Miracle-dz/UniFAR-FTUs huggingface dataset:
Cross-layer optimization for reliability improvement of data delivery in 6LoWPAN-based networks

Internet of Things (IoT) is becoming a reality and new and advanced applications are expected to emerge. For applications with reliability needs to work well in IoT environments, robust data transportation is required. Approaches like TCP are known for not being adequate in sensor network environments, while UDP has been included in the 6LoWPAN stack allowing low-power and limited processing devices to participate in the IoT. However, UDP provides no reliability. One way of providing reliability is to use link-layer acknowledgements but this mechanism may lead to an inefficient use of resources if used unconditionally throughout all the network. Another way is to request the confirmation of messages sent, done at the application layer, but this is an end-to-end process that can only be applied for specific message type transactions. If used for all data then there will be long delays and inefficient use of resources also. Here we address the design of a cross-layer reactive mechanism that improves reliability of data delivery, in order to support applications that require some reliability level when delivering data notifications. This mechanism introduces link layer reliability at specific nodes, gradually and only when needed, having no scaling problems. Results show that this mechanism can improve data delivery and improve the use of network resources.
ENVIRONMENTAL VARIATION AND SEXUAL SELECTION IN THE MOUNTAIN BLUEBIRD (SIALIA CURRUCOIDES)

Sexual selection is an evolutionary force that can result in highly elaborate traits. These traits function to increase mating success through intrasexual or intersexual competition. We studied whether blue coloration in the mountain bluebird (Sialia currucoides) is relevant during intrasexual contests over nest sites. Sexually dimorphic blue coloration in this species has been linked to mating success, but we know little about the function of this signal during aggressive interactions between males. Coloration may signal status and resource holding potential, but it is unclear whether aggressive behavior is based on individual status, the status of a competitor, or mutual assessment of both. We performed simulated territorial intrusions to understand whether male aggressive behavior was linked to his own status, the status of the simulated intruder, or both. We also measured food availability to determine if males with more intense coloration also obtained higher quality territories, as would be expected if plumage brightness honestly signals male resource holding potential (RHP). We found that male aggressive behavior was positively related to his own coloration, but not the coloration of his simulated opponent. However, while a single aggressive behavior was repeatable, our integrated metric of aggression was not. Lastly, we found that males with more saturated coloration obtained territories with greater insect abundance. Overall, our results provide evidence for the function of this signal during agonistic contests, and for the honesty of brightness as an indicator of male resource holding potential.
Audio to the Rescue

Automatic recognition of people is a challenging problem which has received much attention during the recent years due to its many applications in different fields such as law enforcement, security applications or video indexing. Recognition of people can be achieved using different biometrics such as face, voice, fingerprints or iris scans among others. In most cases, the choice of the particular biometric deeply relies on the final application. For instance, retinal scans have shown high recognition accuracy, however their use is limited to the availability of cooperative individuals, which is not always possible. Although relatively high recognition rates have been obtained using separated biometrics, there are some limitations that make very difficult to increase the recognition performance using individual modalities. Examples of these limitations are changes in illumination or pose for the face biometric, and ambient noise and channel distortion for the voice biometric. Although, more powerful recognition schemes for each modality would probably improve the recognition rates, there is another potential way to increase the recognition performance which consists in combining recognition results from different biometrics. The key idea behind this combined approach is that different information sources can complement each other since degradations for each modality are usually uncorrelated. A good example of a system that combine multiple information sources is the human being, e.g. it has been shown that simultaneously seeing and listening a person talking greatly increases intelligibility. In this paper, we will focus on the recognition of people in video sequences for video indexing applications. This is: given a video sequence, we want to locate those clips where a particular person
Nitric oxide and nitric oxide‐generating compounds inhibit hepatocyte protein synthesis

Hepatocytes are stimulated to produce nitric oxide (NO·) from L‐arginine in response to conditioned Kupffer cell medium or a combination of cytokines. Associated with the production of NO· in hepatocytes, there is a profound decrease in total protein synthesis ([3H]leucine incorporation). This report demonstrates that authentic NO· and the NO·‐generating compound S‐nitroso‐N‐acetylpenicillamine inhibit hepatocyte total protein synthesis in a reversible and concentration‐dependent fashion. In parallel with the suppression of hepatocyte total protein synthesis, authentic NO· inhibits the production of two specific hepatocyte proteins, albumin and fibrinogen, without influencing the quantity of albumin mRNA. Although authentic NO· induces a rapid increase in cGMP levels in hepatocytes, the addition of the cGMP analog 8‐bromoguanosine 3‘:5‘ cyclic monophosphate to unstimulated HC cultures does not reproduce the inhibition of total protein synthesis. These data show that NO· is the hepatocyte L‐arginine metabolite that inhibits protein synthesis. Furthermore, these findings indicate that NO· does not inhibit hepatocyte protein synthesis solely through the activation of soluble guanylate cyclase but appears to affect a translational or posttranslational process. —Curran, R. D. ; Ferrari, F. K. ; Kispert, P. H. ; Stadler, J.; Stuehr, D. J.; Simmons, R. L. ; Billiar, T. R. Nitric oxide and nitric oxide‐generating compounds inhibit hepatocyte protein synthesis. FASEB J. 5: 2085–2092; 1991.
Utilization of L‐α‐Nucleobase Amino Acids (NBAs) as Protein Engineering Tools: Construction of NBA‐Modified HIV‐1 Protease Analogues and Enhancement of Dimerization Induced by Nucleobase Interaction

Protein engineering can be a useful technology for constructing novel functional molecules. In this approach, site-directed mutagenesis and directed evolution have been carried out. In many cases, however, this technology has been restricted to genetically encoded amino acids. On the other hand, naturally occurring proteins fold into a compact structure, and this 3D arrangement relates closely to function. A great number of proteins exhibit function after cooperative and noncovalent interactions between two or more subunits. In the field of protein engineering, a powerful tool that can facilitate protein–protein interactions could bring about the construction of novel functional proteins with high ability and stability. Until recently, the approach for association of proteins had been mainly provided by formation of covalent bonds such as disulfide linkage. This method, however, would be complicated if it were to be applied to proteins with three or more subunits. Enhanced protein–protein association by noncovalent and specific interactions could be useful in generating stable 4D structures and protein function. For this purpose, nucleobases are particularly useful due to their ability to form specific interactions. Diederichsen and co-workers reported the construction of a and b peptides with nucleobase moieties at their side chains, and the peptides were functionalized by using Watson–Crick base pairing of duplexes. Garner and co-workers reported the assembly of a helical peptide nucleic acids (aPNAs) that could recognize single-stranded DNA in a complementary manner. We have reported the use of l-a-aminog-nucleobase-butyric acids (nucleobase amino acids or NBAs; Figure 1) for the construction of RNA binding molecules and functional peptides. 7] Furthermore, not only Watson–Crick base pairs but also homo base pairs such as G–G, A–A, T–T and C–C occur in some DNA sequences and designed peptides. 9] The C–C (cytosine–protonated cytosine) interaction is especially strong due to its ability to form three hydrogen bonds, and this homo base pair has been applied to make protein homodimer structures. Therefore, to prove the availability of homo base pairs on the protein–protein association surface, we constructed HIV-1 protease analogues modified with NBAs and their catalytic properties were evaluated.
Improving attending rounds: Qualitative reflections from multidisciplinary providers

Abstract Background. Attending rounds, the time for the attending physician and the team to discuss the team’s patients, take place at teaching hospitals every day, often with little standardization. Objective. This hypothesis-generating qualitative study sought to solicit improvement recommendations for standardizing attending rounds from the perspective of a multi-disciplinary group of providers. Methods. Attending physicians, housestaff (residents and interns), medical students, nurses and pharmacists at an academic medical center participated in a quality improvement initiative between January and April 2013. Participants completed an individual or focus group interview or an e-mail survey with three open-ended questions: (1) What are poor or ineffective practices for attending rounds? (2) How would you change attending rounds structure and function? (3) What do you consider best practices for attending rounds? We undertook content analysis to summarize each clinical stakeholder group’s improvement recommendations. Results. Sixty stakeholders participated in our study including 23 attending hospitalists, 24 housestaff, 7 medical students, 2 pharmacists and 4 nurses. Key improvement recommendations included (1) performing a pre-rounds huddle, (2) planning of the visit schedule based on illness or pending discharge, (3) real-time order writing, (4) patient involvement in rounds with shared decision-making, (5) bedside nurse inclusion and (6) minimizing interruption of intern or student presentations. Conclusions. The practice improvement recommendations identified in this study will require deliberate systems changes and training to implement, and they warrant rigorous evaluation to determine their impact on the clinical and educational goals of rounds.
On Methods to Utilize HIV-RNA Data Measured by Two Different PCR Assays

The plasma HIV-RNA level has been used as the primary efficacy measurement in clinical trials to evaluate antiretroviral regimens in HIV-infected patients. It is measured by polymerase chain reaction (PCR) assays, which usually have limits of reliable quantification (LoQ). For example, the commercially available Amplicor Standard assay has a reliable range of 400–750,000 copies/mL while the Ultrasensitive assay has a range of 50–75,000 copies/mL. Values below the lower LoQ are usually reported as categorical variables such as “ < 400 copies/mL” for the Standard assay and “ < 50 copies/mL” for the Ultrasensitive assay. The Standard assay, which has a higher ceiling of 750,000 copies/mL, is typically used as the first tool to measure HIV-RNA levels; if a value of “ < 400 copies/mL” is reported by the Standard assay, the plasma sample may be re-tested by the Ultrasensitive assay, which has a lower LoQ of 50 copies/mL, in an effort to quantify the HIV-RNA level. However, for the calculation of change from baseline in log10 HIV-RNA, which is an important efficacy endpoint, the additional data measured by the Ultrasensitive assay are usually ignored due to a lack of simple and appropriate statistical methods. The conventional approach, which only uses the Standard assay data, may result in loss of information; the naïve approach, which simply replaces “ < 400 copies/mL” reported by the Standard assay with corresponding Ultrasensitive assay results, may lead to a biased estimate because the two assays may have different assay variability; the likelihood-based approach, which can utilize all data from both assays, is computationally intensive and requires a large sample size, which may limit its use in practice. In this paper, we propose a simple imputation approach that, unlike the naïve method, accounts for the different variability in the two assays. A simulation study is used to compare these approaches. An example from a clinical trial in HIV-infected patients is used to illustrate the proposed approach.
The impact of test case reduction and prioritization on software testing effectiveness

Software testing is critical but most expensive phase of Software Development Life Cycle (SDLC). Development organizations desire to thoroughly test the software. But this exhaustive testing is impractical due to resource constraints. A large number of test suites are generated using automated tools. But the real challenge is the selection of subset of test cases and/or high order test cases crucial to validate the System Under Test (SUT). Test case reduction and prioritization techniques help test manager to solve this problem at a little cost. In this paper, we investigate their impact on testing process effectiveness using previous empirical studies. The results indicate that these techniques improve the testing effectiveness significantly. At the end, a case study is presented that suggests different useful combinations of these techniques, which are helpful for different testing scenarios.
Gestational diabetes: women’s concerns, mood state, quality of life and treatment satisfaction

Objective: The aim of this observational cohort study was to explore concerns, mood state, quality of life (QoL) and treatment satisfaction of women treated for gestational diabetes (GDM). Methods:Twenty-seven diet-treated and 18 insulin-treated women participated in a semi-structured interview and completed a series of three different questionnaires. Results: Qualitative analysis identified “the baby’s health” as dominant concern, but also as main motivational treatment factor. Treatment satisfaction was generally high and further increased, whereas QoL and mood state significantly dropped over time. Conclusions: Acknowledgment of women’s concerns and precise information may improve treatment compliance and outcome.
DC-SCRIPT Regulates Glucocorticoid Receptor Function and Expression of Its Target GILZ in Dendritic Cells

Dendritic cells (DCs) play a central role in the immune system; they can induce immunity or tolerance depending on diverse factors in the DC environment. Pathogens, but also tissue damage, hormones, and vitamins, affect DC activation and maturation. In particular, glucocorticoids (GCs) are known for their immunosuppressive effect on DCs, creating tolerogenic DCs. GCs activate the type I nuclear receptor (NR) glucocorticoid receptor (GR), followed by induced expression of the transcription factor glucocorticoid-inducible leucine zipper (GILZ). GILZ has been shown to be necessary and sufficient for GC-induced tolerogenic DC generation. Recently, we have identified the DC-specific transcript (DC-SCRIPT) as an NR coregulator, suppressing type I steroid NRs estrogen receptor and progesterone receptor. In this study, we analyzed the effect of DC-SCRIPT on GR activity. We demonstrate that DC-SCRIPT coexists with GR in protein complexes and functions as a corepressor of GR-mediated transcription. Coexpression of DC-SCRIPT and GR is shown in human monocyte–derived DCs, and DC-SCRIPT knockdown enhances GR-dependent upregulation of GILZ mRNA expression in DCs. This demonstrates that DC-SCRIPT serves an important role in regulating GR function in DCs, corepressing GR-dependent upregulation of the tolerance-inducing transcription factor GILZ. These data imply that by controlling GR function and GILZ expression DC-SCRIPT is potentially involved in the balance between tolerance and immunity.
Virological and Immunological Studies of Dengue Virus Infection in Pigtail Macaques (Macaca nemestrina).

SUSANA WIDJAJA. Virological and Immunological Studies of Dengue Virus Infection in Pigtail Macaques (Macaca nemestrina). Supervised by DONDIN SAJUTHI, JOKO PAMUNGKAS, DIAH ISKANDRIATI, and PATRICK J BLAIR. A non-human primate (NHP) model is essential for the study of dengue hemorrhagic fever (DHF) pathogenesis and the evaluation of dengue (DEN) vaccine and antiviral drug. Until now, it has been difficult to find an NHP DHF pathogenesis model. Therefore, an evaluation of a DEN vaccine candidate is performed in NHPs that show viremia after infected by DEN virus and the vaccine efficacy is its capability to develop immunity that reduces viremia when vaccinated NHPs are challenged by DEN virus. In this study, the potential of pigtail macaque to serve as an animal model for DEN vaccine testing was evaluated. Homologous sequential DEN challenges were conducted using primary viral isolates from DEN patients in Indonesia. Two parameters, the ability to support dengue viremia and to produce sufficient antibody responses were measured. This study shows that primary infections of all four DEN serotypes cause consistent, measurable viremia in pigtail macaques. The responses of IgM, IgG and avidity antibody following primary and secondary DEN infections are similar with antibody responses in human. The immunity produced by primary infection is sufficient to protect against homologous virus. This species of macaque therefore appears to be a suitable alternative model for testing DEN vaccine candidates. Besides antibody, T lymphocyte also has an important role in the protection and pathogenesis of DEN diseases. DEN specific T lymphocyte measurements, ELISPOT and intracellular cytokine staining-flow cytometry (ICFC), were developed to support DEN studies in pigtail macaque. Peripheral blood mononuclear cells (PBMC) collected before and after DEN infections were tested. ELISPOT results show increase of DEN specific interferon-γ (IFN-γ) producing cells as an individual response of pigtail to primary DEN-1, DEN-3 or DEN-4 infections. Using pools of PBMC taken from several animals, ELISPOT and intracellular cytokine staining-flow cytometry (IC-FC) was run side by side to quantify DEN specific lymphocytes following primary and secondary DEN-2 infections. ELISPOT revealed an increase of DEN specific IFN-γ producing cells following primary infection and a significant increase after secondary infection. Similarly, IC-FC also measured an increase of DEN specific producing IFN-γ CD3+CD4+ and CD3+CD4T lymphocytes. As such, ELISPOT and IC-FC can be applied to measure DEN specific T lymphocytes in pigtail macaques. Therefore, the application of these assays would be useful in elaborating adaptive immunity induced by vaccine and the level of protection. Furthermore, the development of pigtail as DHF model can be evaluated when further research on the cross-reactive T lymphocyte and antibody responses during secondary heterologous is conducted.
Correlation between Body Mass Index and Homa Index in Bariatric Patients

Abstract Background and aims: Overweight and obese individuals are prone to an insulin resistance status assessed in the present study by the HOMA index ("Homeostasis model assessment"). This prospective study assessed the body mass index (BMI) and the insulin resistance status (HOMA index) in obese patients after bariatric surgery (gastric sleeve, gastric by-pass). Material and Methods: The study included 48 patients who were assessed before the bariatric surgery and at 6 months thereafter. The assessment included the body mass index (BMI) and the HOMA index before meal. Results: There was a significant positive correlation between BMI and HOMA index, mostly between weight loss and improvement in insulin resistance status (rho = 0.308, p = 0.0335). Conclusions: BMI decreases significantly after bariatric surgery, which correlates positively with an improvement in insulin resistance status.
Single frame resection of compact digital cameras for UAV imagery

Recently, UAVs (Unmanned Aerial Vehicles) gain a wider acceptance from many disciplines. One major application is for monitoring and mapping. Flying beyond eye sight autonomously and collecting data over large areas are their obvious advantages. To support a large scale urban city mapping, we have developed a UAV system which can carry a compact digital camera as well as a navigational grade of a Global Positioning System (GPS) board mounted on the vehicle. Unfortunately, such a navigational system fails to provide sufficient accuracy required to process images become a large scale map. Ubiquitous digital compact cameras, despite their low cost benefits, are widely known to suffer instabilities in their internal lenses and electronics imaging system. Hence these cameras are less suitable for mapping related purposes. However, this paper presents a photogrammetric technique to precisely determine intrinsic and extrinsic camera parameters of photographed images provided that sufficient numbers of surveyed control points are available. A rigorous Mathematical model is derived to compute each image position with respect to the imaging coordinate system as well as a location of the principal point of an image sensor and the focal length of the camera. An iterative Gaussian-Newton least squares adjustment method is utilized to compute those parameters. Finally, surveyed data are processed and elaborated to justify the mathematical models.
Just how important is spatial coincidence to multisensory integration? Evaluating the spatial rule

This review addresses the question of when spatial coincidence facilitates multisensory integration in humans. According to the spatial rule (which was first formulated on the basis of neurophysiological data in anesthetized animals), multisensory integration is enhanced when stimuli in different sensory modalities are presented from the same spatial location. While the spatial rule fits with the available data from studies of overt and covert spatial attentional orienting, and from the majority of those studies in which space has been somehow relevant to the participant's task, it is inconsistent with the evidence that has emerged from the majority of multisensory studies of stimulus identification and temporal perception. Such a mixed pattern of behavioral results suggests that the spatial rule does not represent a general constraint on multisensory integration in humans. Instead, it would appear to be a much more task‐dependent phenomenon than is often realized. These results, however, are broadly consistent with a distinction between the processing of “where” and “what” (or “how”) information processing in the human brain.