Miracle-dz/UniFAR-FTUs huggingface dataset:
Elevated morning cortisol is a stratified population-level biomarker for major depression in boys only with high depressive symptoms

Significance Clinical depression is a severe and common illness, characterized primarily by persistent low mood and lack of pleasure in usually enjoyable activities, that results in significant impairment in everyday living. It also involves alterations in cognitive and hormonal functions. There is substantial variation between depressed individuals in terms of the causes and therapeutic response, making it difficult to identify those most likely to benefit from intervention and treatment. We derived subtypes of adolescents in the population based on different levels of the hormone cortisol and subclinical depressive symptoms. A group (17%) with both high levels of cortisol and depressive symptoms of both sexes had more depressed thinking. Boys in this group were at high risk for clinical depression. Major depressive disorder (MD) is a debilitating public mental health problem with severe societal and personal costs attached. Around one in six people will suffer from this complex disorder at some point in their lives, which has shown considerable etiological and clinical heterogeneity. Overall there remain no validated biomarkers in the youth population at large that can aid the detection of at-risk groups for depression in general and for boys and young men in particular. Using repeated measurements of two well-known correlates of MD (self-reported current depressive symptoms and early-morning cortisol), we undertook a population-based investigation to ascertain subtypes of adolescents that represent separate longitudinal phenotypes. Subsequently, we tested for differential risks for MD and other mental illnesses and cognitive differences between subtypes. Through the use of latent class analysis, we revealed a high-risk subtype (17% of the sample) demarcated by both high depressive symptoms and elevated cortisol levels. Membership of this class of individuals was associated with increased levels of impaired autobiographical memory recall in both sexes and the greatest likelihood of experiencing MD in boys only. These previously unidentified findings demonstrate at the population level a class of adolescents with a common physiological biomarker specifically for MD in boys and for a mnemonic vulnerability in both sexes. We suggest that the biobehavioral combination of high depressive symptoms and elevated morning cortisol is particularly hazardous for adolescent boys.
Detection number of bipartite graphs and cubic graphs

For a connected graph G of order |V(G)| ≥3 and a k-labelling c : E(G) →{1,2,…,k} of the edges of G, the code of a vertex v of G is the ordered k-tuple (l1,l2,…,lk), where li is the number of edges incident with v that are labelled i. The k-labelling c is detectable if every two adjacent vertices of G have distinct codes. The minimum positive integer k for which G has a detectable k-labelling is the detection number det(G) of G. In this paper, we show that it is NP-complete to decide if the detection number of a cubic graph is 2. We also show that the detection number of every bipartite graph of minimum degree at least 3 is at most 2. Finally, we give some sufficient condition for a cubic graph to have detection number 3.
Vaspin (serpinA12) in obesity, insulin resistance, and inflammation

While genome‐wide association studies as well as candidate gene studies have revealed a great deal of insight into the contribution of genetics to obesity development and susceptibility, advances in adipose tissue research have substantially changed the understanding of adipose tissue function. Its perception has changed from passive lipid storage tissue to active endocrine organ regulating and modulating whole‐body energy homeostasis and metabolism and inflammatory and immune responses by secreting a multitude of bioactive molecules, termed adipokines.
For Better or for Worse: Complexins Regulate SNARE Function and Vesicle Fusion

In contrast to constitutive secretion, SNARE‐mediated synaptic vesicle fusion is controlled by multiple regulatory proteins, which determine the Ca2+ sensitivity of the vesicle fusion process and the speed of excitation–secretion coupling. Complexins are among the best characterized SNARE regulators known to date. They operate by binding to trimeric SNARE complexes consisting of the vesicle protein synaptobrevin and the plasma membrane proteins syntaxin and SNAP‐25. The question as to whether complexins facilitate or inhibit SNARE‐mediated fusion processes is currently a matter of significant controversy. This is mainly because of the fact that biochemical experiments in vitro and studies on vertebrate complexins in vivo have yielded apparently contradictory results. In this review, I provide a summary of available data on the role of complexins in SNARE‐mediated vesicle fusion and attempt to define a model of complexin function that incorporates evidence for both facilitatory and inhibitory roles of complexins in SNARE‐mediated fusion.
A Novel Polymorphism rs1329149 of CYP2E1 and a Known Polymorphism rs671 of ALDH2 of Alcohol Metabolizing Enzymes Are Associated with Colorectal Cancer in a Southwestern Chinese Population

Background: To screen for tagging single nucleotide polymorphisms (tagSNP) in the major alcohol metabolizing enzymes: ADH1B, ALDH2, and CYP2E1, and to evaluate the association between these tagSNPs and colorectal cancer (CRC) in a southwestern Chinese population. Methods: A hospital-based case-control study of 440 CRC patients and 800 cancer-free controls was conducted. Personal information was collected by a Semi-Quantitative Food Frequency Questionnaire. The tagSNPs were screened in the HapMap with Haploview by setting the minor allele frequency at 0.03 with the highest score of r2 form each block. Genotypes were identified by using the SNPLex System. Both crude and adjusted odds ratio (OR) and 95% confidence interval (CI) were used to evaluate the risk of each SNP. Results: Sixteen tagSNPs were selected, and 13 were successfully genotyped. A novel CYP2E1 locus rs1329149 and a known ALDH2 locus rs671 were found to be significantly associated with CRC risk. The adjusted OR was 1.86 (95% CI, 1.12-3.09) for the rs671 A/A genotype and 4.04 for the rs1329149 T/T genotype (95% CI, 2.44-6.70), compared with their common homozygous genotypes. Interaction was found between alcohol consumption and gene polymorphisms on CRC, the adjusted OR was 7.17 (95% CI, 2.01-25.53) for drinking habits combined with rs671 A/A or rs1329149 T/T genotype. Conclusion: The results of this study suggest that rs671 A/A and the first reported locus rs1329149 T/T genotypes increase the susceptibility to CRC, and gene-environmental interaction between the two loci and alcohol use existed for CRC in Southwestern Chinese. Larger studies are warranted to verify our findings. (Cancer Epidemiol Biomarkers Prev 2009;18(9):2522–7)
Cogent: Verifying High-Assurance File System Implementations

We present an approach to writing and formally verifying high-assurance file-system code in a restricted language called Cogent, supported by a certifying compiler that produces C code, high-level specification of Cogent, and translation correctness proofs. The language is strongly typed and guarantees absence of a number of common file system implementation errors. We show how verification effort is drastically reduced for proving higher-level properties of the file system implementation by reasoning about the generated formal specification rather than its low-level C code. We use the framework to write two Linux file systems, and compare their performance with their native C implementations.
A review of mate‐finding Allee effects in insects: from individual behavior to population management

Like other animals and plants, insects may find it difficult to survive and reproduce in small populations, to the extent that their long‐term persistence may be jeopardized. The Allee effect is a theoretical framework that formalizes this decrease in survival or reproduction in small populations, and the resulting decrease in population growth and persistence. Mating failure in low‐density populations is likely to generate an Allee effect and, therefore, has a major effect on the functioning of small populations. Here, I review mate‐finding Allee effects in insect species, and their consequences for individual mating success, population dynamics, and population management. I focus, in particular, on the comparison of theoretical expectations with observational data. Several studies have reported some degree of mating failure at low density. However, almost none of the datasets available allow comparison with the predictions of classical mate‐searching models. A few studies at the population level have reported the co‐occurrence of mating failure at low density and a demographic Allee effect, but no study has yet clearly demonstrated a causal relationship between mating failure and lower rates of population growth. Thus, although the theoretical development of management tactics based on Allee effects is considered promising, the current lack of evidence supporting this strategy limits its potential relevance. I call here for a more rigorous approach to the study of mate‐finding Allee effects and propose new approaches for this purpose.
Cognitive-Behavioral Profiles of Neurodegenerative Dementias: Beyond Alzheimer's Disease

The neurocognitive and behavioral profiles of vascular dementia and vascular cognitive impairment, dementia with Lewy bodies and Parkinson's disease with dementia, and dementia syndromes associated with frontotemporal lobar degenerations are compared and contrasted with Alzheimer's dementia (AD). Vascular dementia/vascular cognitive impairment is characterized by better verbal memory performance, worse quantitative executive functioning, and prominent depressed mood. Dementia with Lewy bodies and Parkinson's disease with dementia are equally contrasted with AD by defective processing of visual information, better performance on executively supported verbal learning tasks, greater attentional variability, poorer qualitative executive functioning, and the presence of mood-congruent visual hallucinations. The frontal variant of frontotemporal lobar degeneration (frontotemporal dementia) differs from AD by better multimodal retention on learning tasks, different patterns of generative word fluency, defective qualitative executive functioning, and by markedly impairment of comportment. For temporal variants of frontotemporal lobar degenerations, progressive aphasia and semantic dementia, worse language performance relative to AD is typically characteristic. (J Geriatr Psychiatry Neurol 2007;20:227-238)
Enhancement of inland penetration of monsoon depressions in the Bay of Bengal due to prestorm ground wetness

Observations of 408 monsoon low‐pressure systems (MLPSs) including 196 monsoon depressions (MDs) that formed in the Bay of Bengal during the 1951–2007 period, and the gridded analysis of daily rainfall fields for the same period, were used to identify the association of antecedent rainfall (1 week average rainfall prior to the genesis of MLPS) with the genesis of MLPS and length of inland penetration by MDs. Prestorm rainfall is treated as a surrogate to prestorm ground wetness conditions due to unavailability of historical soil‐moisture data over the monsoon region. These observations were analyzed using self‐organizing maps (SOMs) to group nine different prestorm monsoon rainfall patterns into different transition states like active, active‐to‐break, break‐to‐active, break, etc. The analysis indicates that MLPS are four times more likely to form on a day during active monsoon state compared to break state. Analysis of MLPSs linked to each monsoon state represented by SOM nodes shows that MDs with higher inland penetration were associated with higher antecedent rainfall. On the other hand, there was no significant difference in low‐level atmospheric circulation for MDs with shortest and longest inland penetration.
Tool Use for Autonomous Agents

The intelligent use of tools is a general and important human competence that AI research has not yet examined in depth. Other fields have studied the topic, however, with results we can compile into a broad characterization of habile (tool-using) agents. In this paper we give an overview of research on the use of physical tools, using this information to motivate the development of artificial habile agents. Specifically, we describe how research goals and methods in animal cognition overlap with those in artificial intelligence. We argue that analysis of activities of tool-using agents offers an informative way to evaluate intelligence.
Stochastic resonance of mixed periodic signal in single-mode laser driven by colored noises

Stochastic resonance (SR) is studied in a gain-noise model of a single-mode, which is driven by two coloured noises and correlated in the form of an e-exponential function. By adopting a linear approximation method, we calculate the laser intensity power spectrum and signal-to-noise ratio (SNR). It is found that the traditional SR appears with the change of intensities of the pump noise and quantum noise, moreover, the phenomenon of SR drivened by the coloured noeses is clearer than the white ones. This paper also shows that when the cross-correlation time between two nosise increases to a certain number, the resonance disappears.
New Zealand triplefin fishes (family Tripterygiidae): contrasting population structure and mtDNA diversity within a marine species flock

Triplefin fishes (Family Tripterygiidae) dominate the New Zealand temperate coastal fish fauna in diversity (26 endemic species, 14 genera). Most species appear to have evolved as a local radiation and mostly occupy sympatric distributions throughout New Zealand. To investigate the forces driving current gene‐flow patterns and past evolutionary histories, we searched for common patterns of population genetic subdivision within eight species sampled throughout their distributions [mitchochondrial DNA (mtDNA) control region, n = 1086]. We hypothesised that common phylogeographical and population differentiation patterns would reveal past or ongoing physical processes, with differences reflecting stochastic or species‐specific processes. Striking differences between species were apparent, with strong phylogeographical structure detected in Grahamina capito and the estuarine species G. nigripenne. G. capito fell into three distinct geographically restricted lineages. G. nigripenne largely separated into northern and southern lineages (ΦST 0.834). Strong population structuring and isolation by distance was evident in Bellapiscis medius, B. lesleyae and Forsterygion lapillum (ΦST 0.686, 0.436 and 0.115, respectively). High gene flow was apparent in G. gymnota and Ruanoho whero, and F. varium. However, for the latter species, isolation was apparent with samples collected from the offshore Three Kings Islands. Overall, a strong relationship was found between habitat depth and population structure among species, and species inhabiting shallower water habitats showed lower genetic diversity with higher levels of population subdivision. High‐latitude populations generally showed low haplotype and nucleotide diversity. These data suggest that processes resulting from intraspecific differences in habitat preference, climatic histories and/or larval ecologies have subdivided populations of shallow water triplefin species.
Neurofeedback in attention-deficit/hyperactivity disorder – different models, different ways of application

In children with attention-deficit/hyperactivity disorder (ADHD), different neurofeedback (NF) protocols have been applied, with the most prominent differentiation between EEG frequency-band (e.g., theta/beta) training and training of slow cortical potentials (SCPs). However, beyond distinctions between such basic NF variables, there are also competing assumptions about mechanisms of action (e.g., acquisition of regulation capability, generalization to daily life behavior). In the present article, we provide a framework for NF models and suppose two hypothetical models, which we call “conditioning-and-repairing model” and “skill-acquisition model,” reflecting extreme poles within this framework. We argue that the underlying model has an impact not only on how NF is applied but also on the selection of evaluation strategies and suggest using evaluation strategies beyond beaten paths of pharmacological research. Reflecting available studies, we address to what extent different views are supported by empirical data. We hypothesize that different models may hold true depending on the processes and behaviors to be addressed by a certain NF protocol. For example, the skill-acquisition model is supported by recent findings as an adequate explanatory framework for the mechanisms of action of SCP training in ADHD. In conclusion, evaluation and interpretation of NF trials in ADHD should be based on the underlying model and the way training is applied, which, in turn, should be stated explicitly in study reports.
Self-triggered control for multi-agent systems under a directed switching graph

This paper presents the design of a self-triggered methodology for control of multi-agent systems. Conditions that guarantee the existence of a self-triggered strategy solving the consensus problem, are provided for first order systems under fixed and switching topologies. A methodology for the computation of the feedback gain and the control update time is given. Simulation results show the effectiveness of the proposed strategy.
Role of ribosome degradation in the death of starved Escherichia coli cells

In Escherichia coli cultures limited for phosphate, the number of ribosomal particles was reduced to a small percentage of its earlier peak value by the time the viable cell count began to drop; the 30S subunits decreased more than the 50S subunits. Moreover, the ribosomal activity was reduced even more: these cells no longer synthesized protein, and their extracts could not translate phage RNA unless ribosomes were added. The translation initiation factors also disappeared, suggesting that they become less stable when released from their normal attachment to 30S subunits. In contrast, elongation factors, aminoacyl-tRNA synthetases, and tRNA persisted. During further incubation, until viability was reduced to 10(-5), the ribosomal particles disappeared altogether, while tRNA continued to be preserved. These results suggest that an excessive loss of ribosomes (and of initiation factors) may be a major cause of cell death during prolonged phosphate starvation.
Ocean Response to Wind Variations, Warm Water Volume, and Simple Models of ENSO in the Low-Frequency Approximation

Abstract Physical processes that control ENSO are relatively fast. For instance, it takes only several months for a Kelvin wave to cross the Pacific basin (Tk ≈ 2 months), while Rossby waves travel the same distance in about half a year. Compared to such short time scales, the typical periodicity of El Nino is much longer (T ≈ 2–7 yr). Thus, ENSO is fundamentally a low-frequency phenomenon in the context of these faster processes. Here, the author takes advantage of this fact and uses the smallness of the ratio ek = Tk/T to expand solutions of the ocean shallow-water equations into power series (the actual parameter of expansion also includes the oceanic damping rate). Using such an expansion, referred to here as the low-frequency approximation, the author relates thermocline depth anomalies to temperature variations in the eastern equatorial Pacific via an explicit integral operator. This allows a simplified formulation of ENSO dynamics based on an integro-differential equation. Within this formulation, .
The Impact of Rapid Weight Loss on Oxidative Stress Markers and the Expression of the Metabolic Syndrome in Obese Individuals

Objective. Obesity is linked with a state of increased oxidative stress, which plays an important role in the etiology of atherosclerosis and type 2 diabetes mellitus. The aim of our study was to evaluate the effect of rapid weight loss on oxidative stress markers in obese individuals with metabolic syndrome (MetS). Design and Methods. We measured oxidative stress markers in 40 obese subjects with metabolic syndrome (MetS+), 40 obese subjects without metabolic syndrome (MetS−), and 20 lean controls (LC) at baseline and after three months of very low caloric diet. Results. Oxidized low density lipoprotein (ox-LDL) levels decreased by 12% in MetS+ subjects, associated with a reduction in total cholesterol (TC), even after adjustment for age and sex. Lipoprotein associated phospholipase A2 (Lp-PLA2) activity decreased by 4.7% in MetS+ subjects, associated with a drop in LDL-cholesterol (LDL-C), TC, and insulin levels. Multivariate logistic regression analysis showed that a model including ox-LDL, LpPLA2 activity, and myeloperoxidase (MPO) improved prediction of MetS status among obese individuals compared to each oxidative stress marker alone. Conclusions. Oxidative stress markers were predictive of MetS in obese subjects, suggesting a higher oxidative stress. Rapid weight loss resulted in a decline in oxidative stress markers, especially in MetS+ patients.
Inflammatory Marker Changes in Postmenopausal Women after a Year-long Exercise Intervention Comparing High Versus Moderate Volumes

This randomized dose comparison trial examined if higher exercise volume decreased inflammatory biomarkers, associated with postmenopausal breast cancer risk, more than moderate exercise volume. The Breast Cancer and Exercise Trial in Alberta was a two-center, two-armed randomized trial in 400 inactive, healthy, postmenopausal women, aged 50 to 74 years, with a body mass index of 22 to 40 kg/m2. Participants were randomized to high (300 minutes/week) or moderate (150 minutes/week) volumes of aerobic exercise while maintaining usual diet. Fasting blood concentrations of C-reactive protein (CRP), IL6, and TNFα were measured at baseline, 6 and 12 months. Intention-to-treat (ITT) analysis was performed using linear mixed models adjusted for baseline biomarker concentrations. ITT analyses of 386 (97%) participants showed no statistically significant group differences for changes in biomarker levels at 6 and 12 months. In addition, we did not observe any modification of this effect by baseline characteristics of participants. In post hoc analyses based on self-selected exercise level (measured in minutes/week), CRP decreased by 22.45% for participants who exercised >246 minutes/week (highest quintile) and increased by 0.07% for those who exercised <110 minutes/week (lowest quintile, Ptrend = 0.04), adjusted for baseline covariates. When this analysis was restricted to include exercise time in the target heart rate zone only, statistically significant trends were observed for both CRP (P < 0.01) and IL6 (P = 0.04). Prescribing 300 minutes/week of moderate-to-vigorous aerobic exercise did not improve inflammatory markers compared with 150 minutes/week in postmenopausal women. Decreases in CRP were observed with higher self-selected exercise volume. Cancer Prev Res; 9(2); 196–203. ©2015 AACR.