Neuroconductor: an R platform for medical imaging analysis

Neuroconductor (https://neuroconductor.org) is an open-source platform for rapid testing and dissemination of reproducible computational imaging software. The goals of the project are to: (i) provide a centralized repository of R software dedicated to image analysis, (ii) disseminate software updates quickly, (iii) train a large, diverse community of scientists using detailed tutorials and short courses, (iv) increase software quality via automatic and manual quality controls, and (v) promote reproducibility of image data analysis. Based on the programming language R (https://www.r-project.org/), Neuroconductor starts with 51 inter-operable packages that cover multiple areas of imaging including visualization, data processing and storage, and statistical inference. Neuroconductor accepts new R package submissions, which are subject to a formal review and continuous automated testing. We provide a description of the purpose of Neuroconductor and the user and developer experience

Interview with Natalia Gherman, candidate for UN Secretary General: “Human rights transcend security, development, and humanitarian responses”

The United Nations will select a new Secretary General this year to take over from Ban Ki-moon, whose term ends on 31 December. In the leadup to the appointment, we will be featuring interviews with some of the candidates for the role. In the second of these discussions, EUROPP editors Tena Prelec and Stuart Brown speak to Natalia Gherman, the candidate from Moldova, on her plans for the UN and what her experience in domestic politics would allow her to bring to the position

Incoherent broadband cavity-enhanced absorption spectroscopy in the near-ultraviolet: application to HONO and NO2

The first application of incoherent broadband cavity-enhanced absorption spectroscopy (IBBCEAS) in the near-ultraviolet for the simultaneous detection of two key atmospheric trace species, HONO and NO2, is reported. For both compounds the absorption is measured between 360 and 380 nm with a compact cavity-enhanced spectrometer employing a high power light-emitting diode. Detection limits of similar to 4 ppbv for HONO and similar to 14 ppbv for NO2 are reported for a static gas cell setup using a 20 s acquisition time. Based on an acquisition time of 10 min and an optical cavity length of 4.5 m detection limits of similar to 0.13 ppbv and similar to 0.38 ppbv were found for HONO and NO2 in a 4 m(3) atmospheric simulation chamber, demonstrating the usefulness of this approach for in situ monitoring of these important species in laboratory studies or field campaigns

Cavity Enhanced Optical Vernier Spectroscopy, Broad Band, High Resolution, High Sensitivity

A femtosecond frequency comb provides a vast number of equidistantly spaced narrow band laser modes that can be simultaneously tuned and frequency calibrated with 15 digits accuracy. Our Vernier spectrometer utilizes all of theses modes in a massively parallel manner to rapidly record both absorption and dispersion spectra with a sensitivity that is provided by a high finesse broad band optical resonator and a resolution that is only limited by the frequency comb line width while keeping the required setup simple.Comment: 11 pages, 3 figures, submitted to PR

High sensitivity in situ monitoring of NO3 in an atmospheric simulation chamber using incoherent broadband cavity-enhanced absorption spectroscopy

We describe the application of incoherent broadband cavity-enhanced absorption spectroscopy (IBBCEAS) for the in situ detection of atmospheric trace gases and radicals (NO3, NO2, O-3, H2O) in an atmospheric simulation chamber under realistic atmospheric conditions. The length of the optical cavity across the reaction chamber is 4.5 m, which is significantly longer than in previous studies that use high finesse optical cavities to achieve high absorption sensitivity. Using a straightforward spectrometer configuration, we show that detection limits corresponding to typical atmospheric concentrations can be achieved with a measurement time of seconds to a few minutes. In particular, with only moderate reflectivity mirrors, we report a measured sensitivity of 4 pptv to NO3 in a 1 min acquisition time. The high spatial and temporal resolution of the IBBCEAS method and its pptv sensitivity to NO3 makes it useful in laboratory studies of atmospheric processes as well as having obvious potential for field measurements.We describe the application of incoherent broadband cavity-enhanced absorption spectroscopy (IBBCEAS) for the in situ detection of atmospheric trace gases and radicals (NO3, NO2, O-3, H2O) in an atmospheric simulation chamber under realistic atmospheric conditions. The length of the optical cavity across the reaction chamber is 4.5 m, which is significantly longer than in previous studies that use high finesse optical cavities to achieve high absorption sensitivity. Using a straightforward spectrometer configuration, we show that detection limits corresponding to typical atmospheric concentrations can be achieved with a measurement time of seconds to a few minutes. In particular, with only moderate reflectivity mirrors, we report a measured sensitivity of 4 pptv to NO3 in a 1 min acquisition time. The high spatial and temporal resolution of the IBBCEAS method and its pptv sensitivity to NO3 makes it useful in laboratory studies of atmospheric processes as well as having obvious potential for field measurements

Structure functions for the three nucleon system

The spectral functions and light-cone momentum distributions of protons and neutrons in 3He and 3H are given in terms of the three-nucleon wave function for realistic nucleon-nucleon interactions. To reduce computational complexity, separable expansions are employed for the nucleon-nucleon potentials. The results for the light-cone momentum distributions suggest that they are not very sensitive to the details of the two-body interaction, as long as it has reasonable short-range repulsion. The unpolarised and polarised structure functions are examined for both 3He and 3H in order to test the usefulness of 3He as a neutron target. It is found that the measurement of the spin structure function of polarised 3H would provide a very clear test of the predicted change in the polarised parton distributions of a bound proton.Comment: 30 pages, REVTeX, 11 figure

A calibration method for broad-bandwidth cavity enhanced absorption spectroscopy performed with supercontinuum radiation

An efficient calibration method has been developed for broad-bandwidth cavity enhanced absorption spectroscopy. The calibration is performed using phase shift cavity ring-down spectroscopy, which is conveniently implemented through use of an acousto-optic tunable filter (AOTF). The AOTF permits a narrowband portion of the SC spectrum to be scanned over the full high-reflectivity bandwidth of the cavity mirrors. After calibration the AOTF is switched off and broad-bandwidth CEAS can be performed with the same light source without any loss of alignment to the set-up. We demonstrate the merits of the method by probing transitions of oxygen molecules O-2 and collisional pairs of oxygen molecules (O-2)(2) in the visible spectral range

Behavioural evidence for self-medication in bumblebees?

The presence of antimicrobial secondary metabolites in nectar suggests that pollinators, which are threatened globally by emergent disease, may benefit from the consumption of nectars rich in these metabolites. We tested whether nicotine, a nectar secondary metabolite common in Solanaceae and Tilia species, is used by parasitized bumblebees as a source of self-medication , using a series of toxicological, microbiological and behavioural experiments. Caged bees infected with Crithidia bombi had a slight preference for sucrose solution laced with the alkaloid and behavioural tests showed that the parasite infection induced an increased consumption of nicotine during foraging activity, though nicotine had an appetite-reducing effect overall. When ingested, nicotine delayed the progression of a gut infection in bumblebees by a few days, but dietary nicotine did not clear the infection, and after 10 days the parasite load approached that of control bees. Moreover, when pathogens were exposed to the alkaloid prior to host ingestion, the protozoan's viability was not directly affected, suggesting that anti-parasite effects were relatively weak. Nicotine consumption in a single dose did not impose any cost even in starved bees but the alkaloid had detrimental effects on healthy bees if consistently consumed for weeks. These toxic effects disappeared in infected bees, suggesting that detoxification costs might have been counterbalanced by the advantages in slowing the progression of the infection. Nicotine consumption did not affect bee lifespan but the reduction in the parasite load may have other likely unexplored subtle benefits both for individual bees and their colony.  Potential evidence for self-medication is discussed. The contention that secondary metabolites in nectar may be under selection from pollinators, or used by plants to enhance their own reproductive success, remains to be confirmed.D.B. was supported by a Marie Curie Intra European Fellowship within the 7th European Community Framework Programm

Cinical – evolutional aspects of acute coronary syndrome without ST segment elevation in diabetics

Congresul III al Medicilor de Familie din Republica Moldova, 17–18 mai, 2012, Chişinău, Republica Moldova, Conferinţa Naţională „Maladii bronhoobstructive la copii”, consacrată profesorului universitar, doctor habilitat Victor Gheţeul, 27 aprilie, Chişinău, Republica MoldovaScopul lucrării. Studierea particularităţilor clinico-evolutive ale sindromului coronarian acut fără elevarea segmentului ST la diabetici. Material şi metode de cercetare Pentru realizarea obiectivelor propuse am efectuat un studiu retrospectiv al fişelor de observaţie a 100 de pacienţi deserviţi de Asistenţa Medicală de Urgenţa din mun. Chişinău, în perioada anului 2009, cu diagnosticul stabilit la etapa de prespital Sindrom Coronarian Acut fără elevarea segmentului ST. Pacienţii evaluaţi au fost repartizaţi în 2 loturi definite în dependenţă de prezenţa sau absenţa diabetului zaharat. Lotul I – 50 de pacienţi cu sindrom coronarian acut fără elevarea segmentului ST; Lotul II – 50 de pacienţi cu sindrom coronarian acut fără elevarea segmentului ST, asociat cu diabetul zaharat. Toţi pacienţii au fost cercetaţi şi analizaţi în baza unei fişe de monitorizare standardizată, care a inclus studierea datelor anamnezice, clinice şi paraclinice. Rezultate proprii şi discuţii Incidenţa SCA fără elevarea segmentului ST în populaţia matură a mun. Chişinău a fost de 3 073 (12%), din totalul SCA, dintre care 1 783 de pacienţi cu diabet zaharat. Din numărul total de 100 de pacienţi, 62 de persoane au fost bărbaţi, ceea ce constituie (62%) şi 38 femei (38%). Distribuţia pacienţilor după sexe în loturile studiate, au relevat următoarele date: în lotul I au fost 34 de bărbaţi (68%) şi 16 femei (32%), iar în lotul II – 28 de bărbaţi (56%) şi 22 de femei (44%). Distribuţia după sexe a evidenţiat o dominanţă a bărbaţilor în ambele grupuri de studiu. Vârsta pacienţilor, incluşi în studiu, a fost cuprinsă între 20 şi 98 de ani. Vârsta medie în lotul I a fost 60,44 ani, iar în lotul II – 54,92 ani. Grupa de vârstă cel mai frecvent întîlnită în lotul I a fost cuprinsă între 51-60 de ani, urmată de grupul de vârstă 61-70 de ani. Cea mai mică frecvenţă a bolii a fost întâlnită la pacienţii din grupul de vârstă < 40 de ani. Concluzii Din numărul total de pacienţi cu sindrom coronarian acut fără supradenivelarea segmentului ST, au predominat bărbaţii, iar femeile diabetice au dezvoltat mai frecvent evenimente coronariene acute decât cele nondiabetice. Categoria socială cea mai afectată este reprezentată de pacienţii de vârsta a treia. Particularităţile clinico-evolutive la pacienţii cu sindrom coronarian acut fără elevarea segmentului ST, asociat cu diabet zaharat, implică manifestări clinice atipice şi dezvoltarea frecventă a complicaţiilor (disritmii, şoc cardiogen, edem pulmonar acut cardiogen, trombembolia arterei pulmonare, anevrism). În cazul pacienţilor cu sindrom coronarian acut fără elevarea segmentului ST, asociat cu diabet, comorbidităţi ca HTA, AVC, IM vechi, dislipidemii au fost depistate într-un număr mai mare

Targeted NGS gene panel identifies mutations in RSPH1 causing primary ciliary dyskinesia and a common mechanism for ciliary central pair agenesis due to radial spoke defects.

Primary ciliary dyskinesia (PCD) is an inherited chronic respiratory obstructive disease with randomized body laterality and infertility, resulting from cilia and sperm dysmotility. PCD is characterized by clinical variability and extensive genetic heterogeneity, associated with different cilia ultrastructural defects and mutations identified in >20 genes. Next generation sequencing (NGS) technologies therefore present a promising approach for genetic diagnosis which is not yet in routine use. We developed a targeted panel-based NGS pipeline to identify mutations by sequencing of selected candidate genes in 70 genetically undefined PCD patients. This detected loss-of-function RSPH1 mutations in four individuals with isolated central pair (CP) agenesis and normal body laterality, from two unrelated families. Ultrastructural analysis in RSPH1-mutated cilia revealed transposition of peripheral outer microtubules into the 'empty' CP space, accompanied by a distinctive intermittent loss of the central pair microtubules. We find that mutations in RSPH1, RSPH4A and RSPH9, which all encode homologs of components of the 'head' structure of ciliary radial spoke complexes identified in Chlamydomonas, cause clinical phenotypes that appear to be indistinguishable except at the gene level. By high-resolution immunofluorescence we identified a loss of RSPH4A and RSPH9 along with RSPH1 from RSPH1-mutated cilia, suggesting RSPH1 mutations may result in loss of the entire spoke head structure. CP loss is seen in up to 28% of PCD cases, in whom laterality determination specified by CP-less embryonic node cilia remains undisturbed. We propose this defect could arise from instability or agenesis of the ciliary central microtubules due to loss of their normal radial spoke head tethering