Miracle-dz/UniFAR-FTUs huggingface dataset:
Loyola eCommons Loyola eCommons Draft Genome Sequence of Streptococcus anginosus UMB7768, Draft Genome Sequence of Streptococcus anginosus UMB7768, Isolated from a Woman with Recurrent UTI Symptoms Isolated from a Woman with Recurrent UTI Symptoms

Streptococcus anginosus recently was implicated as a pathogen involved in urinary tract infections. A strain of S. anginosus was isolated from the female urogenital tract. Here, we present the draft genome sequence of S. anginosus strain UMB7768. S treptococcus anginosus is a catalase-negative Gram-positive bacterium normally associated with a beneﬁcial role in the human gastrointestinal and oropharynx microbiota (1, 2). However, recent studies have shown that S. anginosus is a pathogenic contributor to several abscess-forming infections and potentially plays a role in cystic ﬁbrosis (3, 4). Furthermore, S. anginosus is the predominant member of the S. milleri group (which also includes S. constellatus and S. intermedius ) found in the urogenital tract (5). A prior study found that strains of the bladder and vaginal communities were highly similar, suggesting microbial sharing between these two microbiota (6). S. anginosus is considered an emerging uropathogen; it has been associated with urgency urinary incontinence (7) and urinary tract infections (UTIs) (8, 9). Here, we present the draft genome sequence of S. anginosus UMB7768 from the urinary microbiota of a female with recurrent UTI.
Conquering Cancer Multi-Drug Resistance Using Curcumin and Cisplatin Prodrug-Encapsulated Mesoporous Silica Nanoparticles for Synergistic Chemo- and Photodynamic Therapies

Recently, the development of anti-cancer approaches using different physical or chemical pathways has shifted from monotherapy to synergistic therapy, which can enhance therapeutic effects. As a result, enormous efforts have been devoted to developing various delivery systems encapsulated with dual agents for synergistic effects and to combat cancer cells acquired drug resistance. In this study, we show how to make Institute of Bioengineering and Nanotechnology (IBN)-1-based mesoporous silica nanoparticles (MSNs) for multifunctional drug delivery to overcome drug resistance cancer therapy. Initially, curcumin (Cur)-embedded IBN-1 nanocomposites (IBN-1-Cur) are synthesized in a simple one-pot co-condensation and then immobilized with the prodrug of Cisplatin (CP) on the carboxylate-modified surface (IBN-1-Cur-CP) to achieve photodynamic therapy (PDT) and chemotherapy in one platform, respectively, in the fight against multidrug resistance (MDR) of MES-SA/DX5 cancer cells. The Pluronic F127 triblock copolymer, as the structure-directing agent, in nanoparticles acts as a p-glycoprotein (p-gp) inhibitor. These designed hybrid nanocomposites with excellent structural properties are efficiently internalized by the endocytosis and successfully deliver Cur and CP molecules into the cytosol. Furthermore, the presence of Cur photosensitizer in the nanochannels of MSNs resulted in increased levels of cellular reactive oxygen species (ROS) under light irradiation. Thus, IBN-1-Cur-CP showed excellent anti-cancer therapy in the face of MES-SA/DX5 resistance cancer cells, owing to the synergistic effects of chemo- and photodynamic treatment.
Adaptive tuning, 4-D Var and representers in RKHS

This work was prepared for presentation at the European Centre for Medium-Range Weather Forecasts, Workshop on the Diagnosis of Data Assimilation Systems, Reading, England, November 1998. Four dimensional variational data assimilation, called 4D-Vax in the atmospheric sciences literature, is a method for combining forecast, dynamical systems equations, prior information about properties of the atmosphere, and heterogeneous observations, to get an estimate of the evolving state of the atmosphere. 'Four dimensional' refers to one time and three space variables, as opposed to three space variables alone. In 4D-Var an entire trajectory in time is fit to the available information. Some of my recent research in this area is aimed at studying the use of GCV and GML methods in choosing the numerous tuning parameters in this fitting problem. We (abstractly) generalize the 'toy' weak 4D-Var model in Gong, Wahba, Johnson and Tribbia (1998) to include adaptive tuning of a variety of parameters throughout the 4D-Var variational problem, and note issues of sensitivity and identifiability. We discuss 'models' for model errors which include systematic, short memory and long memory errors. Finally we remark on the role of the theory of representers in reproducing kernel Hubert spaces in the weak 4D-Var setting.
Open Research Online CO drawdown following the middle Miocene expansion of the Antarctic Ice Sheet

[ 1 ] The development of a permanent, stable ice sheet in East Antarctica happened during the middle Miocene, about 14 million years (Myr) ago. The middle Miocene therefore represents one of the distinct phases of rapid change in the transition from the “ greenhouse ” of the early Eocene to the “ icehouse ” of the present day. Carbonate carbon isotope records of the period immediately following the main stage of ice sheet development reveal a major perturbation in the carbon system, represented by the positive d 13 C excursion known as carbon maximum 6 ( “ CM6 ” ), which has traditionally been interpreted as re ﬂ ecting increased burial of organic matter and atmospheric p CO 2 drawdown. More recently, it has been suggested that the d 13 C excursion records a negative feedback resulting from the reduction of silicate weathering and an increase in atmospheric p CO 2 . Here we present high-resolution multi-proxy (alkenone carbon and foraminiferal boron isotope) records of atmospheric carbon dioxide and sea surface temperature across CM6. Similar to previously published records spanning this interval, our records document a world of generally low (~300 ppm) atmospheric p CO 2 at a time generally accepted to be much warmer than today. Crucially, they also reveal a p CO 2 decrease with associated cooling, which demonstrates that the carbon burial hypothesis for CM6 is feasible and could have acted as a positive feedback on global cooling.
The heavy top quark and right-handed currents

We consider a modification of the standard electroweak model with the third quark generation and the $\tau$-lepton in vector representations of $SU(2)\otimes U(1)_Y$ electroweak symmetry. This is a new way to implement right-handed currents which are controlled by the usual Fermi constant, $G_F$, the weak mixing angle, $\sin\theta_W$, and also by the right-handed mixing matrices which survive when the Lagrangian density is written in terms of the mass eigenstates. In this case there are also new CP violation phases.
Comment on 'Reasonable fermionic quantum information theories require relativity'

In [N. Friis, New J. Phys. 18, 033014 (2016)] the non-relativistic description of fermions is considered and in particular the role of the parity superselection rule in relation to the characterization of entanglement. An argument based on the spin-statistics connection is presented as a physical motivation for the parity superselection rule. Since the spin statistics connection was derived in the context of relativistic quantum mechanics it is argued that the inclusion of the parity superselection rule is motivated by Lorentz invariance. Based on this it is further argued that fermionic Quantum Information theory and the theory of special relativity are conceptually inseparable. In this comment a different, and well known, motivation for the parity superselection rule is given that does not rely on arguments from relativistic quantum mechanics, but instead uses the assumptions that the laws of physics are the same for different observers and the no-signalling principle.
Systematic development and feasibility testing of a multibehavioural digital prehabilitation intervention for patients approaching major surgery (iPREPWELL): A study protocol

Improving outcomes for people undergoing major surgery, specifically reducing perioperative morbidity and mortality remains a global health challenge. Prehabilitation involves the active preparation of patients prior to surgery, including support to tackle risk behaviours that mediate and undermine physical and mental health and wellbeing. The majority of prehabilitation interventions are delivered in person, however many patients express a preference for remotely-delivered interventions that provide them with tailored support and the flexibility. Digital prehabilitation interventions offer scalability and have the potential to benefit perioperative healthcare systems, however there is a lack of robustly developed and evaluated digital programmes for use in routine clinical care. We aim to systematically develop and test the feasibility of an evidence and theory-informed multibehavioural digital prehabilitation intervention ‘iPREPWELL’ designed to prepare patients for major surgery. The intervention will be developed with reference to the Behaviour Change Wheel, COM-B model, and the Theoretical Domains Framework. Codesign methodology will be used to develop a patient intervention and accompanying training intervention for healthcare professionals. Training will be designed to enable healthcare professionals to promote, support and facilitate delivery of the intervention as part of routine clinical care. Patients preparing for major surgery and healthcare professionals involved with their clinical care from two UK National Health Service centres will be recruited to stage 1 (systematic development) and stage 2 (feasibility testing of the intervention). Participants recruited at stage 1 will be asked to complete a COM-B questionnaire and to take part in a qualitative interview study and co-design workshops. Participants recruited at stage 2 (up to twenty healthcare professionals and forty participants) will be asked to take part in a single group intervention study where the primary outcomes will include feasibility, acceptability, and fidelity of intervention delivery, receipt, and enactment. Healthcare professionals will be trained to promote and support use of the intervention by patients, and the training intervention will be evaluated qualitatively and quantitatively. The multifaceted and systematically developed intervention will be the first of its kind and will provide a foundation for further refinement prior to formal efficacy testing.
Beyond Questionnaires: Innovative Approaches to Evaluating Mixed Reality

Mixed Reality (MR) technologies, including augmented and virtual reality, are increasingly used in a number of sectors, thanks to their capabilities to immerse users in multisensory interaction environments. However, as indicated by some systematic reviews, questionnaire remains the main method for evaluating the interaction quality of MR. There is a lack of innovative approaches addressing unique features of MR. It can dampen the advances of MR, as evaluation feedback can inform its future development. In this workshop we aim to explore this issue by inviting participants to share their practical experiences or conceptual ideas of evaluating MR in various contexts, using different methods and tools. The ultimate aim is to produce a research agenda on this topic for the community to examine it further in the future.
Weak wind effects in CNO driven winds of hot first stars

Context. During the evolution of rotating first stars, which initially consisted of only hydrogen and helium, CNO elements may emerge to their surface. These stars may therefore have winds that are driven only by CNO elements. Aims. We study weak wind effects (Gayley-Owocki heating and multicomponent effects) in stellar winds of first generation stars driven purely by CNO elements. Methods. We apply our NLTE multicomponent models and hydrodynamical simulations. Results. The multicomponent effects (frictional heating and decoupling) are important particularly for low metallicity winds, but they influence mass loss rate only if they cause decoupling for velocities lower than the escape velocity. The multicomponent effects also modify the feedback from first stars. As a result of the decoupling of radiatively accelerated metals from hydrogen and helium, the first low-energy cosmic ray particles are generated. We study the interaction of these particles with the interstellar medium concluding that these particles easily penetrate the interstellar medium of a given minihalo. We discuss the charging of the first stars by means of their winds. Conclusions. Gayley-Owocki heating, frictional heating, and the decoupling of wind components occur in the winds of evolved low-metallicity stars and the solar metallicity main-sequence stars.
COSMIC SHEAR MEASUREMENT USING AUTO-CONVOLVED IMAGES

We study the possibility of using quadrupole moments of auto-convolved galaxy images to measure cosmic shear. The autoconvolution of an image corresponds to the inverse Fourier transformation of its power spectrum. The new method has the following advantages: the smearing effect due to the point-spread function (PSF) can be corrected by subtracting the quadrupole moments of the auto-convolved PSF; the centroid of the auto-convolved image is trivially identified; the systematic error due to noise can be directly removed in Fourier space; the PSF image can also contain noise, the effect of which can be similarly removed. With a large ensemble of simulated galaxy images, we show that the new method can reach a sub-percent level accuracy under general conditions, albeit with increasingly large stamp size for galaxies of less compact profiles.
Signatures of circumstellar interaction in the Type IIL supernova ASASSN-15oz

Hydrogen-rich, core-collapse supernovae are typically divided into four classes: IIP, IIL, IIn, and IIb. Recent hydrodynamic modelling shows that circumstellar material is required to produce the early light curves of most IIP/IIL supernovae. In this scenario, IIL supernovae experience large amounts of mass-loss before exploding. We test this hypothesis on ASASSN15oz, a Type IIL supernova. With extensive follow-up in the X-ray, UV, optical, IR, and radio, we present our search for signs of interaction and the mass-loss history indicated by their detection. We find evidence of short-lived intense mass-loss just prior to explosion from light-curve modelling, amounting in 1.5 M of material within 1800 R of the progenitor. We also detect the supernova in the radio, indicating mass-loss rates of 10−6 to 10−7 M yr−1 prior to the extreme mass-loss period. Our failure to detect the supernova in the X-ray and the lack of narrow emission lines in the UV, optical, and NIR do not contradict this picture and place an upper limit on the mass-loss rate outside the extreme period of <10−4 M yr−1. This paper highlights the importance gathering comprehensive data on more Type II supernovae to enable detailed modelling of the progenitor and supernova which can elucidate their mass-loss histories and envelope structures and thus inform stellar evolution models.
Space Phasors and Two-Dimensional Frames

This chapter contains sections titled: Introduction Space-Phasor Representation of a Balanced Three-Phase Function Space-Phasor Representation of Three-Phase Systems Power in Three-Wire Three-Phase Systems ? > ? >-Frame Representation and Control of Three-Phase Signals and Systems dq -Frame Representation and Control of Three-Phase Systems
The long helical jet of the Lighthouse nebula, IGR J11014-6103

Jets from rotation-powered pulsars have so far only been observed in systems moving subsonically trough their ambient medium and/or embedded in their progenitor supernova remnant (SNR). Supersonic runaway pulsars are also expected to produce jets, but they have not been confirmed so far. We investigated the nature of the jet-like structure associated to the INTEGRAL source IGR J11014-6103 (the "Lighthouse nebula"). The source is a neutron star escaping its parent SNR MSH 11-61A supersonically at a velocity exceeding 1000 km/s. We observed the Lighthouse nebula and its jet-like X-ray structure through dedicated high spatial resolution observations in X-rays (Chandra) and radio band (ATCA). Our results show that the feature is a true pulsar's jet. It extends highly collimated over >11pc, displays a clear precession-like modulation, and propagates nearly perpendicular to the system direction of motion, implying that the neutron star's spin axis in IGR J11014-6103 is almost perpendicular to the direction of the kick received during the supernova explosion. Our findings suggest that jets are common to rotation-powered pulsars, and demonstrate that supernovae can impart high kick velocities to misaligned spinning neutron stars, possibly through distinct, exotic, core-collapse mechanisms.
Dopachrome tautomerase is a retinoblastoma-specific gene, and its proximal promoter is preferentially active in human retinoblastoma cells

Purpose Retinoblastoma (RB) is a malignant childhood intraocular tumor. Current treatment options for RB have undesirable side effects. A comprehensive understanding of gene expression in human RB is essential for the development of safe and effective new therapies. Methods We reviewed published microarray and RNA sequencing studies in which gene expression profiles were compared between human RB and normal retina tissues. We investigated the expression of genes of interest using quantitative reverse transcription PCR. We examined the activities of cloned promoter DNA fragments with luciferase assay. Results Dopachrome tautomerase (DCT) was among the most overexpressed genes in RB in published studies. We found that DCT was highly expressed in six of 13 samples microdissected from Thai RB tissues. Expression of DCT was absent or barely detected in retina tissues, various human ocular cells, and major organs. We also demonstrated that the −657 to +411 DCT promoter fragment efficiently directs RB cell–specific transcription of the luciferase reporter gene in cell lines. Conclusions The present work highlights that DCT is one of the most RB-specific genes. The regulatory elements required for this cell-specific gene expression are likely located within its proximal promoter.
Sufentanil Combined with Nalbuphine via Patient-Controlled Intravenous Analgesia After Cesarean Section: A Retrospective Evaluation

Purpose This retrospective study evaluated the efficacy, opioid consumption, and safety profile of two patient-controlled intravenous analgesia (PCIA) regimens (sufentanil combined with nalbuphine vs sufentanil alone) after cesarean section (CS). Patients and Methods Parturients (n = 1808) received sufentanil combined with nalbuphine (SN group) or sufentanil alone (S group) as PCIA after CS. The primary outcome was the numeric rating scale (NRS) pain score with movement (NRS-M) at 24 h after CS. Secondary outcomes were NRS scores at rest (NRS-R) at 24 and 48 h after CS, NRS-M at 48 h after CS, cumulative PCIA bolus times, and opioid consumption during the first 24 and 48 h postoperatively, which was measured in morphine-equivalent doses. Results The population comprised 993 and 815 subjects in the SN and S groups, respectively. At 24 and 48 h after CS, the respective NRS-M scores of the SN group (4.62, 3.37) were each significantly lower than those of the S group (5.18, 4.01; P < 0.01 for both). The corresponding NRS-S scores were similarly lower in the SN group (0.96, 0.19) than in the S group (2.05, 0.92; P < 0.01 for both). After adjusting for covariates, the SN group still had lower NRS-M than the S group at 24 h after CS (estimate adjusted = 0.565, P < 0.001). The PCIA bolus times were significantly lower in the SN group than in the S group. The rates of bradycardia and respiratory depression were lower in the SN group than in the S group. However, the rates of dizziness and postoperative hypotension were slightly higher in the SN group, and those of nausea/vomiting were comparable. Conclusion Compared with sufentanil alone, sufentanil combined with nalbuphine for PCIA provided superior analgesia in parturient women after CS.
Recovering $S^1$-invariant metrics on $S^2$ from the equivariant spectrum

We prove an inverse spectral result for $S^1$-invariant metrics on $S^2$ based on the so-called asymptotic equivariant spectrum. This is roughly the spectrum together with large weights of the $S^1$ action on the eigenspaces. Our result generalizes an inverse spectral result of the first and last named authors, together with Victor Guillemin, concerning $S^1$-invariant metrics on $S^2$ which are invariant under the antipodal map. We use higher order terms in the asymptotic expansion of a natural spectral measure associated with the Laplacian and the $S^1$ action.
EV‐ADD, a database for EV‐associated DNA in human liquid biopsy samples

Abstract Extracellular vesicles (EVs) play a key role in cellular communication both in physiological conditions and in pathologies such as cancer. Emerging evidence has shown that EVs are active carriers of molecular cargo (e.g. protein and nucleic acids) and a powerful source of biomarkers and targets. While recent studies on EV‐associated DNA (EV‐DNA) in human biofluids have generated a large amount of data, there is currently no database that catalogues information on EV‐DNA. To fill this gap, we have manually curated a database of EV‐DNA data derived from human biofluids (liquid biopsy) and in‐vitro studies, called the Extracellular Vesicle‐Associated DNA Database (EV‐ADD). This database contains validated experimental details and data extracted from peer‐reviewed published literature. It can be easily queried to search for EV isolation methods and characterization, EV‐DNA isolation techniques, quality validation, DNA fragment size, volume of starting material, gene names and disease context. Currently, our database contains samples representing 23 diseases, with 13 different types of EV isolation techniques applied on eight different human biofluids (e.g. blood, saliva). In addition, EV‐ADD encompasses EV‐DNA data both representing the whole genome and specifically including oncogenes, such as KRAS, EGFR, BRAF, MYC, and mitochondrial DNA (mtDNA). An EV‐ADD data metric system was also integrated to assign a compliancy score to the MISEV guidelines based on experimental parameters reported in each study. While currently available databases document the presence of proteins, lipids, RNA and metabolites in EVs (e.g. Vesiclepedia, ExoCarta, ExoBCD, EVpedia, and EV‐TRACK), to the best of our knowledge, EV‐ADD is the first of its kind to compile all available EV‐DNA datasets derived from human biofluid samples. We believe that this database provides an important reference resource on EV‐DNA‐based liquid biopsy research, serving as a learning tool and to showcase the latest developments in the EV‐DNA field. EV‐ADD will be updated yearly as newly published EV‐DNA data becomes available and it is freely available at www.evdnadatabase. com.
Characterization of decoherence from an environmental perspective

For the case of phase damping (pure decoherence) we investigate the extent to which environmental traits are imprinted on an open quantum system. The dynamics is described using the quantum channel approach. We study what the knowledge of the channel may reveal about the nature of its underlying dynamics and, conversely, what the dynamics tell us about how to consistently model the environment. We find that, for a Markov phase-damping channel (i.e., a channel compatible with a time-continuous Markovian evolution), the environment may adequately be represented by a mixture of only a few coherent states. For arbitrary Hilbert space dimension N{>=}4 we refine the idea of quantum phase damping, for which we show a means of identification. Symmetry considerations are used to identify decoherence-free subspaces of the system.