bluuebunny/crossref_metadata_2025 huggingface dataset:
A brief history of visualizing membrane systems in molecular dynamics simulations
Authors: Corey R. A. , Baaden M. , Chavent M.
Published: May 2023

Understanding lipid dynamics and function, from the level of single, isolated molecules to large assemblies, is more than ever an intensive area of research. The interactions of lipids with other molecules, particularly membrane proteins, are now extensively studied. With advances in the development of force fields for molecular dynamics simulations (MD) and increases in computational resources, the creation of realistic and complex membrane systems is now common. In this perspective, we will review four decades of the history of molecular dynamics simulations applied to membranes and lipids through the prism of molecular graphics.
Multifunctional magnetoliposomes as drug delivery vehicles for the potential treatment of Parkinson’s disease
Authors: Cifuentes Javier , Cifuentes-Almanza Santiago , Ruiz Puentes Paola , Quezada Valentina , González Barrios Andrés Fernando , Calderón-Peláez María-Angélica , Velandia-Romero Myriam Lucia , Rafat Marjan , Muñoz-Camargo Carolina , Albarracín Sonia L. , Cruz Juan C.
Published: May 2023

Parkinson’s disease (PD) is the second most common neurodegenerative disorder after Alzheimer’s disease. Therefore, development of novel technologies and strategies to treat PD is a global health priority. Current treatments include administration of Levodopa, monoamine oxidase inhibitors, catechol-O-methyltransferase inhibitors, and anticholinergic drugs. However, the effective release of these molecules, due to the limited bioavailability, is a major challenge for the treatment of PD. As a strategy to solve this challenge, in this study we developed a novel multifunctional magnetic and redox-stimuli responsive drug delivery system, based on the magnetite nanoparticles functionalized with the high-performance translocating protein OmpA and encapsulated into soy lecithin liposomes. The obtained multifunctional magnetoliposomes (MLPs) were tested in neuroblastoma, glioblastoma, primary human and rat astrocytes, blood brain barrier rat endothelial cells, primary mouse microvascular endothelial cells, and in a PD-induced cellular model. MLPs demonstrated excellent performance in biocompatibility assays, including hemocompatibility (hemolysis percentages below 1%), platelet aggregation, cytocompatibility (cell viability above 80% in all tested cell lines), mitochondrial membrane potential (non-observed alterations) and intracellular ROS production (negligible impact compared to controls). Additionally, the nanovehicles showed acceptable cell internalization (covered area close to 100% at 30 min and 4 h) and endosomal escape abilities (significant decrease in lysosomal colocalization after 4 h of exposure). Moreover, molecular dynamics simulations were employed to better understand the underlying translocating mechanism of the OmpA protein, showing key findings regarding specific interactions with phospholipids. Overall, the versatility and the notable in vitro performance of this novel nanovehicle make it a suitable and promising drug delivery technology for the potential treatment of PD.
Generation and characterization of an inducible renal proximal tubule-specific CreERT2 mouse
Authors: Liang Shiting , Wang Youliang , Kang Meixia , Deng Juan , Chen Liting , Hong Xizhen , Hou Fan Fan , Zhang Fujian
Published: May 2023

Protein reabsorption in renal proximal tubules is essential for maintaining nutrient homeostasis. Renal proximal tubule-specific gene knockout is a powerful method to assess the function of genes involved in renal proximal tubule protein reabsorption. However, the lack of inducible renal proximal tubule-specific Cre recombinase-expressing mouse strains hinders the study of gene function in renal proximal tubules. To facilitate the functional study of genes in renal proximal tubules, we developed an AMNCreERT2 knock-in mouse strain expressing a Cre recombinase–estrogen receptor fusion protein under the control of the promoter of the amnionless (AMN) gene, a protein reabsorption receptor in renal proximal tubules. AMNCreERT2 knock-in mice were generated using the CRISPR/Cas9 strategy, and the tissue specificity of Cre activity was investigated using the Cre/loxP reporter system. We showed that the expression pattern of CreERT2-mEGFP in AMNCreERT2 mice was consistent with that of the endogenous AMN gene. Furthermore, we showed that the Cre activity in AMNCreERT2 knock-in mice was only detected in renal proximal tubules with high tamoxifen induction efficiency. As a proof-of-principle study, we demonstrated that renal proximal tubule-specific knockout of Exoc4 using AMNCreERT2 led to albumin accumulation in renal proximal tubular epithelial cells. The AMNCreERT2 mouse is a powerful tool for conditional gene knockout in renal proximal tubules and should offer useful insight into the physiological function of genes expressed in renal proximal tubules.
Integration of transcriptomics, proteomics, and metabolomics data for the detection of the human pathogenic Prototheca wickerhamii from a One Health perspective
Authors: Guo Jian , Chen Juan , Li Teng , Gao Lei , Jiang Cizhong , Wu Wenjuan
Published: May 2023

Prototheca species are the only microalgae known to cause opportunistic infections in vertebrates and humans. Most cases of protothecosis in humans are caused by Prototheca wickerhamii, but knowledge of the pathogenicity and biology of Prototheca is limited. Globally, the diagnostic rate of Prototheca species infection is much lower than the actual rate of P. wickerhamii. The precise mechanisms underlying the pathogenesis of Prototheca infections remain unclear. In this study, we identified a strain of P. wickerhamii with atypical colony morphology. To reveal the morphological differences between P. wickerhamii S1 (mucous) and the molecular basis of its pathogenicity, the transcriptomics, proteomics, and metabolomics of two pathogenic P. wickerhamii strains and one environmental strain were analysed. Interestingly, mannan endo-1,4-β-mannosidase was significantly downregulated in P. wickerhamii S1, which contributes to a thinner cell wall in S1 compared to strains with typical colony morphology, and the toxicity of macrophages is reduced. Metabolite analysis revealed that the mucoid appearance of P. wickerhamii S1 may have been caused by an increase in linoleic acid, glycerol, and other metabolites. There is still a need to better understand the ecology, aetiology, and pathogenesis of P. wickerhamii, and in particular, its transmission between humans, animals, and the environment, from a One Health perspective.
Implementation of a heart failure educational intervention for patients with recent admissions for acute decompensated heart failure
Authors: Stahlman Sarah , Huizar-Garcia Stephanie , Lipscomb Justina , Frei Christopher , Oliver Ashley
Published: May 2023

Purpose

This study examined whether implementation of a heart failure (HF) education class targeted at patients and their caregivers decreased worsening HF, emergency department (ED) visits and hospital admissions, and improved patient quality of life and confidence in disease state management.

Methods

Patients with HF and a recent hospital admission for acute decompensated heart failure (ADHF) were offered an educational course covering HF pathophysiology, medications, diet, and lifestyle modifications. Patients completed surveys before and 30 days after completion of the educational course. Outcomes of participants at 30 and 90 days after class completion were compared against outcomes for the same patients at 30 and 90 days prior to course attendance. Data was collected using electronic medical records, in-person during the class, and during a phone follow-up.

Results

The primary outcome was a composite of hospital admission, ED visit, and/or outpatient visit for HF at 90 days. A total of twenty-six patients attended classes between September 2018 and February 2019 and were included in the analysis. Median age was 70 years, and most patients were white. All patients were American College of Cardiology/American Heart Association (ACC/AHA) Stage C and a majority had New York Heart Association (NYHA) Class II or III symptoms. Median left ventricular ejection fraction (LVEF) was 40%. The primary composite outcome occurred significantly more frequently in the 90 days prior to class attendance than in the 90 days following attendance (96% vs. 35%, p < 0.01). Likewise, the secondary composite outcome occurred significantly more frequently in the 30 days before class attendance than in the 30 days following (54% vs. 19%, p = 0.02). These results were driven by a decrease in admissions and ED visits for HF symptoms. Survey scores related to patient HF self-management practices and patient confidence in ability to self-manage HF increased numerically from baseline to 30 days after class attendance.

Conclusion

Implementation of an educational class for HF patients improved patient outcomes, confidence, and ability to self-manage HF. Hospital admissions and ED visits also decreased. Adoption of such a course might help to decrease overall health care costs and improve patient quality of life.
Advances in AI for web integrity, equity, and well-being
Authors: Kumar Srijan
Published: May 2023

My research develops data mining, AI, and applied machine learning methods to combat malicious actors (sockpuppets, ban evaders, etc.) and dangerous content (misinformation, hate, etc.) on web platforms. My vision is to create a trustworthy online ecosystem for everyone and the next generation of socially-aware methods that promote health, equity, and integrity of users, communities, and platforms online. Broadly, in my research, I create novel graph, content (NLP, multimodality), and adversarial machine learning methods leveraging terabytes of data to detect, predict, and mitigate online threats. My interdisciplinary research innovates socio-technical solutions that I achieve by amalgamating computer science with social science theories. My research seeks to start a paradigm shift from the current slow and reactive approach against online harms to agile, proactive, and whole-of-society solutions. In this article, I shall describe my research efforts along four thrusts to achieve my goals: (1) Detection of harmful content and malicious actors across platforms, languages, and modalities; (2) Robust detection models against adversarial actors by predicting future malicious activities; (3) Attribution of the impact of harmful content in online and real world; and (4) Mitigation techniques to counter misinformation by professionals and non-expert crowds. Together, these thrusts give a set of holistic solutions to combat cyberharms. I am also passionate about putting my research into practice—my lab's models have been deployed on Flipkart, influenced Twitter's Birdwatch, and now being deployed on Wikipedia.
Politeness strategies used by children in requests in relation to age and gender: a case study of Jordanian elementary school students
Authors: Al-Abbas Linda S.
Published: May 2023

Introduction

Requesting is considered one of the most threatening speech acts that people tend to use politeness strategies to tone down the request and minimize the face loss of the recipient. These strategies develop over years and while children appear to produce polite speech forms at an early age, less is known about the strategies they use when they make requests in the Jordanian context. This study aims to investigate politeness strategies used by Jordanian children in requests at different age levels in relation to their gender.

Methods

The study included 80 subjects divided into two age groups, namely, six years and ten years, with an equal number of boys and girls. They met a lady puppet who had a box of gifts, and they were told to ask her politely to get the gift they wanted. Their requests were recorded and analyzed using Blum-Kulka’s politeness model to find the most common strategies the children used and whether these strategies differed with age and gender.

Results and Discussion

The study concluded that at the age of six, the concept of politeness is present in children’s linguistic competence, but the assignment of polite expressions to the proper speech act is still ill-defined. There were no significant differences in using politeness strategies according to gender. As children grow older, around the age of ten, they become more able to express politeness in requests. Girls preferred the indirect strategies while boys opted for the direct level in making requests. This study may positively help parents and schoolteachers enhance the pragmatic knowledge and linguistic politeness of children.
Are some brightly coloured European wild birds toxic?
Authors: Loxdale Hugh D.
Published: May 2023

Some colourful European wild birds display contrasting bright colours. These are often striking black and white or primary and secondary colours, and with the same basic plumage livery shared by both sexes. These contrasting colours are, one assumes, very obvious to predators when these birds forage diurnally, or continue other aspects of their life history, including courting, nest building and rearing their brood. Here, I posit that such birds may be displaying aposematic warning colouration, possibly enhanced by chemical noxious substances in their flesh and/or feathers, as is already known in certain bird species, including colourful as well as cryptic species. The warning colouration may be Müllerian or Batesian in nature, or maybe is a ruse to suggest to predators that they are in some way noxious, and thus to be avoided. Even if not actually noxious as such, this may give the intended prey time to escape. Certainly, birds like the very obviously blue-black and white patterned Eurasian magpie, Pica pica, are largely avoided by the Eurasian sparrowhawk, Accipiter nisus, although this of course could be a size-related avoidance, as other larger raptorial birds do predate it. These various possibilities are discussed in the present article.
Climate change-related warming-induced shifts in leaf chemical traits favor nutrition of the specialist herbivore Battus polydamas archidamas
Authors: González-Teuber Marcia , Palma-Onetto Valeria , Aguirre Carolina , Ibáñez Alfredo J. , Mithöfer Axel
Published: May 2023

One of the major impacts of climate change is increasing global temperatures. Because warming is expected to affect plant morphological and chemical traits, it may therefore also influence plant interactions with other trophic levels, including herbivores. Here, we simulated a climate warming scenario of +2.7°C in the field using open-top chambers and assessed the effects of warming on plant performance (growth, leaf area, and chlorophyll), leaf nutrients (nitrogen and carbon), and primary (amino acids and carbohydrates) and secondary (toxic aristolochic acids) metabolites in the plantAristolochia chilensis. We performed untargeted metabolomics analyses for estimating general changes in foliar metabolites between ambient control and warming-treated plants. Bioassays were additionally conducted to evaluate how changes in host plant chemistry affected growth and nutritional parameters in first-instar larvae of the specialist lepidopteran herbivoreBattus polydamas archidamas. We found that warming did not significantly affect plant performance, but did result in significant changes in leaf nutrients, and primary and secondary metabolites, although in opposite directions. While primary metabolites (specifically, nitrogen-containing compounds) decreased in response to treatment, aristolochic acids increased. Untargeted metabolomics analyses showed that, of a total of 824 features, 50 were significantly different between ambient control and warming-treated plants; some of these were identified by MS/MS spectra as amino acids. Larvae feeding on warming-treated plants, showed significantly enhanced growth, food conversion efficiency, and lipid concentration. Our study contributes to current understanding of climate change impacts on trophic interactions, showing that projected temperature increases lead to changes in the resistance phenotype of the host plant, favoring nutrition and growth of a unique specialist herbivore.
Structural changes and carbon reduction due to habitat loss in Atlantic Forest
Authors: Rigueira Dary Moreira Gonçalves , Mariano-Neto Eduardo
Published: May 2023

Habitat loss is a significant threat to biodiversity in tropical forests, leading to changes in composition, structure, and function. In this study, we aimed to evaluate the influence of the forest amount at the landscape scale on the structure and the stored carbon of tree communities. Eleven landscape samples of 36 km2 (6 × 6 km), with different amounts of forest cover at the landscape scale (between 5 and 60%), were randomly selected within a wide latitudinal range of Atlantic Forests in Brazil. We also used a sample design to control and avoid some biases in landscape-scale studies during the landscape selection, such as the rescue effect from the surrounding landscapes, differences in matrix permeability in each landscape, and the control for the same vegetation type or successional stage. In each selected landscape, we surveyed all woody individuals with a diameter at breast height (DBH) ≥ 2.5 cm in eight plots of 250 m2, randomly placed in the landscape’s forested areas. The structural variables evaluated were: total abundance, the abundance of prominent families, the abundance of large trees (DBH ≥ 30 cm), mean DBH, and average height, besides carbon storage. From the set of 8,179 individuals, we observed a positive correlation between forest amount and the total abundance, the abundance of large trees, and carbon stock. The abundance of the prominent hardwood tree families were positively correlated with forest amount. When comparing the two landscapes with the lowest proportion of habitats (5–15%) and the highest proportion (55−60%), almost one thousand trees and more than 150 T of carbon per hectare are lost. This reduction in the overall abundance and carbon indicates no compensatory effects on the tree community due to a turnover in composition or substitution of large trees for smaller ones. The Atlantic Forest is undergoing a process of homogenization and functional collapse, derived directly or indirectly from habitat loss, leading to a possible regime shift.
An assessment of the LICOM Forecast System under the IVTT class4 framework
Authors: Zheng Weipeng , Lin Pengfei , Liu Hailong , Luan Yihua , Ma Jinfeng , Mo Huier , Liu Juan
Published: May 2023

This paper evaluates LFS (LICOM Forecast System) forecasts and compares them with other marine forecast systems under the IVTT (Intercomparison and Validation Task Team) Class 4 framework. LFS delivers real-time daily forecasts driven by the GFS (Global Forecast System) atmospheric analyses and surface forecasts. The nudging method in LFS provides the initial state for forecasting, with only the temperature and salinity restored towards the Mercator PSY4 daily analyses. Assessments show that LFS demonstrates a reasonably good capability in short-term marine environment forecast. For the leading 1-6 days forecasts, the root mean square error (RMSE) ranges between 0.53-0.63°C, 0.57-0.66°C and 0.12-0.13 psu for the sea surface temperature, temperature, and salinity profiles, respectively. The overall performance is comparable to other major marine forecast systems, with a slight advantage in forecasting the temperature and salinity profiles. Different nudging time scales are applied to the upper ocean and deep ocean to preserve the effects of mesoscale processes and correct the large-scale biases in temperature and salinity. However, the absence of other observational constraints, such as the sea level height, significantly affects the regional forecast features. Further analyses are required to improve the performance, and the integration of an assimilation system into LFS is urgently needed.
Evidence of the content validity, acceptability, and feasibility of a new Patient-Reported Impact of Dermatological Diseases measure
Authors: Pattinson Rachael , Trialonis-Suthakharan Nirohshah , Hewitt Rachael M. , Valencia López Maria José , Tahmasebi Gandomkari Nasim , Austin Jennifer , FitzGerald Allison , Courtier Nick , Augustin Matthias , Bundy Chris
Published: May 2023

Background

The Global Research on the Impact of Dermatological Diseases (GRIDD) team is developing the new Patient-Reported Impact of Dermatological Diseases (PRIDD) measure of the impact of dermatological conditions on the patient’s life, in partnership with patients. To develop PRIDD, we conducted a systematic review, followed by a qualitative interview study with 68 patients worldwide and subsequently a global Delphi survey of 1,154 patients to ensure PRIDD items were meaningful and important to patients.

Objective

To pilot test PRIDD with patients with dermatological conditions, focusing on its content validity (comprehensiveness, comprehensibility, and relevance), acceptability, and feasibility.

Methods

We conducted a theory-led qualitative study using the Three-Step Test-Interview method of cognitive interviewing. Three rounds of semi-structured interviews were conducted online. Adults (≥ 18 years) living with a dermatological condition and who spoke English sufficiently to take part in the interview were recruited through the International Alliance of Dermatology Patient Organizations’ (GlobalSkin) global membership network. The topic guide met the gold-standard COSMIN (Consensus-based Standards for the Selection of Health Measurement Instruments) standards for cognitive interviewing. Analysis followed the thematic analytical model of cognitive interviewing.

Results

Twelve people (58% male) representing six dermatological conditions from four countries participated. Overall, patients found PRIDD to be comprehensible, comprehensive, relevant, acceptable, and feasible. Participants were able to discern the conceptual framework domains from the items. Feedback resulted in: the recall period being extended from 1 week to 1 month; removal of the ‘not relevant’ response option; and changes to the instructions and item ordering and wording to improve clarity and increase respondents’ confidence in their ability to respond. These evidence-based adjustments resulted in a 26-item version of PRIDD.

Conclusion

This study met the gold-standard COSMIN criteria for the pilot testing of health measurement instruments. The data triangulated our previous findings, in particular the conceptual framework of impact. Our findings illuminate how patients understand and respond to PRIDD and other patient-reported measurement instruments. The results of comprehensibility, comprehensiveness, relevance, acceptability, and feasibility of PRIDD provide evidence of content validity from the target population. The next step in the development and validation of PRIDD is psychometric testing.
Early treatment and toxicity outcomes for small posterior uveal melanomas treated using custom loaded eye plaques
Authors: Medek Sara , Correa Zelia M. , Huth Brad , Takiar Vinita
Published: May 2023

Introduction

Iodine-125 loaded Collaborative Ocular Melanoma Study plaques can achieve excellent tumor control for patients diagnosed with uveal melanomas. Our ocular cancer team hypothesized that use of novel, partially loaded COMS plaques could ease and improve accurate plaque placement during treatment of small, posterior tumors while providing equivalent tumor control.

Materials/methods

Records of 25 patients treated with custom plaques were compared to 20 patients treated with fully loaded plaques, who had received treatment prior to our institution’s adopting the use of these partial plaques. Tumors were matched with regards to location and dimensions as measured by the ophthalmologist. Retrospective analysis of dosing parameters, tumor control and toxicity outcomes were performed.

Results

There were no cancer related deaths, local recurrences or metastases in either cohort at an average follow up of 24 months for patients treated with custom plaques and 60.7 months for patients treated with fully loaded plaques. No statistically significant difference was found in regards to post-operative development of cataracts (χ2 = 0.76) or radiation retinopathy (χ2 = 0.22). Patients treated with custom loaded plaques noted significantly less clinical visual loss (χ2 = 0.006) and were more likely to have vision preserved at ≥20/200 (χ2 = 0.006).

Conclusion

Treatment of small, posterior uveal melanomas with partially loaded COMS plaques results in equivalent survival and recurrence outcomes as treatment with fully loaded plaques, while exposing the patient to less radiation. Additionally, treatment with partially loaded plaques reduces the incidence of clinically significant visual loss. These promising early results support the use of partially loaded plaques in well-selected patients.
Modeling of pulmonary deposition of agents of open and fixed dose triple combination therapies through two different low-resistance inhalers in COPD: a pilot study
Authors: Erdelyi Tamas , Lazar Zsofia , Farkas Árpád , Furi Peter , Nagy Attila , Müller Veronika
Published: May 2023

Introduction

Inhalation therapy is a cornerstone of treating patients with chronic obstructive pulmonary disease (COPD). Inhaler devices might influence the effectiveness of inhalation therapy. We aimed to model and compare the deposition of acting agents of an open and a fixed dose combination (FDC) triple therapy and examine their repeatability.

Methods

We recruited control subjects (Controls, n = 17) and patients with stable COPD (S-COPD, n = 13) and those during an acute exacerbation (AE-COPD, n = 12). Standard spirometry was followed by through-device inhalation maneuvers using a pressurized metered dose inhaler (pMDI) and a soft mist inhaler (SMI) to calculate deposition of fixed dose and open triple combination therapies by numerical modeling. Through-device inspiratory vital capacity (IVCd) and peak inspiratory flow (PIFd), as well as inhalation time (tin) and breath hold time (tbh) were used to calculate pulmonary (PD) and extrathoracic deposition (ETD) values. Deposition was calculated from two different inhalation maneuvers.

Results

There was no difference in forced expiratory volume in 1 s (FEV1) between patients (S-COPD: 42 ± 5% vs. AE-COPD: 35 ± 5% predicted). Spiriva® Respimat® showed significantly higher PD and lower ETD values in all COPD patients and Controls compared with the two pMDIs. For Foster® pMDI and Trimbow® pMDI similar PD were observed in Controls, while ETD between Controls and AE-COPD patients did significantly differ. There was no difference between COPD groups regarding the repeatability of calculated deposition values. Ranking the different inhalers by differences between the two deposition values calculated from separate maneuvers, Respimat® produced the smallest inter-measurement differences for PD.

Discussion

Our study is the first to model and compare PD using pMDIs and an SMI as triple combination in COPD. In conclusion, switching from FDC to open triple therapy in cases when adherence to devices is maintanined may contribute to better therapeutic effectiveness in individual cases using low resistance inhalers.
Thoracic pain in patients with chronic interstitial lung disease—an underestimated symptom
Authors: Scherer Manuela J. , Kampe Sandra , Fredebeul-Beverungen Jonas , Weinreich Gerhard , Costabel Ulrich , Bonella Francesco
Published: May 2023

Introduction

Prevalence and predisposing factors for the development of thoracic pain (TP) in patients with chronic interstitial lung disease (cILD) are largely unknown. Underestimation and insufficient therapy of pain can lead to worsened ventilatory function. Quantitative sensory testing is an established tool for characterization of chronic pain and its neuropathic components. We investigated frequency and intensity of TP in cILD patients and the potential association with lung function and quality of life.

Materials and methods

We prospectively investigated patients with chronic interstitial lung disease to analyze risk factors for the development of thoracic pain and quantify thoracic pain through quantitative sensory testing. In addition, we studied the relationship between pain sensitivity and lung function impairment.

Results

Seventy-eight patients with chronic interstitial lung disease and 36 healthy controls (HCs) were included. Thoracic pain occurred in 38 of 78 patients (49%), most frequently in 13 of 18 (72%, p = 0.02) patients with pulmonary sarcoidosis. The occurrence was mostly spontaneous and not related to thoracic surgical interventions (76%, p = 0.48). Patients with thoracic pain showed a significant impairment of mental well-being (p = 0.004). A higher sensitivity to pinprick stimulation during QST can be observed in patients with thoracic pain (p < 0.001). Steroid treatment was associated with lower sensitivity within thermal (p = 0.034 and p = 0.032) and pressure pain testing (p = 0.046). We observed a significant correlation between total lung capacity and thermal (p = 0.019 and p = 0.03) or pressure pain sensitivity (p = 0.006 and p = 0.024).

Conclusion

This study was performed to investigate prevalence, risk factors and thoracic pain in patients with chronic interstitial lung disease. Thoracic pain mostly occurs spontaneous as a frequent symptom, and seems to be an underestimated symptom in patients with chronic interstitial lung disease, especially those with pulmonary sarcoidosis. Timely identification of thoracic pain may allow starting symptomatic treatment at early stage, before impairment in quality of life occurs.

Clinical Trial Registration

https://www.drks.de/drks_web/, Deutsches Register Klinischer Studien (DRKS) DRKS00022978.
Rare variant burden analysis from exomes of three consanguineous families reveals LILRB1 and PRSS3 as potential key proteins in inflammatory bowel disease pathogenesis
Authors: Jan Rana Mohammed , Al-Numan Huda Husain , Al-Twaty Nada Hassan , Alrayes Nuha , Alsufyani Hadeel A. , Alaifan Meshari A. , Alhussaini Bakr H. , Shaik Noor Ahmad , Awan Zuhier , Qari Yousef , Saadah Omar I. , Banaganapalli Babajan , Mosli Mahmoud Hisham , Elango Ramu
Published: May 2023

Background

Inflammatory bowel disease (IBD) is a chronic autoimmune disorder characterized by severe inflammation and mucosal destruction of the intestine. The specific, complex molecular processes underlying IBD pathogenesis are not well understood. Therefore, this study is aimed at identifying and uncovering the role of key genetic factors in IBD.

Method

The whole exome sequences (WESs) of three consanguineous Saudi families having many siblings with IBD were analyzed to discover the causal genetic defect. Then, we used a combination of artificial intelligence approaches, such as functional enrichment analysis using immune pathways and a set of computational functional validation tools for gene expression, immune cell expression analyses, phenotype aggregation, and the system biology of innate immunity, to highlight potential IBD genes that play an important role in its pathobiology.

Results

Our findings have shown a causal group of extremely rare variants in the LILRB1 (Q53L, Y99N, W351G, D365A, and Q376H) and PRSS3 (F4L and V25I) genes in IBD-affected siblings. Findings from amino acids in conserved domains, tertiary-level structural deviations, and stability analysis have confirmed that these variants have a negative impact on structural features in the corresponding proteins. Intensive computational structural analysis shows that both genes have very high expression in the gastrointestinal tract and immune organs and are involved in a variety of innate immune system pathways. Since the innate immune system detects microbial infections, any defect in this system could lead to immune functional impairment contributing to IBD.

Conclusion

The present study proposes a novel strategy for unraveling the complex genetic architecture of IBD by integrating WES data of familial cases, with computational analysis.
Potency testing of cell and gene therapy products
Authors: Salmikangas Paula , Carlsson Björn , Klumb Christophe , Reimer Tatiana , Thirstrup Steffen
Published: May 2023

Potency is one of the critical quality attributes of biological medicinal products, defining their biological activity. Potency testing is expected to reflect the Mechanism of Action (MoA) of the medicinal product and ideally the results should correlate with the clinical response. Multiple assay formats may be used, both in vitro assays and in vivo models, however, for timely release of the products for clinical studies or for commercial use, quantitative, validated in vitro assays are necessary. Robust potency assays are fundamental also for comparability studies, process validation and for stability testing. Cell and Gene Therapy Products (CGTs, also called Advanced Therapy Medicinal Products, ATMPs) are part of biological medicines, having nucleic acids, viral vectors, viable cells and tissues as starting material. For such complex products potency testing is often challenging and may require a combination of methods to address multiple functional mechanisms of the product. For cells, viability and cell phenotype are important attributes but alone will not be sufficient to address potency. Furthermore, if the cells are transduced with a viral vector, potency probably is related to the expression of the transgene but will also be dependent on the target cells and transduction efficiency/copy number of the transgene in the cells. Genome Editing (GE) together with other cell manipulations can result into multiple changes in the characteristics and activity of the cells, which should be all somehow captured by the potency testing. Non-clinical studies/models may provide valuable support for potency testing, especially for comparability testing. However, sometimes lack of suitable potency data may lead to situations where bridging clinical efficacy data are required to solve the problems of the potency testing, for example where comparability of different clinical batches is unclear. In this article the challenges of potency testing are discussed together with examples of assays used for different CGTs/ATMPs and the available guidance addressing differences between the European Union and the United States.
Characterization and genomic analysis of phage vB_ValR_NF, representing a new viral family prevalent in the Ulva prolifera blooms
Authors: Zhang Xinran , Liang Yantao , Zheng Kaiyang , Wang Ziyue , Dong Yue , Liu Yundan , Ren Linyi , Wang Hongmin , Han Ying , McMinn Andrew , Sung Yeong Yik , Mok Wen Jye , Wong Li Lian , He Jianfeng , Wang Min
Published: May 2023

Introduction

Vibrio is an important bacterial genus containing many pathogenic species. Although more and more Vibrio phages were isolated, the genome, ecology and evolution of Vibrio phages and their roles in bacteriophage therapy, have not been fully revealed.

Methods

Novel Vibrio phage vB_ValR_NF infecting Vibrio alginolyticus was isolated from the coastal waters of Qingdao during the Ulva prolifera blooms, Characterization and genomic feature of phage vB_ValR_NF has been analysed using phage isolation, sequencing and metagenome method.

Results and Discussion

Phage vB_ValR_NF has a siphoviral morphology (icosahedral head 114±1 nm in diameter; a tail length of 231±1 nm), a short latent period (30 minutes) and a large burst size (113 virions per cell), and the thermal/pH stability study showed that phage vB_ValR_NF was highly tolerant to a range of pHs (4-12) and temperatures (-20 - 45 °C), respectively. Host range analysis suggests that phage vB_ValR_NF not only has a high inhibitory ability against the host strain V. alginolyticus, but also can infect 7 other Vibrio strains. In addition, the phage vB_ValR_NF has a double-stranded 44, 507 bp DNA genome, with 43.10 % GC content and 75 open reading frames. Three auxiliary metabolic genes associated with aldehyde dehydrogenase, serine/threonine protein phosphatase and calcineurin-like phosphoesterase were predicted, might help the host V. alginolyticus occupy the survival advantage, thus improving the survival chance of phage vB_ValR_NF under harsh conditions. This point can be supported by the higher abundance of phage vB_ValR_NF during the U. prolifera blooms than in other marine environments. Further phylogenetic and genomic analysis shows that the viral group represented by Vibrio phage vB_ValR_NF is different from other well-defined reference viruses, and can be classified into a new family, named Ruirongviridae. In general, as a new marine phage infecting V. alginolyticus, phage vB_ValR_NF provides basic information for further molecular research on phage–host interactions and evolution, and may unravel a novel insight into changes in the community structure of organisms during the U. prolifera blooms. At the same time, its high tolerance to extreme conditions and excellent bactericidal ability will become important reference factors when evaluating the potential of phage vB_ValR_NF in bacteriophage therapy in the future.
Pseudomonas sivasensis 2RO45 inoculation alters the taxonomic structure and functioning of the canola rhizosphere microbial community
Authors: Świątczak Joanna , Kalwasińska Agnieszka , Szabó Attila , Swiontek Brzezinska Maria
Published: May 2023

Inoculation with plant growth-promoting rhizobacteria (PGPR) is an eco-friendly sustainable strategy for improving crop productivity in diverse environments under different conditions. Our earlier study demonstrated that Pseudomonas sivasensis 2RO45 significantly stimulated canola (Brassica napus L. var. napus) growth. The aim of the present study was to investigate the structural and functional dynamics in the canola rhizosphere microbiome after inoculation with PGPR P. sivasensis 2RO45. The results based on alpha diversity metrics showed that P. sivasensis 2RO45 did not significantly alter the diversity of the native soil microbiota. However, the introduced strain modified the taxonomic structure of microbial communities, increasing the abundance of plant beneficial microorganisms, e.g., bacteria affiliated with families Comamonadaceae, Vicinamibacteraceae, genus Streptomyces, and fungi assigned to Nectriaceae, Didymellaceae, Exophiala, Cyphellophora vermispora, and Mortierella minutissima. The analysis of community level physiological profiling (CLPP) revealed that microbial communities in the P. sivasensis 2RO45 treated canola rhizospheres were more metabolically active than those in the non-treated canola rhizosphere. Four carbon sources (phenols, polymers, carboxylic acids, and amino acids) were better metabolized by the microbial communities from the rhizosphere of plants inoculated with the P. sivasensis 2RO45 than non-inoculated canola rhizospheres. Based on the community-level physiological profiles, the functional diversity of the rhizosphere microbiome was altered by the P. sivasensis 2RO45 inoculation. Substrate utilization Shannon diversity (H) index and evenness (E) index were significantly increased in the treated canola plants. The study provides new insight into PGPR-canola interactions for sustainable agriculture development.
Unexpected decrease of full-length prion protein in macaques inoculated with prion-contaminated blood products
Authors: Jaffré Nina , Delmotte Jérôme , Mikol Jacqueline , Deslys Jean-Philippe , Comoy Emmanuel
Published: May 2023

The presence of prion infectivity in the blood of patients affected by variant Creutzfeldt–Jakob disease (v-CJD), the human prion disease linked to the bovine spongiform encephalopathy (BSE), poses the risk of inter-human transmission of this fatal prion disease through transfusion. In the frame of various experiments, we have previously described that several cynomolgus macaques experimentally exposed to prion-contaminated blood products developed c-BSE/v-CJD, but the vast majority of them developed an unexpected, fatal disease phenotype focused on spinal cord involvement, which does not fulfill the classical diagnostic criteria of v-CJD. Here, we show that extensive analyses with current conventional techniques failed to detect any accumulation of abnormal prion protein (PrPv−CJD) in the CNS of these myelopathic animals, i.e., the biomarker considered responsible for neuronal death and subsequent clinical signs in prion diseases. Conversely, in the spinal cord of these myelopathic primates, we observed an alteration of their physiological cellular PrP pattern: PrP was not detectable under its full-length classical expression but mainly under its physiological terminal-truncated C1 fragment. This observed disappearance of the N-terminal fragment of cellular PrP at the level of the lesions may provide the first experimental evidence of a link between loss of function of the cellular prion protein and disease onset. This original prion-induced myelopathic syndrome suggests an unexpected wide extension in the field of prion diseases that is so far limited to pathologies associated with abnormal changes of the cellular PrP to highly structured conformations.
Odor exploration behavior of the domestic pig (Sus scrofa) as indicator of enriching properties of odors
Authors: Rørvang Maria Vilain , Schild Sarah-Lina Aagaard , Stenfelt Johanna , Grut Rebecca , Gadri Moses A. , Valros Anna , Nielsen Birte L. , Wallenbeck Anna
Published: May 2023

Introduction and aim

Although the sense of smell in pigs is widely recognized as being highly developed, surprisingly little is known about their sensory ability. This study aimed to (a) identify which non-social odors pigs were able to detect and distinguish between, (b) investigate the types of behavior expressed when exploring odors and, (c) compare pigs’ responses to the different odors to evaluate their interest in the odors.

Methods

Growing pigs (N = 192) of crossbred commercial breeds were enrolled in the experiment (32–110 days of age, weighing 64.9 ± 10.1kg). Littermate pairs of opposite sex were tested in test pens with two odor insertion points in the pen wall, 55 cm apart. All pigs were habituated to the test pens and experimenters. Twelve odors were tested (eight essential oils and four synthetic perfumes) in groups of three odors, with each pig pair tested once with one set of three odors (all possible orders of the three odors were tested on 24 pairs in total), always against a non-odor control (demineralized water). In a test, each of the three odors were presented during three trials in a row (a total of 9 trials per test; trial duration: 1 min; inter-trial breaks: 2 min; total test duration: 25 min). Response variables included: duration of sniffing, feeding-related behavior (licking, biting and rooting), agonistic behavior (biting, displacement and pushing) and no approach of the odor or control, recorded throughout each 1-min odor presentation.

Results

All pigs sniffed an odor less when repeatedly presented (LMM: all odors P < 0.05), and significantly longer at the subsequent presentation of a new odor [LMM (3rd vs. 1st presentations): P < 0.001]. Specific odor and odor type (essential oil vs. synthetic perfume) had no significant effect on sniffing duration. Overall, feeding-related behavior and agonistic behavior were expressed significantly more when pigs explored the odor compared with the control insertion point (Paired t-tests: P < 0.001), and specific odor only affected the expression of feeding-related behavior.

Conclusion

Collectively, pigs express sniffing, agonistic, and feeding-related behavior when exploring odors, which suggests that pigs perceive odors of non-social origin as a resource. Odors may thus constitute relevant enrichment material for pigs.
Dysregulation of miR-146a: a causative factor in epilepsy pathogenesis, diagnosis, and prognosis
Authors: Mao Shiqi , Wu Jinhan , Yan Jingkai , Zhang Weijun , Zhu Feng
Published: May 2023

miR-146a is an NF-κB-dependent miRNA that acts as an anti-inflammatory miRNA via the Toll-like receptor (TLR) pathway. miR-146a targets multiple genes and has been identified to directly or indirectly regulate processes other than inflammation, including intracellular Ca changes, apoptosis, oxidative stress, and neurodegeneration. miR-146a is an important regulator of gene expression in epilepsy development and progression. Furthermore, miR-146a-related single nucleotide polymorphisms (SNPs) and single nucleotide variants (SNVs) contribute to the genetic susceptibility to drug resistance and seizure severity in epilepsy patients. This study summarizes the abnormal expression patterns of miR-146a in different types and stages of epilepsy and its potential molecular regulation mechanism, indicating that miR-146a can be used as a novel biomarker for epilepsy diagnosis, prognosis, and treatment.
Case report: A hybrid open and endovascular approach for repairing a life-threatening innominate artery dissection using the simultaneous kissing stent technique
Authors: Kuo Chu-Hsuan , Yang Shun-Tai , Lu Yueh-Hsun , Lu Yu-Chun , Su I-Chang
Published: May 2023

Managing acute innominate artery (IA) dissection associated with severe stenosis is challenging due to its rarity, possible complex dissection patterns, and compromised blood flow to the brain and upper extremities. This report describes our treatment strategy for this challenging disease using the kissing stent technique. A 61-year-old man had worsening of an acute IA dissection secondary to an extension of a treated aortic dissection. Four possible treatment strategies for kissing stent placement were proposed based on different approaches (open surgical or endovascular) and accesses (trans-femoral, trans-brachial, or trans-carotid access). We chose to place two stents simultaneously via a percutaneous retrograde endovascular approach through the right brachial artery and a combined open surgical distal clamping of the common carotid artery with a retrograde endovascular approach through the carotid artery. This hybrid approach strategy highlights the three key points for maintaining safety and efficacy: (1) good guiding catheter support is obtainable through retrograde, rather than antegrade, access to the lesion, (2) concomitant cerebral and upper extremity reperfusion is guaranteed by placing kissing stents into the IA, and (3) peri-procedural cerebral emboli are prevented by surgical exposure of the common carotid artery with distal clamping.