Miracle-dz/UniFAR-FTUs huggingface dataset:
Nrf2 activators provide neuroprotection against 6‐hydroxydopamine toxicity in rat organotypic nigrostriatal cocultures

Oxidative stress and inflammation appear to play a critical role in the progression of Parkinson's disease. As a result, there has been growing interest in antioxidant pathways and how these pathways might be exploited to slow the progressive loss of dopamine neurons. One such pathway that has garnered attention recently is mediated by the transcription factor Nrf2 and is integral in orchestrating cells' antiinflammatory defense. Nrf2 controls the inducible expression of numerous antioxidant and phase 2 detoxification genes, such as glutathione S‐transferase, heme oxygenase‐1, and NAD(P)H:quinone oxidoreductase 1 (NQO1). Once activated, these genes work synergistically to maintain intracellular redox homeostasis. In this study, we test the hypothesis that Nrf2 activation can protect dopaminergic neurons against 6‐hydroxydopamine (6‐OHDA)‐induced toxicity. Treatment of organotypic nigrostriatal cocultures with either tert‐butylhydroquinone (tBHQ) or sulforaphane, known activators of Nrf2, mitigated dopaminergic cell loss. The observed protection appeared to be mediated, at least in part, by an increase in antioxidant activity. Simultaneous treatment of cultures with tBHQ and 6‐OHDA increased NQO1 expression 17‐fold compared with controls. Overall, these results suggest that Nrf2 may play an important role in cellular protection in neurodegenerative diseases and may be a viable therapeutic target in the future. © 2009 Wiley‐Liss, Inc.
Survey of Bacteroides fragilis group susceptibility patterns in Canada

The in vitro activities of penicillin, clindamycin, chloramphenicol, metronidazole, piperacillin, piperacillin-tazobactam, ticarcillin, ticarcillin-clavulanate, ampicillin-sulbactam, cefoxitin, ceftizoxime, cefotetan, moxalactam, and imipenem against 348 Bacteroides fragilis group isolates collected from six Canadian cities during 1990 were determined by the National Committee for Clinical Laboratory Standards (NCCLS) agar dilution technique. All isolates were susceptible to chloramphenicol, metronidazole, piperacillin-tazobactam, and imipenem. For the other antibiotics tested, the following resistance rates were observed: penicillin, 97%; clindamycin, 9%; piperacillin, 19%; ticarcillin, 31%; ticarcillin-clavulanate, 0.28%; ampicillin-sulbactam, 0.85%; cefoxitin, 26%; ceftizoxime, 15%; cefotetan, 53%; and moxalactam, 17%. Susceptibility profiles to beta-lactam antibiotics varied among the different species tested: B. fragilis and Bacteroides vulgatus demonstrated lower resistance rates than Bacteroides distasonis and indole-positive Bacteroides thetaiotaomicron and Bacteroides ovatus. Ceftizoxime results should be interpreted cautiously, because the MICs obtained with the recommended NCCLS control strain were lower than expected.
Evolution of Ime 2 Phosphorylation Sites on Cdk 1 Substrates Provides a Mechanism to Limit the Effects of the Phosphatase Cdc 14 in Meiosis

Progression through meiosis in yeast is governed by the cyclin-dependent kinase Cdk1, in concert with a related kinase called Ime2. It remains unclear how these kinases collaborate to meet the unique demands of meiotic progression. We demonstrate that Ime2 and Cdk1 phosphorylate an overlapping substrate set and that the two kinases overlap functionally as inhibitors of the ubiquitin ligase APC and replication origin licensing. Surprisingly, Ime2 phosphorylates Cdk1 substrates at distinct phosphorylation sites that are highly resistant to dephosphorylation by the phosphatase Cdc14. We propose that Ime2-dependent phosphorylation of a subset of cell-cycle proteins limits the effects of Cdc14 in meiosis.
Nicotinic Receptor Alpha7 Expression Identifies a Novel Hematopoietic Progenitor Lineage

How inflammatory responses are mechanistically modulated by nicotinic acetylcholine receptors (nAChR), especially by receptors composed of alpha7 (α7) subunits, is poorly defined. This includes a precise definition of cells that express α7 and how these impact on innate inflammatory responses. To this aim we used mice generated through homologous recombination that express an Ires-Cre-recombinase bi-cistronic extension of the endogenous α7 gene that when crossed with a reporter mouse expressing Rosa26-LoxP (yellow fluorescent protein (YFP)) marks in the offspring those cells of the α7 cell lineage (α7lin+). In the adult, on average 20–25 percent of the total CD45+ myeloid and lymphoid cells of the bone marrow (BM), blood, spleen, lymph nodes, and Peyers patches are α7lin+, although variability between litter mates in this value is observed. This hematopoietic α7lin+ subpopulation is also found in Sca1+cKit+ BM cells suggesting the α7 lineage is established early during hematopoiesis and the ratio remains stable in the individual thereafter as measured for at least 18 months. Both α7lin+ and α7lin– BM cells can reconstitute the immune system of naïve irradiated recipient mice and the α7lin+:α7lin– beginning ratio is stable in the recipient after reconstitution. Functionally the α7lin+:α7lin– lineages differ in response to LPS challenge. Most notable is the response to LPS as demonstrated by an enhanced production of IL-12/23(p40) by the α7lin+ cells. These studies demonstrate that α7lin+ identifies a novel subpopulation of bone marrow cells that include hematopoietic progenitor cells that can re-populate an animal’s inflammatory/immune system. These findings suggest that α7 exhibits a pleiotropic role in the hematopoietic system that includes both the direct modulation of pro-inflammatory cell composition and later in the adult the role of modulating pro-inflammatory responses that would impact upon an individual’s lifelong response to inflammation and infection.
A new role for the dynamin GTPase in the regulation of fusion pore expansion

The role of dynamin GTPase activity in controlling fusion pore expansion and postfusion granule membrane topology was investigated. The experiments show that, in addition to playing a role in endocytosis, GTPase activity of dynamin regulates the rapidity of fusion pore expansion from tens of milliseconds to seconds after fusion.
FISCAL FORESIGHT: ANALYTICAL ISSUES

Fiscal foresight---the phenomenon that legislative and implementation lags ensure that private agents know the tax rates they face in the future---is intrinsic to the tax policy process. Although acknowledged in empirical work, theoretical analysis of its implications is scant. This paper develops an analytical framework to study the econometric implications of fiscal foresight. A simple example shows that foresight produces equilibrium time series with a non-invertible moving average component, which misaligns the agents' and the econometrician's information sets in estimated VARs. Economically meaningful shocks to taxes, therefore, cannot be easily extracted from statistical innovations. Non-invertibility arises as a natural outgrowth of the fact that optimal decisions discount future tax obligations; non-invertibility, therefore, is likely to be endemic to the study of fiscal policy.
Motor signs predict poor outcomes in Alzheimer disease

Objective: To examine whether the presence of motor signs has predictive value for important outcomes in Alzheimer disease (AD). Methods: A total of 533 patients with AD at early stages (mean Folstein Mini-Mental State Examination [MMSE] 21/30 at entry) were recruited and followed semiannually for up to 13.1 years (mean 3) in five University-based AD centers in the United States and European Union. Four outcomes, assessed every 6 months, were used in Cox models: cognitive endpoint (Columbia Mini-Mental State Examination ≤ 20/57 [∼MMSE ≤ 10/30]), functional endpoint (Blessed Dementia Rating Scale ≥ 10), institutionalization equivalent index, and death. Using a standardized portion of the Unified PD Rating Scale (administered every 6 months for a total of 3,149 visit-assessments, average 5.9 per patient), the presence of motor signs, as well as of individual motor sign domains, was examined as time-dependent predictor. The models controlled for cohort, recruitment center, sex, age, education, a comorbidity index, and baseline cognitive and functional performance. Results: A total of 39% of the patients reached the cognitive, 41% the functional, 54% the institutionalization, and 47% the mortality endpoint. Motor signs were noted for 14% of patients at baseline and for 45% at any evaluation. Their presence was associated with increased risk for cognitive decline (RR, 1.72; 95% CI, 1.24 to 2.38), functional decline (1.80 [1.33 to 2.45]), institutionalization (1.68 [1.26 to 2.25]), and death (1.38 [1.05 to 1.82]). Tremor was associated with increased risk for reaching the cognitive and bradykinesia for reaching the functional endpoints. Postural-gait abnormalities carried increased risk for institutionalization and mortality. Faster rates of motor sign accumulation were associated with increased risk for all outcomes. Conclusions: Motor signs predict cognitive and functional decline, institutionalization, and mortality in Alzheimer disease. Different motor sign domains predict different outcomes.
[Value of tumor markers in the cerebrospinal fluid in the diagnosis of meningeal carcinomatosis].

OBJECTIVE To assess the diagnostic value of tumor markers in the cerebrospinal fluid (CSF) for meningeal carcinomatosis (MC). METHODS Twenty-one MC patients (including 13 adenocarcinoma and 8 non-adenocarcinoma patients), 72 patients with tuberculous meningitis (TBM) and 23 with primary intracerebral tumors (PIT) were enrolled in this study. Blood and CSF tumor markers including CEA, CA125, CA15-3, CA19-9, CA72-4, CYFRA21-1, AFP and NSE were measured by Roche E170 electrochemiluminescence analyzer and sandwich assay. RESULTS CSF tumor markers CEA, CA125, CA199 and CYFRA21-1 and the serum tumor markers CEA, CA125, CA153, CA199 and AFP were significantly higher in MC group than in the other two groups. CSF CEA and CA15-3 were significantly higher in adenocarcinoma MC than in non-adenocarcinoma MC patients, but no significant differences were found in the serum tumor markers between the two groups (P>0.05). CSF tumor markers including CEA, CA125, CA15-3, CA72-4 and CYFRA21-1 were positively correlated to the serum tumor markers (P<0.05). CA199 was positively correlated to the disease course (P<0.05), and age was not correlated to any of the indexes (P>0.05). CONCLUSION Detection of the tumor markers in the CSF, especially CEA, CA125, CA19-9 and CYFRA21-1, may help in the early diagnosis of MC. CEA and CA15-3 can serve as indicators for differential diagnosis of adenocarcinoma and non-adenocarcinoma.
Swept Approximate Message Passing for Sparse Estimation

Approximate Message Passing (AMP) has been shown to be a superior method for inference problems, such as the recovery of signals from sets of noisy, lower-dimensionality measurements, both in terms of reconstruction accuracy and in computational efficiency. However, AMP suffers from serious convergence issues in contexts that do not exactly match its assumptions. We propose a new approach to stabilizing AMP in these contexts by applying AMP updates to individual coefficients rather than in parallel. Our results show that this change to the AMP iteration can provide expected, but hitherto unobtainable, performance for problems on which the standard AMP iteration diverges. Additionally, we find that the computational costs of this swept coefficient update scheme is not unduly burdensome, allowing it to be applied efficiently to signals of large dimensionality.
A Query Expansion Method based on a Weighted Word Pairs Approach

In this paper we propose a query expansion method to improve accuracy of a text retrieval system. Our technique makes use of explicit relevance feedback to expand an initial query with a structured representation called Weighted Word Pairs. Such a structure can be automatically extracted from a set of documents and uses a method for term extraction based on the probabilistic Topic Model. Evaluation has been conducted on TREC-8 repository and performances obtained using standard WWP and Kullback Leibler Divergency query expansion approaches have been compared.
System Cost Minimization in Cloud RAN With Limited Fronthaul Capacity

Cloud radio access network (C-RAN) is emerging as a potential alternative for the next generation RAN by merging RAN and cloud computing together. In this paper, we consider the baseband unit (BBU) pool of C-RAN as a collection of virtual machines (VMs). We allow each user equipment (UE) to associate with multiple VMs in the BBU pool, and each remote radio head (RRH) can only serve a limited number of UEs. Under this model, we jointly optimize the VM activation in the BBU pool and sparse beamforming in the coordinated RRH cluster, which is constrained by limited fronthaul capacity, to minimize the system cost of C-RAN. We formulate this problem as a mixed-integer nonlinear programming problem, and then propose efficient methods to optimize the number of active VMs, as well as the sparse beamforming vectors. Moreover, we derive a closed-form solution for the beamforming vectors. Simulation results suggest that our proposed algorithms have better performance than the benchmark algorithms in terms of both system cost and robustness.
Committee Translation Approach Combined with Cognitive Interviews: A Valuable Translation Method

Many research instruments were originally developed in the English language. However, it is necessary to carefully translate these instruments into the languages of cultures being studied in order to conduct cross-cultural nursing research.1-2 Four common techniques that have been successfully used for instrument translation are back-translation, bilingual techniques, the committee approach, and pretesting.3 Although all these techniques are helpful in maintaining the equivalence of the translated version with the original instrument, 4 the question remains as to whether or not the study participants will be able to understand the meaning of the translated instrument items. To achieve cultural appropriateness as well as equivalence of the translated items with the original items, we would like to offer a valuable translation method that combines the committee translation approach with cognitive interviews. In our study, we wanted to investigate the Theory of Planned Behavior (TPB) constructs influencing nurses’ pain management behavior for hospitalized Thai elderly patients with postoperative pain. However, no existing instruments in Thai addressed all the TPB constructs. Therefore, we prepared and translated the pain assessment questionnaire (PAQ) and pain management questionnaire (PMQ) for use as TPB-based measures of Thai nurses’ beliefs (behavioral, normative, and control), attitudes, perceived norms, perceived behavioral control, and intentions with regard to assessing pain and administering PRN opioid analgesics for the population of interest. Below we describe the committee translation and cognitive interview methods and how we combined them to translate the PAQ and PMQ for use in our research.
The Temperature-Sensitive Ion Channel TRPV2 is Endogenously Expressed and Functional in the Primary Sensory Cell Line F-11

In sensory neurons heat is transduced by a subfamily of TRP channels sharing sequence homology with the capsaicin-sensitive vanilloid receptor subtype 1 (TRPV1), but differing in their thermal response thresholds. To identify a neuronal cell line endogenously expressing noxious heat-transducing ion channels, we examined F-11 cells, a hybridoma derived from rat dorsal root ganglia and mouse neuroblastoma. Using RT-PCR, transcripts homologous to TRPV2 and TRPV4, but not to TRPV1 or TRPV3, were found. We isolated a full-length cDNA of 2.4 kb coding for a 757-amino acid protein corresponding to mouse TRPV2, which was further characterized by immunocytochemistry and electrophysiology. Using the whole-cell patch-clamp technique, we observed a heat-evoked increase in outward and inward currents with a threshold of 51.6 ± 0.2°C. The current-voltage relationship stimulated by a temperature of 52°C was characterized by an outward rectification with a reversal potential close to –10 mV. Heat-evoked currents could be inhibited by ruthenium red. There was no activation by stimulation with capsaicin or 2-aminoethoxydiphenyl borate. Our results indicate that F-11 cells express functional noxious heat-sensitive TRPV2 channels. Thus, we propose that F-11 cells represent a valuable in vitro model to characterize the properties of TRPV2 in a native neuronal environment.
Link-State Routing Can Achieve Optimal Traffic Engineering Dahai

This paper settles a long-standing question with a positive answer: optimal traffic engineering can be realized using ju st link-state routing protocols. In conventional link-state protocols like OSPF and IS-IS, routers compute shortest paths based on link weights, splitting traffic evenly when multipl e shortest paths exist. Unfortunately, in these particular c ases of link-state protocols, computing the optimal link weight s for a given traffic matrix is an NP-hard problem. Even the best setting of the weights can lead to traffic loads that devi ate significantly from the ideal distribution of the traffic. In this work, we show that splitting traffic over multiple paths as an exponential function of path length can achieve optimal traffic engineering. We also present a polynomial-time algorithm for computing the optimal link weights, which in practice is also much more efficient than the local-search heuristics used today. In addition, we show how to apply the algorithm to robust traffic engineering, where one set of link weights must perform well for multiple traffic matrices or failure scenarios. These results are based on our new Network Entropy Maximization framework for routingprotocol design, which parallels the role of Network Utilit y Maximization for congestion control.
White matter integrity as a predictor of response to treatment in first episode psychosis

The integrity of brain white matter connections is central to a patient’s ability to respond to pharmacological interventions. This study tested this hypothesis using a specific measure of white matter integrity, and examining its relationship to treatment response using a prospective design in patients within their first episode of psychosis. Diffusion tensor imaging data were acquired in 63 patients with first episode psychosis and 52 healthy control subjects (baseline). Response was assessed after 12 weeks and patients were classified as responders or non-responders according to treatment outcome. At this second time-point, they also underwent a second diffusion tensor imaging scan. Tract-based spatial statistics were used to assess fractional anisotropy as a marker of white matter integrity. At baseline, non-responders showed lower fractional anisotropy than both responders and healthy control subjects (P < 0.05; family-wise error-corrected), mainly in the uncinate, cingulum and corpus callosum, whereas responders were indistinguishable from healthy control subjects. After 12 weeks, there was an increase in fractional anisotropy in both responders and non-responders, positively correlated with antipsychotic exposure. This represents one of the largest, controlled investigations of white matter integrity and response to antipsychotic treatment early in psychosis. These data, together with earlier findings on cortical grey matter, suggest that grey and white matter integrity at the start of treatment is an important moderator of response to antipsychotics. These findings can inform patient stratification to anticipate care needs, and raise the possibility that antipsychotics may restore white matter integrity as part of the therapeutic response.
Improving the performance of the iterative signature algorithm for the identification of relevant patterns

The iterative signature algorithm (ISA) has become very attractive to detect co‐regulated genes from microarray data matrices and can be a useful tool for the identification of similar patterns in many other kinds of numerical data matrices. Nevertheless, its algorithmic strategy exhibits some limitations since it is based on statistical behavior of the average and considers averages weighted by scores not necessarily positive. Hence, we propose to take the median instead of the average and to use absolutes scores in ISA's structure. Furthermore, a generalized function is also introduced in the algorithm in order to improve its algorithmic strategy for detecting high value or low value biclusters. The effects of these simple modifications on the performance of the biclustering algorithm are evaluated through an experimental comparative study involving synthetic data sets and real data from the organism Saccharomyces cerevisiae. The experimental results show that the proposed variations of ISA outperform the original version in many situations. Absolute scores in ISA are shown to be essential for the correct interpretation of the biclusters found by the algorithm. The median instead of the average turns the biclustering algorithm more resilient to outliers in the data sets. © 2011 Wiley Periodicals, Inc. Statistical Analysis and Data Mining 4: 71–83 2011
Interference and Power Minimization in TDMA-OFDMA Infrastructure Wireless Mesh Networks

This paper examines algorithms to minimize interference in infrastructure wireless mesh networks. A mathematical optimization problem for coloring the active wireless edges in a time-division scheduling frame is formulated. The optimization eliminates primary conflicts and minimizes secondary conflicts. The active wireless edges are specified in an integer zero-one ’edge-specification’ matrix. An ’edge-interference’ matrix is formulated, where each element represents the interference power if two edges share a color. The objective of the optimization problem is to partition the integer edge-specification matrix into a sum of C integer zero-one matrices which specify the active edges assigned to each of the C colors, such that the secondary interference is minimized. The optimal solution requires a constrained partitioning of an integer matrix, which is a combinatorial problem. A polynomial time approximation algorithm called Least-Noise coloring is presented. Simulations of an essentially saturated hexagonal mesh network supporting backhaul traffic flows are reported. It is confirmed that interference and edge transmission powers can be minimized, and that the mesh network can be configured to achieve near-perfect Quality of Service guarantees with essentially 100% throughput.