Miracle-dz/UniFAR-FTUs huggingface dataset:
Deep CNN for Indoor Localization in IoT-Sensor Systems

Currently, indoor localization is among the most challenging issues related to the Internet of Things (IoT). Most of the state-of-the-art indoor localization solutions require a high computational complexity to achieve a satisfying localization accuracy and do not meet the memory limitations of IoT devices. In this paper, we develop a localization framework that shifts the online prediction complexity to an offline preprocessing step, based on Convolutional Neural Networks (CNN). Motivated by the outstanding performance of such networks in the image classification field, the indoor localization problem is formulated as 3D radio image-based region recognition. It aims to localize a sensor node accurately by determining its location region. 3D radio images are constructed based on Received Signal Strength Indicator (RSSI) fingerprints. The simulation results justify the choice of the different parameters, optimization algorithms, and model architectures used. Considering the trade-off between localization accuracy and computational complexity, our proposed method outperforms other popular approaches.
Assessment of the Dose–Response Relationship between Meal Protein Content and Postprandial Thermogenesis: Effect of Sex and the Oral Contraceptive Pill

Implementation of efficacious dietary interventions to regulate energy balance requires understanding of the determinants of individual response. To date, information regarding individual variability in response to elevated meal protein content is lacking. This study investigates whether sex and/or oral contraceptive pill (OCP) use play a role in the response to elevated meal protein in 21 healthy young adults (seven men, seven women not taking OCP, and seven women who were OCP users). Participants consumed each of three standardized isocaloric (590 kcal) meals of differing protein content (11, 23, 31% kcal protein). Resting energy expenditure (EE), respiratory quotient (RQ), hunger and satiety were measured at baseline (fasting) and during 180 min postprandial. Whilst significant dose–response increases in EE were observed in men, meal protein-induced EE in women without OCP reached a maximum at <23% protein. Women taking OCP reported lower postprandial fullness than women without OCP, despite similar body size, but also, most notably, no significant difference in EE response between any of the meals. Whilst the mechanisms underpinning this thermogenic inflexibility in response across a wide-range (three-fold) of protein meal content require further investigation, this highlights the need for careful consideration of factors that may influence an individual’s metabolic response to dietary interventions aimed at optimising postprandial thermogenesis for body weight regulation.
Spindle-shaped viruses infect marine ammonia-oxidizing thaumarchaea

Significance Ammonia-oxidizing archaea (AOA) are major players in global nitrogen cycling. The physicochemical and metabolic factors affecting the composition of AOA communities and their efficiency of resource utilization have been studied extensively. However, viral predation on AOA remains unexplored due to lack of isolated virus–host systems. Here we report on the isolation and characterization of three Nitrosopumilus spindle-shaped viruses (NSVs) that infect AOA hosts. NSVs represent a potentially important group of marine viruses with a chronic infection cycle, providing important insights into the diversity and evolution of the archaeal virosphere. The wide spread of NSVs in AOA-containing marine environments suggests that NSV predation might regulate the diversity and dynamics of AOA communities, thereby affecting the carbon and nitrogen cycling. Ammonia-oxidizing archaea (AOA) from the phylum Thaumarchaeota are ubiquitous in marine ecosystems and play a prominent role in carbon and nitrogen cycling. Previous studies have suggested that, like all microbes, thaumarchaea are infected by viruses and that viral predation has a profound impact on thaumarchaeal functioning and mortality, thereby regulating global biogeochemical cycles. However, not a single virus capable of infecting thaumarchaea has been reported thus far. Here we describe the isolation and characterization of three Nitrosopumilus spindle-shaped viruses (NSVs) that infect AOA and are distinct from other known marine viruses. Although NSVs have a narrow host range, they efficiently infect autochthonous Nitrosopumilus strains and display high rates of adsorption to their host cells. The NSVs have linear double-stranded DNA genomes of ∼28 kb that do not display appreciable sequence similarity to genomes of other known archaeal or bacterial viruses and could be considered as representatives of a new virus family, the “Thaspiviridae. ” Upon infection, NSV replication leads to inhibition of AOA growth, accompanied by severe reduction in the rate of ammonia oxidation and nitrite reduction. Nevertheless, unlike in the case of lytic bacteriophages, NSV propagation is not associated with detectable degradation of the host chromosome or a decrease in cell counts. The broad distribution of NSVs in AOA-dominated marine environments suggests that NSV predation might regulate the diversity and dynamics of AOA communities. Collectively, our results shed light on the diversity, evolution, and potential impact of the virosphere associated with ecologically important mesophilic archaea.
Benchmark dose estimation of urinary and blood cadmium as biomarkers of renal dysfunction among 40‐75‐year‐old non‐smoking women in rural areas of southwest China

This study evaluated the association between urinary cadmium (U‐Cd) and blood Cd (B‐Cd) and several biomarkers of renal dysfunction (α1‐microglobulin [α1‐MG], β2‐microglobulin [β2‐MG], N‐acetyl‐β‐d‐glucosaminidase, metallothionein, retinol‐binding protein and microalbumin [mALB]) and identified the biomarker(s) that was most closely correlated with U‐Cd and B‐Cd among female residents in rural areas of southwest China. U‐Cd, creatinine (Cr), B‐Cd and the above‐mentioned six biomarkers in morning spot urine samples were measured from 288 randomly selected 40‐75‐year‐old non‐smoking women from non‐polluted areas and Cd‐polluted‐areas. The lower 95% confidence limit of the benchmark dose (BMD) corresponding to the 5% (BMDL05) and 10% benchmark response (BMDL10) was calculated with assumed cut‐off values of the 95th and 90th percentile. Among the investigated women, a significant positive association was found among mALB, β2‐MG and U‐Cd as well as B‐Cd. By using the cut‐off value of the 95th percentile, the BMDL05/BMDL10 of U‐Cd and B‐Cd were 4.33/8.89 μg/g Cr for mALB and 1.35/2.77 μg/L for β2‐MG, respectively. The BMDL05/BMDL10 of U‐Cd (B‐Cd) was 2.73/5.60 μg/g Cr (1.00/2.05 μg/L) for mALB, if the cut‐off value was set at the 90th percentile. Therefore, β2‐MG and mALB in urine were good biomarkers for long‐term environmental Cd exposure assessment among the six biomarkers studied for the study pool in southwest China. Our findings may help us to understand the association between nephrotoxicity and Cd exposure, and aid in the decision‐making of authorities for environmental Cd pollution and public health.
Application of a MYC degradation screen identifies sensitivity to CDK9 inhibitors in KRAS-mutant pancreatic cancer

CDK9 inhibitors may treat KRAS-mutant cancers by inducing MYC protein degradation. Screening tumor vulnerability Mutations in the gene encoding the guanosine triphosphatase KRAS are common drivers of various cancers. Because most mutant KRAS proteins are currently too difficult to therapeutically target, alternative targets in KRAS-mutant tumors must be identified. Given a previous observation that KRAS-mutant pancreatic cancers (PDACs) rely on the transcription factor MYC, Blake et al. screened for inhibitors that decreased MYC protein abundance. They found that an inhibitor of the cell cycle–associated kinase CDK9 decreased MYC abundance at both the mRNA and protein levels in a manner independent of KRAS signaling itself. This finding reveals a potential therapeutic target for patients with KRAS-mutant PDAC and possibly also those with more generally MYC-dependent cancers. Stabilization of the MYC oncoprotein by KRAS signaling critically promotes the growth of pancreatic ductal adenocarcinoma (PDAC). Thus, understanding how MYC protein stability is regulated may lead to effective therapies. Here, we used a previously developed, flow cytometry–based assay that screened a library of >800 protein kinase inhibitors and identified compounds that promoted either the stability or degradation of MYC in a KRAS-mutant PDAC cell line. We validated compounds that stabilized or destabilized MYC and then focused on one compound, UNC10112785, that induced the substantial loss of MYC protein in both two-dimensional (2D) and 3D cell cultures. We determined that this compound is a potent CDK9 inhibitor with a previously uncharacterized scaffold, caused MYC loss through both transcriptional and posttranslational mechanisms, and suppresses PDAC anchorage-dependent and anchorage-independent growth. We discovered that CDK9 enhanced MYC protein stability through a previously unknown, KRAS-independent mechanism involving direct phosphorylation of MYC at Ser62. Our study thus not only identifies a potential therapeutic target for patients with KRAS-mutant PDAC but also presents the application of a screening strategy that can be more broadly adapted to identify regulators of protein stability.
glypy - An open source glycoinformatics library.

Glycoinformatics is a critical resource for the study of glycobiology, and glycobiology is a necessary component for understanding the complex interface between intra- and extra-cellular spaces. Despite this, there is limited software available to scientists studying these topics, requiring each to create fundamental data structures and representations anew for each of their applications. This leads to poor uptake of standardization and loss of focus on the real problems. We present glypy, a library written in Python for reading, writing, manipulating, and transforming glycans at several levels of precision. In addition to understanding several standardized formats for textual representation of glycans, the library also provides APIs for major community database, including GlyTouCan and UnicarbKB. The library is freely available under the Apache 2 common license, with source code available at https://github.com/mobiusklein/glypy and documentation at https://glypy.readthedocs. io.
Characterization of epidermal growth factor receptor (EGFR) P848L, an unusual EGFR variant present in lung cancer patients, in a murine Ba/F3 model

Lung cancer patients with mutations in epidermal growth factor receptor (EGFR) benefit from treatments targeting tyrosine kinase inhibitors (TKIs). However, both intrinsic and acquired resistance of tumors to TKIs are common, and EGFR variants have been identified that are resistant to multiple TKIs. In the present study, we characterized selected EGFR variants previously observed in lung cancer patients and expressed in a murine bone marrow pro‐B Ba/F3 cell model. Among these EGFR variants, we report that an exon 20 deletion/insertion mutation S768insVGH is resistant to erlotinib (a first‐generation TKI), but sensitive to osimertinib (a third‐generation TKI). We also characterized a rare exon 21 germline variant, EGFR P848L, which transformed Ba/F3 cells and conferred resistance to multiple EGFR‐targeting TKIs. Our analysis revealed that P848L (a) does not bind erlotinib; (b) is turned over less rapidly than L858R (a common tumor‐derived EGFR mutation); (c) is not autophosphorylated at Tyr 1045 [the major docking site for Cbl proto‐oncogene (c‐Cbl) binding]; and (d) does not bind c‐Cbl. Using viability assays including 300 clinically relevant targeted compounds, we observed that Ba/F3 cells transduced with EGFR P848L, S768insVGH, or L858R have very different drug‐sensitivity profiles. In particular, EGFR P848L, but not L858R or S768insVGH, was sensitive to multiple Janus kinase 1/2 inhibitors. In contrast, cells driven by L858R, but not by P848L, were sensitive to multikinase MAPK/extracellular‐signal‐regulated kinase (ERK) kinase and ERK inhibitors including EGFR‐specific TKIs. These observations suggest that continued investigation of rare TKI‐resistant EGFR variants is warranted to identify optimal treatments for cancer.
Development and Applications of Superfolder and Split Fluorescent Protein Detection Systems in Biology

Molecular engineering of the green fluorescent protein (GFP) into a robust and stable variant named Superfolder GFP (sfGFP) has revolutionized the field of biosensor development and the use of fluorescent markers in diverse area of biology. sfGFP-based self-associating bipartite split-FP systems have been widely exploited to monitor soluble expression in vitro, localization, and trafficking of proteins in cellulo. A more recent class of split-FP variants, named « tripartite » split-FP, that rely on the self-assembly of three GFP fragments, is particularly well suited for the detection of protein–protein interactions. In this review, we describe the different steps and evolutions that have led to the diversification of superfolder and split-FP reporter systems, and we report an update of their applications in various areas of biology, from structural biology to cell biology.
Childhood otitis media: Relationship with daycare attendance, harsh parenting, and maternal mental health

Psychological stress has been linked to developmental problems and poor health in children, but it is unclear whether it is also related to otitis media (OM). As part of a long-term study surveying the characteristics of childcare and development in Taiwan, we analyzed the relationship between OM and sources of psychological stress in children, such as poor maternal mental health and harsh parental discipline. We analyzed the data of 1998 children from the “Kids in Taiwan: National Longitudinal Study of Child Development & Care (KIT) Project” at the age of 3 years. Using bivariate and multivariate logistic regression models, we tested several risk factors as potential independent predictors of two outcomes: parent-reported incidence of OM and child health. The proportion of children who had developed OM in the first 3 years of their life was 12.5%. Daycare attendance (odds ratio [OR]: 1.475; 95% confidence interval [CI]: 1.063–2.046), poor maternal mental health (OR: 1.913; 95% CI: 1.315–2.784), and harsh parental discipline (OR: 1.091; 95% CI: 1.025–1.161) correlated with parent-reported occurrence of OM. These findings suggest that providing psychosocial support to both parents and children might be a novel strategy for preventing OM.
Therapy of 125I particles implantation inhibited the local growth of advanced non-small cell lung cancer: a retrospective clinical study.

BACKGROUND The aim of this study was to investigate the efficacy and safety of 125I particle implantation for treating advanced non-small cell lung cancer (NSCLC). METHODS Data from 56 patients with advanced NSCLC between January 2013 and May 2016 were retrospectively analyzed. The changes of tumor size, objective response rate (ORR), disease control rate (DCR), survival rate of patients and occurrence rate of complications were calculated, and the levels of carcinoembryonic antigen (CEA) and cytokerantin-19-fragment (CYFRA21-1) before and after the treatment were evaluated. RESULTS The 125I particles implantation therapy significantly inhibited the tumor local growth of NSCLC (from 7.75±6.69 to 3.39±2.12 cm) (P<0.001), suggesting a better effectiveness with an RR of 55.4% and DCR of 98.2%. In addition, the 125I particle implantation down-regulated the CEA expression level of lung adenocarcinoma (LAC) patients (P<0.05). The one-year, two-year, three-year survival rate were 41.1%, 39.3% and 19.6% respectively after the implantation therapy. However, patients implanted 125I particles had no serious complications except for slight fever. CONCLUSIONS NSCLC patients at different clinical features all can benefit from the 125I particle implantation therapy. Moreover, the level of CEA can be used as an efficacy predictor for the 125I particle implantation therapy for LAC.
Integration of Phenotype and Hormone Data during Adventitious Rooting in Carnation (Dianthus caryophyllus L.) Stem Cuttings

The rooting of stem cuttings is a highly efficient procedure for the vegetative propagation of ornamental plants. In cultivated carnations, an increased auxin level in the stem cutting base produced by active auxin transport from the leaves triggers adventitious root (AR) formation from the cambium. To provide additional insight into the physiological and genetic basis of this complex trait, we studied AR formation in a collection of 159 F1 lines derived from a cross between two hybrid cultivars (2003 R 8 and 2101-02 MFR) showing contrasting rooting performances. In three different experiments, time-series for several stem and root architectural traits were quantified in detail in a subset of these double-cross hybrid lines displaying extreme rooting phenotypes and their parental genotypes. Our results indicate that the water content and area of the AR system directly contributed to the shoot water content and shoot growth. Moreover, morphometric data and rooting quality parameters were found to be associated with some stress-related metabolites such as 1-aminocyclopropane-1-carboxylic acid (ACC), the ethylene precursor, and the conjugated auxin indol-3-acetic acid-aspartic acid (IAA-Asp).
Essential Oil of Algerian Eryngium campestre: Chemical Variability and Evaluation of Biological Activities

The chemical composition of essential oils extracted from aerial parts of Eryngium campestre collected in 37 localities from Western Algeria was characterized using GC-FID and GC/MS analyses. Altogether, 52 components, which accounted for 70.1 to 86.8% of the total composition oils were identified. The main compounds were Germacrene D (0.4–53.4%), Campestrolide (1.6–35.3%), Germacrene B (0.2–21.5%), Myrcene (0.1–8.4%), α-Cadinol (0.2–7.6%), Spathulenol (0.1–7.6%), Eudesma-4(15)-7-dien-1-β-ol (0.1–7.6%) and τ-Cadinol (0.3–5.5%). The chemical compositions of essential oils obtained from separate organs and during the complete vegetative cycle of the plant were also studied. With the uncommon 17-membered ring lactone named Campestrolide as the main component, Algerian E. campestre essential oils exhibited a remarkable chemical composition. A study of the chemical variability using statistical analysis allowed the discrimination of two main clusters according to the geographical position of samples. The study contributes to the better understanding of the relationship between the plant and its environment. Moreover, the antimicrobial activity of the essential oil was assessed against twelve strains bacteria and two yeasts involved in foodborne and nosocomial infections using paper disc diffusion and dilution agar assays. The in vitro study demonstrated a strong activity against Gram-positive strains such as S. aureus, B. cereus, and E. faecalis. The cytotoxicity and antiparasitic activities (on Lmm and Tbb) of the collective essential oil and one sample rich in campestrolide, as well as some enriched fractions or fractions containing other terpenic compounds, were also analyzed. Campestrolide seems to be one compound responsible for the cytotoxic and antileishmanial effect, while myrcene or/and trans-β-farnesene have a more selective antitrypanosomal activity.
Structural Differences Influence Biological Properties of Glucosylceramides from Clinical and Environmental Isolates of Scedosporium aurantiacum and Pseudallescheria minutispora

Scedosporium/Lomentospora complex is composed of filamentous fungi, including some clinically relevant species, such as Pseudallescheria boydii, Scedosporium aurantiacum, and Scedosporium apiospermum. Glucosylceramide (GlcCer), a conserved neutral glycosphingolipid, has been described as an important cell surface molecule playing a role in fungal morphological transition and pathogenesis. The present work aimed at the evaluation of GlcCer structures in S. aurantiacum and Pseudallescheria minutispora, a clinical and an environmental isolate, respectively, in order to determine their participation in fungal growth and host-pathogen interactions. Structural analysis by positive ion-mode ESI-MS (electrospray ionization mass spectrometer) revealed the presence of different ceramide moieties in GlcCer in these species. Monoclonal antibodies against Aspergillus fumigatus GlcCer could recognize S. aurantiacum and P. minutispora conidia, suggesting a conserved epitope in fungal GlcCer. In addition, these antibodies reduced fungal viability, enhanced conidia phagocytosis by macrophages, and decreased fungal survival inside phagocytic cells. Purified GlcCer from both species led to macrophage activation, increasing cell viability as well as nitric oxide and superoxide production in different proportions between the two species. These results evidenced some important properties of GlcCer from species of the Scedosporium/Lomentospora complex, as well as the effects of monoclonal anti-GlcCer antibodies on fungal cells and host-pathogen interaction. The differences between the two species regarding the observed biological properties suggest that variation in GlcCer structures and strain origin could interfere in the role of GlcCer in host-pathogen interaction.
Quality of Life Associated Factors in a North African Sample of Lower Limbs Amputees

Objective To study factors associated to the quality of life in a North African sample of lower limbs amputees. Methods We conducted a prospective study in the Department Physical Medicine and Rehabilitation, University Hospital of Monastit, Tunisia. A consecutive sample of patients with amputations of the lower limbs was included. The evaluated parameters were quality of life using the Short-Form quality-of-life questionnaire (SF-36), pain using a visual analog scale, function using, the perimeter of walking (PW), the Special Interest Group of the Amputee Medicine (SIGAM) and the Locomotion Capacities Index of the Prosthetic Profile of the Amputee (LCI), and psychological status thanks to the Hospital Anxiety and Depression scale. In the study, the patients were evaluated at the first consultation (T0) and again at 12 months (T1). Results We included 85 patients (age, 59.3±16.7 years) with a sex ratio of 3. The patient quality of life was positively correlated to distal type of amputation, traumatic origin, better LCI (p≤0.001, r=0.349), SIGAM (p=0.046) and PW. A negative correlation was noted with age (p=0.012, r=-0.483) and higher psychological scores (p=0.002, r=-0.321). Conclusion In our sample of North African lower limbs amputees the age and the functional status were the most important predictors of the quality of life.
Effects of the instrument response function and the gate width in time-domain diffuse correlation spectroscopy: model and validations

Abstract. Time-domain diffuse correlation spectroscopy (TD-DCS) is an emerging noninvasive optical technique with the potential to resolve blood flow (BF) and optical coefficients (reduced scattering and absorption) in depth. Here, we study the effects of finite temporal resolution and gate width in a realistic TD-DCS experiment. We provide a model for retrieving the BF from gated intensity autocorrelations based on the instrument response function, which allows for the use of broad time gates. This, in turn, enables a higher signal-to-noise ratio that is critical for in vivo applications. In numerical simulations, the use of the proposed model reduces the error in the estimated late gate BF from 34% to 3%. Simulations are also performed for a wide set of optical properties and source–detector separations. In a homogeneous phantom experiment, the discrepancy between later gates BF index and ungated BF index is reduced from 37% to 2%. This work not only provides a tool for data analysis but also physical insights, which can be useful for studying and optimizing the system performance.