Miracle-dz/UniFAR-FTUs huggingface dataset:
Effects of sodium pyruvate on ameliorating metabolic acidosis

Objective To examine the effects of sodium pyruvate (SP) on metabolic acidosis. Methods For the in vivo experiments, we evaluated effects of SP on an ammonium chloride (NH4Cl)-induced hyperchloremic acidosis rat model. SP was infused at overall doses of 2, 4, and 6 mmol·kg− 1 for the SP1, SP2, and SP3 groups, respectively. Treatment with sodium bicarbonate (SB) was used as a positive control (2 mmol·kg− 1), and treatment with normal saline (NS) was used as a volume control (2 mL·kg− 1). Blood was sampled from the ophthalmic venous plexus for pH, blood gases, electrolytes, glucose, creatinine (Cr), and urea analysis after injection. For the in vitro experiment, propionate was applied to induce intracellular acidosis in human endothelial cells. Intracellular pH (pHi) was fluorimetrically measured after the addition of SP. Results In the in vivo study, the pH of SP1 group showed no significant difference compared with that of the NS group. The SP2 and SP3 groups had a higher pH than the NS group (P < 0.01). The SP3 group had a higher pH than the SB group (P < 0.05) and SP1 group (P < 0.05). Moreover, SP treatment ameliorated the abnormality of calcium and decreased the blood potassium levels. The SP3 group had higher glucose levels than SP1 group (P < 0.05). No significant differences were observed between all the groups in the plasma Cr and urea levels. In the in vitro study, the pHi increased immediately after the addition of SP. Conclusion The data suggest that intravascular treatment with SP represents a novel therapeutic strategy to ameliorate metabolic acidosis.
(R P)-Menthyl (1-hydroxycyclohexyl)phenylphosphinate

The title compound, C22H35O3P, features a tetrahedral P atom bonded to a phenyl ring, a hydroxycyclohexyl unit and the O atom of a menthyl group. The axial chirality at phosphorus is R P. In the crystal, molecules are connected through O—H⋯O hydrogen bonds involving the hydroxy and P=O groups, forming chains along the 21 screw axis. The methyl groups of the isopropyl fragment in the menthyl unit are disordered over two sites of equal occupancy.
Low-density lipoprotein cholesterol/apolipoprotein B ratio may be a useful index that differs in statin-treated patients with and without coronary artery disease: a case control study.

Low density lipoproteins (LDLs) are heterogeneous aggregations of molecules of different particle sizes, and small-size LDLs are more potent risk factors for atherosclerosis. We examined the qualitative characteristics of LDLs in patients with stable coronary artery disease (CAD) receiving statin therapy. LDL-particle size was estimated based on the LDL-cholesterol/apolipoprotein B ratio (LDL-C/apoB) in 214 age-adjusted men receiving statin therapy. The LDL-C/apoB ratio was significantly lower in the CAD (+) group (n = 107) than in the CAD (-) group (n = 107) (median, 1.17 versus 1.19, P = 0.0095). LDL-C/apoB was significantly lower in patients with serum TG ≥ 150 mg/dL than in those with serum TG < 150 mg/dL, and in patients with serum HDL-C < 40 mg/dL than in those with serum HDL-C ≥ 40 mg/dL (1.06 versus 1.18, P = 0.012; 1.08 versus 1.22, P = 0.0023). Stepwise logistic regression analysis revealed that elevated serum TG was an independent predictor for smaller sizes of LDLs, both in the overall subjects (β : -0.165, P = 0.02) as well as in the subset with serum LDL-C < 100 mg/dL (β : -0.252, P = 0.011). This study demonstrated that not only the absolute serum LDL-C level, but also the qualitative characteristics of LDL may be monitored for secondary prevention of CAD. Such monitoring is particularly important in patients with elevated serum TG levels, which is associated with smaller sizes of LDL-particles.
Zinc uptake by Streptococcus pneumoniae depends on both AdcA and AdcAII and is essential for normal bacterial morphology and virulence

Zinc is an essential trace metal for living cells. The ABC transporter AdcABC was previously shown to be required for zinc uptake by Streptococcus pneumoniae. As we have recently described AdcAII as another zinc‐binding lipoprotein, we have investigated the role of both AdcA and AdcAII in S. pneumoniae zinc metabolism. Deletion of either adcA or adcAII but not phtD reduced S. pneumoniae zinc uptake, with dual mutation of both adcA and adcAII further decreasing zinc import. For the Δ(adcA/adcAII) mutant, growth and intracellular concentrations of zinc were both greatly reduced in low zinc concentration. When grown in zinc‐deficient medium, the Δ(adcA/adcAII) mutant displayed morphological defects related to aberrant septation. Growth and morphology of the Δ(adcA/adcAII) mutant recovered after supplementation with zinc. Dual deletion of adcA and adcAII strongly impaired growth of the pneumococcus in bronchoalveolar lavage fluid and human serum, and prevented S. pneumoniae establishing infection in mouse models of nasopharyngeal colonization, pneumonia and sepsis without altering the capsule. Taken together, our results show that AdcA and AdcAII play an essential and redundant role in specifically importing zinc into the pneumococcus, and that both zinc transporters are required for proper cell division and for S. pneumoniae survival during infection.
Signaling Threat

This study examined the cues hypothesis, which holds that situational cues, such as a setting's features and organization, can make potential targets vulnerable to social identity threat. Objective and subjective measures of identity threat were collected from male and female math, science, and engineering (MSE) majors who watched an MSE conference video depicting either an unbalanced ratio of men to women or a balanced ratio. Women who viewed the unbalanced video exhibited more cognitive and physiological vigilance, and reported a lower sense of belonging and less desire to participate in the conference, than did women who viewed the gender-balanced video. Men were unaffected by this situational cue. The implications for understanding vulnerability to social identity threat, particularly among women in MSE settings, are discussed.
High voltage LDMOSFET modeling using BSIM6 as intrinsic-MOS model

Here, we report high voltage MOSFET modeling using BSIM6 model. The model has two components - intrinsic MOSFET channel of LDMOS modeled by BSIM6 and a drift region modeled by non-linear drift resistance. BSIM6 is the next generation bulk MOSFET model in BSIM family of models. It also have the model of Self Heating Effect (SHE) which is very important for high power devices like LDMOS. This model shows good behaviour over wide range of gate and drain bias conditions including convergence. Some of the effects like Quasi-saturation, self-heating and impact ionization are modelled by the combination of BSIM6 and drift-resistance models. We have validated this model on the simulated characteristics generated by TCAD and then, on the measured characteristics of a LDMOS device, where it shows excellent accuracy over entire bias range.
Astrocytes Control Glutamate Receptor Levels at Developing Synapses through SPARC–β-Integrin Interactions

Neurons recruit numerous mechanisms to facilitate the development of synaptic connections. However, little is known about activity-dependent mechanisms that control the timing and fidelity of this process. Here we describe a novel pathway used by neurons to regulate glutamate receptors at maturing central synapses. This pathway relies on communication between neurons and astrocytes and the ability of astrocytes to release the factor SPARC (secreted protein, acidic and rich in cysteine). SPARC expression is dynamically regulated and plays a critical role in determining the level of synaptic AMPARs. SPARC ablation in mice increases excitatory synapse function, causes an abnormal accumulation of surface AMPARs at synapses, and impairs synaptic plasticity during development. We further demonstrate that SPARC inhibits the properties of neuronal β3-integrin complexes, which are intimately coupled to AMPAR stabilization at synapses. Thus neuron–glial signals control glutamate receptor levels at developing synapses to enable activity-driven modifications of synaptic strength.
Genetic and Functional Variation in Denitrifier Populations along a Short-Term Restoration Chronosequence

ABSTRACT Complete removal of plants and soil to exposed bedrock, in order to eradicate the Hole-in-the-Donut (HID) region of the Everglades National Park, FL, of exotic invasive plants, presented the opportunity to monitor the redevelopment of soil and the associated microbial communities along a short-term restoration chronosequence. Sampling plots were established for sites restored in 1989, 1997, 2000, 2001, and 2003. The goal of this study was to characterize the activity and diversity of denitrifying bacterial populations in developing HID soils in an effort to understand changes in nitrogen (N) cycling during short-term primary succession. Denitrifying enzyme activity (DEA) was detected in soils from all sites, indicating a potential for N loss via denitrification. However, no correlation between DEA and time since disturbance was observed. Diversity of bacterial denitrifiers in soils was characterized by sequence analysis of nitrite reductase genes (nirK and nirS) in DNA extracts from soils ranging in nitrate concentrations from 1.8 to 7.8 mg kg−1. High levels of diversity were observed in both nirK and nirS clone libraries. Statistical analyses of clone libraries suggest a different response of nirS- and nirK-type denitrifiers to factors associated with soil redevelopment. nirS populations demonstrated a linear pattern of succession, with individual lineages represented at each site, while multiple levels of analysis suggest nirK populations respond in a grouped pattern. These findings suggest that nirK communities are more sensitive than nirS communities to environmental gradients in these soils.
Interlaboratory Comparison of Methods To Quantify Microsclerotia of Verticillium dahliae in Soil

ABSTRACT In a comparison of different methods for estimatingVerticillium dahliae in soil, 14 soil samples were analyzed in a blinded fashion by 13 research groups in seven countries, using their preferred methods. One group analyzed only four samples. Twelve soil samples were naturally infested, and two had known numbers of microsclerotia of V. dahliae added to them. In addition, a control was included to determine whether transport had an effect on the results. Results differed considerably among the research groups. There was a 118-fold difference between the groups with the lowest and highest mean estimates. Results of the other groups were evenly distributed between these extremes. In general, methods based on plating dry soil samples gave higher numbers of V. dahliae than did plating of an aqueous soil suspension. Recovery of V. dahliae from samples with added microsclerotia varied from 0 to 59%. Most of the variability within each analysis was at the petri dish level. The results indicate the necessity to check the performance of detection assays regularly by comparing recoveries with other laboratories, using a common set of soil samples. We conclude that wet plating assays are less accurate than dry plating assays.
Mitochondrial haplotypes and the New Zealand origin of clonal European Potamopyrgus, an invasive aquatic snail

The small aquatic snail Potamopyrgus antipodarum is an important invading species in Europe, Australia and North America. European populations are generally believed to derive from accidental introductions from New Zealand, probably dating back to the mid‐19th century. We have employed mitochondrial DNA sequences to test the proposed New Zealand origin of European Potamopyrgus, and to learn more about its genealogical history. Using a 481‐bp region of the 16S ribosomal RNA gene, we identified 17 distinct haplotypes among 65 snails from New Zealand. In marked contrast, only two haplotypes were found across all European samples, which cover a large geographical area. Importantly, these two haplotypes are shared with snails from the North Island of New Zealand. Due to sampling limitations we cannot rule out a South Island origin for one of the haplotypes, but our results clearly demonstrate the New Zealand origin of European populations. The marked divergence among the two European haplotypes implies the successful colonization by two distinct mitochondrial lineages, which is consistent with previous data based on nuclear markers.
Hourglass-Incremental Graph Processing on Heterogeneous Infrastructures

Graphs are data structures that can represent relations among entities and enable the extraction of insightful information from their properties. Graph processing systems, that aim at simplifying the computational analysis of graph structures, typically rely on a vertex-centric approach to ease the development of parallel algorithms. In this approach, the computation is modeled as a function that needs to be repeatedly applied to each vertex of the graph, in an iterative process. The irregular structure of graphs and the dynamic nature of the domains that they model, induce load imbalances both in the work performed at each vertex and the number of updates that each region of the graph receives. Knowledge about this load imbalance could be used to provide a more efficient allocation of resources during the execution of the graph processing task. Many graph processing systems are frequently deployed in Infrastructure as a Service (IaaS) platforms but, unfortunately, are oblivious to the heterogeneity of resources that exist in such environments. This prevents them from performing a suitable match among the resources available and the processing needs, which could bring significant cost savings by avoiding the allocation of expensive resources to graph regions that have low computational demand. In this report we advocate the development of a new graph processing system that is aware of the heterogeneity of underlying resources, to enable it to better adapt to different usage patterns and reduce deployment costs.
Managing the teratogenic risk of thalidomide and lenalidomide: an industry perspective

Celgene has developed and operated pregnancy prevention programs since 1998 with the first approval of thalidomide in the US. With the development and marketing of lenalidomide, an analog of thalidomide, the company further advanced its risk management activities, which now cover several territories across the globe. To date, the program is a success in as much as it has minimized the risk of fetal exposure and subsequent development of fetal malformations. Nonetheless, the company understands the need to provide a mechanism for intervention and remediation when at-risk behaviors are identified, and this forms an integral part of the risk management processes. The implementation of the thalidomide and lenalidomide pregnancy prevention program partners patients, healthcare professionals, regulators and the company in a spirit of shared responsibility. This paper also presents the authors' experience and perspective on the challenges of managing a pregnancy prevention program, which at its core aims at ensuring that the product's benefits outweigh the risk of fetal exposure.
Novel method for missing value estimation in gene expression profile based on support vector regression

Gene expression profile is a kind of useful biological resource in recent years. The original data is usually in the form of large matrix with missing values in it. Missing value estimation method is in active demand as many downstream analysis methods suffered from the missing values. Several methods dealing with this problem have been reported (proposed) recently. We proposed a novel missing value estimation method based on support vector regression. Various parameter sets and input coding schemes were employed, and the performance of our method was evaluated over different data sets by comparing with other existing methods. Results show that our method is comparative, if not better than, those previous methods
Minicell-forming mutants of Escherichia coli: suppression of both DicB- and MinD-dependent division inhibition by inactivation of the minC gene product

We have determined the nucleotide sequence of the minB operon of 10 min mutants of Escherichia coli, characterized by impaired inhibition of polar divisions. These mutants were either sensitive or resistant to the division inhibitor DicB. All the mutations were found to lie in minC or minD, confirming the requirement of both gene products in the process of inhibition of polar sites. Mutations conferring resistance to inhibitor DicB were found exclusively in minC. In agreement with de Boer et al. (P. A. J. de Boer, R. E. Crossley, and L. I. Rothfield, Proc. Natl. Acad. Sci. USA 87:1129-1133, 1990), these results provide evidence that, in addition to promoting division inhibition with MinD, protein MinC acts in concert with DicB to inhibit division by a second, MinD-independent process.
Controlling Duration Dependence in Conflict Analyses: A Replication and Extension of "Regime Types and Status Quo Evaluations"

Recent methodological work by Beck, Katz, and Tucker (1998) suggests that existing empirical analyses of binary time-series cross-section (BTSCS) data may be flawed. Analyses using such data fail to account for temporal dependence among observations of the dependent variable. In one such analysis, Lemke and Reed (1996) present a strong altemative to existing theoretical work on the democratic peace proposition. They are able to account for the lack of war between democracies within the theoretical framework provided by Power Transition/Power Parity theory. Since Lemke and Reed's analysis of BTSCS data may be troubled by the nonindependence problem, we replicate and extend their study using grouped duration methods to account for temporal dependence among observations. We find Beck, Katz and Tucker's method to be both useful and simple, and we show Lemnke and Reed's findings to be robust in models controlling for the possible effects of duration dependence.
Wnt3a upregulates transforming growth factor‐β‐stimulated VEGF synthesis in osteoblasts

It is recognized that Wnt3a affects bone metabolism via the canonical Wnt/β‐catenin signalling pathway. We have previously shown that transforming growth factor‐β (TGF‐β) stimulates the synthesis of vascular endothelial growth factor (VEGF) via p44/p42 mitogen‐activated protein (MAP) kinase, stress‐activated protein kinase (SAPK)/c‐Jun N‐terminal kinase (JNK) and p38 MAP kinase in osteoblast‐like MC3T3‐E1 cells. In the present study, we investigated the effect of Wnt3a on TGF‐β‐stimulated VEGF synthesis in these cells. Wnt3a, which alone had little effect on the VEGF levels, significantly enhanced the TGF‐β‐stimulated VEGF release. Lithium chloride and SB216763, inhibitors of glycogen synthase kinase 3β, markedly amplified the TGF‐β‐stimulated VEGF release. Wnt3a failed to affect the TGF‐β‐induced phosphorylation of Smad2, p44/p42 MAP kinase, p38 MAP kinase or SAPK/JNK. Wnt3a and lithium chloride strengthened the VEGF mRNA expression induced by TGF‐β. These results strongly suggest that Wnt3a upregulates VEGF synthesis stimulated by TGF‐β via activation of the canonical pathway in osteoblasts. Copyright © 2011 John Wiley & Sons, Ltd.
Phosphorylation of Exo 1 modulates homologous recombination repair of DNA double-strand breaks

DNA double-strand break (DSB) repair via the homologous recombination pathway is a multistage process, which results in repair of the DSB without loss of genetic information or fidelity. One essential step in this process is the generation of extended single-stranded DNA (ssDNA) regions at the break site. This ssDNA serves to induce cell cycle checkpoints and is required for Rad51 mediated strand invasion of the sister chromatid. Here, we show that human Exonuclease 1 (Exo1) is required for the normal repair of DSBs by HR. Cells depleted of Exo1 show chromosomal instability and hypersensitivity to ionising radiation (IR) exposure. We find that Exo1 accumulates rapidly at DSBs and is required for the recruitment of RPA and Rad51 to sites of DSBs, suggesting a role for Exo1 in ssDNA generation. Interestingly, the phosphorylation of Exo1 by ATM appears to regulate the activity of Exo1 following resection, allowing optimal Rad51 loading and the completion of HR repair. These data establish a role for Exo1 in resection of DSBs in human cells, highlighting the critical requirement of Exo1 for DSB repair via HR and thus the maintenance of genomic stability.
Radiofrequency energy tissue ablation for the treatment of nasal obstruction secondary to turbinate hypertrophy

Objective/Hypothesis: We hypothesized that the success rate of radiofrequency energy (RFe) tissue ablation of the inferior turbinate for nasal obstruction achieved by previous investigators would be improved by using a longer needle electrode and creating two lesions per turbinate. Methods: Ten patients with nasal obstruction secondary to inferior turbinate hypertrophy were prospectively enrolled. A 40‐mm needle delivered RFe to two sites in each inferior turbinate. Patients used a visual analog scale (VAS) to grade nasal obstruction preoperatively and at 1 week and 8 weeks after surgery. Preoperative and postoperative digital images of the nasal cavity were graded for obstruction (0% to 100%) in a blinded manner. Results: All patients (100%) were subjectively improved at 8 weeks. Mean obstruction (VAS) improved from 50% ± 21% to 16% ± 15% (right side) and from 53% ± 29% to 13% ± 13% (left side). Mean improvements were 68% (right side) (P = .004) and 75% (left side) (P = .001). Mean obstruction graded during blinded review of nasal cavity images improved from 73.5% ± 8% to 51% ± 8% (right side) and from 76% ± 6% to 64% ± 7% (left side). Of nine patients using medications for nasal obstruction before treatment, eight (89%) noted no further need for medications at 8 weeks. Conclusion: The use of RFe for submucosal tissue ablation in the hypertrophied inferior turbinate is an effective modality for reducing symptoms of nasal obstruction. Improved results may occur by using a longer needle and creating two lesions per turbinate. Of patients in this study, 100% reported improvement of nasal obstruction.
Statistically optimized FOPID for output force control of SEAs

Abstract Fractional order PID (FOPID) controllers have recently found an increasing application in different fields of control. Comparing to traditional PID algorithms, FOPID controllers provide more flexibility and better performances. The simple and non-model-based structure of FOPID controllers has boosted their usage in real-world applications. However, due to having two more control parameters than regular PID controllers and the non-linear structure of FOPID controllers, the tuning procedure of these controllers is still a challenge. The authors of the present paper have recently proposed a Taguchi-based gain tuning algorithm for tuning of control parameters of FOPID controller. The present paper is an experimental evaluation of the proposed method. A custom made SEA, FUM-LSEA, is used as the test bed in this study. Deriving a dynamic model of the FUM-LSEA, feed-forward terms are added to the controller to compensate for disturbances from motions of the output block. Optimal gains and orders of the controller are obtained through a set of experiments suggested by the Taguchi method. The Taguchi optimized controller is also compared to a Ziegler–Nichols tuned controller. The experimental results indicate 45% improvements in force tracking error.