Miracle-dz/UniFAR-FTUs huggingface dataset:
Single-Molecule Fluorescence Polarization Study of Conformational Change in Archaeal Group II Chaperonin

Group II chaperonins found in archaea and in eukaryotic cytosol mediate protein folding without a GroES-like cofactor. The function of the cofactor is substituted by the helical protrusion at the tip of the apical domain, which forms a built-in lid on the central cavity. Although many studies on the change in lid conformation coupled to the binding and hydrolysis of nucleotides have been conducted, the molecular mechanism of lid closure remains poorly understood. Here, we performed a single-molecule polarization modulation to probe the rotation of the helical protrusion of a chaperonin from a hyperthermophilic archaeum, Thermococcus sp. strain KS-1. We detected approximately 35° rotation of the helical protrusion immediately after photorelease of ATP. The result suggests that the conformational change from the open lid to the closed lid state is responsible for the approximately 35° rotation of the helical protrusion.
Does Aversive Conditioning Reduce Human–Black Bear Conflict?

Abstract Aversive conditioning (AC) has the potential to temporarily reduce conflicts between humans and black bears (Ursus americanus). From 2002 to 2005, I evaluated the effectiveness of projectiles with varying impact intensities, pepper spray, and chasing on approximately 150 bears in Sequoia National Park. Aversive conditioning was successful in keeping bears that were not food-conditioned from becoming food-conditioned. For the bears that were already food-conditioned, 17 of 29 bears subjected to AC abandoned unwanted behaviors, 6 required continual treatments, and 6 were killed or relocated. Success with food-conditioned bears was highest when AC was applied soon after bears obtained human food. Aversive conditioning was less successful on yearlings than adults. Rubber slugs were slightly more effective than lower impact projectiles.
Petiolate wings: effects on the leading-edge vortex in flapping flight

The wings of many insect species including crane flies and damselflies are petiolate (on stalks), with the wing planform beginning some distance away from the wing hinge, rather than at the hinge. The aerodynamic impact of flapping petiolate wings is relatively unknown, particularly on the formation of the lift-augmenting leading-edge vortex (LEV): a key flow structure exploited by many insects, birds and bats to enhance their lift coefficient. We investigated the aerodynamic implications of petiolation P using particle image velocimetry flow field measurements on an array of rectangular wings of aspect ratio 3 and petiolation values of P = 1–3. The wings were driven using a mechanical device, the ‘Flapperatus’, to produce highly repeatable insect-like kinematics. The wings maintained a constant Reynolds number of 1400 and dimensionless stroke amplitude Λ* (number of chords traversed by the wingtip) of 6.5 across all test cases. Our results showed that for more petiolate wings the LEV is generally larger, stronger in circulation, and covers a greater area of the wing surface, particularly at the mid-span and inboard locations early in the wing stroke cycle. In each case, the LEV was initially arch-like in form with its outboard end terminating in a focus-sink on the wing surface, before transitioning to become continuous with the tip vortex thereafter. In the second half of the wing stroke, more petiolate wings exhibit a more detached LEV, with detachment initiating at approximately 70% and 50% span for P = 1 and 3, respectively. As a consequence, lift coefficients based on the LEV are higher in the first half of the wing stroke for petiolate wings, but more comparable in the second half. Time-averaged LEV lift coefficients show a general rise with petiolation over the range tested.
Assessing risk screening methods of malnutrition in geriatric patients: Mini Nutritional Assessment (MNA) versus Geriatric Nutritional Risk Index (GNRI).

INTRODUCTION Elderly subjects are considered a vulnerable group and they have more risk of nutritional problems. The risk of malnutrition increases in hospitalized geriatric patients. OBJECTIVES To compare the correlation between MNA and GNRI with anthropometric, biochemical and Barthel Index in hospitalized geriatric patients and to test the concordance between MNA and GNRI and between Mini Nutritional Assessment Short Form (MNA-SF) and MNA. METHODS It was a cross-sectional study on a sample of 40 hospitalized geriatric patients. For determination nutritional status we used MNA and GNRI; we evaluated the correlation between this both test with biochemical and anthropometric parameters and functional questionnaires. We used Pearson's simple correlation model, oneway ANOVA and multiple logistic regression to evaluate the relationship between MNA and GNRI. RESULTS According to MNA, 17 patients (42.5%) were malnourished and according to GNRI, 13 patients (32.5%) had high risk of nutritional complications. The concordance of MNA and GNRI was 39% and between MNA-SF and MNA was 81%. The most significant differences were detected in weight, BMI, arm and calf circumference and weight loss parameters. Barthel index was significantly different in both tests. The MNA and GRNI had significant correlations with albumin, total protein, transferring, arm and calf circumference, weight loss and BMI parameters. CONCLUSIONS In conclusion, it would be reasonable to use GRNI in cases where MNA is not applicable, or even use GRNI as a complement to MNA in hospitalized elderly patients. There is no reason why they should be deemed incompatible, and patients could benefit from more effective nutritional intervention.
In silico studies of carbon nano tubes and metal clusters

Carbon nanotubes have been envisioned to become a very important material in various applications. This is due to the unique properties of carbon nanotubes which can be exploited in applications on length scales spanning from the nano world to our macroscopic world. For example, the electronic properties of carbon nanotubes makes them utterly suitable for nano electronics while the strength of them makes them suitable for reinforcements in plastics. Both of these applications do however require. mer the ability for systematic production of carbon nanotubes with certain properties. This is called selective carbon nanotube growth and today this has not been achieved with total success. In the work presented in the thesis several diﬀerent computational methods have been applied in our contribution to the systematic search for selective carbon nanotube growth. Put in a context of previous knowledge about carbon nanotube growth our results provide valuable clues to which parameters that control the carbon nanotube growth. In association with the latest results we even dare to, with all modesty, speculate about a plausible control mechanism. The studies presented in the thesis addressed diﬀerent stages of carbon nanotube growth, spanning from the properties aﬀecting the initiation of the growth to the parameters aﬀecting the termination of the growth. In some more detail this included studies of the melting temperatures of nanoscaled metal clusters. The expected size dependence of the melting temperatures was conﬁrmed and the melting temperatures of clusters on substrates were seen to depend both on the material and shape of the surface. As this constitute the premises prior to the carbon nanotube growth it was followed by studies of the interaction between carbon nanotubes and metal clusters of diﬀerent size and constitution. This was done using diﬀerent computational methods and at diﬀerent temperatures. It soon became apparent that the clusters adapted to the carbon nanotube and not vice versa. This held true irrespectively of the constitution of the cluster, that is for both pure metal and metal carbide. It was also seen that there exist a minimum cluster size that prevent the carbon nanotube end from closing. Closure of the carbon nanotube end is likely to lead to the termination of the growth which lead to studies of other reasons for growth termination, e.g., Ostwald ripening of the catalyst particles. This was investigated with the result that the rate of the Ostwald ripening may depend on both the chirality and diameter of the carbon nanotubes. It is suggested that this may provide some answers to the controlled growth of carbon nanotubes.
Preclinical Development Peloruside-and Laulimalide-Resistant Human Ovarian Carcinoma Cells Have b I-Tubulin Mutations and Altered Expression of b II-and b III-Tubulin Isotypes

Peloruside A and laulimalide are potent microtubule-stabilizing natural products with a mechanism of action similar to that of paclitaxel. However, the binding site of peloruside A and laulimalide on tubulin remains poorly understood. Drug resistance in anticancer treatment is a serious problem. We developed peloruside Aand laulimalide-resistant cell lines by selecting 1A9 human ovarian carcinoma cells that were able to grow in the presence of one of these agents. The 1A9-laulimalide resistant cells (L4) were 39-fold resistant to the selecting agent and 39-fold cross-resistant to peloruside A, whereas the 1A9-peloruside A resistant cells (R1) were 6-fold resistant to the selecting agent while they remained sensitive to laulimalide. Neither cell line showed resistance to paclitaxel or other drugs that bind to the taxoid site on b-tubulin nor was there resistance to microtubule-destabilizing drugs. The resistant cells exhibited impaired peloruside A/ laulimalide-induced tubulin polymerization and impaired mitotic arrest. Tubulin mutations were found in the bI-tubulin isotype, R306H or R306C for L4 and A296T for R1 cells. This is the first cell-based evidence to support a b-tubulin–binding site for peloruside A and laulimalide. To determine whether the different resistance phenotypes of the cells were attributable to any other tubulin alterations, the b-tubulin isotype composition of the cells was examined. Increased expression of bIIand bIII-tubulin was observed in L4 cells only. These results provide insight into how alterations in tubulin lead to unique resistance profiles for two drugs, pelorusideA and laulimalide, that have a similarmode of action.Mol Cancer Ther; 10(8); 1419–29. 2011
High abundance and dark CO2 fixation of chemolithoautotrophic prokaryotes in anoxic waters of the Baltic Sea

We determined the abundance and distribution of chemolithoautotrophic prokaryotes in the redoxcline in two basins (Gotland Deep, Landsort Deep) of the central Baltic Sea by combining dark CO2 fixation measurements with flow cytometric cell sorting. Maximum CO2 fixation rates were recorded in sulfidic waters about 20 m below the chemocline. Flow cytometric analyses of deoxyribonucleic acid (DNA)‐stained bacterioplankton revealed the existence of at least five different prokaryotic clusters in water samples collected below the chemocline. Dark CO2 fixation in these clusters was determined by flow cytometric sorting after anoxic incubations with NaH14CO3 tracer. Two clusters, representing about 30% of total prokaryotes, were responsible for 65% to 100% of the total dark fixation. Calculated cell‐specific CO2 fixation rates in the two basins ranged from 3.5 to 24.7 fg C cell−1 d−1 and suggested that these clusters are dominated by chemolithoautotrophic prokaryotes. Mean cell‐specific fixation rates reached more than 10 fg C cell−1 d−1 in most cases, indicating relatively high growth rates (doubling times 1‐2 d) of chemolithoautotrophic prokaryotes. Our results provide the first evidence of such high cell‐specific CO2 uptake and abundance of chemolithoautotrophic prokaryotes in a pelagic marine environment. However, the identity of the organisms as well as the mechanisms fueling CO2 dark fixation in the anoxic zone remain unknown.
Do I really feel it? The contributions of subjective fluency and compatibility in low-level effects on aesthetic appreciation

The causes for the liking of objects are multifaceted. According to the processing fluency account, the ease with which an object is processed leads to a subjective feeling of fluency. This subjective feeling is then interpreted as a positive reaction toward the object resulting higher liking. However, evidence regarding the processes underlying this relation is scarce. To show that the subjective feeling can indeed be responsible for liking, we experimentally manipulated processing ease by providing false physiological feedback (varying skin conductance indicated varying feelings of fluency) and by varying presentation times between 100 and 400 ms while participants viewed line drawings of objects and rated them for liking. A first experiment showed that both false physiological feedback and presentation duration influenced liking. Stimuli primed with a (fake) visualization of a physiological correlate of high ease of processing were liked more than stimuli primed with a low ease of processing. Liking ratings in a no-feedback condition fell between the high and low feedback conditions. To explore possible compatibility effects of coupling visual feedback to the fluency interpretation, in a second experiment we reversed the feedback interpretation—visualization of high skin conductance now indicated low ease of processing. The results show a similar pattern, though the effect was subtler. This indicates that when the coupling of feedback to fluency is less apparent or less compatible, the feeling is less strongly linked to liking. Our results support the claim that variations in the feeling of fluency affect the appreciation of objects in terms of liking. Together, the experiments suggest the contributions of processing ease as well as compatibility to the experience of liking.
Modelling columnar and equiaxed growth

﻿ A novel computer model of the evolution of columnar and equiaxed microstructure during alloy solidification has been developed. A control volume finite difference model of conduction heat transfer is applied to a two-dimensional domain bounded by a relatively cold mould. The initial condition is that of superheated liquid, and nucleation occurs either at the mould wall, leading to columnar dendritic growth, or within the bulk liquid, leading to the growth of equiaxed dendrites. The columnar front or the equiaxed grain boundaries are represented by computationally sharp interfaces, which separate liquid from partially solid alloy. Interpolation between discrete computational markers is employed to describe these interfaces, and a front-tracking technique is used to predict the evolution of the grain structure, via movement of the markers, across the fixed grid. The front velocity is determined via considerations of the kinetics of dendrite growth. The heat equation is fully coupled to the front-tracking algorithm by means of source terms which represent the evolution of latent heat due to the dendritic growth (advancing tips and thickening mushy zone). The model, applied to binary Al-Cu alloys, is computationally efficient. It predicts the variation of the extent of liquid undercooling ahead of the growing columnar front, and new metrics have been established to determine the likelihood of the formation of an equiaxed zone here. The employment of these metrics to establish the influence of heat extraction rate and alloy composition agrees with reports from the literature. The model does not distinguish between individual grains of the columnar zone, but it is shown that this is not an important limitation for most metal casting applications. Direct simulation of the nucleation and growth of multiple equiaxed crystals has been carried out, in which the nucleation and growth of individual grams can be observed via animation, and the influence of melt superheat and heat extraction rate on equiaxed solidification has been determined.
American trees shift their niches when invading Western Europe: evaluating invasion risks in a changing climate

Abstract Four North American trees are becoming invasive species in Western Europe: Acer negundo, Prunus serotina, Quercus rubra, and Robinia pseudoacacia. However, their present and future potential risks of invasion have not been yet evaluated. Here, we assess niche shifts between the native and invasive ranges and the potential invasion risk of these four trees in Western Europe. We estimated niche conservatism in a multidimensional climate space using niche overlap Schoener's D, niche equivalence, and niche similarity tests. Niche unfilling and expansion were also estimated in analogous and nonanalogous climates. The capacity for predicting the opposite range between the native and invasive areas (transferability) was estimated by calibrating species distribution models (SDMs) on each range separately. Invasion risk was estimated using SDMs calibrated on both ranges and projected for 2050 climatic conditions. Our results showed that native and invasive niches were not equivalent with low niche overlap for all species. However, significant similarity was found between the invasive and native ranges of Q. rubra and R. pseudoacacia. Niche expansion was lower than 15% for all species, whereas unfilling ranged from 7 to 56% when it was measured using the entire climatic space and between 5 and 38% when it was measured using analogous climate only. Transferability was low for all species. SDMs calibrated over both ranges projected high habitat suitability in Western Europe under current and future climates. Thus, the North American and Western European ranges are not interchangeable irrespective of the studied species, suggesting that other environmental and/or biological characteristics are shaping their invasive niches. The current climatic risk of invasion is especially high for R. pseudoacacia and A. negundo. In the future, the highest risks of invasion for all species are located in Central and Northern Europe, whereas the risk is likely to decrease in the Mediterranean basin.
[Two year follow-up of acute ischemic syndrome without ST elevation].

OBJECTIVE To analyze the characteristics, treatment, and natural course during two years of the patients with acute coronary ischemic syndrome (ACS) without ST elevation in China as a part of the international multicentre registry of acute ischemic syndrome, Organization to Assess Strategies for Ischemic Syndromes (OASIS). METHODS 2294 patients with ACS without ST elevation, including unstable angina pectoris and non-Q-wave myocardial infarction, aged 63 +/- 8, 62.3% being males, were registered and observed for 2 years based on informed consent in the northwest, north, and northeast China. The specific clinical protocols for patients were decided by the attending physicians without outside intervention. The patients' clinical characteristics, treatments, major events in hospital, and natural course of disease during the period of two years were recorded by filling in Case Report Forms offered by Canadian Cardiovascular Collaboration. RESULTS 89.8% of the patients showed abnormal ECG. The most probable clinical diagnosis on admission was unstable angina in 88.5% of the patients and non-Q-wave myocardial infarction in the other 11.5%. 56.2% of the patients had past history of coronary artery disease, and nearly half of them had myocardial infarction. 57.4%, 18.3%, 47.6%, and 7.1% of them had the prior history of hypertension, diabetes, cigarette smoking and stroke respectively. During hospitalization, anti-platelet therapy and nitrate were used in 94.5% and 96.6% of the cases respectively, and 67.5%, 57.4%, and 59.1%t of them took beta-blockers, calcium antagonists and angiotensin-converting enzyme inhibitor (ACEI) respectively simultaneously. The medication rate dropped by 20.2% approximately 50.2% after discharge from hospital. During the two-year follow up the therapeutic rates of anti-platelets, nitrates, beta-blockers, calcium antagonists, and ACEI were 73.8%, 69.4%, 43.9%, 35.8%, and 31.6% respectively. During the 2 years 43.1%, 23.1%, and 8.2% of the patients underwent coronary angiography, percutaneous coronary intervention (PCI), and coronary artery bypass graft surgery (CABG) respectively. The two-year total mortality was 8.0%. The most common causes of death were severe arrhythmias or sudden death with an incidence of 4.3%. The major events were refractory angina, heart failure, new MI, stroke, and major bleeding with incidence rates of 29.4%, 15.4%, 7.9%, 4.8%, and 0.3%, respectively. CONCLUSION Most patients with acute ischemic syndrome without ST elevation in China are diagnosed as unstable angina. The patients with acute ischemic syndrome are diagnosed as unstable angina mostly in China. More than half of the patients are treated with anti-platelets, nitrates, beta-blockers, calcium antagonists, and ACEI during hospitalization. The medication rate gradually decreases after discharge. The two-year mortality is 8.0%. The most common causes of death include severe arrhythmias and sudden death.
Performance Analysis and Comparison of 6 to 4 Relay Implementations

the depletion of the public IPv4 address pool may speed up the deployment of IPv6. The coexistence of the two versions of IP requires some transition mechanisms. One of them is 6to4 which provides a solution for the problem of an IPv6 capable device in an IPv4 only environment. From among the several 6to4 relay implementations, the following ones were selected for testing: sit under Linux, stf under FreeBSD and stf under NetBSD. Their stability and performance were investigated in a test network. The increasing measure of the load of the 6to4 relay implementations was set by incrementing the number of the client computers that provided the traffic. The packet loss and the response time of the 6to4 relay as well as the CPU utilization and the memory consumption of the computer running the tested 6to4 relay implementations were measured. The implementations were tested also under very heavy load conditions to see if they are safe to be used in production systems. Keywords—IPv6 deployment; IPv6 transition solutions; 6to4; performance analysis
Lacking Control over the Trade-Off between Quality and Quantity in Visual Short-Term Memory

Visual short-term memory (VSTM) is limited in the quantity and quality of items that can be retained over time. Importantly, these two mnemonic parameters interact: increasing the number of items in VSTM reduces the quality with which they are represented. Here, we ask whether this trade-off is under top-down control. Specifically, we test whether participants can strategically optimise the trade-off between quality and quantity for VSTM according to task demands. We manipulated strategic trade-off by varying expectations about the number of to-be-remembered items (Experiments 1–2) or the precision required for the memory-based judgement (Experiment 3). In a final experiment, we manipulated both variables in a complementary way to maximise the motivation to strategically control the balance between number and the quality of items encoded into VSTM. In different blocks, performance would benefit most either by encoding a large number of items with low precision or by encoding a small number of items with high precision (Experiment 4). In all experiments, we compared VSTM performance on trials matched for mnemonic demand, but within contexts emphasising the quality or quantity of VSTM representations. Across all four experiments, we found no evidence to suggest that participants use this contextual information to bias the balance between the number and precision of items in VSTM. Rather, our data suggest that the trade-off may be determined primarily by stimulus-driven factors at encoding.