Windows 11 features major changes to the Windows shell influenced by the canceled Windows 10X, including a redesigned Start menu, the replacement of its "live tiles" with a separate "Widgets" panel on the taskbar, the ability to create tiled sets of windows that can be minimized and restored from the taskbar as a group, and new gaming technologies inherited from Xbox Series X and Series S such as Auto HDR and DirectStorage on compatible hardware. Internet Explorer (IE) has been replaced by the Chromium-based Microsoft Edge as the default web browser, like its predecessor, Windows 10, and Microsoft Teams is integrated into the Windows shell. Microsoft also announced plans to allow more flexibility in software that can be distributed via the Microsoft Store and to support Android apps on Windows 11 (including a partnership with Amazon to make its app store available for the function).
A redesigned user interface is present frequently throughout the operating system, building upon Fluent Design System; translucency, shadows, a new color palette, and rounded geometry are prevalent throughout the UI. A prevalent aspect of the design is an appearance known as "Mica", described as an "opaque, dynamic material that incorporates theme and desktop wallpaper to paint the background of long-lived windows such as apps and settings".[87][88] Much of the interface and start menu takes heavy inspiration from the now-canceled Windows 10X.[89] The Segoe UI font used since Windows Vista has been updated to a variable version, improving its ability to scale between different display resolutions.[90]
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Task View, a feature introduced in Windows 10, features a refreshed design, and supports giving separate wallpapers to each virtual desktop. The window snapping functionality has been enhanced with two additional features; hovering over a window's maximize button displays pre-determined "Snap Layouts" for tiling multiple windows onto a display, and tiled arrangement of windows can be minimized and restored from the taskbar as a "snap group".[77][93] When a display is disconnected in a multi-monitor configuration, the windows that were previously on that display will be minimized rather than automatically moved to the main display. If the same display is reconnected, the windows are restored to their prior location.[94]
At the Build Conference in April 2014, Microsoft's Terry Myerson unveiled an updated version of Windows 8.1 (build 9697) that added the ability to run Windows Store apps inside desktop windows and a more traditional Start menu in place of the Start screen seen in Windows 8. The new Start menu takes after Windows 7's design by using only a portion of the screen and including a Windows 7-style application listing in the first column. The second column displays Windows 8-style app tiles. Myerson said that these changes would occur in a future update, but did not elaborate.[33][34] Microsoft also unveiled the concept of a "universal Windows app", allowing Windows Store apps created for Windows 8.1 to be ported to Windows Phone 8.1 and Xbox One while sharing a common codebase, with an interface designed for different device form factors, and allowing user data and licenses for an app to be shared between multiple platforms. Windows Phone 8.1 would share nearly 90% of the common Windows Runtime APIs with Windows 8.1 on PCs.[33][35][36][37]
A new iteration of the Start menu is used on the Windows 10 desktop, with a list of places and other options on the left side, and tiles representing applications on the right. The menu can be resized, and expanded into a full-screen display, which is the default option in Tablet mode.[42][62][73] A new virtual desktop system was added by a feature known as Task View, which displays all open windows and allows users to switch between them, or switch between multiple workspaces.[42][62] Universal apps, which previously could be used only in full screen mode, can now be used in self-contained windows similarly to other programs.[42][62] Program windows can now be snapped to quadrants of the screen by dragging them to the corner. When a window is snapped to one side of the screen, Task View appears and the user is prompted to choose a second window to fill the unused side of the screen (called "Snap Assist").[62] The Windows system icons were also changed.[73]
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Neutrophils are recruited and activated early on following ischemic stroke. tPA has been shown to promote neutrophil degranulation [16, 17]. Upon degranulation, neutrophils release preformed granules containing proteolytic enzymes, including matrix metalloproteinase-9 (MMP-9), that facilitate migration of leukocytes across the BBB to ischemic brain tissue [18]. The mechanisms by which tPA acts on neutrophils to mediate these effects are unknown. However, products of tPA clot degradation may contribute in part to neutrophil activation and infiltration [19]. A number of the identified tPA regulated genes in our study are associated with neutrophils. In the reperfused-MCAO group, tPA was associated with genes involved in neutrophil activation (SELL, ANXA1, SLPI) and neutrophil migration (MMP9, FGR, FCGR2B). In the permanent-MCAO group, genes involved in neutrophil attachment to endothelium (ITGB2) and genes involved in neutrophil recruitment (SLP1, CSF-1) was observed. Further study is required to delineate the effects of tPA on immune response in ischemic stroke, including determination of the specific immune cells and pathways affected by tPA. These potentially identify new targets to reduce tPA related complications in ischemic stroke and perhaps extend the therapeutic window of tPA.
MMP-9 has been studied in ischemic stroke at both the protein and RNA level in blood and brain. MMP-9 is a protease that degrades extracellular matrix and promotes BBB breakdown. Protein levels of MMP-9 increase in the blood early on after ischemic stroke onset, and this increase is enhanced by tPA [25, 26]. In rats treated with tPA, the rise in blood MMP-9 peaks by 6 hours and return to baseline by 24 hours [25]. In human stroke patients treated with tPA, a similar rise blood MMP-9 occurs by 8 hours and with a return to baseline by 25 hours [26]. MMP-9 mRNA expression in the blood following tPA treated ischemic stroke remains poorly studied. We found MMP-9 mRNA to be reduced at 24 hours. This is consistent with an early rise of MMP-9 levels in the blood by 6-8 hours, followed by a reduction by 24 hours. This is in contrast to the pattern of MMP-9 expression in the brain, where levels remain elevated at the 24-30 hour time point [27, 28]. Further study is required to better delineate MMP-9 mRNA expression patterns in blood, including the relationship with vascular reperfusion, duration of cerebral ischemia, treatment with tPA, and correlation with expression patterns of MMP-9 in cerebral tissue.
To benchmark with another method which used ChIP-seq data during training, we compared Virtual ChIP-seq predictions in 32 chromatin factors across 3 cell types with Avocado imputations. Specifically, we compared the predictions of Virtual ChIP-seq in 200 bp genomic windows with both mean and maximum of Avocado imputations over those windows.
To generate the input matrix for training and validation, we used 200 bp genomic bins with sliding 50 bp windows. We excluded any genomic bin which overlaps with ENCODE blacklist regions ( @@download/ENCFF419RSJ.bed.gz). Except where otherwise specified, we used the Genome Reference Consortium GRCh38/hg38 assembly [39].
We created a non-negative ChIP-seq matrix \(\boldsymbol C \in \mathbb R_\geq 0^M \times N\) (Fig. 1a). We used signal mean among replicate narrowPeak files generated by MACS2 [47] for each of M bins and N cell types and quantile-normalized this matrix.
We created an expression matrix \(\mathbf E \in \mathbb R_\in [0,1]^N \times G\) containing the row-normalized rank of expression each of the G=5000 genes in N cell types (Fig. 1b).
We created an input matrix with rows corresponding to 200 bp genomic windows and columns representing the features described above. Specifically, these features included expression score (Fig. 2a), previous evidence of binding of chromatin factor of interest in publicly available ChIP-seq data (Fig. 2b), chromatin accessibility (Fig. 2c), genomic conservation (Fig. 2d), sequence motif scores (Fig. 2e), HINT footprints, and CREAM peaks. We used sliding genomic bins with 50 bp shifts, where most 200 bp bins overlap six other bins. This provided a maximum resolution of 50 bp in binding prediction. The result is a sparse matrix with 60,620,768 rows representing each bin in the GRCh38 genome assembly [39]. The sparse matrix used in the main model had between 4 and 11 columns, depending on the number of available sequence motifs.
The multi-layer perceptron is a fully connected feed-forward artificial neural network [49]. Our multi-layer perceptron assumes binding at each genomic window is independent of upstream and downstream windows (Fig. 2). For each chromatin factor, we trained the multi-layer perceptron with adaptive momentum stochastic gradient descent [50] and a minibatch size of 200 samples. We used 4-fold cross validation to optimize hyperparameters including activation function (Fig. 2g), number of hidden units per layer (Fig. 2h), number of hidden layers (Fig. 2i), and L2 regularization penalty (Fig. 2j). For training, we only used genomic bins which overlapped chromatin accessibility peaks or previous evidence of chromatin factor binding in any of the training cell types. For assessing performance, however, we used all genomic bins of the chromosome. In each cross validation fold, we iteratively trained on 3 of the 4 chromosomes (5, 10, 15, and 20) at a time and assessed performance in the remaining chromosome. We selected the model with the highest average MCC [15] after 4-fold cross validation. MCC incorporates all four categories of a confusion matrix and assesses performance well even on imbalanced datasets [16]. For 23 chromatin factors, the optimal model had 10 hidden layers. For another set of 23 chromatin factors, the optimal model had 5 hidden layers. For the final 17 chromatin factors, the optimal model had only 2 hidden layers. 2ff7e9595c
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