Miracle-dz/UniFAR-FTUs huggingface dataset:
Phage Therapy Is Effective in a Mouse Model of Bacterial Equine Keratitis

ABSTRACT Bacterial keratitis of the horse is mainly caused by staphylococci, streptococci, and pseudomonads. Of these bacteria, Pseudomonas aeruginosa sometimes causes rapid corneal corruption and, in some cases, blindness. Antimicrobial resistance can make treatment very difficult. Therefore, new strategies to control bacterial infection are required. A bacteriophage (phage) is a virus that specifically infects and kills bacteria. Since phage often can lyse antibiotic-resistant bacteria because the killing mechanism is different, we examined the use of phage to treat horse bacterial keratitis. We isolated Myoviridae or Podoviridae phages, which together have a broad host range. They adsorb efficiently to host bacteria; more than 80% of the ΦR18 phage were adsorbed to host cells after 30 s. In our keratitis mouse model, the administration of phage within 3 h also could kill bacteria and suppress keratitis. A phage multiplicity of infection of 100 times the host bacterial number could kill host bacteria effectively. A cocktail of two phages suppressed bacteria in the keratitis model mouse. These data demonstrated that the phages in this study could completely prevent the keratitis caused by P. aeruginosa in a keratitis mouse model. Furthermore, these results suggest that phage may be a more effective prophylaxis for horse keratitis than the current preventive use of antibiotics. Such treatment may reduce the use of antibiotics and therefore antibiotic resistance. Further studies are required to assess phage therapy as a candidate for treatment of horse keratitis. IMPORTANCE Antibiotic-resistant bacteria are emerging all over the world. Bacteriophages have great potential for resolution of this problem. A bacteriophage, or phage, is a virus that infects bacteria specifically. As a novel therapeutic strategy against racehorse keratitis caused by Pseudomonas aeruginosa, we propose the application of phages for treatment. Phages isolated in this work had in vitro effectiveness for a broad range of P. aeruginosa strains. Indeed, a great reduction of bacterial proliferation was shown in phage therapy for mouse models of P. aeruginosa keratitis. Therefore, to reduce antibiotic usage, phage therapy should be investigated and developed further.
Timing and security analysis of VANET-based intelligent transportation systems: (Invited paper)

With the fast development of autonomous driving and vehicular communication technologies, intelligent transportation systems that are based on VANET (Vehicular Ad-Hoc Network) have shown great promise. For instance, through V2V (Vehicle-to-Vehicle) and V2I (Vehicle-to-Infrastructure) communication, intelligent intersections allow more fine-grained control of vehicle crossings and significantly enhance traffic efficiency. However, the performance and safety of these VANET-based systems could be seriously impaired by communication delays and packet losses, which may be caused by network congestion or by malicious attacks that target communication timing behavior. In this paper, we quantitatively model and analyze some of the timing and security issues in transportation networks with VANET-based intelligent intersections. In particular, we demonstrate how communication delays may affect the performance and safety of a single intersection and of multiple interconnected intersections, and present our delay-tolerant intersection management protocols. We also discuss the issues of such protocols when the vehicles are non-cooperative and how they may be addressed with game theory.
Combined glutamate and glutamine levels in pain-processing brain regions are associated with individual pain sensitivity

Abstract The relationship between glutamate and &ggr;-aminobutyric acid (GABA) levels in the living human brain and pain sensitivity is unknown. Combined glutamine/glutamate (Glx), as well as GABA levels can be measured in vivo with single-voxel proton magnetic resonance spectroscopy. In this cross-sectional study, we aimed at determining whether Glx and/or GABA levels in pain-related brain regions are associated with individual differences in pain sensitivity. Experimental heat, cold, and mechanical pain thresholds were obtained from 39 healthy, drug-free individuals (25 men) according to the quantitative sensory testing protocol and summarized into 1 composite measure of pain sensitivity. The Glx levels were measured using point-resolved spectroscopy at 3 T, within a network of pain-associated brain regions comprising the insula, the anterior cingulate cortex, the mid-cingulate cortex, the dorsolateral prefrontal cortex, and the thalamus. GABA levels were measured using GABA-edited spectroscopy (Mescher–Garwood point-resolved spectroscopy) within the insula, the anterior cingulate cortex, and the mid-cingulate cortex. Glx and/or GABA levels correlated positively across all brain regions. Gender, weekly alcohol consumption, and depressive symptoms were significantly associated with Glx and/or GABA levels. A linear regression analysis including all these factors indicated that Glx levels pooled across pain-related brain regions were positively associated with pain sensitivity, whereas no appreciable relationship with GABA was found. In sum, we show that the levels of the excitatory neurotransmitter glutamate and its precursor glutamine across pain-related brain regions are positively correlated with individual pain sensitivity. Future studies will have to determine whether our findings also apply to clinical populations.
EA-GLES: An Energy-Aware 3D Graphics Library for Mobile Devices

The goal of desktop-class graphics hardware is generally to provide the maximum performances possible to end users. This goal is shared also by mobile hardware designers, although, due the use of a battery as power source, a greater attention needs to be devoted to energy saving. In the last years, a number of approaches to hardware design have been experimented aimed to trade-off the quality of the visual experience with the usage of computational resources, that is to say, with energy consumption. The objective of this work is to tackle energy issues at the software, i.e., at the application level, by introducing a high-level library based on OpenGL ES (often abbreviated GLES) that can be exploited by developers to create energy-aware graphics applications letting end users chose the maximum amount of energy to consume.
Quantum Transport Theory in Graphene

In this thesis, we focus on different aspects of electron transport in nanostructured graphene (such as graphene nanoribbons). We develop and implement numerical methods to study quantum coherent electron transport on an atomistic level, complemented by analytical calculations based on the Dirac approximation valid close to the points $\vec{K}$ and $\vec{K}^\prime$ in the graphene Brillouin zone. By simulating a graphene nanogap bridged with 1,4-phenylene-diamine molecules anchored via $C_{60}$ molecules, we show that a transistor effect can be achieved by back-gating the system. By simulating STM-measurements on nanoribbons with single impurities, we investigate the interplay between size quantization and the local scatterers, and show analytically how the features of the Fourier transformed local density of states can be explained by electrons scattering between different transverse modes of the ribbons. We extend the analys to also include analytical transport calculations, and explain the origin of characteristic dips found in the transmission and their relations to quasi-bound states formed around the ribbon impurities. We construct and simulate graphene ribbons with transverse grain boundaries, and illustrate how such grain boundaries form metallic states bridging the two edges of the ribbon together. This is a plausible candidate to explain the attenuation (or even destruction) of the quantum Hall effect often seen in quantum Hall bar measurements, especially with graphene grown on metals (such as copper) where grain boundaries are common. The introductory chapters also present a basic introduction to the field of graphene and graphene ribbons, and we thoroughly present the tight-binding techniques used for simulation.
Effect of piracetam and nimodipine on full‐thickness skin burns in rabbits

The potential of several drugs for full‐thickness skin burns has been investigated, but the treatment of such burns remains a challenge in plastic surgery. The present study was designed to determine the effect of systemic and topical administration of piracetam and nimodipine on full‐thickness skin burn wound healing. A total of 36 New Zealand male rabbits were divided into six groups. Full‐thickness skin burns were produced in all the groups, except the control group. Piracetam was administered systemically (piracetam‐IV) and topically (piracetam‐C) for 14 days, and nimodipine was administered systemically (nimodipine‐IV) and topically (nimodipine‐C) over the burn wounds for 14 days. The sham group underwent burn injury but was not administered any drug. After 21 days, gross examination and histopathological analysis were performed and the results were compared statistically. Nimodipine‐C and nimodipine‐IV had no effect on burn wound healing. However, both piracetam‐IV and piracetam‐C significantly enhanced the healing of the full‐thickness skin burn wounds, although the latter was more effective, useful and practical in burn wound healing. The histopathological features of the wounds in the piracetam‐C group were closer to those of the control group than those of the other groups. Piracetam‐C rather than piracetam‐IV may promote full‐thickness burn wound healing in rabbits.
Development of reliable techniques for the differential diagnosis of avian tumour viruses by immunohistochemistry and polymerase chain reaction from formalin-fixed paraffin-embedded tissue sections

ABSTRACT A variety of techniques have been developed as diagnostic tools for the differential diagnosis of tumours produced by Marek’s disease virus from those induced by avian leukosis virus and reticuloendotheliosis virus. However, most current techniques are unreliable when used in formalin-fixed paraffin-embedded (FFPE) tissues, which often is the only sample type available for definitive diagnosis. A collection of tumours was generated by the inoculation of different strains of Marek’s disease virus, reticuloendotheliosis virus or avian leukosis virus singularly or in combination. FFPE tissue sections from tumour and non-tumour tissues were analysed by optimized immunohistochemistry (IHC) techniques and traditional as well as quantitative polymerase chain reaction (PCR) with newly designed primers ideal for DNA fragmented by fixation. IHC and PCR results were highly sensitive and specific in tissues from single-infected birds. Virus quantity was higher in tumours compared to non-tumour spleens from Marek’s disease (MD) virus-infected birds. Thus, using FFPE sections alone may be sufficient for the diagnosis of MD by demonstration of high quantities of viral antigens or genome in tumour cells, along with the absence of other tumour viruses by traditional PCR, and if standard criteria are met based on clinical history and histology. IHC furthermore allowed detection of the specific cells that were infected with different viruses in tumours from birds that had been inoculated simultaneously with multiple viruses. Following validation with field samples, these new protocols can be applied for both diagnostic and research purposes to help accurately identify avian tumour viruses in routine FFPE tissue sections.
Possible error in the Danish version of the WHO Quality of Life (WHOQOL-BREF) Questionnaire

Abstract Background: The WHOQOL-BREF is widely used to measure quality of life. Aims: The goal of the present study was to use the questionnaire in a doctoral study. Methods: We studied all the instructions provided by the WHO. Results: In the Danish version of the WHOQOL-BREF there is a discrepancy between the negatively phrased question 9 and both the syntax file and the verbal instructions for coding the data provided by the WHO. Conclusions: This is a notification of possible error interpretations in projects that use the questionnaire. This could be corrected by manual correction in the coding process or by changing the negatively phrased question 9.
Laser‐generated shockwaves enhance antibacterial activity against biofilms in vitro

Bacterial biofilm formation within chronic wound beds, which provides an effective barrier against antibiotics, is a known cause of recalcitrant infections and a significant healthcare burden, often requiring repeated surgical debridements. Laser‐generated shockwaves (LGS) is a novel, minimally invasive, and nonthermal modality for biofilm mechanical debridement which utilizes compressive stress waves, generated by photonic absorption in thin titanium films to mechanically disrupt the biofilm. Prior studies have demonstrated LGS monotherapy to be selectively efficacious for biofilm disruption and safe for host tissues. In this study, we sought to determine if LGS can enhance the antimicrobial activity and biofilm disruption capability of topical antibiotic therapy.
Censored linear regression models for irregularly observed longitudinal data using the multivariate-t distribution

In acquired immunodeficiency syndrome (AIDS) studies it is quite common to observe viral load measurements collected irregularly over time. Moreover, these measurements can be subjected to some upper and/or lower detection limits depending on the quantification assays. A complication arises when these continuous repeated measures have a heavy-tailed behavior. For such data structures, we propose a robust structure for a censored linear model based on the multivariate Student’s t-distribution. To compensate for the autocorrelation existing among irregularly observed measures, a damped exponential correlation structure is employed. An efficient expectation maximization type algorithm is developed for computing the maximum likelihood estimates, obtaining as a by-product the standard errors of the fixed effects and the log-likelihood function. The proposed algorithm uses closed-form expressions at the E-step that rely on formulas for the mean and variance of a truncated multivariate Student’s t-distribution. The methodology is illustrated through an application to an Human Immunodeficiency Virus-AIDS (HIV-AIDS) study and several simulation studies.
VST: A virtual stress testing framework for discovering bugs in SSD flash-translation layers

Flash translation layers (FTLs) are the core embedded software (also known as firmware) of NAND flash-based solid-state drives (SSDs). The relentless pursuit of high-performance SSDs renders FTLs increasingly complex and intricate. Therefore, testing and validating FTLs are crucial and challenging tasks. Directly testing and validating FTLs on SSD hardware are common practices though, they are time-consuming and cumbersome because 1) the testing speed is limited by the hardware speed of SSDs and 2) just reproducing bugs can be challenging, let alone locating and root causing the bugs. This work presents virtual stress testing (VST), a simulation framework to enable executing SSD FTLs on PCs or servers against virtual SRAM, DRAM, and flash emulated by host-side main memory. FTL function calls, such as moving data from flash to DRAM, are served by the VST framework. Therefore, VST can test FTLs without SSD hardware requirements nor SSD speed limitations, and root causing bugs becomes manageable tasks. We apply VST to representative SSD design, OpenSSD, which is actively utilized and maintained by SSD and FTL communities. Experimental results show that VST can test FTLs at a speed up to 375 GB/s, which is several hundred times faster than directly testing FTLs on SSD hardware. Moreover, we successfully discover seven new FTL bugs in the OpenSSD design using VST, which is a solid evidence of VST's bug-discovering effectiveness.
Anaerobic Copper Toxicity and Iron-Sulfur Cluster Biogenesis in Escherichia coli

ABSTRACT While copper is an essential trace element in biology, pollution of groundwater from copper has become a threat to all living organisms. Cellular mechanisms underlying copper toxicity, however, are still not fully understood. Previous studies have shown that iron-sulfur proteins are among the primary targets of copper toxicity in Escherichia coli under aerobic conditions. Here, we report that, under anaerobic conditions, iron-sulfur proteins in E. coli cells are even more susceptible to copper in medium. Whereas addition of 0.2 mM copper(II) chloride to LB (Luria-Bertani) medium has very little or no effect on iron-sulfur proteins in wild-type E. coli cells under aerobic conditions, the same copper treatment largely inactivates iron-sulfur proteins by blocking iron-sulfur cluster biogenesis in the cells under anaerobic conditions. Importantly, proteins that do not have iron-sulfur clusters (e.g., fumarase C and cysteine desulfurase) in E. coli cells are not significantly affected by copper treatment under aerobic or anaerobic conditions, indicating that copper may specifically target iron-sulfur proteins in cells. Additional studies revealed that E. coli cells accumulate more intracellular copper under anaerobic conditions than under aerobic conditions and that the elevated copper content binds to the iron-sulfur cluster assembly proteins IscU and IscA, which effectively inhibits iron-sulfur cluster biogenesis. The results suggest that the copper-mediated inhibition of iron-sulfur proteins does not require oxygen and that iron-sulfur cluster biogenesis is the primary target of anaerobic copper toxicity in cells. IMPORTANCE Copper contamination in groundwater has become a threat to all living organisms. However, cellular mechanisms underlying copper toxicity have not been fully understood up to now. The work described here reveals that iron-sulfur proteins in Escherichia coli cells are much more susceptible to copper in medium under anaerobic conditions than they are under aerobic conditions. Under anaerobic conditions, E. coli cells accumulate excess intracellular copper, which specifically targets iron-sulfur proteins by blocking iron-sulfur cluster biogenesis. Since iron-sulfur proteins are involved in diverse and vital physiological processes, inhibition of iron-sulfur cluster biogenesis by copper disrupts multiple cellular functions and ultimately inhibits cell growth. The results from this study illustrate a new interplay between intracellular copper toxicity and iron-sulfur cluster biogenesis in bacterial cells under anaerobic conditions.
Neighborhood Poverty and 9-1-1 Ambulance Response Time

Abstract Background: Are 9-1-1 ambulances relatively late to poorer neighborhoods? Studies suggesting so often rely on weak measures of neighborhood (e.g., postal zip code), limit the analysis to particular ambulance encounters (e.g., cardiac arrest responses), and do little to account for variations in dispatch priority or intervention severity. Methods: We merged EMS ambulance contact records in a single California county (n = 87,554) with tract-level data from the American Community Survey (n = 300). After calculating tract-level median ambulance response time (MART), we used ordinary least squares (OLS) regression to estimate a conditional average relationship between neighborhood poverty and MART and quantile regression to condition this relationship on 25th, 50th, and 75th percentiles of MART. We also specified each of these outcomes by five dispatch priorities and by three intervention severities. For each model, we estimated the associated changes in MART per 10 percentage point increase in tract-level poverty while adjusting for emergency department proximity, population density, and population size. Results: Our study produced three major findings. First, most of our tests suggested tract-level poverty was negatively associated with MART. Our baseline OLS model estimates that a 10 percentage point increase in tract-level poverty is associated with almost a 24 s decrease in MART (−23.55 s, 95% confidence interval [CI] −33.13 to −13.98). Results from our quantile regression models provided further evidence for this association. Second, we did not find evidence that ambulances are relatively late to poorer neighborhoods when specifying MART by dispatch priority. Third, we were also unable to identify a positive association between tract-level poverty and MART when we specified our outcomes by three intervention severities. Across each of our 36 models, tract-level poverty was either not significantly associated with MART or was negatively associated with MART by a magnitude smaller than a full minute per estimated 10 percentage point increase in poverty concentration. Conclusion: Our study challenges the commonly held assumption that ambulances are later to poor neighborhoods. We scrutinize our findings before cautiously considering their relevance for ambulance response time research and for ongoing conversations on the relationship between neighborhood poverty and prehospital care.
Brain structure differences between Chinese and Caucasian cohorts: A comprehensive morphometry study

Numerous behavioral observations and brain function studies have demonstrated that neurological differences exist between East Asians and Westerners. However, the extent to which these factors relate to differences in brain structure is still not clear. As the basis of brain functions, the anatomical differences in brain structure play a primary and critical role in the origination of functional and behavior differences. To investigate the underlying differences in brain structure between the two cultural/ethnic groups, we conducted a comparative study on education‐matched right‐handed young male adults (age = 22–29 years) from two cohorts, Han Chinese (n = 45) and Caucasians (n = 45), using high‐dimensional structural magnetic resonance imaging (MRI) data. Using two well‐validated imaging analysis techniques, surface‐based morphometry (SBM) and voxel‐based morphometry (VBM), we performed a comprehensive vertex‐wise morphometric analysis of the brain structures between Chinese and Caucasian cohorts. We identified consistent significant between‐group differences in cortical thickness, volume, and surface area in the frontal, temporal, parietal, occipital, and insular lobes as well as the cingulate cortices. The SBM analyses revealed that compared with Caucasians, the Chinese population showed larger cortical structures in the temporal and cingulate regions, and smaller structural measures in the frontal and parietal cortices. The VBM data of the same sample was well‐aligned with the SBM findings. Our findings systematically revealed comprehensive brain structural differences between young male Chinese and Caucasians, and provided new neuroanatomical insights to the behavioral and functional distinctions in the two cultural/ethnic populations.
Virtual Machine Power Accounting with Shapley Value

The ever-increasing power consumption of datacenters has eaten up a large portion of their profit. One possible solution is to charge datacenter users for their actual power usage. However, it poses a great technical challenge as the power of VMs co-existing in a physical machine cannot be measured directly. It is thus critical to develop a fair method to disaggregate the power of a physical machine to individual VMs. We tackle the above challenge by modeling the power disaggregation problem as a cooperative game and propose non-deterministic Shapley value to discover the fair power share of VMs (in the sense of satisfying four desired axiomatic principles), while compensating the negative impact of VM power variation. We demonstrate that the results from existing power model-based solution can deviate from the "ground truth" by 25.22% ∼46.15%. And compared with the exact Shapley value, our non-deterministic Shapley value can achieve less than 5% error for 90% of the time.