gebhart/patrepeval huggingface dataset:
B cell monitoring of transplant patients treated with anti-CD20. (2006)

B cell depletion with the monoclonal anti-CD20 antibody, rituximab, is being used increasingly in clinical transplantation. This chapter reviews the clinical uses and potential immunological consequences of rituximab therapy in the setting of solid organ transplantation. In clinical transplantation, therapy with rituximab is contemplated in cases of rejection that are refractory to conventional immunosuppression. B cell targeted therapy is also being used to lower the risk of allosensitization. The biological effects of rituximab are complex and include a reduction in de novo alloantibody production, shifts in circulating B cell subsets and repertoire, and effects on other immune system cells such as T cells. The chapter concludes with detailed recommendations for clinical laboratory monitoring of rituximab-treated transplant patients, particularly with respect to immunophenotyping of peripheral blood lymphocytes to assess the emergence of transitional B cells during B cell reconstitution. Careful monitoring of the immune system in rituximab-treated transplant patients may yield important insights into B lymphocyte biology and immune tolerance.
On ray tracing parametric surfaces (1985)

A new method for ray tracing parametric surfaces is presented. The new algorithm solves the ray surface intersection directly using multivariate Newton iteration. This provides enough generality to render surfaces which could not be ray traced using existing methods. To overcome the problem of finding a starting point for the Newton algorithm, techniques from Interval Analysis are employed. The results are presented in terms of solving a general nonlinear system of equations f(x)= 0, and thus can be extended to a large class of problems which arise in computer graphics.
Cbfa1/RUNX2 Directs Specific Expression of the Sclerosteosis Gene (SOST) (2004)

Loss-of-function mutations in the sclerosteosis gene (SOST) cause a rare sclerosing bone dysplasia characterized by skeletal overgrowth. Cbfa1/RUNX2 is a key transcriptional regulator of osteoblast function. Here we link these two pathways by demonstrating, via gel shift and transient transfection analyses, that Cbfa1 binding to the proximal SOST promoter contributes to differential SOST expression in two osteosarcoma cell lines. Additionally, an E-box binding motif in the 1.8-kb proximal SOST promoter appears to be functional in SAOS-2 cells, but does not account for SAOS-specific expression of SOST. The regulation of SOST expression by Cbfa1 suggests a potential role for the sclerosteosis gene in homeostatic regulation of osteoblast differentiation and function. Furthermore, the juxtaposition of Cbfa1, E-box, and C/EBP binding sites in the SOST proximal promoter bears an intriguing resemblance to the promoter for osteocalcin, another osteoblast-specific gene with a loss-of-function phenotype of bone overgrowth.
GPU accelerated alignment of 3-D CTA with 2-D X-ray data for improved guidance in coronary interventions (2009)

This paper presents a 2-D/3-D registration method for the alignment of cardiac X-ray images to ECG gated CTA data of the coronary arteries. The purpose of our work is to provide visualization of instruments in relation to pre-operative CTA data during interventional cardiology for improved image guidance, especially in complex procedures. The method utilizes the graphical processing unit (GPU) for rendering of digitally reconstructed radiographs (DRRs) from a 3-D CTA-derived coronary model. Using a multi-scale gradient ascent framework, the normalized cross correlation between the simulated and real X-ray image is optimized. Quantitative evaluation is performed by computing the projection error of the vessel centerlines, which was oPn average 1.34 mm.
JAG1 Mutation Spectrum and Origin in Chinese Children with Clinical Features of Alagille Syndrome (2015)

Alagille syndrome is an autosomal dominant disorder that results from defects in the Notch signaling pathway, which is most frequently due to JAG1 mutations. This study investigated the rate, spectrum, and origin of JAG1 mutations in 91 Chinese children presenting with at least two clinical features of Alagille syndrome (cholestasis, heart murmur, skeletal abnormalities, ocular abnormalities, characteristic facial features, and renal abnormalities). Direct sequencing and/or multiplex-ligation-dependent probe amplification were performed in these patients, and segregation analysis was performed using samples available from the parents. JAG1 disease-causing mutations were detected in 70/91 (76.9%) patients, including 29/70 (41.4%) small deletions, 6/70 (8.6%) small insertions, 16/70 (22.9%) nonsense mutations, 8/70 (11.4%) splice-site mutations, 6/70 (9.4%) missense mutations, and 5/70 (7.1%) gross deletions. Of the mutations detected, 45/62 (72.6%) were novel, and almost all were unique, with the exception of c.439C>T, c.439+1G>A, c.703C>T, c.1382_1383delAC, c.2698C>T, and c.2990C>A, which were detected in two cases each; three cases exhibited entire gene deletions. A majority (69.2%) of the point and frameshift mutations could be detected by the sequencing of eleven exons (exons 3, 5, 6, 11, 14, 16, 18, 21, and 23-25). The mutation detection rate was 50.0% (10/20) in atypical cases that only presented with two or three clinical features of Alagille syndrome. Segregation analysis revealed that 81.1% (30/37) of these mutations were de novo. In conclusion, JAG1 mutations are present in the majority of Chinese pediatric patients with clinical features of Alagille syndrome, and the mutations concentrate on different exons from other reports. Genetic study is important for the diagnosis of atypical Alagille syndrome in Chinese patients.
Higher calcineurin inhibitor levels predict better kidney graft survival in patients with de novo donor-specific anti-HLA antibodies: a cohort study (2017)

The development of de novo anti-HLA donor-specific antibodies (dnDSA) is associated with poorer outcomes in kidney transplant recipients. Despite this, antibody screening post-transplant is not widespread, largely because the optimal management of patients with dnDSA remains undetermined. We hypothesized that in this population, calcineurin inhibitor blood levels would be an independent predictor of graft loss. We analyzed a cohort of unsensitized patients for whom anti-HLA antibody screening was performed prospectively post-transplant. During the screening period between January 2005 and April 2016, 42 patients developed dnDSA. There was no difference in the clinical characteristics or the histological scores of patients biopsied for clinical indication versus those biopsied solely due to detection of dnDSA. Cox modeling revealed a strong relationship between mean tacrolimus levels following dnDSA detection and graft loss, with a hazard ratio of 0.49 (95% CI, 0.33-0.75), which persisted following adjustment for established independent predictors (HR, 0.52, 95% CI, 0.30-0.89). Kaplan-Meier analysis by tertiles of tacrolimus levels and receiver operating curve analysis concurred to show that a threshold of 5.3 ng/ml could be predictive of graft loss. These data suggest that anti-HLA antibody monitoring post-transplant could guide maintenance immunosuppression and improve graft outcomes.
Estimate of indicated torque from crankshaft speed fluctuations: a model for the dynamics of the IC engine (1989)

A contribution is made to the task of constructing a global model for the IC (internal combustion) engine. A robust submodel is formulated for the dynamics of the IC engine, where-in the engine is viewed as a system with input given by cylinder pressure and output corresponding to crankshaft angular acceleration and crankshaft torque. The formulation is well suited to closed-loop engine control and transmission control applications. In the model, cylinder pressure is deterministically related to net engine torque through the geometry and dynamics of the reciprocating assembly. The relationship between net engine torque and crankshaft angular acceleration is explain in terms of a passive second-order electrical circuit model with constant parameters. Experimental results confirm the validity of the model over a wide range of engine operating conditions, including transient conditions. It is concluded that the model provides a powerful tool for estimating average and instantaneous net engine torque based on an inexpensive noncontacting measurement of crankshaft acceleration, thus providing access to one of the primary engine performance variables.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Magnetoresistance of Nanowires Electrodeposited into Anodized Aluminum Oxide Nanochannels (2012)

One-dimensional nanowires with a large aspect ratio have received much attention due to their unique shape anisotropy and extremely large surface area. Metallic nanowires such as Au, Ag and Cu nanowires [1-3] and semiconductor nanowires [4-9] would show unique electron transport properties which are not observed in bulk metals. Ferromagnetic nano‐ wires such as Ni, Co and Fe alloy nanowires as well as Co/Cu multilayered nanowires would be best candidate materials for magnetic field sensors with anisotropic magnetore‐ sistance (AMR) and giant magnetoresistance (GMR) effect. Nanowires can be fabricated by manipulating metallic atoms one by one using scanning tunneling microscopy (STM) or cat‐ alyst-assisted wet chemical etching technique [10], while they can be also prepared by elec‐ trochemically depositing metallic atoms into a nanochannel template with numerous nanochannels [11]. Nanochannel templates such as polycarbonate membrane films or ano‐ dized aluminum oxide films with high density of nanochannels (about 108~1010 cm–2) can be used in the template synthesis technique [12].
Preparation of aromatic polyesters by the direct polycondensation reaction with diphenyl chlorophosphate in pyridine (1983)

Abstract The direct polycondensation reaction of diphenyl chlorophosphate (DPCP) as a new condensing agent in pyridine was used for the preparation of polyarylene esters. High‐molecular‐weight polymers can be prepared by reacting a pyridine solution of dicarboxylic acids and DPCP in the presence of LiCl, followed by treating with a pyridine solution of bisphenols. About an equivalent of LiCl, and 30 mol % excess of DPCP were most favorably added. Effects of the initial reaction of the acids and DPCP, and of dropwise addition of bisphenols on the polycondensation were investigated. Polycondensations of several hydroxybenzoic acids were also carried out with limited success.
Mouse model of carbon tetrachloride induced liver fibrosis: Histopathological changes and expression of CD133 and epidermal growth factor (2010)

Species-specific differences exist with respect to the histopathological and molecular pathogenesis of chronic liver disease. CCl4-induced chronic liver injury in A/J mice has important differences compared to human cirrhosis leading to HCC.
A Heuristic Approach for Offboard-Diagnostics in Advanced Automotive Systems (2009)

&lt;div class="htmlview paragraph"&gt;As the complexity of current automobiles increases, new and innovative diagnostic methods for car maintenance and diagnostic inspection are greatly needed. This paper introduces a new diagnostic approach, which learns from previous repair cases with the help of neural networks in order to assist future diagnostic inspections. Practical experiments have shown that this approach is able to provide promising results even with the data that is already available today.&lt;/div&gt;
Antigenic Differences Between Normal and Malignant Cells as a Basis for Treatment of Intracerebral Neoplasms Using a DNA-Based Vaccine (2006)

Antigenic differences between normal and malignant cells of the cancer patient form the rationale for clinical immunotherapeutic strategies. Because the antigenic phenotype of neoplastic cells varies widely among different cells within the same malignant cell-population, immunization with a vaccine that stimulates immunity to the broad array of tumor antigens expressed by the cancer cells is likely to be more efficacious than immunization with a vaccine for a single antigen. A vaccine prepared by transfer of DNA from the tumor into a highly immunogenic cell line can encompass the array of tumor antigens that characterize the patient's neoplasm. Poorly immunogenic tumor antigens, characteristic of malignant cells, can become strongly antigenic if they are expressed by highly immunogenic cells. A DNA-based vaccine was prepared by transfer of genomic DNA from a breast cancer that arose spontaneously in a C3H/He mouse into a highly immunogenic mouse fibroblast cell line, where genes specifying tumor-antigens were expressed. The fibroblasts were modified in advance of DNA-transfer to secrete an immune augmenting cytokine and to express allogeneic MHC class I-determinants. In an animal model of breast cancer metastatic to the brain, introduction of the vaccine directly into the tumor bed stimulated a systemic cellular anti-tumor immune response measured by two independent in vitro assays and prolonged the lives of the tumor-bearing mice. Furthermore, using antibodies against the various T-cell subsets, it was determined that the systemic cellular anti-tumor immunity was mediated by CD8(+), CD4(+) and NK/LAK cells. The application of DNA-based genomic vaccines for the treatment of a variety of brain tumors is being explored.
Targeting Hepatitis B Virus-Infected Cells with a T-Cell Receptor-Like Antibody (2010)

Virus-specific CD8 T cells are activated when their T-cell receptors (TCRs) recognize the specific viral peptide/major histocompatibility complex (MHC) class I (pMHC) complexes present on the surface of infected cells. Antibodies able to recognize the specific pMHC can mimic TCR specificity and both represent a valuable biological tool to visualize pMHC complexes on infected cells and serve as a delivery system for highly targeted therapies. To evaluate these possibilities, we created a monoclonal antibody able to specifically recognize a hepatitis B virus (HBV) envelope epitope (Env at positions 183 to 91 [Env183-91]) presented by the HLA-A201 molecule, and we tested its ability to recognize HBV-infected hepatocytes and to deliver a cargo to a specific target. We demonstrate that this antibody detects and visualizes the processed product of HBV proteins produced in naturally HBV-infected cells, is not inhibited by soluble HBV proteins present in patient sera, and mediates the intracellular delivery of a fluorescent molecule to target cells. Additionally, compared to CD8 T cells specific for the same HBV epitope, the TCR-like antibody has both a superior sensitivity and a specificity focused on distinct amino acids within the epitope. These data demonstrate that a T-cell receptor-like antibody can be used to determine the quantitative relationship between HBV replication and specific antigen presentation to CD8 T cells and serves as a novel therapeutic delivery platform for personalized health care for HBV-infected patients.
Systematic review and Meta analysis of Chinese medicine for polyhydramnios (2013)

Objective To evaluate efficacy and safety of Chinese medicine for polyhydramnios by systematic review method of evidence-based medicine.Methods The electronic databases,which were PubMed,Embase,and Cochrane library as well as CNKI,VIP,Wanfang and TCM online,were searched.The randomized controlled trials and clinical controlled trials for polyhydramnios,which were Chinese medicine VS single use of western medicine(indomethacin) and Chinese medicine combined with western medicine VS single use of western medicine were included.Data were extracted independently by two reviewers.With quality assessment standard of the Cochrane collaboration and its software RevMan 5.1.2,the Meta analysis was performed.The relative risk and mean difference were adopted as effect index of results,which were both expressed as 95% credibility interval.Results In total,5 trials were included with one thousand and seventeen cases of polyhydramnios.The quality of included Chinese literatures was on the low side in general.Among the trials of Chinese medicine VS western medicine,there was statistical significance only in the index of artery stenosis.As for the total rate of clinical improvement and reduction of AFI score,there were significant differences betweens Chinese medicine combined with western medicine VS single use of western medicine(P0.00001).There were no adverse reaction in Chinese medicine.Conclusion Chinese medicine could have some effects on polyhydramnios,yet the firm conclusion needs more rigorous large-sample clinical trials to prove.
Assessment of whole genome amplification-induced bias through high-throughput, massively parallel whole genome sequencing (2006)

Of the amplification methodologies examined in this paper, the multiple displacement amplification products generated the least bias, and produced significantly higher yields of amplified DNA.
Calixarenes in Action (2000)

Calixarenes in Action is unique among books devoted to this interesting class of synthetic macrocycles. Rather than emphasizing the molecular properties of calixarenes, it covers in depth their supramolecular functions, enlightening the reader as to the peculiar features of calixarenes as hosts and as platforms for the synthesis of more complex receptors and catalysts. Topics covered in detail include the use of calixarenes in:molecular modeling of calixarenesnon-covalent interactionscrystal engineeringcation recognitionanion recognitionsupramolecular devicesnew materialsself-assembly processessupramolecular catalysisThe interest in calixarenes has grown tremendously in the last few years and this book reports, for each topic, the most recent literature critically evaluated by active researchers in the field. Calixarenes in Action is a valuable reference book for researchers in organic, inorganic, analytical and environmental chemistry and can serve as a graduate-level text for students of supramolecular science and technology.
Paracoccus homiensis sp. nov., isolated from a sea-sand sample (2006)

Strain DD-R11(T), isolated from a sea-sand sample from Homi Cape, Pohang city, South Korea, was a Gram-negative, aerobic, motile, non-spore-forming, rod- to ovoid-shaped bacterium. Colonies grown on marine agar were circular, convex and colourless to creamy white. Growth occurred between 10 and 40 degrees C (optimum 25-30 degrees C) and at pH 5.0-9.0 (optimum pH 6.0-8.0). The strain could grow in up to 15 % NaCl (optimum 3-5 % NaCl). According to 16S rRNA gene sequence analysis, the strain was a member of the genus Paracoccus in the Alphaproteobacteria. Sequence similarities to type strains of the genus Paracoccus were between 94.6 and 98.3 %, showing the highest sequence similarity to Paracoccus zeaxanthinifaciens ATCC 21588(T). The DNA-DNA relatedness value of strain DD-R11(T) and P. zeaxanthinifaciens ATCC 21588(T) was 27 %. Strain DD-R11(T) was characterized by having ubiquinone 10 as the major respiratory quinone and C(18 : 1)omega7c as the predominant fatty acid. The DNA G+C content was 63.0 mol%. On the basis of its phenotypic and genotypic characteristics, it is suggested that DD-R11(T) represents a novel species of the genus Paracoccus, for which the name Paracoccus homiensis sp. nov. is proposed, with DD-R11(T) (=KACC 11518(T)=DSM 17862(T)) as the type strain.
The effect of bone marrow aspiration strategy on the yield and quality of human mesenchymal stem cells (2009)

We recommend collection volumes of bone marrow aspirates of at least 8 mL to reduce the risk of obtaining aspirates with low cell numbers. From the same site, a second aspiration or an aspirate of > 10 mL can be drawn without any loss of biological quality due to dilution with peripheral blood.
Topical negative therapy and vacuum assisted closure. New strategies and devices in surgical reconstruction. (2005)

Topical negative pressure (TNP) has been introduced in complex surgical reconstruction and difficult wound healing, having proven to be effective in both drainage of wound secretions and calling for a new, sterile granulating tissue. In the last 15 years many reports have been focusing on TNP in different surgical specialties (orthopedic surgery in exposed fractures, general surgery in eventration, cardiothoracic surgery in sternal dehiscences, plastic surgery in difficult wounds and pressure sores). The authors report their personal experience being among the first Units to use TNP systematically in Italy.
Metabolic and Physiological Impact of Probiotics or Direct-Fed-Microbialson Poultry: A Brief Review of Current Knowledge (2007)

The poultry industry is facing a ban on the use of antibiotic feed additives in many parts of the world. Consequently, there is a growing interest in finding viable alternatives for disease prevention and growth enhancing supplements. The effects of probiotics or direct fed microbials (DFM) on gut health and performance in poultry as well as other species are presented. The interactions between intestinal microbiota, the gut epithelium and the immune system are important in the competitive exclusion process. The mechanisms by which probiotics operate include spatial exclusion, micro-environmental alterations, production of antimicrobial substances and epithelial barrier integrity. The preponderance of research data in this field suggests the likelihood of a small but additive series of beneficial changes from an animal’s exposure to probiotics. Further investigations will be needed to fully characterize the effects and sustained outcomes of probiotic and DFM treatments in poultry.
Chemical Splanchnicectomy in Patients with Unresectable Pancreatic Cancer A Prospective Randomized Trial (1993)

The results suggest that intraoperative chemical splanchnicectomy with alcohol significantly reduces or prevents pain in patients with unresectable pancreatic cancer.
Rubredoxins Involved in Alkane Oxidation (2002)

Rubredoxins (Rds) are essential electron transfer components of bacterial membrane-bound alkane hydroxylase systems. Several Rd genes associated with alkane hydroxylase or Rd reductase genes were cloned from gram-positive and gram-negative organisms able to grow on n-alkanes (Alk-Rds). Complementation tests in an Escherichia coli recombinant containing all Pseudomonas putida GPo1 genes necessary for growth on alkanes except Rd 2 (AlkG) and sequence comparisons showed that the Alk-Rds can be divided in AlkG1- and AlkG2-type Rds. All alkane-degrading strains contain AlkG2-type Rds, which are able to replace the GPo1 Rd 2 in n-octane hydroxylation. Most strains also contain AlkG1-type Rds, which do not complement the deletion mutant but are highly conserved among gram-positive and gram-negative bacteria. Common to most Rds are the two iron-binding CXXCG motifs. All Alk-Rds possess four negatively charged residues that are not conserved in other Rds. The AlkG1-type Rds can be distinguished from the AlkG2-type Rds by the insertion of an arginine downstream of the second CXXCG motif. In addition, the glycines in the two CXXCG motifs are usually replaced by other amino acids. Mutagenesis of residues conserved in either the AlkG1- or the AlkG2-type Rds, but not between both types, shows that AlkG1 is unable to transfer electrons to the alkane hydroxylase mainly due to the insertion of the arginine, whereas the exchange of the glycines in the two CXXCG motifs only has a limited effect.