Miracle-dz/UniFAR-FTUs huggingface dataset:
Fluorescent multiple staining and CASA system to assess boar sperm viability and membranes integrity in short and long-term extenders

The aim of this study was to assess the effect on boar spermatozoa quality of in vitro storage in short and long-term extenders by fluorescent multiple staining (FMS) and computer assisted semen analyzer (CASA). Fresh ejaculates from three healthy, sexually mature boars were diluted with equal volumes of six short-term or three long-term commercial extenders and stored at 19°C for 6 days (short-term) or 12 days (long-term). The integrity of spermatozoa membranes was analyzed by FMS using propidium iodide, 5,5’,6,6’-tetrachloro-1,1’,3,3’ tetraethylbenzimidazolyl-carbocyanine iodide (JC-1) and fluorescein isothiocyanate-conjugated peanut agglutinin (PNA). The results obtained from this staining were compared with spermatozoa motility assessed by CASA. Our study showed that the number of viable spermatozoa with non-reacted acrosomes and intact mitochondria was positively correlated with the rate of motile spermatozoa (r2>0.9) irrespective of the extender used. In all extenders the number of motile spermatozoa significantly decreased as preservation period increased (P<0.05). FMS test is a potent indicator of sperm motility because it analyses mitochondrial integrity independently from observable alterations in motility. The best performing extenders were BTS for short-term storage and TRI-x-Cell for long-term storage.
Left atrial and left atrial appendage functional recovery after cardioversion in patients with recent atrial fibrillation: Serial echocardiographic study.

BACKGROUND The aim of this study is to point out timing of left atrium and its appendage functional recovery after cardioversion (CV) in recent onset atrial fibrillation (AF). METHODS Fifty patients; 27 within 48-h (group I) and 23 after 48-h (group II), of AF onset, who had successful CV underwent transthoracic echocardiography (TTE), before and immediately after CV, then 15, 30 and 90 days later. Transesophageal echocardiography (TEE) was performed for group II before and for all patients immediately after CV and 1 month later. Mitral peak A velocity and left atrial (LA) reversal (Ar) velocity, tissue Doppler imaging (TDI) of septal mitral annular velocity (A1) and LA free wall velocity (A3) were recorded. Absence or peak A velocity < 50 cm/s was taken as a cut off value for atrial stunning. Intra-atrial conduction time (IACT) was measured. LA appendage late emptying (LAALE) velocity was measured by TEE-pulsed TDI of LA appendage. RESULTS Post CV, all group II and 34% of group I experienced stunning. In both groups, peak A, Ar, A1, A3 and LAALE velocities increased (p = 0.000), while IACT decreased (p = 0.000) progressively over time. Partial recovery occurred after 15 and 30 days, while full recovery occurred 30 and 90 days post CV in groups I and II, respectively. IACT1 and IACT2 correlated with LA diameter (r = 0.2778 and r = 0.227, respectively, p < 0.01). CONCLUSIONS Stunning and functional recovery of the LA and its appendage are strongly determined by the duration being in AF. Serial IACT by TDI was a good new parameter for detection of functional recovery of LA and LA appendage.
Incremental Variational Sparse Gaussian Process Regression

Recent work on scaling up Gaussian process regression (GPR) to large datasets has primarily focused on sparse GPR, which leverages a small set of basis functions to approximate the full Gaussian process during inference. However, the majority of these approaches are batch methods that operate on the entire training dataset at once, precluding the use of datasets that are streaming or too large to fit into memory. Although previous work has considered incrementally solving variational sparse GPR, most algorithms fail to update the basis functions and therefore perform suboptimally. We propose a novel incremental learning algorithm for variational sparse GPR based on stochastic mirror ascent of probability densities in reproducing kernel Hilbert space. This new formulation allows our algorithm to update basis functions online in accordance with the manifold structure of probability densities for fast convergence. We conduct several experiments and show that our proposed approach achieves better empirical performance in terms of prediction error than the recent state-of-the-art incremental solutions to variational sparse GPR.
Spatial Cognition and the Brain

Recent advances in the understanding of spatial cognition are reviewed, focusing on memory for locations in large‐scale space and on those advances inspired by single‐unit recording and lesion studies in animals. Spatial memory appears to be supported by multiple parallel representations, including egocentric and allocentric representations, and those updated to accommodate self‐motion. The effects of these representations can be dissociated behaviorally, developmentally, and in terms of their neural bases. It is now becoming possible to construct a mechanistic neural‐level model of at least some aspects of spatial memory and imagery, with the hippocampus and medial temporal lobe providing allocentric environmental representations, the parietal lobe egocentric representations, and the retrosplenial cortex and parieto‐occipital sulcus allowing both types of representation to interact. Insights from this model include a common mechanism for the construction of spatial scenes in the service of both imagery and episodic retrieval and a role for the remainder of Papez's circuit in orienting the viewpoint used. In addition, it appears that hippocampal and striatal systems process different aspects of environmental layout (boundaries and local landmarks, respectively) and do so using different learning rules (incidental learning and associative reinforcement, respectively).
Extracting symbolic rules from trained neural network ensembles

Neural network ensemble can significantly improve the generalization ability of neural network based systems. However, its comprehensibility is even worse than that of a single neural network because it comprises a collection of individual neural networks. In this paper, an approach named REFNE is proposed to improve the comprehensibility of trained neural network ensembles that perform classification tasks. REFNE utilizes the trained ensembles to generate instances and then extracts symbolic rules from those instances. It gracefully breaks the ties made by individual neural networks in prediction. It also employs specific discretization scheme, rule form, and fidelity evaluation mechanism. Experiments show that with different configurations, REFNE can extract rules with good fidelity that well explain the function of trained neural network ensembles, or rules with strong generalization ability that are even better than the trained neural network ensembles in prediction.
From the Southern Association for Vascular Surgery Volumetric analysis of type B aortic dissections treated with thoracic endovascular aortic repair

Background: Type B aortic dissections are being successfully treated by thoracic endovascular aortic repair (TEVAR). Postoperative false lumen patency has been associated with aneurysmal dilatation and rupture of the thoracic aorta, necessitating further intervention. This is the first volumetric analysis of type B aortic dissections comparing patients with and without false lumen thrombosis (FLT) after TEVAR. We hypothesized that a greater increase in postoperative true lumen volume will lead to FLT, and without this change, false lumen patency will result. Methods: Preoperative and postoperative computed tomography angiography (CTA) imaging was analyzed using three-dimensional reconstruction to measure the shortand long-axis diameter and cross-sectional area of the true lumen, false lumen, and total aorta. Measurements were taken at 5-cm intervals from the left subclavian artery to the aortic bifurcation. Preand postoperative volumetric data were calculated and compared in patients with and without postoperative FLT. Results: Between 2006 and 2010, 132 patients underwent thoracic aortic stent grafting. Of these, 31 (23%) had thoracic endografting for type B aortic dissection. Preand postoperative CTA images were available for analysis in 23 patients with a mean age of 59 14 years treated for acute, complicated (n 8, 35%), and chronic (n 15, 65%) indications. Mean follow-up imaging was 9 months (range, 1-39 months). Thirteen patients (56%) had postoperative FLT and 10 (43%) had persistent false lumen patency. The dissections involved the left subclavian artery (n 12), visceral arteries (n 14), renal arteries (n 16), and iliac arteries (n 15). The left subclavian artery was intentionally covered in 15 patients (65%). There were no significant differences in age, acute vs chronic dissection, branch vessel involvement, coverage of the left subclavian artery, or distal extent of the endograft between patients with and without postoperative FLT. Patients with postoperative FLT had a significantly smaller preoperative maximum thoracic aortic diameter (5.05 1.0 vs 6.30 1.4 cm; P .02). Volumetric analysis demonstrated significantly smaller preoperative true lumen volume (141.3 68 vs 230.5 92 cm; P .01) in patients with FLT, but no difference in preoperative false lumen volume. Patients with FLT had a significant increase in the volume percentage of the true lumen from 42.7% to 61.7% (P .02) after stent graft repair, compared with an increase from 46.7% to 47.7% (P .75) in patients with persistent false lumen patency. Conclusions: This volumetric study of type B aortic dissection treated with TEVAR suggests that the ability of the endograft to significantly increase the true lumen volume as a percent of the total aorta most accurately predicts postoperative FLT. This is best demonstrated in a nonaneurysmal dissection regardless of timing since dissection. (J Vasc Surg 2011;54:985-92.)
A novel transverse flux machine for vehicle traction aplications

A novel transverse flux machine topology for electric vehicle traction application using ferrite magnets is presented in this paper. The proposed transverse flux topology utilizes novel magnet arrangements in the rotor that are similar to Halbach-array to boost flux linkage; on the stator side, cores are alternately arranged around a pair of ring windings in each phase to make use of the entire rotor flux that eliminates end windings. Analytical design considerations and finite element methods are used for an optimized design of a scooter in-wheel motor. Simulation results from Finite Element Analysis (FEA) show the motor achieved comparable torque density to conventional rare-earth permanent magnet machines. This machine is a viable candidate for direct drive applications with low cost and high torque density.
Molecular analysis of sarcoidosis lymph nodes for microorganisms: a case–control study with clinical correlates

Introduction Sarcoidosis is an incurable, chronic granulomatous disease primarily involving the lungs and lymph nodes of unknown aetiology, treated with non-specific anti-inflammatory/immunosuppressive drugs. Persistently symptomatic patients worsen with a disabling, potentially fatal clinical course. To determine a possible infectious cause, we correlated in a case-control study the clinical information with the presence of bacterial DNA in sarcoidosis mediastinal lymph nodes compared with control lymph nodes resected during cancer surgery. Methods We retrospectively studied formalin-fixed, paraffin-embedded, mediastinal lymph nodes from 30 patients with sarcoidosis and 30 control patients with lung cancer. Nucleic acids were extracted from nodes, evaluated by ribosomal RNA PCR for bacterial 16S ribosomal DNA and the results were sequenced and compared with a bacterial sequence library. Clinical information was correlated. Results 11/30 (36.7%) of lymph nodes from patients with sarcoidosis had detectable bacterial DNA, significantly more than control patient lymph nodes (2/30, 6.7%), p=0.00516. At presentation, 19/30 (63.3%) patients with sarcoidosis were symptomatic including all patients with detectable bacterial DNA. Radiographically, there were 18 stage I and 12 stage II patients. All stage II patients were symptomatic and 75% had PCR-detectable bacteria. After a mean follow-up of 52.8±32.8 months, all patients with PCR-detectable bacteria in this series were persistently symptomatic requiring treatment. Discussion 36.6% of patients with sarcoidosis had detectable bacterial DNA on presentation, all of these patients were quite symptomatic and most were radiographically advanced stage II. These findings suggest that bacterial DNA-positive, symptomatic patients have more aggressive sarcoidosis that persists long term and might benefit from antimicrobial treatment directed against this presumed chronic granulomatous infection.
Hemodialysis Access Infections, Epidemiology, Pathogenesis and Prevention

Renal replacement therapy (RRT), including various delivery types of haemodialysis, has revolutionised the care of patients with end stage renal disease (ESRD). The most common RRT modality is haemodialysis (ANZ Data 2010, Boddana et al., 2009). Access for dialysis is via arteriovenous fistulae (AVF), arteriovenous grafts (AVG) or via central venous dialysis catheters. The goal of access is to provide a means of accessing the vasculature to undertake RRT in order to deliver the optimal dialysis dose with the minimal associated morbidity and mortality. The National Kidney Foundation (NKF) Kidney Disease Outcome Quality Initiative (KDOQI, 2006) guidelines recommend an AVF prevalence rate of greater than 65%. Arteriovenous fistulae remain the preferred method of access due to improved survival rate and lower associated morbidity and associated medical costs (NKF-KDOQI, 2006). Despite all these measures, dialysis catheters remain commonly used for a variety of reasons. They are now well acknowledged as the harbinger of potential future significant morbidity and mortality. As a result of the significant morbidity burden caused by dialysis catheters, there has been great interest in discovering new and inventive methods of reducing catheter-related infection. Out of this is borne the investigation of preventative measures outlined here. This is particularly important given the immunosuppressed nature of renal patients. The evidence for, and utility of measures, such as topical antimicrobial ointment application, antimicrobial catheter lock solutions, antibiotic impregnated catheters, differing AVF cannulation methods and catheter design, shall be explored below. As we strive for improved outcomes in our patients many more patients are undertaking extended hours home haemodialysis. In those patients with the lowest risk accesses, questions have been raised as to the method of access cannulation and the spectre of increasing associated infectious events. The rope ladder technique involves regular rotation of cannulation sites whereas buttonhole technique uses the same cannulation sites and relies on formation of a track which is then repetitively accessed with blunt needles. This has been a very attractive method for home dialysis patients for a range of reasons. However, despite recent popularity with this technique, a number of studies including from our centre, have now shown that this technique is associated with increased septic events (Birchenough et al., 2008; Nesrallah et al., 2010; Van Eps et al., 2010; Van Loon et al., 2010).
Asymmetrical Interhemispheric Connections Develop in Cat Visual Cortex after Early Unilateral Convergent Strabismus: Anatomy, Physiology, and Mechanisms

In the mammalian primary visual cortex, the corpus callosum contributes to the unification of the visual hemifields that project to the two hemispheres. Its development depends on visual experience. When this is abnormal, callosal connections must undergo dramatic anatomical and physiological changes. However, data concerning these changes are sparse and incomplete. Thus, little is known about the impact of abnormal postnatal visual experience on the development of callosal connections and their role in unifying representation of the two hemifields. Here, the effects of early unilateral convergent strabismus (a model of abnormal visual experience) were fully characterized with respect to the development of the callosal connections in cat visual cortex, an experimental model for humans. Electrophysiological responses and 3D reconstruction of single callosal axons show that abnormally asymmetrical callosal connections develop after unilateral convergent strabismus, resulting from an extension of axonal branches of specific orders in the hemisphere ipsilateral to the deviated eye and a decreased number of nodes and terminals in the other (ipsilateral to the non-deviated eye). Furthermore this asymmetrical organization prevents the establishment of a unifying representation of the two visual hemifields. As a general rule, we suggest that crossed and uncrossed retino-geniculo-cortical pathways contribute successively to the development of the callosal maps in visual cortex.
H-Infinity Stabilization for Singular Networked Cascade Control Systems With State Delay and Disturbance

This paper is concerned with the stabilization and H∞ control problems for a class of singular networked cascade control systems with state delay and disturbance. Via the fact that single loop feedback control shows a shortcoming in that the plant output as nonzero disturbance acts on the systems, a new model of singular networked cascade control system is proposed. In this system, both the network-induced delay and data packed dropout phenomena are considered. Based on the model, sufficient conditions are derived in terms of linear matrix inequalities and the corresponding H∞ stabilizing controller design technique is also developed based on the above conditions. The proposed method emphasizes the implementation issue and employs the cascade control to singular networked control systems. A simulation example is given to illustrate the proposed design procedures and its applications.
Properties of new Escherichia coli Hfr strains constructed by integration of pSC101-derived conjugative plasmids

Conjugative temperature-sensitive plasmids were derived from pSC101. These plasmids are useful in genetic analysis for two reasons: (i) they render possible the construction of new Hfr lines by plasmid integration at predetermined chromosomal loci via Tn10 inverse transposition, and (ii) the Hfr characters are transducible via bacteriophage P1. We also showed that replication from pSC101 origin is deleterious for the plasmid-chromosome fusion.
Wind Power Prediction with Machine Learning Ensembles

For a sustainable integration of wind power into the electricity grid, precise and robust predictions are required. Machine learning methods can be used as purely data-driven, spatio-temporal prediction models that yield better results than traditional physical models based on weather simulations. The objectives of this thesis are the improvement of prediction errors and the reduction of computation times. This thesis proposes a robust and practical prediction framework based on ensembles, which combines the predictions of numerous and preferably diverse models. A comprehensive experimental evaluation shows that the combination of different techniques to an ensemble outperforms state-of-the-art prediction models while requiring shorter computation times. For model selection we employ evolutionary multi-objective optimization algorithms. The methods offer an efficient and comfortable balancing of preferably low prediction errors and moderate computational costs.
Gene Expression Profiling with Cre-Conditional Pseudorabies Virus Reveals a Subset of Midbrain Neurons That Participate in Reward Circuitry

The mesolimbic dopamine pathway receives inputs from numerous regions of the brain as part of a neural system that detects rewarding stimuli and coordinates a behavioral response. The capacity to simultaneously map and molecularly define the components of this complex multisynaptic circuit would thus advance our understanding of the determinants of motivated behavior. To accomplish this, we have constructed pseudorabies virus (PRV) strains in which viral propagation and fluorophore expression are activated only after exposure to Cre recombinase. Once activated in Cre-expressing neurons, the virus serially labels chains of presynaptic neurons. Dual injection of GFP and mCherry tracing viruses simultaneously illuminates nigrostriatal and mesolimbic circuitry and shows no overlap, demonstrating that PRV transmission is confined to synaptically connected neurons. To molecularly profile mesolimbic dopamine neurons and their presynaptic inputs, we injected Cre-conditional GFP virus into the NAc of (anti-GFP) nanobody-L10 transgenic mice and immunoprecipitated translating ribosomes from neurons infected after retrograde tracing. Analysis of purified RNA revealed an enrichment of transcripts expressed in neurons of the dorsal raphe nuclei and lateral hypothalamus that project to the mesolimbic dopamine circuit. These studies identify important inputs to the mesolimbic dopamine pathway and further show that PRV circuit-directed translating ribosome affinity purification can be broadly applied to identify molecularly defined neurons comprising complex, multisynaptic circuits. SIGNIFICANCE STATEMENT The mesolimbic dopamine circuit integrates signals from key brain regions to detect and respond to rewarding stimuli. To further define this complex multisynaptic circuit, we constructed a panel of Cre recombinase-activated pseudorabies viruses (PRVs) that enabled retrograde tracing of neural inputs that terminate on Cre-expressing neurons. Using these viruses and Retro-TRAP (translating ribosome affinity purification), a previously reported molecular profiling method, we developed a novel technique that provides anatomic as well as molecular information about the neural components of polysynaptic circuits. We refer to this new method as PRV-Circuit-TRAP (PRV circuit-directed TRAP). Using it, we have identified major projections to the mesolimbic dopamine circuit from the lateral hypothalamus and dorsal raphe nucleus and defined a discrete subset of transcripts expressed in these projecting neurons, which will allow further characterization of this important pathway. Moreover, the method we report is general and can be applied to the study of other neural circuits.
Why are deep nets reversible: A simple theory, with implications for training

Generative models for deep learning are promising both to improve understanding of the model, and yield training methods requiring fewer labeled samples. Recent works use generative model approaches to produce the deep net's input given the value of a hidden layer several levels above. However, there is no accompanying "proof of correctness" for the generative model, showing that the feedforward deep net is the correct inference method for recovering the hidden layer given the input. Furthermore, these models are complicated. The current paper takes a more theoretical tack. It presents a very simple generative model for RELU deep nets, with the following characteristics: (i) The generative model is just the reverse of the feedforward net: if the forward transformation at a layer is $A$ then the reverse transformation is $A^T$. (This can be seen as an explanation of the old weight tying idea for denoising autoencoders.) (ii) Its correctness can be proven under a clean theoretical assumption: the edge weights in real-life deep nets behave like random numbers. Under this assumption ---which is experimentally tested on real-life nets like AlexNet--- it is formally proved that feed forward net is a correct inference method for recovering the hidden layer. The generative model suggests a simple modification for training: use the generative model to produce synthetic data with labels and include it in the training set. Experiments are shown to support this theory of random-like deep nets; and that it helps the training.