Miracle-dz/UniFAR-FTUs huggingface dataset:
Stress profiling of longevity mutants identifies Afg3 as a mitochondrial determinant of cytoplasmic mRNA translation and aging

Although environmental stress likely plays a significant role in promoting aging, the relationship remains poorly understood. To characterize this interaction in a more comprehensive manner, we examined the stress response profiles for 46 long‐lived yeast mutant strains across four different stress conditions (oxidative, ER, DNA damage, and thermal), grouping genes based on their associated stress response profiles. Unexpectedly, cells lacking the mitochondrial AAA protease gene AFG3 clustered strongly with long‐lived strains lacking cytosolic ribosomal proteins of the large subunit. Similar to these ribosomal protein mutants, afg3Δ cells show reduced cytoplasmic mRNA translation, enhanced resistance to tunicamycin that is independent of the ER unfolded protein response, and Sir2‐independent but Gcn4‐dependent lifespan extension. These data demonstrate an unexpected link between a mitochondrial protease, cytoplasmic mRNA translation, and aging.
Immunodetection of Collagen Types I, II, III, and IV for Differentiation of Liver Fibrosis Stages in Patients with Chronic HCV

Abstract The current study is aimed at evaluating serum collagens and other serum biochemical markers as useful, non‐invasive markers of hepatic fibrosis associated with chronic hepatitis C virus (HCV). Collagen types I, II, III, and IV were detected in serum using ELISA and Western blot techniques. The ELISA levels of collagen I, II, III, and IV increased significantly with the progression of fibrosis staging. Based on receiver‐operating characteristic (ROC) curve analysis, the collagen type III (70 kDa) and type IV (200 kDa) were more useful than other serum bio‐markers for differentiating severe fibrosis from mild fibrosis. Multivariate discriminant analysis (MDA) selected a fibrosis discriminant score (FDS)=[2.345+Collagen III (µg/mL) × 1.923+Collagen IV (µg/mL) × 1.544+ALT (U/mL) × 0.005] ‐ [albumin(g/L) × 0.046]. The FDS correctly classified 87% of the severe fibrosis patients at a cut‐off score=2.2 (i.e., more than 2.2 indicated severe fibrotic liver and less than 2.2 indicated mild fibrotic liver) with specificity of 97%. In a validation study, the FDS was applied to the second cohort of patients and the results were reproduced without significant difference. In conclusion, the developed four‐parameter based FDS is useful for identifying severe liver fibrosis in patients with chronic HCV infection.
Slow Manifolds and Invariant Sets of the Primitive Equations

Abstract The authors review, in a geophysical setting, several recent mathematical results on the forced–dissipative hydrostatic primitive equations with a linear equation of state in the limit of strong rotation and stratification, starting with existence and regularity (smoothness) results and describing their implications for the long-time behavior of the solution. These results are used to show how the solution of the primitive equations in a periodic box comes close to geostrophic balance as t → ∞. Then a review follows of how geostrophic balance could be extended to higher orders in the Rossby number, and it is shown that the solution of the primitive equations also satisfies a higher-order balance up to an exponentially small error. Finally, the connection between balance dynamics in the primitive equations and its global attractor, which is the only known invariant set (for a sufficiently general forcing), is discussed.
Exercise for the treatment of childhood obesity – is it simply too much to ask?

The obesity epidemic that has spread across the western world over the last 20 years requires no introduction to the practicing paediatrician. It is, sadly, almost redundant to point to it as the defining modern issue; an issue where social and lifestyle trends intersect with the health of the population. The consequences will be pervasive, expensive and, yet, almost entirely preventable (1–3). The cause is axiomatic. Whether one can quote it verbatim or not, the law of conservation of energy is obvious to most. Energy can be neither created nor destroyed, only transferred or transformed. Energy can only be lost as a result of work done by a system upon its surroundings. The human body is the ultimate ‘system’, and in modern western societies we simply do not do enough ‘work’. Regrettably, our children are not immune. The anecdotal evidence is all around us. ‘Screen time’ is increasing, and the seduction of the internet and gaming technology grows ever more irresistible to the young and old alike. Children no longer walk or bike to school in favour of being driven or riding the bus. Furthermore, schools, particularly in the United States, are being forced into sacrificing physical education to satisfy ever-increasing educational mandates and new agendas. Communities are changing, becoming more car-dependent and perceived by parents as less safe for children (4,5). As a consequence, the sights and sounds of children cheerfully burning calories as they play together in streets and parks after school are fading images from decades past. Exercise has become the pastime of the privileged, limited to those able to afford it. Yet, these are not just anecdotal observations. There is strong scientific evidence showing that sedentary activity correlates with obesity (6), that children are less active and
The validity of rodent brain-ischemia models is self-evident.

The pointof contention implicit in the title of this article would, at first glance, appear to have little basis in reality. To challenge the validity of rodent studies of brain ischemia would seem on a par, for example, with questioning whether primate kidney cell cultures are a valid model for cultivating the human poliomyelitis virus. 1 A vast body of scientific literature spanning more than 3 decades attests to the utility of the rodent brain in modeling ischemic-anoxic injury. 2 Certain truths deserve emphasis here. As discomfiting as this may appear to certain members of our highly evolved species, it is nonetheless firmly established that there is a very high degree of genetic homology between humans and rodents. 3 Thus, the use of rodents to study genes, messages, enzymes, second messengers, receptors, and neurotransmitters would be expected to lead to insights more relevant than not to the human brain.
Combined optical coherence tomography and hyperspectral imaging using a double-clad fiber coupler

Abstract. This work demonstrates the combination of optical coherence tomography (OCT) and hyperspectral imaging (HSI) using a double-clad optical fiber coupler. The single-mode core of the fiber is used for OCT imaging, while the inner cladding of the double-clad fiber provides an efficient way to capture the reflectance spectrum of the sample. The combination of both methods enables three-dimensional acquisition of the sample morphology with OCT, enhanced with complementary molecular information contained in the hyperspectral image. The HSI data can be used to highlight the presence of specific molecules with characteristic absorption peaks or to produce true color images overlaid on the OCT volume for improved tissue identification by the clinician. Such a system could be implemented in a number of clinical endoscopic applications and could improve the current practice in tissue characterization, diagnosis, and surgical guidance.
Burrow air phase maintenance and respiration by the mudskipper Scartelaos histophorus (Gobiidae: Oxudercinae)

SUMMARY A laboratory burrow and mudflat system was used to examine aspects of burrow air-phase maintenance and utilization by the amphibious mudskipper Scartelaos histophorus. While confined to its burrow during simulated `high tide', this species respires both aquatically and aerially, in the latter case utilizing an air phase it had established by transporting air into the burrow during simulated `low tide'. Over the course of `high-tide' confinement, burrow-water PO2 declines, making the air phase more important for respiration; the burrow-water O2 tension eliciting air-phase respiration is 4.8±0.2 kPa. At `low tide', when the fish has access to air, it deposits new air in the air phase by transporting gulps into the burrow and releasing them. Observed air-deposition rates for both males and females were 12.3±4.5 trips h-1. All of the fish tested (N=8 individuals + 2 pairs) deposited air and responded to experimental air-phase withdrawal by replacing the air (72 of 74 tests, 97.3%). Also, repeated tests with one fish showed that experimental reduction of the air-phase PO2 by mixing with N2 elicited a gas-expelling behavior at O2 levels less than 10.3 kPa. At O2 levels greater than 10.3 kPa, the fish left the air phase intact and added to it by depositing surface air.
Compound heterozygous mutations in the gene PIGP are associated with early infantile epileptic encephalopathy

&NA; There are over 150 known human proteins which are tethered to the cell surface via glycosylphosphatidylinositol (GPI) anchors. These proteins play a variety of important roles in development, and particularly in neurogenesis. Not surprisingly, mutations in the GPI anchor biosynthesis and remodeling pathway cause a number of developmental disorders. This group of conditions has been termed inherited GPI deficiencies (IGDs), a subgroup of congenital disorders of glycosylation; they present with variable phenotypes, often including seizures, hypotonia and intellectual disability. Here, we report two siblings with compound heterozygous variants in the gene phosphatidylinositol glycan anchor biosynthesis, class P (PIGP) (NM_153681.2: c.74T > C;p.Met25Thr and c.456delA;p.Glu153AsnFs*34). PIGP encodes a subunit of the enzyme that catalyzes the first step of GPI anchor biosynthesis. Both children presented with early‐onset refractory seizures, hypotonia, and profound global developmental delay, reminiscent of other IGD phenotypes. Functional studies with patient cells showed reduced PIGP mRNA levels, and an associated reduction of GPI‐anchored cell surface proteins, which was rescued by exogenous expression of wild‐type PIGP. This work associates mutations in the PIGP gene with a novel autosomal recessive IGD, and expands our knowledge of the role of PIG genes in human development.
Can red flowers be conspicuous to bees? Bombus dahlbomii and South American temperate forest flowers as a case in point

SUMMARY It has been argued that trichromatic bees with photoreceptor spectral sensitivity peaks in the ultraviolet (UV), blue and green areas of the spectrum are blind to long wavelengths (red to humans). South American temperate forests (SATF) contain a large number of human red-looking flowers that are reported to be visited by the bumblebee Bombus dahlbomii. In the present study, B. dahlbomii's spectral sensitivity was measured through electroretinogram (ERG) recordings. No extended sensitivity to long wavelengths was found in B. dahlbomii. The spectral reflectance curves from eight plant species with red flowers were measured. The color loci occupied by these flowers in the bee color space was evaluated using the receptor noise-limited model. Four of the plant species have pure red flowers with low levels of chromatic contrast but high levels of negative L-receptor contrast. Finally, training experiments were performed in order to assess the role of achromatic cues in the detection and discrimination of red targets by B. dahlbomii. The results of the training experiments suggest that the bumblebee relies on achromatic contrast provided by the L-receptor to detect and discriminate red targets. These findings are discussed in the context of the evolutionary background under which the relationship between SATF species and their flower visitors may have evolved.
Using Deep Convolutional Neural Networks for Image Retrieval

In content-based image retrieval, the most challenging problem is the “semantic gap” between low-level visual features captured by machines and high-level semantic concepts perceived by human. This paper focuses on the high-level image features learning by the convolutional neural networks (CNN) in image retrieval. As a deep learning framework, CNN can extract meaningful image features in different layers, and transfer the image content into (abstract) semantic concepts. These high-level features descriptors can be better image representations than the hand-crafted feature descriptors, and further improve the image retrieval performance. The experimental results showed that layerwise learning invariant feature hierarchies in CNN is good at feature representations. Using CNN for feature extractions on CIFAR-10 and CIFAR-100 dataset, it achieved 0.707 and 0.244 of mean average precision (MAP), respectively.
Trail Making Test Errors and Executive Function in Schizophrenia and Depression

The Trail Making Test (TMT) frequently is used as a measure of executive cognitive function. However, traditional use of test completion time as the primary outcome score does not give the more detailed information on cognitive processes that analysis of test-taking errors may provide. The present study compared TMT performance of three groups: patients with schizophrenia, patients with major depression, and healthy control participants (n = 30 for each group). Three operationally defined error types were examined: (a) tracking, (b) perseverative, and (c) proximity. Although both patient groups were slower than the healthy control group, only the schizophrenia group made significantly more errors, particularly tracking errors, suggesting a greater degree of cognitive disorganization. Within-group analysis of a larger group of schizophrenia patients (n = 84) revealed that TMT time was most strongly associated with the Withdrawal-Retardation factor of the Brief Psychiatric Rating scale. In contrast, TMT errors were most strongly associated with the Conceptual Disorganization factor. Comparisons of TMT scores and other cognitive tests showed moderate to high associations with tests of working memory, psychomotor speed, and executive function. Stepwise regression analysis revealed an independent association between Digit Cancellation and Part B Time, indicating a unique contribution of visuomotor scanning to performance. In contrast, Part B errors were uniquely associated with the Verbal Series Attention Test and the Token Test, tests of mental tracking and executive-mediated working memory, respectively. These findings demonstrate the utility of TMT error analysis in revealing cognitive deficits not traditionally captured using completion time as the sole outcome variable.
Death-Ritual and Social Structure in Classical Antiquity

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Structures of the Chromophore Binding Sites in BLUF Domains as Studied by Molecular Dynamics and Quantum Chemical Calculations †

BLUF (blue‐light sensing using FAD) domains constitute a new family of flavin‐based blue light photoreceptors. The photocycle of BLUF is unique in the sense that a few hydrogen bond rearrangements are accompanied by only slight structural changes in the bound chromophore. The hydrogen bond rearrangements upon illumination have been inferred from spectral changes in the chromophore: ∼10 nm redshift of the absorption maximum and ∼16 cm−1 downshift of the C4=O stretching frequency. However, the exact features of the hydrogen bond network around the active site are still the subject of some controversy. In particular, the orientation of a conserved Gln (Gln63 in AppA) is presently one of the most questioned topics in the field. Here we perform molecular dynamics simulations for the wild‐type AppA, AppA1‐124C20S, BlrB and T110078 and furthermore quantum chemical calculations to investigate their spectroscopic properties in the dark and signaling states. On the basis of these results, we reveal the dynamic aspect of hydrogen bonding networks at the active site and propose theoretically reasonable models for the dark and signaling states of the BLUF domains.
Computer simulation of the domain dynamics of a quenched system with a large number of nonconserved order parameters: The grain-growth kinetics.

The domain dynamics of a quenched system with many nonconserved order parameters was investigated by using the time-dependent Ginzburg-Landau kinetic equations. Our computer simulation of a model two-dimensional system produced microstructures remarkably similar to experimental observations of normal grain growth. After a short transient, the average domain or grain radius was found to increase with time as ${\mathit{t}}^{1/2}$, in agreement with most of previous mean-field predictions and more recent Q-state Potts model Monte Carlo simulations.
Science is the search for generalizable processes— clinicians solve complex problems: A reply to Wilson on the importance of not confusing these two things

Barbara Wilson is a creative and influential clinician–scientist who has dedicated her working life to finding ways to rehabilitate brain-damaged people in all the confusing complexity of their damaged brains and lives. Her behavioral training at the Institute of Psychiatry in London inspired her to apply the powerful methods of applied behavior analysis to shape functionally relevant behaviors in the real-life contexts in which these people have to learn new ways of living. I, on the other hand, have chosen to work with people who have specific cognitive deficits such as unilateral neglect (Robertson et al., 1998), impaired sustained attention (Robertson et al., 1997) or goal-neglect-type executive deficits (e.g., Manly et al., 2002). I have specifically avoided trying to carry out research on people with complex problems, specifically because I tried to understand how these strange interchanges we call rehabilitation actually work (Robertson, 2002; Robertson & Murre, 1999). In my research (not, I hasten to add, in my clinical practice), I try to identify relatively pure processes that can be replicated anywhere in the world—not to solve the pressing problems of a particular, unique and complex life.
Incident detection from Tweets by neural network with GPGPU

Twitter is an online social network service to supply the place to be released the short sentences as free. Recently, this service has a few hundred million users, and we can collect their Tweets easily. In this paper, we propose the climatic hazard detection method by using Twitter as a social sensor and by using neural network as a machine learning method. However the data size of the text classification is too large. So, it is required to propose the high-speed learning algorithm. On another front, GPU is the dedicated circuit to draw the graphics, so it has a characteristic that the many simple arithmetic circuits are implemented. This characteristic is hoped to apply the massive parallelism not only graphic processing. In this paper, the neural network is applied to be faster by using GPU. Some methods are considered, and the simple one is employed as comparison to compare with the proposed methods. As the result, the proposed method is 6 times faster than comparison method. This neural network learning method is used for the text classification. 35,379 Tweets were gathered and these were deconstructed to the words by using morphological analysis. The feature vectors were constructed by using the nouns and adjectives selected from the words of the Twitter. We used 860 dimensions feature vectors and classified the positive data or negative. As the result of the classification, we achieved 68 percent accuracy to classify the Tweet data.
Intensification of therapy for children with lower-risk acute lymphoblastic leukemia: long-term follow-up of patients treated on Children's Cancer Group Trial 1881.

PURPOSE From December 1988 through December 1992, the Children's Cancer Group (CCG) conducted a randomized trial (CCG-1881) designed to evaluate the impact of adding a single delayed intensification phase of therapy to standard therapy for patients with newly diagnosed low-risk acute lymphoblastic leukemia (ALL). PATIENTS AND METHODS Patients (n = 778) with newly diagnosed ALL, 2 to 9 years of age at diagnosis with an initial WBC count less than 10,000/microL, were eligible for this protocol. All patients received induction, consolidation, and interim maintenance phases of therapy over the first 16 weeks. At week 16, patients remaining in remission were randomly assigned to receive or not receive a single 7-week delayed intensification (DI) phase of therapy. Maintenance therapy was given in lieu of or after DI, with total duration of therapy approximately 3 years for boys and 2 years for girls. RESULTS Patients randomized to receive DI experienced fewer relapse events in all categories. Kaplan-Meier life-table estimates for continuous complete remission (CCR) at 7 years for the randomized regimens were 77% (SE, 2.4%) for the standard regimen and 83% (SE, 2.7%) for the DI regimen (P =.072). The only prognostic factor of significance post-randomization in this selected low-risk population was the day 14 marrow response (P =.0001). CONCLUSION The addition of a single DI phase of therapy was well tolerated and augmented 7-year CCR by 6% (SE of the difference, 3.3%), resulting in 26% fewer adverse events. Overall survival for eligible patients at 7 years is 90% (SE, 1.2%).
Impact of load modeling on small signal stability investigations

In this paper fundamental investigations concerning the influence of load modeling on small signal stability investigations of power systems are presented. For this purpose the effect of different voltage- and frequency-dependent static load models on oscillation damping and frequency was examined by means of a single-machine infinite-bus system. Frequency domain calculations as well as time domain simulations were carried out. Results are presented by both providing the eigenvalues of the electromechanical oscillation modes and by plotting the electromechanical transients of relevant system quantities after a disturbance. It has been found that an increasing voltage- and frequency-dependency of the load model increases the damping and decreases the eigenfrequency of generator rotor oscillations. The reasons for these influences are discussed and analyzed whereas special attention is paid to the interpretation of the load model's impact on oscillation damping.
Supporting Collaborative Information Spaces for Tourists

We show that virtual communities are able to serve individual, highly specific information needs. Our analysis also indicates that existing technology for communities might not support collaborative creation and maintenance of knowledge well and thus improvements to the interaction and visualization mechanisms might be beneficial. We present and briefly discuss an architecture for a community system supporting communication and collaboration on shared material.