Graph-based Semi-Supervised & Active Learning for Edge Flows

We present a graph-based semi-supervised learning (SSL) method for learning edge flows defined on a graph. Specifically, given flow measurements on a subset of edges, we want to predict the flows on the remaining edges. To this end, we develop a computational framework that imposes certain constraints on the overall flows, such as (approximate) flow conservation. These constraints render our approach different from classical graph-based SSL for vertex labels, which posits that tightly connected nodes share similar labels and leverages the graph structure accordingly to extrapolate from a few vertex labels to the unlabeled vertices. We derive bounds for our method's reconstruction error and demonstrate its strong performance on synthetic and real-world flow networks from transportation, physical infrastructure, and the Web. Furthermore, we provide two active learning algorithms for selecting informative edges on which to measure flow, which has applications for optimal sensor deployment. The first strategy selects edges to minimize the reconstruction error bound and works well on flows that are approximately divergence-free. The second approach clusters the graph and selects bottleneck edges that cross cluster-boundaries, which works well on flows with global trends

A new method for estimating the pattern speed of spiral structure in the Milky Way

In the last few decades many efforts have been made to understand the effect of spiral arms on the gas and stellar dynamics in the Milky Way disc. One of the fundamental parameters of the spiral structure is its angular velocity, or pattern speed $\Omega_p$, which determines the location of resonances in the disc and the spirals' radial extent. The most direct method for estimating the pattern speed relies on backward integration techniques, trying to locate the stellar birthplace of open clusters. Here we propose a new method based on the interaction between the spiral arms and the stars in the disc. Using a sample of around 500 open clusters from the {\it New Catalogue of Optically Visible Open Clusters and Candidates}, and a sample of 500 giant stars observed by APOGEE, we find $\Omega_p = 23.0\pm0.5$ km s$^{-1}$ kpc$^{-1}$, for a local standard of rest rotation $V_0=220$~km s$^{-1}$ and solar radius $R_0=8.0$~kpc. Exploring a range in $V_0$ and $R_0$ within the acceptable values, 200-240 km s$^{-1}$ and 7.5-8.5 kpc, respectively, results only in a small change in our estimate of $\Omega_p$, that is within the error. Our result is in close agreement with a number of studies which suggest values in the range 20-25 km s$^{-1}$ kpc$^{-1}$. An advantage of our method is that we do not need knowledge of the stellar age, unlike in the case of the birthplace method, which allows us to use data from large Galactic surveys. The precision of our method will be improved once larger samples of disk stars with spectroscopic information will become available thanks to future surveys such as 4MOST.Comment: 10 pages, 6 figures, 4 tables, accepted for publication in MNRA

The Universal Cut Function and Type II Metrics

In analogy with classical electromagnetic theory, where one determines the total charge and both electric and magnetic multipole moments of a source from certain surface integrals of the asymptotic (or far) fields, it has been known for many years - from the work of Hermann Bondi - that energy and momentum of gravitational sources could be determined by similar integrals of the asymptotic Weyl tensor. Recently we observed that there were certain overlooked structures, {defined at future null infinity,} that allowed one to determine (or define) further properties of both electromagnetic and gravitating sources. These structures, families of {complex} `slices' or `cuts' of Penrose's null infinity, are referred to as Universal Cut Functions, (UCF). In particular, one can define from these structures a (complex) center of mass (and center of charge) and its equations of motion - with rather surprising consequences. It appears as if these asymptotic structures contain in their imaginary part, a well defined total spin-angular momentum of the source. We apply these ideas to the type II algebraically special metrics, both twisting and twist-free.Comment: 32 page

Transcriptome analysis of bacteriophage communities in periodontal health and disease.

BackgroundThe role of viruses as members of the human microbiome has gained broader attention with the discovery that human body surfaces are inhabited by sizeable viral communities. The majority of the viruses identified in these communities have been bacteriophages that predate upon cellular microbiota rather than the human host. Phages have the capacity to lyse their hosts or provide them with selective advantages through lysogenic conversion, which could help determine the structure of co-existing bacterial communities. Because conditions such as periodontitis are associated with altered bacterial biota, phage mediated perturbations of bacterial communities have been hypothesized to play a role in promoting periodontal disease. Oral phage communities also differ significantly between periodontal health and disease, but the gene expression of oral phage communities has not been previously examined.ResultsHere, we provide the first report of gene expression profiles from the oral bacteriophage community using RNA sequencing, and find that oral phages are more highly expressed in subjects with relative periodontal health. While lysins were highly expressed, the high proportion of integrases expressed suggests that prophages may account for a considerable proportion of oral phage gene expression. Many of the transcriptome reads matched phages found in the oral cavities of the subjects studied, indicating that phages may account for a substantial proportion of oral gene expression. Reads homologous to siphoviruses that infect Firmicutes were amongst the most prevalent transcriptome reads identified in both periodontal health and disease. Some genes from the phage lytic module were significantly more highly expressed in subjects with periodontal disease, suggesting that periodontitis may favor the expression of some lytic phages.ConclusionsAs we explore the contributions of viruses to the human microbiome, the data presented here suggest varying expression of bacteriophage communities in oral health and disease

Paleogenomic and ancient DNA

Introduction The DNA is a nucleic acid that contains the genetic information necessary for RNA and protein biosynthesis. DNA extracted from past samples (teeth, bones, faeces, etc.) is defined ancient DNA (aDNA) and needs, to preserve, low level of oxygen, fast decrease in water content and, above all, according to the Arrhenius equation, low temperature. From 1985 (first aDNA extracted from a mummy) with the introduction of the Polymerase Chain Reaction (PCR) several studies of paleogenomic were born, but it is essential to identify some possible errors such as fragmentations, contaminations and post-mortal mutations [1]. The applications of the paleogenomic are: evolutionary biology, population studies, studies of the pathogens and microorganism. Materials and methods We report 3 cases studied by the Division of Paleopathology of Pisa: a) Ferrante I, king of Naples (1431-1494). The natural mummy showed round white formations of the pelvis infiltrating the abdominal wall ( 1a-b). b) Maria of Aragon (1503-1568). The well-preserved artificial mummy had a small peduncolate arborescence neoformation in the right inguinal region. c) Andean female mummy (so-called ‘Fi9’) dated 10th–11th century A.D by radiocarbonium analyses. The natural young mummy presented a marked megavisceral syndrome characterized by megacolon, megaoesophagus and cardiomegaly. It was possible to perform complete autopsies and collect tissue samples utilized for histological analyses and DNA extraction. Results a) Histology performed on the round formations confirmed the diagnosis of colorectal adenocarcinoma. Amplification of aDNA highlighted a point mutation of the codon 12 in K-Ras oncogene responsible for the cancer [2] (fig. 1c). b) Macroscopic and histological aspects seemed peculiar of condyloma acuminatum, a papillomavirus-induced squamous lesion also called “venereal wart”. Molecular study revealed the presence of HPV 18, a virus with high oncogenic potential. Automated sequencing of several clones revealed 100% similarity sequences of both HPV 18 and JC9813 DNA, a putative novel HPV with low oncogenic potential [3] (fig. 2c) c) Analysis of the gut microbiome (paleofeces, descending, transverse and ascending colon) underlined the massive presence of Clostridiceae. Sequences homologous to HPVs in the mummified gut (descending colon) was particularly surprising. It was detected also the Tripanosoma cruzi; by comparing a partial sequence homologous to the large ribosomal subunit alpha of the presumptive ancient T. cruzi with modern strains, we suggest that this pathogen may have a more remote origin than previously expected. We also found sequences associated with putative beta-lactamases, penicillin-binding proteins, resistance to fosfomycin, chloramphenicol, aminoglycosides, macrolides, sulfa, quinolones, tetracycline and vancomycin, and multi-drug transporters [4] (fig. 3c). Conclusion a) The alimentary “environment” of the Neapolitan court of the XV century, with its abundance of natural alimentary alkylating agents (red smoked meat), well explains the acquired mutation of K-Ras. b) This represented the first molecular diagnosis of HPV in mummies. HPV is a very old virus that evolved together with man. c) Streptococcus, Staphylococcus, Bacillus and Pseudomonas sequences were identified in the mummified gut, opening the opportunity to investigate possible mechanisms by which these bacteria are preserved. The detection of sequences homologous to those of pathogens such as T. cruzi and HPV indicate their presence in the Americas prior to European colonization. The presence of antibiotic-resistance genes in an 11th century pre-Columbian Andean mummy is intriguing as antibiotics were introduced recently. The presence of beta-lactam antibiotic resistance is certainly not unexpected in any culture, as would be in the case of resistance to any natural rather than a semi- or completely synthetic antibiotic as a result of exposure to natural antibiotic-producing microbiota originating from the environment (e.g. soil); however, vancomycin, particularly, was discovered more than 50 years ago, and vancomycin-resistance genes have been mainly implicated with the increased use of this antibiotic. The presence of antibiotic-resistance genes in the ancient human gut microbiome clearly indicates that these genes pre-date therapeutical use of these compounds and that they are not necessarily associated to a selective pressure of antibiotics use. Identification of pathogens and antibiotic-resistance genes in ancient human specimens will aid in the understanding of the evolution of pathogens as a way to treat and prevent diseases caused by bacteria, microbial eukaryotes and viruses. References Willerslev E, Cooper A. Review paper. Ancient Dna. Proceedings of the Royal Society of London B: Biological Sciences. 2005; 272(1558):3– 16. Marchetti A, Pellegrini S, Bevilacqua G, Fornaciari G. K-RAS mutation in the tumour of Ferrante I of Aragon, King of Naples. The Lancet; 1996, May 4;347(9010):1272. Fornaciari G, Zavaglia K, Ciranni R. Human papillomavirus in a 16th century mummy. The Lancet; 2003, Oct 3, vol 362. Santiago-Rodriguez TM, Fornaciari G, Luciani S, Dowd SE, Toranzos GA, Marota I, Cano RJ. Gut Microbiome of an 11th Century A.D. PreColumbian Andean Mummy. PLoS One, 2015 Sep 30;10(9)

Reaction of Capsicum peppers commercialized in the Federal District to bacterial wilt.

To verify the bacterial wilt reaction on Capsicum peppers commercialized in the Federal District (DF), fruits of several genotypes within this genus were collected from six different fairs distributed in the satellite cities of Gama, Sobradinho and Guará

Transmission of viruses via our microbiomes.

BackgroundBacteria inhabiting the human body have important roles in a number of physiological processes and are known to be shared amongst genetically-related individuals. Far less is known about viruses inhabiting the human body, but their ecology suggests they may be shared between close contacts.ResultsHere, we report the ecology of viruses in the guts and mouths of a cohort and demonstrate that substantial numbers of gut and oral viruses were shared amongst genetically unrelated, cohabitating individuals. Most of these viruses were bacteriophages, and each individual had distinct oral and gut viral ecology from their housemates despite the fact that some of their bacteriophages were shared. The distribution of bacteriophages over time within households indicated that they were frequently transmitted between the microbiomes of household contacts.ConclusionsBecause bacteriophages may shape human oral and gut bacterial ecology, their transmission to household contacts suggests they could have substantial roles in shaping the microbiota within a household

Coexisting primary Sjögren’s syndrome and sarcoidosis: coincidence, mutually exclusive conditions or syndrome?

Herein, we describe a 44-year-old female diagnosed with histologically proven coexistence of primary Sjögren's syndrome and sarcoidosis with pulmonary and muscular involvement. The differential diagnosis may be difficult, but this is not an exceptional case, which highlights the need to critically revise the consideration of sarcoidosis as an exclusion for primary Sjögren's syndrome, as established in current classification criteria

Psychological factors associated with response to treatment in rheumatoid arthritis

This paper presents a comprehensive review of research relating psychological domains with response to therapy in patients with rheumatoid arthritis. A holistic approach to the disease was adopted by incorporating not only disease activity but also dimensions of the impact of disease on patients' lives. Psychological distress, including depression and anxiety, is common among patients with rheumatoid arthritis and has a significant negative impact on response to therapy and on patients' abilities to cope with chronic illness. Evidence regarding the influence of positive psychological dimensions such as acceptance, optimism, and adaptive coping strategies is scarce. The mechanisms involved in these interactions are incompletely understood, although changes in neuro-endocrine-immune pathways, which are common to depression and rheumatoid arthritis, seem to play a central role. Indirect psychological influences on therapeutic efficacy and long-term effectiveness include a myriad of factors such as adherence, placebo effects, cognition, coping strategies, and family and social support. Data suggest that recognition and appropriate management of psychological distress may improve response to treatment and significantly reduce disease burden