Miracle-dz/UniFAR-FTUs huggingface dataset:
Cytochrome o (cyoABCDE) and d (cydAB) oxidase gene expression in Escherichia coli is regulated by oxygen, pH, and the fnr gene product

The aerobic respiratory chain of Escherichia coli contains two terminal oxidases that catalyze the oxidation of ubiquinol-8 and the reduction of oxygen to water. They are the cytochrome o oxidase complex encoded by cyoABCDE and the cytochrome d oxidase complex encoded by cydAB. To determine how these genes are regulated in response to a variety of environmental stimuli, including oxygen, we examined their expression by using lacZ protein fusions in wild-type and fnr mutant strains of E. coli. Anaerobic growth resulted in a 140-fold repression of cyoA'-'lacZ expression relative to aerobic growth and a 3-fold increase in cydA'-'lacZ expression. Anaerobic repression of both fusions was mediated in part by the fnr gene product, as evidenced by a 30-fold derepression of cyoA'-'lacZ expression and a 4-fold derepression of cydA'-'lacZ expression in an fnr deletion strain. Supplying wild-type fnr in trans restored wild-type repression for both fusions. Fnr thus functions as an anaerobic repressor of both cyoABCDE and cydAB expression. Reduced-minus-oxidized difference spectrum analyses of cell membranes confirmed the effect of the fnr gene product on the production of cytochrome d oxidase in the cell. Based on the pattern of anaerobic cydAB expression observed, we propose the existence of a second, as yet unidentified, regulatory element that must function either to activate cydAB expression as oxygen becomes limiting or to repress cydAB expression aerobically. Whereas cytochrome o oxidase encoded by cyoABCDE appears to be produced only under oxygen-rich growth conditions, in keeping with its biochemical properties, cytochrome d oxidase is expressed moderately aerobically and is elevated yet further when oxygen becomes limiting so that the organism can cope better under oxygen starvation conditions. We also examined cyoABCDE and cydAB expression in response to growth on alternative carbon compounds and to changes in the culture medium pH and osmolarity.
ICMAS '96: Norms, Obligations, and Conventions

The Second International Conference on Multiagent Systems (ICMAS-96) Workshop on Norms, Obligations, and Conventions was held in Kyoto, Japan, from 10 to 13 December 1996. Participants included scientists from deontic logic, database framework, decision theory, agent architecture, cognitive modeling, and legal expert systems. This article summarizes the contributions chosen for presentation and their links to these areas.
Distributed under Creative Commons Cc-by 4.0 Insights on the Structure and Stability of Licanantase: a Trimeric Acid-stable Coiled-coil Lipoprotein from Acidithiobacillus Thiooxidans

Licanantase (Lic) is the major component of the secretome of Acidithiobacillus thiooxidans when grown in elemental sulphur. When used as an additive, Lic improves copper recovery from bioleaching processes. However, this recovery enhancement is not fully understood. In this context, our aim is to predict the 3D structure of Lic, to shed light on its structure-function relationships. Bioinformatics analyses on the amino acid sequence of Lic showed a great similarity with Lpp, an Escherichia coli Lipoprotein that can form stable trimers in solution. Lic and Lpp share the secretion motif, intracellular processing and alpha helix structure, as well as the distribution of hydrophobic residues in heptads forming a hydrophobic core, typical of coiled-coil structures. Cross-linking experiments showed the presence of Lic trimers, supporting our predictions. Taking the in vitro and in silico evidence as a whole, we propose that the most probable structure for Lic is a trimeric coiled-coil. According to this prediction , a suitable model for Lic was produced using the de novo algorithm " Rosetta Fold-and-Dock ". To assess the structural stability of our model, Molecular Dynamics (MD) and Replica Exchange MD simulations were performed using the structure of Lpp and a 14-alanine Lpp mutant as controls, at both acidic and neutral pH. Our results suggest that Lic was the most stable structure among the studied proteins in both pH conditions. This increased stability can be explained by a higher number of both intermonomer hydrophobic contacts and hydrogen bonds, key elements for the stability of Lic's secondary and tertiary structure.
Writer Meets Reader: Emotion Analysis of Social Media from Both the Writer's and Reader's Perspectives

This paper introduces the novel research of emotion analysis from both the writer's and reader's perspectives. A challenge that comes up is the lack of a corpus annotated with both writer and reader emotions. We tackle this problem by combining an online writer-emotion corpus and an online reader-emotion corpus. Statistical analyses are then performed on this newly-generated corpus. It is discovered that there is indeed a relationship between writer and reader emotions.
Epicardial fat volume is correlated with coronary lesion and its severity.

OBJECTIVE To evaluate the correlation of epicardial adipose tissue volume (EATV) with the coronary artery lesion and its severity. METHODS Inpatients with suspicious stable angina of coronary heart lesion were recruited. For patients with coronary artery lesions in CTA, further coronary angiography (CAG) was performed to evaluate the coronary artery lesion. Gensini scoring system was employed to assess the severity of coronary artery lesions. RESULTS Patients were classified as coronary heart disease (CHD) group (n = 160). Results showed the mean EATV was 192.57 ± 30.32 cm(3) in CHD group, which was significantly larger than that in control group (138.56 ± 23.18 cm(3); P < 0.01). The coronary artery stenosis was classified as mild, moderate and severe stenosis according to the extent of coronary artery lesions, and results showed marked difference in the EATV among patients with different severities of coronary artery stenosis (P < 0.005). The Gensini score was positively related to EATV (r = 0.285, P = 0.000). The EATV increased with the increase in the number of affected coronary arteries. Multivariate Logistic regression analysis showed EATV was an independent risk factor of CHD after adjusting other confounding factors (OR = 1.023, P = 0.013). CONCLUSION EATV is closely related to the severity of coronary artery lesions: the larger the EATV, the more severe the coronary artery lesions. Moreover, EATV is an independent risk factor of CHD.
Partial decode-forward for quantum relay channels

A relay channel is one in which a Source and Destination use an intermediate Relay station in order to improve communication rates. We propose the study of relay channels with classical inputs and quantum outputs and prove that a “partial decode and forward” strategy is achievable. We divide the channel uses into many blocks and build codes in a randomized, block-Markov manner within each block. The Relay performs a standard Holevo-Schumacher-Westmoreland quantum measurement on each block in order to decode part of the Source's message and then forwards this partial message in the next block. The Destination performs a novel “sliding-window” quantum measurement on two adjacent blocks in order to decode the Source's message. This strategy achieves non-trivial rates for classical communication over a quantum relay channel.
The NESS Account of Natural Causation: A Response to Criticisms and a Formal MMTS Analysis (forthcoming) (with H. Spector)

The NESS (necessary element of a sufficient set) account of natural (scientific, ‘actual’, ‘factual’) causation is usually acknowledged to be a more satisfactory and comprehensive account than the traditional sine qua non (‘but for’) account. However, objections have been raised to the claim that the NESS account fully captures the concept of natural causation and properly handles all types of situations. Various types of counter-examples have been proposed. More fundamentally, it is argued that the NESS account is viciously circular, since causal terminology often is used in its elaboration and it relies upon the concept of causal laws. Many of the objections raised against the NESS account assume that it is essentially the same as Herbert Hart’s and Tony Honore’s ‘causally relevant factor’ account and John Mackie’s INUS account. In section II of this chapter I distinguish these three accounts, which differ in important ways that make the latter two accounts vulnerable to objections to which the NESS account is immune, and I offer an account of causal laws that I believe rebuts the claim that the NESS account is viciously circular. In section III I argue that the NESS account handles properly the various types of situations that have been raised as alleged counter-examples to its comprehensive validity.
Asynchronous parallel algorithm for mining association rules on a shared-memory multi-processors

Mining association rules from large databases is an important problem in data mining. There is a need to develop parallel algorithm for this problem because it is a very costly computation process. However, all proposed parallel algorithms for mining association rules follow the conventional level-wise approach. On a sharedmemory multi-processors, they will impose a synchronization in every iteration which degrades greatly their performance. The deficiency comes from the contention on the shared I/O channel when all processors are accessing their database partitions in the shared storage synchronously. An asynchronous algorithm APM has been proposed for mining association rules on shared-memory multiprocessors. All participating processors in APM generate candidates and count their supports independently without synchronization. Furthermore, it can finish the computation with less I/O than required in the level-wise approach. The algorithm has been implemented on a Sun Enterprise 4000 multi-processors with 12 nodes. The experiments show that APM has super performance than other proposed synchronous algorithms.
Event-Based Hough Transform in a Spiking Neural Network for Multiple Line Detection and Tracking Using a Dynamic Vision Sensor

Hough Transform has been widely used to detect lines in images captured by conventional cameras. In this paper, we develop an event-based Hough transform and apply it to a new type of camera, namely Dynamic Vision Sensor (DVS). DVS outputs an asynchronous stream of binary events representing illumination change in the scene. We implement the proposed algorithm in a spiking neural network to detect lines on DVS output. Spikes (events) from the DVS sensor are first mapped to Hough transform parameter space and then sent to corresponding spiking neurons for accumulation. A spiking neuron will fire an output spike once it accumulates enough input contributions and then reset itself. The output spikes of the spiking neural network represent the parameters of detected lines. An event-based clustering algorithm is applied on the parameter space spikes to segment multiple lines and track them. In our spiking neural network, a lateral inhibition strategy is applied to suppress noise lines from being detected. This is achieved by resetting a neuron’s neighbors in addition to itself once the neuron fires an output spike. The efficacy of the proposed algorithm is shown by extensive experiments on both artificially generated events and various real DVS outputs.
GM1 erythroimmunoassay for detection and titration of Escherichia coli heat-labile enterotoxin

A GM1 ganglioside erythroimmunoassay for the detection of heat-labile Escherichia coli enterotoxin (LT) was developed for use in poorly equipped laboratories in developing countries. This assay is based on the immunological similarity between Vibrio cholerae toxin and LT and uses cholera toxin antiserum and sheep anti-rabbit immunoglobulin covalently coupled to sheep erythrocytes as conjugate. This assay has the following advantages over other currently available techniques: the reagents it uses are stable, in particular, tanned and sensitized sheep erythrocytes; GM1 ganglioside is commercially available; erythro-adsorption can be read with the naked eye; the test can be completed in 1 day; and as little as 4 ng of V. cholerae toxin or LT per ml can be detected accurately. The GM1 ganglioside erythroimmunoassay showed good quantitative and qualitative correlation with the Vero cell assay and the conventional GM1 enzyme-linked immunosorbent assay. The GM1 ganglioside erythroimmunoassay was somewhat less sensitive than the GM1 enzyme-linked immunosorbent assay but more sensitive than the Vero cell assay. Results obtained for 12 LT-positive and 138 LT-negative E. coli strains correlated with results obtained with GM1 enzyme-linked immunosorbent and Vero cell assays.
New insights in to ancient resistance: the molecular side of cell wall appositions

The epidermis lies at the interface between a plant and its environment. As such, the epidermis is crucial for protecting the plant against environmental insults. We focus primarily on cell wall reinforcement-mediated penetration resistance (papilla-resistance) against fungal pathogen attack. The epidermal cell layer of cereal leaves is the only tissue interacting with the powdery mildew fungus, Blumeria graminis, and papilla formation at sites of fungal penetration attempts provides a basal resistance, hampering fungal invasion irrespective of host specific compatibility or incompatibility. To elucidate the genetic scaffolding of penetration resistance mechanisms, we constructed a cDNA library from wheat leaf epidermis at 24-48 h post inoculation with B. graminis f. sp. tritici. We have sequenced 3,000 expressed sequence tags (ESTs) from this cDNA library. EST analysis revealed a large proportion of genes involved in plant defense/stress responses (1/3) and a low frequency of “house-keeping” genes. Enrichment of defense genes from this EST collection has allowed us to identify several defense and signaling pathways that have been hitherto poorly characterized, including cell wall biosynthesis, vesicle trafficking, redox regulation and metal homeostasis. Our results suggest that a global analysis of transcripts from this epidermis-specific cDNA library makes it feasible to define a full set of genes involved in early plant resistance associated with cell wall modifications.
Optimal Threshold Value for Left Ventricular Hypertrophy in Blacks: The Atherosclerosis Risk in Communities Study

The distribution of echocardiographic left ventricular (LV) mass differs among ethnicities. Because ethnic-specific echocardiographic criteria for LV hypertrophy (LVH) are not established, we determined whether threshold values derived from overwhelmingly white populations are appropriate for blacks, a subgroup having more LVH. Between 1992 and 1994, LV mass was measured echocardiographically in the Jackson, Mississippi, black cohort of the Atherosclerosis Risk in Communities study. Participants free of prevalent cardiovascular disease (CVD) (n=1616; mean±SD, age 59±5.7; 65% women and 57% with hypertension) were included. The optimal LVH threshold value was selected from the continuum of LV mass index (LVMI=LV mass/height2.7) using 3 methods: (1) the best operating point from the area under the resulting receiver-operating characteristic (ROC) curve predicting incident CVD; (2) the value with the smallest probability value associated with incident CVD; and (3) visual inspection of functions of LVMI and CVD in the general additive model (GAM) plot. At a median follow-up of 6.8 years, there were 192 events (coronary heart disease=87, stroke=62, and congestive heart failure=43; incidence=17.6/1000 person-years). The best operating point from the resulting ROC analysis was 51.2 g/m2.7 for sensitivity (53.4%) and specificity (61.5%). The Cox and GAM models adjusted for age, gender, systolic blood pressure, hypertension, diabetes, smoking, total cholesterol-to-high-density lipoprotein ratio, LVH by ECG criterion, and socioeconomic status found 50 to 51 g/m2.7 as the optimal threshold for LVH in middle-aged blacks, corresponding to a minimum probability value and to a log-hazard ratio of zero, respectively. Because these values are close to the 51 g/m2.7 established from predominantly white populations, this cutpoint is appropriate for both groups.
Constitutive Endocytosis and Degradation of the Pre-T Cell Receptor

The pre-T cell receptor (TCR) signals constitutively in the absence of putative ligands on thymic stroma and signal transduction correlates with translocation of the pre-TCR into glycolipid-enriched microdomains (rafts) in the plasma membrane. Here, we show that the pre-TCR is constitutively routed to lysosomes after reaching the cell surface. The cell-autonomous down-regulation of the pre-TCR requires activation of the src-like kinase p56lck, actin polymerization, and dynamin. Constitutive signaling and degradation represents a feature of the pre-TCR because the γδTCR expressed in the same cell line does not exhibit these features. This is also evident by the observation that the protein adaptor/ubiquitin ligase c-Cbl is phosphorylated and selectively translocated into rafts in pre-TCR– but not γδTCR-expressing cells. A role of c-Cbl–mediated ubiquitination in pre-TCR degradation is supported by the reduction of degradation through pharmacological inhibition of the proteasome and through a dominant-negative c-Cbl ubiquitin ligase as well as by increased pre-TCR surface expression on immature thymocytes in c-Cbl–deficient mice. The pre-TCR internalization contributes significantly to the low surface level of the receptor on developing T cells, and may in fact be a requirement for optimal pre-TCR function.
Microsatellite Analysis of Three Phylogenetic Species of Paracoccidioides brasiliensis

ABSTRACT Paracoccidioides brasiliensis is the etiological agent of paracoccidioidomycosis, an important human systemic mycosis in Latin America. Recently, the existence of three different phylogenetic species (S1, PS2, and PS3) of P. brasiliensis was demonstrated. Despite being genetically isolated, all three species were capable of inducing disease in both humans and animals, although lower virulence has been found with the PS2 species. The available molecular methods developed to characterize and type strains have not been useful for assigning isolates to the described species, creating the need for molecular markers capable of distinguishing genetically isolated groups. Here, we describe a PCR and sequencing-based microsatellite marker system that is stable, easy to assay, adaptable to large series of isolates, and discriminatory enough to be used as a typing system in identifying the three proposed species of P. brasiliensis. In addition, this system provides an unambiguous tool for strain discrimination between two (S1 and PS2) of the three phylogenetic species.
Japanese learners' listening to English connected speech

The present study examined the effect of connected speech on second language learners’ listening comprehension, improving some aspects recognized as limitations in an earlier study (Ito, 2006). Although the presence of connected speech was found to negatively influence learners’ listening comprehension in Ito (2006), the participants’ first language (L1) was not controlled. Furthermore, the participants in the study were all studying English in an ESL context, where they are exposed to connected speech on a daily basis. In the present study, participants’ L1 was controlled and limited to Japanese, and their learning context was also limited to an EFL context. The participants took a dictation test which asked them to write down the sentences read with and without connected speech. The results indicated that the presence of connected speech imposes a challenge upon listening comprehension by the Japanese learners of English, regardless of their proficiency levels. The difference in types of connected speech forms was also found to influence their listening comprehension, though its effect differed across the proficiency levels. Listening to English, especially when it is spoken at a natural speed, is one of the big challenges that learners of English often face to. There are many factors that make it challenging for them to catch what is said, one of which is their unfamiliarity with the English sound system. In addition to the differences in segmental phonemes, namely consonants and vowels, between their first language (L1) and English, there are also differences in suprasegmental phonemes.
Is the looping constant of the square grid 5/4?

We define a quantity called the "looping constant" of the integer lattice Z^d, and conjecture that its value for Z^2 is 5/4. A number of striking numerical facts would follow: (1) The first derivative in y of the Tutte polynomial of the N-by-N square grid graph G_N, evaluated at x=y=1 and divided by N^2, has the limiting value 1/8 as N goes to infinity; (2) The expected density of a uniform recurrent state of the abelian sandpile model on G_N has the limiting value 17/8; and (3) The expected length of the cycle in a uniform spanning unicycle of G_N has the limiting value 8.
Memory-based embedded digital ATE

This paper presents memory-based embedded digital ATE (Automatic Test Equipment) - a new logic BIST methodology that can deliver deterministic test stimuli and stores output responses on a chip. The proposed scheme consists of test data compression logic and a new on-chip SRAM structure, which is operated as a ROM when the logic BIST mode is on. The new BIST-oriented RAM (BRAM) implements ROM features in the BIST mode and incurs no performance penalty in the normal SRAM mode of operation. BRAM can be designed by inserting an additional word line in a row to a conventional SRAM bit-cell (no increase in bit-cell area). BRAM stores the compressed test vectors that can be transmitted to on-chip decompressors during test mode. BRAM also accepts compacted output responses. Experimental results show that BRAM performs stable and high-performance ROM operations in the BIST mode. Run-length coding can be incorporated into the proposed test data compression to reduce test data volume further. Test data volume and fault coverage on ISCAS89 benchmark show that the proposed test methodology can be used as a stand-alone BIST scheme while providing test quality of deterministic tests.
Relationships between enzymatic flux capacities and metabolic flux rates: nonequilibrium reactions in muscle glycolysis.

The rules that govern the relationships between enzymatic flux capacities (Vmax) and maximum physiological flux rates (v) at enzyme-catalyzed steps in pathways are poorly understood. We relate in vitro Vmax values with in vivo flux rates for glycogen phosphorylase, hexokinase, and phosphofructokinase, enzymes catalyzing nonequilibrium reactions, from a variety of muscle types in fishes, insects, birds, and mammals. Flux capacities are in large excess over physiological flux rates in low-flux muscles, resulting in low fractional velocities (%Vmax = v/Vmax x 100) in vivo. In high-flux muscles, close matches between flux capacities and flux rates (resulting in fractional velocities approaching 100% in vivo) are observed. These empirical observations are reconciled with current concepts concerning enzyme function and regulation. We suggest that in high-flux muscles, close matches between enzymatic flux capacities and metabolic flux rates (i.e., the lack of excess capacities) may result from space constraints in the sarcoplasm.