Miracle-dz/UniFAR-FTUs huggingface dataset:
Extracorporeal carbon dioxide removal requirements for ultraprotective mechanical ventilation: Mathematical model predictions

Abstract Extracorporeal carbon dioxide (CO2) removal (ECCO2R) facilitates the use of low tidal volumes during protective or ultraprotective mechanical ventilation when managing patients with acute respiratory distress syndrome (ARDS); however, the rate of ECCO2R required to avoid hypercapnia remains unclear. We calculated ECCO2R rate requirements to maintain arterial partial pressure of CO2 (PaCO2) at clinically desirable levels in mechanically ventilated ARDS patients using a six‐compartment mathematical model of CO2 and oxygen (O2) biochemistry and whole‐body transport with the inclusion of an ECCO2R device for extracorporeal veno‐venous removal of CO2. The model assumes steady state conditions. Model compartments were lung capillary blood, arterial blood, venous blood, post‐ECCO2R venous blood, interstitial fluid and tissue cells, with CO2 and O2 distribution within each compartment; biochemistry included equilibrium among bicarbonate and non‐bicarbonate buffers and CO2 and O2 binding to hemoglobin to elucidate Bohr and Haldane effects. O2 consumption and CO2 production rates were assumed proportional to predicted body weight (PBW) and adjusted to achieve reported arterial partial pressure of O2 and a PaCO2 level of 46 mmHg at a tidal volume of 7.6 mL/kg PBW in the absence of an ECCO2R device based on average data from LUNG SAFE. Model calculations showed that ECCO2R rates required to achieve mild permissive hypercapnia (PaCO2 of 46 mmHg) at a ventilation frequency or respiratory rate of 20.8/min during mechanical ventilation increased when tidal volumes decreased from 7.6 to 3 mL/kg PBW. Higher ECCO2R rates were required to achieve normocapnia (PaCO2 of 40 mmHg). Model calculations also showed that required ECCO2R rates were lower when ventilation frequencies were increased from 20.8/min to 26/min. The current mathematical model predicts that ECCO2R rates resulting in clinically desirable PaCO2 levels at tidal volumes of 5‐6 mL/kg PBW can likely be achieved in mechanically ventilated ARDS patients with current technologies; use of ultraprotective tidal volumes (3‐4 mL/kg PBW) may be challenging unless high mechanical ventilation frequencies are used.
MiSet RFC Standards: Defining a Universal Minimum Set of Standards Required for Reproducibility and Rigor in Research Flow Cytometry Experiments

Poor adherence to best practices, insufficient training, and pressure to produce data quickly may lead to publications of suboptimal biomedical research flow cytometry data, which contributes to the body of irreproducible research findings. In addition, documentation of compliance with best flow cytometry practices for submission, visualization, and publication of flow cytometry data is currently endorsed by very few scientific journals, which is particularly concerning as numerous peer‐reviewed flow cytometry publications emphasize instrumentation, experimental design, and data analysis as important sources of variability. Guidelines and resources for adequate reporting, annotation and deposition of flow cytometry experiments are provided by MIFlowCyt and the FlowRepository database, and comprehensive expert recommendations covering principles and techniques of field‐specific flow cytometry applications have been published. To facilitate the integration of quality‐defining parameters into manuscript and grant submission and publication requirements across biomedical fields that rely on the use of flow‐cytometry‐based techniques, a single comprehensive yet easily and universally applicable document is needed. To produce such a list of gold‐standard parameters that assess whether a research flow cytometry experiment has been planned, conducted, interpreted, and reported at the highest standard, a new initiative defining the minimum set of standards a robust and rigorous research flow experiment must fulfill (MiSet RFC Standards) was proposed at CYTO 2019. MiSet RFC Standards will integrate and simplify existing resources to provide a universal benchmark a flow cytometry experiment can easily be measured against. The goal of MiSET RFC Standards is its integration into peer‐review and publication procedures through partnership with stakeholders, journals and publishers in biomedical and translational research. This article introduces the aims and anticipated timeline and discusses strategies for interdisciplinary consensus and implementation. A single‐resource broadly applicable guideline will harmonize standards across different fields of biomedical research and lead to publication of more robust research findings. © 2019 International Society for Advancement of Cytometry
Pulsed Electromagnetic Field Modulates Tendon Cells Response in IL‐1β‐Conditioned Environment

Strategies aiming at controlling and modulating inflammatory cues may offer therapeutic solutions for improving tendon regeneration. This study aims to investigate the modulatory effect of pulsed electromagnetic field (PEMF) on the inflammatory profile of human tendon‐derived cells (hTDCs) after supplementation with interleukin‐1β (IL‐1β). IL‐1β was used to artificially induce inflammatory cues associated with injured tendon environments. The PEMF effect was investigated varying the frequency (5 or 17 Hz), intensity (1.5, 4, or 5 mT), and duty‐cycle (10% or 50%) parameters to which IL‐1β‐treated hTDCs were exposed to. A PEMF actuation with 4 mT, 5 Hz and a 50% duty cycle decreased the production of IL‐6 and tumor necrosis factor‐α (TNF‐α), as well as the expression of TNFα, IL‐6, IL‐8, COX‐2, MMP‐1, MMP‐2, and MMP‐3, while IL‐4, IL‐10, and TIMP‐1 expression increased. These results suggest that PEMF stimulation can modulate hTDCs response in an inflammatory environment holding therapeutic potential for tendon regenerative strategies. © 2019 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 38:160–172, 2020
Prior Exposure to Dry-Cured Meat Promotes Resistance to Simulated Gastric Fluid in Salmonella Typhimurium

This study assessed if exposure of foodborne Salmonella enterica in Brazilian dry-cured loin (BDL) affects pathogen inactivation in simulated gastric fluid (SGF). The acid tolerance responses of three Salmonella enterica serovars, Typhimurium, Derby and Panama, were assessed by an acid challenge trial at pH 3.0 for 4 h following pre-adaptation to three conditions: neutral pH, acidic pH (4.5) or BDL matrix. The influence of Salmonella exposure temperature and time in the BDL on pathogen gastric fluid resistance was evaluated by the response surface methodology. The Salmonella serovars acquired acid tolerance when exposed to the BDL matrix and their response to acid stress was strain-dependent, with S. Typhimurium being the most tolerant strain. S. Typhimuirum exposed to temperatures >25 °C in the BDL matrix displayed increased resistance to SGF. By using the response surface methodology, it was determined that S. Typhimurium becomes less resistant against SGF if maintained in the BDL matrix at temperatures <7 °C, reinforcing the recommendation to store dry-cured meat under refrigeration in order to minimize consumer risks. The results presented herein point to a novel aspect of hurdle technology that should be taken into account to further understand the risks associated with hurdle-stable meat product, such as dry-cured meats, concerning foodborne pathogen contamination.
Letter to the Editor

Biostatistics for Animal Science 2004. By M. Kaps and W. Lamberson. ISBN 0-85199-820-8. Pp 445+13. Wallingford, UK: CABI Publishing. £35:00 (Paperback). www.cabi-publishing.org The target audience for this comprehensive book on statistical methodology is ‘students and researchers of animal sciences’ with a brief to help them ‘learn about and apply appropriate experimental design and statistical methods’. The presentation starts from the very basic level of graphical presentation of data (pie charts and histograms) and calculation of summary descriptive statistics, and concludes with a brief introduction to logistic and log-linear models. On the way the reader will have learnt about probability distributions, hypothesis testing and maximum likelihood estimation through simple linear and multiple regression to non-linear regression methods, a tour of analysis of variance and many different fundamental experimental designs (randomized block, factorial, nested, change-over, Latin square and split-plot) with diversions to the analysis of covariance and repeated measures analysis. Important issues such as sample size determination and power calculation, residual analysis and tests for interactions are not overlooked, though little advice is provided on what to do if these indicate problems. Each topic is introduced by the description of a practical situation and resulting problem to be solved where the technique would be called for. Most are illustrated with analysis of numerical examples using SAS and the output from the program is explained in detail in each case. Some exercises are included, primarily to be performed using SAS. For the benefit of the mathematically inclined reader the full algebraic formulae are given for all the partitions of the sums of squares required to analyse results from the designed experiments. Appendices give basic statistical tables of critical values of the normal, t, F, chi-squared and (less common) the studentized Letter to the Editor
The Relationship between Uterine, Fecal, Bedding, and Airborne Dust Microbiota from Dairy Cows and Their Environment: A Pilot Study

Simple Summary After calving, dairy cows face the risk of negative energy balance, inflammation, and immunosuppression, which may result in bacterial infection and disruption of the normal microbiota, thus encouraging the development of metritis and endometritis. This study characterized uterine, fecal, bedding, and airborne dust microbiota from postpartum dairy cows and their environment during summer and winter. The results clarify the importance of microbiota in cowshed environments, i.e., bedding and airborne dust, in understanding the postpartum uterine microbiota of dairy cows. Abstract The aim of this study was to characterize uterine, fecal, bedding, and airborne dust microbiota from postpartum dairy cows and their environment. The cows were managed by the free-stall housing system, and samples for microbiota and serum metabolite assessment were collected during summer and winter when the cows were at one and two months postpartum. Uterine microbiota varied between seasons; the five most prevalent taxa were Enterobacteriaceae, Moraxellaceae, Ruminococcaceae, Staphylococcaceae, and Lactobacillaceae during summer, and Ruminococcaceae, Lachnospiraceae, Bacteroidaceae, Moraxellaceae, and Clostridiaceae during winter. Although Actinomycetaceae and Mycoplasmataceae were detected at high abundance in several uterine samples, the relationship between the uterine microbiota and serum metabolite concentrations was unclear. The fecal microbiota was stable regardless of the season, whereas bedding and airborne dust microbiota varied between summer and winter. With regards to uterine, bedding, and airborne dust microbiota, Enterobacteriaceae, Moraxellaceae, Staphylococcaceae, and Lactobacillaceae were more abundant during summer, and Ruminococcaceae, Lachnospiraceae, Bacteroidaceae, and Clostridiaceae were more abundant during winter. Canonical analysis of principal coordinates confirmed the relationship between uterine and cowshed microbiota. These results indicated that the uterine microbiota may vary when the microbiota in cowshed environments changes.
A New Model of RGB-D Camera Calibration Based on 3D Control Field

With extensive application of RGB-D cameras in robotics, computer vision, and many other fields, accurate calibration becomes more and more critical to the sensors. However, most existing models for calibrating depth and the relative pose between a depth camera and an RGB camera are not universally applicable to many different kinds of RGB-D cameras. In this paper, by using the collinear equation and space resection of photogrammetry, we present a new model to correct the depth and calibrate the relative pose between depth and RGB cameras based on a 3D control field. We establish a rigorous relationship model between the two cameras; then, we optimize the relative parameters of two cameras by least-squares iteration. For depth correction, based on the extrinsic parameters related to object space, the reference depths are calculated by using a collinear equation. Then, we calibrate the depth measurements with consideration of the distortion of pixels in depth images. We apply Kinect-2 to verify the calibration parameters by registering depth and color images. We test the effect of depth correction based on 3D reconstruction. Compared to the registration results from a state-of-the-art calibration model, the registration results obtained with our calibration parameters improve dramatically. Likewise, the performances of 3D reconstruction demonstrate obvious improvements after depth correction.
Astaxanthin Inhibits Mitochondrial Permeability Transition Pore Opening in Rat Heart Mitochondria

The mitochondrion is the main organelle of oxidative stress in cells. Increased permeability of the inner mitochondrial membrane is a key phenomenon in cell death. Changes in membrane permeability result from the opening of the mitochondrial permeability transition pore (mPTP), a large-conductance channel that forms after the overload of mitochondria with Ca2+ or in response to oxidative stress. The ketocarotenoid astaxanthin (AST) is a potent antioxidant that is capable of maintaining the integrity of mitochondria by preventing oxidative stress. In the present work, the effect of AST on the functioning of mPTP was studied. It was found that AST was able to inhibit the opening of mPTP, slowing down the swelling of mitochondria by both direct addition to mitochondria and administration. AST treatment changed the level of mPTP regulatory proteins in isolated rat heart mitochondria. Consequently, AST can protect mitochondria from changes in the induced permeability of the inner membrane. AST inhibited serine/threonine protein kinase B (Akt)/cAMP-responsive element-binding protein (CREB) signaling pathways in mitochondria, which led to the prevention of mPTP opening. Since AST improves the resistance of rat heart mitochondria to Ca2+-dependent stress, it can be assumed that after further studies, this antioxidant will be considered an effective tool for improving the functioning of the heart muscle in general under normal and medical conditions.
Dicentrine Potentiates TNF-α-Induced Apoptosis and Suppresses Invasion of A549 Lung Adenocarcinoma Cells via Modulation of NF-κB and AP-1 Activation

Numerous studies have indicated that tumor necrosis factor-alpha (TNF-α) could induce cancer cell survival and metastasis via activation of transcriptional activity of NF-κB and AP-1. Therefore, the inhibition of TNF-α-induced NF-κB and AP-1 activity has been considered in the search for drugs that could effectively treat cancer. Dicentrine, an aporphinic alkaloid, exerts anti-inflammatory and anticancer activities. Therefore, we investigated the effects of dicentrine on TNF-α-induced tumor progression in A549 lung adenocarcinoma cells. Our results demonstrated that dicentrine effectively sensitizes TNF-α-induced apoptosis in A549 cells when compared with dicentrine alone. In addition, dicentrine increases caspase-8, -9, -3, and poly (ADP-ribose) polymerase (PARP) activities by upregulating the death-inducing signaling complex and by inhibiting the expression of antiapoptotic proteins including cIAP2, cFLIP, and Bcl-XL. Furthermore, dicentrine inhibits the TNF-α-induced A549 cells invasion and migration. This inhibition is correlated with the suppression of invasive proteins in the presence of dicentrine. Moreover, dicentrine significantly blockes TNF-α-activated TAK1, p38, JNK, and Akt, leading to reduced levels of the transcriptional activity of NF-κB and AP-1. Taken together, our results suggest that dicentrine could enhance TNF-α-induced A549 cell death by inducing apoptosis and reducing cell invasion due to, at least in part, the suppression of TAK-1, MAPK, Akt, AP-1, and NF-κB signaling pathways.
Punishment insensitivity emerges from impaired contingency detection, not aversion insensitivity or reward dominance

Our behaviour is shaped by its consequences – we seek rewards and avoid harm. It has been reported that individuals vary markedly in their avoidance of detrimental consequences, i.e. in their sensitivity to punishment. The underpinnings of this variability are poorly understood; they may be driven by differences in aversion sensitivity, motivation for reward, and/or instrumental control. We examined these hypotheses by applying several analysis strategies to the behaviour of rats (n = 48; 18 female) trained in a task permitting concurrent assessment of punishment, reward-seeking, and Pavlovian fear. We show that punishment insensitivity is a unique phenotype, unrelated to differences in reward-seeking and Pavlovian fear, and due to a failure of instrumental control. Subjects insensitive to punishment are afraid of aversive events, they are simply unable to change their behaviour to avoid them.
RELATIONSHIP BETWEEN GIARDIASIS AND ALLERGY IN CHILDREN REFERRED TO THE ALLERGY CLINIC OF TEHRAN CHILDREN’S MEDICAL CENTER, 2003-2004

Background & Aim: Human giardiasis is an infection produced by the flagellate protozoan, giardia lamblia, that is localized to the small bowel where it produces damage to the mucosa with or without gastrointestinal symptoms. This parasitosis has a worldwide distribution. Its incidence varies from 15 to 30%. Current evidence suggests that both humoral and cellular immune responses are involved in providing immunity to this parasitic infection. A number of reports have described the existence of allergic symptoms in persons with giardiasis. Furthermore, elevated levels of serum IgE and eosinophilia have also occasionally been described in this infection. Due to the importance of this issue in children, it seems essential to evaluate the relationship between giardiasis and allergy so that we can help physicians with the diagnosis and treatment of these patients. Patients & Method: From January 2003 to December 2004, we evaluated a group of 125 children under 15 admitted to the Allergy Clinic of Children’s Medical Center as a case group and also a group of 125 children with no allergic signs admitted to the Internal Clinic of the same center as a control group. Both groups had already been matched when we performed three fecal examinations and measured their total serum IgE and eosinophilia. Results: We found out that 20(16%) out of 125 allergic children were infected with giardia lamblia. In addition, 16 of the children infected with G.lamblia showed significantly higher levels of total IgE. Conclusion: Like previous studies that showed a relationship between giardiasis and skin allergy the results of the present study revealed a relationship between giardiasis and the level of total IgE(P<0.05), which can account for a relationship between giardiasis and skin allergy(p<0.05). However, we didn’t see a clear relationship between giardiasis and peripheral blood eosinophilia(p>0.05).
A Unique Migration: South African Doctors Fleeing to Australia

• Who are the doctors who have left South Africa? • Why did they leave South Africa? • What work are they doing in Australia? • How qualified were they when they left? One can say that this book, based on a thorough scientific survey amongst 469 respondents, gives an overview of this atypical migration. It also shows that one needs to analyse the social backgrounds and life circumstances of those who migrated in order to understand their motives for doing so.
MicroRNAs Involved in Carcinogenesis, Prognosis, Therapeutic Resistance, and Applications in Human Triple-Negative Breast Cancer

Triple-negative breast cancer (TNBC) is the most aggressive, prevalent, and distinct subtype of breast cancer characterized by high recurrence rates and poor clinical prognosis, devoid of both predictive markers and potential therapeutic targets. MicroRNAs (miRNA/miR) are a family of small, endogenous, non-coding, single-stranded regulatory RNAs that bind to the 3′-untranslated region (3′-UTR) complementary sequences and downregulate the translation of target mRNAs as post-transcriptional regulators. Dysregulation miRNAs are involved in broad spectrum cellular processes of TNBC, exerting their function as oncogenes or tumor suppressors depending on their cellular target involved in tumor initiation, promotion, malignant conversion, and metastasis. In this review, we emphasize on masses of miRNAs that act as oncogenes or tumor suppressors involved in epithelial–mesenchymal transition (EMT), maintenance of stemness, tumor invasion and metastasis, cell proliferation, and apoptosis. We also discuss miRNAs as the targets or as the regulators of dysregulation epigenetic modulation in the carcinogenesis process of TNBC. Furthermore, we show that miRNAs used as potential classification, prognostic, chemotherapy and radiotherapy resistance markers in TNBC. Finally, we present the perspective on miRNA therapeutics with mimics or antagonists, and focus on the challenges of miRNA therapy. This study offers an insight into the role of miRNA in pathology progression of TNBC.
Phylostratigraphic Analysis Shows the Earliest Origination of the Abiotic Stress Associated Genes in A. thaliana

Plants constantly fight with stressful factors as high or low temperature, drought, soil salinity and flooding. Plants have evolved a set of stress response mechanisms, which involve physiological and biochemical changes that result in adaptive or morphological changes. At a molecular level, stress response in plants is performed by genetic networks, which also undergo changes in the process of evolution. The study of the network structure and evolution may highlight mechanisms of plants adaptation to adverse conditions, as well as their response to stresses and help in discovery and functional characterization of the stress-related genes. We performed an analysis of Arabidopsis thaliana genes associated with several types of abiotic stresses (heat, cold, water-related, light, osmotic, salt, and oxidative) at the network level using a phylostratigraphic approach. Our results show that a substantial fraction of genes associated with various types of abiotic stress is of ancient origin and evolves under strong purifying selection. The interaction networks of genes associated with stress response have a modular structure with a regulatory component being one of the largest for five of seven stress types. We demonstrated a positive relationship between the number of interactions of gene in the stress gene network and its age. Moreover, genes of the same age tend to be connected in stress gene networks. We also demonstrated that old stress-related genes usually participate in the response for various types of stress and are involved in numerous biological processes unrelated to stress. Our results demonstrate that the stress response genes represent the ancient and one of the fundamental molecular systems in plants.