Miracle-dz/UniFAR-FTUs huggingface dataset:
Hiring the experts: best practices for community-engaged research

Community-engaged approaches to research and practice continue to show success in addressing health equity and making long-term change for partnership relationships and structures of power. The usefulness of these approaches is either diminished or bolstered by community trust, which can be challenging for partnerships to achieve. In this research note we present an example process for recruiting, interviewing, and hiring community researchers as a starting place for capacity building and for laying the foundation for data collection and analysis in health-related community projects.
GENETIC DRIFT AND FOUNDER EFFECT IN NATIVE VERSUS INTRODUCED POPULATIONS OF AN INVADING PLANT, LYTHRUM SALICARIA (LYTHRACEAE)

There are few convincing examples of genetic drift at loci under selection in natural populations. The plant sexual polymorphism tristyly provides an opportunity to investigate genetic drift because stochastic processes interacting with frequency‐dependent selection give rise to a diagnostic pattern of morph‐frequency variation. A previous study of 102 Ontario populations of the introduced tristylous wetland herb Lythrum salicaria provided evidence for the role of stochastic processes during colonization. However, whether stochastic effects are greater in these recently introduced populations compared to native Eurasian populations remains unclear. The propensity of this species to invade disturbed habitats suggests that episodes of colonization and periods of small population size must also occur in the native range. A survey of 102 populations in southwestern France indicated reduced stochastic effects in native populations. Populations exhibited significantly lower morph loss than in Ontario (5% vs. 23%) and significantly higher values of morph evenness. The greater incidence of trimorphism in French populations was not associated with larger population sizes; populations were significantly smaller than those in Ontario (means: 266 vs. 487). Morph evenness was positively correlated with population size among French but not Ontario populations, providing further evidence of nonequilibrium conditions in introduced compared to native populations. The incidence of trimorphism was unexpectedly high in small native populations (N ≤ 25; 22 of 27 populations trimorphic). Computer simulations indicated that levels of gene flow on the order of m ≥ 0.05 can account for the maintenance of tristyly in small populations. The high connectivity of populations within the agricultural landscape typical of southwestern France may facilitate levels of gene flow sufficient to maintain trimorphism in small populations.
An Efficient Recovery Algorithm for Coverage Hole in WSNs †

Failures are inevitable in wireless sensor networks, and it is important to detect and patch the “coverage hole”. In this paper, we propose an efficient recovery algorithm based on minimum distance redundant nodes. By numerical algorithm, the sink node gets the centre of the “coverage hole”, and then wakes up a redundant node, which has the minimum distance to the centre, to recover the hole. Simulation results demonstrate that, by choosing appropriate number of redundant nodes, this algorithm will have great recovery accuracy and coverage quality, also achieve the purpose of prolonging the lifecycle of WSNs.
Proteomic analysis of ampicillin-resistant oral Fusobacterium nucleatum.

INTRODUCTION Fusobacterium nucleatum represents one of the predominant anaerobic species in the oral microbiota. Penicillin-resistant F. nucleatum have been isolated from intra- and extraoral infections. This study aimed to assess ampicillin resistance in F. nucleatum by investigating the synthesis of resistance-associated proteins. METHODS Ampicillin-resistant and ampicillin-susceptible F. nucleatum isolates were obtained from 22 dental plaque samples. Two-dimensional gel electrophoresis and mass spectrometry were used to investigate bacterial protein synthesis. Proteins exhibiting statistically significant quantitative changes between sensitive and resistant isolates were identified using peptide mass mapping and matrix-assisted laser desorption/ionization - time of flight/time of flight (MALDI-TOF/TOF) mass spectrometry. RESULTS Twenty-three F. nucleatum isolates were recovered from plaque samples and their ampicillin minimum inhibitory concentrations ranged between 0.125 microg/ml and 256 microg/ml. Analysis of the bacterial cellular proteins by two-dimensional gel electrophoresis resolved 154-246 distinct protein spots (mean 212, n = 9). Between 32% and 83% of the protein spots were common for the F. nucleatum isolates. Comparisons of the protein profiles of sensitive and resistant isolates revealed the presence of a 29 kDa protein and significant increases in the synthesis of two proteins at 37 and 46 kDa in the ampicillin-resistant F. nucleatum isolates. These proteins were identified as a class D beta-lactamase, ATP-binding cassette (ABC) transporter ATP-binding protein and enolase, respectively. CONCLUSION Synthesis of a class D beta-lactamase by ampicillin-resistant F. nucleatum isolates could complicate antimicrobial treatment because these enzymes might confer resistance to many classes of beta-lactam antibiotics. The differences observed in protein synthesis between ampicillin-resistant and ampicillin-susceptible F. nucleatum may contribute to the antibiotic resistance and virulence of these bacteria.
Using preformed nitrate to infer decadal changes in DOM remineralization in the subtropical North Pacific

The preformed nitrate distribution throughout the subtropical North Pacific is characterized by a negative anomaly between 100 m and the 25.4 σθ surface. Its presence indicates that nitrogen remineralization in the upper thermocline deviates significantly from Redfield stoichiometry. It has been previously suggested that this feature is created during the degradation of nitrogen‐poor dissolved organic matter (DOM) ( Emerson and Hayward, 1995 ). Here we present evidence from two transects in the eastern subtropical North Pacific that degradation of DOM with a high C:N ratio is quantitatively responsible for negative preformed nitrate. We develop a simple isopycnal mass balance to determine preformed nitrate using apparent oxygen utilization (AOU), dissolved organic carbon (DOC), and dissolved organic nitrogen (DON) data. These results agree well with the traditional preformed nitrate calculation and indicate that the intensity of the anomaly is proportional to the magnitude of DOM remineralization and its C:N remineralization ratio. An analysis of preformed nitrate distributions in the eastern subtropical North Pacific between 1980 and 1997 reveals a significant increase in the negative anomaly. While a portion of this change may be attributable to a reduction in ventilation of the gyre, the majority of the signal is due to an increase in the magnitude and/or C:N ratio of DOM remineralization. This conclusion supports recent hypotheses that DOM production and cycling may have increased in this region in the past 2 decades as a result of changes in the phytoplankton community structure.
The Impact of Short-Term Video Games on Performance among Children with Developmental Delays: A Randomized Controlled Trial

This prospective, randomized controlled study investigated the effects of short-term interactive video game playing among children with developmental delays participating in traditional rehabilitation treatment at a rehabilitation clinic. One hundred and one boys and 46 girls with a mean age of 5.8 years (range: 3 to 12 years) were enrolled in this study. All patients were confirmed to suffer from developmental delays, and were participating in traditional rehabilitation treatment. Children participated in two periods of 4 weeks each, group A being offered intervention of eight 30-minute sessions of interactive video games in the first period, and group B in the second, in addition to the traditional rehabilitation treatment. The physical, psychosocial, and total health of the children was periodically assessed using the parent-reported Pediatric Quality of Life Inventory-Generic Core Scales (PedsQL); and the children’s upper extremity and physical function, transfer and basic mobility, sports and physical functioning, and global functioning were assessed using the Pediatric Outcomes Data Collection Instrument. Parental impact was evaluated using the PedsQL-Family Impact Module for family function, PedsQL-Health Satisfaction questionnaire for parents’ satisfaction with their children’s care and World Health Organization-Quality of Life-Brief Version for quality of life. Compared with the baseline, significant improvements of physical function were observed in both groups (5.6 ± 19.5, p = 0.013; 4.7 ± 13.8, p = 0.009) during the intervention periods. No significant improvement of psychosocial health, functional performance, or family impact was observed in children with developmental delays. Short-term interactive video game play in conjunction with traditional rehabilitation treatment improved the physical health of children with developmental delays. Trial Registration: ClinicalTrials.gov NCT02184715
Amplification of ultrafast-rotating ring-shaped optical lattices

A superposition of two optical vortices with different topological charges forms a light wave with azimuthally periodic structure. The beam with such rotational symmetry is called a ring-shaped optical lattice [1]. One of its important features is that it can be flexibly rotated by controlling relative phase difference between them without changing its structure, which offers us rotational degree of freedom in applications such as optical manipulation of micro-or nano-particles. Conventionally, the rotational control has been realized by utilizing mechanical rotation of waveplates, acousto-optic devices or electro-optic modulators. However, their maximum rotational frequency has been limited to GHz regime owing to their response time or bandwidth.
Detecting pauses in continuous sign language

Sign language (SL) segmentation breaks a continuous SL sentence into its basic lexical units by detecting word boundaries. In Speech signal, silence period between two words are detected for a reliable speech parsing. Similarly, for robust SL recognition, majority of direct segmentation approaches exploit these inter-sign pauses in a stream of hand gestures to demarcate the word boundaries. The delayed absolute difference (DAD) signature of the hand positions provides means for analyzing the segmentation features like pauses, repetitions and directional variations in unique tool. In this paper, a novel scheme for detecting pause features is presented.
Preclinical Development Triggering Fbw 7-Mediated Proteasomal Degradation of c-Myc by Oridonin Induces Cell Growth Inhibition and Apoptosis

The transcription factor c-Myc is important in cell fate decisions and is frequently overexpressed in cancer cells, making it an attractive therapeutic target. Natural compounds are among the current strategies aimed at targeting c-Myc, but theirmodes of action still need to be characterized. To explore themechanismsunderlying the anticancer activity of a natural diterpenoid, oridonin, we conducted miRNA expression profiling and statistical analyses that strongly suggested that c-Myc was a potential molecular target of oridonin. Furthermore, experimental data showed that oridonin significantly reduced c-Myc protein levels in vitro and in vivo and that this reductionwasmediatedby theubiquitin-proteasome system. Fbw7, a component of theubiquitinproteasome system and an E3 ubiquitin ligase of c-Myc, was upregulated rapidly in K562 cells and other leukemia and lymphoma cells, resulting in the rapid turnover of c-Myc. In cell lines harboringmutations in the WD domain of Fbw7, the degradation of c-Myc induced by oridonin was attenuated during short-term treatment. GSK-3, an Fbw7 priming kinase, was also activated by oridonin, along with an increase in T58phosphorylated c-Myc. Furthermore, the knockdownof Fbw7 or the forced expression of stable c-Myc resulted in reduced sensitization to oridonin-induced apoptosis. Our observations help to clarify the anticancer mechanisms of oridonin and shed light on the application of this natural compound as an Fbw7-c-Myc pathway targeting agent in cancer treatment. Mol Cancer Ther; 11(5); 1155–65. 2012 AACR.
Cardiovascular effects of the nitric oxide synthase inhibitor NG-methyl-l-arginine hydrochloride (546C88) in patients with septic shock: Results of a randomized, double-blind, placebo-controlled multicenter study (study no. 144-002)*

ObjectiveTo assess the hemodynamic effects of the nitric oxide synthase inhibitor 546C88 in patients with septic shock, although this was not a stated aim of the protocol. The predefined primary efficacy objective of the protocol was resolution of shock determined at the end of a 72-hr treatment period. DesignMulticentered, randomized, placebo-controlled, safety and efficacy study. SettingForty-eight intensive care units in Europe, North America, and Australia. PatientsA total of 312 patients with septic shock diagnosed within 24 hr before randomization. InterventionsPatients were randomly allocated to receive either 546C88 or placebo (5% dextrose) by intravenous infusion for up to 72 hrs. Conventional vasoactive therapy was restricted to norepinephrine, dopamine, and dobutamine. Study drug was initiated at 0.1 mL/kg/hr (5 mg/kg/hr 546C88) and titrated according to response up to a maximum rate of 0.4 mL/kg/hr with the objective to maintain mean arterial pressure at 70 mm Hg while attempting to withdraw any concurrent vasopressor(s). Measurements and Main ResultsRequirement for vasopressors, systemic and pulmonary hemodynamics, indices of oxygen transport, and plasma concentrations of arginine and nitrate were assessed over time. The median mean arterial pressure for both groups was maintained ≥70 mm Hg. There was an early increase in systemic and pulmonary vascular tone and oxygen extraction, whereas both cardiac index and oxygen delivery decreased for patients in the 546C88 cohort. Although these parameters subsequently returned toward baseline values, the observed differences between the treatment groups, except for pulmonary vascular resistance and oxygen extraction, persisted throughout the treatment period, despite a reduced requirement for vasopressors in the 546C88 cohort. These changes were associated with a reduction in plasma nitrate concentrations, which were elevated in both groups before the start of therapy. ConclusionsThe nitric oxide synthase inhibitor 546C88 can reduce the elevated plasma nitrate concentrations observed in patients with septic shock. In this study, treatment with 546C88 for up to 72 hrs was associated with an increase in vascular tone and a reduction in both cardiac index and oxygen delivery. The successful maintenance of a target mean arterial blood pressure ≥70 mm Hg was achieved with a reduction in the requirement for, or withdrawal of, conventional inotropic vasoconstrictor agents (i.e., dopamine and norepinephrine). There were no substantive untoward consequences accompanying these hemodynamic effects. An international, randomized, double-blind, placebo-controlled phase III study has since been conducted in patients with septic shock. Recruitment into the study was discontinued due to the emergence of increased mortality in the 546C88-treated group.
Correction of Intensity Incidence Angle Effect in Terrestrial Laser Scanning

Abstract. In this article, we have studied the incidence angle effect on Terrestrial Laser Scanning (TLS) intensity. In previous tests, it has been found that the backscattered intensity of an object affects the incidence angle effect. We made additional experiments to investigate the potential mixing of distance and incidence angle effects and the role of surface parameters such as object grain size and scanning wavelength. The results indicate that distance and incidence angle effects do not mix and laboratory measured correction values can be used to correct intensity data from field-scanned point clouds. We also compared the laboratory measurements to real world surfaces to validate the correction procedures in practical TLS applications. The idea is also to make practical recommendations for TLS intensity correction in most common TLS applications.
A Novel Varying-Bias Read Scheme for MLC and Wide Temperature Range TMO ReRAM

Resistance of transition metal oxide (TMO) resistive random access memory (ReRAM) depends sharply on temperature, resulting in drastic memory window loss at high temperature. Thus, it is difficult to design the ReRAM that can serve a wide range of operating conditions. It is especially challenging to achieve multi-level-cell (MLC) ReRAM because of the large temperature dependency. This letter investigates both the temperature and read bias dependencies of WOx ReRAM, and found both can be well understood by a modified space-charge limited conduction model. Using this model, we have designed a novel read scheme that varies the read bias according to the device temperature and compensates for the temperature effect on cell resistance. Since TMO ReRAM devices depend on defect states, cell-to-cell and cycle-to-cycle variations are naturally large. An algorithm is designed to address the variability. A 1-Mb WOx ReRAM array is fabricated to both characterize the bias and temperature dependencies and verify the new read scheme. A large and constant memory window is preserved for MLC across a wide temperature range (-40 °C-125 °C), suitable for high-reliability applications.
Pain Correlates with Sleep Disturbances in Parkinson's Disease Patients

Both sleep disorders and pain decrease quality of life in patients with Parkinson's disease (PD). However, little is known about the relationship between objective sleep disturbances and pain in patients with PD. This study aimed to (1) examine the clinical characteristics of pain in PD patients and (2) explore the correlation between pain and sleep disturbances in PD patients.
Perspectives in Magnetic Resonance Probing membrane protein structure using water polarization transfer solid-state NMR

Water plays an essential role in the structure and function of proteins, lipid membranes and other biological macromolecules. Solid-state NMR heteronuclear-detected H polarization transfer from water to biomolecules is a versatile approach for studying water–protein, water–membrane, and water–carbohydrate interactions in biology. We review radiofrequency pulse sequences for measuring water polarization transfer to biomolecules, the mechanisms of polarization transfer, and the application of this method to various biological systems. Three polarization transfer mechanisms, chemical exchange, spin diffusion and NOE, manifest themselves at different temperatures, magic-angle-spinning frequencies, and pulse irradiations. Chemical exchange is ubiquitous in all systems examined so far, and spin diffusion plays the key role in polarization transfer within the macromolecule. Tightly bound water molecules with long residence times are rare in proteins at ambient temperature. The water polarization-transfer technique has been used to study the hydration of microcrystalline proteins, lipid membranes, and plant cell wall polysaccharides, and to derive atomic-resolution details of the kinetics and mechanism of ion conduction in channels and pumps. Using this approach, we have measured the water polarization transfer to the transmembrane domain of the influenza M2 protein to obtain information on the structure of this tetrameric proton channel. At short mixing times, the polarization transfer rates are site-specific and depend on the pH, labile protons, sidechain conformation, as well as the radial position of the residues in this four-helix bundle. Despite the multiple dependences, the initial transfer rates reflect the periodic nature of the residue positions from the water-filled pore, thus this technique provides a way of gleaning secondary structure information, helix tilt angle, and the oligomeric structure of membrane proteins. 2014 Elsevier Inc. All rights reserved.
Multi-functional Interconnect Co-optimization for Fast and Reliable 3 D Stacked

Heat removal and power delivery have become two major reliability concerns in 3D stacked IC technology. For thermal problem, two possible solutions exist: thermal-through-silicon-vias (TTSVs) and micro-fluidic channel (MFC) based liquid cooling. In case of power delivery, a highly complex power distribution network is required to deliver currents reliably to all parts of the 3D stacked IC while suppressing the power supply noise to an acceptable level. However, these thermal and power networks pose major challenges in signal routability and congestion. This is because the signal, power, and thermal interconnects are all competing for routing space. In this paper, we present a co-optimization methodology for the signal, power, and thermal interconnects for 3D stacked ICs based on design of experiments (DOE) and response surface method (RSM). The goal is to improve performance, thermal, noise, and congestion metrics with our holistic approach. We also provide in-depth comparison between T-TSV and MFC based cooling method and discuss how to employ DOE and RSM to best co-optimize the multi-functional interconnects simultaneously.
Mining Evolutionary Data to Reveal the Layered Architecture of Protein Function

Revolutionary advances in sequencing technology have dramatically expanded the set of known, naturallyoccurring protein sequences. Protein sequences arise from an evolutionary process and during evolution proteins experience pressure to maintain and diversity their functions via mutation. Some mutations arise merely from neutral drift, but other changes enable organisms to adapt to their unique niche. Positions that are important for structure or function are expected to be mutationally constrained during evolution. To that end, many algorithms have been devised to identify mutational constraints in the evolutionary record in order to predict the location of functionally important sites. Accurate prediction of functionally important positions would have important practical implications. For example, individual humans each carry about 10,000 exomic sequence polymorphisms. Which of these are functionally and/or clinically significant? Similarly, protein engineers may target such sites for mutagenesis to derive variant functions. To detect these constraints, homologous proteins must first be sorted into protein families, based on sequence similarity, which typically indicates structural and functional similarity. Protein family multiple sequence alignments (MSAs) can then be computationally analyzed to understand the family in light of its evolutionary history. MSA analyses have detect various evolutionary patterns that are thought to confer functional significance. For example, positions that are absolutely conserved across a family are commonly inferred to play important structural or functional roles and, consequently, be intolerant to mutation. Other analyses attempt to identify important non-conserved positions, some of which must be functionally significant for the family to evolve functional variations. One important example is “co-evolutionary” analyses, which seek pairs of positions that vary in a coordinated manner across evolution. MSA analyses make a number of simplifying assumptions to abstract away the full complexity of real proteins. Here, we have (1) assessed the validity of some of these assumptions, and (2) investigated strategies to maximize the usefulness of existing tools in identifying functionally important positions, in light of their limitations, and (3) evaluated the ability of existing tools to identify known-significant positions. To that end, we have applied MSA analyses to the LacI/GalR bacterial transcription regulator family as our primary model system. Our studies have proceeded in three phases.