Miracle-dz/UniFAR-FTUs huggingface dataset:
An in vitro synthetic biology platform for the industrial biomanufacturing of myo‐inositol from starch

Myo‐Inositol (vitamin B8) is widely used in the drug, cosmetic, and food & feed industries. Here, we present an in vitro non‐fermentative enzymatic pathway that converts starch to inositol in one vessel. This in vitro pathway is comprised of four enzymes that operate without ATP or NAD+ supplementation. All enzyme BioBricks are carefully selected from hyperthermophilic microorganisms, that is, alpha‐glucan phosphorylase from Thermotoga maritima, phosphoglucomutase from Thermococcus kodakarensis, inositol 1‐phosphate synthase from Archaeoglobus fulgidus, and inositol monophosphatase from T. maritima. They were expressed efficiently in high‐density fermentation of Escherichia coli BL21(DE3) and easily purified by heat treatment. The four‐enzyme pathway supplemented with two other hyperthermophilic enzymes (i.e., 4‐α‐glucanotransferase from Thermococcus litoralis and isoamylase from Sulfolobus tokodaii) converts branched or linear starch to inositol, accomplishing a very high product yield of 98.9 ± 1.8% wt. /wt. This in vitro (aeration‐free) biomanufacturing has been successfully operated on 20,000‐L reactors. Less costly inositol would be widely added in heath food, low‐end soft drink, and animal feed, and may be converted to other value‐added biochemicals (e.g., glucarate). This biochemical is the first product manufactured by the in vitro synthetic biology platform on an industrial scale. Biotechnol. Bioeng. 2017;114: 1855–1864. © 2017 Wiley Periodicals, Inc.
Interleukin 28B Genetic Polymorphisms Play a Minor Role in Identifying Optimal Treatment Duration in HCV Genotype 1 Slow Responders to Pegylated Interferon plus Ribavirin

Background Pegylated interferon and ribavirin for 72 weeks improve sustained virological response (SVR) in HCV genotype 1 (HCV-1) slow viral responders. Whether interleukin 28B (IL28B) single nucleotide polymorphism (SNP) genotypes and on-treatment viral responses can identify non-rapid virological response (RVR) patients who benefit from 48 or 72 weeks of therapy remains unclear. Methods Treatment-naive HCV-1 patients who failed to achieve RVR were randomly assigned to receive 48 (n=168) or 72 (n=167) weeks of therapy. Baseline factors and on-treatment virological responses at weeks 8 and 12 were evaluated for SVR in 289 compliant patients who received ≥80% of drug dosages and treatment duration, and had end of follow-up viral response. The stratified SVR rates for independent factors were compared by treatment duration. Results Treatment duration, IL28B rs8099917 genotypes, cirrhosis, week-8 viral response (undetectable HCV RNA at treatment week 8) and complete early virological response (cEVR) predicted SVR. In week-8 viral response patients, the SVR rates of 72-week and 48-week treatment were similar (75–88%), regardless of IL28B SNP genotypes or cirrhosis. In non-week-8 viral response patients who achieved cEVR, the SVR rate of 72-week treatment was higher than that of 48-week treatment for non-cirrhotic patients, regardless of IL28B SNP genotypes (91–100% versus 13–44%; P=0.001). Conclusions Although IL28B SNP genotypes predict SVR, they play a minor role when on-treatment viral responses are taken into consideration. On-treatment viral responses at weeks 8 and 12 are the key determinants to decide the optimal treatment duration in HCV-1 patients without RVR.
The clinical evaluation of HER‐2 status: which test to use?

Accurate determination of the status of the type I receptor tyrosine kinase HER‐2 in breast carcinomas provides significant insight into patient prognosis and may also inform selection of chemotherapeutic and hormonal treatments. At present, however, the single most important application of HER‐2 testing is in the selection of patients for treatment with targeted therapies such as Herceptin. Although, based on current literature, fluorescence in situ hybridization (FISH) detection of HER‐2 gene amplification may provide more accurate information in this context, this method is not yet widely available. Therefore, screening by immunohistochemistry (IHC) for HER‐2 protein, backed by rigorous quality controls and FISH testing of equivocal cases with intermediate staining intensity, remains the current practice. In laboratories with highly standardized testing and quality assurance procedures, this protocol appears highly effective. Improvements in fixation procedures, standardization of antibodies, and use of automated image analysis may all increase the precision of IHC testing. However, on the basis of current data, there is a case to be made for the wider implementation of FISH testing to determine HER‐2 status in breast cancer. Copyright © 2003 John Wiley & Sons, Ltd.
Genetic and phenotypic analysis of herpes simplex virus type 1 mutants conditionally resistant to immune cytolysis

Nine temperature-sensitive (ts) mutants of herpes simplex virus type 1 selected for their inability to render cells susceptible to immune cytolysis after infection at the nonpermissive temperature have been characterized genetically and phenotypically. The mutations in four mutants were mapped physically by marker rescue and assigned to functional groups by complementation analysis. In an effort to determine the molecular basis for cytolysis resistance, cells infected with each of the nine mutants were monitored for the synthesis of viral glycoprotein in total cell extracts and for the presence of these glycoproteins in plasma membranes. The four mutants whose ts mutations were mapped were selected with polypeptide-specific antiserum to glycoproteins gA and gB; however, three of the four mutations mapped to DNA sequences outside the limits of the structural gene specifying these glycoproteins. Combined complementation and phenotypic analysis indicates that the fourth mutation also lies elsewhere. The ts mutations in five additional cytolysis-resistant mutants could not be rescued with single cloned DNA fragments representing the entire herpes simplex virus type 1 genome, suggesting that these mutants may possess multiple mutations. Complementation tests with the four mutants whose ts lesions had been mapped physically demonstrated that each represents a new viral gene. Examination of mutant-infected cells at the nonpermissive temperature for the presence of viral glycoproteins in total cell extracts and in membranes at the cell surface demonstrated that (i) none of the five major viral glycoproteins was detected in extracts of cells infected with one mutant, suggesting that this mutant is defective in a very early function; (ii) cells infected with six of the nine mutants exhibited greatly reduced levels of all the major viral glycoproteins at the infected cell surface, indicating that these mutants possess defects in the synthesis or processing of viral glycoproteins; and (iii) in cells infected with one mutant, all viral glycoproteins were precipitable at the surface of the infected cell, despite the resistance of these cells to cytolysis. This mutant is most likely mutated in a gene affecting a late stage in glycoprotein processing, leading to altered presentation of glycoproteins at the plasma membrane. The finding that the synthesis of both gB and gC was affected coordinately in cells infected with six of the nine mutants suggests that synthesis of these two glycoproteins, their transport to the cell surface, or their insertion into plasma membranes is coordinately regulated.
A NUMERICAL INVESTIGATION OF METHANE AIR PARTIALLY PREMIXED FLAMES AT ELEVATED PRESSURES

Abstract A numerical investigation of high pressure, counterflow methane-air partially premixed flames (PPFs) is presented to characterize the effect of pressure on flame structure. Four different mechanisms, namely GRI-2.11, GRI-3.0, the San Diego, and the C2 mechanisms have been examined. The mechanisms have been validated by comparing the predicted laminar flame speeds with experimental data. While there is excellent agreement between the measured and predicted laminar flame speeds based on these mechanisms, there are noticeable discrepancies amongst the mechanisms for the prediction of high-pressure PPFs. The GRI 3.0 mechanism is used to examine the detailed PPF structure at elevated pressures. At low pressures, the PPF exhibits a typical double flame structure that consists of rich premixed and nonpremixed reaction zones, and the separation distance between the reaction zones decreases with increasing pressure. However, for pressure above 10 atm, the separation distance becomes nearly independent of pressure. In addition, a critical pressure is observed, above which the PPF structure exhibits anomalous behavior, characterized by the presence of endothermic reactions and the production of CO in the region between the two reaction zones. A rate of production analysis revealed that the anomalous behavior is attributable to the following reactions: H + H2O → OH + H2, CH2CO + M → CH2 + CO + M, and HCO + M → H + CO + M. The critical pressure at which this behavior is first observed increases with the increase in equivalence ratio and/or strain rate. Thermal radiation is found to have a negligible effect on the flame structure for the range of conditions investigated.
Smelling salts

I was delving into some reference material recently, trying to track down details of early treatment of mild head injury, and I was struck by the repeated mention of smelling salts as a folk remedy for this problem. But just what are smelling salts? Do they work and can they cause injury? Although smelling salts have recently undergone a resurgence of interest by athletes as a pre-game stimulant or as a ‘‘pick me up’’ when performance is flagging, it appears that little is really known or understood about these agents. Over time they have tended to remain a traditional part of the trainer’s kit (along with the ubiquitous sponge and cold sprays) rather than in the medical bag. In the setting of sporting head injury, there are still many individuals and organisations that recommend the use of smelling salts to try and revive the injured athlete. Most recent sports medicine textbooks, however, emphatically state that smelling salts are contraindicated as they cause a withdrawal reaction, with the potential to cause or exacerbate spine injury. Take, for example, this early guideline for the management of unconscious patients from The treatment to restore natural breathing and circulation published in 1878 by Dr Peter Shepherd, Surgeon Major, Army Medical Department and an Associate of the Order of St John of Jerusalem. His approach was fairly dogmatic:
Induction of Immunological Tolerance/Hyporesponsiveness in Baboons with a Nondepleting CD4 Antibody

Tolerance induction with anti-CD4 Abs is well established in rodent transplant and autoimmune disease models, but has yet to be demonstrated in non-human primates or in clinical studies. In retrospect, failure of anti-CD4 Abs to induce tolerance in primates may be technical, a consequence of insufficient dosing and Ab properties influencing immunogenicity and cell depletion. To circumvent these possible limitations, we constructed a novel anti-CD4 mAb, TRX1, humanized to reduce immunogenicity and Fc-modified to prevent cell depletion. Using equine immune globulin (equine Ig) as a model Ag, we examined the tolerance-inducing capacity of TRX1 in baboons. During the induction phase, TRX1 inhibited the humoral response to equine Ig in a dose-dependent manner, with complete suppression of response at the highest dose tested (40 mg/kg). Upon challenge, anti-equine Ig responses were generated in baboons treated with 1 and 10 mg/kg doses of TRX1 and in control animals. In higher dosing cohorts (20 and 40 mg/kg), however, the immune response to equine Ig was modulated in seven of nine animals, including complete unresponsiveness to Ag challenges in two animals. Five of nine were hyporesponsive to equine Ig, generating titers 50- to 250-fold lower than control groups. Repeated challenge resulted in titers falling to baseline or near baseline, with two of five hyporesponsive animals becoming unresponsive to Ag. All animals responded to neoantigen immunization, indicating that the modified response to equine Ig was Ag specific. These studies demonstrate that anti-CD4 Ab-mediated, Ag-specific tolerance can be achieved in baboons without long term immune suppression.
Knowledge Spirals in Higher Education Teaching Innovation

A R&I&i process for a knowledge management system development is presented. It transforms different institutions experiences into organisational knowledge applicable to an entire sector, the higher education one specifically. The knowledge management system allows classifying, organising, distributing and facilitating the application of the knowledge generated by the faculty. A study, with more than 1000 system users, reflects that the system helps to the faculty in the way they perform educational innovation activities. The supported model integrates both Nonaka's epistemological and ontological spirals. This allows defining ontologies and used them in order to transform the individual knowledge into organisational one. The knowledge management system encapsulates complex logic expressions and ontologies management, making easy for the users obtaining successful results that may organise in their own way, becoming a powerful knowledge management process that combines epistemological and ontological knowledge spirals to convert individual experiences in educational innovation into organisational knowledge in the higher education sector.
Role played by Toll-like receptors 2 and 4 in lipoteichoic acid-induced lung inflammation and coagulation.

BACKGROUND The cell wall of Streptococcus pneumoniae consists of lipoteichoic acid (LTA), which is released when pneumococci are killed by either the host immune system or antibiotic treatment. Release of excessive amounts of LTA has been implicated in the toxic sequelae of severe gram-positive infection by virtue of its proinflammatory properties. Several in vitro studies have shown that LTA is recognized by Toll-like receptor (TLR) 2 and CD14. Our objective here was to investigate the inflammatory properties of S. pneumoniae LTA in vivo and the role played by TLR2, TLR4, and CD14 therein. METHODS Wild-type (WT), TLR2 knockout (KO), TLR4 KO, TLR2x4 double-KO, and CD14 KO mice were intranasally inoculated with highly purified pneumococcal LTA. RESULTS LTA induced a dose-dependent inflammatory response and activation of the coagulation and fibrinolytic pathways in a TLR2-dependent fashion. Surprisingly, TLR4 KO mice also displayed a somewhat diminished pulmonary inflammatory and coagulant response compared with WT mice, possibly as a result of absent TLR4 signaling through LTA-induced release of endogenous mediators. CONCLUSION Pneumococcal LTA induces a profound inflammatory response and activation of the coagulation pathway in the lungs in vivo through a TLR2-dependent route, which likely is amplified by endogenous TLR4 ligands.
BREAST SENSATION BEFORE AND AFTER PLASTIC SURGERY

Patients undergoing various plastic surgical procedures on their breasts were studied before and after operations with respect to sensation from crude touch, light pressure, and pain. The more extensive the operation on the breast (the more skin and breast tissue removed) the greater the postoperative decrease in sensation. Reduction mammaplasty and subcutaneous mastectomy were associated with decreased sensation in a significant number of patients. An unexpected finding was that patients having augmentation mammaplasty by either the inframammary or areola route showed a significant decrease in sensation to the nipple and apeola. At two years, 15 percent of the patients still had impaired sensory perception, although crude touch and light pressure appreciation had returned. Many of these patients had normal erectility with normal, and even enhanced, sensuality.
The effects of directional facial cues on electrodermal conditioning to facial stimuli.

The present two Experiments demonstrate that the orientation of angry facial expressions is a critical cue when faces serve as conditioned stimuli during aversive electrodermal conditioning. Experiment 1 demonstrated that responses conditioned to angry faces directed toward the subjects showed significant resistance to extinction whereas responses conditioned to angry faces directed away extinguished immediately during extinction. Experiment 2 was designed to investigate whether the orientation factor was effective only during extinction, i.e. whether the orientation was a performance variable, or if the observed effect originated from factors active during acquisition, i.e. if the orientation primarily influenced learning. When the orientation was shifted between the acquisition and the extinction phase, it was found that it did not matter what direction the faces had during acquisition; it was only during extinction that the faces needed to be directed toward the subjects to evoke persistent responding. These results suggest that the subjects acquired a conditioned response to the angry face regardless of its direction, but that this learning effect remained only when the angry face was directed toward the subject during extinction.
The Hidden Mass and Large Spatial Extent of a Post-Starburst Galaxy Outflow

A galaxy that has experienced a recent burst of star formation has an extended halo of hot, ionized gas surrounding it. Outflowing winds of multiphase plasma have been proposed to regulate the buildup of galaxies, but key aspects of these outflows have not been probed with observations. By using ultraviolet absorption spectroscopy, we show that “warm-hot” plasma at 105.5 kelvin contains 10 to 150 times more mass than the cold gas in a post-starburst galaxy wind. This wind extends to distances > 68 kiloparsecs, and at least some portion of it will escape. Moreover, the kinematical correlation of the cold and warm-hot phases indicates that the warm-hot plasma is related to the interaction of the cold matter with a hotter (unseen) phase at >>106 kelvin. Such multiphase winds can remove substantial masses and alter the evolution of post-starburst galaxies.
A Statistical Model of Rift Valley Fever Activity in Egypt

ABSTRACT: Rift Valley fever (RVF) is a viral disease of animals and humans and a global public health concern due to its ecological plasticity, adaptivity, and potential for spread to countries with a temperate climate. In many places, outbreaks are episodic and linked to climatic, hydrologic, and socioeconomic factors. Although outbreaks of RVF have occurred in Egypt since 1977, attempts to identify risk factors have been limited. Using a statistical learning approach (lasso-regularized generalized linear model), we tested the hypotheses that outbreaks in Egypt are linked to (1) River Nile conditions that create a mosquito vector habitat, (2) entomologic conditions favorable to transmission, (3) socio-economic factors (Islamic festival of Greater Bairam), and (4) recent history of transmission activity. Evidence was found for effects of rainfall and river discharge and recent history of transmission activity. There was no evidence for an effect of Greater Bairam. The model predicted RVF activity correctly in 351 of 358 months (98.0%). This is the first study to statistically identify risk factors for RVF outbreaks in a region of unstable transmission.
Disabled‐2 is transcriptionally regulated by ICSBP and augments macrophage spreading and adhesion

Mice lacking transcription factor interferon consensus sequence binding protein (ICSBP) develop a syndrome similar to human chronic myeloid leukemia and are immunodeficient. In order to define the molecular mechanisms responsible for the cellular defects of ICSBP−/− mice, we used bone marrow‐derived macrophages (BMM) to identify genes deregulated in the absence of ICSBP. Here, we report that disabled‐2 (Dab2), a signal phosphoprotein, is transcriptionally up‐regulated and accumulates in the cytoskeleton/membrane fraction of ICSBP−/− BMM. Moreover, our results revealed Dab2 as a novel IFN‐γ‐response gene. Both ICSBP and the Ets‐transcription factor PU.1 bind to the Dab2 promoter, whereby ICSBP represses PU.1‐induced Dab2 promoter transactivation in vitro. Notably, repression of Dab2 expression by ICSBP is also found in myeloid progenitors. Overexpression of Dab2 leads to accelerated cell adhesion and spreading, accompanied by enhanced actin fiber formation. Furthermore, cell adhesion induces transient Dab2 phosphorylation and its translocation to the cytoskeletal/membrane fraction. Our results identify a novel role of Dab2 as an inducer of cell adhesion and spreading, and strongly suggest that the up‐regulation of Dab2 contributes to the hematopoietic defect seen in ICSBP−/− mice.
Comparing the effect of isotopically labeled or structural analog internal standards on the performance of a LC-MS/MS method to determine ciclosporin A, everolimus, sirolimus and tacrolimus in whole blood

Abstract Background: Liquid chromatography-tandem mass spectrometry (LC-MS/MS) is routinely used for analysis of immunosuppressive drugs. This study investigated whether replacing analog internal standards (ANISs) with isotopically labeled internal standards (ILISs) has an impact on the performance of a LC-MS/MS method for the quantification of tacrolimus (TAC), sirolimus (SIR), ciclosporin A (CsA) and everolimus (EVE) in whole blood. Methods: Following hemolysis, protein precipitation, and extraction with either ANISs (ascomycin, desmethoxy-rapamycin, CsD), or ILISs (TAC-13C,D2; SIR-13C,D3; CsA-D12; EVE-D4), samples were centrifuged and injected into a LC-MS/MS device equipped with a C18 reversed phase column. The effect of the two ISs on the linearity, precision, accuracy, trueness, matrix effects, and carryover was investigated by using the same patient-, proficiency testing-, and quality control samples. Statistical analysis of agreement between results includes a standard random effects model and Passing-Bablok regression. Results: Within-day imprecision was <10%, between-day <8%, and trueness 91%–110% for all the analytes with both ISs. No carryover or matrix effects were observed. The median accuracy was −2.1% for CsA, 9.1% for EVE, 12.2% for SIR, and −1.2% for TAC with the ILISs; and −2% for CsA, 9.8% for EVE, 11.4% for SIR, and 0.2% for TAC with the ANISs. Results of patient and proficiency testing samples were not statistically different. Conclusions: Although ILISs are generally considered superior to ANISs, they may not be always essential. When optimizing a LC-MS/MS method other factors must be also considered.
Dna isolated from DNA/anti-DNA antibody immune complexes in systemic lupus erythematosus is rich in guanine-cytosine content.

DNA fragments were isolated from DNA/anti-DNA antibody immune complexes of systemic lupus erythematosus. Hybridization experiments indicated that DNA isolated from immune complexes originates from human nuclear DNA. Two classes of DNA were identified by polyacrylamide gel electrophoresis. The m.w. of small fragments was 25,000 with 30 to 40 base pairs, and that of large fragments was 100,000 with 150 base pairs. The average guanine-cytosine (G-C) content in the small fragments was 55% of total bases, and that in the large fragments was 45%. Compared with the average 38% G-C content of total human DNA, the antigen DNA is rich in G-C content. Such unusually high G-C content can alter DNA structure, which may serve as the target for antibody production.