Miracle-dz/UniFAR-FTUs huggingface dataset:
Raised circulating soluble growth differentiation factor 15 is negatively associated with testosterone level in hypogonadic men with type 2 diabetes

Epidemiological studies consistently show that decreases in serum testosterone level are observed more frequently in men with type 2 diabetes mellitus (T2DM), while clinical investigations have demonstrated that an increased level of circulating growth differentiation factor‐15 (GDF‐15) are also related closely to T2DM. The aim of this study was to examine the potential relationship between serum GDF‐15 levels and hypogonadism in Chinese male patients with T2DM.
Methods for the Analysis of Visual Motion

Vision is a primary sense that allows human beings to interact with their environment and motion is one of the most important cues that vision can explore and utilize. In this thesis, we present computational approaches to the problems of inferring three-dimensional motion information and perceiving two-dimensional human motions from a sequence of images captured by a camera. The three-dimensional structure of world can be represented by distinguishable features, such as points. Assume all the features move under the same rigid motion in space, this motion can be recovered from the projections of the features in three views by solving a set of trilinear constraints. The trilinear constraints have been considered only as algebraic equations so that their satisfactory performance in motion estimation is not easy to understand. This thesis solves this puzzle by discovering a geometrical interpretation of trilinear constraints. It is showed that those algebraic equations correspond to depth errors appropriately weighted by a function of the relative reliability of the corresponding measurements. When the assumption is relaxed to allowing features to move under different rigid motions, this thesis proposes a three-dimensional motion based expectation-maximization algorithm combined with the modified separation matrix scheme to cluster the features undergoing the same motion into a group and estimate the motion for every group at the same time. The problem of detecting and recognizing human motions arises from many applications in computer vision. This thesis describes an algorithm to detect human body from their motion patterns in a pair of frames which is based on learning an approximate probabilistic model of the positions and velocities of body joints. It then presents a scheme to recognize human actions in a sequence of frames assuming the human body is detected. This scheme enables us to simultaneously recognize both the action and the body poses in the observed sequence. All our theoretical work is supported by experimental results.
A MULTI-WAVELENGTH APPROACH TO THE PROPERTIES OF EXTREMELY RED GALAXY POPULATIONS. I. CONTRIBUTION TO THE STAR FORMATION RATE DENSITY AND ACTIVE GALACTIC NUCLEUS CONTENT

We present a multi-wavelength analysis of the properties of extremely red galaxy (ERG) populations, selected in the GOODS-South/Chandra Deep Field South field. By using all the photometric and spectroscopic information available on large deep samples of extremely red objects (EROs; 645 sources), IRAC EROs (IEROs; 294 sources), and distant red galaxies (DRGs; 350 sources), we derive redshift distributions, identify active galactic nucleus (AGN)-powered and star formation (SF)-powered galaxies, and, using the radio observations of this field, estimate robust (AGN- and dust-unbiased) SF rate densities () for these populations. We also investigate the properties of “pure” (galaxies that conform to only one of the three ERG criteria considered) and “combined” (galaxies that verify all three criteria) sub-populations. Overall, a large number of AGNs are identified (up to ∼30%, based on X-rays and mid-infrared criteria), the majority of which are type-2 (obscured) objects. Among ERGs with no evidence for AGN activity, we identify sub-populations covering a wide range of average SF rates, from below 10 M☉ yr−1 to as high as 200 M☉ yr−1. Applying a redshift separation (1 ⩽ z < 2 and 2 ⩽ z ⩽ 3), we find significant evolution (an increase of a factor of 2 or higher) of for EROs and DRGs, while none is observed for IEROs. The former populations can contribute more than 20% to the global at 2 ⩽ z ⩽ 3. The emission from AGN activity is typically not strong in the ERG population, with AGNs increasing the average radio luminosity of ERG sub-populations by, nominally, less than 20%. AGNs are common, however, and, if no discrimination is attempted, this could significantly increase the estimate (by over 100% in some cases). Thus, and while the contribution of star-forming processes to the radio luminosity in galaxies with AGN remains uncertain, a comprehensive identification of AGNs in these populations is necessary to obtain meaningful results.
Study of nonstandard neutrino interactions with atmospheric neutrino data in Super-Kamiokande i and II

In this paper we study non-standard neutrino interactions as an example of physics beyond the standard model using atmospheric neutrino data collected during the Super-Kamiokande I(1996-2001) and II(2003-2005) periods. We focus on flavor-changing-neutral-currents (FCNC), which allow neutrino flavor transitions via neutral current interactions, and effects which violate lepton non-universality (NU) and give rise to different neutral-current interaction-amplitudes for different neutrino flavors. We obtain a limit on the FCNC coupling parameter, varepsilon_{mu tau}, |varepsilon_{mu tau}|<1.1 x 10^{-2} at 90%C.L. and various constraints on other FCNC parameters as a function of the NU coupling, varepsilon_{e e}. We find no evidence of non-standard neutrino interactions in the Super-Kamiokande atmospheric data.
Spectral classification and HR diagram of pre-main sequence stars in NGC 6530 ,,

Context. Mechanisms involved in the star formation process and in particular the duration of the different phases of the cloud contraction are not yet fully understood. Photometric data alone suggest that objects coexist in the young cluster NGC 6530 with ages from∼1 Myr up to 10 Myrs. Aims. We want to derive accurate stellar parameters and, in particular, stellar ages to be able to constrain a possible age spre ad in the star-forming region NGC6530. Methods. We used low-resolution spectra taken with VIMOS@VLT and literature spectra of standard stars to derive spectral types of a subsample of 94 candidate members of this cluster. Results. We assign spectral types to 86 of the 88 confirmed cluster memb ers and derive individual reddenings. Our data are better fitted by the anomalous reddening law with R V=5. We confirm the presence of strong differential reddening in this region. We derive fundamental stellar parameters, such as effective temperatures, photospheric colors, luminosities, masses, and age s for 78 members, while for the remaining 8 YSOs we cannot determine the interstellar absorption, since they are likely accretors, and the ir V-I colors are bluer than their intrinsic colors. Conclusions. The cluster members studied in this work have masses between 0.4 and 4 M⊙ and ages between 1-2 Myrs and 6-7 Myrs. We find that the SE region is the most recent site of star format ion, while the older YSOs are loosely clustered in the N and W regions. The presence of two distint generations of YSOs with different spatial distribution allows us to conclude that in this re gion there is an age spread of 6-7 Myrs. This is consistent with the scenario of sequential star formation suggested in literature.
CHARACTERIZING THE INFRARED SPECTRA OF SMALL, NEUTRAL, FULLY DEHYDROGENATED POLYCYCLIC AROMATIC HYDROCARBONS

We present the results of a computational study to investigate the infrared spectroscopic properties of a large number of polycyclic aromatic hydrocarbon (PAH) molecules and their fully dehydrogenated counterparts. We constructed a database of fully optimized geometries for PAHs that is complete for eight or fewer fused benzene rings, thus containing 1550 PAHs and 805 fully dehydrogenated aromatics. A large fraction of the species in our database have clearly non-planar or curved geometries. For each species, we determined the frequencies and intensities of their normal modes using density functional theory calculations. Whereas most PAH spectra are fairly similar, the spectra of fully dehydrogenated aromatics are much more diverse. Nevertheless, these fully dehydrogenated species show characteristic emission features at 5.2 μm, 5.5 μm, and 10.6 μm; at longer wavelengths, there is a forest of emission features in the 16–30 μm range that appears as a structured continuum, but with a clear peak centered around 19 μm. We searched for these features in Spitzer-IRS spectra of various positions in the reflection nebula NGC 7023. We find a weak emission feature at 10.68 μm in all positions except that closest to the central star. We also find evidence for a weak 19 μm feature at all positions that is not likely due to C60. We interpret these features as tentative evidence for the presence of a small population of fully dehydrogenated PAHs, and discuss our results in the framework of PAH photolysis and the formation of fullerenes.
Clomipramine inhibits dynamin GTPase activity by L-α-phosphatidyl-L-serine stimulation

Three dynamin isoforms play critical roles in clathrin-dependent endocytosis. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) enters host cells via clathrin-dependent endocytosis. We previously reported that 3-(3-chloro-10,11-dihydro-5H-dibenzo[b,f]azepin-5-yl)-N,N-dimethylpropan-1-amine (clomipramine) inhibits the GTPase activity of dynamin 1, which is in mainly neuron. Therefore, we investigated whether clomipramine inhibits the activity of other dynamin isoforms in this study. We found that, similar to its inhibitory effect on dynamin 1, clomipramine inhibited the L-α-phosphatidyl-L-serine-stimulated GTPase activity of dynamin 2, which is expressed ubiquitously, and dynamin 3, which is expressed in the lung. Inhibition of GTPase activity raises the possibility that clomipramine can suppress SARS-CoV-2 entry into host cells. Graphical Abstract
A “grappling hook” interaction balances self-assembly and chaperone activity of Nucleophosmin 1

How the self-assembly of partially disordered proteins generates functional compartments in the cytoplasm and particularly in the nucleus is poorly understood. Nucleophosmin 1 (NPM1) is an abundant nucleolar protein that forms large oligomers which provide the scaffold for ribosome assembly but also prevent protein aggregation as part of the cellular stress response. Examining the relationship between the self-assembly and chaperone activity of NPM1, we find that oligomerization of full-length NPM1 modulates its ability to retard amyloid formation in vitro. Machine learning and cryo-electron microscopy reveal fuzzy interactions between the disordered region and the C-terminal nucleotide-binding domain that cross-link NPM1 pentamers into oligomers. Ribosomal peptides mediate in a tighter association within the oligomers, reducing their capacity to prevent amyloid formation. We conclude that NPM1 uses a “grappling hook” interaction to form a network-like structure whose chaperone activity is tuned by basic proteins, suggesting a regulatory mechanism for the nucleolar stress response.
On the variable timing behavior of PSR B0540-69: an almost excellent example to study the pulsar braking mechanism

PSR B0540-69 has a braking index measurement in its persistent state: n = 2.129 ± 0.012. Recently, it has been reported to have changes in its spin-down state: a sudden 36% increase in the spin-down rate. Combining the persistent state braking index measurement with different spin-down states, PSR B0540-69 is more powerful than intermittent pulsars in constraining pulsar spin-down models. The pulsar wind model is applied to explain the variable timing behavior of PSR B0540-69. The braking index of PSR B0540-69 in its persistent state results from the combined effect of magnetic dipole radiation and particle wind. The particle density reflects the magnetospheric activity in real-time and may be responsible for the changing spin-down behavior. Corresponding to the 36% increase in the spin-down rate of PSR B0540-69, the relative increase in the particle density is 88% in the vacuum gap model. The braking index calculated with the model in the new state is n = 1.79. Future observations that measure the braking index of PSR B0540-69 in the new spin-down state will be very powerful in distinguishing between different pulsar spin-down models and different particle acceleration models in the wind braking scenario. The variable timing behavior of PSR J1846-0258 is also understandable in the pulsar wind model.
Down the Penrose stairs: How selection for fewer recombination hotspots maintains their existence

In many species, meiotic recombination events tend to occur in narrow intervals of the genome, known as hotspots. In humans and mice, double strand break (DSB) hotspot locations are determined by the DNA-binding specificity of the zinc finger array of the PRDM9 protein, which is rapidly evolving at residues in contact with DNA. Previous models explained this rapid evolution in terms of the need to restore PRDM9 binding sites lost to gene conversion over time, under the assumption that more PRDM9 binding always leads to more DSBs. In recent experimental work, however, it has become apparent that PRDM9 binding on both homologs facilitates DSB repair, and moreover that, in the absence of enough symmetric binding, meiosis no longer progresses reliably. We therefore consider the possibility that the benefit of PRDM9 stems from its role in coupling DSB formation and efficient repair. To this end, we model the evolution of PRDM9 from first principles: from its binding dynamics to the population processes that govern the evolution of the zinc finger array and its binding sites in the genome. As we show, the loss of a small number of strong binding sites leads to the use of a greater number of weaker ones, resulting in a sharp reduction in symmetric binding and favoring new PRDM9 alleles that restore the use of a smaller set of strong binding sites. This decrease in PRDM9 binding symmetry and in its ability to promote DSB repair drive the rapid zinc finger turnover. These results imply that the advantage of new PRDM9 alleles is in limiting the number of binding sites used effectively, rather than in increasing net PRDM9 binding, as previously believed. By extension, our model suggests that the evolutionary advantage of hotspots may have been to increase the efficiency of DSB repair and/or homolog pairing.
Adjusting for genetic confounders in transcriptome-wide association studies leads to reliable detection of causal genes

Expression Quantitative Trait Loci (eQTLs), provide valuable information on the effects of genetic variants. Many methods have been developed to leverage eQTLs to nominate candidate genes of complex traits, including colocalization analysis, transcriptome-wide association studies (TWAS), and Mendelian Randomization (MR)-based methods. All these methods, however, suffer from a key problem: when using the eQTLs of a gene to assess its role in a trait, nearby variants and nearby genetic components of expression of other genes can be correlated with the eQTLs of the test gene, while affecting the trait directly. These “genetic confounders” often lead to false discoveries. We introduced a novel statistical framework to address this challenge. Our method, causal-TWAS (cTWAS), borrowed ideas from statistical fine-mapping, and allowed us to adjust all genetic confounders. In our simulations, we found that existing methods based on TWAS, colocalization or MR all suffered from high false positive rates, often greater than 50%. In contrast, cTWAS showed calibrated false positive rates while maintaining power. Application of cTWAS on several common traits highlighted the weakness of existing methods and discovered novel candidate genes. In conclusion, cTWAS is a novel statistical framework to integrate eQTL and GWAS data, enabling reliable gene discoveries.
Cooling in strongly correlated optical lattices: prospects and challenges

Optical lattices have emerged as ideal simulators for Hubbard models of strongly correlated materials, such as the high-temperature superconducting cuprates. In optical lattice experiments, microscopic parameters such as the interaction strength between particles are well known and easily tunable. Unfortunately, this benefit of using optical lattices to study Hubbard models comes with one clear disadvantage: the energy scales in atomic systems are typically nanokelvin compared with kelvin in solids, with a correspondingly miniscule temperature scale required to observe exotic phases such as d-wave superconductivity. The ultra-low temperatures necessary to reach the regime in which optical lattice simulation can have an impact—the domain in which our theoretical understanding fails—have been a barrier to progress in this field. To move forward, a concerted effort is required to develop new techniques for cooling and, by extension, techniques to measure even lower temperatures. This paper will be devoted to discussing the concepts of cooling and thermometry, fundamental sources of heat in optical lattice experiments, and a review of proposed and implemented thermometry and cooling techniques.
Intrinsic neural timescales in the temporal lobe support an auditory processing hierarchy

During rest, intrinsic neural dynamics manifest at multiple timescales, which progressively increase along visual and somatosensory hierarchies. Theoretically, intrinsic timescales are thought to facilitate processing of external stimuli at multiple stages. However, direct links between timescales at rest and sensory processing, as well as translation to the auditory system are lacking. Here, we used intracranial electroencephalography in humans to show that in the auditory network, intrinsic neural timescales progressively increase, while the spectral slope flattens, from temporal to entorhinal cortex, hippocampus, and amygdala. Within the neocortex, intrinsic timescales exhibit spatial gradients that follow the temporal lobe anatomy. Crucially, intrinsic timescales at rest can explain the latency of auditory responses: as intrinsic timescales increase, so do the single-electrode response onset and peak latencies. Our results suggest that the human auditory network exhibits a repertoire of intrinsic neural dynamics, which manifest in cortical gradients with millimeter resolution and may provide a variety of temporal windows to support auditory processing.
Detectability of bigravity with graviton oscillations using gravitational wave observations

The gravitational waveforms in the ghost-free bigravity theory exhibit deviations from those in general relativity. The main difference is caused by graviton oscillations in the bigravity theory. We investigate the prospects for the detection of the corrections to gravitational waveforms from coalescing compact binaries due to graviton oscillations and for constraining bigravity parameters with the gravitational wave observations. We consider the bigravity model discussed by the De Felice-Nakamura-Tanaka subset of the bigravity model, and the phenomenological model in which the bigravity parameters are treated as independent variables. In both models, the bigravity waveform shows strong amplitude modulation, and there can be a characteristic frequency of the largest peak of the amplitude, which depends on the bigravity parameters. We show that there is a detectable region of the bigravity parameters for the advanced ground-based laser interferometers, such as Advanced LIGO, Advanced Virgo, and KAGRA. This region corresponds to the effective graviton mass of $\mu \geq 10^{-17}~{\rm cm}^{-1}$ for $\tilde{c}-1 \geq 10^{-19}$ in the phenomenological model, while $\mu \geq 10^{-16.5}~{\rm cm}^{-1}$ for $\kappa\xi_c^2 \geq 10^{0.5}$ in the De Felice-Nakamura-Tanaka subset of the bigravity model, respectively, where $\tilde{c}$ is the propagation speed of the massive graviton and $\kappa\xi_c^2$ corresponds to the corrections to the gravitational constant in general relativity. These regions are not excluded by existing solar system tests. We also show that, in the case of $1.4-1.4M_{\rm sun}$ binaries at the distance of $200~{\rm Mpc}$, $\log\mu^2$ is determined with an accuracy of ${\cal O}$(0.1)\% at the 1$\sigma$ level for a fiducial model with $\mu^2=10^{-33}~{\rm cm}^{-2}$ in the case of the phenomenological model.
Structural and Immunological Similarities Between the Metacyclic and Bloodstream Form Variant Surface Glycoproteins of the African Trypanosome

During infection of mammalian hosts, African trypanosomes thwart immunity using antigenic variation of the dense Variant Surface Glycoprotein (VSG) coat, accessing a large repertoire of thousands of genes and pseudogenes and switching to antigenically distinct copies. The parasite is transferred to mammalian hosts through the bite of the tsetse fly. In the salivary glands of the fly, the pathogen adopts the metacyclic form and expresses a limited repertoire of VSG genes specific to that developmental stage. It has remained unknown whether the metacyclic VSGs possess distinct properties associated with this particular and discrete phase of the parasite life cycle. We show here using bioinformatic, crystallographic, and immunological analyses of three metacyclic VSGs that they closely mirror the known classes of bloodstream form VSGs both in structure and in the immunological responses they elicit.
Galactic tide and some properties of the Oort cloud

The paper deals with several properties of the Oort cloud of comets. Sun, Galaxy (and Jupiter) gravitationally act on the comets. New physical model of galactic tide is considered. The main results can be summarized as follows: 1. Mass of the Oort cloud of comets is less than 1 mass of the Earth ($M_{E}$), probably not greater than 1/2 $M_{E}$. 2. Theoretical number of long-period comets with perihelion distance $q$ $<$ 5 AU is about 50-times greater than the conventional approach yields. Gravity of Jupiter was taken into account in finding this result. 3. Semi-major axis $a$ and period of oscillations $P$ of eccentricity (and other orbital elements) are related as $a^{3}$ $P$ $=$ 1 in natural units for a moving Solar System in the Galaxy. The natural unit for time is the orbital period of the Solar System revolution around the galactic center and the natural unit for measuring the semi-major axis is its maximum value for the half-radius of the Solar System corresponding to the half-radius of the Oort cloud. The relation holds for the cases when comets approach the inner part of the Solar System, e.g., perihelion distances are less than $\approx$ 100 AU. 4. The minimum value of semi-major axis for the Oort cloud is $a_{min}$ $\ll$ 1 $\times$ 10$^{4}$ AU. This condition was obtained both from the numerical results on cometary evolution under the action of the galactic tides and from the observational distribution of long-period comets. If the density function of semi-major axis is approximated by proportionality $a^{\alpha}$, then $\alpha$ is - 1/2, approximately. 5. The magnitude of the change in perihelion distance per orbit, $\Delta q$, of a comet due to galactic tides is a strong function of semi-major axis $a$, proportional to $a^{8.25}$.