Miracle-dz/UniFAR-FTUs huggingface dataset:
APOBEC3 degradation is the primary function of HIV-1 Vif for virus replication in the myeloid cell line THP-1

HIV-1 must overcome multiple innate antiviral mechanisms to replicate in CD4+ T lymphocytes and macrophages. Previous studies have demonstrated that the APOBEC3 (A3) family of proteins (at least A3D, A3F, A3G, and stable A3H haplotypes) contribute to HIV-1 restriction in CD4+ T lymphocytes. Virus-encoded virion infectivity factor (Vif) counteracts this antiviral activity by degrading A3 enzymes allowing HIV-1 replication in infected cells. In addition to A3 proteins, Vif also targets other cellular proteins in CD4+ T lymphocytes, including PPP2R5 proteins. However, whether Vif primarily degrades only A3 proteins or has additional essential targets during viral replication is currently unknown. Herein, we describe the development and characterization of A3F-, A3F/A3G-, and A3A-to-A3G-null THP-1 cells. In comparison to Vif-proficient HIV-1, Vif-deficient viruses have substantially reduced infectivity in parental and A3F-null THP-1 cells, and a more modest decrease in infectivity in A3F/A3G-null cells. Remarkably, disruption of A3A–A3G protein expression completely restores the infectivity of Vif-deficient viruses in THP-1 cells. These results indicate that the primary function of Vif during HIV-1 replication in THP-1 cells is the targeting and degradation of A3 enzymes. Importance HIV-1 Vif neutralizes the HIV-1 restriction activity of A3 proteins. However, it is currently unclear whether Vif has additional essential cellular targets. To address this question, we disrupted A3A to A3G genes in the THP-1 myeloid cell line using CRISPR and compared the infectivity of wildtype HIV-1 and Vif mutants with the selective A3 neutralization activities. Our results demonstrate that the infectivity of Vif-deficient HIV-1 and the other Vif mutants is fully restored by ablating the expression of cellular A3A to A3G proteins. These results indicate that A3 proteins are the only essential target of Vif that is required for HIV-1 replication in THP-1 cells.
Global input-to-State stability and stabilization of discrete-Time Piece-Wise Affine Systems

This article presents conditions for global input-to-state stability (ISS) and stabilization of discrete-time,possiblydiscontinuous,piecewiseaffine(PWA)systems.Piecewisequadratic, possibly discontinuous candidate ISS Lyapunov functions are employed for both analysis and synthesis purposes. This enables us to obtain sufficient conditions based on linear matrix inequalities, which can be solved efficiently. One of the advantages of using the ISS framework is that additive disturbance inputs are explicitly taken into account in the analysis and synthesis procedures. Furthermore, the results apply to PWA systems in their full generality, i.e. non-zero affine terms are allowed in the regions in the partition whose closure contains the origin.
A survey of the specificity and mechanism of 1,6 hexanediol-induced disruption of nuclear transport

ABSTRACT Selective transport through the nuclear pore complex (NPC) depends on the dynamic binding of FG-repeat containing nucleoporins, the FG-nups, with each other and with Karyopherins (Kaps). Here, we assessed the specificity and mechanism by which the aliphatic alcohol 1,6-hexanediol (1,6HD) disrupts the permeability barrier of NPCs in live baker’s yeast cells. After a 10-minute exposure to 5% 1,6HD, no notable changes were observed in cell growth, cytosolic pH and ATP levels, or the appearance of organelles. However, effects on the cytoskeleton and Hsp104 were noted. 1,6HD clearly affected the NPC permeability barrier, allowing passive nuclear entry of a 177kDa reporter protein that is normally confined to the cytosol. Moreover, multiple Kaps were displaced from NPCs, and the displacement of Kap122-GFP correlated with the observed passive permeability changes. 1,6HD thus temporarily permeates NPCs, and in line with Kap-centric models, the mechanism includes the release of numerous Kaps from the NPCs.
The human superior colliculus motor region does not respond to finger movements

Electrophysiological studies in macaques and functional neuroimaging in humans revealed a motor region in the superior colliculus (SC) for upper limb reaching movements. Connectivity studies in macaques reported direct connections between this SC motor region and cortical premotor arm, hand, and finger regions. These findings motivated us to investigate if the human SC is also involved in sequential finger tapping movements. We analysed fMRI task data of 130 participants executing simple finger tapping from the Human Connectome Project (HCP). While we found strong signals in the SC for visual cues, we found no signals related to simple finger tapping. Assuming a differential effect owing to simple and complex finger tapping sequences, we searched for responses in the SC corresponding to complex finger tapping above simple finger tapping sequences. We observed expected signal differences in cortical motor and premotor regions, but our analyses provided no evidence for signals related to simple or complex finger tapping in the SC. Despite evidence for direct anatomical connections of the SC motor region and cortical premotor hand and finger areas in macaques, our results suggest that the SC is not involved in simple or complex finger tapping in humans.
Numerical solution of Plateau’s problem by a finite element method

This paper concerns the application of a finite element method to the numerical solution of a nonrestricted form of the Plateau problem, as well as to a free boundary prob- lem of Plateau type. The solutions obtained here are examined for several examples and are considered to be sufficiently accurate. It is also observed that the hysteresis effect, which is a feature of a nonlinear problem, appears in this problem. 1. Introduction. Methods for the numerical solution of the Plateau problem have so far been examined by D. Greenspan (3), (4), using the combination technique of difference and variational methods, and by P. Concus (5), using a finite difference method. These two methods can be applied only to the so-called restricted form of the Plateau problem described by Forsythe and Wasow (2, Section 18.9), that is, to the problems where the boundary condition is represented by a single-valued function. Thus, they cannot be applied to the problem where the boundary condition is repre- sented by a multi-valued function, such as Courant's example described later. This paper shows that such multi-valued boundary-value problems can be solved numerically by a finite element method. In this case, two solution methods, one for a free boundary problem and the other in a cyclindrical coordinate system, are presented.
Limits on Planets around Pulsating White Dwarf Stars

We present limits on planetary companions to pulsating white dwarf stars. A subset of these stars exhibit extreme stability in the period and phase of some of their pulsation modes; a planet can be detected around such a star by searching for periodic variations in the arrival time of these pulsations. We present limits on companions greater than a few Jupiter masses around a sample of 15 white dwarf stars as part of an ongoing survey. One star shows a variation in arrival time consistent with a 2MJ planet in a 4.5 yr orbit. We discuss other possible explanations for the observed signal and conclude that a planet is the most plausible explanation based on the data available.
Hydrodynamic Stability and Turbulence: Beyond Transients to a Self‐Sustaining Process

Transition from laminar to turbulent flows has generally been studied by considering the linear and weakly nonlinear evolution of small disturbances to the laminar flow. That approach has been fruitless for many shear flows, and a last hope for its success has been the existence of transient growth phenomena. The physical origin of those linear transient effects is elucidated, revealing serious limitations both of previous analyses and of the phenomena themselves, which preclude them from causing direct transition. Nonetheless, some transient effects are symptomatic of one element of a nonlinear process that becomes self-sustaining at a small enough dissipation. The process is identified, and its description requires a departure from the traditional focus on the laminar flow. A theory is outlined in which the mean flow has an intrinsic spanwise variation. Evidence indicates this is also the central mechanism in the near wall-region of fully turbulent shear flows.
Watching English grammar change: a case study on complement selection in British and American English

This article traces the complement selection properties of the adjective accustomed from the eighteenth century to the present. The adjective has frequently selected sentential complements, but the study illustrates a major change affecting the form of such complements. In the eighteenth century they were regularly of the to infinitive type, but today they are almost as regularly of the to -ing type. Both syntactic and semantic factors are identified in the article as having an impact on the change. The study also compares the pace of the change in British and American English, arguing that incipient change was discernible in both varieties as early as the nineteenth century. It is argued further that, at the present time, the change has been completed more fully in American English than in British English. This conclusion is reached by considering sentences with extraction or filler–gap dependencies. The data in the article come from large electronic corpora.
Unraveling genetic variation among white spruce families generated through different breeding strategies: Heritability, growth, physiology, hormones and gene expression

Tree improvement programs select genotypes for faster growth, at both early and late stages, to increase yields over unimproved material, and the improvement is frequently attributed to genetic control in growth parameters among genotypes. Underutilized genetic variability among genotypes also has the potential to ensure future gains are possible. However, the genetic variation in growth, physiology and hormone control among genotypes generated from different breeding strategies has not been well characterized in conifers. We assessed growth, biomass, gas exchange, gene expression and hormone levels in white spruce seedlings obtained from three different breeding strategies (controlled crosses, polymix pollination, open pollination) using parents grafted into a clonal seed orchard in Alberta, Canada. A pedigree-based best linear unbiased prediction (ABLUP) mixed model was implemented to quantify variability and narrow-sense heritability for target traits. The levels of several hormones and expression of gibberellin-related genes in apical internodes were also determined. Over the first two years of development, the estimated heritabilities for height, volume, total dry biomass, above ground dry biomass, root:shoot ratio and root length, varied between 0.10 and 0.21, with height having the highest value. The ABLUP values showed large genetic variability in growth and physiology traits both between families from different breeding strategies, and within families. The principal component analysis showed that developmental and hormonal traits explained 44.2% and 29.4% of the total phenotypic variation between the three different breeding strategies and two growth groups. In general, controlled crosses from the fast growth group showed the best apical growth, with more accumulation of indole-3-acetic acid, abscisic acid, phaseic acid, and a 4-fold greater gene expression of PgGA3ox1 in genotypes from controlled crosses versus those from open pollination. However, in some cases, open pollination from the fast and slow growth groups showed the best root development, higher water use efficiency (iWUE and δ13C) and more accumulation of zeatin and isopentenyladenosine. In conclusion, tree domestication can lead to trade-offs between growth, carbon allocation, photosynthesis, hormone levels and gene expression, and we encourage the use of this phenotypic variation identified in improved and unimproved trees to advance white spruce tree improvement programs.
Longitudinal changes in blood pressure and fasting plasma glucose among 5,398 primary care patients with concomitant hypertension and diabetes: An observational study and implications for community-based cardiovascular prevention

Aims To assess longitudinal changes in blood pressure (BP) and fasting plasma glucose (FPG) in primary care patients with concomitant hypertension and type 2 diabetes mellitus (T2DM), and to explore factors associated with patients' inability to improve BP and FPG at follow-up. Methods We constructed a closed cohort in the context of the national basic public health (BPH) service provision in an urbanised township in southern China. Primary care patients who had concomitant hypertension and T2DM were retrospectively followed up from 2016 to 2019. Data were retrieved electronically from the computerised BPH platform. Patient-level risk factors were explored using multivariable logistic regression analysis. Results We included 5,398 patients (mean age 66 years; range 28.9 to 96.1 years). At baseline, almost half [48.3% (2,608/5,398)] of patients had uncontrolled BP or FPG. During follow-up, more than one-fourth [27.2% (1,467/5,398)] of patients had no improvement in both BP and FPG. Among all patients, we observed significant increases in systolic BP [2.31 mmHg, 95% confidence interval (CI): 2.04 to 2.59, p < 0.001], diastolic BP (0.73 mmHg, 0.54 to 0.92, p < 0.001), and FPG (0.12 mmol/l, 0.09 to 0.15, p < 0.001) at follow-up compared to baseline. In addition to changes in body mass index [adjusted odds ratio (aOR)=1.045, 1.003 to 1.089, p = 0.037], poor adherence to lifestyle advice (aOR = 1.548, 1.356 to 1.766, p < 0.001), and unwillingness to actively enrol in health-care plans managed by the family doctor team (aOR = 1.379, 1.128 to 1.685, p = 0.001) were factors associated with no improvement in BP and FPG at follow-up. Conclusion A suboptimal control of BP and FPG remains an ongoing challenge to primary care patients with concomitant hypertension and T2DM in real-world community settings. Tailored actions aiming to improve patients' adherence to healthy lifestyles, expand the delivery of team-based care, and encourage weight control should be incorporated into routine healthcare planning for community-based cardiovascular prevention.
The incidence and risk factors of perioperative cardiac complications in noncardiac major surgery in high-altitude areas: A prospective trial in Tibet autonomous region, China

Background The risk of perioperative cardiac complications (PCCs) in patients living in high-altitude areas may increase with more adverse clinical outcomes due to the special geographical environment, which has not yet been studied. We aimed to determine the incidence and analyze risk factors for PCCs in adult patients undergoing major noncardiac surgery in the Tibet Autonomous Region. Methods This prospective cohort study enrolled resident patients from high-altitude areas receiving major noncardiac surgery in Tibet Autonomous Region People's Hospital in China. Perioperative clinical data were collected, and the patients were followed up until 30 days after surgery. The primary outcome was PCCs during the operation and within 30 days after the surgery. Logistic regression was used to build the prediction models for PCCs. A receiver operating characteristic (ROC) curve was used to evaluate the discrimination. A prognostic nomogram was constructed to generate a numerical probability of PCCs for patients undergoing noncardiac surgery in high-altitude areas. Results Among the 196 patients living in high-altitude areas involved in this study, 33 (16.8%) suffered PCCs perioperatively and within 30 days after surgery. Eight clinical factors were identified in the prediction model, including older age (P = 0.028), extremely high altitude above 4,000 m (P = 0.442), preoperative metabolic equivalent (MET) < 4 (P = 0.153), history of angina within 6 months (P = 0.037), history of great vascular disease (P = 0.073), increased preoperative high sensitivity C-reactive protein (hs-CRP) (P = 0.072), intraoperative hypoxemia (P = 0.025) and operation time >3 h (P = 0.043). The area under the curve (AUC) was 0.766 (95% confidence interval: 0.785–0.697). The score calculated from the prognostic nomogram predicted the risk of PCCs in high-altitude areas. Conclusion The incidence of PCCs in resident patients living in high-altitude areas who underwent noncardiac surgery was high, and the risk factors included older age, high altitude above 4,000 m, preoperative MET < 4, history of angina within 6 months, history of great vascular disease, increased preoperative hs-CRP, intraoperative hypoxemia, and operation time >3 h. The prognostic nomogram of this study could help to assess the PCCs for patients in high-attitude areas undergoing noncardiac surgery. Clinical Trial Registration ClinicalTrials.gov ID: NCT04819698.
Numerical Simulation of Limit-cycle Oscillations of a Cropped Delta Wing Using the Full Navier-Stokes Equations

This paper presents simulations of limit-cycle oscillations of a cropped delta wing using a computational technique that implicitly couples a full Navier-Stokes solver to a linear structural solver. Computational results are compared with existing experimental measurements of the limit-cycle response of the delta wing. The limit-cycle oscillation is shown to consist primarily of a response of the first bending mode and the first torsional mode. Aerodynamic features of the limit cycle identified include a leading-edge vortex and a double shock structure. The leading edge vortex acts like an aerodynamic spring and provides the physical mechanism for the evolution of the limit cycle on the delta wing. Computations are repeated using the Euler equations to determine if the inviscid flow equations adequately simulate the observed limit cycle response.
A review of bioengineering techniques applied to breast tissue: Mechanical properties, tissue engineering and finite element analysis

Female breast cancer was the most prevalent cancer worldwide in 2020, according to the Global Cancer Observatory. As a prophylactic measure or as a treatment, mastectomy and lumpectomy are often performed at women. Following these surgeries, women normally do a breast reconstruction to minimize the impact on their physical appearance and, hence, on their mental health, associated with self-image issues. Nowadays, breast reconstruction is based on autologous tissues or implants, which both have disadvantages, such as volume loss over time or capsular contracture, respectively. Tissue engineering and regenerative medicine can bring better solutions and overcome these current limitations. Even though more knowledge needs to be acquired, the combination of biomaterial scaffolds and autologous cells appears to be a promising approach for breast reconstruction. With the growth and improvement of additive manufacturing, three dimensional (3D) printing has been demonstrating a lot of potential to produce complex scaffolds with high resolution. Natural and synthetic materials have been studied in this context and seeded mainly with adipose derived stem cells (ADSCs) since they have a high capability of differentiation. The scaffold must mimic the environment of the extracellular matrix (ECM) of the native tissue, being a structural support for cells to adhere, proliferate and migrate. Hydrogels (e.g., gelatin, alginate, collagen, and fibrin) have been a biomaterial widely studied for this purpose since their matrix resembles the natural ECM of the native tissues. A powerful tool that can be used in parallel with experimental techniques is finite element (FE) modeling, which can aid the measurement of mechanical properties of either breast tissues or scaffolds. FE models may help in the simulation of the whole breast or scaffold under different conditions, predicting what might happen in real life. Therefore, this review gives an overall summary concerning the human breast, specifically its mechanical properties using experimental and FE analysis, and the tissue engineering approaches to regenerate this particular tissue, along with FE models.
Cross-group friendship and collective action in community solidarity initiatives with displaced people and resident/nationals

Introduction: In Ireland, people seeking asylum (displaced people) receive accommodation in a system called “Direct Provision” (DP) while they wait for their applications for protection to be processed. The living conditions of DP have been described as illegal and inhumane by national and international human rights groups, and the system exacerbates the social exclusion of displaced people. Community responses to DP by displaced people and resident/nationals of Ireland include the creation of informal groups called community solidarity initiatives (CSI), through which cross-group friendships are forged by participation in shared cultural activities. We hypothesized that, compared to non-CSI participants, participants of CSI would report more cross-group friendships, and that more cross-group friendships would predict stronger collective action intentions to support the campaign to end DP, especially among resident/nationals. Methods: We recruited residents/nationals and displaced persons with and without CSI experience to complete a self-report questionnaire (n = 199), measuring cross-group friendship, collective action intentions, and intergroup attitudes. Data were collected between July 2020 and March 2021, using a combination of online and paper surveys. We conducted ANOVA and conditional process analyses on the data to test our hypotheses. Results: As predicted, CSI participants reported more contact with cross-group friends and stronger collective action intentions than non-participators. Conditional process analysis indicated that CSI participation facilitated resident/nationals’ political solidarity with displaced people through cross-group friendship. Discussion: Findings identify the role of group membership in the relationship between contact and collective action for migrant justice, illustrating the potential of CSI to bolster intergroup solidarity and social cohesion through shared activities and cross-group friendship. As such, findings make an important contribution to the literature on intergroup contact, solidarity, and social cohesion, and will be relevant for community practitioners, civil society organisations, NGOs, and policy makers.