gebhart/patrepeval huggingface dataset:
Link between Alginate Reaction Front Propagation and General Reaction Diffusion Theory (2011)

We provide a common theoretical framework reuniting specific models for the Ca(2+)-alginate system and general reaction diffusion theory along with experimental validation on a microfluidic chip. As a starting point, we use a set of nonlinear, partial differential equations that are traditionally solved numerically: the Mikkelsen-Elgsaeter model. Applying the traveling-wave hypothesis as a major simplification, we obtain an analytical solution. The solution indicates that the fundamental properties of the alginate reaction front are governed by a single dimensionless parameter λ. For small λ values, a large depletion zone accompanies the reaction front. For large λ values, the alginate reacts before having the time to diffuse significantly. We show that the λ parameter is of general importance beyond the alginate model system, as it can be used to classify known solutions for second-order reaction diffusion schemes, along with the novel solution presented here. For experimental validation, we develop a microchip model system, in which the alginate gel formation can be carried out in a highly controlled, essentially 1D environment. The use of a filter barrier enables us to rapidly renew the CaCl(2) solution, while maintaining flow speeds lower than 1 μm/s for the alginate compartment. This allows one to impose an exactly known bulk CaCl(2) concentration and diffusion resistance. This experimental model system, taken together with the theoretical development, enables the determination of the entire set of physicochemical parameters governing the alginate reaction front in a single experiment.
演化的政治经济学——在获得凡勃伦-康芒斯奖时的讲话 (2005)

2004年6月号(第38卷第2期)刊登了霍华德·J·谢尔曼的文章.凡勃伦-康芒斯奖是美国演化经济学学会设立的经济学奖,其获奖者均为有独立创见的经济学家,如1976年为约翰·肯尼思·加尔布雷思,1999年为保罗·斯威齐.谢尔曼是加利福尼亚大学教授,在研究商业周期方面取得了卓越的成就,主要著作有、,等等.他在这篇文章中介绍了凡勃伦的演化经济学的观点,阐述了商业(经济制度)对工业(技术)、既得利益者对普通民众、野蛮制度对民主制度这三组对立,说明资本主义制度并非像新古典学派鼓吹的那样是永恒的和不可替代的,它的命运将像此前的原始社会、奴隶制度、封建制度一样走向灭亡.文章重点剖析了美国的资本主义,认为对美国普通民众而言,政治民主是有限的,经济民主更是谈不上.文章摘译如下.
Microwave-Assisted Nonaqueous Sol−Gel Chemistry for Highly Concentrated ZnO-Based Magnetic Semiconductor Nanocrystals (2011)

Various transition metal (TM) doped zinc oxide nanoparticles with the composition TMxZn1−xO (TM = V, Mn, Fe, Co, and Ni; x = 0.01−0.3) were prepared by a microwave-assisted nonaqueous sol−gel route in benzyl alcohol within a few minutes. The high doping levels in the range 20−30 atom % achieved for Co and Fe provide a promising opportunity to study the magnetic properties of such potential diluted magnetic semiconductors. However, only Fe0.2Zn0.8O was ferromagnetic at room temperature. The Co-doped sample showed Curie−Weiss behavior up to a doping level of 30 atom %. According to X-ray absorption fine structure (XAFS) measurements, at high doping levels the Fe-doped ZnO samples contain an increasing fraction of Fe3+ ions (in addition to Fe2+), whereas Co is predominantly in the oxidation state of +2. Clustering of Fe ions into amorphous ferromagnetic Fe3O4 within the ZnO host and the magnetic interactions between the Fe3O4 regions is a possible explanation for the ferromagnetic properties.
Metabolomics analysis reveals large effects of gut microflora on mammalian blood metabolites (2009)

Although it has long been recognized that the enteric community of bacteria that inhabit the human distal intestinal track broadly impacts human health, the biochemical details that underlie these effects remain largely undefined. Here, we report a broad MS-based metabolomics study that demonstrates a surprisingly large effect of the gut "microbiome" on mammalian blood metabolites. Plasma extracts from germ-free mice were compared with samples from conventional (conv) animals by using various MS-based methods. Hundreds of features were detected in only 1 sample set, with the majority of these being unique to the conv animals, whereas approximately 10% of all features observed in both sample sets showed significant changes in their relative signal intensity. Amino acid metabolites were particularly affected. For example, the bacterial-mediated production of bioactive indole-containing metabolites derived from tryptophan such as indoxyl sulfate and the antioxidant indole-3-propionic acid (IPA) was impacted. Production of IPA was shown to be completely dependent on the presence of gut microflora and could be established by colonization with the bacterium Clostridium sporogenes. Multiple organic acids containing phenyl groups were also greatly increased in the presence of gut microbes. A broad, drug-like phase II metabolic response of the host to metabolites generated by the microbiome was observed, suggesting that the gut microflora has a direct impact on the drug metabolism capacity of the host. Together, these results suggest a significant interplay between bacterial and mammalian metabolism.
Post‐translational modification: nature's escape from genetic imprisonment and the basis for dynamic information encoding (2012)

We discuss protein post-translational modification (PTM) from an information processing perspective. PTM at multiple sites on a protein creates a combinatorial explosion in the number of potential 'mod-forms', or global patterns of modification. Distinct mod-forms can elicit distinct downstream responses, so that the overall response depends partly on the effectiveness of a particular mod-form to elicit a response and partly on the stoichiometry of that mod-form in the molecular population. We introduce the 'mod-form distribution'-the relative stoichiometries of each mod-form-as the most informative measure of a protein's state. Distinct mod-form distributions may summarize information about distinct cellular and physiological conditions and allow downstream processes to interpret this information accordingly. Such information 'encoding' by PTMs may facilitate evolution by weakening the need to directly link upstream conditions to downstream responses. Mod-form distributions provide a quantitative framework in which to interpret ideas of 'PTM codes' that are emerging in several areas of biology, as we show by reviewing examples of ion channels, GPCRs, microtubules, and transcriptional co-regulators. We focus particularly on examples other than the well-known 'histone code', to emphasize the pervasive use of information encoding in molecular biology. Finally, we touch briefly on new methods for measuring mod-form distributions.
The Hormonal Control of Organ Formation in Callus of Medicago sativa L. Cultured in Vitro (1978)

Organogenesis in alfalfa callus (Medicago sativa L. cv. ‘Regen S’) has been obtained by the transfer of callus from an induction medium containing growth regulators to a regeneration medium lacking growth regulators. The transfer of callus from induction medium containing high levels of 2,4-D and low levels of kinetin to regeneration medium resulted in the formation of shoots. Conversely, the transfer of callus from induction medium containing low levels of 2,4-D and high levels of kinetin resulted in the formation of roots. The pattern of organogenesis on regeneration medium was modified by the nutritional composition of that medium. When Blaydes medium supplemented with inositol and yeast extract was employed as regeneration medium, root organogenesis was inhibited. Root organogenesis was not inhibited by either Shenk and Hildebrandt medium or Gamborg's B5 medium. Shoot formation occurred on all of these media. A survey of the in vitro organ-forming capacity of 14 genotypic clones from the cv. ‘Regen S’ was conducted. The capacity to form organs differed quantitatively among the clones analyzed. A more detailed analysis of a highly responsive clone (RA3) and a poorly responsive clone (RA5) revealed no significant qualitative difference in their organogenic responses.
Oscillations in exchange coupling and magnetoresistance in metallic superlattice structures: Co/Ru, Co/Cr, and Fe/Cr (1990)

We report the discovery of antiferromagnetic interlayer exchange coupling and enhanced saturation magnetoresistance in two new metallic superlattice systems, Co/Cr and Co/Ru. In these systems and in Fe/Cr superlattices both the magnitude of the interlayer magnetic exchange coupling and the saturation magnetoresistance are found to oscillate with the Cr or Ru spacer layer thickness with a period ranging from 12 \AA{} in Co/Ru to \ensuremath{\simeq}18--21 \AA{} in the Fe/Cr and Co/Cr systems.
Nurses’ descriptions of changes in cognitive function in the acute care setting (2008)

Objective: To describe nurses’ documentation of cognition and behavioural changes in patients in acute care settings. Hospitalised patients often present with multiple co‑morbidities including declining levels of cognitive functioning and this is particularly so for older people. Many older people will experience a delirium during hospitalisation. While prevention or prompt management of delirium is paramount to providing quality care, research suggests that health professionals regularly fail to differentiate between delirium and other cognitive changes in hospitalised patients. Design: Four audits of progress notes were completed over a four week period at a Western Australian tertiary hospital to identify, quantify and categorise cognitive and behavioural changes in hospitalised patients. This paper describes data on nurses’ documentation collected in the course of those audits. On four consecutive Thursdays, the medical records of all patients identified by nursing staff as being confused were reviewed. Where no definitive cause for the confusion was documented, the case notes were examined for evidence of risk factors to determine a probable cause. Setting: A Western Australian tertiary hospital. Subjects: The medical records of all patients identified by nursing staff as being confused. Main outcome measures: Documentation in patient medical records of a patient having cognitive or behavioural changes or being confused; use of a cognitive screening tool; or a diagnosis of delirium. Results: A total of 1209 patients were surveyed over the four audit days with 183 patients (15%) being identified as confused. ‘Confusion’ was the most common descriptor used by nurses to describe cognitive and behavioural changes; in many cases it was the only term used. Many of these changes were indicative of delirium. Little use by any health professional of cognitive screening tools was found. Conclusion: Cognitive and behavioural changes are a common problem in hospitalised patients who are elderly. The use of the term confusion to describe a range of cognitive and behavioural changes is a barrier to accurate identification of delirium, which is often the first indicator of serious underlying illness.
Cervical Kyphosis (2002)

A ratio below 0.3 between the anteroposterior diameter of the medulla-pons junction and the spinal cord at the apex was a risk factor for cervical myelopathy. One of the most predictable risk factors of progression of the cervical kyphosis was osteophyte formation at the anterior aspect of the vertebral body.
Fast Ignition by Intense Laser-Accelerated Proton Beams (2001)

The concept of fast ignition with inertial confinement fusion (ICF) is a way to reduce the energy required for ignition and burn and to maximize the gain produced by a single implosion. Based on recent experimental findings at the PETAWATT laser at Lawrence Livermore National Laboratory, an intense proton beam to achieve fast ignition is proposed. It is produced by direct laser acceleration and focused onto the pellet from the rear side of an irradiated target and can be integrated into a hohlraum for indirect drive ICF.
Dual energy CT via fast kVp switching spectrum estimation (2009)

Recently there has been significant interest in dual energy CT imaging with several acquisition methods being actively pursued. Here we investigate fast kVp switching where the kVp alternates between low and high kVp every view. Fast kVp switching enables fine temporal registration, helical and axial acquisitions, and full field of view. It also presents several processing challenges. The rise and fall of the kVp, which occurs during the view integration period, is not instantaneous and complicates the measurement of the effective spectrum for low and high kVp views. Further, if the detector digital acquisition system (DAS) and generator clocks are not fully synchronous, jitter is introduced in the kVp waveform relative to the view period. In this paper we develop a method for estimation of the resulting spectrum for low and high kVp views. The method utilizes static kVp acquisitions of air with a small bowtie filter as a basis set. A fast kVp acquisition of air with a small bowtie filter is performed and the effective kVp is estimated as a linear combination of the basis vectors. The effectiveness of this method is demonstrated through the reconstruction of a water phantom acquired with a fast kVp acquisition. The impact of jitter due to the generator and detector DAS clocks is explored via simulation. The error is measured relative to spectrum variation and material decomposition accuracy.
Identification of the human c-myc protein nuclear translocation signal. (1988)

We identified and characterized two regions of the human c-myc protein that target proteins into the nucleus. Using mutant c-myc proteins and proteins that fuse portions of c-myc to chicken muscle pyruvate kinase, we found that residues 320 to 328 (PAAKRVKLD; peptide M1) induced complete nuclear localization, and their removal from c-myc resulted in mutant proteins that distributed in both the nucleus and cytoplasm but retained rat embryo cell cotransforming activity. Residues 364 to 374 (RQRRNELKRSP; peptide M2) induced only partial nuclear targeting, and their removal from c-myc resulted in mutant proteins that remained nuclear but were cotransformationally inactive. We conjugated synthetic peptides containing M1 or M2 to human serum albumin and microinjected the conjugate into the cytoplasm of Vero cells. The peptide containing M1 caused rapid and complete nuclear accumulation, whereas that containing M2 caused slower and only partial nuclear localization. Thus, M1 functions as the nuclear localization signal of c-myc, and M2 serves some other and essential function.
Worms to the rescue: Can worm glycans protect from autoimmune diseases? (2010)

Autoimmune and autoinflammatory diseases represent a significant health burden, especially in Western societies. For the majority of these diseases, no cure exists. Recently, research on parasitic worms (helminths) has demonstrated great potential for whole worms, their eggs or their excretory/secretory proteins in down-regulating inflammatory responses both in vitro and in vivo, in various disease models and, in some cases, even in clinical trials. The worms are thought to induce Th2 and regulatory T cells, interfere with Toll-like receptor (TLR) signaling and to down-regulate Th17 and Th1 responses. The molecular mechanisms underlying the worms' ability to modulate the host immune response are not well understood, and many hypotheses have been proposed to explain the observed immune modulation. Increasing evidence suggests that carbohydrate structures (glycans), for example, phosphorylcholine-modified glycans or Galbeta1-4(Fucalpha1-3)GlcNAc- (Lewis X, Le(X)) containing glycans, expressed by the worms contribute to these modulating properties by their interaction with antigen presenting cells. Helminths express a broad variety of protein- and lipid-linked glycans on their surface and on secretory products. These glycans differ in amount and composition and several of these structures are species specific. However, worms also express glycan antigens that are found in a wide variety of different species. Some of these "common" worm glycans are particularly interesting with regard to regulating host responses, because they have the potential to interact with C-type lectins on dendritic cells and thereby may interfere with T-cell polarization. Helminths and helminth-derived molecules form a novel and promising group of therapeutics for autoinflammatory diseases. However, much has to be learned about the molecular mechanisms behind the helminth-mediated antiinflammatory properties. This review will describe some of the emerging evidence in selected disease areas as well as discuss the putative role of glycans in helminth-mediated immunosuppression.
Composing high-performance memory allocators (2001)

article Share on Composing high-performance memory allocators Authors: Emery D. Berger Dept. of Computer Sciences, The University of Texas at Austin, Austin, TX Dept. of Computer Sciences, The University of Texas at Austin, Austin, TXView Profile , Benjamin G. Zorn Microsoft Research, One Microsoft Way, Redmond, WA Microsoft Research, One Microsoft Way, Redmond, WAView Profile , Kathryn S. McKinley Dept. of Computer Science, University of Massachusetts, Amherst, MA Dept. of Computer Science, University of Massachusetts, Amherst, MAView Profile Authors Info & Claims ACM SIGPLAN NoticesVolume 36Issue 5May 2001 pp 114–124https://doi.org/10.1145/381694.378821Online:01 May 2001Publication History 119citation1,262DownloadsMetricsTotal Citations119Total Downloads1,262Last 12 Months49Last 6 weeks4 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access
The Preparation of Acetyl-5-fluorosalicylic Acid (1939)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe Preparation of Acetyl-5-fluorosalicylic AcidC. M. Suter and Arthur W. WestonCite this: J. Am. Chem. Soc. 1939, 61, 9, 2317–2318Publication Date (Print):September 1, 1939Publication History Published online1 May 2002Published inissue 1 September 1939https://pubs.acs.org/doi/10.1021/ja01878a015https://doi.org/10.1021/ja01878a015research-articleACS PublicationsRequest reuse permissionsArticle Views86Altmetric-Citations5LEARN 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
An open-label phase II study of the Hsp90 inhibitor ganetespib (STA-9090) as monotherapy in patients with advanced non-small cell lung cancer (NSCLC). (2011)

7500 Background: Ganetespib is a potent, next-generation Hsp90 inhibitor that is structurally unrelated to the first-generation ansamycin class of Hsp90 inhibitors and has shown superior activity to these agents in preclinical studies. Ganetespib has been well tolerated and has shown promising antitumor activity in early trials in multiple cancers. Methods: Patients (pts) with advanced NSCLC who failed prior treatments received 200 mg/m2 ganetespib as a 1-hr infusion once weekly for 3 of a 4-wk cycle in a Simon two-stage study design assessing primary endpoint of PFS rate at 16 wks. Initial cohorts were defined by mutation status: A) EGFR B) KRAS C) EGFR and KRAS wild type (WT). If ≥2/14 pts in A, B or C were progression-free at 16 wks, enrollment increased to 23 pts for that cohort. Tumor response was assessed every 8 wks. Cohort D was added to include 35 additional EGFR and KRAS WT pts with adenocarcinoma histology. Additional mutational analysis of BRAF, PIK3CA, ERBB2 and MET, as well as FISH analysis for ALK translocation, were performed for Cohorts C and D. Results: 73 pts (31 M, 42 F; median age 62 yrs, range 28-82; ECOG 0-1; prior therapies range 1-10) received a median of 2 cycles (range 1-12) of ganetespib in cohorts A (14), B (17), and C+D (42). AEs reported in ≥20% of pts included diarrhea, fatigue, nausea, anorexia, constipation, and dyspnea and were generally grade 1-2. Expansion criteria were achieved for cohort C, including a durable partial response (PR) and seven pts with prolonged stable disease (≥16 wks). Cohort D continues recruitment. Mutational analyses of Cohort C and D samples will be presented. Conclusions: Ganetespib administered as a single-agent is well-tolerated in pts with NSCLC at 200 mg/m2 once weekly without severe liver, ocular, cardiovascular or renal toxicity. Clinical activity has been observed in pts with advanced NSCLC tumors harboring wild-type EGFR and KRAS.
Effect of heptakis (2,6-O-dimethyl) beta-cyclodextrin on the production of pertussis toxin by Bordetella pertussis (1983)

The effect of heptakis (2,6-O-dimethyl) beta-cyclodextrin (Me beta CD) on the production of pertussis toxin was evaluated. The addition of Me beta CD to the medium stimulated cell growth and pertussis toxin production. Me beta CD enhanced pertussis toxin production 100 times more in synthetic media, such as Stainer-Scholte medium (D. W. Stainer and M. J. Scholte, J. Gen. Microbiol. 63:211-220), than in Me beta CD-free medium in 2-day shake cultures. Maximum production of pertussis toxin was estimated as 50 mg of protein per liter of culture broth both by in vitro and in vivo assays. Purified toxin was demonstrated to be biochemically and biologically identical to the toxin produced in Me beta CD-free static cultures.
The Osteoinductive Activity of Bone Morphogenetic Protein (BMP) Purified by Repeated Extracts of Bovine Bone (2004)

Native bone morphogenetic proteins (BMPs) extracted from bone have been used clinically to stimulate bone regeneration and repair. However, preparation of purified BMP is a laborious process. This study investigated the yield, activity and cost effectiveness of repeatedly extracting the same bone matrix to produce purified BMP. While repeated extraction was able to increase the yield 62% the activity of the partially purified BMP in later extracts decreased both in vitro and in vivo. This decline in activity appears to be due to an increase in non-BMP contaminants, such as collagen, in the extracts. When the first three extracts were combined and processed together activity was equivalent to that of the first extract. A simple analysis based on the cost of reagents used and the time required for purification indicates that separate processing of the extracts is inefficient while combining the first and second extracts and processing them together would result in a small cost saving. Based on this study we would recommend that the demineralized bone matrix be extracted no more than twice and that the extracts be combined for further processing.
Antineoplastic agents. 168. Isolation and structure of axinohydantoin (1990)

Western (Palau) and Eastern (State of Truk) Caroline Islands and Papua New Guinea sponges of the genera Axinella and Hymeniacidon were found to contain the cytostatic (PS ED 50 2.5 and 2.0 (μg/mL) and antineoplastic (PS T/C 143 at 3.6 mg/kg and T/C 138 at 3.6 mg/kg) pyrrologuanidines 1a and 1b. The related hydantoin 2, designated axinohydantoin, was also isolated from an Axinella sp. and its structure was assigned by X-ray crystallographic techniques. Present experience with sponges in the Axinella and Hymeniacidon genera suggests that the previously known hymenialdisine (1b) and analogous imidazole derivatives may be widely distributed among these and related orange colored Porifera. Keywords: axinohydantoin, hymenialdisine, Axinella, Hymeniacidon, cystostatic.