Miracle-dz/UniFAR-FTUs huggingface dataset:
Functional Importance of Deletion Mutant Genotypes in an Insect Nucleopolyhedrovirus Population

ABSTRACT A Nicaraguan isolate of a nucleopolyhedrovirus (SfNIC) that attacks the fall armyworm, Spodoptera frugiperda, survives as a mixture of nine genotypes (SfNIC A to I) that all present genomic deletions, except variant B (complete genotype). Sequencing of cloned restriction fragments revealed that genotypic variants lack between 5 and 16 of the open reading frames present in a contiguous sequence of 18 kb of the SfNIC genome. The absence of oral infectivity of SfNIC-C and -D variants is related to the deletion of the pif and/or pif-2 gene, while that of SfNIC-G remains unexplained. The presence of open reading frame 10, homolog of Se030, also appeared to influence pathogenicity in certain variants. Previous studies demonstrated a significant positive interaction between genotypes B and C. We compared the median lethal concentration of single genotypes (A, B, C, D, and F) and co-occluded genotype mixtures (B+A, B+D, B+F, A+C, and F+C in a 3:1 ratio). Mixtures B+A and B+D showed increased pathogenicity, although only B+D restored the activity of the mixture to that of the natural population. Mixtures of two deletion variants (A+C and F+C) did not show interactions in pathogenicity. We conclude that minority genotypes have an important influence on the overall pathogenicity of the population. These results clearly demonstrate the value of retaining genotypic diversity in virus-based bioinsecticides.
Decoding polyphase migmatites using geochronology and phase equilibria modelling

In this study, in situ U–Pb monazite ages and Lu–Hf garnet geochronology are used to distinguish mineral parageneses developed during Devonian–Carboniferous and Cretaceous events in migmatitic paragneiss and orthogneiss from the Fosdick migmatite–granite complex in West Antarctica. SHRIMP U–Pb monazite ages define two dominant populations at 365–300 Ma (from cores of polychronic grains, dominantly from deeper structural levels in the central and western sectors of the complex) and 120–96 Ma (from rims of polychronic grains, dominantly from the central and western sectors of the complex, and from monochronic grains, mostly from shallower structural levels in the eastern sector of the complex). For five paragneisses and two orthogneisses, Lu–Hf garnet ages range from 116 to 111 Ma, c. 12–17 Ma older than published Sm–Nd garnet ages of 102–99 Ma from three of the same samples. Garnet grains in the analysed samples generally have Lu‐enriched rims relative to Lu‐depleted cores. By contrast, for three of the same samples, individual garnet grains have flat Sm concentrations consistent with high‐T diffusive resetting. Lutetium enrichment of garnet rims is interpreted to record the breakdown of a Lu‐rich accessory mineral during the final stage of garnet growth immediately prior to the metamorphic peak, and/or the preferential retention of Lu in garnet during breakdown to cordierite in the presence of melt concomitant with the initial stages of exhumation. Therefore, garnet is interpreted to be part of the Cretaceous mineral paragenesis and the Lu–Hf garnet ages are interpreted to record the timing of close‐to‐peak metamorphism for this event. For the Devonian–Carboniferous event, phase equilibria modelling of the metasedimentary protoliths to the paragneiss and a diatexite migmatite restrict the peak P–T conditions to 720–800 °C at 0.45–1.0 GPa. For the Cretaceous event, using both forward and inverse phase equilibria modelling of residual paragneiss and orthogneiss compositions, the P–T conditions after decompression are estimated to have been 850–880 °C at 0.65–0.80 GPa. These P–T conditions occurred between c. 106 and c. 96 Ma, determined from Y‐enriched rims on monazite that record the timing of garnet and biotite breakdown to cordierite in the presence of melt. The effects of this younger metamorphic event are dominant throughout the Fosdick complex.
Conformational control of Bax localization and apoptotic activity by Pro168

In healthy cells, Bax resides inactive in the cytosol because its COOH-terminal transmembrane region (TMB) is tucked into a hydrophobic pocket. During apoptosis, Bax undergoes a conformational change involving NH2-terminal exposure and translocates to mitochondria to release apoptogenic factors. How this process is regulated remains unknown. We show that the TMB of Bax is both necessary and sufficient for mitochondrial targeting. However, its availability for targeting depends on Pro168 located within the preceding loop region. Pro168 mutants of Bax lack apoptotic activity, cannot rescue the apoptosis-resistant phenotype of Bax/Bak double knockout cells, and are retained in the cytosol even in response to apoptotic stimuli. Moreover, the mutants have their NH2 termini exposed. We propose that Pro168 links the NH2 and the COOH terminus of Bax and is required for COOH-terminal release and mitochondrial targeting once this link is broken.
Pseudorandom bits for constant depth circuits with few arbitrary symmetric gates

We exhibit an explicitly computable 'pseudorandom' generator stretching l bits into m(l) = l/sup /spl Omega/(log l)/ bits that look random to constant-depth circuits of size m(l) with log m(l) arbitrary symmetric gates (e.g. PARITY, MAJORITY). This improves on a generator by Luby, Velickovic and Wigderson (ISTCS '93) that achieves the same stretch but only fools circuits of depth 2 with one arbitrary symmetric gate at the top. Our generator fools a strictly richer class of circuits than Nisan's generator for constant depth circuits (Combinatorica '91) (but Nisan's generator has a much bigger stretch). In particular, we conclude that every function computable by uniform poly(n)-size probabilistic constant depth circuits with O(log n) arbitrary symmetric gates is in TIME (2/sup no(1)/) This seems to be the richest probabilistic circuit class known to admit a subexponential derandomization. Our generator is obtained by constructing an explicit function f : {0, 1}/sup n/ /spl rarr/ {0, 1} that is very hard on aver-age for constant-depth circuits of size n/sup /spl epsi//spl middot/log n/ with /spl epsi/log/sup 2/ n it arbitrary symmetric gates, and plugging it into the Nisan-Wigderson pseudorandom generator construction (FOCS '88). The proof of the average-case hardness of this function is a modification of arguments by Razborov and Wigderson (IPL '93), and Hansen and Miltersen (MFCS '04), and combines Hdstad's switching lemma (STOC '86) with a multiparty communication complexity lower bound by Babai, Nisan and Szegedy (STOC '89).
Pericardial Fat Is Associated With Prevalent Atrial Fibrillation: The Framingham Heart Study

Background—Obesity represents an important risk factor for atrial fibrillation (AF). We tested the hypothesis that pericardial fat, a unique fat deposit in close anatomic proximity to cardiac structures and autonomic fibers, is associated with prevalent AF. Methods and Results—Participants from the Framingham Heart Study underwent multidetector computed tomography from 2002 to 2005. We estimated the association between quantitative pericardial, intrathoracic and visceral adipose tissue volumes (per standard deviation of volume) with prevalent AF adjusting for established AF risk factors (age, sex, systolic blood pressure, blood pressure treatment, PR interval, and clinically significant valvular disease). Of the 3217 eligible participants (mean age, 50.6±10.1 years; 48% women), 54 had a confirmed diagnosis of AF. Pericardial fat but not intrathoracic or visceral abdominal fat was associated with prevalent AF in multivariable-adjusted models (odds ratio per standard deviation of pericardial fat volume, 1.28; 95% confidence intervals, 1.03 to 1.58). Further adjustments for body mass index, heart failure, myocardial infarction, and intrathoracic fat volume did not materially change the association between pericardial fat and AF. Conclusions—Pericardial fat was associated with prevalent AF even after adjustment for AF risk factors, including body mass index. If this association is replicated, further investigations into the mechanisms linking pericardial fat to AF are merited.
Audiovisual Synchronization and Fusion Using Canonical Correlation Analysis

It is well-known that early integration (also called data fusion) is effective when the modalities are correlated, and late integration (also called decision or opinion fusion) is optimal when modalities are uncorrelated. In this paper, we propose a new multimodal fusion strategy for open-set speaker identification using a combination of early and late integration following canonical correlation analysis (CCA) of speech and lip texture features. We also propose a method for high precision synchronization of the speech and lip features using CCA prior to the proposed fusion. Experimental results show that i) the proposed fusion strategy yields the best equal error rates (EER), which are used to quantify the performance of the fusion strategy for open-set speaker identification, and ii) precise synchronization prior to fusion improves the EER; hence, the best EER is obtained when the proposed synchronization scheme is employed together with the proposed fusion strategy. We note that the proposed fusion strategy outperforms others because the features used in the late integration are truly uncorrelated, since they are output of the CCA analysis.
Neonatal Drug Withdrawal

Maternal use of certain drugs during pregnancy can result in transient neonatal signs consistent with withdrawal or acute toxicity or cause sustained signs consistent with a lasting drug effect. In addition, hospitalized infants who are treated with opioids or benzodiazepines to provide analgesia or sedation may be at risk for manifesting signs of withdrawal. This statement updates information about the clinical presentation of infants exposed to intrauterine drugs and the therapeutic options for treatment of withdrawal and is expanded to include evidence-based approaches to the management of the hospitalized infant who requires weaning from analgesics or sedatives.
A novel concept of a multiphase, multimotor vector controlled drive system supplied from a single voltage source inverter

Since variable speed electric drive systems are supplied from power electronic converters, it is possible to utilize ac machines with a phase number higher than three. It is shown in the paper, using general theory of electrical machines, that an increase of the stator phase number to at least five (or more) enables completely independent vector control of two (or more) multiphase machines that are supplied from a single current-controlled voltage source inverter. In order to achieve such an independent control it is necessary to connect multiphase stator windings of the machines in series and perform an appropriate phase sequence transposition. The concept is equally applicable to any multiphase ac machine type and its major advantage, compared to an equivalent multimotor three-phase drive system, is the saving of a certain number of inverter legs. The actual saving depends on the number of phases. The concept is introduced using an n-phase induction machine as the starting point and further analysis is restricted to an odd number of phases, for the reason explained in the paper. Classification of all the possible cases that may arise is given, followed by presentation of connection diagrams for selected phase numbers. Detailed verification of the proposed concept is provided by simulating the operation of a seven-phase three-motor drive system, controlled using indirect rotor flux oriented control principles. Some preliminary experimental results, which confirm the feasibility of a two-motor series-connected drive system, are included as well. The main advantages and drawbacks of the concept, when compared with an equivalent three-phase multimotor drive system, are finally addressed.
Prognostic, predictive and potential surrogate markers in castration-resistant prostate cancer

Several novel therapeutic agents have demonstrated improvement of overall survival and further patient relevant endpoints in the setting of castration-resistant prostate cancer. Nevertheless, two questions have become increasingly relevant: are there any prognostic or predictive markers that could ease clinical decision-making using risk stratification and risk-adapted treatment in order to provide a benefit for the patient? Furthermore, against the background of increasing possibilities of therapy sequencing in clinical practice and in the clinical trial landscape in castration-resistant prostate cancer, does an isolated evaluation of overall survival reliably mirror the benefit attributable to a single compound? To address both these questions, suitable parameters serving as surrogates for intermediate and long-term endpoints and reflecting individual benefit, respectively, need to be identified and proven.
Evaluating the impact of digital divide on the performance of first year students in an IT course: A case of UKZN

Technology is continuously evolving and has become embedded into the day-to-day activities performed by everyone. Tertiary institutions, like most other institutions, have been greatly impacted and transformed by technology. Studies have shown that technology plays a huge role in the performance of students, because students are expected to make use of various technologies to aid their learning processes. However, with the prevalence of digital divide, some students find it difficult to get access to the Internet, computers and other technological devices before entering the university. Thus, this study examined the effects of “not having access to computers and other technologies before entering the university” on the academic performance of first year students taking an Information Technology (IT) course, in the University of KwaZulu-Natal (UKZN). The results of this study showed that whether or not students had access to computer and other technologies before entering the university, they still achieved good performances in IT courses, especially where the university provides access to computers and other technologies to first year students.
Containment of Conjunctive Regular Path Queries with Inverse

Reasoning on queries is a basic problem both in knowledge representation and databases. A fundamental form of reasoning on queries is checking containment, i.e., verifying whether one query yields necessarily a subset of the result of another query. Query containment is crucial in several contexts, such as query optimization, knowledge base veriflcation, information integration, database integrity checking, and cooperative answering. In this paper we address the problem of query containment in the context of semistructured knowledge bases, where the basic querying mechanism, namely regular path queries, asks for all pairs of objects that are connected by a path conforming to a regular expression. We consider conjunctive regular path queries with inverse, which extend regular path queries with the possibility of using both the inverse of binary relations, and conjunctions of atoms, where each atom specifles that one regular path query with inverse holds between two variables. We present a novel technique to check containment of queries in this class, based on the use of two-way flnite automata. The technique shows the power of two-way automata in dealing with the inverse operator and with the variables in the queries. We also characterize the computational complexity of both the proposed algorithm and the problem.
Revisiting the Robustness of PET-Based Textural Features in the Context of Multi-Centric Trials

Purpose This study aimed to investigate the variability of textural features (TF) as a function of acquisition and reconstruction parameters within the context of multi-centric trials. Methods The robustness of 15 selected TFs were studied as a function of the number of iterations, the post-filtering level, input data noise, the reconstruction algorithm and the matrix size. A combination of several reconstruction and acquisition settings was devised to mimic multi-centric conditions. We retrospectively studied data from 26 patients enrolled in a diagnostic study that aimed to evaluate the performance of PET/CT 68Ga-DOTANOC in gastro-entero-pancreatic neuroendocrine tumors. Forty-one tumors were extracted and served as the database. The coefficient of variation (COV) or the absolute deviation (for the noise study) was derived and compared statistically with SUVmax and SUVmean results. Results The majority of investigated TFs can be used in a multi-centric context when each parameter is considered individually. The impact of voxel size and noise in the input data were predominant as only 4 TFs presented a high/intermediate robustness against SUV-based metrics (Entropy, Homogeneity, RP and ZP). When combining several reconstruction settings to mimic multi-centric conditions, most of the investigated TFs were robust enough against SUVmax except Correlation, Contrast, LGRE, LGZE and LZLGE. Conclusion Considering previously published results on either reproducibility or sensitivity against delineation approach and our findings, it is feasible to consider Homogeneity, Entropy, Dissimilarity, HGRE, HGZE and ZP as relevant for being used in multi-centric trials.
High Humidity Leads to Loss of Infectious Influenza Virus from Simulated Coughs

Background The role of relative humidity in the aerosol transmission of influenza was examined in a simulated examination room containing coughing and breathing manikins. Methods Nebulized influenza was coughed into the examination room and Bioaerosol samplers collected size-fractionated aerosols (<1 µM, 1–4 µM, and >4 µM aerodynamic diameters) adjacent to the breathing manikin’s mouth and also at other locations within the room. At constant temperature, the RH was varied from 7–73% and infectivity was assessed by the viral plaque assay. Results Total virus collected for 60 minutes retained 70.6–77.3% infectivity at relative humidity ≤23% but only 14.6–22.2% at relative humidity ≥43%. Analysis of the individual aerosol fractions showed a similar loss in infectivity among the fractions. Time interval analysis showed that most of the loss in infectivity within each aerosol fraction occurred 0–15 minutes after coughing. Thereafter, losses in infectivity continued up to 5 hours after coughing, however, the rate of decline at 45% relative humidity was not statistically different than that at 20% regardless of the aerosol fraction analyzed. Conclusion At low relative humidity, influenza retains maximal infectivity and inactivation of the virus at higher relative humidity occurs rapidly after coughing. Although virus carried on aerosol particles <4 µM have the potential for remaining suspended in air currents longer and traveling further distances than those on larger particles, their rapid inactivation at high humidity tempers this concern. Maintaining indoor relative humidity >40% will significantly reduce the infectivity of aerosolized virus.
Planar Cycle Covering Graphs

We describe a new variational lower-bound on the minimum energy configuration of a planar binary Markov Random Field (MRF). Our method is based on adding auxiliary nodes to every face of a planar embedding of the graph in order to capture the effect of unary potentials. A ground state of the resulting approximation can be computed efficiently by reduction to minimum-weight perfect matching. We show that optimization of variational parameters achieves the same lower-bound as dual-decomposition into the set of all cycles of the original graph. We demonstrate that our variational optimization converges quickly and provides high-quality solutions to hard combinatorial problems 10-100x faster than competing algorithms that optimize the same bound.
Regional cerebral metabolic correlates of WASO during NREM sleep in insomnia.

STUDY OBJECTIVE To investigate the non-rapid eye movement (NREM) sleep-related regional cerebral metabolic correlates of wakefulness after sleep onset (WASO) in patients with primary insomnia. METHODS Fifteen patients who met DSM-IV criteria for primary insomnia completed 1-week sleep diary (subjective) and polysomnographic (objective) assessments of WASO and regional cerebral glucose metabolic assessments during NREM sleep using [18F] fluoro-2-deoxy-D-glucose positron emission tomography. Whole-brain voxel-by-voxel correlations, as well as region of interest analyses, were performed between subjective and objective WASO and relative regional cerebral metabolism using the statistical software SPM2. RESULTS Subjective WASO was significantly greater than objective WASO, but the 2 measures were positively correlated. Objective WASO correlated positively with the percentage of stage 2 sleep and negatively with the percentage of stages 3 and 4 sleep. Both subjective and objective WASO positively correlated with NREM sleep-related cerebral glucose metabolism in the pontine tegmentum and in thalamocortical networks in a frontal, anterior temporal, and anterior cingulate distribution. CONCLUSIONS Increased relative metabolism in these brain regions during NREM sleep in patients with insomnia is associated with increased WASO measured either subjectively or objectively. These effects are related to the lighter sleep stages of patients with more WASO and may result from increased activity in arousal systems during sleep and or to activity in higher-order cognitive processes related to goal-directed behavior, conflict monitoring, emotional awareness, anxiety, and fear. Such changes may decrease arousal thresholds and/or increase perceptions of wakefulness in insomnia.
Studies on Jacobi–Davidson, Rayleigh quotient iteration, inverse iteration generalized Davidson and Newton updates

We study Davidson‐type subspace eigensolvers. Correction equations of Jacobi–Davidson and several other schemes are reviewed. New correction equations are derived. A general correction equation is constructed, existing correction equations may be considered as special cases of this general equation. The main theme of this study is to identify the essential common ingredient that leads to the efficiency of a diverse form of Davidson‐type methods. We emphasize the importance of the approximate Rayleigh‐quotient‐iteration direction. Copyright © 2006 John Wiley & Sons, Ltd.
Learning Structured Models for Segmentation of 2-D and 3-D Imagery

Efficient and accurate segmentation of cellular structures in microscopic data is an essential task in medical imaging. Many state-of-the-art approaches to image segmentation use structured models whose parameters must be carefully chosen for optimal performance. A popular choice is to learn them using a large-margin framework and more specifically structured support vector machines (SSVM). Although SSVMs are appealing, they suffer from certain limitations. First, they are restricted in practice to linear kernels because the more powerful nonlinear kernels cause the learning to become prohibitively expensive. Second, they require iteratively finding the most violated constraints, which is often intractable for the loopy graphical models used in image segmentation. This requires approximation that can lead to reduced quality of learning. In this paper, we propose three novel techniques to overcome these limitations. We first introduce a method to “kernelize” the features so that a linear SSVM framework can leverage the power of nonlinear kernels without incurring much additional computational cost. Moreover, we employ a working set of constraints to increase the reliability of approximate subgradient methods and introduce a new way to select a suitable step size at each iteration. We demonstrate the strength of our approach on both 2-D and 3-D electron microscopic (EM) image data and show consistent performance improvement over state-of-the-art approaches.