dataesr/scientific-paragraphs-categorization huggingface dataset:
Thermodynamic Experimental Information Vapor pressure of cadmium above solid silver-cadmium alloys was measured by several researchers. Above the α phase, isopiestic method was used by Herasymenko  [38]  in the 873-1173 K temperature range, and by Masson and Sheu  [39]  at 1063 K, electronic spectrophotometer was used by both Scatchard and Boyd  [40]  and Rapperport and Pemsler  [41]  in the 620-875 and 460-633 K temperature ranges respectively. However, Rapperport et al. did not correctly define the alloy composition and hence their data are not usable. A dew point technique was used by Birchenall and al. [42]  in the 793-1153 K temperature range for 3 α phase compositions, and by Filby and Pratt  [37]  in the range of temperature 635-1140 K above the α, β, γ and ε phases. The cadmium activity in the α, β, ζ, γ and ε phases was derived from EMF measurement in the 673-773 K temperature range by Olander  [43].
555 on increasing cadmium concentration from 47 to 81 at. %. These values are very similar, and close to the ideal 1. 63 value corresponding to the close packing of hard spheres. Conversely, the c/a ratio of the η phase (Cd terminal solution) raises from 1. 816 to 1. 886 on increasing cadmium concentration from 97 to 100 at. %, well above the ideal value. As reported in  [6]  for Cd, or in  [54] [55] [56]  for Zn, we consider that the dissimilarity in the interatomic spacings creates an energy difference between the lattice stabilities of the ideal and "non-ideal" hcp cadmium forms. The lattice stability of the hexagonal close-packed cadmium with a "non-ideal" c/a ratio, denoted here hcp_Cd, is taken from the SGTE unary databank  [10]. The lattice stabilities of the metastable "ideal" Cd(hcp_A3) and the metastable Cd(bcc_A2) are estimated at the most suitable values during the optimization process, and then fixed.
Conclusion The thermodynamic assessment of the Ag-Cd-In ternary system based on the exhaustive compilation of literature data and recent experimental investigations  [95]  [7],  [8]  has been carried out. It also takes into account new experimental data related to the liquidus temperatures in cadmium-rich region which are reported in this paper. The liquidus temperatures for ternary compositions have been determined by using the IHDTA protocol. It has been shown in  [8]  that this method, operating closer to equilibrium conditions, considerably reduces the uncertainty in the liquidus determination for this system. The obtained dataset of thermodynamic parameters allows a general good agreement between experimental and calculated results on the binary Ag-In, Ag-Cd and In-Cd subsystems and on the ternary system, at high temperature, in compositions domains where liquid phase is present.
It was placed at 20 °C in a desiccator containing K2CO3 saturated salt during whole time of experiments to ensure constant moisture content. The purity of napin was checked by SDS-PAGE electrophoresis and mass spectrometry as presented in Supplementary data. Two major isoforms of napin were identified ascribed to 2SS3 and 2SS2, respectively. These results were in agreement with those previously described by  Schmidt et al. (2004). Highly methoxylated Pectin (UniPectin QC-100, batch number 47572901) provided by Cargill (France) was used with a degree of methylation of 71 % and a mean molecular weight of 227 kg mol -1. A detailed characterisation is given in Supplementary data. Pectin powder was stored at room temperature during the whole time of experiments. A characterization study performed on individual biopolymer is given in Supplementary data (Figure  S1 ).
II. 5. 2. Optical set-up for droplets observations Biopolymers droplets observations were carried out under continuous flow, directly within the Tygon® tube immersed in an ethylene glycol bath designed with PDMS. The light source was composed of 12 green LED (Radiospares, France) and arranged to obtain a dark field image on the camera. Pictures were taken at a distance of 155 mm from the Tygon tube using an objective with a fixed 1. 5x magnification (OPT-043-216310, Alliance Vision). The objective was connected to a 7x manual zoom (OPT-043-300098, Alliance Vision), a TV-tube (OPT-001 0. 67x, D 35 mm, L 117. 7 mm, Alliance Vision) and a camera (SVS-ECO674MTLGEC, GigE, 2/3'' C'', 1920x2460, Alliance Vision, France) (Figure  1A ). 10 pictures (1 droplet per pictures) were taken. A MatLab procedure was finally used to determine the average grey level.
III. 1. Napin and pectin carry opposite charges in a wide range of pH Electrophoretic mobility was determined as a function of pH to identify conditions where napin and pectin carry opposite charges. Under acidic conditions, napin electrophoretic mobility is positive and decreases to reach 0 at a pH of 9. 5 as reported in Figure  2. This pH value corresponds to the isoelectric point (IEP) of napin in agreement with literature data  (Ericson et al. , 1986; Gehrig, Krzyzaniak, Barciszewski, & Biemann, 1996; Josefsson, Lenman, Ericson, & Rask, 1987; Monsalve & Rodriguez, 1990). For higher pH, electrophoretic mobility is negative. Electrophoretic mobilities of pectin are negative over the entire range of pH and reach a plateau value above pH 6. 0 meaning all carboxylic functions are deprotonated.
The point where napin carried 0 charges is around pH 9. 5 whereas pectin is completely deprotonated above pH 6 as evidenced by the plateau value. Additionally, experimental data obtained for napin are very similar to those calculated using the Uniprot calculator software with napin sequence 2SS3. At pH 4, one napin molecule carries 14 positive charges whereas each pectin molecule carries 160 negative charges. From the knowledge of each biopolymer charge at pH 4 and from phase compositions obtained at thermodynamic equilibrium, Pr/Ps [+]/[-] charge ratio in the dense lower phase was evaluated as a function of initial mixture composition (Figure  7B ). Pr/Ps [+]/[-] charge ratio in the dense lower phase is highly dependent on the initial weight mixing ratio: the higher the initial Pr:Ps weight mixing ratio is, the higher the Pr/Ps [+]/[-] charge ratio in the dense lower phase is.
Acknowledgments The authors acknowledge  Joëlle Davy  and  Patrice Papineau  for their strong technical support for designing the millifluidic device and  Anne-Laure Reguerre  for the image analysis. Marie-Jeanne Crépeau  is thanked for her technical support on the automated Orcinol method,  Véronique Solé-Jamault  for her help with protein purification,  Elisabeth David-Briand  for her technical assistance for interfacial tension measurements,  Thierry Doco ,  Pascale Williams  and  Michael Nigen  for the biochemical and molecular characterization of pectin. This work was carried out with the financial support of the  French Agronomic Research National Institute (INRA)  and the  Region Pays de la Loire.
The 3D structure of integrin α/β heterodimers in a resting state is very similar for both main groups of complexes with or without the α-I domain inserted into the propeller domain, as can be seen for example in existing crystal structures of αXβ2 (PDB ID 4neh;  [12] ) or αIIbβ3 (PDB ID 3fcs;  [13] ). The structure of an activated integrin complex in its open state can be represented by the αIIBβ3 crystal structure (PDB ID 3fcu;  [13] ). Interestingly, up to now, only the α6 subunit has been identified to form a functional heterodimer with β4  [7, 14]. Moreover, all integrins mediate interaction with the actin cytoskeleton; however, α6β4 also interact mainly via plectin with an intermediate filament such as keratin  [15, 16] , which does not compromise its ability to associate with actin filaments and microtubules  [16, 17].
Weak reaction was displayed in protein bands (white arrows) with molecular weights of more than 250 kDa. The band of 48 kDa (grey arrow) was also visible on a negative control blot. Furthermore, we addressed heterodimer formation of the previously identified individual α3, α6 and β1 integrin subunits  [24] , as we were interested in defining integrin heterodimers in separate membrane compartments in the mouse sperm head. We used dual immunofluorescent staining visualized by 3D super resolution microscopy to visualize their localization by using Huygens software to generate a colocalization map based on Pearson's correlation coefficient. The results confirmed the localization of α3 in the plasma membrane covering the acrosomal cap and in the outer acrosomal membrane (Figure  4a ). In order to distinguish between membranes lying in close proximity, we used double immunofluorescent staining with CD46 as a marker of the acrosomal membrane  [25]  (Supplementary Figure  S1 ).
The localization of β1shared the same localization (Figure  4a ), and their mutual interaction as α3β1 heterodimer was confirmed by PLA (Figure  4b ). The share co-localization was confirmed by analysis of SIM data (Figure  4c ) using Huygens software depicting a colocalization map based on Person's coefficient (Figure  4d ). Furthermore, we addressed heterodimer formation of the previously identified individual α3, α6 and β1 integrin subunits  [24] , as we were interested in defining integrin heterodimers in separate membrane compartments in the mouse sperm head. We used dual immunofluorescent staining visualized by 3D super resolution microscopy to visualize their localization by using Huygens software to generate a colocalization map based on Pearson's correlation coefficient. The results confirmed the localization of α3 in the plasma membrane covering the acrosomal cap and in the outer acrosomal membrane (Figure  4a ).
In order to distinguish between membranes lying in close proximity, we used double immunofluorescent staining with CD46 as a marker of the acrosomal membrane  [25]  (Supplementary Figure  S1 ). The localization of β1shared the same localization (Figure  4a ), and their mutual interaction as α3β1 heterodimer was confirmed by PLA (Figure  4b ). The share co-localization was confirmed by analysis of SIM data (Figure  4c ) using Huygens software depicting a colocalization map based on Person's coefficient (Figure  4d ). In intact acrosome mouse sperm heads, the presence of the α6 subunit was shown in both the plasma membrane of acrosomal cap, apical hook and the equatorial segment, in contrast to the localization of β1, which was in the plasma membrane of the acrosomal cap area extending over the apical hook and in the outer acrosomal membrane (Figure  5a ).
The share co-localization was confirmed by analysis of SIM data (Figure  4c ) using Huygens software depicting a colocalization map based on Person's coefficient (Figure  4d ). In intact acrosome mouse sperm heads, the presence of the α6 subunit was shown in both the plasma membrane of acrosomal cap, apical hook and the equatorial segment, in contrast to the localization of β1, which was in the plasma membrane of the acrosomal cap area extending over the apical hook and in the outer acrosomal membrane (Figure  5a ). PLA confirmed the presence of the α6β1 heterodimer specifically in the plasma membrane of the acrosomal cap area and the apical hook (Figure  5b ) and a mutual colocalization of the α6 and β1 subunits was also visibly in the same locations (Figure  5c ), which was confirmed by a colocalization map (Figure  5d , yellow arrows).
A model of probable arrangement of integrin heterodimers in the open state was derived from the results of N-terminal domains docking by a structure superposition of the existing crystal structure of αIIBβ3 in the open state (PDB ID 3fcu;  [13] ), see Figure  6  for a graphical summary. The modeling suggests that complexes of α3β1, α6β1, and α6β4 integrins are, as a consequence of the relative arrangement of their N-terminal domains, found in a conformation with the membrane proximal domains separated  [34] [35] [36] [37]. This leads to the expected cis interaction. On the other hand, the orientation of the α3β4 N-terminal domains would, however, translate to a complex Based on the existing crystal structures combined with the docked homology models, we can further speculate about the functional consequences of the structural differences among α3β1, α6β1, α3β4, and α6β4 complexes.
A model of probable arrangement of integrin heterodimers in the open state was derived from the results of N-terminal domains docking by a structure superposition of the existing crystal structure of αIIBβ3 in the open state (PDB ID 3fcu;  [13] ), see Figure  6  for a graphical summary. The modeling suggests that complexes of α3β1, α6β1, and α6β4 integrins are, as a consequence of the relative arrangement of their N-terminal domains, found in a conformation with the membrane proximal domains separated  [34] [35] [36] [37]. This leads to the expected cis interaction. On the other hand, the orientation of the α3β4 N-terminal domains would, however, translate to a complex with α and β subunits pointing in nearly opposite directions suggesting the trans interaction of the α3β4 integrin heterodimer.
6 ) by a structural superposition of the existing crystal structure of αIIBβ3 in the open state (PDB ID 3fcu;  [13] ). The modelling suggests that while for the α3β1, α6β1 (a), and α6β4 (b) the integrins are involved in a cis interaction adopting the expected conformation with the membrane proximal domains separated  [34] [35] [36] [37] , the orientation of the α3β4 N-terminal domains would lead to a complex with α and β subunits pointing in nearly opposite directions (b) supporting the possible trans interaction (see Supplementary Figure  S2  for more details). We also predict that during the acrosome reaction, when membrane fluidity increases, the α3 and α6 could interchange over the β1 subunit in a more flexible manner to modulate cytoskeletal function during membrane fusion (Figures  7, 8a ).
Moreover, active and inactive forms are known to occupy different clusters when only converting the inactive form into the active form, resulting in signaling activity. The membranes that become surface exposed after the acrosome exocytosis are also rich in integrins. However, to date, it seems that α3β1 and α6β4 integrins pairs are expressed on these sperm membranes which will be in first contact with the oolema (Figure  7 ). With knowledge that, among many others, α3 is also expressed on the egg surface  [38] , it may be of relevance that   6 ) by a structural superposition of the existing crystal structure of αIIBβ3 in the open state (PDB ID 3fcu;  [13] ). The modelling suggests that while for the α3β1, α6β1 (a), and α6β4 (b) the integrins are involved in a cis interaction adopting the expected conformation with the membrane proximal domains separated  [34] [35] [36] [37] , the orientation of the α3β4 N-terminal domains would lead to a complex with α and β subunits pointing in nearly opposite directions (b) supporting the possible trans interaction (see Supplementary Figure  S2  for more details).
In case of dual staining, both primary or secondary antibodies were applied together. After the application of the primary and secondary antibodies, sperm were incubated for 5 min with DAPI (0. 85 µg/mL, Thermo Scientific, Waltham, MA, USA) and washed 3× in PBS. At the end, sperm were washed 1× in distilled water and air-dried. Dry samples were covered with 90% glycerol with 5% anti-fade N-propyl gallate (Sigma-Aldrich). Multi-color SIM super-resolution images were obtained by Zeiss Elyra PS. 1 inverted microscope at Laboratory of confocal and fluorescent microscopy of Faculty of Science (Charles University, Prague, Czech Republic). STED images were obtained by Leica TCS SP8 STED 3X microscope (Microscopy centre-LM and EM, IMG AS, Prague, Czech Republic). Confocal data for colocalization analysis of α6 and β4 subunit was collected with high-end confocal microscope Carl Zeiss LSM 880 NLO (Imaging Methods Core Facility at BIOCEV, Vestec, Czech Republic).
Molecular Modelling of Integrin Heterodimers The all atom models of extracellular parts of integrins α3, α6, β1, and β4 were prepared using a local copy of the I-TASSER  [26]  service, based on the annotation of protein sequences as defined by uniprot accession codes Q62470, Q61739, P09055, and P09055. The flexible side chain protein-protein docking of N-terminal domains was performed using a local copy of the ClusPro server  [27, 28]. The GBSA implicit solvation molecular dynamics simulations were prepared using the OpenMM Zephyr graphical interface  [44]  with the Amber96 force field, 2 fs time step, temperature 295 K, and water collisional interval of 0. 01099 ps. The calculations were performed using the GPU accelerated version of GROMACS program  [45]  collecting geometry every 10 ps.
Data Analysis Huygens Professional version 18. 10 (Scientific Volume Imaging, Hilversum, The Netherlands, Available online: http://svi. nl) was used for visualization mutual position of individual proteins based on surface rendering of the colocalization analysis. A colocalization analyzer computed a Pearson's correlation coefficient and created a 3D colocalization map. The Pearson's correlation coefficient expresses the rate of correlation of colocalizing channels in a dual-color image, giving a value os between minus 1 and plus 1. In this case, 1 means an absolutely positive correlation, 0 means no correlation and -1 means a perfect anti-correlation. The value between 0. 5 and 1 is interpreted as colocalization. The Costes method was used for a background estimation. Ten individual sperm confocal images were analyzed by Fiji software using customized JACoP (Just Another Colocalization Plugin) plugin to calculate Pearson's coefficients  [47] , and the resulting values were statistically evaluated to determine the arithmetic mean and standard deviation.
Acknowledgments: This work was supported by  BIOCEV  project ( CZ. 1. 05/1. 1. 00/02. 0109 )from the  ERDF , by the  Grant Agency of the Czech Republic  No. GA-18-11275S and by the  Institutional support of the Institute of Biotechnology RVO :  86652036. We acknowledge the  Imaging Methods Core Facility at BIOCEV , institution supported by the  Czech-BioImaging large RI projects  ( LM2015062  and  CZ. 02. 1. 01/0. 0/0. 0/16_013/0001775 ,funded by  Ministry of Education, Youth and of Sport Czech Republic)  and  Operational Program Prague Competitiveness  ( CZ. 2. 16/3. 1. 00/21515 )funded by  European Regional Development Fund  for their support with obtaining imaging data presented in this paper. Access to computing and storage facilities owned by parties and projects contributing to the  National Grid Infrastructure MetaCentrum  provided under the programme " Projects of Large Research, Development and Innovations Infrastructures" (Czech Education and Scientific NETwork-CESNET LM2015042 ), is greatly appreciated.
This initiative established a temperature reference baseline for permafrost and led to an increase in the number of accessible boreholes used for temperature monitoring. To analyze the thermal change of permafrost we assembled a global permafrost-temperature data set that includes time series of data attributed to the IPY reference boreholes. We compiled a time series for the decade from 2007 to 2016 that comprises mean annual ground temperatures T, determined from temperatures measured in boreholes within the continuous and discontinuous permafrost zones in the Arctic (including the Subarctic), Antarctica and at high elevations outside the polar regions. The measurements were made at, or as close as possible to the depth of zero annual amplitude Z * , where seasonal changes in ground temperature are negligible (≤0.
Methods Field observations of permafrost temperatures. Boreholes were established and temperatures were recorded during annually repeated fieldwork campaigns in polar high-elevation areas. Temperature was measured either by lowering a calibrated thermistor into a borehole, or recorded using permanently installed multisensor cables  43. Measurements were recorded either manually with a portable temperature system or by automated continuous data logging. At some borehole sites, permafrost thawed at the measurement depth during the period of observations. The criterion to include non-permafrost sites in the global change calculation was that ground temperatures near the depth of the Z * were below 0 °C until the end of the IPY reference period in 2009. Compiling permafrost temperature data. Permafrost temperature data are assembled in the Global Terrestrial Network for Permafrost (GTN-P) Database  16.
Because Z * could not be determined in all boreholes the minimum depth was set to 10 m. However, five boreholes with depths between 6. 7 m and 10 m were included (GTN-P ID's  16  : 137, 860, 861, 877, and 1192), because their depths were equal to Z * , and seasonal fluctuations were less than the instrument precision and accuracy. Boreholes that fulfilled the quality criteria but were not included in this analysis due to depth constraints, represented 22. 6% of the original data set. 8. 6% were excluded from the Arctic continuous data set; 23. 4% from the Arctic discontinuous data set; 30. 0% from the mountain data set; and 57. 1% from the Antarctic data set. Statistically indifferent temperature trends of the remaining shallow (≤12 m) and deeper (>12 m, max. 40 m) boreholes in the utilized data set confirm that the observed depths near Z * (Fig.
6b ) provide a representative sample tracking climate variability coherently. We applied different methods to extract information on permafrost temperature changes in single years, in single boreholes and for decadal changes in the permafrost regions, described as follows: We define a set i = {2007,. ,2016} to identify the years. To identify the boreholes b we use the GTN-P Database ID. Continuous (full-year) records started at a large number of borehole sites in 2008, the second year of the 4 th International Polar Year (IPY). To base the reference period for the annual departure calculation on the largest possible number of boreholes we exclude 2007 and estimate the annual differences in T in year y 2 i and borehole b as Δ T y;b ¼ T y;b À 1=2 T 2008;b þ T 2009;b ð1Þ The last term on the right-hand side of Eq.
The requirement to perform linear regression on b was that i included at least one value y in the IPY period (2007, 2008, or 2009), one value in the modern reference period (2015 or 2016) and a minimum of five values in total. We calculated the rate of temperature change in each borehole as the slope of the linear regression c b using the linear model function (lm) in the R environment. To generate decadal change values, we extrapolated 37. 7% of the borehole data in the Arctic continuous zone, 47. 3% in the Arctic discontinuous zone, 29. 3% in the mountain zone and 100% in Antarctica for 1-3 years. The consistency of temperature time series in boreholes depends on sustained data collection at remote sites. At some boreholes, instrumentation was destroyed, damaged or malfunctioned leading to interruptions in data collection  45.
To avoid broken data runs affecting the annual means, measurements at frequencies greater than monthly (e. g. daily or hourly), were aggregated to monthly means before calculating annual means. Mean annual values were based on at least monthly primary data. Data points based on fewer than one measurement every month were allowed only if the sensor depth was equal to or below the depth of zero annual amplitude. Annual means were calculated from original measurements as calendaryear means in the GTN-P Database. Meteorological years in permafrost areas depend on the onset and termination of the freezing and thaw periods, and in previous studies varied spatially. We therefore indicated the starting month of the period in the data set. Mean values contain only the available valid T data in each year, and thus the number of borehole temperatures included in change-rate calculations varies between years.