Miracle-dz/UniFAR-FTUs huggingface dataset:
TDR estimation of electrical conductivity and saline solute concentration in a volcanic soil

Relative to montmorillonitic or kaolinitic soils, volcanic soils have atypical dielectric characteristics that interfere with the applicability of the Time Domain Reflectometry (TDR) technique for soil moisture (h) determination when common, empirical calibration equations are used. This particular dielectric response affects estimation of salinity in volcanic soils. Six TDR-based methods to estimate bulk electrical conductivity (ra) on a range of KCl saline reference solutions were compared, with Nadler’s method giving the best results (R1:1 2 =0.988). Three models (linear, non-linear and empirical) for predicting soil solution electrical conductivity (rw) based on ra and h, were experimentally tested on 24 hand-packed soil columns varying in salinity (Br ) from 0.2 to 4.0 dS m , each in four h levels (36–58%). Rhoades’ linear model performed better, especially for large water contents, than the other two (R1:1 2 =0.986 vs. 0.976 and 0.983, respectively). An interpretation in terms of mobile vs. immobile volumetric fractions of water present in volcanic soils is suggested as a possible explanation for these results. The empirical model resulted over-parameterized and an alternative equation with fewer non-correlated parameters, ra=(ah 2+bh)rw+ch , is proposed and tested with good results in volcanic soils from the Canary Islands and New Zealand. The equation encompasses both the relative dielectric dominance of the mobile water fraction at high water content typical of volcanic soils, and of the immobile fraction at low water contents. Simultaneous measurements made with a standard fourelectrode probe and TDR gave good correlation (R=0.964). A good linear correlation was also found between tracer concentration in the soil solution and rw (R =0.960). Nadler’s and the new empirical model also tested with good results under dynamic (flow) conditions during a miscible displacement experiment in a large monolith using bromide as a tracer. The method reveals itself as a robust tool for solute transport studies under controlled salinity conditions in a volcanic soil. D 2004 Elsevier B.V. All rights reserved.
Positive and Negative Oxygen Vacancies in Amorphous Silica

We modeled all stable positive and negative charge states of oxygen vacancies originating from the neutral O3 Si=Si O3 defect in amorphous SiO2 (a-SiO2) using an embedded cluster method on a distribution of structural sites. For the first time, we predict the geometry, electronic structure and spectroscopic properties of doubly ionized and negatively charged oxygen vacancies in a-SiO2 and demonstrate that negatively charged vacancies serve as deep electron traps. The results demonstrate that oxygen vacancies can be responsible for both the electron and hole trapping in silica. We compare our findings with the previous calculations and with the recent experimental data.
Real-Time GPS Precise Point Positioning-Based Precipitable Water Vapor Estimation for Rainfall Monitoring and Forecasting

GPS-based precipitable water vapor (PWV) estimation has been proven as a cost-effective approach for numerical weather prediction. Most previous efforts focus on the performance evaluation of post-processed GPS-derived PWV estimates using International GNSS Service (IGS) satellite products with at least 3-9-h latency. However, the suggested timeliness for meteorological nowcasting is 5-30 min. Therefore, the latency has limited the GPS-based PWV estimation in real-time meteorological nowcasting. The limitation has been overcome since April 2013 when IGS released real-time GPS orbit and clock products. This becomes the focus of this paper, which investigates real-time GPS precise point positioning (PPP)-based PWV estimation and its potential for rainfall monitoring and forecasting. This paper first evaluates the accuracy of IGS CLK90 real-time orbit and clock products. Root-mean-square (RMS) errors of <; 5 cm and ~0.6 ns are revealed for real-time orbit and clock products, respectively, during July 4-10, 2013. Second, the real-time GPS PPP-derived PWV values obtained at IGS station WUHN are compared with the post-processed counterparts. The RMS difference of 2.4 mm has been identified with a correlation coefficient of 0.99. Third, two case studies, including a severe rainfall event and a series of moderate rainfall events, have been presented. The agreement between the real-time GPS PPP-derived PWV and ground rainfall records indicates the feasibility of real-time GPS PPP-derived PWV for rainfall monitoring. Moreover, the significantly reduced latency demonstrates a promising perspective of real-time GPS PPP-based PWV estimation as an enhancement to existing forecasting systems for rainfall forecasting.
Towards composition of conformant systems

Motivated by the Model-Based Design process for Cyber-Physical Systems, we consider issues in conformance testing of systems. Conformance is a quantitative notion of similarity between the output trajectories of systems, which considers both temporal and spatial aspects of the outputs. Previous work developed algorithms for computing the conformance degree between two systems, and demonstrated how formal verification results for one system can be re-used for a system that is conformant to it. In this paper, we study the relation between conformance and a generalized approximate simulation relation for the class of Open Metric Transition Systems (OMTS). This allows us to prove a small-gain theorem for OMTS, which gives sufficient conditions under which the feedback interconnection of systems respects the conformance relation, thus allowing the building of more complex systems from conformant components.
Radiolabeling, whole-body single photon emission computed tomography/computed tomography imaging, and pharmacokinetics of carbon nanohorns in mice

In this work, we report that the biodistribution and excretion of carbon nanohorns (CNHs) in mice are dependent on their size and functionalization. Small-sized CNHs (30–50 nm; S-CNHs) and large-sized CNHs (80–100 nm; L-CNHs) were chemically functionalized and radiolabeled with [111In]-diethylenetriaminepentaacetic acid and intravenously injected into mice. Their tissue distribution profiles at different time points were determined by single photon emission computed tomography/computed tomography. The results showed that the S-CNHs circulated longer in blood, while the L-CNHs accumulated faster in major organs like the liver and spleen. Small amounts of S-CNHs- and L-CNHs were excreted in urine within the first few hours postinjection, followed by excretion of smaller quantities within the next 48 hours in both urine and feces. The kinetics of excretion for S-CNHs were more rapid than for L-CNHs. Both S-CNH and L-CNH material accumulated mainly in the liver and spleen; however, S-CNH accumulation in the spleen was more prominent than in the liver.
Neurophysiology of Tactile Perception : A Tribute to Steven Hsiao Chronic recordings reveal tactile stimuli can suppress spontaneous activity of neurons in somatosensory cortex of awake and anesthetized primates

Qi HX, Reed JL, Franca JG, Jain N, Kajikawa Y, Kaas JH. Chronic recordings reveal tactile stimuli can suppress spontaneous activity of neurons in somatosensory cortex of awake and anesthetized primates. J Neurophysiol 115: 2105–000, 2016. First published February 24, 2016; doi:10.1152/jn.00634. 2015. —In somatosensory cortex, tactile stimulation within the neuronal receptive field (RF) typically evokes a transient excitatory response with or without postexcitatory inhibition. Here, we describe neuronal responses in which stimulation on the hand is followed by suppression of the ongoing discharge. With the use of 16-channel microelectrode arrays implanted in the hand representation of primary somatosensory cortex of New World monkeys and prosimian galagos, we recorded neuronal responses from single units and neuron clusters. In 66% of our sample, neuron activity tended to display suppression of firing when regions of skin outside of the excitatory RF were stimulated. In a small proportion of neurons, single-site indentations suppressed firing without initial increases in response to any of the tested sites on the hand. Latencies of suppressive responses to skin indentation (usually 12–34 ms) were similar to excitatory response latencies. The duration of inhibition varied across neurons. Although most observations were from anesthetized animals, we also found similar neuron response properties in one awake galago. Notably, suppression of ongoing neuronal activity did not require conditioning stimuli or multi-site stimulation. The suppressive effects were generally seen following single-site skin indentations outside of the neuron’s minimal RF and typically on different digits and palm pads, which have not often been studied in this context. Overall, the characteristics of widespread suppressive or inhibitory response properties with and without initial facilitative or excitatory responses add to the growing evidence that neurons in primary somatosensory cortex provide essential processing for integrating sensory stimulation from across the hand.
Additive effects and safety of fixed combination therapy with 1% brinzolamide and 0.5% timolol versus 1% dorzolamide and 0.5% timolol in prostaglandin‐treated glaucoma patients

To compare the additive effects and safety of 1% brinzolamide/0.5% timolol fixed combination (BTFC) versus the low‐dose regimen of 1% dorzolamide/0.5% timolol fixed combination (DTFC) in patients with open‐angle glaucoma and ocular hypertension (OAG/OH) following treatment with prostaglandin analogues (PGAs).
Regulation of Schistosoma mansoni Development and Reproduction by the Mitogen-Activated Protein Kinase Signaling Pathway

Background Protein kinases are proven targets for drug development with an increasing number of eukaryotic Protein Kinase (ePK) inhibitors now approved as drugs. Mitogen-activated protein kinase (MAPK) family members connect cell-surface receptors to regulatory targets within cells and influence a number of tissue-specific biological activities such as cell proliferation, differentiation and survival. However, the contributions of members of the MAPK pathway to schistosome development and survival are unclear. Methodology/Principal Findings We employed RNA interference (RNAi) to elucidate the functional roles of five S. mansoni genes (SmCaMK2, SmJNK, SmERK1, SmERK2 and SmRas) involved in MAPK signaling pathway. Mice were injected with post-infective larvae (schistosomula) subsequent to RNAi and the development of adult worms observed. The data demonstrate that SmJNK participates in parasite maturation and survival of the parasites, whereas SmERK are involved in egg production as infected mice had significantly lower egg burdens with female worms presenting underdeveloped ovaries. Furthermore, it was shown that the c-fos transcription factor was overexpressed in parasites submitted to RNAi of SmERK1, SmJNK and SmCaMK2 indicating its putative involvement in gene regulation in this parasite's MAPK signaling cascade. Conclusions We conclude that MAPKs proteins play important roles in the parasite in vivo survival, being essential for normal development and successful survival and reproduction of the schistosome parasite. Moreover SmERK and SmJNK are potential targets for drug development.
ULTRASTRUCTURAL LOCALIZATION OF ALKALINE PHOSPHATASE ACTIVITY IN THE ABSORBING CELLS OF THE DUODENUM OF MOUSE

A direct lead method for the visualization of alkaline phosphatase activity at pH 9 was used in a study on the absorptive cells of the duodenum of the mouse. Lead phosphate precipitate was observed in several structures after a short incubation of glutaraldehyde-fixed frozen sections. On microvilli and in vacuoles below the terminal web, the reaction was intense and persisted even after osmic acid fixation. In the Golgi zone, in the smooth reticulum cisternae and in the dense bodies, the reaction was prominent. In these sites, the deposits were not observed after osmic acid fixation or after short incubation in media containing substrates other than β-glycerophosphate or α-naphthylphosphate.
On the instantaneous frequency of Gaussian stochastic processes

This paper concerns the instantaneous frequency (IF) of continuous-time, zero-mean, complex-valued, proper, mean-square differentiable nonstationary Gaussian stochastic processes. We compute the probability density function for the IF for fixed time, which extends a result known for wide-sense stationary processes to nonstationary processes. For a fixed time the IF has either zero or infinite variance. For harmonizable processes we obtain as a byproduct that the mean of the IF, for fixed time, is the normalized first order frequency moment of the Wigner spectrum.
Correct information unit analysis for determining the characteristics of narrative discourse in individuals with chronic traumatic brain injury

Primary objective: To investigate differences between individuals with traumatic brain injury (TBI) and a control group regarding quantitative characteristics of narrative discourse including correct information units (CIUs). The secondary objective was to explore cognitive correlations with narrative discourse measurements. Research design: Case-control study. Methods: Twenty-six individuals with TBI and 24 age-, gender- and education-matched subjects without brain injury were examined. Four-frame comic strips were used for elicitation of narrative discourse. Six variables of discourse measurements (total time, total number of units and CIUs, units per time, CIUs per time and CIUs per unit) were calculated. The relationships between the 6 discourse measurements and results of standard cognitive tests were also examined, including logical memory, working memory and executive functions. Main outcomes and results: The time efficiency for narrative discourse (i.e. total time, units per time and CIUs per time) was significantly decreased in the TBI group. Moreover, time efficiency was significantly related to measurements of working memory and executive function. The TBI group did not differ from the control group with regard to total number of units and CIUs and CIUs per unit. Conclusion: Decreased time efficiency is the most critical characteristic of narrative discourse in individuals with TBI.
A Strong Dual for Conic Mixed-Integer Programs

Mixed-integer conic programming is a generalization of mixed-integer linear programming. In this paper, we present an extension of the duality theory for mixed-integer linear programming (see [M. Guzelsoy and T. K. Ralphs, Int. J. Oper. Res. (Taichung), 4 (2007), pp. 118--137], [G. L. Nemhauser and L. A. Wolsey, Integer and Combinatorial Optimization, Wiley-Interscience, New York, 1988]) to the case of mixed-integer conic programming. In particular, we construct a subadditive dual for mixed-integer conic programming problems. Under a simple condition on the primal problem, we show that strong duality holds.
Acceleration and Deceleration Capacity of Fetal Heart Rate in an In-Vivo Sheep Model

Background Fetal heart rate (FHR) variability is an indirect index of fetal autonomic nervous system (ANS) integrity. FHR variability analysis in labor fails to detect early hypoxia and acidemia. Phase-rectified signal averaging (PRSA) is a new method of complex biological signals analysis that is more resistant to non-stationarities, signal loss and artifacts. It quantifies the average cardiac acceleration and deceleration (AC/DC) capacity. Objective The aims of the study were: (1) to investigate AC/DC in ovine fetuses exposed to acute hypoxic-acidemic insult; (2) to explore the relation between AC/DC and acid-base balance; and (3) to evaluate the influence of FHR decelerations and specific PRSA parameters on AC/DC computation. Methods Repetitive umbilical cord occlusions (UCOs) were applied in 9 pregnant near-term sheep to obtain three phases of MILD, MODERATE, and SEVERE hypoxic-acidemic insult. Acid-base balance was sampled and fetal ECGs continuously recorded. AC/DC were calculated: (1) for a spectrum of T values (T = 1÷50 beats; the parameter limits the range of oscillations detected by PRSA); (2) on entire series of fetal RR intervals or on “stable” series that excluded FHR decelerations caused by UCOs. Results AC and DC progressively increased with UCOs phases (MILD vs. MODERATE and MODERATE vs. SEVERE, p<0.05 for DC = 2–5, and AC = 1–3). The time evolution of AC/DC correlated to acid-base balance (0.4<<0.9, p<0.05) with the highest for . PRSA was not independent from FHR decelerations caused by UCOs. Conclusions This is the first in-vivo evaluation of PRSA on FHR analysis. In the presence of acute hypoxic-acidemia we found increasing values of AC/DC suggesting an activation of ANS. This correlation was strongest on time scale dominated by parasympathetic modulations. We identified the best performing parameters (), and found that AC/DC computation is not independent from FHR decelerations. These findings establish the basis for future clinical studies.
Improved Stochastic Progressive Photon Mapping with Metropolis Sampling

This paper presents an improvement to the stochastic progressive photon mapping (SPPM), a method for robustly simulating complex global illumination with distributed ray tracing effects. Normally, similar to photon mapping and other particle tracing algorithms, SPPM would become inefficient when the photons are poorly distributed. An inordinate amount of photons are required to reduce the error caused by noise and bias to acceptable levels. In order to optimize the distribution of photons, we propose an extension of SPPM with a Metropolis‐Hastings algorithm, effectively exploiting local coherence among the light paths that contribute to the rendered image. A well‐designed scalar contribution function is introduced as our Metropolis sampling strategy, targeting at specific parts of image areas with large error to improve the efficiency of the radiance estimator. Experimental results demonstrate that the new Metropolis sampling based approach maintains the robustness of the standard SPPM method, while significantly improving the rendering efficiency for a wide range of scenes with complex lighting.
Issues in current management of chronic myeloid leukemia: Importance of molecular monitoring on long term outcome

Abstract Monitoring of CML patients while on therapy is vitally important and ENL has come up with specific guidelines for the same. Since we are currently talking about operational cure, this review shall focus on evaluating the emerging data to optimize response. This requires attention to all outstanding controversial issues. Only careful, accurate and regular monitoring with specific attention to grey areas will help us select first line therapy, decide when to discontinue TKIs and also move to second line TKIs in a timely manner.
Clostridium difficile toxin B-induced necrosis is mediated by the host epithelial cell NADPH oxidase complex

Significance The toxin-producing bacterium Clostridium difficile is the leading cause of antibiotic-associated infection in hospitals worldwide. An estimated 500,000 cases of C. difficile infection (CDI) occur annually in the US, with a cost approaching 3 billion dollars. The principle virulence factors in C. difficile pathogenesis are TcdA and TcdB, two large homologous toxins capable of entering host cells to cause fluid secretion, inflammation, and necrosis of the colonic mucosa. Given that numerous investigators are currently targeting these toxins for the development of novel CDI therapies, understanding the mechanism of toxicity is a significant priority. Clostridium difficile infection (CDI) is a leading cause of health care-associated diarrhea and has increased in incidence and severity over the last decade. Pathogenesis is mediated by two toxins, TcdA and TcdB, which cause fluid secretion, inflammation, and necrosis of the colonic mucosa. TcdB is a potent cytotoxin capable of inducing enzyme-independent necrosis in both cells and tissue. In this study, we show that TcdB-induced cell death depends on assembly of the host epithelial cell NADPH oxidase (NOX) complex and the production of reactive oxygen species (ROS). Treating cells with siRNAs directed against key components of the NOX complex, chemical inhibitors of NOX function, or molecules that scavenge superoxide or ROS confers protection against toxin challenge. To test the hypothesis that chemical inhibition of TcdB-induced cytotoxicity can protect against TcdB-induced tissue damage, we treated colonic explants with diphenyleneiodonium (DPI), a flavoenzyme inhibitor, or N-acetylcysteine (NAC), an antioxidant. TcdB-induced ROS production in colonic tissue was inhibited with DPI, and both DPI and NAC conferred protection against TcdB-induced tissue damage. The efficacy of DPI and NAC provides proof of concept that chemical attenuation of ROS could serve as a viable strategy for protecting the colonic mucosa of patients with CDI.
Use of Genomics To Identify Bacterial Undecaprenyl Pyrophosphate Synthetase: Cloning, Expression, and Characterization of the Essential uppS Gene

ABSTRACT The prenyltransferase undecaprenyl pyrophosphate synthetase (di-trans,poly-cis-decaprenylcistransferase; EC2.5.1.31 ) was purified from the soluble fraction of Escherichia coli by TSK-DEAE, ceramic hydroxyapatite, TSK-ether, Superdex 200, and heparin-Actigel chromatography. The protein was labeled with the photolabile analogue of the farnesyl pyrophosphate analogue (E,E)-[1-3H]-(2-diazo-3-trifluoropropionyloxy)geranyl diphos-phate and was detected on a sodium dodecyl sulfate-polyacrylamide gel as a protein with an apparent molecular mass of 29 kDa. This protein band was cut out from the gel, trypsin digested, and subjected to matrix-assisted laser desorption ionization mass spectrometric analysis. Comparison of the experimental data with computer-simulated trypsin digest data for all E. coliproteins yielded a single match with a protein of unassigned function (SWISS-PROT Q47675 ; YAES_ECOLI). Sequences with strong similarity indicative of homology to this protein were identified in 25 bacterial species, in Saccharomyces cerevisiae, and inCaenorhabditis elegans. The homologous genes (uppS) were cloned from E. coli,Haemophilus influenzae, and Streptococcus pneumoniae, expressed in E. coli as amino-terminal His-tagged fusion proteins, and purified over a Ni2+ affinity column. An untagged version of the E. coli uppS gene was also cloned and expressed, and the protein purified in two chromatographic steps. We were able to detect Upp synthetase activity for all purified enzymes. Further, biochemical characterization revealed no differences between the recombinant untagged E. coli Upp synthetase and the three His-tagged fusion proteins. All enzymes were absolutely Triton X-100 and MgCl2 dependent. With the use of a regulatable gene disruption system, we demonstrated that uppS is essential for growth in S. pneumoniae R6.
Orientation selectivity in pinwheel centers in cat striate cortex.

In primary visual cortex of higher mammals neurons are grouped according to their orientation preference, forming "pinwheels" around "orientation centers. " Although the general structure of orientation maps is largely resolved, the microscopic arrangement of neuronal response properties in the orientation centers has remained elusive. The tetrode technique, enabling multiple single-unit recordings, in combination with intrinsic signal imaging was used to reveal the fine-grain structure of orientation maps in these locations. The results show that orientation centers represent locations where orientation columns converge containing normal, sharply tuned neurons of different orientation preference lying in close proximity.