bluuebunny/crossref_metadata_2025 huggingface dataset:
Use of LoopDeelab during the COVID-19 Pandemic: An Innovative Device for Field Diagnosis
Authors: Dossou Nefert Candace , Gaubert Isidore , Maille Elodie , Morello Remy , Cassier Renaud , Schanen Cécile , Dutheil Jean-Jacques , Rocque Louis-Marie , Vabret Astrid , Ar Gouilh Meriadeg
Published: September 2022

Rapid and accurate diagnosis of SARS-CoV-2 infection is essential for the management of the COVID-19 outbreak. RT-LAMP LoopDeetect COVID-19 (LoopDeescience, France) is a rapid molecular diagnostic tool which operates with the LoopDeelab (LoopDeescience, France) device. RAPID COVID is a prospective double-blind research protocol which was conducted to evaluate the concordance between Loopdeetect COVID-19 and RT-PCR Allplex 2019 n-Cov (Seegene, Korea). Between 11 May 2020 and 14 June 2021, a total of 1122 nasopharyngeal swab specimens were collected, of which 741 were finally analysed. There were 32 “positive” and “indeterminate” RT-PCR results. The intrinsic performances of Loopdeetect COVID-19 are equivalent to other commercial RT-LAMP PCR COVID-19 kits, with a sensitivity and specificity of 69.23% [CI 95%: 48.21–85.67] and 100% [CI 95%: 99.58–100.00], respectively. To the best of our knowledge, LoopDeelab is the only LAMP PCR diagnostic device allowing such a fast and reliable analysis with low-cost equipment; this makes it a new and innovative technology, designed for field use. This device being portable, the development of other detection kits will be useful for the management of epidemics with a high attack rate and would facilitate the rapid application of health measures.
Transmission Patterns of Seasonal Influenza in China between 2010 and 2018
Authors: Lei Hao , Yang Lei , Wang Gang , Zhang Chi , Xin Yuting , Sun Qianru , Zhang Bing , Chen Tao , Yang Jing , Huang Weijuan , Xu Modi , Xie Yu , Wang Yinghan , Xu Pei , Sun Litao , Guo Deyin , Du Xiangjun , Wang Dayan , Shu Yuelong
Published: September 2022

Background Understanding the transmission source, pattern, and mechanism of infectious diseases is essential for targeted prevention and control. Though it has been studied for many years, the detailed transmission patterns and drivers for the seasonal influenza epidemics in China remain elusive. Methods In this study, utilizing a suite of epidemiological and genetic approaches, we analyzed the updated province-level weekly influenza surveillance, sequence, climate, and demographic data between 1 April 2010 and 31 March 2018 from continental China, to characterize detailed transmission patterns and explore the potential initiating region and drivers of the seasonal influenza epidemics in China. Results An annual cycle for influenza A(H1N1)pdm09 and B and a semi-annual cycle for influenza A(H3N2) were confirmed. Overall, the seasonal influenza A(H3N2) virus caused more infection in China and dominated the summer season in the south. The summer season epidemics in southern China were likely initiated in the “Lingnan” region, which includes the three most southern provinces of Hainan, Guangxi, and Guangdong. Additionally, the regions in the south play more important seeding roles in maintaining the circulation of seasonal influenza in China. Though intense human mobility plays a role in the province-level transmission of influenza epidemics on a temporal scale, climate factors drive the spread of influenza epidemics on both the spatial and temporal scales. Conclusion The surveillance of seasonal influenza in the south, especially the “Lingnan” region in the summer, should be strengthened. More broadly, both the socioeconomic and climate factors contribute to the transmission of seasonal influenza in China. The patterns and mechanisms revealed in this study shed light on the precise forecasting, prevention, and control of seasonal influenza in China and worldwide.
Human Virome in Cervix Controlled by the Domination of Human Papillomavirus
Authors: Sasivimolrattana Thanayod , Chantratita Wasun , Sensorn Insee , Chaiwongkot Arkom , Oranratanaphan Shina , Bhattarakosol Parvapan
Published: September 2022

Although other co-viral infections could also be considered influencing factors, cervical human papillomavirus (HPV) infection is the main cause of cervical cancer. Metagenomics have been employed in the NGS era to study the microbial community in each habitat. Thus, in this investigation, virome capture sequencing was used to examine the virome composition in the HPV-infected cervix. Based on the amount of HPV present in each sample, the results revealed that the cervical virome of HPV-infected individuals could be split into two categories: HPV-dominated (HD; ≥60%) and non-HPV-dominated (NHD; <60%). Cervical samples contained traces of several human viral species, including the molluscum contagiosum virus (MCV), human herpesvirus 4 (HHV4), torque teno virus (TTV), and influenza A virus. When compared to the HD group, the NHD group had a higher abundance of several viruses. Human viral diversity appears to be influenced by HPV dominance. This is the first proof that the diversity of human viruses in the cervix is impacted by HPV abundance. However, more research is required to determine whether human viral variety and the emergence of cancer are related.
Autopsy Study Defines Composition and Dynamics of the HIV-1 Reservoir after Allogeneic Hematopoietic Stem Cell Transplantation with CCR5Δ32/Δ32 Donor Cells
Authors: Huyveneers Laura E. P. , Bruns Anke , Stam Arjen , Ellerbroek Pauline , de Jong Dorien , Nagy Noémi A. , Gumbs Stephanie B. H. , Tesselaar Kiki , Bosman Kobus , Salgado Maria , Hütter Gero , Brosens Lodewijk A. A. , Kwon Mi , Diez Martin Jose , van der Meer Jan T. M. , de Kort Theun M. , Sáez-Cirión Asier , Schulze zur Wiesch Julian , Boelens Jaap Jan , Martinez-Picado Javier , Kuball Jürgen H. E. , Wensing Annemarie M. J. , Nijhuis Monique
Published: September 2022

Allo-HSCT with CCR5Δ32/Δ32 donor cells is the only curative HIV-1 intervention. We investigated the impact of allo-HSCT on the viral reservoir in PBMCs and post-mortem tissue in two patients. IciS-05 and IciS-11 both received a CCR5Δ32/Δ32 allo-HSCT. Before allo-HSCT, ultrasensitive HIV-1 RNA quantification; HIV-1-DNA quantification; co-receptor tropism analysis; deep-sequencing and viral characterization in PBMCs and bone marrow; and post-allo-HSCT, ultrasensitive RNA and HIV-1-DNA quantification were performed. Proviral quantification, deep sequencing, and viral characterization were done in post-mortem tissue samples. Both patients harbored subtype B CCR5-tropic HIV-1 as determined genotypically and functionally by virus culture. Pre-allo-HSCT, HIV-1-DNA could be detected in both patients in bone marrow, PBMCs, and T-cell subsets. Chimerism correlated with detectable HIV-1-DNA LTR copies in cells and tissues. Post-mortem analysis of IciS-05 revealed proviral DNA in all tissue biopsies, but not in PBMCs. In patient IciS-11, who was transplanted twice, no HIV-1-DNA could be detected in PBMCs at the time of death, whereas HIV-1-DNA was detectable in the lymph node. In conclusion, shortly after CCR5Δ32/Δ32, allo-HSCT HIV-1-DNA became undetectable in PBMCs. However, HIV-1-DNA variants identical to those present before transplantation persisted in post-mortem-obtained tissues, indicating that these tissues play an important role as viral reservoirs.
COS-7 and SVGp12 Cellular Models to Study JCPyV Replication and MicroRNA Expression after Infection with Archetypal and Rearranged-NCCR Viral Strains
Authors: Prezioso Carla , Passerini Sara , Limongi Dolores , Palamara Anna Teresa , Moens Ugo , Pietropaolo Valeria
Published: September 2022

Since the non-coding control region (NCCR) and microRNA (miRNA) could represent two different and independent modalities of regulating JC polyomavirus (JCPyV) replication at the transcriptional and post-transcriptional levels, the interplay between JC viral load based on NCCR architecture and miRNA levels, following JCPyV infection with archetypal and rearranged (rr)-NCCR JCPyV variants, was explored in COS-7 and SVGp12 cells infected by different JCPyV strains. Specifically, the involvement of JCPyV miRNA in regulating viral replication was investigated for the archetypal CY strain—which is the transmissible form—and for the rearranged MAD-1 strain, which is the first isolated variant from patients with progressive multifocal leukoencephalopathy. The JCPyV DNA viral load was low in cells infected with CY compared with that in MAD-1-infected cells. Productive viral replication was observed in both cell lines. The expression of JCPyV miRNAs was observed from 3 days after viral infection in both cell types, and miR-J1-5p expression was inversely correlated with the JCPyV replication trend. The JCPyV miRNAs in the exosomes present in the supernatants produced by the infected cells could be carried into uninfected cells. Additional investigations of the expression of JCPyV miRNAs and their presence in exosomes are necessary to shed light on their regulatory role during viral reactivation.
Biophysical Modeling of SARS-CoV-2 Assembly: Genome Condensation and Budding
Authors: Li Siyu , Zandi Roya
Published: September 2022

The COVID-19 pandemic caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has spurred unprecedented and concerted worldwide research to curtail and eradicate this pathogen. SARS-CoV-2 has four structural proteins: Envelope (E), Membrane (M), Nucleocapsid (N), and Spike (S), which self-assemble along with its RNA into the infectious virus by budding from intracellular lipid membranes. In this paper, we develop a model to explore the mechanisms of RNA condensation by structural proteins, protein oligomerization and cellular membrane–protein interactions that control the budding process and the ultimate virus structure. Using molecular dynamics simulations, we have deciphered how the positively charged N proteins interact and condense the very long genomic RNA resulting in its packaging by a lipid envelope decorated with structural proteins inside a host cell. Furthermore, considering the length of RNA and the size of the virus, we find that the intrinsic curvature of M proteins is essential for virus budding. While most current research has focused on the S protein, which is responsible for viral entry, and it has been motivated by the need to develop efficacious vaccines, the development of resistance through mutations in this crucial protein makes it essential to elucidate the details of the viral life cycle to identify other drug targets for future therapy. Our simulations will provide insight into the viral life cycle through the assembly of viral particles de novo and potentially identify therapeutic targets for future drug development.
Simultaneous Detection of RIG-1, MDA5, and IFIT-1 Expression Is a Convenient Tool for Evaluation of the Interferon-Mediated Response
Authors: Lozhkov Alexey A. , Plotnikova Marina A. , Egorova Marya A. , Baranovskaya Irina L. , Elpaeva Ekaterina A. , Klotchenko Sergey A. , Vasin Andrey V.
Published: September 2022

In this study, we developed a novel, multiplex qPCR assay for simultaneous detection of RIG-1, MDA5, and IFIT-1 at the mRNA level. The assay was validated in A549 cells transfected with in vitro transcribed RNAs. Both exogenous RNA-GFP and self-amplifying (saRNA-GFP) induced significant expression of RIG-1, MDA5, IFIT-1, as well as type I and III interferons. In contrast, native RNA from intact A549 cells did not upregulate expression of these genes. Next, we evaluated RIG-1, MDA5, and IFIT-1 mRNA levels in the white blood cells of patients with influenza A virus (H3N2) or SARS-CoV-2. In acute phase (about 4 days after disease onset) both viruses induced these genes expression. Clinical observations of SARS-CoV-2 typically describe a two-step disease progression, starting with a mild-to-moderate presentation followed by a secondary respiratory worsening 9 to 12 days after the first onset of symptoms. It revealed that the expression of RIG-1, MDA5, and MxA was not increased after 2 and 3 weeks from the onset the disease, while for IFIT-1 it was observed the second peak at 21 day post infection. It is well known that RIG-1, MDA5, and IFIT-1 expression is induced by the action of interferons. Due to the ability of SOCS-1 to inhibit interferon-dependent signaling, and the distinct antagonism of SARS-CoV-2 in relation to interferon-stimulated genes expression, we assessed SOCS-1 mRNA levels in white blood cells. SARS-CoV-2 patients had increased SOCS-1 expression, while the influenza-infected group did not differ from heathy donors. Moreover, SOCS-1 mRNA expression remained stably elevated during the course of the disease. It can be assumed that augmented SOCS-1 expression is one of multiple mechanisms that allow SARS-CoV-2 to escape from the interferon-mediated immune response. Our results implicate SOCS-1 involvement in the pathogenesis of SARS-CoV-2.
SARS-CoV-2 Variants, Current Vaccines and Therapeutic Implications for COVID-19
Authors: Liang Hong-Yu , Wu Yuyan , Yau Vicky , Yin Huan-Xin , Lowe Scott , Bentley Rachel , Ahmed Mubashir Ayaz , Zhao Wenjing , Sun Chenyu
Published: September 2022

Over the past two years, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused hundreds of millions of infections, resulting in an unprecedented pandemic of coronavirus disease 2019 (COVID-19). As the virus spreads through the population, ongoing mutations and adaptations are being discovered. There is now substantial clinical evidence that demonstrates the SARS-CoV-2 variants have stronger transmissibility and higher virulence compared to the wild-type strain of SARS-CoV-2. Hence, development of vaccines against SARS-CoV-2 variants to boost individual immunity has become essential. However, current treatment options are limited for COVID-19 caused by the SARS-CoV-2 variants. In this review, we describe current distribution, variation, biology, and clinical features of COVID-19 caused by SARS-CoV-2 variants (including Alpha (B.1.1.7 Lineage) variant, Beta (B.1.351 Lineage) variant, Gamma (P.1 Lineage) variant, Delta (B.1.617.2 Lineage) variant, and Omicron (B.1.1.529 Lineage) variant and others. In addition, we review currently employed vaccines in clinical or preclinical phases as well as potential targeted therapies in an attempt to provide better preventive and treatment strategies for COVID-19 caused by different SARS-CoV-2 variants.
In Vivo Oncolytic Virotherapy in Murine Models of Hepatocellular Carcinoma: A Systematic Review
Authors: Ailia Muhammad Joan , Yoo So Young
Published: September 2022

Hepatocellular carcinoma (HCC) is the third leading cause of cancer-related mortality worldwide. Current therapies often provide marginal survival benefits at the expense of undesirable side effects. Oncolytic viruses represent a novel strategy for the treatment of HCC due to their inherent ability to cause direct tumor cell lysis while sparing normal tissue and their capacity to stimulate potent immune responses directed against uninfected tumor cells and distant metastases. Oncolytic virotherapy (OVT) is a promising cancer treatment, but before it can become a standard option in practice, several challenges—systemic viral delivery optimization/enhancement, inter-tumoral virus dispersion, anti-cancer immunity cross-priming, and lack of artificial model systems—need to be addressed. Addressing these will require an in vivo model that accurately mimics the tumor microenvironment and allows the scientific community to design a more precise and accurate OVT. Due to their close physiologic resemblance to humans, murine cancer models are the likely preferred candidates. To provide an accurate assessment of the current state of in vivo OVT in HCC, we have reviewed a comprehensively searched body of work using murine in vivo HCC models for OVT.
Antibody Titers and Protection against Omicron (BA.1 and BA.2) SARS-CoV-2 Infection
Authors: Dimeglio Chloé , Migueres Marion , Bouzid Naémie , Chapuy-Regaud Sabine , Gernigon Caroline , Da-Silva Isabelle , Porcheron Marion , Martin-Blondel Guillaume , Herin Fabrice , Izopet Jacques
Published: September 2022

The emergence of the SARS-CoV-2 variants of concern has greatly influenced the immune correlates of protection, and there are little data about the antibody threshold concentrations to protect against infection with SARS-CoV-2 Omicron BA.1 or BA.2. We analyzed the antibody responses of 259 vaccinated healthcare workers, some of whom had been previously infected by SARS-CoV-2. The median follow-up was 179 days (IQR: 171–182) after blood collection. We detected 88 SARS-CoV-2 Omicron infections during the follow-up period, 55 (62.5%) with SARS-CoV-2 BA.1, and 33 (37.5%) with SARS-CoV-2 BA.2. A neutralizing antibody titer below 8 provided no protection against a BA.1 infection, a titer of 16 or 32 gave 73.2% protection, and a titer of 64 or 128 provided 78.4% protection. Conversely, the BA.2 infection rate did not vary as a function of anti-BA.2 neutralizing antibody titers. Binding antibody concentrations below 6000 BAU/mL provided no protection against Omicron BA.1 infection, 6000–20,000 BAU/mL provided 55.6% protection, and 20,000 or more provided 87.7% protection. There was no difference in BA.2 infection depending on the binding antibody concentration. Further studies are needed to investigate the relationship between antibody concentrations and infection with the Omicron BA.4/5 variants that are becoming predominant worldwide.
Human Respiratory Infections in Nigeria: Influenza and the Emergence of SARS-CoV-2 Pandemic
Authors: Kabantiyok Dennis , Ninyio Nathaniel , Shittu Ismaila , Meseko Clement , Emeto Theophilus I. , Adegboye Oyelola A.
Published: September 2022

The increasing outbreak of zoonotic diseases presents challenging times for nations and calls for a renewed effort to disrupt the chain of events that precede it. Nigeria’s response to the 2006 bird flu provided a platform for outbreak response, yet it was not its first experience with Influenza. This study describes the impact of SARS-CoV-2 on Influenza surveillance and, conversely, while the 1918 Influenza pandemic remains the most devastating (500,000 deaths in 18 million population) in Nigeria, the emergence of SARS CoV-2 presented renewed opportunities for the development of vaccines with novel technology, co-infection studies outcome, and challenges globally. Although the public health Intervention and strategies left some positive outcomes for other viruses, Nigeria and Africa’s preparation against the next pandemic may involve prioritizing a combination of technology, socioeconomic growth, and active surveillance in the spirit of One Health.
Role and Limits of COVID-19 Vaccines in the Delicate Transition from Pandemic Mitigation to Endemic Control
Authors: Mura Marie , Simon Fabrice , Pommier de Santi Vincent , Tangy Frédéric , Tournier Jean-Nicolas
Published: September 2022

The recent surge of COVID-19 related to the Omicron variant emergence has thrown a harsh light upon epidemic control in the near future. This should lead the scientific and medical community to question the long-term vaccine strategy for SARS-CoV-2 control. We provide here a critical point of view regarding the virological evolution, epidemiological aspects, and immunological drivers for COVID-19 control, including a vaccination strategy. Overall, we need more innovations in vaccine development to reduce the COVID-19 burden long term. The most adequate answer might be better cooperation between universities, biotech and pharmaceutical companies
Bioinformatic Analysis for Mucoepidermoid and Adenoid Cystic Carcinoma of Therapeutic Targets
Authors: Ramírez-Martínez Carla Monserrat , Jacinto-Alemán Luis Fernando , Cruz-Hervert Luis Pablo , Portilla-Robertson Javier , Leyva-Huerta Elba Rosa
Published: September 2022

Salivary gland neoplasms are a heterogeneous neoplasm group, including mucoepidermoid carcinoma (MECa), adenoid cystic carcinoma (AdCC), and many others. Objective: We aimed to identify new critical genes of MECa and AdCC using bioinformatics analysis. Methods: Gene expression profile of GSE153283 was analyzed by the GEO2R online tool to use the DAVID software for their subsequent enrichment. Protein–protein interactions (PPI) were visualized using String. Cytoscape with MCODE plugin followed by Kaplan–Meier online for overall survival analysis were performed. Results: 97 upregulated genes were identified for MECa and 86 for AdCC. PPI analysis revealed 22 genes for MECa and 63 for AdCC that were validated by Kaplan–Meier that showed FN1 and SPP1 for MECa, and EGF and ERBB2 for AdCC as more significant candidate genes for each neoplasm. Conclusion: With bioinformatics methods, we identify upregulated genes in MECa and AdCC. The resulting candidate genes as possible therapeutic targets were FN1, SPP1, EGF, and ERBB2, and all those genes had been tested as a target in other neoplasm kinds but not salivary gland neoplasm. The bioinformatic evidence is a solid strategy to select them for more extensive research with clinical impact.
Diplopia, COVID-19 and Vaccination: Results from a Cross-Sectional Study in Croatia
Authors: Škunca Herman Jelena , Marić Goran , Ravlić Maja Malenica , Knežević Lana , Jerković Ivan , Sušić Ena , Marić Vedrana , Vicković Ivanka Petric , Vatavuk Zoran , Polašek Ozren
Published: September 2022

The aim of this study was to explore diplopia as a symptom of undetected COVID-19 infection or as a possible side effect of COVID-19 vaccination. We examined 380 patients with diplopia admitted to the Department of Ophthalmology of the University Hospital Centre Sestre milosrdnice in Zagreb, Croatia, from July 2020 to June 2022. After excluding patients with confirmed organic underlying diplopia causes or monocular diplopia, we linked the patient information with the national COVID-19 and vaccination registries. Among the 91 patients included in this study, previously undetected COVID-19 infection as the possible cause of diplopia was confirmed in five of them (5.5%). An additional nine patients (9.9%) were vaccinated within one month from the onset of their symptoms, while the remaining 77 had neither and were therefore considered as controls. The breakdown according to the mechanism of diplopia showed no substantial difference between the vaccinated patients and the controls. We detected marginally insignificant excess abducens nerve affection in the COVID-positive group compared with that in the controls (p = 0.051). Post-vaccination diplopia was equally common in patients who received vector-based or RNA-based vaccines (21.4 vs. 16.7%; p = 0.694). COVID-19 testing should be performed for all cases of otherwise unexplained diplopia. The risk of post-vaccination diplopia was similar in both types of vaccines administered, suggesting a lack of evidence linking specific vaccine types to diplopia.
Integration of Bulk and Single-Cell RNA-Seq Data to Construct a Prognostic Model of Membrane Tension-Related Genes for Colon Cancer
Authors: Li Jiacheng , Fu Yugang , Zhang Kehui , Li Yong
Published: September 2022

Background: The plasma membrane provides a highly dynamic barrier for cancer cells to interact with their surrounding microenvironment. Membrane tension, a pivotal physical property of the plasma membrane, has attracted widespread attention since it plays a role in the progression of various cancers. This study aimed to identify a prognostic signature in colon cancer from membrane tension-related genes (MTRGs) and explore its implications for the disease. Methods: Bulk RNA-seq data were obtained from The Cancer Genome Atlas (TCGA) database, and then applied to the differentially expressed gene analysis. By implementing a univariate Cox regression and a LASSO-Cox regression, we developed a prognostic model based on four MTRGs. The prognostic efficacy of this model was evaluated in combination with a Kaplan–Meier analysis and receiver operating characteristic (ROC) curve analysis. Moreover, the relationships between the signature and immune cell infiltration, immune status, and somatic mutation were further explored. Lastly, by utilizing single-cell RNA-seq data, cell type annotation, pseudo-time analysis, drug sensitivity, and molecular docking were implemented. Results: We constructed a 4-MTRG signature. The risk score derived from the model was further validated as an independent variable for survival prediction. Two risk groups were divided based on the risk score calculated by the 4-MTRG signature. In addition, we observed a significant difference in immune cell infiltration, such as subsets of CD4 T cells and macrophages, between the high- and low-risk groups. Moreover, in the pseudo-time analysis, TIMP1 was found to be more highly expressed with the progression of time. Finally, three small molecule drugs, elesclomol, shikonin, and bryostatin-1, exhibited a binding potential to TIMP-1. Conclusions: The novel 4-MTRG signature is a promising biomarker in predicting clinical outcomes for colon cancer patients, and TIMP1, a member of the signature, may be a sensitive regulator of the progression of colon cancer.
Multi-Epitope-Based Vaccine Candidate for Monkeypox: An In Silico Approach
Authors: Abdi Sayed Aliul Hasan , Ali Amena , Sayed Shabihul Fatma , Abutahir  , Ali Abuzer , Alam Prawez
Published: September 2022

Currently, there are limited treatment options available for the monkeypox disease. We used a computational strategy to design a specific antigenic vaccine against pathogens. After using various immunoinformatic tools and filters, cytotoxic T-cell lymphocyte (CTL)-, helper T-cell lymphocyte (HTL)-, and interferon gamma (IFN-γ)-inducing epitopes, which comprised the vaccine, in addition to other parameters, such as antigenic and allergic profiles, were assessed to confirm the safety of the vaccine. However, vaccine interaction and stability with Toll-like receptors (TLRs) were assessed by dynamic simulation methods, and it was found that the constructed vaccine was stable. In addition, C-IMMSIM tools were used to determine the immune-response-triggering capabilities of the vaccine. These immunoinformatic findings reveal that constructed vaccine candidates may be capable of triggering an efficient immune response for monkeypox viral infections. However, experimental evaluation is required to verify the safety and immunogenic profile of constructed vaccines.
Vaccination and COVID-19 in Polish Dialysis Patients: Results from the European Clinical Dialysis Database
Authors: Marcinkowski Wojciech , Zuzda Konrad , Zawierucha Jacek , Prystacki Tomasz , Żebrowski Paweł , Małyszko Jacek S. , Wojtaszek Ewa , Małyszko Jolanta
Published: September 2022

Background: Patients with end-stage kidney disease undergoing hemodialysis are particularly vulnerable to severe COVID-19 as a result of older age and multimorbidities. Objectives: Data are still limited and there are no published data on mortality in hemodialyzed patients in Poland, in particular when vaccines became available. We assessed the epidemiologic and clinical data of patients with laboratory-confirmed COVID-19 and assessed the mortality in 2019, 2020, and 2021, as well as the vaccination rate in 2021. Patients and Methods: Retrospectively collected data from 73 Fresenius Nephrocare Poland hemodialysis centers and one public unit were analyzed. Results: In 2021, the vaccination rate was 96%. The unadjusted mortality (number of deaths divided by number of patients) in 2019 was 18.8%, while the unadjusted (after exclusion of COVID-related deaths) mortality in 2020 was 20.8%, and mortality in 2021 was 16.22%. The prevalence of cardiovascular deaths in 2019 and 2020 was almost identical (41.4% vs. 41.2%, respectively), and in 2021, the figures increased slightly to 44.1%. The prevalence of sudden cardiac deaths in 2019 was higher than in 2020 (19.6% vs. 17.3%, respectively) and consequently decreased in 2021 (10.0%), as well as strokes (6.2% vs. 5.4%, and 3.31% in 2021), whereas deaths due to gastrointestinal tract diseases were lower (2.5% vs. 3.2%, and 2.25% in 2021), diabetes complications (0.5% vs. 1.3%, and 0.5% in 2021), sepsis (5.1% vs. 6.3%, and 8.79% in 2021), respiratory failure (1.2 vs. 1.6%, and 2.83% in 2021), and pneumonia (1.4% vs. 2.0%, and 0.82%). There were 1493 hemodialyzed COVID-19 positive patients, and among them, 191 died in 2020 (12.79%). In 2021, there were 1224 COVID-19 positive patients and 260 died (21.24%). The mortality of COVID-19 positive dialyzed patients contributed 13.39% in 2020 and 16.21% in 2021 of all recorded deaths. Conclusions: The mortality among HD patients was higher in 2021 than in 2020 and 2019, despite the very high vaccination rate of up to 96%. The higher non-COVID-19 mortality may be due to the limited possibility of hospitalization and dedicated care during the pandemic. This information is extremely important in order to develop methods to protect this highly vulnerable patient group. Prevention plays a key role; other measures are essential in the mitigation and spread of COVID-19 in HD centers.
Autogenous Escherichia coli Vaccine Application as an Innovative Antimicrobial Therapy in Poultry Farming—A Case Report
Authors: Lozica Liča , Morteza Gholi Céline Sadaf , Kela Adaya , Lošić Ivan , Horvatek Tomić Danijela , Gottstein Željko
Published: September 2022

Escherichia coli (E. coli) is one of the most common bacterial causes of infection in poultry farming. Whether the infection is localized or systemic, a primary or secondary disease, it is most frequently treated through the application of wide-spectrum antimicrobials. Excessive use of antimicrobials in agriculture is significantly contributing to the worldwide rise of antimicrobial resistance, but is also very expensive and often ineffective in the long term. Here, we present a case where a colibacillosis outbreak on a family farm of laying hens was treated using an autogenous vaccine. The birds had septicemia, cellulitis, and severe skin wounds. They were not vaccinated against E. coli, and did not receive any antimicrobials previously. E. coli strains were isolated from the daily mortalities on the farm and used for preparation of the vaccine. Each bird was given an intramuscular injection of the autogenous vaccine. The immunogenicity of the vaccine was tested by the determination of specific antibody levels in the sera of the birds using the in-house ELISA. Shortly after vaccination, the morbidity and mortality rates significantly decreased, and egg production was improved. The application of the autogenous vaccine served as a curative and preventive measure, and has proven to be a very efficient method of antimicrobial therapy.
Exposure of Zero-Dose Children to Multiple Deprivation: Analyses of Data from 80 Low- and Middle-Income Countries
Authors: Wendt Andrea , Santos Thiago M. , Cata-Preta Bianca O. , Arroyave Luisa , Hogan Daniel R. , Mengistu Tewodaj , Barros Aluisio J. D. , Victora Cesar G.
Published: September 2022

The concept of multiple deprivation recognizes that the same individuals, households, and communities are often exposed to several forms of scarcity. We assessed whether lack of immunization is also associated with nutritional, environmental, and educational outcomes. We analyzed data from nationally representative surveys from 80 low- and middle-income countries with information on no-DPT (children aged 12–23 months without any doses of a diphtheria, pertussis and tetanus containing vaccine), stunting, wasting, maternal education and use of contraception, improved water and sanitation, and long-lasting insecticidal nets. Analyses of how these characteristics overlap were performed at individual and ecological levels. Principal component analyses (PCA) provided additional information on indicator clustering. In virtually all analyses, no-DPT children were significantly more likely to be exposed to the other markers for deprivation. The strongest, most consistent associations were found with maternal education, water, and sanitation, while the weakest associations were found for wasting and bed nets. No-DPT prevalence reached 46.1% in the most deprived quintile from first PCA component derived from deprivation indicators. All children were immunized in the two least deprived quintiles of the component. Our analyses provide strong support for the hypothesis that unimmunized children are also affected by other forms of deprivation.
Impact of HLA Polymorphism on the Immune Response to Bacillus Anthracis Protective Antigen in Vaccination versus Natural Infection
Authors: Ascough Stephanie , Ingram Rebecca J. , Chu Karen K. Y. , Moore Stephen J. , Gallagher Theresa , Dyson Hugh , Doganay Mehmet , Metan Gökhan , Ozkul Yusuf , Baillie Les , Williamson E. Diane , Robinson John H. , Maillere Bernard , Boyton Rosemary J. , Altmann Daniel M.
Published: September 2022

The causative agent of anthrax, Bacillus anthracis, evades the host immune response and establishes infection through the production of binary exotoxins composed of Protective Antigen (PA) and one of two subunits, lethal factor (LF) or edema factor (EF). The majority of vaccination strategies have focused upon the antibody response to the PA subunit. We have used a panel of humanised HLA class II transgenic mouse strains to define HLA-DR-restricted and HLA-DQ-restricted CD4+ T cell responses to the immunodominant epitopes of PA. This was correlated with the binding affinities of epitopes to HLA class II molecules, as well as the responses of two human cohorts: individuals vaccinated with the Anthrax Vaccine Precipitated (AVP) vaccine (which contains PA and trace amounts of LF), and patients recovering from cutaneous anthrax infections. The infected and vaccinated cohorts expressing different HLA types were found to make CD4+ T cell responses to multiple and diverse epitopes of PA. The effects of HLA polymorphism were explored using transgenic mouse lines, which demonstrated differential susceptibility, indicating that HLA-DR1 and HLA-DQ8 alleles conferred protective immunity relative to HLA-DR15, HLA-DR4 and HLA-DQ6. The HLA transgenics enabled a reductionist approach, allowing us to better define CD4+ T cell epitopes. Appreciating the effects of HLA polymorphism on the variability of responses to natural infection and vaccination is vital in planning protective strategies against anthrax.
Efficacy, Immunogenicity, and Safety of COVID-19 Vaccines in Randomized Control Trials in the Pre-Delta Era: A Systematic Review and Network Meta-Analysis
Authors: Oh SuA , Purja Sujata , Shin Hocheol , Kim Min Seo , Park Seoyeon , Kronbichler Andreas , Smith Lee , Eisenhut Michael , Shin Jae Il , Kim Eunyoung
Published: September 2022

The most effective method of limiting the coronavirus disease pandemic of 2019 (COVID-19) is vaccination. For the determination of the comparative efficacy and safety of COVID-19 vaccines and their platforms during the pre-Delta era, a systematic review and network meta-analysis was conducted. The MEDLINE, Embase, and MedRxiv databases were searched, and the gray literature was manually searched up to 8 July 2021. The review includes the phase II and III randomized controlled trials (RCTs) that assessed the efficacy, immunogenicity, and safety of the COVID-19 vaccines. The network meta-analysis used a Bayesian model and used the surface under the cumulative ranking to rank the comparisons between the vaccines. All included studies were quality appraised according to their design, and the heterogeneity of the analyses was assessed using I2. In terms of vaccine efficacy, the mRNA-1273 vaccine ranked the highest, and the CoronaVac vaccine ranked the lowest. The mRNA-1273 ranked the highest for neutralizing antibody responses to live SARS-CoV-2. The WIV04 vaccine was associated with the lowest incidence of both local and systemic adverse reactions. All studies except one had a low to moderate risk of bias. The mRNA platform vaccines showed higher efficacy and more adverse reactions than the other vaccines.
A Case of Atypical Unilateral Optic Neuritis Following BNT162b2 mRNA COVID-19 Vaccination
Authors: Motegi Shuntaro , Kanda Takayuki , Takeuchi Masaru
Published: September 2022

Background: We report a case of atypical unilateral optic neuritis after receiving the BNT162b2 mRNA-based COVID-19 vaccine. Case Presentation: An 86-year-old man complained of blurred vision and decreased visual acuity in his right eye 8 days after receiving the second BNT162b2 mRNA-based COVID-19 vaccine and was referred to our hospital. He also had pain with eye movement. Best corrected visual acuity (BCVA) in the right eye was 20/200 and critical flicker frequency dropped to 16 Hz. Relative afferent pupillary defect was positive and central scotomas were observed on visual field analysis. Fundus examination and SD-OCT revealed optic disc swelling and apparent thickening of the retinal nerve fiber layer around the optic disc in the right eye. Although either an increase in CRP or ESR on laboratory tests, demyelinating lesion on MRI, or positive of anti-MOG antibodies or anti-AQP4 antibodies were not observed, fluorescein angiography presented only hyperfluorescence of the optic disc in the right eye, but there were no findings such as papillary deficiency and choroidal delay that would suggest ischemic optic neuropathy. We diagnosed atypical optic neuritis developed after the SARS-CoV-2 mRNA-based vaccination and initiated oral corticosteroid therapy. One month later, the optic disc swelling disappeared and BCVA improved to 20/100; however, the central scotoma remained and no further improvement in visual function OD was obtained. Conclusions: An atypical acute idiopathic optic neuritis can occur after receiving the second vaccination with BNT162b2, which may present a limited response to corticosteroid therapy.
The Longitudinal Analysis on the Anti-SARS-CoV-2 Antibodies among Healthcare Workers in Poland—Before and after BNT126b2 mRNA COVID-19 Vaccination
Authors: Lorent Dagny , Nowak Rafał , Luwański Dawid , Pisarska-Krawczyk Magdalena , Figlerowicz Magdalena , Zmora Paweł
Published: September 2022

One of the groups most vulnerable to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is healthcare workers (HCWs) who have direct contact with suspected and confirmed coronavirus diseases 2019 (COVID-19) patients. Therefore, this study aimed to (i) conduct a longitudinal analysis of the seroprevalence of SARS-CoV-2 infection among HCWs working in two healthcare units (HCUs) in Poland and (ii) identify anti-SARS-CoV-2 IgG antibody (Ab) response factors following infection and anti-COVID-19 vaccination. The overall seroprevalence increased from 0% at baseline in September 2020 to 37.8% in December 2020. It reached 100% in February 2021 after BNT126b2 (Pfizer New York, NY, USA/BioNTech Mainz, Germany) full vaccination and declined to 94.3% in September 2021. We observed significant differences in seroprevalence between the tested high- and low-risk infection HCUs, with the highest seropositivity among the midwives and nurses at the Gynecology and Obstetrics Ward, who usually have contact with non-infectious patients and may not have the proper training, practice and personal protective equipment to deal with pandemic infections, such as SARS-CoV-2. We also found that anti-SARS-CoV-2 Ab levels after coronavirus infection were correlated with disease outcomes. The lowest Ab levels were found among HCWs with asymptomatic coronavirus infections, and the highest were found among HCWs with severe COVID-19. Similarly, antibody response after vaccination depended on previous SARS-CoV-2 infection and its course: the highest anti-SARS-CoV-2 Ab levels were found in vaccinated HCWs after severe COVID-19. Finally, we observed an approximately 90–95% decrease in anti-SARS-CoV-2 Ab levels within seven months after vaccination. Our findings show that HCWs have the highest risk of SARS-CoV-2 infection, and due to antibody depletion, extra protective measures should be undertaken. In addition, in the context of the emergence of new pathogens with pandemic potential, our results highlight the necessity for better infectious disease training and regular updates for the low infection risk HCUs, where the HCWs have only occasional contact with infectious patients.
Market Review and Technical Properties of Electric Vehicles in Germany
Authors: Hecht Christopher , Spreuer Kai Gerd , Figgener Jan , Sauer Dirk Uwe
Published: September 2022

Electromobility has grown rapidly, and especially in China, Europe, and the United States. Within Europe, Germany is the largest market. Our goal in this paper is to provide a data-driven overview of the key data, including the number of vehicles sold, place of registration, battery capacity, and charging power, in Germany. The results were generated by linking car-registration data with the technical details for each car model. We identified more than 84% of the battery electric vehicles in the fleet, but the uncertainty is larger for plug-in hybrid electric vehicles. The number of sold electric vehicles doubled annually over the last two years. Simultaneously, the battery capacity and charging power per vehicle are rising. Combined, the two effects cause the cumulative battery capacity and charging power of the fleet to grow at an even faster pace. The battery energy built into electric vehicles in Germany registered on 1 August 2022 was 50.5 GWh, of which 9.5 GWh belonged to plug-in hybrids. The combined charging system became the dominant charger type for fast charging in Germany, and only 2% of the vehicle fleet used the competing CHAdeMO standard. To allow fellow researchers to work with the data, we published them free of charge on our data platform mobility charts, and we update the data monthly.
Marginal Zinc Deficiency Aggravated Intestinal Barrier Dysfunction and Inflammation through ETEC Virulence Factors in a Mouse Model of Diarrhea
Authors: Wang Peng , Chen Qianqian , Gan Liping , Du Xinyu , Li Qiyue , Qiao Hanzhen , Zhao Yinli , Huang Jin , Wang Jinrong
Published: September 2022

Zinc is both essential and inhibitory for the pathogenesis of enterotoxigenic Escherichia coli (ETEC). However, the accurate effects and underlying mechanism of marginal zinc deficiency on ETEC infection are not fully understood. Here, a marginal zinc-deficient mouse model was established by feeding mice with a marginal zinc-deficient diet, and ETEC k88 was further administrated to mice after antibiotic disruption of the normal microbiota. Marginal zinc deficiency aggravated growth impairment, diarrhea, intestinal morphology, intestinal permeability, and inflammation induced by ETEC k88 infection. In line with the above observations, marginal zinc deficiency also increased the intestinal ETEC shedding, though the concentration of ETEC in the intestinal content was not different or even decreased in the stool. Moreover, marginal zinc deficiency failed to change the host’s zinc levels, as evidenced by the fact that the serum zinc levels and zinc-receptor GPR39 expression in jejunum were not significantly different in mice with ETEC challenge. Finally, marginal zinc deficiency upregulated the relative expression of virulence genes involved in heat-labile and heat-stable enterotoxins, motility, cellular adhesion, and biofilm formation in the cecum content of mice with ETEC infection. These findings demonstrated that marginal zinc deficiency likely regulates ETEC infection through the virulence factors, whereas it is not correlated with host zinc levels.
How Far Should Poles Be Placed? Selecting Positive Feedback Controllers for Damping and Tracking Applications: A Complete Characterisation
Authors: MacLean James , Aleyaasin Majid , Aphale Sumeet S.
Published: September 2022

Designers of Positive Feedback Controllers (PFCs) arbitrarily place poles into the left-hand half-plane of the complex plane without any detailed understanding of where to stop. This works aims to clearly demonstrate, via rigorous mathematical derivation, the conditions for which pole–placement becomes possible. It also highlights the design limits for the family of second–order PFCs—the most popular PFC group. To this end, the complete family of PFCs, namely, Positive Acceleration Velocity Position Feedback and its derivatives, are analysed in great depth with respect to pure damping and also with respect to combined damping and tracking applications. To showcase the practical value and validity of this work, experimental results on a piezoelectric nanopositioner are also presented and discussed.
Green Public Procurement for Accelerating the Transition towards Sustainable Freight Transport
Authors: Karlsson Hampus , Meland Solveig , Ystmark Bjerkan Kristin , Bjørgen Astrid , Bjørge Nina Møllerstuen , Babri Sahar
Published: September 2022

Requests for emission reduction in the freight transport sector will be more intense in the coming years. One possible strategy to reduce emissions from freight transport is through utilising zero emission vehicles, which requires substantial investments both by transporters and by authorities. This paper examines how green public procurement (GPP) can be used to push the market in an environmentally sustainable direction. For this purpose, interviews with both public authorities and freight service providers are conducted. The results show that GPP is considered a useful tool for public authorities to both boost the uptake of zero emission vehicles and to share the investment costs with freight service providers. However, our study shows that there are differences between small and large municipalities. Moreover, to succeed with GPP, public authorities must prioritise such tasks in their daily routines through political decisions and strategies. Additionally, barriers related to financial possibilities are crucial to handle, as public support schemes are important to reduce costs for all involved stakeholders. Altogether, our paper shows that with the right tools and willingness among both public and private stakeholders, GPP can contribute to the use of more environmentally friendly solutions in the freight transport sector.
Eco-Efficiency of Agriculture in the Amazon Biome: Robust Indices and Determinants
Authors: Rosano-Peña Carlos , Silva João Vitor Borges , Serrano André Luiz Marques , Vieira Filho José Eustáquio Ribeiro , Kimura Herbert
Published: September 2022

This study analyzes the municipal agriculture eco-efficiency in the Amazon biome and the influence of exogenous factors. We use a two-stage data envelopment analysis (DEA) method with bootstrap. The results indicate that: (i) the density curve of the corrected eco-efficiency indices is statistically different from the deterministic score curves, suggesting the presence of bias in the latter; (ii) there is evidence of constant returns, demonstrating that small, medium and large municipalities can be equally eco-efficient; (iii) there are relevant eco-inefficient behaviors, showing that it is possible to increase the products (gross revenue and preserved area) and simultaneously reduce environmental damage (impact on biodiversity and greenhouse gas emission indices) with the same inputs, by replicating the best practices; and (iv) eco-efficiency scores are also substantially affected by exogenous factors. Based on the results, strategies can be defined by decision-makers to harmonize economic growth and environmental preservation; in addition, adaptive policies and actions can be adopted to optimize the sustainability of regional agriculture.
Audience Segmentation in Extension Horticultural Programs
Authors: Wagner Katie , Narine Lendel , Hales Rebecca
Published: September 2022

Cluster analysis was used to segment horticulture clientele using data from a needs assessment. Gardeners were segmented into two groups based on their horticulture practices. These groups were described using several factors including age and time spent maintaining different garden areas. Results from this study indicate the importance of considering the target audience prior to design and implementation of a gardening certificate program.