SciMMIR:Benchmarking Scientific Multi-modal Information Retrieval

Multi-modal information retrieval (MMIR) is a rapidly evolving field, where significant progress, particularly in image-text pairing, has been made through advanced representation learning and cross-modality alignment research. However, current benchmarks for evaluating MMIR performance in image-text pairing within the scientific domain show a notable gap, where chart and table images described in scholarly language usually do not play a significant role. To bridge this gap, we develop a specialised scientific MMIR (SciMMIR) benchmark by leveraging open-access paper collections to extract data relevant to the scientific domain. This benchmark comprises 530K meticulously curated image-text pairs, extracted from figures and tables with detailed captions in scientific documents. We further annotate the image-text pairs with two-level subset-subcategory hierarchy annotations to facilitate a more comprehensive evaluation of the baselines. We conducted zero-shot and fine-tuning evaluations on prominent multi-modal image-captioning and visual language models, such as CLIP and BLIP. Our analysis offers critical insights for MMIR in the scientific domain, including the impact of pre-training and fine-tuning settings and the influence of the visual and textual encoders. All our data and checkpoints are publicly available at https://github.com/Wusiwei0410/SciMMIR

Magnetite NPs@C with highly-efficient peroxidase-like catalytic activity as an improved biosensing strategy for selective glucose detection

This work reports the novel application of carbon-coated magnetite nanoparticles (mNPs@C) as catalytic nanomaterial included in a composite electrode material (mNPs@C/CPE) taking advantages of their intrinsic peroxidase-like activity. The nanostructured electrochemical transducer reveals an improved enhancement of the charge transfer for redox processes involving hydrogen peroxide. Likewise, mNPs@C/CPE demonstrated to be highly selective even at elevated concentrations of ascorbic acid and uric acid, the usual interferents of blood glucose analysis. Upon these remarkable results, the composite matrix was further modified by the addition of glucose oxidase as biocatalyst in order to obtain a biosensing strategy (GOx/mNPs@C/CPE) with enhanced properties for the electrochemical detection of glucose. GOx/mNPs@C/CPE exhibit a linear range up to 7.5 x 10-3 mol.L-1 glucose, comprising the entirely physiological range and incipient pathological values. The average sensitivity obtained at –0.100 V was (1.62 ± 0.05)x 105 nA.L.mol-1 (R2 = 0.9992), the detection limit was 2.0 x 10-6 M while the quantification limit was 6.1 x 10-6 mol.L-1. The nanostructured biosensor demonstrated to have an excellent performance for glucose detection in human blood serum even for pathological values.submittedVersionFil: Arana, Mercedes. Universidad Nacional de Córdoba. Facultad de Matemática, Astronomía y Física; Argentina.Fil: Arana, Mercedes. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Física Enrique Gaviola; Argentina.Fil: Tettamanti, Cecilia Soledad. Universidad Nacional de Córdoba. Facultad de Ciencias Químicas. Departamento de Fisicoquímica; Argentina.Fil: Tettamanti, Cecilia Soledad. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Fisicoquímica de Córdoba; Argentina.Fil: Bercoff, Paula Gabriela. Universidad Nacional de Córdoba. Facultad de Matemática, Astronomía y Física; Argentina.Fil: Bercoff, Paula Gabriela. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Física Enrique Gaviola; Argentina.Fil: Rodríguez, Marcela Cecilia. Universidad Nacional de Córdoba. Facultad de Ciencias Químicas. Departamento de Fisicoquímica; Argentina.Fil: Rodríguez, Marcela Cecilia. Consejo Nacional de Investigaciones Científicas y Técnica. Instituto de Investigaciones en Fisicoquímica de Córdoba; Argentina.Otras Ciencias Física

Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data

The impact of TCR-CD3 and TCR-pMHC-CD8 interaction on T cell activation

T cells play important roles in adaptive immunity through mediating clearance of bacteria, virus, and cancer cells. T cell receptor (TCR) recognizes antigen presented on the surface of antigen presenting cells (APC) in the form of peptide major histocompatibility complex (pMHC). TCR does not contain signaling capability by itself. Instead, intracellular signaling is initiated from the signaling motif found on the cytoplasmic tails of neighboring CD3 subunits. Therefore, understanding how TCR and its neighboring CD3 subunits function as a unit is important for deciphering T cell activation and designing therapeutics aimed at shaping T-cell responses. In this thesis, two-dimensional kinetics of TCR interaction with CD3 on the extracellular domain was characterized in the present and absence of force, and the impact of mutations affecting TCR-CD3 interaction on TCR antigen recognition was investigated. Based on these findings, TCR-CD3 interaction in the extracellular domain was identified to play a unique role of relaying force from the pMHC recognition end to the intracellar signaling end of the TCR complex. In the second part, the scope was extended to coreceptor CD8 and the role of force in formation of TCR-pMHC-CD8 trimolecular interaction was investigated in the context of thymocyte selection. The results indicated that force provides a unique readout in functional outcome of thymocytes through differentiating positive selecting ligands from negative selecting ligands. Furthermore, the Lck-dependency in CD8 contribution to the trimolecular interaction was identified, which revealed an inside-out arm of TCR signaling to complement and influence the well-known outside-in path mediated by TCR recognition of pMHC.Ph.D

Characterising the immune response following nasal colonisation of Staphylococcus aureus

© 2019 Chenghao GeStaphylococcus aureus (S. aureus) is an opportunistic pathogen found in the nasal passage of 20%~30% of humans. Persistent nasal carriage of S. aureus is a significant risk factor for various diseases, including secondary bacterial pneumonia. To date, there is no vaccine available against S. aureus and the emergence of multidrug resistant strains limit the use of antibiotics as a treatment option. Little research has been undertaken to define the environmental, physiological and immunological changes that cause S. aureus to shift from the upper to the lower respiratory tract and convert from a commensal organism to pathogenic threat. In this project, we have established a nasal colonisation model of S. aureus in C57BL/6 mice and characterised the role of the innate and adaptive immune response in preventing the dissemination of S. aureus from the upper to the lower airways. Using this model, we have found that while both innate and adaptive immune responses are involved in the clearance of S. aureus from the nasal passage, only neutrophils play a critical role in keeping S. aureus confined to the nose and preventing spread into other organs. While the adaptive immune system does not play a role in preventing the spread of nasal S. aureus, it does play an important role bacterial clearance from this site. Moreover, immunisation with heat-killed S. aureus represents an effective approach to limit mice from being nasally colonised with S. aureus. Collectively our research demonstrates that both arms of the immune system can be harnessed to limit the colonisation and dissemination of S. aureus infection

Analysis of post-marketing requirements for oncology drug conditional approvals in the United States and China

Background: Conditional approvals, also known as accelerated approvals, have been introduced by many pharmaceutical regulators around the world, allowing innovative drugs to enter the market earlier on the basis of limited evidence. This research aims to systematically analyze and compare the post-marketing requirements for conditional approvals of oncology drugs in China and the United States. By collecting and categorizing different types of post-marketing requirements, this study seeks to elucidate how these requirements are proposed and discern the underlying logic and patterns. Methods: This study delved into oncology drug approvals, encompassing FDA accelerated approvals (up to December 31, 2022) and NMPA conditional approvals (from 2017 to December 31, 2022). Leveraging review documents from FDA and NMPA, comprehensive data on product characteristics, all post-marketing commitments and requirements, and especially those related to confirmatory requirements were extracted. The analysis incorporated descriptive statistics, visualizations such as Upset plots, and thorough examination of confirmatory requirement timeframes. Findings: This study examined 168 FDA accelerated approvals and 41 NMPA conditional approvals for oncology indications. Post-marketing requirements displayed diversity: FDA emphasized confirmatory studies, clinical pharmacology studies, and more, while NMPA predominantly focused on confirmatory studies. Confirmatory requirement timeframes indicated higher FDA-required completion times for new confirmatory trials compared to continued completion of original pivotal trials. In contrast, NMPA's requirement patterns were comparatively singular, with relatively fixed timeframes. FDA's evolving trend showed decreasing timeframes over time, suggesting an increasing demand for timely confirmatory data. Interpretation: Conditional approvals offer a unique approach to bring potentially life-saving drugs to the market faster, despite limited supporting evidence. Our analysis of oncology drug conditional approvals in the U.S. and China reveals diverse post-marketing requirement patterns. This study provides valuable insights for regulatory decision-making in a dynamic pharmaceutical landscape. Balancing the risks and rewards of conditional approvals is crucial in ensuring both patient safety and timely access to innovative treatments

Effective femtosecond laser shock peening on a Mg–3Gd alloy at low pulse energy 430 µJ of 1 kHz

In this paper, microstructure evolution and hardness of Mg-3Gd alloy treated by femtosecond (fs) laser shock peening (LSP) with direct and confined ablation modes were investigated in detail. Under a relatively low pulse energy of 430 µJ with a repetition of 1 kHz, the surface hardness of sample has been enhanced by 70% effectively. Compared with ns-LSP with pulse fluence of 71.7 J/cm2, fs-LSP with pulse fluence of 34.2 J/cm2 is superior in the hardness increment, both of which are in the same order of magnitude. A distinct grain refinement of surface layer has been discovered and results in the increase of hardness. Nonuse of absorption and confining layers and the employment of the industry commercial fs laser with high repetition can inspire big potential LSP application in special metal material. Keywords: Laser shock peening, Femtosecond laser, Mg–3Gd alloy hardness, Surface treatmen

Using Fluorescence Quenching Titration to Determine the Orientation of a Model Transmembrane Protein in Mimic Membranes

After synthesis of transmembrane proteins (TMPs), they are transferred and inserted into plasma membranes to play biological functions. Crucially, orientation of TMPs in membranes determines whether they have biological activities. In cellular environments, a number of cofactors, such as translocon, can assist TMPs to be inserted into membranes in defined orientations. During in vitro reconstitution of TMPs with mimic membranes, both insertion and orientation of TMPs are primarily determined by interactions with the membrane. Yet the knowledge is limited, hindering the in vitro applications of TMPs. Here, we take Bacteriorhodopsin (bR) as a model TMP, using fluorescence quenching titration experiment to identify orientation of bR in mimic membranes, examining effects of a number of factors, including lipid composition, pH value, ionic strength and membrane curvature. The most effective determinant is the lipid type, which modulates insertion and orientation of bR in membranes by changing the membrane surface charge and the membrane fluidity. Both the pH value and the ionic strength play secondary roles by tuning the nature of the electrostatic interaction. The membrane curvature was found to have a minor effect on orientation of bR in membranes. By comparing orientations of bR in folded and unfolded states, no obvious change was observed, informing that nascent proteins could be inserted into membranes in defined orientations before folding into the native state inside the membrane

Controllable synthesis of hierarchical porous petal-shaped SAPO-34 zeolite with excellent DTO performance

A hierarchical porous petal-shaped SAPO-34 zeolite was successfully synthesized via one-pot method by using the polymer of polyethylene glycol 20000 (PEG-20000) as structure-directing agents and the low-cost template of morpholine. The physicochemical properties of as-synthesized samples were investigated by XRD, SEM, TEM, FT-IR, EDS, N-2 adsorption-desorption and NH3-TPD measurement. The SEM and TEM results showed that many thin nanosheets with the thickness of 50-100 nm and the slit-porous channels could be observed in the petal-shaped SAPO-34 crystals. The nanosheets could significantly shorten the diffusion length and hierarchical porous structure could enhance the mass transfer. The catalytic test of dimethyl ether to olefins (DTO) revealed that the hierarchical porous petal-shaped SAPO-34 catalysts exhibited higher catalytic performance and longer catalyst lifetime compared with the conventional microporous cube-like SAPO-34 catalysts