gebhart/patrepeval huggingface dataset:
Progress in Myocardial Damage Detection: New Biochemical Markers for Clinicians (1997)

New clinical requirements for triaging chest pain patients challenge the abilities of the current cardiac markers. Serial measurements of myoglobin, creatine kinase (CK) isoenzyme MB (CKMB) mass, or CK isoforms in emergency rooms help to rapidly rule out acute myocardial infarction (AMI). However, within the first 3 to 4 h from chest pain onset, their sensitivities are too low to contribute significantly to AMI diagnosis during this period. CKMB and lactate dehydrogenase (LDH) isoenzyme 1 are not heart-specific, which hampers reliable diagnosis in patients with concomitant skeletal muscle damage. By contrast, the regulatory proteins troponin I and troponin T are expressed in three different isoforms: one for slow-twitch skeletal muscle fibers, one for fast-twitch skeletal muscle fibers, and one for cardiac muscle (cTnI, cTnT); cardiac-specific cTnI and cTnT assays are already available for routine use. cTnT and cTnI are the most promising markers for risk stratification in patients with unstable angina pectoris. Recent reports on increased cTnT in patients with renal failure or myopathy without evidence of myocardial injury and undetectable cTnI suggest that cTnT could be reexpressed similar to CKMB and LDH-1 in chronically damaged human skeletal muscle. Therefore, cTnI is probably the most heart-specific marker. Among the recently proposed new markers for early AMI diagnosis: glycogen phosphorylase isoenzyme BB (GPBB), fatty acid binding protein, phosphoglyceric acid mutase isoenzyme MB, enolase isoenzyme alpha beta, S100a0, and annexin V, GPBB is the most promising because it increases as early as 1 to 4 h from chest pain onset and its early release appears to be essentially dependent on ischemic myocardial injury.
Interleukin-17 gene expression in patients with rheumatoid arthritis (2008)

Interleukin-17 is a proinflammatory cytokine. Recent animal studies have shown that IL-17 plays a role in the initiation and progression of arthritis. However, whether IL-17 has a prominent role in human rheumatoid arthritis (RA) or not remains unclear. Here we investigated the role of IL-17 in patients with RA. cDNA was prepared from knee joint synovial tissues of RA (n = 11) and osteoarthritic (OA, n = 10) patients and PBMC of RA (n = 52) and healthy subjects (n = 34). IL-17 gene expression level was measured by real-time PCR, and was compared with various clinical parameters. IL-17 gene expression in synovial tissues of RA was similar to that in OA. IL-17 gene expression level in PBMC of RA patients was significantly higher than in the control. The response (changes in DAS) to two-week treatment with anti-TNF-α blockers (infliximab or etanercept) did not correlate with changes in IL-17 gene expression levels. The IL-17/TNF-α gene expression ratio at baseline (before treatment) tended to be lower in responders to the treatment. Expression of IL-17 gene in PBMC may be associated with the inflammatory process of RA. IL-17/TNF-α expression ratio is a potentially suitable marker of response to anti-TNF-α therapy.
Alternative isoleucine synthesis pathway in cyanobacterial species (2009)

Cyanothece sp. ATCC 51142 is an aerobic N(2)-fixing and hydrogen-producing cyanobacterium. Isotopomer analysis of its amino acids revealed an identical labelling profile for leucine and isoleucine when Cyanothece 51142 was grown mixotrophically using 2-(13)C-labelled glycerol as the main carbon source. This indicated that Cyanothece 51142 employs the atypical alternative citramalate pathway for isoleucine synthesis, with pyruvate and acetyl-CoA as precursors. Utilization of the citramalate pathway was confirmed by an enzyme assay and LC-MS/MS analysis. Furthermore, the genome sequence of Cyanothece 51142 shows that the gene encoding the key enzyme (threonine ammonia-lyase) in the normal isoleucine pathway is missing. Instead, the cce_0248 gene in Cyanothece 51142 exhibits 53 % identity to the gene encoding citramalate synthase (CimA, GSU1798) from Geobacter sulfurreducens. Reverse-transcription PCR indicated that the cce_0248 gene is expressed and its transcriptional level is lower in medium with isoleucine than in isoleucine-free medium. Additionally, a blast search for citramalate synthase and threonine ammonia-lyase implies that this alternative isoleucine synthesis pathway may be present in other cyanobacteria, such as Cyanothece and Synechococcus. This suggests that the pathway is more widespread than originally thought, as previous identifications of the citramalate pathway are limited to mostly anaerobic bacteria or archaea. Furthermore, this discovery opens the possibility that such autrotrophic micro-organisms may be engineered for robust butanol and propanol production from 2-ketobutyrate, which is an intermediate in the isoleucine biosynthesis pathway.
Dual‐label centromere and telomere FISH identifies human, rat, and mouse cell contribution to Multispecies recombinant urogenital sinus xenografts (2009)

The method is an indispensable tool to analyze xenograft/host interactions and prevent misinterpretation of data using tissue recombination approaches.
Equilibrium Geometries and Electronic Structure of Iron−Porphyrin Complexes:  A Density Functional Study (1997)

We have performed density functional theory (DFT) calculations of iron−porphyrin (FeP) and its complexes with O2, CO, NO, and imidazole (Im). Our fully optimized structures agree well with the available experimental data for synthetic heme models. Comparison with crystallographic data for proteins highlights interesting features of carbon monoxymyoglobin. The diatomic molecule induces a 0.3−0.4 Å displacement of the Fe atom out of the porphyrin nitrogen (Np) plane and a doming of the overall porphyrin ring. The energy of the iron−diatomic bond increases in the order Fe−O2 (9 kcal/mol) < Fe−CO (26 kcal/mol) < Fe−NO (35 kcal/mol). The ground state of FeP(O2) is an open shell singlet. The bent Fe−O2 bond can be formally described as FeIII−O2-, and it is characterized by the anti-ferromagnetic coupling between one of the d electrons of Fe and one of the π* electrons of O2. FeP(CO) is a closed shell singlet, with a linear Fe−C−O bond. The complex with NO has a doublet ground state and a Fe−NO geometry intermediate between that of FeP(CO) and FeP(O2). The bending of the Fe−(diatomic) angle requires a rather low energy for these three complexes, resulting in large-amplitude oscillations of the ligand even at room temperature. The addition of an imidazole ligand to FeP moves the Fe atom out of the porphyrin plane toward the imidazole and decreases significantly the energy differences among the spin states. Moreover, our calculations underline the potential role of the imidazole ligand in controlling the electronic structure of FeP by changing the out-of-planarity of the Fe atom. The presence of the imidazole increases the strength of the Fe−O2 and Fe−CO bonds (15 and 35 kcal/mol, respectively), but does not affect the energy of the Fe−NO bond, while the resulting FeP(Im)(NO) complex exhibits a longer and weaker Fe−Im bond.
Ester enolates from .alpha.-acetoxy esters. Synthesis of arylmalonic and .alpha.-arylalkanoic esters from aryl nucleophiles and .alpha.-keto esters (1982)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTEster enolates from .alpha.-acetoxy esters. Synthesis of arylmalonic and .alpha.-arylalkanoic esters from aryl nucleophiles and .alpha.-keto estersSubrata Ghosh, Simon N. Pardo, and Robert G. SalomonCite this: J. Org. Chem. 1982, 47, 24, 4692–4702Publication Date (Print):November 1, 1982Publication History Published online1 May 2002Published inissue 1 November 1982https://pubs.acs.org/doi/10.1021/jo00145a017https://doi.org/10.1021/jo00145a017research-articleACS PublicationsRequest reuse permissionsArticle Views1288Altmetric-Citations31LEARN 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
A General Diastereoselective Synthesis of Spiroacetals Related to Those in Ionophores via the Reaction of Lactones with Cerium(III) .gamma.-Cerioalkoxide. MAD Reverses the Diastereoselectivity of the Addition of Methylmetallics to a .beta.-Keto Ether (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTA General Diastereoselective Synthesis of Spiroacetals Related to Those in Ionophores via the Reaction of Lactones with Cerium(III) .gamma.-Cerioalkoxide. MAD Reverses the Diastereoselectivity of the Addition of Methylmetallics to a .beta.-Keto EtherYoonmo Ahn and Theodore CohenCite this: J. Org. Chem. 1994, 59, 11, 3142–3150Publication Date (Print):June 1, 1994Publication History Published online1 May 2002Published inissue 1 June 1994https://pubs.acs.org/doi/10.1021/jo00090a036https://doi.org/10.1021/jo00090a036research-articleACS PublicationsRequest reuse permissionsArticle Views402Altmetric-Citations31LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Prevalence of Anticentromere F Protein Autoantibodies in 347 Patients with Non‐Hodgkin's Lymphoma (2005)

An association between autoimmunity and hematological malignancies has been reported including the detection of antinuclear autoantibodies (ANAs) in patients suffering from non-Hodgkin's lymphoma (NHL), with a high prevalence of ANAs directed to components of the mitotic apparatus or the mitosis-associated proteins. Previous studies have demonstrated that one of the targets of such ANAs could be the CENP-F protein, especially in some carcinomas. The prevalence and specificity of anti-CENP-F autoantibodies (aAbs) thus were analyzed in 347 patients with different histological subgroups of NHL before any treatment of NHL, along with 150 controls. The detection of these aAbs was performed using two techniques: a radioimmunological assay (RIA) and an indirect immunofluorescence technique (IIF). Twenty-five (7.2%) NHL patients and 2 (1.3%) control patients displayed anti-CENP-F aAbs using RIA. This difference between the two groups was found to be significant (P < 0.01), with a higher prevalence of aAbs in the follicular (13%) and in the marginal zone B and MALT (10.2%) lymphoma subgroups. By IIF, 10 (2.9%) patients with NHL displayed aAbs with a CENP-F or CENP-F-like pattern, whereas none of the control group did. In conclusion, these data demonstrate that a significant incidence of anti-CENP-F aAbs is observed, before any treatment, in some histological subgroups of NHL patients. In addition to the usefulness of anti-CENP-F aAbs as a marker for some NHL subgroups, prospective studies may be important to evaluate the predictive value of anti-CENP-F aAbs for the development of carcinomas.
Notch3 and Canonical NF-κB Signaling Pathways Cooperatively Regulate Foxp3 Transcription (2011)

Notch3 overexpression has been previously shown to positively regulate the generation and function of naturally occurring regulatory T cells and the expression of Foxp3, in cooperation with the pTα/pre-TCR pathway. In this study, we show that Notch3 triggers the trans activation of Foxp3 promoter depending on the T cell developmental stage. Moreover, we discovered a novel CSL/NF-κB overlapping binding site within the Foxp3 promoter, and we demonstrate that the activation of NF-κB, mainly represented by p65-dependent canonical pathway, plays a positive role in Notch3-dependent regulation of Foxp3 transcription. Accordingly, the deletion of protein kinase C, which mediates canonical NF-κB activation, markedly reduces regulatory T cell number and per cell Foxp3 expression in transgenic mice with a constitutive activation of Notch3 signaling. Collectively, our data indicate that the cooperation among Notch3, protein kinase C, and p65/NF-κB subunit modulates Foxp3 expression, adding new insights in the understanding of the molecular mechanisms involved in regulatory T cell homeostasis and function.
Random Projections for Manifold Learning (2007)

We propose a novel method for linear dimensionality reduction of manifold modeled data. First, we show that with a small number M of random projections of sample points in ℝN belonging to an unknown K-dimensional Euclidean manifold, the intrinsic dimension (ID) of the sample set can be estimated to high accuracy. Second, we rigorously prove that using only this set of random projections, we can estimate the structure of the underlying manifold. In both cases, the number of random projections required is linear in K and logarithmic in N, meaning that K < M ≪ N. To handle practical situations, we develop a greedy algorithm to estimate the smallest size of the projection space required to perform manifold learning. Our method is particularly relevant in distributed sensing systems and leads to significant potential savings in data acquisition, storage and transmission costs.
The prognostic value of modified early warning score of ICU elderly patients in emergency (2013)

Objective To study the prognostic value of modified early warning score (MEWS) and Acute Physiology and Chronic Health Evaluation (APACHE Ⅱ) score in emergency ICU elderly patients.Methods 113 elderly patients were collected in emergency ICU,after admission to calculate the MEWS score and APACHE Ⅱ score,the MEWS score and APACHE Ⅱ score difference were compared between death group and survival group.the differences were compared in MEWS score ≤ 3,4 ～6,7 ～ 9,≥ 10 scores groups respectively;analysis of the MEWS score and APACHE Ⅱ the relevance score.the correlation analysis of the MEWS score and APACHE Ⅱ score was given.Results The MEWS(7.91 ± 2.42) point and APACHE Ⅱ (21.9 ± 4.18) point in death group were greater than that in survival group [(4.51 ± 2.14) point,(19.53 ± 4.37) point] (t =7.49,2.70,all P ＜ 0.01).With MEWS score increasing,the fatality rate rose(P ＜0.01).the MEWS score and APACHE Ⅱ score was correlated(r =0.617,P ＜ 0.01).Conclusion The MEWS score was a simple and quick scoring system,as well as APACHE Ⅱ,it can predict the prognosis of elderly patients in emergency department,it has important application value.

Key words: 
Modified early warning score ;  Health status indicators;  Aged;  Prognosis
A mini-invasive approach to transduodenal sphincteroplasty. (1999)

A right lumbar approach to the duodenum was developed to perform transduodenal sphinctero-plasty for the treatment of retained common bile duct stones. With experience, the procedure was reduced to a mininvasive approach. Nine patients with symptomatic choledocal stones were subjected to translumbar transduodenal sphincteroplasty. Eventually it became obvious that limited dissection was equally effective in exposure of pertinent anatomical structures and ease of performance. Four patients were intervened using the mini-invasive approach. In one instance the procedure was combined with laparoscopic cholecystectomy and cholangiogram. There was no mortality or morbidity and there was universal clearance of the common bile duct.
Neue Methode zur Phasentransfer‐katalysierten Sulfodechlorierung von 1‐Chlor‐2,4‐dinitrobenzol (1981)

Schonende Bedingungen und sehr gute Ausbeuten kennzeichnen die Sulfode‐chlorierung von 1‐Chlor‐2,4‐dinitrobenzol mit Kaliumdisulfit zu 2,4‐Dinitro‐benzolsulfonsäure in Gegenwart protonierter tertiärer Amine als Phasentransfer‐Katalysatoren; dabei hängen Ausbeute und vor allem Reinheit des Produkts von der Kettenlänge der Alkylreste der Amine ab.
DeLight-Net: Decomposing Reflectance Maps into Specular Materials and Natural Illumination (2016)

In this paper we are extracting surface reflectance and natural environmental illumination from a reflectance map, i.e. from a single 2D image of a sphere of one material under one illumination. This is a notoriously difficult problem, yet key to various re-rendering applications. With the recent advances in estimating reflectance maps from 2D images their further decomposition has become increasingly relevant. To this end, we propose a Convolutional Neural Network (CNN) architecture to reconstruct both material parameters (i.e. Phong) as well as illumination (i.e. high-resolution spherical illumination maps), that is solely trained on synthetic data. We demonstrate that decomposition of synthetic as well as real photographs of reflectance maps, both in High Dynamic Range (HDR), and, for the first time, on Low Dynamic Range (LDR) as well. Results are compared to previous approaches quantitatively as well as qualitatively in terms of re-renderings where illumination, material, view or shape are changed.
A Cautionary Note on the Use of Split-YFP/BiFC in Plant Protein-Protein Interaction Studies (2014)

Since its introduction in plants 10 years ago, the bimolecular fluorescence complementation (BiFC) method, or split-YFP (yellow fluorescent protein), has gained popularity within the plant biology field as a method to study protein-protein interactions. BiFC is based on the restoration of fluorescence after the two non-fluorescent halves of a fluorescent protein are brought together by a protein-protein interaction event. The major drawback of BiFC is that the fluorescent protein halves are prone to self-assembly independent of a protein-protein interaction event. To circumvent this problem, several modifications of the technique have been suggested, but these modifications have not lead to improvements in plant BiFC protocols. Therefore, it remains crucial to include appropriate internal controls. Our literature survey of recent BiFC studies in plants shows that most studies use inappropriate controls, and a qualitative rather than quantitative read-out of fluorescence. Therefore, we provide a cautionary note and beginner's guideline for the setup of BiFC experiments, discussing each step of the protocol, including vector choice, plant expression systems, negative controls, and signal detection. In addition, we present our experience with BiFC with respect to self-assembly, peptide linkers, and incubation temperature. With this note, we aim to provide a guideline that will improve the quality of plant BiFC experiments.
Rapid selection of specific MAP kinase-binders from designed ankyrin repeat protein libraries (2006)

We describe here the rapid selection of specific MAP-kinase binders from a combinatorial library of designed ankyrin repeat proteins (DARPins). A combined in vitro/in vivo selection approach, based on ribosome display and the protein fragment complementation assay (PCA), yielded a large number of different binders that are fully functional in the cellular cytoplasm. Ribosome-display selection pools of four successive selection rounds were examined to monitor the enrichment of JNK2-specific DARPins. Surprisingly, only one round of ribosome display with subsequent PCA selection of this pool was necessary to isolate a first specific binder with micromolar affinity. After only two rounds of ribosome-display selection followed by PCA, virtually all DARPins showed JNK2-specific binding, with affinities in the low nanomolar range. The enrichment factor of ribosome display thus approaches 10(5) per round. In a second set of experiments, similar results were obtained with the kinases JNK1 and p38 as targets. Again, almost all investigated DARPins obtained after two rounds of ribosome display showed specific binding to the targets used, JNK1 or p38. In all three selection experiments the identified DARPins possess very high specificity for the target kinase. Taken together, the combination of ribosome display and PCA selections allowed the identification of large pools of binders at unparalleled speed. Furthermore, DARPins are applicable in intracellular selections and immunoprecipitations from the extract of eukaryotic cells.
Patients' treatment beliefs in low back pain (2015)

Choosing the most appropriate treatment for individual patients with low back pain (LBP) can be challenging, and clinical guidelines recommend taking into account patients' preferences. However, no tools exist to assess or compare patients' views about LBP treatments. We report the development and validation of the Low Back Pain Treatment Beliefs Questionnaire (LBP-TBQ) for use across different treatments in clinical practice and research. Using qualitative data, we developed a pool of items assessing perceived credibility, effectiveness, concerns about, and individual "fit" of specific treatments. These items were included in a survey completed by 429 primary care patients with LBP, of whom 115 completed it again 1 to 2 weeks later. We performed psychometric analyses using nonparametric item response theory and classical test theory. The 4 subscales of the resulting 16-item LBP-TBQ showed good homogeneity (H = 0.46-0.76), internal consistency (α = 0.73-0.94), and stability (r = 0.63-0.83), confirmed most convergent and discriminant validity hypotheses, and had acceptable structural validity for 4 guideline-recommended treatments: pain medication, exercise, manual therapy, and acupuncture. Participants with stronger positive treatment beliefs were more likely to rank that treatment as their first choice, indicating good criterion validity (t values = 3.11-9.80, all P < 0.01, except pain medication effectiveness beliefs, t(339) = 1.35; P = 0.18). A short 4-item version also displayed good homogeneity (H = 0.43-0.66), internal consistency (α = 0.70-0.86), and stability (r = 0.82-0.85) and was significantly related to treatment choice (t values = 4.33-9.25, all P < 0.01). The LBP-TBQ can be used to assess treatment beliefs in primary care patients with LBP and to investigate the effects of treatment beliefs on treatment uptake and adherence.