Miracle-dz/UniFAR-FTUs huggingface dataset:
Pregnancy and Lactation in Sprague-Dawley Rats Result in Permanent Reductions of Tibia Trabecular Bone Mineral Density and Structure but Consumption of Red Rooibos Herbal Tea Supports the Partial Recovery

During pregnancy and lactation, maternal bone mineral density (BMD) is reduced as calcium is mobilized to support offspring bone development. In humans, BMD returns to pre-pregnancy levels shortly after delivery, shifting from a high rate of bone resorption during pregnancy and lactation, into a rapid phase of bone formation post-lactation. This rapid change in bone turnover may provide an opportunity to stimulate a greater gain in BMD and stronger trabecular and cortical structure than present pre-pregnancy. Providing polyphenols present in red rooibos herbal tea may promote such an effect. In vitro, red rooibos polyphenols stimulate osteoblast activity, reduce osteoclastic resorption, and increase mineral production. The study objective was to determine if consuming red rooibos from pre-pregnancy through to 4 months post-lactation resulted in a higher BMD and improved trabecular and cortical bone structure in a commonly used rat model. Female Sprague-Dawley rats (n = 42) were randomized to one of the following groups: PREG TEA (pregnant, received supplemental level of red rooibos in water: ~2.6 g /kg body weight/day in water), PREG WATER (pregnant, received water), or NONPREG CON (age-matched, non-pregnant control, received water) from 2 weeks pre-pregnancy (age 8 weeks) through to 4 months post-lactation. Rats were fed AIN-93G (pre-pregnancy through to the end of lactation) and AIN-93M (post-lactation onwards). BMD and trabecular structure (bone volume fraction, trabecular number, trabecular separation) were improved (p < 0.05) by 1- or 2-months post-lactation when comparing PREG TEA to PREG CON, though neither group recovered to the level of NONPREG CON. Cortical outcomes (cortical area fraction, cortical thickness, tissue mineral density) for PREG TEA and PREG CON were reduced (p < 0.05) following lactation but returned to the level of NONPREG CON by 2-months post-lactation, with the exception of cortical thickness. The lack of recovery of BMD and key outcomes of trabecular bone structure was unexpected. While consumption of red rooibos did not result in stronger bone post-lactation, red rooibos did support the partial recovery of trabecular BMD and bone structure following pregnancy and lactation. The findings also provide insight into the timing and dose of polyphenols to study in future interventions.
Copy Number Alterations in Hepatoblastoma: Literature Review and a Brazilian Cohort Analysis Highlight New Biological Pathways

Hepatoblastoma (HB) is a rare embryonal tumor, although it is the most common pediatric liver cancer. The aim of this study was to provide an accurate cytogenomic profile of this type of cancer, for which information in cancer databases is lacking. We performed an extensive literature review of cytogenetic studies on HBs disclosing that the most frequent copy number alterations (CNAs) are gains of 1q, 2/2q, 8/8q, and 20; and losses at 1p and 4q. Furthermore, the CNA profile of a Brazilian cohort of 26 HBs was obtained by array-CGH; the most recurrent CNAs were the same as shown in the literature review. Importantly, HBs from female patients, high-risk stratification tumors, tumors who developed in older patients (> 3 years at diagnosis) or from patients with metastasis and/or deceased carried a higher diversity of chromosomal alterations, specifically chromosomal losses at 1p, 4, 11q and 18q. In addition, we distinguished three major CNA profiles: no detectable CNA, few CNAs and tumors with complex genomes. Tumors with simpler genomes exhibited a significant association with the epithelial fetal subtype of HBs; in contrast, the complex genome group included three cases with epithelial embryonal histology, as well as the only HB with HCC features. A significant association of complex HB genomes was observed with older patients who developed high-risk tumors, metastasis, and deceased. Moreover, two patients with HBs exhibiting complex genomes were born with congenital anomalies. Together, these findings suggest that a high load of CNAs, mainly chromosomal losses, particularly losses at 1p and 18, increases the tendency to HB aggressiveness. Additionally, we identified six hot-spot chromosome regions most frequently affected in the entire group: 1q31.3q42. 3, 2q23.3q37. 3, and 20p13p11.1 gains, besides a 5,3 Mb amplification at 2q24.2q24. 3, and losses at 1p36.33p35. 1, 4p14 and 4q21.22q25. An in-silico analysis using the genes mapped to these six regions revealed several enriched biological pathways such as ERK Signaling, MicroRNAs in Cancer, and the PI3K-Akt Signaling, in addition to the WNT Signaling pathway; further investigation is required to evaluate if disturbances of these pathways can contribute to HB tumorigenesis. The analyzed gene set was found to be associated with neoplasms, abnormalities of metabolism/homeostasis and liver morphology, as well as abnormal embryonic development and cytokine secretion. In conclusion, we have provided a comprehensive characterization of the spectrum of chromosomal alterations reported in HBs and identified specific genomic regions recurrently altered in a Brazilian HB group, pointing to new biological pathways, and relevant clinical associations.
Impact of telecommuting and intelligent transportation systems on residential location choice

The impacts of telecommuting and intelligent transportation systems (ITS) on urban development patterns were investigated in terms of households' residential location choice decisions. A discrete choice modelling approach framework was used. A stated preference (SP) logit analysis was carried out to estimate the parameters of the utility function. An attitude survey of employees of selected public and private sector organizations in the Ottawa-Carleton Region (Canada) yielded the required data for model estimation. In addition to obtaining background information, the survey elicited SP responses by presenting a number of hypothetical residential choice scenarios defined according to the principles of SP experimental design. Results show that telecommuting and ITS measures are highly significant factors in the residential choice model. This leads to the conclusion that these reinforce dispersed residential patterns and encourage moves towards outlying sites. Implications of this conclusion for urban land development planning are noted.
The Elevated Expressions of Anti-lipopolysaccharide Factors After Priming Stimulation Confer Lastingly Humoral Protection in Crab Eriocheir sinensis

Evidence of immune memory in invertebrates (immune priming) has accumulated in various organisms, and both cellular and humoral immune reactions are speculated to be involved in immune priming. However, there is a lack of understanding of the molecular mechanisms involved. In the present study, the protective effect of primed haemolymph was further validated by the increased survival rate of naïve crabs receiving a transfusion of primed haemolymph. By proteomic analysis, there were 474 proteins identified from the primed haemolymph, and most of them were functionally annotated in transport and metabolism classes. A total of 70 proteins were found to be differentially expressed in haemolymph at 12 hours and 7 days after priming stimulation with Aeromonas hydrophila, among which anti-lipopolysaccharide factor 1 (EsALF-1) and 3 (EsALF-3) were identified as the most significant (p < 0.05). After being challenged with A. hydrophila, EsALF-1 and EsALF-3 were highly expressed at both mRNA (in haemocytes) and protein (in haemolymph) levels compared with blank crabs, and the mRNA expressions of components in the EsTLR1-EsMyd88-EsPelle-EsALF pathway also increased significantly (p < 0.05). The EsALF-3 and EsMyd88 were even significantly higher expressed in response to the second A. hydrophila challenge, but their expressions all decreased (p < 0.05) when EsTLR1 was knocked down by RNAi. After the naïve crabs received an injection with the recombinant protein of EsALF-1 (rEsALF-1) or EsALF-3 (rEsALF-3), their survival rate increased significantly (p < 0.05) upon A. hydrophila stimulation. In contrast, the survival rate of the primed crabs reduced significantly (p < 0.05) after they received an injection with the antibody of EsALF-1 or EsALF-3. The enhanced expressions of EsALF-1 and EsALF-3 after A. hydrophilap riming stimulation could sustain for four weeks. All the results suggested that the EsTLR1-mediated productions of EsALF-1 and EsALF-3 in haemolymph played an indispensable role in the month-long humoral immune protection induced by A. hydrophila, which provides solid evidence of immune priming in crabs and a valuable reference for further understanding immune memory in invertebrates.
Flagellin From Pseudomonas aeruginosa Modulates SARS-CoV-2 Infectivity in Cystic Fibrosis Airway Epithelial Cells by Increasing TMPRSS2 Expression

In the coronavirus disease 2019 (COVID-19) health crisis, one major challenge is to identify the susceptibility factors of severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) in order to adapt the recommendations for populations, as well as to reduce the risk of COVID-19 development in the most vulnerable people, especially patients with chronic respiratory diseases such as cystic fibrosis (CF). Airway epithelial cells (AECs) play a critical role in the modulation of both immune responses and COVID-19 severity. SARS-CoV-2 infects the airway through the receptor angiotensin-converting enzyme 2, and a host protease, transmembrane serine protease 2 (TMPRSS2), plays a major role in SARS-CoV-2 infectivity. Here, we show that Pseudomonas aeruginosa increases TMPRSS2 expression, notably in primary AECs with deficiency of the ion channel CF transmembrane conductance regulator (CFTR). Further, we show that the main component of P. aeruginosa flagella, the protein flagellin, increases TMPRSS2 expression in primary AECs and Calu-3 cells, through activation of Toll-like receptor-5 and p38 MAPK. This increase is particularly seen in Calu-3 cells deficient for CFTR and is associated with an intracellular increased level of SARS-CoV-2 infection, however, with no effect on the amount of virus particles released. Considering the urgency of the COVID-19 health crisis, this result may be of clinical significance for CF patients, who are frequently infected with and colonized by P. aeruginosa during the course of CF and might develop COVID-19.
How Is the History of Early Traumatic Exposure Associated With the Psychopathological Outcomes of COVID-19 Related Lockdown and Subsequent Re-opening in People With Eating Disorders?

The negative impact of COVID-19 pandemic on people with Eating Disorders (EDs) has been documented. The aim of this study was to evaluate whether a history of traumatic experiences during childhood or adolescence was associated with a higher degree of psychopathological worsening during COVID-19 related lockdown and in the following re-opening period in this group of people. People with EDs undergoing a specialist ED treatment in different Italian services before the spreading of COVID-19 pandemic (n = 312) filled in an online survey to retrospectively evaluate ED specific and general psychopathology changes after COVID-19 quarantine. Based on the presence of self-reported traumatic experiences, the participants were split into three groups: patients with EDs and no traumatic experiences, patients with EDs and childhood traumatic experiences, patients with EDs and adolescent traumatic experiences. Both people with or without early traumatic experiences reported retrospectively a worsening of general and ED-specific psychopathology during the COVID 19-induced lockdown and in the following re-opening period. Compared to ED participants without early traumatic experiences, those with a self-reported history of early traumatic experiences reported heightened anxious and post-traumatic stress symptoms, ineffectiveness, body dissatisfaction, and purging behaviors. These differences were seen before COVID-19 related restrictions as well as during the lockdown period and after the easing of COVID-19 related restrictions. In line with the “maltreated ecophenotype” theory, these results may suggest a clinical vulnerability of maltreated people with EDs leading to a greater severity in both general and ED-specific symptomatology experienced during the exposure to the COVID-19 pandemic.
Tacrolimus-Induced Neurotrophic Differentiation of Adipose-Derived Stem Cells as Novel Therapeutic Method for Peripheral Nerve Injury

Peripheral nerve injuries (PNIs) are frequent traumatic injuries across the globe. Severe PNIs result in irreversible loss of axons and myelin sheaths and disability of motor and sensory function. Schwann cells can secrete neurotrophic factors and myelinate the injured axons to repair PNIs. However, Schwann cells are hard to harvest and expand in vitro, which limit their clinical use. Adipose-derived stem cells (ADSCs) are easily accessible and have the potential to acquire neurotrophic phenotype under the induction of an established protocol. It has been noticed that Tacrolimus/FK506 promotes peripheral nerve regeneration, despite the mechanism of its pro-neurogenic capacity remains undefined. Herein, we investigated the neurotrophic capacity of ADSCs under the stimulation of tacrolimus. ADSCs were cultured in the induction medium for 18 days to differentiate along the glial lineage and were subjected to FK506 stimulation for the last 3 days. We discovered that FK506 greatly enhanced the neurotrophic phenotype of ADSCs which potentiated the nerve regeneration in a crush injury model. This work explored the novel application of FK506 synergized with ADSCs and thus shed promising light on the treatment of severe PNIs.
Helical post-buckling of a rod in a cylinder: with applications to drill-strings

The helical buckling and post-buckling of an elastic rod within a cylindrical casing arises in many disciplines, but is particularly important in the petroleum industry. Here, a drill-string, subjected to an end twisting moment combined with axial tension or compression, is particularly prone to buckling within its bore-hole—with potentially serious results. In this paper, we make a detailed theoretical study of this type of instability, deriving precise new results for the advanced post-buckling stage when the rod is in continuous contact with the cylinder. Results, including rigorous stability analyses and contact pressure assessments, are presented as equilibrium surfaces to facilitate comparisons with experimental results. Two approximate solutions give insight, universal graphs and parameters, for the practically relevant case of small angles, and highlight the existence of a critical cylinder diameter. Excellent agreement with experiments is achieved.
Early Adolescents’ Social Achievement Goals and Perceived Relational Support: Their Additive and Interactive Effects on Social Behavior

The current study examined the additive and interactive effects of early adolescents’ social achievement goals and perceived relational support from teachers and peers on their social behavior. Adolescents’ social achievement goals (i.e., social development, social demonstration-approach, and social demonstration-avoidance), perceived relational support from teachers and peers, and social behavior (i.e., overt and relational aggression, prosocial behavior, and anxious solitary behavior) were assessed in a sample of fifth and sixth graders (Mage = 12.5; N = 677) nested within 26 classrooms. Multilevel modeling results indicated that social goals and relational support from teachers and peers made additive contributions to adolescents’ social behavior. Results also indicated the evidence of interactive effects, such that relational support from teachers was negatively associated with overt and relational aggression primarily among adolescents who had high social demonstration-approach goals. Findings underscore the need to consider adolescents’ social goals in conjunction with their perceived relational support for educators and practitioners.
A Comparability of Renal Length and Volume Measurements in MRI and Ultrasound in Children

Introduction: Despite the significant increase in use of magnetic resonance imaging (MRI) in children, there is still a lack of normal reference values of renal size in this method and reference values are being interpolated from the ultrasound (US) studies. The study provides comparative analysis of agreement in renal length and volume measurements between MRI and ultrasound. Materials and Methods: Ninety-three children with a mean age of 8.0 ± 6.0 years, who had undergone both renal US and MRI exams, were included in the study. Participants were divided into three subgroups; each kidney was considered separately. Group 1 included 106 kidneys without any anomalies. Group 2 comprised 48 kidneys with a dilated collecting system. Group 3 included 32 kidneys with a duplicated collecting system. Measurements were taken in three dimensions, and renal volume was calculated from the ellipsoid formula. Results: We found no significant difference between US and MRI measurements in Group 1 and Group 2. In Group 3, the difference between measurements in both imaging methods was significant. The mean difference varied from 0.05% in Group 1, 2.95% in Group 2, to 4.99% in Group 3. Conclusion: The US and MRI are comparable methods in renal size measurements. The interpolation of sonographic renal length and volume reference values to the MRI in the pediatric population is justified, as there is a strong agreement between both methods. Both methods can be used interchangeably for following up of the renal size changes in the pediatric population.
The Genetic Landscape of Fiber Flax

Genetic diversity in a breeding program is essential to overcome modern-day environmental challenges faced by humanity and produce robust, resilient crop cultivars with improved agronomic characteristics, as well as to trace crop domestication history. Flax (Linum usitatissimum), one of the first crops domesticated by mankind, has been traditionally cultivated for fiber as well as for medicinal purposes and as a nutritional product. The origins of fiber flax are hidden in the mists of time and can be hypothetically traced back to either the Indo-Afghan region or Fertile Crescent. To shed new light on fiber flax genetic diversity and breeding history, in this study, we presented a comprehensive analysis of the core collection of flax (306 accessions) of different morphotypes and geographic origins maintained by the Russian Federal Research Center for Bast Fiber Crops. We observed significant population differentiation between oilseed and fiber morphotypes, as well as mapped genomic regions affected by recent breeding efforts. We also sought to unravel the origins of kryazhs, Russian heritage landraces, and their genetic relatedness to modern fiber flax cultivars. For the first time, our results provide strong genetic evidence in favor of the hypothesis on kryazh’s mixed origin from both the Indo-Afghan diversity center and Fertile Crescent. Finally, we showed predominant contribution from Russian landraces and kryazhs into the ancestry of modern fiber flax varieties. Taken together, these findings may have practical implications on the development of new improved flax varieties with desirable traits that give farmers greater choice in crop management and meet the aspirations of breeders.
MagNet: Detecting Digital Presentation Attacks on Face Recognition

Presentation attacks on face recognition systems are classified into two categories: physical and digital. While much research has focused on physical attacks such as photo, replay, and mask attacks, digital attacks such as morphing have received limited attention. With the advancements in deep learning and computer vision algorithms, several easy-to-use applications are available where with few taps/clicks, an image can be easily and seamlessly altered. Moreover, generation of synthetic images or modifying images/videos (e.g. creating deepfakes) is relatively easy and highly effective due to the tremendous improvement in generative machine learning models. Many of these techniques can be used to attack the face recognition systems. To address this potential security risk, in this research, we present a novel algorithm for digital presentation attack detection, termed as MagNet, using a “Weighted Local Magnitude Pattern” (WLMP) feature descriptor. We also present a database, termed as ID Age nder, which consists of three different subsets of swapping/morphing and neural face transformation. In contrast to existing research, which utilizes sophisticated machine learning networks for attack generation, the databases in this research are prepared using social media platforms that are readily available to everyone with and without any malicious intent. Experiments on the proposed database, FaceForensic database, GAN generated images, and real-world images/videos show the stimulating performance of the proposed algorithm. Through the extensive experiments, it is observed that the proposed algorithm not only yields lower error rates, but also provides computational efficiency.
Bulk and Single-Cell Profiling of Breast Tumors Identifies TREM-1 as a Dominant Immune Suppressive Marker Associated With Poor Outcomes

Background Triggering receptor expressed on myeloid cells (TREM)-1 is a key mediator of innate immunity previously associated with the severity of inflammatory disorders, and more recently, the inferior survival of lung and liver cancer patients. Here, we investigated the prognostic impact and immunological correlates of TREM1 expression in breast tumors. Methods Breast tumor microarray and RNAseq expression profiles (n=4,364 tumors) were analyzed for associations between gene expression, tumor immune subtypes, distant metastasis-free survival (DMFS) and clinical response to neoadjuvant chemotherapy (NAC). Single-cell (sc)RNAseq was performed using the 10X Genomics platform. Statistical associations were assessed by logistic regression, Cox regression, Kaplan-Meier analysis, Spearman correlation, Student’s t-test and Chi-square test. Results In pre-treatment biopsies, TREM1 and known TREM-1 inducible cytokines (IL1B, IL8) were discovered by a statistical ranking procedure as top genes for which high expression was associated with reduced response to NAC, but only in the context of immunologically “hot” tumors otherwise associated with a high NAC response rate. In surgical specimens, TREM1 expression varied among tumor molecular subtypes, with highest expression in the more aggressive subtypes (Basal-like, HER2-E). High TREM1 significantly and reproducibly associated with inferior distant metastasis-free survival (DMFS), independent of conventional prognostic markers. Notably, the association between high TREM1 and inferior DMFS was most prominent in the subset of immunogenic tumors that exhibited the immunologically hot phenotype and otherwise associated with superior DMFS. Further observations from bulk and single-cell RNAseq analyses indicated that TREM1 expression was significantly enriched in polymorphonuclear myeloid-derived suppressor cells (PMN-MDSCs) and M2-like macrophages, and correlated with downstream transcriptional targets of TREM-1 (IL8, IL-1B, IL6, MCP-1, SPP1, IL1RN, INHBA) which have been previously associated with pro-tumorigenic and immunosuppressive functions. Conclusions Together, these findings indicate that increased TREM1 expression is prognostic of inferior breast cancer outcomes and may contribute to myeloid-mediated breast cancer progression and immune suppression.