Miracle-dz/UniFAR-FTUs huggingface dataset:
Global Diffusion Tractography by Simulated Annealing

<italic>Objective:</italic> Our goal is to develop a robust global tractography method for cardiac diffusion imaging. <italic>Methods:</italic> A graph is stretched over the whole myocardium to represent the fiber structure, and the solutions are minima of a graph energy measuring the fidelity to the data along with the fiber density and curvature. The optimization is performed by a variant of simulated annealing that offers increased design freedom without sacrificing theoretical convergence guarantees. <italic>Results:</italic> Numerical experiments on synthetic and real data demonstrate the capability of our tractography algorithm to deal with low angular resolution, highly noisy data. In particular, our algorithm outperforms the Bayesian model-based algorithm of Reisert <italic>et al. </italic> (<italic>NeuroImage</italic>, vol. 54, no. 2, 2011) and the graph-based algorithm of Frindel <italic> et al.</italic> (<italic>Magn. Reson. Med.</italic>, vol. 64, no. 4, 2010) at the noise levels typical of in vivo imaging. <italic>Conclusion:</italic> The proposed algorithm avoids the drawbacks of local techniques and is very robust to noise, which makes it a promising tool for <italic>in vivo</italic> diffusion imaging of moving organs. <italic>Significance:</italic> Our approach is global in terms of both the fiber structure representation and the minimization problem. It also allows us to adjust the trajectory density by simply changing the vertex-lattice spacing in the graph model, a desirable feature for multiresolution tractography analysis.
Traditional Chinese Medicine (TCM) and Herbal Hepatotoxicity: RUCAM and the Role of Novel Diagnostic Biomarkers Such as MicroRNAs

Background: Traditional Chinese Medicine (TCM) with its focus on herbal use is popular and appreciated worldwide with increased tendency, although its therapeutic efficacy is poorly established for most herbal TCM products. Treatment was perceived as fairly safe but discussions emerged more recently as to whether herb induced liver injury (HILI) from herbal TCM is a major issue; Methods: To analyze clinical and case characteristics of HILI caused by herbal TCM, we undertook a selective literature search in the PubMed database with the search items Traditional Chinese Medicine, TCM, alone and combined with the terms herbal hepatotoxicity or herb induced liver injury; Results: HILI caused by herbal TCM is rare and similarly to drugs can be caused by an unpredictable idiosyncratic or a predictable intrinsic reaction. Clinical features of liver injury from herbal TCM products are variable, and specific diagnostic biomarkers such as microsomal epoxide hydrolase, pyrrole-protein adducts, metabolomics, and microRNAs are available for only a few TCM herbs. The diagnosis is ascertained if alternative causes are validly excluded and causality levels of probable or highly probable are achieved applying the liver specific RUCAM (Roussel Uclaf Causality Assessment Method) as the most commonly used diagnostic tool worldwide. Case evaluation may be confounded by inappropriate or lacking causality assessment, poor herbal product quality, insufficiently documented cases, and failing to exclude alternative causes such as infections by hepatotropic viruses including hepatitis E virus infections; Conclusion: Suspected cases of liver injury from herbal TCM represent major challenges that deserve special clinical and regulatory attention to improve the quality of case evaluations and ascertain patients’ safety and benefit.
Dual-tree $k$-means with bounded iteration runtime

k-means is a widely used clustering algorithm, but for $k$ clusters and a dataset size of $N$, each iteration of Lloyd's algorithm costs $O(kN)$ time. Although there are existing techniques to accelerate single Lloyd iterations, none of these are tailored to the case of large $k$, which is increasingly common as dataset sizes grow. We propose a dual-tree algorithm that gives the exact same results as standard $k$-means; when using cover trees, we use adaptive analysis techniques to, under some assumptions, bound the single-iteration runtime of the algorithm as $O(N + k log k)$. To our knowledge these are the first sub-$O(kN)$ bounds for exact Lloyd iterations. We then show that this theoretically favorable algorithm performs competitively in practice, especially for large $N$ and $k$ in low dimensions. Further, the algorithm is tree-independent, so any type of tree may be used.
Nej1 recruits the Srs2 helicase to DNA double-strand breaks and supports repair by a single-strand annealing-like mechanism

Double-strand breaks (DSBs) represent the most severe DNA lesion a cell can suffer, as they pose the risk of inducing loss of genomic integrity and promote oncogenesis in mammals. Two pathways repair DSBs, nonhomologous end joining (NHEJ) and homologous recombination (HR). With respect to mechanism and genetic requirements, characterization of these pathways has revealed a large degree of functional separation between the two. Nej1 is a cell-type specific regulator essential to NHEJ in Saccharomyces cerevisiae. Srs2 is a DNA helicase with multiple roles in HR. In this study, we show that Nej1 physically interacts with Srs2. Furthermore, mutational analysis of Nej1 suggests that the interaction was strengthened by Dun1-dependent phosphorylation of Nej1 serines 297/298. Srs2 was previously shown to be recruited to replication forks, where it promotes translesion DNA synthesis. We demonstrate that Srs2 was also efficiently recruited to DSBs generated by the HO endonuclease. Additionally, efficient Srs2 recruitment to this DSB was dependent on Nej1, but independent of mechanisms facilitating Srs2 recruitment to replication forks. Functionally, both Nej1 and Srs2 were required for efficient repair of DSBs with 15-bp overhangs, a repair event reminiscent of a specific type of HR called single-strand annealing (SSA). Moreover, absence of Rad51 suppressed the SSA-defect in srs2 and nej1 strains. We suggest a model in which Nej1 recruits Srs2 to DSBs to promote NHEJ/SSA-like repair by dismantling inappropriately formed Rad51 nucleoprotein filaments. This unexpected link between NHEJ and HR components may represent cross-talk between DSB repair pathways to ensure efficient repair.
Quantitative analysis of the thermal requirements for stepwise physical dormancy-break in seeds of the winter annual Geranium carolinianum (Geraniaceae).

BACKGROUND AND AIMS Physical dormancy (PY)-break in some annual plant species is a two-step process controlled by two different temperature and/or moisture regimes. The thermal time model has been used to quantify PY-break in several species of Fabaceae, but not to describe stepwise PY-break. The primary aims of this study were to quantify the thermal requirement for sensitivity induction by developing a thermal time model and to propose a mechanism for stepwise PY-breaking in the winter annual Geranium carolinianum. METHODS Seeds of G. carolinianum were stored under dry conditions at different constant and alternating temperatures to induce sensitivity (step I). Sensitivity induction was analysed based on the thermal time approach using the Gompertz function. The effect of temperature on step II was studied by incubating sensitive seeds at low temperatures. Scanning electron microscopy, penetrometer techniques, and different humidity levels and temperatures were used to explain the mechanism of stepwise PY-break. KEY RESULTS The base temperature (Tb) for sensitivity induction was 17·2 °C and constant for all seed fractions of the population. Thermal time for sensitivity induction during step I in the PY-breaking process agreed with the three-parameter Gompertz model. Step II (PY-break) did not agree with the thermal time concept. Q10 values for the rate of sensitivity induction and PY-break were between 2·0 and 3·5 and between 0·02 and 0·1, respectively. The force required to separate the water gap palisade layer from the sub-palisade layer was significantly reduced after sensitivity induction. CONCLUSIONS Step I and step II in PY-breaking of G. carolinianum are controlled by chemical and physical processes, respectively. This study indicates the feasibility of applying the developed thermal time model to predict or manipulate sensitivity induction in seeds with two-step PY-breaking processes. The model is the first and most detailed one yet developed for sensitivity induction in PY-break.
Protein phosphatase magnesium‐dependent 1A–mediated inhibition of BMP signaling is independent of Smad dephosphorylation

Phosphorylation of Smad1/5/8 at carboxyl‐terminal serine residues by type I receptors activates downstream bone morphogenetic protein (BMP) signaling. Protein phosphatase magnesium‐dependent 1A (PPM1A) has been shown to suppress BMP activity by dephosphorylating phospho‐Smads. We report here that PPM1A suppresses BMP signaling via a novel mechanism. PPM1A inhibited a constitutively activated Smad1 mutant lacking BMP receptor phosphorylation sites. PPM1A reduced the protein levels not only of Smad1 but also of Smad5 and Smad8. A proteasome inhibitor blocked the inhibitory effects of PPM1A on Smad1, but the Smurf‐binding motif in the Smad1 linker region was not involved in this inhibition. The phosphatase activity of PPM1A is essential for inhibition. Taken together, these findings suggest that through the dephosphorylation of unidentified substrate(s), PPM1A inhibits BMP signaling by decreasing Smad protein levels via the proteasome pathway. Moreover, knockdown of endogenous PPM1A stimulated osteoblastic differentiation, suggesting that PPM1A may physiologically suppress BMP signaling via Smads. © 2010 American Society for Bone and Mineral Research
Ageing adversely affects the migration and function of marginal zone B cells

Marginal zone (MZ) B cells are positioned within the spleen to capture blood‐borne antigen and immune complexes and deliver them to follicular dendritic cells in the B‐cell follicles. We show that within the spleens of aged mice antigen capture by MZ B cells, and their ability to shuttle between the follicle and MZ, were impaired. The ability of aged MZ B cells to migrate towards the MZ chemoattractant sphingosine‐1‐phosphate was increased, suggesting that aged MZ B cells had a greater propensity to be retained within the MZ. An extrinsic impairment in aged B‐cell migration towards the MZ was demonstrated using bone marrow chimeras. The follicular shuttling of MZ B cells derived from either young or aged bone marrow was similarly reduced in aged recipient spleens, showing that ageing effects on splenic stromal cells were responsible for the impaired follicular shuttling of MZ B cells. MZ B cells rapidly mount T‐cell‐independent (TI) antibody‐responses to microbial polysaccharide antigen. In aged mice the ability to produce immunoglobulins in response to the TI type 1 antigen TNP‐LPS was impaired. These ageing‐related changes to the MZ and MZ B cells have implications for the clearance of blood‐borne pathogens. Indeed elderly people have increased susceptibility to Streptococcus pneumoniae, a TI antigen, and decreased responses to vaccination. A thorough analysis of the mechanisms that underpin the ageing‐related decline in the status of the MZ and MZ B cells will help the design of novel treatments to improve immunity in the elderly.
Minimum-delay overlay multicast

Delivering delay-sensitive data to a group of receivers with minimum latency is a fundamental problem for various distributed applications. In this paper, we study multicast routing with minimum end-to-end delay to the receivers. The delay to each receiver in a multicast tree consist of the time that the data spends in overlay links as well as the latency incurred at each overlay node, which has to send out a piece of data several times over a finite-capacity network connection. The latter portion of the delay, which is proportional to the degree of nodes in the tree, can be a significant portion of the total delay as we show in the paper. Yet, it is often ignored or only partially addressed by previous multicast algorithms. We formulate the actual delay to the receivers in a multicast tree and consider minimizing the average and the maximum delay in the tree. We show the NP-hardness of these problems and prove that they cannot be approximated in polynomial time to within any reasonable approximation ratio. We then present a number of efficient algorithms to build a multicast tree in which the average or the maximum delay is minimized. These algorithms cover a wide range of overlay sizes for both versions of our problem. The effectiveness of our algorithms is demonstrated through comprehensive experiments on different real-world datasets, and using various overlay network models. The results confirm that our algorithms can achieve much lower delays (up to 60% less) and up to orders of magnitude faster running times (i.e., supporting larger scales) than previous minimum-delay multicast approaches.
Inference of ice cloud properties from high spectral resolution infrared observations

The theoretical basis is explored for inferring the microphysical properties of ice clouds from high spectral resolution infrared (IR) observations. Extensive radiative transfer simulations are carried out to address relevant issues. The single-scattering properties of individual ice crystals are computed from state-of-the-art light scattering computational methods and are subsequently averaged for 30 in situ particle size distributions and for four additional analytical Gamma size distributions. The nonsphericity of ice crystals is shown to have a significant impact on the radiative signatures in the IR spectrum. Furthermore, the errors associated with the use of the Henyey-Greenstein phase function can be larger than 1 K in terms of brightness temperature for large particle effective sizes (/spl sim/80 /spl mu/m) at wavenumbers where the scattering of the IR radiation by ice crystals is not negligible. The simulations undertaken in this paper show that the slope of the IR brightness temperature spectrum between 790-960 cm/sup -1/ is sensitive to the effective particle size. Furthermore, a strong sensitivity of the IR brightness temperature to cloud optical thickness is noted within the 1050-1250-cm/sup -1/ region. Based on these spectral features, a technique is presented for the simultaneous retrieval of the visible optical thickness and effective particle size from high spectral resolution IR data for ice clouds. An error analysis shows that the uncertainties of the retrieved optical thickness and effective particle size have a small range of variation. The error for retrieving particle size in conjunction with an uncertainty of 5 K in cloud temperature, or a surface temperature uncertainty of 2.5 K, is less than 15%. The corresponding errors in the uncertainty of optical thickness are within 5% to 20%, depending on the value of cloud optical thickness. The applicability of the present retrieval technique is demonstrated using airborne high-resolution IR measurements obtained during two field campaigns.
Genre Systems: Structuring Interaction through Communicative Norms

In this paper we demonstrate that teams may use genre systems-sequences of interrelated communicative actions-deliberately or habitually, to structure their collaboration. Using data over a seven-month period from three teams' use of a collaborative electronic technology, Team Room, we illustrate that genre systems are a means of structuring six dimensions of communicative interaction: purpose (why), content (what), participants (who/m), form (how), time (when), and place (where). We suggest that researchers and users may benefit from explicitly recog nizing the role genre systems can play in collaboration and from examining changes in these six dimensions accompanying changes in electronic technology.
Convolutional Attention-based Seq2Seq Neural Network for End-to-End ASR

This thesis introduces the sequence to sequence model with Luong's attention mechanism for end-to-end ASR. It also describes various neural network algorithms including Batch normalization, Dropout and Residual network which constitute the convolutional attention-based seq2seq neural network. Finally the proposed model proved its effectiveness for speech recognition achieving 15.8% phoneme error rate on TIMIT dataset.
Backscatter Error Bounds for the Elastic Lidar Two-Component Inversion Algorithm

Total backscatter-coefficient inversion error bounds for the two-component lidar inversion algorithm (so-called Fernald's or Klett-Fernald-Sasano's method) are derived in analytical form in response to the following three error sources: 1) the measurement noise; 2) the user uncertainty in the backscatter-coefficient calibration; and 3) the aerosol extinction-to-backscatter ratio. The following two different types of error bounds are presented: 1) approximate error bounds using first-order error propagation and 2) exact error bounds using a total-increment method. Both error bounds are formulated in explicit analytical form, which is of advantage for practical physical sensitivity analysis and computational implementation. A Monte Carlo approach is used to validate the error bounds at 355-, 532-, and 1064-nm wavelengths.
A categorization theorem on suffix arrays with applications to space efficient text indexes

In this paper, we design succinct index structures for a text string <i>T</i> of <i>n</i> binary symbols to support efficient searching of a pattern <i>P</i> of length <i>m</i>. Motivated by the fact that the standard representation of suffix arrays uses <i>n</i> lg <i>n</i> bits which is more than the theoretical minimum, we present a theorem that characterizes a permutation as the suffix array of a binary string. Based on the theorem, we design a succinct representation of suffix arrays of binary strings that uses <i>n</i> + <i>o</i>(<i>n</i>) bits, which is the theoretical minimum plus a lower order term, and answers existential and cardinality queries in <i>O(m)</i> time without storing the raw text. With <i>2n</i>+<i>o(n)</i> bits, we can list pattern occurrences in <i>O</i>(<i>m</i> + <i>occ</i> lg <i>n</i>) time in the general case, and for long patterns, when <i>m</i> = Ω(lg<sup>1+∈</sup> <i>n</i>), we answer such listing queries in <i>O</i>(<i>m</i> + <i>occ</i>) time. We also present another implementation that uses <i>O</i>(<i>n</i>) bits and supports pattern searching in <i>O</i>(<i>m</i> + <i>occ</i> lg<sup>λ</sup> <i>n</i>) time for any fixed λ such that 0 < λ < 1. More results and trade-offs are reported in the paper.
Effect of the IL28B Rs12979860 C/T polymorphism on the incidence and features of active cytomegalovirus infection in allogeneic stem cell transplant patients

The current study was aimed at investigating whether the single nucleotide polymorphism (SNP) (rs12979860), upstream of the IL28B gene, had any effect on the incidence rate and the features of active CMV infection in the Allogeneic stem cell transplantation setting. This was a retrospective observational study including 151 patients undergoing T cell‐replete Allo‐SCT. Donor and recipient IL28 SNP genotype was determined by allele‐specific real‐time PCR. The incidence rate of active CMV infection was not significantly associated with either the donor or the recipient IL28B SNP genotype. Nevertheless, a trend towards a lower incidence of active CMV infection was noted in the donor T/T population with respect to the donor C/T and C/C population. The duration of first episodes of CMV DNAemia was significantly shorter in patients carrying the donor T/T genotype with respect to their C/C or C/T counterparts (P = 0.038). Peak CMV DNAmeia levels tended to be lower in patients carrying the T/T genotype (donor or recipient) than in C/C or C/T patients, although statistical significance was not reached. In conclusion the data presented pointed to a protective effect of the T allele (recessive genetic model) against CMV infection in the Allo‐SCT setting. J. Med. Virol. 86:838–844, 2014. © 2013 Wiley Periodicals, Inc.
COMPARISON OF FILTERING ALGORITHMS

To determine the performance of filtering algorithms a study was conducted in which eight groups filtered data supplied to them. The study aimed to determine the general performance of filters, the influence of point resolution on filtering and future research directions. To meet the objectives the filtered data was compared against reference data that was generated manually. In general the filters performed well in landscapes of low complexity. However, complex landscapes as can be found in city areas and discontinuities in the bare earth still pose challenges. Comparison of filtering at lower resolutions confirms that amongst other factors the method of filtering also has an impact on the success of filtering and hence on the choice of scanning resolution. It is suggested that future research be directed at heuristic classification of point-clouds (based on external data), quality reporting, and improving the efficiency of filter strategies.
Urodynamic profile of patients with neurogenic bladder following non-traumatic myelopathies

Objective: To observe the urodynamic profile of the patients following non-traumatic myelopathies (NTMs) with neurogenic bladder. Setting: Neurological rehabilitation department of university tertiary research hospital. Materials and Methods: Seventy-nine patients (44 men) with monophasic NTM, with the age range 8-65 years (31.0 ± 16.0 years), were admitted for inpatients’ rehabilitation. Length of stay in rehabilitation ranged from 6 to 120 days (32.0 ± 24.8 days). Fifty-six patients (70.9%) had spinal lesion above D10, 17 had lesion between D10 and L2 (21.5%), and 6 (7.6%) had cauda equina syndrome. All patients had neurogenic bladder with urinary complaints. Urodynamic study (UDS) was performed in all patients. Results: UDS showed 71.4% patients (40/56) had neurogenic detrusor overactivity (NDO) with or without sphincter dyssynergy (DSD) with lesion above D10; only 52.9% patients (9/17) had NDO with or without DSD detrusor with lesion between D10 and L2; and majority (5/6 patients) had underactive detrusor in the cauda equina group. Bladder management was based on the UDS findings. No significant correlation was found (P > 0.05) between detrusor behavior and the level, severity (ASIA Impairment Scale) of spinal injury, or gender using chi-square test. Conclusions: Neurogenic bladder following NTM was observed in all patients. UDS suggested predominantly NDO in lesions above D10 and mixed pattern in between D10 and L2 lesions. No significant correlation was found between detrusor behavior and the level or severity of NTM in the study.
The Epic 2001 Stratocumulus Study

Abstract Overlaying the cool southeast Pacific Ocean is the most persistent subtropical stratocumulus cloud deck in the world. It produces a profound affect on tropical climate by shading the underlying ocean and radiatively cooling and stirring up turbulence in the atmosphere. In October 2001, the East Pacific Investigation of Climate undertook an exploratory cruise from the Galapagos Islands to Chile. The cruise gathered an unprecedented dataset, integrating radiosonde, surface, cloud remote sensing, aerosol, and ocean measurements. Scientific objectives included measuring the vertical structure of the ABL in this region, understanding what physical processes are determining the stra-tocumulus cloud albedo, and understanding the fluxes of heat and water that couple the atmosphere and ocean in this region. An unexpectedly well-mixed stratocumulus-capped boundary layer as a result of a strong inversion was encountered throughout. A strong diurnal cycle was observed, with thicker clouds and substantial dri.