gebhart/patrepeval huggingface dataset:
Associative memory in gene regulation networks (2010)

The pattern of gene expression in the phenotype of an organism is determined in part by the dynamical attractors of the organism’s gene regulation network. Changes to the connections in this network over evolutionary time alter the adult gene expression pattern and hence the fitness of the organism. However, the evolution of structure in gene expression networks (potentially reflecting past selective environments) and its affordances and limitations with respect to enhancing evolvability is poorly understood in general. In this paper we model the evolution of a gene regulation network in a controlled scenario. We show that selected changes to connections in the regulation network make the currently selected gene expression pattern more robust to environmental variation. Moreover, such changes to connections are necessarily ‘Hebbian’ – ‘genes that fire together wire together’ – i.e. genes whose expression is selected for in the same selective environments become co-regulated. Accordingly, in a manner formally equivalent to well-understood learning behaviour in artificial neural networks, a gene expression network will therefore develop a generalised associative memory of past selected phenotypes. This theoretical framework helps us to better understand the relationship between homeostasis and evolvability (i.e. selection to reduce variability facilitates structured variability), and shows that, in principle, a gene regulation network has the potential to develop ‘recall’ capabilities normally reserved for cognitive systems.
Maternal serum placental protein 13 at 11–13 weeks of gestation in preeclampsia (2009)

PP13 is implicated in the pathogenesis of impaired placentation and subsequent development of early-PE but measurement of this placental product is unlikely to be useful in screening for the disease at 11-13 weeks.
Signal transducer and activator of transcription 3 inhibitors: a patent review (2010)

Numerous groups have shown that in vivo administration of inhibitors of activated Stat3 induce human tumor regression in xenograft models. Indeed, the growing number of preclinical studies in numerous cancer types, as well as the first Phase 0 clinical trial of a Stat3 inhibitor, suggest that Stat3 is a valid and exciting therapeutic target for molecular inhibitors.
SpiroConfidence: Determining the Validity of Smartphone Based Spirometry Using Machine Learning (2018)

Prior work has shown that smartphone spirometry can effectively measure lung function using the phone's built-in microphone and could one day play a critical role in making spirometry more usable, accessible, and cost-effective. Although traditional spirometry is performed with the guidance of a medical expert, smartphone spirometry lacks the ability to provide the patient feedback or guarantee the quality of a patient's spirometry efforts. Smartphone spirometry is particularly susceptible to poorly performed efforts because any sounds in the environment (e.g., a person's voice) or mistakes in the effort (e.g., coughs or short breaths) can invalidate the results. We introduce two approaches to analyze and estimate the quality of smartphone spirometry efforts. A gradient boosting model achieves 98.2% precision and 86.6% recall identifying invalid efforts when given expert tuned audio features, while a Gated-Convolutional Recurrent Neural Network achieves 98.3% precision and 88.0% recall and automatically develops patterns from a Mel-spectrogram, a more general audio feature.
Distinct requirements for Ras oncogenesis in human versus mouse cells (2002)

The spectrum of tumors associated with oncogenic Ras in humans often differs from those in mice either treated with carcinogens or engineered to sporadically express oncogenic Ras, suggesting that the mechanism of Ras transformation may be different in humans. Ras stimulates primarily three main classes of effector proteins, Rafs, PI3-kinase, and RalGEFs, with Raf generally being the most potent at transforming murine cells. Using oncogenic Ras mutants that activate single effectors as well as constitutively active effectors, we find that the RalGEF, and not the Raf or PI3-kinase pathway, is sufficient for Ras transformation in human cells. Thus, oncogenic Ras may transform murine and human cells by distinct mechanisms, and the RalGEF pathway--previously deemed to play a secondary role in Ras transformation--could represent a new target for anti-cancer therapy.
Inhibitors of ATR Kinase for Treatment of Cancer (2013)

ADVERTISEMENT RETURN TO ISSUEPREVPatent HighlightNEXTInhibitors of ATR Kinase for Treatment of CancerAhmed F. Abdel-Magid*View Author Information Therachem Research Medilab (India) Pvt. Ltd., Jaipur, India*Address: 1383 Jasper Drive, Ambler, Pennsylvania 19002, United States. Tel: 215-913-7202. E-mail: [email protected]Cite this: ACS Med. Chem. Lett. 2013, 4, 8, 688–689Publication Date (Web):June 13, 2013Publication History Received10 June 2013Published online13 June 2013Published inissue 8 August 2013https://pubs.acs.org/doi/10.1021/ml4002198https://doi.org/10.1021/ml4002198editorialACS PublicationsCopyright © 2013 American Chemical Society. This publication is available under these Terms of Use. Request reuse permissions This publication is free to access through this site. Learn MoreArticle Views1122Altmetric-Citations-LEARN 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 PDF (192 KB) Get e-AlertscloseSUBJECTS:Assays,Cancer,Cells,Genetics,Peptides and proteins Get e-Alerts
One‐Pot Synthesis and Bioapplication of Amine‐Functionalized Magnetite Nanoparticles and Hollow Nanospheres (2006)

To demonstrate their applications in biological and medical fields such as in immunoassays, magnetic separation of cells or proteins, drug or gene delivery, and magnetic resonance imaging, the template-free syntheses of water-soluble and surface functionalized magnetic nanomaterials have become essential and are challenging. Herein, we developed a facile one-pot template-free method for the preparation of amine-functionalized magnetite nanoparticles and hollow nanospheres by using FeCl(3)6 H(2)O as single iron source. These magnetic nanomaterials were characterized by TEM, SEM, XRD, and FTIR technologies. Their magnetic properties were also studied by using a superconducting quantum interference device (SQUID) magnetometer at room temperature. Then the amine-functionalized magnetite nanoparticles were applied to immunoassays and magnetic resonance imaging in live mice.
Efflux of cellular cholesterol and phospholipid to lipid-free apolipoproteins and class A amphipathic peptides (1995)

The mechanism(s) by which lipid-free apolipoprotein (apo) AI is able to stimulate efflux of cholesterol and phospholipid from cells in cultures has (have) been examined. This process was found to be enhanced when macrophages were enriched with cholesterol. There were 12- and 4-fold increases in cholesterol and phospholipid efflux, respectively, from cholesterol-enriched mouse macrophages when compared to cells not loaded with cholesterol. This enhancement in cholesterol efflux to lipid-free apo AI from macrophages enriched with cholesterol was found to be controlled by the level of free cholesterol in the cells. When cholesterol-enriched mouse macrophages were exposed to lipid-free apo AI at 20 micrograms/mL (706 nM), there was significant efflux of [14C]cholesterol and [3H]phospholipid (20% +/- 0.5%/24 h and 6% +/- 0.3%/24 h, respectively). In comparison, HDL at equivalent protein concentrations only stimulated 11% and 4% efflux of cholesterol and phospholipid, respectively. Synthetic peptides containing amphipathic helical segments that mimic those present in apo AI were used to examine the structural features of the apoprotein which stimulate lipid efflux. Peptides containing only one (18A) or two (37pA) amphipathic helical segments stimulated as much cholesterol efflux from both mouse macrophages and L-cells as apo AI. The order of efficiency, as assessed by the mass concentration at which half-maximal efflux was reached (EC50), was apo AI > 37pA > 18A, indicating that acceptor efficiency was dependent on the number of amphipathic helical segments per molecule. When the helical content of 18A was increased by neutralizing the charges at the ends of the peptide (Ac-18A-NH2), there was a substantial increase in the efficiency for cholesterol efflux (EC50 18A = 17 micrograms/mL vs Ac-18A-NH2 = 6 micrograms/mL). In contrast, when the amphipathicity of the helix in 18A was decreased by scrambling the amino acid sequence, thereby reducing its lipid affinity, cholesterol and phospholipid efflux were not stimulated. The efficiency with which the peptides stimulated cholesterol efflux was in order of their lipid affinity (37pA > Ac-18A-NH2 > 18A), and this order was similar for phospholipid efflux. The time course of lipid release from mouse macrophages and L-cells indicated that phospholipid appeared in the extracellular medium before cholesterol. These results suggest that the apo AI or peptides first interacted with the cell to form protein/phospholipid complexes, that could then accept cholesterol.
Impact of electric vehicles on power distribution networks (2009)

The market for battery powered and plug-in hybrid electric vehicles is currently limited, but this is expected to grow rapidly with the increased concern about the environment and advances in technology. Due to their high energy capacity, mass deployment of electrical vehicles will have significant impact on power networks. This impact will dictate the design of the electric vehicle interface devices and the way future power networks will be designed and controlled. This paper presents the results of an analysis of the impact of electric vehicles on existing power distribution networks. Evaluation of supply/demand matching and potential violations of statutory voltage limits, power quality and imbalance are presented.
Biological activity of a new synthetic muramyl peptide adjuvant devoid of pyrogenicity (1982)

Immunostimulant activities of muramyl dipeptide (enhancement of specific immune responses and of nonspecific resistance to infection) were retained by its N-acetylmuramyl-L-alanyl-D-glutaminyl-n-butyl ester derivative, although very large amounts administered intravenously, or even by the very sensitive intracerebroventricular route, did not elicit fever in the rabbit. This analog also appeared to be devoid of other secondary effects which have been observed after administration of muramyl dipeptide.
Key stages in mammary gland development - The alveolar switch: coordinating the proliferative cues and cell fate decisions that drive the formation of lobuloalveoli from ductal epithelium (2006)

Massive tissue remodelling occurs within the mammary gland during pregnancy, resulting in the formation of lobuloalveoli that are capable of milk secretion. Endocrine signals generated predominantly by prolactin and progesterone operate the alveolar switch to initiate these developmental events. Here we review the current understanding of the components of the alveolar switch and conclude with an examination of the role of the ets transcription factor Elf5. We propose that Elf5 is a key regulator of the alveolar switch.
Final analysis of a phase II study of modified FOLFIRINOX in locally advanced and metastatic pancreatic cancer (2016)

In this first prospective study of modified FOLFIRINOX in MPC and LAPC, we observed decreased AEs compared with historical control patients. In MPC, the efficacy appears comparable with FOLFIRINOX. In LAPC, PFS and OS were prolonged and support the continued use of FOLFIRINOX in this setting.
MatMix 1.0: Using optical mixing to probe visual material perception (2016)

MatMix 1.0 is a novel material probe we developed for quantitatively measuring visual perception of materials. We implemented optical mixing of four canonical scattering modes, represented by photographs, as the basis of the probe. In order to account for a wide range of materials, velvety and glittery (asperity and meso-facet scattering) were included besides the common matte and glossy modes (diffuse and forward scattering). To test the probe, we conducted matching experiments in which inexperienced observers were instructed to adjust the modes of the probe to match its material to that of a test stimulus. Observers were well able to handle the probe and match the perceived materials. Results were robust across individuals, across combinations of materials, and across lighting conditions. We conclude that the approach via canonical scattering modes and optical mixing works well, although the image basis of our probe still needs to be optimized. We argue that the approach is intuitive, since it combines key image characteristics in a "painterly" approach. We discuss these characteristics and how we will optimize their representations.
Structure and dynamics of magnetorheological fluids in rotating magnetic fields (2000)

We report on the orientation dynamics and aggregation processes of magnetorheological fluids subject to rotating magnetic fields using the technique of scattering dichroism. In the presence of stationary fields we find that the mean length of the field-induced aggregates reaches a saturation value due to finite-size effects. When a rotating field is imposed, we see the chains rotate with the magnetic field frequency (synchronous regime) but with a retarded phase angle for all the rotational frequencies applied. However, two different behaviors are found below or above a critical frequency f(c). Within the first regime (low frequency values) the size of the aggregates remains almost constant, while at high frequencies this size becomes shorter due to hydrodynamic drag. Experimental results have been reproduced by a simple model considering a torque balance on the chainlike aggregates.
Glycoprotein biosynthesis in the alg3 Saccharomyces cerevisiae mutant. I. Role of glucose in the initial glycosylation of invertase in the endoplasmic reticulum (1993)

Oligosaccharides on invertase restricted to the endoplasmic reticulum (ER) in alg3,sec18 yeast at 37 degrees C were found to be 20% wild type Man8GlcNAc and 80% Man1 alpha-->2Man1 alpha-->2Man1 alpha-->3(Man1 alpha-->6)Man1 beta-->4GlcNAc2 (Verostek, M.F., Atkinson, P.H., and Trimble, R. B. (1991) J. Biol. Chem. 266, 5547-5551). These results suggested that alg3 was slightly leaky, but did not address whether the oligosaccharide-lipid Man9GlcNAc2 and Man5GlcNAc2 precursors were glucosylated in alg3 yeast. Therefore, an alg3,sec18,gls1 strain was constructed to delete the GLS1-encoded glucosidase I responsible for trimming the terminal alpha 1,2-linked glucose from newly transferred Glc3ManxGlcNAc2 oligosaccharides. Invertase activity was overexpressed 5-10-fold on transforming this strain with a multicopy plasmid (pRB58) carrying the SUC2 gene, and preparative amounts of the ER form of external invertase, derepressed and accumulated at 37 degrees C, were purified. The N-linked glycans were released by sequential treatment with endo-beta-N-acetylglucosaminidase H (endo H) and peptide-N4-N-acetyl-beta-glucosaminyl asparagine amidase. Oligosaccharide pools were sized separately on Bio-Gel P-4, which showed that endo H released about 17% of the carbohydrate as Glc3Man8GlcNAc, while peptide-N4-N-acetyl-beta-glucosaminyl asparagine amidase released the remainder as Hex8GlcNAc2 and Man5GlcNAc2 in a 1:4 ratio. Glycan structures were assigned by 500-MHz two-dimensional DQF-COSY 1H NMR spectroscopy, which revealed that the endo H-resistant Hex8GlcNAc2 pool contained Glc3Man5GlcNAc2 and Man8GlcNAc2 in a 6:4 ratio, the latter a different isomer from that formed by the ER alpha 1,2-mannosidase (Byrd, J. C., Tarentino, A. L., Maley, F., Atkinson, P. H., and Trimble, R. B. (1982) J. Biol. Chem. 257, 14657-14666). Recovery of Glc3Man8GlcNAc and not the ER form of Man8GlcNAc provided an internal control indicating the absence of glucosidase I, which was confirmed by incubation of [3H]Glc3[14C]Man9GlcNAc with solubilized membranes from either alg3,sec18,gls1 or alg3,sec18,GLS1 strains. Chromatographic analysis of the products showed that [3H]Glc was removed only in the presence of the GLS1 gene product. Thus, the vast majority of the N-linked glycosylation in the ER of alg3 yeast (> 75%) occurs by transfer of Man5GlcNAc2 without prior addition of the 3 glucoses normally found on the lipid-linked precursor.
Dominant Weed Species in Peony(Paeonia lactiflora Pallas) Fields (1998)

The experiment was carried out to investigate weed occurrence in peony field. The number of weeds was Compositate 9 species, Gramineae 4 species, Craciferae 3 species, Eugarviaceae, Polygonaceae and Scrophularilaceae 2 species, respectively. Weeds classified by life cycle were annual weed 19 species (57.6%), biennial weed 8 species (24.2%), and perennial weed 6 species (18.2%). Weed species and dominance rate by morphological characteristics were grass weed 4 species (12.1%), broad leaf weed 25 species (84.8%), and sedge weed 1 species (3.1 %) . Major dominant weeds were Capsella bursa-pastoris, Chemopodium album var. centrorubrum and Equisetum arvense in late April, and Digitaria sanguinalis, Erigeron canadensis and Echinochlor crus-galli in late June, and Digitaria sanguinalis, Erigeron canadensis and Echinochlor crus-galli in middle August.
Gabor systems and the Balian-Low Theorem (1998)

The Balian-Low theorem (BLT) is a key result in time-frequency analysis, originally stated by Balian and, independently, by Low, as: If a Gabor system {su2πimbt g(t — na)} m,n∈ℤ with ab = 1 forms an orthonormal basis for L 2(ℝ) then The BLT was later extended from orthonormal bases to exact frames. This paper presents a tutorial on Gabor systems, the BLT, and related topics, such as the Zak transform and Wilson bases. Because of the fact that (g′)⋀(γ) = 2πiγĝ(γ), the role of differentiation in the proof of the BLT is examined carefully. We include the construction of a complete Gabor system of the form {e 2πibmt g(t — a n )} such that {(a n ,b m )} has density strictly less than 1, and an Amalgam BLT that provides distinct restrictions on Gabor systems {e 2πimbt g(t — na)} that form exact frames.
A profile of differentially expressed genes in primary colorectal cancer using suppression subtractive hybridization (1999)

As a step towards understanding the complex differences between normal cells and cancer cells, we have used suppression subtractive hybridization (SSH) to generate a profile of genes overexpressed in primary colorectal cancer (CRC). From a 35¿ omitted¿000 clone SSH-cDNA repertoire, we have screened 400 random clones by reverse Northern blotting, of which 45 clones were scored as overexpressed in tumor compared to matched normal mucosa. Sequencing showed 37 different genes and of these, 16 genes corresponded to known genes in the public databases. Twelve genes, including Smad5 and Fls353, have previously been shown to be overexpressed in CRC. A series of known genes which have not previously been reported to be overexpressed in cancer were also recovered: Hsc70, PBEF, ribophorin II and Ese-3B. The remaining 21 genes have as yet no functional annotation. These results show that SSH in conjunction with high throughput screening provides a very efficient means to produce a broad profile of genes differentially expressed in cancer. Some of the genes identified may provide novel points of therapeutic intervention.
The Structure of the CD4 and CD8 Genes (1987)

The CD4 and CD8 glycoproteins are nonpolymorphic members of the immunoglobulin gene superfamily which are expressed on the surface of functionally distinct populations of T lymphocytes. These molecules, also known respectively as T4/Leu3 and T8/Leu2 in human, and as L3T4 and Lyt2/Lyt3 in mouse, appear to be essential for effective cell-cell inter­ actions, resulting either in target cell lysis or in activation of T lymphocytes. Expression of the CD4 and CD8 molecules correlates with the specificity of T cells for either class-II or class-I major histocompatibility complex (MHC) molecules on target cells (1-7). Thus, CD4 and CD8 may serve to increase the avidity of cell-cell interactions by directly binding to mono­ morphic determinants of the appropriate MHC molecule on target cells (2, 8, 9). The view that the CD4 and CD8 molecules act solely as avidity enhan­ cers has been challenged by recent findings which suggest that these mol­ ecules have a role in transmembrane signal transduction (10-14a). However, no experiments to date have directly tested the ability of CD4 or CD8 to bind ligand or to transduce physiologically relevant signals. It is also not known whether CD4 and CD8 perform analogous functions on separate populations of T cells. The basis for intra thymic selection of CD4+ and CD8+ cells that express appropriate MHC-restricted receptors likewise remains a mystery. The elucidation of these problems awaits functional experiments utilizing the newly isolated genes that encode the CD4 and CD8 glycoproteins (15-24). The emphasis of this review hence is on the isolation and structure of these genes and on the glimpses that the predicted structures of the glycoproteins give us into their potential
Chiral modifications of dolastatin 10: the potent cytostatic peptide (19aR)-isodolastatin 10 (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTChiral modifications of dolastatin 10: the potent cytostatic peptide (19aR)-isodolastatin 10George R. Pettit, Sheo Bux Singh, Fiona Hogan, and Douglas D. BurkettCite this: J. Med. Chem. 1990, 33, 12, 3132–3133Publication Date (Print):December 1, 1990Publication History Published online1 May 2002Published inissue 1 December 1990https://pubs.acs.org/doi/10.1021/jm00174a006https://doi.org/10.1021/jm00174a006research-articleACS PublicationsRequest reuse permissionsArticle Views356Altmetric-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