bluuebunny/crossref_metadata_2025_split huggingface dataset:
Increasing the efficacy of exposure using a whole brain approach to real-time fMRI neurofeedback among female victims of interpersonal violence
Authors: Calvert Maegan L. , Cisler Josh M. , Bush Keith A. 
Published: August 2022

AbstractIndividuals who experience interpersonal violence (IPV) and poly-victimization have an increased likelihood of developing Posttraumatic Stress Disorder (PTSD), and statistically, women are more likely than men to be victims of IPV, experience poly-victimization, and develop PTSD. Current gold-standard PTSD treatments utilize exposure, a key mechanism of change; however, exposure-based treatments suffer from moderate remission rates. This outcome underscores the importance of utilizing knowledge of neural mechanisms to increase treatment effectiveness and PTSD remission rates. The current study used a symptom provocation paradigm, which is conceptually similar to exposure, and whole brain multivariate pattern classifiers (MVPC) to provide participants with neurofeedback on their ability to regulate their brain-states. In the MRI scanner, women (N = 21; control n = 11, PTSD n = 10) completed a symptom provocation paradigm. The MVPC was constructed during the first two runs and neurofeedback was given during the third and fourth run. During all four runs, participants were instructed to increase or decrease their emotional engagement with their stress/trauma script and during the last two runs, participants were provided visual feedback indicating their performance in regulating brain states. Skin conductance response was utilized as an independent measure of physiological arousal. Generalized linear models indicated a significant interaction effect of feedback and condition as well as feedback and group. Generalized linear models of skin conductance response largely mirrored these findings. Results indicate neurofeedback of whole brain activation can be utilized to increase engagement with trauma memories. Thus, exposure-based treatments, possibly with refractory cases of PTSD, may be improved with neurofeedback by providing the therapist and patient insight into their brain-state during exposure which may increase the effectiveness of exposure-based treatments.
LONGITUDINAL CLUSTER ANALYSIS OF HEMODIALYSIS PATIENTS WITH COVID-19 IN THE PRE-VACCINATION ERA
Authors: Esposito Pasquale , Garbarino Sara , Fenoglio Daniela , Cama Isabella , Cipriani Leda , Campi Cristina , Parodi Alessia , Vigo Tiziana , Franciotta Diego , Altosole Tiziana , Grosjean Fabrizio , Viazzi Francesca , Filaci Gilberto , Piana Michele 
Published: August 2022

ABSTRACTCoronavirus disease 2019 (COVID-19) is characterized by a high heterogeneity of clinical presentation and outcomes. This is also true for patients undergoing maintenance hemodialysis (HD), who, due to specific clinical factors and immune status, represent a distinct subgroup of COVID-19 patients.Starting from this observation in this research letter we tested and validated in two cohorts of HD patients with COVID-19 (derivation and validation cohort, respectively) an innovative model which combines linear mixed effect modeling and cluster analysis on longitudinal.This study aimed to describe a methodology allowing patient stratification from simple and widely available data.Our results could be interesting not only to improve COVID-19 management but also to support the application of longitudinal cluster analysis strategy in other clinical settings.
Acquiring thin histological sections of açaí (Euterpe oleracea Mart.) seeds for molecular mapping by mass spectrometry imaging
Authors: Brum Felipe Lopes , Martins Gabriel Rocha , Mohana-Borges Ronaldo , da Silva Ayla Sant’Ana 
Published: August 2022

ABSTRACTRATIONALEMatrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI-IMS) of tissues became popular in the last decade. Consequently, adapting sample preparation methods for different materials turned to be a pivotal step for a successful analysis, due to the requirement of samples slices of 12-20 μm thickness. However, preparing thin sections compatible with MALDI-IMS for unusual samples is challenging, as existing histological protocols may not be suitable, thus requiring new methods. Açaí (Euterpe oleracea Mart.) seed is an example of a challenging material due to its toughness and resistance to crack. Therefore, our goal was to develop a methodology to obtain thin (<20 μm) and entire longitudinal sections of açaí seeds for MALDI-IMS analysis.METHODSDifferent strategies were evaluated for obtaining thin cuts of seeds, being the combination of the following steps the most suitable option: (i) softening of seeds by water immersion for 24 h; (ii) longitudinal cut of seeds to obtain half-seeds using a razor blade and a hammer; (iii) half-seeds imbibition in gelatin; (iv) sectioning using a cryostat at −20 °C to obtain samples with <20 μm thickness; and (v) collection of samples in an indium tin oxide coated glass slide covered by a double-face copper tape to avoid sample wrapping and ensure adhesion after unfreezing. (iv) storage of samples in a −80 °C freezer, if necessary.RESULTSAs a result, this adapted sample preparation method enabled the analysis of açaí seeds by MALDI-IMS providing spatial distribution of carbohydrates in the endosperm.CONCLUSIONSThe adaptations developed for sample preparation will help investigate the metabolic and physiological properties of açaí seeds in future studies.
Rodent Automated Bold Improvement of EPI Sequences (RABIES): A standardized image processing and data quality platform for rodent fMRI
Authors: Desrosiers-Gregoire Gabriel , Devenyi Gabriel A. , Grandjean Joanes , Chakravarty M. Mallar 
Published: August 2022

ABSTRACTFunctional magnetic resonance imaging (fMRI) in rodents holds great potential for advancing our understanding of brain networks. Unlike the human fMRI community, there remains no standardized resource in rodents for image processing, analysis and quality control, posing significant reproducibility limitations. Our software platform, Rodent Automated Bold Improvement of EPI Sequences (RABIES), is a novel pipeline designed to address these limitations for preprocessing, quality control, and confound correction, along with best practices for reproducibility and transparency. We demonstrate the robustness of the preprocessing workflow by validating performance across multiple acquisition sites and both mouse and rat data. Building upon a thorough investigation into data quality metrics across acquisition sites, we introduce guidelines for the quality control of network analysis and offer recommendations for addressing issues. Taken together, the RABIES software will allow the emerging community to adopt reproducible practices and foster progress in translational neuroscience.
Development of Metal organic Framework Based Biosensor to Detect the Coronavirus (Covid-19)
Authors: Alkhodairy Hanoof Fahad , Naeem Muhammad , Helal Aasif , Khalil Amjad Bajis 
Published: August 2022

AbstractRecent outbreak of novel coronavirus (COVID-19) caused around 7 million deaths people worldwide and still afflicting on the global health, economy and social setup. Timely detection and diagnosis are crucial steps to reduce the spread and prevention of any pandemic. Different types of diagnosis methos has been used. In last decade nanomaterials and metal organic frameworks (MOFs) based biosensors has been developed to detect the other viruses. We have designed the Zeolitic imidazolate framework-8 (ZIF-8) based biosensor to detect the COVID-19. ZIF-8 work as fluorescence quenching and re-emergence platform to detect the COVID-19 RNA sequences. ZIF-8 platform is highly sensitive which can distinguish the highly conserved single strand RNA and with 200 pM concentrations. It can distinguish down to the single mismatch nucleotide in RNA sequences.
A Comparison of Representation Learning Methods for Medical Concepts in MIMIC-IV
Authors: Wu Xuan , Zhao Yizheng , Yang Yang , Liu Zhangdaihong , Clifton David A. 
Published: August 2022

AbstractObjectiveTo compare and release the diagnosis (ICD-10-CM), procedure (ICD-10-PCS), and medication (NDC) concept (code) embeddings trained by Latent Dirichlet Allocation (LDA), Word2Vec, GloVe, and BERT, for more efficient electronic health record (EHR) data analysis.Materials and MethodsThe embeddings were pre-trained by the four aforementioned models separately using the diagnosis, procedure, and medication information in MIMIC-IV. We interpreted the embeddings by visualizing them in 2D space and used the silhouette coefficient to assess the clustering ability of these embeddings. Furthermore, we evaluated the embeddings in three downstream tasks without fine-tuning: next visit diagnoses prediction, ICU patients mortality prediction, and medication recommendation.ResultsWe found that embeddings pre-trained by GloVe have the best performance in the downstream tasks and the best interpretability for all diagnosis, procedure, and medication codes. In the next-visit diagnosis prediction, the accuracy of using GloVe embeddings was 12.2% higher than the baseline, which is the random generator. In the other two prediction tasks, GloVe improved the accuracy by 2%-3% over the baseline. LDA, Word2Vec, and BERT marginally improved the results over the baseline in most cases.Discussion and ConclusionGloVe shows superiority in mining diagnoses, procedures, and medications information of MIMIC-IV compared with LDA, Word2Vec, and BERT. Besides, we found that the granularity of training samples can affect the performance of models according to the downstream task and pre-train data.
An Investigation of Lead Concentration in the Breathing Air and the Blood of Automobile Welders in Birjand, Iran
Authors: Motamedrezaei Omolbanin , Gholami Abdolah , Sharifzadeh Gholamreza , Jahani Farnaz , Lotfi Hamed 
Published: August 2022

AbstractIntroductionLead is known as one of the most dangerous toxic metals in the world and its entry into the body can cause acute and chronic intoxication with a wide range of systemic symptoms. Our goal in the current research is to study the level of lead in the breathing zone and blood of the automobile welders in Birjand.MethodsA cross-sectional, descriptive-analytic study was conducted on 47 automobile welders. The criteria for entering the study included, male gender, having at least 1 year of experience in automobile welding, and at least 8 hours of daily employment in welding. The general information required was collected through a questionnaire. At the beginning of the study, in each working environment air samples were taken in accordance with NIOSH 7082 standards. The analysis of the air lead concentration (ALC) was carried out by a flame atomic absorption spectrophotometer. The blood lead concentration (BLC) was measured by NIOSH 8003 method via graphite furnace atomic absorption spectrophotometer.ResultsBased on the data, 12.8% of the workers were smokers and 66% used appropriate personal protective equipment. The average ALC was 0.0458 ± 0.0296 mg/m3 and the average BLC of automobile welders was 9.89 ± 7.32 μg/dL. Although Pearson correlation coefficient showed a positive correlation between ALCs and BLCs, this correlation was not statistically significant (p = 0.38, r = 0.18).ConclusionThe findings of this study showed that the average BLC in cigarette smokers and those who did not use PPE was higher than other people; besides, it was higher in individuals over the age of 30 than those under this age. The mean BLC in automobile welders and the mean ALC corresponded to the standards of the American Conference of Governmental Industrial Hygienists (ACGIH).
Synergistic anti-phage activity of bacterial defence systems
Authors: Wu Yi , Garushyants Sofya K. , van den Hurk Anne , Aparicio-Maldonado Cristian , Kushwaha Simran Krishnakant , King Claire M. , Ou Yaqing , Todeschini Thomas C. , Clokie Martha R.J. , Millard Andrew D. , Gençay Yilmaz Emre , Koonin Eugene V. , Nobrega Franklin L. 
Published: August 2022

ABSTRACTBacterial defence against phage predation involves diverse defence systems acting both individually and concurrently, yet their interactions remain poorly understood. We investigated >100 defence systems in 42,925 bacterial genomes and identified numerous instances of their non-random co-occurrence and mutual exclusion. For several pairs of defence systems significantly co-occurring inEscherichia colistrains, we demonstrate synergistic anti-phage activity, including tmn synergising with defence systems containing sensory switch ATPase domains. Some of the defence system pairs that are mutually exclusive inE. colisignificantly co-occur in other taxa, and one tested mutually exclusive pair showed synergy. These findings demonstrate compatibility and synergy between defence systems, allowing bacteria to adopt flexible strategies for phage defence, driven by specific environmental pressures. The evolution of bacterial immune repertoires seems to be shaped largely by selection for resistance to host-specific phages rather than by negative epistasis.
Tetraploidy-linked sensitization to CENP-E inhibition in human cells
Authors: Yoshizawa Koya , Matsura Akira , Shimada Masaya , Ishida-Ishihara Sumire , Yamamoto Takahiro , Yaguchi Kan , Kawamoto Eiji , Kuroda Taruho , Matsuo Kazuya , Tamaoki Nobuyuki , Sakai Ryuichi , Mishra Mithilesh , Uehara Ryota 
Published: August 2022

AbstractTetraploidy caused by whole-genome duplication is a hallmark of cancer cells, and tetraploidy-selective cell growth suppression is a potential strategy for targeted cancer therapy. However, how tetraploid cells differ from normal diploids in their sensitivity to anti-proliferative treatments remains largely unknown. In this study, we found that tetraploid cells are significantly more susceptible to inhibitors of a mitotic kinesin CENP-E than diploids. CENP-E inhibitor preferentially diminished the tetraploid cell population in diploid-tetraploid co-culture at optimum conditions. Live imaging revealed that tetraploidy-linked increase in unsolvable polar chromosome misalignment caused substantially longer mitotic delay in tetraploids than in diploids upon moderate CENP-E inhibition. This time gap of mitotic arrest resulted in cohesion fatigue and subsequent cell death, specifically in tetraploids, leading to tetraploidy-selective cell growth suppression. In contrast, the microtubule-stabilizing compound paclitaxel caused tetraploidy-selective growth suppression through the aggravation of spindle multipolarization. We also found that CENP-E inhibitor had superior generality to paclitaxel in its tetraploidy selectivity across a broader spectrum of cell lines. Our results highlight the unique properties of CENP-E inhibitors in tetraploidy-selective suppression, giving us clues on the further development of tetraploidy-targeting interventions in cancer.
3D reconstruction of the cerebellar germinal layer reveals intercytoplasmic connections between developing granule cells
Authors: Cordero Cervantes Diégo , Khare Harshavardhan , Wilson Alyssa Michelle , Mendoza Nathaly Dongo , Coulon--Mahdi Orfane , Lichtman Jeff William , Zurzolo Chiara 
Published: August 2022

SummaryThe difficulty of retrieving high-resolution,in vivoevidence of the proliferative- and migratory processes occurring in neural germinal zones has limited our understanding of neurodevelopmental mechanisms. Here, we employed a connectomic approach using a high-resolution, serial-sectioning scanning electron microscopy volume to investigate the laminar cytoarchitecture of the transient external granular layer (EGL) of the developing cerebellum, where granule cells coordinate a series of mitotic and migratory events. By integrating image segmentation, 3D reconstruction, and deep learning approaches, we discovered and characterized anatomically complex intercellular connections bridging pairs of cerebellar granule cells throughout the EGL. Connected cells were either mitotic, migratory, or transitioning between these two cell stages, displaying a chronological continuum of proliferative and migratory events never previously observedin vivoat this resolution. This unprecedented ultra-structural characterization poses intriguing hypotheses about intercellular connectivity between developing progenitors, and its possible role in the development of the central nervous system (CNS).
Climatic variations along an aridity gradient drive significant trait intraspecific variability in Mediterranean species
Authors: Iozia Lorenzo Maria , Crisafulli Virginia , Varone Laura 
Published: August 2022

ABSTRACTSummer drought represents one of the main stress sources stress for plant communities in the Mediterranean region. Plants can adopt several response strategies to cope with stress, reflected in the adoption of specific Plant Functional Traits (PFTs). Trait-based approaches commonly meet three critical issues: they overlook Intraspecific Variability (ITV), they focus on a large spatial scale, or they focus on single trait responses to stress. In this study, we present evidence for a significant amount of ITV in morphological and anatomical trait syndromes observed between three local populations ofPhyllirea latifolia, Pistacia lentiscusandQuercus ilex,distributed along an aridity gradient. Thicker, more physiologically expensive leaves and lower heights found in the drier sites mainly conform to drought-resistance strategies. Interestingly, PFTs fromCistus salviifoliuswere found not to vary between sites. This implies that not all species vary at the same geographical scale, possibly depending on their different successional role. The main implication behind our findings is that climate can easily drive significant ITV in multiple traits among plant populations, even at a local scale, although trait responsiveness might be species-specific. Different plant populations hailing from the same geographical regions might thus respond differently to climate change.HIGHLIGHTVariations in Plant Functional Traits from several Mediterranean species found along an aridity gradient on a local (<60Km radius) scale; responses consistent to reported drought adaptations.
Extant hybrids of RNA viruses and viroid-like elements
Authors: Forgia Marco , Navarro Beatriz , Daghino Stefania , Cervera Amelia , Gisel Andreas , Perotto Silvia , Aghayeva Dilzara N. , Akinyuwa Mary Funmilayo , Gobbi Emanuela , Zheludev Ivan N. , Edgar Robert C. , Chikhi Rayan , Turina Massimo , Babaian Artem , Serio Francesco Di , de la Peña Marcos 
Published: August 2022

AbstractEarth’s life may have originated as self-replicating RNA. Some of the simplest current RNA replicators are RNA viruses, defined by linear RNA genomes encoding an RNA-dependent RNA polymerase (RdRP), and subviral agents with single-stranded, circular RNA genomes, such as viroids encoding paired self-cleaving ribozymes. Amongst a massive expansion of candidate viroid and viroid-like elements, we report that fungal pathogens, ambiviruses, are viroid-like elements which undergo rolling circle replication and encode their own viral RdRP, thus they are a distinct hybrid infectious agent. These findings point to a deep evolutionary history between modern RNA viruses and sub-viral elements and offer new perspectives on the evolution of primordial infectious agents, and RNA life.One-Sentence SummaryNovel infectious agents resembling self-cleaving viroid-like RNAs whilst encoding a viral RNA-dependent RNA polymerase.
Sparsification of Large Ultrametric Matrices: Insights into the Microbial Tree of Life*
Authors: Gorman Evan D. , Lladser Manuel E. 
Published: August 2022

AbstractStrictly ultrametric matrices appear in many domains of mathematics and science; nevertheless, they can be large and dense, making them difficult to store and manipulate, unlike large but sparse matrices. In this manuscript, we exploit that strictly ultrametric matrices can be represented as binary trees to sparsify them via an orthonormal base change based on Haar-like wavelets. We show that, with overwhelmingly high probability, only an asymptotically negligible fraction of the off-diagonal entries in random but large strictly ultrametric matrices remain non-zero after the base change; and develop an algorithm to sparsify such matrices directly from their tree representation. We also identify the subclass of matrices diagonalized by the Haar-like wavelets and supply a sufficient condition to approximate the spectrum of strictly ultrametric matrices outside this subclass. Our methods give computational access to the covariance matrix of the microbiologists’ Tree of Life, which was previously inaccessible due to its size, and motivate introducing a new wavelet-based (beta-diversity) metric to compare microbial environments. Unlike the established (beta-diversity) metrics, the new metric may be used to identify internal nodes (i.e., splits) in the Tree that link microbial composition and environmental factors in a statistically significant manner.MSC codes05C05, 15A18, 42C40, 65F55, 92C70
S-nitrosoglutathione Inhibits the Growth of Androgen-Receptor Dependent and Castration Resistant Prostate Cancer by Modulating FOXM1 Signaling
Authors: Vedenko Anastasia , Shah Khushi , Van Booven Derek , Fridaus Fakiha , Seetham Deepa , Arora Himanshu , Hare Joshua M. , Ramasamy Ranjith 
Published: August 2022

AbstractCastration resistant prostate cancer (CRPC) is an advanced form of prostate cancer associated with loss of androgen receptor activity and resistance to AR-targeted therapies. CRPC is often associated with higher metastasis, invasion, and proliferation. Thus, there’s a strong need for additional molecular markers in CRPC, and therapies that target them directly. Transcriptomic profiling of prostate cancer patients revealed an upregulated signature specific to high-grade tumors in cell cycle progression, E2F targets, G2M checkpoint, DNA repair, Aurora Kinase B, and FOXM1 pathway. Validation in a separate cohort of neuroendocrine prostate cancer patients, the most resistant and invasive form of CRPC which lacks AR expression, showed CCP signature as a dominant driver gene set for NEPC. Moreover, high expression of mRNA targets in each of these pathways is associated with poor overall survival in NEPC patients. Gene set variation analysis revealed a strong inverse correlation between AR signaling and CCP.31, set of 31 markers associated with high proliferation, and a positive correlation between CCP.31 and NEPC signature. FOXM1, a prioritized candidate in CCP is shown to be upregulated in CRPC cell lines and human clinical sections of Gleason 9 patients. GSNO, a nitric oxide donor, known for its inhibitory effect on cell proliferation and an effective inhibitor of cell cycle checkpoints, was able to reverse CCP signature both in-vitro and in-vivo. GSNO exhibits a dependence on AR signaling in-vitro by showing mild effect on CRPC clones, but successfully inhibits tumor growth of AR-null CRPC xenografts. FOXM1 is also targeted by GSNO in-vivo and in-vitro models of both CRPC and AD prostate cancer. This establishes an important link between androgen receptor status in prostate cancer and proposes nitric oxide donors as therapeutic intervention. GSNO is effective against AR-null castration resistant prostate cancer.SignificanceNitric oxide donor, S-glutathione-transferase inhibits tumor growth of castration resistant prostate cancer, regardless of androgen receptor expression status by targeting FOXM1, a critical regulator of cell cycle progression.