Miracle-dz/UniFAR-FTUs huggingface dataset:
Diversity and Abundance of the Bacterial Community of the Red Macroalga Porphyra umbilicalis: Did Bacterial Farmers Produce Macroalgae?

Macroalgae harbor microbial communities whose bacterial biodiversity remains largely uncharacterized. The goals of this study were 1) to examine the composition of the bacterial community associated with Porphyra umbilicalis Kützing from Schoodic Point, ME, 2) determine whether there are seasonal trends in species diversity but a core group of bacteria that are always present, and 3) to determine how the microbial community associated with a laboratory strain (P.um.1) established in the presence of antibiotics has changed. P. umbilicalis blades (n = 5, fall 2010; n = 5, winter 2011; n = 2, clonal P.um.1) were analyzed by pyrosequencing over two variable regions of the 16 S rDNA (V5–V6 and V8; 147,880 total reads). The bacterial taxa present were classified at an 80% confidence threshold into eight phyla (Bacteroidetes, Proteobacteria, Planctomycetes, Chloroflexi, Actinobacteria, Deinococcus-Thermus, Firmicutes, and the candidate division TM7). The Bacteroidetes comprised the majority of bacterial sequences on both field and lab blades, but the Proteobacteria (Alphaproteobacteria, Gammaproteobacteria) were also abundant. Sphingobacteria (Bacteroidetes) and Flavobacteria (Bacteroidetes) had inverse abundances on natural versus P.um. 1 blades. Bacterial communities were richer and more diverse on blades sampled in fall compared to winter. Significant differences were observed between microbial communities among all three groups of blades examined. Only two OTUs were found on all 12 blades, and only one of these, belonging to the Saprospiraceae (Bacteroidetes), was abundant. Lewinella (as 66 OTUs) was found on all field blades and was the most abundant genus. Bacteria from the Bacteroidetes, Proteobacteria and Planctomycetes that are known to digest the galactan sulfates of red algal cell walls were well-represented. Some of these taxa likely provide essential morphogenetic and beneficial nutritive factors to P. umbilicalis and may have had unexpected effects upon evolution of macroalgal form as well as function.
Nano-copper-bearing stainless steel promotes fracture healing by accelerating the callus evolution process

Treatment for fractures requires internal fixation devices, which are mainly produced from stainless steel or titanium alloy without biological functions. Therefore, we developed a novel nano-copper-bearing stainless steel with nano-sized copper-precipitation (317L-Cu SS). Based on previous studies, this work explores the effect of 317L-Cu SS on fracture healing; that is, proliferation, osteogenic differentiation, osteogenesis-related gene expression, and lysyl oxidase activity of human bone mesenchymal stem cells were detected in vitro. Sprague–Dawley rats were used to build an animal fracture model, and fracture healing and callus evolution were investigated by radiology (X-ray and micro-CT), histology (H&E, Masson, and safranin O/fast green staining), and histomorphometry. Further, the Cu2+ content and Runx2 level in the callus were determined, and local mechanical test of the fracture was performed to assess the healing quality. Our results revealed that 317L-Cu SS did not affect the proliferation of human bone mesenchymal stem cells, but promoted osteogenic differentiation and the expression of osteogenesis-related genes. In addition, 317L-Cu SS upregulated the lysyl oxidase activity. The X-ray and micro-CT results showed that the callus evolution efficiency and fracture healing speed were superior for 317L-Cu SS. Histological staining displayed large amounts of fibrous tissues at 3 weeks, and cartilage and new bone at 6 weeks. Further, histomorphometric analysis indicated that the callus possessed higher osteogenic efficiency at 6 weeks, and a high Cu2+ content and increased Runx2 expression were observed in the callus for 317L-Cu SS. Besides, the mechanical strength of the fracture site was much better than that of the control group. Overall, we conclude that 317L-Cu SS possesses the ability to increase Cu2+ content and promote osteogenesis in the callus, which could accelerate the callus evolution process and bone formation to provide faster and better fracture healing.
Management of advanced gastric cancer: An overview of major findings from meta-analysis

This study aims to provide an overview of different treatment for advanced gastric cancer. In the present study, we systematically reviewed the major findings from relevant meta-analyses. A total of 54 relevant papers were searched via the PubMed, Web of Science, and Google scholar databases. They were classified according to the mainstay treatment modalities such as surgery, chemotherapy and others. Primary outcomes including overall survival, response rate, disease-free survival, recurrence-free survival, progression-free survival, time-to-progression, time-to failure, recurrence and safety were summarized. The recommendations and uncertainties regarding the treatment of advanced gastric cancer were also proposed. It was suggested that laparoscopic gastrectomy was a safe and technical alternative to open gastrectomy. Besides, neoadjuvant chemotherapy and adjuvant chemotherapy were thought to benefit the survival over surgery alone. And it was demonstrated in the study that targeted therapy like anti-angiogenic and anti-HER2 agents but anti-EGFR agent might have a significant survival benefit.
Correlation of MET gene amplification and TP53 mutation with PD-L1 expression in non-small cell lung cancer

Background The role of MET amplification in lung cancer, particularly in relation to checkpoint inhibition and EGFR WT, has not been fully explored. In this study, we correlated PD-L1 expression with MET amplification and EGFR, KRAS, or TP53 mutation in primary lung cancer. Methods In this retrospective study, tissue collected from 471 various tumors, including 397 lung cancers, was tested for MET amplification by FISH with a MET/centromere probe. PD-L1 expression was evaluated using clone SP142 and standard immunohistochemistry, and TP53, KRAS, and EGFR mutations were tested using next generation sequencing. Results Our results revealed that PD-L1 expression in non-small cell lung cancer is inversely correlated with EGFR mutation (P=0.0003), and positively correlated with TP53 mutation (P=0.0001) and MET amplification (P=0.004). Patients with TP53 mutations had significantly higher MET amplification (P=0.007), and were more likely (P=0.0002) to be EGFR wild type. There was no correlation between KRAS mutation and overall PD-L1 expression, but significant positive correlation between PD-L1 expression and KRAS with TP53 co-mutation (P=0.0002). A cut-off for the ratio of MET: centromere signal was determined as 1.5%, and 4% of lung cancer patients were identified as MET amplified. Conclusions This data suggests that in lung cancer both MET and TP53 play direct roles in regulating PD-L1 opposing EGFR. Moreover, KRAS and TP53 co-mutation may cooperate to drive PD-L1 expression in lung cancer. Adding MET or TP53 inhibitors to checkpoint inhibitors may be an attractive combination therapy in patients with lung cancer and MET amplification.
Linking Reproduction and Survival Can Improve Model Estimates of Vital Rates Derived from Limited Time-Series Counts of Pinnipeds and Other Species

We propose a method to model the physiological link between somatic survival and reproductive output that reduces the number of parameters that need to be estimated by models designed to determine combinations of birth and death rates that produce historic counts of animal populations. We applied our Reproduction and Somatic Survival Linked (RSSL) method to the population counts of three species of North Pacific pinnipeds (harbor seals, Phoca vitulina richardii (Gray, 1864); northern fur seals, Callorhinus ursinus (L., 1758); and Steller sea lions, Eumetopias jubatus (Schreber, 1776))—and found our model outperformed traditional models when fitting vital rates to common types of limited datasets, such as those from counts of pups and adults. However, our model did not perform as well when these basic counts of animals were augmented with additional observations of ratios of juveniles to total non-pups. In this case, the failure of the ratios to improve model performance may indicate that the relationship between survival and reproduction is redefined or disassociated as populations change over time or that the ratio of juveniles to total non-pups is not a meaningful index of vital rates. Overall, our RSSL models show advantages to linking survival and reproduction within models to estimate the vital rates of pinnipeds and other species that have limited time-series of counts.
Procoagulant Activity of Blood and Endothelial Cells via Phosphatidylserine Exposure and Microparticle Delivery in Patients with Diabetic Retinopathy

Background/Aims: The mechanisms for thrombosis in diabetic retinopathy (DR) are complex and need to be further elucidated. The purpose of this study was to test phosphatidylserine (PS) exposure on microparticles (MPs) and MP-origin cells from the circulation and to analyze cell-/MP-associated procoagulant activity (PCA) in DR patients. Methods: PS-positive MPs and cells from healthy controls (n = 20) and diabetic patients (n = 60) were analyzed by flow cytometry and confocal microscopy. Clotting time and purified coagulation complex assays were used to measure PCA. Results: PS exposure on platelets and monocytes was higher in proliferative DR (PDR) patients than in non-PDR patients or controls. The highest levels of MPs (derived from platelets [30%], erythrocytes [13%], leukocytes [28%], and endothelial cells [10%]) were found in patients with PDR. In addition, PS exposure on blood cells and shed MPs in DR patients led to significantly increased FXa and FIIa generation, fibrin formation, and markedly shortened coagulation time. Moreover, lactadherin reduced 70% of PCA by blocking PS, while an anti-tissue factor antibody had a smaller effect. Conclusion: Our results confirmed that PCA in DR patients may be partly ascribed to PS exposure and MP release from blood and endothelial cells. Lactadherin may act as an efficient anticoagulant factor in this process.
Fluency Interventions and the Impact on Comprehension

Reading fluency is understood to be the rate and accuracy of that which is being read and comprehension is the understanding of what has been read. Many studies support the concept that fluency skills support reading comprehension. Many students with specific learning disabilities lack the fluency skills needed for successful reading comprehension. This study provided fluency interventions to elementary students with specific learning disabilities and evaluated any comprehension gains. Students graphed their own fluency gains during the interventions and a pre-test and post-test were given to monitor comprehension. There was in increase in both the average fluency rate for each group and the average comprehension scores, however, the increases in comprehension were not a statistically significant amount.
Shear strength characteristics of some Indian fly ashes

Thermal power stations using pulverized coal as fuel produce enormous quantities of ash as waste products of combustion. In India, it is estimated that thermal power plants will produce about 100 million t of flyash per year by the year 2000. Hence the problem of ash disposal is expected to become acute due to the limited space available for ash disposal near most of the power plants. This calls for strategies to encourage and establish technological concepts for bulk utilization of fly ash which should not only be cost-effective but also environment friendly. This paper reports an experimental programme carried out to study the shear strength characteristics of fly ash using direct shear tests under different conditions so as to enable its bulk utilization in geotechnical engineering applications. The results are encouraging due to the low unit weight, good frictional properties, low compressibility and high permeability of fly ash.
Statistically Optimal and Computationally Efficient Low Rank Tensor Completion from Noisy Entries

In this article, we develop methods for estimating a low rank tensor from noisy observations on a subset of its entries to achieve both statistical and computational efficiencies. There have been a lot of recent interests in this problem of noisy tensor completion. Much of the attention has been focused on the fundamental computational challenges often associated with problems involving higher order tensors, yet very little is known about their statistical performance. To fill in this void, in this article, we characterize the fundamental statistical limits of noisy tensor completion by establishing minimax optimal rates of convergence for estimating a $k$th order low rank tensor under the general $\ell_p$ ($1\le p\le 2$) norm which suggest significant room for improvement over the existing approaches. Furthermore, we propose a polynomial-time computable estimating procedure based upon power iteration and a second-order spectral initialization that achieves the optimal rates of convergence. Our method is fairly easy to implement and numerical experiments are presented to further demonstrate the practical merits of our estimator.
Monitoring Walker Assistive Devices: A Novel Approach Based on Load Cells and Optical Distance Measurements †

This paper presents a measurement system intended to monitor the usage of walker assistive devices. The goal is to guide the user in the correct use of the device in order to prevent risky situations and maximize comfort. Two risk indicators are defined: one related to force unbalance and the other related to motor incoordination. Force unbalance is measured by load cells attached to the walker legs, while motor incoordination is estimated by synchronizing force measurements with distance data provided by an optical sensor. The measurement system is equipped with a Bluetooth link that enables local supervision on a computer or tablet. Calibration and experimental results are included in the paper.
Elaphroporia ailaoshanensis gen. et sp. nov. in Polyporales (Basidiomycota)

Abstract A new poroid wood-inhabiting fungal genus, Elaphroporia, typified by E. ailaoshanensis sp. nov., is proposed based on a combination of morphological features and molecular evidence. The genus is characterised by an annual growth habit, resupinate basidiocarps, becoming rigid and light-weight up on drying, a monomitic hyphal system with thick-walled generative hyphae bearing both clamp connections and simple septa, slightly amyloid, CB+ and ellipsoid, hyaline, thin-walled, smooth and IKI–, CB– basidiospores. Sequences of ITS and LSU nrRNA gene regions of the studied samples were generated, and phylogenetic analyses were performed with maximum likelihood, maximum parsimony and bayesian inference methods. The phylogenetic analysis based on molecular data of ITS+nLSU sequences showed that Elaphroporia belonged to the residual polyporoid clade and was closely related to Junghuhnia crustacea. Further investigation was obtained for more representative taxa in the Meruliaceae based on ITS+nLSU sequences, in which the result demonstrated that the genus Elaphroporia formed a monophyletic lineage with a strong support (100 % BS, 100 % BP, 1.00 BPP) and then grouped with Flaviporus and Steccherinum.
Rheumatoid Arthritis is Caused by Asymptomatic Proteus Urinary Tract Infections

Urinary tract infections (UTI) are considered as one of the most common groups of infections in humans and affecting either the upper (kidneys--pyelonephritis) or the lower (bladder--cystitis) part of the urinary tract (Thomson and Armitage, 2010). The gastrointestinal tract is a reservoir from which uropathogens emerge. Reflecting this, Enterobacteriaceae are the most important cause of UTI in all population groups, accounting for more than 95% of all UTIs. Among these microbes, E. coli is by far the most common invader, causing some 90% of UTIs in outpatients and approximately 50% in hospitalized patients. Whilst, the frequency of P. mirabilis causing outpatient and inpatients UTIs were 3.2% and 12.7% respectively, these value were reversed to 26.6% and 9.3% when all strains of Proteus species were examined (Talkoff-Robin et al, 2008). In a most recent multicentre study involving nine Spanish hospitals, 784 women with uncomplicated cystitis were evaluated for the frequencies of isolated uropathogens and their susceptibility to antibiotics. Among the 650 pathogens isolated, the first group of the most frequent bacterial agents was Escherichia coli (79.2%) followed by Staphylococcus saprophyticus (4.4%), Proteus mirabilis (4.3%), Enterococcus faecalis (3.3%), and Klebsiella pneumoniae (2.3%) (Palou et al, 2011). In contrast to E. coli strains, it appears that all strains of P. mirabilis, regardless of isolate origin, are capable of infecting the urinary tract (Sosa et al, 2006). Proteus is particularly significant as a renal pathogen especially in causing upper UTI because of its propensity to promote struvite renal calculi (Ronald and Nicolle, 2007).
In vitro evaluation of the anti-leishmanial activity and toxicity of PK11195

BACKGROUND Leishmaniasis, one of the most neglected diseases, is a serious public health problem in many countries, including Brazil. Currently available treatments require long-term use and have serious side effects, necessitating the development of new therapeutic interventions. Because translocator protein (TSPO) levels are reduced in Leishmania amazonensis-infected cells and because this protein participates in apoptosis and immunomodulation, TSPO represents a potential target for Leishmania chemotherapy. The present study evaluated PK11195, a ligand of this protein, as an anti-leishmanial agent. OBJECTIVE To evaluate the leishmanicidal activity of PK11195 against L. amazonensis in infected CBA mouse macrophages in vitro. METHODS The viability of axenic L. amazonensis, Leishmania major, and Leishmania braziliensis promastigotes was assessed after 48 h treatment with PK11195 (0.2-400 µM). Additionally, intracellular parasite viability was evaluated to determine IC50 values and the number of viable parasites in infected macrophages treated with PK11195 (50-100 µM). Infected macrophages were then treated with PK11195 (25-100 µM) to determine the percentage of L. amazonensis-infected cells and the number of parasites per infected cell. Electron microscopy was used to investigate morphological changes caused by PK11195. The production of free oxygen radicals, nitric oxide, and pro-inflammatory cytokines was also evaluated in infected macrophages treated with PK11195 and primed or not primed with IFN-γ. FINDINGS Median IC50 values for PK11195 were 14.2 µM for L. amazonensis, 8.2 µM for L. major, and 3.5 µM for L. braziliensis. The selective index value for L. amazonensis was 13.7, indicating the safety of PK11195 for future testing in mammals. Time- and dose-dependent reductions in the percentage of infected macrophages, the number of parasites per infected macrophage, and the number of viable intracellular parasites were observed. Electron microscopy revealed some morphological alterations suggestive of autophagy. Interestingly, MCP-1 and superoxide levels were reduced in L. amazonensis-infected macrophages treated with PK11195. MAIN CONCLUSIONS PK11195 causes the killing of amastigotes in vitro by mechanisms independent of inflammatory mediators and causes morphological alterations within Leishmania parasites, suggestive of autophagy, at doses that are non-toxic to macrophages. Thus, this molecule has demonstrated potential as an anti-leishmanial agent.
Piezoelectric and Pyroelectric Materials Selection

An attempt has been made to provide the ranking of piezoelectric and pyroelectric materials using technique for order preference by similarity to ideal solution (TOPSIS) method. To calculate weight (priority) for all the attributes (properties) understudy, entropy method is used. Interestingly my results suggest that dielectric constant is a key parameter (after d33 coefficient) which governs selection of piezoelectric materials. PLZT (8/65/35) and LiTaO3 ceramics place on first rank among studied piezoelectric and pyroelectric materials, respectively. These materials are classified using hierarchical clustering which shows similarities between the materials irrespective to their ranking obtained using TOPSIS method.
Models of Experimentally Derived Competitive Effects Predict Biogeographical Differences in the Abundance of Invasive and Native Plant Species

Mono-dominance by invasive species provides opportunities to explore determinants of plant distributions and abundance; however, linking mechanistic results from small scale experiments to patterns in nature is difficult. We used experimentally derived competitive effects of an invader in North America, Acroptilon repens, on species with which it co-occurs in its native range of Uzbekistan and on species with which it occurs in its non-native ranges in North America, in individual-based models. We found that competitive effects yielded relative abundances of Acroptilon and other species in models that were qualitatively similar to those observed in the field in the two ranges. In its non-native range, Acroptilon can occur in nearly pure monocultures at local scales, whereas such nearly pure stands of Acroptilon appear to be much less common in its native range. Experimentally derived competitive effects of Acroptilon on other species predicted Acroptilon to be 4–9 times more proportionally abundant than natives in the North American models, but proportionally equal to or less than the abundance of natives in the Eurasian models. Our results suggest a novel way to integrate complex combinations of interactions simultaneously, and that biogeographical differences in the competitive effects of an invader correspond well with biogeographical differences in abundance and impact.
Phosphorylation of MCAD selectively rescues PINK1 deficiencies in behavior and metabolism

PTEN-induced putative kinase 1 (PINK1) is a mitochondria-targeted kinase whose mutations are a cause of Parkinson’s disease. We set out to better understand PINK1’s effects on mitochondrial proteins in vivo. Using an unbiased phosphoproteomic screen in Drosophila, we found that PINK1 mediates the phosphorylation of MCAD, a mitochondrial matrix protein critical to fatty acid metabolism. By mimicking phosphorylation of this protein in a PINK1 null background, we restored PINK1 null’s climbing, flight, thorax, and wing deficiencies. Owing to MCAD’s role in fatty acid metabolism, we examined the metabolic profile of PINK1 null flies, where we uncovered significant disruptions in both acylcarnitines and amino acids. Some of these disruptions were rescued by phosphorylation of MCAD, consistent with MCAD’s rescue of PINK1 null’s organismal phenotypes. Our work validates and extends the current knowledge of PINK1, identifies a novel function of MCAD, and illuminates the need for and effectiveness of metabolic profiling in models of neurodegenerative disease.
Association between the ratio of triglyceride to high‐density lipoprotein cholesterol and incident type 2 diabetes in Singapore Chinese men and women

Increased triglycerides (TG) and decreased high‐density lipoprotein cholesterol (HDL‐C) are risk factors for type 2 diabetes (T2D). The relationship between TG:HDL‐C ratio and T2D risk is not clear, and it is not known whether the association is modified by gender, body mass index, or fasting status. This study examined the relationship between TG:HDL‐C ratio and risk of incident T2D, and the predictive ability of the ratio on top of other diabetes risk factors.