dataesr/scientific-paragraphs-categorization huggingface dataset:
Acknowledgments: The collection of the urine samples was supported by several organizations ( UNICEF, IRD, ILSI, World Vision , and WFP) and collected by the  Fisheries Administration of Cambodia. The development of the paper was supported by  UNICEF National committees (Australian, Korean , and  Hong Kong ). We would like to thank the  Fisheries Administration of Cambodia and its team  for their support. We would also like to thank  Simon Pfanner  for his editing.
Data analyses Results are reported as means ± standard error of the mean (SEM). For each early biomarker of renal damage, we compared their maximal values after PEGB consumption with previous maximal values reported for healthy dogs. As replicate datasets were collected, linear mixed-effects model analyses could be undertaken to investigate any interaction between PEGB dose, and time. Moreover, an inter-group analysis was performed using a linear model to compare data for each of the experimental groups (4, 20, and 40 mg/kg/d), with the control group, at the beginning and end of the study. Finally, an intra-group analysis was completed using a linear mixed effects model to compare data from the initiation and end of the study. These analyses were completed using the R software (R Core Team (2013)).
Moreover, increasing plasma NGAL would reflect tubular and filtration dysfunction, data already provided by other early biomarkers of renal damage (Plasma CysC, and urinary CysC/Creat, NGAL/Creat, and Clu/Creat ratios). Therefore, we suggest that plasma NGAL measurements represent redundant data and can be omitted. Intermediate measurements were also taken during the 24-week study period for all biomarkers; these did not reveal any significant differences. The PEGB doses ranged from 4 to 40 mg/kg/d, the intentional dose for dogs facing cognitive decline being 4 mg/kg/d [as recommended by the Neurophenols Consortium]. In studies where dogs were fed supplements with grape seed/skin extract at 20 mg/kg/d  [5] , or grape seed proanthocyanidins at 5 mg/kg/d  [6] , symptoms related to acute renal failure were not reported.
Data Management, Statistical Methods, and Definitions The quality of data recorded in the study source documents and case report forms was monitored regularly following good clinical practices principles by the trials' clinical monitor before the data were sent to the centralized database in Manhiça, Mozambique. Data were doubleentered using OpenClinica Enterprise software for clinical data management. The analysis compared infants born to women receiving either SP or MQ, independently of the MQ regimen. The analysis was done on the modified intention-to-treat (mITT) cohort that included all live births born to women who met the inclusion criteria and had data on the outcomes of the main trial. The mITT analyses were adjusted by country. To include seasonality in the adjusted analysis, the duration of women's recruitment was divided into eight periods, and the interaction terms between period of recruitment and country were included in the model, which allows modeling of the effect of period in each country independently.
Congenital abnormalities, hospital admissions, and deaths were considered serious adverse events (SAEs) and were confirmed and reported in specific questionnaires by a study clinician and notified to the sponsor and the data safety monitoring board. Diagnoses for the SAE reporting were codified using Medical Dictionary for Regulatory Activities preferred term and system organ class coding system  [36]. Incidences of clinical malaria, anemia, infant mortality, hospital admissions, and outpatient attendances were estimated as the number of episodes per person over the time at risk. Time at risk was defined as the time from the start of follow-up (day of birth) until the end of follow-up (visit at 12 mo) or withdrawal due to censoring or death, whichever occurred first. In order to avoid counting twice the same episode of clinical malaria, participants did not contribute to the denominator or numerator during an arbitrary period of 28 d after an event of clinical malaria was confirmed.
However, in the first study, MQ was given at a prophylactic dosage (2. 5 mg of base/kg/wk), making it difficult to extrapolate the findings to higher treatment dosages. In the other study, the small sample size was insufficient to appropriately assess differences between groups. In the first trial, weight and weight gain at months 1, 3, 6, and 12 were similar in children born to women who received MQ and those born to women who received placebo  [27]. In the second trial, infant growth outcomes were not assessed. An analysis of a case series of 72 American female soldiers who took weekly MQ prophylaxis without prior knowledge of their pregnancy status found that two out of the 13 live-born infants with available data were small for their ages  [40]. Other than these studies, most of the safety data in children born to women who took MQ while pregnant come from the post-marketing surveillance system of the manufacturer (dominated by exposure as chemoprophylaxis) and from studies in Southeast Asia, none of which assessed the impact of MQ during pregnancy in children older than 1 mo of age  [40] [41] [42] [43] [44].
Additional Information This list of resources contains links that can be accessed when viewing the PDF on a device or via the online version of the article at http://dx. doi. org/10. 1371/journal. pmed. 1001964. • Two PLOS Medicine Research Articles by Gonzalez et al. describe the randomized controlled trial of the efficacy and safety of IPTp with MQ versus SP in HIV-negative women and in HIV-infected women; additional information about the trial is available from ClinicalTrials. gov and the Pan African Clinical Trials Registry • Information is available from the World Health Organization on malaria (in several languages) and on malaria in pregnancy; information on IPTp and the current WHO policy recommendation on IPTp with SP are available; the World Malaria Report 2015 provides details of the current global malaria situation, including information on malaria in individual African countries • The US Centers for Disease Control and Prevention also provides information on malaria and recommendations for the use of MQ during pregnancy; a personal story about malaria in pregnancy is available • Information is available from the Roll Back Malaria Partnership on all aspects of global malaria control • The Malaria in Pregnancy Consortium is undertaking research into the prevention and treatment of malaria in pregnancy • MedlinePlus provides links to additional information on malaria (in English and Spanish).
Acknowledgments We are grateful to all the women who participated in the study. We thank the study staff in the  Malaria in Pregnancy Preventive Alternative Drugs (MiPPAD) partner sites-Allada, Attogon, Sékou (Benin); Fougamou, Lambaréné (Gabon); Manhiça, Maragra (Mozambique) ; and Chamwino and Makole (Tanzania)-for their dedication throughout the study. We wish to thank  Arsenio Nhacolo  for data management, Clinical Monitor Daniel Iñiguez, Project  Assistant Montserrat Pi-Boixadera , the  MiPPAD Safety Monitoring Team-Alberto L. García-Basteiro ,  Anna Llupià , and  Laia Sánchez  from the  Barcelona Centre for International Health Research (Spain)-Elena del Cacho, Carles Codina from the Pharmacy Department , as well as.
This study was funded by the  European Developing Countries Clinical Trials Partnership Instituto de Salud Carlos III  ( PI08/0564 ), Spain;  Federal Ministry of Education and Research  ( BMBF FKZ: da01KA0803 ),  Germany ;  Institut de Recherche pour le Développement (IRD) ,  France. CANTAM  provided infrastructure help in the study. RG and MRu were partially supported by grants from the  Spanish Ministry of Health  (ref. CM07/0015  and  CM11/00278 , respectively). The CISM receives core funding from the  Spanish Agency for International Cooperation (AECI). LLITNs (Permanet) were donated by  Vestergaard Fransen. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Context and Sample The present study is part of the ALIMASSENS Collaborative Project which was launched in France in 2014. It is a five-year multidisciplinary, multicomponent project with the ultimate objective of developing food products of high nutritional quality adapted to the masticatory capacities of non-institutionalized elderly (65+ years)  [23]. The epidemiological component of the ALIMASSENS project is based on data from the ongoing NutriNet-Santé e-cohort. It was launched in France in May 2009, with enrollment and participation taking place exclusively online via a dedicated and secure web site  [24]. Adults with Internet access are recruited via a combination of traditional (e. g. , flyers available in doctors' offices) and online (e. g. , website advertising) strategies including vast, recurrent multimedia campaigns (television, radio, national/regional newspapers, and billboards).
The provision of informed consent and an electronic signature is mandatory for enrollment. The NutriNet-Santé study was approved by the ethics committee of the French Institute for Health and Medical Research (IRB INSERM n ˝0000388FWA00005831) and by the National Commission on Informatics and Liberty (CNIL n ˝908450 and n ˝909216). Upon enrollment, participants are asked to complete a set of five questionnaires: sociodemographics and lifestyle, health status, physical activity, anthropometrics, and diet  [24]. For the present study, we used data from enrolled volunteers aged 65+ years, residing in metropolitan France, with at least three available 24 h dietary records (described below) provided during the first two years following enrollment.
Covariates We used the following sociodemographic and health status data provided via self-administered questionnaires: sex, age, body weight and height, educational level, retirement status, most recent occupational category, smoking, living arrangement, residential area density, prevalent hypertension (self-report and/or antihypertensive treatment), diabetes (self-report and/or anti-diabetic treatment), and history of major cardiovascular disease (myocardial infarction, stroke, acute coronary syndrome).
Acknowledgments: Sources of support: The  ALIMASSENS Collaborative Project  is funded by the  French National Research Agency  (grant #  ANR-14-CE20-0003 ). The epidemiological research work within ALIMASSENS is based on data from the  NutriNet-Santé  study which is supported by the  French Ministry of Health (DGS) , the  French Institute for Health Surveillance (InVS) , the  National Institute for Prevention and Health Education (INPES) , the  Foundation for Medical Research (FRM) , the  National Institute for Health and Medical Research (INSERM) , the  National Institute for Agricultural Research (INRA) , the  National Conservatory of Arts and Crafts (CNAM) , and the  University of Paris 13.
Socio-Economic and Anthropometric Assessment All data and measures were collected by trained field agents. Data on level of education and occupation of children's parents were collected using an auto-administered questionnaire, sent to them few days before the survey, and returned by the children the day of the survey. With respect to anthropometry, standing height was measured to the nearest 0. 1 cm with the use of a wall-mounted stadiometer (Person-check ® , Kirchner and Wilhelm, Germany); weight was measured to the nearest 0. 1 kg on a calibrated scale (Detecto, Webb City, MO, USA). Height-for-age and BMI (Body Mass Index = weight/height 2 ) for-age z-scores were derived from the World Health Organization (WHO) reference for school-age children: Stunting was defined as height-for-age <-2 z, thinness was defined as BMI-for-age <-2 z, and overweight as BMI-for-age ≥+1 z [23].
Data Management and Statistical Analyses Epidata software version 3. 1 (The Epidata Association, Odense, Denmark, 2008) was used for data entry and validation by double entry and Stata 14 (Stata Corporation, College Station, TX, USA, 2015) for data management and statistical analyses. The type I error risk was 0. 05. Results are presented as estimates and standard error (between parentheses) or a 0. 95 confidence interval (between brackets). For the UIC and iodine content of the salt used in the households, results were expressed as medians and/or percentages using the categorizations defined above. Associations between UIC or salt iodine content with gender, age, and area or region, were graphed using box and whisker plots of quantitative variables and assessed using chi-square tests, using UIC or salt iodine content in quintiles.
General Characteristics of the Samples A total of 780 boys and 780 girls were surveyed, from which urine and salt samples, and socio-demographic and anthropometric data were collected. Two thirds were from urban areas and weighted proportions by regions were in accordance with national data for the same age-class (Table  1 ). Mean age was 9. 3 (0. 04) years, the minimum was 6. 1 years and maximum was 12. 9 years in accordance with the inclusion criteria. Most fathers and mothers had primary schooling or more, but seven mothers out of 10 had no professional occupation vs. only a fraction of the fathers. Mean weight was 30. 5 (0. 5) kg, mean height 134. 3 (0. 5) cm, mean height-for-age was 0. 0 (0. 1) z-scores, mean BMI-for-age was -0. 18 z-scores of the reference. Less than a 10th of the children were thin.
Acknowledgments: The work was supported by the  Tunisian National Institute of Nutrition and Food Technology of the Tunisian Ministry of Health  and by grants from  UNICEF Tunisia. The authors wish to thank the Tunisian national and regional delegates, health directors, education directors, as well as parents of selected children who facilitated the fieldwork of this survey. The founding sponsors had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, and in the decision to publish the results.
Study population We performed a retrospective single-centre observational study: 118 biopsy samples were retrospectively retrieved from a key-word search of the computed database of the Department of Pathology of the University Hospital of Lille. The selection terms consisted of "calcification", "crystal" and "graft kidney". The selection criteria included availability of the paraffin-embedded kidney allograft biopsy tissue. These 118 biopsies were performed in 72 allograft recipients. One hundred patients without crystals in their biopsy were randomised as controls. All patients consented to participate in the protocol. Patients were treated with double immunosuppressant of calcineurin inhibitor and mycophenolate mofetil, and prednisolone was added in case of sensitisation. This study was approved by our local ethics committee.
IR-MS analysis IR-MS was performed on an IN10MX microscope (Thermo Scientific, ZA Courtaboeuf, Les Ulis, France). Tissue samples were deposited on Low-e microscope slides (Mir-rIR, Kevley Technologies, Tienta Sciences, Indianapolis) and then chemically treated with xylene to remove paraffin in order to improve crystal detection. All spectra were collected in ultrafast mode using a 50 mm Â 50 mm aperture. The spectra were collected in the 4000e800 cm À1 mid-IR range at a resolution of 16 cm À1 with one spectrum per pixel. Data analysis of IR spectra and chemical images was performed using OMNIC software. Infrared spectroscopy was also carried out on a PerkinElmer Spotlight 400 FTIR microspectrometer fitted with a liquid nitrogen cooled, 16element linear array mercury cadmium telluride (MCT) detector.
Sample collection and analyses All relevant clinical and biochemical data of both donors and recipients were collected prospectively in a database. Serum and urine sample analyses were performed at the first ambulatory consultation (day 18) and at months 3, 6, 12 and 24 after transplantation. Serum concentrations of PTH were determined by third generation chemiluminescence assay. This assay detects full-length and not the N-terminal truncated fragments with a normal range of 15e68 pg/ml.
Statistics SPSS statistical software package, version 22. 0 (SPSS Inc, Chicago, Illinois, USA), was used for the statistical analyses. Results are expressed as mean ± SD. Numerical data were compared with the student t-test or the ManneWitney Utest, depending on the results of analysis for a normal distribution using the ShapiroeWilk test. Comparisons of categorical data between groups were performed with the Chi-square test or the Fischer exact-test as indicated. Graft survival Kaplan Meier-curves were compared with the logrank test. Differences with p < 0. 05 were considered as being statistically significant.
In the preference assay, hungry flies are given a choice between two sugars mixed with different colors; after 5 min color of the abdomen is used to assess consumption. (B) Schematic of selected pectic polysaccharides present in fruits' cell Figure  1  continued on next page threshold for D-arabinose is reported to be five times lower than that of L-arabinose  (Hassett et al. , 1950). When we measured consumption by Capillary Feeder (CAFE ´) assays over a concentration range (Figure  2 -figure supplement 3B) or by mixing radioactive [32]P in the food in fixed concentration (Figure  2 -figure supplement 3C), the flies consumed more D-than L-arabinose. Over time, however, flies consumed less D-and L-arabinose than nutritious sugars (data not shown), consistent with other studies  (Dus et al.
Statistical analysis and number of trials (n) All statistical analyses were performed using Graphpad Prism 5. All the data met the assumption of homogeneity of variance, therefore unpaired two-tailed t-test or one-way analysis of variance (ANOVA) was performed with Tukey post-hoc test between pairs of samples. ANOVA tests for significance were performed a probability value of 0. 05 and more stringent values are listed in each figure where applicable. For all experiments, each n is considered a biological replicate; separate trials used independent samples of genetically identical flies. For two-choice experiments, a single n constitutes a population measure generated from 50 male flies. The preference index indicates the proportion of flies eating the sugar, which was determined by scoring visible color in the abdomen or thorax.
For each box, images were acquired at a rate of one image/ min for 2 hr using the software VisionGS, Germany. The stack of images was then transferred to ImageJ  (Abramoff et al. , 2004 ) and the liquid level of each capillary was analyzed using a Java plugin, and subsequently transferred to Excel. Results are expressed as the mean of the change of the liquid level in each capillary (D-arabinose: n = 12; L-arabinose: n = 10 boxes). Error bars are computed as the standard error to the mean (s. e. m. ).
A reference electrode was connected to the abdomen of the fly, using a drop of electrocardiogram gel. Each stimulation lasted 2 s and was digitized at 10 kHz, 16 bits during 2 s (DT9818, Data Translation, USA). The data acquisition, spike detection and sorting was performed under a program, dbWave. The results were subsequently transferred to Excel, and expressed as the mean (n = 8-15 measures). Error bars were computed as the s. e. m.
Acknowledgements KS and JM conceived of the project, designed the experiments, analyzed the data, and prepared the manuscript. JM, HJ, AVA. , and CPS performed the experiments. JU, BS, and JL assisted with imaging and image analysis. ZY built the optogenetic apparatus. KS and JM wrote the paper and made the figures. MAA performed the electrophysiological observations, Palak Rawat performed CAFE experiments, and FMP analyzed the  CAFE  and electrophysiology data. We are especially grateful to  Dr. John Carlson  of  Yale University  for reagents and suggestions in the early stages of the project. We thank  Wanda Colon Cesario ,  Adrienne van Antwerp , and  Abiel Trevino  for assistance with sugar preference tests and calcium imaging. We thank  Tony Torello  for help in constructing the optogenetic apparatus.
Design of TAL modules and rat Lepr locus targeting in vivo According to the rat Lepr nucleic acid sequence obtained from the NCBI (National Center for Biotechnology Information) genbank database, we designed a pair of TALE modular arrays targeting two adjacent sites with an 18 bp interval (spacer) on exon 2 of the rat Lepr gene. The TALE arrays were fused to the N terminus of the catalytic domain of Fok I nuclease. In vitro transcribed mRNA of the TALEN pair was injected into 153 rat one-cell embryos and this resulted in 3 F 0 newborns. Using the T7 endonuclease I (T7EI) digestion assay, we identified two F 0 pups that were founders containing mutations in the Lepr locus. Interestingly, founder 2 rat carried a bi-allelic mutation and no wild-type PCR band was identified (Figure  1A ). To determine the exact mutation sequence, PCR products were TA cloned and at least ten colonies were sequenced.
This indicated that the corresponding PCR products (871 bp) were melted, and annealed with a similar amount of PCR products amplified from wild-type mouse genomic DNA to form heteroduplex DNA. The DNA heteroduplex was then subjected to mismatch sensitive endonuclease (T7E1) assays and the products were resolved in 1. 5% agarose gels. Underlined data indicated rat bearing mutations. M, DNA marker. E, Sequences of TALEN-induced mutations in F 1 of Lepr founder 1. The binding sites of the TALEN half-site are shown in blue and underlined. A dash represents a single base deletion. Insertions or substitutions are indicated by red letters and underlining. Allele that appeared in F 1 but was not originally identified in the founder is highlighted in yellow. The number of F 1 rats with each genotype is listed on the right.
TALEN expression vector construction We identified target sites of the Lepr using the online software (http://boglabx. plp. iastate. edu/TALENT/help. php) (Cer- ALT, alanine aminotransferase. Analytes were measured in serum and these data were tested in ADICON Clinical Laboratories. Data are given as means±SEM for surviving animals (n=5 for WT and Lepr in18/in18 rats, respectively). mak et al. , 2011). Nucleotide-recognizing TALE single-unit vectors and TALEN expression vectors were obtained from Bo Zhang (Peking University). We constructed TALE repeat arrays and TALE nuclease expression vectors according to the methods as described  (Huang et al. , 2011).
A dash represents a single base deletion. Insertions or substitutions are indicated in red letters. The length and frequency of indels are labeled to the right of each sequence. C, 18-week-old Lepr founder 2 (right) and its wild-type littermate (left) were anesthetized and photographed. D, Identification of F 1 of Lepr founder 1 using T7 endonuclease assay. PCR primers were designed flanking the TALEN binding sites of Lepr. PCR products (871 bp) were melted, and annealed with a similar amount of PCR products amplified from wild-type mouse genomic DNA to form heteroduplex DNA. The DNA heteroduplex was then subjected to mismatch sensitive endonuclease (T7E1) assays and the products were resolved in 1. 5% agarose gels. Underlined data indicated rat bearing mutations. M, DNA marker. E, Sequences of TALEN-induced mutations in F 1 of Lepr founder 1.
, 2008). The forward and reverse primer sequences used are shown in Table  2. The specificity and identity of the amplified products were verified by the melting curve analysis showing a single melting peak after amplification and by sequencing the amplified PCR products using the Big Dye Terminator v1. 1 and an ABI3130 sequencer (Applied Biosystems). Data analysis was performed using the Roche's E-method of relative quantification, which uses standard curve derived efficiencies, of the LightCycler 480 1. 5 version software. In this study we used the β2-microglobulin (BMG) housekeeping gene as the reference gene since its expression level was unaffected by our experimental conditions. The results are expressed as the target/reference ratio divided by the target/reference ratio of the calibrator.