gebhart/patrepeval huggingface dataset:
The systematic synthesis of complexes containing µ<sub>3</sub>-CS ligands as two-electron donors. The preparation and structure of [{Co(η-C<sub>5</sub>H<sub>5</sub>)}<sub>2</sub>{Fe(PPh<sub>3</sub>)(CO)<sub>2</sub>}(µ<sub>3</sub>-S)(µ<sub>3</sub>-CS)] (1992)

The η2-(CS)-CS2 ligand in [Fe{PPh3}2(CO)2(η2-CS2)] is cleaved by [Co(η-C5H5)[PPh3}2] at room temperature with formation of [{Co(η-C5H5)}2{Fe(PPh3)(CO)2](µ3-S)] in which the CS ligand acts as a µ3 two-electron donor to the Co2Fe triangle.
Using Rogowski coils for transient current measurements (1993)

In recent years the Rogowski-coil method of measuring electric current has developed from a ‘laboratory curiosity’ to a versatile measuring system with many applications throughout industry and in research. The technique possesses many features which offer an advantage over iron-cored current measuring devices and these are well illustrated by considering how it can be used for measuring transient currents. The paper describes the principle of operation of Rogowski coils and the practical aspects of using them and gives several examples of their use in making transient measurements. The Rogowski coil is a conceptually simple device. Its theory of operation illustrates some basic principles of electromagnetism applied in a practical device. The coil itself provides an elegant demonstration of Ampère&apos;s Law and, because of its inherent linearity, the response of a coil under extreme measuring situations is much easier to treat theoretically than iron-cored measuring instruments. The educational aspects of studying Rogowski coils should not be overlooked.
A Novel Approach to the Synthesis of Cytotoxic C2—C3 Unsaturated Pyrrolo[2,1‐c][1,4]benzodiazepines (PBDs) with Conjugated Acrylyl C2‐Substituents. (2004)

Abstract For Abstract see ChemInform Abstract in Full Text.
Evaluation of malignant glioma patients during the postirradiation period (1979)

✓ The syndrome of increased focal or generalized central nervous system (CNS) dysfunction in the early postirradiation period in patients treated with radiation therapy (RT) for malignant gliomas has not been well documented. The authors have undertaken retrospective study of 51 patients with supratentorial malignant gliomas who survived longer than 26 weeks from the time of diagnosis. All patients received irradiation and chemotherapy and were evaluated at 8-week intervals. Each evaluation consisted of a neurological examination, computerized tomography (CT) and radionuclide scans, Karnofsky rating, and an evaluation of glucocorticoid levels needed to maintain neurological function. In all, 263 evaluable periods, consisting of 1290 individual evaluable tests (parameters), were analyzed. In the first 18 weeks after RT, 26 of the 51 patients studied (51%) showed deterioration in one or more tests; 14 of the 26 (53%) did not improve. These 14 patients had a median time to tumor progression (MTP) of 31 weeks. The remaining 12 patients in this group (47%) improved and had an MTP of 73 weeks. Of the 51 patients, 25 (49%) showed deterioration significant enough to presume tumor progression (two of the following three tests were unequivocally worse: neurological examination, CT scan, and radionuclide scan), seven improved with no change in therapy and had an MTP of 66 weeks, while the other 18 had an MTP of 32 weeks. Excluding the Karnofsky rating, any individual test that showed worsening during the first 18-week period had a 33% probability of significant improvement at a subsequent evaluation period. After 18 weeks the probability of the test improving was only 4%. The authors conclude that CNS decompensation up to 18 weeks after RT, as ascertained from clinical examination, scans, or glucocorticoid dosage, does not invariably predict tumor progression, because in 28% (7/25) of such cases there will be subsequent improvement.
The sweetness inhibitor ‘Lactisole’ attenuates postprandial hyperglycaemia (2009)

Postprandial hyperglycaemia is associated with an increased risk of macrovascular disease and higher rates of CVD mortality (1) . Glucose absorption from the gut is facilitated by the Na-dependent glucose transporter SGLT1 (2) , and methods to reduce SGLT1-mediated glucose absorption would be an interesting therapeutic strategy. The presence of glucose in the intestine may increase the expression and activity of SGLT1, possibly via activation of the heterodimeric (T1R3/T1R2) 'sweet' taste receptors (3) . Lactisole is known to act on T1R3 (4) , and the aim of the present study was to investigate whether the presence of lactisole would reduce glucose uptake from the gut in vivo.
Analysis of Modified Human Papillomavirus Type 16 L1 Capsomeres: the Ability To Assemble into Larger Particles Correlates with Higher Immunogenicity (2009)

L1 capsomeres purified from Escherichia coli represent an economic alternative to the recently launched virus-like particle (VLP)-based prophylactic vaccines against infection with human papillomavirus types 16 and 18 (HPV-16 and HPV-18), which are causative agents of cervical cancer. It was recently reported that capsomeres are much less immunogenic than VLPs. Numerous modifications of the L1 protein leading to the formation of capsomeres but preventing capsid assembly have been described, such as the replacement of the cysteine residues that form capsid-stabilizing disulfide bonds or the deletion of helix 4. So far, the influence of these modifications on immunogenicity has not been thoroughly investigated. Here, we describe the purification of eight different HPV-16 L1 proteins as capsomeres from Escherichia coli. We compared them for yield, structure, and immunogenicity in mice. All L1 proteins formed almost identical pentameric structures yet differed strongly in their immunogenicity, especially regarding the humoral immune responses. Immunization of TLR4(-/-) mice and DNA immunization by the same constructs confirmed that immunogenicity was independent of different degrees of contamination with copurifying immune-stimulatory molecules from E. coli. We hypothesize that immunogenicity correlates with the intrinsic ability of the capsomeres to assemble into larger particles, as only assembly-competent L1 proteins induced high antibody responses. One of the proteins (L1DeltaN10) proved to be the most immunogenic, inducing antibody titers equivalent to those generated in response to VLPs. However, preassembly prior to injection did not increase immunogenicity. Our data suggest that certain L1 constructs can be used to produce highly immunogenic capsomeres in bacteria as economic alternatives to VLP-based formulations.
Clay–Chitosan Nanobrick Walls: Completely Renewable Gas Barrier and Flame-Retardant Nanocoatings (2012)

Thin films prepared via a layer-by-layer (LbL) assembly of renewable materials exhibit exceptional oxygen barrier and flame-retardant properties. Positively charged chitosan (CH), at two different pH levels (pH 3 and pH 6), was paired with anionic montmorillonite (MMT) clay nanoplatelets. Thin-film assemblies prepared with CH at high pH are thicker, because if the low polymer charge density. A 30-bilayer (CH pH 6-MMT) nanocoating (~100 nm thick) reduces the oxygen permeability of a 0.5-mm-thick polylactic acid film by four orders of magnitude. This same coating system completely stops the melting of a flexible polyurethane foam, when exposed to direct flame from a butane torch, with just 10 bilayers (~30 nm thick). Cone calorimetry confirms that this coated foam exhibited a reduced peak heat-release rate, by as much as 52%, relative to the uncoated control. These environmentally benign nanocoatings could prove beneficial for new types of food packaging or a replacement for environmentally persistent antiflammable compounds.
Kinetic versus thermodynamic control. An organic chemistry experiment (1971)

The authors report an experiment which does not involve the competition of different starting materials for a common reagent, but rather one in which a kinetically-controlled and a thermodynamically-controlled products may be obtained from exactly the same starting materials. The experiment has the added advantage of illustrating certain principles of the use of infrared and ultraviolet spectra for the identification of compounds of similar structures.
TCA‐100 tumour chemosensitivity assay: Differences in sensitivity between cultured tumour cell lines and clinical studies (1994)

The BATLE LE TCA-100 tumour chemosensitivity assay has been used to evaluate chemotherapeutic drug sensitivity of cultured tumour cell lines. Studies were performed using test drug concentrations calibrated to discriminate sensitivity and resistance of clinical specimens. Strong sensitivity which appeared to be inconsistent with clinical experience was detected for some drugs and cell lines. Findings of strong sensitivity were consistent with basic differences between sensitivity testing cultured cell lines and clinical specimens. Results with cell lines frequently may not apply directly to clinical applications. Characterization of differences between cell lines and clinical specimens may assist in application of cell line findings to clinical trials.
High-Dose Bupivacaine Remotely Loaded into Multivesicular Liposomes Demonstrates Slow Drug Release Without Systemic Toxic Plasma Concentrations After Subcutaneous Administration in Humans (2010)

Peak plasma bupivacaine concentrations were not different in the 2 groups, despite a 4-fold increase in total bupivacaine dose administered in the novel liposomal preparation. The delayed elimination and prolonged redistribution of liposomal bupivacaine to plasma is compatible with the depot-related slow-release effect leading to the prolonged pharmacodynamic effect previously reported.
Functional interaction among catalytic residues in subtilisin BPN′ (1990)

Variants of the serine protease, subtilisin BPN', in which the catalytic triad residues (Ser-221, His-64, and Asp-32) are replaced singly or in combination by alanine retain activities with the substrate N-succinyl-L-Ala-L-Ala-L-Pro-L-Phe-p-nitroanilide (sAAPF-pna) that are at least 10(3) to 10(4) above the non-enzymatic rate [Carter, P., Wells, J.A. Nature (London) 322:564-568, 1988]. A possible source of the residual activity was the hydrogen bond with the N delta 2 of Asn-155 that helps to stabilize the oxyanion generated in the tetrahedral transition state during amide bond hydrolysis by the wild-type enzyme. Replacing Asn-155 by Gly (N155G) lowers the turnover number (kcat) for sAAPF-pna by 150-fold with virtually no change in the Michaelis constant (KM). However, upon combining the N155G and S221A mutations to give N155G:S221A, kcat is actually 5-fold greater than for the S221A enzyme. Thus, the catalytic role of Asn-155 is dependent upon the presence of Ser-221. The residual activity of the N155G:S221A enzyme (approximately 10(4)-fold above the uncatalyzed rate) is not an artifact because it can be completely inhibited by the third domain of the turkey ovomucoid inhibitor (OMTKY3), which forms a strong 1:1 complex with the active site. The mutations N155G and S221A individually weaken the interaction between subtilisin and OMTKY3 by 1.8 and 2.0 kcal/mol, respectively, and in combination by 2.1 kcal/mol. This is consistent with disruption of stabilizing interactions around the reactive site carbonyl of the OMTKY3 inhibitor.(ABSTRACT TRUNCATED AT 250 WORDS)
Genomic Diversity and Relatedness of Bifidobacteria Isolated from a Porcine Cecum (2003)

This study initially involved the isolation of a number of bifidobacteria from either the lumen or the epithelium of a porcine cecum. A total of 160 isolates were selected at random on MRS plates containing cysteine hydrochloride (0.5 g/liter) and mupirocin (50 mg/liter). All were identified as bifidobacteria based on fructose-6-phosphate phosphoketolase activity. Following genomic digestion with the restriction enzyme XbaI and pulsed-field gel electrophoresis (PFGE), the isolates produced 15 distinct macro-restriction patterns. Several of the PFGE patterns differed by only 1, 2, or 3 DNA fragments and were grouped as related patterns into seven PFGE types, termed A through G. The related patterns appeared to show genomic plasticity within the isolates arising from chromosomal mutations or possibly horizontal transfer of plasmids. The relative frequency of each PFGE type was maintained within each cecal sample, with PFGE type E representing approximately 50% of the isolates. Randomly amplified polymorphic DNA PCR, cell morphology, whole-cell protein profiling, 16S ribosomal DNA sequencing, and DNA-DNA hybridization were used to determine if the seven apparently unrelated PFGE types represented genetically distinct isolates. Four groups were identified: PFGE types A, C/D/G, B/E, and F, and these appeared to represent Bifidobacterium minimum, Bifidobacterium pseudolongum subsp. pseudolongum, and Bifidobacterium pseudolongum subsp. globosum and two new species, respectively. The data demonstrate the presence of considerable genomic diversity within a relatively simple bifidobacteria population, consisting of 15 distinct strains representing four groups, which was maintained throughout the porcine cecal contents and epithelial layer.
Sequence feature-based prediction of protein stability changes upon amino acid substitutions (2010)

Relevant sequence features can be used to accurately predict protein stability changes upon amino acid substitutions. Predictive results at this level of accuracy may provide useful information to distinguish between deleterious and tolerant alterations in disease candidate genes. To make the classifier accessible to the genetics research community, we have developed a new web server, called MuStab (http://bioinfo.ggc.org/mustab/).
Electric current and electric field induced in the human body when exposed to an incident electric field near the resonant frequency (2000)

The electric field and current density induced in the human body when this is exposed to electric fields near the resonant frequency, 53 MHz, are determined analytically. Since this frequency range includes an important amateur radio band of 50-60 MHz and exposure to electric fields at this frequency has been shown to be hazardous, the study has a specific motivation. A cylindrical model of the body is used to derive formulas for the total axial current and current density induced in the body subject to skin effect. Tabulations and graphical representations illuminate the results.
Human MAP Tau Based Targeted Cytolytic Fusion Proteins (2017)

Some of the most promising small molecule toxins used to generate antibody drug conjugates (ADCs) include anti-mitotic agents (e.g., auristatin and its derivatives) which are designed to attack cancerous cells at their most vulnerable state during mitosis. We were interested in identifying a human cystostatic protein eventually showing comparable activities and allowing the generation of corresponding targeted fully human cytolytic fusion proteins. Recently, we identified the human microtubule associated protein tau (MAP tau), which binds specifically to tubulin and modulates the stability of microtubules, thereby blocking mitosis and presumably vesicular transport. By binding and stabilizing polymerized microtubule filaments, MAP tau-based fusion proteins skew microtubule dynamics towards cell cycle arrest and apoptosis. This biological activity makes rapidly proliferating cells (e.g., cancer and inflammatory cells) an excellent target for MAP tau-based targeted treatments. Their superior selectivity for proliferating cells confers additional selectivity towards upregulated tumor-associated antigens at their surface, thereby preventing off-target related toxicity against normal cells bearing tumor-associated antigens at physiologically normal to low levels. In this review, we highlight recent findings on MAP tau-based targeted cytolytic fusion proteins reported in preclinical immunotherapeutic studies.
Cationic liposome–microtubule complexes: Pathways to the formation of two-state lipid–protein nanotubes with open or closed ends (2005)

Intermolecular interactions between charged membranes and biological polyelectrolytes, tuned by physical parameters, which include the membrane charge density and bending rigidity, the membrane spontaneous curvature, the biopolymer curvature, and the overall charge of the complex, lead to distinct structures and morphologies. The self-assembly of cationic liposome-microtubule (MT) complexes was studied, using synchrotron x-ray scattering and electron microscopy. Vesicles were found to either adsorb onto MTs, forming a "beads on a rod" structure, or undergo a wetting transition and coating the MT. Tubulin oligomers then coat the external lipid layer, forming a tunable lipid-protein nanotube. The beads on a rod structure is a kinetically trapped state. The energy barrier between the states depends on the membrane bending rigidity and charge density. By controlling the cationic lipid/tubulin stoichiometry it is possible to switch between two states of nanotubes with either open ends or closed ends with lipid caps, a process that forms the basis for controlled chemical and drug encapsulation and release.
Effects of Coordination to Transition Metals on the Hydration and Electroactivity of the Chelating Ligand 1,10-Phenanthroline-5,6-dione (1996)

The intrinsically electroactive ligand in the title was coordinated to Co2+, Fe2+, Ni2+, Zn2+, and Cu+, and the resulting hydration of the carbonyl groups of a portion of the coordinated ligand eliminated its electroactivity. The extent of hydration of the coordinated ligand was evaluated by means of rotating disk voltammetry. Estimates were obtained for the equilibrium constants governing the hydration reaction. The hydration induced by coordination of the ligand to the metal cations varied in parallel with the magnitude of the first association constant for the metal−ligand coordination.
Malignant transformation of human fibroblasts by a transfected N-ras oncogene. (1990)

The only ras oncogene as yet identified in cells from human fibrosarcomas is N-ras, but the relationship between N-ras oncogene expression and the malignant state of these cell lines is not known. To determine if expression of an N-ras oncogene causes human cells to become malignant, we transfected the N-ras oncogene from human leukemia cell line 8402, cloned into a high expression vector pSV N-ras, into MSU-1.1 cells, a nontumorigenic, infinite life span fibroblast cell strain with a normal morphology and a stable near-diploid karyotype. The transformants formed distinct foci composed of morphologically transformed cells. Cells from such foci expressed higher than normal levels of N-ras protein, exhibited growth factor independence, and formed large colonies in soft agar at a high frequency. Injection of progeny of these focus-derived cells s.c. into athymic mice resulted in progressively growing, invasive malignant tumors (round cell, spindle cell, or giant cell sarcomas) which reached a diameter of 6 mm in 3 to 4 weeks. Injection of focus-derived or tumor-derived cells i.v. resulted in tumors in various organs of the mice. The focus-derived cell strain tested, as well as the majority of the cells derived from the tumor it produced, exhibited the same near-diploid karyotype as the parental MSU-1.1 cells. Cells transfected with an N-ras oncogene that was expressed at a normal level formed only a single, indistinct focus, and cells from that focus were not malignant.
Gradient Projection for Sparse Reconstruction: Application to Compressed Sensing and Other Inverse Problems (2007)

Many problems in signal processing and statistical inference involve finding sparse solutions to under-determined, or ill-conditioned, linear systems of equations. A standard approach consists in minimizing an objective function which includes a quadratic (squared ) error term combined with a sparseness-inducing regularization term. Basis pursuit, the least absolute shrinkage and selection operator (LASSO), wavelet-based deconvolution, and compressed sensing are a few well-known examples of this approach. This paper proposes gradient projection (GP) algorithms for the bound-constrained quadratic programming (BCQP) formulation of these problems. We test variants of this approach that select the line search parameters in different ways, including techniques based on the Barzilai-Borwein method. Computational experiments show that these GP approaches perform well in a wide range of applications, often being significantly faster (in terms of computation time) than competing methods. Although the performance of GP methods tends to degrade as the regularization term is de-emphasized, we show how they can be embedded in a continuation scheme to recover their efficient practical performance.
Substitution of 3′-Phosphate Cap with a Carbon-Based Blocker Reduces the Possibility of Fluorescence Resonance Energy Transfer Probe Failure in Real-Time PCR Assays (2004)

During the last decade, research and clinical use of real-time PCR applications has continued to grow in importance (1). Many laboratories that use real-time PCR with fluorescent probes experience an unexplained loss of probe fluorescence at some stage, in particular with pairs of fluorescence resonance energy transfer (FRET) probes. Photobleaching is often assumed to be the cause. Structural integrity of the oligonucleotides is also a major factor, and its loss has been shown to correlate with repeated freeze–thaw cycles (2). Laboratories guard against these two problems by aliquoting probes and protecting them from light. Despite these precautions, inexplicable FRET probe failures are still observed. In one recent such case, we were able to determine an additional mechanism for FRET probe failure: loss of the phosphate cap from the 3′ end of a probe. To our knowledge, this has not been described previously. Our studies revealed that this may be a common and important problem, intrinsic to 3′-phosphate-blocking chemistry. We also found that alternative terminating groups may be a preferable option to 3′-phosphate blocking.

A 3-nmol/L synthesis-scale LightCycler™ hybridization probe set was purchased from Idaho Technology Inc. Biochem in April 2003. As is common practice, the manufacturer produced a large-scale synthesis and, after shipping our order, archived the remainder for a possible future reorder. The first half of the batch (α-probe set) was sent immediately, whereas the second half (β-probe set) was stored lyophilized for 6 months at −20 °C and then shipped with our next order.

Oligonucleotides from the first shipment were used in PCR reactions in a LightCycler with satisfactory results. PCR conditions were as follows: 1× LightCycler FastStart DNA Master Hybridization Probe Mix (Roche Diagnostics), MgCl2 (final concentration, 3.5 mM), 0.5 μM each of the forward (5′-GGCCTTTCTGAAGCAAG-3′) and reverse (5′-GACGATTTCTTATTTCACAGCTCC-3′) primers, 0.2 μM each of the donor …