bluuebunny/crossref_metadata_2025_split huggingface dataset:
Superspreading of airborne pathogens in a heterogeneous world
Authors: Kirkegaard Julius B. , Mathiesen Joachim , Sneppen Kim 
Published: May 2021

AbstractEpidemics are regularly associated with reports of superspreading: single individuals infecting many others. How do we determine if such events are due to people inherently being biological superspreaders or simply due to random chance? We present an analytically solvable model for airborne diseases which reveal the spreading statistics of epidemics in socio-spatial heterogeneous spaces and provide a baseline to which data may be compared. In contrast to classical SIR models, we explicitly model social events where airborne pathogen transmission allows a single individual to infect many simultaneously, a key feature that generates distinctive output statistics. We find that diseases that have a short duration of high infectiousness can give extreme statistics such as 20% infecting more than 80%, depending on the socio-spatial heterogeneity. Quantifying this by a distribution over sizes of social gatherings, tracking data of social proximity for university students suggest that this can be a approximated by a power law. Finally, we study mitigation efforts applied to our model. We find that the effect of banning large gatherings works equally well for diseases with any duration of infectiousness, but depends strongly on socio-spatial heterogeneity.
Metabolomic analysis of skeletal muscle before and after strenuous exercise to fatigue
Authors: Ohmura Hajime , Mukai Kazutaka , Takahashi Yuji , Takahashi Toshiyuki 
Published: May 2021

AbstractThoroughbreds have high maximal oxygen consumption and show hypoxemia and hypercapnia during intense exercise, suggesting that the peripheral environment in skeletal muscle may be severe. Changes in metabolites following extreme alterations in the muscle environment in horses after exercise may provide useful evidence. We compared the muscle metabolites before and after supramaximal exercise to fatigue in horses. Six well-trained horses ran until exhaustion in incremental exercise tests. Biopsy samples were obtained from the gluteus medius muscle before and immediately after exercise for capillary electrophoresis–mass spectrometry analysis. In the incremental exercise test, the total running time and speed of the last step were 10.4 ± 1.3 (mean ± standard deviation) min and 12.7 ± 0.5 m/s, respectively. Of 73 metabolites, 18 and 11 were significantly increased and decreased after exercise, respectively. The heat map of the hierarchical cluster analysis of muscle metabolites showed that changes in metabolites were clearly distinguishable before and after exercise. Strenuous exercise increased many metabolites in the glycolytic pathway and the tricarboxylic acid cycle in skeletal muscle. Targeted metabolomic analysis of skeletal muscle may clarify the intramuscular environment caused by exercise and explain the response of working muscles to strenuous exercise that induces hypoxemia and hypercapnia in Thoroughbred horses.
Correlation between amide proton transfer-related signal intensity and diffusion and perfusion magnetic resonance imaging parameters in high-grade glioma
Authors: Nakajo Masanori , Bohara Manisha , Kamimura Kiyohisa , Higa Nayuta , Yoshiura Takashi 
Published: May 2021

AbstractAmide proton transfer (APT) imaging is a magnetic resonance (MR) molecular imaging technique that is sensitive to mobile proteins and peptides in living tissue. Studies have shown that APT-related signal intensity (APTSI) parallels with the malignancy grade of gliomas, allowing the preoperative assessment of tumor grades. An increased APTSI in malignant gliomas has been attributed to cytosolic proteins and peptides in proliferating tumor cells; however, the exact underlying mechanism is poorly understood. To get an insight into the mechanism of high APTSI in malignant gliomas, we investigated the correlations between APTSI and several MR imaging parameters including apparent diffusion coefficient (ADC), relative cerebral blood volume and pharmacokinetic parameters obtained in the same regions-of-interest in 22 high-grade gliomas. We found a significant positive correlation between APTSI and ADC (ρ = 0.625 and 0.490 for observers 1 and 2, respectively; p < 0.001 for both), which is known to be inversely correlated with cell density. Multiple regression analysis revealed that ADC was significantly associated with APTSI (p < 0.001 for both observers). Our results suggest possible roles of extracellular proteins and peptides in high APTSI in malignant gliomas.
Spray coagulation with snare-tip versus argon plasma coagulation: An ex vivo study evaluating tissue effects
Authors: Fetz Andrew , Farnell David , Irani Shayan , Gan S. Ian 
Published: May 2021

Abstract
Background and study aims Argon plasma coagulation (APC) is an effective and safe modality for many gastrointestinal conditions requiring hemostasis and/or ablation. However, it can be quite costly. A potentially more cost-effective alternative is snare-tip spray coagulation (SC). This study aimed to determine whether SC would be a safe and effective alternative to APC using an ex-vivo model.
Methods Using two resected porcine stomach, 36 randomized gastric areas were ablated for 2 seconds with either APC at 1.0 L/min 20 W (APC20) and 1.4 L/min 40 W (APC40) or SC with Effect 2 60 W (SC60) and 80 W (SC80) from 3 mm. Extent of tissue injury was then analyzed histopathologically.
Results The mean coagulation depth was 790 ± 159 µm and 825 ± 467 µm for SC60 (n = 9) and SC80 (n = 8), respectively. This was compared to 539 ± 151 µm for APC20 (n = 8) and 779 ± 267 µm for APC40 (n = 9). Mean difference (MD) in coagulation depth between SC60 and APC40 was 12 µm (95 % confidence interval [CI], –191 to 214 µm; P = 0.91) and was 47 µm (95 %CI, –162 to 255 µm; P = 0.81) between SC80 and APC40. There was a greater depth of injury with APC40 (MD, 240 µm; 95 %CI, 62 to 418 µm; P = 0.04) and with SC60 (MD, 252 µm; 95 %CI, 141 to 362 µm; P = 0.004) when compared to APC20. Mean cross-sectional area of coagulation was 2.39 ± 0.852 mm² for SC60 and 2.54 ± 1.83 mm² for SC80 compared to 1.22 ± 0.569 mm² for APC20 and 1.99 ± 0.769 mm² for APC40. Seventy-eight percent reached the muscularis mucosa (MM) and 11 % the submucosa in the SC60 group compared to 50 % and 38 % in SC80 and 56 % and 11 % in APC40, respectively. Thirty-eight percent of APC20 specimens reached the MM. The muscularis propria was unaffected.
Conclusions This small ex-vivo study suggests that SC60 and SC80 may be safe alternatives to APC40 with comparable coagulation depths and area effects.
Feasibility and safety of colonoscopy performed by nonexperts for acute lower gastrointestinal bleeding: post hoc analysis
Authors: Nishida Tsutomu , Niikura Ryota , Nagata Naoyoshi , Honda Tetsuro , Sunagozaka Hajime , Shiratori Yasutoshi , Tsuji Shigetsugu , Sumiyoshi Tetsuya , Fujita Tomoki , Kiyotoki Shu , Yada Tomoyuki , Yamamoto Katsumi , Shinozaki Tomohiro , Nakamatsu Dai , Yamada Atsuo , Fujishiro Mitsuhiro 
Published: May 2021

Abstract
Background and study aims It remains unclear whether the experience of endoscopists affects clinical outcomes for acute lower gastrointestinal bleeding (ALGIB). We aimed to determine the feasibility and safety of colonoscopies performed by nonexperts using secondary data from a randomized controlled trial for ALGIB.
Patients and methods We analyzed clinical outcomes in 159 patients with ALGIB who underwent colonoscopies performed by two groups of endoscopists: experts and nonexperts. We compared endoscopy outcomes, including identification of stigmata of recent hemorrhage (SRH), successful endoscopic treatment, adverse events (AEs), and clinical outcomes between the two groups, including 30-day rebleeding, transfusion, length of stay, thrombotic events, and 30-day mortality.
Results Expert endoscopists alone performed colonoscopies in 96 patients, and nonexperts performed colonoscopies in 63 patients. The use of antiplatelets and warfarin was significantly higher in the expert group. The SRH identification rate (24.0 and 17.5 %), successful endoscopic treatment rate (95.0 and 100 %), rate of AEs during colonoscopy (0 and 0 %), transfusion rate (6.3 and 4.8 %), length of stay (8.0 and 6.4 days), rate of thrombotic events (0 and 1.8 %), and mortality (0 and 0 %) were not different between the expert and nonexpert groups. Rebleeding within 30 days occurred more often in the expert group than in the nonexpert group (14.3 vs. 5.4 % P = 0.0914).
Conclusions The performance of colonoscopies for ALGIB by nonexperts did not result in worse clinical outcomes, suggesting that its use could be feasible for nonexperts for diagnosis and treatment of ALGIB.
DOP69 Ozanimod for induction treatment of Moderate-to-Severe Ulcerative Colitis: Results from a systematic literature review and network meta-analyses
Authors: Eaton K , Duperrouzel C , Bhandari P , Craigie S , Bonner A , Cameron C , Tencer T , Kumar J 
Published: May 2021

Abstract

Background
Ozanimod (OZA) is an orally administered, selective sphingosine-1-phosphate receptor modulator that has been evaluated versus placebo (PBO) in the phase 3 True North trial in the treatment of adult patients with moderate-to-severe ulcerative colitis (UC). The objective of this study was to compare the relative efficacy of OZA versus other approved moderate-to-severe UC therapies via network meta-analyses (NMA).

Methods
A systematic literature review was conducted to identify randomised clinical trials published from Jan 1, 2000 to Oct 21, 2020 that evaluated biological therapies (infliximab [IFX], adalimumab [ADA], golimumab [GOL], vedolizumab [VEDO], and ustekinumab [UST]) or an oral small molecule (tofacitinib [TOF]) for adults with moderate-to-severe UC. Bayesian NMAs were performed to determine the comparative efficacy of these therapies based on clinical remission, clinical response, and endoscopic improvement in the induction phase (6 to 14 weeks). Three populations were considered: all patients (overall), first-line (biologic-naïve), or those with exposure to or failure of prior biologic therapy (biologic-experienced). All six comparator therapies were included in the overall and biologic-naive populations, whereas the biologic-experienced population included ADA, VEDO, UST, and TOF due to lack of biologic-experienced data for IFX and GOL.

Results
Twenty-two RCTs examining 10,269 patients in the induction phase were included (Figure 1). All therapies offered significant improvement over PBO across networks apart from ADA in the analysis of clinical remission and clinical response in the biologic-experienced population and ADA, VEDO, and OZA in the analysis of endoscopic improvement in the biologic-experienced population. In the overall and biologic-naïve populations, OZA offered similar efficacy to all other therapies across endpoints except for a significant improvement in endoscopic improvement over ADA (overall: OR 2.01, 95% CrI 1.14, 3.66 [Figure 2]; biologic-naïve: OR 2.13, 95% CrI 1.02, 4.50 [Figure 3]). OZA also offered similar efficacy to all other therapies across endpoints in the biologic-experienced population except for an improvement in clinical remission (OR 4.16, 95% CrI 1.55, 11.24) and clinical response (OR 3.11, 95% CrI 1.40, 7.08) over ADA (Figure 4).

Conclusion
This NMA suggests that OZA provides similar induction efficacy on clinical remission, clinical response, and endoscopic improvement versus other approved moderate-to-severe UC therapies regardless of prior biologic treatment status.
OP11 Longitudinal profiling of mucosal immune cell composition using multiplex immunohistochemistry identifies drug- and response-specific patterns in Ulcerative Colitis
Authors: Volk V , Aden K , Tran F , Mishra N , Bernardes J , Röcken C , Schreiber S , Feuerhake F , Rosenstiel P 
Published: May 2021

Abstract

Background
Interventions targeting key inflammatory mechanisms have expanded the therapeutic repertoire for ulcerative colitis (UC). However, exact molecular mechanisms associated with clinical response remain elusive. We conducted a multiplex-immunohistochemistry (IHC) study to monitor immune cell composition in biopsies from UC patients under 2 approved therapies targeting TNF (infliximab) and integrin (vedolizumab), and a phase IIa clinical trial with the selective IL-6 transsignalling inhibitor olamkicept, to identify spatiotemporal changes of mucosal immune cell compartments in relation to each mechanism of action.

Methods
Sigmoid biopsies from UC patients exposed to infliximab, vedolizumab or olamkicept (26 patients in total) at baseline and week 2, 6 and 14 after therapy induction were subjected to multiplex IHC for CD3, CD15, CD20, CD68, pSTAT3, and pan-cytokeratin (OPAL/Vectra Polaris, Akoya). Quantitative and spatial immune cell patterns captured by advanced image analysis (inForm, Akoya; R package PhenoptrReports) were analysed for differences between baseline and subsequent time points using Dunnett’s multiple comparisons test (GraphPad Prism 8.4.3). Accepted significance levels: *p&lt;0.05,**p&lt;0.01, ***p&lt;0.001.

Results
Targeted therapies resulted in overall decrease of immune cell infiltrates (range 1.15–1.22 fold; p=0.017-0.007), irrespective of drug or specified endpoint (remission at week 14) (Fig. 1). Significant drug-specific changes of spatial immune cell distributions were discernible (Fig. 2). Anti-TNF treatment was mainly associated with decrease in CD3+ T cells (p=0.005) localized in the submucosa close to epithelium or in tertiary lymphoid organs. In contrast, integrin targeting resulted in fewer CD15+ neutrophils, mainly in the submucosal compartment (p=0.046). Olamkicept treatment resulted in unique depletion of pSTAT3+ cells in patients achieving remission at week 14 (not observed in remission after infliximab or vedolizumab). To decipher drug-independent features of clinical remission we assessed distance metrics between immune and intestinal epithelial cells in remission and non-remission patients and observed increase (endpoint compared to baseline) of the average distance to the nearest CD20 or CD15 cell in the remission (p=0.0054, p=0.0004) but not in the non-remission group (n.s.).

Conclusion
Our study strongly suggests that multiplexed spatiotemporally resolved immune cell phenotyping may provide novel insights into the dynamic shifts of immune cell compartments in UC patients undergoing targeted therapy. We propose that such highly resolved digital maps of immune cells could lead to novel tools for therapeutic stratification of IBD patients.
OP29 Long-term dietary patterns are associated with pro-inflammatory and anti-inflammatory features of the gut microbiome
Authors: Bolte L , Vich Vila A , Imhann F , Collij V , Peters V , Fu J , Kurilshikov A , Campmans-Kuijpers M , Dijkstra G , Wijmenga C , Zhernakova A , Weersma R 
Published: May 2021

Abstract

Background
The gut microbiome directly affects the balance of pro-inflammatory and anti-inflammatory responses in the gut. As microbes thrive on dietary substrates, the question arises whether we can nourish an anti-inflammatory gut ecosystem. In this study, we investigated the relation between 173 dietary factors and the microbiome of 1425 individuals spanning four cohorts: Crohn’s disease, ulcerative colitis, irritable bowel syndrome and the general population.

Methods
Shotgun metagenomic sequencing was performed to profile gut microbial composition and function. Dietary intake was assessed through food frequency questionnaires. We performed unsupervised clustering to identify dietary patterns and microbial clusters. Next, linear models were conducted between dietary intake and microbial species and pathways, adding age, sex, caloric intake and sequencing read depth as covariates. Analyses were conducted per cohort, followed by a meta-analysis and heterogeneity estimation. Multiple testing correction was performed on the obtained p-values and a FDR &lt;0.05 was defined as significance cut-off.

Results
We identified 38 associations between dietary patterns and microbial clusters. Moreover, 61 individual foods and nutrients were associated with 61 species and 249 metabolic pathways in the meta-analysis across healthy individuals and patients with IBS, Crohn’s disease and UC (FDR&lt;0.05, heterogeneity p-value&gt;0.05). Processed foods and animal-derived foods were consistently associated with higher abundances of Firmicutes, Ruminococcus species of the Blautia genus and endotoxin synthesis pathways. The opposite associations were found for clusters comprising fish, nuts, bread and legumes. Moreover, while total plant protein intake was associated with a higher Bifidobacterium abundance (FDR=0.048, coef=4.98), animal-derived protein showed a negative association (FDR=1.30x10-05, coef= -4.1). Lastly, we observed positive associations of fecal calprotectin with a fast food cluster (FDR=4.14x10-4, coef=0.24) and a cluster comprised of high-fat meat, potatoes and gravy (FDR=0.003, coef =0.22), while the opposite was seen for clusters of fish and nuts (FDR=0.038, coef= -0.1) and bread and legumes (FDR=0.005, coef= -2.48).

Conclusion
We identified dietary patterns that consistently correlate with groups of bacteria with shared functional roles in both, health and disease. Moreover, specific foods and nutrients were associated with species known to infer mucosal protection and anti-inflammatory effects. A decrease in these bacteria has already been associated with both IBS and IBD. We propose microbial mechanisms through which the diet affects inflammatory responses in the gut as a rationale for future intervention studies.
P009 Disease classifier and microbial dysbiosis index tools cross-predict various pathogenic conditions due to general microbial signal
Authors: Abbas Egbariya H , Braun T , Hadar R , Gal-Mor O , Shental N , Haberman Y , Amir A 
Published: May 2021

Abstract

Background
Microbial dysbiosis is widely described in inflammatory bowel disease (IBD), and has been shown to predict IBD state. However, many other diseases including neuro-psychiatric, metabolic, and malignancies, most of which do not result in gut inflammation, are also linked with gut microbial alteration. Since most studies focus on a single disease, the extent of similarity between different diseases is usually not examined.

Methods
We reanalyzed raw sequencing data from 12,838 human gut V4 16Sseq samples, spanning 59 case-controls comparisons and 28 unique diseases. Novel statistical approach was applied to reduce the effect of the different cohorts; all samples were processed uniformly, and differentially expressed amplicon sequence variants (ASVs) were identified within each cohort. The resulting behavior (direction of change and effect size) of each ASV were then combined across all studies. We used random forest as our classifier and generated non-specific dysbiosis index (NSDI).

Results
For the disease prediction, each cohort was randomly subsampled to 23 healthy and 23 disease samples. Random forest classifier was trained on one disease/control cohort, and the trained classifier was then used to predict the status of a different disease/control cohort. Disease classifiers performed well in identifying many sick vs. healthy states but failed to differentiate between different diseases. For example, a classifier trained on IBD cohort classified relatively good also disease/control in lupus, schizophrenia, or Parkinson’s from different cohorts. We show this cross-identification is due to a large number of shared disease-associated bacteria and utilize these bacteria to define a novel non-specific dysbiosis index (NSDI). After, we identified 114 non-disease specific ASVs (86 up and 28 down regulated ASVs across diseases in comparison to controls), we calculate the per-sample NSDI by rank-transforming the bacteria within the sample and computing the normalized log ratio of the sum of the ranks of the 86 down and 28 up regulated ASVs. The resulting NSDI is shown to perform better than the previously published CD dysbiosis index (Gevers et al, 2014; PMID: 24629344) indicating that NSDI can successfully differentiate between most cases and controls across a wide variety of diseases.

Conclusion
A robust non-specific general response of the gut microbiome is detected across different diseases, some of which is shared with IBD. Classifiers trained on a single disease may identify the general non-specific signal and therefore care should be taken when interpreting the classifier predictions. Finally, our NSDI can be used to prioritize the per-sample degree of dysbiosis.
P020 Mapping the changing intercellular communication and its downstream effect in Ulcerative Colitis
Authors: Potari-gul L , Modos D , Turei D , Valdeolivas A , Madgwick M , Saez-Rodriguez J , Korcsmaros T 
Published: May 2021

Abstract

Background
Intercellular communication is essential for growing and differentiating in multicellular organisms by transducing the signal from cell to cell. Despite its importance, the molecular background is less discovered due to the lack of data. This gap has started to be addressed with the appearance of single-cell omics approaches providing an insight among others into the gene expression of individual cells.

Methods
We have developed a method to predict and compare cell-cell signalling interactions using single-cell RNAseq data from colon biopsies. Transcriptomic data alone is not capable of connecting the cells, a reliable network resource is needed to mediate the signal via protein-protein interactions between the source and target cells. Here we used OmniPath - a resource providing not only intra- and intercellular interactions but also annotations of proteins involved in the interplay of cells - to reconstruct signalling networks. We examined intercellular communication among five cell-types (regulatory T cell, macrophage, dendritic cell, goblet cell and myofibroblast) in healthy colon and during Ulcerative Colitis.

Results
Our analysis shows that there are significant differences in the type of cell-cell communication (ligand-receptor connections, adherens junctions, etc.) between the healthy and Ulcerative Colitis (UC) conditions, and these differences lead to altered downstream effects in the signal receiving cell. In both conditions, the ligand-receptor and adhesion connections were overrepresented, however cell junctions were less abundant in UC. Regarding the communication among the five cell-types, in healthy condition, cells are tightly connected to dendritic cells while in diseased condition to regulatory T cells. Focusing on ligand-receptor interactions between myofibroblasts and regulatory T cells, our pipeline identified the MAPK, Toll-like receptor (TLR) 2/6 and TLR 7/8 pathways enriched downstream in healthy conditions. In contrast, TLR3 and TLR4 pathways were affected by the myofibroblast in Ulcerative Colitis.

Conclusion
We found key intercellular mechanisms leading to well-defined differential pathway activation profiles. We showed that in uninflamed UC condition myofibroblasts disrupt the anti-inflammatory effect of regulatory T cells. Our pipeline is able to predict and analyse cell-cell interactions and their downstream effects and to highlight the differences in healthy and diseased states.