Miracle-dz/UniFAR-FTUs huggingface dataset:
Study on carbapenemase-producing bacteria by matrix-assisted laser desorption/ionization approach

The development of new techniques for the detection of carbapenemase activity is of great importance since the increased incident of resistance against carbapenems represents a serious threat to global public health. In this context, the matrix-assisted laser desorption/ionization approach already demonstrated to be a reliable tool for rapid carbapenemase detection. As a newly developed test, there is still a lack of in-depth analysis of its robustness and possible wider application. The main goal of this study was to evaluate the potential for using the design MBT STAR-Carba assay as the pre-characterization method for Enterobacterales and P. aeruginosa strains in terms of the produced classes of carbapenemases using modified procedure parameters—various suspension densities and incubation times. Moreover, its usefulness for the in-depth analysis and characterization of metallo-β-lactamases (MBL) was tested by applying inhibition assays. In this study, the designed assay proved to be a sensitive tool for the detection of carbapenemase hydrolytic activity, which can be successfully used to partially classify the class of carbapenemase present. Additionally, the use of defined high concentration suspensions would allow to shorten the incubation time to 1 minute for certain strains. Considering that the assay was also suitable to investigate the effect of different inhibitors on the MBL activity, it demonstrates far higher discriminatory potential than only a rapid routine carbapenemase detection tool and could be used as a susceptibility assay.
Neocortical Layer 1: An Elegant Solution to Top-Down and Bottom-Up Integration.

Many of our daily activities, such as riding a bike to work or reading a book in a noisy cafe, and highly skilled activities, such as a professional playing a tennis match or a violin concerto, depend upon the ability of the brain to quickly make moment-to-moment adjustments to our behavior in response to the results of our actions. Particularly, they depend upon the ability of the neocortex to integrate the information provided by the sensory organs (bottom-up information) with internally generated signals such as expectations or attentional signals (top-down information). This integration occurs in pyramidal cells (PCs) and their long apical dendrite, which branches extensively into a dendritic tuft in layer 1 (L1). The outermost layer of the neocortex, L1 is highly conserved across cortical areas and species. Importantly, L1 is the predominant input layer for top-down information, relayed by a rich, dense mesh of long-range projections that provide signals to the tuft branches of the PCs. Here, we discuss recent progress in our understanding of the composition of L1 and review evidence that L1 processing contributes to functions such as sensory perception, cross-modal integration, controlling states of consciousness, attention, and learning. Expected final online publication date for the Annual Review of Neuroscience, Volume 44 is July 2021. Please see http://www.annualreviews. org/page/journal/pubdates for revised estimates.
Left‐behind children's social adjustment and relationship with parental coping with children's negative emotions during the COVID‐19 pandemic in China

Using data collected from two provinces in China through an online survey, the current study aimed to investigate left‐behind children's emotional and academic adjustment during the COVID‐19 pandemic in China. The participants included 1780 left‐behind (960 boys) and 1500 non‐left‐behind (811 boys) children in elementary and junior high school with a mean age of 11.23. Self‐reported questionnaires concerning children's depression, loneliness, anxiety, and academic adjustment, and parents' coping with children's negative emotions were completed. The results suggested that compared with non‐left‐behind children, left‐behind children's depression and anxiety symptoms were more severe and their academic adjustment was poorer. However, left‐behind children had lower levels of loneliness than non‐left‐behind children. Additionally, supportive coping types, especially emotion‐focused and problem‐focused reactions, were significantly negatively correlated with children's depression and anxiety. Unsupportive coping types, especially distress and punitive reactions, were significantly positively correlated with children's depression and anxiety symptoms. Moreover, the relationships between punitive reactions and depression, ignoring and loneliness and problem‐focused reactions and academic adjustment were significantly stronger in left‐behind children. Hence, during the pandemic, left‐behind children were still at a disadvantage even with their parents' company. However, parents' coping style towards left‐behind children's negative emotions played a significant role in their adjustment.
Control of High Pretilt Angle for Nematic Liquid Crystal on Homeotropic Alignment Layer by In-situ Photoalignment Method

Pretilt angle generation and liquid crystal (LC) aligning capabilities for a nematic (N) LC with obliquely polarized UV exposure on a homeotropic polyimide (PI) surface by an in-situ photoalignment method were studied. The high pretilt angle of 30θ for NLC with obliquely polarized UV exposure on the PI surface for 20 min can be achieved. The pretilt angle generated in NLC by the in-situ photoalignment method was higher than that generated by a conventional photoalignment method on a homeotropic alignment layer. Also, we suggest that the generation of pretilt angle in NLC with obliquely polarized UV exposure during imidization of the polymer for homeotropic alignment is a promising method to generate a high pretilt angle. Lastly, the good electro-optical (EO) characteristics of the photoaligned vertical alignment (VA)-liquid crystal display (LCD) by UV exposure on the PI surface for 10 min were observed.
INTEGRATION Large-Scale Modeling Framework of Direct Cellular Vehicle-to-All (C-V2X) Applications

The transportation system has evolved into a complex cyber-physical system with the introduction of wireless communication and the emergence of connected travelers and connected automated vehicles. Such applications create an urgent need to develop high-fidelity transportation modeling tools that capture the mutual interaction of the communication and transportation systems. This paper addresses this need by developing a high-fidelity, large-scale dynamic and integrated traffic and direct cellullar vehicle-to-vehicle and vehicle-to-infrastructure (collectively known as V2X) modeling tool. The unique contributions of this work are (1) we developed a scalable implementation of the analytical communication model that captures packet movement at the millisecond level; (2) we coupled the communication and traffic simulation models in real-time to develop a fully integrated dynamic connected vehicle modeling tool; and (3) we developed scalable approaches that adjust the frequency of model coupling depending on the number of concurrent vehicles in the network. The proposed scalable modeling framework is demonstrated by running on the Los Angeles downtown network considering the morning peak hour traffic demand (145,000 vehicles), running faster than real-time on a regular personal computer (1.5 h to run 1.86 h of simulation time). Spatiotemporal estimates of packet delivery ratios for downtown Los Angeles are presented. This novel modeling framework provides a breakthrough in the development of urgently needed tools for large-scale testing of direct (C-V2X) enabled applications.
Monte Carlo simulation of electron thermalization in scintillator materials: Implications for scintillator nonproportionality

The lack of reliable quantitative estimates of the length and time scales associated with hot electron thermalization after a gamma-ray induced energy cascade obscures the interplay of various microscopic processes controlling scintillator performance and hampers the search for improved detector materials. We apply a detailed microscopic kinetic Monte Carlo model of the creation and subsequent thermalization of hot electrons produced by gamma irradiation of six important scintillating crystals to determine the spatial extent of the cloud of excitations produced by gamma rays and the time required for the cloud to thermalize with the host lattice. The main ingredients of the model are ensembles of microscopic track structures produced upon gamma excitation (including the energy distribution of the excited carriers), numerical estimates of electron-phonon scattering rates, and a calculated particle dispersion to relate the speed and energy of excited carriers. All these ingredients are based on first-princi.
HIV testing and seroprevalence among couples of people diagnosed with HIV in China: A meta-analysis

Background Partner notification and testing could expand HIV testing and link infections to care. We performed a meta-analysis on HIV testing rate and prevalence among couples of people diagnosed with HIV in China. Methods Six electronic databases (PubMed, Cochrane Library, Embase, Web of Science, the China National Knowledge Internet, and WanFang) and abstracts of five HIV/sexually transmitted infections conferences were searched up to February 1, 2020. Meta-analysis was conducted using a random-effects model to assess HIV testing rate and prevalence among couples of Chinese people diagnosed with HIV. Results Of 3,657 records retrieved, 42 studies were identified. Among them, three studies were conducted among pregnant women and 10 among men who have sex with men. The pooled uptake rate of couples HIV testing among Chinese people diagnosed with HIV was 65% (95% confidence interval, 57% -73%; 23 studies). The pooled HIV prevalence among couples who had an HIV test was 28% [24%-32%] (38 studies). Subgroup analyses showed that the pooled couples HIV testing uptake rates among pregnant women and men who have sex with men were 76% [66%-86%] (3 studies) and 49% [30%-68%] (8 studies), and the pooled HIV prevalence in two populations was 53% [27%-78%] (3 studies) and 14% [10%-17%] (10 studies), respectively. Conclusions Nearly two-thirds of couples of people diagnosed with HIV have had an HIV test, of whom 28% were positive. Couples of MSM with a positive HIV diagnosis had a lower testing rate, which indicates more effective strategies need to be carried out to improve couples HIV testing among Chinese MSM.
Export of reactive nitrogen from North America during summertime: Sensitivity to hydrocarbon chemistry

The global influence on tropospheric chemistry of nitrogen oxides (NOx = NO + NO2) emitted by fossil fuel combustion may be strongly modulated by nonmethane hydrocarbon (NMHC) chemistry taking place in the continental boundary layer. This effect is investigated using a three-dimensional, continental-scale model of tropospheric O3-NOx-NMHC chemistry over North America in summer. The model includes detailed representation of NMHC chemistry including in particular isoprene. Model results are evaluated with observations for ozone, reactive nitrogen species, and photochemical tracers at a number of sites in North America. Sensitivity analyses are conducted to explore the effects of assumptions regarding the aerosol chemistry of peroxy radicals and the fate of hydroxy organic nitrates produced from the oxidation of isoprene. A budget analysis for the United States in the model indicates that 9% Of NOx. emitted from fossil fuel combustion is exported out of the continental boundary layer as NOx, 3.5% is exported as peroxyacetyl nitrate (PAN), and 3.7% is exported as other organic nitrates. Isoprene is the principal NMHC responsible for the formation and export of organic nitrates, which eventually decompose to provide a source of NOx in the remote troposphere. Export of NOx. and organic nitrates from the U.S. boundary layer is found to be a major source of NOx. on the scale of the northern hemisphere troposphere and on the scale of the upper troposphere at northern midlatitudes. Proper representation of isoprene chemistry in the continental boundary layer is important for simulation Of NOx in global tropospheric chemistry models.
Low-Frequency Ultrasound to Improve Dead-End Ultrafiltration Performance

Low-frequency ultrasound (20 kHz) has been used to facilitate dead-end ultrafiltration of polymer solutions. The influence of ultrasonic irradiation on permeate fluxes and retention ratios was investigated and compared with conventional stirred and unstirred operations. In addition, the effect of the ultrasonic field on the membrane permeability and on the polymer solution was examined. The efficiency of ultrasound in enhancing ultrafiltration performance was demonstrated. This improvement is due to a decrease of the boundary layer resistance against permeation flow, which may be attributed to disturbance induced within the cell and at the membrane surface by physical effects associated with ultrasonic waves propagation.
Training focal lung pathology detection using an eye movement modeling example

Abstract. Purpose: Published reports suggest that nonoptimal visual search behavior is associated with false negatives in chest x-ray interpretation. Eye movement modeling example (EMME)-based training interventions, that is, interventions showing models of visual search to trainees, have been shown to improve visual search as well as task accuracy. Approach: We examined the detection of focal lung pathology on chest x-rays before and after two different EMME training interventions that have been shown to be efficient: (i) an EMME showing moving fixations on a blurred background (spotlight group) and (ii) an EMME showing moving fixations on a nonblurred background (circle group). These two experimental groups were compared to a control group that was only provided with the correct location of pathologies on the chest x-rays. Results: Performance outcomes showed improved detection sensitivity and specificity in all groups (also the control group). It appears that repetitive exposure to pathologies on chest x-rays with feedback resulted in enhanced pattern recognition. In addition, visual search strategies became more efficient during post-tests. Conclusion: Repetitive exposure to a focal lung pathology detection task with feedback improves overall performance. However, the specific EMME training interventions did not add any further advantages. Similar training interventions can be provided online to assess feasibility and reproducibility of such (or similar) training formats. Such training can, for example, reduce the number of false negative errors, especially for novices.
Validation of the Personality Assessment Inventory (PAI) scale of scales in a mixed clinical sample

Abstract Objective: This exploratory study examined the classification accuracy of three derived scales aimed at detecting cognitive response bias in neuropsychological samples. The derived scales are composed of existing scales from the Personality Assessment Inventory (PAI). A mixed clinical sample of consecutive outpatients referred for neuropsychological assessment at a large Midwestern academic medical center was utilized. Participants and Methods: Participants included 332 patients who completed study’s embedded and free-standing performance validity tests (PVTs) and the PAI. PASS and FAIL groups were created based on PVT performance to evaluate the classification accuracy of the derived scales. Three new scales, Cognitive Bias Scale of Scales 1–3, (CB-SOS1-3) were derived by combining existing scales by either summing the scales together and dividing by the total number of scales summed, or by logistically deriving a variable from the contributions of several scales. Results: All of the newly derived scales significantly differentiated between PASS and FAIL groups. All of the derived SOS scales demonstrated acceptable classification accuracy (i.e. CB-SOS1 AUC = 0.72; CB-SOS2 AUC = 0.73; CB-SOS3 AUC = 0.75). Conclusions: This exploratory study demonstrates that attending to scale-level PAI data may be a promising area of research in improving prediction of PVT failure.
Comparative analysis of differences between preoperative endoscopic biopsy and postoperative pathological examination for diagnosis of gastric intraepithelial neoplasia

Objective This study was performed to compare the differences between preoperative endoscopic biopsy (PEB) and postoperative pathological examination (PPE) for diagnosis of gastric intraepithelial neoplasia (GIN). Methods From September 2016 to July 2019, 188 consecutive patients with GIN at Yuyao People’s Hospital were retrospectively analyzed. The 188 patients had 218 GIN lesions. All patients underwent PEB and either endoscopic submucosal dissection or surgical treatment. PPE was performed on pathological tissues that had been surgically removed. Results Among 138 cases of low-grade dysplasia (LGD) diagnosed by PEB, 46 were upgraded to high-grade dysplasia (HGD), 20 were upgraded to early gastric cancer (EGC), and 2 were downgraded to inflammation after PPE. Among 42 cases of HGD, 23 were upgraded to EGC, 2 were downgraded to LGD, and 2 were downgraded to inflammation after PPE. Among 38 cases of EGC, 1 was downgraded to HGD and 2 were downgraded to LGD after PPE. The original diagnosis was maintained after the operation in 120 cases of GIN. Conclusion Biopsy did not fully reflect the lesions of GIN. Biopsy review should be actively performed, and the lesions should be clarified by endoscopic submucosal dissection or surgery.
Assessment of Agreement Between Human Ratings and Lexicon-Based Sentiment Ratings of Open-Ended Responses on a Behavioral Rating Scale

To date, there is a paucity of research conducting natural language processing (NLP) on the open-ended responses of behavior rating scales. Using three NLP lexicons for sentiment analysis of the open-ended responses of the Behavior Assessment System for Children-Third Edition, the researchers discovered a moderately positive correlation between the human composite rating and the sentiment score using each of the lexicons for strengths comments and a slightly positive correlation for the concerns comments made by guardians and teachers. In addition, the researchers found that as the word count increased for open-ended responses regarding the child’s strengths, there was a greater positive sentiment rating. Conversely, as word count increased for open-ended responses regarding child concerns, the human raters scored comments more negatively. The authors offer a proof-of-concept to use NLP-based sentiment analysis of open-ended comments to complement other data for clinical decision making.
Distinct transcriptomic signature of mRNA and microRNA in ulcerative colitis and irritable bowel syndrome

Background: Ulcerative colitis (UC) and irritable bowel syndrome (IBS) are both chronic bowel diseases involving stress. To identify genes differentially expressed in UC and IBS, and to determine whether psychological stress can influence those gene expressions, we conducted this pilot study. Methods: Patients of UC, irritable bowel syndrome (IBS) and normal controls (NC) (n=5 in each group) were recruited. Perceived stress scale (PSS) was adopted to assess psychological stress level. Sigmoid mucosa samples were collected during colonoscopy. Differentially expressed genes (DEGs) of both mRNA and microRNA (DEG-mRNA and DEG-miRNA) were identified by RNA-Seq and microarray, respectively. Weighted gene co-expression network analysis (WGCNA), gene ontology, and microRNA target analysis were performed to identify regulatory relationships and pathways involved. Pearson correlation was performed to identify the relationship between DEGs and PSS score. Results: In total, 1,770 and 938 DEG-mRNAs, 107 and 3 DEG-miRNAs were identified in UC and IBS (nominal P<0.05), respectively. The transcriptome changes in UC and IBS were highly correlated but transcriptome severity was larger in UC. There were 268 overlapped DEG-mRNAs and 3 overlapped DEG-miRNAs between UC and IBS. Median PSS score was 27.5 (24.7, 40.0) in UC, 27.0 (17.5, 32.5) in IBS and 22.0 (12.0, 28.5) in NC. Five of the UC DEG-mRNAs were significantly correlated to PSS scores, including SLC4A7, PLCB1, SPATA33, DECR2, RP11-792A8.4. There were no DEGs correlate with PSS scores in IBS. One module enriched for immunological pathways was upregulated in UC. Metabolic pathways were enriched in IBS. Within the UC-related co-expression module, we identified 18 DEG-mRNAs that were also targets of DEG-miRNA. Conclusions: Integration of microRNA and mRNA expression profiles identified changes of gene expression in both UC and IBS. Although the two diseases have significant overlapped transcriptomic changes, they have distinct signature. Immunological pathways are involved prominently in UC while metabolic pathways in IBS. Psychological stress is uniquely associated with the transcriptome changes of UC.
Over-parametrized deep neural networks minimizing the empirical risk do not generalize well

Recently it was shown in several papers that backpropagation is able to find the global minimum of the empirical risk on the training data using over-parametrized deep neural networks. In this paper, a similar result is shown for deep neural networks with the sigmoidal squasher activation function in a regression setting, and a lower bound is presented which proves that these networks do not generalize well on a new data in the sense that networks which minimize the empirical risk do not achieve the optimal minimax rate of convergence for estimation of smooth regression functions.
Fe b 20 21 Meissner effect in nonstandard superconductors

It was recently pointed out that so-called “superhydrides”, hydrogen-rich materials that appear to become superconducting at high temperatures and pressures, exhibit physical properties that are different from both conventional and unconventional standard type I and type II superconductors [1, 2]. Here we consider magnetic field expulsion in the first material in this class discovered in 2015, sulfur hydride [3]. A nuclear resonant scattering experiment has been interpreted as demonstration that the Meissner effect takes place in this material [4, 5]. However, here we point out that the observed effect implies a Meissner pressure [6] in this material that is much larger than that of standard superconductors. This provides strong evidence that hydride superconductors are qualitatively different from the known standard superconductors if they are superconductors.
Coupling Poisson–Nernst–Planck and density functional theory to calculate ion flux

Ion transport between two baths of fixed ionic concentrations and applied electrostatic (ES) potential is analysed using a one-dimensional drift-diffusion (Poisson–Nernst–Planck, PNP) transport system designed to model biological ion channels. The ions are described as charged, hard spheres with excess chemical potentials computed from equilibrium density functional theory (DFT). The method of Rosenfeld (Rosenfeld Y 1993 J. Chem. Phys. 98 8126) is generalized to calculate the ES excess chemical potential in channels. A numerical algorithm for solving the set of integral–differential PNP/DFT equations is described and used to calculate flux through a calcium-selective ion channel.
Simulation of Quadcopter's Complex Spatial Motion in Virtual Environment Systems

The paper considers the task of simulation quadcopter motion control in vir-tual environment systems. The proposed solution of this task is based on the application of a mathematical model of quadcopter dynamics, in which quaternion and axis-angle representation of the attitude are used. In this work, a feedback linearization method for the equations of quadcopter and its elec-tric motors dynamics is proposed to control the quadcopter. With the application of this approach, quadcopter motion is achieved by the obtained expressions for linear acceleration and the desired quaternion. The proposed methods and approaches for quadcopter simulation were implemented in the software package of virtual environment and tested using examples of the motion of a quadcopter model along a given path.