Low Replication Rate Research Articles

Feline infectious peritonitis virus ORF7a is a virulence factor involved in inflammatory pathology in cats

A hyperinflammatory response is a prominent feature of feline infectious peritonitis (FIP), but the mechanisms behind the feline infectious peritonitis virus (FIPV)-induced cytokine storm in the host have not been clarified. Studies have shown that coronaviruses encode accessory proteins that are involved in viral replication and associated with viral virulence, the inflammatory response and immune regulation. Here, we found that FIPV ORF7a gene plays a key role in viral infection and host proinflammatory responses. The recombinant FIPV strains lacking ORF7a (rQS-79Δ7a) exhibit low replication rates in macrophages and do not induce dramatic upregulation of inflammatory factors. Furthermore, through animal experiments, we found that the rQS-79Δ7a strain is nonpathogenic and do not cause symptoms of FIP in cats. Unexpectedly, after three vaccinations with rQS-79Δ7a strain, humoral and cellular immunity was increased and provided protection against virulent strains in cats, and the protection rate reaches 40%. Importantly, our results demonstrated that ORF7a is a key virulence factor that exacerbates FIPV infection and inflammatory responses. Besides, our findings will provide novel implications for future development of live attenuated FIPV vaccines.

Reinterpretation of the results of randomized clinical trials.

Randomized clinical trials (RCTs) shape our clinical practice. Several studies report a mediocre replicability rate of the studied RCTs. Many researchers believe that the relatively low replication rate of RCTs is attributed to the high p value significance threshold. To solve this problem, some researchers proposed using a lower threshold, which is inevitably associated with a decrease in the study power. The results of 22 500 RCTs retrieved from the Cochrane Database of Systematic Reviews (CDSR) were reinterpreted using 2 fixed p significance threshold (0.05 and 0.005), and a recently proposed flexible threshold that minimizes the weighted sum of errors in statistical inference. With p < 0.05 criterion, 28.5% of RCTs were significant; p < 0.005, 14.2%; and p < flexible threshold, 9.9% (2/3 of significant RCTs based on p < 0.05 criterion, were found not significant). Lowering the p cut-off, although decreases the false-positive rate, is not generally associated with a lower weighted sum of errors; the false-negative rate increases (the study power decreases); important treatments may be left undiscovered. Accurate calculation of the optimal p value thresholds needs knowledge of the variance in each study arm, a posteriori. Lowering the p value threshold, as it is proposed by some researchers, is not reasonable as it might be associated with an increase in false-negative rate. Using a flexible p significance threshold approach, although results in a minimum error in statistical inference, might not be good enough too because only a rough estimation may be calculated a priori; the data necessary for the precise computation of the most appropriate p significance threshold are only available a posteriori. Frequentist statistical framework has an inherent conflict. Alternative methods, say Bayesian methods, although not perfect, would be more appropriate for the data analysis of RCTs.

Improved discovery of RNA-binding protein binding sites in eCLIP data using DEWSeq.

Enhanced crosslinking and immunoprecipitation (eCLIP) sequencing is a method for transcriptome-wide detection of binding sites of RNA-binding proteins (RBPs). However, identified crosslink sites can deviate from experimentally established functional elements of even well-studied RBPs. Current peak-calling strategies result in low replication and high false positive rates. Here, we present the R/Bioconductor package DEWSeq that makes use of replicate information and size-matched input controls. We benchmarked DEWSeq on 107 RBPs for which both eCLIP data and RNA sequence motifs are available and were able to more than double the number of motif-containing binding regions relative to standard eCLIP processing. The improvement not only relates to the number of binding sites (3.1-fold with known motifs for RBFOX2), but also their subcellular localization (1.9-fold of mitochondrial genes for FASTKD2) and structural targets (2.2-fold increase of stem-loop regions for SLBP. On several orthogonal CLIP-seq datasets, DEWSeq recovers a larger number of motif-containing binding sites (3.3-fold). DEWSeq is a well-documented R/Bioconductor package, scalable to adequate numbers of replicates, and tends to substantially increase the proportion and total number of RBP binding sites containing biologically relevant features.

Genotypic and Phenotypic Characterization of Replication-Competent HIV-2 Isolated from Controllers and Progressors.

Although some individuals with HIV-2 develop severe immunodeficiency and AIDS-related complications, most may never progress to AIDS. Replication-competent HIV-2 isolated from asymptomatic long-term non-progressors (controllers) have lower replication rates than viruses from individuals who progress to AIDS (progressors). To investigate potential retroviral factors that correlate with disease progression in HIV-2, we sequenced the near full-length genomes of replication-competent viruses previously outgrown from controllers and progressors and used phylogeny to seek genotypic correlates of disease progression. We validated the integrity of all open reading frames and used cell-based assays to study the retroviral transcriptional activity of the long terminal repeats (LTRs) and Tat proteins of HIV-2 from controllers and progressors. Overall, we did not identify genotypic defects that may contribute to HIV-2 non-progression. Tat-induced, LTR-mediated transcription was comparable between viruses from controllers and progressors. Our results were obtained from a small number of participants and should be interpreted accordingly. Overall, they suggest that progression may be determined before or during integration of HIV-2.

Insights into ageing rates comparison across tissues from recalibrating cerebellum DNA methylation clock

DNA methylation (DNAm)-based age clocks have been studied extensively as a biomarker of human ageing and a risk factor for age-related diseases. Despite different tissues having vastly different rates of proliferation, it is still largely unknown whether they age at different rates. It was previously reported that the cerebellum ages slowly; however, this claim was drawn from a single clock using a relatively small sample size and so warrants further investigation. We collected the largest cerebellum DNAm dataset (N = 752) to date. We found the respective epigenetic ages are all severely underestimated by six representative DNAm age clocks, with the underestimation effects more pronounced in the four clocks whose training datasets do not include brain-related tissues. We identified 613 age-associated CpGs in the cerebellum, which accounts for only 14.5% of the number found in the middle temporal gyrus from the same population (N = 404). From the 613 cerebellum age-associated CpGs, we built a highly accurate age prediction model for the cerebellum named CerebellumClockspecific (Pearson correlation=0.941, MAD=3.18 years). Ageing rate comparisons based on the two tissue-specific clocks constructed on the 201 overlapping age-associated CpGs support the cerebellum has younger DNAm age. Nevertheless, we built BrainCortexClock to prove a single DNAm clock is able to unbiasedly estimate DNAm ages of both cerebellum and cerebral cortex, when they are adequately and equally represented in the training dataset. Comparing ageing rates across tissues using DNA methylation multi-tissue clocks is flawed. The large underestimation of age prediction for cerebellums by previous clocks mainly reflects the improper usage of these age clocks. There exist strong and consistent ageing effects on the cerebellar methylome, and we suggest the smaller number of age-associated CpG sites in cerebellum is largely attributed to its extremely low average cell replication rates.

Study on skin infection model of Staphylococcus aureus based on analytic hierarchy process and Delphi method

PurposeInfectious skin diseases are a type of inflammatory skin lesions caused by pathogenic microorganisms. Because of the uncertainty of methodology, the skin infection model usually have low replication rate and lack of good evaluation system. We aimed to establish multi-index and comprehensive evaluation method for Staphylococcus aureus (S.aureus) skin-infection models through Analytic hierarchy process (AHP) and Delphi method, and screen high quality animal models through it. Materials and methodsFirstly, the evaluation indicators of skin infection were collected basing on literature research. The weight of the evaluation indicators were decided according to AHP and Delphi method. Then different ulcer models (mouse or rat) infected by S. aureus were selected as the research objects. ResultsThe evaluation indicators were classified into four groups of criteria (including ten sub-indicators) and given different weights, physical sign changes (0.0518), skin lesion appearance (0.2934), morphological observation (0.3184), etiological examination (0.3364). Through the evaluation system, we screened and found that the mouse ulcer model which caused by a round wound and 1.0 × 1010 CFU/mL (0.1 mL) bacterial concentration got the highest comprehensive score, and also found that the model which caused by a 1.5 cm-round wound and 1.0 × 1010 CFU/mL (0.2 mL) maybe the best rat ulcer model. ConclusionsThis study has established an evaluation system based on AHP and Delphi method, also provided the best skin ulcer models selected by this system, the models are suitable for disease research and drug development research of skin ulcer.

The synergistic effect of genetic and environmental factors in the development of attention-deficit/hyperactivity disorder symptoms in children and adolescents

Gene-environment interactions (GxE) have been increasingly explored in psychiatry but with low replication rates. Attention-deficit/hyperactivity disorder (ADHD) is a suitable candidate for studying GxE due to its high heritability and well-defined environmental risk factors. Here, we explored GxE using polygenic risk score (PRS) to represent the genetic liability to ADHD (ADHD-PRS) and environmental risk score (ERS) to represent the combined effects of environmental risk factors. We analyzed longitudinal data of 2,046 individuals (6-14 years of age at baseline and 14-23 at the last follow-up) from the Brazilian High-Risk Cohort Study for Psychiatric Disorders. Psychiatric evaluation included the Child Behavior Checklist and the Strength and Difficulties Questionnaire. Statistical analyses were performed using mixed-effects models. We observed statistically significant interactions between ADHD-PRS and ERS, suggesting that environmental and genetic factors act synergistically in the development of ADHD symptoms. These effects were not present for depression or anxiety symptoms. No evidence of GxE correlation was detected. Mechanistically, our findings suggest that environmental stressors modulate the genetic risk for ADHD. Future studies should investigate whether the reduction of environmental risks can prevent the development of symptoms of ADHD, especially in children with a family history of the disorder.

New insights into diversity of the upper respiratory tract microbiota and its relationship with SARS-CoV-2 viral load in the nasopharyngeal epithelial cells in patients with COVID-19.

The effects of SARS‑CoV‑2 infection on the composition of the upper respiratory tract (URT) microbiota are yet to be established, and more attention to this topic is needed. The study aimed to assess the bacterial profile and the possible association between the URT microbiota composition and the SARS‑CoV‑2 viral load. Nasopharyngeal swabs were taken from 60 adult patients with SARS‑CoV‑2 infection who were divided into 3 groups based on the quantification cycle (Cq) value in the quantitative polymerase chain reaction test: group I (n = 20), Cq lower than or equal to 31 (high replication rate); group II (n = 20), Cq greater than 31 and lower than 38 (low replication rate), and group III (n = 20), Cq higher than or equal to 38 (virus eliminated from the nasopharyngeal epithelial cells). The obtained genetic libraries of 16S rRNA were sequenced and taxonomic diversity profiling was performed to determine the α- and β‑biodiversity in each group. A significantly lower abundance of Prevotella species was noted in group I, as compared with groups II and III. Akkermansia muciniphila, Faecalibacterium prausnitzii, Fusicatenibacterium saccharivorans, and Bacteroides dorei abundance was characteristic of and significantly greater in group I than in groups II and III. Overall, the microbiota composition was the most diverse in group I, whereas groups II and III were more homogenous in terms of taxonomic diversity. The arbitrary division of patients according to the SARS‑CoV‑2 viral load was reflected in diverse composition of their bacterial microbiota, which implies an association between these 2 factors. The patients with a low viral replication rate and those who eliminated the virus from the epithelial cells belonged to a group with a less diverse microbiota community than the patients with a high viral replication rate.

Refocus on stopping! Replication of reduced right amygdala reactivity to negative, visual primes during inhibition of motor responses

Several practices contribute to low replication rates in neuroimaging; unreported analytical flexibility, publication biases, the lack of data sharing, the use of underpowered samples, and many more. In the current study, we tried to replicate emotional interference during motor response inhibition in a sample of N = 57 healthy students at a different study site. The failure to inhibit impulses in highly emotional situations is a characteristic of many mental disorders. Apart from this, exaggerated emotional responses can debilitate social and cognitive functioning in healthy participants. Functional magnetic resonance imaging was acquired while participants performed a combined stop signal and Simon task with neutral and negative, visual primes. Negative, visual primes led to prolonged reaction times and stopping latencies. FMRI data showed that negative, visual primes led to increased activation in the bilateral amygdala and enhanced visual processing. Consistent with other studies on emotional interference, we observed decreased activation in regions of the central-executive network and reduced deactivation in the ventromedial prefrontal cortex for negative trials. Replicating the results of our former studies (Kampa et al., 2018, 2020), we found an interaction effect in the right amygdala. Concurrent inhibition of motor responses thus seemed to downregulate the processing of negative stimuli in the right amygdala. We performed exploratory brain-behavior correlation analyses to test if increased right amygdala activation to negative primes was associated with a decrement in performance. We found no such relationship; however, because of the low statistical power, we cannot decide conclusively on the relationship between the right amygdala, and behavioral interference. We discuss potential solutions for overcoming the power problem associated with brain-behavior correlation analyses.

Variation and Covariation in Large-scale Replication Projects: An Evaluation of Replicability

Over the last decade, large-scale replication projects across the biomedical and social sciences have reported relatively low replication rates. In these large-scale replication projects, replication has typically been evaluated based on a single replication study of some original study and dichotomously as successful or failed. However, evaluations of replicability that are based on a single study and are dichotomous are inadequate, and evaluations of replicability should instead be based on multiple studies, be continuous, and be multi-faceted. Further, such evaluations are in fact possible due to two characteristics shared by many large-scale replication projects. In this article, we provide such an evaluation for two prominent large-scale replication projects, one which replicated a phenomenon from cognitive psychology and another which replicated 13 phenomena from social psychology and behavioral economics. Our results indicate a very high degree of replicability in the former and a medium to low degree of replicability in the latter. They also suggest an unidentified covariate in each, namely ocular dominance in the former and political ideology in the latter, that is theoretically pertinent. We conclude by discussing evaluations of replicability at large, recommendations for future large-scale replication projects, and design-based model generalization. Supplementary materials for this article are available online.

Poor Agreement Between Next-Generation DNA Sequencing and Bacterial Cultures in Orthopaedic Trauma Procedures.

Next-generation DNA sequencing (NGS) detects bacteria-specific DNA corresponding to the 16S ribosomal RNA gene and can identify bacterial presence with greater accuracy than traditional culture methods. The clinical relevance of these findings is unknown. The purpose of the present study was to compare the results from bacterial culture and NGS in order to characterize the potential use of NGS in orthopaedic trauma patients. A prospective cohort study was performed at a single academic, level-I trauma center. Three patient groups were enrolled: (1) patients undergoing surgical treatment of acute closed fractures (presumed to have no bacteria), (2) patients undergoing implant removal at the site of a healed fracture without infection, and (3) patients undergoing a first procedure for the treatment of a fracture nonunion who might or might not have subclinical infection. Surgical site tissue was sent for culture and NGS. The proportions of culture and NGS positivity were compared among the groups. The agreement between culture and NGS results was assessed with use of the Cohen kappa statistic. Bacterial cultures were positive in 9 of 111 surgical sites (110 patients), whereas NGS was positive in 27 of 111 surgical sites (110 patients). Significantly more cases were positive on NGS as compared with culture (24% vs. 8.1%; p = 0.001), primarily in the acute closed fracture group. No difference was found in terms of the percent positivity of NGS when comparing the acute closed fracture, implant removal, and nonunion groups. With respect to bacterial identification, culture and NGS agreed in 73% of cases (κ = 0.051; 95% confidence interval, -0.12 to 0.22) indicating only slight agreement compared with expected chance agreement of 50%. NGS identified bacterial presence more frequently than culture, but with only slight agreement between culture and NGS. It is possible that the increased frequency of bacterial detection with molecular methods is reflective of biofilm presence on metal or colonization with nonpathogenic bacteria, as culture methods have selection pressure posed by restrictive, artificial growth conditions and there are low metabolic activity and replication rates of bacteria in biofilms. Our data suggest that NGS should not currently substitute for or complement conventional culture in orthopaedic trauma cases with low suspicion of infection. Diagnostic Level II. See Instructions for Authors for a complete description of levels of evidence.

Profiling Hepatitis B Viral Load: Treatment and Epidemiological Implications in a West African Hospital

Background: Chronic hepatitis B virus (HBV) infection is one of the largest public health problems with nearly 350 million chronic carriers and 500,000 deaths each year. These deaths are most often associated with disease progression to cirrhosis or hepatocellular carcinoma, which some studies have shown is associated with long-term viral replication in chronic carriers. Viral load quantification, a key element of disease management, is expensive and difficult to access. Viral load plays a crucial role in patient classification and treatment initiation. Four years after the implementation of viral load platform, the objective of this study was to assess viral load profile in HBs chronic carriers in a sub-Saharan Hospital and to determine the potential impact of this distribution on preventive and therapeutic strategies against hepatitis B infection. Materials and Method: The study was carried out between April 2016 and October 2020 in the laboratory of the PRINCIPAL Hospital in Dakar. All patients referred for HBV DNA viral load testing following a positive AgHBs test were included. Incomplete medical records were excluded from the study. Only the first quantification test performed on each patient is recorded. DNA extraction was performed with COBAS AmpliPrep (Roche Molecular Systems, Inc., Branchburg, NJ, USA). Amplification was performed using COBAS TaqMan48 (Roche Molecular Systems, Inc., Branchburg, NJ, USA). Data were collected from the laboratory’s computer system and entered into Microsoft Excel (2007). Statistical analyzes were performed using Epi-Info 7 software. Results: A total of 3002 patients, 76.1% (2285/3002) men and 33.9% (717/3002) women, were included in the study. Young adults were most represented among the subjects (23.2%) and (20.1%) in the age groups 25 - 30 and 30 - 35. The majority (52.7%) of patients had viral loads between 20 and 2000 IU. Patients with undetectable viral loads and patients with viral loads below 20 IU comprised 14.6% and 7.53% of the study population, respectively. Patients with viral loads between 2000 and 20,000 IU/ml and those with viral loads greater than 20,000 IU/ml represented 16.3% and 8.89% of the study population, respectively. Viral load was higher in males than females, with corresponding median and interquartile ranges of 2.7 log IU (2.2, 2.75) and 2.23 log IU (2.1, 2.4) (p < 0.001). This viral load also decreases with age. There were more patients with an undetectable viral load over 30 years than those under 30 years, with a ratio of 1.62 (IC95% = 1.29 - 2.05) (p = 0.009). Conclusion: This study shows a successful implementation of virus quantification in the context of resource-constrained countries. The second finding of this study is the high prevalence of adolescents with high plasma viral loads, indicating the need for additional investigations to initiate therapy. The large population with a low HBV replication rate points to the problem of financing follow-up care for chronically infected people. Studying this population in the context of an unknown genomic profile indicates the need to deepen virological laboratory testing through a sequencing platform. Finally, regular viral load reporting in major hospital cities could be a powerful and accessible management tool for hepatitis B programs in resource-constrained countries.

Replication target selection in clinical psychology: A Bayesian and qualitative reevaluation.

Low replication rates and ill-informed selection of replication targets can harm clinical practice. We take a pragmatic approach to suggest which studies to replicate in clinical psychology. We propose a 2-step process entailing a quantitative assessment of evidence strength using Bayes factors, and a qualitative assessment concerning theory and methodology. We provide proof of concept on a series of published clinical studies. We included 75 studies with 94 individual effects. Step 1 yielded 42 effects (45%) with Bayes Factors suggesting ambiguous evidence or absence of an effect. These 42 effects were qualitatively assessed by 2 raters. We illustrate their decision process and discuss advantages and disadvantages of the proposed steps.

The Costs of HARKing

Kerr ([1998]) coined the term ‘HARKing’ to refer to the practice of ‘hypothesizing after the results are known’. This questionable research practice has received increased attention in recent years because it is thought to have contributed to low replication rates in science. The present article discusses the concept of HARKing from a philosophical standpoint and then undertakes a critical review of Kerr’s ([1998]) twelve potential costs of HARKing. It is argued that these potential costs are either misconceived, misattributed to HARKing, lacking evidence, or that they do not take into account pre- and post-publication peer review and public availability to research materials and data. It is concluded that it is premature to conclude that HARKing has led to low replication rates.

An experimental design tool to optimize inference precision in data-driven mathematical models of bacterial infections in vivo.

The management of bacterial diseases calls for a detailed knowledge about the dynamic changes in host-bacteria interactions. Biological insights are gained by integrating experimental data with mechanistic mathematical models to infer experimentally unobservable quantities. This inter-disciplinary field would benefit from experiments with maximal information content yielding high-precision inference. Here, we present a computationally efficient tool for optimizing experimental design in terms of parameter inference in studies using isogenic-tagged strains. We study the effect of three experimental design factors: number of biological replicates, sampling timepoint selection and number of copies per tagged strain. We conduct a simulation study to establish the relationship between our optimality criterion and the size of parameter estimate confidence intervals, and showcase its application in a range of biological scenarios reflecting different dynamics patterns observed in experimental infections. We show that in low-variance systems with low killing and replication rates, predicting high-precision experimental designs is consistently achieved; higher replicate sizes and strategic timepoint selection yield more precise estimates. Finally, we address the question of resource allocation under constraints; given a fixed number of host animals and a constraint on total inoculum size per host, infections with fewer strains at higher copies per strain lead to higher-precision inference.

High-throughput analysis suggests differences in journal false discovery rate by subject area and impact factor but not open access status

BackgroundA low replication rate has been reported in some scientific areas motivating the creation of resource intensive collaborations to estimate the replication rate by repeating individual studies. The substantial resources required by these projects limits the number of studies that can be repeated and consequently the generalizability of the findings. We extend the use of a method from Jager and Leek to estimate the false discovery rate for 94 journals over a 5-year period using p values from over 30,000 abstracts enabling the study of how the false discovery rate varies by journal characteristics.ResultsWe find that the empirical false discovery rate is higher for cancer versus general medicine journals (p = 9.801E−07, 95% CI: 0.045, 0.097; adjusted mean false discovery rate cancer = 0.264 vs. general medicine = 0.194). We also find that false discovery rate is negatively associated with log journal impact factor. A two-fold decrease in journal impact factor is associated with an average increase of 0.020 in FDR (p = 2.545E−04). Conversely, we find no statistically significant evidence of a higher false discovery rate, on average, for Open Access versus closed access journals (p = 0.320, 95% CI − 0.015, 0.046, adjusted mean false discovery rate Open Access = 0.241 vs. closed access = 0.225).ConclusionsOur results identify areas of research that may need additional scrutiny and support to facilitate replicable science. Given our publicly available R code and data, others can complete a broad assessment of the empirical false discovery rate across other subject areas and characteristics of published research.

Tyrosine Kinase Inhibitors Play an Antiviral Action in Patients Affected by Chronic Myeloid Leukemia: A Possible Model Supporting Their Use in the Fight Against SARS-CoV-2.

SARS-CoV-2 is the viral agent responsible for the pandemic that in the first months of 2020 caused about 400,000 deaths. Among compounds proposed to fight the SARS-CoV-2-related disease (COVID-19), tyrosine kinase inhibitors (TKIs), already effective in Philadelphia-positive acute lymphoblastic leukemia (Ph+ ALL) and chronic myeloid leukemia (CML), have been proposed on the basis of their antiviral action already demonstrated against SARS-CoV-1. Very few cases of COVID-19 have been reported in Ph+ ALL and in CML Italian cohorts; authors suggested that this low rate of infections might depend on the use of TKIs, but the biological causes of this phenomenon remain unknown. In this study, the CML model was used to test if TKIs would sustain or not the viral replication and if they could damage patient immunity. Firstly, the infection and replication rate of torquetenovirus (TTV), whose load is inversely proportional to the host immunological control, have been measured in CML patients receiving nilotinib. A very low percentage of subjects were infected at baseline, and TTV did not replicate or at least showed a low replication rate during the follow-up, with a mean load comparable to the measured one in healthy subjects. Then, after gene expression profiling experiments, we found that several “antiviral” genes, such as CD28 and IFN gamma, were upregulated, while genes with “proviral” action, such as ARG-1, CEACAM1, and FUT4, were less expressed during treatment with imatinib, thus demonstrating that TKIs are not detrimental from the immunological point of view. To sum up, our data could offer some biological explanations to the low COVID-19 occurrence in Ph+ ALL and CML patients and sustain the use of TKIs in COVID-19, as already proposed by several international ongoing studies.

Replication kinetics of a CHIKV Asian strain with 76 aa duplication in the nsP3 HVD, in comparison to the wild-type Asian and ECSA strains

Introduction: Chikungunya virus (CHIKV) is a mosquito-borne alphavirus which causes fever, rash and polyarthralgia. CHIKV has expanded its circulating regions to the Indian Ocean islands, Europe, Americas and Southeast Asia. Two CHIKV lineages, the ASIAN and ECSA are circulating in Malaysia. In 2009, a CHIKV strain with a 76 amino acid (aa) duplication in its nsP3 hypervariable domain (HVD), identified as CHIKvASIAN09MUM-Dup+ was isolated from a patient co-infected with DENV-2. Indels and duplication have been found in many other alphaviruses, and suggested to play a role in the survivality of the viruses. Objectives: We aim to compare and relate the replication kinetics and virulency in-vitro of CHIKvASIAN09MUM-Dup+ with the wild-type Asian and ECSA strains. Methods &amp; Results: Genotypic analysis was conducted on three CHIKV strains in Malaysia, the CHIKvASIAN06UM-Dup-, CHIKvECSA08UM-Dup- and CHIKvASIAN09MUM-Dup+. We found that CHIKvASIAN09MUM-Dup+ has significant low replication rates in Vero, C6/36 and Rhabdosarcoma cells as compared to the wild-type strains. The highest titers were reached by CHIKvASIAN09MUM-Dup+ in all cells are 6.5 to 6.75 log10 TCID50/mL, which is 100 fold lower compared to the wild-type strains. Conclusion: The significantly low replication rate of Dup+ strain in all the cells, maybe suggestive to be due to co-infection and co-existence with DENV, where the aa duplication may play a role in overcoming competitive suppression. This preliminary finding agrees with reported events, where alphaviruses use insertion, deletion and duplication of amino acid in nsP3 HVD as strategies to influence replication in host, viral virulency, pathogenesis and survivality for evolution adaptation.

Cathelicidin bovine myeloid antimicrobial peptide (BMAP) 28 is involved in the inflammatory response against alpha-herpesviruses in the bovine nervous system

The role of the local innate immune response in the neuropathogenesis of bovine herpesvirus (BoHV) type 1 and 5 remains largely unknown. This study determined the gene transcriptional expression of relevant bovine cathelicidins, TNFα and IFNβ in the nervous system of experimentally-infected cattle during the different stages of BoHV-1 and BoHV-5 infectious cycle. We studied the modulation of bovine myeloid antimicrobial peptide (BMAP) 27 and 28 by alpha-herpesviruses during acute infection of the central nervous system (CNS). However, BMAP28 was the main cathelicidin modulated. BoHV-5 supressed BMAP28 expression mainly in frontal cortex and cervical medulla whereas BoHV-1 slightly induced the expression of cathelicidins in the olfactory and posterior cortex. The differences in the regulation of the innate response are likely related to distinct replication rates of both alpha-herpesviruses in the CNS. During latency and reactivation, BoHV-1 and -5 decreased BMAP28 and BMAP27 expression, accompanied by high levels of TNFα and IFNβ transcripts in the posterior brain region and medulla during BoHV reactivation. In terms of cytokines, a remarkably overexpression of IFNβ was induced by BoHV-5 (133.8-fold). In trigeminal ganglion (TG) both alpha-herpesviruses induced cathelidicins gene expression at all stages of the infection cycle, while only acute BoHV-5 infection increased TNFα (129-fold) mRNA levels. This study suggests that the pronounced downregulation of BMAP28 in BoHV-5-acutely-infected CNS is due to a decreased immune stimulation during viral infection, favouring its establishment in the CNS with a low replication rate until latency. Thus, cathelicidins, together with IFNβ and TNFα, are differentially regulated by BoHV-5 and BoHV-1 infections and this regulation is dependent on the stage of virus infection in the bovine nervous system.

The (im)precision of scholarly consumer behavior research

Knowing related empirical facts as precisely as possible is crucial to knowledge development. Does the sampling precision of published consumer research ensure it contributes meaningfully to marketing science? To answer this question, the sampling precision of four consumer-centric journals selected for their relative impact factors—Journal of Consumer Research (JCR), Journal of Consumer Psychology (JCP), Journal of Consumer Marketing (JCM), and International Journal of Consumer Studies (IJCS)—is compared. Based on a recently developed a priori procedure, analyses of articles published between 2000 and 2016 determined the precision of the reported sample means that estimate corresponding population means. Results show studies in all journals lack sufficient precision, with JCR and JCP studies half as precise as JCM and IJCS studies. Sampling precision’s value to scientific advancement partly reflects its connection to replication probabilities. Given low replication rates, the most cited consumer-related studies, which strongly influence subsequent research, may be the most misdirecting.