Miracle-dz/UniFAR-FTUs huggingface dataset:
Sets of integrating plasmids and gene disruption cassettes containing improved counter‐selection markers designed for repeated use in budding yeast

Counter‐selection is a useful gene manipulation technique for repeated gene disruptions, gene shufflings and gene replacements in yeasts. We developed a novel counter‐selection system using a galactose‐inducible growth inhibitory sequence (Kawahata et al. 1999 . Yeast 15: 1–10). This counter‐selection marker, named GAL10p–GIN11, has several advantages over previous counter‐selection markers, i.e. use of an inexpensive galactose medium for counter‐selection, combined use with any transformation markers for gene introduction, and no requirement of specific mutations in the host strains. The GIN11 sequence, which is a part of an X‐element of the subtelomeric regions, contained a conserved autonomously replicating sequence, causing the possibility of inefficient chromosomal integration. We isolated GIN11 mutants that lost the replication activity but retained the growth‐inhibitory effect when overexpressed. A mutant GIN11M86 sequence was selected and fused to the CUP1 promoter for the counter‐selection on a copper‐containing medium. The GALp–GIN11M86 and the CUPp–GIN11M86 were used for constructing sets of integrating plasmids containing auxotrophic markers involving HIS3, TRP1, LEU2, URA3 or ADE2, or a drug‐resistant marker PGKp–YAP1. In addition, a set of gene disruption cassettes that contained each of the auxotrophic markers and the GALp–GIN11M86, which were flanked by direct repeats of a hisG sequence, were constructed. The counter‐selectable integrating plasmids and the gene disruption cassettes can allow the markers to be used repeatedly for yeast gene manipulations. Copyright © 2002 John Wiley & Sons, Ltd.
Combination of Transient Lymphodepletion With Busulfan and Fludarabine and Peptide Vaccination in a Phase I Clinical Trial for Patients With Advanced Melanoma

Taking advantage of homeostatic mechanisms to boost tumor-specific cellular immunity is raising increasing interest in the development of therapeutic strategies in the treatment of melanoma. Here, we have explored the potential of combining homeostatic proliferation, after transient immunosuppression, and antigenic stimulation of Melan-A/Mart-1 specific CD8+ T-cells. In an effort to develop protocols that could be readily applicable to the clinic, we have designed a phase I clinical trial, involving lymphodepleting chemotherapy with Busulfan and Fludarabine, reinfusion of Melan-A specific CD8+ T-cell containing peripheral blood mononuclear cells (exempt of growth factors), and Melan-A peptide vaccination. Six patients with advanced melanoma were enrolled in this outpatient regimen that demonstrated good feasibility combined with low toxicity. Consistent depletion of lymphocytes with persistent increased CD4/CD8 ratios was induced, although the proportion of circulating CD4+ regulatory T-cells remained mostly unchanged. The study of the immune reconstitution period showed a steady recovery of whole T-cell numbers overtime. However, expansion of Melan-A specific CD8+ T-cells, as measured in peripheral blood, was mostly inconsistent, accompanied with marginal phenotypic changes, despite vaccination with Melan-A/Mart-1 peptide. On the clinical level, 1 patient presented a partial but objective antitumor response following the beginning of the protocol, even though a direct effect of Busulfan/Fludarabine cannot be completely ruled out. Overall, these data provide further ground for the development of immunotherapeutic approaches to be both effective against melanoma and applicable in clinic.
Evaluation of High-Resolution Precipitation Estimates from Satellites during July 2012 Beijing Flood Event Using Dense Rain Gauge Observations

Satellite-based precipitation estimates products, CMORPH and PERSIANN-CCS, were evaluated with a dense rain gauge network over Beijing and adjacent regions for an extremely heavy precipitation event on July 21 2012. CMORPH and PEERSIANN-CSS misplaced the region of greatest rainfall accumulation, and failed to capture the spatial pattern of precipitation, evidenced by a low spatial correlation coefficient (CC). CMORPH overestimated the daily accumulated rainfall by 22.84% while PERSIANN-CCS underestimated by 72.75%. In the rainfall center, both CMORPH and PERSIANN-CCS failed to capture the temporal variation of the rainfall, and underestimated rainfall amounts by 43.43% and 87.26%, respectively. Based on our results, caution should be exercised when using CMORPH and PERSIANN-CCS as input for monitoring and forecasting floods in Beijing urban areas, and the potential for landslides in the mountainous zones west and north of Beijing.
Interaction of Silymarin Flavonolignans with Organic Anion-Transporting Polypeptides

Organic anion-transporting polypeptides (OATPs) are multispecific transporters mediating the uptake of endogenous compounds and xenobiotics in tissues that are important for drug absorption and elimination, including the intestine and liver. Silymarin is a popular herbal supplement often used by patients with chronic liver disease; higher oral doses than those customarily used (140 mg three times/day) are being evaluated clinically. The present study examined the effect of silymarin flavonolignans on OATP1B1-, OATP1B3-, and OATP2B1-mediated transport in cell lines stably expressing these transporters and in human hepatocytes. In overexpressing cell lines, OATP1B1- and OATP1B3-mediated estradiol-17β-glucuronide uptake and OATP2B1-mediated estrone-3-sulfate uptake were inhibited by most of the silymarin flavonolignans investigated. OATP1B1-, OATP1B3-, and OATP2B1-mediated substrate transport was inhibited efficiently by silymarin (IC50 values of 1.3, 2.2 and 0.3 µM, respectively), silybin A (IC50 values of 9.7, 2.7 and 4.5 µM, respectively), silybin B (IC50 values of 8.5, 5.0 and 0.8 µM, respectively), and silychristin (IC50 values of 9.0, 36.4, and 3.6 µM, respectively). Furthermore, silymarin, silybin A, and silybin B (100 µM) significantly inhibited OATP-mediated estradiol-17β-glucuronide and rosuvastatin uptake into human hepatocytes. Calculation of the maximal unbound portal vein concentrations/IC50 values indicated a low risk for silymarin-drug interactions in hepatic uptake with a customary silymarin dose. The extent of silymarin-drug interactions depends on OATP isoform specificity and concentrations of flavonolignans at the site of drug transport. Higher than customary doses of silymarin, or formulations with improved bioavailability, may increase the risk of flavonolignan interactions with OATP substrates in patients.
Extracellular Disulfide Bridges Serve Different Purposes in Two Homologous Chemokine Receptors, CCR1 and CCR5

In addition to the 7 transmembrane receptor (7TM)-conserved disulfide bridge between transmembrane (TM) helix 3 and extracellular loop (ECL)-2, chemokine receptors (CCR) contain a disulfide bridge between the N terminus and what previously was believed to be ECL-3. Recent crystal and NMR structures of the CXC chemokine receptors (CXCR) CXCR4 and CXCR1, combined with structural analysis of all endogenous chemokine receptors indicate that this chemokine receptor–conserved bridge in fact connects the N terminus to the top of TM-7. By employing chemokine ligands that mainly target extracellular receptor regions and small-molecule ligands that predominantly interact with residues in the main binding crevice, we show that the 7TM-conserved bridge is essential for all types of ligand-mediated activation, whereas the chemokine-conserved bridge is dispensable for small-molecule activation in CCR1. However, in striking contrast to previous studies in other chemokine receptors, high-affinity CCL3 chemokine binding was maintained in the absence of either bridge. In the highly related CCR5, a completely different dependency was observed as neither activation nor binding of the same chemokines was retained in the absence of either bridge. In contrast, both bridges were dispensable for activation by the same small molecules. This indicates that CCR5 activity is independent of extracellular regions, whereas in CCR1 the preserved folding of ECL-2 is necessary for activation. These results indicate that conserved structural features in a receptor subgroup do not necessarily provide specific traits for the whole subgroup but rather provide unique traits to the single receptors.
Physicochemical Requirement for the Vegetative Growth of Schizophyllum commune Collected from Different Ecological Origins

Schizophyllum commune is an edible and medicinal mushroom widely distributed in the world. The optimal growth conditions for the mycelia of 10 strains of the fungus were investigated. The temperature suitable for the mycelial growth and density was obtained at 30~35°C. Among the tested conditions, the minimum mycelial growth was found at 15°C. In case of pH, the most favorable growth was found at pH 5. The results indicated that this mushroom well adapted to high temperature and low pH for its mycelial growth. Considering growth phenotype of mycelia, Hamada, Hennerberg, PDA and YM were the most suitable and Lilly, Glucose triptone, Glucose peptone and Hoppkins were the most unfavorable among tested media for the mycelial growth of S. commune. Out of tested carbon sources, dextrin and fructose were the most suitable and lactose, mannose and sorbitol were the unsuitable for the fungus. Compact mycelial density was obtained from most of the carbon sources. Among used nitrogen sources, calcium nitrate, potassium nitrate and alanine were the most appropriate and the most incompatible were ammonium phosphate, histidine, urea and arginine for mycelial growth of S. commune on the culture media. Calcium nitrate, histidine and potassium nitrate showed moderately thin or thin, and rest of nitrogen sources showed compact or moderately compact mycelial density.
A Distributed Algorithm for Solving Positive Definite Linear Equations Over Networks With Membership Dynamics

This paper considers the problem of solving a symmetric positive definite system of linear equations over a network of agents with arbitrary asynchronous interactions and membership dynamics. The latter implies that each agent is allowed to join and leave the network at any time, for infinitely many times, and lose all its memory upon leaving. We develop Subset Equalizing (SE), a distributed asynchronous algorithm for solving such a problem. To design and analyze SE, we introduce a novel time-varying Lyapunov-like function, defined on a state space with changing dimension, and a generalized concept of network connectivity, capable of handling such interactions and membership dynamics. Based on them, we establish the boundedness, asymptotic convergence, and exponential convergence of SE, along with a bound on its convergence rate. Finally, through extensive simulation, we show that SE is effective in a volatile agent network and that a special case of SE, termed Groupwise Equalizing, is significantly more bandwidth/energy efficient than two existing algorithms in multi-hop wireless networks.
Treatment of Liver Metastases in Patients with Neuroendocrine Tumors of Gastroesophageal and Pancreatic Origin

Well-to-moderately differentiated neuroendocrine tumors of gastroesophageal and pancreatic origin (GEP-NETs) with liver metastasis are a heterogeneous group of malignancies for which a range of therapeutic options have been employed. Surgical resection of hepatic metastases or hepatic artery embolization may be beneficial in patients with hepatic-predominant metastatic disease. Patients with “carcinoid” syndrome and syndromes associated with functional pancreatic NET (PNET) can be effectively treated with somatostatin analogs. On the other hand, the efficacy of systemic chemotherapy for these patients is limited. A placebo-controlled, double-blind, prospective, and randomized study showed that octreotide LAR improves progression-free survival in patients with advanced midgut functional “carcinoids. ” In patients with advanced pancreatic NET, randomized, placebo-controlled studies have recently demonstrated that treatment with the tyrosine kinase inhibitor sunitinib or with mTOR inhibitor everolimus is associated with improved progression-free survival. Based on these studies, octreotide LAR, sunitinib, or everolimus are now considered as first-line therapeutic options in patients with advanced NET. Future studies will likely further define the role of these agents in patients with carcinoid liver metastasis and pancreatic NET liver metastasis.
Bistability of a coupled Aurora B kinase-phosphatase system in cell division

Aurora B kinase, a key regulator of cell division, localizes to specific cellular locations, but the regulatory mechanisms responsible for phosphorylation of substrates located remotely from kinase enrichment sites are unclear. Here, we provide evidence that this activity at a distance depends on both sites of high kinase concentration and the bistability of a coupled kinase-phosphatase system. We reconstitute this bistable behavior and hysteresis using purified components to reveal co-existence of distinct high and low Aurora B activity states, sustained by a two-component kinase autoactivation mechanism. Furthermore, we demonstrate these non-linear regimes in live cells using a FRET-based phosphorylation sensor, and provide a mechanistic theoretical model for spatial regulation of Aurora B phosphorylation. We propose that bistability of an Aurora B-phosphatase system underlies formation of spatial phosphorylation patterns, which are generated and spread from sites of kinase autoactivation, thereby regulating cell division. DOI: http://dx.doi. org/10.7554/eLife.10644. 001
Select Overexpression of Homer1a in Dorsal Hippocampus Impairs Spatial Working Memory

Long Homer proteins forge assemblies of signaling components involved in glutamate receptor signaling in postsynaptic excitatory neurons, including those underlying synaptic transmission and plasticity. The short immediate-early gene (IEG) Homer1a can dynamically uncouple these physical associations by functional competition with long Homer isoforms. To examine the consequences of Homer1a-mediated “uncoupling” for synaptic plasticity and behavior, we generated forebrain-specific tetracycline (tet) controlled expression of Venus-tagged Homer1a (H1aV) in mice. We report that sustained overexpression of H1aV impaired spatial working but not reference memory. Most notably, a similar impairment was observed when H1aV expression was restricted to the dorsal hippocampus (HP), which identifies this structure as the principal cortical area for spatial working memory. Interestingly, H1aV overexpression also abolished maintenance of CA3-CA1 long-term potentiation (LTP). These impairments, generated by sustained high Homer1a levels, identify a requirement for long Homer forms in synaptic plasticity and temporal encoding of spatial memory.
Discovering Relations between Noun Categories

Traditional approaches to Relation Extraction from text require manually defining the relations to be extracted. We propose here an approach to automatically discovering relevant relations, given a large text corpus plus an initial ontology defining hundreds of noun categories (e.g., Athlete, Musician, Instrument). Our approach discovers frequently stated relations between pairs of these categories, using a two step process. For each pair of categories (e.g., Musician and Instrument) it first co-clusters the text contexts that connect known instances of the two categories, generating a candidate relation for each resulting cluster. It then applies a trained classifier to determine which of these candidate relations is semantically valid. Our experiments apply this to a text corpus containing approximately 200 million web pages and an ontology containing 122 categories from the NELL system [Carlson et al., 2010b], producing a set of 781 proposed candidate relations, approximately half of which are semantically valid. We conclude this is a useful approach to semi-automatic extension of the ontology for large-scale information extraction systems such as NELL.
Molecular Cloud Turbulence and Star Formation

We review the properties of turbulent molecular clouds (MCs), focusing on the physical processes that influence star formation (SF). MC formation appears to occur during large-scale compression of the diffuse ISM driven by supernovae, magnetorotational instability, or gravitational instability in galactic disks of stars and gas. The compressions generate turbulence that can accelerate molecule production and produce the observed morphology. We then review the properties of MC turbulence, including density enhancements observed as clumps and cores, magnetic field structure, driving scales, the relation to observed scaling relations, and the interaction with gas thermodynamics. We argue that MC cores are dynamical, not quasistatic, objects with relatively short lifetimes not exceeding a few megayears. We review their morphology, magnetic fields, density and velocity profiles, and virial budget. Next, we discuss how MC turbulence controls SF. On global scales turbulence prevents monolithic collapse of the clouds; on small scales it promotes local collapse. We discuss its effects on the SF efficiency, and critically examine the possible relation between the clump mass distribution and the initial mass function, and then turn to the redistribution of angular momentum during collapse and how it determines the multiplicity of stellar systems. Finally, we discuss the importance of dynamical interactions between protostars in dense clusters, and the effect of the ionization and winds from those protostars on the surrounding cloud. We conclude that the interaction of self-gravity and turbulence controls MC formation and behavior, as well as the core and star formation processes within them.
Autonomic Correlates at Rest and during Evoked Attention in Children with Attention-Deficit/Hyperactivity Disorder and Effects of Methylphenidate

Objective: The aim of this study was to assess autonomic nervous system functioning in children with attention-deficit/hyperactivity disorder (ADHD) and to examine the effects of methylphenidate and focussed attention. Method: Children with ADHD (n = 19) were tested while they were stimulant free and during a period in which they were on stimulants. On both occasions, autonomic nervous system functioning was tested at baseline and during focussed attention. Autonomic nervous system functioning of control subjects was also tested at baseline and during focussed attention. Autonomic nervous system activity was determined by means of heart rate variability (HRV) and skin conductivity analyses. Attention was evoked by means of the BioGraph Infiniti biofeedback apparatus. HRV was determined by time domain, frequency domain and Poincaré analysis of RR interval data. Skin conductivity was determined by the BioGraph Infiniti biofeedback apparatus. Results: The main findings of this study were (a) that stimulant-free children with ADHD showed a sympathetic underarousal and parasympathetic overarousal of the sympathovagal balance relative to control subjects; (b) methylphenidate shifted the autonomic balance of children with ADHD towards normal levels; however, a normal autonomic balance was not reached, and (c) stimulant-free children with ADHD exhibited a shift in the sympathovagal balance towards the sympathetic nervous system from baseline to focussed attention; however, methylphenidate appeared to abolish this shift. Conclusions: Stimulant-free children with ADHD have a parasympathetic dominance of the autonomic balance, relative to control subjects. Methylphenidate attempts to restore the normal autonomic balance in children with ADHD, but inhibits the normal autonomic nervous system response to a cognitive challenge. Clinical Applications: These results indicate that methylphenidate may have a suppressive effect on the normal stress response. Although this may be of benefit to those who interact with children who suffer from ADHD, the implications for the physiological and psychological well-being of the children themselves are debatable. Further research is needed. Limitations of the Study: Only 19 children with ADHD and 18 control subjects were tested. Further studies should include prior testing in order to exclude children with possible co-existing learning disabilities. Cognitive function and emotional responses of children with ADHD were not tested.
Assessment of the deamination of aminoacetone, an endogenous substrate for semicarbazide-sensitive amine oxidase.

Methylglyoxal, a toxic aldehyde, has been reported to be increased in diabetes and has been claimed to be related to diabetic complications. Aminoacetone, an intermediate in the metabolism of threonine and glycine, has been proposed to be an endogenous substrate for semicarbazide-sensitive amine oxidase (SSAO). Methylglyoxal is the product. An HPLC procedure for the determination of SSAO activity toward aminoacetone in vitro is described. It was observed in previous assays that methylglyoxal formed via deamination of aminoacetone was quite unstable and led to erroneous results. o-Phenylenediamine (o-PD) was therefore employed for derivatization of methylglyoxal. o-PD does not affect SSAO activity and can be included in the enzyme reaction mixture for continuous trapping of methylglyoxal. This can avoid the loss of methylglyoxal during incubation. Deamination of aminoacetone by human umbilical artery SSAO was confirmed with this improved assay. The values of Km and Vmax, are 125.9 +/- 20.5 microM and 332.2 +/- 11.7 nmol/h/mg protein, respectively. Deamination of aminoacetone was nearly completely inhibited by 1 mM semicarbazide and 1 microM MDL-72974A, a potent selective SSAO inhibitor, whereas MAO inhibitors clorgyline (1 mM) and deprenyl (1 mM) had no inhibitory effect.
Clinical outcomes and safety with trabectedin therapy in patients with advanced soft tissue sarcomas following failure of prior chemotherapy: results of a worldwide expanded access program study.

BACKGROUND This expanded access program (EAP) was designed to provide trabectedin access for patients with incurable soft tissue sarcoma (STS) following progression of disease with standard therapy. The outcomes of trial participants accrued over approximately 5 years are reported. PATIENTS AND METHODS Adult patients with advanced STS of multiple histologies, including leiomyosarcoma and liposarcoma (L-sarcomas), following relapse or disease progression following standard-of-care chemotherapy, were enrolled. Trabectedin treatment cycles (1.5 mg/m(2), intravenously over 24 h) were repeated q21 days. Objective response, overall survival (OS), and safety were evaluated. RESULTS Of 1895 patients enrolled, 807 (43%) had evaluable objective response data, with stable disease reported in 343 (43%) as best response. L-sarcoma patients exhibited longer, OS compared with other histologies [16.2 months (95% confidence interval (CI) 14.1-19.5) versus 8.4 months (95% CI 7.1-10.7)], and a slightly higher objective response rate [6.9% (95% CI 4.8-9.6) versus 4.0% (95% CI 2.1-6.8)]. The median treatment duration was 70 days representing a median of three treatment cycles; 30% of patients received ≥ 6 cycles. Safety and tolerability in this EAP were consistent with prior clinical trial data. CONCLUSION Results of this EAP are consistent with previous reports of trabectedin, demonstrating disease control despite a low incidence of objective responses in advanced STS patients after failure of standard chemotherapy. CLINICALTRIALS.GOV: NCT00210665.
Malignant transformation of the cultured human hepatocytes induced by hepatitis C virus core protein

Abstract: Background/Aim: Hepatitis C virus core protein (HCV‐C) has been known to play an important role in hepatocarcinogenesis. But, up to now there is no certain evidence in pathomorphology directly supporting this standpoint. In this study, a human hepatocytes model expressing HCV‐C was established for investigating the influence of HCV‐C on hepatocytes biological properties.