Miracle-dz/UniFAR-FTUs huggingface dataset:
Enrichment with Carbon-13 and Deuterium during Monooxygenase-Mediated Biodegradation of 1,4-Dioxane

Recent technical developments have enabled the application of compound-specific isotope analysis (CSIA) of low (parts per billion) concentrations of 1,4-dioxane that are often found in groundwater at 1,4-dioxane-contaminated sites. However, to quantify 1,4-dioxane biodegradation, isotopic enrichment factors are needed to interpret the CSIA data obtained from field samples. In this study, the carbon and hydrogen isotopic enrichment factors (eC and eH, respectively) for 1,4-dioxane biodegradation have been determined for axenic propane- or isobutane-grown cultures of Rhodococcus rhodochrous ATCC 21198 and for tetrahydrofuran-grown cultures of Pseudonocardia tetrahydrofuranoxidans K1. The enrichment factors for propane-grown (eC = −2.7 ± 0.3‰, and eH = −21 ± 2‰) and isobutane-grown (eC = −2.5 ± 0.3‰, and eH = −28 ± 6‰) cells of strain 21198 were similar and substantially smaller than those determined for tetrahydrofuran-grown cells of strain K1 (eC = −4.7 ± 0.9‰, and eH = −147 ± 22‰). The presence of 1-butyn.
Protracted yet Coordinated Differentiation of Long-Lived SARS-CoV-2-Specific CD8+ T Cells during Convalescence

Key Points Longitudinal CyTOF analysis of tetramer+ SARS-CoV-2–specific CD8+ T cells was performed. Nucleocapsid-specific T and Ab responses are coordinated. Self-renewing potential and polyfunctionality of tetramer+ cells change over convalescence. Visual Abstract CD8+ T cells can potentiate long-lived immunity against COVID-19. We screened longitudinally-sampled convalescent human donors against SARS-CoV-2 tetramers and identified a participant with an immunodominant response against residues 322 to 311 of nucleocapsid (Nuc322–331), a peptide conserved in all variants of concern reported to date. We conducted 38-parameter cytometry by time of flight on tetramer-identified Nuc322–331–specific CD8+ T cells and on CD4+ and CD8+ T cells recognizing the entire nucleocapsid and spike proteins, and took 32 serological measurements. We discovered a coordination of the Nuc322–331–specific CD8+ T response with both the CD4+ T cell and Ab pillars of adaptive immunity. Over the approximately six month period of convalescence monitored, we observed a slow and progressive decrease in the activation state and polyfunctionality of Nuc322–331–specific CD8+ T cells, accompanied by an increase in their lymph node–homing and homeostatic proliferation potential. These results suggest that following a typical case of mild COVID-19, SARS-CoV-2–specific CD8+ T cells not only persist but continuously differentiate in a coordinated fashion well into convalescence into a state characteristic of long-lived, self-renewing memory.
Conductive and injectable hyaluronic acid/gelatin/gold nanorod hydrogels for enhanced surgical translation and bioprinting.

There is growing evidence indicating the need to combine the rehabilitation and regenerative medicine fields to maximize functional recovery after spinal cord injury (SCI), but there are limited methods to synergistically combine the fields. Conductive biomaterials may enable synergistic combination of biomaterials with electric stimulation (ES), which may enable direct ES of neurons to enhance axon regeneration and reorganization for better functional recovery; however, there are three major challenges in developing conductive biomaterials: (1) low conductivity of conductive composites, (2) many conductive components are cytotoxic, and (3) many conductive biomaterials are pre-formed scaffolds and are not injectable. Pre-formed, noninjectable scaffolds may hinder clinical translation in a surgical context for the most common contusion-type of SCI. Alternatively, an injectable biomaterial, inspired by lessons from bioinks in the bioprinting field, may be more translational for contusion SCIs. Therefore, in the current study, a conductive hydrogel was developed by incorporating high aspect ratio citrate-gold nanorods (GNRs) into a hyaluronic acid and gelatin hydrogel. To fabricate nontoxic citrate-GNRs, a robust synthesis for high aspect ratio GNRs was combined with an indirect ligand exchange to exchange a cytotoxic surfactant for nontoxic citrate. For enhanced surgical placement, the hydrogel precursor solution (i.e., before crosslinking) was paste-like, injectable/bioprintable, and fast-crosslinking (i.e., 4 min). Finally, the crosslinked hydrogel supported the adhesion/viability of seeded rat neural stem cells in vitro. The current study developed and characterized a GNR conductive hydrogel/bioink that provided a refinable and translational platform for future synergistic combination with ES to improve functional recovery after SCI.
Réponse des cellules épithéliales pulmonaires à l'exposition au perflurocarbone dans le contexte des applications de la ventilation liquide totale

Au cours de la ventilation liquide totale (VLT), les cellules pulmonaires sont exposees a des perfluorocarbones (PFC) dont les proprietes physiques different fortement du milieu standard de culture cellulaire (DMEM) et encore plus des proprietes de l'air. Dans cette these nous etudions les effets d’une exposition au PFC sur la reponse des cellules epitheliales pulmonaires, en effectuant une etude approfondie des proprietes structurales, mecaniques et fonctionnelles. La reponse des cellules A549 (alveolaire), HBE (bronchique) et AM (Macrophage alveolaire) exposees au PFC est etudiee par comparaison au DMEM. Les variations de la structure de F-actine, de la densite d'adhesion focale et de la distribution du glycocalyx sont evaluees par fluorescence. Les changements de proprietes mecaniques et de parametres d’adhesion sont mesures par la Magnetocymetrie (MTC) etendue a l’analyse multiechelle. La mecanique cellulaire est caracterisee par deux modeles microrheologiques refletant deux types de comportement possibles du cytosquelette (CSK). L'adhesion a la matrice cellulaire est analysee par un modele stochastique de de-adhesion, decrivant la composante non-reversible de la reponse cellulaire. Les roles fondamentaux de la structure de F-actine et de la couche de glycocalyx sont respectivement evalues par depolymerisation de F-actine et en degradant le glycocalyx. Les resultats montrent que l'exposition au PFC induit un remodelage de la structure de F-actine, un affaiblissement du CSK et une diminution de l'adhesion. Ces resultats demontrent que le PFC declenche une reponse particuliere des cellules epitheliales caracterisee par une diminution de la tension intracellulaire, l'affaiblissement de l'adhesion et la redistribution du glycocalyx. L’origine de cette adaptation cellulaire est physique et tres probablement reliee a l’augmentation de l'energie interfaciale associee a la basse tension de surface d’un PFC chimiquement apolaire. La faible tension de surface du PFC est egalement responsable d'une augmentation de la compliance pulmonaire pendant VLT et a des impacts profonds dans les parametres respiratoires, parallelement a la modification de la reponse cellulaire.
Contributions of Preterm Delivery to Cardiovascular Disease Risk Prediction in Women.

Background: Preterm delivery is associated with a 1.4- to 2-fold increased risk of cardiovascular disease (CVD), but inclusion of preterm delivery in CVD risk prediction algorithms has not been tested. We evaluated whether including preterm delivery and parity in CVD risk scores improved identification of women at high risk versus scores based on traditional risk factors. Methods: We predicted 10-year CVD risk using 119,587 observations contributed by 76,512 women ≥40 years of age and 20-year CVD risk with 72,533 women ≥40 years of age and 72,872 women ≥30 years of age from the Nurses' Health Study II. Cox proportional hazards models were fit with established CVD risk factors (Model 1) and established risk factors plus preterm delivery and parity (Model 2). We evaluated model fit, calibration, discrimination, and risk reclassification. Results: Very preterm delivery (<32 weeks) was associated with CVD in all 10- and 20-year models that included the established CVD risk factors (e.g., hazard ratio: 1.61, 95% confidence interval: 1.19 to 2.20 in 10-year risk model). Model 2 had improved fit relative to Model 1, but discrimination was not improved in Model 2 based on the C-difference or net reclassification index. Similar models for 20-year CVD risk prediction at age ≥30 years indicated improved discrimination when including preterm delivery and parity. Conclusions: Incorporating preterm delivery and parity into CVD risk scores appears most useful when women are young, before they develop established CVD risk factors. Observed improvements in risk prediction were small and warrant further investigation to confirm our findings and assess utility in a clinical setting.
Application of arti ﬁ cial neural network (ANN-MLP) for the prediction of fouling resistance in heat exchanger to MgO-water and CuO-water nano ﬂ uids

In this work, an arti ﬁ cial neural network (ANN) model was developed with the aim of predicting fouling resistance for heat exchanger, the network was designed and trained by means of 375 experimental data points that were selected from the literature. These data points contain six inputs, including time, volumetric concentration, heat ﬂ ux, mass ﬂ ow rate, inlet temperature, thermal conductivity and fouling resistance as an output. The experimental data are used for training, testing and validation of the ANN using multiple layer perceptron (MLP). The comparison of statistical criteria of different networks shows that the optimal structure for predicting the fouling resistance of the nano ﬂ uid is the MLP network with 20 hidden neurons, which has been trained with Levenberg – Marquardt (LM) algorithm. The accuracy of the model was assessed based on three known statistical metrics including mean square error (MSE), mean absolute percentage error (MAPE) and coef ﬁ cient of determination (R 2 ). The obtained model was found with the performance of {MSE ¼ 6.5377 (cid:2) 10 (cid:3) 4 , MAPE ¼ 2.40% and R 2 ¼ 0.99756} for the training stage, {MSE ¼ 3.9629 (cid:2) 10 (cid:3) 4 , MAPE ¼ 1.8922% and R 2 ¼ 0.99835} for the test stage and {MSE ¼ 5.8303 (cid:2) 10 (cid:3) 4 , MAPE ¼ 2.57% and R 2 ¼ 0.99812} for the validation stage. In order to control the fouling procedure, and after conducting a sensitivity analysis, it found that all input variables have strong effect on the estimation of the fouling resistance. Reduction of fouling resistance in heat exchangers. A high determination coef ﬁ cient has been reached (R 2 ¼ 0.99770). Developing a program and an interface to facilitate the calculation for users.
Southern rice black‐streaked dwarf virus hijacks SNARE complex of its insect vector for its effective transmission to rice

Abstract Vesicular trafficking is an important dynamic process that facilitates intracellular transport of biological macromolecules and their release into the extracellular environment. However, little is known about whether or how plant viruses utilize intracellular vesicles to their advantage. Here, we report that southern rice black‐streaked dwarf virus (SRBSDV) enters intracellular vesicles in epithelial cells of its insect vector by engaging VAMP7 and Vti1a proteins in the soluble N‐ethylmaleimide‐sensitive factor attachment protein receptor (SNARE) complex. The major outer capsid protein P10 of SRBSDV was shown to interact with VAMP7 and Vti1a of the white‐backed planthopper and promote the fusion of vesicles into a large vesicle, which finally fused with the plasma membrane to release virions from midgut epithelial cells. Downregulation of the expression of either VAMP7 or Vti1a did not affect viral entry and accumulation in the gut, but significantly reduced viral accumulation in the haemolymph. It also did not affect virus acquisition, but significantly reduced the virus transmission efficiency to rice. Our data reveal a critical mechanism by which a plant reovirus hijacks the vesicle transport system to overcome the midgut escape barrier in vector insects and provide new insights into the role of the SNARE complex in viral transmission and the potential for developing novel strategies of viral disease control.
Impact of Binge Drinking During College on Resting State Functional Connectivity

Aim The current study aimed to examine the longitudinal effects of standard binge drinking (4+/5+ drinks for females/males in 2 hours) and extreme binge drinking (8+/10+ drinks for females/males in 2 hours) on resting state functional connectivity. Method 119 college students with distinct alcohol bingeing patterns (35 non-bingeing controls, 44 standard bingers, and 40 extreme bingers) were recruited to ensure variability in bingeing frequency. Resting state fMRI scans were obtained at time 1 when participants were college freshmen and sophomores and again approximately two years later. On four occasions during the 2-year period between scans, participants reported monthly standard and extreme binge drinking for the past 6 months. Association between bingeing and change in functional connectivity was studied using both network-level and edge-level analysis. Network connectivity was calculated by aggregating multiple edges (a functional connection between any two brain regions) affiliated with the same network. The network-level analysis used mixed-effects models to assess the association between standard/extreme binge drinking and change in network connectivity, focusing on canonical networks often implicated in substance misuse. On the other hand, the edge-level analysis tested the relationship between bingeing and change in whole-brain connectivity edges using connectome-based predictive modeling (CPM). Results For network-level analysis, higher standard bingeing was associated with a decrease in connectivity between Default Mode Network-Ventral Attention Network (DMN-VAN) from time 1 to time 2, controlling for the initial binge groups at time 1, longitudinal network changes, in-scanner motion and other demographic covariates. For edge-level analysis, the CPM failed to identify a generalizable predictive model of cumulative standard/extreme bingeing from change in connectivity edges. Conclusions Our findings suggest that binge drinking is associated with abnormality in networks implicated in attention allocation and self-focused processes, which, in turn, have been implicated in rumination, craving, and relapse. More extensive alterations in functional connectivity might be observed with heavier or longer binge drinking pattern.
‘Phantom’ atoms and thermal motion in fullerene C60 revealed by x-ray and neutron diffraction

The additional atomic occupancy in the octahedral and the tetrahedral voids of the face-centered cubic lattice (fcc) of fullerene C60 was detected by neutron and x-ray powder diffraction. The observed occupancy exactly tracks the rearrangement of the orientation order with temperature decreases and results from the large atomic vibrations of the carbon atoms constituting the fullerene molecules. This motion assumes a small but finite probability to find the carbon atoms in the fcc interstitial voids, which is modeled by the detected ‘phantom’ occupancies.
Evaluation of the implant disease risk assessment (IDRA) tool: A retrospective study in patients with treated periodontitis and implant‐supported fixed dental prostheses (FDPs)

Abstract Aim To evaluate the Implant Disease Risk Assessment (IDRA) tool for the prediction of peri‐implantitis in treated periodontitis patients with implant‐supported fixed dental prostheses (FDPs) after at least 5 years of function. Material and methods From the patient pool of implant patients enrolled in a regular supportive periodontal therapy programme (SPT) for at least 5 years, 239 patients were screened. Eighty patients met the inclusion criteria and underwent evaluation through the criteria of the IDRA tool. Areas under the curve (AUCs) for receiver operating characteristic (ROC) curves including 95% confidence intervals were estimated. Results Seventy‐nine patients (43 males and 36 females, 8 smokers), aged on average 59.0 years (range: 40–79 years) at baseline (i.e. FDP delivery) were analysed. The calculated IDRA‐risk was in 34 patients (42.5%) a moderate risk, while 45 patients (56.3%) were considered at high IDRA‐risk. One patient categorized at low IDRA‐risk was excluded from the analysis. The AUC was 0.613 (95% CI: 0.464–0.762) if the IDRA‐risk was associated with prevalence of peri‐implantitis at the most recent follow‐up. Peri‐implantitis was diagnosed in 4 patients (12%) at moderate and in 12 patients (27%) at high IDRA‐risk, respectively. The calculated odds ratio for developing peri‐implantitis in patients with high IDRA‐risk compared with patients with moderate IDRA‐risk was 2.727 with no statistically significant difference between the two groups (95% CI: 0.793–9.376). Conclusion Within the limitations of the present retrospective study, the IDRA algorithm might represent a promising tool to assess patients at moderate or high risk of developing peri‐implantitis.
Poly-Cauchy numbers of the second kind - the combinatorics behind

We introduce poly-Cauchy permutations of the second kind that are enumerated by the polyCauchy numbers of the second kind. We provide combinatorial proofs for several identities involving polyCauchy numbers of the second kind and some of their generalizations. The aim of this work is to demonstrate the power and beauty of the elementary combinatorial approach.
Metric Entropy and Nonlinear Partial Differential Equations by

DUTTA, PRERONA. Metric Entropy and Nonlinear Partial Differential Equations. (Under the direction of Tien Khai Nguyen.) The metric entropy (or "-entropy) has been studied extensively in a variety of literature and disciplines. This notion was introduced by Kolmogorov and Tikhomirov in 1959 as the minimum number of bits needed to represent a point in a given subset K of a metric space (E ,ρ), up to an accuracy " with respect to the metric ρ. Recently, the "-entropy has also been used to measure the set of solutions of various nonlinear partial differential equations (PDEs). In this context, it provides a measure of the order of “resolution” and the “complexity” of a numerical scheme. This dissertation is motivated by the above points of view and demonstrates techniques emerging from the field of nonlinear analysis, that are used to estimate the metric entropy for different classes of bounded variation (BV) functions. Since Helly’s theorem states that a set of uniformly bounded total variation functions is compact in L-space, a natural question arises on how to quantify the degree of compactness and we answer this using the concept of "-entropy. Subsequently, we apply the obtained results to measure solution sets of conservation laws and Hamilton-Jacobi equations. In the first half of this thesis, we elucidate the foundational principles involved in our work and show that the minimal number of functions needed to represent a bounded total variation function in L1([0, L ]d ,R) up to an error " with respect to L1-distance, is of the order "−d . We use this outcome to examine the metric entropy for sets of viscosity solutions to the Hamilton-Jacobi equation. Earlier works on this topic considered a uniformly convex Hamiltonian. We extend the analysis to the case when the Hamiltonian H ∈C 1(Rd ) is strictly convex, coercive and a uniformly directionally convex function. Under these assumptions, we establish sharp estimates on the "-entropy for sets of viscosity solutions to the HamiltonJacobi equation with respect to W1,1-distance in multi-dimensional cases. The second half of the thesis focuses on finding sharp estimates for the metric entropy of a class of bounded total generalized variation functions taking values in a general totally bounded metric space (E ,ρ) upto an accuracy of " with respect to the L1–distance. We rely on the ideas of covering and packing in (E ,ρ) to derive such bounds and utilize them to study a scalar conservation law in one-dimensional space, which yields an upper bound on the "-entropy of a set of entropy admissible weak solutions to it, in case of weakly genuinely nonlinear fluxes, i.e., for fluxes with no affine parts. In particular, for fluxes admitting finitely many inflection points with a polynomial degeneracy, this estimate is sharp. © Copyright 2021 by Prerona Dutta All Rights Reserved Metric Entropy and Nonlinear Partial Differential Equations
Defining meaningful units. Challenges in sign segmentation and segment-meaning mapping (short paper)

This paper addresses the tasks of sign segmentation and segment-meaning mapping in the context of sign language (SL) recognition. It aims to give an overview of the linguistic properties of SL, such as coarticulation and simultaneity, which make these tasks complex. A better understanding of SL structure is the necessary ground for the design and development of SL recognition and segmentation methodologies, which are fundamental for machine translation of these languages. Based on this preliminary exploration, a proposal for mapping segments to meaning in the form of an agglomerate of lexical and non-lexical information is introduced.
Approaching Sign Language Gloss Translation as a Low-Resource Machine Translation Task

A cascaded Sign Language Translation system first maps sign videos to gloss annotations and then translates glosses into a spoken languages. This work focuses on the second-stage gloss translation component, which is challenging due to the scarcity of publicly available parallel data. We approach gloss translation as a low-resource machine translation task and investigate two popular methods for improving translation quality: hyperparameter search and backtranslation. We discuss the potentials and pitfalls of these methods based on experiments on the RWTH-PHOENIX-Weather 2014T dataset.
Product Review Translation using Phrase Replacement and Attention Guided Noise Augmentation

Product reviews provide valuable feedback of the customers and however and they are available today only in English on most of the e-commerce platforms. The nature of reviews provided by customers in any multilingual country poses unique challenges for machine translation such as code-mixing and ungrammatical sentences and presence of colloquial terms and lack of e-commerce parallel corpus etc. Given that 44% of Indian population speaks and operates in Hindi language and we address the above challenges by presenting an English–to–Hindi neural machine translation (NMT) system to translate the product reviews available on e-commerce websites by creating an in-domain parallel corpora and handling various types of noise in reviews via two data augmentation techniques and viz. (i). a novel phrase augmentation technique (PhrRep) where the syntactic noun phrases in sentences are replaced by the other noun phrases carrying different meanings but in similar context; and (ii). a novel attention guided noise augmentation (AttnNoise) technique to make our NMT model robust towards various noise. Evaluation shows that using the proposed augmentation techniques we achieve a 6.67 BLEU score improvement over the baseline model. In order to show that our proposed approach is not language-specific and we also perform experiments for two other language pairs and viz. En-Fr (MTNT18 corpus) and En-De (IWSLT17) that yield the improvements of 2.55 and 0.91 BLEU points and respectively and over the baselines.