bluuebunny/crossref_metadata_2025 huggingface dataset:
Expired But Not Yet Dead: Examining the Red Blood Cell Storage Lesion in Extended-Storage Whole Blood
Authors: Pulliam Kasiemobi E. , Joseph Bernadin , Veile Rosalie A. , Friend Lou Ann , Makley Amy T. , Caldwell Charles C. , Lentsch Alex B. , Goodman Michael D. , Pritts Timothy A.
Published: August 2020

Whole blood is a powerful resuscitation strategy for trauma patients but has a shorter shelf life than other blood products. The red blood cell storage lesion in whole blood has not previously been investigated beyond the standard storage period. In the present study, we hypothesized that erythrocytes in stored whole blood exhibit similar aspects of the red blood cell storage lesion and that transfusion of extended storage whole blood would not result in a more severe inflammatory response after hemorrhage in a murine model. To test this hypothesis, we stored low-titer, O-positive, whole blood units, and packed red blood cells (pRBCs) for up to 42 days, then determined aspects of the red blood cell storage lesion. Compared with standard storage pRBCs, whole blood demonstrated decreased microvesicle and free hemoglobin at 21 days of storage and no differences in osmotic fragility. At 42 days of storage, rotational thromboelastometry demonstrated that clotting time was decreased, alpha angle was increased, and clot formation time and maximum clot firmness similar in whole blood as compared with pRBCs with the addition of fresh frozen plasma. In a murine model, extended storage whole blood demonstrated decreased microvesicle formation, phosphatidylserine, and cell-free hemoglobin. After hemorrhage and resuscitation, TNF-a, IL-6, and IL-10 were decreased in mice resuscitated with whole blood. Red blood cell survival was similar at 24 h after transfusion. Taken together, these data suggest that red blood cells within whole blood stored for an extended period of time demonstrate similar or reduced accumulation of the red blood cell storage lesion as compared with pRBCs. Further examination of extended-storage whole blood is warranted.
Sepsis Induces Deregulation of IL-13 Production and PD-1 Expression in Lung Group 2 Innate Lymphoid Cells
Authors: Akama Yuichi , Park Eun Jeong , Satoh-Takayama Naoko , Gaowa Arong , Ito Atsushi , Kawamoto Eiji , Darkwah Samuel , Appiah Michael G. , Myint Phyoe Kyawe , Ohno Hiroshi , Imai Hiroshi , Shimaoka Motomu
Published: August 2020

Deregulation of the immune system in sepsis plays the central role in the pathogenesis of multiple organ failure including septic lung injury. Group 2 innate lymphoid cells (ILC2s) have emerged as a new player in regulating immune homeostasis in the lung; however, the role of ILC2s in lung injury in sepsis remains poorly understood. Here, we investigated temporal changes in stimulatory and inhibitory receptor expression and intracellular type 2 cytokine expression of ILC2s in the lung using a cecal ligation and puncture mouse sepsis model. We found that IL-13 production by ILC2s, which were predominately composed of the resident natural ILC2 subset rather than the migratory inflammatory ILC2 subset, was reduced in the lungs of sepsis mice on day 1 and gradually restored through day 7. Although the expression levels of ST2 and inducible T-cell costimulator (stimulatory receptors) were high, IL-13 production by ILC2s was reduced while showing high programmed cell death 1 (PD-1) (inhibitory receptor) expression. Furthermore, using IL-33 knockout mice, we have shown that IL-33 regulates the capacity of ILC2s to produce IL-13, possibly through the modulation of ST2 and PD-1 expression and signaling in the septic lung. To the best of our knowledge, this is the first report showing differential costimulatory/inhibitory receptor expression on ILC2s in a septic lung in the context of an IL-33/IL-13 pathway-mediated type 2 immune response in the progression and resolution of inflammation. Our present findings contribute to a better understanding of the underlying immunological mechanism of ILC2s and may fill the critical knowledge gap regarding immune homeostasis in the lung that hampers the development of new therapeutic strategies for sepsis-induced acute lung injury.
Septic Stability? Gut Microbiota in Young Adult Mice Maintains Overall Stability After Sepsis Compared to Old Adult Mice
Authors: Mankowski Robert T. , Thomas Ryan M. , Darden Dijoia B. , Gharaibeh Raad Z. , Hawkins Russell B. , Cox Michael C. , Apple Camille , Nacionales Dina C. , Ungaro Ricardo F. , Dirain Marvin L. , Moore Fredrick A. , Leeuwenburgh Christiaan , Brakenridge Scott C. , Clanton Thomas L. , Laitano Orlando , Moldawer Lyle L. , Mohr Alicia M. , Efron Philip A.
Published: August 2020

Background:

Older adults have worse outcomes after sepsis than young adults. Additionally, alterations of the gut microbiota have been demonstrated to contribute to sepsis-related mortality. We sought to determine if there were alterations in the gut microbiota with a novel sepsis model in old adult mice, which enter a state of persistent inflammation, immunosuppression, and catabolism (PICS), as compared with young adult mice, which recover with the sepsis model.

Methods:

Mixed sex old (∼20 mo) and young (∼4 mo) C57Bl/6J mice underwent cecal ligation and puncture with daily chronic stress (CLP+DCS) and were compared with naive age-matched controls. Mice were sacrificed at CLP+DCS day 7 and feces collected for bacterial DNA isolation. The V3–V4 hypervariable region was amplified, 16S rRNA gene sequencing performed, and cohorts compared. α-Diversity was assessed using Chao1 and Shannon indices using rarefied counts, and β-diversity was assessed using Bray-Curtis dissimilarity.

Results:

Naive old adult mice had significantly different α and β-diversity compared with naive adult young adult mice. After CLP+DCS, there was a significant shift in the α and β-diversity (FDR = 0.03 for both) of old adult mice (naive vs. CLP+DCS). However, no significant shift was displayed in the microbiota of young mice that underwent CLP+DCS in regards to α-diversity (FDR = 0.052) and β-diversity (FDR = 0.12), demonstrating a greater overall stability of their microbiota at 7 days despite the septic insult. The taxonomic changes in old mice undergoing CLP+DCS were dominated by decreased abundance of the order Clostridiales and genera Oscillospira.

Conclusion:

Young adult mice maintain an overall microbiome stability 7 days after CLP+DCS after compared with old adult mice. The lack of microbiome stability could contribute to PICS and worse long-term outcomes in older adult sepsis survivors. Further studies are warranted to elucidate mechanistic pathways and potential therapeutics.
Dependence Clusters in Alzheimer Disease and Medicare Expenditures
Authors: Zhu Carolyn W. , Lee Seonjoo , Ornstein Katherine A. , Cosentino Stephanie , Gu Yian , Andrews Howard , Stern Yaakov
Published: August 2020

Introduction:

Dependence in Alzheimer disease has been proposed as a holistic, transparent, and meaningful representation of disease severity. Modeling clusters in dependence trajectories can help understand changes in disease course and care cost over time.

Methods:

Sample consisted of 199 initially community-living patients with probable Alzheimer disease recruited from 3 academic medical centers in the United States followed for up to 10 years and had ≥2 Dependence Scale recorded. Nonparametric K-means cluster analysis for longitudinal data (KmL) was used to identify dependence clusters. Medicare expenditures data (1999-2010) were compared between clusters.

Results:

KmL identified 2 distinct Dependence Scale clusters: (A) high initial dependence, faster decline, and (B) low initial dependence, slower decline. Adjusting for patient characteristics, 6-month Medicare expenditures increased over time with widening between-cluster differences.

Discussion:

Dependence captures dementia care costs over time. Better characterization of dependence clusters has significant implications for understanding disease progression, trial design and care planning.
Aquitalea aquatilis sp. nov., isolated from Jungwon waterfall
Authors: Ngo Hien T.T. , Kim HongYong , Trinh Huan , Yi Tae-Hoo
Published: August 2020

A Gram-stain-negative, facultative anaerobic, motile, short rods and yellow-pigmented bacterium, designated strain THG-DN7.12T, was isolated from water collected at Jungwon waterfall on Yongmun mountain, Republic of Korea. According to 16S rRNA gene sequence comparisons, strain THG-DN7.12T was found to be most closely related to

Aquitalea denitrificans

5YN1-3T (98.9 % sequence similarity),

Aquitalea magnusonii

TRO-001DR8T (98.7 %) and

Aquitalea pelogenes

P1297T (98.0 %). The DNA–DNA relatedness between strain THG-DN7.12T and its phylogenetically closest neighbours was below 70.0 %. The strain's DNA G+C content was 59.7 mol%. The major polar lipid was found to be phosphatidylethanolamine. Summed feature 3 (C16 : 1
 ω7c and/or C16 : 1
 ω6c) and C16 : 0 were identified as the major fatty acids. Ubiquinone Q-8 was detected as the only respiratory quinone. These data supported the affiliation of strain THG-DN7.12T to the genus

Aquitalea

. Strain THG-DN7.12T was distinguished from related

Aquitalea

species by physiological and biochemical tests. Therefore, the novel isolate represents a novel species, for which the name Aquitalea aquatilis sp. nov. is proposed, with THG-DN7.12T as the type strain (=KACC 18847T=CCTCC AB 2016185T).
Streptomyces lycii sp. nov., an endogenous actinomycete isolated from Lycium ruthenicum
Authors: Ma Liran , Zeng Hong , Xia Zhanfeng , Luo Xiaoxia , Zhang Lili , Wan Chuanxing
Published: August 2020

A novel endogenous actinobacteria strain, designated TRM 66187T, was isolated from Lycium ruthenicum sampled at Alar, Xinjiang, Northwest PR China, and characterized using a polyphasic taxonomic approach. Phylogenetic analysis based on 16S rRNA gene sequences affiliated strain TRM 66187T with the genus

Streptomyces

. The whole-cell sugar pattern of TRM 66187T consisted of galactose, glucose and ribose. The predominant menaquinones were MK-9(H4) and MK-9(H6). Major cellular fatty acids were iso-C14:0, iso-C15:0, anteiso-C15:0 and anteiso-C16:0. The detected polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannoside and two unidentified polar lipids. The G+C content of strain TRM 66187T was 71.8 mol%. Results of phylogenetic analysis showed that strain TRM 66187T had 98.48% 16S rRNA gene sequence similarity to the closest described species

Streptomyces qinglanensis

DSM 42035T. The average nucleotide identity value between strain TRM 66187T and the closest related strain

Streptomyces qinglanensis

DSM 42035T was calculated to be 77.2%. The digital DNA–DNA hybridization value between them was 22.4%. Multilocus sequence analyses based on five housekeeping genes (atpD, gyrB, recA, rpoB and trpB) also indicated that strain TRM 66187T should be assigned to the genus

Streptomyces

. On the basis of evidence from this polyphasic study, strain TRM 66187T should be designated as representing a novel species of the genus

Streptomyces

, for which the name Streptomyces lycii sp. nov. is proposed. The type strain is TRM 66187T (=LMG 31493T=CCTCC AA 2018094T).
Salinimicrobium nanhaiense sp. nov. and Salinimicrobium oceani sp. nov., two novel species of the family Flavobacteriaceae isolated from the South China Sea
Authors: Cao Wen-Rui , Zhang Lan-Zeng , Hu Yi-Hao , Jiang Ming-Yu , Li Ying-Jie
Published: August 2020

Strains J15B81-2T and J15B91T were isolated from a sediment sample collected from the South China Sea. Cells of both strains were observed to be rod-shaped, non-gliding, Gram-stain-negative, yellow-pigmented, facultatively anaerobic, catalase-positive, oxidase-negative and showing optimum growth at 30 °C. Strains J15B81-2T and J15B91T could tolerate up to 9 and 10  % (w/v) NaCl concentration and grow at pH 6.5–9.5 and 6.0–9.0, respectively. The strains shared 97.4 % 16S rRNA gene sequence similarity to each other but were identified as two distinct species based on 81.1–85.8 % ANIb and 31.5 % dDDH values calculated using whole genome sequences. Strains J15B81-2T and J15B91T shared highest 16S rRNA gene sequence similarity to

Salinimicrobium xinjiangense

CGMCC 1.12522T (98.4 %) and

Salinimicrobium sediminis

CGMCC 1.12641T (98.0 %), respectively. Among species with validly published names,

S. sediminis

CGMCC 1.12641T shared close genetic relatedness with strains J15B81-2T [85.1–85.3% average nucleotide identity based on blastBlast+ (ANIb) and 30.6 % digital DNA–DNA hybridization (dDDH)] and J15B91T (76.6–79.1 % ANIb and 21.5 % dDDH). The major fatty acid of strains J15B81-2T and J15B91T were identified as iso-C15 : 0 and iso-C16 : 0, respectively, and the major polar lipids of the two strains consisted of phosphatidylethanolamine, one unidentified phospholipid, one unidentified aminolipid and one unidentified lipid. The strains contained MK-6 as their predominant menaquinone. The genomic G+C contents of strains J15B81-2T and J15B91T were determined to be 41.7 and 41.8 mol %, respectively. Both strains are considered to represent two novel species of the genus

Salinimicrobium

and the names Salinimicrobium nanhaiense sp. nov. and Salinimicrobium oceani sp. nov. are proposed for strains J15B81-2T (=KCTC 72867T=MCCC 1H00410T) and J15B91T (=KCTC 72869T=MCCC 1H00411T), respectively.
Discriminatory cytokine profiles predict muscle function, fatigue and cognitive function in patients with Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS)
Authors: Gusnanto A , Earl KE , Sakellariou GK , Owens DJ , Lightfoot A , Fawcett S , Owen E , Staunton CA , Shu T , Croden FC , Fenech M , Sinclair M , Ratcliffe L , Whysall KA , Haynes R , Wells NM , Jackson MJ , Close GL , Lawton C , Beadsworth MBJ , Dye L , McArdle A
Published: August 2020

Myalgic Encephalomyelitis (ME) /Chronic Fatigue Syndrome (CFS) is a severely debilitating and complex illness of uncertain aetiology, affecting the lives of millions and characterised by prolonged fatigue. The initiating factors and mechanisms leading to chronic debilitating muscle fatigue in ME/CFS are unknown and are complicated by the time required for diagnosis. Both mitochondrial dysfunction and inflammation have been proposed to be central to the pathogenesis of ME/CFS. This original and extensive study demonstrated that although there was little dysfunction evident in the muscle mitochondria of patients with ME/CFS, particular blood plasma and skeletal muscle cytokines, when adjusted for age, gender and cytokine interactions could predict both diagnosis and a number of measures common to patients with ME/CFS. These included MVC and perceived fatigue as well as cognitive indices such as pattern and verbal reaction times. We employed advanced multivariate analyses to cytokine profiles that leverages covariation and intrinsic redundancy to identify patterns of immune signaling that can be evaluated for their predictions of disease phenotype. The current study identified discriminatory cytokine profiles that can be sufficiently used to distinguish HCs from patients with ME/CFS and provides compelling evidence that a limited number of cytokines are associated with diagnosis and fatigue. Moreover, this study demonstrates significant potential of using multiplex cytokine profiles and bioinformatics as diagnostic tools for ME/CFS, potentiating the possibility of not only diagnosis, but also being able to individually personalise therapies.

Significance

Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) is a complex, chronic, debilitating and potentially life-changing medical condition affecting children and adults of all ages, races and socio-economic groupings. Clinical presentation includes fluctuating fatigue of varying severity, with other symptoms, including myalgia, arthralgia, post-exertional fatigue, unrefreshed sleep, headache, upper respiratory tract symptoms, and cognitive impairment. With no biomarkers, or diagnostic tests, aetiology, epidemiology and pathophysiology remain unclear. This extensive study employed advanced multivariate analyses that leveraged covariation and intrinsic redundancy and identified discriminatory cytokine profiles that can be used to distinguish Healthy Controls (HCs) from patients with ME/CFS and a limited number of cytokines were associated with physical and cognitive fatigue. These findings are relevant to the potential of increasing numbers of patients developing chronic fatigue following Coronavirus disease 2019.
Blood donor exposome and impact of common drugs on red blood cell metabolism
Authors: Nemkov Travis , Stefanoni Davide , Bordbar Aarash , Issaian Aaron , Palsson Bernhard O. , Dumont Larry J , Hay Ariel , Song Anren , Xia Yang , Redzic Jasmina S. , Eisenmesser Elan Z. , Zimring James C , Kleinman Steve , Hansen Kirk C. , Busch Michael P. , D’Alessandro Angelo ,   for the Recipient Epidemiology and Donor Evaluation Study-III (REDS-III) RBC-Omics Study
Published: August 2020

Computational models based on recent maps of the red blood cell proteome suggest that mature erythrocytes may harbor targets for common drugs. This prediction is relevant to red blood cell storage in the blood bank, in which the impact of small molecule drugs or other xenometabolites deriving from dietary, iatrogenic or environmental exposures (“exposome”) may alter erythrocyte energy and redox metabolism and, in so doing, affect red cell storage quality and post-transfusion efficacy. To test this prediction, here we provide a comprehensive characterization of the blood donor exposome, including the detection of common prescription and off-the-counter drugs in 250 units donated by healthy volunteers from the REDS-III RBC Omics study. Based on high-throughput drug screenings of 1,366 FDA-approved drugs, we report a significant impact of ∼65% of the tested drugs on erythrocyte metabolism. Machine learning models built using metabolites as predictors were able to accurately predict drugs for several drug classes/targets (bisphosphonates, anticholinergics, calcium channel blockers, adrenergics, proton-pump inhibitors, antimetabolites, selective serotonin reuptake inhibitors, and mTOR) suggesting that these drugs have a direct, conserved, and significant impact on erythrocyte metabolism. We then focused on ranitidine – a common antiacid – as a representative drug with the potential to improve human erythrocyte storage quality and post-transfusion performances in mice. By combining tracing experiments with 1,2,3-13C3-glucose, proteome integral solubility alteration assays, genetic ablation of S1P synthesis capacity, in silico docking and 1D NMR, we show that ranitidine triggers metabolic mechanisms involving sphingosine 1-phosphate (S1P)-dependent modulation of erythrocyte glycolysis and/or direct binding to hemoglobin.

Graphical Abstract

RBC exposome from the REDS III study revealed that blood from a subset of donors contains traces of the most common drugs in the United States. RBCs can uptake these drugs, in some cases can metabolize them to their bioactive metabolites and in others the drug can directly impact RBC metabolism during storage.

Key points

Blood donor exposomes include metabolites of environmental exposure, traces of common prescription or off-the-counter drugs;

65% of 1366 FDA- approved drug significantly affect RBC metabolism. Ranitidine significantly impacts glycolysis and S1P metabolism.
Look before diving into pooling of SARS-CoV-2 samples on high throughput analyzers
Authors: LeBlanc Jason J. , Patriquin Glenn , Pettipas Janice , Warhuus Michelle , Sarty Darren , Jackson Colleen , Heinstein Charles , MacDonald James , Haldane David , Hatchette Todd F
Published: August 2020

Given the unprecedented demand for SARS-CoV-2 testing during the COVID-19 pandemic, the benefits of specimen pooling have recently been explored. As previous studies were limited to mathematical modeling or testing on low throughput PCR instruments, this study aimed to assess pooling on high throughput analyzers. To assess the impact of pooling, SARS-CoV-2 dilutions were performed at varying pool depths (i.e. 1:2, 1:4, and 1:8) into test-negative nasopharyngeal or oropharynx/anterior nares swabs matrix. Testing was evaluated on the automated Roche Cobas 6800 system, or the Roche MagNApure LC 2.0 or MagNAPure 96 instruments paired with a laboratory-developed test using a 96-well PCR format. The frequency of detection in specimens with low viral loads was evaluated using archived specimens collected throughout the first pandemic wave. The proportion of detectable results per pool depths was used to estimate the potential impact. In addition, workflow at the analytical stage, and pre-and post-stages of testing were also considered. The current study estimated that pool depths of 1:2, 1:4, and 1:8 would have allowed the detection of 98.3%, 96.0%, and 92.6% of positive SARS-CoV-2 results identified in the first wave of the pandemic in Nova Scotia. Overall, this study demonstrated that pooling on high throughput instrumentation can dramatically increase the overall testing capacity to meet increased demands, with little compromising to sensitivity at low pool depths. However, the human resources required at the pre-analytical stage of testing is a particular challenging to achieve.
Gmo labeling in food products in montevideo, uruguay
Authors: Arleo M. , Benavente P. , Cardozo V. , Katz A. , Vázquez S. , Da Silva Tavares A. , Legnani M. , Martínez Debat C.
Published: August 2020

Montevideo establishes the mandatory labeling of foods containing genetically modified material through the Departmental Decree No. 36.554, positioning Uruguay within the 65 countries that have incorporated this type of regulation.

The Food Regulation Service, in its role of sanitary police, and through its Laboratory of Bromatology, in agreement with the Food Molecular Traceability Laboratory (Faculty of Sciences, University of the Republic), carried out the analysis of 206 products made with ingredients derived from corn and/or soybean, during the 2015-2017 period, within the framework of compliance with the aforementioned Decree.

The strategy used consisted of the application of molecular techniques (Real Time PCR), for the detection of common sequences present in the transgenic events of soybean and corn, and the subsequent quantification of the content of GM material, in relation to an established labeling threshold of 1%.

As a result of this study, it was found that 36.9% of the analyzed foods presented sequences derived from genetically modified plant organisms (GMOs); and in 95% of the cases, its content exceeded the threshold established for its labeling.

This study, constitutes the first approach to the knowledge of different transgenic elements distribution in food commercialized in Montevideo.

These results provide valuable information to both the consumer, for decision making about the food to be consumed, and also for the official control organizations, which must enforce the regulations.

This type of work has demonstrated, once again, the importance of the interrelation between academy and state agencies, in the generation of knowledge and in the implementation of new analytical methodologies, as well as in the training of qualified human resources and in the compliance with current regulations.
Exhaled SARS-CoV-2 quantified by face-mask sampling in hospitalised patients with covid-19
Authors: Williams Caroline M. , Pan Daniel , Decker Jonathan , Fletcher Eve , Wisniewska Anika , Sze Shirley , Assadi Sara , Haigh Richard , Abdulwhhab Mohamad , Bird Paul , Holmes Christopher W , Al-Taie Alaa , Saleem Baber , Pan Jingzhe , Garton Natalie J , Pareek Manish , Barer Michael R
Published: August 2020

Background

Human to human transmission of SARS-CoV-2 is driven by the respiratory route but little is known about the pattern and quantity of virus output from exhaled breath. We have previously shown that face-mask sampling (FMS) can detect exhaled tubercle bacilli and have adapted its use to quantify exhaled SARS-CoV-2 RNA in patients admitted to hospital with covid-19.

Methods

Between May and December 2020, we took two concomitant FMS and nasopharyngeal samples (NPS) over two days, starting within 24 hours of a routine virus positive NPS in patients hospitalised with covid-19, at University Hospitals of Leicester NHS Trust, UK. Participants were asked to wear a modified duckbilled facemask for 30 minutes, followed by a nasopharyngeal swab. Demographic, clinical, and radiological data, as well as International Severe Acute Respiratory and emerging Infections Consortium (ISARIC) mortality and deterioration scores were obtained.

Exposed masks were processed by removal, dissolution and analysis of sampling matrix strips fixed within the mask by RT-qPCR. Viral genome copy numbers were determined and results classified as Negative; Low: ≤999 copies; Medium: 1,000-99,999 copies and High ≥ 100,000 copies per strip for FMS or per 100µl for NPS.

Results

102 FMS and NPS were collected from 66 routinely positive patients; median age: 61 (IQR 49 - 77), of which FMS was positive in 37% of individuals and concomitant NPS was positive in 50%. Positive FMS viral loads varied over five orders of magnitude (<10-3.3 × 106 genome copies/strip); 21 (32%) patients were asymptomatic at the time of sampling. High FMS viral load was associated with respiratory symptoms at time of sampling and shorter interval between sampling and symptom onset (FMS High: median (IQR) 2 days (2-3) vs FMS Negative: 7 days (7-10), p=0.002). On multivariable linear regression analysis, higher FMS viral loads were associated with higher ISARIC mortality (Medium FMS vs Negative FMS gave an adjusted coefficient of 15.7, 95% CI 3.7-27.7, p=0.01) and deterioration scores (High FMS vs Negative FMS gave an adjusted coefficient of 37.6, 95% CI 14.0 to 61.3, p=0.002), while NPS viral loads showed no significant association.

Conclusion

We demonstrate a simple and effective method for detecting and quantifying exhaled SARS-CoV-2 in hospitalised patients with covid-19. Higher FMS viral loads were more likely to be associated with developing severe disease compared to NPS viral loads. Similar to NPS, FMS viral load was highest in early disease and in those with active respiratory symptoms, highlighting the potential role of FMS in understanding infectivity.
Breastmilk; a source of SARS-CoV-2 specific IgA antibodies
Authors: van Keulen Britt J. , Romijn Michelle , Bondt Albert , Dingess Kelly A. , Kontopodi Eva , van der Straten Karlijn , den Boer Maurits A. , Bosch Berend J. , Brouwer Philip J.M. , de Groot Christianne J.M. , Hoek Max , Li Wentao , Pajkrt Dasja , Sanders Rogier W. , Schoonderwoerd Anne , Tamara Sem , Timmermans Rian A.H. , Vidarsson Gestur , Stittelaar Koert J. , Rispens Theo T. , Hettinga Kasper A. , van Gils Marit J. , Heck Albert J.R. , van Goudoever Johannes B.
Published: August 2020

Background

Since the outbreak of COVID-19, many put their hopes in the rapid development of effective immunizations. For now patient isolation, physical distancing and good hygiene are the sole measures for prevention. Processed breast milk with antibodies against SaRS-CoV-2 may serve as additional protection. We aimed to determine the presence and neutralization capacity of antibodies against SaRS-CoV-2 in breastmilk of mothers who have recovered from COVID-19.

Methods

This prospective case control study included lactating mothers, recovered from (suspected) COVID-19 and healthy controls. Serum and breastmilk was collected. To assess the presence of antibodies in breastmilk and serum, we used multiple complementary assays, namely ELISA with the SARS-CoV-2 spike protein, SARS-CoV-2 receptor binding domain (RBD) and with the SARS-CoV-2 nucleocapsid (N) protein for IgG and bridging ELISA with the SARS-CoV-2 RBD and N protein for total Ig. To assess the effect of pasteurization breastmilk was exposed to Holder Pasteurization and High Pressure Pasteurization.

Results

Breastmilk contained antibodies against SARS-CoV-2 using any of the assays in 24 out of 29 (83%) proven cases, in six out of nine (67%) suspected cases and in none of the 13 controls.In vitroneutralization of SARS-CoV-2 clinical isolate virus strain was successful in a subset of serum (13%) and milk samples (26%). Although after pasteurization of the milk SARS-CoV-2 antibodies were detected with both methods of pasteurization, virus neutralizing capacity of those antibodies was only retained with the HPP approach.

Conclusion

Breastmilk of mothers who recovered from COVID-19 contains significant amounts of IgA against SARS-CoV-2, both before and after pasteurization.

Key Points

Question

Does breastmilk of mothers who have recovered from coronavirus disease 2019 (COVID-19) contain antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)?

Findings

We provide multiple lines of evidence on the presence of a variety of antibodies against SARS-CoV-2, with no such antibodies present in the controls. These antibodies are capable of neutralizing a clinical isolate of SARS-CoV-2in vitro. We furthermore show that high pressure pasteurization hardly affects antibody levels and efficacy.

Meaning

Breastmilk, obtained from mothers who have recovered from COVID-19, may serve as a safe and widely applicable preventive strategy for vulnerable high risk populations
Accurately Differentiating COVID-19, Other Viral Infection, and Healthy Individuals Using Multimodal Features via Late Fusion Learning
Authors: Xu Ming , Ouyang Liu , Gao Yan , Chen Yuanfang , Yu Tingting , Li Qian , Sun Kai , Bao Forrest Sheng , Safarnejad Lida , Wen Jing , Jiang Chao , Chen Tianyang , Han Lei , Zhang Hengdong , Gao Yue , Yu Zhengmin , Liu Xiaowen , Yan Tianyu , Li Hebi , Robinson Patrick , Zhu Baoli , Liu Jie , Liu Yang , Zhang Zengli , Ge Yaorong , Chen Shi
Published: August 2020

Effectively identifying COVID-19 patients using non-PCR clinical data is critical for the optimal clinical outcomes. Currently, there is a lack of comprehensive understanding of various biomedical features and appropriate technical approaches to accurately detecting COVID-19 patients. In this study, we recruited 214 confirmed COVID-19 patients in non-severe (NS) and 148 in severe (S) clinical type, 198 non-infected healthy (H) participants and 129 non-COVID viral pneumonia (V) patients. The participants’ clinical information (23 features), lab testing results (10 features), and thoracic CT scans upon admission were acquired as three input feature modalities. To enable late fusion of multimodality data, we developed a deep learning model to extract a 10-feature high-level representation of the CT scans. Exploratory analyses showed substantial differences of all features among the four classes. Three machine learning models (k-nearest neighbor kNN, random forest RF, and support vector machine SVM) were developed based on the 43 features combined from all three modalities to differentiate four classes (NS, S, V, and H) at once. All three models had high accuracy to differentiate the overall four classes (95.4%-97.7%) and each individual class (90.6%-99.9%). Multimodal features provided substantial performance gain from using any single feature modality. Compared to existing binary classification benchmarks often focusing on single feature modality, this study provided a novel and effective breakthrough for clinical applications. Findings and the analytical workflow can be used as clinical decision support for current COVID-19 and other clinical applications with high-dimensional multimodal biomedical features.

One sentence summary

We trained and validated late fusion deep learning-machine learning models to predict non-severe COVID-19, severe COVID-19, non-COVID viral infection, and healthy classes from clinical, lab testing, and CT scan features extracted from convolutional neural network and achieved predictive accuracy of > 96% to differentiate all four classes at once based on a large dataset of 689 participants.
Intertumoral Genetic Heterogeneity Generates Distinct Tumor Microenvironments in a Novel Murine Synchronous Melanoma Model
Authors: Qin Shuyang S. , Han Booyeon J. , Williams Alyssa , Jackson Katherine M. , Jewell Rachel , Chacon Alexander C. , Lord Edith M. , Linehan David C. , Kim Minsoo , Reuben Alexandre , Gerber Scott A. , Prieto Peter A.
Published: August 2020

Synchronous metastatic melanoma, clinically defined as multiple lesions diagnosed within 6 months, has a poor prognosis. Despite recent advances in systemic immunotherapy, a majority of patients fail to respond or exhibit lesion-specific responses. While intertumoral heterogeneity has been clinically associated with lesion-specific therapeutic responses, no clear mechanism has been identified, largely due to the scarcity of preclinical models. We developed a novel murine synchronous melanoma model that recapitulates clinical intertumoral heterogeneity. We show that genetic differences between tumors generate distinct tumor immune microenvironments (TIME). These TIMEs can independently upregulate PD-1/PD-L1 expression in response to ongoing anti-tumor immunity and the presence of interferon-gamma. The simultaneous presence of multiple tumors can additionally alter the TIME of each tumor. As such, our model provides a unique approach to investigate the effects of intertumoral heterogeneity on mechanisms of immunotherapy resistance.
Long-range sequential dependencies precede complex syntactic production in language acquisition
Authors: Sainburg Tim , Mai Anna , Gentner Timothy Q
Published: August 2020

To convey meaning, human language relies on hierarchically organized, long-range relationships spanning words, phrases, sentences, and discourse. The strength of the relationships between sequentially ordered elements of language (e.g., phonemes, characters, words) decays following a power law as a function of sequential distance. To understand the origins of these relationships, we examined long-range statistical structure in the speech of human children at multiple developmental time points, along with non-linguistic behaviors in humans and phylogenetically distant species. Here we show that adult-like power-law statistical dependencies precede the production of hierarchically-organized linguistic structures, and thus cannot be driven solely by these structures. Moreover, we show that similar long-range relationships occur in diverse non-linguistic behaviors across species. We propose that the hierarchical organization of human language evolved to exploit pre-existing long-range structure present in much larger classes of non-linguistic behavior, and that the cognitive capacity to model long-range hierarchical relationships preceded language evolution. We call this the Statistical Scaffolding Hypothesis for language evolution.

1

Significance Statement

Human language is uniquely characterized by semantically meaningful hierarchical organization, conveying information over long timescales. At the same time, many non-linguistic human and animal behaviors are also often characterized by richly hierarchical organization. Here, we compare the long-timescale statistical dependencies present in language to those present in non-linguistic human and animal behaviors as well as language production throughout childhood. We find adult-like, long-timescale relationships early in language development, before syntax or complex semantics emerge, and we find similar relationships in non-linguistic behaviors like cooking and even housefly movement. These parallels demonstrate that long-range statistical dependencies are not unique to language and suggest a possible evolutionary substrate for the long-range hierarchical structure present in human language.
Susceptibility of raccoon dogs for experimental SARS-CoV-2 infection
Authors: Freuling Conrad M. , Breithaupt Angele , Müller Thomas , Sehl Julia , Balkema-Buschmann Anne , Rissmann Melanie , Klein Antonia , Wylezich Claudia , Höper Dirk , Wernike Kerstin , Aebischer Andrea , Hoffmann Donata , Friedrichs Virginia , Dorhoi Anca , Groschup Martin H. , Beer Martin , Mettenleiter Thomas C.
Published: August 2020

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in China at the end of 2019, and became pandemic. The zoonotic virus most likely originated from bats, but definite intermediate hosts have not yet been identified. Raccoon dogs (Nyctereutes procyonoides) are kept for fur production, in particular in China, and were suspected as potential intermediate host for both SARS-CoV6 and SARS-CoV2. Here we demonstrate susceptibility of raccoon dogs for SARS-CoV-2 infection after intranasal inoculation and transmission to direct contact animals. Rapid, high level virus shedding, in combination with minor clinical signs and pathohistological changes, seroconversion and absence of viral adaptation highlight the role of raccoon dogs as a potential intermediate host. The results are highly relevant for control strategies and emphasize the risk that raccoon dogs may represent a potential SARS-CoV-2 reservoir. Our results support the establishment of adequate surveillance and risk mitigation strategies for kept and wild raccoon dogs.

Article Summary Line

Raccoon dogs are susceptible to and efficiently transmit SARS-CoV2 and may serve as intermediate host
Resolving Individual-Atom of Protein Complex using Commonly Available 300-kV Cryo-electron Microscopes
Authors: Zhang Kaiming , Pintilie Grigore D. , Li Shanshan , Schmid Michael F. , Chiu Wah
Published: August 2020

Breakthroughs in single-particle cryo-electron microscopy (cryo-EM) technology have made near-atomic resolution structure determination possible. Here, we report a ∼1.35-Å structure of apoferritin reconstructed from images recorded on a Gatan K3 or a Thermo Fisher Falcon 4 detector in a commonly available 300-kV Titan Krios microscope (G3i) equipped with or without a Gatan post-column energy filter. Our results demonstrate that the atomic-resolution structure determination can be achieved by single-particle cryo-EM with a fraction of a day of automated data collection. These structures resolve unambiguously each heavy atom (C, N, O, and S) in the amino acid side chains with an indication of hydrogen atoms’ presence and position, as well as the unambiguous existence of multiple rotameric configurations for some residues. We also develop a statistical and chemical based protocol to assess the positions of the water molecules directly from the cryo-EM map. In addition, we have introduced a B’ factor equivalent to the conventional B factor traditionally used by crystallography to annotate the atomic resolution model for determined structures. Our findings will be of immense interest among protein and medicinal scientists engaging in both basic and translational research.
A geometrical framework forf–statistics
Authors: Oteo–García Gonzalo , Oteo José–Angel
Published: August 2020

A detailed derivation of thef–statistics formalism is made from a geometrical framework. It is shown that thef–statistics appear when a genetic distance matrix is constrained to describe a four population phylogenetic tree. The choice of genetic metric is crucial and plays an outstanding role as regards the tree–like–ness criterion. The case of lack of treeness is interpreted in the formalism as presence of population admixture. In this respect, four formulas are given to estimate the admixture proportions. One of them is the so–calledf4–ratio estimate and we show that a second one is related to a known result developed in terms of the fixation indexFST. An illustrative numerical simulation of admixture proportion estimates is included. Relationships of the formalism with coalescence times and pairwise sequence differences are also provided.
Primary visual cortex injury produces loss of inhibitory neurons and long-term visual circuit dysfunction
Authors: Frankowski Jan C. , Foik Andrzej T. , Machhor Jiana R. , Lyon David C. , Hunt Robert F.
Published: August 2020

Primary sensory areas of the mammalian neocortex have a remarkable degree of plasticity, allowing neural circuits to adapt to dynamic environments. However, little is known about the effect of traumatic brain injury on visual system function. Here we applied a mild focal contusion injury to primary visual cortex (V1) in adult mice. We found that, although V1 was largely intact in brain-injured mice, there was a reduction in the number of inhibitory interneurons that extended into deep cortical layers. In general, we found a preferential reduction of interneurons located in superficial layers, near the impact site, while interneurons positioned in deeper layers were better preserved. Three months after injury, V1 neurons showed dramatically reduced responses to visual stimuli and weaker orientation selectivity and tuning, consistent with the loss of cortical inhibition. Our results demonstrate that V1 neurons no longer robustly and stably encode visual input following a mild traumatic injury.

Highlights

Inhibitory neurons are lost throughout brain injured visual cortex

Visually-evoked potentials are severely degraded after injury

Injured V1 neurons show weaker selectivity and tuning consistent with reduced interneurons
Genomic evolution of antibiotic resistance is contingent on genetic background following a long-term experiment withEscherichia coli
Authors: Card Kyle J. , Thomas Misty D. , Graves Joseph L. , Barrick Jeffrey E. , Lenski Richard E.
Published: August 2020

Antibiotic resistance is a growing health concern. Efforts to control resistance would benefit from an improved ability to forecast when and how it will evolve. Epistatic interactions between mutations can promote divergent evolutionary trajectories, which complicates our ability to predict evolution. We recently showed that differences between genetic backgrounds can lead to idiosyncratic responses in the evolvability of phenotypic resistance, even among closely relatedEscherichia colistrains. In this study, we examined whether a strain’s genetic background also influences the genotypic evolution of resistance. Do lineages founded by different genotypes take parallel or divergent mutational paths to achieve their evolved resistance states? We addressed this question by sequencing the complete genomes of antibiotic-resistant clones that evolved from several different genetic starting points during our earlier experiments. We first validated our statistical approach by quantifying the specificity of genomic evolution with respect to antibiotic treatment. As expected, mutations in particular genes were strongly associated with each drug. Then, we determined that replicate lines evolved from the same founding genotypes had more parallel mutations at the gene level than lines evolved from different founding genotypes, although these effects were more subtle than those showing antibiotic specificity. Taken together with our previous work, we conclude that historical contingency can alter both genotypic and phenotypic pathways to antibiotic resistance.

Significance

A fundamental question in evolution is the repeatability of adaptation. Will independently evolving populations respond similarly when facing the same environmental challenge? This question also has important public-health implications related to the growing problem of antibiotic resistance. For example, efforts to control resistance might benefit from accurately predicting mutational paths to resistance. However, this goal is complicated when a lineage’s prior history alters its subsequent evolution. We recently found that differences between genetic backgrounds can lead to unpredictable responses in phenotypic resistance. Here, we report that genetic background can similarly alter genotypic paths to resistance. This historical contingency underscores the importance of accounting for stochasticity, in the past as well as at present, when designing evolutionarily informed treatment strategies.
Rethinking glottal midline detection
Authors: Kist Andreas M. , Zilker Julian , Gómez Pablo , Schützenberger Anne , Döllinger Michael
Published: August 2020

A healthy voice is crucial for verbal communication and hence in daily as well as professional life. The basis for a healthy voice are the sound producing vocal folds in the larynx. A hallmark of healthy vocal fold oscillation is the symmetric motion of the left and right vocal fold. Clinically, videoendoscopy is applied to assess the symmetry of the oscillation and evaluated subjectively. High-speed videoendoscopy, an emerging method that allows quantification of the vocal fold oscillation, is more commonly employed in research due to the amount of data and the complex, semi-automatic analysis. In this study, we provide a comprehensive evaluation of methods that detect fully automatically the glottal midline. We use a biophysical model to simulate different vocal fold oscillations, extended the openly available BAGLS dataset using manual annotations, utilized both, simulations and annotated endoscopic images, to train deep neural networks at different stages of the analysis workflow, and compared these to established computer vision algorithms. We found that classical computer vision perform well on detecting the glottal midline in glottis segmentation data, but are outper-formed by deep neural networks on this task. We further suggest GlottisNet, a multi-task neural architecture featuring the simultaneous prediction of both, the opening between the vocal folds and the symmetry axis, leading to a huge step forward towards clinical applicability of quantitative, deep learning-assisted laryngeal endoscopy, by fully automating segmentation and midline detection.
Suboptimal intermediates underlie evolution of the Bicoid homeodomain
Authors: Onal Pinar , Gunasinghe Himari Imaya , Yui Umezawa Kristaley , Zheng Michael , Ling Jia , Azeez Leen , Dalmeus Anecine , Tazin Tasmima , Small Stephen
Published: August 2020

Changes in regulatory networks generate materials for evolution to create phenotypic diversity. For transcription networks, multiple studies have shown that alterations in binding sites of cis-regulatory elements correlate well with the gain or loss of specific features of the body plan. Less is known about alterations in the amino acid sequences of the transcription factors (TFs) that bind these elements. Here we study the evolution of Bicoid (Bcd), a homeodomain (HD) protein that is critical for anterior embryo patterning inDrosophila. The ancestor of Bcd (AncBcd) emerged after a duplication of a Zerknullt (Zen)-like ancestral protein (AncZB) in a suborder of flies. AncBcd diverged from AncZB, gaining novel transcriptional and translational activities. We focus on the evolution of the HD of AncBcd, which binds DNA and RNA, and is comprised of four subdomains: an N-terminal arm (NT) and three helices; H1, H2, and Recognition Helix (RH). Using chimeras of subdomains and gene rescue assays inDrosophila, we show that robust patterning activity of the Bcd HD (high frequency rescue to adulthood) is achieved only when amino acid substitutions in three separate subdomains (NT, H1, and RH) are combined. Other combinations of subdomains also yield full rescue, but with lower penetrance, suggesting alternative suboptimal activities. Our results suggest a multi-step pathway for the evolution of the Bcd HD that involved intermediate HD sequences with suboptimal activities, which constrained and enabled further evolutionary changes. They also demonstrate critical epistatic forces that contribute to the robust function of a DNA-binding domain.