Miracle-dz/UniFAR-FTUs huggingface dataset:
Antibiotic susceptibility of the bacteria causing odontogenic infections.

AIMS An evaluation is made of bacterial species and susceptibility to various antibiotics used in application to odontogenic infections of periapical location and in pericoronitis of the lower third molar, with the aim of optimizing the antibiotherapy of such infections and thus preventing unnecessary side effects and over-treatment. MATERIAL AND METHODS Sixty-four patients with odontogenic infection were selected on the basis of a series of inclusion and exclusion criteria. Samples were collected from lesions under maximally aseptic conditions, avoiding oral saprophytic contamination. The samples were cultured and incubated under aerobic and anaerobic conditions, followed by bacteriological identification and antibiotic susceptibility testing. RESULTS A total of 184 bacterial strains were isolated and identified, comprising grampositive facultative anaerobes (68%), gramnegative strict anaerobes (30%) and grampositive facultative anaerobes (2%). Regardless of the origin of the odontogenic infection, the causal bacteria yielded the best results in terms of increased sensitivity and lesser resistance with amoxicillin / clavulanate and amoxicillin, respectively (p<0.05). DISCUSSION There are increasingly numerous reports in the literature of growing bacterial resistance to antibiotics in infectious processes affecting non-buccodental territories. This same tendency has not been observed in relation to oral infections, though important resistance has been documented for certain concrete antibiotics. According to our results, the common-use antibiotics with the greatest sensitivity and lowest resistance were shown to be amoxicillin/clavulanate followed by amoxicillin alone.
Partitioning longleaf pine soil respiration into its heterotrophic and autotrophic components through root exclusion

Rapid and accurate estimations of the heterotrophic and autotrophic components of total soil respiration (Rs) are important for calculating forest carbon budgets and for understanding carbon dynamics associated with natural and management-related disturbances. The objective of this study was to use deep (60 cm) root exclusion tubes and paired control (i.e., no root exclusion) collars to estimate heterotrophic respiration (Rh) and Rs, respectively, in three 26-year-old longleaf pine (Pinus palustris Mill.) stands in western Georgia. Root biomass was measured in root exclusion tubes and control collars after 102–104 days of incubation and fine root biomass loss from root exclusion was used to quantify root decay. Mean Rs from control collars was 3.3 micromol·CO2·m−2·s−1. Root exclusion tubes decreased Rs, providing an estimate of Rh. Mean Rh was 2.7 micromol·CO2·m−2·s−1 when uncorrected by pretreatment variation, root decay, or soil moisture compared to 2.1 micromol·CO2·m−2·s−1 when Rh was corrected for root decay. The corresponding ratio of Rh to Rs ranged from 66% to 82%, depending on the estimation method. This study provides an estimate of Rh in longleaf pine forests, and demonstrates the potential for deep root exclusion tubes to provide relatively rapid assessments (i.e., ~40 days post-treatment) of Rh in similar forests. The range in Rh to Rs is comparable to other reports for similar temperate coniferous ecosystems.
Molecular Characterization and Subtyping of Blastocystis Species in Irritable Bowel Syndrome Patients from North India

Blastocystis species has been extensively studied in recent few years to establish its pathogenecity. Present study was designed to identify and examine the association of Blastocystis sp. and its subtypes with Irritable Bowel Syndrome (IBS). Blastocystis sp. detected using wet-mount microscopy, trichrome staining, in-vitro culture and Polymerase Chain Reaction (PCR) assay in a cohort of IBS patients (n = 150) and healthy controls (n = 100). Isolates of Blastocystis sp.were subtyped using Sequence Tagged Site and representative samples were sequenced at SSUrRNA locus.A total of sixty five isolates of Blastocystis sp. were identified [IBS (n = 50); Controls (n = 15)] of which 91% belonged to ST3 and 9% belonged to ST1. No other subtypes could be identified. Statistically significant association was observed between Blastocystis sp. and IBS patients; however no particular subtype could be ascertained to any particular clinical type of IBS.The frequency of occurrence of Blastocystis sp. was more in IBS patients as compared to the controls and ST3 being the most prevalent subtype. The genetic polymorphism of SSU-rRNA gene amongst the different Blastocystis sp.isolates found in this study reinforces the fact that these organisms are genetically highly divergent.
Common Genetic Risk of Major Depression and Nicotine Dependence: The Contribution of Antisocial Traits in a United States Veteran Male Twin Cohort

Abstract Many studies that found associations between depression and nicotine dependence have ignored possible shared genetic influences associated with antisocial traits. The present study examined the contribution of genetic and environmental effects associated with conduct disorder (CD) and antisocial personality disorder (ASPD) to the comorbidity of major depression (MD) and nicotine dependence (ND). A telephone diagnostic interview, the Diagnostic Interview Schedule-III-R, was administered to eligible twins from the Vietnam Era Twin (VET) Registry in 1992. Multivariate genetic models were fitted to 3360 middle-aged and predominantly white twin pairs (1868 monozygotic, 1492 dizygotic pairs) of which both members completed the pertinent diagnostic interview sections. Genetic influences on CD accounted for 100%, 68%, and 50% of the total genetic variance in risk for ASPD, MD and ND, respectively. After controlling for genetic influences on CD, the partial genetic correlation between MD and ND was no longer statistically significant. Nonshared environmental contributions to the comorbidity among these disorders were not significant. This study not only demonstrates that the comorbidity between ND and MD is influenced by common genetic risk factors, but also further suggests that the common genetic risk factors overlapped with those for antisocial traits such as CD and ASPD in men.
The Histone Demethylase, Jmjd1a, Interacts With the Myocardin Factors to Regulate SMC Differentiation Marker Gene Expression

We and others have previously shown that the myocardin transcription factors play critical roles in the regulation of smooth muscle cell (SMC) differentiation marker gene expression. In a yeast 2-hybrid screen for proteins that interact with myocardin-related transcription factor-A (MRTF-A), we identified the histone 3 lysine 9 (H3K9)-specific demethylase, Jmjd1a. GST pull-down assays demonstrated that Jmjd1a bound all 3 myocardin family members, and further mapping studies showed that the jumonjiC domain of Jmjd1a was sufficient to mediate this interaction. Overexpression of Jmjd1a in multipotential 10T1/2 cells decreased global levels of di-methyl H3K9, stimulated the SM &agr;-actin and SM22 promoters, and synergistically enhanced MRTF-A- and myocardin-dependent transactivation. Using chromatin immunoprecipitation assays, we also demonstrated that TGF-&bgr;–mediated upregulation of SMC differentiation marker gene expression in 10T1/2 cells was associated with decreased H3K9 dimethylation at the CArG-containing regions of the SMC differentiation marker gene promoters. Importantly, knockdown of Jmjd1a in 10T1/2 cells and primary rat aortic SMCs by retroviral delivery of siRNA attenuated TGF-&bgr;–induced upregulation of endogenous SM myosin heavy chain expression. These effects were concomitant with increased H3K9 dimethylation at the SMC differentiation marker gene promoters and with inhibition of MRTF-A-dependent transactivation of the SMC-specific transcription. These results suggest, for the first time, that SMC differentiation marker gene expression is regulated by H3K9 methylation and that the effects of the myocardin factors on SMC-specific transcription may involve the recruitment of Jmjd1a to the SMC-specific promoters.
Thermal behavior and melt fragility number of Cu100-x Zrx glassy alloys in terms of crystallization and viscous flow

Six Cu100-xZrx amorphous alloys (x in the range 35.7 - 60 at. percent) were prepared via chill block melt spinning (CBMS) method under low pressure Helium atmosphere. Their crystallization and viscous flow behavior was studied with the aid of Perkin Elmer DSC 2C and Perkin Elmer TMS 2 devices, respectively. The viscous flow temperature dependencies at a heating rate of 20 K min-1 were interpreted on the basis of the f ree volume model. The DSC and TMS data were used to determine the fragility number m of Angell in three different ways as a function of alloy composition. It has been shown that the fragility number goes over a maximum and has a minimum at x very near to the alloy composition Cu64Zr36 in good agreement with the results of Donghua Xu et al. and Wang D et al. The experimental techniques and model interpretation used provide a tool for understanding the glass forming ability (GFA) and relaxation phenomena in metallic glasses.
UpaG, a New Member of the Trimeric Autotransporter Family of Adhesins in Uropathogenic Escherichia coli

ABSTRACT The ability of Escherichia coli to colonize both intestinal and extraintestinal sites is driven by the presence of specific virulence factors, among which are the autotransporter (AT) proteins. Members of the trimeric AT adhesin family are important virulence factors for several gram-negative pathogens and mediate adherence to eukaryotic cells and extracellular matrix (ECM) proteins. In this study, we characterized a new trimeric AT adhesin (UpaG) from uropathogenic E. coli (UPEC). Molecular analysis of UpaG revealed that it is translocated to the cell surface and adopts a multimeric conformation. We demonstrated that UpaG is able to promote cell aggregation and biofilm formation on abiotic surfaces in CFT073 and various UPEC strains. In addition, UpaG expression resulted in the adhesion of CFT073 to human bladder epithelial cells, with specific affinity to fibronectin and laminin. Prevalence analysis revealed that upaG is strongly associated with E. coli strains from the B2 and D phylogenetic groups, while deletion of upaG had no significant effect on the ability of CFT073 to colonize the mouse urinary tract. Thus, UpaG is a novel trimeric AT adhesin from E. coli that mediates aggregation, biofilm formation, and adhesion to various ECM proteins.
Fabrication and characterization of porous alumina with denser surface layer by direct foaming

Porous alumina with a denser surface layer is fabricated from an alumina/novolac composite body containing hexamethylenetetramine (HMT) that is used as a blowing agent and a curing agent for the novolac resin. A gas blown from HMT leads to the formation of pores up to submillimeter inside the alumina/novolac composite body. On the other hand, the denser surface layer without large pores is formed by the gas released from the surface during blowing. The blowing condition for the alumina/ novolac composite body is examined as a function of heat-treatment temperature in order to investigate the formation of the pore and the surface layer. Porous alumina with the denser surface layer is obtained through de-binding and sintering of the body. This paper also describes the microstructure and mechanical strength of the sintered porous alumina, and advantages of the denser surface layer.
Assessment of bronchodilator responsiveness in preschool children using forced oscillations

Background: The forced oscillation technique (FOT) requires minimal patient cooperation and is feasible in preschool children. Few data exist on respiratory function changes measured using FOT following inhaled bronchodilators (BD) in healthy young children, limiting the clinical applications of BD testing in this age group. A study was undertaken to determine the most appropriate method of quantifying BD responses using FOT in healthy young children and those with common respiratory conditions including cystic fibrosis, neonatal chronic lung disease and asthma and/or current wheeze. Methods: A pseudorandom FOT signal (4–48 Hz) was used to examine respiratory resistance and reactance at 6, 8 and 10 Hz; 3–5 acceptable measurements were made before and 15 min after the administration of salbutamol. The post-BD response was expressed in absolute and relative (percentage of baseline) terms. Results: Significant BD responses were seen in all groups. Absolute changes in BD responses were related to baseline lung function within each group. Relative changes in BD responses were less dependent on baseline lung function and were independent of height in healthy children. Those with neonatal chronic lung disease showed a strong baseline dependence in their responses. The BD response in children with cystic fibrosis, asthma or wheeze (based on both group mean data and number of responders) was not greater than in healthy children. Conclusions: The BD response assessed by the FOT in preschool children should be expressed as a relative change to account for the effect of baseline lung function. The limits for a positive BD response of −40% and 65% for respiratory resistance and reactance, respectively, are recommended.
Minimization of L2-Sensitivity for 2-D Separable-Denominator State-Space Digital Filters Subject to L2-Scaling Constraints

For two-dimensional (2D) separable-denominator state-space digital filters, the minimization problem of an L<sub>2</sub>-sensitivity measure subject to L<sub>2</sub>-scaling constraints was investigated. First, the coefficient sensitivity is analyzed by using a pure L<sub>2 </sub>norm. Next, an iterative algorithm is developed for minimizing an L<sub>2</sub>-sensitivity measure subject to L<sub>2</sub>-scaling constraints. This approach largely relies on the use of a Lagrange function and some matrix-theoretic techniques
Phonetic learning as a pathway to language: new data and native language magnet theory expanded (NLM-e)

Infants' speech perception skills show a dual change towards the end of the first year of life. Not only does non-native speech perception decline, as often shown, but native language speech perception skills show improvement, reflecting a facilitative effect of experience with native language. The mechanism underlying change at this point in development, and the relationship between the change in native and non-native speech perception, is of theoretical interest. As shown in new data presented here, at the cusp of this developmental change, infants' native and non-native phonetic perception skills predict later language ability, but in opposite directions. Better native language skill at 7.5 months of age predicts faster language advancement, whereas better non-native language skill predicts slower advancement. We suggest that native language phonetic performance is indicative of neural commitment to the native language, while non-native phonetic performance reveals uncommitted neural circuitry. This paper has three goals: (i) to review existing models of phonetic perception development, (ii) to present new event-related potential data showing that native and non-native phonetic perception at 7.5 months of age predicts language growth over the next 2 years, and (iii) to describe a revised version of our previous model, the native language magnet model, expanded (NLM-e). NLM-e incorporates five new principles. Specific testable predictions for future research programmes are described.
Distributed Gradient Optimization with Embodied Approximation

We present an informal description of a general approach for developing decentralized distributed gradient descent optimization algorithms for teams of embodied agents that need to rearrange their configuration over space and/or time, into some optimal and initially unknown configuration. Our approach relies on using embodiment and spatial embeddedness as a surrogate for computational resources, permitting the reduction or elimination of communication or shared memory for conventional parallel computation. Intermediate stages of the gradient descent process are manifested by the locations of the robots, instead of being represented symbolically. Each point in the space-time evolution of the system can be considered an approximation of the solution, which is refined by the agents’ motion in response to sensor measurements. For each agent, motion is approximately in the direction of the local antigradient of the global cost function. We illustrate this approach by giving solutions to two non-trivial realistic optimization tasks from the robotics domain. We suggest that embodied approximations can be used by living distributed systems to find affordable solutions to the optimization tasks they face.
Receptor‐operated Ca2+ entry mediated by TRPC3/TRPC6 proteins in rat prostate smooth muscle (PS1) cell line

Prostate smooth muscle cells predominantly express α1‐adrenoceptors (α1‐AR). α1‐AR antagonists induce prostate smooth muscle relaxation and therefore they are useful therapeutic compounds for the treatment of benign prostatic hyperplasia symptoms. However, the Ca2+ entry pathways associated with the activation of α1‐AR in the prostate have yet to be elucidated. In many cell types, mammalian homologues of transient receptor potential (TRP) genes, first identified in Drosophila, encode TRPC (canonical TRP) proteins. They function as receptor‐operated channels (ROCs) which are involved in various physiological processes such as contraction, proliferation, apoptosis, and differentiation. To date, the expression and function of TRPC channels have not been studied in prostate smooth muscle. In fura‐2 loaded PS1 (a prostate smooth muscle cell line) which express endogenous α1A‐ARs, α‐agonists epinephrine (EPI), and phenylephrine (PHE) induced Ca2+ influx which depended on the extracellular Ca2+ and PLC activation but was independent of PKC activation. Thus, we have tested two membrane‐permeable analogues of diacylglycerol (DAG), oleoyl‐acyl‐sn‐glycerol (OAG) and 1,2‐dioctanoyl‐sn‐glycerol (DOG). They initiated Ca2+ influx whose properties were similar to those induced by the α‐agonists. Sensitivity to 2‐aminoethyl diphenylborate (2‐APB), SKF‐96365 and flufenamate implies that Ca2+‐permeable channels mediated both α‐agonist‐ and OAG‐evoked Ca2+ influx. Following the sarcoplasmic reticulum (SR) Ca2+ store depletion by thapsigargin (Tg), a SERCA inhibitor, OAG and PHE were both still able to activate Ca2+ influx. However, OAG failed to enhance Ca2+ influx when added in the presence of an α‐agonist. RT‐PCR and Western blotting performed on PS1 cells revealed the presence of mRNAs and the corresponding TRPC3 and TRPC6 proteins. Experiments using an antisense strategy showed that both α‐agonist‐ and OAG‐induced Ca2+ influx required TRPC3 and TRPC6, whereas the Tg‐activated (“capacitative”) Ca2+ entry involved only TRPC3 encoded protein. It may be thus concluded that PS1 cells express TRPC3 and TRPC6 proteins which function as receptor‐ and store‐operated Ca2+ entry pathways. © 2005 Wiley‐Liss, Inc.
Sex‐Dependent, Osteoblast Stage‐Specific Effects of Progesterone Receptor on Bone Acquisition

The role of the progesterone receptor (PR) in the regulation of sexual dimorphism in bone has yet to be determined. Here we utilized genetic fate mapping and Western blotting to demonstrate age‐dependent PR expression in the mouse femoral metaphysis and diaphysis. To define sex‐dependent and osteoblast stage–specific effects of PR on bone acquisition, we selectively deleted PR at different stages of osteoblast differentiation. We found that when Prx1‐Cre mice were crossed with PR floxed mice to generate a mesenchymal stem cell (MSC) conditional KO model (Prx1; PRcKO), the mutant mice developed greater trabecular bone volume with higher mineral apposition rate and bone formation. This may be explained by increased number of MSCs and greater osteogenic potential, particularly in males. Age‐related trabecular bone loss was similar between the Prx1; PRcKO mice and their WT littermates in both sexes. Hormone deficiency during the period of rapid bone growth induced rapid trabecular bone loss in both the WT and the Prx1; PRcKO mice in both sexes. No differences in trabecular bone mass was observed when PR was deleted in mature osteoblasts using osteocalcin‐Cre (Bglap‐Cre). Also, there were no differences in cortical bone mass in all three PRcKO mice. In conclusion, PR inactivation in early osteoprogenitor cells but not in mature osteoblasts influenced trabecular bone accrual in a sex‐dependent manner. PR deletion in osteoblast lineage cells did not affect cortical bone mass. © 2017 American Society for Bone and Mineral Research.
Characterizing the Relationship between Steady State and Response Using Analytical Expressions for the Steady States of Mass Action Models

The steady states of cells affect their response to perturbation. Indeed, diagnostic markers for predicting the response to therapeutic perturbation are often based on steady state measurements. In spite of this, no method exists to systematically characterize the relationship between steady state and response. Mathematical models are established tools for studying cellular responses, but characterizing their relationship to the steady state requires that it have a parametric, or analytical, expression. For some models, this expression can be derived by the King-Altman method. However, King-Altman requires that no substrate act as an enzyme, and is therefore not applicable to most models of signal transduction. For this reason we developed py-substitution, a simple but general method for deriving analytical expressions for the steady states of mass action models. Where the King-Altman method is applicable, we show that py-substitution yields an equivalent expression, and at comparable efficiency. We use py-substitution to study the relationship between steady state and sensitivity to the anti-cancer drug candidate, dulanermin (recombinant human TRAIL). First, we use py-substitution to derive an analytical expression for the steady state of a published model of TRAIL-induced apoptosis. Next, we show that the amount of TRAIL required for cell death is sensitive to the steady state concentrations of procaspase 8 and its negative regulator, Bar, but not the other procaspase molecules. This suggests that activation of caspase 8 is a critical point in the death decision process. Finally, we show that changes in the threshold at which TRAIL results in cell death is not always equivalent to changes in the time of death, as is commonly assumed. Our work demonstrates that an analytical expression is a powerful tool for identifying steady state determinants of the cellular response to perturbation. All code is available at http://signalingsystems.ucsd. edu/models-and-code/ or as supplementary material accompanying this paper.