Miracle-dz/UniFAR-FTUs huggingface dataset:
The Complexity of Relational Queries over Extractions from Text

Large amounts of textual data with high potential value are prevalent nowadays. Incorporating textual data within traditional database systems usually consists of two stages (a) extracting relations from the text using primitive extractors and (b) manipulating the extracted relations with relational algebra operations. Document spanners is a formal framework proposed by Fagin, Kimelfeld, Reiss, and Vansummeren, that captures the relational philosophy of commercial database systems for text analytics. A document spanner (or spanner, for short) is a function that maps a string (document) into a relation over spans which are interval positions of the string. Evaluating spanners is a computational problem that involves both the atomic extractors, the relational algebra expression, and the document. We investigate the complexity of this problem from various angles, each regarding some components as fixed and regarding the rest as input. We focus on regular atomic extractor specified by means of either regular expressions or finite state automata. We present lower bounds and devise different restrictions and approaches to establish efficient upper bounds. We study the expressive power of spanners that involve recursion and the implications of extensions that support partial extractions in the flavor of SPARQL.
Application of the Sampling Theorem to Optical Diffraction Theory

The sampling theorem is applied to optical diffraction theory as a computational tool. Formulas are developed in terms of sampled values of the point spread function for the transfer function, total illuminance, line spread function and cumulative line spread function. Typical numerical examples are presented. The theory is presented for general point spread functions for slit and square apertures, but only for rotationally symmetric point spread functions for circular apertures. In the case of the slit aperture, the following question is answered: Given the real part of the incoherent transfer function, determine its imaginary part and vice versa. The theory of conjugate Fourier series and finite Hilbert transforms is introduced in order to answer this question.
Changes in humpback whale song structure and complexity reveal a rapid evolution on a feeding ground in Northern Norway

Singing behaviour by male humpback whales (Megaptera novaeangliae) has traditionally been associated with low-latitude breeding grounds. However, in recent years, this vocal behaviour has been increasingly reported outside these areas. All singers in a given population sing the same version of a song and this song is continually evolving over time with modifications on different levels within the song structure. Tracing changes in whale song will help to undercover the drivers underlying this vocal display and contribute to the understanding of animal culture and its evolution. To determine the progressive changes in songs found on a subarctic feeding ground and migratory stopover, a detailed analysis of humpback whale song recordings from Northern Norway was conducted. Passive acoustic data from the Lofoten-Vesterålen Ocean Observatory (LoVe), collected using a bottom-moored underwater hydrophone, were used from January - April 2018 and January 2019. Two measures of the song structure were examined: (1) sequence similarities using the Levenshtein distance and (2) song complexity using a principal component analysis (PCA). In total, 21 distinct themes were identified which presented highly directional, structural changes over time. Two themes from 2018 reoccurred in 2019, whereas all other themes in 2019 appeared to be evolved versions of 2018 themes. All songs grouped into three general clusters, reflecting the rapid evolution over the study period. With all sampled animals singing the same version of the song, this might indicate that the singers are either from the same breeding population or that song learning occurred before the study period. Song complexity appeared to follow the trend of song progression; songs became more complex as they evolved over the months in 2018 and decreased in complexity between the years, returning to a more simplified song in 2019. The results confirm that humpback whale song exhibits a rapid progression on a shared subarctic feeding ground, with strong potential for song exchange and opportunities for cultural transmission between populations in the North Atlantic.
Investigating the impact of pre-slaughter management factors on meat quality outcomes in cattle raised for beef: A scoping review

Introduction The pre-slaughter management period is a critical juncture in the beef supply chain, having implications not only for animal welfare and product quality, but also for profitability. During this period, cattle are exposed to many stressors in a short time, many of which have been shown to impact meat quality. Understanding how cattle management during this terminal step in the production chain affects meat quality and economic outcomes is crucial. Methods The objective of this study was to investigate, synthesize, and report on research evaluating the impact of management factors during the pre-slaughter period on beef meat quality. A systematic approach was used to search for peer-reviewed and primary studies published in English in CAB Abstracts, PubMed, and Web of Science. A total of 3,217 non-duplicate records were screened for eligibility; articles were deemed eligible for inclusion if they included beef cattle in the pre-slaughter period and reported at least one meat quality outcome. After three screening rounds, 85 articles met all inclusion criteria. Data pertinent to the scoping review’s aims were extracted, including study location, population characteristics, pre-slaughter factors reported, and outcomes of interest. Results Europe (35, 41%) and South America (21, 25%) represented approximately two-thirds of the studies. Bulls (37, 43.5%) and steers (34, 40.0%) were the most reported sex classes, with the most frequent breed types reported as predominantly British or Continental and Bos indicus breeds (24, 28.2%; 24, 28.2%, respectively). Transportation (n=46), lairage (n=36), and handling (n=35) practices were the most reported pre-slaughter factors. Overall, 59 studies reported pH as an outcome of interest – almost double that of the next highest outcome, bruising (n=35). Muscle pH was most assessed with predictors at the abattoir (n=37); conversely, the effects of transportation were most evaluated on bruising (n=23). Discussion A trend across all the categories was that there were relatively few studies evaluating the impact of pre-transport factors on meat quality. Charting the relevant literature is a critical step towards understanding the relationship between pre-slaughter management and end-product quality; doing so will help industry stakeholders in the beef production chain optimize management practices that improve meat quality and enhance profitability.
fNIRS-based brain functional response to robot-assisted training for upper-limb in stroke patients with hemiplegia

Background Robot-assisted therapy (RAT) has received considerable attention in stroke motor rehabilitation. Characteristics of brain functional response associated with RAT would provide a theoretical basis for choosing the appropriate protocol for a patient. However, the cortical response induced by RAT remains to be fully elucidated due to the lack of dynamic brain functional assessment tools. Objective To guide the implementation of clinical therapy, this study focused on the brain functional responses induced by RAT in patients with different degrees of motor impairment. Methods A total of 32 stroke patients were classified into a low score group (severe impairment, n = 16) and a high score group (moderate impairment, n = 16) according to the motor function of the upper limb and then underwent RAT training in assistive mode with simultaneous cerebral haemodynamic measurement by functional near-infrared spectroscopy (fNIRS). Functional connectivity (FC) and the hemisphere autonomy index (HAI) were calculated based on the wavelet phase coherence among fNIRS signals covering bilateral prefrontal, motor and occipital areas. Results Specific cortical network response related to RAT was observed in patients with unilateral moderate-to-severe motor deficits in the subacute stage. Compared with patients with moderate dysfunction, patients with severe impairment showed a wide range of significant FC responses in the bilateral hemispheres induced by RAT with the assistive mode, especially task-related involvement of ipsilesional supplementary motor areas. Conclusion Under assisted mode, RAT-related extensive cortical response in patients with severe dysfunction might contribute to brain functional organization during motor performance, which is considered the basic neural substrate of motor-related processes. In contrast, the limited cortical response related to RAT in patients with moderate dysfunction may indicate that the training intensity needs to be adjusted in time according to the brain functional state. fNIRS-based assessment of brain functional response assumes great importance for the customization of an appropriate protocol training in the clinical practice.
Molecular characterization of immunogenic cell death indicates prognosis and tumor microenvironment infiltration in osteosarcoma

Introduction Osteosarcoma (OS) is a highly aggressive bone malignancy with a poor prognosis, mainly in children and adolescents. Immunogenic cell death (ICD) is classified as a type of programmed cell death associated with the tumor immune microenvironment, prognosis, and immunotherapy. However, the feature of the ICD molecular subtype and the related tumor microenvironment (TME) and immune cell infiltration has not been carefully investigated in OS. Methods The ICD-related genes were extracted from previous studies, and the RNA expression profiles and corresponding data of OS were downloaded from The Cancer Genome Atlas and Gene Expression Omnibus database. The ICD-related molecular subtypes were classed by the "ConsensusclusterPlus" package and the construction of ICD-related signatures through univariate regression analysis. ROC curves, independent analysis, and internal validation were used to evaluate signature performance. Moreover, a series of bioinformatic analyses were used for Immunotherapy efficacy, tumor immune microenvironments, and chemotherapeutic drug sensitivity between the high- and low-risk groups. Results Herein, we identified two ICD-related subtypes and found significant heterogeneity in clinical prognosis, TME, and immune response signaling among distinct ICD subtypes. Subsequently, a novel ICD-related prognostic signature was developed to determine its predictive performance in OS. Also, a highly accurate nomogram was then constructed to improve the clinical applicability of the novel ICD-related signature. Furthermore, we observed significant correlations between ICD risk score and TME, immunotherapy response, and chemotherapeutic drug sensitivity. Notably, the in vitro experiments further verified that high GALNT14 expression is closely associated with poor prognosis and malignant progress of OS. Discussion Hence, we identified and validated that the novel ICD-related signature could serve as a promising biomarker for the OS's prognosis, chemotherapy, and immunotherapy response prediction, providing guidance for personalized and accurate immunotherapy strategies for OS.
Prenatal exposure to phenols and benzophenones in relation to markers of male reproductive function in adulthood

Introduction Environmental exposure during fetal life may disrupt testicular development. In humans, a limited number of studies have investigated whether these adverse effects persist into adulthood. Using data from a prospective, population-based birth cohort study, The Copenhagen Mother-Child cohort, the objective was to assess if there is an association between fetal exposure to selected phenols and benzophenones and markers of testicular function in adult men. Methods Pregnant women were recruited in 1997–2001. Their sons were examined clinically at 18-20 years of age, with focus on adult markers of reproductive function (anogenital distance (AGD), semen quality and reproductive hormones). In total, 101 18–20-year-old men were included, whose mothers during pregnancy had a serum sample drawn and analyzed for bisphenol A (BPA) and seven other simple phenols, as well as six benzophenones. To investigate the association between chemical levels (in tertiles, T1-T3) in relation to markers of reproductive function, univariate and multiple linear regression analyses were performed. Results In fully adjusted analyses, increased levels of luteinizing hormone (LH) were observed with higher fetal exposure to BPA (percentage difference (95%CI)) (T2: 12% (-8%,36%) and T3: 33% (10%,62%), compared to T1) and benzophenone-3 (BP-3) (T2: 21% (-2%,49%), T3: 18% (-4%,45%)), while no clear association was seen to total testosterone (TT). Higher levels of BPA and BP-3 were associated with a lower TT/LH ratio, although only significant for BPA (p-trend=0.01). No associations were seen to AGD or markers of semen quality. Conclusion In conclusion, high exposure to BPA and BP-3 was associated with a compensated reduced Leydig cell function but no other changes in markers of reproductive health. As maternal levels of BPA and BP-3 were not correlated, separate effects may be at play. Larger studies on long-term reproductive consequences of prenatal exposures are warranted to validate our findings.
Editorial: Biodiversity in a changing world: How do species traits reflect anthropogenic changes in aquatic ecosystems?

Laboratory of Plankton Ecology, Department of Zoology, Institute of Biology, Federal University of Juiz de Fora, Juiz de Fora, Brazil, Department of Geosciences and Geography, University of Helsinki, Helsinki, Finland, Laboratory of Protozoology, Department of Zoology, Institute of Biology, Federal University of Juiz de Fora, Juiz de Fora, Brazil, Department of Oceanography and Limnology, Federal University of Rio Grande do Norte, Natal, Brazil
Responses of root system architecture to water stress at multiple levels: A meta-analysis of trials under controlled conditions

Plants are exposed to increasingly severe drought events and roots play vital roles in maintaining plant survival, growth, and reproduction. A large body of literature has investigated the adaptive responses of root traits in various plants to water stress and these studies have been reviewed in certain groups of plant species at a certain scale. Nevertheless, these responses have not been synthesized at multiple levels. This paper screened over 2000 literatures for studies of typical root traits including root growth angle, root depth, root length, root diameter, root dry weight, root-to-shoot ratio, root hair length and density and integrates their drought responses at genetic and morphological scales. The genes, quantitative trait loci (QTLs) and hormones that are involved in the regulation of drought response of the root traits were summarized. We then statistically analyzed the drought responses of root traits and discussed the underlying mechanisms. Moreover, we highlighted the drought response of 1-D and 2-D root length density (RLD) distribution in the soil profile. This paper will provide a framework for an integrated understanding of root adaptive responses to water deficit at multiple scales and such insights may provide a basis for selection and breeding of drought tolerant crop lines.
Application of nanomaterials in diagnosis and treatment of glioblastoma

Diagnosing and treating glioblastoma patients is currently hindered by several obstacles, such as tumor heterogeneity, the blood-brain barrier, tumor complexity, drug efflux pumps, and tumor immune escape mechanisms. Combining multiple methods can increase benefits against these challenges. For example, nanomaterials can improve the curative effect of glioblastoma treatments, and the synergistic combination of different drugs can markedly reduce their side effects. In this review, we discuss the progression and main issues regarding glioblastoma diagnosis and treatment, the classification of nanomaterials, and the delivery mechanisms of nanomedicines. We also examine tumor targeting and promising nano-diagnosis or treatment principles based on nanomedicine. We also summarize the progress made on the advanced application of combined nanomaterial-based diagnosis and treatment tools and discuss their clinical prospects. This review aims to provide a better understanding of nano-drug combinations, nano-diagnosis, and treatment options for glioblastoma, as well as insights for developing new tools.
Large-scale Vietnamese point-of-interest classification using weak labeling

Point-of-Interests (POIs) represent geographic location by different categories (e.g., touristic places, amenities, or shops) and play a prominent role in several location-based applications. However, the majority of POIs category labels are crowd-sourced by the community, thus often of low quality. In this paper, we introduce the first annotated dataset for the POIs categorical classification task in Vietnamese. A total of 750,000 POIs are collected from WeMap, a Vietnamese digital map. Large-scale hand-labeling is inherently time-consuming and labor-intensive, thus we have proposed a new approach using weak labeling. As a result, our dataset covers 15 categories with 275,000 weak-labeled POIs for training, and 30,000 gold-standard POIs for testing, making it the largest compared to the existing Vietnamese POIs dataset. We empirically conduct POI categorical classification experiments using a strong baseline (BERT-based fine-tuning) on our dataset and find that our approach shows high efficiency and is applicable on a large scale. The proposed baseline gives an F1 score of 90% on the test dataset, and significantly improves the accuracy of WeMap POI data by a margin of 37% (from 56 to 93%).
Potent immunomodulatory and antitumor effect of anti-CD20-IL2no-alpha tri-functional immunocytokine for cancer therapy

Introduction The anti-CD20 antibody rituximab (RTX) has substantially improved outcomes of patients with B-cell lymphomas, although more efficient therapies are needed for refractory or relapsing lymphomas. An approach to increase the clinical effectiveness of anti-tumor therapy is the use of antibody-cytokine fusion proteins (immunocytokines (ICKs)) to deliver at the tumor site the antibody effector functions and cytokines that trigger anti-tumor activities. In particular, IL-2-based ICKs have shown significant results in preclinical studies but not in clinical trials due to the toxicity profile associated to high doses IL-2 and the undesired expansion of Tregs. Methods To improve the efficacy of RTX therapy, we fused a murine (mIgG2a) or a human (hIgG1) version of RTX to a mutated IL-2 (no-alpha mutein), which has a disrupted affinity for the high affinity IL-2 receptor (IL-2R) to prevent the stimulation of Tregs and reduce the binding to endothelial cells expressing CD25, the α chain of high affinity IL-2R. Characterization of anti-CD20-IL2no-alpha ICKs was performed by SDS-PAGE, Western-blotting and SEC-HPLC and also by several functional in vitro techniques like T-cell proliferation assays, apoptosis, CDC and ADCC assays. The in vivo activity was assessed by using murine tumor cells expressing huCD20 in C57/Bl6 mice. Results Both ICKs exhibited similar in vitro specific activity of their IL2no-alpha mutein moieties and kept CD20-binding capacity. Anti-CD20-IL2no-alpha (hIgG1) retained antibody effector functions as complement-dependent cytotoxicity and enhanced direct apoptosis, NK cell activation and antibody-dependent cellular cytotoxicity relative to RTX. In addition, both ICKs demonstrated a higher antitumor efficacy than parental molecules or their combination in an EL4-huCD20 tumor model in immunocompetent mice. Anti-CD20-IL2no-alpha (hIgG1) strongly expanded NK and CD8+ T cells but not Tregs in tumor-bearing mice. Discussion These findings suggest that anti-CD20-IL2no-alpha could represent an alternative treatment for B cell lymphoma patients, mainly those refractory to RTX therapy.
Pharmacokinetics and pharmacodynamics of anti-tuberculosis drugs: An evaluation of in vitro, in vivo methodologies and human studies

There has been an increased interest in pharmacokinetics and pharmacodynamics (PKPD) of anti-tuberculosis drugs. A better understanding of the relationship between drug exposure, antimicrobial kill and acquired drug resistance is essential not only to optimize current treatment regimens but also to design appropriately dosed regimens with new anti-tuberculosis drugs. Although the interest in PKPD has resulted in an increased number of studies, the actual bench-to-bedside translation is somewhat limited. One of the reasons could be differences in methodologies and outcome assessments that makes it difficult to compare the studies. In this paper we summarize most relevant in vitro, in vivo, in silico and human PKPD studies performed to optimize the drug dose and regimens for treatment of tuberculosis. The in vitro assessment focuses on MIC determination, static time-kill kinetics, and dynamic hollow fibre infection models to investigate acquisition of resistance and killing of Mycobacterium tuberculosis populations in various metabolic states. The in vivo assessment focuses on the various animal models, routes of infection, PK at the site of infection, PD read-outs, biomarkers and differences in treatment outcome evaluation (relapse and death). For human PKPD we focus on early bactericidal activity studies and inclusion of PK and therapeutic drug monitoring in clinical trials. Modelling and simulation approaches that are used to evaluate and link the different data types will be discussed. We also describe the concept of different studies, study design, importance of uniform reporting including microbiological and clinical outcome assessments, and modelling approaches. We aim to encourage researchers to consider methods of assessing and reporting PKPD of anti-tuberculosis drugs when designing studies. This will improve appropriate comparison between studies and accelerate the progress in the field.
Editorial: Perioperative hemodynamic monitoring and management

COPYRIGHT © 2022 Tu, Monnet, Vieillard-Baron, Dobrilovic and Yin. 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: Perioperative hemodynamic monitoring and management