Miracle-dz/UniFAR-FTUs huggingface dataset:
Structure and Function Relationships between ATPase Family, AAA Domain Containing Protein 5, Proliferating Cell Nuclear Antigen, and USP1-Associated Factor 1

The genome is constantly damaged by intracellular and extracellular factors. At sites of DNA damage, replication forks are stalled, leading to monoubiquitination of proliferating cell nuclear antigen (PCNA). Monoubiquitination of PCNA promotes the switch from regular high-fidelity polymerases to Y-family polymerases for bypassing damaged DNA. Prolonged replication by these polymerases may lead to increased mutagenesis, so tight regulation of this process is required. ATAD5 recruits a deubiquitinase complex consisting of ubiquitin-specific protease 1 (USP1) and USP1associated factor 1 (UAF1) to control PCNA monoubiquitination. The mechanism by which ATAD5 and PCNA interact has been previously unexplored. We show through biochemical and structural studies that ATAD5 contains a non-canonical PCNAinteracting protein motif that interacts with PCNA in the low μM range. Our structural studies indicate that the binding of ATAD5’s PIP Box to PCNA is topologically conserved with respect to canonical PIP Boxes from other proteins. Furthermore, we detected we interactions between ATAD5’s and UAF1’s protein interacting motifs. This suggests that ATAD5 acts as an adapter between PCNA and the UAF1-USP1 deubiquitinase complex. Characterization of these interactions will increase our understanding of DNA damage tolerance and may lead to the design of better cancer therapeutics.
Amyloid precursor protein processing in human neurons with an allelic series of the PSEN1 intron 4 deletion mutation and total presenilin-1 knockout

Abstract Mutations in presenilin-1 (PSEN1), encoding the catalytic subunit of the amyloid precursor protein-processing enzyme γ-secretase, cause familial Alzheimer’s disease. However, the mechanism of disease is yet to be fully understood and it remains contentious whether mutations exert their effects predominantly through gain or loss of function. To address this question, we generated an isogenic allelic series for the PSEN1 mutation intron 4 deletion; represented by control, heterozygous and homozygous mutant induced pluripotent stem cells in addition to a presenilin-1 knockout line. Induced pluripotent stem cell-derived cortical neurons reveal reduced, yet detectable amyloid-beta levels in the presenilin-1 knockout line, and a mutant gene dosage-dependent defect in amyloid precursor protein processing in PSEN1 intron 4 deletion lines, consistent with reduced processivity of γ-secretase. The different effects of presenilin-1 knockout and the PSEN1 intron 4 deletion mutation on amyloid precursor protein-C99 fragment accumulation, nicastrin maturation and amyloid-beta peptide generation support distinct consequences of familial Alzheimer’s disease-associated mutations and knockout of presenilin-1 on the function of γ-secretase.
Intelligent Edge Control with Deterministic-IP based Industrial Communication in Process Automation

In the past years, the Industry 4.0, also known as the Fourth Industrial Revolution, has emerged by the advancement of manufacturing technologies with the Internet of Things (IoT) to enable interconnected manufacturing machines and systems with higher productivity. One of the interesting scenarios in the context of I4.0 is to provide control from the edge, which will improve the efficiency and flexibility of the system at a reduced cost. The industrial automation, especially the process automation (PA) aims for a converged network for data communication. Traditionally internet protocol (IP) is being used for standard IT communication to connect machines to the enterprise network, but not used as much for field network due to lack of determinism. Recent, research has been focused on the design and development of deterministic IP communication, and some preliminary results have been standardized in the IETF Deterministic Network (DetNet) group. In this paper, we investigate on extending the deterministic IP communication to operational technology (OT) domain to support real time industrial Ethernet (RTE) communications. We have integrated IEC-61131-3 based soft PLC (Programmable Logic Controller) runtime system into an Edge computing gateway. The RTE frames are wrapped up with custom UDP/IP header by a proxy and delivered to the deterministic routers. The routers forward packets with a bounded delay of less than 30us per hop. We validate our approach using an experimental test setup, a virtualized PLC (vPLC) inside the edge device remotely controlling the PA application (bioreactor) by passing through proxies and deterministic routers in a heterogeneous network.
The Behavioural Economics of Social Media: A Study of Self Commitment Devices and the Facebook Privacy Paradox

Despite mounting public concern over the issue of social media overusage, there is limited evidence that the time individuals spend on social media platforms is excessive from a welfare standpoint. I implement a randomised intervention over 6 weeks, encouraging a subset of 629 participants recruited over Facebook to adopt a voluntary soft commitment device designed to help limit their phone, Facebook, and Instagram usage. Utilising data from 4 surveys and direct measurement of social media use, I find that: (i) individuals persistently underestimate how much time they actually spend on social media; (ii) they spend much more time on their phones and Facebook than they profess to ideally desire; (iii) users are willing to set application limits even in the absence of incentives to do so; (iv) and lastly, the adoption of such limits significantly reduces phone and Facebook use, with reductions in the latter persisting even after a month. These results all suggest that individuals spend more time on social media than is optimal as a result of their limited ability to exercise self-control. Additionally, in a second experimental arm of the study, I investigate the effect of nudging individuals to review and report their Facebook privacy settings on their behaviour, finding that it results in limited changes to privacy-protective choices; instead, I find that individuals respond by reducing their usage of Facebook. ∗Email address: ruruhoong@alumni.stanford. edu. I am indebted to my thesis advisor, Matthew Gentzkow, for his invaluable guidance and unparalleled support, without which this paper would not be possible. I additionally wish to thank him for his generous sponsorship of this project, as well as UAR for funding the pilot. I also wish to thank Marcelo Clerici-Arias and my peers in the undergraduate honours programme for their constructive comments, as well as Jacob Goldin, Matthew Rabin, and others who provided helpful suggestions along the way. The study was approved by the Institutional Review Board at Stanford
Changes in antioxidant systems and biomass in response to selenate in blue-green microalgae Spirulina platensis تغییر سیستم آنتی اکسیدانی و بیوماس

The effects of selenium (Se) on growth and antioxidant activity in Spirulina platensis were investigated. S. platensis was grown in zarrouk medium containing three different concentrations of selenate (Na2SeO4) (0 as a control, 5 and 10 mg l ) for 7 days. Selenate, at the concentration of 5 mg lwas found to improve S. platensis growth. However, selenate was toxic to S. platensis at the concentration of 10 mg l. Selenium increased the activity of enzymatic (peroxidase and catalase) and non-enzymatic (carotenoids) antioxidants when Se was applied to the microalgae at low concentration (5 mgl). Phenolic compounds were significantly increased in Se-treated samples. The contents of chlorophyll a and carotenoids in Se-treated S. platensis did not significantly change as compared to control. The FTIR analysis clearly indicated that the spectra of cells grown on different Se concentrations did not significantly change as compared to control. In addition, the variety of different compounds such as aromatic, phosphine, alcohols and carboxylic acids were synthesized in all examined treatments. The present results suggested that Se at low concentration had suitable effects on the physiology of S. platensis.
IFT 6760 A-Lecture 14 Johnson − Lindenstrauss theorem

In the previous lectures we presented some dimensionality reduction algorithms such as PCA and LLE. The purpose of these methods is, given a high dimensional dataset, find a lower dimensional space to project the data into that manages to keep some of the important structural characteristics of the original dataset. For example, in the case of the PCA, we aim at preserving as much variance as possible. One important assumption that both PCA and LLE leverage to perform ”good” dimensionality reduction is that the dataset intrinsically lives in a lower dimensional subspace than the one it is embedded in.
Läs- och skrivinlärning via dator hos elever i årskurs 1

Den formella las- och skrivundervisningen i Sverige inleds i arskurs 1. Hur las- och skrivundervisning bedrivs kan skilja sig at mellan olika klasser. Trageton (2005) har utvecklat en las- och skri .
基於加式弦波模型之國語歌聲合成方法 A Mandarin Singing-Voice Synthesis Method Based on Additive Sinusoidal Model 古鴻炎 陳安璿

作歌聲合成時,一個基本的、必需顧慮的是音 色(timbre)一致性的問題,即不管音高(基本頻率)變 高或變低,音色都需保持為同一個人的[6],一般常 犯的錯誤是音色隨著音調高低在改變,就如同錄音 機快速或慢速播放時發生的情形一樣。 此外,國語 歌曲裡常會聽到轉音(sweeping)之唱法,即一個字 要唱 2 個甚至 3 個音符,比起一個字唱一個音符是 較為困難的,前人所研究的弦波模型之合成方法, 並未嘗試作轉音的合成,而在本論文裡,我們嘗試 作轉音合成的研究,希望合成出像人一樣平順的轉 音歌唱聲。 在轉音之外,國語歌聲合成時也需要特 別注意的是,音節前面無聲子音(如/s, ts/)部分的處 理,因為前面提到的合成方法,都只著重於有聲 (voiced)部分,然而無聲子音若處理不當,不只是子 音本身變得不清楚,也會使拍子、節奏錯掉,因此 我們考慮了無聲子音的合成問題。 除此之外,真人 歌聲裡可聽到的一個現象是抖音(vibrato),抖音形 成的原因是,音高變得不固定隨著時間作慢速(每秒 5 次左右)擺動[6, 7, 13],依據此原理,本論文也嘗 試了抖音的合成。
Improving the evaluation and impact of mental health and other supportive school-based programmes on students' academic outcomes

Schools are under increased pressure to demonstrate that all programming promotes student academic achievement. As a result, school-based programmes originally designed to address non-academic issues are now being asked to demonstrate the impact on academic outcomes. The current special issue is the first of two that will examine the association between school-based non-academic services (such as school mental health, family support and mentoring) and students' academic success. These papers provide empirical tests of three programmes and commentary on theoretically and empirically based recommendations for improvement. The final paper provides evidence for the effectiveness of one approach. As these articles highlight, tying the activities of these supportive programmes more closely to academic outcomes, setting clear academic goals, monitoring academic progress and providing feedback to practitioners about progress towards these goals may help increase the probability of non-academic programmes positively impacting academic outcomes.
IDEA AND PERSPECT IVE The dissimilarity of species interaction networks

Timothée Poisot, Elsa Canard, David Mouillot, Nicolas Mouquet and Dominique Gravel Abstract In a context of global changes, and amidst the perpetual modification of community structure undergone by most natural ecosystems, it is more important than ever to understand how species interactions vary through space and time. The integration of biogeography and network theory will yield important results and further our understanding of species interactions. It has, however, been hampered so far by the difficulty to quantify variation among interaction networks. Here, we propose a general framework to study the dissimilarity of species interaction networks over time, space or environments, allowing both the use of quantitative and qualitative data. We decompose network dissimilarity into interactions and species turnover components, so that it is immediately comparable to common measures of b-diversity. We emphasise that scaling up b-diversity of community composition to the b-diversity of interactions requires only a small methodological step, which we foresee will help empiricists adopt this method. We illustrate the framework with a large dataset of hosts and parasites interactions and highlight other possible usages. We discuss a research agenda towards a biogeographical theory of species interactions.
Adaptive Density Map Generation for Crowd Counting

Crowd counting is an important topic in computer vision due to its practical usage in surveillance systems. The typical design of crowd counting algorithms is divided into two steps. First, the ground-truth density maps of crowd images are generated from the ground-truth dot maps (density map generation), e.g., by convolving with a Gaussian kernel. Second, deep learning models are designed to predict a density map from an input image (density map estimation). Most research efforts have concentrated on the density map estimation problem, while the problem of density map generation has not been adequately explored. In particular, the density map could be considered as an intermediate representation used to train a crowd counting network. In the sense of end-to-end training, the hand-crafted methods used for generating the density maps may not be optimal for the particular network or dataset used. To address this issue, we first show the impact of different density maps and that better ground-truth density maps can be obtained by refining the existing ones using a learned refinement network, which is jointly trained with the counter. Then, we propose an adaptive density map generator, which takes the annotation dot map as input, and learns a density map representation for a counter. The counter and generator are trained jointly within an end-to-end framework. The experiment results on popular counting datasets confirm the effectiveness of the proposed learnable density map representations.
Genetic variations in connection

• A submitted manuscript is the version of the article upon submission and before peer-review. There can be important differences between the submitted version and the official published version of record. People interested in the research are advised to contact the author for the final version of the publication, or visit the DOI to the publisher's website. • The final author version and the galley proof are versions of the publication after peer review. • The final published version features the final layout of the paper including the volume, issue and page numbers.
The Development of an Application that supports Body Awareness for Children with Visual Impairments and Additional Disabilities

Abstract The manuscript reports a case study of a design-based research effort to create an app that promotes body awareness among students with visual impairments (VIs) and additional disabilities. Since 2012, a multidisciplinary team has been developing and testing an app called “Body Awareness through Movement and Music,” designed to help children with VIs and additional disabilities improve their body awareness. The app is embedded with features grounded in structured movement routine (SMR) theory. The research effort examines whether a well-designed, intuitive user interface can support improved body awareness of students with VIs and multiple disabilities when used within the itinerant teaching model. A prototype of the app was presented at an international conference where attendees reacted positively to the possibility of using the tool to support body awareness. The prototype was used in a case study with one participant through a multi-sensory approach, with consistency and repetition. Initial findings indicate use of the app provided a SMR that enabled the participant to exhibit appropriate behavior.Keywords
Victor: theWeb-PageCleaning Tool

In this paper we present a completesolution for automatic cleaning of arbitrary HTML pages with a goal of using web data as a corpus in the areaof natural languageprocessing andcomputational linguistics. We employ asequence-labeling approach based onConditional Random Fields (CRF). Every block of text in analyzed web page is assigned a set of features extracted from the textual content and HTML structure of the page. The blocks are automatically labeled either as content segments containing main web page content, which should bepreserved, or asnoisy segmentsnot suitable for further linguistic processing, which should be eliminated. Our solution is based on the tool introduced at theCLEANEVAL 2007shared task workshop. In this paper, wepresent new CRF features, ahandyannotation tool, and new evaluation metrics. Evaluation itself is performed ona random sample of web pages automatically downloaded from the Czech web domain.
RESEARCH OF THE CHARACTERISTICS OF A STEGANOGRAPHY ALGORITHM BASED ON LSB METHOD OF EMBEDDING INFORMATION IN IMAGES

: The article deals with the steganography system which hides text inside images without losing data . The secret message is hidden in the cover image using Last Significant Bit (LSB) algorithm. To evaluate steganography system properties the measures like Signal-to-Noise Ratio (SNR), Peak Signal-to-Noise Ratio (PRSN), Mean Squared Error (MSE) and Structural Similarity Index for measuring (SSIM) are used. Experimental results show the advantages of the described steganography system.
DiscoNet: Shapes Learning on Disconnected Manifolds for 3D Editing

Editing 3D models is a very challenging task, as it requires complex interactions with the 3D shape to reach the targeted design, while preserving the global consistency and plausibility of the shape. In this work, we present an intelligent and user-friendly 3D editing tool, where the edited model is constrained to lie onto a learned manifold of realistic shapes. Due to the topological variability of real 3D models, they often lie close to a disconnected manifold, which cannot be learned with a common learning algorithm. Therefore, our tool is based on a new deep learning model, DiscoNet, which extends 3D surface autoencoders in two ways. Firstly, our deep learning model uses several autoencoders to automatically learn each connected component of a disconnected manifold, without any supervision. Secondly, each autoencoder infers the output 3D surface by deforming a pre-learned 3D template specific to each connected component. Both advances translate into improved 3D synthesis, thus enhancing the quality of our 3D editing tool.
AN EVALUATION OF RESIDUALS FOR TIlE COX MOOEL

Residuals are often helpful in detecting model departures. This paper compares two residuals for the Cox regression model, the Schoenfeld (19S2) score residuals and the Barlow and Prentice (1988) integrated residuals, in their ability to detect nonproportional hazards. Simulation results indicate that the Schoenfeld residuals m~ have greater specificity. The integrated residual does ~stimate the empirical influence function, however.
What is inside Distributed Representations? Encoding and Decoding Structures in Vectors without Learning

Encoding linguistic information in distributed representations is a strong and promising trend in Natural Language Processing. In fact, these distributed representations are vectors or tensors which are successfully used in learning over linguistic data. Distributed representations are linguistic representations ready to be used as feature vectors. However, this success starts to pose legitimate questions: what is exactly concealed in these distributed representations? And more importantly, is it possible to decode distributed representations to recover back the encoded linguistic information? In this paper, we propose decoders to invert very complex encoding functions: the distributed tree encoders [1] which embed trees in low dimensional vectors without learning. As these functions are not invertible per se, we treated this problem as a parsing problem. Hence, we propose two classes of decoders based on parsing algorithms: one for binary trees based on CYK and one for general trees based on CYK+. Experiments show that, with a sufficient dimensionality, the encoding-decoding process has a high accuracy.
SD-FAST: A Packet Rerouting Architecture in SDN

Communication link failure is common in any network. In Software Defined Network (SDN), protection-based recovery scheme reduces the failure recovery delay by installing alternative routes at the data plane switches. We can deploy Fast Failure Group (FFG) of OpenFlow protocol if a switch has an alternative path towards the destination; otherwise, the switch can use crankback approach to send the affected traffic towards the traversed route to find an alternative path. These existing recovery schemes force every packet to traverse a chain of matching tables even in the absence of a link failure, which impacts packet processing time and end-to-end delay. In this paper, we propose a packet rerouting architecture, called SD-FAST, that invokes recovery scheme only after facing failure and reduces both the packet processing and crankback backtracking time. We evaluate SD-FAST in Mininet, considering real and simulated traffic on real network topologies. The evaluation results confirm that SD-FAST can reduce around 73% crankback backtracking time and 64% delay compared to its counterparts.
Similar Impacts of Alien and Native Tree Species on Understory Light Availability in a Temperate Forest

Research Highlights: We evaluated influence of alien and native trees and shrubs on stand leaf area index to basal area ratio, indicating that both groups provide similar amounts of foliage. Background and Objectives: Foliage traits determine tree species effect on understory light availability. Direct comparisons of understory light availability due to different foliage traits of tree species are conducted less often at the stand level. We hypothesized that light availability is driven by canopy leaf area, and alien species contribution to canopy foliage will be similar to native species due to analogous patterns of biomass allocation in tree species. Materials and Methods: We studied forests dominated by alien and native tree species in Wielkopolski National Park (Western Poland). We measured light availability using the LAI-2200 canopy analyzer (Li-Cor Inc., Lincoln, NE, USA) and we calculated leaf area index (LAI) in 170 stands using published models of foliage biomass and data on specific leaf area. Results: Our study confirmed an impact of LAI on light availability in the understory layer. Analyzing the proportion of contribution to stand LAI and basal area (BA) we found that most alien species did not differ in LAI to BA ratio from native species. The exception was Prunus serotina Ehrh. , with a LAI to BA ratio higher than all native and alien trees. However, the highest LAI to BA ratios we found were for the alien shrub Cotoneaster lucidus Schltdl. and native shrubs of fertile broadleaved forests. Conclusions: Our study showed that alien species contribution to shading the understory is comparable to native species, with the exception of P. serotina due to its dominance in the higher shrub canopy strata where it exhibits different patterns of biomass allocation than native trees. Our study explained that invasive tree species impact on light availability in forest ecosystems is mainly mediated by the increased quantity of foliage, not by more effective LAI to BA ratio.