Miracle-dz/UniFAR-FTUs huggingface dataset:
Accelerating Similarity Search for Elastic Measures: A Study and New Generalization of Lower Bounding Distances

Similarity search is a core analytical task, and its performance critically depends on the choice of distance measure. For time-series querying, elastic measures achieve state-of-the-art accuracy but are computationally expensive. Thus, fast lower bounding (LB) measures prune unnecessary comparisons with elastic distances to accelerate similarity search. Despite decades of attention, there has never been a study to assess the progress in this area. In addition, the research has disproportionately focused on one popular elastic measure, while other accurate measures have received little or no attention. Therefore, there is merit in developing a framework to accumulate knowledge from previously developed LBs and eliminate the notoriously challenging task of designing separate LBs for each elastic measure. In this paper, we perform the first comprehensive study of 11 LBs spanning 5 elastic measures using 128 datasets. We identify four properties that constitute the effectiveness of LBs and propose the Generalized Lower Bounding (GLB) framework to satisfy all desirable properties. GLB creates cache-friendly summaries, adaptively exploits summaries of both query and target time series, and captures boundary distances in an unsupervised manner. GLB outperforms all LBs in speedup (e.g., up to 13.5× faster against the strongest LB in terms of pruning power), establishes new state-of-the-art results for the 5 elastic measures, and provides the first LBs for 2 elastic measures with no known LBs. Overall, GLB enables the effective development of LBs to facilitate fast similarity search.
Emergence of Aeromonas veronii strain co-harboring blaKPC–2, mcr-3.17, and tmexC3.2-tmexD3.3-toprJ1b cluster from hospital sewage in China

Introduction The raise of multi-drug resistant bacteria involving carbapenem, colistin, or tigecycline resistance constitutes a threat to public health, which partly results from the transmission of corresponding mobile resistance genes, such as blaKPC and blaNDM for carbapenem, mcr for colistin, and tmexCD-toprJ gene cluster for tigecycline. Herein, we described the emergence of an Aeromonas veronii strain HD6454 co-harboring blaKPC–2, mcr-3.17, and tmexC3.2-tmexD3.3-toprJ1b gene cluster from hospital sewage. Methods Whole genome sequencing (WGS) was used to determine the genome sequence of HD6454, and the detailed genomic analysis of genetic elements or regions carrying key antimicrobial resistance genes (ARGs) from HD6454 were performed. Cloning experiment was conducted to confirm the function of key ARGs in mediating antimicrobial resistance. Conjugation experiment was conducted to determine the mobility of the plasmid. Results The results showed that this strain belonged to a novel sequence type (ST) variant ST1016, and carried 18 important ARGs. Among them, the blaKPC–2 was carried by non-self-transmissible IncP-6 plasmid, while tmexC3.2-tmexD3.3-toprJ1b gene cluster and mcr-3.17 were carried by integrative and mobilizable element (IME) or IME-related region in chromosome. The mcr-3.17, mcr-3.6, and mcr-3-like3 genes were further inferred to originate from IMEs of Aeromonas species. Additionally, for the first time, the mcr-3.17 was confirmed to confer low-level resistance to colistin under inducible expression, while tmexC3.2-tmexD3.3-toprJ1b gene cluster was confirmed to confer low-level resistance to tigecycline. Discussion This is the first report of a strain co-harboring blaKPC–2, mcr-3.17, and tmexC3.2-tmexD3.3-toprJ1b gene cluster. Although the resistance and/or mobility of these ARGs are limited in this strain, the emergence of this multiple important ARGs-carrying strain deserves further attention.
Efficacy of ICI-based treatment in advanced NSCLC patients with PD-L1≥50% who developed EGFR-TKI resistance

Introduction Platinum-based chemotherapy is still the standard of care for Epidermal growth factor receptor (EGFR) mutated non-small cell lung cancer (NSCLC) patients after developing EGFR-TKI resistance. However, no study focusing on the role of immuno checkpoint inhibitor (ICI) based treatments for EGFR mutated NSCLC patients who carried programmed death ligand 1 (PD-L1) tumor proportion score (TPS) greater than 50% progressed after EGFR-TKI therapy. In this study, we retrospectively investigated the outcomes of ICI-based treatments for EGFR mutated NSCLC patients carried PD-L1 TPS≥50% after developing EGFR-TKI resistance and to explore the population that may benefited from ICI-based treatment. Methods We retrospectively collected data of advanced NSCLC patients with EGFR mutations and PD-L1 TPS≥50% who have failed prior EGFR-TKI therapies without T790M mutation at Shanghai Chest Hospital between January 2018 and June 2021. Progression-free survival (PFS) and overall survival (OS) were utilized to evaluate the outcomes of this study. Results A total of 146 patients were included. Up to June 20th, 2022, median follow-up was 36.7 months (IQR, 12.5-44.2 months). Among the population, 66 patients (45.2%) received chemotherapy, the remaning (54.8%) received ICI-based treatment, including 56 patients(70.0%) received ICI combined with chemotherapy (IC) and 24 patients (30.0%) received ICI monotherapy (IM). In IC group,31 patients received ICI combined with chemotherapy,19 patients received ICI combined with antiangiogenic therapy and remaing received ICI combined with chemotherapy and antiangiogenic therapy. Survival analysis shown that patients who received ICI-based treatment had better progress-free survival (PFS) and overall survival (OS) compared with those treated with other therapy (median PFS, 10.0 vs. 4.0 months, P<0.001; median OS, 39.5 vs. 24.2 months, P<0.001). What’s more, patients who treated with IC treatment had a superior survival time than those received IM treatment (median PFS, 10.3 vs. 7.0 months, P<0.001; median OS, 41.6 vs. 32.4 months, P<0.001). Subgroup analysis found that the PFS and OS benefit of IC was evident in all subgroups. Conclusions For advanced NSCLC patients with EGFR mutations and PD-L1 TPS≥50% who have failed prior EGFR-TKI therapies without T790M mutation, ICI-based treatment could provide a more favorable survival than classical chemotherapy. What’ s more, compared with ICI monotherapy, ICI combined with chemotherapy seems to be the preferred treatment.
Soluble monomeric human programmed cell death-ligand 1 inhibits the functions of activated T cells

Introduction The presence of soluble human programmed cell death-ligand 1 (shPD-L1) in the blood of patients with cancer has been reported to be negatively correlated with disease prognosis. However, little information exists about the mechanisms underlying high levels of shPD-L1 for promoting disease progression. Methods In this study, we first analyzed the correlations between shPD-L1 and apoptosis of T cells in patients with cancer, then tested the effect of shPD-L1 on T-cell functions and the production of regulatory T cells. Results We found that the apoptosis of human peripheral PD-1+CD4+ T cells was significantly elevated in patients with cancer compared with healthy donors and was positively correlated with circulating PD-L1 levels in patients with cancer. In vitro, monomeric shPD-L1 significantly inhibited the proliferation, cytokine secretion, and cancer cell-killing activity of peripheral blood mononuclear cells (PBMCs) activated by either agonist antibodies or HATac (high-affinity T cell activation core)-NYE (NY-ESO-1 antigen). It also promoted CD4+ T cells to express forkhead family transcription factor 3 (FoxP3) for the conversion of induced T regulatory cells, which was more significant than that mediated by soluble human PD-L1 fusion protein (shPD-L1-Fc). Discussion These results confirm that soluble PD-L1 could be a candidate for inhibiting the functions of activated T cells, promoting peripheral tolerance to tumor cells, and implicating in system tumor immune escape in addition to the tumor microenvironment. This is an important mechanism explaining the negative correlation between peripheral blood PD-L1 levels and cancer prognosis. Therefore, understanding the roles of hPD-L1 in peripheral blood will be helpful for the development of precision immunotherapy programs in treating various tumors.
Impact of early pericardial fluid chymase activation after cardiac surgery

Introduction Chymase is a highly destructive serine protease rapidly neutralized in the circulation by protease inhibitors. Here we test whether pericardial fluid (PCF) chymase activation and other inflammatory biomarkers determine intensive care unit length of stay, and explore mechanisms of chymase delivery by extracellular vesicles to the heart. Methods PCF was collected from adult patients (17 on-pump; 13 off-pump) 4 h after cardiac surgery. Extracellular vesicles (EVs) containing chymase were injected into Sprague–Dawley rats to test for their ability to deliver chymase to the heart. Results The mean intensive care unit (ICU) stay and mean total length of stay was 2.17 ± 3.8 days and 6.41 ± 1.3 days respectively. Chymase activity and 32 inflammatory markers did not differ in on-pump vs. off-pump cardiac surgery. Society of Thoracic Surgeons Predicted Risk of Morbidity and Mortality Score (STS-PROM), 4-hour post-surgery PCF chymase activity and C-X-C motif chemokine ligand 6 (CXCL6) were all independent predictors of ICU and total hospital length of stay by univariate analysis. Mass spectrometry of baseline PCF shows the presence of serine protease inhibitors that neutralize chymase activity. The compartmentalization of chymase within and on the surface of PCF EVs was visualized by immunogold labeling and transmission electron microscopy. A chymase inhibitor prevented EV chymase activity (0.28 fmol/mg/min vs. 14.14 fmol/mg/min). Intravenous injection of PCF EVs obtained 24 h after surgery into Sprague Dawley rats shows diffuse human chymase uptake in the heart with extensive cardiomyocyte damage 4 h after injection. Discussion Early postoperative PCF chymase activation underscores its potential role in cardiac damage soon after on- or off-pump cardiac surgery. In addition, chymase in extracellular vesicles provides a protected delivery mechanism from neutralization by circulating serine protease inhibitors.
Editorial: The earliest-born cortical neurons as multi-tasking pioneers: expanding roles for subplate neurons in cerebral cortex organization and function, volume II

COPYRIGHT © 2023 Oka, Sato and Chou. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. Editorial: The earliest-born cortical neurons as multi-tasking pioneers: expanding roles for subplate neurons in cerebral cortex organization and function, volume II
The carboxypeptidase B and carbonic anhydrase genes play a reproductive regulatory role during multiple matings in Ophraella communa

Seminal fluid proteins (SFPs) are key factors in sexual reproduction and are transferred to females during mating with sperm. SFPs have a nutritional value because they protect and activate sperm storage and release to optimize fecundity. Multiple matings promote ovipositioning in several insect species. Therefore, insects may obtain more SFP through multiple matings to maximize reproduction, but this process has not yet been clearly confirmed. Here, the relationship between multiple matings and the SFPs in Ophraella communa (Coleoptera: Chrysomelidae), a biological control agent of the common ragweed Ambrosia artemisiifolia (Asterales: Asteraceae), was studied. Multiple matings significantly increased female fecundity and ovary egg deposition. Carboxypeptidase B (OcCpb) and carbonic anhydrase (OcCa) genes were identified as putative SFP genes in O. communa and they showed strong male-biased expression. Additionally, OcCpb and OcCa expression was upregulated in the bursa copulatrix of mating females compared to that in virgin females, but their expression gradually declined after copulation. Furthermore, OcCpb and OcCa knockdown in males led to a decrease in insect fecundity compared to that in the control. The reproductive tract of females mated with dsRNA-treated males was dissected and observed and, notably, the ovaries produced significantly fewer eggs. These data suggest that OcCpb and OcCa play regulatory roles during multiple matings in O. communa.
Biomass and lipid production by the native green microalgae Chlorella sorokiniana in response to nutrients, light intensity, and carbon dioxide: experimental and modeling approach

Introduction: Microalgae are photosynthetic cells that can produce third-generation biofuels and other commercial compounds. Microalgal growth is influenced by two main parameters: light intensity and carbon dioxide concentration, which represent the energy and carbon source, respectively. For photosynthesis, the optimum values of abiotic factors vary among species. Methods: In this study, the microalga Chlorella sorokiniana was isolated from a freshwater lake. It was identified using molecular analysis of the ribosomal internal transcribed spacer. A single-factor design of experiments in 250-mL Erlenmeyer flasks was used to evaluate which concentrations of nitrogen and phosphorus increase the production of biomass and lipids. The response surface methodology was used with a 32-factorial design (light intensity and CO2 were used to evaluate its effect on biomass, lipid production, and specific growth rates, in 200-mL tubular photobioreactors (PBRs)). Results and Discussion: Low levels of light lead to lipid accumulation, while higher levels of light lead to the synthesis of cell biomass. The highest biomass and lipid production were 0.705 ± 0.04 g/L and 55.1% ± 4.1%, respectively. A mathematical model was proposed in order to describe the main phenomena occurring in the culture, such as oxygen and CO2 mass transfer and the effect of light and nutrients on the growth of microalgae. The main novelties of this work were molecular identification of the strain, optimization of culture conditions for the indigenous microalgae species that were isolated, and formulation of a model that describes the behavior of the culture.
Development and validity of a short web-based semi-quantitative Food Frequency Questionnaire applicable in both clinical and research setting: an evolution over time

Background Assessing dietary intake is valuable both in clinical practice and in research. In research and in clinical practice, long-term habitual dietary intake is most often of interest. Therefore, a web-based semi-quantitative Food Frequency Questionnaire (FFQ) was developed to measure habitual intake of nutrients and foods. Aim This study aimed to assess content validity, convergent validity, and reliability of a 32-item semi-quantitative FFQ for adults. Methods A total of three different cohorts of Flemish adults were recruited in the past 10 years. The first cross-sectional validation study took place in 2013, consequently in 2019 and 2021. Content validity was assessed in 2019 through a semi-structured cognitive interview. Convergent validity was assessed by examining mean differences, Wilcoxon signed-rank test, Spearman's correlation coefficients (SCC), and Bland–Altman analysis for energy, nutrient, and food group intake compared with a 3-day food record (FR). Additionally, consumers-only analysis was performed together with cross-classification analysis by assessing the ranking capabilities of the FFQ into quartiles and weighted kappa. Reliability was assessed through the evaluation of SCC and intra-class correlation (ICC) of test–retest assessment of the FFQ. Results Spearman's correlation coefficient (SCC) for energy and absolute nutrient intake between the FFQ and the FR ranged from 0.02 to 0.54. Compared with absolute macronutrients, higher SCC was found for the majority of the relative macronutrient intake and most food groups. Bland–Altman plots showed improved agreement and decreasing bias between the FFQ and the FR over time. Misclassification of the FFQ for nutrients was acceptable and decreased over time (7.4, 7.5, and 6.8% in 2013, 2019, and 2021, respectively), but weighted kappa remained mostly fair (κ ≤ 0.20). The reliability of the FFQ was good and improved over time (mean SCC of 0.65 and 0.66 p <0.001 in 2013 and 2019). Conclusion The short web-based FFQ is an easy, low-cost, and feasible tool with good reliability, low misclassification, and acceptable validity to compare nutrient densities and food group intake at the population level. The measurement of absolute intake remains debatable.
The Gal/GalNac lectin as a possible acetylcholine receptor in Entamoeba histolytica

Entamoeba histolytica (E. histolytica) is a protozoan responsible for intestinal amebiasis in at least 500 million people per year, although only 10% of those infected show severe symptoms. It is known that E. histolytica captures molecules released during the host immune response through membrane receptors that favor its pathogenetic mechanisms for the establishment of amebic invasion. It has been suggested that E. histolytica interacts with acetylcholine (ACh) through its membrane. This promotes the increase of virulence factors and diverse mechanisms carried out by the amoeba to produce damage. The aim of this study is to identify a membrane receptor in E. histolytica trophozoites for ACh. Methods included identification by colocalization for the ACh and Gal/GalNAc lectin binding site by immunofluorescence, western blot, bioinformatic analysis, and quantification of the relative expression of Ras 5 and Rab 7 GTPases by RT-qPCR. Results show that the Gal/GalNAc lectin acts as a possible binding site for ACh and this binding may occur through the 150 kDa intermediate subunit. At the same time, this interaction activates the GTPases, Ras, and Rab, which are involved in the proliferation, and reorganization of the amoebic cytoskeleton and vesicular trafficking. In conclusion, ACh is captured by the parasite, and the interaction promotes the activation of signaling pathways involved in pathogenicity mechanisms, contributing to disease and the establishment of invasive amebiasis.
Urban cultural heritage is mentally restorative: an experimental study based on multiple psychophysiological measures

Introduction Urban cultural heritage sites bear the cultural functions of a city, hold spiritual and cultural value, can recall emotional memories, and serve the cultural leisure activities of the residents. Urban cultural heritage sites can help citizens perceive a sense of belonging and a feeling of relaxation, but whether and to what extent cultural heritage sites affect mental health remains unknown. Methods Based on attention restoration theory, multiple research methods are adopted in this study to examine the impact of cultural heritage on human restorative mechanisms. Five representative cultural heritage sites from the cultural heritage-rich city of Xi'an are selected as the research object. In addition, a questionnaire survey and physiological experiments are conducted. Perceived restorative scale, skin conductance response, heart rate variability, and eye movement data while viewing photographs of the cases are collected from the participants. Results Results show that cultural heritage sites have psychophysiological restorative effects, which are especially significant in the fascination dimension. Moreover, historical buildings can promote the restorative effects of cultural heritage sites. Discussion This finding may lead to new conservation and innovation planning strategies considering the mental health effects of cultural heritage.
Dynamic models for musical rhythm perception and coordination

Rhythmicity permeates large parts of human experience. Humans generate various motor and brain rhythms spanning a range of frequencies. We also experience and synchronize to externally imposed rhythmicity, for example from music and song or from the 24-h light-dark cycles of the sun. In the context of music, humans have the ability to perceive, generate, and anticipate rhythmic structures, for example, “the beat. ” Experimental and behavioral studies offer clues about the biophysical and neural mechanisms that underlie our rhythmic abilities, and about different brain areas that are involved but many open questions remain. In this paper, we review several theoretical and computational approaches, each centered at different levels of description, that address specific aspects of musical rhythmic generation, perception, attention, perception-action coordination, and learning. We survey methods and results from applications of dynamical systems theory, neuro-mechanistic modeling, and Bayesian inference. Some frameworks rely on synchronization of intrinsic brain rhythms that span the relevant frequency range; some formulations involve real-time adaptation schemes for error-correction to align the phase and frequency of a dedicated circuit; others involve learning and dynamically adjusting expectations to make rhythm tracking predictions. Each of the approaches, while initially designed to answer specific questions, offers the possibility of being integrated into a larger framework that provides insights into our ability to perceive and generate rhythmic patterns.
A Search for Light Weakly-Interacting Massive Particles with SuperCDMS and Applications to Neutrino Physics

Cosmological and astrophysical evidence indicates that 85% of the matter content of the universe is in the form of non-baryonic dark matter. A large number of experiments are currently undertaking searches for weakly-interacting massive particles (WIMPs), the leading class of particle candidates for dark matter. This thesis describes the results of such a search with the SuperCDMS experiment, which uses Ge detectors cooled to 50 mK to detect ionization and phonons produced by particle interactions. We perform a blind analysis of 577 kg d of exposure on 7 detectors targeting WIMPs with masses < 30 GeV/c2 , where anomalous results have been reported by previous experiments. No significant excess is observed and we set an upper limit on the spin-independent WIMP-nucleon cross section of 1.2 x 10-42 cm 2 at 8 GeV/c2 . We also set constraints on dark matter interactions independent of the dark matter halo physics, as well as on annual modulation of a dark matter signal. Cryogenic detectors similar to SuperCDMS also have potential applications in neutrino physics. We study several configurations in which dark matter detectors could be used with an intense neutrino source to detect an unmeasured Standard Model process called coherent neutrino scattering. This process may be useful, for example, as a calibration for next-generation dark matter detectors, and for constraining eV-scale sterile neutrinos. In addition, small cryogenic X-ray detectors on sounding rockets with large fields-of-view have the unique ability to constrain sterile neutrino dark matter. We set limits on sterile neutrino dark matter using an observation by the XQC instrument, and discuss prospects for a future observation of the galactic center using the Micro-X instrument. Thesis Supervisor: Enectali Figueroa-Feliciano Title: Associate Professor of Physics