Miracle-dz/UniFAR-FTUs huggingface dataset:
Near Maximum-Likelihood Sequential-Search Decoding Algorithms for Binary Convolutional Codes

In this work, the maximum-likelihood sequential-search decoding algorithm proposed in [17] is revisited. By replacing the conventional Fano metric with one that is derived based on the Wagner rule, the sequential-search decoding in [17] guarantees the maximum-likelihood (ML) performance, and was therefore named the maximum-likelihood sequential decoding algorithm (MLSDA). It was then concluded by simulations that when the MLSDA is operated over the convolutional code trellis, its software computational complexity is in general considerably smaller than that of the Viterbi algorithm. A common problem on sequential-type decoding is that at the signal-to-noise ratio (SNR) below the one corresponding to the cut off rate, the average decoding complexity and the required stack size grow rapidly with the information length [25]. This problem, to some extent, prevents the practical use of sequential-type decoding from codes with long information sequence. In order to alleviate the problem in the MLSDA, we propose to directly eliminate the top path whose end node is ∆-trellis-level prior to the farthest one among all nodes that have been expanded thus far by the sequential search, which we termed the early elimination. We then analyze the early-elimination window that results in negligible performance degradation for the MLSDA. Our asymptotic-based analytical result indicates that the required early elimination window for negligible performance degradation is around three times (resp. 2.2-fold) of the constraint length for rate one-half convolutional codes under additive white Gaussian (resp. binary symmetric) channel. For rate one-third convolutional codes, the required early-elimination window reduces to two times (resp. 1.2-fold) of the constraint length for the same channel. The theoretical level thresholds almost coincide with the simulation results. As a consequence of small early elimination window required for near maximum-likelihood performance, the MLSDA with early elimination modification iv rules out considerable computational burdens, as well as memory requirement, by directly eliminating a big number of the top paths. This makes the MLSDA with early elimination suitable for applications that dictate a low-complexity software implementation with near maximum-likelihood performance. The upper bounds of decoding complexity of both the MLSDAs with and without early elimination are subsequently derived by utilizing the Berry-Esseen inequality. Both the upper bound and the simulated complexity indicate that the average decoding complexity per output bit for the MLSDA with early elimination is almost irrelevant to the memory order, as well as the message length, for medium to high SNRs.
Prevalence of mitochondrial DNA disease in adults

Diverse and variable clinical features, a loose genotype–phenotype relationship, and presentation to different medical specialties have all hindered attempts to gauge the epidemiological impact of mitochondrial DNA (mtDNA) disease. Nevertheless, a clear understanding of its prevalence remains an important goal, particularly about planning appropriate clinical services. Consequently, the aim of this study was to accurately define the prevalence of mtDNA disease (primary mutation occurs in mtDNA) in the working‐age population of the North East of England.
Benchmarking confound regression strategies for the control of motion artifact in studies of functional connectivity

Since initial reports regarding the impact of motion artifact on measures of functional connectivity, there has been a proliferation of confound regression methods to limit its impact. However, recent techniques have not been systematically evaluated using consistent outcome measures. Here, we provide a systematic evaluation of 12 commonly used confound regression methods in 193 young adults. Specifically, we compare methods according to three benchmarks, including the residual relationship between motion and connectivity, distance-dependent effects of motion on connectivity, and additional degrees of freedom lost in confound regression. Our results delineate two clear trade-offs among methods. First, methods that include global signal regression minimize the relationship between connectivity and motion, but unmask distance-dependent artifact. In contrast, censoring methods mitigate both motion artifact and distance-dependence, but use additional degrees of freedom. Taken together, these results emphasize the heterogeneous efficacy of proposed methods, and suggest that different confound regression strategies may be appropriate in the context of specific scientific goals.
MiR-210 Is Induced by Oct-2, Regulates B Cells, and Inhibits Autoantibody Production

MicroRNAs (MiRs) are small, noncoding RNAs that regulate gene expression posttranscriptionally. In this study, we show that MiR-210 is induced by Oct-2, a key transcriptional mediator of B cell activation. Germline deletion of MiR-210 results in the development of autoantibodies from 5 mo of age. Overexpression of MiR-210 in vivo resulted in cell autonomous expansion of the B1 lineage and impaired fitness of B2 cells. Mice overexpressing MiR-210 exhibited impaired class-switched Ab responses, a finding confirmed in wild-type B cells transfected with a MiR-210 mimic. In vitro studies demonstrated defects in cellular proliferation and cell cycle entry, which were consistent with the transcriptomic analysis demonstrating downregulation of genes involved in cellular proliferation and B cell activation. These findings indicate that Oct-2 induction of MiR-210 provides a novel inhibitory mechanism for the control of B cells and autoantibody production.
Adaptive Rate Allocation Scheme for Uplink TH-UWB Networks

In this paper, an efficient rate allocation scheme to maximize the throughput in uplink multi-rate time-hopping ultra-wideband (TH-UWB) communications is proposed. This is a challenging task due to the lack of a suitable closed form expression of the multiuser interference in a multi-rate context. Moreover, an exhaustive search for the optimal solution would be too prohibitive due to the high complexity induced. Our contribution can be summarized as follows: i) A new expression of the multiuser interference variance accounting for multi-rate communications is proposed. ii) Thanks to this, a computational efficient multi-rate allocation scheme is proposed. The algorithm allows to achieve high throughput while keeping a relatively low starvation rate and it outperforms a Max-Min algorithm with a fix rate for all users. Moreover, the simulations based on the theoretical analysis give insights on the influence of the different UWB parameters on the global throughput.
Sources of Variation in a Two-Step Monitoring Protocol for Species Clustered in Conspicuous Points: Dolichotis patagonum as a Case Study

In species showing distributions attached to particular features of the landscape or conspicuous signs, counts are commonly made by making focal observations where animals concentrate. However, to obtain density estimates for a given area, independent searching for signs and occupancy rates of suitable sites is needed. In both cases, it is important to estimate detection probability and other possible sources of variation to avoid confounding effects on measurements of abundance variation. Our objective was to assess possible bias and sources of variation in a two-step protocol in which random designs were applied to search for signs while continuously recording video cameras were used to perform abundance counts where animals are concentrated, using mara (Dolichotis patagonum) as a case study. The protocol was successfully applied to maras within the Península Valdés protected area, given that the protocol was logistically suitable, allowed warrens to be found, the associated adults to be counted, and the detection probability to be estimated. Variability was documented in both components of the two-step protocol. These sources of variation should be taken into account when applying this protocol. Warren detectability was approximately 80% with little variation. Factors related to false positive detection were more important than imperfect detection. The detectability for individuals was approximately 90% using the entire day of observations. The shortest sampling period with a similar detection capacity than a day was approximately 10 hours, and during this period, the visiting dynamic did not show trends. For individual mara, the detection capacity of the camera was not significantly different from the observer during fieldwork. The presence of the camera did not affect the visiting behavior of adults to the warren. Application of this protocol will allow monitoring of the near-threatened mara providing a minimum local population size and a baseline for measuring long-term trends.
Is a Coded Physical Activity Diary Valid for Assessing Physical Activity Level and Energy Expenditure in Stroke Patients?

Objectives to determine the concurrent validity of a physical activity diary for measuring physical activity level and total energy expenditure in hospitalized stroke patients. Method Sixteen stroke patients kept coded activity diaries and wore SenseWear Pro2 multi-sensor activity monitors during daytime hours for one day. A researcher observed the patients and completed a diary. Data from the patients' diaries were compared with observed and measured data to determine total activity (METs*minutes), activity level and total energy expenditure. Results Spearman correlations between the patients' and researchers' diaries revealed a high correlation for total METs*minutes (rs = 0.75, p<0.01) for sedentary (rs = 0.74,p<0.01) and moderate activities (rs = 0.71,p<0.01) and a very high correlation (rs = 0.92, p<0.01) for the total energy expenditure. Comparisons between the patients' diaries and activity monitor data revealed a low correlation (rs 0.29) for total METs*minutes and energy expenditure. Conclusion Coded self-monitoring activity diaries appear feasible as a low-tech alternative to labor-intensive observational diaries for determining sedentary, moderate, and total physical activity and for quantifying energy expenditure in hospitalized stroke patients. Given the poor correlation with objective measurements of physical activity, however, further research is needed to validate its use against a gold-standard measure of physical activity intensity and energy expenditure.
Arterial-Venous Segregation by Selective Cell Sprouting: An Alternative Mode of Blood Vessel Formation

Making Split Decisions Development of the vertebrate vasculature has been thought to involve just two mechanisms of blood vessel formation. Herbert et al. (p. 294; see the Perspective by Benedito and Adams) identified a third mechanism in zebrafish in which two distinct, unconnected vessels can be derived from a single precursor vessel. Several vascular endothelial growth factors and signaling pathways, including ephrin and notch signaling, coordinated the sorting and segregation of a mixture of arterial and venous-fated precursor cells into distinct arterial and venous vessels. These findings provide a mechanistic framework for how mixed populations of cells can coordinate their behavior to segregate and form distinct blood vessels. An alternative developmental pathway for vertebrate vasculature segregates a precursor vessel into two separate vessels. Blood vessels form de novo (vasculogenesis) or upon sprouting of capillaries from preexisting vessels (angiogenesis). With high-resolution imaging of zebrafish vascular development, we uncovered a third mode of blood vessel formation whereby the first embryonic artery and vein, two unconnected blood vessels, arise from a common precursor vessel. The first embryonic vein formed by selective sprouting of progenitor cells from the precursor vessel, followed by vessel segregation. These processes were regulated by the ligand EphrinB2 and its receptor EphB4, which are expressed in arterial-fated and venous-fated progenitors, respectively, and interact to orient the direction of progenitor migration. Thus, directional control of progenitor migration drives arterial-venous segregation and generation of separate parallel vessels from a single precursor vessel, a process essential for vascular development.
Using natural products for drug discovery: the impact of the genomics era

ABSTRACT Introduction: Evolutionarily selected over billions of years for their interactions with biomolecules, natural products have been and continue to be a major source of pharmaceuticals. In the 1990s, pharmaceutical companies scaled down their natural product discovery programs in favor of synthetic chemical libraries due to major challenges such as high rediscovery rates, challenging isolation, and low production titers. Propelled by advances in DNA sequencing and synthetic biology technologies, insights into microbial secondary metabolism provided have inspired a number of strategies to address these challenges. Areas covered: This review highlights the importance of genomics and metagenomics in natural product discovery, and provides an overview of the technical and conceptual advances that offer unprecedented access to molecules encoded by biosynthetic gene clusters. Expert opinion: Genomics and metagenomics revealed nature’s remarkable biosynthetic potential and her vast chemical inventory that we can now prioritize and systematically mine for novel chemical scaffolds with desirable bioactivities. Coupled with synthetic biology and genome engineering technologies, significant progress has been made in identifying and predicting the chemical output of biosynthetic gene clusters, as well as in optimizing cluster expression in native and heterologous host systems for the production of pharmaceutically relevant metabolites and their derivatives.
Frontiers in Source Modeling for Near-Source Ground-Motion Prediction

Accurate prediction of the intensity and variability of strong ground motions for future large earthquakes depends on our ability to simulate realistic earthquake source models. While there has been considerable progress in characterizing the complexity of earthquake ruptures, recent devastating earthquakes have exhibited rather unexpected behavior. Moderate-size events occurred with surprisingly large ground motions, in contrast to very large ruptures that showed relatively low ground motions in the frequency range of 0.1 – 3.0 sec. These observations are at odds with standard ground-motion attenuation relationships, and fundamentally challenge current strong-motion prediction methods. A related issue is the question about the upper limits of near-source ground motions. These topics can only be reconciled by considering the complexity of earthquake faulting and the dynamic processes of rupture nucleation, propagation and arrest. In this paper we discuss recent improvements to generate physically consistent earthquake rupture models for strong-motion simulation. We combine simulated slip distributions (realization of spatial random fields, consistent in scaling and spatial variability with slip distributions of past earthquakes) with constraints on the rupture nucleation and energy budget of earthquake rupture. Efficient stress-drop calculations in the spectral domain serve as input to estimate the temporal evolution of the rupture process through a set of empirical relationships derived from the analysis of spontaneous dynamic rupture models. Long-term earthquake-cycle simulations with realistic variability in rate-and-state friction parameters provide constraints on the generation, long-term behavior and characterization of earthquake source complexity for fault zones at different evolutionary stages. The pseudo-dynamic source characterization is inherently kinematic, but emulates the most important characteristics of dynamic rupture. While the relationships between dynamic source parameters are simplifications of the true complexity in rupture physics, they help identify the interaction between source properties that are relevant for strong ground motion prediction, and provide an improvement over purely kinematic models.
Cadmium Toxicity to Microcystis aeruginosa PCC 7806 and Its Microcystin-Lacking Mutant

The adverse effects of microcystin (MC) produced by cyanobacteria have drawn considerable attention from the public. Yet it remains unclear whether MC confers any benefits to the cyanobacteria themselves. One suggested function of MC is complexation, which may influence the bioaccumulation and toxicity of trace metals. To test this hypothesis, we examined Cd toxicity to wild-type Microcystis aeruginosa PCC 7806 (WT) and its MC-lacking mutant (MT) under nutrient-enriched (+NP), phosphorus-limited (-P), and nitrogen-limited (-N) conditions. The accumulation of Cd and the biochemical parameters associated with its detoxification [total phosphorus (TP), inorganic polyphosphate (Poly-P), and glutathione (GSH) in the cells as well as intra- and extra-cellular carbohydrates] were quantified. Although the –P cyanobacteria accumulated less Cd than their +NP and –N counterparts, the different nutrient-conditioned cyanobacteria were similarly inhibited by similar free ion concentration of Cd in the medium ([Cd2+]F). Such good toxicity predictability of [Cd2+]F was ascribed to the synchronous decrease in the intracellular concentrations of Cd and TP. Nevertheless, Cd toxicity was still determined by the intracellular Cd to phosphorus ratio (Cd/P), in accordance with what has been reported in the literature. On the other hand, the concentrations of TP, Poly-P, and carbohydrates went up, but GSH concentration dropped down with the enhancement of [Cd2+]F, indicating their association with Cd detoxification. Although the inactivation of MC peptide synthetase gene had some nutrient and Cd concentration dependent effects on the parameters above, both cyanobacterial strains showed the same Cd accumulation ability and displayed similar Cd sensitivity. These results suggest that MC cannot affect metal toxicity either by regulating metal accumulation or by altering the detoxification ability of the cyanobacteria. Other possible functions of MC need to be further investigated.
A Functional Neuroimaging Description of Two Deep Dyslexic Patients

Deep dyslexia is a striking reading disorder that results from left-hemisphere brain damage and is characterized by semantic errors in reading single words aloud (e.g., reading spirit as whisky). Two types of explanation for this syndrome have been advanced. One is that deep dyslexia results from a residual left-hemisphere reading system that has lost the ability to pronounce a printed word without reference to meaning. The second is that deep dyslexia reflects right-hemisphere word processing. Although previous attempts to adjudicate between these hypotheses have been inconclusive, the controversy can now be addressed by mapping functional anatomy. In this study, we demonstrate that reading by two deep dyslexic patients (CJ and JG) involves normal or enhanced activity in spared left-hemisphere regions associated with naming (Broca's area and the left posterior inferior temporal cortex) and with the meanings of words (the left posterior temporo-parietal cortex and the left anterior temporal cortex). In the right-hemisphere homologues of these regions, there was inconsistent activation within the normal group and between the deep dyslexic patients. One (CJ) showed enhanced activity (relative to the normals) in the right anterior inferior temporal cortex, the other (JG) in the right Broca's area, and both in the right frontal operculum. Although these differential right-hemisphere activations may have influenced the reading behavior of the patients, their activation patterns primarily reflect semantic and phonological systems in spared regions of the left hemisphere. These results preclude an explanation of deep dyslexia in terms of purely right-hemisphere word processing.
Thermodynamic Model for Energy-Constrained Open-System Evolution of Crustal Magma Bodies Undergoing Simultaneous Recharge, Assimilation and Crystallization: the Magma Chamber Simulator

The Magma Chamber Simulator quantifies the impact of simultaneous recharge, assimilation and crystallization through mass and enthalpy balance in a multicomponent^multiphase (melt þ solids (cid:2) fluid) composite system. As a rigorous thermodynamic model, the Magma Chamber Simulator computes phase equilibria and geochemical evolution self-consistently in resident magma, recharge magma and wallrock, all of which are connected by specified thermodynamic boundaries, to model an evolving open-system magma body. In a simulation, magma cools from its liquidus temperature, and crystals (cid:2) fluid are incrementally fractionated to a separate cumulate reservoir. Enthalpy from cooling, crystallization, and possible magma recharge heats wallrock from its initial subsolidus temperature. Assimilation begins when a critical wallrock melt volume fraction (0 · 04^0 · 12) in a range consistent with the rheology of partially molten rock systems is achieved.The mass of melt above this limit is removed from the wallrock and homogenized with the magma body melt. New equilibrium states for magma and wallrock are calculated that reflect conservation of total mass, mass of each element and enthalpy. Magma cooling and crystallization, addition of recharge magma and anatectic melt to the magma body (where ap-propriate), and heating and arguments, does not occur because assimilation suppresses crystallization by modifying the topology of multicomponent phase saturation surfaces. As a consequence, contaminated magma composition and crystallizing solids are distinct compared with the FC-only case. (2) At similar stages ofevolution, contaminated melt is more vo-luminous ( (cid:3) 3 · 5 (cid:4) ) than melt formed by FC-only. (3) In AFC, some trace element concentrations are lower than their FC-only counterparts at the same stage of evolution. Elements that typically behave incompatibly in mafic and intermediate magmas (e.g. La, Nd, Ba) may not be ‘enriched’ by crustal contamination, and the most ‘crustal’ isotope signatures may not correlate with the highest concentrations of such elements. (4) The proportion of an element contributed by anatectic melt to resident magma is typically different for each element, and thus the extent of mass exchange between crust and magma should be quantified using total mass rather than the mass of a single element. Based on these sometimes unexpected results, it can be argued that progress in quantifying the origin and evolution of open magmatic systems and documenting how mantle-derived magmas and the crust interact rely not only on improvements in instrumentation and generation of larger datasets, but also on continued development of computational tools that couple thermodynamic assessment of phase equilibria in multicomponent systems with energy and mass conservation.
PeerSearch: Efficient Information Retrieval in Peer-to-Peer Networks

In this paper, we propose an efficient peer-to-peer information retrieval system PeerSearch that supports state-of-the-art content and semantic searches. PeerSearch avoids the scalability problem of existing systems that employ centralized indexing, index flooding, or query flooding. It also avoids the non-determinism that exhibited by heuristic-based approaches. PeerSearch achieves both efficiency and determinism through an elegant combination of index placement and query routing. Given a query, PeerSearch only needs to search a small number of nodes to identify matching documents.