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The recent success of Large Language Models (LLM) in a wide range of Natural Language Processing applications opens the path towards novel Question Answering Systems over Knowledge Graphs leveraging LLMs. However, one of the main obstacles preventing their implementation is the scarcity of training data for the task of translating questions into corresponding SPARQL queries, particularly in the case of domain-specific KGs. To overcome this challenge, in this study, we evaluate several strategies for fine-tuning the OpenLlama LLM for question answering over life science knowledge graphs. In particular, we propose an end-to-end data augmentation approach for extending a set of existing queries over a given knowledge graph towards a larger dataset of semantically enriched question-to-SPARQL query pairs, enabling fine-tuning even for datasets where these pairs are scarce. In this context, we also investigate the role of semantic "clues" in the queries, such as meaningful variable names and inline comments. Finally, we evaluate our approach over the real-world Bgee gene expression knowledge graph and we show that semantic clues can improve model performance by up to 33% compared to a baseline with random variable names and no comments included., Comment: To appear in Proceedings of SWAT4HCLS 2024: Semantic Web Tools and Applications for Healthcare and Life Sciences

We introduce the RIKEN Microstructural Imaging Metadatabase, a semantic web-based imaging database in which image metadata are described using the Resource Description Framework (RDF) and detailed biological properties observed in the images can be represented as Linked Open Data. The metadata are used to develop a large-scale imaging viewer that provides a straightforward graphical user interface to visualise a large microstructural tiling image at the gigabyte level. We applied the database to accumulate comprehensive microstructural imaging data produced by automated scanning electron microscopy. As a result, we have successfully managed vast numbers of images and their metadata, including the interpretation of morphological phenotypes occurring in sub-cellular components and biosamples captured in the images. We also discuss advanced utilisation of morphological imaging data that can be promoted by this database.

Imaging data is one of the most important fundamentals in the current life sciences. We aimed to construct an ontology to describe imaging metadata as a data schema of the integrated database for optical and electron microscopy images combined with various bio-entities. To realise this, we applied Resource Description Framework (RDF) to an Open Microscopy Environment (OME) data model, which is the de facto standard to describe optical microscopy images and experimental data. We translated the XML-based OME metadata into the base concept of RDF schema as a trial of developing microscopy ontology. In this ontology, we propose 18 upper-level concepts including missing concepts in OME such as electron microscopy, phenotype data, biosample, and imaging conditions.

In April 2020, the QUality Assessment and REProducibility for Instruments and Images in Light Microscopy (QUAREP-LiMi) initiative was formed. This initiative comprises imaging scientists from academia and industry who share a common interest in achieving a better understanding of the performance and limitations of microscopes and improved quality control (QC) in light microscopy. The ultimate goal of the QUAREP-LiMi initiative is to establish a set of common QC standards, guidelines, metadata models, and tools, including detailed protocols, with the ultimate aim of improving reproducible advances in scientific research. This White Paper 1) summarizes the major obstacles identified in the field that motivated the launch of the QUAREP-LiMi initiative; 2) identifies the urgent need to address these obstacles in a grassroots manner, through a community of stakeholders including, researchers, imaging scientists, bioimage analysts, bioimage informatics developers, corporate partners, funding agencies, standards organizations, scientific publishers, and observers of such; 3) outlines the current actions of the QUAREP-LiMi initiative, and 4) proposes future steps that can be taken to improve the dissemination and acceptance of the proposed guidelines to manage QC. To summarize, the principal goal of the QUAREP-LiMi initiative is to improve the overall quality and reproducibility of light microscope image data by introducing broadly accepted standard practices and accurately captured image data metrics., Comment: 17 pages, 3 figures, shortened abstract, Co-Lead Authors: Glyn Nelson and Ulrike Boehm, Corresponding author: Roland Nitschke

To investigate the origin of the enhanced $T_c$ ($\approx$ 110 K) of the trilayer cuprate superconductor Bi$_{2}$Sr$_{2}$Ca$_{2}$Cu$_{3}$O$_{10+\delta}$ (Bi-2223), we have performed systematic magnetoresistance (MR) measurements on this superconductor, as well as on the bilayer superconductor, Bi$_{2}$Sr$_{2}$CaCu$_{2}$O$_{8+\delta}$ (Bi-2212). The in-plane coherence length, $\xi_{ab}$, and the specific-heat jump, ${\Delta}C$, have been estimated using the theory of renormalized superconductive fluctuations, and the doping dependence of these parameters has been qualitatively explained using the Fermi arc approach. A detailed comparison of the superconducting parameters with $T_c$ for these compounds suggests that an additional superconducting condensation energy exists, due to an increase in the number of stacking CuO$_{2}$ planes in a unit cell., Comment: 17 pages, 5 figures, to appear in JPSJ

We have measured the thermal conductivity along different directions of the S = 1/2 one-dimensional (1D) spin system Sr2V3O9 in magnetic fields up to 14 T. It has been found that the thermal conductivity along the [10-1] direction, \k{appa}[10-1], is large and markedly suppressed by the application of magnetic field, indicating that there is a large contribution of spinons to \k{appa}[10-1] and that the spin chains run along the [10-1] direction. The maximum value of the thermal conductivity due to spinons is ~14 W/Km along the [10-1] direction, supporting the empirical law that the magnitude of the thermal conductivity due to spinons is roughly proportional to the antiferromagnetic interaction between the nearest neighboring spins., Comment: 22 pages, 6 figures, 1 table

To investigate the relationship between the pseudogap and superconductivity, we measured both the in-plane ($\rho_{ab}$) and out-of-plane ($\rho_c$) resistivity for oxygen-controlled Bi$_{2}$Sr$_{2}$CaCu$_{2}$O$_{8+\delta}$ single crystals subject to magnetic fields (parallel to the $c$ axis) of up to 17.5 T. The onset temperature for the superconductive fluctuation, $T_{scf}$, is determined by the large positive in-plane magnetoresistance (MR) and negative out-of-plane MR observed near $T_c$, whereas the pseudogap opening temperature $T^*$ is determined by the semiconductive upturn of the zero-field $\rho_c$. $T_{scf}$ was found to scale roughly as $T_c$, with a decreasing temperature interval between them upon doping. On the other hand, $T^*$ starts out much higher than $T_{scf}$ but decreases monotonically upon doping; finally, at a heavily overdoped state, it is not observed above $T_{scf}$. These results imply that the pseudogap is not a simple precursor of superconductivity, but that further study is needed to determine whether or not $T^*$ exists below $T_{scf}$ in the heavily overdoped state., Comment: 17 pages, 7 figures, to appear in JPSJ

The ground state of the quantum spin system kappa-(BEDT-TTF)2Cu2(CN)3 in which antiferromagnetically-interacting S=1/2 spins are located on a nearly equilateral triangular lattice attracts considerable interest both from experimental and theoretical aspects, because a simple antiferromagnetic order may be inhibited because of the geometrical frustration and hence an exotic ground state is expected. Furthermore, recent two reports on the ground state of this system have made it further intriguing by showing completely controversial results; one indicates the gapless state and the other gapped. By utilizing microscopic probe of muSR, we have investigated its spin dynamics below 0.1 K, unveiling its microscopically phase separated ground state at zero field.

We have demonstrated the effect of pressure on the steplike metamagnetic transition and its associated magnetostriction in (Eu$_{1-x}$Gd$_{x}$)$_{0.6}$Sr$_{0.4}$MnO$_{3}$ ($x=0$ and 0.1). The critical field initiating the field induced ferromagnetic transition in both samples is lowered by the applied pressure. The further application of external pressure up to 1.2 GPa on the $x=0$ parent sample causes a spontaneous ferromagnetic transition with a second-oder like character, leading to collapses of the steplike transition and its concomitant lattice striction. These findings indicate a crucial role of the low-temperature phase separated state characterized by a suppressed magnetization upon decreasing temperature., Comment: 8 pages, 6 figures. arXiv admin note: text overlap with arXiv:1006.1459

In order to clarify the origin of the enhancement of the thermal conductivity in the Bose-Einstein Condensed (BEC) state of field-induced triplons, we have measured the thermal conductivity along the [101] direction parallel to spin-chains, $kappa_{\|[101]}$, and perpendicular to spin-chains, $kappa_{\perp[101]}$, of the S=1/2 bond-alternating spin-chain system Pb2V3O9 in magnetic fields up to 14 T. With increasing field at 3 K, it has been found that both $kappa_{\|[101]}$ and $kappa_{\perp[101]}$ are suppressed in the gapped normal state in low fields. In the BEC state of field-induced triplons in high fields, on the other hand, $kappa_{\|[101]}$ is enhanced with increasing field, while $kappa_{\perp[101]}$ is suppressed. That is, the thermal conductivity along the direction, where the magnetic interaction is strong, is markedly enhanced in the BEC state. Accordingly, our results suggest that the enhancement of $kappa_{\|[101]}$ in the BEC state is caused by the enhancement of the thermal conductivity due to triplons on the basis of the two-fluid model, as in the case of the superfluid state of liquid 4He., Comment: 5 pages, 3 figures

We have demonstrated the effect of pressure on magnetization jump and its associated magnetostriction in Eu$_{0.58}$Sr$_{0.42}$MnO$_{3}$. The critical field lowered by the applied pressure is explained by a suppression of the metastable blocked state, which is inherent to the phase separated manganite system exhibiting the magnetic avalanche. To reduce a factor of the bad thermal coupling in the bulk sample, and to further examine the nature of the magnetization jump, we have performed the influence of pressure on the isothermal magnetization of the powder sample. There is no discrepancy in the critical field between the bulk and powder samples although the $MH$ curve of the latter is not saturated at high fields. These findings indicate a crucial role of the frozen phase separated state in the abrupt transition., Comment: 6 pages,5 figures

We have measured and analyzed the dielectric constant of the dimer Mott insulator $\kappa-$(BEDT-TTF)$_2$Cu$_2$(CN)$_3$, which is known as a playground for a spin-liquid state. Most unexpectedly, this particular organic salt has nontrivial charge degrees of freedom, being characterized by a dipole-glass-like dielectric relaxation below around 60 K. This is ascribed to the charge disproportionation within the dimer due to the intersite Coulomb repulsion. In this respect, the dipole observed here is purely quantum mechanical, and thereby exhibits unexpected responses., Comment: 5 pages, 5 figures

The characteristic pseudogap temperature T* in Bi2Sr2CaCu2O8 system has been systematically evaluated as a function of doping, especially focusing on its overdoped region, by measuring the out-of-plane resistivity under the magnetic fields. Overdoped samples have been prepared by annealing TSFZ-grown Bi2Sr2CaCu2O8 single crystals under the high oxygen pressures (990 kgf/cm2). At a zero field, the out-of-plane resistivity showed a metallic behavior down to Tc (= 62 K), while under the magnetic fields of over 3 T,it showed typical upturn behavior from around 65 K upon decreasing temperature. This result suggests that the pseudogap and superconductivity are different phenomena., Comment: 2 pages, 2 figures. Final version accepted for the Proceedings of the M2S-IX Conference (Tokyo, September 2009)

We have fabricated a metallic structure in an organic Mott insulator $\kappa$-(BEDT-TTF)$_2$Cu[N(CN)$_2$]Cl. The periodic metallic domains of approximately 90$\times$90 $\mu$m$^2$ obtained by X-ray irradiation through a molybdenum mesh mask are visualized by scanning microregion infrared reflectance spectroscopy technique. No deterioration by irradiation is found in a range of nanometer to micrometer scales. We demonstrate that the present processing method is applicable for the fabrication of molecular electronic devices., Comment: 3 pages, submitted to APEX

We have measured the thermal conductivity of the one-dimensional (1D) S=1/2 Heisenberg antiferromagnetic spin system of Sr2Cu1-xPdxO3 single crystals including nonmagnetic impurities of Pd2+. It has been found that the mean free path of spinons along the 1D spin chain at low temperatures is very close to the average length of finite spin chains between spin defects estimated from the magnetic susceptibility measurements. This proves that the thermal conduction due to spinons at low temperatures in Sr2CuO3 is ballistic as theoretically expected [Zotos et al.: Phys. Rev. Lett. 55 (1997) 11029].

We report an impurity effect in the organic superconductor $\kappa$-(ET)$_2$Cu(NCS)$_2$ by substitution of the ET molecule with an analogue, bis(methyleneditio)tetrathiafulvalene (MT). The superconducting transition temperature decreases with increasing substitution. The in-plane magnetic penetration depth is enhanced with substitution, which is quantitatively attributed to the decrease in the in-plane mean free path. The enhancement of the penetration depth can also explain the reduction of the effective pinning in terms of the condensation energy., Comment: 4 pages, submitted to J. Phys. Soc. Jpn

High-field magnetic torque measurements were carried out in the spin gap system (CH$_3$)$_2$CHNH$_3$CuCl$_3$. It was observed that the magnitude of the magnetic torque $\tau$ is almost zero until the critical field and then increases rapidly, which indicates the existence of the magnetic quantum phase transition from the spin-gap phase to the field-induced magnetic ordered phase. From the temperature dependence of the magnetic torque $\tau$, the cusp-like minimum indicative of the Bose-Einstein condensation (BEC) of magnons was observed for $H \perp$ C-plane, while the kink-anomaly was observed for $H \perp$ A-plane at the field-induced transition temperature. It was found that this different behavior between $H \perp$ A-plane and $H \perp$ C-plane can be interpreted as the breaking of the magnon BEC picture due to the rotational symmetry breaking. The additional anomaly was also observed in the field-induced magnetic ordered phase at the intermediate angle of the applied magnetic field in the A-plane and discussed in terms of the spin-flop transition, the spin-reorientation transition and the spin-lattice correlations. In order to investigate the spin-lattice correlations in (CH$_3$)$_2$CHNH$_3$CuCl$_3$, we performed the magnetostriction measurements and observed that the magnetostriction appears by vanishing of the spin gap., Comment: It was found that the results presented in the old version "v1" include some artifacts due to the experimental problem so that the old version is withdrawn. We carried out the same measurements again and present the obtained results as new version "v2", which will appear in J. Phys. Soc. Jpn. vol.76 (2007) No. 8

We report the in-plane resistivity and magnetic susceptibility of the layered cobalt oxide Na$_{0.35}$CoO$_{2}{\cdot}1.3$H$_{2}$O single crystal. The temperature dependence of the resistivity shows metallic behavior from room temperature to the superconducting transition temperature $T_{c}$ of 4.5 K. Sharp resistive transition, zero resistivity and almost perfect superconducting volume fraction below $T_{c}$ indicate the good quality and the bulk superconductivity of the single crystal. The upper critical field $H_{c2}$ and the coherence length $\xi$ are obtained from the resistive transitions in magnetic field parallel to the c-axis and the $ab$-plane. The anisotropy of $\xi$, $\xi_{ab} / \xi_{c} =$ 12 nm/1.3 nm $\simeq$ 9.2, suggests that this material is considered to be an anisotropic three dimensional superconductor. In the field parallel to the $ab$-plane, $H_{c2}$ seems to be suppressed to the value of Pauli paramagnetic limit. It may indicate the spin singlet superconductivity in the cobalt oxide., Comment: 4 pages, 4 figures

We investigate the superconductivity in the deuterated BEDT-TTF molecular substitution system $\kappa$-[(h8-BEDT-TTF)$_{1-x}$(d8-BEDT-TTF)$_x$]$_2$Cu[N(CN)$_2$]Br, where h8 and d8 denote fully hydrogenated and deuterated molecules, respectively. Systematic and wide range ($x$ = 0 -- 1) substitution can control chemical pressure finely near the Mott boundary, which results in the modification of the superconductivity. After cooling slowly, the increase of $T_{\textrm{c}}$ observed up to $x \sim$ 0.1 is evidently caused by the chemical pressure effect. Neither reduction of $T_{\textrm{c}}$ nor suppression of superconducting volume fraction is found below $x \sim$ 0.5. This demonstrates that the effect of disorder by substitution is negligible in the present system. With further increase of $x$, both $T_{\textrm{c}}$ and superconducting volume fraction start to decrease toward the values in $x$ = 1., Comment: J. Phys. Soc. Jpn

The electromagnetic response to microwaves in the mixed state of YBa2Cu3Oy(YBCO) was measured in order to investigate the electronic state inside and outside the vortex core. The magnetic-field dependence of the complex surface impedance at low temperatures was in good agreement with a general vortex dynamics description assuming that the field-independent viscous damping force and the linear restoring force were acting on the vortices. In other words, both real and imaginary parts of the complex resistivity, \rho_1, and \rho_2, were linear in B. This is explained by theories for d-wave superconductors. Using analysis based on the Coffey-Clem description of the complex penetration depth, we estimated that the vortex viscosity \eta at 10 K was (4 \sim 5) \times 10^{-7} Ns/m^2. This value corresponds to \omega_0 \tau \sim 0.3 - 0.5, where \omega_0 and \tau are the minimal gap frequency and the quasiparticle lifetime in the vortex core, respectively. These results suggest that the vortex core in YBCO is in the moderately clean regime. Investigation of the moderately clean vortex core in high-temperature superconductors is significant because physically new effects may be expected due to d-wave characteristics and to the quantum nature of cuprate superconductors. The behavior of Z_s as a function of B across the first order transition (FOT) of the vortex lattice was also investigated. Unlike Bi2Sr2CaCu2Oy (BSCCO), no distinct anomaly was observed around the FOT in YBCO. Our results suggest that the rapid increase of X_s due to the change of superfluid density at the FOT would be observed only in highly anisotropic two-dimensional vortex systems like BSCCO. We discuss these results in terms of the difference of the interlayer coupling and the energy scale between the two materials., Comment: 10 pages, 6 figures, to be published in Phys. Rev. B, one reference added