Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of determinants for inhibitor binding within the RNA active site of human telomerase using PNA scanning.

Telomerase is a ribonucleoprotein that participates in the maintenance of telomere length. Its activity is up-regulated in many tumor types, suggesting that it may be a novel target for chemotherapy. The RNA component of telomerase contains an active site that plays at least two roles&sbd;binding telomere ends and templating their replication [Greider, C. W. , & Blackburn, E. H. (1989) Nature 337, 331-337]. The accessibility of RNA nucleotides for inhibitor binding cannot be assumed because of the potential for RNA secondary structure and RNA-protein interactions. Here we use high-affinity recognition by overlapping peptide nucleic acids (PNAs) [Nielsen, P. E. , et al. (1991) Science 254, 1497-1500] to identify nucleotides within the RNA active site of telomerase that are determinants for inhibitor recognition. The IC50 for inhibition decreases from 30 microM to 10 nM as cytidines 50-52 (C50-52) at the boundary between the alignment and elongation domains are recognized by PNAs overlapping from the 5' direction. As C50-52 are uncovered in the 3' direction, IC50 increases from 10 nM to 300 nM. As cytidine 56 at the extreme 3' end of the active site is uncovered, IC50 values increase from 0.5 microM to 10 microM. This analysis demonstrates that C50-C52 and C56 are important for PNA recognition and are physically accessible for inhibitor binding. We use identification of these key determinants to minimize the size of PNA inhibitors, and knowledge of these determinants should facilitate design of other small molecules capable of targeting telomerase. The striking differences in IC50 values for inhibition of telomerase activity by related PNAs emphasize the potential of PNAs to be sensitive probes for mapping complex nucleic acids. We also find that PNA hybridization is sensitive to nearest-neighbor interactions, and that consecutive guanine bases within a PNA strand increase binding to complementary DNA and RNA sequences.
A Forward Genetic Approach in Chlamydomonas reinhardtii as a Strategy for Exploring Starch Catabolism

A screen was recently developed to study the mobilization of starch in the unicellular green alga Chlamydomonas reinhardtii. This screen relies on starch synthesis accumulation during nitrogen starvation followed by the supply of nitrogen and the switch to darkness. Hence multiple regulatory networks including those of nutrient starvation, cell cycle control and light to dark transitions are likely to impact the recovery of mutant candidates. In this paper we monitor the specificity of this mutant screen by characterizing the nature of the genes disrupted in the selected mutants. We show that one third of the mutants consisted of strains mutated in genes previously reported to be of paramount importance in starch catabolism such as those encoding β-amylases, the maltose export protein, and branching enzyme I. The other mutants were defective for previously uncharacterized functions some of which are likely to define novel proteins affecting starch mobilization in green algae.
The Impact of Posttraumatic Stress Disorder on Partners and Children of Australian Vietnam Veterans

Objective: This study explored the emotional and physical health of a group of families of Australian Vietnam veterans suffering posttraumatic stress disorder (PTSD). The aim was to study the impact of PTSD upon the families of the sufferers. Method: The families of a random sample of Vietnam veterans receiving treatment at a specialist PTSD Unit were invited to participate in this study. Partners of the veterans and children over the age of 15 years were eligible to participate. Four selfreport psychometric inventories were administered assessing psychological distress, social climate within their families, self-esteem, and a range of lifestyle issues, including physical health. A control group, consisting of a sample of volunteers, was also surveyed. Results: The partners of the Vietnam veterans showed significantly higher levels of somatic symptoms, anxiety and insomnia, social dysfunction and depression than the control group. They reported significantly less cohesion and expressiveness in their families and significantly higher levels of conflict. The partners also had significantly lower levels of self-esteem. The children of the veterans reported significantly higher levels of conflict in their families. However, the children showed no significant differences on measures of psychological distress and self-esteem from their matched counterparts. Conclusions: These findings support overseas studies that indicate that the families of PTSD sufferers are also impacted by the disorder. In this study, the families of Australian Vietnam veterans experienced more conflict and their partners were significantly more psychologically distressed (i.e. somatic symptoms, anxiety, insomnia, social dysfunction, depression and low self-esteem) than a matched control group.
A molecular dynamics analysis of protein structural elements

The relation between protein secondary structure and internal motions was examined by using molecular dynamics to calculate positional fluctuations of individual helix, β‐sheet, and loop structural elements in free and substrate‐bound hen egg‐white lysozyme. The time development of the fluctuations revealed a general correspondence between structure and dynamics; the fluctuations of the helices and β‐sheets converged within the 101 psec period of the simulation and were lower than average in magnitude, while the fluctuations of theloop regions were not converged and were mostly larger than average in magnitude. Notable exceptions to this pattern occurred in the substrate‐bound simulation. A loop region (residues 101–107) of the active site cleft had significantly reduced motion due to interactions withthe substrate. Moreover, part of a loop and a 310 helix (residues of 67–88) not in contact with the substrate showeda marked increase in fluctuations. That these differences in dynamics of free and substrate‐bound lysozyme did not result simply from sampling errors was established by an analysis of the variations in the fluctuationsof the two halves of the 101 psec simulation of free lysozyme. Concerted transitions of four to five mainchain ϕ and ψ angles between dihedral wells were shown to be responsible for large coordinate shifts in the loops. These transitions displaced six or fewer residues and took place eitherabruptly, in 1 psec or less, or with a diffusive character over 5–10 psec. Displacements of rigid secondary structures involved longer timescale motions in bound lysozyme; a 0.5 Å rms change in the position of a helix occurred over the 55 psec simulation period. This helix reorientation within the protein appears to be a response to substrate binding. There was little correlation between the solvent accessible surface areaand the dynamics of the different structural elements.
熊本大学学術リポジトリ Kumamoto University Repository System Title Wireless LAN Based Indoor Positioning System WiPS and Its Simulation

The wireless LAN(Wi-Fi) infrastructure is widely used and many location-aware systems and services are researched. In this paper, wireless LAN based indoor positioning system WiPS is proposed. WiPS uses wireless LAN technology to measure the location of each mobile terminal. Mobile terminals equip only wireless LAN device to communicate and measure its location, so it can be made without any additional devices for location sensing. Existing wireless LAN based location systems measure the signal strength by only access points. On WiPS, each mobile terminal also measures the signal strength of neighboring terminals. Thereby WiPS can achieve more precise location estimation than existing systems, where there are many mobile terminals. We simulate the case that disntance measurement has probablistic error. The result shows improvement of accuracy in WiPS.
Comparing Performance of Committee Based Approaches to Active Learning

In this paper we study the use of Query by Committee strategies in active learning from unlabeled examples. In this framework we compare four algorithms for creating ensembles of classifiers: bagging, boosting, decorate and random forests. We consider the use of different measures of disagreement among components classifiers to select the most informative example to query an oracle for its label. Moreover, we introduce a new technique, based on analysing the neighborhood of examples, which is applied to create a starting training set for generating the first ensemble. The usefulness of all these approaches is experimentally evaluated. Results of our experiments confirm that accurate final classifiers could be created using a relatively small number of queries to label examples, in particular for active decorate. Simpler disagreement measures, as margins of examples or median difference are usually more effective than more advanced ones, however mainly for multi-class data. Finally, the new technique for selecting starting examples has proved to be definitely more effective than simple sampling.
An analytical model for bounded WSNs with unreliable cluster heads and links

In Wireless Sensor Networks (WSNs), performance and availability are important in providing Quality of Service (QoS). WSNs are prone to failures that may result from software and hardware malfunctions, battery drain, tampering and link failures. In addition, sensors are resource constrained in terms of inadequate processing capacity, limited storage memory and restricted power supply. Alternating sensor operations between sleep and active modes whilst saving energy, has also introduced more challenges to the performance and dependability of WSN systems. This paper therefore seeks to investigate performance and availability concerns resulting from link and node failures in addition to the buffer restrictions and challenges caused by alternating sensor operations between active and sleep states. First, a finite queue capacity analytical model integrating performance and availability in the presence of node and channel failures and repairs is developed. Using the model, we analyse performance and availability of WSNs in terms of network throughput, delays and dependability. Finally, the model is used to evaluate tradeoffs between performance metrics. The analytical solutions using Spectral Expansion and Kolmogorov Forward equations as well as the simulation results are in good agreement.
Vibrotactile feedback and visual cues for arm posture replication

For rehabilitation applications using multiple types of feedback can help speed up posture correction of the subject - visual cues are particularly helpful in providing global information to the subjects. This paper presents a system that aids students to mimic a master's arm posture using vibrotactile feedback and visual cues. The design of the vibrotactile feedback unit as well as the posture correction protocol are discussed in details. Experiments comparing student's posture correction time using only vibrotactile feedback and vibrotactile feedback with visual cue are conducted to show the difference in using multi-modal feedback over unimodal feedback systems. An improved design of vibration pattern for better user perception and interpretation of the vibrotactile feedback information is also presented at the end of the paper.
Legislative Mandates for Use of Active Surveillance Cultures to Screen for Methicillin-Resistant Staphylococcus aureus and Vancomycin-Resistant Enterococci: Position Statement From the Joint SHEA and APIC Task Force

Legislation aimed at controlling antimicrobial-resistant pathogens through the use of active surveillance cultures to screen hospitalized patients has been introduced in at least 2 US states. In response to the proposed legislation, the Society for Healthcare Epidemiology of America (SHEA) and the Association of Professionals in Infection Control and Epidemiology (APIC) have developed this joint position statement. Both organizations are dedicated to combating healthcare-associated infections with a wide array of methods, including the use of active surveillance cultures in appropriate circumstances. This position statement reviews the proposed legislation and the rationale for use of active surveillance cultures, examines the scientific evidence supporting the use of this strategy, and discusses a number of unresolved issues surrounding legislation mandating use of active surveillance cultures. The following 5 consensus points are offered. (1) Although reducing the burden of antimicrobial-resistant pathogens, including methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant enterococci (VRE), is of preeminent importance, APIC and SHEA do not support legislation to mandate use of active surveillance cultures to screen for MRSA, VRE, or other antimicrobial-resistant pathogens. (2) SHEA and APIC support the continued development, validation, and application of efficacious and cost-effective strategies for the prevention of infections caused by MRSA, VRE, and other antimicrobial-resistant and antimicrobial-susceptible pathogens. (3) APIC and SHEA welcome efforts by healthcare consumers, together with private, local, state, and federal policy makers, to focus attention on and formulate solutions for the growing problem of antimicrobial resistance and healthcare-associated infections. (4) SHEA and APIC support ongoing additional research to determine and optimize the appropriateness, utility, feasibility, and cost-effectiveness of using active surveillance cultures to screen both lower-risk and high-risk populations. (5) APIC and SHEA support stronger collaboration between state and local public health authorities and institutional infection prevention and control experts.
Long-Term Follow-up and Results of Thoracoscopic Sympathectomy for Primary Palmar Hyperhidrosis

The goal of this retrospective study was to evaluate the long-term outcomes of bilateral video-assisted thoracoscopic (VATS) sympathectomy for primary hyperhydrosis. Between January 2008 and October 2012, 56 cases underwent VATS sympathectomy for primary palmar hyperhidrosis. All patients' intraoperative and postoperative outcomes were collected. Data of the procedure and complications, midterm and long term outcome were collected by telephone interview. Mean age was 22.5 years (range, 16–38 years), and mean operative time to complete the bilateral procedure was 52 minutes (range, 40–85 minutes). The procedure was successfully completed in all patients without the need to enlarge the incision. The hands of all patients were dry and warm after operation. Postoperatively, there was no mortality and no residual palmar hyperhidrosis. Postoperative stay range was 2 to 4 days. Neurologic complications (radial paralysis, Horner syndrome and dysesthesia of the arm) were not occurred. Compensatory sweating occurred in 12.5% of the patients. Despite this 89.9% of the patients were satisfied or very satisfied. This study confirms that VATS sympathectomy is a suitable choice for severe palmar hyperhidrosis. Long-term follow-up proved that mild compensatory hyperhidrosis is the main side effect associated with this technique.
On the Convergence of GMRES with Invariant-Subspace Deflation

We consider the solution of large and sparse linear systems of equations by GMRES. Due to the appearance of unfavorable eigenvalues in the spectrum of the coefficient matrix, the convergence of GMRES may hamper. To overcome this, a deflated variant of GMRES can be used, which treats those unfavorable eigenvalues effectively. In the literature, several deflated GMRES variants are applied successfully to various problems, while a theoretical justification is often lacking. In contrast to deflated CG, the convergence of deflated GMRES seems to be harder to analyze and to understand. This paper presents some new theoretical insights into deflated GMRES based on A-invariant deflation subspaces. Fundamental results regarding the convergence of deflated GMRES are proved in order to show the effectiveness and robustness of this method. Numerical experiments are provided to illustrate the theoretical results and to show some further properties of deflated GMRES. Consequently, practical variants of deflated GMRES from the literature can be better understood based on the results presented in this paper.
Olfactory Neurons Expressing Closely Linked and Homologous Odorant Receptor Genes Tend to Project Their Axons to Neighboring Glomeruli on the Olfactory Bulb

We have characterized two separate odorant receptor (OR) gene clusters to examine how olfactory neurons expressing closely linked and homologous OR genes project their axons to the olfactory bulb. Murine OR genes, MOR28, MOR10, and MOR83, share 75–95% similarities in the amino acid sequences and are tightly linked on chromosome 14. In situ hybridization has demonstrated that the three genes are expressed in the same zone, at the most dorsolateral and ventromedial portions of the olfactory epithelium, and are rarely expressed simultaneously in individual neurons. Furthermore, we have found that olfactory neurons expressing MOR28, MOR10, or MOR83 project their axons to very close but distinct subsets of glomeruli on the medial and lateral sides of the olfactory bulb. Similar results have been obtained with another murine OR gene cluster for A16 and MOR18 on chromosome 2, sharing 91% similarity in the amino acid sequences. These results may indicate an intriguing possibility that olfactory neurons expressing homologous OR genes within a cluster tend to converge their axons to proximal but distinct subsets of glomeruli. These lines of study will shed light on the molecular basis of topographical projection of olfactory neurons to the olfactory bulb.
Issues in the Management of Acute Agitation: How Much Current Guidelines Consider Safety?

Agitated behavior constitutes up to 10% of emergency psychiatric interventions. Pharmacological tranquilization is often used as a valid treatment for agitation but a strong evidence base does not underpin it. Available literature shows different recommendations, supported by research data, theoretical considerations, or clinical experience. Rapid tranquilization (RT) is mainly based on parenteral drug treatment and the few existing guidelines on this topic, when suggesting the use of first generation antipsychotics and benzodiazepines, include drugs with questionable tolerability profile such as chlorpromazine, haloperidol, midazolam, and lorazepam. In order to systematically evaluate safety concerns related to the adoption of such guidelines, we reviewed them independently from principal diagnosis while examining tolerability data for suggested treatments. There is a growing evidence about safety profile of second generation antipsychotics for RT but further controlled studies providing definitive data in this area are urgently needed.
Experimental evidence of impacts of an invasive parakeet on foraging behavior of native birds

Lay Summary Invasive rose-ringed parakeets caused behavioral changes in native garden birds that reduced their feeding rates. Understanding how invasive species impact native species can be complex, especially in urban environments where many other factors are also at play. We therefore used an experiment to disentangle these factors and demonstrate that parakeets are more disruptive than a dominant native competitor.
Evaluation of emergency tourniquets for prehospital use in China.

OBJECTIVE Massive hemorrhage is life-threatening during armed conflicts. Tourniquets are important medical devices used to reduce severe bleeding in trauma. The aim of this study was to empirically evaluate the current tourniquets used in China and provide information to emergency nurses in selecting the appropriate tourniquet. METHODS Five tourniquets were self-applied by 20 healthy participants. The blood flow distal to the tourniquet site was assessed using vascular Doppler ultrasound. Application time, pain, numbness, and other parameters were evaluated. RESULTS The bladder tourniquet and windlass tourniquet effectively occluded arterial blood flow with success rates higher than 75% in both the upper and lower extremities. The Cargo-strap was the fastest to apply, taking (7.22+/-2.30) s for the upper extremity and (6.48+/-2.40) s for the lower extremity. The rubber tube was the most painful, and the improvised tourniquet was the least efficient. The success rates were higher in the lower extremity than in the upper extremity (P less than 0.05, X(2) equal to 5.714). CONCLUSIONS The bladder tourniquet and the windlass tourniquet are efficient tourniquets, although the windlass is superior with respect to portability and pain. The Cargo-strap and rubber tourniquets have several disadvantages that reduce their suitability for field use. The improvised tourniquet is not recommended because of low efficiency and severe pain during implementation.
Exploring the Challenges of Making Data Physical

Physical representations of data have existed for thousands of years. However, it is only now that advances in digital fabrication, actuated tangible interfaces, and shape-changing displays can support the emerging area of 'Data Physicalization' [6]: the study of computer-supported, physical representations of data and their support for cognition, communication, learning, problem solving and decision making. As physical artifacts, data physicalizations can tap more deeply into our perceptual exploration skills than classical computer setups, while their dynamic physicality alleviates some of the main drawbacks of static artifacts by facilitating their crafting, supporting adaptation to different data, and encouraging sharing between different users.
SISS: Extending semantic interoperability to support collaborative system development and execution

Middleware infrastructure has been widely adopted to support the development and execution of collaborative systems. With these systems many challenges arise, those related to interoperability gained remarkable importance. This work aims to increase the semantic interoperability support in an infrastructure named Web-based Groupware Service-Oriented Architecture (WGWSOA) that uses middleware services to support the development and execution of collaborative systems. Services were built on this infrastructure to extend the interoperability semantic support. Evidences pointing to the validity of the proposed solution, to support the development and execution of collaborative systems, were produced through an experimental study.