Miracle-dz/UniFAR-FTUs huggingface dataset:
Anaerobic Methane Oxidation Driven by Microbial Reduction of Natural Organic Matter in a Tropical Wetland

ABSTRACT Wetlands constitute the main natural source of methane on Earth due to their high content of natural organic matter (NOM), but key drivers, such as electron acceptors, supporting methanotrophic activities in these habitats are poorly understood. We performed anoxic incubations using freshly collected sediment, along with water samples harvested from a tropical wetland, amended with 13C-methane (0.67 atm) to test the capacity of its microbial community to perform anaerobic oxidation of methane (AOM) linked to the reduction of the humic fraction of its NOM. Collected evidence demonstrates that electron-accepting functional groups (e.g., quinones) present in NOM fueled AOM by serving as a terminal electron acceptor. Indeed, while sulfate reduction was the predominant process, accounting for up to 42.5% of the AOM activities, the microbial reduction of NOM concomitantly occurred. Furthermore, enrichment of wetland sediment with external NOM provided a complementary electron-accepting capacity, of which reduction accounted for ∼100 nmol 13CH4 oxidized · cm−3 · day−1. Spectroscopic evidence showed that quinone moieties were heterogeneously distributed in the wetland sediment, and their reduction occurred during the course of AOM. Moreover, an enrichment derived from wetland sediments performing AOM linked to NOM reduction stoichiometrically oxidized methane coupled to the reduction of the humic analogue anthraquinone-2,6-disulfonate. Microbial populations potentially involved in AOM coupled to microbial reduction of NOM were dominated by divergent biota from putative AOM-associated archaea. We estimate that this microbial process potentially contributes to the suppression of up to 114 teragrams (Tg) of CH4 · year−1 in coastal wetlands and more than 1,300 Tg · year−1, considering the global wetland area. IMPORTANCE The identification of key processes governing methane emissions from natural systems is of major importance considering the global warming effects triggered by this greenhouse gas. Anaerobic oxidation of methane (AOM) coupled to the microbial reduction of distinct electron acceptors plays a pivotal role in mitigating methane emissions from ecosystems. Given their high organic content, wetlands constitute the largest natural source of atmospheric methane. Nevertheless, processes controlling methane emissions in these environments are poorly understood. Here, we provide tracer analysis with 13CH4 and spectroscopic evidence revealing that AOM linked to the microbial reduction of redox functional groups in natural organic matter (NOM) prevails in a tropical wetland. We suggest that microbial reduction of NOM may largely contribute to the suppression of methane emissions from tropical wetlands. This is a novel avenue within the carbon cycle in which slowly decaying NOM (e.g., humic fraction) in organotrophic environments fuels AOM by serving as a terminal electron acceptor.
Co‐evolution of specific amino acid in sigma 1.2 region and nucleotide base in the discriminator to act as sensors of small molecule effectors of transcription initiation in mycobacteria

The transcription from rrn and a number of other promoters is regulated by initiating ribonucleotides (iNTPs) and guanosine tetra/penta phosphate [(p)ppGpp], either by strengthening or by weakening of the RNA polymerase (RNAP)–promoter interactions during initiation. Studies in Escherichia coli revealed the importance of a sequence termed discriminator, located between −10 and the transcription start site of the responsive promoters in this mode of regulation. Instability of the open complex at these promoters is attributed to the lack of stabilizing interactions between the suboptimal discriminator and the 1.2 region of sigma 70 (Sig70) in RNAP holoenzyme. We demonstrate a different pattern of interaction between the promoters and sigma A (SigA) of Mycobacterium tuberculosis to execute similar regulation. Instead of cytosine and methionine, thymine at three nucleotides downstream to −10 element and leucine 232 in SigA are found to be essential for iNTPs and pppGpp mediated response at the rrn and gyr promoters of the organism. The specificity of the interaction is substantiated by mutational replacements, either in the discriminator or in SigA, which abolish the nucleotide mediated regulation in vitro or in vivo. Specific yet distinct bases and the amino acids appear to have ‘co‐evolved’ to retain the discriminator‐sigma 1.2 region regulatory switch operated by iNTPs/pppGpp during the transcription initiation in different bacteria.
Intelligent systems’ Holistic Evolving Analysis of Real-life Universal speaker characteristics

In this position paper we present the FP7 ERC starting grant project iHEARu (Intelligent systems’ Holistic Evolving Analysis of Real-life Universal speaker characteristics). This project addresses several fundamental shortcomings in state of the art methods for computational paralinguistics, by introducing holistic analysis, evolving learning of features and models, and collection of real-life, large-scale data annotated in multiple dimensions (‘universally’). We discuss the first aspect of the project, holistic analysis, in more detail, and give benchmark results using state of the art multi-target learning methods on the INTERSPEECH 2012 Speaker Trait Challenge dataset (Likability Sub-Challenge). The results clearly indicate the need for improved machine learning methods and data collection to learn holistic speaker classification.
A monoclonal antibody to a constant determinant of the rat T cell antigen receptor that induces T cell activation. Differential reactivity with subsets of immature and mature T lymphocytes

mAb R73 detects a T cell-specific surface molecule consisting of two disulfide-linked subunits of 40 and 46 kD, respectively, on 97% of peripheral rat T cells, as defined by the OX-52 marker. Of the few OX- 52+ R73- cells, none are CD4+ but many express the CD8 antigen known to be present on rat NK cells. mAb R73 is mitogenic for unseparated spleen cells and for purified T cells. In the absence of non-T "accessory cells", stimulation by R73 requires artificial crosslinking of the mAb and is largely dependent on exogenous IL-2. Overnight incubation of purified T cells with crosslinked R73 mAb induces blastoid transformation, IL-2-R expression, and modulation of the R73 antigen. In the rat thymus, mature medullary cells express the R73 determinant at the same level as peripheral T cells, whereas 94% of CD4-CD8- thymocytes are R73-. The major CD4+8+ thymocyte population contains 25% R73- and 70% R73low cells. Thymocytes of the CD4-CD8+OX-44- subpopulation that are the direct precursors of CD4+CD8+ cells display a continuum of R73 antigen density from undetectable to very low levels. We conclude that R73 is most likely directed at a constant determinant of the rat alpha/beta heterodimeric TCR and suggest that CD8+ immature thymocytes are the first cells in the T cell differentiation pathway to express this molecule at their surface.
HyperPlex: a World of 3D Interactive Digital Movies

We present a new environment for browsing a visual landscape inhabited by digital movies that live interact and play in a graphical vir tual world The movies are modeled as au tonomous agents which have their own sensors and goals and which can interpret the actions of the participant and react to them Our en vironment allows one or more people to in teract with the HyperPlex world through the use of vision techniques No goggles gloves or wires are needed interaction takes place with the use of computer vision techniques that an alyze the image of the person An extension of this system to a multi user game is currently being considered
Rationale for the Surgical Treatment of Lumbar Degenerative Spondylolisthesis

Study Design. A questionnaire survey. Objective. The aim of this study was to determine the effect of patient age, dynamic instability, and/or low back pain on the treatment of patients with a degenerative spondylolisthesis, and if the operative approach is affected by surgeon specialty, location, or practice model. Summary of Background Data. The classic treatment for patients with symptomatic degenerative spondylolisthesis is decompression and fusion; however in a select group of patients, an isolated decompression may be reasonable. Methods. A survey was sent to surgeon members of the Lumbar Spine Research Society and AOSpine requesting information regarding their preferred treatment of degenerative spondylolisthesis for a number of different clinical scenarios. Determinants included patient age, the presence of instability, symptoms of low back pain, surgeon's location, surgeon's specialty, and practice model. Results. A total of 223 spine surgeons completed the survey. Age of the patient, the presence of instability, and low back pain all significantly (P < 0.0001) affected the recommended treatment, which were independent of surgeon factors. Older patients were significantly less likely to be offered an interbody fusion and more likely to be recommended for an isolated decompression (P < 0.0001), and the presence of dynamic instability made an interbody fusion more likely than an isolated decompression (P < 0.0001). Of those who responded, 53.2% of surgeons reported they would recommend an isolated decompression for a properly selected patient with a degenerative spondylolisthesis. Conclusion. The most common operative treatment for a degenerative spondylolisthesis is a decompression and fusion; however, the results of this survey demonstrate that surgeons consider degenerative spondylolisthesis a heterogeneous condition that requires an individualized surgical plan. Future studies are needed to evaluate the effect of variables such as age, the presence of low back pain, and the presence of dynamic instability on patient reported outcomes from various surgical options. Level of Evidence: N/A.
Us hunters: interactive communication for young cavemen

This paper presents a multi-user virtual heritage application that allows children to experience and learn the hunting strategies depicted in a cave painting from 6000 B.C. The application is based on a multi-touch vertical screen that allows for full-body interaction through carefully defined gestures that provide sufficient ecological naturalness and experimentation freedom to the users. This paper gives a detailed account on the experience and interaction design, agent programming and multi-touch technology.
Airline Yield Management with Overbooking, Cancellations, and No-Shows

We formulate and analyze a Markov decision process (dynamic programming) model for airline seat allocation (yield management) on a single-leg flight with multiple fare classes. Unlike previous models, we allow cancellation, no-shows, and overbooking. Additionally, we make no assumptions on the arrival patterns for the various fare classes. Our model is also applicable to other problems of revenue management with perishable commodities, such as arise in the hotel and cruise industries. We show how to solve the problem exactly using dynamic programming. Under realistic conditions, we demonstrate that an optimal booking policy is characterized by state- and time-dependent booking limits for each fare class. Our approach exploits the equivalence to a problem in the optimal control of admission to a queueing system, which has been well studied in the queueing-control literature. Techniques for efficient implementation of the optimal policy and numerical examples are also given. In contrast to previous models, we show that 1) the booking limits need not be monotonic in the time remaining until departure; 2) it may be optimal to accept a lower-fare class and simultaneously reject a higher-fare class because of differing cancellation refunds, so that the optimal booking limits may not always be nested according to fare class; and 3) with the possibility of cancellations, an optimal policy depends on both the total capacity and the capacity remaining. Our numerical examples show that revenue gains of up to 9% are possible with our model, compared with an equivalent model omitting the effects of cancellations and no-shows. We also demonstrate the computational feasibility of our approach using data from a real-life airline application.
TPM1 polymorphisms and nonsyndromic orofacial clefts susceptibility in a Chinese Han population

Located at 15q22 a susceptibility region for nonsyndromic orofacial clefts (NSOC), TPM1 encodes a group of highly conserved ubiquitous actin‐binding proteins involved in the muscle contraction and cytoskeleton organization. Considering the multiple functions of TPM1 gene, we investigated the potential relationship between TPM1 polymorphisms and risk of NSOC in a Chinese Han population. Four tag single nucleotide polymorphisms (tSNPs) of TPM1 (rs11071720, rs3803499, rs12148828, and rs1972041) were selected to conduct a case‐control study with 673 NSOC patients and 705 unrelated healthy controls from a Chinese Han population. The SNPs were genotyped by the IPLEX Sequenom MassARRAY platform. SNP rs1972041GA showed a decreased risk of NSOC in heterozygotes (P = 0.038, OR = 0.77, 95%CI = [0.61, 0.99]). Further stratified analysis revealed an enhanced protective effect of the minor allele G at rs197204 on lip with cleft palate (CLP) and cleft lip with or without cleft palate (CL/P) groups under a codominant or dominant model. No association was observed between the remaining three markers (rs11071720, rs3803499, and rs12148828) and NSOC as well as its subgroups. TPM1 polymorphisms might contribute to the etiology of NSOC, and more emphasis should be placed on TPM1 during craniofacial development. © 2016 Wiley Periodicals, Inc.
Control of Neural Stem Cell Survival by Electroactive Polymer Substrates

Stem cell function is regulated by intrinsic as well as microenvironmental factors, including chemical and mechanical signals. Conducting polymer-based cell culture substrates provide a powerful tool to control both chemical and physical stimuli sensed by stem cells. Here we show that polypyrrole (PPy), a commonly used conducting polymer, can be tailored to modulate survival and maintenance of rat fetal neural stem cells (NSCs). NSCs cultured on PPy substrates containing different counter ions, dodecylbenzenesulfonate (DBS), tosylate (TsO), perchlorate (ClO4) and chloride (Cl), showed a distinct correlation between PPy counter ion and cell viability. Specifically, NSC viability was high on PPy(DBS) but low on PPy containing TsO, ClO4 and Cl. On PPy(DBS), NSC proliferation and differentiation was comparable to standard NSC culture on tissue culture polystyrene. Electrical reduction of PPy(DBS) created a switch for neural stem cell viability, with widespread cell death upon polymer reduction. Coating the PPy(DBS) films with a gel layer composed of a basement membrane matrix efficiently prevented loss of cell viability upon polymer reduction. Here we have defined conditions for the biocompatibility of PPy substrates with NSC culture, critical for the development of devices based on conducting polymers interfacing with NSCs.
The Xircus Search Engine

Nowadays, XML is the document model in favour for both documentand data-centric web applications. Its influence in other, more traditional projects and applications grows as the web and associated techniques become the de-facto standard in user interfaces in such systems. We present an XML-sensitive search engine (Xircus) suited for processing semi-structured queries over large collections of XML documents. Xircus is based on state of the art information retrieval techniques. It is a test bed for research in query processing for XML and semistructured data in general.
Steganalysis of data hiding in binary text images

We present a technique for the steganalysis of electronic binary text images. The proposed method makes use of the similarity between the same characters or symbols for the purpose of detection. The idea of soft pattern matching is used to pair similar characters or symbols together for comparison. The proposed method can estimate the length of the message embedded by the targeted embedding algorithm.
Designing Self-Modifying Agents

Agents need to be able to adapt to changes in their environment. One way to achieve this, is to provide agents with the ability of self-modifica tion. Self-modification requires reflection and strategies with which new knowledge can be acquired, a necessary condition for creativity. This paper describes a knowledge-leve l model for the design of self-modifyin g agents and explores the feasibility of automatically designing self-modifying agents.
enDNA-Prot: Identification of DNA-Binding Proteins by Applying Ensemble Learning

DNA-binding proteins are crucial for various cellular processes, such as recognition of specific nucleotide, regulation of transcription, and regulation of gene expression. Developing an effective model for identifying DNA-binding proteins is an urgent research problem. Up to now, many methods have been proposed, but most of them focus on only one classifier and cannot make full use of the large number of negative samples to improve predicting performance. This study proposed a predictor called enDNA-Prot for DNA-binding protein identification by employing the ensemble learning technique. Experiential results showed that enDNA-Prot was comparable with DNA-Prot and outperformed DNAbinder and iDNA-Prot with performance improvement in the range of 3.97–9.52% in ACC and 0.08–0.19 in MCC. Furthermore, when the benchmark dataset was expanded with negative samples, the performance of enDNA-Prot outperformed the three existing methods by 2.83–16.63% in terms of ACC and 0.02–0.16 in terms of MCC. It indicated that enDNA-Prot is an effective method for DNA-binding protein identification and expanding training dataset with negative samples can improve its performance. For the convenience of the vast majority of experimental scientists, we developed a user-friendly web-server for enDNA-Prot which is freely accessible to the public.
ABEY: an Incremental Personalized Method Based on Attribute Entropy for Recommender Systems (S)

Recording attribute frequencies and calculating user preferences on attributes are generally used in current personalized method – user profile for recommender system. In this paper, we propose a new personalized method, namely ABEY, to do the personalization in another way. ABEY firstly uses attribute entropies to calculates user preferences on attribute classes. ABEY refines these preferences by wiping off some interferences, and allocates a group of such preferences for each user at the end of measurement. ABEY could re-rank given recommendations, according to aggregate attribute class preferences for them. Experiments are conducted on data sets collected from three E-commerce sites in real world. The effectiveness of ABEY, including accuracy, coverage and novelty, has been evaluated and the results indicate that ABEY can be a superior alternative to user profile on finding related items for individuals.
Load Balance Algorithms for Anycast

Increasingly, replicated anycast servers are being used to deliver network applications and service ever increasing user requests. Therefore, the strategies used to guarantee network bandwidth prerequisites and perform load balancing across the nodes of an anycast group are critical to the performance of online applications. In this paper, we model user requests, network congestion and latency, and server load using a combination of hydro-dynamics and queuing theory to develop an efficient job distribution strategy. Current, anycast research does not explicitly consider the system load of nodes within an anycast groups when distributing requests. Therefore, the performance of a heavily loaded anycast system can quickly become congested and uneven as jobs are routed to closely linked nodes which are already saturated with requests. In comparison, the nodes of further away systems remain relatively unused because of other issues such as network bandwidth and latency during these times. Our system redirects requests from busy systems to the idle, remotely linked nodes, to process requests faster in spite of slower network access. Using an empirical study, we show this technique can improve request performance, and throughput with minimal network probing overhead.
Some Systolic Array Developments in the United Kingdom

For the last five or six years, there has been an active program of research on systolic array processors (SAPs) in the United Kingdom. In this article, the authors describe two key projects initiated at the Royal Signals and Radar Establishment (RSRE) and carried out in collaboration with a number of major electronics companies and several universities. The success of these projects demonstrates clearly that the systolic approach to system design is not just an academic concept but a practical means of exploiting large amounts of parallelism and hence achieving orders of magnitude improvement in performance for digital signal processing (DSP). This type of application not only demands but also fully utilizes the SAP architecture. The first project was aimed at developing an electronic processor capable of computing the vector of complex weights required to form the receive beam for an adaptive antenna array.
Interaction of Heparan Sulfate from Mammary Cells with Acidic Fibroblast Growth Factor (FGF) and Basic FGF

We have determined the relationship between the binding sites for acidic fibroblast growth factor (aFGF) and basic FGF (bFGF) in heparan sulfate (HS) prepared from a panel of mammary cell lines and the ability of the HS to activate aFGF and bFGF in DNA synthesis assays. The k a of the HS for aFGF fell into three groups, whereas the k d (0.0015–0.016 s−1) and the K d (0.4–8.6 μm) formed a continuum. bFGF possessed a high affinity binding site (K d 22–30 nm) with a fastk a (320,000–550,000 m −1s−1), termed “fast/high,” and a lower affinity site (K d 47–320 nm) with a slowerk a (35,000–150,000 m −1s−1), termed “slow/low. ” Most of the species of HS possessed the latter binding site, which was able to activate bFGF in HS-deficient fibroblasts. However, the HS from the culture medium of the mammary fibroblasts and the myoepithelial-like cells possessed both a fast/high and a slow/low binding site and could not activate bFGF, although it could potentiate the growth-stimulatory activity of aFGF. Treatment of the HS possessing two binding sites for bFGF with heparitinase 1 released oligosaccharides that were able to restore the activity of bFGF in HS-deficient fibroblasts.
Simulation of the behavior of aluminum alloys welded in Friction Stir Welding FSW

The friction stir welding FSW is a topical technique to date, either for experimental or numerical research topics. Based on the fact that the majority of the heat generated, comes from the contact between the workpiece and the shoulder, and from the work of friction done by the pin. Thus, it is crucial to approach the reality, by simulating the most of the conditions, related to the FSW process. The development of a numerical model allows us, not only to simulate the FSW welding process, but also to conduct a parametric study and vary the welding conditions as desired. Therefore, a numerical study is conducted on the friction stir welding of AA 5083H111 work piece, in order to perceive the optimal settings. A three dimensional model designed by ANSYS APDL was used. Before proceeding with this, a preliminary experimental study was carried out on FSW welded AA 6082 –T6 specimens and base material, using tensile and fatigue tests. The numerical results obtained, essentially longitudinal residual stresses, are compared to other studies, experimental and numerical.