Miracle-dz/UniFAR-FTUs huggingface dataset:
An Emergent Model for Mimicking Human Neuronal Pathways in Silico

In this study, our aim is to mimick human neuronal pathways without assuming the transition from microscopic to macroscopic scales depend upon mathematical arguments. Human neuronal pathways are natural complex systems in which large sets of neurons interact locally and give bottomup rise to collective macroscopic behaviors. In this sense, correct knowledge of the synaptic effective connections between neurons is a key prerequisite for relating them to the operation of their central nervous system (CNS). However, estimating these effective connections between neurons in the human CNS poses a great challenge since direct recordings are impossible. Consequently, the network between human neurons is often expressed as a black box and the properties of connections between neurons are estimated using indirect methods (Turker and Powers, 2005). In indirect methods a particular receptor system is stimulated and the responses of neurons that are affected by the stimulus recorded to estimate the properties of the circuit. However, these neuronal circuits in human subjects are only estimations and their existence cannot be directly proven. Furthermore, there is no satisfactory theory on how these unknown parts of the CNS operate.
A human monocytic NF-κB fluorescent reporter cell line for detection of microbial contaminants in biological samples

Sensing of pathogens by innate immune cells is essential for the initiation of appropriate immune responses. Toll-like receptors (TLRs), which are highly sensitive for various structurally and evolutionary conserved molecules derived from microbes have a prominent role in this process. TLR engagement results in the activation of the transcription factor NF-κB, which induces the expression of cytokines and other inflammatory mediators. The exquisite sensitivity of TLR signalling can be exploited for the detection of bacteria and microbial contaminants in tissue cultures and in protein preparations. Here we describe a cellular reporter system for the detection of TLR ligands in biological samples. The well-characterized human monocytic THP-1 cell line was chosen as host for an NF-ᴋB-inducible enhanced green fluorescent protein reporter gene. We studied the sensitivity of the resultant reporter cells for a variety of microbial components and observed a strong reactivity towards TLR1/2 and TLR2/6 ligands. Mycoplasma lipoproteins are potent TLR2/6 agonists and we demonstrate that our reporter cells can be used as reliable and robust detection system for mycoplasma contaminations in cell cultures. In addition, a TLR4-sensitive subline of our reporters was engineered, and probed with recombinant proteins expressed in different host systems. Bacterially expressed but not mammalian expressed proteins induced strong reporter activity. We also tested proteins expressed in an E. coli strain engineered to lack TLR4 agonists. Such preparations also induced reporter activation in THP-1 cells highlighting the importance of testing recombinant protein preparations for microbial contaminations beyond endotoxins. Our results demonstrate the usefulness of monocytic reporter cells for high-throughput screening for microbial contaminations in diverse biological samples, including tissue culture supernatants and recombinant protein preparations. Fluorescent reporter assays can be measured on standard flow cytometers and in contrast to established detection methods, like luciferase-based systems or Limulus Amebocyte Lysate tests, they do not require costly reagents.
Patient assistive system for the shoulder joint

Abstract The mobility of the upper extremity is essential for everyday activities and for independent living. Shoulder disorders affect the range of motion, therefore a patient assistive system (PAS) for the shoulder joint can be used to compensate the restrictions. The developed PAS supports up to 120° of flexion and abduction. The portable dynamic orthotic consists of two levers and is attached to a hip belt. The upper arm of the patient is connected to the device using a brace. The prototype is driven by one motor and controlled by surface electromyography (EMG). The functionality of the system was successfully verified by tests with healthy subjects. For further development, a study with shoulder patients will be performed and health professionals will evaluate the PAS.
The Incubation Period of Buruli Ulcer (Mycobacterium ulcerans Infection)

Introduction Buruli Ulcer (BU) is caused by the environmental microbe Mycobacterium ulcerans. Despite unclear transmission, contact with a BU endemic region is the key known risk factor. In Victoria, Australia, where endemic areas have been carefully mapped, we aimed to estimate the Incubation Period (IP) of BU by interviewing patients who reported defined periods of contact with an endemic area prior to BU diagnosis. Method A retrospective review was undertaken of 408 notifications of BU in Victoria from 2002 to 2012. Telephone interviews using a structured questionnaire and review of notification records were performed. Patients with a single visit exposure to a defined endemic area were included and the period from exposure to disease onset determined (IP). Results We identified 111 of 408 notified patients (27%) who had a residential address outside a known endemic area, of whom 23 (6%) reported a single visit exposure within the previous 24 months. The median age of included patients was 30 years (range: 6 to 73) and 65% were male. 61% had visited the Bellarine Peninsula, currently the most active endemic area. The median time from symptom onset to diagnosis was 71 days (range: 34–204 days). The midpoint of the reported IP range was utilized to calculate a point estimate of the IP for each case. Subsequently, the mean IP for the cohort was calculated at 135 days (IQR: 109–160; CI 95%: 113.9–156), corresponding to 4.5 months or 19.2 weeks. The shortest IP recorded was 32 days and longest 264 days (Figure 1 & 2). IP did not vary for variables investigated. Conclusions The estimated mean IP of BU in Victoria is 135 days (IQR: 109–160 days), 4.5 months. The shortest recorded was IP 34 days and longest 264 days. A greater understanding of BU IP will aid clinical risk assessment and future research.
Sphingolipid Long-Chain Base Hydroxylation Is Important for Growth and Regulation of Sphingolipid Content and Composition in Arabidopsis[W]

Sphingolipids are structural components of endomembranes and function through their metabolites as bioactive regulators of cellular processes such as programmed cell death. A characteristic feature of plant sphingolipids is their high content of trihydroxy long-chain bases (LCBs) that are produced by the LCB C-4 hydroxylase. To determine the functional significance of trihydroxy LCBs in plants, T-DNA double mutants and RNA interference suppression lines were generated for the two Arabidopsis thaliana LCB C-4 hydroxylase genes Sphingoid Base Hydroxylase1 (SBH1) and SBH2. These plants displayed reductions in growth that were dependent on the content of trihydroxy LCBs in sphingolipids. Double sbh1 sbh2 mutants, which completely lacked trihydroxy LCBs, were severely dwarfed, did not progress from vegetative to reproductive growth, and had enhanced expression of programmed cell death associated–genes. Furthermore, the total content of sphingolipids on a dry weight basis increased as the relative amounts of trihydroxy LCBs decreased. In trihydroxy LCB–null mutants, sphingolipid content was ∼2.5-fold higher than that in wild-type plants. Increases in sphingolipid content resulted from the accumulation of molecular species with C16 fatty acids rather than with very-long-chain fatty acids, which are more commonly enriched in plant sphingolipids, and were accompanied by decreases in amounts of C16-containing species of chloroplast lipids. Overall, these results indicate that trihydroxy LCB synthesis plays a central role in maintaining growth and mediating the total content and fatty acid composition of sphingolipids in plants.
System Level Methodology for Interconnect Aware and Temperature Constrained Power Management of 3-D MP-SOCs

Modern 3-D multiprocessor systems-on-chip (MP-SoC) incorporate processing elements (PEs) and memories within die-stacks interconnected using through-silicon vias (TSVs). The resulting power density of these systems necessitates the inclusion of thermal effects in the architecture space exploration stage of the design process. The number and placement of TSVs influences the thermal conductivity in the vertical direction in die-stacks, and consequently these must be considered during thermal analysis. However, the special requirement of keep out zones (KOZs) for TSVs due to mechanical stress considerations complicates the design of the vertical interconnect, potentially impacting its electrical performance as well. This paper presents an integrated methodology that allows for TSV topology exploration to evaluate the best vertical interconnect structure while considering crosstalk, area overheads, and KOZ requirements using an initial system floorplan. After incorporating feedback from the exploration, the resulting vertical interconnect is included within a temperature-power simulation that estimates the thermal profile of the 3-D stack. Within this methodology, a novel power management scheme for 3-D MP-SoCs that considers both temperature as well as positional information and thermal relationships between PEs, while performing dynamic voltage-frequency scaling (DVFS), is introduced. The scheme effectively maintains smooth temperature profiles, decreases fluctuations in voltage-frequency levels, and increases the aggregate frequency of operation at a lower total power dissipation. Further, the scheme is applied to a stack partitioned into voltage islands, where it is shown to match the conventional per-core DVFS schemes in its performance.
Dissecting abdominal aortic aneurysm in Ang II-infused mice : the importance of imaging

Introduction. Since the initial publication in 2000, Angiotensin II-infused mice have become the model of choice to study abdominal aortic aneurysm in a pre-clinical setting. We recently used phase contrast X-ray based computed tomography to challenge the existing paradigm and demonstrated that these animals develop an apparent luminal dilatation and an intramural hematoma, both related to mural ruptures in the tunica media in the vicinity of suprarenal side branches, providing evidence that the main lesion is rather a mere dissection without previous
DU Electronic Theses and Dissertations Graduate Studies 1-1-2012 Student School Engagement as a Potential Predictor of High School Completion

There is a dropout epidemic in the United States. In the US, 25% of high school students do not graduate on time. For Latinos, the number is worse, with only 64% graduating from high school. Current research is clear that 9 th grade is a critical year for keeping students in school. Students that earn all their credits for their core classes in 9 th grade are more likely to graduate than students who fail one or more class during their freshman year. Prior to this study, engagement has been connected to dropout in the literature, but with differing ideas of how to measure engagement. The Student School Engagement Measure (SSEM) could be one tool used to estimate levels of engagement and identify students at risk of dropping out. This study used structural equation modeling to identify whether 8 th grade SSEM scores were a significant predictor of credits earned by the end of 9 th grade. The results of this study indicated that 8 th grade SSEM scores were not a significant predictor of credits earned at the end of 9 th grade, supporting previous research has found that engagement changes from year to year. These findings suggest that measuring engagement over the course of a single year, instead of using the SSEM as a long term predictor, might be a more useful use of the SSEM.
Dynamic Panel Estimation and Homogeneity Testing Under Cross Section Dependence

This paper deals with cross section dependence, homogeneity restrictions and small sample bias issues in dynamic panel regressions. To address the bias problem we develop a panel approach to median unbiased estimation that takes account of cross section dependence. The new estimators given here considerably reduce the effects of bias and gain precision from estimating cross section error correlation. The paper also develops an asymptotic theory for tests of coefficient homogeneity under cross section dependence, and proposes a modified Hausman test to test for the presence of homogeneous unit roots. An orthogonalization procedure is developed to remove cross section dependence and permit the use of conventional and meta unit root tests with panel data. Some simulations investigating the finite sample performance of the estimation and test procedures are reported.
Chimeric antigen receptor-T cell therapy for solid tumors require new clinical regimens

ABSTRACT Introduction: Chimeric antigen receptor modified T cell (CAR-T) therapy has achieved encouraging breakthroughs in the treatment of hematological malignancies. Nevertheless, this success has not yet been extrapolated to solid tumors. This review focuses on new clinical regimens that could improve the therapeutic efficacy of CAR-T in solid tumors. Areas covered: Herein, the authors reviewed recent clinical trials using CAR-T therapies for the treatment of solid tumors. Specifically, this review covered the following areas: (1) the current status of CAR-T cells in the treatment of solid tumors; (2) the major factors constraining the efficacy of CAR-T cells in solid tumors; and (3) opinions regarding the future of CAR-T as a treatment for solid tumors. Expert commentary: While some recent studies have shown promising results, the ultimate success of CAR-T therapies in solid tumor patients will require the following improvements to clinical regimens: (1) local delivery of CAR-T cells; (2) combination of CAR-T cells with chemotherapeutic drugs to treat metastatic tumors; (3) combination of CAR-T with immune checkpoint inhibitors; (4) combination therapy using CAR-T cells targeting two different antigens; and (5) the use of CAR-T as a strategy to prevent tumor recurrence and metastasis after radical resection.
Assessment of Blood-Brain Barrier Permeability by Dynamic Contrast-Enhanced MRI in Transient Middle Cerebral Artery Occlusion Model after Localized Brain Cooling in Rats

Objective The purpose of this study was to evaluate the effects of localized brain cooling on blood-brain barrier (BBB) permeability following transient middle cerebral artery occlusion (tMCAO) in rats, by using dynamic contrast-enhanced (DCE)-MRI. Materials and Methods Thirty rats were divided into 3 groups of 10 rats each: control group, localized cold-saline (20℃) infusion group, and localized warm-saline (37℃) infusion group. The left middle cerebral artery (MCA) was occluded for 1 hour in anesthetized rats, followed by 3 hours of reperfusion. In the localized saline infusion group, 6 mL of cold or warm saline was infused through the hollow filament for 10 minutes after MCA occlusion. DCE-MRI investigations were performed after 3 hours and 24 hours of reperfusion. Pharmacokinetic parameters of the extended Tofts-Kety model were calculated for each DCE-MRI. In addition, rotarod testing was performed before tMCAO, and on days 1-9 after tMCAO. Myeloperoxidase (MPO) immunohisto-chemistry was performed to identify infiltrating neutrophils associated with the inflammatory response in the rat brain. Results Permeability parameters showed no statistical significance between cold and warm saline infusion groups after 3-hour reperfusion 0.09 ± 0.01 min-1 vs. 0.07 ± 0.02 min-1, p = 0.661 for Ktrans; 0.30 ± 0.05 min-1 vs. 0.37 ± 0.11 min-1, p = 0.394 for kep, respectively. Behavioral testing revealed no significant difference among the three groups. However, the percentage of MPO-positive cells in the cold-saline group was significantly lower than those in the control and warm-saline groups (p < 0.05). Conclusion Localized brain cooling (20℃) does not confer a benefit to inhibit the increase in BBB permeability that follows transient cerebral ischemia and reperfusion in an animal model, as compared with localized warm-saline (37℃) infusion group.
Autojoin: Providing Freedom from Specifying Joins

SQL is not appropriate for casual users as it requires understanding relational schemas and how to construct joins. Many new query interfaces insulate users from the logical structure of the database, but they require the automatic discovery of valid joins. Although specific query interfaces implement join determination algorithms, they are tied to the specific language and typically limited in scope or scalability. AutoJoin provides a general solution to the query inference problem, which allows more complex queries to be executed on larger and more complicated schemas. It enumerates query interpretations at least an order of magnitude faster than previous methods. In addition, the engine reduces the number of queries considered ambiguous. Experimental results demonstrate that query inference can be efficiently performed on large, complex schemas allowing simpler access to databases through keyword search or conceptual query languages. AutoJoin also provides programmers with a tool to iteratively create SQL queries without requiring explicit knowledge of the structure of a database.
Impact of novel therapies for mantle cell lymphoma in the real world setting: a report from the UK's Haematological Malignancy Research Network (HMRN)

The treatment landscape for mantle cell lymphoma (MCL) has changed dramatically in recent years, with findings from clinical trials reporting improvements in survival. Data on the general patient population are, however, sparse; and it is unclear whether the effects observed in clinical trials have translated into the real‐world setting. To investigate this, we examined first‐line and relapsed/refractory (RR) disease management in 335 MCL patients diagnosed between 2004 and 2015 in an established population‐based patient cohort, along with data on demographic, diagnostic and prognostic factors. Marked treatment and survival changes were observed; first‐line rituximab immunotherapy, for example, increased from 32% to 86% over the 11‐year period, and median survival increased from 2·0 years among those first treated in 2004–2011 to 3·5 years among those treated in 2012–2015. Outcomes for RR disease also improved, from 8 months in 2004–2011 to 16·8 months in 2012–2015, coinciding with the introduction of agents, such as bendamustine and ibrutinib. Encouragingly, improvements were seen across all ages; 1‐year overall survival among patients over 70 years treated for RR disease almost doubled. Our analyses underscore the importance of monitoring the impact of treatment changes in the real‐world setting.
Identification of Structural Systems Using Particle Swarm Optimization

Abstract Particle swarm optimization (PSO) is a new heuristic method that has yielded promising results for solving complex optimization problems. Its advantages are a simple structure, ease of use, quality of solution, and robustness. This paper utilizes the PSO algorithm for parameter estimation of structural systems, which could be formulated as a multi-modal numerical optimization problem with high dimension. Simulation results for identifying the parameters of multiple degree-of-freedom (DOF) linear and nonlinear structural systems are presented to demonstrate the effectiveness of the proposed method.
A Dissociation between Categorization and Similarity to Exemplars

Research in category learning has been dominated by a ‘reference point’ view in which items are classified based on attention-weighted similarity to reference points (e.g., prototypes, exemplars, clusters) in a multidimensional space. Although much work has attempted to distinguish between particular types of reference point models, they share a core design principle that items will be classified as belonging to the category of the most proximal reference point(s). In this paper, we present an original experiment challenging this distance assumption. After classification training on a modified XOR category structure, we find that many learners generalize their category knowledge to novel exemplars in a manner that violates the distance assumption. This pattern of performance reveals a fundamental limitation in the reference point framework and suggests that stimulus generalization is not a reliable foundation for explaining human category learning.
THE HEALTH SUITE CONCEPT : A SOCIAL MEDIA PLATFORM FOR PUBLIC HEALTH APPLICATIONS

Social media interventions addressing public health issues have proliferated at an unprecedented rate in the past decade. However, despite its nimble and flexible nature, social media has been applied to health issues in silos. By this, we mean that social media affordances have either been applied to addressing specific aspects of a health issue, or have focused on addressing one issue at a time, such as infectious diseases. Given the apparent commonalities in the technological characteristics of social media for health interventions, applying the same features to a distinct set of health issues leads to reinventing the wheel and, more important, redundancy in technological deliverables. This paper addresses this issue by proposing the general architecture of Health Suite, an integrative common platform built on a plug-and-play model for health-related social media solutions. We present summary findings from formative research studies that informed our idea, offer a detailed description of Health Suite and its various modules, and demonstrate how Health Suite’s modules have been adapted for designing a social media-based dengue prevention intervention in Colombo, Sri Lanka. The paper culminates with a brief discussion of challenges and future directions for this e-health architecture.