bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identifiability and experimental design in perturbation studies
Authors: Gross Torsten , Blüthgen Nils 
Published: April 2020

AbstractMotivationA common strategy to infer and quantify interactions between components of a biological system is to deduce them from the network’s response to targeted perturbations. Such perturbation experiments are often challenging and costly. Therefore, optimizing the experimental design is essential to achieve a meaningful characterization of biological networks. However, it remains difficult to predict which combination of perturbations allows to infer specific interaction strengths in a given network topology. Yet, such a description of identifiability is necessary to select perturbations that maximize the number of inferable parameters.ResultsWe show analytically that the identifiability of network parameters can be determined by an intuitive maximum-flow problem. Furthermore, we used the theory of matroids to describe identifiability relationships between sets of parameters in order to build identifiable effective network models. Collectively, these results allowed to device strategies for an optimal design of the perturbation experiments. We benchmarked these strategies on a database of human pathways. Remarkably, full network identifiability was achieved, on average, with less than a third of the perturbations that are needed in a random experimental design. Moreover, we determined perturbation combinations that additionally decreased experimental effort compared to single-target perturbations. In summary, we provide a framework that allows to infer a maximal number of interaction strengths with a minimal number of perturbation experiments.Availability and implementationIdentiFlow is available at github.com/GrossTor/IdentiFlow.Supplementary informationSupplementary data are available at Bioinformatics online.
Regression-adjusted average treatment effect estimates in stratified randomized experiments
Authors: Liu Hanzhong , Yang Yuehan 
Published: April 2020

Summary
Linear regression is often used in the analysis of randomized experiments to improve treatment effect estimation by adjusting for imbalances of covariates in the treatment and control groups. This article proposes a randomization-based inference framework for regression adjustment in stratified randomized experiments. We re-establish, under mild conditions, the finite-population central limit theorem for a stratified experiment, and we prove that both the stratified difference-in-means estimator and the regression-adjusted average treatment effect estimator are consistent and asymptotically normal; the asymptotic variance of the latter is no greater and typically less than that of the former. We also provide conservative variance estimators that can be used to construct large-sample confidence intervals for the average treatment effect.
Effects of Growth Phase and Ultraviolet-B Pretreatment in Perilla Leaves on the Two-Spotted Spider Mite
Authors: Tomimori Daichi , Hosokawa Munetaka , Aoki Shinichi , Osakabe Masahiro 
Published: April 2020

AbstractPerilla, Perilla frutescens (L.) Britton var. crispa (Thunb.) H. Deane, is traditionally cultivated as an edible/medicinal crop in East Asia. Its essential oil contains many bioactive compounds that are expected to have high pharmacological functionality, as well as antimicrobial and insecticidal activity. Spider mites are a major pest group for perilla cultivation. The two-spotted spider mite, Tetranychus urticae Koch, possesses divergent detoxification enzymes and has developed resistance against most acaricides. The essential oil content of perilla halves from the pre-flowering phase to the flowering phase, and ultraviolet (UV)-B radiation generally increases defense compounds. To clarify the effects of this change in essential oil content and the effects of UV-B pretreatment, we investigated the developmental success and egg production of T. urticae on leaves from the preflowering and flowering phases cultivated with and without nighttime UV-B irradiation. Both the parameters significantly increased on leaves from the flowering phase in comparison with that from the preflowering phase, suggesting that constitutively produced essential oil provided protection against mite pests in a growth phase-specific manner. The defense system also extended the developmental period of mites on red perilla leaves, but not on green perilla leaves, in preflowering phase. Although egg production was lower on red perilla leaves pretreated with UV-B, no negative effects were caused on the developmental success and duration on red and green perilla and the egg production on green perilla by UV-B pretreatment. Our findings reveal a significant impact of investment allocation of perilla plants and a small contribution of UV-B irradiation to the plant defense system.
Oesophageal-pericardial fistula: a rare complication of radiation-induced oesophagitis
Authors: Denglos Pauline , Nuytens Frederiek , Piessen Guillaume 
Published: April 2020

Abstract
Oesophageal-pericardial fistula after radiation therapy for lung cancer is a rare complication associated with a high mortality. In this case report, we present the case of 52-year-old women with late radiation-induced oesophagitis after chemoradiotherapy for a pulmonary adenocarcinoma, complicated by an oesophageal-pericardial fistula for which a transthoracic oesophagectomy with pericardial drainage was performed. The postoperative course was complicated by a fatal hypovolaemic shock due to a perforation of the descending aorta near the initial fistula track. In this case report, we illustrate the importance of thorough inspection of diagnostic images in this context and emphasize the role of endovascular repair in case an associated aortic perforation is suspected.
Two-step treatment of dysphagia lusoria: robotic-assisted resection of aberrant right subclavian artery following aortic debranching
Authors: La Regina Davide , Prouse Giorgio , Mongelli Francesco , Pini Ramon 
Published: April 2020

Abstract
A 69-year-old female suffering from severe dysphagia due to an aberrant right subclavian artery was treated with a two-step approach. A right carotid-subclavian bypass was followed 2 weeks later by a robotic-assisted thoracoscopic resection of the aberrant right subclavian artery. The postoperative course was uneventful, and the patient immediately recovered from her dysphagia. In our case, the robotic-assisted technology offered major advantages and, based on our experience, may be useful in the treatment of this rare disease.
Haemorrhagic stroke and major bleeding after intervention with biological aortic valve prosthesis: risk factors and antithrombotic treatment
Authors: Christersson Christina , Ståhle Elisabeth , Lindhagen Lars , James Stefan 
Published: April 2020

Introduction
The majority of patients with severe aortic stenosis are recommended intervention with a surgical biological prosthesis (bioSAVR) or a transcatheter aortic valve intervention (TAVI). The antithrombotic strategies after aortic valve intervention vary and include drugs targeting both platelets and the coagulation cascade. Long-term exposure and changes of antithrombotic treatment influence the risk of both bleeding and thromboembolic events.The aim was to describe an unselected sample of patients who have experienced haemorrhagic stroke and other major bleeding events after biological aortic prosthesis, their antithrombotic treatment and changes of treatments in relation to the bleeding event.All patients performing an bioSAVR or a TAVI 2008–2014 were identified in the SWEDEHEART registry and included in the study (n = 10 711). The outcome events were haemorrhagic stroke and other major bleeding event. Information of drug exposure was collected from the dispensed drug registry.The incidence rate of any bleeding event was 2.85/100 patient-years the first year after aortic valve intervention. Heart failure and atrial fibrillation were present more often in patients with a first haemorrhagic stroke or other major bleeding event compared to without. The proportion of exposure to warfarin was 28.7% vs. 21.3% in patients with and without a haemorrhagic stroke. Comparable figures were 31.2% vs. 19.0% in patients with and without other major bleeding event. During 1 month prior a haemorrhagic stroke or other major bleeding event 39.4% and 38.0%, respectively, of the patients not previously exposed to antithrombotic treatment started warfarin or single antiplatelet therapy.Major bleeding events are not uncommon after aortic valve intervention with a biological prosthesis. Evaluation of comorbidities and previous bleeding might improve risk stratification for bleeding in these elderly patients. The pattern of change of antithrombotic treatment was similar in the groups with and without a bleeding event and in most patients the antithrombotic regime was unchanged the month before an event.
Characterization and survey in cattle of a rumen Pyrimadobacter sp. which degrades the plant toxin fluoroacetate
Authors: Kang Seungha , Khan Shahjalal , Webb Rick , Denman Stuart , McSweeney Chris 
Published: April 2020

ABSTRACTAmong the natural halogenic compounds, the plant toxin fluoroacetate (FA) causes livestock fatalities in southern hemisphere countries. Here, we report on the isolation of a rumen bacterium, strain C12–8 that degrades FA under anaerobic conditions. 16S rRNA gene sequence analysis showed this bacterium belonged to the Pyramidobacter genus within the Synergistetes phylum and was 98% similar to Pyramidobacter piscolens W5455 isolated from the human oral cavity. Transmission electron microscopy showed the cell envelope to be unusual, with only one membrane and no obvious external wall. Growth and FA degradation were enhanced by peptide-rich protein hydrolysates but not carbohydrates. End products of metabolism were mainly acetate, propionate/isovalerate and isobutyrate. Strain C12-8 preferentially used peptide-bound amino acids rather than free amino acids. Glycine, serine, threonine, leucine, histidine and isoleucine were utilized as free and peptide-bound amino acids, but there was minimal utilization of alanine, proline, methionine, aspartic acid, lysine and arginine in either form. A survey of several cattle properties in northern Australia showed that strain C12-8 and other FA degrading bacteria affiliated with Cloacibacillus porcorum strain MFA1 were endemic to cattle in the northern beef herd and may help to reduce toxicity.
The marine intertidal zone shapes oyster and clam digestive bacterial microbiota
Authors: Offret Clément , Paulino Sauvann , Gauthier Olivier , Château Kevin , Bidault Adeline , Corporeau Charlotte , Miner Philippe , Petton Bruno , Pernet Fabrice , Fabioux Caroline , Paillard Christine , Blay Gwenaelle Le 
Published: April 2020

ABSTRACTDigestive microbiota provide a wide range of beneficial effects on host physiology and are therefore likely to play a key role in marine intertidal bivalve ability to acclimatize to the intertidal zone. This study investigated the effect of intertidal levels on the digestive bacterial microbiota of oysters (Crassostrea gigas) and clams (Ruditapes philippinarum), two bivalves with different ecological niches. Based on 16S rRNA region sequencing, digestive glands, seawater and sediments harbored specific bacterial communities, dominated by operational taxonomic units assigned to the Mycoplasmatales,Desulfobacterales and Rhodobacterales orders, respectively. Field implantation modified digestive bacterial microbiota of both bivalve species according to their intertidal position. Rhodospirillales and Legionellales abundances increased in oysters and clams from the low intertidal level, respectively. After a 14-day depuration process, these effects were still observed, especially for clams, while digestive bacterial microbiota of oysters were subjected to more short-term environmental changes. Nevertheless, 3.5 months stay on an intertidal zone was enough to leave an environmental footprint on the digestive bacterial microbiota, suggesting the existence of autochthonous bivalve bacteria. When comparing clams from the three intertidal levels, 20% of the bacterial assemblage was shared among the levels and it was dominated by an operational taxonomic unit affiliated to the Mycoplasmataceae and Spirochaetaceae families.
Effect of stevia on the gut microbiota and glucose tolerance in a murine model of diet-induced obesity
Authors: Becker Sarah L , Chiang Edna , Plantinga Anna , Carey Hannah V , Suen Garret , Swoap Steven J 
Published: April 2020

ABSTRACTArtificial sweeteners have been shown to induce glucose intolerance by altering the gut microbiota; however, little is known about the effect of stevia. Here, we investigate whether stevia supplementation induces glucose intolerance by altering the gut microbiota in mice, hypothesizing that stevia would correct high fat diet-induced glucose intolerance and alter the gut microbiota. Mice were split into four treatment groups: low fat, high fat, high fat + saccharin and high fat + stevia. After 10 weeks of treatment, mice consuming a high fat diet (60% kcal from fat) developed glucose intolerance and gained more weight than mice consuming a low fat diet. Stevia supplementation did not impact body weight or glucose intolerance. Differences in species richness and relative abundances of several phyla were observed in low fat groups compared to high fat, stevia and saccharin. We identified two operational taxonomic groups that contributed to differences in beta-diversity between the stevia and saccharin groups: Lactococcus and Akkermansia in females and Lactococcus in males. Our results demonstrate that stevia does not rescue high fat diet-induced changes in glucose tolerance or the microbiota, and that stevia results in similar alterations to the gut microbiota as saccharin when administered in concordance with a high fat diet.
Limitations of right ventricular annular parameters in the early postoperative period following pulmonary endarterectomy: an observational study
Authors: Rézaiguia-Delclaux Saida , Haddad François , Pilorge Catherine , Amsallem Myriam , Fadel Elie , Stéphan François 
Published: April 2020

Abstract

OBJECTIVES
Echocardiographic right ventricular (RV) annular parameters are probably not as reliable to evaluate the surgical success in the postoperative period after pulmonary endarterectomy (PEA), whereas RV end-diastolic/left ventricular end-diastolic area ratio (RVEDA/LVEDA ratio) could be more useful. This study examined the relationship between RV annular parameters or RVEDA/LVEDA ratio and ideal cardiac index (ICI), before and after PEA.

METHODS
Among 80 patients who underwent PEA, the relationships between RVEDA/LVEDA ratio (21 patients), or tricuspid annular plane systolic excursion (32 patients), or systolic tricuspid annular velocity (55 patients) and ICI were modelled.

RESULTS
Forty-eight hours following PEA, mean pulmonary artery pressure decreased (26 ± 6 vs 46 ± 12 mmHg, P &lt; 0.0001) and ICI improved (2.8 ± 0.8 vs 3.0 ± 0.9 l/min/m2, P = 0.02). In contrast to the moderate association between RV annular indices and ICI in the preoperative period, no significant relationship was found in the postoperative period (r = 0.54 and 0.17 for tricuspid annular plane systolic excursion and r = 0.46 and 0.16 for systolic tricuspid annular velocity, respectively). The RVEDA/LVEDA ratio significantly decreased postoperatively (0.97 ± 0.21 vs 1.19 ± 0.43, P = 0.002) and was correlated with ICI both in preoperative and postoperative periods (r = 0.57 and 0.57, respectively). There was a significant correlation between changes in RVEDA/LVEDA ratio and changes in total pulmonary resistance

CONCLUSIONS
Improved ICI and RVEDA/LVEDA ratio reflected the surgical success of PEA and lowering of total pulmonary resistances. In contrast to the RV/left ventricular area ratio, annular RV indices associated poorly with postoperative ICI. Recognizing this limitation is important in minimizing the overdiagnosis of RV dysfunction after PEA.
Complex Microbiota in Laboratory Rodents: Management Considerations
Authors: Franklin Craig L , Ericsson Aaron C 
Published: April 2020

Abstract
Our bodies and those of our animal research subjects are colonized by bacterial communities that occupy virtually every organ system, including many previously considered sterile. These bacteria reside as complex communities that are collectively referred to as microbiota. Prior to the turn of the century, characterization of these communities was limited by a reliance on culture of organisms on a battery of selective media. It was recognized that the vast majority of microbes, especially those occupying unique niches of the body such as the anaerobic environment of the intestinal tract, were uncultivatable. However, with the onset and advancement of next-generation sequencing technology, we are now capable of characterizing these complex communities without the need to cultivate, and this has resulted in an explosion of information and new challenges in interpreting data generated about, and in the context of, these complex communities. We have long known that these microbial communities often exist in an intricate balance that, if disrupted (ie, dysbiosis), can lead to disease or increased susceptibility to disease. Because of many functional redundancies, the makeup of these colonies can vary dramatically within healthy individuals [1]. However, there is growing evidence that subtle differences can alter the phenotype of various animal models, which may translate to the varying susceptibility to disease seen in the human population. In this manuscript, we discuss how to include complex microbiota as a consideration in experimental design and model reproducibility and how to exploit the extensive variation that exists in contemporary rodent research colonies. Our focus will be the intestinal or gut microbiota (GM), but it should be recognized that microbial communities exist in many other body compartments and these too likely influence health and disease [2, 3]. Much like host genetics, can we one day harness the vast genetic capacity of the microbes we live with in ways that will benefit human and animal health?
Initial evaluation of nivolumab in patients with post-operative recurrence of malignant pleural mesothelioma
Authors: Nakamura Akifumi , Kondo Nobuyuki , Nakamichi Toru , Kuroda Ayumi , Hashimoto Masaki , Matsumoto Seiji , Yokoi Takashi , Kuribayashi Kozo , Kijima Takashi , Hasegawa Seiki 
Published: April 2020

Abstract

Background
Limited options exist for treating post-recurrence patients with malignant pleural mesothelioma (MPM). This study aimed to evaluate the efficacy and feasibility of nivolumab in patients with post-operative recurrence of MPM in a real-world setting.

Methods
This study included 35 patients with post-operative recurrence of MPM. Treatment consisted of 240-mg intravenous nivolumab administration every 2 weeks until progressive disease (PD) or serious adverse events (AEs). Additional post-treatment data were evaluated, including objective response rate (ORR), disease control rate (DCR), progression-free survival (PFS), post-treatment survival and AEs. Tumor response was assessed using the modified Response Evaluation Criteria in Solid Tumors. Survival analysis was performed using the Kaplan–Meier method. The feasibility analysis including AEs was performed with the National Cancer Institute Common Terminology Criteria for Adverse Events version 5.0.

Results
Of the 35 patients who received nivolumab, median follow-up was 6 months. The median treatment duration was 3 months (range: 1–14 months), and median of 8 cycles (range: 2–32 cycles) was administered. Best overall responses were follows: 1 patient had complete response, 6 had partial response, 18 had stable disease and 8 had PD. The ORR was 20.0%, and the DCR was 77.1%. The median overall survival and PFS were 13.1 and 4.4 months, respectively. There were grade-3 AEs in four patients (11.4%). No grade-4 or -5 AEs were observed.

Conclusion
Nivolumab treatment in patients with post-operative recurrence of MPM seems safe and clinical efficacy.
A unique case report of a high-pressure paint injection injury of the hand with associated carbapenemase resistant Pseudomonas aeruginosa infection
Authors: Barger Kurt , Jenkins Ryne , Weng Bruce , Fan Juston , Tholcke Loren , French Michael 
Published: April 2020

AbstractHigh pressure injection injuries to the hand should not be taken lightly as urgent surgical debridement is required to ensure favorable outcomes. Empiric antibiotic administration is recommended; however, few studies focus on the secondary infection risk associated with these high pressure injection injuries. We present a rare case of a patient presenting with carbapenem resistant Pseudomonas aeruginosa following a high pressure paint gun injury of the thumb. Urgent surgical debridement with administration of broad-spectrum antibiotic coverage for both gram-negative and gram-positive bacteria is recommended. The injection of foreign materials can cause extensive tissue damage and immunosuppression facilitating growth of opportunistic bacteria that are often rare in healthy adults. We advocate for obtaining cultures at initial debridement to optimize treatment in these unique and rare injection injuries. Concerns should be raised as carbapenem resistant bacteria become more prevalent in the community.
A syntactic dependency network approach to the study of translational language
Authors: Fan Lu , Jiang Yue 
Published: April 2020

Abstract
Complex network approach provides language research with quantitative measures that can capture global features of language. Although translational language has been recognized as a ‘third code’ by some researchers, its independence still calls for further and quantitative validation in an overall manner. In this study, we intend to examine this independence and explore comprehensively its features. We investigated macroscopically translational language from English into Chinese and from Chinese into English by comparing with its source language and native language through syntactic dependency networks. The results show that: (1) translational language presents small-world and scale-free properties like most languages do; (2) however, it is independent of and different from both source language and native language in terms of its network parameters; (3) its network parameters show values eclectic between source language and native language, and this eclectic tendency may be regarded as a new candidate for universal features of translational language, which certainly needs further validation in other genres and language pairs. This study also corroborates that quantitative linguistic method of complex network approach can be well utilized in the study of translational language.