dataesr/scientific-paragraphs-categorization huggingface dataset:
, 2009)  and Brazil  (Amaral, et al. , 2006). Light alone may not be a perfect proxy to measure populations but, combined with other sources, it can substantially add value. It is worth noting that the Gridded Population of the World (GPW) 7  , which is one of the most widespread databases of the global population density, uses nighttime lights as one of its many inputs. Also using nighttime light images,  Elvidge, et al. (2009)  constructed a global Poverty Index (PI) by dividing population numbers by the average light. This shows the regions where people are living without satellite detectable stable light, which is, according to the authors, an indicator for poverty. After calibrating the index with official statistics on poverty, it was estimated that 2. 2 billion people live with an income below $2 a day.
It can be seen in Exhibit A1 that most publications fail to mention explicitly the specific version. This may complicate the reproduction and comparison of different studies. In this research, we tried to follow a best-practice by inter-calibrating and reprojecting the different images and removing the gas flares. The Stable Lights dataset version 4 (NGDC, 2012) was used. The inter-calibrated nighttime light images that are at our disposal cover the period between 1992 and 2009. This includes exactly the period of the dramatic regime shift that can be seen in the MGI study. Therefore, we decided to challenge this fascinating study and compare the dynamics of the economic center of gravity with the center of gravity of nighttime light emissions.
Acknowledgements This paper is an outgrowth of the master thesis completed in Nov. 2012 by  Nicola Pestalozzi  entitled " Earth Nighttime Lights  to study economic and urban growth", performed under the supervision of the other authors. Additional material, including images and videos that were made for the master thesis project, can be found on www. worldatnight. ethz. ch. The thesis is available online at www. er. ethz. ch/publications/MAS-Nicola_Pestalozzi_Dec12. pdf. We wish to heartily thank the whole  Land Use Engineering Research Group (LUE) of Professor Hans Rudolf Heinimann. We would like to mention Daniel Trüssel and  Monika Niederhuber  in particular for sharing their expertise on ArcGIS. Thanks also to  Luc Girardin  and  Sebastian Schutte  from the  International Conflict Research Group (ICR)  of  Professor Lars-Erik Cedermann  for their help, especially in the initial phase of the work.
Results Diploid heterothallic SK1 MATa/α cells were cultivated in YPA until mid-exponential growth phase. They were transferred to sporulation medium containing potassium acetate as the carbon source and trace amounts of nitrogen introduced by amino acid supplements that complemented the auxotrophies of the strain. Samples from at least two independent sporulation time courses were taken hourly until completion of meiotic differentiation for the measurement of genome-wide transcriptional activity, intracellular metabolite concentrations, and enzymatic activities. Our study focused on the regulation of the central metabolism that orchestrates carbon and nitrogen flux repartitioning and assures energetic homeostasis. Therefore, the transcriptome data released in our previous study  [7]  were re-analyzed with particular regard to the transcriptional activity of genes in glycolysis, pentose phosphate pathway (PPP), Krebs and glyoxylate cycle, gluconeogenesis, reserve carbohydrate metabolism, purine nucleotide metabolism, and glutamate metabolism.
Accordingly, several enzymatic activities and metabolite pools located in these pathways were monitored, and a metabolic flux analysis was carried out at mid-stage meiosis. This allowed information on metabolic reprogramming to be inferred from four different datasets, and provided a high resolution analysis of metabolic reprogramming. To identify meiosis-specific metabolic regulation from the starvation response caused by the absence of nutrients, the behavior of the sporulating SK1 MATa/α strain was compared to a sporulation-deficient homothallic SK1 MATα/α control strain cultivated in the same conditions. To minimize a potential impact of differing auxotrophic markers in both strains, all experiments were carried out using media with exactly the same composition, irrespective of the actual metabolic requirement of the strains for a particular supplement.
Visual comparison of the transcription profiles of the above listed metabolic genes with the earlier transcriptome study of Primig et al. [6]  showed that their transcription patterns were highly similar in both studies. In particular, the meiosis-specific transcriptional down-regulation of the entire glycolytic pathway can also be observed in this earlier released dataset. However,  Primig and  (See figure on previous page. ) Figure  1  Comparison of expression profiles of selected genes during meiotic development and progress in meiotic differentiation. (a) Experimentally monitored and (b) schematically represented timing of meiotic landmark events. (c, d) Clustered gene expression patterns where rows correspond to a gene and columns correspond to time points after transfer from YPA to sporulation medium.
Transcriptome, transcription factor, and gene ontology term analyses Raw transcriptome data were published in an earlier study  [7]. They are available via the European Bioinformatics Institute's repository ArrayExpress  [59]  [accession no. E-TABM-915 (MATa/α and MATα/α)]. In our TF analysis we referred to the dataset provided by MacIsaac et al. [25]  who identified associations between TFs and genes based on the TF binding motif and its conservation among different yeast species (supplementary data of  [25] , file 'TF_binding_p0001_cons1. txt'). To identify enrichment of TF targets among a given gene cluster, a hyper-geometric test was performed according to  [60]  using Equation  4 : p ¼ 1- X k-1 i¼0 M i N-M n-i N n ð4Þ wherein N is the total number of genes, M is the number of annotated targets of a specific TF, n is the number of genes in the analyzed cluster, and k is the number of genes from that cluster that are annotated targets of the specific TF.
Acknowledgements This project was supported by a post-doctoral  DFG  fellowship (WA2163) awarded to TW, an FRM fourth-year PhD fellowship awarded to YL,  Inserm Avenir grant  ( R07216NS ) and  Région Bretagne   CREATE grant  ( R11016NN ) awarded to MP, and research grants  ANR  ( NT05-2_448 ) and  BLAN07-2_200101  awarded to JMF. We thank the students  Utsav Agrawal ,  Bastian Bechter , and  Shuyang Guo  for their valuable help in this study. The authors wish to thank  Ulrich Schlecht  ( Genome Technology Center, Palo Alto, CA, USA ) for providing strains and critical reading of the manuscript, and  Jürgen Heinisch  ( Universität Osnabrück, Germany ) for providing the Pfk1 antibody.
It is generally admitted that the biology of cancers in adolescents and young adults differs dramatically in terms of pathways alteration from those striking later in lifespan  [7]. Moreover, due to their rarity, our knowledge about early-life HCCs is lacking. In order to gain insights into the molecular changes occurring in the unusual clinical presentation of HCC in young Peruvian individuals, we conducted a comparative analysis of mutations with age of 80 HCCs obtained from patients admitted at INEN, i. e. 41 persons below age 40 (,40) and 39 persons above or equal age 40 ($40). Thirty-one exons covering 17 kb in nine genes considered as mutation hotspots in HCC were analyzed. The purpose of the present study was to determine whether genetic variations exist between younger and older Peruvian HCC patients and to compare this spectrum with data published from elsewhere.
Statistical analyses The age distribution of the patients was analyzed using a Gaussian mixture model for detecting bimodality and calculating bimodality index (BI)  [11, 12]. Pearson's second skewness coefficients were calculated as described  [13]. Comparisons between prevalence of alterations were performed using the Chi-square and Fisher's exact tests. Continuous variables were analyzed with Student's t-test and Mann-Whitney U test. Statistical analyses were performed with an alpha significance level 0. 05, using InStat package (GraphPad Software Inc. ). Class discovery was performed by unsupervised hierarchical clustering, using the DNA-Chip Analyzer (dChip) software version 2010 (HSPH). Mean values are presented with standard deviation (¡SD).
Acknowledgments The authors wish to acknowledge all patients whose participation was essential to the achievement of this study. The authors are grateful to  Macarena Farı  ´as from the  Department of Urologic Surgery of INEN  and  Luis Cano ,  Juan-Pablo Cerapio ,  Dany Cordova ,  Lourdes Huanca ,  Marlene Nun ˜ez , and  Patricia Webb  from the  Department of Pathology of INEN  for their leadership in aggregating the medical records and collecting the biomedical specimens;  Sylviane Bouchier  and  Catherine Gouyette  from the  Institut Pasteur Genomic Platform One  for their technical support;  Nathalie Jolly  from the  Integrated Research Clinic Center of the Institut Pasteur  for her critical discussions; and  David D. Parker Jr. for his suggestions in preparing the manuscript. The authors thank the  Laboratoire Ando-Amazonien de Chimie du Vivant (LMI-LAVI ),  IRD-UPCH , for its logistic support.
This work was funded by the  French National League against Cancer  (team label LNCC) and Odyssey-RE; SB and ED (PI) were supported by the  Third Cancer Plan, ITMO Cancer of the French National Alliance for Life Sciences and Health (Aviesan)  ( ENV201408 ); FD (PI) and ER were supported by the  Young Teams Associated  to  IRD Program (INCAnCER) ; TRR was a recipient of a doctoral fellowship from the  Peruvian FINCyT Science and Technology Program's Scholarships for Doctoral Studies Abroad  ( BECA-1-P-155-13 ). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
The Ag/Ag 1 reference electrode was obtained by introducing a silver wire in the reference compartment containing silver ions (AgNO 3 , 0. 01M) and tetrabutylammonium perchlorate (TBAP, 0. 1 M) in acetonitrile. The measured redox potential were expressed vs ferrocene used herein as internal reference. The triarylamine solutions were prepared in dichloromethane solvent added with 0. 1 M of tetrabutylammonium hexafluorophosphate (Bu 4 NPF 6 ) as a supporting electrolyte (Sigma-Aldrich). The solutions were deoxygenated by argon bubbling prior to each experiment. Cyclic voltammograms (CVs) were performed with VSP potentiostat controlled by EC-Lab 10. 02 software. Both potentiostat and software were purchased from Bio-Logic Instruments-France. 1PA and 2PA measurements. Triarylamine derivatives/toluene solutions were prepared with concentrations of 1310  16  molecules/cm 3 and on order of 10 18 molecules/c-m 3 for linear and nonlinear optical measurements, respectively.
The time-to-amplitude converter was from Tennelec. Pulse deconvolution was performed from the time profile of the exciting pulse recorded under the same conditions by using a Ludox solution. The fluorescence data were analyzed by a nonlinear least-squares global method using the Globals software package developed at the Laboratory for Fluorescence Dynamics at the University of Illinois at Urbana-Champaign (Globals software, Irvine, CA, USA). Computational details. In this paper, quantum chemical calculations were employed to investigate the molecular and electronic structures of triarylamine molecules containing trifluoromethyl and determine their one-photon and two-photon transitions and related electronic structure parameters. For this purpose, quantum chemical calculations using the Kohn-Sham formulation of density functional theory (KS-DFT) were performed.
The equilibrium molecular geometry of the molecules was determined in both gas-phase and solvent environment. The solvation effects on the equilibrium molecular geometry, the electronic structure and the one-photon and two-photon properties of each investigated molecule were taken into account by employing a Polarizable Continuum Model (PCM) and assuming the toluene solvent. The gas-phase geometry optimizations were performed employing the B3LYP/6-311G(d,p) approach  [50] [51] [52]. In the case of the geometry optimization taking into account the solvent environment, the PCM using the integral equation formalism variant (IEF-PCM)  10  was employed in combination with the B3LYP/6-311G(d,p) approach. All the geometry optimizations were performed using the Gaussian 2009 package  53. The IEF-PCM method was combined with the United Atom for Hartree-Fock (UAHF) model to build the solute cavity.
Subsequently, to determine the lowest energy one-and two-photon allowed transitions and related molecular parameters of the investigated molecules, the response function calculations  39, 40  within the DFT framework were performed using the DALTON program  54. In this approach, the excitation energies and transition dipole moments (two-photon probabilities) are analytically computed as, respectively, poles and single residues of the linear (quadratic) response function of the molecular electronic density. Moreover, by computing the double residue of the quadratic response function the excited states dipole moments and the transition dipole moment between excited states were also determined. All the response function calculations were performed employing the CAM-B3LYP/6-311G(d) approach  55  for the investigated molecules in both gas-phase and solvent environment.
In the case of the response function calculations, the PCM as implemented in DALTON program was employed  56. To be consistent, for all molecules the van der Waals surface used in the response function calculations was defined by adopting the set of van der Waals radius and atomic centers determined at the geometry optimization stage using the Gaussian 2009 package. A preliminary assessment of the exchange-correlation functionals revealed that the standard hybrid B3LYP and PBE0 functionals and also the standard long-range corrected CAM-B3LYP functional, fail to well reproduce the experimental UV-vis spectra of the triarylamine molecules containing trifluoromethyl investigated (for a recent exhaustive summary of TD-DFT benchmarks we refer to excellent reviews  [57] [58] [59]. Therefore, in this study the successful strategy of K.
However, another point that can contribute to such differences is that in the present study the values adopted for the CAM-B3LYP functional parameters were determined by performing linear response function calculations in combination with a PCM, while in the work conducted by K. Okuno et al. the values were determined based on the results of gas-phase calculations. Finally, to confirm the donor-acceptor charge transfers involved on the main oneand two-photon transitions of the substitutes, the percentage contribution of the excitations to the transitions, and the KS molecular orbitals involved, were determined. The KS molecular orbitals were determined by DFT calculations using the tuned CAM-B3LYP/6-311G(d) approach in combination with IEF-PCM and using the Gaussian 2009 package  53.
Acknowledgments Financial support from  FAPESP (Fundaça ˜o de Amparo aPesquisa do estado de Sa ˜o Paulo , processo n o :  2011/12399-0  e n o :  2009/11810-8 ),  CNPq  ( Conselho Nacional de Desenvolvimento Cientı ´fico e Tecnologico) ,  Coordenaça ˜o de Aperfeiçoamento de Pessoal de Nı ´vel Superior (CAPES)  and the  Air Force Office of Scientific Research  ( FA9550-12-1-0028 ) are acknowledged. R. Z. is a  Wenner-Gren   Foundations scholar. This work was also supported by a computational Grant from the  Swedish Infrastructure Committee (SNIC)  for the Project ' 'Multiphysics Modeling of Molecular Materials '' ( SNIC 025/12-38 ).
Reversed-Phase High-performance Liquid Chromatography (RP-HPLC) A volume of 50 µL containing 5 mg of lyophilized CN or CN-H was loaded onto a Lichrospher C 18 analytical column (150 × 2 mm, 5-µm particle size, 10-nm porosity; Cluzeau, Sainte-Foy-La-Grande, France) connected to an Alliance HPLC unit 2690 (Waters Corp. , Milford, MA, USA) equipped with a photodiode array detector DAD 996 (Waters). Peptides were then eluted for 90 min by a linear gradient from 5 to 50 % of acetonitrile in water and in the presence of 0. 1 % trifluoroacetic acid. The flow rate was 0. 25 mL min -1 , detection was carried out at 215 nm, and the separation was analysed with the Millennium 32 version 3. 05. 01 software (Waters).
, 2014). Camel b-CN showed high antioxidant activity after hydrolysis with chymotrypsin  (Salami et al. , 2011). The camel b-CN (Swiss-Prot accession number Q9TVD0) includes 8 residues of Phe, a highly antiradicalar aromatic amino acid, whereas bovine b-CN contains 5 Phe residues (Swiss-Prot accession number P02666) and might be one explanation of the potential antioxidant activity of the camel protein. Tsopmo et al. (2011)  have reported that the presence of aromatic residues confers high free radical scavenging activity to synthetic peptides, the most efficient residue being Trp. The antioxidant activity of peptides has been attributed to certain amino acid sequences  (Suetsuna et al. , 2000)  as well as to the presence of peptide bonds present or structural conformation arrangement (Hernandez-L edesma et al.
The median follow-up was estimated according to the « reverse Kaplan-Meier method » and presented with 95% CIs. Survival curves were drawn and the log-rank test was performed to assess differences between groups. Multivariate analyses were carried out using Cox proportional hazards regressions with a stepwise selection procedure to investigate known prognostic factors. Hazards Ratios (HR) with 95% CIs show the risk of experiencing the event (death from any cause) during the follow-up period. All reported P values are two-sided and the significance level was set at 5% (p < 0. 05). Statistical analyses were performed using the STATA 11 software (Stata Corporation, College Station, TX).
Histologic evaluation For each site, a portion of the EMR specimen was fixed in 4 % paraformaldehyde in phosphate-buffered saline. After tissue washing in phosphate-buffered saline, the specimen was dehydrated and embedded in paraffin. Sequential sections of mucosa (5 µm) were obtained and, after staining in hematoxylin and eosin, were analyzed with an Olympus IX50 microscope (Olympus America, Center Valley, Pennsylvania, USA). Pictures were captured with a DP71 digital camera (Olympus) connected to a computer through a frame grabber card (Cell^B software, Olympus). To assess the mucosal morphology, we analyzed mucosal thickness, determined by measuring the distance between the surface epithelium and the underlying muscularis mucosae (only in study 1).
The prevalence of DM in the general population aged above 40 years is estimated at 24%, and 10 million DM patients are estimated to be living now in Iran  [5]. It is recognized that blood glucose levels can temporarily increase as a result of infection with TB, which is a chronic infectious disease  [6]. This interaction, and the rise in blood glucose levels, can result in false positive diagnoses of DM if blood glucose levels are measured at the time of registration of TB patients  [7, 8]. There are limited data to show whether blood glucose levels stay the same, decrease or even increase with TB treatment and whether there are any associations between these changes in blood glucose levels and final TB treatment outcomes. In Iran, we have been assessing blood glucose status by measurement of glycosylated haemoglobin (HbA1c).
Data variables, data sources and data collection Patient data were obtained from a patient TB register into a paper-based proforma. Data variables included age, sex, a new or known diagnosis of DM, smoking status, drug abuse history, duration of symptoms, type of TB, cavitary lesion in chest x-ray, grade of sputum smear at base line, FBG level, HbA1c level, and final TB treatment outcomes. The grade of sputum smear at base line was defined as: 10? 99 bacilli in 100 high power field = 1 + ; 1? 10 bacilli in one high power field = 2 + ; more than 10 bacilli in one high power field = 3 + ; scanty as less than 10 bacilli in 100 high power fields. These data were single entered into SPSS version 11. 5 [SPSS Inc, Chicago, IL, USA]. All records were checked for completeness, reliability and precision.
Data analysis and statistics All demographic and clinical information of TB patients were transported from SPSS to STATA and analyzed using Stata, version 12. 1 (Statacorp. College Station, Texas, USA). Patients with TB were divided into four groups based on the measurements of HbA1c at the two different time points: 1. Normal-Normal (NN): The patients who had HbA1c less than 6. 5% at two time points. They were defined as normal 2. Elevated-Normal (EN): The patients who had HbA1c ≥6. 5% at the baseline and at the third month had <6. 5%. They were defined as uncertain DM status.
Then, to visualize the blood vessels with 2PEM, 100 mL of Evans Blue (10 mg/ mL in PBS, E-2129 Sigma-Aldrich) was administered to the anesthetized mouse C. Z-projection of a typical 2PEM dataset obtained from the mouse ear that was injected with GFP-expressing tumor cells (green). SHG signal of the collagen fibers is shown in blue. Evans Blue stains blood vessels and is depicted in red. Scale bar: 100 mm. See Movie S1. D. Cartoon of the NIRB process representing the imaged volume containing a vessel (red), collagen fibers (blue), and tumor cells (green). Our NIRB-procedure entails drawing a frame at the surface of the skin with a high-powered laser, above and away from the ROI. The imaged volumes presented in this work were in between 60 and 200 mm in depth and ranging from 270 to 440 mm in xy.
Intravital Two-Photon Excitation Microscopy (2PEM) and Near-Infrared Branding (NIRB) The anesthetized mouse was mounted on a custom built holder inspired by Li et al. [29]. The holder keeps the ear flat under the lens of the microscope without interfering with second harmonic generation signal captured by a trans detector. The stage bearing the mouse was mounted on an upright confocal microscope (TCS SP8, Leica Microsystems, operating under Leica Application Suite Advanced Fluorescence (LAS AF) software), in an environmental chamber set to 28 ˚C. 2PEM was performed by a single excitation wavelength at 940 nm (Chameleon Ultra II, Coherent), using a 2560. 95 N. A. water immersion objective. Emission wavelengths of 510 nm and 680 nm were chosen to collect the fluorescent signal of Life-Act (tumor cells) and Evans Blue (blood vessels), respectively, and the signal was collected by hybrid non-descanned photo-detectors (HyD, Leica Microsystems).
The second harmonic generation (SHG, collagen) was imaged at a wavelength of 470 nm, using a photomultiplier detector (PMT, Leica Microsystems). The 2PEM datasets were captured at a scan speed of 400 Hz. The ROI was marked by NIRB  [12, 13] , as described in the text. The frame contour was scanned with a pulsed laser at 800 nm (Coherent Chameleon Ultra II, coherent mean power 3,5W at 800 nm), and at a low scan speed (10 Hz, line average: 2, frame average: 2 and picture dimensions: 102461024 pixels) at the level of the skin surface, above the ROI. The branding was repeated until the square was clearly visible with transmitted light. A. Cartoon of the sectioning approach. Following 2PEM, NIRB and processing as described before, a few thick sections were produced from the sample to verify the orientation of the block and the presence of the NIRB markings ('Approach').