Miracle-dz/UniFAR-FTUs huggingface dataset:
Adaptive Multiple Subtraction Based on an Accelerating Iterative Curvelet Thresholding Method

In the seismic exploration, recorded data contain primaries and multiples, where primaries, as signals of interest, can be used to image the subsurface geology. Surface-related multiple elimination (SRME), one important class of multiple attenuation algorithms, operates in two stages, multiple prediction and subtraction. Due to the phase and amplitude errors in the predicted multiples, adaptive multiple subtraction (AMS) is the key step of SRME. The main challenge of this technique resides in removing multiples without distorting primaries. The curvelet-based AMS methods, which exploit the sparsity of primary and multiple in curvelet domain and the misfit between the original and estimated signals in data domain, have shown outstanding performances in real seismic data processing. These methods are realized by using the iterative curvelet thresholding (ICT), which has heavy computation burden since it includes two forward/inverse curvelet transform (CuT) pairs in each iteration. To ameliorate the computational cost, we propose an accelerating ICT method by exploiting the misfit between the original and estimated signals in curvelet domain directly. Since the proposed method only needs do one forward/inverse CuT pair, it is faster than the traditional ICT method. Considering that the error of the predicted multiple is frequency-dependent, we furthermore introduce the joint constraints within different frequency bands to stabilize and improve the multiple attenuation. Synthetic and field examples demonstrate that the proposed method outperforms the traditional ICT method. In addition, the proposed method has shown to be suitable for refining other AMS methods’ results, yielding a SNR improvement of 0.5–2.8 dB.
Altered Salivary Microbiome in the Early Stage of HIV Infections among Young Chinese Men Who Have Sex with Men (MSM)

Human immunodeficiency virus (HIV) infections are spiking in Chinese young men who have sex with men (MSM). To explore alterations in the salivary microbiome and its correlation with demographic characteristics, CD4+ T cell count and viral load (VL) in HIV infections, samples of unstimulated whole saliva were analyzed by 16S rRNA gene sequencing using the Illumina MiSeq platform in 20 HIV newly infected patients before the initiation of antiretroviral therapy (ART) and at three and six months after, and in 20 age- and gender-paired healthy Chinese people. The results showed that the alpha diversity of salivary microbiota in HIV infections did not show differences from the healthy controls, but was reduced after six months under ART treatment. Comparative analysis revealed that Streptococcus was enriched in HIV-infected individuals, while Neisseria was enriched in the healthy control group. After effective ART, the salivary microbiota composition was not completely restored, although some microbiota recovered. In addition, we found Provotella_7, Neisseria and Haemophilus were correlated negatively with CD4+ T cell count, while Neisseria was correlated positively with VL. We conclude that HIV infections experience a dysbiosis of the salivary microbiome. The salivary microbiome test could be a substitute for the blood tests in the diagnosis and prognosis of diseases.
Phylogenomics and the Genetic Architecture of the Placental Mammal Radiation.

The genomes of placental mammals are being sequenced at an unprecedented rate. Alignments of hundreds, and one day thousands, of genomes spanning the rich living and extinct diversity of species offer unparalleled power to resolve phylogenetic controversies, identify genomic innovations of adaptation, and dissect the genetic architecture of reproductive isolation. We highlight outstanding questions about the earliest phases of placental mammal diversification and the promise of newer methods, as well as remaining challenges, toward using whole-genome data to resolve placental mammal phylogeny. The next phase of mammalian comparative genomics will see the completion and application of finished-quality, gapless genome assemblies from many ordinal lineages and closely related species. Interspecific comparisons between the most hypervariable genomic loci will likely reveal large, but heretofore mostly underappreciated, effects on population divergence, morphological innovation, and the origin of new species. Expected final online publication date for the Annual Review of Animal Biosciences, Volume 9 is February 16, 2021. Please see http://www.annualreviews. org/page/journal/pubdates for revised estimates.
GP4: an integrated Gram-Positive Protein Prediction Pipeline for subcellular localization mimicking bacterial sorting

Abstract Subcellular localization is a critical aspect of protein function and the potential application of proteins either as drugs or drug targets, or in industrial and domestic applications. However, the experimental determination of protein localization is time consuming and expensive. Therefore, various localization predictors have been developed for particular groups of species. Intriguingly, despite their major representation amongst biotechnological cell factories and pathogens, a meta-predictor based on sorting signals and specific for Gram-positive bacteria was still lacking. Here we present GP4, a protein subcellular localization meta-predictor mainly for Firmicutes, but also Actinobacteria, based on the combination of multiple tools, each specific for different sorting signals and compartments. Novelty elements include improved cell-wall protein prediction, including differentiation of the type of interaction, prediction of non-canonical secretion pathway target proteins, separate prediction of lipoproteins and better user experience in terms of parsability and interpretability of the results. GP4 aims at mimicking protein sorting as it would happen in a bacterial cell. As GP4 is not homology based, it has a broad applicability and does not depend on annotated databases with homologous proteins. Non-canonical usage may include little studied or novel species, synthetic and engineered organisms, and even re-use of the prediction data to develop custom prediction algorithms. Our benchmark analysis highlights the improved performance of GP4 compared to other widely used subcellular protein localization predictors. A webserver running GP4 is available at http://gp4.hpc. rug.nl/
Plasma Phospholipid n-3/n-6 Polyunsaturated Fatty Acids and Desaturase Activities in Relation to Moderate-to-Vigorous Physical Activity through Pregnancy: A Longitudinal Study within the NICHD Fetal Growth Studies

Maternal plasma phospholipid polyunsaturated fatty acids (PUFAs) play critical roles in maternal health and fetal development. Beyond dietary factors, maternal moderate-to-vigorous physical activity (MVPA) has been linked to multiple health benefits for both the mother and offspring, but studies investigating the influence of maternal MVPA on maternal PUFA profile are scarce. The objective of present study was to examine the time-specific and prospective associations of MVPA with plasma PUFA profile among pregnant women. This study included 321 participants from the National Institute of Child Health and Human Development (NICHD) Fetal Growth Studies–Singletons cohort. Maternal plasma phospholipid PUFAs and MPVA were measured at four visits during pregnancy (10–14, 15–26, 23–31, and 33–39 gestational weeks (GW)). Associations of maternal MVPA with individual plasma PUFAs and desaturase activity were examined using generalized linear models. Maternal MVPA was associated inversely with plasma phospholipid linoleic acid, gamma-linolenic acid, and Δ6-desaturase in late pregnancy (23–31 or 33–39 GW), independent of maternal age, race, education, parity, pre-pregnancy body mass index, and dietary factors. Findings from this longitudinal study indicate that maternal habitual MVPA may play a role on PUFAs metabolism, particular by alerting plasma n-6 subclass and desaturase activity in late pregnancy. These associations are novel and merit confirmation in future studies.
White matter hyperintensities at critical crossroads for executive function and verbal abilities in small vessel disease

The presence of white matter lesions in patients with cerebral small vessel disease (SVD) is among the main causes of cognitive decline. We investigated the relation between white matter hyperintensity (WMH) locations and executive and language abilities in 442 SVD patients without dementia with varying burden of WMH. We used Stroop Word Reading, Stroop Color Naming, Stroop Color‐Word Naming, and Category Fluency as language measures with varying degrees of executive demands. The Symbol Digit Modalities Test (SDMT) was used as a control task, as it measures processing speed without requiring language use or verbal output. A voxel‐based lesion–symptom mapping (VLSM) approach was used, corrected for age, sex, education, and lesion volume. VLSM analyses revealed statistically significant clusters for tests requiring language use, but not for SDMT. Worse scores on all tests were associated with WMH in forceps minor, thalamic radiations and caudate nuclei. In conclusion, an association was found between WMH in a core frontostriatal network and executive‐verbal abilities in SVD, independent of lesion volume and processing speed. This circuitry underlying executive‐language functioning might be of potential clinical importance for elderly with SVD. More detailed language testing is required in future research to elucidate the nature of language production difficulties in SVD.
Developing Rapid Antimicrobial Susceptibility Testing for Motile/Non-Motile Bacteria Treated with Antibiotics Covering Five Bactericidal Mechanisms on the Basis of Bead-Based Optical Diffusometry

Rapid antimicrobial susceptibility testing (AST) is an effective measure in the treatment of infections and the prevention of bacterial drug resistance. However, diverse antibiotic types and bacterial characteristics have formed complicated barriers to rapid diagnosis. To counteract these limitations, we investigated the interactions between antibiotic-treated bacteria and functionalized microbeads in optical diffusometry. The conjugation with bacteria increased the effective microbead complex size, thereby resulting in a temporal diffusivity change. The yielded data were sorted and analyzed to delineate a pattern for the prediction of antimicrobial susceptibility. The outcome showed that a completed rapid AST based on the trend of microbead diffusivity could provide results within 3 h (2 h measurement + 1 h computation). In this research, we studied four bacterial strains, including Escherichia coli, Pseudomonas aeruginosa, Klebsiella pneumoniae, and Staphylococcus aureus, and six antibiotics. Despite the different inhibitory effects caused by various antibiotics, similar trends in diffusivity alteration for all susceptible and resistant cases in the last 40 min of the 2-h measurement period were deduced. In addition, the AST results obtained using optical diffusometry showed good agreement with those acquired from the commercial instrument and conventional culture methods. Finally, we conducted a single-blinded clinical test, and the sensitivity, specificity, and accuracy of the system reached 92.9%, 91.4%, and 91.8%, respectively. Overall, the developed optical diffusometry showcased rapid AST with a small sample volume (20 μL) and low initial bacterial count (105 CFU/mL). This technique provided a promising way to achieve early therapy against microbial diseases in the future.
Effects of three different rehabilitation games’ interaction on brain activation using functional near-infrared spectroscopy

Objective: This study reveals the changes in brain activation due to different game interaction states based on functional near-infrared spectroscopy signals and discusses their significance for stroke rehabilitation. Approach: The oxygenated hemoglobin concentration (Delta [HbO2]) signals and the deoxygenated hemoglobin (Delta [HbR]) signals were recorded from the prefrontal cortex (PFC), the motor cortex (MC), the occipital lobe (OL) and the temporal lobe of 21 subjects (mean age: 24.6 ± 1.9 years old) in three game interaction states: physical, motion-sensing, and button-push training. The subjects were also asked to complete user-satisfaction survey scales after the experiment. Main results: Compared with the button-training state, several channels in the PFC and MC region of the physical-training state were significantly altered as were several channels in the RMC region of the motion-sensing training state (P < 0.05 after adjustment). The motion-sensing state of the PFC had a significant correlation with that of the MC and the OL. The subjective scale results show that the acceptability of the physical and motion-sensing states was greater than the acceptability of the button-push training state. Significance: The results show that the brain regions responded more strongly when activated by the physical and motion-sensing states compared with the button-push training state, and the physical and motion-sensing states are more conducive to the rehabilitation of the nervous system. The design of rehabilitation products for stroke patients is discussed and valuable insights are offered to support the selection of better interactive training methods.
Redox Potential and Antioxidant Capacity of Bovine Bone Collagen Peptides towards Stable Free Radicals, and Bovine Meat Lipids and Proteins. Effect of Animal Age, Bone Anatomy and Proteases—A Step Forward towards Collagen-Rich Tissue Valorisation

Collagen antioxidant peptides are being widely studied. However, no research has paid attention to biological parameters such as the age and anatomy of collagen-rich tissues, which can determine a change in tissue structure and composition, and then in bioactivity. Moreover, only few research works have studied and assessed peptides antioxidant activity on the food matrix. This work aimed to investigate the effect of bovine’s bone age and anatomy, and of six different enzymes, on the antioxidant activity of collagen peptides. Collagen was extracted from young and old bovine femur and tibia; six different enzymes were used for peptides’ release. The redox potential, the quenching of stable free radicals, and the antioxidant capacity on bovine meat lipids and proteins was evaluated, under heating from ambient temperature to 80 °C. Age and anatomy showed a significant effect; the influence of anatomy becomes most important with age. Each enzyme’s effectiveness toward age and anatomy was not the same. The greatest amount of peptides was released from young bones’ collagen hydrolysed with papain. The antioxidant activity was higher at higher temperatures, except for meat proteins. Assessing the effect of age and anatomy of collagen-rich tissues can promote a better application of collagen bioactive peptides.
MEA Preparation for Direct Formate/Formic Acid Fuel Cell—Comparison of Palladium Black and Palladium Supported on Activated Carbon Performance on Power Generation in Passive Fuel Cell

Membrane electrode assemblies (MEAs) with palladium catalysts were successfully prepared by using a home-made manual pressing system with Nafion glue application that contributed to a decrease of additional energy consumption. The catalyst coated membranes were prepared with supported palladium on activated carbon (PdC) and unsupported palladium black (PdB) for comparison. The performance of passive, air breathing, functioning under ambient conditions and with low concentration (1 M) formate/formic acid fuel cell was evaluated. Based on polarization curves, the best result was obtained with carbon supported catalyst and HCOOK fuel, achieving 21.01 mW/mgPd. Still, constant current discharge with PdC showed an energy generation efficiency of 14% with HCOOH over 3% with HCOOK caused by lower potassium ion conductivity and its permeability through the proton exchange membrane. The faradic efficiency of conversion in the cell is equal to the overall energy efficiency and makes the cell self-sufficient.
Sensors for the quantification, localization and analysis of the dynamics of plant hormones

Summary Plant hormones play important roles in plant growth and development and physiology, and in acclimation to environmental changes. The hormone signaling networks are highly complex and interconnected. It is thus important to not only know where the hormones are produced, how they are transported and how and where they are perceived, but also to monitor their distribution quantitatively, ideally in a non‐invasive manner. Here we summarize the diverse set of tools available for quantifying and visualizing hormone distribution and dynamics. We provide an overview over the tools that are currently available, including transcriptional reporters, degradation sensors, and luciferase and fluorescent sensors, and compare the tools and their suitability for different purposes.
Estimation of Heights and Body Masses of Tuberculosis Patients in the Canadian Fluoroscopy Cohort Study for Use in Individual Dosimetry

Abstract This paper documents the estimation of mean heights and body masses, by age and sex, used in development of organ-specific dose conversion coefficients for external radiation for a historical cohort of about 64,000 patients from the Canadian Fluoroscopy Cohort Study. Patients were exposed to repeated fluoroscopy and chest radiography examinations in the course of treatment for tuberculosis in residential medical facilities throughout Canada between 1930 and 1969. Using Canadian national survey data and extensive literature review, mean heights and masses were obtained for the White population of Canada during the time period of interest, and the differences in mean body mass between tuberculosis patients and the general population were estimated. Results in terms of mean height and body mass of Canadian tuberculosis patients, with uncertainties, are reported for selected age groups (children of ages 1, 5, 10, and 15 y and adults age 20+) and for both sexes. Use of estimated average heights and body masses by age and sex permits the adjustment of computerized phantoms for body mass for a given age, thereby increasing the relevance of the organ-specific dose conversion coefficients for the cohort and improving the accuracy of the resulting estimated organ doses.
Inference of Regulatory System for TAG Biosynthesis in Lipomyces starkeyi

Improving the bioproduction ability of efficient host microorganisms is a central aim in bioengineering. To control biosynthesis in living cells, the regulatory system of the whole biosynthetic pathway should be clearly understood. In this study, we applied our network modeling method to infer the regulatory system for triacylglyceride (TAG) biosynthesis in Lipomyces starkeyi, using factor analyses and structural equation modeling to construct a regulatory network model. By factor analysis, we classified 89 TAG biosynthesis-related genes into nine groups, which were considered different regulatory sub-systems. We constructed two different types of regulatory models. One is the regulatory model for oil productivity, and the other is the whole regulatory model for TAG biosynthesis. From the inferred oil productivity regulatory model, the well characterized genes DGA1 and ACL1 were detected as regulatory factors. Furthermore, we also found unknown feedback controls in oil productivity regulation. These regulation models suggest that the regulatory factor induction targets should be selected carefully. Within the whole regulatory model of TAG biosynthesis, some genes were detected as not related to TAG biosynthesis regulation. Using network modeling, we reveal that the regulatory system is helpful for the new era of bioengineering.
Ribosomal Protein L10: From Function to Dysfunction

Eukaryotic cytoplasmic ribosomes are highly structured macromolecular complexes made up of four different ribosomal RNAs (rRNAs) and 80 ribosomal proteins (RPs), which play a central role in the decoding of genetic code for the synthesis of new proteins. Over the past 25 years, studies on yeast and human models have made it possible to identify RPL10 (ribosomal protein L10 gene), which is a constituent of the large subunit of the ribosome, as an important player in the final stages of ribosome biogenesis and in ribosome function. Here, we reviewed the literature to give an overview of the role of RPL10 in physiologic and pathologic processes, including inherited disease and cancer.
Association of sleep disturbance and freezing of gait in Parkinson disease: prevention/delay implications.

STUDY OBJECTIVES Freezing of gait (FOG) severely impairs life quality of Parkinson disease (PD) patients. It remains unclear about the relationship between sleep disturbance and FOG in PD. In this study, we aimed to investigate the relationship between sleep disturbance and FOG in PD. METHODS First, we assessed clinical characteristics of freezers and nonfreezers in PD patients. Next, we assessed clinical characteristics of PD patients with different PDSS1 score. Finally, we prospectively followed a cohort of nonfreezers at baseline clinical visit for a maximum of 18 months, and performed a Cox regression analysis to further investigate the relationship between PDSS1 score and FOG in PD. RESULTS A total of 163 participants with PD were included into the baseline analysis. The freezers had significantly worse sleep compared with the nonfreezers. The proportion of freezers in the patients with low PDSS1 score (PDSS1<6) was significantly higher than that in the patients with high PDSS1 score (PDSS1≥6). A total of 52 nonfreezers were prospectively followed. During a maximum of 18-month follow-up, FOG incidence (73%) in the PDSS1<6 group was significantly higher than that (24%) in the PDSS1≥6 group (p =.008). Low PDSS1 score (HR=4.23, 95% CI 1.64-10.92, p =.003) and high L-dopa equivalent daily dose (HR=4.18, 95% CI 1.62-10.75, p =.003) were significantly associated with an increased hazard of FOG. CONCLUSIONS Our study indicated that low PDSS1 score may be a risk factor for the development of FOG and provided important insights into potential targets for the prevention/delay of FOG in PD.
Danggui Sini Decoction (herbal medicine) for the treatment of primary dysmenorrhoea: a systematic review and meta-analysis

Abstract Danggui Sini Decoction (DSD), a traditional herbal prescription, has been commonly used in the treatment of primary dysmenorrhoea (PD). We investigated the current evidence of randomised controlled trials (RCTs) and performed a systematic review to evaluate the efficacy of DSD in the treatment of PD. We registered the protocol for this systemic review in PROSPERO with the registration number CRD 42017074062 on August 10, 2017. Nine databases were searched from inception to August 2019. Eleven RCTs with 1005 patients were included. DSD was shown to have more favourable effects on the clinical effective rate than western medicine, which support the clinical use of DSD in the treatment of PD. However, considering the high risk of bias in the included studies, more well-designed RCTs are needed to further evaluate the efficacy of DSD in the treatment of PD.