gebhart/patrepeval huggingface dataset:
Detection of functional modules from protein interaction networks (2003)

Complex cellular processes are modular and are accomplished by the concerted action of functional modules (Ravasz et al., Science 2002;297:1551-1555; Hartwell et al., Nature 1999;402:C47-52). These modules encompass groups of genes or proteins involved in common elementary biological functions. One important and largely unsolved goal of functional genomics is the identification of functional modules from genomewide information, such as transcription profiles or protein interactions. To cope with the ever-increasing volume and complexity of protein interaction data (Bader et al., Nucleic Acids Res 2001;29:242-245; Xenarios et al., Nucleic Acids Res 2002;30:303-305), new automated approaches for pattern discovery in these densely connected interaction networks are required (Ravasz et al., Science 2002;297:1551-1555; Bader and Hogue, Nat Biotechnol 2002;20:991-997; Snel et al., Proc Natl Acad Sci USA 2002;99:5890-5895). In this study, we successfully isolate 1046 functional modules from the known protein interaction network of Saccharomyces cerevisiae involving 8046 individual pair-wise interactions by using an entirely automated and unsupervised graph clustering algorithm. This systems biology approach is able to detect many well-known protein complexes or biological processes, without reference to any additional information. We use an extensive statistical validation procedure to establish the biological significance of the detected modules and explore this complex, hierarchical network of modular interactions from which pathways can be inferred.
The Spectrophotometric Absorbance of Intralipid® (1980)

The spectral absorbance of Intralipid, a phospholipid emulsion, was investigated to discern its effect, when parenterally administered, on the spectrophotometric measurement of hemoglobin (Hb), oxyhemoglobin (HbO2), and carboxyhemoglobin (HbCO). While accounting for dilutional factors, various concentrations of Intralipid in both water and hemoglobin solutions were analyzed at six wavelengths commonly used to measure Hb, HbO2 and HbCO. Absorbance increased linearly with Intralipid concentration at all wavelengths, and ranged from 0.034 at 505 nm to 0.019 at 626.6 nm per mg of Intralipid. Therefore, in patients receiving Intralipid, significant errors in Hb, HbO2 and HbCO measurements can be introduced if these measurements are made by oximetry, and the authors suggest that such measurements should be accomplished by methods other than spectrophotometry.
Trefoil Factor 3, Cholinesterase and Homocysteine: Potential Predictors for Parkinson’s Disease Dementia and Vascular Parkinsonism Dementia in Advanced Stage (2018)

Our findings suggest that serum TFF3, ChE activity and Hcy levels may underlie the pathophysiological mechanisms of PDD and VPD. As the race to find biomarkers or predictors for these diseases intensifies, a better understanding of the roles of TFF3, ChE activity and Hcy may yield insights into the pathogenesis of PDD and VPD.
Performance of a Turbo-Coded CDMA System in an Indoor Wireless Infrared Channel (2009)

Turbo-coded CDMA system is analyzed and simulated in an indoor wireless infrared channel. The indoor infrared channel is modeled as a non-directed diffuse link. From the simulation results, it is confirmed that the turbo coding is very effective in improving BER (bit error rate) performance, and outperforms BCH code.
Neurophysiologic analyses of low- and high-level visual processing in Alzheimer disease (2007)

We conclude that visual evoked potentials (EPs) are abnormal in all patients with Alzheimer disease (AD): Those with small pattern and motion onset EPs may have greater AD pathology in visual cortex, whereas those with larger pattern onset EPs may have greater AD pathology in higher centers. These findings highlight the utility of visual EPs in distinguishing between syndromic variants of AD associated with particular patterns of functional decline.
Catalytic activity of unpromoted and promoted nickel molybdate in butane selective oxidation (1996)

Stoichiometric α- and β-phases of NiMoO4 show remarkable differences in the selective oxidation of butane to butenes and butadiene; modification of the surface acid–base properties of the catalysts by doping with K and Ca results in an increase in catalytic activity, especially with the α-phase.
Electron beam dynamics and self-cooling up to PeV level due to betatron radiation in plasma-based accelerators (2012)

In plasma-based accelerators, electrons are accelerated by ultrahigh gradient of $1--100\text{ }\text{ }\mathrm{GV}/\mathrm{m}$ and undergo the focusing force with the same order as the accelerating force. Heated electrons are injected in a plasma wake and exhibit the betatron oscillation that generates synchrotron radiation. Intense betatron radiation from laser-plasma accelerators is attractive x-ray/gamma-ray sources, while it produces radiation loss and significant effects on energy spread and transverse emittance via the radiation reaction force. In this article, electron beam dynamics on transverse emittance and energy spread with considering radiation reaction effects are studied numerically. It is found that the emittance growth and the energy spread damping initially dominate and balance with radiative damping due to the betatron radiation. Afterward the emittance turns to decrease at a constant rate and leads to the equilibrium at a nanometer radian level with growth due to Coulomb scattering at PeV-level energies. A constant radiation loss rate ${R}_{T}=2/3$ is found without regard to the electron beam and plasma conditions. Self-cooling of electron beams due to betatron radiation may guarantee TeV-range linear colliders and give hints on astrophysical ultrahigh-energy phenomena.
Proteolytic Cleavage of the β1 Subunit of Platelet α2β1 Integrin by the Metalloproteinase Jararhagin Compromises Collagen-stimulated Phosphorylation of pp72 (1997)

Early signaling events in the stimulation of platelets by collagen include the tyrosine phosphorylations of FcR gamma-chain, pp72(syk) and phospholipase Cgamma2. These events are dependent on the main platelet collagen receptor, alpha2beta1 integrin (glycoprotein Ia-IIa complex). We recently found that jararhagin, a 52-kDa snake venom metalloproteinase, selectively inhibits collagen-induced platelet secretion and aggregation in parallel with the cleavage of the beta1 subunit of the alpha2beta1 integrin. The present study demonstrates that jararhagin also interferes with collagen-induced phosphorylation of the protein-tyrosine kinase pp72(syk). This effect is not observed when the platelet aggregation response to collagen is inhibited by two venom RGD-containing disintegrins, contortrostatin and echistatin. These disintegrins inhibit platelet aggregation through their high affinity binding to the platelet alphaIIbbeta3 integrin (glycoprotein IIb-IIIa complex). We also show that mild stimulation by ADP of jararhagin-treated platelets, but not of platelets treated with the RGD-containing disintegrins, restores the collagen-induced platelet aggregation. ADP also restored both pp72(syk) and pleckstrin phosphorylation of jararhagin-treated platelets in response to collagen, presumably via interaction of collagen with ADP-activated alphaIIbbeta3 integrin. Thus, RGD-containing disintegrins do not interfere with agonist-induced pp72(syk) phosphorylation but inhibit aggregation through occupancy of the alphaIIbbeta3 integrin. Conversely, jararhagin affects early platelet signaling events in response to collagen through its effects on the alpha2beta1 integrin without interfering with the function of the alphaIIbbeta3 integrin. Our demonstration that the degradation of the beta1 subunit of alpha2beta1 by jararhagin results in the loss of pp72(syk) phosphorylation, suggests that this subunit is critically involved in collagen-induced platelet signaling.
Pretreatment Thrombocytosis as a Prognostic Factor in Metastatic Breast Cancer (2013)

Background. An elevated platelet count is often associated with malignancies, and it has been confirmed as an adverse prognostic factor in various cancers including early stage breast cancer. We sought to determine if thrombocytosis is also a prognostic factor in metastatic breast cancer. Patients and Methods. The records of 165 metastatic breast cancer patients with complete follow-up that had thrombocytosis or normal platelet counts were reviewed. Kaplan-Meier curves were constructed, and the survivals of the two groups were compared using the LogRank test. A Cox regression analysis was used to determine if thrombocytosis is an independent factor for overall and progression free survival. Results. There was a statistically significant difference in overall and progression free survival favoring the normal platelets group (LogRank test and 0.008, resp.). Thrombocytosis remained a significant adverse prognostic factor in multivariate analysis. Other independent prognostic factors for overall survival included age, ER/PR status, and grade. Conclusion. Thrombocytosis represents an independent adverse prognostic factor in patients with metastatic breast cancer. Thus metastatic breast cancer joins a range of cancers in which this easily measurable value can be used for clinical prognostication. Further use as a predictive value for specific treatments has a rationale and deserves to be investigated.
Missing Data in Randomized Clinical Trials for Weight Loss: Scope of the Problem, State of the Field, and Performance of Statistical Methods (2009)

Our analysis offers an equation for predictions of dropout rates useful for future study planning. Our raw data analyses suggests that multiple imputation is better than other methods for handling missing data in obesity randomized controlled trials, followed closely by mixed models. We suggest these methods supplant last observation carried forward as the primary method of analysis.
Resistance switching in the metal deficient-type oxides: NiO and CoO (2007)

The resistance switching properties in Pt∕Ni–O∕Pt and Pt∕Co–O∕Pt synthesized by the magnetron sputtering have been investigated. The oxygen partial pressure during sputtering and the post-thermal process are crucial to forming of the trilayer. By investigating x-ray photoemission spectroscopy spectra, the increase of initial resistance in Ni–O was caused by the variation of the stoichiometry, while that in the Co–O was accompanied by the phase transformation between CoO and Co3O4. The resistance switching in Pt∕Co–O∕Pt and Pt∕Ni–O∕Pt exhibits the analogous electrode area and temperature dependences. As a result of the I-V measurements at the elevated temperature, the assistance of Joule heating in the reset process is implied.
Highly resolving two-dimensional gels for protein sequencing. (1991)

Two-dimensional (2D) PAGE, using carrier ampholytes for the first-dimension separation, has provided a tool for the simultaneous analysis of cellular proteins. To extend the utility of 2D PAGE to the preparative level, we have investigated the use of immobilized pH gradients (IPG) for the first-dimension separation. The results we have obtained indicate that as much as 1 mg of cellular protein can be loaded onto a single IPG gel without loss of resolution. Mutant polypeptides previously detected in carrier ampholyte-based 2D gels were equally detectable in IPG-based 2D gels. With IPG gels several hundred cellular polypeptides can be isolated, from as few as 10 gels, in sufficient amount for sequencing with current sequencing technology. We therefore conclude that IPG greatly enhances the prospects for the large-scale sequencing of cellular proteins for the development of 2D gel-related protein data bases and for the identification of new polypeptide gene products, with the attendant implications for a genome sequencing effort.
Polyphenylated cyclobuten-4-ones from squaryl dichloride (1974)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPolyphenylated cyclobuten-4-ones from squaryl dichlorideEberhard W. Neuse and Brian R. GreenCite this: J. Org. Chem. 1974, 39, 11, 1585–1587Publication Date (Print):May 1, 1974Publication History Published online1 May 2002Published inissue 1 May 1974https://pubs.acs.org/doi/10.1021/jo00924a029https://doi.org/10.1021/jo00924a029research-articleACS PublicationsRequest reuse permissionsArticle Views80Altmetric-Citations4LEARN 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
On the theory of thermal stresses in a thin bonding layer (1995)

Thin bonding layers made of solders or metal-filled adhesives are widely used in electronics. They are mostly responsible for the integrity and reliability of computers and other electronic devices. Major concerns are due to thermal stresses arising in the process of electronic packaging. In this article, the analytical theory of thermal stresses is constructed under some natural simplifying assumptions. The assumptions include the thermoelastic behavior of the bonded materials and thermoelastic–plastic behavior of a bonding layer, after the latter is deposited and the composite system is cooled to an operational temperature. The closed system of governing partial differential equations for thermal stresses in a thin bonding layer is derived for any in-plane shape of the layer. Some particular problems are solved in an explicit form and the implication of the solutions for the prediction of planar voids and cracks formation are discussed.
Atomic layer deposition of ZrO2 on W for metal–insulator–metal capacitor application (2003)

A metal–insulator–metal (MIM) capacitor using ZrO2 on tungsten (W) metal bottom electrode was demonstrated and characterized in this letter. Both ZrO2 and W metal were synthesized by an atomic layer deposition (ALD) method. High-quality 110∼115 Å ZrO2 films were grown uniformly on ALD W using ZrCl4 and H2O precursors at 300 °C, and polycrystalline ZrO2 in the ALD regime could be obtained. A 13∼14-Å-thick interfacial layer between ZrO2 and W was observed after fabrication, and it was identified as WOx through angle-resolved x-ray photoelectron spectroscopy analysis with wet chemical etching. The apparent equivalent oxide thickness was 20∼21 Å. An effective dielectric constant of 22∼25 including an interfacial WOx layer was obtained by measuring capacitance and thickness of MIM capacitors with Pt top electrodes. High capacitance per area (16∼17 fF/μm2) and low leakage current (10−7 A/cm2 at ±1 V) were achieved.
Heteroatomic Aroma Compounds (2002)

Techniques to determine volatile sulfur compounds in foods including: distillation, co-distillation, SDE, liquid-liquid extraction and sublimation are discussed in terms of efficiencies and potential artifact formation. Advantages, limitations and potential problems using SPME as well as purge, and trap concentration techniques are discussed. Sample-analyte dependent concentration techniques such as, adsorption on mercury based solid sorbents, metal foils, and impregnated filters are presented. Separation techniques including HPLC and GC are compared in terms of separation power, sample capacity and detector sensitivity. Limits of detection, sensitivity, selectivity and cost of flame photometric, chemilluminescence, atomic emission and pulsed flame photometric GC detectors are discussed. Advantages and limitations of isotope dilution analysis are presented.
Dissecting the role of milk components on gut microbiota composition (2012)

The composition of human milk is tailored to contribute to the development of the gastrointestinal (GI) tract of newborns and infants. Importantly, human milk contains the antimicrobial compounds lysozyme and lactoferrin that are thought to contribute to the formation of a health-promoting microbiota. As these protective factors are lacking in the milk of dairy animals, we genetically engineered goats expressing human lysozyme in their milk and have recently reported a new animal model to dissect out the role of milk components on gut microbiota formation. Using the pig as a more human-relevant animal model, we demonstrated that consumption of lysozyme-rich milk enriched the abundance of bacteria associated with GI health and decreased those associated with disease, much like human milk. This work demonstrated that the pig is a valid animal model for gut microbiome studies on the effects of dietary components on microbiota composition, host-microbe interactions and state of the intestine.
Properties of amorphous alloy films mainly composed of Co--Nb (1983)

Amorphous alloy films, mainly composed of Co-Nb, have been studied by radio frequency (RF) sputtering. These amorphous films having small magnetostriction show excellent soft magnetic properties after the magnetic annealing we have developed. One of them with the composition of (Co <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">83.5</inf> Fe <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> ) <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">92/85.5</inf> Nb <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">8</inf> was found to have very high saturation magnetization <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">B_{s} = 14300</tex> (gauss). The effects of additives such as Zr to the alloys have been investigated and amorphous films having high crystallization temperature as well as high saturation magnetization were successfully obtained. These amorphous films show fairly good wear and corrosion resistance as well as excellent thermal stability of the magnetic properties.
Endocannabinoids in the rat basolateral amygdala enhance memory consolidation and enable glucocorticoid modulation of memory (2009)

Extensive evidence indicates that the basolateral complex of the amygdala (BLA) modulates the consolidation of memories for emotionally arousing experiences, an effect that involves the activation of the glucocorticoid system. Because the BLA expresses high densities of cannabinoid CB1 receptors, the present experiments investigated whether the endocannabinoid system in the BLA influences memory consolidation and whether glucocorticoids interact with this system. The CB1 receptor agonist WIN55,212-2 (5-50 ng per 0.2 microL per side), infused bilaterally into the BLA of male Sprague-Dawley rats immediately after inhibitory avoidance training, induced dose-dependent enhancement of 48-h retention. Conversely, the CB1 receptor antagonist AM251 (0.07-0.28 ng per 0.2 microL per side) administered after training into the BLA induced inhibitory avoidance retention impairment. Furthermore, intra-BLA infusions of a low and nonimpairing dose of AM251 (0.14 ng per 0.2 microL per side) blocked the memory enhancement induced by concurrent administration of WIN55,212-2. Delayed infusions of WIN55,212-2 or AM251 administered into the BLA 3 h after training or immediate posttraining infusions of these drugs into the adjacent central amygdala did not significantly alter retention performance. Last, intra-BLA infusions of a low and otherwise nonimpairing dose of AM251 (0.14 ng per 0.2 microL per side) blocked the memory-enhancing effect induced by systemic administration of corticosterone (3 mg/kg, s.c.). These findings indicate that endocannabinoids in the BLA enhance memory consolidation and suggest that CB1 activity within this brain region is required for enabling glucocorticoid effects on memory consolidation enhancement.
Methylprednisolone-rituximab is an effective salvage therapy for patients with relapsed chronic lymphocytic leukemia including those with unfavorable cytogenetic features (2007)

Chronic lymphocytic leukemia (CLL) patients with aggressive molecular characteristics such as deletion of 17p13.1 do not respond to conventional treatments and have a shorter survival. Studies suggest that high-dose methylprednisolone (HDMP) has activity in such patients and combining HDMP with rituximab may enhance efficacy. We identified 37 patients with CLL treated with the HDMP-rituximab who had follow-up at Mayo Clinic. Nine of 27 (33%) had deletion of 17p13.1 and six of 27 (22%) had deletion of 11q22.3. After a median of one cycle of HDMP-rituximab, 29 (78%) patients had an objective response according to the National Cancer Institute CLL Working Group Criteria including five of nine patients with deletion of 17p13.1. Eight (22%) patients had a complete clinical response. Although well tolerated, 11 (29%) patients developed infectious complications before completing one month of therapy. Three-year survival was 41% (95% CI: 26 - 66%). HDMP-rituximab is an active regimen in patients with relapsed, refractory, and cytogenetically high-risk CLL. Further evaluation of this regimen in controlled trials appears warranted.
Occam's inversion; a practical algorithm for generating smooth models from electromagnetic sounding data (1987)

Abstract The inversion of electromagnetic sounding data does not yield a unique solution, but inevitably a single model to interpret the observations is sought. We recommend that this model be as simple, or smooth, as possible, in order to reduce the temptation to overinterpret the data and to eliminate arbitrary discontinuities in simple layered models.To obtain smooth models, the nonlinear forward problem is linearized about a starting model in the usual way, but it is then solved explicitly for the desired model rather than for a model correction. By parameterizing the model in terms of its first or second derivative with depth, the minimum norm solution yields the smoothest possible model.Rather than fitting the experimental data as well as possible (which maximizes the roughness of the model), the smoothest model which fits the data to within an expected tolerance is sought. A practical scheme is developed which optimizes the step size at each iteration and retains the computational efficiency of layered models, resulting in a stable and rapidly convergent algorithm. The inversion of both magnetotelluric and Schlumberger sounding field data, and a joint magnetotelluric-resistivity inversion, demonstrate the method and show it to have practical application.