Miracle-dz/UniFAR-FTUs huggingface dataset:
Freeze-dried strawberries lower serum cholesterol and lipid peroxidation in adults with abdominal adiposity and elevated serum lipids.

Dietary flavonoid intake, especially berry flavonoids, has been associated with reduced risks of cardiovascular disease (CVD) in large prospective cohorts. Few clinical studies have examined the effects of dietary berries on CVD risk factors. We examined the hypothesis that freeze-dried strawberries (FDS) improve lipid and lipoprotein profiles and lower biomarkers of inflammation and lipid oxidation in adults with abdominal adiposity and elevated serum lipids. In a randomized dose-response controlled trial, 60 volunteers [5 men and 55 women; aged 49 ± 10 y; BMI: 36 ± 5 kg/m(2) (means ± SDs)] were assigned to consume 1 of the following 4 beverages for 12 wk: 1) low-dose FDS (LD-FDS; 25 g/d); 2) low-dose control (LD-C); 3) high-dose FDS (HD-FDS; 50 g/d); and 4) high-dose control (HD-C). Control beverages were matched for calories and total fiber. Blood draws, anthropometrics, blood pressure, and dietary data were collected at screening (0 wk) and after 12-wk intervention. Dose-response analyses revealed significantly greater decreases in serum total and LDL cholesterol and nuclear magnetic resonance (NMR)-derived small LDL particle concentration in HD-FDS [33 ± 6 mg/dL, 28 ± 7 mg/dL, and 301 ± 78 nmol/L, respectively (means ± SEMs)] vs. LD-FDS (-3 ± 11 mg/dL, -3 ± 9 mg/dL, and -28 ± 124 nmol/L, respectively) over 12 wk (0-12 wk; all P < 0.05). Compared with controls, only the decreases in total and LDL cholesterol in HD-FDS remained significant vs. HD-C (0.7 ± 12 and 1.4 ± 9 mg/dL, respectively) over 12 wk (0-12 wk; all P < 0.05). Both doses of strawberries showed a similar decrease in serum malondialdehyde at 12 wk (LD-FDS: 1.3 ± 0.2 μmol/L; HD-FDS: 1.2 ± 0.1 μmol/L) vs. controls (LD-C: 2.1 ± 0.2 μmol/L; HD-C: 2.3 ± 0.2 μmol/L) (P < 0.05). In general, strawberry intervention did not affect any measures of adiposity, blood pressure, glycemia, and serum concentrations of HDL cholesterol and triglycerides, C-reactive protein, and adhesion molecules. Thus, HD-FDS exerted greater effects in lowering serum total and LDL cholesterol and NMR-derived small LDL particles vs. LD-FDS in the 12-wk study. These findings warrant additional investigation in larger trials. This trial was registered at clinicaltrials.gov as NCT01883401.
Burden of respiratory comorbidities in patients with atopic dermatitis and psoriasis

DEAR EDITOR, Atopic dermatitis (AD), a skin disease with an estimated lifetime prevalence of up to 20%, represents a major global healthcare burden. Patients with AD have a propensity to develop asthma due to a combination of genetic, immunological and environmental factors, yet descriptive studies on the impact of respiratory diseases in adults with AD are scarce. In contrast, psoriasis, another chronic inflammatory skin disease, has been associated with respiratory comorbidities such as chronic obstructive pulmonary disease (COPD), asthma and obstructive sleep apnoea (OSA). Respiratory diseases cause considerable morbidity and mortality worldwide. Quantitative assessments of the respiratory comorbidity associated with AD and psoriasis are pivotal, yet this topic remains understudied. We investigated the burden of respiratory diseases in Danish adults with AD compared with patients with psoriasis and general population controls, respectively. Utilizing data from Danish administrative registries we identified all Danish adults (aged ≥ 18 years) with an inpatient or outpatient (ambulatory) diagnosis of AD or psoriasis during the study period (1 January 1995 to 31 December 2012). Patients with AD were matched (on age and sex) with 10 general population controls. Patients were classified as having severe AD and severe psoriasis, respectively, if they received appropriate systemic therapy. A detailed description of the methodology is available on request. In total, 7937 patients with AD, 24 505 patients with psoriasis and 79 370 general population controls were identified. Asthma was highly prevalent in the AD group (18.0%), compared with patients with psoriasis (2.8%) and general population controls (2.0%) (Table 1). Logistic regression analyses yielded pronounced associations between asthma and AD, compared with psoriasis [adjusted odds ratio (aOR) 5.95, 95% confidence interval (CI) 5.38–6.59] and general population controls (aOR 8.79, 95% CI 8.08–9.56). Similar trends were found for status asthmaticus and asthma-related therapies (inhaled corticosteroids and inhaled adrenergics). COPD occurred less frequently in patients with AD than in those with psoriasis (7.4% vs. 2.6%; aOR 0.62, 95% CI 0.53– 0.72), as did use of COPD-related therapies (anticholinergics). However, in patients with severe AD, COPD risk was significantly increased compared with controls (3.5% vs. 2.1%; aOR 1.42, 95% CI 1.17–1.73). The prevalence of OSA was significantly lower in patients with AD compared with psoriasis
Joint Beamforming Design and Time Allocation for Wireless Powered Communication Networks

This paper investigates a multi-input single-output (MISO) wireless powered communication network (WPCN) under the protocol of harvest-then-transmit. The power station (PS) with reliable power supply first replenishes the passive user nodes by radio-frequency wireless power transfer (WPT) in the downlink, then each user node transmits independent information to the sink by a time division multiple access (TDMA) scheme in the uplink. We consider the joint time allocation and beamforming design to maximize the system sum-throughput. With perfect channel station information (CSI) at the PS, a semi-closed form solution is proposed by exploiting the strict concavity of the joint design problem. Then, in the case with Gaussian CSI errors, a robust algorithm is proposed to maximize the system throughput subject to the signal-to-noise ratio (SNR) outage probability constraints. Simulation results demonstrate the efficiency of the proposed fast algorithm and validate the robust algorithm.
Static and dynamic heterogeneities in water

The thermodynamic behaviour of water seems to be related to static heterogeneities. These static heterogeneities are related to the local structure of water molecules and, when properly characterized, may offer an economical explanation of thermodynamic data. ‘What matters’ most in determining some of the unusual properties of liquid water may be the fact that the local geometry of the liquid molecules is not spherical or oblong, but rather tetrahedral. In respect to static heterogeneities, this local geometry is critical. The dynamic behaviour of water seems to be related to dynamic heterogeneities, which seem to explain the dynamics of supercooled liquid water well.
Identifying time-varying neuromuscular system with a recursive least-squares algorithm: a Monte-Carlo simulation study

A human-centered design of haptic aids aims at tuning the force feedback based on the effect it has on human behavior. For this goal, a better understanding of the influence of haptic aids on the pilot neuromuscular response becomes crucial. In realistic scenarios, the neuromuscular response can continuously vary depending on many factors, such as environmental factors or pilot fatigue. This paper presents a method that online estimates time-varying neuromuscular dynamics during force-related tasks. This method is based on a Recursive Least Squares (RLS) algorithm and assumes that the neuromuscular response can be approximated by a Finite Impulse Response filter. The reliability and the robustness of the method were investigated by performing a set of Monte-Carlo simulations with increasing level or remnant noise. Even with high level of remnant noise, the RLS algorithm provided accurate estimates when the neuromuscular dynamics were constant or changed slowly. With instantaneous changes, the RLS algorithm needed almost 8s to converge to a reliable estimate. These results seem to indicate that RLS algorithm is a valid tool for estimating online time-varying admittance.
UNIpedia: A Unified Ontological Knowledge Platform for Semantic Content Tagging and Search

The emergence of an ever increasing number of documents makes it more and more difficult to locate them when desired. An approach for improving search results is to make use of user-generated tags. This approach has led to improvements. However, they are limited because tags are (1) free from context and form, (2) user generated, (3) used for purposes other than description, and (4) often ambiguous. As a formal, declarative knowledge representation model, Ontologies provide a foundation upon which machine understandable knowledge can be obtained and tagged, and as a result, it makes semantic tagging and search possible. With an ontology, semantic web technologies can be utilized to automatically generate semantic tags. WordNet has been used for this purpose. However, this approach falls short in tagging documents that refer to new concepts and instances. To address this challenge, we present UNIpedia - a platform for unifying different ontological knowledge bases by reconciling their instances as WordNet concepts. Our mapping algorithms use rule based heuristics extracted from ontological and statistical features of concept and instances. UNIpedia is used to semantically tag contemporary documents. For this purpose, the Wikipedia and Open Cyc knowledge bases, which are known to contain up to date instances and reliable metadata about them, are selected. Experiments show that the accuracy of the mapping between WordNet and Wikipedia is 84% for the most relevant concept name and 90% for the appropriate sense.
An Improved Structural EM to Learn Dynamic Bayesian Nets

This paper addresses the problem of learning structure of Bayesian and Dynamic Bayesian networks from incomplete data based on the Bayesian Information Criterion. We describe a procedure to map the problem of the dynamic case into a corresponding augmented Bayesian network through the use of structural constraints. Because the algorithm is exact and anytime, it is well suitable for a structural Expectation--Maximization (EM) method where the only source of approximation is due to the EM itself. We show empirically that the use a global maximizer inside the structural EM is computationally feasible and leads to more accurate models.
Geometric Signal Processing on Polygonal Meshes

Very large polygonal models, which are used in more and more graphics applications today, are routinely generated by a variety of methods such as surface reconstruction algorithms from 3D scanned data, isosurface construction algorithms from volumetric data, and photogrametric methods from aerial photography. In this report we provide an overview of several closely related methods developed during the last few yers, to smooth, denoise, edit, compress, transmit, and animate very large polygonal models.
Optimal Distributed Control of Reactive Power Via the Alternating Direction Method of Multipliers

We formulate the control of reactive power generation by photovoltaic inverters in a power distribution circuit as a constrained optimization that aims to minimize power losses subject to finite inverter capacity and upper and lower voltage limits at all nodes in the circuit. When voltage variations along the circuit are small and losses of both real and reactive powers are small compared with the respective flows, the resulting optimization problem is convex. Moreover, the cost function is separable enabling a distributed online implementation with node-local computations using only local measurements augmented with limited information from the neighboring nodes communicated over cyber channels. Such an approach lies between the fully centralized and local policy approaches previously considered. We explore protocols based on the dual-ascent method and on the alternating direction method of multipliers (ADMMs), and find that the ADMM protocol performs significantly better.
Structural Disorder Provides Increased Adaptability for Vesicle Trafficking Pathways

Vesicle trafficking systems play essential roles in the communication between the organelles of eukaryotic cells and also between cells and their environment. Endocytosis and the late secretory route are mediated by clathrin-coated vesicles, while the COat Protein I and II (COPI and COPII) routes stand for the bidirectional traffic between the ER and the Golgi apparatus. Despite similar fundamental organizations, the molecular machinery, functions, and evolutionary characteristics of the three systems are very different. In this work, we compiled the basic functional protein groups of the three main routes for human and yeast and analyzed them from the structural disorder perspective. We found similar overall disorder content in yeast and human proteins, confirming the well-conserved nature of these systems. Most functional groups contain highly disordered proteins, supporting the general importance of structural disorder in these routes, although some of them seem to heavily rely on disorder, while others do not. Interestingly, the clathrin system is significantly more disordered (∼23%) than the other two, COPI (∼9%) and COPII (∼8%). We show that this structural phenomenon enhances the inherent plasticity and increased evolutionary adaptability of the clathrin system, which distinguishes it from the other two routes. Since multi-functionality (moonlighting) is indicative of both plasticity and adaptability, we studied its prevalence in vesicle trafficking proteins and correlated it with structural disorder. Clathrin adaptors have the highest capability for moonlighting while also comprising the most highly disordered members. The ability to acquire tissue specific functions was also used to approach adaptability: clathrin route genes have the most tissue specific exons encoding for protein segments enriched in structural disorder and interaction sites. Overall, our results confirm the general importance of structural disorder in vesicle trafficking and suggest major roles for this structural property in shaping the differences of evolutionary adaptability in the three routes.
Bimanual Elbow Robotic Orthoses: Preliminary Investigations on an Impairment Force-Feedback Rehabilitation Method

Modern rehabilitation practices have begun integrating robots, recognizing their significant role in recovery. New and alternative stroke rehabilitation treatments are essential to enhance efficacy and mitigate associated health costs. Today’s robotic interventions can play a significant role in advancing rehabilitation. In addition, robots have an inherent ability to perform tasks accurately and reliably and are typically well suited to measure and quantify performance. Most rehabilitation strategies predominantly target activation of the paretic arm. However, bimanual upper-limb rehabilitation research suggests potential in enhancing functional recovery. Moreover, studies suggest that limb coordination and synchronization can improve treatment efficacy. In this preliminary study, we aimed to investigate and validate our user-driven bimanual system in a reduced intensity rehab practice. A bimanual wearable robotic device (BWRD) with a Master–Slave configuration for the elbow joint was developed to carry out the investigation. The BWRD incorporates position and force sensors for which respective control loops are implemented, and offers varying modes of operation ranging from passive to active training. The proposed system enables the perception of the movements, as well as the forces applied by the hemiparetic arm, with the non-hemiparetic arm. Eight participants with chronic unilateral stroke were recruited to participate in a total of three 1-h sessions per participant, delivered in a week. Participants underwent pre- and post-training functional assessments along with proprioceptive measures. The post-assessment was performed at the end of the last training session. The protocol was designed to engage the user in an assortment of static and dynamic arm matching and opposing tasks. The training incorporates force-feedback movements, force-feedback positioning, and force matching tasks with same and opposite direction movements. We are able to suggest identification of impairment patterns in the position-force plot results. In addition, we performed a proprioception evaluation with the system. We set out to design innovative and user immersive training tasks that utilize the BWRD capabilities, and we demonstrate that the subjects were able to cooperate and accomplish the protocol. We found that the Fugl–Meyer and Wolf Motor Function Test (pre to post) measured improvements (15 and 19%, respectively). Recognizing the brevity of the training, we focus our report primarily on the proprioception testing (32% significant improvement, pprop = 0.033) and protocol distinctive features and results. This paper presents the electromechanical features and performance of the BWRD, the testing protocol, and the assessments utilized. Outcome measures and results are presented and demonstrate the successful application and operation of the system.
Occurrence and determinants of selective reporting of clinical drug trials: design of an inception cohort study

Introduction Responsible conduct of research implies that results of clinical trials should be completely and adequately reported. This article describes the design of a cohort study that aims to investigate the occurrence and the determinants of selective reporting in an inception cohort of all clinical drug trials that were reviewed by the Dutch Institutional Review Boards (IRBs) in 2007. It also describes the characteristics of the study cohort. Methods and analysis In 2007, Dutch IRBs reviewed 622 clinical drug trials. For each trial, we assessed the stages of progress. We discriminated five intermediate stages and five definite stages. Intermediate stages of progress are: approved by an IRB; started inclusion; completed as planned; terminated early; published as article. The definite stages of progress are: rejected by an IRB; never started inclusion; not published as article; completely reported; selectively reported. We will use univariate and multivariate Cox regression models to identify trial characteristics associated with non-publication. We will identify seven trial-specific discrepancy items, including the objectives, inclusion and exclusion criteria, end points, sample size, additional analyses, type of population analysis and sponsor acknowledgement. The percentage of trials with discrepancies between the protocol and the publication will be scored. We will investigate the association between trial characteristics and the occurrence of discrepancies. Ethics and dissemination No IRB-approval is required for this study. Access to confidential research protocols was provided by the Central Committee on Research Involving Human Subjects. We plan to finish data collection in June 2015, and expect to complete data cleaning, analysis and manuscript preparation within the next 3 months. Hence, a first draft of an article containing the results is expected before the end of October 2015.
Relationship between nitrogen-fixing sulfate reducers and fermenters in salt marsh sediments and roots of Spartina alterniflora

A combination of inhibitors and carbon substrates was used to determine the relative contribution of sulfate-reducing bacteria (SRB) and fermenting bacteria to nitrogen fixation in a salt marsh sediment and on the roots of Spartina alterniflora. Because a lag period precedes acetylene-reducing activity (ARA) in amended sediments, an extensive analysis was done to be sure that this activity was due to the activation of dormant cells, not simply to cell proliferation. Since ARA was not affected by metabolic inhibitors such as rifampin, nalidixic acid, or methionine sulfoximine, it appeared that cell growth was not responsible for this activity. Instead, dormant cells were being activated by the added energy source. Molybdate inhibition studies with glucose-amended sediment slurries indicated that ARA in the upper 5 cm of the salt marsh was due primarily (70%) to SRB and that below that level (5 to 10 cm) it was due primarily (greater than 90%) to fermenting bacteria. ARA associated with washed roots of intact S. alterniflora plants was not inhibited by molybdate, which indicates that bacteria other than SRB were responsible. However, when the roots were excised from the plant, the activity (per unit of root mass) was 10-fold higher and was severely inhibited by molybdate. While this high activity is probably an artifact, due to the release of oxidizable substrates from the excised roots, it indicates that SRB are present in high numbers on Spartina roots.
Space–Time Coding Techniques With Bit-Interleaved Coded Modulations for MIMO Block-Fading Channels

The space-time bit-interleaved coded modulation (ST-BICM) is an efficient technique to obtain high diversity and coding gain on a block-fading multiple-input multiple-output (MIMO) channel. Its maximum-likelihood (ML) performance is computed under ideal interleaving conditions, which enables a global optimization taking into account channel coding. Thanks to a diversity upper bound derived from the Singleton bound, an appropriate choice of the time dimension of the space-time coding is possible, which maximizes diversity while minimizing complexity. Based on the analysis, an optimized interleaver and a set of linear precoders, called dispersive nucleo algebraic (DNA) precoders are proposed. The proposed precoders have good performance with respect to the state of the art and exist for any number of transmit antennas and any time dimension. With turbo codes, they exhibit a frame error rate which does not increase with frame length.
Pyk2 and FAK differentially regulate progression of the cell cycle.

We have previously identified FAK and its associated signaling pathways as a mediator of cell cycle progression by integrins. In this report, we have analyzed the potential role and mechanism of Pyk2, a tyrosine kinase closely related to FAK, in cell cycle regulation by using tetracycline-regulated expression system as well as chimeric molecules. We have found that induction of Pyk2 inhibited G(1) to S phase transition whereas comparable induction of FAK expression accelerated it. Furthermore, expression of a chimeric protein containing Pyk2 N-terminal and kinase domain and FAK C-terminal domain (PFhy1) increased cell cycle progression as FAK. Conversely, the complementary chimeric molecule containing FAK N-terminal and kinase domain and Pyk2 C-terminal domain (FPhy2) inhibited cell cycle progression to an even greater extent than Pyk2. Biochemical analyses indicated that Pyk2 and FPhy2 stimulated JNK activation whereas FAK or PFhy1 had little effect on it, suggesting that differential activation of JNK by Pyk2 may contribute to its inhibition of cell cycle progression. In addition, Pyk2 and FPhy2 to a greater extent also inhibited Erk activation in cell adhesion whereas FAK and PFhy1 stimulated it, suggesting a role for Erk activation in mediating differential regulation of cell cycle by Pyk2 and FAK. A role for Erk and JNK pathways in mediating the cell cycle regulation by FAK and Pyk2 was also confirmed by using chemical inhibitors for these pathways. Finally, we showed that while FAK and PFhy1 were present in focal contacts, Pyk2 and FPhy2 were localized in the cytoplasm. Interestingly, both Pyk2 and FPhy2 (to a greater extent) were tyrosine phosphorylated and associated with Src and Fyn. This suggested that they may inhibit Erk activation in an analogous manner as the mislocalized FAK mutant (&Dgr;)C14 described previously by competing with endogenous FAK for binding signaling molecules such as Src and Fyn. This model is further supported by an inhibition of endogenous FAK association with active Src by Pyk2 and FPhy2 and a partial rescue by FAK of Pyk2-mediated cell cycle inhibition.