Two Decades of Wildlife Pathogen Surveillance: Case Study of Choclo orthohantavirus and Its Wild Reservoir Oligoryzomys costaricensis

The Costa Rican pygmy rice rat (Oligoryzomys costaricensis) is the primary reservoir of Choclo orthohantavirus (CHOV), the causal agent of hantavirus disease, pulmonary syndrome, and fever in humans in Panama. Since the emergence of CHOV in early 2000, we have systematically sampled and archived rodents from >150 sites across Panama to establish a baseline understanding of the host and virus, producing a permanent archive of holistic specimens that we are now probing in greater detail. We summarize these collections and explore preliminary habitat/virus associations to guide future wildlife surveillance and public health efforts related to CHOV and other zoonotic pathogens. Host sequences of the mitochondrial cytochrome b gene form a single monophyletic clade in Panama, despite wide distribution across Panama. Seropositive samples were concentrated in the central region of western Panama, consistent with the ecology of this agricultural commensal and the higher incidence of CHOV in humans in that region. Hantavirus seroprevalence in the pygmy rice rat was >15% overall, with the highest prevalence in agricultural areas (21%) and the lowest prevalence in shrublands (11%). Host-pathogen distribution, transmission dynamics, genomic evolution, and habitat affinities can be derived from the preserved samples, which include frozen tissues, and now provide a foundation for expanded investigations of orthohantaviruses in Panama.

Comparison of PvLAP5 and Pvs25 qRT-PCR assays for the detection of Plasmodium vivax gametocytes in field samples preserved at ambient temperature from remote malaria endemic regions of Panama

BACKGROUND

As the elimination of malaria in Mesoamerica progresses, detection of Plasmodium vivax using light microscopy (LM) becomes more difficult. Highly sensitive molecular tools have been developed to help determine the hidden reservoir of malaria transmission in low transmission settings. In this study we compare the performance of PvLAP5 and Pvs25 qRT-PCR assays to LM for the detection of Plasmodium vivax gametocytes in field samples preserved at ambient temperature from malaria endemic regions of Panama.

METHODS

For this purpose, we collected a total of 83 malaria field samples during 2017-2020 preserved in RNAprotect (RNAp) of which 63 (76%) were confirmed P. vivax by LM and selected for further analysis. Additionally, 16 blood samples from local healthy malaria smear negative volunteers, as well as, from 15 malaria naïve lab-bred Aotus monkeys were used as controls. To optimize the assays, we first determined the minimum blood volume sufficient for detection of PvLAP5 and Pv18SrRNA using P. vivax infected Aotus blood that was preserved in RNAp and kept either at ambient temperature for up to 8 days before freezing or was snap-frozen at -80° Celsius at the time of bleeding. We then compared the mean differences in gametocyte detection rates of both qRT-PCR assays to LM and performed a multivariate correlation analysis of study variables. Finally, we determined the sensitivity (Se) and specificity (Sp) of the assays at detecting gametocytes compared to LM.

RESULTS

Blood volume optimization indicated that a blood volume of at least 60 μL was sufficient for detection of PvLAP5 and Pv18SrRNA and no significant differences were found between RNA storage conditions. Both PvLAP5 and Pvs25 qRT-PCR assays showed a 37-39% increase in gametocyte detection rate compared to LM respectively. Strong positive correlations were found between gametocytemia and parasitemia and both PvLAP5 and Pvs25 gametocyte markers. However, no significant differences were detected in the Se and Sp of the Pvs25 and PvLAP5 qRT-PCR assays, even though data from control samples suggested Pvs25 to be more abundant than PvLAP5.

CONCLUSIONS

This study shows that the PvLAP5 qRT-PCR assay is as Se and Sp as the gold standard Pvs25 assay and is at least 37% more sensitive than LM at detecting P. vivax gametocytes in field samples preserved in RNAp at ambient temperature from malaria endemic regions of Panama.

AUTHOR SUMMARY

Plasmodium vivax is one of the five species of malaria (P. falciparum, P. malariae, P. ovale and P. knowlesi) that are transmitted to man by the bite of female anopheles mosquitoes. It causes ~14.3 million cases mainly in Southeast Asia, India, the Western Pacific and the Americas annually. In the Americas, malaria remains a major problem in underdeveloped areas and indigenous communities in the Amazon region and eastern Panama, where it is endemic and difficult to eliminate. As malaria elimination progresses, detection of P. vivax by light microscopy (LM) becomes more difficult. Therefore, highly sensitive molecular tools have been developed that use genetic markers for the parasite to help determine the hidden reservoir of malaria transmission. This study compares the performance of two molecular assays based on the genetic markers of mature gametocytes PvLAP5 and Pvs25 with LM. The study shows that the PvLAP5 qRT-PCR assay is as sensitive and specific as the gold standard Pvs25 assay and is at least 37% more sensitive than LM at detecting P. vivax gametocytes. These data suggest that the PvLAP5 qRT-PCR assay can be a useful tool to help determine the hidden reservoir of transmission in endemic foci approaching elimination.

Statistical analysis of thermal conductivity experimentally measured in water-based nanofluids

Nanofluids are suspensions of nanoparticles in a base heat-transfer liquid. They have been widely investigated to boost heat transfer since they were proposed in the 1990s. We present a statistical correlation analysis of experimentally measured thermal conductivity of water-based nanofluids available in the literature. The influences of particle concentration, particle size, temperature and surfactants are investigated. For specific particle materials (alumina, titania, copper oxide, copper, silica and silicon carbide), separate analyses are performed. The conductivity increases with the concentration in qualitative agreement with Maxwell’s theory of homogeneous media. The conductivity also increases with the temperature (in addition to the improvement due to the increased conductivity of water). Surprisingly, only silica nanofluids exhibit a statistically significant effect of the particle size, whereby smaller particles lead to faster heat transfer. Overall, the large scatter in the experimental data prevents a compelling, unambiguous assessment of these effects. Taken together, the results of our analysis suggest that more comprehensive experimental characterizations of nanofluids are necessary to estimate their practical potential.

Population genomics of Plasmodium vivax in Panama to assess the risk of case importation on malaria elimination

Malaria incidence in Panama has plateaued in recent years in spite of elimination efforts, with almost all cases caused by Plasmodium vivax. Notwithstanding, overall malaria prevalence remains low (fewer than 1 case per 1000 persons). We used selective whole genome amplification to sequence 59 P. vivax samples from Panama. The P. vivax samples were collected from two periods (2007-2009 and 2017-2019) to study the population structure and transmission dynamics of the parasite. Imported cases resulting from increased levels of human migration could threaten malaria elimination prospects, and four of the samples evaluated came from individuals with travel history. We explored patterns of recent common ancestry among the samples and observed that a highly genetically related lineage (termed CL1) was dominant among the samples (47 out of 59 samples with good sequencing coverage), spanning the entire period of the collection (2007-2019) and all regions of the country. We also found a second, smaller clonal lineage (termed CL2) of four parasites collected between 2017 and 2019. To explore the regional context of Panamanian P. vivax we conducted principal components analysis and constructed a neighbor-joining tree using these samples and samples collected worldwide from a previous study. Three of the four samples with travel history clustered with samples collected from their suspected country of origin (consistent with importation), while one appears to have been a result of local transmission. The small number of Panamanian P. vivax samples not belonging to either CL1 or CL2 clustered with samples collected from Colombia, suggesting they represent the genetically similar ancestral P. vivax population in Panama or were recently imported from Colombia. The low diversity we observe in Panama indicates that this parasite population has been previously subject to a severe bottleneck and may be eligible for elimination. Additionally, while we confirmed that P. vivax is imported to Panama from diverse geographic locations, the lack of impact from imported cases on the overall parasite population genomic profile suggests that onward transmission from such cases is limited and that imported cases may not presently pose a major barrier to elimination.

Molecular analysis in cytological samples obtained by endobronchial or oesophageal ultrasound guided needle aspiration in non-small cell lung cancer

INTRODUCTION

Cytological samples obtained by endobronchial ultrasound (EBUS) are capital for diagnosis, staging and molecular profile in non-small cell lung carcinoma (NSCLC).

OBJECTIVE

To assess the success rate of complete, partial and individual of molecular analysis in samples obtained by EBUS-guided transbronchial needle aspiration (TBNA) and/or by oesophageal ultrasound-guided fine needle aspiration with an echobronchoscope (EUS-B-FNA) in patients with NSCLC.

METHODS

Prospective study including 90 patients with non-squamous NSCLC, or non-smoking squamous. Cytological samples were classified into two groups. Group 1: PEN membrane slide and/or cell blocks for the determination of mutations of EGFR, KRAS, ERBB2 and BRAF. Group 2: silane coated slides or cell blocks for rearrangements of ALK, ROS1 and MET amplification.

RESULTS

The success rate was 78.6% for 4 molecular alterations (EGFR, KRAS, ALK and ROS1), and 44% for 7 determinations. The individual success rate for EGFR was 97%, KRAS 96.3%, ALK 85%, ROS1 82.3%, ERBB2 71.4%, BRAF 67.7% and MET 81.1%. There were no significant differences (p=0.489) in the number of molecular analyses (1-3 vs. 4) in group 1, depending on the types of samples (cell block vs. PEN membrane slide vs. cell block and PEN membrane slide).

CONCLUSIONS

In patients with NSCLC, the cytological material obtained by ultrasound-guided needle aspiration is sufficient for individual and partial molecular analysis in the vast majority of cases. Membrane slides such as cell blocks are valid samples for molecular analysis.

Ley caótica exponencial de los sistemas dinámicos cardiacos para evaluación del Holter: 16 horas

Introducción. En un estudio previo se realizó una reducción a 16 horas en la evaluación de la ley exponencial de la dinámica cardiaca caótica, mostrando su efectividad en la caracterización de enfermedad y normalidad. Objetivo. Confirmar la aplicabilidad clínica de la ley matemática exponencial para evaluar la dinámica cardiaca caótica a partir de los registros Holter en 16 horas, observando su utilidad diagnóstica al disminuir su tiempo de evaluación. Diseño. Estudio observacional de corte trasversal donde se avaluó los parámetros electrocardiográficos mediante metodologías físico matemáticas inductivas con una confirmación estadística. Metodología. Se tomaron 100 registros Holter con diferentes tipos de patología, y 40 Holter que fueron diagnosticados como normales. Para cada Holter se construyó un atractor caótico, y midiendo sus espacios de ocupación y dimensión fractal se aplicó la evaluación matemática para diferenciar normalidad de enfermedad. Finalmente se realizaron medidas de concordancia diagnostica respecto al estándar de oro. Resultados. La ocupación espacial de todos los atractores estuvieron dentro de los valores esperados; los registros normales presentaron en la rejilla Kp valores entre 205 y 423. Para los registros con enfermedad aguda, estos valores oscilaron entre 21 y 65; y para los registros de enfermedad crónica estos valores estuvieron entre 104 y 195. Los valores de sensibilidad y especificidad fueron de 100% y el coeficiente Kappa fue de 1. Conclusión. El presente estudio muestra la aplicabilidad clínica de esta metodología para la evaluación en 16 horas de registros electrocardiográficos continuos o Holter.

Identification of oestrogen, progesterone receptor and human epidermal growth factor receptor 2 expression in mediastinal metastases of breast cancer obtained by endobronchial ultrasound-guided transbronchial needle aspiration

BACKGROUND

In breast cancer patients, the expression statuses of oestrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2) are crucial in the choice of treatment. Receptor expression in metastatic lesions can differ from the primary tumour. The aim of our study was to analyse the utility of endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) to obtain samples allowing the identification of ER, PR and HER2 expression in patients with mediastinal metastases of breast cancer.

PATIENTS AND METHODS

The clinical files of all patients with a final diagnosis of breast cancer mediastinal metastases diagnosed by EBUS-TBNA in our institution were retrospectively analysed. The ability of EBUS-TBNA to obtain samples that allowed hormone receptor and HER2 expression analysis was calculated.

RESULTS

Twenty-four patients were included. ER, PR and HER2 assessments could be performed in 22, 20 and 22 patients, respectively. In 20 of the 24 patients it was possible to investigate all three types of receptor expression. In the remaining four cases, where ER, PR or HER2 expression tests could not be performed, it was due to a lack of tissue. In cases with adequate results for EBUS-TBNA and the primary tumour agreement was greater for ER (16/19) and HER2 (12/14) than PR (8/17). Based on receptor status, there was a change in the choice of treatment for five patients.

CONCLUSION

In patients with breast cancer mediastinal metastases, ER, PR and HER2 expression can be assessed in samples obtained by EBUS-TBNA whenever a sufficient tissue sample is collected.

O rural na formação e na evolução do Brasil contemporâneo

Resenha:WANDERLEY, Maria de Nazareth Baudel. Um saber necessário: os estudos rurais no Brasil. Campinas: Editora da UNICAMP, 2012. 151p. ISBN: 978-85-268-0957-4

Autosomal recessive IFT57 hypomorphic mutation cause ciliary transport defect in unclassified oral-facial-digital syndrome with short stature and brachymesophalangia

The 13 subtypes of oral-facial-digital syndrome (OFDS) belong to the heterogeneous group of ciliopathies. Disease-causing genes encode for centrosomal proteins, components of the transition zone or proteins implicated in ciliary signaling. A unique consanguineous family presenting with an unclassified OFDS with skeletal dysplasia and brachymesophalangia was explored. Homozygosity mapping and exome sequencing led to the identification of a homozygous mutation in IFT57, which encodes a protein implicated in ciliary transport. The mutation caused splicing anomalies with reduced expression of the wild-type transcript and protein. Both anterograde ciliary transport and sonic hedgehog signaling were significantly decreased in subjects' fibroblasts compared with controls. Sanger sequencing of IFT57 in 13 OFDS subjects and 12 subjects with Ellis-Van Creveld syndrome was negative. This report identifies the implication of IFT57 in human pathology and highlights the first description of a ciliary transport defect in OFDS, extending the genetic heterogeneity of this subgroup of ciliopathies.

Chemical and electrochemical characterization of Nafion containing silver nanoparticles in a stripe-like distribution

Study of the effect of Ag-NPs stripes in Nafion: evaluation of chemical, electrochemical and mechanical properties.

Clinical reappraisal of SHORT syndrome with PIK3R1 mutations: toward recommendation for molecular testing and management

SHORT syndrome has historically been defined by its acronym: short stature (S), hyperextensibility of joints and/or inguinal hernia (H), ocular depression (O), Rieger abnormality (R) and teething delay (T). More recently several research groups have identified PIK3R1 mutations as responsible for SHORT syndrome. Knowledge of the molecular etiology of SHORT syndrome has permitted a reassessment of the clinical phenotype. The detailed phenotypes of 32 individuals with SHORT syndrome and PIK3R1 mutation, including eight newly ascertained individuals, were studied to fully define the syndrome and the indications for PIK3R1 testing. The major features described in the SHORT acronym were not universally seen and only half (52%) had four or more of the classic features. The commonly observed clinical features of SHORT syndrome seen in the cohort included intrauterine growth restriction (IUGR) <10th percentile, postnatal growth restriction, lipoatrophy and the characteristic facial gestalt. Anterior chamber defects and insulin resistance or diabetes were also observed but were not as prevalent. The less specific, or minor features of SHORT syndrome include teething delay, thin wrinkled skin, speech delay, sensorineural deafness, hyperextensibility of joints and inguinal hernia. Given the high risk of diabetes mellitus, regular monitoring of glucose metabolism is warranted. An echocardiogram, ophthalmological and hearing assessments are also recommended.

The CD4:CD8 ratio is associated with markers of age-associated disease in virally suppressed HIV-infected patients with immunological recovery

OBJECTIVES

Inversion of the CD4:CD8 ratio (< 1) has been identified as a hallmark of inmmunosenescence and an independent predictor of mortality in the general population. We aimed to assess the association between the CD4:CD8 ratio and markers of age-associated disease in treated HIV-infected patients with good immunovirological response.

METHODS

A cross-sectional analysis was conducted in 132 HIV-infected adults on antiretroviral therapy (ART), with plasma HIV RNA < 50 HIV-1 RNA copies/mL for at least 1 year, CD4 count > 350 cells/μL and age < 65 years. We analysed the associations between the CD4:CD8 ratio and subclinical atherosclerosis [assessed using carotid intima-media thickness (IMT)], arterial stiffness [assessed using the augmentation index (AIx)], the estimated glomerular filtration rate (eGFR), muscle wasting and sarcopenia [assessed using appendicular lean mass/height(2) (ALM) measured by dual-energy X-ray absorptiometry (DEXA)].

RESULTS

CD4:CD8 ratio inversion was associated with higher IMT, lower eGFR and lower ALM (all values P < 0.05), but not with AIx. In multivariate analyses adjusted for age, sex, hypertriglyceridaemia, tobacco use and cumulative ART exposure, inversion of the CD4:CD8 ratio was independently associated with higher IMT [odds ratio (OR) 2.9; 95% confidence interval (CI) 1.2-7.1], arterial stiffness (OR 4.8; 95% CI 1.0-23.5) and lower eGFR (OR 5.2; 95% CI 1.0-64.4), but not sarcopenia (OR 0.7; 95% CI 0.2-2.7). These associations persisted when models were applied to subjects with nadir CD4 counts > 200 cells/μL and those with CD4 counts > 500 cells/μL.

CONCLUSIONS

The CD4:CD8 ratio in treated HIV-infected subjects with good immunovirological response is independently associated with markers of age-associated disease. Hence, it might be a clinically useful predictor of non-AIDS-defining conditions.

Nature of laminar-turbulence intermittency in shear flows

In pipe, channel, and boundary layer flows turbulence first occurs intermittently in space and time: at moderate Reynolds numbers domains of disordered turbulent motion are separated by quiescent laminar regions. Based on direct numerical simulations of pipe flow we argue here that the spatial intermittency has its origin in a nearest neighbor interaction between turbulent regions. We further show that in this regime turbulent flows are intrinsically intermittent with a well-defined equilibrium turbulent fraction but without ever assuming a steady pattern. This transition scenario is analogous to that found in simple models such as coupled map lattices. The scaling observed implies that laminar intermissions of the turbulent flow will persist to arbitrarily large Reynolds numbers.

Streamwise-localized solutions at the onset of turbulence in pipe flow

Although the equations governing fluid flow are well known, there are no analytical expressions that describe the complexity of turbulent motion. A recent proposition is that in analogy to low dimensional chaotic systems, turbulence is organized around unstable solutions of the governing equations which provide the building blocks of the disordered dynamics. We report the discovery of periodic solutions which just like intermittent turbulence are spatially localized and show that turbulent transients arise from one such solution branch.

[HPV detection in the mouth and cervix of patients with histological diagnosis suggestive of genital infection]

This work evaluated HPV infection in the oral cavity (using oroscopy and exfoliative oral cytology) and its relation to genital infection in women with cytological diagnosis suggestive of HPV infection. The sample consisted of 60 patients who underwent oroscopy, cytology and viral determination in mouth and cervix by PCR using generic primers MY09/MY11 and MPCR. HPV DNA was detected in oral and genital mucosa in 48.33% and 73.3% of patients, respectively, yielding a concordance of 44.2% (k=0.44, moderate agreement). The most common viral types were low risk, especially type 6, found in 86.2% of oral samples and 65.9% of cervical specimens, alone or in combination with other types of low (11) or high oncogenic risk (16, 18, 33), with a concordance of 10.45% (k = 0.1, insignificant agreement). However, in relation to type 6, there was a concordance of 75.86% (k=0.7, high agreement). The cytology of the oral cavity had a sensitivity of 3.5% and a specificity of 93.6%. For oroscopy, sensitivity was 27.6% and specificity was 74.2%. The results indicate that HPV infection in the oral cavity of patients with genital infection could be frequent. The low concordance between HPV types suggests that HPV infection in the mouth and cervix has a different biological behavior.

Measurement of the -3 keV resonance in the reaction 13C(α,n)16O of importance in the s-process

The (13)C(α,n)(16)O reaction is the neutron source for the main component of the s-process, responsible for the production of most nuclei in the mass range 90</~A</~204. It is active inside the helium-burning shell in asymptotic giant branch stars, at temperatures </~10(8) K, corresponding to an energy interval where the (13)C(α,n)(16)O is effective from 140 to 230 keV. In this region, the astrophysical S(E)-factor is dominated by the -3 keV subthreshold resonance due to the 6.356 MeV level in (17)O, giving rise to a steep increase of the S(E)-factor. Notwithstanding that it plays a crucial role in astrophysics, no direct measurements exist inside the s-process energy window. The magnitude of its contribution is still controversial as extrapolations, e.g., through the R matrix and indirect techniques, such as the asymptotic normalization coefficient (ANC), yield inconsistent results. The discrepancy amounts to a factor of 3 or more right at astrophysical energies. Therefore, we have applied the Trojan horse method to the (13)C((6)Li,n(16)O)d quasifree reaction to achieve an experimental estimate of such contribution. For the first time, the ANC for the 6.356 MeV level has been deduced through the Trojan horse method as well as the n-partial width, allowing to attain an unprecedented accuracy in the (13)C(α,n)(16)O study. Though a larger ANC for the 6.356 MeV level is measured, our experimental S(E)-factor agrees with the most recent extrapolation in the literature in the 140-230 keV energy interval, the accuracy being greatly enhanced thanks to this innovative approach.

Edge state in pipe flow experiments

Recent numerical studies suggest that in pipe and related shear flows, the region of phase space separating laminar from turbulent motion is organized by a chaotic attractor, called an edge state, which mediates the transition process. We here confirm the existence of the edge state in laboratory experiments. We observe that it governs the dynamics during the decay of turbulence underlining its potential relevance for turbulence control. In addition we unveil two unstable traveling wave solutions underlying the experimental flow fields. This observation corroborates earlier suggestions that unstable solutions organize turbulence and its stability border.

Stability and angular-momentum transport of fluid flows between corotating cylinders

Turbulent transport of angular momentum is a necessary process to explain accretion in astrophysical disks. Although the hydrodynamic stability of disklike flows has been tested in experiments, results are contradictory and suggest either laminar or turbulent flow. Direct numerical simulations reported here show that currently investigated laboratory flows are hydrodynamically unstable and become turbulent at low Reynolds numbers. The underlying instabilities stem from the axial boundary conditions, affect the flow globally, and enhance angular-momentum transport.

Incidence rate for hantavirus infections without pulmonary syndrome, Panama

During 2001–2007, to determine incidence of all hantavirus infections, including those without pulmonary syndrome, in western Panama, we conducted 11 communitywide surveys. Among 1,129 persons, antibody prevalence was 16.5%–60.4%. Repeat surveys of 476 found that patients who seroconverted outnumbered patients with hantavirus pulmonary syndrome by 14 to 1.

Optimal Order of Markov Models Applied to Bankchecks

The aim of this study is to show that the optimal order of Markov Model of cursive words can be rigorously stated in order to fit the structural properties of the observed data using Akaike information criterion. The method has been tested on French Postal check amounts up to order 4. An original structural representation of cursive words based on graphemes is used. The conditional probability to have a word model given an observed sequence of graphemes is computed independently of the length of the sequence. The recognition results obtained confirm the optimal order found using Akaike criterion.

Proteolysis, lipolysis, volatile compounds, texture, and flavor of Hispánico cheese made using frozen ewe milk curds pressed for different times

Hispánico cheese is manufactured in Spain from a mixture of cow and ewe milk. Production of ewe milk varies throughout the year, with a peak in spring and a valley in summer and autumn. To overcome this seasonal shortage, curd from spring ewe milk may be frozen and used for cheese manufacture some months later. In the present work, ewe milk curds pressed for 15, 60, or 120 min were held at -24 degrees C for 4 mo, thawed, cut to 1-mm pieces, and mixed with fresh cow milk curd for the manufacture of experimental Hispánico cheeses. Control cheese was made from a mixture of pasteurized cow and ewe milk in the same (80:20) proportion. Cheeses, made in duplicate experiments, were analyzed throughout a 60-d ripening period. No significant differences between cheeses were found for lactic acid bacteria counts, dry matter content, hydrophilic peptides, 47 out of 68 vol.tile compounds, texture, and flavor characteristics. On the other hand, differences of minor practical significance between experimental and control cheeses, unrelated to the use of frozen ewe milk curd or the pressing time of ewe milk curd, were found for pH value, aminopeptidase activity, proteolysis, hydrophobic peptides, free amino acids, free fatty acids, and the remaining 21 vol.tile compounds. It may be concluded that the use of frozen ewe milk curd in the manufacture of Hispánico cheese does not alter its main characteristics.