Miracle-dz/UniFAR-FTUs huggingface dataset:
Redundant Proteolytic Mechanisms Process Seed Storage Proteins in the Absence of Seed-Type Members of the Vacuolar Processing Enzyme Family of Cysteine Proteases

Seed-type vacuolar processing enzyme (VPE) activity is predicted to be essential for post-translational proteolysis of seed storage proteins in the protein storage vacuole of developing seeds. To test this hypothesis, we examined the protein profiles of developing and germinating seeds from Arabidopsis plants containing transposon-insertional knockout mutations in the genes that encode the two seed-type VPEs in Arabidopsis, βVPE, which was identified previously, and δVPE, which is described here. The effects of these mutations were studied individually in single mutants and together in a double mutant. Surprisingly, we found that most of the seed protein still was processed proteolytically in seed-type VPE mutants. The minor differences observed in polypeptide accumulation between wild-type and βVPE mutant seeds were characterized using a two-dimensional gel/mass spectrometric analysis approach. The results showed increased amounts of propolypeptide forms of legumin-type globulins accumulating in mutant seeds. However, the majority of protein (>80%) still was processed to mature α- and β-chains, as observed in wild-type seeds. Furthermore, we identified several legumin-type globulin polypeptides, not corresponding to pro or mature forms, that increased in accumulation in βVPE mutant seeds compared with wild-type seeds. Together, these results indicate the existence of both redundant and alternative processing activities in seeds. The latter was substantiated by N-terminal sequencing of a napin-type albumin protein, indicating cleavage consistent with previous in vitro studies using purified aspartic protease. Analysis of genome-wide transcript profiling data sets identified six protease genes (including an aspartic protease gene and βVPE) that shared spatial and temporal expression patterns with seed storage proteins. From these results, we conclude that seed-type VPEs constitute merely one pathway for processing seed storage protein and that other proteolytic enzymes also can process storage proteins into chains capable of stable accumulation in mature seeds.
Joint transmitter receiver diversity for efficient space division multiaccess

The beamforming problem is studied in wireless networks where both the transmitters and receivers have linear adaptive antenna arrays. Algorithms are proposed that find the antenna array weight vectors at both the transmitters and receivers as well as the transmitter powers with one of the following two objectives: (1) to maximize the minimum signal-to-interference-and-noise ratio (SINR) over all receivers and (2) to minimize the sum of the total transmitted power satisfying the SINR requirements at all links. A numerical study is performed to compare the network capacity and the power consumption among systems having a different number of antenna array elements in a code division multiple access network.
Comparison of Glaucoma Probability Score and Moorfields Regression Analysis to Discriminate Glaucomatous and Healthy Eyes

Purpose To compare sensitivity and specificity values of glaucoma probability score (GPS) and Moorfields regression analysis (MRA) of Heidelberg retina tomograph (HRT) to discriminate between glaucomatous and healthy eyes. Methods A total of 160 eyes of 160 individuals (80 glaucoma patients and 80 healthy subjects) were enrolled in this prospective cross-sectional study. Confocal scanning laser ophthalmoscopy was performed with HRT. Performance of GPS and MRA were evaluated by considering borderline (BL) cases as within normal limits (WNL) or as outside normal limits (ONL). For further analysis glaucoma group was divided into two subsets: initial and moderate/severe damage group. Results There was no difference between glaucoma patients and normal subjects in terms of gender, disc area, and pachymetry (p>0.05). The GPS was higher, average visual field MD and PSD values were worse, and patients were older in glaucoma group (p=0.001). Sensitivity and specificity values were 72.5% and 93.8% respectively for MRA and 75.0% and 88.8% for GPS when BL cases considered as WNL, and when BL cases considered as ONL these values were 83.8% and 73.8% for MRA and 88.8% and 70.0% for GPS. There was no difference between sensitivity and specificity values of GPS and MRA for either situation (p>0.05). Sensitivity of GPS (76.2%) was higher than of MRA (61.9%) in initial glaucomatous eyes (p=0.317). Conclusions Diagnostic performance of GPS was similar to MRA. It was found that GPS might differentiate between glaucomatous and healthy eyes with relatively better sensitivity but worse specificity and represent considerable advantage over MRA in early glaucoma cases.
Consensus on context-specific strategies for reducing the stigma of human immunodeficiency virus/acquired immunodeficiency syndrome in Zambézia Province, Mozambique

Abstract Stigma has been implicated in poor outcomes of human immunodeficiency virus (HIV)/acquired immunodeficiency syndrome (AIDS) care. Reducing stigma is important for HIV prevention and long-term treatment success. Although stigma reduction interventions are conducted in Mozambique, little is known about the current nature of stigma and the efficacy and effectiveness of stigma reduction initiatives. We describe action research to generate consensus on critical characteristics of HIV stigma and anti-stigma interventions in Zambézia Province, Mozambique. Qualitative data gathering methods, including in-depth key-informant interviews, community interviews and consensus group sessions, were utilized. Delphi methods and the strategic options development analysis technique were used to synthesize qualitative data. Key findings are that stigma enacted by the general public might be declining in tandem with the HIV/AIDS epidemic in Mozambique, but there is likely excessive residual fear of HIV disease and community attitudes that sustain high levels of perceived stigma. HIV-positive women accessing maternal and child health services appear to shoulder a disproportionate burden of stigma. Unintentional biases among healthcare providers are currently the critical frontier of stigmatization, but there are few interventions designed to address them. Culturally sensitive psychotherapies are needed to address psychological distress associated with internalized stigma and these interventions should complement current supports for voluntary counseling and testing. While advantageous for defining stakeholder priorities for stigma reduction efforts, confirmatory quantitative studies of these consensus positions are needed before the launch of specific interventions.
Status of the Microbial Census

SUMMARY Over the past 20 years, more than 78,000 16S rRNA gene sequences have been deposited in GenBank and the Ribosomal Database Project, making the 16S rRNA gene the most widely studied gene for reconstructing bacterial phylogeny. While there is a general appreciation that these sequences are largely unique and derived from diverse species of bacteria, there has not been a quantitative attempt to describe the extent of sequencing efforts to date. We constructed rarefaction curves for each bacterial phylum and for the entire bacterial domain to assess the current state of sampling and the relative taxonomic richness of each phylum. This analysis quantifies the general sense among microbiologists that we are a long way from a complete census of the bacteria on Earth. Moreover, the analysis indicates that current sampling strategies might not be the most effective ones to describe novel diversity because there remain numerous phyla that are globally distributed yet poorly sampled. Based on the current level of sampling, it is not possible to estimate the total number of bacterial species on Earth, but the minimum species richness is 35,498. Considering previous global species richness estimates of 107 to 109, we are certain that this estimate will increase with additional sequencing efforts. The data support previous calls for extensive surveys of multiple chemically disparate environments and of specific phylogenetic groups to advance the census most rapidly.
Regional Instability and Economic Growth: Thy Neighbor's Curse

We show that regional instability defined as political instability in neighboring countries has strong negative effects on a countrys income per capita growth rate. The magnitude of this negative externality is found to be equivalent to the effect from an identical increase in domestic political instability. We find that there are three main channels in which regional instability hurt growth. First regional instability disrupts trade flows. The shares of merchandise and manufactured trade are substantially lower in countries with high regional instability. Second regional instability require increases in military outlays at the expense of other productive activities. Third the composition of investment is found to be skewed against the share of equipment investment in countries with high regional instability. To the extent that equipment investment has a higher social rate of return than transport or structure investment this shift can reduce aggregate returns to capital and hamper growth. (authors)
Template Trackingwith Observation Relevance Determination

This paper addresses the problem of template tracking in the presence of occlusions, clutter and rapid motion. We adopt a learning approach, using a Bayesian Mixture of Experts (BME), in which observations at each frame yield direct predictions of the state (e.g. position / scale) of the tracked target. In contrast to other methods in the literature, we explicitly address the problem that the prediction accuracy can deteriorate drastically for observations that are not similar to the ones in the training set; such observations are common in case of partial occlusions or of fast motion. To do so, we couple the BME with a probabilistic kernel-based classifier which, when trained, can determine the probability that a new/unseen observation can accurately predict the state of the target (the 'relevance' of the observation in question). In addition, in the particle filtering framework, we derive a recursive scheme for maintaining an approximation of the posterior probability of the target's state in which the probabilistic predictions of multiple observations are moderated by their corresponding relevance. We apply the algorithm in the problem of 2D template tracking and demonstrate that the proposed scheme outperforms classical methods for discriminative tracking in case of motions large in magnitude and of partial occlusions.
The Lone Wolf – Solo Terrorism and the Challenge ofPreventative Prosecution

On September 11, 2001, as we will never forget, al-Qaeda’s elaborate planning and deployment of numerous terrorist agents resulted in shocking destruction and 2,976 deaths. Since the time of those shattering atrocities, though, threats within our borders have centered increasingly not on concerted activities but on solo actors of terrorism. This emerging threat – often described as “Lone Wolf Terrorism” – has seen efforts that were tragically successful including the 2009 shooting rampage that left thirteen dead at Fort Hood. Others have come frighteningly close to carnage, such as the 2010 attempt to detonate explosives in Times Square. Reports indicate that in recent years most Islamic terrorist plots in the United States do not employ multiple agents in concert and instead are perpetrated by a “Lone Wolf. ” Recognizing this growing danger, President Barack Obama observed that single actor terrorism was “the most likely scenario that we have to guard against right now. ” When an individual acts alone – and does not communicate destructive intentions to others – that per-
Estimates of the Contribution of Single Neurons to Perception Depend on Timescale and Noise Correlation

The sensitivity of a population of neurons, and therefore the amount of sensory information available to an animal, is limited by the sensitivity of single neurons in the population and by noise correlation between neurons. For decades, therefore, neurophysiologists have devised increasingly clever and rigorous ways to measure these critical variables (Parker and Newsome, 1998). Previous studies examining the relationship between the responses of single middle temporal (MT) neurons and direction-discrimination performance uncovered an apparent paradox. Sensitivity measurements from single neurons suggested that small numbers of neurons may account for a monkey's psychophysical performance (Britten et al., 1992), but trial-to-trial variability in activity of single MT neurons are only weakly correlated with the monkey's behavior, suggesting that the monkey's decision must be based on the responses of many neurons (Britten et al., 1996). We suggest that the resolution to this paradox lies (1) in the long stimulus duration used in the original studies, which led to an overestimate of neural sensitivity relative to psychophysical sensitivity, and (2) mistaken assumptions (because no data were available) about the level of noise correlation in MT columns with opposite preferred directions. We therefore made new physiological and psychophysical measurements in a reaction time version of the direction-discrimination task that matches neural measurements to the actual decision time of the animals. These new data, considered together with our recent data on noise correlation in MT (Cohen and Newsome, 2008), provide a substantially improved account of psychometric performance in the direction-discrimination task.
Final trial report of sentinel-node biopsy versus nodal observation in melanoma.

BACKGROUND Sentinel-node biopsy, a minimally invasive procedure for regional melanoma staging, was evaluated in a phase 3 trial. METHODS We evaluated outcomes in 2001 patients with primary cutaneous melanomas randomly assigned to undergo wide excision and nodal observation, with lymphadenectomy for nodal relapse (observation group), or wide excision and sentinel-node biopsy, with immediate lymphadenectomy for nodal metastases detected on biopsy (biopsy group). Results No significant treatment-related difference in the 10-year melanoma-specific survival rate was seen in the overall study population (20.8% with and 79.2% without nodal metastases). Mean (± SE) 10-year disease-free survival rates were significantly improved in the biopsy group, as compared with the observation group, among patients with intermediate-thickness melanomas, defined as 1.20 to 3.50 mm (71.3 ± 1.8% vs. 64.7 ± 2.3%; hazard ratio for recurrence or metastasis, 0.76; P=0.01), and those with thick melanomas, defined as >3.50 mm (50.7 ± 4.0% vs. 40.5 ± 4.7%; hazard ratio, 0.70; P=0.03). Among patients with intermediate-thickness melanomas, the 10-year melanoma-specific survival rate was 62.1 ± 4.8% among those with metastasis versus 85.1 ± 1.5% for those without metastasis (hazard ratio for death from melanoma, 3.09; P<0.001); among patients with thick melanomas, the respective rates were 48.0 ± 7.0% and 64.6 ± 4.9% (hazard ratio, 1.75; P=0.03). Biopsy-based management improved the 10-year rate of distant disease-free survival (hazard ratio for distant metastasis, 0.62; P=0.02) and the 10-year rate of melanoma-specific survival (hazard ratio for death from melanoma, 0.56; P=0.006) for patients with intermediate-thickness melanomas and nodal metastases. Accelerated-failure-time latent-subgroup analysis was performed to account for the fact that nodal status was initially known only in the biopsy group, and a significant treatment benefit persisted. CONCLUSIONS Biopsy-based staging of intermediate-thickness or thick primary melanomas provides important prognostic information and identifies patients with nodal metastases who may benefit from immediate complete lymphadenectomy. Biopsy-based management prolongs disease-free survival for all patients and prolongs distant disease-free survival and melanoma-specific survival for patients with nodal metastases from intermediate-thickness melanomas. (Funded by the National Cancer Institute, National Institutes of Health, and the Australia and New Zealand Melanoma Trials Group; ClinicalTrials.gov number, NCT00275496.).
Cardiac surgery-associated acute kidney injury: risk factors analysis and comparison of prediction models.

OBJECTIVES Cardiac surgery-associated acute kidney injury (AKI) is a well-known factor influencing patients' long-term morbidity and mortality. Several prediction models of AKI requiring dialysis (AKI-D) have been developed. Only a few direct comparisons of these models have been done. Recently, a new, more uniform and objective definition of AKI has been proposed [Kidney Disease: Improve Global Outcomes (KDIGO)-AKI]. The performance of these prediction models has not yet been tested. METHODS Preoperative demographic and clinical characteristics of 1056 consecutive adult patients undergoing cardiac surgery were collected retrospectively for the period 2012-2014. Multivariable logistic regression analysis was used to determine the independent predictors of AKI-D and the KDIGO-AKI stages. Risk scores of five prediction models were calculated using corresponding subgroups of patients. The discrimination of these models was calculated by the c-statistics (area under curve, AUC) and the calibration was evaluated for the model with the highest AUC by calibration plots. RESULTS The incidence of AKI-D was 3.5% and for KDIGO-AKI 23% (17.3% for Stage 1, 2.1% for Stage 2 and 3.6% for Stage 3). Older age, atrial fibrillation, NYHA class III or IV heart failure, previous cardiac surgery, higher preoperative serum creatinine and endocarditis were independently associated with the development of AKI-D. For KDIGO-AKI, higher body mass index, older age, female gender, chronic obstructive pulmonary disease, previous cardiac surgery, atrial fibrillation, NYHA class III or IV heart failure, higher preoperative serum creatinine and the use of cardiopulmonary bypass were independent predictors. The model by Thakar et al. showed the best performance in the prediction of AKI-D (AUC 0.837; 95% CI = 0.810-0.862) and also in the prediction of KDIGO-AKI stage 1 and higher (AUC = 0.731; 95% CI = 0.639-0.761), KDIGO-AKI stage 2 and higher (AUC = 0.811; 95% CI = 0.783-0.838) and for KDIGO-AKI stage 3 (AUC = 0.842; 95% CI = 0.816-0.867). CONCLUSIONS The performance of known prediction models for AKI-D was found reasonably well in the prediction of KDIGO-AKI, with the model by Thakar having the highest predictive value in the discrimination of patients with risk for all KDIGO-AKI stages.
Treatment of lactic acidosis with dichloroacetate in dogs.

Lactic acidosis is a clinical condition due to accumulation of H(+) ions from lactic acid, characterized by blood lactate levels >5 mM and arterial pH <7.25. In addition to supportive care, treatment usually consists of intravenous NaHCO(3), with a resultant mortality >60%. Dichloroacetate (DCA) is a compound that lowers blood lactate levels under various conditions in both man and laboratory animals. It acts to increase pyruvate oxidation by activation of pyruvate dehydrogenase. We evaluated the effects of DCA in the treatment of two different models of type B experimental lactic acidosis in diabetic dogs: hepatectomy-lactic acidosis and phenformin-lactic acidosis. The metabolic and systemic effects examined included arterial blood pH and levels of bicarbonate and lactate; the intracellular pH (pHi) in liver and skeletal muscle; cardiac index, arterial blood pressure and liver blood flow; liver lactate uptake and extrahepatic splanchnic (gut) lactate production; and mortality. Effects of DCA were compared with those of either NaCl or NaHCO(3). The infusion of DCA and NaHCO(3), delivered equal amounts of volume and sodium, although the quantity of NaHCO(3) infused (2.5 meq/kg per h) was insufficient to normalize arterial pH. In phenformin-lactic acidosis, DCA-treated animals had a mortality of 22%, vs. 89% in those treated with NaHCO(3). DCA therapy increased arterial pH and bicarbonate, liver pHi and cardiac index, with increased liver lactate uptake and a fall in blood lactate. With NaHCO(3) therapy, there were decrements of cardiac index and liver pHi, with an increase in venous pCO(2) and gut production of lactate. Dogs with hepatectomy-lactic acidosis were either treated or pretreated with DCA. Treatment with DCA resulted in stabilization of cardiac index, a fall in blood lactate, and 17% mortality. NaHCO(3) was associated with a continuous decline of cardiac index, rise in blood lactate, and 67% mortality. In dogs pretreated with NaCl, mortality was 33%, but all dogs pretreated with DCA survived. Dogs pretreated with DCA also had lower blood lactate and higher arterial pH and bicarbonate than did those pretreated with NaCl.Thus, in either of two models of type B experimental lactic acidosis, treatment with DCA improves cardiac index, arterial pH, bicarbonate and lactate, and liver pHi. The mortality in dogs with type B lactic acidosis was significantly less in DCA-treated animals than in those treated with other modalities.
Extraction of multiresolution watermark images for resolving rightful ownership

Digital watermarking has been recently proposed as the mean for intellectual property right protection of multimedia data. We present some ways to 'visualize' the invisible watermarks, both statistically and perceptually, for proving the ownership. A system which is capable of embedding a good resolution meaningful binary watermark image and later extracting different versions of that watermark image with varying resolutions is proposed. The system has the nice feature that the watermark detector (rather than encoder) is allowed to adaptively choose the trade-off between robustness degree and resolution of the extracted watermark image. It takes advantage of the high spatial correlation of the watermark image and the human visual system's super ability to recognize a correlated pattern to enhance the detection performance. While a statistical technique which can quantify the false alarm detection probability should be considered as a fundamental measure for a valid ownership claim, the ability to extract a meaningful watermark image will greatly facilitate the process of convincing the jury of an ownership claim.
Dynamic Variable Ordering Based Concurrent Search for Distributed CSPs

Concurrent search is an efficient technique for solving distributed constraint satisfaction problems (DisCSPs). dynamic variable ordering (DVO) impacts performance of search greatly. In this paper, we present a distributed dynamic variable ordering based concurrent search algorithm, in which domain sizes of variables are calculated approximately during search. Experiments on randomly generated DisCSPs demonstrate that the proposed algorithm improves concurrent search drastically.