Miracle-dz/UniFAR-FTUs huggingface dataset:
Taxonomic Note: A Place for DNA-DNA Reassociation and 16S rRNA Sequence Analysis in the Present Species Definition in Bacteriology

Because a natural entity “species” cannot be recognized as a group of strains that is genetically well separated from its phylogenetic neighbors, a pragmatic approach was taken to define a species by a polyphasic approach (L. G. Wayne, D. J. Brenner, R. R. Colwell, P. A. D. Grimont, O. Kandler, M. I. Krichevsky, L. H. Moore, W. E. C. Moore, R. G. E. Murray, E. Stackebrandt, M. P. Starr, and H. G. Truper, Int. J. Syst. Bacteriol. 37:463-464, 1987), in which a DNA reassociation value of about 70% plays a dominant role. With the establishment of rapid sequence analysis of 16S rRNA and the recognition of its potential to determine the phylogenetic position of any prokaryotic organism, the role of 16S rRNA similarities in the present species definition in bacteriology needs to be clarified. Comparative studies clearly reveal the limitations of the sequence analysis of this conserved gene and gene product in the determination of relationships at the strain level for which DNA-DNA reassociation experiments still constitute the superior method. Since today the primary structure of 16S rRNA is easier to determine than hybridization between DNA strands, the strength of the sequence analysis is to recognize the level at which DNA pairing studies need to be performed, which certainly applies to similarities of 97% and higher.
The smart service proxy — A middlebox for a semantic Web of things

Within the last decade a lot of effort was put into the development of novel technologies to realize an Internet of Things. With 6LowPAN the resource constrained devices such as sensor nodes can be seamlessly integrated with the (IPv6 enabled) Internet [1]. With CoAP they are even able to run Web Servers and thereby integrate their data with the Web [2]. However, direct and open access for arbitrary Web Clients from the Internet is often not desirable for scalability reasons and sometimes not even possible. Thus, in this paper the Smart Service Proxy (SSP) is presented which provides documents to the (semantic) Web on behalf of sensor nodes and other data sources without any loss of actuality. It borrows and combines some concepts of several IETF CoRE drafts (e.g. [3], [4], [5]) in a single piece of software1. Furthermore, due to Semantic Web technologies such as RDF, the SSPs are even able to infer and provide additional knowledge.
Equiphase Precoder Design for Cooperative Communication with Complex Field Network Coding

Complex field network coding (CFNC) can be employed to achieve ideal throughput as high as 1/2 symbol per source per time slot (sym/S/TS) in relay-based cooperative communications. In this paper, equiphase precoder (EP) scheme for CFNC-based system (EP-CFNC) is proposed to achieve better symbol error probability (SEP) performance. The distribution of transmitted symbol's constellation is carefully designed against noise. The theoretical analysis provides a method to estimate the SEP and verifies the coding gain obtained by equiphase precoder. Moreover, simulation results, in both additive complex White Gaussian noise (AWGN) channels and Rayleigh fading channels, show that SEP can be substantially reduced via the proposed EP-CFNC algorithm.
Observation of a new inner-orbital molecular transition at 55.8 nm in N22+ produced by multiphoton coupling.

Etude experimentale de cette bande a 55,8 nm qui presente des decompositions vibrationnelles, de duree de vie ∼ 100 ps. Attribution a une transition de type excimere 3 Π u → 3 Π g par production multiphotonique indirecte de niveaux moleculaires a lacune 2σ g
A Cooperative Framework for Integrating Ontologies in a Networked Surveillance System

In a networked surveillance system distributed ontology construction processes are required for the better inference. To make use of a cooperative framework for integrating ontologies, we describe a computing framework for the integration of ontologies supplied by a predetermined set of data source servers, who may be interconnected through a peer to peer network. In our approach, every data source server agent consults the derived ontology constructed by the neighbors in order to refine its private local ontology. In addition, the model proposed in this paper allows the agents involved in the construction of the distributed ontology to use their own recognition technology. Common APIs are supplied for querying the global ontology. For such a P2P network, an effective cache framework that can handle heterogeneous devices is provided. Keywords-component; Networked Surveillance Systems, Multimedia Data, Biometric Data. Peer to Peer Computing
Effect of rifampicin-based antitubercular therapy and the cytochrome P450 2B6 516G>T polymorphism on efavirenz concentrations in adults in South Africa

Background Rifampicin induces expression of the cytochrome P450 isoenzyme 2B6 (CYP2B6), which metabolizes efavirenz. The CYP2B6 516G>T polymorphism impairs efavirenz metabolism and occurs more commonly in Africans than in Caucasians. We explored the effect of rifampicin-based antitubercular therapy and the 516G>T polymorphism on efavirenz concentrations in HIV- infected patients in South Africa. Methods Between-patient and within-patient comparisons were made of mid-dosing interval efavirenz plasma concentrations in adults on antiretroviral therapy including efavirenz 600 mg daily, with and without antitubercular therapy. Results There were 142 participants (40 were on antitubercular therapy and 102 were controls), the mean weight was 66 kg. Median efavirenz concentration was 2.4 mg/l (interquartile range [IQR] 1.3–3.1) and 1.8 mg/l (IQR 1.4–4.4) in participants on antitubercular therapy and controls, respectively (P=0.734). Paired efavirenz concentrations during and after antitubercular therapy in 17 participants were also similar (P=0.113). Genotyping results were 60 (49%) G/G homozygotes, 46 (38%) G/T heterozygotes and 16 (13%) T/T homozygotes. In a multivariate logistic regression model adjusted for sex, weight and concomitant antitubercular therapy, the 516G>T polymorphism was strongly associated with high (>4 mg/l) efavirenz concentrations: odds ratio (OR) 4.4 (95% confidence interval [CI] 1.3–14.9) for G/T versus G/G and 31.1 (95% CI 6.6–146.6) for T/T versus G/G. High efavirenz concentrations were associated with severe sleep disturbance (P=0.048). Low (<1 mg/l) efavirenz concentrations were associated with virological failure (OR 12.5, 95% CI 2.7–57.3). Conclusions Efavirenz can be used together with rifampicin-based antitubercular therapy without dose adjustment in this population. The 516G>T polymorphism occurred commonly and was associated with high efavirenz concentrations.
Aging with Traumatic Brain Injury: Effects of Age at Injury on Behavioral Outcome following Diffuse Brain Injury in Rats

Development and aging are influenced by external factors with the potential to impact health throughout the life span. Traumatic brain injury (TBI) can initiate and sustain a lifetime of physical and mental health symptoms. Over 1.7 million TBIs occur annually in the USA alone, with epidemiology suggesting a higher incidence for young age groups. Additionally, increasing life spans mean more years to age with TBI. While there is ongoing research of experimental pediatric and adult TBI, few studies to date have incorporated animal models of pediatric, adolescent, and adult TBI to understand the role of age at injury across the life span. Here, we explore repeated behavioral performance between rats exposed to diffuse TBI at five different ages. Our aim was to follow neurological morbidities across the rodent life span with respect to age at injury. A single cohort of male Sprague-Dawley rats (n = 69) was received at postnatal day (PND) 10. Subgroups of this cohort (n = 11-12/group) were subjected to a single moderate midline fluid percussion injury at age PND 17, PND 35, 2 months, 4 months, or 6 months. A control group of naïve rats (n = 12) was assembled from this cohort. The entire cohort was assessed for motor function by beam walk at 1.5, 3, 5, and 7 months of age. Anxiety-like behavior was assessed with the open field test at 8 months of age. Cognitive performance was assessed using the novel object location task at 8, 9, and 10 months of age. Depression-like behavior was assessed using the forced swim test at 10 months of age. Age at injury and time since injury differentially influenced motor, cognitive, and affective behavioral outcomes. Motor and cognitive deficits occurred in rats injured at earlier developmental time points, but not in rats injured in adulthood. In contrast, rats injured during adulthood showed increased anxiety-like behavior compared to uninjured control rats. A single diffuse TBI did not result in chronic depression-like behaviors or changes in body weight among any groups. The interplay of age at injury and aging with an injury are translationally important factors that influence behavioral performance as a quality of life metric. More complete understanding of these factors can direct rehabilitative efforts and personalized medicine for TBI survivors.
Endosymbiotic Bacteria Associated with the Mealy Bug, Rhizoecus amorphophalli (Hemiptera: Pseudococcidae)

The mealy bug, Rhizoecus amorphophalli, is a menace to the aroid farmers due to the intensive infestation on stored tubers. Spraying of pesticides was able to control this pest but it always left a chance for fungal growth. Bacterial endosymbionts associated with the insects provide several benefits to their host. Since such endosymbionts play a vital role even in the physiology of their host, revealing the types of bacteria associated with mealy bug will give basic information, which may throw light on the management of this noxious pest. The present study is the first to identify bacterial endosymbionts associated with R. amorphophalli employing phenotypic characterization and 16S rDNA sequencing. Three culturable bacteria, namely, Bacillus subtilis, Staphylococcus gallinarum, and Staphylococcus saprophyticus, were isolated from R. amorphophalli. Moreover, the antibiotic susceptibility tests against the isolated bacteria showed that all the isolates were susceptible to the three antibiotics tested, except cephalexin. Recently, endosymbionts are used as effective biocontrol agents (BCAs) and the present study will stand as a connecting link in identification and effective utilization of these endosymbionts as BCAs for management of R. amorphophalli.
On the robustness of AQM mechanisms against non-responsive traffic

Active Queue Management (AQM) mechanisms have come a long way, with an initial goal to avoid congestion to the recent most focus on reducing queue delay. The benefits of using AQM mechanisms at routers are being thoroughly studied nowadays, mainly to avoid the problem of bufferblaat. Although a lot of work has focused on analyzing the behavior of AQM mechanisms, the nature of traffic used while deriving inferences is mainly responsive (TCP), with small numbers of unresponsive flows (UDP) used in the background. The usage of UDP in Internet has increased significantly in the recent past, owing to a great demand for time sensitive multimedia applications. Since UDP flows do not respond to congestion signals, controlling the queue length at routers by using AQM mechanisms becomes a non-trivial task. In this paper, we study the robustness of popular AQM mechanisms in the presence of a large number of unresponsive UDP flows using ns-2. Further, we provide guidelines to effectively tune the AQM knobs and enhance their robustness against non-responsive UDP flows.
An aminoacyl-tRNA synthetase that specifically activates pyrrolysine.

Pyrrolysine, the 22nd cotranslationally inserted amino acid, was found in the Methanosarcina barkeri monomethylamine methyltransferase protein in a position that is encoded by an in-frame UAG stop codon in the mRNA. M. barkeri encodes a special amber suppressor tRNA (tRNA(Pyl)) that presumably recognizes this UAG codon. It was reported that Lys-tRNA(Pyl) can be formed by the aminoacyl-tRNA synthetase-like M. barkeri protein PylS [Srinivasan, G. , James, C. M. & Krzycki, J. A. (2002) Science 296, 1459-1462], whereas a later article showed that Lys-tRNA(Pyl) is synthesized by the combined action of LysRS1 and LysRS2, the two different M. barkeri lysyl-tRNA synthetases. Pyrrolysyl-tRNA(Pyl) formation was presumed to result from subsequent modification of lysine attached to tRNA(Pyl). To investigate whether pyrrolysine can be directly attached to tRNA(Pyl) we chemically synthesized pyrrolysine. We show that PylS is a specialized aminoacyl-tRNA synthetase for charging pyrrolysine to tRNA(Pyl); lysine and tRNA(Lys) are not substrates of the enzyme. In view of the properties of PylS we propose to name this enzyme pyrrolysyl-tRNA synthetase. In contrast, the LysRS1:LysRS2 complex does not recognize pyrrolysine and charges tRNA(Pyl) with lysine. These in vitro data suggest that Methanosarcina cells have two pathways for acylating the suppressor tRNA(Pyl). This would ensure efficient translation of the in-frame UAG codon in case of pyrrolysine deficiency and safeguard the biosynthesis of the proteins whose genes contain this special codon.
Sequence Analysis and Comparative Study of the Protein Subunits of Archaeal RNase P

RNase P, a ribozyme-based ribonucleoprotein (RNP) complex that catalyzes tRNA 5′-maturation, is ubiquitous in all domains of life, but the evolution of its protein components (RNase P proteins, RPPs) is not well understood. Archaeal RPPs may provide clues on how the complex evolved from an ancient ribozyme to an RNP with multiple archaeal and eukaryotic (homologous) RPPs, which are unrelated to the single bacterial RPP. Here, we analyzed the sequence and structure of archaeal RPPs from over 600 available genomes. All five RPPs are found in eight archaeal phyla, suggesting that these RPPs arose early in archaeal evolutionary history. The putative ancestral genomic loci of archaeal RPPs include genes encoding several members of ribosome, exosome, and proteasome complexes, which may indicate coevolution/coordinate regulation of RNase P with other core cellular machineries. Despite being ancient, RPPs generally lack sequence conservation compared to other universal proteins. By analyzing the relative frequency of residues at every position in the context of the high-resolution structures of each of the RPPs (either alone or as functional binary complexes), we suggest residues for mutational analysis that may help uncover structure-function relationships in RPPs.
Studies of a primitive mammalian spleen, the opossum (Didelphis virginiana)

Light microscopic sections of the adult opossum (Didelphis virginiana) spleen were observed to lack venous sinuses; this primitive mammalian spleen may be classified as non‐sinusal in nature. In the spleen of the opossum, the capillary segments of the penicillar arteries lacked ellipsoid sheaths characteristic of certain mammalian spleens.
Viability Assessment for Artificial Gametes: The Need for Biomarkers of Functional Competency1

ABSTRACT Assisted reproductive technology (ART) has resulted in more than 5 million births worldwide. However, mainstream ART techniques are not always successful for an estimated 30% of infertile patients in whom gametes are nonviable. Most patients would clearly prefer genetic parenthood, currently possible only via the use of donated gametes or, in future, via the clinical use of artificial gametes (AGs) incorporating parental DNA. Despite much recent progress in the derivation of AGs, significant obstacles remain. Although it is possible to create artificial cells exhibiting some of the molecular and physiological traits of human gametes, they do not yet exhibit the same level of functionality as their in vivo counterparts. Most current effort pays scant attention to confirmation of molecular integrity and clinical applicability of AGs. Here we discuss the various clinical parameters used to assess gamete and embryo viability and discuss markers of gamete function that may be used within future studies attempting to derive AGs. The use of AGs may prove controversial to some members of the general public, and, as such, there is significant need for an appropriate ethical and legal framework governing the clinical use of such cells. However, provided these issues can be successfully overcome, it is highly likely that AGs will represent powerful biological tools for reproductive science, a valuable training resource for embryologists and for potential use in the clinical treatment of human infertility.
Research on System Design and Control Technology of Vision-Based CyberCar

In this paper the vehicle structure, performance parameters and dynamic model of JLUIV5-CyberCar are discussed. An optimal controller is designed to achieve the line path tracking ability, while the curve path tracking ability is guaranteed by a fuzzy controller. To improve the tracking performance of the vehicle steering system in different conditions, controller output collections of JLUIV5-CyberCar are established combined with variable structure control theory. Design the state observer based on Kalman filter theory to estimate the lateral velocity and yaw rate. Simulations and experimental results have confirmed the effectiveness of the proposed method
The RNA ligands for mouse proline-rich RNA-binding protein (mouse Prrp) contain two consensus sequences in separate loop structure

Mouse proline-rich RNA-binding protein (mPrrp) is a mouse ortholog of Xenopus Prrp, which binds to a vegetal localization element (VLE) in the 3′-untranslated region (3′-UTR) of Vg1 mRNA and is expected to be involved in the transport and/or localization of Vg1 mRNA to the vegetal cortex of oocytes. In mouse testis, mPrrp protein is abundantly expressed in the nuclei of pachytene spermatocytes and round spermatids, and shifts to the cytoplasm in elongating spermatids. To gain an insight into the function of mPrrp in male germ cells, we performed in vitro RNA selection (SELEX) to determine the RNA ligand sequence of mPrrp. This analysis revealed that many of the selected clones contained both of two conserved elements, AAAUAG and GU1–3AG. RNA-binding study on deletion mutants and secondary structure analyses of the selected RNA revealed that a two-loop structure containing the conserved elements is required for high-affinity binding to mPrrp. Furthermore, we found that the target mRNAs of Xenopus Prrp contain intact AAAUAG and GU1–3AG sequences in the 3′-UTR, suggesting that these binding sequences are shared by Prrps of Xenopus and mouse.
Marking focus in Chatino

Abstract This paper presents and analyzes new data from the officially endangered language Chatino. We investigate the behavior of a Chatino preposition, jį? į which is sometimes found preceding direct objects. Its patterning, with respect to when it will and when it will not precede a direct object, has so far eluded characterization. Using both natural discourse and elicited data, we examine and reject hypotheses of jį? į's occurrence based on various properties of the direct object: animacy, specificity, thematic role, 3 → 2 advancement (i.e., the marked direct objects are underlyingly indirect objects). We propose an analysis in which jį? į marks the discourse focus. We argue that the Chatino data support Lambrechts (1994) position that focus is nonidentical with “new information”, and that the Chatino data necessitate an expansion of the definition of focus beyond the propositional level. Our analysis incorporates a disambiguating function of jį? į to separate the subject and object when they are potentially parsed as a single NP.
Premature senescence of highly proliferative endothelial progenitor cells is induced by tumor necrosis factor‐α via the p38 mitogen‐activated protein kinase pathway

Senescence of endothelial cells increases with systemic aging and is thought to contribute to the development of atherosclerosis. Cell therapy with highly proliferative endothelial progenitor cells (EPCs) is an emerging therapeutic option to promote endothelial regeneration, but little is known about their senescence and their vulnerability to inflammatory stressors. We therefore studied the senescence of proliferative human EPCs and investigated the effects of the proinflammatory cytokine tumor necrosis factor‐α (TNF‐α) on their senescence. Human EPCs had a significantly lower rate of senescence at baseline, compared with that of mature endothelial cells. However, EPCs up‐regulated the expression of the senescence‐associated cell cycle arrest protein p16INK4aand markedly increased measured senescence levels when exposed to chronic TNF‐α treatment. Analysis of telomere length showed that the increases in senescence were not related to changes in telomere length. Inhibition of the p38 mitogen‐activated protein kinase pathway blocked the induction of p16INK4a and cellular senescence. In conclusion, highly proliferative EPCs have a low rate of intrinsic senescence but are vulnerable to premature senescence induction by chronic proinflammatory stimulation. These findings will lead to a better understanding of physiological endothelial regeneration as well as to targeted therapies with the aim of promoting endothelial regeneration through endothelial progenitor cells. — Zhang, Y. , Herbert, B. ‐S. , Rajashekhar, G. , Ingram, D. A. , Yoder, M. C. , Clauss, M. , Rehman. J. Premature senescence of highly proliferative endothelial progenitor cells is induced by tumor necrosis factor‐α via the p38 mitogen‐activated protein kinase pathway. FASEBJ. 23, 1358–1365 (2009)
The significance of altered temperature after traumatic brain injury: an analysis of investigations in experimental and human studies: Part 2

Raised body temperature is a common occurrence after severe traumatic brain injury (TBI). It is widely accepted that experimental evidence points to a harmful effect of raised temperature both during and after TBI. Consequently, the policy of many neurocritical care units is to implement therapies for body temperature control. This article reviews the evidence that links spontaneous temperature changes with worsened outcome after experimentally-induced and human brain trauma. The current evidence-base and rationale for treatment of raised temperature after TBI is presented with discussion positing areas for further work to explore the notion that raised temperature may not be deleterious in all neurosurgical patients.
An Exploratory Study of User Perceptions of Payment Methods in UK and the US

This paper presents the design and the results of a cross-cultural study of user perceptions and attitudes toward electronic payment methods. We conduct a series of semi-structured interviews involving forty participants (20 in London, UK, and 20 in Manhattan, KS, USA) to explore how individuals use the mechanisms available to them within their routine payment and banking activities. We also study their comprehension of payment processes, the perceived effort and impact of using different methods, as well as direct or indirect recollections of (suspected or actual) fraud and related interactions with banks and retailers. By comparing UK and US participants, we also elicit commonalities and differences that may help better understand, if not predict, attitudes of US customers once technologies like Chip-and-PIN are rolled out – for instance, several US participants were confused by how to use it, while UK participants found it convenient. Our results show that purchasing habits as well as the availability of rewards schemes are primary criteria influencing choices relating to payment technologies, and that inconsistencies, glitches, and other difficulties with newer technologies generate frustration sometimes leading to complete avoidance of new payment methods.