Miracle-dz/UniFAR-FTUs huggingface dataset:
Matrix completion with side information and its applications in predicting the antigenicity of influenza viruses

Motivation Low‐rank matrix completion has been demonstrated to be powerful in predicting antigenic distances among influenza viruses and vaccines from partially revealed hemagglutination inhibition table. Meanwhile, influenza hemagglutinin (HA) protein sequences are also effective in inferring antigenic distances. Thus, it is natural to integrate HA protein sequence information into low‐rank matrix completion model to help infer influenza antigenicity, which is critical to influenza vaccine development. Results We have proposed a novel algorithm called biological matrix completion with side information (BMCSI), which first measures HA protein sequence similarities among influenza viruses (especially on epitopes) and then integrates the similarity information into a low‐rank matrix completion model to predict influenza antigenicity. This algorithm exploits both the correlations among viruses and vaccines in serological tests and the power of HA sequence in predicting influenza antigenicity. We applied this model into H3N2 seasonal influenza virus data. Comparing to previous methods, we significantly reduced the prediction root‐mean‐square error in a 10‐fold cross validation analysis. Based on the cartographies constructed from imputed data, we showed that the antigenic evolution of H3N2 seasonal influenza is generally S‐shaped while the genetic evolution is half‐circle shaped. We also showed that the Spearman correlation between genetic and antigenic distances (among antigenic clusters) is 0.83, demonstrating a globally high correspondence and some local discrepancies between influenza genetic and antigenic evolution. Finally, we showed that 4.4%±1.2% genetic variance (corresponding to 3.11 ± 1.08 antigenic distances) caused an antigenic drift event for H3N2 influenza viruses historically. Availability and implementation The software and data for this study are available at http://bi.sky. zstu.edu. cn/BMCSI/. Contact jialiang.yang@mssm.edu or pinganhe@zstu.edu. cn Supplementary information Supplementary data are available at Bioinformatics online.
Biocompatible Materials Based on Self-Assembling Peptides on Ti25Nb10Zr Alloy: Molecular Structure and Organization Investigated by Synchrotron Radiation Induced Techniques

In this work, we applied advanced Synchrotron Radiation (SR) induced techniques to the study of the chemisorption of the Self Assembling Peptide EAbuK16, i.e., H-Abu-Glu-Abu-Glu-Abu-Lys-Abu-Lys-Abu-Glu-Abu-Glu-Abu-Lys-Abu-Lys-NH2 that is able to spontaneously aggregate in anti-parallel β-sheet conformation, onto annealed Ti25Nb10Zr alloy surfaces. This synthetic amphiphilic oligopeptide is a good candidate to mimic extracellular matrix for bone prosthesis, since its β-sheets stack onto each other in a multilayer oriented nanostructure with internal pores of 5–200 nm size. To prepare the biomimetic material, Ti25Nb10Zr discs were treated with aqueous solutions of EAbuK16 at different pH values. Here we present the results achieved by performing SR-induced X-ray Photoelectron Spectroscopy (SR-XPS), angle-dependent Near Edge X-ray Absorption Fine Structure (NEXAFS) spectroscopy, FESEM and AFM imaging on Ti25Nb10Zr discs after incubation with self-assembling peptide solution at five different pH values, selected deliberately to investigate the best conditions for peptide immobilization.
In situ near-infrared spectroscopy for soil organic matter prediction in paddy soil, Pasak watershed, Thailand

Romsonthi C. , Tawornpruek S. , Watana S. (2018): In situ near-infrared spectroscopy for soil organic matter prediction in paddy soil, Pasak watershed, Thailand. Plant Soil Environ. , 64: 70–75. Soil organic matter (SOM) is a major index of soil quality assessment because it is one of the key soil properties controlling nutrient budgets in agricultural production systems. The aim of the in situ near-infrared spectroscopy (NIRS) for SOM prediction in paddy area is evaluation of the potential of SOM and prediction of other soil properties. There are keys for soil fertility and soil quality assessments. A spectral reflectance of 130 soil samples was collected by field spectroradiometer in a region of near-infrared. Spectral reflectance collections were processed by the first derivative transformation with the Savitsky-Golay algorithms. Partial least square regression method was used to develop a calibration model between soil properties and spectral reflectance, which was used for prediction and validation processes. Finally, the results of this study demonstrate that NIRS is an effective method that can be used to predict SOM (R2 = 0.73, RPD (ratio of performance to deviation) = 1.82) and total nitrogen (R2 = 0.72, RPD = 1.78). Therefore, NIRS is a potential tool for soil properties predictions. The use of these techniques will facilitate the implementation of soil management with a decreasing cost and time of soil study in a large scale. However, further works are necessary to develop more accurate soil properties prediction and to apply this method to other areas.
Explorer Lawsonia intracellularis infection of intestinal crypt cells is associated with specific depletion of secreted MUC 2 in goblet cells

The expression patterns of secreted (MUC2 and MUC5AC) and membrane-tethered (MUC1, MUC4, MUC12 and MUC13) mucins were monitored in healthy pigs and pigs challenged orally with Lawsonia intracellularis. These results showed that the regulation of mucin gene expression is distinctive along the GI tract of the healthy pig, and may reflect an association between the function of the mucin subtypes and different physiological demands at various sites. We identified a specific depletion of secreted MUC2 from goblet cells in infected pigs that correlated with the increased level of intracellular bacteria in crypt cells. We concluded that L. intracellularis may influence MUC2 production, thereby altering the mucus barrier and enabling cellular invasion. © 2015 The Authors. Published by Elsevier B.V. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
Treatment outcomes of TB‐infected individuals attending public sector primary care clinics in rural Liberia from 2015 to 2017: a retrospective cohort study

In June 2015, Partners in Health (PIH) and the Liberian Ministry of Health began a community health worker (CHW) programme containing food support, reimbursement of transport and social assistance to address gaps in tuberculosis (TB) treatment exacerbated by the 2014‐2015 Ebola virus disease (EVD) epidemic. The purpose of this article was to analyse the performance of routine clinical TB care and the effects of this CHW programme.
Use of Online Forums for Perinatal Mental Illness, Stigma, and Disclosure: An Exploratory Model

Background Perinatal mental illness is a global health concern; however, many women with the illness do not get the treatment they need to recover. Interventions that reduce the stigma around perinatal mental illness have the potential to enable women to disclose their symptoms to health care providers and consequently access treatment. There are many online forums for perinatal mental illness and thousands of women use them. Preliminary research suggests that online forums may promote help-seeking behavior, potentially because they have a role in challenging stigma. This study draws from these findings and theoretical concepts to present a model of forum use, stigma, and disclosure. Objective This study tested a model that measured the mediating role of stigma between online forum use and disclosure of affective symptoms to health care providers. Methods A Web-based survey of 200 women who were pregnant or had a child younger than 5 years and considered themselves to be experiencing psychological distress was conducted. Women were recruited through social media and questions measured forum usage, perinatal mental illness stigma, disclosure to health care providers, depression and anxiety symptoms, barriers to disclosure, and demographic information. Results There was a significant positive indirect effect of length of forum use on disclosure of symptoms through internal stigma, b=0.40, bias-corrected and accelerated (BCa) 95% CI 0.13-0.85. Long-term forum users reported higher levels of internal stigma, and higher internal stigma was associated with disclosure of symptoms to health care providers when controlling for symptoms of depression and anxiety. Conclusions Internal stigma mediates the relationship between length of forum use and disclosure to health care providers. Findings suggest that forums have the potential to enable women to recognize and reveal their internal stigma, which may in turn lead to greater disclosure of symptoms to health care providers. Clinicians could refer clients to trustworthy and moderated online forums that facilitate expression of perinatal mental illness stigma and promote disclosure to health care providers.
Short‐term treatment of equine wounds with orf virus IL‐10 and VEGF‐E dampens inflammation and promotes repair processes without accelerating closure

Healing is delayed in limb wounds relative to body wounds of horses, partly because of sustained inflammation and inefficient angiogenesis. In laboratory animals, proteins derived from orf virus modulate these processes and enhance healing. We aimed to compare immune cell trafficking and the inflammatory, vascular, and epidermal responses in body and limb wounds of horses and then to investigate the impact of orf virus interleukin‐10 and vascular endothelial growth factor‐E on these processes. Standardized excisional wounds were created on the body and forelimb of horses and their progression monitored macroscopically until healed. Tissue samples were harvested to measure the expression of genes regulating inflammation and repair (quantitative polymerase chain reaction) and to observe epithelialization (histology), innate immune cell infiltration, and angiogenesis (immunofluorescence). Delayed healing of limb wounds was characterized by intensified and extended pro‐inflammatory signaling and exacerbated innate immune response, concomitant with the absence of anti‐inflammatory eIL‐10. Blood vessels were initially more permeable and then matured belatedly, concomitant with retarded production of angiogenic factors. Epithelial coverage was achieved belatedly in limb wounds. Viral proteins were administered to wounds of one body and one limb site/horse at days 1–3, while wounds at matching sites served as controls. Treatment dampened pro‐inflammatory gene expression and the innate immune response in all wounds. It also improved angiogenic gene expression, but primarily in body wounds, where it altered blood vessel density and myofibroblast persistence. Moreover, the viral proteins increased epithelialization of all wounds. The short‐term viral protein therapy did not, however, improve the healing rate of wounds in either location, likely due to suboptimal dosing. In conclusion, we have further detailed the processes contributing to protracted healing in limb wounds of horses and shown that short‐term administration of viral proteins exerts several promising though transient effects that, if optimized, may positively influence healing.
Sex-Related Differences in Reproductive Allocation, Growth, Defense and Herbivory in Three Dioecious Neotropical Palms

Background Frequently, in dioecious plants, female plants allocate more resources to reproduction than male plants. Therefore it is expected that asymmetrical allocation to reproduction may lead to a reproduction-growth tradeoff, whereby female plants grow less than male plants, but invest more in defenses and thus experience lower herbivory than male plants. Methodology/Principal Findings We tested these expectations by comparing resource allocation to reproduction, growth and defense and its consequences on herbivory in three sympatric dioecious Chamaedorea palms (C. alternans, C. pinnatifrons and C. ernesti-augusti) using a pair-wise design (replicated male/female neighboring plants) in a Mexican tropical rain forest. Our findings support the predictions. Biomass allocation to reproduction in C. pinnatifrons was 3-times higher in female than male plants, consistent with what is known in C. alternans and C. ernesti-augusti. Growth (height and leaf production rate and biomass production) was higher in male plants of all three species. Female plants of the three species had traits that suggest greater investment in defense, as they had 4–16% tougher leaves, and 8–18% higher total phenolic compounds concentration. Accordingly, female plants sustained 53–78% lower standing herbivory and 49–87% lower herbivory rates than male plants. Conclusions/Significance Our results suggests that resource allocation to reproduction in the studied palms is more costly to female plants and this leads to predictable intersexual differences in growth, defense and herbivory. We conclude that resource allocation to reproduction in plants can have important consequences that influence their interaction with herbivores. Since herbivory is recognized as an important selective force in plants, these results are of significance to our understanding of plant defense evolution.
Age- and sex-based recovery curves to track functional outcomes in older adults with total knee arthroplasty

Background older adults with total knee arthroplasty (TKA) frequently undergo rehabilitation to address limited knee flexion range-of-motion, quadriceps weakness and gait speed limitations. This study aimed to develop age- and sex-specific recovery curves of knee flexion range-of-motion, quadriceps strength and fast gait speed post-TKA. Methods a population-based sample of 2,987 patients undergoing primary TKA participated, of whom 2015 (68%) were 65 years of age or older. At 4, 8 and 12 weeks post surgery, knee flexion range-of-motion, quadriceps strength and fast gait speed were quantified. Quantile regression was used to determine the percentiles of the knee and gait measures. Results the various knee and gait measures improved nonlinearly over time, with substantial improvements observed in the 1st 8-10 weeks post surgery. Age-specific, sex-specific recovery curves were developed to show the recovery patterns at multiple percentile levels. A web interface was created to facilitate easy computation of the percentile rank for a given outcome value. Conclusions we have provided reference percentile values for knee flexion range-of-motion, quadriceps strength and gait speed recovery post-TKA. Such information may assist rehabilitation professionals in interpreting outcomes and quantifying deviations from the expected recovery pattern.
Mechanism of Stx17 recruitment to autophagosomes via IRGM and mammalian Atg8 proteins

Autophagy is a conserved eukaryotic process with metabolic, immune, and general homeostatic functions in mammalian cells. Mammalian autophagosomes fuse with lysosomes in a SNARE-driven process that includes syntaxin 17 (Stx17). How Stx17 translocates to autophagosomes is unknown. In this study, we show that the mechanism of Stx17 recruitment to autophagosomes in human cells entails the small guanosine triphosphatase IRGM. Stx17 directly interacts with IRGM, and efficient Stx17 recruitment to autophagosomes requires IRGM. Both IRGM and Stx17 directly interact with mammalian Atg8 proteins, thus being guided to autophagosomes. We also show that Stx17 is significant in defense against infectious agents and that Stx17–IRGM interaction is targeted by an HIV virulence factor Nef.
Phytoremediation potential of water caltrop (Trapa natans L.) using municipal wastewater of the activated sludge process-based municipal wastewater treatment plant

ABSTRACT Phytoremediation experiments were carried out to assess the phytoremediation potential of water caltrop (Trapa natans L.) using municipal wastewater collected from the activated sludge process- (ASP) based municipal wastewater treatment plant. The results revealed that T. natans significantly (P ≤ .05/P ≤ .01/P ≤ .001) reduced the contents of total dissolved solids (TDS), electrical conductivity (EC), biochemical oxygen demand (BOD5), chemical oxygen demand, total Kjeldahl nitrogen, phosphate (), sodium (Na+), potassium (K+), calcium (Ca2+), magnesium (Mg2+), cadmium (Cd), chromium (Cr), copper (Cu), iron (Fe), manganese (Mn), lead (Pb), zinc (Zn), standard plate count, and most probable number of the municipal wastewater after phytoremediation experiments. The maximum removal of these parameters was obtained at 60 days of the phytoremediation experiments, but the removal rate of these parameters was gradually increased from 15 to 45 days and it was slightly decreased at 60 days. Most contents of Cd, Cu, Fe, Mn and Zn were translocated in the leaves of T. natans, whereas most contents of Cr and Pb were accumulated in the root of T. natans after phytoremediation experiments. The contents of different biochemical components were recorded in the order of total sugar > crude protein > total ash > crude fiber > total fat in T. natans after phytoremediation of municipal wastewater. Therefore, T. natans was found to be effective for the removal of different parameters of municipal wastewater and can be used effectively to reduce the pollution load of municipal wastewater drained from the ASP-based treatment plants.
Leveraging Unlabeled Data for Crowd Counting by Learning to Rank

We propose a novel crowd counting approach that leverages abundantly available unlabeled crowd imagery in a learning-to-rank framework. To induce a ranking of cropped images, we use the observation that any sub-image of a crowded scene image is guaranteed to contain the same number or fewer persons than the super-image. This allows us to address the problem of limited size of existing datasets for crowd counting. We collect two crowd scene datasets from Google using keyword searches and query-by-example image retrieval, respectively. We demonstrate how to efficiently learn from these unlabeled datasets by incorporating learning-to-rank in a multi-task network which simultaneously ranks images and estimates crowd density maps. Experiments on two of the most challenging crowd counting datasets show that our approach obtains state-of-the-art results.
Comparison and optimization of machine learning methods for automated classification of circulating tumor cells

Advances in rare cell capture technology have made possible the interrogation of circulating tumor cells (CTCs) captured from whole patient blood. However, locating captured cells in the device by manual counting bottlenecks data processing by being tedious (hours per sample) and compromises the results by being inconsistent and prone to user bias. Some recent work has been done to automate the cell location and classification process to address these problems, employing image processing and machine learning (ML) algorithms to locate and classify cells in fluorescent microscope images. However, the type of machine learning method used is a part of the design space that has not been thoroughly explored. Thus, we have trained four ML algorithms on three different datasets. The trained ML algorithms locate and classify thousands of possible cells in a few minutes rather than a few hours, representing an order of magnitude increase in processing speed. Furthermore, some algorithms have a significantly (P < 0.05) higher area under the receiver operating characteristic curve than do other algorithms. Additionally, significant (P < 0.05) losses to performance occur when training on cell lines and testing on CTCs (and vice versa), indicating the need to train on a system that is representative of future unlabeled data. Optimal algorithm selection depends on the peculiarities of the individual dataset, indicating the need of a careful comparison and optimization of algorithms for individual image classification tasks. © 2016 International Society for Advancement of Cytometry
Mitochondrial Fission Is Required for Angiotensin II-Induced Cardiomyocyte Apoptosis Mediated by a Sirt1-p53 Signaling Pathway

Hypertension-induced cardiac apoptosis is a major contributor to early-stage heart-failure. Our previous studies have found that p53-mediated mitochondrial fission is involved in aldosterone-induced podocyte apoptosis. However, it is not clear that whether p53-induced mitochondrial fission is critical for hypertensive Angiotensin II (AngII)-induced cardiomyocyte apoptosis. In this study, we found that inhibition of the mitochondrial fission protein Drp1 (dynamin-related protein 1) by Mdivi-1 prevented cardiomyocyte apoptosis and cardiac remodeling in SHRs. In vitro we found that treatment of cultured neonatal rat cardiomyocytes with AngII induced Drp1 expression, mitochondrial fission, and apoptosis. Knockdown of Drp1 inhibited AngII-induced mitochondrial fission and cardiomyocyte apoptosis. Furthermore, AngII induced p53 acetylation. Knockdown of p53 inhibited AngII-induced Drp1 expression, mitochondrial fission, and cardiomyocyte apoptosis. Besides, we found that Sirt1 was able to reverse AngII-induced p53 acetylation and its binding to the Drp1 promoter, which subsequently inhibited mitochondrial fission and eventually attenuated cardiomyocyte apoptosis. Collectively, these results suggest that AngII degrades Sirt1 to increase p53 acetylation, which induces Drp1 expression and eventually results in cardiomyocyte apoptosis. Sirt1/p53/Drp1dependent mitochondrial fission may be a valuable therapeutic target for hypertension induced heart failure.
HYDRATION MECHANISM AND STRENGTH OF OPC AND BLENDED OPC WITH FLY ASH IN THE PRESENCE OF METAKAOLIN

The infrastructural development is an important aspect for the overall development of country. In all construction works concrete is an important and costly issue, this governs the total cost of project. To reduce cement consumption for environmental and economical concern, use of supplementary materials is required. In this work fly ash and metakaolin were used to decrease the cement contents and increase the strength as well as durability of cement. The main objective of this research work is to know the cement hydration mechanism, its strength with different ratio of fly ash and metakaolin. All mixes were made with water-to-binder ratio of 0.40. The results are evidences by chemical analysis, XRD, SEM, DSC, etc.
Visual Comparison of Two Data Sets: Do People Use the Means and the Variability?

In our everyday lives, we are required to make decisions based upon our statistical intuitions. Often, these involve the comparison of two groups, such as luxury versus family cars and their suitability. Research has shown that the mean difference affects judgements where two sets of data are compared, but the variability of the data has only a minor influence, if any at all. However, prior research has tended to present raw data as simple lists of values. Here, we investigated whether displaying data visually, in the form of parallel dot plots, would lead viewers to incorporate variability information. In Experiment 1, we asked a large sample of people to compare two fictional groups (children who drank ‘Brain Juice’ versus water) in a one-shot design, where only a single comparison was made. Our results confirmed that only the mean difference between the groups predicted subsequent judgements of how much they differed, in line with previous work using lists of numbers. In Experiment 2, we asked each participant to make multiple comparisons, with both the mean difference and the pooled standard deviation varying across data sets they were shown. Here, we found that both sources of information were correctly incorporated when making responses. Taken together, we suggest that increasing the salience of variability information, through manipulating this factor across items seen, encourages viewers to consider this in their judgements. Such findings may have useful applications for best practices when teaching difficult concepts like sampling variation.