bluuebunny/crossref_metadata_2025_split huggingface dataset:
North American Society for Pediatric Gastroenterology, Hepatology, and Nutrition Position Paper
Authors: Merritt Russell J. , Fleet Sarah E. , Fifi Amanda , Jump Candi , Schwartz Sally , Sentongo Timothy , Duro Debora , Rudolph Jeffrey , Turner Justine ,   NASPGHAN Committee on Nutrition
Published: May 2020

ABSTRACTParents and caretakers are increasingly feeding infants and young children plant‐based “milk” (PBM) alternatives to cow milk (CM). The US Food and Drug Administration currently defines “milk” and related milk products by the product source and the inherent nutrients provided by bovine milk. Substitution of a milk that does not provide a similar nutritional profile to CM can be deleterious to a child's nutritional status, growth, and development. Milk's contribution to the protein intake of young children is especially important. For almond or rice milk, an 8 oz serving provides only about 2% or 8%, respectively, of the protein equivalent found in a serving of CM. Adverse effects from the misuse of certain plant‐based beverages have been well‐documented and include failure to gain weight, decreased stature, kwashiorkor, electrolyte disorders, kidney stones, and severe nutrient deficiencies including iron deficiency anemia, rickets, and scurvy. Such adverse nutritional outcomes are largely preventable. It is the position of the North American Society for Pediatric Gastroenterology, Hepatology, and Nutrition (NASPGHAN) Nutrition Committee, on behalf of the society, that only appropriate commercial infant formulas be used as alternatives to human milk in the first year of life. In young children beyond the first year of life requiring a dairy‐free diet, commercial formula may be a preferable alternative to cow's milk, when such formula constitutes a substantial source of otherwise absent or reduced nutrients (eg, protein, calcium, vitamin D) in the child's restricted diet. Consumer education is required to clarify that PBMs do not represent an equivalent source of such nutrients. In this position paper, we provide specific recommendations for clinical care, labelling, and needed research relative to PBMs.
Clinical presentation of paroxysmal supraventricular tachycardia: evaluation of usual and unusual symptoms
Authors: Yetkin Ertan , Ozturk Selcuk , Cuglan Bilal , Turhan Hasan 
Published: May 2020

ObjectiveClinical presentation of paroxysmal supraventricular tachycardia may vary from asymptomatic occurrence or mild perception of palpitation to severe chest pain or syncope. This variation is the most challenging issue in the diagnostic evaluation of rhythm disturbances and paroxysmal supraventricular tachycardia as well. This study sought to evaluate the symptoms during the tachycardia attack or index event in patients who underwent electrophysiological study and ablation procedure.MethodsThis retrospective study included 100 consecutive patients who underwent electrophysiological study and ablation procedures due to supraventricular tachycardia. Structural heart disease, moderate/severe valvular pathology, systemic pathologies, such as connective tissue disease and chronic obstructive lung disease, history of pacemaker implantation was defined as exclusion criteria. In addition, medically managed patients and patients with unsuccessful ablation were not included in the study.ResultsPalpitation was the most frequently observed symptom in 84% of patients, followed by chest pain in 47%, dyspnea in 38%, syncope 26%, lightheadedness in 19%, and sweating in 18% of the patients. The most common symptoms after tachycardia event were fatigue and lightheadedness with frequencies of 56% and 55%, respectively. Forty-five percent of the patients reported more than one, unusually frequent urination within the following 1–3 hours after the index event.ConclusionsParoxysmal supraventricular tachycardia might manifest itself as gastrointestinal, neurological, psychosomatic symptoms, and unusual complaints in association with or without main symptoms, including palpitation, chest pain, syncope, and dyspnea. Symptoms after tachycardia or index event should be questioned systematically.
Magnesium Sulfate Attenuates Lethality and Oxidative Damage Induced by Different Models of Hypoxia in Mice
Authors: Mohammadi Hamidreza , Shamshirian Amir , Eslami Shafagh , Shamshirian Danial , Ebrahimzadeh Mohammad Ali 
Published: May 2020

AbstractMg2+is an important cation in our body. It is an essential co-factor for many enzymes. Despite many works, nothing is known about the protective effects of MgSO4against hypoxia-induced lethality and oxidative damage in brain mitochondria. In this study, antihypoxic and antioxidative activities of MgSO4were evaluated by three experimental models of induced-hypoxia (asphyctic, haemic, and circulatory) in mice. Mitochondria protective effects of MgSO4were evaluated in mice brain after induction of different models of hypoxia. Antihypoxic activity was especially pronounced in asphyctic hypoxia where MgSO4at dose 600 mg/kg showed the same activity as phenytoin which used as a positive control (P<0.001). In the haemic model, MgSO4at all used doses significantly prolonged latency of death. In circulatory hypoxia, MgSO4(600 mg/kg) doubles the survival time. MgSO4significantly decreased Lipid peroxidation, protein carbonyl, and improved mitochondrial function and glutathione content in brain mitochondria compared to control groups. The results obtained in this study showed that MgSO4administration has protective effects against lethality induced by different models of hypoxia and improves brain mitochondria oxidative damage.
Nanaerobic growth enables direct visualization of dynamic cellular processes in human gut symbionts
Authors: García-Bayona Leonor , Coyne Michael J. , Hantman Noam , Montero-Llopis Paula , Von Salena , Ito Takeshi , Malamy Michael H. , Basler Marek , Barquera Blanca , Comstock Laurie E. 
Published: May 2020

AbstractMechanistic studies of anaerobic gut bacteria have been hindered by the lack of a fluorescent protein system to track and visualize proteins and dynamic cellular processes in actively growing bacteria. Although underappreciated, many gut “anaerobes” are able to respire using oxygen as the terminal electron acceptor. The oxygen continually released from gut epithelial cells creates an oxygen gradient from the mucus layer to the anaerobic lumen (1), with oxygen available to bacteria growing at the mucus layer. Using a combination of analyses, we show thatBacteroidesspecies are metabolically and energetically robust and do not mount stress responses in the presence of 0.10 - 0.14% oxygen, defined as nanaerobic conditions (2). Taking advantage of this metabolic capability, we show that nanaerobic growth provides sufficient oxygen for the maturation of oxygen-requiring fluorescent proteins inBacteroidesspecies. Type strains of four differentBacteroidesspecies show bright GFP fluorescence when grown nanaerobically versus anaerobically. We compared four different red fluorescent proteins and found that mKate2 yields high fluorescence intensity in our assay. We show that GFP-tagged proteins can be localized in nanaerobically growing bacteria. In addition, we used time-lapse fluorescence microscopy to image dynamic Type VI secretion system processes in metabolically activeB. fragilis. The ability to visualize fluorescently-labeledBacteroidesand fluorescently-linked proteins in actively growing nanaerobic gut symbionts ushers in a new age of imaging analyses in these bacteria.SignificanceDespite many recent technological advances to study the human gut microbiota, we still lack a facile system to image dynamic cellular processes in most abundant gut species due to the requirement of oxygen for chromophore maturation of commonly used fluorescent proteins. Here, we took advantage of the ability of anaerobes of the gut microbiota to respire aerobically and grow robustly at 0.10– 0.14% oxygen. This physiologic concentration of oxygen is sufficient for fluorescent proteins to mature, allowing for visualization of biological processes never before imaged in these bacteria. This advance will allow for numerous types of analyses in actively-growing “nanaerobic” gut bacteria including subcellular protein localizations, single-cell analyses, biofilm imaging, and protein interactions with other microbes and the host.
Digitization of Electrocardiogram Using Bilateral Filtering
Authors: Sankar S Hari , Patni Anchit , Mulleti Satish , Seelamantula Chandra Sekhar 
Published: May 2020

ABSTRACTElectrocardiogram (ECG) is one of the most basic tools available for the detection of cardiovascular disease (CVD) which has evolved as one of the major causes of death in recent times, spanning countries. Conventionally, ECGs are printed on graph sheets which keep fading away with time. Hence, the preservation of ECG graph sheets is difficult. Digitization of printed ECG graph sheets is a solution to this problem. Digitization also helps in faster analysis and interpretation of ECG signals. Although the previous works have succeeded in smoothing ECG after extracting the signal from graph sheet, the cost amounts to loss of peak amplitude characteristics leading to wrong diagnosis. In this work, we propose a digitization technique to extract ECG signals from graph sheets. The proposed bilateral filter based method achieves a high degree of smoothness with all the peak characteristics intact when compared to other implementations using Butterworth filters. With this technique, it is now possible to create extensive databases similar to MIT–BIH from printed ECG graph sheets. A high level of automation is achieved, and results verified with over 60 ECGs and compared.
Regional activity in the rat anterior cingulate cortex and insula during persistence and quitting in a physical-effort task
Authors: Porter Blake S. , Li Kunling , Hillman Kristin L. 
Published: May 2020

AbstractAs animals carry out behaviors, particularly costly ones, they must constantly assess whether or not to persist in the behavior or quit. The anterior cingulate cortex (ACC) has been shown to assess the value of behaviors and to be especially sensitive to physical effort costs. Complimentary to these functions, the insula is thought to represent the internal state of the animal including factors such as hunger, thirst, and fatigue. Utilizing a novel weight lifting task for rats, we characterized the local field potential (LFP) activity of the ACC and anterior insula (AI) during effort expenditure. In the task male rats are challenged to work for sucrose reward, which costs progressively more effort over time to obtain. Rats are able to quit the task at any point. We found modest shifts in LFP theta (7-9 Hz) activity as the task got progressively more difficult in terms of absolute effort expenditure. However, when the LFP data were analyzed based on the rat’s relative progress towards quitting the task, or performance state, substantial shifts in LFP power in the theta and gamma (55-100 Hz) frequency bands were observed in ACC and AI. Both ACC and AI theta power decreased as the rats got closer to quitting, while ACC and AI gamma power increased. Furthermore, coherency between ACC and AI in the delta (2-4 Hz) range shifted alongside the rat’s performance state. Overall we show that ACC and AI LFP activity changes correlate to the rats’ relative performance state in an effort-based task.Significance StatementAnimals need to assess whether or not a behavior is worth pursuing based on their internal states (e.g., hunger, fatigue) and the costs and benefits of the behavior. However, internal states often change as behaviors are carried out, such as becoming fatigued, necessitating constant reassessment as to whether to continue the behavior or quit. We characterized brain activity in the anterior cingulate cortex and insula, brain regions involved in cost-benefit decision making and internal state representations, respectively, as rats carried out a challenging physical-effort task. Both brain regions showed significant shifts in activity as the rats approached their quitting point. Our study provides one of the first characterizations of neural activity as an animal decides to quit an effortful task.
For-profit nursing homes and the risk of COVID-19 outbreaks and resident deaths in Ontario, Canada
Authors: Stall Nathan M. , Jones Aaron , Brown Kevin A. , Rochon Paula A. , Costa Andrew P. 
Published: May 2020

AbstractBackgroundNursing homes have become the epicentre of the coronavirus disease 2019 (COVID-19) pandemic in Canada. Previous research demonstrates that for-profit nursing homes deliver inferior care across a variety of outcome and process measures, raising the question of whether for-profit homes have had worse COVID-19 outcomes than non-profit homes.MethodsWe conducted a retrospective cohort study of all nursing homes in Ontario, Canada from March 29-May 20, 2020 using a COVID-19 outbreak database maintained by the Ontario Ministry of Long-Term Care. We used hierarchical logistic and count-based methods to model the associations between nursing home profit status (for-profit, non-profit or municipal) and nursing home COVID-19 outbreaks, COVID-19 outbreak sizes, and COVID-19 resident deaths.ResultsThe analysis included all 623 Ontario nursing homes, of which 360 (57.7%) were for-profit, 162 (26.0%) were non-profit, and 101 (16.2%) were municipal homes. There were 190 (30.5%) COVID-19 nursing home outbreaks involving 5218 residents (mean of 27.5 ± 41.3 residents per home), resulting in 1452 deaths (mean of 7.6 ± 12.7 residents per home) with an overall case fatality rate of 27.8%. The odds of a COVID-19 outbreak was associated with the incidence of COVID-19 in the health region surrounding a nursing home (adjusted odds ratio [aOR], 1.94; 95% confidence interval [CI] 1.23-3.09) and number of beds (aOR, 1.40; 95% CI 1.20-1.63), but not profit status. For-profit status was associated with both the size of a nursing home outbreak (adjusted risk ratio [aRR], 1.96; 95% CI 1.26-3.05) and the number of resident deaths (aRR, 1.78; 95% CI 1.03-3.07), compared to non-profit homes. These associations were mediated by a higher prevalence of older nursing home design standards in for-profit homes.Interpretation: For-profit status is associated with the size of a COVID-19 nursing home outbreak and the number of resident deaths, but not the likelihood of outbreaks. Differences between for profit and non-profit homes are largely explained by older design standards, which should be a focus of infection control efforts and future policy.
Constraining the contribution of aerobic nitrite oxidation to oxygen consumption in oceanic oxygen minimum zones
Authors: Beman J.M. , Vargas S.M. , Wilson J.M. , Perez-Coronel E. , Karolewski J.S. , Vazquez S. , Yu A. , Cairo A.E. , White M.E. , Koester I. , Aluwihare L. I. , Wankel S.D. 
Published: May 2020

AbstractOceanic oxygen minimum zones (OMZs) are globally significant sites of biogeochemical cycling where microorganisms deplete dissolved oxygen (DO) to concentrations <20 µM. Amid intense competition for DO in these metabolically challenging environments, aerobic nitrite oxidation may consume significant amounts of DO and help maintain low DO concentrations, but this remains unquantified. Using parallel measurements of oxygen consumption rates and15N-nitrite oxidation rates applied to both water column profiles and oxygen manipulation experiments, we show that the contribution of nitrite oxidation to overall DO consumption systematically increases as DO declines below 2 µM. Nitrite oxidation could account for all DO consumption only under DO concentrations <393 nM found in and below the secondary chlorophyll maximum. These patterns were consistent across sampling stations and experiments, reflecting coupling between nitrate reduction and nitrite-oxidizingNitrospinawith high oxygen affinity (based on isotopic and omic data). Collectively our results provide new insight into the contribution of nitrite oxidation to the maintenance and biogeochemical dynamics of OMZs.
Non-Canonical Ago Loading of EV-Derived Exogenous miRNA Generates Foreign miRNPs on Endosomes to Arbitrate Gene Expression in Recipient Cells
Authors: Ghoshal Bartika , Bertrand Edouard , Bhattacharyya Suvendra N. 
Published: May 2020

AbstractMicroRNAs, the tiny regulators of gene expression, can be transferred between neighbouring cells via Extracellular Vesicles (EV) to control the expression of genes in both donor and recipient cells. How the Extracellular Vesicles-derived miRNAs are getting internalized and become functional in target cells is an unresolved question. We found that EV-associated miRNAs are primarily single stranded and, to become functional, get loaded with the Ago proteins present in the recipient cells without requiring host Dicer1. Following endocytosis of miRNA-containing extracellular vesicles, loading of host Ago occurs on the endosomal membrane where pH-dependent membrane fusion triggers the release of internalized miRNAs to form exogenous miRNP pool. In addition, loading of exogenous miRNA to host Ago also depends on the mitochondrial activity of recipient cells. Internalization of hepatocyte derived miR-122 containing EVs in macrophage activates the recipient cell by targeting cytokine expression.Leishmania donovani, a protozoan parasite known to affect endocytosis and to cause mitochondrial depolarization in infected macrophages, restricts the EV-internalization process and thereby preventing inflammatory cytokine expression and ensuring internalized pathogen survival in macrophage.
Simeprevir potently suppresses SARS-CoV-2 replication and synergizes with remdesivir
Authors: Lo Ho Sing , Hui Kenrie Pui Yan , Lai Hei-Ming , Khan Khadija Shahed , Kaur Simranjeet , Huang Junzhe , Li Zhongqi , Chan Anthony K. N. , Cheung Hayley Hei-Yin , Ng Ka-Chun , Wang Ho John Chi , Chen Yu Wai , Ma Bowen , Cheung Peter Man-Hin , Shin Donghyuk , Wang Kaidao , Lee Meng-Hsuan , Selisko Barbara , Eydoux Cecilia , Guillemot Jean-Claude , Canard Bruno , Wu Kuen-Phon , Liang Po-Huang , Dikic Ivan , Zuo Zhong , Chan Francis K. L. , Hui David S. C. , Mok Vincent C. T. , Wong Kam-Bo , Ko Ho , Aik Wei Shen , Chan Michael Chi Wai , Ng Wai-Lung 
Published: May 2020

AbstractThe outbreak of coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a global threat to human health. Using a multidisciplinary approach, we identified and validated the hepatitis C virus (HCV) protease inhibitor simeprevir as an especially promising repurposable drug for treating COVID-19. Simeprevir potently reduces SARS-CoV-2 viral load by multiple orders of magnitude and synergizes with remdesivirin vitro. Mechanistically, we showed that simeprevir inhibits the main protease (Mpro) and unexpectedly the RNA-dependent RNA polymerase (RdRp). Our results thus reveal the viral protein targets of simeprevir, and provide preclinical rationale for the combination of simeprevir and remdesivir for the pharmacological management of COVID-19 patients.One Sentence SummaryDiscovery of simeprevir as a potent suppressor of SARS-CoV-2 viral replication that synergizes with remdesivir.
A global data-driven census of Salmonella small proteins and their potential functions in bacterial virulence
Authors: Venturini Elisa , Svensson Sarah L. , Maaß Sandra , Gelhausen Rick , Eggenhofer Florian , Li Lei , Cain Amy K. , Parkhil Julian , Becher Dörte , Backofen Rolf , Barquist Lars , Sharma Cynthia M. , Westermann Alexander J. , Vogel Jörg 
Published: May 2020

ABSTRACTSmall proteins are an emerging class of gene products with diverse roles in bacterial physiology. However, a full understanding of their importance has been hampered by insufficient genome annotations and a lack of comprehensive characterization in microbes other than Escherichia coli. We have taken an integrative approach to accelerate the discovery of small proteins and their putative virulence-associated functions in Salmonella Typhimurium. We merged the annotated small proteome of Salmonella with new small proteins predicted with in silico and experimental approaches. We then exploited existing and newly generated global datasets that provide information on small open reading frame expression during infection of epithelial cells (dual RNA-seq), contribution to bacterial fitness inside macrophages (TraDIS), and potential engagement in molecular interactions (Grad-seq). This integrative approach suggested a new role for the small protein MgrB beyond its known function in regulating PhoQ. We demonstrate a virulence and motility defect of a Salmonella ΔmgrB mutant and reveal an effect of MgrB in regulating the Salmonella transcriptome and proteome under infection-relevant conditions. Our study highlights the power of interpreting available “omics” datasets with a focus on small proteins, and may serve as a blueprint for a data integration-based survey of small proteins in diverse bacteria.
Cataract-associated New Mutants S175G/H181Q of βB2-Crystallin and P24S/S31G of γD-Crystallin are Involved in Protein aggregation by Structural Changes
Authors: Song In-Kang , Na Seungjin , Paek Eunok , Lee Kong-Joo 
Published: May 2020

ABSTRACTβ/γ-Crystallins, the main structural protein in human lenses, have highly stable structure for keeping the lens transparent. Their mutations have been linked to congenital cataracts. In this study, we identified 10 new mutations of β/γ-crystallins in lens proteomic dataset of cataract patients using bioinformatic tools. Of these, two double mutants, S175G/H181Q of βΒ2-crystallin and P24S/S31G of γD-crystallin, were found mutations occurred in the largest loop linking the distant β-sheets in the Greek key motif. We selected these double mutants for identifying the properties of these mutations, employing biochemical assay, the identification of protein modifications with nanoUPLC-ESI-TOF tandem MS and examining their structural dynamics with hydrogen/deuterium exchange-mass spectrometry (HDX-MS). We found that both double mutations decrease protein stability and induce the aggregation of β/γ-crystallin, possibly causing cataracts. This finding suggests that both the double mutants can serve as biomarkers of congenital cataracts.
Study of cell to cell transmission of SARS CoV 2 virus particle using gene network from microarray data
Authors: Basu Anamika , Sarkar Anasua , Maulik Ujjwal 
Published: May 2020

AbstractMicroarray data from SARS CoV2 patients helps to construct a gene network relating to this disease. Analysis of these genes, present in network, highlights their biological functions and related cellular pathways. With the assistance of these information, a drug(s) can be identified to treat COVID-19. A detailed analysis of the human host response to SARS CoV 2 with expression profiling by high throughput sequencing has executed with primary human lung epithelium cell lines. Clustered genes annotation and gene network construction are performed with the help of String database. Among four cluster of genes from microarray data, cluster 1 is identified as basal cells with p= 1.37e−05 with 44 genes. Functional enrichment analysis of genes present in gene network has completed using String database, ToppFun online tool and NetworkAnalyst tool. For SARS CoV2 virus particles, keratin proteins, which are part of cytoskeleton structure of host cell, play a major role in cell to cell virus particle transmission. Among three types of cell- cell communication, only anchoring junction between basal cell membrane and basal lamina, is involved in this virus transmission. In this junction point, hemidesmosome structure play a vital role in virus spread from one cell to basal lamina in respiratory tract. In this protein complex structure, keratin, integrin and laminin proteins of host cell is used to promote the spread of virus infection into extracellular matrix. So, small molecular blockers of different anchoring junction proteins i.e. ITGA3, ITGA2 can provide efficient protection against this deadly virus disease. Understanding the human host response against this virus is very important to develop novel therapeutics for the treatment of SARS-CoV 2.