Miracle-dz/UniFAR-FTUs huggingface dataset:
Population Levels Assessment of the Distribution of Disease-Associated Variants With Emphasis on Armenians – A Machine Learning Approach

Background: During the last decades a number of genome-wide association studies (GWASs) has identified numerous single nucleotide polymorphisms (SNPs) associated with different complex diseases. However, associations reported in one population are often conflicting and did not replicate when studied in other populations. One of the reasons could be that most GWAS employ a case-control design in one or a limited number of populations, but little attention was paid to the global distribution of disease-associated alleles across different populations. Moreover, the majority of GWAS have been performed on selected European, African, and Chinese populations and the considerable number of populations remains understudied. Aim: We have investigated the global distribution of so far discovered disease-associated SNPs across worldwide populations of different ancestry and geographical regions with a special focus on the understudied population of Armenians. Data and Methods: We have used genotyping data from the Human Genome Diversity Project and of Armenian population and combined them with disease-associated SNP data taken from public repositories leading to a final dataset of 44,234 markers. Their frequency distribution across 1039 individuals from 53 populations was analyzed using self-organizing maps (SOM) machine learning. Our SOM portrayal approach reduces data dimensionality, clusters SNPs with similar frequency profiles and provides two-dimensional data images which enable visual evaluation of disease-associated SNPs landscapes among human populations. Results: We find that populations from Africa, Oceania, and America show specific patterns of minor allele frequencies of disease-associated SNPs, while populations from Europe, Middle East, Central South Asia, and Armenia mostly share similar patterns. Importantly, different sets of SNPs associated with common polygenic diseases, such as cancer, diabetes, neurodegeneration in populations from different geographic regions. Armenians are characterized by a set of SNPs that are distinct from other populations from the neighboring geographical regions. Conclusion: Genetic associations of diseases considerably vary across populations which necessitates health-related genotyping efforts especially for so far understudied populations. SOM portrayal represents novel promising methods in population genetic research with special strength in visualization-based comparison of SNP data.
Corilagin Interferes With Toll-Like Receptor 3-Mediated Immune Response in Herpes Simplex Encephalitis

Herpes simplex encephalitis (HSE) is the most common infectious disease of the central nervous system worldwide. However, the pathogenesis of HSE is not clear. Research has shown that the immune response mediated by the toll-like receptor 3 (TLR3) signaling pathway is essential to protect the central nervous system against herpes simplex virus (HSV) infection. However, an excessive immune response may cause tissue damage accompanied by pathological changes. The aim of this study was to explore the molecular mechanism via which corilagin controls HSE through the TLR3 signaling pathway in vitro and in vivo. Cells and mice were pre-treated with polyriboinosinic polyribocytidylic acid [poly(I:C)] or HSV type 1, and then treated with corilagin. After treatment, the mRNA and protein levels of TLR3, TLR-like receptor-associated interferon factor (TRIF), tumor necrosis factor (TNF) receptor type 1-associated DEATH domain protein (TRADD), TNF receptor-associated factor (TRAF) 3 and 6, nuclear factor-kappa-B (NF-κB) essential modulator (NEMO), P38, and interferon regulatory factor 3 (IRF3) were decreased. Interleukin-6 (IL-6), TNF-α, and type 1 interferon-β were also decreased. When TLR3 expression was silenced or increased, corilagin still inhibited the expression of TLR3 and its downstream mediators. Hematoxylin-eosin (HE) staining and immunohistochemical examinations of mouse brain tissues revealed that corilagin lessened the degree of brain inflammation. Altogether, these results suggest that corilagin may regulate the immune response in HSE and relieve inflammatory injury by interfering with the TLR3 signaling pathway.
Preliminary Comparison and Analyses of Air Temperature at 2m Height between Three Reanalysis Data-Sets and Observation in the East of Qinghai-Xiang Plateau

The monthly mean surface air temperature at 2mfrom the NCEP/DOE,ERA-interim and JRA-25reanalysis data-sets were respectively compared with those observed value at meteorological stations in the east of Qinghai-Xizang Plateau area from 1989to 2009.The results show that the reanalysis air temperature is higher credibility in summer than in winter,the NCEP/DOE reanalysis data is systematically smaller than the observation,while JRA-25is systematically higher.The datasets of ERA-interim,JRA-25and the observation value all show similar warming trends in the east of Qinghai-Xizang Plateau from 1989to 2009,while NCEP/DOE shows a cooling trend instead.When considering the interannual change,the JRA-25reanalysis data shows the best consistency with the observation records,while NCEP/DOE shows the worst.After the analyzing the quality index of three datasets,it is clear that the quality of ERA-interim is better than that of the other two datasets and is improving with time.Another conclusion is that the quality of 2mair temperature from the reanalysis data is partly effected by ENSO,East Asian and plateau monsoons.
Effect of Ultra-Small Chitosan Nanoparticles Doped with Brimonidine on the Ultra-Structure of the Trabecular Meshwork of Glaucoma Patients

Abstract Brimonidine, an anti-glaucoma medicine, acts as an adrenergic agonist which decreases the synthesis of aqueous humour and increases the amount of drainage through Schlemm's canal and trabecular meshwork, but shows dose-dependent (0.2% solution thrice daily) toxicity. To reduce the side effects and improve the efficacy, brimonidine was nanoencapsulated on ultra-small-sized chitosan nanoparticles (nanobrimonidine) (28 ± 4 nm) with 39% encapsulation efficiency, monodispersity, freeze–thawing capability, storage stability, and 2% drug loading capacity. This nanocomplex showed burst, half, and complete release at 0.5, 45, and 100 h, respectively. Nanobrimonidine did not show any in vitro toxicity and was taken up by caveolae-mediated endocytosis. The nanobrimonidine-treated trabeculectomy tissue of glaucoma patients showed better dilation of the trabecular meshwork under the electron microscope. This is direct evidence for better bioavailability of nanobrimonidine after topical administration. Thus, the developed nanobrimonidine has the potential to improve the efficacy, reduce dosage and frequency, and improve delivery to the anterior chamber of the eye.
Distributionally Robust Chance-Constrained Bin Packing

Chance-constrained bin packing problem allocates a set of items into bins and, for each bin, bounds the probability that the total weight of packed items exceeds the bin's capacity. Different from the stochastic programming approaches relying on full distributional information of the random item weights, we assume that only the information of the mean and covariance matrix is available. Accordingly, we consider distributionally robust chance-constrained bin packing (DCBP) models. Using two types of ambiguity sets, we equivalently reformulate the DCBP models as 0-1 second-order cone (SOC) programs. Furthermore, we exploit the submodularity of the 0-1 SOC constraints under special and general covariance matrices, and derive extended polymatroid inequalities to strengthen the 0-1 SOC formulations. We then incorporate these valid inequalities in a branch-and-cut algorithm for efficiently solving the DCBP models. Finally, we demonstrate the computational efficacy of our approaches and performance of DCBP solutions on test instances with diverse problem sizes, parameters, and item weight uncertainty.
A New Class of Changing-look LINERs

We report the discovery of six active galactic nuclei (AGNs) caught “turning on” during the first nine months of the Zwicky Transient Facility (ZTF) survey. The host galaxies were classified as low-ionization nuclear emission-line region galaxies (LINERs) by weak narrow forbidden line emission in their archival SDSS spectra, and detected by ZTF as nuclear transients. In five of the cases, we found via follow-up spectroscopy that they had transformed into broad-line AGNs, reminiscent of the changing-look LINER iPTF16bco. In one case, ZTF18aajupnt/AT2018dyk, follow-up Hubble Space Telescope ultraviolet and ground-based optical spectra revealed the transformation into a narrow-line Seyfert 1 with strong [Fe vii, x, xiv] and He ii λ 4686 coronal lines. Swift monitoring observations of this source reveal bright UV emission that tracks the optical flare, accompanied by a luminous soft X-ray flare that peaks ∼60 days later. Spitzer follow-up observations also detect a luminous mid-infrared flare, implying a large covering fraction of dust. Archival light curves of the entire sample from CRTS, ATLAS, and ASAS-SN constrain the onset of the optical nuclear flaring from a prolonged quiescent state. Here we present the systematic selection and follow-up of this new class of changing-look LINERs, compare their properties to previously reported changing-look Seyfert galaxies, and conclude that they are a unique class of transients well-suited to test the uncertain physical processes associated with the LINER accretion state.
Design of a RADA16-based self-assembling peptide nanofiber scaffold for biomedical applications

Abstract RADA16 (RADARADARADARADA) is an amphiphilic polypeptide composed of 16 amino acids, which is composed of alternating positively charged arginine (R), hydrophobic alanine (A) and negatively charged aspartic acid (D) that repeat periodically throughout the composition. This structure allows RADA16 to form an extremely stable and highly ordered β-sheet structure by noncovalent bonding (ionic bonds, hydrogen bonds, hydrophobic action, π-π bonds, etc.). Moreover, it can form a three-dimensional (3D) nanofiber hydrogel scaffold in neutral pH with water content higher than 99% and with a physiological saline solution, having excellent biocompatibility and low immunogenicity, etc. Its degradation products are amino acids, which can reduce the possibility of an inflammatory reaction and have little effect on the normal healing process of damaged tissue. In addition, the special 3D structure of RADA16 facilitates the proliferation and differentiation of cells, making it widely used in cell culture scaffolds. Subsequent studies have found that the C-terminus or N-terminus of RADA16 is modified by a specific functional peptide, which not only retains the original function of RADA16 but also gives the RADA16 self-assembling hydrogel a more powerful function. In recent years, RADA16 and RADA16-based fusion peptides have been applied in biomedical fields, such as 3D cell culture, tissue repair, rapid hemostasis, and delivery systems, which have broad prospects. This review focuses on recent research and applications of RADA16 and RADA16-based self-assembling peptide nanofiber scaffold (SAPNS) in biomedicine.
Deep Constrained Dominant Sets for Person Re-Identification

In this work, we propose an end-to-end constrained clustering scheme to tackle the person re-identification (re-id) problem. Deep neural networks (DNN) have recently proven to be effective on person re-identification task. In particular, rather than leveraging solely a probe-gallery similarity, diffusing the similarities among the gallery images in an end-to-end manner has proven to be effective in yielding a robust probe-gallery affinity. However, existing methods do not apply probe image as a constraint, and are prone to noise propagation during the similarity diffusion process. To overcome this, we propose an intriguing scheme which treats person-image retrieval problem as a constrained clustering optimization problem, called deep constrained dominant sets (DCDS). Given a probe and gallery images, we re-formulate person re-id problem as finding a constrained cluster, where the probe image is taken as a constraint (seed) and each cluster corresponds to a set of images corresponding to the same person. By optimizing the constrained clustering in an end-to-end manner, we naturally leverage the contextual knowledge of a set of images corresponding to the given person-images. We further enhance the performance by integrating an auxiliary net alongside DCDS, which employs a multi-scale ResNet. To validate the effectiveness of our method we present experiments on several benchmark datasets and show that the proposed method can outperform state-of-the-art methods.
Frequency of DNA end joining in trans is not determined by the predamage spatial proximity of double-strand breaks in yeast

Significance DNA double-strand breaks (DSBs) are severe insults that lead to different types of genome rearrangements if repaired incorrectly. We explored the genesis of genomic rearrangements mediated by the nonhomologous end-joining pathway of DSB repair. Previous studies suggested that the efficiency of trans repair (i.e., rearrangements) is strongly influenced by the distance between two stretches of DNA incurring DSBs. We systematically investigated the impact of predamage spatial proximity on trans repair frequency in yeast and found no correlation between them, which has important implications for understanding chromosome movement and disease-causing rearrangements. DNA double-strand breaks (DSBs) are serious genomic insults that can lead to chromosomal rearrangements if repaired incorrectly. To gain insight into the nuclear mechanisms contributing to these rearrangements, we developed an assay in yeast to measure cis (same site) vs. trans (different site) repair for the majority process of precise nonhomologous end joining (NHEJ). In the assay, the HO endonuclease gene is placed between two HO cut sites such that HO expression is self-terminated upon induction. We further placed an additional cut site in various genomic loci such that NHEJ in trans led to expression of a LEU2 reporter gene. Consistent with prior reports, cis NHEJ was more efficient than trans NHEJ. However, unlike homologous recombination, where spatial distance between a single DSB and donor locus was previously shown to correlate with repair efficiency, trans NHEJ frequency remained essentially constant regardless of the position of the two DSB loci, even when they were on the same chromosome or when two trans repair events were put in competition. Repair of similar DSBs via single-strand annealing of short terminal direct repeats showed substantially higher repair efficiency and trans repair frequency, but still without a strong correlation of trans repair to genomic position. Our results support a model in which yeast cells mobilize, and perhaps compartmentalize, multiple DSBs in a manner that no longer reflects the predamage position of two broken loci.
Analysis of Equatorial Currents Observed by Eastern Indian Ocean Cruises in 2010 and 2011

Abstract Hydrographic and direct current measurements were made in the Eastern Equatorial Indian Ocean in May 2010 and April 2011 as part of the Eastern Indian Ocean Cruises (EIOC) organized by the South China Sea Institute of Oceanology (SCSIO). Analyses of the ship-drift Acoustic Doppler Current Profiler (ADCP) data indicate that the equatorial currents observed in May 2010 are characterized by a strongly eastward surface current (Wyrtki Jets, WJs) with a maximum velocity of 0.9 m s-1, while that observed in April 2011 is weak and without a consistent direction. The strongly eastward WJ transports the surface water eastward, resulting in a deeper upper mixed layer, as shown in the temperature and salinity pro-files. However, it was found that the Equatorial Under-current (EUC) in the Eastern Indian Ocean is strong in April 2011 and weak in May 2010. The EUC was located approximately at the position of the thermocline, and it had higher salinity (up to approximately 35.5 psu) than the upper and lower waters.
UvA-DARE (Digital Academic Repository) Rethinking the biopolitical: Borders, refugees, mobilities…

This Symposium reflects on the growing relevance of biopolitical perspectives in camps studies, border studies, refugee studies, and in particular in research at the intersection between mobility studies and political geography. The five interventions accordingly engage with questions regarding the use of biopolitics as an analytical framework, but also as a pervasive strategy and governmental tool in Western societies. Through an analysis of several empirical cases – most notably hotspots on the Greek Aegean Island, refugee’s forced hyper mobility in Europe, speech acts connected to the ethnic cleansing of the Rohingya people in Myanmar and the ‘voluntary return’ policies in Europe, and the paper borders created by visa systems – the
Little Ice Age

The term Little Ice Age was originally coined by F Matthesin 1939 to describe the most recent 4000 year climaticinterval (the Late Holocene) associated with a particularlydramatic series of mountain glacier advances and retreats,analogous to, though considerably more moderate than, thePleistocene glacial ﬂuctuations. This relatively prolongedperiod has now become known as the Neoglacial period.The term Little Ice Age is, instead, reserved for the mostextensive recent period of mountain glacier expansion and isconventionally deﬁned as the 16th–mid 19th century periodduring which European climate was most strongly impacted.This period begins with a trend towards enhanced glacialconditions in Europe following the warmer conditions ofthe so-called medieval warm period or medieval climaticoptimum of Europe (
The polymodal frequency-magnitude relationship of earthquakes

Earthquake frequency-magnitude relationships can be well described as a polymodal composite of normal distributions, a pattern consistent with varying causal mechanisms in different tectonic settings and/or magnitude ranges but a pattern also in conflict with the assumption of self-similarity or the fractal nature of earthquakes. From the Giardini Catalog, 4660 deep (> 350 km) worldwide earthquakes presumably homogeneous with respect to causal mechanism, are well described as a single normally distributed population. Analysis of 10,341 earthquakes ranging in magnitude from 2.0 to 8.2 from the 1989 to 1991 National Earthquake Information Center - Quick Epicenter Determination catalogue yields three populations each of whose magnitude frequency is expressed in terms of probability. Some nonsimilar frequency-magnitude distributions for low magnitudes are also explicable as the result of one or more normally distributed populations. In our model, b is a measure of the dispersion of the population.
Proceedings of Meetings on Acoustics

The radiation of finite-amplitude waves from the open end of a baffled, circular pipe is considered as a direct continuation of work begun by Kuhn, Blackstock, and Wright more than three decades ago [Kuhn et al., J. Acoust. Soc. Am. 63, S1, S84 (1978)]. In this paper, a 1 kHz sinusoidal pulse with initial peak pressure amplitude of nearly 1.2 kPa has been propagated down a 6.1 m pipe, whose open end (5.1 cm inner diameter) has been placed off-center in a large rectangular baffle. As the steepened or shock-like waves exit the pipe, the measured waveforms are comprised of sharp impulses that are delta function-like in nature, particularly on axis. Although linear piston theory predicts similar waveform shapes, there is also evidence that nonlinear propagation of these impulses, which exceed a peak pressure amplitude of 1.5 kPa near the pipe opening, is occurring. http://asadl.org/jasa/resource/1/jasman/v63/iS1/pS84_s5
Proceedings of Meetings on Acoustics

Acoustic fields in shallow water have a statistical nature due to complex, time-evolving sound speed fields and scattering from rough boundaries. Previously, coupled-mode transport theory [Raghukumar and Colosi (2012)] was applied to high frequency acoustic fluctuations in an environment typical of the Shallow Water 2006 (SW06) experiment on the New Jersey continental shelf. As a consequence of the strong adiabatic component in SW06 propagation, a hybrid approach was used to calculate mode coherences where mode energies from the DozierTappert approach were combined with adiabatic phase terms. Mode energies, coherences and acoustic intensities were examined and it was found that internal and surface waves preferentially couple low and high modes respectively. Here, we extend that study to include higher moments such as scintillation index and shift focus to modes that are coupled by both internal and surface waves. Oceanographic and sea surface measurements are used to constrain the internal wave and sea surface models. The relative importance of linear internal waves and surface scattering effects are studied using transport theory and Monte Carlo simulations.
Proceedings of Meetings on Acoustics

Numerical mode matching (NMM) method is developed to predict the acoustic attenuation performance of expansion chambers with singleinlet and double-outlets. The two-dimensional finite element method is employed to calculate the transversal eigenvalues and eigenvectors, and the mode matching technique is used to determine the modal amplitudes and transmission loss of expansion chamber silencers by combining the boundary conditions at inlet and outlets. For the purpose of validation, the transmission loss predictions of elliptical expansion chambers with single-inlet and double-outlets from the present NMM method and the three-dimensional finite element method (FEM) are compared, and good agreements between them are observed. Then the NMM method is used to investigate the effects of extended lengths of outlets on the acoustic attenuation performance of elliptical expansion chambers.
Proceedings of Meetings on Acoustics

Hearing Protection Devices (HPD), such as earmuffs, are widely used to protect workers from noisy environments. Numerical predictive tools can be used to simulate the vibroacoustic behaviour of earmuffs and thus assess their sound attenuation and improve their acoustical design. The present work describes the implementation of a vibroacoustic finite element numerical model of an earmuff coupled to a rigid baffle in the frequency range from 20Hz to 5000Hz. An experimental assessment of the sound transfer paths through each element of the earmuff (cup, cushion, foam lining) using a specific acoustical test bench is first proposed. This analysis is then used to target the right level of model complexity for each component. An experimental validation of the FEM model is then carried out.
EVALUATION OF FLOOD INUNDATION IN JAKARTA USING FLOOD INUNDATION MODEL CALIBRATED BY RADAR RAINFALL

1Member of JSCE, Department of Civil and Environmental Engineering, Tohoku University (Aoba 468-1 Aoba-ku Sendai-shi Miyagi, 980-0845, Japan) 2Member of JSCE, Assistant Professor, International Research Institute of Disaster Science, Tohoku University (Aoba 468-1 Aoba-ku Sendai-shi Miyagi, 980-0845, Japan) 3 Researcher, Water Resources Engineering Research Group, Faculty of Civil and Environmental Engineering, Bandung Institute of Technology (Jalan Ganesha 10 Bandung 40132, Indonesia) 4Member of JSCE, Associate Professor, International Research Institute of Disaster Science, Tohoku University (Aoba 468-1 Aoba-ku Sendai-shi Miyagi, 980-0845, Japan) 5 Member of JSCE, Professor, Department of Civil and Environmental Engineering, Tohoku University (Aoba 6-6-06 Aoba-ku Sendai-shi Miyagi, 980-8579, Japan) 6Member of JSCE, Professor, International Research Institute of Disaster Science, Tohoku University (Aoba 468-1 Aoba-ku Sendai-shi Miyagi, 980-0845, Japan)