Miracle-dz/UniFAR-FTUs huggingface dataset:
A Novel lncRNA HOXC-AS3 Acts as a miR-3922-5p Sponge to Promote Breast Cancer Metastasis

Abstract Purpose: The function of long noncoding RNAs (lncRNA) in breast cancer metastasis remains largely unknown. In this work, the role of HOXC-AS3 in breast cancer progression was investigated. Methods: By using Cancer Genome Atlas (TCGA) Database, we investigated the expression of HOXC-AS3 in breast cancer and explored the association between HOXC-AS3 expression and prognosis. Then, we studied the biological function of HOXC-AS3 in cell migration and invasion both in vitro and in vivo. Furthermore, the target miRNA of HOXC-AS3, and the target mRNA of miR-3922-5p were proved. Results: HOXC-AS3 is aberrantly overexpressed in breast cancers especially the HER2+ type. Moreover, high expression of HOXC-AS3 has a relationship with poor clinical outcomes of breast cancer. In addition, HOXC-AS3 regulates cell Invasion and migration both in vitro and in vivo. Our results demonstrated that miR-3922-5p was a direct target of HOXC-AS3, and PPP1R1A was a target of miR-3922-5p in breast cancer. Conclusions: The novel lncRNA HOXC-AS3 acts as a miR-3922-5p sponge to upregulate PPP1R1A protein expression, and thus results in promoting breast cancer metastasis. HOXC-AS3 could be a novel therapeutic target for breast cancer therapeutics.
Serum uric acid levels of patients with multiple sclerosis and other neurological diseases

The serum uric acid (UA) levels were measured in 112 patients with multiple sclerosis (MS) and 794 patients with different types of other neurological diseases (OND) or healthy control group. Serum UA levels, along with relevant clinical parameters of MS and OND, were also investigated. MS patients had significantly lower UA levels than those with transient ischemia attack (344.6 130.6 μmol/L, P 0.000), cerebral hemorrhage (311.9 104.7 μmol/L, P 0.000), cerebral infarction (291.3 101.6 μmol/L, P 0.014) and the healthy control group (312.1 92.8 μmol/L, P 0.000). MS patients had significantly higher serum UA levels than those with cryptococcus meningitis or meningoencephalitis (178.9 107.0 μmol/L, P 0.000) and tuberculous meningitis or meningoencephalitis patients (175.7 99.9 μmol/L, P 0.000). There were no significant differences in UA levels between patients with MS and those with facial neuritis, viral meningitis or encephalitis, pulmonary tuberculosis, polymyositis or dermatomyositis, myasthenia gravis, subarachnoid hemorrhage, migraine, Guillain–Barre syndrome and myelitis. In addition, UA levels were independently correlated with gender and duration of MS, but neither with MRI activity, disability nor subtypes of the disease in MS patients. Our data suggest that UA has two biphasic functions: neuroprotective and injurious. Our studies may help physicians to deal with conditions having abnormal UA levels. Multiple Sclerosis 2008; 14: 188–196. http://msj.sagepub. com
Incidence and Outcomes of Mental Disorders in a Regional Population: The Northern Rivers Mental Health Study

Objectives: To estimate the incidence of mental disorders in a cohort of previously symptom-free individuals who are representatives of a regional Australian population. To map changing patterns of diagnosis and comorbidity within the cohort over a 2 year period. Method: Two year follow-up of a community-based cohort drawn from a telephone screening of 9191 randomly selected adults. Subjects were administered a comprehensive face-to-face interview which included the Composite International Diagnostic Interview. A total of 1407 subjects were interviewed at baseline, and 968 subjects were reinterviewed (a 68.8% follow-up rate). Results: There was considerable change in disorder status over the study period, and analysis of the Composite International Diagnostic Interview scoring suggests that these changes reflected real changes in symptomatology. Of subjects interviewed at both baseline and follow-up, 638 were classified as disorder-free at their entry to the study. After 2 years, 98 of these met criteria for a mental disorder during the preceding 12 months. After adjusting for sampling and gender, the 12 month incidence of any mental disorder among subjects who had been disorder-free 2 years previously was 9.95 per hundred person-years at risk. At baseline, a further 330 subjects met ICD-10 criteria for a mental disorder during the previous 12 months. Two years later, 167 of these subjects (50.6%) were disorder-free, and 163 still met the criteria for a mental disorder, although there had often been considerable change in their diagnosis. Subjects with a mental disorder at the commencement of the study were significantly more likely than those without a disorder to have a positive diagnosis 2 years later (p < 0.001). The number of diagnoses at baseline was a strong predictor of the number of diagnoses at follow-up (p < 0.001), and each additional comorbid diagnosis at baseline also increased the probability of a persisting disorder at follow-up (p < 0.001). Conclusions: Over a 2 year period, the majority of subjects with a mental disorder will become disorder-free, while a significant number of previously disorder-free individuals will develop a positive diagnosis. Health services need to be designed to meet this labile demand.
Dimensional and Geometrical Quality Enhancement in Additively Manufactured Parts: Systematic Framework and A Case Study

In order to compete with traditional manufacturing processes, Additive Manufacturing (AM) should be capable of producing medium to large batches at industrial-degree quality and competitive cost-per-unit. This paper proposes a systematic framework approach to the problem of fulfilling dimensional and geometric requirements for medium batch sizes of AM parts, which has been structured as a three-step optimization methodology. Firstly, specific work characteristics are analyzed so that information is arranged according to an Operation Space (factors that could have an influence upon quality) and a Verification Space (formed by quality indicators and requirements). Standard process configuration leads to characterization of the standard achievable quality. Secondly, controllable factors are analyzed to determine their relative influence upon quality indicators and the optimal process configuration. Thirdly, optimization of part dimensional and/or geometric definition at the design level is performed in order to improve part quality and meet quality requirements. To evaluate the usefulness of the proposed framework under quasi-industrial condition, a case study is presented here which is focused on the dimensional and geometric optimization of surgical-steel tibia resection guides manufactured by Laser-Power Bed Fusion (L-PBF). The results show that the proposed approach allows for part quality improvement to a degree that matches the initial requirements.
Expanding the editable genome and CRISPR–Cas9 versatility using DNA cutting-free gene targeting based on in trans paired nicking

Abstract Genome editing typically involves recombination between donor nucleic acids and acceptor genomic sequences subjected to double-stranded DNA breaks (DSBs) made by programmable nucleases (e.g. CRISPR–Cas9). Yet, nucleases yield off-target mutations and, most pervasively, unpredictable target allele disruptions. Remarkably, to date, the untoward phenotypic consequences of disrupting allelic and non-allelic (e.g. pseudogene) sequences have received scant scrutiny and, crucially, remain to be addressed. Here, we demonstrate that gene-edited cells can lose fitness as a result of DSBs at allelic and non-allelic target sites and report that simultaneous single-stranded DNA break formation at donor and acceptor DNA by CRISPR–Cas9 nickases (in trans paired nicking) mostly overcomes such disruptive genotype-phenotype associations. Moreover, in trans paired nicking gene editing can efficiently and precisely add large DNA segments into essential and multiple-copy genomic sites. As shown herein by genotyping assays and high-throughput genome-wide sequencing of DNA translocations, this is achieved while circumventing most allelic and non-allelic mutations and chromosomal rearrangements characteristic of nuclease-dependent procedures. Our work demonstrates that in trans paired nicking retains target protein dosages in gene-edited cell populations and expands gene editing to chromosomal tracts previously not possible to modify seamlessly due to their recurrence in the genome or essentiality for cell function.
An Empirical Comparison of Multivariable Methods for Estimating Risk of Death from Coronary Heart Disease

Background Logistic regression and, more recently, Cox regression have been the predominant methods for identifying risk factors and developing risk estimation equations for coronary heart disease (CHD). Software for the regression tree method is now available for binary and survival outcomes and thus offers an alternative methodology. This paper compares these four methods for identifying significant risk factors from among a set of candidate factors and for estimating the risk of death from CHD using baseline and mortality follow-up data on 1701 men participating in the Busselton Health Study. The candidate risk factors were age, body mass index, systolic and diastolic blood pressure, treatment for hypertension, cholesterol and smoking.
Paradoxical Changes Underscore Epigenetic Reprogramming During Adult Zebrafish Extraocular Muscle Regeneration

Purpose Genomic reprogramming and cellular dedifferentiation are critical to the success of de novo tissue regeneration in lower vertebrates such as zebrafish and axolotl. In tissue regeneration following injury or disease, differentiated cells must retain lineage while assuming a progenitor-like identity in order to repopulate the damaged tissue. Understanding the epigenetic regulation of programmed cellular dedifferentiation provides unique insights into the biology of stem cells and cancer and may lead to novel approaches for treating human degenerative conditions. Methods Using a zebrafish in vivo model of adult muscle regeneration, we utilized chromatin immunoprecipitation followed by massively parallel DNA sequencing (ChIP-seq) to characterize early changes in epigenetic signals, focusing on three well-studied histone modifications—histone H3 trimethylated at lysine 4 (H3K4me3), and histone H3 trimethylated or acetylated at lysine 27 (H3K27me3 and H3K27Ac, respectively). Results We discovered that zebrafish myocytes undergo a global, rapid, and transient program to drive genomic remodeling. The timing of these epigenetic changes suggests that genomic reprogramming itself represents a distinct sequence of events, with predetermined checkpoints, to generate cells capable of de novo regeneration. Importantly, we uncovered subsets of genes that maintain epigenetic marks paradoxical to changes in expression, underscoring the complexity of epigenetic reprogramming. Conclusions Within our model, histone modifications previously associated with gene expression act for the most part as expected, with exceptions suggesting that zebrafish chromatin maintains an easily editable state with a number of genes paradoxically marked for transcriptional activity despite downregulation.
Inactivation of Genes Encoding MutL and MutS Proteins Influences Adhesion and Biofilm Formation by Neisseria gonorrhoeae

Neisseria gonorrhoeae is an etiological agent of gonorrhea, which remains a global health problem. This bacterium possesses MutL and MutS DNA repair proteins encoded by mutL and mutS genes, whose inactivation causes a mutator phenotype. We have demonstrated the differential gene expression in N. gonorrhoeae mutL and mutS mutants using DNA microarrays. A subset of differentially expressed genes encodes proteins that can influence adhesion and biofilm formation. Compared to the wild-type strain, N. gonorrhoeae mutL and mutS mutants formed denser biofilms with increased biofilm-associated biomass on the abiotic surface. The N. gonorrhoeae mutS::km, but not the mutL mutant, was also more adherent and invasive to human epithelial cells. Further, during infection of epithelial cells with N. gonorrhoeae mutS::km, the expression of some bacterial genes encoding proteins that can influence gonococcal adhesion was changed compared with their expression in cells infected with the wild-type gonococcus, as well as of human genes’ encoding receptors utilized by N. gonorrhoeae (CD46, CEACAM 1, HSPG 2). Thus, deficiency in the mutS gene resulting in increased mutation frequency in singular organisms can be beneficial in populations because these mutants can be a source of features linked to microbial fitness.
A dual role of dLsd1 in oogenesis: regulating developmental genes and repressing transposons

Abstract The histone demethylase LSD1 is a key chromatin regulator that is often deregulated in cancer. Its ortholog, dLsd1 plays a crucial role in Drosophila oogenesis; however, our knowledge of dLsd1 function is insufficient to explain its role in the ovary. Here, we have performed genome-wide analysis of dLsd1 binding in the ovary, and we document that dLsd1 is preferentially associated to the transcription start site of developmental genes. We uncovered an unanticipated interplay between dLsd1 and the GATA transcription factor Serpent and we report an unexpected role for Serpent in oogenesis. Besides, our transcriptomic data show that reducing dLsd1 levels results in ectopic transposable elements (TE) expression correlated with changes in H3K4me2 and H3K9me2 at TE loci. In addition, our results suggest that dLsd1 is required for Piwi dependent TE silencing. Hence, we propose that dLsd1 plays crucial roles in establishing specific gene expression programs and in repressing transposons during oogenesis.
The spectro-photometric calibration of the JWST NIRSpec instrument

NIRSpec is the main near-infrared spectrograph on board the James Webb Space Telescope, offering multi-object capabilities as well as an integral field unit and a number of fixed slits for studies of individual objects. In this paper, we describe the unique challenges in calibrating this complex instrument, and the approach taken to deal with them, both in terms of operational procedures and via automated processing of NIRSpec data. We provide a high-level description of the sequence of processing steps required for NIRSpec science data, and the necessary on-ground calibration files. We focus our discussion on the case of a typical multi-object observation with the MSA, in which adjacent micro-shutters are used to sample the science object and the sky background in an alternating way. This dithering strategy is particularly well suited for faint targets, but its guiding principles also apply to other NIRSpec modes.
Learning Deep Hierarchical Spatial–Spectral Features for Hyperspectral Image Classification Based on Residual 3D-2D CNN

Every pixel in a hyperspectral image contains detailed spectral information in hundreds of narrow bands captured by hyperspectral sensors. Pixel-wise classification of a hyperspectral image is the cornerstone of various hyperspectral applications. Nowadays, deep learning models represented by the convolutional neural network (CNN) provides an ideal solution for feature extraction, and has made remarkable achievements in supervised hyperspectral classification. However, hyperspectral image annotation is time-consuming and laborious, and available training data is usually limited. Due to the “small-sample problem”, CNN-based hyperspectral classification is still challenging. Focused on the limited sample-based hyperspectral classification, we designed an 11-layer CNN model called R-HybridSN (Residual-HybridSN) from the perspective of network optimization. With an organic combination of 3D-2D-CNN, residual learning, and depth-separable convolutions, R-HybridSN can better learn deep hierarchical spatial–spectral features with very few training data. The performance of R-HybridSN is evaluated over three public available hyperspectral datasets on different amounts of training samples. Using only 5%, 1%, and 1% labeled data for training in Indian Pines, Salinas, and University of Pavia, respectively, the classification accuracy of R-HybridSN is 96.46%, 98.25%, 96.59%, respectively, which is far better than the contrast models.
Sperm enter glands of preovulatory bovine endometrial explants and initiate inflammation.

We previously reported that sperm binding to cultured monolayers of bovine uterine epithelial cells induces an acute inflammatory response involving the Toll-like receptor (TLR2) signaling pathway. This response serves to clear the uterus of sperm and thereby prepares the endometrium for implantation. The endometrium is lined by surface epithelial cells; however, epithelial cells also line uterine glands. To investigate the source of the immune response, we used an explant model. Explants of bovine endometrium were incubated with bull sperm illuminated by JC1 fluorescent labeling in their mitochondria. The sperm glided over the surface epithelium until they encountered and entered uterine glands, where they remained. Scanning electron microscopy of explants revealed polymorphonuclear neutrophils (PMNs) in uterine glands along with the sperm. In the absence of sperm, PMNs were not seen in glands. Incubation of sperm with explants resulted in an acute inflammatory response, seen as upregulation of mRNA expression of IL8, TNFA, IL1B, PGES, and TLR2 in whole explants, as well as increased TNFA protein expression in uterine glands. TLR1/2 antagonist reduced sperm numbers in the glands and inhibited the increase of TNFA. Our observations suggest that uterine glands serve as a site where sperm interact with uterine epithelium to trigger the innate immune response to clear excess sperm from the uterus.
Online joint power control for cooperative jamming systems with energy harvesting

To maximize the long-term time-averaged secrecy rate of an energy harvesting wireless communication system, an online power control algorithm based on the Lyapunov optimization framework is proposed. The system is composed of a source node, a cooperative jamming node, and two destination nodes. The source node and the jamming node are powered by the energy harvesting device. Information sent to the two destination nodes is mutually confidential. Using the Lyapunov optimization framework, the original stochastic optimization problem is transformed into a per-time-slot optimization problem, and the power of the signal and that of the artificial noise are determined based on the current system state such as the power level of the batteries and channel coefficients. The fairness between the two destination nodes is considered too. Simulation results demonstrate that the proposed algorithm can effectively utilize the harvested energy and significantly improve the long-term averaged secrecy rate.
Trekstock Meet & Move: The Impact of One-Day Health and Well-Being Events for Young Adults with Cancer.

Purpose: To evaluate the impact of a series of one-day events delivered by Trekstock, a cancer charity supporting young adults with cancer in the United Kingdom. Methods: Data on physical activity, mood, perceived support, self-efficacy, and confidence to be active were collected at three time points: before, after, and 2 weeks following the Meet & Move events. Results: Ninety-seven young adults with cancer (mean age: 29 years, 35% still receiving active treatment) attended a Trekstock Meet & Move event and participated within the evaluation. Baseline data demonstrated that before attending a Meet & Move event, 27.4% (n = 23) of young adults reported feeling their cancer excluded them from engaging in exercise, 44% (n = 37) reported they worry exercise will cause pain or injury, and only 38.6% (n = 32) knew what exercise they could do. Data collected post-event and at follow-up indicated that Meet & Move had a positive impact upon attendees' self-efficacy and confidence to be active with more than half reporting they felt inspired after attending. There was also a significant reduction in reported worry that exercise may cause pain or injury and reported perception of feeling left out of exercise because of cancer (p < 0.05). Following engagement in the Meet & Move events, 45% of attendees had either signed up for an additional Trekstock physical activity program or initiated engagement in a new type of physical activity on their own. Conclusion: Trekstock Meet & Move events inspire and motivate young adults with cancer in their 20s and 30s to be active.
Gas Detection Using Portable Deep-UV Absorption Spectrophotometry: A Review

Several gas molecules of environmental and domestic significance exhibit a strong deep-UV absorption. Therefore, a sensitive and a selective gas detector based on this unique molecular property (i.e., absorption at a specific wavelength) can be developed using deep-UV absorption spectrophotometry. UV absorption spectrometry provides a highly sensitive, reliable, self-referenced, and selective approach for gas sensing. This review article addresses the recent progress in the application of deep-UV absorption for gas sensing owing to its inherent features and tremendous potentials. Applications, advancements, and challenges related to UV emission sources, gas cells, and UV photodetectors are assessed and compared. We present the relevant theoretical aspects and challenges associated with the development of portable sensitive spectrophotometer. Finally, the applications of UV absorption spectrometry for ozone, NO2, SO2, and aromatic organic compounds during the last decades are discussed and compared. A portable UV absorption spectrophotometer can be developed by using LEDs, hollow core waveguides (HCW), and UV photodetectors (i.e., photodiodes). LED provides a portable UV emission source with low power input, low-intensity drifts, low cost, and ease of alignment. It is a quasi-chromatic UV source and covers the absorption band of molecules without optical filters for absorbance measurement of a target analyte. HCWs can be applied as a miniature gas cell for guiding UV radiation for measurement of low gas concentrations. Photodiodes, on the other hand, offer a portable UV photodetector with excellent spectral selectivity with visible rejection, minimal dark current, linearity, and resistance against UV-aging.
Room-temperature compression and equation of state of body-centered cubic zirconium

Zirconium (Zr) has properties conducive to nuclear applications and exhibits complex behavior at high pressure with respect to the effects of impurities, deviatoric stress, kinetics, and grain growth which makes it scientifically interesting. Here, we present experimental results on the 300 K equation of state of ultra-high purity Zr obtained using the diamond-anvil cell coupled with synchrotron-based x-ray diffraction and electrical resistance measurements. Based on quasi-hydrostatic room-temperature compression in helium to pressure P = 69.4(2) GPa, we constrain the bulk modulus and its pressure derivative of body-centered cubic (bcc) β-Zr to be K = 224(2) GPa and K′ = 2.6(1) at P = 37.0(1) GPa. A Monte Carlo approach was developed to accurately quantify the uncertainties in K and K′. In the Monte Carlo simulations, both the unit-cell volume and pressure vary according to their experimental uncertainty. Our high-pressure studies do not indicate additional isostructural volume collapse in the bcc phase of Zr in the 56–58 GPa pressure range.