Miracle-dz/UniFAR-FTUs huggingface dataset:
Quantitative evaluation of the pyramidal tract segmented by diffusion tensor tractography: feasibility study in patients with amyotrophic lateral sclerosis.

PURPOSE Diffusion tensor imaging can evaluate the cerebral white matter quantitatively using fractional anisotropy (FA) and also can extract a certain tract by tractography, but these two have been used separately and not combined. The purpose of this study was to assess the clinical feasibility of ROI analysis using diffusion tensor tractography (DTT) in patients with amyotrophic lateral sclerosis (ALS). MATERIALS AND METHODS Sixteen patients with ALS (9 limb-onset type, 7 bulbar-onset type) and nine age-matched volunteers were studied. DTT of the corticobulbar tract (DTT-CBT) and corticospinal tract (DTT-CST) were visualized by free software (dTV/VOLUME-ONE). Regions-of-interest (ROIs) were semi-automatically placed on the tracts defined by DTT methods, and FA values within the ROIs were measured. RESULTS Mean FA values of ALS patients in the ROIs along the DTT-CST (bulbar-onset: 0.574, limb-onset: 0.594) were significantly lower than those of controls (DTT-CST: 0.629) (p<0.05). The mean FA of DTT-CBT of the bulbar-onset type (0.509) was significantly lower than that of the limb-onset type (0.558) and that of volunteers (0.561). CONCLUSION DTT could segmentate certain white matter tracts and evaluate them quantitatively. It could depict the subtle changes between subtypes of ALS as well as the changes between the patients and volunteers.
Robust monitoring of network-wide aggregates through gossiping

We investigate the use of gossip protocols for continuous monitoring of network-wide aggregates under crash failures. Aggregates are computed from local management variables using functions such as SUM, MAX, or AVERAGE. For this type of aggregation, crash failures offer a particular challenge due to the problem of mass loss, namely, how to correctly account for contributions from nodes that have failed. In this paper we give a partial solution. We present G-GAP, a gossip protocol for continuous monitoring of aggregates, which is robust against failures that are discontiguous in the sense that neighboring nodes do not fail within a short period of each other. We give formal proofs of correctness and convergence, and we evaluate the protocol through simulation using real traces. The simulation results suggest that the design goals for this protocol have been met. For instance, the tradeoff between estimation accuracy and protocol overhead can be controlled, and a high estimation accuracy (below some 5% error in our measurements) is achieved by the protocol, even for large networks and frequent node failures. Further, we perform a comparative assessment of GGAP against a tree-based aggregation protocol using simulation. Surprisingly, we find that the tree-based aggregation protocol consistently outperforms the gossip protocol for comparative overhead, both in terms of accuracy and robustness.
Deep Gaussian Conditional Random Field Network: A Model-Based Deep Network for Discriminative Denoising

We propose a novel end-to-end trainable deep network architecture for image denoising based on a Gaussian Conditional Random Field (GCRF) model. In contrast to the existing discriminative denoising methods that train a separate model for each individual noise level, the proposed deep network explicitly models the input noise variance and hence is capable of handling a range of noise levels. Our deep network, which we refer to as deep GCRF network, consists of two sub-networks: (i) a parameter generation network that generates the pairwise potential parameters based on the noisy input image, and (ii) an inference network whose layers perform the computations involved in an iterative GCRF inference procedure. We train two deep GCRF networks (each network operates over a range of noise levels: one for low input noise levels and one for high input noise levels) discriminatively by maximizing the peak signal-to-noise ratio measure. Experiments on Berkeley segmentation and PASCALVOC datasets show that the proposed approach produces results on par with the state of-the-art without training a separate network for each individual noise level.
Combination of COX-2 expression and PIK3CA mutation as prognostic and predictive markers for celecoxib treatment in breast cancer

COX-2 expression level and prognostic value are still a matter of debate in breast cancer (BC). We addressed these points in the context of PIK3CA mutational status. Based on an interesting study of aspirin efficacy in colorectal cancer, we hypothesized that celecoxib antitumoral activity may be restricted to PIK3CA mutated BC. COX-2 mRNA expression was analyzed in 446 BC samples and in 61 BC patient-derived xenografts (PDX) using quantitative RT-PCR. The prognostic impact of COX-2 expression level was assessed independently and according to PIK3CA mutational status in our cohort and in a validation set of 817 BC. The antitumoral activity of celecoxib was tested in two triple-negative (TN) PDX with a PIK3CA wild-type (wt) or mutated genotype. COX-2 mRNA was overexpressed in 2% of BC and significantly associated with TN subtype. Metastasis-free survival (MFS) was significantly better in patients with high COX-2 expression level, the prognosis of whom was similar to patients with PIK3CA mutations. TCGA validation cohort confirmed that patients with low COX-2 expression PIK3CA wt tumors had the worse disease-free survival (DFS) compared to all other subgroups. Celecoxib had a significant antitumoral effect in PIK3CA mutated PDX only. Celecoxib antitumoral activity involved S6 ribosomal protein and AKT phosphorylation. Low expression of COX-2 has a significant negative impact on the MFS/DFS of BC patients. Antitumoral effect of celecoxib is restricted to PIK3CA mutated PDX. These results suggest that PIK3CA mutation may be a new predictive biomarker for celecoxib efficacy.
Sensory and Motor Systems Organization of the Mammalian Locomotor CPG: Review of Computational Model and Circuit Architectures Based on Genetically Identified Spinal Interneurons

The organization of neural circuits that form the locomotor central pattern generator (CPG) and provide flexor–extensor and left–right coordination of neuronal activity remains largely unknown. However, significant progress has been made in the molecular/genetic identification of several types of spinal interneurons, including V0 (V0D and V0V subtypes), V1, V2a, V2b, V3, and Shox2, among others. The possible functional roles of these interneurons can be suggested from changes in the locomotor pattern generated in mutant mice lacking particular neuron types. Computational modeling of spinal circuits may complement these studies by bringing together data from different experimental studies and proposing the possible connectivity of these interneurons that may define rhythm generation, flexor–extensor interactions on each side of the cord, and commissural interactions between left and right circuits. This review focuses on the analysis of potential architectures of spinal circuits that can reproduce recent results and suggest common explanations for a series of experimental data on genetically identified spinal interneurons, including the consequences of their genetic ablation, and provides important insights into the organization of the spinal CPG and neural control of locomotion.
Hazelnut: a bidirectionally typed structure editor calculus

Structure editors allow programmers to edit the tree structure of a program directly. This can have cognitive benefits, particularly for novice and end-user programmers. It also simplifies matters for tool designers, because they do not need to contend with malformed program text. This paper introduces Hazelnut, a structure editor based on a small bidirectionally typed lambda calculus extended with holes and a cursor. Hazelnut goes one step beyond syntactic well-formedness: its edit actions operate over statically meaningful incomplete terms. Naïvely, this would force the programmer to construct terms in a rigid "outside-in" manner. To avoid this problem, the action semantics automatically places terms assigned a type that is inconsistent with the expected type inside a hole. This meaningfully defers the type consistency check until the term inside the hole is finished. Hazelnut is not intended as an end-user tool itself. Instead, it serves as a foundational account of typed structure editing. To that end, we describe how Hazelnut's rich metatheory, which we have mechanized using the Agda proof assistant, serves as a guide when we extend the calculus to include binary sum types. We also discuss various interpretations of holes, and in so doing reveal connections with gradual typing and contextual modal type theory, the Curry-Howard interpretation of contextual modal logic. Finally, we discuss how Hazelnut's semantics lends itself to implementation as an event-based functional reactive program. Our simple reference implementation is written using js_of_ocaml.
Effect of increased level of fertilizers on Bt cotton and green fodder yield under cotton + legume fodder intercropping system of western zone of Tamil Nadu

A Field experiment was conducted during Kharif 2015-16 and 2016-17 at Krishi Vigyan Kendra, Veterinary College and Research Institute campus, Namakkal, Tamil Nadu to assess the performance of increased level of fertilizers on yield of Bt cotton and green fodder yield under intercropping situation as part of Ph.D., research programme. Cotton yield was significantly higher (2029 and 1507 kg ha-1) in the Bt cotton + moth bean intercropping system during both years experimentation and lower was recorded under Bt cotton + fodder cowpea intercropping system. Application of 150% RDF resulted that the significantly higher cotton yield of 1991 kg ha-1 and 1474 kg ha-1 during 2015-2016 and 2016-2017, respectively. But, intercropping of fodder cowpea with Bt cotton had higher seed cotton equivalent yield and net returns with application of 150% recommended dose of fertilizers. Fodder cowpea with application of 150% RDF produced higher green fodder yield 17407 and 14431 kg ha-1 during first and second year respectively. Lower fodder yield was recorded under Bt cotton + pillipesera with 100% RDF application and it recorded 2788 kg ha-1 and 1112 kg ha-1 during 2015-2016 and 2016-2017, respectively.
Estimation of soil moisture with the combined L-band radar and radi ometer measurements

This study demonstrates a technique of estimating soil moisture using the combined passive/active L-band microwave measurements. It shows 1) evaluation of the small albedo assumption for using dual polarization passive measurements, 2) development of a synthesized technique to estimate soil moisture, and 3) evaluation with ground soil moisture measurements from the SMEX02 experiment data. In this study, we study a combined active/passive technique to estimate surface soil moisture with the focus on the short vegetated surfaces. We first simulated a database for both active and passive signals under Hydros's sensor configurations using the radiative transfer model with a wide range of conditions for surface soil moisture, roughness and vegetation properties that we considered as the random orientated cylinders. Using this database, we developed 1) the techniques to estimate surface soil moisture. We will demonstrate this technique with the model simulated data and its validation with the airborne PALS image data from the soil moisture SMEX'02 experimental data. II. INVERSION MODEL DESCRIPTION The simulation models used in this study are based on the commonly used three components emission and backscattering model concept with no consideration on the polarization dependence of the vegetation extinction properties. They are given as
Enhanced Osteoclastic Resorption and Responsiveness to Mechanical Load in Gap Junction Deficient Bone

Emerging evidence suggests that connexin mediated gap junctional intercellular communication contributes to many aspects of bone biology including bone development, maintenance of bone homeostasis and responsiveness of bone cells to diverse extracellular signals. Deletion of connexin 43, the predominant gap junction protein in bone, is embryonic lethal making it challenging to examine the role of connexin 43 in bone in vivo. However, transgenic murine models in which only osteocytes and osteoblasts are deficient in connexin 43, and which are fully viable, have recently been developed. Unfortunately, the bone phenotype of different connexin 43 deficient models has been variable. To address this issue, we used an osteocalcin driven Cre-lox system to create osteoblast and osteocyte specific connexin 43 deficient mice. These mice displayed bone loss as a result of increased bone resorption and osteoclastogenesis. The mechanism underlying this increased osteoclastogenesis included increases in the osteocytic, but not osteoblastic, RANKL/OPG ratio. Previous in vitro studies suggest that connexin 43 deficient bone cells are less responsive to biomechanical signals. Interestingly, and in contrast to in vitro studies, we found that connexin 43 deficient mice displayed an enhanced anabolic response to mechanical load. Our results suggest that transient inhibition of connexin 43 expression and gap junctional intercellular communication may prove a potentially powerful means of enhancing the anabolic response of bone to mechanical loading.
A Bacteriophage for Myxococcus xanthus: Isolation, Characterization and Relation of Infectivity to Host Morphogenesis

Burchard, Robert P. (University of Minnesota, Minneapolis), and M. Dworkin. A bacteriophage for Myxococcus xanthus: isolation, characterization and relation of infectivity to host morphogenesis. J. Bacteriol. 91:1305–1313. 1966. —A bacteriophage (MX-1) infecting Myxococcus xanthus FBt has been isolated from cow dung. The bacteriophage particle is approximately 175 mμ long. A tail about 100 mμ in length is encased in a contractile sheath and terminates in a tail plate. The head is polyhedral with a width of about 75 mμ. The nucleic acid of the bacteriophage is deoxyribonucleic acid and has a guanine plus cytosine content of 55.5%. The bacteriophage requires 10−3m Ca++ and 10−2m monovalent cation for optimal adsorption. Grown on vegetative cells of M. xanthus FBt at 30 C in 2% Casitone medium, the bacteriophage has a latent period of 120 min and a burst size of approximately 100. Host range studies indicate that three strains of M. xanthus including a morphogenetic mutant are sensitive to the bacteriophage, whereas M. fulvus, Cytophaga, Sporocytophaga myxococcoides, and a fourth strain of M. xanthus are not. Of the two cellular forms characteristic of the Myxococcus life cycle, the bacteriophage infect only the vegetative cells; they do not adsorb to microcysts. Ability to adsorb bacteriophage is lost between 65 and 75 min after initiation of the relatively synchronous conversion of vegetative cells to microcysts. The bacteriophage does not adsorb to spheroplasts. After the appearance of visible morphogenesis and before the loss of bacteriophage receptor sites, addition of bacteriophage results in the formation of microcysts which give rise to infective centers only upon germination. The possibility that the infected microcysts are harboring intact bacteriophages has been eliminated.
Multitemporal synthetic aperture radar for bridges monitoring

The present work is devoted to analyze the potentiality of satellite-based techniques for structural monitoring of bridges. Specifically, the well-known case study of the cable stayed bridge across the river Garigliano and Ausente stream is presented. The available “in situ” data have been compared and integrated with satellite-based measurements (ERS, ENVISAT satellites) for the common monitoring period (1993-2004); thus, the temporal observation window has been extended until 2010 (ENVISAT satellite). DInSAR represents a consolidated tool for deformation monitoring and its application on man-made structures and infrastructures can make easier the detection of potential problems with a consequent improvement of risks management.
A Comparison between Characterization and Biological Properties of Brazilian Fresh and Aged Propolis

Objective. As propolis is a highly valued bee product, we aimed to verify the quality of aged propolis, investigating their phenolic and flavonoid composition, levels of toxic metals, radical scavenging and antimicrobial activities. Material and Methods. Samples of fresh and aged propolis of six different beekeepers, from the same geographical location, were investigated in terms of their phenolic and flavonoid composition and levels of Pb, Cd, and Cr, as well as radical scavenging and antimicrobial activities. Results. The two groups of propolis had similar qualitative composition by HPLC-PDA and ESI(-)-MS. Fresh propolis and aged propolis show no differences when average values of extraction yield, flavonoids, EC50, or MIC were compared and both types of propolis showed good antimicrobial activity at low concentrations. Only levels of phenolic compounds were higher in fresh propolis. Conclusion. The propolis samples considered in this study, aged or fresh, had similar qualitative composition, although they were collected in different periods. Samples only differed in their levels of total phenolic content. Moreover, aged propolis conserves significant radical scavenging and antimicrobial properties. We suggest that aged propolis should not be discarded but explored for alternative applications.
Counting the Founders: The Matrilineal Genetic Ancestry of the Jewish Diaspora

The history of the Jewish Diaspora dates back to the Assyrian and Babylonian conquests in the Levant, followed by complex demographic and migratory trajectories over the ensuing millennia which pose a serious challenge to unraveling population genetic patterns. Here we ask whether phylogenetic analysis, based on highly resolved mitochondrial DNA (mtDNA) phylogenies can discern among maternal ancestries of the Diaspora. Accordingly, 1,142 samples from 14 different non-Ashkenazi Jewish communities were analyzed. A list of complete mtDNA sequences was established for all variants present at high frequency in the communities studied, along with high-resolution genotyping of all samples. Unlike the previously reported pattern observed among Ashkenazi Jews, the numerically major portion of the non-Ashkenazi Jews, currently estimated at 5 million people and comprised of the Moroccan, Iraqi, Iranian and Iberian Exile Jewish communities showed no evidence for a narrow founder effect, which did however characterize the smaller and more remote Belmonte, Indian and the two Caucasus communities. The Indian and Ethiopian Jewish sample sets suggested local female introgression, while mtDNAs in all other communities studied belong to a well-characterized West Eurasian pool of maternal lineages. Absence of sub-Saharan African mtDNA lineages among the North African Jewish communities suggests negligible or low level of admixture with females of the host populations among whom the African haplogroup (Hg) L0-L3 sub-clades variants are common. In contrast, the North African and Iberian Exile Jewish communities show influence of putative Iberian admixture as documented by mtDNA Hg HV0 variants. These findings highlight striking differences in the demographic history of the widespread Jewish Diaspora.
Wood Cellular Dendroclimatology: Testing New Proxies in Great Basin Bristlecone Pine

Dendroclimatic proxies can be generated from the analysis of wood cellular structures, allowing for a more complete understanding of the physiological mechanisms that control the climatic response of tree species. Century-long (1870–2013) time series of anatomical parameters were developed for Great Basin bristlecone pine (Pinus longaeva D.K. Bailey) by capturing strongly contrasted microscopic images through a Confocal Laser Scanning Microscope. Environmental information embedded in wood anatomical series was analyzed in comparison with ring-width series using measures of empirical signal strength. Response functions were calculated against monthly climatic variables to evaluate climate sensitivity of cellular features (e.g., lumen area; lumen diameter) for the period 1950–2013. Calibration-verification tests were used to determine the potential to generate long climate reconstructions from these anatomical proxies. A total of eight tree-ring parameters (two ring-width and six chronologies of xylem anatomical parameters) were analyzed. Synchronous variability among samples varied among tree-ring parameters, usually decreasing from ring-width to anatomical features. Cellular parameters linked to plant hydraulic performance (e.g., tracheid lumen area and radial lumen diameter) showed empirical signal strength similar to ring-width series, while noise was predominant in chronologies of lumen tangential width and cell wall thickness. Climatic signals were different between anatomical and ring-width chronologies, revealing a positive and temporally stable correlation of tracheid size (i.e., lumen and cell diameter) with monthly (i.e., March) and seasonal precipitation. In particular, tracheid lumen diameter emerged as a reliable moisture indicator and was then used to reconstruct total March–August precipitation from 1870 to 2013. Wood anatomy holds great potential to refine and expand dendroclimatic records by allowing estimates of plant physiological adaptations to external stressors. Integrating xylem cellular features with ring-width chronologies can widen our understanding of past climatic variability (including annual extreme events) and improve the evaluation of long-term plant response to drought, especially in connection with future warming scenarios.
Spatial distribution pattern of oviposition in the mosquito Aedes aegypti in relation to urbanization in Buenos Aires: southern fringe bionomics of an introduced vector

Abstract The distribution of Aedes aegypti (L) (Diptera: Culicidae) oviposition in Buenos Aires City is spatially heterogeneous. Oviposition activity was monitored for a year with a grid of 279 traps at 850‐m intervals that were serviced weekly. Geostatistics were used for the spatial analysis and generalized linear regression to model oviposition as a function of demographic and environmental variables. The proportion of weeks infested and the total number of eggs showed spatial continuity and were higher in areas that had higher densities of houses and were closer to industrial sites; they were lower in areas with higher human populations or higher densities of flats. When all sites were considered, the spatial structure showed a strong trend, but after regression, the residuals presented lower spatial dependence. When only infested sites were considered, the oviposition variables were spatially autocorrelated and the regression residuals showed little or no spatial dependence. The spatial pattern of Ae. aegypti oviposition in a highly urbanized city such as Buenos Aires seems to be related to the urbanization gradient. These urban environments might present different resource availability or continuity between patches of resources.