Brain or Mind?

This short creative prose illustrates an experience that I had while rotating at the Worcester Recovery Center and Hospital. I hope readers will reflect on the philosophical tension between neurology and psychiatry and also deepen their appreciation for the human behind the label of a refractory patient

Global transpiration data from sap flow measurements : the SAPFLUXNET database

Plant transpiration links physiological responses of vegetation to water supply and demand with hydrological, energy, and carbon budgets at the land-atmosphere interface. However, despite being the main land evaporative flux at the global scale, transpiration and its response to environmental drivers are currently not well constrained by observations. Here we introduce the first global compilation of whole-plant transpiration data from sap flow measurements (SAPFLUXNET, https://sapfluxnet.creaf.cat/, last access: 8 June 2021). We harmonized and quality-controlled individual datasets supplied by contributors worldwide in a semi-automatic data workflow implemented in the R programming language. Datasets include sub-daily time series of sap flow and hydrometeorological drivers for one or more growing seasons, as well as metadata on the stand characteristics, plant attributes, and technical details of the measurements. SAPFLUXNET contains 202 globally distributed datasets with sap flow time series for 2714 plants, mostly trees, of 174 species. SAPFLUXNET has a broad bioclimatic coverage, with woodland/shrubland and temperate forest biomes especially well represented (80 % of the datasets). The measurements cover a wide variety of stand structural characteristics and plant sizes. The datasets encompass the period between 1995 and 2018, with 50 % of the datasets being at least 3 years long. Accompanying radiation and vapour pressure deficit data are available for most of the datasets, while on-site soil water content is available for 56 % of the datasets. Many datasets contain data for species that make up 90 % or more of the total stand basal area, allowing the estimation of stand transpiration in diverse ecological settings. SAPFLUXNET adds to existing plant trait datasets, ecosystem flux networks, and remote sensing products to help increase our understanding of plant water use, plant responses to drought, and ecohydrological processes. SAPFLUXNET version 0.1.5 is freely available from the Zenodo repository (https://doi.org/10.5281/zenodo.3971689; Poyatos et al., 2020a). The "sapfluxnetr" R package - designed to access, visualize, and process SAPFLUXNET data - is available from CRAN.Peer reviewe

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

A Study on the Thermomechanical Reliability Risks of Through-Silicon-Vias in Sensor Applications

Reliability risks for two different types of through-silicon-vias (TSVs) are discussed in this paper. The first is a partially-filled copper TSV, if which the copper layer covers the side walls and bottom. A polymer is used to fill the rest of the cavity. Stresses in risk sites are studied and ranked for this TSV structure by FEA modeling. Parametric studies for material properties (modulus and thermal expansion) of TSV polymer are performed. The second type is a high aspect ratio TSV filled by polycrystalline silicon (poly Si). Potential risks of the voids in the poly Si due to filling defects are studied. Fracture mechanics methods are utilized to evaluate the risk for two different assembly conditions: package assembled to printed circuit board (PCB) and package assembled to flexible substrate. The effect of board/substrate/die thickness and the size and location of the void are discussed

Early Mechanisms of Pathobiology Are Revealed by Transcriptional Temporal Dynamics in Hippocampal CA1 Neurons of Prion Infected Mice

<div><p>Prion diseases typically have long pre-clinical incubation periods during which time the infectious prion particle and infectivity steadily propagate in the brain. Abnormal neuritic sprouting and synaptic deficits are apparent during pre-clinical disease, however, gross neuronal loss is not detected until the onset of the clinical phase. The molecular events that accompany early neuronal damage and ultimately conclude with neuronal death remain obscure. In this study, we used laser capture microdissection to isolate hippocampal CA1 neurons and determined their pre-clinical transcriptional response during infection. We found that gene expression within these neurons is dynamic and characterized by distinct phases of activity. We found that a major cluster of genes is altered during pre-clinical disease after which expression either returns to basal levels, or alternatively undergoes a direct reversal during clinical disease. Strikingly, we show that this cluster contains a signature highly reminiscent of synaptic N-methyl-D-aspartic acid (NMDA) receptor signaling and the activation of neuroprotective pathways. Additionally, genes involved in neuronal projection and dendrite development were also altered throughout the disease, culminating in a general decline of gene expression for synaptic proteins. Similarly, deregulated miRNAs such as miR-132-3p, miR-124a-3p, miR-16-5p, miR-26a-5p, miR-29a-3p and miR-140-5p follow concomitant patterns of expression. This is the first in depth genomic study describing the pre-clinical response of hippocampal neurons to early prion replication. Our findings suggest that prion replication results in the persistent stimulation of a programmed response that is mediated, at least in part, by synaptic NMDA receptor activity that initially promotes cell survival and neurite remodelling. However, this response is terminated prior to the onset of clinical symptoms in the infected hippocampus, seemingly pointing to a critical juncture in the disease. Manipulation of these early neuroprotective pathways may redress the balance between degeneration and survival, providing a potential inroad for treatment.</p> </div

The list of genes we further investigated using qRT-PCR.

<p>Student's t-test statistic was employed such that a deregulation in fold change between infected and control samples showed at least a p-value≤0.1. The+or−represents a 1–2 fold change; 2.1–3.0 fold change is represented by++or−−while a ≥3.1 is annotated as +++. Blank spaces represent a lack of significant signal between infected and control samples. Relative microarray fold changes are highlighted in parenthesis. Pre-clinical time period spans up to and including 110 DPI while clinical represents 130 DPI and EP.</p

A novel bioluminescence orthotopic mouse model for advanced lung cancer

info:eu-repo/semantics/publishe

The distribution of resident immune cells in the CA1 hippocampal region of both control and prion infected mice.

<p>(<b>A</b>) The expression levels of microglia (AIF1) and astrocyte (GFAP) cell markers determined by microarrays in both control and infected samples. The bars represent log signal intensity values where dark gray bars indicate infected samples while light gray bars represent control levels of AIF1. Statistical significance was calculated by the Student's t-test where * reflects a p-value≤0.05 and ** for p-value≤0.01. The AIF1 log fold change is plotted as a line graph. The red bar reflects GFAP signal in prion infected sample as we did not detect any signal in control samples. The horizontal dotted red line represents the signal intensity threshold set at 100. (<b>B</b>) Immunoflourescence images for both control and infected mice at 70 and EP times post infection showing the presence of GFAP (red) within the CA1 nuclear cell layer (blue). Scale bar reflects a 50 µm region. (<b>C</b>) Representative immunohistochemistry images of microglial CA1 regions of control and prion infected samples. Images represent 70 and end point (EP) DPIs showing microglial cells stained brown contrasted against the blue nuclear stain. Scale bar reflects a 50 µm region. (<b>D</b>) The quantified presence of microglia in control and prion infected samples during the course of disease. The star for the DPI 90 time point indicates insufficient replicates for accurate statistical analysis. Statistical significance was calculated by the Student's t-test; ns means no significance; * for a p-value of ≤0.05 and ** for a p-value of ≤0.0005.</p