gebhart/patrepeval huggingface dataset:
Hospital based superconducting cyclotron for neutron therapy: Medical physics perspective (2001)

The neutron therapy facility at the Gershenson Radiation Oncology Center, Harper University Hospital in Detroit has been operational since September 1991. The d(48.5)+Be beam is produced in a gantry mounted superconducting cyclotron designed and built at the National Superconducting Cyclotron Laboratory (NSCL). Measurements were performed in order to obtain the physical characteristics of the neutron beam and to collect the data necessary for treatment planning. This included profiles of the dose distribution in a water phantom, relative output factors and the design of various beam modifiers, i.e., wedges and tissue compensators. The beam was calibrated in accordance with international protocol for fast neutron dosimetry. Dosimetry and radiobiology intercomparions with three neutron therapy facilities were performed prior to clinical use. The radiation safety program was established in order to monitor and reduce the exposure levels of the personnel. The activation products were identified and the exposure in the treatment room was mapped. A comprehensive quality assurance (QA) program was developed to sustain safe and reliable operation of the unit at treatment standards comparable to those for conventional photon radiation. The program can be divided into three major parts: maintenance of the cyclotron and related hardware; QA of the neutron beam dosimetry and treatment delivery; safety and radiation protection. In addition the neutron beam is used in various non-clinical applications. Among these are the microdosimetric characterization of the beam, the effects of tissue heterogeneity on dose distribution, the development of boron neutron capture enhanced fast neutron therapy and variety of radiobiology experiments.
Preclinical Evaluation of Two Neutralizing Human Monoclonal Antibodies against Hepatitis C Virus (HCV): a Potential Treatment To Prevent HCV Reinfection in Liver Transplant Patients (2006)

Passive immunotherapy is potentially effective in preventing reinfection of liver grafts in hepatitis C virus (HCV)-associated liver transplant patients. A combination of monoclonal antibodies directed against different epitopes may be advantageous against a highly mutating virus such as HCV. Two human monoclonal antibodies (HumAbs) against the E2 envelope protein of HCV were developed and tested for the ability to neutralize the virus and prevent human liver infection. These antibodies, designated HCV-AB 68 and HCV-AB 65, recognize different conformational epitopes on E2. They were characterized in vitro biochemically and functionally. Both HumAbs are immunoglobulin G1 and have affinity constants to recombinant E2 constructs in the range of 10(-10) M. They are able to immunoprecipitate HCV particles from infected patients' sera from diverse genotypes and to stain HCV-infected human liver tissue. Both antibodies can fix complement and form immune complexes, but they do not activate complement-dependent or antibody-dependent cytotoxicity. Upon complement fixation, the monoclonal antibodies induce phagocytosis of the immune complexes by neutrophils, suggesting that the mechanism of viral clearance includes endocytosis. In vivo, in the HCV-Trimera model, both HumAbs were capable of inhibiting HCV infection of human liver fragments and of reducing the mean viral load in HCV-positive animals. The demonstrated neutralizing activities of HCV-AB 68 and HCV-AB 65 suggest that they have the potential to prevent reinfection in liver transplant patients and to serve as prophylactic treatment in postexposure events.
Combined head and eye tracking system for dynamic testing of the vestibular system (1996)

We present a combined head-eye tracking system suitable for use with free head movement during natural activities. This system provides an integrated head and eye position measurement while allowing for a large range of head movement (approx 1.8 m of head translation is tolerated). Six degrees of freedom of head motion and two degrees of freedom of eye motion are measured by the system. The system was designed to be useful for the evaluation of the vestibulo-ocular reflex (VOR). The VOR generates compensatory eye movements in order to stabilize gaze during linear or rotational motion of the head. Current clinical and basic research evaluation of the VOR has used a restricted range of head motion, mainly low-frequency, yaw rotation. An integrated eye-head tracking system such as the one presented here allows the VOR response to linear and angular head motion to be studied in a more physiologically relevant manner. Two examples of the utility of the integrated head and eye tracking system in evaluating the vestibular response to linear and angular motion are presented.
The bradykinin B2 Receptor knockout mouse is protected from thrombosis (2003)

Peer Reviewed
Coniferyl Ferulate Incorporation into Lignin Enhances the Alkaline Delignification and Enzymatic Degradation of Cell Walls (2008)

Incorporating ester interunit linkages into lignin could facilitate fiber delignification and utilization. In model studies with maize cell walls, we examined how partial substitution of coniferyl alcohol (a normal monolignol) with coniferyl ferulate (an ester conjugate from lignan biosynthesis) alters the formation and alkaline extractability of lignin and the enzymatic hydrolysis of structural polysaccharides. Coniferyl ferulate moderately reduced lignification and cell-wall ferulate copolymerization with monolignols. Incorporation of coniferyl ferulate increased lignin extractability by up to 2-fold in aqueous NaOH, providing an avenue for producing fiber with less noncellulosic and lignin contamination or of delignifying at lower temperatures. Cell walls lignified with coniferyl ferulate were more readily hydrolyzed with fibrolytic enzymes, both with and without alkaline pretreatment. Based on our results, bioengineering of plants to incorporate coniferyl ferulate into lignin should enhance lignocellulosic biomass saccharification and particularly pulping for paper production.
Development and use of the H strain of avian infectious bronchitis virus from the Netherlands as a vaccine: a review (2004)

The H strain of infectious bronchitis (IB) was one of the earliest live attenuated IB vaccines to be developed and has continued to be use in most parts of the world for almost 50 years. It was developed for used at both the 52nd (H52) and 120th (H120) vaccine levels and, because of it ability to provide heterologous cross-protection against a number of IB viruses of different serotypes, has proved to be one of the most enduring live attenuated IB vaccines. In fact, the H120 vaccine is possibly the most widely used live attenuated IB vaccine globally to this day. The use of H52 has, however, declined with the introduction of safe and highly efficacious inactivated IB vaccines. This review documents the original studies to isolate and attenuate the H strain by serial embryo passage, and describes the early studies to demonstrate its efficacy in laboratory studies and under field conditions. The efficacy of the H vaccine in providing cross-protection against some of the many IB variants now reported worldwide is also discussed, and possible future vaccination strategies for IB considered.
Design, Synthesis, and Evaluation of Linker-Duocarmycin Payloads: Toward Selection of HER2-Targeting Antibody–Drug Conjugate SYD985 (2015)

Antibody-drug conjugates (ADCs) that are currently on the market or in clinical trials are predominantly based on two drug classes: auristatins and maytansinoids. Both are tubulin binders and block the cell in its progression through mitosis. We set out to develop a new class of linker-drugs based on duocarmycins, potent DNA-alkylating agents that are composed of a DNA-alkylating and a DNA-binding moiety and that bind into the minor groove of DNA. Linker-drugs were evaluated as ADCs by conjugation to the anti-HER2 antibody trastuzumab via reduced interchain disulfides. Duocarmycin 3b, bearing an imidazo[1,2-a]pyridine-based DNA-binding unit, was selected as the drug moiety, notably because of its rapid degradation in plasma. The drug was incorporated into the linker-drugs in its inactive prodrug form, seco-duocarmycin 3a. Linker attachment to the hydroxyl group in the DNA-alkylating moiety was favored over linking to the DNA-binding moiety, as the first approach gave more consistent results for in vitro cytotoxicity and generated ADCs with excellent human plasma stability. Linker-drug 2 was eventually selected based on the properties of the corresponding trastuzumab conjugate, SYD983, which had an average drug-to-antibody ratio (DAR) of about 2. SYD983 showed subnanomolar potencies against multiple human cancer cell lines, was highly efficacious in a BT-474 xenograft model, and had a long half-life in cynomolgus monkeys, in line with high stability in monkey and human plasma. Studies comparing ADCs with a different average DAR showed that a higher average DAR leads to increased efficacy but also to somewhat less favorable physicochemical and toxicological properties. Fractionation of SYD983 with hydrophobic interaction chromatography resulted in SYD985, consisting of about 95% DAR2 and DAR4 species in an approximate 2:1 ratio and having an average DAR of about 2.8. SYD985 combines several favorable properties from the unfractionated ADCs with an improved homogeneity. It was selected for further development and recently entered clinical Phase I evaluation.
Parallelizing stateful operators in a distributed stream processing system (2012)

We consider a distributed stream processing application, expressed as a data-flow graph with operators as vertices connected by streams and deployed over a cluster of compute nodes, where a small subset of the operators are often the performance bottlenecks for the entire application. In cases where a bottleneck operator is stateless, it is obvious that parallelization by splitting the incoming stream among multiple parallel operators deployed on different nodes can help improve performance. However, it is not so obvious when the bottleneck operator is stateful. In such a case, parallelization is much more challenging as it often requires a state sharing mechanism for the parallel operators. Moreover, it incurs additional overheads of required accesses by the parallel operators to shared state and synchronization constructs. In this paper, we propose a parallelization framework for stateful stream processing operators. The framework not only addresses issues related to the system model and support for operator parallelization, but also delves into the theoretical details that model the suitability of parallelization and the optimal degree of parallelism. We have implemented and evaluated our framework in the context of IBM's System S distributed stream processing middleware. While microbenchmarks are used to validate the proposed theoretical model, a parallelized implementation of a moving KNN application is used for the purpose of evaluation.
Mutations in the fatty acid elongation 1 gene are associated with a loss of β‐ketoacyl‐CoA synthase activity in low erucic acid rapeseed (2001)

Low erucic acid rapeseed (LEAR) is characterised by a near absence of very long chain fatty acids in the seed oil which has been correlated with a lack of acyl-CoA elongation activity. Here we show that the absence of acyl-CoA and ATP-dependent elongation activities in microsomes isolated from LEAR embryos is associated with an absence of beta-ketoacyl-CoA synthase activity encoded by the Bn-fatty acid elongation 1 (FAE1) genes. Size exclusion chromatography of solubilised microsomes revealed the presence of a high molecular mass acyl-CoA elongase complex in high erucic acid rapeseed which was absent in microsomes isolated from LEAR seeds. Although transcripts for the Bn-FAE1 genes were detected in LEAR embryos, immunoblots using antisera raised against the beta-ketoacyl-CoA synthase indicated an absence of this protein. Comparison of the deduced amino acid sequences of immature embryo cDNAs reveals that LEAR alleles of Bn-FAE1 encode variant beta-ketoacyl-CoA synthase proteins.
Nuts and bolts of chemical exchange saturation transfer MRI (2013)

Chemical exchange saturation transfer (CEST) has emerged as a novel MRI contrast mechanism that is well suited for molecular imaging studies. This new mechanism can be used to detect small amounts of contrast agent through the saturation of rapidly exchanging protons on these agents, allowing a wide range of applications. CEST technology has a number of indispensable features, such as the possibility of simultaneous detection of multiple 'colors' of agents and of changes in their environment (e.g. pH, metabolites, etc.) through MR contrast. Currently, a large number of new imaging schemes and techniques are being developed to improve the temporal resolution and specificity and to correct for the influence of B0 and B1 inhomogeneities. In this review, the techniques developed over the last decade are summarized with the different imaging strategies and post-processing methods discussed from a practical point of view, including the description of their relative merits for the detection of CEST agents. The goal of the present work is to provide the reader with a fundamental understanding of the techniques developed, and to provide guidance to help refine future applications of this technology. This review is organized into three main sections ('Basics of CEST contrast', 'Implementation' and 'Post-processing'), and also includes a brief Introduction and Summary. The 'Basics of CEST contrast' section contains a description of the relevant background theory for saturation transfer and frequency-labeled transfer, and a brief discussion of methods to determine exchange rates. The 'Implementation' section contains a description of the practical considerations in conducting CEST MRI studies, including the choice of magnetic field, pulse sequence, saturation pulse, imaging scheme, and strategies to separate magnetization transfer and CEST. The 'Post-processing' section contains a description of the typical image processing employed for B0 /B1 correction, Z-spectral interpolation, frequency-selective detection and improvement of CEST contrast maps.
Spectrum of mutations in the gene encoding the adrenoleukodystrophy protein. (1995)

X-linked adrenoleukodystrophy (ALD) has been associated with mutations in a gene encoding an ATP-binding transporter, which is located in the peroxisomal membrane. Deficiency of the gene leads to impaired peroxisomal beta-oxidation. Systematic analysis of the open reading frame of the ALD gene, using reverse transcriptase-PCR, followed by direct sequencing, revealed mutations in all 28 unrelated kindreds analyzed. No entire gene deletions or drastic promoter mutations were detected. In only one kindred did the mutation involve multiple exons. The other mutations were small alterations leading to missense (13 of 28) or nonsense mutations, a single amino acid deletion, frameshifts, or splice acceptor-site defects. Mutations affecting a single amino acid were concentrated in the region between the third and fourth putative transmembrane domains and in the ATP-binding domain. Mutations were detected in all investigated ALD kindreds, suggesting that this gene is the only gene responsible for X-linked ALD. This overview of mutations is useful in the determination of structurally and functionally important regions and provides an efficient screening strategy for identification of mutations in the ALD gene.
The Potential Role of Probiotics in the Management of Childhood Autism Spectrum Disorders (2011)

Gastrointestinal (GI) dysfunction has been reported in a substantial number of children with autism spectrum disorders (ASD). Activation of the mucosal immune response and the presence of abnormal gut microbiota are repeatedly observed in these children. In children with ASD, the presence of GI dysfunction is often associated with increased irritability, tantrums, aggressive behaviour, and sleep disturbances. Moreover, modulating gut bacteria with short-term antibiotic treatment can lead to temporary improvement in behavioral symptoms in some individuals with ASD. Probiotics can influence microbiota composition and intestinal barrier function and alter mucosal immune responses. The administration of probiotic bacteria to address changes in the microbiota might, therefore, be a useful novel therapeutic tool with which to restore normal gut microbiota, reduce inflammation, restore epithelial barrier function, and potentially ameliorate behavioural symptoms associated with some children with ASD. In this review of the literature, support emerges for the clinical testing of probiotics in ASD, especially in the context of addressing GI symptoms.
Clinical features of adrenal insufficiency in patients with acquired immunodeficiency syndrome (1996)

Adrenal insufficiency features in AIDS patients with advanced disease, without specific findings and with a history of previous opportunistic diseases. Basal cortisol values at 0830 h lower than 275 nmol/l are highly suggestive of adrenal insufficiency in patients with AIDS.
Cancer Cachexia in the Age of Obesity: Skeletal Muscle Depletion Is a Powerful Prognostic Factor, Independent of Body Mass Index (2013)

CT images reveal otherwise occult muscle depletion. Patients with cancer who are cachexic by the conventional criterion (involuntary weight loss) and by two additional criteria (muscle depletion and low muscle attenuation) share a poor prognosis, regardless of overall body weight.
Trial watch: Tumor-targeting monoclonal antibodies for oncological indications (2015)

An expanding panel of monoclonal antibodies (mAbs) that specifically target malignant cells or intercept trophic factors delivered by the tumor stroma is now available for cancer therapy. These mAbs can exert direct antiproliferative/cytotoxic effects as they inhibit pro-survival signal transduction cascades or activate lethal receptors at the plasma membrane of cancer cells, they can opsonize neoplastic cells to initiate a tumor-targeting immune response, or they can be harnessed to specifically deliver toxins or radionuclides to transformed cells. As an indication of the success of this immunotherapeutic paradigm, international regulatory agencies approve new tumor-targeting mAbs for use in cancer patients every year. Moreover, the list of indications for previously licensed molecules is frequently expanded to other neoplastic disorders as the results of large, randomized clinical trials become available. Here, we discuss recent advances in the preclinical and clinical development of tumor-targeting mAbs for oncological indications.
Serum protein markers for early detection of ovarian cancer (2005)

Early diagnosis of epithelial ovarian cancer (EOC) would significantly decrease the morbidity and mortality from this disease but is difficult in the absence of physical symptoms. Here, we report a blood test, based on the simultaneous quantization of four analytes (leptin, prolactin, osteopontin, and insulin-like growth factor-II), that can discriminate between disease-free and EOC patients, including patients diagnosed with stage I and II disease, with high efficiency (95%). Microarray analysis was used initially to determine the levels of 169 proteins in serum from 28 healthy women, 18 women newly diagnosed with EOC, and 40 women with recurrent disease. Evaluation of proteins that showed significant differences in expression between controls and cancer patients by ELISA assays yielded the four analytes. These four proteins then were evaluated in a blind cross-validation study by using an additional 106 healthy females and 100 patients with EOC (24 stage I/II and 76 stage III/IV). Upon sample decoding, the results were analyzed by using three different classification algorithms and a binary code methodology. The four-analyte test was further validated in a blind binary code study by using 40 additional serum samples from normal and EOC cancer patients. No single protein could completely distinguish the cancer group from the healthy controls. However, the combination of the four analytes exhibited the following: sensitivity 95%, positive predictive value (PPV) 95%, specificity 95%, and negative predictive value (NPV) 94%, a considerable improvement on current methodology.
Peptide mimicry of the meningococcal group C capsular polysaccharide. (1995)

Sequence analysis of the variable regions of the heavy and light chains of the anti-idiotypic antibody 6F9, which mimics the meningococcal group C capsular polysaccharide (MCP), was performed. The immunogenic site on 6F9 responsible for inducing an anti-MCP antibody response was determined by means of sequence and computer model analysis of these data. Complementarity-determining region 3 (CDR3) was found to be unique in that the sequence tract YRY was exposed on the surface. A synthetic peptide spanning the CDR3 domain was synthesized and complexed to proteosomes (meningococcal group B outer membrane protein). Immunizations of BALB/c mice with the peptide-proteosome complex resulted in a significant anti-MCP antibody response. Immunized mice were protected against infection with a lethal dose of Neisseria meningitidis serogroup C.
Ceramide-mediated biology. Determination of structural and stereospecific requirements through the use of N-acyl-phenylaminoalcohol analogs. (1992)

Ceramide is a postulated intracellular modulator of cell growth and differentiation (Okazaki, T., Bielawska, A., Bell, R.M., and Hannun, Y. A. (1990) J. Biol. Chem. 265, 15823-15831). In order to determine the structural and stereospecific requirements for ceramide effects on HL-60 cells, N-acyl-phenylaminoalcohol analogs were synthesized and evaluated for their ability to mimic the effects of ceramide on cell proliferation and differentiation. These compounds share with ceramide a similar polar headgroup that allows the investigation of the roles of the primary and secondary hydroxyls, the hydrophobicity of the molecule, and stereospecificity. N-Myristoyl derivatives of phenylamino alcohols showed optimal activity over other chain length analogs and were able to mimic the effects of C2-ceramide on cell growth and differentiation. Neither the primary nor the secondary alcohol was necessary for activity, but the amide-linked acyl chain was required. Stereospecificity of action was demonstrated with an enantiomeric pair: D-erythro-N-myristoyl-2-amino-1-phenyl-1-propanol (C14-D-e-APP-1) and L-erythro-N-myristoyl-2-amino-1-phenyl-1-propanol (C14-L-e-APP-1). The D stereoisomer was as effective as C2-ceramide in inhibiting HL-60 cell growth and in inducing cell differentiation, whereas the L enantiomer lacked activity in both assays. These results suggest stereospecific action of ceramide and strongly support a physiologic role for ceramide as an intracellular mediator with primary roles in regulation of cell growth and differentiation.