bluuebunny/crossref_metadata_2025 huggingface dataset:
scDEA: differential expression analysis in single-cell RNA-sequencing data via ensemble learning
Authors: Li Hui-Sheng , Ou-Yang Le , Zhu Yuan , Yan Hong , Zhang Xiao-Fei
Published: September 2021

The identification of differentially expressed genes between different cell groups is a crucial step in analyzing single-cell RNA-sequencing (scRNA-seq) data. Even though various differential expression analysis methods for scRNA-seq data have been proposed based on different model assumptions and strategies recently, the differentially expressed genes identified by them are quite different from each other, and the performances of them depend on the underlying data structures. In this paper, we propose a new ensemble learning-based differential expression analysis method, scDEA, to produce a more stable and accurate result. scDEA integrates the P-values obtained from 12 individual differential expression analysis methods for each gene using a P-value combination method. Comprehensive experiments show that scDEA outperforms the state-of-the-art individual methods with different experimental settings and evaluation metrics. We expect that scDEA will serve a wide range of users, including biologists, bioinformaticians and data scientists, who need to detect differentially expressed genes in scRNA-seq data.
A multi-step and multi-scale bioinformatic protocol to investigate potential SARS-CoV-2 vaccine targets
Authors: Russo Giulia , Di Salvatore Valentina , Sgroi Giuseppe , Parasiliti Palumbo Giuseppe Alessandro , Reche Pedro A , Pappalardo Francesco
Published: September 2021

The COVID-19 pandemic has highlighted the need to come out with quick interventional solutions that can now be obtained through the application of different bioinformatics software to actively improve the success rate. Technological advances in fields such as computer modeling and simulation are enriching the discovery, development, assessment and monitoring for better prevention, diagnosis, treatment and scientific evidence generation of specific therapeutic strategies. The combined use of both molecular prediction tools and computer simulation in the development or regulatory evaluation of a medical intervention, are making the difference to better predict the efficacy and safety of new vaccines. An integrated bioinformatics pipeline that merges the prediction power of different software that act at different scales for evaluating the elicited response of human immune system against every pathogen is proposed. As a working example, we applied this problem solving protocol to predict the cross-reactivity of pre-existing vaccination interventions against SARS-CoV-2.
VOLTA: adVanced mOLecular neTwork Analysis
Authors: Pavel Alisa , Federico Antonio , del Giudice Giusy , Serra Angela , Greco Dario
Published: September 2021

Motivation

Network analysis is a powerful approach to investigate biological systems. It is often applied to study gene co-expression patterns derived from transcriptomics experiments. Even though co-expression analysis is widely used, there is still a lack of tools that are open and customizable on the basis of different network types and analysis scenarios (e.g. through function accessibility), but are also suitable for novice users by providing complete analysis pipelines.

Results

We developed VOLTA, a Python package suited for complex co-expression network analysis. VOLTA is designed to allow users direct access to the individual functions, while they are also provided with complete analysis pipelines. Moreover, VOLTA offers when possible multiple algorithms applicable to each analytical step (e.g. multiple community detection or clustering algorithms are provided), hence providing the user with the possibility to perform analysis tailored to their needs. This makes VOLTA highly suitable for experienced users who wish to build their own analysis pipelines for a wide range of networks as well as for novice users for which a ‘plug and play’ system is provided.

Availability and implementation

The package and used data are available at GitHub: https://github.com/fhaive/VOLTA and 10.5281/zenodo.5171719.

Supplementary information

Supplementary data are available at Bioinformatics online.
LipidQuant 1.0: automated data processing in lipid class separation–mass spectrometry quantitative workflows
Authors: Wolrab Denise , Cífková Eva , Čáň Pavel , Lísa Miroslav , Peterka Ondřej , Chocholoušková Michaela , Jirásko Robert , Holčapek Michal
Published: September 2021

We present the LipidQuant 1.0 tool for automated data processing workflows in lipidomic quantitation based on lipid class separation coupled with high-resolution mass spectrometry. Lipid class separation workflows, such as hydrophilic interaction liquid chromatography or supercritical fluid chromatography, should be preferred in lipidomic quantitation due to the coionization of lipid class internal standards with analytes from the same class. The individual steps in the LipidQuant workflow are explained, including lipid identification, quantitation, isotopic correction and reporting results. We show the application of LipidQuant data processing to a small cohort of human serum samples.

Availability and implementation

The LipidQuant 1.0 is freely available at Zenodo https://doi.org/10.5281/zenodo.5151201 and https://holcapek.upce.cz/lipidquant.php.

Supplementary information

Supplementary data are available at Bioinformatics online.
Genetic Contribution to Concern for Nature and Proenvironmental Behavior
Authors: Chang Chia-chen , Nghiem Thi Phuong Le , Fan Qiao , Tan Claudia L Y , Oh Rachel Rui Ying , Lin Brenda B , Shanahan Danielle F , Fuller Richard A , Gaston Kevin J , Carrasco L Roman
Published: September 2021

Earth is undergoing a devastating extinction crisis caused by human impacts on nature, but only a fraction of society is strongly concerned and acting on the crisis. Understanding what determines people's concern for nature, environmental movement activism, and personal conservation behavior is fundamental if sustainability is to be achieved. Despite its potential importance, the study of the genetic contribution to concern for nature and proenvironmental behaviors has been neglected. Using a twin data set (N = 2312), we show moderate heritability (30%–40%) for concern for nature, environmental movement activism, and personal conservation behavior and high genetic correlations between them (.6–.7), suggesting a partially shared genetic basis. Our results shed light on the individual variation in sustainable behaviors, highlighting the importance of understanding both the environmental and genetic components in the pursuit of sustainability.
KCNQ variants and pain modulation: a missense variant in Kv7.3 contributes to pain resilience
Authors: Yuan Jun-Hui , Estacion Mark , Mis Malgorzata A , Tanaka Brian S , Schulman Betsy R , Chen Lubin , Liu Shujun , Dib-Hajj Fadia B , Dib-Hajj Sulayman D , Waxman Stephen G
Published: September 2021

There is a pressing need for understanding of factors that confer resilience to pain. Gain-of-function mutations in sodium channel Nav1.7 produce hyperexcitability of dorsal root ganglion neurons underlying inherited erythromelalgia, a human genetic model of neuropathic pain. While most individuals with erythromelalgia experience excruciating pain, occasional outliers report more moderate pain. These differences in pain profiles in blood-related erythromelalgia subjects carrying the same pain-causative Nav1.7 mutation and markedly different pain experience provide a unique opportunity to investigate potential genetic factors that contribute to inter-individual variability in pain. We studied a patient with inherited erythromelalgia and a Nav1.7 mutation (c.4345T>G, p. F1449V) with severe pain as is characteristic of most inherited erythromelalgia patients, and her mother who carries the same Nav1.7 mutation with a milder pain phenotype. Detailed six-week daily pain diaries of pain episodes confirmed their distinct pain profiles. Electrophysiological studies on subject-specific induced pluripotent stem cell-derived sensory neurons from each of these patients showed that the excitability of these cells paralleled their pain phenotype. Whole-exome sequencing identified a missense variant (c.2263C>T, p. D755N) in KCNQ3 (Kv7.3) in the pain resilient mother. Voltage-clamp recordings showed that co-expression of Kv7.2-wild type (WT)/Kv7.3-D755N channels produced larger M-currents than that of Kv7.2-WT/Kv7.3-WT. The difference in excitability of the patient-specific induced pluripotent stem cell-derived sensory neurons was mimicked by modulating M-current levels using the dynamic clamp and a model of the mutant Kv7.2-WT/Kv7.3-D755N channels. These results show that a ‘pain-in-a-dish’ model can be used to explicate genetic contributors to pain, and confirm that KCNQ variants can confer pain resilience via an effect on peripheral sensory neurons.
Quality of Service Estimation Enabled With Trust-Based Resource Allocation in Collaborative Cloud Using Improved Grey Wolf Optimization
Authors: Pol Pooja Shashank , Pachghare Vinod K
Published: September 2021

Collaborative cloud computing utilizes information technology to successfully provide service over the network and serve the end users with tremendously stronger computational capability and enormous memory space at lower costs. Moreover, providing highly trustworthy service is the most fundamental task even on this platform. So far, only some contributions are there that meet the requirements of trust computing in this scenario. This proposal estimates the Quality of Service and trust by analyzing the system behavior using a new trust computing model. This is handled using Neural Network model. Further, a parallel resource matching framework is introduced using the concept of MapReduce concept, thereby the resource allocation is performed without any conflicts. Particularly, the resource allocation is performed precisely by optimization logic, where an Improved Grey Wolf Optimizer is introduced to do the same. In fact, the proposed algorithm is the enhanced version of traditional Grey Wolf Optimizer. Finally, the performance of the projected model is compared over other state-of-the-art models concerning different performance measures.
Interest clustering coefficient: a new metric for directed networks like Twitter
Authors: Trolliet Thibaud , Cohen Nathann , Giroire Frédéric , Hogie Luc , Pérennes Stéphane
Published: September 2021

The clustering coefficient has been introduced to capture the social phenomena that a friend of a friend tends to be my friend. This metric has been widely studied and has shown to be of great interest to describe the characteristics of a social graph. But, the clustering coefficient is originally defined for a graph in which the links are undirected, such as friendship links (Facebook) or professional links (LinkedIn). For a graph in which links are directed from a source of information to a consumer of information, it is no more adequate. We show that former studies have missed much of the information contained in the directed part of such graphs. In this article, we introduce a new metric to measure the clustering of directed social graphs with interest links, namely the interest clustering coefficient. We compute it (exactly and using sampling methods) on a very large social graph, a Twitter snapshot with 505 million users and 23 billion links, as well as other various datasets. We additionally provide the values of the formerly introduced directed and undirected metrics, a first on such a large snapshot. We observe a higher value of the interest clustering coefficient than classic directed clustering coefficients, showing the importance of this metric. By studying the bidirectional edges of the Twitter graph, we also show that the interest clustering coefficient is more adequate to capture the interest part of the graph while classic ones are more adequate to capture the social part. We also introduce a new model able to build random networks with a high value of interest clustering coefficient. We finally discuss the interest of this new metric for link recommendation.
Does Habituation Affect the Efficacy of Semiochemical Oviposition Repellents Developed Against Drosophila suzukii?
Authors: Stockton Dara G , Cha Dong H , Loeb Greg M
Published: September 2021

The application of feeding and oviposition repellents is limited to arthropod systems in which habituation does not occur. Although several compounds appear to reduce Drosophila suzukii Matsumura (Dipetra: Drosophilidae) oviposition in berries, previous studies have yet to address whether habituation is a significant risk following preexposure. We tested the response of adult female D. suzukii to three previously identified semiochemical oviposition repellents, 1-octen-3-ol (octenol), ±-geosmin, and 2-n-pentylfuran, following adult and larval preexposure. Using a two-choice gated trap capture assay, we assessed captures in repellent-treated versus blank traps, female survival, and oviposition frequency in the selected trap. We did not find evidence of habituation to octenol or 2-pentylfuran in adult flies preexposed for 24, 48, or 72 hr. When exposed to each of the repellents as larvae, D. suzukii showed similar deterrence as those exposed as adults alone. However, mortality did decrease in F1 octenol treated flies. In contrast with previous investigations we did not observe repellent effects in response to geosmin. Our results suggest that neither exposure during the adult life stage nor during larval development inhibited the effectiveness of octenol and 2-pentylfuran. However, greater survivorship on octenol treated baits in F1 flies, combined with apparent neurotoxic effects of this compound, indicate that octenol may be less suited for field applications. For this reason, 2-pentylfuran appears to be a better candidate for ongoing research aimed at developing an effective push–pull system of behavioral management.
Engineering of molybdenum-cofactor-dependent nitrate assimilation in Yarrowia lipolytica
Authors: Perli Thomas , Borodina Irina , Daran Jean-Marc
Published: September 2021

Engineering a new metabolic function in a microbial host can be limited by the availability of the relevant cofactor. For instance, in Yarrowia lipolytica, the expression of a functional nitrate reductase is precluded by the absence of molybdenum cofactor (Moco) biosynthesis. In this study, we demonstrated that the Ogataea parapolymorpha Moco biosynthesis pathway combined with the expression of a high affinity molybdate transporter could lead to the synthesis of Moco in Y. lipolytica. The functionality of Moco was demonstrated by expression of an active Moco-dependent nitrate assimilation pathway from the same yeast donor, O. parapolymorpha. In addition to 11 heterologous genes, fast growth on nitrate required adaptive laboratory evolution which, resulted in up to 100-fold increase in nitrate reductase activity and in up to 4-fold increase in growth rate, reaching 0.13h-1. Genome sequencing of evolved isolates revealed the presence of a limited number of non-synonymous mutations or small insertions/deletions in annotated coding sequences. This study that builds up on a previous work establishing Moco synthesis in S. cerevisiae demonstrated that the Moco pathway could be successfully transferred in very distant yeasts and, potentially, to any other genera, which would enable the expression of new enzyme families and expand the nutrient range used by industrial yeasts.
The long history of child sponsorship, c.1700–1950
Authors: Kaell Hillary
Published: September 2021

The invention of child sponsorship, a fundraising tool that raises billions of dollars a year for global projects, is widely credited to the Save the Children Fund in 1919. This article is the first to revise that history, as it follows sponsorship through multiple iterations across more than two centuries. Doing so, it uncovers sponsorship’s roots in transatlantic Protestant missionary networks that combined new theologies of child saving with early capitalism’s ‘share holding’ system. Turning to the early twentieth century, it then shows how sponsorship mobilized ‘non-sectarian’ Christianity to lend authority to humanitarian appeals while opening up broader markets.
The 2001 ILC Articles on State Responsibility—An Annotated Bibliography
Authors: Gore Kiran Nasir , Alvarez Dr Gloria M
Published: September 2021

In this Special Issue, commemorating the twentieth anniversary of the International Law Commission’s Draft Articles on the Responsibility of States for Internationally Wrongful Acts, as adopted in August 2001 (‘ILC Articles’ or ‘ARSIWA’), we curate a bibliography annotating important contributions to scholarship and literature concerning the ILC Articles. It is organized topically, including focus on attribution, elements of international breach (including acts, omissions, defences and justifications), the State–individual relationship, State responsibility for judicial acts, various redress doctrines and contributory fault. Each entry is accompanied by a few comments. This annotated bibliography aims to be useful to practitioners and scholars alike, as it presents a centralized corpus of relevant literature, reflecting the topics that have captured popular interest, while also illuminating possible gaps where further scholarly attention is needed.
On Conjugates and the Asymptotic Distortion of One-Dimensional C1+bv Diffeomorphisms
Authors: Navas Andrés
Published: September 2021

We show that a $C^{1+bv}$ circle diffeomorphism with absolutely continuous derivative and irrational rotation number can be conjugated to diffeomorphisms that are $C^{1+bv}$ arbitrary close to the corresponding rotation. This improves a theorem of M. Herman, who established the same result but starting with a $C^2$ diffeomorphism. We prove that the same holds for countable Abelian groups of circle diffeomorphisms acting freely, a result that is new even in the $C^{\infty }$ context. Related results and examples concerning the asymptotic distortion of diffeomorphisms are presented. Along this path, we provide a straightened version of the classical Denjoy–Kocsma inequality for absolutely continuous potentials.$\hfill$In memory of Jean-Christophe Yoccoz
Improving first-pass success rates during emergency intubation at an academic emergency department: a quality improvement initiative
Authors: Bakhsh Abdullah , Alharbi Ahd , Almehmadi Raghad , Kamfar Sara , Aldhahri Arwa , Aledeny Ahmed , Ashour Yasmeen , Khojah Imad
Published: September 2021

Background

Airway management is a high-stakes procedure in emergency medicine. Continuously monitoring this procedure allows performance improvement while revealing safety issues. We instituted a quality improvement initiative in the emergency department to improve first-pass success rates in the emergency department.

Methods

This was a quality improvement initiative at an academic emergency department from 2018 to 2020. We developed a rapid sequence intubation guideline for procedure standardization and introduced an intubation procedure note for performance monitoring. Data were entered directly by the primary physician and nurse during intubation. The quality improvement team thereafter collected the data retrospectively and entered into a local airway database. More importantly, we introduced a culture of quality improvement and safety in airway management via regular education and feedback.

Results

We included a total of 146 intubations. The first-pass success rate started at 57.1% and increased to 80.0% during the study period (P < 0.01). Fifty-six percent were male, and the mean age (±SD) was 55.56 (±17.64). Video laryngoscopy was used in 101 (69.2%) patients, while direct laryngoscopy was used in only 44 (30.8%) patients. A logistic regression analysis was conducted to determine the independent factors associated with first-pass success. These factors included the use of video laryngoscopy (odds ratio (OR) 2.47 95% confidence interval (95% CI) [1.62–3.76]) (adjusted OR 3.87 [1.13–13.23]) and good Cormack–Lehane views (grades 1–2) (OR 2.71 95% CI [1.74–4.20]) (adjusted OR 7.88 [2.43–25.53]).

Conclusion

Our study shows that implementing and maintaining an airway quality improvement program improves first-pass intubation success. Moreover, the use of video laryngoscopy and obtaining good Cormack–Lehane views (grades 1–2) are independently associated with improved first-pass success.
Deep engagement and public opinion toward the United States: U.S. military presence and threat perceptions
Authors: Shinomoto Sou
Published: September 2021

Under what conditions are a country’s residents likely to express favorable or unfavorable attitudes toward the United States? I discuss this question using survey data from 38 countries, focusing on the possible impacts that the active approach by the United States toward security threats has on the psychology of countries’ residents. The results show that the larger the U.S. military presence in a country, the more likely that its residents are to express negative attitudes toward the United States. Meanwhile, citizens who feel threatened by specific types of global actors that the U.S. government actively confronts as security threats are less likely to express negative attitudes toward the United States, and particularly less likely to do so the larger the U.S. military presence in their country. These findings contribute significantly to understanding the shifts in the socio-political dynamics of regions such as the Asia-Pacific, where the United States has long implemented an active approach.
Voices in the Background: Environmental Degradation and Climate Change as Driving Forces of Violence Against Indigenous Women
Authors: Csevár Szilvia
Published: September 2021

Adopted on the fifteenth anniversary of resolution 1325, Security Council resolution 2242 has recognized for the first time the substantial link between climate change and the “Women, Peace and Security” (WPS) framework. Despite this landmark resolution, the intersections of environmental factors, conflict and violence against women remain largely absent from the Security Council's WPS agenda. Competition over natural resources is generally understood as a driver of conflict. The risk of insecurity and conflict are further increased by environmental degradation and climate change. It is therefore clear that the environment and natural resources must be integrated into the WPS agenda. This should necessarily include a discussion of indigenous rights to land and the gender-related dimensions of environmental factors. Indigenous women are disproportionately affected by environmental degradation, caused by resource extraction and increasingly compounded by climatic changes. This in turn exacerbates other vulnerabilities, including sexual and gender-based violence and other forms of marginalization. This article argues, by reference to the situation in West Papua, that unfettered resource extraction not only amplifies vulnerabilities and exacerbates preexisting inequalities stemming from colonial times, it also gives rise to gendered consequences flowing from the damage wreaked on the natural environment and thus poses a danger to international peace and security. As such, the Security Council's failure to recognize the continuous struggle of women in indigenous and rural communities against extractive economies and climate change impact as a security risk forms a serious lacuna within its WPS agenda.
Taking the Research Experience Seriously: A Framework for Reflexive Applied Research in Development
Authors: Krystalli Roxani , Hoffecker Elizabeth , Leith Kendra , Wilson Kim
Published: September 2021

Interdisciplinary scholarly literature considers how research processes may adversely affect their participants. Building on this work, this article addresses the processes and practices of applied research in contexts in which imbalances of power exist between researchers and those being researched. We argue that research activities in international development and humanitarian work that are typically operational, such as needs assessments, baseline studies, and monitoring and evaluation, represent interventions in the lives of participants, with the potential to create value or harm, delight or distress. The ethical and methodological dilemmas of this intervention have received less attention than purely academic discussions of human subject research. How can applied researchers meaningfully reckon with the effects of the research process on both those conducting it and those participating in it throughout the research cycle? In response, we introduce an approach co-developed over seven years through engagement with applied researchers across sectors. We discuss four interrelated principles—relevance, respect, right-sizing, and rigor—intended to invite a commitment to ongoing process improvement in the conduct of applied research. We also propose a framework to guide the implementation of these principles and illustrate the tensions that may arise in the process of its application. These contributions extend conversations about research ethics and methods to the operational research realm, as well as provide concrete tools for reflecting on the processes of operational research as sites of power that ought to be considered as seriously as the findings of data collection activities.
Design Strategies for Collaborative Learning in Tangible Tabletops: Positive Interdependence and Reflective Pauses
Authors: Wise Alyssa Friend , Antle Alissa N , Warren Jillian
L
Published: September 2021

This mixed methods study examined the impact of two design strategies on interactional processes in a collaborative tangible-tabletop land-use planning simulation. Twenty pairs of fifth grade children used the simulation to create a world they would want to live in. To investigate the impact of positive interdependence half the pairs were assigned one of two roles, each with an associated set of tangible ‘land-use’ stamp tools. All pairs were given access to pause and reflect tools. Quantitative results showed that children in the positive interdependence condition gave more one-way explanations to their partners than control pairs. They also had fewer but longer instances of bilaterally resolved conflict. Qualitative findings indicated the importance of pause and reflect tools for provoking explanations and resolving conflict. This study has revealed important considerations for the instantiation of positive interdependence and reflective pauses in collaborative tabletop learning systems, showing both quantitative and qualitative differences in the interactional processes that result from these design strategies.

CCS CONCEPTS.

Human-centered computing → Empirical studies in collaborative and social computing.
Alternative Causes of Infectious Diarrhea in Patients with Negative Tests for Clostridoides Difficile
Authors: Kwon Jennie H , O’Neil Caroline A , Hink Tiffany , Reske Kimberly A , Bosserman Rachel E , Dubberke Erik R , Burnham Carey-Ann D
Published: September 2021

Background

Hospitalized patients with diarrhea who have a negative Clostridoides difficile (C. difficile) test are not routinely evaluated for alternative causes of infectious diarrhea. This study assessed for potential infectious causes of diarrhea in hospitalized patients with an order for repeat C. difficile toxin enzyme immunoassay (tEIA) testing after an initial tEIA test was negative.

Methods

For patients age ≥18 years who had a second C. difficile tEIA test ordered within 96 h after a negative tEIA test, remnant fecal specimens from the first (negative) tEIA test were evaluated using the BioFire FilmArray Gastrointestinal Panel PCR, C. difficile toxigenic culture, and culture on a blood agar plate (BAP) to identify other potential causes of infectious diarrhea. Growth of organisms on the BAP was also used to assess potential disruptions in the gastrointestinal microbiota.

Results

Among 84 remnant specimens, toxigenic C. difficile was identified in 9 (11%) by culture or PCR, while potential alternative causes of infectious diarrhea, including norovirus, rotavirus, enteropathogenic Escherichia coli, and Salmonella, were identified in 11 specimens (13%) by PCR. For the majority of patients, no infectious cause of diarrhea was identified, but 84% exhibited disrupted gastrointestinal microbiota, which may contribute to diarrhea.

Conclusions

When a hospitalized patient has a negative C. difficile tEIA test but continues to have diarrhea, alternative infectious and noninfectious causes of diarrhea should be considered. If the patient has clinical signs and symptoms suggestive of infection or risk factors for gastrointestinal infection, laboratory testing for other etiologic agents may be appropriate.
Living on the EDGE: Canadian Experience With EUS-directed Transgastric ERCP (EDGE) in Patients With Roux-en-Y Gastric Bypass Anatomy
Authors: Barclay Robert L , Jain Avni , Buteau Ferland Anne-Sophie , Chen Yen-I , Donnellan Fergal
Published: September 2021

Introduction

Roux-en-Y gastric bypass (RYGB) surgery imposes anatomic barriers to endoscopic retrograde cholangiopancreatography (ERCP). Potential options for biliary access in these patients include laparoscopic-assisted ERCP or balloon enteroscopy. However, these approaches require specialized equipment and/or operating room personnel and are associated with high rates of failure and adverse events compared to conventional ERCP. A recently described technique, EDGE, is an endoscopic approach which involves accessing the excluded stomach to facilitate ERCP.

Objective

The objective of this study is to describe the results of EDGE procedures performed in Canada.

Methods

Data were collected from patient cases who had undergone an EDGE procedure across centers in Canada. All patients had a history of RYGB bariatric surgery. In each procedure, a 20-mm diameter lumen-apposing metal stent (LAMS) was deployed under EUS guidance to allow access from the gastric remnant/proximal jejunum to the excluded stomach. Subsequently, during a separate procedure, a duodenoscope was passed through the LAMS to perform ERCP. Following ERCP, the LAMS was replaced with a pigtail stent or APC was used to facilitate closure of the gastro-jejunal/gastro-gastric fistula.

Results

The indication for EDGE in the seven included cases was for the treatment of choledocholithiasis (six) or gallstone pancreatitis (one). The technical success rate of the EDGE procedure in these cases was 100%. Clinical success, defined by normalization of bilirubin and symptomatic relief, was observed in all cases. There were no adverse events reported.

Conclusion

The results of this series support EDGE as a safe and minimally invasive approach to biliary access and therapy in patients with previous RYGB surgery.
Understanding Perceived Stress in Adolescent Inflammatory Bowel Disease
Authors: Sunavsky Adam , Moreau Julia , Tripp Dean A
Published: September 2021

Background

Inflammatory bowel disease (IBD) is a chronic and debilitating illness associated with psychosocial comorbidities. Adolescents are vulnerable to the additive stress of managing IBD and navigating developmental milestones. Psychosocial factors, such as catastrophizing, illness stigma, illness uncertainty, and illness-related shame, often contribute to perceived stress in chronic illnesses. However, the combination of these variables on perceived stress in adolescents with IBD has not been examined.

Methods

Participants completed a cross-sectional online self-report survey. Model 4 of PROCESS Macro in SPSS was used to test the parallel mediation model of the relationship between disease severity and perceived stress using catastrophizing, stigma, uncertainty, and shame as mediators using 10,000 bootstrap samples. T-tests were run to assess systematic differences in the dependent variable between subjects.

Results

One hundred and thirty-one adolescents (Mage = 18.95 years; 100 females) completed the survey. Females had higher stress scores than males (P =0.002), and there were no difference in stress between younger and older participants (P = 0.085), location (P = 0.484), or IBD type (P = 0.515). The total effect of disease stress on perceived stress operating through the mediators was significant, b = 0.168, SE = 0.028, 95% CI [0.112, 0.224]. Helplessness catastrophizing, illness uncertainty, and illness-related shame, but not illness stigma, were equally strong, positive mediators.

Conclusions

The present results suggest that helplessness catastrophizing, illness uncertainty, and illness-related shame are central elements to target in stress interventions for adolescents with IBD.
Effects of artificial substrates on the growth and immunology of postlarvae of Marsupenaeus japonicus (Spence Bate, 1888) (Decapoda: Dendrobranchiata: Penaeidae) reared in biofloc
Authors: Kim Su-Kyoung , Jang In-Kwon , Kim Seok Ryel , Jeon Jea Chun , Kim Su Kyoung
Published: September 2021

We investigated the effects of biofloc and artificial substrates (net and brush) on the growth and immunology of the postlarvae of Marsupenaeus japonicus (Spence Bate, 1888) reared for 30 days. The mRNA expressions of innate immune-related genes (prophenoloxidase, masquerade-like serine proteinase, and lysozyme) in the postlarvae were analyzed using quantitative reverse transcription PCR (qRT-PCR). The highest specific growth rate of larvae (3.66 ± 0.02% d–1, 3.75 ± 0.02% d–1) were shown in the net and control groups. The highest survival rate (90 ± 7.1%) was observed in the brush group (P < 0.05). The net yield was significantly higher in the artificial substrate groups (brush 36.60 ± 6.19 g m–2, net 36.46 ± 2.36 g m–2) than in the control (33.79 ± 0.16 g m–2) (P < 0.05). Total suspended, volatile suspended, and suspended solids were significantly lower in the brush group than in the other groups. The immune-related genes showed significantly higher expressions in the artificial substrate groups than in the control. These results support the benefits of artificial substrate in M. japonicus nursery culture to mitigate space competition and suppress cannibalism, with a positive effect on survival. The additional surface area provided by the biofloc, which the larvae can graze on, enhanced the expression of immune-related genes in individuals.
Development of Economic Thresholds Toward Bollworm (Lepidoptera: Noctuidae), Management in Bt Cotton, and Assessment of the Benefits From Treating Bt Cotton With Insecticide
Authors: Calvin Wilfrid , Yang Fei , Brown Sebe A , Catchot Angus L , Crow Whitney D , Cook Donald R , Gore Jeffrey , Kurtz Ryan , Lorenz Gustav M , Seiter Nicholas J , Stewart Scott D , Towles Tyler , Kerns David L
Published: September 2021

Widespread field-evolved resistance of bollworm [Helicoverpa zea (Boddie)] to Cry1 and Cry2 Bt proteins has threatened the utility of Bt cotton for managing bollworm. Consequently, foliar insecticide applications have been widely adopted to provide necessary additional control. Field experiments were conducted across the Mid-South and in Texas to devise economic thresholds for foliar insecticide applications targeting bollworm in cotton. Bt cotton technologies including TwinLink (TL; Cry1Ab+Cry2Ae), TwinLink Plus (TLP; Cry1Ab+Cry2Ae+Vip3Aa), Bollgard II (BG2; Cry1Ac+Cry2Ab), Bollgard 3 (BG3; Cry1Ac+Cry2Ab+Vip3Aa), WideStrike (WS; Cry1Ac+Cry1F), WideStrike 3 (WS3; Cry1Ac+Cry1F+Vip3Aa), and a non-Bt (NBT) variety were evaluated. Gain threshold, economic injury level, and economic thresholds were determined. A 6% fruiting form injury threshold was selected and compared with preventive treatments utilizing chlorantraniliprole. Additionally, the differences in yield from spraying bollworms was compared among Bt cotton technologies. The 6% fruiting form injury threshold resulted in a 25 and 75% reduction in insecticide applications relative to preventive sprays for WS and BG2, respectively. All Bt technologies tested in the current study exhibited a positive increase in yield from insecticide application. The frequency of yield increase from spraying WS was comparable to that of NBT. Significant yield increases due to insecticide application occurred less frequently in triple-gene Bt cotton. However, their frequencies were close to the dual-gene Bt cotton, except for WS. The results of our study suggest that 6% fruiting form injury is a viable threshold, and incorporating a vetted economic threshold into an Integrated Pest Management program targeting bollworm should improve the sustainability of cotton production.
Ethyl Formate as a Methyl Bromide Alternative for Fumigation of Citrus: Efficacy, Fruit Quality, and Workplace Safety
Authors: Park Min-Goo , Lee Byung-Ho , Yang Jeong-Oh , Kim Bong-Soo , Roh Gwang Hyun , Kendra Paul E , Cha Dong H
Published: September 2021

Ethyl formate (EF) was evaluated as a potential alternative to methyl bromide (MB) for phytosanitary treatment of imported citrus fruit in the Republic of Korea. Planococcus citri (Risso) (Hemiptera: Pseudococcidae), a mealybug with known tolerance against EF and MB, was used as a representative pest to test efficacy of the two fumigants against eggs. In nine commercial-scale refrigerated container (67.5 m3) trials using imported orange, lemon and grapefruit, EF applied at the currently approved dose for citrus (70 g·m-3 at 5°C for 4 h, developed for Aspidiotus excisus Green (Hemiptera: Diaspididae), a species less EF tolerant than P. citri) resulted in 76.9–98.3% mortality of P. citri eggs. The EF treatment did not affect the sugar content or the color of peel and pulp of the treated fruit. When oranges were treated according to the current MB (64 g·m-3 at >5°C for 2 h) or EF treatment guidelines, the concentration of fumigant around the fruit fluctuated between 9.4 and 185.1 ppm for EF and 9.5–203.0 ppm for MB during the 72-h post-fumigation processes (venting [0–2 h], transportation to storage [2–24 h], and storage periods [24–72 h]) with both EF and MB maintained between 10 and 100 ppm during the storage period. Considering the efficacy of EF, its apparent lack of phytotoxicity, and its more manageable threshold limit value for humans (100 ppm EF compared to 1 ppm MB for an 8-h time weighted average exposure), our results suggest that EF may be a promising alternative to MB for the phytosanitary treatment of imported citrus in Korea.
The Lari-Leuco Container: A Novel Collection Arena for Separating Insects Ascending or Descending From a Plant Foliage Sample
Authors: Mayfield Albert E , Dietschler Nicholas J , Whitmore Mark C
Published: September 2021

Efficient separation of insects from plant material for quantification and collection is an important component of entomological research. This paper reports on a novel, easily replicable container designed to efficiently collect two different biological control agents dispersing from hemlock (Tsuga spp.) foliage infested with the invasive hemlock woolly adelgid (HWA), Adelges tsugae Annand (Hemiptera: Adelgidae). The container utilizes a simplified Berlese-style funnel design to collect Laricobius spp. (Coleoptera: Derodontidae) larvae dropping from the foliage into a removable bottom jar, a central jar to house the foliage sample, and a removable top jar to collect adult silver flies (Leucopis spp., Diptera: Chamaemyiidae) emerging from puparia on the twigs. The efficacy of two designs (with and without a funnel leading to the top collection jar) was evaluated using western hemlock [Tsuga heterophylla (Raf.) Sarg.] foliage naturally colonized with HWA and the two predator genera. All Laricobius larvae were effectively collected in the bottom jar, and the addition of an inverted funnel leading to the top collection jar increased the proportion of Leucopis flies reaching the target jar from 60% to 94%. This ‘Lari-Leuco’ container is presented as a research and motoring tool to benefit the integrated pest management program for HWA in eastern North America and for potential use in simultaneously separating ascending and descending life stages in other insect-plant or predator-prey systems.
Rudolf Weisker’s anatomical and developmental wax models: New evidence and contexts concerning his career and sources
Authors: Charwat Elaine
Published: September 2021

The institute for wax modelling founded in Leipzig by Rudolf Weisker (1845–1887) can be considered an important competitor to the earlier established and more successful producers of nineteenth-century developmental and anatomical wax models, Adolf and Friedrich Ziegler. This article establishes previously unknown aspects relating to Weisker, his background and sources. It examines why models from these producers were collected by universities and university-affiliated museums, and considers important differences affecting the production and ‘status’ of their models. It argues that Weisker’s career and models exemplify the impact of increasing specialization, as well as scientific controversies, during the second half of the nineteenth century, concerning scientific practice, publishing (both two- and three-dimensional) and collecting. It suggests that one reason Weisker was unable to thrive in competition with the Zieglers was that the emphasis of developmental models, especially, moved from illustrative to analytical during this period; Weisker, for reasons suggested here, was unable to respond to these changes.
Within-Canopy Distribution of Stenoma catenifer (Lepidoptera: Elachistidae) Infestation in Avocado Orchards
Authors: Vacari Alessandra M , Damato Felipe , Dami Bruno Gomes , de Lima Mateus Levi Feliz , Lima Lucas S M Ubiali , Figueiredo Gustavo Pincerato , Cabral Eder de Oliveira , Rodriguez-Saona Cesar
Published: September 2021

Native to the neotropics, the avocado seed moth Stenoma catenifer Walsingham (Lepidoptera: Elachistidae) is a specialist pest of the family Lauraceae and considered one of the most important pests of avocados worldwide. However, little is known regarding its spatial distribution within a single tree. Therefore, we designed a study to evaluate the effects of canopy height and aspect (i.e., side of the tree) on fruit infestation by S. catenifer larvae in avocados. The study was conducted in three commercial organic avocado orchards located in São Paulo, Brazil. At each orchard, 40 fruit from 30 random trees were sampled weekly from October 2017 through February 2018, evaluating the number of fruits infested by S. catenifer larvae at three tree heights (bottom, middle, and top). In addition, fruits on the ground were also sampled. We also evaluated the effect of the side of the tree where the fruits were collected, i.e., whether they were on the side facing the east (sunrise) or the west (sunset). Within the avocado canopy, the level of fruit infestation by S. catenifer larvae was significantly higher at the top of the trees than in the middle and bottom. Fruit on the ground had lower levels of infestation than those on the tree canopy. The level of fruit infestation was also higher on the side of avocado trees facing the east (sunrise). Understanding the within-tree distribution of S. catenifer will help to better target monitoring and control activities against this pest in avocados.
Hygiene-Eliciting Brood Semiochemicals as a Tool for Assaying Honey Bee (Hymenoptera: Apidae) Colony Resistance to Varroa (Mesostigmata: Varroidae)
Authors: Wagoner K , Millar J G , Keller J , Bello J , Waiker P , Schal C , Spivak M , Rueppell O
Published: September 2021

Despite numerous interventions, the ectoparasitic mite Varroa (Varroa destructor Anderson and Trueman [Mesostigmata: Varroidae]) and the pathogens it vectors remain a primary threat to honey bee (Apis mellifera Linnaeus [Hymenoptera: Apidae]) health. Hygienic behavior, the ability to detect, uncap, and remove unhealthy brood from the colony, has been bred for selectively for over two decades and continues to be a promising avenue for improved Varroa management. Although hygienic behavior is expressed more in Varroa-resistant colonies, hygiene does not always confer resistance to Varroa. Additionally, existing Varroa resistance selection methods trade efficacy for efficiency, because those achieving the highest levels of Varroa resistance can be time-consuming, and thus expensive and impractical for apicultural use. Here, we tested the hypothesis that hygienic response to a mixture of semiochemicals associated with Varroa-infested honey bee brood can serve as an improved tool for predicting colony-level Varroa resistance. In support of our hypothesis, we demonstrated that a mixture of the compounds (Z)-10-tritriacontene, (Z)-8-hentriacontene, (Z)-8-heptadecene, and (Z)-6-pentadecene triggers hygienic behavior in a two-hour assay, and that high-performing colonies (hygienic response to ≥60% of treated cells) have significantly lower Varroa infestations, remove significantly more introduced Varroa, and are significantly more likely to survive the winter compared to low-performing colonies (hygienic response to <60% of treated cells). We discuss the relative efficacy and efficiency of this assay for facilitating apiary management decisions and selection of Varroa-resistant honey bees, as well as the relevance of these findings to honey bee health, pollination services, and social insect communication.
Influence of the Color, Shape, and Size of the Clay Model on Arthropod Interactions in Turfgrass
Authors: Khan Fawad Z A , Joseph Shimat V
Published: September 2021

Many predatory arthropods occur naturally in turfgrass, and they provide adequate control of lepidopteran pests, such as fall armyworm, Spodoptera frugiperda (JE Smith) (Lepidoptera: Noctuidae), and black cutworm, Agrotis ipsilon (Hufnagel) (Lepidoptera: Noctuidae). Recording predation is challenging under field conditions because predators rarely leave any evidence. Clay models were successfully employed for studying predation, and this technique is underutilized in turfgrass. Little is known about whether the characteristics of clay models, such as color, shape, and size, influence arthropod interactions in turfgrass. To improve the utility of clay models in turfgrass, the influence of the color, shape, and size of clay models on arthropod interactions was studied by exposing clay models during daytime and nighttime in a turfgrass field. The results showed that arthropods interacted with clay models, and various types of impressions were recorded, including paired marks, scratches, cuts, and pricks. Although the color of the clay model had no significant effects on arthropod interactions during the night, significantly greater numbers of impressions were noticed on the blue and green models than on the yellow models during the daytime. The caterpillar-shaped models captured significantly greater densities of impressions than the beetle-shaped models. Additionally, the number of impressions significantly increased with an increase in the size of the model regardless of shape.
Fully Bayesian Estimation Under Dependent and Informative Cluster Sampling
Authors: León-Novelo Luis G , Savitsky Terrance D
Published: September 2021

Survey data are often collected under multistage sampling designs where units are binned to clusters that are sampled in a first stage. The unit-indexed population variables of interest are typically dependent within cluster. We propose a Fully Bayesian method that constructs an exact likelihood for the observed sample to incorporate unit-level marginal sampling weights for performing unbiased inference for population parameters while simultaneously accounting for the dependence induced by sampling clusters of units to produce correct uncertainty quantification. Our approach parameterizes cluster-indexed random effects in both a marginal model for the response and a conditional model for published, unit-level sampling weights. We compare our method to plug-in Bayesian and frequentist alternatives in a simulation study and demonstrate that our method most closely achieves correct uncertainty quantification for model parameters, including the generating variances for cluster-indexed random effects. We demonstrate our method in an application with NHANES data.

KEY WORDS: Inclusion probabilities; Mixed-effects linear model; NHANES; Primary stage sampling unit; Sampling weights; Survey sampling.