Miracle-dz/UniFAR-FTUs huggingface dataset:
Muramyl Dipeptide, a Shared Structural Motif of Peptidoglycans, Is a Novel Inducer of Bone Formation through Induction of Runx2

Peptidoglycan fragments released from gut microbiota can be delivered to the bone marrow and affect bone metabolism. We investigated the regulation of bone metabolism by muramyl dipeptide (MDP), which is a shared structural unit of peptidoglycans. Increased bone and mineral density by enhanced bone formation were observed in mice administered with MDP. Remarkably, pretreatment or posttreatment with MDP alleviated bone loss in RANKL‐induced osteoporosis mouse models. MDP directly augmented osteoblast differentiation and bone‐forming gene expression by Runx2 activation. Despite no direct effect, MDP indirectly attenuated osteoclast differentiation through downregulation of the RANKL/osteoprotegerin (OPG) ratio. MDP increased the expression of the MDP receptor, Nod2, and MDP‐induced bone formation and osteoblast activation did not occur during Nod2 deficiency. Other Nod2 ligands also increased bone formation through the induction of Runx2, as MDP did. In conclusion, we suggest that MDP is a novel inducer of bone formation that could potentially be a new therapeutic molecule to protect against osteoporosis. © 2017 American Society for Bone and Mineral Research.
A novel Group Template Pattern Classifiers (GTPCs) method in protein secondary structure prediction

Protein secondary structure prediction is a fundamental problem and is much more challenging. In this study we propose a novel method called Group Template Pattern Classifiers (GTPCs), which captures the long-range interactions of the whole protein at a great degree. Firstly the protein dataset is divided into several groups based on the length of proteins. The proteins with “similar” length in each group are used to build the prediction model. Then Wavelets are used to extract the features of PSSM profile, and characterize the changing information of PSSM profile. A new protein can be predicted by the corresponding GTPCs model based on the new protein length. Experiments are performed on 25PDB, CB513, CASP9, CASP10, CASP11, and CASP12 datasets, and the good performance of 86.38%, 84.11%, 83.92%, 83.07%, 81.98%, and 82.35% is achieved respectively using 6 GTPCs model. Our experimental results are better than other state of the art methods. (http://qilubio.qlu.edu.cn /protein_GTPC)
Vermicompost Amended Pine Bark Substrate Improves Nursery Crop Production

MCGINNIS, MICHELLE S. Vermicompost Amended Pine Bark Substrate Improves Nursery Crop Production. (Under the direction of Stuart L. Warren and Ted E. Bilderback.) Several field, greenhouse, and laboratory studies were conducted to evaluate the effects of vermicomposted (VC) hog manure amended to pine bark (PB) on substrate physical properties, plant growth and flower production, water use efficiency of productivity (WUEP), effluent nitrogen and phosphorus content, substrate solution pH, macronutrient release rate characteristics, and the ability of VC to replace conventional fertilizer nutrient inputs. Nitrogen and phosphorus budgets were determined, and nutrient use efficiencies of nitrogen (NUEN) and phosphorus (NUEP) were calculated. Container capacity and available water increased linearly and air space decreased linearly with increasing rate of VC. Growth of several species increased linearly with increasing VC rate with no traditional amendments of limestone and micronutrients; and 20% VC resulted in greater plant dry weights than the PB control (amended with limestone and micronutrients). However, there were species where growth decreased linearly with increased VC rate, while the 20% VC maintained equivalent dry weights to the PB control. The WUEP of several species were improved compared to the control. Liming effects of 5% VC were equivalent to the control receiving limestone, whereas VC rates >10% had greater liming effects compared to the respective control. Twenty percent VC provided sufficient quantities of P, Ca, Mg, S, and micronutrients such that an additional supply of these nutrients need not be applied. Although 20% VC did not supply K in quantities comparable to traditional inputs, the reduction of K did not affect growth or flower bud production of hibiscus. Macronutrient release rates (determined on a volume basis) of N and S from VC followed a first-order model, Ca and Mg followed a two pool first/zero-order model, and P followed a zero-order model. The tissue nutrient content of N, Ca, Mg, and S increased with increasing VC rate while P decreased with decreasing VC rate. Vermicompost in the substrate increased N and P effluent content, but reducing the leaching fraction decreased nutrient contents. The NUEN ranged from 9% to 20% with no major differences between substrate or leaching fraction treatments. However, the NUEP was improved when VC was amended to the substrate. Vermicompost Amended Pine Bark Substrate Improves Nursery Crop Production by Michelle S. McGinnis A dissertation submitted to the Graduate Faculty of North Carolina State University in partial fulfillment of the requirements for the Degree of Doctor of Philosophy Horticultural Science Raleigh, North Carolina
Genetic Programming-Evolved Spatio-Temporal Descriptor for Human Action Recognition

The potential value of human action recognition has led to it becoming one of the most active research subjects in computer vision. In this paper, we propose a novel method to automatically generate low-level spatio-temporal descriptors showing good performance, for high-level human-action recognition tasks. We address this as an optimization problem using genetic programming (GP), an evolutionary method, which produces the descriptor by combining a set of primitive 3D operators. As far as we are aware, this is the first report of using GP for evolving spatio-temporal descriptors for action recognition. In our evolutionary architecture, the average cross-validation classification error calculated using the support-vector machine (SVM) classifier is used as the GP fitness function. We run GP on a mixed dataset combining the KTH and the Weizmann datasets to obtain a promising feature-descriptor solution for action recognition. To demonstrate generalizability, the best descriptor generated so far by GP has also been tested on the IXMAS dataset leading to better accuracies compared with some previous hand-crafted descriptors.
Simultaneous determination of thermodynamic and kinetic parameters of aminopolycarbonate complexes of cobalt(II) and nickel(II) based on isothermal titration calorimetry data

The influence of the different side chain residues on the thermodynamic and kinetic parameters for complexation reactions of the Co2+ and Ni2+ ions has been investigated by using the isothermal titration calorimetry (ITC) technique supported by potentiometric titration data. The study was concerned with the 2 common tripodal aminocarboxylate ligands, namely, nitrilotriacetic acid and N‐(2‐hydroxyethyl) iminodiacetic acid. Calorimetric measurements (ITC) were run in the 2‐(N‐morpholino)ethanesulfonic acid hydrate (2‐(N‐morpholino) ethanesulfonic acid), piperazine‐N,N′‐bis(2‐ethanesulfonic acid), and dimethylarsenic acid buffers (0.1 mol L−1, pH 6) at 298.15 K. The quantification of the metal‐buffer interactions and their incorporation into the ITC data analysis enabled to obtain the pH‐independent and buffer‐independent thermodynamic parameters (K, ΔG, ΔH, and ΔS) for the reactions under study. Furthermore, the kinITC method was applied to obtain kinetic information on complexation reactions from the ITC data. Correlations, based on kinetic and thermodynamic data, between the kinetics of formation of Co2+ and Ni2+ complexes and their thermodynamic stabilities are discussed.
Overlapping T cell antigenic sites on a synthetic peptide fragment from herpes simplex virus glycoprotein D, the degenerate MHC restriction elicited, and functional evidence for antigen-Ia interaction

Analysis of the B10.A T cell response to synthetic peptides representing the NH2-terminal 23 amino acids from the HSV glycoprotein D sequence revealed two antigenic determinants for T cells: one localized between residues 1-16 and the other between residues 8-23. The 1-16 site, which is helical, was recognized in the context of the Ia molecule, whereas the 8-23 site, which is nonhelical, was recognized in the context of the I-E molecule. The I-E-restricted response was found to be highly MHC degenerate in that T cell hybridomas specific for the 8-23 peptide responded to antigen on APCs derived from B10.A, B10.A(5R), and B10.A(9R) mice and showed differences in antigenic fine specificity with APCs of different haplotypes. These data support the idea of antigen-Ia interaction.
Incidence and risk factors associated with the development of pressure ulcers in an intensive care unit

AIMS AND OBJECTIVES To determinate the incidence, incidence rate and risk factors of pressure ulcers in critical care patients. BACKGROUND Pressure ulcers represent one of the most frequent health problems in clinical practice. Specifically, critical patients who are hospitalised in intensive care units have a higher risk of developing a pressure ulcer, with an incidence that fluctuates between 3.3-39.3% according to previous studies. DESIGN Prospective cohort study. METHODS Three hundred and thirty-five adult patients (over 18 years old) who were hospitalised in intensive care units for at least 24 hr were monitored for a maximum of 32 days. They were excluded if they had a pressure ulcers at admission. The survival rate for pressure ulcers, from stages I-IV, was calculated using the Kaplan-Meier method. A multivariate Cox regression model was adjusted to identify the main risk factors for pressure ulcers: demographic, clinical, prognostic and therapeutic variables. RESULTS The incidence of pressure ulcers in critical patients was 8.1%, and the incidence rate was 11.72 pressure ulcers for 1,000 days of intensive care units stay; 40.6% of pressure ulcers were of stage I and 59.4% of stage II, mainly in the sacrum. According to the Cox model, the main risk factors for pressure ulcers were in-hospital complications, prognostic scoring system (SAPS III) and length of immobilisation. CONCLUSIONS The incidence of pressure ulcers is lower than that shown in recent studies. Complications on the unit and the prognosis score were risk factors associated with pressure ulcers but, surprisingly, length of immobilisation was a protective factor. RELEVANCE TO CLINICAL PRACTICE Survival analysis of pressure ulcer allows for identification of risk factors associated with this health problem in the intensive care units. Identifying these factors can help nurses establish interventions to prevent pressure ulcers in this healthcare scenario, given that pressure ulcers prevention is an indicator of nursing quality.
Characterization, Quantification and Compound-specific Isotopic Analysis of Pyrogenic Carbon Using Benzene Polycarboxylic Acids (BPCA)

Fire-derived, pyrogenic carbon (PyC), sometimes called black carbon (BC), is the carbonaceous solid residue of biomass and fossil fuel combustion, such as char and soot. PyC is ubiquitous in the environment due to its long persistence, and its abundance might even increase with the projected increase in global wildfire activity and the continued burning of fossil fuel. PyC is also increasingly produced from the industrial pyrolysis of organic wastes, which yields charred soil amendments (biochar). Moreover, the emergence of nanotechnology may also result in the release of PyC-like compounds to the environment. It is thus a high priority to reliably detect, characterize and quantify these charred materials in order to investigate their environmental properties and to understand their role in the carbon cycle. Here, we present the benzene polycarboxylic acid (BPCA) method, which allows the simultaneous assessment of PyC's characteristics, quantity and isotopic composition (13C and 14C) on a molecular level. The method is applicable to a very wide range of environmental sample materials and detects PyC over a broad range of the combustion continuum, i.e., it is sensitive to slightly charred biomass as well as high temperature chars and soot. The BPCA protocol presented here is simple to employ, highly reproducible, as well as easily extendable and modifiable to specific requirements. It thus provides a versatile tool for the investigation of PyC in various disciplines, ranging from archeology and environmental forensics to biochar and carbon cycling research.
Challenges and recent advances in MOF–polymer composite membranes for gas separation

Membrane technology has attracted tremendous attention in the field of gas separation due to its low cost and energy consumption. Polymer membranes are used in some industrial-scale gas separation processes, however, they often suffer a trade-off between permeability and selectivity. To overcome this limitation, porous materials with molecular sieve properties have been combined with polymers to give membranes with enhanced gas separation performance. Metal–organic frameworks (MOFs) are nanoporous materials possessing ultrahigh porosity, large surface area, structural diversity and rich functionalities, which make them promising candidates for gas separation. This review primarily focuses on the fabrication methods of MOF–polymer composite membranes including MOF-based mixed-matrix membranes (MMMs) and polymer supported MOF membranes. Recent progress in MOF membrane fabrication, incorporating the challenges and difficulties faced, are presented. Furthermore, corresponding solutions and strategies are given in detail to offer instructions to fabricate membranes with ideal morphology and performance.
Corpus Callosotomy for Intractable Epilepsy Revisited: The Children’s Hospital of Michigan Series

Corpus callosotomy is a palliative procedure performed to reduce the severity of drug-resistant epilepsy. The authors assessed its efficacy on different seizure types in 20 subjects (age range 5-19 years); 8 with active vagus nerve stimulator. Fifteen had complete callosotomy, 3 had anterior 2/3, and 2 had anterior 2/3 followed later by complete callosotomy. Ten had endoscopic approach. In all, 65% had ≥ 50% reduction of generalized seizures leading to falls (atonic, tonic, myoclonic); 35% became seizure-free (follow-up period: 6 months to 9 years; mean 3 years). Seizure outcome distribution was better for generalized than for partial seizures (P = .003). Endoscopic approach was as effective as transcranial approach. Seven subjects who failed vagus nerve stimulator therapy responded with ≥50% seizure reduction. Corpus callosotomy is an effective treatment for intractable generalized epilepsy leading to falls with significant seizure reduction or even elimination of seizures, in the majority of children.
Experimental study and statistical evaluation for impact resistance of steel fiber reinforced lightweight aggregate concrete

The impact resistance of steel fiber reinforced lightweight aggregate concrete (SFLWC) was presented in a drop-weight test. In this test,5 groups of discal specimens with different steel fiber volume fractions including 0,0.5%,1.0%,1.5% and 2.0% were tested. The experimental results indicate that the impact resistance of lightweight aggregate concrete is improved with the increase in fiber volume fraction. As the variation in experimental results,a statistical evaluation was performed to study the influence of impact resistance of SFLWC with different steel fiber volume fractions. Furthermore,the impact resistance was simulated with probability distribution by log-normal distribution and two-parameters Weibull distribution,respectively. And the goodnees-of-fit tests indicate that the log-normal distribution and Weibull distribution both have good fitness to the impact resistance of steel fiber reinforced lightweight aggregate concrete. Lastly,the impact resistance formulas for SFLWC with each steel fiber addition are developed to facilitate the application.
Apportioning bacterial carbon source utilization in soil using 14C isotope analysis of FISH‐targeted bacterial populations sorted by fluorescence activated cell sorting (FACS): 14C‐FISH‐FACS

An unresolved need in microbial ecology is methodology to enable quantitative analysis of in situ microbial substrate carbon use at the population level. Here, we evaluated if a novel combination of radiocarbon-labelled substrate tracing, fluorescence in situ hybridisation (FISH) and fluorescence-activated cell sorting (FACS) to sort the FISH-targeted population for quantification of incorporated radioactivity (14 C-FISH-FACS) can address this need. Our test scenario used FISH probe PSE1284 targeting Pseudomonas spp. (and some Burkholderia spp.) and salicylic acid added to rhizosphere soil. We examined salicylic acid-14 C fate (mineralized, cell-incorporated, extractable and non-extractable) and mass balance (0-24 h) and show that the PSE1284 population captured ∼ 50% of the Nycodenz extracted biomass 14 C. Analysis of the taxonomic distribution of the salicylic acid biodegradation trait suggested that PSE1284 population success was not due to conservation of this trait but due to competitiveness for the added carbon. Adding 50KBq of 14 C sample-1 enabled detection of 14 C in the sorted population at ∼ 60-600 times background; a sensitivity which demonstrates potential extension to analysis of rarer/less active populations. Given its sensitivity and compatibility with obtaining a C mass balance, 14 C-FISH-FACS allows quantitative dissection of C flow within the microbial biomass that has hitherto not been achieved.
CCLBR: Congestion Control-Based Load Balanced Routing in Unstructured P2P Systems

Given the growing popularity of the peer-to-peer (P2P) network systems in the recent years, efficient query routing under highly dynamic environments is still lacking in several P2P network systems. In response to this challenge, this paper proposes a new churn-resilient system to find alternative routing paths for the purpose of balancing the query loads under higher network churns and heavy workloads, ultimately to improve the search efficiency. Two novel methods are devised to balance the network query loads among both inter- and intragroup level peers. First, a resource grouping and a rewiring method is proposed to spontaneously organize and cluster the peers having same resources together. This strategy facilitates the peers to evolve the network into a cluster-like topology and balances the query loads among the intergroup peers. Second, a collaborative Q-learning method is proposed to balance the query loads among the intragroup peers in order to intelligently avoid queries being forwarded to the congested peers in the network. Experiments conducted under dynamic network scenarios demonstrate that our proposed method achieves better search performances with a more balanced network load than the existing methods, and further exhibits higher robustness and adaptability under higher network churns and heavy network loads.
Classification of normal and dysphagia in patients with GERD using swallowing sound analysis

In recent years, acoustical analysis of the swallowing mechanism has received considerable attention and because of many damages of invasive methods, it is preferred. This paper proposes acoustic-based method to separate dysphagia patients with reflux disorder from normal persons. In this work, we have used swallowing sound of 22 individuals (11 normal and 11 abnormal). Swallowing sound signals were recorded with sound recorder over the trachea and ambient noise was removed and spectral features were extracted from the sounds. Classification is done by non-linear support vector machines, using leave-one-out. According to the experimental results, the system can classify 66.1% of total swallow signals correctly (signal accuracy) and 95.7% of the total subject in a group of healthy and dysphagia patients (subject accuracy). The experimental results show that the proposed system can provide concrete features for clinicians to diagnose dysphagia in reflux patients.
Expression of androgen receptor in mouse eye tissues.

PURPOSE To test the possibility that androgen directly affects the corneal cells, the possible occurrence of androgen receptor (AR) in the cornea and other eye tissues of mice was examined. METHODS To examine the occurrence of AR protein in the mouse eye tissues, an immunocytochemical method was used. To examine the occurrence of AR mRNA in the cornea and lens, reverse transcription-polymerase chain reaction (RT-PCR) was used. RESULTS Immunocytochemical examination revealed that antigenicity for AR antibody exists in cell nuclei of cornea, lens, iris, and ciliary body of both male and female mice. RT-PCR revealed that mRNA of AR occurs in the cornea and lens of both male and female mice. CONCLUSIONS It is concluded that AR occurs in cells of cornea, lens, iris, and ciliary body of the mouse eye. Androgen may affect cells in these tissues directly through interaction with AR.
Multitask Feature Learning for Low-Resource Query-by-Example Spoken Term Detection

We propose a novel technique that learns a low-dimensional feature representation from unlabeled data of a target language, and labeled data from a nontarget language. The technique is studied as a solution to query-by-example spoken term detection (QbE-STD) for a low-resource language. We extract low-dimensional features from a bottle-neck layer of a multitask deep neural network, which is jointly trained with speech data from the low-resource target language and resource-rich nontarget language. The proposed feature learning technique aims to extract acoustic features that offer phonetic discriminability. It explores a new way of leveraging cross-lingual speech data to overcome the resource limitation in the target language. We conduct QbE-STD experiments using the dynamic time warping distance of the multitask bottle-neck features between the query and the search database. The QbE-STD process does not rely on an automatic speech recognition pipeline of the target language. We validate the effectiveness of multitask feature learning through a series of comparative experiments.
Micro-epidemiological structuring of Plasmodium falciparum parasite populations in regions with varying transmission intensities in Africa. [version 1; referees: awaiting peer review]

Background The first models of malaria transmission assumed a completely mixed and homogeneous population of parasites. Recent models include spatial heterogeneity and variably mixed populations. However, there are few empiric estimates of parasite mixing with which to parametize such models. Methods Here we genotype 276 single nucleotide polymorphisms (SNPs) in 5199 P. isolates from two Kenyan sites and one Gambian site to determine falciparum the spatio-temporal extent of parasite mixing, and use Principal Component Analysis (PCA)