Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of the catalytic sites of a papain-like cysteine proteinase of murine coronavirus

The murine coronavirus mouse hepatitis virus gene 1 is expressed as a polyprotein, which is cleaved into multiple proteins posttranslationally. One of the proteins is p28, which represents the amino-terminal portion of the polyprotein and is presumably generated by the activity of an autoproteinase domain of the polyprotein (S. C. Baker, C. K. Shieh, L. H. Soe, M.-F. Chang, D. M. Vannier, and M. M. C. Lai, J. Virol. 63:3693-3699, 1989). In this study, the boundaries and the critical amino acid residues of this putative proteinase domain were characterized by deletion analysis and site-directed mutagenesis. Proteinase activity was monitored by examining the generation of p28 during in vitro translation in rabbit reticulocyte lysates. Deletion analysis defined the proteinase domain to be within the sequences encoded from the 3.6- to 4.4-kb region from the 5' end of the genome. A 0.7-kb region between the substrate (p28) and proteinase domain could be deleted without affecting the proteolytic cleavage. However, a larger deletion (1.6 kb) resulted in the loss of proteinase activity, suggesting the importance of spacing sequences between proteinase and substrate. Computer-assisted analysis of the amino acid sequence of the proteinase domain identified potential catalytic cysteine and histidine residues in a stretch of sequence distantly related to papain-like cysteine proteinases. The role of these putative catalytic residues in the proteinase activity was studied by site-specific mutagenesis. Mutations of Cys-1137 or His-1288 led to a complete loss of proteinase activity, implicating these residues as essential for the catalytic activity. In contrast, most mutations of His-1317 or Cys-1172 had no or only minor effects on proteinase activity. This study establishes that mouse hepatitis virus gene 1 encodes a proteinase domain, in the region from 3.6 to 4.4 kb from the 5' end of the genome, which resembles members of the papain family of cysteine proteinases and that this proteinase domain is responsible for the cleavage of the N-terminal peptide.
Response of Planar and Cylindrical Ion Counters to a Corona Ion Source

Because of the environmental and economic applications of small air ions near HVDC power lines, it is desirable to have accurate and reliable ion counters. A parallel-screen small air ion source using corona discharge was constructed for evaluating two aspiration ion counters in the range 5000 to 1,000,000 cm with positive and negative ions. A planar electrode ion counter and a cylindrical electrode ion counter were exposed to the ion source. Comparisons were made between predicted theoretical ion densities and those measured by two instruments. For a theoretical ion density of 10000 cm/sup -3/ and a calibration-region spacing of 10 cm, both ion counters measured ion concentrations up to two times larger than the theoretical ion concentration in the calibration region. With the same theoretical ion density but with a calibration-region spacing of 30 cm, the planar ion counter measured within about 10% of the theoretical ion density. >
Molecular Basis for Nitric Oxide Dynamics and Affinity with Alcaligenes xylosoxidans Cytochrome ć *

The bacterial heme protein cytochrome ć from Alcaligenes xylosoxidans (AXCP) reacts with nitric oxide (NO) to form a 5-coordinate ferrous nitrosyl heme complex. The crystal structure of ferrous nitrosyl AXCP has previously revealed that NO is bound in an unprecedented manner on the proximal side of the heme. To understand how the protein structure of AXCP controls NO dynamics, we performed absorption and Raman time-resolved studies at the heme level as well as a molecular computational dynamics study at the entire protein structure level. We found that after NO dissociation from the heme iron, the structure of the proximal heme pocket of AXCP confines NO close to the iron so that an ultrafast (7 ps) and complete (99 ± 1%) geminate rebinding occurs, whereas the proximal histidine does not rebind to the heme iron on the timescale of NO geminate rebinding. The distal side controls the initial NO binding, whereas the proximal heme pocket controls its release. These dynamic properties allow the trapping of NO within the protein core and represent an extreme behavior observed among heme proteins.
A new labeling approach using stable isotopes to study in vivo plasma cholesterol metabolism in humans.

A method to study reverse cholesterol transport in humans was developed using stable isotopes and kinetic analysis. Three normolipidemic subjects received simultaneous intravenous infusions of deuterated leucine and (13)C-acetate for 14 and 8 hours, respectively. Deuterium enrichment was measured in protein-bound leucine in apolipoproteins (apo) B-100 and A-I (using gas chromatography coupled with mass spectrometry [GCMS]) and (13)C-enrichment in unesterified cholesterol and cholesteryl ester (using gas chromatography coupled to isotope ratio mass spectrometry [GC-C-IRMS]) in very-low-density lipoprotein (VLDL), low-density lipoprotein (LDL), and high-density lipoprotein (HDL) during the tracer infusion. Curves were analyzed using multicompartmental analysis. This protocol is suitable to quantify the different processes involved in reverse cholesterol transport (RCT) in humans, including cholesterol esterification, transfer of cholesteryl ester from HDL towards apo B-100-containing lipoproteins, and the contribution of VLDL, LDL, and HDL in the final steps of RCT. In agreement with previous data from kinetic analysis of radiotracer experiments, our results suggest that in fasting normolipidemic subjects the major fraction of cholesteryl ester enters plasma through esterification in HDL (more than 95%). The major fraction of cholesteryl ester disappears through apo B-100-containing lipoproteins (VLDL and LDL) catabolism (mean of 82%) rather than through removal from HDL (mean of 18% with approximately an equal part for apo AI-dependent and independent catabolism, respectively, 7% and 11%). We conclude that this protocol could be applied to study the modulation of these processes by nutrition, diseases, or pharmacologic treatments.
A jellyfish distribution management system using an unmanned aerial vehicle and unmanned surface vehicles

In this paper, we propose a jellyfish distribution management system using an UAV (unmanned aerial vehicle) and USVs (unmanned surface vehicle). The UAV was designed to satisfy the requirements for flight in ocean environment. The target jellyfish, aurelia aurita, is recognized through a convolution neural network and its distribution is calculated. A high-speed deep neural network architecture has been developed to have reliable recognition accuracy and fast operation speed. We also propose a method for selecting candidates that are inputs to the proposed network. The recognition accuracy of the jellyfish is increased by removing the probability value of the meaningless class among the probability vectors of the evaluated input image and re-evaluating it by normalization. The jellyfish distribution is calculated based on the unit jellyfish image thus recognized. The distribution level is defined by using the novelty concept of the distribution map buffer. The proposed algorithm has a frame rate of 8 Hz or higher without any GPU and a recognition rate of over 90%.
Factors related to diagnostic yield of transbronchial biopsy using endobronchial ultrasonography with a guide sheath in small peripheral pulmonary lesions.

STUDY OBJECTIVES To evaluate factors predicting the diagnostic yield of transbronchial biopsy (TBB) using endobronchial ultrasonography with a guide sheath (EBUS-GS) in small peripheral pulmonary lesions (PPLs) </= 30 mm in mean diameter. DESIGN Retrospective analysis. PATIENTS AND METHODS One hundred fifty-five consecutive patients with 158 small PPLs underwent TBB using EBUS-GS. RESULTS A definitive diagnosis was established by TBB using EBUS-GS in 106 PPLs (67%). The diagnostic yield of PPLs </= 15 mm in mean diameter (40%) was significantly lower than that of PPLs > 15 mm and </= 30 mm in mean diameter (76%; p < 0.001). PPLs in which the probe was positioned within the PPL on the endobronchial ultrasonography (EBUS) image had a higher diagnostic yield (83%) than PPLs in which the probe was positioned adjacent to the PPL (61%) or outside the PPL (4%; p < 0.001). There were no significant differences in diagnostic yield for underlying disease, location, CT scan bronchus sign, operator, or type of EBUS probe. In the multivariate analysis, only the position of the probe (within or adjacent to the PPL when judged against outside the PPL) was determined to be a significant factor predicting diagnostic yield. On the other hand, a pathologic diagnosis was established with the first, second, third, fourth, and fifth biopsy specimens in 65%, 80%, 87%, 91%, and 97% of PPLs, respectively. CONCLUSIONS The position of the probe (ie, within or adjacent to the PPL) is a significant factor in predicting the diagnostic yield of TBB using EBUS-GS for small PPLs; the optimum number of biopsy specimens is at least five.
Changing Patterns of Mental Health Care Use: The Role of Integrated Mental Health Services in Veteran Affairs Primary Care

Objective: Aiming to foster timely, high-quality mental health care for Veterans, VA's Primary Care–Mental Health Integration (PC-MHI) embeds mental health specialists in primary care and promotes care management for depression. PC-MHI and patient-centered medical home providers work together to provide the bulk of mental health care for primary care patients with low-to-moderate-complexity mental health conditions. This study examines whether increasing primary care clinic engagement in PC-MHI services is associated with changes in patient health care utilization and costs. Methods: We performed a retrospective longitudinal cohort study of primary care patients with identified mental health needs in 29 Southern California VA clinics from October 1, 2008 to September 30, 2013, using electronic administrative data (n = 66,638). We calculated clinic PC-MHI engagement as the proportion of patients receiving PC-MHI services among all primary care clinic patients in each year. Capitalizing on variation in PC-MHI engagement across clinics, our multivariable regression models predicted annual patient use of 1) non-primary care based mental health specialty (MHS) visits, 2) total mental health visits (ie, the sum of MHS and PC-MHI visits), and 3) health care utilization and costs. We controlled for year- and clinic-fixed effects, other clinic interventions, and patient characteristics. Results: Median clinic PC-MHI engagement increased by 8.2 percentage points over 5 years. At any given year, patients treated at a clinic with 1 percentage-point higher PC-MHI engagement was associated with 0.5% more total mental health visits (CI, 0.18% to 0.90%; P = .003) and 1.0% fewer MHS visits (CI, −1.6% to −0.3%; P = .002); this is a substitution rate, at the mean, of 1.5 PC-MHI visits for each MHS visit. There was no PC-MHI effect on other health care utilization and costs. Conclusions: As intended, greater clinic engagement in PC-MHI services seems to increase realized accessibility to mental health care for primary care patients, substituting PC-MHI for MHS visits, without increasing acute care use or total costs. Thus, PC-MHI services within primary care clinics may improve mental health care value at the patient population level. More research is needed to understand the relationship between clinic PC-MHI engagement and clinical quality of mental health care.
Meridional Heat Transport Variability at 26.5°N in the North Atlantic

Abstract Data from almost five years of current meter moorings located across the Bahamas Escarpment at 26.5°N are used to investigate meridional heat transport variability in the section and its impact on transatlantic heat flux. Estimates of heat transport derived from the moored arrays are compared to results from the Community Modeling Effort (CME) Atlantic basin model and to historical hydrographic section data. A large fraction of the entire transatlantic heat flux is observed in this western boundary region, due to the opposing warm and cold water flows associated with the Antilles Current in the thermocline and the deep western boundary current at depth. Local heat transport time series derived from the moored arrays exhibit large variability over a range of ± 2 PW relative to 0°C, on timescales of roughly 100 days. An annual cycle of local heat transport with a range of 1.4 PW is observed with a summer maximum and fall minimum, qualitatively similar to CME model results. Breakdown of the total he.
Performance Assessment of Dynamic Spiral Scan Modes With Variable Pitch for Quantitative Perfusion Computed Tomography

Purpose:Perfusion computed tomography is increasingly being used in diagnostic radiology. Axial coverage of the traditional approach is limited to the width of the detector. Using continuous periodic table movement coverage can be increased beyond this limit. In this study, we compared tissue flow values determined from scans with a periodic spiral implementation with variable pitch with ones determined from standard dynamic scan modes. Methods:A flow phantom (preserved porcine kidney) was scanned with 2 settings of a periodic spiral (Adaptive 4D Spiral) with a range of 100 and 148 mm and a temporal sampling of 1.5 seconds. Additionally, the whole phantom was scanned with the standard dynamic mode (detector width 38.4 mm, temporal sampling 1.0 seconds) at various overlapping positions as a reference. Scan parameters (80 kV, 140 mAs, 40s scan time) were selected similar to a typical brain perfusion study. All scans were repeated 5 times. Tissue flow was calculated with a dedicated deconvolution algorithm. In a center slice and 3 additional slices at various off center positions flow values were recorded in a total of 126 regions of interest (ROI). Reproducibility was determined from the variation of the repeat scans. Agreement between periodic spirals and standard mode was determined by Bland Altman plots and correlation analysis. Results:The reproducibility of the tissue flow determination ranged from 2.7 to 4.4 mL/100 mL/min and was similar for all scan modes. The coefficient of variation ranged from 3.9% to 6.1%. Mean tissue flow in the 126 ROIs ranged from 35 to 121 mL/100 mL/min. There was excellent correlation between both periodic spiral ranges and the standard dynamic mode with a Pearson correlation coefficient of r = 0.97. The regression slope (intercept 0) for the 100 mm range was 1.01, for the 148 mm range it was 0.97. The absolute differences per ROI varied between 1.5 and 4.1 mL/100 mL/min, the relative differences between 1.9% and 6.5%. Differences did not depend on the slice location. Conclusions:Periodic spiral scan modes with variable pitch and a sampling rate of 1.5 seconds can be used for the quantitative determination of tissue flow. Their performance is equivalent to equidistant sampling with standard dynamic scan modes. The ranges of 100 and 148 mm investigated allow coverage of the whole brain or an entire organ for perfusion imaging.
A Broadside-Split-Ring Resonator-Based Coil for MRI at 7 T

A coil design termed as broadside-coupled loop (BCL) coil and based on the broadside-coupled split ring resonator (BC-SRR) is proposed as an alternative to a conventional loop design at 7T. The BCL coil has an inherent uniform current which assures the rotational symmetry of the radio-frequency field around the coil axis. A comparative analysis of the signal-to-noise ratio provided by BCL coils and conventional coils has been carried out by means of numerical simulations and experiments in a 7T whole body system.
Wheelchair Users' Perceptions of and Experiences with Power Assist Wheels

Giacobbi PR, Jr, Levy CE, Dietrich FD, Winkler SH, Tillman MD, Chow JW: Wheelchair users' perceptions of and experiences with power assist wheels. Objective:To assess wheelchair users' perceptions of and experiences with power assist wheels using qualitative interview methods. Design:Qualitative evaluations were conducted in a laboratory setting with a focus on users' experiences using power assist wheel in their naturalistic environments. Participants consisted of seven women and 13 men (Mage = 42.75, SD = 14.68) that included one African American, one Hispanic, 17 whites, and one individual from Zambia. Qualitative interviews were conducted before, during, and after use of a power assist wheel. Main outcome measures included the wheelchair users' evaluations and experiences related to the use of power assist wheels. Results:The primary evaluations included wheeling on challenging terrains, performance of novel activities, social/family aspects, fatigue, and pain. These descriptions indicated that most participants perceived positive experiences with the power assist wheels, including access to new and different activities. Secondary evaluations indicated that the unit was cumbersome and prohibitive for some participants because of difficulties with transport in and out of a vehicle and battery life. Most participants felt that power assist wheels provided more independence and social opportunities. Conclusions:The power assist wheel seems to offer physical and social benefits for most wheelers. Clinicians should consider users' home environment and overall life circumstances before prescribing.
Educational Needs as Perceived by IS and End-User Personnel: A Survey of Knowledge and Skill Requirements

One of the fundamental issues inherent to both practice and academia emanates from the need to know what knowledge and skills personnel must possess to successfully perform their jobs. This article addresses this issue by performing an educational needs assessment, one that considers the deficiencies of both IS and end-user personnel. To this end, an instrument has been developed, tested, and completed by 275 employees within eight different organizations. The findings of this study suggest that among six different knowledge and skill areas, both IS and end-user personnel are most deficient in the area of "general IS knowledge" (e.g., IS policies and plans, fit between IS and organization, etc.). In addition, IS personnel appear to be in need of more "organizational knowledge" (e.g., organizational goals and objectives, critical success factors, etc.). End users, on the other hand, seem to require more IS-related skills (e.g., data access, use of software packages, etc.). The implications of these findings for practitioners and academicians focus on finding ways to improve the education and training programs currently in place.
Intrainstitutional EHR collections for patient‐level information retrieval

Research in clinical information retrieval has long been stymied by the lack of open resources. However, both clinical information retrieval research innovation and legitimate privacy concerns can be served by the creation of intrainstitutional, fully protected resources. In this article, we provide some principles and tools for information retrieval resource‐building in the unique problem setting of patient‐level information retrieval, following the tradition of the Cranfield paradigm. We further include an analysis of parallel information retrieval resources at Oregon Health & Science University and Mayo Clinic that were built on these principles.
Chromosomal studies of species of Rubiaceae (A. L. de Jussieu) from the Brazilian cerrado

Abstract – The chromosomes of 14 species belonging to two subfamilies of the family Rubiaceae collected in the Brazilian cerrado were studied. In the subfamily Ixoroideae, five species (Alibertia concolor, A. edulis, A. sessilis, Genipa americana and Tocoyena formosa) had a chromosome number of 2n = 22 and one (Amaioua intermedia) showed polyploidy, with 2n = 66. All of the chromosome numbers were multiples of the more common basic number for this family (x = 11). In the subfamily Rubioideae, variations in the number of chromosomes were observed among tribes and genera, with 2n = 20 in the tribe Coccocypseleae (Coccocypselum lanceolatum), 2n = 28 in Spermacoceae (Borreria latifolia, B. verticillata and Richardia brasiliensis) and n = 11 in Coussareeae (Coussarea hydrangeifolia). In the tribe Psychotrieae, the variations included n = 11 (Palicourea rigida), 2n = 22 (Psychotria hoffmannseggiana) and 2n = 32 (Psychotria deflexa). The ideograms elaborated for 12 species were symmetrical (TF% varied from 47.45 to 38.01). The size of the chromosomes ranged from 1.26 to 7.33 μm and most were metacentric. The results show that chromosome size and morphology were insufficient to differentiate among groups within the Rubiaceae.
Application of related data automatic semantic annotation technology in Internet of things

specific to semi-supervised learning method based on graph ignoring the problem of video correlation in research and application of multimedia, a kind of video annotation algorithm based on related kernel mapping linear neighborhood propagation is put forward. Firstly, the propagation coefficient of the iteration annotation is calculated in the algorithm with the kernel function according to the adjusted distance of semi-supervised learning; secondly, the sample of the low-lever feature space is obtained by using the propagation coefficient; thirdly, the correlation table between the semantic concepts is constructed according to video correlation modeling; finally, the structure of the nearest neighborhood graph is constructed; use the labeled video information to carry out iterative propagation to unlabeled video so as to complete video annotation. Experimental results show that: this algorithm can not only improve the accuracy of video annotation but also can make up for the lack of the number of video data labeled.
A study on WK-recursive topology using gpNoCsim++ simulator and comparison to Other topologies

Network-on-Chip (NoC) was first invented to tackle with the problem of communication in System-on-Chip (SoC). SoC uses a shared bus to communicate between components. All architectures based on a shared bus have some inherent problems as limited scalability and shared bus becoming a bottleneck. NoC offers a scalable architecture and capability of complex topological design. The architecture is inspired from computer networks. Although it is similar to computer networks from routing, switching and topology point of view but consumption of energy and space is too important for NoC. This article studies WK-recursive topology for NoC. The topology is simulated with gnNoCSim++ and performance metrics is compared to Fat Tree, Extended-Butterfly Fat Tree Interconnetion (EFTI), Mesh, Torus and Octagon. The comparison shows strengths and weaknesses of WK-recursive.