nils-herrmann/clean_scirepeval huggingface dataset:
AMPKa Is Suppressed in Bladder Cancer through Macrophage Mediated Mechanisms12
Venue: Translational oncology

Bladder cancer presents as either low or high grade disease, each with distinct mutational profiles; however, both display prominent mTORC1 activation. One major negative regulator of mTORC1 is AMPK, which is a critical metabolic regulator that suppresses cellular growth in response to metabolic stress by negatively regulating mTORC1. Alterations in the activation and protein levels of AMPK have been reported in breast, gastric, and hepatocellular carcinoma. To investigate whether AMPK suppression is responsible for mTOR activation in bladder cancer, the levels of AMPKa were quantified in a cohort of primary human bladder cancers and adjacent nontumor tissues. The levels of p AMPKa,  AMPKa2, and total AMPKa were significantly suppressed in both low and high grade disease when compared with nontumor tissue. To elucidate the AMPKa suppression mechanism, we focused on inflammation, particularly tumor infiltrating macrophages, due to their reported role in regulating AMPK expression. Treatment of HTB2 cancer cells with varying doses of differentiated U937 macrophage conditioned medium (CM) demonstrated a dose dependent reduction of AMPKa protein. Additionally, macrophage CM treatment of HTB2 and HT1376 bladder cells for various times also reduced AMPKa protein but not mRNA levels. Direct TNFa treatment also suppressed AMPKa at the protein but not RNA level. Finally, staining of the human cohort for CD68, a macrophage marker, revealed that CD68+ cell counts correlated with reduced AMPKa levels. In summary, these data demonstrate the potential role for inflammation and inflammatory cytokines in regulating the levels of AMPKa and promoting mTORC1 activation in bladder cancer.
Metal fate and effects in estuaries: A review and conceptual model for better understanding of toxicity.
Venue: The Science of the total environment

Metal pollution is a global problem in estuaries due to the legacy of historic contamination and currently increasing metal emissions. However, the establishment of water and sediment standards or management actions in brackish systems has been difficult because of the inherent transdisciplinary nature of estuarine processes. According to the European Commission, integrative comprehension of fate and effects of contaminants in different compartments of these transitional environments (estuarine sediment, water, biota) is still required to better establish, assess and monitor the good ecological status targeted by the Water Framework Directive. Thus, the present study proposes a holistic overview and conceptual model for the environmental fate of metals and their toxicity effects on aquatic organisms in estuaries. This includes the analysis and integration of biogeochemical processes and parameters, metal chemistry and organism physiology. Sources of particulate and dissolved metal, hydrodynamics, water chemistry, and mechanisms of toxicity are discussed jointly in a multidisciplinary manner. It is also hypothesized how these different drivers of metal behaviour might interact and affect metal concentrations in diverse media, and the knowledge gaps and remaining research challenges are pointed. Ultimately,estuarine physicochemical gradients, biogeochemical processes, and organism physiology are jointly coordinating the fate and potential effects of metals in estuaries, and both realistic model approaches and attempts.
State of charge estimation in lithium ion batteries: A particle filter approach

The dynamics of lithium ion batteries are complex and are often approximated by models consisting of partial differential equations (PDEs) relating the internal ionic concentrations and potentials. The Pseudo two dimensional model (P2D) is one model that performs sufficiently accurately under various operating conditions and battery chemistries. Despite its widespread use for prediction, this model is too complex for standard estimation and control applications. This article presents an original algorithm for state of charge estimation using the P2D model. Partial differential equations are discretized using implicit stable algorithms and reformulated into a nonlinear state space model. This discrete, high dimensional model (consisting of tens to hundreds of states) contains implicit, nonlinear algebraic equations. The uncertainty in the model is characterized by additive Gaussian noise. By exploiting the special structure of the pseudo two dimensional model, a novel particle filter algorithm that sweeps in time and spatial coordinates independently is developed. This algorithm circumvents the degeneracy problems associated with high dimensional state estimation and avoids the repetitive solution of implicit equations by defining a 'tether' particle. The approach is illustrated through extensive simulations.
Macrophage Phenotype and Function in Different Stages of Atherosclerosis.
Venue: Circulation research

The remarkable plasticity and plethora of biological functions performed by macrophages have enticed scientists to study these cells in relation to atherosclerosis for >50 years, and major discoveries continue to be made today. It is now understood that macrophages play important roles in all stages of atherosclerosis, from initiation of lesions and lesion expansion, to necrosis leading to rupture and the clinical manifestations of atherosclerosis, to resolution and regression of atherosclerotic lesions. Lesional macrophages are derived primarily from blood monocytes, although recent research has shown that lesional macrophage like cells can also be derived from smooth muscle cells. Lesional macrophages take on different phenotypes depending on their environment and which intracellular signaling pathways are activated. Rather than a few distinct populations of macrophages, the phenotype of the lesional macrophage is more complex and likely changes during the different phases of atherosclerosis and with the extent of lipid and cholesterol loading, activation by a plethora of receptors, and metabolic state of the cells. These different phenotypes allow the macrophage to engulf lipids, dead cells, and other substances perceived as danger signals; efflux cholesterol to high density lipoprotein; proliferate and migrate; undergo apoptosis and death; and secrete a large number of inflammatory and proresolving molecules. This review article, part of the Compendium on Atherosclerosis, discusses recent advances in our understanding of lesional macrophage phenotype and function in different stages of atherosclerosis. With the increasing understanding of the roles of lesional macrophages, new research areas and treatment strategies are beginning to emerge.
Senescent intimal foam cells are deleterious at all stages of atherosclerosis
Venue: Science

Wreaking havoc while (growth )arrested Cells enter a state of senescence in response to certain stresses. Studying mouse models, Childs et al. examined the role of senescent lipid loaded macrophages (so called "foam cells" in the pathogenesis of atherosclerosis. At early stages of atherosclerosis, senescent foam cells promoted the expression of inflammatory cytokines. At later stages, they promoted the expression of matrix metalloproteases implicated in the rupture of atherosclerotic plaque, which can lead to blood clots. Experimental removal of the senescent cells had beneficial effects at both stages of the disease. Science, this issue p. 472 Senescent macrophages contribute to early and late stages of atherosclerosis and are potential targets for therapy. Advanced atherosclerotic lesions contain senescent cells, but the role of these cells in atherogenesis remains unclear. Using transgenic and pharmacological approaches to eliminate senescent cells in atherosclerosis prone low density lipoprotein receptor deficient (Ldlr mice, we show that these cells are detrimental throughout disease pathogenesis. We find that foamy macrophages with senescence markers accumulate in the subendothelial space at the onset of atherosclerosis, where they drive pathology by increasing expression of key atherogenic and inflammatory cytokines and chemokines. In advanced lesions, senescent cells promote features of plaque instability, including elastic fiber degradation and fibrous cap thinning, by heightening metalloprotease production. Together, these results demonstrate that senescent cells are key drivers of atheroma formation and maturation and suggest that selective clearance of these cells by senolytic agents holds promise for the treatment of atherosclerosis.
Dynamic Neural Turing Machine with Soft and Hard Addressing Schemes
Venue: ArXiv

We extend neural Turing machine (NTM) model into a dynamic neural Turing machine (D NTM) by introducing a trainable memory addressing scheme. This addressing scheme maintains for each memory cell two separate vectors, content and address vectors. This allows the D NTM to learn a wide variety of location based addressing strategies including both linear and nonlinear ones. We implement the D NTM with both continuous, differentiable and discrete, non differentiable read/write mechanisms. We investigate the mechanisms and effects of learning to read and write into a memory through experiments on Facebook bAbI tasks using both a feedforward and GRUcontroller. The D NTM is evaluated on a set of Facebook bAbI tasks and shown to outperform NTM and LSTM baselines. We have done extensive analysis of our model and different variations of NTM on bAbI task. We also provide further experimental results on sequential pMNIST, Stanford Natural Language Inference, associative recall and copy tasks.
Game Accessibility for the Blind: Current Overview and the Potential Application of Audio Description as the Way Forward

Over the past four decades video games have become a worldwide phenomenon and one of the preferred leisure options for many. However, game accessibility remains a pending issue, due to the visual and interactive nature of the medium. Mangiron and Zhang analyse the current state of game accessibility, particularly for the blind and visually impaired. They discuss the barriers and gaming options for this target group, such as audio games and 'video less' games. Finally, the chapter explores the feasibility of applying audio description to video games, which would potentially enhance game accessibility for blind and visually impaired players.
Design of a Curriculum Framework for Raising Awareness of Game Accessibility
Venue: ICCHP

While game accessibility is well researched, many game developers lack awareness of issues and solutions and there is no framework to support educators in teaching about game accessibility. This study is based on an international survey to accessibility researchers, as well as people in the game industry and related communities. The quantitative data shows the most weighted topics in a curriculum, and the qualitative data provides detailed quotes to explain how a curriculum framework could be designed. Results also show that there is a need to change attitudes to game accessibility, but also to focus on practice, basic concepts and needs of disabled in an introductory course, while an advanced course could focus more on theory and solutions which are harder to implement. Future research is to follow up this study to further validate our conclusions.
N fixing trees in wetland restoration plantings: effects on nitrogensupply and soil microbial communities
Venue: Environmental Science and Pollution Research

To investigate the impact of an exotic Frankia nodulated tree (Alnus trabeculosa) on soil nitrogen content, soil microbial composition, and the abundance of N turnover related functional microorganism community, we compared the community structure and abundance of key functional genes (nifH, bacterial/archaeal amoA, and nosZ) in the rhizosphere and nonrhizosphere of monoculture of Phragmites australis and A.trabeculosa P.australis mixed communities by MiSeq Illumina sequencing and real time PCR, respectively. The introduction of Frankia nodulated tree to recover degraded wetland was effective in the accumulation of soil organic carbon and nitrogen, which was the key factor to impact on the bacterial community composition revealed by canonical correspondence analysis. Acidobacteria and Proteobacteria were the dominant bacterial phylums while seven rare phyla appeared the most phylogenetically different among the investigated soil of two vegetations, including Chlorobi, Cyanobacteria, OD1, OP11, TM6, TM7, and GN02. The gene copy numbers of nifH were ranged from 2.28 x 108 to 2.96 x 109 copies g 1 dry soil in the wetland, and which were significantly higher in soil samples from P. australis than that from A.trabeculosa. While the abundance of nosZ in both rhizosphere and nonrhizosphere soils of A.trabeculosa P.australis mixed communities was significantly lower compared with P.australis monoculture. The potential nitrification (PNA) (0.15 0.41 mg NOx N kg 1 dry soil d 1) in the rhizosphere of A. trabeculosa was significantly higher than that of P. australis, and the soil denitrification enzyme activity (DEA) (0.42 0.90 nmol N2O N g 1 dry soil h 1) was lower in the mixed community compared with monoculture of P. australis. The introduced planting of Frankia nodulated tree effectively accumulated soil organic carbon and nitrogen and reduce the relative abundance and activity of nitrogen fixing bacteria and denitrification bacteria.
Characterisation of Damaged Tubular Composites by Acoustic Emission, Thermal Diffusivity Mapping and TSR RGB Projection Technique
Venue: Applied Composite Materials

An increase in the use of composite materials, owing to improved design and fabrication processes, has led to cost reductions in many industries. Resistance to corrosion, high specific strength, and stiffness are just a few of their many attractive properties. However, damage tolerance remains a major concern in the implementation of composites and uncertainty regarding component lifetimes can lead to over design and under use of such materials. A combination of non destructive evaluation (NDE) and structural health monitoring (SHM) have shown promise in improving confidence by enabling data collection in situ and in real time. In this work, infrared thermography (IRT) is employed for NDE of tubular composite specimens before and after impact. Four samples are impacted with energies of 5 J, 7.5 J, and 10 J by an un instrumented falling weight set up. Acoustic emissions (AE) are monitored using bonded piezoelectric sensors during one of the four impact tests. IRT data is used to generate diffusivity and thermal depth mappings of each sample using the thermographic signal reconstruction (TSR) red green blue (RGB) projection technique. Analysis of AE data alone for a 10 J impact suggest significant damage to the fibres and matrix; this is in good agreement with the generated thermal depth mappings for each sample, which indicate damage through multiple fibre layers. IRT and AE data are correlated and validated by optical micrographs taken along the cross section of damage.
A framework for verification of SystemC TLM programs with model slicing: A case study
Venue: 2016 53nd ACM/EDAC/IEEE Design Automation Conference (DAC)

In this paper, we evaluate the effectiveness of model slicing to provide assurance about correctness of SystemC TLM programs. The need for such assurance is important since SystemC has become a de facto standard for building systems with hardware/software co design. Existing approaches that enable one to transform the given SystemC TLM program into an UPPAAL model that can be verified suffer from models that result in state space explosion. This problem becomes even more complex when verifying fault tolerance. Model slicing has the potential to provide a solution to this problem. Therefore, we focus on developing a model slicer that extends existing work on model slicing and combines it with tools to generate UPPAAL models from SystemC TLM programs and tools to add the impact of faults to those UP PAAL models. The experimental results show that with the proposed framework, the designer is capable of verifying even very complex SystemC TLM models, which would have been impossible without the proposed approach.
Existing Bridge Formulas for Truck Weight Regulation from International Jurisdictions and Resulting Load Stresses on Single Span Bridges

AbstractThis paper identifies and characterizes existing bridge formulas from international regions and presents the results of an analysis of the allowable gross vehicle weights and bridge load stress effects on single span bridges resulting from these formulas. This is done to provide insight into this method of regulating truck size and weight to identify influencing factors and considerations for future decisions regarding the creation of new bridge formulas, or modification of existing ones. It is found that bridge formulas vary significantly in terms of the level of restrictiveness of allowable loads and imposed load effects due to the design criteria used in their development including truck configurations, bridge design methods, design loads, and allowable load rating. Bridge formulas should be designed to limit the imposed stresses on bridges based on criteria suitable to a jurisdiction's truck fleet and infrastructure characteristics in order to adequately regulate truck sizes and weights.
Fournier's Gangrene: Epidemiology and Outcomes in the General US Population
Venue: Urologia Internationalis

Case series reported 20 40% mortality rates for patients with Fournier's gangrene with some series as high as 88% This literature comes almost exclusively from referral centers.  We identified and analyzed inpatients with Fournier's gangrene who had a surgical debridement or died in the US State Inpatient Databases.  One thousand six hundred and forty one males and 39 females with Fournier's gangrene represented <0.02% of hospital admissions. Overall, the incidence was 1.6 cases per 100,000 males and case fatality was 7.5% Sixty six percent of hospitals cared for no cases per year, 17% cared for 1 case per year, 10% cared for 2 cases per year, 4% cared for 3 cases per year, 1% cared for 4 cases per year, and only 1% cared for =5 cases per year. Teaching hospitals had higher mortality (adjusted OR 1.9) due primarily to more acutely ill patients. Hospitals treating more than 1 Fournier's gangrene case per year had an adjusted 42 84% lower mortality (p 0.0001)  Most hospitals rarely care for Fournier's gangrene patients. The population based mortality rate (7.5% was substantially lower than the case series from tertiary care centers. Hospitals that treated more number of Fournier's gangrene patients had lower mortality rates, thereby supporting the rationale that regionalized care worked well for patients with this rare disease.
Fournier's gangrene. A clinical review.
Venue: Archivio italiano di urologia, andrologia organo ufficiale [di] Societa italiana di ecografia urologica e nefrologica

's gangrene is a rare, necrotising fasciitis of the external genitalia, perineal or perianal regions. The disease has a higher incidence in males and risk factors for development include diabetes, HIV, alcoholism and other immune compromised states. The aggressive disease process is associated with a high mortality rate of 20 30% In addition, the increasing age and prevalence of diabetes in the population, begs the need for increased clinical awareness of Fournier's gangrene with emphasis on early diagnosis and management. This review aims to highlight the relevant research surrounding Fournier's gangrene, in particular the various prognostic indicators and management strategies.  A search was conducted on the MEDLINE database for all applicable research; clinical reviews, retrospective studies and case reports. In addition to which a search of the European Association of Urology, the British Association for Urological Surgeons and the British Medical Journal was conducted for the most recent recommendations.  Immediate broad spectrum antibiotic therapy and urgent surgical debridement are the core managerial principles of Fournier's gangrene. The use of adjunctive therapies such as hyperbaric oxygen and vacuum assisted closure are supported in some aspects of the literature and disputed in others. The lack of randomized controlled studies limits the use of these potential additional therapies to patients unresponsive to conventional management. The value of unprocessed honey as a topical antimicrobial agent has been highlighted in the literature for small lesions in uncomplicated patients.  Fournier's gangrene is a urological emergency with a high mortality rate despite advances in the medical and surgical fields. The aggressive nature of the infection advocates the need for early recognition allowing immediate surgical intervention. The opposing results of available research as well as the lack of high quality evidence surrounding emergent therapies prevents their routine use in the management of Fournier's gangrene. The absence of a specific care pathway may hinder efficient management of Fournier's gangrene, thus based on current guidelines a management pathway is suggested.
Fournier's gangrene current approaches
Venue: International wound journal

Fournier's gangrene is a rare but highly mortal infectious disease characterised by fulminant necrotising fasciitis involving the genital and perineal regions. The objective of this study is to analyse the demographics, clinical feature and treatment approaches as well as outcomes of Fournier's gangrene. Data were collected retrospectively from medical records and operative notes. Patient data were analysed by demographics, aetiological factors, clinical features, treatment approaches and outcomes. Twelve patients (five female and seven male) were enrolled in this study. The most common aetiology was perianal abscess (41*6% Wound cultures showed a mixture of microorganisms in six (50% patients. For faecal diversion, while colostomy was performed in six cases (50% Flexi Seal was used in two cases (16*6% In four patients (33*4% no faecal diversion was performed. Negative pressure wound therapy (NPWT) system was effective in the last four patients (33*4% The mean hospitalisation period in patients who used NPWT was 18 days, while it was 20 days in the others. NPWT in Fournier's gangrene is a safe dressing method. It promotes granulation formation.  Seal faecal management is an alternative method to colostomy and provides protection from its associated complications. The combination of two devices (Flexi Seal and NPWT) is an effective and comfortable method in the management of Fournier's gangrene in appropriate patients.
Clinical characteristics and predictors of gangrene in patients with systemic sclerosis and digital ulcers in the Digital Ulcer Outcome Registry: a prospective, observational cohort
Venue: Annals of the rheumatic diseases

Digital vasculopathy in systemic sclerosis (SSc) consists of a spectrum of Raynaud's phenomenon (RP) digital ulcers (DUs) critical digital ischaemia and escalation to gangrene. The complications of severe digital vasculopathy often require hospital based management with intravenous therapies and  3 Although gangrene is not infrequent in the clinic, data on the prevalence and implications of gangrene in patients with SSc are scarce.3 7 The DU Outcomes (DUO) Registry is a European, prospective, multicentre, observational cohort of patients with SSc and past and/or current DUs at enrolment.8 10 The aims of the current study were (i) to describe the characteristics of an SSc DU population according to the presence/history of gangrene and (ii) to identify the risk factors for the development of incident gangrene. All patients in the participating centres with SSc and a history or presence of DUs are eligible for inclusion in the DUO Registry, irrespective of their treatment regimen. At enrolment, data were collected on demographic and clinical variables. Patients were categorised into three groups according to their past history of gangrene