gebhart/patrepeval huggingface dataset:
High-affinity binding of plasminogen-activator inhibitor 1 complexes to LDL receptor–related protein 1 requires lysines 80, 88, and 207 (2019)

It is well-established that complexes of plasminogen-activator inhibitor 1 (PAI-1) with its target enzymes bind tightly to low-density lipoprotein (LDL) receptor-related protein 1 (LRP1), but the molecular details of this interaction are not well-defined. Furthermore, considerable controversy exists in the literature regarding the nature of the interaction of free PAI-1 with LRP1. In this study, we examined the binding of free PAI-1 and complexes of PAI-1 with low-molecular-weight urokinase-type plasminogen activator to LRP1. Our results confirmed that uPA:PAI-1 complexes bind LRP1 with ∼100-fold increased affinity over PAI-1 alone. Chemical modification of PAI-1 confirmed an essential requirement of lysine residues in PAI-1 for the interactions of both PAI-1 and uPA:PAI-1 complexes with LRP1. Results of surface plasmon resonance measurements supported a bivalent binding model in which multiple sites on PAI-1 and uPA:PAI-1 complexes interact with complementary sites on LRP1. An ionic-strength dependence of binding suggested the critical involvement of two charged residues for the interaction of PAI-1 with LRP1 and three charged residues for the interaction of uPA:PAI-1 complexes with LRP1. An enhanced affinity resulting from the interaction of three regions of the uPA:PAI-1 complex with LDLa repeats on LRP1 provided an explanation for the increased affinity of uPA:PAI-1 complexes for LRP1. Mutational analysis revealed an overlap between LRP1 binding and binding of a small-molecule inhibitor of PAI-1, CDE-096, confirming an important role for Lys-207 in the interaction of PAI-1 with LRP1 and of the orientations of Lys-207, -88, and -80 for the interaction of uPA:PAI-1 complexes with LRP1.
Combinatorial and high-throughput measurements of the modulus of thin polymer films (2005)

We describe the design and refinement of a high-throughput buckling-based metrology for ascertaining the mechanical properties (e.g., modulus) of combinatorial thin polymer film libraries. We provide critical details for the construction of a suitable strain stage, describe sample preparation, and highlight methods for high-throughput data acquisition and data analysis. To illustrate the combinatorial and high-throughput capability of this metrology, we prepare and evaluate films possessing a gradient in the elastic modulus and compare the results with an analytical expression derived from composite beam theory. Application of this metrology is very simple and practically any laboratory, academic or industrial, can perform such measurements with only modest investment in equipment. Although developed as a platform for investigating combinatorial libraries, researchers can take advantage of the high-throughput nature of this metrology to measure noncombinatorial film specimens as well.
Molecular orbital theory of the electron structure of organic compounds. XXIV. Geometries and energies of small boron compounds. Comparisons with carbocations (1975)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMolecular orbital theory of the electron structure of organic compounds. XXIV. Geometries and energies of small boron compounds. Comparisons with carbocationsJ. D. Dill, P. v. R. Schleyer, and J. A. PopleCite this: J. Am. Chem. Soc. 1975, 97, 12, 3402–3409Publication Date (Print):June 1, 1975Publication History Published online1 May 2002Published inissue 1 June 1975https://pubs.acs.org/doi/10.1021/ja00845a021https://doi.org/10.1021/ja00845a021research-articleACS PublicationsRequest reuse permissionsArticle Views744Altmetric-Citations178LEARN 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
EFFECT OF VESSEL COMPLIANCE ON THE IN-VITRO PERFORMANCE OF A PULSATING RESPIRATORY SUPPORT CATHETER (2001)

Intravenous oxygenation is a potential extra-pulmonary method of supplementing gas exchange in acute respiratory failure patients. A respiratory support catheter is being developed which consists of a polyurethane pulsating balloon located concentrically within a bundle of microporous hollow fiber membranes. Tne catheter will be inserted through the femoral vein and will lie within the vena cava. The balioon-generated flow interacts with the natural blood flow in the vena cava increasing gas exchange efficiency. The purpose of this study was to examine the influence of blood vessel compliance on the gas exchange performance of the respiratory support catheter. The catheter was placed in an in-vitro circulatory loop with a section of either rigid tube or polyurethane tube serving as a “mock” vena cava. The compliance of the custom fabricated tube was comparable to the compliance measured in bovine vena cava. The gas exchange of the respiratory catheter was measured at several balloon pulsation rates for each “mock” vena cava material. Balloon pulsation rates up to 120 bpm enhanced gas exchange comparably in both the rigid and compliant tubes. Within the rigid tube, the gas exchange further increased up to pulsation rate of 300 bpm. However, no additional gain in gas exchange was observed at balloon pulsation rates higher than 120 bpm. Our acute in-vivo studies of the respiratory support catheter have not indicated that a decrease in gas exchange as balloon pulsation rate increases above a particular value. The differences above pulsation rates of 120 bpm may reflect differences in the compliance of the polyurethane tube versus the natural vena cava.
Gene Dosage Effect of <scp>l</scp> -Proline Biosynthetic Enzymes on <scp>l</scp> -Proline Accumulation and Freeze Tolerance in <i>Saccharomyces cerevisiae</i> (2003)

We have previously reported that L-proline has cryoprotective activity in Saccharomyces cerevisiae. A freeze-tolerant mutant with L-proline accumulation was recently shown to carry an allele of the PRO1 gene encoding gamma-glutamyl kinase, which resulted in a single amino acid substitution (Asp154Asn). Interestingly, this mutation enhanced the activities of gamma-glutamyl kinase and gamma-glutamyl phosphate reductase, both of which catalyze the first two steps of L-proline synthesis and which together may form a complex in vivo. Here, we found that the Asp154Asn mutant gamma-glutamyl kinase was more thermostable than the wild-type enzyme, which suggests that this mutation elevated the apparent activities of two enzymes through a stabilization of the complex. We next examined the gene dosage effect of three L-proline biosynthetic enzymes, including Delta(1)-pyrroline-5-carboxylate reductase, which converts Delta(1)-pyrroline-5-carboxylate into L-proline, on L-proline accumulation and freeze tolerance in a non-L-proline-utilizing strain. Overexpression of the wild-type enzymes has no influence on L-proline accumulation, which suggests that the complex is very unstable in nature. However, co-overexpression of the mutant gamma-glutamyl kinase and the wild-type gamma-glutamyl phosphate reductase was effective for L-proline accumulation, probably due to a stabilization of the complex. These results indicate that both enzymes, not Delta(1)-pyrroline-5-carboxylate reductase, are rate-limiting enzymes in yeast cells. A high tolerance for freezing clearly correlated with higher levels of L-proline in yeast cells. Our findings also suggest that, in addition to its cryoprotective activity, intracellular L-proline could protect yeast cells from damage by oxidative stress. The approach described here provides a valuable method for breeding novel yeast strains that are tolerant of both freezing and oxidative stresses.
ChemInform Abstract: Inter‐ and Intramolecular Alcohol Additions to exo‐Glycals. (2002)

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.
Relapsed childhood acute lymphoblastic leukemia in the Nordic countries: prognostic factors, treatment and outcome (2015)

Relapse is the main reason for treatment failure in childhood acute lymphoblastic leukemia. Despite improvements in the up-front therapy, survival after relapse is still relatively poor, especially for high-risk relapses. The aims of this study were to assess outcomes following acute lymphoblastic leukemia relapse after common initial Nordic Society of Paediatric Haematology and Oncology protocol treatment; to validate currently used risk stratifications, and identify additional prognostic factors for overall survival. Altogether, 516 of 2735 patients (18.9%) relapsed between 1992 and 2011 and were included in the study. There were no statistically significant differences in outcome between the up-front protocols or between the relapse protocols used, but an improvement over time was observed. The 5-year overall survival for patients relapsing in the period 2002-2011 was 57.5±3.4%, but 44.7±3.2% (P<0.001) if relapse occurred in the period 1992-2001. Factors independently predicting mortality after relapse included short duration of first remission, bone marrow involvement, age ten years or over, unfavorable cytogenetics, and Down syndrome. T-cell immunophenotype was not an independent prognostic factor unless in combination with hyperleukocytosis at diagnosis. The outcome for early combined pre-B relapses was unexpectedly poor (5-year overall survival 38.0±10.6%), which supports the notion that these patients need further risk adjustment. Although survival outcomes have improved over time, the development of novel approaches is urgently needed to increase survival in relapsed childhood acute lymphoblastic leukemia.
Aero engines lose weight thanks to composites (2012)

Aircraft engines have traditionally been the domain of metal but aero engine manufacturers are now saving substantial weight by using composites in the fan blades and containment case. George Marsh reports on the latest developments.
Misclassified Tissue Volumes in Alzheimer Disease Patients With White Matter Hyperintensities (2008)

MRI-based volumetric studies of Alzheimer Disease that do not account for WMH can expect an erroneous inflation of gray or white matter volumes, especially in the frontal and inferior parietal regions. To avoid this source of error, MRI-based volumetric studies in patient populations susceptible to hyperintensities should include a WMH segmentation protocol.
Therapy with nCPAP: incomplete elimination of Sleep Related Breathing Disorder (2000)

Correct assessment of the overall treatment effectiveness requires knowledge about therapy compliance and efficacy. This study aimed to determine overall long-term apnoea alleviation after continuous positive airway pressure (CPAP) in a complete sleep laboratory cohort. Out of 209 consecutive CPAP candidates (mean age 57+/-12 yrs, body mass index (BMI) 30.0+/-5.1 kg x m2, respiratory disturbance index (RDI) 32.9+/-29 h), follow-up treatment was performed in 149 of them at 9, 18 and 30 months after CPAP prescription. Compliance with CPAP (machine run time/days CPAP available) was adjusted for the individual subjective sleep-time. Apnoea alleviation was defined as adjusted compliance multiplied by the CPAP effect (RDI with CPAP applied), remaining RDI was calculated. The baseline RDI, age or BMI in 75 patients, who did not tolerate nasal continuous positive airway pressure (nCPAP), did not differ from those accepting CPAP (acceptors, n=74). In acceptors at 9 months follow-up RDI with CPAP applied was 1.4+/-2.6 (CPAP effect, n=66), mean CPAP use was 3.6+/-2.5 x 24 h(-1) (n=68), mean apnoea alleviation was 52.4+/-32.0% (range 1-100%, n=47), the average remaining whole-night RDI was 17.8+/-26. At 9, 18 and 30 months (n=47), the mean daily CPAP use increased from 3.6+/-2.5 h to 4.1+/-2.5 h and 4.4+/-2.4 h (p<0.01). Effectiveness of continuous positive airway pressure is potentially high but acceptance was low. When accounting for sleep-time, its actual effect and use, only 50% adjusted continuous positive airway pressure effectiveness was observed.
Effect of Metals in Biomimetic Dimetal Complexes on Affinity and Gas-Phase Protection of Phosphate Esters (2015)

Although the biomimetic dimetal complex [LGa2(OH)2(H2O)2](3+) [L = 2,6-bis((N,N'-bis(2-picolyl)amino)methyl)-4-tertbutylphenolate] provides efficient protection against phosphate loss in phosphopeptides upon collision-induced dissociation tandem mass spectrometry (CID MS/MS), the underlying mechanism remains unknown. Here, we explored the mechanism in detail and investigated the selective binding to phosphate groups in solution. Dimetal complexes containing combinations of Ga(3+), In(3+), Fe(3+), Co(3+), Zn(2+), Cu(2+), and V(2+) were reacted with HPO4(2-), phosphoserine, and a phosphopeptide (FQpSEEQQQTEDELQDK, abbreviated "βcas") and studied with isothermal titration calorimetry (ITC), CID MS/MS, and density functional theory (DFT). Ka for HPO4(2-) binding scaled with the metal charge and was 35-fold larger for [LGa2(OH)2(H2O)2](3+) (3.08 ± 0.31 × 10(6) M(-1)) than for [LZn2(HCOO)2](+). CID MS/MS of [LGa2(βcas)](n+) revealed protection against phosphate detachment (<3% of the total ion intensity). Phosphate detachment from βcas was 22-40% and increased to 42-71% when bound to dimetal complexes of lower charge than {LGa2}(5+). CID data suggests that facile metal-phosphate dissociation is associated with proton transfer from the intermediate oxazoline ring formed in the phosphopeptide to the metal-phosphate complex. The observed phosphate stabilization was attributed to a significant reduction in the gas-phase basicity (GB) of the phosphate group when bound to {LGa2}(5+)/{LIn2}(5+) complex cores. Absence of proton transfer results in formation of an ion-zwitterion intermediate with a greater dissociation threshold. This hypothesis is supported by DFT calculations for [LGa2(PO4)](2+), [LGaZn(PO4)](+), [LZn2(PO4)], and 2,4-dimethyl-3-oxazoline showing that [LGa2(PO4)](2+) is the only compound with a substantial lower GB (321 kJ/mol less) than 2,4-dimethyl-3-oxazoline.
Efficient Adaptive Resource Allocation for Multiuser OFDM Systems with Minimum Rate Constraints (2007)

This work investigates the adaptive resource allocation scheme for the downlink of multiuser OFDM systems. We focus on the problem of maximizing the overall spectral efficiency while maintaining the QoS requirements of users, including bit error rate and individual minimum rate requirements. Under the assumption of equal power allocation, an efficient algorithm is proposed to obtain the suboptimal solution of the resource allocation. In this algorithm, we first introduce some positive multipliers, one for each user, according to their minimum rate constraints (MRC), and then a parallel subcarrier-and-bit allocation scheme is designed using these multipliers with low complexity. The numerical results show that our algorithm not only substantially reduces the computational complexity of the existing algorithm, but also provides a noticeable performance improvement.
A Low-Cost Wireless Sensor System and Its Application in Dental Retainers (2009)

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> In this paper, a wireless interrogable sensor device based on an ultra low-power microcontroller for data collection and a radio frequency identification (RFID) interface for data transmission is presented. Wireless sensor systems utilizing RFID transponders offer a new and exciting means of measurement and identification suitable for many biomedical applications. For the majority of these applications, small, inexpensive radio request sensor systems are desirable. In this paper, an ultra-low-power and low-cost wireless temperature data logger system is presented with its application in observing dental retainer use. For this purpose, the retainer's ambient temperature is measured by an integrated sensor and recorded using a microcontroller which acts like a temperature data logger storing the thermal history of several months. For a self powered wireless data transmission from the sensor to the interrogation unit a RFID transponder, operating in the 13.56 MHz ISM band, is used. The presented sensor system includes hard- and software power saving modes reducing the sensor idle current consumption to 1 <formula formulatype="inline"><tex Notation="TeX">$\mu$</tex> </formula>A. This allows a battery powered operation of the device for up to two years. For dental and biomedical applications, the device is hermetically sealed using a biocompatible polymeric encapsulation. Results of the first clinical trials observing the patient's dental retainer usage by a set of retainers equipped with the RFID temperature sensor/data logger device are presented. The stored temperature values are analyzed and a clear temperature characteristic indicating the retainer usage was found. </para>
Nanoparticle Dynamics:  A Multiscale Analysis of the Liouville Equation (2005)

A theory of nanoparticle dynamics based on scaling arguments and the Liouville equation is presented. We start with a delineation of the scales characterizing the behavior of the nanoparticle/host fluid system. Asymptotic expansions, multiple time and space scale techniques, the resulting coarse-grained dynamics of the probability densities of the Fokker-Planck-Chandrasekhar (FPC) type for the nanoparticle(s), and the hydrodynamic models of the host medium are obtained. Collections of nanoparticles are considered so that problems such as viral self-assembly and the transition from a particle suspension to a solid porous matrix can be addressed via a deductive approach that starts with the Liouville equation and a calibrated atomic force field, and yields a generalized FPC equation. Extensions allowing for the investigation of the rotation and deformation of the nanoparticles are considered in the context of the space-warping formalism. Thermodynamic forces and dissipative effects are accounted for. The notion of configuration-dependent drag coefficients and their implications for coagulation and consolidation are shown to be natural consequences of the analysis. All results are obtained via formal asymptotic expansions in mass, size, and other physical and kinetic parameter ratios.
From normal respiratory mucosa to epidermoid carcinoma: Expression of human mucin genes (2000)

Mucous cells in the respiratory tract contribute to the maintenance of the normal epithelial cell population via mechanisms of cell proliferation and differentiation. Mucous cell hyperplasia often occurs as a basic response to injury in the tracheobronchial epithelium. These cells are also thought to be involved in the histogenesis of epidermoid metaplasia. A typical biochemical feature of these cells is mucus secretion. Aberrant glycosylation or under-glycosylation of mucins is well known in cancer; however, the specific role played by mucin genes is at present unclear. To provide information regarding the expression of these genes in squamous metaplasia and squamous cell carcinoma, we analyzed and compared the expression of MUC1-MUC7 genes by in situ hybridization in control respiratory mucosa and lesions associated with neoplasia (hyperplasia, metaplasia and dysplasia) and squamous cell carcinomas. MUC4 was expressed independently of mucus secretion since it was expressed weakly by basal cells and probably by ciliated cells as well as collecting ducts, epidermoid metaplasia with complete squamous cell differentiation, and most of epidermoid carcinomas even well differentiated and keratinized. In squamous metaplasia and dysplasia, MUC4 gene expression was diffuse and less intense than in normal epithelium. MUC5AC was overexpressed in dysplasia as well as in mucous cell and basal cell hyperplasia and undetectable when squamous differentiation was achieved.
Stool microbiome reveals diverse bacterial ureases as confounders of oral urea breath testing for <i>Helicobacter pylori</i> and <i>Mycobacterium tuberculosis</i> in Bamako, Mali (2016)

Detection of bacterial urease activity has been utilized successfully to diagnose Helicobacter pylori (H. pylori). While Mycobacterium tuberculosis (M. tuberculosis) also possesses an active urease, it is unknown whether detection of mycobacterial urease activity by oral urease breath test (UBT) can be exploited as a rapid point of care biomarker for tuberculosis (TB) in humans. We enrolled 34 individuals newly diagnosed with pulmonary TB and 46 healthy subjects in Bamako, Mali and performed oral UBT, mycobacterial sputum culture and H. pylori testing. Oral UBT had a sensitivity and specificity (95% CI) of 70% (46-88%) and 11% (3-26%), respectively, to diagnose culture-confirmed M. tuberculosis disease among patients without H. pylori, and 100% sensitivity (69-100%) and 11% specificity (3-26%) to diagnose H. pylori among patients without pulmonary TB. Stool microbiome analysis of controls without TB or H. pylori but with positive oral UBT detected high levels of non-H. pylori urease producing organisms, which likely explains the low specificity of oral UBT in this setting and in other reports of oral UBT studies in Africa.
Analysis of algorithms on threaded trees (1981)

This paper investigates the performances of various algorithms operating on binary trees. In particular the expected times necessary to compute the different successor and predecessor nodes of a random node in a random threaded binary tree are presented. Based on these results it is then shown that the inorder traversal algorithm using threads is about 25% better performing than the corresponding algorithm using stacks, while for preorder and postorder little or no improvement in traversal times is gained by the use of threads. Finally the presence of threads in a binary tree is briefly discussed with respect to the performance of insertion and deletion algorithms.
Estimation of Flood Discharge for Ungauged Rural Catchments in Victoria (1985)

A regional flood estimation procedure is presented for ungauged rural catchments in the southeastern region of Victoria. Flood frequency analyses were based on the partial duration series model which was jointly represented by the Poisson and log-Pearson Type 3 distributions. The study region was divided into three hydrologically homogeneous regions and multiple regression was used to determine expressions for probability of exceedance discharges in terms of catchment characteristics.
메이커산업과 디자인ㆍ공학 융합교육의 방향 (2017)

메이커산업에 필요한 교육은 많은 정보와 지식을 통하여 학생 스스로 이를 습득하고 문제를 인식하며 해결해 줄 수 있는 교육이다. 메이커 무브먼트는 많은 가능성을 가진 신산업의 일부이다. 이 연구의 메이커 양성을 위한 교육설계는 대학교 공학과 디자인교육 사이의 연결을 시도한다. 내용은 공학도들에게 디자인을 수행할 수 있는 기본교육의 실천 가능성을 찾는 과정으로...