Miracle-dz/UniFAR-FTUs huggingface dataset:
Whole genome sequencing and analysis reveal insights into the genetic structure, diversity and evolutionary relatedness of luxI and luxR homologs in bacteria belonging to the Sphingomonadaceae family

Here we report the draft genomes and annotation of four N-acyl homoserine lactone (AHL)-producing members from the family Sphingomonadaceae. Comparative genomic analyses of 62 Sphingomonadaceae genomes were performed to gain insights into the distribution of the canonical luxI/R-type quorum sensing (QS) network within this family. Forty genomes contained at least one luxR homolog while the genome of Sphingobium yanoikuyae B1 contained seven Open Reading Frames (ORFs) that have significant homology to that of luxR. Thirty-three genomes contained at least one luxI homolog while the genomes of Sphingobium sp. SYK6, Sphingobium japonicum, and Sphingobium lactosutens contained four luxI. Using phylogenetic analysis, the sphingomonad LuxR homologs formed five distinct clades with two minor clades located near the plant associated bacteria (PAB) LuxR solo clade. This work for the first time shows that 13 Sphingobium and one Sphingomonas genome(s) contain three convergently oriented genes composed of two tandem luxR genes proximal to one luxI (luxR-luxR-luxI). Interestingly, luxI solos were identified in two Sphingobium species and may represent species that contribute to AHL-based QS system by contributing AHL molecules but are unable to perceive AHLs as signals. This work provides the most comprehensive description of the luxI/R circuitry and genome-based taxonomical description of the available sphingomonad genomes to date indicating that the presence of luxR solos and luxI solos are not an uncommon feature in members of the Sphingomonadaceae family.
Intestinal Adaptation Following Massive Ileocecal Resection in 20-day-old Weanling Rats

Objective: Few infant animal models have been used to study infantile short bowel syndrome (SBS). Most SBS models involve removal of the proximal small bowel followed by jejunoileal anastomosis, which has unclear clinical relevance to human infantile SBS that often results from surgical treatment for necrotizing enterocolitis and involves removal of the ileum, ileocecal valve, and part of or the entire colon. Our objective was to develop a more appropriate SBS model in developing rats. Materials and Methods: Twenty-day-old weanling rats were divided into 2 surgery groups, ileocecal resection (ICR) and sham groups, and a control group that did not undergo surgery. All were fed a liquid diet ad libitum for 7 days after surgery or for 7 days in the controls, and body weight, food intake, and stool changes were recorded daily. The rats were then euthanized and intestinal lengths and weights were recorded. Samples of intestine from the distal jejunum and proximal colon were collected for histology. Mucosal samples from the middle, distal jejunum, and colon were collected for measurements of mucosal weights, DNA, RNA, and protein levels. Maltase activity was determined in the small intestine. Results: Eighty-five percent of rats survived the ICR with subsequent development of diarrhea, hyperphagia, and poor growth. Adaptive responses to ICR, as compared with sham, were evidenced by increased intestinal and mucosal weights, DNA, RNA, and protein levels, increased maltase activity and villous thickness in distal jejunum, and increased mucosal thickness in the colon. Conclusions: This ICR model in weanling rats is appropriate for studying human infantile SBS.
TRIP-Assisted Steels?

The weight of an automobile can be reduced by using high-strength steels as long as they have the ductility essential in metal-forming operations. One class of suitable alloys is known as the “TRIP-assisted steels”, in which the microstructure is a mixture of allotriomorphic ferrite and bainite; the term TRIP stands for transformation-induced plasticity. The typical chemical composition is Fe–0.15C– 1.5Si–1.5Mn wt%; the high silicon concentration ensures that cementite is not precipitated during the growth of upper bainite. The carbon that is partitioned from bainitic ferrite stabilises the residual austenite, enabling it to be retained at ambient temperature. The final microstructure typically contains 20% bainitic ferrite, 10% retained austenite with the remainder being allotriomorphic ferrite. There have been many publications on the microstructure and property relationships of TRIP-assisted steels. Most of these studies highlight the presence of the retained austenite and many imply that the observed high uniform elongation is a consequence of the martensitic transformation of the retained austenite under the influence of an applied stress or strain. The purpose of the present work was to investigate theoretically, the magnitude of the contribution that transformation plasticity can make to the total elongation.
Signaling pathways activated by epidermal growth factor receptor or fibroblast growth factor receptor differentially regulate branching morphogenesis in fetal mouse submandibular glands

Although growth factor signaling is required for embryonic development of organs, individual signaling mechanisms regulating these organotypic processes are just beginning to be defined. We compared signaling activated in fetal mouse submandibular glands (SMGs) by three growth factors, epidermal growth factor (EGF), fibroblast growth factor (FGF) 7, or FGF10, and correlated it with specific events of branching morphogenesis. Immunoblotting showed that EGF strongly stimulated phosphorylation of extracellular signal‐regulated kinase‐1/2 (ERK‐1/2) and weakly stimulated phosphorylation of phospholipase Cγ1 (PLCγ1) and phosphatidylinositol‐3 kinase (PI3K) in cultured E14 SMG. However, FGF7 and FGF10 stimulated phosphorylation of both PLCγ1 and PI3K, but elicited only minimal phosphorylation of ERK‐1/2. Morphological study of mesenchyme‐free SMG epithelium cultured in Matrigel revealed that EGF induced cleft formation of endpieces, that FGF7 stimulated both cleft formation and stalk elongation, but that FGF10 induced only stalk elongation. In mesenchyme‐free SMG epithelium cultured with EGF, FGF7 and FGF10, U0126 (MEK inhibitor) completely blocked cleft formation, whereas U73122 (PLCγ1 inhibitor) suppressed stalk elongation. These finding suggest that EGF stimulates cleft formation and drives branch formation via ERK‐1/2, and that FGF7 stimulates both cleft formation and stalk elongation via PLCγ1 and partly via ERK‐1/2, but that FGF10 stimulates stalk elongation mainly via PLCγ1.
Intranasal Microemulsion of Sildenafil Citrate: In Vitro Evaluation and In Vivo Pharmacokinetic Study in Rabbits

The purpose of the present study was to prepare intranasal delivery system of sildenafil citrate and estimate its relative bioavailability after nasal administration in rabbits to attain rapid onset of action with good efficacy at lower doses. Sildenafil citrate saturated solubility was determined in different solvents, cosolvents, and microemulsion systems. For nasal application, sildenafil citrate was formulated in two different systems: the first was a cosolvent system (S3) of benzyl alcohol/ethanol/water/Transcutol/taurodeoxy cholate/Tween 20 (0.5:16.8:47.7:15.9:1:18.1% w/w). The second was a microemulsion system (ME6) containing Oleic acid: Labrasol/Transcutol/water (8.33:33.3:16.66:41.66% w/w). The prepared systems were characterized in relation to their clarity, particle size, viscosity, pH, and nasal ciliotoxicity. In vivo pharmacokinetic performance of the selected system ME6 (with no nasal ciliotoxicity) was evaluated in a group of six rabbits in a randomized crossover study and compared to the marketed oral tablets. The targeted solubility (>20 mg/ml) of sildenafil citrate was achieved with cosolvent systems S1, S3, and S5 and with microemulsion systems ME3–ME6. The saturated solubility of sildenafil citrate in cosolvent system S3 and microemulsion system ME6 were 22.98 ± 1.26 and 23.79 ± 1.16 mg/ml, respectively. Microemulsion formulation ME6 showed shorter tmax (0.75 h) and higher AUC(0-∞) (1,412.42 ng h/ml) compared to the oral tablets which showed tmax equals 1.25 h and AUC(0-∞) of 1,251.14 ng h/ml after administration to rabbits at dose level of 5 mg/kg. The relative bioavailability was 112.89%. In conclusion, the nasal absorption of sildenafil citrate microemulsion was found to be fast, indicating the potential of nasal delivery instead of the conventional oral administration of such drug.
A High Order Stable Conservative Method for Solving Hyperbolic Conservation Laws on Arbitrarily Distributed Point Clouds

In this paper, we aim to solve one- and two-dimensional hyperbolic conservation laws on arbitrarily distributed point clouds. The initial condition is given on such a point cloud, and the algorithm solves for point values of the solution at later time also on this point cloud. By using the Voronoi technique and by introducing a grouping algorithm, we divide the computational domain into nonoverlapping cells. Each cell is a polygon and contains a minimum number of the given points to ensure accuracy. We carefully select points in each cell during the grouping procedure and hence are able to interpolate or fit the discrete initial values with piecewise polynomials. By adapting the traditional discontinuous Galerkin method on the constructed polygonal mesh, we obtain a stable, conservative, and high order method. Numerical results for both one- and two-dimensional scalar equations and Euler systems of compressible gas dynamics are provided to illustrate the good behavior of our mesh generation algorithm as w.
Learning Schemata for Natural Language Processing

This paper describes a natural language system which improves its own performance through learning. The system processes short English narratives and is able to acquire, from a single narrative, a new schema for a stereotypical set of actions. During the understanding process, the system attempts to construct explanations for characters' actions in terms of the goals their actions were meant to achieve. When the system observes that a character has achieved an interesting goal in a novel way, it generalizes the set of actions they used to achieve this goal into a new schema. The generalization process is a knowledge-based analysis of the causal structure of the narrative which removes unnecessary details while maintaining the validity of the causal explanation. The resulting generalized set of actions is then stored as a new schema and used by the system to correctly process narratives which were previously beyond its capabilities.
Bioefficiency of different tocopherols in chicken as assessed by haemolysis test and microsomal pentane production

Bioefficiencies of α-, γ- and δ-tocopherol in comparison with all-rac-α-tocopherol were established in broiler chickens. For this, 1-d-old male broiler chickens received a diet deficient in vitamin E and supplemented with increasing doses of the corresponding tocopheryl acetates. After 2 and 3 weeks of feeding, the animals were killed to obtain blood and liver samples. The ex vivo tests used were detergent induced haemolysis and pentane production by liver microsomes. Bioefficiencies were calculated by comparison of the dose–response curves. It is concluded that haemolysis and pentane production are appropriate indicators of the bioefficiency of tocopherols in broiler chickens. The values obtained by both tests hardly differed and agree well with the figures previously obtained from rats and other species.
Hypertriglyceridemia-Induced Acute Pancreatitis During Pregnancy: Editorial Comment

30 cute pancreatitis is encountered in approximately 3/10000 pregnancies. Most common predisposing factors are gall-stone disease and hypertriglyceridemia. Lipid and lipoprotein levels are increased during pregnancy especially in the third trimester up to three fold. Thus, triglyceride levels may increase up to 300 mg/dL but not more than that in a normal pregnancy. Levels between 750-1000 mg/dL may induce an acute pancreatitis. Alcohol abuse and cystic fibrosis are other rare causes.
An Exponential Monte-Carlo Local Search Algorithm for the Berth Allocation Problem

Over the years, the demand for maritime transportation has rapidly increased [1], [2]. This usually leads to an increasing in competition among different ports in providing efficient services. Port managers face significant challenges in efficiently utilizing the given resources to provide a cost-effective service [1]. Among many optimization and decision making problems in the port management system, the berth allocation problem (BAP) is considered as one of the most challenging and it has a critical role in the ports effectiveness and competitiveness. The BAP seeks an allocation for a given set of vessels berthing positions and berthing times. The main objective of the BAP is to minimize the total waiting time for all vessels in a port [2].
Effect of Fabric Properties on Thermal Signature and Burn Injury

Abstract : Thermal signature reduction and flame/thermal protection are two important protections for the survivability of the U.S. soldiers operating in the battlefield. Among many parameters that influence the degree of thermal signature reduction and flame/thermal protection, thermal radiation is the most important one. The dominant heat transfer mode between a fire and clothing surface is radiation, as much as 80%. Thermal image is a contrast of different thermal radiance between the target and the background. The optical properties of a material are major factors influencing thermal radiance from the material surface. Therefore, controlling the optical properties of military clothing fabrics is a viable means to improve thermal protection and thermal camouflage of future force warriors.
Effects of anodization voltage on CaP/Al2O3–Ti nanometre biocomposites

Nanometre CaP/Al2O3–Ti biocomposites for implant applications were successfully fabricated using a hybrid technique of anodization and hydrothermal treatment, in which CaP/Al2O3 formed a double-layer coating on titanium with porous CaP as the top layer and anodic Al2O3 film as the intermediate layer. Techniques, such as x-ray diffraction (XRD), electron scanning microscopy and energy disperse x-ray analysis (SEM + EDX), transmission electron microscopy (TEM) and atomic force microscopy (AFM), were used to investigate the composition, microstructure and morphology of the fabricated CaP/Al2O3 composite coating and the CaP/Al2O3–Ti biocomposites. XRD results showed that the fabricated composite coating contained Al2O3 and various calcium phosphate phases. SEM and TEM micrographs confirmed that CaP crystals were in nanometres, embedded in situ in the walls of the cylindrical structure of anodic alumina, and finally formed a thin and porous top layer on the anodic alumina intermediate layer. The nanometre and T-shape effects of the CaP top layer, and the porous and cylindrical microstructure of CaP/Al2O3 composite coating could produce an excellent combination of bioactivity and mechanical integrity of the CaP/Al2O3–Ti biocomposites. It was also found that the anodization voltage of the anodization process played an important role on the composition and microstructure of the fabricated CaP/Al2O3–Ti biocomposites. The contents of Ca and P incorporated in anodic alumina depended strongly on the anodization voltage. Their variations could result in different CaP phases, CaP crystal shapes and sizes, and topography of the CaP/Al2O3–Ti biocomposites. The optimal anodization voltage in this study was found to be in the range 40–60 V.
A multidimensional blood stimulation assay reveals immune alterations underlying systemic juvenile idiopathic arthritis

The etiology of sporadic human chronic inflammatory diseases remains mostly unknown. To fill this gap, we developed a strategy that simultaneously integrates blood leukocyte responses to innate stimuli at the transcriptional, cellular, and secreted protein levels. When applied to systemic juvenile idiopathic arthritis (sJIA), an autoinflammatory disease of unknown etiology, this approach identified gene sets associated with specific cytokine environments and activated leukocyte subsets. During disease remission and off treatment, sJIA patients displayed dysregulated responses to TLR4, TLR8, and TLR7 stimulation. Isolated sJIA monocytes underexpressed the IL-1 inhibitor aryl hydrocarbon receptor (AHR) at baseline and accumulated higher levels of intracellular IL-1&bgr; after stimulation. Supporting the demonstration that AHR down-regulation skews monocytes toward macrophage differentiation, sJIA monocytes differentiated in vitro toward macrophages, away from the dendritic cell phenotype. This might contribute to the increased incidence of macrophage activation syndrome in these patients. Integrated analysis of high-dimensional data can thus unravel immune alterations predisposing to complex inflammatory diseases.
Quality Factor Effect on the Wireless Range of Microstrip Patch Antenna Strain Sensors

Recently introduced passive wireless strain sensors based on microstrip patch antennas have shown great potential for reliable health and usage monitoring in aerospace and civil industries. However, the wireless interrogation range of these sensors is limited to few centimeters, which restricts their practical application. This paper presents an investigation on the effect of circular microstrip patch antenna (CMPA) design on the quality factor and the maximum practical wireless reading range of the sensor. The results reveal that by using appropriate substrate materials the interrogation distance of the CMPA sensor can be increased four-fold, from the previously reported 5 to 20 cm, thus improving considerably the viability of this type of wireless sensors for strain measurement and damage detection.
Associations Between Paternally Transmitted Fetal IGF2 Variants and Maternal Circulating Glucose Concentrations in Pregnancy

OBJECTIVE To test the hypothesis that polymorphic variation in the paternally transmitted fetal IGF2 gene is associated with maternal glucose concentrations in the third trimester of pregnancy. RESEARCH DESIGN AND METHODS A total of 17 haplotype tag single nucleotide polymorphisms in the IGF2 gene region were genotyped in 1,160 mother/partner/offspring trios from the prospective Cambridge Baby Growth Study (n = 845 trios) and the retrospective Cambridge Wellbeing Study (n = 315 trios) (3,480 samples in total). Associations were tested between inferred parent-of-origin fetal alleles, z scores of maternal glucose concentrations 60 min. after an oral glucose load performed at week 28 of pregnancy, and offspring birth weights. RESULTS Using the minimum P value test, paternally transmitted fetal IGF2 polymorphisms were associated with maternal glucose concentrations; specifically, paternally transmitted fetal rs6578987 (P = 0.006), rs680 (P = 0.01), rs10770125 (P = 0.0002), and rs7924316 (P = 0.01) alleles were associated with increased maternal glucose concentrations in the third trimester of pregnancy and placental IGF-II contents at birth (P = 0.03). In contrast, there were no associations between maternal glucose concentrations and maternal or maternally transmitted fetal IGF2 genotypes. CONCLUSIONS Polymorphic variation in paternally transmitted fetal IGF2 is associated with increased maternal glucose concentrations in pregnancy and could potentially alter the risk of gestational diabetes in the mother. The association may be at least partially mediated by changes in placental IGF2 expression.
Optimal Jamming Attack Strategies and Network Defense Policies in Wireless Sensor Networks

We consider a scenario where a sophisticated jammer jams an area in which a single-channel random-access-based wireless sensor network operates. The jammer controls the probability of jamming and the transmission range in order to cause maximal damage to the network in terms of corrupted communication links. The jammer action ceases when it is detected by the network (namely by a monitoring node), and a notification message is transferred out of the jammed region. The jammer is detected by employing an optimal detection test based on the percentage of incurred collisions. On the other hand, the network defends itself by computing the channel access probability to minimize the jamming detection plus notification time. The necessary knowledge of the jammer in order to optimize its benefit consists of knowledge about the network channel access probability and the number of neighbors of the monitor node. Accordingly, the network needs to know the jamming probability of the jammer. We study the idealized case of perfect knowledge by both the jammer and the network about the strategy of each other and the case where the jammer and the network lack this knowledge. The latter is captured by formulating and solving optimization problems where the attacker and the network respond optimally to the worst-case or the average-case strategies of the other party. We also take into account potential energy constraints of the jammer and the network. We extend the problem to the case of multiple observers and adaptable jamming transmission range and propose a meaningful heuristic algorithm for an efficient jamming strategy. Our results provide valuable insights about the structure of the jamming problem and associated defense mechanisms and demonstrate the impact of knowledge as well as adoption of sophisticated strategies on achieving desirable performance.
Detection of Subtle Brain Changes Using Subvoxel Registration and Subtraction of Serial MR Images

Objective The aim of this study was to examine the potential of accurate image registration for detecting subtle changes in the brain. Materials and Methods Isotropic T1-weighted volume images were obtained in 10 normal subjects and five patients on two or more occasions (including pre- and postcontrast studies). The images were segmented and a 3D rigid body translation and rotation technique was used with sine interpolation to precisely match the images using a x2-test. The registered images and the subtraction images produced from them were used to detect changes in signal intensity, site, shape, and size of the brain. Results Small changes due to differences in orientation of the head, growth, and development as well as inhalation of oxygen and carbogen (95% O2/5% CO2) were observed in normal subjects. Changes were also observed in patients with minor head trauma, a meningioma, an astrocytoma, and multiple sclerosis. Differences due to contrast enhancement and surgery and/or anesthesia were also seen. Conclusion With use of subvoxel registration, subtle changes in the brain were detected in a variety of physiological and clinical situations where differences have hitherto been difficult or impossible to detect.