Miracle-dz/UniFAR-FTUs huggingface dataset:
Semi-Quantitative Parameter Analysis of DCE-MRI Revisited: Monte-Carlo Simulation, Clinical Comparisons, and Clinical Validation of Measurement Errors in Patients with Type 2 Neurofibromatosis

Purpose To compare semi-quantitative (SQ) and pharmacokinetic (PK) parameters for analysis of dynamic contrast enhanced MR data (DCE-MRI) and investigate error-propagation in SQ parameters. Methods Clinical data was collected from five patients with type 2-neurofibromatosis (NF2) receiving anti-angiogenic therapy for rapidly growing vestibular schwannoma (VS). There were 7 VS and 5 meningiomas. Patients were scanned prior to therapy and at days 3 and 90 of treatment. Data was collected using a dual injection technique to permit direct comparison of SQ and PK parameters. Monte Carlo modeling was performed to assess potential measurement errors in SQ parameters in persistent, washout, and weakly enhancing tissues. The simulation predictions for five semi-quantitative parameters were tested using the clinical DCE-MRI data. Results In VS, SQ parameters and Ktrans showed close correlation and demonstrated similar therapy induced reductions. In meningioma, only the denoised Signal Enhancement Ratio (Rse1/se2(DN)) showed a significant therapy induced reduction (p<0.05). Simulation demonstrated: 1) Precision of SQ metrics normalized to the pre-contrast-baseline values (MSErel and ∑MSErel) is improved by use of an averaged value from multiple baseline scans; 2) signal enhancement ratio Rmse1/mse2 shows considerable susceptibility to noise; 3) removal of outlier values to produce a new parameter, Rmse1/mse2(DN), improves precision and sensitivity to therapy induced changes. Direct comparison of in-vivo analysis with Monte Carlo simulation supported the simulation predicted error distributions of semi-quantitative metrics. Conclusion PK and SQ parameters showed similar sensitivity to anti-angiogenic therapy induced changes in VS. Modeling studies confirmed the benefits of averaging baseline signal from multiple images for normalized SQ metrics and demonstrated poor noise tolerance in the widely used signal enhancement ratio, which is corrected by removal of outlier values.
Protein Primary Structure of the Vaccinia Virion at Increased Resolution

ABSTRACT Here we examine the protein covalent structure of the vaccinia virus virion. Within two virion preparations, >88% of the theoretical vaccinia virus-encoded proteome was detected with high confidence, including the first detection of products from 27 open reading frames (ORFs) previously designated “predicted,” “uncharacterized,” “inferred,” or “hypothetical” polypeptides containing as few as 39 amino acids (aa) and six proteins whose detection required nontryptic proteolysis. We also detected the expression of four short ORFs, each of which was located within an ORF (“ORF-within-ORF”), including one not previously recognized or known to be expressed. Using quantitative mass spectrometry (MS), between 58 and 74 proteins were determined to be packaged. A total of 63 host proteins were also identified as candidates for packaging. Evidence is provided that some portion of virion proteins are “nicked” via a combination of endoproteolysis and concerted exoproteolysis in a manner, and at sites, independent of virus origin or laboratory procedures. The size of the characterized virion phosphoproteome was doubled from 189 (J. Matson, W. Chou, T. Ngo, and P. D. Gershon, Virology 452-453:310–323, 2014, doi:http://dx.doi.org/10.1016/j.virol.2014.01.012) to 396 confident, unique phosphorylation sites, 268 of which were within the packaged proteome. This included the unambiguous identification of phosphorylation “hot spots” within virion proteins. Using isotopically enriched ATP, 23 sites of intravirion kinase phosphorylation were detected within nine virion proteins, all at sites already partially occupied within the virion preparations. The clear phosphorylation of proteins RAP94 and RP19 was consistent with the roles of these proteins in intravirion early gene transcription. In a blind search for protein modifications, cysteine glutathionylation and O-linked glycosylation featured prominently. We provide evidence for the phosphoglycosylation of vaccinia virus proteins. IMPORTANCE Poxviruses are among the most complex and irregular virions, about whose internal structure little is known. To better understand poxvirus virion structure, imaging should be supplemented with other tools. Here, we provide a deep study of the covalent structure of the vaccinia virus virion using the various tools of contemporary mass spectrometry.
Correlates of nursing care burden among institutionalized patients with dementia

ABSTRACT Background: The stress associated with care of patients with dementia has led to high nursing staff turnover. This study aims to explore patient factors that are related to nursing burden. Methods: The present study examined nursing care burden related to 55 institutionalized dementia patients using the Modified Nursing Care Assessment Scale (M-NCAS). Cognition was assessed with the Severe Impairment Battery (SIB), activities of daily living (ADLs) were measured with the Alzheimer's Disease Functional Assessment of Change Scale (ADFACS), aggression was measured with the Aggressive Behavior Scale (ABS), and the Charlson Comorbidity Index (CCI) was used to assess medical comorbidity. Finally, the Dementia Cognitive Fluctuation Scale (DCFS) was used to assess the presence and severity of cognitive fluctuations (CFs). Linear regression models were used to assess their relationships with nursing care burden. Results: The mean age of the patients was 90.41 years (SD=2.84) and 89.10% were males. ADFACS total score (B = 0.36, β = 0.42, p = 0.002) and ABS score (B = 2.933, β = 0.37, p = 0.002) significantly predicted the M-NCAS Attitude score. ABS score was the only significant predictor of M-NCAS Strain score (B = 2.57, β = 0.35, p = 0.009). Conclusions: In the long-term care setting, aggressive behavior plays an important role in both subjective and objective nursing burden, while impaired ADLs increase the objective burden for nursing staff.
Of ‘Disgrace’ and ‘Pain’ – Corticolimbic Interaction Patterns for Disorder-Relevant and Emotional Words in Social Phobia

Limbic hyperactivation and an impaired functional interplay between the amygdala and the prefrontal cortex are discussed to go along with, or even cause, pathological anxiety. Within the multi-faceted group of anxiety disorders, the highly prevalent social phobia (SP) is characterized by excessive fear of being negatively evaluated. Although there is widespread evidence for amygdala hypersensitivity to emotional faces in SP, verbal material has rarely been used in imaging studies, in particular with an eye on disorder-specificity. Using functional magnetic resonance imaging (fMRI) and a block design consisting of (1) overall negative, (2) social-phobia related, (3) positive, and (4) neutral words, we studied 25 female patients with social phobia and 25 healthy female control subjects (HC). Results demonstrated amygdala hyperactivation to disorder-relevant but not to generally negative words in SP patients, with a positive correlation to symptom severity. A functional connectivity analysis revealed a weaker coupling between the amygdala and the left middle frontal gyrus in patients. Symptom severity was negatively related to connectivity strength between the amygdala and the ventromedial prefrontal and orbitofrontal cortex (Brodmann Area 10 and 11). The findings clearly support the view of a hypersensitive threat-detection system, combined with disorder-related alterations in amygdala-prefrontal cortex connectivity in pathological anxiety.
Fractional-order complementary filters for small unmanned aerial system attitude estimation

For small unmanned aerial systems (sUAS), the problem of estimation of orientation angles relative to the Earths surface (attitude) is of major importance. Usually, this estimation is performed by the combination of several kinds of sensor data by a Kalman filter or complementary-style filter producing a navigation-quality solution. Kalman filters make assumptions about linearity and statistical properties of the sensor noise, which must be accurate for proper functioning of the filter. Another option, the complementary filter, is more simple, and does not make these assumptions. Although the applications of the complementary filter have been researched in depth, the complementary filter can be combined in a novel way with fractional-order filters for the purpose of small UAS flight. In this paper, a roll-pitch fractional-order estimator is shown in flight configuration (real-time code) on a small sUAS. With fewer tunable parameters, we show that the fractional-order filter is more simple to implement. Realtime results are shown which indicate adequate performance relative to an existing quaternion-based Kalman filter-based estimator.
Adaptive Memory Fusion: Towards Transparent, Agile Integration of Persistent Memory

The great promise of in-memory computing inspires en-gineers to scale their main memory subsystems in a timely and efficient manner. Offering greatly expanded capacity at near-DRAM speed, today’s new-generation persistent memory (PM) module is no doubt an ideal candidate for system upgrade. However, integrating DRAM-comparable PMs in current enterprise systems faces big barriers in terms of huge system modifications for software compati-bility and complex runtime support. In addition, the very large PM capacity unavoidably results in massive metadata, which introduces significant performance and energy overhead. The inefficiency issue becomes even acute when the memory system reaches its capacity limit or the application requires large memory space allocation. In this paper we propose adaptive memory fusion (AMF), a novel PM integration scheme that jointly solves the above issues. Rather than struggle to adapt to the persistence property of PM through modifying the full software stack, we focus on exploiting the high capacity feature of emerging PM modules. AMF is designed to be totally transparent to user applications by carefully hiding PM devices and managing the available PM space in a DRAM-like way. To further improve the performance, we devise holistic optimization scheme that allows the system to efficiently utilize system resources. Specifically, AMF is able to adaptively release PM based on memory pressure status, smartly reclaim PM pages, and enable fast space expansion with direct PM pass-through. We implement AMF as a kernel subsystem in Linux. Compared to traditional approaches, AMF could decrease the page faults number of high-resident-set benchmarks by up to 67.8% with an average of 46.1%. Using realistic in-memory database, we show that AMF outperforms existing solutions by 57.7% on SQLite and 21.8% on Redis. Overall, AMF represents a more lightweight design approach and it would greatly encourage rapid and flexible adoption of PM in the near future.
Failure investigation of fused deposition modelling parts fabricated at different raster angles under tensile and flexural loading

Fused deposition modelling is an efficient rapid prototyping process used to rapidly fabricate three-dimensional solid objects with complicated geometries. Many process parameters affect the fused deposition modelling process and their settings influence the quality of the specimen. This article investigates the effect of raster angle on surface roughness (along and across the length direction) and mechanical properties (tensile and flexural strength) of fused deposition modelling parts built at 10 different raster angles (0°–90° at 10° interval). All parts are built using acrylonitrile butadiene styrene P430 material. Surface roughness for circular and parabolic curved surfaces is also measured when specimens are built at different raster angles. Fracture surfaces are inspected with scanning electron microscope to study the modes of failure under different loading conditions. The samples where raster angle is 0° and layers are deposited along the length of the specimen exhibited optimal mechanical strength and good surface finish (when measured along the length). Scanning electron microscope results reveal that for 0° raster angle, failures are mainly due to pulling and rupture of fibres and for 30° and 60° raster angle, failure is due to brittle shear in a direction parallel to raster orientation. Due to the presence of number of heating and cooling cycle in 90° raster orientation, interlayer cracking and distortion of raster take place leading to lower strength.
The “Lévy or Diffusion” Controversy: How Important Is the Movement Pattern in the Context of Trapping?

Many empirical and theoretical studies indicate that Brownian motion and diffusion models as its mean field counterpart provide appropriate modeling techniques for individual insect movement. However, this traditional approach has been challenged, and conflicting evidence suggests that an alternative movement pattern such as Levy walks can provide a better description. Levy walks differ from Brownian motion since they allow for a higher frequency of large steps, resulting in a faster movement. Identification of the ‘correct’ movement model that would consistently provide the best fit for movement data is challenging and has become a highly controversial issue. In this paper, we show that this controversy may be superficial rather than real if the issue is considered in the context of trapping or, more generally, survival probabilities. In particular, we show that almost identical trap counts are reproduced for inherently different movement models (such as the Brownian motion and the Levy walk) under certain conditions of equivalence. This apparently suggests that the whole ‘Levy or diffusion’ debate is rather senseless unless it is placed into a specific ecological context, e.g., pest monitoring programs.
Development and Application of Noncontact Near-Infrared Spectroscopy System for Measuring Biological Tissue

The in vivo application of near-infrared spectroscopy (NIRS) for brain-activity measurements was first described by Jöbsis in 1977. Over the past 35 years, this technique has been developed as a useful tool for the clinical monitoring of tissue oxygenation, for neuroimaging studies, and for the measurement of tissue structures. The NIRS system for detecting the absorption change in deep biological tissues must currently use contact fiber-optic probes on the skin in order to avoid artifacts induced by direct skin-reflected light or tissue movement. On the other hand, noncontact NIRS imaging may have many promising applications such as for monitoring the biological state of drivers and sleeping people. The purpose of this thesis is the development and application of a noncontact NIRS system. To establish a noncontact NIRS system for the measurement of deep biological tissues, a noncontact brain activity measurement system using a phosphor which is excited by and emits near-infrared light was developed. To optimize and validate this system, the influence of the fluorescence lifetime on the amplitude of the lock-in detection was investigated to determine the optimal frequency of the light source’s intensity modulation. The sensitivity of the system to the internal absorbance change was estimated using a phantom measurement. To clearly show that this system can detect the absorbance changes in the cerebral blood instead of those in the superficial regions, the hemoglobin changes in the same area of the prefrontal cortex were measured during a working memory task by simultaneously using this system and a conventional contact optical topography system. The precision of the system was also evaluated. As an example of promising applications, the noncontact system was extended to a system with flexible source positions using a galvano scanner. An 808-nm laser, whose focal point on the surface of the biological tissue is controlled by the galvano scanner, is used as the light source. The system is used to measure twenty points on the tissue surface at which the source-detector (S-D) distances are 7–45 mm (with
An Adaptive, Finite Difference Solver for the Nonlinear Poisson-Boltzmann Equation with Applications to Biomolecular Computations

We present a solver for the Poisson-Boltzmann equation and demonstrate its applicability for biomolecular electrostatics computation. The solver uses a level set framework to represent sharp, complex interfaces in a simple and robust manner. It also uses non-graded, adaptive octree grids which, in comparison to uniform grids, drastically decrease memory usage and runtime without sacriﬁcing accuracy. The basic solver was introduced in earlier works [16, 27], and here is extended to address biomolecular systems. First, a novel approach of calculating the solvent excluded and the solvent accessible surfaces is explained; this allows to accurately represent the location of the molecule’s surface. Next, a hybrid ﬁnite difference/ﬁnite volume approach is presented for discretizing the nonlinear Poisson-Boltzmann equation and enforcing the jump boundary conditions at the interface. Since the interface is implicitly represented by a level set function, imposing the jump boundary conditions is straightforward and efﬁcient.
Feedback control of functional electrical stimulation for arbitrary upper extremity movements

Functional electrical stimulation (FES) is a type of neuroprosthesis in which muscles are stimulated by electrical pulses in order to compensate for the loss of voluntary movement control. Modulating the stimulation intensities to reliably generate movements is a challenging control problem. For the first time, this paper presents a feedback controller for FES to control arm movements in a 2D (table-top) task space. This feedback controller is based on a recent human motor control model, which uses muscle synergies to simplify the calculations and improve control performance. The experimental results show that this control scheme can produce arbitrary movements in the 2D task space, with less than 2 cm hand position error from the specified targets.
Human Metapneumovirus M2-2 Protein Inhibits Innate Immune Response in Monocyte-Derived Dendritic Cells

Human metapneumovirus (hMPV) is a leading cause of lower respiratory infection in young children, the elderly and immunocompromised patients. Repeated hMPV infections occur throughout life. However, immune evasion mechanisms of hMPV infection are largely unknown. Recently, our group has demonstrated that hMPV M2-2 protein, an important virulence factor, contributes to immune evasion in airway epithelial cells by targeting the mitochondrial antiviral-signaling protein (MAVS). Whether M2-2 regulates the innate immunity in human dendritic cells (DC), an important family of immune cells controlling antigen presenting, is currently unknown. We found that human DC infected with a virus lacking M2-2 protein expression (rhMPV-ΔM2-2) produced higher levels of cytokines, chemokines and IFNs, compared to cells infected with wild-type virus (rhMPV-WT), suggesting that M2-2 protein inhibits innate immunity in human DC. In parallel, we found that myeloid differentiation primary response gene 88 (MyD88), an essential adaptor for Toll-like receptors (TLRs), plays a critical role in inducing immune response of human DC, as downregulation of MyD88 by siRNA blocked the induction of immune regulatory molecules by hMPV. Since M2-2 is a cytoplasmic protein, we investigated whether M2-2 interferes with MyD88-mediated antiviral signaling. We found that indeed M2-2 protein associated with MyD88 and inhibited MyD88-dependent gene transcription. In this study, we also identified the domains of M2-2 responsible for its immune inhibitory function in human DC. In summary, our results demonstrate that M2-2 contributes to hMPV immune evasion by inhibiting MyD88-dependent cellular responses in human DC.
Sex differences in associations of arginine vasopressin and oxytocin with resting‐state functional brain connectivity

Oxytocin (OT) and arginine vasopressin (AVP) exert robust and sexually dimorphic influences on cognition and emotion. How these hormones regulate relevant functional brain systems is not well understood. OT and AVP serum concentrations were assayed in 60 healthy individuals (36 women). Brain functional networks assessed with resting‐state functional magnetic resonance imaging (rs‐fMRI) were constructed with graph theory–based approaches that characterize brain networks as connected nodes. Sex differences were demonstrated in rs‐fMRI. Men showed higher nodal degree (connectedness) and efficiency (information propagation capacity) in left inferior frontal gyrus (IFG) and bilateral superior temporal gyrus (STG) and higher nodal degree in left rolandic operculum. Women showed higher nodal betweenness (being part of paths between nodes) in right putamen and left inferior parietal gyrus (IPG). Higher hormone levels were associated with less intrinsic connectivity. In men, higher AVP was associated with lower nodal degree and efficiency in left IFG (pars orbitalis) and left STG and less efficiency in left IFG (pars triangularis). In women, higher AVP was associated with lower betweenness in left IPG, and higher OT was associated with lower nodal degree in left IFG (pars orbitalis). Hormones differentially correlate with brain networks that are important for emotion processing and cognition in men and women. AVP in men and OT in women may regulate orbital frontal cortex connectivity, which is important in emotion processing. Hormone associations with STG and pars triangularis in men and parietal cortex in women may account for well‐established sex differences in verbal and visuospatial abilities, respectively. © 2016 Wiley Periodicals, Inc.
SMARTLOG: Place error log statement by deep understanding of log intention

Failure-diagnosis logs can dramatically reduce the system recovery time when software systems fail. Log automation tools can assist developers to write high quality log code. In traditional designs of log automation tools, they define log placement rules by extracting syntax features or summarizing code patterns. These approaches are, however, limited since the log placements are far beyond those rules but are according to the intention of software code. To overcome these limitations, we design and implement SmartLog, an intention-aware log automation tool. To describe the intention of log statements, we propose the Intention Description Model (IDM). SmartLog then explores the intention of existing logs and mines log rules from equivalent intentions. We conduct the experiments based on 6 real-world open-source projects. Experimental results show that SmartLog improves the accuracy of log placement by 43% and 16% compared with two state-of-the-art works. For 86 real-world patches aimed to add logs, 57% of them can be covered by SmartLog, while the overhead of all additional logs is less than 1%.
Tannic Acid Modified Silver Nanoparticles Show Antiviral Activity in Herpes Simplex Virus Type 2 Infection

The interaction between silver nanoparticles and herpesviruses is attracting great interest due to their antiviral activity and possibility to use as microbicides for oral and anogenital herpes. In this work, we demonstrate that tannic acid modified silver nanoparticles sized 13 nm, 33 nm and 46 nm are capable of reducing HSV-2 infectivity both in vitro and in vivo. The antiviral activity of tannic acid modified silver nanoparticles was size-related, required direct interaction and blocked virus attachment, penetration and further spread. All tested tannic acid modified silver nanoparticles reduced both infection and inflammatory reaction in the mouse model of HSV-2 infection when used at infection or for a post-infection treatment. Smaller-sized nanoparticles induced production of cytokines and chemokines important for anti-viral response. The corresponding control buffers with tannic acid showed inferior antiviral effects in vitro and were ineffective in blocking in vivo infection. Our results show that tannic acid modified silver nanoparticles are good candidates for microbicides used in treatment of herpesvirus infections.