Miracle-dz/UniFAR-FTUs huggingface dataset:
A MASSIVE PROGENITOR OF THE LUMINOUS TYPE IIn SUPERNOVA 2010jl

The bright, nearby, recently discovered supernova (SN) 2010jl is a luminous Type IIn SN. Here, we report archival Hubble Space Telescope (HST) observations of its host galaxy UGC 5189A taken roughly 10 yr prior to explosion, as well as early-time optical spectra of the SN. The HST images reveal a luminous, blue point source at the position of the SN, with an absolute magnitude of −12.0 in the F300W filter. If it is not just a chance alignment, the source at the SN position could be (1) a massive young (<6 Myr) star cluster in which the SN resided, (2) a quiescent, luminous blue star with an apparent temperature around 14,000 K, (3) a star caught during a bright outburst akin to those of luminous blue variables, or (4) a combination of option (1) and option (2) or (3). Although we cannot confidently choose between these possibilities with the present data, any of them imply that the progenitor of SN 2010jl had an initial mass above 30 M☉. This reinforces mounting evidence that many SNe IIn result from very massive stars, that massive stars can produce visible SNe without collapsing quietly to black holes, and that massive stars can sometimes retain their H envelopes until shortly before explosion. Standard stellar evolution models fail to account for these observed properties.
Salmonella typhimurium

The involvement of an outer membrane transport component for vitamin B12 uptake in Salmonella typhimurium, analogous to the btuB product in Escherichia coli, was investigated. Mutants of S. typhimurium selected for resistance to bacteriophage BF23 carried mutations at the btuB locus (butBs) (formerly called bfe, at the analogous map position as the E. coli homolog) and were defective in high-affinity vitamin B,2 uptake. The cloned E. coli btuB gene (btuBE) hybridized to S. typhimurium genomic DNA and restored vitamin B12 transport activity to S. typhimurium btuBs mutants. An Mr-60000 protein in the S. typhimurium outer membrane was repressed by growth with vitamin B12 and was eliminated in a btuBs mutant. The btuBs product thus appears to play the same role in vitamin B,2 transport by S. typhimurium as does the E. coli btuBE product. A second vitamin B12 transport system that is not present in E. coli was found by cloning a fragment of S. typhimurium DNA that complemented btuB mutants for vitamin B12 utilization. In addition to this plasmid with a 6-kilobase insert of S. typhimurium DNA, vitamin B,2 utilization by E. coli btuB strains required the btuC and btuD products, necessary for transport across the cytoplasmic membrane, but not the btuE or tonB product. The plasmid conferred low levels of vitamin B12-binding and energy-dependent transport activity but not susceptibility to phage BF23 or utilization of dicyanocobinamide. The cloned S. typhimurium DNA encoding this new transport system did not hybridize to the btuBE gene or to E. coli chromosomal DNA and therefore does not carry the S. typhimurium btuBs locus. Increased production of an Mr-84,000 polypeptide associated with the outer membrane was seen. The new locus appears to be carried on the large plasmid in most S. typhimurium strains. Thus, S. typhimurium possesses both highand low-affinity systems for uptake of cobalamins across the outer membrane.
Trends in Antibiotic Susceptibility in Staphylococcus aureus in Boston, Massachusetts, from 2000 to 2014

ABSTRACT The rate of infection by methicillin-resistant Staphylococcus aureus (MRSA) has declined over the past decade, but it is unclear whether this represents a decline in S. aureus infections overall. To evaluate the trends in the annual rates of infection by S. aureus subtypes and mean antibiotic resistance, we conducted a 15-year retrospective observational study at two tertiary care institutions in Boston, MA, of 31,753 adult inpatients with S. aureus isolated from clinical specimens. We inferred the gain and loss of methicillin resistance through genome sequencing of 180 isolates from 2016. The annual rates of infection by S. aureus declined from 2003 to 2014 by 4.2% (2.7% to 5.6%), attributable to an annual decline in MRSA of 10.9% (9.3% to 12.6%). Penicillin-susceptible S. aureus (PSSA) increased by 6.1% (4.2% to 8.1%) annually, and rates of methicillin-susceptible penicillin-resistant S. aureus (MSSA) did not change. Resistance in S. aureus decreased from 2000 to 2014 by 0.8 antibiotics (0.7 to 0.8). Within common MRSA clonal complexes, 3/14 MSSA and 2/21 PSSA isolates arose from the loss of resistance-conferring genes. Overall, in two tertiary care institutions in Boston, MA, a decline in S. aureus infections has been accompanied by a shift toward increased antibiotic susceptibility. The rise in PSSA makes penicillin an increasingly viable treatment option.
Preoperative Chemotherapy for Breast Cancer : Theoretical Considerations , Summary of Research Findings , and Clinical Recommendations

This review summarises the literature on non-randomised and randomised clinical trials on preoperative chemotherapy in breast cancer. The effectiveness and survival benefits of adjuvant anthracycline-based chemotherapy and, more recently, taxane-containing regimens have led to more frequent use of preoperative chemotherapy as neoadjuvant treatment in operable breast cancers. However, survival benefit has not been shown in randomised controlled trials comparing preoperative chemotherapy with the same regimens used postoperatively or in studies that add taxanes sequentially to anthracycline-containing regimens. Nevertheless, the neoadjuvant setting is an ideal platform for testing new regimens for non–cross-resistance to established regimens and for identifying predictive factors for specific therapies. For the latter, multigene profiling has produced some preliminary and exciting results that may lead to the better selection of patients for specific treatment or that may suggest clues to more effective salvage therapies.
High WT1 gene expression before haematopoietic stem cell transplant in children with acute myeloid leukaemia predicts poor event‐free survival

WT1 gene expression has been proposed as a useful marker of minimal residual disease in leukaemia. Its utility in paediatric haematopoietic stem cell transplantation (HSCT) has not been studied. We studied the prognostic value of WT1 expression in peripheral blood prior to HSCT in 36 children with acute myeloid leukaemia (AML). Samples were obtained 2 weeks pre‐transplant to determine the level of WT1 expression. WT1 expression was normalized using K562 cells as a control and a relative value of 0·5 was chosen as the cut‐off point between high and low WT1 expression. The median level of pre‐transplant WT1 expression in the 36 patients was 0·09 (range 0·0001–11·0), with 11patients having WT1 ≥ 0·5 and 25, WT1 < 0·5. After HSCT, 76% of patients with high pre‐transplant WT1 expression relapsed, in contrast to 0% of the patients with low WT1 expression. Those with high WT1 expression had significantly lower 5‐year event‐free survival (EFS) (18%, 95% CI 0–40%) as compared to those with low WT1 expression (68%, 95% CI 50–86%, P = 0·007). Multivariate analysis showed that pre‐transplant WT1 level is the only significant prognostic factor for the difference in EFS. Our finding suggests that elevated WT1 gene expression before HSCT in paediatric AML predicts relapse and poor long‐term EFS. A larger prospective study is warranted to compare the value of high WT1 expression and other markers of minimal residue disease in predicting clinical outcomes after HSCT.
On the mechanism of transient instability of power systems

In recent studies, it has been verifiedheuristically andexperimentally (via simulations) that instability in power systems due to a fault occurs when one machine or a group of machines, called thecritical group, loses synchronism with the remaining machines. Using energy functions associated with a critical group (rather than system-wide functions), transient stability results which are less conservative than other existing results, have been obtained. The existence and identity of a critical group is ascertained in these studies byoff-line simulations.In this paper, we present results, for power systems with uniform damping, which establishanalytically theexistence and theidentity of the critical group of machines due to a given fault. We also present a result to determine estimates of the domain of attraction of asymptotically stable equilibrium points in power systems. The results presented herein can potentially be usedon-line to determine which machines belong to a critical group, and to use this information for corrective action (e.g.,shedding of the critical generators orfast valving for these generators). The applicability of the present results is demonstrated by means of a specific example (a 162-bus, 17-generator model of the power network of the State of Iowa).
A study of quetiapine: efficacy and tolerability in psychotic adolescents.

OBJECTIVE To study the effectiveness, safety, and tolerability of quetiapine in adolescents with psychotic disorders. METHODS This study was an 8-week, open trial using quetiapine with 15 adolescents, ages 13-17 years, mean age 15.1 years, with a diagnosis of a psychotic disorder. Our primary instruments focused on psychotic symptomatology as measured by the Brief Psychiatric Rating Scale (BPRS), Clinical Global Impression (CGI), Positive and Negative Syndrome Scale (PANSS), and the Young Mania Rating Scale (YMRS). Other measures included adverse events, clinical laboratory tests, vital signs, electrocardiogram (ECG), extrapyramidal (EPS) measures, and ophthalmologic examination. RESULTS Quetiapine significantly reduced psychotic symptoms as measured by the BPRS, PANSS, YMRS, CGI, and CGI Severity of Illness scale. The average weight gain was 4.1 kg. After correction for expected weight gain, the mean weight gain over the 8-week period was 3.4 kg. Prolactin and cholesterol remained unchanged. Trends were found for a decrease in T4 and an increase in thyroid-stimulating hormone. Common adverse effects were somnolence, agitation, drowsiness, and headache. No significant findings were noted on repeat ECGs, EPS measures, or ophthalmic examination. The final average treatment dose was 467 mg/day (range 300-800 mg/day). CONCLUSIONS Quetiapine is suggested to be effective treatment of youths with psychotic disorders and to have a favorable side-effect profile.
ISHair: Importance Sampling for Hair Scattering

We present an importance sampling method for the bidirectional scattering distribution function (bsdf) of hair. Our method is based on the multi‐lobe hair scattering model presented by Sadeghi et al. [ SPJT10 ]. We reduce noise by drawing samples from a distribution that approximates the bsdf well. Our algorithm is efficient and easy to implement, since the sampling process requires only the evaluation of a few analytic functions, with no significant memory overhead or need for precomputation. We tested our method in a research raytracer and a production renderer based on micropolygon rasterization. We show significant improvements for rendering direct illumination using multiple importance sampling and for rendering indirect illumination using path tracing.
Biochemical Basis of Resistance of Tobacco Callus Tissue Cultures to Hydroxyphenylethylamines

It has been reported that hydroxyphenylethylamines, such as tyramine and octopamine, are toxic to tobacco (Nicotiana tabacum L.) callus cultures grown in the presence of auxins, whereas calli grown in the presence of cytokinins and crown gall cultures are resistant to these amines (P. Christou and K.A. Barton [1989] Plant Physiol 89: 564-568). In an attempt to understand the underlying mechanism of this resistance, we compared the fates of tyramine in tyramine-sensitive and tyramine-resistant tobacco tissue cultures (cv Xanthi nc). The very rapid formation of black-colored oxidation products from tyramine in sensitive tissues suggested that the toxicity might be caused by the oxidation of tyramine by phenol oxidases present in the tissues or released into the medium after subculture. This was confirmed through many indirect procedures (effect of exogenously added tyrosinase, induction of polyphenol oxidase [PPO] activity by auxin, etc.). The study of tyramine structure-activity relationships further suggested that the toxicity of tyramine might be due to the formation of indolequinones after oxidation by PPO. Subculture of calli grown on 2,4-dichlorophenoxyacetic acid in a medium containing benzyladenine triggered a slow decrease in PPO activity and dramatic increases in peroxidase and tyramine hydroxycinnamoyl transferase (THT) activities. THT was undetectable in calli grown on 2,4-dichlorophenoxyacetic acid but very active in tyramine-resistant crown gall cultures. Moreover, when [3H]tyramine was fed in vivo to tyramine-resistant tissues, it was rapidly integrated into cell walls in the wound periderm formed at the periphery of the calli. Both the conjugation of tyramine and its integration into cell walls could compete with the formation of toxic quinones and therefore play a part in the resistance. Thus, it seems likely that the control of the toxicity of hydroxyphenylethylamines by cytokinins results primarily from changes in the metabolism and the compartmentation of these amines.
Evaluation of fecal microbiomes associated with obesity in captive cynomolgus monkeys (Macaca fascicularis)

Microorganisms play important roles in obesity; however, the role of the gut microbiomes in obesity is controversial because of the inconsistent findings. This study investigated the gut microbiome communities in obese and lean groups of captive healthy cynomolgus monkeys reared under strict identical environmental conditions, including their diet. No significant differences in the relative abundance of Firmicutes, Bacteroidetes and Prevotella were observed between the obese and lean groups, but a significant difference in Spirochetes (p < 0.05) was noted. Microbial diversity and richness were similar, but highly variable results in microbial composition, diversity, and richness were observed in individuals, irrespective of their state of obesity. Distinct clustering between the groups was not observed by principal coordinate analysis using an unweighted pair group method. Higher sharedness values (95.81% ± 2.28% at the genus level, and 79.54% ± 5.88% at the species level) were identified among individual monkeys. This paper reports the association between the gut microbiome and obesity in captive non-human primate models reared under controlled environments. The relative proportion of Firmicutes and Bacteroidetes as well as the microbial diversity known to affect obesity were similar in the obese and lean groups of monkeys reared under identical conditions. Therefore, obesity-associated microbial changes reported previously appear to be associated directly with environmental factors, particularly diet, rather than obesity.
Refining near‐native protein–protein docking decoys by local resampling and energy minimization

How to refine a near‐native structure to make it closer to its native conformation is an unsolved problem in protein‐structure and protein–protein complex‐structure prediction. In this article, we first test several scoring functions for selecting locally resampled near‐native protein–protein docking conformations and then propose a computationally efficient protocol for structure refinement via local resampling and energy minimization. The proposed method employs a statistical energy function based on a Distance‐scaled Ideal‐gas REference state (DFIRE) as an initial filter and an empirical energy function EMPIRE (EMpirical Protein‐InteRaction Energy) for optimization and re‐ranking. Significant improvement of final top‐1 ranked structures over initial near‐native structures is observed in the ZDOCK 2.3 decoy set for Benchmark 1.0 (74% whose global rmsd reduced by 0.5 Å or more and only 7% increased by 0.5 Å or more). Less significant improvement is observed for Benchmark 2.0 (38% versus 33%). Possible reasons are discussed. Proteins 2009. © 2008 Wiley‐Liss, Inc.
Pseudomonas aeruginosa population biology in chronic obstructive pulmonary disease.

BACKGROUND The role played by airway infections with Pseudomonas aeruginosa in the course and pathogenesis of chronic obstructive pulmonary disease (COPD) has not yet been resolved. We report on the molecular epidemiology and population biology of P. aeruginosa in COPD. METHODS P. aeruginosa isolates collected from adults with COPD during a 10-year prospective study were genotyped in 56 binary marker loci of core and accessory genomes. RESULTS The typing of 134 P. aeruginosa COPD isolates uncovered 60 unrelated bacterial clones. The worldwide dominant clones in the P. aeruginosa population were also the most abundant clones among the COPD isolates. Sporadic or intermittent infection with P. aeruginosa was typical for the airways of patients with COPD. Sequential isolates with the same genotype of the core genome diversified the composition of their accessory genome during the course of the infection. CONCLUSIONS Intraclonal microevolution and the frequent turnover or loss of clones are typical for infections with P. aeruginosa in COPD. This epidemiological signature differs from that of the chronic carriage of the same P. aeruginosa clone in patients with cystic fibrosis.
Visual Guidance for Encountered Type Haptic Display: A feasibility study

Virtual/mixed reality leveraging an encountered type haptic display will suffer difficulty if virtual and real objects are spatially discrepant. We propose a new method for resolving this issue, visual guidance. The visual guidance algorithm is defined and described in detail, and contrasted with a previously explored approach. The feasibility of the proposed algorithm is experimentally verified.
Plasma Insulin‐Like Growth Factor‐I and Its Binding Proteins 1 and 3 During Continuous Nonoral and Oral Combined Hormone Replacement Therapy

OBJECTIVE We determined the effects of continuous combined nonoral and oral estrogen-progestin therapy on plasma levels of insulin-like growth factor-I (IGF-I) and its binding proteins 1 (IGFBP-1) and 3 (IGFBP-3). DESIGN Forty women complaining of climacteric symptoms were randomized to receive either transdermal estradiol patches (50 microg daily) in combination with an intrauterine system releasing 20 microg of levonorgestrel daily or an established regimen of an oral dose of 2 mg of estradiol and 1 mg of norethisterone acetate daily for 1 year. Fifteen women in the nonoral therapy group and 17 in the oral therapy group completed the 1-year prospective study. RESULTS Plasma levels of IGF-I decreased significantly in the oral therapy group, but no changes were observed in the plasma levels of its binding proteins. Transdermal estrogen in combination with intrauterine levonorgestrel did not induce any change in plasma IGF-I, whereas the plasma levels of IGFBP-3 decreased. IGFBP-1 concentrations increased, which may be related to the induction of this protein into the endometrium by the intrauterine levonorgestrel delivery. CONCLUSIONS Both the nonoral and oral continuous combined estrogen-progestin therapies used in this study produced only minor changes in the circulating concentrations of IGF-I and its binding proteins.
The prognostic relevance of the nonstructural 5A gene interferon sensitivity determining region is different in infections with genotype 1b and 3a isolates of hepatitis C virus.

Hepatitis C virus (HCV) RNA serum concentration, quasispecies complexity, and sequence and phylogenetic analysis of the nonstructural 5A gene (NS5A) interferon sensitivity determining region (ISDR) were determined in pretreatment serum samples from 47 patients with chronic hepatitis C (36 infected by HCV genotype 1b and 11 by 3a). Among HCV genotype 1b-infected patients, virus load was lower (P = .003) and the number of NS5A-ISDR amino acid changes was higher (P = .001) in long-term responders than in non-long-term responders, but there were no differences in quasispecies complexity. Multivariate analysis showed a close association between response to interferon and NS5A-ISDR phenotype. Phylogenetic analysis showed that isolates from non-long-term responders clustered apart from the majority of isolates from long-term responders. There was no association between virologic features and therapeutic response in HCV genotype 3a-infected patients. In conclusion, low virus load and mutant NS5A-ISDR phenotype are closely associated with long-term response to interferon in HCV genotype 1b- but probably not in 3a-infected patients.
Patrik Holm Single-chain antibody construction and functional mapping of the monoclonal antibody TS 1 Single-chain antibody construction and functional mapping of the monoclonal antibody TS 1

Antibodies are proteins with the ability to bind antigens rapidly and specifically. Antibodies consist of several different parts. The complementary determining regions (CDR) are the parts that recognize the antigen are the focus of this study. The aims of this study were to synthesize and produce a single-chain antibody (scFv) of the anti-cytokeratin 8 monoclonal IgG antibody TS1 and to functionally map amino acid residues important for the interaction with its antigen and the anti-idiotypic antibody αTS1. Cytokeratins are present in significant amount in the necrotic areas of carcinomas and are not released into the circulation since they have low solubility. The TS1 antibody has been shown to be effective in binding cytokeratin 8 (CK8) exposed in tumors in vivo and is proposed to be useful in immunotargeting and/or immunotherapy. The anti-idiotypic antibody αTS1 can be used to regulate the tumor:non-tumor ratio. Mutagenesis of certain amino acid residues can be used to alter the affinity to improve the tumor:nontumor ratio further. In the present study, the TS1 IgG was chemically modified to specify groups of amino acid residues important for the interaction with both CK8 and αTS1. If important residues were found in the CDRs, they were mutated in the TS1 scFv construct and the effect was studied using ELISA. The main conclusions drawn from this study are that the important amino acid residues in TS1 for the interaction with both CK8 and αTS1 are mainly tyrosines, charged residues and a tryptophan. A central interacting interface was identified with the somewhat unusual participation of residues in the CDR 2 of the light chain. Mutations which resulted in increased affinity to both CK8 and αTS1 were also identified.
Challenges in teaching the pumping lemma in automata theory course

2. THE PROBLEM In Automata Theory course, Pumping Lemma is learned as one of the major methods used to prove irregularity of languages. Our experience shows that students face some typical difficulties when studying the Lemma and applying it in problem solution. These are caused by problems in employing formal reasoning methods (that by themselves are common in theoretical CS courses), and relate mainly to misunderstanding of the Lemma's conditions and their necessity for its correctness. As a result, the Lemma is often used in a wrong way, leading to incorrect proofs. Another danger is that a student may complete the course and be able to mechanically solve standard problems using the Lemma (following canonical procedures found in the textbook), but without having developed an appropriate understanding of underlying concepts and nuances.