gebhart/patrepeval huggingface dataset:
Mass spectrometry of N‐linked oligosaccharides using atmospheric pressure infrared laser ionization from solution (2004)

An atmospheric pressure (AP) infrared (IR) laser ionization technique, implemented on a quadrupole ion trap mass spectrometer, was used to analyze underivatized, N-linked oligosaccharides in solution. Experiments were conducted on an atmospheric pressure infrared ionization from solution (AP-IRIS) ion source which differed from previous AP IR matrix-assisted laser desorption/ionization (MALDI) interfaces in that the ion source operated in the absence of an extraction electric field with a higher power 2.94 microm IR laser. The general term 'IRIS' is used as the mechanism of ionization differs from that of MALDI, and is yet to be fully elucidated. The AP-IRIS ion source demonstrated femtomole-level sensitivity for branched oligosaccharides. AP-IRIS showed approximately 16 times improved sensitivity for oligomannose-6 and the core-fucosylated glycan M3N2F over optimal results obtainable on a AP UV-MALDI with a 2,4,6-trihydroxyacetophenone matrix. Comparison between IR and UV cases also showed less fragmentation in the IR spectrum for a glycan with a conserved trimannosyl core, core-substituted with fucose. A mixture of complex, high-mannose and sialylated glycans resulted in positive ion mass spectra with molecular ion peaks for each sugar. Tandem mass spectrometry of the sodiated molecular ions in a mixture of glycans revealed primarily glycosidic (B, Y) cleavages. The reported results show the practical utility of AP-IRIS while the ionization mechanism is still under investigation.
MAF file for mutations from Real-time Genomic Characterization of Advanced Pancreatic Cancer to Enable Precision Medicine (2023)

&lt;p&gt;MAF file for mutations identified in the cohort&lt;/p&gt;
Downstaging of Rectal Cancer Following Neoadjuvant Chemoradiotherapy; How Far Could Functional MRI Support Organ Preservation Approach (2023)

Background: Rectal cancer constitutes a distinct subset of colorectal carcinoma necessitating a dedicated multidisciplinary approach through the journey of diagnosis and treatment. Neoadjuvant chemoradiotherapy (CRT) has the advantage of tumor down staging, with a chance of pathologic complete response (pCR) with reflection on locoregional recurrence rates, and increased overall survival. In this study we aim to assess the response to neoadjuvant chemoradiotherapy offered to patients with locally advanced rectal cancer using functional MRI then to be validated through final pathological result following standard surgical management.Patients and Methods: This study included 29 patients with rectal cancer eligible for neoadjuvant therapy. Patients had their MRI before and after neoadjuvant CRT, then they underwent surgical intervention in the form of anterior resection with total mesorectal excision (TME) or abdominoperineal resection (APR). Final pathological results were compared to post CRT functional MRI results. Results: We found that neoadjuvant CRT downstaged our patients to the extent that rendered around 15 percent of patients with complete pathological response could have made benefit from organ preservation approach with either ‘watch-and-wait’ or local excision, a chance could be offered in regards to good standardized functional multiparametric MRI assessment.Conclusion: Response to neoadjuvant treatment in locally advanced rectal cancer could be assessed with multiparametric functional MRI giving the patient good chances regarding the best tailored surgical options that influence disease control and overall survival.
GPCR-induced migration of breast carcinoma cells depends on both EGFR signal transactivation and EGFR-independent pathways (2005)

The epidermal growth factor receptor (EGFR) plays a key role in the regulation of important cellular processes under normal and pathophysiological conditions such as cancer. In human mammary carcinomas the EGFR is involved in regulating cell growth, survival, migration and metastasis and its activation correlates with the lack of response in hormone therapy. Here, we demonstrate in oestrogen receptor-positive and -negative human breast cancer cells and primary mammary epithelial cells a cross-communication between G protein-coupled receptors (GPCRs) and the EGFR. We present evidence that specific inhibition of ADAM15 or TACE blocks GPCR-induced and proHB-EGF-mediated EGFR tyrosine phosphorylation, downstream mitogenic signalling and cell migration. Notably, activation of the PI3K downstream mediator PKB/Akt by GPCR ligands involves the activity of sphingosine kinase (SPHK) and is independent of EGFR signal transactivation. We conclude that GPCR-induced chemotaxis of breast cancer cells is mediated by EGFR-dependent and -independent signalling pathways, with both parallel pathways having to act in concert to achieve a complete migratory response.
Probabilistic Random Forests: Predicting Data Point Specific Misclassification Probabilities ; CU-CS-954-03 (2003)

Recently proposed classification algorithms give estimates or worst-case bounds for the probability of misclassification [Lanckriet et al., 2002][L.Breiman, 2001].These accuracy estimates are for all future predictions, even though some predictions are more likely to be correct than others.This paper introduces Probabilistic Random Forests (PRF), which is based on two existing algorithms, Minimax Probability Machine Classification and Random Forests, and gives data point dependent estimates of misclassification probabilities for binary classification.A PRF model outputs both a classification and a misclassification probability estimate for the data point.PRF makes it possible to assess the risk of misclassification, one prediction at a time, without detailed distribution assumptions or density estimation.Experiments show that PRFs give good estimates of the error probability for each classification.
Development of a Scalable Process for the Crop Protection Agent Isoclast (2015)

A scalable process to the insecticide Isoclast manufactured by Dow AgroSciences LLC is described. The process involves the de novo construction of a fully elaborated pyridine sulfide using enamine-mediated cyclization followed by two efficient and inexpensive oxidations to introduce the sulfoximine.
CT arthrography of the intra-articular long head of biceps tendon: Diagnostic performance outside the labral-bicipital complex (2019)

CT arthrography demonstrates good sensitivity and excellent specificity for the detection of intra-articular LHB tendinopathy and tear.
An In-Comparator Aperture-Time Equalization in a 7-nm FinFET CMOS 40-Gb/s Receiver (2020)

This letter proposes an in-comparator aperture-time equalization scheme using the impulse response of a clocked comparator. The technique is applied in a wireline link receiver prototype, implemented in CMOS 7-nm FinFET technology. The proposed method controls the aperture properties of the slicers by shaping their impulse sensitivity functions. We demonstrate an aperture skew control range of 4.7 ps with 147-fs accuracy for NRZ signaling at 40 Gb/s. PAM4 signaling at 80 Gb/s is also showcased using the proposed technique. These results serve as a proof of concept for next-generation source-synchronous chip-to-chip dense I/O links where aperture-time skews could be fine adjusted inside each comparator.
Effect of Angiogenesis and Lymphangiogenesis in Diesel Exhaust Particles Inhalation in Mouse Model of LPS Induced Acute Otitis Media (2022)

Lymphangiogenesis and angiogenesis might have significant involvement in the pathogenesis of otitis media with effusion. This study investigated the effect of diesel exhaust particles (DEP) on inflammation and lymphangiogenesis in a mouse model of acute otitis media (AOM). BALB/c mice were injected with LPS and exposed to 100 µg/m<sup>3</sup> DEP. The mice were divided into four groups: control (no stimulation), AOM, AOM + DEP, and DEP + AOM. The effects of DEP inhalation pre- and post-DEP induction were estimated based on measurements of the auditory brainstem response, mRNA levels of lymphangiogenesis-related genes and cytokines, and histology of the middle ear. Cell viability of human middle ear epithelial cells decreased in a dose-response manner at 24 and 48 hours post-DEP exposure. DEP alone did not induce AOM. AOM-induced mice with pre- or post-DEP exposure showed thickened middle ear mucosa and increased expression of TNF-α and IL1-β mRNA levels compared to the control group, but increased serum IL-1β levels were not found in the AOM + Post DEP. The mRNA expression of TLR4, VEGFA, VEGFAC, and VEGFR3 was increased by pre-AOM DEP exposure. The expression of VEFGA protein was stronger in the AOM + Post DEP group than in any other group. The expression of CD31 and CD45 markers in the mouse middle ear tissue was higher in the Pre DEP + AOM group than in the AOM group. This result implies that pre-exposure to DEP more strongly increases inflammation and lymphangiogenesis in a mouse model of acute otitis media.
In situ x-ray diffraction study of metal induced crystallization of amorphous germanium (2009)

Metal induced crystallization (MIC) is a technique that lowers the crystallization temperature of amorphous semiconductors. The process has mainly been used to influence the crystallization of amorphous silicon (a-Si) and multiple studies on this subject have already been performed. The research of the MIC of amorphous Ge (a-Ge) has been mostly limited to the use of a Ni or Al film. This paper focuses on the characterization of the crystallization behavior of a-Ge films in the presence of 20 transition metals (Ti, Zr, Hf, V, Nb, Ta, Cr, Mo, W, Mn, Re, Fe, Ru, Co, Rh, Ir, Ni, Pd, Pt, Cu, Ag, Au, and Al). The kinetics of the crystallization process are also systematically studied for the seven metals that lower the initial crystallization temperature the most. In addition, the influence of the thickness of the metal film was determined for the case of a Au and Al film. A comparison of the influence of the various metals on a-Ge and a-Si is made and the similarities and differences are discussed using existing models for the MIC process.
Directing Stem Cell Fate by Controlling the Affinity and Density of Ligand–Receptor Interactions at the Biomaterials Interface (2012)

Die Differenzierung mesenchymaler Stammzellen kann durch die Affinität und Dichte eines immobilisierten Liganden für den Integrinrezeptor beeinflusst werden. Zellen an Monoschichten, die das hochaffine cyclische RGD-Peptid (links) präsentieren, zeigen eine erhöhte Expression von osteogenen Markern, während Zellen an Monoschichten, die das weniger affine lineare RGD-Peptid (rechts) präsentieren, frühe myogene Marker bei hoher Ligandendichte und neurogene Marker bei niedriger Ligandendichte exprimieren. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
An allosteric potentiator suggests a role for M4 muscarinic acetylcholine receptor (mAChR) in modulating excitatory hippocampal synaptic transmission (2008)

Numerous animal and human studies suggest that muscarinic acetylcholine receptors (mAChRs), specifically M 1 and M 4 , may be viable targets for the treatment of neurodegenerative disorders such as Alzheimer's disease (AD). We have used cheminformatic and medicinal chemistry to develop novel, highly selective M 4 allosteric potentiators. VU10010, the lead compound, potentiates the M 4 response to acetylcholine (ACh) 47‐fold while having no activity at other mAChR subtypes. This compound binds to an allosteric site on the receptor and increases affinity for ACh and coupling to G proteins. Whole cell patch clamp recordings revealed that selective potentiation of M 4 with VU10010 increased carbachol‐induced depression of transmission at excitatory but not inhibitory synapses in the hippocampus. The effect was not mimicked by an inactive analog of VU10010 and was absent in M 4 knockout (KO) mice. This provides compelling evidence for selective regulation of excitatory transmission in this important forebrain structure by M 4 . We are now examining the effects of selective M 1 and M 4 activation on field excitatory postsynaptic potentials in the CA1 region to understand the involvement of these receptors in muscarinic long‐term potentiation and depression. This work supported by NIMH grants MH073676‐01A1 and 1 F31 MH80559‐01.
(Auto) mobile communication in a heterogeneous and converged world (2001)

We discuss services and system architecture issues for future wireless communication in the vehicular environment. We consider the problem of wireless network heterogeneity that will be a consequence of emerging technologies such as wireless LANs, ad hoc networks, and broadcast systems, in addition to third-generation cellular standards like UMTS. In particular, a communication gateway architecture is proposed as an essential building block in future automobile systems. It enables services and applications within the car to transparently use different wireless communication systems. Our article gives a high-level view of the component architecture of the gateway and its adaptation layer to the wireless infrastructure.
Ignoring Your Neighbors: Moment Correlations Dominated by Indirect or Distant Interactions in an Ordered Nanomagnet Array (2011)

We have studied the moment correlations within triangular lattice arrays of single-domain coaligned nanoscale ferromagnetic islands. Independent variation of lattice spacing along and perpendicular to the island axis tunes the magnetostatic interactions between islands through a broad range of relative strengths. For certain lattice parameters, the sign of the correlations between near-neighbor island moments is opposite to that favored by the pairwise interaction. This finding, supported by analysis of the total correlation in terms of direct and convoluted indirect contributions across multiple pairwise interactions, indicates that indirect interactions and/or those mediated by further neighbors can be tuned to be dominant, with implications for the wide range of systems composed of interacting nanomagnets.
Uso de Metodologias Criativas no Processo de Ensino da Disciplina Engenharia de Requisitos (2019)

Developing the ability to define the requirements of a system is one of the core competencies and objectives of the Requirements Engineering course. Several traditional teaching methods are used by the academy for this purpose, also trying to support experiences closer to reality and the generation of solutions more in line with the demands of stakeholders. However, they do not seem to meet the students' learning needs, who show a growing interest in more creative, interactive, engaging and participatory approaches. This paper evaluates the perception of graduate students in Software Engineering about creative teaching methodologies in the discipline of Requirements Engineering. For this purpose, an exploratory-descriptive study was carried out, where a questionnaire was applied to the students. The results show a favourable perception of the involved students in applying creative techniques.
ChemInform Abstract: A Novel Class of Cyclic β‐Dicarbonyl Leaving Groups and Their Use in the Design of Benzisothiazolone Human Leukocyte Elastase (HLE) Inhibitors. (1996)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
The Development of Nanoparticles for the Detection and Imaging of Ovarian Cancers (2021)

Ovarian cancer remains as one of the most lethal gynecological cancers to date, with major challenges associated with screening, diagnosis and treatment of the disease and an urgent need for new technologies that can meet these challenges. Nanomaterials provide new opportunities in diagnosis and therapeutic management of many different types of cancers. In this review, we highlight recent promising developments of nanoparticles designed specifically for the detection or imaging of ovarian cancer that have reached the preclinical stage of development. This includes contrast agents, molecular imaging agents and intraoperative aids that have been designed for integration into standard imaging procedures. While numerous nanoparticle systems have been developed for ovarian cancer detection and imaging, specific design criteria governing nanomaterial targeting, biodistribution and clearance from the peritoneal cavity remain key challenges that need to be overcome before these promising tools can accomplish significant breakthroughs into the clinical setting.
The nexus of syntrophy‐associated microbiota in anaerobic digestion revealed by long‐term enrichment and community survey (2014)

Anaerobic digestion (AD) processes are known to effectively convert organic waste to CO2 and CH4 , but much of the microbial ecology remains unclear. Specifically, we have limited insights into symbiotic syntroph and methanogen ('syntrophy') acid degradation, although they are essential for preventing process deterioration. Also, we often observed many uncharacterized or uncultivated organisms, but poorly understood their role(s) in relation to syntrophy. To define syntrophy-associated populations, this study enriched methanogenic communities with propionate, butyrate, benzoate, acetate, formate and H2 from two different inocula over 3 years. 16S pyrotag analysis revealed core populations of known syntrophs (six clades) and methanogens (nine clades) associated with acid degradation, and evidence for substrate- and/or inoculum-dependent specificity in syntrophic partnerships. Based on comprehensive re-evaluation of publically available microbial community data for AD, the known syntrophs and methanogens identified were clearly representatives of the AD-associated syntrophs and methanogens. In addition, uncultivated clades related to Bacteroidetes, Firmicutes, Actinobacteria and Chloroflexi were ubiquitously found in AD and enrichments. These organisms may be universally involved in AD syntrophic degradation, but only represented <23% of the yet-to-be-cultivated organisms (89 of 390 clades). Thus, the contribution of these uncultured organisms in AD remains unclear and warrants further investigation.
An O-band Metamaterial Converter Interfacing Standard Optical Fibers to Silicon Nanophotonic Waveguides (2015)

A metamaterial interface between standard optical fibers and silicon waveguides was fabricated in a CMOS production facility and shows −1.3dB peak efficiency with 0.8dB penalty over a 100 nm bandwidth and all polarizations.
Endorsed E-Cash (2007)

An electronic cash (e-cash) scheme lets a user withdraw money from a bank and then spend it anonymously. E-cash can be used only if it can be securely and fairly exchanged for electronic goods or services. In this paper, we introduce and realize endorsed e-cash. An endorsed e-coin consists of a lightweight endorsement x and the rest of the coin which is meaningless without x. We reduce the problem of exchanging e-cash to that of exchanging endorsements. We demonstrate the usefulness of endorsed e-cash by exhibiting simple and efficient solutions to two important problems: (1) optimistic and unlinkable fair exchange of e-cash for digital goods and services; and (2) onion routing with incentives and accountability for the routers. Finally, we show how to represent a set of n endorsements using just one endorsement; this means that the complexity of the fair exchange protocol for n coins is the same as for one coin, making e-cash all the more scalable and suitable for applications. Our fair exchange of multiple e-coins protocol can be applied to fair exchanges of (almost) any secrets.
New synthesis of 7‐bromo‐1, 3‐dihydro‐3‐hydroxy‐5‐(2′‐pyridyl)‐2H‐1,4‐benzodiazepin‐2‐one (1981)

Abstract A new synthesis of 7‐bromo‐1,3‐dihydro‐3‐hydroxy‐5‐(2′‐pyridyl)‐2 H ‐1,4‐benzodiazepin‐2‐one ( 5 ) is described. Starting from bromazepam ( 3 ), C(3) acylation with lead tetraacetate/potassium iodide in acetic acid affords 4 , while its mild hydrolysis according to our recently described method (5) gives 5 . Improved hexamine cyclization of 1 into 3 , via quaternary hexaminium salt 2 , is discussed, and identification of the intermediates 7 and 8 is performed. Compound 5 undergoes on melting, or on brief heating in glacial acetic acid, the thermal rearrangement into quinazolin‐2‐aldehyde ( 13 ), the structure of which is confirmed by oxidation into the ester 14 , which in turn was hydrolyzed to the acid 15 . The same compound ( 5 ) rearranges on heating with manganese(III) acetate in acetic acid into the 3‐amino‐2‐quinolone derivative 6 . On heating in glacial acetic acid in the presence of lead tetraacetate/potassium iodide (or iodine), compound 4 , in addition to giving the aldehyde 13 , ester 14 and acid 15 rearrangement products, affords 1,2‐dihydroquinazolin‐2‐carboxylic acid 16 .
Retraction: Evaluation of Co‐Digestion at a Commercial Dairy Anaerobic Digester (2011)

Abstract The above article published online on 16 June 2011 in Wiley Online Library ( http://www.onlinelibrary.wiley.com ), and in Volume 39, pp. 697‐704, has been retracted by agreement between the Editor‐in‐Chief, Prisca Henheik, and Wiley‐VCH Verlag GmbH &amp; Co. KgaA. The retraction has been agreed following an investigation carried out by Washington State University (WSU) which determined that research misconduct had occurred with respect to fabricating experimental data and falsifying data that formed the basis of a section of this article on the part of the corresponding author. Furthermore, WSU determined that the corresponding author did not declare an existing commercial conflict of interest when submitting the paper to the peer‐&amp;#x2010;reviewed journal CLEAN ‐ Soil, Air, Water.
Hydrogen-bond-mediated folding in depsipeptide models of .beta.-turns and .alpha.-helical turns (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTHydrogen-bond-mediated folding in depsipeptide models of .beta.-turns and .alpha.-helical turnsElizabeth A. Gallo and Samuel H. GellmanCite this: J. Am. Chem. Soc. 1993, 115, 21, 9774–9788Publication Date (Print):October 1, 1993Publication History Published online1 May 2002Published inissue 1 October 1993https://pubs.acs.org/doi/10.1021/ja00074a052https://doi.org/10.1021/ja00074a052research-articleACS PublicationsRequest reuse permissionsArticle Views1002Altmetric-Citations55LEARN 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