Miracle-dz/UniFAR-FTUs huggingface dataset:
Clinical Course, Outcomes and Complications of Thai Pediatric Pure Type versus Mixed Type Lupus Membranous Nephritis.

Background Due to the relative infrequency of lupus membranous nephritis (LMN) compared to other types of lupus nephritis (LN) in pediatric patients, the current literature on pediatric LMN is limited. The knowledge regarding clinical manifestations, outcomes and infectious complications are mainly based on studies in the adult population. Similar to disease expression in SLE, the renal manifestations of LMN are affected by environmental factors and vary among racial and ethnic groups. Objective To describing clinical features, common infectious complications, and outcomes of pediatric-onset LMN in Thailand and the correlation between pure and mixed types of LMN classified by renal pathology. Material and Method This was a retrospective analysis of 40 patients with LMN as seen in the Pediatric Nephrology Clinic, Maharaj Nakorn Chiang Mai from January, 2003 to December, 2012. Patients were categorized into pure and mixed types of LMN the comparisons of the clinical course, results of treatment and infectious complications between the two types had been analyzed and recorded data for 2 years. Results Kidney biopsy was performed. Of the 40 patients with LMN, 50% were diagnosed as mixed-type LMN. The clinical symptoms presented including rash, hypertension, edema, serositis and arthritis were found at 57.7%, 45%, 40%, 25% and 25% respectively. All of the patients were treated with an immunosuppressive drug such as: Cyclophosphamide, Azathioprine, Cyclosporine or Mycophenolate mofetil, together with systemic steroids. During the two years follow up, every patient had normal GFR. Twenty nine patients (72.5%) had renal remission in proteinuria with complete remission in 7 patients (17.5%) and partial remission in 22 patients (55%). An average time from the onset to remission was 12 months. GFR and proteinuria were not significant difference between the two groups after treatment. The infections found in patients who received cyclophosphamide include herpes infection, salmonellosis, lung abscess, nocardiosis, giardia intestinalis and cerebral cysticercosis. Furthermore, steroid side effect was avascular necrosis of the hip joint. Conclusion The mixed-type LMN patients had a higher blood pressure, higher BUN and positive LE cell than those of the pure-type LMN patients. Hypertension at initial presentation can be a predictor of proliferative lesion in renal pathology. However, a proliferative lesion accompanied with LMN does not affect renal outcomes. With similar renal outcomes, the immunosuppressive with low adverse effects may be considered as a preferable treatment.
The CoLoMoTo Interactive Notebook: Accessible and Reproducible Computational Analyses for Qualitative Biological Networks

Analysing models of biological networks typically relies on workflows in which different software tools with sensitive parameters are chained together, many times with additional manual steps. The accessibility and reproducibility of such workflows is challenging, as publications often overlook analysis details, and because some of these tools may be difficult to install, and/or have a steep learning curve. The CoLoMoTo Interactive Notebook provides a unified environment to edit, execute, share, and reproduce analyses of qualitative models of biological networks. This framework combines the power of different technologies to ensure repeatability and to reduce users’ learning curve of these technologies. The framework is distributed as a Docker image with the tools ready to be run without any installation step besides Docker, and is available on Linux, macOS, and Microsoft Windows. The embedded computational workflows are edited with a Jupyter web interface, enabling the inclusion of textual annotations, along with the explicit code to execute, as well as the visualisation of the results. The resulting notebook files can then be shared and re-executed in the same environment. To date, the CoLoMoTo Interactive Notebook provides access to software tools including GINsim, BioLQM, Pint, MaBoSS, and Cell Collective for the modelling and analysis of Boolean and multi-valued networks. More tools will be included in the future. We developed a Python interface for each of these tools to offer a seamless integration in the Jupyter web interface and ease the chaining of complementary analyses.
A Study of the Self-Reported Resilience of APC Chaplains

Approximately 5000 members of the Association of Professional Chaplains were surveyed using the Professional Quality of Life instrument in order to assess levels of Compassion Satisfaction and Compassion Fatigue and its associated subscales, Burnout and Secondary Traumatic Stress; 1299 surveys were completed. The most significant finding of this study is that Board Certified Chaplains have remarkably low scores of Burnout and Secondary Traumatic Stress and significantly high levels of Compassion Satisfaction.
On Controlling the Attack Surface of Object-Oriented Refactorings

: The results of this work have originally been published in [Ru18]. Refactorings constitute an effective means to improve quality and maintainability of evolving object-oriented programs. Search-based techniques have shown promising results in Ąnding near-optimal sequences of behavior-preserving program transformations that (1) maximize code-quality metrics and (2) minimize the number of code changes. However, the impact of refactorings on non-functional properties like security has received little attention so far. To this end, we propose, as a further objective, to minimize the attack surface of object-oriented programs (i.e., to maximize strictness of declared accessibility of class members). Minimizing the attack surface naturally competes with applicability of established refactorings like MoveMethod , frequently used for improving code quality in terms of coupling/cohesion measures. Our tool implementation is based on an EMF meta-model for J ava -like programs and utilizes MOMoT , a search-based model-transformation and optimization framework. Our experimental results gained from applying different accessibility-control strategies to a collection of real-world Java programs show the impact of attack surface minimization on design-improving refactorings. We further compare the results to those of existing refactoring tools.
The relationship between neuroticism and night eating: exploring the mediating roles of psychological distress and maladaptive coping

ABSTRACT Night Eating Syndrome has been shown to be associated with various negative physical and psychological consequences. This study explored the relationship between neuroticism and night eating, which had not been studied before. We also examined the possible mediating roles of psychological distress and maladaptive coping for the relationship between neuroticism and night eating. A sample of 578 Chinese college students were assessed on several measures: The Revised Eysenck Personality Questionnaire Short Scale, the Night Eating Questionnaire, the Depression Anxiety Stress Scales, and the Simplified Coping Style Questionnaire. Results indicated that neuroticism was significantly and positively related to night eating (r = .38, p < .01), and the relationship between neuroticism and night eating was partially mediated by psychological distress, but not by maladaptive coping. The results not only revealed a medium-sized relationship between neuroticism and night eating, but also pointed out the importance of psychological distress as related to the relationship between neuroticism and night eating. Unlike neuroticism, which is a personality trait, psychological distress is an emotional state, and it is much more malleable through appropriate intervention. The treatment and intervention for night eating may benefit from our attention to the psychological distress.
Efficiency and Optimality of Largest Deficit First Prioritization

An increasing number of real-time applications with compute and/or communication deadlines are being supported on a shared infrastructure. Such applications can often tolerate occasional deadline violations without substantially impacting their Quality of Service (QoS). This article explores the efficient allocation of shared resources to satisfy such QoS requirements. We study a simple framework which decouples this problem into two subproblems: (1) dynamic prioritization of users based on arbitrary functions of their deficits (difference of achieved vs. required QoS), and (2) priority-based resource allocation on the underlying compute fabric. In this article, we shall assume the solution to the latter is fixed, e.g., as realized in the task prioritization capabilities of current hardware/software, and focus on compatible solutions to the former. We first characterize the set of feasible QoS requirements and show the optimality of max weight-like prioritization. We then consider simple weighted Largest Deficit First (w-LDF) prioritization policies, where users with higher weighted QoS deficits are given higher priority. The article gives an inner bound for the feasible set under w-LDF policies, and, under an additional monotonicity assumption, characterizes its geometry leading to a sufficient condition for optimality. Additional insights on the efficiency ratio of w-LDF policies, the optimality of hierarchical-LDF, and characterization of clustering of failures are also discussed.
Stimulation of the Internal Ribosome Entry Site (IRES)-Dependent Translation of Enterovirus 71 by DDX3X RNA Helicase and Viral 2A and 3C Proteases

The translation of enterovirus 71 (EV71) is mediated by an internal ribosome entry site (IRES)-dependent manner. EV71 IRES comprises five highly structured domains (domains II-VI) in the 5′-untranslated region of the viral mRNA. A conserved AUG triplet residing in domain VI is proposed to be the ribosome entry site. It is thus envisaged that the highly structured conformation of domain VI may actually reduce the accessibility of the AUG triplet to the ribosome. This study identified a DEAD-box family RNA helicase, DDX3X, that positively regulated the EV71 IRES-dependent translation. The helicase activity of DDX3X was required for the stimulation of EV71 IRES activity; however, DDX3X was no longer important for the IRES activity when the secondary structure of domain VI was destabilized. DDX3X interacted with the truncated eIF4G which bound specifically to domain V. Thus, we proposed that DDX3X might bind to domain VI or a region nearby via the interaction with the truncated eIF4G, and subsequently unwound the secondary structure of domain VI to facilitate ribosome entry. Additionally, we demonstrated that the viral 2Apro and 3Cpro enhanced the IRES-dependent translation via their protease activities. Together, these results indicate that DDX3X is an important RNA helicase involved in EV71 IRES-dependent translation and that IRES translation is enhanced by viral infection, partly mediated by viral protease activity.
Health Promotion Behaviors and Its Predictors Among the College Students in Iran

The health-promoting behaviors form typically during adolescence and youth. This study was conducted to determine the status of the health-promoting behaviors in the students of Babol University of Medical Sciences and its predictors. This cross-sectional study was done on 350 students from April 2016 to July 2016. The applied questionnaires were health-promoting lifestyle profile II, general self-efficacy scale, and sociodemographic variables. Data were analyzed using the SPSS software by descriptive tests, one-way analysis of variance, and multivariable linear regression. The mean total health-promoting lifestyle profile II score was 126.79 ± 19.28. In the subscales, the participants scored the highest in interpersonal relations (24.62 ± 4.59) and the lowest in physical activity (16.53 ± 4.17). Analyses of the data showed that there was a significant association among some subscales of health-promoting behaviors and gender, family size, living in dormitory and also showed that self-efficacy remained as significant factor in relation to all subscales of health-promoting behaviors.
Examination of Water Quantification and Incorporation in Transition Zone Minerals: Wadsleyite, Ringwoodite and Phase D Using ERDA (Elastic Recoil Detection Analysis)

Hydrous wadsleyite, ringwoodite, and phase D have been synthesized in the MgO-SiO$_2$-H$_2$O and MgO-FeO-SiO$_2$-H$_2$O systems at mantle transition zone conditions (15–21 GPa and 1,100–1,700 • C) to investigate their water incorporation using Elastic Recoil Detection Analysis (ERDA), which is an absolute quantitative method. Wadsleyite and ringwoodite water contents vary from 0.1 to 3.2 wt% H$_2$O and for ringwoodite containing up to 1.16 wt% H$_2$O we observe that the (Mg+Fe)/Si ratio vs. water content follows the same trend as for wadsleyite, indicating that H is substituting for Mg as for wadsleyite. We also measured, for the first time, the water content of phase D and observed that it varies from 6.7 to 11.2 wt% H$_2$O, up to twice less than estimated from electron microprobe analysis totals. Using these experiments, we were able to determine the absorptivity coefficient for OH infrared absorption bands in four wadsleyite and five ringwoodite samples. The average for the two iron-free wadsleyite samples leads to an absorptivity of 69,000 ± 7,000 L/moles H$_2$O/cm$^2$ , in very good agreement with previous determinations. The wadsleyite with 8 mole% Fe displays an absorptivity of 67,000 ± 5,000 L/moles H$_2$O/cm$^2$. The absorptivity values vary from 118,500 ± 5,000 for Fe-free ringwoodite to ±135,000 ± 9,000 for Fe-bearing ringwoodite (10% mole Fe). Our results show that absorptivity coefficient for OH infrared absorption of ringwoodite do not drastically change with Fe content and that the frequency-based calibration of Paterson (1982) underestimates its water determinations by 50%. This is very important to know when comparing data from different studies where different extinction coefficients have been used.
3D modeling and segmentation of diffusion weighted MRI data

Diffusion weighted magnetic resonance imaging (DW MRI) is a technique that measures the diffusion properties of water molecules to produce a tensor-valued volume dataset. Because water molecules can diffuse more easily along fiber tracts, for example in the brain, rather than across them, diffusion is anisotropic and can be used for segmentation. Segmentation requires the identification of regions with different diffusion properties. In this paper we propose a new set of rotationally invariant diffusion measures which may be used to map the tensor data into a scalar representation. Our invariants may be rapidly computed because they do not require the calculation of eigenvalues. We use these invariants to analyze a 3D DW MRI scan of a human head and build geometric models corresponding to isotropic and anisotropic regions. We then utilize the models to perform quantitative analysis of these regions, for example calculating their surface area and volume.
DPS: Dynamic Precision Scaling for Stochastic Computing-based Deep Neural Networks*

Stochastic computing (SC) is a promising technique with advantages such as low-cost, low-power, and error-resilience. However so far SC-based CNN (convolutional neural network) accelerators have been kept to relatively small CNNs only, primarily due to the inherent precision disadvantage of SC. At the same time, previous SC architectures do not exploit the dynamic precision capability, which can be crucial in providing efficiency as well as flexibility in SC-CNN implementations. In this paper we present a DPS (dynamic precision scaling) SC-CNN that is able to exploit dynamic precision with very low overhead, along with the design methodology for it. Our experimental results demonstrate that our DPS SC-CNN is highly efficient and accurate up to ImageNet-targeting CNNs, and show efficiency improvements over conventional digital designs ranging in 50~00% in operations-per-area depending on the DNN and the application scenario, while losing less than 1% in recognition accuracy.
Antibacterial Activity of Human Simulated Epithelial Lining Fluid Concentrations of Ceftazidime-Avibactam Alone or in Combination with Amikacin Inhale (BAY41-6551) against Carbapenem-Resistant Pseudomonas aeruginosa and Klebsiella pneumoniae

ABSTRACT The role of inhalational combination therapy when treating carbapenem-resistant Pseudomonas aeruginosa and Klebsiella pneumoniae with newer beta-lactam/beta-lactamase inhibitors has not been established. Using a 72-h in vitro pharmacodynamic chemostat model, we simulated the human exposures achieved in epithelial lining fluid (ELF) following intravenous treatment with ceftazidime-avibactam (CZA) 2.5 g every 8 h (q8h) alone and in combination with inhaled amikacin (AMK-I) 400 mg q12h, a reformulated aminoglycoside designed for inhalational administration, against three P. aeruginosa isolates (CZA [ceftazidime/avibactam] MICs, 4/4 to 8/4 μg/ml; AMK-I MICs, 8 to 64 μg/ml) and three K. pneumoniae isolates (CZA MICs, 1/4 to 8/4 μg/ml; AMK-I MICs, 32 to 64 μg/ml). Combination therapy resulted in a significant reduction in 72-h CFU compared with that of CZA monotherapy against two of three P. aeruginosa isolates (−4.14 log10 CFU/ml, P = 0.027; −1.42 log10 CFU/ml, P = 0.020; and −0.4 log10 CFU/ml, P = 0.298) and two of three K. pneumoniae isolates (0.04 log10 CFU/ml, P = 0.963; −4.34 log10 CFU/ml, P < 0.001; and −2.34 log10 CFU/ml, P = 0.021). When measured by the area under the bacterial growth curve (AUBC) over 72 h, significant reductions were observed in favor of the combination regimen against all six isolates tested. AMK-I combination therapy successfully suppressed CZA resistance development in one K. pneumoniae isolate harboring blaKPC-3 that was observed during CZA monotherapy. These studies suggest a beneficial role for combination therapy with intravenous CZA and inhaled AMK when treating pneumonia caused by carbapenem-resistant Gram-negative bacteria.
Approximate On-The-Fly Coarse-Grained Reconfigurable Acceleration for General-Purpose Applications

Approximate functional unit designs have the potential to reduce power consumption significantly compared to their precise counterparts; however, few works have investigated composing them to build generic accelerators. In this work, we do a design-space exploration of state-of-the-art approximate designs, propose a flow for designing approximate coarse-grained reconfigurable arrays (CGRAs), and discuss compilation and runtime reconfiguration issues. We compare the energy savings of precise and approximate reconfigurable acceleration and show that the latter can provide up to 50% additional power savings under a 10% quality loss constraint for the applications in the AxBench suite.
Immunoregulatory role of 15‐lipoxygenase in the pathogenesis of bacterial keratitis

Although autacoids primarily derived from the cyclooxygenase‐2 and 5‐lipoxygenase (LOX) pathways are essential mediators of inflammation, endogenous specialized proresolving mediators (SPMs) act as robust agonists of resolution. SPM biosynthesis is initiated by the conversion of arachidonic acid, eicosa‐pentaenoic acid, and docosahexaenoic acid primarily via the 12/15‐LOX pathway. Although 12/15‐LOX activity is prominent in the cornea, the role of SPM pathway activation during infection remains largely unknown and is the focus of the current study. Pseudomonas keratitis was induced in resistant BALB/c and susceptible C57BL/6 (B6) mice. Biosynthetic pathways for proinflammatory autacoids and SPMs were assessed. Divergent lipid mediator profiles demonstrate the importance of 15‐LOX pathways in the pathogenesis of ocular infectious disease. Results indicate that an imbalance of LOX enzymatic pathways contributes to susceptibility observed in B6 mice where deficient activation of SPM circuits, as indicated by reduced 15‐hydroxy‐eicosatetraenoic acid and 17‐hydroxydocosahexaenoic acid levels, prevented transition toward resolution and led to chronic inflammation. In sharp contrast, BALB/c mice demonstrated a well‐balanced axis of 5‐LOX/12‐LOX/15‐LOX pathways, resulting in sufficient proresolving bioactive metabolite formation and immune homeostasis. Furthermore, a novel immunoregulatory role for 15‐LOX was revealed in inflammatory cells (polymorphonuclear leukocytes and macrophages), which influenced phagocytic activity. These data provide evidence that SPM circuits are essential for host defense during bacterial keratitis. —Carion, T.W. , Greenwood, M. , Ebrahim, A. S. , Jerome, A. , Suvas, S. , Gronert, K. , Berger, E. A. Immunoregulatory role of 15‐lipoxygenase in the pathogenesis of bacterial keratitis. FASEB J. 32, 5026–5038 (2018). www.fasebj. org
Crystal structures of a [NiFe] hydrogenase large subunit HyhL in an immature state in complex with a Ni chaperone HypA

Significance The large subunit of [NiFe] hydrogenase undergoes Ni insertion into the active site by the Ni chaperone HypA during its posttranslational process (maturation process). However, the detailed mechanism of the Ni insertion has been elusive. Here, we report the structures of an immature large subunit HyhL in complex with HypA, which enable us to infer a series of conformational changes involved in the Ni delivery. The structures show that the N-terminal tail of HyhL interacts with the Ni-binding domain of HypA. Structural comparison of the immature large subunit HyhL with a mature one reveals that the Ni insertion may induce spatial rearrangement of the N- and C-terminal tails of HyhL. Ni-Fe clusters are inserted into the large subunit of [NiFe] hydrogenases by maturation proteins such as the Ni chaperone HypA via an unknown mechanism. We determined crystal structures of an immature large subunit HyhL complexed with HypA from Thermococcus kodakarensis. Structure analysis revealed that the N-terminal region of HyhL extends outwards and interacts with the Ni-binding domain of HypA. Intriguingly, the C-terminal extension of immature HyhL, which is cleaved in the mature form, adopts a β-strand adjacent to its N-terminal β-strands. The position of the C-terminal extension corresponds to that of the N-terminal extension of a mature large subunit, preventing the access of endopeptidases to the cleavage site of HyhL. These findings suggest that Ni insertion into the active site induces spatial rearrangement of both the N- and C-terminal tails of HyhL, which function as a key checkpoint for the completion of the Ni-Fe cluster assembly.