bluuebunny/crossref_metadata_2025 huggingface dataset:
Amicitia
Authors: Rollinger Christian
Published: August 2020

The question of what constitutes friendship—a true friend—is one that has been asked in many societies and historically contingent periods, and from a number of different vantage points. Just as the Romans interrogated themselves as to the precise nature of their amicitiae, so, too, have ancient historians and classicists investigated the vast field of that relationship. They have asked widely divergent questions: What was the philosophical or emotional basis of Roman friendship? How did Roman authors, from the comedies of the middle republic to later imperial works, discuss friendship? What role did it play in society, in economic or political contexts? How was the traditional notion of amicitia changed by the changing circumstances first of the imperial period and, more profoundly, by the advent of Christendom? Ancient historians and classicists have been attempting to answer these questions for a long time. Scholarly discourse can be broadly divided into two large fields, the first of which was (and is) concerned with the development of Roman philosophical thought on amicitia and, particularly, with Cicero’s famous treatise Laelius de amicitia. As the study of Roman amicitiae is rendered exceedingly complicated by the intentionally vague semantics of Roman terminology, which employs amicitia for a variety of social relationships, not all of which a majority of people would now term “friendships,” little consensus has been reached beyond strictly philological questions. In addition to these philological and philosophical enquiries, however, a second field emerged in the early 1980s, which emphasized the importance of Roman institutions of personal relationships for the study of Roman history, particularly in the field of politics. This perspective has been enlarged in recent years by a renewed interest in the role of amicitia in, e.g., the Roman economy and in the communicative and affiliative strategies that were essential in creating and maintaining amicitiae. Additionally, there appeared what might be called a “democratization” of friendship studies, with amicitia no longer seen as an exclusive phenomenon between elite Roman males. The advent of Christianity (but also of new philosophical schools) in Late Antiquity was accompanied by a distinct rethinking of amicitia from a Neoplatonic and Christian perspective. Schramm 2013 and White 1992 (both cited under General Overviews) offer exemplary approaches and further references, but the changing interpretations of amicitia in the later Roman world make this a distinctly different subject and consequently this period is excluded from this bibliography.
Geographies of Diplomacy
Authors: Jackson Thomas
Published: August 2020

From the micro-geographies of specific diplomatic sites to the global imaginations of world politics that inform diplomatic relations, diplomacy has countless spatial dimensions. In recent years, scholars from various disciplines, including geography and International Relations (IR), have begun the task of critically engaging with geographical questions that diplomacy raises. At the core of this endeavor is foregrounding the often overlooked significance of space in diplomatic practice. At a micro-scale, diplomacy is comprised of a collection of activities and materials that are necessarily located somewhere in space. These specific “sites” of diplomacy have their own spatial organization—from the seating plan of a state dinner to the offices and corridors of embassies and foreign ministries—and these locations are shaped by their unique micro-geographies. The spatial dynamics of both spectacular and mundane diplomatic sites have led scholars to draw on the core geographical concept of “place” in analyzing diplomatic practice. Location has an emotional and affective agency that influences our perception of events; decisions as to where diplomacy takes place are as significant as the diplomatic actions themselves. Beyond specific sites, scholars have also considered how diplomacy plays a much wider role in the spatialization of world politics. First, diplomacy is an act closely associated with the functionality of the state. Performing the capacity to represent a polity through engagement with external actors is a legitimacy-building process and a key tool of statecraft. Second, the act of diplomacy also has transformative potential. Encounters between states that take place in diplomatic settings can mediate disputes, ignite arguments, and generally reshape how relations between actors are imagined. Research into the geographies of diplomacy benefits from a great breadth of perspectives. At a time when technological innovation and forces of globalization have given rise to “new” diplomatic actors and practices, multiple disciplinary perspectives have highlighted the changing spatial dynamics of diplomacy. In particular, innovative theoretical and methodological approaches have been developed to study alternative diplomatic actors both “above” and “below” the state. This challenge to traditional notions of who and what might be considered as diplomatic actors suggests that scholarly work on the geographies of diplomacy sits at the forefront of engagement with the rapidly changing terrain of contemporary diplomatic practice. The works included in this bibliography were selected to reflect current trends in this vibrant and rapidly evolving subfield. They are, however, only a sample of the wider work associated with the geographies of diplomacy and should be seen as a starting point for engagement with the literature.
Identification of a Unique Type of Isoflavone O-Methyltransferase, GmIOMT1, Based on Multi-Omics Analysis of Soybean under Biotic Stress
Authors: Uchida Kai , Sawada Yuji , Ochiai Koji , Sato Muneo , Inaba Jun , Hirai Masami Yokota
Published: August 2020

Isoflavonoids are commonly found in leguminous plants. Glycitein is one of the isoflavones produced by soybean. The genes encoding the enzymes in the isoflavone biosynthetic pathway have mostly been identified and characterized. However, the gene(s) for isoflavone O-methyltransferase (IOMT), which catalyzes the last step of glycitein biosynthesis, has not yet been identified. In this study, we conducted multi-omics analyses of fungal-inoculated soybean and indicated that glycitein biosynthesis was induced in response to biotic stress. Moreover, we identified a unique type of IOMT, which participates in glycitein biosynthesis. Soybean seedlings were inoculated with Aspergillus oryzae or Rhizopus oligosporus and sampled daily for 8 d. Multi-omics analyses were conducted using liquid chromatography–tandem mass spectrometry and RNA sequencing. Metabolome analysis revealed that glycitein derivatives increased following fungal inoculation. Transcriptome co-expression analysis identified two candidate IOMTs that were co-expressed with the gene encoding flavonoid 6-hydroxylase (F6H), the key enzyme in glycitein biosynthesis. The enzymatic assay of the two IOMTs using respective recombinant proteins showed that one IOMT, named as GmIOMT1, produced glycitein. Unlike other IOMTs, GmIOMT1 belongs to the cation-dependent OMT family and exhibited the highest activity with Zn2+ among cations tested. Moreover, we demonstrated that GmIOMT1 overexpression increased the levels of glycitein derivatives in soybean hairy roots when F6H was co-expressed. These results strongly suggest that GmIOMT1 participates in inducing glycitein biosynthesis in response to biotic stress.
A Sicilian–Cretan biogeographical disjunction in the land snail genusCornu(Gastropoda: Helicidae)
Authors: Hausdorf Bernhard , Bamberger Sonja , Walther Frank
Published: August 2020

We report an unusual biogeographical disjunction between the western and the eastern Mediterranean region. Cornu (Gastropoda: Helicidae) is a western Mediterranean land snail genus. It includes Cornu (Cornu) aspersum, which originated in north-western Africa and was distributed by humans for food or accidentally, first throughout the Mediterranean region and, subsequently, to all continents except Antarctica. It also includes three species belonging to the subgenus Erctella, which are all endemic to Sicily. We discovered a new species of Cornu on the Greek island of Crete. The morphological and molecular genetic analyses showed that the species from Crete is a disjunct representative of the subgenus Erctella. We hypothesize that the disjunction originated by a long-distance dispersal event of the ancestors of the Cretan species from Sicily by birds or by sea currents, perhaps facilitated by a tsunami or a similar event. The Cretan lineage separated from the Sicilian species in the Late Miocene or Early Pliocene. This divergence time is compatible with the hypothesis that the ancestor of Cornu cretense sp. nov. was washed from Sicily to Crete by the Zanclean flood that refilled the Mediterranean basin after it had dried up during the Messinian salinity crisis.
Revision shock in Pacific oysters taxonomy: the genusMagallana(formerlyCrassostreain part) is well-founded and necessary
Authors: Salvi Daniele , Mariottini Paolo
Published: August 2020

The description of the genus Magallana provoked taxonomic ‘revision shock’ among Bayne and colleagues, who criticised: (1) the supporting evidence for this taxonomic change, (2) the procedure used and (3) its impact on the nomenclatural stability of oysters. Here, we demonstrate that the description of the genus Magallana fulfils the norms of taxonomic and indexing revisions, and is well-founded on a scientific basis. The clade named Magallana is supported by a robust phylogeny based on comprehensive taxon sampling, independent datasets and varied analytical methods. A new maximum likelihood phylogenetic analysis of oysters, based on mitochondrial gene order data (representing molecular phenotypes above the sequence level), has provided additional support for this classification. These results are fully consistent with all previously published phylogenetic studies, thus providing an unambiguous indication of the stability of the clade that meets all the currently accepted criteria for naming clades as taxa. We show that, while the criterion of ‘morphological diagnosability’ is not applicable at any level of oyster classification, several striking molecular phenotypes are diagnostic of Magallana, both at the nuclear and the mitochondrial genome level. The classification with three genera Magallana, Crassostrea and Talonostrea reflects the evolutionary diversity of Crassostreinae and is consistent with taxonomic ranking criteria adopted for other oyster subfamilies.
Laboratory Assays Used to Rank Potato Cultivar Tolerance to Blackleg Showed That Tuber Vacuum Infiltration Results Correlate With Field Observations
Authors: Taylor Damar , Charkowski Amy O. , Zeng Yuan
Published: August 2020

Seed potato certification data collected in Colorado from 2012 to 2016 was used to rank potato cultivar tolerance to blackleg. Five cultivars with different tolerance levels to blackleg (‘Chipeta’ ≈ ‘Alegria’ ≈ ‘Lamoka’ < ‘Classic Russet’ < ‘Yukon Gem’) were tested to determine whether we could validate field data with laboratory assays. A strain isolated from Colorado, Pectobacterium atrosepticum CW1-4, and the P. atrosepticum type strain, 33260, were used to inoculate plants through vacuum infiltration of tubers or stem inoculation. Disease was assessed with time-lapse video and by measuring lesion length and disease incidence. After vacuum infiltration of tubers with P. atrosepticum CW1-4 and 33260, cultivars varied in tolerance to soft rot (‘Lamoka’ < ‘Classic Russet’ < ‘Alegria’ ≈ ‘Yukon Gem’ < ‘Chipeta’). Blackleg tolerance of the five cultivars also varied after vacuum infiltration (‘Lamoka’ < ‘Alegria’ ≈ ‘Chipeta’ < ‘Classic Russet’ ≈ ‘Yukon Gem’). All cultivars were susceptible after stem inoculation with either strain. In this assay, ‘Chipeta’ had the longest lesions, and ‘Lamoka’ had the smallest lesions. Time-lapse video was used to assess ‘Classic Russet’ and ‘Yukon Gem.’ ‘Yukon Gem’ developed disease symptoms faster than ‘Classic Russet,’ but the difference was not significant. These results indicate that relative susceptibility of the five cultivars to P. atrosepticum depends on the assay used and that laboratory and greenhouse results differed from field observations.
The Burden of Resilience Should Not Fall Solely on Nurses
Authors: Cunningham Tim
Published: August 2020

Health care organizations should manage burnout from the top down.
How State Scope-of-Practice Policies Impact NP Care
Authors: Taylor Lauren N. , Gilchrist Siobhan
Published: August 2020

Three projects examine the effect of NP practice acts on access to health care.
Treatment Approved for Severe Malaria
Authors: Aschenbrenner Diane S.
Published: August 2020

Artesunate for injection has been approved as initial treatment for severe malaria in both adults and children; artesunate should be followed by a full course of treatment with an oral antimalarial drug to prevent relapse.
Antihyperglycemic Drug Approved to Treat Heart Failure
Authors: Aschenbrenner Diane S.
Published: August 2020

Dapagliflozin (Farxiga) has been approved to reduce the risk of hospitalization and cardiovascular death in adults who have New York Heart Association class II to IV heart failure with reduced ejection fraction.
CE: Trauma-Related Hemorrhagic Shock: A Clinical Review
Authors: Caldwell Nicole W. , Suresh Mithun , Garcia-Choudary Tricia , VanFosson Christopher A.
Published: August 2020

Optimal management of trauma-related hemorrhagic shock begins at the point of injury and continues throughout all hospital settings. Several procedures developed on the battlefield to treat this condition have been adopted by civilian health care systems and are now used in a number of nonmilitary hospitals. Despite the important role nurses play in caring for patients with trauma-related hemorrhagic shock, much of the literature on this condition is directed toward paramedics and physicians. This article discusses the general principles underlying the pathophysiology and clinical management of trauma-related hemorrhagic shock and updates readers on nursing practices used in its management.
High Burden of Brain Lesions in Patients with Atrial Fibrillation
Authors: Rosenberg Karen
Published: August 2020

According to this study:

Patients with atrial fibrillation have a high burden of vascular brain lesions, as revealed by systematic brain MRI. Most lesions are clinically unrecognized (silent).

Even silent lesions are associated with worse cognitive function.
Early Exposure to Racial Segregation Linked to Poorer Cognitive Function in Midlife
Authors: Rosenberg Karen
Published: August 2020

According to this study:

Exposure to racial residential segregation during young adulthood is associated with worse cognitive function in Black adults as early as midlife.
Formula vs. Donor Breast Milk for Preterm or Low-Birth-Weight Infants
Authors: Ireson Deborah
Published: August 2020

Editor's note: The mission of Cochrane Nursing is to provide an international evidence base for nurses involved in delivering, leading, or researching nursing care. Cochrane Corner provides summaries of recent systematic reviews from the Cochrane Library. For more information, see https://nursing.cochrane.org.
Can Pediatric Orthopaedic Surgery be Done Safely in a Freestanding Ambulatory Surgery Center? Review of 3780 Cases
Authors: Sheffer Benjamin W. , Kelly Derek M. , Spence David D. , Walker Kent L. , Westbrooks Timothy J. , Palm Preston H. , Nolan Vikki G. , Sawyer Jeffrey R.
Published: August 2020

Background:

The purpose of this study was to determine the intraoperative and 30-day postoperative complication rates in a large consecutive cohort of pediatric patients who had orthopaedic surgery at a freestanding ambulatory surgery center (ASC). The authors also wanted to identify the rates of same-day, urgent hospital transfers, and 30-day hospital admissions. The authors hypothesized that pediatric orthopaedic procedures at a freestanding ASC can be done safely with a low rate of complications.

Methods:

A retrospective review identified patients aged 17 years or younger who had surgery at a freestanding ASC over a 9-year period. Adverse outcomes were divided into intraoperative complications, postoperative complications, need for the secondary procedure, unexpected hospital admission on the same day of the procedure, and unexpected hospital admission within 30 days of the index procedure. Complications were graded as grade 1, the complication could be treated without additional surgery or hospitalization; grade 2, the complication resulted in an unplanned return to the operating room (OR) or hospital admission; or grade 3, the complication resulted in an unplanned return to the OR or hospitalization with a change in the overall treatment plan.

Results:

Adequate follow-up was available for 3780 (86.1%) surgical procedures. Overall, there were 9 (0.24%) intraoperative complications, 2 (0.08%) urgent hospital transfers, 114 (3%) complications, and 16 (0.42%) readmissions. Seven of the 9 intraoperative complications resolved before leaving the OR, and 2 required return to the OR.

Neither complications nor hospitalizations correlated with age, race, gender, or length or type of surgery. There was no correlation between the presence of medical comorbidities, body mass index, or American Society of Anesthesiologists score and complication or hospitalization.

Conclusions:

Pediatric orthopaedic surgical procedures can be performed safely in an ASC because of multiple factors that include dedicated surgical teams, single-purpose ORs, and strict preoperative screening criteria. The rates of an emergency hospital transfer, surgical complications, and 30-day readmission, even by stringent criteria, are lower than those reported for outpatient procedures performed in the hospital setting.

Level of Evidence:

Level IV—case series.
The Economics of New Technology
Authors: Dvorzhinskiy Aleksey , Fragomen Austin T. , Rozbruch S. Robert
Published: August 2020

Emerging technologies have been implicated in the steady rise in healthcare expenditures. Although expensive, new technology has allowed for the treatment of very severe deformities within the field of limb lengthening and reconstruction. Beginning as early as the Ilizarov method of distraction osteogenesis, many of the treatments have resulted in impressive clinical results at the cost of being resource intensive. In addition to the economic cost, the treatments placed a significant burden on the patient who was forced to remain in external fixation for long periods of time. To decrease time in external fixation, lengthening over a nail and lengthening and then nailing were developed. Although certainly an improvement, external fixation was still a major component of treatment, and complications associated with its use remained. The advent of the motorized internal lengthening nail (MLN) has obviated the use of external fixation in a select group of patients and seems to be a step forward for the field. Still, the high upfront costs related to the price of the implant have served to limit its use in resource-poor areas and decrease adoption among cost-conscious surgeons. Although seemingly more expensive, the costs of MLN may be offset by the fact that this treatment requires fewer surgical procedures and may have fewer complications. This article reviews the available evidence with regards to the hospital, surgeon, and total cost when comparing lengthening over a nail versus MLN in the femur and lengthening and then nailing versus MLN in the tibia.
Management of Anticoagulation and Antiplatelet Therapy in Glaucoma Surgery
Authors: Shukla Aakriti G. , Ramulu Pradeep Y.
Published: August 2020

The use of antithrombotic therapy is rising as the population of older adults grows and novel agents with wider indications emerge. Likewise, surgical treatment of glaucoma may become increasingly common as the prevalence of glaucoma increases and innovative treatment options are developed. These trends highlight the need to understand how best to manage antithrombotic therapy in the context of glaucoma surgery. This review article describes current literature on antithrombotic therapy and perioperative thromboembolic risk evaluation based on individual factors. In addition, guidance is offered on the management of antithrombotic therapy in the setting of each type of glaucoma surgery, with an emphasis on a multidisciplinary approach involving the patients’ treating physicians.
In-Hospital Management Might Reduce Induction Deaths in Pediatric Patients With Acute Lymphoblastic Leukemia: Results From a Japanese Cohort
Authors: Nakagawa Shunsuke , Kato Motohiro , Imamura Toshihiko , Imai Chihaya , Koh Katsuyoshi , Kawano Yoshifumi , Shimomura Yasuto , Watanabe Arata , Kikuta Atsushi , Saito Akiko , Horibe Keizo , Manabe Atsushi , Ohara Akira , Okamoto Yasuhiro
Published: August 2020

Induction deaths (ID) remain a critical issue in the treatment of pediatric patients with acute lymphoblastic leukemia (ALL). The reported rate of ID in this population is 1% or higher. We speculate that this proportion might be lower in Japan because of mandatory hospitalization during induction therapy to manage complications. We retrospectively analyzed the incidence of ID among children with ALL enrolled in 4 Japanese study groups between 1994 and 2013. Among 5620 children, 41 (0.73%) cases of ID were noted. The median age was 6.5 years; 24 children were female, and 7 had T-cell ALL. Infection was the most common cause of ID (n=22), but the incidence (0.39%) was lower than that reported in western countries. Mortality within 48 hours from the onset of infection was low, comprising 25% of infection-related deaths. The incidence of infections caused by Bacillus species was low. Only 1 patient died because of Aspergillus infection. Fatal infections mostly occurred during the third week of induction therapy. Our findings suggest that close monitoring, stringent infection control, and immediate administration of appropriate antibiotics through hospitalization might be important strategies in reducing the rate of infection-related ID in pediatric patients with ALL.
Nonomuraea antri sp. nov., an actinomycete isolated from cave soil in Thailand
Authors: Lipun Kenika , Teo Wee Fei Aaron , Suksaard Paweena , Pathom-aree Wasu , Duangmal Kannika
Published: August 2020

A novel actinobacterium, designated strain NN258T, was isolated from a cave soil sample collected from a karst cave at Khao No-Khao Kaeo, Nakhon Sawan province, Thailand. The morphological, chemotaxonomic and phylogenetic characteristics were consistent with its classification in the genus

Nonomuraea

. Strain NN258T showed the highest 16S rRNA gene sequence similarity values to

Nonomuraea candida

HMC10T,

Nonomuraea mesophila

6K102T,

Nonomuraea rubra

DSM 43768T,

Nonomuraea diastatica

KC712T and

Nonomuraea helvata

IFO 14681T. The strain formed an extensively branched substrate and aerial mycelia. The whole-cell hydrolysates contained meso-diaminopimelic acid as the diagnostic diamino acid, with glucose, madurose, mannose and ribose as the whole-cell sugars. The polar lipids were diphosphatidylglycerol, phosphotidylmethylethanolamine, phosphatidylethanolamine, hydroxy-phosphatidylmonomethylethanolamine, hydroxy-phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannoside, two unidentified phospholipids, three unidentified sugar-containing phosphoaminolipids, an unidentified glycolipid and two unidentified lipids. The predominant menaquinone was MK-9(H4), with minor amounts of MK-9(H0), MK-9(H2) and MK-9(H6). Major cellular fatty acids (>10%) were iso-C16 : 0 and 10-methyl-C17 : 0. The G+C content of the genomic DNA was 71.0 mol%. The average nucleotide identity and digital DNA–DNA hybridization values between strain NN258T and the reference strains were 79.9–80.9 % and 26.1–27.0 %, respectively. On the basis of phenotypic, genotypic and phylogenetic data, strain NN258T represents a novel species of the genus

Nonomuraea

, for which the name Nonomuraea antri sp. nov. is proposed. The type strain is NN258T (=TBRC 11478T=NBRC 114269T).
Yersinia artesiana sp. nov., Yersinia proxima sp. nov., Yersinia alsatica sp. nov., Yersina vastinensis sp. nov., Yersinia thracica sp. nov. and Yersinia occitanica sp. nov., isolated from humans and animals
Authors: Le Guern Anne-Sophie , Savin Cyril , Angermeier Hilde , Brémont Sylvie , Clermont Dominique , Mühle Estelle , Orozova Petya , Najdenski Hristo , Pizarro-Cerdá Javier
Published: August 2020

Thirty-three

Yersinia

strains previously characterized by the French

Yersinia

National Reference Laboratory (YNRL) and isolated from humans and animals were suspected to belong to six novel species by a recently described core genome multilocus sequence typing scheme. These strains and five additional strains from the YNRL were characterized using a polyphasic taxonomic approach including a phylogenetic analysis based on 500 core genes, determination of average nucleotide identity (ANI), determination of DNA G+C content and identification of phenotypic features. Phylogenetic analysis confirmed that the 38 studied strains formed six well-demarcated clades. ANI values between these clades and their closest relatives were <94.7 % and ANI values within each putative novel species were >97.5 %. Distinctive biochemical characteristics were identified in five out of the six novel species. All of these data demonstrated that the 38 strains belong to six novel species of the genus

Yersinia

: Yersinia artesiana sp. nov., type strain IP42281T (=CIP 111845T=DSM 110725T); Yersinia proxima sp. nov., type strain IP37424T (=CIP 111847T=DSM 110727T); Yersinia alsatica sp. nov., type strain IP38850T (=CIP 111848T=DSM 110726T); Yersinia vastinensis sp. nov., type strain IP38594T (=CIP 111844T=DSM 110738T); Yersinia thracica sp. nov., type strain IP34646T (=CIP 111842T=DSM 110736T); and Yersinia occitanica sp. nov., type strain IP35638T (=CIP 111843T=DSM 110739T).
Pooling of samples to optimize SARS-CoV-2 diagnosis by RT-qPCR: comparative analysis of two protocols
Authors: Volpato Fabiana , Lima-Morales Daiana , Wink Priscila Lamb , Willig Julia , Paris Fernanda , Ashton-Prolla Patricia , Barth Afonso Luís
Published: August 2020

RT-qPCR for SARS-CoV-2 is the main diagnostic test used to identify the novel coronavirus. Several countries have used large scale SARS-CoV-2 RT-qPCR testing as one of the important strategies for combating the pandemic. In order to process the massive needs for coronavirus testing, the usual throughput of routine clinical laboratories has reached and often surpassed its limits and new approaches to cope with this challenge must be developed. This study has aimed to evaluate the use pool of samples as a strategy to optimize the diagnostic of SARS-CoV-2 by RT-qPCR in a general population. A total of 220 naso/orofaryngeal swab samples were collected and tested using two different protocols of sample pooling. In the first protocol (Protocol A); 10 clinical samples were pooled before RNA extraction. The second protocol (Protocol B) consisted of pooling the already extracted RNAs from 10 individual samples. Results from Protocol A were identical (100% agreement) with the individual results. However, for results from Protocol B, reduced agreement (91%) was observed in relation to results obtained by individual testing. Inconsistencies observed were related to RT-qPCR results with higher Cycle Thresholds (Ct > 32.73). Furthermore, in pools containing more than one positive individual, the Ct of the pool was equivalent to the lowest Ct among the individual results. These results provide additional evidence in favor of the clinical use of pooled samples for SARS-CoV-2 diagnosis by RT-qPCR and suggest that pooling of samples before RNA extraction is preferrable in terms of diagnostic yield.
MicroRNA variants and HLA-miRNA interactions are novel rheumatoid arthritis susceptibility factors
Authors: Guo Shicheng , Jin Yehua , Zhou Jieru , Zhu Qi , Jiang Ting , Bian Yanqin , Zhang Runrun , Chang Cen , Xu Lingxia , Shen Jie , Zheng Xinchun , Shen Yi , Qin Yingying , Chen Jihong , Tang Xiaorong , Cheng Peng , Ding Qin , Zhang Yuanyuan , Liu Jia , Cheng Qingqing , Guo Mengru , Liu Zhaoyi , Qiu Weifang , Qian Yi , Sun Yang , Shen Yu , Nie Hong , Schrodi Steven J , He Dongyi
Published: August 2020

Objective

Althogh Genome-wide association studies have identified >100 variants for rheumatoid arthritis (RA),the reported genetic variants only explain <40% of RA heritability. We conducted a systemic association study between common East-Asian miRNA SNPs with RA in a large Han Chinese cohort to explain missing heritability and identify miRNA epistatic interactions.

Methods

4 HLA SNPs (HLA-DRB1, HLA-DRB9, HLA-DQB1 and TNFAIP3) and 225 common SNPs located in miRNA which might influence the miRNA target binding or pre-miRNA stability were genotyped in 1,607 rheumatoid arthritis and 1,580 matched normal individuals. A meta-analysis with previous GWAS studies (4,873 RA cases and 17,642 controls) was performed to discovery another novel miRNA RA-associated SNPs.

Results

2 novel SNPs including rs1414273 (miR-548ac, OR=0.84, P=8.26×10-4) and rs2620381 (miR-627, OR=0.77, P=2.55×10-3) conferred significant association with RA. Individuals carried 8 risk alleles showed 15.38 (95%CI: 4.69-50.49, P<1.0×10-6) times more risk to be affected by RA. In addition, rs5997893 (miR-3928) showed significant epistasis effect with rs4947332 (HLA-DRB1, OR=4.23, P=0.04) and rs2967897 (miR-5695) with rs7752903 (TNFAIP3, OR=4.43, P=0.03). Finally, we demonstrated targets of the significant miRNAs showed enrichment in immune related genes (P=2.0×10-5) and FDA approved drug target genes (P=0.014).

Conclusions

6 novel miRNA SNPs including rs1414273 (miR-548ac, P=8.26×10-4), rs2620381 (miR-627, P=2.55×10-3), rs4285314 (miR-3135b, P=1.10×10-13), rs28477407 (miR-4308, P=3.44×10-5), rs5997893 (miR-3928, P=5.9×10-3) and rs45596840 (miR-4482, P=6.6×10-3) were confirmed to be significantly associated with RA in a Chinese population. Our study suggests that miRNAs might be interesting targets to accelerate the understanding of the pathogenesis and drug development for rheumatoid arthritis.
Identification of a polymorphism in the N gene of SARS-CoV-2 that adversely impacts detection by a widely-used RT-PCR assay
Authors: Vanaerschot Manu , Mann Sabrina A. , Webber James T. , Kamm Jack , Bell Sidney M. , Bell John , Hong Si Noon , Nguyen Minh Phuong , Chan Lienna Y. , Bhatt Karan D. , Tan Michelle , Detweiler Angela M. , Espinosa Alex , Wu Wesley , Batson Joshua , Dynerman David ,   CLIAHUB Consortium, Wadford Debra A. , Puschnik Andreas S. , Neff Norma , Ahyong Vida , Miller Steve , Ayscue Patrick , Tato Cristina M. , Paul Simon , Kistler Amy , DeRisi Joseph L. , Crawford Emily D.
Published: August 2020

We identify a mutation in the N gene of SARS-CoV-2 that adversely affects annealing of a commonly used RT-PCR primer; epidemiologic evidence suggests the virus retains pathogenicity and competence for spread. This reinforces the importance of using multiple targets, preferably in at least 2 genes, for robust SARS-CoV-2 detection.

Article Summary Line

A SARS-CoV-2 variant that occurs worldwide and has spread in California significantly affects diagnostic sensitivity of an N gene assay, highlighting the need to employ multiple viral targets for detection.
Multi-omics phenotyping of the gut-liver axis allows health risk predictability fromin vivosubchronic toxicity tests of a low-dose pesticide mixture
Authors: Mesnage Robin , Teixeira Maxime , Mandrioli Daniele , Falcioni Laura , Ducarmon Quinten Raymond , Zwittink Romy Daniëlle , Amiel Caroline , Panoff Jean-Michel , Bourne Emma , Savage Emanuel , Mein Charles A , Belpoggi Fiorella , Antoniou Michael N
Published: August 2020

Human health effects from chronic exposure to mixtures of pesticide residues are little investigated. We compared standard histopathology and serum biochemistry measures and multi-omics analyses in anin vivosubchronic toxicity test of a mixture of six pesticide active ingredients frequently detected in foodstuffs (azoxystrobin, boscalid, chlorpyrifos, glyphosate, imidacloprid and thiabendazole). Sprague-Dawley rats were administered with the pesticide mixture with each ingredient at its regulatory permitted acceptable daily intake. Analysis of water and feed consumption, body weight, histopathology and serum biochemistry showed little or no physiological effects from exposure to the pesticide mixture. In marked contrast, analysis of the host-gut microbiome axis using serum and caecum metabolomics revealed that nicotinamide and tryptophan metabolism were affected, which suggested the initiation of a cell danger response, including adaptation to oxidative stress. Only limited effects were detected on the caecum microbiota by shotgun metagenomics. Further analyses ofin vitrobacterial cultures showed that growth ofLactobacillus rhamnosusandEscherichia colistrains was negatively impacted by the pesticide mixture at concentrations that were not inhibitory when exposure was to a single agent. Transcriptomics of the liver showed that 257 genes had their expression changed. Gene functions affected included those involved in the regulation of response to hormones and correlated with previously reported transcriptome changes following administration of nicotinamide. Genome-wide DNA methylation analysis of the same liver samples showed that 4255 CpG sites were differentially methylated (> 10% difference). Overall, we demonstrated that unlike standard blood biochemical and organ histological analysis, in-depth molecular profiling using a combination of high-throughput ‘-omics’ methods in laboratory animals exposed to low concentrations of pesticides reveals metabolic effects on the gut-liver axis, which can potentially be used as biomarkers for the prediction of future negative health outcomes. Our data suggest that adoption of multi-omics as part of regulatory risk assessment procedures will result in more accurate outcome measures, with positive public health implications.
PieParty: Visualizing cells from scRNA-seq data as pie charts
Authors: Kurtenbach Stefan , Dollar James J. , Cruz Anthony M. , Durante Michael A. , Harbour J. William
Published: August 2020

Single cell RNA sequencing (scRNA-seq) has been a transformative technology in many research fields. Dimensional reduction techniques such as UMAP and tSNE are used to visualize scRNA-seq data in two or three dimensions in order for cells to be clustered in biologically meaningful ways. Subsequently, gene expression is frequently mapped onto these plots to show the distribution of gene expression across the plots, for instance to distinguish cell types. However, plotting each cell with only one color leads to repetitive and unintuitive representations. Here, we present Pie Party, which allows scRNA-seq data to be plotted such that every cell is represented as a pie chart, and every slice in the pie charts corresponds to the gene expression of individual genes. This allows for the simultaneous visualization of the expression of multiple genes and gene networks. The resulting figures are information dense, space efficient and highly intuitive. PieParty is publicly available on GitHub athttps://github.com/harbourlab/PieParty.
Optimization and scaling of patient-derived brain organoids uncovers deep phenotypes of disease
Authors: Shah Kevan , Bedi Rishi , Rogozhnikov Alex , Ramkumar Pavan , Tong Zhixiang , Rash Brian , Stanton Morgan , Sorokin Jordan , Apaydin Cagsar , Batarse Anthony , Bergamaschi Julia , Blattner Robert , Brown Spencer , Bosshardt Anthony , Castrillo Carlos , Dang Brenda , Drusinsky Shiron , Enriquez Luigi , Grayson David , Hilliard Juliana , Hsu Pei-Ken , Johnson Chili , Jones Ryan , Lash Andy , Lee Chia-Yao , Li Kelly , McKay Austin , Mount Elliot , Nicola Justin , Oumzil Ismael , Paek Justin , Pascoe Deborah , Piepho Arden , Poust Sean , Quang Daphne , Schultz Matthew , Sims Jessica , Taylor Patrick , Treiman Geffen , Wueseke Oliver , Young Noah , Pollen Alex , Flanzer Doug , Chao Daniel , Skibinski Gaia , Kato Saul , Escola G. Sean
Published: August 2020

Cerebral organoids provide unparalleled access to human brain development in vitro. However, variability induced by current culture methodologies precludes using organoids as robust disease models. To address this, we developed an automated Organoid Culture and Assay (ORCA) system to support longitudinal unbiased phenotyping of organoids at scale across multiple patient lines. We then characterized organoid variability using novel machine learning methods and found that the contribution of donor, clone, and batch is significant and remarkably consistent over gene expression, morphology, and cell-type composition. Next, we performed multi-factorial protocol optimization, producing a directed forebrain protocol compatible with 96-well culture that exhibits low variability while preserving tissue complexity. Finally, we used ORCA to study tuberous sclerosis, a disease with known genetics but poorly representative animal models. For the first time, we report highly reproducible early morphological and molecular signatures of disease in heterozygous TSC+/− forebrain organoids, demonstrating the benefit of a scaled organoid system for phenotype discovery in human disease models.
Network asynchrony underlying increased broadband gamma power
Authors: Guyon Nicolas , Zacharias Leonardo Rakauskas , de Oliveira Eliezyer Fermino , Kim Hoseok , Leite João Pereira , Lopes-Aguiar Cleiton , Carlén Marie
Published: August 2020

Synchronous activity of cortical inhibitory interneurons expressing parvalbumin (PV) underlies the expression of cortical gamma rhythms. Paradoxically, deficient PV inhibition is associated with increased broadband gamma power. Increased baseline broadband gamma is also a prominent characteristic in schizophrenia, and a hallmark of network alterations induced by N-methyl-D-aspartate receptor (NMDAR) antagonists such as ketamine. It has been questioned if enhanced broadband gamma power is a true rhythm, and if rhythmic PV inhibition is involved or not. It has been suggested that asynchronous and increased firing activities underlie broadband power increases spanning the gamma band. Using mice lacking NMDAR activity specifically in PV neurons to model deficient PV inhibition, we here show that local LFP (local field potential) oscillations and neuronal activity with decreased synchronicity generate increases in prefrontal broadband gamma power. Specifically, reduced spike time precision of both local PV interneurons and wide-spiking (WS) excitatory neurons contribute to increased firing rates, and spectral leakage of spiking activity (spike “contamination”) affecting the broadband gamma band. Desynchronization was evident at multiple time scales, with reduced spike-LFP entrainment, reduced cross-frequency coupling, and fragmentation of brain states. While local application of S(+)-ketamine in wildtype mice triggered network desynchronization and increases in broadband gamma power, our investigations suggest that disparate mechanisms underlie increased power of broadband gamma caused by genetic alteration of PV interneurons, and ketamine-induced power increases in broadband gamma. Our studies, thus, confirm that broadband gamma increases can arise from asynchronous activities, and demonstrate that long-term deficiency of PV inhibition can be a contributor.
Differences in structure and hibernation mechanism highlight diversification of the microsporidian ribosome
Authors: Ehrenbolger Kai , Jespersen Nathan , Sharma Himanshu , Sokolova Yuliya Y. , Tokarev Yuri S. , Vossbrinck Charles R. , Barandun Jonas
Published: August 2020

Assembling and powering ribosomes are energy-intensive processes requiring fine-tuned cellular control mechanisms. In organisms operating under strict nutrient limitations, such as pathogenic microsporidia, conservation of energy via ribosomal hibernation and recycling is critical. The mechanisms by which hibernation is achieved in microsporidia, however, remain poorly understood. Here, we present the cryo-EM structure of the ribosome from Paranosema locustae spores, bound by the conserved eukaryotic hibernation and recycling factor Lso2. The microsporidian Lso2 homolog adopts a V-shaped conformation to bridge the mRNA decoding site and the large subunit tRNA binding sites, providing a reversible ribosome inactivation mechanism. Although microsporidian ribosomes are universally highly compacted, the P. locustae ribosome retains several rRNA segments absent in other microsporidia, and represents an intermediate state of rRNA reduction. In one case, the near complete reduction of an expansion segment has resulted in a single bound nucleotide, which acts as an architectural co-factor to stabilize a protein-protein interface. The presented structure highlights the reductive evolution in these emerging pathogens and sheds light on a conserved mechanism for eukaryotic ribosome hibernation.
Multi-species ELISA for the detection of antibodies against SARS-CoV-2 in animals
Authors: Wernike Kerstin , Aebischer Andrea , Michelitsch Anna , Hoffmann Donata , Freuling Conrad , Balkema-Buschmann Anne , Graaf Annika , Müller Thomas , Osterrieder Nikolaus , Rissmann Melanie , Rubbenstroth Dennis , Schön Jacob , Schulz Claudia , Trimpert Jakob , Ulrich Lorenz , Volz Asisa , Mettenleiter Thomas , Beer Martin
Published: August 2020

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a pandemic with millions of infected humans and hundreds of thousands of fatalities. As the novel disease - referred to as COVID-19 - unfolded, occasional anthropozoonotic infections of animals by owners or caretakers were reported in dogs, felid species and farmed mink. Further species were shown to be susceptible under experimental conditions. The extent of natural infections of animals, however, is still largely unknown. Serological methods will be useful tools for tracing SARS-CoV-2 infections in animals once test systems are validated for use in different species. Here, we developed an indirect multi-species ELISA based on the receptor-binding domain (RBD) of SARS-CoV-2. The newly established ELISA was validated using 59 sera of infected or vaccinated animals including ferrets, raccoon dogs, hamsters, rabbits, chickens, cattle and a cat, and a total of 220 antibody-negative sera of the same animal species. Overall, a diagnostic specificity of 100.0% and sensitivity of 98.31% was achieved, and the functionality with every species included in this study could be demonstrated. Hence, a versatile and reliable ELISA protocol was established that enables high-throughput antibody detection in a broad range of animal species, which may be used for outbreak investigations, to assess the seroprevalence in susceptible species or to screen for reservoir or intermediate hosts.
Production of biopolymer precursors beta-alanine and L-lactic acid from CO2with metabolically versatileRhodococcus opacusDSM 43205
Authors: Salusjärvi Laura , Ojala Leo , Peddinti Gopal , Lienemann Michael , Jouhten Paula , Pitkänen Juha-Pekka , Toivari Mervi
Published: August 2020

Hydrogen oxidizing autotrophic bacteria are promising hosts for CO2conversion into chemicals. In this work, we engineered the metabolically versatile lithoautotrophic bacteriumRhodococcus opacusstrain DSM 43205 for synthesis of polymer precursors. Aspartate decarboxylase (panD) or lactate dehydrogenase (ldh) were expressed for beta-alanine or L-lactic acid production, respectively. The heterotrophic cultivations on glucose produced 25 mg L-1beta-alanine and 742 mg L-1L-lactic acid, while autotrophic cultivations with CO2, H2and O2resulted in the production of 1.8 mg L-1beta-alanine and 146 mg L-1L-lactic acid. Beta-alanine was also produced at 345 µg L-1from CO2in electrobioreactors, where H2and O2were provided by water electrolysis. This work demonstrates thatR. opacusDSM 43205 can be readily engineered to produce chemicals from CO2and provides base for its further metabolic engineering.
Modulation of the cAMP levels with a conserved actinobacteria phosphodiesterase enzyme reduces antimicrobial tolerance in mycobacteria
Authors: Thomson Michael , Nunta Kanokkan , Cheyne Ashleigh , liu Yi , Garza-Garcia Acely , Larrouy-Maumus Gerald
Published: August 2020

Antimicrobial tolerance (AMT) is the gateway to the development of antimicrobial resistance (AMR) and is therefore a major issue that needs to be addressed.

The second messenger cyclic-AMP (cAMP), which is conserved across all taxa, is involved in propagating signals from environmental stimuli and converting these into a response. In bacteria, such asM. tuberculosis,P. aeruginosa,V. choleraeandB. pertussis, cAMP has been implicated in virulence, metabolic regulation and gene expression. However, cAMP signalling in mycobacteria is particularly complex due to the redundancy of adenylate cyclases, which are enzymes that catalyse the formation of cAMP from ATP, and the poor activity of the only known phosphodiesterase (PDE) enzyme, which degrades cAMP into 5’- AMP.

Based on these two features, the modulation of this system with the aim of investigating cAMP signalling and its involvement in AMT in mycobacteria id difficult.

To address this pressing need, we identified a new cAMP-degrading phosphodiesterase enzyme (Rv1339) and used it to significantly decrease the intrabacterial levels of cAMP in mycobacteria. This analysis revealed that this enzyme increased the antimicrobial susceptibility ofM. smegmatismc2155. Using a combination of metabolomics, RNA-sequencing, antimicrobial susceptibility assays and bioenergetics analysis, we were able to characterize the molecular mechanism underlying this increased susceptibility.

This work represents an important milestone showing that the targeting of cAMP signalling is a promising new avenue for antimicrobial development and expands our understanding of cAMP signalling in mycobacteria.
One-step multiple site-specific base editing by direct embryo injection for precision and pyramid pig breeding
Authors: Song Ruigao , Wang Yu , Zheng Qiantao , Yao Jing , Cao Chunwei , Wang Yanfang , Zhao Jianguo
Published: August 2020

Precise and simultaneous acquisition of multiple beneficial alleles in the genome to improve pig performance are pivotal for making elite breeders. Cytidine base editors (CBEs) have emerged as powerful tools for site-specific single nucleotide replacement. Here, we compare the editing efficiency of four CBEs in porcine embryonic cells and embryos to show that hA3A-BE3-Y130F and hA3A-eBE3-Y130F consistently results in higher base-editing efficiency and lower toxic effects to in vitro embryo development. We also show that zygote microinjection of hA3A-BE3-Y130F results in one-step generation of pigs (3BE pigs) harboring C-to-T point mutations, including a stop codon in CD163 and in MSTN and induce beneficial allele in IGF2. The 3BE pigs showed improved growth performance, hip circumference, food conversion rate. Our results demonstrate that CBEs can mediate high throughput genome editing by direct embryo microinjection. Our approach allows immediate introduction of novel alleles for beneficial traits in transgene-free animals for pyramid breeding.