Miracle-dz/UniFAR-FTUs huggingface dataset:
Applications of Microstereolithography in Tissue Engineering

Microstereolithography is a microfabrication technique based on the light induced crosslinking of a prepolymer according to a computer based design. The technology emerged in the 1980’s as a rapid prototyping technique for the fabrication of small parts and devices. The technique has evolved into an important research tool with a diverse range of applications ranging from photonics to tissue engineering. Two distinctly different branches of microstereolithography exist, differentiated by the fundamental mechanics involved. The first branch, based on the initiation of curing by the interaction of one photon of light with an initiator is a surface based technique. The photosensitised prepolymer or ‘resin’ is illuminated typically with ultraviolet light in order to cure the material within the first hundred micrometers of the surface and structures are constructed in a layer-by-layer fashion. The second, more recently developed ‘branch’ of microstereolithography was developed in the last decade of the twentieth century (although the underlying principles were predicted as early as the 1930’s). Multiphoton polymerization is a technique similar to multiphoton microscopy, in which two or more photons interact with the photoinitiator within the lifetime of a virtual intermediate state, initiating curing. Due to the low probability of this occurrence curing is only initiated in areas of very high photon density, achieved by focusing a laser beam through a high numerical aperture objective into the resin. Photocuring then occurs in the central area of the focal point, within the volume of the resin. The aim of this thesis was to investigate the applications of this technology (both one and two photon) in tissue engineering, for the fabrication of bespoke tissue scaffolds and other implantable devices. Photocurable oligomers based on bioresorbable materials already in clinical use were also explored and their suitability for tissue engineering applications investigated, with a focus on structuring and biocompatibility.
Accelerating Software Engineering Research Adoption with Analysis Bots

An important part of software engineering (SE) research is to develop new analysis techniques and to integrate these techniques into software development practice. However, since access to developers is non-trivial and research tool adoption is slow, new analyses are typically evaluated as follows: a prototype tool that embeds the analysis is implemented, a set of projects is identified, their revisions are selected, and the tool is run in a controlled environment, rarely involving the developers of the software. As a result, research artifacts are brittle and it is unclear if an analysis tool would actually be adopted. In this paper, we envision harnessing the rich interfaces provided by popular social coding platforms for automated deployment and evaluation of SE research analysis. We propose that SE analyses can be deployed as analysis bots. We focus on two specific benefits of such an approach: (1) analysis bots can help evaluate analysis techniques in a less controlled, and more realistic context, and (2) analysis bots provide an interface for developers to "subscribe" to new research techniques without needing to trust the implementation, the developer of the new tool, or to install the analysis tool locally. We outline basic requirements for an analysis bots platform, and present research challenges that would need to be resolved for bots to flourish.
Shear wave estimation by using Shear Wave Holography with normal vibration: Preliminary results

Mechanical properties of soft human tissue are linked to their pathological state. One way to assess these properties is through the Young modulus measurement, which is related to the shear wave speed in the medium when considering tissues as nearly incompressible. In order to characterize its elastic properties using sonoelastography, we introduce a new technique for shear wave estimation from a static interference pattern based on Shear Wave Holography. A relation between the mathematical representation of the interference pattern and the local shear speed is derived using the Phase Derivative approach. The experimental scheme is presented, detailing the advantages of the new configuration. Homogeneous and heterogeneous elastic media were simulated, generating an interference pattern on them. The shear speed estimation algorithm was explained and applied to obtain the speed map, calculating the mean value over each medium. The technique was tested on a nearly incompressible homogeneous elastic phantom, yielding a maximum and a mean estimation error of 6% and 4.6% respectively. Overall, Shear Wave Holography using normal vibration is feasible and shows promising results in estimating shear wave speed in elastic materials.
Improved Bat Algorithm Based Energy Efficient Congestion Control Scheme for Wireless Sensor Networks

Energy conservation and congestion control are widely researched topics in Wireless Sensor Networks in recent years. The main objective is to develop a model to find the optimized path on the basis of distance between source and destination and the residual energy of the node. This paper shows an implementation of nature inspired improved Bat Algorithm to control congestion in Wireless Sensor Networks at transport layer. The Algorithm has been applied on the fitness function to obtain an optimum solution. Simulation results have shown improvement in parameters like network lifetime and throughput as compared with CODA (Congestion Detection and Avoidance), PSO (Particle Swarm Optimization) algorithm and ACO (Ant Colony Optimization).
Which kind of science is construction management

It is argued that the mainstream views on the nature of construction management are insufficient, and as one consequence of this, the relevance of construction management has been questioned. As a solution to this situation, construction management is suggested to be repositioned as a design science, rather than as an explanatory science. A historical consideration reveals that design science equals to one of the sciences proposed by Aristotle, however, the suggestion of Aristotle has been forgotten. Thus, there has been a long-standing neglect of the design science, which explains the present fragmentation of this field. It is argued that this redefinition of construction management will solve several problems plaguing this discipline, including the problem of relevance.
Knowledge Fusion in the Large - taking a cue from the brain

Even the most commonplace cognitive behaviors such as vision and languageunderstandinginvolve large-scale fusion of disparate pieces of evidence. Therefore,our capacity to rapidly and effortlessly produce coherent interpretations of visual and verbal inputs points to the remarkable ability of the human mind/brain to fuse evidence. We discuss a neurally motivated computational model that attempts to replicate some of this remarkable ability, and illustrate the functioning of the model with the help of a few examples.
Functional characterization of hub proteins in weighted yeast protein-protein interaction networks

The centrality-lethality rule reveals that topological prominence of a protein indicates its functional importance. But are all hub proteins in PPI network essential? Using P-value to weight PPI networks, we classified hub proteins into two types: essential hub and nonessential hub. The weighted centrality measure of weighted PPI networks showed that the weighted method can give greater support for functional characterization of hub proteins. We found that essential hubs are vital and they tend to be intra-modular hubs, while nonessential hubs are useful in maintaining the overall network connectivity and tend to be inter-modular hubs.
Age-related hypertension and salt sensitivity are associated with unique cortico-medullary distribution of D1R, AT1R, and NADPH-oxidase in FBN rats

Abstract We examined effects of normal (NS) and high salt (HS) on blood pressure (BP) and cortico-medullary distribution of dopamine D1 receptor (D1R), angiotensin AT1 receptor (AT1R), NADPH oxidase-gp91phox, and sodium transporters (NHE-3, Na, K ATPase) in adult and aged rats. Aged rats fed with NS diet had higher BP, which further increased with HS. HS increased D1R mRNA and protein levels in cortex and medulla of adult rats. NS or HS fed-aged rats had higher AT1R and gp91phox mRNA levels in cortex and medulla. Aged rats fed with NS diet had higher gp91phox protein levels in cortex. HS diet increased AT1R and gp91phox protein levels in medulla of aged rats. Aged rats fed with NS or HS diet had higher NHE-3 protein levels in medulla. HS increased Na, K ATPase protein levels in medulla of aged rats. HS increased urinary kidney injury molecule-1 (KIM-1) but not protein or albumin levels in aged rats. These results suggest that cortical gp91phox and medullary NHE-3 contribute to age-related hypertension. Whereas D1R (cortical and medullary) together with medullary AT1R, gp91phox and Na, K-ATPase contribute to salt sensitivity in aged rats. And, KIM-1 may be a better marker for kidney damage.
New Symmetric Cipher Enhanced by Rotor in Real & Gaussian Domains (SCER)

This paper gives a new symmetric cryptosystem using twelve rounds enhanced by sixteen wheels rotor operating on all the 256 characters indicated by the ASCII. It uses thirty-two bits S-boxes implemented using thirty-two bits affine transformation modulo 232 addition and thirty-two bits XORING are used followed by modulo 232+1 multiplication. Numerical results are used to implement the proposed cryptosystem. The strength of this system is compared with the well known DES and IDEA symmetric systems and gives excellent results from the point of view of the security characteristics and the statistics of the ciphertext.
A second protease of foot-and-mouth disease virus

Foot-and-mouth disease virus (FMDV) genes are expressed as a polyprotein which is rapidly processed into the four primary cleavage products L, P1, P2, and P3. In secondary cleavage reactions, these are further processed into the mature proteins. The FMDV L protein is located at the N terminus of the polyprotein and is the first gene product released from the nascent polyprotein. For analysis of its biological function, the L gene was mutated by site-directed mutagenesis of cloned cDNA. In vitro translation of in vitro transcripts of these DNAs and expression studies in Escherichia coli showed that the L mutants affect the processing of the viral polyprotein. The mutants isolated were partially or totally defective in processing the polyprotein at the L/P1 junction. These mutants could, however, be processed in the presence of the wild-type L protein. Furthermore, an antiserum directed against the L protein inhibited processing at the L/P1 cleavage site, so that the release of the L protein from the polyprotein was blocked. These data reveal that the L gene product represents a viral protease which catalyzes its own release from the nascent polyprotein.
Modularization Metrics: Assessing Package Organization in Legacy Large Object-Oriented Software

There exist many large object-oriented software systems consisting of several thousands of classes that are organized into several hundreds of packages. In such software systems, classes cannot be considered as units for software modularization. In such context, packages are not simply classes containers, but they also play the role of modules: a package should focus to provide well identified services to the rest of the software system. Therefore, understanding and assessing package organization is primordial for software maintenance tasks. Although there exist a lot of works proposing metrics for the quality of a single class and/or the quality of inter-class relationships, there exist few works dealing with some aspects for the quality of package organization and relationship. We believe that additional investigations are required for assessing package modularity aspects. The goal of this paper is to provide a complementary set of metrics that assess some modularity principles for packages in large legacy object-oriented software: Information-Hiding, Changeability and Reusability principles. Our metrics are defined with respect to object-oriented dependencies that are caused by inheritance and method call. We validate our metrics theoretically through a careful study of the mathematical properties of each metric.
HBV Reactivation in Patients Treated with Antitumor Necrosis Factor-Alpha (TNF-α) Agents for Rheumatic and Dermatologic Conditions: A Systematic Review and Meta-Analysis

Introduction. Antitumor necrosis factor-alpha (TNF-α) agents are widely used for treatment of rheumatic and dermatological diseases. We conducted the systematic review and meta-analysis to assess the prevalence of HBV reactivation among patients treated with anti-TNF-α. Methods and Findings. A comprehensive literature search of MEDLINE, Scopus, and ISI Web of Knowledge databases was conducted. From 21 studies included in the systematic review, 9 included patients with occult chronic HBV infection and 6 included patients with overt infection while 6 addressed both groups. Based on 10 studies eligible for meta-analysis we report pooled estimate of HBV reactivation of 4.2% (95% CI: 1.4–8.2%, I 2: 74.7%). The pooled prevalence of reactivation was 3.0% (95% CI: 0.6–7.2, I 2: 77.1%) for patients with occult infection, and 15.4% (95% CI: 1.2–41.2%, I 2: 79.9%) for overt infection. The prevalence of reactivation was 3.9% (95% CI: 1.1–8.4%, I 2: 51.1%) for treatment with etanercept and 4.6% (95% CI: 0.5–12.5%, I 2: 28.7%) for adalimumab. For subgroup of patients without any antiviral prophylaxis the pooled reactivation was 4.0% (95% CI: 1.2–8.3%, I 2: 75.6%). Conclusion. Although HBV reactivation rate is relatively low in patients treated with anti-TNF-α for rheumatic and dermatological conditions, the antiviral prophylaxis would be recommended in patients with overt chronic HBV infection.
A New VLSI Architecture of Parallel Multiplier–Accumulator Based on Radix-2 Modified Booth Algorithm

In this paper, we proposed a new architecture of multiplier-and-accumulator (MAC) for high-speed arithmetic. By combining multiplication with accumulation and devising a hybrid type of carry save adder (CSA), the performance was improved. Since the accumulator that has the largest delay in MAC was merged into CSA, the overall performance was elevated. The proposed CSA tree uses 1's-complement-based radix-2 modified Booth's algorithm (MBA) and has the modified array for the sign extension in order to increase the bit density of the operands. The CSA propagates the carries to the least significant bits of the partial products and generates the least significant bits in advance to decrease the number of the input bits of the final adder. Also, the proposed MAC accumulates the intermediate results in the type of sum and carry bits instead of the output of the final adder, which made it possible to optimize the pipeline scheme to improve the performance. The proposed architecture was synthesized with 250, 180 and 130 ¿m, and 90 nm standard CMOS library. Based on the theoretical and experimental estimation, we analyzed the results such as the amount of hardware resources, delay, and pipelining scheme. We used Sakurai's alpha power law for the delay modeling. The proposed MAC showed the superior properties to the standard design in many ways and performance twice as much as the previous research in the similar clock frequency. We expect that the proposed MAC can be adapted to various fields requiring high performance such as the signal processing areas.
A comparative study of two molecular mechanics models based on harmonic potentials

We show that the two molecular mechanics models, the stick-spiral and the beam models, predict considerably different mechanical properties of materials based on energy equivalence. The difference between the two models is independent of the materials since all parameters of the beam model are obtained from the harmonic potentials. We demonstrate this difference for finite width graphene nanoribbons and a single polyethylene chain comparing results of the molecular dynamics (MD) simulations with harmonic potentials and the finite element method with the beam model. We also find that the difference strongly depends on the loading modes, chirality and width of the graphene nanoribbons, and it increases with decreasing width of the nanoribbons under pure bending condition. The maximum difference of the predicted mechanical properties using the two models can exceed 300% in different loading modes. Comparing the two models with the MD results of AIREBO potential, we find that the stick-spiral model overestima.
A morphometries analysis method for craniofacial differences of ancient humans

In the paper, we present the way of using the statistical shape analysis methods, by using the ancient human fossil craniofacial form data. In Indonesia, Homo floresiensis was discovered in the isolated island named Flores. The controversial issue rose whether Homo floresiensis was a microcephalic modern human or a new species. Then we analyze the deformations of Homo floresiensis from Homo sapiens and Homo erectus. As the deformation analysis method, we used the new morphometric statistical analysis which is called the statistical shape analysis or the geometry driven statistics analysis. The resultant partial warp data show distinctive features among them and we can verify that the method is accurate for analyzing the craniofacial differences of ancient humans.
Annotating Object Instances with a Polygon-RNN

We propose an approach for semi-automatic annotation of object instances. While most current methods treat object segmentation as a pixel-labeling problem, we here cast it as a polygon prediction task, mimicking how most current datasets have been annotated. In particular, our approach takes as input an image crop and sequentially produces vertices of the polygon outlining the object. This allows a human annotator to interfere at any time and correct a vertex if needed, producing as accurate segmentation as desired by the annotator. We show that our approach speeds up the annotation process by a factor of 4.7 across all classes in Cityscapes, while achieving 78:4% agreement in IoU with original ground-truth, matching the typical agreement between human annotators. For cars, our speed-up factor is 7.3 for an agreement of 82:2%. We further show generalization capabilities of our approach to unseen datasets.
Contrasting Effects of Singlet Oxygen and Hydrogen Peroxide on Bacterial Community Composition in a Humic Lake

Light excitation of humic matter generates reactive oxygen species (ROS) in surface waters of aquatic ecosystems. Abundant ROS generated in humic matter rich lakes include singlet oxygen (1O2) and hydrogen peroxide (H2O2). Because these ROS differ in half-life time and toxicity, we compared their effects on microbial activity (14C-Leucine incorporation) and bacterial community composition (BCC) in surface waters of humic Lake Grosse Fuchskuhle (North-eastern Germany). For this purpose, experiments with water samples collected from the lake were conducted in July 2006, September 2008 and August 2009. Artificially increased 1O2 and H2O2 concentrations inhibited microbial activity in water samples to a similar extent, but the effect of the respective ROS on BCC varied strongly. BCC analysis by 16S rRNA gene clone libraries and RT-PCR DGGE revealed ROS specific changes in relative abundance and activity of major bacterial groups and composition of dominating phylotypes. These changes were consistent in the three experiments performed in different years. The relative abundance of Polynucleobacter necessarius, Limnohabitans-related phylotypes (Betaproteobacteria), and Novosphingobium acidiphilum (Alphaproteobacteria) increased or was not affected by photo-sensitized 1O2 exposure, but decreased after H2O2 exposure. The opposite pattern was found for Actinobacteria of the freshwater AcI-B cluster which were highly sensitive to 1O2 but not to H2O2 exposure. Furthermore, group-specific RT-PCR DGGE analysis revealed that particle-attached P. necessarius and Limnohabitans-related phylotypes exhibit higher resistance to 1O2 exposure compared to free-living populations. These results imply that 1O2 acts as a factor in niche separation of closely affiliated Polynucleobacter and Limnohabitans-related phylotypes. Consequently, oxidative stress caused by photochemical ROS generation should be regarded as an environmental variable determining abundance, activity, and phylotype composition of environmentally relevant bacterial groups, in particular in illuminated and humic matter rich waters.
Toward Automated Detection of Logic Vulnerabilities in Web Applications

Web applications are the most common way to make services and data available on the Internet. Unfortunately, with the increase in the number and complexity of these applications, there has also been an increase in the number and complexity of vulnerabilities. Current techniques to identify security problems in web applications have mostly focused on input validation flaws, such as crosssite scripting and SQL injection, with much less attention devoted to application logic vulnerabilities. Application logic vulnerabilities are an important class of defects that are the result of faulty application logic. These vulnerabilities are specific to the functionality of particular web applications, and, thus, they are extremely difficult to characterize and identify. In this paper, we propose a first step toward the automated detection of application logic vulnerabilities. To this end, we first use dynamic analysis and observe the normal operation of a web application to infer a simple set of behavioral specifications. Then, leveraging the knowledge about the typical execution paradigm of web applications, we filter the learned specifications to reduce false positives, and we use model checking over symbolic input to identify program paths that are likely to violate these specifications under specific conditions, indicating the presence of a certain type of web application logic flaws. We developed a tool, called Waler, based on our ideas, and we applied it to a number of web applications, finding previously-unknown logic vulnerabilities.
RABBIT, an interface for information retrieval by reformulation

A new kind of user interface for information retrieval has been designed and implemented. This interface, named RABlIT, relies upon a new paradigm for retrieval, retrieval by reformulation, based on a psychological theory of human remembering. To make a query, the user interactively constructs a description of his target item(s) by criticizing successive example (and counterexample) instances. These instances from the database are presented to the user from a well-defined perspective inferred from the user's query description. This restricted presentation, which makes use of the KL-ONE formalism, prevents the user from creating semantically improper query descriptions. RABBIT is intended for users who work infrequently with a complex database or who must deal with a multitude of databases. A second class of users for which this interface should prove useful are users who approach a database with only a vague idea of what it is that they want and who thus, need to be guided in the (re)formulation of their queries. Academic Thesis Supervisor: Fernando J. Corbatb Title: Professor of Computer Science and Engineering Company Thesis Supervisor: D. Austin Henderson, Jr. Title: Member of the Research Staff, Xerox Palo Alto Research Centers Company Thesis Supervisor: Michael D. Williams Title: Member of the Research Staff, Xerox Palo Alto Research Centers