Miracle-dz/UniFAR-FTUs huggingface dataset:
Neuronal Activity Distributed in Multiple Cortical Areas during Voluntary Control of the Native Arm or a Brain-Computer Interface

Abstract Voluntary control of visually-guided upper extremity movements involves neuronal activity in multiple areas of the cerebral cortex. Studies of brain-computer interfaces (BCIs) that use spike recordings for input, however, have focused largely on activity in the region from which those neurons that directly control the BCI, which we call BCI units, are recorded. We hypothesized that just as voluntary control of the arm and hand involves activity in multiple cortical areas, so does voluntary control of a BCI. In two subjects (Macaca mulatta) performing a center-out task both with a hand-held joystick and with a BCI directly controlled by four primary motor cortex (M1) BCI units, we recorded the activity of other, non-BCI units in M1, dorsal premotor cortex (PMd) and ventral premotor cortex (PMv), primary somatosensory cortex (S1), dorsal posterior parietal cortex (dPPC), and the anterior intraparietal area (AIP). In most of these areas, non-BCI units were active in similar percentages and at similar modulation depths during both joystick and BCI trials. Both BCI and non-BCI units showed changes in preferred direction (PD). Additionally, the prevalence of effective connectivity between BCI and non-BCI units was similar during both tasks. The subject with better BCI performance showed increased percentages of modulated non-BCI units with increased modulation depth and increased effective connectivity during BCI as compared with joystick trials; such increases were not found in the subject with poorer BCI performance. During voluntary, closed-loop control, non-BCI units in a given cortical area may function similarly whether the effector is the native upper extremity or a BCI-controlled device.
Coding Methods to Evaluate Patient-Centered Interactions.

In a recent issue of Psychosomatic Medicine, Boucher et al. (1) report a systematic review of assessment tools for evaluating physicians’ communication skills. They found 45 different assessment tools but were concerned that most were poorly validated. They wisely advised the need for more rigorous research. We were concerned, however, to find that Boucher et al. had omitted the following recent articles of ours from rigorous, controlled research. They were coding methods that evaluated physicians for their communication skills regarding the following:
Relations of Mindfulness and Illness Acceptance With Psychosocial Functioning in Patients With Metastatic Breast Cancer and Caregivers.

OBJECTIVES To examine relationships in mindfulness and illness acceptance and psychosocial functioning in patients with metastatic breast cancer and their family caregivers. SAMPLE & SETTING 33 dyads from an academic cancer center in the United States. METHODS & VARIABLES Participants completed questionnaires on mindfulness, illness acceptance, relationship quality, anxiety, and depressive symptoms. Dyadic, cross-sectional data were analyzed using actor-partner interdependence models. RESULTS Greater nonjudging, acting with awareness, and illness acceptance among caregivers were associated with patients' and caregivers' perceptions of better relationship quality. Higher levels of these processes were associated with reduced anxiety and depressive symptoms in patients and caregivers. IMPLICATIONS FOR NURSING Aspects of mindfulness and illness acceptance in dyads confer benefits that are primarily intrapersonal in nature. Nurses may consider introducing mindfulness and acceptance-based interventions to patients and caregivers with adjustment difficulties.
Particle size and substrate wettability dependent patterns in dried pendant drops

The particle laden sessile drops when dried on solid surfaces under certain conditions leave a deposit pattern wherein all the particles are confined to a narrow region close to the edge of the deposit. Such patterns which often form when coffee drops dry are referred to as the coffee ring patterns or the coffee stains. Recent research points to the formation of intriguing patterns when colloidal particle laden drops are dried in configurations other than sessile mode. In this article, the combined effect of particle size and wettability of the substrate on the patterns formed by drying drops in sessile and pendant configurations is investigated via experiments. Our results demonstrate a transition from coffee ring to central dome-like deposit morphology with decrease in wettability of the substrates when drops containing 3 μm diameter particles are dried in pendent mode. A similar transition in the deposit morphology is observed with increase in the diameter of the particles in pendant drops dried on substrates of near neutral wettability (θ = 86 ± 3°). The influence of particles size, substrate wettability and drop configuration on the kinetics of deposition of particles at the three phase contact line will also be discussed. We compare our experimental observations with particle based simulations wherein the dried patterns are generated by accounting for three particle transport modes, namely, advective particle transport resulting from capillary flow, gravity driven settling of particles and particle capture by descending interface.
Benchmarking DNA methylation assays in a reef‐building coral

Interrogation of chromatin modifications, such as DNA methylation, has the potential to improve forecasting and conservation of marine ecosystems. The standard method for assaying DNA methylation (whole genome bisulphite sequencing), however, is currently too costly to apply at the scales required for ecological research. Here, we evaluate different methods for measuring DNA methylation for ecological epigenetics. We compare whole genome bisulphite sequencing (WGBS) with methylated CpG binding domain sequencing (MBD‐seq), and a modified version of MethylRAD we term methylation‐dependent restriction site‐associated DNA sequencing (mdRAD). We evaluate these three assays in measuring variation in methylation across the genome, between genotypes, and between polyp types in the reef‐building coral Acropora millepora. We find that all three assays measure absolute methylation levels similarly for gene bodies (gbM), as well as exons and 1 Kb windows with a minimum Pearson correlation 0.66. Differential gbM estimates were less correlated, but still concurrent across assays. We conclude that MBD‐seq and mdRAD are reliable and cost‐effective alternatives to WGBS. The considerably lower sequencing effort required for mdRAD to produce comparable methylation estimates makes it particularly useful for ecological epigenetics.
Evaluation of 3D PLLA scaffolds coated with nano-thick collagen as carrier for hepatocytes.

Orthotopic liver transplantation is presently the most effectual method for the treatment of end-stage liver diseases. Though, one major issue is the restricted number of donor organs that are accessible. Hence, liver tissue engineering is under investigation with the goal of restoring liver functions. In this study, we investigated 3D porous scaffolds made of PLLA coated with a nano thick collagen layer (matrices). Primary rat dermal fibroblasts were used in a first study phase to check matrices' cytocompatibility. More than 70% of seeded cells could adhere and remain viable 24 and 48 hours after the seeding. To test the suitability of the matrices for human primary hepatocytes, HepaRG cells were seeded and analyzed for viability, adhesion rate, and functionality such as albumin secretion. About 80% of seeded HepaRG adhered to the scaffolds remaining viable up to 72 hours. Cells were homogeneously distributed in the entire scaffold with albumin secretion increasing with time. Our results indicate that PLLA collagen-coated matrices allow hepatocytes attachment and distribution throughout the 3D structure, as well as support cell functionality. Such matrices have been applied in our clinical phase II trial. Functional hepatocytes were successfully implanted in patients suffering from liver-cirrhosis with higher cell numbers and adhesions rate compared to our previous trial with the first matrix type and a general improvement in clinical condition.
A PRACTICAL GUIDE TO OPTIMIZING THE BENEFITS OF POST-STROKE SPASTICITY INTERVENTIONS WITH BOTULINUM TOXIN A: AN INTERNATIONAL GROUP CONSENSUS

This consensus paper is derived from a meeting of an international group of 19 neurological rehabilitation specialists with a combined experience of more than 250 years (range 4–25 years; mean 14.1 years) in treating post-stroke spasticity with botulinum toxin A. The group undertook critical assessments of some recurring practical challenges, not yet addressed in guidelines, through an extensive literature search. They then discussed the results in the light of their individual clinical experience and developed consensus statements to present to the wider community who treat such patients. The analysis provides a comprehensive overview of treatment with botulinum toxin A, including the use of adjunctive therapies, within a multidisciplinary context, and is aimed at practicing clinicians who treat patients with post-stroke spasticity and require further practical guidance on the use of botulinum toxin A. This paper does not replicate information published elsewhere, but instead aims to provide practical advice to help optimize the use of botulinum toxin A and maximize clinical outcomes. The recommendations for each topic are summarized in a series of statements. Where published high-quality evidence exists, the recommendations reflect this. However, where evidence is not yet conclusive, the group members issued statements and, in some cases, made recommendations based on their clinical experience. LAY ABSTRACT A group of doctors from around the world, who are experts in treating muscle stiffness and spasm (also called spasticity), reviewed the current scientific evidence supporting the effectiveness of using botulinum toxin injections in treatment of spasticity that results from a stroke. When evidence is not available, they discussed and agreed on the best way to treat spasticity using botulinum toxin. The recommendations made by these expert doctors can be used by less-experienced doctors as a guide to how best to use botulinum toxin injection in treating spasticity after a stroke.
Parallel ddRAD and Genome Skimming Analyses Reveal a Radiative and Reticulate Evolutionary History of the Temperate Bamboos

Abstract Rapid evolutionary radiations are among the most challenging phylogenetic problems, wherein different types of data (e.g., morphology and molecular) or genetic markers (e.g., nuclear and organelle) often yield inconsistent results. The tribe Arundinarieae, that is, the temperate bamboos, is a clade of tetraploid originated 22 Ma and subsequently radiated in East Asia. Previous studies of Arundinarieae have found conflicting relationships and/or low support. Here, we obtain nuclear markers from ddRAD data for 213 Arundinarieae taxa and parallel sampling of chloroplast genomes from genome skimming for 147 taxa. We first assess the feasibility of using ddRAD-seq data for phylogenetic estimates of paleopolyploid and rapidly radiated lineages, optimize clustering thresholds, and analysis workflow for orthology identification. Reference-based ddRAD data assembly approaches perform well and yield strongly supported relationships that are generally concordant with morphology-based taxonomy. We recover five major lineages, two of which are notable (the pachymorph and leptomorph lineages), in that they correspond with distinct rhizome morphologies. By contrast, the phylogeny from chloroplast genomes differed significantly. Based on multiple lines of evidence, the ddRAD tree is favored as the best species tree estimation for temperate bamboos. Using a time-calibrated ddRAD tree, we find that Arundinarieae diversified rapidly around the mid-Miocene corresponding with intensification of the East Asian monsoon and the evolution of key innovations including the leptomorph rhizomes. Our results provide a highly resolved phylogeny of Arundinarieae, shed new light on the radiation and reticulate evolutionary history of this tribe, and provide an empirical example for the study of recalcitrant plant radiations. [Arundinarieae; ddRAD; paleopolyploid; genome skimming; rapid diversification; incongruence. ]
Six Months of Hybrid Closed-Loop Versus Manual Insulin Delivery With Fingerprick Blood Glucose Monitoring in Adults With Type 1 Diabetes: A Randomized, Controlled Trial

OBJECTIVE To investigate glycemic and psychosocial outcomes with hybrid closed-loop (HCL) versus user-determined insulin dosing with multiple daily injections (MDI) or insulin pump (i.e., standard therapy for most adults with type 1 diabetes). RESEARCH DESIGN AND METHODS Adults with type 1 diabetes using MDI or insulin pump without continuous glucose monitoring (CGM) were randomized to 26 weeks of HCL (Medtronic 670G) or continuation of current therapy. The primary outcome was masked CGM time in range (TIR; 70–180 mg/dL) during the final 3 weeks. RESULTS Participants were randomized to HCL (n = 61) or control (n = 59). Baseline mean (SD) age was 44.2 (11.7) years, HbA1c was 7.4% (0.9%) (57 [10] mmol/mol), 53% were women, and 51% used MDI. HCL TIR increased from (baseline) 55% (13%) to (26 weeks) 70% (10%) with the control group unchanged: (baseline) 55% (12%) and (26 weeks) 55% (13%) (difference 15% [95% CI 11, 19]; P < 0.0001). For HCL, HbA1c was lower (median [95% CI] difference −0.4% [−0.6, −0.2]; −4 mmol/mol [−7, −2]; P < 0.0001) and diabetes-specific positive well-being was higher (difference 1.2 [95% CI 0.4, 1.9]; P < 0.0048) without a deterioration in diabetes distress, perceived sleep quality, or cognition. Seventeen (9 device-related) versus 13 serious adverse events occurred in the HCL and control groups, respectively. CONCLUSIONS In adults with type 1 diabetes, 26 weeks of HCL improved TIR, HbA1c, and their sense of satisfaction from managing their diabetes compared with those continuing with user-determined insulin dosing and self-monitoring of blood glucose. For most people living with type 1 diabetes globally, this trial demonstrates that HCL is feasible, acceptable, and advantageous.
Genome-wide association of phenotypes based on clustering patterns of hand osteoarthritis identify WNT9A as novel osteoarthritis gene

Background Despite recent advances in the understanding of the genetic architecture of osteoarthritis (OA), only two genetic loci have been identified for OA of the hand, in part explained by the complexity of the different hand joints and heterogeneity of OA pathology. Methods We used data from the Rotterdam Study (RSI, RSII and RSIII) to create three hand OA phenotypes based on clustering patterns of radiographic OA severity to increase power in our modest discovery genome-wide association studies in the RS (n=8700), and sought replication in an independent cohort, the Framingham Heart Study (n=1203). We used multiple approaches that leverage different levels of information and functional data to further investigate the underlying biological mechanisms and candidate genes for replicated loci. We also attempted to replicate known OA loci at other joint sites, including the hips and knees. Results We found two novel genome-wide significant loci for OA in the thumb joints. We identified WNT9A as a possible novel causal gene involved in OA pathogenesis. Furthermore, several previously identified genetic loci for OA seem to confer risk for OA across multiple joints: TGFa, RUNX2, COL27A1, ASTN2, IL11 and GDF5 loci. Conclusions We identified a robust novel genetic locus for hand OA on chromosome 1, of which WNT9A is the most likely causal gene. In addition, multiple genetic loci were identified to be associated with OA across multiple joints. Our study confirms the potential for novel insight into the genetic architecture of OA by using biologically meaningful stratified phenotypes.
RepoMan stimulates the chromosome-dependent pathway of microtubule assembly

ABSTRACT RepoMan is a chromosome-associated scaffold protein that integrates signaling of multiple kinases and phosphatases to coordinate spindle-kinetochore interactions, chromosome (de)condensation and nuclear envelope (dis)assembly during mitosis. Another key mitotic event is the assembly of a microtubule-based spindle, which involves redundant pathways emanating from the centrosomes, microtubules and chromosomes. Here we describe a novel mitotic function of RepoMan in regulating chromosome-dependent microtubule assembly. At limiting concentrations of microtubule-destabilizing agents, RepoMan-depleted cells showed enhanced chromosome clustering. This clustering was completely dependent on the partial inhibition of microtubule growth originating from the chromosome-dependent pathway. We also demonstrated that RepoMan interacts with prime regulators of the chromosome-dependent spindle assembly such as NuSAP1, NuMA, and TPX2. In addition, RepoMan was required to enable or maintain phosphorylation of NuSAP1 at CDK sites, thereby enabling activation of NuSAP1 through dissociation of inhibitory importin β/7. Our data identify RepoMan as an enhancer of microtubule assembly at chromosomes.
The combined effects of probiotics and restricted calorie diet on the anthropometric indices, eating behavior, and hormone levels of obese women with food addiction: a randomized clinical trial

ABSTRACT Background and aim Food addiction (FA) is an important contributor to obesity. Alterations in gut microbiota (GM) diversity and composition have also been proposed to play a pivotal role in obesity pathogenesis. This trial aimed to assess the effects of probiotic supplementation on the anthropometric indices, eating behavior, and hormone levels of obese women with FA Methods This randomized, double-blind, placebo-controlled clinical trial was conducted among obese women with FA. Participants (n = 62) received a restricted calorie diet (RCD) plus either probiotic, or placebo for 12 weeks. Anthropometric measurements, biochemical markers, eating behavior and appetite were assessed during the study period. Results Probiotics administration significantly reduced weight, body mass index (BMI), waist circumference (WC), waist to hip ratio (WHR), body fat percentage (BFP), and trunk fat percentage (TFP) compared to the placebo group (p < 0.001). Also, a significant improvement was observed in eating behavior in the probiotic group compared to the placebo group (p < 0.001). Serum levels of oxytocin increased and NPY decreased significantly in the probiotic group compared to the placebo group (p = 0.02, p = 0.002, respectively). Moreover, leptin level significantly decreased in the probiotic group compared to the baseline values (p < 0.001), while probiotics did not cause a greater significant reduction in leptin level, compared to the placebo group. Conclusion Multi-probiotic supplementation may have beneficial effects on anthropometric indices, eating behavior, and some appetite-regulating hormones in obese women with FA. Trial registration: Iranian Registry of Clinical Trials identifier: IRCT20131228015968N5.
Why thermal conductivity of CaO is lower than that of CaS: a study from the perspective of phonon splitting of optical mode

Generally speaking, for materials with the same structure, the thermal conductivity is higher for lighter atomic masses. However, we found that the thermal conductivity of CaO is lower than that of CaS, despite the lighter atomic mass of O than S. To uncover the underlying physical mechanisms, the thermal conductivity of CaM (M = O, S, Se, Te) and the corresponding response to strain is investigated by performing first-principles calculations along with the phonon Boltzmann transport equation. For unstrained system, the order of thermal conductivity is CaS > CaO > CaSe > CaTe. This order remains unchanged in the strain range of −2% to 5%. When the compressive strain is larger than 2%, the thermal conductivity of CaO surpasses that of CaS and becomes the highest thermal conductivity material among the four compounds. By analyzing the mode-dependent phonon properties, the phonon lifetime is found to be dominant over other influential factors and leads to the disparate response of thermal conductivity under strain. Moreover, the changing trend of three-phonon scattering phase space is consistent with that of phonon lifetime, which is directly correlated to the phonon frequency gap induced by the LO-TO splitting. The variation of Born effective charge is found to be opposite for CaM. The Born effective charge of CaO decreases with tensile strain increasing, demonstrating stronger charge delocalization and lower ionicity, while the Born effective charges of CaS, CaSe, and CaTe show a dramatic increase. Such variation indicates that the bonding nature can be effectively tuned by external strain, thus affecting the phonon anharmonic properties and thermal conductivity. The difference of bonding nature is further confirmed by the band structure. Our results show that the bonding nature of CaM can be modulated by external strain and leads to disparate strain dependent thermal conductivity.
THE ROLE OF TAXIMETRICS IN ANGIOSPERM TAXONOMY

SUMMARY This paper indicates one way in which taximetrics can contribute to the taxonomic work currently being carried out in herbaria and universities. Taximetric and orthodox studies of African species of Crotalaria L. (Leguminosae) carried out separately by the two authors produced classifications which were similar in essential features. It was possible to resolve twenty discrepancies between the two classifications which varied from the delimitation of major groupings to the placing of individual species and the treatment of outliers. In some cases Polhill's orthodox scheme was upheld and in others Bisby's taximetric results provided evidence for making improvements. The outcome was an amended classification for which the nomenclatural changes are set out. The authors suggest that parallel studies of this sort may prove one of the most useful contributions that taximetrics can make. Not only is maximum use made of both types of procedure but also such studies contribute to knowledge of the relative performance of the taximetric and orthodox procedures. Only when there is much more confidence and experience in using taximetric procedures will it be useful to apply them in situations where there is no immediate check from orthodox work.