Miracle-dz/UniFAR-FTUs huggingface dataset:
First Insights into Human Fingertip Regeneration by Echo-Doppler Imaging and Wound Microenvironment Assessment

Fingertip response to trauma represents a fascinating example of tissue regeneration. Regeneration derives from proliferative mesenchymal cells (blastema) that subsequently differentiate into soft and skeletal tissues. Clinically, conservative treatment of the amputated fingertip under occlusive dressing can shift the response to tissue loss from a wound repair process towards regeneration. When analyzing by Immunoassay the wound exudate from occlusive dressings, the concentrations of brain-derived neurotrophic factor (BDNF) and leukemia inhibitory factor (LIF) were higher in fingertip exudates than in burn wounds (used as controls for wound repair versus regeneration). Vascular endothelial growth factor A (VEGF-A) and platelet-derived growth factor (PDGF) were highly expressed in both samples in comparable levels. In our study, pro-inflammatory cytokines were relatively higher expressed in regenerative fingertips than in the burn wound exudates while chemokines were present in lower levels. Functional, vascular and mechanical properties of the regenerated fingertips were analyzed three months after trauma and the data were compared to the corresponding fingertip on the collateral uninjured side. While sensory recovery and morphology (pulp thickness and texture) were similar to uninjured sides, mechanical parameters (elasticity, vascularization) were increased in the regenerated fingertips. Further studies should be done to clarify the importance of inflammatory cells, immunity and growth factors in determining the outcome of the regenerative process and its influence on the clinical outcome.
Multi-institutional positioning test feedback dashboard for aspiring students: lessons learnt from a case study in flanders

Our work focuses on a multi-institutional implementation and evaluation of a Learning Analytics Dashboards (LAD) at scale, providing feedback to N=337 aspiring STEM (science, technology, engineering and mathematics) students participating in a region-wide positioning test before entering the study program. Study advisors were closely involved in the design and evaluation of the dashboard. The multi-institutional context of our case study requires careful consideration of external stakeholders and data ownership and portability issues, which gives shape to the technical design of the LAD. Our approach confirms students as active agents with data ownership, using an anonymous feedback code to access the LAD and to enable students to share their data with institutions at their discretion. Other distinguishing features of the LAD are the support for active content contribution by study advisors and LATEX type-setting of question item feedback to enhance visual recognizability. We present our lessons learnt from a first iteration in production.
TU-Tagging: A Method for Identifying Layer-Enriched Neuronal Genes in Developing Mouse Visual Cortex

Abstract Thiouracil (TU)-tagging is an intersectional method for covalently labeling newly transcribed RNAs within specific cell types. Cell type specificity is generated through targeted transgenic expression of the enzyme uracil phosphoribosyl transferase (UPRT); temporal specificity is generated through a pulse of the modified uracil analog 4TU. This technique has been applied in mouse using a Cre-dependent UPRT transgene, CA>GFPstop>HA-UPRT, to profile RNAs in endothelial cells, but it remained untested whether 4TU can cross the blood-brain barrier (BBB) or whether this transgene can be used to purify neuronal RNAs. Here, we crossed the CA>GFPstop>HA-UPRT transgenic mouse to a Sepw1-cre line to express UPRT in layer 2/3 of visual cortex or to an Nr5a1-cre line to express UPRT in layer 4 of visual cortex. We purified thiol-tagged mRNA from both genotypes at postnatal day (P)12, as well as from wild-type (WT) mice not expressing UPRT (background control). We found that a comparison of Sepw1-purified RNA to WT or Nr5a1-purified RNA allowed us to identify genes enriched in layer 2/3 of visual cortex. Here, we show that Cre-dependent UPRT expression can be used to purify cell type-specific mRNA from the intact mouse brain and provide the first evidence that 4TU can cross the BBB to label RNA in vivo.
A 51.6 Mb/s Experimental VLC System Using a Monochromic Organic LED

An organic light emitting diode (OLED) shows characteristics different from a traditional semiconductor LED when both are applied to visible light communication (VLC). This paper first experimentally characterizes its static and dynamic communication properties with varying input signals. This band-limited and power-limited light source leads to unique communication channel and noise models. Accordingly, the orthogonal frequency-division multiplexing in conjunction with offset quadrature amplitude modulation (OFDM-OQAM) is applied, and its performance is compared against the traditional dc-biased optical OFDM. To further enhance the communication performance, a bit and power loading algorithm and a proper equalization algorithm are jointly implemented to combat the channel frequency selectivity and increase the data rate. A bit-rate of 51.6 Mb/s based on a monochromic OLED is experimentally achieved through the proposed design. The rate is comparable to the multicolor OLEDs-based VLC link in the literature.
CTD-2020K17.1, a Novel Long Non-Coding RNA, Promotes Migration, Invasion, and Proliferation of Serous Ovarian Cancer Cells In Vitro

Background Ovarian cancer is the most lethal malignant tumor of the female reproductive system, and the metastasis is one of the major factors that contribute to the poor outcome of patients with OC. Accumulating evidence indicates that lncRNAs are expressed and play important regulatory roles in ovarian cancer. Material/Methods Aberrant lncRNAs in primary ovarian cancer tissues (POCTs) and paired omental metastasis tissues (OMTs) of patients with HGSOC were studied via lncRNA microarray. Real-time PCR was performed to examine CTD-2020K17.1 expression in HGSOC tissues from 38 patients, a normal ovarian surface epithelium cell line, and 4 ovarian cancer cell lines. Additionally, Transwell assays, wound healing assays, CCK-8 proliferation assays, and flow cytometry were used to explore the biological function of CTD-2020K17.1 in ovarian cancer cells. Finally, Western blot analysis was used to verify the potential target gene of CTD-2020K17.1. Results A novel lncRNA named CTD-2020K17.1 was identified via microarray analysis. Expression of CTD-2020K17.1 was significantly increased in OMTs and in 4 ovarian cancer cell lines compared with POCTs (P<0.05) or normal ovarian surface epithelial cell line (P<0.05). Moreover, CTD-2020K17.1 overexpression promoted migration, invasion, and proliferation of ovarian cancer cells, and CTD-2020K17.1 regulated the expression of CARD11. Conclusions CTD-2020K17.1 is significantly upregulated in OMTs and ovarian cancer cell lines. It can promote the migration, invasion, and proliferation of ovarian cancer cells, and CARD11 is regulated by CTD-2020K17.1.
An Improved Method of Total Variation Superiorization Applied to Reconstruction in Proton Computed Tomography

Previous work has shown that total variation superiorization (TVS) improves reconstructed image quality in proton computed tomography (pCT). The structure of the TVS algorithm has evolved since then and this paper investigated if this new algorithmic structure provides additional benefits to pCT image quality. Structural and parametric changes introduced to the original TVS algorithm included: (1) inclusion or exclusion of TV reduction requirement, (2) a variable number, <inline-formula> <tex-math notation="LaTeX">$N$ </tex-math></inline-formula>, of TV perturbation steps per feasibility-seeking iteration, and (3) introduction of a perturbation kernel <inline-formula> <tex-math notation="LaTeX">$0< \alpha < 1$ </tex-math></inline-formula>. The structural change of excluding the TV reduction requirement check tended to have a beneficial effect for <inline-formula> <tex-math notation="LaTeX">$3\le N\le 6$ </tex-math></inline-formula> and allows full parallelization of the TVS algorithm. Repeated perturbations per feasibility-seeking iterations reduced total variation (TV) and material dependent standard deviations for <inline-formula> <tex-math notation="LaTeX">$3\le N\le 6$ </tex-math></inline-formula>. The perturbation kernel <inline-formula> <tex-math notation="LaTeX">$\alpha $ </tex-math></inline-formula>, effectively equal to <inline-formula> <tex-math notation="LaTeX">$\alpha =0.5$ </tex-math></inline-formula> in the original TVS algorithm, reduced TV and standard deviations as <inline-formula> <tex-math notation="LaTeX">$\alpha $ </tex-math></inline-formula> was increased beyond <inline-formula> <tex-math notation="LaTeX">$\alpha =0.5$ </tex-math></inline-formula>, but negatively impacted reconstructed relative stopping power (RSP) values for <inline-formula> <tex-math notation="LaTeX">$\alpha >0.75$ </tex-math></inline-formula>. The reductions in TV and standard deviations allowed feasibility-seeking with a larger relaxation parameter <inline-formula> <tex-math notation="LaTeX">$\lambda $ </tex-math></inline-formula> than previously used, without the corresponding increases in standard deviations experienced with the original TVS algorithm. This paper demonstrates that the modifications related to the evolution of the original TVS algorithm provide benefits in terms of both pCT image quality and computational efficiency for appropriately chosen parameter values.
Biochemical characterization of metabolism‐based atrazine resistance in Amaranthus tuberculatus and identification of an expressed GST associated with resistance

Summary Rapid detoxification of atrazine in naturally tolerant crops such as maize (Zea mays) and grain sorghum (Sorghum bicolor) results from glutathione S‐transferase (GST) activity. In previous research, two atrazine‐resistant waterhemp (Amaranthus tuberculatus) populations from Illinois, U.S.A. (designated ACR and MCR), displayed rapid formation of atrazine‐glutathione (GSH) conjugates, implicating elevated rates of metabolism as the resistance mechanism. Our main objective was to utilize protein purification combined with qualitative proteomics to investigate the hypothesis that enhanced atrazine detoxification, catalysed by distinct GSTs, confers resistance in ACR and MCR. Additionally, candidate AtuGST expression was analysed in an F2 population segregating for atrazine resistance. ACR and MCR showed higher specific activities towards atrazine in partially purified ammonium sulphate and GSH affinity‐purified fractions compared to an atrazine‐sensitive population (WCS). One‐dimensional electrophoresis of these fractions displayed an approximate 26‐kDa band, typical of GST subunits. Several phi‐ and tau‐class GSTs were identified by LC‐MS/MS from each population, based on peptide similarity with GSTs from Arabidopsis. Elevated constitutive expression of one phi‐class GST, named AtuGSTF2, correlated strongly with atrazine resistance in ACR and MCR and segregating F2 population. These results indicate that AtuGSTF2 may be linked to a metabolic mechanism that confers atrazine resistance in ACR and MCR.
The Effect of the 2009 U.S. Preventive Services Task Force Breast Cancer Screening Recommendations on Mammography Rates.

OBJECTIVE To examine the effect of a change in U.S. Preventive Services Task Force (USPSTF) screening guidelines on mammography rates in the United States. PRINCIPAL FINDINGS In 2010, the year following the change in guidelines, 12-month mammography prevalence among women aged 40-49 years fell by 2.09 percentage points (95 percent confidence interval [CI]: -2.87 to -1.31) from 54.63 percent in 2008. For women aged 50-74 years, and aged 75 years and older, 12-month screening rates were 2.21 (95 percent CI: -2.65 to -1.77) and 3.60 (95 percent CI: -4.48 to -2.70) percentage points lower than those in 2008. In 2012, for women aged 40-49 years, 12-month prevalence fell to 52.51 percent, a decline of 2.12 percentage points (95 percent CI: -2.79 to -1.32) relative to screening rates prior the USPSTF announcement. For women aged 50-74 years and aged 75 years and older screening rates were 2.45 (95 percent CI: -2.96 to -2.07) and 5.71 (95 percent CI: -6.61 to -4.81) percentage points lower, respectively, in 2012 than in 2008. CONCLUSION This study demonstrates an immediate and lasting reduction in the rates of breast cancer screening among women of all age groups after the 2009 revision of screening guidelines by the USPSTF.
Long-Term Outcomes in Patients Surviving Large Burns: The Skin

The objective of this study was to evaluate persons who have survived severe burns and to describe the long-term residual problems relating to the skin. This is a cross-sectional descriptive study that included a one-time evaluation of 98 burn survivors (18 years old or older) who survived ≥30% TBSA burns, were ≥3 years postinjury, and consented to participate. Study participants were required to undergo a physical examination conducted by the Physical Medicine and Rehabilitation physicians in addition to completing study questionnaires. Participants were predominantly male (63%) and Caucasian (69%). The average time from injury was 17 years (range 3–53 years), and the average TBSA burn was 57% (range 30–97%). Problems with hot and cold temperature, sensory loss, raised scars, and itching continued to pose problems many years after burn injury. Reports of open wounds, skin rash, painful scars, and shooting pain in scars tended to decrease over time, whereas reports of fragile burns, including cuts and tears, tended to increase over time. Findings from the physical examination of the participants include hypertrophic scars in grafted areas (92%) and in nongrafted areas (38%), decreased sensation to pin in grafted areas (71%), hyperpigmentation in grafted areas (53%), fingernail deformities (35%), and skin breakdown (32%). Individuals with large burns deserve more long-term attention. As survivors of large burns continue to face significant burn-related issues, there is a critical need for long-term follow-up both in the clinic and in research.
The Φ-Operator : A Rotation Operator For Flow Analysis and Visualization ∗

A prevalent strategy in vector field data analysis is to extract and classify the integral curves derived from flow data. With the exception of topology-based methods, many of these classifications depend on the choice of algorithm thresholds. However, topology-based methods have yet to be fully developed for time-varying vector field analysis. In this paper, we introduce a novel descriptor, called the Φ−operator for flow data analysis that is based on the signed curvature of an integral curve. With this descriptor, the vector-valued data analysis is reduced to a scalar field analysis problem. We present the definition and computation of the Φ field and show how to utilize it to achieve a flow domain partitioning based on the behaviors of the integral curves seeded at different spatial locations. A unified framework for the computation of the Φ field and its gradient field, |∇Φ|, is introduced. This framework is easy to implement and can be applied to the characterization of streamlines, pathlines, and streaklines based on their different geometric attributes. A new flow feature, referred to as cycloid boundary curves, corresponding to the ridges of the |∇Φ| field is revealed that classifies the flow domain into regions with different rotational behavior. We apply this framework to the analysis and visualization of a number of synthetic and simulation flow data sets. Finally, we provide a detailed comparison of this new structure with a number of wellknown flow features, including vector field topology, vortex regions, FTLE ridges, and singularity paths. Our comparison shows that collectively the Φ and |∇Φ| fields encode more flow information than previous individual feature descriptors alone. ∗This work was supported by the National Science Foundation, IIS-1352722. †Guoning Chen and Lei Zhang are with University of Houston ‡ David Thompson and Adrian Sescu are with Mississippi State University §Robert S. Laramee is with the Swansea University, UK.
On Trojan side channel design and identification

Trojan side channels (TSCs) are serious threats to the security of cryptographic systems because they facilitate to leak secret keys to attackers via covert side channels that are unknown to designers. To tackle this problem, we present a new hardware Trojan detection technique for TSCs. To be specific, we first investigate general power-based TSC designs and discuss the tradeoff between their hardware cost and the complexity of the key cracking process. Next, we present our TSC identification technique based on the correlation between the key and the covert physical side channels used by attackers. Experimental results demonstrate the effectiveness of the proposed solution.
Real time on-chip implementation of dynamical systems with spiking neurons

Simulation of large-scale networks of spiking neurons has become appealing for understanding the computational principles of the nervous system by producing models based on biological evidence. In particular, networks that can assume a variety of (dynamically) stable states have been proposed as the basis for different behavioural and cognitive functions. This work focuses on implementing the Neural Engineering Framework (NEF), a formal method for mapping attractor networks and control-theoretic algorithms to biologically plausible networks of spiking neurons, on the SpiNNaker system, a massive programmable parallel architecture oriented to the simulation of networks of spiking neurons. We describe how to encode and decode analog values to patterns of neural spikes directly on chip. These methods take advantage of the full programmability of the ARM968 cores constituting the processing base of a SpiNNaker node, and exploit the fast Network-on-chip for spike communication. In this paper we focus on the fundamentals of representing, transforming and implementing dynamics in spiking networks. We show real time simulation results demonstrating the NEF principles and discuss advantages, precision and scalability. More generally, the present approach can be used to state and test hypotheses with large-scale spiking neural network models for a range of different cognitive functions and behaviours.
The genome of the marine medaka Oryzias melastigma

Marine medaka (Oryzias melastigma) is considered to be a useful fish model for marine and estuarine ecotoxicology studies and has good potential for field‐based population genomics because of its geographical distribution in Asian estuarine and coastal areas. In this study, we present the first whole‐genome draft of O. melastigma. The genome assembly consists of 8,602 scaffolds (N50 = 23.737 Mb) and a total genome length of 779.4 Mb. A total of 23,528 genes were predicted, and 12,670 gene families shared with three teleost species (Japanese medaka, mangrove killifish and zebrafish) were identified. Genome analyses revealed that the O. melastigma genome is highly heterozygous and contains a large number of repeat sequences. This assembly represents a useful genomic resource for fish scientists.
Achieving an efficient and fair equilibrium through taxation

It is well known that a game equilibrium can be far from efficient or fair, due to the misalignment between individual and social objectives. The focus of this paper is to design a new mechanism framework that induces an efficient and fair equilibrium in a general class of games. To achieve this goal, we propose a taxation framework, which first imposes a tax on each player based on the perceived payoff (income), and then redistributes the collected tax to other players properly. By turning the tax rate, this framework spans the continuum space between strategic interactions (of selfish players) and altruistic interactions (of unselfish players), hence provides rich modelling possibilities. The key challenge in the design of this framework is the proper taxing rule (i.e., the tax exemption and tax rate) that induces the desired equilibrium in a wide range of games. First, we propose a flat tax rate (i.e., a single tax rate for all players), which is necessary and sufficient for achieving an efficient equilibrium in any static strategic game with common knowledge. Then, we provide several tax exemption rules that achieve some typical fairness criterions (such as the Max-min fairness) at the equilibrium. We further illustrate the implementation of the proposed taxation framework in the game of Prisoners' Dilemma.
Simulation of the effect of an external GHz electric field on the potential energy profile of Ca2+ ions in the selectivity filter of the CaVAb channel

CaV channels are transmembrane proteins that mediate and regulate ion fluxes across cell membranes, and they are activated in response to action potentials to allow Ca2+ influx. Since ion channels are composed of charge or polar groups, an external alternating electric field may affect the ion‐selective membrane transport and the performance of the channel. In this article, we have investigated the effect of an external GHz electric field on the dynamics of calcium ions in the selectivity filter of the CaVAb channel. Molecular dynamics (MD) simulations and the potential of mean force (PMF) calculations were carried out, via the umbrella sampling method, to determine the free energy profile of Ca2+ ions in the CaVAb channels in presence and absence of an external field. Exposing CaVAb channel to 1, 2, 3, 4, and 5 GHz electric fields increases the depth of the potential energy well and this may result in an increase in the affinity and strength of Ca2+ ions to binding sites in the selectivity filter the channel. This increase of strength of Ca2+ ions binding in the selectivity filter may interrupt the mechanism of Ca2+ ion conduction, and leads to a reduction of Ca2+ ion permeation through the CaVAb channel.
E3DOAS: Balancing QoE and Energy-Saving for Multi-Device Adaptation in Future Mobile Wireless Video Delivery

Smart devices (e.g., smartphones, tablets, smart-home devices, etc.) have become important companions to most people in their daily activities, and are very much used for multimedia content exchange (i.e., video sharing, real-time/non-real-time multimedia streaming), contributing to the exponential increase in mobile traffic over the current wireless networks. While the next generation mobile networks will provide higher capacity than the current 4G systems, the network operators will face important challenges associated with the outstanding increase of both video traffic and user expectations in terms of their levels of perceived quality or quality of experience (QoE). Furthermore, the heterogeneity of mobile devices (e.g., screen resolution, battery life, and hardware performance) also impacts severely the end-user QoE. In this context, this paper proposes an evolved QoE-aware energy-saving device-oriented adaptive scheme (E3DOAS) for mobile multimedia delivery over future wireless networks. E3DOAS makes use of a coalition game-based rate allocation strategy within the multi-device heterogeneous environment, and optimizes the trade-off between the end-user perceived quality of the multimedia delivery and the mobile device energy-saving. Testing has involved a prototype of E3DOAS, a crowd-sourcing-based QoE assessment method to model non-reference perceptual video quality, and an energy measurement testbed introduced to collect power consumption parameters of the mobile devices. Simulation-based performance evaluation showed how E3DOAS outperformed other state of the art multimedia adaptive solutions in terms of energy saving, end-to-end quality of service metrics and end-user perceived quality.