Miracle-dz/UniFAR-FTUs huggingface dataset:
More Than Just a Weed: An Exploration of the Antimicrobial Activity of Rumex crispus using a Multivariate Data Analysis Approach

Abstract Plants have a long history of use for their medicinal properties. The complexity of botanical extracts presents unique challenges and necessitates the application of innovative approaches to correctly identify and quantify bioactive compounds. For this study, we used untargeted metabolomics to explore the antimicrobial activity of Rumex crispus (yellow dock), a member of the Polygonaceae family used as an herbal remedy for bacterial infections. Ultra-performance liquid chromatography coupled with high resolution mass-spectrometry (UPLC-MS) was used to identify and quantify the known antimicrobial compound emodin. In addition, we used biochemometric approaches to integrate data measuring antimicrobial activity from R. crispus root starting material and fractions against methicillin-resistant Staphylococcus aureus (MRSA) with UPLC-MS data. Our results support the hypothesis that multiple constituents, including the anthraquinone emodin, contribute to the antimicrobial activity of R. crispus against MRSA.
Ropivacaine suppresses tumor biological characteristics of human hepatocellular carcinoma via inhibiting IGF-1R/PI3K/AKT/mTOR signaling axis

ABSTRACT Ropivacaine, a common local anesthetic in the clinic, has anti-proliferative and pro-apoptotic effects in numerous cancers, however, the underlying regulatory mechanism of ropivacaine in hepatocellular carcinoma remains unclear. In the current study, human HepG2 cells were stimulated with different ropivacaine concentrations. Cell Counting Kit-8 assay, cell colony formation, and cell cycle were used to monitor cell viability. Cell apoptosis, migration, and invasion were determined by flow cytometry and transwell assays. Tumor xenograft experiments were performed to prove the anti-cancer effect of ropivacaine in vivo. A high dose of ropivacaine inhibited proliferation and promoted apoptosis of HepG2 cells in a dose-dependent manner. Ropivacaine challenge also arrested cells in the G2 phase, followed by a decline in the protein expression of cyclin D1 and cyclin-dependent kinase 2, and an increase in p27 levels in HepG2 cells. Additionally, different ropivacaine doses suppressed cell migration and invasion by upregulating E-cadherin expression and downregulating N-cadherin expression. Mechanically, ropivacaine challenge gradually restrained insulin-like growth factor-1 receptor (IGF-1 R) expression and the activities of phosphorylated-PI3K, AKT, and mTOR in HepG2 cells with increased ropivacaine doses. In the tumor xenograft experiment, ropivacaine was confirmed to inhibit tumor growth, accompanied by inhibition of the IGF-1 R/PI3K/AKT/mTOR signaling axis. In conclusion, ropivacaine suppressed tumor biological characteristics and promoted apoptosis, resulting in the suppression of hepatocellular carcinoma progression by targeting the IGF-1 R/PI3K/AKT/mTOR signaling pathway. It is possible that ropivacaine-mediated local anesthesia may be developed as a novel surgical adjuvant drug for treating hepatocellular carcinoma. Graphical Abstract
Extractive Financial Narrative Summarisation using SentenceBERT Based Clustering

We participate in the FNS-2021 Shared Task: “Financial Narrative Summarisation” organized by at 3rd Financial Narrative Processing Workshop (FNP-2021). We build an unsupervised extractive automatic ﬁnancial summarisation system for the speciﬁc task. In our approach to the FNS-2021 shared task, the documents are ﬁrst analyzed and an intermediate bespoke document set created containing the most salient sections of the reports. Next, vector representations are created for the intermediate document set based on SentenceBERT. Finally, the vectors are then clustered and sentences from each cluster are chosen for the ﬁ-nal generated report summaries. The achieved results support the proposed method’s effectiveness.
Human influence on brown trout juvenile body size during metapopulation expansion

Change in body size can be driven by social (density) and non-social (environmental and spatial variation) factors. In expanding metapopulations, spatial sorting by means of dispersal on the expansion front can further drive the evolution of body size. However, human intervention can dramatically affect these founder effects. Using long-term monitoring of the colonization of the remote Kerguelen islands by brown trout, a facultative anadromous salmonid, we analyse body size variation in 32 naturally founded and 10 human-introduced populations over 57 years. In naturally founded populations, we find that spatial sorting promotes slow positive changes in body size on the expansion front, then that body size decreases as populations get older and local density increases. This pattern is, however, completely different in human-introduced populations, where body size remains constant or even increases as populations get older. The present findings confirm that changes in body size can be affected by metapopulation expansion, but that human influence, even in very remote environments, can fully alter this process.
Comparing dream to reality: an assessment of adherence of the first generation of preregistered studies

Preregistration is a method to increase research transparency by documenting research decisions on a public, third-party repository prior to any influence by data. It is becoming increasingly popular in all subfields of psychology and beyond. Adherence to the preregistration plan may not always be feasible and even is not necessarily desirable, but without disclosure of deviations, readers who do not carefully consult the preregistration plan might get the incorrect impression that the study was exactly conducted and reported as planned. In this paper, we have investigated adherence and disclosure of deviations for all articles published with the Preregistered badge in Psychological Science between February 2015 and November 2017 and shared our findings with the corresponding authors for feedback. Two out of 27 preregistered studies contained no deviations from the preregistration plan. In one study, all deviations were disclosed. Nine studies disclosed none of the deviations. We mainly observed (un)disclosed deviations from the plan regarding the reported sample size, exclusion criteria and statistical analysis. This closer look at preregistrations of the first generation reveals possible hurdles for reporting preregistered studies and provides input for future reporting guidelines. We discuss the results and possible explanations, and provide recommendations for preregistered research.
The impact of moderate heating on human bones: an infrared and neutron spectroscopy study

This study aims to analyse human bones exposed to low/medium temperatures (200–650°C) under experimentally controlled conditions, both oxidizing and reducing, using complementary optical and neutron vibrational spectroscopy techniques. Clear differences were observed between the aerobically and anaerobically heated bones. The organic constituents disappeared at lower temperatures for the former (ca 300°C), while they lingered for higher temperatures in anaerobic environments (ca 450–550°C). Unsaturated non-graphitizing carbon species (chars) were detected mainly for anaerobically heated samples, and cyanamide formation occurred only at 650°C in reducing settings. Overall, the main changes were observed from 300 to 400°C in anaerobic conditions and from 450 to 500°C in aerobic environments. The present results enabled the identification of specific spectroscopic biomarkers of the effect of moderate temperatures (less than or equal to 650°C) on human bone, thus contributing to a better characterization of forensic and archaeological skeletal remains subject to heating under distinct environmental settings. In particular, these data may provide information regarding cannibalism or ancient bone boiling and defleshing rituals.
Life-history traits and habitat availability shape genomic diversity in birds: implications for conservation

More than 25% of species assessed by the International Union for Conservation of Nature (IUCN) are threatened with extinction. Understanding how environmental and biological processes have shaped genomic diversity may inform management practices. Using 68 extant avian species, we parsed the effects of habitat availability and life-history traits on genomic diversity over time to provide a baseline for conservation efforts. We used published whole-genome sequence data to estimate overall genomic diversity as indicated by historical long-term effective population sizes (Ne) and current genomic variability (H), then used environmental niche modelling to estimate Pleistocene habitat dynamics for each species. We found that Ne and H were positively correlated with habitat availability and related to key life-history traits (body mass and diet), suggesting the latter contribute to the overall genomic variation. We found that H decreased with increasing species extinction risk, suggesting that H may serve as a leading indicator of demographic trends related to formal IUCN conservation status in birds. Our analyses illustrate that genome-wide summary statistics estimated from sequence data reflect meaningful ecological attributes relevant to species conservation.
The role of DDK and Treslin–MTBP in coordinating replication licensing and pre-initiation complex formation

Treslin/Ticrr is required for the initiation of DNA replication and binds to MTBP (Mdm2 Binding Protein). Here we show that in Xenopus egg extract, MTBP forms an elongated tetramer with Treslin containing two molecules of each protein. Immunodepletion and add-back experiments show that Treslin-MTBP is rate-limiting for replication initiation. It is recruited onto chromatin before S phase starts and recruitment continues during S phase. We show that DDK activity both increases and strengthens the interaction of Treslin-MTBP with licensed chromatin. We also show that DDK activity cooperates with CDK activity to drive the interaction of Treslin-MTBP with TopBP1 which is a regulated crucial step in pre-Initiation Complex formation. These results suggest how DDK works together with CDKs to regulate Treslin-MTBP and plays a crucial in selecting which origins will undergo initiation.
Audit of Looked After Children (LAC) in residential care and BMI increase in one UK local authority

The rise of obesity among the UK’s child population has become a serious public health issue. Looked after children (LAC) have been highlighted as a vulnerable group, with increased health needs compared to other children and young people from comparable socio-economic backgrounds. Among the risks of serious complications related to obesity in children and young adults are cardiovascular disease, type 2 diabetes, hypertension, lipid abnormalities, sleep apnoea and musculoskeletal disorders. This health note summarises findings from a recent cross-sectional study of 14 children in five residential care homes in one UK local authority.
Medical Nutrition Therapy for Adult Patients receiving Extracorporeal Membrane Oxygenation

Extracorporeal membrane oxygenation (ECMO) has been widely used as a maintenance treatment in clinical practice. It provides circulatory and respiratory support for the most critically ill patients to sustain their life. These patients have unstable hemodynamics, high metabolic states, and may combine multiple organ failures. Therefore, it is difficult to provide reasonable and effective nutritional intervention for them although they are in a malnutrition state. The current clinical nutrition guideline is for all patients in the intensive care unit (ICU), but it is not enough to provide reliable and specific guidance for patients receiving ECMO. So how to implement medical nutrition therapy (MNT) for these patients will be the challenge we are facing now and in the future. This article analyzes the studies of ECMO and nutrition to summarize the current clinical practice and research. Meanwhile, according to the "EADMIF Six-Principle” proposed by the author in 2020, to provide innovative ideas for clinical standardization of MNT in patients receiving ECMO.
Voltage and reactive power correlation in multi-objective optimization of an offshore grid

In the last few years, many offshore wind power plants are installed at North Sea and more are under construction. Offshore grid would be vital in the integration of future offshore wind power plant with the main land grid. Both, multi-terminal DC and AC cable systems are under consideration in the concept of future offshore grid. The reactive power and voltage operating point for such a network is important for the optimized operation. This article presents an optimization criterion of voltage and reactive power control for an offshore AC grid having a parallel connecting grid-forming converter. Multi-objective optimization problem is formulated considering four reactive power management strategies. The solution of the optimization algorithm is analysed and compared with respect to active power losses in the network, voltage variation, and reactive power contribution by the sources. The research presents a methodology to apply a suitable reactive power management strategy to achieve the best optimum operating points. The solution provides the optimum operating points for offshore wind farm reactive power, frequency and voltage droop gain values for VSC-HVDC system, and reactive power sharing factor of HVDC transmission.
Modulation of elasto-inertial transitions in Taylor–Couette flow by small particles

Abstract Particle suspensions in non-Newtonian liquid matrices are frequently encountered in nature and industrial applications. We here study the Taylor–Couette flow (TCF) of semidilute spherical particle suspensions (volume fraction $\leq 0.1$) in viscoelastic, constant-viscosity liquids (Boger fluids). We describe the influence of particle load on various flow transitions encountered in TCF of such fluids, and on the nature of these transitions. Particle addition is found to delay the onset of first- and second-order transitions, thus stabilising laminar flows. It also renders them hysteretic, suggesting an effect on the nature of bifurcations. The transition to elasto-inertial turbulence (EIT) is shown to be delayed by the presence of particles, and the features of EIT altered, with preserved spatio-temporal large scales. These results imply that particle loading and viscoelasticity, which are known to destabilise the flow when considered separately, can on the other hand compete with one another and ultimately stabilise the flow when considered together.
The linguistic dimensions of concrete and abstract concepts: lexical category, morphological structure, countability, and etymology

Abstract The distinction between abstract and concrete concepts is fundamental to cognitive linguistics and cognitive science. This distinction is commonly operationalized through concreteness ratings based on the aggregated judgments of many people. What is often overlooked in experimental studies using this operationalization is that ratings are attributed to words, not to concepts directly. In this paper we explore the relationship between the linguistic properties of English words and conceptual abstractness/concreteness. Based on hypotheses stated in the existing linguistic literature we select a set of variables (part of speech, morphological structure, countability, etymology) and verify whether they are statistically associated with concreteness ratings. We show that English nouns are rated as more concrete compared to other parts of speech, but mass nouns are rated as less concrete than count nouns. Furthermore, a more complex morphological structure is associated with abstractness, and as for etymology, French- and Latin-derived words are more abstract than words of other origin. This shows that linguistic properties of words are indeed associated with the degree of concreteness that we attribute to the underlying concepts, and we discuss the implications that these findings have for linguistic theory and for empirical investigations in the cognitive sciences.
A positively Tuned Voltage Indicator Reveals Electrical Correlates of Calcium Activity in the Brain

Neuronal spiking activity is routinely recorded using genetically encoded calcium indicators (GECIs), but calcium imaging is limited in temporal resolution and does not report subthreshold voltage changes. Genetically encoded voltage indicators (GEVIs) offer better temporal resolution and subthreshold sensitivity, but spike detection with fast GEVIs has required specialized imaging equipment. Here, we report the ASAP4 subfamily of genetically encoded voltage indicators (GEVIs) that brighten in response to membrane depolarization, inverting the fluorescence-voltage relationship of previous ASAP GEVIs. Two variants, ASAP4b and ASAP4e, feature 128% and 178% fluorescence increases over 100-mV of depolarization, respectively, facilitating spike detection in single trials in vivo with standard 1 and 2-photon imaging systems. Simultaneous voltage and calcium imaging confirms improved temporal resolution and spike discernment by ASAP4 GEVIs. Thus, positively tuned ASAP4 voltage indicators enable recording of neuronal spiking activity using similar equipment as calcium imaging, while providing higher temporal resolution. One Sentence Summary Upward ASAPs increase detection capability of GEVIs in vivo.
Inactivation of SARS Coronavirus 2 and COVID-19 patient samples for contemporary immunology and metabolomics studies

In late 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged from Wuhan, China spurring the Coronavirus Disease-19 (COVID-19) pandemic that has resulted in over 219 million confirmed cases and nearly 4.6 million deaths worldwide. Intensive research efforts ensued to constrain SARS-CoV-2 and reduce COVID-19 disease burden. Due to the severity of this disease, the US Centers for Disease Control and Prevention (CDC) and World Health Organization (WHO) recommend that manipulation of active viral cultures of SARS-CoV-2 and respiratory secretions from COVID-19 patients be performed in biosafety level 3 (BSL3) containment laboratories. Therefore, it is imperative to develop viral inactivation procedures that permit samples to be transferred and manipulated at lower containment levels (i.e., BSL2), and maintain the fidelity of downstream assays to expedite the development of medical countermeasures (MCMs). We demonstrate optimal conditions for complete viral inactivation following fixation of infected cells with paraformaldehyde solution or other commonly-used branded reagents for flow cytometry, UVC inactivation in sera and respiratory secretions for protein and antibody detection assays, heat inactivation following cDNA amplification of single-cell emulsions for droplet-based single-cell mRNA sequencing applications, and extraction with an organic solvent for metabolomic studies. Thus, we provide a suite of protocols for viral inactivation of SARS-CoV-2 and COVID-19 patient samples for downstream contemporary immunology assays that facilitate sample transfer to BSL2, providing a conceptual framework for rapid initiation of high-fidelity research as the COVID-19 pandemic continues.
Methane in Lakes: Variability in Stable Carbon Isotopic Composition and the Potential Importance of Groundwater Input

Methane (CH4) is an important component of the carbon (C) cycling in lakes. CH4 production enables carbon in sediments to be either reintroduced to the food web via CH4 oxidation or emitted as a greenhouse gas making lakes one of the largest natural sources of atmospheric CH4. Large stable carbon isotopic fractionation during CH4 oxidation makes changes in 13C:12C ratio (δ13C) a powerful and widely used tool to determine the extent to which lake CH4 is oxidized, rather than emitted. This relies on correct δ13C values of original CH4 sources, the variability of which has rarely been investigated systematically in lakes. In this study, we measured δ13C in CH4 bubbles in littoral sediments and in CH4 dissolved in the anoxic hypolimnion of six boreal lakes with different characteristics. The results indicate that δ13C of CH4 sources is consistently higher (less 13C depletion) in littoral sediments than in deep waters across boreal and subarctic lakes. Variability in organic matter substrates across depths is a potential explanation. In one of the studied lakes available data from nearby soils showed correspondence between δ13C-CH4 in groundwater and deep lake water, and input from the catchment of CH4 via groundwater exceeded atmospheric CH4 emissions tenfold over a period of 1 month. It indicates that lateral hydrological transport of CH4 can explain the observed δ13C-CH4 patterns and be important for lake CH4 cycling. Our results have important consequences for modelling and process assessments relative to lake CH4 using δ13C, including for CH4 oxidation, which is a key regulator of lake CH4 emissions.
Using Digital Speech Assessments to Detect Early Signs of Cognitive Impairment

Detecting early signs of cognitive decline is crucial for early detection and treatment of Alzheimer's Disease. Most of the current screening tools for Alzheimer's Disease represent a significant burden, requiring invasive procedures, or intensive and costly clinical testing. Recent findings have highlighted changes to speech and language patterns that occur in Alzheimer's Disease, and may be detectable prior to diagnosis. Automated tools to assess speech have been developed that can be used on a smartphone or tablet, from one's home, in under 10 min. In this study, we present the results of a study of older adults who completed a digital speech assessment task over a 6-month period. Participants were grouped according to those who scored above (N = 18) or below (N = 18) the recommended threshold for detecting cognitive impairment on the Montreal Cognitive Assessment (MoCA) and those with diagnoses of mild cognitive impairment (MCI) or early Alzheimer's Disease (AD) (N = 14). Older adults who scored above the MoCA threshold had better performance on speech composites reflecting language coherence, information richness, syntactic complexity, and word finding abilities. Those with MCI and AD showed more rapid decline in the coherence of language from baseline to 6-month follow-up, suggesting that this score may be useful both for detecting cognitive decline and monitoring change over time. This study demonstrates that automated speech assessments have potential as sensitive tools to detect early signs of cognitive impairment and monitor progression over time.
Ultrafast Terahertz Complex Conductivity Dynamics of Layered MoS2 Crystal Probed by Time-Resolved Terahertz Spectroscopy

Ultrafast carrier dynamics, including the carrier photoexcitation and relaxation processes, plays an essential role in improving the performance of molybdenum disulfide (MoS2)-based optoelectronic devices. Herein, we investigate the photo-generated carrier dynamics in layered MoS2 crystal using a time-resolved terahertz (THz) spectroscopy. We have analyzed the ultrafast changes of the THz complex photoconductivity deduced from the peak and zero-crossing of THz waveforms. The decay time of the real part of the THz photoconductivity in layered MoS2 crystal is independent with the pump power, while the imaginary part increases with the pump power. We attribute the decay time of the real part to the carrier recombination process via phonon-assistance and the decay time of the imaginary part to the defect-assisted exciton recombination. The peak values of the complex photoconductivity show a trend of saturation with the increase of the pump power because of the many-body effect at high carrier concentration. This work deepens the understanding of the basic ultrafast physical process in MoS2 crystal, which is enlightening for the design of novel optoelectronic devices.