gebhart/patrepeval huggingface dataset:
Evaluation of CHROMagar Orientation for differentiation and presumptive identification of gram-negative bacilli and Enterococcus species (1996)

A new chromogenic plate medium, CHROMagar Orientation, was evaluated for use in the differentiation and presumptive identification of gram-negative bacilli and Enterococcus species by a multipoint inoculation (replicator) technique. In this study, 1,404 gram-negative bacilli and 74 enterococcal isolates were tested on CHROMagar Orientation. Six control American Type Culture Collection strains were also included with the testing to ensure quality control of the media. Of the Escherichia coli isolates (n = 588) tested, 99.3% produced a pink-to-red color. Only in four isolates that were O-nitrophenyl-beta-D-galactopyranoside (ONPG) negative did this result differ. Proteus mirabilis and P. vulgaris were well differentiated on this medium. P. mirabilis (n = 184) produced a clear colony with diffusible brown pigment around the periphery. By contrast, 15 of 16 P. vulgaris isolates produced bluish-green colonies with a slight brown background. All Aeromonas hydrophila isolates (n = 26) tested produced clear to pink colonies at 35 to 37 degrees C. This colony color changed to blue after 2 to 3 h of incubation at room temperature. A. hydrophila exhibited stronger color and better growth at 30 degrees C. Serratia marcescens (n = 29) demonstrated an aqua blue color that deepened to a darker blue when exposed to room temperature. All enterococcal isolates (n = 74) resulted in a blue color and gave pinpoint colonies on purity subcultures at 35 to 37 degrees C after 18 h of incubation. Similarity in color resulted in failure to discriminate accurately between Klebsiella, Enterobacter, and Citrobacter species. However, these species could be readily differentiated from other members of the family Enterobacteriaceae. Pseudomonas aeruginosa (n = 151) was easily differentiated from members of the Enterobacteriaceae but was less easily distinguishable from other gram-negative nonmembers of the Enterobacteriaceae. The medium was found to facilitate easy visual detection of mixed bacterial isolates in culture. When used in a replicator system, it easily detected mixed growths of organisms which may have otherwise led to false antibiotic susceptibility results. These mixed growths were not obvious on the routine susceptibility testing medium (Isosensitest).
Hole-Doped Semiconductor Nanowire on Top of ans-Wave Superconductor: A New and Experimentally Accessible System for Majorana Fermions (2012)

Majorana fermions were envisioned by Majorana in 1935 to describe neutrinos. Recently, it has been shown that they can be realized even in a class of electron-doped semiconductors, on which ordinary s-wave superconductivity is proximity induced, provided the time reversal symmetry is broken by an external Zeeman field above a threshold. Here we show that in a hole-doped semiconductor nanowire the threshold Zeeman field for Majorana fermions can be very small for some magic values of the hole density. In contrast to the electron-doped systems, smaller Zeeman fields and much stronger spin-orbit coupling and effective mass of holes allow the hole-doped systems to support Majorana fermions in a parameter regime which is routinely realized in current experiments.
A New Approach to Generating Fracture Conductivity (2010)

Abstract The primary goal of a hydraulic fracturing treatment is to create a highly conductive flow path to the wellbore that economically increases well production. In moderate and high permeability wells the lack of adequate fracture conductivity is a limiting factor in the production potential of the well, whereas in tight gas reservoirs the limiting factor is often the effective fracture half-length. Even in the last case, adequate fracture conductivity is important to allow efficient recovery of the fracturing fluid. Traditionally, efforts to enhance conductivity have been directed to improve the ability to flow through a porous proppant pack. The industry has extended significant efforts towards the goal of increasing proppant pack permeability through the development of less damaging carrier fluids, higher strength man-made proppants, more efficient fracturing fluid breakers and so on. As an industry however, we continue to struggle with the fact that well testing frequently indicates disappointingly shorter or less conductive fractures than designed. Multiple studies indicate that proppant-pack retained permeability is often a small fraction of the maximum expected value. This manuscript describes a novel hydraulic fracturing technique that enables a step-change approach towards increasing fracture conductivity. The technique is based on the creation of a network of open channels inside the fracture. Modeling and experimental work indicates that the new technique can deliver conductivities in excess of ten-times those obtained from conventional fracture treatments. Extensive lab-, yard- and field- scale experiments combined with theoretical work allowed creating the framework that describes the physical processes occurring during the application of this new technique. By providing significantly higher fracture conductivity, this new fracturing approach delivers a number of consequential benefits: better fracture cleanup; lower pressure loss within the fracture; longer effective fracture half-lengths, all of which will contribute to improved short- and long-term production. A 15-well field study, selected from over fifty treatments performed up to date with this technique, is presented to show posttreatment results with significant gains in well production and expected ultimate recovery with respect to offset wells treated with conventional fracturing methods.
RNA Viruses and RNAi: Quasispecies Implications for Viral Escape (2015)

Due to high mutation rates, populations of RNA viruses exist as a collection of closely related mutants known as a quasispecies. A consequence of error-prone replication is the potential for rapid adaptation of RNA viruses when a selective pressure is applied, including host immune systems and antiviral drugs. RNA interference (RNAi) acts to inhibit protein synthesis by targeting specific mRNAs for degradation and this process has been developed to target RNA viruses, exhibiting their potential as a therapeutic against infections. However, viruses containing mutations conferring resistance to RNAi were isolated in nearly all cases, underlining the problems of rapid viral evolution. Thus, while promising, the use of RNAi in treating or preventing viral diseases remains fraught with the typical complications that result from high specificity of the target, as seen in other antiviral regimens.
Sleep Disorders During Pregnancy (2004)

This paper reviews the topic of sleep disorders in pregnant women. We describe changes in sleep architecture and sleep pattern during pregnancy, discuss the impact of the physical and biochemical changes of pregnancy on sleep in pregnant women and examine whether maternal-fetal outcomes may be adversely affected in women with disordered sleep. The literature on common sleep disorders affecting pregnant women, including insomnia, sleep-disordered breathing and restless legs syndrome, is reviewed and recommendations are made for the management of these disorders during pregnancy.
High-spin five-co-ordinate nickel(II) and cobalt(II) complexes with 2,6-diacetylpyridinebis(imines) (1968)

The Schiff bases obtained from 2,6-diacetylpyridine and various aliphatic amines behave as tridentate ligands with set of donor atoms NNN in nickel(II) and cobalt(II) complexes. The complexes have the general formula MLX2(M = Ni or Co; L = 2,6-diacetylpyridinebisimine; and X = halogen or pseudohalogen) and are all of the high-spin type. The nickel and cobalt halide complexes are five-co-ordinate both in the solid state and in solution, while the nickel and cobalt nitrate complexes are octahedral. The cobalt thiocyanate complexes are monomeric and five-co-ordinate, while the nickel thiocyanate complexes achieve a polymeric octahedral structure, presumably through intermolecular bridging linkages of the thiocyanate groups.
Resonance-Assisted Hot Electron Femtochemistry at Surfaces (1996)

A theory of resonance-assisted, hot-electron-induced femtochemical processing at surfaces (HEFATS) has been developed in terms of inelastic electron scattering via negative-molecular-ion shape resonances associated with molecules adsorbed on solid surfaces. Two examples, one involving a broad band of laser-excited hot electrons and the other a tunable narrow band produced by a solid state tunnel junction, are used to illustrate the potential of HEFATS in chemical bond breaking as, for instance, in desorption.
Attenuated Measles Vaccine in Children with Acute Leukemia (1962)

It has been shown by Mitus and her associates 1-3 that infection with measles virus in children with acute leukemia may occasionally terminate fatally. At autopsy in such cases, pathological changes characteristic of giant-cell pneumonia are present. The etiologic agent in all cases of this condition examined thus far has proved to be measles virus. These workers also found that prophylactic administration of γ-globulin cannot be relied upon to prevent the development of measles giant-cell pneumonia. Accordingly, the possibility of protecting this unusually vulnerable sort of patient by means of vaccination with attenuated measles virus vaccine was considered. The decision to vaccinate a small selected group of children was taken only after carefully weighing the possible untoward effects of the vaccine against the grave risk attendant upon infection naturally acquired. In the first part of this communication, abnormal as well as normal reactions to measles of different children with acute
Histone mRNA degradation in vivo: the first detectable step occurs at or near the 3' terminus. (1986)

The first detectable step in the degradation of human H4 histone mRNA occurs at the 3' terminus in a cell-free mRNA decay system (J. Ross and G. Kobs, J. Mol. Biol. 188:579-593, 1986). Most or all of the remainder of the mRNA is then degraded in a 3'-to-5' direction. The experiments described here were designed to determine whether a similar degradation pathway is followed in whole cells. Two sets of short-lived histone mRNA decay products were detected in logarithmically growing erythroleukemia (K562) cells. These products, designated the -5 and -12 RNAs, were generated by the loss of approximately 4 to 6 and 11 to 13 nucleotides, respectively, from the 3' terminus of histone mRNA. The same decay products were observed after a brief incubation in vitro. They were in low abundance or absent from cells that were not degrading histone mRNA. In contrast, they were readily detectable in cells that degraded the mRNA at an accelerated rate, i.e., in cells cultured with a DNA synthesis inhibitor, either cytosine arabinoside or hydroxyurea. During the initial stages of the decay process, as the 3' terminus of the mRNA was being degraded, the 5'-terminal region remained intact. These results indicate that the first detectable step in human H4 histone mRNA decay occurs at the 3' terminus and that degradation proceeds 3' to 5', both in cells and in cell-free reactions.
The synthesis of oligoribonucleotides containing O6-methylguanosine: the role of conserved guanosine residues in hammerhead ribozyme cleavage (1993)

The synthesis is described of oligoribonucleotides containing the modified nucleoside O6-methylguanosine. Solid-phase oligoribonucleotide assembly was carried out by use of 2'-silyl-protected nucleoside phosphoramidites, a new O6-methylguanosine-containing synthon and a mild deprotection method. The O6-methylguanosine-modified oligonucleotides were used in the study of the role of conserved residues G5, G8 and G12 in hammerhead ribozyme cleavage. Hammerheads thus substituted at any of these positions showed an approximately 75-fold reduction in kcat whereas Km was unaffected. Hammerheads with modifications at G5 or G8 showed a significant reduction in magnesium binding affinity whereas modification at G12 had no effect. The results show that the three conserved G residues play crucial but different role sin hammerhead cleavage.
The effect of a bacterial vaccine on tumors and the immune response of ICR/Ha mice. (1990)

This study examined the effect of mixed bacterial vaccine (MBV), a biological response modifier prepared from Streptococcus pyogenes and Serratia marcescens, on the immune system of mice and on the regression of a transplantable mouse tumor sarcoma 37. The study examined MBV's biological properties and analyzed its chemical composition. The chemical composition varied with the growth media. A typical centrifuged, dialyzed supernate of the serum-containing preparation was found to consist mainly of protein and minimal amounts of carbohydrate and endotoxin, while MBV made with synthetic medium contained similar amounts of all three. MBV was nontoxic for mice, which gained weight following the injection of 0.5-1.0 ml of MBV. MBV caused regression of 20-100% of well-established mouse tumors without appreciable toxicity. MBV also had a striking effect on the immune response of mice to sheep red blood cells. When administered simultaneously with antigen injection, MBV increased the number of antibody-secreting splenocytes measured by the plaque-forming assay threefold. Serum antibody levels also increased two- to threefold. MBV did not enhance the immune response to pneumococcal polysaccharide type III, a B-cell-dependent response. However, the in vivo administration of MBV increased the in vitro response to MBV and the B-cell mitogen lipopolysaccharide. MBV compares favorably with other biological response modifiers because of its enhancing effect on the immune response and its oncolytic properties at nontoxic levels.
Insulin-Like Growth Factor 1 Receptor Signaling Regulates Skin Development and Inhibits Skin Keratinocyte Differentiation (2006)

The insulin-like growth factor 1 receptor (IGF-1R) is a multifunctional receptor that mediates signals for cell proliferation, differentiation, and survival. Genetic experiments showed that IGF-1R inactivation in skin results in a disrupted epidermis. However, because IGF-1R-null mice die at birth, it is difficult to study the effects of IGF-1R on skin. By using a combined approach of conditional gene ablation and a three-dimensional organotypic model, we demonstrate that IGF-1R-deficient skin cocultures show abnormal maturation and differentiation patterns. Furthermore, IGF-1R-null keratinocytes exhibit accelerated differentiation and decreased proliferation. Investigating the signaling pathway downstream of IGF-1R reveals that insulin receptor substrate 2 (IRS-2) overexpression compensates for the lack of IGF-1R, whereas IRS-1 overexpression does not. We also demonstrate that phosphatidylinositol 3-kinase and extracellular signal-regulated kinase 1 and 2 are involved in the regulation of skin keratinocyte differentiation and take some part in mediating the inhibitory signal of IGF-1R on differentiation. In addition, we show that mammalian target of rapamycin plays a specific role in mediating IGF-1R impedance of action on keratinocyte differentiation. In conclusion, these results reveal that IGF-1R plays an inhibitory role in the regulation of skin development and differentiation.
A preliminary note on the use of enzymes in conservation: the removal of aged acrylic resin coatings with lipase (1999)

Lipases, hydrolytic enzymes that act on glycerol-ester bonds, are often used in conservation for their ability to degrade aged oil films, as a non-toxic and often less aggressive alternative to highly polar organic solvents and/or alkaline mixtures. One such enzyme has been used to remove layers of an aged acrylic resin (Paraloid B72) in two instances, a fifteenth-century tempera painting on panel and a nineteenth-century oil painting on canvas. A plausible mechanism for the action of the enzyme is discussed.
Cytokine Signaling Through Nonreceptor Protein Tyrosine Kinases (1995)

Cytokines are a family of soluble mediators of cell-to-cell communication that includes interleukins, interferons, and colony-stimulating factors. The characteristic features of cytokines lie in their functional redundancy and pleiotropy. Most of the cytokine receptors that constitute distinct superfamilies do not possess intrinsic protein tyrosine kinase (PTK) domains, yet receptor stimulation usually invokes rapid tyrosine phosphorylation of intracellular proteins, including the receptors themselves. It is now clear that these receptors are capable of recruiting or activating (or both) a variety of nonreceptor PTKs to induce downstream signaling pathways. Thus, the intracytoplasmic structure of cytokine receptors has evolved so as to allow the combined action of different PTK family members expressed in different cell types, which may ultimately determine the activity of cytokines.
Synthesis and Characterization of Silicone‐Based Surfactants as Anti‐Foaming Agents (2011)

Abstract Silicone‐based amphiphilic surfactants were synthesized as anti‐foaming agents through a polycondensation reaction between chlorine‐terminated polysiloxane and polyethers. Poly(ethylene glycol) (PEG) and poly(propylene glycol) of different molecular weights were used. The structures of these tri‐block co‐polymers were characterized by FTIR, 1 H NMR and ESI–MS analysis. Surface tension, foam height and foam destruction properties of these co‐polymers were determined. Spectroscopic analysis confirmed that bonding of polyether to polysiloxane was successful and two types of different tri‐block co‐polymers were obtained. The anti‐foaming efficiency of these co‐polymers tended to increase with an increase in the hydrophilic character of the co‐polymer chains. The synthesized tri‐block co‐polymers, which can be used as anti‐foaming agents in paper‐coating applications of poly(vinyl acetate‐ co ‐butyl acrylate) latexes, showed low surface tension values, fast liquid drainage and efficient foam destruction. PEG 200‐ b ‐PDMS‐ b ‐PEG 200 was determined to be the most efficient anti‐foaming agent among all co‐polymers synthesized.
Fossil sister group of craniates: Predicted and found (2003)

This study investigates whether the recently described Cambrian fossil Haikouella (and the very similar Yunnanozoon) throws light on the longstanding problem of the origin of craniates. In the first rigorous cladistic analysis of the relations of this animal, we took 40 anatomical characters from Haikouella and other taxa (hemichordates, tunicates, cephalochordates, conodont craniates and other craniates, plus protostomes as the outgroup) and subjected these characters to parsimony analysis. The characters included several previously unrecognized traits of Haikouella, such as upper lips resembling those of larval lampreys, the thick nature of the branchial bars, a mandibular branchial artery but no mandibular branchial bar, muscle fibers defining the myomeres, a dark fibrous sheath that defines the notochord, conclusive evidence for paired eyes, and a large hindbrain and diencephalon in the same positions as in the craniate brain. The cladistic analysis produced this tree: (protostomes, hemichordates (tunicates, (cephalochordates, (Haikouella, (conodonts + other craniates))))), with the "Haikouella + craniate" clade supported by bootstrap values that ranged from 81-96%, depending on how the analysis was structured. Thus, Haikouella is concluded to be the sister group of the craniates. Alternate hypotheses that unite Haikouella with hemichordates or cephalochordates, or consider it a basal deuterostome, received little or no support. Although it is the sister group of craniates, Haikouella is skull-less and lacks an ear, but it does have neural-crest derivatives in its branchial bars. Its craniate characters occur mostly in the head and pharynx; its widely spaced, robust branchial bars indicate it ventilated with branchiomeric muscles, not cilia. Despite its craniate mode of ventilation, Haikouella was not a predator but a suspension feeder, as shown by its cephalochordate-like endostyle, and tentacles forming a screen across the mouth. Haikouella was compared to pre-craniates predicted by recent models of craniate evolution and was found to fit these predictions closely. Specifically, it fits Northcutt and Gans' prediction that the change from ciliary to muscular ventilation preceded the change from suspension feeding to predatory feeding; it fits Butler's claim that vision was the first craniate sense to start elaborating; it is consistent with the ideas of Donoghue and others about the ancestor of conodont craniates; and, most strikingly, it resembles Mallatt's prediction of the external appearance of the ancestral craniate head. By contrast, Haikouella does not fit the widespread belief that ancestral craniates resembled hagfishes, because it has no special hagfish characters. Overall, Haikouella agrees so closely with recent predictions about pre-craniates that we conclude that the difficult problem of craniate origins is nearly solved.
Effect of allogeneic hematopoietic cell transplantation in first complete remission on post-relapse complete remission rate and survival in acute myeloid leukemia (2015)

47 (29%) 31 (27%) 6 (23%) 10 (53%) 0.068 No. of induction courses to attain CR1, n (%) 0.027 1 134 (83%) 102 (88%) 18 (69%) 14 (74%) 2 27 (17%) 14 (12%) 8 (31%) 5 (26%) Post-remission therapy in CR1, n (%) 0.064 No 25 (16%) 14 (12%) 8 (31%) 3 (16%) Yes 136 (84%) 102 (88%) 18 (69%) 16 (84%) No. of post-remission courses in CR1, n (%) 0.003 0 25 (16%) 14 (12%) 8 (31%) 3 (16%) 1 35 (22%) 20 (17%) 7 (27%) 8 (42%) 2 36 (22%) 26 (22%) 6 (23%) 5 (26%) 3 65 (40%) 59 (49%) 5 (19%) 3 (16%) Median CR1 duration, m (range) 8.0 (0.5-163) 6.4 (0.5-79.5) 11.6 (3.9-163) 10.0 (3.4-82) < 0.001 Performance status at 1st relapse, n (%) 0.042 0-1 129 (81%) 97 (84%) 21 (81%) 11 (60%) 2 32 (19%) 19 (16%) 5 (19%) 8 (40%) Cytogenetics at 1 st relapse, n (%) 0.35 Favorable 11 (7%) 10 (9%) 1 (4%) 0 (0%) Intermediate 94 (58%) 70 (60%) 13 (50%) 11 (58%) Adverse 34 (21%) 24 (21%) 7 (27%) 3 (16%) Missing/Insufficient 22 (14%) 12 (10%) 5 (19%) 5 (26%) Molecular studies at 1st relapse FLT3, n (%) 0.78 Positive 22 (13.5%) 18 (15.5%) 3 (11.5%) 1 (5%) Negative 64 (40%) 47 (40.5%) 9 (34.5%) 8 (42%) N/A 75 (46.5%) 51 (44%) 14 (54%) 10 (53%) NPM1, n (%) 0.05 Positive 20 (12.5%) 19 (16%) 1 (4%) 0 (0%) Negative 33 (20.5%) 24 (21%) 3 (11.5%) 6 (31.5%) N/A 108 (67%) 73 (63%) 22 (84.5%) 13 (68.5%)
Protein engineering by chemical means? (1987)

Journal Article Protein engineering by chemical means? Get access R.E. Offord R.E. Offord Départment de Biochimie Médicale, Université de Genève1211 Genève 4, Switzerland Search for other works by this author on: Oxford Academic PubMed Google Scholar Protein Engineering, Design and Selection, Volume 1, Issue 3, June 1987, Pages 151–157, https://doi.org/10.1093/protein/1.3.151 Published: 01 June 1987