Miracle-dz/UniFAR-FTUs huggingface dataset:
Nuclear Pore Complex Proteins in Alzheimer Disease

Ultrastructural studies of neurofibrillary tangles in Alzheimer disease (AD) have demonstrated a close relationship between nuclear pores and the cytoplasmic paired helical filaments comprising the tangles, as well as nuclear irregularity in many tangle-bearing neurons; nuclear pore aggregation has been observed in nearby neurons. These observations prompted examination of the nuclear pore complex (NPC) and proteins critical to nucleocytoplasmic transport in neurons with and without tangles in AD and control cases. Light microscopic study of hippocampus and neocortex in AD and controls revealed that all nuclei were labeled by antibodies to NPC proteins, including the central transporter nucleoporin Nup62. Nucleoporin and tau label revealed significantly more nuclear irregularity in AD, often associated with neurofibrillary tangles. Double label of Nup62 with apoptotic markers (TUNEL and active caspase-3) and a cell-cycle protein (cyclin B1) revealed no clear relationship of nuclear irregularity to apoptosis or cell-cycle protein expression. However, cytoplasmic accumulation of nuclear transport factor 2 (NTF2), a protein that transports cargo from the cytoplasm into the nucleus, was observed in a subset of hippocampal neurons with and without tangles in AD but not control cases. Further investigation of the NPC and nucleocytoplasmic transport in AD is warranted.
Vasopressin and epinephrine vs. epinephrine alone in cardiopulmonary resuscitation.

BACKGROUND During the administration of advanced cardiac life support for resuscitation from cardiac arrest, a combination of vasopressin and epinephrine may be more effective than epinephrine or vasopressin alone, but evidence is insufficient to make clinical recommendations. METHODS In a multicenter study, we randomly assigned adults with out-of-hospital cardiac arrest to receive successive injections of either 1 mg of epinephrine and 40 IU of vasopressin or 1 mg of epinephrine and saline placebo, followed by administration of the same combination of study drugs if spontaneous circulation was not restored and subsequently by additional epinephrine if needed. The primary end point was survival to hospital admission; the secondary end points were return of spontaneous circulation, survival to hospital discharge, good neurologic recovery, and 1-year survival. RESULTS A total of 1442 patients were assigned to receive a combination of epinephrine and vasopressin, and 1452 to receive epinephrine alone. The treatment groups had similar baseline characteristics except that there were more men in the group receiving combination therapy than in the group receiving epinephrine alone (P=0.03). There were no significant differences between the combination-therapy and the epinephrine-only groups in survival to hospital admission (20.7% vs. 21.3%; relative risk of death, 1.01; 95% confidence interval [CI], 0.97 to 1.05), return of spontaneous circulation (28.6% vs. 29.5%; relative risk, 1.01; 95% CI, 0.97 to 1.06), survival to hospital discharge (1.7% vs. 2.3%; relative risk, 1.01; 95% CI, 1.00 to 1.02), 1-year survival (1.3% vs. 2.1%; relative risk, 1.01; 95% CI, 1.00 to 1.02), or good neurologic recovery at hospital discharge (37.5% vs. 51.5%; relative risk, 1.29; 95% CI, 0.81 to 2.06). CONCLUSIONS As compared with epinephrine alone, the combination of vasopressin and epinephrine during advanced cardiac life support for out-of-hospital cardiac arrest does not improve outcome. (ClinicalTrials.gov number, NCT00127907.)
Targeted pseudorandom generators, simulation advice generators, and derandomizing logspace

Assume that for every derandomization result for logspace algorithms, there is a pseudorandom generator strong enough to nearly recover the derandomization by iterating over all seeds and taking a majority vote. We prove under a precise version of this assumption that BPL ⊆ ∩α > 0 DSPACE(log1 + α n). We strengthen the theorem to an equivalence by considering two generalizations of the concept of a pseudorandom generator against logspace. A targeted pseudorandom generator against logspace takes as input a short uniform random seed and a finite automaton; it outputs a long bitstring that looks random to that particular automaton. A simulation advice generator for logspace stretches a small uniform random seed into a long advice string; the requirement is that there is some logspace algorithm that, given a finite automaton and this advice string, simulates the automaton reading a long uniform random input. We prove that ∩α > 0 prBPSPACE(log1 + α n) = ∩α > 0 prDSPACE(log1 + α n) if and only if for every targeted pseudorandom generator against logspace, there is a simulation advice generator for logspace with similar parameters. Finally, we observe that in a certain uniform setting (namely, if we only worry about sequences of automata that can be generated in logspace), targeted pseudorandom generators against logspace can be transformed into simulation advice generators with similar parameters.
Developing a Prognostic Model for 90-day Mortality After Liver Transplantation Based on Pretransplant Recipient Factors

Background. Current statistical prognostic models for mortality after liver transplantation do not have good discriminatory ability. Furthermore, the methodology used to develop these models is often flawed. The objective of this paper is to develop a prognostic model for 90-day mortality after liver transplantation based on pretransplant recipient factors, employing a rigorous model development method. Methods. We used data on 4,829 patient that were prospectively collected for the UK & Ireland Liver Transplant Audit. Switching regression was employed to impute missing values combined with a bootstrapping approach for variable selection. Results. In all, 452 patients (9.4%) died within 90 days of their transplantation. The final prognostic model was well calibrated and discriminated moderately well between patients who did and who did not die (c-statistic 0.65, 95% CI [0.63, 0.68]). Although discrimination was not excellent overall, the results showed that those patients with a “low” chance of dying within 90 days of their transplant and those with a “high” chance of dying could be differentiated from patients with a “intermediate” chance. Conclusions. Our model can provide transplant candidates with predictions of their early posttransplantation prospects before any donor information is known, which is essential information for patients with end-stage liver disease for whom liver transplantation is a treatment option.
Phenotypic plasticity of coralline algae in a High CO2 world

It is important to understand how marine calcifying organisms may acclimatize to ocean acidification to assess their survival over the coming century. We cultured the cold water coralline algae, Lithothamnion glaciale, under elevated pCO2 (408, 566, 770, and 1024 μatm) for 10 months. The results show that the cell (inter and intra) wall thickness is maintained, but there is a reduction in growth rate (linear extension) at all elevated pCO2. Furthermore a decrease in Mg content at the two highest CO2 treatments was observed. Comparison between our data and that at 3 months from the same long-term experiment shows that the acclimation differs over time since at 3 months, the samples cultured under high pCO2 showed a reduction in the cell (inter and intra) wall thickness but a maintained growth rate. This suggests a reallocation of the energy budget between 3 and 10 months and highlights the high degree plasticity that is present. This might provide a selective advantage in future high CO2 world.
Growth Limits of Listeria monocytogenesas a Function of Temperature, pH, NaCl, and Lactic Acid

ABSTRACT Models describing the limits of growth of pathogens under multiple constraints will aid management of the safety of foods which are sporadically contaminated with pathogens and for which subsequent growth of the pathogen would significantly increase the risk of food-borne illness. We modeled the effects of temperature, water activity, pH, and lactic acid levels on the growth of two strains ofListeria monocytogenes in tryptone soya yeast extract broth. The results could be divided unambiguously into “growth is possible” or “growth is not possible” classes. We observed minor differences in growth characteristics of the two L. monocytogenes strains. The data follow a binomial probability distribution and may be modeled using logistic regression. The model used is derived from a growth rate model in a manner similar to that described in a previously published work (K. A. Presser, T. Ross, and D. A. Ratkowsky, Appl. Environ. Microbiol. 64:1773–1779, 1998). We used “nonlinear logistic regression” to estimate the model parameters and developed a relatively simple model that describes our experimental data well. The fitted equations also described well the growth limits of all strains of L. monocytogenesreported in the literature, except at temperatures beyond the limits of the experimental data used to develop the model (3 to 35°C). The models developed will improve the rigor of microbial food safety risk assessment and provide quantitative data in a concise form for the development of safer food products and processes.
Phase noise measurements of 10-MHz BVA quartz crystal resonators

In this paper, we review a new piece of equipment that allows one to characterize the phase noise of crystal resonators using a phase bridge system with carrier suppression. This equipment allows one to measure the inherent phase stability of quartz crystal resonators in a passive circuit without the noise usually associated with an active oscillator. We achieved a system noise floor of approximately -150 dBc/Hz at 1 Hz and -160 dBc/Hz, at 10 Hz. A SPICE characterization of the carrier suppression system is given. An investigation of the phase modulation (PM) noise in 10 MHz BVA, SC-cut quartz crystal resonator pairs is presented.
Harmonic Power Harvesting System for Passive RFID Sensor Tags

This paper introduces a relevant concept of energy harvesting for passive UHF radio frequency identification (RFID) relying on the exploitation of the power carried by the third harmonic signal generated by the RFID chip. The idea consists on the use of the sole third harmonic energy to power up an associated sensor to the RFID tag. The proposed concept is first demonstrated in simulation thanks to an equivalent model for the RF front-end of a passive UHF RFID chip. Although the proposed model is simplified, it considers the generated nonlinear signals, allowing an efficient design of the rectifier circuit, which is responsible of harvesting the third harmonic power besides ensuring the activation of the RFID chip in order to communicate with the reader. The power driving between the RFID chip, third harmonic harvester, and antenna at the fundamental and third harmonic frequencies is achieved by designing a low-loss distributed three-port impedance matching network. Simulation results confirm the operation of the matching network and the exploitation of the third harmonic signal by analyzing the power at different nodes in the circuit. Measurement results validate the proposed nonlinear chip model. A prototype of the RFID tag harmonic-harvester produces 39 μW of dc power harvested from the harmonic signal, showing good agreement with the simulation results. Finally, a sensor application exploiting the harmonic harvested power to energize a commercial temperature sensor at a distance of 80 cm from the reader is demonstrated.
GROWING GREEN: THE EMERGENT ROLE OF NON-TILAPIA ATTRIBUTES IN MARKETING TILAPIA

This paper is focused upon the emergent emphasis of environmentally friendly (ENVF) attributes in fish with particular regard to tilapia in the UK. The focus is upon the technical production issues, marketing implications, public health and adoption responses from a 3-year multi-disciplinary Research Councils UK project, which examined the prospects for UK (agricultural) farmers to diversify into production of warmwater tilapia. The proposed production process and product characteristics abound with green credentials, consistent with emergent market demands. This combination might enable small-scale producers to access growing UK niche markets for fresh fish and to compete through upmarket positions with expanding EU tilapia imports. Having ascertained the wider market characteristics, primary research was undertaken through consumer focus groups and in-depth interviews with organizational channel members. The results supported the initial premise of niche markets existing for tilapia produced from local, small-scale environmentally friendly units. Three target groups in the UK were identified: ethnic consumers, green consumers and discrete segments (gastro-pubs and upscale fish restaurants) within foodservice. Having established favorable market prospects the propensity of farmers to diversify into this novel area of activity was explored. Investigation of farmer entrepreneurship, undertaken in 2006 and 2007, explored perceived challenges in the new aquaculture venture. In-depth face to face and telephone interviews with agricultural farmers identified a number of factors that both encouraged and dissuaded them from diversification into tilapia. Despite the ongoing interests of some, and other emergent adopters, the majority seem disinclined to commercialize their interest. The paper concludes that a more holistic support perspective will be required to promote a more favorable reaction and reviews the prognosis for the success of local fish production.
Effect of isolation in a constant environment on periodicity of physiological functions and performance levels.

Abstract : In an effort to determine the extent to which the day/night cycles of physiological and psychological functions normally synchronized with the environment in 24-hour cycles might change in isolation in an environment where there were no external clues, two medical students were studied. These subjects were isolated for nine days in a constant environment, in which temperature, humidity, barometric pressure, light intensity, and noise levels were closely controlled. In brief, the findings showed that they experienced a shift of 1.7 hours away from local clock time. Their average total periodicity being 25.8 hours. The cycles of body temperature, pulse rate, and basal skin resistance followed the phaseshift of the sleep-wakefulness cycle, while the cycle of respiratory rate became dissociated in both subjects. Most of the urine functions remained synchronized for five days but dissociated from the sleep- wakefulness cycle during the subsequent three days of the isolation period. The two subjects were of different body build and demonstrated distinctly different personality trait configurations, which were reflected in their temporal organization. Twelve-hour and six-hour periodicities were shown by power spectral analysis to dominate temporarily the 24-hour periodicity cycle during the adjustment to and recovery from the effects of isolation, in heart-rate, body temperature, and basal skin resistance, and respiratory rate of both subjects. This temporary breakdown of the temporal organization might be involved in the subjectively experienced difficulties of adjustment to living in a constant environment.
Overexpression of PAK1 Correlates with Aberrant Expression of EMT Markers and Poor Prognosis in Non-Small Cell Lung Cancer

Objective: p21-activated kinases (PAKs) are serine/threonine protein kinases. PAK1 and epithelial-mesenchymal transition (EMT) are key therapeutic targets in cancer. The clinical significance of PAK1 and its potential association with EMT phenotype in non-small cell lung cancer (NSCLC) was investigated. Methods: Immunohistochemistry was used to detect the expression of PAK1, and mesenchymal and epithelial markers (vimentin, N-cadherin, and E-cadherin) in 186 cases of NSCLC tissues and 50 cases of tumor-adjacent normal tissues. The correlation of PAK1 with the clinicopathological characteristics, prognosis, and mesenchymal and epithelial markers in NSCLC were analyzed. Results: Compared with the non-tumor tissues, PAK1, vimentin, and N-cadherin levels were markedly elevated in NSCLC tissues, whereas the E-cadherin levels were significantly decreased (P<0.05). The aberrant expression of PAK1 was significantly associated with TNM stage and metastasis (P<0.001). Patients who displayed high expression of PAK1 may achieve a poorer progression-free survival (PFS) and overall survival (OS), compared to those with low expression of PAK1 (P=0.001 and P<0.001). Univariate and multivariate analysis showed that high expression of PAK1 was an independent predictor of poor prognosis [hazard ratio (HR) =2.121, P<0.001, HR=1.928, P=0.001, respectively]. In addition, significant correlations were observed between the EMT markers and OS or PFS (P<0.01). Interestingly, PAK1 expression was positively correlated with vimentin and N-cadherin levels (r=0.473, P<0.001; r=0.526, P<0.001, respectively) and negatively correlated with E-cadherin levels (r=-0.463, P<0.001) in NSCLC tissues. Conclusion: PAK1 may promote NSCLC progression and metastasis through EMT, thereby exhibiting the potential of an efficient prognostic predictor in NSCLC patients.
Constrained Unfolding of a Helical Peptide: Implicit versus Explicit Solvents

Steered Molecular Dynamics (SMD) has been seen to provide the potential of mean force (PMF) along a peptide unfolding pathway effectively but at significant computational cost, particularly in all-atom solvents. Adaptive steered molecular dynamics (ASMD) has been seen to provide a significant computational advantage by limiting the spread of the trajectories in a staged approach. The contraction of the trajectories at the end of each stage can be performed by taking a structure whose nonequilibrium work is closest to the Jarzynski average (in naive ASMD) or by relaxing the trajectories under a no-work condition (in full-relaxation ASMD—namely, FR-ASMD). Both approaches have been used to determine the energetics and hydrogen-bonding structure along the pathway for unfolding of a benchmark peptide initially constrained as an α-helix in a water environment. The energetics are quite different to those in vacuum, but are found to be similar between implicit and explicit solvents. Surprisingly, the hydrogen-bonding pathways are also similar in the implicit and explicit solvents despite the fact that the solvent contact plays an important role in opening the helix.
Drought-Adaptation Potential in Fagus sylvatica: Linking Moisture Availability with Genetic Diversity and Dendrochronology

Background Microevolution is essential for species persistence especially under anticipated climate change scenarios. Species distribution projection models suggested that the dominant tree species of lowland forests in Switzerland, European beech (Fagus sylvatica L.), might disappear from most areas due to expected longer dry periods. However, if genotypes at the moisture boundary of the species climatic envelope are adapted to lower moisture availability, they can serve as seed source for the continuation of beech forests under changing climates. Methodology/Principal Findings With an AFLP genome scan approach, we studied neutral and potentially adaptive genetic variation in Fagus sylvatica in three regions containing a dry and a mesic site each (n ind. = 241, n markers = 517). We linked this dataset with dendrochronological growth measures and local moisture availabilities based on precipitation and soil characteristics. Genetic diversity decreased slightly at dry sites. Overall genetic differentiation was low (F st = 0.028) and Bayesian cluster analysis grouped all populations together suggesting high (historical) gene flow. The Bayesian outlier analyses indicated 13 markers with three markers differing between all dry and mesic sites and the others between the contrasting sites within individual regions. A total of 41 markers, including seven outlier loci, changed their frequency with local moisture availability. Tree height and median basal growth increments were reduced at dry sites, but marker presence/absence was not related to dendrochronological characteristics. Conclusion and Their Significance The outlier alleles and the makers with changing frequencies in relation to moisture availability indicate microevolutionary processes occurring within short geographic distances. The general genetic similarity among sites suggests that ‘preadaptive’ genes can easily spread across the landscape. Yet, due to the long live span of trees, fostering saplings originating from dry sites and grown within mesic sites might increase resistance of beech forests during the anticipated longer dry periods.
Relationships between glucose fluctuations and oxidative stress in short duration type 2 diabetes treated with sensor-augmented insulin pump

This study aims to explore the relationships between oxidative stress and glucose fluctuations in patients with short duration type 2 diabetes treated with sensor-augmented insulin pump (SAP). Sixty type 2 diabetes patients with duration < 1 year and HbA1c ≥ 9% were enrolled and randomly divided into the SAP group or the multiple daily injection (MDI) group, and all of them were performed 6-day enhanced treatments. Furthermore, the patients were also assigned to the severe oxidative group (group SO) or the weak oxidative group (group WO) according to median level of 8-iso-prostaglandin F2a (8-iso-PGF2a), an oxidative stress parameter. Compared with the baseline, the following parameters which indicate glucose fluctuations: the mean blood glucose (MBG), mean amplitude of glycemic excursion (MAGE), absolute mean of daily differences (MODD) and incremental area under the curve (IAUC) in group SAP were significantly decreased after 6-day therapy (P < 0.05), while no difference was found on terms of serum 8-iso-PGF2a levels (P > 0.05). After SAP therapy, the levels of MBG, MAGE, MODD and IAUC in group SAP were significantly lower than group MDI (P < 0.05). There was no difference in serum 8-iso-PGF2a levels and insulin daily dosage (IDD) between the groups (P > 0.05). The values of IDD and waistline in group SO were significantly higher than group WO (P < 0.05). The multiple regression analysis showed IDD (t=2.146, P=0.035) and waistline (t=4.502, P=0.011) were independently correlated with 8-iso-PGF2a. No relationship was found between oxidative stress and glucose fluctuations in short duration type 2 diabetes patients under the condition of short-term intensive SAP therapy, IDD and waistline were independent risk factors toward the activation of oxidative stress.
QUALITY CONTROL AND LOW-LEVEL STATISTICAL ANALYSIS OF ILLUMINA BEADARRAYS

• The Illumina BeadArrayTM platform is a novel microarray technology based on randomly assembled arrays of beads. Each bead on the array carries copies of a single gene-specific probe with, on average, about 30 replicates of each bead type on an array. Given the encouraging results regarding the reproducibility of BeadArrayTM data and high profile studies already being carried out using the BeadArrayTM technology, there is likely to be an increase in the volume of BeadArrayTM data available. A major advantage of BeadArrayTM technology is the high degree of replication of beads of a given type. However, current analysis methods give summarised information for each bead type as output rather than information for each individual bead on the array. The beadarray R package is able to recreate individual bead information for arrays using raw images as input. Here, we use a particular experiment to illustrate the image processing steps used by Illumina and corresponding methods available in beadarray. Our investigations into BeadArrayTM data have demonstrated a high degree of reproducibility both within and between arrays. However, we identified some aspects of the low-level analysis that could be improved. Key-Words: • Illumina; BeadArray; beadarray; Bioconductor; microarray. AMS Subject Classification: • 62P10, 92C40, 92-08. 2 M. Dunning, N. Thorne, I. Camilier, M. Smith and S. Tavaré Quality Control of BeadArrays 3