Optimized bone sampling protocols for the retrieval of ancient DNA from archaeological remains

The methods presented here seek to maximize the chances for the recovery of human DNA from ancient archaeological remains while limiting input sample material. This was done by targeting anatomical sampling locations previously determined to yield the highest amounts of ancient DNA (aDNA) in a comparative analysis of DNA recovery across the skeleton. Prior research has suggested that these protocols maximize the chances for the successful recovery of ancient human and pathogen DNA from archaeological remains. DNA yields were previously assessed by Parker et al. 2020 in a broad survey of aDNA preservation across multiple skeletal elements from 11 individuals recovered from the medieval (radiocarbon dated to a period of circa (ca.) 1040-1400 CE, calibrated 2-sigma range) graveyard at Krakauer Berg, an abandoned medieval settlement near Peißen Germany. These eight sampling spots, which span five skeletal elements (pars petrosa, permanent molars, thoracic vertebra, distal phalanx, and talus) successfully yielded high-quality ancient human DNA, where yields were significantly greater than the overall average across all elements and individuals. Yields were adequate for use in most common downstream population genetic analyses. Our results support the preferential use of these anatomical sampling locations for most studies involving the analyses of ancient human DNA from archaeological remains. Implementation of these methods will help to minimize the destruction of precious archaeological specimens.Introduction Protocol 1. Considerations before sample processing 2. Pretreatment 3. Bone powder generation Representative Results Discussio

Stimulus- and Neural-Referred Visual Receptive Field Properties following Hemispherectomy:A Case Study Revisited

Contains fulltext : 208072.pdf (publisher's version ) (Open Access

Preserved retinotopic brain connectivity in macular degeneration

PURPOSE: The eye disease macular degeneration (MD) is a leading cause of blindness worldwide. There is no cure for MD, but several promising treatments aimed at restoring vision at the level of the retina are currently under investigation. These treatments assume that the patient's brain can still process appropriately the retinal input once it is restored, but whether this assumption is correct has yet to be determined. METHODS: We used functional magnetic resonance imaging (fMRI) and connective field modelling to determine whether the functional connectivity between the input-deprived portions of primary visual cortex (V1) and early extrastriate areas (V2/3) is still retinotopically organised. Specifically, in both patients with juvenile macular degeneration and age-matched controls with simulated retinal lesions, we assessed the extent to which the V1-referred connective fields of extrastriate voxels, as estimated on the basis of spontaneous fMRI signal fluctuations, adhered to retinotopic organisation. RESULTS: We found that functional connectivity between the input-deprived portions of visual areas V1 and extrastriate cortex is still largely retinotopically organised in MD, although on average less so than in controls. Patients with stable fixation exhibited normal retinotopic connectivity, however, suggesting that for the patients with unstable fixation, eye-movements resulted in spurious, homogeneous signal modulations across the entire input-deprived cortex, which would have hampered our ability to assess their spatial structure of connectivity. CONCLUSIONS: Despite the prolonged loss of visual input due to MD, the cortico-cortical connections of input-deprived visual cortex remain largely intact. This suggests that the restoration of sight in macular degeneration can rely on a largely unchanged retinotopic representation in early visual cortex following loss of central retinal function

Linking cortical visual processing to viewing behavior using fMRI

One characteristic of natural visual behavior in humans is the frequent shifting of eye position. It has been argued that the characteristics of these eye movements can be used to distinguish between distinct modes of visual processing (Unema et al., 2005). These viewing modes would be distinguishable on the basis of the eye-movement parameters fixation duration and saccade amplitude and have been hypothesized to reflect the differential involvement of dorsal and ventral systems in saccade planning and information processing. According to this hypothesis, on the one hand, while in a “pre-attentive” or ambient mode, primarily scanning eye movements are made; in this mode fixation are relatively brief and saccades tends to be relatively large. On the other hand, in “attentive” focal mode, fixations last longer and saccades are relatively small, and result in viewing behavior which could be described as detailed inspection. Thus far, no neuroscientific basis exists to support the idea that such distinct viewing modes are indeed linked to processing in distinct cortical regions. Here, we used fixation-based event-related (FIBER) fMRI in combination with independent component analysis (ICA) to investigate the neural correlates of these viewing modes. While we find robust eye-movement-related activations, our results do not support the theory that the above mentioned viewing modes modulate dorsal and ventral processing. Instead, further analyses revealed that eye-movement characteristics such as saccade amplitude and fixation duration did differentially modulate activity in three clusters in early, ventromedial and ventrolateral visual cortex. In summary, we conclude that evaluating viewing behavior is crucial for unraveling cortical processing in natural vision

Assessing Uncertainty and Reliability of Connective Field Estimations From Resting State fMRI Activity at 3T

Connective Field (CF) modeling estimates the local spatial integration between signals in distinct cortical visual field areas. As we have shown previously using 7T data, CF can reveal the visuotopic organization of visual cortical areas even when applied to BOLD activity recorded in the absence of external stimulation. This indicates that CF modeling can be used to evaluate cortical processing in participants in which the visual input may be compromised. Furthermore, by using Bayesian CF modeling it is possible to estimate the co-variability of the parameter estimates and therefore, apply CF modeling to single cases. However, no previous studies evaluated the (Bayesian) CF model using 3T resting-state fMRI data. This is important since 3T scanners are much more abundant and more often used in clinical research compared to 7T scanners. Therefore in this study, we investigate whether it is possible to obtain meaningful CF estimates from 3T resting state (RS) fMRI data. To do so, we applied the standard and Bayesian CF modeling approaches on two RS scans, which were separated by the acquisition of visual field mapping data in 12 healthy participants. Our results show good agreement between RS- and visual field (VF)- based maps using either the standard or Bayesian CF approach. In addition to quantify the uncertainty associated with each estimate in both RS and VF data, we applied our Bayesian CF framework to provide the underlying marginal distribution of the CF parameters. Finally, we show how an additional CF parameter, beta, can be used as a data-driven threshold on the RS data to further improve CF estimates. We conclude that Bayesian CF modeling can characterize local functional connectivity between visual cortical areas from RS data at 3T. Moreover, observations obtained using 3T scanners were qualitatively similar to those reported for 7T. In particular, we expect the ability to assess parameter uncertainty in individual participants will be important for future clinical studies

Three-Body and One-Body Channels of the Auger Core-Valence-Valence decay: Simplified Approach

We propose a computationally simple model of Auger and APECS line shapes from open-band solids. Part of the intensity comes from the decay of unscreened core-holes and is obtained by the two-body Green's function $G^{(2)}_{\omega}$, as in the case of filled bands. The rest of the intensity arises from screened core-holes and is derived using a variational description of the relaxed ground state; this involves the two-holes-one-electron propagator $G_{\omega}$, which also contains one-hole contributions. For many transition metals, the two-hole Green's function $G^{(2)}_{\omega}$ can be well described by the Ladder Approximation, but the three-body Green's function poses serious further problems. To calculate $G_{\omega}$, treating electrons and holes on equal footing, we propose a practical approach to sum the series to all orders. We achieve that by formally rewriting the problem in terms of a fictitious three-body interaction. Our method grants non-negative densities of states, explains the apparent negative-U behavior of the spectra of early transition metals and interpolates well between weak and strong coupling, as we demonstrate by test model calculations.Comment: AMS-LaTeX file, 23 pages, 8 eps and 3 ps figures embedded in the text with epsfig.sty and float.sty, submitted to Phys. Rev.

Pion-Lambda-Sigma Coupling Extracted from Hyperonic Atoms

The latest measurements of the atomic level width in Sigma-hyperonic Pb atom offer the most accurate datum in the region of low-energy Sigma-hyperon physics. Atomic widths are due to the conversion of Sigma-nucleon into Lambda-nucleon. In high angular momentum states this conversion is dominated by the one-pion exchange. A joint analysis of the data of the scattering of negative-Sigma on proton converting into a Lambda and a neutron and of the atomic widths allows to extract a pseudovector pion-hyperon-Sigma coupling constant of 0.048 with a statistical error of +-0.005 and a systematic one of +-0.004. This corresponds to a pseudoscalar coupling constant of 13.3 with a statistical uncertainty of 1.4 and a systematic one of 1.1.Comment: 12 pages, 1 figure, Use of Revtex.st