Miracle-dz/UniFAR-FTUs huggingface dataset:
Exploring the role of LIAS-related cuproptosis in systemic lupus erythematosus

Background Cuproptosis is a novel mode of cell death, which is strongly related to energy metabolism in mitochondria and regulated by protein lipoylation. Currently, the molecular mechanisms of cuproptosis-related genes (CRGs) involved in systemic lupus erythematosus (SLE) largely remained unclear, our study is aimed to explore the mechanisms of cuproptosis and CRGs involved in SLE. Methods Bulk RNA-seq datasets were collected to display the expressions of CRGs in peripheral blood mononuclear cells (PBMCs) of SLE and healthy individuals, and then ROC analysis was used to establish the diagnostic models of CRGs. Next, the immune infiltration analyses were applied to reveal the difference of immune cells infiltration in LIAS-low and LIAS-high group. Additionally, WGCNA analysis was performed to find the gene modules significantly correlated with the LIAS expression level. We also performed the functional enrichment analyses for LIAS-related gene modules to determine the potential pathways involved in the development of SLE. Finally, scRNA-seq dataset was used to cluster immune cell subsets, reveal the activated pathways, and study cell-cell interactions in LIAS-low and LIAS-high cells. Result We found CDKN2A was significantly increased and LIAS was significantly decreased in SLE patients compared with healthy individuals. The AUC score showed that LIAS had a great diagnostic value than other CRGs. Additionally, the results of immune infiltration analyses showed that immune cells proportion were diverse in LIAS-low and LIAS-high samples. The gene sets related to LIAS expression level were involved in dephosphorylation of JAK1 by SHP1, phosphorylation of STAT2, cytokine signaling in immune system, expression of interferon-alpha and beta, inhibition of JAK kinase activity by SOCS1/3, and so on. Finally, the results of cell-cell communication showed that CCL- (CCL5 + CCR1) and ANNEXIN- (ANXA1 + FPR1) might play an essential role in the communication network between LIAS-low and LIAS-high cells. Conclusion Above findings inferred that LIAS-mediated cuproptosis might involve in a comprehensive cellular and molecular mechanism to cause the occurrence and development of SLE.
Cell Population Growth Kinetics in the Presence of Stochastic Heterogeneity of Cell Phenotype

Recent studies at individual cell resolution have revealed phenotypic heterogeneity in nominally clonal tumor cell populations. The heterogeneity affects cell growth behaviors, which can result in departure from the idealized uniform exponential growth of the cell population. Here we measured the stochastic time courses of growth of an ensemble of populations of HL60 leukemia cells in cultures, starting with distinct initial cell numbers to capture a departure from the uniform exponential growth model for the initial growth (“take-off”). Despite being derived from the same cell clone, we observed significant variations in the early growth patterns of individual cultures with statistically significant differences in growth dynamics, which could be explained by the presence of inter-converting subpopulations with different growth rates, and which could last for many generations. Based on the hypothesis of existence of multiple subpopulations, we developed a branching process model that was consistent with the experimental observations.
Cross-cohort single-nucleotide-variant profiling of gut microbiota suggests a novel gut-health assessment approach

ABSTRACT Adaptive evolutionary changes can precede the ecological changes in the gut microbial communities under constant host selection pressure, yet their association with host diseased status was underexplored. Explore shared disease-associated single-nucleotide variants (SNVs) in gut microbes spanning diverse human diseases. We performed a meta-analysis of 1,711 gut metagenomic samples from 16 case-control studies spanning 12 human diseases and included an additional 446-member cohort for validation. Overall, healthy individuals carried more mutated resident gut microbes, and more SNVs, mainly involving the short-chain fatty acids (SCFAs) producing bacteria. Furthermore, the widespread differences in base variant bias of gut microbes were observed between healthy and nonhealthy subjects suggesting divergent gut microbial evolutionary directions under different host medical conditions. We further found that nonsynonymous SNVs can lead to the loss of function of four SCFA-production genes in nonhealthy populations, among which two genes (i.e., ack and scpC) from Faecalibacterium prausnitzii C and Bacteroides stercoris, respectively, were externally validated. Subsequently, we developed a novel gut microbiome health index based on the SNV rate of all mutated strains, classifying host health states with 74.23% accuracy, and validated with high accuracy (AUROC = 69.28%). Our study highlights the importance of employing the genetic variability in gut microbiome to characterize the gut microbial adaptation that can also predict human chronic diseases. IMPORTANCE Most studies focused much on the change in abundance and often failed to explain the microbiome variation related to disease conditions, Herein, we argue that microbial genetic changes can precede the ecological changes associated with the host physiological changes and, thus, would offer a new information layer from metagenomic data for predictive modeling of diseases. Interestingly, we preliminarily found a few genetic biomarkers on SCFA production can cover most chronic diseases involved in the meta-analysis. In the future, it is of both scientific and clinical significance to further explore the dynamic interactions between adaptive evolution and ecology of gut microbiota associated with host health status. Most studies focused much on the change in abundance and often failed to explain the microbiome variation related to disease conditions, Herein, we argue that microbial genetic changes can precede the ecological changes associated with the host physiological changes and, thus, would offer a new information layer from metagenomic data for predictive modeling of diseases. Interestingly, we preliminarily found a few genetic biomarkers on SCFA production can cover most chronic diseases involved in the meta-analysis. In the future, it is of both scientific and clinical significance to further explore the dynamic interactions between adaptive evolution and ecology of gut microbiota associated with host health status.
2011 Mars Science Laboratory Mission Design Overview

Scheduled to launch in the fall of 2011 with arrival at Mars occurring in the summer of 2012, NASA’s Mars Science Laboratory will explore and assess whether Mars ever had conditions capable of supporting microbial life. In order to achieve its science objectives, the Mars Science Laboratory will be equipped with the most advanced suite of instruments ever sent to the surface of the Red Planet. Delivering the next mobile science laboratory safely to the surface of Mars has various key challenges derived from a strict set of requirements which include launch vehicle performance, spacecraft mass, communications coverage during Entry, Descent, and Landing, atmosphere-relative entry speeds, latitude accessibility, and dust storm season avoidance among others. The Mars Science Laboratory launch/arrival strategy selected after careful review satisfies all these mission requirements.
Assessing the effectiveness of imperviousness on stormwater runoff in micro urban catchments by model simulation

Imperviousness, considered as a critical indicator of the hydrologic impacts of urbanization, has gained increasing attention both in the research field and in practice. However, the effectiveness of imperviousness on rainfall–runoff dynamics has not been fully determined in a fine spatiotemporal scale. In this study, 69 drainage subareas <1 ha of a typical residential catchment in Beijing were selected to evaluate the hydrologic impacts of imperviousness, under a typical storm event with a 3‐year return period. Two metrics, total impervious area (TIA) and effective impervious area (EIA), were identified to represent the impervious characteristics of the selected subareas. Three runoff variables, total runoff depth (TR), peak runoff depth (PR), and lag time (LT), were simulated by using a validated hydrologic model. Regression analyses were developed to explore the quantitative associations between imperviousness and runoff variables. Then, three scenarios were established to test the applicability of the results in considering the different infiltration conditions. Our results showed that runoff variables are significantly related to imperviousness. However, the hydrologic performances of TIA and EIA were scale dependent. Specifically, with finer spatial scale and the condition heavy rainfall, TIA rather than EIA was found to contribute more to TR and PR. EIA tended to have a greater impact on LT and showed a negative relationship. Moreover, the relative significance of TIA and EIA was maintained under the different infiltration conditions. These findings may provide potential implications for landscape and drainage design in urban areas, which help to mitigate the runoff risk. Copyright © 2015 John Wiley & Sons, Ltd.
Autophagy in normal hematopoiesis and leukemia: Biological and therapeutic implications

All together the studies in this thesis show that autophagy is an essential survival mechanism for both normal hematopoietic and AML cells and MDS erythroblasts. Altered expression of autophagy-associated genes might have consequences for drug resistance. Therefore, these findings suggest that inhibition of autophagy might be a promising therapeutic strategy for the treatment of AML.
Male and female reproductive systems

Humans and Puberty (pg. 80): Examine Fig. 3.1 Most humans first experience the effects of reproductive ___________________ in their early to mid ________. This period, called _________________, is when hormonal signals change the body so that it is able to _____________________. When puberty begins, the _____________________ gland at the base of the brain starts to produce ___________________ ______________________ hormone (FSH). FSH travels to the ______________________ -the ________________ in females and the ________________ in males. FSH signals the testes to produce _________________ and the ovaries to produce mature ____________. Other hormones help in development and maintenance of additional characteristics associated with male or femaleness, these are called the ___________________ ___________________ characteristics.
A cross-generational study of the perception and construction of South Africans of Indian descent as foreigners by fellow citizens.

ion is one of the modern mind’s principal powers. When applied to humans, that power means effacing the face: whatever marks remain of the face serve as badges of membership, the signs of belonging to a category, and the fate meted out to the owner of the face is nothing more yet nothing less either than the treatment reserved for the category, of which the owner of the face is but a specimen. The overall effect of abstraction is that rules routinely followed in personal interaction, ethical rules most prominent among them, do not interfere where the handling of a category is concerned, including every entity classified into that category just on account of having been so classified. Although Bauman (2000) was writing about a different context, his theory of abstraction can nevertheless be applied to this situation of labour exploitation under indenture as the Indian indentured labourers were perceived as nothing more than a category of people, grouped together, with all distinguishing features and personal characteristics which make them unique individuals, removed, but were only seen as units of labour, brought to the colony for a specific purpose, and any traces of their common humanity was ignored. In addition, the comparison of the Indian immigrants to the local African population in the articles published in The Mercury is also significant in that it illustrates that the colonial discourse around African people centred on notions of an ‘uncivilised’ ‘race’. Colonial discourse in Natal at this time served to legitimate economic interests. The division of the colony into the discrete categories of ‘white’ and ‘native’, as ‘races’ or species was not simply descriptive, but was about constructing certain people as ‘whites’ and superior, others as ‘blacks’ and inferior. As Miles (1989) argues, the dominant groups in society distort social reality through racist ideology 69 Report of the Indian Immigrants Commission: 1885-1887 in Meer (1980:522-526). In 1885, a commission was appointed under Justice Wragg to investigate the consequences of the free and passenger Indians on the colony. The report was delivered in 1887.
Performance analysis of the IEEE 802 . 11 MAC protocol for wireless LANs

Wireless local area networks (WLANs) are extremely popular being almost everywhere including business, office and home deployments. The IEEE 802.11 protocol is the dominating standard for WLANs. The essential medium access control (MAC) mechanism of 802.11 is called distributed co-ordination function (DCF). This paper provides a simple and accurate analysis using Markov chain modelling to compute IEEE 802.11 DCF performance, in the absence of hidden stations and transmission errors. This mathematical analysis calculates in addition to the throughput efficiency, the average packet delay, the packet drop probability and the average time to drop a packet for both basic access and RTS/CTS medium access schemes. The derived analysis, which takes into account packet retry limits, is validated by comparison with OPNET simulation results. We demonstrate that a Markov chain model presented in the literature, which also calculates throughput and packet delay by introducing an additional transition state to the Markov chain model, does not appear to model IEEE 802.11 correctly, leading to ambiguous conclusions for its performance. We also carry out an extensive and detailed study on the influence on performance of the initial contention window size (CW), maximum CW size and data rate. Performance results are presented to identify the dependence on the backoff procedure parameters and to give insights on the issues affecting IEEE 802.11 DCF performance. Copyright # 2005 John Wiley & Sons, Ltd.
Eyespot-dependent determination of the phototactic sign in Chlamydomonas reinhardtii

Significance The phototactic behavior of the unicellular green alga Chlamydomonas reinhardtii is thought to rely on photoreception by the eyespot apparatus. Here, we isolated an eyespot-less mutant that clearly exhibits phototaxis. Intriguingly, the phototactic sign (the direction of cell migration) in this mutant is opposite to that of the wild type after treatment with reagents that enhance the sign, a property that we also detected in previously reported eyespot-less mutants. The reversed phototactic-sign phenotype was attributed to the fact that the photoreceptors were exposed to condensed light from their rear side. This report demonstrates the importance of the eyespot, in which carotenoid layers shield the photoreceptors from light condensed by the cell body, which functions as a convex lens. The biflagellate green alga Chlamydomonas reinhardtii exhibits both positive and negative phototaxis to inhabit areas with proper light conditions. It has been shown that treatment of cells with reactive oxygen species (ROS) reagents biases the phototactic sign to positive, whereas that with ROS scavengers biases it to negative. Taking advantage of this property, we isolated a mutant, lts1-211, which displays a reduction-oxidation (redox) dependent phototactic sign opposite to that of the wild type. This mutant has a single amino acid substitution in phytoene synthase, an enzyme that functions in the carotenoid-biosynthesis pathway. The eyespot contains large amounts of carotenoids and is crucial for phototaxis. Most lts1-211 cells have no detectable eyespot and reduced carotenoid levels. Interestingly, the reversed phototactic-sign phenotype of lts1-211 is shared by other eyespot-less mutants. In addition, we directly showed that the cell body acts as a convex lens. The lens effect of the cell body condenses the light coming from the rear onto the photoreceptor in the absence of carotenoid layers, which can account for the reversed-phototactic-sign phenotype of the mutants. These results suggest that light-shielding property of the eyespot is essential for determination of phototactic sign.
Agent-based fractal architecture and modelling for developing distributed manufacturing systems

For their timely response to the rapidly changing manufacturing environment and markets, future manufacturing systems must be flexible, adaptable, and reusable. Recently, bionic (or biological), holonic, and fractal manufacturing systems (FrMS) have been discussed as potential candidates for the next generation of manufacturing systems. This study focuses on the FrMS, which is based on the concept of autonomous cooperating agents referred to as fractals. The major component of the FrMS is a basic fractal unit (BFU). It consists of five functional modules: observing module (observer), analysing module (analyser), resolving and executing module (resolver), organizing module (organizer), and reporting module (reporter). Although the FrMS has many conceptual advantages, the implementation of the system has been known to be difficult. This paper is a preliminary study of the basic components and the architecture with an eye toward the future implementation of FrMS. In order to describe the characteristics of a fractal, this paper presents several models including function models using IDEF0, working models using Petri-net, and static/dynamic models using the unified modelling language (UML).
Privacy in Social Networks : A Survey

Social network sites are extensively use for communication by social user. This communication among the sites produces an immense amount of data within the networks. The data that are associated with these sites hold essential information about users. To reveal the privacy of this essential information from unauthorized access is a critical issue in social networks. In this survey paper, we study various types of privacy disruption in social network and appraise the privacy technique for keeping up the privacy in social network in three categories: anonymization, hybridization of anonymity with clustering.
Hunting success of lions in a semi-arid environment

Parameters that influence the hunting success of lions in a semi-arid region in Namibia were assessed by means of generalized linear models. Results indicate that when combined, hunting techniques employed by lionesses, lioness group size, prey species, time of day (day/night), terrain, and the interaction between terrain and day/ night had significant independent effects on the probabiliry that a hunt would be successful. Hunts that involved co-ordinated stalking were more likely to succeed than other hunt categories. Success of hunting the five major prey species increased linearly with lioness group size. Lionesses were also more successful during hunts on moonless nights in undulating terrain. Under the semi-arid conditions in Namibia, where lions are exposed to eight months of food scarciry in an open habitat, group hunting and co-ordinated co-operation are the most important variables influencing the outcome of hunts and therefore also per capita food intake. In this environment group hunting may be an important factor in the evolution of socialiry in the species.
Ice loss in High Mountain Asia and the Gulf of Alaska observed by
CryoSat-2 swath altimetry between 2010 and 2019

Abstract. Glaciers and ice caps are currently the largest non-steric contributor to sea level rise, contributing ~30 % to sea level budget. Global monitoring of these regions remains a challenging task since global estimates rely on a variety of observations and models to achieve the required spatial and temporal coverage, and significant differences remain between current estimates. Here we report the first application of a novel approach to retrieve spatially-resolved elevation and mass change from Radar Altimetry over entire mountain glaciers areas. We apply interferometric swath altimetry to CryoSat-2 data acquired between 2010 and 2019 over High Mountain Asia (HMA) and in the Gulf of Alaska (GoA). In addition, we extract monthly time series of elevation change, exploiting CryoSat's high temporal repeat, to reveal seasonal and multiannual variation in rates of glaciers' thinning at unprecedented spatial detail. We find that during this period, HMA and GoA have lost an average of −27.9 ± 2.4 Gt yr−1 (−0.29 ± 0.03 m w.e. yr−1) and −76.3 ± 5.6 Gt yr−1 (−0.89 ± 0.07 m w.e. yr−1) respectively, corresponding to a contribution to sea level rise of 0.048 ± 0.004 mm yr−1 and 0.217 ± 0.015 mm yr−1. Glacier thinning is ubiquitous except for the Karakoram-Kunlun region experiencing stable or slightly positive mass balance. In the GoA region the intensity of thinning varies spatially and temporally and correlates with the strength of the Pacific Decadal Oscillation. In HMA we observe sustained multiannual trends until 2015-6, and decreased loss or even mass gain from 2016-17 onwards.
Hydrostatic gas distributions: global estimates of temperature and abundance

Estimating the temperature and metal abundance of the intracluster and the intragroup media is crucial to determine their global metal content and to determine fundamental cosmological parameters. When a spatially resolved temperature or abundance profile cannot be recovered from observations (e.g. for distant objects), or deprojection is difficult (e.g. due to a significant non-spherical shape), only global average temperature and abundance are derived. After introducing a general technique to build hydrostatic gaseous distributions of prescribed density profile in potential wells of any shape, we compute the global mass-weighted and emission-weighted temperature and abundance for a large set of barotropic equilibria and an observationally motivated abundance gradient. We also compute the spectroscopic-like temperature that is recovered from a single temperature fit of observed spectra. The derived emission-weighted abundance and temperatures are higher by 50 to 100 per cent than the corresponding mass-weighted quantities, with overestimates that increase with the gas mean temperature. Spectroscopic temperatures are intermediate between mass and luminosity-weighted temperatures. Dark matter flattening does not lead to significant differences in the values of the average temperatures or abundances with respect to the corresponding spherical case (except for extreme cases).
Risk factors for the introduction and within-herd transmission of Mycobacterium avium subspecies paratuberculosis (MAP) infection on 59 Irish dairy herds

Title Risk factors for the introduction and within-herd transmission of Mycobacterium avium subspecies paratuberculosis (MAP) infection on 59 Irish dairy herds Authors(s) Cashman, W. ; Buckley, J.; Quigley, T. ; et al. Publication date 2008 Publication information Irish Veterinary Journal, 61 (7): Publisher Springer (Biomed Central Ltd.) Item record/more information http://hdl.handle. net/10197/5756 Publisher's version (DOI) 10.1186/2046-0481-61-7-464