Miracle-dz/UniFAR-FTUs huggingface dataset:
Accuracy of electron density, effective atomic number, and iodine concentration determination with a dual‐layer dual‐energy computed tomography system

PURPOSE This study aimed to quantitate the accuracy of the determination of electron density (ED), effective atomic number (Zeff ), and iodine concentration, directed for more accurate radiation therapy planning, with a new dual-layer dual-energy computed tomography (DL-DECT) system. The dependence of the accuracy of these values on the scan and reconstruction parameters, as well as on the phantom size, was also examined. METHODS Measurements were performed on a commercial DECT system with a DL detector (IQon Spectral CT, Philips Healthcare), using phantoms with various tissue-equivalent inserts as well as iodine and calcium inserts of different concentrations. The expected values of ED and Zeff for the insert materials were derived from the chemical compositions provided by the vendors. The nominal scan condition for the accuracy measurements was 120 kVp, 20 mGy CTDIvol, 0.812 pitch, 16 × 0.625 mm collimation, and 0.33-second gantry rotation. RESULTS The median deviation of ED ranged from -0.1% to 1.1% for all Gammex tissue inserts. The median deviation of Zeff ranged from -2.3% to 1.7% for soft tissue and bone inserts and was ≤7% for lung inserts. The absolute deviations for ED and Zeff in lung inserts were within 1% of the ED of water and 1 a.u. , respectively. For two different phantom sizes, the ED values agreed to within 0.7% and the Zeff values agreed to within 2%, except for the lung inserts. When the scan parameters were changed from 120 kVp/20 mGy to 140 kVp/30 mGy, the ED differed within [-0.51%, 0.65%] and the Zeff differed within [-1.1%, 0.23%] for all materials except lungs, in which Zeff increased by 2.4%. The accuracy of ED and Zeff measurement at 120 kVp was no worse than that at 140 kVp. For iodine quantitation, the median absolute deviations from the nominal values were up to 0.3 mg/mL for iodine concentrations of 2-20 mg/mL, with an overall median deviation of -0.1 mg/mL. Iodine and calcium were well separated on the ED-Zeff scatter plot, even at the lowest concentrations (2 mg/mL for iodine and 50 mg/mL for calcium). CONCLUSIONS The accuracy of ED measurement, Zeff determination, and iodine quantitation derived from DL-DECT was demonstrated with phantom measurements. The accuracies were not sensitive to scan and reconstruction parameters, namely tube potential, dose, rotation time, and spectral reconstruction level, especially in the case of electron density.
An improved achievable rate region for causal cognitive radio

This paper studies two-user causal cognitive radio channels, in which the secondary user has causal knowledge about the message being sent by the primary user. An inner bound on the capacity region of such channels is established by employing a coding strategy consisting of block Markov superposition and dirty paper encoding, and backward decoding. An illustrative example in the Gaussian case is provided.
NKT cells are phenotypically and functionally diverse

NK1.1+α βTCR+ (NKT) cells have several important roles including tumor rejection and prevention of autoimmune disease. Although both CD4+ and CD4–CD8– double‐negative (DN) subsets of NKT cells have been identified, they are usually described as one population. Here, we show that NKT cells are phenotypically, functionally and developmentally heterogeneous, and that three distinct subsets (CD4+, DN and CD8+) are differentially distributed in a tissue‐specific fashion. CD8+ NKT cells are present in all tissues but the thymus, and are highly enriched for CD8α+β– cells. These subsets differ in their expression of a range of cell surface molecules (Vβ8, DX5, CD69, CD45RB, Ly6C) and in their ability to produce IL‐4 and IFN‐γ, with splenic NKT cell subsets producing lower levels than thymic NKT cells. Developmentally, most CD4+ and DN NKT cells are thymus dependent, in contrast to CD8+ NKT cells, and are also present amongst recent thymic emigrants in spleen and liver. TCR Jα281‐deficient mice show a dramatic deficiency in thymic NKT cells, whereas a significant NKT cell population (enriched for the DN and CD8+ subsets) is still present in the periphery. Taken together, this study reveals a far greater level of complexity within the NKT cell population than previously recognized.
A mutagenesis-based approach identifies amino acids in the N-terminal part of Francisella tularensis IglE that critically control Type VI system-mediated secretion

ABSTRACT The Gram-negative bacterium Francisella tularensis is the etiological agent of the zoonotic disease tularemia. Its life cycle is characterized by an ability to survive within phagocytic cells through phagosomal escape and replication in the cytosol, ultimately causing inflammasome activation and host cell death. Required for these processes is the Francisella Pathogenicity Island (FPI), which encodes a Type VI secretion system (T6SS) that is active during intracellular infection. In this study, we analyzed the role of the FPI-component IglE, a lipoprotein which we previously have shown to be secreted in a T6SS-dependent manner. We demonstrate that in F. tularensis LVS, IglE is an outer membrane protein. Upon infection of J774 cells, an ΔiglE mutant failed to escape from phagosomes, and subsequently, to multiply and cause cytopathogenicity. Moreover, ΔiglE was unable to activate the inflammasome, to inhibit LPS-stimulated secretion of TNF-α, and showed marked attenuation in the mouse model. In F. novicida, IglE was required for in vitro secretion of IglC and VgrG. A mutagenesis-based approach involving frameshift mutations and alanine substitution mutations within the first ∼ 38 residues of IglE revealed that drastic changes in the sequence of the extreme N-terminus (residues 2–6) were well tolerated and, intriguingly, caused hyper-secretion of IglE during intracellular infection, while even subtle mutations further downstream lead to impaired protein function. Taken together, this study highlights the importance of IglE in F. tularensis pathogenicity, and the contribution of the N-terminus for all of the above mentioned processes.
HD-Index: Pushing the Scalability-Accuracy Boundary for Approximate kNN Search in High-Dimensional Spaces

Nearest neighbor searching of large databases in high-dimensional spaces is inherently difficult due to the curse of dimensionality. A flavor of approximation is, therefore, necessary to practically solve the problem of nearest neighbor search. In this paper, we propose a novel yet simple indexing scheme, HD-Index, to solve the problem of approximate k-nearest neighbor queries in massive high-dimensional databases. HD-Index consists of a set of novel hierarchical structures called RDB-trees built on Hilbert keys of database objects. The leaves of the RDB-trees store distances of database objects to reference objects, thereby allowing efficient pruning using distance filters. In addition to triangular inequality, we also use Ptolemaic inequality to produce better lower bounds. Experiments on massive (up to billion scale) high-dimensional (up to 1000+) datasets show that HD-Index is effective, efficient, and scalable.
Rotation-bed magnetic refrigeration apparatus

Rotary magnetic refrigeration apparatus has a ring (21) a magnetic reproducing beds arranged in (22), this ring is mounted for rotation about a central axis, each bed, the ring (21) is rotated to moved into the magnetic field formed by the magnet (29) when and out from there. Heat transfer fluid, the dispensing valve (24) is guided to the reproduction bed (22) and from there, the distribution valve is connected to the hot end and cold end of the bed by conduit, bed (22) ring (21 ) rotates together with. The dispensing valve (24) has a fixed valve member connected to the hot heat exchanger (34) and the cold heat exchanger (38) by conduit. Magnetocaloric material contained in the bed is a porous, it can flow heat transfer fluid therethrough. The dispensing valve (24) directs the heat transfer fluid to the hot end of the bed that is outside the magnetic field, the fluid flows to the cold end through which, where, back to the distribution valve (24), and bed there when in the magnetic field, the distribution valve (24) directs the fluid to the cold end of the bed, through which flow the hot end, where the fluid is returned to the distribution valve, completing an active magnetic regeneration cycle. Fluid flowing through the conduit, remains however, or still not flow in a single direction, to minimize the dead volume of the conduit.
IP3-4 kinase Arg1 regulates cell wall homeostasis and surface architecture to promote Cryptococcus neoformans infection in a mouse model

ABSTRACT We previously identified a series of inositol polyphosphate kinases (IPKs), Arg1, Ipk1, Kcs1 and Asp1, in the opportunistic fungal pathogen Cryptococcus neoformans. Using gene deletion analysis, we characterized Arg1, Ipk1 and Kcs1 and showed that they act sequentially to convert IP3 to PP-IP5 (IP7), a key metabolite promoting stress tolerance, metabolic adaptation and fungal dissemination to the brain. We have now directly characterized the enzymatic activity of Arg1, demonstrating that it is a dual specificity (IP3/IP4) kinase producing IP5. We showed previously that IP5 is further phosphorylated by Ipk1 to produce IP6, which is a substrate for the synthesis of PP-IP5 by Kcs1. Phenotypic comparison of the arg1Δ and kcs1Δ deletion mutants (both PP-IP5-deficient) reveals that arg1Δ has the most deleterious phenotype: while PP-IP5 is essential for metabolic and stress adaptation in both mutant strains, PP-IP5 is dispensable for virulence-associated functions such as capsule production, cell wall organization, and normal N-linked mannosylation of the virulence factor, phospholipase B1, as these phenotypes were defective only in arg1Δ. The more deleterious arg1Δ phenotype correlated with a higher rate of arg1Δ phagocytosis by human peripheral blood monocytes and rapid arg1Δ clearance from lung in a mouse model. This observation is in contrast to kcs1Δ, which we previously reported establishes a chronic, confined lung infection. In summary, we show that Arg1 is the most crucial IPK for cryptococcal virulence, conveying PP-IP5–dependent and novel PP-IP5–independent functions.
Body size downgrading of mammals over the late Quaternary

Megafaunal loss Today, it is well known that human activities put larger animals at greater risk of extinction. Such targeting of the largest species is not new, however. Smith et al. show that biased loss of large-bodied mammal species from ecosystems is a signature of human impacts that has been following hominin migrations since the Pleistocene. If the current trend continues, terrestrial mammal body sizes will become smaller than they have been over the past 45 million years. Megafaunal mammals have a major impact on the structure of ecosystems, so their loss could be particularly damaging. Science, this issue p. 310 Hominins have caused size-selective extinctions of large mammals since the Pleistocene. Since the late Pleistocene, large-bodied mammals have been extirpated from much of Earth. Although all habitable continents once harbored giant mammals, the few remaining species are largely confined to Africa. This decline is coincident with the global expansion of hominins over the late Quaternary. Here, we quantify mammalian extinction selectivity, continental body size distributions, and taxonomic diversity over five time periods spanning the past 125,000 years and stretching approximately 200 years into the future. We demonstrate that size-selective extinction was already under way in the oldest interval and occurred on all continents, within all trophic modes, and across all time intervals. Moreover, the degree of selectivity was unprecedented in 65 million years of mammalian evolution. The distinctive selectivity signature implicates hominin activity as a primary driver of taxonomic losses and ecosystem homogenization. Because megafauna have a disproportionate influence on ecosystem structure and function, past and present body size downgrading is reshaping Earth’s biosphere.
Surface Vulnerability of Cerebral Cortex to Major Depressive Disorder

Major depressive disorder (MDD) is accompanied by atypical brain structure. This study first presents the alterations in the cortical surface of patients with MDD using multidimensional structural patterns that reflect different neurodevelopment. Sixteen first-episode, untreated patients with MDD and 16 matched healthy controls underwent a magnetic resonance imaging (MRI) scan. The cortical maps of thickness, surface area, and gyrification were examined using the surface-based morphometry (SBM) approach. Increase of cortical thickness was observed in the right posterior cingulate region and the parietal cortex involving the bilateral inferior, left superior parietal and right paracentral regions, while decreased thickness was noted in the parietal cortex including bilateral pars opercularis and left precentral region, as well as the left rostral-middle frontal regions in patients with MDD. Likewise, increased or decreased surface area was found in five sub-regions of the cingulate gyrus, parietal and frontal cortices (e.g., bilateral inferior parietal and superior frontal regions). In addition, MDD patients exhibited a significant hypergyrification in the right precentral and supramarginal region. This integrated structural assessment of cortical surface suggests that MDD patients have cortical alterations of the frontal, parietal and cingulate regions, indicating a vulnerability to MDD during earlier neurodevelopmental process.
Injuries in Runners; A Systematic Review on Risk Factors and Sex Differences

Background The popularity of running continues to increase, which means that the incidence of running-related injuries will probably also continue to increase. Little is known about risk factors for running injuries and whether they are sex-specific. Objectives The aim of this study was to review information about risk factors and sex-specific differences for running-induced injuries in adults. Search Strategy The databases PubMed, EMBASE, CINAHL and Psych-INFO were searched for relevant articles. Selection Criteria Longitudinal cohort studies with a minimal follow-up of 1 month that investigated the association between risk factors (personal factors, running/training factors and/or health and lifestyle factors) and the occurrence of lower limb injuries in runners were included. Data Collection and Analysis Two reviewers’ independently selected relevant articles from those identified by the systematic search and assessed the risk of bias of the included studies. The strength of the evidence was determined using a best-evidence rating system. Sex differences in risk were determined by calculating the sex ratio for risk factors (the risk factor for women divided by the risk factor for men). Main Results Of 400 articles retrieved, 15 longitudinal studies were included, of which 11 were considered high-quality studies and 4 moderate-quality studies. Overall, women were at lower risk than men for sustaining running-related injuries. Strong and moderate evidence was found that a history of previous injury and of having used orthotics/inserts was associated with an increased risk of running injuries. Age, previous sports activity, running on a concrete surface, participating in a marathon, weekly running distance (30–39 miles) and wearing running shoes for 4 to 6 months were associated with a greater risk of injury in women than in men. A history of previous injuries, having a running experience of 0–2 years, restarting running, weekly running distance (20–29 miles) and having a running distance of more than 40 miles per week were associated with a greater risk of running-related injury in men than in women. Conclusions Previous injury and use of orthotic/inserts are risk factors for running injuries. There appeared to be differences in the risk profile of men and women, but as few studies presented results for men and women separately, the results should be interpreted with caution. Further research should attempt to minimize methodological bias by paying attention to recall bias for running injuries, follow-up time, and the participation rate of the identified target group.
Tensor Matched Subspace Detection

The problem of testing whether an incomplete tensor lies in a given tensor subspace, called \textit{tensor matched subspace detection}, is significant when it is unavoidable to have missing entries. Compared with the matrix case, the tensor matched subspace detection problem is much more challenging due to the curse of dimensionality and the intertwinement between the sampling operator and the tensor product operation. In this paper, we investigate the subspace detection problem for the transform-based tensor models. Under this framework, tensor subspaces and the orthogonal projection onto a given subspace are defined, and the energies of a tensor outside the given subspace (also called \textit{residual energy} in statistics) with tubal-sampling and elementwise-sampling are derived. We have proved that the residual energy of sampling signals is bounded with high probability. Based on the residual energy, the reliable detection is feasible.
Spermatogenesis‐associated proteins at different developmental stages of buffalo testicular seminiferous tubules identified by comparative proteomic analysis

The testicular seminiferous tubules contain Sertoli cells and different types of spermatogenic cells. They provide the microenvironment for spermatogenesis, but the precise molecular mechanism of spermatogenesis is still not well known. Here, we have employed tandem mass tag coupled to LC‐MS/MS with the high‐throughput quantitative proteomics technology to explore the protein expression from buffalo testicular seminiferous tubules at three different developmental stages (prepuberty, puberty, and postpuberty). The results show 304 differentially expressed proteins with a ≥2‐fold change, and bioinformatics analysis indicates that 27 of these may be associated with spermatogenesis. Expression patterns of seven selected proteins were verified via Western blot and quantitative RT‐PCR analysis, and further cellular localizations of these proteins by immunohistochemical or immunofluorescence analysis. Taken together, the results provide potential molecular markers of spermatogenesis and provide a rich resource for further studies on male reproduction regulation.
A reliable controller deployment strategy based on network condition evaluation in SDN

As a new network paradigm, Software Defined Networking (SDN) decouples control plane from data plane and has the programmability. With the network size increases, the control plane usually deploys multiple controllers to solve the scalability of SDN. However, it also introduces a new issue that is how to place controller reliably in the network. Meanwhile, the unreliable multi-controller deployment will bring about low network stability and high packet loss rate. In order to address this problem, we propose a Reliable Controller Deployment (RCD) strategy based on network condition evaluation. Firstly, we build a multi-controller network model and define the evaluation parameters for network condition, which include the node reliability and path quality. Then, through considering the weighted node reliability and path quality simultaneously, RCD assesses the controller nodes and selects the optimal locations for controller deployment. Moreover, we design the corresponding algorithm with the help of simulated annealing to implement this strategy. Finally, the simulation results show that RCD has the better performance in controller reliability and network stability.
Analysis and classification of ECG-waves and rhythms using circular statistics and vector strength

Abstract The most common way to analyse heart rhythm is to calculate the RR-interval and the heart rate variability. For further evaluation, descriptive statistics are often used. Here we introduce a new and more natural heart rhythm analysis tool that is based on circular statistics and vector strength. Vector strength is a tool to measure the periodicity or lack of periodicity of a signal. We divide the signal into non-overlapping window segments and project the detected R-waves around the unit circle using the complex exponential function and the median RR-interval. In addition, we calculate the vector strength and apply circular statistics as wells as an angular histogram on the R-wave vectors. This approach enables an intuitive visualization and analysis of rhythmicity. Our results show that ECG-waves and rhythms can be easily visualized, analysed and classified by circular statistics and vector strength.
Anti social comment classification based on kNN algorithm

Billions of contributions are made every day across multiple online communities and social media websites in the form of social messages, social blogs and online discussion. The aim of this paper is to identify such comments and posts which are racist and malicious in nature so that they could be effetely banned and removed in order to counter them. This article uses set of documents with racist comments as text corpus on which appropriate machine learning algorithm is applied to detect racist comments or meaning. To detect anti-social content there is a need to find the extent of similarity between a pair of text messages as a source and classified terms which are antisocial or in discriminating terms. The approach devised in this article to detect antisocial behavior is a technique based on term frequency based content classification.
Microbiota promotes systemic T-cell survival through suppression of an apoptotic factor

Significance Little is known about the molecular mechanisms by which the microbiota influences T-cell responses. We have determined that a secreted protein, Erdr1, is highly upregulated in germfree T cells and that microbial products can suppress Erdr1 through MyD88. Erdr1 functions to induce apoptosis through a Fas-dependent pathway that can impact the process of immunization and dictate the clinical course of autoimmunity. Thus, microbial colonization functions to regulate T-cell survival through suppression of the cytokine Erdr1, revealing a potentially new T-cell factor that can be therapeutically targeted. Symbiotic microbes impact the severity of a variety of diseases through regulation of T-cell development. However, little is known regarding the molecular mechanisms by which this is accomplished. Here we report that a secreted factor, Erdr1, is regulated by the microbiota to control T-cell apoptosis. Erdr1 expression was identified by transcriptome analysis to be elevated in splenic T cells from germfree and antibiotic-treated mice. Suppression of Erdr1 depends on detection of circulating microbial products by Toll-like receptors on T cells, and this regulation is conserved in human T cells. Erdr1 was found to function as an autocrine factor to induce apoptosis through caspase 3. Consistent with elevated levels of Erdr1, germfree mice have increased splenic T-cell apoptosis. RNA sequencing of Erdr1-overexpressing cells identified the up-regulation of genes involved in Fas-mediated cell death, and Erdr1 fails to induce apoptosis in Fas-deficient cells. Importantly, forced changes in Erdr1 expression levels dictate the survival of auto-reactive T cells and the clinical outcome of neuro-inflammatory autoimmune disease. Cellular survival is a fundamental feature regulating appropriate immune responses. We have identified a mechanism whereby the host integrates signals from the microbiota to control T-cell apoptosis, making regulation of Erdr1 a potential therapeutic target for autoimmune disease.