Miracle-dz/UniFAR-FTUs huggingface dataset:
Obesity and Diabetic Kidney Disease: Role of Oxidant Stress and Redox Balance.

SIGNIFICANCE Reactive oxygen species (ROS) reactive nitrogen species (RNS) and redox processes are of key importance in obesity- and diabetes-related kidney disease; however, there remains significant controversy in the field. RECENT ADVANCES New data from imaging and in vivo models of obesity and diabetic kidney disease have shed new insights into this field. In the setting of obesity- and diabetes-related kidney injury, there is a growing recognition that the major moieties of ROS and RNS are hydrogen peroxide and peroxynitrite with the enzymatic sources being NADPH oxidases and nitric oxide synthase, respectively. However, the role of mitochondrial superoxide as a driver of renal complications remains unclear. CRITICAL ISSUES Several key issues that are often not discussed are the specific ROS and RNS molecules, the source of generation, the location of production, and downstream targets. FUTURE DIRECTIONS Further understanding of the role of ROS/RNS/redox and their relationship with key signaling and metabolic pathways such as AMP-activated protein kinase (AMPK) and hypoxia-inducible factor 1-α (HIF1α) will be critical to a new understanding of kidney complications of caloric challenges and new therapeutic approaches. Antioxid. Redox Signal. 25, 208-216.
In situ near-tip normal strain evolution of a growing fatigue crack

Normal strains near a growing fatigue crack have been studied in situ using the Digital Image Correlation (DIC) technique in a compact tension specimen of stainless steel 316L under tension-tension cyclic loading. An error analysis of the measured displacements and strains has been carried out, and the results show that the precisions of displacements and strains in the direction perpendicular to the crack plane and ahead of the crack are better than those parallel to the crack plane and in the wake of the crack. The errors in the measured displacements are in the range of 0.06 to 0.1 m and between 0.2% and 0.4% for the measured strains, the latter are well below the critical strain at the onset of crack growth about 8%. Strain ratchetting was found ahead of the growing fatigue crack tip, albeit very close to the crack tip.
Fishing in the stream: Similarity search over endless data

Similarity search is the task of retrieving data items that are similar to a given query. In this paper, we introduce the time-sensitive notion of similarity search over endless data-streams (SSDS), which takes into account data quality and temporal characteristics in addition to similarity. SSDS is challenging as it needs to process unbounded data, while computation resources are bounded. We propose Stream-LSH, a randomized SSDS algorithm that bounds the index size by retaining items according to their freshness, quality, and dynamic popularity attributes. We show that Stream-LSH increases recall when searching for similar items compared to alternative approaches using the same space capacity.
Routability-Driven TSV-Aware Floorplanning Methodology for Fixed-Outline 3-D ICs

Although 3-D floorplanning has been studied widely, routability which is a very important issue in modern integrated circuit (IC) designs is rarely discussed. Floorplanning in 3-D ICs is much difficult than that in 2-D ICs because of large difference in sizes between modules and through silicon vias (TSVs), which are key components in 3-D ICs. And the locations of TSVs have great impact on wirelength and routability in resulting floorplans. Hence, this paper proposes a TSV-aware 3-D floorplanning methodology which can consider wirelength and routability at the same time under the fixed-outline constraint. Unlike most of previous works which completely apply the simulated annealing algorithm, our methodology mainly apply deterministic algorithms to resolve the problem. Thus, our approach is more efficient and flexible than previous works. Experimental results have demonstrated that the proposed methodology can significantly reduce routing congestion in 3-D ICs with a slight increase in wirelength.
Imitating human reaching motions using physically inspired optimization principles

We present an end-to-end framework which equips robots with the capability to perform reaching motions in a natural human-like fashion. A markerless, high-accuracy, model-based human motion tracker is used to observe how humans perform everyday activities in real-world scenarios. The obtained trajectories are clustered to represent different types of manipulation and reaching motions occurring in a kitchen environment. Using bilevel optimization methods a combination of physically inspired optimization principles is determined that describes the human motions best. For humanoid robots like the iCub these principles are used to compute reaching motion trajectories which are similar to human behavior and respect the individual requirements of the robotic hardware.
Entity Matching across Heterogeneous Sources

Given an entity in a source domain, finding its matched entities from another (target) domain is an important task in many applications. Traditionally, the problem was usually addressed by first extracting major keywords corresponding to the source entity and then query relevant entities from the target domain using those keywords. However, the method would inevitably fails if the two domains have less or no overlapping in the content. An extreme case is that the source domain is in English and the target domain is in Chinese. In this paper, we formalize the problem as entity matching across heterogeneous sources and propose a probabilistic topic model to solve the problem. The model integrates the topic extraction and entity matching, two core subtasks for dealing with the problem, into a unified model. Specifically, for handling the text disjointing problem, we use a cross-sampling process in our model to extract topics with terms coming from all the sources, and leverage existing matching relations through latent topic layers instead of at text layers. Benefit from the proposed model, we can not only find the matched documents for a query entity, but also explain why these documents are related by showing the common topics they share. Our experiments in two real-world applications show that the proposed model can extensively improve the matching performance (+19.8% and +7.1% in two applications respectively) compared with several alternative methods.
Evaluation of a pilot intervention to redesign the decentralised vaccine supply chain system in Nigeria

ABSTRACT Responsibility for immunisation in Nigeria is decentralised to sub-national governments. So far, they have failed to achieve optimal coverage for their populations. We evaluated a pilot intervention implemented between 2013 and 2014 to redesign a vaccine supply chain management system in Kano, Nigeria. The intervention included financing immunisation services from a designated pool of government and donor funds, a visibility tool to track vaccine stock, and a private vendor engaged to deliver vaccines directly to health facilities. The number of local government areas within the state with adequate vaccine stock increased from 21% to 98% after 10 months. To understand how the intervention achieved this outcome, we analysed immunisation coverage for the period and interviewed 18 respondents across different levels of government. We found that the intervention worked by improving ownership and accountability for immunisation by sub-national governments and their capacity for generating resources and management (of data and the supply chain). While the intervention focused on improving immunisation coverage, we identified gaps in the demand for services. Efforts to improve immunisation coverage and vaccine supply systems should streamline decentralised structures, empower sub-national governments with financial and technical capacity, and promote strategies to improve the demand and use of services.
Effectiveness of Probiotic, Prebiotic, and Synbiotic Therapies in Reducing Postoperative Complications: A Systematic Review and Network Meta-analysis.

Background Microbiome-directed therapies are increasingly used preoperatively and postoperatively to improve postoperative outcomes. Recently, the effectiveness of probiotics, prebiotics, and synbiotics in reducing postoperative complications (POCs) has been questioned. This systematic review aimed to examine and rank the effectiveness of these therapies on POCs in adult surgical patients. Methods We searched for articles from PubMed, Embase, Cochrane, Web of Science, Scopus, and CINAHL plus. From 2002 to 2015, 31 articles meeting the inclusion criteria were identified in the literature. Risk of bias and heterogeneity were assessed. Network meta-analyses (NMA) were performed using random-effects modeling to obtain estimates for study outcomes. Risk ratios (RRs) and 95% confidence intervals (CIs) were estimated. We then ranked the comparative effects of all regimens with the surface under the cumulative ranking (SUCRA) probabilities. Results A total of 2,952 patients were included. We found that synbiotic therapy was the best regimen in reducing surgical site infection (SSI) (RR = 0.28; 95% CI, 0.12-0.64) in adult surgical patients. Synbiotic therapy was also the best intervention to reduce pneumonia (RR = 0.28; 95% CI, 0.09-0.90), sepsis (RR = 0.09; 95% CI, 0.01-0.94), hospital stay (mean = 9.66 days, 95% CI, 7.60-11.72), and duration of antibiotic administration (mean = 5.61 days, 95% CI, 3.19-8.02). No regimen significantly reduced mortality. Conclusions This network meta-analysis suggests that synbiotic therapy is the first rank to reduce SSI, pneumonia, sepsis, hospital stay, and antibiotic use. Surgeons should consider the use of synbiotics as an adjunctive therapy to prevent POCs among adult surgical patients. Increasing use of synbiotics may help to reduce the use of antibiotics and multidrug resistance.
Computing the fundamental interactions between carbon nanotubes and pulmonary surfactant proteins

Molecular dynamic computation is one of the most direct and detailed approaches for investigating protein and carbon nanotube interaction at the atomic level. Molecular dynamic computation can address the events occurring in a protein’s structure and on the surface of the carbon nanotube. Molecular dynamic computation can also explain the structural changes in protein, including (i) secondary and tertiary structure changes, (ii) orientation and reorientation of the protein before and after adsorption, (iii) behavior of each amino acid residual group, (iv) hydrogen-bonding, (v) pi-pi stacking of carbon atoms of proteins and carbon nanotube, and other things as well. These fundamental properties have to address the adsorption of protein on a carbon nanotube surface, and estimates of this process are produced by molecular dynamic computations. Also, molecular dynamic computation is an attractive method for 3D imaging in bionanotechnology because it can give a complete trajectory over time (tens or hundreds of nanoseconds) of all atoms of protein interacting with carbon nanotubes and thus clarify their behavior in a given environment. vi This work presents the fundamental understanding of the human pulmonary surfactant proteins SP-A, SP-B, SP-C, and SP-D and their interaction with a singlewalled carbon nanotube. This is accomplished using nanoscale molecular dynamic computation. Atomistic molecular dynamic simulation is performed and a trajectory over 100 ns is computed. Results show that all four pulmonary surfactant proteins are adsorbed on the surface of a carbon nanotube. The main driving force of interaction is the Van der Waals force of attraction. From the root mean square deviation of all four protein trajectories, stability is achieved. Both hydrophobic and hydrophilic residues of proteins are adsorbed on the surface of a carbon nanotube. These results will be helpful in developing nano-electro-chemical biosensors in the future.
Phylogenetic Revision of the Genus Peltigera (Lichen‐Forming Ascomycota) Based on Morphological, Chemical, and Large Subunit Nuclear Ribosomal DNA Data

Peltigera (Peltigerineae, lichenized Ascomycota) is one of the most widespread lichen genera incorporating bi‐ and trimembered associations involving fungi, green algae (cf. Coccomyxa), and cyanobacteria (cf. Nostoc). A wide range of morphological and chemical (secondary compounds) variation at both the intra‐ and interspecific levels is present in this genus. Compared to many other genera of macrolichens, its taxonomy, including chemotaxonomy, still remains poorly understood. Existing infrageneric classifications of Peltigera are almost exclusively based on photobiont composition of the thallus. These classifications assumed that bi‐ and trimembered taxa were distinct monophyletic entities. The genus Peltigera has never been the focus of a comprehensive phylogenetic study. The most recent and widely accepted subdivision of the genus into seven groups is based mainly on morphological and chemical characters. Relationships among species of Peltigera are investigated here using chemical, morphological, and large subunit nuclear ribosomal DNA (LSU nrDNA) data. We test the monophyly of these seven morpho‐chemical Peltigera groups and propose a classification based on a phylogenetic approach. Data sets of 42 chemical characters (terpenoids), 31 morphological characters, and 1135 LSU nrDNA characters for 96 samples representing 38 Peltigera species, eight undescribed putative Peltigera species, and nine species from seven potentially closely related genera from Peltigerineae were subjected to maximum parsimony analyses. Morphological, chemical, and molecular analyses were carried out independently and on a combined data set. Monophyly of Peltigera, including Hydrothyria, was confirmed. The genus Hydrothyria is transferred to Peltigera and a new combination Peltigera hydrothyria Miadlikowska & Lutzoni is proposed. Eight monophyletic sections within the genus Peltigera, with high bootstrap support, are circumscribed: sections Peltigera, Polydactylon Miadlikowska & Lutzoni, Chloropeltigera Gyeln. , Peltidea (Ach.) Vain. , Horizontales Miadlikowska & Lutzoni, Retifoveatae Miadlikowska & Lutzoni, Phlebia Wallr. , and Hydrothyriae Miadlikowska & Lutzoni. Unequivocal morphological and chemical synapomorphies for all sections except section Peltidea are recognized and presented. A key for identification of the sections is provided. In addition, a key based on four main terpenoids for determination of the chemotypes and species within section Polydactylon is included. Five terpenoids (50–54) identified on thin‐layer chromatography plates for P. elisabethae and P. horizontalis chemotype I are added to the list of substances found in Peltigera. Five chemotypes, mainly from Poland and Norway, are reported from Peltigera thalli for the first time: P. malacea chemotype V, P. leucophlebia chemotype II, P. hymenina chemotypes II and III, and P. collina chemotype IV. Three main types of vein structure in Peltigera were recognized based on SEM studies.
Progress in Understanding the Molecular Basis Underlying Functional Diversification of Cyclic Dinucleotide Turnover Proteins

ABSTRACT Cyclic di-GMP was the first cyclic dinucleotide second messenger described, presaging the discovery of additional cyclic dinucleotide messengers in bacteria and eukaryotes. The GGDEF diguanylate cyclase (DGC) and EAL and HD-GYP phosphodiesterase (PDE) domains conduct the turnover of cyclic di-GMP. These three unrelated domains belong to superfamilies that exhibit significant variations in function, and they include both enzymatically active and inactive members, with a subset involved in synthesis and degradation of other cyclic dinucleotides. Here, we summarize current knowledge of sequence and structural variations that underpin the functional diversification of cyclic di-GMP turnover proteins. Moreover, we highlight that superfamily diversification is not restricted to cyclic di-GMP signaling domains, as particular DHH/DHHA1 domain and HD domain proteins have been shown to act as cyclic di-AMP phosphodiesterases. We conclude with a consideration of the current limitations that such diversity of action places on bioinformatic prediction of the roles of GGDEF, EAL, and HD-GYP domain proteins.
Lubricant Provides Poor Rectal Mucosal HIV Coverage.

Given the rising HIV incidence in men who have sex with men (MSM) despite repeatedly proven effectiveness of oral HIV pre-exposure prophylaxis, behaviorally congruent periodic dosing strategies, such as dosing microbicides as lubricants, are now in demand. Rectal microbicide gel studies largely administer gels using vaginal applicators, which have not been well received and do not mimic lubricant use. We compared rectal gel manually dosed as lubricant with applicator dosing in five healthy, HIV-negative MSM who received 10 or 3.5 ml of 99mTc-DTPA-radiolabeled hydroxyethyl cellulose universal placebo gel intrarectally. After washout, participants received 10 ml of radiolabeled Wet® Original® lubricant to apply to the anus with fingers and/or a phallus in a manner typical of sexual lubricant use with a partner, followed by simulated receptive anal intercourse. Single-photon emission computed tomography with transmission computed tomography was performed 4 h after each gel administration. Manual dosing was associated with more variable rectosigmoid distribution, 4.4-15.3 cm from the anorectal junction, compared with more uniform distribution, 5.9-7.4 and 5.3-7.6 cm after 10 and 3.5 ml applicator dosing, respectively. A significantly smaller fraction of the initial 10 ml dose was retained within the colon after manual dosing, 3.4%, compared with 94.9% and 88.4% after 10 and 3.5 ml applicator dosing, respectively (both p < .001). Manual dosing of a sexual lubricant delivered a small, variable fraction of the dose with variable rectosigmoid distribution compared with applicator dosing. These results raise concern that dosing a rectal microbicide gel as a sexual lubricant may not provide adequate or predictable mucosal coverage for HIV protection.
Models and Information Rates for Wiener Phase Noise Channels

A waveform channel is considered where the transmitted signal is corrupted by Wiener phase noise and additive white Gaussian noise. A discrete-time channel model that considers the effect of filtering on the phase noise is developed. The model is based on a multi-sample receiver, i.e., an integrate-and-dump filter whose output is sampled at a rate higher than the signaling rate. It is shown that, at high Signal-to-Noise Ratio (SNR), the multi-sample receiver achieves a rate that grows logarithmically with the SNR if the number of samples per symbol (oversampling factor) grows with the cubic root of the SNR. Moreover, the pre-log factor is at least 1/2 and can be achieved by amplitude modulation. For an approximate discrete-time model of the multi-sample receiver, the capacity pre-log at high SNR is shown to be at least 3/4 if the number of samples per symbol grows with the square root of the SNR. The analysis shows that phase modulation achieves a pre-log of at least 1/4, while amplitude modulation still achieves a pre-log of 1/2. This is strictly greater than the capacity pre-log of the (approximate) discrete-time Wiener phase noise channel with only one sample per symbol, which is 1/2. Numerical simulations are used to compute lower bounds on the information rates achieved by the multi-sample receiver. The simulations show that oversampling is beneficial for both strong and weak phase noise at high SNR. In fact, the information rates are sometimes substantially larger than when using commonly-used approximate discrete-time models.
Genome Sequences of 12 Pseudomonas lundensis Strains Isolated from the Lungs of Humans

ABSTRACT We report here the first complete genome sequence of a human Pseudomonas lundensis isolate, strain AU1044, and the draft genomes of 11 other clinical P. lundensis strains, isolated from the lungs of cystic fibrosis patients. The genome of strain AU1044 is 4.81 Mb and encodes seven 16S rRNAs.
SteadyCom: Predicting microbial abundances while ensuring community stability

Genome-scale metabolic modeling has become widespread for analyzing microbial metabolism. Extending this established paradigm to more complex microbial communities is emerging as a promising way to unravel the interactions and biochemical repertoire of these omnipresent systems. While several modeling techniques have been developed for microbial communities, little emphasis has been placed on the need to impose a time-averaged constant growth rate across all members for a community to ensure co-existence and stability. In the absence of this constraint, the faster growing organism will ultimately displace all other microbes in the community. This is particularly important for predicting steady-state microbiota composition as it imposes significant restrictions on the allowable community membership, composition and phenotypes. In this study, we introduce the SteadyCom optimization framework for predicting metabolic flux distributions consistent with the steady-state requirement. SteadyCom can be rapidly converged by iteratively solving linear programming (LP) problem and the number of iterations is independent of the number of organisms. A significant advantage of SteadyCom is compatibility with flux variability analysis. SteadyCom is first demonstrated for a community of four E. coli double auxotrophic mutants and is then applied to a gut microbiota model consisting of nine species, with representatives from the phyla Bacteroidetes, Firmicutes, Actinobacteria and Proteobacteria. In contrast to the direct use of FBA, SteadyCom is able to predict the change in species abundance in response to changes in diets with minimal additional imposed constraints on the model. By randomizing the uptake rates of microbes, an abundance profile with a good agreement to experimental gut microbiota is inferred. SteadyCom provides an important step towards the cross-cutting task of predicting the composition of a microbial community in a given environment.
Complementary Perception for Handheld SLAM

We present a novel method for mapping general three-dimensional environments, where sufficient geometric or visual information is not everywhere guaranteed and where the device motion is unconstrained as with handheld systems. The continuous-time simultaneous localization and mapping algorithm integrates a lidar, camera, and inertial measurement unit in a complementary fashion whereby all sensors contribute constraints to the optimization. The proposed algorithm is designed to expand the domain of mappable environments and therefore increase the reliability and utility of general purpose mobile mapping. A key component of the proposed algorithm is the incorporation of depth uncertainty into visual features, which is effective for noisy surfaces and allows features with and without depth estimates to be modeled in a unified manner. Results demonstrate a wider mappable domain on challenging environments compared to the state-of-the-art lidar or vision-based localization and mapping algorithms.