physical Exercise Exacerbates Acute Kidney Injury Induced by LPS via Toll-Like Receptor 4

Introduction: Lipopolysaccharide (LPS) is a systemic response-triggering endotoxin, which has the kidney as one of its first targets, thus causing acute injuries to this organ. Physical exercise is capable of promoting physiological alterations and modulating inflammatory responses in the infectious process through multiple parameters, including the toll-like receptor (TLR)-4 pathway, which is the main LPS signaling in sepsis. Additionally, previous studies have shown that physical exercise can be both a protector factor and an aggravating factor for some kidney diseases. This study aims at analyzing whether physical exercise before the induction of LPS endotoxemia can protect kidneys from acute kidney injury. Methods: C57BL/6J male mice, 12 weeks old, were distributed into four groups: (1) sedentary (control, N = 7); (2) sedentary + LPS (N = 7); (3) trained (N = 7); and (4) trained + LPS (N = 7). In the training groups, the animals exercised 5×/week in a treadmill, 60 min/day, for 4 weeks (60% of max. velocity). Sepsis was induced in the training group by the application of a single dose of LPS (5 mg/kg i.p.). Sedentary animals received LPS on the same day, and the non-LPS groups received a saline solution instead. All animals were euthanized 24 h after the administration of LPS or saline. Results: The groups receiving LPS presented a significant increase in serum urea (p < 0.0001) and creatinine (p < 0.001) concentration and renal gene expression of inflammatory markers, such as tumor necrosis factor alpha and interleukin-6, as well as TLRs. In addition, LPS promoted a decrease in reduced glutathione. Compared to the sedentary + LPS group, trained + LPS showed overexpression of a gene related to kidney injury (NGAL, p < 0.01) and the protein levels of LPS receptor TLR-4 (p < 0.01). Trained + LPS animals showed an expansion of the tubulointerstitial space in the kidney (p < 0.05) and a decrease in the gene expression of hepatic AOAH (p < 0.01), an enzyme involved in LPS clearance. Conclusion: In contrast to our hypothesis, training was unable to mitigate the renal inflammatory response caused by LPS. On the contrary, it seems to enhance injury by accentuating endotoxin-induced TLR-4 signaling. This effect could be partly due to the modulation of a hepatic enzyme that detoxifies LPS.
Virulence Phenotypes of Siberian Wheat Stem Rust Population in 2017–2018

Management of wheat stem rust in Western Siberia has gained importance since the first outbreaks in 2007–2010 and 2016. The race composition and virulence patterns were investigated for the enlarged Puccinia graminis f. sp. tritici (Pgt) samples collected in three neighboring regions Omsk, Novosibirsk, and Altai during 2017–2018. Most of Pgt isolates were identified as virulent to wheat lines with genes Sr5, Sr9a, Sr10, Sr38, SrMcN, and avirulent to Sr24, Sr31. Differentiation ability of genes Sr6, Sr7b, Sr8a, Sr9b, Sr9d, Sr9g, Sr9e, Sr11, Sr17, Sr21, Sr30, Sr36, and SrTmp to distinguish between the regional populations was established. A total of 33 virulence phenotypes or races were detected among 115 Pgt isolates tested. Based on virulence phenotypes, two different Pgt subpopulations were identified in the Altai and Omsk regions likely originating from asexual and sexual cycles, respectively. The Novosibirsk pathogen population seems to be a mixture of isolates originated from both neighboring regions with virulence phenotypes that developed in the west, Omsk (TKRPF, QHHSF, and MLLTF), and in the south, Altai (NFMSF, LKCSF, LKMSF, and PKCSF), of Western Siberia.