Miracle-dz/UniFAR-FTUs huggingface dataset:
On-Site Nurse-Led Cancer Genetics Program Increases Cancer Genetic Testing Completion in Black Veterans

PURPOSE Telegenetics services can expand access to guideline-recommended cancer genetic testing. However, access is often not distributed equitably to all races and ethnicities. We evaluated the impact of an on-site nurse-led cancer genetics service in a diverse Veterans Affairs Medical Center (VAMC) oncology clinic on likelihood of germline testing (GT) completion. METHODS We conducted an observational retrospective cohort study of patients who were referred for cancer genetics services at the Philadelphia VAMC between October 1, 2020, and February 28, 2022. We evaluated the association between genetics service (on-site v telegenetics) and likelihood of GT completion in a subcohort of new consults, excluding patients with prior consults and those referred for known history of germline mutations. RESULTS A total of 238 Veterans, including 108 (45%) seen on site, were identified for cancer genetics services during the study period, with the majority referred for a personal (65%) or family (26%) history of cancer. In the subcohort of new consults, 121 Veterans (54% self-identified race/ethnicity [SIRE]-Black), including 60 (50%) seen on site, were included in the analysis of germline genetic testing completion. In a univariate analysis, patients who were seen by the on-site genetics service had 3.2-fold higher likelihood of completing GT (relative risk, 3.22; 95% CI, 1.89 to 5.48) compared with the telegenetics service. In multivariable regression analysis, the on-site genetics service was associated with higher likelihood of GT completion, but this association was only statistically significant in SIRE-Black compared with SIRE-White Veterans (adjusted RR, 4.78; 95% CI, 1.53 to 14.96; P < .001; P-interaction of race × genetics service = .016). CONCLUSION An on-site nurse-led cancer genetics service embedded in a VAMC Oncology practice was associated with higher likelihood of germline genetic testing completion than a telegenetics service among self-identified Black Veterans.
New Metric to Evaluate Cardiac Anisotropic Mechanics by Directional High-Frequency Ultrasound-Based Transverse Wave Elastography

The evaluation of cardiac anisotropic mechanics is important in the diagnosis of heart disease. However, other representative ultrasound imaging-based metrics, which are capable of quantitatively evaluating anisotropic cardiac mechanics, are insufficient for accurately diagnosing heart disease due to the influence of viscosity and geometry of cardiac tissues. In this study, we propose a new ultrasound imaging-based metric, maximum cosine similarity (MaxCosim), for quantifying anisotropic mechanics of cardiac tissues by evaluating the periodicity of the transverse wave speeds depending on the measurement directions using ultrasound imaging. We developed a high-frequency ultrasound-based directional transverse wave imaging system to measure the transverse wave speed in multiple directions. The ultrasound imaging-based metric was validated by performing experiments on 40 rats randomly assigned to four groups; three doxorubicin (DOX) treatment groups received 10, 15, or 20 mg/kg DOX, while the control group received 0.2 mL/kg saline. In each heart sample, the developed ultrasound imaging system allowed measuring transverse wave speeds in multiple directions, and the new metric was then calculated from 3-D ultrasound transverse wave images to evaluate the degree of anisotropic mechanics of the heart sample. The results of the metric were compared with histopathological changes for validation. A decrease in the MaxCosim value was observed in the DOX treatment groups, with the degree of decrease depending on the dose. These results are consistent with the histopathological features, suggesting that our ultrasound imaging-based metric can quantify the anisotropic mechanics of cardiac tissues and potentially be used for the early diagnosis of heart disease.
Recent advances in antifungal drug development targeting lanosterol 14α‐demethylase (CYP51): A comprehensive review with structural and molecular insights

Fungal infections are posing serious threat to healthcare system due to emerging resistance among available antifungal agents. Among available antifungal agents in clinical practice, azoles (diazole, 1,2,4‐triazole and tetrazole) remained most effective and widely prescribed antifungal agents. Now their associated side effects and emerging resistance pattern raised a need of new and potent antifungal agents. Lanosterol 14α‐demethylase (CYP51) is responsible for the oxidative removal of 14α‐methyl group of sterol precursors lanosterol and 24(28)‐methylene‐24,25‐dihydrolanosterol in ergosterol biosynthesis hence an essential component of fungal life cycle and prominent target for antifungal drug development. This review will shed light on various azole‐ as well as non‐azoles‐based derivatives as potential antifungal agents that target fungal CYP51. Review will provide deep insight about structure activity relationship, pharmacological outcomes, and interactions of derivatives with CYP51 at molecular level. It will help medicinal chemists working on antifungal development in designing more rational, potent, and safer antifungal agents by targeting fungal CYP51 for tackling emerging antifungal drug resistance.
Lie groups with square integrable representations

Let G be a separable locally compact group, Z a closed subgroup contained in the center of G such that center (G)/Z is compact. An irreducible unitary representation X of G is said to be square integrable mod Z (or a member of the discrete series of G) if there exist non-zero vectors qA, / in the representation space g(w) such that G 1(wr(g)(p: V)12 dg < oo, where dg is the right Haar measure of G/Z. The problem of classifying semi-simple Lie groups and connected, simply connected nilpotent Lie groups having discrete series has been solved by Harish-Chandra, and J. Wolf and C. C. Moore. In this paper we shall consider the problem for another class of Lie groups whose radicals are connected, simply connected nilpotent Lie groups (these are called U-groups). Thus let G be a connected U-group, N its radical, and S a maximal connected semi-simple subgroup of G. Apart from some technical requirements on S it will be proved that G has discrete series if and only if: (A) The center of N is the connected component of the identity in the center of G, and (B) Both N and S have discrete series. Furthermore every member of the discrete series of G may be written as the "tensor product" of a member of the discrete series of S extended trivially to N with an irreducible representation of G whose restriction to N is a member of the discrete series of N. Finally an algorithm to determine U-groups having discrete series as successive extensions of simpler U-groups is also described. Roughly speaking, Mackey's theory of group extensions ([10]) will be applied to solve the problem by induction. Thus let H be a closed normal
A co-adaptive duality-aware framework for biomedical relation extraction

Abstract Motivation Biomedical relation extraction is a vital task for electronic health record mining and biomedical knowledge base construction. Previous work often adopts pipeline methods or joint methods to extract subject, relation, and object while ignoring the interaction of subject–object entity pair and relation within the triplet structure. However, we observe that entity pair and relation within a triplet are highly related, which motivates us to build a framework to extract triplets that can capture the rich interactions among the elements in a triplet. Results We propose a novel co-adaptive biomedical relation extraction framework based on a duality-aware mechanism. This framework is designed as a bidirectional extraction structure that fully takes interdependence into account in the duality-aware extraction process of subject–object entity pair and relation. Based on the framework, we design a co-adaptive training strategy and a co-adaptive tuning algorithm as collaborative optimization methods between modules to promote better mining framework performance gain. The experiments on two public datasets show that our method achieves the best F1 among all state-of-the-art baselines and provides strong performance gain on complex scenarios of various overlapping patterns, multiple triplets, and cross-sentence triplets. Availability and implementation Code is available at https://github.com/11101028/CADA-BioRE.
Gut microbiota fermentation profiles of pre-digested mycoprotein (Quorn) using faecal batch cultures in vitro: a preliminary study

Abstract High-fibre diets are beneficial for many health outcomes via a wide range of mechanisms including gut microbiota fermentation-derived short-chain fatty acid (SCFAs) production. Mycoprotein (marketed as Quorn) is a food high in fibre (>6 g/100 g wet weight (ww)) and protein (13 g/100 g ww) which has been shown to have positive effects on glycemic control and appetite in humans. Nevertheless, the mechanisms underpinning this are poorly understood. Here, we investigate the changes in gut microbiota α- and β-diversity, pH and SCFAs production in faecal batch cultures supplemented with pre-digested mycoprotein (Quorn), soy, chicken and control (unsupplemented) using eight fresh stools from healthy donors. The results showed that pre-digested mycoprotein did not alter pH (p = .896), α- or β-diversity of the gut microbiota when compared to the control, soy, and chicken. Nevertheless, chicken led to a significant increase in total SCFAs post-24 h vs. control (+57.07 mmol/L, p = .01). In particular, propionate increased when compared to soy (+19.59 mmol/L, p = .03) and the control (+23.19 mmol/L, p < .01). No other differences in SCFAs were detected. In conclusion, pre-digested mycoprotein was not fermented in vitro by healthy gut microbiota in the settings of this experiment.
CRISPR/Cas9‐Mediated Gene Knockout in Cells and Tissues Using Lentivirus

CRISPR‐Cas9 has become a powerful and popular gene editing tool. However, successful application of this tool in the lab can still be quite daunting to many newcomers to molecular biology, mostly because it is a relatively lengthy process involving multiple steps with variations of each step. Here, we provide a reliable, stepwise, and newcomer‐friendly protocol to knock out a target gene in wild‐type human fibroblasts. This protocol involves sgRNA design using CRISPOR, construction of an “all‐in‐one” vector expressing both sgRNA and Cas9 using Golden Gate cloning, streamlined production of high‐titer lentiviruses in 1 week after molecular cloning, and transduction of cells to generate a knockout cell pool. We further introduce a protocol for lentiviral transduction of ex vivo mouse embryonic salivary epithelial explants. In summary, our protocol is useful for new researchers to apply CRISPR‐Cas9 to generate stable gene knockout cells and tissue explants using lentivirus. Published 2023. This article is a U.S. Government work and is in the public domain in the USA.
FOURIER TRANSFORM CODING OF IMAGES

The scientific advantages are pointed out from the Fourier transform encoding optical and electron microscope images and source data for computer-plotted Fourier-plane holograms, especially if bit compression ratios may be achieved, with comparable reconstructions, at the level found for the adaptive cosine transform. The relative importance is considered of image reconstruction based on the Fourier phase data alone and on combined phase and amplitude data. It is shown that bit rates as low as 0.3 bit per pixel can be achieved by encoding a combination of the Fourier phase and amplitude data. This is achieved by low-pass filtering together with a clustering procedure in the Fourier plane which seeks out the more important Fourier amplitude coefficients and their associated phases.
Numerical Simulation of Chua's Circuit Oriented to Circuit Synthesis

The application of numerical methods based on polynomial approximation and multistep algorithm is presented to simulate the behavior of a chaotic oscillator, e.g. Chua's circuit, which consists of five circuit elements: one linear resistor, one inductor, two capacitors and one nonlinear resistor known as Chua's diode. The last element is modeled by an I-V piecewise-linear function to formulate a system of linear dynamic equations. This initial value problem is solved numerically to compute a sequence of chaotic phenomena. Values of the circuit elements can be determined by this numerical method, and the synthesis of Chua's diode can be realized directly using novel active devices. Numerical results are in good agreement with experiment data.
Coupled anaerobic methane oxidation and metal reduction in soil under elevated CO2

Continued current emissions of carbon dioxide (CO2) and methane (CH4) by human activities will increase global atmospheric CO2 and CH4 concentrations and surface temperature significantly. Fields of paddy rice, the most important form of anthropogenic wetlands, account for about 9% of anthropogenic sources of CH4. Elevated atmospheric CO2 may enhance CH4 production in rice paddies, potentially reinforcing the increase in atmospheric CH4. However, what is not known is whether and how elevated CO2 influences CH4 consumption under anoxic soil conditions in rice paddies, as the net emission of CH4 is a balance of methanogenesis and methanotrophy. In this study, we used a long‐term free‐air CO2 enrichment experiment to examine the impact of elevated CO2 on the transformation of CH4 in a paddy rice agroecosystem. We demonstrate that elevated CO2 substantially increased anaerobic oxidation of methane (AOM) coupled to manganese and/or iron oxides reduction in the calcareous paddy soil. We further show that elevated CO2 may stimulate the growth and metabolism of Candidatus Methanoperedens nitroreducens, which is actively involved in catalyzing AOM when coupled to metal reduction, mainly through enhancing the availability of soil CH4. These findings suggest that a thorough evaluation of climate‐carbon cycle feedbacks may need to consider the coupling of methane and metal cycles in natural and agricultural wetlands under future climate change scenarios.
Association of C‐reactive protein gene polymorphisms with the risk of ischemic stroke: A systematic review and meta‐analysis

The heterogeneous, complex condition known as ischemic stroke (IS) is brought on by the interaction of a number of risk factors and genetic variables. The association between C‐reactive protein (CRP) gene polymorphisms and IS has, however, been the subject of inconsistent findings. Therefore, we conducted a meta‐analysis to comprehensively address possible associations of CRP genes with the risk of IS.
Instability of unbounded transverse mixing layer in shallow waters

This paper examines the role of waves in the development of the instability of an unbounded transverse mixing layer in shallow waters. In supercritical state waves become significant. The matching of the wave-like asymptotic solution in the far field to the solutions near the inflection and the returning surfaces poses a difficult mathematical problem. We therefore conducted numerical simulations to find solutions directly from the shallow water equations. The simulations found that the growing waves in the unstable current had a consistent structure throughout the linear stage of the instability’s development. The excitation, reflection, and transmission of waves produced a modulating instability that maintained a consistent structure as the amplitude of the instability increased over many orders of magnitude. This role of the waves on the supercritical instability, as delineated by our numerical simulations, is not solely describable by the classical analytical method.
Taming Reversible Halftoning via Predictive Luminance

Traditional halftoning usually drops colors when dithering images with binary dots, which makes it difficult to recover the original color information. We proposed a novel halftoning technique that converts a color image into a binary halftone with full restorability to its original version. Our novel base halftoning technique consists of two convolutional neural networks (CNNs) to produce the reversible halftone patterns, and a noise incentive block (NIB) to mitigate the flatness degradation issue of CNNs. Furthermore, to tackle the conflicts between the blue-noise quality and restoration accuracy in our novel base method, we proposed a predictor-embedded approach to offload predictable information from the network, which in our case is the luminance information resembling from the halftone pattern. Such an approach allows the network to gain more flexibility to produce halftones with better blue-noise quality without compromising the restoration quality. Detailed studies on the multiple-stage training method and loss weightings have been conducted. We have compared our predictor-embedded method and our novel method regarding spectrum analysis on halftone, halftone accuracy, restoration accuracy, and the data embedding studies. Our entropy evaluation evidences our halftone contains less encoding information than our novel base method. The experiments show our predictor-embedded method gains more flexibility to improve the blue-noise quality of halftones and maintains a comparable restoration quality with a higher tolerance for disturbances.
Fast stereo matching based on probability assignment and ORB operator

Abstract A stereo matching algorithm based on probability assignment is proposed to meet the real-time demand of stereo matching using SURF(Speeded Up Robust Features). In order to accelerate search of matching points, probability assignment of feature points is acquired based on the correlation between fuzzy clustering and probability assignment, as well as the necessary conditions of information entropy; then, when extracting ORB feature points, a data set is used to record the sequence of feature points after decreasing the edge effect; epipolar line, uniqueness and sequence constraints narrow down the search space; the Hamming distance between descriptors are calculated and the nearest neighbor matching becomes the stereo matching result. Experimental results show that the proposed algorithm accelerates matching and maintains high accuracy, even when applied to non-standard pictures.
LFQ-Based Peptide and Protein Intensity Differential Expression Analysis

Testing for significant differences in quantities at the protein level is a common goal of many LFQ-based mass spectrometry proteomics experiments. Starting from a table of protein and/or peptide quantities from a given proteomics quantification software, many tools and R packages exist to perform the final tasks of imputation, summarization, normalization, and statistical testing. To evaluate the effects of packages and settings in their substeps on the final list of significant proteins, we studied several packages on three public data sets with known expected protein fold changes. We found that the results between packages and even across different parameters of the same package can vary significantly. In addition to usability aspects and feature/compatibility lists of different packages, this paper highlights sensitivity and specificity trade-offs that come with specific packages and settings.
Comparison between two different systems by using linear first order differential equations

This study deals with the reliability and availability characteristics of two different system, the second system differs from the first system due to the additional feature of preventive maintenance. Reliability and availability analysis of system having one active unit and one warm standby unit with self-reset function and one maintenance facility is presented. The failure unit is repaired through self-reset or maintenance according to different failure models. We drive the MTSF and Steady-state availability for the two systems using linear first order differential equations and perform comparisons theoretically and graphically to observe the effect of the preventive maintenance on system performance.
A hybrid-exchange density functional study of Ca-doped LaMnO3

In this work, hybrid-exchange density functional theory calculations are carried out to determine the effects of A-site doping on the electronic and magnetic properties of the manganite series La1−xCaxMnO3. This study focuses on the nature of the ground state for an ordered Ca distribution. We show that the hybrid exchange functional, B3LYP, provides an accurate and consistent description of the electronic structure for LaMnO3 and La0.75Ca0. 25MnO3. The magnetic ground states for the compositions studied are predicted correctly and comparisons have been made to available experimental data. This provides a basis for a first principles description of the magnetocaloric effect in La1−xCaxMnO3.
Refining Timely Diagnosis of Early Syphilis by Using Treponema pallidum PCR or IgM Immunoblotting Next to Conventional Serology for Syphilis

Treponema pallidum subsp. pallidum is a fastidious spirochete and the etiologic agent of syphilis, a sexually transmitted infection (STI). Syphilis diagnoses and disease staging are based on clinical findings and serologic testing. ABSTRACT Treponema pallidum subsp. pallidum is a fastidious spirochete and the etiologic agent of syphilis, a sexually transmitted infection (STI). Syphilis diagnoses and disease staging are based on clinical findings and serologic testing. Moreover, according to most international guidelines, PCR analysis of swab samples from genital ulcers is included in the screening algorithm where possible. It has been suggested that PCR might be omitted from the screening algorithm due to low added value. As an alternative to PCR, IgM serology might be used. In this study, we wanted to establish the added value of PCR and IgM serology for diagnosing primary syphilis. Added value was defined as finding more cases of syphilis, preventing overtreatment, or limiting the extent of partner notification to more recent partners. We found that both PCR and IgM immunoblotting could aid the timely diagnosis of early syphilis in ~24% to 27% of patients. PCR has the greatest sensitivity and can be applied to cases with an ulcer with suspected reinfection or primary infection. In the absence of lesions, the IgM immunoblot could be used. However, the IgM immunoblot has better performance in cases with suspected primary infection than in reinfections. The target population, testing algorithm, time pressures, and costs should determine whether either test provides sufficient value to be implemented in clinical practice.
Pulse-mode measurement of electron beam halo using diamond-based detector

RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan(Received 16 September 2011; published 6 February 2012)Using a diamond-based detector, the electron beam halo in a high-energy accelerator can be measuredwith a lower detection limit than that using other instruments, such as a core monitor, a dose meter, or anoptical ﬁber. We have successfully measured an electron beam halo using diamond-based detectorsoperating in the ionization mode, which were installed in the beam duct to measure the intensity of thebeam halo directly. Pulse-by-pulse measurements were adopted to suppress the background noiseefﬁciently. Feasibility tests on the diamond-based detector and beam halo monitor were performed inthe beam dump area of the 8 GeV SPring-8 synchrotron booster and at the 250 MeV SPring-8 CompactSASE Source test accelerator for the SPring-8 Angstrom Compact free electron LAser (SACLA),respectively.Weachievedalowerdetectionlimitof2 10