Miracle-dz/UniFAR-FTUs huggingface dataset:
How Robust is the Association of Life Satisfaction with Value Congruence? A Study of Constructed Socio-Demographic Groups in a Russian National Sample

Congruence between own values and those of one’s reference groups has been found to promote life satisfaction. Actual or anticipated support or sanctions from reference others presumably explains this effect. Does the effect extend to congruence with the values of others who are similar only in socio-demographic characteristics with whom one does not interact? We constructed 36 socio-demographic groups by crossing age, gender, religion, education level, and region of residence in a representative Russian national sample (N=961). We derived value congruence scores by correlating individuals’ values with the mean values of their constructed group. Value congruence and life satisfaction correlated significantly across individuals even in these groups. The less important self-direction values to individuals, the stronger the correlation. A meta-analysis of the correlations in the 36 groups also confirmed the positive association of value congruence with life satisfaction. The characteristics used to construct the groups did not moderate this association.
Managing Security Work in Scrum: Tensions and Challenges

We advocate a change of perspective in the question of agile secure software development and analyze what makes it diﬃcult to address security needs in Scrum. The literature focuses on the integration of security activities into agile development processes. However, detailed prescriptions for security work would be misplaced in a generic management framework like Scrum. Therefore we take a closer look at the tensions between Scrum’s way of organizing work and the characteristics of security requirements. Our previous work suggests that Scrum works well as a management model and security development requires iterations as in agile development, yet Scrum teams can fail to address security needs due to their low visibility, competing objectives, and Scrum’s division of labor. Tensions arise as Scrum is optimized to fulﬁll explicit requirements and maximize business value, whereas security is often an implicit requirement with a diﬀerent value proposition, which neverthe-less requires substantial work and cannot be addressed by bug ﬁxing or quality assurance alone. As a consequence, promising research directions are the reﬂective discovery of security needs, the valuation and prioritization of security work, collaboration between Scrum teams and security experts, and veriﬁcation and feedback mechanisms for security.
Rescue of mutant rhodopsin traffic by metformin-induced AMPK activation accelerates photoreceptor degeneration

Abstract Protein misfolding caused by inherited mutations leads to loss of protein function and potentially toxic ‘gain of function’, such as the dominant P23H rhodopsin mutation that causes retinitis pigmentosa (RP). Here, we tested whether the AMPK activator metformin could affect the P23H rhodopsin synthesis and folding. In cell models, metformin treatment improved P23H rhodopsin folding and traffic. In animal models of P23H RP, metformin treatment successfully enhanced P23H traffic to the rod outer segment, but this led to reduced photoreceptor function and increased photoreceptor cell death. The metformin-rescued P23H rhodopsin was still intrinsically unstable and led to increased structural instability of the rod outer segments. These data suggest that improving the traffic of misfolding rhodopsin mutants is unlikely to be a practical therapy, because of their intrinsic instability and long half-life in the outer segment, but also highlights the potential of altering translation through AMPK to improve protein function in other protein misfolding diseases.
Hidden Hamiltonian Cycle Recovery via Linear Programming

We introduce the problem of hidden Hamiltonian cycle recovery, where there is an unknown Hamiltonian cycle in an $n$-vertex complete graph that needs to be inferred from noisy edge measurements. The measurements are independent and distributed according to $\calP_n$ for edges in the cycle and $\calQ_n$ otherwise. This formulation is motivated by a problem in genome assembly, where the goal is to order a set of contigs (genome subsequences) according to their positions on the genome using long-range linking measurements between the contigs. Computing the maximum likelihood estimate in this model reduces to a Traveling Salesman Problem (TSP). Despite the NP-hardness of TSP, we show that a simple linear programming (LP) relaxation, namely the fractional $2$-factor (F2F) LP, recovers the hidden Hamiltonian cycle with high probability as $n \to \infty$ provided that $\alpha_n - \log n \to \infty$, where $\alpha_n \triangleq -2 \log \int \sqrt{d P_n d Q_n}$ is the R\'enyi divergence of order $\frac{1}{2}$. This condition is information-theoretically optimal in the sense that, under mild distributional assumptions, $\alpha_n \geq (1+o(1)) \log n$ is necessary for any algorithm to succeed regardless of the computational cost. Departing from the usual proof techniques based on dual witness construction, the analysis relies on the combinatorial characterization (in particular, the half-integrality) of the extreme points of the F2F polytope. Represented as bicolored multi-graphs, these extreme points are further decomposed into simpler "blossom-type" structures for the large deviation analysis and counting arguments. Evaluation of the algorithm on real data shows improvements over existing approaches.
A DAC With an Impedance Attenuator and Distortion Analysis Using Volterra Series

An impedance attenuator is implemented to reduce digital-to-analog converter (DAC) distortion, and two techniques to further reduce the distortion are discussed: the first is to use cross-coupled capacitors to cancel nonlinear currents; the second is to optimize the common-mode bandwidth of the differential amplifier for cancellation of distortion. To support these techniques, DAC distortion has been analyzed with the Volterra series, and the analysis is compared with simulation results and measurement data. The analysis uncovers a previously unknown nonlinear cancellation mechanism for the DAC and confirms the proposed techniques. Each technique can contribute 3–6 dB of improvement, and about a 6-dB improvement when combined. The 0.708-mm2 DAC is fabricated in a 28-nm metal-gate digital CMOS process with the proposed impedance attenuator, and it achieves −89 dBc of average HD3 at a 5-MHz input frequency and sampling rate of 230.4 MHz.
Solving the shrinkage-induced PDMS alignment registration issue in multilayer soft lithography

Shrinkage of polydimethylsiloxane (PDMS) complicates alignment registration between layers during multilayer soft lithography fabrication. This often hinders the development of large-scale microfabricated arrayed devices. Here we report a rapid method to construct large-area, multilayered devices with stringent alignment requirements. This technique, which exploits a previously unrecognized aspect of sandwich mold fabrication, improves device yield, enables highly accurate alignment over large areas of multilayered devices and does not require strict regulation of fabrication conditions or extensive calibration processes. To demonstrate this technique, a microfabricated Braille display was developed and characterized. High device yield and accurate alignment within 15 µm were achieved over three layers for an array of 108 Braille units spread over a 6.5 cm2 area, demonstrating the fabrication of well-aligned devices with greater ease and efficiency than previously possible.
Cerebral dopaminergic and glutamatergic transmission relate to different subjective responses of acute alcohol intake: an in vivo multimodal imaging study

Converging preclinical evidence links extrastriatal dopamine release and glutamatergic transmission via the metabotropic glutamate receptor 5 (mGluR5) to the rewarding properties of alcohol. To date, human evidence is lacking on how and where in the brain these processes occur. Mesocorticolimbic dopamine release upon intravenous alcohol administration and mGluR5 availability were measured in 11 moderate social drinkers by single‐session [18F]fallypride and [18F]FPEB positron emission tomography, respectively. Additionally, baseline and postalcohol glutamate and glutamine levels in the anterior cingulate cortex (ACC) were measured by using proton‐magnetic resonance spectroscopy. To investigate differences in reward domains linked to both neurotransmitters, regional imaging data were related to subjective alcohol responses. Alcohol induced significant [18F]fallypride displacement in the prefrontal cortex (PFC), temporal and parietal cortices and thalamus (P < 0.05, corrected for multiple comparisons). Dopamine release in the ACC and orbitofrontal and ventromedial PFCs were correlated with subjective ‘liking’ and ‘wanting’ effects (P < 0.05). In contrast, baseline mGluR5 availability was positively correlated with the ‘high’ effect of alcohol in dorsolateral, ventrolateral and ventromedial PFCs and in the medial temporal lobe, thalamus and caudate nucleus (P < 0.05). Although neither proton‐magnetic resonance spectroscopy glutamate nor glutamine levels were affected by alcohol, baseline ACC glutamate levels were negatively associated with the alcohol ‘liking’ effect (P < 0.003). These data reveal new mechanistic understanding and differential neurobiological underpinnings of the effects of acute alcohol consumption on human behavior. Specifically, prefrontal dopamine release may encode alcohol ‘liking’ and ‘wanting’ effects in specific areas underlying value processing and motivation, whereas mGluR5 availability in distinct prefrontal–temporal–subcortical regions is more related to the alcohol ‘high’ effect.
Deep‐targeted sequencing of endothelial nitric oxide synthase gene exons uncovers exercise intensity and ethnicity‐dependent associations with post‐exercise hypotension

In previous studies, we found an endothelial nitric oxide synthase gene (NOS3) variant rs2070744 associated with the ambulatory blood pressure (BP) response following bouts of moderate and vigorous intensity acute exercise, termed post‐exercise hypotension (PEH). In a validation cohort, we sequenced NOS3 exons for associations with PEH. Obese (30.9 ± 3.6 kg.m−2) African American (n = 14) [AF] and Caucasian (n = 9) adults 42.0 ± 9.8 years with hypertension (139.8 ± 10.4/84.6 ± 6.2 mmHg) performed three random experiments: bouts of vigorous and moderate intensity cycling and control. Subjects were attached to an ambulatory BP monitor for 19 h. We performed deep‐targeted exon sequencing with the Illumina TruSeq Custom Amplicon kit. Variant genotypes were coded as number of minor alleles (#MA) and selected for additional statistical analysis based upon Bonferonni or Benjamini–Yekutieli multiple testing‐corrected P‐values under time‐adjusted linear models for 19 hourly BP measurements for each subject. After vigorous intensity over 19 h, among NOS3 variants passing multiple testing thresholds, as the #MA increased in rs891512 (P = 6.4E‐04), rs867225 (P = 6.5E‐04), rs743507 (P = 2.6E‐06), and rs41483644 (P = 2.4E‐04), systolic (SBP) decreased from 17.5 to 33.7 mmHg; and in rs891512 (P = 9.7E‐05), rs867225 (P = 2.6E‐05), rs41483644 (P = 1.6E‐03), rs3730009 (P = 2.6E‐04), and rs77325852 (P = 5.6E‐04), diastolic BP decreased from 11.1 mmHg to 20.3 mmHg among AF only. In contrast, after moderate intensity over 19 h in NOS3 rs3918164, as the #MA increased, SBP increased by 16.6 mmHg (P = 2.4E‐04) among AF only. NOS3 variants exhibited associations with PEH after vigorous, but not moderate intensity exercise among AF only. NOS3 should be studied further for its effects on PEH in a large, ethnically diverse sample of adults with hypertension to confirm our findings.
The Repeat Sequences and Elevated Substitution Rates of the Chloroplast accD Gene in Cupressophytes

The plastid accD gene encodes a subunit of the acetyl-CoA carboxylase (ACCase) enzyme. The length of accD gene has been supposed to expand in Cryptomeria japonica, Taiwania cryptomerioides, Cephalotaxus, Taxus chinensis, and Podocarpus lambertii, and the main reason for this phenomenon was the existence of tandemly repeated sequences. However, it is still unknown whether the accD gene length in other cupressophytes has expanded. Here, in order to investigate how widespread this phenomenon was, 18 accD sequences and its surrounding regions of cupressophyte were sequenced and analyzed. Together with 39 GenBank sequence data, our taxon sampling covered all the extant gymnosperm orders. The repetitive elements and substitution rates of accD among 57 gymnosperm species were analyzed, the results show: (1) Reading frame length of accD gene in 18 cupressophytes species has also expanded. (2) Many repetitive elements were identified in accD gene of cupressophyte lineages. (3) The synonymous and non-synonymous substitution rates of accD were accelerated in cupressophytes. (4) accD was located in rearrangement endpoints. These results suggested that repetitive elements may mediate the chloroplast genome rearrangement and accelerated the substitution rates.
Bi-directional Association of Cerebrospinal Fluid Immune Markers with Stage of Alzheimer’s Disease Pathogenesis

Immune mechanisms may be important in the pathogenesis of Alzheimer’s disease (AD). Yet, studies comparing cerebrospinal fluid (CSF) and plasma immune marker levels of healthy and demented individuals have yielded conflicting results. We analyzed CSF from 101 members of the parental history-positive PREVENT-AD cohort of healthy aging adults, and 237 participants without dementia from the initial cohort of the Alzheimer’s Disease Neuroimaging Initiative (ADNI-1). Following recent practice, we used the biomarkers total-tau and amyloid-β1-42 to allocate participants from each study into four stages of AD pathogenesis: Stage 0 (no abnormality), Stage 1 (reduced amyloid-β1-42), Stage 2 (reduced amyloid-β1-42 and increased total-tau), or “Suspected Non-Alzheimer Pathology” (elevated total-tau only). Investigating the PREVENT-AD participants’ CSF assay results for 19 immune/inflammatory markers, we found six that showed a distinct bi-directional relationship with pathogenetic stage. Relative to Stage 0, these were diminished at Stage 1 but strongly increased at Stage 2. Among the ADNI participants (90 healthy controls and 147 with mild cognitive impairment), we found that 23 of 83 available CSF markers also showed this distinct pattern. These results support recent observations that immune activation may become apparent only after the onset of both amyloid and tau pathologies. Unexpectedly, they also suggest that immune marker activity may diminish along with earliest appearance of amyloid-β plaque pathology. These findings may explain discordant results from past studies, and suggest the importance of characterizing the extent of AD pathology when comparing clinical groups.
Predicting User Views in Online News

We analyze user viewing behavior on an online news site. We collect data from 64,000 news articles, and use text features to predict frequency of user views. We compare predictiveness of the headline and “teaser” (viewed before clicking) and the body (viewed after clicking). Both are predictive of clicking behavior, with the full article text being most predictive.
Evolving Construction Ordering Heuristics for Educational Timetabling Problems

Construction heuristics play an important role in solving combinatorial optimization problems. These heuristics are usually used to create an initial solution to the problem which is improved using optimization techniques such as metaheuristics. For examination timetabling and university course timetabling problems essentially graph colouring heuristics have been used for this purpose. The process of deriving heuristics manually for educational timetabling is a time consuming task. Furthermore, according to the no free lunch theorem di↵erent heuristics will perform well for di↵erent problems and problem instances. This research presents generation hyper-heuristics [1] to evolve low-level construction heuristics for the examination timetabling and university course timetabling problems. The hyper-heuristics use genetic programming [2]. The following section presents the genetic programming (GP) hyperheuristics, the experimental setup and preliminary results.
Evaluation of a novel cardiac output index on healthy elderly, cardiovascular and heart failure patients during dynamic exercise

We have recently proposed a novel CO index, namely pulse time reflection ratio (PTRR), which is extracted from photoplethysmogram and electrocardiogram and measurable from wearable devices, and proved that this index is potentially useful for dynamic CO monitoring in a preliminary study carried out on young, healthy subjects. In this study, we presented an evaluation of this technique against impedance cardiography on 64 subjects undergoing incremental maximal exercise testing, including 15 healthy elderly, 19 cardiovascular patients and 30 heart failure patients. Results showed significant intra-subject correlations (r) between PTRR and reference CO in all subjects (mean r: 0.93, p<0.05) and no significant differences on mean r among subject populations (one-way ANOVA, p=0.48). With further development and testing on mobile subjects, this technique can be applied for long-term CO monitoring at home or in other dynamic situations.
The Sporothrix schenckii Gene Encoding for the Ribosomal Protein L6 Has Constitutive and Stable Expression and Works as an Endogenous Control in Gene Expression Analysis

Sporothrix schenckii is one of the causative agents of sporotrichosis, a worldwide-distributed mycosis that affects humans and other mammals. The interest in basic and clinical features of this organism has significantly increased in the last years, yet little progress in molecular aspects has been reported. Gene expression analysis is a set of powerful tools that helps to assess the cell response to changes in the extracellular environment, the genetic networks controlling metabolic pathways, and the adaptation to different growth conditions. Most of the quantitative methodologies used nowadays require data normalization, and this is achieved measuring the expression of endogenous control genes. Reference genes, whose expression is assumed to suffer minimal changes regardless the cell morphology, the stage of the cell cycle or the presence of harsh extracellular conditions are commonly used as controls in Northern blotting assays, microarrays, and semi-quantitative or quantitative RT-PCR. Since the biology of the organisms is usually species specific, it is difficult to find a reliable group of universal genes that can be used as controls for data normalization in experiments addressing the gene expression, regardless the taxonomic classification of the organism under study. Here, we compared the transcriptional stability of the genes encoding for elongation factor 1A, Tfc1, a protein involved in transcription initiation on Pol III promoters, ribosomal protein L6, histone H2A, β-actin, β-tubulin, glyceraldehyde 3-phosphate dehydrogenase, UAF30, the upstream activating factor 30, and the transcription initiation factor TFIID subunit 10, during the fungal growth in different culture media and cell morphologies. Our results indicated that only the gene encoding for the ribosomal protein L6 showed a stable and constant expression. Furthermore, it displayed not transcriptional changes when S. schenckii infected larvae of Galleria mellonella or interacted with immune cells. Therefore, this gene could be used as control for data normalization in expression assays. As a proof of concept, this gene was used to assess the expression of genes encoding for glycosidases involved in the protein N-linked glycosylation pathway, a histidine kinase whose expression is regulated during the fungal dimorphism, and a glycosidase that participates in sucrose assimilation.
Acoustic Funnel and Buncher for Nanoparticle Injection

Acoustics-based techniques are investigated to focus and bunch nanoparticle beams. This allows to overcome the prominent problem of the longitudinal and transverse mismatch of particle stream and x-ray beam in single-particle/single molecule imaging at x-ray free-electron lasers (XFEL). It will also enable synchronised injection of particle streams at kHz repetition rates. Transverse focusing concentrates the particle flux to the (sub)micrometer x-ray focus. In the longitudinal direction, focused acoustic waves can be used to bunch the particle to the same repetition rate as the x-ray pulses. The acoustic manipulation is based on simple mechanical recoil effects and could be advantageous over light-pressure-based methods, which rely on absorption. The acoustic equipment is easy to implement and can be conveniently inserted into current XFEL endstations. With the proposed method, data collection times could be reduced by a factor of $10^4$. This work does not just provide an efficient method for acoustic manipulation of streams of arbitrary gas phase particles, but also opens up wide avenues for acoustics-based particle optics.
Rhythms of Locomotion Expressed by Limulus polyphemus, the American Horseshoe Crab: I. Synchronization by Artificial Tides

Limulus polyphemus, the American horseshoe crab, has an endogenous clock that drives circatidal rhythms of locomotor activity. In this study, we examined the ability of artificial tides to entrain the locomotor rhythms of Limulus in the laboratory. In experiments one and two, the activity of 16 individuals of L. polyphemus was monitored with activity boxes and “running wheels. ” When the crabs were exposed to artificial tides created by changes in water depth, circatidal rhythms were observed in animals exposed to 12.4-h “tidal” cycles of either water depth changes (8 of 8 animals) or inundation (7 of 8 animals). In experiment three, an additional 8 animals were exposed to water depth changes under cyclic conditions of light and dark and then monitored for 10 days with no imposed artificial tides. Most animals (5) clearly synchronized their activity to the imposed artificial tidal cycles, and 3 of these animals showed clear evidence of entrainment after the artificial tides were terminated. Overall, these results demonstrate that the endogenous tidal clock that influences locomotion in Limulus can be entrained by imposed artificial tides. In the laboratory, these tidal cues override the influence of light/dark cycles. In their natural habitat, where both tidal and photoperiod inputs are typically always present, their activity rhythms are likely to be much more complex.
Fluorescence lifetime imaging for viscosity and diffusion measurements

Imaging viscosity and its spatiotemporal patterns can provide valuable insight into the underlying physical conditions of biochemical reactions and biological processes in cells and tissues. One way to measure viscosity and diffusion is the use of fluorescence recovery after photobleaching (FRAP). We combine FRAP with FLIM and time-resolved fluorescence anisotropy imaging (tr-FAIM), by acquiring time- and polarization-resolved fluorescence images in every frame of a FRAP series. This allows us to simultaneously monitor translational and rotational diffusion. This approach can be applied to measuring diffusion in homogeneous and heterogeneous environments, and in principle also allows the study of homo-FRET. Another way to measure viscosity and diffusion is through specific flexible dyes, e.g. fluorescent molecular rotors, whose fluorescence quantum yield and fluorescence lifetime depend on the viscosity of the environment, in combination with fluorescence lifetime imaging (FLIM). We show that a bodipybased fluorescent molecular rotor targeting mitochondria reports on their viscosity, which changes under physiological stimuli. Both methods can optically measure viscosity and diffusion on the micrometer scale.