Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic characterization of HIV-1 viruses among antiretroviral therapy failure individuals in Suzhou City, China

Background: This retrospective study was aimed to characterize the distribution of HIV-1 genotypes and prevalence of drug-resistance mutations in antiretroviral therapy (ART) failure individuals in Suzhou City, China. Methods: Polgene of HIV-1 viruses in EDTA anticoagulant plasma samples of 398 ART failure HIV-infected individuals were successfully ampli�ed by using an in-house assay. Drug resistance mutations were analyzed by using the Stanford HIV Drug Resistance Database system (https://hivdb.stanford.edu/hivdb/by-mutations/). HIV-1 genotypes were determined by REGA HIV subtyping tool (version 3.46, https://www.genomedetective.com/app/typingtool/hiv). Near full-length genomes (NFLG) of HIV-1 viruses were obtained by next generation sequencing method. Results: Sequences analysis of the pol gene revealed that CRF 01_AE (57.29%, 228/398) was the dominant subtype circulating in Suzhou City, followed by CRF 07_BC (17.34%, 69/398), subtype B (7.54%, 30/398), CRF 08_BC (6.53%, 26/398), CRF 67_01B (3.02%, 12/398) and CRF55_01B (2.51%, 10/398). The overall prevalence of drug-resistant mutations in ART failure HIV-infected individuals was 64.57% (257/398), including 45.48% (181/398) for nucleotide reverse transcriptase inhibitors (NRTIs) mutations, 63.32% (252/398) for non-nucleoside reverse transcriptase inhibitors (NNRTIs) mutations, and 3.02% (12/398) for protease inhibitors (PIs) mutations. Ten near full-length genomes (NFLG) of HIV-1 viruses were identi�ed, including six recombinants of CRF 01_AE and subtype B, two recombinants of CRF 01_AE, subtype B and subtype C sequences, one recombinant of CRF 01_AE and subtype C and one recombinant of CRF 01_AE, subtype A1 and subtype C. Conclusions: The high prevalence of drug-resistant HIV-1 viruses was a serious challenge for HIV prevention and HIV-infected individuals’ treatment. Therapeutic regimens of ART failure HIV-infected individuals should be adjusted in time according to drug resistance test results. NFLG sequencing facilitates the identi�cation of new HIV-1 recombinant strains.
Dietary enzymatically treated yeast and coccidia challenge effects on the growth performance, nutrient digestibility, and intestinal health of broiler chickens

Background: There is a growing search for natural feed additives to alleviate the deleterious effects of coccidia infection in poultry production. This study aimed to investigate the effect of enzymatically treated yeast (ETY) on the growth performance, nutrient digestibility, and intestinal health of coccidia-challenged broiler chickens. Methods: From d 1 to 14 post hatching, 480 broiler chickens were allocated to 3 corn-soybean meal-based experimental diets with increasing concentrations of ETY (0, 1, or 2 g/kg). The experiment was designed as a randomized complete block design with body weight (BW) used as a blocking factor. On d 14 post hatching, the birds were re-randomized within each of the 3 experimental diets. Each of the 3 diet groups was split into a challenge or no-challenge group. This resulted in a 3 × 2 factorial arrangement of treatments. The coccidia challenge was administered on d 15 by an oral gavage. Results: Dietary ETY improved (P < 0.05) the G:F of birds on d 21 regardless of the challenge state and linearly increased (P < 0.01) the apparent ileal digestibility of dry matter (DM), nitrogen, and gross energy (GE). The coccidia challenge decreased (P < 0.01) BW gain, feed intake, and G:F of broiler chickens, and reduced (P < 0.01) the apparent total tract digestibility of DM, GE, and nitrogen. The coccidia challenge increased (P< 0.01) the mRNA gene expression of TNF α , IL-1 β , IL-10, and IL-6 in the cecal mucosa. There was a tendency (P = 0.08) for ETY to linearly reduce IL-1 β expression. Additionally, ETY supplementation increased (P < 0.05) the gene expression of OCLN. Serum catalase increased (P < 0.05) with dietary ETY in broiler chickens on d 21. Dietary ETY linearly increased (P < 0.05) the ileal villus height to crypt depth ratio, and ileal goblet cell density in broiler chickens. The ileal and excreta oocyst
Fixed points of inhomogeneous smoothing transforms

We consider the inhomogeneous version of the fixed-point equation of the smoothing transformation, that is, the equation , where means equality in distribution, is a given sequence of non-negative random variables and is a sequence of i.i. d. copies of the non-negative random variable X independent of . In this situation, X (or, more precisely, the distribution of X) is said to be a fixed point of the (inhomogeneous) smoothing transform. In the present paper, we give a necessary and sufficient condition for the existence of a fixed point. Furthermore, we establish an explicit one-to-one correspondence with the solutions to the corresponding homogeneous equation with C = 0. Using this correspondence and the known theory on the homogeneous equation, we present a full characterization of the set of fixed points under mild assumptions.
Structural and Functional Insights into Non-Structural Proteins of 3 Coronaviruses

: Coronaviruses (CoVs) are causing a number of human and animal diseases because of 15 their zoonotic nature such as Middle East respiratory syndrome (MERS), severe acute respiratory 16 syndrome (SARS) and coronavirus disease 2019 (COVID-19). These viruses can infect 17 respiratory, gastrointestinal, hepatic and central nervous systems of human, livestock, birds, bat, 18 mouse, and many wild animals. The severe acute respiratory syndrome coronavirus 2 (SARS- 19 CoV-2) is a newly emerging respiratory virus and is causing CoVID-19 with high morbidity and 20 considerable mortality. All CoVs belong to the order Nidovirales , family Coronaviridae , are 21 enveloped positive-sense RNA viruses, characterised by club-like spikes on their surfaces and 22 large RNA genome with a distinctive replication strategy. Coronavirus have the largest RNA 23 genomes ( ~ 26–32 kilobases) and their expansion was likely enabled by acquiring enzyme 24 functions that counter the commonly high error frequency of viral RNA polymerases. Non- 25 structural proteins (nsp) 7-16 are cleaved from two large replicase polyproteins and guide the 26 replication and processing of coronavirus RNA. Coronavirus replicase has more or less universal 27 activities, such as RNA polymerase (nsp 12) and helicase (nsp 13), as well as a variety of unusual 28 or even special mRNA capping (nsp 14, nsp 16) and fidelity regulation (nsp 14) domains. Besides 29 that, several smaller subunits (nsp 7– nsp 10) serve as essential cofactors for these enzymes and 30 contribute to the emerging “nsp interactome. ” In spite of the significant progress in studying 31 coronaviruses structural and functional properties, there is an urgent need to understand the 32 coronaviruses evolutionary success that will be helpful to develop enhanced control strategies. 33 Therefore, it is crucial to understand the structure, function, and interactions of coronaviruses RNA 34 synthesizing machinery and their replication strategies.
THE START OF THE SAGITTARIUS SPIRAL ARM (SAGITTARIUS ORIGIN) AND THE START OF THE NORMA SPIRAL ARM (NORMA ORIGIN): MODEL-COMPUTED AND OBSERVED ARM TANGENTS AT GALACTIC LONGITUDES −20° < l < +23°

Here, we fitted a four-arm spiral model to the more accurate data on global arm pitch angle and arm longitude tangents to get the start of each spiral arm near the galactic nucleus. We find that the tangent to the “start of the Sagittarius” spiral arm (arm middle) is at l = −17° ± 0. °5, while the tangent to the “start of the Norma” spiral arm (arm middle) is at l = +20° ± 0. °5. Earlier, we published a compilation of observations and analysis of the tangent to each spiral arm tracer from longitudes +23° to +340°; in this paper we cover the arm tracers in the remaining longitudes +340 (=−20°) to +23°. Our model arm tangents are confirmed through the recent observed masers data (at the arm's inner edge). Observed arm tracers in the inner Galaxy show an offset from the mid arm; this was also found elsewhere in the Milky Way disk. In addition, we collated the observed tangents to the so-called 3 kpc arm features; statistically they are found to be near l = −18° ± 2° and near l = +21° ± 2°, after excluding misidentified spiral arms. We find that the model-computed arm tangents in the inner Galaxy are spatially coincident with the mean longitude of the observed tangents to the 3 kpc arm features (same galactic longitudes, within the errors). These spatial similarities may be suggestive of a contiguous space.
Routeing Properties in a Gibbsian Model for Highly Dense Multihop Networks

We investigate a probabilistic model for routeing in a multihop ad hoc communication network, where each user sends a message to the base station. Messages travel in hops via other users, used as relays. Their trajectories are chosen at random according to a Gibbs distribution, which favors trajectories with low interference, measured in terms of signal-to-interference ratio. This model was introduced in our earlier paper, where we expressed, in the limit of a high density of users, the typical distribution of the family of trajectories in terms of a law of large numbers. In this paper, we derive its qualitative properties. We analytically identify the emerging typical scenarios in three extreme regimes. We analyze the typical number of hops and the typical length of a hop and the deviation of the trajectory from the straight line, regime 1 in the limit of a large communication area and large distances and regime 2 in the limit of a strong interference weight. In both the regimes, the typical trajectory approaches a straight line quickly, in regime 1 with equal hop lengths. Interestingly, in regime 2, the typical length of a hop diverges logarithmically in the distance of the transmitter to the base station. We further analyze (regime 3) local and global repulsive effects of a densely populated subarea on the trajectories.
New scale factor measure

The computation of probabilities in an eternally inflating universe requires a regulator or ``measure. '' The scale factor time measure truncates the Universe when a congruence of timelike geodesics has expanded by a fixed volume factor. This definition breaks down if the generating congruence is contracting\char22{}a serious limitation that excludes from consideration gravitationally bound regions such as our own. Here we propose a closely related regulator which is well defined in the entire spacetime. The new scale factor cutoff restricts to events with a scale factor below a given value. Since the scale factor vanishes at caustics and crunches, this cutoff always includes an infinite number of disconnected future regions. We show that this does not lead to divergences. The resulting measure combines desirable features of the old scale factor cutoff and of the light-cone time cutoff, while eliminating some of the disadvantages of each.
Estimating the Just Noticeable Difference of Tactile Feedback in Oculus Quest 2 Controllers

In virtual reality (VR) applications, humans experience the provided content not only through the visual and auditory systems but also through the somatosensory system. Thus, we decided to conduct a VR study to further explore the just noticeable difference (JND) of tactile feedback to understand humans’ perceptions of tactile stimuli. Our VR study examined the JND in terms of the intensity, duration, and frequency of tactile feedback provided through commercially available vibrotactile motion controllers, the Oculus Quest 2 controllers. We instructed participants to report whether they perceived a difference between a reference (variation) and a testing stimulus at each point in the experiment for a different property (intensity, duration, and frequency) of tactile feedback. We report both positive and negative JND values for the three properties of tactile feedback. We discuss our findings and limitations and provide directions for future studies regarding tactile perception for commercially available tactile feedback devices.
A NOTE ON ARTINIAN LOCAL RINGS

In this note, we prove that an Artinian local ring is G-semisimple (resp., SG-semisimple, 2-SG-semisimple) if and only if its maximal ideal is G-projective (resp., SG-projective, 2-SG-projective). As a corollary, we obtain the global statement of the above. We also give some examples of local G-semisimple rings whose maximal ideals are n generated for some positive integer n .
THE EXTENDED MAIN-SEQUENCE TURNOFF CLUSTERS OF THE LARGE MAGELLANIC CLOUD—MISSING LINKS IN GLOBULAR CLUSTER EVOLUTION

Recent observations of intermediate-age (1–3 Gyr) massive star clusters in the Large Magellanic Cloud have revealed that the majority possess bifurcated or extended main-sequence turnoff (EMSTO) morphologies. This effect can be understood to arise from subsequent star formation among the stellar population with age differences between constituent stars amounting to 50–300 Myr. Age spreads of this order are similarly invoked to explain the light-element abundance variations witnessed in ancient globular clusters (GCs). In this paper, we explore the proposition that the clusters exhibiting the EMSTO phenomenon are a general phase in the evolution of massive clusters, one that naturally leads to the particular chemical properties of the ancient GC population. We show that the isolation of EMSTO clusters to intermediate ages is the consequence of observational selection effects. In our proposed scenario, the EMSTO phenomenon is identical to that which establishes the light-element abundance variations that are ubiquitous in the ancient GC population. Our scenario makes a strong prediction: EMSTO clusters will exhibit abundance variations in the light-elements characteristic of the ancient GC population.
Aspect of Consumer Behavioural Theory in the Context of Graphic Design

Research findings on consumers’ behaviour are few in the context of graphic design. This study contributes to the knowledge by delving into the available source of information on consumers’ behaviour in order to bring its relationship with graphic design into the limelight. The study is based on the notion that understanding the mindset of consumers will help avert dissonance in interpretations of graphic design obvious in the consumers’ environment. In this study, the extent to which graphic design operates in a commensal relationship with consumers’ behaviour has been explored with the notion of unfolding the ever extension of the scope of graphic design to consumer-based themes beyond the studio environment. Based on this intention, the study has been based on the review of prior literature purposively sampled using a random sample. This study as literature of consumer behaviour reveals a crucial aspect of effective communication design; it assists a graphic designer to realize, consider and predict consumer behaviour. Perhaps, ideas posited through the findings of this paper may inspire more research that is based on graphic design adaptation to the changing world of the consumers’ behaviour.
Non-Gaussian Entangled States and Entangled Orthonormal Basis

We provide a family of non-Gaussian pure entangled states in a bipartite system as the eigenstates of a quadratic Hamiltonian composed of Einstein–Podolsky–Rosen-like operators. The ground state of the Hamiltonian corresponds to the two-mode-squeezed vacuum and belongs to the Gaussian states. In contrast, all of the excited states are non-Gaussian states. A separable inequality maximally violated by the eigenstates is derived.
Kitaev-Heisenberg-J2-J3model for the iridatesA2IrO3

A Kitaev-Heisenberg-J2-J3 model is proposed to describe the Mott-insulating layered iridates A2IrO3 (A=Na,Li). The model is a combination of the Kitaev honeycomb model and the Heisenberg model with all three nearest neighbor couplings J1, J2 and J3. A rich phase diagram is obtained at the classical level, including the experimentally suggested zigzag ordered phase; as well as the stripy phase, which extends from the Kitaev-Heisenberg limit to the J1-J2-J3 one. Combining the experimentally observed spin order with the optimal fitting to the uniform magnetic susceptibility data gives an estimate of possible parameter values, which in turn reaffirms the necessity of including both the Kitaev and farther neighbor couplings.
Toward a minimum branching fraction for dark matter annihilation into electromagnetic final states

Observational limits on the high-energy neutrino background have been used to place general constraints on dark matter that annihilates only into standard model particles. Dark matter particles that annihilate into neutrinos will also inevitably branch into electromagnetic final states through higher-order tree and loop diagrams that give rise to charged leptons, and these charged particles can transfer their energy into photons via synchrotron radiation or inverse Compton scattering. In the context of effective field theory, we calculate the loop-induced branching ratio to charged leptons and show that it is generally quite large, typically > or approx. 1%, when the scale of the dark matter mass exceeds the electroweak scale, M{sub W}. For a branching fraction >or approx. 3%, the synchrotron radiation bounds on dark matter annihilation are currently stronger than the corresponding neutrino bounds in the interesting mass range from 100 GeV to 1 TeV. For dark matter masses below M{sub W}, our work provides a plausible framework for the construction of a model for 'neutrinos-only' dark matter annihilations.
Fast entanglement detection for unknown states of two spatial qutrits

We investigate the practicality of the method proposed by Maciel et al. [Phys. Rev. A. 80, 032325 (2009). ] for detecting the entanglement of two spatial qutrits (three-dimensional quantum systems), which are encoded in the discrete transverse momentum of single photons transmitted through a multislit aperture. The method is based on the acquisition of partial information of the quantum state through projective measurements, and a data processing analysis done with semidefinite programs. This analysis relies on generating gradually an optimal entanglement witness operator, and numerical investigations have shown that it allows for the entanglement detection of unknown states with a cost much lower than full state tomography.
Regularized solution of a nonlinear problem in electromagnetic sounding

Non destructive investigation of soil properties is crucial when trying to identify inhomogeneities in the ground or the presence of conductive substances. This kind of survey can be addressed with the aid of electromagnetic induction measurements taken with a ground conductivity meter. In this paper, starting from electromagnetic data collected by this device, we reconstruct the electrical conductivity of the soil with respect to depth, with the aid of a regularized damped Gauss–Newton method. We propose an inversion method based on the low-rank approximation of the Jacobian of the function to be inverted, for which we develop exact analytical formulae. The algorithm chooses a relaxation parameter in order to ensure the positivity of the solution and implements various methods for the automatic estimation of the regularization parameter. This leads to a fast and reliable algorithm, which is tested on numerical experiments both on synthetic data sets and on field data. The results show that the algorithm produces reasonable solutions in the case of synthetic data sets, even in the presence of a noise level consistent with real applications, and yields results that are compatible with those obtained by electrical resistivity tomography in the case of field data.
The Insufficiency of Statistics for Detecting Racial Discrimination by Police

Benchmark tests are employed when testing for racial discrimination by police. Neil and Winship (2019) emphasize that such tests are threatened by Simpson’s paradox, but avoid analyzing the paradox causally. They consequently cannot elucidate the link between statistical quantities and discrimination hypotheses. Simpson’s paradox reveals that the statistics given by benchmark tests are not invariant to conditioning on additional variables. On this basis, I argue that benchmark statistics should not by themselves be taken to provide any evidence regarding discrimination, absent additional assumptions. Causal models can represent these assumptions.
Chapter 1 Conditional generative models

To motivate this use case, consider the following problem. We wish to colorize a black and white photo, that is, we wish to predict the color of each pixel in a black and white photo. Now, we already have seen some tools we could apply to this problem. First we will try to solve it with least-squares regression. Second, with softmax classification. We will see that both approaches fall short of a good solution. This will motivate the necessity of conditional generative models, which turn out to solve the colorization problem quite nicely, and can produce nearly photorealistic results.
Study of axial strain-induced torsion of single-wall carbon nanotubes using the 2D continuum anharmonic anisotropic elastic model

Recent molecular dynamic simulations have found that chiral single-walled carbon nanotubes (SWCNTs) twist during stretching, resembling the motion of a screw. Obviously this phenomenon, as a type of curvature–chirality effect, cannot be explained by the usual isotropic elastic theory of SWCNTs. More interestingly, with larger axial strains (before buckling), the axial strain-induced torsion (a-SIT) shows asymmetric behaviors for axial tensile and compressing strains, which suggests the anharmonic elasticity of SWCNTs plays an important role in real a-SIT responses. In order to study the a-SIT of chiral SWCNTs with actual sizes, and to avoid possible deviation of computer simulation results due to the finite-size effect, we propose a two-dimensional (2D) analytical continuum model which can be used to describe SWCNTs of arbitrary chirality, curvature, and length, and which is concerned with their anisotropic and anharmonic elasticity. The elastic energy of the present model comes from the continuum limit of lattice energy based on second generation reactive empirical bond order potential (REBO-II), a well-established empirical potential for solid carbons. Our model has no adjustable parameters, except for those presented in REBO-II, and all the coefficients in the model can be calculated analytically. Using our method, we obtain the a-SIT responses of chiral SWCNTs with arbitrary radii, chiralities and lengths. Our results are in reasonable agreement with recent molecular dynamic simulations (Liang et al 2006 Phys. Rev. Lett. 96 165501). Our approach can also be used to calculate other curvature–chirality-dependent anharmonic mechanical responses of SWCNTs.
C 4 interpolation and smoothing exponential splines based on a sixth order differential operator with two parameters

In this work, a class of interpolation and smoothing exponential splines with respect to a sixth order differential operator with two parameters is constructed. All the square matrices involved in the construction are proved to be tridiagonal symmetric and diagonally dominant, which results in algorithms for computing this class of exponential splines. The obtained splines have C 4 continuity and are the minimum solution of the combination of interpolation and a generalized smoothing energy integral. The performances of the resulting splines in financial data from the S &P500 index and the effect of fitting multi-exponential decay data are given. Numerical experiments show that the resulting splines have more freedom to adjust the shape and control the energy of the curves and perform better than previous methods in fitting multi-exponential decay data. And cross validation and generalized cross validation for determining an appropriate smoothing parameter are also developed.