dataesr/scientific-paragraphs-categorization huggingface dataset:
ICN deployments will allow improving substantially the quality of service for indoor user equipments (UEs), and bring real competition to Wi-Fi technologies for the increasingly remunerative indoor market. The emergence of pervasive ICNs makes it important to comprehend how such networks will be used. In this context, a considerable volume of research has focused on methods related to the modeling of radio propagation in indoor environments  [46, 36, 4] , the impact of the building layout on network performance  [26, 59, 58, 6]  or the efficient planning of ICNs  [19, 55, 54, 5]. However, the dynamics and distinguishing features of the traffic data generated by in-building radio access network components have not been studied yet. Unlike outdoor base stations (BSs) that tend to observe a general-purpose use, i.
However, all these approaches build upon the cellular data recorded at outdoor BSs, disregarding the ICN traffic and its peculiarities. The literature on the characteristics of ICN traffic demands is in fact rather limited  [44, 60, 24]. The works in  [44, 60]  compared the characteristics of outdoor BSs and wireline traffic demands, pronouncing that there are distinct differences in terms of packet, flow, and session-level statistics, as well as in the temporal traffic patterns. However, despite wireline networks being installed indoors, their operation is fundamentally different from that of wireless ICNs, and thus the conclusions of  [44, 60]  cannot be straightforwardly extended to our case study. The traffic from ICNs was considered in  [24] , exploring the mobile application utilization profiles in Santiago de Chile for a 15-day period.
The authors discussed how the urban context and time of the day affect human activities and application usage. More specifically, along with the application traffic patterns of outdoor BSs, they presented these of indoor BSs, but without expanding on their specific characteristics or how they fluctuate across different indoor environments. Our work fills that gap, building upon a rich Internet measurement data set to evince that various application utilization clusters exist inherently in ICN traffic, revealing the particularities of each cluster, and correlating them with the indoor environment in which they are generated.
INTERNET MEASUREMENT DATA The measurement traffic data used in our work was collected in the production network of a major MNO providing services throughout a nationwide network in France. To conduct the measurement collection, the operator deploys passive measurement probes to monitor the Gi, SGi, and Gn interfaces that connect Gateway GPRS Support Nodes (GGSNs) and Packet Data Network Gateway (PGWs) to external Public Data Networks (PDNs), gathering data about the traffic generated by mobile subscribers using 4G and 5G connectivity. Indeed, the MNO is presently operating a 5G non-standalone (NSA) deployment, which allows gathering data about both 4G and 5G traffic via measurements limited to the 4G Evolved Packet Core (EPC) network that is shared by 4G eNodeBs and 5G gNodeBs in the Radio Access Network (RAN).
The MNO identifies the mobile service associated with each TCP and UDP session recorded by the probes, by running Deep Packet Inspection (PDI) and analyzing the results via proprietary traffic classifiers. Each such IP session is also geo-referenced at the level of Base Transceiver Station (BTS), by exploiting the User Location Information (ULI) field present in the Packet Data Protocol (PDP) Contexts and Evolved Packet System (EPS) Bearers over the GPRS Tunneling Protocol control plane (GTP-C). Based on this information, it is possible to estimate the traffic demand for each mobile application at an individual BTS, by aggregating the traffic of all IP sessions from/to the same BTS. Such data is aggregated over time within intervals of one hour for the purpose of our study. Overall, the data used throughout the paper comprise per-hour downlink and uplink traffic of various mobile services at all indoor cellular antennas managed by the MNO in the target country.
This includes 4, 762 ICN antennas installed at more than 1, 000 sites, comprising different types of indoor environments located at an urban, suburban, or rural surrounding. We note that the vast majority of those antennas are 4G, as apparently 5G is scarcely used for ICN at this stage of roll-out of the technology in France. The recording period was approximately two months, starting from the 21 st of November 2022 and extending until the 24 th of January 2023. The mobile services considered span a diverse range of mobile applications used throughout daily life related to activities such as social networking, messaging, audio and video streaming, transportation, professional activities, and well-being. The ethical considerations related to the data collection and processing are discussed in detail in the Ethics sections in the Appendix.
Measuring relative ICN service usage To probe the dynamics of the ICN mobile traffic demands across the network, we pursue an unsupervised learning approach. In particular, we consider the aggregated sum of the downlink and uplink traffic recorded for each mobile service over the target twomonth period as a distinct feature, and we form a matrix, 𝑇 𝑁 ×𝑀 , comprising the overall traffic in megabytes (MB) for the 𝑁 indoor antennas and 𝑀 applications included in our data set. In particular, for the rest of our study, we consider 𝑁 = 4, 762 indoor antennas and 𝑀 = 73 mobile services. Our aim is to pass this matrix to an unsupervised learning algorithm, which will be able to identify patterns and existing hidden structures within the traffic data, without further guidance. However, the overall traffic is not a defining feature per se, and it will inevitably instigate bias in the clustering algorithm for two reasons.
ETHICS Our work builds on mobile network traffic generated by users of a nationwide cellular infrastructure, focusing on the traffic generated by ICNs. Specifically, we leverage the hourly traffic demands at the level of individual cells, which are generated from network measurements carried out in the target infrastructure as detailed in Section 3. The traffic measurements used to compute the measures introduced in Section 4. 2 were collected by the operator for network management and research purposes, and temporarily stored within a secure platform at their own premises. The hour-level aggregation was also carried out in the same platform by personnel of the network operator, in full compliance with Article 89 of the General Data Protection Regulation (GDPR)  [15]  of the European Commission.
g. farm casual labour, the disconnection between the work and the worker). All of these cases comprise innovations which reconfigure how farming is practiced, integrating new elements, knowledge and ways of working. For full case study reports see the AgriLink project website (www. agrilink2020. eu). The research utilised a standardised approach to identifying farmers' microAKIS. Case studies were identified in regions at NUTS 3 level. Study farmers were primarily identified utilising a snowball methodology, with an emphasis on identifying as wide a variety of respondents as possible. In the French case study, a database from another research project on outsourcing practices was utilised to ensure a broad range of activities was covered. As is characteristic of qualitative research, farmer interviews continued until saturation was reached, typically comprising between 30 and 50 interviews per case study (see Table  1 ).
e. identifying the extent to which the microAKIS identified by individual farmers reflected the infrastructural AKIS at regional level). In all four case studies, research was undertaken in regions where the innovations had been establishing for several years, so that researchers could assess change over time in knowledge sources. The purposes of the studies were not to be representative, but to garner a wide range of situations. Data was collected face-to-face or by telephone in 2019. Interviews were audio-recorded with informed consent from the interviewees, transcribed in note form in their native languages, and initially analysed in relation to the overall research questions of the project. This analysis is available in projects reports on the AgriLink website. The data presented is this paper is a re-analysis of the data collected for the AgriLink project, applying assemblage theory.
e. it's historicity). The data on materialities was derived from questions about the barriers to adoption, the most important types of knowledge and skills the farmers needed to assess the innovation, risks and uncertainties associated with the innovation, and negative side effects. AKIS actor respondents also offered insights into materialities through their responses to questions about the sustainability implications (social, environmental and economic) of the innovation. The focus of the dataset on farmers microAKIS supported an analysis of assemblages at farm level. Data were reanalysed in table form for comparative analysis across the four cases, with separate lines focusing on the themes presented in this paper: historicity and ruptures, elements of the assemblage and knowledge, and the materialities of the innovation.
Consideration of a dataset from multiple theoretical perspectives is not unusual in rural studies, although there are some limitations to this approach. A dataset specifically designed for consideration using assemblage theory would have more directly interrogated the materialities and territorialisation processes. Pursuing characterisation of the microAKIS as a method necessarily places the farmer at the centre of the farm assemblage, as the primary territorialising force. This is at odds with the orientation of more-than-human research towards decentralising human agency. However, as we demonstrate, the data provides a useful starting point for considering how assemblage theory can advance  AKIS concepts.
Acknowledgements We wish to thank  Adam Calo  for his comments on an earlier draft and  Mark Redman  for his summary of policy approaches to AKIS in the AgriLink conceptual framework, which we drew on for this paper. We wish to thank the data collectors for the case studies:  Gunn-Turid Kvam  and  Renate M Butli Hårstad  both from  Ruralis ,  Emils Kilis  and  Talis Tisenkopfs  from the  Baltic Studies Centre ;  Geneviève Nguyen  and  Eloïse Bergeret  from  INRAE  and  Helen Zarokosta  from the  Agricultural University of Athens. We also wish to thank two anonymous reviewers who provided detailed and very constructive feedback on earlier versions of this paper. The research presented in this paper was funded by the  European Union 's  Horizon 2020 research and innovation programme  under grant agreement No  727577  (AgriLink).
Stage 3: after the final SC layer, the network uses a global averaging stage before a classification layer, while the saliency masks are integrated and contribute to generate the final output of the network. (B) Spontaneous emergence of spatial frequency tuning and orientation sensitivity. Discrimination performance across gratings of different spatial frequencies (upper) and orientation (lower) in the SC model and in the AlexNet model that approximate V1 responses. (C) Example of bubbles analysis on three subjects from the test dataset. (D) Effect of face manipulation toward M and P channels in the SC model and in the fMRI activity of the human SC. Scatterplots and marginal distributions of classification probability for LSF and HSF filtered faces compared to original images. The y-axis corresponds to the probability of belonging to the correct category assigned by the model to each unfiltered image, while the x-axis represents the probability assigned when the instances are spatial frequency filtered.
Despite advances in cardioprotection, new therapeutic strategies capable of preventing ischemia-reperfusion injury of patients are still needed. Here, we discover that sarcoplasmic/endoplasmic reticulum Ca 2+ ATPase (SERCA2) phosphorylation at serine 663 is a clinical and pathophysiological event of cardiac function. Indeed, the phosphorylation level of SERCA2 at serine 663 is increased in ischemic hearts of patients and mouse. Analyses on different human cell lines indicate that preventing serine 663 phosphorylation significantly increases SERCA2 activity and protects against cell death, by counteracting cytosolic and mitochondrial Ca 2+ overload. By identifying the phosphorylation level of SERCA2 at serine 663 as an essential regulator of SERCA2 activity, Ca 2+ homeostasis and infarct size, these data contribute to a more comprehensive understanding of the excitation/contraction coupling of cardiomyocytes and establish the pathophysiological role and the therapeutic potential of SERCA2 modulation in acute myocardial infarction, based on the hotspot phosphorylation level of SERCA2 at serine 663 residue.
Ratio signals were normalized as following: [1+ (R -R t=600s )/(R t=180s. -R t=600s )]. B Violin plot of ER Ca 2+ refilling slope over two minutes from time 630 s of control (n = 199, on 11 experimental days), TDZD8 (n = 210, on 7 experimental days), thapsigargin (n = 42, on 2 experimental days) and 1 µM SB216763 (N = 212 cells, on 6 experimental days). Median with a 95% confidence interval is shown and one-way ANOVA followed by Tukey's multiple comparisons test was used to assess significance versus Control condition (****p < 0. 0001). C Motif of the GSK3β substrate sequence (from PhosphoSitePlus database). D Listing of in silico analysis of putative GSK3β target sites on SERCA2 determined by NetPhos3. 1 and PhosphoSitePlus public databases. E Mass spectrometry analysis of SERCA2 phosphorylation at serine 663 residue (Sp663) in left ventricle of C57BL/6 mice in basal (Control; n = 10) and after 60 min ischemia followed by 30 minutes reoxygenation (IR; n = 10).
0002). L Resting cytosol Ca 2+ evaluated with the ratiometric FuraRed sensor in rWT (N = 6) and rS663A (N = 8) SERCA2 rescued mice. Median with interquartile interval is shown and two-tailed unpaired t test with Welch's correction was used to assess significance (*p = 0. 0105). M-P Quantification of sarcomere shortening in mouse cardiomyocytes isolated from the AR after the in vivo ischemia-reperfusion insult measured with the software IonWizard; Ionoptix system. M Evaluation of peak h in µm in rWT (N = 135) and rS663A (N = 245) SERCA2 rescued cardiomyocytes. Median with interquartile interval is shown and two-tailed unpaired t test with Welch's correction was used to assess significance (****p < 0. 0001). N Evaluation of time to peak 50% in rWT (N = 135) and rS663A (N = 245) SERCA2 rescued cardiomyocytes.
In silico analysis The putative GSK3β binding sites on SERCA2 were predicted using NetPhos 3. 1  33  [https://services. healthtech. dtu. dk/services/NetPhos-3. 1/] and PhosphoSitePlus  34  [https://www. phosphosite. org/homeAction. action] public databases. Cell culture HEK293-T (ATCC, CRL-3216), MEF-T cell lines and their derivatives were routinely cultured in Dulbecco's Modified Eagle Medium (Gibco) supplemented with 10% fetal calf serum (PAN-biotech), 100 µM nonessential amino acids (Gibco), 100 U/mL penicillin (Gibco), 100 µg/mL streptomycin (Gibco), 2 mM L-glutamine (Gibco), 1 mM sodium pyruvate (Gibco) and incubated at 37 °C in 5% CO 2 in a damp atmosphere. Cells were regularly passaged by single-cell dissociation with 0. 05% trypsin-EDTA (Gibco). Generation of transient transfectants.
The impact of H/R was evaluated regarding the percentage of dead PI-positive cells measured using the 561 nm laser on a LSRFortessa X-20 (BD-Biosciences) and then analyzed using FACSDiva 8. 0. 1 software (BD-Biosciences). Acquisition thresholds were set to select for cell population without debris and a live/dead gate set to 5% using a no-PI treated sample. A total of 10,000 cells per tubes were acquired in triplicate and then averaged.
We first analyzed the donor-alone images, we extracted the variables of the exponential fit of donor spectral bleed-through as a function of fluorescence intensity. We finally averaged these variables to generate to donor spectral bleed-through correction factor. In a second time, we proceed in the same way for the acceptor-alone images and extracted a constant value for the acceptor spectral bleed-through. Finally, we analyzed the three channels of FRET images and we sorted out the FRET efficiency maps. Pixel distribution histograms of these FRET efficiency maps were extracted and fitted with a robust Gaussian regression (Prism, GraphPad Software) prior their averaging. The mean value of each Gaussian regression was averaged for each condition.
Cardiomyocytes were then collected and homogenized for imaging or proteomic analysis. Mitochondrial characterization. Live ACM were labeled with 5 µM MitoSOX red reagent (Invitrogen, M36008) for detecting mitochondrial reactive oxygen species (ROS) and 20 nM MitoProbe Tetramethylrhodamine (Invitrogen, M20036) for determining mitochondrial membrane potential. Percentage of stained cells was measured using the 561 nm laser on a LSRFortessa X-20 (Becton-Dickinson) and then analyzed using FACSDiva 8. 0. 1 software (Becton-Dickinson). The total ACM number threshold for flow cytometry was set at 10,000 cells. Mitochondrial respiration. Mitochondrial oxygen consumption rate was measured on intact cardiomyocytes (500 µg), incubated in CCB buffer (140 mM NaCl, 5 mM KCl, 10 mM HEPES, 1 mM MgCl2, 2 mM CaCl 2 , 10 mM glucose; adjusted to pH 7.
Caffeine response parameters were further analyzed with OriginPRO (OriginLab9. 0. 0. 87)  65. Sarcomere shortening. Isolated Cardiomyocytes were paced using a field stimulator at a frequency of 1 Hz, 20 V and movement of cardiomyocytes was measured and analyzed with the IonWizard software Ionoptix  68. Patch-clamp electrophysiology. Current recordings were made at room temperature under voltage clamp using the whole-cell configuration of the patch-clamp technique. Command voltage and data acquisition were performed with pClamp software (Axon Instruments, Foster city, CA, USA). The holding potential (HP) was kept at -80 mV. Membrane capacitance (C m ) was systematically measured and was calculated by analyzing the capacitive surge produced by a small voltage step as previously described  69.
Statistics Data processing and statistical analyses were conducted with Excel (Microsoft 2016), Prism (GraphPad5. 0. 0), OriginPro (Origi-nLab9. 0. 0. 87) and R (R Core Team 2020) software. Mean with 95% confidence interval or Median with an interquartile range, calculated from at least three independent experiments, are shown. Two-tailed unpaired t test with Welch's correction, two-tailed paired with Wilcoxon test, one-and two-way ANOVA followed by Tukey's multiple comparisons or a Mann-Whitney test were used to assess significance (ns p ≥ 0. 05, *p < 0. 05, **p < 0. 01, ***p < 0. 001, ****p < 0. 0001).
Acknowledgements We would like to acknowledge our fundings from the  French National Research Agency   ANR-JCJC 16-CE17-0020-01  to L. G and  OPeRa IHU  research program  ANR-10-IBHU-0004  to M. O, and from the  Leducq Transatlantic Network of Excellence "Targeting mitochondria  to treat heart disease" (MitoCardia,  16CVD04 ) to M. P and M. O. We are very grateful to  William Edward Louch  for the generous gift of the Serca2 flox/flox Tg(αMHC-MerCreMer) and Serca2 flox/flox transgenic mice, and his advice in maintaining the SERCA transgenic mice. We would like to thank the iXplora [https://sfrsantelyonest. univ-lyon1. fr/ixplora/index. php] platform (Celphedia) [https://celphedia. eu/en/]for in vivo expertise and help in analysis; the  Tissue-Tumorotheque Est  ( CRB-HCL, HCL's biobank ) for the human biological samples; the contribution of Protein.
MβL Fold Enzymes in Archaea 4. 1. Reconstruction of Common Ancestral Sequences and Blast Analyses In our previous research, to investigate MβL sequences from unsuspected microorganisms such as archaea, which are naturally resistant to all antibiotics including β-lactams because they lack peptidoglycans, we performed the reconstruction of ancestral bacterial β-lactamases, especially class B metallo-β-lactamases based on the maximum likelihood phylogenetic tree analysis using 174 class B MβL variants retrieved from the Arg-annot database  [60]. Using an inferred MβL fold ancestor sequence as the query term in a BlastP analysis performed against the archaea database, we were able to identify a huge number of archaeal MβL fold sequences, while BlastP analysis, using contemporary bacterial sequences did not detect these archaeal sequences  [6].
Discovery of MβL Fold Enzymes in Giant Viruses With the existence of evidence of MβL fold enzymes in all domains of life, including Bacteria, Archaea, and Eukaryotes, as mentioned above, we similarly conducted, as part of our research into these MβL fold enzymes, a search for MβL fold enzymes in Giant viruses. By searching for the conserved MβL motif against a protein database of giant viruses retrieved from the NCBI (n = 72,993 proteins), we were able to identify fifteen confirmed MβL fold sequences (based on a protein length of at least 200 aa). Default protein annotations of these gvMβL sequences from the NCBI database included ribonuclease Z, the ribonuclease BN/tRNA processing enzyme, the MβL fold metallo-hydrolase/oxidoreductase superfamily, the metallo-β-lactamase superfamily protein, the Ankyrin repeat domain-containing protein, and proteins with unknown function.
Among these AR-like enzymes, especially β-lactam resistance proteins, the search for an MβL signature (HxHxDH) revealed their existence in this domain of life, as shown in Figure  2  for representative sequences. The default annotations of these CPR proteins from the NCBI database are mainly "MβL fold metallo-hydrolase", "β-lactamase domain protein", or "RNA-metabolising metallo-β-lactamase". Interestingly, as shown in Figure  1 , the identified MβL fold sequences in CPR microorganisms constitute one branch from the phylogenetic tree in which archaeal and Asgard sequences can be identified, and one of them, from Sulfolobus tokodaii, was reported to have a function associated with the quorum sensing mechanism  [38]. This may suggest a native function of these CPR MβL fold enzymes, associated with communication processes with bacteria, with which they share an obligate symbiotic lifestyle, as reported in the literature  [70].
e. , PSI-BLAST: Position-Specific Iterated BLAST; PHI-BLAST: Pattern Hit Initiated BLAST; DELTA-BLAST: Domain Enhanced Lookup Time Accelerated BLAST). More sensitive search approaches including the search for Hidden Markov Models (HMM) profile, Sequence Similarity Network analysis (SSN), and the use of inferred common ancestor sequences as targets are more appropriate and more useful when it comes to detecting and identifying homologous sequences in any organism. This review highlights a great example of the misleading annotations of proteins in public sequence databases, which is not only limited to MβL fold proteins but applied to many classes of sequences proteins as previously reported, greatly reducing our perception of the multifunctionality of some proteins, due to the unique attributed function by the default protein annotation  [85].