gebhart/patrepeval huggingface dataset:
Spreading of X chromosome inactivation via a hierarchy of defined Polycomb stations (2012)

X chromosome inactivation (XCI) achieves dosage balance in mammals by repressing one of two X chromosomes in females. During XCI, the long noncoding Xist RNA and Polycomb proteins spread along the inactive X (Xi) to initiate chromosome-wide silencing. Although inactivation is known to commence at the X-inactivation center (Xic), how it propagates remains unknown. Here, we examine allele-specific binding of Polycomb repressive complex 2 (PRC2) and chromatin composition during XCI and generate a chromosome-wide profile of Xi and Xa (active X) at nucleosome-resolution. Initially, Polycomb proteins are localized to ∼150 strong sites along the X and concentrated predominantly within bivalent domains coinciding with CpG islands ("canonical sites"). As XCI proceeds, ∼4000 noncanonical sites are recruited, most of which are intergenic, nonbivalent, and lack CpG islands. Polycomb sites are depleted of LINE repeats but enriched for SINEs and simple repeats. Noncanonical sites cluster around the ∼150 strong sites, and their H3K27me3 levels reflect a graded concentration originating from strong sites. This suggests that PRC2 and H3K27 methylation spread along a gradient unique to XCI. We propose that XCI is governed by a hierarchy of defined Polycomb stations that spread H3K27 methylation in cis.
Cognitive Enhancers (Nootropics). Part 1: Drugs Interacting with Receptors (2012)

Cognitive enhancers (nootropics) are drugs to treat cognition deficits in patients suffering from Alzheimer's disease, schizophrenia, stroke, attention deficit hyperactivity disorder, or aging. Cognition refers to a capacity for information processing, applying knowledge, and changing preferences. It involves memory, attention, executive functions, perception, language, and psychomotor functions. The term nootropics was coined in 1972 when memory enhancing properties of piracetam were observed in clinical trials. In the meantime, hundreds of drugs have been evaluated in clinical trials or in preclinical experiments. To classify the compounds, a concept is proposed assigning drugs to 18 categories according to their mechanism(s) of action, in particular drugs interacting with receptors, enzymes, ion channels, nerve growth factors, re-uptake transporters, antioxidants, metal chelators, and disease-modifying drugs meaning small molecules, vaccines, and monoclonal antibodies interacting with amyloid-β and tau. For drugs, whose mechanism of action is not known, they are either classified according to structure, e.g., peptides, or their origin, e.g., natural products. The review covers the evolution of research in this field over the last 25 years.
May the Force Be with You (2018)

The use of ultrasound haptic feedback for mid-air gestures in cars has been proposed to provide a sense of control over the user's intended actions and to add touch to a touchless interaction. However, the impact of ultrasound feedback to the gesturing hand regarding lane deviation, eyes-off-the-road time (EORT) and perceived mental demand has not yet been measured. This paper investigates the impact of uni- and multimodal presentation of ultrasound feedback on the primary driving task and the secondary gesturing task in a simulated driving environment. The multimodal combinations of ultrasound included visual, auditory, and peripheral lights. We found that ultrasound feedback presented unimodally and bimodally resulted in significantly less EORT compared to visual feedback. Our results suggest that multimodal ultrasound feedback for mid-air interaction decreases EORT whilst not compromising driving performance nor mental demand and thus can increase safety while driving.
α-Conotoxin EpI, a Novel Sulfated Peptide from Conus episcopatusThat Selectively Targets Neuronal Nicotinic Acetylcholine Receptors (1998)

We have isolated and characterized α-conotoxin EpI, a novel sulfated peptide from the venom of the molluscivorous snail, Conus episcopatus. The peptide was classified as an α-conotoxin based on sequence, disulfide connectivity, and pharmacological target. EpI has homology to sequences of previously described α-conotoxins, particularly A, PnIB, and ImI. However, EpI differs from previously reported conotoxins in that it has a sulfotyrosine residue, identified by amino acid analysis and mass spectrometry. Native EpI was shown to coelute with synthetic EpI. The peptide sequence is consistent with most, but not all, recognized criteria for predicting tyrosine sulfation sites in proteins and peptides. The activities of synthetic EpI and its unsulfated analogue [Tyr15]EpI were similar. Both peptides caused competitive inhibition of nicotine action on bovine adrenal chromaffin cells (neuronal nicotinic ACh receptors) but had no effect on the rat phrenic nerve-diaphragm (muscle nicotinic ACh receptors). Both EpI and [Tyr15]EpI partly inhibited acetylcholine-evoked currents in isolated parasympathetic neurons of rat intra. cardiac ganglia. These results indicate that EpI and [Tyr15]EpI selectively inhibit α3B2 and a3134 nicotinic acetylcholine receptors.
180nm gate length amorphous InGaZnO thin film transistor for high density image sensor applications (2010)

In this article, we propose a novel hybrid complementary metal oxide semiconductor (CMOS) image sensor architecture utilizing nanometer scale amorphous In-Ga-Zn-O (a-IGZO) thin film transistors (TFT) combined with a conventional Si photo diode. This approach will overcome the loss of quantum efficiency and image quality due to the downscaling of the photodiode. The 180nm gate length a-IGZO TFT exhibits remarkable short channel device performance including a low 1/f noise and a high output gain, despite fabrication temperatures as low as 200°C. The excellent device performance has been achieved by a double layer gate dielectric (Al <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> /SiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> ) and a trapezoidal active region formed by a tailored etching process. A self aligned top gate structure was employed for low parasitic capacitance. 3D process simulation tools were applied to optimize a four pixel CMOS image sensor structure. The results demonstrate how our stacked hybrid device approach contributes to new device strategies in image sensor architectures. We expect that this approach is applicable to numerous devices and systems in future micro- and nano-electronics.
A molecular theory of lipid—protein interactions in the plasma lipoproteins (1974)

Abbreviations: VLDL, very low density lipoproteins; HDL, high density lipoproteins; apoprotein, a lipid-free protein component from a lipoprotein; apoLP-Ala and apoLP-Ser, two apoproteins from human VLDL, with carboxyl-terminal alanine and serine, respectively; apoLP-Gln-I (A-l), and apoLP-Gln-II (A-II), the two major apoproteins of human HDL, each with carboxyl-terminal glutamine.
Experimental Syphilis in Guinea Pig (1989)

The infrequent use of guinea pig in experimental syphilis, the not well genetically and immunologically characterized strains of animals originating from places with unspecified conditions of husbandry, and the various strains of Treponema pallidum used for infection provided inconsistent and discouraging results. For eight decades the rabbit has been the major animal model in studies of syphilis. However, the lack of readily available inbred strains of rabbits--necessary for adoptive transfer experiments--has been a stumbling block in revealing the mechanisms responsible for immunity, susceptibility, and resistance to T. pallidum infection. These difficulties have recently been overcome by demonstration of inbred strains susceptible to T. pallidum infection, paving the way to studies of adoptive immunity. The guinea pig may also be a better model than the rabbit for immunomanipulations (irradiation, injection with antibodies specific to various cell populations), allowing a closer insight into the immunopathologic mechanism operating during the course of syphilitic infection. The "rediscovery" of the guinea pig as a model for experimental syphilis and recent years of intensive studies justify a review summarizing older data and providing the most recent information. The authors, having first-hand experience with this model, will provide detailed information on (1) historical background; (2) course of infection with T. pallidum in inbred and outbred strains of guinea pigs; (3) the ID50 for various strains; (4) various routes of infection; (5) age and sex-dependent susceptibility to infection; (6) kinetic of the humoral response to specific and non-specific treponemal antigens; (7) appearance of autoantibodies and immune complexes; (8) cellular response, including lymphoproliferative response, macrophage inhibitory factor(s) production, chemotaxis and adoptive transfer of immunity by purified T cells; and (9) a complete list of references.
Activation of chitin synthetase in permeabilized cells of a Saccharomyces cerevisiae mutant lacking proteinase B (1982)

Digitonin treatment at 30 degrees C of a Saccharomyces cerevisiae mutant lacking proteinase B permeabilized the cells and caused rapid and extensive activation of chitin synthetase in situ. The same result was obtained with a mutant generally defective in vacuolar proteases. By lowering the temperature and using different permeabilization procedures, we showed that increases in permeability and activation are distinct processes. Activation was inhibited by the protease inhibitors antipain and leupeptin, but by pepstatin or chymostatin. Metal chelators were also inhibitory, and their effect was reversed by the addition of Ca2+ but not by Mg2+. Antipain added together with Ca2+ after incubation of the cells in the presence of a chelating agent prevented reversal of inhibition, a result that was interpreted as indicating that antipain acts either on the same step affected by Ca2+ or on a subsequent step. Efforts to obtain activation in cell-free extracts were unsuccessful, but it was possible to extract the synthetase, once activated, by breaking permeabilized cells with glass beads. Treatment of the cell-free extracts with trypsin led not only to increased activity of chitin synthetase, but also to a change in the pH-activity curve and a diminished requirement by the enzyme for free N-acetylglucosamine. These observations suggest that the modification undergone by the synthetase during endogenous activation is different from that brought about by trypsin treatment.
SYNTHESIS OF A NOVEL POLYSACCHARIDE HYDROGEL (1999)

ABSTRACT A modified hyaluronic acid (HA) biopolymer was synthesized that can be photocrosslinked to form a stable hydrogel. The chemical and physical properties including the amount of modification of the polymer with methacrylate anhydride, the viscosity of the modified biopolymer, and the solute diffusion characteristics of the polymer have been determined.
Detection of North American Eastern and Western Equine Encephalitis Viruses by Nucleic Acid Amplification Assays (2003)

We have developed nucleic acid sequence-based amplification (NASBA), standard reverse transcription PCR (RT-PCR), and TaqMan nucleic acid amplification assays for the rapid detection of North American eastern equine encephalitis (EEE) and western equine encephalitis (WEE) viral RNAs from samples collected in the field and clinical samples. The sensitivities of these assays have been compared to that of virus isolation. While all three types of nucleic acid amplification assays provide rapid detection of viral RNAs comparable to the isolation of viruses in Vero cells, the TaqMan assays for North American EEE and WEE viral RNAs are the most sensitive. We have shown these assays to be specific for North American EEE and WEE viral RNAs by testing geographically and temporally distinct strains of EEE and WEE viruses along with a battery of related and unrelated arthropodborne viruses. In addition, all three types of nucleic acid amplification assays have been used to detect North American EEE and WEE viral RNAs from mosquito and vertebrate tissue samples. The sensitivity, specificity, and rapidity of nucleic acid amplification demonstrate the usefulness of NASBA, standard RT-PCR, and TaqMan assays, in both research and diagnostic settings, to detect North American EEE and WEE viral RNAs.
Expression of the MHC Class II Pathway in Triple-Negative Breast Cancer Tumor Cells Is Associated with a Good Prognosis and Infiltrating Lymphocytes (2016)

Triple-negative breast cancer (TNBC) is a subtype with heterogeneous patient outcomes. Approximately 40% of patients experience rapid relapse, while the remaining patients have long-term disease-free survival. To determine if there are molecular differences between primary tumors that predict prognosis, we performed RNA-seq on 47 macrodissected tumors from newly diagnosed patients with TNBC (n = 47; 22 relapse, 25 no relapse; follow-up median, 8 years; range, 2-11 years). We discovered that expression of the MHC class II (MHC II) antigen presentation pathway in tumor tissue was the most significant pathway associated with progression-free survival (HR, 0.36; log-rank P = 0.0098). The association between MHC II pathway expression and good prognosis was confirmed in a public gene expression database of 199 TNBC cases (HR, 0.28; log-rank P = 4.5 × 10(-8)). Further analysis of immunohistochemistry, laser-capture microdissected tumors, and TNBC cell lines demonstrated that tumor cells, in addition to immune cells, aberrantly express the MHC II pathway. MHC II pathway expression was also associated with B-cell and T-cell infiltration in the tumor. Together, these data support the model that aberrant expression of the MHC II pathway in TNBC tumor cells may trigger an antitumor immune response that reduces the rate of relapse and enhances progression-free survival. Cancer Immunol Res; 4(5); 390-9. ©2016 AACR.
A Randomized Trial of Acyclovir for 7 Days or 21 Days with and without Prednisolone for Treatment of Acute Herpes Zoster (1994)

In acute herpes zoster, treatment with acyclovir for 21 days or the addition of prednisolone to acyclovir therapy confers only slight benefits over standard 7-day treatment with acyclovir. Neither additional treatment reduces the frequency of postherpetic neuralgia.
Radiosensitization of Hypoxic HeLa S3 Cells in Vitro by a New Type of Radiosensitizer: Spermine and Spermidine Amides with Nitro Groups (1983)

A new type of hypoxic cell sensitizer (FNT-series compounds) has been developed and tested on HeLa S3 cells. They have two nitrobenzoyl groups at both ends of the spermine or spermidine in their chemical structures. Their ability to sensitize hypoxic cells is greater than that of misonidazole. Among them, N1, N10-bis(4-nitrobenzoyl)-spermidine (FNT-1) was most effective. 1 mM FNT-1 gave a corrected enhancement ratio of 1.71 compared to 1.32 for the same concentration of misonidazole. Its electron affinity, in terms of the half-wave reduction potential, was - 350 mV and higher than that of misonidazole (-395 mV). These FNT-series compounds are thought to interact with DNA in two ways; noncovalent linkage between the basic groups of the polyamine and highly acidic phosphate moieties of the nucleic acid and, secondly, the insertion of the nitrobenzoyl groups between base pairs of the DNA double helix. Since spermine and spermidine themselves did not show any sensitizing activities, it is suggested that the nitrobenzoyl groups which are introduced in spermine and spermidine, play an important role in sensitization.
Valence-band and core photoelectron spectroscopic studies of molybdenum aqueous oxidation and the influence of argon-ion etching (1995)

The behaviour of a polished molydenum metal surface upon exposure to both aerated and deaerated water and 1.0 mol dm–3 sodium chloride solution, in a previously described anaerobic cell, has been studied by X-ray photoelectron spectroscopy (XPS). No oxidation was found on metal samples exposed to deaerated solutions. Exposure to aerated sodium chloride solution also produced no oxide formation. However, exposing the polished metal surface to aerated water produced significant oxidation, in agreement with previous results. The valence band studies complement the core-level data, as well as providing information not available in the core spectra. We find that metal surfaces cleaned by argon-ion etching rather than by mechanical polishing of the molybdenum are inert to oxidation by aerated water. These etched surfaces show differences in the valenceband region that are consistent with the generation of a defect molybdenum structure, possibly containing oxygen. This defect structure, generated by argon-ion etching, appears to passivate the metal. The valenceband data were interpreted by calculated spectra generated by multiple-scattered-wave X-α cluster calculations.
Spectrum of Disease Due to Rapidly Growing Mycobacteria (1983)

One hundred twenty-five cases of disease due to rapidly growing mycobacteria were observed over a four-year period. Cutaneous infections accounted for 74 cases (59%). Of these, 40 followed surgical procedures (especially augmentation mammaplasty or median sternotomy), and 34 were due to accidental penetrating trauma. Among the 24 patients with pulmonary disease, the mean age was approximately 60 years, the majority of patients (63%) were women, and most had unilateral noncavitary disease. Other infections included disseminated disease with multiple nodular skin lesions and positive blood cultures, cervical lymphadenitis, keratitis, and endocarditis associated with a prosthetic valve. Infected tissues showed mixed acute and granulomatous inflammation; acid-fast bacilli, when present, occurred in extracellular clumps within microabscesses. Mycobacterium fortuitum and Mycobacterium chelonei were encountered with approximately equal frequency; 80% of isolates of M. chelonei were subspecies abscessus, and 83% of isolates of M. fortuitum were biovariant fortuitum. The outcome in these infections was generally good, although 9% of the patients, including all those with endocarditis, died. Infections due to M. fortuitum and M. chelonei are probably markedly under-diagnosed, and these organisms are capable of causing a wide spectrum of clinical disease.
Methods of measuring solar and terrestrial atmospheric circulations (1966)

In order either to support or to cast doubt upon the mode of study of the circulation of the solar photosphere recently employed by Ward, a comparable use of his methods is made in a test study of the terrestrial atmosphere for which extensive investigations by independent procedures are available. In a qualified over-all manner, Ward's procedures for measuring the large-scale horizontal eddy components from sunspot displacements are given vindication.
PPAR: a Key Nuclear Factor in Nutrient / Gene Interactions? (1995)

Retinoids as well as steroid and thyroid hormones are small lipophilic molecules that exert an intricate array of combinatorial effects during embryogenesis, cellular differentiation, and homeostasis in the adult organism. Complexity in the signalling pathway of these hormones results from the functional association of low affinity cytoplasmic hormone binding proteins and high affinity nuclear hormone receptors. The latter interact with polymorphic response elements linked to target genes and mediate the hormonal response at the transcriptional level.
Mutations in Steroid 21-Hydroxylase (CYP21) (1994)

The inherited inability to synthesize cortisol is termed congenital adrenal hyperplasia. More than 90% of cases are caused by 21-hydroxylase deficiency. This syndrome is characterized by signs of androgen excess and often mineralocorticoid deficiency. Steroid 21-hydroxylase (P450c21) is a microsomal enzyme expressed in the adrenal gland that catalyzes conversion of 17-hydroxyprogesterone and progesterone to 11-deoxycortisol and deoxycorticosterone respectively. In man, this enzyme is encoded by the CYP21 (CYP21B) gene which is located in the HLA major histocompatibility complex along with a pseudogene, CYP21P (CYP21A). Mutations in CYP21 causing congenital adrenal hyperplasia are almost all generated by recombinations between CYP21 and CYP21P. These recombinations either delete CYP21 or transfer deleterious mutations from CYP21P to CYP21, a process termed apparent gene conversion. The degree of enzymatic compromise caused by each mutation is correlated with the clinical severity of the deficiency observed in patients carrying that mutation.
Systematic Search for Placental DNA-Methylation Markers on Chromosome 21: Toward a Maternal Plasma-Based Epigenetic Test for Fetal Trisomy 21 (2008)

Twenty-two (19%) of the 114 studied CGIs on chromosome 21 showed epigenetic differences between samples of placenta and maternal blood cells; these CGIs may provide a rich source of markers for noninvasive prenatal diagnosis.
Asymmetric Intramolecular C−H Insertions of Aryldiazoacetates (2001)

[reaction: see text] The enantioselectivity of Rh(2)(S-DOSP)(4) catalyzed C-H insertion of aryldiazoacetates is very dependent on the site of the C-H insertion. The highest enantioselectivity is obtained for insertion into methine C-H bonds.
CO2-neutral fuels (2015)

The need for storage of renewable energy (RE) generated by photovoltaic, concentrated solar and wind arises from the fact that supply and demand are ill-matched both geographically and temporarily. This already causes problems of overcapacity and grid congestion in countries where the fraction of RE exceeds the 20% level. A system approach is needed, which focusses not only on the energy source, but includes conversion, storage, transport, distribution, use and, last but not least, the recycling of waste. Furthermore, there is a need for more flexibility in the energy system, rather than relying on electrification, integration with other energy systems, for example the gas network, would yield a system less vulnerable to failure and better adapted to requirements. For example, long-term large-scale storage of electrical energy is limited by capacity, yet needed to cover weekly to seasonal demand. This limitation can be overcome by coupling the electricity net to the gas system, considering the fact that the Dutch gas network alone has a storage capacity of 552 TWh, sufficient to cover the entire EU energy demand for over a month. This lecture explores energy storage in chemicals bonds. The focus is on chemicals other than hydrogen, taking advantage of the higher volumetric energy density of hydrocarbons, in this case methane, which has an approximate 3.5 times higher volumetric energy density. More importantly, it allows the ready use of existing gas infrastructure for energy storage, transport and distribution. Intermittent wind electricity generated is converted into synthetic methane, the Power to Gas (P2G) scheme, by splitting feedstock CO2 and H2O into synthesis gas, a mixture of CO and H2. Syngas plays a central role in the synthesis of a range of hydrocarbon products, including methane, diesel and dimethyl ether. The splitting is accomplished by innovative means; plasmolysis and high-temperature solid oxygen electrolysis. A CO2-neutral fuel cycle is established by powering the conversion step by renewable energy and recapturing the CO2 emitted after combustion, ultimately from the surrounding air to cover emissions from distributed source. Carbon Capture and Utilisation (CCU) coupled to P2G thus creates a CO2-neutral energy system based on synthetic hydrocarbon fuel. It would enable a circular economy where the carbon cycle is closed by recovering the CO2 emitted after reuse of synthetic hydrocarbon fuel. The critical step, technically as well as economically, is the conversion of feedstock CO2/H2O into syngas rather than the capture of CO2 from ambient air.