Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Chlamydia muridarum Can Invade the Central Nervous System via the Olfactory and Trigeminal Nerves and Infect Peripheral Nerve Glial Cells

Chlamydia pneumoniae can infect the brain and has been linked to late-onset dementia. Chlamydia muridarum, which infects mice, is often used to model human chlamydial infections. While it has been suggested to be also important for modelling brain infection, nervous system infection by C. muridarum has not been reported in the literature. C. pneumoniae has been shown to infect the olfactory bulb in mice after intranasal inoculation, and has therefore been suggested to invade the brain via the olfactory nerve; however, nerve infection has not been shown to date. Another path by which certain bacteria can reach the brain is via the trigeminal nerve, but it remains unknown whether Chlamydia species can infect this nerve. Other bacteria that can invade the brain via the olfactory and/or trigeminal nerve can do so rapidly, however, whether Chlamydia spp. can reach the brain earlier than one-week post inoculation remains unknown. In the current study, we showed that C. muridarum can within 48 h invade the brain via the olfactory nerve, in addition to infecting the trigeminal nerve. We also cultured the glial cells of the olfactory and trigeminal nerves and showed that C. muridarum readily infected the cells, constituting a possible cellular mechanism explaining how the bacteria can invade the nerves without being eliminated by glial immune functions. Further, we demonstrated that olfactory and trigeminal glia differed in their responses to C. muridarum, with olfactory glia showing less infection and stronger immune response than trigeminal glia.</p

Burkholderia pseudomallei invades the olfactory nerve and bulb after epithelial injury in mice and causes the formation of multinucleated giant glial cells in vitro

The infectious disease melioidosis is caused by the bacterium Burkholderia pseudomallei. Melioidosis is characterised by high mortality and morbidity and can involve the central nervous system (CNS). We have previously discovered that B. pseudomallei can infect the CNS via the olfactory and trigeminal nerves in mice. We have shown that the nerve path is dependent on mouse strain, with outbred mice showing resistance to olfactory nerve infection. Damage to the nasal epithelium by environmental factors is common, and we hypothesised that injury to the olfactory epithelium may increase the vulnerability of the olfactory nerve to microbial insult. We therefore investigated this, using outbred mice that were intranasally inoculated with B. pseudomallei, with or without methimazole-induced injury to the olfactory neuroepithelium. Methimazole-mediated injury resulted in increased B. pseudomallei invasion of the olfactory epithelium, and only in pre-injured animals were bacteria found in the olfactory nerve and bulb. In vitro assays demonstrated that B. pseudomallei readily infected glial cells isolated from the olfactory and trigeminal nerves (olfactory ensheathing cells and trigeminal Schwann cells, respectively). Bacteria were degraded by some cells but persisted in other cells, which led to the formation of multinucleated giant cells (MNGCs), with olfactory ensheathing cells less likely to form MNGCs than Schwann cells. Double Cap mutant bacteria, lacking the protein BimA, did not form MNGCs. These data suggest that injuries to the olfactory epithelium expose the primary olfactory nervous system to bacterial invasion, which can then result in CNS infection with potential pathogenic consequences for the glial cells.</p

Chlamydia pneumoniae can infect the central nervous system via the olfactory and trigeminal nerves and contributes to Alzheimer’s disease risk

Chlamydia pneumoniae is a respiratory tract pathogen but can also infect the central nervous system (CNS). Recently, the link between C. pneumoniae CNS infection and late-onset dementia has become increasingly evident. In mice, CNS infection has been shown to occur weeks to months after intranasal inoculation. By isolating live C. pneumoniae from tissues and using immunohistochemistry, we show that C. pneumoniae can infect the olfactory and trigeminal nerves, olfactory bulb and brain within 72 h in mice. C. pneumoniae infection also resulted in dysregulation of key pathways involved in Alzheimer’s disease pathogenesis at 7 and 28 days after inoculation. Interestingly, amyloid beta accumulations were also detected adjacent to the C. pneumoniae inclusions in the olfactory system. Furthermore, injury to the nasal epithelium resulted in increased peripheral nerve and olfactory bulb infection, but did not alter general CNS infection. In vitro, C. pneumoniae was able to infect peripheral nerve and CNS glia. In summary, the nerves extending between the nasal cavity and the brain constitute invasion paths by which C. pneumoniae can rapidly invade the CNS likely by surviving in glia and leading to Aβ deposition.</p

Estimation of reactive inorganic iodine fluxes in the Indian and Southern Ocean marine boundary layer

22 pags., 10 figs., 2 tabs.Iodine chemistry has noteworthy impacts on the oxidising capacity of the marine boundary layer (MBL) through the depletion of ozone (O3) and changes to HOx (OH=HO2) and NOx (NO=NO2) ratios. Hitherto, studies have shown that the reaction of atmospheric O3 with surface seawater iodide (I-) contributes to the flux of iodine species into the MBL mainly as hypoiodous acid (HOI) and molecular iodine (I2). Here, we present the first concomitant observations of iodine oxide (IO), O3 in the gas phase, and sea surface iodide concentrations. The results from three field campaigns in the Indian Ocean and the Southern Ocean during 2015 2017 are used to compute reactive iodine fluxes in the MBL. Observations of atmospheric IO by multi-axis differential optical absorption spectroscopy (MAX-DOAS) show active iodine chemistry in this environment, with IO values up to 1 pptv (parts per trillion by volume) below latitudes of 40° S. In order to compute the sea-to-air iodine flux supporting this chemistry, we compare previously established global sea surface iodide parameterisations with new regionspecific parameterisations based on the new iodide observations. This study shows that regional changes in salinity and sea surface temperature play a role in surface seawater iodide estimation. Sea air fluxes of HOI and I2, calculated from the atmospheric ozone and seawater iodide concentrations (observed and predicted), failed to adequately explain the detected IO in this region. This discrepancy highlights the need to measure direct fluxes of inorganic and organic iodine species in the marine environment. Amongst other potential drivers of reactive iodine chemistry investigated, chlorophyll a showed a significant correlation with atmospheric IO (R D 0:7 above the 99 % significance level) to the north of the polar front. This correlation might be indicative of a biogenic control on iodine sources in this region.The authors thank the Ministry of Earth Sciences for funding the expeditions and IITM for providing a research fellowship to Swaleha Inamdar. We would particularly like to thank the ISOE and IIOE-2 teams for their tireless contribution to manually recording and compiling atmospheric and oceanic observations during the expedition. We express gratitude to the officers, crew, and scientists on board RV S.A. Agulhas and RV Sagar Kanya for their support. Financial support. Lucy J. Carpenter, Liselotte Tinel, Rosie Chance, and Tomás Sherwen received funding from the UK NERC through the grant “Iodide in the ocean: distribution and impact on iodine flux and ozone loss” (grant no. NE/N009983/1

Hybrid recoil mass analyzer at IUAC - First results using gas-filled mode and future plans

Hybrid recoil mass analyzer (HYRA) is a unique, dual-mode spectrometer designed to carry out nuclear reaction and structure studies in heavy and medium-mass nuclei using gas-filled and vacuum modes, respectively and has the potential to address newer domains in nuclear physics accessible using high energy, heavy-ion beams from superconducting LINAC accelerator (being commissioned) and ECR-based high current injector system (planned) at IUAC. The first stage of HYRA is operational and initial experiments have been carried out using gas-filled mode for the detection of heavy evaporation residues and heavy quasielastic recoils in the direction of primary beam. Excellent primary beam rejection and transmission efficiency (comparable with other gas-filled separators) have been achieved using a smaller focal plane detection system. There are plans to couple HYRA to other detector arrays such as Indian national gamma array (INGA) and 4Ï spin spectrometer for ER tagged spectroscopic/spin distribution studies and for focal plane decay measurements. © Indian Academy of Sciences