dataesr/scientific-paragraphs-categorization huggingface dataset:
Only data collected before ART initiation were considered for immunogenicity analyses, and data collected after that timepoint were censored. Immunogenicity results were summarized using descriptive statistics for continuous variables and percentages with 95% CIs for categorical variables. ICS results were expressed as the percentage of the total CD40L þ CD4 þ and CD8 þ T-cells expressing IL-2 and/or IFN-g and/or TNF-a in response to stimulation with p17, p24, RT, or Nef antigen minus the response measured upon in-vitro stimulation with medium only. F4-specific CD4 þ or CD8 þ T-cell responses were estimated from the sum of specific CD4 þ or CD8 þ T-cell frequencies in response to each individual antigen. F4-specific CD4 þ Tcell measures were characterized based on their magnitude (frequencies of CD40L þ CD4 þ T-cells expressing at least IL-2 and at least 1 cytokine), cytokine coexpression profiles, and breadth (percentage of responders after in-vitro stimulation with each individual antigen and with at least 1, 2, 3, or 4 antigens).
ACKNOWLEDGEMENTS The authors thank all trial participants, and acknowledge the contributions of the clinicians, nurses, and laboratory technicians. The authors also thank  Michel Janssens  for the CMI assays and  Muriel Feyssaguet  for the antibody assays,  Wouter Houthoofd  ( XPE Pharma and Science , on behalf of  GSK Vaccines ) for publication management, and  Claire Verbelen  ( XPE Pharma and Science , on behalf of  GSK Vaccines ) for initial drafting of the manuscript and incorporation of comments received from the authors.
Data Availability The results summary for this study (GSK study number 111679-NCT01218113) is currently available on the GSK Clinical Study Register and can be accessed at http://www. gsk-clinicalstudyregister. com/study/111679. Upon authorization or termination of development of this medicine, anonymized patient-level data underlying this study will be made available to independent researchers, subject to review by an independent panel, at www. clinicalstudydatarequest. com. To further protect the privacy of patients and individuals involved in our studies, GSK does not publically disclose subject level data.
This tendency arises because of the oscillatory nature of the agent. Given an attractive odour (i. e. a negative gain g<0), large re-orientations are more likely to be triggered when a negative p nÀ1 has been perceived during the previous step. And since a negative p nÀ1 is more likely to be  perceived when turning away from the odour, the subsequent turn, in the opposite direction, is thus more likely to be directed towards the odour side. Nonetheless, this bias is weak and requires a large dataset to appear significant. Our model predicts that the bias should increase together with increasing odour attraction, whether from stronger gain due to appetitive learning; stronger sensory input due to increased odour concentration, or both (Figure  7A ); it should also become more apparent when the odour is located on one side of the larvae (Figure  7B ).
Real larvae path analysis We analysed the tracks from 42 wild-type larvae, the data recorded for  Gomez-Marin et al. (2011) , which was supplied by Matthieu Louis. Each 3rd-instar foraging-larva path was recorded for 5 min at 7fps after releasing each larva on a rectangular agarose slab opposite to an odour source given by an ethyl butyrate droplet suspended from the lid. Tail, centroid, and head positions were extracted from each frame of the video using custom tracking software. Having obtained the processed data we used Matlab to analyse the tracks. Body bending was calculated as the angle formed between the tail-to-centroid axis and centroid-to-head axis. The variable 'angular velocity of the anterior part of the body' was obtained as the derivative across time of the centroid-to-head axis orientation.
Study design and inclusion criteria This prospective multicentre phase 2 study included 24 patients diagnosed with AML in primary treatment failure who underwent allogeneic SCT between 2010 and 2013. The trial was approved by each participating center's institutional review board, the Comité de Protection des Personnes de Tours (CPP Ouest-1, ref. 2009-R29) and the national Agence Française de Sécurité Sanitaire des Produits de Santé (AFSSAPS). This study was registered with ClinicalTrials. gov, identifier number: NCT01188174. Informed consent from patients and donors was obtained before their inclusion in the study. Patients aged between 18 and 55 years were eligible for the study if they had a confirmed diagnosis of AML in the status of primary induction failure, i. e. patients alive after induction treatment but who failed to fulfill the criteria for CR or CR with incomplete recovery.
20. Overall and leukemia-free survival rates were calculated using the Kaplan-Meier method. Overall survival was defined as the time from allogeneic SCT to death, regardless of the cause. Leukemia-free survival was defined as survival with no evidence of leukemia after achieving complete remission. The probability of NRM was calculated using the cumulative incidence procedure. We defined NRM as death with no evidence of leukemia relapse or progression. Data were computed using SPSS and EZR version 1. 27 (Saitama Medical Center, Jichi Medical University, Japan), which is a graphical user interface for R (The R Foundation for Statistical Computing, version 3. 1. 1). 28.
Furthermore, among patients treated with DLI, half died from relapse. The use of DLI to enhance the antileukemic effect and decrease relapse in our study was, therefore, a disappointing strategy. In addition, as previously described,  38  we observed a relatively high incidence of GvHD after pDLI. It does, therefore, seem indispensable to develop new strategies to prevent relapse after allogeneic SCT. One way to overcome these difficulties would be to perform earlier pDLI while patients are still under immunosuppressive therapy. Furthermore, Goodyear et   Table  3. Non-hematologic organ toxicity according to WHO criteria. well tolerated, and was associated with a low incidence of GvHD. 39 This strategy appears promising and a prospective trial evaluating preemptive azacytidine and DLI in high-risk AML patients is ongoing (NCT01541280).
Acknowledgments The authors would like to thank the nursing staff for providing excellent care for our patients. MM thanks  Prof. J. V. Melo  for critical reading of the manuscript. The study was supported by the  "Association for Training, Education and Research in Hematology, Immunology and Transplantation" (ATERHIT). Sanofi (France)  provided clofarabine used as part of this study. However, Sanofi was not involved in the study design, data analyses, or manuscript writing.
, 2014) , which questions the reliability of rate models developed on such datasets. As a matter of fact, aside from a limited number of studies which managed to reconcile experimental and field data at specific sites (e. g. Maher et al. , 2009) , upscaling laboratory results to the field without adjustments of several modeling parameters has essentially remained an elusive goal. The source for the above-mentioned discrepancies remains an open question: aside from identified complicating factors including aqueous transport-limitations  (Ruiz-Agudo et al. , 2012; Laanait et al. , 2015)  or passivation by surface layers  (Daval et al. , 2011 (Daval et al. , , 2013)) , a handful of recent studies has pointed out that mineral surfaces do not homogeneously and isotropically react with aqueous fluids  (Godinho et al.
g. Yanina and Rosso, 2008; Bandstra and Brantley, 2008; Kubicki et al. , 2012; Daval et al. ,2013; Lüttge et al. , 2013; Kurganskaya and Lüttge, 2013; Fenter et al. , 2014). Taken together, these recent observations motivated the present study, aimed at clarifying the validity and limitations of the conventional protocol commonly used to measure and upscale mineral dissolution rates. Below, we provide measurements of K-feldspar (orthoclase, KAlSi 3 O 8 ) dissolution, considered as a model mineral. Orthoclase was selected because of (1) its chemical composition and low-symmetry space-group, which substantially deviate from simple oxides/hydroxides for which the SCM/TST model putatively applies, (2) the fairly large dataset related to the bulk dissolution kinetics and dissolving surface structure of orthoclase (see  Gautier et al.
In fact, our main concern was to propose an ad hoc curve which could adequately fit our experimental datasets to ultimately provide overall r-ΔG relations for the arbitrary crystal morphologies reported in Fig. 4. Solid red lines are rate-curves based on the transition state theory. The relation between r (hkl) and ΔG is apparently specific to the crystallographic orientation which is considered, since the dissolution rate plateau value observed at far-from-equilibrium conditions is different for each face (Fig. 2 ). The face-specific dissolution rates r (hkl) observe the following trend:. A tenfold factor is measured between the rate plateau value of the slowest dissolving face (001) and the fastest dissolving face. In addition, the shape of the r-ΔG relations also depends on the crystallographic orientation.
Conclusions Overall, this combined experimental and modeling study illustrates some limitations of the conventional treatment of aqueous mineral reactivity. In particular, our results suggest that the mechanistic basis for the bottom-up simulations of chemical weathering that rely on overall kinetic rate laws may not be as robust as commonly expected. Although the current reactive transport simulations cannot be simply abandoned, one has to keep in mind that most of the so-called kinetic rate laws that can be retrieved in thorough database and review papers may probably not reflect more than empirical relations, such that one has to remain careful with respect to the predictive ability of the outputs of such simulations. Alternative approaches are therefore necessary to improve the reliability of such simulations.
White, A. F. and Brantley, S. L. (2003). The effect of time on the weathering of silicate minerals: why do weathering rates differ in the laboratory and field? Chem. Geol. The fitting parameters are listed in Table  4  note that the actual values of the fitted parameters are not meant to be related to any specific molecular mechanism. In fact, our main concern was to propose an ad hoc curve which could adequately fit our experimental datasets to ultimately provide overall r-ΔG relations for the arbitrary crystal morphologies reported in For the and faces, which belong to the F2 category, no obvious modification of etch pit density can be seen for ΔG < ~ -10 kJ. mol -1. These results illustrate that the TST framework fails to predict the r-ΔG relations and emphasizes the control exerted by the crystallographic structure on the reaction rate and rate law.
Acknowledgements This work has been funded through a grant attributed to  D. D. for the project "Feldspar reactivity in the context of Soultz-sous-Forêts: From microstructural characterizations to numerical modeling" under the framework of the LABEX  ANR-11-LABX-0050_G-EAU-THERMIE-PROFONDE  which benefits from a funding from the state managed by the  French National Research Agency  as part of the  French "Investissements d'avenir ". M. P. -V. thanks the  Région Alsace and LABEX "G-EAU-THERMIE PROFONDE"  for funding her PhD contract. K. G. K. effort at LBL was supported by the Director,  Office of Science, Office of Basic Energy Sciences, Chemical Sciences, Geosciences, and Biosciences Division , of the  U. S. Department of Energy  under Contract No. DE-AC02-05CH11231. We are indebted to  G.
B. Experimental method For the multi-body configurations, the receiver body incidence was typically varied between -15≤σ R ≤15°. A 5s settling period was employed at the start of each tunnel run. At each incidence, the receiver body paused and the forces and moments were measured using an ABLE MKXIV 6-component, internal balance. The force and moment balance output was filtered using a 5Hz low-pass filter and the data was acquired at a sample rate of 100 kHz with a typical sample duration of 2s. A shadowgraph image was also taken at each incidence setting. A light source was focused using a 0. 38m diameter lens and the illuminated flowfield was projected onto a transparent screen on the opposite tunnel window where a still image was taken with a PCO Sensicam qe camera. This same experiment procedure was used for different axial stagger configurations, different generator bodies as well as the isolated receiver configurations.
C. Measurement uncertainty The experimental uncertainties were calculated using the approach of Taylor  25  and are mostly expressed as a fractional uncertainty of the measured value (Table  1 ). All measurement uncertainties were estimated from systematic and random sources of error which included the instrument calibration, instrument accuracy given by the manufacturer and the data acquisition resolution. Based on the isolated receiver measurements, a flow angularity correction of σ cor =-0. 05° was applied to the measured data which ensured zero normal force at zero incidence for the isolated configuration.
B. Computational grids All the 3D computational grids were created using the grid generation software Gridgen 29 and were based on a hybrid meshing approach. The computational domain modeled one-half of the flowfield since the sideslip angles for both bodies were zero. This assumption was supported by the measurements of side force and yawing moment for the receiver body which were found to be nominally zero. The computational domain extended from a short distance upstream of the leading edge of the foremost body to approximately 3D downstream of the base of the aftmost body (Fig. 5a ). The base and supporting sting were also included for each body where appropriate. The surrounding flowfield domain boundary was arranged so that the bow shock of both bodies exited through the downstream outlet face.
Grid convergence A selection of configurations which are representative of the dataset as a whole were further investigated to assess the solution sensitivity to spatial resolution and to provide an estimate of the discretization error using the approach of Roache  31. A grid convergence study was completed for each of the selected configurations over three grid levels. For the hybrid grids used in this investigation it was necessary to use an effective grid refinement ratio  31. This was based on the relative total grid sizes and was approximately r eff ≈1. 5 for this investigation (Eqn. (1) shows r eff between the fine and medium grid levels). 3 / 1          med fine eff N N r (1) The integrated force and moment coefficients (C X , C Z , C m ) were used as the comparison parameters in the grid convergence study.
B. Effect of axial stagger In multi-body configurations, the disturbance flowfield includes a primary shockwave which emanates from the generator forebody and impacts on the receiver body. It also includes the associated expansion wave which arises downstream of the primary shock. The axial impingement location of the primary shockwave is known to have a marked effect on the magnitude and sign of the interference loads acting on an un-finned slender body  6, 22, 24. The fins on the receiver body in the current investigation were expected to intensify this effect. In this section, the interference aerodynamics for a selection of key cases from the measurement database are investigated which includes configurations with the sharp generator and the finned receiver at five different incidence angles (σ R =-15, -8, 0, 8, 15°) placed in four axial stagger arrangements (∆x w /D=-1.
Ideally, an analytical method is developed that can measure specific neurogranin metabolites independent of antibodies, similar to what has been developed for A␤ 1-42  [48]. In addition, harmonization studies are preferably conducted collaboratively, as it has also been done for the A␤ 1-42 immuno-assays  [49]. Finally, our postmortem analysis on human brain tissue with the mAb ADxNGCI2 confirmed data acquired in the rat brain. Golgi methods and electron microscopy, in the rat, demonstrated a post-synaptic localization of neurogranin  [13]  where it mediates long-term potentiation through its interaction with calmodulin  [10, 13, 50 ]. Yet, ADxNGCI2 also labeled the cell body of the neurons, a large part of their dendritic tree as well as synapses. Moreover, the distribution of the protein was not limited to the somato-dendritic compartment but also involved some axons and particularly the mossy fibers of the hippocampus.
ACKNOWLEDGMENTS The authors kindly acknowledge  Leentje Demeyer ,  Kimberley Mauroo , and  Erik Stoops  for their technical assistance in the development of the BACE1 assay. We also would like to thank the team of  Wim Maes and Nick Geukens (PharmAbs, KU Leuven, Belgium ) as well as the team of  Els Saesen  and  Laurence Padel  ( BIOTEM, France ) for the joined efforts in the generation of neurogranin mAbs. Finally, we acknowledge  Jill Luyckx ,  Naomi De Roeck ,  Joery Goossens , and  Ellis Niemantsverdriet  ( BIODEM, UAntwerp ) for CSF sample processing and classical  A. De Vos  et al. / Neurogranin/BACE1 and Cognition Correlate biomarker analyses with Innotest kits. This work was in part supported by the  University Research Fund of the University of Antwerp ; the  Institute Born-Bunge ; the  Alzheimer Research Foundation  ( SAO-FRA ); the  Research Foundation -Flanders (FWO) ; the  Agency for Innovation by Science and Technology (IWT O&O   140105 ;  IWT Baekeland 140262 ); the  Interuniversity Attraction Poles (IAP) program  of the  Belgian Science Policy Office ; the  Flanders Impulse Program on Networks for Dementia Research (VIND).
This proof-of-concept paper is meant to introduce here a novel method aimed at subtyping AZFc rearrangements. It is able to differentiate the partial deletion and partial duplication subtypes of the Deleted in Azoospermia (DAZ) gene family. The keystone of the method is the determination of the copy number of the gene family member-specific variant(s) in a series of sequence family variant (SFV) positions. Most importantly, we present a novel approach for the correct interpretation of the variant copy number data to determine the copy number of the individual DAZ family members in the context of frequent interloci gene conversion. Besides DAZ1/ DAZ2 and DAZ3/DAZ4 deletions, not yet described rearrangements such as DAZ2/DAZ4 deletion and three duplication subtypes were also found by the utilization of the novel approach.
The lack of the entire AZFc region has long been shown to cause azoospermia or oligozoospermia  [6]. Many studies have been conducted so far to screen for partial AZFc rearrangements in relationship with male infertility with findings that are not easy to reconcile. [3, 5, [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18]. According to a comprehensive review, DAZ (GeneBank accession number: NG_004755. 2) and CDY1 families represent key AZFc spermatogenic determinants  [19]. A meta-analysis including 18 studies with more than 12,000 men showed that gr/gr deletion occurred more frequently in infertile than control men. Furthermore, the association was dependent on ethnicity and geographic region  [20]. A population-based survey of 20,000 Y-chromosomes also states that gr/gr deletion doubles the risk of severe spermatogenic failure  [21].
This is necessary since in addition to deletion, duplication and inversion, the members of gene families located in AZFc are also subjected to interlocus gene conversion  [14, 27, 28]. This phenomenon can detach gene family member-specific variants from their host family member, thereby contributing to the variability of the variant ratio at a SFV position across a population. Partial deletion and partial duplication samples are then subtyped utilizing the markers' newly derived applicability. Finally, the concordance of data pointing to the assigned subtypes is evaluated to check the probability of the conclusions. The four DAZ genes were chosen as the targets of variant ratio analysis, but it can be extended to other gene families. The studied SFV positions were selected by aligning the sequences of the four DAZ family members extracted from the human reference genome.
Analysis of control DNA mixtures To adjust the concentration of the DAZ inserts to the value typical of DAZ genes in individual DNA samples in our lab, the control mixtures were diluted 1:500,000. Six aliquots of mixture 1 and three aliquots of mixtures 2-9 were amplified parallel and sequenced as described above. The area-under-the-curve (AUC) ratio was determined from the sequencing electropherograms at each studied SFV position in each aliquot of every DNA mixture. The AUC of the signal given by the DAZ family member-specific variant (AUC spec ) and that given by the non-specific variant (AUC non-spec ) was measured separately with the use of ImageJ software  [30]  in a standardized way. The AUC ratio was calculated using the following formula: 100 x AUC spec /(AUC spec + AUC non-spec ).
Validation methods Multiplex PCR assays to detect deletions in AZFc region. Two multiplex PCR reactions were assembled to amplify three and four STS markers, respectively, which are located in AZFc region (except for sY1201). Multiplex I amplified sY1197 (NCBI GenBank Accession Number:  G67168), sY1206 (G67171) and sY1201 (G67170). Multiplex II tested for the presence of sY1191 (G73809), sY1291 (G72340), sY1258 (G75499) and sY1201. Lying outside the AZFc region, sY1201 was used as a control for the presence of chromosome Y and the functionality of the PCR reaction in both multiplex assemblies. The reactions were carried out using the Qiagen Multiplex PCR Kit according to the manufacturer's instructions. The ratios of the primers were optimized so that each band would exhibit approximately equal intensity on agarose gels.
All processes are listed below. 1/ Aligning the sequences of the four DAZ genes extracted from the human reference genome in order to select amplifiable fragments which i) consist of four amplicons belonging to the four DAZ genes, respectively, and ii) contain as many SFV positions as possible (Fragments I and II) (  ). 5/ Amplification of selected regions to get Fragment I in control mixtures. 6/ Sequencing Fragment I in control mixtures. 7/ Measuring AUCs by ImageJ software and calculating the AUC ratio at each SFV position in every control mixture. 8/ Correlating the AUC ratios measured in control mixtures with known variant ratios (S5 Table ). 9/ Measuring AUCs and calculating the AUC ratio at each SFV position in all individual samples. 10/ Plotting AUC ratios throughout all samples for each studied position to visualize AUC ratio clustering (Fig  3 ).
For example, no exploitable information remained for DAZ4 in the other five deletion and two duplication samples (Ydup_01, Ydup_05). In contrast, stage 3 analysis led to the successful evaluation of our all deletion and duplication samples by making it possible to retain a considerable part of the data which would otherwise have been excluded from the analysis at stage 2 (S8C and S9C Tables). It was the first association which allowed to infer the lack of DAZ4 from the absence of the DAZ4-specific C 1820 in the concomitant presence of the DAZ1specific A 972 in Ydel_07, Ydel_09 and Ydel_10. At the same time, the second association made 0 0 0 0 - - 0 1 0 1 - - 1 0 no conclusion no conclusion - - 1 1 1 1 1 1 2 0 1 1 1 1 2 1 - - no conclusion no conclusion 3 0 - - no conclusion no conclusion 1 2 - - 1 2 2 2 - - 2 2 4 0 - - 2 2 3 1 - - 2 2 Conclusions allowed to be drawn for the copy number of DAZ3 and DAZ4 in partial deletion and partial duplication samples, based on the combined analysis of the class II/a DAZ3-and class II/b DAZ4-specific markers located in Fragment II, are shown.