Miracle-dz/UniFAR-FTUs huggingface dataset:
Extracting Phonetic Posterior-Based Features for Detecting Multiple Sclerosis From Speech

Multiple sclerosis (MS) is a chronic inflammatory disease of the central nervous system which, in addition to affecting motor and cognitive functions, may also lead to specific changes in the speech of patients. Speech production, comprehension, repetition and naming tasks, as well as structural and content changes in narratives, might indicate a limitation of executive functions. In this study we present a speech-based machine learning technique to distinguish speakers with relapsing-remitting subtype MS and healthy controls (HC). We exploit the fact that MS might cause a motor speech disorder similar to dysarthria, which, with our hypothesis, might affect the phonetic posterior estimates supplied by a Deep Neural Network acoustic model. From our experimental results, the proposed posterior posteriorgram-based feature extraction approach is useful for detecting MS: depending on the actual speech task, we obtained Equal Error Rate values as low as 13.3%, and AUC scores up to 0.891, indicating a competitive and more consistent classification performance compared to both the x-vector and the openSMILE ‘ComParE functionals’ attributes. Besides this discrimination performance, the interpretable nature of the phonetic posterior features might also make our method suitable for automatic MS screening or monitoring the progression of the disease. Furthermore, by examining which specific phonetic groups are the most useful for this feature extraction process, the potential utility of the proposed phonetic features could also be utilized in the speech therapy of MS patients.
Comparing the Expression of Canonical and Non-Canonical Inflammasomes Across Glioma Grades: Evaluating Their Potential as an Aggressiveness Marker

Background Inflammasomes are key in the initiation of inflammatory responses and serve to defend the organism. However, when the immune system is imbalanced, these complexes contribute to tumor progression. The purpose of this study was to investigate the effect of non-canonical inflammasomes on glioma malignancy. Methods We performed bioinformatics analysis to confirm the expression of canonical and non-canonical inflammasome-related molecules according to the degree of malignancy through immunohistochemical examination of glioma tissues obtained with patient consent from our institution. Results Bioinformatics analysis confirmed that the expression levels of non-canonical inflammasome-related molecules were significantly higher in tumor tissues than in normal tissues, and they also increased according to malignancy, which adversely affected the survival rate. Furthermore, in gliomas, positive correlations were found between N-form gasdermin-D, a key molecule associated with the non-canonical inflammasome, and other related molecules, including NLRP3, caspase-1, caspase-4, and caspase-5. These results were verified by immunohistochemical examination of glioma tissues, and the expression levels of these molecules also increased significantly with increasing grade. In addition, the features of pyroptosis were confirmed. Conclusion This study identified the potential of non-canonical inflammasomes as aggressiveness markers for gliomas and presented a perspective for improving glioma treatment.
Dielectric equilateral triangle microresonators: integral equations and semiclassical physics approaches

Abstract. We investigate in detail the resonant properties of a two-dimensional dielectric cavity with an equilateral triangle shape, using a numerical integral equations approach and a semiclassical approach. The homogeneous Müller boundary equations are used to calculate the resonant modes of a dielectric triangle in a wide range of frequencies. It is shown that the modes of dielectric triangles localized on families of periodic orbits can be well described in terms of a semiclassical superscar model. Special attention is given to the families of resonances based on the inscribed triangle periodic orbit.
UvA-DARE ( Digital Academic Repository ) Hybrid resonators for light trapping and emission control

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Speaking Stata: From Rounding to Binning

This is a basic review of how to bin variables in Stata, meaning how to divide their range or support into disjoint intervals. I survey rounding functions with emphasis on floor and ceiling functions as tools to get clearly defined intervals of equal width. Using a specific display format is usually a better idea than rounding to multiples of a fraction. Quantile binning is popular in several fields. I give tips and tricks on how to produce such bins and also on how to show their limitations. Experimentation with the display command or Mata is a good way to learn about functions and to test binning rules.
Comparison of three common inbred mouse strains reveals substantial differences in hippocampal GABAergic interneuron populations and in vitro network oscillations

A major challenge in neuroscience is to pinpoint neurobiological correlates of specific cognitive and neuropsychiatric traits. At the mesoscopic level, promising candidates for establishing such connections are brain oscillations that can be robustly recorded as local field potentials with varying frequencies in the hippocampus in vivo and in vitro. Inbred mouse strains show natural variation in hippocampal synaptic plasticity (e.g. long‐term potentiation), a cellular correlate of learning and memory. However, their diversity in expression of different types of hippocampal network oscillations has not been fully explored. Here, we investigated hippocampal network oscillations in three widely used inbred mouse strains: C57BL/6J (B6J), C57BL/6NCrl (B6N) and 129S2/SvPasCrl (129) with the aim to identify common oscillatory characteristics in inbred mouse strains that show aberrant emotional/cognitive behaviour (B6N and 129) and compare them to “control” B6J strain. First, we detected higher gamma oscillation power in the hippocampal CA3 of both B6N and 129 strains. Second, higher incidence of hippocampal sharp wave‐ripple (SPW‐R) transients was evident in these strains. Third, we observed prominent differences in the densities of distinct interneuron types and CA3 associative network activity, which are indispensable for sustainment of mesoscopic network oscillations. Together, these results add further evidence to profound physiological differences among inbred mouse strains commonly used in neuroscience research.
The choline-binding proteins PspA, PspC, and LytA of Streptococcus pneumoniae and their interaction with human endothelial and red blood cells

ABSTRACT Streptococcus pneumoniae is a Gram-positive opportunistic pathogen that can colonize the upper respiratory tract. It is a leading cause of a wide range of infectious diseases, including community-acquired pneumonia and meningitis. Pneumococcal infections cause 1–2 million deaths per year, most of which occur in developing countries. Here, we focused on three choline-binding proteins (CBPs), i.e., PspC, PspA, and LytA. These pneumococcal proteins have different surface-exposed regions but share related choline-binding anchors. These surface-exposed pneumococcal proteins are in direct contact with host cells and have diverse functions. We explored the role of the three CBPs on adhesion and pathogenicity in a human host by performing relevant imaging and functional analyses, such as electron microscopy, confocal laser scanning microscopy, and functional quantitative assays, targeting biofilm formation and the hemolytic capacity of S. pneumoniae. In vitro biofilm formation assays and electron microscopy experiments were used to examine the ability of knockout mutant strains lacking the lytA, pspC, or pspA genes to adhere to surfaces. We found that LytA plays an important role in robust synthesis of the biofilm matrix. PspA and PspC appeared crucial for the hemolytic effects of S. pneumoniae on human red blood cells. Furthermore, all knockout mutants caused less damage to endothelial cells than wild-type bacteria, highlighting the significance of each CPB for the overall pathogenicity of S. pneumoniae. Hence, in addition to their structural function within the cell wall of S. pneumoniae, each of these three surface-exposed CBPs controls or mediates multiple steps during bacterial pathogenesis.
The impact of thawing duration on leptin and adiponectin levels in frozen human milk samples

Measurements of hormone concentrations in human milk from understudied populations across the world is of growing scientific interest. Due to limited access to suitable laboratory facilities at many research sites, human milk samples are often shipped frozen to distant laboratories for analysis. Shipping and handling exposes samples to the risk of thawing and degradation as the results of delays, mishandling, or other unforeseen circumstances. Similar degradation risk factors are well known in serum samples. However, the vulnerability of hormone degradation in human milk to thawing during transportation is largely unexplored. Leptin and adiponectin are of particular importance due to their roles in feeding behavior and metabolism in infants, hence our focus on these two hormones. In addition, leptin and adiponectin have been shown to be vulnerable to pasteurization temperature degradation in human milk samples.
Decamethylcyclopentasiloxane affects estradiol production in female rats but not H295R cells

Sex hormones, such as androgens and estrogens, are predominantly produced in the gonads (ovaries and testes) and adrenal cortex. Endocrine‐disrupting chemicals (EDCs) are substances that mimic, block, or interfere with hormones in the endocrine systems of humans and organisms. EDCs mainly act via nuclear receptors and steroidogenesis‐related enzymes. In the OECD conceptual framework for testing and assessment of EDCs, several well‐known assays are used to identify the potential disruption of nuclear receptors both in vivo and in vitro, whereas the H295R steroidogenesis assay is the only assay that detects the disruption of steroidogenesis. Forskolin and prochloraz are often used as positive controls in the H295R steroidogenesis assay. Decamethylcyclopentasiloxane (D5) was suspected one of EDCs, but the effects of D5 on steroidogenesis remain unclear. To establish a short‐term in vivo screening method that detects the disruption of steroidogenesis, rats in the present study were fed a diet containing forskolin, prochloraz, or D5 for 14 days. Forskolin increased plasma levels of 17β‐estradiol (E2) and testosterone as well as the mRNA level of Cyp19 in both the adrenal glands and ovaries. Prochloraz induced the loss of cyclicity in the sexual cycle and decreased plasma levels of E2 and testosterone. D5 increased E2 levels and shortened the estrous cycle in a dose‐dependent manner; however, potential endocrine disruption was not detected in the H295R steroidogenesis assay. These results demonstrate the importance of comprehensively assessing the endocrine‐disrupting effects of chemicals on steroidogenesis in vivo.
Evaluation of deep marginal feedback cancellation for hearing aids using speech and music

Speech and music both play fundamental roles in daily life. Speech is important for communication while music is important for relaxation and social interaction. Both speech and music have a large dynamic range. This does not pose problems for listeners with normal hearing. However, for hearing-impaired listeners, elevated hearing thresholds may result in low-level portions of sound being inaudible. Hearing aids with frequency-dependent amplification and amplitude compression can partly compensate for this problem. However, the gain required for low-level portions of sound to compensate for the hearing loss can be larger than the maximum stable gain of a hearing aid, leading to acoustic feedback. Feedback control is used to avoid such instability, but this can lead to artifacts, especially when the gain is only just below the maximum stable gain. We previously proposed a deep-learning method called DeepMFC for controlling feedback and reducing artifacts and showed that when the sound source was speech DeepMFC performed much better than traditional approaches. However, its performance using music as the sound source was not assessed and the way in which it led to improved performance for speech was not determined. The present paper reveals how DeepMFC addresses feedback problems and evaluates DeepMFC using speech and music as sound sources with both objective and subjective measures. DeepMFC achieved good performance for both speech and music when it was trained with matched training materials. When combined with an adaptive feedback canceller it provided over 13 dB of additional stable gain for hearing-impaired listeners.
A critical inter‐subunit interaction for the transmission of the allosteric signal in the Agrobacterium tumefaciens ADP‐glucose pyrophosphorylase

ADP‐glucose pyrophosphorylase is a key regulatory enzyme involved in starch and glycogen synthesis in plants and bacteria, respectively. It has been hypothesized that inter‐subunit communications are important for the allosteric effect in this enzyme. However, no specific interactions have been identified as part of the regulatory signal. The enzyme from Agrobacterium tumefaciens is a homotetramer allosterically regulated by fructose 6‐phosphate and pyruvate. Three pairs of distinct subunit‐subunit interfaces are present. Here we focus on an interface that features two symmetrical interactions between Arg11 and Asp141 from one subunit with residues Asp141 and Arg11 of the neighbor subunit, respectively. Previously, scanning mutagenesis showed that a mutation at the Arg11 position disrupted the activation of the enzyme. Considering the distance of these residues from the allosteric and catalytic sites, we hypothesized that the interaction between Arg11 and Asp141 is critical for allosteric signaling rather than effector binding. To prove our hypothesis, we mutated those two sites (D141A, D141E, D141N, D141R, R11D, and R11K) and performed kinetic and binding analysis. Mutations that altered the charge affected the regulation the most. To prove that the interaction per se (rather than the presence of specific residues) is critical, we partially rescued the R11D protein by introducing a second mutation (R11D/D141R). This could not restore the activator effect on kcat, but it did rescue the effect on substrate affinity. Our results indicate the critical functional role of Arg11 and Asp141 to relay the allosteric signal in this subunit interface.
Integrated morphological and transcriptome profiles reveal a highly-developed extrusome system associated to virulence in the notorious fish parasite, Ichthyophthirius multifiliis

ABSTRACT Ichthyophthirius multifiliis is an obligate parasitic ciliate that causes severe economic damage in aquaculture. The parasite contains numerous extrusive organelles (extrusomes) that assist in its pathogenesis and reproduction. However, the structure of these extrusomes and the molecular profiles involved in exocytosis remain unclear. In the present study, through comparative ultrastructural observations across the life cycle of I. multifiliis, we demonstrated that all three of its life stages (theront, trophont, and tomont) exhibited an abundance of extrusomes. In addition, two different types of extrusomes were identified according to their unique structures. Type I extrusomes (mucocysts) are crystalline, oval-shaped, 0.7–1.4 × 0.6–1.1 μm, and distributed as “rosettes” below the trophont membrane. Type II extrusomes, 2.0–3.0 × 0.2–0.3 μm, are rod-shaped with tubular cores and identified as toxicysts, the aggregation of which in the anterior part of the theront and cortex of the trophont revealed their potential roles in I. multifiliis invasion. This was confirmed by our transcriptome investigations of the three stages of I. multifiliis, which revealed that a set of genes involved in proteolysis and DNA/protein biogenesis was highly expressed in the theront and trophont. Furthermore, to map the molecular mechanisms of extrusome release, we characterized 25 Rab family genes in I. multifiliis and determined their expression profiles across the life cycle, reflecting the distribution patterns of the two extrusomes. Collectively, our data revealed that a highly developed extrusome system could play a potential role in the virulence of I. multifiliis, which facilitates a better understanding of the parasite’s development.
Nanomechanoelectrical approach to highly sensitive and specific label-free DNA detection

Significance Miniaturized, high-precision DNA analysis holds significant potential for advancing biotechnology development and enabling applications in diagnostics, healthcare, and drug discovery. DNA detection using all-electronic devices offers a promising pathway to unlock this potential. However, existing all-electronic methods are prone to limited specificity and detection limit due to interference from nonspecific electrostatic and electrochemical interactions induced by prevalent charged species in solutions. To address this challenge, we drive nanostructural DNA strands, tethered to a graphene transistor, to oscillate in an alternating electric field. We find that the resulting transistor-current spectral characteristics are resistant to the interference interactions, leading to ultrahigh specificity and a detection limit improved by two orders of magnitude compared to existing methods.
A safety review of recently approved and late-stage trial treatments for metastatic melanoma: systemic and regional therapies

ABSTRACT Introduction Advanced melanoma accounts for the majority of skin cancer-associated deaths. Over the past 15 years, there has been a dramatic change in the treatment options and prognosis for patients with advanced melanoma secondary to the development of novel systemic immunotherapies (IO) and targeted therapies. In addition to these novel systemic therapies, regional therapies (intralesional and perfusional) also continue to play a major role in the management of these patients. Areas covered In this article, we review recent updates in the management of advanced melanoma via Medline (PubMed) and Google Scholar, including recently published trials in the metastatic, adjuvant, and neoadjuvant settings. We also review recently published trials for regional therapies and discuss future directions in the management of patients with advanced melanoma. Expert opinion A significant portion of patients with advanced melanoma will develop recurrent or progressive disease following treatment with IO or targeted therapy. Therefore, identifying not only the appropriate therapeutic agent but also the sequence and duration of treatment is pivotal for these patients.
Impacts of climate change on herpetofauna diversity in the Qinghai‐Tibetan Plateau

Although numerous studies on the impacts of climate change on biodiversity have been published, only a handful are focused on the intraspecific level or consider population‐level models (separate models per population). We endeavored to fill this knowledge gap relative to the Qinghai‐Tibetan plateau (QTP) by combining species distribution modeling (SDMs) with population genetics (i.e., population‐level models) and phylogenetic methods (i.e., phylogenetic tree reconstruction and phylogenetic diversity analyses). We applied our models to 11 endemic and widely distributed herpetofauna species inhabiting high elevations in the QTP. We aimed to determine the influence of environmental heterogeneity on species’ responses to climate change, the magnitude of climate‐change impacts on intraspecific diversity, and the relationship between species range loss and intraspecific diversity losses under 2 shared socioeconomic pathways (SSP245 and SSP585) and 3 future periods (2050s, 2070s, and 2090s). The effects of global climatic change were more pronounced at the intraspecific level (22% of haplotypes lost and 36% of populations lost) than the morphospecies level in the SSP585 climate change scenario. Maintenance of genetic diversity was in general determined by a combination of factors including range changes, species genetic structure, and the part of the range predicted to be lost. This is owing to the fact that the loss and survival of populations were observed in species irrespective of the predicted range changes (contraction or expansion). In the southeast (mountainous regions), climate change had less of an effect on range size (>100% in 3 species) than in central and northern QTP plateau regions (range size <100% in all species). This may be attributed to environmental heterogeneity, which provided pockets of suitable climate in the southeast, whereas ecosystems in the north and central regions were homogeneous. Generally, our results imply that mountainous regions with high environmental heterogeneity and high genetic diversity may buffer the adverse impacts of climate change on species distribution and intraspecific diversity. Therefore, genetic structure and characteristics of the ecosystem may be crucial for conservation under climate change.
Friendly Visiting Programs for Older People Experiencing Social Isolation: A Realist Review of what Works, for whom, and under what Conditions

Abstract Many social interventions have been developed with the hopes of reducing and preventing social isolation among older people (e.g., recreation, arts-based programs and social prescription). Friendly visiting programs, also known as befriending schemes, have been a mainstay in this area for decades and are largely thought to be effective at reconnecting older people (≥ 60 years of age) experiencing isolation. Research and evaluations have yet to determine, however, how and why these programs may be most successful, and under what conditions. This article presents the findings of a realist synthesis aimed at identifying the critical mechanisms and contextual factors that lead to successful outcomes in friendly visiting programs. Seven studies are synthesized to inform a friendly visiting program theory accounting for key mechanisms (e.g., provision of informal support) and underlying contexts (e.g., training of volunteers) that can be used to inform future programs. Recommendations for future research are also presented.
Recent advancements on use of essential oils as preservatives against fungi and mycotoxins spoiling food grains

Abstract Spoilage of grains by mycotoxigenic fungi poses a great threat to food security and human health. Conventionally used chemical agents to prevent grain fungi contamination cause increasingly significant problems such as microbial resistance, residual toxicity and environmental unfriendliness. In recent years, plant essential oils (EOs) have become a hot spot in the research of control of grain fungi and mycotoxins, due to their extensive sources, non-toxicity, environmental friendliness and good antifungal efficiency. The current review aims to provide an overview of the prevention of fungi and mycotoxins in grain through EOs. The antifungal and toxin inhibition efficiency of different EOs and their effective components are investigated. The inhibition mechanism of EOs on fungi and mycotoxins in grains is introduced. The influence of EOs treatment on the change of grain quality is also discussed. In addition, the formulations and techniques used to overcome the disadvantages of EOs application are introduced. The results of recent studies have confirmed that EOs provide great potential for controlling common fungi and mycotoxins in grains, and enhancing quantity and quality safety of grains.