gebhart/patrepeval huggingface dataset:
Oxygen Glucose Deprivation Model of Cerebral Stroke in PC-12 Cells: Glucose as a Limiting Factor (2008)

Optimum time points for oxygen-glucose deprivation (OGD) and re-oxygenation have been identified to suggest the suitability of PC-12 cells as rapid and sensitive in vitro model of cerebral stroke. Further, the precise role of glucose as one of the limiting factors was ascertained. PC-12 cells were subjected to receive OGD of 1-8 h followed by re-oxygenation for 6 to 96 h in medium having glucose 0-10 mg/ml. Loss of cell viability was assessed using trypan blue dye exclusion and MTT assays. The significant (p < 0.05) reduction in percent viable cell count was started at 2 h of OGD (80.7 +/- 2.0) and continued in further OGD periods (3, 4, 5, 6, 7, and 8 h), i.e. 65.7 +/- 3.5, 59.7 +/- 4.6, 54.3 +/- 3.2, 44.7 +/- 2.9, 20.3 +/- 4.3, 5.7 +/- 2.0 of counted cells, respectively. Cells growing in glucose-free medium have shown a gradual (p < 0.001) decrease in cell viability throughout the re-oxygenation. Re-oxygenation of 24 h was found to be first statistically significant time point for all the glucose concentrations. Glucose concentration during re-oxygenation was found to be one of the key factors involved in the growth and proliferation in PC-12 cells. The OGD of 6 h followed by a re-oxygenation period of 24 h with 4-6 mg/ml glucose concentration could be recorded as optimum conditions under our experimental conditions.
Palladium-Catalyzed Cross-Coupling Reactions of 2-Indolyldimethylsilanols with Substituted Aryl Halides (2004)

[reaction: see text] A mild and general cross-coupling reaction of 2-indolylsilanols has been developed. The experimental variables that lead to successful coupling are (1) the use of sodium tert-butoxide as the activator, (2) the use of copper(I) iodide in stoichiometric quantities, and (3) the use of Pd2(dba)3.CHCl3 as the catalyst. Under these conditions N-(Boc)-2-indolyldimethylsilanol reacts with a variety of aromatic iodides to afford the coupling products in good yield (70-84%).
Extension of the range of DNA sequences available for triple helix formation: Stabilization of mismatched triplexes by acridine-containing oligonucleotides (1997)

Triple helix formation usually requires an oligopyrimidine*oligopurine sequence in the target DNA. A triple helix is destabilized when the oligopyrimidine*oligopurine target contains one (or two) purine*pyrimidine base pair inversion(s). Such an imperfect target sequence can be recognized by a third strand oligonucleotide containing an internally incorporated acridine intercalator facing the inverted purine*pyrimidine base pair(s). The loss of triplex stability due to the mismatch is partially overcome. The stability of triplexes formed at perfect and imperfect target sequences was investigated by UV thermal denaturation experiments. The stabilization provided by an internally incorporated acridine third strand oligonucleotide depends on the sequences flanking the inverted base pair. For triplexes containing a single mismatch the highest stabilization is observed for an acridine or a propanediol tethered to an acridine on its 3'-side facing an inverted A*T base pair and for a cytosine with an acridine incorporated to its 3'-side or a guanine with an acridine at its 5'-side facing an inverted G*C base pair. Fluorescence studies provided evidence that the acridine was intercalated into the triplex. The target sequences containing a double base pair inversion which form very unstable triplexes can still be recognized by oligonucleotides provided they contain an appropriately incorporated acridine facing the double mismatch sites. Selectivity for an A*T base pair inversion was observed with an oligonucleotide containing an acridine incorporated at the mismatched site when this site is flanked by two T*A*T base triplets. These results show that the range of DNA base sequences available for triplex formation can be extended by using oligonucleotide intercalator conjugates.
An Improved Green Fluorescent Protein Gene as a Vital Marker in Plants (1996)

A synthetic green fluorescent protein (GFP) gene (pgfp) was constructed to improve GFP expression in plants. Corn and tobacco protoplast transient assays showed that pgfp gave about 20-fold brighter fluorescence than the wild-type gene (gfp). Replacement of the serine at position 65 with a threonine (S65Tpgfp) or a cysteine (S65Cpgfp) yielded 100- to 120-fold brighter fluorescence than wild-type gfp upon excitation with 490-nm light. Incorporation of a plant intron into the coding region yielded an additional 1.4-fold improvement, for a cumulative improvement of about 150-fold in fluorescence at 490-nm excitation. Various versions of pgfp were also stably introduced into corn, wheat, tobacco, and Arabidopsis plants. Bright-green fluorescence was observed with a fluorescence microscope in virtually all examined tissues of transgenic monocots and dicots. In the case of Arabidopsis, expression of the pgfp gene under the enhanced 355 promoter of the cauliflower mosaic virus produced green fluorescence that was readily detectable by eye using a hand-held, long-wave ultraviolet lamp and/or a black-light source.
Two New Steroidal Saponins from the Rhizomes of Dioscorea panthaica and their Cytotoxic Activity (2001)

Two new steroidal saponins, dioscoresides C (1) and D (2), along with a new natural product, pregnadienolone 3-O-beta-gracillimatriose (3), and two known compounds, pregnadienolone 3-O-beta-chacotrioside (4) and pseudoprotodioscin (5), were isolated from the rhizomes of Dioscorea panthaica Prain et Burkill. On the basis of extensive NMR studies and chemical evidence, dioscoresides C and D were determined to be 26-O-beta-D-glucopyranosyl-3 beta,26-dihydroxy-23(S)-methoxy-25(R)-furosta-5,20(22)-dien-3-O-alpha-L-rhamnopyranosyl-(1-->2)-[alpha-L-rhamnopyranosyl-(1-->4)]-beta-D-glucopyranoside and 26-O-beta-D-glucopyranosyl-3 beta,26-dihydroxy-20,22-seco-25(R)-furosta-5-en-20,22-dine-3-O-alpha-L-rhamnopyranosyl-(1-->2)-[alpha-L-rhamnopyranosyl-(1--> 4)]-beta-D-glucopyranoside. These compounds showed mild cytotoxicity against the cancer cell lines, A375, L929, and HeLa, in a dose-dependent manner.
The Potential Link between Gut Microbiota and IgE-Mediated Food Allergy in Early Life (2013)

There has been a dramatic rise in the prevalence of IgE-mediated food allergy over recent decades, particularly among infants and young children. The cause of this increase is unknown but one putative factor is a change in the composition, richness and balance of the microbiota that colonize the human gut during early infancy. The coevolution of the human gastrointestinal tract and commensal microbiota has resulted in a symbiotic relationship in which gut microbiota play a vital role in early life immune development and function, as well as maintenance of gut wall epithelial integrity. Since IgE mediated food allergy is associated with immune dysregulation and impaired gut epithelial integrity there is substantial interest in the potential link between gut microbiota and food allergy. Although the exact link between gut microbiota and food allergy is yet to be established in humans, recent experimental evidence suggests that specific patterns of gut microbiota colonization may influence the risk and manifestations of food allergy. An understanding of the relationship between gut microbiota and food allergy has the potential to inform both the prevention and treatment of food allergy. In this paper we review the theory and evidence linking gut microbiota and IgE-mediated food allergy in early life. We then consider the implications and challenges for future research, including the techniques of measuring and analyzing gut microbiota, and the types of studies required to advance knowledge in the field.
ENHANZE® drug delivery technology: a novel approach to subcutaneous administration using recombinant human hyaluronidase PH20 (2019)

ENHANZE<sup>®</sup> drug delivery technology is based on the proprietary recombinant human hyaluronidase PH20 enzyme (rHuPH20; Halozyme Therapeutics, Inc.) that facilitates the subcutaneous (SC) delivery of co-administered therapeutics. rHuPH20 works by degrading the glycosaminoglycan hyaluronan (HA), which plays a role in resistance to bulk fluid flow in the SC space, limiting large volume SC drug delivery, dispersion, and absorption. Co-administration of rHuPH20 with partner therapies can overcome administration time and volume barriers associated with existing SC therapeutic formulations, and has been shown to reduce the burden on patients and healthcare providers compared with intravenous formulations. rHuPH20 (as HYLENEX<sup>®</sup> recombinant) is currently FDA-approved for subcutaneous fluid administration for achieving hydration, to increase the dispersion and absorption of other injected drugs, and in subcutaneous urography for improving resorption of radiopaque agents. rHuPH20 is also co-formulated with two anticancer therapies, trastuzumab (i.e. Herceptin<sup>®</sup> SC) and rituximab (i.e. RITUXAN HYCELA<sup>®</sup>/RITUXAN<sup>®</sup> SC/MabThera<sup>®</sup> SC) and dosed sequentially with human immunoglobin to treat primary immunodeficiency (i.e. HyQvia<sup>®</sup>/HYQVIA<sup>®</sup>). This article reviews pharmaceutical properties of rHuPH20, its current applications with approved therapeutics, and the potential for future developments.
Photothermal Heterodyne Imaging of Individual Nonfluorescent Nanoclusters and Nanocrystals (2004)

We introduce a new, highly sensitive, and simple heterodyne optical method for imaging individual nonfluorescent nanoclusters and nanocrystals. A 2 order of magnitude improvement of the signal is achieved compared to previous methods. This allows for the unprecedented detection of individual small absorptive objects such as metallic clusters (of 67 atoms) or nonluminescent semiconductor nanocrystals. The measured signals are in agreement with a calculation based on the scattering field theory from a photothermal-induced modulated index of refraction profile around the nanoparticle.
A Synthesis of Tetrahydrooxocrinine Methine (1965)

Tetrahydrooxocrinine methine (XLIII) has been synthesized by a sequence of reactions including ring enlargement of a tetralone (XXXVI) to a seven-membered nitrogenous ring compound (XXXVIII) by the use of Schmidt reaction.
Water photolysis at 12.3% efficiency via perovskite photovoltaics and Earth-abundant catalysts (2014)

Although sunlight-driven water splitting is a promising route to sustainable hydrogen fuel production, widespread implementation is hampered by the expense of the necessary photovoltaic and photoelectrochemical apparatus. Here, we describe a highly efficient and low-cost water-splitting cell combining a state-of-the-art solution-processed perovskite tandem solar cell and a bifunctional Earth-abundant catalyst. The catalyst electrode, a NiFe layered double hydroxide, exhibits high activity toward both the oxygen and hydrogen evolution reactions in alkaline electrolyte. The combination of the two yields a water-splitting photocurrent density of around 10 milliamperes per square centimeter, corresponding to a solar-to-hydrogen efficiency of 12.3%. Currently, the perovskite instability limits the cell lifetime.
A simple model of mechanotransduction in primate glabrous skin (2012)

Tactile stimulation of the hand evokes highly precise and repeatable patterns of activity in mechanoreceptive afferents; the strength (i.e., firing rate) and timing of these responses have been shown to convey stimulus information. To achieve an understanding of the mechanisms underlying the representation of tactile stimuli in the nerve, we developed a two-stage computational model consisting of a nonlinear mechanical transduction stage followed by a generalized integrate-and-fire mechanism. The model improves upon a recently published counterpart in two important ways. First, complexity is dramatically reduced (at least one order of magnitude fewer parameters). Second, the model comprises a saturating nonlinearity and therefore can be applied to a much wider range of stimuli. We show that both the rate and timing of afferent responses are predicted with remarkable precision and that observed adaptation patterns and threshold behavior are well captured. We conclude that the responses of mechanoreceptive afferents can be understood using a very parsimonious mechanistic model, which can then be used to accurately simulate the responses of afferent populations.
Analysis of DNA From Recurrent Genital Herpes Simplex Virus Isolates by Restriction Endonuclease Digestion (1986)

In a blind study, DNA from 40 clinical isolates of herpes simplex viruses was analyzed by restriction endonucleases to determine whether serial isolates from an individual patient could be identified and whether exogenous reinfection occurred within this population. Five of the 40 isolates served as controls. Based on restriction patterns obtained following Bam H1 cleavage of DNA, 35 isolates were assigned to 15 patients. Isolates from two patients displayed variation in the electrophoretic mobility of certain Bam H1 fragments. However, the isolates from one patient were identical when digested with four additional enzymes. One of three sequential isolates from a patient, when cleaved with Eco R1 and Hind III, showed variable fragments in the terminal and joint regions of the S segment of the genome. The appearance of the fragments was not due to the addition of a known restriction site. We conclude that exogenous reinfection with a genetically distinct strain of herpes simplex virus type 2 (HSV-2) did not occur among these 15 patients with recurrent genital HSV infections.
A rare CYP19 (aromatase) variant may increase the risk of breast cancer (1998)

The aromatase P450 (coded by the CYP19 gene) is responsible for the rate limiting step in the metabolism of C19 steroids to estrogens and is expressed in most breast carcinomas. A polymorphic tetranucleotide repeat (TTTA)n in intron 5, about 80 nucleotides downstream of exon 4 has previously been described. The allele frequencies of the polymorphic repeat were studied in series of 182 sporadic and 185 familial breast cancer patients as well as in 252 healthy control individuals. Five different alleles containing 7, 8, 9, 11 and 12-TTTA-repeats were detected. A relatively rare allele (A1) containing the longest repeat (TTTA)12 was found significantly more frequently in breast cancer patients than in control individuals. This indicates that individuals carrying the A1 allele of CYP19 may have an increased risk of developing breast cancer, OR 2.42 (95% confidence interval [CI] 1.03-5.80). The higher frequency was observed in both sporadic and familial patients, although when each of the groups was compared to the control group only a borderline significance was seen. A higher frequency of A1 allele carriers was also found in the group of patients with positive estrogen receptor and progesterone receptor positive tumors. These data suggest that the CYP19 gene may be involved as a low penetrance gene in breast cancer susceptibility.
The species specificity of growth hormone requires the cooperative interaction of two motifs (2000)

Primate growth hormones (GH) activate both primate and non-primate somatotrophic receptors (GH receptors), but non-primate GHs do not activate primate GH receptors. Previous studies argued the interaction of Asp(171) of human GH and Arg(43) of the receptor produced an attractive ionic interaction. In non-primate GHs, His(170) replaces the homologous Asp(171), producing a repulsive interaction with Arg(43) of the primate receptor which was believed to reduce the attraction of non-primate GH for the human GH receptor, thus providing species specificity. In this report, H170D bovine GH had activity and affinity for human GH receptors approaching those of human GH. In contrast, replacing Asp(171) of human GH with His did not significantly reduce somatotrophic activity, indicating that species specificity is not wholly explained by this residue's interaction with Arg(43) of the receptor. Deletion of either Phe(44) (a residue present only in primate GHs) or residues 32-46 (20-kDa form of human GH) each only marginally reduced somatotrophic activities. But the combination of the D171H mutation with either DeltaPhe(44) or Delta32-46 in human GH reduced binding and activity in a greater than additive fashion, indicated a functional interaction between these distant structural features. In bovine GH addition of phenylalanine at position 44 increased the somatotrophic activity and receptor affinity in cells containing the human GH receptor. The combination of the H170D mutation and the addition of phenylalanine at position 44 created a bovine GH with activity indistinguishable from wild-type human GH. Based on evidence from both bovine and human GHs, the cooperative interaction of these two distant motifs determined the species specificity and indicated that structural plasticity was a critical feature necessary for the species specificity of somatotrophic activity.
Centrifugal microfluidic platforms: advanced unit operations and applications (2015)

Centrifugal microfluidics has evolved into a mature technology. Several major diagnostic companies either have products on the market or are currently evaluating centrifugal microfluidics for product development. The fields of application are widespread and include clinical chemistry, immunodiagnostics and protein analysis, cell handling, molecular diagnostics, as well as food, water, and soil analysis. Nevertheless, new fluidic functions and applications that expand the possibilities of centrifugal microfluidics are being introduced at a high pace. In this review, we first present an up-to-date comprehensive overview of centrifugal microfluidic unit operations. Then, we introduce the term "process chain" to review how these unit operations can be combined for the automation of laboratory workflows. Such aggregation of basic functionalities enables efficient fluidic design at a higher level of integration. Furthermore, we analyze how novel, ground-breaking unit operations may foster the integration of more complex applications. Among these are the storage of pneumatic energy to realize complex switching sequences or to pump liquids radially inward, as well as the complete pre-storage and release of reagents. In this context, centrifugal microfluidics provides major advantages over other microfluidic actuation principles: the pulse-free inertial liquid propulsion provided by centrifugal microfluidics allows for closed fluidic systems that are free of any interfaces to external pumps. Processed volumes are easily scalable from nanoliters to milliliters. Volume forces can be adjusted by rotation and thus, even for very small volumes, surface forces may easily be overcome in the centrifugal gravity field which enables the efficient separation of nanoliter volumes from channels, chambers or sensor matrixes as well as the removal of any disturbing bubbles. In summary, centrifugal microfluidics takes advantage of a comprehensive set of fluidic unit operations such as liquid transport, metering, mixing and valving. The available unit operations cover the entire range of automated liquid handling requirements and enable efficient miniaturization, parallelization, and integration of assays.
Synthesis, central nervous system activity and teratogenicity of a homothalidomide. (1990)

The optical isomers of alpha-phthalimidoadipinimide (1) were synthesized by a route based on D(+)- and L(-)-amino-epsilon-caprolactam (5) as synthon. The isomers of 1 were obtained in high yields by treating D(+)- and L(-)-amino-epsilon-caprolactam (5) with N-carboethoxyphthalimide (4), followed by oxidation with benzeneseleninic anhydride (7). The teratogenic potency of both isomers of 1 was studied by the HET-(Hen's Egg Test); 1 caused distinctly lower teratogenic effects in contrast to thalidomide (2). D(-)-1 and L(+)-1 showed sedative effects with a lower activity than 2. Both are more stable in alkaline solution at the same time with a smaller tendency for racemization.
Catching bad guys with graph mining (2011)

Suspicious network patterns may be the key to detecting criminals and fraudsters on e-commerce sites.
Selection of Smart Small-Molecule Ligands: The Proof of Principle (2008)

The development of drugs and diagnostics with desirable characteristics requires smart small-molecule ligandsligands with predefined binding parameters of interaction with the target. Here, we propose a general approach for selection of such ligands from highly diverse combinatorial libraries of small molecules by methods of kinetic capillary electrophoresis (KCE). We deduct three fundamental requirements for the combinatorial library to suit the KCE-based selection of smart ligands and suggest a universal design of the library for selecting smart small-molecule ligands: every small molecule in the library is tagged with DNA that encodes the structure of the molecule. Finally, we use several DNA-tagged small molecules, which represent a hypothetical library, to prove experimentally selection of smart small-molecule ligands by the proposed approach.
Conjugation with (111)In-DTPA-poly(ethylene glycol) improves imaging of anti-EGF receptor antibody C225. (2001)

These findings indicate that (111)In-DTPA-PEG-C225 selectively localized to the tumors expressing high levels of EGFR. PEG-modification of C225 significantly reduced its liver uptake, resulting in improved visualization of EGFR-positive tumors. Using PEG as a linker between the monoclonal antibody and metal chelator is a useful strategy to optimize the imaging characteristics of antibody-based scintigraphic agents.
Immunochemical Protocols (1992)

Molecular biologists can no longer afford to be experts in only one par ticular area. They need to be equally competent at handling DNA, RNA, and proteins, moving from one area to another as required
High Resolution Crystal Structure of Pyruvate Decarboxylase from Zymomonas mobilis (1998)

The crystal structure of tetrameric pyruvate decarboxylase from Zymomonas mobilis has been determined at 1.9 A resolution and refined to a crystallographic R-factor of 16.2% and Rfree of 19.7%. The subunit consists of three domains, all of the alpha/beta type. Two of the subunits form a tight dimer with an extensive interface area. The thiamin diphosphate binding site is located at the subunit-subunit interface, and the cofactor, bound in the V conformation, interacts with residues from the N-terminal domain of one subunit and the C-terminal domain of the second subunit. The 2-fold symmetry generates the second thiamin diphosphate binding site in the dimer. Two of the dimers form a tightly packed tetramer with pseudo 222 symmetry. The interface area between the dimers is much larger in pyruvate decarboxylase from Z. mobilis than in the yeast enzyme, and structural differences in these parts result in a completely different packing of the subunits in the two enzymes. In contrast to other pyruvate decarboxylases, the enzyme from Z. mobilis is not subject to allosteric activation by the substrate. The tight packing of the dimers in the tetramer prevents large rearrangements in the quaternary structure as seen in the yeast enzyme and locks the enzyme in an activated conformation. The architecture of the cofactor binding site and the active site is similar in the two enzymes. However, the x-ray analysis reveals subtle but significant structural differences in the active site that might be responsible for variations in the biochemical properties in these enzymes.
Atomic Layer Deposition of ZrO2 Thin Films with High Dielectric Constant on TiN Substrates (2008)

thin films were grown on substrates by atomic layer deposition. A high dielectric constant was obtained due to the formation of a high-temperature crystalline form, tetragonal or cubic. The origin of the formation of the high-temperature form was examined by depositing films on two types of surfaces, anatase and rutile. Tetragonal or cubic films were formed on both substrates. This suggests that growth-controlled selection is responsible for the formation of the metastable phase , not the minimization of interfacial energy.