An accurate aging clock developed from large-scale gut microbiome and human gene expression data

Accurate measurement of the biological markers of the aging process could provide an "aging clock" measuring predicted longevity and enable the quantification of the effects of specific lifestyle choices on healthy aging. Using machine learning techniques, we demonstrate that chronological age can be predicted accurately from (1) the expression level of human genes in capillary blood and (2) the expression level of microbial genes in stool samples. The latter uses a very large metatranscriptomic dataset, stool samples from 90,303 individuals, which arguably results in a higher quality microbiome-aging model than prior work. Our analysis suggests associations between biological age and lifestyle/health factors, e.g., people on a paleo diet or with IBS tend to have higher model-predicted ages and people on a vegetarian diet tend to have lower model-predicted ages. We delineate the key pathways of systems-level biological decline based on the age-specific features of our model.

Detecting salivary host and microbiome RNA signature for aiding diagnosis of oral and throat cancer

OBJECTIVE

Oral squamous cell carcinoma (OSCC) and oropharyngeal squamous cell carcinoma (OPSCC) can go undetected resulting in late detection and poor outcomes. We describe the development and validation of CancerDetect for Oral & Throat cancer™ (CDOT), to detect markers of OSCC and/or OPSCC within a high-risk population.

MATERIAL AND METHODS

We collected saliva samples from 1,175 individuals who were 50 years or older, or adults with a tobacco use history. 945 of those were used to train a classifier using machine learning methods, resulting in a salivary microbial and human metatranscriptomic signature. The classifier was then independently validated on the 230 remaining samples prospectively collected and unseen by the classifier, consisting of 20 OSCC (all stages), 76 OPSCC (all stages), and 134 negatives (including 14 pre-malignant).

RESULTS

On the validation cohort, the specificity of the CDOT test was 94 %, sensitivity was 90 % for participants with OSCC, and 84.2 % for participants with OPSCC. Similar classification results were observed among people in early stage (stages I & II) vs late stage (stages III & IV).

CONCLUSIONS

CDOT is a non-invasive test that can be easily administered in dentist offices, primary care centres and specialised cancer clinics for early detection of OPSCC and OSCC. This test, having received FDA's breakthrough designation for accelerated review, has the potential to enable early diagnosis, saving lives and significantly reducing healthcare expenditure.

The salivary metatranscriptome as an accurate diagnostic indicator of oral cancer

Despite advances in cancer treatment, the 5-year mortality rate for oral cancers (OC) is 40%, mainly due to the lack of early diagnostics. To advance early diagnostics for high-risk and average-risk populations, we developed and evaluated machine-learning (ML) classifiers using metatranscriptomic data from saliva samples (n = 433) collected from oral premalignant disorders (OPMD), OC patients (n = 71) and normal controls (n = 171). Our diagnostic classifiers yielded a receiver operating characteristics (ROC) area under the curve (AUC) up to 0.9, sensitivity up to 83% (92.3% for stage 1 cancer) and specificity up to 97.9%. Our metatranscriptomic signature incorporates both taxonomic and functional microbiome features, and reveals a number of taxa and functional pathways associated with OC. We demonstrate the potential clinical utility of an AI/ML model for diagnosing OC early, opening a new era of non-invasive diagnostics, enabling early intervention and improved patient outcomes.

The Role of Movement Patterns in Epidemic Models on Complex Networks

In this paper, we analyze the influence of the usual movement variables on the spread of an epidemic. Specifically, given two spatial topologies, we can deduce which topology produces less infected individuals. In particular, we determine the topology that minimizes the overall number of infected individuals. It is worth noting that we do not assume any of the common simplifying assumptions in network theory such as all the links have the same diffusion rate or the movement of the individuals is symmetric. Our main conclusion is that the degree of mobility of the population plays a critical role in the spread of a disease. Finally, we derive theoretical insights to management of epidemics.

Interdisciplinary Approaches to COVID-19

The coronavirus disease 2019 (COVID-19) pandemic has been a significant concern worldwide. The pandemic has demonstrated that public health issues are not merely a health concern but also affect society as a whole. In this chapter, we address the importance of bringing together the world's scientists to find appropriate solutions for controlling and managing the COVID-19 pandemic. Interdisciplinary cooperation, through modern scientific methods, could help to handle the consequences of the pandemic and to avoid the recurrence of future pandemics.

Optimal Network Architectures for Spatially Structured Populations with Heterogeneous Diffusion

The motivation of this article is to derive new management guidelines to maximize the overall population size using popular management and conservation strategies, such as protected marine areas and ecological corridors. These guidelines are based on the identification of the network architectures for which the total population size is maximized. Describing the biological roles of the typical network variables in the fate of the population is a classic problem with many practical applications. This article suggests that the optimal network architecture relies heavily on the degree of mobility of the population. The recommended network architecture for populations with reduced mobility (in the absence of cost of dispersal and landscapes made up of many sources) is a graph with a patch that has routes toward any other patch with a lower growth rate. However, for highly mobile populations there are many possible network architectures for which the total population size is maximized (e.g., any cyclic graph). We have paid special attention to species with symmetric movement in heterogeneous landscapes. A striking result is that the network architecture does not have any influence on the total population size for highly mobile populations when any pair of different patches can be connected by a sequence of paths.

The urgent need for integrated science to fight COVID-19 pandemic and beyond

The COVID-19 pandemic has become the leading societal concern. The pandemic has shown that the public health concern is not only a medical problem, but also affects society as a whole; so, it has also become the leading scientific concern. We discuss in this treatise the importance of bringing the world's scientists together to find effective solutions for controlling the pandemic. By applying novel research frameworks, interdisciplinary collaboration promises to manage the pandemic's consequences and prevent recurrences of similar pandemics.

Global phylogeography and ancient evolution of the widespread human gut virus crAssphage

Microbiomes are vast communities of microorganisms and viruses that populate all natural ecosystems. Viruses have been considered to be the most variable component of microbiomes, as supported by virome surveys and examples of high genomic mosaicism. However, recent evidence suggests that the human gut virome is remarkably stable compared with that of other environments. Here, we investigate the origin, evolution and epidemiology of crAssphage, a widespread human gut virus. Through a global collaboration, we obtained DNA sequences of crAssphage from more than one-third of the world's countries and showed that the phylogeography of crAssphage is locally clustered within countries, cities and individuals. We also found fully colinear crAssphage-like genomes in both Old-World and New-World primates, suggesting that the association of crAssphage with primates may be millions of years old. Finally, by exploiting a large cohort of more than 1,000 individuals, we tested whether crAssphage is associated with bacterial taxonomic groups of the gut microbiome, diverse human health parameters and a wide range of dietary factors. We identified strong correlations with different clades of bacteria that are related to Bacteroidetes and weak associations with several diet categories, but no significant association with health or disease. We conclude that crAssphage is a benign cosmopolitan virus that may have coevolved with the human lineage and is an integral part of the normal human gut virome.

Global phylogeography and ancient evolution of the widespread human gut virus crAssphage

Microbiomes are vast communities of microorganisms and viruses that populate all natural ecosystems. Viruses have been considered to be the most variable component of microbiomes, as supported by virome surveys and examples of high genomic mosaicism. However, recent evidence suggests that the human gut virome is remarkably stable compared with that of other environments. Here, we investigate the origin, evolution and epidemiology of crAssphage, a widespread human gut virus. Through a global collaboration, we obtained DNA sequences of crAssphage from more than one-third of the world's countries and showed that the phylogeography of crAssphage is locally clustered within countries, cities and individuals. We also found fully colinear crAssphage-like genomes in both Old-World and New-World primates, suggesting that the association of crAssphage with primates may be millions of years old. Finally, by exploiting a large cohort of more than 1,000 individuals, we tested whether crAssphage is associated with bacterial taxonomic groups of the gut microbiome, diverse human health parameters and a wide range of dietary factors. We identified strong correlations with different clades of bacteria that are related to Bacteroidetes and weak associations with several diet categories, but no significant association with health or disease. We conclude that crAssphage is a benign cosmopolitan virus that may have coevolved with the human lineage and is an integral part of the normal human gut virome.

Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Effects of moderate, voluntary ethanol consumption on the rat and human gut microbiome

Many alcohol-induced health complications are directly attributable to the toxicity of alcohol or its metabolites, but another potential health impact of alcohol may be on the microbial communities of the human gut. Clear distinctions between healthy and diseased-state gut microbiota have been observed in subjects with metabolic diseases, and recent studies suggest that chronic alcoholism is linked to gut microbiome dysbiosis. Here, we investigated the effects of moderate levels of alcohol consumption on the gut microbiome in both rats and humans. The gut microbiota of rats voluntarily consuming a 20 percent ethanol solution, on alternate days, were compared with a non-exposed control group to identify differential taxonomic and functional profiles. Gut microbial diversity profiles were determined using culture-independent amplification, next-generation sequencing and bioinformatic analysis of bacterial 16S ribosomal RNA gene sequence libraries. Our results showed that, compared with controls, ethanol-consuming rats experienced a significant decline in the biodiversity of their gut microbiomes, a state generally associated with dysbiosis. We also observed significant shifts in the overall diversity of the gut microbial communities and a dramatic change in the relative abundance of particular microbes, such as the Lactobacilli. We also compared our results to human fecal microbiome data collected as part of the citizen science American Gut Project. In contrast to the rat data, human drinkers had significantly higher gut microbial biodiversity than non-drinkers. However, we also observed that microbes that differed among the human subjects displayed similar trends in the rat model, including bacteria implicated in metabolic disease.

Exposure to a Healthy Gut Microbiome Protects Against Reproductive and Metabolic Dysregulation in a PCOS Mouse Model

Polycystic ovary syndrome (PCOS) is a common endocrine disorder affecting ∼10% to 15% of reproductive-aged women worldwide. Diagnosis requires two of the following: hyperandrogenism, oligo-ovulation or anovulation, and polycystic ovaries. In addition to reproductive dysfunction, many women with PCOS display metabolic abnormalities associated with hyperandrogenism. Recent studies have reported that the gut microbiome is altered in women with PCOS and rodent models of the disorder. However, it is unknown whether the gut microbiome plays a causal role in the development and pathology of PCOS. Given its potential role, we hypothesized that exposure to a healthy gut microbiome would protect against development of PCOS. A cohousing study was performed using a letrozole-induced PCOS mouse model that recapitulates many reproductive and metabolic characteristics of PCOS. Because mice are coprophagic, cohousing results in repeated, noninvasive inoculation of gut microbes in cohoused mice via the fecal-oral route. In contrast to letrozole-treated mice housed together, letrozole mice cohoused with placebo mice showed significant improvement in both reproductive and metabolic PCOS phenotypes. Using 16S rRNA gene sequencing, we also observed that the overall composition of the gut microbiome and the relative abundance of Coprobacillus and Lactobacillus differed in letrozole-treated mice cohoused with placebo mice compared with letrozole mice housed together. These results suggest that dysbiosis of the gut microbiome may play a causal role in PCOS and that modulation of the gut microbiome may be a potential treatment option for PCOS.

Seasonal dynamics of DNA and RNA viral bioaerosol communities in a daycare center

BACKGROUND

Viruses play an important role in ecosystems, including the built environment (BE). While numerous studies have characterized bacterial and fungal microbiomes in the BE, few have focused on the viral microbiome (virome). Longitudinal microbiome studies provide insight into the stability and dynamics of microbial communities; however, few such studies exist for the microbiome of the BE, and most have focused on bacteria. Here, we present a longitudinal, metagenomic-based analysis of the airborne DNA and RNA virome of a children's daycare center. Specifically, we investigate how the airborne virome varies as a function of season and human occupancy, and we identify possible sources of the viruses and their hosts, mainly humans, animals, plants, and insects.

RESULTS

Season strongly influenced the airborne viral community composition, and a single sample collected when the daycare center was unoccupied suggested that occupancy also influenced the community. The pattern of influence differed between DNA and RNA viromes. Human-associated viruses were much more diverse and dominant in the winter, while the summertime virome contained a high relative proportion and diversity of plant-associated viruses.

CONCLUSIONS

This airborne microbiome in this building exhibited seasonality in its viral community but not its bacterial community. Human occupancy influenced both types of communities. By adding new data about the viral microbiome to complement burgeoning information about the bacterial and fungal microbiomes, this study contributes to a more complete understanding of the airborne microbiome.

Letrozole treatment of adult female mice results in a similar reproductive phenotype but distinct changes in metabolism and the gut microbiome compared to pubertal mice

BACKGROUND

A majority of women with polycystic ovary syndrome (PCOS) have metabolic dysfunction that results in an increased risk of type 2 diabetes. We previously developed a pubertal mouse model using the aromatase inhibitor, letrozole, which recapitulates many of the reproductive and metabolic features of PCOS. To further our understanding of the effects of androgen excess, we compared the effects of letrozole treatment initiated in puberty versus adulthood on reproductive and metabolic phenotypes as well as on the gut microbiome.

RESULTS

Letrozole treatment of both pubertal and adult female mice resulted in reproductive hallmarks of PCOS, including hyperandrogenemia, anovulation and polycystic ovaries. However, unlike pubertal mice, treatment of adult female mice resulted in modest weight gain and abdominal adiposity, minimal elevation in fasting blood glucose and insulin levels, and no detectable insulin resistance. In addition, letrozole treatment of adult mice was associated with a distinct shift in gut microbial diversity compared to letrozole treatment of pubertal mice.

CONCLUSIONS

Our results indicate that dysregulation of metabolism and the gut microbiome in PCOS may be influenced by the timing of androgen exposure. In addition, the minimal weight gain and lack of insulin resistance in adult female mice after letrozole treatment indicates that this model may be useful for investigating the effects of hyperandrogenemia on the hypothalamic-pituitary-gonadal axis and the periphery without the influence of substantial metabolic dysregulation.

Discovery of a Novel Periodontal Disease-Associated Bacterium

One of the world's most common infectious disease, periodontitis (PD), derives from largely uncharacterized communities of oral bacteria growing as biofilms (a.k.a. plaque) on teeth and gum surfaces in periodontal pockets. Bacteria associated with periodontal disease trigger inflammatory responses in immune cells, which in later stages of the disease cause loss of both soft and hard tissue structures supporting teeth. Thus far, only a handful of bacteria have been characterized as infectious agents of PD. Although deep sequencing technologies, such as whole community shotgun sequencing have the potential to capture a detailed picture of highly complex bacterial communities in any given environment, we still lack major reference genomes for the oral microbiome associated with PD and other diseases. In recent work, by using a combination of supervised machine learning and genome assembly, we identified a genome from a novel member of the Bacteroidetes phylum in periodontal samples. Here, by applying a comparative metagenomics read-classification approach, including 272 metagenomes from various human body sites, and our previously assembled draft genome of the uncultivated Candidatus Bacteroides periocalifornicus (CBP) bacterium, we show CBP's ubiquitous distribution in dental plaque, as well as its strong association with the well-known pathogenic "red complex" that resides in deep periodontal pockets.

PAHs contamination in edible gastropods from north Patagonian harbor areas

PAHs are persistent pollutants released into the environment by fossil fuels burning and leak during petroleum operations. Associated with suspended particles upon entering marine ecosystem are accumulated by benthic fauna. Human exposure occurs mainly from ingestion such as gastropods consumption. The objective was to determine PAHs in sediments and in the marine gastropod Buccinanops globulosus in sites with different maritime and urban influences. In sampling sites located 20 km from the harbor, PAHs were non-detected; while in harbor gastropods, the level of PAH4 was exceeded according to international normative. Level of dibenzo[a,h]anthracene in sediments was between the ISQG and PEL. Since these are the first results of PAHs in edible gastropods in South America, we concluded that PAHs can be dangerous for consumers according to ingestion frequency. Integrative studies are necessary to evaluate the interaction among pollutants in maritime areas and the incidence in human health due to shellfish consumption.

The role of intragestational ghrelin on postnatal development and reproductive programming in mice

The purpose of this study was to evaluate the intragestational role of ghrelin in offspring development and reproductive programming in a mouse model of ghrelin imbalance during pregnancy. Female mice were injected with ghrelin (supraphysiological levels: 4 nmol/animal/day), antagonist (endogenous ghrelin inhibition with (D-Lys3)GHRP-6, 6 nmol/animal/day) or vehicle (control = normal ghrelin levels) throughout the pregnancy. Parameters evaluated in litters were growth, physical, neurobiological and sexual development and, at adulthood, reproductive function. Litter size and initial weight did not vary between treatments. Male pups from dams treated with ghrelin showed higher body weight increase until adulthood (31.7 ± 0.8 vs control = 29.7 ± 0.7, n = 11–14 litters/treatment; P < 0.05). Postnatal physical and neurobiological development was not modified by treatments. The antagonist accelerated male puberty onset, evidenced as earlier testis descent and increased relative testicular weight (antagonist = 0.5 ± 0.0% vs ghrelin = 0.4 ± 0.0% and control = 0.4 ± 0.0%, n = 5–10 litters/treatment; P < 0.05). At adulthood, these males exhibited lower relative testicular weight and reduced sperm motility (63.9 ± 3.6% vs control = 70.9 ± 3.3 and ghrelin = 75.6 ± 3.0, n = 13–15 animals; P < 0.05), without changes in plasma testosterone or fertility. Female pups intragestationally exposed to the antagonist showed earlier vaginal opening (statistically significant only at Day 25) and higher ovarian volume (antagonist = 1085.7 ± 64.0 mm3 vs ghrelin = 663.3 ± 102.8 mm3 and control = 512.3 ± 116.4 mm3; n = 4–6 animals/treatment; P < 0.05), indicating earlier sexual maturation. At adulthood, these females and those exposed to ghrelin showed a tendency to higher percentages of embryo loss and/or foetal atrophy. In conclusion, ghrelin participates in reproductive foetal programming: alterations in ghrelin activity during pregnancy modified body weight increase and anticipated puberty onset, exerting (or tending to) negative effects on adult reproductive function.

PARTIE: a partition engine to separate metagenomic and amplicon projects in the Sequence Read Archive

Motivation

The Sequence Read Archive (SRA) contains raw data from many different types of sequence projects. As of 2017, the SRA contained approximately ten petabases of DNA sequence (10¹⁶ bp). Annotations of the data are provided by the submitter, and mining the data in the SRA is complicated by both the amount of data and the detail within those annotations. Here, we introduce PARTIE, a partition engine optimized to differentiate sequence read data into metagenomic (random) and amplicon (targeted) sequence data sets.

Results

PARTIE subsamples reads from the sequencing file and calculates four different statistics: k-mer frequency, 16S abundance, prokaryotic- and viral-read abundance. These metrics are used to create a RandomForest decision tree to classify the sequencing data, and PARTIE provides mechanisms for both supervised and unsupervised classification. We demonstrate the accuracy of PARTIE for classifying SRA data, discuss the probable error rates in the SRA annotations and introduce a resource assessing SRA data.

Availability and Implementation

PARTIE and reclassified metagenome SRA entries are available from https://github.com/linsalrob/partie

Supplementary information

Supplementary data are available at Bioinformatics online.

Gut Microbial Diversity in Women With Polycystic Ovary Syndrome Correlates With Hyperandrogenism

CONTEXT

A majority of women with polycystic ovary syndrome (PCOS) have metabolic abnormalities that result in an increased risk of developing type 2 diabetes and heart disease. Correlative studies have shown an association between changes in the gut microbiome and metabolic disorders. Two recent studies reported a decrease in α diversity of the gut microbiome in women with PCOS compared with healthy women.

OBJECTIVE

We investigated whether changes in the gut microbiome correlated with specific clinical parameters in women with PCOS compared with healthy women. We also investigated whether there were changes in the gut microbiome in women with polycystic ovarian morphology (PCOM) who lacked the other diagnostic criteria of PCOS.

PARTICIPANTS

Subjects were recruited at the Poznan University of Medical Sciences. Fecal microbial diversity profiles of healthy women (n = 48), women with PCOM (n = 42), and women diagnosed with PCOS using the Rotterdam criteria (n = 73) were analyzed using 16S ribosomal RNA gene sequencing.

RESULTS

Lower α diversity was observed in women with PCOS compared with healthy women. Women with PCOM had a change in α diversity that was intermediate between that of the other two groups. Regression analyses showed that hyperandrogenism, total testosterone, and hirsutism were negatively correlated with α diversity. Permutational multivariate analysis of variance in UniFrac distances showed that hyperandrogenism was also correlated with β diversity. A random forest identified bacteria that discriminated between healthy women and women with PCOS.

CONCLUSION

These results suggest that hyperandrogenism may play a critical role in altering the gut microbiome in women with PCOS.

Effects of diffusion on total biomass in simple metacommunities

This paper analyzes the effects of diffusion on the overall population size of the different species of a metacommunity. Depending on precise thresholds, we determine whether increasing the dispersal rate of a species has a positive or negative effect on population abundance. These thresholds depend on the interaction type of the species and the quality of the patches. The motivation for researching this issue is that spatial structure is a source of new biological insights with management interest. For instance, in a metacommunity of two competitors, the movement of a competitor could lead to a decrease of the overall population size of both species. On the other hand, we discuss when some classic results of metapopulation theory are preserved in metacommunities. Our results complement some recent experimental work by Zhang and collaborators.

Sampling, Extraction, and High-Throughput Sequencing Methods for Environmental Microbial and Viral Communities

The emergence of high-throughput sequencing technologies has deepened our understanding of complex microbial communities and greatly facilitated the study of as-yet uncultured microbes and viruses. Studies of complex microbial communities require high-quality data to generate valid results. Here, we detail current methods of microbial and viral community sample acquisition, DNA extraction, sample preparation, and sequencing on Illumina high-throughput platforms. While using appropriate analytical tools is important, it must not overshadow the need for establishing a proper experimental design and obtaining sufficient numbers of samples for statistical purposes. Researchers must also take care to sample biologically relevant sites and control for potential confounding factors (e.g., contamination).

Endosymbiont interference and microbial diversity of the Pacific coast tick, Dermacentor occidentalis, in San Diego County, California

The Pacific coast tick, Dermacentor occidentalis Marx, is found throughout California and can harbor agents that cause human diseases such as anaplasmosis, ehrlichiosis, tularemia, Rocky Mountain spotted fever and rickettsiosis 364D. Previous studies have demonstrated that nonpathogenic endosymbiotic bacteria can interfere with Rickettsia co-infections in other tick species. We hypothesized that within D. occidentalis ticks, interference may exist between different nonpathogenic endosymbiotic or nonendosymbiotic bacteria and Spotted Fever group Rickettsia (SFGR). Using PCR amplification and sequencing of the rompA gene and intergenic region we identified a cohort of SFGR-infected and non-infected D. occidentalis ticks collected from San Diego County. We then amplified a partial segment of the 16S rRNA gene and used next-generation sequencing to elucidate the microbiomes and levels of co-infection in the ticks. The SFGR R. philipii str. 364D and R. rhipicephali were detected in 2.3% and 8.2% of the ticks, respectively, via rompA sequencing. Interestingly, next generation sequencing revealed an inverse relationship between the number of Francisella-like endosymbiont (FLE) 16S rRNA sequences and Rickettsia 16S rRNA sequences within individual ticks that is consistent with partial interference between FLE and SFGR infecting ticks. After excluding the Rickettsia and FLE endosymbionts from the analysis, there was a small but significant difference in microbial community diversity and a pattern of geographic isolation by distance between collection locales. In addition, male ticks had a greater diversity of bacteria than female ticks and ticks that weren’t infected with SFGR had similar microbiomes to canine skin microbiomes. Although experimental studies are required for confirmation, our findings are consistent with the hypothesis that FLEs and, to a lesser extent, other bacteria, interfere with the ability of D. occidentalis to be infected with certain SFGR. The results also raise interesting possibilities about the effects of putative vertebrate hosts on the tick microbiome.

Characterization of the salivary microbiome in patients with pancreatic cancer

Clinical manifestations of pancreatic cancer often do not occur until the cancer has undergone metastasis, resulting in a very low survival rate. In this study, we investigated whether salivary bacterial profiles might provide useful biomarkers for early detection of pancreatic cancer. Using high-throughput sequencing of bacterial small subunit ribosomal RNA (16S rRNA) gene, we characterized the salivary microbiota of patients with pancreatic cancer and compared them to healthy patients and patients with other diseases, including pancreatic disease, non-pancreatic digestive disease/cancer and non-digestive disease/cancer. A total of 146 patients were enrolled at the UCSD Moores Cancer Center where saliva and demographic data were collected from each patient. Of these, we analyzed the salivary microbiome of 108 patients: 8 had been diagnosed with pancreatic cancer, 78 with other diseases and 22 were classified as non-diseased (healthy) controls. Bacterial 16S rRNA sequences were amplified directly from salivary DNA extractions and subjected to high-throughput sequencing (HTS). Several bacterial genera differed in abundance in patients with pancreatic cancer. We found a significantly higher ratio of Leptotrichia to Porphyromonas in the saliva of patients with pancreatic cancer than in the saliva of healthy patients or those with other disease (Kruskal–Wallis Test; P < 0.001). Leptotrichia abundances were confirmed using real-time qPCR with Leptotrichia specific primers. Similar to previous studies, we found lower relative abundances of Neisseria and Aggregatibacter in the saliva of pancreatic cancer patients, though these results were not significant at the P < 0.05 level (K–W Test; P = 0.07 and P = 0.09 respectively). However, the relative abundances of other previously identified bacterial biomarkers, e.g., Streptococcus mitis and Granulicatella adiacens, were not significantly different in the saliva of pancreatic cancer patients. Overall, this study supports the hypothesis that bacteria abundance profiles in saliva are useful biomarkers for pancreatic cancer though much larger patient studies are needed to verify their predictive utility.

Periodic oscillations of a model for membrane permeability with fluctuating environmental conditions

We perform an analytical study of the dynamics of a multi-solute model for water transport across a cell membrane under periodic fluctuations of the extracellular solute molalities. Under the presence of non-permeating intracellular solute, water volume experiences periodic oscillations if and only if the extracellular non-permeating solute molality is positive in the average. On the other hand, in the absence of non-permeating intracellular solute, a sufficient condition for the existence of an infinite number of periodic solutions of the model is provided. Such sufficient condition holds automatically in the case of only one permeating solute. The proofs are based on classical tools from the qualitative theory of differential equations, namely Brouwer degree, upper and lower solutions and comparison arguments.

Dynamics of a few corotating vortices in Bose-Einstein condensates

We study the dynamics of small vortex clusters with a few (2-4) corotating vortices in Bose-Einstein condensates by means of experiments, numerical computations, and theoretical analysis. All of these approaches corroborate the counterintuitive presence of a dynamical instability of symmetric vortex configurations. The instability arises as a pitchfork bifurcation at sufficiently large values of the vortex system angular momentum that induces the emergence and stabilization of asymmetric rotating vortex configurations. The latter are quantified in the theoretical model and observed in the experiments. The dynamics is explored both for the integrable two-vortex particle system, where a reduction of the phase space of the system provides valuable insight, as well as for the nonintegrable three- (or more) vortex case, which additionally admits the possibility of chaotic trajectories.

Lie symmetries and solitons in nonlinear systems with spatially inhomogeneous nonlinearities

Using Lie group theory and canonical transformations, we construct explicit solutions of nonlinear Schrödinger equations with spatially inhomogeneous nonlinearities. We present the general theory, use it to show that localized nonlinearities can support bound states with an arbitrary number solitons, and discuss other applications of interest to the field of nonlinear matter waves.

The births of five Spanish babies from cryopreserved donated oocytes

BACKGROUND

The technique of freezing oocytes is still not widely used. Reasons cited for this include the technique's low efficacy and the risk of aneuploidy. However, the introduction of technical changes (the type and concentration of cryoprotective substances; slow freezing and rapid thawing; and fertilization by ICSI) has led to improved results. We present four pregnancies obtained using mature oocytes (in metaphase II) that had been frozen and thawed. The oocytes were donated by young women who were not patients.

METHODS

The frozen oocytes (n = 88) came from seven donors aged 18-25 years. The metaphase II oocytes, morphologically normal in appearance, were denuded of their cumulus-corona complex. The cryoprotective freezing solution contained 1,2-propanediol (1.5 mol/l) and sucrose (0.3 mol/l). Freezing was slow and thawing rapid. The oocytes were fertilized by ICSI.

RESULTS

Seventy-nine of the 88 thawed oocytes survived (89.8%); 58 were fertilized (73.4% of all those microinjected); and 26 were transferred (44.8% of all those fertilized). Four pregnancies were produced after seven transfers (57.1%). Five children were born from four pregnancies.

CONCLUSIONS

With the freezing/thawing technique used, oocyte survival was high ( approximately 90%). The pregnancy rate with frozen oocytes was similar to that obtained using fresh oocytes from donors ( approximately 50%).

Does the use of contraception reduce the risk of pregnancy-induced hypertension?

To estimate the impact of the exposure to spermatozoa on the risk of developing pregnancy-induced hypertension, the duration of sexual cohabitation with the father and the use of contraceptive methods were evaluated among 113 primigravid women with pregnancy-induced hypertension and 109 age- and parity-matched controls. The duration of unprotected sexual cohabitation was approximately 50% shorter in women with pregnancy-induced hypertension (2.3 versus 4.7, P < 0.0001), regardless of the contraceptive method previously used. However, the duration of oral contraception use was similar in cases and controls (22.1 versus 23.4 months). Also, of the total group of women who developed pregnancy-induced hypertension, 85.5% (97) became pregnant during the first 3 months of unprotected sexual intercourse in comparison with 54.1% (59) in the control group (P < 0.0001). Results suggest that the risk of pregnancy-induced hypertension in primigravidae is reduced with duration of sexual cohabitation, and therefore with exposure to paternal spermatozoa. However, the protective effect of exposure is not achieved while using oral contraceptives. Considering the present options for nulliparous women, contraception does not appear to be a viable public health policy to reduce the risk of pregnancy induced hypertension.

Platelet sensitivity to prostaglandin E1 inhibition is reduced in pre-eclampsia but not in nonproteinuric gestational hypertension

OBJECTIVE

Platelet aggregometry was used to discriminate platelet sensitivity to prostaglandin E1 (PGE1) inhibition, to evaluate whether platelet behaviour in pre-eclamptic women was different in this respect than from that in nonproteinuric hypertensive women.

METHODS

The amount of PGE1 required to inhibit in vitro platelet aggregation induced by arachidonic acid was determined in samples from 60 women: 20 nonpregnant controls, 20 women with normal pregnancies, 10 women with gestational hypertension and 10 with pre-eclampsia.

RESULTS

The response to arachidonic acid was similar among the four groups. Amounts of PGE1 necessary to inhibit platelet aggregation were significantly higher in normal pregnant women compared with nonpregnant controls (P<0.001). Platelets from pre-eclamptic women required significantly higher concentrations of PGE1 to inhibit aggregation than the other groups studied (P<0.001). However, there was no significant difference between normal and nonproteinuric hypertensive pregnant women.

CONCLUSIONS

Our findings support the notion that increased platelet reactivity during late pregnancy is exacerbated in pre-eclamptic women but not in nonproteinuric hypertensive women. This is in agreement with the hypothesis that pre-eclampsia and gestational hypertension are different conditions. Prospective studies are required to confirm if this simple test may be useful in the early identification of pregnant women at risk for pre-eclampsia.

Prevalence and clinical significance of anticardiolipin antibodies in pregnancies complicated by parvovirus B19 infection

Anticardiolipin antibodies were measured in 60 pregnant women with acute parvovirus B19 infection. Test results for eight (13.3 per cent) women were positive for anticardiolipin antibody. Six of these eight women became negative later, yielding a prevalence of anticardiolipin antibodies of 3.3 per cent (2/60) 6 months after acute parvovirus B19 infection. Anticardiolipin antibody positivity was not associated with an increased risk of abortion, fetal death, or maternal complications. This study suggests that there is an elevated frequency of anticardiolipin antibodies in pregnant women with acute parvovirus B19, probably representing an epiphenomenon. However, this is not associated with an adverse maternal or perinatal outcome.

The incidence of human parvovirus B19 infection during pregnancy and its impact on perinatal outcome

A prospective study of parvovirus B19 infection during pregnancy was conducted at a large teaching hospital in Barcelona, Spain. Women (1610) who were < 28 weeks pregnant at enrollment were screened for parvovirus infection. The prevalence of IgG positivity was 35.03% (564/1610). The incidence of acute infection during pregnancy was 3.7% (60/1610). There were five abortions among the B19-infected women but only one was caused by parvovirus, as assessed by histologic examination and polymerase chain reaction assay. The incidence of fetal loss caused by parvovirus was, therefore, 1.66% (1/60). The remaining 55 pregnancies were uneventful, and at 1 year of age, none of the infants had serious abnormalities. The incidence of vertical transmission of infection was estimated at 25%. This study provides evidence that although acute parvovirus infection may occur relatively commonly during pregnancy, an adverse fetal outcome is a rare complication.

Umbilical artery Doppler ultrasound predicts low birth weight and fetal death in hypertensive pregnancies

BACKGROUND

Doppler ultrasound is nowadays common in the management of pregnancies complicated with hypertension, as an indirect assessment of fetal well-being. However, the value of abnormal umbilical artery Doppler results in predicting poor fetal outcome in hypertensive pregnancies has been studied in only a small number of patients. We designed a study to investigate the relation between abnormal umbilical artery Doppler velocimetry and fetal outcome in hypertensive pregnancies.

DESIGN

A prospective observational study over a 2-year period was performed at the Hospital Clinic, University of Barcelona. Pulsed Doppler examinations of the umbilical artery were performed in one hundred and seventy-two hypertensive pregnant women. The physicians managing the case were not aware of the Doppler results. The incidence of low birth weight and fetal death were considered as the main outcome measures.

RESULTS

When low birth weight was used as an end-point, abnormal resistance index showed a high specificity (95.16%), positive predictive value (83.33%), and negative predictive value (86.76%). Sensitivity was 62.5%. The absence of end-diastolic velocity predicted low birth weight in 100% of pregnancies and fetal death in 66.66%. All stillbirths had absence of end-diastolic velocity (sensitivity 100%).

CONCLUSION

This study demonstrates that umbilical artery Doppler velocimetry is a useful tool to assess fetal well being in hypertensive pregnancies.

Screening and treatment of asymptomatic bacteriuria in pregnancy prevent pyelonephritis

Although asymptomatic bacteriuria during pregnancy is associated with an increased risk of developing pyelonephritis, the effectiveness of screening programs to reduce this risk is controversial. A sharp reduction in the annual incidence of pyelonephritis (1.8% to 0.6%, P < .001) occurred after the introduction of a program to screen and treat asymptomatic bacteriuria among pregnant women followed at a large teaching hospital. The data provide retrospective and prospective evidence that screening and treatment programs for asymptomatic bacteriuria during pregnancy reduce the risk of pyelonephritis in a population with a moderate to high prevalence of bacteriuria.

Maternal primary pulmonary hypertension associated with pregnancy

Primary pulmonary hypertension (PPH) is a very uncommon clinical entity, with a high mortality when associated with pregnancy. Three cases of PPH associated with gestation and different outcomes are reported, and a literature review concerning its management and outcome is made. We emphasize the importance of a strict control of such patients, with the supportive cardiovascular measures and surveillance of fetal well-being. The peculiar handling of the course of delivery and the type of anaesthesia is discussed.