Miracle-dz/UniFAR-FTUs huggingface dataset:
Test and Evaluation of ff99IDPs Force Field for Intrinsically Disordered Proteins

Over 40% of eukaryotic proteomic sequences have been predicted to be intrinsically disordered proteins (IDPs) or intrinsically disordered regions (IDRs) and confirmed to be associated with many diseases. However, widely used force fields cannot well reproduce the conformers of IDPs. Previously the ff99IDPs force field was released to simulate IDPs with CMAP energy corrections for the eight disorder-promoting residues. In order to further confirm the performance of ff99IDPs, three representative IDP systems (arginine-rich HIV-1 Rev, aspartic proteinase inhibitor IA3, and α-synuclein) were used to test and evaluate the simulation results. The results show that for free disordered proteins, the chemical shifts from the ff99IDPs simulations are in quantitative agreement with those from reported NMR measurements and better than those from ff99SBildn. Thus, ff99IDPs can sample more clusters of disordered conformers than ff99SBildn. For structural proteins, both ff99IDPs and ff99SBildn can well reproduce the conformations. In general, ff99IDPs can successfully be used to simulate the conformations of IDPs and IDRs in both bound and free states. However, relative errors could still be found at the boundaries of ordered residues scattered in long disorder-promoting sequences. Therefore, polarizable force fields might be one of the possible ways to further improve the performance on IDPs.
Modification of the ultrasonic properties of elastomers loaded with magnetic particles by applying magnetic fields during curing

Particle loaded polymers and elastomers have been largely used in different ultrasonic applications like backing materials and matching layers because composite properties (velocity, attenuation, density and impedance) can be easily engineered by changing the filler concentration. Recently, the use of magnetic particles has been theoretically proposed as a means to produce active matching layers whose response can be modified upon the application of magnetic fields. In this paper, we propose to introduce modifications of the composite properties by using magnetic particles and applying magnetic fields during curing to establish well defined patterns in the spatial distribution of the particles within the elastomer that induce material anisotropy that effectively modify ultrasonic properties.
The Performance Impact of Elliptic Curve Cryptography on DNSSEC for Constrained Hardware Architectures

The Domain Name System (DNS) is an Internet protocol, with one of its tasks being the translation and mapping of human memorable domain names to computer usable IP addresses. Due to major security flaws in the DNS, security measures were needed. DNS Security Extensions (DNSSEC) are a suite of extensions that provide authenticity and integrity to DNS responses, using digital signatures. Unfortunately, DNSSEC is not without its flaws as well. Earlier research has shown that many of these issues are caused by the use of RSA as default cryptosystem for DNSSEC. Switching to an Elliptic Curve Cryptography (ECC-)based cryptosystem, will significantly mitigate these problems; however, verification of an ECC-based signature requires much more computing power. Earlier research has shown that for server-class architectures this is not an issue. However, local DNS resolving comes with privacy benefits for users. Therefore, we analyse whether the performance impact is problematic for home routers with a constrained hardware architecture. We examine the question “Will switching the cryptosystem of DNSSEC to an ECC-based one lead to performance issues for DNS resolvers on a constrained hardware architecture? ” In this research, we construct a DNS scenario test and adopt a model to determine a worst-case value for the amount of signatures a constrained hardware resolver should be able to verify. Subsequently, we benchmark a variety of ECC verification algorithms and implementations to determine whether this amount is obtainable for mentioned architectures. Provided that certain implementation choices are made, we conclude that switching the cryptosystem of DNSSEC to an ECC-based one is feasible for home routers.
On the Attractiveness of Product Recovery: The Forces that Shape Reverse Markets

Product recovery is a major contributor for implementing sustainable business practices. Within such operations, which are either driven by legislation or economic rationales, practitioners face strategic issues concerning reverse market entry and positioning. Although the complexity of acting on reverse markets is widely acknowledged, a comprehensive framework to facilitate decision making in this area is lacking. In an attempt to fill that gap, we develop a model that supports original equipment manufacturers’ (OEMs’) assessment of the attractiveness of reverse markets. We identify, from a comprehensive literature analysis, in‐depth interviews, and engagement with a dozen companies from different countries, factors that influence key characteristics of reverse markets, and consolidate this lengthy list into a comprehensive model intuitively applicable to business practice. The model combines five forces that drive reverse markets: access to recoverable products; threat of independent recovery companies’ (IRCs’) market entry; rivalry for recoverable products; adverse effects on core business; and remarketing opportunities. We propose for each a set of attributes that influences its power and direction. To demonstrate the efficacy of the model, we apply it in two industry settings: recovery of white goods in the United Kingdom and paper recycling in Germany. The present research enables OEMs to understand the structure and forces that drive reverse markets, identify levers to influence those markets, anticipate market developments, and formulate resilient strategies for product recovery.
Wolf in Sheep's Clothing - The Downscaling Attack Against Deep Learning Applications

This paper considers security risks buried in the data processing pipeline in common deep learning applications. Deep learning models usually assume a fixed scale for their training and input data. To allow deep learning applications to handle a wide range of input data, popular frameworks, such as Caffe, TensorFlow, and Torch, all provide data scaling functions to resize input to the dimensions used by deep learning models. Image scaling algorithms are intended to preserve the visual features of an image after scaling. However, common image scaling algorithms are not designed to handle human crafted images. Attackers can make the scaling outputs look dramatically different from the corresponding input images. This paper presents a downscaling attack that targets the data scaling process in deep learning applications. By carefully crafting input data that mismatches with the dimension used by deep learning models, attackers can create deceiving effects. A deep learning application effectively consumes data that are not the same as those presented to users. The visual inconsistency enables practical evasion and data poisoning attacks to deep learning applications. This paper presents proof-of-concept attack samples to popular deep-learning-based image classification applications. To address the downscaling attacks, the paper also suggests multiple potential mitigation strategies.
Hyperbolic Metamaterials

Hyperbolic metamaterials were originally introduced to overcome the diffraction limit of optical imaging. Soon thereafter it was realized that hyperbolic metamaterials demonstrate a number of novel phenomena resulting from the broadband singular behavior of their density of photonic states. These novel phenomena and applications include super resolution imaging, new stealth technologies, enhanced quantum-electrodynamic effects, thermal hyperconductivity, superconductivity, and interesting gravitation theory analogues. Here we briefly review typical material systems, which exhibit hyperbolic behavior and outline important applications of hyperbolic metamaterials.
INO-8875, a Highly Selective A1 Adenosine Receptor Agonist: Evaluation of Chronotropic, Dromotropic, and Hemodynamic Effects in Rats

Selective pharmacological activation of the adenosine 1 receptor (A1R) is a promising new approach to achieve a potent block of atrioventricular (A-V)–nodal conduction without significant cardiovascular side effects. The purpose of the present study was to evaluate the cardiovascular profile of INO-8875, a highly selective A1R agonist, and to compare its properties with N-[3(R)-tetrahydrofuranyl]-6-aminopurine riboside (CVT-510), which has already been shown to induce negative dromotropic effects with minimal cardiovascular side effects in animals and in clinical studies. Dose-response experiments in the isolated hearts of rats were used to evaluate the functional selectivity of INO-8875 for the slowing of A-V–nodal conduction. Ventilated adult rats were used to study the effects of INO-8875, in vivo, on arterial blood pressure as well as on supraventricular electrophysiology. Ex vivo, INO-8875 (100 nM to 3 μM) progressively prolonged A-V–nodal conduction without reducing left ventricular function or coronary resistance. In vivo, INO-8875 up to a dose of 50 μg/kg did not reduce the carotid arterial blood pressure (n = 4). INO-8875 (1–50 μg/kg) and CVT-510 (20 and 50 μg/kg) both induced a dose-dependent decrease in heart rate and atrial refractoriness, as well as slowing of A-V–nodal conduction. However, compared with CVT-510, the activity of INO-8875 was more pronounced in A-V–nodal function. INO-8875 exhibited a greater duration of action, lasting up to 2.5 hours post dosing, whereas the effects of CVT-510 dissipated over 1 hour. INO-8875 demonstrates functional properties of a highly selective A1R agonist. INO-8875 exhibits an increased dromotropic effect and greater duration of action compared with CVT-510.
Nisin as a Food Preservative: Part 2: Antimicrobial Polymer Materials Containing Nisin

Nisin is the only bacteriocin approved as a food preservative because of its antibacterial effectiveness and its negligible toxicity for humans. Typical problems encountered when nisin is directly added to foods are mainly fat adsorption leading to activity loss, heterogeneous distribution in the food matrix, inactivation by proteolytic enzymes, and emergence of resistance in normally sensitive bacteria strains. To overcome these problems, nisin can be immobilized in solid matrices that must act as diffusional barriers and allow controlling its release rate. This strategy allows maintaining a just sufficient nisin concentration at the food surface. The design of such antimicrobial materials must consider both bacterial growth kinetics but also nisin release kinetics. In this review, nisin incorporation in polymer-based materials will be discussed and special emphasis will be on the applications and properties of antimicrobial food packaging containing this bacteriocin.
Inhibition of Auxin Signaling in Frankia Species-Infected Cells in Casuarina glauca Nodules Leads to Increased Nodulation1

Inhibition of auxin signaling in plant cells infected by endosymbiotic nitrogen-fixing bacteria increases nodulation. Actinorhizal symbioses are mutualistic interactions between plants and the soil bacteria Frankia spp. that lead to the formation of nitrogen-fixing root nodules. The plant hormone auxin has been suggested to play a role in the mechanisms that control the establishment of this symbiosis in the actinorhizal tree Casuarina glauca. Here, we analyzed the role of auxin signaling in Frankia spp. -infected cells. Using a dominant-negative version of an endogenous auxin-signaling regulator, INDOLE-3-ACETIC ACID7, we established that inhibition of auxin signaling in these cells led to increased nodulation and, as a consequence, to higher nitrogen fixation per plant even if nitrogen fixation per nodule mass was similar to that in the wild type. Our results suggest that auxin signaling in Frankia spp. -infected cells is involved in the long-distance regulation of nodulation in actinorhizal symbioses.
Outcomes of a community-based treatment programme for people with acquired brain injury in the chronic phase: a pilot study

ABSTRACT The objective of the study was to evaluate the outcomes of Brainz, a low intensity community-based treatment programme for people with acquired brain injury (ABI). Participants were 62 people with sustained ABI (5.2 years post-injury, SD = 4.5) and 35 family caregivers. Participants attended two to five cognitive and physical group modules and received two hours of individual home treatment every two weeks. Primary outcomes for people with ABI were participation, perceived difficulties in daily life and need of care, level of goal attainment, and self-esteem. Primary family caregiver outcome was perceived burden of care. Attrition rate of people with ABI was 24% (n = 15), and of family caregivers was 31% (n = 11). People with ABI were more satisfied with the level of their participation after completing Brainz (p < .01), but showed no change in participation frequency or in restrictions (both ps > .01). They perceived fewer difficulties in daily life and less need of care (both ps < .01). Also, in two cognitive modules people improved on their goal achievement (p < .01). However, their self-esteem was reduced (p < .01). Caregiver burden was reduced (p < .01). This study has provided preliminary evidence of the effectiveness of a combined group-based clinical and individual home-based treatment programme, but more research is needed, preferably in larger controlled studies.
Recording Infant ERP Data for Cognitive Research

Researchers from different backgrounds have an increasing interest in investigating infant cognitive development using electroencephalogram (EEG) recordings. Although EEG measurements are suitable for infants, the method poses several challenges including setting up an infant-friendly, but interference-free lab environment and designing age-appropriate stimuli and paradigms. Certain specifics of infant EEG data have to be considered when deriving event-related potentials (ERPs) to investigate cognitive processes in the developing brain. The present article summarizes the practical aspects of conducting ERP research with infants and describes how researchers typically deal with the specific challenges entailed in this work.
Experimental miniature piglet model for the infection of human norovirus GII

Ten Yucatan miniature piglets were challenged with the human norovirus (NoV) GII.12/GII.3 CAU140599 strain and five piglets were used as negative controls. Stool, serum, and organs were collected and processed from two NoV‐infected piglets and one negative piglet at 1, 2, 3, 5, and 7 days post‐inoculation (dpi). NoV was detected in stool and serum samples by real‐time RT‐PCR. Mild diarrhea was observed at 1‐3 dpi. Fecal shedding and viremia were detected intermittently at 1, 3, and 7 dpi. While interferon‐α was significantly elevated at 2‐3 dpi, interferon‐γ was not changed. Immunohistochemistry demonstrated that the NoV capsid antigen was present in macrophages, lymphocytes, and dendritic cells of the stomach, intestines, lymph nodes, spleen, and tonsils. Intestinal epithelium did not exhibit a positive signal for NoV. In addition, negative‐sense viral RNA was confirmed in immune cells by fluorescence in situ hybridization. Therefore, NoV might be associated with macrophages and lymphocytes in gastrointestinal tract and immune organs of experimentally infected miniature piglets.
Investigation of the Interaction Between Human Serum Albumin and Antitumor Palladium(II) Complex Containing 1,10-Phenanthroline and Dithiocarbamate Ligands

The interaction between [Pd(But-dtc)(phen)]NO3 (where But-dtc = butyldithiocarbamate and phen = 1,10-phenanthroline) with HSA (Human Serum Albumin) was investigated by applying fluorescence, UV–Vis and circular dichroism techniques under physiological conditions. The results of fluorescence spectra indicated that the Pd(II) complex could effectively quench the fluorescence intensity of HSA molecules via static mechanism. The number of binding sites and binding constant of HSA–Pd(II) complex were calculated. Analysis of absorption titration data on the interaction between Pd(II) complex and HSA revealed the formation of HSA–Pd(II) complex with high-binding affinity. Thermodynamic parameters indicated that hydrophobic forces play a major role in this interaction. Furthermore, CD measurements were taken to explore changes in HSA secondary structure induced by the Pd(II) complex.
A pilot study exploring the effects of a 12-week t'ai chi intervention on somatic symptoms of depression in patients with heart failure.

BACKGROUND Patients with chronic heart failure (HF) and with elevated depression symptoms are at greater risk of morbidity and mortality. Somatic symptoms of depression are particularly prevalent in HF and are related to worse disease prognosis. T'ai chi practice is related to increased emotional well-being in various clinical populations; however, relatively little is known about t'ai chi's effects on somatic versus cognitive symptom dimensions of depression in HF. PURPOSE The objective of the study was to measure whether a t'ai chi intervention effectively reduces somatic and/or cognitive symptoms of depression in patients with HF. METHODS Patients with HF were assigned to either t'ai chi training (n=16) or a usual-care group (n=12). At baseline and after the 12-week intervention period, participants were evaluated for changes in depressive symptoms using Beck Depression Inventory (BDI) total scores (BDI-t) and subcategorized scores of BDI-somatic (BDI-s) and BDI-cognitive (BDI-c), and for symptoms of fatigue using the Multidimensional Fatigue Symptom Inventory-Short Form. RESULTS Patients with HF in the t'ai chi group compared to the usual-care group had reduced BDI-s (p≤0.017), but not BDI-c (p=0.50) scores from pre- to postintervention. Although t'ai chi did not significantly reduce fatigue, changes in physical fatigue (p≤0.05) were independently associated with changes in BDI-t scores. CONCLUSIONS T'ai chi practice reduced somatic symptoms of depression, which have been linked to worse prognosis in HF. Reductions in fatigue appear to explain some but not all of the reductions in somatic symptoms of depression.
Impedance spectroscopy of a vibrating wire for viscosity measurements

Many routine viscosity measurement systems suffer from low accuracy and some are also operator dependant which creates repeatability problems. This paper describes the ongoing developments of a viscosity measurement system based on a vibrating wire cell. The proposed improvements include the simultaneous fitting of the magnitude and phase of the measured impedance and the test of different equivalent impedance circuits. Since the fitting function has a high number of search variables and contains many local minima, a hybrid method involving genetic algorithms as well as a traditional search algorithm is used. The system is tested with liquid diisodecyl phthalate (DIDP) and the viscosity results are compared to reference values available in the literature. A new equivalent impedance circuit is also suggested as one of the possible circuits to model the cell behavior in the future, when used with ionic liquids.
Mediating the Electoral Connection: The Information Effects of Voter Signals on Legislative Behavior

We develop and assess an information account of representation. Accordingly, politicians face uncertainty about voter opinion and use previous vote margins to gauge future electoral outcomes. Losses in vote support elicit ideological moderation given new information about electorates. To test this account, we use rain around Election Day as a natural experiment in voting in the US House races from 1956 to 2008. We find that each additional inch of rainfall exogenously dampens Democratic vote margins by 1.4–2.0 percentage points and shifts incumbents rightward in their roll call positions in subsequent Congresses. We find responsiveness mainly in competitive districts with the greatest risk of defeat, and by Democrats rather than Republicans, suggesting an asymmetry in party representation. Overall, we highlight the importance of elite information uncertainty as a mechanism driving the electoral connection, and we show that idiosyncratic electoral effects can meaningfully impact legislative behavior.
Thromboxane biosynthesis and platelet function in type II diabetes mellitus.

It has been suggested that platelet hyperreactivity in patients with diabetes mellitus is associated with increased platelet production of thromboxane. We therefore compared the excretion of a thromboxane metabolite and platelet function in 50 patients with Type II diabetes mellitus who had normal renal function and clinical evidence of macrovascular disease and in 32 healthy controls. The mean (+/- SD) excretion rate of urinary 11-dehydro-thromboxane B2 was significantly higher in the patients than in the controls (5.94 +/- 3.68 vs. 1.50 +/- 0.79 nmol per day; P less than 0.001), irrespective of the type of macrovascular complication. Tight metabolic control achieved with insulin therapy reduced the levels of 11-dehydro-thromboxane B2 by approximately 50 percent. The fractional conversion of exogenous thromboxane B2 (infused at a rate of 4.5, 45.3, or 226.4 fmol per kilogram of body weight per second) to urinary 11-dehydro-thromboxane B2 was assessed in four patients, in whom it averaged 5.4 +/- 0.1 percent; this value did not differ from that measured in healthy subjects. Aspirin in low doses (50 mg per day for seven days) reduced urinary excretion of the metabolite by approximately 80 percent in four patients. The fact that thromboxane biosynthesis recovered over the following 10 days was consistent with a platelet origin of the urinary metabolite. (ABSTRACT TRUNCATED AT 250 WORDS)
Ecosystem nitrogen fixation throughout the snow‐free period in subarctic tundra: effects of willow and birch litter addition and warming

Nitrogen (N) fixation in moss‐associated cyanobacteria is one of the main sources of available N for N‐limited ecosystems such as subarctic tundra. Yet, N2 fixation in mosses is strongly influenced by soil moisture and temperature. Thus, temporal scaling up of low‐frequency in situ measurements to several weeks, months or even the entire growing season without taking into account changes in abiotic conditions cannot capture the variation in moss‐associated N2 fixation. We therefore aimed to estimate moss‐associated N2 fixation throughout the snow‐free period in subarctic tundra in field experiments simulating climate change: willow (Salix myrsinifolia) and birch (Betula pubescens spp. tortuosa) litter addition, and warming. To achieve this, we established relationships between measured in situ N2 fixation rates and soil moisture and soil temperature and used high‐resolution measurements of soil moisture and soil temperature (hourly from May to October) to model N2 fixation. The modelled N2 fixation rates were highest in the warmed (2.8 ± 0.3 kg N ha−1) and birch litter addition plots (2.8 ± 0.2 kg N ha−1), and lowest in the plots receiving willow litter (1.6 ± 0.2 kg N ha−1). The control plots had intermediate rates (2.2 ± 0.2 kg N ha−1). Further, N2 fixation was highest during the summer in the warmed plots, but was lowest in the litter addition plots during the same period. The temperature and moisture dependence of N2 fixation was different between the climate change treatments, indicating a shift in the N2 fixer community. Our findings, using a combined empirical and modelling approach, suggest that a longer snow‐free period and increased temperatures in a future climate will likely lead to higher N2 fixation rates in mosses. Yet, the consequences of increased litter fall on moss‐associated N2 fixation due to shrub expansion in the Arctic will depend on the shrub species’ litter traits.