gebhart/patrepeval huggingface dataset:
Differentiation factors, including nerve growth factor, fibroblast growth factor, and interleukin-6, induce an accumulation of an active Ras.GTP complex in rat pheochromocytoma PC12 cells. (1992)

Ras has been thought to be involved in neuronal differentiation of rat pheochromocytoma PC12 cells. PC12 cells are immature adrenal chromaffin-like cells which undergo differentiation to sympathetic neuron-like cells in response to nerve growth factor (NGF). Fibroblast growth factor (FGF) and interleukin (IL)-6 can also induce differentiation of PC12 cells. In this paper, we report that NGF, FGF, and IL-6 induce an accumulation of an active Ras.GTP complex. In the serum-starved culture of PC12 cells, 6% of the Ras protein was complexed with GTP. Upon stimulation with NGF, the percentage of Ras.GTP increased to 24% after 2 min, and the high level of Ras.GTP was maintained for at least 16 h. On the other hand, the activation of Ras by FGF and IL-6 showed distinct kinetics; about 3-fold increase of Ras.GTP was detected at 10 min, and afterward, the level returned to the basal level within 60 min. These observations provide direct evidence that activation of Ras is involved in signal transduction from these differentiation factors. In addition, it was found that growth factors, including epidermal growth factor, insulin, and insulin-like growth factor-I, and a tumor promoter, 12-O-tetradecanoylphorbol-13-acetate (TPA), can also activate Ras under the same conditions. A tyrosine kinase-specific inhibitor, genistein, inhibited the increase of Ras.GTP induced by NGF and other factors. On the other hand, down-regulation of protein kinase C (PKC) by prolonged treatment with TPA, which sufficiently blocked TPA-induced Ras activation, did not abolish the formation of Ras.GTP by NGF. These results suggest that tyrosine kinases rather than PKC play a major role in the NGF-induced activation of Ras in PC12 cells.
Structural Studies of Amyloid Proteins at the Molecular Level (2017)

Dozens of proteins are known to convert to the aggregated amyloid state. These include fibrils associated with systemic and neurodegenerative diseases and cancer, functional amyloid fibrils in microorganisms and animals, and many denatured proteins. Amyloid fibrils can be much more stable than other protein assemblies. In contrast to globular proteins, a single protein sequence can aggregate into several distinctly different amyloid structures, termed polymorphs, and a given polymorph can reproduce itself by seeding. Amyloid polymorphs may be the molecular basis of prion strains. Whereas the Protein Data Bank contains some 100,000 globular protein and 3,000 membrane protein structures, only a few dozen amyloid protein structures have been determined, and most of these are short segments of full amyloid-forming proteins. Regardless, these amyloid structures illuminate the architecture of the amyloid state, including its stability and its capacity for formation of polymorphs.
Clonally related follicular lymphomas and histiocytic/dendritic cell sarcomas: evidence for transdifferentiation of the follicular lymphoma clone (2008)

Rare cases of histiocytic and dendritic cell (H/DC) neoplasms have been reported in patients with follicular lymphoma (FL), but the biologic relationship between the 2 neoplasms is unknown. We studied 8 patients with both FL and H/DC neoplasms using immunohistochemistry, fluorescence in situ hybridization (FISH) for t(14;18), and polymerase chain reaction (PCR)/sequencing of BCL2 and IGH rearrangements. There were 5 men and 3 women (median age, 59 years). All cases of FL were positive for t(14;18). The H/DC tumors included 7 histiocytic sarcomas, 5 of which showed evidence of dendritic differentiation, and 1 interdigitating cell sarcoma. Five H/DC tumors were metachronous, following FL by 2 months to 12 years; tumors were synchronous in 3. All 8 H/DC tumors showed presence of the t(14;18) either by FISH, or in 2 cases by PCR with the major breakpoint region (MBR) probe. PCR and sequencing identified identical IGH gene rearrangements or BCL2 gene breakpoints in all patients tested. All H/DC tumors lacked PAX5, and up-regulation of CEBPbeta and PU.1 was seen in all cases tested. These results provide evidence for a common clonal origin of FL and H/DC neoplasms when occurring in the same patient, and suggest that lineage plasticity may occur in mature lymphoid neoplasms.
Heavy-atom derivatization (2003)

Most of the standard methods of solving macromolecular structures involve producing a protein crystal that is derivatized by an anomalous scatterer or heavy atom (MIR, SIRAS, MAD, SAD etc.). The theoretical methodology which underpins the extraction of phase information from such derivatives is widely available in the literature. In addition, there are comprehensive sources of information on the chemistry of heavy-atom compounds and the ligands with which they are known to interact, as well as the Heavy Atom Databank accessible on the World Wide Web. This contribution therefore aims to provide some information on the less well documented practical problems of firstly deciding on an overall strategy for derivatization and secondly performing the physical manipulations involved in producing heavy-atom derivatives from native protein crystals and then cryocooling them. Ways to optimize the chances of isomorphous unit cells are suggested. Methods of determining whether or not the heavy atom is bound are outlined, including the powerful technique of PIXE (particle-induced X-ray emission).
ChemInform Abstract: DERIVATE VON 4‐AZAHOMOADAMANTAN, SYNTH. UND BIOLOGISCHE AUSWERTUNG (1971)

Abstract Die Azahomoadamantanderivate (II), (IV) und (VI) werden aus dem 4‐Azahomoadamantan‐5‐on (I) hergestellt.
Development of Single-Well Gas Assisted Gravity Drainage Process for Enhanced Oil Recovery (2016)

EOR application in prolific deepwater Gulf of Mexico (DGOM) reservoirs has remained a challenge. Exorbitant well cost (>200M$) precludes having extensive injection patterns and very characteristics of the reservoirs themselves are partly to blame for negligible EOR activity in DGOM. We have been able to develop and demonstrate a novel design in the form of Single Well – Gas Assisted Gravity Drainage (SW-GAGD) process, which is potentially cost effective, at the same time ensuring very high oil recoveries. In this design, a single well acts as an injector as well as a producer, thereby minimizing well cost. The efficacy of the process has been demonstrated using partially scaled visual glass models and material balance calculations. The recovery factor is in the range of 70-80% in the immiscible mode and near 100% in the miscible mode at abandonment. Such high recoveries are as a result of highly efficient film flow aided gravity drainage process. Being a forced gravity drainage process, SW-GAGD is, however, an order of magnitude faster and thus expected to be an economically viable recovery process. For example, at just 2.5 SCCM (2.3 ft/day), the process was 23 times faster than pure gravity drainage for recovering 61% OOIP (ultimate recovery factor for pure gravity drainage). This process has also been shown to be immune to reservoir heterogeneities like vertical fractures, reservoir permeability layering and reservoir dip and hence laboratory results are more likely to be translatable to the field. In fact reservoir layering with low permeability layering near horizontal lateral was shown to improve the sweep and recovery efficiency compared to no layering case by 6-7% at abandonment. Among various models, semi-analytical Hagoort model was found to best represent forced gravity process in an analytical fashion. It used a non-dimensional form of solution with velocity incorporated in the gravity no. definition to account for forced gravity drainage process. A reasonable match was obtained for SW-GAGD recoveries, with slight under prediction of recoveries post breakthrough. This is attributed to non-consideration of film drainage, which is anticipated to play an important role, especially post breakthrough.
PROGESTERONE AND PROGESTERONE THERAPY IN PREGNANCY (1965)

From the Department of Obstetrics and Gynecology, University of Colorado School of Medicine, Denver
Voltage clamp of rat and human skeletal muscle: measurements with an improved loose‐patch technique. (1984)

Intact fibres of human intercostal and rat omohyoid muscles were studied at 23 degree C with a loose-patch voltage-clamp technique that employed two concentric micropipettes to electrically isolate small-diameter (10-15 microns) patches of sarcolemma. This method allows investigation of membrane excitability under highly physiological conditions. Step depolarizations to 0 mV elicited sodium inward currents that reached peak values of up to 20 mA/cm2 within 250 microseconds, and then declined. In human muscle, the reversal potential (ENa) was approximately 40 mV, and maximal conductances (GNa) ranged from 44 to 360 mS/cm2. In rat muscle, ENa was 42 mV and GNa ranged from 100 to 250 mS/cm2. Sodium channels in rat and human muscle were indistinguishable in most aspects of their kinetic behaviour and voltage dependence. Outward potassium currents were small by comparison (usually less than 2 mA/cm2) and saturated at positive potentials. The maximum potassium conductance (GK) ranged from 0 to 19 mS/cm2 (human) and from 4 to 12 mS/cm2 (rat muscle).
Synthesis of layered silicon-graphene hetero-structures by wet jet milling for high capacity anodes in Li-ion batteries (2020)

Abstract While silicon-based negative electrode materials have been extensively studied, to develop high capacity lithium-ion batteries (LIBs), implementing a large-scale production method that can be easily transferred to industry, has been a crucial challenge. Here, a scalable wet-jet milling method was developed to prepare a silicon-graphene hybrid material to be used as negative electrode in LIBs. This synthesized composite, when used as an anode in lithium cells, demonstrated high Li ion storage capacity, long cycling stability and high-rate capability. In particular, the electrode exhibited a reversible discharge capacity exceeding 1763 mAh g −1 after 450 cycles with a capacity retention of 98% and a coulombic efficiency of 99.85% (with a current density of 358 mA g −1 ). This significantly supersedes the performance of a Si-dominant electrode structures. The capacity fade rate after 450 cycles was only 0.005% per cycle in the 0.05–1 V range. This superior electrochemical performance is ascribed to the highly layered, silicon-graphene porous structure, as investigated via focused ion beam in conjunction with scanning electron microscopy tomography. The hybrid electrode could retain 89% of its porosity (under a current density of 358 mA g −1 ) after 200 cycles compared with only 35% in a Si-dominant electrode. Moreover, this morphology can not only accommodate the large volume strains from active silicon particles, but also maintains robust electrical connectivity. This confers faster transportation of electrons and ions with significant permeation of electrolyte within the electrode. Physicochemical characterisations were performed to further correlate the electrochemical performance with the microstructural dynamics. The excellent performance of the hybrid material along with the scalability of the synthesizing process is a step forward to realize high capacity/energy density LIBs for multiple device applications.
Trifluoromethylated Butadienes (1954)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTTrifluoromethylated ButadienesAlbert L. Henne and Paul E. HinkampCite this: J. Am. Chem. Soc. 1954, 76, 20, 5147–5148Publication Date (Print):October 1, 1954Publication History Published online1 May 2002Published inissue 1 October 1954https://pubs.acs.org/doi/10.1021/ja01649a044https://doi.org/10.1021/ja01649a044research-articleACS PublicationsRequest reuse permissionsArticle Views184Altmetric-Citations14LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Systematic review: the chemoprevention of oesophageal adenocarcinoma (2005)

The incidence of oesophageal adenocarcinoma is increasing in the UK faster than any other malignancy. Despite its relatively poor prognosis and the limited success of existing treatments, there is enthusiasm that chemopreventive agents might be able to stem the transition from normal squamous epithelium to adenocarcinoma. We discuss gastro-oesophageal reflux as the main risk factor for the development of Barrett's metaplasia, the only known precursor of oesophageal adenocarcinoma. Treatment options for reflux disease are considered with regard to their effects on cancer risk. Recent advances in the molecular and cell biology of Barrett's are outlined, and potential targets for chemoprevention examined. Available treatments for reflux disease have not convincingly altered the likelihood of cancer development. Epidemiological and animal studies support the use of non-steroidal anti-inflammatory drugs as potential chemopreventive agents. Dietary agents, however, have a more favourable side-effect profile and may prove to be an attractive alternative, although more work is needed to fully explore this prospect.
The expansion of urbanisation in the Balearic Islands (1956–2006) (2014)

Since the mid-20th century the Balearic Islands have experienced significant changes as a result of their incorporation into the global economy as a mass tourism destination. The expansion of urbanisation has become a main change, given that the archipelago’s urbanised surface has increased fivefold since 1956. The territory of the islands has been organised internally to meet the demands of, first, tourism, and, second, the residential demands of Central European countries. The process has generated a whole new territorial model, dominated by new urban coastal and metropolitan areas in larger cities. This new model overlaps the regular traditional scattered centres inland with some walled coastal towns, from the pretourist model. This paper quantifies, describes, and explains these changes based on data from a series of land cover maps of 1956, 1973, 1995, and 2006, paying special attention to the particularities of each of the islands: Mallorca, Menorca, Ibiza and Formentera.
White matter injury, cholesterol dysmetabolism, and APP/Abeta dysmetabolism interact to produce Alzheimer’s disease (AD) neuropathology: A hypothesis and review (2023)

We postulate that myelin injury contributes to cholesterol release from myelin and cholesterol dysmetabolism which contributes to Abeta dysmetabolism, and combined with genetic and AD risk factors, leads to increased Abeta and amyloid plaques. Increased Abeta damages myelin to form a vicious injury cycle. Thus, white matter injury, cholesterol dysmetabolism and Abeta dysmetabolism interact to produce or worsen AD neuropathology. The amyloid cascade is the leading hypothesis for the cause of Alzheimer's disease (AD). The failure of clinical trials based on this hypothesis has raised other possibilities. Even with a possible new success (Lecanemab), it is not clear whether this is a cause or a result of the disease. With the discovery in 1993 that the apolipoprotein E type 4 allele (APOE4) was the major risk factor for sporadic, late-onset AD (LOAD), there has been increasing interest in cholesterol in AD since APOE is a major cholesterol transporter. Recent studies show that cholesterol metabolism is intricately involved with Abeta (Aβ)/amyloid transport and metabolism, with cholesterol down-regulating the Aβ LRP1 transporter and upregulating the Aβ RAGE receptor, both of which would increase brain Aβ. Moreover, manipulating cholesterol transport and metabolism in rodent AD models can ameliorate pathology and cognitive deficits, or worsen them depending upon the manipulation. Though white matter (WM) injury has been noted in AD brain since Alzheimer's initial observations, recent studies have shown abnormal white matter in every AD brain. Moreover, there is age-related WM injury in normal individuals that occurs earlier and is worse with the APOE4 genotype. Moreover, WM injury precedes formation of plaques and tangles in human Familial Alzheimer's disease (FAD) and precedes plaque formation in rodent AD models. Restoring WM in rodent AD models improves cognition without affecting AD pathology. Thus, we postulate that the amyloid cascade, cholesterol dysmetabolism and white matter injury interact to produce and/or worsen AD pathology. We further postulate that the primary initiating event could be related to any of the three, with age a major factor for WM injury, diet and APOE4 and other genes a factor for cholesterol dysmetabolism, and FAD and other genes for Abeta dysmetabolism.
Parental Chromosome-specific Chromatin Conformation in the Imprinted U2af1-rs1 Gene in the Mouse (1997)

The imprinted U2af1-rs1 gene on mouse chromosome 11 is expressed exclusively from the paternal allele. We found that U2af1-rs1 resides in a chromosomal domain that displays marked differences in chromatin conformation and DNA methylation between the parental chromosomes. Chromatin conformation was assayed in brain and liver, in fetuses, and in embryonic stem cells by sensitivity to nucleases in nuclei. In all these tissues, the unmethylated paternal chromosome is sensitive to DNase-I and MspI and has two DNase-I hypersensitive sites in the 5'-untranslated region. In brain and in differentiated stem cells, which display high levels of U2af1-rs1 expression, a paternal DNase-I hypersensitive site is also readily apparent in the promoter region. On the maternal chromosome, in contrast, the entire U2af1-rs1 gene and its promoter are highly resistant to DNase-I and MspI in all tissues analyzed and are fully methylated. No differential MNase sensitivity was detected in this imprinted domain. The parental chromosome-specific DNA methylation and chromatin conformation were also present in parthenogenetic and androgenetic cells and in tissues from animals maternally or paternally disomic for chromosome 11. This demonstrates that these parental chromosome-specific epigenotypes are independently established and maintained and provides no evidence for interallelic trans-sensing and counting mechanisms in U2af1-rs1.
Transcutaneous RF-Powered Implantable Minipump Driven by a Class-E Transmitter (2006)

We describe the design and testing of an inductive coupling system used to power an implantable minipump for applications in ambulating rats. A 2 MHz class-E oscillator driver powered a coil transmitter wound around a 33-cm-diameter rat cage. A receiver coil, a filtered rectifier, and a voltage-sensitive switch powered the implant. The implant DC current at the center of the primary coil (5.1 V) exceeded the level required to activate the solenoid valve in the pump. The variations of the implant current in the volume of the primary coil reflected the variations of the estimated coupling coefficient between the two coils. The pump could be activated in-vivo, while accommodating the vertical and horizontal movements of the animal. Advantages of this design include a weight reduction for the implant, an operation independent from a finite power source, and a remote activation/deactivation.
Adsorption and Thermal Chemistry of Nitroethane on Si(100)-2 × 1 (2003)

Surface chemistry of nitroethane on Si(100)-2 × 1 has been investigated using multiple internal reflection Fourier transform infrared spectroscopy (MIR−FTIR), Auger electron spectroscopy (AES), and thermal desorption mass spectrometry. Molecular adsorption of nitroethane at submonolayer coverages dominates at cryogenic temperatures (95 K). As the surface temperature is increased to 140 K, chemical reaction involving nitro group occurs, whereas the ethyl entity remains intact. Similar behavior is observed for nitromethane. Thus, a barrier of approximately 36 kJ/mol is established for the interaction of nitroalkane molecules with the Si(100)-2 × 1 surface in contrast to the essentially barrierless transformation predicted previously theoretically for nitromethane. Further annealing of the silicon surface leads to the decomposition of nitroethane. The concentration of nitrogen and oxygen remains constant on a surface within the temperature interval studied here, whereas approximately half of the ethyl groups undergo hydrogen elimination, which releases ethylene and produces surface hydrogen. The rest of the ethyl groups decompose leading to the formation of surface carbon as confirmed by AES.
MfSAT: Detect simple sequence repeats in viral genomes (2011)

Simple sequence repeats (SSRs) are ubiquitous short tandem repeats, which are associated with various regulatory mechanisms and have been found in viral genomes. Herein, we develop MfSAT (Multi-functional SSRs Analytical Tool), a new powerful tool which can fast identify SSRs in multiple short viral genomes and then automatically calculate the numbers and proportions of various SSR types (mono-, di-, tri-, tetra-, penta- and hexanucleotide repeats). Furthermore, it also can detect codon repeats and report the corresponding amino acid.
PHOTOCHEMICAL INTERACTION OF FUROCOUMARINS WITH BROMODEOXYURIDINE AND POLYDEOXY‐NUCLEOTIDES CONTAINING BROMODEOXYURIDINE: ITS BIOLOGICAL IMPLICATIONS (1978)

Abstract— The photoreaction of 5‐bromodeoxyuridine (BUdR) exposed to 360 nm light in the presence of the furocoumarins, 4,5′,8‐trimethylpsoralen (TMP) and 8‐methoxypsoralen (&amp;MOP), was studied and compared to those of thymidine. BUdR reacted with furocoumarins, producing cyclobutane‐containing adducts, as does thymidine. Furocoumarins reacted also with BUdR‐containing polymer, poly(dA‐BUdR) in the double stranded form, at a rate similar to that of thymidine‐containing polymer, poly(dA‐dT). Polyamines, which slow the photoreactions of TMP with DNA, had no effect on its binding to the two former polynucleotides. It is suggested that because of the similar photoreactions of BUdR and thymidine with furocoumarins, this combination could be used to elucidate the mechanism by which BUdR sensitizes biological systems. In Escherichia coli some sensitization by BUdR of TMP plus 360 nm light killing was observed. It is therefore concluded that at least part of the sensitization of bacteria by BUdR to UV and ionizing radiation is caused by interference with the repair processes. Since no such sensitization was observed in a uvr B mutant, BUdR apparently impairs the efficiency of the excision resynthesis pathway of repair.