gebhart/patrepeval huggingface dataset:
Discovery of Novel, Dual Mechanism ERK Inhibitors by Affinity Selection Screening of an Inactive Kinase (2014)

An affinity-based mass spectrometry screening technology was used to identify novel binders to both nonphosphorylated and phosphorylated ERK2. Screening of inactive ERK2 identified a pyrrolidine analogue 1 that bound to both nonphosphorylated and phosphorylated ERK2 and inhibited ERK2 kinase activity. Chemical optimization identified compound 4 as a novel, potent, and highly selective ERK1,2 inhibitor which not only demonstrated inhibition of phosphorylation of ERK substrate p90RSK but also demonstrated inhibition of ERK1,2 phosphorylation on the activation loop. X-ray cocrystallography revealed that upon binding of compound 4 to ERK2, Tyr34 undergoes a rotation (flip) along with a shift in the poly-Gly rich loop to create a new binding pocket into which 4 can bind. This new binding mode represents a novel mechanism by which high affinity ATP-competitive compounds may achieve excellent kinase selectivity.
1-Oxo-2-oxa-1-phosphabicyclo[2.2.2]octane:  A New Mechanistic Probe for the Basic Hydrolysis of Phosphate Esters (1996)

Synthesis of the title compound 2 was accomplished in a multistep sequence starting from hypophosphorous acid. In strong base, the bicyclic phosphinate 2 hydrolyzes 2 orders of magnitude faster than the bicyclic phosphate OP(OCH2)3CCH3 (1a) and the acceleration is entirely enthalpic. This rate enhancement is attributed to the greater ease with which 2 achieves the five-coordinate transition state. The molecular structure of 2, determined by X-ray means, compared with that of 1a reveals no evidence of strain within either bicyclic framework. The observed acceleration does not support the contribution of a stereoelectronic effect in the hydrolysis of six-membered ring phosphates.
Gabapentin: An Alternative to the Cyclooxygenase-2 Inhibitors for Perioperative Pain Management (2005)

The cyclooxygenase-2 inhibitor, rofecoxib, was a popular analgesic adjuvant for improving perioperative pain management. We designed this placebo-controlled study to test the hypothesis that gabapentin could produce similar reductions in postoperative pain and opioid analgesic usage, thereby improving the recovery process. One hundred patients undergoing abdominal hysterectomy procedures were randomly assigned to one of four treatment groups: 1) control group received placebo capsules and pills before and for 2 days after surgery, 2) rofecoxib group received 50 mg/d PO and placebo capsules before and after surgery and, 3) gabapentin group received 1.2 g/d PO and placebo pills before and after surgery, and 4) combination group received rofecoxib 50 mg/d and gabapentin 1.2 g/d PO before and after surgery. The anesthetic technique was standardized and the postoperative assessments included verbal rating scales for pain and sedation, IV morphine usage, quality of recovery assessment, recovery of bowel function, resumption of normal activities, and patient satisfaction with their pain management. Postoperative pain scores were significantly reduced in all three analgesic treatment groups (versus control group). Compared with the control group, patient-controlled analgesia morphine usage was also significantly reduced in the 3 analgesic treatment groups at 1, 8, 24, and 30 h after surgery. Total PCA morphine usage was decreased by 43%, 24%, and 50% in groups 2, 3, and 4, respectively, compared with group 1. Oral analgesic consumption was also smaller in groups 2 and 4 when compared with the control group. The opioid-sparing effects of rofecoxib and gabapentin lead to a faster recovery of bowel function. Discharge eligibility scores in groups 2 and 4 were improved at 24 h when compared with group 1, and patient satisfaction with postoperative pain management was significantly higher at 24 h in all 3 analgesic treatment groups. At the 72 h follow-up, all of the patients in group 4 were completely satisfied with their pain management compared with only 32%, 64%, and 72% in groups 1, 2, and 3, respectively. Gabapentin (1.2 g/d PO) appears to be an acceptable alternative to rofecoxib (50 mg/d PO) for short-term use as an adjuvant to opioid analgesics in patients undergoing lower abdominal surgery.
Purification, characterization, and properties of an aryl aldehyde oxidoreductase from Nocardia sp. strain NRRL 5646 (1997)

An aryl aldehyde oxidoreductase from Nocardia sp. strain NRRL 5646 was purified 196-fold by a combination of Mono-Q, Reactive Green 19 agarose affinity, and hydroxyapatite chromatographies. The purified enzyme runs as a single band of 140 kDa on sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The molecular mass was estimated to be 163 +/- 3.8 kDa by gel filtration, indicating that this enzyme is a monomeric protein. The binding of the enzyme to Reactive Green 19 agarose was Mg2+ dependent. The binding capacity was estimated to be about 0.2 mg of Reactive Green agarose per ml in the presence of 10 mM MgCl2. This enzyme can catalyze the reduction of a wide range of aryl carboxylic acids, including substituted benzoic acids, phenyl-substituted aliphatic acids, heterocyclic carboxylic acids, and polyaromatic ring carboxylic acids, to produce the corresponding aldehydes. The Km values for benzoate, ATP, and NADPH were determined to be 645 +/- 75, 29.3 +/- 3.1, and 57.3 +/- 12.5 microM, respectively. The Vmax was determined to be 0.902 +/- 0.04 micromol/min/mg of protein. Km values for (S)-(+)-alpha-methyl-4-(2-methylpropyl)-benzeneacetic acid (ibuprofen) and its (R)-(-) isomer were determined to be 155 +/- 18 and 34.5 +/- 2.5 microM, respectively. The Vmax for the (S)-(+) and (R)-(-) isomers were 1.33 and 0.15 micromol/min/mg of protein, respectively. Anthranilic acid is a competitive inhibitor with benzoic acid as a substrate, with a Ki of 261 +/- 30 microM. The N-terminal and internal amino acid sequences of a 76-kDa peptide from limited alpha-chymotrypsin digestion were determined.
Effect of tumor promoting contraceptive steroids on growth and drug metabolizing enzymes in rat liver. (1986)

Liver tumor formation in rats treated with oral contraceptive steroids for long periods has been associated with the tumor promoting potential of these agents. As other known liver tumor promoters, e.g., phenobarbital and hexachlorocyclohexane, induce liver growth and hepatic monooxygenases, we investigated whether or not estrogens have similar effects. Female rats were treated with a wide range of doses of ethinylestradiol, including human contraceptive doses, which are approximately 1 microgram/kg. The physiological estrogen estradiol was studied for comparison. Also included were norethynodrel and norethisteron and its acetate and enanthate because these human progestins act predominantly estrogenic in rats. Daily s.c. doses of ethinylestradiol (0.5 mg/kg) produced a rapid increase of liver mass, DNA, RNA, and protein which was almost maximal after 7 days. The percentages of parenchymal cells involved in DNA synthesis and mitosis were enhanced up to 20-fold, suggesting parenchymal hyperplasia as the main cause of liver growth. Sinus wall cells showed a proportionate increase of number and DNA synthesis. Likewise, all other steroids tested produced significant increases of liver mass and DNA. For ethinylestradiol and estradiol extrapolated threshold doses were in the range of 1 microgram/kg. These doses are below those used in previous tumor promotion studies in rats. Using 5 different substrates to check monooxygenase activities of isolated liver microsomes, no induction or only very weak induction by estrogens was found. These studies suggest that induction of liver growth may be a property relevant for the tumor promoting activity of estrogens; in contrast, induction of hepatic monooxygenases does not appear to be necessary for liver tumor promotion in the rat.
Functional agonism of insect odorant receptor ion channels (2011)

In insects, odor cues are discriminated through a divergent family of odorant receptors (ORs). A functional OR complex consists of both a conventional odorant-binding OR and a nonconventional coreceptor (Orco) that is highly conserved across insect taxa. Recent reports have characterized insect ORs as ion channels, but the precise mechanism of signaling remains unclear. We report the identification and characterization of an Orco family agonist, VUAA1, using the Anopheles gambiae coreceptor (AgOrco) and other orthologues. These studies reveal that the Orco family can form functional ion channels in the absence of an odor-binding OR, and in addition, demonstrate a first-in-class agonist to further research in insect OR signaling. In light of the extraordinary conservation and widespread expression of the Orco family, VUAA1 represents a powerful new family of compounds that can be used to disrupt the destructive behaviors of nuisance insects, agricultural pests, and disease vectors alike.
The use of targeted muscle reinnervation for improved myoelectric prosthesis control in a bilateral shoulder disarticulation amputee (2004)

A novel method for the control of a myoelectric upper limb prosthesis was achieved in a patient with bilateral amputations at the shoulder disarticulation level. Four independently controlled nerve-muscle units were created by surgically anastomosing residual brachial plexus nerves to dissected and divided aspects of the pectoralis major and minor muscles. The musculocutaneous nerve was anastomosed to the upper pectoralis major; the median nerve was transferred to the middle pectoralis major region; the radial nerve was anastomosed to the lower pectoralis major region; and the ulnar nerve was transferred to the pectoralis minor muscle which was moved out to the lateral chest wall. After five months, three nerve-muscle units were successful (the musculocutaneous, median and radial nerves) in that a contraction could be seen, felt and a surface electromyogram (EMG) could be recorded. Sensory reinnervation also occurred on the chest in an area where the subcutaneous fat was removed. The patient was fitted with a new myoelectric prosthesis using the targeted muscle reinnervation. The patient could simultaneously control two degrees-of-freedom with the experimental prosthesis, the elbow and either the terminal device or wrist. Objective testing showed a doubling of blocks moved with a box and blocks test and a 26% increase in speed with a clothes pin moving test. Subjectively the patient clearly preferred the new prosthesis. He reported that it was easier and faster to use, and felt more natural.
Nusinersen versus Sham Control in Later-Onset Spinal Muscular Atrophy (2018)

Among children with later-onset SMA, those who received nusinersen had significant and clinically meaningful improvement in motor function as compared with those in the control group. (Funded by Biogen and Ionis Pharmaceuticals; CHERISH ClinicalTrials.gov number, NCT02292537 .).
Triggering of the proteinase dipeptidyl peptidase IV (CD26) amplifies human T lymphocyte proliferation (1991)

CD26 (Ta1, dipeptidyl peptidase IV) is a Mr 105,000 protein expressed at high levels on activated T lymphocytes and is a potential marker of memory T cells. Reciprocal immunodepletion and solid phase double determinant binding studies showed that mAb AC7 and the CD26-specific mAb anti-Ta1 reacted with spatially distinct sites on the same molecule. The proteinase dipeptidyl peptidase IV (DPP IV) was immunoprecipitated with mAb AC7 and its enzymatic activity directly assayed using an enzyme overlay membrane system. High levels of DPP IV activity were detected on the T cell tumor line CCRF-HSB-2 and on PBMC stimulated by a variety of methods. By itself, soluble mAb AC7 was not mitogenic for T cells but enhanced T cell proliferation that resulted from treatment with phorbol myristic acetate (PMA) in the presence of accessory cells. T cell proliferation was also induced by co-immobilized mAb AC7 and mAb OKT3 (anti-CD3). Cultures of T cells growing in the presence of IL-2 responded with accelerated growth when exposed to a combination of immobilized mAb AC7 and soluble mAb OKT3, a result not seen with freshly isolated T cells.
Electrolyte system for fast preparative focusing in wide pH range based on bidirectional isotachophoresis (2014)

In this paper, we suggest new electrolyte system for fast preparative electrofocusing in wide pH range. It is based on bidirectional ITP with multiple counterions and spacers created by commercially available defined simple buffers. The migration course of proposed focusing model can be simulated in advance by using separation conditions and electrolyte components that are consequently applied during the experiments. The suggested electrolyte system allows high current densities at the initial stages of focusing without danger of local overheating, which strongly reduces the time needed for analysis completion. The performance of the electrolyte system is demonstrated by the focusing of synthetic colored low molecular weight indicators and proteins in the arrangements with both linear narrow strip and nonwoven fabric sheet with continuous flow.
Carbohydrate Modifications in Antisense Research (1994)

This book presents a review of recent developments and progress in the carbohydrate-related chemistry of novel nucleic acid mimics and their applications in antisense therapeutics. In recent years, significant advances have been made in understanding the essential elements of designing more effective antisense molecules. One of the main focal points has been on the modifications of the carbohydrate portion of an oligonucleotide to achieve stability towards nuclease degradation and to enhance the binding affinity for a given target. The successes and failures of this research in our laboratory and others are discussed. The possible future directions of research in carbohydrate-related modifications of antisense molecules are projected. The focus on potential improvements in stability against cellular nucleases, affinity towards designated targets, and cellular uptake of these novel oligomers remains a high priority.
The use of precolumns for solvent focusing in capillary column gas chromatography (1994)

Abstract In trace analysis by capillary GC it is often desirable to use larger than normal injection volumes to obtain sufficient sensitivity. This, however, results in a wider solvent peak and tailing, and may reduce column efficiency. This paper describes the use of a short length of a capillary precolumn coated with a stationary phase of polarity similar to that of the sample solvent and a film thickness greater than that of the analytical column; provided the right combination of polarities of injection solvent and liquid phases are used, the precolumn focuses the solvent band, thereby enabling the maximum injection volume to be increased without measurably reducing efficiency. Typical precolumn dimensions are 1 m length, 0.32 mm i.d., and 0.5 μm stationary phase film thickness. Using a precolumn increases the maximum injection volume up to 8 or 10 μl, or three times that appropriate for a conventional analytical column, with little or no loss in efficiency.
On a Path to Unfolding the Biological Mechanisms of Orthodontic Tooth Movement (2009)

Orthodontic forces deform the extracellular matrix and activate cells of the paradental tissues, facilitating tooth movement. Discoveries in mechanobiology have illuminated sequential cellular and molecular events, such as signal generation and transduction, cytoskeletal re-organization, gene expression, differentiation, proliferation, synthesis and secretion of specific products, and apoptosis. Orthodontists work in a unique biological environment, wherein applied forces engender remodeling of both mineralized and non-mineralized paradental tissues, including the associated blood vessels and neural elements. This review aims at identifying events that affect the sequence, timing, and significance of factors that determine the nature of the biological response of each paradental tissue to orthodontic force. The results of this literature review emphasize the fact that mechanoresponses and inflammation are both essential for achieving tooth movement clinically. If both are working in concert, orthodontists might be able to accelerate or decelerate tooth movement by adding adjuvant methods, whether physical, chemical, or surgical.
Development of hot-pressed and chemical-vapor-deposited zinc sulfide and zinc selenide in the United States for optical windows (2007)

By the mid 1950s, there was a need for infrared-transmitting materials with improved optical and mechanical characteristics for military and commercial instruments. The newly invented "heat-seeking" missile also required a more durable infrared-transmitting dome. Some properties of ZnS were known from studies of natural minerals. More properties of pure ZnS and ZnSe were measured with single crystals grown in Air Force and industrial laboratories in the 1950s. In 1956, a team led by William Parsons at the Eastman Kodak Hawk-Eye Works in Rochester, New York began to apply the technique of hot pressing to make infrared-transmitting ceramics from powders. This work led to commercial production of six materials, including ZnS (IRTRAN® 2) and ZnSe (IRTRAN® 4) in the 1960s. Because the hot pressed materials could not be made in very large sizes and suffered from undesirable optical losses, the Air Force began to look for alternative manufacturing methods around 1970. Almost immediately, highly successful materials were produced by chemical vapor deposition under Air Force sponsorship by a team led by James Pappis at the Raytheon Research Division in Waltham, Massachusetts. Chemical-vapor-deposited materials replaced hot pressed materials in most applications within a few years. From a stream of Air Force contracts in the 1970s and early 1980s, Raytheon produced two different grades of ZnS for windows and domes, one grade of ZnSe for high-energy CO<sub>2</sub> laser windows, and a composite ZnS/ZnSe window for aircraft sensor pods. In 1980, a competitor called CVD, Inc., was formed by Robert Donadio, who came from the Raytheon Research Division. CVD began with a license from Raytheon, but soon sued Raytheon, arguing that the license violated the Sherman Antitrust Act. Raytheon countersued for breach of employment contracts and misappropriation of trade secrets. In 1984, a jury ruled in favor of CVD, which went on to build a lucrative business in ZnSe and ZnS. CVD was eventually purchased, first by Morton, and later by Rohm & Haas. II-VI, Inc. was formed in 1971 by Carl J. Johnson and James E. Hawkey to produce CdTe optics for industrial CO<sub>2</sub> lasers. When Raytheon introduced ZnSe into the market in 1974, it was obvious that ZnSe was superior to CdTe, so II-VI purchased ZnSe from Raytheon to produce optical components. The supply of ZnSe was never stable enough for II-VI, which therefore began its own effort to deposit ZnSe in 1975. In 1980, II-VI became an investor in and customer of CVD, Inc., buying a substantial portion of the ZnSe that could be supplied by both Raytheon and CVD. Still pressed to meet customer demand, II-VI built its first ZnSe production furnace in the period 1983-1986. A second furnace came on line in 1988 and two more were operational by 1990. Finally attaining excess capacity, II-VI became a supplier of ZnS as well as ZnSe. In 1990, Raytheon exited the ZnS and ZnSe business, leaving it mainly to CVD and II-VI.
Overexpression of the SR proteins ASF/SF2 and SC35 influences alternative splicing in vivo in diverse ways. (1995)

The SR proteins are a family of essential splicing factors highly conserved throughout metazoa. Here we examine the effects of two prototypical SR proteins, ASF/SF2 and SC35, when overexpressed by transfection in cultured cells together with plasmids encoding alternatively spliced model transcripts. As expected from past work, both proteins were found to affect alternative splicing, but differences as well as similarities in their behavior were observed. With adenovirus E1a pre-mRNA, ASF/SF2 caused shifts in alternative splicing similar to those observed previously, and the effects of mutations, in the protein and the pre-mRNA, were largely consistent with in vitro results. For example, the C-terminal RS domain was not required to alter splice site selection. SC35 overexpression also altered E1a splicing, but the pattern was distinct from that detected with ASF/SF2, indicating that the two proteins can function differently in vivo. Unexpectedly, with SV40 early pre-mRNA, overexpression of either protein resulted in a marked inhibition of splicing, with the downstream small t 5' splice site more sensitive than the upstream large T 5' splice site. This is essentially the opposite of what has been observed when the concentration of these proteins is increased in vitro. The RS domain was necessary but not sufficient for this effect. Finally, overexpression of SC35, but not ASF/SF2, resulted in substantial accumulation of the unspliced SV40 pre-mRNA, which was efficiently transported to the cytoplasm. This finding suggests that SC35 may play an unanticipated role in mRNA stability and/or transport.
On a General Relation Involving the Glass Temperature and Coefficients of Expansion of Polymers (1962)

Treating the glass temperature TG of polymers as an iso-free volume state allows one to derive the result (αL—αG). TG=K1, a constant; or the approximate result αLTG=K2, another constant. The α's are the coefficients of cubical expansion for 100% amorphous polymer above and below TG. K1 is 0.113 for a wide variety of polymers differing in cohesive energy density, chain stiffness, and geometry. We thus have a general criterion for TG. K2 is 0.164. This latter relation combined with the principle of corresponding states, results in an expression for Tg as a function of cohesive energy density and chain rigidity. The polyalkyl methacrylates which have side-chain transitions below TG follow the first equation if αG is replaced by αG′, the expansion coefficient below the side-chain transition. Polymer-solvent systems are similar to the polyalkylmethacrylates. Two additional products, αL·TM and ΔCP·TG, where TM is the melting point of the polymer and ΔCP is the jump in specific heat at TG, are approximately constant.
Brain-targeted delivery of paclitaxel using glutathione-coated nanoparticles for brain cancers (2011)

Paclitaxel is not effective for treatment of brain cancers because it cannot cross the blood-brain barrier (BBB) due to efflux by P-glycoprotein (P-gp). In this work, glutathione-coated poly-(lactide-co-glycolide) (PLGA) nanoparticles (NPs) of paclitaxel were developed for brain targeting for treatment of brain cancers. P-gp ATPase assay was used to evaluate the NP as potential substrates. The NP showed a particle size suitable for BBB permeation (particle size around 200 nm) and higher cellular uptake of the NP was demonstrated in RG2 cells. The P-gp ATPase assay suggested that the NP were not substrate for P-gp and would not be effluxed by P-gp present in the BBB. The in vitro release profile of the NP exhibited no initial burst release and showed sustained drug release. The proposed coated NP showed significantly higher cytotoxicity in RG2 cells compared with uncoated NP (p ≤ 0.05). Tubulin immunofluorescent study showed higher cell death by the NP due to increased microtubule stabilization. In vivo brain uptake study in mice showed higher brain uptake of the NP containing coumarin-6 compared with solution. The proposed brain-targeted NP delivery of paclitaxel could be an effective treatment for the brain cancers.