Miracle-dz/UniFAR-FTUs huggingface dataset:
Migratory transient osteoporosis: atypical migration to the bilateral knee after childbirth

Transient osteoporosis (TO) is a rare self-limiting disease, characterized by bone marrow edema (BME). [1] It was first described in 1959 by Curtiss and Kincaid in pregnant women in their third trimester. [2] The term “transient osteoporosis” was first used in 1968 by Lequesue. [3] Transient osteoporosis is a disorder which primary affects women in their third trimester of pregnancy. However, it may also be seen in middle aged men and non-pregnant women. [4] Typically, its course involves unilateral or bilateral hip joints. But, it may also affect knee, ankle and foot joints. [5,6] Rarely, the disorder may start from one joint and migrate to others. In this article, we presented an interesting case of TO, which started with involvement of the hip joint in a pregnant woman in her third trimester and continued with dissemination to bilateral knee joints in the postpartum period. It is the first time in the literature that a case was presented where the disorder showed migration to other joints after childbirth.
Investigation of fascin1, a marker of mature dendritic cells, reveals a New role for IL-6 signaling in chemotaxis

Migration of mature dendritic cells (DCs) to lymph nodes is critical for the initiation of adaptive immunity. While CCR7, a a G-protein-coupled receptor for CCL19/21 chemokines, is known to be essential for chemotaxis of mature DCs, the molecular mechanism linking inflammation to chemotaxis remains unclear. We previously demonstrated that fascin1, an actin-bundling protein, increases chemotaxis of mature DCs. In this paper we showed that fascin1 enhanced Interleukin (IL)-6 secretion and signaling. Furthermore, we demonstrated that IL-6 signaling is required for chemotaxis. Blockage of IL-6 signaling in WT DCs with an anti-IL-6 receptorα (IL-6Rα) antibody inhibited chemotaxis toward CCL19. Likewise, knockout (KO) of IL-6Rα inhibited chemotaxis of BMDCs. The addition of soluble IL-6Rα and IL-6 rescued chemotaxis of IL-6Rα KO BMDCs, underscoring the role of IL-6 signaling in chemotaxis. We found that IL-6 signaling is required for internalization of CCR7, the initial step of CCR7 recycling. CCR7 recycling is known to be essential for CCR7-mediated chemotaxis, explaining why IL-6 signaling is needed for chemotaxis of mature DCs. Our results have identified IL-6 signaling as a new regulatory pathway for CCR7/CCL19-mediated chemotaxis, and suggest that rapid migration of mature DCs to lymph nodes depends on inflammation-associated IL-6 signaling.
Evaluation of a Caries Risk Assessment Model in an Adult Population

The purpose of this study was to evaluate a multifactorial caries risk assessment model by comparing the risk factor scores with caries increment. Secondary data analysis included a chart review of 434 dental patients in which basic caries risk scores, total risk score and caries increment were collected. ANOVA and logistic regression were conducted to assess the statistical significance of the difference between caries increments across categories of risk factors. Mean tooth caries increments of the risk groups were 0.20±0.8 (low), 1.13±1.59 (moderate), 2.09±2.63 (high), which were statistically significant (p<0.001). Past and present caries experience, carbohydrates, mucogingival bleeding index, and stimulated salivary flow showed statistically significant associations with caries increment (p<0.05) but the total risk score proved to be the most powerful predictor of future caries activity (p<0.001). The multifactorial etiology of caries necessitates the use of a risk assessment model that includes various factors that contribute to caries development.
Evaluation of a Behavioral Self-Care Intervention for Public Health Students

ABSTRACT Background: Postgraduate education is recognized as a time of intense stress. Rates of anxiety and depression are elevated among graduate students, and longitudinal studies have documented increases in clinical symptoms over the course of training. Purpose: The current study was to evaluate whether an academically sponsored self-care intervention would increase engagement in health promotion activities. The primary goal was to determine whether self-care behaviors completed in the midst of a challenging academic program would prevent the worsening of student mental health. Methods: The self-care intervention included behavior change projects designed to increase health-promoting behaviors within 4 domains (nutrition, physical activity, mental health, social support). Students received incentives in the way of bonus points for maintaining health behaviors for the duration of the 12-week semester. Results: Results revealed significant increases in health-promoting behaviors. Importantly, mental health symptoms did not worsen over the course of the semester. Discussion: The study provides preliminary support for the utility of a brief self-care intervention for students in the health sciences. Translation to Health Education Practice: Future studies should examine the applicability of this intervention to students in other fields of study and through online education formats.
Patterns of anisotropic temperature factors in bovine trypsin crystals with and without 0.5 THz irradiation

Vibrational oscillations in amide and side chain groups are well studied in proteins, but these are not occupied at ambient temperatures and they have a short lifespan when infrared radiation is present. Active vibrational modes in proteins lie in the terahertz (THz) range at physiological temperatures, and their experimental descriptions of them in this range are lacking. In this paper, we present the effect of 0.5 THz irradiation on atomic displacement parameters (ADP) in bovine trypsin. The crystals were subjected to terahertz radiation in an alternating manner and two states of the crystals were recovered using X-ray crystallography. The clustering of ADPs uniquely identified atoms from the different crystals. The ADP similarities tended to develop between chemically similar atoms and between atoms of the catalytic triad. This pattern of ADP similarity is likely created by delocalized polar vibration modes rather than, as frequently assumed, elastic and rigid-body motions.
Single-cell RNA-Seq reveals the link between CD45 isoforms and tumor-infiltrating T cells heterogeneity in liver cancer

CD45 isoforms play a major role in characterizing T cell function, phenotype, and development. However, there is lacking comprehensive interrogation about the relationship between CD45 isoforms and T lymphocytes from cancer patients at the single-cell level yet. Here, we investigated the CD45 isoforms component of published 5,063 T cells of hepatocellular carcinoma (HCC), which has been assigned functional states. We found that the distribution of CD45 isoforms in T lymphocytes cells depended on tissue resource, cell type, and functional state. Further, we demonstrated that CD45RO and CD45RA dominate in characterizing the phenotype and function of T cell though multiple CD45 isoforms coexist in T cells, through a novel alternative splicing pattern analysis. We identified a novel development trajectory of tumor-infiltrating T cells from Tcm to Temra (effector memory T cells re-expresses CD45RA) after detecting two subpopulations in state of transition, Tcm (central memory T) and Tem (effector memory T). Temra, capable of high cytotoxic characteristics, was discovered to be associated with the stage of HCC and may be a target of immunotherapy. Our study presents a comprehension of the connection between CD45 isoforms and the function, states, sources of T lymphocytes cells in HCC patients at the single-cell level, providing novel insight for the effect of CD45 isoforms on T cell heterogeneity.
Global impact of phosphorylation on protein endurance

Post-translational modifications such as phosphorylation can have profound effects on the physicochemical and biological properties of proteins. However, high-throughput and systematic approaches have not yet been developed to assess the effects of specific modification types and sites on protein lifetime, which represents a key parameter for understanding signaling rewiring and drug development. Here we describe a proteomic method, DeltaSILAC, to quantify the impact of site-specific phosphorylation on the endurance of thousands of proteins in live cells. Being configured on the reproducible data-independent acquisition mass spectrometry (DIA-MS), the pulse labeling approach using stable isotope-labeled amino acids in cells (SILAC), together with a novel peptide-level matching strategy, this multiplexed assay revealed the global delaying effect of phosphorylation on protein turnover in growing cancer cells. Further, we identified local sequence and structural features in proximity to the phosphorylated sites that could be associated with protein endurance alterations. We found that phosphorylated sites accelerating protein turnover are functionally selected for cell fitness and evolutionarily conserved. DeltaSILAC provides a generalizable approach for prioritizing the effects of phosphorylation sites on protein lifetime in the context of cell signaling and disease biology, which is highly complementary to existing methods. Finally, DeltaSILAC is widely applicable to diverse post-translational modification types and different cell systems.
Recapitulating Evolutionary Divergence in a Single Cis-Regulatory Element Is Sufficient to Cause Expression Changes of the Lens Gene Tdrd7

Mutations in cis-regulatory elements play important roles for phenotypic changes during evolution. Eye degeneration in the blind mole rat (BMR) and other subterranean mammals is significantly associated with widespread divergence of eye regulatory elements, but the effect of these regulatory mutations on eye development and function has not been explored. Here, we investigate the effect of mutations observed in the BMR sequence of a conserved non-coding element upstream of Tdrd7, a pleiotropic gene required for lens development and spermatogenesis. We first show that this conserved element is a transcriptional repressor in lens cells and that the BMR sequence partially lost repressor activity. Next, we recapitulated the evolutionary changes by precisely replacing the endogenous regulatory element in a mouse line by the orthologous BMR sequence with CRISPR-Cas9. Strikingly, this repressor element has a large effect, causing a more than two-fold up-regulation of Tdrd7 in developing lens. Interestingly, the increased mRNA level does not result in a corresponding increase in TDRD7 protein nor an obvious lens phenotype, likely explained by buffering at the posttranscriptional level. Our results are consistent with eye degeneration in subterranean mammals having a polygenic basis where many small-effect mutations in different eye-regulatory elements collectively contribute to phenotypic differences.
A survey of rare epigenetic variation in 23,116 human genomes identifies disease-relevant epivariations and novel CGG expansions

There is growing recognition that epivariations, most often recognized as promoter hypermethylation events that lead to gene silencing, are associated with a number of human diseases. However, little information exists on the prevalence and distribution of rare epigenetic variation in the human population. In order to address this, we performed a survey of methylation profiles from 23,116 individuals using the Illumina 450k array. Using a robust outlier approach, we identified 4,452 unique autosomal epivariations, including potentially inactivating promoter methylation events at 384 genes linked to human disease. For example, we observed promoter hypermethylation of BRCA1 and LDLR at population frequencies of ~1 in 3,000 and ~1 in 6,000 respectively, suggesting that epivariations may underlie a fraction of human disease which would be missed by purely sequence-based approaches. Using expression data, we confirmed that many epivariations are associated with outlier gene expression. Analysis of SNV data and monozygous twin pairs suggests that approximately two thirds of epivariations segregate in the population secondary to underlying sequence mutations, while one third are likely sproradic events that occur post-zygotically. We identified 25 loci where rare hypermethylation coincided with the presence of an unstable CGG tandem repeat, and validated the presence of novel CGG expansions at several of these, identifying the molecular defect underlying most of the known folate-sensitive fragile sites in the genome. Our study provides a catalog of rare epigenetic changes in the human genome, gives insight into the underlying origins and consequences of epivariations, and identifies many novel hypermethylated CGG repeat expansions.
Plant cell wall integrity maintenance and pattern-triggered immunity modulate jointly plant stress responses in Arabidopsis thaliana

Plant cells are surrounded by walls, which must often meet opposing functional requirements during plant growth and defense. The cells meet them by modifying wall structure and composition in a tightly controlled and adaptive manner. The modifications seem to be mediated by a dedicated cell wall integrity (CWI) maintenance mechanism. Currently the mode of action of the mechanism is not understood and it is unclear how its activity is coordinated with established plant defense signaling. We investigated responses to induced cell wall damage (CWD) impairing CWI and the underlying mechanism in Arabidopsis thaliana. Interestingly inhibitor- and enzyme-derived CWD induced similar, turgor-sensitive stress responses. Genetic analysis showed that the receptor-like kinase (RLK) FEI2 and the mechano-sensitive, plasma membrane-localized Ca2+- channel MCA1 function downstream of the THE1 RLK in CWD perception. Phenotypic clustering with 27 genotypes identified a core group of RLKs and ion channels, required for activation of CWD responses. By contrast, the responses were repressed by pattern-triggered immune (PTI) signaling components including PEPR1 and 2, the receptors for the immune signaling peptide AtPep1. Interestingly AtPep1 application repressed CWD-induced phytohormone accumulation in a PEPR1/2-dependent manner. These results suggest that PTI suppresses CWD-induced defense responses through elicitor peptide-mediated signaling during defense response activation. If PTI is impaired, the suppression of CWD-induced responses is alleviated, thus compensating for defective PTI. Significance statement Stress resistance and plant growth determine food crop yield and efficiency of bioenergy production from ligno-cellulosic biomass. Plant cell walls are essential elements of the biological processes, therefore functional integrity of the cell walls must be maintained throughout. Here we investigate the plant cell wall integrity maintenance mechanism. We characterize its mode of action, identify essential signaling components and show that the AtPep1 signaling peptide apparently coordinates pattern triggered immunity (PTI) and cell wall integrity maintenance in plants. These results suggest how PTI and cell wall modification coordinately regulate biotic stress responses with plants possibly compensating for PTI impairment through enhanced activation of stress responses regulated by the CWI maintenance mechanism.
Circulating long non-coding RNAs as biomarkers of acute myocardial infarction

For the past decades, acute myocardial infarction (AMI) has been the most common cause of death in both genders. The invention of percutaneous intervention (PCI) has saved thousands of lives. The most important prognostic factor for AMI is the time between the onset of AMI and revascularization. Heart centers around the world have devoted themselves to improving the evaluation tools for AMI. Among these evaluation tools, MI biomarkers have undergone the most evolution over the past decade. Traditionally used protein biomarkers like CK-MB and troponin are limited by serum instability and low sensitivity, especially if patient is admitted right after chest pain. Because both biomarkers require 4–6 hours to be detectable. Recently, the researches of one type of noncoding RNA namely long non-coding RNA (lncRNA) in the MI field has become popular. Even not coding any protein in most cases, lncRNA has an astounding effect on protein expression and modification. Expressions of lncRNA in the peripheral blood have been found to change during AMI. Both basic and clinical studies suggest that circulating lncRNA can be potentially used as a biomarker for myocardial injury.
Generating links that are both quasi-alternating and almost alternating

We construct an infinite family of links which are both almost alternating and quasi-alternating from a given either almost alternating diagram representing a quasi-alternating link, or connected and reduced alternating tangle diagram. To do that we use what we call a dealternator extension which consists in replacing the dealternator by a rational tangle extending it. We note that all not alternating and quasi-alternating Montesinos links can be obtained in that way. We check that all the obtained quasi-alternating links satisfy Conjecture 3.1 of Qazaqzeh et al. (JKTR 22 (06), 2013), that is the crossing number of a quasi-alternating link is less than or equal to its determinant. We also prove that the converse of the Theorem 3.3 of Qazaqzeh et al. (JKTR 24 (01), 2015) is false.
BANet: Bidirectional Aggregation Network With Occlusion Handling for Panoptic Segmentation

Panoptic segmentation aims to perform instance segmentation for foreground instances and semantic segmentation for background stuff simultaneously. The typical top-down pipeline concentrates on two key issues: 1) how to effectively model the intrinsic interaction between semantic segmentation and instance segmentation, and 2) how to properly handle occlusion for panoptic segmentation. Intuitively, the complementarity between semantic segmentation and instance segmentation can be leveraged to improve the performance. Besides, we notice that using detection/mask scores is insufficient for resolving the occlusion problem. Motivated by these observations, we propose a novel deep panoptic segmentation scheme based on a bidirectional learning pipeline. Moreover, we introduce a plug-and-play occlusion handling algorithm to deal with the occlusion between different object instances. The experimental results on COCO panoptic benchmark validate the effectiveness of our proposed method. Codes will be released soon at https://github.com/Mooonside/BANet.
3D-MPA: Multi-Proposal Aggregation for 3D Semantic Instance Segmentation

We present 3D-MPA, a method for instance segmentation on 3D point clouds. Given an input point cloud, we propose an object-centric approach where each point votes for its object center. We sample object proposals from the predicted object centers. Then, we learn proposal features from grouped point features that voted for the same object center. A graph convolutional network introduces inter-proposal relations, providing higher-level feature learning in addition to the lower-level point features. Each proposal comprises a semantic label, a set of associated points over which we define a foreground-background mask, an objectness score and aggregation features. Previous works usually perform non-maximum-suppression (NMS) over proposals to obtain the final object detections or semantic instances. However, NMS can discard potentially correct predictions. Instead, our approach keeps all proposals and groups them together based on the learned aggregation features. We show that grouping proposals improves over NMS and outperforms previous state-of-the-art methods on the tasks of 3D object detection and semantic instance segmentation on the ScanNetV2 benchmark and the S3DIS dataset.
Understanding Cross-Lingual Syntactic Transfer in Multilingual Recurrent Neural Networks

It is now established that modern neural language models can be successfully trained on multiple languages simultaneously without changes to the underlying architecture, providing an easy way to adapt a variety of NLP models to low-resource languages. But what kind of knowledge is really shared among languages within these models? Does multilingual training mostly lead to an alignment of the lexical representation spaces or does it also enable the sharing of purely grammatical knowledge? In this paper we dissect different forms of cross-lingual transfer and look for its most determining factors, using a variety of models and probing tasks. We find that exposing our LMs to a related language does not always increase grammatical knowledge in the target language, and that optimal conditions for lexical-semantic transfer may not be optimal for syntactic transfer.
The Fornax 3D project: Globular clusters tracing kinematics and metallicities

Globular clusters (GCs) are found ubiquitously in massive galaxies and due to their old ages, they are regarded as fossil records of galaxy evolution. Spectroscopic studies of GC systems are often limited to the outskirts of galaxies, where GCs stand out against the galaxy background and serve as bright tracers of galaxy assembly. In this work, we use the capabilities of the Multi Unit Explorer Spectrograph (MUSE) to extract a spectroscopic sample of 722 GCs in the inner regions (≲3 Reff) of 32 galaxies in the Fornax cluster. These galaxies were observed as part of the Fornax 3D project, a MUSE survey that targets early and late-type galaxies within the virial radius of Fornax. After accounting for the galaxy background in the GC spectra, we extracted line-of-sight velocities and determined metallicities of a sub-sample of 238 GCs. We found signatures of rotation within GC systems, and comparing the GC kinematics and that of the stellar body shows that the GCs trace the spheroid of the galaxies. While the red GCs prove to closely follow the metallicity profile of the host galaxy, the blue GCs show a large spread of metallicities but they are generally more metal-poor than the host.
Investigation of the parameters of spiral pattern in galaxies: the arm width

In this work, we determine the parameters of spiral structure for a sample of face-on spiral galaxies. In practice, the solution to this problem is a hard task because of the diversity of observed characteristics associated with spiral structure, such as the number of arms, their shape, arm contrast, etc. We study spiral structure in galaxies based on an analysis of photometric cuts perpendicular to the arm direction. The method is based on an approximation of these slices with an analytical function and derivation of the parameters of spiral structure (arm width, asymmetry, pitch angle) using the fitted parameters from this approximation. The algorithm has been applied to a sample of 155 galaxies selected from the Sloan Digital Sky Survey in different passbands. In this paper, we only consider the results on arm width: most spirals exhibit an increase in their width with galactocentric distance. Only 14 per cent of galaxies in our sample show an opposite trend or have an almost constant arm width at all radii.
The Boltzmann legacy revisited: kinetic models of social interactions

The application of classical methods of statistical mechanics, originally developed by Ludwig Boltzmann in gas dynamics, to the description of social phenomena is a successful story that we try to outline in this paper. On one hand, it is nowadays a flourishing research line, which is more and more permeating different contexts such as the econophysics, sociophysics, biomathematics, transportation engineering to name just a few of them. On the other hand, it is a fascinating mathematical challenge, because it requires the interplay of various complementary expertises: modelling, model analysis, numerics. In this paper, we try to give a taste of all of this using the social phenomenon of opinion formation as a motivating example.