Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparative effectiveness of positron emission mammography and MRI in the contralateral breast of women with newly diagnosed breast cancer.

OBJECTIVE The objective of our study was to compare the performance of positron emission mammography (PEM) with that of MRI in the evaluation of the contralateral breast of women with newly diagnosed cancer. SUBJECTS AND METHODS Four hundred seventy-two women with newly diagnosed breast cancer offered breast-conserving surgery from September 2006 through November 2008 consented to participate in a multicenter protocol. Participants underwent contrast-enhanced breast MRI and 18F-FDG PEM in randomized order, and the examinations were interpreted independently. The performance characteristics of the imaging modalities were compared using the McNemar test and generalized estimating equations. A retrospective blinded review of PEM images was performed by four experienced observers to understand the reasons for false-negatives. RESULTS Three hundred sixty-seven women (median age, 58 years; age range, 26-93 years) eligible for analysis completed the appropriate follow-up for study inclusion. Fifteen women (4.1%) were found to have contralateral cancer (11 invasive [mean tumor size, 12 mm; median, 10 mm; range, 1-22 mm] and four ductal carcinoma in situ). Of the 15 cases, both PEM and MRI showed three (20%), only MRI showed 11 (73%), and one (6.7%) was found at prophylactic mastectomy. MRI sensitivity at 14 of 15 (93%; 95% CI, 66-94) was higher than PEM at three of 15 (20%; 95% CI, 5.3-46) (p<0.001). On PEM, three additional cancers were seen prospectively but were considered probably benign and two other cancers were visible in retrospect at the site. Of 352 contralateral breasts without cancer, findings were negative or benign on PEM for 335 (95.2%; 95% CI, 92.2-97.0), which is more than MRI at 315 (89.5%; 95% CI, 85.7-92.4; p=0.002). The positive predictive value (PPV) of PEM-prompted biopsies (3/14 [21%]) was not significantly different from the PPV of MRI (15/54 [28%], p=0.58). On blinded retrospective PEM review of the 15 contralateral cancers, PEM findings for 11 (73%) were considered suspicious. CONCLUSION Contralateral cancer was found in 15 of 367 women (4.1%), with MRI showing 14 (93%). Eleven contralateral cancers (73%) were visible on PEM, but only three (20%) were recognized prospectively as suspicious. Lesions that are visible on PEM should be viewed as suspicious unless known to be benign by prior breast imaging or biopsy.
Symmetry-Aware Marginal Density Estimation

The Rao-Blackwell theorem is utilized to analyze and improve the scalability of inference in large probabilistic models that exhibit symmetries. A novel marginal density estimator is introduced and shown both analytically and empirically to outperform standard estimators by several orders of magnitude. The developed theory and algorithms apply to a broad class of probabilistic models including statistical relational models considered not susceptible to lifted probabilistic inference.
Low adherence of HIV providers to practice guidelines for hepatocellular carcinoma screening in HIV/hepatitis B coinfection.

BACKGROUND In the era of combination therapy for human immunodeficiency virus (HIV), liver disease, and hepatocellular carcinoma (HCC) are major causes of death for patients coinfected with HIV and hepatitis B virus (HBV). This study compared HIV provider and hepatologist awareness of and adherence to the American Association for the Study of Liver Diseases (AASLD) practice guidelines for chronic HBV management. The primary endpoint of HIV provider adherence to HCC screening recommendations was compared to that of hepatologists at a large metropolitan academic medical center. METHODS Medical record database searches by ICD-9 codes were used to identify HIV/HBV coinfected (n = 144) and HBV monoinfected (n = 225) patients who were seen at least twice over a 2-year period in outpatient clinics. Adherence to AASLD guidelines was assessed by chart review. Provider awareness was evaluated through a voluntary anonymous survey with knowledge-based questions. RESULTS Over a 2-year period, only 36.0% of HIV/HBV coinfected patients seen in HIV practices completed HCC screening compared to 81.8% of HBV monoinfected patients in hepatology practices (P < .00001). Similarly, HIV providers less frequently monitored HBV viral load (P < .0001), HBeAg/anti-HBe (P < .00001), HBsAg/anti-HBs (P < .00001) than hepatologists but screened more often for hepatitis A immunity (P = .028). Self-reported adherence and knowledge scores were similar among 19 HIV providers and 16 hepatologists. CONCLUSIONS HIV providers ordered significantly fewer HCC screening and HBV monitoring tests than hepatologists within a single academic medical center. In the setting of increased reliance on quality indicators for care, both patients and providers will benefit from greater adherence to established guidelines.
Adaptive Radio Modes in Sensor Networks: How Deep to Sleep?

Energy-efficient performance is a central challenge in sensor network deployments, and the radio is a major contributor to overall energy node consumption. Current energy- efficient MAC protocols for sensor networks use a fixed low power radio mode for putting the radio to sleep. Fixed low power modes involve an inherent tradeoff: deep sleep modes have low current draw and high energy cost and latency for switching the radio to active mode, while light sleep modes have quick and inexpensive switching to active mode with a higher current draw. This paper proposes adaptive radio low power sleep modes based on current traffic conditions in the network, as an enhancement to our recent RFID impulse low power wake-up mechanism. The paper also introduces a comprehensive node energy model, that includes energy components for radio switching, transmission, reception, listening, and sleeping, as well as the often disregarded micro-controller energy component to evaluate energy performance for both MicaZ and TelosB platforms, which use different MCU's. We then use the model for comparing the energy-related performance of RFIDImpulse enhanced with adaptive low power modes with BMAC and IEEE 802.15. 4 for the two node platforms under varying data rates. The comparative analysis confirms that RFIDImpulse with adaptive low power modes provides up to 20 times lower energy consumption than IEEE 802.15. 4 in low traffic scenario. The evaluation also yields the optimal settings of low power modes on the basis of data rates for each node platform, and it provides guidelines for the selection of appropriate MAC protocol, low power mode, and node platform for a given set of traffic requirements of a sensor network application.
Ultra High Throughput Sequencing in Human DNA Variation Detection: A Comparative Study on the NDUFA3-PRPF31 Region

Background Ultra high throughput sequencing (UHTS) technologies find an important application in targeted resequencing of candidate genes or of genomic intervals from genetic association studies. Despite the extraordinary power of these new methods, they are still rarely used in routine analysis of human genomic variants, in part because of the absence of specific standard procedures. The aim of this work is to provide human molecular geneticists with a tool to evaluate the best UHTS methodology for efficiently detecting DNA changes, from common SNPs to rare mutations. Methodology/Principal Findings We tested the three most widespread UHTS platforms (Roche/454 GS FLX Titanium, Illumina/Solexa Genome Analyzer II and Applied Biosystems/SOLiD System 3) on a well-studied region of the human genome containing many polymorphisms and a very rare heterozygous mutation located within an intronic repetitive DNA element. We identify the qualities and the limitations of each platform and describe some peculiarities of UHTS in resequencing projects. Conclusions/Significance When appropriate filtering and mapping procedures are applied UHTS technology can be safely and efficiently used as a tool for targeted human DNA variations detection. Unless particular and platform-dependent characteristics are needed for specific projects, the most relevant parameter to consider in mainstream human genome resequencing procedures is the cost per sequenced base-pair associated to each machine.
RNase P Ribozymes Inhibit the Replication of Human Cytomegalovirus by Targeting Essential Viral Capsid Proteins

An engineered RNase P-based ribozyme variant, which was generated using the in vitro selection procedure, was used to target the overlapping mRNA region of two proteins essential for human cytomegalovirus (HCMV) replication: capsid assembly protein (AP) and protease (PR). In vitro studies showed that the generated variant, V718-A, cleaved the target AP mRNA sequence efficiently and its activity was about 60-fold higher than that of wild type ribozyme M1-A. Furthermore, we observed a reduction of 98%–99% in AP/PR expression and an inhibition of 50,000 fold in viral growth in cells with V718-A, while a 75% reduction in AP/PR expression and a 500-fold inhibition in viral growth was found in cells with M1-A. Examination of the antiviral effects of the generated ribozyme on the HCMV replication cycle suggested that viral DNA encapsidation was inhibited and as a consequence, viral capsid assembly was blocked when the expression of AP and PR was inhibited by the ribozyme. Thus, our study indicates that the generated ribozyme variant is highly effective in inhibiting HCMV gene expression and blocking viral replication, and suggests that engineered RNase P ribozyme can be potentially developed as a promising gene-targeting agent for anti-HCMV therapy.
Technological Aptitude and Applications of Leuconostoc mesenteroides Bioactive Strains Isolated from Algerian Raw Camel Milk

Two strains (B7 and Z8) of the Leuconostoc mesenteroides subspecies mesenteroides that were isolated from Algerian camel milk from an initial pool of 13 strains and demonstrated a high ability to inhibit the growth of Listeria spp. were selected and characterised at the phenotypic and genotypic levels. Probiotic profiling and inhibition spectra against food borne pathogens in mixed cultures were also investigated. The bacteriocin produced by L. mesenteroides strain B7 was identified as leucocin B by specific PCR. In vitro studies demonstrated that both Leuconostoc mesenteroides strains exhibited a marked probiotic profile, showing high survival at low pH (2-3 and 4) in the presence of 0.5%, 1%, and 2% of bile salts and at pH 3 in the presence of 3 mg/mL pepsin. Susceptibility testing against antimicrobial agents was also performed for both strains. When tested in a mixed culture with Listeria innocua, Listeria ivanovii, or Staphylococcus aureus, strain B7 reduced the numbers of these species by 1.87, 1.78, and 1.38 log units, respectively. Consequently, these two strains were found to possess good probiotic properties in vitro and a high capacity for Listeria spp. inhibition in mixed cultures. Therefore, these strains have a favourable technological aptitude and a potential application as novel probiotic starters.
Ramifications of kinetic partitioning on usher‐mediated pilus biogenesis

The biogenesis of diverse adhesive structures in a variety of Gram‐negative bacterial species is dependent on the chaperone/usher pathway. Very little is known about how the usher protein translocates protein subunits across the outer membrane or how assembly of these adhesive structures occurs. We have discovered several mechanisms by which the usher protein acts to regulate the ordered assembly of type 1 pili, specifically through critical interactions of the chaperone–adhesin complex with the usher. A study of association and dissociation events of chaperone–subunit complexes with the usher in real time using surface plasmon resonance revealed that the chaperone–adhesin complex has the tightest and fastest association with the usher. This suggests that kinetic partitioning of chaperone–adhesin complexes to the usher is a defining factor in tip localization of the adhesin in the pilus. Furthermore, we identified and purified a chaperone–adhesin–usher assembly intermediate that was formed in vivo. Trypsin digestion assays showed that the usher in this complex was in an altered conformation, which was maintained during pilus assembly. The data support a model in which binding of the chaperone–adhesin complex to the usher stabilizes the usher in an assembly‐competent conformation and allows initiation of pilus assembly.
The Cr3C2 thermal spray coating on Al-Si substrate

Purpose: The objective of this work was to present the changes between the plasma sprayed and high velocity oxy-fuel (HVOF) wear Cr3C2 resistant coats. The differences in microstructure and microhardness of coatings were investigated. The characterization of fully melted, unmelted and partly melted areas was performed. Design/methodology/approach: The investigated coats contained very differentiate areas, especially plasma sprayed layers. Systematic investigations of microstructure by using optical, electron scanning microscopy and transmission electron microscopy selected fully melted, unmelted or partly melted areas and their characteristic features were performed. Microhardness of coats was measured and compared with the similar literature results. Findings: Microstructure of plasma sprayed coats was finding as consisting from elongating splats, additionally contained un-melted previous particle of powder and some voids and oxides. Contrary to this the HFOV coatingss were more uniform containing almost equiaxial grains. The microhardness of HFOV coatings was almost two times higher than plasma sprayed ones. Practical implications: The performed investigations provide information, which could be useful in the industrial practice about the essential features of wear resistant plasma sprayed coatings. Originality/value: It was assumed that HVOF coatings have more uniform microstructure, higher microhardness, which could suggests better resistance before the wear and grindability.
N-myc downstream regulated gene 1 modulates Wnt-β-catenin signalling and pleiotropically suppresses metastasis

Wnt signalling has pivotal roles in tumour progression and metastasis; however, the exact molecular mechanism of Wnt signalling in the metastatic process is as yet poorly defined. Here we demonstrate that the tumour metastasis suppressor gene, NDRG1, interacts with the Wnt receptor, LRP6, followed by blocking of the Wnt signalling, and therefore, orchestrates a cellular network that impairs the metastatic progression of tumour cells. Importantly, restoring NDRG1 expression by a small molecule compound significantly suppressed the capability of otherwise highly metastatic tumour cells to thrive in circulation and distant organs in animal models. In addition, our analysis of clinical cohorts data indicate that Wnt+/NDRG−/LRP+ signature has a strong predictable value for recurrence‐free survival of cancer patients. Collectively, we have identified NDRG1 as a novel negative master regulator of Wnt signalling during the metastatic progression, which opens an opportunity to define a potential therapeutic target for metastatic disease.
Reduction of Theta Rhythm Dissociates Grid Cell Spatial Periodicity from Directional Tuning

Inhibition of neuronal activity in the medial septum stops grid cells in the medial entorhinal cortex from firing in a grid. Grid cells recorded in the medial entorhinal cortex of freely moving rats exhibit firing at regular spatial locations and temporal modulation with theta rhythm oscillations (4 to 11 hertz). We analyzed grid cell spatial coding during reduction of network theta rhythm oscillations caused by medial septum (MS) inactivation with muscimol. During MS inactivation, grid cells lost their spatial periodicity, whereas head-direction cells maintained their selectivity. Conjunctive grid–by–head-direction cells lost grid cell spatial periodicity but retained head-direction specificity. All cells showed reduced rhythmicity in autocorrelations and cross-correlations. This supports the hypothesis that spatial coding by grid cells requires theta oscillations, and dissociates the mechanisms underlying the generation of entorhinal grid cell periodicity and head-direction selectivity.
Detection of elevated levels of tumour‐associated microRNAs in serum of patients with diffuse large B‐cell lymphoma

Circulating nucleic acids have been shown to have potential as non‐invasive diagnostic markers in cancer. We therefore investigated whether microRNAs also have diagnostic utility by comparing levels of tumour‐associated MIRN155 (miR‐155), MIRN210 (miR‐210) and MIRN21 (miR‐21) in serum from diffuse large B‐cell lymphoma (DLBCL) patients (n = 60) with healthy controls (n = 43). Levels were higher in patient than control sera (P = 0·009, 0·02 and 0·04 respectively). Moreover, high MIRN21 expression was associated with relapse‐free survival (P = 0·05). This is the first description of circulating microRNAs and suggests that microRNAs have potential as non‐invasive diagnostic markers for DLBCL and possibly other cancers.
Mechanical flutter stimulation induces a lasting response in the sensorimotor cortex as revealed with BOLD fMRI

It has been recently shown that 20 min of mechanical flutter stimulation induces lasting motor cortical excitability changes, as assessed by transcranial magnetic stimulation in relaxed hand muscles. The present functional magnetic resonance imaging (fMRI) study aims to examine if such neuromodulatory changes are reflected in the BOLD signal during a motor test. Therefore, two groups were recruited: one group receiving whole‐hand flutter stimulation with a frequency of 25 Hz (FSTIM group, n = 22) and a second group receiving no stimulation (NOSTIM group, n = 22). As motor test finger‐to‐thumb tapping was performed to activate a wide sensorimotor network during the fMRI measurements. Three fMRI measurements were obtained with this test: before stimulation (PRE), after stimulation (POST1), and 1 h after stimulation (POST2). Three regions of interest (ROIs) were defined: primary motor area (M1), primary somatosensory area (S1), and supplementary motor area. In the absence of baseline differences between both groups, the FSTIM group showed increased movement‐related brain activations compared with the NOSTIM group, both at POST1 and POST2. ROI analysis revealed increased blood‐oxygenation‐level‐dependent (BOLD) responses within contralateral S1 (+20%) and M1 (+25%) at POST1, which lasted until POST2. These poststimulatory effects within S1 and M1 obviously reflect neuroplastic changes associated with augmented cortical excitability. These findings are of high clinical relevance, for example, to improve the treatment of stroke patients. Hum Brain Mapp 34:2767–2774, 2013. © 2012 Wiley Periodicals, Inc.
STRUCTURAL VULNERABILITY AND RISK ASSESSMENT OF HARGHITA COUNTY’S INNER ROAD NETWORK

Structural Vulnerability and Risk Assessment of Harghita County’s Inner Road Network. Road transportation systems has become indispensable in everyday life. They have a high importance in global economic circuit, thus their vulnerability and risk analysis is indispensable. In this paper we want to make an intrinsic characterization the road network infrastructure of Harghita’s county. Our vulnerability assessment was based on the internal structure of the road network using elements from graph theory. We identified that the majority of the settlements are loosely coupled with each other, after three random edge failure the road network becomes unconnected. We also identified the heavily loaded route segments with the assumption of using the shortest distance path. These are the most vulnerable parts of road network. The failure of two of these route segments can lead to the isolation of the county seat from the other major cities. By developing a simulation environment in R we could model the consequences of any edge failure in terms of detour length and number of traveling persons which couldn’t reach their destination. Through this latter evaluation we made the risk assessment of the road network, calculating the number of traveling persons which are locked to their destination.
New Zealand weather extremes and climate-related events; a model-based assessment

Extreme weather and climate-related events can have pronounced environmental, economic and societal impacts, yet large natural variability within Earth’s constantly evolving climate system challenges the understanding of how these phenomena are changing. Increasingly powerful climate models have made it possible to study how certain factors, including anthropogenic forcings, have modified the likelihood and magnitude of extreme events. This study examines climate observations, reanalysis fields and model output to assess how weather extremes and climate-related events have changed. Part 1 investigates the detection and attribution of surface climate changes in relation to ozone depletion. Part 2 uses probabilistic event attribution and storyline frameworks to evaluate the role of anthropogenic forcings in altering the risk of extreme 1-day rainfall (RX1D) events for Christchurch, New Zealand in light of an unprecedented rainfall event that occurred in March 2014. Extremely large simulations of possible weather generated by the weather@home Australia-New Zealand (w@h ANZ) model found ozone forcings induced significant changes globally (< 3 hPa) in simulations of mean sea level pressure for 2013. A clear seasonal response was detected in the Southern Hemisphere (SH) circulation that was consistent with prior studies. Ozone-induced changes to average monthly rainfall were not significant in New Zealand with large natural variability and the limitation of one-year simulations challenging attribution to this climate forcing. In Christchurch, model and observational data give evidence of human activity increasing the likelihood and magnitude (+17%) of RX1D events despite significant drying trends for mean total rainfall (-66%) in austral summer. For events similar to that observed during March 2014, the fraction of attributable risk (FAR) is estimated to be 27.4%. This result was robust across different spatial averaging areas though is sensitive to the rainfall threshold examined. Unique meteorological conditions in combination with anomalously high sea surface temperatures (SSTs) in the tropical South Pacific were likely important to the occurrence of this extreme event. These results demonstrate how human influence can be detected in present-day weather and climate events.
From Slab Coupling to Slab Pull: Stress Segmentation in the Subducting Nazca Plate

We investigate the stress field that the Nazca slab experiences during subduction beneath the South American plate by determining the focal mechanisms of moderate subduction‐related earthquakes continuously from 20‐ to 120‐km depth and inverting for the stress directions of four slab regions. Our results show the sharp termination of the coupling zone, which is characterized by compressional stresses, uplift of the overlying mountain range, and likely the activation of preexisting slab structures. Beyond and below this zone slab pull is the dominant stress. Near the slab surface, we also find signatures of the activation of inherited structures. Deeper in the slab, fault orientations are more likely controlled by the stress field alone. Along the subduction pathway, we find indication for an increase of the absolute slab pull component of the stress field that correlates with an increase in event rate and the occurrence possibility of M > 7 intermediate depth earthquakes.