Miracle-dz/UniFAR-FTUs huggingface dataset:
The regulatory locus cinRI in Rhizobium leguminosarum controls a network of quorum‐sensing loci

N‐(3‐hydroxy‐7‐cis‐tetradecenoyl)‐l‐homoserine lactone (3OH,C14:1‐HSL) is a quorum‐sensing signalling molecule produced by Rhizobium leguminosarum. It is unusual in that it inhibits the growth of several strains of R. leguminosarum and was previously known as ‘small bacteriocin’. The cinRI locus responsible for the production of 3OH,C14:1‐HSL has been characterized; it is predicted to be on the chromosome, based on DNA hybridization. The cinR and cinI genes are in different transcriptional units, separated by a predicted transcription terminator. CinR regulates cinI expression to a very high level in a cell‐density dependent manner, and cinI expression is positively autoregulated by 3OH,C14:1‐HSL, the only identified N‐acyl homoserine lactone (AHL) produced by CinI. No other AHLs were identified that strongly induced cinI expression. Mutation of cinI or cinR abolishes the production of 3OH,C14:1‐HSL and also reduces the production of several other AHLs. This is thought to result from the expression of three other AHL production loci being affected by the absence of 3OH,C14:1‐HSL. AHLs produced by these other loci include N‐hexanoyl‐ and N‐octanoyl‐l‐homoserine lactones and, unexpectedly, N‐heptanoyl‐l‐homoserine lactone (C7‐HSL). The expression of the rhiI gene on the symbiotic plasmid is greatly reduced in a cinI mutant, and the major regulatory effect appears to be mediated at least in part as a result of an effect on expression of RhiR, the regulator of rhiI. Thus, cinR and cinI appear to be at the top of a regulatory cascade or network that influences several AHL‐regulated quorum‐sensing loci. The expression of cinI–lacZ fusions is significantly reduced (but not abolished) when the symbiosis plasmid pRL1JI is present, resulting in a reduction in the level of 3OH,C14:1‐HSL produced. Mutation of cinI had little effect on growth or nodulation. However, plasmid transfer was affected, and the results obtained indicate that 3OH,C14:1‐HSL produced by either the donor or the recipient in mating experiments can stimulate transfer of pRL1JI.
Prognostic impact of perineural invasion in hypopharyngeal squamous cell carcinoma

Abstract Objectives: The aim of this study was to evaluate the role of PNI in HPSCC. Methods: The medical records of 105 patients who underwent surgery-based treatment for HPSCC were reviewed. Clinicopathologic parameters including disease-specific survival were correlated with PNI. Results: PNI was identified in 27 of the 105 (25.7%) cases of HPSCC. Correlation analysis demonstrated that PNI in HPSCC was significantly correlated with pN classification (10.3% in N0/N1 vs 34.8% in N2/N3, p = 0.006). Patients with PNI had decreased 5-year disease-specific survival with borderline significance (p = 0.065). In a sub-set of 31 patients who did not receive post-operative radiotherapy, PNI was determined to be a significant prognostic predictor (p = 0.033). In multivariate analysis, extracapsular invasion was the only independent prognostic factor for disease-specific survival (p = 0.001). Conclusion: Perineural invasion (PNI) should be considered an independent predictor for cervical lymph node involvement. PNI status in primary hypopharyngeal squamous cell carcinoma (HPSCC) specimens should be considered in decisions concerning adjuvant radiotherapy.
An undersampling 14-bit cyclic ADC

An undersampling 14-bit 357 kSps cyclic ADC is designed for radio frequency identification (RFID) transceiver system. Modified passive capacitor error-average (PCEA) technique is adopted for high accuracy. Opamp sharing and the removal of front-end SHA are utilized for low power dissipation and small chip area. The proposed chip is fabricated in a 180 nm CMOS process, and it occupies 0.65 mm × 1.6 mm. With 2.431 MHz input, the ADC achieves 70.4 dB signal-to-noise and distortion ration (SNDR), 85.6 dB spurious free dynamic range (SFDR) and 11.4 effective number of bits (ENOB). When the input frequency increases to 15.59 MHz, the measured SNDR, SFDR and ENOB are 67.3 dB, 88.1 dB and 10.9 bit, respectively. With 3 V supply, it consums 4.2 mW with FOM of 4.3 pJ/Step.1
The statistical analysis of genetic sequencing and rare variant association studies

Eugene Urrutia: The Statistical Analysis of Genetic Sequencing and Rare Variant Association Studies (Under the direction of Michael Wu) Understanding the role of genetic variability in complex traits is a central goal of modern human genetics research. So far, genome wide association tests have not been able to discover SNPs that explain a large proportion of the heritability of disease. It is hoped that with the advent of accessible DNA sequencing data, investigators can uncover more of the socalled missing heritability. The added information contained in sequencing data includes rare variants, that is, minor alleles whose population frequency is low. We examine several existing region based rare variant association tests including burden based tests and similarity based tests and show that each is most powerful under a certain set of conditions which is unknown to the investigator. While some have proposed tests that combine the features of several existing tests, none as yet has provided a test to combine the features of all existing tests. Here, we propose one such test under the framework of the SKAT test, and show that it is nearly as powerful as the most appropriately chosen test under a range of scenarios. Existing methods do not allow for missing values in the covariates. Standard use of complete case analysis may yield misleading results, including false positives and biased parameter estimates. To address this problem, we extend an existing maximum likelihood strategy for accommodating partially missing covariates to the SKAT framework for rare variant association testing. This results in a test with high power to identify genetic regions associated with quantitative traits while still providing unbiased estimation and correct control of type I error when covariates are missing at random. Since the framework is generic, we also consider the application of this approach to epigenetic data.
IDENTIFICATION OF ETHYLENE AS A VOLATILE PRODUCT OF THE FUNGUS PENICILLIUM DIGITATUM.

Experiments reported independently by BIALE (1) and MILLER, WINSTON, and FISHER (8) revealed that the common green mold of citrus fruits, P. digitatum, produces a physiologically active emanation whose effects on plant tissue are the same as those caused by ethylene gas. It was shown by the latter authors and by BIALE and SHEPHERD (3) that this fungus produces this emanation whether grown on its natural host or in culture, and PRATT (10) showed that production of the emanation does not depend on major nutrient components of the culture solution but does appear to be related to active growth and respiration of the culture. Production of the active gas by fungus-infected fruit has been further studied by ROHRBAUGH (12) and BIALE (2). Except for recent evidence of NICKERSON (9) that ethylene may be produced by Blastomyces dermatitidis and two other human pathogens, P. digitatum is the only fungus reported to have this activity. Biological testing of various other plant pathogens has given negative results (1, 14). Since P. digitatum is a particularly promising organism for the study of the mechanism of ethylene formation, it was of interest to verify chemllically the identity of the active gas produced.
Angle estimation of coherent targets for bistatic MIMO radar

Angel estimation is considered for bi-static MIMO radar in the case where there exist both coherent and incoherent targets. Firstly, the bis-tatic MIMO radar data model is introduced and data covariance matrix is given. secondly, a matrix is formed using a column of the bi-static MIMO radar data covariance matrix. The rank of the formed matrix is only related to the number of the targets. Finally, the estimation of signal parameter via rotational invariance techniques (ESPRIT) algorithm is applied on the formed data matrix to estimate the direction of departure (DOD) and the direction of arrival (DOA). The numerical results show the effectiveness of the method.
Residential Revitalization and Displacement in a Growth Region

REVITALIZATION of central-city neighborhoods was one of the most publicized and debated urban developments of the past decade. In stark contrast to more than three decades of continued and seemingly unpreventable decline, the process of privately sponsored urban renewal became a much celebrated affair. ' The reasons for the celebration are obvious and range from the growth of a new tax base to the physical improvement of the inner-city environment. In spite of these advantages, inner-city revitalization became the focus of bitter debate.2
Prevalence of TT virus DNA in eastern Taiwan aborigines

We studied the prevalence of TT virus (TTV) DNA in the general population of the eastern Taiwan aborigine villages, about 11% (34 of 317). There is no association between the presence of HBsAg and TTV DNA or betwen the presence of HCV RNA and TTV DNA. Therefore, the infection of HBV or HCV and the presence of TTV DNA appear to be independent from each other. The association between the presence of TTV DNA and the elevated alanine aminotransferase (and/or aspartate aminotransferase) activity was also investigated. The presence of TTV DNA was not found to be correlated with abnormal liver function (P = 0.574) when age, gender, and the presence of HBsAg, HCV RNA, and HGV RNA were all considered in the assay. The sequence homology of TTV DNA fragments between different isolates from Taiwan and N22 (the clone obtained from the original prototype strain) from Japan ranged from 84 to 97%. The recombinant protein encoded by the TTV DNA fragment corresponding to the open reading frame of N22 was expressed in E. coli successfully. However, no serum response against the recombinant protein was detected. J. Med. Virol. 59:198–203, 1999. © 1999 Wiley‐Liss, Inc.
Amplified warming projections for high altitude regions of the northern hemisphere mid-latitudes from CMIP5 models

We use output from global climate models available from the Coupled Model Intercomparison Project Phase 5 (CMIP5) for three different greenhouse gas emission scenarios to investigate whether the projected warming in mountains by the end of the 21st century is significantly different from that in low elevation regions. To remove the effects of latitudinal variation in warming rates, we focus on seasonal changes in the mid-latitude band of the northern hemisphere between 27.5° N and 40° N, where the two major mountain systems are the Tibetan Plateau/Himalayas in Asia and the Rocky Mountains in the United States. Results from the multi-model ensemble indicate that warming rates in mountains will be enhanced relative to non-mountain regions at the same latitude, particularly during the cold season. The strongest correlations of enhanced warming with elevation are obtained for the daily minimum temperature during winter, with the largest increases found for the Tibetan Plateau/Himalayas. The model projections indicate that this occurs, in part, because of proportionally greater increases in downward longwave radiation at higher elevations in response to increases in water vapor. The mechanisms for enhanced increases in winter and spring maximum temperatures in the Rockies appear to be influenced more by increases in surface absorption of solar radiation owing to a reduced snow cover. Furthermore, the amplification of warming with elevation is greater for a higher greenhouse gas emission scenario.
Use of medium-chain triglyceride diets in children with malabsorption.

Medium-chain triglyceride (MCT) contains fatty acids with 8 or 10 carbon atoms and differs from long-chain triglyceride (LCT, containing fatty acids with 12 or more carbon atoms) in its water miscibility, its faster hydrolysis by pancreatic lipase, its ability to enter the intestinal mucosal cell unhydrolyzed and to undergo hydrolysis within the cell
Breath Acetone Concentration Measured Using a Palm-Size Enzymatic Sensor System

A palm-size electrochemical sensor was developed that utilizes an acetone sensitive enzyme system to amperometrically measure the acetone concentration in human breath. A study of dieting individuals showed an increase in breath acetone from baseline to elevated concentrations as the diet progressed, demonstrating the utility of the device as an indication of the rate of fat metabolism. The sensor response current linearly increased with increasing vapor acetone concentration. The sensor was tested using human breath, and the current response was linear from 0.2 to 10 ppm (v/v). Simulated and human breath results were shown to be comparable, and acetone concentrations out to 24 ppm (v/v) were measured. The enzymatic sensor was capable of detecting the low baseline breath acetone concentrations found in nondieting, nonexercising individuals. The correlation of the enzymatic sensor to the gas chromatograph possessed a linear correlation coefficient greater than 0.950 in all cases.
Public health perspectives on noise and cardiovascular disease

Introduction: Emerging research suggests that noise impacts human health beyond simply the auditory system. There have been recent amendments to acceptable noise level thresholds within the occupational setting and new European Union directives for noise in the community from air and road sources. The purpose of this review will be to assess the relationship between noise and cardiovascular disease in different settings. Methods: A literature review was conducted using PubMed on noise and more cardiovascular disease endpoints. All studies published in the English language between 2000-present were included. Studies on noise annoyance were excluded. Results: There is a strong positive association between occupational noise exposure and cardiovascular outcomes. There is a moderate association with noise in the community setting from road sources and a weak association with aircraft noise. The strength of the association across settings is dependent on the outcome type, interaction with age and sex of subjects, and time of measurement. Road source noise had the strongest association with myocardial infarction, notably in women during night exposures. The association with hypertension and road noise, when stratified by sex, was significant in men during night-time exposures and in pregnant older women. Only nighttime aircraft noise was associated with statistically significant findings in adults. All sources of noise demonstrate a dose response relationship, which peaks at different noise thresholds. Occupational noise exposure had the strongest association with noise > 85 dB (A) and duration of exposure. Conclusion: There is sufficient evidence to warrant the precautionary public health principle to reduce noise at the population levels for industry workers through stronger legislation, regular compliance inspections, and health promotion. Where population wide noise legislation has not yet been enacted, noise exposure reduction at the individual level may be beneficial.
Le traitement des spondylodiscites infectieuses non tuberculeuses. Analyse des pratiques thérapeutiques chez 110 patients hospitalisés dans 12 CHU en France

Les modalites du traitement des spondylodiscites infectieuses (SDI) a germes banals ne sont pas consensuelles. Aucun essai therapeutique randomise evaluant l'interet d'une antibiotherapie courte ou par voie orale n'a ete publie a ce jour. En raison de ce manque d'informations, il nous a paru interessant de decrire les traitements des patients hospitalises pour une SDI, dans 12 services de rhumatologie travaillant en reseau. Ces services ont accepte d'inclure dans cette etude transversale et descriptive, les dix premiers patients hospitalises a partir de janvier 1997 pour le traitement d'une SDI a germe banal. Apres verification des criteres d'inclusion, les observations de 110 patients ont ete analysees. Il s'agit de 67 hommes et de 43 femmes dont l'âge moyen est de 60,6 ± 13,7 ans (de 17 a 86 ans). Le delai separant les premiers signes de la date du diagnostic est en moyenne de 39,6 ± 39,8 jours (de 24 heures a 240 jours). Le taux de positivite des hemocultures est de 47,3 % tandis que celui de la ponction-biopsie discovertebrale est de 63,6 %. Ces deux examens permettent d'identifier un germe responsable de la SDI dans 79 observations (72,8 %). La duree d'hospitalisation dans le service de rhumatologie est en moyenne de 31,3 ± 14,1 jours (de 4 a 78 jours). Le traitement antibiotique est administre par voie intraveineuse (i.v.) chez 103 patients (93,6 %) pour une duree moyenne de 25,5 ± 17,6 jours (de 4 a 124 jours) mais qui depasse quatre semaines chez 36,5 % des patients. Le traitement antibiotique est administre par voie orale exclusivement et d'emblee chez sept patients (6,4 %). Dans 100 observations, ce traitement est utilise en complement puis en relais de la voie intraveineuse pour une duree moyenne de 87,2 ± 43,6 jours (de 20 a 278 jours). La duree totale du traitement antibiotique est de 103,0 ± 40,4 jours (de 42 a 285 jours). Quatre-vingt dix-huit patients (89,1 %) ont beneficie d'un corset. L'analyse des pratiques therapeutiques montre que si les choix d'antibiotiques sont coherents et respectent les recommandations en vigueur, il existe d'importantes differences entre les centres pour la duree du traitement par voie intraveineuse, la duree d'hospitalisation et la duree totale de traitement.
Registration of 3D diffusion weighted images using maximisation of mutual information

Diffusion tensor imaging (DTI) characterises anisotropic diffusion of water in the human body. For accurate estimation of tensor parameters it is essential that the diffusion weighted images are spatially aligned. In this study, we demonstrate the use of mutual information to register 3D diffusion weighted images. Specifically, diffusion weighted as opposed to non-diffusion-weighted images are used as the reference for registration and a rigid transformation is used to correct the distortions caused in the images because of patient movement. The results demonstrate that the proposed registration scheme can consistently and effectively characterise the motion induced distortion by minimising the mis-registration of images. Potential applications for this method are discussed.
Unique Profile of Visuo-Perceptual Skills in a Genetic Syndrome

Williams syndrome (WS) and Down syndrome (DS) are genetic disorders with characteristic neuropsychological profiles. Subjects with WS show surface similarities to subjects with right hemisphere damage (RHD) in their relative preservation of linguistic skills, their poor visuo-constructive skills, and their hierarchical processing biases. Ten adolescents and young adults with WS and nine matched subjects with DS were administered a battery of visuospatial perceptual tasks to test whether the profile of performance in WS would resemble that in RHD. It was found instead that the WS subjects showed a distinctive clustering of skills, with particular preservation of facial discrimination, but impairment of other perceptual skills. Subjects with DS showed a more homogeneous profile. The WS profile may map onto the functional dichotomy between ventral and dorsal visual pathways in the cerebral cortex.
Exposure Effects on the Psychophysical Scaling Methods of Magnitude Estimation and Cross-Modal Matching for Vibrotactile Stimulation of the Tongue and Hand

The purpose of the present study was to investigate possible effects of exposure upon psychophysical scaling responses when vibrotactile magnitude estimation and cross-modal matching are conducted within the same experiment. Four groups of 10 subjects each, with an over-all age range of 18–23 yr. , were employed. Groups 1 and 2 performed magnitude estimation for lingual vibrotaction and cross-modal matching with the lingual vibrotactile stimulus as the standard. Group 1 received the magnitude-estimation task first and Group 2 received the cross-modal-matching task first. Groups 3 and 4 performed magnitude estimation for vibrotaction applied to the thenar eminence of the hand and cross-modal matching with the vibrotactile stimulus applied to the thenar eminence of the hand as the standard. Group 3 received the magnitude-estimation task first and Group 4 received the cross-modal-matching task first. The psychophysical scaling methods of magnitude estimation and cross-modal matching showed very little exposure effect of one upon the other when used in the same experiment. Also, magnitude scaling responses tended to increase more rapidly with increases in vibrotactile stimulus intensity when the test site was the thenar eminence of the hand as opposed to the dorsum of the tongue.
Mixed Infections, Cryptic Diversity, and Vector-Borne Pathogens: Evidence from Polygenis Fleas and Bartonella Species

ABSTRACT Coinfections within hosts present opportunities for horizontal gene transfer between strains and competitive interactions between genotypes and thus can be a critical element of the lifestyles of pathogens. Bartonella spp. are Alphaproteobacteria that parasitize mammalian erythrocytes and endothelial cells. Their vectors are thought to be various biting arthropods, such as fleas, ticks, mites, and lice, and they are commonly cited as agents of various emerging diseases. Coinfections by different Bartonella strains and species can be common in mammals, but little is known about specificity and coinfections in arthropod vectors. We surveyed the rate of mixed infections of Bartonella in flea vectors (Polygenis gwyni) parasitizing cotton rats (Sigmodon hispidus) in which previous surveys indicated high rates of infection. We found that nearly all fleas (20 of 21) harbored one or more strains of Bartonella, with rates of coinfection approaching 90%. A strain previously identified as common in cotton rats was also common in their fleas. However, another common strain in cotton rats was absent from P. gwyni, while a rare cotton rat strain was quite common in P. gwyni. Surprisingly, some samples were also coinfected with a strain phylogenetically related to Bartonella clarridgeiae, which is typically associated with felids and ruminants. Finally, a locus (pap31) that is characteristically borne on phage in Bartonella was successfully sequenced from most samples. However, sequence diversity in pap31 was novel in the P. gwyni samples, relative to other Bartonella previously typed with pap31, emphasizing the likelihood of large reservoirs of cryptic diversity in natural populations of the pathogen.