Miracle-dz/UniFAR-FTUs huggingface dataset:
Effectiveness of radiotherapy for local control in T3N0 rectal cancer managed with total mesorectal excision: a meta-analysis

Introduction: The total mesorectal excision (TME) significantly improved rectal cancer outcomes. Radiotherapy’s benefit in T3N0 rectal cancer patients managed with TME has not been clearly demonstrated. A systematic review and meta-analysis were undertaken to determine whether radiotherapy altered the risk of locoregional recurrence (LR) in T3N0 rectal cancer patients managed with a TME. Materials and Methods: Studies indexed on PubMed or Embase were systematically searched from inception to October 18, 2020. Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines were observed for the literature search, study screening, and data extraction; the Newcastle Ottawa Scale evaluated bias; Grades of Recommendation, Assessment, Development, and Evaluation Working Group system evaluated certainty; and all were performed independently by at least two investigators. Studies that reported LR data specific to T3N0 rectal cancer patients managed with TME, treated with and without radiotherapy, were included. Data was pooled using a random-effects model. Meta-analyses of the relative risk of local recurrence were conducted. Results: Five retrospective cohort studies involving 932 unique patients reported LR outcomes; no prospective studies met eligibility criteria. Median follow-up ranged from 38.4–78 months. Adjuvant radiotherapy was provided in 3 studies. Chemotherapy was delivered and reported in 4 studies, providing both concurrent and adjuvant chemotherapy. A non-significant LR reduction with radiotherapy alongside TME was estimated, mean relative risk (RR) 0.63 (95% Confidence Interval 0.31–1.29; I2 = 41.8%). Conclusions: A non-significant LR benefit with radiotherapy’s addition was estimated. Meta-analysis of exclusively retrospective cohort studies was concerning for biased results. Adequately powered randomized trials are warranted.
Plasma Exchange May Enhance Antitumor Effects by Removal of Soluble Programmed Death-Ligand 1 and Extracellular Vesicles: Preliminary Study

The antitumor effect of antibody-drug conjugates (ADC) is the main factor in achieving cures. Although the mechanism of tumor resistance to treatment is multifaceted, tumor-derived extracellular vesicles (T-EVs) have been implicated as contributing to the attenuation of ADC therapeutic efficacy. Thus, strategies to eliminate T-EVs are highly promising for overcoming drug resistance. Here we demonstrate plasma exchange therapy to remove T-EVs, decreasing their amount in vitro by 75%. Although trastuzumab emtansine (T-DM1) treatment alone was effective in our rat tumor model, the combination therapy of T-DM1 and T-EV filtration achieved early tumor shrinkage. Our results indicate that T-EV filtration plus ADC is a promising strategy for overcoming drug resistance.
VPsearch: fast exact sequence similarity search for genomic sequences

Similarity search is a central task in computational biology, and in genomics in particular. In genomics, similarity search usually takes the following form: given an unknown nucleotide or protein sequence (the query), what are the most similar sequences in a given database of known sequences? In this context, similarity search is important for taxonomic determination, to establish phylogenetic relationships, or to annotate sequences and genes with functional information. With the advent of easily accessible high-throughput sequencing technologies, the amount of available genomic data continues to grow rapidly, and the demands for computationally efficient and accurate similarity search implementations have increased accordingly.
“It’s about Taking the Risk”: Exploring Toddlers’ Risky Play in a Redesigned Outdoor Space

Physically challenging, risky play is a natural part of children’s outdoor play behaviour, yet risky play is often limited by the environmental affordances as well as educators’ reluctance to allow this type of play due to safety concerns. This case study explored the influence of the redesign of the outdoor environment on 18–26-month-old children’s play behaviours and their educators’ attitudes and responses to the children’s risky play. Video recorded observations examined the children’s play behaviours and adult interactions with the children during their usual outdoor play time. Interviews with educators explored their conceptions of risk-taking and attitudes towards the risky elements included in the redesigned space, whilst their attitudes towards children’s risky play and personal risk-taking behaviours were examined using the Tolerance of Risk in Play Scale and Attitudes Towards Risk questionnaire. Findings indicate that despite initial concerns, educators were supportive of the children’s risky play in the new environment and the environment afforded opportunities for diverse play including risky play.
Whole-Exome Sequencing Revealed New Candidate Genes for Human Dilated Cardiomyopathy

Dilated cardiomyopathy (DCM) is a complex disease affecting young adults. It is a pathological condition impairing myocardium activity that leads to heart failure and, in the most severe cases, transplantation, which is currently the only possible therapy for the disease. DCM can be attributed to many genetic determinants interacting with environmental factors, resulting in a highly variable phenotype. Due to this complexity, the early identification of causative gene mutations is an important goal to provide a genetic diagnosis, implement pre-symptomatic interventions, and predict prognosis. The advent of next-generation sequencing (NGS) has opened a new path for mutation screening, and exome sequencing provides a promising approach for identifying causal variants in known genes and novel disease-associated candidates. We analyzed the whole-exome sequencing (WES) of 15 patients affected by DCM without overloading (hypertension, valvular, or congenital heart disease) or chronic ischemic conditions. We identified 70 pathogenic or likely pathogenic variants and 1240 variants of uncertain clinical significance. Gene ontology enrichment analysis was performed to assess the potential connections between affected genes and biological or molecular function, identifying genes directly related to extracellular matrix organization, transcellular movement through the solute carrier and ATP-binding cassette transporter, and vitamin B12 metabolism. We found variants in genes implicated to a different extent in cardiac function that may represent new players in the complex genetic scenario of DCM.
VLT X-shooter spectroscopy of the nearest brown dwarf binary

The aim of the project is to characterise both components of the nearest brown dwarf sytem to the Sun, WISE J104915.57-531906.1 (=Luhman16AB) at optical and near-infrared wavelengths. We obtained high signal-to-noise intermediate-resolution (R~6000-11000) optical (600-1000 nm) and near-infrared (1000-2480nm) spectra of each component of Luhman16AB, the closest brown dwarf binary to the Sun, with the X-Shooter instrument on the Very Large Telescope. We classify the primary and secondary of the Luhman16 system as L6-L7.5 and T0+/-1, respectively, in agreement with previous measurements published in the literature. We present measurements of the lithium pseudo-equivalent widths, which appears of similar strength on both components (8.2+/-1.0 Angstroms and 8.4+/-1.5 Angstroms for the L and T components, respectively). The presence of lithium (Lithium 7) in both components imply masses below 0.06 Msun while comparison with models suggests lower limits of 0.04 Msun. The detection of lithium in the T component is the first of its kind. Similarly, we assess the strength of other alkali lines (e.g. pseudo-equivalent widths of 6-7 Angstroms for RbI and 4-7 Angstroms for CsI) present in the optical and near-infrared regions and compare with estimates for L and T dwarfs. We also derive effective temperatures and luminosities of each component of the binary: -4.66+/-0.08 dex and 1305(+180)(-135) for the L dwarf and -4.68+/-0.13 dex and 1320(+185)(-135) for the T dwarf, respectively. Using our radial velocity determinations, the binary does not appear to belong to any of the well-known moving group. Our preliminary theoretical analysis of the optical and J-band spectra indicates that the L- and T-type spectra can be reproduced with a single temperature and gravity but different relative chemical abundances which impact strongly the spectral energy distribution of L/T transition objects.
Time Dependent Quantum Transport Through Graphene Nanoribbons

Time-dependent quantum transport for graphene nanoribbons (GNR) are calculated by the hierarchical equation of motion (HEOM) method based on the nonequilibrium Green's function (NEGF) theory (Xie et.al, J. Chem. Phys. 137, 044113, 2012). In this paper, a new steady state calculation technique is introduced and accelerated by the contour integration, which is suitable for large systems. Three Lorentzian fitting schemes for the self-energy matrices are developed based on the nonlinear least square method. Within these schemes, the number of Lorentzians is effectively reduced and the fitting results are good and convergent. With these two developments in HEOM, we have calculated the transient currents in GNR. We find a new type of edge state with delta-function-like density of states in many semi-infinite armchair-type GNR.
Controlling the density of the two-dimensional electron gas at the SrTiO 3 /LaAlO 3 interface

The polar discontinuity at the SrTiO3/LaAlO3 interface (STO/LAO) can in principle sustain an electron density of 3.3E14 cm-2 (0.5 electrons per unit cell). However, experimentally observed densities are more than an order of magnitude lower. Using a combination of first-principles and Schrodinger-Poisson simulations we show that the problem lies in the asymmetric nature of the structure, i.e., the inability to form a second LAO/STO interface that is a mirror image of the first, or to fully passivate the LAO surface. Our insights apply to oxide interfaces in general, explaining for instance why the SrTiO3/GdTiO3 interface has been found to exhibit the full density of 3.3E14 cm-2.
Antisymmetric rank--2 tensor unparticle physics

We present the phenomenology of antisymmetric rank-2 tensor unparticle operator O{sub U,A}{sup {mu}}{sup {nu}} with scaling dimension d{sub U}. We consider the physical effects of operator O{sub U,A}{sup {mu}}{sup {nu}} in Z{sup 0} boson invisible decays Z{sup 0}{yields}U, Z{sup 0}{yields}bb channel, the electroweak precision observable S parameter, and the muon anomalous magnetic dipole moment. The Z{sup 0} boson invisible decay gives a very stringent constraint in the ({lambda}{sub U},M{sub U}) plane, and only small r{identical_to}{lambda}{sub U}/M{sub U} < or approx. 0.1 is favored, when {lambda}{sub U} is order of several 100 GeV. When the phenomenological parameter {mu}, which parameterizes the scale invariance breaking, goes to 0, the S parameter and the muon (g-2) diverge for 1<d{sub U}<2, while for nonzero {mu}, there will be constraints on ({lambda}{sub U},M{sub U}) which are more stringent than those obtained from collider experiments.
Initial-data contribution to the error budget of gravitational waves from neutron-star binaries

As numerical calculations of inspiraling neutron-star binaries reach values of accuracy that are comparable with those of black-hole binaries, a fine budgeting of the various sources of error becomes increasingly important. Among such sources, the initial data are normally not accounted for, the rationale being that the error on the initial spacelike hypersurface is always far smaller than the error gained during the evolution. We here consider critically this assumption and perform a comparative analysis of the gravitational waveforms relative to essentially the same physical binary configuration when computed with two different initial-data codes, and then evolved with the same evolution code. More specifically, we consider the evolution of irrotational neutron-star binaries computed either with the pseudospectral code lorene, or with the newly developed finite-difference code cocal; both sets of initial data are subsequently evolved with the high-order-evolution code whiskythc. In this way we find that although global quantities of the system, like the mass and angular momentum, have differences of the order of $\ensuremath{\lesssim}0.02%$, local quantities, like rest-mass density, extrinsic curvature or angular velocity, show pointwise differences that are much larger, of the order of $\ensuremath{\lesssim}1%$. These local differences are then responsible for a dephasing in the gravitational waves at the merger time (after approximately three orbits) of $\ensuremath{\sim}1.4$ radians. Our results highlight the importance of using initial data that are pointwisely the same when comparative studies are done and physical parameters are estimated.
Design Theory of Equal Split Dual- Band Power Divider without Reactive Elements

In this paper, a design approach for getting dual-band working in a Wilkinson-based power divider (WPD) without adding any reactive elements or open- or short-circuited stubs is presented. The transfer matrix approach is used to get the analytical solutions of the required design equations. Admittance representation with respect to the input and output ports is done to perform even-odd mode analysis. In this impedance of each section is kept constant but the electrical length varies. Different combinations of electrical lengths are taken such that the overall length remains constant. The electrical lengths are selected based on dual-band analysis and depend on the tuning ratio. The conditions for attaining the impedance matching are applied to the obtained design equations and hence found out the values of the matching resistors to be placed between the transmission line sections. The proposed power divider centered at 2.5GHz and 7GHz is theoretically calculated simulated and fabricated. Finally, design procedures and experiments show good agreement with theoretical simulation.
Spherically Symmetric Perfect Fluid Distributions in General Relativity

Various methods of obtaining an exact solution of Einstein field equations representing shear-free motion of a spherically symmetric perfect fluid have been discussed. The methods due to McVittie (1967) and Nariai (1967), where one assumes the metric in a convenient form form one group, and the methods due to Kustaanheimo and Qvist (1948), Chakravarty et al. (1976) and Wyman (1976) where one chooses suitably an arbitrary function of integration form the other group.
Cycle-Inhibiting Factor Is Associated with Burkholderia pseudomallei Invasion in Human Neuronal Cells

Simple Summary Neurological melioidosis, caused by Burkholderia pseudomallei, can lead to the development of severe symptoms associated with the nervous system. However, the pathogenic mechanism through which this bacterium infects neuronal cells has not been studied. This study showed that B. pseudomallei can infect human neuronal SH-SY5Y cells in vitro. Cycle-inhibiting factor (Cif), a type III secreted effector, is one of the virulence factors produced by B. pseudomallei upon infection. The B. pseudomallei cif-deleted mutant reduced the ability to invade neuronal cells compared with the parental strain. Our finding indicates that Cif is associated with B. pseudomallei invasion of human neuronal cells. Abstract Burkholderia pseudomallei is a pathogenic bacterium that causes human melioidosis, which is associated with a high mortality rate. However, the underlying mechanisms of B. pseudomallei pathogenesis are largely unknown. In this study, we examined the infection of human neuronal SH-Sy5y cells by several clinically relevant B. pseudomallei strains. We found that all tested B. pseudomallei strains can invade SH-Sy5y cells, undergo intracellular replication, cause actin-tail formation, and form multinucleated giant cells. Additionally, a deletion mutant of B. pseudomallei cycle-inhibiting factor (cif) was constructed that exhibited reduced invasion in SH-Sy5y cells. Complementation of cif restored invasion of the B. pseudomallei cif-deleted mutant. Our findings enhance understanding of B. pseudomallei pathogenicity in terms of the virulence factor Cif and demonstrate the function of Cif in neurological melioidosis. This may eventually lead to the discovery of novel targets for treatment and a strategy to control the disease.
The 2XMMi/SDSS Galaxy Cluster Survey - III. Clusters associated with spectroscopically targeted luminous red galaxies in SDSS-DR10

We present a sample of 383 X-ray selected galaxy groups and clusters with spectroscopic redshift measurements (up to z ∼ 0.79) from the 2XMMi/SDSS Galaxy Cluster Survey. The X-ray cluster candidates were selected as serendipitously detected sources from the 2XMMi-DR3 catalogue that were located in the footprint of the Sloan Digital Sky Survey (SDSS-DR7). The cluster galaxies with available spectroscopic redshifts were selected from the SDSS-DR10. We developed an algorithm for identifying the cluster candidates that are associated with spectroscopically targeted luminous red galaxies and for constraining the cluster spectroscopic redshift. A cross-correlation of the constructed cluster sample with published optically selected cluster catalogues yielded 264 systems with available redshifts. The present redshift measurements are consistent with the published values. The current cluster sample extends the optically confirmed cluster sample from our cluster survey by 67 objects. Moreover, it provides spectroscopic confirmation for 78 clusters among our published cluster sample, which previously had only photometric redshifts. Of the new cluster sample that comprises 67 systems, 55 objects are newly X-ray discovered clusters and 52 systems are sources newly discovered as galaxy clusters in optical and X-ray wavelengths. Based on the measured redshifts and the fluxes given in the 2XMMi-DR3 catalogue, we estimated the X-ray luminosities and masses of the cluster sample.
Clusters: age scales for stellar physics

Ages are key to truly understand a large plethora of astrophysical phenomena. On the other hand, stellar clusters are open windows to understand stellar evolution, specifically, the change with time and mass of different stellar properties. As such, they are our laboratories where different theories can be tested, but without accurate ages, our knowledge would impaired. We revisit here a large number of age-dating techniques and discuss their advantages and draw-backs. In addition, a step-by step process is suggested in order to built a coherent age scale ladder, minimizing the error budget and the sources of uncertainty.
Terahertz Electrodynamics of Dirac Fermions in Graphene

Charge carriers in graphene mimic two-dimensional massless Dirac fermions with linear energy dispersion, resulting in unique optical and electronic properties. They exhibit high mobility and strong interaction with electromagnetic radiation over a broad frequency range. Interband transitions in graphene give rise to pronounced optical absorption in the mid-infrared to visible spectral range, where the optical conductivity is close to a universal value σ0 = πe2/2h. Free-carrier intraband transitions, on the other hand, cause lowfrequency absorption, which varies significantly with charge density and results in strong light extinction at high carrier density. These properties together suggest a rich variety of possible optoelectronic applications for graphene. In this thesis, we investigate the optoelectronic properties of graphene by measuring transient photoconductivity with optical pump-terahertz probe spectroscopy. We demonstrate that graphene exhibits semiconducting positive photoconductivity near zero carrier density, which crosses over to metallic negative photoconductivity at high carrier density. These observations are accounted for by the interplay between photoinduced changes of both the Drude weight and carrier scattering rate. Our findings provide a complete picture to explain the opposite photoconductivity behavior reported in (undoped) graphene grown epitaxially and (doped) graphene grown by chemical vapor deposition. Our measurements also reveal the non-monotonic temperature dependence of the Drude weight in graphene, a unique property of two-dimensional massless Dirac fermions.
High Hemin Concentration Induces Escape from Senescence of Normoxic and Hypoxic Colon Cancer Cells

Simple Summary High red-meat consumption as well as bleeding or bruising can promote oxidative stress and, in consequence, cancer development. However, the mechanism of that phenomenon is not understood. The induction of therapy-induced senescence (TIS) might also be induced by oxidative stress. Recently, TIS cells, despite their inhibited proliferation potential, have been identified as one of the sources of tumor re-growth. Here, with the use of molecular analyses, we found that oxidative stress, promoted by high doses of hemin or H2O2, can trigger TIS escape and cell re-population. It is closely related to the activity of antioxidative enzymes, especially heme oxygenase-1. Hypoxia might accelerate these effects. Therefore, we propose that the prevention of excessive oxidative stress could be a potential target in senolytic therapies. Abstract Hemoglobin from either red meat or bowel bleeding may promote oxidative stress and increase the risk of colorectal cancer (CRC). Additionally, solid cancers or their metastases may be present with localized bruising. Escape from therapy-induced senescence (TIS) might be one of the mechanisms of tumor re-growth. Therefore, we sought to study whether hemin can cause escape from TIS in CRC. To induce senescence, human colon cancer cells were exposed to a chemotherapeutic agent irinotecan (IRINO). Cells treated with IRINO exhibited common hallmarks of TIS. To mimic bleeding, colon cancer cells were additionally treated with hemin. High hemin concentration activated heme oxygenase-1 (HO-1), induced escape from TIS and epithelial-to-mesenchymal transition, and augmented progeny production. The effect was even stronger in hypoxic conditions. Similar results were obtained when TIS cells were treated with another prooxidant agent, H2O2. Silencing of antioxidative enzymes such as catalase (CAT) or glutathione peroxidase-1 (GPx-1) maintained colon cancer cells in a senescent state. Our study demonstrates that a high hemin concentration combined with an increased activity of antioxidative enzymes, especially HO-1, leads to escape from the senescence of colon cancer cells. Therefore, our observations could be used in targeted anti-cancer therapy.