Miracle-dz/UniFAR-FTUs huggingface dataset:
Supplemental Material for Experimental and computational validation of models of uorescent and luminescent reporter genes in bacteria

Hidde de Jong Caroline Ranquet Delphine Ropers Corinne Pinel Johannes Geiselmann Laboratoire Adaptation et Pathogénie des Microorganismes (CNRS UMR 5163) Institut Jean Roget, Campus Santé, Université Joseph Fourier Domaine de la Merci, 38700 La Tronche, France Institut National de Recherche en Informatique et en Automatique (INRIA) Research center Grenoble Rhône-Alpes 655 avenue de l'Europe, Montbonnot, 38334 Saint Ismier Cedex, France
From xylogenesis to tree rings: wood traits to investigate tree response to environmental changes

It is noteworthy that the largest part of global vegetation biomass depends on a thin layer of cells: the vascular cambium. Understanding the wood formation processes and relationships with environmental factors is a crucial and timely research question requiring interdisciplinary efforts, also to upscale the information gained and to evaluate implications for tree growth and forest productivity.We provide an overview of wood formation processes up to tree-ring development, bearing in mind that the combined action of intrinsic factors and environmental drivers determines the anatomical traits of a tree ring formed at a specific time and position within the tree’s architecture. After briefly reviewing intrinsic factors, we focus attention on environmental drivers highlighting how a correct interpretation of environmental signals in tree rings must be grounded in a deep knowledge of xylogenesis and consequent wood anatomical traits. We provide guidelines on novel methods and approaches recently developed to study xylem formation. We refer to existing literature on established techniques for retrospective analyses in tree-ring series of anatomical and isotopic traits, to assess long-term ecophysiological responses to environmental variations, also giving advice on possible bias because of interand within-tree variability.Finally, we highlight that, once the temporal axis of intra-annual tree-ring variability of xylem traits is established by xylogenesis analysis, a multidisciplinary approach linking classical dendro-ecology, wood functional traits (dendro-anatomy) and eco-physiology (here focusing on dendro-isotopes) allows a better interpretation of past environmental events hidden in tree rings, and more reliable forecasts of wood growth in response to climate change.
Do Immigrants Affect Firm‐Specific Wages?

In this paper, we propose and test a novel effect of immigration on the wages of native workers. Existing studies have focused on the wage effects that result from changes in the aggregate labour supply in a competitive labour market. We argue that if labour markets are not fully competitive, the use of immigrants may also affect wage formation at the most disaggregate level – the workplace. Using linked employeremployee data, we find that an increased use of workers from less developed countries has a significantly negative effect on the wages of native workers at the workplace – also when controlling for potential endogeneity of the immigrant share using both fixed effects and IV. Additional evidence suggests that this effect works at least partly through a general effect on the wage norm in the firm of hiring employees with poor outside options (the immigrants).
Privacy-Preserving Triangle Counting in Distributed Graphs

Together with the popularity of graph structure in real world data, graph analysis has become an attractive research topic. Triangle counting is one of typical graph mining tasks and plays a significant role in complex network analysis, with a wide range of applications in social network analysis, spam detection, and computer-aided design applications. Given the sensitive nature of graph data, the disclosure of graph content for the purpose of analysis may raise a major privacy concern to both individuals and organizations. In this paper, we propose a protocol for privacy-preserving triangle counting when the overall graph is distributed to different parties. We firstly present the solution in a two-party scenario and then extend the protocol to any number of participating parties. The graph structure is represented by an adjacency matrix, and cryptographic secure matrix computation is utilized to tackle the problem. A secure multi-party power of matrix sum protocol is proposed to serve as a building block for the solution. We have evaluated the computational complexity and scalability of the proposed protocols both analytically and empirically. The results show that the protocols are efficient and scalable for small and medium size data.
Increase in Modified Condition/Decision Coverage using program code transformer

Modified Condition / Decision Coverage (MC / DC) is a white box testing criteria aiming to prove that all conditions involved in a predicate can influence the predicate value in the desired way. Though MC/DC is a standard coverage criterion, existing automated test data generation approaches like CONCOLIC testing do not support MC/DC. To address this issue we present an automated approach to generate test data that helps to achieve an increase in MC/DC coverage of a program under test. We use code transformation techniques which consist of the following major steps: Identification of predicates, Simplification of sum of product by QUINE-McMLUSKY method, and generating empty true-false if-else statements. This transformed program is inserted into the CONCOLIC tester (CREST TOOL) to generate test data for increased MC/DC coverage. Our approach helps to achieve an increase in MC/DC coverage as compared to the traditional CONCOLIC testing.
Kinematic design of a PKM-type composite actuator

Nowadays one development trend of machines is to grow bigger and bigger in size and hence larger actuators are required. To develop a larger servo mechanical press, a composite actuator scheme is proposed to combine two or more programmable actuators to act as one actuator through a two- or multi- degree of freedom (dof) parallel kinematic mechanism (PKM). In this paper, the performance indices for the compositie actuator are proposed to describe the mechanical adavantages of a general mechanism. The kinematic model is built based on Assur's Group method. The dimensional design are introduced to make the composite actuator having a nearly constant mechanical advantage. Based on the discussions, a pending patent is applied for a new servo mechanical press developed in the laboratory.
Injection of HGF Plasmid cDNA to Prevent Manifestation of Parkinson Disease: A Preclinical Study using a Primate Model

Parkinson disease (PD) is a neurodegenerative disorder characterized by the loss of dopaminergic neurons. Current therapies provide symptomatic treatment only and thus fail to prevent the process of neurodegeneration. Recently, it has been reported that neurotrophic factors could support the survival and enhance the function of dopaminergic neurons. Thus, gene therapy using neurotrophic factors has become the center of interest. From this viewpoint, we focused on hepatocyte growth factor (HGF) as a novel neurotrophic and angiogenic growth factor. In this study, we examined the effects of over-expression of HGF on clinical symptoms induced in a monkey model of PD, aiming toward human gene therapy. Stereotaxic transfection of naked plasmid DNA encoding human HGF cDNA into the striatum resulted in significant prevention of behavioral, immunohistochemical, HPLC and PET scan findings. Overall, the present study demonstrated that over-expression of HGF prevented neuronal death in a PD primate model, providing a potential novel therapy for PD.
Tau Oligomers: Cytotoxicity, Propagation, and Mitochondrial Damage

Aging has long been considered as the main risk factor for several neurodegenerative disorders including a large group of diseases known as tauopathies. Even though neurofibrillary tangles (NFTs) have been examined as the main histopathological hallmark, they do not seem to play a role as the toxic entities leading to disease. Recent studies suggest that an intermediate form of tau, prior to NFT formation, the tau oligomer, is the true toxic species. However, the mechanisms by which tau oligomers trigger neurodegeneration remain unknown. This review summarizes recent findings regarding the role of tau oligomers in disease, including release from cells, propagation from affected to unaffected brain regions, uptake into cells, and toxicity via mitochondrial dysfunction. A greater understanding of tauopathies may lead to future advancements in regards to prevention and treatment.
Mitotic phosphorylation of SUN1 loosens its connection with the nuclear lamina while the LINC complex remains intact

At the onset mitosis in higher eukaryotes, the nuclear envelope (NE) undergoes dramatic deconstruction to allow separation of duplicated chromosomes. Studies have shown that during this process of nuclear envelope breakdown (NEBD), the extensive protein networks of the nuclear lamina are disassembled through phosphorylation of lamins and several inner nuclear membrane (INM) proteins. The LINC complex, composed of SUN and nesprin proteins, is involved in multiple interactions at the NE and plays vital roles in nuclear and cellular mechanics by connecting the nucleus to the cytoskeleton. Here, we show that SUN1, located in the INM, undergoes mitosis-specific phosphorylation on at least 3 sites within its nucleoplasmic N-terminus. We further identify Cdk1 as the kinase responsible for serine 48 and 333 phosphorylation, while serine 138 is phosphorylated by Plk1. In mitotic cells, SUN1 loses its interaction with N-terminal domain binding partners lamin A/C, emerin, and short nesprin-2 isoforms. Furthermore, a triple phosphomimetic SUN1 mutant displays increased solubility and reduced retention at the NE. In contrast, the central LINC complex interaction between the SUN1 C-terminus and the KASH domain of nesprin-2 is maintained during mitosis. Together, these data support a model whereby mitotic phosphorylation of SUN1 disrupts interactions with nucleoplasmic binding partners, promoting disassembly of the nuclear lamina and, potentially, its chromatin interactions. At the same time, our data add to an emerging picture that the core LINC complex plays an active role in NEBD.
Sensitivity of signal reconstruction

A method of assessing the quality of reconstructing signals from finite sets of samples is presented. The assessment uses a sensitivity function that provides information about the reliability of the reconstructed signal at every time instant. The sensitivity function equals zero where the reconstruction is perfect (sampling instants) and achieve global maximum where the available samples do not provide any information about the original signal (typically at /spl plusmn//spl prop/). The proposed method measures the quality of reconstructing before the actual samples of the signal are taken.
Feature Concatenation Multiview Subspace Clustering

Multi-view clustering aims to achieve more promising clustering results than single-view clustering by exploring the multi-view information. Since statistic properties of different views are diverse, even incompatible, few approaches implement multi-view clustering based on the concatenated features directly. However, feature concatenation is a natural way to combine multiple views. To this end, this paper proposes a novel multi-view subspace clustering approach dubbed Feature Concatenation Multi-view Subspace Clustering (FCMSC). Specifically, by exploring the consensus information, multi-view data are concatenated into a joint representation firstly, then, l2,1-norm is integrated into the objective function to deal with the sample-specific and cluster-specific corruptions of multiple views for benefiting the clustering performance. Furthermore, by introducing graph Laplacians of multiple views, a graph regularized FCMSC is also introduced to explore both the consensus information and complementary information for clustering. It is noteworthy that the obtained coefficient matrix is not derived by directly applying the Low-Rank Representation (LRR) to the joint view representation simply. Finally, an effective algorithm based on the Augmented Lagrangian Multiplier (ALM) is designed to optimized the objective functions. Comprehensive experiments on six real world datasets illustrate the superiority of the proposed methods over several state-of-the-art approaches for multi-view clustering.
FastFlow: Efficient Parallel Streaming Applications on Multi-core

Shared memory multiprocessors come back to popularity thanks to rapid spreading of commodity multi-core architectures. As ever, shared memory programs are fairly easy to write and quite hard to optimise; providing multi-core programmers with optimising tools and programming frameworks is a nowadays challenge. Few efforts have been done to support effective streaming applications on these architectures. In this paper we introduce FastFlow, a low-level programming framework based on lock-free queues explicitly designed to support high-level languages for streaming applications. We compare FastFlow with state-of-the-art programming frameworks such as Cilk, OpenMP, and Intel TBB. We experimentally demonstrate that FastFlow is always more efficient than all of them in a set of micro-benchmarks and on a real world application; the speedup edge of FastFlow over other solutions might be bold for fine grain tasks, as an example +35% on OpenMP, +226% on Cilk, +96% on TBB for the alignment of protein P01111 against UniProt DB using Smith-Waterman algorithm.
Multi-criteria evaluation of interesting dependencies according to a data mining approach

This paper addresses the problem of the goodness of dependency rules extracted by mining data. Our approach is experimental and based on the idea that model quality such as accuracy, interestingness or domain-dependent criteria. Most works on model quality are focusing on one criterion at a time only and do not take into account multiple factors simultaneously. A few works combine different measures in weighted expressions. In order to combine multiple measures, we have first realized a comparative study which highlights the relative contribution of different factors and reveals trade-offs among some of them. This situation suggests looking in the rules which may not exist. Thus, we show that a multi-objective evolutionary approach is able to reveal interesting rules which are ignored by standard solutions.
Voice based control command signal generation for intelligent system

The speech processing and its application to intelligent system is the state of the art research. The systems are getting smarter day by day with the introduction of the speech signal to control the machine. The basic model of human speech system is used to design the algorithm which is able to detect words as well as an alphabetical letter to generate commands and control machine. The speech enhancement followed by feature extraction algorithm is used to extract the information embedded in speech signal. Once the speech is enhanced and the valued information is extracted, automatic speech recognition system is used to continuously detect the environmental sound and capture the portion of sound which is in the range of human speech frequency. Feature classification algorithm is further used to detect words or letter following different class.
Demographic fitness of Belminus ferroae (Hemiptera: Triatominae) on three different hosts under laboratory conditions

Triatominae are widely recognised for their role as vectors of Trypanosoma cruzi. One of the main biological characteristics of this subfamily is their obligate haematophagous condition. However, previous studies on Belminus herreri and Belminus ferroae suggested that cockroaches are their principal hosts in domiciles. Due to this peculiar behaviour, the aim of this study was to analyse several demographic and reproductive parameters of B. ferroae fed on three different hosts (mice, cockroaches and Rhodnius prolixus) and relate B. ferroae fitness to these alternative hosts. The cohorts were reared under constant conditions. The egg hatching rate was similar for cohorts fed on cockroaches (69.4%) and R. prolixus (63.8%), but was much lower for the cohort fed on mice (16%). The development time from the nymph to adult stage and the average age of first reproduction (α) presented lower values in the cohort fed on cockroaches, which is consistent with the higher population growth rate associated with this host. Demographic parameters [intrinsic rate of natural increase, finite rate of population growth, net reproductive rate and damping ratio] showed statistically significant differences between the cohorts. Analysis of the life history of B. ferroae revealed a higher fitness related to the cockroach. The implications of these results for the origin of the subfamily are discussed.
A Posthuman-Xenofeminist Analysis of the Discourse on Autonomous Weapons Systems and Other Killing Machines

Abstract In this article, I critique the current debates surrounding autonomous weapons systems, using feminist posthuman theory to make sense of such systems – and the relation between human and machine – in terms of automation and autonomy. The dominant narratives about autonomous weapons tend to present them as exceptional; they are distinct from all the other kinds of human inventions that can kill. Further attention is required, not on autonomous weapons themselves but on the delegation of killing to a far broader range of technologies across the human–machine/autonomous–automated spectrum. While current attempts at legal regulation distinguish between civil and military technologies, such a distinction becomes impossible in light of the links between civil and military technologies and the killing potential of many technologies, including artificial intelligence.
Roentgen stereophotogrammetric analysis as a predictor of mechanical loosening of knee prostheses.

The tibial components in 143 patients with total knee replacements performed before 1988 were assessed for micromotion using roentgen stereophotogrammetric analysis (RSA) over a period of 13 years. The fixation of the prostheses remained clinically sound in all cases, although revision had been required for other reasons in seven. In a second group taken from all cases with RSA available on our full database to 1990, 15 tibial components had been followed by RSA from the insertion until, 1 to 11 years after the initial arthroplasty, they were revised for mechanical loosening of the tibial component; 12 of these comprised all the loosenings in the base group, thus making a total of 155 consecutive cases, while an additional three were inserted after the base material had been compiled. The mean migration in the first group was about 1 mm at one year, but subsequent migration was slower, reaching a mean of about 1.5 mm after ten years. About one-third migrated continuously throughout follow-up, while two-thirds ceased to migrate after one to two years. In the revision group, 14 components had migrated continuously and at one year significantly more than those in the first group. One revision case lacked the crucial one-year follow-up and could not be classified. These findings suggest that mechanical loosening begins early in the postoperative period. Clinical symptoms which necessitate revision, seen at this stage in 20% of abnormally migrating tibial components, may not appear until up to ten years after the operation. (ABSTRACT TRUNCATED AT 250 WORDS)
DG-JFET for Low Power Applications and Behavior of It as a MOS Capacitor

In this work a 22 nm Dual Gate Enhancement Mode Junction Field Effect Transistor (DG-JFET) structure is proposed and its behavior as a MOS capacitor is studied. The results have shown that, the proposed DG-JFET has better short channel effect (SCE) suppression and a lower threshold voltage than MOSFETs. DG-JFETs were recognized as one of the possible choice to continue the scaling beyond the conventional limits. DAVINCI (a Synopsys® 3D-device simulation tool) is used to analyze the device architecture and performance initially. The numerical device simulation results show that the enhancement mode DG-JFETs as an emerging technology to extend the scaling and the parasitic behavior of the device is analyzed from the carrier profile.
A Study of Techniques for Facial Detection and Expression Classification

Automatic recognition of facial expressions is an important component for human-machine interfaces. It has lot of attraction in research area since 1990's.Although humans recognize face without effort or delay, recognition by a machine is still a challenge. Some of its challenges are highly dynamic in their orientation, lightening, scale, facial expression and occlusion. Applications are in the fields like user authentication, person identification, video surveillance, information security, data privacy etc. The various approaches for facial recognition are categorized into two namely holistic based facial recognition and feature based facial recognition. Holistic based treat the image data as one entity without isolating different region in the face where as feature based methods identify certain points on the face such as eyes, nose and mouth etc. In this paper, facial expression recognition is analyzed with various methods of facial detection,facial feature extraction and classification.
Participation in further education in England and Wales: an analysis of post-war trends

The paper examines the time-series evidence relating to participation rates in further education in England and Wales and, using cointegration analysis, identifies a long-run statistical relationship in the data consistent with an augmented human-capital model. The recent rapid growth of participation is largely attributable to the improvements in GCSE attainment, coupled with the expansion of higher education, of the last decade. Fluctuations in labour demand play a significant role in determining the movements of participation rates over time, and the substantial rise in youth unemployment of the early 1990s contributed to the growth in participation at this time. Copyright 2001 by Oxford University Press.
Slow potentials in spontaneous ganglion cells of the lobster heart

Summary The slow potential was recorded from the large cell of the lobster cardiac ganglion, and effects of polarizing currents on its initiation were observed. 1. Depolarization of Cell 5 at a sufficient interval after the preceding slow potential elicited synaptic potentials and slow potential. Hyperpolarization impeded the development of the slow potential. 2. Synaptic potentials occurred repetitively during depolarization. They were evoked by stimulus given at varying phases during the spontaneous activity, differing from the slow potential which was elicited with a critical interval. This fact indicates that the slow potential is the independent depolarization of the membrane of large cell, separated from synaptic potentials. 3. Axon produced trains of full-sized spikes, but it did not exhibit the slow potential, suggesting that the slow potential was generated at the soma and dendrites of large cell. 4. The spontaneous burst of the large cell was composed of the slow potentials and spikes. When the small cells that induced synaptic potentials were inactive, the large cells became pacemakers which initiated only the slow potential with superimposed spikes. 5. Synchronous discharges of the cardiac ganglion are considered to be performed by the coordination of the activities of both large and small cells.