Miracle-dz/UniFAR-FTUs huggingface dataset:
CD44s Assembles Hyaluronan Coat on Filopodia and Extracellular Vesicles and Induces Tumorigenicity of MKN74 Gastric Carcinoma Cells

CD44 is a multifunctional adhesion molecule typically upregulated in malignant, inflamed and injured tissues. Due to its ability to bind multiple ligands present in the tumor microenvironment, it promotes multiple cellular functions related to tumorigenesis. Recent data has shown that CD44 and its principal ligand hyaluronan (HA) are carried by extracellular vesicles (EV) derived from stem and tumor cells, but the role of CD44 in EV shedding has not been studied so far. To answer this question, we utilized CD44-negative human gastric carcinoma cell line MKN74 manipulated to stably express CD44 standard form (CD44s). The effect of CD44s expression on HA metabolism, EV secretion, morphology and growth of these cells was studied. Interestingly, HAS2 and HYAL2 expression levels were significantly upregulated in CD44s-expressing cells. Cell-associated HA levels were significantly increased, while HA levels in the culture medium of CD44s-positive cells was lower compared to CD44s-negative MOCK cells. CD44s expression had no significant effect on the proliferation capacity of cells, but cells showed diminished contact inhibition. Superresolution imaging revealed that CD44s and HA were accumulated on filopodia and EVs secreted from CD44s-positive cells, but no differences in total numbers of secreted EV between CD44s-negative and -positive cells was detected. In 3D cultures, CD44s-expressing cells had an enhanced invasion capacity in BME gel and increased spheroidal growth when cultured in collagen I gel. No significant differences in mitotic activity, tumor size or morphology were detected in CAM assays. However, a significant increase in HA staining coverage was detected in CD44s-positive tumors. Interestingly, CD44s-positive EVs embedded in HA-rich matrix were detected in the stromal areas of tumors. The results indicate that CD44s expression significantly increases the HA binding capacity of gastric cancer cells, while the secreted HA is downregulated. CD44s is also carried by EVs secreted by CD44s-expressing cells. These findings highlight the potential usefulness of CD44s and its ligands as multipurpose EV biomarkers, because they are upregulated in inflammatory, injured, and cancer cells and accumulate on the surface of EVs secreted in these situations.
Electronic Children’s Books: Promises Not Yet Fulfilled

The infant-toddler period is increasingly recognized as crucial for early brain and child development and school readiness.1 Parents can support cognitive, language, and social-emotional development during this period through positive parenting activities, such as reading aloud and playing together. Although parents are inundated with information suggesting that new technology can enhance or even replace books to enhance child development, little is known about whether this is true, especially in early childhood. In this issue of Pediatrics , Munzer et al2 have sought to narrow the data gap by studying interactions that take place when parents and children engage using electronic children’s books. Ideally, electronic books could increase access to a range of children’s literature through adaptation to ubiquitous digital platforms, such as tablets and electronic readers, and by offering books in multiple languages. They could make developmentally and culturally appropriate reading materials easily accessible at low cost to low-income families in the United States and globally. However, it could also be that tablet-based interfaces are less effective at supporting beneficial interactions than reading print books, especially … Address correspondence to Suzy Tomopoulos, MD, Department of Pediatrics, NYU School of Medicine550 First Ave, New York, NY 10016. E-mail: tomops01{at}nyulangone.org
Effects of Different Dietary Calcium Levels on the Performance, Egg Quality, and Albumen Transparency of Laying Pigeons

Simple Summary The transparency of pigeon egg albumen is a special phenotypic trait that different from other poultry eggs, and calcium is one of the main factors. This experiment aimed to study the effects of added dietary Ca on production performance, egg quality, and albumen transparency. It will guide producers on how to feed their laying pigeons and provide a scientific basis for special feed research and the development of laying pigeons with transparent eggs. Abstract In order to confirm the dietary calcium (Ca) requirement to keep a balance of the production performance and the albumen transparency, the study examined the effects of different dietary Ca levels on the production performance, egg quality, and albumen transparency of laying pigeons. 1080 pigeon pairs were randomly allocated into six treatment groups, each consisting of six replicates of 30 pigeon pairs per treatment. Ca levels of 0.60, 0.90, 1.20, 1.80, 2.40, and 3.00% were fed. The results showed that the laying rate, average egg weight, and feed to egg ratio were significantly influenced by Ca levels (p < 0.05). Albumen percentage, albumen height, Haugh unit, and eggshell thickness at 8 w and 16 w were significantly influenced by Ca levels (p < 0.05). The L*, a*, b*, and c* values of cooked albumen at 8 w and 16 w were all significantly influenced by Ca levels (p < 0.05). After 16 w of feeding different Ca levels, the percentage of transparent eggs had an early increasing and later decreasing trend. In conclusion, taking the transparency of pigeon eggs as an assessment index and considering production performance secondly, the optimal level of dietary Ca for laying White King pigeons is 0.90%.
Dynamic response reconstruction for structural health monitoring using densely connected convolutional networks

This article proposes a novel dynamic response reconstruction approach for structural health monitoring using densely connected convolutional networks. Skip connection and dense block techniques are carefully applied in the designed network architecture, which greatly facilitates the information flow, and increases the training efficiency and accuracy of feature extraction and propagation with fewer parameters in the network. Sub-pixel shuffling and dropout techniques are used in the designed network and applied to reduce the computational demand and improve training efficiency. The network is trained in a supervised manner, where the input and output are the measurements of the available channels at response available locations and desired channels at response unavailable locations. The proposed densely connected convolutional networks automatically extract the high-level features of the input data and construct the complicated nonlinear relationship between the responses of available and desired locations. Experimental studies are conducted using the measured acceleration responses from Guangzhou New Television Tower to investigate the effects of the locations of available responses, the numbers of available and unavailable channels, and measurement noise. The results demonstrate that the proposed approach can accurately reconstruct the responses in both time and frequency domains with strong noise immunity. The reconstructed response is further used for modal identification to demonstrate the usability and accuracy of the reconstructed responses. The applicability of the proposed approach for structural health monitoring is further proved by the highly consistent modal parameters identified from the reconstructed and true responses.
Anti-allodynic effects of the selective NaV1.7 inhibitor Pn3a in a mouse model of acute post-surgical pain: evidence for analgesic synergy with opioids and baclofen.

Pain is the leading cause of disability in the developed world but remains a poorly treated condition. Specifically, post-surgical pain continues to be a frequent and undermanaged condition. Here, we investigate the analgesic potential of pharmacological NaV1.7 inhibition in a mouse model of acute post-surgical pain, based on incision of the plantar skin and underlying muscle of the hind paw. We demonstrate that local and systemic treatment with the selective NaV1.7 inhibitor μ-theraphotoxin-Pn3a is effectively anti-allodynic in this model and completely reverses mechanical hypersensitivity in the absence of motor adverse effects. In addition, the selective NaV1.7 inhibitors ProTx-II and PF-04856264 as well as the clinical candidate CNV1014802 also reduced mechanical allodynia. Interestingly, co-administration of the opioid receptor antagonist naloxone completely reversed analgesic effects of Pn3a, indicating an involvement of endogenous opioids in the analgesic activity of Pn3a. Additionally, we found super-additive antinociceptive effects of sub-therapeutic Pn3a doses not only with the opioid oxycodone but also with the GABAB receptor agonist baclofen. Transcriptomic analysis of gene expression changes in dorsal root ganglia of mice post-surgery did not reveal any changes in mRNA expression of endogenous opioids or opioid receptors, however several genes involved in pain, including Runx1 (Runt related transcription factor 1), Cacna1a (CaV2.1) and Cacna1b (CaV2.2) were downregulated. In summary, these findings suggest that pain after surgery can be successfully treated with NaV1.7 inhibitors alone or in combination with baclofen or opioids, which may present a novel and safe treatment strategy for this frequent and poorly managed condition.
Aloe vera (L.) Burm. F. as a Potential Anti-COVID-19 Plant: A Mini-review of Its Antiviral Activity

Aims: A novel β-coronavirus (2019-nCoV) has become a pandemic affecting hundreds of thousands of people worldwide. Since there is no effective treatment, the need of finding alternative methods which can help to curb this pandemic is urgent. This study aims to review the literature on the virucidal and cytotoxic properties of Aloe vera, one of the most studied plants considered as a nutraceutical in order to propose it as an alternative solution against COVID-19. Methodology: The literature review was based mainly on the COVID-19 resources that have been made freely available to the scientific community but also on the usual databases such as Pubmed and Google scholar. Mini-review Article Mpiana et al.; EJMP, 31(8): 86-93, 2020; Article no.EJMP. 56842 87 Results: The literature review shows that the plant has antiviral activity on several types of virus (Haemorrhagic Viral Rhobdavirus Septicaemia, Herpes simplex virus type 1, Herpes simplex virus type 2, Varicella-Zoster virus, human immunodeficiency virus, Influenza virus, poliovirus, Cytomegalovirus, Human papillomavirus) including coronavirus SARS-CoV-1. The plant is consumed orally in several forms and is safe. It is possible that molecules of this plant that have already shown effectiveness on other viruses by some mechanisms such as interaction of virus enzyme, breakdown of the viral envelope etc. could participate in the action of the plant. Also, the presence of minerals such as Zinc, which have shown an effect on SARS-CoV-1, could be involved in the antiviral effect of Aloe vera. Conclusion: Molecular docking of the main molecules of Aloe vera with SARS-CoV-2 protease is in progress and clinical trials are necessary to confirm the activity of Aloe vera on COVID-19.
Lifetime cancer prevalence and life history traits in mammals

Abstract Background Cancer is a common diagnosis in many mammalian species, yet they vary in their vulnerability to cancer. The factors driving this variation are unknown, but life history theory offers potential explanations to why cancer defense mechanisms are not equal across species. Methodology Here we report the prevalence of neoplasia and malignancy in 37 mammalian species, representing 11 mammalian orders, using 42 years of well curated necropsy data from the San Diego Zoo and San Diego Zoo Safari Park. We collected data on life history components of these species and tested for associations between life history traits and both neoplasia and malignancy, while controlling for phylogenetic history. Results These results support Peto’s paradox, in that we find no association between lifespan and/or body mass and the prevalence of neoplasia or malignancy. However, a positive relationship exists between litter size and prevalence of malignancy (P = 0.005, Adj. R2 = 0.212), suggesting that a species’ life history strategy may influence cancer vulnerabilities. Lastly, we tested for the relationship between placental invasiveness and malignancy. We find no evidence for an association between placental depth and malignancy prevalence (P = 0.618, Adj. R2 = 0.068). Conclusions Life history theory offers a powerful framework to understand variation in cancer defenses across the tree of life. These findings provide insight into the relationship between life history traits and cancer vulnerabilities, which suggest a trade-off between reproduction and cancer defenses. Lay summary Why are some mammals more vulnerable to cancer than others? We test whether life history trade-offs may explain this variation in cancer risk. Bigger, longer-lived animals do not develop more cancer compared to smaller, shorter-lived animals. However, we find a positive association between litter size and cancer prevalence in mammals.
Diagnosis of Lymphoma Using Fine-Needle Aspiration Biopsy and Core-Needle Biopsy: A Single-Institution Experience

Objective: The objective is to study the efficacy of fine-needle aspiration biopsy (FNAB) and core-needle biopsy (CNB) in the diagnosis of lymphoma in a single institution. Study Design: We retrospectively reviewed 635 FNAB/CNB cases performed in our institution to rule out lymphoma during a 4-year period and collected the relevant clinical and pathological information for statistical analysis. Results and Conclusions: This cohort comprised 275 males and 360 females, with a median age of 57 years. Among the 593 cases with adequate diagnostic materials for lymphoma work-up, 226 were positive for lymphoma, 286 were negative for lymphoma, and 81 were nondiagnostic. Each case had an FNAB, and 191 cases also underwent a CNB. The subclassification rate according to the WHO (2008) was 67% overall, 81% for the FNAB with CNB group, and 40% for the FNAB group. In the FNAB with CNB group, the subclassification rates for cases with and without a history of lymphoma were not significantly different. A definitive diagnosis of lymphoma relied on ancillary studies, but was not affected by location, or the needle gauge of CNB. Follow-up data revealed a high diagnostic accuracy of FNAB with CNB. In conclusion, the use of FNAB and CNB with ancillary studies is effective in providing a definitive diagnosis of lymphoma in our experience at the Northwell Health System.
The value of combined hemodynamic, respiratory and intra-abdominal pressure monitoring in predicting acute kidney injury after major intraabdominal surgeries

Abstract Background: The incidence of postoperative acute kidney injury (AKI) is predominantly determined by renal hemodynamics. Beside arterial blood pressure, the role of factors causing a deterioration of venous congestion (intraabdominal pressure, central venous pressure, mechanical ventilation) has emerged. The value of combined hemodynamic, respiratory and intra-abdominal pressure (IAP) monitoring in predicting postoperative acute kidney injury has received only limited exploration to date. Methods: Data were collected for adult patients admitted after major abdominal surgery at nine Hungarian ICUs. Hemodynamic parameters were compared in AKI vs. no-AKI patients at the time of admission and 48 h thereafter. Regarding ventilatory support, we tested mean airway pressures (Pmean). Effective renal perfusion pressure (RPP) was calculated as MAP−(IAP + CVP + Pmean). The Mann–Whitney U and the chi-square tests were carried out for statistical analysis with forward stepwise logistic regression for AKI as a dependent outcome. Results: A total of 84 patients (34 ventilated) were enrolled in our multicenter observational study. The median values of MAP were above 70 mmHg, IAP not higher than 12 mmHg and CVP not higher than 8 mmHg at all time-points. When we combined those parameters, even those belonging to the ‘normal’ range with Pmean, we found significant differences between no-AKI and AKI groups only at 12 h after ICU admission (median and IQR: 57 (42–64) vs. 40 (36–52); p < . 05). Below it’s median (40.7 mmHg) on admission, AKI developed in all patients. If above 40.7 mmHg on admission, they were protected against AKI, but only if it did not decrease within the first 12 h. Conclusions: Calculated effective RPP with the novel formula MAP−(IAP + CVP + Pmean) may predict the onset of AKI in the surgical ICU with a great sensitivity and specificity. Maintaining effective RPP appears important not only at ICU admission but during the next 12 h, as well. Additional, larger studies are needed to explore therapeutic interventions targeting this parameter.
Electrostatics of Tau Protein by Molecular Dynamics

Tau is a microtubule-associated protein that promotes microtubule assembly and stability. This protein is implicated in several neurodegenerative diseases, including Alzheimer’s. To date, the three-dimensional (3D) structure of tau has not been fully solved, experimentally. Even the most recent information is sometimes controversial in regard to how this protein folds, interacts, and behaves. Predicting the tau structure and its profile sheds light on the knowledge about its properties and biological function, such as the binding to microtubules (MT) and, for instance, the effect on ionic conductivity. Our findings on the tau structure suggest a disordered protein, with discrete portions of well-defined secondary structure, mostly at the microtubule binding region. In addition, the first molecular dynamics simulation of full-length tau along with an MT section was performed, unveiling tau structure when associated with MT and interaction sites. Electrostatics and conductivity were also examined to understand how tau affects the ions in the intracellular fluid environment. Our results bring a new insight into tau and tubulin MT proteins, their characteristics, and the structure–function relationship.
Diversified crop rotation and management system influence durum yield and quality

Diversified crop rotation, sequence of crops within a rotation, and management system may affect durum (Triticum turgidum L.) yield and quality. This study investigated the impact of stacked vs. alternate‐year rotation and conventional vs. ecological management system on dryland durum growth, yield, quality, and N relations from 2008 to 2011 in the northern Great Plains. Stacked rotations were durum–durum–canola (Brassica napus L.)–pea (Pisum sativum L.) (DDCP) and durum–durum–flax (Linum usitatissimum L.)–pea (DDFP). Alternate‐year rotations were durum–canola–durum–pea (DCDP) and durum–flax–durum–pea (DFDP). Continuous durum (CD) was also included for comparison. Conventional management included the combination of tillage, recommended seed rate, broadcast N fertilization, and reduced stubble height; ecological management included no‐tillage, increased seed rate, banded N fertilization, and greater stubble height. Durum height was 4–7 cm taller in the ecological than the conventional management with DCDP, DDCP, and DFDP. Plant height, spike number, grain yield, aboveground biomass, N accumulation, N removal index, and N‐use efficiency were 8–46% greater in the ecological than the conventional management in wet years, but were 15–26% greater in the conventional management in dry years. Plant height, spike number, aboveground biomass, and seed weight varied with crop rotations and years. The ecological management improved durum growth, yield, and N relations in wet years, but the conventional management was superior in dry year. Producers can enhance dryland durum yield and quality by using the ecological management, especially in wet years, rather than relying on crop rotations. Disciplines Agricultural Science | Agriculture Comments This article is published as Lenssen, Andrew W. , Upendra M. Sainju, Brett L. Allen, William B. Stevens, and Jalal D. Jabro. "Diversified crop rotation and management system influence durum yield and quality. " Agronomy Journal 112 (2020): 4407-4419. doi: 10.1002/agj2.20311. This article is available at Iowa State University Digital Repository: https://lib.dr.iastate.edu/agron_pubs/660 Received: 26 February 2020 Accepted: 20 May 2020 Published online: 24 June 2020 DOI: 10.1002/agj2.20311
Allele frequency analysis of variants reported to cause autosomal dominant inherited retinal diseases question the involvement of 19% of genes and 10% of reported pathogenic variants

Background Next generation sequencing (NGS) generates a large amount of genetic data that can be used to better characterise disease-causing variants. Our aim was to examine allele frequencies of sequence variants reported to cause autosomal dominant inherited retinal diseases (AD-IRDs). Methods Genetic information was collected from various databases, including PubMed, the Human Genome Mutation Database, RETNET and gnomAD. Results We generated a database of 1223 variants reported in 58 genes, including their allele frequency in gnomAD that contains NGS data of over 138 000 individuals. While the majority of variants are not represented in gnomAD, 138 had an allele count of >1 and were examined carefully for various aspects including cosegregation and functional analyses. The analysis revealed 122 variants that were reported pathogenic but unlikely to cause AD-IRDs. Interestingly, in some cases, these unlikely pathogenic variants were the only ones reported to cause disease in AD inheritance pattern for a particular gene, therefore raising doubt regarding the involvement of 11 (19%) of the genes in AD-IRDs. Conclusion We predict that these data are not limited to a specific disease or inheritance pattern since non-pathogenic variants were mistakenly reported as pathogenic in various diseases. Our results should serve as a warning sign for geneticists, variant database curators and sequencing panels’ developers not to automatically accept reported variants as pathogenic but cross-reference the information with large databases.
CRISPR‐LbCas12a‐mediated modification of citrus

Summary Recently, CRISPR‐Cas12a (Cpf1) from Prevotella and Francisella was engineered to modify plant genomes. In this report, we employed CRISPR‐LbCas12a (LbCpf1), which is derived from Lachnospiraceae bacterium ND2006, to edit a citrus genome for the first time. First, LbCas12a was used to modify the CsPDS gene successfully in Duncan grapefruit via Xcc‐facilitated agroinfiltration. Next, LbCas12a driven by either the 35S or Yao promoter was used to edit the PthA4 effector binding elements in the promoter (EBEP thA4‐CsLOBP) of CsLOB1. A single crRNA was selected to target a conserved region of both Type I and Type II CsLOBPs, since the protospacer adjacent motif of LbCas12a (TTTV) allows crRNA to act on the conserved region of these two types of CsLOBP. CsLOB1 is the canker susceptibility gene, and it is induced by the corresponding pathogenicity factor PthA4 in Xanthomonas citri by binding to EBEP thA4‐CsLOBP. A total of seven 35S‐LbCas12a‐transformed Duncan plants were generated, and they were designated as #D35s1 to #D35s7, and ten Yao‐LbCas12a‐transformed Duncan plants were created and designated as #Dyao1 to #Dyao10. LbCas12a‐directed EBEP thA4‐CsLOBP modifications were observed in three 35S‐LbCas12a‐transformed Duncan plants (#D35s1, #D35s4 and #D35s7). However, no LbCas12a‐mediated indels were observed in the Yao‐LbCas12a‐transformed plants. Notably, transgenic line #D35s4, which contains the highest mutation rate, alleviates XccΔpthA4:dCsLOB1.4 infection. Finally, no potential off‐targets were observed. Therefore, CRISPR‐LbCas12a can readily be used as a powerful tool for citrus genome editing.