Miracle-dz/UniFAR-FTUs huggingface dataset:
Title Diversity and abundance of ammonia-oxidizing prokaryotes in sediments from the coastal Pearl River estuary to the South China Sea

In the present study the diversity and abundance of nitrifying microbes including ammonia-oxidizing archaea (AOA) and betaproteobacteria (beta-AOB) were investigated, along with the physicochemical parameters potentially affecting them, in a transect of surface sediments from the coastal margin adjacent to the Pearl River estuary to the slope in the deep South China Sea. Nitrifying microbial diversity was determined by detecting the amoA (ammonia monooxygenase subunit A) gene. An obvious community structure shift for both AOA and beta-AOB from the coastal marginal areas to the slope in the deep-sea was detected, while the OTU numbers of AOA amoA were more stable than those of the beta-AOB. The OTUs of beta-AOB increased with the distance from the coastal margin areas to the slope in the deep-sea. Beta-AOB showed lower diversity with dominant strains in a polluted area but higher diversity without dominant strains in a clean area. Moreover, the diversity of beta-AOB was correlated with pH values, while no noticeable relationships were established between AOA and physicochemical parameters. Beta-AOB was more sensitive to transect environmental variability and might be a potential indicator for environmental changes. Additionally, the surface sediments surveyed in the South China Sea harboured diverse and distinct AOA and beta-AOB phylotypes different from other environments, suggesting the endemicity of some nitrifying prokaryotes in the South China Sea.
Prioritization of Overflow Tasks to Improve Performance of Mobile Cloud

Mobile devices may offload their applications to a virtual machine running on a cloud host. This application may fork new tasks which require virtual machines of their own on the same physical machine. Achieving satisfactory performance level in such a scenario requires flexible resource allocation mechanisms in the cloud data center. In this paper we present two such mechanisms which use prioritization: one in which forked tasks are given full priority over newly arrived tasks, and another in which a threshold is established to control the priority so that full priority is given to the forked tasks if their number exceeds a predefined threshold. We analyze the performance of both mechanisms using a Markovian multiserver queueing system with two priority levels to model the resource allocation process, and a multi-dimensional Markov system based on a Birth-Death queueing system with finite population, to model virtual machine provisioning. Our performance results indicate that the threshold-based priority scheme not only performs better, but can also be tuned to achieve the desired performance level.
PHYLOGENETIC RELATIONSHIPS OF B ETULA SPECIES ( BETULACEAE ) BASED ON NUCLEAR ADH AND CHLOROPLAST MAT K SEQUENCES

The phylogenetic relationships within the genus Betula (Betulaceae) were investigated using a part of the nuclear ADH gene and DNA sequences of the chloroplast matK gene with parts of its flanking regions. Two well-supported phylogenetic groups could be identified in the chloroplast DNA sequence: one containing the three American species B. lenta, B. alleghaniensis, and B. papyrifera and the other including all the other species studied. The ADH gene displayed more variation, and three main groups could be identified. In disagreement with the classical division of the genus Betula, B. schmidtii and B. nana grouped with the species in subgenus Betula, and B. ermanii grouped with species in subgenus Chamaebetula, including B. humilis and B. fruticosa. The ADH phylogeny suggests that several independent polyploidizations within the genus Betula could have taken place. The ADH and chloroplast phylogenies were in part incongruent due to the placement of B. papyrifera. The most likely reason for this seems to be cytoplasmic introgression.
Therapeutic Advantage in Selective Ligament Augmentation for Partial Tears of the Anterior Cruciate Ligament

Background: As a result of recent studies describing the double-bundle anterior cruciate ligament (ACL), selected ACL augmentation procedures, either anteromedial (AM) or posterolateral (PL), have been introduced as the treatment of choice for partial ACL ruptures. The preserved mechanoreceptor and vascularity of the remnant ACL are considered to provide additional biological benefits. Although enhanced knee joint proprioception in ACL augmented patients has been previously reported, there is no study assessing biological healing advantages of the graft after the ACL augmentation procedure. Hypothesis: Selected ACL augmentation for partial tears can accelerate the healing process of the grafted tendon, which promotes better biomechanical recovery of the tendon, compared with conventional ACL reconstruction of complete tears. Study Design: Controlled laboratory study. Methods: Two rat models were established in this study: an ACL augmentation partial tear model and conventional ACL reconstruction for a complete tear. Biological assessments of cellularity and angiogenesis were measured by hematoxylin and eosin staining and immunostaining, respectively. Additionally, rat-specific type III collagen and α-smooth muscle actin were evaluated by immunohistochemical staining to analyze the healing process, whereas anti-rat neurofilament antigen was assessed to examine proprioceptive recovery. Biological assessments of the augmented and reconstructed grafts were conducted postoperatively at week 2, whereas biomechanical testing was performed postoperatively at week 8. Results: An increase in cellularity and angiogenesis was observed in the augmented grafts compared with the conventionally reconstructed grafts. Also, increased amounts of rat-specific type III collagen, α-smooth muscle actin, and anti-rat neurofilament antigen were expressed in the augmented grafts. Biomechanical testing showed that failure to load was significantly higher in the augmentation group compared with the conventional reconstruction group (augmentation, 15.9 ± 1.0; reconstruction, 7.0 ± 1.3; P < .01). Clinical Relevance: Selected ACL augmentation could be a good choice for the repair of partial ACL injury by preserving the uninjured portion of the ACL, which in turn could maintain the anatomic position of the ligament and its biomechanical function.
Analysis and Classification of Airborne Radar Signal Types Using Time-Frequency Analysis

An electronic support (ES) system is used by the military for intelligence gathering, threat detection, and as a support to the electronic attack system. Its main feature is to determine the frequency parameters and pulse characteristics of the received radar signal. The estimated signal parameters are then used as input to a classifier network to determine the identity of the received signal. This paper describes airborne radar signal type analysis and classification (ARTAC) system that uses the spectrogram to obtain the time-frequency representation (TFR) and apply analysis tools such as the instantaneous energy, instantaneous frequency and other related tools to estimate various signal parameters. The estimated parameters are used as input to the rule-based classifier which classifies the signal appropriately. Monte-Carlo simulation is then carried out to determine the accuracy of signal classification at various signal-to-noise ratios (SNRs) in additive white Gaussian noise (AWGN). The method used achieves 90 percent classification accuracy at SNR of 6.2dB.
Inhibition of Inflammatory Cytokine Production in Human Corneal Cells by Dexamethasone, but Not Cyclosporin

Purpose: To evaluate the modulatory effects of anti-inflammatory agents, dexamethasone (Dex) and cyclosporin A (CsA), on the production of cytokines and chemokines by human corneal cells in vitro following stimulation by the pro-inflammatory cytokine after interleukin 1β (IL-1β). Methods: A human corneal epithelial (HCE) cell line and human corneal fibroblasts (HCFs) were stimulated in culture with IL-1β and treated with Dex or CsA. The gene expression for selected cytokines and chemokines was determined by reverse transcriptase-polymerase chain reaction (RT-PCR). The secretion of cytokines and chemokines was measured by enzyme-linked immunosorbent assay. Results: IL-1β enhanced the mRNA and/or protein levels of granulocyte-macrophage colony-stimulating factor (GM-CSF), IL-8, and monocyte chemotactic protein (MCP)-1 in HCE and IL-6, IL-8, MCP-3, and regulated on T-cell activation expressed secreted (RANTES) in HCFs. Treatment with CsA did not inhibit cytokine production in either HCE or HCFs. In contrast, Dex treatment inhibited the IL-1β-induced production of GM-CSF, IL-6, IL-8, MCP-3, and RANTES, but not MCP-1. Conclusion: These results show that Dex, but not CsA, has direct immunosuppressive effects on the resident corneal cells, HCE and HCFs. This suggests that the clinically observed immunosuppressive effects of topical CsA are mediated primarily through the immune cells.
Automatic segmentation of breast and fibroglandular tissue in breast MRI using local adaptive thresholding

Breast density is considered as an important risk factor associated with the development of breast cancer. Breast and fibroglandular tissue segmentation is the main step to compute breast density in Magnetic Resonance Imaging (MRI). This study presents an automatic algorithm to segment breast and fibroglandular tissue in MRI. It is a difficult task due to bias field and similar signal intensity between fibroglandular tissue and pectoral muscle. Our proposed segmentation approach has been developed based on the local adaptive thresholding to dominate on intensity inhomogeneity due to bias field and the low contrast intensity of the boundary between breast and pectoral muscle. The presented approach is validated with a dataset of 2520 bilateral axial breast MR images from 45 women that include all of Breast Imaging Reporting and Data System (BI-RADS) breast density range. Five quantitative metrics as Dice Similarity Coefficient (DSC), Jaccard Coefficient (JC), total overlap, False Negative (FN) and False Positive (FP) are employed to compare similarity between manual and automatic segmentations. For breast segmentation, the presented approach achieves DSC, JC, total overlap, FN and FP values of 0.90, 0.82, 0.89, 0.1 and 0.09, respectively. For fibroglandular tissue segmentation, we attain DSC, JC, total overlap, FN and FP values of 0.96, 0.94, 0.98, 0.02 and 0.04, respectively.
A delay line based CMOS time digitizer IC with 13 ps single-shot precision

This paper introduces an integrated digital CMOS time-to-digital converter which measures time periods with picosecond-level resolution. The circuit was fabricated in a 0.35 /spl mu/m standard digital CMOS process. 13 ps rms single-shot precision was achieved by using a counter and a two-level nested DLL interpolation. Interpolators, which divide the cycle time of the 145 MHz reference clock to 512 pieces, provided 13.5 ps LSB width. The temperature drift was below 0.05 ps//spl deg/C. The power consumption with a 3.3 V operating voltage was 55 mW.
Low voltage ride through capability enhancement of wind farms' generators: DVR versus STATCOM

This paper investigates the application of dynamic voltage restorer (DVR) versus static compensator (STATCOM) to enhance low voltage ride through (LVRT) capability of wind farms. The research done in the area of LVRT focused on a single machine compensation analysis; however, no such analysis was done for entire wind farms generators. Therefore, the main contribution of this paper is to study LVRT compensation through STATCOM and/or DVR in order to provide guidelines for the implementation of each solution within large wind farms. In this paper, squirrel cage induction generators (SCIGs) are studied using a simplified approach based on torque-speed characteristics of induction machines. The transient stability margin is proposed as indicator of LVRT capability. Analytical calculations are verified against simulation results using PSCAD/EMTDC package.
How Well Quantified Is the Limit of Quantification?

Background: Raw data on the relationship between known and measured values of an analyte are collected and analyzed to determine the limit of quantification (LOQ) of an assay. In most LOQ problems, the researcher is given an observed value for the marker of interest if this value is greater than the LOQ, and a missing value (<LOQ) otherwise. From a statistical perspective, the implicit assumption is that there is no measurement error for values greater than the LOQ, and unacceptable measurement error for values less than the LOQ. A more plausible assumption is that there is measurement error throughout the measure's support. Methods: We describe a Bayesian measurement error model that yields prediction intervals for the true assay value throughout the range of analyte values, and allows for heteroscedasticity of the measurement errors. Results: We illustrate our model on calibration data for fat-soluble vitamins, focusing particularly on beta-cryptoxanthin. Prediction intervals for values above the LOQ are wide, and the width increases with the measured value. Prediction intervals below the LOQ provide more information than the statement that the value is less than the LOQ. Conclusion: The current approach to transmitting data from calibration assays is flawed, since it provides a distorted picture of the actual measurement error. Implications for subsequent analyses of assay measurements are discussed.
Data masking for privacy-sensitive learning

We study the problem of data release with privacy, where data is made available with privacy guarantees while keeping the usability of the data as high as possible. This is important in healthcare and other domains with sensitive data. In particular, we propose a method of masking sensitive parts of private data while ensuring that a learner trained using the masked data is similar to the learner trained on the original data, to maintain usability. We provide theoretical guarantees about the lower bound of the distance between the masked and the true underlying data, and illustrate the effectiveness of the proposed method of data masking for privacy-sensitive learning on synthetic and real-world data.
Prevention of distal embolization during saphenous vein graft lesion angioplasty. Experience with a new temporary occlusion and aspiration system.

BACKGROUND Repeat coronary artery bypass graft surgery (CABG) is associated with a high morbidity and mortality, rendering percutaneous treatment of saphenous vein graft (SVG) lesions an attractive alternative. However, percutaneous interventions of degenerated SVGs carries high risk of distal embolization. METHODS AND RESULTS This study reports our initial experience with the PercuSurge GuardWire, a new device developed to prevent embolization during treatment of degenerated SVG. This device consists of a 190-cm-long, hollow 0.014-in guidewire with a central lumen connected to a distal occlusion balloon. A dedicated inflation device (the MicroSeal Adapter) was used to inflate the distal balloon and maintain complete lumen occlusion during balloon dilatation and stent implantation. A monorail aspiration catheter, connected to a vacuum syringe, was used to evacuate atherosclerotic and thrombotic debris. Angioplasty with stent implantation was performed in 15 degenerated SVGs (18 lesions). Procedural success was achieved in all patients with normal postprocedure flow (Thrombolysis in Myocardial Infarction grade 3). No distal embolization was observed. There were no major in-hospital adverse clinical events, including Q-wave or non-Q-wave myocardial infarction, emergency CABG, or death. All patients were asymptomatic at discharge. CONCLUSIONS This preliminary series supports the feasible use of the PercuSurge GuardWire for retrieval of plaque debris and prevention of embolization in degenerated SVGs. The good tolerance of temporary occlusions without angiographic or clinical evidence of distal embolization represents encouraging early findings.
Rapid tranquillisation of violent or agitated patients in a psychiatric emergency setting

Background The pharmacological management of violence in people with psychiatric disorders is under-researched. Aims To compare interventions commonly used for controlling agitation or violence in people with serious psychiatric disorders. Method We randomised 200 people to receive intramuscular lorazepam (4 mg) or intramuscular haloperidol (10 mg) plus promethazine (25–50 mg mix). Results At blinded assessments 4 h later (99.5% follow-up), equal numbers in both groups (96%) were tranquil or asleep. However, 76% given the haloperidol-promethazine mix were asleep compared with 45% of those allocated lorazepam (RR=2.29, 95% CI 1.59–3.39; NNT=3.2, 95% CI 2.3–5.4). The haloperidol-promethazine mix produced a faster onset of tranquillisation/sedation and more clinical improvement over the first 2 h. Neither intervention differed significantly in the need for additional intervention or physical restraints, numbers absconding, or adverse effects. Conclusions Both interventions are effective for controlling violent/agitated behaviour. If speed of sedation is required, the haloperidol-promethazine combination has advantages over lorazepam.
Psychological interventions to reduce suicidality in high-risk patients with major depression: a randomized controlled trial

Background Positive psychological constructs have been associated with reduced suicidal ideation, and interventions to cultivate positive feelings have the potential to reduce suicide risk. This study compares the efficacy of a 6-week, telephone-based positive psychology (PP) intervention against a cognition-focused (CF) control intervention among patients recently hospitalized for depression and suicidal ideation or behavior. Method A total of 65 adults with a current major depressive episode reporting suicidal ideation or a recent suicide attempt were enrolled from participating in-patient psychiatric units. Prior to discharge, participants were randomized to the PP (n = 32) or CF (n = 33) intervention. In both interventions, participants received a treatment manual, performed weekly PP (e.g. gratitude letter) or CF (e.g. recalling daily events) exercises, and completed weekly one-on-one telephone sessions over 6 weeks. Between-group differences in hopelessness (primary outcome), depression, suicidality and positive psychological constructs at 6 and 12 weeks were tested using mixed-effects models accounting for intensity of post-hospitalization psychiatric treatment. Results Compared with PP, the CF intervention was associated with significantly greater improvements in hopelessness at 6 weeks (β = −3.15, 95% confidence interval −6.18 to −0.12, effect size = −0.84, p = 0.04), but not 12 weeks. Similarly, the CF intervention led to greater improvements in depression, suicidal ideation, optimism and gratitude at 6 and 12 weeks. Conclusions Contrary to our hypothesis, the CF intervention was superior to PP in improving hopelessness, other suicide risk factors and positive psychological constructs during a key post-discharge period among suicidal patients with depression. Further study of this CF intervention is warranted in populations at high suicide risk.
[Clinical observation on Qidi Yiqi Yangyin Huoxue Recipe in treating diabetic nephropathy at stage III and IV].

OBJECTIVE To observe the clinical effect of Qidi Yiqi Yangyin Huoxue Recipe (QYYHR) on diabetic nephropathy (DN) at stage III and IV. METHODS One hundred type 2 DN patients of qi-yin deficiency with blood-stasis syndrome were randomly divided into two groups, all were treated with basal hypoglycemic treatment but with QYYHR given to the treatment group additionally for 3 months. The symptoms were observed, blood glucose, urinary albumin excretion rate (UAER), blood urea nitrogen (BUN), creatinine (Cr) and hemorheological parameters were detected before and after treatment. RESULTS The total effective rate was higher in the treatment group than that in the control group (89.6% vs. 68.1%, P < 0.01), and the improvement of UAER, BUN, Cr and hemorheological parameters was also significantly better in the former than in the latter (P < 0.05). CONCLUSION QYYHR has favorable effects on type 2 DN of qi-yin deficiency with blood-stasis syndrome.
Selection of Marker Genes Using Whole-Genome DNA Polymorphism Analysis

Molecular markers serve to assign individual samples to specific groups. Such markers should be easily identified and have a high discrimination power, being highly conserved within groups while showing sufficient variability between the groups that are to be distinguished. The availability of a large number of complete genomic sequences now enables the informed selection of genes as molecular markers based on the observed patterns of variability. We derived a new scoring system based on observed DNA polymorphic differences, and which uses the Bayes theorem as adapted by Wilcox. For validation, we applied this system to the problem of identifying individual species within a prokaryotic (Vibrio) and a eukaryotic (Diphyllobothrium) genus for validation. Top-scoring candidates genes Chromosome segregation ATPase and ATPase-subunit 6 showed better discrimination power in Vibrio and Diphyllobothrium, respectively, as compared to standard molecular markers (recA, dnaJ and atpA for Vibrio, and 18s rRNA, ITS and COX1 for Diphyllobothrium).
Equiatomic Quaternary Rare Earth Element Zinc Pnictide Oxides RZnPO and RZnAsO.

The twelve phosphide oxides RZnPO (R = Y, La-Nd, Sm, Gd-Tm) and the nine arsenide oxides (R = Y, La-Nd, Sm, Gd-Dy) have been prepared by reaction of the rare earth elements, ZnO, and phosphorus or arsenic, respectively, in a NaCl/KCl flux. The compounds RZnPO (R = Y, Pr, Nd, Sm, Gd-Tm) crystallize with a new trigonal rhombohedral structure type, determined from single-crystal X-ray diffractometer data of NdZnPO: R&thremacr;m, a = 397.7(1) pm, c = 3097.5(5) pm, Z = 6. The other eleven compounds are isotypic with ZrCuSiAs (P4/nmm, Z = 2). This tetragonal structure was refined from single-crystal X-ray data of LaZnPO (a = 404.0(1) pm, c = 890.8(2) pm) and NdZnAsO (a = 403.0(1) pm, c = 894.9(4) pm). In both structure types rare earth element-oxygen layers alternate with zinc-pnictogen layers. The rare earth element atoms have four oxygen and three (NdZnPO) or four (LaZnPO, NdZnAsO) pnictogen neighbors. The zinc atoms have tetrahedral pnictogen coordination. The arsenide oxides as well as the tetragonal phosphide oxides LaZnPO and CeZnPO are black, while the other (trigonal) phosphide oxides are transparent. The more metallic character of the tetragonal compounds is ascribed to their more delocalized chemical bonding, as is indicated by their higher coordination numbers, which in part also result through significant Zn-Zn bonding.
Triplet of FCM classifiers

This paper proposes an additional version of the fuzzy c-means based classifier (FCMC). The classifier FCMC-R treats relational data instead of object data. FCMCs use covariance structures to represent flexible shapes of clusters. Despite its effectiveness, the intense computation of covariance matrices is an impediment for classifying a set of high-dimensional feature data. In order to tackle with this problem, we proposed a way of directly handling high-dimensional data, i.e., FCMC-H. The third type of the FCM classifier is the relational classifier FCMC-R, which is derived from FCMC-H. The relational data represented by a relational matrix are based on dissimilarities or distances between object data. The triplets, i.e., FCMC, FCMC-H, and FCMC-R are equivalent when the dimensionality of feature vectors is not very high and the dissimilarity is represented by Euclidean distances. The randomized test set performance of FCMC on the sets of object data from UCI repository is comparable to that of the support vector machine (SVM) classifier. The performances of the triplet in terms of 100 times three way data splits (3-WDS) procedure are compared. The triplet surpasses the k-nearest neighbor (k-NN) classifier, which is a well established and very popular relational classifier.