Replication research: opportunities, experiences and challenges

Replication is one of the main principles of the scientific method. In the physical sciences, new knowledge is often not considered valid until the original study has been replicated in other labs and the original results are not refuted Replication will either improve confidence in our research findings or identify important boundary conditions. Replications also enhance various scientific processes and offer methodical and educational improvements. The purpose of this panel is twofold. First, to explore the opportunities for scientific development that replication research enables by reflecting on the experiences of encouraging, doing, and publishing replication studies. Second, to explore the various challenges that replication research raises about its value to individual scholars as well as to our collective understanding of phenomena within the information systems field

A Multi-Epoch Study of the Radio Continuum Emission of Orion Source I: Constraints on the Disk Evolution of a Massive YSO and the Dynamical History of Orion BN/KL

We present new 7mm continuum observations of Orion BN/KL with the VLA. We resolve the emission from the protostar radio Source I and BN at several epochs. Source I is highly elongated NW-SE, and remarkably stable in flux density, position angle, and overall morphology over nearly a decade. This favors the extended emission component arising from an ionized disk rather than a jet. We have measured the proper motions of Source I and BN for the first time at 43 GHz. We confirm that both sources are moving at high speed (12 and 26 km/s, respectively) approximately in opposite directions, as previously inferred from measurements at lower frequencies. We discuss dynamical scenarios that can explain the large motions of both BN and Source I and the presence of disks around both. Our new measurements support the hypothesis that a close (~50 AU) dynamical interaction occurred around 500 years ago between Source I and BN as proposed by Gomez et al. From the dynamics of encounter we argue that Source I today is likely to be a binary with a total mass on the order of 20 Msun, and that it probably existed as a softer binary before the close encounter. This enables preservation of the original accretion disk, though truncated to its present radius of ~50 AU. N-body numerical simulations show that the dynamical interaction between a binary of 20 Msun total mass (I) and a single star of 10 Msun mass (BN) may lead to the ejection of both and binary hardening. The gravitational energy released in the process would be large enough to power the wide-angle flow traced by H2 and CO emission in the BN/KL nebula. Assuming the proposed dynamical history is correct, the smaller mass for Source I recently estimated from SiO maser dynamics (>7 Msun) by Matthews et al., suggests that non-gravitational forces (e.g. magnetic) must play an important role in the circumstellar gas dynamics.Comment: 17 pages, 7 figures, 4 tables, accepted by Ap

The genome evolution and domestication of tropical fruit mango

Background: Mango is one of the world’s most important tropical fruits. It belongs to the family Anacardiaceae, which includes several other economically important species, notably cashew, sumac and pistachio from other genera. Many species in this family produce family-specific urushiols and related phenols, which can induce contact dermatitis. Results: We generate a chromosome-scale genome assembly of mango, providing a reference genome for the Anacardiaceae family. Our results indicate the occurrence of a recent whole-genome duplication (WGD) event in mango. Duplicated genes preferentially retained include photosynthetic, photorespiration, and lipid metabolic genes that may have provided adaptive advantages to sharp historical decreases in atmospheric carbon dioxide and global temperatures. A notable example of an extended gene family is the chalcone synthase (CHS) family of genes, and particular genes in this family show universally higher expression in peels than in flesh, likely for the biosynthesis of urushiols and related phenols. Genome resequencing reveals two distinct groups of mango varieties, with commercial varieties clustered with India germplasms and demonstrating allelic admixture, and indigenous varieties from Southeast Asia in the second group. Landraces indigenous in China formed distinct clades, and some showed admixture in genomes. Conclusions: Analysis of chromosome-scale mango genome sequences reveals photosynthesis and lipid metabolism are preferentially retained after a recent WGD event, and expansion of CHS genes is likely associated with urushiol biosynthesis in mango. Genome resequencing clarifies two groups of mango varieties, discovers allelic admixture in commercial varieties, and shows distinct genetic background of landraces

Virulence behavior of uropathogenic Escherichia coli strains in the host model Caenorhabditis elegans

Urinary tract infections (UTIs) are among the most common bacterial infections in humans. Although a number of bacteria can cause UTIs, most cases are due to infection by uropathogenic Escherichia coli (UPEC). UPEC are a genetically heterogeneous group that exhibit several virulence factors associated with colonization and persistence of bacteria in the urinary tract. Caenorhabditis elegans is a tiny, free-living nematode found worldwide. Because many biological pathways are conserved in C. elegans and humans, the nematode has been increasingly used as a model organism to study virulence mechanisms of microbial infections and innate immunity. The virulence of UPEC strains, characterized for antimicrobial resistance, pathogenicity-related genes associated with virulence and phylogenetic group belonging was evaluated by measuring the survival of C. elegans exposed to pure cultures of these strains. Our results showed that urinary strains can kill the nematode and that the clinical isolate ECP110 was able to efficiently colonize the gut and to inhibit the host oxidative response to infection. Our data support that C. elegans, a free-living nematode found worldwide, could serve as an in vivo model to distinguish, among uropathogenic E. coli, different virulence behavior

Effects of monoculture and polyculture farming in oil palm smallholdings on terrestrial arthropod diversity

Oil palm agriculture has become one of the economic mainstays for biodiversity-rich countries in the tropics. The conversion of native forests to oil palm monoculture plantation has caused unprecedented biodiversity loss in Southeast Asia. Little is known about the effects of oil palm polyculture farming on arthropod diversity. In this study, arthropods were sampled using pitfall traps at 120 sites in Peninsular Malaysia. We examined how arthropod biodiversity responded to different oil palm farming practices and local-scale vegetation structure characteristics. We found that the number of arthropod orders was significantly greater in polyculture than monoculture smallholdings. However, we did not detect a significant difference in arthropod order composition nor abundance between monoculture and polyculture practices. In situ habitat characteristics explained 16% of the variation in arthropod order richness, with key predictor variables including farming practice, height of oil palm stands, and number of immature palm. The findings of this study suggest that polyculture farming together with management for in situ habitat complexity may be a useful strategy in supporting biodiversity within in oil palm plantations

Coronary Artery Disease in Patients Undergoing Transvalvular Aortic Valve Implantation

Coronary artery disease (CAD) is common in patients with severe aortic stenosis. With the advent of transcatheter aortic valve implantation (TAVI) as a therapeutic option, management of CAD in such patients has undergone a revolution. Younger patients are now candidates for treatment, and have a greater life-time probability of requiring post-TAVI coronary access. Considerations include pre-procedural assessment and revascularisation, procedural planning to avoid coronary obstruction as well as optimisation of post-procedural coronary access. The authors review the challenges of managing CAD in TAVI patients, shed light on the evidence base, and provide guidance on how to optimise management

Resequencing and comparative genomics of stagonospora nodorum: Sectional gene absence and effector discovery

Stagonospora nodorum is an important wheat (Triticum aestivum) pathogen in many parts of the world, causing major yield losses. It was the first species in the large fungal Dothideomycete class to be genome sequenced. The reference genome sequence (SN15) has been instrumental in the discovery of genes encoding necrotrophic effectors that induce disease symptoms in specific host genotypes. Here we present the genome sequence of two further S. nodorum strains (Sn4 and Sn79) that differ in their effector repertoire from the reference. Sn79 is avirulent on wheat and produces no apparent effectors when infiltrated onto many cultivars and mapping population parents. Sn4 is pathogenic on wheat and has virulences not found in SN15. The new strains, sequenced with short-read Illumina chemistry, are compared with SN15 by a combination of mapping and de novo assembly approaches.Each of the genomes contains a large number of strain-specific genes, many of which have no meaningful similarity to any known gene. Large contiguous sections of the reference genome are absent in the two newly sequenced strains. We refer to these differences as “sectional gene absences.” The presence of genes in pathogenic strains and absence in Sn79 is added to computationally predicted properties of known proteins to produce a list of likely effector candidates. Transposon insertion was observed in the mitochondrial genomes of virulent strains where the avirulent strain retained the likely ancestral sequence. The study suggests that short-read enabled comparative genomics is an effective way to both identify new S. nodorum effector candidates and to illuminate evolutionary processes in this species

On the Formation of Compact Stellar Disks Around Sgr A*

The recent identification of one or two sub-parsec disks of young, massive stars orbiting the ~4e6 solar mass black hole Sgr A* has prompted an "in-situ" scenario for star formation in disks of gas formed from a cloud captured from the Galactic center environment. To date there has been no explanation given for the low angular momentum of the disks relative to clouds passing close to the center. Here we show that the partial accretion of extended Galactic center clouds, such as the 50 km/s giant molecular cloud, that temporarily engulf Sgr A* during their passage through the central region of the Galaxy provide a natural explanation for the angular momentum and surface density of the the observed stellar disks. The captured cloud material is gravitationally unstable and forms stars as it circularizes, potentially explaining the large eccentricity and range of inclinations of the observed stellar orbits. The application of this idea to the formation of the circumnuclear ring is also discussed.Comment: 12 pages, 2 figs, minor changes, ApJ Letters accepte

Type 1 diabetes, COVID-19 vaccines and short-term safety: Subgroup analysis from the global COVAD study

AIMS/INTRODUCTION Coronavirus disease 2019 (COVID-19) vaccinations have been proven to be generally safe in healthy populations. However, the data on vaccine safety in patients with type 1 diabetes are scarce. This study aimed to evaluate the frequency and severity of short-term (<7-day) adverse vaccination events (AEs) and their risk factors among type 1 diabetes patients. MATERIALS AND METHODS This study analyzed data from the COVID-19 vaccination in Autoimmune Diseases (COVAD) survey database (May to December 2021; 110 collaborators, 94 countries), comparing <7-day COVID-19 vaccine AE among type 1 diabetes patients and healthy controls (HCs). Descriptive statistics; propensity score matching (1:4) using the variables age, sex and ethnicity; and multivariate analyses were carried out. RESULTS This study analyzed 5,480 completed survey responses. Of all responses, 5,408 were HCs, 72 were type 1 diabetes patients (43 females, 48.0% white European ancestry) and Pfizer was the most administered vaccine (39%). A total of 4,052 (73.9%) respondents had received two vaccine doses. Patients with type 1 diabetes had a comparable risk of injection site pain, minor and major vaccine AEs, as well as associated hospitalizations to HCs. However, type 1 diabetes patients had a higher risk of severe rashes (3% vs 0.4%, OR 8.0, 95% confidence interval 1.7-36), P = 0.007), although reassuringly, these were rare (n = 2 among type 1 diabetes patients). CONCLUSIONS COVID-19 vaccination was safe and well tolerated in patients with type 1 diabetes with similar AE profiles compared with HCs, although severe rashes were more common in type 1 diabetes patients