Miracle-dz/UniFAR-FTUs huggingface dataset:
Status and Epidemiology of Maize Lethal Necrotic Disease in Northern Tanzania

Sustainable control of plant diseases requires a good understanding of the epidemiological aspects such as the biology of the causal pathogens. In the current study, we used RT-PCR and Next Generation Sequencing (NGS) to contribute to the characterization of maize lethal necrotic (MLN) viruses and to identify other possible viruses that could represent a future threat in maize production in Tanzania. RT-PCR screening for Maize Chlorotic Mottle Virus (MCMV) detected the virus in the majority (97%) of the samples (n = 223). Analysis of a subset (n = 48) of the samples using NGS-Illumina Miseq detected MCMV and Sugarcane Mosaic Virus (SCMV) at a co-infection of 62%. The analysis further detected Maize streak virus with an 8% incidence in samples where MCMV and SCMV were also detected. In addition, signatures of Maize dwarf mosaic virus, Sorghum mosaic virus, Maize yellow dwarf virus-RMV and Barley yellow dwarf virus were detected with low coverage. Phylogenetic analysis of the viral coat protein showed that isolates of MCMV and SCMV were similar to those previously reported in East Africa and Hebei, China. Besides characterization, we used farmers’ interviews and direct field observations to give insights into MLN status in different agro-ecological zones (AEZs) in Kilimanjaro, Mayara, and Arusha. Through the survey, we showed that the prevalence of MLN differed across regions (P = 0.0012) and villages (P < 0.0001) but not across AEZs (P > 0.05). The study shows changing MLN dynamics in Tanzania and emphasizes the need for regional scientists to utilize farmers’ awareness in managing the disease.
Magnetic Silica-Coated Iron Oxide Nanochains as Photothermal Agents, Disrupting the Extracellular Matrix, and Eradicating Cancer Cells

Cancerous cells and the tumor microenvironment are among key elements involved in cancer development, progression, and resistance to treatment. In order to tackle the cells and the extracellular matrix, we herein propose the use of a class of silica-coated iron oxide nanochains, which have superior magnetic responsiveness and can act as efficient photothermal agents. When internalized by different cancer cell lines and normal (non-cancerous) cells, the nanochains are not toxic, as assessed on 2D and 3D cell culture models. Yet, upon irradiation with near infrared light, the nanochains become efficient cytotoxic photothermal agents. Besides, not only do they generate hyperthermia, which effectively eradicates tumor cells in vitro, but they also locally melt the collagen matrix, as we evidence in real-time, using engineered cell sheets with self-secreted extracellular matrix. By simultaneously acting as physical (magnetic and photothermal) effectors and chemical delivery systems, the nanochain-based platforms offer original multimodal possibilities for prospective cancer treatment, affecting both the cells and the extracellular matrix.
Extending the Battery Life of the ZigBee Routers and Coordinator by Modifying Their Mode of Operation

Wireless sensor networks proliferate more and more in all social scopes and sectors. Such networks are implemented in smart homes, smart cities, security systems, medical resources, agriculture, automotive industry, etc. Communication devices and sensors of such networks are powered with batteries: the enlarging of battery life is a hot research topic. We focus on wireless sensor networks based on ZigBee technology. While sleep standard operation mode is defined for end devices, it is not the case for the rest of devices (routers and Coordinator), which usually always remain in active mode. We designed a formal optimization model for maximizing the enlarging of the battery life of routers and Coordinator, allowing us to delimit practical successful conditions. It was successfully tested with a standard ZigBee datasheet comprising technical data for sensors, routers, and coordinators. It was tested in a practical wireless sensor network assembly with XBee S2C devices. We derived, from the previous model, a novel but simple protocol of communication among routers and coordinators. It was tested in different use cases. We showed that when end devices generate traffic at regular intervals, the enlarging of the battery life of routers and Coordinator was possible only under certain use cases.
Reduction of thrombotic and inflammatory complications of polystyrene-block-polyisoprene-block-polystyrene (SIS) with one-step electrospinning

Abstract Polystyrene-block-polyisoprene-block-polystyrene (SIS) has been used as biomaterials due to its soft and stable properties under physiological conditions. However, the thrombotic and inflammatory complications caused by SIS restrain its application as blood-contacting implant. To overcome this problem, the hydrophilic core-shell structured SIS-based microfiber with antioxidant encapsulation is fabricated with one-step reactive electrospinning. We demonstrate that the phase separation of SIS and acylated Pluronic F127 (F127-DA) components and crosslinking during electrospinning renders the microfiber blood compatible and stable under physiological condition; the encapsulation of 2-O-d-glucopyranosyl-l-ascorbic acid (AA-2G) in microfiber and subsequent release of AA-2G detoxifies the excess reactive oxygen species (ROS). The microfibers are nontoxic to cells and promote the fast growth and proliferation of human umbilical vein endothelial cells (HUVECs) in the presence of ROS; the thrombotic and inflammatory complications are effectively reduced with implant evaluation in vivo. Therefore, our work paves a new way to improve the biocompatibility of SIS, making it a promising candidate for blood contact materials.
Racial discrimination in medical care settings and opioid pain reliever misuse in a U.S. cohort: 1992 to 2015

Background In the United States whites are more likely to misuse opioid pain relievers (OPRs) than blacks, and blacks are less likely to be prescribed OPRs than whites. Our objective is to determine whether racial discrimination in medical settings is protective for blacks against OPR misuse, thus mediating the black-white disparities in OPR misuse. Methods We used data from 3528 black and white adults in the Coronary Artery Risk Development in Young Adults (CARDIA) study, an ongoing multi-site cohort. We employ causal mediation methods, with race (black vs white) as the exposure, lifetime discrimination in medical settings prior to year 2000 as the mediator, and OPR misuse after 2000 as the outcome. Results We found black participants were more likely to report discrimination in a medical setting (20.3% vs 0.9%) and less likely to report OPR misuse (5.8% vs 8.0%, OR = 0.71, 95% CI = 0.55, 0.93, adjusted for covariates). Our mediation models suggest that when everyone is not discriminated against, the disparity is wider with black persons having even lower odds of reporting OPR misuse (OR = 0.63, 95% CI = 0.45, 0.89) compared to their white counterparts, suggesting racial discrimination in medical settings is a risk factor for OPR misuse rather than protective. Conclusions These results suggest that racial discrimination in a medical setting is a risk factor for OPR misuse rather than being protective, and thus could not explain the seen black-white disparity in OPR misuse.
Comparison of quality control methods for automated diffusion tensor imaging analysis pipelines

The processing of brain diffusion tensor imaging (DTI) data for large cohort studies requires fully automatic pipelines to perform quality control (QC) and artifact/outlier removal procedures on the raw DTI data prior to calculation of diffusion parameters. In this study, three automatic DTI processing pipelines, each complying with the general ENIGMA framework, were designed by uniquely combining multiple image processing software tools. Different QC procedures based on the RESTORE algorithm, the DTIPrep protocol, and a combination of both methods were compared using simulated ground truth and artifact containing DTI datasets modeling eddy current induced distortions, various levels of motion artifacts, and thermal noise. Variability was also examined in 20 DTI datasets acquired in subjects with vascular cognitive impairment (VCI) from the multi-site Ontario Neurodegenerative Disease Research Initiative (ONDRI). The mean fractional anisotropy (FA), mean diffusivity (MD), axial diffusivity (AD), and radial diffusivity (RD) were calculated in global brain grey matter (GM) and white matter (WM) regions. For the simulated DTI datasets, the measure used to evaluate the performance of the pipelines was the normalized difference between the mean DTI metrics measured in GM and WM regions and the corresponding ground truth DTI value. The performance of the proposed pipelines was very similar, particularly in FA measurements. However, the pipeline based on the RESTORE algorithm was the most accurate when analyzing the artifact containing DTI datasets. The pipeline that combined the DTIPrep protocol and the RESTORE algorithm produced the lowest standard deviation in FA measurements in normal appearing WM across subjects. We concluded that this pipeline was the most robust and is preferred for automated analysis of multisite brain DTI data.
Hormone replacement therapy and lung cancer risk in women: a meta-analysis of cohort studies

Abstract Background: Discordant results about the causal relationship between hormone replacement therapy use (HRT) and lung cancer risk in women had been reported. We therefore conducted a meta-analysis of cohort studies to evaluate this association. Methods: The PubMed and Embase databases were searched. Fixed- or random-effects model was used to pool the study-specific relative risks (RRs) with corresponding 95% confidence intervals (CIs). Sensitivity analysis, publication bias, and subgroup analysis were performed. Results: A total of 13 cohort studies met the inclusion criteria. Combined results indicated that compared with nonusers, women with HRT use were at a decreased risk (RR: 0.95, 95% CI: 0.91-0.99, I2 = 30.8%, P for heterogeneity = .137). In subgroup analysis by geographic area, smoking statue, type of hormones, and histology type of lung cancer, no significant association between HRT use and lung cancer was observed in most subgroups except in those studies which reported risk estimates adjusted for age, body mass index, smoking, and other confounders (RR: 0.95, 95 CI: 0.91-0.99, I2 = 33.0%, P for heterogeneity = .214). Both Begg funnel plot and Egger test (P = .243) suggested no evidence for publication bias. Conclusion: Our meta-analysis suggests ever use of HRT is associated with a decreased risk of lung cancer in women.
Engineered Maturation Approaches of Human Pluripotent Stem Cell-Derived Ventricular Cardiomyocytes

Heart diseases such as myocardial infarction and myocardial ischemia are paroxysmal and fatal in clinical practice. Cardiomyocytes (CMs) differentiated from human pluripotent stem cells provide a promising approach to myocardium regeneration therapy. Identifying the maturity level of human pluripotent stem cell-derived cardiomyocytes (hPSC-CMs) is currently the main challenge for pathophysiology and therapeutics. In this review, we describe current maturity indicators for cardiac microtissue and microdevice cultivation technologies that accelerate cardiac maturation. It may provide insights into regenerative medicine, drug cardiotoxicity testing, and preclinical safety testing.
Bionic Upper Limb Reconstruction: A Valuable Alternative in Global Brachial Plexus Avulsion Injuries—A Case Series

Global brachial plexopathies including multiple nerve root avulsions may result in complete upper limb paralysis despite surgical treatment. Bionic reconstruction, which includes the elective amputation of the functionless hand and its replacement with a mechatronic device, has been described for the transradial level. Here, we present for the first time that patients with global brachial plexus avulsion injuries and lack of biological shoulder and elbow function benefit from above-elbow amputation and prosthetic rehabilitation. Between 2012 and 2017, forty-five patients with global brachial plexus injuries approached our centre, of which nineteen (42.2%) were treated with bionic reconstruction. While fourteen patients were amputated at the transradial level, the entire upper limb was replaced with a prosthetic arm in a total of five patients. Global upper extremity function before and after bionic arm substitution was assessed using two objective hand function tests, the action research arm test (ARAT), and the Southampton hand assessment procedure (SHAP). Other outcome measures included the DASH questionnaire, VAS to assess deafferentation pain and the SF-36 health survey to evaluate changes in quality of life. Using a hybrid prosthetic arm mean ARAT scores improved from 0.6 ± 1.3 to 11.0 ± 6.7 (p = 0.042) and mean SHAP scores increased from 4.0 ± 3.7 to 13.8 ± 9.2 (p = 0.058). After prosthetic arm replacement mean DASH scores improved from 52.5 ± 9.4 to 31.2 ± 9.8 (p = 0.003). Deafferentation pain decreased from mean VAS 8.5 ± 1.0 to 6.7 ± 2.1 (p = 0.055), while the physical and mental component summary scale as part of the SF-36 health survey improved from 32.9 ± 6.4 to 40.4 ± 9.4 (p = 0.058) and 43.6 ± 8.9 to 57.3 ± 5.5 (p = 0.021), respectively. Bionic reconstruction can restore simple but robust arm and hand function in longstanding brachial plexus patients with lack of treatment alternatives.
Dynamic time warping-based transfer learning for improving common spatial patterns in brain–computer interface

Objective. Common spatial patterns (CSP) is a prominent feature extraction algorithm in motor imagery (MI)-based brain–computer interfaces (BCIs). However, CSP is computed using sample-based covariance-matrix estimation. Hence, its performance deteriorates if the number of training trials is small. To address this problem, this paper proposes a novel regularized covariance matrix estimation framework for CSP (i.e. DTW-RCSP) based on dynamic time warping (DTW) and transfer learning. Approach. The proposed framework combines the subject-specific covariance matrix () estimated using the available trials from the new subject, with a novel DTW-based transferred covariance matrix () estimated using previous subjects’ trials. In the proposed , the available labelled trials from the previous subjects are temporally aligned to the average of the available trials of the new subject from the same class using DTW. This alignment aims to reduce temporal variations and non-stationarities between previous subjects’ trials and the available trials from the new subjects. Moreover, to tackle the problem of regularization parameter selection when only a few trials are available for training, an online method is proposed, where the best regularization parameter is selected based on the confidence scores of the trained classifier on the upcoming first few labelled testing trials. Main results. The proposed framework is evaluated on two datasets against two baseline algorithms. The obtained results reveal that DTW-RCSP significantly outperformed the baseline algorithms at various testing scenarios, particularly, when only a few trials are available for training. Significance. Impressively, our results show that successful BCI interactions could be achieved with a calibration session as small as only one trial per class.
Preparation of Calcipotriol Emulsion Using Bacterial Exopolysaccharides as Emulsifier for Percutaneous Treatment of Psoriasis Vulgaris

An exopolysaccharides/calcipotriol (EPS/CPT) emulsion was prepared using bacterial EPS as emulsifier, sunflower oil as an oil phase and CPT as the loaded drug, and the effect of this emulsion on psoriasis vulgaris treatment was evaluated. An EPS composed of mannose (70.56%) and glucose (29.44%) was obtained from the marine mangrove bacteria Bacillus amyloliquefaciens ZWJ (Zhu Wenjing) strain. The EPS has significant emulsifying activity at the concentration of 1.5%. The prepared EPS/CPT emulsion has small and stable particle size, with a drug content of 0.00492%, and good spreading properties. The in vitro drug release results revealed that the emulsion showed a certain sustained release effect. In vitro and in vivo animal experiments show that the EPS/CPT emulsion can effectively treat psoriasis vulgaris by increasing the accumulation of CPT in psoriatic skin lesions and reducing the levels of inflammatory cells and inflammatory factors (TNF and IL6). Additionally, it has a certain effect on reducing the side effects associated with CPT. This study lays a foundation for the research of EPS in the topical application of medical materials and treatment of psoriasis.
Valorization of Lignin as an Immobilizing Agent for Bioinoculant Production using Azospirillum brasilense as a Model Bacteria

Plant growth-promoting bacteria (PGPB) have been largely considered as beneficial in harsh and limiting environments given their effects on alleviating plant stress. For practical applications, most of the PGPB are prepared in immobilization matrices to improve the stability and benefits of bacteria. Despite the long list of immobilizing agents/carriers tested to date, a long list of desired requirements is yet to be achieved. Here, lignin stands as a scarcely tested immobilizer for bioinoculants with great potential for this purpose. The aim of this work was to demonstrate the feasibility of lignin as a carrier of the nitrogen-fixing Azospirillum brasilense. These bacteria were cultured in liquid media with recovered organosolv lignin added for bacterial immobilization. Then, lignin was recovered and the immobilized biomass was quantified gravimetrically by DNA extraction and serial dilution plating. Fluorescent microscopy as well as Congo red agar plating showed the immobilization of the bacterial cells in the lignin matrix and crystal violet dyeing showed the biofilms formation in lignin particles. A high number of cells were counted per gram of dried lignin. Lignin can be readily used as low-cost, health-safe bioinoculant carrier to be used in soil and agricultural applications.
Crossover interference and sex-specific genetic maps shape identical by descent sharing in close relatives

Simulations of close relatives and identical by descent (IBD) segments are common in genetic studies, yet most past efforts have utilized sex averaged genetic maps and ignored crossover interference, thus omitting features known to affect the breakpoints of IBD segments. We developed Ped-sim, a method for simulating relatives that can utilize either sex-specific or sex averaged genetic maps and also either a model of crossover interference or the traditional Poisson model for inter-crossover distances. To characterize the impact of previously ignored mechanisms, we simulated data for all four combinations of these factors. We found that modeling crossover interference decreases the standard deviation of the IBD proportion by 10.4% on average in full siblings through second cousins. By contrast, sex-specific maps increase this standard deviation by 4.2% on average, and also impact the number of segments relatives share. Most notably, using sex-specific maps, the number of segments half-siblings share is bimodal; and when combined with interference modeling, the probability that sixth cousins have non-zero IBD ranges from 9.0 to 13.1%, depending on the sexes of the individuals through which they are related. We present new analytical results for the distributions of IBD segments under these models and show they match results from simulations. Finally, we compared IBD sharing rates between simulated and real relatives and find that the combination of sex-specific maps and interference modeling most accurately captures IBD rates in real data. Ped-sim is open source and available from https://github.com/williamslab/ped-sim. Author summary Simulations are ubiquitous throughout statistical genetics in order to generate data with known properties, enabling tests of inference methods and analyses of real world processes in settings where experimental data are challenging to collect. Simulating genetic data for relatives in a pedigree requires the synthesis of chromosomes parents transmit to their children. These chromosomes form as a mosaic of a given parent’s two chromosomes, with the location of switches between the two parental chromosomes known as crossovers. Detailed information about crossover generation based on real data from humans now exists, including the fact that men and women have overall different rates (women produce ~1.6 times more crossovers) and that real crossovers are subject to interference—whereby crossovers are further apart from one another than expected under a model that selects their locations randomly. Our new method, Ped-sim, can simulate pedigree data using these less commonly modeled crossover features, and we used it to evaluate the importance of sex-specific rates and interference in real data. These comparisons show that both factors shape the amount of DNA two relatives share identically, and that their inclusion in models of crossover better fit data from real relatives.
Eriodictyol ameliorates lipopolysaccharide‐induced acute lung injury by suppressing the inflammatory COX‐2/NLRP3/NF‐κB pathway in mice

The purpose of this paper is to observe the protective action and its effective mechanism of eriodictyol on lipopolysaccharide (LPS)‐induced acute lung injury (ALI). In this study, our results indicated that eriodictyol could dramatically suppress the inflammatory mediators, including interleukin‐6 (IL‐6), IL‐1β, prostaglandin E2, and tumor necrosis factor‐α in bronchoalveolar lavage fluid of LPS‐challenged mice. Eriodictyol also alleviated the wet/dry ratio and improved pathological changes of the lung. In addition, eriodictyol significantly decreased myeloperoxidase activity and malondialdehyde content as well as increased superoxide dismutase activity. Moreover, eriodictyol inhibited the COX‐2/NLRP3/NF‐κB signaling pathway in the lung tissues of ALI mice. In conclusion, our observations validated that eriodictyol processed the protective effects on ALI mice, which was related to the regulation of the COX‐2/NLRP3/NF‐κB signaling pathway.
Fab-Arm Exchange Combined with Selective Protein A Purification Results in a Platform for Rapid Preparation of Monovalent Bispecific Antibodies Directly from Culture Media

Bispecific antibody (bsAb) applications have exponentially expanded with the advent of molecular engineering strategies that have addressed many of the initial challenges, including improper light chain pairing, heterodimer purity, aggregation, and pharmacokinetics. However, the lack of high-throughput methods for the generation of monovalent bsAbs has resulted in a bottleneck that has hampered their therapeutic evaluation, as current technologies can be cost-prohibitive and impractical. To address this issue, we incorporated single-matched point mutations in the CH3 domain to recapitulate the physiological process of human IgG4 Fab-arm exchange to generate monovalent bsAbs. Furthermore, we utilized the substitutions H435R and Y436F in the CH3 domain of IgG1, which incorporates residues from human IgG3, thus ablating protein A binding. By exploiting this combination of mutations and optimizing the reduction and reoxidation conditions for Fab arm exchange, highly pure monovalent bsAbs can be rapidly purified directly from combined culture media using standard protein A purification. This methodology, reported herein for the first time, allows for the high-throughput generation of monovalent bsAbs, thus increasing the capacity for evaluating monovalent bsAb iterations for therapeutic potential.