Miracle-dz/UniFAR-FTUs huggingface dataset:
Loss of FliL Alters Proteus mirabilis Surface Sensing and Temperature-Dependent Swarming

ABSTRACT Proteus mirabilis is a dimorphic motile bacterium well known for its flagellum-dependent swarming motility over surfaces. In liquid, P. mirabilis cells are 1.5- to 2.0-μm swimmer cells with 4 to 6 flagella. When P. mirabilis encounters a solid surface, where flagellar rotation is limited, swimmer cells differentiate into elongated (10- to 80-μm), highly flagellated swarmer cells. In order for P. mirabilis to swarm, it first needs to detect a surface. The ubiquitous but functionally enigmatic flagellar basal body protein FliL is involved in P. mirabilis surface sensing. Previous studies have suggested that FliL is essential for swarming through its involvement in viscosity-dependent monitoring of flagellar rotation. In this study, we constructed and characterized ΔfliL mutants of P. mirabilis and Escherichia coli. Unexpectedly and unlike other fliL mutants, both P. mirabilis and E. coli ΔfliL cells swarm (Swr+). Further analysis revealed that P. mirabilis ΔfliL cells also exhibit an alteration in their ability to sense a surface: e.g., ΔfliL P. mirabilis cells swarm precociously over surfaces with low viscosity that normally impede wild-type swarming. Precocious swarming is due to an increase in the number of elongated swarmer cells in the population. Loss of fliL also results in an inhibition of swarming at <30°C. E. coli ΔfliL cells also exhibit temperature-sensitive swarming. These results suggest an involvement of FliL in the energetics and function of the flagellar motor.
A Comparison of Two Open Source LiDAR Surface Classification Algorithms

With the progression of LiDAR (Light Detection and Ranging) towards a mainstream resource management tool, it has become necessary to understand how best to process and analyze the data. While most ground surface identification algorithms remain proprietary and have high purchase costs; a few are openly available, free to use, and are supported by published results. Two of the latter are the multiscale curvature classification and the Boise Center Aerospace Laboratory LiDAR (BCAL) algorithms. This study investigated the accuracy of these two algorithms (and a combination of the two) to create a digital terrain model from a raw LiDAR point cloud in a semi-arid landscape. Accuracy of each algorithm was assessed via comparison with >7,000 high precision survey points stratified across six different cover types. The overall performance of both algorithms differed by only 2%; however, within specific cover types significant differences were observed in accuracy. The results highlight the accuracy of both algorithms across a variety of vegetation types, and ultimately suggest specific scenarios where one approach may outperform the other. Each algorithm produced similar results except in the ceanothus and conifer cover types where BCAL produced lower errors.
Efficient matching of SPARQL subscriptions using rete

Ubiquitous domains such as smart spaces, location-aware mobile systems, or internet-of-things are characterized by large and volatile sets of heterogeneous and independently behaving entities like devices, services, and other identified objects. This study focuses on efficient implementation of an event processing system to manage interaction among these entities. The approach is based on expressive semantic representations: information sharing in RDF and content-based publish/subscribe with SPARQL as the subscription language. SPARQL can be used to construct elaborate queries for detecting complex states resulting from receiving events produced by multiple interrelated entities. The notification system should aim at short notification times while simultaneously allowing high throughput of events. We study incremental matching of SPARQL queries on RDF data using Rete algorithm. The results obtained demonstrate that an efficient and fast semantic notification framework can be implemented by representing SPARQL queries and RDF triples as rules and facts in a Rete engine.
Nonsteroidal Anti-inflammatory Drug Use and Serum Total Estradiol in Postmenopausal Women

Laboratory and epidemiologic evidence suggest that nonsteroidal anti-inflammatory drug (NSAID) use may be inversely related to the risk of breast cancer; however, the mechanism by which NSAIDs may protect against the development of this disease is uncertain. The objective of this observational study was to assess the relationship between current NSAID use and endogenous estradiol levels, an established breast cancer risk factor. To evaluate this aim, we conducted a cross-sectional investigation among 260 postmenopausal women who were not recently exposed to exogenous hormones. Information on current NSAID use (aspirin, cyclooxygenase-2 inhibitors, and other NSAIDs combined) was collected using a questionnaire at the time of blood draw. Estradiol was quantified in serum by radioimmunoassay. General linear models were used to evaluate the association between NSAID use and serum total estradiol. The age-adjusted and body mass index–adjusted geometric mean serum estradiol concentration among NSAID users (n = 124) was significantly lower than nonusers of NSAIDs (n = 136; 17.8 versus 21.3 pmol/L; P = 0.03). Further adjustment for additional potential confounding factors did not substantially alter estimates (17.7 versus 21.2 pmol/L; P = 0.03). To our knowledge, this report is the first to examine the relationship between NSAID use and serum estradiol in postmenopausal women. These cross-sectional findings suggest that NSAID use may be associated with lower circulating estradiol levels, potentially representing one mechanism through which NSAIDs exert protective effects on breast cancer. (Cancer Epidemiol Biomarkers Prev 2008;17(3):680–7)
Clinical impact of first and early second trimester fetal echocardiography on high risk pregnancies

Objective: To evaluate the clinical impact of fetal echocardiography before 16 weeks’ gestation on the management of pregnancies with fetuses at risk of congenital heart disease. Design and setting: Observational study in a fetal medicine unit. Participants and methods: 222 consecutive women with high risk pregnancies (230 fetuses) underwent transabdominal fetal echocardiography at a median gestation of 14+1 weeks. For 10%, transvaginal scans were also performed. Criteria for normal scans were normal sequential segmental analysis, symmetrical four chamber view, normal semilunar valves, arterial outflow tracts, and ductal and aortic arches. Early scans were compared with mid-second trimester fetal echocardiography. Postmortem and postnatal data were added. Adverse pregnancy outcomes were diagnosis of a major cardiac or extracardiac abnormality, chromosomal defects, intrauterine death, or termination of pregnancy. Results: There were 21 abnormal cardiac scans (9%): 14 major structural defects (eight isolated, six with chromosomal or extracardiac abnormalities) in pregnancies resulting in three live births, one intrauterine death, and 10 terminated pregnancies. Seven scans showed asymmetry between right and left sided structures (two isolated, five with chromosomal or extracardiac abnormalities); six of the seven pregnancies were terminated. The scans were normal in 199 cases (87%). Cardiac follow up of 184 of 199 babies (93%) confirmed situs and connections. One case each of pulmonary stenosis and ventricular septal defect requiring postnatal intervention were diagnosed at later scans. In 28 of 199 (14%) babies there was a non-cardiac adverse outcome. First examination was not diagnostic for 10 (4%). Conclusion: Early fetal echocardiography in high risk pregnancies was diagnostic in 96%. Abnormal cardiac scans (isolated in 48%, major structrual defects in 67%) led to termination of pregnancy in 76%. Most cardiac scans were normal, allowing family reassurance. The high number of adverse outcomes with normal cardiac anatomy stresses the need for a multidisciplinary approach to early fetal echocardiography.
Convolutional Codes for Network-Error Correction

In this work, we introduce convolutional codes for network-error correction in the context of coherent network coding. We give a construction of convolutional codes that correct a given set of error patterns, as long as consecutive errors are separated by a certain interval. We also give some bounds on the field size and the number of errors that can get corrected in a certain interval. Compared to previous network error correction schemes, using convolutional codes is seen to have advantages in field size and decoding technique. Some examples are discussed which illustrate the several possible situations that arise in this context.
The myeloid-cell-specific c-fes promoter is regulated by Sp1, PU.1, and a novel transcription factor

The protein product of the c-fps/fes (c-fes) proto-oncogene has been implicated in the normal development of myeloid cells (macrophages and neutrophils). mRNA for c-fes has been detected exclusively in myeloid cells and vascular endothelial cells in adult mammals. Although a 13-kilobase-pair (kb) human c-fes transgene exhibits high levels of expression in mice, the sequences that confer myeloid-cell-specific expression of the human c-fes gene have not been defined. Transient-transfection experiments demonstrated that plasmids containing 446 bp of c-fes 5'-flanking sequences linked to a luciferase reporter gene were active exclusively in myeloid cells. No other DNA element within the 13-kb human c-fes locus contained positive cis-acting elements, with the exception of a weakly active region within the 3'-flanking sequences. DNase I footprinting assays revealed four distinct sites that bind myeloid nuclear proteins (-408 to -386, -293 to -254, -76 to -65, and -34 to +3). However, the first two footprints resided in sequences that were largely dispensable for transient activity. Plasmids containing 151 bp of 5'-flanking sequences confer myeloid-cell-specific gene expression. Electrophoretic mobility shift analyses demonstrated that the 151-bp region contains nuclear protein binding sites for Sp1, PU.1, and/or Elf-1, and a novel factor. This unidentified factor binds immediately 3' of the PU.1/Elf-1 sites and appears to be myeloid cell specific. Mutation of the PU.1/Elf-1 site or the 3' site (FP4-3') within the context of the c-fes promoter resulted in substantially reduced activity in transient transfections. Furthermore, transient-cotransfection assay demonstrated that PU.1 (and not Elf-1) can transactivate the c-fes promoter in nonmyeloid cell lines. We conclude that the human c-fes gene contains a strong myeloid-cell-specific promoter that is regulated by Sp1, PU.1, and a novel transcription factor.
Antimicrobial properties of platelet-rich preparations. A systematic review of the current pre-clinical evidence

Abstract In recent years autologous platelet concentrates (APCs) have become popular in several medicine fields, representing a valuable adjunct to regenerative surgical procedures. Beneficial effects in the control of postsurgical discomfort and infection have also been frequently reported, suggesting that APC may possess anti-inflammatory and antimicrobial properties. The aim of the present review was to summarize the current evidence regarding the antimicrobial effects of platelet concentrates, investigated by in vitro and animal studies. This review was conducted following a systematic approach. An electronic search was performed on MEDLINE, EMBASE and Scopus databases using appropriate search terms, without language or time restrictions. Preclinical studies assessing the antimicrobial activity of APC were included and divided according to the experimental design. Twenty in vitro studies and four animal studies, investigating APC effects on a broad range of microorganisms, were included. In in vitro studies APC reduced the growth of microorganisms during the first hours of incubation, while they could not completely break down the microbial load. In fact, over time a recovery of bacterial growth was always observed, suggesting that APCs display a bacteriostatic rather than a microbicidal activity. All animal studies showed that APC administered by local injections were able to reduce the infection caused by different microorganisms, although to a lesser extent compared to antibiotics. In conclusion, although the exact action mechanisms of interaction with microbial pathogens need further investigation, platelet concentrates proved to have antimicrobial properties, and therefore could represent a useful natural substance for controlling postoperative infections at surgical sites.
Pretreatment direct bilirubin and total cholesterol are significant predictors of overall survival in advanced non‐small‐cell lung cancer patients with EGFR mutations

This study was designed to examine the prediction of pretreatment circulating bilirubin and cholesterol for overall survival in 459 advanced non‐small‐cell lung cancer (NSCLC) patients with epidermal growth factor receptor (EGFR) mutations. Circulating total bilirubin, direct bilirubin (DB), total cholesterol (TC), high‐density lipoprotein cholesterol (HDL‐C) and low‐density lipoprotein cholesterol (LDL‐C) levels were measured at baseline. The mean age (standard deviation) of all study patients was 58.7 (10.5) years, and 42.9% of them was males. Ever smokers accounted for 27.0% and lung adenocarcinoma for 90.4%. The median follow‐up time and survival time were 29.5 and 34.9 months, respectively. Patients with higher DB had a 1.68‐fold increased risk of death compared with patients with lower DB (hazard ratio [HR] = 1.68, 95% confidence interval [CI]: 1.22–2.30, p = 0.001), while patients with higher TC were at a 63% reduced risk of death compared with patients with lower TC (HR = 0.37, 95% CI: 0.20–0.67, p = 0.001). As for HDL‐C, patients with higher levels had the risk of death reduced by 46% (HR = 0.54, 95% CI: 0.29–1.00, p = 0.049) compared with patients with lower levels. After the Bonferroni correction, only DB and TC were significantly associated with NSCLC survival. Our findings demonstrate for the first time that pretreatment DB was identified as a significant risk factor, yet TC as a protective factor, for overall survival in NSCLC patients with EGFR mutations.
Foveolar choroidal blood flow in age-related macular degeneration.

PURPOSE To compare measurements of the foveolar choroidal blood circulation in subjects with nonexudative, age-related macular degeneration (AMD) with those of control subjects. METHODS Laser Doppler flowmetry was used to assess relative choroidal blood velocity (ChBVel), volume (ChBVol), and flow (ChBFlow) in the center of the fovea. Measurements were obtained in 20 eyes of 20 subjects with 10 or more large drusen, visual acuity of 20/32 or better, and no evidence of choroidal neovascularization. Findings obtained in these subjects were compared with those of 10 eyes of 10 age- and blood pressure-matched control subjects with no large drusen. Foveolar choroidal blood flow measurements were obtained by asking the study participants to fixate on a probing laser beam. RESULTS No significant differences in average age, blood pressure, or intraocular pressure were observed between subjects with AMD and control subjects. In subjects with AMD, average ChBVol was 0.24 +/- 0.08 (+/- 1 SD) arbitrary units (AU); this value was 33% lower than that of control subjects (0.36 +/- 0.11 AU; two-tailed, independent Student's t-test, P = 0.005). Average ChBVel, conversely, was not significantly different from normal (0.44 +/- 0.07 AU) in subjects with AMD (0.44 +/- 0.10 AU). Average ChBFlow in subjects with AMD (8.7 +/- 3.1 AU) was 37% lower than that of control subjects (13.7 +/- 3.5 AU) (P = 0.0005). Average blood flow pulsatility was 6% higher in subjects with AMD (0.71 +/- 0.15) than in control subjects (0.66 +/- 0.14), but this difference was not statistically significant (P = 0.42). CONCLUSIONS Average ChBFlow in the nonexudative stages of AMD is lower than that of age-matched controls, and the effect is caused mainly by a decrease in ChBVol. Further studies are needed to elucidate whether decreased ChBFlow plays a role in the development of choroidal neovascularization, and whether ChBFlow measurements may help identify subjects with AMD at risk for developing choroidal neovascularization.
Preferences for nesting material as environmental enrichment for laboratory mice

Behavioural and psychological needs of laboratory animals generally cannot adequately be met in standard laboratory cages. Environmental enrichment, which provides a more structured environment can enhance the well-being of laboratory animals. They may perform more of their species-specific behaviour and may control their environment in a better way. An easily applicable form of enrichment for laboratory mice is nesting material. Six different types of nesting materials were evaluated in a preference test with male and female animals of two strains (C57BL/6J or BALB/c, n=48). No significant differences in preference were found between the strains or between the sexes. All mice showed a clear preference for cages with tissues or towels as compared to paper strips or no nesting material, and for cages with cotton string or wood-wool as compared to wood shavings or no nesting material. Paper-derived materials were preferred over wood-derived materials, although the results also suggest that the nature (paper or wood) of the nesting material is less important than its structure, which determines the nestability of the material. Nesting material may be a relatively simple method to contribute to the well-being of laboratory mice.
The accuracy of blood velocity measurement using ultrasound

In this study we explore the use of colour flow imaging to quantify blood velocity and wall shear rate. A known velocity profile was obtained using a straight tube flow rig. Colour Doppler ultrasound images were obtained and velocity profiles extracted off-line. There was a small discrepancy (2.6%) in maximum velocity, which was not present after convolution with the colour flow point spread function, hence is likely to be due to velocity gradient broadening within the sample volume. There was disagreement at the edge of the vessel due to loss of velocities below the clutter filter. At a typical clinical colour flow scale (12.8 cms/sup -1/) the error in wall shear measurement is 62 % and at a lower scale setting (4.4 cms/sup -1/) the error is 11%. This improvement seems to be due to the lower level of clutter filter that is used as the velocity scale decreases.
Auditory Evoked Responses in Musicians during Passive Vowel Listening Are Modulated by Functional Connectivity between Bilateral Auditory-related Brain Regions

Currently, there is striking evidence showing that professional musical training can substantially alter the response properties of auditory-related cortical fields. Such plastic changes have previously been shown not only to abet the processing of musical sounds, but likewise spectral and temporal aspects of speech. Therefore, here we used the EEG technique and measured a sample of musicians and nonmusicians while the participants were passively exposed to artificial vowels in the context of an oddball paradigm. Thereby, we evaluated whether increased intracerebral functional connectivity between bilateral auditory-related brain regions may promote sensory specialization in musicians, as reflected by altered cortical N1 and P2 responses. This assumption builds on the reasoning that sensory specialization is dependent, at least in part, on the amount of synchronization between the two auditory-related cortices. Results clearly revealed that auditory-evoked N1 responses were shaped by musical expertise. In addition, in line with our reasoning musicians showed an overall increased intracerebral functional connectivity (as indexed by lagged phase synchronization) in theta, alpha, and beta bands. Finally, within-group correlative analyses indicated a relationship between intracerebral beta band connectivity and cortical N1 responses, however only within the musicians' group. Taken together, we provide first electrophysiological evidence for a relationship between musical expertise, auditory-evoked brain responses, and intracerebral functional connectivity among auditory-related brain regions.
An Updated Meta-Analysis on the Association of MDM2 SNP309 Polymorphism with Colorectal Cancer Risk

Background The mouse double minute 2 (MDM2) gene encodes a phosphoprotein that interacts with P53 and negatively regulates its activity. The SNP309 polymorphism (T-G) in the promoter of MDM2 gene has been reported to be associated with enhanced MDM2 expression and tumor development. Studies investigating the association between MDM2 SNP309 polymorphism and colorectal cancer (CRC) risk reported conflicting results. We performed a meta-analysis of all available studies to explore the association of this polymorphism with CRC risk. Methods All studies published up to July 2013 on the association between MDM2 SNP309 polymorphism and CRC risk were identified by searching electronic databases PubMed, EMBASE, and Chinese Biomedical Literature database (CBM) databases. The association between the MDM2 SNP309 polymorphism and CRC risk was assessed by odds ratios (ORs) together with their 95% confidence intervals (CIs). Results A total of 14 case-control studies including 4460 CRC cases and 4828 controls were identified. We did not find a significant association between the MDM2 SNP309 polymorphism and CRC risk in all genetic models in overall population. However, in subgroup analysis by ethnicity, significant associations were found in Asians (TG vs. TT: OR = 1.197, 95% CI = 1.055–1.358, P=0.005; GG+TG vs. TT: OR = 1.246, 95% CI = 1.106–1.404, P=0.000) and Africans. When stratified by HWE in controls, significantly increased risk was also found among the studies consistent with HWE (TG vs. TT: OR = 1.166, 95% CI = 1.037–1.311, P= 0.010). In subgroup analysis according to p53 mutation status, and gender, no any significant association was detected. Conclusions The present meta-analysis suggests that the MDM2 is a candidate gene for CRC susceptibility. The MDM2 SNP309 polymorphism may be a risk factor for CRC in Asians.
Preliminary Evaluation of the Use of the sefA Fimbrial Gene to Elicit Immune Response Against Salmonella enterica Serotype Enteritidis in Chickens

Abstract In the last 2 decades, the prevalence of Salmonella enterica serotype Enteritidis (Salmonella Enteritidis) has dramatically increased worldwide, becoming the leading cause of food-borne illnesses and an important public health issue. Many studies have suggested the role of the SEF14 fimbrial protein in the adhesion of Salmonella Enteritidis to the host. In the present study, the sefA gene, which encodes the main subunit of the SEF14 fimbrial protein, was cloned into a temperature-sensitive expression vector and transformed into a nonpathogenic, avirulent strain of Escherichia coli. The recombinant strain was used as a vaccine to elicit specific immune response against the SefA protein of Salmonella Enteritidis in 1-day-old chickens. The recombinant strain was reisolated from the intestines of treated birds for up to 21 days posttreatment, demonstrating its ability to colonize the intestinal tracts of 1-day-old chickens. In addition, immunoglobulin A (IgA) against the SefA protein was detected in intestinal secretions from treated birds at 7 days posttreatment and in bile samples from 14 to 21 days posttreatment by enzyme-linked immunosorbent assay. Nontreated birds did not show any evidence of intestinal colonization by the recombinant strain or anti-SefA IgA response in their bile or intestinal secretions. Preliminary evaluation of the recombinant strain showed a potential use of this strain to elicit protection against Salmonella Enteritidis infection in chickens. Further experiments are needed to study the ability of the recombinant strain to protect birds against Salmonella Enteritidis colonization.