Miracle-dz/UniFAR-FTUs huggingface dataset:
Handheld Real-Time LED-Based Photoacoustic and Ultrasound Imaging System for Accurate Visualization of Clinical Metal Needles and Superficial Vasculature to Guide Minimally Invasive Procedures

Ultrasound imaging is widely used to guide minimally invasive procedures, but the visualization of the invasive medical device and the procedure’s target is often challenging. Photoacoustic imaging has shown great promise for guiding minimally invasive procedures, but clinical translation of this technology has often been limited by bulky and expensive excitation sources. In this work, we demonstrate the feasibility of guiding minimally invasive procedures using a dual-mode photoacoustic and ultrasound imaging system with excitation from compact arrays of light-emitting diodes (LEDs) at 850 nm. Three validation experiments were performed. First, clinical metal needles inserted into biological tissue were imaged. Second, the imaging depth of the system was characterized using a blood-vessel-mimicking phantom. Third, the superficial vasculature in human volunteers was imaged. It was found that photoacoustic imaging enabled needle visualization with signal-to-noise ratios that were 1.2 to 2.2 times higher than those obtained with ultrasound imaging, over insertion angles of 26 to 51 degrees. With the blood vessel mimicking phantom, the maximum imaging depth was 38 mm. The superficial vasculature of a human middle finger and a human wrist were clearly visualized in real-time. We conclude that the LED-based system is promising for guiding minimally invasive procedures with peripheral tissue targets.
Quantitative Proteomic Approach Identifies Vpr Binding Protein as Novel Host Factor Supporting Influenza A Virus Infections in Human Cells*

Influenza A virus (IAV) infections are a major cause for respiratory disease in humans, which affects all age groups and contributes substantially to global morbidity and mortality. IAV have a large natural host reservoir in avian species. However, many avian IAV strains lack adaptation to other hosts and hardly propagate in humans. While seasonal or pandemic IAV strains replicate efficiently in permissive human cells, many avian IAV cause abortive nonproductive infections in these hosts despite successful cell entry. However, the precise reasons for these differential outcomes are poorly defined. We hypothesized that the distinct course of an IAV infection with a given virus strain is determined by the differential interplay between specific host and viral factors. By using Spike-in SILAC mass spectrometry-based quantitative proteomics we characterized sets of cellular factors whose abundance is specifically up- or downregulated in the course of permissive versus nonpermissive IAV infection, respectively. This approach allowed for the definition and quantitative comparison of about 3500 proteins in human lung epithelial cells in response to seasonal or low-pathogenic avian H3N2 IAV. Many identified proteins were similarly regulated by both virus strains, but also 16 candidates with distinct changes in permissive versus nonpermissive infection were found. RNAi-mediated knockdown of these differentially regulated host factors identified Vpr binding protein (VprBP) as proviral host factor because its downregulation inhibited efficient propagation of seasonal IAV whereas overexpression increased viral replication of both seasonal and avian IAV. These results not only show that there are similar differences in the overall changes during permissive and nonpermissive influenza virus infections, but also provide a basis to evaluate VprBP as novel anti-IAV drug target.
Genetic absence of PD-1 promotes accumulation of terminally differentiated exhausted CD8+ T cells

Using PD-1–deficient mice and co-adoptive transfer approaches, Odorizzi et al. demonstrate that PD-1 is not required for the induction of CD8+ T cell exhaustion (TEX) in chronic LCMV infection. The absence of PD-1 leads to more cytotoxic, but terminally differentiated TEX, with compromised long-term durability. PD-1 may well serve to protect TEX from excessive overstimulation, proliferation, and terminal differentiation.
Caregiver maltreatment causes altered neuronal DNA methylation in female rodents

Abstract Negative experiences with a caregiver during infancy can result in long-term changes in brain function and behavior, but underlying mechanisms are not well understood. It is our central hypothesis that brain and behavior changes are conferred by early childhood adversity through epigenetic changes involving DNA methylation. Using a rodent model of early-life caregiver maltreatment (involving exposure to an adverse caregiving environment for postnatal days 1–7), we have previously demonstrated abnormal methylation of DNA associated with the brain-derived neurotrophic factor (Bdnf) gene in the medial prefrontal cortex (mPFC) of adult rats. The aim of the current study was to characterize Bdnf DNA methylation in specific cell populations within the mPFC. In the prefrontal cortex, there is approximately twice as many neurons as glia, and studies have recently shown differential and distinctive DNA methylation patterns in neurons versus nonneurons. Here, we extracted nuclei from the mPFC of adult animals that had experienced maltreatment and used fluorescence-activated cell sorting to isolate cell types before performing bisulfite sequencing to estimate methylation of cytosine–guanine sites. Our data indicate that early-life stress induced methylation of DNA associated with Bdnf IV in a cell-type and sex-specific manner. Specifically, females that experienced early-life maltreatment exhibited greater neuronal cytosine–guanine methylation compared to controls, while no changes were detected in Bdnf methylation in males regardless of cell type. These changes localize the specificity of our previous findings to mPFC neurons and highlight the capacity of maltreatment to cause methylation changes that are likely to have functional consequences for neuronal function.
Correlation between changes in blood fatty acid composition and visual sustained attention performance in children with inattention : effect of dietary n 3 fatty acids containing phospholipids 1 – 3

Background: Increasing evidence supports n 3 fatty acid (FA) supplementation for patients with psychiatric disorders, such as attention deficit hyperactivity disorder. However, the exact metabolic fate of dietary eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) on different glyceride carriers remains unclear. Objective: We investigated whether conjugation of EPA and DHA to phospholipid (PL-n 3) or to triacylglycerol (fish oil; FO) affects their incorporation in blood compartments and influences executive functioning. Design: Children aged 8–13 y with impaired visual sustained attention performance received placebo, 250 mg/d EPA DHA esterified to PL-n 3 (300 mg/d phosphatidylserine), or FO for 3 mo in a randomized double-blind manner. Main outcome measures included plasma and erythrocyte FA profile and continuous performance test results (Test of Variables of Attention; TOVA). Results: Sixty of the 83 children enrolled completed the interventions (n 18–21 per group). There was an enrichment of EPA (1.5–2.2-fold), docosapentaenoic acid (DPA; 1.2-fold), and DHA (1.3-fold) in the PL fraction in the plasma of FOand PL-n 3–fed children. In erythrocytes, only PL-n 3 resulted in a significant reduction ( 30%) of very-long-chain saturated FAs (C20-24) and in an increase (1.2and 2.2-fold, respectively) in linoleic acid and DPA. Total TOVA scores increased in the PL-n 3 (x SD: 3.35 1.86) and FO (1.72 1.67) groups but not in the placebo group ( 0.42 2.51) (PL-n 3 FO placebo; P 0.001). A significant correlation between the alterations in FAs and increased TOVA scores mainly occurred in the PL-n 3 group. Conclusion: Consumption of EPA DHA esterified to different carriers had different effects on the incorporation of these FAs in blood fractions and on the visual sustained attention performance in children. This trial was registered at clinicaltrials.gov as NCT00382616. Am J Clin Nutr 2008;87:1170–80.
Variable Responses of Benthic Communities to Anomalously Warm Sea Temperatures on a High-Latitude Coral Reef

High-latitude reefs support unique ecological communities occurring at the biogeographic boundaries between tropical and temperate marine ecosystems. Due to their lower ambient temperatures, they are regarded as potential refugia for tropical species shifting poleward due to rising sea temperatures. However, acute warming events can cause rapid shifts in the composition of high-latitude reef communities, including range contractions of temperate macroalgae and bleaching-induced mortality in corals. While bleaching has been reported on numerous high-latitude reefs, post-bleaching trajectories of benthic communities are poorly described. Consequently, the longer-term effects of thermal anomalies on high-latitude reefs are difficult to predict. Here, we use an autonomous underwater vehicle to conduct repeated surveys of three 625 m2 plots on a coral-dominated high-latitude reef in the Houtman Abrolhos Islands, Western Australia, over a four-year period spanning a large-magnitude thermal anomaly. Quantification of benthic communities revealed high coral cover (>70%, comprising three main morphospecies) prior to the bleaching event. Plating Montipora was most susceptible to bleaching, but in the plot where it was most abundant, coral cover did not change significantly because of post-bleaching increases in branching Acropora. In the other two plots, coral cover decreased while macroalgal cover increased markedly. Overall, coral cover declined from 73% to 59% over the course of the study, while macroalgal cover increased from 11% to 24%. The significant differences in impacts and post-bleaching trajectories among plots underline the importance of understanding the underlying causes of such variation to improve predictions of how climate change will affect reefs, especially at high-latitudes.
Process Oriented Information Systems Architectures in Healthcare

In order to create value for customers efficiently and to avoid unnecessary or redundant activity, organizations need IT support that interacts well with their business processes. In addition, healthcare organizations require transparent communication between the various actors and between IT systems. A new type of process oriented integration architecture has been developed using software devices known as process managers. These use simple graphical models to visualize business process integration and facilitate its management and monitoring. This article discusses the benefits and difficulties of introducing process manager technology into healthcare, based on a project to integrate IT systems over the patient process and across several organizations. Particular problems are caused by communication across organizational boundaries, e.g. due to security issues. However, the technology is able to manage and monitor processes and to make communication simpler and saf
Diversity of Human Copy Number Variation and Multicopy Genes

Evolution, Gene Number, and Disease Slight variations in the numbers of copies of genes influence human disease and other characters. Variants can be hard to detect when they lie in heavily duplicated and widely similar regions of sequence known as “dark matter. ” Sudmant et al. (p. 641) have methods to tease apart the duplicated regions to reveal singly unique nucleotide identifiers. These have turned out to be among the most variable seen in different human population groups—most notably among genes for neurodevelopment and neurological diseases. Such polymorphisms can be genotyped with specificity and may help us understand how variation in copy number may affect human evolution and disease. Specific gene copies can be identified in regions of high copy number variability in the human genome. Copy number variants affect both disease and normal phenotypic variation, but those lying within heavily duplicated, highly identical sequence have been difficult to assay. By analyzing short-read mapping depth for 159 human genomes, we demonstrated accurate estimation of absolute copy number for duplications as small as 1.9 kilobase pairs, ranging from 0 to 48 copies. We identified 4.1 million “singly unique nucleotide” positions informative in distinguishing specific copies and used them to genotype the copy and content of specific paralogs within highly duplicated gene families. These data identify human-specific expansions in genes associated with brain development, reveal extensive population genetic diversity, and detect signatures consistent with gene conversion in the human species. Our approach makes ~1000 genes accessible to genetic studies of disease association.
Automated Debugging with Tractable Probabilistic Programming

Probabilistic programming languages allow domain experts to specify generative models in a high-level language, and reason about those models using domainindependent algorithms. Given an input, a probabilistic program generates a distribution over outputs. In this work, we instead use probabilistic programming to explicitly reason about the distribution over programs, rather than outputs. We propose Tractable Probabilistic Programs (TPP), a language to represent rich probabilistic dependencies between different parts of a program; we make use of the recent work on sum-product networks to ensure that inference remains tractable. We explain how TPP can be applied to the problem of automated program debugging; given a corpus of buggy programs, a TPP model can be learned to capture a probability distribution over the location of the bug. The model can also incorporate additional sources of information, such as coverage statistics on test suites. We also briefly outline how TPP can be used to solve the more ambitious problem of fault correction, i.e. predicting the most probable true program conditioned on a buggy one. The ability to learn common patterns of bugs and incorporate multiple sources of information potentially makes TPP useful as a unifying framework for automated program debugging.
Optimization of query streams using semantic prefetching

Streams of relational queries submitted by client applications to database servers contain patterns that can be used to predict future requests. We present the Scalpel system, which detects these patterns and optimizes request streams using context-based predictions of future requests. Scalpel uses its predictions to provide a form of semantic prefetching, which involves combining a predicted series of requests into a single request that can be issued immediately. Scalpel's semantic prefetching reduces not only the latency experienced by the application but also the total cost of query evaluation. We describe how Scalpel learns to predict optimizable request patterns by observing the application's request stream during a training phase. We also describe the types of query pattern rewrites that Scalpels cost-based optimizer considers. Finally, we present empirical results that show the costs and benefits of Scalpel's optimizations.
Probabilistic Integration

A research frontier has emerged in scientific computation, founded on the principle that numerical error entails epistemic uncertainty that ought to be subjected to statistical analysis. This viewpoint raises several interesting challenges, including the design of statistical methods that enable the coherent propagation of probabilities through a (possibly deterministic) computational pipeline. This paper examines thoroughly the case for probabilistic numerical methods in statistical computation and a specific case study is presented for Markov chain and Quasi Monte Carlo methods. A probabilistic integrator is equipped with a full distribution over its output, providing a measure of epistemic uncertainty that is shown to be statistically valid at finite computational levels, as well as in asymptotic regimes. The approach is motivated by expensive integration problems, where, as in krigging, one is willing to expend, at worst, cubic computational effort in order to gain uncertainty quantification. There, probabilistic integrators enjoy the "best of both worlds", leveraging the sampling efficiency of Monte Carlo methods whilst providing a principled route to assessment of the impact of numerical error on scientific conclusions. Several substantial applications are provided for illustration and critical evaluation, including examples from statistical modelling, computer graphics and uncertainty quantification in oil reservoir modelling.
Type 2 Innate Immunity in Helminth Infection Is Induced Redundantly and Acts Autonomously following CD11c+ Cell Depletion

ABSTRACT Infection with gastrointestinal helminths generates a dominant type 2 response among both adaptive (Th2) and innate (macrophage, eosinophil, and innate lymphoid) immune cell types. Two additional innate cell types, CD11chigh dendritic cells (DCs) and basophils, have been implicated in the genesis of type 2 immunity. Investigating the type 2 response to intestinal nematode parasites, including Heligmosomoides polygyrus and Nippostrongylus brasiliensis, we first confirmed the requirement for DCs in stimulating Th2 adaptive immunity against these helminths through depletion of CD11chigh cells by administration of diphtheria toxin to CD11c.DOG mice. In contrast, responsiveness was intact in mice depleted of basophils by antibody treatment. Th2 responses can be induced by adoptive transfer of DCs, but not basophils, exposed to soluble excretory-secretory products from these helminths. However, innate type 2 responses arose equally strongly in the presence or absence of CD11chigh cells or basophils; thus, in CD11c.DOG mice, the alternative activation of macrophages, as measured by expression of arginase-1, RELM-α, and Ym-1 (Chi3L3) in the intestine following H. polygyrus infection or in the lung following N. brasiliensis infection, was unaltered by depletion of CD11c-expressing DCs and alveolar macrophages or by antibody-mediated basophil depletion. Similarly, goblet cell-associated RELM-β in lung and intestinal tissues, lung eosinophilia, and expansion of innate lymphoid (“nuocyte”) populations all proceeded irrespective of depletion of CD11chigh cells or basophils. Thus, while CD11chigh DCs initiate helminth-specific adaptive immunity, innate type 2 cells are able to mount an autonomous response to the challenge of parasite infection.
Performance Analysis of Proactive, Reactive and Hybrid MANET Routing Protocols on IEEE 802.11 Standard

MANET consists of mobile nodes which exchange information dynamically among them over wireless links. The most important element of MANET is Routing Protocols which are needed to handle dynamic communication and also find route so as to deliver data packets to the correct destination. Performance of routing protocols is an important issue because of dynamic nature of MANET. In this paper performance of AODV, OLSR and GRP routing protocols is evaluated for FTP based application traffic on IEEE 802.11 WLAN Standard and 48 Mbps data rate. The network performance is evaluated by using OPNET simulator based on various quantitative metrics- Network Load, Throughput, Retransmission Attempts and Media Access Delay by varying physical characteristics and number of nodes. A comparative performance analysis of these protocols have been carried out in this paper and in the last conclusion will be presented which demonstrate that performance of routing protocols differs by varying the network and selection of accurate routing protocol according to the network ultimately influences the efficiency of the network in a magnificent way.
Testing Attribute Selection Algorithms for Classification Performance on Real Data

We have developed an e-learning platform which records all activity done by students. We try to create an analysis framework that may be used for proving whether or not the platform can classify the students according to their accumulated knowledge. In this process, attribute selection is one of the major initial steps that must be accomplished. In this paper we show what implications may have attribute selection for classification performance and which are the best techniques that may lead to concluding results
LAAT-1 Is the Lysosomal Lysine/Arginine Transporter That Maintains Amino Acid Homeostasis

Lysosomal Amino Acid Transporter Cystinosis is characterized by intralysosomal accumulation of free cystine, which results in age-dependent problems in the kidney, muscle, retina, and central nervous system. The disease-causing gene encodes a lysosomal cystine transporter. The most effective therapeutic agent for cystinosis, cysteamine, depletes lysosomal free cystine by converting it to cysteine and the mixed disulfide cysteine-cysteamine, which can then be exported from lysosomes as a lysine analog through a putative lysine/cationic amino acid transporter. Using an unbiased genetic screen for Caenorhabditis elegans mutants with increased accumulation of apoptotic cells or autophagosomes, Liu et al. (p. 351) now reveal the molecular identity of a lysosomal lysine/arginine transporter that plays a role in maintaining lysosome function and amino acid homeostasis and that can explain how cysteamine alleviates a lysosomal storage disease. A lysosomal membrane protein identified in nematodes can explain how cysteamine alleviates a lysosomal storage disease. Defective catabolite export from lysosomes results in lysosomal storage diseases in humans. Mutations in the cystine transporter gene CTNS cause cystinosis, but other lysosomal amino acid transporters are poorly characterized at the molecular level. Here, we identified the Caenorhabditis elegans lysosomal lysine/arginine transporter LAAT-1. Loss of laat-1 caused accumulation of lysine and arginine in enlarged, degradation-defective lysosomes. In mutants of ctns-1 (C. elegans homolog of CTNS), LAAT-1 was required to reduce lysosomal cystine levels and suppress lysosome enlargement by cysteamine, a drug that alleviates cystinosis by converting cystine to a lysine analog. LAAT-1 also maintained availability of cytosolic lysine/arginine during embryogenesis. Thus, LAAT-1 is the lysosomal lysine/arginine transporter, which suggests a molecular explanation for how cysteamine alleviates a lysosomal storage disease.
Interference aware MMSE equalization for MIMO TxAA

Closed loop transmission diversity will be an important part of the enhancements of todays wireless technologies, e.g. in double-stream transmit antenna array (D-TxAA). Despite the promise of performance gains, closed loop beamforming will introduce an interference scenario in the downlink that cannot easily be handled by the conventional MMSE equalization approach. In this paper, we derive an interference aware MMSE equalizer that uses the information about the beamforming vectors. The proposed equalizer can be calculated by utilizing a virtual channel description incorporating the beamforming weights. To assess the performance, we performed fading simulations with a system level description of the transmission. The derived equalizer shows only a small increase in complexity compared to the conventional approach, but perfectly restores the orthogonality.
Gluten-Free Diet Indications, Safety, Quality, Labels, and Challenges

A gluten-free diet (GFD) is the safest treatment modality in patient with coeliac disease (CD) and other gluten-related disorders. Contamination and diet compliance are important factors behind persistent symptoms in patients with gluten related-disorders, in particular CD. How much gluten can be tolerated, how safe are the current gluten-free (GF) products, what are the benefits and side effects of GFD? Recent studies published in Nutrients on gluten-free products’ quality, availability, safety, as well as challenges related to a GFD are discussed.