Miracle-dz/UniFAR-FTUs huggingface dataset:
The complete mitochondrial genome of the pen shell Atrina pectinata (Mollusca: Bivalvia: Pinnidae): The first representative from the family Pinnidae

In this study, we described the complete mitochondrial genome of the pen shell Atrina pectinata. It was 16,811 bp in length and consisted of 35 genes including 12 protein-coding genes, 2 ribosomal RNAs, and 21 transfer RNAs (trnS2 and atp8 lacked). All genes were encoded on the same strand. In gene order, there was no completely identical block compared to those of Mytilus edulis, Crassostrea gigas, Chlamys farreri and Venerupis philippinarum. It may be a ground pattern of Pinnidae mitochondrial genomes.
Pain Prediction From ECG in Vascular Surgery

Varicose vein surgeries are routine outpatient procedures, which are often performed under local anaesthesia. The use of local anaesthesia both minimises the risk to patients and is cost effective, however, a number of patients still experience pain during surgery. Surgical teams must therefore decide to administer either a general or local anaesthetic based on their subjective qualitative assessment of patient anxiety and sensitivity to pain, without any means to objectively validate their decision. To this end, we develop a 3-D polynomial surface fit, of physiological metrics and numerical pain ratings from patients, in order to model the link between the modulation of cardiovascular responses and pain in varicose vein surgeries. Spectral and structural complexity features found in heart rate variability signals, recorded immediately prior to 17 varicose vein surgeries, are used as pain metrics. The so obtained pain prediction model is validated through a leave-one-out validation, and achieved a Kappa coefficient of 0.72 (substantial agreement) and an area below a receiver operating characteristic curve of 0.97 (almost perfect accuracy). This proof-of-concept study conclusively demonstrates the feasibility of the accurate classification of pain sensitivity, and introduces a mathematical model to aid clinicians in the objective administration of the safest and most cost-effective anaesthetic to individual patients.
References and Notes Materials and Methods Som Text Figs. S1 to S9 Tables S1 to S3 References and Notes Protein Displacement by Dexh/d " Rna Helicases " without Duplex Unwinding

DNA transfer into eukaryotic cells (25). The absence of TFSS genes necessary for DNA transfer in the UWE25 genome suggests that in this organism TFSS is responsible for secreting effector proteins into the amoebal host and thus fulfills a function similar to that of the TTSS. The arrangement of UWE25 TFSS genes adjacent to each other in a single region on the chromosome, their higher GϩC content (41.9%, 37.9% in the third codon position) compared with the genomic GϩC content (35.8%, 26.9% in the third codon position), and the presence of several transposases in proximity to TFSS genes indicates that the TFSS was recently acquired by UWE25 from a donor with a genomic GϩC content greater than 42% [es-timated according to (26)]. The TFSS genes thus represent the only recognized example for a possible recent lateral transfer of genes (coding for proteins with known function) to UWE25 after the split of the chlamydial lin-eage into its two sister groups. A recently recognized virulence factor of pathogenic chlamydiae, the protease-like activity factor (CPAF) (27), is also encoded in the UWE25 genome (pc0916). CPAF is one of the few proteins that have been shown to be secreted (possibly by means of the TTSS) by patho-genic chlamydiae into the host cytoplasm. Its function is still unknown, but CPAF is able to degrade the human transcription factors required for major histocompatibility complex (MHC) expression (27). The presence of CPAF in UWE25, which resides in a host that does not possess a MHC system, indicates that CPAF has evolved from a protease with a different specific function in lower eukaryotic hosts. Chlamydiae are among the most successful bacterial pathogens of humans and have recently also been associated with chronic diseases (1, 9). Comparative and phylogenetic genome analysis of a chlamydia-related symbiont of amoebae showed that it has retained several key features of the last common chlamydial ancestor and provided evidence that major virulence mechanisms of present-day pathogenic chla-mydiae have evolved from the interaction of ancestral chlamydiae with early eukaryotes. Subsequent adaptation of pathogenic chlamyd-iae to animal and human host cells was most likely mediated by proteins found in modern pathogenic chlamydiae but not detectable by sequence homology in the UWE25 genome (table S3). However, the presence of key viru-lence factors in environmental chlamydiae, together with their documented ability to multiply in human macrophages (28), suggests that these protozoan symbionts have the genetic tools to allow …
A study of networking software induced latency

For long time, high-speed packet processing has been reserved for specialized hardware devices since software based solutions were not able to achieve the required performance. However, off-the-shelf packet processing hardware and software improved over the last years, which is why software based solutions cope with high-speed traffic nowadays. Due to the flexibility of software there is a trend towards doing packet processing in software, e.g. using OpenFlow or virtual switches. Although packet processing in software offers many capabilities, the complexity of such software bases solutions makes it hard to evaluate, optimize, or predict the networking performance of servers, end user hosts, or routers. We present a study that investigates the packet latency caused by the packet processing in the Linux network stack. We develop a simulation model in ns-3 for packet processing via the Linux network stack that helps understanding of its performance implications. We validate our simulation model based on measurements with nanosecond accuracy and software profiling.
A Knitro-based real-time locomotion method for imitating the caterpillar-like climbing strategy

This paper presents a novel locomotion method to imitate the caterpillar-like climbing strategy. Caterpillar-like climbing is in fact slow, but a caterpillar's multi-segmented body trunk enhances the climbing versatility and dexterity, which motivates us to develop a caterpillar-like climbing method. In this paper, we introduce the characteristics of the climbing locomotion observed on natural caterpillars first, and then propose a three-stage climbing method to imitate the caterpillar-like climbing patterns. An energy efficient strategy is then formulated, aiming for the minimization of robot joint energy expenditure over a locomotion period. For real-time implementation and singularity avoidance within the energy efficient framework, we incorporate the Knitro method to search for kinematical optimal solutions over a period of time. Successful simulation and experimental results show the effectiveness of the proposed caterpillar-like climbing locomotion strategy.
Effect of Membrane Cholesterol on BSEP/Bsep Activity: Species Specificity Studies for Substrates and Inhibitors

The efflux transporter responsible for the canalicular elimination of bile salts from the hepatocytes is the bile salt export pump (BSEP, ABCB11). Absence or inhibition of this transporter leads to bile salt retention in the hepatocyte and in turn can lead to cholestatic liver disease. We expressed the BSEP/Bsep protein from three species (human, rat, and mouse) in a baculovirus-infected Sf9 system. Vesicles prepared from these cells were used to evaluate bile salt transport of four conjugated bile salts. Because the Sf9 system contains less membrane cholesterol than the liver canalicular membrane, the effect of added cholesterol on the kinetics of BSEP/Bsep-mediated bile salt transport was also investigated. Cholesterol treatment increased the Vmax values in all the species, with the most pronounced effect observed in the rat transporter. In contrast, Km values, with the exception of glycochenodeoxycholate, remained largely unchanged. The species-specific bile salt transport inhibition potential of three compounds known to cause clinical cholestasis was investigated in vesicles containing BSEP/Bsep. Troglitazone and glibenclamide inhibited the BSEP/Bsep-mediated transport of different bile salts with similar affinities, whereas the potential of cyclosporine A to inhibit bile salt transport showed species- and bile salt-specific variations. In conclusion, the cholesterol-loaded Sf9 vesicles overexpressing BSEP/Bsep seem to be a useful system for the identification of potential cholestatic compounds and can also be used for the investigation of species specificity. We observed greater differences in IC50 values for inhibitors than in Km values for substrates between species.
The Mechanism for Type I Interferon Induction by Mycobacterium tuberculosis is Bacterial Strain-Dependent

Type I interferons (including IFNαβ) are innate cytokines that may contribute to pathogenesis during Mycobacterium tuberculosis (Mtb) infection. To induce IFNβ, Mtb must gain access to the host cytosol and trigger stimulator of interferon genes (STING) signaling. A recently proposed model suggests that Mtb triggers STING signaling through bacterial DNA binding cyclic GMP-AMP synthase (cGAS) in the cytosol. The aim of this study was to test the generalizability of this model using phylogenetically distinct strains of the Mtb complex (MTBC). We infected bone marrow derived macrophages with strains from MTBC Lineages 2, 4 and 6. We found that the Lineage 6 strain induced less IFNβ, and that the Lineage 2 strain induced more IFNβ, than the Lineage 4 strain. The strains did not differ in their access to the host cytosol and IFNβ induction by each strain required both STING and cGAS. We also found that the three strains shed similar amounts of bacterial DNA. Interestingly, we found that the Lineage 6 strain was associated with less mitochondrial stress and less mitochondrial DNA (mtDNA) in the cytosol compared with the Lineage 4 strain. Treating macrophages with a mitochondria-specific antioxidant reduced cytosolic mtDNA and inhibited IFNβ induction by the Lineage 2 and 4 strains. We also found that the Lineage 2 strain did not induce more mitochondrial stress than the Lineage 4 strain, suggesting that additional pathways contribute to higher IFNβ induction. These results indicate that the mechanism for IFNβ by Mtb is more complex than the established model suggests. We show that mitochondrial dynamics and mtDNA contribute to IFNβ induction by Mtb. Moreover, we show that the contribution of mtDNA to the IFNβ response varies by MTBC strain and that additional mechanisms exist for Mtb to induce IFNβ.
Mathematical theory of the h- and g-index in case of fractional counting of authorship

This paper studies the h-index (Hirsch index) and the g-index of authors, in case one counts authorship of the cited articles in a fractional way. There are two ways to do this: or one counts the citations to these papers in a fractional way or one counts the ranks of the papers in a fractional way as credit for an author. In both cases we define the fractional hand g-indexes and we present inequalities (both upper and lower bounds) between these fractional hand g-indexes and their corresponding unweighted values (also involving, of course, the co-authorship distribution). Wherever applicable, examples and counterexamples are provided. 1 Permanent address
Case Report of a Prostatic Abscess with a Review of the Literature

A middle age male with type 2 diabetes mellitus presented with urinary symptoms. Blood and urine cultures were consistent with Methicillin Resistant Staphylcoccal Aureus (MRSA). A computed tomography demonstrated mutiple prostatic microabscessess. No other hematogenous source was identified. Transurethral prostatic drainage and intravenous Vancomycin followed by oral doxcycline led to clinical success for this likely Community acquired case of MRSA (CA-MRSA). We discuss our case report and discuss the current literature on the trends, causation, diagnosis and treatment of MRSA induced prostatic abscess.
Tenacibaculum soleae sp. nov., isolated from diseased sole (Solea senegalensis Kaup).

A novel Gram-negative, rod-shaped, gliding bacterial strain designated LL04 12.1. 7T was isolated from diseased sole (Solea senegalensis Kaup) in Galicia, Spain. Colonies were yellow-pigmented with uneven edges and did not adhere to the agar. The DNA G+C content of the strain was 29.8 mol%. 16S rRNA gene sequence similarity analysis indicated that strain LL04 12.1. 7T is a member of the genus Tenacibaculum in the family Flavobacteriaceae. Sequence similarities between the isolate and the type strains of other members of the genus were 96.7-94.8 %. The major fatty acids (>10 % of total fatty acids) were iso-C15 : 0 (23.1 %), iso-C15 : 0 3-OH (10.6 %), C15 : 1 omega 6c (12.2 %) and summed feature 3 (comprising C16 : 1 omega 7c and/or iso-C15 : 0 2-OH, 11.0 %). Genotypic and phenotypic data distinguished strain LL04 12.1. 7T from the 11 recognized Tenacibaculum species, indicating that it represents a novel species, for which the name Tenacibaculum soleae sp. nov. is proposed. The type strain is strain LL04 12.1. 7T (=CECT 7292T =NCIMB 14368T).
Stochastic modelling and analysis of cloud computing data center

Cloud data centers (CDC) are an integral part of today's internet services. Enterprises and Businesses around the world rely heavily on data centers for their daily computation and IT operations. In fact, every time we search for an information on the internet, or we use an application on our smartphones, we access data centers. In CDC, most compute resources are represented as virtual machines (VMs) which are mapped into physical machines (PMs). Performance is often is a key metric for CDC. This paper presents a stochastic model based on queuing theory to aid in studying and analyzing performance in CDC. CDC platforms are modeled with an open queuing system that can be used to estimate the expected Quality of Service (QoS) guarantees the cloud can offer. We give numerical examples to show how the model estimates the number of required VM instances needed to satisfy a given the QoS parameters. In particular, we plot the response time, drop rate and CPU utilization while varying the incoming request arrival rate, and for different number of VM instances. We cross-validate our analytical model using a DES (Discrete Event Simulator). Our analysis and simulation results show that the proposed model is able to estimate the number of VMs needed to achieve QoS targets when varying the arrival request rate.
Disentangling the fuzzy front-end: an integrative literature review

Within the vast body of research on new product development (NPD), the so-called ‘fuzzy front end (FFE) of innovation received and continues to receive considerable attention. The importance of the FFE can hardly be underestimated as it has been widely established that improvements to this early phase of the innovation process far exceed advances in later stages of the innovation cycle (Poskela and Martinsuo, 2009; Verworn, 2009). Even though its importance cannot be mistaken, FFE research results have been widely dispersed; scholars for example still have problems to settle upon a clear definition of the term ‘fuzziness’ (Brun, Saetre and Gjelsvik, 2009) and different research approaches and focal points of research are used interchangeably (Reid and de Bretani, 2004). This dissertation is an attempt to understand and synthesize the ‘fuzzy front end’ field of research. In doing so, it attempts to answer two research questions: (1) In the FFE research field, what are the different research streams and how have they developed over time and (2) what are the empirically proven success and contingency factors related to managing the fuzzy front end successfully? By means of an exhaustive integrative literature review, 103 publications were reviewed and close-read. The dissertation contributions to the literature in the following ways: first, a visual overview regarding the definitions on the terms ‘fuzziness’ and the ‘front-end’ is provided. Next, literature is categorized on (1) methodology type, (2) innovation dimension and (3) conceptual group. Third, success and contingency factors are identified and discussed and a tool is constructed that allows decision-makers, managers and entrepreneurs to understand how the FFE should be managed for their specific situation and context. Besides a theoretical contribution on the actual content of the FFE-literature field and the way it has developed over time, this dissertation also is of practical use for managers and entrepreneurs as it provides insights to move towards more successful FFE-processes.
Transmural Myocardial Deformation in the Canine Left Ventricle: Normal in Vivo Three‐Dimensional Finite Strains

To examine transmural finite deformation in the wall of the canine left ventricle, closely spaced columns of lead beads were implanted at a single site on the left ventricular free wall. The three-dimensional coordinates of these myocardial markers were obtained with highspeed biplane cineradiography. Any four noncoplanar markers forming small tetrahedral volumes (±0.1 cc) were used to calculate finite normal and shear strains with respect to a cardiac coordinate system at end diastole. Due to the symmetry of the finite strain tensor, the algebraic eigenvalue problem could be solved to compute principal strains and the directions of the principal axes of deformation with respect to the reference coordinates. An examination of the principal strains in a number of tetrahedra in five animals indicates that deformation increases with depth beneath the epicardium. For example, the transmural variation of principal shortening strain averages −0.014 ± 0.009 per 10% increment in thickness from epicardium to endocardium. Furthermore, shortening and thickening strains at midwall and deeper are too large (0.10 to 0.40) to be described accurately by infinitesimal theory. These strains are often accompanied by substantial in-plane and transverse shears which are not predicted by typical membrane or shell theories, indicating that these theories must be applied with caution when computing indices of regional ventricular performance. The directions of the principal axes of shortening vary substantially less than the fiber direction varies across the wall (20±-40± compared with 100±-140± for fiber direction), supporting the concept that there are substantial interactions between neighboring fibers in the left ventricular wall.
XYY Karyotype in a Pair of Monozygotic Twins: A 17-Year Life-History Study

We have recently had the opportunity to investigate clinical and behavioural characteristics of a pair of 17-year-old twin boys who were discovered to have the XYY karyotype (18). Since these twins, known to this department since infancy, had been studied at the age of three, early direct findings as well as retrospective data are available regarding their symptoms and development.
Natural Shell: An Assistant for End-User Scripting

Scripting is a widely-used way to automate the execution of tasks. Despite the popularity of scripting, it remains difficult to use for both beginners and experts: because of the cryptic commands for the first group, and incompatible syntaxes across different systems, for the latter group. The authors introduce Natural Shell, an assistant for enabling end-users to generate commands and scripts for various purposes. Natural Shell automatically synthesizes scripts for different shell systems based on natural language descriptions. By interacting with Natural Shell, new users can learn the basics of scripting languages without the obstacles from the incomprehensible syntaxes. On the other hand, the authors' tool frees more advanced users from manuals when they switch shell systems. The authors have developed a prototype system and demonstrate its effectiveness with a benchmark of 50 examples of popular shell commands collected from online forums. In addition, the authors analyzed the usage of Natural Shell in a lab study that involves 10 participants with different scripting skill levels. Natural Shell effectively assists the users to generate commands in assigned syntaxes and greatly streamlines their learning and using experience.
S'engager dans la lecture : un investissement au service des compétences

une facette cognitive qui correspond aux savoirs et competences en lecture. Les resultats pour cette facette ont ete developpes dans le premier rapport international publie par LOCDE [2001]; une facette non cognitive : le concept designe aussi lengagement dans la lecture (les pratiques de lecture, les attitudes, la motivation, linteret pour la lecture). Ces resultats ont ete developpes dans le rapport La lecture, moteur de changement. Performances et engagement dun pays a lautre [2003].
Differential Voltage current conveyor transconductance amplifier based wave active filter

This paper presents Differential Voltage current conveyor transconductance amplifier (DVCCTA) voltage mode wave active filter. This method emulates reflected and incident wave for basic building block i.e. series inductor which may then be configured for other passive element realization. The functionality of the proposed method is verified for a 4th order low pass prototype filter using SPICE simulation with 0. 25µm TSMC CMOS technology parameters.
‘Fasting and prayer don't concern the doctors … they don't even know what it is': communication, decision-making and perceived social relations of Pakistani Muslim patients with long-term illnesses

Objectives. Pakistani Muslims have the poorest overall health profile in Britain, for reasons which at present remain poorly understood. We sought to explore the impact of religious identity and beliefs on self-management of long-term conditions, on patient–professional communication and decision-making and health inequalities within Pakistani Muslim communities. Design. Ethnographic study involving in-depth interviews and participant observation. Results. Religious identity plays a central role in many individuals' attempts to make sense of their personal illness narrative. Practitioners and patients are typically unwilling to engage in discussion about religious influences on patient decision-making, reflecting patients' lack of confidence in the appropriateness of raising such issues, and professionals' lack of awareness of their importance. Patients consequently receive little or no support from professionals about decisions involving such influences on self-care. The policy vacuum and lack of patient–professional engagement in this area allows the use of stereotypes of Pakistani Muslims by practitioners to remain unchallenged in most healthcare settings. Social dynamics within these settings reflect those in wider UK society, in which many Pakistani respondents believe they are unwelcome. These factors affect the psychosocial well-being of Pakistani Muslims and on their ability to manage long-term conditions. Conclusion. Shared understanding about the context in which patients manage long-term conditions is a precursor to effective lay–professional partnerships. Religious identity influences the health beliefs and practices of many British Pakistani Muslim patients. Failure to acknowledge and discuss this influence on long-term illness management leads to a vacuum in professional knowledge, inadequate support for patients' decision-making and poor responses to their requests for assistance. Findings indicate a need for practitioners to initiate more open discussion and raise questions about the pathways leading to higher rates of complications and the relationship between social status and health inequalities in this population.