Miracle-dz/UniFAR-FTUs huggingface dataset:
Nanomechanical characterization of SU8/ZnO nanocomposite films for applications in energy-harvesting microsystems

Integration of piezoelectric zinc oxide (ZnO) nanoparticles with SU8 in the form of photo-patternable nanocomposite films can lead to the development of a new generation of energy-harvesting microdevices. Design of such energy-harvesting micro/nano-systems will require knowledge of the mechanical properties of the SU8/ZnO nanocomposite thin films for various loadings of ZnO. This work presents characterization of mechanical properties of SU8/ZnO nanocomposite films with ZnO concentration varying in the range of 0–25 wt% via quasi-static and dynamic nanoindentation. These films were fabricated using conventional microfabrication steps involving dispersion of ZnO in SU8 by ultrasonication, followed by spin-coating and UV exposure. The elastic modulus obtained via quasi-static nanoindentation varies from ~6.2 GPa for pristine SU8 to ~8.8 GPa for SU8/25 wt% ZnO nanocomposite, while hardness varies from 402 MPa to ~520 MPa for SU8/ZnO nanocomposites in the same range of ZnO wt%. The experimentally-obtained elastic modulus has also been compared with estimates obtained via Eshelby–Mori–Tanaka micromechanics. Storage modulus, loss modulus and loss factor obtained via dynamic nanoindentation tests indicate that the SU8/ZnO nanocomposites exhibit viscoelastic behavior in the studied frequency-range of 10 Hz to 201.5 Hz. Microstructural characterization via scanning electron microscopy and optical characterization via UV–vis spectrometry of the nanocomposites have also been reported.
Haemodynamic effects of haemorrhage during xenon anaesthesia in pigs.

BACKGROUND It was hypothesized that xenon would stabilize mean arterial pressure (MAP) in haemorrhagic shock, recovery, and volume resuscitation, because a higher MAP has been observed with xenon, when compared with isoflurane anaesthesia. The responses to haemorrhage and subsequent volume replacement were therefore compared between xenon and isoflurane anaesthesia, in pigs. METHODS Pigs were randomized to anaesthesia with xenon 0.55 MAC (group Xe, n=9) or isoflurane 0.55 MAC (group Iso, n=9), each with remifentanil 0.5 microg kg(-1) min(-1). MAP, heart rate, cardiac output (CO), and left ventricular fractional area change (FAC) were collected at control (1), after haemorrhage (20 ml kg(-1)) (2), after 10 min of recovery (3), after volume replacement (4), and 30 min later (5). Data were analysed by two-way repeated measures anova. RESULTS Blood loss decreased MAP (Xe: 103 [21] to 53 [24] mm Hg; Iso: 92 [18] to 55 [14] mm Hg) and CO (Xe: 4.1 [0.8] to 2.6 [0.5] litre min(-1); Iso: 5.1 [1.1] to 3.8 [1.2] litre min(-1)), in spite of significant tachycardia. MAP and CO recovered to about 75% of control, and subsequent volume replacement completely reversed symptoms in both groups, but increased FAC only with xenon. CONCLUSION Haemodynamic response to acute haemorrhage appeared faster with xenon/remifentanil than with isoflurane/remifentanil anaesthesia. In particular MAP decrease and short-term recovery were more marked with xenon (P<0.02). In the xenon group, volume replacement increased FAC compared with control and isoflurane (P<0.02).
The Grafting of Universal T-Helper Epitopes Enhances Immunogenicity of HIV-1 Tat Concurrently Improving Its Safety Profile

Extracellular Tat (eTat) plays an important role in HIV-1 pathogenesis. The presence of anti-Tat antibodies is negatively correlated with disease progression, hence making Tat a potential vaccine candidate. The cytotoxicity and moderate immunogenicity of Tat however remain impediments for developing Tat-based vaccines. Here, we report a novel strategy to concurrently enhance the immunogenicity and safety profile of Tat. The grafting of universal helper T-lymphocyte (HTL) epitopes, Pan DR Epitope (PADRE) and Pol711 into the cysteine rich domain (CRD) and the basic domain (BD) abolished the transactivation potential of the Tat protein. The HTL-Tat proteins elicited a significantly higher titer of antibodies as compared to the wild-type Tat in BALB/c mice. While the N-terminal epitope remained immunodominant in HTL-Tat immunizations, an additional epitope in exon-2 was recognized with comparable magnitude suggesting a broader immune recognition. Additionally, the HTL-Tat proteins induced cross-reactive antibodies of high avidity that efficiently neutralized exogenous Tat, thus blocking the activation of a Tat-defective provirus. With advantages such as presentation of multiple B-cell epitopes, enhanced antibody response and importantly, transactivation-deficient Tat protein, this approach has potential application for the generation of Tat-based HIV/AIDS vaccines.
NIX is required for programmed mitochondrial clearance during reticulocyte maturation

The regulated clearance of mitochondria is a well recognized but poorly understood aspect of cellular homeostasis, and defects in this process have been linked to aging, degenerative diseases, and cancer. Mitochondria are recycled through an autophagy-related process, and reticulocytes, which completely eliminate their mitochondria during maturation, provide a physiological model to study this phenomenon. Here, we show that mitochondrial clearance in reticulocytes requires the BCL2-related protein NIX (BNIP3L). Mitochondrial clearance does not require BAX, BAK, BCL-XL, BIM, or PUMA, indicating that NIX does not function through established proapoptotic pathways. Similarly, NIX is not required for the induction of autophagy during terminal erythroid differentiation. NIX is required for the selective elimination of mitochondria, however, because mitochondrial clearance, in the absence of NIX, is arrested at the stage of mitochondrial incorporation into autophagosomes and autophagosome maturation. These results yield insight into the mechanism of mitochondrial clearance in higher eukaryotes. Furthermore, they show a BAX- and BAK-independent role for a BCL2-related protein in development.
Integration of a clinical trial database with a PACS

Many clinical trials use Electronic Case Report Forms (ECRF), e.g., from OpenClinica. Trial data is augmented if DICOM scans, dose cubes, etc. from the Picture Archiving and Communication System (PACS) are included for data mining. Unfortunately, there is as yet no structured way to collect DICOM objects in trial databases. In this paper, we obtain a tight integration of ECRF and PACS using open source software. Methods: DICOM identifiers for selected images/series/studies are stored in associated ECRF events (e.g., baseline) as follows: 1) JavaScript added to OpenClinica communicates using HTML with a gateway server inside the hospitals firewall; 2) On this gateway, an open source DICOM server runs scripts to query and select the data, returning anonymized identifiers; 3) The scripts then collects, anonymizes, zips and transmits selected data to a central trial server; 4) Here data is stored in a DICOM archive which allows authorized ECRF users to view and download the anonymous images associated with each event. Results: All integration scripts are open source. The PACS administrator configures the anonymization script and decides to use the gateway in passive (receiving) mode or in an active mode going out to the PACS to gather data. Our ECRF centric approach supports automatic data mining by iterating over the cases in the ECRF database, providing the identifiers to load images and the clinical data to correlate with image analysis results. Conclusions: Using open source software and web technology, a tight integration has been achieved between PACS and ECRF.
Refactoring Inspection Support for Manual Refactoring Edits

Refactoring is commonly performed manually, supported by regression testing, which serves as a safety net to provide confidence on the edits performed. However, inadequate test suites may prevent developers from initiating or performing refactorings. We propose RefDistiller, a static analysis approach to support the inspection of manual refactorings. It combines two techniques. First, it applies predefined templates to identify potential missed edits during manual refactoring. Second, it leverages an automated refactoring engine to identify extra edits that might be incorrect. RefDistiller also helps determine the root cause of detected anomalies. In our evaluation, RefDistiller identifies 97 percent of seeded anomalies, of which 24 percent are not detected by generated test suites. Compared to running existing regression test suites, it detects 22 times more anomalies, with 94 percent precision on average. In a study with 15 professional developers, the participants inspected problematic refactorings with RefDistiller versus testing only. With RefDistiller, participants located 90 percent of the seeded anomalies, while they located only 13 percent with testing. The results show RefDistiller can help check the correctness of manual refactorings.
Noise suppression and speech enhancement for hearing aid applications using smartphones

In our hearing aid research supported by NIH-NIDCD, smartphone is used as a powerful platform to implement complex signal processing algorithms for facilitating hearing study and improving hearing aid applications. As part of the hearing aid signal processing pipeline is speech enhancement (SE) algorithm aimed at suppressing the noise and enhancing the speech. In this paper, we present a review of some new single- and two-channel SE algorithms developed for operating under different types of noise and different signal to noise ratios. These algorithms aim at improving the quality (noise suppression) and intelligibility (perception) of enhanced speech for hearing aid applications through their real-time implementations on smartphones. Performance of these algorithms are presented and compared using various objective and subjective tests.
Parameters of laser ionization of explosives for ion mobility spectrometry

The possibility of optimizing the parameters of laser radiation for increasing the efficiency of ionization of vapors of explosives in a laser field asymmetric ion mobility spectrometer (FAIMS) was investigated. The dependences of TNT ion signal on intensity of laser radiation, pulse energy and repetition frequency of laser pulses were obtained. Optimum value of the intensity of laser radiation for ionization in air was experimentally obtained - 3•107 W/cm2. It is shown that defocusing of laser radiation and expansion of the ionization region increase the TNT signal if the radiation intensity remains at the optimum level. It is shown that repetition rate should be such that the interval between pulses is shorter than the time of diffusion of non-ionized molecules into the laser irradiation region. A scheme for a multi-pass laser beam through the ion source of a spectrometer was proposed. The scheme will effectively use laser radiation and improve the ionization efficiency of nitro aromatic molecules.
Insulin receptor substrate-2 (IRS-2) rs1805097 G>A polymorphism is associated with colorectal cancer susceptibility: a meta-analysis involving 11,234 subjects

To assess the role of the insulin receptor substrate-2 (IRS-2) rs1805097 G>A polymorphism in colorectal cancer (CRC) susceptibility, we conducted a comprehensive meta-analysis, which included 5,220 CRC cases and 6,014 controls in six case-control studies published up to September 30, 2015. We used the crude odds ratios (ORs) with their 95% confidence intervals (95% CIs) to assess the relationship of IRS-2 rs1805097 G>A variants with CRC risk. Overall, IRS-2 rs1805097 G>A polymorphism was associated with the decreased risk of overall CRC risk (AA+GA vs. GG: OR, 0.91; 95% CI, 0.84-0.99; P=0.022). In a subgroup analysis by the region of CRC, IRS-2 rs1805097 G>A polymorphism was associated with a significantly decreased risk of colon cancer (AA+GA vs. GG: OR, 0.84; 95% CI, 0.76-0.94; P=0.002), but not mixed colorectal cancer and rectal cancer. In a subgroup analysis by ethnicity, a significantly decreased CRC risk was identified among American populations (AA+GA vs. GG: OR, 0.88; 95% CI, 0.80-0.97; P=0.007), but not Caucasians. Our meta-analysis suggested the IRS-2 rs1805097 G>A polymorphism might act as a CRC protective factor, especially in colon cancer and American populations subgroups.
Is there a UV/X-ray connection in IRAS 13224-3809?

We present results from the optical, ultraviolet, and X-ray monitoring of the NLS1 galaxy IRAS 13224−3809 taken with Swift and XMM–Newton during 2016. IRAS 13224−3809 is the most variable bright AGN in the X-ray sky and shows strong X-ray reflection, implying that the X-rays strongly illuminate the inner disc. Therefore, it is a good candidate to study the relationship between coronal X-ray and disc UV emission. However, we find no correlation between the X-ray and UV flux over the available ∼40 d monitoring, despite the presence of strong X-ray variability and the variable part of the UV spectrum being consistent with irradiation of a standard thin disc. This means either that the X-ray flux which irradiates the UV emitting outer disc does not correlate with the X-ray flux in our line of sight and/or that another process drives the majority of the UV variability. The former case may be due to changes in coronal geometry, absorption or scattering between the corona and the disc.
Semi-Orthogonal Low-Rank Matrix Factorization for Deep Neural Networks

Time Delay Neural Networks (TDNNs), also known as one-dimensional Convolutional Neural Networks (1-d CNNs), are an efﬁcient and well-performing neural network architecture for speech recognition. We introduce a factored form of TDNNs (TDNN-F) which is structurally the same as a TDNN whose layers have been compressed via SVD, but is trained from a random start with one of the two factors of each matrix constrained to be semi-orthogonal. This gives substantial improvements over TDNNs and performs about as well as TDNN-LSTM hybrids.
G-Miner: an efficient task-oriented graph mining system

Graph mining is one of the most important areas in data mining. However, scalable solutions for graph mining are still lacking as existing studies focus on sequential algorithms. While many distributed graph processing systems have been proposed in recent years, most of them were designed to parallelize computations such as PageRank and Breadth-First Search that keep states on individual vertices and propagate updates along edges. Graph mining, on the other hand, may generate many subgraphs whose number can far exceed the number of vertices. This inevitably leads to much higher computational and space complexity rendering existing graph systems inefficient. We propose G-Miner, a distributed system with a new architecture designed for general graph mining. G-Miner adopts a unified programming framework for implementing a wide range of graph mining algorithms. We model subgraph processing as independent tasks, and design a novel task pipeline to streamline task processing for better CPU, network and I/O utilization. Our extensive experiments validate the efficiency of G-Miner for a range of graph mining tasks.
Terrestrial activity, movements and spatial ecology of an Australian freshwater turtle, Chelodina longicollis, in a temporally dynamic wetland system

Animal movements, use of space, activity patterns and habitat use are in part determined by proximal factors such as the landscapes they occupy,seasonal or environmental cues and individual attributes such as sex and body size. Using radio-telemetry and a drift fence, we examined the contribution of these factors to variation in movements, use of space and terrestrial activity in a freshwater turtle, Chelodina longicollis (Testudines: Chelidae), in south-east Australia. Movements and use of space depended strongly on landscape attributes, while sex and body size were less important.Movements and use of space also varied seasonally and were partly correlated with rainfall. The high overall vagility of turtles, irrespective of sex and adult body size (13.8 2.8 ha (SE) home range, 2608 305 m total distance moved, 757 76 m range length), probably reflects a common need to be mobile in a landscape characterized by fluctuating resources in temporary wetlands. Use of temporary wetlands also drives C. longicollis into terrestrial habitats for movements between wetlands and extended refuge.Timing of inter-wetland movements was associated with rainfall, but most notably for immature individuals and for those moving towards temporary wetlands. Movements of adults, evacuation of the drying wetland and periods of extended refuge (i.e. aestivation) were less dependent upon rainfall if at all.We conclude that movements about and use of the landscape by C. longicollis are under the strong influence of several interacting factors such as patch configuration,seasonal and environmental cues, and in part, body size.We argue that such behaviours are also ultimately under selection from the costs and benefits of these behaviours in the context of fluctuating resources.
Mitochondrial nicotinamide adenine dinucleotide reduced (NADH) oxidation links the tricarboxylic acid (TCA) cycle with methionine metabolism and nuclear DNA methylation

Mitochondrial function affects many aspects of cellular physiology, and, most recently, its role in epigenetics has been reported. Mechanistically, how mitochondrial function alters DNA methylation patterns in the nucleus remains ill defined. Using a cell culture model of induced mitochondrial DNA (mtDNA) depletion, in this study we show that progressive mitochondrial dysfunction leads to an early transcriptional and metabolic program centered on the metabolism of various amino acids, including those involved in the methionine cycle. We find that this program also increases DNA methylation, which occurs primarily in the genes that are differentially expressed. Maintenance of mitochondrial nicotinamide adenine dinucleotide reduced (NADH) oxidation in the context of mtDNA loss rescues methionine salvage and polyamine synthesis and prevents changes in DNA methylation and gene expression but does not affect serine/folate metabolism or transsulfuration. This work provides a novel mechanistic link between mitochondrial function and epigenetic regulation of gene expression that involves polyamine and methionine metabolism responding to changes in the tricarboxylic acid (TCA) cycle. Given the implications of these findings, future studies across different physiological contexts and in vivo are warranted.
History, Expectations, and Leadership in the Evolution of Social Norms

We study the evolution of a social norm of `cooperation' in a dynamic environment. Each agent lives for two periods and interacts with agents from the previous and next generations via a coordination game. Social norms emerge as patterns of behavior that are stable in part due to agents' interpretations of private information about the past, influenced by occasional commonly-observed past behaviors. For sufficiently backward-looking societies, history completely drives equilibrium play, leading to a social norm of high or low cooperation. In more forward-looking societies, there is a pattern of 'reversion' whereby play starting with high (low) cooperation reverts toward lower (higher) cooperation. The impact of history can be countered by occasional 'prominent' agents, whose actions are visible by all future agents and who can leverage their greater visibility to influence expectations of future agents and overturn social norms of low cooperation.
Odd surface waves in two-dimensional incompressible fluids

We consider free surface dynamics of a two-dimensional incompressible fluid with odd viscosity. The odd viscosity is a peculiar part of the viscosity tensor which does not result in dissipation and is allowed when parity symmetry is broken. For the case of incompressible fluids, the odd viscosity manifests itself through the free surface (no stress) boundary conditions. We first find the free surface wave solutions of hydrodynamics in the linear approximation and study the dispersion of such waves. As expected, the surface waves are chiral and even exist in the absence of gravity and vanishing shear viscosity. In this limit, we derive effective nonlinear Hamiltonian equations for the surface dynamics, generalizing the linear solutions to the weakly nonlinear case. Within the small surface angle approximation, the equation of motion leads to a new class of non-linear chiral dynamics governed by what we dub the chiral Burgers equation. The chiral Burgers equation is identical to the complex Burgers equation with imaginary viscosity and an additional analyticity requirement that enforces chirality. We present several exact solutions of the chiral Burgers equation. For generic multiple pole initial conditions, the system evolves to the formation of singularities in a finite time similar to the case of an ideal fluid without odd viscosity. We also obtain a periodic solution to the chiral Burgers corresponding to the non-linear generalization of small amplitude linear waves.
Dermatologic toxicity from novel therapy using antimicrobial peptide LL‐37 in melanoma: A detailed examination of the clinicopathologic features

LL‐37 is a naturally occurring 37‐amino‐acid peptide that is part of the innate immune system in human skin. Preclinical studies have showed that intra‐tumoral injections of LL‐37 stimulate the innate immune system by activation of plasmacytoid dendritic cells, which mediate tumor destruction. LL‐37 intra‐tumoral injections have been utilized in a phase 1 clinical trial for melanoma patients with cutaneous metastases. We report dermatologic toxicity in a 63‐year‐old woman with stage IIIC melanoma of the right calf and inguinal lymph nodes. She was previously treated with nivolumab and combination chemotherapy (cisplatin, vinblastine and dacarbazine) and subsequently treated with LL‐37 injections upon progression of both prior regimens. She received a total of 8 weekly LL‐37 injections, with interval clinical shrinkage of injected lesions. However, approximately 45 days after initiation of this therapy, she presented with multiple verrucous papules and a vesiculo‐bullous lesion on the trunk and extremities. Clinically, most of these lesions were thought to be either squamous cell carcinoma or inflamed seborrheic keratosis. Histologically, 11 of the total 12 skin biopsies showed similar histopathologic features, with a prominent lichenoid inflammatory infiltrate admixed with eosinophils and an overlying atypical squamous epithelial proliferation with verrucous and keratoacanthoma‐like features and varying degrees of keratinocytic atypia. Interestingly, a majority of the lesions did not show spongiosis (11/12). All lesions resolved within 2 months of cessation of LL‐37 injection therapy. This case highlights adverse dermatological manifestations of LL‐37 therapy, similar to the consequences of other novel therapies.