Miracle-dz/UniFAR-FTUs huggingface dataset:
Optimal In-Place Learning and the Lobe Component Analysis

It is difficult to map many existing learning algorithms onto biological networks because the former require a separate learning network. The computational basis of biological cortical learning is still poorly understood. This paper rigorously introduces a concept called in-place learning. With in-place learning, every networked neuron in-place is responsible for the learning of its signal processing characteristics (e.g., efficacies of synapses) within its connected network environment. There is no need for a separate learning network. With this in-place hypothesis, consequently, each neuron does not have extra space to compute and store the second and higher order statistics (e.g., correlations) of its input fibers. This work first provides a classification of learning algorithms. Then, it shows that the two well-known in-place biological mechanisms, the Hebbian rule and lateral inhibition, are sufficient to develop orientation selective cells, similar to those found in VI, from inputs of natural images. Many other cells that have not been fully understood have emerged as well. The presented computational study of these two in-place learning mechanisms leads to a new concept- these cells correspond to what are called lobe components, which are high concentrations in the probability of the neuronal input space. Further analysis explains how every neuron can learn efficiently (i.e., near-optimal efficiency) by scheduling its plasticity while interacting with other connected neurons. A simple, in-place (Type-5) learning algorithm is presented. The experimental results showed that this simple biologically inspired algorithm is superior to some well-known state-of-the-art ICA algorithms, thanks to its near-optimal efficiency.
Five-Year Study of Tacrolimus as Secondary Intervention Versus Continuation of Cyclosporine in Renal Transplant Patients at Risk for Chronic Renal Allograft Failure

Background. Chronic allograft nephropathy is the most frequent cause of long-term kidney allograft loss. Studies are desperately needed to improve long-term survival. Tacrolimus has been associated with less rejection and better kidney function compared with cyclosporine in clinical trials. This study tested the hypothesis that conversion from cyclosporine to tacrolimus might improve long-term outcomes in patients with chronic allograft damage. Methods. In this multicenter Canadian clinical trial, cyclosporine-treated patients with biopsy-proven chronic allograft nephropathy and impaired renal function were randomly assigned (2:1) to convert to tacrolimus or continue on cyclosporine therapy. A total of 106 (70 tacrolimus and 36 cyclosporine treated) patients were followed-up for up to 5 years. The primary outcome was graft survival. Results. In an intention to treat analysis, subsequent graft (73% vs. 81%, P=0.2835, log-rank test) and patient survival (91% vs. 92%, P=0.8668, log-rank test) were not different between the tacrolimus and cyclosporine groups, respectively. Changes in Chronic Allograft Damage Index scores on protocol biopsies from baseline to 3 years were not different (+0.4±1.8 vs. +1.3±3.2, P=0.5910, cyclosporine vs. tacrolimus, respectively). There were no significant differences in biopsy-proven acute rejection (6 [8.6%] vs. 2 [5.6%], tacrolimus vs. cyclosporine, respectively, P=0.5906). Conclusions. In this study, patients with chronic allograft damage converted from cyclosporine to tacrolimus demonstrated no apparent benefit.
Antigenic Variation in Plasmodium falciparum Malaria Involves a Highly Structured Switching Pattern

Many pathogenic bacteria, fungi, and protozoa achieve chronic infection through an immune evasion strategy known as antigenic variation. In the human malaria parasite Plasmodium falciparum, this involves transcriptional switching among members of the var gene family, causing parasites with different antigenic and phenotypic characteristics to appear at different times within a population. Here we use a genome-wide approach to explore this process in vitro within a set of cloned parasite populations. Our analyses reveal a non-random, highly structured switch pathway where an initially dominant transcript switches via a set of switch-intermediates either to a new dominant transcript, or back to the original. We show that this specific pathway can arise through an evolutionary conflict in which the pathogen has to optimise between safeguarding its limited antigenic repertoire and remaining capable of establishing infections in non-naïve individuals. Our results thus demonstrate a crucial role for structured switching during the early phases of infections and provide a unifying theory of antigenic variation in P. falciparum malaria as a balanced process of parasite-intrinsic switching and immune-mediated selection.
dbSUPER: a database of super-enhancers in mouse and human genome

Super-enhancers are the clusters of transcriptional enhancers that can drive cell-type-specific gene expression and also crucial in cell identity. Many disease-associated sequence variations are enriched in super-enhancer regions of disease-relevant cell types. Thus, super-enhancers can be used as potential biomarkers for disease diagnosis and therapeutics. Current studies have identified super-enhancers in more than 100 cell types and demonstrated their functional importance. However, no centralized resource to integrate all these findings is available yet. We developed dbSUPER (http://bioinfo.au.tsinghua.edu.cn/dbsuper/), the first integrated and interactive database of super-enhancers, with the primary goal of providing a resource for assistance in further studies related to transcriptional control of cell identity and disease. dbSUPER provides a responsive and user-friendly web interface to facilitate efficient and comprehensive search and browsing. The data can be easily sent to Galaxy instances, GREAT and Cistrome web servers for downstream analysis, and can be visualized in UCSC genome browser while custom tracks added automatically. The data can be downloaded and exported in variety of formats. Further, dbSUPER lists genes associated with the super-enhancers and links to various other databases such as GeneCards, UniProt and Entrez. dbSUPER also provides an overlap analysis tool, to annotate user defined regions. We believe dbSUPER is a valuable resource for the biologists and genetic research communities.
Creating mobile traffic grids based on geospatial data and using cell assignment probabilities

Mobile operators' investments depend largely on the costs of the radio network. The efficiency of building and maintaining the radio network is determined largely by the quality of the radio planning process. The planning tool, the propagation predictions and the spatial traffic input together are the key ingredients of the planning process. In this paper we describe a method to create high quality spatial traffic grid by combining network measurements and propagation predictions with demographic, vector and clutter type data in a statistical model. This gives results of a precision that commonly applied traffic spreading methods in planning tools cannot achieve and gets more and more important when planning micro cells. Operators can achieve large savings on network investments and manual optimisation, while delivering the desired quality by applying these traffic grids.
Coronary Flow Velocity and Disturbed Flow Predict Adverse Clinical Outcome After Coronary Angioplasty

Objective—Laminar flow becomes disturbed at high velocities, reducing shear stress and augmenting vascular inflammation and proliferation, processes that are pivotal in restenosis and atherogenesis. We hypothesized that disturbed blood flow after coronary angioplasty is associated with adverse long-term clinical outcome. Methods and Results—The cineangiograms from 97 patients undergoing laser-assisted coronary angioplasty were analyzed. Coronary blood flow velocity, the residual lesion dimensions, and the Reynolds number (an index of disturbed flow) were measured by using a frame-counting technique and quantitative coronary angiography. Cox proportional hazards were used to assess the relative risk of adverse events (target-vessel revascularization, myocardial infarction, or death) over a mean 2.5 years after the index procedure. There were 41 adverse events during 245 patient years of follow-up (17% per year of follow-up). The risk of an adverse event was increased for patients with a high flow velocity (>250 mm/s; relative risk 2.5, 95% CI 1.3 to 4.7) or a high Reynolds number (>200) at the stenosis inlet (relative risk 2.1, 95% CI 1.1 to 4.1) at the end of the procedure. Adjustment for other factors did not alter these results. Conclusions—High Reynolds numbers, indicating disturbed blood flow after coronary angioplasty, increase the risk of adverse clinical events, potentially through shear-stress–related molecular mechanisms that promote restenosis and atherogenesis.
Who Becomes an Inventor in America? The Importance of Exposure to Innovation

We characterize the factors that determine who becomes an inventor in America by using de-identified data on 1.2 million inventors from patent records linked to tax records. We establish three sets of results. First, children from high-income (top 1%) families are ten times as likely to become inventors as those from below-median income families. There are similarly large gaps by race and gender. Differences in innate ability, as measured by test scores in early childhood, explain relatively little of these gaps. Second, exposure to innovation during childhood has significant causal effects on children's propensities to become inventors. Growing up in a neighborhood or family with a high innovation rate in a specific technology class leads to a higher probability of patenting in exactly the same technology class. These exposure effects are gender-specific: girls are more likely to become inventors in a particular technology class if they grow up in an area with more female inventors in that technology class. Third, the financial returns to inventions are extremely skewed and highly correlated with their scientific impact, as measured by citations. Consistent with the importance of exposure effects and contrary to standard models of career selection, women and disadvantaged youth are as under-represented among high-impact inventors as they are among inventors as a whole. We develop a simple model of inventors' careers that matches these empirical results. The model implies that increasing exposure to innovation in childhood may have larger impacts on innovation than increasing the financial incentives to innovate, for instance by reducing tax rates. In particular, there are many "lost Einsteins" - individuals who would have had highly impactful inventions had they been exposed to innovation.
Texture image retrieval using Phase-based features in the complex wavelet domain

The phase holds crucial information about image structures and features, but only the real part or the magnitude of the transform coefficients is often used for image processing applications. In this paper, a method for the feature extraction of images called Phase-based LBP is presented. Proposed method is based on the combination of phase of complex wavelet coefficients and the Local Binary Pattern operator (LBP). We also perform the comparative analysis about retrieval effectiveness of phase information of some complex wavelet transforms using for Phase-based LBP. Experimental results, achieved with the standard rotated Brodatz dataset, show the interest of this method comparing with another methods only based on the real part or the magnitude of the wavelet coefficients for texture image retrieval.
A PhoP/PhoQ-induced Lipase (PagL) That Catalyzes 3-O-Deacylation of Lipid A Precursors in Membranes ofSalmonella typhimurium *

Pathogenic bacteria modify the structure of the lipid A portion of their lipopolysaccharide in response to environmental changes. Some lipid A modifications are important for virulence and resistance to cationic antimicrobial peptides. The two-component system PhoP/PhoQ plays a central role in regulating lipid A modification. We now report the discovery of a PhoP/PhoQ-activated gene (pagL) in Salmonella typhimurium, encoding a deacylase that removes the R-3-hydroxymyristate moiety attached at position 3 of certain lipid A precursors. The deacylase gene (pagL) was identified by assaying for loss of deacylase activity in extracts of 14 random TnphoA::pag insertion mutants. ThepagL gene encodes a protein of 185 amino acid residues unique to S. typhimurium and closely related organisms such as Salmonella typhi. Heterologous expression ofpagL in Escherichia coli on plasmid pWLP21 results in loss of the R-3-hydroxymyristate moiety at position 3 in ∼90% of the lipid A molecules but does not inhibit cell growth. PagL is synthesized with a 20-amino acidN-terminal signal peptide and is localized mainly in the outer membrane, as judged by assays of separated S. typhimurium membranes and by SDS-polyacrylamide gel analysis of membranes from E. coli cells that overexpress PagL. The function of PagL is unknown, given that S. typhimuriummutants lacking pagL display no obvious phenotypes, but PagL might nevertheless play a role in pathogenesis if it serves to modulate the cytokine response of an infected animal host.
Endothelial Nitric Oxide Synthase: A New Paradigm for Gene Regulation in the Injured Blood Vessel

Abstract—Advances in our understanding of the molecular mechanisms involved in the constitutive and regulated expression of endothelial nitric oxide synthase (eNOS) mRNA expression present a new level of complexity to the study of endothelial gene regulation in health and disease. Recent studies highlight the contribution of both transcription and RNA stability to net steady-state mRNA levels of eNOS in vascular endothelium, introducing a new paradigm to gene regulation in the injured blood vessel. Constitutive eNOS expression is dependent on basal transcription machinery in the core promoter, involving positive and negative protein–protein and protein–DNA interactions. Chromatin-based mechanisms and epigenetic events also regulate expression of eNOS at the transcriptional level in a cell-restricted fashion. Although constitutively active, important physiological and pathophysiologic stimuli alter eNOS gene transcription rates. For instance, eNOS transcription rates increase in response to lysophosphatidylcholine, shear stress, and TGF-&bgr;, among others. Under basal conditions, eNOS mRNA is extremely stable. Surprisingly, posttranscriptional mechanisms have emerged as important regulatory pathways in the observed decreases in eNOS expression in some settings. In models of inflammation, proliferation/injury, oxidized low-density lipoprotein treatment, and hypoxia, eNOS mRNA destabilization plays a significant role in the rapid downregulation of eNOS mRNA levels.
CSP: A Novel System Architecture for Scalable Internet and Communication Services

The boundary between the network edge and the front-end servers of the data center is blurring. Appliance vendors are flooding the market with new capabilities, while switch/router vendors scramble to add these services to their traditional transport services. The result of this competition is a set of ad-hoc technologies and capabilities to provide services at the network edge. This paper describes the Comm Services Platform (CSP); a system architecture for this new 'communication services tier' of the data center. CSP enumerates a set of architectural components to provide scalable communication services built from standard building blocks that utilize emerging server, I/O and network technologies. The building blocks of CSP include a System Area Network, the Virtual Interface Architecture, programmable network processors, and standard high-density servers.
Living Safety Arguments for Open Systems

In recent years, there has been a shift from closed systems, with clearly defined borders, whose behavior is completely determined a priori, towards open systems. An open system is an independently developed system, which is able to communicate and cooperate with other open systems in an ad-hoc manner, at runtime. Moreover, due to their openness, such systems may be used in various contexts. Whenever open systems collaborate in a safety-critical context at runtime, the functional safety of both the individual open systems and emerged system of open systems needs to be assured. More and more regulations nowadays require a safety argumentation of the system. I thereby propose an approach for automatically adapting the safety argumentation built manually, during design time, according to the new operational environment information. To evaluate and validate the proposed solution, the approach will be applied to 1) a system of autonomous drones cooperating for intelligent intersection management, and 2) a system of cooperative transport robots in an industrial setting.
Analysis and hardware design of a scalable dual JPEG-2000 entropy coder

The JPEG-2000 image compression standard is increasingly gaining widespread importance. The rich variety of features makes it highly suitable for a large spectrum of applications but at the same time its associated complexity makes it hard to optimize for particular implementations. One the key step during the processing is entropy coding which takes about 70% of the execution time. We propose in this paper an analysis and hardware design of a dual entropy coder with the goal of being used as a coprocessor to the general JPEG-2000 flow.
Automated Extraction of Weather Variables from Camera Imagery

Thousands of traffic and safety monitoring cameras are deployed or are being deployed all across the country and throughout the world. These cameras serve a wide range of uses from monitoring building access to adjusting timing cycles of traffic lights at clogged intersections. Currently, these images are typically viewed on a wall of monitors in a traffic operations or security center where observers manually monitor potentially hazardous or congested conditions and notify the appropriate authorities. However, the proliferation of camera imagery taxes the ability of the manual observer to track and respond to all incidents. In addition, the images contain a wealth of information, including visibility, precipitation type, road conditions, camera outages, etc., that often goes unreported because these variables are not always critical or go undetected. Camera deployments continue to expand and the corresponding rapid increases in both the volume and complexity of camera imagery demand that automated algorithms be developed to condense the discernable information into a form that can be easily used operationally by users. MIT Lincoln Laboratory (MIT/LL) under funding from the Federal Highway Administration (FHWA) is investigating new techniques to extract weather and road condition parameters from standard traffic camera imagery. To date, work has focused on developing an algorithm to measure atmospheric visibility and prove the algorithm concept. The initial algorithm examines the natural edges within the image (the horizon, tree lines, roadways, permanent buildings, etc) and performs a comparison of each image with a historical composite image. This comparison enables the system to determine the visibility in the direction of the sensor by detecting which edges are visible and which are not. A primary goal of the automated camera imagery feature extraction system is to ingest digital imagery with limited specific site information such as location, height, angle, and visual extent, thereby making the system easier for users to implement. There are, of course, many challenges in providing a reliable automated estimate of the visibility under all conditions (camera blockage/movement, dirt/raindrops on lens, etc) and the system attempts to compensate for these situations. This paper details the work-to-date on the visibility algorithm and defines a path for further development of the overall system.
Multi-Fisheye for Interactive Visualization of Large Graphs

By selectively zooming in and zooming out visualizations, the fisheye technique allows users to study details while maintaining context. In this paper, we introduce a multifisheye technique, which amounts to introducing several fisheyes in a visualization at the same time. Our multifisheye technique is based on partitioning the visualization's display area and applying a fisheye algorithm inside each partition. While we demonstrate the potential of applying our multifisheye technique using a social network, it clearly can be applied in other areas and types of networks, including in probabilistic graphical models such as Bayesian networks.
Electronic Ordering System Improves Postoperative Pain Management after Total Knee or Hip Arthroplasty

Summary Objectives: The authors investigated the impact of computerized provider order entry (CPOE) on the delivery times of analgesia and subsequent patient outcomes. We hypothesized that patients would report less pain and use less pain medications compared with the previous paper-based system. Methods: Two groups of patients after a total hip (THA) or knee arthroplasty (TKA) were retrospectively compared: one comprising 106 patients when the paper-based ordering system was in effect (conventional group), and one comprising 96 patients after CPOE was installed (electronic group). All patients received a regional anaesthetic at surgery (combined spinal-epidural). TKA patients also received a single-injection femoral nerve block. After transfer to the postoperative anaesthesia care unit (PACU), a patient-controlled epidural analgesia (PCEA) infusion was initiated. The following data was collected from the PACU record: time to initiation of analgesia, visual analog scale (VAS) pain scores at initiation of analgesia and hourly for the first postoperative day (POD), volume of pain medication used, length of stay (LOS) in the PACU and the hospital. Results: The time to initiation of analgesia from arrival in the PACU was significantly lower in the electronic group compared to the conventional group (24.5 ± 28.3 minutes vs. 51.1 ± 26.2 minutes; mean ± SD, p < 0.001), as were VAS pain scores (0.82 ± 1.08 vs. 1.5 ± 1.52, p < 0.001) and the volume of PCEA needed to control pain (27.9 ± 20.2 ml vs. 34.8 ± 20.3 ml, p = 0.001) at 4 hours postoperatively. PACU LOS and hospital LOS did not significantly differ in the two groups. Conclusions: After implementation of CPOE, patients received their postoperative analgesia faster, had less pain, and required less medication. Citation: Urban M,Chiu T, Wolfe S, Magid S. Electronic Ordering System Improves Postoperative Pain Management after Total Knee or Hip Arthroplasty. Appl Clin Inform 2015;6: 591–599 http://dx.doi. org/10.4338/ACI-2014-12-RA-0114