Miracle-dz/UniFAR-FTUs huggingface dataset:
Mean Field and Capacity in Realistic Networks of Spiking Neurons Storing Sparsely Coded Random Memories

Mean-field (MF) theory is extended to realistic networks of spiking neurons storing in synaptic couplings of randomly chosen stimuli of a given low coding level. The underlying synaptic matrix is the result of a generic, slow, long-term synaptic plasticity of two-state synapses, upon repeated presentation of the fixed set of the stimuli to be stored. The neural populations subtending the MF description are classified by the number of stimuli to which their neurons are responsive (multiplicity). This involves 2p + 1 populations for a network storing p memories. The computational complexity of the MF description is then significantly reduced by observing that at low coding levels (f), only a few populations remain relevant: the population of mean multiplicity pf and those of multiplicity of order pf around the mean. The theory is used to produce (predict) bifurcation diagrams (the onset of selective delay activity and the rates in its various stationary states) and to compute the storage capacity of the network (the maximal number of single items used in training for each of which the network can sustain a persistent, selective activity state). This is done in various regions of the space of constitutive parameters for the neurons and for the learning process. The capacity is computed in MF versus potentiation amplitude, ratio of potentiation to depression probability and coding level f. The MF results compare well with recordings of delay activity rate distributions in simulations of the underlying microscopic network of 10,000 neurons.
Aortic valve calcium scoring is a predictor of significant paravalvular aortic insufficiency in transapical-aortic valve implantation.

OBJECTIVE Transapical-aortic valve implantation (TA-AVI) has evolved as routine for selected high-risk patients. However, paravalvular leaks >1+ remain an unsolved issue using current generations of transcatheter valve devices. The purpose of this study was to investigate the impact of native aortic valve calcification on paravalvular leaks and outcomes using the Edwards SAPIEN™ prosthesis. METHODS One hundred and twenty consecutive patients (out of 307 TA-AVIs) with preoperative computed tomography aged 82.6 ± 6.2 years, 75.0% female were included. Implanted prosthetic valve sizes were 23 mm (n = 31) and 26 mm (n = 89), respectively. Mean logistic European System for Cardiac Operative Risk Evaluation-Score was 30.1 ± 15.5% and mean Society of Thoracic Surgeons-Score was 12.8 ± 7.9%. Electrocardiographic (ECG)-gated cardiac computed tomography allowed to quantify the amount of calcification of aortic valve leaflets using a scoring analogous to the Agatston calcium scoring of coronary arteries [Aortic Valve Calcium Scoring (AVCS)]. Paravalvular leaks were assessed intraoperatively by echocardiography and root angiography. RESULTS All valves were implanted successfully. The mean AVCS in patients without paravalvular leaks (n = 66) was 2704 ± 1510; with mild paravalvular leaks (n = 31) was 3804 ± 2739 (P = 0.05); and with moderate paravalvular leaks (n = 4) was 7387 ± 1044 (P = 0.002). There was a significant association between the AVCS and paravalvular leaks [odds ratio (OR; per AVCS of 1000), 11.38; 95% confidence interval (CI) 2.33-55.53; P = 0.001)] and a trend towards a higher incidence of new pacemaker implantation (OR 1.27; 95% CI 0.85-1.89; P = 0.26). No association was found to 30-day mortality, major cardiac events and stroke rate (OR 1.05; 95% CI 0.84-1.32; P = 0.68; OR 0.92; 95% CI 0.68-1.25; P = 0.57 and OR 0.90; 95% CI 0.41-1.96; P = 0.79, respectively). Overall 30-day mortality was 14.2%. CONCLUSION Severe native valve calcifications are predictive for postoperative relevant paravalvular leak. AVCS prior to TA-AVI might serve as an additional tool to reconsider the TAVI indication to reduce the risk of paravalvular leaks especially in so-called operable patients.
Mild segregation in the breeding preferences of an invasive anuran (Discoglossus pictus) and its main native competitor (Epidalea calamita) in ephemeral ponds

The choice of breeding sites by pond-breeding anurans has notable consequences for the fitness of larvae. Hence, beyond pond typology and phenology, adults can also discriminate according to several other features, for instance to favour allotopy with potential competitors. However, the lack of shared evolutionary history might impede proper ecological differentiation with alien species during the first stages of invasions. Here, we studied several possible sources of ecological segregation between the invasive Discoglossus pictus and the native Epidalea calamita in ephemeral ponds, where the native toad hardly had competition before the arrival of the invasive frog. During spring of 2016, we periodically surveyed 69 ephemeral ponds in three areas with different invasion histories to detect the presence/absence of eggs and tadpoles of these species. Invasive D. pictus started breeding earlier than E. calamita, but differences were not significant. Similarly, there were not clear differences among areas with different invasion histories. However, we found for both species a mutual tendency to directly avoid larval syntopy at the end of the reproductive season. We also found interspecific differences in the features that both species use for pond choice, preferring the native species shallower and less vegetated ephemeral ponds. Globally however, co-occurrence was high, pointing at other processes as key to the coexistence between both species in these habitats.
Phase-Shifted Full-Bridge Series-Resonant DC-DC Converters for Wide Load Variations

This paper presents the design of a phase-shifted full-bridge series resonant converter (PS-FB SRC). The proposed FB SRC features a novel two-mode operation. It is operated in series resonant mode at normal loads. The switching frequency is varied to regulate the output voltage. The fixed-frequency phase-shifted pulse width modulation, on the other hand, is used to adjust the effective duty cycle and regulate the output voltage at light loads. The proposed converter exhibits high conversion efficiency for wide-range load conditions. The relationships among the voltage gain, the switching frequency, and the effective duty cycle are discussed and analyzed. Finally, a 48-V/42-A prototype is implemented. Experiments are conducted to verify the theoretical analysis.
Sparse Bayesian Multi-Task Learning

We propose a new sparse Bayesian model for multi-task regression and classification. The model is able to capture correlations between tasks, or more specifically a low-rank approximation of the covariance matrix, while being sparse in the features. We introduce a general family of group sparsity inducing priors based on matrix-variate Gaussian scale mixtures. We show the amount of sparsity can be learnt from the data by combining an approximate inference approach with type II maximum likelihood estimation of the hyperparameters. Empirical evaluations on data sets from biology and vision demonstrate the applicability of the model, where on both regression and classification tasks it achieves competitive predictive performance compared to previously proposed methods.
Differential Patterns of Large Tumor Antigen-Specific Immune Responsiveness in Patients with BK Polyomavirus-Positive Prostate Cancer or Benign Prostatic Hyperplasia

ABSTRACT The role of the polyomavirus BK (BKV) large tumor antigen (L-Tag) as a target of immune response in patients with prostate cancer (PCa) has not been investigated thus far. In this study, we comparatively analyzed humoral and cellular L-Tag-specific responsiveness in age-matched patients bearing PCa or benign prostatic hyperplasia, expressing or not expressing BKV L-Tag-specific sequences in their tissue specimens, and in non-age-matched healthy individuals. Furthermore, results from patients with PCa were correlated to 5-year follow-up clinical data focusing on evidence of biochemical recurrence (BR) after surgery (prostate specific antigen level of ≥0.2 ng/ml). In peripheral blood mononuclear cells (PBMC) from patients with PCa with evidence of BR and BKV L-Tag-positive tumors, stimulation with peptides derived from the BKV L-Tag but not those derived from Epstein-Barr virus, influenza virus, or cytomegalovirus induced a peculiar cytokine gene expression profile, characterized by high expression of interleukin-10 (IL-10) and transforming growth factor β1 and low expression of gamma interferon genes. This pattern was confirmed by protein secretion data and correlated with high levels of anti-BKV L-Tag IgG. Furthermore, in PBMC from these PCa-bearing patients, L-Tag-derived peptides significantly expanded an IL-10-secreting CD4+ CD25+(high) CD127− FoxP3+ T cell population with an effector memory phenotype (CD103+) capable of inhibiting proliferation of autologous anti-CD3/CD28-triggered CD4+ CD25− T cells. Collectively, our findings indicate that potentially tolerogenic features of L-Tag-specific immune response are significantly associated with tumor progression in patients with BKV+ PCa.
Bacterial Community Structure Associated with a Dimethylsulfoniopropionate-Producing North Atlantic Algal Bloom

ABSTRACT The bacteria associated with oceanic algal blooms are acknowledged to play important roles in carbon, nitrogen, and sulfur cycling, yet little information is available on their identities or phylogenetic affiliations. Three culture-independent methods were used to characterize bacteria from a dimethylsulfoniopropionate (DMSP)-producing algal bloom in the North Atlantic. Group-specific 16S rRNA-targeted oligonucleotides, 16S ribosomal DNA (rDNA) clone libraries, and terminal restriction fragment length polymorphism analysis all indicated that the marine Roseobacter lineage was numerically important in the heterotrophic bacterial community, averaging >20% of the 16S rDNA sampled. Two other groups of heterotrophic bacteria, the SAR86 and SAR11 clades, were also shown by the three 16S rRNA-based methods to be abundant in the bloom community. In surface waters, the Roseobacter, SAR86, and SAR11 lineages together accounted for over 50% of the bacterial rDNA and showed little spatial variability in abundance despite variations in the dominant algal species. Depth profiles indicated thatRoseobacter phylotype abundance decreased with depth and was positively correlated with chlorophyll a, DMSP, and total organic sulfur (dimethyl sulfide plus DMSP plus dimethyl sulfoxide) concentrations. Based on these data and previous physiological studies of cultured Roseobacter strains, we hypothesize that this lineage plays a role in cycling organic sulfur compounds produced within the bloom. Three other abundant bacterial phylotypes (representing a cyanobacterium and two members of the α Proteobacteria) were primarily associated with chlorophyll-rich surface waters of the bloom (0 to 50 m), while two others (representing Cytophagales and δProteobacteria) were primarily found in deeper waters (200 to 500 m).
The Influence of Extracellular Matrix on Gene Expression: Is Structure the Message?

SUMMARY The study of the regulation of gene expression in cultured cells, particularly in epithelial cells, has been both hampered and facilitated by the loss of function that accompanies culture on traditional plastic substrata. Initially, investigations of differentiated function were thwarted by the inadequacy of tissue culture methods developed to support growth of mesenchymal cells. However, with the recognition that the unit of function in higher organisms is larger than the cell itself, and that gene expression is dependent upon cell interactions with hormones, substrata and other cells, came the understanding that the epithelial cell phenotype is profoundly influenced by the extra-cellular environment. In the last decade research on epithelial cells has centred on culture conditions that recreate the appropriate environment for function with very promising and important results. The investigations into the modulation of phenotype in culture produced not only a better model, but also contributed to a better understanding of the regulation of normal function. Using cultured mammary gland epithelial cells as a primary model of these interactions, our studies of gene expression are based on three premises. That the extracellular matrix (ECM) on which the cells sit is an extension of the cells and an active participant in the regulation of cellular function; i.e. the ECM is an ‘informational’ entity in the sense that it receives, imparts and integrates structural and functional signals. That ECM-induced functional differentiation in the mammary gland is mediated through changes in cell shape, i.e. that the structure is in large part ‘the message’ required to maintain differentiated gene expression. That the unit of function includes the cell plus its extracellular matrix; in a larger context, the unit is the organ itself. These tenets and the data presented below are consistent with a model of ‘Dvnamic Reciprocity’, where the ECM is postulated to exert an influence on gene expression via transmembrane proteins and cytoskeletal components. In turn, cytoskeletal association with polyribosomes affects mRNA stability and rates of protein synthesis, while its interaction with the nuclear matrix could affect mRNA processing and, possibly, rates of transcription.
Dog bite injuries.

AIMS To describe the extent of the dog bite problem in New Zealand for the period 1989 to 2001. METHODS Fatalities and cases requiring public-hospital treatment identified from the New Zealand Health Information Service databases. RESULTS There was one fatality and 3119 hospitalisations, an average of 240 per year. Those most at risk were males and children under 9 years of age. The incidence rate of dog bites has continued to increase from that reported previously. There has been a increase in recent years but it is difficult to determine whether this is real effect or an artefact of coding. CONCLUSIONS Dog bite injuries represent a significant public health problem in New Zealand. Ongoing monitoring is required to determine if dog control policies are having the intended effect.
Multicenter, Prospective, Longitudinal Study of the Recurrence, Surgical Site Infection, and Quality of Life After Contaminated Ventral Hernia Repair Using Biosynthetic Absorbable Mesh

Objective: The aim of the study was to evaluate biosynthetic absorbable mesh in single-staged contaminated (Centers for Disease Control class II and III) ventral hernia (CVH) repair over 24 months. Background: CVH has an increased risk of postoperative infection. CVH repair with synthetic or biologic meshes has reported chronic biomaterial infections and high hernia recurrence rates. Methods: Patients with a contaminated or clean-contaminated operative field and a hernia defect at least 9 cm2 had a biosynthetic mesh (open, sublay, retrorectus, or intraperitoneal) repair with fascial closure (n = 104). Endpoints included overall Kaplan-Meier estimates for hernia recurrence and postoperative wound infection rates at 24 months, and the EQ-5D and Short Form 12 Health Survey (SF-12). Analyses were conducted on the intent-to-treat population, and health outcome measures evaluated using paired t tests. Results: Patients had a mean age of 58 years, body mass index of 28 kg/m2, 77% had contaminated wounds, and 84% completed 24-months follow-up. Concomitant procedures included fistula takedown (n = 24) or removal of infected previously placed mesh (n = 29). Hernia recurrence rate was 17% (n = 16). At the time of CVH repair, intraperitoneal placement of the biosynthetic mesh significantly increased the risk of recurrences (P ⩽ 0.04). Surgical site infections (19/104) led to higher risk of recurrence (P < 0.01). Mean 24-month EQ-5D (index and visual analogue) and SF-12 physical component and mental scores improved from baseline (P < 0.05). Conclusions: In this prospective longitudinal study, biosynthetic absorbable mesh showed efficacy in terms of long-term recurrence and quality of life for CVH repair patients and offers an alternative to biologic and permanent synthetic meshes in these complex situations.
Neurophysiology of Tactile Perception : A Tribute to Steven Hsiao The tactile speed aftereffect depends on the speed of adapting motion across the skin rather than other spatiotemporal features X

McIntyre S, Seizova-Cajic T, Holcombe AO. The tactile speed aftereffect depends on the speed of adapting motion across the skin rather than other spatiotemporal features. J Neurophysiol 115: 1112–1121, 2016. First published December 2, 2015; doi:10.1152/jn.00821. 2014. —After prolonged exposure to a surface moving across the skin, this felt movement appears slower, a phenomenon known as the tactile speed aftereffect (tSAE). We asked which feature of the adapting motion drives the tSAE: speed, the spacing between texture elements, or the frequency with which they cross the skin. After adapting to a ridged moving surface with one hand, participants compared the speed of test stimuli on adapted and unadapted hands. We used surfaces with different spatial periods (SPs; 3, 6, 12 mm) that produced adapting motion with different combinations of adapting speed (20, 40, 80 mm/s) and temporal frequency (TF; 3.4, 6.7, 13.4 ridges/s). The primary determinant of tSAE magnitude was speed of the adapting motion, not SP or TF. This suggests that adaptation occurs centrally, after speed has been computed from SP and TF, and/or that it reflects a speed cue independent of those features in the first place (e.g., indentation force). In a second experiment, we investigated the properties of the neural code for speed. Speed tuning predicts that adaptation should be greatest for speeds at or near the adapting speed. However, the tSAE was always stronger when the adapting stimulus was faster (242 mm/s) than the test (30–143 mm/s) compared with when the adapting and test speeds were matched. These results give no indication of speed tuning and instead suggest that adaptation occurs at a level where an intensive code dominates. In an intensive code, the faster the stimulus, the more the neurons fire.
High performance of combined HPV testing and genotyping for HPV16/18/52/58 in triaging women with minor cervical cytological abnormalities in northern Thailand

Human papillomavirus (HPV) infection is an important cause of cervical cancer. Screening with cytology or combined cytology and HPV testing helps to detect early cervical cancers and precancerous lesions (high‐grade squamous intraepithelial lesion or worse [HSIL+]). Minor cytological abnormalities (atypical squamous cells of undetermined significance and low‐grade squamous intraepithelial lesion) account for the majority of abnormal cervical cytology results, but only 10–20% of women with minor cytological abnormalities have histologic HSIL+. Triage tests are useful to identify the high‐risk patients and reduce the colposcopy burden. This study was aimed to evaluate the triage performance of combined HPV DNA testing and genotyping. Cervical samples from women with minor cytological abnormalities, who underwent colposcopy at Chiang Mai University Hospital in northern Thailand between October 2010 and February 2014, were tested for HPV DNA using Hybrid Capture 2 (HC2). Genotyping was performed using Linear Array assay. Of 223 women with cervical histology confirmation, histologic HSIL+ was detected in 25 women (11.2%). The sensitivity, specificity, positive predictive value, and negative predictive value of 3 triage methods for histologic HSIL+ were; 100%, 47.5%, 19.4%, and 100% by HC2 only; 40.0%, 88.4%, 30.3%, and 92.1% by combined HC2 and genotypes HPV16/18; and 96.0%, 75.8%, 33.3%, and 99.3% by combined HC2 and genotypes HPV16/18/52/58. Triage using combined HC2 and genotypes HPV16/18/52/58 showed significantly greater area under the receiver operating curve than the other 2 methods (P < 0.001). Combined HPV DNA testing and genotyping for HPV16/18/52/58 is useful for triaging women with minor cervical cytological abnormalities in northern Thailand. J. Med. Virol. 88:135–143, 2016. © 2015 Wiley Periodicals, Inc.
New Variants of Malignant Glioneuronal Tumors: A Clinicopathological Study of 40 Cases

OBJECTIVE:To demonstrate that malignant glioneuronal tumors comprise a large spectrum of neoplasms, without mature ganglion-like cells, that may histologically resemble any malignant glioma (World Health Organization Grade III or IV) but have a distinct biological behavior. METHODS:This series includes all tumors diagnosed as malignant glioneuronal tumors (MGNTs) in our routine practice during a 2-year period during which neurofilament protein (NFP) immunostaining was performed in any case of suspected malignant glioma with unusual clinical, radiographic, and/or histological features. Immunostaining using neuronal markers (NFP, NeuN, synaptophysin, and chromogranin) and glial fibrillary acidic protein was done on paraffin sections after antigen retrieval. The presence of NFP-positive tumor cells, including those in mitosis, was used as a hallmark diagnostic criterion of MGNT. RESULTS:All tumors coexpressed glial fibrillary acidic protein and NFP. Other neuronal markers tested were inconstantly expressed. No recurrence was observed at the primary site in 36.4% of patients who underwent gross total resection. Twelve patients (33.3%) developed intra-axial and/or systemic metastases, and 4 were free of disease at 39 to 184 months. Univariate analysis revealed that gross total surgical resection was the most important prognostic factor predicting survival (44 versus 15 mo; P < 0.0001), followed by a long duration of symptoms (>1 yr; P = 0.005), young age at symptom onset (children versus adults; P = 0.045), and absence of necrosis (P = 0.02). Gross total surgical resection (P = 0.001) and a long duration of symptoms (symptoms > 1 yr; P = 0.013) proved to be independent and statistically significant prognostic factors in the multivariate analysis. CONCLUSION:NFP immunostaining is required to identify MGNTs accurately. Their distinction from malignant gliomas is of paramount clinical importance, particularly for neurosurgeons, because gross total surgical resection may be curative in some cases. Finally, MGNTs may account for the long-term survival and/or occurrence of metastases demonstrated in a subset of malignant gliomas.