Miracle-dz/UniFAR-FTUs huggingface dataset:
Day–night cycles and the sleep-promoting factor, Sleepless, affect stem cell activity in the Drosophila testis

Significance Daily rhythms in light coordinate many biological functions over the 24-h day, facilitating the adaptation of organisms to the environment. A crucial task accomplished routinely by all multicellular organisms is the maintenance of tissue homeostasis through the activity of adult stem cells, which generate new cells when required. Using a classic Drosophila stem cell niche, we show that the frequency of stem cell divisions is rhythmic in a day–night cycle. In addition, our data, which show that stem cell divisions are increased in a short-sleeping mutant, suggest that mechanisms regulating sleep–wake rhythms may also influence stem cell activity. Our findings provide links between environmental cycles, behavioral states, and maintenance of tissue integrity by stem cells. Adult stem cells maintain tissue integrity and function by renewing cellular content of the organism through regulated mitotic divisions. Previous studies showed that stem cell activity is affected by local, systemic, and environmental cues. Here, we explore a role of environmental day–night cycles in modulating cell cycle progression in populations of adult stem cells. Using a classic stem cell system, the Drosophila spermatogonial stem cell niche, we reveal daily rhythms in division frequencies of germ-line and somatic stem cells that act cooperatively to produce male gametes. We also examine whether behavioral sleep–wake cycles, which are driven by the environmental day–night cycles, regulate stem cell function. We find that flies lacking the sleep-promoting factor Sleepless, which maintains normal sleep in Drosophila, have increased germ-line stem cell (GSC) division rates, and this effect is mediated, in part, through a GABAergic signaling pathway. We suggest that alterations in sleep can influence the daily dynamics of GSC divisions.
Life Course Socioeconomic Position: Associations with Cardiac Structure and Function at Age 60-64 Years in the 1946 British Birth Cohort

Although it is recognized that risks of cardiovascular diseases associated with heart failure develop over the life course, no studies have reported whether life course socioeconomic inequalities exist for heart failure risk. The Medical Research Council’s National Survey of Health and Development was used to investigate associations between occupational socioeconomic position during childhood, early adulthood and middle age and measures of cardiac structure [left ventricular (LV) mass index and relative wall thickness (RWT)] and function [systolic: ejection fraction (EF) and midwall fractional shortening (mFS); diastolic: left atrial (LA) volume, E/A ratio and E/e’ ratio)]. Different life course models were compared with a saturated model to ascertain the nature of the relationship between socioeconomic position across the life course and each cardiac marker. Findings showed that models where socioeconomic position accumulated over multiple time points in life provided the best fit for 3 of the 7 cardiac markers: childhood and early adulthood periods for the E/A ratio and E/e’ ratio, and all three life periods for LV mass index. These associations were attenuated by adjustment for adiposity, but were little affected by adjustment for other established or novel cardio-metabolic risk factors. There was no evidence of a relationship between socioeconomic position at any time point and RWT, EF, mFS or LA volume index. In conclusion, socioeconomic position across multiple points of the lifecourse, particularly earlier in life, is an important determinant of some measures of LV structure and function. BMI may be an important mediator of these associations.
VIP21, a 21-kD membrane protein is an integral component of trans-Golgi- network-derived transport vesicles

In simple epithelial cells, apical and basolateral proteins are sorted into separate vesicular carriers before delivery to the appropriate plasma membrane domains. To dissect the putative sorting machinery, we have solubilized Golgi-derived transport vesicles with the detergent CHAPS and shown that an apical marker, influenza haemagglutinin (HA), formed a large complex together with several integral membrane proteins. Remarkably, a similar set of CHAPS-insoluble proteins was found after solubilization of a total cellular membrane fraction. This allowed the cloning of a cDNA encoding one protein of this complex, VIP21 (Vesicular Integral-membrane Protein of 21 kD). The transiently expressed protein appeared on the Golgi-apparatus, the plasma membrane and vesicular structures. We propose that VIP21 is a component of the molecular machinery of vesicular transport.
Multiway range trees: scalable IP lookup with fast updates

In this paper, we introduce a new IP lookup scheme with worst-case search and update time of O(log n), where n is the number of prefixes in the forwarding table. Our scheme is based on a new data structure, a multiway range tree. While existing lookup schemes are good for IPv4, they do not scale well in both lookup speed and update costs when addresses grow longer as in the IPv6 proposal. Thus our lookup scheme is the first lookup scheme to offer fast lookups and updates for IPv6 while remaining competitive for IPv4.
Survey of Computer Vision and Machine Learning in Gastrointestinal Endoscopy

This paper attempts to provide the reader a place to begin studying the application of computer vision and machine learning to gastrointestinal (GI) endoscopy. They have been classified into 18 categories. It should be be noted by the reader that this is a review from pre-deep learning era. A lot of deep learning based applications have not been covered in this thesis.
Morphological Biosignatures in Volcanic Rocks – Applications for Life Detection on Mars

The exploration of Mars is largely based on comparisons with Earth analogue environments and processes. The up-coming NASA Mars mission 2020 and ExoMars 2020 has the explicit aim to search for signs of life on Mars. During preparations for the missions, glaring gaps in one specific field was pointed out: the lack of a fossil record in igneous and volcanic rock. Earth´s fossil record is almost exclusively based on findings in sedimentary rocks, while igneous rocks have been considered barren of life, including a fossil record of past life. Since martian volcanic rocks will be targeted in the search for biosignatures, the lack of a terrestrial analogue fossil record is an obvious impediment to the scientific aim of the mission. Here we will briefly review the knowledge of microscopic life in deep rock and deep time. Focus will be on underexplored environments in subseafloor crustal rocks, and on ancient environments harbouring early prokaryotic and eukaryotic lineages. We will highlight some of the aspects that need immediate attention and further investigations to meet the scientific goals of the missions. The current paper is a first step towards the long-term aim is to establish an atlas of the fossil record in volcanic rocks, which can be of use for the up-coming space missions.
Testing for Panel Unit Roots under General Cross-sectional Dependence

In this article, we generalize four tests of multivariate linear hypothesis to panel data unit root testing. The test statistics are invariant to certain linear transformations of data and therefore simulated critical values may conveniently be used. It is demonstrated that all four tests remains well behaved in cases of where there are heterogeneous alternatives and cross-correlations between marginal variables. A Monte Carlo simulation is included to compare and contrast the tests with two well-established ones.
Concrete Types for TypeScript

Typescript extends JavaScript with optional type annotations that are, by design, unsound and, that the Typescript compiler discards as it emits code. This design point preserves programming idioms developers are familiar with, and allows them to leave their legacy code unchanged, while offering a measure of static error checking in parts of the program that have type annotations. We present an alternative design for TypeScript, one where it is possible to support the same degree of dynamism, but where types can be strengthened to provide hard guarantees. We report on an implementation, called StrongScript, that improves runtime performance of typed programs when run on a modified version of the V8 JavaScript engine.
Analyzing onset of nonlinearity of a colloidal gel at the critical point

In this work we study onset of nonlinear rheological behavior of a colloidal dispersion of a synthetic hectorite clay, Laponite, at the critical gel state while undergoing sol-gel transition. When subjected to step strain in the nonlinear regime, the relaxation modulus shifts vertically to the lower values such that the deviation from linearity can be accommodated using a strain dependent damping function. We also perform creep-recovery and start-up shear experiments on the studied colloidal dispersion at the critical gel state and monitor deviation in response as the flow becomes nonlinear. A quasi-linear integral model is developed with the time-strain separable relaxation modulus to account for the effect of nonlinear deformation. Remarkably, the proposed model predicts the deviation from linearity in the creep-recovery and start-up shear experiments very well leading to a simple formulation to analyze the onset of nonlinear rheological behavior in the critical gels. We also analyze the energy dissipation during the nonlinear deformation and validate the Bailey criterion using the developed viscoelastic framework.
Ultraviolet Extinction Properties of the 30 Dor Nebula and Interpreting Observations of Starburst Clusters

Recent investigations of the extinction law in 30 Dor and the Tarantula Nebula, at optical and near-infrared wavelengths, have revealed a ratio of total to selective extinction RV = AV/E(B − V) of about 4.5. This indicates a larger fraction of big grains than in the Galactic diffuse interstellar medium (ISM). Possible origins include coalescence of small grains, small grain growth, selective destruction of small grains, and fresh injection of big grains. From a study of the ultraviolet extinction properties of three massive stars in the 30 Dor nebula (R139, R140, R145), observed with the International Ultraviolet Explorer, we show that the excess of big grains does not come at the expense of small grains, which are still present and possibly even more abundant. Fresh injection of large grains appears to be the dominant mechanism. A process able to naturally account for this in environments such as the Tarantula nebula, where formation of massive stars has been ongoing for over ∼20 Myr, is the explosion of massive stars as SNe II. The ensuing change in the conditions of the ISM is only temporary, lasting less than ∼100 Myr, because shattering and shocks will eventually break and destroy the bigger grains. However, this is the only time when star-forming regions are detectable as such in starburst and high-redshift galaxies, and we highlight the complexity inherent in interpreting observations of star-forming regions in these environments. If the extinction characteristics are not known properly, any attempts to derive quantitative physical parameters are bound to fail.
Estimation of Human Internal Temperature from Wearable Physiological Sensors

We evaluated a Kalman filter (KF) approach to modeling the physiology of internal temperature viewed through “noisy” non-invasive observations of heart rate. Human core body temperature (Tcore) is an important measure of thermal state, e.g., hypo- or hyperthermia, but is difficult to measure using non-invasive wearable sensors. We estimated parameters for a discrete KF model from data collected during several Military training events and from distance runners (n=38). Model performance was evaluated in 25 physically-active subjects who participated in various laboratory and field studies involving exercise of 2-to-8 h duration at ambient temperatures of 20 to 40°C. Overall, the KF model’s estimate of Tcore had a root mean square error of 0.30±0.13 ºC from the observed Tcore, and was within ± 0.5 ºC over 85% of the time. The benefit of the KF approach is that it requires only one input while current state of the art models typically require multiple inputs including individual anthropometrics, metabolic rate, clothing characteristics, and environmental conditions. This state estimation problem in computational physiology illustrates the potential for collaboration between the artificial intelligence and ambulatory physiological monitoring communities.
Establishment in MANET ’ s : Swarm Intelligence

We present some properties of trust establishment in mobile , ad-hoc networks and illustrate how they differ from those of trust establishment in the Internet. We present a framework for trust establishment in mobile ad-hoc networks and argue that peer-to-peer networks are especially suitable to solve the problems of generation, distribution, and discovery of trust evidence in mobile ad-hoc networks. We develop a new scheme based on swarm intelligence and demonstrate its advantages over the peer to peer scheme. We evaluate our approach through simulation with NS-2.
Gene Expression, Molecular Class Changes, and Pathway Analysis after Neoadjuvant Systemic Therapy for Breast Cancer

Purpose: To examine gene expression differences between pre- and post-neoadjuvant systemic therapy (NST) specimens of breast cancers and identify biologic changers that may lead to new therapeutic insights. Methods: Gene expression data from prechemotherapy fine needle aspiration specimens were compared with resected residual cancers in 21 patients after 4 to 6 months of NST. We removed stroma-associated genes to minimize confounding effects. PAM50 was used to assign molecular class. Paired t test and gene set analysis were used to identify differentially expressed genes and pathways. Results: The ER and HER2 status based on mRNA expression remained stable in all but two cases, and there were no changes in proliferation metrics (Ki67 and proliferating cell nuclear antigen expression). Molecular class changed in 8 cases (33.3%), usually to normal-like class, which was associated with low residual cancer cell cellularity. The expression of 200 to 600 probe sets changed between baseline and post-NST samples. In basal-like cancers, pathways driven by increased expression of phosphoinositide 3-kinase, small G proteins, and calmodulin-dependent protein kinase II and energy metabolism were enriched, whereas immune cell–derived and the sonic hedgehog pathways were depleted in residual cancer. In non–basal-like breast cancers, notch signaling and energy metabolism (e.g., fatty acid synthesis) were enriched and sonic hedgehog signaling and immune-related pathways were depleted in residual cancer. There was no increase in epithelial–mesenchymal transition or cancer stem cell signatures. Conclusions: Our data indicate that energy metabolism related processes are upregulated and immune-related signals are depleted in residual cancers. Targeting these biologic processes may represent promising adjuvant treatment strategies for patients with residual cancer. Clin Cancer Res; 18(4); 1109–19. ©2012 AACR.
An update on cutaneous aging treatment using herbs

Skin aging is caused by several factors. Ultraviolet (UV) exposure as well as oxidative stress elevates inflammatory mediators causing degradation of the extracellular matrix, which is regarded as the major cause of skin wrinkles, one of the signs of aging. Topical applications of active ingredients protect against dermal photodamage and scavenge radicals that can delay skin aging. Matrix metalloproteinase inhibitors against degradation of collagen, elastin, and hyaluronan are the key strategy to combat cutaneous aging. In addition, active ingredients with the efficacy to enhance extracellular matrix production, including those with UV protection efficacy, play an important role in protecting the skin from aging. Naturally derived compounds for combating skin wrinkles are gaining more interest among the consumers as they are perceived to be milder, safer, and healthier. This article, therefore, briefly addresses the causes of skin aging and extensively summarizes on herbs appraisal for skin wrinkles treatment. Therefore, delaying aging of skin using the functional herbs would maintain the individual's appearance with high esthetic and psychosocial impacts.
Antiepileptic drugs induce subcritical dynamics in human cortical networks

Significance Activity propagation in cortex must be carefully balanced to prevent premature die-out and runaway excitation. In this study, large-scale human electrophysiology data and systematic pharmacological control of cortical network interactions are used to provide evidence that cortical network dynamics is controlled by network interactions according to a branching process. The results provide a missing link to the branching process theory of cortical network function with implications for understanding the foundations of cortical excitability, its monitoring in conditions like epilepsy, and how the balance of excitation and inhibition shapes the capacity of temporal information integration in cortical networks. Cortical network functioning critically depends on finely tuned interactions to afford neuronal activity propagation over long distances while avoiding runaway excitation. This importance is highlighted by the pathological consequences and impaired performance resulting from aberrant network excitability in psychiatric and neurological diseases, such as epilepsy. Theory and experiment suggest that the control of activity propagation by network interactions can be adequately described by a branching process. This hypothesis is partially supported by strong evidence for balanced spatiotemporal dynamics observed in the cerebral cortex; however, evidence of a causal relationship between network interactions and cortex activity, as predicted by a branching process, is missing in humans. Here this cause–effect relationship is tested by monitoring cortex activity under systematic pharmacological reduction of cortical network interactions with antiepileptic drugs. This study reports that cortical activity cascades, presented by the propagating patterns of epileptic spikes, as well as temporal correlations decline precisely as predicted for a branching process. The results provide a missing link to the branching process theory of cortical network function with implications for understanding the foundations of cortical excitability and its monitoring in conditions like epilepsy.
Drosophila Neurotrophins Reveal a Common Mechanism for Nervous System Formation

Neurotrophic interactions occur in Drosophila, but to date, no neurotrophic factor had been found. Neurotrophins are the main vertebrate secreted signalling molecules that link nervous system structure and function: they regulate neuronal survival, targeting, synaptic plasticity, memory and cognition. We have identified a neurotrophic factor in flies, Drosophila Neurotrophin (DNT1), structurally related to all known neurotrophins and highly conserved in insects. By investigating with genetics the consequences of removing DNT1 or adding it in excess, we show that DNT1 maintains neuronal survival, as more neurons die in DNT1 mutants and expression of DNT1 rescues naturally occurring cell death, and it enables targeting by motor neurons. We show that Spätzle and a further fly neurotrophin superfamily member, DNT2, also have neurotrophic functions in flies. Our findings imply that most likely a neurotrophin was present in the common ancestor of all bilateral organisms, giving rise to invertebrate and vertebrate neurotrophins through gene or whole-genome duplications. This work provides a missing link between aspects of neuronal function in flies and vertebrates, and it opens the opportunity to use Drosophila to investigate further aspects of neurotrophin function and to model related diseases.
Worldwide Doublets of Large Shallow Earthquakes 1149

We investigated all the pairs of Mw >-7.5 shallow earthquakes in the Harvard catalog that occurred at a centroid distance of less than 100 km. We showed that most of these pairs have similar focal mechanisms. Because these earthquakes generally should have focal regions in excess of 100 km diameter, their rupture zones apparently intersect. For all these pairs, the time interval is significantly less than the time span needed for plate motion to accumulate the strain released by the first event. These observations conflict strongly with quasi-periodic recurrence models on which the seismic gap hypothesis is based. Power-law recurrence fits these earthquake observations much better.
Endocardial Border Delineation during Dobutamine Infusion Using Contrast Echocardiography

Background: A significant percentage of pharmacologic stress echocardiograms produce suboptimal images despite the use of second harmonic imaging. Intravenous continuous infusion of myocardial ultrasound contrast may enhance endocardial border delineation during dobutamine‐atropine stress echocardiography (DASE), improving wall‐motion analysis. Patients and Methods: We prospectively studied 68 patients (41 males and 27 females), mean age 58 years, with DASE during intravenous infusion of contrast using second harmonic imaging. Dobutamine was infused in scalar doses of 5 μg/kg/min to 40 μg/kg/min, and atropine was administered in doses of up to 1 mg. We diluted 0.1 mL of perfluorocarbon‐exposed sonicated dextrose albumin (PESDA) microbubbles into 80 mL of saline solution, which was used for continuous intravenous infusion. Blinded reviewers used a 16‐segment model at rest and peak DASE to analyze segmental wall delineation in two sets of images for each patient, with and without contrast. An endocardial delineation score of 0–3 (nondelineated to excellent delineation) was given to each segment. An endocardial delineation score index (EDSI), the number of endocardial delineation scores for each set of images divided by 16, was created. Results: The analysis of the mean EDSI for the 2176 segments was 1.46 (± 0.43) at rest and 1.30 (± 0.48) at peak for noncontrast images and 2.22 (± 0.52) and 2.29 (± 0.52) for contrast images. Complete left ventricle opacification was obtained in all patients, with a mean dose of 4 mL/min, although in 15 (22%) patients, signs of apical bubble destruction occurred. There were 1768 (81%) of 2176 segments delineated without contrast enhancement and 2057 (95%) of 2176 with enhancement (P < 0.05). Conclusion: Continuous infusion of myocardial ultrasound contrast improves endocardial border delineation using second harmonic imaging in patients undergoing DASE.