Miracle-dz/UniFAR-FTUs huggingface dataset:
Optimizing Data Science Applications using Static Analysis

Data science applications are often coded in Python, using Pandas and similar APIs. Pandas requires data to be in memory, and when run on larger datasets, these applications may run out of memory, or suffer from poor performance. We describe the SCIRPy system for optimizing such applications by source to source transformations, using static analysis and transformation rules. SCIRPy implements a number of optimizations like data selection, drop column removal, multistage data fetch, and efficient data representation based on metadata analysis. The application source code is transformed into a custom-built intermediate representation (IR) and these optimizations are performed in this IR. The optimized IR is then transformed back to Python source. Our experiments show that our approach reduces the memory footprint and time consumption of a number of data science applications.
Unpacking Cultural Intelligence: Cultivating Ethnorelativism in International Business Education

ABSTRACT In light of diverse designs of the international business (IB) curriculum, this study investigates how the IB curriculum that requires students to major in a functional area enhances students’ cultural intelligence as well as differentiates the effect of students’ study abroad experience above and beyond various functional IB courses. By conducting qualitative focus groups and a quantitative survey in the United States, we find that although students’ past study abroad experiences improved their cultural intelligence (CQ), the IB education curriculum, even without a study abroad component, plays a pivotal role in improving students’ ethnorelativism, which leads to increased CQ. The finding of the current study supports that IB programs focusing on curriculum that enhances students’ ethnorelativism will help students develop CQ despite lacking study-abroad opportunities due to various travel restrictions, such as the ones caused by the COVID-19 pandemic. In addition, ethnorelativism in its own right has become a salient issue in the current climate of rising intolerance against minorities of different cultural backgrounds. We offer suggestions in the IB curriculum to further foster students’ ethnorelativism and CQ.
Detection of Turkish Sign Language Using Deep Learning and Image Processing Methods

ABSTRACT Sign language is a physical language that enables people with disabilities to communicate using hand and facial gestures. For this reason, it is very important for people with disabilities to express themselves freely in society and to make the sign language understandable to everyone. In this study, the data set was created by taking 10223 images for 29 letters in the Turkish Sign Language Alphabet. Images are made suitable for education by using image enhancement techniques. In the final stage of the study, classification processes on images were carried out by using CapsNet, AlexNet and ResNet-50, DenseNet, VGG16, Xception, InceptionV3, NasNet, EfficentNet, Hitnet, Squeezenet architectures and TSLNet, which was designed for the study. When the deep learning models were examined, it was found that CapsNet and TSLNet models were the most successful models with 99.7% and 99.6% accuracy rates, respectively.
Syntheses, structures and fluorescence properties of two Ce/Zn-Ce complexes with an open-chain ether Schiff base ligand

Abstract Reaction of bis(3-methoxysalicylidene)-3-oxapentane-1,5-diamine (H2L) with Ce(NO3)3 afforded a new Ce(III) complex with composition [Ce(H2L)(NO3)3] (1). Complex 1 reacts with zinc acetate and terephthalic acid to prepare complex 2, [Zn4Ce2(L)4(terephthalate)2][Ce(DMF)(NO3)5]. They have been characterized by elemental analysis, UV/Vis and IR spectroscopy, and single-crystal X-ray diffraction. The structure analysis revealed that 1 is mononuclear, whereas 2 is d-f heteronuclear. The fluorescence properties of the ligand and complexes 1 and 2 were studied in the solid state. The significantly blue-shifted emissions and enhancement of fluorescence in 1 and 2 relative to the ligand were attributed to coordination of ligand with metal ions. The results show that the structure and fluorescence of the Ce(III) complexes can be modified by introducing Zn(II) ion and auxiliary ligand terephthalate.
SNP rs4971059 predisposes to breast carcinogenesis and chemoresistance via TRIM46‐mediated HDAC1 degradation

Identification of the driving force behind malignant transformation holds the promise to combat the relapse and therapeutic resistance of cancer. We report here that the single nucleotide polymorphism (SNP) rs4971059, one of 65 new breast cancer risk loci identified in a recent genome‐wide association study (GWAS), functions as an active enhancer of TRIM46 expression. Recreating the G‐to‐A polymorphic switch caused by the SNP via CRISPR/Cas9‐mediated homologous recombination leads to an overt upregulation of TRIM46. We find that TRIM46 is a ubiquitin ligase that targets histone deacetylase HDAC1 for ubiquitination and degradation and that the TRIM46‐HDAC1 axis regulates a panel of genes, including ones critically involved in DNA replication and repair. Consequently, TRIM46 promotes breast cancer cell proliferation and chemoresistance in vitro and accelerates tumor growth in vivo. Moreover, TRIM46 is frequently overexpressed in breast carcinomas, and its expression is correlated with lower HDAC1 expression, higher histological grades, and worse prognosis of the patients. Together, our study links SNP rs4971059 to replication and to breast carcinogenesis and chemoresistance and support the pursuit of TRIM46 as a potential target for breast cancer intervention.
Myeloid Clonal Infiltrate Identified With Next-Generation Sequencing in Skin Lesions Associated With Myelodysplastic Syndromes and Chronic Myelomonocytic Leukemia: A Case Series

Background Myelodysplastic syndromes (MDS) and chronic myelomonocytic leukemia (CMML) are associated with cutaneous manifestations. Next-generation sequencing (NGS) is a tool capable of identifying clonal myeloid cells in the skin infiltrate and thus better characterize the link between hematological diseases and skin lesions. Objective To assess whether skin lesions of MDS/CMML are clonally related to blood or bone marrow cells using NGS. Methods Comparisons of blood or bone marrow and skin samples NGS findings from patients presenting with MDS/CMML and skin lesions in three French hospitals. Results Among the 14 patients recruited, 12 patients (86%) had mutations in the skin lesions biopsied, 12 patients (86%) had a globally similar mutational profile between blood/bone marrow and skin, and 10 patients (71%) had mutations with a high variant allele frequency (>10%) found in the myeloid skin infiltrate. Mutations in TET2 and DNMT3A, both in four patients, were the most frequent. Two patients harbored a UBA1 mutation on hematopoietic samples. Limitations Limited number of patients and retrospective collection of the data. Blood and skin sampling were not performed at the exact same time point for two patients. Conclusion Skin lesions in the setting of MDS/CMML are characterized by a clonal myeloid infiltrate in most cases.
Transcriptome Analysis Reveals the Senescence Process Controlling the Flower Opening and Closure Rhythm in the Waterlilies (Nymphaea L.)

Most waterlily flowers open at dawn and close after noon usually for three to four days, and thereafter wilt. The short lifespan of flowers restricts the development of the flower postharvest industry. The termination of flower movements is a key event during flower aging process. However, it is still unclear when the senescence process initiates and how it terminates the movement rhythm. In this study, we observed that the opening diameter of flowers was the smallest on the fourth (last) flowering day. Subsequent transcriptome profiles generated from petals at different flowering stages showed that the multiple signaling pathways were activated at the last closure stage (Time 3, T3) of the flowers, including Ca2+, reactive oxygen species and far red light signaling pathways, as well as auxin, ethylene and jasmonic acid signaling pathways. Moreover, In terms of cell metabolism regulation, the genes related to hydrolase (protease, phospholipase, nuclease) were upregulated at T3 stage, indicating that petals entered the senescence stage at that time; and the genes related to water transport and cell wall modification were also differentially regulated at T3 stage, which would affect the ability of cell expand and contract, and eventually lead to petal not open after the fourth day. Collectively, our data provided a new insight into the termination of flower opening in the waterlilies, and a global understanding of the senescence process of those opening-closure rhythm flowers.
Sex Differences in Characteristics and Outcomes in Elderly Heart Failure Patients With Preserved Ejection Fraction: A Post-hoc Analysis From TOPCAT

Introduction: Although the impact of sex on patient outcomes for heart failure (HF) with preserved ejection fraction (HFpEF) has been reported, it is still unclear whether this impact is applicable for elderly patients with HFpEF. This study was conducted as a secondary analysis from a large randomized controlled trial—The Treatment of Preserved Cardiac Function Heart Failure with an Aldosterone Antagonist Trial (TOPCAT)—to evaluate the impact of sex differences on the baseline characteristics and outcomes of HFpEF patients who were older than 70 years. Methods: Baseline characteristic of elderly patients were compared between men and women. Primary outcomes were cardiovascular (CV) mortality and HF-related hospitalization, whereas secondary outcomes were all-cause mortality and all-cause hospitalization. Cox regression models were used to determine the effect of sex differences on patient outcomes. Results: A total of 1,619 patients were included in the study: 898 (55.5%) women and 721 (44.5%) men. Age was similar between women and men. Women had fewer comorbidities but worse cardiac function than men. The rate of primary outcomes was lower in women than in men (18.4 vs. 27.5%; p < 0.001), including rate of CV mortality (8.9 vs. 14.8%; p < 0.001) and HF-related hospitalization (13.4 vs. 18.2%; p = 0.008). All-cause mortality was also lower in women than in men (15.6 vs. 25.4%; p < 0.001). After adjustment for baseline characteristics, Cox regression analysis showed that female sex was a protective factor for CV mortality [hazard ratio (HR): 0.53; 95% confidence interval (CI): 0.40–0.73], HF-related hospitalization (HR: 0.71; 95% CI: 0.55–0.93), and all-cause mortality (HR: 0.59; 95% CI: 0.47–0.75). Although spironolactone significantly reduced the rate of all-cause mortality in women even after adjusting for baseline characteristics (HR: 0.68; 95% CI: 0.48–0.96; p = 0.028), no significant multivariate association was noted between sex and treatment effects (p = 0.190). Conclusion: Among elderly patients with HFpEF, women had worse cardiac function but better survival and lower HF-related hospitalization rate than men. Clinical Trial Registration: NCT00094302 (TOPCAT). Registered October 15, 2004, https://www.clinicaltrials. gov/ct2/show/NCT00094302.
Ferroptosis-Related Genes in Bronchoalveolar Lavage Fluid Serves as Prognostic Biomarkers for Idiopathic Pulmonary Fibrosis

Background: Idiopathic pulmonary fibrosis (IPF) is a chronic progressive disease with unknown etiology and unfavorable prognosis. Ferroptosis is a form of regulated cell death with an iron-dependent way that is involved in the development of various diseases. Whereas the prognostic value of ferroptosis-related genes (FRGs) in IPF remains uncertain and needs to be further elucidated. Methods: The FerrDb database and the previous studies were screened to explore the FRGs. The data of patients with IPF were obtained from the GSE70866 dataset. Wilcoxon's test and univariate Cox regression analysis were applied to identify the FRGs that are differentially expressed between normal and patients with IPF and associated with prognosis. Next, a multigene signature was constructed by the least absolute shrinkage and selection operator (LASSO)-penalized Cox model in the training cohort and evaluated by using calibration and receiver operating characteristic (ROC) curves. Then, 30% of the dataset samples were randomly selected for internal validation. Finally, the potential function and pathways that might be affected by the risk score-related differently expressed genes (DEGs) were further explored. Results: A total of 183 FRGs were identified by the FerrDb database and the previous studies, and 19 of them were differentially expressed in bronchoalveolar lavage fluid (BALF) between IPF and healthy controls and associated with prognosis (p < 0.05). There were five FRGs (aconitase 1 [ACO1], neuroblastoma RAS viral (v-ras) oncogene homolog [NRAS], Ectonucleotide pyrophosphatase/phosphodiesterase 2 [ENPP2], Mucin 1 [MUC1], and ZFP36 ring finger protein [ZFP36]) identified as risk signatures and stratified patients with IPF into the two risk groups. The overall survival rate in patients with high risk was significantly lower than that in patients with low risk (p < 0.001). The calibration and ROC curve analysis confirmed the predictive capacity of this signature, and the results were further verified in the validation group. Risk score-related DEGs were found enriched in ECM-receptor interaction and focal adhesion pathways. Conclusion: The five FRGs in BALF can be used for prognostic prediction in IPF, which may contribute to improving the management strategies of IPF.
Scorpion Venom Heat-Resistant Peptide Attenuates Microglia Activation and Neuroinflammation

Background: Intervention of neuroinflammation in central nervous system (CNS) represents a potential therapeutic strategy for a host of brain disorders. The scorpion Buthus martensii Karsch (BmK) and its venom have long been used in the Orient to treat inflammation-related diseases such as rhumatoid arthritis and chronic pain. Scorpion venom heat-resistant peptide (SVHRP), a component from BmK venom, has been shown to reduce seizure susceptibility in a rat epileptic model and protect against cerebral ischemia-reperfusion injury. As neuroinflammation has been implicated in chronic neuronal hyperexcitability, epileptogenesis and cerebral ischemia-reperfusion injury, the present study aimed to investigate whether SVHRP has anti-inflammatory property in brain. Methods: An animal model of neuroinflammation induced by lipopolysacchride (LPS) injection was employed to investigate the effect of SVHRP (125 µg/kg, intraperitoneal injection) on inflammagen-induced expression of pro-inflammatory factors and microglia activation. The effect of SVHRP (2–20 μg/ml) on neuroinflammation was further investigated in primary brain cell cultures containing microglia as well as the immortalized BV2 microglia culture stimulated with LPS. Real-time quantitative PCR were used to measure mRNA levels of inducible nitric oxide synthase (iNOS), tumor necrosis factor-α (TNF-α), interleukin (IL)-1β and IL-6 in hippocampus of animals. Protein levels of TNF-α, iNOS, P65 subunit of nuclear factor-κB (NF-κB) and mitogen-activated protein kinases (MAPKs) were examined by ELISA or western blot. Microglia morphology in animal hippocampus or cell cultures and cellular distribution of p65 were shown by immunostaining. Results: Morphological study demonstrated that activation of microglia, the main component that mediates the neuroinflammatory process, was inhibited by SVHRP in both LPS mouse and cellular model. Our results also showed dramatic increases in the expression of iNOS and TNF-α in hippocampus of LPS-injected mice, which was significantly attenuated by SVHRP treatment. In vitro results showed that SVHRP attenuated LPS-elicited expression of iNOS and TNF-α in different cultures without cell toxicity, which might be attributed to suppression of NF-κB and MAPK pathways by SVHRP. Conclusion: Our study demonstrates that SVHRP is able to inhibit neuroinflammation and microglia activation, which may underlie the therapeutic effects of BmK-derived materials, suggesting that BmK venom could be a potential source for CNS drug development.
Key Bioturbator Species Within Benthic Communities Determine Sediment Resuspension Thresholds

Abundant research has shown that macrobenthic species are able to increase sediment erodibility through bioturbation. So far, however, this has been at the level of individual species. Consequently, we lack understanding on how such species effects act on the level of bioturbator communities. We assessed the isolated and combined effects of three behaviorally contrasting macrobenthic species, i.e., Corophium volutator, Hediste diversicolor, and Limecola balthica, at varying densities on the critical bed shear stress for sediment resuspension (τcr). Overall, the effect of a single species on sediment erodibility could be described by a power function, indicating a relatively large effect of small bioturbator densities which diminishes toward higher individual density. In contrast to previous studies, our results could not be generalized between species using total metabolic rate, indicating that metabolic rate may be only suitable to integrate bioturbation effects within and between closely related species; highly contrasting species require consideration of species-specific bioturbation strategies. Experiments at the benthic community level revealed that the ability of a benthic community to reduce τcr is mainly determined by the species that has the largest individual effect in reducing τcr, as opposed to the species that is dominant in terms of metabolic rate. Hence, to predict and accurately model the net effect of bioturbator communities on the evolution of tidal flats and estuaries, identification of the key bioturbating species with largest effects on τcr and their spatial distribution is imperative. Metabolic laws may be used to describe their actual activity.
Interactions Among Nerve Regeneration, Angiogenesis, and the Immune Response Immediately After Sciatic Nerve Crush Injury in Sprague-Dawley Rats

To preliminarily explore the primary changes in the expression of genes involved in peripheral nerve processes, namely, regeneration, angiogenesis, and the immune response, and to identify important molecular therapeutic targets, 45 Sprague-Dawley (SD) rats were randomly divided into a control group and an injury group. In the injury group, tissue samples were collected at 4 and 7 days after the injury for next-generation sequencing (NGS) analysis combined with gene ontology (GO) analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis and Venn diagram construction to identify the differentially expressed mRNAs (DEmRNAs) associated with regeneration, angiogenesis, and the immune response of the nerve. The expression of genes in the distal and proximal ends of the injured nerve after injury was analyzed by qRT-PCR. NGS revealed that compared with the control group, the injury group had 4020 DEmRNAs 4 days after injury and 3278 DEmRNAs 7 days after injury. A bioinformatics analysis showed that C-C chemokine receptor type 5 (CCR5), Thy1 cell surface antigen (Thy1), Notch homolog 1 (Notch1), and semaphorin 4A (Sema4A) were all associated with regeneration, angiogenesis, and the immune response of the nerve at both 4 and 7 days after injury, but qPCR revealed no significant difference in the expression of Thy1 (P = 0.29) or Sema4A (P = 0.82) in the proximal end, whereas a significant difference was observed in CCR5 and Notch1 (P < 0.05). The trend in the Notch1 change was basically consistent with the RNA-seq result after injury, which implied its indispensable role during endothelial cell proliferation and migration, macrophage recruitment, and neurotrophic factor secretion.
Real-Time Shape Estimation for Concentric Tube Continuum Robots with a Single Force/Torque Sensor

Shape-sensing in real-time is a key requirement for the development of advanced algorithms for concentric tube continuum robots when safe interaction with the environment is important e.g., for path planning, advanced control, and human-machine interaction. We propose a real-time shape-estimation algorithm for concentric tube continuum robots based on the force-torque information measured at the tubes’ basis. It extends a shape estimation algorithm for elastic rods based on discrete Kirchhoff rod theory. For simplicity and efficiency of calculation, we combine it with a model under piece-wise constant curvature assumption, in which we model a concentric tube continuum robot as a combination of segments of planar constant curvatures lying on different equilibrium planes. We evaluate our approach for a single and two combined additively manufactured tubes and achieve an estimation frequency of 333 Hz for two combined tubes with a mean deviation along the backbone of the tubes of 1.91–5.22 mm.
Identification of Candidate Olfactory Genes in Scolytus schevyrewi Based on Transcriptomic Analysis

The bark beetle, Scolytus schevyrewi (S. schevyrewi), is an economically important pest in China that causes serious damage to the fruit industry, particularly, in Xinjiang Province. Chemical signals play an important role in the behavior of most insects, accordingly, ecofriendly traps can be used to monitor and control the target pests in agriculture. In order to lay a foundation for future research on chemical communication mechanisms at the molecular level, we generate antennal transcriptome databases for male and female S. schevyrewi using RNA sequencing (RNA-seq) analysis. By assembling and analyzing the adult male and female antennal transcriptomes, we identified 47 odorant receptors (ORs), 22 ionotropic receptors (IRs), 22 odorant-binding proteins (OBPs), and 11 chemosensory proteins (CSPs). Furthermore, expression levels of all the candidate OBPs and CSPs were validated in different tissues of male and female adults by semiquantitative reverse transcription PCR (RT-PCR). ScosOBP2 and ScosOBP18 were highly expressed in female antennae. ScosCSP2, ScosCSP3, and ScosCSP5 were specifically expressed in the antennae of both males and females. These results provide new potential molecular targets to inform and improve future management strategies of S. schevyrewi.