dataesr/scientific-paragraphs-categorization huggingface dataset:
In Vitro Wound Healing Assay ECFCs and HUVECs were seeded in 6-well 0. 2% gelatin coated plates at a density of 1 ˆ10 5 cells/well. Three days later, cells were placed overnight in EBM-2 + 5% FCS. Cells were then treated with wortmanin 100 nM (Calbiochem) and with 10 µg/mL of LMWF or LMWH in EBM-2 + 5% FCS for 24 h (0. 1% DMSO was present in all treatment conditions). A wound was created in the center of each well, by scratching the cell monolayer with a sterile plastic pipette tip. Cellular debris were removed as the wells were washed with PBS and the medium replaced by EBM-2 + 5% FCS. The wells were observed and imaged using a phased microscope just after the creation of the wound and 6 h later. The uncovered surface was measured by a blinded observer using Histolab software (Microvisions, Evry, France).
Data were extracted and normalized using GeneSpring GX (Per Chip: Normalize to 50th percentile; Per Gene: Normalize to median). The working lists were created, filtering probes with detection p-values < 0. 05 for at least half of the arrays. To control for systematic bias, unsupervised hierarchical clustering was performed, showing that samples are segregated according to the treatment groups. Differentially expressed genes with an expression fold change greater than 1. 5 fold were selected using the Student test, with a significance p-value < 0. 05, including Bonferroni and Benjamini Hochberg false discovery detection. Differential expression of the chosen genes was assessed using supervised hierarchical clustering. The interpretation of the resulting gene lists was performed using the Ingenuity interface.
Acknowledgments: We thank the staff of the  Hôpital des Diaconesses and of the Maternité des Lilas  for providing umbilical cord blood and umbilical cord samples. We thank the staff of the  Plateforme P3S-Université Pierre et Marie Curie and Nicolas Cagnard  from the  Plateforme Bioinformatique-Université Paris Descartes  for their precious help and expertise. C. B. was supported by a grant from the  French Ministry of Research and Education  and from the  French Society of Hematology. These institutions had no other involvement in this study.
Single cells were isolated from a mass culture (passage V) of RDEB keratinocytes infected with SIN retroviruses bearing a COL7A1 cDNA. Clonal types were determined  (Barrandon & Green, 1987)  and listed in Supplementary Table  S1. Growing clones were expanded for further characterisation. S2 ) that codes for a sub-unit of a metabolic enzyme  (Taft et al, 2013). We thus determined by RT-PCR that the level of DARS expression was unchanged in the corrected stem cell compared to uninfected cells (Fig  5C ). We also used NGS data to gain information on insertion/deletion (indel) and single nucleotide polymorphism (SNP) identified in the DARS sequence of clone 6. None of the annotated indel or SNP was associated with disorders described in the genomic database (GWAS catalogue and Cosmic GS5). However, two undescribed indels and one SNP were identified  (Fig 5D).
Small insertion-deletions and SNP calling were performed and compared to GWAS databases. The mapping highlighted two indels and one SNP in the DARS genomic sequence. The indels were not associated with disease and the SNP was synonymous (CCU-CCG both codons correspond to proline). ª that the entire procedure from initial isolation of a population of epidermal stem cells from the biopsy to the transplantation of cloned genetically corrected CEA necessitates a maximum of 30 divisions. This is a reasonable number when a holoclone can undergo at least 180 doublings in culture  (Rochat et al, 1994; Mathor et al, 1996). Second, one must favour a friendly cell-sorting technology over fluorescence-activated cell sorting (FACS) as it is well documented that the FACS procedure is a source of stress for epidermal stem cells  (Barrandon et al, 2012).
Whole-genome sequencing Whole-genome sequencing was performed by Microsynth, Switzerland. Raw data are accessible on http://ncbi. nlm. nih. gov/sra/ accession number SRP050326. Briefly, 3 lg genomic DNA from clone 6 was sequenced using SOLiD 5500xl (Life Technologies) mate-pair reads. The reads were mapped to the hg19 reference sequence and to the vector reference sequence from the viral producer clone Flp293A-E1aColVII1. Mate pairs that span from the viral sequence to a human chromosome were extracted. Specific primers for the predicted integration sites were designed, and amplified products were sequenced to resolve the proviral integration sites at the base-pair level. Based on the mapping, SNP calling was performed and SNP were compared to dbSNP. Mapping, SNP and small indel calling were performed using LifeScope 2.
Acknowledgements We are grateful to Genethon for providing us with retroviral supernatants through the  Therapeuskin consortium , to  Dagmar Wirth  for the Flp293A-E1aColVII1 producer clone and to  Alain Hovnanian  for stimulating discussions. We are also grateful to  Steeve Vermot  and  Jeanne Vannod  for excellent technical help, to  Patrick Reichenbach  and  Giulietta Maruggi  for the help in Southern blotting, to  Matthias Titeux  for sharing his grafting protocol and to  Stéphanie Rosset  for technical assistance with TEM. We also thank  Olivier Dormond  for pRb, p21, Ras and GAPDH antibodies,  Alessandro Amici  for help with the tumorigenic assay and critical reading of the manuscript,  Jean-Daniel Tissot  for supplying us with human plasma,  Alvaro Baptista  and the  Department of Pathology  at the CHUV with skin samples and  Rainer Follador  from Microsynth for helpful discussion.
Raw data are accessible on http://ncbi. nlm. nih. gov/sra/accessionnumberSRP050326. Integration sites were then individually characterised by conventional sequencing with a definition at a base-pair level(Fig 5B). Sequencing data confirmed the integrations identified by LM-PCR on chromosomes 2 and 22 and confirmed the integration on chromosome 11 discovered by FISH. Most importantly, these experiments demonstrated that the proviruses did not integrate in or in the vicinity of known oncogenes, therefore diminishing or even alleviating the risk of uncontrolled cell proliferation. One provirus was inserted in the first intron of the DARS gene (chromosome 2)(Fig 5B and Supplementary Table.
Purpose: Cervical dystonia (CD) is a hypertonic condition caused by damage to the central nervous system. Very few studies have assessed the overall economic burden of the disease. The objective of this study was to describe the utilization of health care resources of patients with CD in the UK primary care setting, using a large population-based database. Patients and methods: Adults with a first diagnosis of CD between January 1, 2007 and January 31, 2011, who were registered to a general practitioner (GP) practice contributing to The Health Improvement Network (THIN), were included. Sociodemographic and clinical characteristics were assessed at the time of diagnosis. Health care resource utilization and pharmacological treatment were investigated at the end of the first and second year after diagnosis.
Differences in costs across patients were explained by the frequency of BoNT-A administration and duration of effect. 22 However, at the present time, there are no other European studies that have estimated the overall economic burden of CD, including the UK. The primary objective of this study was to describe the utilization of health care resources of patients with CD in the primary care UK setting, using a large population-based database. Both health care resource utilization and frequency of prescriptions by the general practitioner (GP) of the most common pharmacological treatments during the first and second year after diagnosis were assessed. Additional data variables described in the study included the sociodemographic and clinical characteristics of patients newly diagnosed with CD.
Material and methods This retrospective study was conducted using data from individuals registered to a GP practice contributing to The Health Improvement Network (THIN) database. THIN database includes primary care records from 532 general practices representative of the UK population, with 3. 7 million registered patients as of the end of September 2011. 23 Available records include anonymized sociodemographic data, medical signs, symptoms and diagnoses described using Read codes (a standardized clinical coding system used by GPs in the UK), diagnostic and laboratory tests, referrals, and prescriptions of any medications issued by the GP.
inclusion and exclusion criteria This study included adults aged 18 years old and above at the time of first diagnosis of CD (index date) between January 1, 2007 and January 31, 2011. The diagnosis was identified by a single Read code -"F138200: spasmodic torticollis"; no other codes with the specific term "cervical dystonia" existed. All the available patient data up to January 31, 2013 was extracted. To ensure only newly diagnosed cases were captured, patients were excluded if they were first diagnosed within 6 months of registering with the GP practice. The study time frame included patient records from 12 months prior to index date (baseline period) until end of follow up, which was defined as death, transfer out of the practice, or last data collection at the practice. Patients were required to have a minimum of 24 months of follow up after diagnosis so that resources could be investigated at two cross-sectional time points after diagnosis: at 12 and 24 months.
For categorical variables, the number and proportion at each level of the variable, with 95% confidence intervals (CI) around the proportion, were reported. The number and percentage of missing values, as applicable, were reported for each variable. All analyses were conducted using commercially available statistical software (SAS version 9. 2; SAS Institute Inc. , Cary, NC, USA). The study was approved by the international Scientific Review Committee (SRC) to ensure appropriate analysis and interpretation of the data (SRC protocol 13-074).
Results Overall, 6,352 patients had their first Read code for CD recorded between January 1, 2007 and January 31, 2011 (Figure  1 ). Patients were excluded for the following reasons: aged younger than 18 years old (n=1,068), less than 6 months between registration and index date (n=576), and less than 24 months of follow up after index date (n=684). Reasons for having less than 24 months follow up included: 37 patients who had died, 408 who had transferred out of the GP practice and the remaining 239 were enrolled in a practice for which the last data collection was earlier than January 31, 2013. When comparing patients with at least 24 months of follow up and those with less than 24 months follow up, the only investigated characteristic that was significantly different between the two groups was age, as patients with less than 24 months of follow up were younger on average (mean age 41.
9% of patients were current smokers, defined in their most recent smoking status as "current smoker" at baseline. Socioeconomic status was assessed and scored to indicate patients' deprivation level geographically, with 1 being least deprived and 5 being most deprived. This was recorded in 95. 6% of the patients, of which 22. 9% came from the least-deprived category, followed by 21. 6% from category 2, 21. 2% from category 3, 19. 3% from category 4, and 15. 2% from category 5, the most-deprived area. This distribution was consistent with that of the overall THIN population (data provided by Cegedim Strategic Data Medical Research UK (CSD MR UK). Overall, most patients (82. 5%) did not have any of the comorbidities investigated. Depression in the last year before diagnosis was the most common comorbidity, present in 8.
Discussion This study used a population-based primary care database to describe sociodemographic and clinical characteristics as well as health care resource utilization in patients with CD in the UK. A total of 4,024 patients with CD were identified between January 1, 2007 and January 31, 2011. Based on the prior incidence estimates of between 8 and 12 cases per million person-years,  4, 25, 26  the number of cases identified in THIN was larger than that previously reported in the literature. However, prior studies were considered to have low estimates  27  owing to the way they had been designed. They mostly evaluated patients who attended secondary care facilities specializing in treatment of this condition, whereas in THIN, a wider population was included, namely all subjects coded by their GP as "spasmodic torticollis", and in the UK, some of them would be managed in the primary care setting only.
After adjusting by age, sex, and socioeconomic status, the usage of primary care resources was found to be similar to that of other patients. Secondary care, as captured in the database, was found to be higher in patients with CD compared with that in the rest of the population in THIN. Oral medications were generally prescribed by the GP, including treatment continuation for chronic conditions that were initiated in the specialist setting. The most common treatments for CD were analgesics and benzodiazepines. Pain has been reported in the literature as affecting up to 75% of patients with CD,  24  which appears to be consistent with the high prescription rates of analgesics. However, in THIN, only the data on prescription type are available, whereas the reason for prescription cannot be determined.
Treatments chosen or prescribed (at any time) included: BoNT-A (86%), oral medication (53%), physiotherapy (31%), psychological support (11%), and surgery/deep brain stimulation (9%). There are limitations associated with this study, which suggest the results should be interpreted with appropriate caution. This study was descriptive in nature, and although the health care resources that were investigated are those associated with CD, given the nature of the database and lack of detailed reason for prescription or visit, it was not possible to specifically attribute them to CD. This is a common limitation in retrospective studies. Additionally, detailed data on resources from the secondary care setting are not well captured in THIN, including medical treatment and procedures. Read codes related to treatment with BoNT-A were investigated as part of this study, and only 0.
35% and 0. 29% of the patients recorded in the first and second year after diagnosis, respectively, were found to have one of the Read codes. This could reflect the initial stages of the disease in the first 2 years after diagnosis or a predominance of patients with CD with mild symptoms. Still, percentages were lower than expected for this patient population, and it is possible that there were a number of treatments with BoNT-A that were not captured within the database, which could account for the low numbers. Further prospective studies from supplementary data sources that capture more elements of secondary care are needed to fully understand the overall economic burden associated with CD. Despite the limitations, this study has a number of strengths. First, THIN records are broadly representative of the UK population in terms of age, sex, and geographical locations, and have been widely used for many cohort studies in many conditions.
Acknowledgments The authors would like to thank  Hannah Kurth  ( Global Market Access and Pricing, Ipsen Pharma ), and  Dimitra Lambrelli  and  Andrew Cox  ( Research Scientists, Evidera ) for their valuable input throughout the study, and  Sharon MacLachlan  ( Research Associate, Evidera ) for excellent data programming work. The authors are also grateful to  Evan Davies  ( Research Associate, Evidera ) for his revision and edits on the manuscript.
The stunning diversity of cichlid fishes has greatly enhanced our understanding of speciation and radiation. Little is known about the evolution of cichlid parasites. Parasites are abundant components of biodiversity, whose diversity typically exceeds that of their hosts. In the first comprehensive phylogenetic parasitological analysis of a vertebrate radiation, we study monogenean parasites infecting tropheine cichlids from Lake Tanganyika. Monogeneans are flatworms usually infecting the body surface and gills of fishes. In contrast to many other parasites, they depend only on a single host species to complete their lifecycle. Our spatially comprehensive combined nuclear-mitochondrial DNA dataset of the parasites covering almost all tropheine host species (N = 18), reveals species-rich parasite assemblages and shows consistent host-specificity.
Results Sequence diversity and host-specificity. The dataset based on a rDNA fragment of 1399 bp length contained 82 haplotypes and 575 variable sites, of which 323 were parsimony-informative. As two rDNA sequences each from parasite of Petrochromis trewavasae trewavasae and from Petrochromis trewavasae ephippium and three from parasites of Tropheus brichardi differed to the extent that meaningful alignment was hampered, they were excluded from further analyses. For COI, the dataset amounted to 583 bp, 73 haplotypes, 278 variable sites and 230 parsimony-informative sites. The concatenated dataset included 62 haplotypes and totaled 1935 nucleotide positions. This alignment contained 621 bp of ITS-1, 157 bp of 5. 8S rDNA, 574 bp of ITS-2 and 583 bp of COI. There were 861 variable sites, of which 659 parsimony-informative.
Phylogenetic analyses. Tree reconstruction on the basis of the concatenated dataset (Fig. 1 ) showed that all Tanganyika monogeneans are grouped in a well-supported clade. In the tree, the parasites of the following taxa are grouped together: the non-tropheine Tanganyika endemic Neolamprologus fasciatus, the haplochromine Astatotilapia burtoni, which is endemic to the Tanganyika Basin but not to the lake proper, and the Tropheini. Within this group, Cichlidogyrus infecting tropheines is supported as a monophyletic group. Cichlidogyrus sclerosus and its congener C. zambezensis, the latter hosted on the riverine haplochromine Serranochromis robustus jallae, are clearly separated from the Tanganyikan parasites. Well-supported clusters of Cichlidogyrus are organised according to host species. Irrespective of sampling locality, 'Ctenochromis' horei, 'Gnathochromis' pfefferi, Limnotilapia dardennii, Lobochilotes labiatus, Simochromis diagramma and southern Pseudosimochromis babaulti all harbour monophyletic parasite clades.
This difference was significant as it outnumbered all differences in AIC scores comparing the same models for 5000 randomly generated trees of the same size. Cophylogenetic analyses. The two best solutions proposed by the CoRe-Pa software, either based on a resolved parasite tree or a parasite tree with a basal polytomy, are presented in Table  3. The best solution for the resolved tree and the second best solution in the polytomy case invoked no host-switching and an unrealistically high cost for it, in comparison to the costs inferred for other events. These scenarios are not biologically plausible. Cost schemes should not only be judged on a purely statistical basis but also include the biological context  33. Hence these reconstructions were not further considered and, in case of the resolved tree scenario, replaced by the second best proposal (Fig.
3 ). The two retained solutions, with and without a polytomy in the parasite tree, proposed comparable numbers for all events, with a high number (33-40) of sortings, similar frequencies of cospeciation (11-13) and within-host speciation events (12-11) and a low number of host-switches (4-3) (Table  3 ; Fig. 3 ). In the software package TreeMap the inferred number of 12 cospeciation events was found statistically significant at a level of 0. 05, because only 421 out of 10 4 random reconciliations included 12 or more cospeciation events. This indicates topological congruence between host and parasite trees. Overall congruence between the host and parasite mitochondrial genotypes was significant in a distance-based cophylogenetic analysis (P < 0. 01) although only 11 out of 47 links were reported as significant at a level of 0.
Methods Sampling and data collection. Cichlidogyrus specimens were collected on 18 of the 23 nominal species of Tropheini. Nominal species excluded are Tropheus kasabae Nelissen, 1977, a junior synonym of T. moorii  65  ; T. polli Axelrod, 1977, a junior synonym of T. annectens  65  ; Petrochromis horii Takahashi & Koblmüller, 2014, which was unknown at the time of sampling; Petrochromis orthognathus Matthes, 1959 and Simochromis margaretae Axelrod and Harrison, 1978. The latter species is known only from four museum specimens, none of which suited for molecular analyses; inspection of two of these individuals did not yield gill monogeneans. We distinguish between northern and southern Ps. babaulti. Indeed, the southern populations form a separate clade  8  and were classified at the time of sampling as a separate species: Ps.
Gills were inspected for monogeneans under an Olympus SZX12 stereomicroscope. Parasites were isolated with a dissection needle and stored in 5 μ l of milli-Q H 2 0 at -20 °C awaiting further processing. A small number of flatworms were stored in the field on FTA Classic Cards (Whatman). In total, sequences were obtained from 220 parasite specimens, retrieved from 84 cichlid individuals. DNA extraction, PCR amplification and sequencing followed Vanhove  23  (Supplementary Methods S1). Table  4  shows the GenBank accession numbers of the parasite sequences obtained. Phylogenetic analyses of parasites belonging to Cichlidogyrus. The closest BLAST hit from GenBank, the complete ITS-1 sequence of Cichlidogyrus sclerosus Paperna and Thurston, 1969 (DQ537359) was included as additional outgroup for rooting.
Sequence alignment was performed by MUSCLE v. 3. 8  66  under default distance measures and sequence weighting schemes. The resulting alignments were visually inspected and improved in MEGA v. 5  67. In the case of COI, alignment was straightforward as there were no gaps and translation into amino acids (using the echinoderm and flatworm mitochondrial code) did not result in nonsense or stop codons. These nuclear and mitochrondrial datasets were used separately for an assessment of genetic diversity. jModelTest v. 0. 1. 1  68  was used to select the optimal molecular evolution model starting from a maximum likelihood (ML) optimized tree. Based on the corrected Akaike information criterion (AICc), the TVM + Γ model was selected for the nuclear alignment and the TIM2 + I + Γ model for the mitochondrial dataset (with gamma shape parameter of 0.
40 for ITS rDNA and 0. 11 for COI). Gamma-corrected pairwise genetic distances were calculated in PAUP* v. 4. 01b (Swofford, 2001, Sinauer Associates). As a rough estimate of the species diversity contained in the sample, the number of haplotypes displaying at least 1% (for ITS rDNA) and 2% divergence (for COI) was determined. This follows the ITS divergence cut-off proposed to match morphospecies boundaries in the best-studied monogenean, Gyrodactylus 57 , and the threshold of sequence divergence between species commonly used in barcoding  69. For tree reconstruction, a concatenated dataset was built on the basis of the specimens that yielded both nuclear and mitochondrial sequences. For an assessment of the phylogenetic content of the dataset, we performed a likelihood mapping analysis based on quartet puzzling  70  implemented in TREE-PUZZLE v.