Miracle-dz/UniFAR-FTUs huggingface dataset:
Distinct RPA functions promote eukaryotic DNA replication initiation and elongation

Single-stranded DNA binding proteins (SSBs) are essential for DNA replication across all domains of life, but vary significantly in their structure and subunit composition. The eukaryotic SSB, Replication Protein A (RPA), serves critical functions in DNA replication, the DNA damage response, and DNA repair. We sought to determine the requirements for RPA during eukaryotic DNA replication initiation and elongation. To determine whether the ssDNA-binding activity is sufficient, we tested SSBs from different domains of life in reconstituted S. cerevisiae origin unwinding and DNA replication reactions. Interestingly, E. coli SSB, but not T4 bacteriophage Gp32, fully substitutes for RPA in promoting origin DNA unwinding. Using RPA mutants, we found that only large, multimeric complexes with multiple DNA-binding domains support origin unwinding. In contrast, our studies demonstrated that eukaryotic replication fork function requires specific RPA domains for normal leading- and lagging-strand DNA synthesis. Together, these results reveal new requirements for ssDNA-binding proteins in eukaryotic replication origin unwinding and uncover RPA domains that are critical for faithful replication fork function.
Towards Overcoming Practical Obstacles to Deploying Deep Active Learning

Active learning (AL) is a prominent technique 001 for reducing the annotation effort required for 002 training machine learning models. Deep learn-003 ing offers a solution for several essential obsta-004 cles to deploying AL in practice but introduces 005 many others. One of such problems is the 006 excessive computational resources required to 007 train an acquisition model and estimate its un-008 certainty on instances in the unlabeled pool. 009 We propose two techniques that tackle this is-010 sue for text classiﬁcation and tagging tasks, of-011 fering a substantial reduction of AL iteration 012 duration and the computational overhead in-013 troduced by deep acquisition models in AL. 014 We also demonstrate that our algorithm that 015 leverages pseudolabeling and distilled models 016 overcomes one of the obstacles revealed previ-017 ously in the literature. Namely, it was shown 018 that due to differences between an acquisition 019 model used to select instances during AL and 020 a successor model trained on the labeled data, 021 the beneﬁts of AL can diminish. We show 022 that our algorithm, despite using a smaller and 023 faster acquisition model, is capable of training 024 a more expressive successor with higher per-025 formance. 026
Munich Personal RePEc Archive Physics Laws of Social Science

Economics, and other fields of social science are often criticized as unscientific for their apparent failures to formulate universal laws governing human societies. Whether economics is truly a science is one of the oldest questions. This paper attempts to create such universal laws, and asserts that economics is a branch of quantum physics just like chemistry. Choice is a central concept in economics and other fields of social science, yet there is no corresponding concept of choice in modern physics. This article suggests that by introducing the concept of choice to the existing framework of physics, one can formulate five new physics laws, which establishes a common physics foundation for all fields of social and natural science. Applications in economics, biology, history, and finance prove that these new laws remove the invisible wall, which has been artificially separating social science from natural science. One implication of this article is that to establish a sound scientific foundation for social science requires not only advances in psychology and neurobiology but also a new interpretation of quantum mechanics.
Quantum optical diode with semiconductor microcavities

The semiconductor diode, which acts as an electrical rectifier and allows unidirectional electronic transports, is the key to information processing in integrated circuits. Analogously, an optical rectifier (or diode) working at specific target wavelengths has recently becomes a dreaming device in optical communication and signal processing. In this paper, we propose a scheme to realize an optical diode for photonic transport at the level of few photons. The system consists of two spatially overlapping single-mode semiconductor microcavities coupled via ${\chi ^{(2)}}$ nonlinearities. The photon blockade is predicted to take place in this system. These photon blockade effects can be achieved by tuning the frequency of the input laser field (driving field). Based on those blockades, we derive analytically the single- and two-photon current in terms of zero and finite-time delayed two-order correlation function. The results suggest that the system can serve as an single- and two-photon quantum optical diodes which allow transmission of photons in one direction much more efficiently than in the other.
Preliminary study: quantification of chronic pain from physiological data

Supplemental Digital Content is Available in the Text. Preliminary evidence suggests that physiological variables collected with our low-cost pain meter are correlated with chronic pain, both for individuals and populations. Abstract Introduction: It is unknown if physiological changes associated with chronic pain could be measured with inexpensive physiological sensors. Recently, acute pain and laboratory-induced pain have been quantified with physiological sensors. Objectives: To investigate the extent to which chronic pain can be quantified with physiological sensors. Methods: Data were collected from chronic pain sufferers who subjectively rated their pain on a 0 to 10 visual analogue scale, using our recently developed pain meter. Physiological variables, including pulse, temperature, and motion signals, were measured at head, neck, wrist, and finger with multiple sensors. To quantify pain, features were first extracted from 10-second windows. Linear models with recursive feature elimination were fit for each subject. A random forest regression model was used for pain score prediction for the population-level model. Results: Predictive performance was assessed using leave-one-recording-out cross-validation and nonparametric permutation testing. For individual-level models, 5 of 12 subjects yielded intraclass correlation coefficients between actual and predicted pain scores of 0.46 to 0.75. For the population-level model, the random forest method yielded an intraclass correlation coefficient of 0.58. Bland–Altman analysis shows that our model tends to overestimate the lower end of the pain scores and underestimate the higher end. Conclusion: This is the first demonstration that physiological data can be correlated with chronic pain, both for individuals and populations. Further research and more extensive data will be required to assess whether this approach could be used as a “chronic pain meter” to assess the level of chronic pain in patients.
Integrative single cell and spatial transcriptomics of colorectal cancer reveals multicellular functional units that support tumor progression

While advances in single cell genomics have helped to chart the cellular components of tumor ecosystems, it has been more challenging to characterize their specific spatial organization and functional interactions. Here, we combine single cell RNA-seq and spatial transcriptomics by Slide-seq, to create a detailed spatial map of healthy and dysplastic colon cellular ecosystems and their association with disease progression. We profiled an inducible genetic CRC mouse model that recapitulates key features of human CRC, assigned cell types and epithelial expression programs to spatial tissue locations in tumors, and computationally used them to identify the regional features spanning different cells in the same spatial niche. We find that tumors were organized in cellular neighborhoods, each with a distinct composition of cell subtypes, expression programs, and local cellular interactions. Three cellular neighborhood archetypes were associated with tumor progression, were active at the same time in different spatial parts of the same tumor, involved dysplasia-specific cellular layouts, and relied on distinct mechanisms: (1) inflammatory epithelial regions with endothelial cells and monocytes expressing angiogenesis, inflammation and invasion programs; (2) epithelial stem-like regions, associated with plasma and B cell activity; and (3) epithelial-to-mesenchymal transition (EMT) regions with dysplastic cells expressing a Wnt signaling program. Comparing to scRNA-seq and Slide-seq data from human CRC, we find that both cell composition and layout features were conserved in both species, with mouse archetypal neighborhoods correlated with malignancy and clinical outcome in human patient tumors, highlighting the relevance of our findings to human disease.
Molecular view of ER membrane remodeling by the Sec61/TRAP translocon

Protein translocation across the endoplasmic reticulum (ER) membrane is an essential initial step in protein entry into the secretory pathway. The conserved Sec61 protein translocon facilitates polypeptide translocation and coordinates cotranslational polypeptide processing events. In cells, the majority of Sec61 is stably associated with a heterotetrameric membrane protein complex, the translocon associated protein complex (TRAP), yet the mechanism by which TRAP assists in polypeptide translocation or cotranslational modifications such as N-glycosylation remains unknown. Here, we demonstrate the structure of the core Sec61/TRAP complex bound to a mammalian ribosome by Cryo-EM. The interactions with ribosome anchor the Sec61/TRAP complex in a conformation that renders the ER membrane locally thinner by significantly curving its the lumenal leaflet. We propose a model for how TRAP stabilizes the ribosome exit tunnel to assist nascent polypeptide insertion through Sec61 and provides a ratcheting mechanism into the ER lumen by direct polypeptide interactions.
Integrated Bioinformatics Analysis Reveals Novel miRNA as Biomarkers Associated with Preeclampsia

Preeclampsia is a leading cause of perinatal maternal-foetal mortality and morbidity. This study aims to identify the key microRNAs (miRNA) in preeclampsia and uncover their potential functions. We downloaded the miRNA expression profile of GSE119799 for plasma and GSE177049 for the placenta. Each dataset consisted of five patients (PE) and five controls (N). From a technical point of view, we analysed the counts per million (CPM) for both datasets, highlighting 358 miRNAs in common, 78 unique for plasma and 298 unique for placenta. At the same time, we performed an expression differential analysis (|logFC| ≥ 1|and FDR ≤ 0.05) to evaluate the biological impact of the miRNAs. This approach allowed us to highlight 321 miRNAs in common between plasma and placenta, within which four were upregulated in plasma. Furthermore, the same analysis revealed five miRNAs expressed exclusively in plasma; these were also upregulated. In conclusion, the in-depth bioinformatics analysis conducted during our study will allow us, on the one hand, to verify the targets of each of the nine identified miRNAs; on the other hand, to use them both as new non-invasive biomarkers and as therapeutic targets for the development of personalised treatments.
Genetic basis of a seasonal life-history polyphenism

Seasonal polyphenisms are common across the animal and plant kingdom yet we understand the explicit interactions between genetics and environment for only a few taxa. Are the genomic regions and their variants associated with the trait the same or different across environments? Is the response to selection shared or different across different “background” selection environments? Offspring type in the sacoglossan sea slug Alderia willowi is a seasonally modulated interaction between genotype and phenotype that results in offspring of wildly different developmental trajectories. In a genome-wide association test I found 41 SNPs associated with offspring type. In an evolve and resequence experiment I found thousands of loci changed in frequency following selection. These loci were partially shared (37%) between low and high salinity. Of the 41 candidate SNPs identified in the GWAS only seven also showed significant allele frequency change across replicates in the selection experiments with four in high salinity, two in low and one in both. This reveals a broad pattern of allele frequency change that is largely unique to the environment in which selection for the same phenotype occurs. The results presented in this paper showcase the ability of phenotypic plasticity to move the phenotype independent of the genotype and thus maintain the polyphenism that is so striking in this species.
Research Online Research Online Behavioral Market Segmentation of Binary Guest Survey Data with Bagged Behavioral Market Segmentation of Binary Guest Survey Data with Bagged Clustering Clustering

Abstract Binary survey data from the Austrian National Guest Survey conducted in the summer season of 1997 were used to identify behavioural market segments on the basis of vacation activity information. Bagged clustering overcomes a number of diffculties typically encountered when partitioning large binary data sets: The partitions have greater structural stability over repetitions of the algorithm and the question of the "correct" number of clusters is less important because of the hierarchical step of the cluster analysis. Finally, the bootstrap part of the algorithm provides means for assessing and visualizing segment stability for each input variable. Abstract. Binary survey data from the Austrian National Guest Survey conducted in the summer season of 1997 were used to identify behavioral market segments on the basis of vacation activity information. Bagged clustering overcomes a number of diﬃculties typically encountered when partitioning large binary data sets: The partitions have greater structural stability over repetitions of the algorithm and the question of the “correct” number of clusters is less important because of the hierarchical step of the cluster analysis. Finally, the bootstrap part of the algorithm provides means for assessing and visualizing segment stability for each input variable.
Robust and adjustable C-shaped electron vortex beams

Wavefront engineering is an important quantum technology, often applied to the production of states carrying orbital angular momentum (OAM). Here, we demonstrate the design and production of robust C-shaped beam states carrying OAM, in which the usual doughnut-shaped transverse intensity structure of the vortex beam contains an adjustable gap. We find that the presence of the vortex lines in the core of the beam is crucial for maintaining the stability of the C-shape structure during beam propagation. The topological charge of the vortex core controls mainly the size of the C-shape, while its opening angle is related to the presence of vortex–anti-vortex loops. We demonstrate the generation and characterisation of C-shaped electron vortex beams, although the result is equally applicable to other quantum waves. C-shaped electron vortex beams have potential applications in nanoscale fabrication of planar split-ring structures and three-dimensional chiral structures as well as depth sensing and magnetic field determination through rotation of the gap in the C-shape.
AN ANTENNA ARRAY OF MILLIMETER WAVE FREQUENCY FOR 5G APPLICATIONS

— Nowadays there is a rapid increase in the usage of moblies for either voice calls or for the browsing or for watching HD videos online. There is a huge traffic in the usage of frequency[1] band of present technology that is 4G technology. So to overcome this problem so many scientists did research and came up with a solution that to upgrade to 5G technology.5G technology is very fast and has higher bandwidth with higher datarate which is used to over come the problems caused due to higher traffic in the network. One of the important device in the 5G technology is antenna. In this paper, we are going to present the design and Time domain Analysis[2] for Dipole Patch array antenna. The Antenna is made with Rogers substrate of Di-electric constant which has High Dielectric Strength ε=3.55 to operate at millimeter wave frequencies and is designed to have Compact size, and model. The antenna is taken care of by Co-planar Waveguide Transmission line and has a smaller absolute size.
Erythrocyte, Whole Blood, Plasma, and Blubber Fatty Acid Profiles in Oceanaria-Based versus Wild Alaskan Belugas (Delphinapterus leucas)

This investigation compared the fatty acid (FA) levels found in erythrocyte (RBC) membranes, plasma, whole blood (WB), and blubber from wild Alaskan (Bristol Bay) belugas (Delphinapterus leucas) (BBB, n = 9) with oceanaria-based belugas (OBB, n = 14) fed a controlled diet consisting of primarily herring (Clupea harengus) and capelin (Mallotus villosus). FA patterns in RBCs, WB, and plasma varied considerably between BBB and OBB animals. Focusing on RBC FA levels of known dietary origin, the OBBs had markedly higher levels of 20:1n9,11 and 22:1n9,11. RBC levels of these fatty acids were 1% and 0.2% in the BBBs, but 8.2% and 4.5%, respectively, in the OBBs (p < 0.05 both). These long-chain mono-unsaturated FAs (LC-MUFAs) are rich in herring and capelin but not in the prey species (i.e., salmonids, smelt, cod, and shrimp) generally available to BBBs. As for the marine omega-3 poly-unsaturated fatty acids [PUFAs; 20:5n3 (eicosapentaenoic acid) and 22:6n3 (docosahexaenoic acid)], the former was higher in the OBBs vs. BBBs (16% vs. 11%, p < 0.05), but the latter was low and similar in both (3.8% vs. 4%). Similar patterns were seen in the other sample types, except that DHA% was higher in BBB than OBB animals in both plasma (12.6% vs. 8.7%) and in blubber (12% vs. 4.9%) (p < 0.05). A physiologically important omega-6 PUFA, 20:4n6 (arachidonic acid) was approximately 2× higher in BBB than OBB within RBC (22% vs. 12%), WB (16% vs. 7%), plasma (11.5% vs. 4.6%) and blubber (4.6% vs. 2.4%), respectively. While blubber FAs have been evaluated historically and relatively easy to procure with biopsy darts in the field, this study proposes that blood-based FAs collected during health assessments or subsistence hunts, especially RBC or WB FAs, may be more convenient to handle using dried blood spot cards (DBS) with limited cold storage and simplifies shipping requirements, and may more accurately reflect tissue FA status.
Effects of different inorganic selenium levels in laying quails (Coturnix coturnix Japonica) diets on performance, egg quality, and serum biochemical parameters

Inorganic selenium supplementation in poultry diet has been controversial. It has been linked that the excess and deficiency of this mineral can lead to health problems in these animals. However, this fact is not so evident in quails. In this research 120 female quails (220.6 ± 8.2 g) at 10 weeks of age were allocated to five treatment groups with six replicates of four quails in each. Experimental diets were formed by adding 0, 0.25, 0.50, 0.75 or1.00 mg/kg of inorganic selenium (sodium-selenite) to the diet containing 0.12 mg/kg of selenium. We observed that performance parameters, mortality, egg external, and internal quality of quails were not affected by the supplementation of inorganic selenium to the diet Serum glucose (P = 0.0020) and creatinine (P = 0.0333) levels were affected by inorganic selenium supplementation, but no differences were found for other parameters among those treatments. The addition of 0.50 mg/kg of inorganic selenium to the diet increased serum glucose levels of laying quails compared with the control group. While serum creatinine level was maximized with the addition of 0.25 mg/kg inorganic selenium to the diet, and it was minimized with the addition of 0.50 mg/kg inorganic selenium. Supplementation with inorganic selenium (0 to 1.00 mg/kg) in laying quail diets did not have any adverse effect on performance, mortality, and egg quality during the study. No abnormalities were found in the serum parameters that would lead to the suspicion of metabolic disease in the quails.
In Vitro Shoot Regeneration of Hibiscus acetosella, Muskmelon, Watermelon, and Winged Bean1

Shoot regeneration has been obtained from leaf and/or cotyledon explants of winged bean [Psophocarpus tetragonolobus (L.) D.C.], Hibiscus acetoseiia Welw. ex. Hiern, muskmelon (Cucumis melo L.), and watermelon [Citrullus lanatus (Thunb.) Mat-sum & Nakai] on 2 media designated HC and BR-1.
150 years old and still alive: eigenproblems

Linear eigenproblems continue to be an important and highly relevant area of research in numerical linear algebra. Therefore, it should be no surprise that numerical algorithms for eigenproblems are among the oldest known in the modern literature. In 1846, exactly 150 years ago, Jacobi [33] wrote his famous paper on the computation of solutions for the problem Ax = x, with AT = A. Strictly speaking, this is not correct, since matrix notation was unknown at that time. So Jacobi formulated the problem in terms of systems of equations, written out elementwise. His paper contains computational elements that are still in use, like the plane rotations for making a system more diagonally dominant, and the (Gauss)-Jacobi iteration method for diagonally dominant systems. These elements were combined in his approach for the computation of eigenvalues, together with a clever way of setting up a correction equation for eigenvalue and eigenvector approximations.
COLLECTIVE OUTFLOW FROM A SMALL MULTIPLE STELLAR SYSTEM

The formation of high-mass stars is usually accompanied by powerful protostellar outflows. Such high-mass outflows are not simply scaled-up versions of their lower-mass counterparts, since observations suggest that the collimation degree degrades with stellar mass. Theoretically, the origins of massive outflows remain open to question because radiative feedback and fragmentation of the accretion flow around the most massive stars, with M > 15 M☉, may impede the driving of magnetic disk winds. We here present a three-dimensional simulation of the early stages of core fragmentation and massive star formation that includes a subgrid-scale model for protostellar outflows. We find that stars that form in a common accretion flow tend to have aligned outflow axes, so that the individual jets of multiple stars can combine to form a collective outflow. We compare our simulation to observations with synthetic H2 and CO observations and find that the morphology and kinematics of such a collective outflow resembles some observed massive outflows, such as Cepheus A and DR 21. We finally compare physical quantities derived from simulated observations of our models to the actual values in the models to examine the reliability of standard methods for deriving physical quantities, demonstrating that those methods indeed recover the actual values to within a factor of two to three.
Sensitivity of the transverse flow to the symmetry energy

We study the sensitivity of transverse flow to symmetry energy in the Fermi energy region as well as at high energies. We find that transverse flow is sensitive to symmetry energy and its density dependence in the Fermi energy region. We also show that the transverse flow can address the symmetry energy at densities about twice the saturation density; however, it shows insensitivity to the symmetry energy at densities {rho}/{rho}{sub 0}>2. The mechanism for the sensitivity of transverse flow to symmetry energy and its density dependence is also discussed.