gebhart/patrepeval huggingface dataset:
Estrogen-Receptor Biology: Continuing Progress and Therapeutic Implications (2005)

Endocrine therapies, first used more than 100 years ago, are the most effective treatments for breast cancers expressing the estrogen receptor (ER). All endocrine therapies are designed to block ER function in some way, thereby making them the first targeted therapies used for cancer. Selective ER modulators (SERMs) such as tamoxifen bindERandpartially block its activity.Ovarian ablation, luteinizing hormone–releasing hormone agonists, and aromatase inhibitors reduce the level of estrogen and inhibit ligand-induced activation of ER. Steroidal antiestrogens such as fulvestrant bind ER, more completely block its function, and induce receptor degradation.While all of these therapies are effective in certain patients, de novo and acquired resistance remain major problems. New information on the biology of ER provides insight into the mechanisms of treatment resistance and new strategies to overcome it, thereby potentially making these therapies even more effective.
Single-step purification of Proteus mirabilis urease accessory protein UreE, a protein with a naturally occurring histidine tail, by nickel chelate affinity chromatography (1994)

Proteus mirabilis urease, a nickel metalloenzyme, is essential for the virulence of this species in the urinary tract. Escherichia coli containing cloned structural genes ureA, ureB, and ureC and accessory genes ureD, ureE, ureF, and ureG displays urease activity when cultured in M9 minimal medium. To study the involvement of one of these accessory genes in the synthesis of active urease, deletion mutations were constructed. Cultures of a ureE deletion mutant did not produce an active urease in minimal medium. Urease activity, however, was partially restored by the addition of 5 microM NiCl2 to the medium. The predicted amino acid sequence of UreE, which concludes with seven histidine residues among the last eight C-terminal residues (His-His-His-His-Asp-His-His-His), suggested that UreE may act as a Ni2+ chelator for the urease operon. To exploit this potential metal-binding motif, we attempted to purify UreE from cytoplasmic extracts of E. coli containing cloned urease genes. Soluble protein was loaded onto a nickel-nitrilotriacetic acid column, a metal chelate resin with high affinity for polyhistidine tails, and bound protein was eluted with a 0 to 0.5 M imidazole gradient. A single polypeptide of 20-kDa apparent molecular size, as shown by sodium dodecyl sulfate-10 to 20% polyacrylamide gel electrophoresis, was eluted between 0.25 and 0.4 M imidazole. The N-terminal 10 amino acids of the eluted polypeptide exactly matched the deduced amino acid sequence of P. mirabilis UreE. The molecular size of the native protein was estimated on a Superdex 75 column to be 36 kDa, suggesting that the protein is a dimer. These data suggest that UreE is a Ni(2)+-binding protein that is necessary for synthesis of a catalytically active urease at low Ni(2+) concentrations.
“Click” synthesis of small molecule probes for activity-based fingerprinting of matrix metalloproteases (2006)

By using "Click Chemistry", we achieved the facile synthesis of various affinity-based hydroxamate probes that enable generation of activity-based fingerprints of a variety of metalloproteases, including matrix metalloproteases (MMPs), in proteomics experiments.
Interaction of monoclonal antibodies with cell surface antigens of human ovarian carcinomas. (1984)

Two monoclonal antibodies, OC 125 and OC 133, bind to distinct determinants on the surface of human epithelial ovarian carcinoma cell lines. OC 125 and OC 133 recognize determinants on molecules with molecular weights greater than 200,000 and 80,000, respectively. When binding to four different cell lines was compared, apparent affinity constants for OC 125 ranged from 3.1 X 10(9) to 6.0 X 10(7) M-1, whereas those for OC 133 ranged from 1.6 X 10(9) to 8.5 X 10(8) M-1. An estimate of the number of antigenic determinants per cell ranged from 1.0 X 10(7) to 2.8 X 10(5) for OC 125 and from 4.0 X 10(5) to 3.4 X 10(4) for OC 133. Antigenic determinants recognized by OC 125 and OC 133 could be detected in spent culture medium. When radiolabeled OC 125 was incubated with each of four ovarian tumor cell lines, approximately 90% of the antibody remained bound to the tumor cell surfaces for more than 20 hr. Similar binding of OC 133 was observed with three of the four ovarian tumor cell lines. By contrast, greater than 70% of OC 133 antibody was either shed or endocytosed after binding to OVCA 433 cells over the same period. Antigenic modulation was not induced by either antibody interacting with any of the four cell lines. These data suggest that antigen may be lost from the surface of human ovarian carcinoma cells by several different mechanisms and that antigen release is not inconsistent with binding of radiolabeled antibody to the tumor cell surface for prolonged periods.
Pasture response to gibberellins: A review and recommendations (2009)

Abstract Gibberellins are plant hormones that activate dormant enzyme systems. Applied to pasture, they can stimulate out‐of‐season growth or accelerate growth through reserve mobilisation, leaf and stem elongation, and promotion of flowering. When evaluating gibberellin as a potential pasture production stimulant, historical investigations frequently used rates ranging from 25–700 g/ha of active ingredient. Responses were found to be uneconomic, and there were often side effects including a decrease in tillering, decreased root mass, and a yield depression subsequent to the initial response. With gibberellic acid now available from China at comparatively cheaper prices than applied historically, and emerging understanding that application rates as low as 5–10 g/ha active ingredient can produce more cost‐effective responses, possibly with reduced side effects, there is renewed interest in gibberellin use to increase winter and spring pasture production or manipulate seasonality of production. Arationale for delivery of extension advice is presented.
Accurate Camera Calibration with New Minimizing Function (2006)

Camera calibration has been studied extensively in computer vision and photogrammetry. But almost all the camera calibration techniques iterate with the general minimizing function by minimizing the discrepancy between the real position in pixels of a 2D image point and the calculated projection of the 3D object point on the image plane. Though the imaging distance errors are equal, the spatial anti-projection distance errors are not identical at different distance before the camera. As far as vision measurement system, its final object is to obtain the accurate space coordinate of the measured point. Theoretically, the space point should on the optical ray generated by its projection image point and the center of camera. To satisfy the special request of vision measurement system for camera calibration parameters, we present a valid camera calibration method based on new minimizing function using high precision virtual stereo calibration pattern, which is formed by moving an infrared light-emitting diode (IR LED) feature point with CMM on pre-defined paths. Radial distortion and decentering distortion are molded. The proposed technique consists of linear optimization parameter estimation and nonlinear refinement, which is carried out by minimizing the distance of all the 3D space points from the corresponding optical ray generated by their projections image points and the center of camera. Simulated data and real data are both shown that the calibration precision of the proposed method is better than that of the general minimizing the distance between the imaged points and the modeled projections. This method considerable reduces the distance of all the 3D space points from the corresponding optical ray generated from their projections image points and the center of camera, enhances the precision of camera calibration parameters, and improves the precision of the vision measurement system.
Identification of residues of the H-ras protein critical for functional interaction with guanine nucleotide exchange factors. (1994)

Ras proteins are activated in vivo by guanine nucleotide exchange factors encoded by genes homologous to the CDC25 gene of Saccharomyces cerevisiae. We have taken a combined genetic and biochemical approach to probe the sites on Ras proteins important for interaction with such exchange factors and to further probe the mechanism of CDC25-catalyzed GDP-GTP exchange. Random mutagenesis coupled with genetic selection in S. cerevisiae was used to generate second-site mutations within human H-ras-ala15 which could suppress the ability of the Ala-15 substitution to block CDC25 function. We transferred these second-site suppressor mutations to normal H-ras and oncogenic H-rasVal-12 to test whether they induced a general loss of function or whether they selectively affected CDC25 interaction. Four highly selective mutations were discovered, and they affected the surface-located amino acid residues 62, 63, 67, and 69. Two lines of evidence suggested that these residues may be involved in binding to CDC25: (i) using the yeast two-hybrid system, we demonstrated that these mutants cannot bind CDC25 under conditions where the wild-type H-Ras protein can; (ii) we demonstrated that the binding to H-Ras of monoclonal antibody Y13-259, whose epitope has been mapped to residues 63, 65, 66, 67, 70, and 73, is blocked by the mouse sos1 and yeast CDC25 gene products. We also present evidence that the mechanism by which CDC25 catalyzes exchange is more involved than simply catalyzing the release of bound nucleotide and passively allowing nucleotides to rebind. Most critically, a complex of Ras and CDC25 protein, unlike free Fas protein, possesses significantly greater affinity for GTP than for GDP. Furthermore, the Ras CDC25 complex is more readily dissociated into free subunits by GTP than it is by GDP. Both of these results suggest a function for CDC25 in promoting the selective exchange of GTP for GDP.
Contractile activity and passive stretch regulate tubulin mRNA and protein content in cardiac myocytes (1996)

Accumulation of tubulin protein and an increased array of microtubules have been associated with contractile dysfunction in cardiac myocytes after pressure overload in vivo. Experiments were performed to assess the ability of mechanical stimuli experienced by ventricular cardiac myocytes during the progression of hypertrophic and dilated pathology to increase beta-tubulin production in cultured neonatal rat cardiac myocytes. Results indicate that both contractile activity and load due to passive stretch increase beta-tubulin protein content in neonatal rat cardiac myocytes through accumulation of beta-tubulin mRNA, which occurs without increased beta-tubulin gene transcription. Western blot analysis demonstrated that contraction resulted in the accumulation of beta-tubulin in neonatal rat cardiac myocytes above increases observed in the content of total cellular protein. Northern blot analysis indicated that beta-tubulin mRNA content increased in response to both stretch and contraction. alpha-Adrenergic agonists that lead to pathophysiological growth in cardiac myocytes also stimulated an increase in beta-tubulin mRNA content. Treatment of contracting neonatal cardiac myocytes with angiotensin II (ANG II) further increased beta-tubulin mRNA content, whereas ANG II treatment in arrested neonatal cardiac myocytes failed to increase beta-tubulin mRNA. Nuclear run-on experiments indicate that contraction stimulates beta-tubulin mRNA accumulation without an increase in beta-tubulin gene transcription. These results imply that tubulin production in cultured cardiac myocytes can be regulated directly by mechanical forces. In mechanically challenged hearts, the accumulation of beta-tubulin and the development of contractile dysfunction may be directly related to the mechanical forces imposed on the myocardium during the onset and progression of cardiovascular disease.
Sodium valproate for painful diabetic neuropathy: a randomized double-blind placebo-controlled study (2003)

Sodium valproate is well-tolerated, and provides significant subjective improvement in painful diabetic neuropathy.
Plasma Insulin-like Growth Factor I and IGF Binding Protein 3 Levels in Patients With Acute Cerebral Ischemic Injury (1997)

IGF-I and IGFBP-3 plasma levels are decreased in patients after cerebral ischemia. After acute ischemic stroke, increased demand for growth factors, altered tissue distribution, and accelerated metabolic clearance rate or central inhibition of the somatotrophic axis may contribute to these low plasma concentrations. Growth factors such as IGF-I and IGFBP-3 may play an important role in the pathophysiology of acute cerebral ischemia, and growth factors may have a considerable effect on future therapeutic regimens.
An extensible dynamically-typed hierarchy of exceptions (2006)

In this paper we address the lack of extensibility of the exception type in Haskell. We propose a lightweight solution involving the use of existential types and the Typeable class only, and show how our solution allows a fully extensible hierarchy of exception types to be declared, in which a single overloaded catch operator can be used to catch either specific exception types, or exceptions belonging to any subclass in the hierarchy. We also show how to combine the existing object-oriented framework OOHaskell with our design, such that OOHaskell objects can be thrown and caught as exceptions, with full support for implicit OOHaskell subtyping in the catch operator.
Measurements of Quasiparticle Tunneling Dynamics in a Band-Gap-Engineered Transmon Qubit (2012)

We have engineered the band gap profile of transmon qubits by combining oxygen-doped Al for tunnel junction electrodes and clean Al as quasiparticle traps to investigate energy relaxation due to quasiparticle tunneling. The relaxation time ${T}_{1}$ of the qubits is shown to be insensitive to this band gap engineering. Operating at relatively low-${E}_{J}/{E}_{C}$ makes the transmon transition frequency distinctly dependent on the charge parity, allowing us to detect the quasiparticles tunneling across the qubit junction. Quasiparticle kinetics have been studied by monitoring the frequency switching due to even-odd parity change in real time. It shows the switching time is faster than $10\text{ }\text{ }\ensuremath{\mu}\mathrm{s}$, indicating quasiparticle-induced relaxation has to be reduced to achieve ${T}_{1}$ much longer than $100\text{ }\text{ }\ensuremath{\mu}\mathrm{s}$.
Serum exosomal hnRNPH1 mRNA as a novel marker for hepatocellular carcinoma (2017)

These findings suggested that serum exosomal hnRNPH1 mRNA could be an effective marker for HCC in high HBV prevalence areas.
Telmisartan in incipient and overt diabetic renal disease (2011)

The effects of telmisartan on kidney function support its use in patients with microalbuminuria or overt diabetic nephropathy.
Recent Advances in the Research and Development of RAF Kinase Inhibitors (2006)

The RAS-RAF-MEK-ERK signaling pathway (ERK pathway) plays a key role in tumorigenesis and cancer progression. Mutations of RAS or B-RAF lead to a constitutive activation of the ERK pathway, which ultimately results in increased cell division, and cell survival. This review article focuses on the recent literature related to ERK pathway inhibitors, with a particular emphasis on RAF kinase inhibitors. Preclinical and clinical data for the RAF kinase inhibitor sorafenib (BAY 43-9006 tosylate), that was recently approved in the US for the treatment of advanced renal cell carcinoma, are also outlined.
Programming language evolution via source code query languages (2012)

Programming languages evolve just like programs. Language features are added and removed, for example when programs using them are shown to be error-prone. When language features are modified, deprecated, removed or even deemed unsuitable for the project at hand, it is necessary to analyse programs to identify occurrences to refactor.
Gene Reactivation in Erythrocytes: Nuclear Transplantation in Oocytes and Eggs of Rana (1983)

Adult erythrocyte nuclei of Rana, transplanted and incubated in the cytoplasm of maturing oocytes, direct matured oocytes to form swimming tadpoles. These results demonstrate that nuclei of noncycling and terminally differentiated erythrocytes contain the genes to specify tadpole development, and conditioning these nuclei in the cytoplasm of oocytes leads to a widespread reactivation of dormant genes.
A structural census of genomes: comparing bacterial, eukaryotic, and archaeal genomes in terms of protein structure (1997)

Representative genomes from each of the three kingdoms of life are compared in terms of protein structure, in particular, those of Haemophilus influenzae (a bacteria), Methanococcus jannaschii (an archaeon), and yeast (a eukaryote). The comparison is in the form of a census (or comprehensive accounting) of the relative occurrence of secondary and tertiary structures in the genomes, which particular emphasis on patterns of supersecondary structure. Comparison of secondary structure shows that the three genomes have nearly the same overall secondary-structure content, although they differ markedly in amino acid composition. Comparison of super-secondary structure, using a novel "frequent-words" approach, shows that yeast has a preponderance of consecutive strands (e.g. beta-beta-beta patterns), Haemophilus, consecutive helices (alpha-alpha-alpha), and Methanococcus, alternating helix-strand structures (beta-alpha-beta). Yeast also has significantly more helical membrane proteins than the other two genomes, with most of the differences concentrated in proteins containing two transmembrane segments. Comparison of tertiary structure (by sequence matching and domain-level clustering) highlights the substantial duplication in each genome (approximately 30% to 50%), with the degree of duplication following similar patterns in all three. Many sequence families are shared among the genomes, with the degree of overlap between any two genomes being roughly similar. In total, the three genomes contain 148 of the approximately 300 known protein folds. Forty-five of these 148 that are present in all three genomes are especially enriched in mixed super-secondary structures (alpha/beta). Moreover, the five most common of these 45 (the "top-5") have a remarkably similar super-secondary structure architecture, containing a central sheet of parallel strands with helices packed onto at least one face and beta-alpha-beta connections between adjacent strands. These most basic molecular parts, which, presumably, were present in the last common ancestor to the three Kingdoms, include the TIM-barrel, Rossmann, flavodoxin, thiamin-binding, and P-loop-hydrolase folds.
A digital acoustic recording tag for measuring the response of wild marine mammals to sound (2003)

Definitive studies on the response of marine mammals to anthropogenic sound are hampered by the short surface time and deep-diving lifestyle of many species. A novel archival tag, called the DTAG, has been developed to monitor the behavior of marine mammals, and their response to sound, continuously throughout the dive cycle. The tag contains a large array of solid-state memory and records continuously from a built-in hydrophone and suite of sensors. The sensors sample the orientation of the animal in three dimensions with sufficient speed and resolution to capture individual fluke strokes. Audio and sensor recording is synchronous so the relative timing of sounds and motion can be determined precisely. The DTAG has been attached to more than 30 northern right whales (Eubalaena glacialis) and 20 sperm whales (Physeter macrocephalus) with recording duration of up to 12 h per deployment. Several deployments have included sound playbacks to the tagged whale and a transient response to at least one playback is evident in the tag data.
Improved Cerebral Resuscitation From Cardiac Arrest in Dogs With Mild Hypothermia Plus Blood Flow Promotion (1996)

After normothermic cardiac arrest of 11 minutes in dogs, resuscitative mild hypothermia plus cerebral blood flow promotion can achieve functional recovery with the least histological brain damage yet observed with the same model and comparable insults.
An overview of the regulation of influenza vaccines in the United States (2016)

Influenza virus vaccines are unique among currently licensed viral vaccines. The vaccines designed to protect against seasonal influenza illness must be updated periodically in an effort to match the vaccine strain with currently circulating viruses, and the vaccine manufacturing timeline includes multiple, overlapping processes with a very limited amount of flexibility. In the United States (U.S.), over 150 million doses of seasonal trivalent and quadrivalent vaccine are produced annually, a mammoth effort, particularly in the context of a vaccine with components that usually change on a yearly basis. In addition, emergence of an influenza virus containing an HA subtype that has not recently circulated in humans is an ever present possibility. Recently, pandemic influenza vaccines have been licensed, and the pathways for licensure of pandemic vaccines and subsequent strain updating have been defined. Thus, there are formidable challenges for the regulation of currently licensed influenza vaccines, as well as for the regulation of influenza vaccines under development. This review describes the process of licensing influenza vaccines in the U.S., the process and steps involved in the annual updating of seasonal influenza vaccines, and some recent experiences and regulatory challenges faced in development and evaluation of novel influenza vaccines.
Detection and Quantification of Left Atrial Structural Remodeling With Delayed-Enhancement Magnetic Resonance Imaging in Patients With Atrial Fibrillation (2009)

DE-MRI provides a noninvasive means of assessing left atrial myocardial tissue in patients suffering from AF and might provide insight into the progress of the disease. Preablation DE-MRI holds promise for predicting responders to AF ablation and may provide a metric of overall disease progression.
Hydrogenation of Benzonitrile to Benzylamine Catalyzed by Ruthenium Hydride Complexes with P−NH−NH−P Tetradentate Ligands:  Evidence for a Hydridic−Protonic Outer Sphere Mechanism (2007)

The reaction of RuHCl(PPh3)3 with the tetradentate ligand [PPh2((ortho-C6H4)CH2NHCH2-)]2 {ethP2(NH)2} in THF produces the new complex trans-RuHCl{ethP2(NH)2} (1) as a mixture of two isomers. The complex RuHCl{ethP2(NH)2} (1) when activated with KOtBu/KH is a very active catalyst for the hydrogenation of benzonitrile to benzylamine in toluene, more active than the known catalyst Ru(H2)2H2(PCy3)2 (2). A mixture of 1 and 2 and base also results in efficient conversion of benzonitrile to benzylamine. The complex RuHCl{tmeP2(NH)2} (3) where tmeP2(NH)2 is [PPh2((ortho-C6H4)CH2NHCMe2-)]2 is a less active catalyst for this reaction. These catalyst systems are air sensitive and extremely moisture sensitive. Experimental and theoretical (DFT) evidence is presented for a new mechanism for nitrile hydrogenation: the successive hydrogenation of the CN triple bond and then the CN double bond of the intermediate imine by H+/H- transfer from a trans dihydride active catalyst. The amido complex RuH{tmeP2N(NH)} (4) has similar activity to 3/base for the base-free hydrogenation of benzonitrile and is moderately active for the catalytic hydration of benzonitrile. The new complex RuH(BH4){ethP2(NH)2} (7) was prepared by reacting 1 with NaBH4 but is found to be a poor catalyst for nitrile hydration.