Miracle-dz/UniFAR-FTUs huggingface dataset:
Gray Matter Abnormalities in Type 1 and Type 2 Diabetes: A Dual Disorder ALE Quantification

Aims/hypothesis: Diabetes mellitus (DM) is associated with comorbid brain disorders. Neuroimaging studies in DM revealed neuronal degeneration in several cortical and subcortical brain regions. Previous studies indicate more pronounced brain alterations in type 2 diabetes mellitus (T2DM) than in type 1 diabetes mellitus (T1DM). However, a comparison of both types of DM in a single analysis has not been done so far. The aim of this meta-analysis was to conduct an unbiased objective investigation of neuroanatomical differences in DM by combining voxel-based morphometry (VBM) studies of T1DM and T2DM using dual disorder anatomical likelihood estimation (ALE) quantification. Methods: PubMed, Web of Science and Medline were systematically searched for publications until June 15, 2020. VBM studies comparing gray matter volume (GMV) differences between DM patients and controls at the whole-brain level were included. Study coordinates were entered into the ALE meta-analysis to investigate the extent to which T1DM, T2DM, or both conditions contribute to gray matter volume differences compared to controls. Results: Twenty studies (comprising of 1,175 patients matched with 1,013 controls) were included, with seven studies on GMV alterations in T1DM and 13 studies on GMV alterations in T2DM. ALE analysis revealed seven clusters of significantly lower GMV in T1DM and T2DM patients relative to controls across studies. Both DM subtypes showed GMV reductions in the left caudate, right superior temporal lobe, and left cuneus. Conversely, GMV reductions associated exclusively with T2DM (>99% contribution) were found in the left cingulate, right posterior lobe, right caudate and left occipital lobe. Meta-regression revealed no significant influence of study size, disease duration, and HbA1c values. Conclusions/interpretation: Our findings suggest a more pronounced gray matter atrophy in T2DM compared to T1DM. The increased risk of microvascular or macrovascular complications, as well as the disease-specific pathology of T2DM may contribute to observed GMV reductions. Systematic Review Registration: [PROSPERO], identifier [CRD42020142525].
Novel Volumetric and Surface-Based Magnetic Resonance Indices of the Aging Brain – Does Male and Female Brain Age in the Same Way?

Introduction: Novel post-processing methods allow not only for assessment of brain volumetry or cortical thickness based on magnetic resonance imaging (MRI) but also for more detailed analysis of cortical shape and complexity using parameters such as sulcal depth, gyrification index, or fractal dimension. The aim of this study was to analyze changes in brain volumetry and other cortical indices during aging in men and women. Material and Methods: Material consisted of 697 healthy volunteers (aged 38–80 years; M/F, 264/443) who underwent brain MRI using a 1.5-T scanner. Voxel-based volumetry of total gray matter (GM), white matter (WM), and cerebrospinal fluid (CSF) was performed followed by assessment of cortical parameters [cortical thickness (CT), sulcal depth (SD), gyrification index (GI), and fractal dimension (FD)] in 150 atlas locations using surface-based morphometry with a region-based approach. All parameters were compared among seven age groups (grouped every 5 years) separately for men and women. Additionally, percentile curves for men and women were provided for total volumes of GM, WM, and CSF. Results: In men and women, a decrease in GM and WM volumes and an increase in CSF volume seem to progress slowly since the age of 45. In men, significant GM and WM loss as well as CSF increase start above 55 years of age, while in women, significant GM loss starts above 50 and significant WM loss as well as CSF increase above 60. CT was found to significantly decrease with aging in 39% of locations in women and in 36% of locations in men, SD was found to increase in 13.5% of locations in women and in 1.3% of locations in men, GI was decreased in 3.4% of locations in women and in 2.0% of locations in men, and FD was changed in 2.7% of locations in women compared to 2.0% in men. Conclusions: Male and female brains start aging at the similar age of 45. Compared to men, in women, the cortex is affected earlier and in the more complex pattern regarding not only cortical loss but also other alterations within the cortical shape, with relatively longer sparing of WM volume.
Neural Evidence of Language Membership Control in Bilingual Word Recognition: An fMRI Study of Cognate Processing in Chinese–Japanese Bilinguals

This study aims to examine the neural mechanisms of resolving response competition during bilingual word recognition in the context of language intermixing. During fMRI scanning, Chinese–Japanese unbalanced bilinguals were required to perform a second-language (L2) lexical decision task composed of cognates, interlingual homographs, matched control words from both Chinese (first language) and Japanese (L2), and pseudowords. Cognate word processing showed longer reaction times and greater activation in the supplementary motor area (SMA) than L2 control word processing. In light of the orthographic and semantic overlap of cognates, these results reflect the cognitive processing involved in resolving response conflicts enhanced by the language membership of non-target language during bilingual word recognition. A significant effect of L2 proficiency was also observed only in the SMA, which is associated with the task decision system. This finding supports the bottom-up process in the BIA+ model and the Multilink model. The task/decision system receives the information from the word identification system, making appropriate responses during bilingual word recognition.
Dynamics of Soil Bacterial and Fungal Communities During the Secondary Succession Following Swidden Agriculture IN Lowland Forests

Elucidating dynamics of soil microbial communities after disturbance is crucial for understanding ecosystem restoration and sustainability. However, despite the widespread practice of swidden agriculture in tropical forests, knowledge about microbial community succession in this system is limited. Here, amplicon sequencing was used to investigate effects of soil ages (spanning at least 60 years) after disturbance, geographic distance (from 0.1 to 10 km) and edaphic property gradients (soil pH, conductivity, C, N, P, Ca, Mg, and K), on soil bacterial and fungal communities along a chronosequence of sites representing the spontaneous succession following swidden agriculture in lowland forests in Papua New Guinea. During succession, bacterial communities (OTU level) as well as its abundant (OTU with relative abundance > 0.5%) and rare (<0.05%) subcommunities, showed less variation but more stage-dependent patterns than those of fungi. Fungal community dynamics were significantly associated only with geographic distance, whereas bacterial community dynamics were significantly associated with edaphic factors and geographic distance. During succession, more OTUs were consistently abundant (n = 12) or rare (n = 653) for bacteria than fungi (abundant = 6, rare = 5), indicating bacteria were more tolerant than fungi to environmental gradients. Rare taxa showed higher successional dynamics than abundant taxa, and rare bacteria (mainly from Actinobacteria, Proteobacteria, Acidobacteria, and Verrucomicrobia) largely accounted for bacterial community development and niche differentiation during succession.
Brain-Computer Interface Coupled to a Robotic Hand Orthosis for Stroke Patients’ Neurorehabilitation: A Crossover Feasibility Study

Brain-Computer Interfaces (BCI) coupled to robotic assistive devices have shown promise for the rehabilitation of stroke patients. However, little has been reported that compares the clinical and physiological effects of a BCI intervention for upper limb stroke rehabilitation with those of conventional therapy. This study assesses the feasibility of an intervention with a BCI based on electroencephalography (EEG) coupled to a robotic hand orthosis for upper limb stroke rehabilitation and compares its outcomes to conventional therapy. Seven subacute and three chronic stroke patients (M = 59.9 ± 12.8) with severe upper limb impairment were recruited in a crossover feasibility study to receive 1 month of BCI therapy and 1 month of conventional therapy in random order. The outcome measures were comprised of: Fugl-Meyer Assessment of the Upper Extremity (FMA-UE), Action Research Arm Test (ARAT), motor evoked potentials elicited by transcranial magnetic stimulation (TMS), hand dynamometry, and EEG. Additionally, BCI performance and user experience were measured. All measurements were acquired before and after each intervention. FMA-UE and ARAT after BCI (23.1 ± 16; 8.4 ± 10) and after conventional therapy (21.9 ± 15; 8.7 ± 11) were significantly higher (p < 0.017) compared to baseline (17.5 ± 15; 4.3 ± 6) but were similar between therapies (p > 0.017). Via TMS, corticospinal tract integrity could be assessed in the affected hemisphere of three patients at baseline, in five after BCI, and four after conventional therapy. While no significant difference (p > 0.05) was found in patients’ affected hand strength, it was higher after the BCI therapy. EEG cortical activations were significantly higher over motor and non-motor regions after both therapies (p < 0.017). System performance increased across BCI sessions, from 54 (50, 70%) to 72% (56, 83%). Patients reported moderate mental workloads and excellent usability with the BCI. Outcome measurements implied that a BCI intervention using a robotic hand orthosis as feedback has the potential to elicit neuroplasticity-related mechanisms, similar to those observed during conventional therapy, even in a group of severely impaired stroke patients. Therefore, the proposed BCI system could be a suitable therapy option and will be further assessed in clinical trials.
The Effects of In Ovo Injection of Synbiotics on the Early Growth Performance and Intestinal Health of Chicks

In this study, the effects of synbiotic inclusion at the intra-amniotic stage in layer chicks were evaluated with different parameters, such as performance, immunological function, intestinal development, and cecal microflora content. A total of 1,200 eggs with fertile embryos were allocated into four treatment groups. For every treatment, five replicates were used, and 60 eggs were included in each replicate. The following four treatment groups were established: the non-injected group, 0.9% physiological saline injection (saline) group, 1 × 106 CFU/egg Lactobacillus plantarum injection (probiotic) group, and 1 × 106 CFU/egg L. plantarum + 2 mg/egg Astragalus polysaccharide injection (synbiotic) group. In ovo injection was carried out at 18.5 days of incubation. The results showed that in ovo injection of probiotics or synbiotics did not affect the hatching or growth performance of the chicks but significantly increased their feed intake (FI), body weight (BW), and the feed conversion ratio (FCR). Additionally, in ovo injection of synbiotics enhanced the levels of serum interleukin-2 (IL-2), interferon-γ (IFN-γ), and secretory immunoglobulin A (SIgA) in intestinal lavage fluid and the histomorphological development of the small intestine. Our results also indicated that intra-amniotic synbiotic injection significantly increased Lactobacillus and Bifidobacterium colonization while decreasing the relative abundance of Escherichia coli in the chicken cecum (P < 0.05). In summary, in ovo injection of synbiotics had positive impacts on the performance, immunological function, gut development, and microbiota of growing chicks.
Identifying the ‘Active Ingredients' of an Effective Psychological Intervention to Reduce Fear of Cancer Recurrence: A Process Evaluation

Purpose: Psychological interventions targeting fear of cancer recurrence (FCR) are effective in reducing fear and distress. Process evaluations are an important, yet scarce adjunct to published intervention trials, despite their utility in guiding the interpretation of study outcomes and optimizing intervention design for broader implementation. Accordingly, this paper reports the findings of a process evaluation conducted alongside a randomized controlled trial of a psychological intervention for melanoma patients. Methods: Men and women with a history of Stage 0–II melanoma at high-risk of developing new primary disease were recruited via High Risk Melanoma Clinics across Sydney, Australia and randomly allocated to receive the psychological intervention (n = 80) or usual care (n = 84). Intervention participants received a tailored psycho-educational resource and three individual psychotherapeutic sessions delivered via telehealth. Qualitative and quantitative data on intervention context, processes, and delivery (reach, dose, and fidelity), and mechanisms of impact (participant responses, moderators of outcome) were collected from a range of sources, including participant surveys, psychotherapeutic session audio-recordings, and clinical records. Results: Almost all participants reported using the psycho-educational resource (97%), received all intended psychotherapy sessions (96%), and reported high satisfaction with both intervention components. Over 80% of participants would recommend the intervention to others, and a small proportion (4%) found discussion of melanoma-related experiences confronting. Perceived benefits included enhanced doctor-patient communication, talking more openly with family members about melanoma, and improved coping. Of potential moderators, only higher FCR severity at baseline (pre-intervention) was associated with greater reductions in FCR severity (primary outcome) at 6-month follow-up (primary endpoint). Conclusions: Findings support the acceptability and feasibility of a psychological intervention to reduce FCR amongst individuals at high risk of developing another melanoma. Implementation into routine melanoma care is an imperative next step, with FCR screening recommended to identify those most likely to derive the greatest psychological benefit.
Blood Flow Within Bioengineered 3D Printed Vascular Constructs Using the Porcine Model

Recently developed biofabrication technologies are enabling the production of three-dimensional engineered tissues containing vascular networks which can deliver oxygen and nutrients across large tissue volumes. Tissues at this scale show promise for eventual regenerative medicine applications; however, the implantation and integration of these constructs in vivo remains poorly studied. Here, we introduce a surgical model for implantation and direct in-line vascular connection of 3D printed hydrogels in a porcine arteriovenous shunt configuration. Utilizing perfusable poly(ethylene glycol) diacrylate (PEGDA) hydrogels fabricated through projection stereolithography, we first optimized the implantation procedure in deceased piglets. Subsequently, we utilized the arteriovenous shunt model to evaluate blood flow through implanted PEGDA hydrogels in non-survivable studies. Connections between the host femoral artery and vein were robust and the patterned vascular channels withstood arterial pressure, permitting blood flow for 6 h. Our study demonstrates rapid prototyping of a biocompatible and perfusable hydrogel that can be implanted in vivo as a porcine arteriovenous shunt, suggesting a viable surgical approach for in-line implantation of bioprinted tissues, along with design considerations for future in vivo studies. We further envision that this surgical model may be broadly applicable for assessing whether biomaterials optimized for 3D printing and cell function can also withstand vascular cannulation and arterial blood pressure. This provides a crucial step toward generated transplantable engineered organs, demonstrating successful implantation of engineered tissues within host vasculature.
Classifying Vulnerability to Sleep Deprivation Using Resting-State Functional MRI Graph Theory Metrics

Sleep deprivation (SD) has become very common in contemporary society, where people work around the clock. SD-induced cognitive deficits show large inter-individual differences and are trait-like with known neural correlates. However, few studies have used neuroimaging to predict vulnerability to SD. Here, resting state functional magnetic resonance imaging (fMRI) data and psychomotor vigilance task (PVT) data were collected from 60 healthy subjects after resting wakefulness and after one night of SD. The number of PVT lapses was then used to classify participants on the basis of whether they were vulnerable or resilient to SD. We explored the viability of graph-theory-based degree centrality to accurately classify vulnerability to SD. Compared with during resting wakefulness, widespread changes in degree centrality (DC) were found after SD, indicating significant reorganization of sleep homeostasis with respect to activity in resting state brain network architecture. Support vector machine (SVM) analysis using leave-one-out cross-validation achieved a correct classification rate of 84.75% [sensitivity 82.76%, specificity 86.67%, and area under the receiver operating characteristic curve (AUC) 0.94] for differentiating vulnerable subjects from resilient subjects. Brain areas that contributed most to the classification model were mainly located within the sensorimotor network, default mode network, and thalamus. Furthermore, we found a significantly negative correlation between changes in PVT lapses and DC in the thalamus after SD. These findings suggest that resting-state network measures combined with a machine learning algorithm could have broad potential applications in screening vulnerability to SD.
Solving the Problem of Assessing Synergy and Antagonism for Non-Traditional Dosing Curve Compounds Using the DE/ZI Method: Application to Nrf2 Activators

Multi-drug combination therapy carries significant promise for pharmacological intervention, primarily better efficacy with less toxicity and fewer side effects. However, the field lacks methodology to assess synergistic or antagonistic interactions for drugs with non-traditional dose response curves. Specifically, our goal was to assess small-molecule modulators of antioxidant response element (ARE)-driven gene expression, which is largely regulated by the Nrf2 transcription factor. Known as Nrf2 activators, this class of compounds upregulates a battery of cytoprotective genes and shows significant promise for prevention of numerous chronic diseases. For example, sulforaphane sourced from broccoli sprouts is the subject of over 70 clinical trials. Nrf2 activators generally have non-traditional dose response curves that are hormetic, or U-shaped. We introduce a method based on the principles of Loewe Additivity to assess synergism and antagonism for two compounds in combination. This method, termed Dose-Equivalence/Zero Interaction (DE/ZI), can be used with traditional Hill-slope response curves, and it also can assess interactions for compounds with non-traditional curves, using a nearest-neighbor approach. Using a Monte-Carlo method, DE/ZI generates a measure of synergy or antagonism for each dosing pair with an associated error and p-value, resulting in a 3D response surface. For the assessed Nrf2 activators, sulforaphane and di-tert-butylhydroquinone, this approach revealed synergistic interactions at higher dosing concentrations consistently across data sets and potential antagonistic interactions at lower concentrations. DE/ZI eliminates the need to determine the best fit equation for a given data set and values experimentally-derived results over formulated fits.
Evaluating Assisted Gene Flow in Marginal Populations of a High Mountain Species

Many species cannot either migrate or adapt at the rate of temperature increases due to climate warming. Therefore, they need active conservation strategies to avoid extinction. Facilitated adaptation actions, such assisted gene flow, aim at the increase of the evolutionary resilience of species affected by global change. In elevational gradients, marginal populations at the lower elevation edges are experiencing earlier snowmelt and higher temperatures, which force them to adapt to the new conditions by modifying their phenology. In this context, advancing the onset of flowering and seed germination times are crucial to ensure reproductive success and increase seedling survival prior to summer drought. Assisted gene flow may bring adaptive alleles and increase genetic diversity that can help throughout ontogeny. The main aim of this work is to assess the effects that different gene flow treatments could have on the desired trait changes in marginal populations. Accordingly, we established a common garden experiment in which we assayed four different gene flow treatments between Silene ciliata Pourr. (Caryophyllaceae) populations located in similar and different elevation edges, belonging to the same and different mountains. As a control treatment, within-population crosses of low elevation edge populations were performed. The resulting seeds were sown and the germination and flowering onset dates of the resulting plants recorded, as well as the seedling survival. Gene flow between populations falling on the same mountain and same elevation and gene flow from high-elevation populations from a different mountain to low-elevation populations advanced seed germination time with respect to control crosses. No significant effects of gene flow on seedling survival were found. All the gene flow treatments delayed the onset of flowering with respect to control crosses and this effect was more pronounced in among-mountain gene flows. The results of this study highlight two important issues that should be thoroughly studied before attempting to apply assisted gene flow in practical conservation situations. Firstly, among-populations gene flow can trigger different responses in crucial traits throughout the ontogeny of plant species. Secondly, the population provenance of gene flow is determinant and plays a significant role on the effects of gene flow.
Glycans in Virus-Host Interactions: A Structural Perspective

Many interactions between microbes and their hosts are driven or influenced by glycans, whose heterogeneous and difficult to characterize structures have led to an underappreciation of their role in these interactions compared to protein-based interactions. Glycans decorate microbe glycoproteins to enhance attachment and fusion to host cells, provide stability, and evade the host immune system. Yet, the host immune system may also target these glycans as glycoepitopes. In this review, we provide a structural perspective on the role of glycans in host-microbe interactions, focusing primarily on viral glycoproteins and their interactions with host adaptive immunity. In particular, we discuss a class of topological glycoepitopes and their interactions with topological mAbs, using the anti-HIV mAb 2G12 as the archetypical example. We further offer our view that structure-based glycan targeting strategies are ready for application to viruses beyond HIV, and present our perspective on future development in this area.