Miracle-dz/UniFAR-FTUs huggingface dataset:
AZT resistance of simian foamy virus reverse transcriptase is based on the excision of AZTMP in the presence of ATP

Azidothymidine (AZT, zidovudine) is one of the few nucleoside inhibitors known to inhibit foamy virus replication. We have shown previously that up to four mutations in the reverse transcriptase gene of simian foamy virus from macaque (SFVmac) are necessary to confer high resistance against AZT. To characterize the mechanism of AZT resistance we expressed two recombinant reverse transcriptases of highly AZT-resistant SFVmac in Escherichia coli harboring three (K211I, S345T, E350K) or four mutations (K211I, I224T, S345T, E350K) in the reverse transcriptase gene. Our analyses show that the polymerization activity of these mutants is impaired. In contrast to the AZT-resistant reverse transcriptase of HIV-1, the AZT resistant enzymes of SFVmac reveal differences in their kinetic properties. The SFVmac enzymes exhibit lower specific activities on poly(rA)/oligo(dT) and higher KM-values for polymerization but no change in KD-values for DNA/DNA or RNA/DNA substrates. The AZT resistance of the mutant enzymes is based on the excision of the incorporated inhibitor in the presence of ATP. The additional amino acid change of the quadruple mutant appears to be important for regaining polymerization efficiency.
A Hybrid Multi-Objective Scheme Applied to Redundant Robot Manipulators

In this paper, a hybrid multi-objective scheme is proposed to complete simultaneously four objectives, i.e., the specified primary task for the end-effector, obstacle avoidance, joint-physical limits avoidance, and repetitive motion of redundant robot manipulators. In addition, corresponding theoretical analysis is given, which guarantees the validity of the proposed scheme. Then, the proposed hybrid multi-objective scheme is reformulated as a dynamical quadratic program (DQP) problem. The optimal solution of the DQP problem is found by the PLPE (piecewise-linear projection equation) neural network, i.e., PLPENN, and also by the corresponding numerical algorithm implemented on the computer. Furthermore, simulation and comparison based on a six-link planar redundant robot manipulator substantiate the effectiveness and accuracy of the proposed scheme. At last, a hardware experiment is conducted on a six-link physical robot manipulator system, which substantiates the physical realizability, operational stability, and safety of the proposed hybrid multi-objective scheme.
Neurolymphomatosis—diagnosis and assessment of treatment response by FDG PET‐CT

Neurolymphomatosis (NL) is lymphomatous infiltration of peripheral nerves, and is an uncommon manifestation of non‐Hodgkin's lymphoma (NHL). Although nerve biopsy is the main method for histological diagnosis, a blind nerve biopsy may not be diagnostic. While CT and MRI have been used to detect NL, recent reports demonstrated the benefit of integrated positron emission tomography (PET) using F18‐2‐fluoro‐2‐deoxy‐D‐glucose (FDG) combined with computed tomography (CT). We described the utility of FDG PET‐CT in this uncommon subgroup of NHL where it can assist in establishing the diagnosis, the potential to guide sites for biopsy and in the assessment of response to therapy. Copyright © 2007 John Wiley & Sons, Ltd.
Approximate Capacity Region of the Two-User MISO Broadcast Channels with Delayed CSIT

We consider the problem of multiple-input single-output Broadcast Channels with Rayleigh fading where the transmitter has access to delayed knowledge of the channel state information. We first characterize the capacity region of this channel with two users to within constant number of bits for all values of the transmit power. The proposed signaling strategy utilizes the delayed knowledge of the channel state information and the previously transmitted signals, in order to create a signal of common interest for both receivers. This signal would be the quantized version of the summation of the previously transmitted signals. A challenge that arises in deriving the result for finite signal-to-noise ratio regimes is the correlation that exists between the quantization noise and the signal. To guarantee the independence of quantization noise and signal, we extend the framework of lattice quantizers with dither together with an interleaving step. For converse, we use the fact that the capacity region of this problem is upper-bounded by the capacity region of a physically degraded broadcast channel with no channel state information where one receiver has two antennas. Then, we derive an outer-bound on the capacity region of this degraded broadcast channel. Finally, we show how to extend our results to obtain the approximate capacity of the $K$-user multiple-input single-output Broadcast Channel with delayed knowledge of the channel state information at the transmitter to within $2 \log_2 \left( K + 2 \right)$ bits/s/Hz.
Architectures and Protocols for Capacity Efficient, Highly Dynamic and Highly Resilient Core Networks [Invited]

The Core Optical Networks (CORONET) program addresses the development of architectures, protocols, and network control and management to support the future advanced requirements of both commercial and government networks, with a focus on highly dynamic and highly resilient multi-terabit core networks. CORONET encompasses a global network supporting a combination of IP and wavelength services. Satisfying the aggressive requirements of the program required a comprehensive approach addressing connection setup, restoration, quality of service, network design, and nodal architecture. This paper addresses the major innovations developed in Phase 1 of the program by the team led by Telcordia and AT&T. The ultimate goal is to transfer the technology to commercial and government networks for deployment in the next few years.
“Hard” and “soft” lesions underlying the HLA class I alterations in cancer cells: Implications for immunotherapy

The ability of cancer cells to escape from the natural or immunotherapy‐induced antitumor immune response is often associated with alterations in the tumor cell surface expression of Major Histocompatibility Complex (MHC) Class I antigens. Considerable knowledge has been gained on the prevalence of various patterns of MHC Class I defects and the underlying molecular mechanisms in different types of cancer. In contrast, few data are available on the changes in MHC Class I expression happening during the course of cancer immunotherapy. We have recently proposed that the progression or regression of a tumor lesion in cancer patients undergoing immunotherapy could be predetermined by the molecular mechanism responsible for the MHC Class I alteration and not by the type of immunotherapy used, i.e., interleukin‐2 (IL‐2), Bacillus Calmette‐Guèrin (BCG), interferon‐alpha (IFN‐α), peptides alone, dendritic cells loaded with peptides, protein‐bound polysaccharide etc. If the molecular alteration responsible for the changes in MHC Class I expression is reversible by cytokines (“soft” lesion), the MHC Class I expression will be upregulated, the specific T cell–mediated response will increase and the lesion will regress. However, if the molecular defect is structural (“hard” lesion), the MHC Class I expression will remain low, the escape mechanism will prevail and the primary tumor or the metastatic lesion will progress. According to this idea, the nature of the preexisting MHC Class I lesion in the cancer cell has a crucial impact determining the final outcome of cancer immunotherapy. In this article, we discuss the importance of these two types of molecular mechanisms of MHC Class I–altered expression.
Sparse Codes and Spikes

In order to make progress toward understanding the sensory coding strategies employed by the cortex, it will be necessary to draw upon guiding principles that provide us with reasonable ideas for what to expect and what to look for in the neural circuitry. The unifying theme behind all of the chapters in this book is that probabilistic inference—i.e., the process of inferring the state of the world from the activities of sensory receptors and a probabilistic model for interpreting their activity—provides a major guiding principle for understanding sensory processing in the nervous system. Here, I shall propose a model for how inference may be instantiated in the neural circuitry of the visual cortex, and I will show how it may help us to understand both the form of the receptive fields found in visual cortical neurons as well as the nature of spiking activity in these neurons.
Detection of grlA and gyrA Mutations in 344 Staphylococcus aureus Strains

ABSTRACT Mutations in the grlA and gyrA genes of 344 clinical strains of Staphylococcus aureus isolated in 1994 in Japan were identified by combinations of single-strand conformation polymorphism analysis, restriction fragment length analysis, and direct sequencing to identify possible relationships to fluoroquinolone resistance. Five types of single-point mutations and four types of double mutations were observed in the grlA genes of 204 strains (59.3%). Four types of single-point mutations and four types of double mutations were found in the gyrA genes of 188 strains (54.7%). Among them, the grlA mutation of TCC→TTC or TAC (Ser-80→Phe or Tyr) and the gyrAmutation of TCA→TTA (Ser-84→Leu) were principal, being detected in 137 (39.8%) and 121 (35.9%) isolates, respectively. ThegrlA point mutations of CAT→CAC (His-77 [silent]), TCA→CCA (Ser-81→Pro), and ATA→ATT (Ile-100 [silent]) were novel, as was the GAC→GGC (Asp-73→Gly) change in gyrA. A total of 15 types of mutation combinations within both genes were related to ciprofloxacin resistance (MIC ≥ 3.13 μg/ml) and were present in 193 mutants (56.1%). Strains containing mutations in both genes were highly resistant to ciprofloxacin (MIC at which 50% of the isolates are inhibited [MIC50] = 50 μg/ml). Those with the Ser-80→Phe or Tyr alteration in grlA but wild-typegyrA showed a lower level of ciprofloxacin resistance (MIC50 ≤ 12.5 μg/ml). Levofloxacin was active against 68 of 193 isolates (35.2%) with mutations at codon 80 of grlAin the presence or absence of a concomitant mutation at codon 73, 84, or 88 in gyrA (MIC ≤ 6.25 μg/ml). The new fluoroquinolone DU-6859a showed good activity with 186 of 193 isolates (96.4%) for which the MIC was ≤6.25 μg/ml.
Chronic sub-clinical inflammation in the abdominal adipose tissue – Evaluation of inflammatory cytokines and their link with insulin resistance in metabolically obese South Indians: A cross-sectional observational study

Objective: To measure the levels of proinflammatory cytokines tumor necrosis factor-alpha (TNF-α), interleukin-6(IL-6), and high-sensitive C-reactive protein (hs-CRP) and the anti-inflammatory cytokine adiponectin (AN) in obese South Indian subjects and to ascertain whether or not a causal role could be ascribed to these cytokines in the development of insulin resistance (IR). Materials and Methods: Forty obese and forty nonobese volunteers of both genders were recruited. Parameters such as body mass index (BMI), waist circumference (WC), and blood pressure were evaluated. Fasting blood sugar (FBS), fasting insulin level, hemoglobin A1c (HbA1C), lipid profile, TNF-α, IL-6, hs-CRP, and AN levels were measured. IR was evaluated by homeostatic model assessment-IR method. Abdominal adiposity was measured by ultrasonography. The results were statistically evaluated by appropriate tests. Results: BMI, WC, and visceral fat were high in the obese group. Females had higher subcutaneous fat in both groups. HbA1C was marginally high in the obese group (P = 0.014). IR was high in all the groups, obese males showing higher values (not significant[NS]). Total cholesterol and low-density lipoprotein were high in the obese group (P = 0.028, P = 0.003). TNF-α was high in obese males (NS), IL-6 was high in both groups, higher in nonobese females (NS), hs-CRP was high in both groups, higher in females of both groups (NS). AN was high in females of both groups (P = 0.002). Conclusions: In this study on South Indian subjects, proinflammatory cytokines such as IL-6 and hs-CRP, despite being high, did not show any causal correlation either with abdominal obesity or with IR. TNF-α being normal showed some correlation which was inconsistent. Even the anti-inflammatory adipokine, AN did not show any correlation with IR. Cytokines had an inconsistent correlation with the components of metabolic syndrome hence were not useful.
Prevalence of occult hepatitis C in Egyptian patients with non alcoholic fatty liver disease

This study aim is to assess the prevalence of occult HCV infection among Egyptian patients with non alcoholic fatty liver disease (NAFLD) with elevated AST and ALT, and to correlate presence of occult HCV with severity of liver disease. Patients and Methods: After informed consent 27 patients with elevateed liver enzymes diagnosed as NAFLD were examined for demographic, clinical, laboratory data and Ultrasonography. Liver biopsy was done and tested for HCV RNA in tissue. Genotyping using RFLP analysis of PCR products in the 5’NCR was done for positive cases. Results: HCV RNA in tissue was positive in 11/27 patients (40.7%); genotype was 4a in all positive cases. AST and ALT values showed significantly lower values in occult HCV than the non HCV NAFLD group. Liver biopsy of studied patients showed no significant difference as regard inflammation and fibrosis according to METAVIR score. Conclusions: Occult HCV is highly prevalent among Egyptian NAFLD patients. It seems to induce a mild liver disease. Patients with elevated ALT and negative HCV RNA in sera might be investigated for tissue HCV RNA. Follow up is recommended for the occult HCV patients to monitor progression to overt disease.
Infectivity of blood components with low hepatitis B virus DNA levels identified in a lookback program

BACKGROUND: Japanese Red Cross (JRC) blood centers implemented anti‐hepatitis B core antigen (HBc) screening in 1989 and 50‐minipool (MP)‐nucleic acid testing (NAT) in 2000. A systematic lookback study has been conducted to determine the hepatitis B virus (HBV) transmission risk of donations drawn in the pre‐hepatitis B surface antigen (HBsAg) and/or MP‐NAT window phase and by donors with occult HBV infection.
Oxidative Stress in HPV-Driven Viral Carcinogenesis: Redox Proteomics Analysis of HPV-16 Dysplastic and Neoplastic Tissues

Genital infection by high risk Human Papillomavirus (HR-HPV), although recognized as the main etio-pathogenetic factor of cervical cancer, is not per se sufficient to induce tumour development. Oxidative stress (OS) represents an interesting and under-explored candidate as a promoting factor in HPV-initiated carcinogenesis. To gain insight into the role of OS in cervical cancer, HPV-16 positive tissues were collected from patients with invasive squamous cervical carcinoma, from patients with High Grade dysplastic HPV lesions and from patients with no clinical evidence of HPV lesions. After virological characterization, modulation of proteins involved in the redox status regulation was investigated. ERp57 and GST were sharply elevated in dysplastic and neoplastic tissues. TrxR2 peaked in dysplastic samples while iNOS was progressively reduced in dysplastic and neoplastic samples. By redox proteomic approach, five proteins were found to have increased levels of carbonyls in dysplastic samples respect to controls namely: cytokeratin 6, actin, cornulin, retinal dehydrogenase and GAPDH. In carcinoma samples the peptidyl-prolyl cis-trans isomerase A, ERp57, serpin B3, Annexin 2 and GAPDH were found less oxidized than in dysplastic tissues. HPV16 neoplastic progression seems associated with increased oxidant environment. In dysplastic tissues the oxidative modification of DNA and proteins involved in cell morphogenesis and terminal differentiation may provide the conditions for the neoplastic progression. Conversely cancer tissues seem to attain an improved control on oxidative damage as shown by the selective reduction of carbonyl adducts on key detoxifying/pro-survival proteins.
Can We Validate the Results of Twin Studies? A Census-Based Study on the Heritability of Educational Achievement

As for most phenotypes, the amount of variance in educational achievement explained by SNPs is lower than the amount of additive genetic variance estimated in twin studies. Twin-based estimates may however be biased because of self-selection and differences in cognitive ability between twins and the rest of the population. Here we compare twin registry based estimates with a census-based heritability estimate, sampling from the same Dutch birth cohort population and using the same standardized measure for educational achievement. Including important covariates (i.e., sex, migration status, school denomination, SES, and group size), we analyzed 893,127 scores from primary school children from the years 2008–2014. For genetic inference, we used pedigree information to construct an additive genetic relationship matrix. Corrected for the covariates, this resulted in an estimate of 85%, which is even higher than based on twin studies using the same cohort and same measure. We therefore conclude that the genetic variance not tagged by SNPs is not an artifact of the twin method itself.
Group-Based Negotiations in P2P Systems

In P2P systems, groups are typically formed to share resources and/or to carry on joint tasks. In distributed environments formed by a large number of peers conventional authentication techniques are inadequate for the group joining process, and more advanced ones are needed. Complex transactions among peers may require more elaborate interactions based on what peers can do or possess instead of peers' identity. In this work, we propose a novel peer group joining protocol. We introduce a highly expressive resource negotiation language, able to support the specification of a large variety of conditions applying to single peers or groups of peers. Moreover, we define protocols to test such resource availability customized to the level of assurance required by the peers. Our approach has been tested and evaluated on an extension of the JXTA P2P platform. Our results show the robustness of our approach in detecting malicious peers, detected both during the negotiation and during the peer group lifetime. Regardless of the peer group cardinality and interaction frequency, the peers always detect possible free riders within a small time frame.
Photon-induced total-internal-reflection all-optical switches

An all-optical switch is demonstrated. The switch is based on the photon-induced carrier effect and the principle of the total internal reflection (TIR). An asymmetric Y-branch with multimode waveguides is designed and fabricated on GaAlAs/GaAs epitaxial materials. The 805-nm light is used to activate the carrier effects and generate the total-reflection effect at the branch. The device is characterized at the wavelength of 1.31 /spl mu/m. Its extinction ratio is larger than 18.0 dB when the injected optical density is 15/spl times/10/sup 1/ W/mm/sup 2/.
A Fuzzy-Rule-Based Approach for Single Frame Super Resolution

In this paper, a novel fuzzy rule-based prediction framework is developed for high-quality image zooming. In classical interpolation-based image zooming, resolution is increased by inserting pixels using certain interpolation techniques. Here, we propose a patch-based image zooming technique, where each low-resolution (LR) image patch is replaced by an estimated high-resolution (HR) patch. Since an LR patch can be generated from any of the many possible HR patches, it would be natural to develop rules to find different possible HR patches and then to combine them according to rule strength to get the estimated HR patch. Here, we generate a large number of LR-HR patch pairs from a collection of natural images, group them into different clusters, and then generate a fuzzy rule for each of these clusters. The rule parameters are also learned from these LR-HR patch pairs. As a result, an efficient mapping from LR patch space to HR patch space can be formulated. The performance of the proposed method is tested on different images, and is also compared with other representative as well as state-of-the-art image zooming techniques. Experimental results show that the proposed method is better than the competing methods and is capable of reconstructing thin lines, edges, fine details, and textures in the image efficiently.
Lived experience in patients with recurrent glioblastoma in Japan: A narrative study

Glioblastoma (GBM) is well known to have one of the poorest prognoses among all cancers. Patients with GBM in progression-free survival (PFS) may be relatively stable and can often maintain their quality of life. Thus, PFS is a desirable goal. In Japan, the median PFS is 11 months. It is difficult to grasp a patient's thoughts and hopes when, after PFS, they are readmitted due to recurrence or acute deterioration. Therefore, this study aimed to describe the lived experience of illness in patients with recurrent GBM, focusing on PFS. We enrolled five patients into the study; however, only four patients completed data collection. Data were collected using semi-structured interviews. We also conducted a thematic narrative analysis. As a result, we generated one overall theme: Even in vulnerable and constrained daily lives, the aim was gaining a sense of stability—and maintaining it steadily—as far as possible, on their own. That sense of stability is fragile so that maintaining equilibrium is a precarious enterprise. Moreover, in PFS, participants were trying to maintain equilibrium by reevaluating themselves and sometimes giving up something, although they received support from people around them. We infer that it is important for nurses to assess and understand the fluctuations in that sense of stability through continuous involvement with patients. An interdisciplinary approach and lateral integration of care are important to meet the needs of GBM patients. This understanding will lead to nursing supports that help patients live with stability, pride, and dignity.
Reasoning about actions with sensing under qualitative and probabilistic uncertainty

We focus on the aspect of sensing in reasoning about actions under qualitative and probabilistic uncertainty. We first define the action language E for reasoning about actions with sensing, which has a semantics based on the autoepistemic description logic ALCKNF, and which is given a formal semantics via a system of deterministic transitions between epistemic states. As an important feature, the main computational tasks in E can be done in linear and quadratic time. We then introduce the action language E+ for reasoning about actions with sensing under qualitative and probabilistic uncertainty, which is an extension of E by actions with nondeterministic and probabilistic effects, and which is given a formal semantics in a system of deterministic, nondeterministic, and probabilistic transitions between epistemic states. We also define the notion of a belief graph, which represents the belief state of an agent after a sequence of deterministic, nondeterministic, and probabilistic actions, and which compactly represents a set of unnormalized probability distributions. Using belief graphs, we then introduce the notion of a conditional plan and its goodness for reasoning about actions under qualitative and probabilistic uncertainty. We formulate the problems of optimal and threshold conditional planning under qualitative and probabilistic uncertainty, and show that they are both uncomputable in general. We then give two algorithms for conditional planning in our framework. The first one is always sound, and it is also complete for the special case in which the relevant transitions between epistemic states are cycle-free. The second algorithm is a sound and complete solution to the problem of finite-horizon conditional planning in our framework. Under suitable assumptions, it computes every optimal finite-horizon conditional plan in polynomial time. We also describe an application of our formalism in a robotic-soccer scenario, which underlines its usefulness in realistic applications.