Miracle-dz/UniFAR-FTUs huggingface dataset:
Aberrant topographical organization in default-mode network in first-episode remitted geriatric depression: a graph-theoretical analysis

ABSTRACT Background: Neuroimaging studies have shown that major depressive disorder is associated with altered activity patterns of the default-mode network (DMN). In this study, we sought to investigate the topological organization of the DMN in patients with remitted geriatric depression (RGD) and whether RGD patients would be more likely to show disrupted topological configuration of the DMN during the resting-state. Methods: Thirty-three RGD patients and thirty-one healthy control participants underwent clinical and cognitive evaluations as well as resting-state functional magnetic resonance imaging scans. The functional connectivity (FC) networks were constructed by thresholding Pearson correlation metrics of the DMN regions defined by group independent component analysis, and their topological properties (e.g. small-world and network efficiency) were analyzed using graph theory-based approaches. Results: Relative to the healthy controls, the RGD patients showed decreased FC in the posterior regions of the DMN (i.e. the posterior cingulate cortex/precuneus, angular gyrus, and middle temporal gyrus). Furthermore, the RGD patients showed abnormal global topology of the DMN (i.e. increased characteristic path length and reduced global efficiency) when compared with healthy controls. Importantly, significant correlations between these network measures and cognitive performance indicated their potential use as biomarkers of cognitive dysfunction in RGD. Conclusions: The present study indicated disrupted FC and topological organization of the DMN in the context of RGD, and further implied their contribution to cognitive deficits in RGD patients.
Radical Scavenging and Anti-Inflammatory Activities of Representative Anthocyanin Groupings from Pigment-Rich Fruits and Vegetables

Anthocyanins, the naturally occurring pigments responsible for most red to blue colours of flowers, fruits and vegetables, have also attracted interest because of their potential health effects. With the aim of contributing to major insights into their structure–activity relationship (SAR), we have evaluated the radical scavenging and biological activities of selected purified anthocyanin samples (PASs) from various anthocyanin-rich plant materials: two fruits (mahaleb cherry and blackcurrant) and two vegetables (black carrot and “Sun Black” tomato), differing in anthocyanin content (ranging from 4.9 to 38.5 mg/g DW) and molecular structure of the predominant anthocyanins. PASs from the abovementioned plant materials have been evaluated for their antioxidant capacity using Trolox Equivalent Antioxidant Capacity (TEAC) and Oxygen Radical Absorbance Capacity (ORAC) assays. In human endothelial cells, we analysed the anti-inflammatory activity of different PASs by measuring their effects on the expression of endothelial adhesion molecules VCAM-1 and ICAM-1. We demonstrated that all the different PASs showed biological activity. They exhibited antioxidant capacity of different magnitude, higher for samples containing non-acylated anthocyanins (typical for fruits) compared to samples containing more complex anthocyanins acylated with cinnamic acid derivatives (typical for vegetables), even though this order was slightly reversed when ORAC assay values were expressed on a molar basis. Concordantly, PASs containing non-acylated anthocyanins reduced the expression of endothelial inflammatory antigens more than samples with aromatic acylated anthocyanins, suggesting the potential beneficial effect of structurally diverse anthocyanins in cardiovascular protection.
Adaptive weights for mass conservation in a least-squares finite element method

ABSTRACT In this paper, we develop a least-squares (LS) finite element method for the Stokes equations. The LS method uses the -norm of the residuals of the continuity equation multiplied by appropriately adjusted weights. To adjust the weight, we employ an adaptive weight iteration approach based on a residual type a posteriori error estimator for the LS functional. This LS method is applied to flows through a planar channel, lid-driven cavity flows, and flows past a transverse slot. The results demonstrate that mass conservation of the LS method in fluid simulations can be significantly improved by appropriately adjusting weights, and that this can be accomplished using low-order basis functions, without substantial complications in coding. We provide a posteriori error estimates for the linearized velocity–vorticity–pressure first-order system and show numerical results supporting the estimate. Numerical results reveal that the mass conservation constant is problem dependent.
Clinicopathological Evaluation of Chronic Traumatic Encephalopathy in Players of American Football

Importance Players of American football may be at increased risk of long-term neurological conditions, particularly chronic traumatic encephalopathy (CTE). Objective To determine the neuropathological and clinical features of deceased football players with CTE. Design, Setting, and Participants Case series of 202 football players whose brains were donated for research. Neuropathological evaluations and retrospective telephone clinical assessments (including head trauma history) with informants were performed blinded. Online questionnaires ascertained athletic and military history. Exposures Participation in American football at any level of play. Main Outcomes and Measures Neuropathological diagnoses of neurodegenerative diseases, including CTE, based on defined diagnostic criteria; CTE neuropathological severity (stages I to IV or dichotomized into mild [stages I and II] and severe [stages III and IV]); informant-reported athletic history and, for players who died in 2014 or later, clinical presentation, including behavior, mood, and cognitive symptoms and dementia. Results Among 202 deceased former football players (median age at death, 66 years [interquartile range, 47-76 years]), CTE was neuropathologically diagnosed in 177 players (87%; median age at death, 67 years [interquartile range, 52-77 years]; mean years of football participation, 15.1 [SD, 5.2]), including 0 of 2 pre–high school, 3 of 14 high school (21%), 48 of 53 college (91%), 9 of 14 semiprofessional (64%), 7 of 8 Canadian Football League (88%), and 110 of 111 National Football League (99%) players. Neuropathological severity of CTE was distributed across the highest level of play, with all 3 former high school players having mild pathology and the majority of former college (27 [56%]), semiprofessional (5 [56%]), and professional (101 [86%]) players having severe pathology. Among 27 participants with mild CTE pathology, 26 (96%) had behavioral or mood symptoms or both, 23 (85%) had cognitive symptoms, and 9 (33%) had signs of dementia. Among 84 participants with severe CTE pathology, 75 (89%) had behavioral or mood symptoms or both, 80 (95%) had cognitive symptoms, and 71 (85%) had signs of dementia. Conclusions and Relevance In a convenience sample of deceased football players who donated their brains for research, a high proportion had neuropathological evidence of CTE, suggesting that CTE may be related to prior participation in football.
The complete mitochondrial genome sequence of Cirrhinus mrigala (♀) × Labeo rohita (♂)

Abstract We cloned and sequenced the complete mitochondrial DNA (mtDNA) of Cirrhinus mrigala (♀) × Labeo rohita (♂) by PCR-based method. The total of the mtDNA was 16,595 bp. It consisted of 13 protein-coding genes, 22 tRNAs, 2 rRNA genes, and one putative control region (D-loop region). The overall base composition on strand was as follows A: 32.09%, G: 15.51%, C: 27.95%, T: 24.45%, and the A + T content 56.54%. All the protein-coding genes initiated by typical ATG codon, and ten genes ended with the complete stop codon TAA or TAG, while COII2, ND4 and Cytb genes terminated with GCC, TAT and GCT. The control region contains a thiolases active site, EGF-like domain signature and two anaphylatoxin domain signature. This mitogenome sequence data would play an important role in population genetics and phylogenetics of the hybrid fish in the Cyprinidae family.
Raman spectroscopy of transition metal dichalcogenides

Raman spectroscopy of transition metal dichalcogenides (TMDs) is reviewed based on our recent theoretical and experimental works. First, we discuss the semi-classical and quantum mechanical description for the polarization dependence of Raman spectra of TMDs in which the optical dipole transition matrix elements as a function of laser excitation energy are important for understanding the polarization dependence of the Raman intensity and Raman tensor. Overviewing the symmetry of TMDs, we discuss the dependence of the Raman spectra of TMDs on layer thickness, polarization, laser energy and the structural phase. Furthermore, we discuss the Raman spectra of twisted bilayer and heterostructures of TMDs. Finally, we give our perspectives on the Raman spectroscopy of TMDs.
Evaluation of P53 Protein Overexpression, Ki67 Proliferative Activity and Mitotic Index as Markers of Tumour Recurrence in Superficial Transitional Cell Carcinoma of the Bladder

Objectives: To confirm the interrelationship between p53, ki67, mitotic index with others known prognostic factors such us stage, grade, multifocality, tumour size, history of recurrence in transitional cell carcinoma (TCC) of the bladder and to determine the prognostic impact of p53, Ki67 and mitotic index in predicting recurrence in superficial bladder cancer.Methods: Two hundred and fourteen patients with apparently superficial TCC of the bladder underwent TURBT and the 192 histologically Ta–T1 were divided into 104 primary lesions (group 1, mean follow–up 26 months) and 88 recurrent tumours (group 2, mean follow–up 28 months). Data concerning focality, tumour size, number of recurrences and recurrence–free survival were considered in each patients. All samples were immunohistochemically stained with p53 and Ki67 monoclonal antibodies. Mitotic index (MI) was calculated on haematoxylin and eosin stained sections.Results: Recurrence–free survival was significantly lower in superficial recurrent tumours (group 2) compared with primary tumours (group 1). P53 staining was correlated with grade and stage for both 5 and 20% positivity thresholds. Ki67 and MI were significantly different over strata defined by stage, grade and focality in both patients groups but only Ki67 showed a correlation with p53 status. Recurrence–free survival could not be predicted either by p53 status or MI. A 20% cut–off level of Ki67 staining resulted a good predictor of recurrence in group 1 Ta–T1/G1–G2 tumours (p = 0.03). Only Ki67 and multifocality were found to be independent prognostic factors of recurrence in multivariate analysis. Stratifying Ta–T1/G1–G2 patients according to these variables, Ki67 provided a useful tool to predict early recurrence in monofocal lesions from both groups.Conclusions: P53 and MI despite a fairly good correlation with traditional prognostic factors in bladder TCC seem to play no role in the prediction of tumoural recurrence. A Ki67 index over 20% predicts those single well–differentiated (Ta–T1/G1–G2) tumours which are likely to recur within one year of treatment
Host‐specific associations affect the microbiome of Philornis downsi, an introduced parasite to the Galápagos Islands

The composition and diversity of bacteria forming the microbiome of parasitic organisms have implications for differential host pathogenicity and host–parasite co‐evolutionary interactions. The microbiome of pathogens can therefore have consequences that are relevant for managing disease prevalence and impact on affected hosts. Here, we investigate the microbiome of an invasive parasitic fly Philornis downsi, recently introduced to the Galápagos Islands, where it poses extinction threat to Darwin's finches and other land birds. Larvae infest nests of Darwin's finches and consume blood and tissue of developing nestlings, and have severe mortality impacts. Using 16s rRNA sequencing data, we characterize the bacterial microbiota associated with P. downsi adults and larvae sourced from four finch host species, inhabiting two islands and representing two ecologically distinct groups. We show that larval and adult microbiomes are dominated by the phyla Proteobacteria and Firmicutes, which significantly differ between life stages in their distributions. Additionally, bacterial community structure significantly differed between larvae retrieved from strictly insectivorous warbler finches (Certhidea olivacea) and those parasitizing hosts with broader dietary preferences (ground and tree finches, Geospiza and Camarhynchus spp., respectively). Finally, we found no spatial effects on the larval microbiome, as larvae feeding on the same host (ground finches) harboured similar microbiomes across islands. Our results suggest that the microbiome of P. downsi changes during its development, according to dietary composition or nutritional needs, and is significantly affected by host‐related factors during the larval stage. Unravelling the ecological significance of bacteria for this parasite will contribute to the development of novel, effective control strategies.
Radical Prostatectomy Can Provide a Cure For Well–Selected Clinical Stage T3 Prostate Cancer

Objective: Radical prostatectomy is commonly believed not to achieve the eradication of locally advanced disease. This retrospective study aimed to elucidate the role of radical prostatectomy in this condition.Methods: A retrospective study of 158 patients surgically treated for clinical stage T3N0M0 prostate cancer was undertaken. Thirty patients had postoperative hormonal treatment, rendering prostate–specific antigen (PSA) follow–up unreliable, and were considered to be progressive at 1 month. Eighteen other patients received postoperative radiotherapy. One hundred and ten patients had radical prostatectomy only. PSA–relapse–free survival was analyzed. The mean follow–up time was 30 months.Results: Seventy–nine percent of the resected specimens were pathologically T3 (pT3), and about 25% were pT3c. Thirteen percent were pT2 and 8% were pT4. Ninety–five specimens (60%) had positive surgical margins. There was poor accordance between the biopsy Gleason score and that of the specimen. A multivariate analysis showed that seminal vesicle and nodal invasion, margin status and a PSA level above 10 ng/ml were independent prognostic factors. In 47 cT3a patients with PSA <10 ng/ml, the PSA–free survival rate exceeded 70% at 24 months and the 5–year estimated PSA–free survival rate was more than 60%. Conclusions: Radical prostatectomy has a place in the treatment of clinical stage T3 prostate cancer patients with a PSA value lower than 10 ng/ml. There is a need to definitively rule out nodal or seminal vesicle invasion in order to select those patients that can benefit from surgery.
Interferon-Gamma Release Assay is Not Appropriate for the Diagnosis of Active Tuberculosis in High-Burden Tuberculosis Settings: A Retrospective Multicenter Investigation

Background: Interferon-gamma release assay (IGRA) has been used in latent tuberculosis (TB) infection and TB diagnosis, but the results from different high TB-endemic countries are different. The aim of this study was to investigate the value of IGRA in the diagnosis of active pulmonary TB (PTB) in China. Methods: We conducted a large-scale retrospective multicenter investigation to further evaluate the role of IGRA in the diagnosis of active PTB in high TB-epidemic populations and the factors affecting the performance of the assay. All patients who underwent valid T-SPOT.TB assays from December 2012 to November 2015 in six large-scale specialized TB hospitals in China and met the study criteria were retrospectively evaluated. Patients were divided into three groups: Group 1, sputum culture-positive PTB patients, confirmed by positive Mycobacterium tuberculosis sputum culture; Group 2, sputum culture-negative PTB patients; and Group 3, non-TB respiratory diseases. The medical records of all patients were collected. Chi-square tests and Fisher's exact test were used to compare categorical data. Multivariable logistic analyses were performed to evaluate the relationship between the results of T-SPOT in TB patients and other factors. Results: A total of 3082 patients for whom complete information was available were included in the investigation, including 905 sputum culture-positive PTB cases, 914 sputum culture-negative PTB cases, and 1263 non-TB respiratory disease cases. The positive rate of T-SPOT.TB was 93.3% in the culture-positive PTB group and 86.1% in the culture-negative PTB group. In the non-PTB group, the positive rate of T-SPOT.TB was 43.6%. The positive rate of T-SPOT.TB in the culture-positive PTB group was significantly higher than that in the culture-negative PTB group (&khgr;2 = 25.118, P < 0.01), which in turn was significantly higher than that in the non-TB group (&khgr;2 = 566.116, P < 0.01). The overall results were as follows: sensitivity, 89.7%; specificity, 56.37%; positive predictive value, 74.75%; negative predictive value, 79.11%; and accuracy, 76.02%. Conclusions: High false-positive rates of T-SPOT.TB assays in the non-TB group limit the usefulness as a single test to diagnose active TB in China. We highly recommend that IGRAs not be used for the diagnosis of active TB in high-burden TB settings.
Second-order BDF time approximation for Riesz space-fractional diffusion equations

ABSTRACT Second-order backward difference formula (BDF2) is considered for time approximation of Riesz space-fractional diffusion equations. The Riesz space derivative is approximated by the second-order fractional centre difference formula. To improve the computational efficiency, an alternating directional implicit scheme is also proposed for solving two-dimensional space-fractional diffusion problems. Numerical experiments are provided to verify our theory and to show the effectiveness of numerical algorithms.
Implications of the degree of controllability of controlled plants in the sense of LQR optimal control

ABSTRACT In this paper, the relationship between the degree of controllability (DOC) of controlled plants and the corresponding quadratic optimal performance index in LQR control is investigated for the electro-hydraulic synchronising servo control systems and wind turbine systems, respectively. It is shown that for these two types of systems, the higher the DOC of a controlled plant is, the better the quadratic optimal performance index is. It implies that in some LQR controller designs, the measure of the DOC of a controlled plant can be used as an index for the optimisation of adjustable plant parameters, by which the plant can be controlled more effectively.
Nodule size as predictive factor of efficacy of radiofrequency ablation in treating autonomously functioning thyroid nodules

Abstract Context: No defined pre-treatment factors are able to predict the response to radiofrequency ablation (RFA) of an autonomously functioning thyroid nodule (AFTN). Objective: Primary endpoint was to evaluate the success rate of RFA to restore euthyroidism in a cohort of adult patients with small solitary AFTN compared with medium-sized nodules. Secondary endpoints included nodule volume reduction and rate of conversion from hot nodules to cold using scintiscan. Methods: This was a 24-month prospective monocentric open parallel-group trial. Twenty-nine patients with AFTN were divided into two groups based on thyroid volume: 15 patients with small nodules (<12 mL) in group A and 14 patients with medium nodules (>12 mL) in group B. All patients underwent a single session of RFA and were clinically, biochemically, and morphologically evaluated at baseline and at 1, 6, 12 and 24 months after treatment. Results: After RFA, there was greater nodule volume reduction in group A compared with group B (p < 0.001 for each follow-up point). In group A, there was a greater increase in TSH levels than in group B at 6 (p = 0.01), 12 (p = 0.005), and 24 months (p < 0.001). At 24 months, the rate of responders was greater in group A than in group B (86 vs. 45%; p < 0.001). In group A, 86% of nodules converted from hot to cold compared with 18% in group B (p < 0.001). Conclusions: A single session of RFA was effective in restoring euthyroidism in patients with small AFTNs. Nodule volume seems to be a significant predictive factor of the efficacy of RFA in treating AFTN.
Similarities and Differences between the Effects of Amino Acids and Nitroprusside on Peritoneal Permeability during CAPD

Objective: Intraperitoneal administration of amino acid based dialysis solutions affects the surface area available for diffusion, with almost no effect on the intrinsic permeability to macromolecules. Intraperitoneally administered nitroprusside affects the vascular surface area and the intrinsic permeability without effect on the peritoneal blood flow. In the present study, these differences were translated into different effects on the radii of the pores in the peritoneal membrane. Methods: Effects of amino acid based dialysate and nitroprusside on peritoneal permeability characteristics were evaluated in standard peritoneal permeability analyses with L-arginine-containing amino acid dialysate (10 patients) or with 1.36% glucose dialysate with nitroprusside (10 patients). In each patient a control experiment with 1.36% glucose was performed. Kinetic modeling was done to analyze the effects in terms of the pore theory. Results: Both interventions increased the mass transfer area coefficients of low molecular weight solutes. This is in accordance with an increase in the unrestricted area over diffusion distance found with modeling. With amino acids almost no effect was found on the protein clearances; the increase in the large-pore radius was only small. Nitroprusside induced a marked increase in protein clearances. This was in accordance with an evident increase in the average large-pore radius. Conclusions: Amino acids affect the radii of the small pores and the large pores to the same extent. Nitroprusside influences especially the large pores. Both amino acids and nitroprusside are vasoactive, although the effects on the peritoneal microcirculation are different.
Semantic context improves speech intelligibility and reduces listening effort for listeners with hearing impairment

Abstract Objective: We investigated whether speech intelligibility and listening effort for hearing-aid users is affected by semantic context and hearing-aid setting. Design: Participants heard target sentences spoken in a reverberant background of cafeteria noise and competing speech. Participants reported each sentence verbally. Eight participants also rated listening effort after each sentence. Sentence topic was either the same as, or different from, the previous target sentence. Study sample: Twenty participants with sensorineural hearing loss were fit binaurally with Signia receiver-in-the-canal hearing aids. Participants performed the task twice: once using the hearing aid’s omnidirectional setting and once using the “Reverberant Room” setting, designed to aid listening in reverberant environments. Results: Participants achieved better speech intelligibility for same-topic than different-topic sentences, and when they used the “Reverberant Room” than the omnidirectional hearing-aid setting. Participants who rated effort showed a reliable reduction in listening effort for same-topic sentences and for the “Reverberant Room” hearing-aid setting. The improvement in speech intelligibility from semantic context (i.e. same-topic compared to different-topic sentences) was greater than the improvement gained from changing hearing-aid setting. Conclusions: These findings highlight the enormous potential of cognitive (specifically, semantic) factors for improving speech intelligibility and reducing perceived listening effort in noise for hearing-aid users.