julilili42/papers huggingface dataset:
Upscaling Reputation Communication Simulations
2022-12-26

Social communication is omnipresent and a fundamental basis of our daily lives. Especially due to the increasing popularity of social media, communication flows are becoming more complex, faster and more influential. It is therefore not surprising that in these highly dynamic communication structures, strategies are also developed to spread certain opinions, to deliberately steer discussions or to inject misinformation. The reputation game is an agent-based simulation that uses information theoretical principles to model the effect of such malicious behavior taking reputation dynamics as an example. So far, only small groups of 3 to 5 agents have been studied, whereas now, we extend the reputation game to larger groups of up to 50 agents, also including one-to-many conversations. In this setup, the resulting group dynamics are examined, with particular emphasis on the emerging network topology and the influence of agents&amp;rsquo; personal characteristics thereon. In the long term, the reputation game should thus help to determine relations between the arising communication network structure, the used communication strategies and the recipients&amp;rsquo; behavior, allowing us to identify potentially harmful communication patterns, e.g., in social media.
War and the city: Lessons from urbicide in Ukraine
2022-12-27

This article explores urbicide during Europe’s largest ongoing war of the 21st century. Urbicide in Ukraine is not just another story in a long list of well-covered destroyed cities; it has new manifestations and needs to be rethought. Despite the variety of forms and concepts associated with urbicide, it has some common features such as non-selective ness, simultaneous destruction of symbolic and mundane, ordinary places, both physical structures and values, is aimed at ‘killing’ the heterogeneous urbanity for its own sake, and even being carefully planned causes reconfiguration of urban spaces in unexpected ways. The article has three focuses; it concentrates on the extent and causes of direct ur bicide in Ukraine, the relation of urban life under occupation and indirect urbicide, and narratives of (non)return to occupied cities. All these foci are united by the main purpose of the study to understand the urbicide caused by the warfare and global geopolitical changes that are ‘exploding’ (in a literal and relative sense) in Ukraine’s cities. This re search is based on the analysis of semi-structured in-depth interviews, thematic analysis, as well as mapping of warfare and urbicide in Ukraine.
Health-related quality of life, continuity of care and patient satisfaction: long-term outcomes of former patients of the Tuebingen Transition Program (TTP) – a retrospective cohort study
2022-12-27

Abstract Background A significant number of patients in pediatric rheumatology suffer from ongoing disease activity into adulthood and thus need to be transferred into adult care. Transition as a structured individual process of preparation and patient empowerment can reduce risks of adverse long-term outcomes. The aim of this study was to measure long-term transition outcomes such as health-related quality of life (HR-QoL), patient satisfaction, and continuity of care in former patients of the interdisciplinary Tuebingen Transition Program (TTP). Methods In an iterative team process, a standardized questionnaire was developed including the EQ-5D-5L to measure HR-QoL, visual analogue scales to measure various items of patient satisfaction, further questions on continuity of care and physical activity and physician global assessment (PGA) to determine disease activity. HR-QoL and physical activity were compared to data from the average German population. Data was analyzed descriptively, and a logistic regression analysis was performed to identify possible predictive factors for negative outcomes. Results Response rate was 28.8% (85/295), 70.6% were female and median age was 24.1 years. 70.6% were diagnosed with juvenile idiopathic arthritis (JIA). Overall, HR-QoL was high (79.8 on the EQ VAS), yet lower than in the average population. The study cohort was more physically active than the respective average age groups. Mean patient satisfaction with pediatric care (8.4; standard deviation (SD) 1.7) and with the transition program (7.9; SD 2.6) was higher than with adult care (7.7; SD 2.2). 76.5% of participants received regular rheumatologic care after transfer. After excluding all participants in remission, the drop-out rate was 4.7%. A low PGA at the time of transfer was associated with higher HR-QoL and patient satisfaction after transfer. Conclusions HR-QoL of adult patients after successful transfer to adult rheumatology is reduced compared to the general population but physical activity and achievement of clinical remission could help to prevent negative long-term outcomes. Patient satisfaction and self-management of TTP patients were generally high, whereas youth-specific issues and their impact on the disease mandate greater attention. Treatment discontinuation rates were low and mostly due to remission. Further studies should focus on the identification of early predictors of long-term outcome to improve the process and outcome of transition.
Global Gene Expression Analysis Reveals Complex Cuticle Organization of the Tribolium Compound Eye
2022-12-27

Abstract The red flour beetle Tribolium castaneum is a resource-rich model for genomic and developmental studies. To extend previous studies on Tribolium eye development, we produced transcriptomes for normal-eyed and eye-depleted heads of pupae and adults to identify differentially transcript-enriched (DE) genes in the visual system. Unexpectedly, cuticle-related genes were the largest functional class in the pupal compound eye DE gene population, indicating differential enrichment in three distinct cuticle components: clear lens facet cuticle, highly melanized cuticle of the ocular diaphragm, which surrounds the Tribolium compound eye for internal fortification, and newly identified facet margins of the tanned cuticle, possibly enhancing external fortification. Phylogenetic, linkage, and high-throughput gene knockdown data suggest that most cuticle proteins (CPs) expressed in the Tribolium compound eye stem from the deployment of ancient CP genes. Consistent with this, TcasCPR15, which we identified as the major lens CP gene in Tribolium, is a beetle-specific but pleiotropic paralog of the ancient CPR RR-2 CP gene family. The less abundant yet most likely even more lens-specific TcasCP63 is a member of a sprawling family of noncanonical CP genes, documenting a role of local gene family expansions in the emergence of the Tribolium compound eye CP repertoire. Comparisons with Drosophila and the mosquito Anopheles gambiae reveal a steady turnover of lens-enriched CP genes during insect evolution.
Treatment of Acute Mesenteric Ischemia: Individual Challenges for Interventional Radiologists and Abdominal Surgeons
2022-12-27

Background: Acute mesenteric ischemia (AMI) is a life-threatening condition resulting from occlusion of the mesenteric arterial vessels. AMI requires immediate treatment with revascularization of the occluded vessels. Purpose: to evaluate the technical success, clinical outcomes and survival of patients receiving endovascular treatment for AMI followed by surgery. Material and Methods: A search of our institution’s database for AMI revealed 149 potential patients between 08/2016 and 08/2021, of which 91 were excluded due to incomplete clinical data, insufficient imaging or missing follow-up laparoscopy. The final cohort included 58 consecutive patients [(median age 73.5 years [range: 43–96 years], 55% female), median BMI 26.2 kg/m2 (range:16.0–39.2 kg/m2)]. Periinterventional imaging regarding the cause of AMI (acute-embolic or acute-on-chronic) was evaluated by two radiologists in consensus. The extent of AMI and the degree of technical success was graded according to a modified TICI (Thrombolysis in Cerebral Infarction scale) score (TICI-AMI) classification (0: no perfusion; 1: minimal; 2a &lt; 50% filling; 2b &gt; 50%; 2c: near complete or slow; 3: complete). Lab data and clinical data were collected, including the results of follow-up laparoscopy. Non-parametric statistics were used. Results: All interventions were considered technically successful. The most common causes of AMI were emboli (51.7%) and acute-on-chronic thrombotic occlusions (37.9%). Initial imaging showed a TICI-AMI score of 0, 1 or 2a in 87.9% (n = 51) of patients. Post-therapeutic TICI-AMI scores improved significantly with 87.9% of patients grade 2b and better. Median lactate levels reduced from 2.7 (IQR 2.0–3.7) mg/dL (1–18) to 1.45 (IQR 0.99–1.90). Intestinal ischemia was documented in 79.1% of cases with resection of the infarcted intestinal loops. In total, 22/58 (37.9%) patients died during the first 30 days after intervention and surgery. According to CIRSE criteria, we did not observe any SAE scores of grade 2 or higher. Conclusions: AMI is a serious disease with high lethality within the first 30 days despite optimal treatment. However, interventional revascularization before surgery with resection of the infarcted bowel can save two out of three of critically ill patients.
Plasma glial fibrillary acidic protein in autosomal dominant Alzheimer's disease: Associations with Aβ‐PET, neurodegeneration, and cognition
2022-12-28

Abstract Background Glial fibrillary acidic protein (GFAP) is a promising candidate blood‐based biomarker for Alzheimer's disease (AD) diagnosis and prognostication. The timing of its disease‐associated changes, its clinical correlates, and biofluid‐type dependency will influence its clinical utility. Methods We evaluated plasma, serum, and cerebrospinal fluid (CSF) GFAP in families with autosomal dominant AD (ADAD), leveraging the predictable age at symptom onset to determine changes by stage of disease. Results Plasma GFAP elevations appear a decade before expected symptom onset, after amyloid beta (Aβ) accumulation and prior to neurodegeneration and cognitive decline. Plasma GFAP distinguished Aβ‐positive from Aβ‐negative ADAD participants and showed a stronger relationship with Aβ load in asymptomatic than symptomatic ADAD. Higher plasma GFAP was associated with the degree and rate of neurodegeneration and cognitive impairment. Serum GFAP showed similar relationships, but these were less pronounced for CSF GFAP. Conclusion Our findings support a role for plasma GFAP as a clinical biomarker of Aβ‐related astrocyte reactivity that is associated with cognitive decline and neurodegeneration. Highlights Plasma glial fibrillary acidic protein (GFAP) elevations appear a decade before expected symptom onset in autosomal dominant Alzheimer's disease (ADAD). Plasma GFAP was associated to amyloid positivity in asymptomatic ADAD. Plasma GFAP increased with clinical severity and predicted disease progression. Plasma and serum GFAP carried similar information in ADAD, while cerebrospinal fluid GFAP did not.
MuLan-Methyl—multiple transformer-based language models for accurate DNA methylation prediction
2022-12-28

Abstract Transformer-based language models are successfully used to address massive text-related tasks. DNA methylation is an important epigenetic mechanism, and its analysis provides valuable insights into gene regulation and biomarker identification. Several deep learning–based methods have been proposed to identify DNA methylation, and each seeks to strike a balance between computational effort and accuracy. Here, we introduce MuLan-Methyl, a deep learning framework for predicting DNA methylation sites, which is based on 5 popular transformer-based language models. The framework identifies methylation sites for 3 different types of DNA methylation: N6-adenine, N4-cytosine, and 5-hydroxymethylcytosine. Each of the employed language models is adapted to the task using the “pretrain and fine-tune” paradigm. Pretraining is performed on a custom corpus of DNA fragments and taxonomy lineages using self-supervised learning. Fine-tuning aims at predicting the DNA methylation status of each type. The 5 models are used to collectively predict the DNA methylation status. We report excellent performance of MuLan-Methyl on a benchmark dataset. Moreover, we argue that the model captures characteristic differences between different species that are relevant for methylation. This work demonstrates that language models can be successfully adapted to applications in biological sequence analysis and that joint utilization of different language models improves model performance. Mulan-Methyl is open source, and we provide a web server that implements the approach.
X-Ray Polarization Observations of BL Lacertae
2022-12-28

Abstract Blazars are a class of jet-dominated active galactic nuclei with a typical double-humped spectral energy distribution. It is of common consensus that the synchrotron emission is responsible for the low frequency peak, while the origin of the high frequency hump is still debated. The analysis of X-rays and their polarization can provide a valuable tool to understand the physical mechanisms responsible for the origin of high-energy emission of blazars. We report the first observations of BL Lacertae (BL Lac) performed with the Imaging X-ray Polarimetry Explorer, from which an upper limit to the polarization degree Π X &lt; 12.6% was found in the 2–8 keV band. We contemporaneously measured the polarization in radio, infrared, and optical wavelengths. Our multiwavelength polarization analysis disfavors a significant contribution of proton-synchrotron radiation to the X-ray emission at these epochs. Instead, it supports a leptonic origin for the X-ray emission in BL Lac.
In vitro and ex vivo modeling of enteric bacterial infections
2022-12-28

Enteric bacterial infections contribute substantially to global disease burden and mortality, particularly in the developing world. <i>In vitro</i> 2D monolayer cultures have provided critical insights into the fundamental virulence mechanisms of a multitude of pathogens, including <i>Salmonella enterica</i> serovars Typhimurium and Typhi, <i>Vibrio cholerae, Shigella</i> spp., <i>Escherichia coli</i> and <i>Campylobacter jejuni</i>, which have led to the identification of novel targets for antimicrobial therapy and vaccines. In recent years, the arsenal of experimental systems to study intestinal infections has been expanded by a multitude of more complex models, which have allowed to evaluate the effects of additional physiological and biological parameters on infectivity. Organoids recapitulate the cellular complexity of the human intestinal epithelium while 3D bioengineered scaffolds and microphysiological devices allow to emulate oxygen gradients, flow and peristalsis, as well as the formation and maintenance of stable and physiologically relevant microbial diversity. Additionally, advancements in <i>ex vivo</i> cultures and intravital imaging have opened new possibilities to study the effects of enteric pathogens on fluid secretion, barrier integrity and immune cell surveillance in the intact intestine. This review aims to present a balanced and updated overview of current intestinal <i>in vitro</i> and <i>ex vivo</i> methods for modeling of enteric bacterial infections. We conclude that the different paradigms are complements rather than replacements and their combined use promises to further our understanding of host-microbe interactions and their impacts on intestinal health.
Curcumin loaded gold nanoparticles–chitosan/sodium alginate nanocomposite for nanotheranostic applications
2022-12-28

A solvent casting technique was used for the preparation of biomimetic nanocomposites scaffolds at three various concentrations of Curcumin loaded gold nanoparticles (Cur-AuNPs-1, 1.5, and 2 ml) as filler materials with chitosan-sodium alginate composite. The physico-chemical properties of prepared Cu-Au NPs and biomimetic nanocomposites were analyzed using various characterization techniques. <i>In vitro</i> biocompatibility of biomimetic nanocomposites are determined using simulated body fluid for biomineralization property, HAp formation and phosphate buffer saline (PBS) for swelling property, protein adsorption. Antibacterial activity of Cur-Au NPs and their nanocomposites carried out against <i>Escherichia coli</i> (<i>E. coli</i>) and <i>Staphylococcus aureus. In vitro</i> cytotoxicity of Cur-AuNPs is identified against UC-6 and MDA-MB 231 cell lines. The use of above studies and activity of Cur-AuNPs with contain biomimetic nanocomposites can adoptable for nanotheranostics.
Prediction of Honeydew Contaminations on Cotton Samples by In-Line UV Hyperspectral Imaging
2022-12-28

UV hyperspectral imaging (225 nm–410 nm) was used to identify and quantify the honeydew content of real cotton samples. Honeydew contamination causes losses of millions of dollars annually. This study presents the implementation and application of UV hyperspectral imaging as a non-destructive, high-resolution, and fast imaging modality. For this novel approach, a reference sample set, which consists of sugar and protein solutions that were adapted to honeydew, was set-up. In total, 21 samples with different amounts of added sugars/proteins were measured to calculate multivariate models at each pixel of a hyperspectral image to predict and classify the amount of sugar and honeydew. The principal component analysis models (PCA) enabled a general differentiation between different concentrations of sugar and honeydew. A partial least squares regression (PLS-R) model was built based on the cotton samples soaked in different sugar and protein concentrations. The result showed a reliable performance with R2cv = 0.80 and low RMSECV = 0.01 g for the validation. The PLS-R reference model was able to predict the honeydew content laterally resolved in grams on real cotton samples for each pixel with light, strong, and very strong honeydew contaminations. Therefore, inline UV hyperspectral imaging combined with chemometric models can be an effective tool in the future for the quality control of industrial processing of cotton fibers.
Ozone Disinfection for Elimination of Bacteria and Degradation of SARS-CoV2 RNA for Medical Environments
2022-12-28

Pathogenic bacteria and viruses in medical environments can lead to treatment complications and hospital-acquired infections. Current disinfection protocols do not address hard-to-access areas or may be beyond line-of-sight treatment, such as with ultraviolet radiation. The COVID-19 pandemic further underscores the demand for reliable and effective disinfection methods to sterilize a wide array of surfaces and to keep up with the supply of personal protective equipment (PPE). We tested the efficacy of Sani Sport ozone devices to treat hospital equipment and surfaces for killing Escherichia coli, Enterococcus faecalis, Bacillus subtilis, and Deinococcus radiodurans by assessing Colony Forming Units (CFUs) after 30 min, 1 h, and 2 h of ozone treatment. Further gene expression analysis was conducted on live E. coli K12 immediately post treatment to understand the oxidative damage stress response transcriptome profile. Ozone treatment was also used to degrade synthetic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA as assessed by qPCR CT values. We observed significant and rapid killing of medically relevant and environmental bacteria across four surfaces (blankets, catheter, remotes, and syringes) within 30 min, and up to a 99% reduction in viable bacteria at the end of 2 h treatment cycles. RNA-seq analysis of E. coli K12 revealed 447 differentially expressed genes in response to ozone treatment and an enrichment for oxidative stress response and related pathways. RNA degradation of synthetic SARS-CoV-2 RNA was seen an hour into ozone treatment as compared to non-treated controls, and a non-replicative form of the virus was shown to have significant RNA degradation at 30 min. These results show the strong promise of ozone treatment of surfaces for reducing the risk of hospital-acquired infections and as a method for degradation of SARS-CoV-2 RNA.
Success concepts for causal discovery
2022-12-28

Abstract Existing causal discovery algorithms are often evaluated using two success criteria, one that is typically unachievable and the other which is too weak for practical purposes. The unachievable criterion—uniform consistency—requires that a discovery algorithm identify the correct causal structure at a known sample size. The weak but achievable criterion— pointwise consistency—requires only that one identify the correct causal structure in the limit. We investigate two intermediate success criteria— decidability and progressive solvability —that are stricter than mere consistency but weaker than uniform consistency. To do so, we review several topological theorems characterizing which discovery problems are decidable and/or progressively solvable. These theorems apply to any problem of statistical model selection, but in this paper, we apply the theorems only to selection of causal models. We show, under several common modeling assumptions, that there is no uniformly consistent procedure for identifying the direction of a causal edge, but there are statistical decision procedures and progressive solutions. We focus on linear models in which the error terms are either non-Gaussian or contain no Gaussian components ; the latter modeling assumption is novel to this paper. We focus especially on which success criteria remain feasible when confounders are present.