Miracle-dz/UniFAR-FTUs huggingface dataset:
Model for interface defect and positive charge generation in ultrathin SiO2/ZrO2 gate dielectric stacks

The generation of interface defects and positive charge during the injection of electrons in p-Si/SiO2/ZrO2/TiN structures is investigated. The kinetics of generation of both type of defects are found to be very similar. A model is proposed to explain the interface defect generation, based on the depassivation of trivalent silicon dangling bonds (Si3≡SiH→Si3≡Si⋅) at the (100)Si/SiO2 interface by the injected electrons. A Gaussian spread for the activation energy Ed related to the dissociation of the Si–H bond is included in this model. Comparison with experimental results reveals that the mean value of the activation energy Edi decreases linearly with the electric field Eox across the SiO2 layer. This behavior is attributed to the alignment of the Si–H dipole moment with respect to Eox, which favors dissociation of the Si–H bond. The hint of a correlation between the interface defect and positive charge generation suggests that the positively charged centers might be hydrogen-induced overcoordinated oxyge.
Forward-looking infrared 3D target tracking via combination of particle filter and SIFT

Aiming at the problem of tracking 3D target in forward-looking infrared (FLIR) image, this paper proposes a high-accuracy robust tracking algorithm based on SIFT and particle filter. The main contribution of this paper is the proposal of a new method of estimating the affine transformation matrix parameters based on Monte Carlo methods of particle filter. At first, we extract SIFT features on infrared image, and calculate the initial affine transformation matrix with optimal candidate key points. Then we take affine transformation parameters as particles, and use SIR (Sequential Importance Resampling) particle filter to estimate the best position, thus implementing our algorithm. The experiments demonstrate that our algorithm proves to be robust with high accuracy.
Searching for DNA methylation in patients triple-negative breast cancer: a liquid biopsy approach

ABSTRACT Introduction Liquid biopsies are proving to have diagnostic and prognostic value in many different cancers, and in breast cancer they have the potential to improve outcomes by providing valuable information throughout a patient’s cancer journey. However, patients with triple negative breast cancer (TNBC) have received little benefit from such liquid biopsies due to underlying limitations in the discovery and utility of robust biomarkers. Here, we examine the development of DNA methylation-based liquid biopsy assays for breast cancer and how they pertain to TNBC. Areas Covered We conducted a systematic review of liquid biopsy assays for breast cancer and analyzed their relevance in TNBC. We show that the utility of DNA mutation-based assays is poor for TNBC due to the low mutational frequencies across the genome in this subtype. We offer a detailed review of mDETECT – a liquid biopsy specifically designed for assessing tumor burden in TNBC patients. Expert Opinion DNA methylation are foundational and robust events that occur in cancer evolution and may differentiate almost all forms of cancer, including TNBC. Longitudinal patient monitoring using DNA methylation-based liquid biopsies offers great potential for improving the detection and management of TNBC.
An algebraic reconstruction of a moving point source for a scalar wave equation

We discuss an identification problem of a single point source for a three-dimensional scalar wave equation. In this problem, the location and magnitude of the point source are assumed to be unknown. The location moves in a compact region, and the magnitude changes with time. As given data, we use the observed values of the retarded potential and its derivatives obtained at a single observation point and time. For this problem, we propose a direct identification method for the location and magnitude of the source. Our method consists only of the methods of linear algebra, though the problem is formulated by a partial differential equation. Numerical examples are also given to illustrate the effectiveness of our method.
Roughness/error trade-offs in neural network time series models

Radial basis function neural network models of a time series may be developed or trained using samples from the series. Each model is a continuous curve that can be used to represent the series or predict future vales. Model development requires a tradeoff between a measure of roughness of the curve and a measure of its error relative to the samples. For roughness defined as the root integrated squared second derivative and for error defined as the root sum squared deviation (which are among the most common definitions), an optimal tradeoff conjecture is proposed and illustrated. The conjecture states that the curve that minimizes roughness subject to given error is a weighted mean of the least squares line and the natural cubic spline through the samples.
Weighted Sensitivity Minimization for Causal, Linear, Discrete Time--Varying Systems

The weighted sensitivity minimization problem for discrete time--varying systems is treated in a state space framework. Given a controllable and causal (stable) state space realization of the plant to be controlled, the first step in the solution is the computation of an outer-inner factorization of the plant. The key algorithmic step here is the solution of a Lyapunov type of equation running backward in time. Based on the part of the realization of the inner (isometric) factor related to its output state space we then formulate and solve a Nevanlinna--Pick interpolation problem. This second step is also characterized by a Lyapunov equation. It is shown that the solution to the sensitivity minimization problem exists when the solution to this Lyapunov equation is positive definite for all time instances. Finally, we pay special attention to the minimal disturbance attenuation level when the latter is assumed to be equal to a constant scalar for all time instances as well as to a square root implementation of the recursive equations.
U-box E3 ubiquitin ligase PUB8 attenuates abscisic acid responses during early seedling growth

Abstract ABSCISIC ACID-INSENSITIVE3 (ABI3) and ABI5 are 2 crucial transcription factors in abscisic acid (ABA) signaling, and their homeostasis at the protein level plays a decisive role in seed germination and subsequent seedling growth. Here, we found that PLANT U-BOX 8 (PUB8), a U-box E3 ubiquitin ligase, physically interacts with ABI3 and ABI5 and negatively regulates ABA responses during early Arabidopsis (Arabidopsis thaliana) seedling growth. Loss-of-function pub8 mutants were hypersensitive to ABA-inhibited cotyledon greening, while lines overexpressing PUB8 with low levels of ABI5 protein abundance were insensitive to ABA. Genetic analyses showed that ABI3 and ABI5 were required for the ABA-sensitive phenotype of pub8, indicating that PUB8 functions upstream of ABI3 and ABI5 to regulate ABA responses. Biochemical analyses showed that PUB8 can associate with ABI3 and ABI5 for degradation through the ubiquitin-mediated 26S proteasome pathway. Correspondingly, loss-of-function of PUB8 led to enhanced ABI3 and ABI5 stability, while overexpression of PUB8 impaired accumulation of ABI3 and ABI5 in planta. Further phenotypic analysis indicated that PUB8 compromised the function of ABI5 during early seedling growth. Taken together, our results reveal the regulatory role of PUB8 in modulating the early seedling growth by controlling the homeostasis of ABI3 and ABI5.
Variations in the 24 h temporal patterns and time budgets of grazing, rumination, and idling behaviors in grazing dairy cows in a New Zealand system

Abstract This study investigated the variations in the temporal distributions and the lengths of times utilized for grazing, ruminating, and idling behaviors by grazing dairy cows over 24 h. Spring-calved lactating dairy cows (N = 54) from three breeds, Holstein-Friesian (HFR), Jersey (JE), and KiwiCross (KC) in different lactations (1st, 2nd, 3rd) and with different breeding worth index values (103 < BW > 151) were selected. The cows were managed through a rotational grazing scheme and milked once a day at 0500 hours. The cows grazed mainly pasture and consumed additional feeds (maize silage and turnips) in the summer and autumn seasons. AfiCollar was used to record grazing and rumination behaviors (min/h) in the individual cows throughout the lactation period (~270 d). The time neither utilized for grazing nor rumination was counted as idling behavior (min/h). A repeat measure design with PROC MIXED was performed in SAS considering the effects of breed, lactation, individual cow, the hour of the day, season, day within the season, and supplementary feed within the season to evaluate the difference in grazing, rumination, and idling behaviors. Hour of the day, season, day within season, and supplementary feed had significant effects on grazing, rumination, and idling behaviors. Regardless of the season and supplementary feed, cows spent most of the daytime grazing and most of the nighttime ruminating. Grazing activity remained consistently high throughout the day with two peaks around dawn and dusk and a short peak around midnight. Rumination activity remained high from the late evening until early morning. Grazing and ruminating patterns were similar between different breeds and lactations, however, JE cows grazed slightly longer than HFR and KC, and first-lactation cows grazed slightly longer than those in higher lactations. The onset and cessation of grazing activity by the cows were adjusted according to varying day lengths by season. Cows finished grazing earlier when they consumed additional supplements or silage along with pasture. Cows from different breed groups and lactations spent most of their 24 h grazing followed by ruminating and idling. Season and supplementary feed potentially affected the variations in behavior time budgets. These findings should support improving measures for grazing management to address pasture allocation and additional feed demands, and animal welfare in varying environmental and/or managemental conditions.
Generalized Kittel-Van Vleck Relation between g and g ′ ; Validity for Negative g Factors

It is pointed out that a generalized exact relationship exists between the spectroscopic splitting factor $g$ and the magnetomechanical ratio ${g}^{\ensuremath{'}}$ for paramagnetic centers: ${g}^{\ensuremath{'}}=\frac{g}{(g\ensuremath{-}\ensuremath{\rho})}$ with $\ensuremath{\rho}=\frac{〈{S}_{z}〉}{{{S}_{z}}^{\ensuremath{'}}}$. Here ${S}^{\ensuremath{'}}$ is the fictitious spin in the spin Hamiltonian and $〈{S}_{z}〉$ is the expectation value of the real spin in the state labeled by ${{S}_{z}}^{\ensuremath{'}}$; the $z$ axis is defined by the direction of magnetic field. Several classes of magnetic systems are considered, where for each system $\ensuremath{\rho}$ is constant over a wide range of physical parameters such as cubic crystal field and spin-orbit coupling, expressing an underlying symmetry of the magnetic ion in its environment. It is shown that the sole criterion for validity of the Kittel-Van Vleck relation ${g}^{\ensuremath{'}}=\frac{g}{(g\ensuremath{-}1)}$ is that $〈{S}_{z}〉={{S}_{z}}^{\ensuremath{'}}$ and that this may occur even when the admixed orbital angular momentum is very large so that the departure of $g$ from 2 is very large. The generalized relation between $g$ and ${g}^{\ensuremath{'}}$ is also applied to cases where $g$ is negative while ${g}^{\ensuremath{'}}$ is positive. The extension of the relation between $g$ and ${g}^{\ensuremath{'}}$ to cases of interacting magnetic centers is discussed.
Luminescence excitation spectra in diamond

Photoluminescence excitation (PLE) spectra, measured at varying temperatures and for different luminescent energies, are applied systematically to the study of defects in $\mathrm{I}a,$ $\mathrm{I}b,$ $\mathrm{II}b,$ and chemical-vapor-deposited (CVD) diamond. It is shown that the green luminescent band in CVD diamond films consists of two distinct components. The first one is attributed to recombination in the amorphous carbon phase. The second component increases with surface hydrogenation in CVD films, but an analogous band remains almost unchanged in Ib diamond. This band is ascribed to the donor-acceptor pair recombination. The photoionization threshold for transitions from the valence band to the donor level is determined as 3.25 eV. Based on PLE measurements the broad blue band is assigned to the vibronic band of a dislocation-related center with the ground state position in the range from ${E}_{V}$ to ${E}_{V}+0.37$ eV. A series of undocumented photoluminescence (PL) lines at 1.81, 1.84, 1.91, 2.02, 2.1, and 2.2 eV is characterized by PL and PLE techniques as belonging to radiative transitions from different excited states to the same ground state of a divacancy-related center. Oscillatory behavior in the PLE spectra from CVD diamond is used to deduce ${E}_{C}\ensuremath{-}2.24 \mathrm{eV}$ and ${E}_{C}\ensuremath{-}2.05 \mathrm{eV}$ as the optical ionization thresholds to the conduction band for the divacancy-related and the 1.68 eV centers, respectively.
Mixed Nonlinear Complementarity Problems via Nonlinear Optimization: Numerical Results on Multi-Rigid-Body Contact Problems with Friction

Abstract In this work we show that the mixed nonlinear complementarity problem may be formulated as an equivalent nonlinear bound-constrained optimization problem that preserves the smoothness of the original data. One may thus take advantage of existing codes for bound-constrained optimization. This approach is implemented and tested by means of an extensive set of numerical experiments, showing promising results. The mixed nonlinear complementarity problems considered in the tests arise from the discretization of a motion planning problem concerning a set of rigid 3D bodies in contact in the presence of friction. We solve the complementarity problem associated with a single time frame, thus calculating the contact forces and accelerations of the bodies involved.
Synthesis of magnetic fields

The paper deals with some problems of magnetic fields synthesis, depending on determination of the current density distribution, which generates the required magnetic field in the investigated region. Such problems can be reduced to the linear, or nonlinear Fredholm integral equations of the first kind, or to the set of these equations. Fredholm integral equation of the first kind belongs to the class of the ill-posed problems, and for its solving the method of regularisation has been used. In the paper there are given some useful results of synthesis of magnetic fields in few practical configurations.
Comparing ice composition in dark molecular clouds

Abstract We present 5–20 μm Spitzer/IRS spectroscopy toward stars behind dark molecular clouds. We present preliminary results from the Serpens dark cloud to show the variation between environments within a cloud. We are surveying 3 clouds with varying levels of star formation activity. Serpens has the highest level of activity from our 3 clouds. We show that location as well extinction can cause variations in ice composition. We also find that some lines of sight contain organic molecules such as methane and methanol, and the first detection of acetylene ice in the interstellar medium. We believe the high extinction lines of sight have been enriched by star formation activity near those lines of sight.
Determination of vancomycin exposure target and individualized dosing recommendations for critically ill patients undergoing continuous renal replacement therapy

Few studies have been conducted to quantify the exposure target of vancomycin in intensive care unit (ICU) patients undergoing continuous renal replacement therapy (CRRT) and provide optimized dosage regimens. We aimed to determine vancomycin exposure target and dosing recommendations using data from an open database in critically ill patients undergoing CRRT.
Analysis of the bacterial communities associated with pupae and winged or wingless adults of Lipoptena fortisetosa collected from cervids in Italy

The hippoboscid Lipoptena fortisetosa Maa, 1965 is a hematophagous ectoparasite of cervids that can bite humans. This fly is expanding its geographical range and is of concern for animal and human health since it can potentially harbour harmful microorganisms. This study was aimed at characterizing the bacterial communities of L. fortisetosa in its different life‐cycle stages. Pupae and wingless adults were collected from cervids hunted in Tuscan‐Emilian Apennines (central Italy) and pooled into groups of 10 by life stage (30 individual pupae; 1420 individual wingless adults). Winged flies were caught by sweep netting and separated into five pools of 10 insects. After DNA extraction, the bacterial content of each pool was analysed using 16 S metabarcoding. Results revealed that the composition and relative abundance of different taxa greatly differed in the three analysed groups. Wingless adults showed a high abundance of Bartonella (33.07%), which is almost absent in winged flies and pupae. Among the detected pathogens, four genera of concern for human health were found: Bartonella, Moraxella, Mycobacterium and Rickettsia. Interestingly reads similar to Bartonella bovis, Moraxella osloensis and Arsenophonus lipopteni Operational Taxonomic Unit (OTUs) were detected. These findings suggest the possible role of L. fortisetosa as a reservoir of pathogenic microorganisms, confirming the need for further investigation to ascertain its vectorial capacity.
Recognition of the CCT5 di‐Glu degron by CRL4DCAF12 is dependent on TRiC assembly

Assembly Quality Control (AQC) E3 ubiquitin ligases target incomplete or incorrectly assembled protein complexes for degradation. The CUL4‐RBX1‐DDB1‐DCAF12 (CRL4DCAF12) E3 ligase preferentially ubiquitinates proteins that carry a C‐terminal double glutamate (di‐Glu) motif. Reported CRL4DCAF12 di‐Glu‐containing substrates include CCT5, a subunit of the TRiC chaperonin. How DCAF12 engages its substrates and the functional relationship between CRL4DCAF12 and CCT5/TRiC is currently unknown. Here, we present the cryo‐EM structure of the DDB1‐DCAF12‐CCT5 complex at 2.8 Å resolution. DCAF12 serves as a canonical WD40 DCAF substrate receptor and uses a positively charged pocket at the center of the β‐propeller to bind the C‐terminus of CCT5. DCAF12 specifically reads out the CCT5 di‐Glu side chains, and contacts other visible degron amino acids through Van der Waals interactions. The CCT5 C‐terminus is inaccessible in an assembled TRiC complex, and functional assays demonstrate that DCAF12 binds and ubiquitinates monomeric CCT5, but not CCT5 assembled into TRiC. Our biochemical and structural results suggest a previously unknown role for the CRL4DCAF12 E3 ligase in overseeing the assembly of a key cellular complex.
Parental exposure to ocean acidification impacts gamete production and physiology but not offspring performance in Nematostella vectensis

ABSTRACT Ocean acidification (OA) resulting from anthropogenic CO2 emissions is impairing the reproduction of marine organisms. While parental exposure to OA can protect offspring via carryover effects, this phenomenon is poorly understood in many marine invertebrate taxa. Here, we examined how parental exposure to acidified (pH 7.40) versus ambient (pH 7.72) seawater influenced reproduction and offspring performance across six gametogenic cycles (13 weeks) in the estuarine sea anemone Nematostella vectensis. Females exhibited reproductive plasticity under acidic conditions, releasing significantly fewer but larger eggs compared to ambient females after 4 weeks of exposure, and larger eggs in two of the four following spawning cycles despite recovering fecundity, indicating long-term acclimatization and greater investment in eggs. Males showed no changes in fecundity under acidic conditions but produced a greater percentage of sperm with high mitochondrial membrane potential (MMP; a proxy for elevated motility), which corresponded with higher fertilization rates relative to ambient males. Finally, parental exposure to acidic conditions did not significantly influence offspring development rates, respiration rates, or heat tolerance. Overall, this study demonstrates that parental exposure to acidic conditions impacts gamete production and physiology but not offspring performance in N. vectensis, suggesting that increased investment in individual gametes may promote fitness.
NMDA Receptor Antibodies and Neuropsychiatric Symptoms in Parkinson's Disease.

OBJECTIVE N-methyl-d-aspartate receptor (NMDAR) encephalitis is an autoantibody-mediated neurological syndrome with prominent cognitive and neuropsychiatric symptoms. The clinical relevance of NMDAR antibodies outside the context of encephalitis was assessed in this study. METHODS Plasma from patients with Parkinson's disease (PD) (N=108) and healthy control subjects (N=89) was screened at baseline for immunoglobulin A (IgA), IgM, and IgG NMDAR antibodies, phosphorylated tau 181 (p-tau181), and the neuroaxonal injury marker neurofilament light (NfL). Clinical assessment of the patients included measures of cognition (Mini-Mental State Examination [MMSE]) and neuropsychiatric symptoms (Hospital Anxiety and Depression Scale; Non-Motor Symptoms Scale for Parkinson's Disease). A subgroup of patients (N=61) was followed annually for up to 6 years. RESULTS Ten (9%) patients with PD tested positive for NMDAR antibodies (IgA, N=5; IgM, N=6; IgG, N=0), and three (3%) healthy control subjects had IgM NMDAR antibodies; IgA NMDAR antibodies were detected significantly more commonly among patients with PD than healthy control subjects (χ2=4.23, df=1, p=0.04). Age, gender, and disease duration were not associated with NMDAR antibody positivity. Longitudinally, antibody-positive patients had significantly greater decline in annual MMSE scores when the analyses were adjusted for education, age, disease duration, p-tau181, NfL, and follow-up duration (adjusted R2=0.26, p=0.01). Neuropsychiatric symptoms were not associated with antibody status, and no associations were seen between NMDAR antibodies and p-tau181 or NfL levels. CONCLUSIONS NMDAR antibodies were associated with greater cognitive impairment over time in patients with PD, independent of other pathological biomarkers, suggesting a potential contribution of these antibodies to cognitive decline in PD.
Maturation of consonant perception, but not vowel perception, predicts lexical skills at 12 months.

Consonants and vowels differentially contribute to lexical acquisition. From 8 months on, infants' preferential reliance on consonants has been shown to predict their lexical outcome. Here, the predictive value of German-learning infants' (n = 58, 29 girls, 29 boys) trajectories of consonant and vowel perception, indicated by the electrophysiological mismatch response, across 2, 6, and 10 months for later lexical acquisition was studied. The consonant-perception trajectory from 2 to 6 months (β = -2.95) and 6 to 10 months (β = -.91), but not the vowel-perception trajectory, significantly predicted receptive vocabulary at 12 months. These results reveal an earlier predictive value of consonant perception for word learning than previously found, and a particular role of the longitudinal maturation of this skill in lexical acquisition.