Improved Performance of Near infrared Excitation Raman Spectroscopy Using Reflective Thin-film Gold on Glass Substrates for Cytology Samples

Confocal near-infrared Raman spectroscopy has been shown to have applications in the area of clinical biology. A source wavelength in the near infrared is preferred over visible wavelengths for inspecting biological samples due to superior wave number resolution and reduced photo damage. However, these excitation sources have a number of drawbacks when compared to lasers in the visible wavelength region, including the requirement to use expensive highly pure crystal substrates such as Raman grade calcium fluoride as well as long acquisition times due to the lower Raman scattering efficiency. This paper investigates the use of a reflective substrate comprising a low cost 100 nm thin-film gold on glass substrate, as an alternative. Similar to recent work that used stainless steel substrates, it is demonstrated that the thin-film gold coated substrates, which are relatively inexpensive, produce cell spectra with 1.65 times the signal to noise ratio when compared with spectra obtained from calcium fluoride under identical conditions, with no apparent background signal in the fingerprint region. Two prostate cell lines are examined having been deposited on glass, calcium fluoride, and thin-film gold on glass substrates using the Thin Prep standard. Background spectra from, and cell adhesion on, these three substrates are compared. A comparison of the intensities and signal to noise ratios of the resulting spectra, and their viability for classification using principle components analysis is performed, which further demonstrates the benefit of reflective substrates

Weak axial nuclear heavy meson exchange currents and interactions of solar neutrinos with deuterons

Starting from the axial heavy meson exchange currents, constructed earlier in conjunction with the Bethe--Salpeter equation, we first present the axial $\rho$--, $\omega$-- and $a_1$ meson exchange Feynman amplitudes that satisfy the partial conservation of the axial current. Employing these amplitudes, we derive the corresponding weak axial heavy meson exchange currents in the leading order in the 1/M expansion ($M$ is the nucleon mass), suitable for the nuclear physics calculations beyond the threshold energies and with wave functions obtained by solving the Schr\"odinger equation with one--boson exchange potentials. The constructed currents obey the nuclear form of the partial conservation of the axial current. We apply the space component of these currents in calculations of the cross sections for the disintegration of deuterons by low energy (anti)neutrinos. The deuteron and the final state nucleon--nucleon wave functions are derived (i) from a variant of the OBEPQB potential, and (ii) from the Nijmegen 93 and Nijmegen I nucleon-nucleon interaction. The extracted values of the constant $L_{1, A}$, entering the axial exchange currents of the pionless effective field theory, are in a reasonable agreement with its value predicted by the dimensional analysis.Comment: 34 pages, 3 figures, 11 table

Among-year and within-population variation in foraging distribution of European shags Phalacrocorax aristotelis over two decades: implications for marine spatial planning

Marine spatial planning aims to deliver sustainable use of marine resources by minimizing environmental impacts of human activities and designating Marine Protected Areas. This poses a challenge where species’ distributions show spatio-temporal heterogeneity. However, due to logistic constraints and challenging timescales many studies of distribution are undertaken over few years or on a restricted subset of the population. Long-term studies can help identify the degree of uncertainty in those less comprehensive in space and time. We quantify inter-annual and sub-colony variation in the summer foraging distribution of a population of European shags Phalacrocorax aristotelis, using a tracking data set comprising 320 individuals and 1106 foraging trips in 15 years from 1987 to 2010. Foraging distribution over the study period was concentrated in three areas. Data from one and two years captured an average of 54% and 64% of this distribution, respectively, but it required 8 years’ data to capture over 90% of the distribution. Foraging range increased with population size when breeding success was low, suggesting interplay between extrinsic and intrinsic effects. Furthermore, females had foraging ranges on average 36% greater than males. Finally, sub-colony segregation occurred in foraging areas up to 4 km from the colony and in the most distant locations (>10 km), whilst there was considerable overlap at intermediate distances (6–10 km). Our study highlights important considerations for marine spatial planning in particular, and species conservation in general, notably the proportion of the population distribution identified, the prevailing conditions experienced and the need for balanced sampling across the population

Atmospheric Circulation of Eccentric Hot Neptune GJ436b

GJ436b is a unique member of the transiting extrasolar planet population being one of the smallest and least irradiated and possessing an eccentric orbit. Because of its size, mass and density, GJ436b could plausibly have an atmospheric metallicity similar to Neptune (20-60 times solar abundances), which makes it an ideal target to study the effects of atmospheric metallicity on dynamics and radiative transfer in an extrasolar planetary atmosphere. We present three-dimensional atmospheric circulation models that include realistic non-gray radiative transfer for 1, 3, 10, 30, and 50 times solar atmospheric metallicity cases of GJ436b. Low metallicity models (1 and 3 times solar) show little day/night temperature variation and strong high-latitude jets. In contrast, higher metallicity models (30 and 50 times solar) exhibit day/night temperature variations and a strong equatorial jet. Spectra and light curves produced from these simulations show strong orbital phase dependencies in the 50 times solar case and negligible variations with orbital phase in the 1 times solar case. Comparisons between the predicted planet/star flux ratio from these models and current secondary eclipse measurements support a high metallicity atmosphere (30-50 times solar abundances) with disequilibrium carbon chemistry at play for GJ436b. Regardless of the actual atmospheric composition of GJ436b, our models serve to illuminate how metallicity influences the atmospheric circulation for a broad range of warm extrasolar planets.Comment: 25 pages, 13 figure

The driver landscape of sporadic chordoma.

Chordoma is a malignant, often incurable bone tumour showing notochordal differentiation. Here, we defined the somatic driver landscape of 104 cases of sporadic chordoma. We reveal somatic duplications of the notochordal transcription factor brachyury (T) in up to 27% of cases. These variants recapitulate the rearrangement architecture of the pathogenic germline duplications of T that underlie familial chordoma. In addition, we find potentially clinically actionable PI3K signalling mutations in 16% of cases. Intriguingly, one of the most frequently altered genes, mutated exclusively by inactivating mutation, was LYST (10%), which may represent a novel cancer gene in chordoma.Chordoma is a rare often incurable malignant bone tumour. Here, the authors investigate driver mutations of sporadic chordoma in 104 cases, revealing duplications in notochordal transcription factor brachyury (T), PI3K signalling mutations, and mutations in LYST, a potential novel cancer gene in chordoma

Recurrent mutation of IGF signalling genes and distinct patterns of genomic rearrangement in osteosarcoma

Osteosarcoma is a primary malignancy of bone that affects children and adults. Here, we present the largest sequencing study of osteosarcoma to date, comprising 112 childhood and adult tumours encompassing all major histological subtypes. A key finding of our study is the identification of mutations in insulin-like growth factor (IGF) signalling genes in 8/112 (7%) of cases. We validate this observation using fluorescence in situ hybridization (FISH) in an additional 87 osteosarcomas, with IGF1 receptor (IGF1R) amplification observed in 14% of tumours. These findings may inform patient selection in future trials of IGF1R inhibitors in osteosarcoma. Analysing patterns of mutation, we identify distinct rearrangement profiles including a process characterized by chromothripsis and amplification. This process operates recurrently at discrete genomic regions and generates driver mutations. It may represent an age-independent mutational mechanism that contributes to the development of osteosarcoma in children and adults alike

Pathologic tearfulness after limbic encephalitis: A novel disorder and its neural basis

Objective We investigated the nature and neural foundations of pathologic tearfulness in a uniquely large cohort of patients who had presented with autoimmune limbic encephalitis (aLE). Methods We recruited 38 patients (26 men, 12 women; median age 63.06 years; interquartile range [IQR] 16.06 years) in the postacute phase of aLE who completed questionnaires probing emotion regulation. All patients underwent structural/functional MRI postacutely, along with 67 age- and sex-matched healthy controls (40 men, 27 women; median age 64.70 years; IQR 19.87 years). We investigated correlations of questionnaire scores with demographic, clinical, neuropsychological, and brain imaging data across patients. We also compared patients diagnosed with pathologic tearfulness and those without, along with healthy controls, on gray matter volume, resting-state functional connectivity, and activity. Results Pathologic tearfulness was reported by 50% of the patients, while no patient reported pathologic laughing. It was not associated with depression, impulsiveness, memory impairment, executive dysfunction in the postacute phase, or amygdalar abnormalities in the acute phase. It correlated with changes in specific emotional brain networks: volume reduction in the right anterior hippocampus, left fusiform gyrus, and cerebellum, abnormal hippocampal resting-state functional connectivity with the posteromedial cortex and right middle frontal gyrus, and abnormal hemodynamic activity in the left fusiform gyrus, right inferior parietal lobule, and ventral pons. Conclusions Pathologic tearfulness is common following aLE, is not a manifestation of other neuropsychiatric features, and reflects abnormalities in networks of emotion regulation beyond the acute hippocampal focus. The condition, which may also be present in other neurologic disorders, provides novel insights into the neural basis of affective control and its dysfunction in disease

Cross-talk between motor neurons and myotubes via endogenously secreted neural and muscular growth factors.

Neuromuscular junction (NMJ) research is vital to advance the understanding of neuromuscular patho-physiology and development of novel therapies for diseases associated with NM dysfunction. In vivo, the micro-environment surrounding the NMJ has a significant impact on NMJ formation and maintenance via neurotrophic and differentiation factors that are secreted as a result of cross-talk between muscle fibers and motor neurons. Recently we showed the formation of functional NMJs in vitro in a co-culture of immortalized human myoblasts and motor neurons from rat-embryo spinal-cord explants, using a culture medium free from serum and neurotrophic or growth factors. The aim of this study was to assess how functional NMJs were established in this co-culture devoid of exogenous neural growth factors. To investigate this, an ELISA-based microarray was used to compare the composition of soluble endogenously secreted growth factors in this co-culture with an a-neural muscle culture. The levels of seven neurotrophic factors brain-derived neurotrophic factor (BDNF), glial-cell-line-derived neurotrophic factor (GDNF), insulin-like growth factor-binding protein-3 (IGFBP-3), insulin-like growth factor-1 (IGF-1), neurotrophin-3 (NT-3), neurotrophin-4 (NT-4), and vascular endothelial growth factor (VEGF) were higher (p < 0.05) in the supernatant of NMJ culture compared to those in the supernatant of the a-neural muscle culture. This indicates that the cross-talk between muscle and motor neurons promotes the secretion of soluble growth factors contributing to the local microenvironment thereby providing a favourable regenerative niche for NMJs formation and maturation

Production, Decay, and Polarization of Excited Heavy Hadrons

We discuss the production via fragmentation of excited heavy mesons and baryons, and their subsequent decay. In particular, we consider the question of whether a net polarization of the initial heavy quark may be detected, either in a polarization of the final ground state or in anisotropies in the decay products of the excited hadron. The result hinges in part on a nonperturbative parameter which measures the net transverse alignment of the light degrees of freedom in the fragmentation process. We use existing data on charmed mesons to extract this quantity for certain excited mesons. Using this result, we estimate the polarization retention of charm and bottom baryons.Comment: 37 pages, 3 figures available upon request, uses phyzzx forma

Think Outside the Color Box: Probabilistic Target Selection and the SDSS-XDQSO Quasar Targeting Catalog

We present the SDSS-XDQSO quasar targeting catalog for efficient flux-based quasar target selection down to the faint limit of the Sloan Digital Sky Survey (SDSS) catalog, even at medium redshifts (2.5 <~ z <~ 3) where the stellar contamination is significant. We build models of the distributions of stars and quasars in flux space down to the flux limit by applying the extreme-deconvolution method to estimate the underlying density. We convolve this density with the flux uncertainties when evaluating the probability that an object is a quasar. This approach results in a targeting algorithm that is more principled, more efficient, and faster than other similar methods. We apply the algorithm to derive low-redshift (z < 2.2), medium-redshift (2.2 <= z 3.5) quasar probabilities for all 160,904,060 point sources with dereddened i-band magnitude between 17.75 and 22.45 mag in the 14,555 deg^2 of imaging from SDSS Data Release 8. The catalog can be used to define a uniformly selected and efficient low- or medium-redshift quasar survey, such as that needed for the SDSS-III's Baryon Oscillation Spectroscopic Survey project. We show that the XDQSO technique performs as well as the current best photometric quasar-selection technique at low redshift, and outperforms all other flux-based methods for selecting the medium-redshift quasars of our primary interest. We make code to reproduce the XDQSO quasar target selection publicly available