Miracle-dz/UniFAR-FTUs huggingface dataset:
Clinical Significance in Oral Cavity Squamous Cell Carcinoma of Pathogenic Somatic Mitochondrial Mutations

Somatic mutations affecting the mitochondrial DNA (mtDNA) have been frequently observed in human cancers and proposed as important oncological biomarkers. However, the clinical significance of mtDNA mutations in cancer remains unclear. This study was therefore performed to explore the possible clinical use in assessing oral squamous cell carcinoma (OSCC) of pathogenic mtDNA mutations. The entire mitochondrial genome of 300 OSCC with their matched control DNAs was screened by direct sequencing and criteria were set to define a pathogenic somatic mutation. The patients' TP53 R72P genotypes were determined by polymerase chain reaction-restriction fragment length polymorphism. The relationships between pathogenic somatic mutations, clinicopathogical features, TP53 R72P genotype and clinical prognosis were analyzed. Overall, 645 somatic mtDNA mutations were identified and 91 of these mutations were defined as pathogenic. About one quarter (74/300) of the OSCC tumor samples contained pathogenic mutations. Individuals with the TP53 R allele had a higher frequency of pathogenic somatic mutation than those with the PP genotype. Kaplan-Meier analysis indicated that TP53 R allele patients with pathogenic somatic mutations demonstrated a significant association with a poorer disease-free survival than other individuals (HR = 1.71; 95% CI, 1.15–2.57; p = 0.009) and this phenomenon still existed after adjusting for mtDNA haplogroup, tumor stage with treatment regimens, differentiation and age at diagnosis (HR = 1.59; 95% CI, 1.06–2.40; p = 0.03). Subgroup analyses showed that this phenomenon was limited to patients who received adjuvant radiotherapy/chemo-radiotherapy after surgery. The results strongly indicated that pathogenic mtDNA mutations are a potential prognostic marker for OSCCs. Furthermore, functional mitochondria may play an active role in cancer development and the patient's response to radiotherapy/chemo-radiotherapy.
IGMN : An Incremental Gaussian Mixture Network that Learns Instantaneously from Data Flows

This works proposes IGMN (standing for Incremental Gaussian Mixture Network), a new connectionist approach for incremental concept formation and robotic tasks. It is inspired on recent theories about the brain, specially the Memory-Prediction Framework and the Constructivist Artificial Intelligence, which endows it with some unique features that are not present in most ANN models such as MLP and GRNN. Moreover, IGMN is based on strong statistical principles (Gaussian mixture models) and asymptotically converges to the optimal regression surface as more training data arrive. Through several experiments using the proposed model it is demonstrated that IGMN is also robust to overfitting, does not require fine-tunning its configuration parameters and has a very good computational performance, thus allowing its use in real time control applications. Therefore, IGMN is a very useful machine learning tool for incremental function approximation.
Cyber Security Awareness Campaigns: Why do they fail to change behaviour?

The present paper focuses on Cyber Security Awareness Campaigns, and aims to identify key factors regarding security which may lead them to failing to appropriately change people's behaviour. Past and current efforts to improve information-security practices and promote a sustainable society have not had the desired impact. It is important therefore to critically reflect on the challenges involved in improving information-security behaviours for citizens, consumers and employees. In particular, our work considers these challenges from a Psychology perspective, as we believe that understanding how people perceive risks is critical to creating effective awareness campaigns. Changing behaviour requires more than providing information about risks and reactive behaviours - firstly, people must be able to understand and apply the advice, and secondly, they must be motivated and willing to do so - and the latter requires changes to attitudes and intentions. These antecedents of behaviour change are identified in several psychological models of behaviour. We review the suitability of persuasion techniques, including the widely used 'fear appeals'. From this range of literature, we extract essential components for an awareness campaign as well as factors which can lead to a campaign's success or failure. Finally, we present examples of existing awareness campaigns in different cultures (the UK and Africa) and reflect on these.
Does Central Bank Transparency Impact Financial Markets? A Cross-country Econometric Analysis

Blinder et al. (2001) argues that more open public disclosure of central bank policies may enhance the efficiency of markets. We examine this claim by studying for a set of seven industrialized countries whether selected central banks' moves toward more open disclosure during the 1990s improved or worsened the predictability of the corresponding national financial markets. Employing methodologies analogous to Campbell and Shiller (1991), we find that for all countries, the forecasting error has decreased for interest rates on the respective government bonds across most maturity lengths, and that the expectations hypothesis has generally performed better at the short end of the yield curve. Our results also tentatively show that the effects are stronger for central banks that made the move to greater disclosure, compared to those banks that resisted increasing the public's information set. These findings are consistent with Tabellini's (1987) view that central bank secrecy will hinder the smooth functioning of financial markets.
Swift recovery of severe acute hypoxemic respiratory failure under non-invasive ventilation.

BACKGROUND In the setting of severe acute respiratory distress syndrome (ARDS; PaO2/FiO2 < 100), the cut-off point for switching from non-invasive ventilation to intubation combined to mechanical ventilation is poorly defined. RESULTS The swift resolution over 10 h of a severe acute hypoxemic respiratory failure (P/F = 57) caused by aspiration following heroin overdose, using non-invasive ventilation (NIV)-high PEEP (15-20 cm H2O)-low pressure support (8 cm H20) is reported. The success in treating non-invasively severe hypoxia was presumably linked to a highly restricted subset: healthy young patient, minimal alteration of consciousness, non-combativeness, absence of severe metabolic acidosis, quick resolution of supraventricular arrhythmia, one-to-one supervision by the intensivist in the critical care unit. CONCLUSION Given the complications associated with tracheal intubation and mechanical ventilation on the one hand and with delayed intubation on the other hand, high PEEP-NIV may warrant study in a restricted set of patients closely monitored in a critical care environment.
The Search for Meaning: What Do the Narratives of Grieving Individuals Reveal?

This qualitative research project is a narrative inquiry into the loss experiences of four bereaved individuals who have lost an immediate family member; one of them is myself. In particular, the meanings assigned to the losses and how those meanings impacted the grieving process were explored by listening to in-depth narratives of the participants’ experiences of loss and grief. A narrative methodology was used, based on a constructivist epistemology that describes a human tendency to put events in narrative forms in order to give them a sense of continuity and meaning. Four narratives, along with their respective analysis, were presented in separate chapters, with my own narrative presented as the last narrative chapter. Of the four of us, two are males: one from Jewish-American and the other from GermanRomanian descent, and two are females: both from Persian descent. The four participants ranged from 39 to 71 years of age at the time of the interviews, with the losses occurring 3 to 25 years before the interviews. Findings of this research reveal the unique and complex grieving processes of the participants. A variety of meanings were assigned to the losses with each meaning having its own possible impact on the course of bereavement. Each participant expressed her/his own personal assumptions about the nature of life, love, suffering, human vulnerabilities, and death
Association of Body Mass Index with Depression, Anxiety and Suicide—An Instrumental Variable Analysis of the HUNT Study

Objective While high body mass index is associated with an increased risk of depression and anxiety, cumulative evidence indicates that it is a protective factor for suicide. The associations from conventional observational studies of body mass index with mental health outcomes are likely to be influenced by reverse causality or confounding by ill-health. In the present study, we investigated the associations between offspring body mass index and parental anxiety, depression and suicide in order to avoid problems with reverse causality and confounding by ill-health. Methods We used data from 32,457 mother-offspring and 27,753 father-offspring pairs from the Norwegian HUNT-study. Anxiety and depression were assessed using the Hospital Anxiety and Depression Scale and suicide death from national registers. Associations between offspring and own body mass index and symptoms of anxiety and depression and suicide mortality were estimated using logistic and Cox regression. Causal effect estimates were estimated with a two sample instrument variable approach using offspring body mass index as an instrument for parental body mass index. Results Both own and offspring body mass index were positively associated with depression, while the results did not indicate any substantial association between body mass index and anxiety. Although precision was low, suicide mortality was inversely associated with own body mass index and the results from the analysis using offspring body mass index supported these results. Adjusted odds ratios per standard deviation body mass index from the instrumental variable analysis were 1.22 (95% CI: 1.05, 1.43) for depression, 1.10 (95% CI: 0.95, 1.27) for anxiety, and the instrumental variable estimated hazard ratios for suicide was 0.69 (95% CI: 0.30, 1.63). Conclusion The present study’s results indicate that suicide mortality is inversely associated with body mass index. We also found support for a positive association between body mass index and depression, but not for anxiety.
Thioredoxin‐ASK1 complex levels regulate ROS‐mediated p38 MAPK pathway activity in livers of aged and long‐lived Snell dwarf mice

We have proposed that the age‐associated increase of reactive oxygen species (ROS) by electron transport chain (ETC) dysfunction may cause the elevated basal level of p38 MAPK stress response pathway activity. However, the mechanism by which ROS activates this pathway is not clear. Here we propose that activation of the p38 MAPK pathway by complex I (CI) generated ROS, in response to rotenone (ROT) treatment, is based on the ability of reduced Trx to bind to and inhibit ASK 1 and its release from the complex upon oxidation. This balance of free vs. bound ASK1 regulates the level of p38 MAPK pathway activity. To support this mechanism we demonstrate that the production of ROS by ROT treated AML12 hepatocyte cells dissociates the Trx‐ASK1 complex, thereby increasing p38 MAPK pathway activity. This mechanism is supported by the ability of N‐acetyl cysteine (NAC) to prevent dissociation of Trx‐ASK1 and activation of the p38 MAPK pathway. We also demonstrated that the ratio of ASK1/Trx‐ASK1 increases in aged mouse livers and that this correlates with the increased basal activity of the p38 MAPK pathway. The longevity of Snell dwarf mice has been attributed to their resistance to oxidative stress. A comparison of the levels of Trx‐ASK1 in young and aged dwarfs showed a higher abundance of the complex than in their age‐matched controls. These results, which are indicative of a decreased level of oxidative stress, suggest that increased ROS production in aged liver may alter the ratio of ASK1 and Trx‐ASK1, thereby increasing the age‐associated basal level of p38 MAPK pathway activity. —Hsieh, C. ‐C. , Papaconstantinou, J. Thioredoxin‐ASK1 complex levels regulate ROS‐mediated p38 MAPK pathway activity in livers of aged and long‐lived Snell dwarf mice. FASEB J. 20, 259–268 (2006)
In-Hive Behavior of Pollen Foragers (Apis mellifera) in Honey Bee Colonies Under Conditions of High and Low Pollen Need

Pollen collection in honey bees is regulated around a homeostatic set-point. How the control of pollen collection is achieved is still unclear. DiAerent feedback mechanisms have been proposed but little is known about the experience of pollen foragers in the hive. A detailed documentation of the behavior of pollen foragers in the hive under diAerent pollen need conditions is presented here. Taking a broad observational approach, we analyze the behavior of individual pollen foragers in the hive between collecting trips and quantify the diAerent variables constituting the in-hive stay. Comparing data from two colonies and 143 individuals during experimentally induced times of low vs. times of high pollen need, we show that individual foragers modulate their in-hive working tempo according to the actual pollen need of the colony: pollen foragers slowed down and stayed in the hive longer when pollen need was low and spent less time in the hive between foraging trips when pollen need by their colony was high. Furthermore, our data show a significant change in the trophallactic experience of pollen foragers with changing pollen need conditions of their colony. Pollen foragers had more short (< 3 s) trophallactic contacts when pollen need was high, resulting in an increase of total number of trophallactic contacts. Thus, our results support the hypothesis that trophallactic experience is one of the various information pathways used by pollen foragers to assess their colony’s pollen need.
Lesion to the Nigrostriatal Dopamine System Disrupts Stimulus-Response Habit Formation

Acquisition and performance of instrumental actions are assumed to require both action-outcome and stimulus-response (S-R) habit processes. Over the course of extended training, control over instrumental performance shifts from goal-directed action-outcome associations to S-R associations that progressively gain domination over behavior. Lesions of the lateral part of the dorsal striatum disrupt this process, and rats with lesions to the lateral striatum showed selective sensitivity to devaluation of the instrumental outcome (Yin et al., 2004), indicating that this area is necessary for habit formation. The present experiment further explored the basis of this dysfunction by examining the ability of rats subjected to bilateral 6-hydroxydopamine lesions of the nigrostriatal dopaminergic pathway to develop behavioral autonomy with overtraining. Rats were given extended training on two cued instrumental tasks associating a stimulus (a tone or a light) with an instrumental action (lever press or chain pull) and a food reward (pellets or sucrose). Both tasks were run daily in separate sessions. Overtraining was followed by a test of goal sensitivity by satiety-specific devaluation of the reward. In control animals, one action (lever press) was insensitive to reward devaluation, indicating that it became a habit, whereas the second action (chain pull) was still sensitive to goal devaluation. This result provides evidence that the development of habit learning may depend on the characteristics of the response. In dopamine-depleted rats, lever press and chain pull remained sensitive to reward devaluation, evidencing a role of striatal dopamine transmission in habit formation.
Functional Coupling from Simple to Complex Cells in the Visually Driven Cortical Circuit

In the classic model of the primary visual cortex, upper-layer complex cells are driven by feedforward inputs from layer 4 simple cells. Based on spike cross-correlation, previous in vivo work has suggested that this connection is strong and dense, with a high probability of connection (50%) and significant strength in connected pairs. A much sparser projection has been found in brain slices, however, with the probability of layer 4 cells connecting to layer 2/3 cells being relatively low (10%). Here, we explore this connection in vivo in the cat primary visual cortex by recording simultaneously spikes of layer 4 simple cells and the membrane potential (Vm) of layer 2/3 complex cells. By triggering the average of the complex cell's Vm on the spikes of the simple cell (Vm-STA), we found functional coupling to be very common during visual stimulation: the simple cell's spikes tended to occur near the troughs of the complex cell's Vm fluctuations and were, on average, followed by a significant (∼1 mV) fast-rising (10 ms) depolarization in the complex cell. In the absence of visual stimulation, however, when single simple cells were activated electrically through the recording electrode, no significant depolarization, or at most a very weak input (0.1–0.2 mV), was detected in the complex cell. We suggest that the functional coupling observed during visual stimulation arises from coordinated or nearly synchronous activity among a large population of simple cells, only a small fraction of which are presynaptic to the recorded complex cell.
Use of risk-adjusted change in health status to assess the performance of integrated service networks in the Veterans Health Administration.

OBJECTIVE Health outcome assessments have become an expectation of regulatory and accreditation agencies. We examined whether a clinically credible risk adjustment methodology for the outcome of change in health status can be developed for performance assessment of integrated service networks. STUDY DESIGN Longitudinal study. SETTING Outpatient. STUDY PARTICIPANTS Thirty-one thousand eight hundred and twenty-three patients from 22 Veterans Health Administration (VHA) integrated service networks were followed for 18 months. MAIN MEASURE The physical (PCS) and mental (MCS) component scales from the Veterans Rand 36-items Health Survey (VR-36) and mortality. The outcomes were decline in PCS (decline in PCS scores greater than -6.5 points or death) and MCS (decline in MCS scores greater than -7.9 points). RESULTS Four thousand three hundred and twenty-eight (13.6%) patients showed a decline in PCS scores greater than -6.5 points, 4322 (13.5%) had a decline in MCS scores by more than -7.9 points, and 1737 died (5.5%). Multivariate logistic regression models were used to adjust for case-mix. The models performed reasonably well in cross-validated tests of discrimination (c-statistics = 0.72 and 0.68 for decline in PCS and MCS, respectively) and calibration. The resulting risk-adjusted rates of decline in PCS and MCS and ranks of the networks differed considerably from unadjusted ratings. CONCLUSION It is feasible to develop clinically credible risk adjustment models for the outcomes of decline in PCS and MCS. Without adequate controls for case-mix, we could not determine whether poor patient outcomes reflect poor performance, sicker patients, or other factors. This methodology can help to measure and report the performance of health care systems.
An Accurately Controlled Antagonistic Shape Memory Alloy Actuator with Self-Sensing

With the progress of miniaturization, shape memory alloy (SMA) actuators exhibit high energy density, self-sensing ability and ease of fabrication, which make them well suited for practical applications. This paper presents a self-sensing controlled actuator drive that was designed using antagonistic pairs of SMA wires. Under a certain pre-strain and duty cycle, the stress between two wires becomes constant. Meanwhile, the strain to resistance curve can minimize the hysteresis gap between the heating and the cooling paths. The curves of both wires are then modeled by fitting polynomials such that the measured resistance can be used directly to determine the difference between the testing values and the target strain. The hysteresis model of strains to duty cycle difference has been used as compensation. Accurate control is demonstrated through step response and sinusoidal tracking. The experimental results show that, under a combination control program, the root-mean-square error can be reduced to 1.093%. The limited bandwidth of the frequency is estimated to be 0.15 Hz. Two sets of instruments with three degrees of freedom are illustrated to show how this type actuator could be potentially implemented.
INTERACTIONAL FEEDBACK AND INSTRUCTIONAL COUNTERBALANCE

This comparative analysis of teacher-student interaction in two different instructional settings at the elementary-school level (18.3 hr in French immersion and 14.8 hr Japanese immersion) investigates the immediate effects of explicit correction, recasts, and prompts on learner uptake and repair. The results clearly show a predominant provision of recasts over prompts and explicit correction, regardless of instructional setting, but distinctively varied student uptake and repair patterns in relation to feedback type, with the largest proportion of repair resulting from prompts in French immersion and from recasts in Japanese immersion. Based on these findings and supported by an analysis of each instructional setting's overall communicative orientation, we introduce the counterbalance hypothesis, which states that instructional activities and interactional feedback that act as a counterbalance to a classroom's predominant communicative orientation are likely to prove more effective than instructional activities and interactional feedback that are congruent with its predominant communicative orientation.This research was supported by Standard Research Grants (410-98-0175 and 410-2002-0988) awarded to the first author from the Social Sciences and Humanities Research Council of Canada and by a Nihon University Individual Research Grant for 2005 awarded to the second author. A version of this study was presented at the Second Language Research Forum held at Columbia University in October 2005. We are especially grateful to the participating teachers and their students and also to Yingli Yang for her role as research assistant in aggregating the datasets. We thank Sue Gass, Alison Mackey, Iliana Panova, Leila Ranta, and two SSLA reviewers for their helpful comments on earlier versions of this paper.
Modeling Clone Evolution

During the maintenance of a program, not only the source code but also the code clones contained in it evolve. Some recent studies focused on detecting patterns in the history of code clones to evaluate the harmfulness of clones. Since clone evolution is a rather novel field of study, there is still need for more comprehensive models and improved methodologies. Current approaches are limited to detecting only a small specialized set of patterns in a clone’s evolution, they generally lack scalability and the way they collect data has to be discussed. We provide an overview of existing methods to model clone evolution by describing the patterns that can be observed and the respective detection procedure. We discuss their shortcomings and point out open questions towards more detailed models of clone evolution.