Miracle-dz/UniFAR-FTUs huggingface dataset:
Current Trends in Neoantigen-Based Cancer Vaccines

Cancer immunotherapies are treatments that use drugs or cells to activate patients’ own immune systems against cancer cells. Among them, cancer vaccines have recently been rapidly developed. Based on tumor-specific antigens referred to as neoantigens, these vaccines can be in various forms such as messenger (m)RNA and synthetic peptides to activate cytotoxic T cells and act with or without dendritic cells. Growing evidence suggests that neoantigen-based cancer vaccines possess a very promising future, yet the processes of immune recognition and activation to relay identification of a neoantigen through the histocompatibility complex (MHC) and T-cell receptor (TCR) remain unclear. Here, we describe features of neoantigens and the biological process of validating neoantigens, along with a discussion of recent progress in the scientific development and clinical applications of neoantigen-based cancer vaccines.
Physical performance and muscle strength rather than muscle mass are predictor of all-cause mortality in hemodialysis patients

Objectives Patients undergoing maintenance hemodialysis usually suffer a high burden of poor functional status. The aim of this study was to investigate the association between muscle mass, muscle strength as well as physical performance with all-cause mortality in hemodialysis patients. Methods 923 hemodialysis patients (565 men, mean aged 61.3 ± 12.7 years) were included from eight facilities in Tianjin and Shanghai of China from 2019 to 2021. Muscle mass was evaluated by skeletal muscle index (SMI) and muscle strength was assessed by handgrip strength. Different measures of physical performance were measured via gait speed, Timed Up and Go Test (TUGT) and short physical performance battery (SPPB). Cox proportional hazards regression models were used to determine the adjusted hazard ratios (HRs) of mortality with 95% confidence intervals (95% CIs) for baseline muscle mass, muscle strength and different measures of physical performance. Additionally, the area under the Receiver Operating Characteristic (ROC) curves were constructed to determine which index is a better predictor of mortality. Results During a median follow-up of 14 (12–17 months), 79 (8.6%) patients died. Using the Cox regression analysis, we founded that muscle strength and physical performance rather than muscle mass were significantly negatively associated with mortality. The C-index for different measures of physical performance in predicting mortality were 0.709 for SPPB, 0.7 for TUGT and 0.678 for gait speed, respectively. The C-index for muscle strength was 0.635, and the ability of prediction was significantly lower than the physical performance. Conclusions Physical performance seems to a better indicator of mortality than muscle mass and strength in hemodialysis patients. Simple measures of physical performance may be appropriately used as a screening tool targeting high-risk hemodialysis patients for the prevention of mortality.
Biofilm formation of two genetically diverse Staphylococcus aureus isolates under beta-lactam antibiotics

Purpose Our aim was to evaluate the biofilm formation of 2 genetically diverse Staphylococcus aureus isolates, 10379 and 121940, under different concentrations of beta-lactam antibiotics on biomass content and biofilm viability. Methods Biofilm formation and methicillin resistance genes were tested using PCR and multiplex PCR. PCR was combined with bioinformatics analysis to detect multilocal sequence typing (MLST) and SCCmec types, to study the genetical correlation between the tested strains. Then, the crystal violet (CV) test and XTT were used to detect biomass content and biofilm activity. Antibiotic susceptibility was tested using a broth dilution method. According to their specific MIC, different concentrations of beta-lactam antibiotics were used to study its effect on biomass content and biofilm viability. Results Strain 10379 carried the icaD, icaBC, and MRSA genes, not the icaA, atl, app, and agr genes, and MLST and SCCmec typing was ST45 and IV, respectively. Strain 121940 carried the icaA, icaD, icaBC, atl, and agr genes, not the aap gene, and MLST and SCCmec typed as ST546 and IV, respectively. This suggested that strains 10379 and 121940 were genotypically very different. Two S. aureus isolates, 10379 and 121940, showed resistance to beta-lactam antibiotics, penicillin, ampicillin, meropenem, streptomycin and kanamycin, some of which promoted the formation of biofilm and biofilm viability at low concentrations. Conclusion Despite the large differences in the genetic background of S. aureus 10379 and 121940, some sub-inhibitory concentrations of beta-lactam antibiotics are able to promote biomass and biofilm viability of both two isolates.
A Neural Network-Based Application to Identify Cubic Structures in Multi Component Crystalline Materials using X- Ray Diffraction Data

††† Summary One of the crystalline materials structures is cubic. An experimental study has been done about developing a scheme to identify the cubic structure types in single or multi component materials. This scheme is using fingerprints created from the calculation of quadratic Miller indices ratios and matches it with the ratio of the sin 2 θ values from the diffracted data of material obtained by X-Ray Diffraction (XRD) method. These manual matching processes are complicated and sometimes are tedious because the diffracted data are complex and may have more than one fingerprint inside. This paper proposes an application of multi-layered back-propagation neural network in matching the fingerprints with the diffracted data of crystalline material to quickly and correctly identify its cubic structure component types.
Mapping Gendered Communications, Film, and Media Studies: Seven Author Clusters and Two Discursive Communities

This study examined and mapped the extent to which gender became incorporated into the intersecting research fields of communications, film, and media studies. A total of 8054 academic publications from these disciplines, indexed in the Web of Science between 1975 and 2022 (ndocs = 8054), were extracted to create two types of bibliometric maps: (a) an author co-citation map, and (b) a co-occurrence map of key terms (taken from keyword lists, titles, and abstracts of publications). Our results revealed a pattern of seven distinct clusters of 995 authors (nauthors = 995) in the field. Additional research is needed to analyze the internal structure of these seven clusters, and label them accordingly. The key terms in the same authors’ works, however, show a distinctively different pattern, namely a divided, dichotomous, polarized structure (nterms = 720). Judging from this, we hypothesize that gender is discussed in two main ways: either as a critical concept concerning discourses, representations, and other social and cultural constructs, or as a variable in more formal sociological and psychological research designs. The conceptual framework and results of the present study lay the foundation for further research regarding the diverse academic agendas of the seven author clusters, the split nature of their discursive communities, as well as the key difference between the two patterns.
BROYDEN`S METHOD FOR OPERATORS WITH REGULARLY CONTINUOUS DIVIDED DIFFERENCES

We present a new convergence analysis of popular Broyden's method in the Banach/Hilbert space setting which is applicable to non- smooth operators. Moreover, we do not assume a priori solvability of the equation under consideration. Nevertheless, without these simplifying as- sumptions our convergence theorem implies existence of a solution and superlinear convergence of Broyden's iterations. To demonstrate practi- cal merits of Broyden's method, we use it for numerical solution of three nontrivial infinite-dimensional problems.
1480 nm Diode-Pumped Er3+:Yb3+ Co-Doped Phospho-Alumino-Silicate Fiber for Extending the L-Band Gain Up to 1625 nm

In this article, we report erbium/ytterbium (Er/Yb) co-doped phospho-alumino-silicate fibers (EYDFs) fabricated by the modified chemical vapor deposition (MCVD) and solution doping technique, to extend the L-band gain up to 1625 nm. Fibers with different doping concentrations and Yb-to-Er ratios were studied in terms of the spectroscopic properties and optical amplification in the L-band when pumped at 1480 nm. A higher Yb-to-Er ratio suppressed the signal-induced excited-state absorption (ESA) effect and also improved the amplifier gain in the L-band. A maximum gain of 15.5 dB at 1625 nm was achieved for the fiber with an Yb-to-Er ratio of 3.5. The gain coefficient was 0.039 dB/mW and the saturation output power was 21.5 dBm at 1600 nm. On the other hand, one highly doped fiber with the Er2O3 concentration of 0.5 mol% and an Yb-to-Er ratio of 2 was demonstrated to have the controlled Er concentration quenching and a reduced amplifier device length, exhibiting 12.9 dB gain and 6.3 dB noise figure (NF) at 1625 nm, with <5.8 dB NF from 1575 to 1623 nm. What's more, the temperature-dependent amplifier performance was studied, over the temperature range of −60 to 80 °C. The temperature-dependent-gain (TDG) coefficient and its zero-point wavelength were reported. An increased L-band gain was achieved by cooling the fiber.
LIMIT THEOREMS FOR QUADRATIC FORMS WITH APPLICATIONS TO WHITTLE'S ESTIMATE

We establish strong and weak approximations for quadratic forms of weakly and strongly dependent random variables and obtain necessary and sufcient conditions for the weak convergence of weighted functions of quadratic forms. The results are applied to get the asymptotic distributions of some tests which can be used to detect possible changes in the longmemory parameter.
Convolutional Neural Network Based Unmanned Ground Vehicle Control via Deep Reinforcement Learning

In order to reduce the cost of human resources and material resources and improve the power line inspection efficiency, unmanned ground vehicle (UGV), which utilizes the modern artificial intelligence such as deep learning and reinforcement learning, is commonly introduced to replace of human to inspect power lines in the grid system. This paper provides a deep Q network (DQN) and convolutional neural network (CNN) based end-to-end control model to drive UGV to inspect automatically, and meanwhile to avoid obstacles. Specifically, we utilize the preprocessed grayscale image as the input of the CNN, and output the final Q value. This model simulates human learning behavior by interaction between UGV and the environment. Through repeated self-learning and reward value increasing in a simulation environment, the UGV successfully reaches the target position in a shortest time and meanwhile avoiding a variety of obstacles.
Nucleosome Remodeling at the Yeast PHO8 and PHO84 Promoters without the Putatively Essential SWI/SNF Remodeler

Chromatin remodeling by ATP-dependent remodeling enzymes is crucial for all genomic processes, like transcription or replication. Eukaryotes harbor many remodeler types, and it is unclear why a given chromatin transition requires more or less stringently one or several remodelers. As a classical example, removal of budding yeast PHO8 and PHO84 promoter nucleosomes upon physiological gene induction by phosphate starvation essentially requires the SWI/SNF remodeling complex. This dependency on SWI/SNF may indicate specificity in remodeler recruitment, in recognition of nucleosomes as remodeling substrate or in remodeling outcome. By in vivo chromatin analyses of wild type and mutant yeast under various PHO regulon induction conditions, we found that overexpression of the remodeler-recruiting transactivator Pho4 allowed removal of PHO8 promoter nucleosomes without SWI/SNF. For PHO84 promoter nucleosome removal in the absence of SWI/SNF, an intranucleosomal Pho4 site, which likely altered the remodeling outcome via factor binding competition, was required in addition to such overexpression. Therefore, an essential remodeler requirement under physiological conditions need not reflect substrate specificity, but may reflect specific recruitment and/or remodeling outcomes.
Navier-Stokes/Darcy Coupling: Modeling, Analysis, and Numerical Approximation

This paper is an overview of known and new results about the coupling of Navier-Stokes and Darcy equations to model the filtration of incompressible fluids through porous media. We discuss coupling conditions and we analyze the global coupled model in order to prove its well-posedness and to characterize effective algorithms to compute the solution of its numerical approximation.
Chemistry and Bioactivity of Croton Essential Oils: Literature Survey and Croton hirtus from Vietnam

Using essential oils to control vectors, intermediate hosts, and disease-causing microorganisms is a promising approach. The genus Croton in the family Euphorbiaceae is a large genus, with many species containing large amounts of essential oils, however, essential oil studies are limited in terms of the number of Croton species investigated. In this work, the aerial parts of C. hirtus growing wild in Vietnam were collected and analyzed by gas chromatography/mass spectrometry (GC/MS). A total of 141 compounds were identified in C. hirtus essential oil, in which sesquiterpenoids dominated, comprising 95.4%, including the main components β-caryophyllene (32.8%), germacrene D (11.6%), β-elemene (9.1%), α-humulene (8.5%), and caryophyllene oxide (5.0%). The essential oil of C. hirtus showed very strong biological activities against the larvae of four mosquito species with 24 h LC50 values in the range of 15.38–78.27 μg/mL, against Physella acuta adults with a 48 h LC50 value of 10.09 μg/mL, and against ATCC microorganisms with MIC values in the range of 8–16 μg/mL. In order to provide a comparison with previous works, a literature survey on the chemical composition, mosquito larvicidal, molluscicidal, antiparasitic, and antimicrobial activities of essential oils of Croton species was conducted. Seventy-two references (seventy articles and one book) out of a total of two hundred and forty-four references related to the chemical composition and bioactivity of essential oils of Croton species were used for this paper. The essential oils of some Croton species were characterized by their phenylpropanoid compounds. The experimental results of this research and the survey of the literature showed that Croton essential oils have the potential to be used to control mosquito-borne and mollusk-borne diseases, as well as microbial infections. Research on unstudied Croton species is needed to search for species with high essential oil contents and excellent biological activities.
Spanwise structure and scale growth in turbulent boundary layers

Spanwise structure and growth mechanisms in a turbulent boundary layer are investigated experimentally. PIV measurements are obtained in the streamwise–spanwise ($x$–$z$)-plane from the buffer layer to the top of the logarithmic region at Re$_\theta = 1015$ and 7705. The dominant motions of the flow are shown to be large-scale regions of momentum deficit elongated in the streamwise direction. Throughout the logarithmic layer, the regions are consistently bordered by vortices organized in the streamwise direction, offering strong support for a vortex packet model. Additionally, evidence is presented for the existence and organization of hairpin vortices in the region $y^+ < 60$. Statistical evidence is also presented for two important aspects of the vortex packet paradigm: vortex organization in the streamwise direction, and the clear association of the hairpin signature with local minima in streamwise velocity. Several spanwise lengthscales are shown to vary linearly with distance from the wall, revealing self-similar growth of spanwise structure in an average sense. Inspection of the data, however, suggests that individual structures do not grow strictly self-similarly in time. It is proposed that additional scale growth occurs by the merging of vortex packets on an eddy-by-eddy basis via a vortex re-connection mechanism similar to that suggested by Wark & Nagib (1989). The proposed mechanism provides a link between vortex-pairing concepts and the observed coalescence of streaky low-speed regions in the inner layer.
Phenotypic and genotypic characterization of Shiga toxin-producing Escherichia coli strains recovered from bovine carcasses in Uruguay

Introduction Shiga toxin-producing Escherichia coli (STEC) is a zoonotic pathogen that cause food-borne diseases in humans. Cattle and derived foodstuffs play a known role as reservoir and vehicles, respectively. In Uruguay, information about the characteristics of circulating STEC in meat productive chain is scarce. The aim was to characterize STEC strains recovered from 800 bovine carcasses of different slaughterhouses. Methods To characterize STEC strains we use classical microbiological procedures, Whole Genome Sequencing (WGS) and FAO/WHO risk criteria. Results We analyzed 39 STEC isolated from 20 establishments. They belonged to 21 different O-groups and 13 different H-types. Only one O157:H7 strain was characterized and the serotypes O130:H11(6), O174:H28(5), and O22:H8(5) prevailed. One strain showed resistance in vitro to tetracycline and genes for doxycycline, sulfonamide, streptomycin and fosfomycin resistance were detected. Thirty-three strains (84.6%) carried the subtypes Stx2a, Stx2c, or Stx2d. The gene eae was detected only in two strains (O157:H7, O182:H25). The most prevalent virulence genes found were lpfA (n = 38), ompA (n = 39), ompT (n = 39), iss (n = 38), and terC (n = 39). Within the set of STEC analyzed, the majority (81.5%) belonged to FAO/WHO’s risk classification levels 4 and 5 (lower risk). Besides, we detected STEC serotypes O22:H8, O113:H21, O130:H11, and O174:H21 belonged to level risk 2 associate with diarrhea, hemorrhagic colitis or Hemolytic-Uremic Syndrome (HUS). The only O157:H7 strain analyzed belonged to ST11. Thirty-eight isolates belonged to the Clermont type B1, while the O157:H7 was classified as E. Discussion The analyzed STEC showed high genomic diversity and harbor several genetic determinants associated with virulence, underlining the important role of WGS for a complete typing. In this set we did not detect non-O157 STEC previously isolated from local HUS cases. However, when interpreting this findings, the low number of isolates analyzed and some methodological limitations must be taken into account. Obtained data suggest that cattle constitute a local reservoir of non-O157 serotypes associated with severe diseases. Other studies are needed to assess the role of the local meat chain in the spread of STEC, especially those associated with severe diseases in humans.
Phase Transformation and Deformation Processes in Oriented Polyethylene

Plastic deformation processes in oriented polyethylene are investigated by the X-ray method, and changes in texture produced by transverse compression are interpreted in terms of twinning, slip and phase transformation. The crystal structure of the new form produced by the phase transformation is determined, and the unit cell is a monoclinic one with a=8.09, b=2.53, c=4.79 Å and β=107.9°. The phase transformation is considered to be of diffusion-less type and a transition mechanism similar to that of twinning is proposed.
Comparisons of RCM Generation Algorithms for Vision-Controlled Robotic Endoscope

In minimally invasive surgery (MIS), a surgical endoscope is an essential instrument that provides visualization for the surgeon. One principal characteristic of surgical instruments is that remote center of motion (RCM) must be respected. To meet such a practical requirement, many physical RCM mechanisms and software-based RCM generation algorithms have been proposed. As compared with physical RCM mechanisms, RCM generation algorithms possess more flexibility due to the fact that the RCM point can be adjusted if required. This paper conducts comparisons of four typical RCM generation algorithms applied to a vision-controlled robotic endoscope under joint constraints. Kinematic models of the robotic endoscope and the four RCM generation algorithms are first briefly introduced. Then, a unified control formulation based on quadratic programming (QP) is constructed to incorporate kinematic, RCM, and physical constraints of the robotic endoscope. Based on the unified control scheme, comparative simulations and experiments are performed. The advantages and disadvantages of the four typical RCM generation algorithms are analyzed and discussed. When performing a same peg transfer task in the simulations, the RCM errors synthesized by RCM generation algorithms designed using a plane equation and an insertion equation are smaller. In the physical experiments, there are few differences in the RCM errors. Nevertheless, it is revealed that the joint velocities corresponding to the RCM generation algorithm based on a plane equation are the smallest, which means that the joint angles change more gently and it can be more friendly to MIS.
Relationship of Extravascular Lung Water and Pulmonary Vascular Permeability to Respiratory Mechanics in Patients with COVID-19-Induced ARDS

During acute respiratory distress syndrome (ARDS), the increase in pulmonary vascular permeability and lung water induced by pulmonary inflammation may be related to altered lung compliance. A better understanding of the interactions between respiratory mechanics variables and lung water or capillary permeability would allow a more personalized monitoring and adaptation of therapies for patients with ARDS. Therefore, our main objective was to investigate the relationship between extravascular lung water (EVLW) and/or pulmonary vascular permeability index (PVPI) and respiratory mechanic variables in patients with COVID-19-induced ARDS. This is a retrospective observational study from prospectively collected data in a cohort of 107 critically ill patients with COVID-19-induced ARDS from March 2020 to May 2021. We analyzed relationships between variables using repeated measurements correlations. We found no clinically relevant correlations between EVLW and the respiratory mechanics variables (driving pressure (correlation coefficient [CI 95%]: 0.017 [−0.064; 0.098]), plateau pressure (0.123 [0.043; 0.202]), respiratory system compliance (−0.003 [−0.084; 0.079]) or positive end-expiratory pressure (0.203 [0.126; 0.278])). Similarly, there were no relevant correlations between PVPI and these same respiratory mechanics variables (0.051 [−0.131; 0.035], 0.059 [−0.022; 0.140], 0.072 [−0.090; 0.153] and 0.22 [0.141; 0.293], respectively). In a cohort of patients with COVID-19-induced ARDS, EVLW and PVPI values are independent from respiratory system compliance and driving pressure. Optimal monitoring of these patients should combine both respiratory and TPTD variables.
Improved Quantitative Real-Time PCR Protocol for Detection and Quantification of Methanogenic Archaea in Stool Samples

Methanogenic archaea are an important component of the human and animal intestinal microbiota, and yet their presence is rarely reported in publications describing the subject. One of the methods of quantifying the prevalence of methanogens is quantitative real-time PCR (qPCR) of the methanogen-specific mcrA gene, and one of the possible reasons for detection failure is usually a methodology bias. Here, we refined the existing protocol by changing one of the primers and improving the conditions of the qPCR reaction. As a result, at the expense of a slightly lower yet acceptable PCR efficiency, the new assay was characterized by increased specificity and sensitivity and a wider linear detection range of 7 orders of magnitude. The lowest copy number of mcrA quantified at a frequency of 100% was 21 copies per reaction. The other validation parameters tested, such as reproducibility and linearity, also gave satisfactory results. Overall, we were able to minimize the negative impacts of primer dimerization and other cross-reactions on qPCR and increase the number of not only detectable but also quantifiable stool samples—or in this case, chicken droppings.