Miracle-dz/UniFAR-FTUs huggingface dataset:
Production of Indole from l-Tryptophan and Effects of These Compounds on Biofilm Formation by Fusobacterium nucleatum ATCC 25586

ABSTRACT The l-tryptophan degradation product indole is a purported extracellular signaling molecule that influences biofilm formation in various bacteria. Here we analyzed the mechanisms of indole production in Fusobacterium nucleatum and the effects of tryptophan and indole on F. nucleatum planktonic and biofilm cells. The amino acid sequence deduced from the fn1943 gene in F. nucleatum ATCC 25586 was 28% identical to that deduced from tnaA in Escherichia coli, which encodes tryptophanase catalyzing the β-elimination of l-tryptophan to produce indole. The fn1943 gene was cotranscribed with the downstream gene fn1944, which is a homolog of tnaB encoding low-affinity tryptophan permease. The transcript started at position −68 or −153 from the first nucleotide of the fn1943 translation initiation codon. Real-time quantitative PCR showed that much more F. nucleatum fn1943 transcripts were obtained from log-phase cells than from stationary-phase cells. Indole production by the purified recombinant protein encoded by fn1943 was examined using high-performance liquid chromatography. The Km and kcat of the enzyme were 0.26 ± 0.03 mM and 0.74 ± 0.04 s−1, respectively. F. nucleatum biofilm formation and the biofilm supernatant concentration of indole increased dose dependently with increasing tryptophan concentrations. Exogenous indole also increased F. nucleatum biofilm formation in a dose-dependent manner. Even at very high concentrations, tryptophan did not affect fn1943 expression, whereas similar indole concentrations decreased expression. Thus, exogenous tryptophan and indole were suggested to increase F. nucleatum biofilms.
100-mV 44-µW 2.4-GHz LNA in 16 nm FinFET technology

To achieve both ultra-low-voltage (ULV) and ultra-low-power (ULP), we adopted the sub-threshold design on gate and near-triode design on drain terminals. The proposed low-noise amplifier (LNA) achieves a power gain of 6.9 dB and a noise figure (NF) of 3.0 dB at 2.4 GHz. The PDC is 44 μW under a VDD of 100 mV. The input and output matching are -10.4 dB and -5.7 dB, respectively. The LNA is fabricated in TSMC FinFET Plus CMOS technology.
Robust bounds for classification via selective sampling

We introduce a new algorithm for binary classification in the selective sampling protocol. Our algorithm uses Regularized Least Squares (RLS) as base classifier, and for this reason it can be efficiently run in any RKHS. Unlike previous margin-based semi-supervised algorithms, our sampling condition hinges on a simultaneous upper bound on bias and variance of the RLS estimate under a simple linear label noise model. This fact allows us to prove performance bounds that hold for an arbitrary sequence of instances. In particular, we show that our sampling strategy approximates the margin of the Bayes optimal classifier to any desired accuracy ε by asking Õ (d/ε2) queries (in the RKHS case d is replaced by a suitable spectral quantity). While these are the standard rates in the fully supervised i.i. d. case, the best previously known result in our harder setting was Õ (d3/ε4). Preliminary experiments show that some of our algorithms also exhibit a good practical performance.
A micro-pool model for decision-related signals in visual cortical areas

The study of sensory signaling in the visual cortex has been greatly advanced by the recording of neural activity simultaneously with the performance of a specific psychophysical task. Individual nerve cells may also increase their firing leading up to the particular choice or decision made on a single psychophysical trial. Understanding these signals is important because they have been taken as evidence that a particular nerve cell or group of nerve cells in the cortex is involved in the formation of the perceptual decision ultimately signaled by the organism. However, recent analyses show that the size of a decision-related change in firing in a particular neuron is not a secure basis for concluding anything about the contribution of a single neuron to the formation of a decision: rather the size of the decision-related firing is expected to be dominated by the extent to which the activation of a single neuron is correlated with the firing of the pool of neurons. The critical question becomes what defines membership of a population of neurons. This article presents the proposal that groups of neurons are naturally linked together by their connectivity, which in turn reflects the previous history of sensory stimulations. When a new psychophysical task is performed, a group of neurons relevant to the judgment becomes involved because the firing of some neurons in that group is strongly relevant to the task. This group of neurons is called a micro-pool. This article examines the consequences of such a proposal within the visual nervous system. The main focus is on the signals available from single neurons, but it argued that models of choice-related signals must scale up to larger numbers of neurons because MRI and MEG studies also show evidence of similar choice signals.
Operational dissection of β‐amyloid cytopathic effects on cultured neurons

Alzheimer disease (AD) affects mainly people over the age of 65 years, suffering from different clinical symptoms such as progressive decline in memory, thinking, language, and learning capacity. The toxic role of β‐amyloid peptide (Aβ) has now shifted from insoluble Aβ fibrils to smaller, soluble oligomeric Aβ aggregates. The urgent need for efficient new therapies is high; robust models dissecting the physiopathological aspects of the disease are needed. We present here a model allowing study of four cytopathic effects of Aβ oligomers (AβO): oxidative stress, loss of synapses, disorganization of the neurite network, and cellular death. By generating a solution of AβO and playing on the concentration of and time of exposure to AβO, we have shown that it was possible to reproduce early effects (oxidative stress) and the long‐term development of structural alterations (death of neurons). We have shown that 1) all toxic events were linked to AβO according to a specific timing and pathway and 2) AβO were probably the key intermediates in AD pathogenesis. The present model, using Aβ peptide solution containing AβO, reproduced essential neuropathological features of AD; the effects involved were similar whatever the kind of neurons tested (cortical vs. hippocampal). By using a single system, it was possible to embrace all toxic mechanisms at defined times and concentrations, to study each involved pathway, and to study the effects of new molecules on the different neurotoxic pathways responsible for development of AD. © 2013 Wiley Periodicals, Inc.
A Comprehensive Functional Analysis of NTRK1 Missense Mutations Causing Hereditary Sensory and Autonomic Neuropathy Type IV (HSAN IV)

Hereditary sensory and autonomic neuropathy type IV (HSAN IV) is an autosomal recessive disorder characterized by a complete lack of pain perception and anhidrosis. Here, we studied a cohort of seven patients with HSAN IV and describe a comprehensive functional analysis of seven novel NTRK1 missense mutations, c.1550G >A, c.1565G >A, c.1970T >C, c.2096T >C, c.2254T >A, c.2288G >C, and c.2311C >T, corresponding to p.G517E, p.G522E, p.L657P, p.I699T, p.C752S, p.C763S, and p.R771C, all of which were predicted pathogenic by in silico analysis. The results allowed us to assess the pathogenicity of each mutation and to gain novel insights into tropomyosin receptor kinase A (TRKA) downstream signaling. Each mutation was systematically analyzed for TRKA glycosylation states, intracellular and cell membrane expression patterns, nerve growth factor stimulated TRKA autophosphorylation, TRKA‐Y496 phosphorylation, PLCγ activity, and neurite outgrowth. We showed a diverse range of functional effects: one mutation appeared fully functional, another had partial activity in all assays, one mutation affected only the PLCγ pathway and four mutations were proved null in all assays. Thus, we conclude that complete abolition of TRKA kinase activity is not the only pathogenic mechanism underlying HSAN IV. By corollary, the assessment of the clinical pathogenicity of HSAN IV mutations is more complex than initially predicted and requires a multifaceted approach.
GM3 suppresses anchorage‐independent growth via Rho GDP dissociation inhibitor beta in melanoma B16 cells

Ly‐GDI, Rho GTPase dissociation inhibitor beta, was found to be expressed parallel to the GM3 level in mouse B16 cells whose GM3 contents were modified by B4galt6 sense, B4galt6 antisense cDNA, or St3galt5 siRNA transfection. Ly‐GDI expression was increased on GM3 addition to these cells and decreased with D‐PDMP treatment, a glucosylceramide synthesis inhibitor. Suppression of GM3 or Ly‐GDI by RNAi was concomitantly associated with an increase in anchorage‐independent growth in soft agar. These results clearly indicate that GM3 suppresses anchorage‐independent growth through Ly‐GDI. GM3 signals regulating Ly‐GDI expression was inhibited by LY294002, siRNA against Akt1 and Akt2 and rapamycin, showing that GM3 signals are transduced via the PI3K/Akt/mTOR pathway. Either siRNA towards Rictor or Raptor suppressed Ly‐GDI expression. The Raptor siRNA suppressed the effects of GM3 on Ly‐GDI expression and Akt phosphorylation at Thr308, suggesting GM3 signals to be transduced to mTOR‐Raptor and Akt‐Thr308, leading to Ly‐GDI stimulation. siRNA targeting Pdpk1 reduced Akt phosphorylation at Thr308 and rendered the cells insensitive to GM3 stimulation, indicating that Akt‐Thr308 plays a critical role in the pathway. The components aligned in this pathway showed similar effects on anchorage‐independent growth as GM3 and Ly‐GDI. Taken together, GM3 signals are transduced in B16 cells through PI3K, Pdpk1, AktThr308 and the mTOR/Raptor pathway, leading to enhanced expression of Ly‐GDI mRNA, which in turn suppresses anchorage‐independent growth in melanoma B16 cells. (Cancer Sci 2011; 102: 1476–1485)
Translating basic attentional paradigms to schizophrenia research: Reconsidering the nature of the deficits

Abnormalities in attention have long been viewed as one of the fundamental underlying cognitive deficits in schizophrenia, likely contributing both to formation of some types of symptoms and particularly to the substantial work and social impairments that often accompany schizophrenia. Yet, the precise nature of the attentional deficits in schizophrenia remains poorly understood. Translating advances in cognitive psychology to clinical research brings paradigms with greater analytic power to the study of attention in schizophrenia. In particular, these paradigms should shed light on whether the attentional dysfunction in schizophrenia is best conceptualized as arising from limitations in amount or allocation of processing capacity or from more specific structural bottlenecks that do not allow certain processes to be carried out in two tasks simultaneously. Certain types of dual-task paradigms are particularly well suited to make distinctive predictions, particularly those involving a psychological refractory period paradigm. The background and design of a series of ongoing studies of prodromal, first-episode, and chronic schizophrenia patients are described that are addressing the developmental course of attentional dysfunction in this disorder. These refined paradigms should substantially increase our understanding of the specific forms of attentional impairment characterizing schizophrenia and their connections to symptom development and functional outcome.
A greedy tree growing algorithm for the design of variable rate vector quantizers [image compression]

A technique for directly designing a variable-rate tree-structured vector quantizer by growing the tree one node at a time rather than one layer at time is presented. The technique is a natural extension of a tree growing method for decision trees. When the tree is pruned with a generalized algorithm for optimally pruning trees, improvement is measured in the signal-to-noise ratio at high rates over pruning a fixed-rate tree-structured vector quantizer of the same initial rate. The growing algorithm can be interpreted as a constrained inverse of the pruning algorithm. >
Intergroup Contact Effects via Ingroup Distancing among Majority and Minority Groups: Moderation by Social Dominance Orientation

Five studies tested whether intergroup contact reduces negative outgroup attitudes through a process of ingroup distancing. Based on the deprovincialization hypothesis and Social Dominance Theory, we hypothesized that the indirect effect of cross-group friendship on outgroup attitudes via reduced ingroup identification is moderated by individuals’ Social Dominance Orientation (SDO), and occurs only for members of high status majority groups. We tested these predictions in three different intergroup contexts, involving conflictual relations between social groups in Germany (Study 1; N = 150; longitudinal Study 2: N = 753), Northern Ireland (Study 3: N = 160; Study 4: N = 1,948), and England (Study 5; N = 594). Cross-group friendship was associated with reduced ingroup identification and the link between reduced ingroup identification and improved outgroup attitudes was moderated by SDO (the indirect effect of cross-group friendship on outgroup attitudes via reduced ingroup only occurred for individuals scoring high, but not low, in SDO). Although there was a consistent moderating effect of SDO in high-status majority groups (Studies 1–5), but not low-status minority groups (Studies 3, 4, and 5), the interaction by SDO was not reliably stronger in high- than low-status groups. Findings are discussed in terms of better understanding deprovincialization effects of contact.
The assessment of the malnutrition in traumatic ICU patients in Iran

Background Despite recognition of the importance of nutritional feedings, the delivery of optimal nutrition remains difficult to achieve in most intensive care units (ICU). Objective To assess the status of malnutrition in traumatically ill patients hospitalized in an ICU in Iran. Methods This descriptive, cross-sectional study was conducted in Hamadan, Iran, on 123 patients in an ICU ward over six months with the purpose of assessing malnutrition status. Malnutrition and its severity were assessed based on the defined chemical parameters on admission and the end of stay times. Also, body mass index (BMI), weight (W), and height (H) anthropometric indices were assessed simultaneously to be compared with the chemical results. For statistical analysis we used SPSS version 16 software. Results Overall, 83% of patients had malnutrition on admission to ICU, which was 90% on discharge or near-death condition, indicating increase of the prevalence of malnutrition within hospitalization in this ward. On admission, 11% of patients had mild, 61% moderate, and 11% severe malnutrition that reached to 4%, 63%, and 23%, respectively, by the end of the stay. BMI was significantly different in the patients who completed two weeks in the ICU (p<0.05). Assessment of the correlation between admission and two week completed stay showed that BMI, H, and W were positively correlated (r=0.85), (r=1.0), and (r=0.638), (p<0.05), respectively. There were no significant correlations in these parameters in the fourth week. Assessing the changes in anthropometric parameters showed downward trends of both weight and body mass index within ICU hospitalization. Conclusion As shown in our study, inattention to needs of critically ill patients or lack of facilities results in developing and worsening of malnutrition, which, in turn, considerably worsens the outcome. To supply the needs of these in-hypermetabolic state patients, the importance of nutrition and its effect on outcome must be understood by medical staff; close monitoring of the nutritional status of these patients, along with meticulous calculations and team work, must be done and appropriate supportive routs be used.
Acute Stress Increases Sex Differences in Risk Seeking in the Balloon Analogue Risk Task

Background Decisions involving risk often must be made under stressful circumstances. Research on behavioral and brain differences in stress responses suggest that stress might have different effects on risk taking in males and females. Methodology/Principal Findings In this study, participants played a computer game designed to measure risk taking (the Balloon Analogue Risk Task) fifteen minutes after completing a stress challenge or control task. Stress increased risk taking among men but decreased it among women. Conclusions/Significance Acute stress amplifies sex differences in risk seeking; making women more risk avoidant and men more risk seeking. Evolutionary principles may explain these stress-induced sex differences in risk taking behavior.
Dreaming of electric sheep? Exploring the functions of dream-like mechanisms in the development of mental imagery simulations

According to the simulation hypothesis, mental imagery can be explained in terms of predictive chains of simulated perceptions and actions, i.e., perceptions and actions are reactivated internally by our nervous system to be used in mental imagery and other cognitive phenomena. Our previous research shows that it is possible but not trivial to develop simulations in robots based on the simulation hypothesis. While there are several previous approaches to modelling mental imagery and related cognitive abilities, the origin of such internal simulations has hardly been addressed. The inception of simulation (InSim) hypothesis suggests that dreaming has a function in the development of simulations by forming associations between experienced, non-experienced but realistic, and even unrealistic perceptions. Here, we therefore develop an experimental set-up based on a simple simulated robot to test whether such dream-like mechanisms can be used to instruct research into the development of simulations and mental imagery-like abilities. Specifically, the hypothesis is that ‘dreams’ informing the construction of simulations lead to faster development of good simulations during waking behaviour. The paper presents initial results in favour of the hypothesis.
Free radical activity of PM10: iron-mediated generation of hydroxyl radicals.

The purpose of this study was to test the hypothesis that particulate matter < or = 10 microns in aerodynamic diameter (PM10) particles have the ability to generate free radical activity at their surface. We collected PM10 filters from the Edinburgh, United Kingdom, Enhanced Urban Network sampling site, removed particles from the filter, and tested their ability to cause free radical damage to supercoiled plasmid DNA. We found that the PM10 particles did cause damage to the DNA that was mediated by hydroxyl radicals, as shown by inhibition of the injury with mannitol. The PM10-associated hydroxyl radical activity was confirmed using a high-performance liquid chromatography-based assay to measure the hydroxyl radical adduct of salicylic acid. Desferrioxamine abolished the hydroxyl radical-mediated injury, which suggests that iron was involved. Analysis of PM10 filters confirmed the presence of large amounts of iron and leaching studies confirmed that the PM10 samples could release substantial amounts of Fe(III) and lesser amounts of Fe(II). To investigate the size of the particles involved in the hydroxyl radical injury, we centrifuged the suspension of PM10 to clarity, tested the clear supernatant, and found that it had all of the suspension activity. We conclude, therefore, that the free radical activity is derived either from a fraction that is not centrifugeable on a bench centrifuge, or that the radical generating system is released into solution. ImagesFigure 1.
On the optimization of the daily operation of a wind-hydro power plant

This paper proposes the utilization of water storage ability to improve wind park operational economic gains and to attenuate the active power output variations due to the intermittence of the wind-energy resource. An hourly-discretized optimization algorithm is proposed to identify the optimum daily operational strategy to be followed by the wind turbines and the hydro generation pumping equipments, provided that a wind-power forecasting is available. The stochastic characteristics of the wind power are exploited in the approach developed in order to identify an envelope of recommended operational conditions. Three operational conditions were analyzed and the obtained results are presented and discussed.
Ensuring implementation success: how should coach injury prevention education be improved if we want coaches to deliver safety programmes during training sessions?

Coaches play a major role in encouraging and ensuring that participants of their teams adopt appropriate safety practices. However, the extent to which the coaches undertake this role will depend upon their attitudes about injury prevention, their perceptions of what the other coaches usually do and their own beliefs about how much control they have in delivering such programmes. Fifty-one junior netball coaches were surveyed about incorporating the teaching of correct (safe) landing technique during their delivery of training sessions to junior players. Overall, >94% of coaches had strongly positive attitudes towards teaching correct landing technique and >80% had strongly positive perceptions of their own control over delivering such programmes. Coaches’ ratings of social norms relating to what others think about teaching safe landing were more positive (>94%) than those relating to what others actually do (63–74%). In conclusion, the junior coaches were generally receptive towards delivering safe landing training programmes in the training sessions they led. Future coach education could include role modelling by prominent coaches so that more community-level coaches are aware that this is a behaviour that many coaches can, and do, engage in.
Extending object-oriented systems with roles

In many class-based object-oriented systems the association between as instance and a class is exclusive and permanent. Therefore these systems have serious difficulties in representing objects taking on different roles over time. Such objects must be reclassified any time they evolve (e.g., if a person becomes a student and later an employee). Class hierarchies must be planned carefully and may grow exponentially if entities may take on serveral independent roles. The problem is even more servere for object-oriented databases than for common object-oriented programming. Databases store objects over longer periods, during which the represented entities evolve. This article shows how class-based object-oriented systems can be extended to handle evolving objects well. Class hierarchies are complemented by role hierarchies, whose nodes represent role types an object classified in the root may take on. At any point in time, an entity is represented by an instance of the root and an instance of every role type whose role it currently plays. In a natural way, the approach extends traditional object-oriented concepts, such as classification, object identity, specialization, inheritance, and polymorphism in a natural way. The practicability of the approach is demonstrated by an implementation in Smalltalk. Smalltalk was chosen because it is widely known, which is not true for any particular class-based object-oriented database programming language. Roles can be provided in Smalltalk by adding a few classes. There is no need to modify the semantics of Smalltalk itself. Role hierarchies are mapped transparently onto ordinary classes. The presented implementation can easily be ported to object-oriented database programming languages based on Smalltalk, such as Gemstone's OPAL hierarchies are complemented by role hierarchies, whose nodes represent role types an object classified in the root may take on. At any point in time, an entity is represented by an instance of the root and an instance of every role type whose role in currently plays.