Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification and Isolation of a Castellaniella Species Important during Biostimulation of an Acidic Nitrate- and Uranium-Contaminated Aquifer

ABSTRACT Immobilization of uranium in groundwater can be achieved through microbial reduction of U(VI) to U(IV) upon electron donor addition. Microbial community structure was analyzed in ethanol-biostimulated and control sediments from a high-nitrate (>130 mM), low-pH, uranium-contaminated site in Oak Ridge, TN. Analysis of small subunit (SSU) rRNA gene clone libraries and polar lipid fatty acids from sediments revealed that biostimulation resulted in a general decrease in bacterial diversity. Specifically, biostimulation resulted in an increase in the proportion of Betaproteobacteria (10% of total clones in the control sediment versus 50 and 79% in biostimulated sediments) and a decrease in the proportion of Gammaproteobacteria and Acidobacteria. Clone libraries derived from dissimilatory nitrite reductase genes (nirK and nirS) were also dominated by clones related to Betaproteobacteria (98% and 85% of total nirK and nirS clones, respectively). Within the nirK libraries, one clone sequence made up 59 and 76% of sequences from biostimulated sediments but only made up 10% of the control nirK library. Phylogenetic analysis of SSU rRNA and nirK gene sequences from denitrifying pure cultures isolated from the site indicate that all belong to a Castellaniella species; nearly identical sequences also constituted the majority of biostimulated SSU rRNA and nirK clone libraries. Thus, by combining culture-independent with culture-dependent techniques, we were able to link SSU rRNA clone library information with nirK sequence data and conclude that a potentially novel Castellaniella species is important for in situ nitrate removal at this site.
Screening for psychiatric symptoms: PAS-ADD Checklist norms for adults with intellectual disabilities.

BACKGROUND The Psychiatric Assessment Schedule for Adults with Developmental Disabilities Checklist (PAS-ADD Checklist) is a screening instrument designed to help carers recognize likely mental health problems in people with intellectual disabilities (ID). To date there are no published PAS-ADD Checklist data on a large nonpsychiatric population of adults with ID, an important step towards developing norms for comparative purposes. METHODS Informants who had known participants for a median 24 months completed the PAS-ADD Checklist on 1155 adults with ID living in community, residential care and hospital settings in a county district in the North-east of England. RESULTS Normative data were obtained for the PAS-ADD Checklist for the study population with reference to gender, age, and type of residence. The overall prevalence of mental health problems was 20.1%, and the rates for affective/neurotic, organic and psychotic disorders were 14%, 3.9%, and 10.2%, respectively. Significant differences in the rates for particular disorders were found across gender, age and, residence type. CONCLUSIONS The rates of mental disorders found in the study population were consistent with previous studies of general populations of people with ID using over-inclusive screening instruments. The PAS-ADD Checklist appears to be an easy-to-use and sensitive tool for identifying mental health cases in ID populations, but further investigation is required concerning the specificity of the instrument.
A western-style diet reduces bone mass and biomechanical bone strength to a greater extent in male compared with female rats during development

Evidence from epidemiological and animal-feeding trials suggests that a western-style diet that is high in fat, and low in Ca, vitamin D and folic acid may result in low bone mass and poor bone quality: this leads to an increased risk of fragility fracture. The overall objective of the present study was to determine the effect of feeding a western-style diet (low in Ca (0·4 g/kg diet, Ca:P ratio 1:10), cholecalciferol (3 μg/kg diet), folic acid (0·23 mg/kg diet) and fibre (20 g/kg diet), and high in fat (200 g/kg diet)) for 17 weeks on bone mineral content (BMC) and the biomechanical bone strength of rat femurs. A secondary objective was to determine whether femurs from male and female rats (seven to eight rats per group) respond differently to the western-style diet. Male and female rats weighing 150–180 g were fed a western-style diet or a control diet for 17 weeks. At the end of the feeding trial, femur BMC was measured by ashing, and biomechanical properties were determined by three-point bending. Femur BMC and the majority of biomechanical properties measured were lower (P<0·05) among male and female rats fed a western-style diet compared with a control diet, despite similar weight gain and final body weight within genders. However, the western-style diet had a greater negative effect on femur BMC and biomechanical strength properties among male rats compared with females. This may be because male rats experienced greater overall body growth, as assessed by weight gain, than female rats, and suggests that the nutrient composition of the western-style diet did not support the development of strong femurs.
Sparse-view x-ray CT reconstruction via total generalized variation regularization

Sparse-view CT reconstruction algorithms via total variation (TV) optimize the data iteratively on the basis of a noise- and artifact-reducing model, resulting in significant radiation dose reduction while maintaining image quality. However, the piecewise constant assumption of TV minimization often leads to the appearance of noticeable patchy artifacts in reconstructed images. To obviate this drawback, we present a penalized weighted least-squares (PWLS) scheme to retain the image quality by incorporating the new concept of total generalized variation (TGV) regularization. We refer to the proposed scheme as ‘PWLS-TGV’ for simplicity. Specifically, TGV regularization utilizes higher order derivatives of the objective image, and the weighted least-squares term considers data-dependent variance estimation, which fully contribute to improving the image quality with sparse-view projection measurement. Subsequently, an alternating optimization algorithm was adopted to minimize the associative objective function. To evaluate the PWLS-TGV method, both qualitative and quantitative studies were conducted by using digital and physical phantoms. Experimental results show that the present PWLS-TGV method can achieve images with several noticeable gains over the original TV-based method in terms of accuracy and resolution properties.
Pattern matching intrusion detection technique for Wireless Sensor Networks

Wireless Sensor Network (WSN) is a network with large number of tiny sensor devices which are of low cost, and minimum consumption of power called as sensor nodes. These type of nodes have great sensing technology which are specifically designed for applications such as military, smart homes and other security related areas. Due its wireless nature, network can be deployed anywhere in the environment, which becomes more vulnerable for attackers to destroy the network. Most importantly, WSN should be protected from malicious activities to take place and thus security becomes a major issue. However, such security can be provided by applying mechanisms for both intrusion detection and prevention. In our study, pattern matching is one of the mechanism that can be used for security of WSN. We also discuss some of the preventive measures that can be considered for protecting the sensor network.
Assessing frequency effects on verb inflection use by Spanish-speaking individuals with agrammatism: Theoretical and clinical implications

The resistance of high-frequency linguistic elements to aphasic impairment suggests that frequency of occurrence may be implicated in verb use differences in agrammatic aphasia. The highly-inflected Spanish verb system allows for the examination of frequency of occurrence along two main metrics, daily usage frequency and paradigmatic frequency. In this study, we explored the role of those two frequency dimensions in verb repetition by Spanish speakers with agrammatism. Six native Spanish-speaking individuals with agrammatic oral expression were matched for age, education and Spanish dialect with six speakers with typical language. The speakers participated in a sentence repetition task involving simple verb tenses. Results revealed that high frequency in daily usage can have a stronger facilitating effect on verb repetition than paradigmatic frequency. Theoretical and clinical implications of the findings are discussed to highlight some plausible repercussions of typical discourse patterns in providing a socio-cognitive dimension to agrammatism theory and in supporting the use of frequency-based linguistic features in agrammatism therapy.
Detection of depth in binocular visual systems using Kuramoto models

Animals routinely rely on their eyes to localize fixed and moving targets especially with the goal of either avoiding or capturing them. Detection of position of targets in space is an important problem in such a localization process for the motor control circuit to actuate a successful movement. The purpose of this paper is to sketch a binocular visual system that includes image capturing, retinal projection, sparse representation and data fusion, multi-neural encoding in the cortex down to detection of depth of objects from activity waves using nonlinear dynamics of an oscillatory network. The general strategies from visual circuitry, some of which may not be employed by the animal, could perhaps be employed in building machines with multiple sensors
Comparison of three pretreatment protocols to prevent anaphylactoid reactions to radiocontrast media.

Three pretreatment regimens were compared for prevention of anaphylactoid reactions in 149 patients who previously had reacted to radiocontrast media (RCM) administration. From 1976 to 1980, 52 patients were treated with 50 mg of oral prednisone 13, 7, and 1 hour before and 50 mg intramuscular diphenhydramine 1 hour before procedures (group I). From 1980 to 1984, 48 patients received 300 mg oral cimetidine one hour before procedure in addition to the other regimen (group II). From 1984 to 1989, 49 patients received the three drugs and 25 mg oral ephedrine one hour before procedures (group III). Previous reactions were similar in each group, consisting of urticaria and/or angioedema in all patients, hypotension in some (groups I, 5; II, 6; III, 4), and wheezing in two (group I). Readministration of RCM was intraarterial (groups I, 18; II, 20; III, 20) or intravenous. Generalized reactions upon readministration of RCM occurred in 4 (8%) of group I and 3 (6%) of both groups II and III. All reactions consisted of urticaria and/or angioedema, were mild, and required no specific treatment. In a separate group of ten patients whose previous reactions to RCM were life threatening (shock), pretreatment was accompanied by a provocative dosing regimen. Two patients (20%) experienced systemic reactions that resulted in termination of the procedure. All our pretreatment regimens were equally effective; however, we favor a more comprehensive pretreatment protocol (regimen III) based upon our lack of demonstrated adverse effects and a possible therapeutic advantage as reported by other investigators. (ABSTRACT TRUNCATED AT 250 WORDS)
Deformative stress associated with an abnormal clivo-axial angle: A finite element analysis

Background: Chiari malformation, functional cranial settling and subtle forms of basilar invagination result in biomechanical neuraxial stress, manifested by bulbar symptoms, myelopathy and headache or neck pain. Finite element analysis is a means of predicting stress due to load, deformity and strain. The authors postulate linkage between finite element analysis (FEA)-predicted biomechanical neuraxial stress and metrics of neurological function. Methods: A prospective, Internal Review Board (IRB)-approved study examined a cohort of 5 children with Chiari I malformation or basilar invagination. Standardized outcome metrics were used. Patients underwent suboccipital decompression where indicated, open reduction of the abnormal clivo-axial angle or basilar invagination to correct ventral brainstem deformity, and stabilization/ fusion. FEA predictions of neuraxial preoperative and postoperative stress were correlated with clinical metrics. Results: Mean follow-up was 32 months (range, 7-64). There were no operative complications. Paired t tests/ Wilcoxon signed-rank tests comparing preoperative and postoperative status were statistically significant for pain, bulbar symptoms, quality of life, function but not sensorimotor status. Clinical improvement paralleled reduction in predicted biomechanical neuraxial stress within the corticospinal tract, dorsal columns and nucleus solitarius. Conclusion: The results are concurrent with others, that normalization of the clivo-axial angle, fusion-stabilization is associated with clinical improvement. FEA computations are consistent with the notion that reduction of deformative stress results in clinical improvement. This pilot study supports further investigation in the relationship between biomechanical stress and central nervous system (CNS) function.
Resurrection of the flagellar rotary motor near zero load

Flagellated bacteria, such as Escherichia coli, are propelled by helical flagellar filaments, each driven at its base by a reversible rotary motor, powered by a transmembrane proton flux. Torque is generated by the interaction of stator proteins, MotA and MotB, with a rotor protein FliG. The physiology of the motor has been studied extensively in the regime of relatively high load and low speed, where it appears to operate close to thermodynamic equilibrium. Here, we describe an assay that allows systematic study of the motor near zero load, where proton translocation and movement of mechanical components are rate limiting. Sixty-nanometer-diameter gold spheres were attached to hooks of cells lacking flagellar filaments, and light scattered from a sphere was monitored at the image plane of a microscope through a small pinhole. Paralyzed motors of cells carrying a motA point mutation were resurrected at 23°C by expression of wild-type MotA, and speeds jumped from zero to a maximum value (≈300 Hz) in one step. Thus, near zero load, the speed of the motor is independent of the number of torque-generating units. Evidently, the units act independently (they do not interfere with one another), and there are no intervals during which a second unit can add to the speed generated by the first (the duty ratio is close to 1).
A delta-sigma modulator for a 1-bit digital switching amplifier

A seventh-order single-loop single-bit delta-sigma modulator for a 1-bit digital audio switching amplifier is presented. To achieve high SNR and ensure the modulator stability for a large input range, the positions of the modulator loop filter poles and zeros are optimized, and a feedback comparator is used. A test chip was fabricated in a 0.35-/spl mu/m CMOS process with optional 5-V transistors. The modulator achieves an SNR of 111 dB and 0.0015-% THD+N over the audio band. The normalized maximum allowable input range is 0.89. There are two modulators on one chip, one for each left and right audio channel. The isolation between both channels is over 135 dB. The chip area is 12.6 mm/sup 2/ and it draws 60 mA from a 5-V supply.
Reducing the saliency of intentional stimuli results in greater contextual-dependent performance

Wright and Shea (1991) described intentional stimuli as explicitly identified information necessary to successfully perform a task, whereas incidental stimuli are not explicitly identified as crucial to task performance but have the potential to become associated with particular responses because of their selective presence in the training environment. Shea and Wright (1995), using a speeded-choice RT task, indicated that manipulating the strength of association between incidental information and the responses, by changing the discriminibility of incidental stimuli while fixing the strength of the association between the intentional stimuli and each response, had a significant impact on task performance. The present experiment further examined the role played by incidential stimuli when the strength of association between the intentional stimuli and the associated responses was reduced, by minimising stimulus– response compatibility. It was assumed that this latter manipulation would have a similar impact as increasing the strength of incidential stimuli–response relationships. That is, the relative contribution of the incidental stimuli would increase, resulting in an increase in context-dependent behaviour during tests in which the intentional and incidental stimuli activated different responses. The results were in agreement with this prediction and consistent with a model for contextual-dependent performance proposed by Shea and Wright (1995) as well as with the outshining hypothesis forwarded by Smith (1988, 1994).
Cryptosporidium parvum-Specific Mucosal Immune Response in C57BL/6 Neonatal and Gamma Interferon-Deficient Mice: Role of Tumor Necrosis Factor Alpha in Protection

ABSTRACT Both neonatal and C57BL/6 gamma interferon (IFN-γ) knockout (C57BL/6-GKO) mice are susceptible to Cryptosporidium parvum, but the course of infection is different. Neonatal mice are able to clear the parasite within 3 weeks, whereas C57BL/6-GKO mice, depending on age, die rapidly or remain chronically infected. The mechanism by which IFN-γ leads to a protective immunity is yet poorly understood. In order to investigate the effect of IFN-γ on other cytokines expressed in the intestinal mucosa during C. parvum infection, we studied cytokine mRNA expression in the neonates and GKO (neonatal and adult) mice by quantitative reverse transcription-PCR (RT-PCR) at 4 and 9 days after infection. IFN-γ mRNA levels were quickly and strongly up-regulated in the mucosa of neonatal mice. In GKO mice, the Th1-type response was dramatically altered during the infection, whereas the mRNA expression levels of the Th2-type cytokines interleukin 4 (IL-4) and IL-10 were increased in both mouse models. In the absence of IFN-γ, the adult knockout mice up-regulated the mRNA levels of inflammatory cytokines, such as IL-1β, IL-6, and granulocyte-macrophage colony-stimulating factor, in the mucosa, but not tumor necrosis factor alpha (TNF-α), whereas all these cytokines were up-regulated in the infected neonatal mice. Further experiments indicated that injections of TNF-α into GKO adult mice significantly reduced oocyst shedding. The results of the present study indicate that the resolution of infection is dependent on the expression of Th1-type cytokines in the mucosa of C57BL/6 mice and that TNF-α may participate in the control of parasite development.
A proteomic characterization of water buffalo milk fractions describing PTM of major species and the identification of minor components involved in nutrient delivery and defense against pathogens

Water buffalo has been studied in relation to the exclusive use of its milk for the manufacture of high‐quality dairy products. Buffalo milk presents physicochemical features different from that of other ruminant species, such as a higher content of fatty acids and proteins. We report here a detailed proteomic analysis of buffalo skim milk, whey and milk fat globule membrane fractions. Notwithstanding the poor information available on buffalo genome, identification of protein isoforms corresponding to 72 genes was achieved by a combined approach based on 2‐DE/MALDI‐TOF PMF and 1‐DE/μLC‐ESI‐IT‐MS‐MS. Major protein components, i.e. αSl‐, αS2‐, β‐, κ‐caseins, α‐lactalbumin and β‐lactoglobulin, were characterized for PTM, providing a scientific basis to coagulation/cheese making processes used in dairy productions. Minor proteins detected emphasized the multiple functions of milk, which besides affording nutrition to the newborn through its major components, also promotes development and digestive tract protection in the neonate, and ensures optimal mammary gland function in the mother. Defense against pathogens is guaranteed by an arsenal of antimicrobial/immunomodulatory proteins, which are directly released in milk or occur on the surface of secreted milk‐lipid droplets. Proteins associated with cell signaling or membrane/protein trafficking functions were also identified, providing putative insights into major secretory pathways in mammary epithelial cells.
The su(Hw) protein insulates expression of the Drosophila melanogaster white gene from chromosomal position‐effects.

Mutations in the suppressor of Hairy‐wing [su(Hw)] locus reverse the phenotype of a number of tissue‐specific mutations caused by insertion of a gypsy retrotransposon. The su(Hw) gene encodes a zinc finger protein which binds to a 430 bp region of gypsy shown to be both necessary and sufficient for its mutagenic effects. su(Hw) protein causes mutations by inactivation of enhancer elements only when a su(Hw) binding region is located between these regulatory sequences and a promoter. To understand the molecular basis of enhancer inactivation, we tested the effects of su(Hw) protein on expression of the mini‐white gene. We find that su(Hw) protein stabilizes mini‐white gene expression from chromosomal position‐effects in euchromatic locations by inactivating negative and positive regulatory elements present in flanking DNA. Furthermore, the su(Hw) protein partially protects transposon insertions from the negative effects of heterochromatin. To explain our current results, we propose that su(Hw) protein alters the organization of chromatin by creating a new boundary in a pre‐existing domain of higher order chromatin structure. This separates enhancers and silencers distal to the su(Hw) binding region into an independent unit of gene activity, thereby causing their inactivation.
Androgens activate mitogen‐activated protein kinase signaling: Role in neuroprotection

Recent evidence indicates that testosterone is neuroprotective, however, the underlying mechanism(s) remains to be elucidated. In this study, we investigated the hypothesis that androgens induce mitogen‐activated protein kinase (MAPK) signaling in neurons, which subsequently drives neuroprotection. We observed that testosterone and its non‐aromatizable metabolite dihydrotestosterone (DHT) rapidly and transiently activate MAPK in cultured hippocampal neurons, as evidenced by phosphorylation of extracellular signal‐regulated kinase (ERK)‐1 and ERK‐2. Importantly, pharmacological suppression of MAPK/ERK signaling blocked androgen‐mediated neuroprotection against β‐amyloid toxicity. Androgen activation of MAPK/ERK and neuroprotection also was observed in PC12 cells stably transfected with androgen receptor (AR), but in neither wild‐type nor empty vector‐transfected PC12 cells. Downstream of ERK phosphorylation, we observed that DHT sequentially increases p90 kDa ribosomal S6 kinase (Rsk) phosphorylation and phosphorylation‐dependent inactivation of Bcl‐2‐associated death protein (Bad). Prevention of androgen‐induced phosphorylation of Rsk and Bad blocked androgen neuroprotection. These findings demonstrate AR‐dependent androgen activation of MAPK/ERK signaling in neurons, and specifically identify a neuroprotective pathway involving downstream activation of Rsk and inactivation of Bad. Elucidation of androgen‐mediated neural signaling cascades will provide important insights into the mechanisms of androgen action in brain, and may present a framework for therapeutic intervention of age‐related neurodegenerative disorders.