dataesr/scientific-paragraphs-categorization huggingface dataset:
One possible explanation for this discrepancy between studies may relate to the timing of T-cell assessment relative to that of the resolution of HEV infection-assuming the same contraction of Tcell responses observed in immune-competent HEVexposed subjects occurs in immunosuppressed patients, those who had cleared infection would have reduced responses if assessed at significantly later time points. In our study, the median time between HEV onset and assessment was 24 months for organ transplant recipients, but data relating to timing of resolution of viremia were not available for all subjects. We next assessed the diagnostic utility of a commercially available QuantiFERON assay that uses HEV antigen 239 (a truncated capsid protein) to confirm HEV exposure in immune-competent subjects. Although there has been significant improvement in the diagnostic sensitivity of serological assays for HEV infection, the possibility that they lack specificity has been raised by reports of high HEV IgG seroprevalences in regions where acute HEV is diagnosed only rarely.
Acknowledgments: We thank  Wantai Pharmaceuticals  for providing HEV diagnostic ELISA kits free of charge. We thank the hepatology research nurses (in particular,  Mark Ainsworth ) for supporting the recruitment of HEV patients to this study. We also acknowledge the team of research staff at the  Oxford Vaccine Group  (in particular,  Andrew Pollard ,  Simon Kerridge , and  Amber Thompson ) and thank the many volunteers who contributed to this research.
Study Design The SAKURA Study 1 is the first of 2 Phase III, randomized, double-masked, multinational studies conducted in the European Union, India, Israel, Japan, Latin America, and the United States. Both studies are registered at ClinicalTrials. gov (NCT01358266). Subjects randomized up to March 31, 2013 comprise the population of SAKURA Study 1, and subjects enrolling from April 1, 2013 were randomized into SAKURA Study 2 (ongoing). SAKURA Study 1 consists of a 6-month double-masked treatment period, followed by a 6-month open-label treatment period and a 12-month re-treatment period during which eligible subjects were to receive 880-mg injections. The results from the double-masked treatment period of SAKURA Study 1 are reported here. Subject eligibility criteria included age !18 years; an investigator-determined diagnosis of active NIU of the posterior segment (which in this study includes intermediate, posterior, or panuveitis), defined as a vitreous haze (VH) score of >1þ in the study eye; and a best-corrected visual acuity (BCVA) of !19 Early Treatment of Diabetic Retinopathy Study letters (!20/400 Snellen equivalent) in the study eye and !20/200 in the fellow eye.
Statistical Analyses In accordance with the intent-to-treat principle, all randomized subjects comprised the primary population for efficacy analyses. For the primary analyses of all VH response end points, subjects rescued before Month 5 were treated as nonresponders. For subjects not rescued before Month 5, missing VH data at Month 5 were imputed using the last observation carried forward approach. For the sensitivity analyses, a per-protocol population was used, which consisted of the intent-to-treat population excluding subjects with significant protocol violations or missing a Month 5 VH score. For the assessment of corticosteroid tapering success, the analysis included all subjects who were taking systemic corticosteroid(s) at baseline with an overall prednisone-equivalent dose >5 mg/day (intent-to-taper population).
Study Oversight An ethics committee or institutional review board at each participating site reviewed and approved the clinical study protocol, informed consent form, and all other appropriate study-related documents. The study was conducted in accordance with Good Clinical Practice guidelines and the principles of the Declaration of Helsinki. Study sites in the United States complied with the provisions of the Health Insurance Portability and Accountability Act. Before undergoing any study-related activity or administration of study medication, subjects were required to understand and sign the informed consent form. The SAKURA Study included a data monitoring committee that met periodically to conduct an independent review of unmasked aggregated and individual-level data related to study safety, data integrity, and overall study conduct.
Subject Disposition A total of 347 subjects (348 study eyes) were randomized at 103 sites in the European Union, India, Israel, Japan, Latin America, and the United States from May 31, 2011, to March 31, 2013 (Fig 2). One subject was inadvertently enrolled twice and was randomized to receive the 880-mg dose each time. The second identification number was excluded from the efficacy analyses. The safety population included all randomized subject identification numbers, excluding 2 subjects who were randomized but not treated, yielding a safety population of 346 study eyes. A total of 69 subjects (19. 9%) who were receiving systemic corticosteroid(s) in a prednisone-equivalent dose of !7. 5 mg/day at baseline comprised the intent-to-taper population. The database of SAKURA Study 1 was locked on April 22, 2015, after completion of the open-label treatment phase; data from this phase of the study will be reported at a later date.
In summary, the results of the SAKURA Study 1 demonstrated 5-month improvement in VH combined with preservation of BCVA and reduction in corticosteroid treatment burden in patients with active NIU of the posterior segment who received repeated intravitreal injections of sirolimus 440 mg. There were no clinically relevant systemic safety issues and there was a low incidence of adverse events typically associated with corticosteroid therapy. The data provide level 1 evidence supporting the strategy of mTOR inhibition in NIU of the posterior segment using a locally administered therapy. Future research on intravitreal sirolimus will likely explore its potential role in combination therapy regimens, its corticosteroid-sparing efficacy in a larger population, and its longer-term safety and efficacy (currently being evaluated in the open-label treatment phase of the SAKURA Study 1).
Acknowledgments. The authors acknowledge the important intellectual contributions to the article from  Dr. Yusuf Ali ,  Dr. Vincent Baeyens ,  Dr. Masaaki Kageyama ,  Dr. Sri Mudumba ,  Dr. Michelle Chernock ,  Dr. Kavitha Damal  (all employees of  Santen, Inc. ), and  Mary Ellen Valentine  (previous employee of  Santen, Inc. ). The authors also thank the members of the SAKURA Data Monitoring Committee ( Dr. Henry J. Kaplan  of the  Kentucky Lions Eye Center, University of Louisville , Kentucky;  Dr. Jennifer Lim  of the  Illinois Eye and Ear Infirmary, University of Illinois College of Medicine at Chicago ; and  Dr. H. Nida Sen  of the  National Eye Institute, National Institutes of Health, Bethesda, MD ) for their work on the trial, especially  Dr. Kaplan  for his review of the manuscript.
b, Western blotting analysis of untagged and His 6 -tagged bGP. Western blotting analysis was first conducted using a polyclonal antibody against the six-histidine tag and then reprobed using a monoclonal antibody against bGP. c, plot of the activity of glycogenolysis as a function of the purified bGP concentration. Various concentrations of purified protein were assayed for enzymatic activity in the direction of glycogen breakdown in the presence of 1 mM AMP and 0. 25% glycogen. The data represent the averages of initial velocities (expressed as mAbs/min) of three experiments Ϯ S. D. The curve was fitted to the data using linear regression. d, glycogen saturation curve of purified bGP. Purified recombinant bGP (100 nM) activity was measured in the direction of glycogen breakdown in the presence of a saturating concentration of AMP (1 mM) and various concentrations of glycogen (0 -0.
35%). The data shown represent the means of initial velocities of three different experiments (expressed as mean Abs/min Ϯ S. D. ). e, activation of bGP by phosphorylation and AMP. Specific phosphorylation of bGP Ser 14 was performed prior to the assay by incubating the recombinant enzyme with phosphorylase kinase in the presence of ATP for 2 h at room temperature. bGP and phosphorylated bGP was then assayed for activity with or without 1 mM AMP. Activity was expressed as the percentage of the control (bGP activity in the presence of AMP alone). The data shown represent the means of initial velocities of three different experiments Ϯ S. D. ***, p Ͻ 0. 001. f, Western blotting of phosphorylated and non-phosphorylated bGP. Recombinant bGP was incubated with (lane 1) or without (lane 2) phosphorylase kinase and subjected to Western blotting analysis using an antiphosphoserine antibody.
The resulting n Hill coefficient of 0. 994 indicated that AMP binding to bGP was not cooperative (Fig. 1g ). All these characteristics are in accordance with previously published data  (23, 24). We thus used this functional enzyme for further crystallographic studies. The Overall Structure of bGP-We performed several trials to obtain the human bGP structure in its active and inactive conformations. We first attempted to crystallize the enzyme alone and complexed with allosteric effectors such as AMP, ATP, caffeine, glucose, or ammonium sulfate. We obtained bGP crystals in 0. 2 M calcium chloride dihydrate, 0. 1 M NaHepes, pH 7. 5, using 28% (v/v) PEG 400 as precipitant. We did not obtain bGP co-crystals with ligands, despite the high number of crystallization conditions tested. We thus performed soaking experiments of the bGP crystals with several allosteric effectors.
Finally, we collected diffraction data sets from bGP crystals, at 2. 5 Å resolution and from bGP in complex with AMP at 3. 4 Å resolution. The three-dimensional structures were determined by molecular replacement, using a homology model based on human muscle glycogen phosphorylase (PDB code 1Z8D) as a search model (Table  1 ). bGP shares a high percentage of amino acid sequence identity with the muscle (83%) and liver (80%) isozymes. Accordingly, bGP displays a global structure similar to the other isoforms with monomer and dimer RMSD in alpha carbon positions of Ͻ1 Å (Table  2 ). In both crystals, we have one molecule by asymmetric unit, but a bGP tetramer is formed by crystallographic symmetry (Figs. 2a  and 3a ). The tetrameric arrangement of GPs has only been observed for the activated (or R state) of mGP (in the presence of AMP and/or when phosphorylated).
In the absence of AMP or phosphorylation, mGP crystallizes as a dimer in the asymmetric unit (PDB code 2GPB). It was thus surprising to observe that in absence of AMP, bGP also formed a tetramer. We attribute this quaternary arrangement to the presence of a PEG 400 molecule, used as precipitant, in the AMP binding site (supplemental Fig. S2 ) (see "Results" and "Discussion"). Each tetramer is composed by the association of two functional dimers that interact through the catalytic face located at the tetramer interface  (29). The regulatory face on the other side is exposed to the solvent (Fig. 2, b  and c ). The monomer is composed of two domains: the N-terminal domain from residues 22 to 484 and the C-terminal domain from residues 485 to 822 (Fig. 2, b  and c ). The catalytic site, found at the interface between the two domains, is marked by the presence of the electron density of the co-factor pyridoxal phosphate attached to the protein through a Schiff base linkage to Lys 680 , as observed in the mGP and lGP structures  (27) (28) (29).
GP monomers mGP (PDB code 1PYG) 0. 63 0. 69 lGP (PDB code 1FA9) 0. 7 bGP (PDB code 5IKP) observed in PEG-bound bGP crystals is sufficiently close to the active state to allow all the structural changes induced by the addition of AMP without altering the crystal integrity. Indeed, soaking experiments with allosteric inhibitors, such as ATP or caffeine, altered the crystal integrity within seconds (visible cracks and poor diffraction). By contrast, several diffraction data sets were collected from crystals of AMP-complexed bGP obtained by soaking, and the solved structures were similar (monomer RMSD of 0. 34 Å and dimer RMSD of 0. 35 Å). Changes induced by the addition of AMP were conserved in all the AMP-bound bGP structures. Additionally, the correct and reproducible coordination of AMP in the AMP-binding site and the slight structural changes accompanying PEG 400 replacement by AMP (Fig.
025%) and various concentrations of AMP (0 -3 mM). Initial velocities were determined, and cooperativity of AMP binding was assessed by fitting the data to the Hill equation, Log͑Y/͑1 Ϫ Y͒͒ ϭ nlog͓AMP͔ Ϫ logK A (Eq. 1) where Y is the ratio V i /V max , n is the Hill coefficient, [AMP] is the corresponding concentration of AMP, and K A is the affinity constant. Phosphorylation of Ser 14 and Activation by Phosphorylation-bGP was phosphorylated using phosphorylase kinase from rabbit muscle (Sigma-Aldrich) (1 unit/mg bGP) activated by preincubation for 1 h in phosphorylation buffer containing 20 mM Tris-HCl buffer, pH 7. 7, 0. 22 mM ATP, 3. 3 mM MgCl 2 , 0. 5 mM CaCl 2 , 0. 5 mM NaF for activation. Phosphorylation was performed by the addition of activated phosphorylase kinase to the bGP solution and in phosphorylation buffer and incubation for 2 h at room temperature.
The best crystals were obtained using a solution of 28% (v/v) PEG 400, 0. 2 M calcium chloride, and 0. 1 M Hepes, pH 7. 5. Crystals with dimensions of up to 0. 05 mm ϫ 0. 05 mm ϫ 0. 1 mm appeared within 2 weeks. The crystal of protein complexed with AMP (AMP-bound bGP) was obtained by soaking the apo-form crystal for 3 h in 50 mM of AMP dissolved into the crystallization solution. For data collection, the crystals were flash-cooled in liquid nitrogen using the mother crystallization solution as cryoprotectant. All x-ray diffraction data were collected on the PROXIMA-1 Beamline at the Soleil Synchrotron (St. Aubin, France) and the ID23-2 at European Synchrotron Radiation Facility (Grenoble, France). Diffraction images were integrated using the XDS program  (42). Structure Determination, Refinement, and Analysis-For the resolution of the structure, molecular replacement phases were obtained using Phaser  (43)  implemented in the CCP4 program suite (Collaborative Computational Project, Number 4 (  44 )).
The model for molecular replacement was built by homology modeling using SWISS-MODEL  (45)  based on the template structure of human muscle glycogen phosphorylase (PDB code 1Z8D). The initial models were completed and adjusted using the COOT program  (46). Refinement was performed using REFMAC as implemented in CCP4  (47). The crystal structure of the PEG-bound GPb at 2. 5 Å resolution was refined to R and R free crystallographic factors of 18 and 24%, respectively (see statistics in Table  1 ). The crystal structure of the AMP-bound bGP at 3. 4 Å resolution was refined to R and R free crystallographic factors of 21 and 29%, respectively (see statistics in Table  1 ). Atomic coordinates and structure factors were deposited in the Protein Data Bank under accession codes 5IKO and 5IKP for the PEG-bound GPb and the AMP-bound bGP, respectively.
Details about these DEGs are given in Additional file 2. There is no significant difference in terms of the number of upregulated or downregulated genes in both genotypes and brain regions (Fig. 1a ). When considering each brain area analyzed, there is little difference in the number of dysregulated genes for a given genotype (Fig. 1b ). In Wt mice, about 10 % of DEGs are common to both tissues while 13 % shared DEGs can be observed in Tg animals (Fig. 1b ). Interestingly, a number of DEGs are common to both genotypes in both brain areas (Fig. 1c ). Up to 366 genes are commonly dysregulated after vitamin D3 treatment in both Wt and Tg mice (Fig. 1d ). Using Ingenuity Pathway Analysis (IPA) software, the clustering of the 366 genes indicates that among the top canonical pathways, the ones displaying the largest number of DEGs are: Axon guidance signaling (13 genes), Protein kinase A signaling  (13) , ILK signaling (9), Huntington's disease signaling  (9) , Glioblastoma Multiform signaling  (8) , Cdc42 signaling  (8) , IL8 signaling  (8) , Agranulocyte adhesion and diapedesis  (8) , Tight junction signaling  (7) , Embryonic stem cell pluripotency  (6) , Corticotropin Releasing Hormone signaling  (6) , Communication between innate and adaptive immune cells  (5) , Glutamate receptor signaling  (5)  and Dopamine receptor signaling  (5).
An intriguing expression of hormone transcripts in the cortex and hippocampus One of the aims of this transcriptomic analysis was to extract information about genes whose expression is modified in the nervous system after 5 months of vitamin D3 supplementation, regardless of the pathological context. One way to obtain such information is to refine the working dataset to include only genes that are commonly dysregulated in all tested conditions. Table  1  shows the list of genes found to be dysregulated in Wt and Tg mice, in both the hippocampus and cortex. In these four conditions, we found 28 DEGs, with varying fold changes according to the genotype and brain region studied, that are consistently regulated after 5 months of vitamin D3 supplementation. To gain better sense of the biological functions represented by the differentially expressed genes, we performed a Functional Annotation Clustering using the NIH David tool.
This analysis revealed that the genes in this dataset are related to five different biological clusters: regulation of phosphorylation, hormone activity, membrane trafficking, nucleotide binding and metal ion binding. A less restrictive additional analysis was performed on DEGs found in at least three out of the four conditions. Table  2  represents the top ten biological clusters associated with this dataset. One hundred thirty-six genes were differentially expressed (Additional file 3) and when performing functional annotation clustering of these DEGs, the number one biological function is hormone activity (Table  2 ). Eight genes fall into this ontological category: Avp, Igf1, Igf2, Nppa, Oxt, Pmch, Prl, Trh. Bearing in mind that several of these neuropeptides are largely found in the pituitary axis, it is extremely intriguing to find them differentially expressed in the cortex or hippocampus of 5XFAD mice.
The effects of vitamin D3 supplementation vary according to the health status of the animal To move further and comprehensively assess the effect of vitamin D on brain functioning, we analyzed the Dysregulated transcripts in the hippocampus and cortex of vitamin D3 supplemented wild type and transgenic mice in comparison with unsupplemented littermates. The gene symbol, the full name and the fold change of each gene are indicated record of dysregulated genes, in accordance with their role in well-described metabolic pathways. For each strain, we combined transcriptomic data from the hippocampus and the neocortex at M9 and, using Ingenuity software, we listed the main canonical pathways that were modified by the vitamin D3-enriched diet. We then compared the two strains of animals (Wt vs Tg).
Vitamin D3, a potent upstream regulator altering the expression of Alzheimer's disease-associated genes To further decipher the detailed role of vitamin D in brain functioning, we narrowed our analysis to the genes that are directly or indirectly regulated by vitamin D or its related-metabolites. Using Ingenuity software, we listed all dysregulated molecules whose expression has been associated, in the literature, to this steroid. As summarized in Fig. 3 , we observed 290 and 249 vitamin D-related DEGs respectively, when comparing vitamin D3-supplemented Wt and Tg mice with their unsupplemented littermates. Within these two pools, 188 and 151 genes are part of the initial list of 784 vitamin D-associated transcripts whose expression is altered in the brain of transgenic animals (Additional file 5).
On top of that, the majority of the   2  Top canonical metabolic pathways associated to gene dysregulation in the cortex and hippocampus of mice after 5 months of vitamin D3 supplementation: common versus strain-specific processes. Metabolic pathways associated to gene expression dysregulation were identified using Ingenuity Pathway Analysis (IPA). Data from both the cortex and hippocampus were analyzed as one dataset and the main metabolic pathways affected were clustered according to their association to the nervous (a) or the immune (b) system vitamin D-related genes are associated to Alzheimer's disease, in both the Wt and Tg brains. We show that vitamin D action in the brain of this AD mouse model likely involves signaling through ESR1 and IGF1 and that a 5-month therapeutic intervention reduces the histological markers of the disease and restores learning and memory capacities.
A cross examination of our data with those reported in these studies reveals that the dysregulated expression of 46 genes -Aaas, Aldoa, Atp2b4, Bcam, Bmp1, C3, Cat, Ccl2, Cntn4, Col16a1, Dpp6, Epas1, Fam120c, Fam70a, Fbln1, Fkbp1a, Foxc1, Gfap, Grp, Hspa12a, Htr2c, Igf1, Kdr, Kif1a, Lcat, Lpl, Ndst4, Nmbr, Nr4a2, Pde3b, Pmch, Polr1b, Ppp2r2b, Rab33b, Sdc4, Senp7, Serinc2, Slc17a6, Syt2, Thbd, Tia1, Trhr, Ttc39c, Vcam1, Vdr and Vps13cwas formerly observed. The newly generated list may appear relatively restricted when compared to our initial dataset of 3488 dysregulated genes. However, given the variety of scientific paradigms (depletion vs supplementation), the nature of the samples (cells vs different brain regions), the molecular diversity of the administered molecule (vitamin D3 vs 1,25(OH)2D3) and the heterogeneous size of the datasets, it is not of minor importance to be able to establish an inventory of commonly misexpressed genes in nervous cells or brain areas after vitamin D3 treatment.
We chose to perform a literature-based analysis of possible VDRE-containing DEGs in our datasets. To avoid discrepancies between study designs, we initially based our search on a large in silico and microarray-based study by Wang and colleagues  [6]. This revealed the presence of a very limited number of putative VDREs in our dataset. However, although ChiP-seq and genome-wide studies have found that the most frequent sequence located in VDR binding regions is the classic consensus VDRE motif, these data also suggest the presence of other motifs whose configuration diverge from the classic one and that might or might not interact directly with the VDR  [33]. Moreover, there appears to be 1000-10,000 possible chromatin VDR binding sites, according to the cell-type considered. In contrast the number of primary 1,25(OH)2D3 target genes is thought to be around 100-1000 per tissue, suggesting that some genes are controlled by more than one VDR binding site  [33].
It is therefore difficult to conclude on the complete list of VDR direct targets in our dataset. For instance, the study by Latimer and coworkers, reported putative VDRE sequences in three genes from our dataset -Cntn4, Ppp2r2b and Syt2 -which were not previously identified by Wang and colleagues  [6, 30]. These potential VDRE-containing DEGs are involved in synaptic vesicle trafficking and neurotransmission, indicating a possible direct modulation of these processes by 1,25(OH)2D3 in the 5XFAD animal model. Since the determination of true VDRE sequences would require further investigation and that vitamin D metabolites are also known to interact with various membrane-based signaling pathways, the search for indirect actions, for instance through modulation of immune processes, is not to be excluded.
As with clinical trials, there is a great need for additional work in rodents before deciphering the exact mechanisms of action of vitamin D in the nervous system. However, we feel confident that the present dataset is a useful public resource which reflects the variety and pleiotropy of vitamin D3 actions in the brain with particular emphasis on the crosstalk between vitamin D3 activated pathways and those affected in AD and should allow future studies to further validate the use of vitamin D3 as a potent therapeutic agent in AD.