Miracle-dz/UniFAR-FTUs huggingface dataset:
Transcriptional profiles of drought-responsive genes in modulating transcription signal transduction, and biochemical pathways in tomato

To unravel the molecular mechanisms of drought responses in tomato, gene expression profiles of two drought-tolerant lines identified from a population of Solanum pennellii introgression lines, and the recurrent parent S. lycopersicum cv. M82, a drought-sensitive cultivar, were investigated under drought stress using tomato microarrays. Around 400 genes identified were responsive to drought stress only in the drought-tolerant lines. These changes in genes expression are most likely caused by the two inserted chromosome segments of S. pennellii, which possibly contain drought-tolerance quantitative trait loci (QTLs). Among these genes are a number of transcription factors and signalling proteins which could be global regulators involved in the tomato responses to drought stress. Genes involved in organism growth and development processes were also specifically regulated by drought stress, including those controlling cell wall structure, wax biosynthesis, and plant height. Moreover, key enzymes in the pathways of gluconeogenesis (fructose-bisphosphate aldolase), purine and pyrimidine nucleotide biosynthesis (adenylate kinase), tryptophan degradation (aldehyde oxidase), starch degradation (β-amylase), methionine biosynthesis (cystathionine β-lyase), and the removal of superoxide radicals (catalase) were also specifically affected by drought stress. These results indicated that tomato plants could adapt to water-deficit conditions through decreasing energy dissipation, increasing ATP energy provision, and reducing oxidative damage. The drought-responsive genes identified in this study could provide further information for understanding the mechanisms of drought tolerance in tomato.
A three-tier SDN architecture for DenseNets

Traffic demand in terms of total traffic volume and bit rate of mobile users is expected to increase exponentially over the coming years. As a result, current cellular networks are rapidly reaching their capacity limitations. Rescaling existing networks and protocols will not solve the problem due to a number of reasons. Firstly, the cost of upgrading backhaul networks is very high. Secondly, the bottleneck is moving from the Radio Access Network (RAN) to the core network. Finally, difficulty of mobility management and operational cost are becoming very high. Therefore, a recent direction in research has been to deploy high dense heterogeneous networks called DenseNets. In this paper, a novel three-tiered Software Defined Networking (SDN) architecture is proposed to support heterogeneous DenseNets. SDN architecture with the proposed 3-tiers, identified as physical, control and management layers, is capable of tackling the aforementioned problems, as well as mitigating network bottlenecks, latency and interference.
Comparative Phyloclimatic Analysis and Evolution of Ecological Niches in the Scimitar Babblers (Aves: Timaliidae: Pomatorhinus)

We present the first extensive and integrative analysis of niche evolution based on climatic variables and a dated molecular phylogeny of a heterogeneous avian group of Southeast Asian scimitar babblers of the genus Pomatorhinus. The four main clades of scimitar babblers have species that co-occur in similar areas across southern Asia but some have diverged at different timeframes, with the most recently evolved clade harboring the highest number of species. Ecological niche models and analysis of contributing variables within a phylogenetic framework indicate instances of convergent evolution of members of different clades onto similar ecological parameter space, as well as divergent evolution of members from within clades. Pomatorhinus species from different clades occupying Himalayan foothills show convergence towards similar climatic tolerances, whereas within a clade, allopatric sister-species occurring in the Himalayas have diverged to occupy different climatic parameter spaces. Comparisons of climatic tolerances of Himalayan foothills taxa with species distributed further south in Assam/Burma and Burma/Thailand indicate convergence towards similar parameter spaces in several climatic variables. Niche overlap was observed to be lower among species of the youngest clade (ruficollis) and higher among species of older clades (ferruginosus). Analysis of accumulation of ecological disparity through time indicates rapid divergence within recent time frames. As a result, Himalayan taxa originating at different temporal scales within the four main scimitar babbler clades have differentiated ecologically only in recently diverged taxa. Our study suggests that the repeated orogenic and climatic fluctuations of the Pliocene and Pleistocene within mainland Southeast Asia served as an important ecological speciation driver within scimitar babblers, by providing opportunities for rapid geographic expansion and filling of novel environmental niches.
Developments in Multivariate Time Series Modeling

We consider modeling procedures for multiple time series which aim to address the challenge of providing both a good representation of the structure, and an efficient parameterization. We first review a method, applied to vector autoregressions of low order, which uses conditional independence graphs to identify a sparse structural autoregressive representation. We show by an example how this may be extended to identify a sparse structural form of an ARMA(1,1) model for a series of seven daily US dollar term rates. The identified structure reveals the pivotal role of the series of two year rates, and highlights sources of heteroscedasticity. Vector autoregressions of high order are widely used to provide an empirical approximation to multiple time series structure, but the large number of parameters in these models restricts the possible maximum lag when the series is of moderate length. We present, and illustrate by example, a simple extension of the vector autoregression in which the predictors are smoothed functions of the past variables. This allows information from higher lags to be used in a model of relatively low order, and can improve forecasts at higher lead times.
Acute fractures of the odontoid process. An analysis of 45 cases.

✓ Between 1969 and 1974, 45 cases of acute odontoid fracture were diagnosed and treated at this institution. The group consisted of 35 men and 10 women; 24 were between 19 and 40 years of age, and 21 were over 40 years old. Detectable myelopathy was appreciated in eight cases (18%). Diagnosis was established within 72 hours of the traumatic event. Initial evaluation disclosed displacement of the fracture in 17 cases (38%). Following reduction, the initial treatment was posterior fusion in three cases, and external immobilization in 42 cases. Excluding two deaths within the first week of treatment, 40 cases were available for follow-up analysis. Bone union failed to occur following periods of immobilization ranging from 4 to 6 months in 13 cases (33%). Fibrous union with no evidence of instability was apparent in two cases. Nonunion in displaced fractures was seen in 60%, with a rate of 88% in those displaced more than 4 mm. The rate of nonunion in undisplaced fractures was 16%. The rates of incidence of d.
A Quantum Version of Wielandt's Inequality

In this paper, Wielandt's inequality for classical channels is extended to quantum channels. That is, an upper bound to the number of times a channel must be applied, so that it maps any density operator to one with full rank, is found. Using this bound, dichotomy theorems for the zero-error capacity of quantum channels and for the Matrix Product State (MPS) dimension of ground states of frustration-free Hamiltonians are derived. The obtained inequalities also imply new bounds on the required interaction-range of Hamiltonians with unique MPS ground state.
Synaptic vesicles and exocytosis.

Neurons transmit information by releasing neurotransmitters from presynaptic nerve endings, In the resting stage , transmitters are stored in small organelles of uniform size and shape , the synaptic vesicles . When an action potential arrives in the nerve terminal , the membrane depolarizes and voltage-gated Ca2+ channels open . The resulting Ca2+ influx triggers exocytosis of synaptic vesicles , resulting in the release of neurotransmitter. The synaptic vesicle membrane is rapidly retrieved by endocytosis and reutilized for the formation of synaptic vesicles. These vesicles are reloaded with transmitter for another round of exocytosis . This cycle is repeated many times and can be studied in nerve terminals that have no connection with the neuronal cell body . Thus , the presynaptic compartment consists of an autonomous unit that contains all components required for repetitive exocytosis and membrane recycling . In contrast, release of neuropeptides involves large dense core vesicles that follow a different route; they will not be considered in this discussion (for review, see Thureson-Klein & Klein 1990) . Although the principles o f synaptic vesicle membrane traffic were worked out many years ago (reviewed by Ceccarelli & Hurlbut 1980) , it remains a major challenge to define the molecular events underlying the individual
Smooth functional and structural maps on the neocortex via orthonormal bases of the Laplace-Beltrami operator

Functional and structural maps, such as a curvature, cortical thickness, and functional magnetic resonance imaging (MRI) maps, indexed over the local coordinates of the cortical manifold play an important role in neuropsychiatric studies. Due to the highly convoluted nature of the cerebral cortex and image quality, these functions are generally uninterpretable without proper methods of association and smoothness onto the local coordinate system. In this paper, we generalized the spline smoothing problem (Wahba, 1990) from a sphere to any arbitrary two-dimensional (2-D) manifold with boundaries. We first seek a numerical solution to orthonormal basis functions of the Laplace-Beltrami (LB) operator with Neumann boundary conditions for a 2-D manifold M then solve the spline smoothing problem in a reproducing kernel Hilbert space (r.k.h.s.) of real-valued functions on manifold M with kernel constructed from the basis functions. The explicit discrete LB representation is derived using the finite element method calculated directly on the manifold coordinates so that finding discrete LB orthonormal basis functions is equivalent to solving an algebraic eigenvalue problem. And then smoothed functions in r.k. h.s can be represented as a linear combination of the basis functions. We demonstrate numerical solutions of spherical harmonics on a unit sphere and brain orthonormal basis functions on a planum temporale manifold. Then synthetic data is used to quantify the goodness of the smoothness compared with the ground truth and discuss how many basis functions should be incorporated in the smoothing. We present applications of our approach to smoothing sulcal mean curvature, cortical thickness, and functional statistical maps on submanifolds of the neocortex
CALL FOR PAPERS Mechanisms of Diastolic Dysfunction in Cardiovascular Disease A mouse model of heart failure with preserved ejection fraction due to chronic infusion of a low subpressor dose of angiotensin II

Jessica A. Regan, Adolfo Gabriele Mauro, Salvatore Carbone, Carlo Marchetti, Rabia Gill, Eleonora Mezzaroma, Juan Valle Raleigh, Fadi N. Salloum, Benjamin W. Van Tassell, Antonio Abbate, and X Stefano Toldo VCU Pauley Heart Center, Virginia Commonwealth University, Richmond, Virginia; Victoria Johnson Research Center, Virginia Commonwealth University, Richmond, Virginia; and School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia
Electrotonic Signals along Intracellular Membranes May Interconnect Dendritic Spines and Nucleus

Synapses on dendritic spines of pyramidal neurons show a remarkable ability to induce phosphorylation of transcription factors at the nuclear level with a short latency, incompatible with a diffusion process from the dendritic spines to the nucleus. To account for these findings, we formulated a novel extension of the classical cable theory by considering the fact that the endoplasmic reticulum (ER) is an effective charge separator, forming an intrinsic compartment that extends from the spine to the nuclear membrane. We use realistic parameters to show that an electrotonic signal may be transmitted along the ER from the dendritic spines to the nucleus. We found that this type of signal transduction can additionally account for the remarkable ability of the cell nucleus to differentiate between depolarizing synaptic signals that originate from the dendritic spines and back-propagating action potentials. This study considers a novel computational role for dendritic spines, and sheds new light on how spines and ER may jointly create an additional level of processing within the single neuron.
Extracellular matrix environment influences chondrogenic pattern formation in limb bud micromass culture: Experimental verification of theoretical models

Various theoretical models have been proposed to explain the periodicity in the pattern of limb chondrogenesis, but experimental comparison of these models have seldom been performed properly. In the present study, micromass culture of limb bud mesenchyme cells was undertaken to test the validity of three theoretical models: the reaction‐diffusion model, the cell sorting model, and the mechanochemical model. Computer simulations were undertaken to predict the factors that can affect the coarseness of the chondrogenic pattern. According to the predictions, we performed micromass culture of limb mesenchyme in collagen and agarose gel. Then we carried out time‐lapse observation to analyze the cell movement during pattern formation. From computer simulations it was theoretically predicted that changes in the surrounding extracellular matrix should alter the periodicity of the chondrogenic pattern in vitro, and we found that pattern changes actually occurred under different culture conditions. When compared with the culture in a liquid medium, the chondrogenic pattern became less coarse when the cells were cultured in collagen or agarose gel, and the pattern change appeared to be independent of the cell differentiation. Time‐lapse observation revealed a decrease in cell motility when the cells were cultured in gel. It was found that both the reaction‐diffusion and cell sorting models fit the pattern change produced and that the mechanochemical model is not primarily important in the chondrogenic pattern formation in vitro. Anat Rec 258:100–107, 2000. © 2000 Wiley‐Liss, Inc.
Responses to GABAA Receptor Activation Are Altered in NTS Neurons Isolated From Renal-Wrap Hypertensive Rats

Abstract—The inhibitory amino acid GABA is a potent modulator of the spontaneous discharge and the responses to afferent inputs of neurons in the nucleus of the solitary tract (NTS). To determine if responses to activation of GABAA receptors are altered in hypertension, GABAA receptor–evoked whole cell currents were measured in enzymatically dispersed NTS neurons from 33 normotensive (NT, 109±4 mm Hg, n=7) and 24 hypertensive (HT, 167±5 mm Hg, n=24) rats. GABAA receptor–evoked currents reversed at the calculated equilibrium potential for chloride and were blocked by bicuculline (n=6). Membrane capacitance was the same in neurons from NT (7.5±0.6 pF, n=62) and HT (6.8±0.6 pF, n=51) rats. The EC50 for peak GABA-evoked currents cells was significantly greater in neurons from HT (21.0±2.6 &mgr;mol/L, n=16) compared with NT rats (13.0±1.8 &mgr;mol/L, n=14, P =0.01). The EC50 of neurons exhibiting DiA labeling of presumptive aortic nerve terminals was no different than that observed in the nonlabeled cells (19.0±4.9 &mgr;mol/L, n=4). The time constant for desensitization of GABAA-evoked currents was the same in neurons from HT (4.5±0.3 seconds, n=17) and NT rats (3.8±0.3 seconds, n=17, P >0.05). Repetitive pulse application of GABA revealed a more rapid decline in the evoked current in neurons from HT compared with NT rats. The amplitude of the 5th pulse of GABA (5-second duration, 2-second interval) was 21±2% the amplitude of the 1st pulse in NT rats (n=10) and 14±2% in HT rats (n=11, P <0.05). These alterations in GABAA-receptor evoked currents could render the neurons less sensitive to GABAA receptor inhibition and influence afferent integration by NTS neurons in HT.
Aging‐associated Changes in Human Brain

A wide varicty of anatomic and histological alterations are common in brains of aged individuals. However, identification of intrinsic aging changes—as distinct from changes resulting from cumulative environmental insult—is problematic. Some degree of neuronal and volume loss would appear to be inevitable, but recent studies have suggested that the magnitudes of such changes are much less than previously thought, and studies of dendritic complexity in cognitively intact individuals suggest continuing neuronal plasticity into the eighth decade. A number of vascular changes become more frequent with age, many attributable to systemic conditions such as hypertension and atherosclerosis. Age-associated vascular changes not clearly linked to such conditions include hyaline arteriosclerotic changes with formation of arterial tortuosities in small intracranial vessels and the radiographic changes in deep cerebral white matter known as “leukoaralosis. ” Aging is accompanied by increases in glial cell activation, in oxidative damage to proteins and lipids, in irreversible protein glycation, and in damage to DNA, and such changes may underlie in part the age-associated increasing incidence of “degenerative” conditions such as Alzheimer disease and Parkinson disease. A small number of histological changes appear to be universal in aged human brains. These include increasing numbers of corpora amylacea within astrocytic processes near blood-brain or cerebrospinal fluid-brain interfaces, accumulation of the “aging” pigment lipofuscin in all brain regions, and appearance of Alzheimer-type neurofibrillary tangles (but not necessarily amyloid plaques) in mesial temporal structures.
Chronic Otitis Media and Sequelae in the Population of Greenland

It is generally recognized that chronic otitis media and sequelae of this disease are frequently encountered among the native population of Greenland, but the prevalence of chronic otitis in Greenland has not previously been systematically traced. Treatment for this disease has improved and we expect an increased demand for treatment of this disease among Greenland natives. To evaluate the need of treatment the prevalence of chronic otitis media in two large Greenland towns was assessed. The study population included 303 persons aged 11–20 years and 305 aged 41–50 years. Medical histories were recorded and objective examinations were performed using e.g. oto-micro-scopy. Among the young participants, 8% had chronic suppurative otitis and 14% sequelae of chronic otitis media. Among the older participants, 2% had suppurative otitis and 13% sequelae of chronic otitis. It is estimated, using Scandinavian criteria, that 8.6% of the participants would have benefitted from an ear operation either to stop otorrhea and/or to improve the hearing. The launching of an oto-surgical effort in Greenland is considered justifiable on the grounds of the importance of hearing to communication and the isolation in point of the native Greenland population.
Immunogenicity of recombinant hepatitis B vaccine in treatment-naive and treatment-experienced chronic hepatitis C patients: the effect of pegylated interferon plus ribavirin treatment.

AIM To retrospectively evaluate the vaccination-induced anti-HBs seroconversion rates in treatment-naive and treatment-experienced chronic hepatitis C (CHC) patients. Also to prospectively evaluate the seroconversion rates in CHC patients during pegylated interferon (PEG) plus ribavirin (RIB) treatment. METHODS Seventy treatment-naive CHC patients (group A), 22 sustained virological responders-SVR following interferon (IFN) plus RIB treatment CHC patients (group B) and 121 healthy subjects (group C) had been participated in the same HBV vaccination schedule (20 microg, 0-1-6 mo). Seroconversion was considered if anti-HBs levels were above 10 mIU/mL within 3 mo following the third dose of the vaccine. Moreover, we prospectively selected 30 non-cirrhotic CHC patients and evaluated them for the efficacy of the same vaccine schedule randomizing them in two groups: Group-1, 15 CHC patients received the first dose of the vaccine in parallel with the initiation of PEG plus RIB treatment and Group-2, 15 patients received the same vaccination schedule without concomitant treatment. Determination of anti-HBs was performed at mo 1, 2, and 7. Statistical analysis of data was based on ANOVA student's t-test and chi-square analysis (P < 0.05). RESULTS Fifty-eight of 70 group A patients (82.85%), 20/22 group B (90.9%) and 112/121 healthy subjects (92.56%) had been seroconverted. The seroconversion rates were significantly higher in the control group than in treatment-naive CHC patients (P = 0.04). The corresponding rates were comparable between group A and group B CHC patients (P = 0.38). The vast majority of non-responders (10/14, 71.43%) had been infected by genotype-1 of HCV. The seroconversion rates were comparable between group 1 and 2 CHC patients at mo 1 (20% versus 26.7%, P = 0.67), mo 2 (46.7% vs 60%, P = 0.46) and mo 7 (86.7% versus 93.3%, P = 0.54) of follow-up. CONCLUSION The immunogenicity of HBV vaccine seems to be lower in CHC patients compared to healthy subjects. SVR following IFN plus RIB treatment does not affect the antibody response to HBV vaccine. Infection by genotype-1 seems to negatively influence the seroconversion rates. Vaccination against HBV during PEG plus RIB combination treatment is not beneficial in terms of anti-HBs seroconversion rates.
Correlates of physical activity in a national sample of girls and boys in grades 4 through 12.

Psychological, biological, social, and physical environmental variables were examined for their association with physical activity of young people. A national sample of 1,504 parents and children in Grades 4-12 were interviewed by telephone. Twenty-two potential determinants were assessed along with an 11-item child physical activity index (alpha = .76). Hierarchical multiple regressions were conducted separately for 6 age-sex subgroups. Percentage of variance explained ranged from 18% for boys in Grades 4-6 to 59% for girls in Grades 10-12. Three variables had strong and consistent associations with the child physical activity index that generalized across subgroups: use of afternoon time for sports and physical activity, enjoyment of physical education, and family support for physical activity. These 3 variables should be targeted for change to promote physical activity in all groups of young people.