#### BMC Research Notes

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Tracey J. Harvey, Raul Ayala Davila, Diana Vidovic, Sazia Sharmin, ,
Published: 13 July 2021
BMC Research Notes, Volume 14, pp 1-4; doi:10.1186/s13104-021-05687-5

Abstract:
Objective Sulfation is an essential physiological process that regulates the function of a wide array of molecules involved in brain development. We have previously shown expression levels for the sulfate transporter Slc13a4 to be elevated during postnatal development, and that sulfate accumulation in the brains of Slc13a4 +/− mice is reduced, suggesting a role for this transporter during this critical window of brain development. In order to understand the pathways regulated by cellular sulfation within the brain, we performed a bulk RNA-sequencing analysis of the forebrain of postnatal day 20 (P20) Slc13a4 heterozygous mice and wild-type litter mate controls. Data description We performed an RNA transcriptomic based sequencing screen on the whole forebrain from Slc13a4 +/− and Slc13a4 +/+mice at P20. Differential expression analysis revealed 90 differentially regulated genes in the forebrain of Slc13a4 +/− mice (a p-value of 0.1 was considered as significant). Of these, 55 were upregulated, and 35 were downregulated in the forebrain of heterozygous mice. Moreover, when we stratified further with a ± 1.2 fold-change, we observed 38 upregulated, and 16 downregulated genes in the forebrain of heterozygous mice. This resource provides a useful tool to interrogate which pathways may require elevated sulfate levels to drive normal postnatal development of the brain.
Published: 13 July 2021
BMC Research Notes, Volume 14, pp 1-6; doi:10.1186/s13104-021-05654-0

Abstract:
Objective Canine visceral leishmaniasis (CVL) is the main source of human visceral leishmaniosis (HVL) in Mediterranean region, including Iran and is spread from domestic dogs to Phlebotomine sand flies vectors to humans. To control the transmission of HVL, early and accurate detection of infected dogs is paramount importance despite it remains a confronting challenge. Herein, we evaluated the performance of direct agglutination test (DAT) against gold standard nested polymerase chain reaction (nested-PCR) for CVL diagnosis in symptomatic and asymptomatic domestic dogs from endemic areas of Iran. Results Venous blood samples were collected from dogs without clinical signs (n = 30) and with clinical signs (n = 35) suggestive of Leishmania infantum infection. Among 65 samples examined, Leishmania DNA was detected by nested-PCR in 89.23% (58/65). Furthermore, 86.15% (56/65) nested-PCR positive samples were also DAT positive. The results of the DAT sensitivity test were 96.43% and 96.67% in symptomatic and asymptomatic dogs, respectively, while the specificity was 100.00% and 60.00% in symptomatic and asymptomatic dogs, respectively. The results of this study also pointed out substantial concordance between DAT test and nested-PCR method in both symptomatic dogs (Κ = 0.783; P < 0.001) and asymptomatic dogs (Κ = 0.618; P < 0.001). Thus, DAT represents as a simple and economic tool for initial diagnosis of CVL particularly in endemic areas of the disease.
Correction
Darshan M. Sivaloganathan,
Published: 12 July 2021
BMC Research Notes, Volume 14, pp 1-2; doi:10.1186/s13104-021-05669-7

Published: 12 July 2021
BMC Research Notes, Volume 14, pp 1-4; doi:10.1186/s13104-021-05679-5

Abstract:
Objectives The “Integrating a neonatal healthcare package for Malawi” (IMCHA#108030) project conducted mixed-methods to understand facility-based implementation factors for newborn health innovations in low-resourced health settings. The objective of the two datasets was to evaluate: (a) capacity of quality newborn care in three districts in southern Malawi, and (b) barriers and facilitators the scale up of bubble continuous positive airway pressure (CPAP), a newborn health innovation to support babies with respiratory distress. Data description The Integrated Maternal, Neonatal and Child Quality of Care Assessment and Improvement Tool (version April-2014) is a standardized facility assessment tool developed by the World Health Organization (WHO) that examines quality as well as quantity and availability. The facility survey is complemented by a qualitative dataset of illustrative quotes from health service providers and supervisors on bubble CPAP implementation factors. Research was conducted in one primary health centre (facility assessment only), three district-level hospitals (both) and a tertiary hospital (qualitative only) in southern Malawi. These datasets may be used by other researchers for insights into health systems of low-income countries and implementation factors for the roll-out of neonatal health innovations as well as to frame future research questions or preliminary exploratory research on similar topics.
Tomoaki Mori, Chiaki Warner, Serika Ohno, Koichi Mori, Takamasa Tobimatsu,
Published: 10 July 2021
BMC Research Notes, Volume 14, pp 1-7; doi:10.1186/s13104-021-05683-9

Abstract:
Objective To find mutations that may have recently occurred in Plum pox virus (PPV), we collected six PPV-infected plum/peach trees from the western part of Japan and one from the eastern part. After sequencing the full-length PPV genomic RNAs, we compared the amino acid sequences with representative isolates of each PPV strain. Results All new isolates were found to belong to the PPV-D strain: the six isolates collected from western Japan were identified as the West-Japan strain while the one collected from eastern Japan as the East-Japan strain. Amino acid sequence analysis of these seven isolates suggested that the 1407th and 1529th amino acid residues are characteristic of the West-Japan and the East-Japan strains, respectively. Comparing them with the corresponding amino acid residues of the 47 non-Japanese PPV-D isolates revealed that these amino acid residues are undoubtedly unique. A further examination of the relevant amino acid residues of the other 210 PPV-D isolates collected in Japan generated a new hypothesis regarding the invasion route from overseas and the subsequent diffusion route within Japan: a PPV-D strain might have invaded the western part of Japan from overseas and spread throughout Japan.
Published: 10 July 2021
BMC Research Notes, Volume 14, pp 1-7; doi:10.1186/s13104-021-05680-y

Abstract:
Objective This study aimed to investigate the short-term effect of ovariohysterectomy on urine levels of serotonin and its relation to levels of cortisol, testosterone and progesterone in female dogs. Seven bitches were studied before surgical ovariohysterectomy and then once a week during 4 weeks. Spontaneously voided urine samples were collected and concentration ratios of hormone/creatinine in urine were analysed. Results The bitches had significantly lower levels of cortisol, testosterone, and progesterone 1 week after ovariohysterectomy compared with before and the levels stayed low throughout the study (P ≤ 0.05). Interestingly, serotonin levels tended to increase 4 weeks after surgery (P = 0.08). A positive correlation between cortisol and progesterone was found before and after surgery. After surgery, serotonin was positively correlated with cortisol and progesterone (P ≤ 0.05).
Published: 8 July 2021
BMC Research Notes, Volume 14, pp 1-7; doi:10.1186/s13104-021-05652-2

Abstract:
Objective There has been much discussion and debate around the underreporting of COVID-19 infections and deaths in India. In this short report we first estimate the underreporting factor for infections from publicly available data released by the Indian Council of Medical Research on reported number of cases and national seroprevalence surveys. We then use a compartmental epidemiologic model to estimate the undetected number of infections and deaths, yielding estimates of the corresponding underreporting factors. We compare the serosurvey based ad hoc estimate of the infection fatality rate (IFR) with the model-based estimate. Since the first and second waves in India are intrinsically different in nature, we carry out this exercise in two periods: the first wave (April 1, 2020–January 31, 2021) and part of the second wave (February 1, 2021–May 15, 2021). The latest national seroprevalence estimate is from January 2021, and thus only relevant to our wave 1 calculations. Results Both wave 1 and wave 2 estimates qualitatively show that there is a large degree of “covert infections” in India, with model-based estimated underreporting factor for infections as 11.11 (95% credible interval (CrI) 10.71–11.47) and for deaths as 3.56 (95% CrI 3.48–3.64) for wave 1. For wave 2, underreporting factor for infections escalate to 26.77 (95% CrI 24.26–28.81) and to 5.77 (95% CrI 5.34–6.15) for deaths. If we rely on only reported deaths, the IFR estimate is 0.13% for wave 1 and 0.03% for part of wave 2. Taking underreporting of deaths into account, the IFR estimate is 0.46% for wave 1 and 0.18% for wave 2 (till May 15). Combining waves 1 and 2, as of May 15, while India reported a total of nearly 25 million cases and 270 thousand deaths, the estimated number of infections and deaths stand at 491 million (36% of the population) and 1.21 million respectively, yielding an estimated (combined) infection fatality rate of 0.25%. There is considerable variation in these estimates across Indian states. Up to date seroprevalence studies and mortality data are needed to validate these model-based estimates.
Shweta Sinha, Ajay Prakash, Bikash Medhi, Alka Sehgal, Daniela I. Batovska,
Published: 8 July 2021
BMC Research Notes, Volume 14, pp 1-7; doi:10.1186/s13104-021-05684-8

Abstract:
Objective Malaria is a major global health concern with the urgent need for new treatment alternatives due to the alarming increase of drug-resistant Plasmodium strains. Chalcones and its derivatives are important pharmacophores showing antimalarial activity. Determination of the pharmacokinetic variables at the preliminary step of drug development for any drug candidates is an essential component of in vivo antimalarial efficacy tests. Substandard pharmacokinetic variables are often responsible for insufficient therapeutic effect. Therefore, three chalcone derivatives, 1, 2, and 3, having antimalarial potency were studied further for potential therapeutic efficacy. Results In vivo pharmacokinetic studies of these three derivatives were performed on New Zealand White rabbits. The three derivatives were administered intra-peritoneally or orally at effective dose concentration and blood samples at different time points were collected. The determination of drug concentration was done through reverse phase-high performance liquid chromatography. The peak plasma concentration of derivative 1, 2, and 3 were 1.96 ± 0.46 µg/mL (intraperitoneal route), 69.89 ± 5.49 µg/mL (oral route), and 3.74 ± 1.64 µg/mL (oral route). The results indicate a very low bioavailability of these derivatives. The present study gives a benchmark to advance the investigation of more derivatives in order to revamp the pharmacokinetic variables while maintaining both potency and metabolic constancy.
Published: 8 July 2021
BMC Research Notes, Volume 14, pp 1-11; doi:10.1186/s13104-021-05649-x

Abstract:
Objectives We explore the existence of a fixed point as well as the uniqueness of a mapping in an ordered b-metric space using a generalized $$({\check{\psi }}, \hat{\eta })$$ ( ψ ˇ , η ^ ) -weak contraction. In addition, some results are posed on a coincidence point and a coupled coincidence point of two mappings under the same contraction condition. These findings generalize and build on a few recent studies in the literature. At the end, we provided some examples to back up our findings. Result In partially ordered b-metric spaces, it is discussed how to obtain a fixed point and its uniqueness of a mapping, and also investigated the existence of a coincidence point and a coupled coincidence point for two mappings that satisfying generalized weak contraction conditions.
Published: 7 July 2021
BMC Research Notes, Volume 14, pp 1-4; doi:10.1186/s13104-021-05675-9

Abstract:
Objectives Sengon (Falcataria moluccana) is a popular tree species in community plantation forests in Java, Indonesia due to its fast-growing and multipurpose characteristics. However, without effective control measures sengon plantations are vulnerable to boktor stem borer (Xystrocera festiva) infestation. Previous research found some boktor-resistant trees amid mostly susceptible individuals. Resistant trees have higher levels of enzyme inhibitory activity than susceptible ones. However, efforts to differentiate between the two accessions using microsatellite markers failed to provide satisfactory answers. This dataset was created to study differences in gene expressions between resistant and susceptible accessions, and to identify candidate genes involved in boktor resistance in sengon. Data description RNA was extracted from fresh wood samples collected from two individual trees: one heavily infested with boktor larvae, and the other showing no signs of infestation. The sample trees grow in close proximity to each other within the same plantation. The RNA was sequenced using the BGISEQ-500 platform and produced 78.5 million raw reads. De novo transcriptome were assembled using Trinity and produced 96,164 contigs after filtering and clustering. This transcriptome data is important for understanding pest resistance mechanisms in sengon trees, serving as basis for an improvement program for resistance to boktor pest.