dataesr/scientific-paragraphs-categorization huggingface dataset:
Electrophysiology. Stereotactic EEG (sEEG) was recorded with (depth) macro-electrodes (AdTech) of 4-12 platinum contacts 1 mm in diameter, with nickel-chromium wiring and polyurethane tubing. The macro-micro probes of Behnke-Fried type consisted of 8 platinum macro-contacts embedded on the surface of a polyurethane tube with a hollow lumen (diameter 1, 3 mm). Eight 40-μ m platinum-iridium micro-wires were protruded 3-6 mm beyond the macro-electrode tip into the cerebral tissue (Fig. 1A , inset). During surgery, wires were trimmed to ensure they entered grey matter. Signals from macro-and micro-contacts were acquired simultaneously, at sampling rates of 4 kHz and 32 kHz respectively, with a 160-channel Atlas recording system (Neuralynx Inc. , Tucson, AZ, Cheetah acquisition software). Bandpass filter settings for the macro-and micro-electrode recordings were 0.
Training procedure. The training protocol included a short screening procedure and the actual training. During the screening the subjects explored different cognitive strategies to control the sphere movement. We suggested to try out several cognitive tasks, depending on the position of the target electrode and using a cognitive functional atlas database (www. linkrbrain. org. Tasks included visual, auditory, linguistic or spatial imagery, mathematical exercises, memory retrieval or executive functions. If a successful strategy could be identified, we asked the subjects to maintain it for the training condition. Subsequently, three to six training sessions of 5 minutes each were conducted per day on 2-4 successive days, according to subjects' willingness and capability to participate (session number: min = 7, max = 19, mean = 15.
Offline analysis. After training was completed, signals from all macro-contacts were re-referenced to a common average reference montage of at least 30 artifact-free channels for offline analysis. Possible muscle, movement or epileptic artifacts were screened visually across complete data sets. In total 403 macro-contacts were recorded, and signal from 326 artifact-free channels was used for further analysis (see Supplementary Figure  S1  for individual electrode positions and Supplementary Table  ST1  for anatomical regions). Electrical 50 Hz noise was suppressed by the same zero-phase forward-backward digital infinite impulse response (IIR) type II Chebyshev bandstop filter as used for real-time analysis. All analyses were implemented in MATLAB (The MathWorks).
Oscillatory event detection. To analyze successful modulation periods in more detail, we extracted intervals of strong theta activity from all sessions. Automatic detection of these 'oscillatory events' was based on two criteria: amplitude threshold > mean + 1 SD of baseline (above the 68 th percentile of the baseline distribution), and a duration of at least 600 ms (about 4 theta cycles). Detection based on power or envelope yielded comparable results. Detected events were selected for further offline analysis from each subject, after visual inspection and removal of possible artifacts (number of selected events per subject, S1 to S6 in order: 886, 255, 384, 645, 255, 433, total 2858 events). The timing of identified events was consistent with threshold crossings detected online during experiments (data not shown).
Regression analysis. Individual control indices for each session were regressed to a single linear predictor term, namely the number of connections per session. Models were generated with Matlab function 'fitlm' and resulting regression coefficients were used to fit the data. Theta-Gamma modulation index. Coupling of theta and gamma frequency was assessed in several stages. We first visually inspected time-frequency representations of all oscillatory events split into non-overlapping theta cycles aligned at the troughs. Time-frequency representations were calculated separately for each cycle and then averaged to preserve induced oscillatory phenomena. Gabor wavelet transform with a modulated Gaussian window was used to derive time-frequency decompositions  42. Visual inspection suggested theta-gamma occurred at frequencies in the range 30-120 Hz.
We then generated phase-and amplitude-time series for all sessions. Phase times series in the theta range were calculated with an IIR Chebyshev filter with a forward-backward filtering algorithm to avoid phase distortion  43. Amplitude times series in the gamma range were extracted using Gabor wavelet transform. Theta-gamma modulation was then estimated using procedures as described  44. To evaluate the coupling strength induced specifically through training, we calculated the MI as the difference between training and baseline modulation indices. Increase in coupling was assessed as correlation between time (individual session numbers) and MI. Firing rate and spike-field locking analysis. Spike sorting was performed offline with Wave_Clus software  45  and verified with a second method Klustakwik  46.
We distinguished between multi-unit (MUA) and single-unit activity (SUA) using the criterion that less than 1% of spikes should show inter-spike-intervals (ISI) below 3 ms. We classed units recorded from the same channel but on different days as distinct cells. In the following we use the term neuron to refer to a putative multi-or single-unit. Binary data containing spike trains were converted to instantaneous firing rate using a Gaussian kernel convolution (kernel width 3 s). We classed neuronal activity during oscillatory events from all subjects (1641 events with spikes) according to increasing, decreasing or stable firing frequency and measure their distance to target electrode. A threshold of 40% was used to define changes in firing rate over 1000 ms before and after event onset (post-pre > 40%: increase; post-pre < -40%: decrease; -40% < post-pre < 40%: stable).
Spike-field locking was calculated from LFP phase-times series of the target electrode, extracted at the times of spiking, with distances between target zone and micro-electrodes ranging between 5 and 37 mm (see section Electrophysiology). Phase-locking was statistically evaluated with the Matlab toolbox for circular statistics  47. We distinguished increasing, decreasing or sustained phase-locking, from Rayleigh Z-statistics for each session and their correlation with time (n = 9). Different patterns were assigned as for firing rate analysis (threshold at r = ± 0. 4).
Limitations of the study. There are several limitations of the present study. Most importantly, the anatomical heterogeneity and the small number of electrode locations (and thus training target) across subjects make it difficult to fully investigate the anatomical specificity of the response. A larger group of subject would allow studying voluntary control of oscillations across the whole cortex. A second concern is that our data were obtained from patients suffering from medically intractable epilepsy and some abnormal activities (such as interictal spikes or high-amplitude slow waves) constitute a source of signal artifacts. In our case, we minimized this contamination by selecting for recording sites that are virtually free from epileptiform activity. Still, there could be some significant alterations caused by the pathology or due to the medication.
Results In this paper, we first attempt to observe the difference of the spatial patterns during the sessions: visual, FES and visual+FES. For this purpose, we determine the power spectral density (PSD)13 of each spatial filters. The PSD distribution for six spatial filters of subject 1 is shown in Fig. 2. As observed from the figure, the patterns are highly discriminable for the first four filters and they overlap in the last two. it is also noted that FES+Visual session (in black) has the highest power followed by Visual (in blue) session and lastly FES session (in red) for the first three filters. A similar trend is noted for the other two subjects too. Next, we employ 10 cross validation12 on the dataset, where at every iteration, one block of data is randomly selected for testing and the rest of the block are employed for training.
Introduction The last decade has seen a significant number of new retinal treatment paradigms commencing clinical trials. 4] [5]  While all of these approaches hold promise, only retinal prostheses have reached the market for the restoration of some visual function in patients blind from retinitis pigmentosa. The Argus II System was the first and remains one of only two retinal prostheses to be approved for commercialization in the European Economic Area (receiving CE Mark in 2011) and the only prosthesis to date to receive FDA approval for commercialization in the USA (Humanitarian Device Exemption approval in 2013) and Health Canada approval (in 2014). Thirty patients implanted with the Argus II Retinal Prosthesis System (Second Sight Medical Products, Inc. , Sylmar, CA, USA) for the Argus II feasibility study (http:// clinicaltrials.
K. and France). Exclusion criteria included: diseases or conditions that may have prevented successful implantation (e. g. , axial length out of a certain range) or prevented the device from working correctly (e. g. , damaged optic nerve function). The trial was and continues to be conducted in accordance with the Declaration of Helsinki and the national regulations for medical device clinical trials in the respective countries where the study is being conducted: the United States, the United Kingdom, France, and Switzerland. The study has been approved by the national ministries of health in these countries and the ethics committees or institutional review boards of participating institutions. All patients signed informed consent to participate. The clinical trial is posted on www. clinicaltrials.
Information about device reliability, stability, and robustness over time was gathered by tracking the number of device failures. Data on partial or complete explantation of devices were also captured. Post-explant follow-up visits were performed at 1 day, 1 week, 4 weeks, 3 months, 6 months, and 12 months post-explant except as noted below. Post-explant visits included eye exam, retinal photography, ocular coherence tomography, and Fluorescein Angiography. The primary endpoint for efficacy was visual function, as measured by three customdesigned objective assessments. Square Localization measured the ability to locate and touch a high-contrast white square of light on a black background, on a touch screen monitor; Direction of Motion assessed patients' ability to determine and indicate the direction of a high-contrast bar that moved across the monitor; and Grating Visual Acuity measured patients' visual acuity using square-wave gratings of different spatial frequencies presented on a computer monitor.
The FLORA and VisQoL were performed only through post-implant year 3 (as per the clinical trial protocol), and the FLORA has been described and reported elsewhere. 10, 11 The Activity Inventory was not fully validated in this patient population (e. g. , with very low vision patients) and as such the data are not included in this report. The Door and Line Tasks were scored by percent success -the mean percent of correct responses (touching the door or ending at the line) for System ON and OFF was calculated over the group.
Patient Demographics Enrollment of 30 patients at 10 centers was completed in 26 months (between June 2007 and August 2009), including a pause in enrollment of about 6 months after the first 15 patients were implanted. Basic demographics are shown in Table  1. Patients Lost to Follow-up-No patients were completely lost to follow-up as of five years post-implant. However, the number of patients included in the analysis of safety and efficacy did decline over time. Safety data were gathered to five years for 27 patients, with drop-out occurring for explanted patients at 1. 2 years, 3. 5 years, and 4. 3 years. Performance data were gathered for N=21 or N=20 patients at five years post-implant as described below.
Safety Previous reports presented serious adverse event (SAE) data at 1 year and 3 years postimplant. 6, 7 Here, we reprint the 0-3 years cumulative SAE rates and report SAEs that occurred up to 5 years post-implant (Table  2 ). As of 5 years post-implant, 60% of patients (18/30) had experienced no device-or surgery-related SAEs. There were 24 SAEs among 12 patients. All SAEs were treatable with standard ophthalmic approaches, and there were no lost eyes (enucleated) in the study. As shown in Table  2 , only one additional serious adverse event had occurred up to year five since the last analysis at three years post-implant. A rhegmatogenous retinal detachment was noted in the implanted eye of one patient during a routine follow-up visit about 4. 5 years post-implant. The detachment remained stable for over a year, when neovascular glaucoma associated with rubeosis was noted.
Visual Function Mean results over time on visual function tasks are shown in Figure  2. The number of patients included in the analysis for each time point is indicated in the axis label. Square Localization and Direction of Motion were introduced partway through the study, so baseline and year 1 follow-up results do not represent a complete data set. Later time points also include fewer patients, due to the explants and device failures described above as well as a few instances of missed protocol visits in years 4 and 5. Missed visits were due to health reasons (1), method deviation (1), and consent to safety follow-up only after year 3 or 4 (2). One additional patient did not complete the Direction of Motion, Line Task, or Door Task at year 5 due to fatigue. As a group, patients perform better on Square Localization with the System ON (lower mean error) than using their residual vision at all time points (Figure  2A ).
There were no lost eyes and there was no damaged residual vision in the study. However, it is clear that any chronic implant in the eye carries a continual risk of serious adverse events. While outside the scope of this paper, additional instances of SAEs were found in four patients after the 5-year time point. In two patients, these represented recurrences or worsening of previous SAEs; in two, they were new events (conjunctival erosion and subsequent endophthalmitis in one patient, and a rhegmatogenous retinal detachment in another). These will be reported in a future paper when the dataset is complete and events have been adjudicated. It is therefore critical for any patient considering being implanted with the Argus II System to understand the long-term and ongoing risks; both the patient and his or her ophthalmologist must commit to at least a yearly evaluation of eye health for as long as the System remains implanted.
Conclusions As of October 15, 2015, over 200 patient-years of data had been collected on the 30 patients implanted with the Argus II Retinal Prosthesis System. The longest implant duration to date is 8. 4 years -and this device, as well as 23 others, continues to function, reliably enhancing basic visual function for these patients who otherwise can see almost nothing. The outcome of the functional tests described in this report and the acceptable safety profile of the Argus II System in this clinical trial led to its regulatory approval in EU, the USA, and in Canada. The device has gone on to be implanted in many patients and, in many countries, remains the only currently available treatment for profound vision loss in RP and outer retinal dystrophy. These new long-term data from the original study continue to demonstrate that this therapy remains an option for patients with retinitis pigmentosa and may allow for stable and reliable restoration of some basic visual function.
Acknowledgments The authors thank  Suber Huang, MD , who served as the independent medical safety monitor for the Argus II Clinical Trial. Funded by  National Institutes of Health  grant no. 5R01EY012893-10  (R. J. G. , principal investigator) 07/2000e02/2011  National Eye Institute, Research/Development of Artificial Retinas  for the Blind and  National Institutes of Health  grant no. 1RC3EY020778-01  (R. J. G. , principal investigator),  Development and Testing of Low Vision Assessment Tools for Retinal Prostheses. The clinical trial was sponsored by  Second Sight Medical Products, Inc. The sponsor participated in the design and conduct of the study; data management, analysis, and interpretation; and preparation and review of the manuscript.
Acknowledgments We thank  Eric Trinquet  ( Cisbio Bioassays ) for providing fluorescent leptin. We also would like to thank  Li Liu  for the expert technical assistance. This work was supported by the  National Institutes of Health  (Grants  DK84142 ,  DK102780 , and  P01ES022845  to SGB), the  United States Environment Protection Agency  (Grant  RD83544101 ), and the  EU   FP7  integrated project (grant agreement n°  266408 , "Ful l4Health", to SGB).
2011). In this chapter, we will first present the current knowledge and hypotheses regarding the anatomical and functional support of HS. Second, we will discuss the consequences of recent literature describing the developmental time course of anatomical and functional inter-hemispheric organization. Third, we will present results and hypotheses regarding the relationships between HS, cognitive abilities and developmental/psychiatric illness. Lastly, we will comment on a tool we have designed to study HS in healthy humans, the BIL&GIN database, with the aim of investigating the lateralization of motor, verbal, and visuospatial functions.
BIL&GIN: A Multimodal Database for Investigating HS To address some of the issues raised in this chapter and to make progress in our understanding of the role of HS in shaping the large-scale organization of the human brain, we acquired a multimodal (neuroimaging, cognitive/behavioral abilities, genetic) database designed for the investigation of HS. This database, named BIL&GIN (Brain Imaging of Lateralization by the Groupe d'Imagerie Neurofonctionnelle), included a sample of 453 healthy adults (aged 18-54 years), balanced for sex and handedness  (Mazoyer et al. 2015). For each participant, we recorded manual skills, hand and eye preference, and familial sinistrality. Verbal, spatial, and numerical abilities were assessed with a large battery of tests. Finally, multimodal MRI data were acquired in each participant, namely T1 and DTI for conducting morphometric analysis of gray matter and WM, and resting-state fMRI data for assessing intrinsic connectivity.
Human Study The Angers University Hospital ethics committee approved the protocol and the study was conducted in accordance with the Helsinki Declaration and French law. All participants provided written informed consent before being included in the study. The study was registered at ClinicalTrials. gov (Identifier: NCT01390129). A total of 50 patients scheduled for elective aortic valve replacement because of aortic valve stenosis underwent RIPC under anesthesia prior to cardiac surgery. The exclusion criteria were as follows: combined surgery with another valve or coronary artery bypass graft, emergency surgery, coronary stenosis >70%, left ventricular ejection fraction <35%, history of MI, coronary revascularization, and preoperative treatment with nicorandil, metformin, or sulfonylurea within 8 days before surgery.
Based on the results of the exploratory analysis, amino acid chromatography was conducted on these samples in order to confirm changes of these metabolites in humans. C, Administration of potentially cardioprotective metabolites found in (B). MI was induced in rats as described in (A). In the treated groups (n=39), metabolites alone or in combination were injected intraperitoneally 10 minutes before coronary occlusion. In the Vehicle+MI group, rats received vehicle only intraperitoneally (n=12). data, the mean difference for each metabolite represents the mean of the difference (after RIPCÀbefore RIPC) calculated over all the subjects. When the normal distribution or ratios between 2normally distributed variables could not be reasonably assessed, the nonparametric Mann-Whitney test or its version for paired data were used for means comparison, respectively.
5) were not retained. The model with the best predictive capabilities, ie, the highest Q² value, was selected based on the variable importance for the projection (VIP) and coefficient values. VIP values summarize the importance of each variable for the orthogonal partial least-squares discriminant analysis model, while coefficient values summarize the relationship between the Y (RIPC/Control) and X (matrix of measured metabolites) variables. Coefficient values are very similar to coefficients obtained from multiple regression analysis. By plotting VIP versus coefficient values ("volcano" plot), the significant variables of orthogonal partial least-squares discriminant analysis models can be detected and selected. The multivariate data analysis was conducted using SIMCA-P software 13. 0 (Umetrics, Umeả, Sweden).
LC-MS/MS Targeted Metabolomic Analysis Plasma samples from both the RIPC (n=10) and control (n=10) groups were analyzed using the AbsoluteIDQ â p180 kit. All 6 groups of molecules measured in the kit, namely acylcarnitines, amino acids, biogenic amines, glycerophospholipids, sphingolipids, and sugars, were examined. The difference between the mean concentrations of each group of rats was not statistically significant for any of the 6 families. Similarly, RIPC/ Control ratios were close to 1 for the 6 groups of molecules. Principal component analysis score plot revealed no outliers, yet could not distinguish RIPC from Control samples (Figure  3A ). However, a model obtained using the supervised orthogonal partial least-squares discriminant analysis method fitted our data well (R 2 X=0. 66, R 2 Y=0.
Acknowledgements The authors are grateful to  Peter C Rimensberger, MD, PhD  ( University Hospital of Geneva, Switzerland ) and  Tom Leenhoven  for sharing ideas about NHFOV and for the critical review of this manuscript. The authors are also grateful to  Ascanio Tridente, MD  for linguistic revision of the manuscript. Finally authors thanks  Luigi Bertogalli  for the help in preparing the vectorial graphics. Contributors DDL wrote the first paper draft and no honorarium was provided for that. DDL conceived the paper and both the authors participated in its preparation. DDL provided and analysed data from previous unpublished bench experiments. VDO performed bibliographic research and both the authors analysed the literature data. VDO also provided and prepared clinical data of illustrative case and took care of the online supplementary video contents.
Computational Details The ground state geometry of the native D-luciferin molecule has been optimized both in gas phase, C 2 H 5 OH, C 6 H 5 CH 3 , and C 6 H 12 solvents using hybrid B3LYP functional and Pople's 6-31G(d,p) basis set for C, H, N, O, and an effective core potential (ECP)-corrected LANL2DZ basis set for S atoms. In the following work, ECP has been used to save some computational time. The TP cross-section obtained with or without ECP is expected to have the same order of magnitude, because TPA does not involve the inner electrons, and hence a suitable pseudopotential (which is the case for S-atom) should not affect the process-and hence the computational results-drastically. The solvent phase geometry optimizations have been carried out within a polarizable continuum model (PCM)  [29, 30] , as implemented in Gaussian 09 program package  [31].