Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of Putative Drug Targets in Highly Resistant Gram-Negative Bacteria; and Drug Discovery Against Glycyl-tRNA Synthetase as a New Target

Background: Gram-negative bacterial infections are on the rise due to the high prevalence of multidrug-resistant bacteria, and efforts must be made to identify novel drug targets and then new antibiotics. Methods: In the upstream part, we retrieved the genome sequences of 4 highly resistant Gram-negative bacteria (e.g., Acinetobacter baumannii, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Enterobacter cloacae). The core proteins were assessed to find common, cytoplasmic, and essential proteins with no similarity to the human proteome. Novel drug targets were identified using DrugBank, and their sequence conservancy was evaluated. Protein Data Bank files and STRING interaction networks were assessed. Finally, the aminoacylation cavity of glycyl-tRNA synthetase (GlyQ) was virtually screened to identify novel inhibitors using AutoDock Vina and the StreptomeDB library. Ligands with high binding affinity were clustered, and then the pharmacokinetics properties of therapeutic agents were investigated. Results: A total of 6 common proteins (e.g., RP-L28, RP-L30, RP-S20, RP-S21, Rnt, and GlyQ) were selected as novel and widespread drug targets against highly resistant Gram-negative superbugs based on different criteria. In the downstream analysis, virtual screening revealed that Rimocidin, Flavofungin, Chaxamycin, 11,11′-O-dimethyl-14′-deethyl-14′-methylelaiophylin, and Platensimycin were promising hit compounds against GlyQ protein. Finally, 11,11′-O-dimethyl-14′-deethyl-14′-methylelaiophylin was identified as the best potential inhibitor of GlyQ protein. This compound showed high absorption capacity in the human intestine. Conclusion: The results of this study provide 6 common putative new drug targets against 4 highly resistant and Gram-negative bacteria. Moreover, we presented 5 different hit compounds against GlyQ protein as a novel therapeutic target. However, further in vitro and in vivo studies are needed to explore the bactericidal effects of proposed hit compounds against these superbugs.
Prediction Equation for Physical Activity Energy Expenditure in 11–13-Year-Old Sri Lankan Children

This study aimed to develop a regression equation to predict physical activity energy expenditure (PAEE) using accelerometry. Children aged 11–13 years were recruited and randomly assigned to validation (n = 54) and cross-validation (n = 25) groups. The doubly labelled water (DLW) technique was used to assess energy expenditure and accelerometers were worn by participants across the same period. A preliminary equation was developed using stepwise multiple regression analysis with sex, height, weight, body mass index, fat-free mass, fat mass and counts per minute (CPM) as independent variables. Goodness-of-fit statistics were used to select the best prediction variables. The PRESS (predicted residual error sum of squares) statistical method was used to validate the final prediction equation. The preliminary equation was cross-validated on an independent group and no significant (p > 0.05) difference was observed in the PAEE estimated from the two methods. Independent variables of the final prediction equation (PAEE = [0.001CPM] − 0.112) accounted for 70.6% of the variance. The new equation developed to predict PAEE from accelerometry was found to be valid for use in Sri Lankan children.
Black Holes and Entropy

There are a number of similarities between black-hole physics and thermodynamics. Most striking is the similarity in the behaviors of black-hole area and of entropy: Both quantities tend to increase irreversibly. In this paper we make this similarity the basis of a thermodynamic approach to black-hole physics. After a brief review of the elements of the theory of information, we discuss black-hole physics from the point of view of information theory. We show that it is natural to introduce the concept of black-hole entropy as the measure of information about a black-hole interior which is inaccessible to an exterior observer. Considerations of simplicity and consistency, and dimensional arguments indicate that the black-hole entropy is equal to the ratio of the black-hole area to the square of the Planck length times a dimensionless constant of order unity. A different approach making use of the specific properties of Kerr black holes and of concepts from information theory leads to the same conclusion, and suggests a definite value for the constant. The physical content of the concept of black-hole entropy derives from the following generalized version of the second law: When common entropy goes down a black hole, the common entropy in the black-hole exterior plus the black-hole entropy never decreases. The validity of this version of the second law is supported by an argument from information theory as well as by several examples.
Optical coherence tomography in material deformation by using short pulse laser irradiation

We demonstrate the feasibility of OCT imaging for the investigation of samples, which are processed by the short pulse laser. The use of short pulse lasers in various material processing have provided the advantages such as a high peak power and a small heat affected zone over conventional methods based on mechanical treatment. However, due to the improper application of the lasers, the unwanted surface or structural deformation of materials and the thermal damages around an irradiation spot can be caused. Thus, the real-time monitoring/evaluation of laser processing performance in-situ is needed to prevent the excessive deformation of the material and to determine optimal processing conditions. As a standard method to investigation of the material processing by using the lasers, the scanning electron microscopy (SEM) or the transmission electron microscopy (TEM) observation of a physically cleaved surface is used although sample damages are given during the cleaving and polishing process. In this paper, we utilized the OCT advantages such as high resolution and non-invasive investigation to evaluate the laser processing performance. OCT images for the deformation monitoring of the ABS plastic present correlation with images obtained from conventional investigation methods. OCT images of the maxillary bone clearly show the difference in the pit formation of the biological sample at different irradiation conditions. We prove the potential of OCT for the evaluation of laser-processed various samples. Integrating OCT system into a laser processing system, we can visualize the effect of laser-based treatments in clinical and industrial fields.
Spatial Vector Autoregressions

Abstract A spatial vector autoregressive model (SpVAR) is defined as a VAR which includes spatial as well as temporal lags among a vector of stationary state variables. SpVARs may contain disturbances that are spatially as well as temporally correlated. Although the structural parameters are not fully identified in SpVARs, contemporaneous spatial lag coefficients may be identified by weakly exogenous state variables. Dynamic spatial panel data econometrics is used to estimate SpVARs. The incidental parameter problem is handled by bias correction rather than more popular alternatives such as generalised methods of moments (GMM). The interaction between temporal and spatial stationarity is discussed. The impulse responses for SpVARs are derived, which naturally depend upon the temporal and spatial dynamics of the model. We provide an empirical illustration using annual spatial panel data for Israel. The estimated SpVAR is used to calculate impulse responses between variables, over time, and across space. Finally, weakly exogenous instrumental variables are used to identify contemporaneous spatial lag coefficients.
Online multiple object tracker with enhanced features

Abstract. The online multiobject tracking (MOT), which integrates object detection and tracking into a single network, has made breakthroughs in recent years. However, most online trackers have a more monotonous prediction of the tracking offset in two consecutive frames, which may not be reliable when facing extreme situations such as occlusion and object deformation. Once the tracking offset of an object is biased, its corresponding tracklet will no longer maintain temporal consistency, which will seriously affect the tracking performance. In this paper, we propose a new online multiple object tracker with feature enhancement mechanism, namely En-Tracker. In En-Tracker, a multibranch kinematic analysis network (MKANet) is designed to address the above problems. MKANet estimates the pixel offset and instance offset of the object in parallel based on imitating the human thinking to joint position and appearance representations. Note that these two types of offsets compensate and facilitate each other to effectively deal with some extreme scenarios. In addition, we propose a kinematic-assisted feature synthesis enhancement (KFSE) module, which has a more comprehensive enhancement mechanism. Specifically, KFSE propagates previous tracking information to the current frame based on kinematic trend analysis while enhancing the characterization of detection features and appearance embeddings, which not only assists in object detection but also ensures the uniqueness of the appearance embeddings. Extensive experiments on MOT16 and MOT17 verify the effectiveness and advantage of our model.
Psychological Adjustment Profiles of LGBTQ+ Young Adults Residing with Their Parents during the COVID-19 Pandemic: An International Study

The COVID-19 pandemic has been associated with poor mental health symptoms, particularly among vulnerable populations such as LGBTQ+ individuals. In the present study, we aimed to (i) identify different psychological adjustment profiles among LGBTQ+ young adults during the COVID-19 pandemic and compare LGBTQ+ young adults in relation to (ii) sociodemographic characteristics and COVID-19-related experiences and (iii) the internal and external protective resources associated with each adjustment profile. An online questionnaire was administered to 1699 LGBTQ+ young adults from six countries (Brazil, Chile, Italy, Portugal, Sweden, and the UK). A cluster analysis was conducted, and four profiles of psychological adjustment were identified: unchallenged, resilient, distressed, and at-risk. The at-risk cluster scored lowest in social support (particularly from family). The profiles of participants who experienced the highest levels of pandemic adversity (at-risk and resilient) comprised mostly South American participants, those under lockdown at the time of survey completion, those who self-identified as transgender and non-binary, and those with a plurisexual sexual orientation. Interventions should consider strategies to help young adults maintain support systems and reinforce the value of positive family relationships. Specific groups within the LGBTQ+ community that seem to be in a particularly vulnerable situation may need additional tailored support.
Systemic lupus erythematosus is causally associated with hypothyroidism, but not hyperthyroidism: A Mendelian randomization study

Background The relationship between systemic lupus erythematosus (SLE) and thyroid diseases is still controversial. Due to confounders and reverse causation, previous studies were not convincing. We aimed to investigate the relationship between SLE and hyperthyroidism or hypothyroidism by Mendelian randomization (MR) analysis. Methods We performed a two-step analysis using bidirectional two-sample univariable and multivariable MR (MVMR) to explore the causality of SLE and hyperthyroidism or hypothyroidism in three genome-wide association studies (GWAS) datasets, including 402,195 samples and 39,831,813 single-nucleotide polymorphisms (SNPs). In the first step analysis, with SLE as exposure and thyroid diseases as outcomes, 38 and 37 independent SNPs strongly (P < 5*10-8) associated with SLE on hyperthyroidism or SLE on hypothyroidism were extracted as valid instrumental variables (IVs). In the second step analysis, with thyroid diseases as exposures and SLE as outcome, 5 and 37 independent SNPs strongly associated with hyperthyroidism on SLE or hypothyroidism on SLE were extracted as valid IVs. In addition, MVMR analysis was performed in the second step analysis to eliminate the interference of SNPs that were strongly associated with both hyperthyroidism and hypothyroidism. 2 and 35 valid IVs for hyperthyroidism on SLE and hypothyroidism on SLE were obtained in MVMR analysis. MR results of two steps analysis were estimated respectively by multiplicative random effects-inverse variance weighted (MRE-IVW), simple mode (SM), weighted median (WME) and MR-Egger regression methods. Sensitivity analysis and visualization of MR results were performed by heterogeneity test, pleiotropy test, leave-one-out test, scatter plots, forest plots and funnel plots. Results The MRE-IVW method in the first step of MR analysis revealed that SLE was causally associated with hypothyroidism (OR = 1.049, 95% CI = 1.020-1.079, P < 0.001), but not causally associated with hyperthyroidism (OR = 1.045, 95% CI = 0.987-1.107, P = 0.130). In the inverse MR analysis, the MRE-IVW method revealed that both hyperthyroidism (OR = 1.920, 95% CI = 1.310-2.814, P < 0.001) and hypothyroidism (OR = 1.630, 95% CI = 1.125-2.362, P = 0.010) were causally associated with SLE. Results from other MR methods were consistent with MRE-IVW. However, when MVMR analysis was performed, there was no longer a causal relationship of hyperthyroidism on SLE (OR = 1.395, 95% CI = 0.984-1.978, P = 0.061), nor was there a causal relationship of hypothyroidism on SLE (OR = 1.290, 95% CI = 0.823-2.022, P = 0.266). The stability and reliability of the results were confirmed by sensitivity analysis and visualization. Conclusions Our univariable and multivariable MR analysis revealed that systemic lupus erythematosus was causally associated with hypothyroidism, but did not provided evidence to support a causal relationship of hypothyroidism on SLE or between SLE and hyperthyroidism.
Double degenerates among DA white dwarfs

The results of a spectroscopic survey of catalog white dwarfs in search of radial velocity variations indicative of a binary motion are reported. In a sample of 54 DA white dwarfs, one Double Degenerate (DD) system with a period of 1.15 days (the shortest period DD system yet discovered) is found. Two other excellent and two good DD candidates, and two white dwarf + red dwarf pairs were also found. If all the candidates should be confirmed, this would indicate a frequency of about 13 percent of interacting binaries in an unbiased sample of evolved stars, with a DD frequency of about 10 percent. These results suggest fairly large values for the common-envelope parameter alpha, implying that a source of energy other than orbital may be required to eject the envelope during common-envelope events. Finally, in combination with previous evidence our result implies that DDs with WD components of the DA variety are unlikely to be the precursors of Type I supernovae, but DDs with non-DA components remain very attractive candidates. 20 refs.
The band gap of ultrathin amorphous and well-ordered Al2O3 films on CoAl(100) measured by scanning tunneling spectroscopy

The structural and electronic properties of ultrathin insulator Al2O3 films on CoAl(100) have been studied using a combination of scanning tunneling spectroscopy and microscopy. The analysis of the differential conductance yields a band gap of 2.6–2.9eV for amorphous Al2O3. In the case of a well-ordered alumina film, the band gap is increased to 4.5eV. On each of the oxide phases, the barrier height is to a large extent independent of local variations such as the surface corrugations or oxide steps.
Phononic Crystal Made of Silicon Ridges on a Membrane for Liquid Sensing

We propose the design of a phononic crystal to sense the acoustic properties of a liquid that is constituted by an array of silicon ridges on a membrane. In contrast to other concepts, the ridges are immersed in the liquid. The introduction of a suitable cavity in the periodic array gives rise to a confined defect mode with high localization in the cavity region and strong solid–liquid interaction, which make it sensitive to the acoustic properties of the liquid. By using a finite element method simulation, we theoretically study the transmission and cavity excitation of an incident flexural wave of the membrane. The observation of the vibrations of this mode can be achieved either outside the area of the phononic crystal or just above the cavity. We discuss the existence of the resonant modes, as well as its quality factor and sensitivity to liquid properties as a function of the geometrical parameters. The performance of the proposed sensor has then been tested to detect the variation in NaI concentration in a NaI–water mixture.
Temporal and spatial evolution of embodied carbon transfer network in the context of the domestic economic cycle

Abstract Under accelerated domestic economic cycle, it is significant to predict the embodied carbon transfer network (ECTNs) to identify key emission regions to improve emission reduction efficiency. Based on the existing China Multi-regional Input-Output Table (CMRIOs) for 2002, 2007, 2010, 2012, 2015 and 2017, the CMRIOs for 2002-2017 were updated, then the ECTNs were predicted and constructed from 2018 to 2025 through Particle Swarm Optimization- Support Vector Model. Finally, the spatial and temporal evolution trends of the ECTNs’ features were explored through complex networks analysis. The results showed that carbon leakage between provinces has been becoming increasingly serious. The small-world features of the ECTNs were becoming increasingly obvious. The distribution of provinces with great influence on carbon transfer was transferred from north to south, and then to the central region. Hebei, Jiangsu, Henan, Zhejiang, Inner Mongolia, and other resource-intensive and manufacturing provinces played an important "bridge" role in the trade between economic developed and developing provinces. Trade ties between non neighboring provinces have become increasingly close, which means the development of China’s integration has strengthened. This study provides a theoretical reference for the formulation of China’s overall carbon emission reduction policy. Graphical Abstract
Identifying Preferences for Conditional Cooperation Using Individual Beliefs

The relationship between contributions and elicited beliefs in a repeated two-person public good experiment is modeled with the help of a parsimounious random-utility function that allows for conditionally cooperative, opportunistic, and altruistic patterns of behavior. Under standard assumptions, a latent-class mixed logit specification with three sub-populations is shown to capture well heterogeneity in individual contribution levels over time, while also accomodating for different degrees of heteroscedasticity. The estimation results are consistent with the conjecture that the majority of players in public goods games are strongly conditional cooperators, with smaller fractions of the population leaning to opportunistic or altruistic behavior.
Insights into taxonomy and phylogenetic relationships of eleven Aristolochia species based on chloroplast genome

Introduction The Aristolochia, as an important genus comprised of over 400 species, has attracted much interest because of its unique chemical and pharmacological properties. However, the intrageneric taxonomy and species identification within Aristolochia have long been difficult because of the complexity of their morphological variations and lack of high-resolution molecular markers. Methods In this study, we sampled 11 species of Aristolochia collected from distinct habitats in China, and sequenced their complete chloroplast (cp) genomes. Results The 11 cp genomes of Aristolochia ranged in size from 159,375bp (A. tagala) to 160,626 bp (A. tubiflora), each containing a large single-copy (LSC) region (88,914-90,251 bp), a small single-copy (SSC) region (19,311-19,917 bp), and a pair of inverted repeats (IR) (25,175-25,698 bp). These cp genomes contained 130-131 genes each, including 85 protein-coding genes (CDS), 8 ribosomal RNA genes, and 37-38 transfer RNA genes. In addition, the four types of repeats (forward, palindromic, reverse, and complement repeats) were examined in Aristolochia species. A. littoralis had the highest number of repeats (168), while A. tagala had the lowest number (42). The total number of simple sequence repeats (SSRs) is at least 99 in A. kwangsiensis, and, at most, 161 in A. gigantea. Interestingly, we detected eleven highly mutational hotspot regions, including six gene regions (clpP, matK, ndhF, psbT, rps16, trnK-UUU) and five intergenic spacer regions (ccsA-ndhD, psbZ-trnG-GCC, rpl33-rps18, rps16-trnQ-UUG, trnS-GCU-trnG-UCC). The phylogenetic analysis based on the 72 protein-coding genes showed that 11 Aristolochia species were divided into two clades which strongly supported the generic segregates of the subgenus Aristolochia and Siphisia. Discussion This research will provide the basis for the classification, identification, and phylogeny of medicinal plants of Aristolochiaceae.
Systemic Inflammation/Nutritional Status Scores Are Prognostic but Not Predictive in Metastatic Non-Small-Cell Lung Cancer Treated with First-Line Immune Checkpoint Inhibitors

Biomarkers of systemic inflammation/nutritional status have been associated with outcomes in advanced-stage non-small-cell lung cancer (NSCLC) treated with immune checkpoint inhibitors (ICIs). However, most of them were not tested in cohorts of patients treated with ICIs in combination with chemotherapy (CT) (ICI + CT) or with CT alone, making it impossible to discriminate a predictive from a prognostic effect. We conducted a single-center retrospective study to search for associations between various baseline biomarkers/scores that reflected the systemic inflammation/nutritional status (Lung Immune Prognostic Index, Modified Lung Immune Prognostic Index, Scottish Inflammatory Prognostic Score, Advanced Lung Cancer Inflammation Index, EPSILoN, Prognostic Nutritional Index, Systemic Immune-Inflammation Index, Gustave Roussy Immune Score, Royal Marsden Hospital Prognostic Score, Lung Immuno-oncology Prognostic Score 3, Lung Immuno-oncology Prognostic Score 4, score published by Holtzman et al., and Glasgow Prognostic Score) and outcomes in metastatic NSCLC treated in a first-line setting either with ICI in monotherapy (cohort 1; n = 75), ICI + CT (cohort 2; n = 56), or CT alone (cohort 3; n = 221). In the three cohorts, the biomarkers/scores were moderately associated with overall survival (OS) and progression-free survival (PFS). Their prognostic performance was relatively poor, with a maximum c-index of 0.66. None of them was specific to ICIs and could help to choose the best treatment modality. The systemic inflammation/nutritional status, associated with outcomes independently of the treatment, is therefore prognostic but not predictive in metastatic NSCLC.
Dynamic Parameterization for Path Following Control

Path following is a basic skill for robots in industrial use. Since the objective of path following is to make a robot follow the reference path, the velocity of the robot or the timing of the motion does not need to be strictly controlled. In this paper, the reference path is defined as a function of the parameter that has dynamics. Using this parameter, we can define the contour error, which is the error that enables us to measure the distance from the reference path to the configuration of the robot. Although the contour error is suitable for use in path following, the dynamics of the parameter contain singular points at which the dynamics cannot be defined. In order to overcome this difficulty, globally defined dynamics are introduced, and two dynamics are integrated with a switching scheme. In this paper, the asymptotic stability of the whole system is proved theoretically. Computer simulation results also show the effectiveness of the method.