Miracle-dz/UniFAR-FTUs huggingface dataset:
A nomogram predicting the histologic activity of lupus nephritis from clinical parameters

ABSTRACT Background The 2021 clinical guidelines of the Kidney Disease: Improving Global Outcomes emphasize the importance of the histological activity index (AI) in the management of lupus nephritis (LN). Patients with LN and a high AI have poor renal outcomes and high rates of nephritic relapse. In this study we constructed prediction models for the AI in LN. Methods The study population comprised 337 patients diagnosed with LN using kidney biopsy. The participants were randomly divided into training and testing cohorts. They were further divided into high-activity (AI >2) and low-activity (AI ≤2) groups. This study developed two clinical prediction models using logistic regression and least absolute shrinkage and selection operator (LASSO) analyses with laboratory test results collected at the time of kidney biopsy. The performance of models was assessed using 5-fold cross-validation and validated in the testing cohort. A nomogram for individual assessment was constructed based on the preferable model. Results Multivariate analysis showed that higher mean arterial pressure, lower estimated glomerular filtration rate, lower complement 3 level, higher urinary erythrocytes count and anti-double-stranded DNA seropositivity were independent risk factors for high histologic activity in LN. Both models performed well in the testing cohort regarding the discriminatory ability to identify patients with an AI >2. The average area under the curve of 5-fold cross-validation was 0.855 in the logistic model and 0.896 in the LASSO model. A webtool based on the LASSO model was created for clinicians to enter baseline clinical parameters to produce a probability score of an AI >2. Conclusions The established nomogram provides a quantitative auxiliary tool for distinguishing LN patients with a high AI and helps physicians make clinical decisions in their comprehensive assessment.
Changing What You Like: Modifying Contour Properties Shifts Aesthetic Valuations of Scenes

To what extent do aesthetic experiences arise from the human ability to perceive and extract meaning from visual features? Ordinary scenes, such as a beach sunset, can elicit a sense of beauty in most observers. Although it appears that aesthetic responses can be shared among humans, little is known about the cognitive mechanisms that underlie this phenomenon. We developed a contour model of aesthetics that assigns values to visual properties in scenes, allowing us to predict aesthetic responses in adults from around the world. Through a series of experiments, we manipulate contours to increase or decrease aesthetic value while preserving scene semantic identity. Contour manipulations directly shift subjective aesthetic judgments. This provides the first experimental evidence for a causal relationship between contour properties and aesthetic valuation. Our findings support the notion that visual regularities underlie the human capacity to derive pleasure from visual information.
Prevalence of human papilloma virus and Chlamydia trachomatis in endometrial and cervical carcinoma: a comparative study in North Indian women

Abstract Cervical cancer (Cacx) is the second and endometrial cancer (Ec) is the third most common gynecological cancer worldwide. The present study aims to understand the complex and unexplored conditions occurring in cervix and endometrium of the female genital tract caused due to the infection of the human papilloma viruses (HPVs) and Chlamydia trachomatis (CT). A total of 300 tissue biopsy samples of cervix and endometrium were included in the present study and tested for the presence of HPV and CT deoxyribonucleic acid (DNA) by using polymerase chain reaction (PCR) technique. The odds ratios and 95% confidence interval were considered for the calculation of the association of HPV and CT infection with the risk of cervical or Ec. Among endometrial patients, samples were 5% positive for HPV and 5% positive for CT infection. Among endometrial control group, no sample was found positive for either HPV or CT infection. Among cervical patients, 72% samples were positive for only HPV infection and 1% samples were positive for only CT infection. Among control group, 7% of samples were positive for only HPV infection and 3% were positive for only CT infection. The co-infection of CT with HPV in 9% of Cacx cases and in 2% of cervical control samples was also observed. This is the first study in Indian women to detect the prevalence of HPV and CT infections in endometrium cases and control. An updated estimate regarding the HPV and CT prevalence in cervix cases and control samples was also provided.
Simultaneous warming and acidification limit population fitness and reveal phenotype costs for a marine copepod

Phenotypic plasticity and evolutionary adaptation allow populations to cope with global change, but limits and costs to adaptation under multiple stressors are insufficiently understood. We reared a foundational copepod species, Acartia hudsonica, under ambient (AM), ocean warming (OW), ocean acidification (OA), and combined ocean warming and acidification (OWA) conditions for 11 generations (approx. 1 year) and measured population fitness (net reproductive rate) derived from six life-history traits (egg production, hatching success, survival, development time, body size and sex ratio). Copepods under OW and OWA exhibited an initial approximately 40% fitness decline relative to AM, but fully recovered within four generations, consistent with an adaptive response and demonstrating synergy between stressors. At generation 11, however, fitness was approximately 24% lower for OWA compared with the AM lineage, consistent with the cost of producing OWA-adapted phenotypes. Fitness of the OWA lineage was not affected by reversal to AM or low food environments, indicating sustained phenotypic plasticity. These results mimic those of a congener, Acartia tonsa, while additionally suggesting that synergistic effects of simultaneous stressors exert costs that limit fitness recovery but can sustain plasticity. Thus, even when closely related species experience similar stressors, species-specific costs shape their unique adaptive responses.
Introduction to Thematic Set: Aeolian Processes, Landforms and Chronologies

Studies of aeolian processes and landforms, especially on millen-nial to decadal timescales, provide a natural laboratory for understanding their response to forcing factors, including climate change and variability and human impacts, that determine the supply, availability, and mobility of sediment. This Thematic Set of articles is derived from a Topical Session
Proceedings of the 9th ACM international symposium on Modeling analysis and simulation of wireless and mobile systems

Welcome to the 9th ACM/IEEE International Symposium on Modeling, Analysis and Simulation of Wireless and Mobile Systems (MSWiM). This year the technical program includes 51 high quality papers on wireless and mobile systems, poster and demo sessions plus two keynote addresses from well-known experts in the field. We would like to thank Prof. Alois Ferscha (Johannes Kepler Universitat Linz, Austria) and Prof. George C. Polyzos (Athens University of Economics and Business, Greece) for accepting our invitation to be the keynote speakers.MSWiM 2006 also includes four tutorials on quality of service in IP for wireless systems, wireless and multimedia, future open mobile services, and WiFi versus WiMax. Besides, several workshops (MobiWAC, PE-WASUN, Q2SWinet, WMuNeP, PM2HW2N) will be hold focusing on mobility management and wireless access, security, multimedia, and heterogeneous wireless networks.
The Impact of the Web on Information Retrieval

of physical servers [Berners-Lee 1989]. At the time, his proposal went further than others in considering not only information resources (documents) as part of this graph but also non-information resources, that is, abstract concepts and entities of all kinds, in what would be later termed the Semantic Web. Further, while this information space was primarily intended to be explored by human navigation as was the case with hypertext implementations of the past, Berners-Lee did foresee the opportunity for the automated analysis of the Web graph. As it turns out, his key ideas, the representation of information as a graph, adding a semantic layer to information, and the potential for automated analysis of these structures would come to revolutionize an entire subfield of computer science, the field of information retrieval (IR). In this chapter, we trace the impact of Berners-Lee’s ideas on the development of IR, both within the academic field and its applications in industry, particularly web search engines. Indeed, today, web search engines are tools that are a crucial component of our daily lives. In Section 7.2, we will first look at how Berners-Lee’s ideas of structuring the Web brought about a set of challenges and opportunities that reinvigorated the field of IR and led to the emergence of web search, both in academia and industry. In Section 7.3, we will consider how Berners-Lee’s ideas around the extension of the hypertext Web to a Semantic Web and its implementation in technical standards at the W3C provided further new opportunities for developing semantic search engines with capabilities well beyond what was possible using the techniques of the past. Last, in Section 7.4, we will consider some of The Impact of the Web on Information Retrieval
An Identification Algorithm of Rice Seedling Rows with Seedlings Absence Based on CS-Yolov5 Model

The identification of rice seedling rows is crucial for precision agriculture and automatic navigation. In this paper, an identification algorithm of rice seedling rows with seedlings absence based on CS-Yolov5 model is proposed, which can effectively solve the influence of complex paddy backgrounds, different density of weed distribution, light intensity change and seedlings absence. The algorithm mainly includes the detection of rice seedlings based on CS-Yolov5 model, the classification of seedling feature points based on clustering and PCA compression in the case of seedlings absence and the extraction of seedling band lines for each seedling row. Field experiments showed that the average identification angle deviation was less than 1° and the average pixel offset did not exceed 2 pixels.
Long-sequence model for traffic forecasting in suboptimal situation

Accurate traffic prediction generally depends on reliable and noise-free data, which may not reflect real-world scenarios. Additionally, the high sampling rate poses challenges in capturing the inherent temporal periodicity present in traffic data. To address these issues and achieve long-term traffic prediction, this paper proposes a novel approach called as Spatio-Temporal State Space Probabilistic Diffusion (ST-SSPD). The proposed method utilizes state space modeling to decompose the historical signal of an ego-graph into the frequency domain, thereby reducing the impact of missing data during the subsequent reconstruction phase. The reconstructed signal is then employed to condition a probabilistic denoising diffusion model, enabling the learning of the underlying data distribution by the gradual denoising of pure Gaussian noise into the desired prediction. This technique facilitates the modeling of long-range dependencies by representing an optimal historical approximation through a high-order polynomial projection, resulting in significantly enhanced traffic prediction accuracy. Extensive experiments were conducted on real-world traffic datasets with varying levels of data loss to evaluate the effectiveness of the proposed model. The results demonstrate the model's robustness to data loss and its superior performance compared to existing state-of-the-art architectures in traffic forecasting.
Exploiting Flat Namespace to Improve File System Metadata Performance on Ultra-fast, Byte-addressable NVMs

The conventional file system provides a hierarchical namespace by structuring it as a directory tree. Tree-based namespace structure leads to inefficient file path walk and expensive namespace tree traversal, underutilizing ultra-low access latency and superior sequential performance provided by non-volatile memories (NVMs). This paper proposes FlatFS+, an NVM file system that features a flat namespace architecture while providing a compatible hierarchical namespace view. FlatFS+ incorporates three novel techniques: direct file path walk model, range-optimized Br tree, and compressed index key design with scan and write dual optimization, to fully exploit flat namespace to improve file system metadata performance on ultra-fast, byte-addressable NVMs. Evaluation results demonstrate that FlatFS+ achieves significant performance improvements for metadata-intensive benchmarks and real-world applications compared to other file systems.
Altered DNA methylation underlies monocyte dysregulation and innate exhaustion memory in sepsis

Innate immune memory is the process by which pathogen exposure elicits cell-intrinsic states to alter the strength of future immune challenges. Such altered memory states drive monocyte dysregulation during sepsis, promoting pathogenic behavior characterized by pro-inflammatory, immunosuppressive gene expression in concert with emergency hematopoiesis. Epigenetic changes, notably in the form of histone modifications, have been shown to underlie innate immune memory, but the contribution of DNA methylation to this process remains poorly understood. Using an ex vivo sepsis model, we discovered broad changes in DNA methylation throughout the genome of exhausted monocytes, including at several genes previously implicated as major drivers of immune dysregulation during sepsis and Covid-19 infection (e.g. Plac8). Methylome alterations are driven in part by Wnt signaling inhibition in exhausted monocytes, and can be reversed through treatment with DNA methyltransferase inhibitors, Wnt agonists, or immune training molecules. Importantly, these changes are recapitulated in septic mice following cecal slurry injection, resulting in stable changes at critical immune genes that support the involvement of DNA methylation in acute and long-term monocyte dysregulation during sepsis.
EfpA is required for re-growth of Mycobacterium tuberculosis following isoniazid exposure

Efflux of antibiotics is a survival strategy in bacteria. Mycobacterium tuberculosis has approximately sixty efflux pumps, but little is known about the role of each pump, or which moieties that they efflux. The putative efflux pump, EfpA, is a member of the major facilitator superfamily that has been shown to be essential by saturation transposon mutagenesis studies. It has been implicated in the efflux of the frontline drug isoniazid (INH) in M. tuberculosis. This is supported by evidence from transcriptional profiling that efpA is induced in response to INH exposure. However, its role in physiology and adaptation of M. tuberculosis to antibiotics, have yet to be determined. Here, we describe the repression of efpA using CRISPR interference and the direct effect of this on the ability of M. tuberculosis to survive exposure to INH over a 45-day time-course. We determined that wild-type levels of efpA were required for the recovery of M. tuberculosis cultures following INH exposure and that, after 45-days of INH exposure, no viable colonies were recoverable from efpA-repressed M. tuberculosis cultures. We postulate that EfpA is required for the recovery of M. tuberculosis following INH-exposure and that EfpA may have a role in the development of resistance, during treatment and contributes to relapse in patients.
Comparative omics reveals unanticipated metabolic rearrangements in a high-oil mutant of plastid acetyl-CoA carboxylase

Heteromeric acetyl-CoA carboxylase (ACCase) catalyzes the ATP-dependent carboxylation of acetyl-CoA to produce malonyl-CoA, the committed step for de novo fatty acid synthesis. In plants, ACCase activity is controlled at multiple levels, including negative regulation by biotin attachment domain-containing (BADC) proteins, of which the badc1/3 double mutant leads to increased seed triacylglycerol accumulation. Unexpectedly, the Arabidopsis badc1/3 mutant also accumulates more protein. The metabolic consequences from both higher oil and protein was investigated in developing badc1/3 seed using global transcriptomics, translatomics, proteomics, and metabolomics. Changes include: reduced plastid pyruvate dehydrogenase; increased acetyl-CoA synthetase; increased storage and lipid-droplet packaging proteins; increased lipases; and increased β-oxidation fatty acid catabolism. We present a model of how Arabidopsis adapted to deregulated ACCase, limiting total oil accumulation, and altering flux through pathways of carbon accumulation that presents possible targets for future bioengineering of valuable seed storage reserves.
Ultralow background membrane editors for spatiotemporal control of lipid metabolism and signaling

Phosphatidic acid (PA) is a multifunctional lipid with important metabolic and signaling functions, and efforts to dissect its pleiotropy demand strategies for perturbing its levels with spatiotemporal precision. Previous membrane editing approaches for generating local PA pools used light-mediated induced proximity to recruit a PA-synthesizing enzyme, phospholipase D (PLD), from the cytosol to the target organelle membrane. Whereas these optogenetic PLDs exhibited high activity, their residual activity in the dark led to undesired chronic lipid production. Here, we report ultralow background membrane editors for PA wherein light directly controls PLD catalytic activity, as opposed to localization and access to substrates, exploiting a LOV domain-based conformational photoswitch inserted into the PLD sequence and enabling their stable and non-perturbative targeting to multiple organelle membranes. By coupling organelle-targeted LOVPLD activation to lipidomics analysis, we discovered different rates of metabolism for PA and its downstream products depending on the subcellular location of PA production. We also elucidated signaling roles for PA pools on different membranes in conferring local activation of AMP-activated protein kinase signaling. This work illustrates how membrane editors featuring acute, optogenetic conformational switches can provide new insights into organelle-selective lipid metabolic and signaling pathways. TOC Graphic
Explainable machine learning for the identification of proteome states via the data processing kitchen sink

The application of machine learning algorithms to facilitate the understanding of changes in proteome states has emerged as a promising methodology in proteomics research. Unfortunately, these methods can prove difficult to interpret, as it may not be immediately obvious how models reach their predictions. We present the data processing kitchen sink (DPKS) which provides reproducible access to classic statistical methods and advanced explainable machine learning algorithms to build highly accurate and fully interpretable predictive models. In DPKS, explainable machine learning methods are used to calculate the importance of each protein towards the prediction of a model for a particular proteome state. The calculated importance of each protein can enable the identification of proteins that drive phenotypic change in a data-driven manner while classic techniques rely on arbitrary cutoffs that may exclude important features from consideration. DPKS is a free and open source Python package available at https://github.com/InfectionMedicineProteomics/DPKS.
Analysis of The Recreational Value of The Coral-Surrounded Hon Mun Islands In Vietnam

Understanding the recreational value of natural resources is crucial to effective conservation programmes. When natural resources are threatened with dire consequences by human activities, their recreational value is greatly reduced, thus affecting their contribution to conservation programmes. The purpose of this research is to explore the recreational value of the coral-surrounded Hon Mun Islands. The islands contain the richest coral biodiversity in the country and are only about six km from a port, which has been earmarked for expansion. This research employs the travel cost method and the contingent valuation method to measure and analyse impacts on the recreational value of the islands. The zonal travel cost model (ZTCM) estimates the annual recreational value at approximately USD 17.9 million while the result from the individual travel cost model (ITCM) is about USD 8.7 million. A 20% loss of the recreational value that is expected to ensue from the proposed port expansion is still larger than the expanded port's projected annual revenue of USD 3.1 million. Therefore, the port expansion proposal seriously needs reevaluation.
Precision Proteoform Design for 4R Tau Isoform Selective Templated Aggregation

Prion-like spread of disease-specific tau conformers is a hallmark of all tauopathies. A 19-residue probe peptide containing a P301L mutation and spanning the R2/R3 splice junction of tau, folds and stacks into seeding-competent fibrils and induces aggregation of 4R, but not 3R tau. These tau peptide fibrils propagate aggregated intracellular tau over multiple generations, have a high β- sheet content, a colocalized lipid signal, and adopt a well-defined U-shaped fold found in 4R tauopathy brain-derived fibrils. Fully atomistic replica exchange molecular dynamics (MD) simulations were used to compute the free energy landscapes of the conformational ensemble of the peptide monomers. These identified an aggregation-prohibiting β-hairpin structure and an aggregation-competent U-fold unique to 4R tauopathy fibrils. Guided by MD simulations, we identified that the N-terminal-flanking residues to PHF6, which slightly vary between 4R and 3R isoforms, modulate seeding. Strikingly, when a single amino acid switch at position 305 replaced the serine of 4R tau with a lysine from the corresponding position in the first repeat of 3R tau, the seeding induced by the 19-residue peptide was markedly reduced. Conversely, a 4R tau mimic with three repeats, prepared by replacing those amino acids in the first repeat with those amino acids uniquely present in the second repeat, recovered aggregation when exposed to the 19- residue peptide. These peptide fibrils function as partial prions to recruit naïve 4R tau—ten times the length of the peptide—and serve as a critical template for 4R tauopathy propagation. These results hint at opportunities for tau isoform-specific therapeutic interventions. Significance Statement A structural motif corresponding to a short junction sequence spanning R2 and R3 forms fibrils that adopt a fold characteristic of 4R tauopathy fibrils and induces misfolding of the larger tau protein with loss of microtubule binding and a prion-like specificity for 4R tau. Simulations, validated experimentally, pinpointed the specific amino acids in the peptide that can toggle its properties between aggregation competent and incompetent. The modifications suggest design principles for a therapeutic intervention potentially capable of disaggregating tau or preventing its aggregation in the 4R tauopathies.