gebhart/patrepeval huggingface dataset:
OR23-01 Intrapatient ACTH Variability in Cushing’s Disease: Prognostic Significance (2020)

Abstract Introduction: In patients with Cushing’s Disease (CD), intrapatient variability of hormone measurements creates significant clinical challenges, therefore multiple measurements are recommended.1 Urinary and salivary cortisol variation has been well described. However, intrapatient variation of adrenocorticotropic hormone (ACTH) in CD remains unknown. In CD patients, ACTH levels are inherently elevated from baseline but the coefficient of diurnal variation is reduced.2Additionally, at each diurnal time point, these exists a significant variation around the mean for the ACTH levels. In this study, we first analyzed the intrapatient variablility of ACTH at each diurnal timepoint in patients with CD. CD is primarily a disorder of ACTH excess, and treatment directed at pituitary adenomas would presumably perturb ACTH levels prior to affecting serum or urine cortisol. We hypothesized that the coefficient of variation at each diurnal time-point can help predict remission from CD following surgery. Methods: We conducted a retrospective review of patients (n = 645) who had histopathologically confirmed diagnosis of CD from 2005-2019 (NCT NCT00060541). We selected patients that had ≥ 3 plasma ACTH values over a 7 day span prior to surgical or medical intervention. We grouped the ACTH measurements into morning (AM) and midnight (PM) values to account for diurnal variation in ACTH secretion. We then analyzed post-operative hormone measurements performed every 6 hours prior to administration of replacement corticosteroids. Remission was assigned to patients with nadir serum cortisol level ≤5 mcg/dL within ten days post-operatively3,4. Results: We found 54 patients with multiple PM (n = 27) and AM (n = 41) ACTH measurements within a 7 day span. We found that the median coefficient of variation (CV) of intra-patient variability was 19.7% (N=41) (95% CI:12.5-27.5) for the AM and was 24% (N=27) (95% CI: 9.6-31.8) for the PM. Age, the number of tests, or the length of test period were not correlated with CV or absolute levels of ACTH. The intraclass correlation coefficient (ICC) of the AM data set was 0.59 and the PM data set was 0.79 which demonstrates a good and excellent reliability respectively. We found that that, in general, 30-60% decrease from pre-operative ACTH levels predicted remission from CD. ACTH decrease &amp;gt;50% on POD2 and 3 had 100% specificity and sensitivity in predicting remission. The decrease in ACTH preceded cortisol nadir in 3/10 patients by 24 hours. Conclusion: We found significant intra-patient variability in plasma levels of ACTH at individual diurnal timepoints in CD patients. We also found that the change in ACTH &amp;gt;50% on POD2 or 3 is an excellent predictor of remission from CD.
A transgenic mouse model for tumour immunotherapy: induction of an anti-idiotype response to human MUC1 (2000)

MUC1 is a membrane bound, polymorphic epithelial mucin expressed at the luminal surface of glandular epithelium. It is highly expressed in an underglycosylated form on carcinomas and metastatic lesions and is, therefore, a potential target for immunotherapy of cancer. The monoclonal antibody HMFG1 binds the linear core protein sequence, PDTR, contained within the immunodominant domain of the tandem repeat of MUC1. The efficacy of murine and humanized HMFG1 (Ab1) used as an anti-idiotypic vaccine was examined in mice transgenic for human MUC1 (MUC1.Tg) challenged with murine epithelial tumour cells transfected with human MUC1. Humoral idiotypic cascade through Ab2 and Ab3 antibodies was observed in MUC1.Tg mice following multiple antibody inoculations in the presence of adjuvant. Impaired tumour growth at day 35 and highest Ab3 levels were found in mice that had received mHMFG1 with RAS adjuvant. However, comparison of Ab3 levels in individual mice with tumour size in all treatment groups did not show a correlation between smaller tumours and increased levels of anti-idiotype antibody. This suggests that the anti-tumour effects of anti-idiotype vaccination are not solely related to the induction of idiotypic antibody cascades and probably involve other mechanisms.
Dichloro{[2-(1-methylethoxy-O)phenyl]-methylene} tricyclohexylphosphine ruthenium (Hoveyda-Grubbs Catalyst) (2003)

[203714-71-0] C28H45Cl2OPRu (MW 600.61) InChI = 1S/C18H33P.C10H12O.2ClH.Ru/c1-4-10-16(11-5-1)19(17-12-6-2-7-13-17)18-14-8-3-9-15-18;1-8(2)11-10-7-5-4-6-9(10)3;;;/h16-18H,1-15H2;3-8H,1-2H3;2*1H;/q;;;;+2/p-2 InChIKey = KMKCJXPECJFQPQ-UHFFFAOYSA-L (well-defined, stable ruthenium carbene used as a recyclable olefin metathesis catalyst) Physical Data: mp 200–201 °C. Solubility: dichloromethane, chloroform, benzene, alcohols, and other organic solvents. Form Supplied in: dark brown crystalline solid. Analysis of Reagent Purity: carbene proton appears as a doublet (JPH = 4.4 Hz) by 1H NMR at 17.44 ppm. Preparative Methods: prepared by the treatment of Cl2Ru(PPh3)3 with 2-isopropoxyphenyldiazomethane in dichloromethane at −78 °C for 10 min. The PPh3 ligand is readily exchanged upon treatment with 2.0 equiv of PCy3 in dichloromethane. Purification: silica gel chromatography and recrystallization as thin needles by dissolution in warm hexanes and subsequent storage at 0 °C. Handling, Storage, and Precautions: stable indefinitely in air as a solid; oxidation of the carbene unit occurs slowly (weeks or months) when dissolved in non-distilled, non-degassed solvents.
Search for proteins with similarity to the CFTR R domain using an optimized RDBMS solution, mBioSQL (2006)

Abstract The cystic fibrosis transmembrane conductance regulator (CFTR) comprises ATP binding and transmembrane domains, and a unique regulatory (R) domain not found in other ATP binding cassette proteins. Phosphorylation of the R domain at different sites by PKA and PKC is obligatory for the chloride channel function of CFTR. Sequence similarity searches on the R domain were uninformative. Furthermore, R domains from different species show low sequence similarity. Since these R domains resemble each other only in the location of the phosphorylation sites, we generated different R domain patterns masking amino acids between these sites. Because of the high number of the generated patterns we expected a large number of matches from the UniProt database. Therefore, a relational database management system (RDBMS) was set up to handle the results. During the software development our system grew into a general package which we term Modular BioSQL (mBioSQL). It has higher performance than other solutions and presents a generalized method for the storage of biological result-sets in RDBMS allowing convenient further analysis. Application of this approach revealed that the R domain phosphorylation pattern is most similar to those in nuclear proteins, including transcription and splicing factors.
Fetal Mesenchymal Stromal Cells Differentiating towards Chondrocytes Acquire a Gene Expression Profile Resembling Human Growth Plate Cartilage (2012)

We used human fetal bone marrow-derived mesenchymal stromal cells (hfMSCs) differentiating towards chondrocytes as an alternative model for the human growth plate (GP). Our aims were to study gene expression patterns associated with chondrogenic differentiation to assess whether chondrocytes derived from hfMSCs are a suitable model for studying the development and maturation of the GP. hfMSCs efficiently formed hyaline cartilage in a pellet culture in the presence of TGFβ3 and BMP6. Microarray and principal component analysis were applied to study gene expression profiles during chondrogenic differentiation. A set of 232 genes was found to correlate with in vitro cartilage formation. Several identified genes are known to be involved in cartilage formation and validate the robustness of the differentiating hfMSC model. KEGG pathway analysis using the 232 genes revealed 9 significant signaling pathways correlated with cartilage formation. To determine the progression of growth plate cartilage formation, we compared the gene expression profile of differentiating hfMSCs with previously established expression profiles of epiphyseal GP cartilage. As differentiation towards chondrocytes proceeds, hfMSCs gradually obtain a gene expression profile resembling epiphyseal GP cartilage. We visualized the differences in gene expression profiles as protein interaction clusters and identified many protein clusters that are activated during the early chondrogenic differentiation of hfMSCs showing the potential of this system to study GP development.
FcR Interactions Do Not Play a Major Role in Inhibition of Experimental Autoimmune Encephalomyelitis by Anti-CD154 Monoclonal Antibodies (2004)

It has been demonstrated that anti-CD154 mAb treatment effectively inhibits the development of experimental autoimmune encephalomyelitis (EAE). However, although it appears to prevent the induction of Th1 cells and reactivation of encephalitogenic T cells within the CNS, little information is available regarding the involvement of alternative mechanisms, nor has the contribution of Fc effector mechanisms in this context been addressed. By contrast, efficacy of anti-CD154 mAbs in models of allotransplantation has been reported to involve long-term unresponsiveness, potentially via activation of T regulatory cells, and recently was reported to depend on Fc-dependent functions, such as activated T cell depletion through FcgammaR or complement. In this study we demonstrate that anti-CD154 mAb treatment inhibits EAE development in SJL mice without apparent long-term unresponsiveness or active suppression of disease. To address whether the mechanism of inhibition of EAE by anti-CD154 mAb depends on its Fc effector interactions, we compared an anti-CD154 mAb with its aglycosyl counterpart with severely impaired FcgammaR binding and reduced complement binding activity with regard to their ability to inhibit clinical signs of EAE and report that both forms of the Ab are similarly protective. This observation was largely confirmed by the extent of leukocyte infiltration of the CNS; however, mice treated with the aglycosyl form may display slightly more proteolipid protein 139-151-specific immune reactivity. It is concluded that FcR interactions do not play a major role in the protective effect of anti-CD154 mAb in the context of EAE, though they may contribute to the full abrogation of peripheral peptide-specific lymphocyte responses.
Failure to confirm association of a polymorphism in ABCB1 with multidrug-resistant epilepsy (2004)

Alteration of ATP-binding cassette subfamily B member 1 transporter (ABCB1) can plausibly cause drug-resistant epilepsy as it influences brain penetration of drugs. The CC genotype at the ABCB1 C3435T polymorphism was reported to be associated with multidrug resistance. A replication study in 401 drug-resistant and 208 drug-responsive subjects with epilepsy showed no significant association between the CC genotype and drug-resistant epilepsy. The authors suggest the initial association may have arisen by chance.
Distance spectrum computation for equalized MIMO multipath fading channels (2002)

We estimate bit error probability bounds for finite-length delay-optimised multi-input multi-output (MIMO) equalizers. These equalizers shorten the impulse response memory of frequency-selective MIMO channels by minimizing the average energy of the error sequence between the equalized MIMO channel impulse response and the target impulse response. We answer an important question in this paper namely, how much asymptotic loss in SNR do we expect as a result of this shortening? A partial distance spectrum for a 2/spl times/2 MIMO channel is evaluated with or without channel shortening equalisers. The union bound is then used to upper bound the bit error probability. Similarly, the lower bound is computed from the squared minimum Euclidean distance. Numerical results show that the expected loss is in the order of 2.5 dB for realistic wireless channel environments.
Processing of an Aluminum‐6061 Metal Matrix Composite by Equal‐Channel Angular Pressing (2002)

An Al-6061 metal matrix composite, reinforced with 10 vol.% Al2O3 particulates, was subjected to equal-channel angular pressing (ECAP). The grain size of the composite was reduced by a factor of approximately 2× through ECAP processing. The mechanical properties of the material were investigated using tensile testing at high temperatures over a range of strain rates. This paper describes and discusses the mechanical properties of the composite after ECAP and presents representative microstructures obtained using transmission electron microscopy.
Design and Synthesis of Novel Sulfonamide-Containing Bradykinin hB2Receptor Antagonists. 1. Synthesis and SAR of α,α-Dimethylglycine Sulfonamides (2006)

We recently published the extensive in vivo pharmacological characterization of MEN 16132 (J. Pharmacol. Exp. Ther. 2005, 616-623; Eur. J. Pharmacol. 2005, 528, 7), a member of the sulfonamide-containing human B(2) receptor (hB(2)R) antagonists. Here we report, in detail, how this family of compounds was designed, synthesized, and optimized to provide a group of products with subnanomolar affinity for the hB(2)R and high in vivo potency after topical administration to the respiratory tract. The series was designed on the basis of indications from the X-ray structures of the key structural motifs A and B present in known antagonists and is characterized by the presence of an alpha,alpha-dialkyl amino acid. The first lead (17) of the series was submitted to extensive chemical work to elucidate the structural requirements to increase hB(2) receptor affinity and antagonist potency in bioassays expressing the human B(2) receptor (hB(2)R). The following structural features were selected: a 2,4-dimethylquinoline moiety and a piperazine linker acylated with a basic amino acid. The representative lead compound 68 inhibited the specific binding of [(3)H]BK to hB(2)R with a pKi of 9.4 and antagonized the BK-induced inositolphosphate (IP) accumulation in recombinant cell systems expressing the hB(2)R with a pA(2) of 9.1. Moreover, compound 68 when administered (300 nmol/kg) intratracheally in the anesthetized guinea pig, was able to significantly inhibit BK-induced bronchoconstriction for up to 120 min after its administration, while having a lower and shorter lasting effect on hypotension.
Pathways-driven Sparse Regression Identifies Pathways and Genes Associated with High-density Lipoprotein Cholesterol in Two Asian Cohorts (2013)

Standard approaches to analysing data in genome-wide association studies (GWAS) ignore any potential functional relationships between genetic markers. In contrast gene pathways analysis uses prior information on functional structure within the genome to identify pathways associated with a trait of interest. In a second step, important single nucleotide polymorphisms (SNPs) or genes may be identified within associated pathways. Most pathways methods begin by testing SNPs one at a time, and so fail to capitalise on the potential advantages inherent in a multi-SNP, joint modelling approach. Here we describe a dual-level, sparse regression model for the simultaneous identification of pathways, genes and SNPs associated with a quantitative trait. Our method takes account of various factors specific to the joint modelling of pathways with genome-wide data, including widespread correlation between genetic predictors, and the fact that variants may overlap multiple pathways. We use a resampling strategy that exploits finite sample variability to provide robust rankings for pathways, SNPs and genes. We test our method through simulation, and use it to perform pathways-driven SNP selection in a search for pathways, genes and SNPs associated with variation in serum high-density lipoprotein cholesterol (HDLC) levels in two separate GWAS cohorts of Asian adults. By comparing results from both cohorts we identify a number of candidate pathways including those associated with cardiomyopathy, and T cell receptor and PPAR signalling. Highlighted genes include those associated with the L-type calcium channel, adenylate cyclase, integrin, laminin, MAPK signalling and immune function.
Bcl-2-Mediated Cell Survival Promotes Metastasis of EpH4 βMEKDD Mammary Epithelial Cells (2004)

The majority of patients who succumb to cancer die from metastatic disease progression rather than from the primary tumor. Elucidation of the mechanisms underlying tissue-specific metastasis is essential to the development of effective therapies. The mitogen-activated protein kinase kinase (MEK) pathway is frequently activated in human tumors and has been shown to regulate genes involved in proliferation, migration, and invasion. Studies with MEK-transformed EpH4 mouse mammary epithelial cells showed that these cells are highly tumorigenic but have a limited metastatic ability. Detachment of epithelial cells from the extracellular matrix causes disruption of the actin cytoskeleton and induces apoptosis. Several metastatic breast carcinoma cell lines have been shown to be resistant to cell death following actin disruption. This death-resistant phenotype can be modeled by overexpressing the antiapoptotic Bcl-2 protein in cells. This suggests that mechanisms that regulate survival of extravasated tumor cells may enhance metastatic efficiency. Therefore, we examined whether expression of Bcl-2 in MEK-transformed EpH4 mammary epithelial cells could provide a survival advantage and promote metastasis. Expression of Bcl-2 in parental EpH4 mammary epithelial cells or MEK-transformed cells was insufficient to induce increased migration, invasion, or tumor development. However, Bcl-2 expression markedly enhanced spontaneous lung metastasis from orthotopically implanted primary tumors. These results clearly show that mechanisms that regulate primary tumor development are distinct from those that promote metastasis and that assays designed to isolate genes involved in transformation may fail to identify genes that are critical regulators of metastasis.
A Novel SnO2 Sensor and its Selectivity Improvement with Catalytic Filter (2014)

We present a new organometallic approach for the preparation of nanostructured SnO2 gas sensitive layer. The deposited sensitive layer on a silicon device shows high response to 100 ppm of CO and C3H8. In order to improve the sensor selectivity we have implemented a catalytic filter material in a cap placed just above the sensing device. The catalytic filter is made of zinc oxide supported gold nanoparticles (Au@ZnO) prepared by deposition-precipitation by urea (DPU) method. This catalytic filter, operated at room temperature and under humid atmosphere (HR 50%), allowed to selectively eliminate the sensor response under 100 ppm of CO, whereas the sensor always responds to 100 ppm of C3H8.
Exploiting redundancy for robust sensing (2005)

In this thesis, we explore the challenges in making an Internet-scale heterogeneous sensing system more robust. We target end-to-end robustness in that we address failures in collecting data from a large collection of wired and wireless sensors, and problems in making sensor readings available to end-users from storage on Internet-connected nodes. Although often overlooked, robustness is extremely crucial for such systems because they are often deployed in harsh environments and are not typically very well-maintained. Traditional robustness techniques generally involve tradeoffs between robustness and resource-efficiency; i.e., they mask failures by using additional resources (e.g., energy, storage). Unfortunately, these traditional tradeoffs are not well suited to resource constraints and large scales of typical sensing systems. 
This dissertation puts forth the claim that more practical solutions can be developed by exploiting several unique deployment- and application-specific properties of typical sensing systems. We show that by slightly relaxing the requirements of exact or fresh answers, we can significantly improve the robustness of a system, without additional resource overheads. We argue that this approach is well suited to sensing systems since optimizing resource usage is one of the important goals of their designs and the applications can often tolerate approximate or slightly stale data. We support the above claim by proposing efficient solutions for robust data collection and storage in a sensing system. 
For robust collection of data from wireless sensors, we present Synopsis Diffusion, a novel data aggregation scheme that exploits wireless sensors' broadcast communication and sensing applications' tolerance for approximate aggregate answers. Synopsis Diffusion, unlike previous schemes, decouples aggregation algorithms from underlying aggregation topologies, enabling highly robust aggregation with energy-efficient multi-path routing. We also present Tributary-Delta, a novel adaptive aggregation scheme that efficiently combines the benefits of existing schemes and uses application-aware adaptation to cope with the dynamics of deployment environments. Under typical loss rates, our techniques can provide five times more accurate results than existing energy-efficient schemes, without additional energy overhead. 
For storing sensor readings on Internet-connected nodes, we show that existing design principles used to build highly available storage systems do not work well for an Internet-scale system where failures are often correlated. (Abstract shortened by UMI.)
Correction of Serum Sodium for Glucose Concentration in Hemodialysis Patients With Poor Glucose Control (2010)

As a rule of thumb in clinical medicine, the serum sodium concentration decreases by 1.6 mEq/l for every 100 mg/dl increase in glucose concentration due to water shifts from the intracellular to the extracellular compartment (1). This correction factor is based on theoretical considerations and has not been well validated. An experimental study in healthy subjects found significantly greater decreases in sodium concentration than expected when using the standard correction factor, especially when glucose concentrations were above 400 mg/dl (2). It was suggested that a correction factor of 2.4 mEq/l per 100 mg/dl increase in glucose concentration might be a better overall estimate of the association between the serum sodium and glucose concentrations (2).

Exact …
Teenager: should one use a child or adult low dose computed tomography protocol? (2020)

Poster: ECR 2020 / C-04435 / Teenager: should one use a child or adult low dose computed tomography protocol? by: C. Cox , M. Segbers, M. van Straten; Rotterdam/NL
Transparent p-type semiconductor: LaCuOS layered oxysulfide (2000)

La 1−x Sr x CuOS (x=0, 0.05) thin films prepared by radio-frequency sputtering were found to have high optical transmission (⩾70%) at the visible and near-infrared wavelengths and an energy gap of about 3.1 eV. The dc electrical conductivities of x=0 and 0.05 thin films at room temperature were 1.2×10−2 and 2.6×10−1 S cm−1, respectively. The Seebeck coefficients of these samples were positive, indicating that p-type electrical conduction is dominant in these materials. A sharp photoluminescence peak, probably originating from an interband transition, was observed at the optical absorption edge. The present study demonstrates that LaCuOS is a promising transparent p-type semiconductor for optoelectronic applications. Moreover, our material design, based on chemical modulation of the valence band, was successfully extended to oxysulfide systems.
Ultrafast Coherent X-Rays - from Femtoseconds to Zeptoseconds (2011)

Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text M. Murnane and H. Kapteyn, "Ultrafast Coherent X-Rays - from Femtoseconds to Zeptoseconds," in Frontiers in Optics 2011/Laser Science XXVII, OSA Technical Digest (Optica Publishing Group, 2011), paper FTuB2. Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article