Miracle-dz/UniFAR-FTUs huggingface dataset:
Use of IBASPM atlas-based automatic segmentation toolbox in pathological brains: Effect of template selection

IBASPM software is an atlas-based method for automatic segmentation of brain structures, available as a freeware toolbox for the SPM package. To test the influence of the atlas when segmenting normal and pathologic brains, manual segmentation of the caudate nucleus head was compared to automatic segmentations using four different atlases: the default MNI AAL atlas; a customized atlas created from a combined sample of patients (n=20) and controls (n=18); and a customized atlas obtained separately for each group. Maximum average ratio of overlapping voxels (dice overlap) between manual and automatic segmentation was 71% for controls and 52% for patients. In both groups, overlap ratios were better when using the customized atlases, instead of the standard MNI AAL atlas. Accuracy of the method was biased between left and right hemispheres, and also between groups, individual variability being higher in patients than in controls. Volumetric measurements using the customized atlases were also more accurate than using the MNI AAL atlas. Volume data were closer to manual segmentation values than dice overlap ratio (average differences ranging from 22.7% for MNI AAL atlas to 10.1% for customized atlas of patients and controls combined). Results suggests a low overall performance of IBASPM as an automatic segmentation method for the head of the caudate nucleus. Because of the biases observed, the use of this method for analyzing caudate nucleus in patients presenting anatomical abnormalities should be cautiously carried out.
Knowledge and Information Systems REGULAR PAPER

In this paper, we define time series query filtering, the problem of monitoring the streaming time series for a set of predefined patterns. This problem is of great practical importance given the massive volume of streaming time series available through sensors, medical patient records, financial indices and space telemetry. Since the data may arrive at a high rate and the number of predefined patterns can be relatively large, it may be impossible for the comparison algorithm to keep up. We propose a novel technique that exploits the commonality among the predefined patterns to allow monitoring at higher bandwidths, while maintaining a guarantee of no false dismissals. Our approach is based on the widely used envelope-based lower-bounding technique. As we will demonstrate on extensive experiments in diverse domains, our approach achieves tremendous improvements in performance in the offline case, and significant improvements in the fastest possible arrival rate of the data stream that can be processed with guaranteed no false dismissals. As a further demonstration of the utility of our approach, we demonstrate that it can make semisupervised learning of time series classifiers tractable.
MRI multicomponent relaxometry based on compressive sensing

A novel application of ℓ1-norm minimization in the MRI field is presented. The novel methodology, called Intra Voxel Analysis (IVA), by combining different acquisitions with standard resolution, is able to investigate the presence of different contributions, i.e., of different tissues, inside each imaged voxel. The approach is somehow similar to spectroscopy, but instead of searching different resonance frequencies, it discriminates within each voxel the tissues characterized by different spin-spin relaxation times. The proposed methodology is able to work on MR images acquired at full resolution by using any acquisition scheme. A phantom has been built and images for testing the approach.
Single Gene Deletions of mrpA to mrpG and mrpE Point Mutations Affect Activity of the Mrp Na+/H+ Antiporter of Alkaliphilic Bacillus and Formation of Hetero-Oligomeric Mrp Complexes

ABSTRACT Mrp antiporters catalyze secondary Na+(Li+)/H+ antiport and/or K+/H+ antiport that is physiologically important in diverse bacteria. An additional capacity for anion flux has been observed for a few systems. Mrp is unique among antiporters in that it requires all six or seven hydrophobic gene products (MrpA to MrpG) of the mrp operon for full antiporter activity, but MrpE has been reported to be dispensable. Here, the membrane complexes formed by Mrp proteins were examined using a cloned mrp operon from alkaliphilic Bacillus pseudofirmus OF4. The operon was engineered so that the seven Mrp proteins could be detected in single samples. Membrane extracts of an antiporter-deficient Escherichia coli strain expressing this construct were analyzed by blue native-sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Mrp complexes of two sizes were identified containing all seven Mrp proteins. Studies of the single nonpolar mrp gene deletions in the construct showed that a subcomplex of MrpA, MrpB, MrpC, and MrpD was formed in the absence of MrpE, MrpF, or MrpG. By contrast, MrpE, MrpF, and MrpG were not observed in membranes lacking MrpA, MrpB, MrpC, or MrpD. Although MrpA and MrpD have been hypothesized to be the antiporter proteins, the MrpA-to-D complex was inactive. Every Mrp protein was required for an activity level near that of the wild-type Na+/H+ antiporter, but a very low activity level was observed in the absence of MrpE. The introduction of an MrpE(P114G) mutation into the full Mrp complex led to antiport activity with a greatly increased apparent Km value for Na+. The results suggested that interactions among the proteins of heterooligomeric Mrp complexes strongly impact antiporter properties.
Influence of humidity on the decomposition products and insulating characteristics of CF3I

Recent studies show that CF3I is possible to take the place of SF6 used in gas insulated switchgear (GIS) as insulating gas. H2O is one of the key factors influencing the categories and quantities of decomposition products of SF6 in discharge. The process of decomposition of CF3I and the influence from H2O on the insulating property of CF3I have not been studied. In this paper, we analyzed the process of decomposition of CF3I with micro-moisture at ambient temperature and pressure using simulation by density functional theory (DFT). The changes in energy of reactions were calculated and compared according to thermodynamic theories and the most likely reaction pathways and decomposition products were found. The results show that CF3I may break down after attaching electron in strong electric field, which is reversible. CF3I can react with H- and OH-coming from H2O collided by high-energy electron and produce various and complex products, which breaks the dynamic balance of CF3I. Partial discharge experimental results show that the discharge in CF3I becomes more violent when the micro-moisture content increases. The result of simulation and experiment verifies H2O can destroy the insulating property of CF3I.
Analysis of the H19ICR Insulator

ABSTRACT Transcriptional insulators are specialized cis-acting elements that protect promoters from inappropriate activation by distal enhancers. The H19 imprinting control region (ICR) functions as a CTCF-dependent, methylation-sensitive transcriptional insulator. We analyzed several insertional mutations and demonstrate that the ICR can function as a methylation-regulated maternal chromosome-specific insulator in novel chromosomal contexts. We used chromosome conformation capture and chromatin immunoprecipitation assays to investigate the configuration of cis-acting elements at these several insertion sites. By comparing maternal and paternal organizations on wild-type and mutant chromosomes, we hoped to identify mechanisms for ICR insulator function. We found that promoter and enhancer elements invariably associate to form DNA loop domains at transcriptionally active loci. Conversely, active insulators always prevent these promoter-enhancer interactions. Instead, the ICR insulator forms novel loop domains by associating with the blocked promoters and enhancers. We propose that these associations are fundamental to insulator function.
Biological characteristics of a manganese resistant microorgnism

Rhizosphere soils of Chenopodium album Linn were collected by means of filed surveys on Xiangtan manganese tailings. One red manganese- resistant strain numbered XY was isolated from the rhizosphere of exarid plant through concentration gradient screening technique. The cellular form, physiological and biochemical tests were conducted using the growth curve, and effects of temperature, pH, NaCl concentration to growth of the strain tested were investigated. The results of the tests showed that 1) the strain reached logarithmic phase in 5-26h; 2) the optimal temperature range for growth of the strain was from 35°C to 40°C; 3) the optimal pH range for growth of the strain was from 7.0 to 7.3; 4) the optimal NaCl concentration range for growth of the strain was 10g/L. In this study, the strain XY was identified, and status of the strain in the taxonomy and phylogeny has been conformed according to 16S rDNA sequences, demonstrating that the strain XY belongs to Serratia genus.
The anal sphincter in fecal incontinence.

Anal sphincter characteristics were studied in eight children who had repair of an imperforate anus. Six of the eight had problems with fecal impaction and soiling. Resting yield pressure (RYP) was measured by gradual distension of a balloon within the sphincter and defined as the point at which a pressure plateau was reached and further distension of the balloon produced no further increase in recorded pressure. At this point the patients were asked to "squeeze down on the balloon" and this superimposed voluntary pressure was termed the "squeeze pressure. " Both of these pressures were lower in the patients who had been operated on than in age-matched controls. Two patients who had developed continence had pressures approaching normal. Six patients with psychogenic constipation had sphincter pressures similar to the normal controls. This simple method of recording anal pressures may help to differentiate organic from non-organic types of fecal soiling.
Validating the effects of drug treatment on blood pressure in the General Practice Research Database

Observational studies using clinical databases, such as the United Kingdom's General Practice Research Database (GPRD), may provide an alternative to clinical trial data for detecting longitudinal changes in blood pressure due to drug exposures that vary over time. Blood pressure data which are measured at variable intervals and are often missing present a particular methodological challenge to the analysis of such studies.
An Analysis of Active End-to-end Bandwidth Measurements in Wireless Networks

For active, probing-based bandwidth measurements performed on top of the unifying IP layer, it may seem reasonable to expect the measurement problem in wireless networks to be no different than the one in wired networks. However, in networks with 802.11 wireless bottleneck links we show that this is not the case. The results from the experiments presented in this paper show that the measured available bandwidth is dependent on the probe packet size (contrary to what is observed in wired networks). Another equally important finding is that the measured link capacity, using the well known TOPP model, is dependent on the probe packet size and on the cross-traffic intensity. The underlying reasons for the observed differences are analyzed by incorporating the characteristics of 802.11 wireless networks into the TOPP model. The extended model is applicable to other end-to-end bandwidth measurement methods as well, such as BART, Pathload and PTR.
Comparative pharmacology of epibatidine: a potent agonist for neuronal nicotinic acetylcholine receptors.

Pharmacological properties of the (+)- and (-)-isomers of synthetic epibatidine, exo-2-(6-chloro-3-pyridyl)-7-azabicyclo-[2.2. 1]heptane, were compared with nicotine and acetylcholine on several subtypes of chicken and human nicotinic acetylcholine receptors (AChRs). Both isomers of epibatidine behaved as extremely potent full agonists on chicken (alpha 3 beta 2, alpha 3 beta 4, alpha 4 beta 2, alpha 7, and alpha 8) and human (alpha 3 beta 2, alpha 3 beta 4, and alpha 7) neuronal AChRs expressed in Xenopus oocytes. Currents induced by epibatidine were effectively blocked by the nicotinic antagonists hexamethonium and mecamylamine. Apparent affinity was 100 to 1000-fold higher for epibatidine than for nicotine or acetylcholine. EC50 values ranged from 1 nM (for homomeric chicken alpha 8) to 2 microM (for homomeric chicken alpha 7). Epibatidine showed comparatively lower affinity for muscle-type AChRs from Torpedo and humans (EC50 values, 1.6 and 16 microM respectively). In binding assays, epibatidine was used on AChR subtypes immunoisolated from chicken brain and retina (alpha 4 beta 2, alpha 7, and alpha 8), the human neuronal cell line SH-SY5Y (alpha 3 and alpha 7), Torpedo electric organ (alpha 1 beta 1 gamma delta), or the human rhabdomyosarcoma cell line TE671 (alpha 1 beta 1 gamma delta). Both isomers of epibatidine exhibited extremely high affinity for all neuronal AChRs tested, with KI values ranging from 0.6 pM (human alpha 3 AChRs) to 0.6 microM (chicken alpha 7 AChRs). In contrast, epibatidine had lower affinity for Torpedo muscle-type AChRs (KI approximately 5 microM). Racemic [3H]epibatidine was an effective labeling reagent for human alpha 3 beta 2 AChRs, exhibiting a KD (0.14 nM) similar to the KI values observed for unlabeled (+)-epibatidine (0.23 nM) or (-)-epibatidine (0.16 nM).
Micro Data, Heterogeneity and the Evaluation of Public Policy Part 1

This paper summarizes the contributions of microeconometrics to economic knowledge. Four main themes are developed. (1) Microeconometricians developed new tools to respond to econometric problems raised by the analysis of the new sources of micro data produced after the Second World War. (2) Microeconometrics improved on aggregate time series methods by building models that linked economic models for individuals to data on individual behaviour. (3) An important empirical regularity detected by the field is the diversity and heterogeneity of behaviour. This heterogeneity has profound consequences for economic theory and for econometric practice. (4) Microeconometrics has contributed substantially to the scientific evaluation of public policy.
Premenopausal Plasma Ferritin Levels, HFE Polymorphisms, and Risk of Breast Cancer in the Nurses' Health Study II

Background: Evidence from the Nurses' Health Study II (NHSII) suggests that red meat consumption is associated with increased breast cancer risk in premenopausal women. Iron may be responsible by contributing to oxidative stress or effects on immune function. Methods: We conducted a case–control study nested within the NHSII, examining prediagnostic plasma ferritin (n = 795 cases, 795 controls), 15 hemochromatosis gene (HFE) single-nucleotide polymorphisms (SNP; n = 765 cases, 1,368 controls), and breast cancer risk. Cases were diagnosed after providing blood samples between 1996 and 1999. ORs and 95% confidence intervals (CI) were calculated for ferritin levels by conditional logistic regression and for HFE SNPs by unconditional logistic regression. Results: We did not observe a significant association between ferritin levels and breast cancer (top vs. bottom quartile multivariate OR: 1.05; 95% CI, 0.77–1.45; PTrend = 0.77). Results did not change when restricted to women who were premenopausal at blood draw, and were similar when cases were examined by hormone receptor status, and menopausal status at diagnosis. No HFE SNPs were significantly associated with breast cancer in a log-additive manner. Among controls, ferritin levels were nominally associated with SNPs rs9366637 (PTrend = 0.04), rs6918586 (PTrend = 0.06), and rs13161 (PTrend = 0.07), but results did not remain significant after adjusting for multiple testing. Conclusions: Ferritin levels and HFE SNPs were not associated with breast cancer risk in this population. Impact: Components of red meat other than iron are likely responsible for its positive association with breast cancer in premenopausal women. Cancer Epidemiol Biomarkers Prev; 23(3); 516–24. ©2014 AACR.
Polarization-Manipulated Dual-Band Enhanced Optical Transmission Through Subwavelength Rectangular Hole Array on Metallic Film

We proposed and experimentally demonstrated the polarization-controlled dual-band optical transmission through metallic hole array. It is utilized the anisotropic enhanced transmission through metallic array of subwavelength rectangular holes. The meaning is that the incident polarization state can decide the output wavelength. Two polarization-manipulated resonant transmissions at 632 nm (red) and 532 nm (green) have been demonstrated. It can be applied for achieving integrated polarization-controlled red-green light switching devices. Also, it can be used as a wavelength-dependent micropolarizer.
A High Power Density Series-Stacked Energy Buffer for Power Pulsation Decoupling in Single-Phase Converters

A high-efficiency, high-power-density buffer architecture is proposed for power pulsation decoupling in power conversion between dc and single-phase ac. We present an active decoupling solution that yields improved efficiency and reduced circuit complexity compared to existing solutions. In the proposed architecture, the main energy storage capacitor is connected in series with an active buffer converter across the dc bus. The series-stacked capacitor blocks the majority of the dc bus voltage to reduce the voltage stress on the buffer converter, such that fast, low-voltage transistors can be employed for the buffer converter. Moreover, the series capacitor provides the majority of the power pulsation decoupling through a wide voltage swing, and the buffer converter only needs to process a small fraction of the total power of the entire architecture, allowing a very small active circuit volume and very high system efficiency. The circuit operation and design constraints are analyzed in detail. In the proposed buffer architecture, the series stacking of a nearly lossless capacitor and a lossy converter presents a challenge of capacitor voltage balancing and power loss compensation. We propose a control scheme exploiting the small ripple in the bus voltage and dc input current to compensate for the power loss in the buffer converter while maintaining the voltage balance. Light-load techniques are also introduced to ensure that the buffer architecture meets strict ripple requirements while providing sufficient loss compensation. A 2-kW hardware prototype based on low-voltage GaN switches has been built to demonstrate the performance of the proposed solution. A power density of 25 W/cm $^3$ (410 W/in $^3$) by rectangular box volume and an efficiency above 98.9% across a wide load range has been experimentally verified.
Water‐Borne Endovascular Embolics Inspired by the Undersea Adhesive of Marine Sandcastle Worms

Transcatheter embolization is used to treat vascular malformations and defects, to control bleeding, and to selectively block blood supply to tissues. Liquid embolics are used for small vessel embolization that require distal penetration. Current liquid embolic agents have serious drawbacks, mostly centered around poor handling characteristics and toxicity. In this work, a water‐borne in situ setting liquid embolic agent is described that is based on electrostatically condensed, oppositely charged polyelectrolytes–complex coacervates. At high ionic strengths, the embolic coacervates are injectable fluids that can be delivered through long narrow microcatheters. At physiological ionic strength, the embolic coacervates transition into a nonflowing solid morphology. Transcatheter embolization of rabbit renal arteries demonstrated capillary level penetration, homogeneous occlusion, and 100% devascularization of the kidney, without the embolic crossing into venous circulation. The benign water‐borne composition and setting mechanism avoids many of the problems of current liquid embolics, and provides precise temporal and spatial control during endovascular embolization.
A high-fidelity method for genomic sequencing of single somatic cells reveals a very high mutational burden

Postzygotic mutations in somatic cells lead to genome mosaicism and can be the cause of cancer, possibly other human diseases and aging. Somatic mutations are difficult to detect in bulk tissue samples. Here, we review the available assays for measuring somatic mutations, with a focus on recent single-cell, whole genome sequencing methods. Impact statement Somatic mutations cause cancer, possibly other diseases and aging. Yet, very little is known about the frequency of such mutations in vivo, their distribution across the genome, and their possible functional consequences other than cancer. Even in cancer, we do not know the heterogeneity of mutations within a tumor and if seemingly normal cells in its surroundings already have elevated mutation frequencies. Here, we review a new, whole genome amplification system that allows accurate quantification and characterization of single-cell mutational landscapes in human cells and tissues in relation to disease.
Perifosine plus lenalidomide and dexamethasone in relapsed and relapsed/refractory multiple myeloma: a Phase I Multiple Myeloma Research Consortium study

The combination of lenalidomide–dexamethasone is active in multiple myeloma (MM). Preclinical data showed that the Akt inhibitor, perifosine, sensitized MM cells to lenalidomide and dexamethasone, providing the rationale for this Phase I, multicentre, single‐arm study to assess the safety and determine the maximum‐tolerated dose (MTD) of perifosine–lenalidomide–dexamethasone in relapsed and relapsed/refractory MM. Patients received escalating doses of perifosine 50–100 mg daily and lenalidomide 15–25 mg once daily on days 1–21 of each 28‐d cycle, plus dexamethasone 20–40 mg weekly thereafter, as indicated. Thirty‐two patients were enrolled across four dose cohorts. MTD was not reached, with 31 patients evaluable for safety/tolerability. The most common all‐causality grade 1‐2 adverse events were fatigue (48%) and diarrhoea (45%), and grade 3–4 neutropenia (26%), hypophosphataemia (23%), thrombocytopenia (16%), and leucopenia (13%). Among 30 evaluable patients, 73% (95% confidence interval, 57·5–89·2%) achieved a minimal response or better, including 50% with a partial response or better. Median progression‐free survival was 10·8 months and median overall survival 30·6 months. Response was associated with phospho‐Akt in pharmacodynamic studies. Perifosine–lenalidomide–dexamethasone was well tolerated and demonstrated encouraging clinical activity in relapsed and relapsed/refractory MM.
Surface-Consistent Sparse Multichannel Blind Deconvolution of Seismic Signals

We describe a method that allows for blind surface consistent estimation of the source and receiver wavelets of seismic signals. This is very relevant for surface-consistent deconvolution where current processing standards focus on the removal of the source and receiver effects under the minimum phase assumption. The proposed method, which is an extension of the Euclid deconvolution method, employs an iterative algorithm that simultaneously estimates the source and receiver wavelets that are consistent with the data. Unlike most deconvolution methods, the algorithm requires no prior phase assumptions. Another important feature of the algorithm is that we questioned the Gaussian density assumption of the reflectivity series and instead implemented a sparse regularizer to constrain the solution space of our desired reflectivity series. In other words, we assume that the reflectivity series can be cast as a sparse vector with few nonzero coefficients.