Miracle-dz/UniFAR-FTUs huggingface dataset:
Functional neuroanatomy of performance monitoring: fMRI, ERP, and Patient Studies

Performance monitoring, an indispensable prerequisite of goal-directed, flexible behavior has attracted the interest of many researchers. Performance monitoring impairment may result in major daily-life problems in neurological and psychiatric patients. In this paper, I review the recent advances in clinical studies on performance monitoring in different populations of neurological and psychiatric patients. The findings are discussed with respect to current models of performance monitoring that have mostly arisen from correlational approaches. Moreover, perspectives for clinical use are given and methodological issues for patient studies of performance monitoring will be discussed. D 2005 Elsevier B.V. All rights reserved.
Isgur-wise Function

Using the framework of the Heavy Quark Effective Theory we have re-analyzed the Isgur-Wise function describing semileptonic Λ b → Λ c decays in the QCD sum rule approach. The slope parameter of the Isgur-Wise function is found to be ρ 2 = 1.35 ± 0.12, which is consistent with an experimental measurement and a lattice calculation. To O(1/m b , 1/m c) of the heavy quark expansion the integrated Λ b decay width is used to extract the CKM
Stochastic stability for discrete-time Markov jump Lur'e systems

This paper analyzes the stochastic stability problem of discrete-time Markov jump Lur'e systems. We consider that the switching parameter defining the active mode for both the linear and the cone-bounded nonlinearity is governed by a finite state Markov chain. Based on Linear Matrix Inequalities (LMIs), sufficient conditions are provided for the stability analysis, considering two different assumptions for the transition probability matrix: the case in which it is supposed to be known and the case in which it is supposed to be partially known. As the main tool we employ a stochastic Lur'e type Lyapunov function using the sector condition assumption for the nonlinearities. An academic example is presented in order to illustrate the proposed methods.
Autobiographical Memory in Mild and Moderate Dementia of the Alzheimer's Type.

Alzheimer’s disease (AD) is a progressive disease that particularly affects memory with difficulties starting insidiously and gradually progressing. Anterograde amnesia for semantic and episodic types of declarative knowledge becomes the most prominent and disproportionately impaired cognitive symptom. By the middle stages of the disease, this memory loss progresses to severe impairment. The neuropathology of early AD involves the hippocampal complex, which is involved in new learning and storage of recent experiences. As the disease progresses, it involves neocortical areas, which are involved in the storage o f more remote memories. Participants, including minimal stage AD, mild stage AD, moderate stage AD, and normal controls were interviewed using the Autobiographical Memory Interview (AMI), which consists of an autobiographical incidents component and a personal semantic component. They were also administered a brief mental status exam and tests of remote memory, anterograde memory, semantic category word fluency, and reading. Autobiographical memory was impaired in all three groups of AD patients. There was a temporally graded loss (poorer recall o f recent than childhood memories) for the minimal and mild AD groups on the autobiographical incidents schedule o f the AMI. The moderate group showed equal impairment across life periods. On the personal semantic memory schedule of the AMI, the mild and moderate AD groups showed a temporal gradient. Remote public memory was also impaired in all three groups o f AD patients. All AD groups performed worse on the recent life period than on earlier time periods. Overall, there were low correlations between remote public memory and autobiographical memory for the AD groups, supporting the separability o f these
A novel persulfide detection method reveals protein persulfide- and polysulfide-reducing functions of thioredoxin and glutathione systems

Protein Persulfide Detection Protocol reveals vital roles for thioredoxin and glutathione systems in maintaining sulfane sulfur homeostasis in cells and in vivo. Hydrogen sulfide signaling involves persulfide formation at specific protein Cys residues. However, overcoming current methodological challenges in persulfide detection and elucidation of Cys regeneration mechanisms from persulfides are prerequisites for constructing a bona fide signaling model. We here establish a novel, highly specific protein persulfide detection protocol, ProPerDP, with which we quantify 1.52 ± 0.6 and 11.6 ± 6.9 μg/mg protein steady-state protein persulfide concentrations in human embryonic kidney 293 (HEK293) cells and mouse liver, respectively. Upon treatment with polysulfides, HEK293 and A549 cells exhibited increased protein persulfidation. Deletion of the sulfide-producing cystathionine-γ-lyase or cystathionine-β-synthase enzymes in yeast diminished protein persulfide levels, thereby corroborating their involvement in protein persulfidation processes. We here establish that thioredoxin (Trx) and glutathione (GSH) systems can independently catalyze reductions of inorganic polysulfides and protein persulfides. Increased endogenous persulfide levels and protein persulfidation following polysulfide treatment in thioredoxin reductase-1 (TrxR1) or thioredoxin-related protein of 14 kDa (TRP14) knockdown HEK293 cells indicated that these enzymes constitute a potent regeneration system of Cys residues from persulfides in a cellular context. Furthermore, TrxR1-deficient cells were less viable upon treatment with toxic amounts of polysulfides compared to control cells. Emphasizing the dominant role of cytosolic disulfide reduction systems in maintaining sulfane sulfur homeostasis in vivo, protein persulfide levels were markedly elevated in mouse livers where hepatocytes lack both TrxR1 and glutathione reductase (TR/GR-null). The different persulfide patterns observed in wild-type, GR-null, and TR/GR-null livers suggest distinct roles for the Trx and GSH systems in regulating subsets of protein persulfides and thereby fine-tuning sulfide signaling pathways.
Towards Automated Test Sequence Generation

The article presents a novel control-flow based test sequence generation technique using UML 2.0 activity diagram, which is a behavioral type of UML diagram. Like other model-based techniques, this technique can be used in the earlier phases of the development process owing to the availability of the design models of the system. The activity diagram model is seamlessly converted into a colored Petri net. We proposed a technique that enables the automatic generation of test sequences according to a given coverage criteria from the execution of the colored Petri nets model. Two types of structural coverage criteria for AD based models, namely sequential and concurrent coverage are described. The proposed technique was applied to an example to demonstrate its feasibility and the generated test sequences were evaluated against selected coverage criteria. This technique can potentially be adapted to service oriented applications, workflows, and concurrent applications.
Genetic Evaluation of Physiological Functions of Thiolase Isozymes in the n-Alkane-Assimilating YeastCandida tropicalis

ABSTRACT The n-alkane-assimilating diploid yeast Candida tropicalis possesses three thiolase isozymes encoded by two pairs of alleles: cytosolic and peroxisomal acetoacetyl-coenzyme A (CoA) thiolases, encoded by CT-T1A and CT-T1B, and peroxisomal 3-ketoacyl-CoA thiolase, encoded by CT-T3A andCT-T3B. The physiological functions of these thiolases have been examined by gene disruption. The homozygousct-t1aΔ/t1bΔ null mutation abolished the activity of acetoacetyl-CoA thiolase and resulted in mevalonate auxotrophy. The homozygous ct-t3aΔ/t3bΔ null mutation abolished the activity of 3-ketoacyl-CoA thiolase and resulted in growth deficiency on n-alkanes (C10 to C13). All thiolase activities in this yeast disappeared with thect-t1aΔ/t1bΔ and ct-t3aΔ/t3bΔ null mutations. To further clarify the function of peroxisomal acetoacetyl-CoA thiolases, the site-directed mutation leading acetoacetyl-CoA thiolase without a putative C-terminal peroxisomal targeting signal was introduced on the CT-T1A locus in thect-t1bΔ null mutant. The truncated acetoacetyl-CoA thiolase was solely present in cytoplasm, and the absence of acetoacetyl-CoA thiolase in peroxisomes had no effect on growth on all carbon sources employed. Growth on butyrate was not affected by a lack of peroxisomal acetoacetyl-CoA thiolase, while a retardation of growth by a lack of peroxisomal 3-ketoacyl-CoA thiolase was observed. A defect of both peroxisomal isozymes completely inhibited growth on butyrate. These results demonstrated that cytosolic acetoacetyl-CoA thiolase was indispensable for the mevalonate pathway and that both peroxisomal acetoacetyl-CoA thiolase and 3-ketoacyl-CoA thiolase could participate in peroxisomal β-oxidation. In addition to its essential contribution to the β-oxidation of longer-chain fatty acids, 3-ketoacyl-CoA thiolase contributed greatly even to the β-oxidation of a C4 substrate butyrate.
Damp housing and asthma: a case-control study.

BACKGROUND: Several epidemiological studies have reported a higher prevalence of respiratory symptoms in subjects living in damp housing, but links with specific respiratory diseases such as asthma have not been satisfactorily established. METHODS: One hundred and two subjects with physician diagnosed asthma and 196 age and sex matched controls were interviewed; 222 (75%) then agreed to have their dwelling surveyed for dampness. The prevalence of both self-reported and observed dampness in the homes of the asthmatic subjects and controls were compared. Both asthma and the severity of the dampness were quantified so that the possibility of a dose-response relationship could be investigated. RESULTS: Asthmatic subjects reported dampness in their current (odds ratio (OR) 1.92, 95% confidence interval (CI) 1.18 to 3.12) and previous (OR 2.11, 95% CI 1.29 to 3.47) dwellings more frequently than control subjects. The surveyor confirmed dampness in 58 of 90 (64%) dwellings of asthmatic subjects compared with 54 of 132 (41%) dwellings of control subjects (OR 2.62, 95% CI 1.50 to 4.55). This association persisted after controlling for socioeconomic and other confounding variables (adjusted OR 3.03, 95% CI 1.65 to 5.57). The severity of asthma was found to correlate statistically with measures of total dampness (r = 0.30, p = 0.006) and mould growth (r = 0.23, p = 0.035) in the dwelling. Patients living in homes with confirmed areas of dampness had greater evidence of airflow obstruction than those living in dry homes (mean difference in forced expiratory volume in one second (FEV1) 10.6%, 95% CI 1.0 to 20.3). CONCLUSIONS: Asthma is associated with living in damp housing and there appears to be a dose-response relationship. Action to improve damp housing conditions may therefore favourably influence asthma morbidity.
On the intraspecific variability in basal metabolism and the food habits hypothesis in birds

The food habits hypothesis (FHH) stands as one of the most striking and often-cited interspecific patterns to emerge from comparative studies of endothermic energetics. The FHH identifies three components of diet that potentially produce vari- ability in mass-independent BMR, i.e. food quality, food availability, and food predictability or environmental productivity. The hypothesis predicts that species with diets of low energy content and/or low digestibility should evolve low mass-independent BMRs. The effects of food habits on BMR have been widely investigated at the interspecific level, but the variation between in- dividuals and populations has been largely ignored. Our focus is to compare predictions derived from interspecific studies with data collected from within-species studies to explore the mechanisms and functional significance of adaptive responses predicted by the food-habits hypothesis among birds. We conclude that if BMR is correlated with daily energy expenditure, then organisms that can lower BMR will reduce daily energy expenditure and hence, food requirements. Birds that lower BMR in stressful envi- ronments may increase survival. Nevertheless, the mechanism (s) by which birds eating a low quality diet reduce BMR and whether lower BMR affects fitness remain to be determined (Current Zoology 56 (6): 759-766, 2010).
Inferring method specifications from natural language API descriptions

Application Programming Interface (API) documents are a typical way of describing legal usage of reusable software libraries, thus facilitating software reuse. However, even with such documents, developers often overlook some documents and build software systems that are inconsistent with the legal usage of those libraries. Existing software verification tools require formal specifications (such as code contracts), and therefore cannot directly verify the legal usage described in natural language text in API documents against code using that library. However, in practice, most libraries do not come with formal specifications, thus hindering tool-based verification. To address this issue, we propose a novel approach to infer formal specifications from natural language text of API documents. Our evaluation results show that our approach achieves an average of 92% precision and 93% recall in identifying sentences that describe code contracts from more than 2500 sentences of API documents. Furthermore, our results show that our approach has an average 83% accuracy in inferring specifications from over 1600 sentences describing code contracts.
Ecosystem responses in the southern Caribbean Sea to global climate change

Over the last few decades, rising greenhouse gas emissions have promoted poleward expansion of the large-scale atmospheric Hadley circulation that dominates the Tropics, thereby affecting behavior of the Intertropical Convergence Zone (ITCZ) and North Atlantic Oscillation (NAO). Expression of these changes in tropical marine ecosystems is poorly understood because of sparse observational datasets. We link contemporary ecological changes in the southern Caribbean Sea to global climate change indices. Monthly observations from the CARIACO Ocean Time-Series between 1996 and 2010 document significant decadal scale trends, including a net sea surface temperature (SST) rise of ∼1.0 ± 0.14 °C (±SE), intensified stratification, reduced delivery of upwelled nutrients to surface waters, and diminished phytoplankton bloom intensities evident as overall declines in chlorophyll a concentrations (ΔChla = −2.8 ± 0.5%⋅y−1) and net primary production (ΔNPP = −1.5 ± 0.3%⋅y−1). Additionally, phytoplankton taxon dominance shifted from diatoms, dinoflagellates, and coccolithophorids to smaller taxa after 2004, whereas mesozooplankton biomass increased and commercial landings of planktivorous sardines collapsed. Collectively, our results reveal an ecological state change in this planktonic system. The weakening trend in Trade Winds (−1.9 ± 0.3%⋅y−1) and dependent local variables are largely explained by trends in two climatic indices, namely the northward migration of the Azores High pressure center (descending branch of Hadley cell) by 1.12 ± 0.42°N latitude and the northeasterly progression of the ITCZ Atlantic centroid (ascending branch of Hadley cell), the March position of which shifted by about 800 km between 1996 and 2009.
Cell cycle-dependent regulation of the RNA-binding protein Staufen1

Staufen1 (Stau1) is a ribonucleic acid (RNA)-binding protein involved in the post-transcriptional regulation of gene expression. Recent studies indicate that Stau1-bound messenger RNAs (mRNAs) mainly code for proteins involved in transcription and cell cycle control. Consistently, we report here that Stau1 abundance fluctuates through the cell cycle in HCT116 and U2OS cells: it is high from the S phase to the onset of mitosis and rapidly decreases as cells transit through mitosis. Stau1 down-regulation is mediated by the ubiquitin-proteasome system and the E3 ubiquitin ligase anaphase promoting complex/cyclosome (APC/C). Stau1 interacts with the APC/C co-activators Cdh1 and Cdc20 via its first 88 N-terminal amino acids. The importance of controlling Stau155 levels is underscored by the observation that its overexpression affects mitosis entry and impairs proliferation of transformed cells. Microarray analyses identified 275 Stau155-bound mRNAs in prometaphase cells, an early mitotic step that just precedes Stau1 degradation. Interestingly, several of these mRNAs are more abundant in Stau155-containing complexes in cells arrested in prometaphase than in asynchronous cells. Our results point out for the first time to the possibility that Stau1 participates in a mechanism of post-transcriptional regulation of gene expression that is linked to cell cycle progression in cancer cells.
Results of patch testing with a special series of rubber allergens

The purpose of this study was to examine the results of patch testing with the rubber components on a standard screening tray and compare them with the results of testing with a special series of 27 rubber components (rubber tray). 1670 patients were patch tested with the screening tray and 317 of these were also tested with the rubber tray 16% of those tested with the rubber tray had a positive response to at least 1 of the rubber allergens on the screening tray and 22% had a positive response to at least 1 of the allergens on the rubber tray. The most common positive response to the rubber tray allergens was to tetramethylthiuram monosulfide. There were no responses to 3 of the components on the rubber tray and there was only 1 positive response to a further 4 components. The diagnostic test characteristics of the rubber components on the screening tray were examined using the rubber tray as the gold standard. The sensitivity of the screening tray was 94%, specificity 51%, positive predictive value 87%, and negative predictive value 71% Of the 317 tested. 11%, were found to have a positive to a substance on the rubber tray that was not evident from the results of the screening tray patch testing technique: allergic contact dermatitis; rubber allergens: false‐negative reactions: fake‐positive reactions.
Altered Oncogene Activity Contributes to Compensation for Antisense Suppression of Bcl-2 and Tumor Resistance

Antisense oligonucleotides (oligos) have targeted growth regulatory proteins in prostate cancer models. To identify compensatory alterations in the expression of non-targeted genes we evaluate mono- and bispecific oligos targeting and equally suppressing the expression of the apoptosis inhibitory protein bcl-2. Bcl-2 is chosen because oligos directed towards it have entered clinical trials to restore apoptosis in cancer patients. Treated LNCaP cells compensate for the diminished bcl-2 by suppressing caspase-3 (an apoptosis promoter) while enhancing expression of AKT-1 (another apoptosis inhibitor), androgen receptor (AR) and its (p300 and IL-6) coactivators. Additional proteins are enhanced including PD-1, its ligand PD-L1 (immune checkpoint blockade markers) and fas-ligand, which activate apoptosis through the signal transduction, along with suppressor protein p53, polymerase transcription mediator MED-12 and signal transducer STAT-3. These alterations in expression may contribute to a greatly enhanced expression of the proliferation marker KI-67. This suggests that therapeutic approaches to restore apoptosis through suppression of bcl-2 lead to an altered expression in non-targeted genes involving apoptosis, androgen sensitivity, transcriptional activity and immune responsiveness, leads to an increase in proliferation (and a more androgen driven aggressive phenotype). In this study we evaluate the expression of two oncogenes (v-myc and K-ras) and find a large and significant enhancement of v-myc activity, which is produced by oligos targeting bcl-2 at the 5’ position. For K-ras, although significant suppression is produced by the bispecific targeting bcl-2 at the 3’ position, the percent change is relatively small compared with other compensatory alterations we have measured, and much less than in v-myc. Therefore, for the two oncogenes being evaluated, only increased v-myc activity is probably large enough to contribute to increased tumor aggressiveness in compensation for bcl-2 suppression.
Politics of education for Japanese returnee children

Business expansion in the 1960s and its associated international strategies have meant that many Japanese company employees and their families were sent abroad on long‐term assignments. The children who accompanied their parents on such assignments and then returned to Japan were first described as ‘educational refugees’ and were regarded as culturally ambiguous, socially marginalized and academically disadvantaged. The Japanese government considered that special measures were needed for these children, as they had missed out on the standard education that they would otherwise have received. Consequently, it introduced various educational options so that they could reintegrate smoothly into Japanese society and its educational system. Later, in the 1980s, when ‘globalization’ became vital to Japan, the attributes associated with such children were recast and they began to be regarded as ‘valuable national assets’ for their supposed rich cross‐cultural awareness and bilingual abilities, the very qualities the government sought in the new generations of Japanese. They were now seen as a barometer of Japan's globalization and, with their new high‐flying, global image, universities and companies began to actively enrol them. However, were these variously ascribed attributes based on fact? My research in the UK into their English and Japanese abilities has demonstrated that the claims, whether of disadvantage or of ability, were exaggerated or misleading. Furthermore, with the rapid increase in people's mobility, information and technology and with the multicultural orientation that many host communities, including the UK, now adopt their sojourn lifestyle has become increasingly Japanese, making the gap between assumption and reality even greater.
Mechanisms of Electroacupuncture-Induced Analgesia on Neuropathic Pain in Animal Model

Neuropathic pain remains as one of the most difficult clinical pain syndromes to treat. Electroacupuncture (EA), involving endogenous opioids and neurotransmitters in the central nervous system (CNS), is reported to be clinically efficacious in various fields of pain. Although multiple experimental articles were conducted to assess the effect of EA-induced analgesia, no review has been published to assess the efficacy and clarify the mechanism of EA on neuropathic pain. To this aim, this study was firstly designed to evaluate the EA-induced analgesic effect on neuropathic pain and secondly to guide and help future efforts to advance the neuropathic pain treatment. For this purpose, articles referring to the analgesic effect of acupuncture on neuropathic pain and particularly the work performed in our own laboratory were analyzed. Based on the articles reviewed, the role of spinal opioidergic, adrenergic, serotonergic, cholinergic, and GABAergic receptors in the mechanism of EA-induced analgesia was studied. The results of this research demonstrate that μ and δ opioid receptors, α 2-adrenoreceptors, 5-HT1A and 5-HT3 serotonergic receptors, M1 muscarinic receptors, and GABAA and GABAB GABAergic receptors are involved in the mechanisms of EA-induced analgesia on neuropathic pain.