Miracle-dz/UniFAR-FTUs huggingface dataset:
Structural and Functional Characterization of the Mumps Virus Phosphoprotein

ABSTRACT The phosphoprotein (P) is virally encoded by the Rhabdoviridae and Paramyxoviridae in the order Mononegavirales. P is a self-associated oligomer and forms complexes with the large viral polymerase protein (L), the nucleocapsid protein (N), and the assembled nucleocapsid. P from different viruses has shown structural diversities even though their essential functions are the same. We systematically mapped the domains in mumps virus (MuV) P and investigated their interactions with nucleocapsid-like particles (NLPs). Similar to other P proteins, MuV P contains N-terminal, central, and C-terminal domains with flexible linkers between neighboring domains. By pulldown assays, we discovered that in addition to the previously proposed nucleocapsid binding domain (residues 343 to 391), the N-terminal region of MuV P (residues 1 to 194) could also bind NLPs. Further analysis of binding kinetics was conducted using surface plasmon resonance. This is the first observation that both the N- and C-terminal regions of a negative-strand RNA virus P are involved in binding the nucleocapsid. In addition, we defined the oligomerization domain (POD) of MuV P as residues 213 to 277 and determined its crystal structure. The tetrameric MuV POD is formed by one pair of long parallel α-helices with another pair in opposite orientation. Unlike the parallel orientation of each α-helix in the tetramer of Sendai virus POD, this represents a novel orientation of a POD where both the N- and the C-terminal domains are at either end of the tetramer. This is consistent with the observation that both the N- and the C-terminal domains are involved in binding the nucleocapsid.
Reflections on the INEX structure extraction competition

After two participations to the INEX competition in the Structure Extraction task, which consists in building navigation tools for digitised books by constructing hyperlinked table of contents from OCR text and layout information, we present in this paper some reflections about this competition regarding its dataset, and its evaluation measure. We point out some issues, and propose some recommendations for improving the groundtruth and the measures.
On the Discrepancy Between Kleinberg's Clustering Axioms and k-Means Clustering Algorithm Behavior

This paper investigates the validity of Kleinberg's axioms for clustering functions with respect to the quite popular clustering algorithm called $k$-means. While Kleinberg's axioms have been discussed heavily in the past, we concentrate here on the case predominantly relevant for $k$-means algorithm, that is behavior embedded in Euclidean space. We point at some contradictions and counter intuitiveness aspects of this axiomatic set within $\mathbb{R}^m$ that were evidently not discussed so far. Our results suggest that apparently without defining clearly what kind of clusters we expect we will not be able to construct a valid axiomatic system. In particular we look at the shape and the gaps between the clusters. Finally we demonstrate that there exist several ways to reconcile the formulation of the axioms with their intended meaning and that under this reformulation the axioms stop to be contradictory and the real-world $k$-means algorithm conforms to this axiomatic system.
Pose search: Retrieving people using their pose

We describe a method for retrieving shots containing a particular 2D human pose from unconstrained movie and TV videos. The method involves first localizing the spatial layout of the head, torso and limbs in individual frames using pictorial structures, and associating these through a shot by tracking. A feature vector describing the pose is then constructed from the pictorial structure. Shots can be retrieved either by querying on a single frame with the desired pose, or through a pose classifier trained from a set of pose examples. Our main contribution is an effective system for retrieving people based on their pose, and in particular we propose and investigate several pose descriptors which are person, clothing, background and lighting independent. As a second contribution, we improve the performance over existing methods for localizing upper body layout on unconstrained video. We compare the spatial layout pose retrieval to a baseline method where poses are retrieved using a HOG descriptor. Performance is assessed on five episodes of the TV series 'Buffy the Vampire Slayer', and pose retrieval is demonstrated also on three Hollywood movies.
Dynamic reconfiguration and routing algorithms for IP-over-WDM networks with stochastic traffic

We develop algorithms for joint IP layer routing and WDM logical topology reconfiguration in IP-over-WDM networks experiencing stochastic traffic. At the WDM layer, we associate a non-negligible tuning latency with WDM reconfiguration, during which time tuned transceivers cannot service backlogged data. The IP layer is modeled as a queueing system. We demonstrate that our algorithms achieve asymptotic throughput optimality by using frame-based maximum weight scheduling decisions. We study both deterministic and random frame durations. In addition to dynamically triggering WDM reconfiguration, our algorithms specify precisely how to route packets over the IP layer during the phases in which the WDM layer remains fixed. Our algorithms remain valid under a variety of optical layer constraints. We provide an analysis of the specific case of WDM networks with multiple ports per node. In order to gauge the delay properties of our algorithms, we conduct a simulation study and demonstrate an important tradeoff between WDM reconfiguration and IP layer routing. We find that multi-hop routing is extremely beneficial at low throughput levels, while single-hop routing achieves improved delay at high throughput levels. For a simple access network, we demonstrate through simulation the benefit of employing multi-hop IP layer routes.
Paedomorphosis as an Evolutionary Driving Force: Insights from Deep-Sea Brittle Stars

Heterochronic development has been proposed to have played an important role in the evolution of echinoderms. In the class Ophiuroidea, paedomorphosis (retention of juvenile characters into adulthood) has been documented in the families Ophiuridae and Ophiolepididae but not been investigated on a broader taxonomic scale. Historical errors, confusing juvenile stages with paedomorphic species, show the difficulties in correctly identifying the effects of heterochrony on development and evolution. This study presents a detailed analysis of 40 species with morphologies showing various degrees of juvenile appearance in late ontogeny. They are compared to a range of early ontogenetic stages from paedomorphic and non-paedomorphic species. Both quantitative and qualitative measurements are taken and analysed. The results suggest that strongly paedomorphic species are usually larger than other species at comparable developmental stage. The findings support recent notions of polyphyletic origin of the families Ophiuridae and Ophiolepididae. The importance of paedomorphosis and its correct recognition for the practice of taxonomy and phylogeny are emphasized.
Diagnostic challenges in osteoporosis. Indications for bone densitometry and establishing secondary causes.

OBJECTIVE To review indications for assessing bone mineral density (BMD) and to review patient characteristics and diseases associated with osteoporosis. QUALITY OF EVIDENCE This paper is based on data from longitudinal observational studies of how BMD and other risk factors affect development of fragility fractures and on several peer-reviewed publications describing pathophysiology of bone turnover and pathogenesis of osteoporosis. Indications for obtaining BMD and monitoring treatment are based on the recommendations of the Osteoporosis Society of Canada derived from the consensus opinion of a panel of experts in osteoporosis and based on their review of the primary literature. MAIN MESSAGE Measurement of BMD provides the best single objective predictor of the relative risk of fracture at sites such as the vertebrae, hip, and wrist, predicting the likelihood of fracture with as much accuracy as measurement of elevated blood pressure predicts stroke. In addition to making the diagnosis of osteoporosis, BMD measurements are used to monitor progression of osteoporosis and effects of therapy. At this date, dual energy x-ray absorptiometry is preferred for measuring BMD. The most likely causes of osteoporosis in any patient are age, hormone withdrawal (in both men and women), and drugs (particularly corticosteroids). Secondary causes, particularly hyperparathyroidism and multiple myeloma, should be excluded by performing appropriate laboratory tests. CONCLUSION A BMD measurement should be obtained for patients at high risk of osteoporosis and fragility fractures to guide initiation and monitor success of therapy.
Hand-eye calibration

Deals with the hand-eye calibration problem. The question is to find the relative position and orientation between a camera rigidly mounted on the robot's last joint and the gripper. Hand-eye calibration is useful in many cases as for example, grasping objects or reconstructing 3D scenes. Almost all existing solutions lead to solving for homogeneous transformation equations of the form AX=XB. We propose a new formulation. Our method determines simultaneously the hand-eye transformation and the location of a calibration object with respect to the robot world coordinate system. The main advantage is that the number of unknowns remains constant and the solution is constrained to be consistent with the whole set of calibration data. Results of simulation experiments and comparisons with classical techniques are reported and analysed. Real experiments with a Cartesian robot are described and the results accuracy discussed.
Design of disulfide bridge as an alternative mechanism for color shift in firefly luciferase and development of secreted luciferase

The bioluminescence reaction, which uses luciferin, Mg^2+-ATP and molecular oxygen to yield an electronically excited oxyluciferin, is carried out by luciferase and emits visible light. The bioluminescence color of firefly luciferases is determined by the luciferase structure and assay conditions. It is proposed that the stability of a protein can be increased by introduction of disulfide bridge that decreases the configurational entropy of unfolding. A disulfide bridge is introduced into Photinus pyralis firefly luciferase to make three separate mutant enzymes with a single bridge. Moreover, C^81-A^105C mutant luciferase was modified and successfully secreted to the extracellular medium. By introduction of disulfide bridges using site-directed mutagenesis in Photinus pyralis luciferase the color of emitted light was changed to red and the optimum temperature of activity was also increased (up to 10 °C more than wild type). Amongst mutants with a disulfide bridge, P^451C-V^469C and L^306C-L^309C mutants exhibit a single peak in the red region of the spectrum at pH 7.8. It is worthwhile to note that with the design of a secreted luciferase, the increased optimum temperature, thermostability and emission of red light might make mutant luciferase suitable reporters for the study of gene expression in high through-put screening.
On the Activity of the Corticostriatal Networks during Spike-and-Wave Discharges in a Genetic Model of Absence Epilepsy

Absence seizures are characterized by impairment of consciousness associated with widespread bilaterally synchronous spike-and-wave discharges (SWDs) in the electroencephalogram (EEG), which reflect highly synchronized oscillations in thalamocortical networks. Although recent pharmacological studies suggest that the basal ganglia could provide a remote control system for absence seizures, the mechanisms of propagation of epileptic discharges in these subcortical nuclei remain unknown. In the present study, we provide the first description of the electrical events in the corticostriatal pathway during spontaneous SWDs in the genetic absence epilepsy rats from Strasbourg (GAERS), a genetic model of absence epilepsy. In corticostriatal neurons, the SWDs were associated with suprathreshold rhythmic depolarizations in-phase with local EEG spikes. Consistent with this synchronized firing in their excitatory cortical afferents, striatal output neurons (SONs) exhibited, during SWDs, large-amplitude rhythmic synaptic depolarizations. However, SONs did not discharge during SWDs. Instead, the rhythmic synaptic excitation of SONs was shunted by a Cl--dependent increase in membrane conductance that was temporally correlated with bursts of action potentials in striatal GABAergic interneurons. The reduced SON excitability accompanying absence seizures may participate in the control of SWDs by affecting the flow of cortical information within the basal ganglia circuits.
Relationship between bond energy and total work of fracture for asphalt binder-aggregate systems

Surface free energy is a thermodynamic material property representing the work required to create new surfaces of unit area in a vacuum. Surface free energy has been used to quantify and screen both the cohesive bond energy of asphalt binders and the adhesive bond energy of asphalt binder–aggregate interfaces in wet and dry conditions. The bond energy is computed based on the surface free energies of the constituent materials. The total work of fracture is the cumulative effect of energies applied to the sample to create two new surfaces of unit area. These energies include the bond energy, calculated from surface free energy, dissipated plastic energy, and dissipated viscoelastic energy. This paper presents experimental results from a series of pull-off tests using asphalt binder-aggregate samples that demonstrate the relationship between bond energy and total work of fracture. In order to fully explore this relationship, temperature, loading rate, specimen geometry, and moisture content were varied.
Laparoscopic total extraperitoneal repair under spinal anesthesia versus general anesthesia: a randomized prospective study

Background Laparoscopic total extraperitoneal (TEP) inguinal hernia repair is a well-known approach to inguinal hernia repair that is usually performed under general anesthesia (GA). To date, no reports compare the efficacy of spinal anesthesia (SA) with that of GA for laparoscopic hernia repairs. The purpose of this study was to compare the surgical outcome of TEP inguinal hernia repair performed when the patient was treated under SA with that performed under GA. Materials and methods Between July 2015 and July 2016, 50 patients were prospectively randomized to either the GA TEP group (Group I) or the SA TEP group (Group II). Propofol, fentanyl, rocuronium, sevoflurane, and tracheal intubation were used for GA. Hyperbaric bupivacaine (15 mg) and fentanyl (10 µg) were used for SA to achieve a sensorial level of T3. Intraoperative events related to SA, operative and anesthesia times, postoperative complications, and pain scores were recorded. Each patient was asked to evaluate the anesthetic technique by using a direct questionnaire filled in 3 months after the operation. Results All the procedures were completed by the allocated method of anesthesia as there were no conversions from SA to GA. Pain was significantly less for 1 h (P<0.0001) and 4 h (P=0.002) after the procedure for the SA and GA groups, respectively. There was no difference between the two groups regarding complications, hospital stay, recovery, or surgery time. Generally, patients were more satisfied with SA than GA (P<0.020). Conclusion TEP inguinal hernia repair can be safely performed under SA, and SA was associated with less postoperative pain, better recovery, and better patient satisfaction than GA.
Web-Based and Mobile Delivery of an Episodic Future Thinking Intervention for Overweight and Obese Families: A Feasibility Study

Background The bias toward immediate gratification is associated with maladaptive eating behaviors and has been cross-sectionally and prospectively related to obesity. Engaging in episodic future thinking, which involves mental self-projection to pre-experience future events, reduces this bias and energy intake in overweight/obese adults and children. To examine how episodic future thinking can be incorporated into clinical interventions, a Web-based system was created to provide training for adults and children in their everyday lives. Objective Our study examined the technical feasibility, usability, and acceptability of a Web-based system that is accessible by mobile devices and adapts episodic future thinking for delivery in family-based obesity interventions. Methods We recruited 20 parent-child dyads (N=40) from the surrounding community and randomized to episodic future thinking versus a nutritional information thinking control to test the feasibility of a 4-week Web-based intervention. Parents were 44.1 (SD 7.8) years of age with BMI of 34.2 (SD 6.8) kg/m2. Children were 11.0 (SD 1.3) years of age with BMI percentile of 96.0 (SD 1.8). Families met weekly with a case manager for 4 weeks and used the system daily. Adherence was collected through the Web-based system, and perceived acceptance of the Web-based system was assessed postintervention. Measurements of body composition and dietary intake were collected at baseline and after the 4 weeks of intervention. Results All 20 families completed the intervention and attended all sessions. Results showed parents and children had high adherence to the Web-based system and perceived it to be easy to use, useful, and helpful. No differences between conditions were found in adherence for parents (P=.65) or children (P=.27). In addition, results suggest that basic nutrition information along with episodic future thinking delivered through our Web-based system may reduce energy intake and weight. Conclusions We showed that our Web-based system is an accepted technology and a feasible utility. Furthermore, results provide initial evidence that our system can be incorporated into family-based treatments targeting behaviors related to weight control. These results show promising utility in using our Web-based system in interventions.
against Secondary Nematode Infection Eosinophils Mediate Protective Immunity

James J. Lee and Judith A. AppletonMaura C. Ruyechan, Kierstin L. Luber, Nancy A. Lee, Lu Huang, Nebiat G. Gebreselassie, Lucille F. Gagliardo,ol.1402219http://www.jimmunol.org/content/early/2014/11/26/jimmunJ Immunol€ published online 26 November 2014Subscriptionshttp://jimmunol.org/subscriptionsInformation about subscribing to The Journal of Immunology is online at: Permissionshttp://www.aai. org/ji/copyright.htmlSubmit copyright permission requests at: Email Alertshttp://jimmunol.org/cgi/alerts/etocReceive free email-alerts when new articles cite this article. Sign up at:
Seroprevalence of Toxocara canis infection among children in Swaziland, southern Africa

Abstract As there appeared to be no data available on Toxocara canis infection in the children of Swaziland, a serological survey of T. canis infection was recently conducted among 92 children aged 3–12 years from rural slums in the low- and middle-veld. A child was considered seropositive if, in western blots based on the excretory–secretory antigens of larval T. canis, his or her serum gave a positive result when diluted 1 : 64. Forty-one (44.6%) of the children were found seropositive. There were no statistically significant differences in seroprevalence between the 49 boys and 43 girls investigated (46.9% v. 41.8%) or between the eight subjects aged 12 years and the 47 aged ≤5 years (62.5% v. 38.3%); the corresponding odds ratios were 0.81 (95% confidence interval=0.36–1.86; P=0.62) and 2.69 (95% confidence interval=0.57–12.62; P=0.20), respectively. The 66 subjects from the middleveld were, however, significantly more likely to be seropositive than the 26 subjects from the lowveld (54.5% v. 19.2%; odds ratio=5.04, with a 95% confidence interval of 1.70–14.98; P<0.01). It seems likely that T. canis infection is common among the children who live in slums in Swaziland, particularly in the country's middleveld, probably as the result of poor hygiene and poor sanitation.
Immunohistochemical Characterization of Spontaneous and Acrylonitrile-induced Brain Tumors in the Rat

Twenty-eight spontaneously occurring glial tumors (previously diagnosed as astrocytomas, oligodendrogliomas, and gliomas) and eleven granular cell tumors (GCTs) were selected for evaluation using a panel of immunohistochemistry (IHC) stains (Ricinus communis agglutinin type 1 [RCA-1], ionized calcium-binding adapter molecule 1 [Iba-1], OX-6/major immunohistocompatibility complex class II, oligodendrocytes transcription factor 2 [Olig2], glial fibrillary acidic protein [GFAP], S100 beta, glutamine synthetase, neurofilament, proliferating cell nuclear antigen). In addition, nine brain tumors from a 2-year drinking water study for acrylonitrile were obtained from the Acrylonitrile Group, Inc. Based on IHC staining characteristics, Olig2+ oligodendrogliomas were the most commonly diagnosed spontaneous tumor in these animals. Many of the spontaneous tumors previously diagnosed as astrocytomas were RCA-1+, Iba-1+ and negative for GFAP, S100beta, and glutamine synthetase; the diagnosis of malignant microglial tumor is proposed for these neoplasms. Three mixed tumors were identified with Olig2+ (oligodendrocytes) and Iba-1+ (macrophage/microglia) cell populations. The term mixed glioma is not recommended for these tumors, as it is generally used to refer to oligoastrocytomas, which were not observed in this study. GCT were positive for RCA-1 and Iba-1. All acrylonitrile tumors were identified as malignant microglial tumors. These results may indicate that oligodendrogliomas are more common as spontaneous tumors, while acrylonitrile-induced neoplasms are microglial/histiocytic in origin. No astrocytomas (GFAP, S100 beta, and/or glutamine synthetase-positive neoplasms) were observed.
Fast packet classification using field-level trie

Packet classification plays an important role in next-generation Internet routers in providing various services such as packet filtering, policy routing, traffic policing, and load balancing. In this paper, we propose an original field-level trie classification (FLTC) scheme that accommodates classifier (rule database) with multiple fields specified in different forms (prefix and range). The FLTC achieves a high classification speed with reasonable storage. It is also highly scalable regarding the size and the number of fields of classifiers.
THE COMPOSITION OF STAPHYLOCOCCUS AUREUS IN RELATION TO THE WATER ACTIVITY OF THE GROWTH MEDIUM.

Summary: Staphylococcus aureus organisms, grown in basal medium of water activity (aw) 0·993 and in basal medium adjusted to several different aw values by addition of NaCl, were analysed for the following components: sodium, potassium, calcium, magnesium, total amino acids, inorganic phosphate, chloride, water, DNA, RNA, protein. Cell water decreased from 1·66 to 0·83 g. /g. dry weight when aw was decreased from 0·993 to 0·90. Internal concentrations of solutes generally increased with decrease in aw, potassium and phosphate concentrations being greatest at 0·92 aw and sodium, chloride, magnesium, and amino acids at 0·90 aw, the lowest aw value studied. Increases in potassium and amino acid concentrations resulted largely from the decreased water contents of cocci grown at low aw values. Intracellular sodium and chloride concentrations were much lower than and proportional to the NaCl concentration in the medium. The predominant cell solute was potassium at 0·92 aw and above, and sodium below 0·92 aw. The data are discussed in relation to the inhibition of bacterial growth at low aw values.