bluuebunny/crossref_metadata_2025_split huggingface dataset:
P672 A tertiary multicenter cohort of patients with chronic intestinal pseudo-obstruction and Crohn’s disease: a rare association with a high prevalence of monogenic disorders
Authors: De castelbajac F , Charbit-Henrion F , Goulet O , Cerf-Bensussan N , Treton X , Stefanescu C , Cazals-Hatem D , Billiauws L , Bouhnik Y , Joly F , Uzzan M 
Published: May 2021

Abstract

Background
Chronic intestinal pseudo-obstruction (CIPO) is a rare condition that is not commonly associated with Crohn’s disease (CD).
We performed a cohort study aiming at identifying clinical, immunological and genetic features as well as response to conventional CD treatments of patients co-affected with CIPO and CD.

Methods
We conducted an observational retrospective cohort study in two tertiary CIPO and IBD centers.
Patients with parenteral nutrition-dependent CIPO and features of CD including large intestinal or perianal ulcers, strictures, abscesses and fistula with pathology findings compatible with CD, were included.
We used flow-cytometry and targeted-next generation sequencing to identify immune defects and monogenic causes in 129 predefined genes responsible for monogenic enteropathies

Results
Eight unrelated patients were studied. 5 had a myogenic phenotype and 3 had a neurogenic form with histological exam for all patients. CD involved small bowel in all cases whereas one patient had ileocolonic involvement. Two patients had perianal complex fistula. Seven patients had a stricturing form and 1 had an inflammatory-only behavior. No patient had a penetrating form. All patients were diagnosed with CIPO prior to CD. Median age at CIPO diagnosis was 11.5 years old (IQR 0,31.5) while it was 22.5 (IQR 19,29) at CD diagnosis. At CD diagnosis, mean fecal calprotectin level was 551 ug/g (range 390 - 1200) and citrulline averaged 23.6 umol/l (range 15–35 umol/l).
Histopathological analyses of intestinal specimens revealed ulcerations for half of the patients, increase in intraepithelial lymphocytes in 3, granuloma and cryptitis in 1 patient.
Abnormalities in peripheral lymphocytes’ subsets were found in 2 patients. 5 patients were ultimately diagnosed with monogenic forms of enteropathy: 2 in ACTG2, with an autosomal dominant inheritance, 1 with a STAT1gain of function, (GOF) and two with recessive inheritance: TYMP. All patients received steroids with clinical response in 2. 6 patients received antiTNF, with only one sustained remission. Two patients received vedolizumab and 2 were treated with ustekinumab. Except for antiTNF in 1 patient, common CD treatments did not lead to any improvement. Of note, antiJAK therapy in a patient with STAT1GOF failed to induce remission.

Conclusion
Herein is described the first cohort of extensively genetically and immunologically explored patients co-affected with CIPO and CD. Immune defects were common and monogenic forms were found with a high prevalence. Rates of response to biologic treatment were very low. Identification of monogenic cause through immunological and genetic explorations is warranted in patient with CIPO-CD association as it could lead to targeted therapy and genetic counseling.
P675 Flavonoid-degrading bacteria have central positions in correlation network analysis in patients with Inflammatory Bowel Disease
Authors: Pisani A , Rausch P , Ellul S , Bang C , Tabone T , Marantidis Cordina C , Zahra G , Ellul P , Franke A 
Published: May 2021

Abstract

Background
Correlation networks are employed to assess the interactions between different bacteria. The aim of this study was to assess which bacterial species had central positions in a network analysis in faecal samples of patients with IBD who are in remission.

Methods
The fecal microbiota of 98 Maltese patients with IBD who were in remission and a control group (97 controls) were analyzed by 16S rRNA sequencing.
To generate co-abundance networks the SparCC algorithm as implemented in mothur was employed (50 samplings, 100 iterations, 10,000 permutations) based on Amplicon sequence variants (ASV) abundances (shared among 10% samples) at a P-value cutoff of PFDR≤0.05 and a correlation strength above the median of non-zero correlations.

Results
Correlation network analysis identified two flavonoid-degrading bacteria to be more important than expected by chance. Flavonifractor plautii (previously known as Clostridium Orbiscindens and Eubacterium plautii) which associated to IBD more than to controls and Eggertella lenta, which associated to patients with Ulcerative colitis (UC), had a high network importance on several levels, with a very central position (betweenness) and many associations to other community members (node degree), which are themselves important mediators (PageRank®) (Figure 1) Other bacteria occupying highly central positions in the community network included Oscillibacter uncl., Alistipes shahii and members of the order Clostridiales. These associated to controls and are known butyrate producers, usually associated with a beneficial effect on gut homeostasis. Eigenvalue centrality identified a strongly correlated group of Enterobacteriaceae.

Figure 1: The barplots show the top 50 bacteria within the network based on their centrality measures (Betweenness, Degree, Eigenvalue centrality, PageRank).
Highlighted in red are network members with a higher importance than expected by chance, based on a Z-test against 10’000 randomized networks (P ≤ 0.05). Highlighted as well are the associations of the respective ASVs to various factors, as detected by indicator species analysis (p≤0.05).

Conclusion
Flavonoids have been described to have anti-inflammatory properties and flavonoid-degrading bacteria have been associated with the prevention of malignancy, cardiovascular disease, diabetes type 2 and cognitive decline. In mice studies, oral administration of Flavinofractor plautii was noted to suppress Th2 immune responses. Thus, one may postulate that their presence may be important in the maintenance of IBD, although in a state of remission. Future studies should provide more evidence on their role and whether the colonization of flavonoid degrading bacteria can induce remission or conversely increase chronicity or severity of IBD.
P678 Definition of a microbial signature as a predictor of post-surgical recurrence in patients with Crohn’s disease
Authors: Oliver L , Amoedo J , Julià D , Camps B , Ramió-Pujol S , Malagón M , Torres P , Domènech E , Guardiola J , Serra-Pagès M , Garcia-Gil J , Aldeguer X 
Published: May 2021

Abstract

Background
Although there are several effective drugs for the treatment of Crohn’s disease (CD), almost 80% of patients will end up needing a surgical resection throughout their lives. This procedure is not always curative, as the disease often reappears in the intestine. Endoscopic recurrence occurs in 65%-90% of patients after one year from surgery. The aetiology of the recurrence is unknown; however, several studies have shown how the resident microbiota is modified after surgery.
The aim of this study is to evaluate samples from patients with CD before and after an intestinal resection to determine if at baseline there are differences in the abundance of different microbial markers, which could be capable of predicting endoscopic recurrences.

Methods
In this observational study, a stool sample was obtained from 20 patients with CD before undergoing surgery, recruited at Hospital Universitari Dr. Josep Trueta, Hospital Universitari of Bellvitge, and the Hospital Universitari Germans Trias i Pujol.
From each sample, DNA was purified and the relative abundance of the following microbial markers was quantified using qPCR: F. prausnitzii (Fpra) and its phylogroups (PHG-I and PHG-II), E. coli (Eco ), A. muciniphila (Akk), Ruminococcus sp. (Rum), Bacteroidetes (Bac), M. smithii (Msm), and total bacterial load (Eub).

Results
Individually, none of the biomarkers demonstrated the ability to differentiate patients who will develop post-surgical recurrence from those who will not. In contrast, the combination of 4 microbial markers (Eco, PHGI, Bac, and Eub) showed a high capacity of discrimination between the 2 groups. The algorithm that incorporates these three markers shows a sensitivity and specificity of 100% and 90.91%, respectively, and a positive and negative predictive value of 90.00% and 100%, respectively.

Conclusion
A microbial signature to determine patients who will have post-surgical recurrence has been identified. This tool can be very useful in daily clinical practice allowing to schedule a personalized therapy, enabling preventive treatment only in that subgroup of patients who really require it. A broader prospective study will be needed to validate these results.
Comparison of Sex Pheromone and Kairomone-Enhanced Pheromone Lures for Monitoring Oriental Fruit Moth (Lepidoptera: Tortricidae) in Mating Disruption and Non-Disruption Tree Fruit Orchards
Authors: Walgenbach James F , Schoof Steven C , Bosch Dolors , Escudero-Colomar Lucia-Adriana , Lingren Bill , Krawczyk Grzegorz 
Published: May 2021

Abstract
Oriental fruit moth, Grapholita molesta (Busck), populations were monitored using standard sex pheromone lures (OFM L2) and kairomone-enhanced lures to aid the interpretation of trap captures with enhanced relative to conventional lures. Initially, comparison of 10 different lures showed that a10X load of OFM pheromone, codlemone, terpinyl acetate, and acetic acid were key components of the most attractive lures (TRE11034 and 1123). Subsequent trapping studies in mating disruption and non-disrupted orchards in the United States and Spain compared trap captures with TRE1123 and OFM L2 lures. Compared to the OFM L2 lure, the TRE1123 lure captured more moths in mating disruption and non-disrupted orchards, caught female moths, improved the precision of mean population estimates, and led to greater resolution of generational flights. Suppression of trap captures in mating disruption versus non-disrupted orchards was similar with both lures. There were significant linear correlations between weekly trap captures with the two lures in the majority of mating disruption and non-disrupted orchards across locations and years. Furthermore, regression of the slopes of trap capture regressions (i.e., attractiveness of enhanced lures relative to sex pheromone lures alone) versus moth density (as measured by mean cumulative moth capture with TRE1123 and OFM L2 lures) exhibited a significant positive relationship in non-disrupted orchards, indicating enhanced lures were relatively more attractive under high population densities. This relationship was not significant in mating disruption orchards, likely due to the density independent, non-competitive mechanism of mating disruption for oriental fruit moth when using high-dose reservoir dispensers.
What causes hot markets for equity IPOs? An analysis of initial public offerings in the Netherlands, 1876–2015
Authors: de Jong Abe , Legierse Wilco 
Published: May 2021

AbstractThis paper explains fluctuations in the number of initial public offerings (IPOs) between 1876 and 2015 in the Netherlands. We test an econometric model and find that the number of IPOs is strongly related to the economic growth and the size of the stock exchange. We also find that IPOs are timed to coincide with favorable market conditions. Our model explains almost 50 percent of the fluctuations and most of the hot markets. To further understand IPO waves, we conduct a descriptive analysis, which yields two additional causes for hot markets, i.e., high capital needs and investors’ expectations for specific industries.
Quality of child healthcare in European countries: common measures across international databases and national agencies
Authors: Rocco Ilaria , Tamburis Oscar , Pecoraro Fabrizio , Luzi Daniela , Corso Barbara , Minicuci Nadia 
Published: May 2021

Abstract

Background
The evaluation of child healthcare is not yet widely explored, especially from a cross-country comparison perspective. The routine adoption of measures by national assessment agencies is under-investigated. Though the guiding principles developed at international level call for a child-centric multi-dimensional evaluation of child care, its feasibility is hampered by the availability of robust and harmonized data.

Methods
To explore the data availability, international databases (IDBs) were scrutinized and measures dealing with child health-related issues were collated. In parallel, an ad hoc questionnaire was administrated to 30 Country Agents (CAs) to gather measures routinely adopted at local level. To facilitate the comparison of measures, a three-level conceptual map was developed.

Results
The IDBs yielded at 207 measures that pertained mainly to non-health determinants of health, whereas the 352 measures obtained from CAs focused on process and outcome. A set of 33 common measures that related to immunization, morbidity and mortality were identified.

Conclusions
A limited set of measures used both in IDBs and at national level identify common areas of concerns that certainly capture crucial issues with child prevention and health outcomes. However, they are far from satisfying a child-centric multi-dimensional approach to the evaluation of child well-being and well-becoming. There is room for improvement at both international and national levels. IDBs should include and harmonize measures that concern the provision of child-centric services and encompass physical, social and mental development. At the national level, efforts towards the inclusion of measures that concern non-health determinants of health should be pursued.
Were immigrants on the frontline during the lockdown? Evidence from France
Authors: Gosselin Anne , Melchior Maria , Desprat Diane , Devetter François-Xavier , Pannetier Julie , Valat Emmanuel , Memmi Sarah 
Published: May 2021

Abstract
In France, immigrants’ excess of mortality was higher than natives’ during the Spring 2020 lockdown. Were immigrants in frontline jobs and more exposed to Covid-19? Based on a nationally representative survey, we model the probability to work in a frontline job according to migratory status, taking sociodemographic and occupational characteristics into account. Compared to natives (Metropolitan France), being an African immigrant was associated to higher probability to work in a frontline job [adjusted odds ratio (aOR) = 1.82 (1.23–2.71)], as well as being born in French Overseas Departments [aOR = 1.64 (1.23–2.18)], reflecting racial division of work and higher Sars-Cov-2 exposure of immigrant and minority populations.
Genome-wide analysis in Drosophila reveals diet-by-gene interactions and uncovers diet-responsive genes
Authors: Francis Deanne , Ghazanfar Shila , Havula Essi , Krycer James R , Strbenac Dario , Senior Alistair , Minard Annabel Y , Geddes Thomas , Nelson Marin E , Weiss Fiona , Stöckli Jacqueline , Yang Jean Y H , James David E 
Published: May 2021

Abstract
Genetic and environmental factors play a major role in metabolic health. However, they do not act in isolation, as a change in an environmental factor such as diet may exert different effects based on an individual’s genotype. Here, we sought to understand how such gene–diet interactions influenced nutrient storage and utilization, a major determinant of metabolic disease. We subjected 178 inbred strains from the Drosophila genetic reference panel (DGRP) to diets varying in sugar, fat, and protein. We assessed starvation resistance, a holistic phenotype of nutrient storage and utilization that can be robustly measured. Diet influenced the starvation resistance of most strains, but the effect varied markedly between strains such that some displayed better survival on a high carbohydrate diet (HCD) compared to a high-fat diet while others had opposing responses, illustrating a considerable gene × diet interaction. This demonstrates that genetics plays a major role in diet responses. Furthermore, heritability analysis revealed that the greatest genetic variability arose from diets either high in sugar or high in protein. To uncover the genetic variants that contribute to the heterogeneity in starvation resistance, we mapped 566 diet-responsive SNPs in 293 genes, 174 of which have human orthologs. Using whole-body knockdown, we identified two genes that were required for glucose tolerance, storage, and utilization. Strikingly, flies in which the expression of one of these genes, CG4607 a putative homolog of a mammalian glucose transporter, was reduced at the whole-body level, displayed lethality on a HCD. This study provides evidence that there is a strong interplay between diet and genetics in governing survival in response to starvation, a surrogate measure of nutrient storage efficiency and obesity. It is likely that a similar principle applies to higher organisms thus supporting the case for nutrigenomics as an important health strategy.
Genomic prediction and QTL mapping of root system architecture and above-ground agronomic traits in rice (Oryza sativa L.) with a multitrait index and Bayesian networks
Authors: Sharma Santosh , Pinson Shannon R M , Gealy David R , Edwards Jeremy D 
Published: May 2021

Abstract
Root system architecture (RSA) is a crucial factor in resource acquisition and plant productivity. Roots are difficult to phenotype in the field, thus new tools for predicting phenotype from genotype are particularly valuable for plant breeders aiming to improve RSA. This study identifies quantitative trait loci (QTLs) for RSA and agronomic traits in a rice (Oryza sativa) recombinant inbred line (RIL) population derived from parents with contrasting RSA traits (PI312777 × Katy). The lines were phenotyped for agronomic traits in the field, and separately grown as seedlings on agar plates which were imaged to extract RSA trait measurements. QTLs were discovered from conventional linkage analysis and from a machine learning approach using a Bayesian network (BN) consisting of genome-wide SNP data and phenotypic data. The genomic prediction abilities (GPAs) of multi-QTL models and the BN analysis were compared with the several standard genomic prediction (GP) methods. We found GPAs were improved using multitrait (BN) compared to single trait GP in traits with low to moderate heritability. Two groups of individuals were selected based on GPs and a modified rank sum index (GSRI) indicating their divergence across multiple RSA traits. Selections made on GPs did result in differences between the group means for numerous RSA. The ranking accuracy across RSA traits among the individual selected RILs ranged from 0.14 for root volume to 0.59 for lateral root tips. We conclude that the multitrait GP model using BN can in some cases improve the GPA of RSA and agronomic traits, and the GSRI approach is useful to simultaneously select for a desired set of RSA traits in a segregating population.
The Assembled and Annotated Genome of the Fairy-Ring Fungus Marasmius oreades
Authors: Hiltunen Markus , Ament-Velásquez Sandra Lorena , Johannesson Hanna 
Published: May 2021

Abstract
Marasmius oreades is a basidiomycete fungus that grows in so called “fairy rings,” which are circular, underground mycelia common in lawns across temperate areas of the world. Fairy rings can be thought of as natural, long-term evolutionary experiments. As each ring has a common origin and expands radially outwards over many years, different sectors will independently accumulate mutations during growth. The genotype can be followed to the next generation, as mushrooms producing the sexual spores are formed seasonally at the edge of the ring. Here, we present new genomic data from 95 single-spore isolates of the species, which we used to construct a genetic linkage map and an updated version of the genome assembly. The 44-Mb assembly was anchored to 11 linkage groups, producing chromosome-length scaffolds. Gene annotation revealed 13,891 genes, 55% of which contained a pfam domain. The repetitive fraction of the genome was 22%, and dominated by retrotransposons and DNA elements of the KDZ and Plavaka groups. The level of assembly contiguity we present is so far rare in mushroom-forming fungi, and we expect studies of genomics, transposons, phylogenetics, and evolution to be facilitated by the data we present here of the iconic fairy-ring mushroom.
Closer Appendage Spacing Augments Metachronal Swimming Speed by Promoting Tip Vortex Interactions
Authors: Ford Mitchell P , Santhanakrishnan Arvind 
Published: May 2021

Abstract
Numerous species of aquatic invertebrates, including crustaceans, swim by oscillating multiple closely spaced appendages. The coordinated, out-of-phase motion of these appendages, known as “metachronal paddling,” has been well-established to improve swimming performance relative to synchronous paddling. Invertebrates employing this propulsion strategy cover a wide range of body sizes and shapes, but the ratio of appendage spacing (G) to the appendage length (L) has been reported to lie in a comparatively narrow range of 0.2 &lt; G/L ≤ 0.65. The functional role of G/L on metachronal swimming performance is unknown. We hypothesized that for a given Reynolds number and stroke amplitude, hydrodynamic interactions promoted by metachronal stroke kinematics with small G/L can increase forward swimming speed. We used a dynamically scaled self-propelling robot to comparatively examine swimming performance and wake development of metachronal and synchronous paddling under varying G/L, phase lag, and stroke amplitude. G/L was varied from 0.4 to 1.5, with the expectation that when G/L is large, there should be no performance difference between metachronal and synchronous paddling due to a lack of interaction between vortices that form on the appendages. Metachronal stroking at nonzero phase lag with G/L in the biological range produced faster swimming speeds than synchronous stroking. As G/L increased and as stroke amplitude decreased, the influence of phase lag on the swimming speed of the robot was reduced. For smaller G/L, vortex interactions between adjacent appendages generated a horizontally oriented wake and increased momentum fluxes relative to larger G/L, which contributed to increasing swimming speed. We find that while metachronal motion augments swimming performance for closely spaced appendages (G/L &lt;1), moderately spaced appendages (1.0 ≤ G/L ≤ 1.5) can benefit from the metachronal motion only when the stroke amplitude is large.
Deterrence in the Cyber Realm: Public versus Private Cyber Capacity
Authors: Kostyuk Nadiya 
Published: May 2021

AbstractCan cyber deterrence work? Existing scholarly works argue that deterrence by punishment using cyberattacks is ineffective because the difficulty of attributing the origin of cyberattacks makes the threat of future attacks less credible. However, these works have told us relatively little about the deterrence ability of public cyberinstitutions (PCIs), defined as publicly observable proactive efforts aimed at signaling a country’s level of cyber offensive and defensive capability. This research shows that middle powers (that have scarce cyber arsenals) can use PCIs to deter cyber attacks that cause significant damage to their economy and prosperity; however, this deterrent capability is rather limited. Using an incomplete-information model, we demonstrate that PCIs only deter adversaries that are susceptible to the costs created by these institutions. Despite this limited deterrence ability, middle powers tend to over-invest resources in these cyberinstitutions: Weak cyber states tend to over-invest to convince strong cyber adversaries that they are strong, whereas strong cyber states over-invest so that adversaries do not believe that they are weak states pretending to be strong. By doing so, states reduce their overall cybercapacity. We establish the empirical plausibility of these results using election interference campaigns as examples of strategic attacks. Our focus on the strategic use of PCIs as a deterrent represents a departure from existing literature—which has focused only on cyberoperations—and has important policy implications.