Miracle-dz/UniFAR-FTUs huggingface dataset:
The hexokinase Gene Family in Cotton: Genome-Wide Characterization and Bioinformatics Analysis

Hexokinase (HXK) is involved in hexose phosphorylation, sugar sensing, and signal transduction, all of which regulate plant growth and adaptation to stresses. Gossypium hirsutum L. is one of the most important fiber crops in the world, however, little is known about the HXKs gene family in G. hirsutum L. We identified 17 GhHXKs from the allotetraploid G. hirsutum L. genome (AADD). G. raimondii (DD) and G. arboreum (AA) are the diploid progenitors of G. hirsutum L. and contributed equally to the At_genome and Dt_genome GhHXKs genes. The chromosomal locations and exon-intron structures of GhHXK genes among cotton species are conservative. Phylogenetic analysis grouped the HXK proteins into four and three groups based on whether they were monocotyledons and dicotyledons, respectively. Duplication event analysis demonstrated that HXKs in G. hirsutum L. primarily originated from segmental duplication, which prior to diploid hybridization. Experiments of qRT-PCR, transcriptome and promoter cis-elements demonstrated that GhHXKs’ promoters have auxin and GA responsive elements that are highly expressed in the fiber initiation and elongation stages, while the promoters contain ABA-, MeJA-, and SA-responsive elements that are highly expressed during the synthesis of the secondary cell wall. We performed a comprehensive analysis of the GhHXK gene family is a vital fiber crop, which lays the foundation for future studies assessing its role in fiber development.
Bacterial Communities in the Fruiting Bodies and Background Soils of the White Truffle Tuber magnatum

Tuber magnatum Picco is a greatly appreciated truffle species mainly distributed in Italy. Its price and characteristics mostly depend on its geographical origin. Truffles represent a fundamental step of the life cycle of Tuber species promoting spore dissemination. They consist of two main parts, gleba, the inner part, and peridium, which is in direct contact with ground soil. Within the truffle and around in the growing soil, both the occurrence and abundance of different microbial species seem to play an essential role in truffle production. The development of the next-generation sequencing (NGS) based technology has greatly improved to deepen the role of the composition of microbial communities, thus improving the knowledge of the existing relationships between microbial taxa in a specific condition. Here, we applied a metabarcoding approach to assess the differences in T. magnatum samples collected from three areas in Tuscany (Italy). Peridium and gleba were analyzed separately with the aim to distinguish them based on their microbial composition. Also, soil samples were collected and analyzed to compare productive and unproductive truffle grounds to confirm the presence of specific patterns linked to truffle production. Results indicate that differences occurred between truffle compartments (gleba and peridium) as well as between analyzed soils (productive and unproductive), with distinctive taxa associated. Furthermore, findings also demonstrated specific characteristics associated with truffle collection areas, thus indicating a degree of microbial selection related to different environments.
Dissecting Tissue Compartment-Specific Protein Signatures in Primary and Metastatic Oropharyngeal Squamous Cell Carcinomas

Head and neck squamous cell carcinoma (HNSCC) often presents with locoregional or distant disease, despite multimodal therapeutic approaches, which include surgical resection, chemoradiotherapy, and more recently, immunotherapy for metastatic or recurrent HNSCC. Therapies often target the primary and nodal regional HNSCC sites, and their efficacy at controlling occult distant sites remains poor. While our understanding of the tumor microenvironment conducive to effective therapies is increasing, the biology underpinning locoregional sites remains unclear. Here, we applied targeted spatial proteomic approaches to primary and lymph node metastasis from an oropharyngeal SCC (OPSCC) cohort to understand the expression of proteins within tumors, and stromal compartments of the respective sites in samples of both matched and unmatched patients. In unmatched analyses of n = 43 primary and 11 nodal metastases, our data indicated that tumor cells in nodal metastases had higher levels of Ki-67, PARP, BAD, and cleaved caspase 9, suggesting a role for increased proliferation, DNA repair, and apoptosis within these metastatic cells. Conversely, in matched analyses (n = 7), pro-apoptotic markers BIM and BAD were enriched in the stroma of primary tumors. Univariate, overall survival (OS) analysis indicated CD25 in tumor regions of primary tumors to be associated with reduced survival (HR = 3.3, p = 0.003), while progesterone receptor (PR) was associated with an improved OS (HR = 0.33, p = 0.015). This study highlights the utility of spatial proteomics for delineating the tumor and stromal compartment composition, and utility toward understanding these properties in locoregional metastasis. These findings indicate unique biological properties of lymph node metastases that may elucidate further understanding of distant metastatic in OPSCC.
Decreased Efficiency of Between-Network Dynamics During Early Memory Consolidation With Aging

Aging is associated with memory decline and progressive disabilities in the activities of daily living. These deficits have a significant impact on the quality of life of the aging population and lead to a tremendous burden on societies and health care systems. Understanding the mechanisms underlying aging-related memory decline is likely to inform the development of compensatory strategies promoting independence in old age. Research on aging-related memory decline has mainly focused on encoding and retrieval. However, some findings suggest that memory deficits may at least partly be due to impaired consolidation. To date, it remains elusive whether aging-related memory decline results from defective consolidation. This study examined age effects on consolidation-related neural mechanisms and their susceptibility to interference using functional magnetic resonance imaging data from 13 younger (20–30 years, 8 female) and 16 older (49–75 years, 5 female) healthy participants. fMRI was performed before and during a memory paradigm comprised of encoding, consolidation, and retrieval phases. Consolidation was variously challenged: (1) control (no manipulation), (2) interference (repeated stimulus presentation with interfering information), and (3) reminder condition (repeated presentation without interfering information). We analyzed the fractional amplitude of low-frequency fluctuations (fALFF) to compare brain activity changes from pre- to post-encoding rest. In the control condition, fALFF was decreased in the left supramarginal gyrus, right middle temporal gyrus, and left precuneus but increased in parts of the occipital and inferior temporal cortex. Connectivity analyses between fALFF-derived seeds and network ROIs revealed an aging-related decrease in the efficiency of functional connectivity (FC) within the ventral stream network and between salience, default mode, and central executive networks during consolidation. Moreover, our results indicate increased interference susceptibility in older individuals with dynamics between salience and default mode networks as a neurophysiological correlate. Conclusively, aging-related memory decline is partly caused by inefficient consolidation. Memory consolidation requires a complex interplay between large-scale brain networks, which qualitatively decreases with age.
Physiological Mechanisms and Significance of Intracranial B Waves

Objective Recently published studies have described slow spontaneous cerebral blood flow (CBF) and cerebrospinal fluid (CSF) oscillations measured by magnetic resonance imaging (MRI) as potential drivers of brain glymphatic flow, with a similar frequency as intracranial B-waves. Aiming to establish the relationship between these waveforms, we performed additional analysis of frequency and waveform parameters, of our previously published transcranial Doppler (TCD) and intracranial pressure (ICP) recordings of intracranial B waves, to compare to published MRI frequency measurements of CBF and CSF slow oscillations. Patients and Methods We analyzed digital recordings of B waves in 29 patients with head injury, including middle cerebral artery (MCA) flow velocity (FV), ICP, end tidal CO2, and arterial blood pressure (ABP). A subset of these recordings demonstrated high B wave activity and was further analyzed for parameters including frequency, interaction, and waveform distribution curve features. These measures were compared to published similar measurements of spontaneous CBF and CSF fluctuations evaluated using MRI. Results In patients with at least 10% amplitude B wave activity, the MCA blood flow velocity oscillations comprising the B waves, had a maximum amplitude at 0.0245 Hz, and time derivative a maximum amplitude at 0.035 Hz. The frequency range of the B waves was between 0.6–2.3 cycles per min (0.011-0.038 Hz), which is in the same range as MRI measured CBF slow oscillations, reported in human volunteers. Waveform asymmetry in MCA velocity and ICP cycles during B waves, was also similar to published MRI measured CBF slow oscillations. Cross-correlation analysis showed equivalent time derivatives of FV vs. ICP in B waves, compared to MRI measured CBF slow oscillations vs. CSF flow fluctuations. Conclusions The TCD and ICP recordings of intracranial B waves show a similar frequency range as CBF and CSF flow oscillations measured using MRI, and share other unique morphological wave features. These findings strongly suggest a common physiological mechanism underlying the two classes of phenomena. The slow blood flow and volume oscillations causing intracranial B waves appear to be part of a cascade that may provide a significant driving force for compartmentalized CSF movement and facilitate glymphatic flow.
Identification of Novel Characteristics in TP53-Mutant Hepatocellular Carcinoma Using Bioinformatics

Background: TP53 mutations are the most frequent mutations in hepatocellular carcinoma (HCC) and affect the occurrence and development of this cancer type. Therefore, it is essential to clarify the function and mechanism of TP53 mutations in HCC. Methods: We performed a sequence of bioinformatic analyses to elucidate the characteristics of TP53 mutations in HCC. We downloaded the data of hepatocellular carcinoma from The Cancer Genome Atlas database and used different R packages for serial analyses, including gene mutation analysis, copy number variation analysis, analysis of the tumor mutational burden and microsatellite instability, differential gene expression analysis, and functional enrichment analysis of TP53 mutations, and performed gene set enrichment analysis. We established a protein-protein interaction network using the STRING online database and used the Cytoscape software for network visualization, and hub gene screening. In addition, we performed anticancer drug sensitivity analysis using data from the Genomics of Drug Sensitivity in Cancer. Immune infiltration and prognosis analyses were also performed. Results: Missense mutations accounted for a great proportion of HCC mutations, the frequency of single nucleotide polymorphisms was high, and C > T was the most common form of single nucleotide variations. TP53 had a mutation rate of 30% and was the most commonly mutated gene in HCC. In the TP53 mutant group, the tumor mutational burden (p < 0.001), drug sensitivity (p < 0.05), ESTIMATE score (p = 0.038), and stromal score (p < 0.001) dramatically decreased. The Cytoscape software screened ten hub genes, including CT45A1, XAGE1B, CT55, GAGE2A, PASD1, MAGEA4, CTAG2, MAGEA10, MAGEC1, and SAGE1. The prognostic model showed a poor prognosis in the TP53 mutation group compared with that in the wild-type group (overall survival, p = 0.023). Univariate and multivariate cox regression analyses revealed that TP53 mutation was an independent risk factor for the prognosis of HCC patients (p <0.05). The constructed prognostic model had a favorable forecast value for the prognosis of HCC patients at 1 and 3 years (1-year AUC = 0.752, 3-years AUC = 0.702). Conclusion: This study further deepened our understanding of TP53-mutated HCC, provided new insights into a precise individualized therapy for HCC, and has particular significance for prognosis prediction.
Hearing From Men Living With HIV: Experiences With HIV Testing, Treatment, and Viral Load Suppression in Four High-Prevalence Countries in Sub-Saharan Africa

Engaging men in HIV services remains a challenge across sub-Saharan Africa. There is a critical need to better understand facilitators of men's successful engagement with HIV services and assess if there are similarities across contexts. We conducted in-depth interviews and focus group discussions with 92 men living with HIV (MLHIV) across Malawi, Uganda, South Africa, and Eswatini, most of whom had been diagnosed with HIV within the last 5 years. We coded interviews for themes using a constant-comparative approach. We contextualized our findings within a socioecological framework. HIV testing was primarily motivated by illness (individual level), though illness was sometimes accompanied by prompting and support from healthcare providers and/or intimate partners. Once diagnosed, nearly all participants reported immediate linkage to care, initiation of antiretroviral therapy (ART), and subsequent ART adherence. ART initiation and adherence were facilitated by men's sense of agency and ownership over their health (individual level), social support from intimate partners, friends, and family (interpersonal/network level), supportive-directive counseling from healthcare providers (institutional/health systems level), and male-friendly services, i.e., rapid, respectful, private (institutional/health systems level). Health literacy regarding viral suppression (individual level), strengthened by patient-provider communication (institutional/health systems level), was highest in Uganda, where most men could discuss viral load testing experiences, report their viral load status (most reported suppressed), and demonstrate an understanding of treatment as prevention. Elsewhere, few participants understood what viral load suppression was and even fewer knew their viral load status. Our findings reveal socioecological-level facilitators of men's progress across the HIV-care continuum. Programs may want to leverage facilitators of ART initiation and adherence that span socioecological levels—e.g., healthcare ownership and agency, social support, supportive-directive counseling—and apply them to each end of the continuum to encourage early HIV testing/diagnosis and improve health literacy to help men understand and achieve viral load suppression.
Is Balance Control Affected by Sleep Deprivation? A Systematic Review of the Impact of Sleep on the Control of Balance

Background Sleep is a complex physiological function that should be addressed from different perspectives and consider the circadian rhythm. Sleep deprivation, either acute or chronic, negatively affects several functions, including motor control. Balance control is essential in several daily life activities and balance problems are related to falls. Research Question This review focuses on how sleep conditions impact balance control. Methods Systematic literature review according to PRISMA guidelines. Results The literature provided strong evidence that acute sleep deprivation impairs postural control. Chronic sleep deprivation as well as low sleep quality had similar effects, although there is a lower number of works addressing this issue. Furthermore, time awake worsens postural controls and it can be used to detect sleepiness and fatigue. The sleep deprivation showed a stronger negative effect on postural control when removing the visual information (eyes closed) than when reducing proprioceptive feedback (soft surface). There is scarce literature about the effects of chronotype, circadian patterns and chronic sleep deprivation, a frequent problem, on balance control; however they consistently indicate that there is an relationship between them. Most of the studies only consider one-night (acute) sleep deprivation without monitoring prior sleep conditions and the circadian rhythm phase of the participants. However, a few studies indicated that these factors must be considered. Significance These results suggest that the sleep conditions of a subject should be considered for several days prior to balance control tests. Therefore, we propose a revision of current postural measurement protocols to include sleep assessment, such as sleep quality questionnaires or actimetry, and to consider the circadian rhythm of the participants to plan the hour of the tests.
Relationship Between Hypertension and Cognitive Function in an Elderly Population: A Population-Based Study in Rural Northern China

The burden of cognitive impairment and dementia is particularly severe in low- and middle-income countries. Although hypertension is an important risk factor for cognitive impairment, the influence of different hypertension classification on cognitive impairment remains controversial. To explore the impact of hypertension and hypertension classification on cognitive function, this study was based on a low-income population aged over 60 years in northern China. This population-based, cross-sectional study was conducted from April 2014 to January 2015 in rural areas of Tianjin, China. A total of 1,171 participants aged ≥ 60 years were included. Participants were interviewed by professional researchers face-to-face, using the pre-designed questionnaire. Cognitive function was assessed using the Mini-mental State Examination (MMSE). Multivariate regression analysis was used to calculate the odds ratio (OR) value. There was a significant association between hypertension and cognitive impairment (OR, 1.415; 95% CI: 1.005–1.992; P = 0.047) and a significant positive association between stage 3 hypertension (OR, 1.734; 95% CI: 1.131–2.656; P = 0.012) and the prevalence of cognitive impairment. To prevent dementia, clinicians should consider the cognitive function and blood pressure control of low-income individuals aged over 60 years with hypertension in northern China, especially those with stage 3 hypertension. In addition, the inconsistent effects of blood pressure on different cognitive functions should also be considered; special attention should be paid to orientation and concentration.
Vestibular Stimulation Causes Contraction of Subjective Time

As the cerebellum is involved in vestibular and time-keeping processes, we asked if the latter are related. We conducted three experiments to investigate the effects of vestibular stimulation on temporal processing of supra-second durations. In Experiment 1, subjects had to perform temporal productions of 10- and 15-s intervals either standing on both feet or while being engaged in the difficult balancing task of standing on one foot with their eyes closed (or open for control purposes). In Experiment 2, participants were required to produce intervals of 5, 10, 15, and 20 s while standing on both feet with their eyes open or closed, which constituted an easier balancing task. In Experiment 3, we removed the active balancing; temporal productions of the same four durations had to be performed with the eyes open or closed during the passive vestibular stimulation induced by the oscillatory movements of a swing. Participants produced longer intervals when their eyes were closed, but active balancing was not the culprit. On the contrary, temporal over-production was particularly pronounced during the passive vestibular stimulation brought about by the swing movements. Taken together, the experiments demonstrate that the contraction of the subjective time during balancing tasks with closed eyes is most likely of vestibular origin.
Deep Learning-Based Protein Features Predict Overall Survival and Chemotherapy Benefit in Gastric Cancer

Gastric cancer (GC) is one of the most common malignant tumors with a high mortality rate worldwide and lacks effective methods for prognosis prediction. Postoperative adjuvant chemotherapy is the first-line treatment for advanced gastric cancer, but only a subgroup of patients benefits from it. Here, we used 833 formalin-fixed, paraffin-embedded resected tumor samples from patients with TNM stage II/III GC and established a proteomic subtyping workflow using 100 deep-learned features. Two proteomic subtypes (S-I and S-II) with overall survival differences were identified. S-I has a better survival rate and is sensitive to chemotherapy. Patients in the S-I who received adjuvant chemotherapy had a significant improvement in the 5-year overall survival rate compared with patients who received surgery alone (65.3% vs 52.6%; log-rank P = 0.014), but no improvement was observed in the S-II (54% vs 51%; log-rank P = 0.96). These results were verified in an independent validation set. Furthermore, we also evaluated the superiority and scalability of the deep learning-based workflow in cancer molecular subtyping, exhibiting its great utility and potential in prognosis prediction and therapeutic decision-making.
Transcriptomic Responses of Adult Versus Juvenile Atlantids to Ocean Acidification

Shelled holoplanktonic gastropods are among the most vulnerable calcifiers to ocean acidification. They inhabit the pelagic environment and build thin and transparent shells of aragonite, a metastable form of calcium carbonate. While shelled pteropods have received considerable attention and are widely regarded as bioindicators of ocean acidification, atlantids have been much less studied. In the open ocean, atlantids are uniquely positioned to address the effects of ocean acidification at distinct trophic levels. From juvenile to adult, they undergo dramatic metamorphosis. As adults they are predatory, feeding primarily on shelled pteropods, copepods and other zooplankton, while as juveniles they feed on algae. Here we investigated the transcriptome and the impact of a three-day CO2 exposure on the gene expression of adults of the atlantid Atlanta ariejansseni and compared these to results previously obtained from juveniles. Individuals were sampled in the Southern Subtropical Convergence Zone (Atlantic Ocean) and exposed to ocean chemistry simulating past (~mid-1960s), present (ambient) and future (2050) conditions. In adults we found that the changes in seawater chemistry had significantly affected the expression of genes involved in biomineralization and the immune response, although there were no significant differences in shell growth between the three conditions. In contrast, juveniles experienced substantial changes in shell growth and a broader transcriptomic response. In adults, 1170 genes had the same direction of expression in the past and future treatments when compared to the ambient. Overall, this type of response was more common in adults (8.6% of all the genes) than in juveniles (3.9%), whereas a linear response with decreasing pH was more common in juveniles (7.7%) than in adults (4.5%). Taken together, these results suggest that juveniles are more sensitive to increased acidification than adults. However, experimental limitations including short incubation times, one carboy used for each treatment and two replicates for transcriptome analysis, require us to be cautious about these conclusions. We show that distinct transcriptome profiles characterize the two life stages, with less than 50% of shared transcripts. This study provides an initial framework to understand how ocean acidification may affect the molecular and calcification responses of adult and juvenile atlantids.