Miracle-dz/UniFAR-FTUs huggingface dataset:
Dictionary Learning and Time Sparsity for Dynamic MR Data Reconstruction

The reconstruction of dynamic magnetic resonance data from an undersampled k-space has been shown to have a huge potential in accelerating the acquisition process of this imaging modality. With the introduction of compressed sensing (CS) theory, solutions for undersampled data have arisen which reconstruct images consistent with the acquired samples and compliant with a sparsity model in some transform domain. Fixed basis transforms have been extensively used as sparsifying transforms in the past, but recent developments in dictionary learning (DL) have been shown to outperform them by training an overcomplete basis that is optimal for a particular dataset. We present here an iterative algorithm that enables the application of DL for the reconstruction of cardiac cine data with Cartesian undersampling. This is achieved with local processing of spatio-temporal 3D patches and by independent treatment of the real and imaginary parts of the dataset. The enforcement of temporal gradients is also proposed as an additional constraint that can greatly accelerate the convergence rate and improve the reconstruction for high acceleration rates. The method is compared to and shown to systematically outperform k- t FOCUSS, a successful CS method that uses a fixed basis transform.
CLASSIFYING SPACES, VIRASORO EQUIVARIANT BUNDLES, ELLIPTIC COHOMOLOGY AND MOONSHINE

This work explores some connections between the elliptic cohomology of classifying spaces for finite groups, Virasoro equivariant bundles over their loop spaces and Moonshine for finite groups. Our motivation is as follows: up to homotopy we can replace the loop group LBG by the disjoint union ⨿ [γ]BCG(γ) of classifying spaces of centralizers of elements γ representing conjugacy classes of elements in G. An elliptic object over LBG then becomes a compatible family of graded infinite dimensional representations of the subgroups CG(γ), which in turn defines an element in J. Devoto’s equivariant elliptic cohomology ring EllG. Up to localization (inversion of the order of G) and completion with respect to powers of the kernel of the homomorphism EllG −→ Ell{1}, this ring is isomorphic to Ell ∗(BG), see [5, 6]. Moreover, elliptic objects of this kind are already known: for example the 2-variable Thompson series forming part of the Moonshine associated with the simple groups M24 and the Monster M. Indeed the compatibility condition between the characters of the representations of CG(γ) mentioned above was originally formulated by S. Norton in an Appendix to [21], independently of the work on elliptic genera by various authors leading to the definition of elliptic cohomology (see the various contributions to [17]). In a slightly different direction, J-L. Brylinski [2] introduced the group of Virasoro equivariant bundles over the loop space LM of a simply connected manifold M as part of his investigation of a Dirac operator on LM with coefficients in a suitable vector bundle. Our suggested definition of an elliptic object (= equivariant bundle over a not necessarily simply-connected space) starts from this, and builds in additional structure suggested by Moonshine. We propose it as only provisional, for while it fits in well with Devoto’s construction, the localization which this requires suggests that, even in the very special case of X = BG, further refinement will be necessary to obtain a geometric definition of an elliptic-like cohomology theory. The following example may help the reader to follow our general construction. Accepting for the moment that up to completion and localization a class in Ell(BG) is represented by an infinite dimensional bundle over the loop space LBG, restriction to the subspace of constant loops defines a map Ell∗(BG) −→ K∗(BG)((q)). The image of the representation ring R(G) in the coefficients of the power series ring on the right is dense, giving a privileged position to representations whose characters satisfy a modularity condition. The 1-dimensional Thompson series of [4, 21, 32] are certainly of this type. For the Mathieu group M24 we have a particularly
A Nucleolin-Binding 3′ Untranslated Region Element Stabilizes β-Globin mRNA In Vivo

ABSTRACT The normal expression of human β globin is critically dependent upon the constitutively high stability of its encoding mRNA. Unlike with α-globin mRNA, the specific cis-acting determinants and trans-acting factors that participate in stabilizing β-globin mRNA are poorly described. The current work uses a linker-scanning strategy to identify a previously unknown determinant of mRNA stability within the β-globin 3′ untranslated region (3′UTR). The new determinant is positioned on an mRNA half-stem opposite a pyrimidine-rich sequence targeted by αCP/hnRNP-E, a factor that plays a critical role in stabilizing human α-globin mRNA. Mutations within the new determinant destabilize β-globin mRNA in intact cells while also ablating its 3′UTR-specific interaction with the polyfunctional RNA-binding factor nucleolin. We speculate that 3′UTR-bound nucleolin enhances mRNA stability by optimizing αCP access to its functional binding site. This model is favored by in vitro evidence that αCP binding is enhanced both by cis-acting stem-destabilizing mutations and by the trans-acting effects of supplemental nucleolin. These studies suggest a mechanism for β-globin mRNA stability that is related to, but distinct from, the mechanism that stabilizes human α-globin mRNA.
Ravens, New Caledonian crows and jackdaws parallel great apes in motor self-regulation despite smaller brains

Overriding motor impulses instigated by salient perceptual stimuli represent a fundamental inhibitory skill. Such motor self-regulation facilitates more rational behaviour, as it brings economy into the bodily interaction with the physical and social world. It also underlies certain complex cognitive processes including decision making. Recently, MacLean et al. (MacLean et al. 2014 Proc. Natl Acad. Sci. USA 111, 2140–2148. (doi:10.1073/pnas.1323533111)) conducted a large-scale study involving 36 species, comparing motor self-regulation across taxa. They concluded that absolute brain size predicts level of performance. The great apes were most successful. Only a few of the species tested were birds. Given birds' small brain size—in absolute terms—yet flexible behaviour, their motor self-regulation calls for closer study. Corvids exhibit some of the largest relative avian brain sizes—although small in absolute measure—as well as the most flexible cognition in the animal kingdom. We therefore tested ravens, New Caledonian crows and jackdaws in the so-called cylinder task. We found performance indistinguishable from that of great apes despite the much smaller brains. We found both absolute and relative brain volume to be a reliable predictor of performance within Aves. The complex cognition of corvids is often likened to that of great apes; our results show further that they share similar fundamental cognitive mechanisms.
Soil Organic Matter Composition in the Subhumid Ethiopian Highlands as Influenced by Deforestation and Agricultural Management

Physical fractionation, degradative wet-chemical analysis and liquid-state 13 C nuclear magnetic resonance (NMR) spectroscopy were used to assess the impact of land use changes on the amount and structural composition of soil organic matter (SOM) in bulk soils and size separates in the subhumid highlands of southern Ethiopia. Soil samples (0-10 cm) were collected from natural forest, tea plantations, 25-yr cultivated fields at Wushwush (Paleudalf), Podocarpus-dominated natural forest, Cupressus plantations, and 30-yr cultivated fields at Munesa (Palehumults) sites. Forest clearing and continuous cultivation led to significant depletion (P < 0.05) of total soil organic C (SOC) (55% and 63%) and N (52% and 60%) in the surface soils, respectively. Compared with the cultivated fields, lower proportions of SOC (51 and 27%) and N (49 and 13%) were lost from the tea and Cupressus plantations, respectively. The largest depletion occurred from the labile SOM associated with the sand separates concurrent with higher oxidation states of lignin. However, substantial amounts of these organic substrates were also lost from the stable SOM fraction. Particularly, SOM, associated with the silt-size separates, decreased suggesting that the SOM in silt was quite susceptible to land use changes and represents a moderately labile SOM pool in the soils under study. Solution 13 C NMR spectra revealed larger proportions of protonated and C- and O-substituted aryl-C in the silt than in clay-size separates. In contrast, O-alkyl-C structures were more prominent in the clay than in silt-size separates, coinciding with the lignin distribution obtained by wet-chemical analysis. Deforestation and subsequent agricultural management not only resulted in SOM depletion but also markedly altered the chemical composition of SOM in the subhumid highland ecosystems.
Derivation and validation of an index to predict early death or unplanned readmission after discharge from hospital to the community

Background: Readmissions to hospital are common, costly and often preventable. An easy-to-use index to quantify the risk of readmission or death after discharge from hospital would help clinicians identify patients who might benefit from more intensive post-discharge care. We sought to derive and validate an index to predict the risk of death or unplanned readmission within 30 days after discharge from hospital to the community. Methods: In a prospective cohort study, 48 patient-level and admission-level variables were collected for 4812 medical and surgical patients who were discharged to the community from 11 hospitals in Ontario. We used a split-sample design to derive and validate an index to predict the risk of death or nonelective readmission within 30 days after discharge. This index was externally validated using administrative data in a random selection of 1 000 000 Ontarians discharged from hospital between 2004 and 2008. Results: Of the 4812 participating patients, 385 (8.0%) died or were readmitted on an unplanned basis within 30 days after discharge. Variables independently associated with this outcome (from which we derived the nmemonic “LACE”) included length of stay (“L”); acuity of the admission (“A”); comorbidity of the patient (measured with the Charlson comorbidity index score) (“C”); and emergency department use (measured as the number of visits in the six months before admission) (“E”). Scores using the LACE index ranged from 0 (2.0% expected risk of death or urgent readmission within 30 days) to 19 (43.7% expected risk). The LACE index was discriminative (C statistic 0.684) and very accurate (Hosmer–Lemeshow goodness-of-fit statistic 14.1, p = 0.59) at predicting outcome risk. Interpretation: The LACE index can be used to quantify risk of death or unplanned readmission within 30 days after discharge from hospital. This index can be used with both primary and administrative data. Further research is required to determine whether such quantification changes patient care or outcomes.
First-In-Class Small Molecule ONC201 Induces DR5 and Cell Death in Tumor but Not Normal Cells to Provide a Wide Therapeutic Index as an Anti-Cancer Agent

We previously identified ONC201 (TIC10) as a first-in-class orally active small molecule with robust antitumor activity that is currently in clinical trials in advanced cancers. Here, we further investigate the safety characteristics of ONC201 in preclinical models that reveal an excellent safety profile at doses that exceed efficacious doses by 10-fold. In vitro studies indicated a strikingly different dose-response relationship when comparing tumor and normal cells where maximal effects are much stronger in tumor cells than in normal cells. In further support of a wide therapeutic index, investigation of tumor and normal cell responses under identical conditions demonstrated large apoptotic effects in tumor cells and modest anti-proliferative effects in normal cells that were non-apoptotic and reversible. Probing the underlying mechanism of apoptosis indicated that ONC201 does not induce DR5 in normal cells under conditions that induce DR5 in tumor cells; DR5 is a pro-apoptotic TRAIL receptor previously linked to the anti-tumor mechanism of ONC201. GLP toxicology studies in Sprague-Dawley rats and beagle dogs at therapeutic and exaggerated doses revealed no dose-limiting toxicities. Observations in both species at the highest doses were mild and reversible at doses above 10-fold the expected therapeutic dose. The no observed adverse event level (NOAEL) was ≥42 mg/kg in dogs and ≥125 mg/kg in rats, which both correspond to a human dose of approximately 1.25 g assuming standard allometric scaling. These results provided the rationale for the 125 mg starting dose in dose escalation clinical trials that began in 2015 in patients with advanced cancer.
Comparative Biochemical and Computational Study of the Role of Naturally Occurring Mutations at Ambler Positions 104 and 170 in GES β-Lactamases

ABSTRACT In GES-type β-lactamases, positions 104 and 170 are occupied by Glu or Lys and by Gly, Asn, or Ser, respectively. Previous studies have indicated an important role of these amino acids in the interaction with β-lactams, although their precise role, especially that of residue 104, remains uncertain. In this study, we constructed GES-1 (Glu104, Gly170), GES-2 (Glu104, Asn170), GES-5 (Glu104, Ser170), GES-6 (Lys104, Ser170), GES-7 (Lys104, Gly170), and GES-13 (Lys104, Asn170) by site-specific mutagenesis and compared their hydrolytic properties. Isogenic comparisons of β-lactam resistance levels conferred by these GES variants were also performed. Data indicated the following patterns: (i) Lys104-containing enzymes exhibited enhanced hydrolysis of oxyimino-cephalosporins and reduced efficiency against imipenem in relation to enzymes possessing Glu104, (ii) Asn170-containing enzymes showed reduced hydrolysis rates of penicillins and older cephalosporins, (iii) Ser170 enabled GES to hydrolyze cefoxitin efficiently, and (iv) Asn170 and Ser170 increased the carbapenemase character of GES enzymes but reduced their activity against ceftazidime. Molecular dynamic simulations of GES apoenzyme models, as well as construction of GES structures complexed with cefoxitin and an achiral ceftazidime-like boronic acid, provided insights into the catalytic behavior of the studied mutants. There were indications that an increased stability of the hydrogen bonding network of Glu166-Lys73-Ser70 and an altered positioning of Trp105 correlated with the substrate spectra, especially with acylation of GES by imipenem. Furthermore, likely effects of Ser170 on GES interactions with cefoxitin and of Lys104 on interactions with oxyimino-cephalosporins were revealed. Overall, the data unveiled the importance of residues 104 and 170 in the function of GES enzymes.
ADsafety: Type-Based Verification of JavaScript Sandboxing

Web sites routinely incorporate JavaScript programs from several sources into a single page. These sources must be protected from one another, which requires robust sandboxing. The many entry-points of sandboxes and the subtleties of JavaScript demand robust verification of the actual sandbox source. We use a novel type system for JavaScript to encode and verify sandboxing properties. The resulting verifier is lightweight and efficient, and operates on actual source. We demonstrate the effectiveness of our technique by applying it to ADsafe, which revealed several bugs and other weaknesses.
Who donates their body to science? An international, multicenter, prospective study

The altruistic act of body donation provides a precious resource for both teaching and researching human anatomy. However, relatively little is known about individuals who donate their bodies to science (donors), and in particular whether donors in different geographical locations share similar characteristics. A multicenter prospective survey of donors registering during 2010 in three different geographical locations, New Zealand, Ireland, and the Republic of South Africa, was conducted to identify donor characteristics. The 28‐question survey included sections on body donation program awareness, reasons for donating, giving tendency, education, ethnicity, relationship status, occupation, religion, and political preference. Two hundred surveys (81%) were returned [New Zealand 123 (85% response rate), Republic of South Africa 41 (67%), and Ireland 36 (92%)]. Results indicate that donors share certain characteristics including reason for donating (80% cited a desire to aid medical science as the main reason for wishing to donate their body); family structure (most donors are or have been in long‐term partnerships and ≥85% have siblings); and a higher proportion with no religious affiliation compared to their reference population. Some variations between locations were noted including donor age, the mode of program awareness, occupation, relationship status, political preference, organ donor status and with whom donors had discussed their decision to donate. This information could be important for assisting the identification of potential body donors in new and established bequest programs. Anat Sci Educ. © 2012 American Association of Anatomists.
Recognition acuity, grating acuity, contrast sensitivity, and visual fields in 6-year-old children.

OBJECTIVE To measure monocular distance visual acuity (VA), grating VA, contrast sensitivity, and visual field extent in full-term, 6-year-old children. METHODS Subjects were 59 healthy full-term children aged 5.8 to 6.3 years who had no ocular abnormalities and no myopia of 1.00 diopter (D) or greater, hyperopia of 4.00 D or greater, astigmatism of 1.50 D or greater, or anisometropia of 1.50 D or greater spherical equivalent or cylinder, as evaluated by a standard eye examination with cycloplegic refraction. All were tested monocularly for recognition acuity (Early Treatment Diabetic Retinopathy Study VA charts), grating acuity (Teller acuity cards), contrast sensitivity (Pelli-Robson contrast sensitivity charts), and visual field extent (white-sphere kinetic perimetry). RESULTS Right and left eye values did not differ significantly. Mean values for the right eye were 0.040 logMAR (SD, 0.075 log units) for Early Treatment Diabetic Retinopathy Study VA, 24.5 cycles per degree (SD, 0.3 octaves) for grating acuity, and 1.63 (SD, 0.12 log units) for contrast sensitivity. Mean visual field extent for the inferonasal, superonasal, superotemporal, and inferotemporal meridians was 59.1 degrees (SD, 9.7 degrees), 57.8 degrees (SD, 9.6 degrees), 71.2 degrees (SD, 12.3 degrees), and 100.4 degrees (SD, 6.6 degrees), respectively. CONCLUSIONS The results provide additional normative monocular data on visual function in 6-year-old children and indicate that their thresholds are less than those of adults for distance recognition VA, grating VA, and contrast sensitivity, but similar to those of adults for white-sphere kinetic perimetry.
Bone morphogenetic protein 2 stimulates articular cartilage proteoglycan synthesis in vivo but does not counteract interleukin-1alpha effects on proteoglycan synthesis and content.

OBJECTIVE To study the effect of bone morphogenetic protein 2 (BMP-2) on articular cartilage proteoglycan (PG) synthesis in vivo and to investigate whether BMP-2 is able to counteract the effects of interleukin-1 (IL-1) on articular cartilage PG synthesis and content. METHODS BMP-2 alone or in combination with IL-1alpha was injected into murine knee joints. PG synthesis was measured by 35S-sulfate incorporation using an ex vivo method or autoradiography. Cartilage PG content was analyzed by measuring Safranin O staining intensity on histologic sections. RESULTS BMP-2 appeared to be a potent stimulator of articular cartilage PG synthesis in vivo. However, BMP-2 was not able to counteract the deleterious effects of IL-1alpha on articular cartilage PG synthesis and content. In addition, intraarticular injections of BMP-2 induced chondrophytes. CONCLUSION Although BMP-2 is a very potent stimulator of cartilage PG synthesis in vivo, the therapeutic applications of BMP-2 are limited due to the inability of BMP-2 to counteract the effects of IL-1 and the induction of chondrophytes.
Telomerase Deficiency Affects the Formation of Chromosomal Translocations by Homologous Recombination in Saccharomyces cerevisiae

Telomerase is a ribonucleoprotein complex required for the replication and protection of telomeric DNA in eukaryotes. Cells lacking telomerase undergo a progressive loss of telomeric DNA that results in loss of viability and a concomitant increase in genome instability. We have used budding yeast to investigate the relationship between telomerase deficiency and the generation of chromosomal translocations, a common characteristic of cancer cells. Telomerase deficiency increased the rate of formation of spontaneous translocations by homologous recombination involving telomere proximal sequences during crisis. However, telomerase deficiency also decreased the frequency of translocation formation following multiple HO-endonuclease catalyzed DNA double-strand breaks at telomere proximal or distal sequences before, during and after crisis. This decrease correlated with a sequestration of the central homologous recombination factor, Rad52, to telomeres determined by chromatin immuno-precipitation. This suggests that telomerase deficiency results in the sequestration of Rad52 to telomeres, limiting the capacity of the cell to repair double-strand breaks throughout the genome. Increased spontaneous translocation formation in telomerase-deficient yeast cells undergoing crisis is consistent with the increased incidence of cancer in elderly humans, as the majority of our cells lack telomerase. Decreased translocation formation by recombinational repair of double-strand breaks in telomerase-deficient yeast suggests that the reemergence of telomerase expression observed in many human tumors may further stimulate genome rearrangement. Thus, telomerase may exert a substantial effect on global genome stability, which may bear significantly on the appearance and progression of cancer in humans.
Plateletpheresis concentrate produced with Fresenius cell separator Iraqi experience

The beneficial effect of platelets in the control and prevention of thrombocytopenic hemorrhage was noted early in this century. In 1910 Duke was the first who showed that the platelets contained in the transfused whole blood decreases the bleeding time and controlled bleeding. General improvement of the technique of separating platelets from whole blood & availability of Plateletpheresis concentrate produced with Fresenius cell separator Iraqi experience