Miracle-dz/UniFAR-FTUs huggingface dataset:
Laser Generated Shockwave Therapy of Bacterial Biofilms: From Benchtop to Pre-Clinical Studies

Author(s): Yao, William | Advisor(s): Grundfest, Warren S. | Abstract: The presence of bacterial biofilms in wounds presents a major complication in wound treatments, significantly increasing morbidity and mortality. Biofilms delay wound healing, promote the growth of bacteria, and are a persistent source of pathogens that can infect other wounds. They are natively resistant to surfactants, antibiotics, and antiseptics, causing many current anti-bacterial treatments to remain ineffective at improving patient outcomes. Alternative methods for wound management often remove healthy tissue, along with the biofilm, resulting in unacceptable injuries to the patient. This work investigated a novel method of mechanically disrupting and removing persistent biofilms with laser generated shockwaves (LGS). We have demonstrated that LGS therapy can eliminate bacterial biofilms without damaging the surrounding tissue. This study further developed practical and effective methods of delivering LGS in patients. We have developed a portable raster scanner, capable of delivering LGS at a rate of 5 shockwaves per second, with peak pressures of g200 MPa, computer-aided targeting, and a treatment area of 4 x 6 cm2. Using this system, we have demonstrated that LGS can remove 99.4% of biofilm matrix and 97.7% of surface CFUs.This study also investigated the ability of LGS therapy to facilitate antibiotic delivery through biofilms. We have shown that LGS can increase the effectiveness of gentamicin by 21.4%, when used against Staphylococcus epidermidis biofilm grown in vitro, indicating that LGS can help restore the effectiveness of treatments that were hindered by the presence of biofilms. When used against S. epidermidis biofilm grown on ex vivo tissue, LGS can still remove 69% of CFUs and cause a 52% reduction in biofilm coverage, without damage to the underlying tissue.In bringing this technology forward, we have demonstrated that LGS is safe and well-tolerated when used on intact skin in rodents. When used at the maximal therapeutic window of 295.6 i? ½ 35.4 MPa, no hemorrhages nor damage to the dermis were seen after treatment. The only damage observed were minor injuries to the epidermis that resolve within three days. Preliminary followup results in rodents showed that these minor injuries cause no statistical differences in healing times between LGS-treated excisional wounds and controls.
Twenty-Two Years of Warming, Fertilisation and Shading of Subarctic Heath Shrubs Promote Secondary Growth and Plasticity but Not Primary Growth

Most manipulation experiments simulating global change in tundra were short-term or did not measure plant growth directly. Here, we assessed the growth of three shrubs (Cassiope tetragona, Empetrum hermaphroditum and Betula nana) at a subarctic heath in Abisko (Northern Sweden) after 22 years of warming (passive greenhouses), fertilisation (nutrients addition) and shading (hessian fabric), and compare this to observations from the first decade of treatment. We assessed the growth rate of current-year leaves and apical stem (primary growth) and cambial growth (secondary growth), and integrated growth rates with morphological measurements and species coverage. Primary- and total growth of Cassiope and Empetrum were unaffected by manipulations, whereas growth was substantially reduced under fertilisation and shading (but not warming) for Betula. Overall, shrub height and length tended to increase under fertilisation and warming, whereas branching increased mostly in shaded Cassiope. Morphological changes were coupled to increased secondary growth under fertilisation. The species coverage showed a remarkable increase in graminoids in fertilised plots. Shrub response to fertilisation was positive in the short-term but changed over time, likely because of an increased competition with graminoids. More erected postures and large, canopies (requiring enhanced secondary growth for stem reinforcement) likely compensated for the increased light competition in Empetrum and Cassiope but did not avoid growth reduction in the shade intolerant Betula. The impact of warming and shading on shrub growth was more conservative. The lack of growth enhancement under warming suggests the absence of long-term acclimation for processes limiting biomass production. The lack of negative effects of shading on Cassiope was linked to morphological changes increasing the photosynthetic surface. Overall, tundra shrubs showed developmental plasticity over the longer term. However, such plasticity was associated clearly with growth rate trends only in fertilised plots.
Why are Features Deprecated? An Investigation Into the Motivation Behind Deprecation

In this study, we investigate why API producers deprecate features. Previous work has shown us that knowing the rationale behind deprecation of an API aids a consumer in deciding to react, thus hinting at a diversity of deprecation reasons. We manually analyze the Javadoc of 374 deprecated methods pertaining four mainstream Java APIs to see whether the reason behind deprecation is mentioned. We find that understanding the rationale from just the Javadoc is insufficient; hence we add other data sources such as the source code, issue tracker data and commit history. We observe 12 reasons that trigger API producers to deprecate a feature. We evaluate an automated approach to classify these motivations.
Lyapunov-Based Nonlinear Disturbance Observer for n-Links Flexible Joint Robot Manipulators

In this paper, the nonlinear disturbance observer (NDO) is presented for serial flexible joint robot manipulators (FJM). To this end, a planar robot manipulator with n flexible joints is considered. After deriving the general form of dynamic equations for serial n-links FJM, a nonlinear disturbance observer is proposed on the basis of the system dynamic equations. The main challenge here is to obtain the acceptable range of the observer gain which guarantees the stability condition. So by choosing the proper Lyapunov candidate, stability analysis of the proposed observer is performed by using the Lyapunov’s direct method. Since the proposed NDO makes the system robust against internal and external disturbances, no accurate dynamic model is required to achieve the high precision motion control. The effectiveness of the proposed observer in the regulation problem is investigated by numerical simulations for a two-links robot manipulator. To this end an optimal LQR controller is designed to stabilize the system besides the optimal state observer in order to estimate the angular velocity of the links and motors. Simulation results show the ability of the proposed method to properly estimate and compensate different disturbances.
The Relationship between Health Literacy and General Health Level of Hemodialysis Patients: A Case Study in Iran

Background: Healthliteracyincludesthesocialcognitiveskillsthatdeterminethemotivationandabilityof individualsinachiev-ing, understanding, and utilizing information to maintain and enhance health. People with inadequate health literacy have a weaker health condition. The present study aimed at investigating the relationship between health literacy and the general health level of hemodialysis patients. Methods: This descriptive - analytical study was performed on 130 hemodialysis patients of Baharlu Hospital in Tehran. Data were collected using Health Literacy and General Health Assessment Tool. The collected data were analyzed using SPSS 21.0 software and Spearman correlation test. Results: Theresultsrevealedthatthehealthliteracymeanscorewas46.81 ± 22.87andthatthestudiedindividualsdidnothavesuf-ﬁcienthealthliteracy. Thegeneralhealthmeanscorewas14.20 ± 6.50,andtherewasastatisticallysigniﬁcantrelationshipbetween health literacy and general health (P < 0.05). Conclusions: In this study, it was found that those with higher health literacy score had better general health. Dialysis causes many clinical and psychological problems, limiting physical and mental activities of the patients. The decrease in health literacy is associated with a decrease in health including physical and psychological problems. In general, dialysis patients still need to learn more about health literacy and general health.
Advances in Model Learning for Software Systems

Finding minimal separating sequences for all pairs of inequivalent states in a finite state machine is a classic problem in automata theory. Sets of minimal separating sequences, for instance, play a central role in many conformance testing methods. Moore has already outlined a partition refinement algorithm that constructs such a set of sequences in O(mn) time, where m is the number of transitions and n is the number of states. In this chapter, we present an improved algorithm based on the minimization algorithm of Hopcroft that runs in O(m log n) time. The efficiency of our algorithm is empirically verified and compared to the traditional algorithm.
Risks of spreading foot and mouth disease through milk and dairy products

: A review of epidemics of foot and mouth disease (FMD) has highlighted the important role which raw (untreated) milk can play in the spread of the disease in a country which is normally free of FMD and whose cattle are not routinely vaccinated. The greatest hazard is likely to be in the early stages of an outbreak, before disease control measures have been implemented. The spread of FMD through milk can be prevented by the effective application of control measures combined with 'codes of practice' for the treatment of potentially infected milk. The author considers the probable mechanisms of transmission of FMD by milk and dairy products. These mechanisms are based on the quantities of virus excreted in milk, the survival of the virus under various management and manufacturing conditions and the minimum doses required to initiate infection in susceptible animals by different routes. The key points for consideration when making a risk assessment of the importation of milk and dairy products are also discussed.
Identification of cellular functions of cardiolipin as physiological modifiers of barth syndrome

IDENTIFICATION OF CELLULAR FUNCTIONS OF CARDIOLIPIN AS PHYSIOLOGICAL MODIFIERS OF BARTH SYNDROME by AMIT S. JOSHI December 2012 Advisor: Dr. Miriam L. Greenberg Major: Biological Sciences Degree: Doctor of Philosophy Cardiolipin (CL) is an anionic phospholipid synthesized in the mitochondrial inner membrane. Perturbation of CL metabolism leads to Barth syndrome (BTHS), a life threatening genetic disorder. I utilized genetic, biochemical and cell biological approaches in yeast to elucidate the cellular functions of CL. Understanding the functions of CL is expected to shed light on the pathology and possible treatments for BTHS. BTHS is caused by mutations in TAZ1, which encodes a CL remodeling enzyme called tafazzin. BTHS patients exhibit a wide range of clinical presentations, indicating that physiological modifiers influence the BTHS phenotype. A targeted synthetic lethality screen was performed to identify physiological modifiers of CL deficiency. Using this approach, synthetic genetic interactions of CL mutants were identified with genes encoding mitochondrial outer membrane proteins, specifically in the TOM, MDM and SAM complexes, which are involved in mitochondrial protein import, suggesting that CL plays a role in this process. Consistent with this, we
The Prevalence and Clinical Significance of Coronary Artery Calcification in Cardiac Catheterization

Objective: To determine the prevalence of coronary artery calcification, its pattern of distribution, relative frequency in each coronary artery and its association with coronary artery stenosis. Methods: This is a retrospective study conducted in Queen Alia Heart Institute in Amman-Jordan in the period between 2012 and 2015. A total number of 1137 adult patients who had coronary angiography were reviewed looking for coronary calcification, its frequency according to gender, age and distribution. Calcification was diagnosed as radiopacities within the vessel wall seen during selective coronary angiogram. Results: The total numbers of angiography reviewed were 1137. Coronary calcification was diagnosed in 111 patients, most of them were males, left anterior descending artery was the commonest artery involved, isolated calcification of right coronary artery and circumflex artery was rare, obstructive coronary artery disease was highly associated with coronary artery calcifications. Conclusion: Coronary artery calcification is highly associated with coronary artery stenosis, it may be seen in any part of the coronary circulation, Left Anterior Descending was most commonly affected, it was usually seen in proximal segments and was found in 10% of population, with male gender being the majority.
Product Ranking on Online Platforms

On online platforms, consumers face an abundance of options that are displayed in the form of a position ranking. Only products placed in the first few positions are readily accessible to the consumer, and she needs to exert effort to access more options. For such platforms, we develop a two-stage sequential search model where in the first stage, the consumer sequentially screens positions to observe the preference weight of the products placed in them and forms a consideration set. In the second stage, she observes the additional idiosyncratic utility that she can derive from each product and chooses the highest-utility product within her consideration set. For this model, we first characterize the optimal sequential search policy of a welfare-maximizing consumer. We then study how platforms with different objectives should rank products. We focus on two objectives: (i) maximizing the platform's market share and (ii) maximizing the consumer's welfare. Somewhat surprisingly, we show that ranking products in decreasing order of their preference weights does not necessarily maximize market share or consumer welfare. Such a ranking may shorten the consumer's consideration set due to the externality effect of high-positioned products on low-positioned ones, leading to insufficient screening. We then show that both problems---maximizing market share and maximizing consumer welfare---are NP-complete. We develop novel near-optimal polynomial-time ranking algorithms for each objective. Further, we show that even though ranking products in decreasing order of their preference weights is suboptimal, such a ranking enjoys strong performance guarantees for both objectives. We complement our theoretical developments with numerical studies using synthetic data in which we show (1) that heuristic versions of our algorithms that do not rely on model primitives perform well and (2) that our model can be effectively estimated using a maximum likelihood estimator.
Three dimensional geometric morphometric study of the Ethiopian Myomys - Stenocephalemys complex (Murinae, Rodentia)

Abstract Geometric morphometrics was used to investigate the Ethiopian Myomys - Stenocephalemys complex, and to suggest possible explanations for differences in size and shape. The four species of the complex ( M. albipes , M. ruppi , S. griseicauda , S. albocaudata ) and a Kenyan species, M. fumatus , were studied using Procrustes analysis of three dimensional landmarks collected over the skull. All these species occur in very different habitats, from forests at 1000 m up to the Afro Alpine moorlands above 4000 m. There is a substantial contradiction between phylogenetic relationships based on chromosomal rearrangements and allozymes (two distinct lineages corresponding to the two genera), and mtDNA ( Stenocephalemys being paraphyletic). Geometric morphometrics supports the former hypothesis. Partial Least-Squares analysis shows a significant relation between variation in size and shape and altitude, which strongly suggests that adaptation is a major causal factor for divergence in the morphology of the skull. Size increases with altitude, paralleling a clinal change in shape, which involves stenocephaly as characterising the highland species. This shape modification allows the rodents to scan the sky efficiently for birds, which represent the main category of predators in the Afro Alpine moorlands.
Regenesis: How Synthetic Biology Will Reinvent Nature and Ourselves

Imagine a future in which human beings have become immune to all viruses, in which bacteria can custom-produce everyday items, like a drinking cup, or generate enough electricity to end oil dependency. Building a house would entail no more work than planting a seed in the ground. These scenarios may seem far-fetched, but pioneering geneticist George Church and science writer Ed Regis show that synthetic biology is bringing us ever closer to making such visions a reality. In Regenesis, Church and Regis explore the possibilities--and perils--of the emerging field of synthetic biology. Synthetic biology, in which living organisms are selectively altered by modifying substantial portions of their genomes, allows for the creation of entirely new species of organisms. Until now, nature has been the exclusive arbiter of life, death, and evolution; with synthetic biology, we now have the potential to write our own biological future. Indeed, as Church and Regis show, it even enables us to revisit crucial points in the evolution of life and, through synthetic biological techniques, choose different paths from those nature originally took. Such exploits will involve far more than just microbial tinkering. Full-blown genomic engineering will make possible incredible feats, from resurrecting woolly mammoths and other extinct organisms to creating mirror life forms with a molecular structure the opposite of our own. These technologies--far from the out-of-control nightmare depicted in science fiction--have the power to improve human and animal health, increase our intelligence, enhance our memory, and even extend our life span. A breathtaking look at the potential of this world-changing technology, Regenesis is nothing less than a guide to the future of life.
Variation In Extra-Pair Mating Systems In Tachycineta Swallows: A Life-History Approach

Despite the fact that the majority of bird species inhabit the tropics and southern hemisphere, studies of north temperate birds have historically driven much of the development of avian behavioral ecology and life history evolution. Here we characterize the genetic mating system of a south temperate breeder, the Whiterumped Swallow Tachycineta leucorrhoa, and examine the effects of breeding density and synchrony on extra-pair paternity in this species. White-rumped Swallows nesting in Buenos Aires Province, Argentina, show notably high rates of extra-pair paternity, with 77% of nests (N = 78) having extra-pair young and 56% of nestlings (N = 342) in the sampled population being extra-pair. Within broods, one to four males fathered extra-pair offspring, and in 29% of nests all offspring were from extra-pair sires. In those cases where we could identify extra-pair sires (N = 31 males), the median distance between their own social nests and the nests where they fathered nestlings was 165m. We did not find a relationship between breeding synchrony and extra-pair paternity rates, nor between density of neighbors and extra-pair paternity. Previous comparative studies on life history traits have found most variation in extra-pair paternity to be concentrated at the taxonomic levels of family and order. Extra-pair paternity rates in our White-rumped Swallow populations are similar to those found in the north temperate congener, Tree Swallow T. bicolor (73-89% nests, 35-69% young), but quite different from those of their tropical relative, Mangrove Swallow T.
Studies on Indo-Australian and East-Asiatic Eumenidae (Hymenoptera, Vespoidea)

CONTENTS Introduction 3 1. On Labus Saussure and a related new genus. 5 Labus Saussure 5 Cyrtolabus gen. n 11 2. On Pareumenes Saussure and related genera. 14 Pareumenes Saussure 16 Pseumenes Giordani Soika 25 Ectopioglossa Perkins 29 Nortozumia van der Vecht 39 Pseudozumia Saussure 41 Coeleumenes gen. n 45 3. On Anterhynchium Saussure and some related genera. 57 Allorhynchium gen. n 58 Anterhynchium Saussure 73 Subg. Anterhynchium Saussure 74 „ Dirhynchium subg. n 77 „ Epiodynerus Giordani Soika 88 Pararrhynchium Saussure 94 Orancistrocerus gen. n 99 Rhynchium Spinola 109 4. A new genus for Rhynchium nitidulum (Fabricius). 111 Xenorhynchium gen. n 111 Literature 113 Index 114
Efficient Scheduling of Scientific Workflows Using Hot Metadata in a Multisite Cloud

Large-scale, data-intensive scientific applications are often expressed as scientific workflows (SWfs). In this paper, we consider the problem of efficient scheduling of a large SWf in a multisite cloud, i.e., a cloud with geo-distributed cloud data centers (sites). The reasons for using multiple cloud sites to run a SWf are that data is already distributed, the necessary resources exceed the limits at a single site, or the monetary cost is lower. In a multisite cloud, metadata management has a critical impact on the efficiency of SWf scheduling as it provides a global view of data location and enables task tracking during execution. Thus, it should be readily available to the system at any given time. While it has been shown that efficient metadata handling plays a key role in performance, little research has targeted this issue in multisite cloud. In this paper, we propose to identify and exploit hot metadata (frequently accessed metadata) for efficient SWf scheduling in a multisite cloud, using a distributed approach. We implemented our approach within a scientific workflow management system, which shows that our approach reduces the execution time of highly parallel jobs up to 64 percent and that of the whole SWfs up to 55 percent.
ITERATIVE METHOD FOR BLIND EVALUATION OF MIXED NOISE CHARACTERISTICS ON IMAGES

A new method for blind estimation of mixed noise parameters is proposed. The method is based on line fitting into a set of cluster centers obtained from scatter-plot of local variance and mean estimates. Improved estimation of cluster centers is performed on basis of fourth-order statistical moment analysis. The estimation results for the proposed method are compared to the results for other known methods using images from TID2008 database. It is shown that the proposed method provides estimation accuracy comparable to the estimation accuracy of the method based on maximum likelihood estimation of image and noise characteristics (which is considered the best among the existing methods). An advantage of our method is that it is considerably faster.
Semi-Supervised Learning for Diagnosing Faults in Electromechanical Systems

Safe and reliable operation of the systems relies on the use of online condition monitoring and diagnostic systems that aim to take immediate actions upon the occurrence of a fault. Machine learning techniques are widely used for designing data-driven diagnostic models. The training procedure of a data-driven model usually requires a large amount of labeled data, which may not be always practical. This problem can be untangled by resorting to semi-supervised learning approaches, which enables the decision making procedure using only a few numbers of labeled samples coupled with a large number of unlabeled samples. Thus, it is crucial to conduct a critical study on the use of semi-supervised learning for the purpose of fault diagnosis. Another issue of concern is fault diagnosis in non-stationary environments, where data streams evolve over time, and as a result, model-based and most of the datadriven models are impractical. In this work, this has been addressed by means of an adaptive data-driven diagnostic model.