julilili42/papers huggingface dataset:
Using Conversational AI to Facilitate Mental Health Assessments and Improve Clinical Efficiency Within Psychotherapy Services: Real-World Observational Study
2023-10-20

Background Most mental health care providers face the challenge of increased demand for psychotherapy in the absence of increased funding or staffing. To overcome this supply-demand imbalance, care providers must increase the efficiency of service delivery. Objective In this study, we examined whether artificial intelligence (AI)–enabled digital solutions can help mental health care practitioners to use their time more efficiently, and thus reduce strain on services and improve patient outcomes. Methods In this study, we focused on the use of an AI solution (Limbic Access) to support initial patient referral and clinical assessment within the UK’s National Health Service. Data were collected from 9 Talking Therapies services across England, comprising 64,862 patients. Results We showed that the use of this AI solution improves clinical efficiency by reducing the time clinicians spend on mental health assessments. Furthermore, we found improved outcomes for patients using the AI solution in several key metrics, such as reduced wait times, reduced dropout rates, improved allocation to appropriate treatment pathways, and, most importantly, improved recovery rates. When investigating the mechanism by which the AI solution achieved these improvements, we found that the provision of clinically relevant information ahead of clinical assessment was critical for these observed effects. Conclusions Our results emphasize the utility of using AI solutions to support the mental health workforce, further highlighting the potential of AI solutions to increase the efficiency of care delivery and improve clinical outcomes for patients.
Multicentric pilot study to standardize clinical whole exome sequencing (WES) for cancer patients
2023-10-20

Abstract A growing number of druggable targets and national initiatives for precision oncology necessitate broad genomic profiling for many cancer patients. Whole exome sequencing (WES) offers unbiased analysis of the entire coding sequence, segmentation-based detection of copy number alterations (CNAs), and accurate determination of complex biomarkers including tumor mutational burden (TMB), homologous recombination repair deficiency (HRD), and microsatellite instability (MSI). To assess the inter-institution variability of clinical WES, we performed a comparative pilot study between German Centers of Personalized Medicine (ZPMs) from five participating institutions. Tumor and matched normal DNA from 30 patients were analyzed using custom sequencing protocols and bioinformatic pipelines. Calling of somatic variants was highly concordant with a positive percentage agreement (PPA) between 91 and 95% and a positive predictive value (PPV) between 82 and 95% compared with a three-institution consensus and full agreement for 16 of 17 druggable targets. Explanations for deviations included low VAF or coverage, differing annotations, and different filter protocols. CNAs showed overall agreement in 76% for the genomic sequence with high wet-lab variability. Complex biomarkers correlated strongly between institutions (HRD: 0.79–1, TMB: 0.97–0.99) and all institutions agreed on microsatellite instability. This study will contribute to the development of quality control frameworks for comprehensive genomic profiling and sheds light onto parameters that require stringent standardization.
Middle and Upper Paleolithic occupations of Fumane Cave (Italy): a geoarchaeological investigation of the anthropogenic features.
2023-10-20

Here we present the results of a microcontextual analysis of purported combustion features recovered from Middle and Upper Paleolithic occupations at the cave site of Fumane, Italy. Our analyses, which integrate micromorphology with organic petrology, show that only a few of the features represent primary, intact hearths; some of them show evidence for various phases of anthropogenic reworking, either through trampling or sweeping and dumping. Several of the features are multi-layered and reflect a complex formation history of various activities related to combustion and site maintenance. Many appear to be the remnants of occupation horizons only partially preserved and peripherally related to combustion. Within several of the intact hearths from the Mousterian, we were able to identify variable fuel sources in different features, implying a degree of flexibility in the fuel-selection strategies of the Neanderthal occupants of Fumane. In this study we design a classification system of the anthropogenic features and also conduct a spatial analysis, through which we can infer diachronic patterns in the frequency and intensity of site occupation and the spatial distribution of activities. We note a decrease in frequency of combustion features throughout the Mousterian which continues into the Uluzzian. The features associated with the Protoaurignacian occupation, in contrast with those from the Mousterian, are multi-layered and well-defined. We argue that these trends, which correspond with other trends in artefact frequency, imply changes in the settlement dynamics of the site during the transition from the last Neanderthal occupation of the cave to the arrival of modern humans.
Humoral immune response to SARS-CoV-2 and endemic coronaviruses in urban and indigenous children in Colombia
2023-10-20

Abstract Background Although anti-SARS-CoV-2 humoral immune responses and epidemiology have been extensively studied, data gaps remain for certain populations such as indigenous people or children especially in low- and middle-income countries. To address this gap, we evaluated SARS-CoV-2 seroprevalence and humoral immunity towards the parental B.1 strain, local SARS-CoV-2 variants, and endemic coronaviruses in children from Colombia from March to April 2021. Methods We performed a cross-sectional seroprevalence study with 80 children from Bogotá and expanded our analysis by comparing results with an independent observational study of 82 children from the Wiwa community living in the north-eastern Colombian territories. Antibody IgG titers towards SARS-CoV-2 and the endemic coronaviruses as well as ACE2 binding inhibition as a proxy for neutralization towards several SARS-CoV-2 variants were analyzed using two multiplex-based immunoassays. Results While we find seroprevalence estimates of 21.3% in children from Bogotá, seroprevalence is higher with 34.1% in Wiwa children. We observe a robust induction of antibodies towards the surface-exposed spike protein, its S1-, S2- and receptor-binding-subdomains in all SARS-CoV-2 seropositive children. Only nucleocapsid-specific IgG is significantly lower in the indigenous participants. ACE2 binding inhibition is low for all SARS-CoV-2 variants examined. We observe a dominance of NL63 S1 IgG levels in urban and indigenous children which suggests an early exposure to this respiratory virus independent of living conditions and geographic location. SARS-CoV-2 seropositivity does not correlate with antibody levels towards any of the four endemic coronaviruses indicating the absence of cross-protective immunity. Conclusions Overall, antibody titers, but in particular ACE2 binding inhibition are low within Colombian samples, requiring further investigation to determine any potential clinical significance.
Revealing biogeographic patterns in genetic diversity of native and invasive plants and their association with soil community diversity in the Chinese coast
2023-10-20

Within‐species genetic diversity is shaped by multiple evolutionary forces within the confines of geography, and has cascading effects on the biodiversity of other taxa and levels. Invasive species are often initially limited in genetic diversity but still respond rapidly to their new range, possibly through ‘pre‐adapted' genotypes or multiple sources of genetic diversity, but little is known about how their genetic structure differs from that of native species and how it alters the genetic‐species diversity relationship. Here, we selected a widespread native species Phragmites australis and its co‐occurring invasive competitor Spartina alterniflora as our model plant species. We investigated the genetic structure of P. australis using two chloroplast fragments and ten nuclear microsatellites in 13 populations along the Chinese coastal wetlands. We discovered a distinct geographical differentiation, showing that the northern and southern populations harbored unique genotypes. We also found a significant increase in genetic diversity (allelic richness and expected heterozygosity) from south to north. Combined with previous studies of S. alterniflora , the Mantel tests revealed a significant correlation of genetic distances between P. australis and S. alterniflora even when controlling for geographic distance, suggesting that the invasive species S. alterniflora might exhibit a phylogeographic pattern similar to that of the native species to some extent. Furthermore, our results suggest that the S. alterniflora invasion has altered the relationship between the genetic diversity of the dominant native plant and the associated species richness of soil nematodes. The reason for the alteration of genetic‐species diversity relationship might be that the biological invasion weakens the environmental impact on both levels of biodiversity. Our findings contribute to understanding the latitudinal patterns of intraspecific genetic diversity in widespread species. This work on the genetic diversity analysis of native species also provides significant implications for the invasion stage and ecological consequences of biological invasions.
Active Suppression of the Nigrostriatal Pathway during Optogenetic Stimulation Revealed by Simultaneous fPET/fMRI
2023-10-20

Abstract The dopaminergic system is a central component of the brain’s neurobiological framework, governing motor control, reward responses, and playing an essential role in various brain disorders such as Parkinson’s disease and schizophrenia. Within this complex network, the nigrostriatal pathway represents a critical circuit for dopamine transmission from the substantia nigra to the striatum, a connection that is vital to understanding many of the disease-related dysfunctions. However, stand-alone functional magnetic resonance imaging (fMRI) is unable to study the intricate interplay between brain activation and its molecular underpinnings. In our study, the simultaneous use of [ 18 F]FDG functional positron emission tomography (fPET)/BOLD-fMRI provided a new insight that allowed us to demonstrate an active suppression of the nigrostriatal activity during optogenetic stimulation via presynaptic autoinhibition. Our in vivo observation emphasizes that the observed BOLD signal depression during neuronal stimulation does not correlate with neuronal inactivity, but results from an active suppression of neuronal firing as shown by the high [ 18 F]FDG signal increase. This result not only illustrates the potential of simultaneous fPET/fMRI to understand the molecular mechanisms of brain function but also provides a new perspective on how neurotransmitters such as dopamine influence hemodynamic responses in the brain.
High Resolution Biological and Physical Sampling Reveals Expression of Domoic Acid Biosynthetic Genes at Frontal Zones
2023-10-20

Abstract Ocean microbes are the foundation of marine food webs, regulating carbon cycling and ecosystem dynamics. How they proliferate, die, move, and interact is regulated by physical, chemical, and biological factors that are dynamic and challenging to quantify in the natural environment. A significant limitation in many marine field studies is the inability to continuously sample the ever-changing ocean environment over space and time. In this study, we integrated spatiotemporal and multi-omic sample collection in an intensive sampling effort of phytoplankton ecology in Monterey Bay, California during the spring of 2021. Sampling methods coupled: (1) manual shipboard CTD sampling, (2) autonomous sampling using a Long-Range Autonomous Underwater Vehicle (LRAUV) equipped with an Environmental Sampling Processor (ESP), and (3) high-resolution physical measurements by an autonomous vertical profiler (Wirewalker). Sampling occurred as upwelling waned alongside declining domoic acid (DA) and low abundances of toxigenic Pseudo-nitzschia . Conditions needed to spark a widespread and toxic Pseudo-nitzschia bloom were absent, yet low-level DA was driven by similar mechanisms to those causing elevated DA. Three DA biosynthetic intermediate molecules were reported in the environment for the first time. Both shipboard and ESP sampling approaches identified DA biosynthetic gene expression at frontal zones. DA and expression of dabA , the gene encoding the first committed step of DA biosynthesis, were higher in association with recently upwelled water that supplied nutrients for growth and DA biosynthesis. Detection of subtle variations in dab gene expression in response to environmental variation provide a window into the ecological dynamics underpinning major toxic events. Graphical Abstract
Environment-induced heritable variations are common
2023-10-20

<title>Abstract</title> Parental or ancestral environments can induce heritable phenotypic changes, but whether such environment-induced heritable changes are a common phenomenon remains unexplored. Here, we subjected 14 genotypes of <italic>Arabidopsis thaliana</italic> to 10 different environmental treatments and observed phenotypic and genome-wide gene expression changes over successive generations. We found that all environmental treatments caused heritable phenotypic and gene expression changes, with a substantial proportion stably transmitted over all observed generations. Intriguingly, the susceptibility of a genotype to environmental inductions could be predicted based on the transposon abundance in the genome. Our study thus challenges the classic view that the environment only participates in the selection of heritable variation and suggests that the environment can broadly contribute to the generation of heritable variation.
Discarded sequencing reads uncover natural variation in pest resistance inThlaspi arvense
2023-10-20

Abstract Understanding the genomic basis of natural variation in plant pest resistance is an important goal in plant science, but it usually requires large and labour-intensive phenotyping experiments. Here, we explored the possibility that non-target reads from plant DNA sequencing can serve as phenotyping proxies for addressing such questions. We used data from a whole-genome and -epigenome sequencing study of 207 natural lines of field pennycress ( Thlaspi arvense ) that were grown in a common environment and spontaneously colonized by aphids, mildew and other microbes. We found that the numbers of non-target reads assigned to the pest species differed between populations, had significant SNP-based heritability, and were associated with climate of origin and baseline glucosinolates content. Specifically, pennycress lines from cold and thermally fluctuating habitats, presumably less favorable to aphids, showed higher aphid DNA load, i.e. decreased aphid resistance. Genome-wide association analyses identified genetic variants at known defense genes but also novel genomic regions associated with variation in aphid and mildew DNA load. Moreover, we found several differentially methylated regions associated with pathogen loads, in particular differential methylation at transposons and hypomethylation in the promoter of a gene involved in stomatal closure, likely induced by pathogens. Our study provides first insights into the defense mechanisms of Thlaspi arvense , a rising crop and model species, and demonstrates that non-target whole genome sequencing reads, usually discarded, can be leveraged to estimate intensities of plant biotic interactions. With rapidly increasing numbers of large sequencing datasets worldwide, this approach should have broad application in fundamental and applied research.
Systematic optimization of siRNA productive uptake into resting and activated T cellsex vivo
2023-10-20

Abstract RNA-based medicines are ideally suited for precise modulation of T cell phenotypes in anti-cancer immunity, in autoimmune diseases and for ex vivo modulation of T-cell-based therapies. Therefore, understanding productive siRNA uptake to T cells is of particular importance. Most studies used unmodified siRNAs or commercially available siRNA with undisclosed chemical modifications patterns to show functionality in T cells. Despite being an active field of research, robust siRNA delivery to T cells still represents a formidable challenge. Therefore, a systematic approach is needed to further optimize and understand productive siRNA uptake pathways to T cells. Here we compared conjugate-mediated and nanoparticle-mediated delivery of siRNAs to T cells in the context of fully chemically modified RNA constructs. We showed that lipid-conjugate-mediated delivery outperforms lipid-nanoparticle-mediated and extracellular-vesicle-mediated delivery in activated T cells ex vivo . Yet, ex vivo manipulation of T cells without the need of activation is of great therapeutic interest for CAR-T, engineered TCR-T and allogeneic donor lymphocyte applications. We are first to report productive siRNA uptake into resting T cells using lipid-conjugate mediated delivery. Interestingly, we observed strong dependence of silencing activity on lipid-conjugate-identity in resting T cells but not in activated T cells. This phenomenon is consistent with our early uptake kinetics data. Lipid-conjugates also enabled delivery of siRNA to all mononuclear immune cell types, including both lymphoid and myeloid lineages. These findings are expected to be broadly applicable for ex vivo modulation of immune cell therapies.
Sub-millimeter bSSFP BOLD-fMRI accelerated with 3D stack-of-spirals at 9.4 T
2023-10-20

This work aims to improve the speed of balanced steady-state free precession (bSSFP) acquisition with segmented 3D stack-of-spirals for functional brain studies at 9.4 T (see protocols.zip). Functional experiments were performed with full-field flickering checkerboard pattern (see radial_checkerboard.zip). The resulting data were reconstructed using an iterative algorithm with corrections for system imperfections such as trajectory deviations and B0 inhomogeneity using SpiralReco package. In the first set of experiments, we evaluated the signal change and stability with respect to echo and repetition time for a full field checkerboard stimulus. To demonstrate the high spatio-temporal resolution of the developed method, the results of three optimized protocols at submillimeter resolution (0.6 mm & 0.8 mm) and at 1.2 mm isotropic resolution for whole brain coverage were performed. Data organization TR/TE scans and high resolution scans: Sub-01[-06].tar.gz . ├── anat │ ├── GRE_TE16.nii.gz │ └── T1w.nii.gz (skull stripped) └── func ├── glm │ ├── smooth_0p6_moco_M397_peSpiral_R4_p6_run1_B0MTI_DCFJackson.feat │ ├── smooth_0p8_moco_M414_peSpiral_R4_p8_run1_B0MTI_DCFJackson.feat │ ├── smooth_1p0_moco_M418_peSpiral_R4_TE2_TR10_vTR3_B0MTI_DCFJackson.feat │ ├── smooth_1p0_moco_M420_peSpiral_R4_TE4_TR10_vTR3_B0MTI_DCFJackson.feat │ ├── smooth_1p0_moco_M425_peSpiral_R4_TE6_TR10_vTR3_B0MTI_DCFJackson.feat │ ├── smooth_1p0_moco_M428_peSpiral_R4_TE2_TR6_vTR3_B0MTI_DCFJackson.feat │ └── smooth_1p0_moco_M433_peSpiral_R4_TE2_TR8_vTR3_B0MTI_DCFJackson.feat ├── M397_peSpiral_R4_p6_run1_B0MTI_DCFJackson.nii.gz ├── M414_peSpiral_R4_p8_run1_B0MTI_DCFJackson.nii.gz ├── M418_peSpiral_R4_TE2_TR10_vTR3_B0MTI_DCFJackson.nii.gz ├── M420_peSpiral_R4_TE4_TR10_vTR3_B0MTI_DCFJackson.nii.gz ├── M425_peSpiral_R4_TE6_TR10_vTR3_B0MTI_DCFJackson.nii.gz ├── M428_peSpiral_R4_TE2_TR6_vTR3_B0MTI_DCFJackson.nii.gz └── M433_peSpiral_R4_TE2_TR8_vTR3_B0MTI_DCFJackson.nii.gz Whole brain: Sub-07.tar.gz ├── anat │ └── T1w.nii (skull stripped) └── func ├── M366_peSpiral_R4x2_1p2iso_ss_sWE_run_B0MTI_DCFJackson.nii.gz ├── M377_peSpiral_R4x2_1p2iso_ss_sWE_run_B0MTI_DCFJackson.nii.gz ├── smooth_1p2_moco_M366_peSpiral_R4x2_1p2iso_ss_sWE_run_B0MTI_DCFJackson.feat └── smooth_1p2_moco_M377_peSpiral_R4x2_1p2iso_ss_sWE_run_B0MTI_DCFJackson.feat
Supporting dataset for "Evoked EEG responses to TMS targeting regions outside the primary motor cortex and their test-retest reliability"
2023-10-20

This repository contains a dataset supporting results in the manuscript: Evoked EEG responses to TMS targeting regions outside the primary motor cortex and their test-retest reliability. Song, Y., Gordon, P. C., Metsomaa, J., Rostami, M., Belardinelli, P., & Ziemann, U. in submission, 2023. Summary: We aimed to investigate TEPs and their test-retest reliability when targeting regions outside M1, specifically the left angular gyrus (AG), supplementary motor area (SMA), and medial prefrontal cortex (mPFC), using an optimized sham procedure. We conducted three identical TMS–EEG sessions one week apart involving 24 healthy participants. In each session, we targeted the three areas separately using a figure−of−eight TMS coil for active TMS, while a second coil away from the head produced auditory input for sham TMS. Masking noise and electric scalp stimulation were applied in both conditions to achieve matched EEG responses to peripheral sensory inputs. TMS-EEG recording: For each TMS-EEG session, we divided into three TMS-EEG blocks that correspond to three cortical targets: AG, SMA, and mPFC. EEG signals were recorded with a TMS-compatible system (NeurOne, Bittium). Electrodes were placed according to the International 10-5 system in an elastic cap (EasyCap BC-TMS-64, EasyCap). EEG was sampled at 5 kHz (device filter DC-1250Hz), and electrode CPz served as the reference online. We recorded 150 pulses for the active conditions per cortical target and 150 for sham conditions. Visual analog scale (VAS): Participants rated their perception of auditory and somatosensory inputs from the active and sham conditions, ranging from 0 to 10. 0 represented no perception, and 10 described maximal perception. The VAS included items assessing the intensity of auditory sensation, the intensity of scalp sensation, the area size of scalp sensation, and the intensity of pain or discomfort. Each item rating was replicated twice. Dataset: The present dataset consists of: 24 data files from 24 healthy participants, each includes preprocessed eeg signals stored in fieldtrip data structure per cortical target per session [Note: each dataset is merged with active ('1') and sham ('2') events]. Leadfield matrix per session. Head model. An example tms-eeg dataset before preprocessing from a participant (in eeglab data structure). The preprocessing steps are described in the method section of the manuscript and in the code: tms_eeg_Cleaningpipeline.m (available in GitHub). A generic head model VAS scores Session information Data analysis: The code used to preprocess the TMS-EEG signal and produce results in the manuscript is available in GitHub: https://github.com/Song-Yufei/tms-eeg-using-optimized-sham-outside-M1